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25
docs/pyerrors.html
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@ -1151,19 +1151,18 @@ The following entries are optional:</li>
</span><span id="L-477"><a href="#L-477"><span class="linenos">477</span></a> </span><span id="L-477"><a href="#L-477"><span class="linenos">477</span></a>
</span><span id="L-478"><a href="#L-478"><span class="linenos">478</span></a><span class="sd">Julia I/O routines for the json.gz format, compatible with [ADerrors.jl](https://gitlab.ift.uam-csic.es/alberto/aderrors.jl), can be found [here](https://github.com/fjosw/ADjson.jl).</span> </span><span id="L-478"><a href="#L-478"><span class="linenos">478</span></a><span class="sd">Julia I/O routines for the json.gz format, compatible with [ADerrors.jl](https://gitlab.ift.uam-csic.es/alberto/aderrors.jl), can be found [here](https://github.com/fjosw/ADjson.jl).</span>
</span><span id="L-479"><a href="#L-479"><span class="linenos">479</span></a><span class="sd">&#39;&#39;&#39;</span> </span><span id="L-479"><a href="#L-479"><span class="linenos">479</span></a><span class="sd">&#39;&#39;&#39;</span>
</span><span id="L-480"><a href="#L-480"><span class="linenos">480</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">.obs</span><span class="w"> </span><span class="kn">import</span> <span class="o">*</span> </span><span id="L-480"><a href="#L-480"><span class="linenos">480</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">.</span><span class="w"> </span><span class="kn">import</span> <span class="n">dirac</span> <span class="k">as</span> <span class="n">dirac</span>
</span><span id="L-481"><a href="#L-481"><span class="linenos">481</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">.correlators</span><span class="w"> </span><span class="kn">import</span> <span class="o">*</span> </span><span id="L-481"><a href="#L-481"><span class="linenos">481</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">.</span><span class="w"> </span><span class="kn">import</span> <span class="nb">input</span> <span class="k">as</span> <span class="nb">input</span>
</span><span id="L-482"><a href="#L-482"><span class="linenos">482</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">.fits</span><span class="w"> </span><span class="kn">import</span> <span class="o">*</span> </span><span id="L-482"><a href="#L-482"><span class="linenos">482</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">.</span><span class="w"> </span><span class="kn">import</span> <span class="n">integrate</span> <span class="k">as</span> <span class="n">integrate</span>
</span><span id="L-483"><a href="#L-483"><span class="linenos">483</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">.misc</span><span class="w"> </span><span class="kn">import</span> <span class="o">*</span> </span><span id="L-483"><a href="#L-483"><span class="linenos">483</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">.</span><span class="w"> </span><span class="kn">import</span> <span class="n">linalg</span> <span class="k">as</span> <span class="n">linalg</span>
</span><span id="L-484"><a href="#L-484"><span class="linenos">484</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">.</span><span class="w"> </span><span class="kn">import</span> <span class="n">dirac</span> <span class="k">as</span> <span class="n">dirac</span> </span><span id="L-484"><a href="#L-484"><span class="linenos">484</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">.</span><span class="w"> </span><span class="kn">import</span> <span class="n">mpm</span> <span class="k">as</span> <span class="n">mpm</span>
</span><span id="L-485"><a href="#L-485"><span class="linenos">485</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">.</span><span class="w"> </span><span class="kn">import</span> <span class="nb">input</span> <span class="k">as</span> <span class="nb">input</span> </span><span id="L-485"><a href="#L-485"><span class="linenos">485</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">.</span><span class="w"> </span><span class="kn">import</span> <span class="n">roots</span> <span class="k">as</span> <span class="n">roots</span>
</span><span id="L-486"><a href="#L-486"><span class="linenos">486</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">.</span><span class="w"> </span><span class="kn">import</span> <span class="n">linalg</span> <span class="k">as</span> <span class="n">linalg</span> </span><span id="L-486"><a href="#L-486"><span class="linenos">486</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">.</span><span class="w"> </span><span class="kn">import</span> <span class="n">special</span> <span class="k">as</span> <span class="n">special</span>
</span><span id="L-487"><a href="#L-487"><span class="linenos">487</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">.</span><span class="w"> </span><span class="kn">import</span> <span class="n">mpm</span> <span class="k">as</span> <span class="n">mpm</span> </span><span id="L-487"><a href="#L-487"><span class="linenos">487</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">.correlators</span><span class="w"> </span><span class="kn">import</span> <span class="o">*</span>
</span><span id="L-488"><a href="#L-488"><span class="linenos">488</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">.</span><span class="w"> </span><span class="kn">import</span> <span class="n">roots</span> <span class="k">as</span> <span class="n">roots</span> </span><span id="L-488"><a href="#L-488"><span class="linenos">488</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">.fits</span><span class="w"> </span><span class="kn">import</span> <span class="o">*</span>
</span><span id="L-489"><a href="#L-489"><span class="linenos">489</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">.</span><span class="w"> </span><span class="kn">import</span> <span class="n">integrate</span> <span class="k">as</span> <span class="n">integrate</span> </span><span id="L-489"><a href="#L-489"><span class="linenos">489</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">.misc</span><span class="w"> </span><span class="kn">import</span> <span class="o">*</span>
</span><span id="L-490"><a href="#L-490"><span class="linenos">490</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">.</span><span class="w"> </span><span class="kn">import</span> <span class="n">special</span> <span class="k">as</span> <span class="n">special</span> </span><span id="L-490"><a href="#L-490"><span class="linenos">490</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">.obs</span><span class="w"> </span><span class="kn">import</span> <span class="o">*</span>
</span><span id="L-491"><a href="#L-491"><span class="linenos">491</span></a> </span><span id="L-491"><a href="#L-491"><span class="linenos">491</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">.version</span><span class="w"> </span><span class="kn">import</span> <span class="n">__version__</span> <span class="k">as</span> <span class="n">__version__</span>
</span><span id="L-492"><a href="#L-492"><span class="linenos">492</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">.version</span><span class="w"> </span><span class="kn">import</span> <span class="n">__version__</span> <span class="k">as</span> <span class="n">__version__</span>
</span></pre></div> </span></pre></div>

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@ -131,7 +131,7 @@
</span><span id="L-32"><a href="#L-32"><span class="linenos"> 32</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Have to specify position of cov-element belonging to mean!&#39;</span><span class="p">)</span> </span><span id="L-32"><a href="#L-32"><span class="linenos"> 32</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Have to specify position of cov-element belonging to mean!&#39;</span><span class="p">)</span>
</span><span id="L-33"><a href="#L-33"><span class="linenos"> 33</span></a> <span class="k">else</span><span class="p">:</span> </span><span id="L-33"><a href="#L-33"><span class="linenos"> 33</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="L-34"><a href="#L-34"><span class="linenos"> 34</span></a> <span class="k">if</span> <span class="n">pos</span> <span class="o">&gt;</span> <span class="bp">self</span><span class="o">.</span><span class="n">N</span><span class="p">:</span> </span><span id="L-34"><a href="#L-34"><span class="linenos"> 34</span></a> <span class="k">if</span> <span class="n">pos</span> <span class="o">&gt;</span> <span class="bp">self</span><span class="o">.</span><span class="n">N</span><span class="p">:</span>
</span><span id="L-35"><a href="#L-35"><span class="linenos"> 35</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;pos </span><span class="si">%d</span><span class="s1"> too large for covariance matrix with dimension </span><span class="si">%d</span><span class="s1">x</span><span class="si">%d</span><span class="s1">!&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">pos</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">N</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">N</span><span class="p">))</span> </span><span id="L-35"><a href="#L-35"><span class="linenos"> 35</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;pos </span><span class="si">{</span><span class="n">pos</span><span class="si">}</span><span class="s1"> too large for covariance matrix with dimension </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">N</span><span class="si">}</span><span class="s1">x</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">N</span><span class="si">}</span><span class="s1">!&#39;</span><span class="p">)</span>
</span><span id="L-36"><a href="#L-36"><span class="linenos"> 36</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">_grad</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="bp">self</span><span class="o">.</span><span class="n">N</span><span class="p">,</span> <span class="mi">1</span><span class="p">))</span> </span><span id="L-36"><a href="#L-36"><span class="linenos"> 36</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">_grad</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="bp">self</span><span class="o">.</span><span class="n">N</span><span class="p">,</span> <span class="mi">1</span><span class="p">))</span>
</span><span id="L-37"><a href="#L-37"><span class="linenos"> 37</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">_grad</span><span class="p">[</span><span class="n">pos</span><span class="p">]</span> <span class="o">=</span> <span class="mf">1.</span> </span><span id="L-37"><a href="#L-37"><span class="linenos"> 37</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">_grad</span><span class="p">[</span><span class="n">pos</span><span class="p">]</span> <span class="o">=</span> <span class="mf">1.</span>
</span><span id="L-38"><a href="#L-38"><span class="linenos"> 38</span></a> <span class="k">else</span><span class="p">:</span> </span><span id="L-38"><a href="#L-38"><span class="linenos"> 38</span></a> <span class="k">else</span><span class="p">:</span>
@ -171,7 +171,7 @@
</span><span id="L-72"><a href="#L-72"><span class="linenos"> 72</span></a> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">N</span><span class="p">):</span> </span><span id="L-72"><a href="#L-72"><span class="linenos"> 72</span></a> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">N</span><span class="p">):</span>
</span><span id="L-73"><a href="#L-73"><span class="linenos"> 73</span></a> <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">i</span><span class="p">):</span> </span><span id="L-73"><a href="#L-73"><span class="linenos"> 73</span></a> <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">i</span><span class="p">):</span>
</span><span id="L-74"><a href="#L-74"><span class="linenos"> 74</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_cov</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="n">j</span><span class="p">]</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">_cov</span><span class="p">[</span><span class="n">j</span><span class="p">][</span><span class="n">i</span><span class="p">]:</span> </span><span id="L-74"><a href="#L-74"><span class="linenos"> 74</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_cov</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="n">j</span><span class="p">]</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">_cov</span><span class="p">[</span><span class="n">j</span><span class="p">][</span><span class="n">i</span><span class="p">]:</span>
</span><span id="L-75"><a href="#L-75"><span class="linenos"> 75</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Covariance matrix is non-symmetric for (</span><span class="si">%d</span><span class="s1">, </span><span class="si">%d</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">))</span> </span><span id="L-75"><a href="#L-75"><span class="linenos"> 75</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;Covariance matrix is non-symmetric for (</span><span class="si">{</span><span class="n">i</span><span class="si">}</span><span class="s1">, </span><span class="si">{</span><span class="n">j</span><span class="si">}</span><span class="s1">)&#39;</span><span class="p">)</span>
</span><span id="L-76"><a href="#L-76"><span class="linenos"> 76</span></a> </span><span id="L-76"><a href="#L-76"><span class="linenos"> 76</span></a>
</span><span id="L-77"><a href="#L-77"><span class="linenos"> 77</span></a> <span class="n">evals</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linalg</span><span class="o">.</span><span class="n">eigvalsh</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_cov</span><span class="p">)</span> </span><span id="L-77"><a href="#L-77"><span class="linenos"> 77</span></a> <span class="n">evals</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linalg</span><span class="o">.</span><span class="n">eigvalsh</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_cov</span><span class="p">)</span>
</span><span id="L-78"><a href="#L-78"><span class="linenos"> 78</span></a> <span class="k">for</span> <span class="n">ev</span> <span class="ow">in</span> <span class="n">evals</span><span class="p">:</span> </span><span id="L-78"><a href="#L-78"><span class="linenos"> 78</span></a> <span class="k">for</span> <span class="n">ev</span> <span class="ow">in</span> <span class="n">evals</span><span class="p">:</span>
@ -247,7 +247,7 @@
</span><span id="Covobs-33"><a href="#Covobs-33"><span class="linenos"> 33</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Have to specify position of cov-element belonging to mean!&#39;</span><span class="p">)</span> </span><span id="Covobs-33"><a href="#Covobs-33"><span class="linenos"> 33</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Have to specify position of cov-element belonging to mean!&#39;</span><span class="p">)</span>
</span><span id="Covobs-34"><a href="#Covobs-34"><span class="linenos"> 34</span></a> <span class="k">else</span><span class="p">:</span> </span><span id="Covobs-34"><a href="#Covobs-34"><span class="linenos"> 34</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="Covobs-35"><a href="#Covobs-35"><span class="linenos"> 35</span></a> <span class="k">if</span> <span class="n">pos</span> <span class="o">&gt;</span> <span class="bp">self</span><span class="o">.</span><span class="n">N</span><span class="p">:</span> </span><span id="Covobs-35"><a href="#Covobs-35"><span class="linenos"> 35</span></a> <span class="k">if</span> <span class="n">pos</span> <span class="o">&gt;</span> <span class="bp">self</span><span class="o">.</span><span class="n">N</span><span class="p">:</span>
</span><span id="Covobs-36"><a href="#Covobs-36"><span class="linenos"> 36</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;pos </span><span class="si">%d</span><span class="s1"> too large for covariance matrix with dimension </span><span class="si">%d</span><span class="s1">x</span><span class="si">%d</span><span class="s1">!&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">pos</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">N</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">N</span><span class="p">))</span> </span><span id="Covobs-36"><a href="#Covobs-36"><span class="linenos"> 36</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;pos </span><span class="si">{</span><span class="n">pos</span><span class="si">}</span><span class="s1"> too large for covariance matrix with dimension </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">N</span><span class="si">}</span><span class="s1">x</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">N</span><span class="si">}</span><span class="s1">!&#39;</span><span class="p">)</span>
</span><span id="Covobs-37"><a href="#Covobs-37"><span class="linenos"> 37</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">_grad</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="bp">self</span><span class="o">.</span><span class="n">N</span><span class="p">,</span> <span class="mi">1</span><span class="p">))</span> </span><span id="Covobs-37"><a href="#Covobs-37"><span class="linenos"> 37</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">_grad</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="bp">self</span><span class="o">.</span><span class="n">N</span><span class="p">,</span> <span class="mi">1</span><span class="p">))</span>
</span><span id="Covobs-38"><a href="#Covobs-38"><span class="linenos"> 38</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">_grad</span><span class="p">[</span><span class="n">pos</span><span class="p">]</span> <span class="o">=</span> <span class="mf">1.</span> </span><span id="Covobs-38"><a href="#Covobs-38"><span class="linenos"> 38</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">_grad</span><span class="p">[</span><span class="n">pos</span><span class="p">]</span> <span class="o">=</span> <span class="mf">1.</span>
</span><span id="Covobs-39"><a href="#Covobs-39"><span class="linenos"> 39</span></a> <span class="k">else</span><span class="p">:</span> </span><span id="Covobs-39"><a href="#Covobs-39"><span class="linenos"> 39</span></a> <span class="k">else</span><span class="p">:</span>
@ -287,7 +287,7 @@
</span><span id="Covobs-73"><a href="#Covobs-73"><span class="linenos"> 73</span></a> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">N</span><span class="p">):</span> </span><span id="Covobs-73"><a href="#Covobs-73"><span class="linenos"> 73</span></a> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">N</span><span class="p">):</span>
</span><span id="Covobs-74"><a href="#Covobs-74"><span class="linenos"> 74</span></a> <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">i</span><span class="p">):</span> </span><span id="Covobs-74"><a href="#Covobs-74"><span class="linenos"> 74</span></a> <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">i</span><span class="p">):</span>
</span><span id="Covobs-75"><a href="#Covobs-75"><span class="linenos"> 75</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_cov</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="n">j</span><span class="p">]</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">_cov</span><span class="p">[</span><span class="n">j</span><span class="p">][</span><span class="n">i</span><span class="p">]:</span> </span><span id="Covobs-75"><a href="#Covobs-75"><span class="linenos"> 75</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_cov</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="n">j</span><span class="p">]</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">_cov</span><span class="p">[</span><span class="n">j</span><span class="p">][</span><span class="n">i</span><span class="p">]:</span>
</span><span id="Covobs-76"><a href="#Covobs-76"><span class="linenos"> 76</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Covariance matrix is non-symmetric for (</span><span class="si">%d</span><span class="s1">, </span><span class="si">%d</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">))</span> </span><span id="Covobs-76"><a href="#Covobs-76"><span class="linenos"> 76</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;Covariance matrix is non-symmetric for (</span><span class="si">{</span><span class="n">i</span><span class="si">}</span><span class="s1">, </span><span class="si">{</span><span class="n">j</span><span class="si">}</span><span class="s1">)&#39;</span><span class="p">)</span>
</span><span id="Covobs-77"><a href="#Covobs-77"><span class="linenos"> 77</span></a> </span><span id="Covobs-77"><a href="#Covobs-77"><span class="linenos"> 77</span></a>
</span><span id="Covobs-78"><a href="#Covobs-78"><span class="linenos"> 78</span></a> <span class="n">evals</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linalg</span><span class="o">.</span><span class="n">eigvalsh</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_cov</span><span class="p">)</span> </span><span id="Covobs-78"><a href="#Covobs-78"><span class="linenos"> 78</span></a> <span class="n">evals</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linalg</span><span class="o">.</span><span class="n">eigvalsh</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_cov</span><span class="p">)</span>
</span><span id="Covobs-79"><a href="#Covobs-79"><span class="linenos"> 79</span></a> <span class="k">for</span> <span class="n">ev</span> <span class="ow">in</span> <span class="n">evals</span><span class="p">:</span> </span><span id="Covobs-79"><a href="#Covobs-79"><span class="linenos"> 79</span></a> <span class="k">for</span> <span class="n">ev</span> <span class="ow">in</span> <span class="n">evals</span><span class="p">:</span>
@ -361,7 +361,7 @@
</span><span id="Covobs.__init__-33"><a href="#Covobs.__init__-33"><span class="linenos">33</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Have to specify position of cov-element belonging to mean!&#39;</span><span class="p">)</span> </span><span id="Covobs.__init__-33"><a href="#Covobs.__init__-33"><span class="linenos">33</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Have to specify position of cov-element belonging to mean!&#39;</span><span class="p">)</span>
</span><span id="Covobs.__init__-34"><a href="#Covobs.__init__-34"><span class="linenos">34</span></a> <span class="k">else</span><span class="p">:</span> </span><span id="Covobs.__init__-34"><a href="#Covobs.__init__-34"><span class="linenos">34</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="Covobs.__init__-35"><a href="#Covobs.__init__-35"><span class="linenos">35</span></a> <span class="k">if</span> <span class="n">pos</span> <span class="o">&gt;</span> <span class="bp">self</span><span class="o">.</span><span class="n">N</span><span class="p">:</span> </span><span id="Covobs.__init__-35"><a href="#Covobs.__init__-35"><span class="linenos">35</span></a> <span class="k">if</span> <span class="n">pos</span> <span class="o">&gt;</span> <span class="bp">self</span><span class="o">.</span><span class="n">N</span><span class="p">:</span>
</span><span id="Covobs.__init__-36"><a href="#Covobs.__init__-36"><span class="linenos">36</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;pos </span><span class="si">%d</span><span class="s1"> too large for covariance matrix with dimension </span><span class="si">%d</span><span class="s1">x</span><span class="si">%d</span><span class="s1">!&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">pos</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">N</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">N</span><span class="p">))</span> </span><span id="Covobs.__init__-36"><a href="#Covobs.__init__-36"><span class="linenos">36</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;pos </span><span class="si">{</span><span class="n">pos</span><span class="si">}</span><span class="s1"> too large for covariance matrix with dimension </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">N</span><span class="si">}</span><span class="s1">x</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">N</span><span class="si">}</span><span class="s1">!&#39;</span><span class="p">)</span>
</span><span id="Covobs.__init__-37"><a href="#Covobs.__init__-37"><span class="linenos">37</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">_grad</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="bp">self</span><span class="o">.</span><span class="n">N</span><span class="p">,</span> <span class="mi">1</span><span class="p">))</span> </span><span id="Covobs.__init__-37"><a href="#Covobs.__init__-37"><span class="linenos">37</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">_grad</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="bp">self</span><span class="o">.</span><span class="n">N</span><span class="p">,</span> <span class="mi">1</span><span class="p">))</span>
</span><span id="Covobs.__init__-38"><a href="#Covobs.__init__-38"><span class="linenos">38</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">_grad</span><span class="p">[</span><span class="n">pos</span><span class="p">]</span> <span class="o">=</span> <span class="mf">1.</span> </span><span id="Covobs.__init__-38"><a href="#Covobs.__init__-38"><span class="linenos">38</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">_grad</span><span class="p">[</span><span class="n">pos</span><span class="p">]</span> <span class="o">=</span> <span class="mf">1.</span>
</span><span id="Covobs.__init__-39"><a href="#Covobs.__init__-39"><span class="linenos">39</span></a> <span class="k">else</span><span class="p">:</span> </span><span id="Covobs.__init__-39"><a href="#Covobs.__init__-39"><span class="linenos">39</span></a> <span class="k">else</span><span class="p">:</span>

313
docs/pyerrors/dirac.html
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@ -105,100 +105,99 @@
<div class="pdoc-code codehilite"><pre><span></span><span id="L-1"><a href="#L-1"><span class="linenos"> 1</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span> <div class="pdoc-code codehilite"><pre><span></span><span id="L-1"><a href="#L-1"><span class="linenos"> 1</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
</span><span id="L-2"><a href="#L-2"><span class="linenos"> 2</span></a> </span><span id="L-2"><a href="#L-2"><span class="linenos"> 2</span></a>
</span><span id="L-3"><a href="#L-3"><span class="linenos"> 3</span></a> </span><span id="L-3"><a href="#L-3"><span class="linenos"> 3</span></a><span class="n">gammaX</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span>
</span><span id="L-4"><a href="#L-4"><span class="linenos"> 4</span></a><span class="n">gammaX</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span> </span><span id="L-4"><a href="#L-4"><span class="linenos"> 4</span></a> <span class="p">[[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="n">j</span><span class="p">],</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="n">j</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="n">j</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="n">j</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">]],</span>
</span><span id="L-5"><a href="#L-5"><span class="linenos"> 5</span></a> <span class="p">[[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="n">j</span><span class="p">],</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="n">j</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="n">j</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="n">j</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">]],</span> </span><span id="L-5"><a href="#L-5"><span class="linenos"> 5</span></a> <span class="n">dtype</span><span class="o">=</span><span class="nb">complex</span><span class="p">)</span>
</span><span id="L-6"><a href="#L-6"><span class="linenos"> 6</span></a> <span class="n">dtype</span><span class="o">=</span><span class="nb">complex</span><span class="p">)</span> </span><span id="L-6"><a href="#L-6"><span class="linenos"> 6</span></a><span class="n">gammaY</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span>
</span><span id="L-7"><a href="#L-7"><span class="linenos"> 7</span></a><span class="n">gammaY</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span> </span><span id="L-7"><a href="#L-7"><span class="linenos"> 7</span></a> <span class="p">[[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">],</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">]],</span>
</span><span id="L-8"><a href="#L-8"><span class="linenos"> 8</span></a> <span class="p">[[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">],</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">]],</span> </span><span id="L-8"><a href="#L-8"><span class="linenos"> 8</span></a> <span class="n">dtype</span><span class="o">=</span><span class="nb">complex</span><span class="p">)</span>
</span><span id="L-9"><a href="#L-9"><span class="linenos"> 9</span></a> <span class="n">dtype</span><span class="o">=</span><span class="nb">complex</span><span class="p">)</span> </span><span id="L-9"><a href="#L-9"><span class="linenos"> 9</span></a><span class="n">gammaZ</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span>
</span><span id="L-10"><a href="#L-10"><span class="linenos">10</span></a><span class="n">gammaZ</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span> </span><span id="L-10"><a href="#L-10"><span class="linenos">10</span></a> <span class="p">[[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="n">j</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="n">j</span><span class="p">],</span> <span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="n">j</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="n">j</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">]],</span>
</span><span id="L-11"><a href="#L-11"><span class="linenos">11</span></a> <span class="p">[[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="n">j</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="n">j</span><span class="p">],</span> <span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="n">j</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="n">j</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">]],</span> </span><span id="L-11"><a href="#L-11"><span class="linenos">11</span></a> <span class="n">dtype</span><span class="o">=</span><span class="nb">complex</span><span class="p">)</span>
</span><span id="L-12"><a href="#L-12"><span class="linenos">12</span></a> <span class="n">dtype</span><span class="o">=</span><span class="nb">complex</span><span class="p">)</span> </span><span id="L-12"><a href="#L-12"><span class="linenos">12</span></a><span class="n">gammaT</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span>
</span><span id="L-13"><a href="#L-13"><span class="linenos">13</span></a><span class="n">gammaT</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span> </span><span id="L-13"><a href="#L-13"><span class="linenos">13</span></a> <span class="p">[[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">],</span> <span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">]],</span>
</span><span id="L-14"><a href="#L-14"><span class="linenos">14</span></a> <span class="p">[[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">],</span> <span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">]],</span> </span><span id="L-14"><a href="#L-14"><span class="linenos">14</span></a> <span class="n">dtype</span><span class="o">=</span><span class="nb">complex</span><span class="p">)</span>
</span><span id="L-15"><a href="#L-15"><span class="linenos">15</span></a> <span class="n">dtype</span><span class="o">=</span><span class="nb">complex</span><span class="p">)</span> </span><span id="L-15"><a href="#L-15"><span class="linenos">15</span></a><span class="n">gamma</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">gammaX</span><span class="p">,</span> <span class="n">gammaY</span><span class="p">,</span> <span class="n">gammaZ</span><span class="p">,</span> <span class="n">gammaT</span><span class="p">])</span>
</span><span id="L-16"><a href="#L-16"><span class="linenos">16</span></a><span class="n">gamma</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">gammaX</span><span class="p">,</span> <span class="n">gammaY</span><span class="p">,</span> <span class="n">gammaZ</span><span class="p">,</span> <span class="n">gammaT</span><span class="p">])</span> </span><span id="L-16"><a href="#L-16"><span class="linenos">16</span></a><span class="n">gamma5</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span>
</span><span id="L-17"><a href="#L-17"><span class="linenos">17</span></a><span class="n">gamma5</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span> </span><span id="L-17"><a href="#L-17"><span class="linenos">17</span></a> <span class="p">[[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">]],</span>
</span><span id="L-18"><a href="#L-18"><span class="linenos">18</span></a> <span class="p">[[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">]],</span> </span><span id="L-18"><a href="#L-18"><span class="linenos">18</span></a> <span class="n">dtype</span><span class="o">=</span><span class="nb">complex</span><span class="p">)</span>
</span><span id="L-19"><a href="#L-19"><span class="linenos">19</span></a> <span class="n">dtype</span><span class="o">=</span><span class="nb">complex</span><span class="p">)</span> </span><span id="L-19"><a href="#L-19"><span class="linenos">19</span></a><span class="n">identity</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span>
</span><span id="L-20"><a href="#L-20"><span class="linenos">20</span></a><span class="n">identity</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span> </span><span id="L-20"><a href="#L-20"><span class="linenos">20</span></a> <span class="p">[[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">]],</span>
</span><span id="L-21"><a href="#L-21"><span class="linenos">21</span></a> <span class="p">[[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">]],</span> </span><span id="L-21"><a href="#L-21"><span class="linenos">21</span></a> <span class="n">dtype</span><span class="o">=</span><span class="nb">complex</span><span class="p">)</span>
</span><span id="L-22"><a href="#L-22"><span class="linenos">22</span></a> <span class="n">dtype</span><span class="o">=</span><span class="nb">complex</span><span class="p">)</span> </span><span id="L-22"><a href="#L-22"><span class="linenos">22</span></a>
</span><span id="L-23"><a href="#L-23"><span class="linenos">23</span></a> </span><span id="L-23"><a href="#L-23"><span class="linenos">23</span></a>
</span><span id="L-24"><a href="#L-24"><span class="linenos">24</span></a> </span><span id="L-24"><a href="#L-24"><span class="linenos">24</span></a><span class="k">def</span><span class="w"> </span><span class="nf">epsilon_tensor</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">,</span> <span class="n">k</span><span class="p">):</span>
</span><span id="L-25"><a href="#L-25"><span class="linenos">25</span></a><span class="k">def</span><span class="w"> </span><span class="nf">epsilon_tensor</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">,</span> <span class="n">k</span><span class="p">):</span> </span><span id="L-25"><a href="#L-25"><span class="linenos">25</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Rank-3 epsilon tensor</span>
</span><span id="L-26"><a href="#L-26"><span class="linenos">26</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Rank-3 epsilon tensor</span> </span><span id="L-26"><a href="#L-26"><span class="linenos">26</span></a>
</span><span id="L-27"><a href="#L-27"><span class="linenos">27</span></a> </span><span id="L-27"><a href="#L-27"><span class="linenos">27</span></a><span class="sd"> Based on https://codegolf.stackexchange.com/a/160375</span>
</span><span id="L-28"><a href="#L-28"><span class="linenos">28</span></a><span class="sd"> Based on https://codegolf.stackexchange.com/a/160375</span> </span><span id="L-28"><a href="#L-28"><span class="linenos">28</span></a>
</span><span id="L-29"><a href="#L-29"><span class="linenos">29</span></a> </span><span id="L-29"><a href="#L-29"><span class="linenos">29</span></a><span class="sd"> Returns</span>
</span><span id="L-30"><a href="#L-30"><span class="linenos">30</span></a><span class="sd"> Returns</span> </span><span id="L-30"><a href="#L-30"><span class="linenos">30</span></a><span class="sd"> -------</span>
</span><span id="L-31"><a href="#L-31"><span class="linenos">31</span></a><span class="sd"> -------</span> </span><span id="L-31"><a href="#L-31"><span class="linenos">31</span></a><span class="sd"> elem : int</span>
</span><span id="L-32"><a href="#L-32"><span class="linenos">32</span></a><span class="sd"> elem : int</span> </span><span id="L-32"><a href="#L-32"><span class="linenos">32</span></a><span class="sd"> Element (i,j,k) of the epsilon tensor of rank 3</span>
</span><span id="L-33"><a href="#L-33"><span class="linenos">33</span></a><span class="sd"> Element (i,j,k) of the epsilon tensor of rank 3</span> </span><span id="L-33"><a href="#L-33"><span class="linenos">33</span></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="L-34"><a href="#L-34"><span class="linenos">34</span></a><span class="sd"> &quot;&quot;&quot;</span> </span><span id="L-34"><a href="#L-34"><span class="linenos">34</span></a> <span class="n">test_set</span> <span class="o">=</span> <span class="nb">set</span><span class="p">((</span><span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">,</span> <span class="n">k</span><span class="p">))</span>
</span><span id="L-35"><a href="#L-35"><span class="linenos">35</span></a> <span class="n">test_set</span> <span class="o">=</span> <span class="nb">set</span><span class="p">((</span><span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">,</span> <span class="n">k</span><span class="p">))</span> </span><span id="L-35"><a href="#L-35"><span class="linenos">35</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="p">(</span><span class="n">test_set</span> <span class="o">&lt;=</span> <span class="nb">set</span><span class="p">((</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">3</span><span class="p">))</span> <span class="ow">or</span> <span class="n">test_set</span> <span class="o">&lt;=</span> <span class="nb">set</span><span class="p">((</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">))):</span>
</span><span id="L-36"><a href="#L-36"><span class="linenos">36</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="p">(</span><span class="n">test_set</span> <span class="o">&lt;=</span> <span class="nb">set</span><span class="p">((</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">3</span><span class="p">))</span> <span class="ow">or</span> <span class="n">test_set</span> <span class="o">&lt;=</span> <span class="nb">set</span><span class="p">((</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">))):</span> </span><span id="L-36"><a href="#L-36"><span class="linenos">36</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;Unexpected input&quot;</span><span class="p">,</span> <span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">,</span> <span class="n">k</span><span class="p">)</span>
</span><span id="L-37"><a href="#L-37"><span class="linenos">37</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;Unexpected input&quot;</span><span class="p">,</span> <span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">,</span> <span class="n">k</span><span class="p">)</span> </span><span id="L-37"><a href="#L-37"><span class="linenos">37</span></a>
</span><span id="L-38"><a href="#L-38"><span class="linenos">38</span></a> </span><span id="L-38"><a href="#L-38"><span class="linenos">38</span></a> <span class="k">return</span> <span class="p">(</span><span class="n">i</span> <span class="o">-</span> <span class="n">j</span><span class="p">)</span> <span class="o">*</span> <span class="p">(</span><span class="n">j</span> <span class="o">-</span> <span class="n">k</span><span class="p">)</span> <span class="o">*</span> <span class="p">(</span><span class="n">k</span> <span class="o">-</span> <span class="n">i</span><span class="p">)</span> <span class="o">/</span> <span class="mi">2</span>
</span><span id="L-39"><a href="#L-39"><span class="linenos">39</span></a> <span class="k">return</span> <span class="p">(</span><span class="n">i</span> <span class="o">-</span> <span class="n">j</span><span class="p">)</span> <span class="o">*</span> <span class="p">(</span><span class="n">j</span> <span class="o">-</span> <span class="n">k</span><span class="p">)</span> <span class="o">*</span> <span class="p">(</span><span class="n">k</span> <span class="o">-</span> <span class="n">i</span><span class="p">)</span> <span class="o">/</span> <span class="mi">2</span> </span><span id="L-39"><a href="#L-39"><span class="linenos">39</span></a>
</span><span id="L-40"><a href="#L-40"><span class="linenos">40</span></a> </span><span id="L-40"><a href="#L-40"><span class="linenos">40</span></a>
</span><span id="L-41"><a href="#L-41"><span class="linenos">41</span></a> </span><span id="L-41"><a href="#L-41"><span class="linenos">41</span></a><span class="k">def</span><span class="w"> </span><span class="nf">epsilon_tensor_rank4</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">,</span> <span class="n">k</span><span class="p">,</span> <span class="n">o</span><span class="p">):</span>
</span><span id="L-42"><a href="#L-42"><span class="linenos">42</span></a><span class="k">def</span><span class="w"> </span><span class="nf">epsilon_tensor_rank4</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">,</span> <span class="n">k</span><span class="p">,</span> <span class="n">o</span><span class="p">):</span> </span><span id="L-42"><a href="#L-42"><span class="linenos">42</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Rank-4 epsilon tensor</span>
</span><span id="L-43"><a href="#L-43"><span class="linenos">43</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Rank-4 epsilon tensor</span> </span><span id="L-43"><a href="#L-43"><span class="linenos">43</span></a>
</span><span id="L-44"><a href="#L-44"><span class="linenos">44</span></a> </span><span id="L-44"><a href="#L-44"><span class="linenos">44</span></a><span class="sd"> Extension of https://codegolf.stackexchange.com/a/160375</span>
</span><span id="L-45"><a href="#L-45"><span class="linenos">45</span></a><span class="sd"> Extension of https://codegolf.stackexchange.com/a/160375</span> </span><span id="L-45"><a href="#L-45"><span class="linenos">45</span></a>
</span><span id="L-46"><a href="#L-46"><span class="linenos">46</span></a> </span><span id="L-46"><a href="#L-46"><span class="linenos">46</span></a>
</span><span id="L-47"><a href="#L-47"><span class="linenos">47</span></a> </span><span id="L-47"><a href="#L-47"><span class="linenos">47</span></a><span class="sd"> Returns</span>
</span><span id="L-48"><a href="#L-48"><span class="linenos">48</span></a><span class="sd"> Returns</span> </span><span id="L-48"><a href="#L-48"><span class="linenos">48</span></a><span class="sd"> -------</span>
</span><span id="L-49"><a href="#L-49"><span class="linenos">49</span></a><span class="sd"> -------</span> </span><span id="L-49"><a href="#L-49"><span class="linenos">49</span></a><span class="sd"> elem : int</span>
</span><span id="L-50"><a href="#L-50"><span class="linenos">50</span></a><span class="sd"> elem : int</span> </span><span id="L-50"><a href="#L-50"><span class="linenos">50</span></a><span class="sd"> Element (i,j,k,o) of the epsilon tensor of rank 4</span>
</span><span id="L-51"><a href="#L-51"><span class="linenos">51</span></a><span class="sd"> Element (i,j,k,o) of the epsilon tensor of rank 4</span> </span><span id="L-51"><a href="#L-51"><span class="linenos">51</span></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="L-52"><a href="#L-52"><span class="linenos">52</span></a><span class="sd"> &quot;&quot;&quot;</span> </span><span id="L-52"><a href="#L-52"><span class="linenos">52</span></a> <span class="n">test_set</span> <span class="o">=</span> <span class="nb">set</span><span class="p">((</span><span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">,</span> <span class="n">k</span><span class="p">,</span> <span class="n">o</span><span class="p">))</span>
</span><span id="L-53"><a href="#L-53"><span class="linenos">53</span></a> <span class="n">test_set</span> <span class="o">=</span> <span class="nb">set</span><span class="p">((</span><span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">,</span> <span class="n">k</span><span class="p">,</span> <span class="n">o</span><span class="p">))</span> </span><span id="L-53"><a href="#L-53"><span class="linenos">53</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="p">(</span><span class="n">test_set</span> <span class="o">&lt;=</span> <span class="nb">set</span><span class="p">((</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">4</span><span class="p">))</span> <span class="ow">or</span> <span class="n">test_set</span> <span class="o">&lt;=</span> <span class="nb">set</span><span class="p">((</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">3</span><span class="p">))):</span>
</span><span id="L-54"><a href="#L-54"><span class="linenos">54</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="p">(</span><span class="n">test_set</span> <span class="o">&lt;=</span> <span class="nb">set</span><span class="p">((</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">4</span><span class="p">))</span> <span class="ow">or</span> <span class="n">test_set</span> <span class="o">&lt;=</span> <span class="nb">set</span><span class="p">((</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">3</span><span class="p">))):</span> </span><span id="L-54"><a href="#L-54"><span class="linenos">54</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;Unexpected input&quot;</span><span class="p">,</span> <span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">,</span> <span class="n">k</span><span class="p">,</span> <span class="n">o</span><span class="p">)</span>
</span><span id="L-55"><a href="#L-55"><span class="linenos">55</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;Unexpected input&quot;</span><span class="p">,</span> <span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">,</span> <span class="n">k</span><span class="p">,</span> <span class="n">o</span><span class="p">)</span> </span><span id="L-55"><a href="#L-55"><span class="linenos">55</span></a>
</span><span id="L-56"><a href="#L-56"><span class="linenos">56</span></a> </span><span id="L-56"><a href="#L-56"><span class="linenos">56</span></a> <span class="k">return</span> <span class="p">(</span><span class="n">i</span> <span class="o">-</span> <span class="n">j</span><span class="p">)</span> <span class="o">*</span> <span class="p">(</span><span class="n">j</span> <span class="o">-</span> <span class="n">k</span><span class="p">)</span> <span class="o">*</span> <span class="p">(</span><span class="n">k</span> <span class="o">-</span> <span class="n">i</span><span class="p">)</span> <span class="o">*</span> <span class="p">(</span><span class="n">i</span> <span class="o">-</span> <span class="n">o</span><span class="p">)</span> <span class="o">*</span> <span class="p">(</span><span class="n">j</span> <span class="o">-</span> <span class="n">o</span><span class="p">)</span> <span class="o">*</span> <span class="p">(</span><span class="n">o</span> <span class="o">-</span> <span class="n">k</span><span class="p">)</span> <span class="o">/</span> <span class="mi">12</span>
</span><span id="L-57"><a href="#L-57"><span class="linenos">57</span></a> <span class="k">return</span> <span class="p">(</span><span class="n">i</span> <span class="o">-</span> <span class="n">j</span><span class="p">)</span> <span class="o">*</span> <span class="p">(</span><span class="n">j</span> <span class="o">-</span> <span class="n">k</span><span class="p">)</span> <span class="o">*</span> <span class="p">(</span><span class="n">k</span> <span class="o">-</span> <span class="n">i</span><span class="p">)</span> <span class="o">*</span> <span class="p">(</span><span class="n">i</span> <span class="o">-</span> <span class="n">o</span><span class="p">)</span> <span class="o">*</span> <span class="p">(</span><span class="n">j</span> <span class="o">-</span> <span class="n">o</span><span class="p">)</span> <span class="o">*</span> <span class="p">(</span><span class="n">o</span> <span class="o">-</span> <span class="n">k</span><span class="p">)</span> <span class="o">/</span> <span class="mi">12</span> </span><span id="L-57"><a href="#L-57"><span class="linenos">57</span></a>
</span><span id="L-58"><a href="#L-58"><span class="linenos">58</span></a> </span><span id="L-58"><a href="#L-58"><span class="linenos">58</span></a>
</span><span id="L-59"><a href="#L-59"><span class="linenos">59</span></a> </span><span id="L-59"><a href="#L-59"><span class="linenos">59</span></a><span class="k">def</span><span class="w"> </span><span class="nf">Grid_gamma</span><span class="p">(</span><span class="n">gamma_tag</span><span class="p">):</span>
</span><span id="L-60"><a href="#L-60"><span class="linenos">60</span></a><span class="k">def</span><span class="w"> </span><span class="nf">Grid_gamma</span><span class="p">(</span><span class="n">gamma_tag</span><span class="p">):</span> </span><span id="L-60"><a href="#L-60"><span class="linenos">60</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Returns gamma matrix in Grid labeling.&quot;&quot;&quot;</span>
</span><span id="L-61"><a href="#L-61"><span class="linenos">61</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Returns gamma matrix in Grid labeling.&quot;&quot;&quot;</span> </span><span id="L-61"><a href="#L-61"><span class="linenos">61</span></a> <span class="k">if</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;Identity&#39;</span><span class="p">:</span>
</span><span id="L-62"><a href="#L-62"><span class="linenos">62</span></a> <span class="k">if</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;Identity&#39;</span><span class="p">:</span> </span><span id="L-62"><a href="#L-62"><span class="linenos">62</span></a> <span class="n">g</span> <span class="o">=</span> <span class="n">identity</span>
</span><span id="L-63"><a href="#L-63"><span class="linenos">63</span></a> <span class="n">g</span> <span class="o">=</span> <span class="n">identity</span> </span><span id="L-63"><a href="#L-63"><span class="linenos">63</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;Gamma5&#39;</span><span class="p">:</span>
</span><span id="L-64"><a href="#L-64"><span class="linenos">64</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;Gamma5&#39;</span><span class="p">:</span> </span><span id="L-64"><a href="#L-64"><span class="linenos">64</span></a> <span class="n">g</span> <span class="o">=</span> <span class="n">gamma5</span>
</span><span id="L-65"><a href="#L-65"><span class="linenos">65</span></a> <span class="n">g</span> <span class="o">=</span> <span class="n">gamma5</span> </span><span id="L-65"><a href="#L-65"><span class="linenos">65</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;GammaX&#39;</span><span class="p">:</span>
</span><span id="L-66"><a href="#L-66"><span class="linenos">66</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;GammaX&#39;</span><span class="p">:</span> </span><span id="L-66"><a href="#L-66"><span class="linenos">66</span></a> <span class="n">g</span> <span class="o">=</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
</span><span id="L-67"><a href="#L-67"><span class="linenos">67</span></a> <span class="n">g</span> <span class="o">=</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> </span><span id="L-67"><a href="#L-67"><span class="linenos">67</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;GammaY&#39;</span><span class="p">:</span>
</span><span id="L-68"><a href="#L-68"><span class="linenos">68</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;GammaY&#39;</span><span class="p">:</span> </span><span id="L-68"><a href="#L-68"><span class="linenos">68</span></a> <span class="n">g</span> <span class="o">=</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
</span><span id="L-69"><a href="#L-69"><span class="linenos">69</span></a> <span class="n">g</span> <span class="o">=</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> </span><span id="L-69"><a href="#L-69"><span class="linenos">69</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;GammaZ&#39;</span><span class="p">:</span>
</span><span id="L-70"><a href="#L-70"><span class="linenos">70</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;GammaZ&#39;</span><span class="p">:</span> </span><span id="L-70"><a href="#L-70"><span class="linenos">70</span></a> <span class="n">g</span> <span class="o">=</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
</span><span id="L-71"><a href="#L-71"><span class="linenos">71</span></a> <span class="n">g</span> <span class="o">=</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> </span><span id="L-71"><a href="#L-71"><span class="linenos">71</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;GammaT&#39;</span><span class="p">:</span>
</span><span id="L-72"><a href="#L-72"><span class="linenos">72</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;GammaT&#39;</span><span class="p">:</span> </span><span id="L-72"><a href="#L-72"><span class="linenos">72</span></a> <span class="n">g</span> <span class="o">=</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span>
</span><span id="L-73"><a href="#L-73"><span class="linenos">73</span></a> <span class="n">g</span> <span class="o">=</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> </span><span id="L-73"><a href="#L-73"><span class="linenos">73</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;GammaXGamma5&#39;</span><span class="p">:</span>
</span><span id="L-74"><a href="#L-74"><span class="linenos">74</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;GammaXGamma5&#39;</span><span class="p">:</span> </span><span id="L-74"><a href="#L-74"><span class="linenos">74</span></a> <span class="n">g</span> <span class="o">=</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma5</span>
</span><span id="L-75"><a href="#L-75"><span class="linenos">75</span></a> <span class="n">g</span> <span class="o">=</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma5</span> </span><span id="L-75"><a href="#L-75"><span class="linenos">75</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;GammaYGamma5&#39;</span><span class="p">:</span>
</span><span id="L-76"><a href="#L-76"><span class="linenos">76</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;GammaYGamma5&#39;</span><span class="p">:</span> </span><span id="L-76"><a href="#L-76"><span class="linenos">76</span></a> <span class="n">g</span> <span class="o">=</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma5</span>
</span><span id="L-77"><a href="#L-77"><span class="linenos">77</span></a> <span class="n">g</span> <span class="o">=</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma5</span> </span><span id="L-77"><a href="#L-77"><span class="linenos">77</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;GammaZGamma5&#39;</span><span class="p">:</span>
</span><span id="L-78"><a href="#L-78"><span class="linenos">78</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;GammaZGamma5&#39;</span><span class="p">:</span> </span><span id="L-78"><a href="#L-78"><span class="linenos">78</span></a> <span class="n">g</span> <span class="o">=</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma5</span>
</span><span id="L-79"><a href="#L-79"><span class="linenos">79</span></a> <span class="n">g</span> <span class="o">=</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma5</span> </span><span id="L-79"><a href="#L-79"><span class="linenos">79</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;GammaTGamma5&#39;</span><span class="p">:</span>
</span><span id="L-80"><a href="#L-80"><span class="linenos">80</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;GammaTGamma5&#39;</span><span class="p">:</span> </span><span id="L-80"><a href="#L-80"><span class="linenos">80</span></a> <span class="n">g</span> <span class="o">=</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma5</span>
</span><span id="L-81"><a href="#L-81"><span class="linenos">81</span></a> <span class="n">g</span> <span class="o">=</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma5</span> </span><span id="L-81"><a href="#L-81"><span class="linenos">81</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;SigmaXT&#39;</span><span class="p">:</span>
</span><span id="L-82"><a href="#L-82"><span class="linenos">82</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;SigmaXT&#39;</span><span class="p">:</span> </span><span id="L-82"><a href="#L-82"><span class="linenos">82</span></a> <span class="n">g</span> <span class="o">=</span> <span class="mf">0.5</span> <span class="o">*</span> <span class="p">(</span><span class="n">gamma</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">-</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
</span><span id="L-83"><a href="#L-83"><span class="linenos">83</span></a> <span class="n">g</span> <span class="o">=</span> <span class="mf">0.5</span> <span class="o">*</span> <span class="p">(</span><span class="n">gamma</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">-</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> </span><span id="L-83"><a href="#L-83"><span class="linenos">83</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;SigmaXY&#39;</span><span class="p">:</span>
</span><span id="L-84"><a href="#L-84"><span class="linenos">84</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;SigmaXY&#39;</span><span class="p">:</span> </span><span id="L-84"><a href="#L-84"><span class="linenos">84</span></a> <span class="n">g</span> <span class="o">=</span> <span class="mf">0.5</span> <span class="o">*</span> <span class="p">(</span><span class="n">gamma</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">-</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
</span><span id="L-85"><a href="#L-85"><span class="linenos">85</span></a> <span class="n">g</span> <span class="o">=</span> <span class="mf">0.5</span> <span class="o">*</span> <span class="p">(</span><span class="n">gamma</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">-</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> </span><span id="L-85"><a href="#L-85"><span class="linenos">85</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;SigmaXZ&#39;</span><span class="p">:</span>
</span><span id="L-86"><a href="#L-86"><span class="linenos">86</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;SigmaXZ&#39;</span><span class="p">:</span> </span><span id="L-86"><a href="#L-86"><span class="linenos">86</span></a> <span class="n">g</span> <span class="o">=</span> <span class="mf">0.5</span> <span class="o">*</span> <span class="p">(</span><span class="n">gamma</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">-</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
</span><span id="L-87"><a href="#L-87"><span class="linenos">87</span></a> <span class="n">g</span> <span class="o">=</span> <span class="mf">0.5</span> <span class="o">*</span> <span class="p">(</span><span class="n">gamma</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">-</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> </span><span id="L-87"><a href="#L-87"><span class="linenos">87</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;SigmaYT&#39;</span><span class="p">:</span>
</span><span id="L-88"><a href="#L-88"><span class="linenos">88</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;SigmaYT&#39;</span><span class="p">:</span> </span><span id="L-88"><a href="#L-88"><span class="linenos">88</span></a> <span class="n">g</span> <span class="o">=</span> <span class="mf">0.5</span> <span class="o">*</span> <span class="p">(</span><span class="n">gamma</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">-</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
</span><span id="L-89"><a href="#L-89"><span class="linenos">89</span></a> <span class="n">g</span> <span class="o">=</span> <span class="mf">0.5</span> <span class="o">*</span> <span class="p">(</span><span class="n">gamma</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">-</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> </span><span id="L-89"><a href="#L-89"><span class="linenos">89</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;SigmaYZ&#39;</span><span class="p">:</span>
</span><span id="L-90"><a href="#L-90"><span class="linenos">90</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;SigmaYZ&#39;</span><span class="p">:</span> </span><span id="L-90"><a href="#L-90"><span class="linenos">90</span></a> <span class="n">g</span> <span class="o">=</span> <span class="mf">0.5</span> <span class="o">*</span> <span class="p">(</span><span class="n">gamma</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">-</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
</span><span id="L-91"><a href="#L-91"><span class="linenos">91</span></a> <span class="n">g</span> <span class="o">=</span> <span class="mf">0.5</span> <span class="o">*</span> <span class="p">(</span><span class="n">gamma</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">-</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> </span><span id="L-91"><a href="#L-91"><span class="linenos">91</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;SigmaZT&#39;</span><span class="p">:</span>
</span><span id="L-92"><a href="#L-92"><span class="linenos">92</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;SigmaZT&#39;</span><span class="p">:</span> </span><span id="L-92"><a href="#L-92"><span class="linenos">92</span></a> <span class="n">g</span> <span class="o">=</span> <span class="mf">0.5</span> <span class="o">*</span> <span class="p">(</span><span class="n">gamma</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">-</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
</span><span id="L-93"><a href="#L-93"><span class="linenos">93</span></a> <span class="n">g</span> <span class="o">=</span> <span class="mf">0.5</span> <span class="o">*</span> <span class="p">(</span><span class="n">gamma</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">-</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span> </span><span id="L-93"><a href="#L-93"><span class="linenos">93</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="L-94"><a href="#L-94"><span class="linenos">94</span></a> <span class="k">else</span><span class="p">:</span> </span><span id="L-94"><a href="#L-94"><span class="linenos">94</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s1">&#39;Unkown gamma structure&#39;</span><span class="p">,</span> <span class="n">gamma_tag</span><span class="p">)</span>
</span><span id="L-95"><a href="#L-95"><span class="linenos">95</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s1">&#39;Unkown gamma structure&#39;</span><span class="p">,</span> <span class="n">gamma_tag</span><span class="p">)</span> </span><span id="L-95"><a href="#L-95"><span class="linenos">95</span></a> <span class="k">return</span> <span class="n">g</span>
</span><span id="L-96"><a href="#L-96"><span class="linenos">96</span></a> <span class="k">return</span> <span class="n">g</span>
</span></pre></div> </span></pre></div>
@ -341,21 +340,21 @@
</div> </div>
<a class="headerlink" href="#epsilon_tensor"></a> <a class="headerlink" href="#epsilon_tensor"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="epsilon_tensor-26"><a href="#epsilon_tensor-26"><span class="linenos">26</span></a><span class="k">def</span><span class="w"> </span><span class="nf">epsilon_tensor</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">,</span> <span class="n">k</span><span class="p">):</span> <div class="pdoc-code codehilite"><pre><span></span><span id="epsilon_tensor-25"><a href="#epsilon_tensor-25"><span class="linenos">25</span></a><span class="k">def</span><span class="w"> </span><span class="nf">epsilon_tensor</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">,</span> <span class="n">k</span><span class="p">):</span>
</span><span id="epsilon_tensor-27"><a href="#epsilon_tensor-27"><span class="linenos">27</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Rank-3 epsilon tensor</span> </span><span id="epsilon_tensor-26"><a href="#epsilon_tensor-26"><span class="linenos">26</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Rank-3 epsilon tensor</span>
</span><span id="epsilon_tensor-28"><a href="#epsilon_tensor-28"><span class="linenos">28</span></a> </span><span id="epsilon_tensor-27"><a href="#epsilon_tensor-27"><span class="linenos">27</span></a>
</span><span id="epsilon_tensor-29"><a href="#epsilon_tensor-29"><span class="linenos">29</span></a><span class="sd"> Based on https://codegolf.stackexchange.com/a/160375</span> </span><span id="epsilon_tensor-28"><a href="#epsilon_tensor-28"><span class="linenos">28</span></a><span class="sd"> Based on https://codegolf.stackexchange.com/a/160375</span>
</span><span id="epsilon_tensor-30"><a href="#epsilon_tensor-30"><span class="linenos">30</span></a> </span><span id="epsilon_tensor-29"><a href="#epsilon_tensor-29"><span class="linenos">29</span></a>
</span><span id="epsilon_tensor-31"><a href="#epsilon_tensor-31"><span class="linenos">31</span></a><span class="sd"> Returns</span> </span><span id="epsilon_tensor-30"><a href="#epsilon_tensor-30"><span class="linenos">30</span></a><span class="sd"> Returns</span>
</span><span id="epsilon_tensor-32"><a href="#epsilon_tensor-32"><span class="linenos">32</span></a><span class="sd"> -------</span> </span><span id="epsilon_tensor-31"><a href="#epsilon_tensor-31"><span class="linenos">31</span></a><span class="sd"> -------</span>
</span><span id="epsilon_tensor-33"><a href="#epsilon_tensor-33"><span class="linenos">33</span></a><span class="sd"> elem : int</span> </span><span id="epsilon_tensor-32"><a href="#epsilon_tensor-32"><span class="linenos">32</span></a><span class="sd"> elem : int</span>
</span><span id="epsilon_tensor-34"><a href="#epsilon_tensor-34"><span class="linenos">34</span></a><span class="sd"> Element (i,j,k) of the epsilon tensor of rank 3</span> </span><span id="epsilon_tensor-33"><a href="#epsilon_tensor-33"><span class="linenos">33</span></a><span class="sd"> Element (i,j,k) of the epsilon tensor of rank 3</span>
</span><span id="epsilon_tensor-35"><a href="#epsilon_tensor-35"><span class="linenos">35</span></a><span class="sd"> &quot;&quot;&quot;</span> </span><span id="epsilon_tensor-34"><a href="#epsilon_tensor-34"><span class="linenos">34</span></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="epsilon_tensor-36"><a href="#epsilon_tensor-36"><span class="linenos">36</span></a> <span class="n">test_set</span> <span class="o">=</span> <span class="nb">set</span><span class="p">((</span><span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">,</span> <span class="n">k</span><span class="p">))</span> </span><span id="epsilon_tensor-35"><a href="#epsilon_tensor-35"><span class="linenos">35</span></a> <span class="n">test_set</span> <span class="o">=</span> <span class="nb">set</span><span class="p">((</span><span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">,</span> <span class="n">k</span><span class="p">))</span>
</span><span id="epsilon_tensor-37"><a href="#epsilon_tensor-37"><span class="linenos">37</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="p">(</span><span class="n">test_set</span> <span class="o">&lt;=</span> <span class="nb">set</span><span class="p">((</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">3</span><span class="p">))</span> <span class="ow">or</span> <span class="n">test_set</span> <span class="o">&lt;=</span> <span class="nb">set</span><span class="p">((</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">))):</span> </span><span id="epsilon_tensor-36"><a href="#epsilon_tensor-36"><span class="linenos">36</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="p">(</span><span class="n">test_set</span> <span class="o">&lt;=</span> <span class="nb">set</span><span class="p">((</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">3</span><span class="p">))</span> <span class="ow">or</span> <span class="n">test_set</span> <span class="o">&lt;=</span> <span class="nb">set</span><span class="p">((</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">))):</span>
</span><span id="epsilon_tensor-38"><a href="#epsilon_tensor-38"><span class="linenos">38</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;Unexpected input&quot;</span><span class="p">,</span> <span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">,</span> <span class="n">k</span><span class="p">)</span> </span><span id="epsilon_tensor-37"><a href="#epsilon_tensor-37"><span class="linenos">37</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;Unexpected input&quot;</span><span class="p">,</span> <span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">,</span> <span class="n">k</span><span class="p">)</span>
</span><span id="epsilon_tensor-39"><a href="#epsilon_tensor-39"><span class="linenos">39</span></a> </span><span id="epsilon_tensor-38"><a href="#epsilon_tensor-38"><span class="linenos">38</span></a>
</span><span id="epsilon_tensor-40"><a href="#epsilon_tensor-40"><span class="linenos">40</span></a> <span class="k">return</span> <span class="p">(</span><span class="n">i</span> <span class="o">-</span> <span class="n">j</span><span class="p">)</span> <span class="o">*</span> <span class="p">(</span><span class="n">j</span> <span class="o">-</span> <span class="n">k</span><span class="p">)</span> <span class="o">*</span> <span class="p">(</span><span class="n">k</span> <span class="o">-</span> <span class="n">i</span><span class="p">)</span> <span class="o">/</span> <span class="mi">2</span> </span><span id="epsilon_tensor-39"><a href="#epsilon_tensor-39"><span class="linenos">39</span></a> <span class="k">return</span> <span class="p">(</span><span class="n">i</span> <span class="o">-</span> <span class="n">j</span><span class="p">)</span> <span class="o">*</span> <span class="p">(</span><span class="n">j</span> <span class="o">-</span> <span class="n">k</span><span class="p">)</span> <span class="o">*</span> <span class="p">(</span><span class="n">k</span> <span class="o">-</span> <span class="n">i</span><span class="p">)</span> <span class="o">/</span> <span class="mi">2</span>
</span></pre></div> </span></pre></div>
@ -384,22 +383,22 @@ Element (i,j,k) of the epsilon tensor of rank 3</li>
</div> </div>
<a class="headerlink" href="#epsilon_tensor_rank4"></a> <a class="headerlink" href="#epsilon_tensor_rank4"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="epsilon_tensor_rank4-43"><a href="#epsilon_tensor_rank4-43"><span class="linenos">43</span></a><span class="k">def</span><span class="w"> </span><span class="nf">epsilon_tensor_rank4</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">,</span> <span class="n">k</span><span class="p">,</span> <span class="n">o</span><span class="p">):</span> <div class="pdoc-code codehilite"><pre><span></span><span id="epsilon_tensor_rank4-42"><a href="#epsilon_tensor_rank4-42"><span class="linenos">42</span></a><span class="k">def</span><span class="w"> </span><span class="nf">epsilon_tensor_rank4</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">,</span> <span class="n">k</span><span class="p">,</span> <span class="n">o</span><span class="p">):</span>
</span><span id="epsilon_tensor_rank4-44"><a href="#epsilon_tensor_rank4-44"><span class="linenos">44</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Rank-4 epsilon tensor</span> </span><span id="epsilon_tensor_rank4-43"><a href="#epsilon_tensor_rank4-43"><span class="linenos">43</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Rank-4 epsilon tensor</span>
</span><span id="epsilon_tensor_rank4-45"><a href="#epsilon_tensor_rank4-45"><span class="linenos">45</span></a> </span><span id="epsilon_tensor_rank4-44"><a href="#epsilon_tensor_rank4-44"><span class="linenos">44</span></a>
</span><span id="epsilon_tensor_rank4-46"><a href="#epsilon_tensor_rank4-46"><span class="linenos">46</span></a><span class="sd"> Extension of https://codegolf.stackexchange.com/a/160375</span> </span><span id="epsilon_tensor_rank4-45"><a href="#epsilon_tensor_rank4-45"><span class="linenos">45</span></a><span class="sd"> Extension of https://codegolf.stackexchange.com/a/160375</span>
</span><span id="epsilon_tensor_rank4-46"><a href="#epsilon_tensor_rank4-46"><span class="linenos">46</span></a>
</span><span id="epsilon_tensor_rank4-47"><a href="#epsilon_tensor_rank4-47"><span class="linenos">47</span></a> </span><span id="epsilon_tensor_rank4-47"><a href="#epsilon_tensor_rank4-47"><span class="linenos">47</span></a>
</span><span id="epsilon_tensor_rank4-48"><a href="#epsilon_tensor_rank4-48"><span class="linenos">48</span></a> </span><span id="epsilon_tensor_rank4-48"><a href="#epsilon_tensor_rank4-48"><span class="linenos">48</span></a><span class="sd"> Returns</span>
</span><span id="epsilon_tensor_rank4-49"><a href="#epsilon_tensor_rank4-49"><span class="linenos">49</span></a><span class="sd"> Returns</span> </span><span id="epsilon_tensor_rank4-49"><a href="#epsilon_tensor_rank4-49"><span class="linenos">49</span></a><span class="sd"> -------</span>
</span><span id="epsilon_tensor_rank4-50"><a href="#epsilon_tensor_rank4-50"><span class="linenos">50</span></a><span class="sd"> -------</span> </span><span id="epsilon_tensor_rank4-50"><a href="#epsilon_tensor_rank4-50"><span class="linenos">50</span></a><span class="sd"> elem : int</span>
</span><span id="epsilon_tensor_rank4-51"><a href="#epsilon_tensor_rank4-51"><span class="linenos">51</span></a><span class="sd"> elem : int</span> </span><span id="epsilon_tensor_rank4-51"><a href="#epsilon_tensor_rank4-51"><span class="linenos">51</span></a><span class="sd"> Element (i,j,k,o) of the epsilon tensor of rank 4</span>
</span><span id="epsilon_tensor_rank4-52"><a href="#epsilon_tensor_rank4-52"><span class="linenos">52</span></a><span class="sd"> Element (i,j,k,o) of the epsilon tensor of rank 4</span> </span><span id="epsilon_tensor_rank4-52"><a href="#epsilon_tensor_rank4-52"><span class="linenos">52</span></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="epsilon_tensor_rank4-53"><a href="#epsilon_tensor_rank4-53"><span class="linenos">53</span></a><span class="sd"> &quot;&quot;&quot;</span> </span><span id="epsilon_tensor_rank4-53"><a href="#epsilon_tensor_rank4-53"><span class="linenos">53</span></a> <span class="n">test_set</span> <span class="o">=</span> <span class="nb">set</span><span class="p">((</span><span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">,</span> <span class="n">k</span><span class="p">,</span> <span class="n">o</span><span class="p">))</span>
</span><span id="epsilon_tensor_rank4-54"><a href="#epsilon_tensor_rank4-54"><span class="linenos">54</span></a> <span class="n">test_set</span> <span class="o">=</span> <span class="nb">set</span><span class="p">((</span><span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">,</span> <span class="n">k</span><span class="p">,</span> <span class="n">o</span><span class="p">))</span> </span><span id="epsilon_tensor_rank4-54"><a href="#epsilon_tensor_rank4-54"><span class="linenos">54</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="p">(</span><span class="n">test_set</span> <span class="o">&lt;=</span> <span class="nb">set</span><span class="p">((</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">4</span><span class="p">))</span> <span class="ow">or</span> <span class="n">test_set</span> <span class="o">&lt;=</span> <span class="nb">set</span><span class="p">((</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">3</span><span class="p">))):</span>
</span><span id="epsilon_tensor_rank4-55"><a href="#epsilon_tensor_rank4-55"><span class="linenos">55</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="p">(</span><span class="n">test_set</span> <span class="o">&lt;=</span> <span class="nb">set</span><span class="p">((</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">4</span><span class="p">))</span> <span class="ow">or</span> <span class="n">test_set</span> <span class="o">&lt;=</span> <span class="nb">set</span><span class="p">((</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">3</span><span class="p">))):</span> </span><span id="epsilon_tensor_rank4-55"><a href="#epsilon_tensor_rank4-55"><span class="linenos">55</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;Unexpected input&quot;</span><span class="p">,</span> <span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">,</span> <span class="n">k</span><span class="p">,</span> <span class="n">o</span><span class="p">)</span>
</span><span id="epsilon_tensor_rank4-56"><a href="#epsilon_tensor_rank4-56"><span class="linenos">56</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;Unexpected input&quot;</span><span class="p">,</span> <span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">,</span> <span class="n">k</span><span class="p">,</span> <span class="n">o</span><span class="p">)</span> </span><span id="epsilon_tensor_rank4-56"><a href="#epsilon_tensor_rank4-56"><span class="linenos">56</span></a>
</span><span id="epsilon_tensor_rank4-57"><a href="#epsilon_tensor_rank4-57"><span class="linenos">57</span></a> </span><span id="epsilon_tensor_rank4-57"><a href="#epsilon_tensor_rank4-57"><span class="linenos">57</span></a> <span class="k">return</span> <span class="p">(</span><span class="n">i</span> <span class="o">-</span> <span class="n">j</span><span class="p">)</span> <span class="o">*</span> <span class="p">(</span><span class="n">j</span> <span class="o">-</span> <span class="n">k</span><span class="p">)</span> <span class="o">*</span> <span class="p">(</span><span class="n">k</span> <span class="o">-</span> <span class="n">i</span><span class="p">)</span> <span class="o">*</span> <span class="p">(</span><span class="n">i</span> <span class="o">-</span> <span class="n">o</span><span class="p">)</span> <span class="o">*</span> <span class="p">(</span><span class="n">j</span> <span class="o">-</span> <span class="n">o</span><span class="p">)</span> <span class="o">*</span> <span class="p">(</span><span class="n">o</span> <span class="o">-</span> <span class="n">k</span><span class="p">)</span> <span class="o">/</span> <span class="mi">12</span>
</span><span id="epsilon_tensor_rank4-58"><a href="#epsilon_tensor_rank4-58"><span class="linenos">58</span></a> <span class="k">return</span> <span class="p">(</span><span class="n">i</span> <span class="o">-</span> <span class="n">j</span><span class="p">)</span> <span class="o">*</span> <span class="p">(</span><span class="n">j</span> <span class="o">-</span> <span class="n">k</span><span class="p">)</span> <span class="o">*</span> <span class="p">(</span><span class="n">k</span> <span class="o">-</span> <span class="n">i</span><span class="p">)</span> <span class="o">*</span> <span class="p">(</span><span class="n">i</span> <span class="o">-</span> <span class="n">o</span><span class="p">)</span> <span class="o">*</span> <span class="p">(</span><span class="n">j</span> <span class="o">-</span> <span class="n">o</span><span class="p">)</span> <span class="o">*</span> <span class="p">(</span><span class="n">o</span> <span class="o">-</span> <span class="n">k</span><span class="p">)</span> <span class="o">/</span> <span class="mi">12</span>
</span></pre></div> </span></pre></div>
@ -428,43 +427,43 @@ Element (i,j,k,o) of the epsilon tensor of rank 4</li>
</div> </div>
<a class="headerlink" href="#Grid_gamma"></a> <a class="headerlink" href="#Grid_gamma"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="Grid_gamma-61"><a href="#Grid_gamma-61"><span class="linenos">61</span></a><span class="k">def</span><span class="w"> </span><span class="nf">Grid_gamma</span><span class="p">(</span><span class="n">gamma_tag</span><span class="p">):</span> <div class="pdoc-code codehilite"><pre><span></span><span id="Grid_gamma-60"><a href="#Grid_gamma-60"><span class="linenos">60</span></a><span class="k">def</span><span class="w"> </span><span class="nf">Grid_gamma</span><span class="p">(</span><span class="n">gamma_tag</span><span class="p">):</span>
</span><span id="Grid_gamma-62"><a href="#Grid_gamma-62"><span class="linenos">62</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Returns gamma matrix in Grid labeling.&quot;&quot;&quot;</span> </span><span id="Grid_gamma-61"><a href="#Grid_gamma-61"><span class="linenos">61</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Returns gamma matrix in Grid labeling.&quot;&quot;&quot;</span>
</span><span id="Grid_gamma-63"><a href="#Grid_gamma-63"><span class="linenos">63</span></a> <span class="k">if</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;Identity&#39;</span><span class="p">:</span> </span><span id="Grid_gamma-62"><a href="#Grid_gamma-62"><span class="linenos">62</span></a> <span class="k">if</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;Identity&#39;</span><span class="p">:</span>
</span><span id="Grid_gamma-64"><a href="#Grid_gamma-64"><span class="linenos">64</span></a> <span class="n">g</span> <span class="o">=</span> <span class="n">identity</span> </span><span id="Grid_gamma-63"><a href="#Grid_gamma-63"><span class="linenos">63</span></a> <span class="n">g</span> <span class="o">=</span> <span class="n">identity</span>
</span><span id="Grid_gamma-65"><a href="#Grid_gamma-65"><span class="linenos">65</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;Gamma5&#39;</span><span class="p">:</span> </span><span id="Grid_gamma-64"><a href="#Grid_gamma-64"><span class="linenos">64</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;Gamma5&#39;</span><span class="p">:</span>
</span><span id="Grid_gamma-66"><a href="#Grid_gamma-66"><span class="linenos">66</span></a> <span class="n">g</span> <span class="o">=</span> <span class="n">gamma5</span> </span><span id="Grid_gamma-65"><a href="#Grid_gamma-65"><span class="linenos">65</span></a> <span class="n">g</span> <span class="o">=</span> <span class="n">gamma5</span>
</span><span id="Grid_gamma-67"><a href="#Grid_gamma-67"><span class="linenos">67</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;GammaX&#39;</span><span class="p">:</span> </span><span id="Grid_gamma-66"><a href="#Grid_gamma-66"><span class="linenos">66</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;GammaX&#39;</span><span class="p">:</span>
</span><span id="Grid_gamma-68"><a href="#Grid_gamma-68"><span class="linenos">68</span></a> <span class="n">g</span> <span class="o">=</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> </span><span id="Grid_gamma-67"><a href="#Grid_gamma-67"><span class="linenos">67</span></a> <span class="n">g</span> <span class="o">=</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
</span><span id="Grid_gamma-69"><a href="#Grid_gamma-69"><span class="linenos">69</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;GammaY&#39;</span><span class="p">:</span> </span><span id="Grid_gamma-68"><a href="#Grid_gamma-68"><span class="linenos">68</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;GammaY&#39;</span><span class="p">:</span>
</span><span id="Grid_gamma-70"><a href="#Grid_gamma-70"><span class="linenos">70</span></a> <span class="n">g</span> <span class="o">=</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> </span><span id="Grid_gamma-69"><a href="#Grid_gamma-69"><span class="linenos">69</span></a> <span class="n">g</span> <span class="o">=</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
</span><span id="Grid_gamma-71"><a href="#Grid_gamma-71"><span class="linenos">71</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;GammaZ&#39;</span><span class="p">:</span> </span><span id="Grid_gamma-70"><a href="#Grid_gamma-70"><span class="linenos">70</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;GammaZ&#39;</span><span class="p">:</span>
</span><span id="Grid_gamma-72"><a href="#Grid_gamma-72"><span class="linenos">72</span></a> <span class="n">g</span> <span class="o">=</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> </span><span id="Grid_gamma-71"><a href="#Grid_gamma-71"><span class="linenos">71</span></a> <span class="n">g</span> <span class="o">=</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
</span><span id="Grid_gamma-73"><a href="#Grid_gamma-73"><span class="linenos">73</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;GammaT&#39;</span><span class="p">:</span> </span><span id="Grid_gamma-72"><a href="#Grid_gamma-72"><span class="linenos">72</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;GammaT&#39;</span><span class="p">:</span>
</span><span id="Grid_gamma-74"><a href="#Grid_gamma-74"><span class="linenos">74</span></a> <span class="n">g</span> <span class="o">=</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> </span><span id="Grid_gamma-73"><a href="#Grid_gamma-73"><span class="linenos">73</span></a> <span class="n">g</span> <span class="o">=</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span>
</span><span id="Grid_gamma-75"><a href="#Grid_gamma-75"><span class="linenos">75</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;GammaXGamma5&#39;</span><span class="p">:</span> </span><span id="Grid_gamma-74"><a href="#Grid_gamma-74"><span class="linenos">74</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;GammaXGamma5&#39;</span><span class="p">:</span>
</span><span id="Grid_gamma-76"><a href="#Grid_gamma-76"><span class="linenos">76</span></a> <span class="n">g</span> <span class="o">=</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma5</span> </span><span id="Grid_gamma-75"><a href="#Grid_gamma-75"><span class="linenos">75</span></a> <span class="n">g</span> <span class="o">=</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma5</span>
</span><span id="Grid_gamma-77"><a href="#Grid_gamma-77"><span class="linenos">77</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;GammaYGamma5&#39;</span><span class="p">:</span> </span><span id="Grid_gamma-76"><a href="#Grid_gamma-76"><span class="linenos">76</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;GammaYGamma5&#39;</span><span class="p">:</span>
</span><span id="Grid_gamma-78"><a href="#Grid_gamma-78"><span class="linenos">78</span></a> <span class="n">g</span> <span class="o">=</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma5</span> </span><span id="Grid_gamma-77"><a href="#Grid_gamma-77"><span class="linenos">77</span></a> <span class="n">g</span> <span class="o">=</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma5</span>
</span><span id="Grid_gamma-79"><a href="#Grid_gamma-79"><span class="linenos">79</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;GammaZGamma5&#39;</span><span class="p">:</span> </span><span id="Grid_gamma-78"><a href="#Grid_gamma-78"><span class="linenos">78</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;GammaZGamma5&#39;</span><span class="p">:</span>
</span><span id="Grid_gamma-80"><a href="#Grid_gamma-80"><span class="linenos">80</span></a> <span class="n">g</span> <span class="o">=</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma5</span> </span><span id="Grid_gamma-79"><a href="#Grid_gamma-79"><span class="linenos">79</span></a> <span class="n">g</span> <span class="o">=</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma5</span>
</span><span id="Grid_gamma-81"><a href="#Grid_gamma-81"><span class="linenos">81</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;GammaTGamma5&#39;</span><span class="p">:</span> </span><span id="Grid_gamma-80"><a href="#Grid_gamma-80"><span class="linenos">80</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;GammaTGamma5&#39;</span><span class="p">:</span>
</span><span id="Grid_gamma-82"><a href="#Grid_gamma-82"><span class="linenos">82</span></a> <span class="n">g</span> <span class="o">=</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma5</span> </span><span id="Grid_gamma-81"><a href="#Grid_gamma-81"><span class="linenos">81</span></a> <span class="n">g</span> <span class="o">=</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma5</span>
</span><span id="Grid_gamma-83"><a href="#Grid_gamma-83"><span class="linenos">83</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;SigmaXT&#39;</span><span class="p">:</span> </span><span id="Grid_gamma-82"><a href="#Grid_gamma-82"><span class="linenos">82</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;SigmaXT&#39;</span><span class="p">:</span>
</span><span id="Grid_gamma-84"><a href="#Grid_gamma-84"><span class="linenos">84</span></a> <span class="n">g</span> <span class="o">=</span> <span class="mf">0.5</span> <span class="o">*</span> <span class="p">(</span><span class="n">gamma</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">-</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> </span><span id="Grid_gamma-83"><a href="#Grid_gamma-83"><span class="linenos">83</span></a> <span class="n">g</span> <span class="o">=</span> <span class="mf">0.5</span> <span class="o">*</span> <span class="p">(</span><span class="n">gamma</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">-</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
</span><span id="Grid_gamma-85"><a href="#Grid_gamma-85"><span class="linenos">85</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;SigmaXY&#39;</span><span class="p">:</span> </span><span id="Grid_gamma-84"><a href="#Grid_gamma-84"><span class="linenos">84</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;SigmaXY&#39;</span><span class="p">:</span>
</span><span id="Grid_gamma-86"><a href="#Grid_gamma-86"><span class="linenos">86</span></a> <span class="n">g</span> <span class="o">=</span> <span class="mf">0.5</span> <span class="o">*</span> <span class="p">(</span><span class="n">gamma</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">-</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> </span><span id="Grid_gamma-85"><a href="#Grid_gamma-85"><span class="linenos">85</span></a> <span class="n">g</span> <span class="o">=</span> <span class="mf">0.5</span> <span class="o">*</span> <span class="p">(</span><span class="n">gamma</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">-</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
</span><span id="Grid_gamma-87"><a href="#Grid_gamma-87"><span class="linenos">87</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;SigmaXZ&#39;</span><span class="p">:</span> </span><span id="Grid_gamma-86"><a href="#Grid_gamma-86"><span class="linenos">86</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;SigmaXZ&#39;</span><span class="p">:</span>
</span><span id="Grid_gamma-88"><a href="#Grid_gamma-88"><span class="linenos">88</span></a> <span class="n">g</span> <span class="o">=</span> <span class="mf">0.5</span> <span class="o">*</span> <span class="p">(</span><span class="n">gamma</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">-</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> </span><span id="Grid_gamma-87"><a href="#Grid_gamma-87"><span class="linenos">87</span></a> <span class="n">g</span> <span class="o">=</span> <span class="mf">0.5</span> <span class="o">*</span> <span class="p">(</span><span class="n">gamma</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">-</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
</span><span id="Grid_gamma-89"><a href="#Grid_gamma-89"><span class="linenos">89</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;SigmaYT&#39;</span><span class="p">:</span> </span><span id="Grid_gamma-88"><a href="#Grid_gamma-88"><span class="linenos">88</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;SigmaYT&#39;</span><span class="p">:</span>
</span><span id="Grid_gamma-90"><a href="#Grid_gamma-90"><span class="linenos">90</span></a> <span class="n">g</span> <span class="o">=</span> <span class="mf">0.5</span> <span class="o">*</span> <span class="p">(</span><span class="n">gamma</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">-</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> </span><span id="Grid_gamma-89"><a href="#Grid_gamma-89"><span class="linenos">89</span></a> <span class="n">g</span> <span class="o">=</span> <span class="mf">0.5</span> <span class="o">*</span> <span class="p">(</span><span class="n">gamma</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">-</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
</span><span id="Grid_gamma-91"><a href="#Grid_gamma-91"><span class="linenos">91</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;SigmaYZ&#39;</span><span class="p">:</span> </span><span id="Grid_gamma-90"><a href="#Grid_gamma-90"><span class="linenos">90</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;SigmaYZ&#39;</span><span class="p">:</span>
</span><span id="Grid_gamma-92"><a href="#Grid_gamma-92"><span class="linenos">92</span></a> <span class="n">g</span> <span class="o">=</span> <span class="mf">0.5</span> <span class="o">*</span> <span class="p">(</span><span class="n">gamma</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">-</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> </span><span id="Grid_gamma-91"><a href="#Grid_gamma-91"><span class="linenos">91</span></a> <span class="n">g</span> <span class="o">=</span> <span class="mf">0.5</span> <span class="o">*</span> <span class="p">(</span><span class="n">gamma</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">-</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
</span><span id="Grid_gamma-93"><a href="#Grid_gamma-93"><span class="linenos">93</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;SigmaZT&#39;</span><span class="p">:</span> </span><span id="Grid_gamma-92"><a href="#Grid_gamma-92"><span class="linenos">92</span></a> <span class="k">elif</span> <span class="n">gamma_tag</span> <span class="o">==</span> <span class="s1">&#39;SigmaZT&#39;</span><span class="p">:</span>
</span><span id="Grid_gamma-94"><a href="#Grid_gamma-94"><span class="linenos">94</span></a> <span class="n">g</span> <span class="o">=</span> <span class="mf">0.5</span> <span class="o">*</span> <span class="p">(</span><span class="n">gamma</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">-</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span> </span><span id="Grid_gamma-93"><a href="#Grid_gamma-93"><span class="linenos">93</span></a> <span class="n">g</span> <span class="o">=</span> <span class="mf">0.5</span> <span class="o">*</span> <span class="p">(</span><span class="n">gamma</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">-</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">@</span> <span class="n">gamma</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
</span><span id="Grid_gamma-95"><a href="#Grid_gamma-95"><span class="linenos">95</span></a> <span class="k">else</span><span class="p">:</span> </span><span id="Grid_gamma-94"><a href="#Grid_gamma-94"><span class="linenos">94</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="Grid_gamma-96"><a href="#Grid_gamma-96"><span class="linenos">96</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s1">&#39;Unkown gamma structure&#39;</span><span class="p">,</span> <span class="n">gamma_tag</span><span class="p">)</span> </span><span id="Grid_gamma-95"><a href="#Grid_gamma-95"><span class="linenos">95</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s1">&#39;Unkown gamma structure&#39;</span><span class="p">,</span> <span class="n">gamma_tag</span><span class="p">)</span>
</span><span id="Grid_gamma-97"><a href="#Grid_gamma-97"><span class="linenos">97</span></a> <span class="k">return</span> <span class="n">g</span> </span><span id="Grid_gamma-96"><a href="#Grid_gamma-96"><span class="linenos">96</span></a> <span class="k">return</span> <span class="n">g</span>
</span></pre></div> </span></pre></div>

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@ -79,224 +79,226 @@
<label class="view-source-button" for="mod-misc-view-source"><span>View Source</span></label> <label class="view-source-button" for="mod-misc-view-source"><span>View Source</span></label>
<div class="pdoc-code codehilite"><pre><span></span><span id="L-1"><a href="#L-1"><span class="linenos"> 1</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">os</span> <div class="pdoc-code codehilite"><pre><span></span><span id="L-1"><a href="#L-1"><span class="linenos"> 1</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">fnmatch</span>
</span><span id="L-2"><a href="#L-2"><span class="linenos"> 2</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">fnmatch</span> </span><span id="L-2"><a href="#L-2"><span class="linenos"> 2</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">os</span>
</span><span id="L-3"><a href="#L-3"><span class="linenos"> 3</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">re</span> </span><span id="L-3"><a href="#L-3"><span class="linenos"> 3</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">re</span>
</span><span id="L-4"><a href="#L-4"><span class="linenos"> 4</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">struct</span> </span><span id="L-4"><a href="#L-4"><span class="linenos"> 4</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">struct</span>
</span><span id="L-5"><a href="#L-5"><span class="linenos"> 5</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">warnings</span> </span><span id="L-5"><a href="#L-5"><span class="linenos"> 5</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">warnings</span>
</span><span id="L-6"><a href="#L-6"><span class="linenos"> 6</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span> <span class="c1"># Thinly-wrapped numpy</span> </span><span id="L-6"><a href="#L-6"><span class="linenos"> 6</span></a>
</span><span id="L-7"><a href="#L-7"><span class="linenos"> 7</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">matplotlib.pyplot</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">plt</span> </span><span id="L-7"><a href="#L-7"><span class="linenos"> 7</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">matplotlib.pyplot</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">plt</span>
</span><span id="L-8"><a href="#L-8"><span class="linenos"> 8</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">matplotlib</span><span class="w"> </span><span class="kn">import</span> <span class="n">gridspec</span> </span><span id="L-8"><a href="#L-8"><span class="linenos"> 8</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span> <span class="c1"># Thinly-wrapped numpy</span>
</span><span id="L-9"><a href="#L-9"><span class="linenos"> 9</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">..obs</span><span class="w"> </span><span class="kn">import</span> <span class="n">Obs</span> </span><span id="L-9"><a href="#L-9"><span class="linenos"> 9</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">matplotlib</span><span class="w"> </span><span class="kn">import</span> <span class="n">gridspec</span>
</span><span id="L-10"><a href="#L-10"><span class="linenos"> 10</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">..fits</span><span class="w"> </span><span class="kn">import</span> <span class="n">fit_lin</span> </span><span id="L-10"><a href="#L-10"><span class="linenos"> 10</span></a>
</span><span id="L-11"><a href="#L-11"><span class="linenos"> 11</span></a> </span><span id="L-11"><a href="#L-11"><span class="linenos"> 11</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">..fits</span><span class="w"> </span><span class="kn">import</span> <span class="n">fit_lin</span>
</span><span id="L-12"><a href="#L-12"><span class="linenos"> 12</span></a> </span><span id="L-12"><a href="#L-12"><span class="linenos"> 12</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">..obs</span><span class="w"> </span><span class="kn">import</span> <span class="n">Obs</span>
</span><span id="L-13"><a href="#L-13"><span class="linenos"> 13</span></a><span class="k">def</span><span class="w"> </span><span class="nf">fit_t0</span><span class="p">(</span><span class="n">t2E_dict</span><span class="p">,</span> <span class="n">fit_range</span><span class="p">,</span> <span class="n">plot_fit</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">observable</span><span class="o">=</span><span class="s1">&#39;t0&#39;</span><span class="p">):</span> </span><span id="L-13"><a href="#L-13"><span class="linenos"> 13</span></a>
</span><span id="L-14"><a href="#L-14"><span class="linenos"> 14</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Compute the root of (flow-based) data based on a dictionary that contains</span> </span><span id="L-14"><a href="#L-14"><span class="linenos"> 14</span></a>
</span><span id="L-15"><a href="#L-15"><span class="linenos"> 15</span></a><span class="sd"> the necessary information in key-value pairs a la (flow time: observable at flow time).</span> </span><span id="L-15"><a href="#L-15"><span class="linenos"> 15</span></a><span class="k">def</span><span class="w"> </span><span class="nf">fit_t0</span><span class="p">(</span><span class="n">t2E_dict</span><span class="p">,</span> <span class="n">fit_range</span><span class="p">,</span> <span class="n">plot_fit</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">observable</span><span class="o">=</span><span class="s1">&#39;t0&#39;</span><span class="p">):</span>
</span><span id="L-16"><a href="#L-16"><span class="linenos"> 16</span></a> </span><span id="L-16"><a href="#L-16"><span class="linenos"> 16</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Compute the root of (flow-based) data based on a dictionary that contains</span>
</span><span id="L-17"><a href="#L-17"><span class="linenos"> 17</span></a><span class="sd"> It is assumed that the data is monotonically increasing and passes zero from below.</span> </span><span id="L-17"><a href="#L-17"><span class="linenos"> 17</span></a><span class="sd"> the necessary information in key-value pairs a la (flow time: observable at flow time).</span>
</span><span id="L-18"><a href="#L-18"><span class="linenos"> 18</span></a><span class="sd"> No exception is thrown if this is not the case (several roots, no monotonic increase).</span> </span><span id="L-18"><a href="#L-18"><span class="linenos"> 18</span></a>
</span><span id="L-19"><a href="#L-19"><span class="linenos"> 19</span></a><span class="sd"> An exception is thrown if no root can be found in the data.</span> </span><span id="L-19"><a href="#L-19"><span class="linenos"> 19</span></a><span class="sd"> It is assumed that the data is monotonically increasing and passes zero from below.</span>
</span><span id="L-20"><a href="#L-20"><span class="linenos"> 20</span></a> </span><span id="L-20"><a href="#L-20"><span class="linenos"> 20</span></a><span class="sd"> No exception is thrown if this is not the case (several roots, no monotonic increase).</span>
</span><span id="L-21"><a href="#L-21"><span class="linenos"> 21</span></a><span class="sd"> A linear fit in the vicinity of the root is performed to exctract the root from the</span> </span><span id="L-21"><a href="#L-21"><span class="linenos"> 21</span></a><span class="sd"> An exception is thrown if no root can be found in the data.</span>
</span><span id="L-22"><a href="#L-22"><span class="linenos"> 22</span></a><span class="sd"> two fit parameters.</span> </span><span id="L-22"><a href="#L-22"><span class="linenos"> 22</span></a>
</span><span id="L-23"><a href="#L-23"><span class="linenos"> 23</span></a> </span><span id="L-23"><a href="#L-23"><span class="linenos"> 23</span></a><span class="sd"> A linear fit in the vicinity of the root is performed to exctract the root from the</span>
</span><span id="L-24"><a href="#L-24"><span class="linenos"> 24</span></a><span class="sd"> Parameters</span> </span><span id="L-24"><a href="#L-24"><span class="linenos"> 24</span></a><span class="sd"> two fit parameters.</span>
</span><span id="L-25"><a href="#L-25"><span class="linenos"> 25</span></a><span class="sd"> ----------</span> </span><span id="L-25"><a href="#L-25"><span class="linenos"> 25</span></a>
</span><span id="L-26"><a href="#L-26"><span class="linenos"> 26</span></a><span class="sd"> t2E_dict : dict</span> </span><span id="L-26"><a href="#L-26"><span class="linenos"> 26</span></a><span class="sd"> Parameters</span>
</span><span id="L-27"><a href="#L-27"><span class="linenos"> 27</span></a><span class="sd"> Dictionary with pairs of (flow time: observable at flow time) where the flow times</span> </span><span id="L-27"><a href="#L-27"><span class="linenos"> 27</span></a><span class="sd"> ----------</span>
</span><span id="L-28"><a href="#L-28"><span class="linenos"> 28</span></a><span class="sd"> are of type float and the observables of type Obs.</span> </span><span id="L-28"><a href="#L-28"><span class="linenos"> 28</span></a><span class="sd"> t2E_dict : dict</span>
</span><span id="L-29"><a href="#L-29"><span class="linenos"> 29</span></a><span class="sd"> fit_range : int</span> </span><span id="L-29"><a href="#L-29"><span class="linenos"> 29</span></a><span class="sd"> Dictionary with pairs of (flow time: observable at flow time) where the flow times</span>
</span><span id="L-30"><a href="#L-30"><span class="linenos"> 30</span></a><span class="sd"> Number of data points left and right of the zero</span> </span><span id="L-30"><a href="#L-30"><span class="linenos"> 30</span></a><span class="sd"> are of type float and the observables of type Obs.</span>
</span><span id="L-31"><a href="#L-31"><span class="linenos"> 31</span></a><span class="sd"> crossing to be included in the linear fit.</span> </span><span id="L-31"><a href="#L-31"><span class="linenos"> 31</span></a><span class="sd"> fit_range : int</span>
</span><span id="L-32"><a href="#L-32"><span class="linenos"> 32</span></a><span class="sd"> plot_fit : bool</span> </span><span id="L-32"><a href="#L-32"><span class="linenos"> 32</span></a><span class="sd"> Number of data points left and right of the zero</span>
</span><span id="L-33"><a href="#L-33"><span class="linenos"> 33</span></a><span class="sd"> If true, the fit for the extraction of t0 is shown together with the data. (Default: False)</span> </span><span id="L-33"><a href="#L-33"><span class="linenos"> 33</span></a><span class="sd"> crossing to be included in the linear fit.</span>
</span><span id="L-34"><a href="#L-34"><span class="linenos"> 34</span></a><span class="sd"> observable: str</span> </span><span id="L-34"><a href="#L-34"><span class="linenos"> 34</span></a><span class="sd"> plot_fit : bool</span>
</span><span id="L-35"><a href="#L-35"><span class="linenos"> 35</span></a><span class="sd"> Keyword to identify the observable to print the correct ylabel (if plot_fit is True)</span> </span><span id="L-35"><a href="#L-35"><span class="linenos"> 35</span></a><span class="sd"> If true, the fit for the extraction of t0 is shown together with the data. (Default: False)</span>
</span><span id="L-36"><a href="#L-36"><span class="linenos"> 36</span></a><span class="sd"> for the observables &#39;t0&#39; and &#39;w0&#39;. No y label is printed otherwise. (Default: &#39;t0&#39;)</span> </span><span id="L-36"><a href="#L-36"><span class="linenos"> 36</span></a><span class="sd"> observable: str</span>
</span><span id="L-37"><a href="#L-37"><span class="linenos"> 37</span></a> </span><span id="L-37"><a href="#L-37"><span class="linenos"> 37</span></a><span class="sd"> Keyword to identify the observable to print the correct ylabel (if plot_fit is True)</span>
</span><span id="L-38"><a href="#L-38"><span class="linenos"> 38</span></a><span class="sd"> Returns</span> </span><span id="L-38"><a href="#L-38"><span class="linenos"> 38</span></a><span class="sd"> for the observables &#39;t0&#39; and &#39;w0&#39;. No y label is printed otherwise. (Default: &#39;t0&#39;)</span>
</span><span id="L-39"><a href="#L-39"><span class="linenos"> 39</span></a><span class="sd"> -------</span> </span><span id="L-39"><a href="#L-39"><span class="linenos"> 39</span></a>
</span><span id="L-40"><a href="#L-40"><span class="linenos"> 40</span></a><span class="sd"> root : Obs</span> </span><span id="L-40"><a href="#L-40"><span class="linenos"> 40</span></a><span class="sd"> Returns</span>
</span><span id="L-41"><a href="#L-41"><span class="linenos"> 41</span></a><span class="sd"> The root of the data series.</span> </span><span id="L-41"><a href="#L-41"><span class="linenos"> 41</span></a><span class="sd"> -------</span>
</span><span id="L-42"><a href="#L-42"><span class="linenos"> 42</span></a><span class="sd"> &quot;&quot;&quot;</span> </span><span id="L-42"><a href="#L-42"><span class="linenos"> 42</span></a><span class="sd"> root : Obs</span>
</span><span id="L-43"><a href="#L-43"><span class="linenos"> 43</span></a> </span><span id="L-43"><a href="#L-43"><span class="linenos"> 43</span></a><span class="sd"> The root of the data series.</span>
</span><span id="L-44"><a href="#L-44"><span class="linenos"> 44</span></a> <span class="n">zero_crossing</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">argmax</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span> </span><span id="L-44"><a href="#L-44"><span class="linenos"> 44</span></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="L-45"><a href="#L-45"><span class="linenos"> 45</span></a> <span class="p">[</span><span class="n">o</span><span class="o">.</span><span class="n">value</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">t2E_dict</span><span class="o">.</span><span class="n">values</span><span class="p">()])</span> <span class="o">&gt;</span> <span class="mf">0.0</span><span class="p">)</span> </span><span id="L-45"><a href="#L-45"><span class="linenos"> 45</span></a>
</span><span id="L-46"><a href="#L-46"><span class="linenos"> 46</span></a> </span><span id="L-46"><a href="#L-46"><span class="linenos"> 46</span></a> <span class="n">zero_crossing</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">argmax</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span>
</span><span id="L-47"><a href="#L-47"><span class="linenos"> 47</span></a> <span class="k">if</span> <span class="n">zero_crossing</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span> </span><span id="L-47"><a href="#L-47"><span class="linenos"> 47</span></a> <span class="p">[</span><span class="n">o</span><span class="o">.</span><span class="n">value</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">t2E_dict</span><span class="o">.</span><span class="n">values</span><span class="p">()])</span> <span class="o">&gt;</span> <span class="mf">0.0</span><span class="p">)</span>
</span><span id="L-48"><a href="#L-48"><span class="linenos"> 48</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Desired flow time not in data&#39;</span><span class="p">)</span> </span><span id="L-48"><a href="#L-48"><span class="linenos"> 48</span></a>
</span><span id="L-49"><a href="#L-49"><span class="linenos"> 49</span></a> </span><span id="L-49"><a href="#L-49"><span class="linenos"> 49</span></a> <span class="k">if</span> <span class="n">zero_crossing</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
</span><span id="L-50"><a href="#L-50"><span class="linenos"> 50</span></a> <span class="n">x</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">t2E_dict</span><span class="o">.</span><span class="n">keys</span><span class="p">())[</span><span class="n">zero_crossing</span> <span class="o">-</span> <span class="n">fit_range</span><span class="p">:</span> </span><span id="L-50"><a href="#L-50"><span class="linenos"> 50</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Desired flow time not in data&#39;</span><span class="p">)</span>
</span><span id="L-51"><a href="#L-51"><span class="linenos"> 51</span></a> <span class="n">zero_crossing</span> <span class="o">+</span> <span class="n">fit_range</span><span class="p">]</span> </span><span id="L-51"><a href="#L-51"><span class="linenos"> 51</span></a>
</span><span id="L-52"><a href="#L-52"><span class="linenos"> 52</span></a> <span class="n">y</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">t2E_dict</span><span class="o">.</span><span class="n">values</span><span class="p">())[</span><span class="n">zero_crossing</span> <span class="o">-</span> <span class="n">fit_range</span><span class="p">:</span> </span><span id="L-52"><a href="#L-52"><span class="linenos"> 52</span></a> <span class="n">x</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">t2E_dict</span><span class="o">.</span><span class="n">keys</span><span class="p">())[</span><span class="n">zero_crossing</span> <span class="o">-</span> <span class="n">fit_range</span><span class="p">:</span>
</span><span id="L-53"><a href="#L-53"><span class="linenos"> 53</span></a> <span class="n">zero_crossing</span> <span class="o">+</span> <span class="n">fit_range</span><span class="p">]</span> </span><span id="L-53"><a href="#L-53"><span class="linenos"> 53</span></a> <span class="n">zero_crossing</span> <span class="o">+</span> <span class="n">fit_range</span><span class="p">]</span>
</span><span id="L-54"><a href="#L-54"><span class="linenos"> 54</span></a> <span class="p">[</span><span class="n">o</span><span class="o">.</span><span class="n">gamma_method</span><span class="p">()</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">y</span><span class="p">]</span> </span><span id="L-54"><a href="#L-54"><span class="linenos"> 54</span></a> <span class="n">y</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">t2E_dict</span><span class="o">.</span><span class="n">values</span><span class="p">())[</span><span class="n">zero_crossing</span> <span class="o">-</span> <span class="n">fit_range</span><span class="p">:</span>
</span><span id="L-55"><a href="#L-55"><span class="linenos"> 55</span></a> </span><span id="L-55"><a href="#L-55"><span class="linenos"> 55</span></a> <span class="n">zero_crossing</span> <span class="o">+</span> <span class="n">fit_range</span><span class="p">]</span>
</span><span id="L-56"><a href="#L-56"><span class="linenos"> 56</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mi">2</span> <span class="o">*</span> <span class="n">fit_range</span><span class="p">:</span> </span><span id="L-56"><a href="#L-56"><span class="linenos"> 56</span></a> <span class="p">[</span><span class="n">o</span><span class="o">.</span><span class="n">gamma_method</span><span class="p">()</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">y</span><span class="p">]</span>
</span><span id="L-57"><a href="#L-57"><span class="linenos"> 57</span></a> <span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span><span class="s1">&#39;Fit range smaller than expected! Fitting from </span><span class="si">%1.2e</span><span class="s1"> to </span><span class="si">%1.2e</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">x</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]))</span> </span><span id="L-57"><a href="#L-57"><span class="linenos"> 57</span></a>
</span><span id="L-58"><a href="#L-58"><span class="linenos"> 58</span></a> </span><span id="L-58"><a href="#L-58"><span class="linenos"> 58</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mi">2</span> <span class="o">*</span> <span class="n">fit_range</span><span class="p">:</span>
</span><span id="L-59"><a href="#L-59"><span class="linenos"> 59</span></a> <span class="n">fit_result</span> <span class="o">=</span> <span class="n">fit_lin</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">)</span> </span><span id="L-59"><a href="#L-59"><span class="linenos"> 59</span></a> <span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;Fit range smaller than expected! Fitting from </span><span class="si">{</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="si">:</span><span class="s1">1.2e</span><span class="si">}</span><span class="s1"> to </span><span class="si">{</span><span class="n">x</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="si">:</span><span class="s1">1.2e</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">,</span> <span class="n">stacklevel</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span>
</span><span id="L-60"><a href="#L-60"><span class="linenos"> 60</span></a> </span><span id="L-60"><a href="#L-60"><span class="linenos"> 60</span></a>
</span><span id="L-61"><a href="#L-61"><span class="linenos"> 61</span></a> <span class="k">if</span> <span class="n">plot_fit</span> <span class="ow">is</span> <span class="kc">True</span><span class="p">:</span> </span><span id="L-61"><a href="#L-61"><span class="linenos"> 61</span></a> <span class="n">fit_result</span> <span class="o">=</span> <span class="n">fit_lin</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">)</span>
</span><span id="L-62"><a href="#L-62"><span class="linenos"> 62</span></a> <span class="n">plt</span><span class="o">.</span><span class="n">figure</span><span class="p">()</span> </span><span id="L-62"><a href="#L-62"><span class="linenos"> 62</span></a>
</span><span id="L-63"><a href="#L-63"><span class="linenos"> 63</span></a> <span class="n">gs</span> <span class="o">=</span> <span class="n">gridspec</span><span class="o">.</span><span class="n">GridSpec</span><span class="p">(</span><span class="mi">2</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="n">height_ratios</span><span class="o">=</span><span class="p">[</span><span class="mi">3</span><span class="p">,</span> <span class="mi">1</span><span class="p">],</span> <span class="n">wspace</span><span class="o">=</span><span class="mf">0.0</span><span class="p">,</span> <span class="n">hspace</span><span class="o">=</span><span class="mf">0.0</span><span class="p">)</span> </span><span id="L-63"><a href="#L-63"><span class="linenos"> 63</span></a> <span class="k">if</span> <span class="n">plot_fit</span> <span class="ow">is</span> <span class="kc">True</span><span class="p">:</span>
</span><span id="L-64"><a href="#L-64"><span class="linenos"> 64</span></a> <span class="n">ax0</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">subplot</span><span class="p">(</span><span class="n">gs</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> </span><span id="L-64"><a href="#L-64"><span class="linenos"> 64</span></a> <span class="n">plt</span><span class="o">.</span><span class="n">figure</span><span class="p">()</span>
</span><span id="L-65"><a href="#L-65"><span class="linenos"> 65</span></a> <span class="n">xmore</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">t2E_dict</span><span class="o">.</span><span class="n">keys</span><span class="p">())[</span><span class="n">zero_crossing</span> <span class="o">-</span> <span class="n">fit_range</span> <span class="o">-</span> <span class="mi">2</span><span class="p">:</span> <span class="n">zero_crossing</span> <span class="o">+</span> <span class="n">fit_range</span> <span class="o">+</span> <span class="mi">2</span><span class="p">]</span> </span><span id="L-65"><a href="#L-65"><span class="linenos"> 65</span></a> <span class="n">gs</span> <span class="o">=</span> <span class="n">gridspec</span><span class="o">.</span><span class="n">GridSpec</span><span class="p">(</span><span class="mi">2</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="n">height_ratios</span><span class="o">=</span><span class="p">[</span><span class="mi">3</span><span class="p">,</span> <span class="mi">1</span><span class="p">],</span> <span class="n">wspace</span><span class="o">=</span><span class="mf">0.0</span><span class="p">,</span> <span class="n">hspace</span><span class="o">=</span><span class="mf">0.0</span><span class="p">)</span>
</span><span id="L-66"><a href="#L-66"><span class="linenos"> 66</span></a> <span class="n">ymore</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">t2E_dict</span><span class="o">.</span><span class="n">values</span><span class="p">())[</span><span class="n">zero_crossing</span> <span class="o">-</span> <span class="n">fit_range</span> <span class="o">-</span> <span class="mi">2</span><span class="p">:</span> <span class="n">zero_crossing</span> <span class="o">+</span> <span class="n">fit_range</span> <span class="o">+</span> <span class="mi">2</span><span class="p">]</span> </span><span id="L-66"><a href="#L-66"><span class="linenos"> 66</span></a> <span class="n">ax0</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">subplot</span><span class="p">(</span><span class="n">gs</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
</span><span id="L-67"><a href="#L-67"><span class="linenos"> 67</span></a> <span class="p">[</span><span class="n">o</span><span class="o">.</span><span class="n">gamma_method</span><span class="p">()</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">ymore</span><span class="p">]</span> </span><span id="L-67"><a href="#L-67"><span class="linenos"> 67</span></a> <span class="n">xmore</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">t2E_dict</span><span class="o">.</span><span class="n">keys</span><span class="p">())[</span><span class="n">zero_crossing</span> <span class="o">-</span> <span class="n">fit_range</span> <span class="o">-</span> <span class="mi">2</span><span class="p">:</span> <span class="n">zero_crossing</span> <span class="o">+</span> <span class="n">fit_range</span> <span class="o">+</span> <span class="mi">2</span><span class="p">]</span>
</span><span id="L-68"><a href="#L-68"><span class="linenos"> 68</span></a> <span class="n">ax0</span><span class="o">.</span><span class="n">errorbar</span><span class="p">(</span><span class="n">xmore</span><span class="p">,</span> <span class="p">[</span><span class="n">yi</span><span class="o">.</span><span class="n">value</span> <span class="k">for</span> <span class="n">yi</span> <span class="ow">in</span> <span class="n">ymore</span><span class="p">],</span> <span class="n">yerr</span><span class="o">=</span><span class="p">[</span><span class="n">yi</span><span class="o">.</span><span class="n">dvalue</span> <span class="k">for</span> <span class="n">yi</span> <span class="ow">in</span> <span class="n">ymore</span><span class="p">],</span> <span class="n">fmt</span><span class="o">=</span><span class="s1">&#39;x&#39;</span><span class="p">)</span> </span><span id="L-68"><a href="#L-68"><span class="linenos"> 68</span></a> <span class="n">ymore</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">t2E_dict</span><span class="o">.</span><span class="n">values</span><span class="p">())[</span><span class="n">zero_crossing</span> <span class="o">-</span> <span class="n">fit_range</span> <span class="o">-</span> <span class="mi">2</span><span class="p">:</span> <span class="n">zero_crossing</span> <span class="o">+</span> <span class="n">fit_range</span> <span class="o">+</span> <span class="mi">2</span><span class="p">]</span>
</span><span id="L-69"><a href="#L-69"><span class="linenos"> 69</span></a> <span class="n">xplot</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="n">x</span><span class="p">),</span> <span class="n">np</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="n">x</span><span class="p">))</span> </span><span id="L-69"><a href="#L-69"><span class="linenos"> 69</span></a> <span class="p">[</span><span class="n">o</span><span class="o">.</span><span class="n">gamma_method</span><span class="p">()</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">ymore</span><span class="p">]</span>
</span><span id="L-70"><a href="#L-70"><span class="linenos"> 70</span></a> <span class="n">yplot</span> <span class="o">=</span> <span class="p">[</span><span class="n">fit_result</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="n">fit_result</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">*</span> <span class="n">xi</span> <span class="k">for</span> <span class="n">xi</span> <span class="ow">in</span> <span class="n">xplot</span><span class="p">]</span> </span><span id="L-70"><a href="#L-70"><span class="linenos"> 70</span></a> <span class="n">ax0</span><span class="o">.</span><span class="n">errorbar</span><span class="p">(</span><span class="n">xmore</span><span class="p">,</span> <span class="p">[</span><span class="n">yi</span><span class="o">.</span><span class="n">value</span> <span class="k">for</span> <span class="n">yi</span> <span class="ow">in</span> <span class="n">ymore</span><span class="p">],</span> <span class="n">yerr</span><span class="o">=</span><span class="p">[</span><span class="n">yi</span><span class="o">.</span><span class="n">dvalue</span> <span class="k">for</span> <span class="n">yi</span> <span class="ow">in</span> <span class="n">ymore</span><span class="p">],</span> <span class="n">fmt</span><span class="o">=</span><span class="s1">&#39;x&#39;</span><span class="p">)</span>
</span><span id="L-71"><a href="#L-71"><span class="linenos"> 71</span></a> <span class="p">[</span><span class="n">yi</span><span class="o">.</span><span class="n">gamma_method</span><span class="p">()</span> <span class="k">for</span> <span class="n">yi</span> <span class="ow">in</span> <span class="n">yplot</span><span class="p">]</span> </span><span id="L-71"><a href="#L-71"><span class="linenos"> 71</span></a> <span class="n">xplot</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="n">x</span><span class="p">),</span> <span class="n">np</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="n">x</span><span class="p">))</span>
</span><span id="L-72"><a href="#L-72"><span class="linenos"> 72</span></a> <span class="n">ax0</span><span class="o">.</span><span class="n">fill_between</span><span class="p">(</span><span class="n">xplot</span><span class="p">,</span> <span class="n">y1</span><span class="o">=</span><span class="p">[</span><span class="n">yi</span><span class="o">.</span><span class="n">value</span> <span class="o">-</span> <span class="n">yi</span><span class="o">.</span><span class="n">dvalue</span> <span class="k">for</span> <span class="n">yi</span> <span class="ow">in</span> <span class="n">yplot</span><span class="p">],</span> <span class="n">y2</span><span class="o">=</span><span class="p">[</span><span class="n">yi</span><span class="o">.</span><span class="n">value</span> <span class="o">+</span> <span class="n">yi</span><span class="o">.</span><span class="n">dvalue</span> <span class="k">for</span> <span class="n">yi</span> <span class="ow">in</span> <span class="n">yplot</span><span class="p">])</span> </span><span id="L-72"><a href="#L-72"><span class="linenos"> 72</span></a> <span class="n">yplot</span> <span class="o">=</span> <span class="p">[</span><span class="n">fit_result</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="n">fit_result</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">*</span> <span class="n">xi</span> <span class="k">for</span> <span class="n">xi</span> <span class="ow">in</span> <span class="n">xplot</span><span class="p">]</span>
</span><span id="L-73"><a href="#L-73"><span class="linenos"> 73</span></a> <span class="n">retval</span> <span class="o">=</span> <span class="p">(</span><span class="o">-</span><span class="n">fit_result</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">/</span> <span class="n">fit_result</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> </span><span id="L-73"><a href="#L-73"><span class="linenos"> 73</span></a> <span class="p">[</span><span class="n">yi</span><span class="o">.</span><span class="n">gamma_method</span><span class="p">()</span> <span class="k">for</span> <span class="n">yi</span> <span class="ow">in</span> <span class="n">yplot</span><span class="p">]</span>
</span><span id="L-74"><a href="#L-74"><span class="linenos"> 74</span></a> <span class="n">retval</span><span class="o">.</span><span class="n">gamma_method</span><span class="p">()</span> </span><span id="L-74"><a href="#L-74"><span class="linenos"> 74</span></a> <span class="n">ax0</span><span class="o">.</span><span class="n">fill_between</span><span class="p">(</span><span class="n">xplot</span><span class="p">,</span> <span class="n">y1</span><span class="o">=</span><span class="p">[</span><span class="n">yi</span><span class="o">.</span><span class="n">value</span> <span class="o">-</span> <span class="n">yi</span><span class="o">.</span><span class="n">dvalue</span> <span class="k">for</span> <span class="n">yi</span> <span class="ow">in</span> <span class="n">yplot</span><span class="p">],</span> <span class="n">y2</span><span class="o">=</span><span class="p">[</span><span class="n">yi</span><span class="o">.</span><span class="n">value</span> <span class="o">+</span> <span class="n">yi</span><span class="o">.</span><span class="n">dvalue</span> <span class="k">for</span> <span class="n">yi</span> <span class="ow">in</span> <span class="n">yplot</span><span class="p">])</span>
</span><span id="L-75"><a href="#L-75"><span class="linenos"> 75</span></a> <span class="n">ylim</span> <span class="o">=</span> <span class="n">ax0</span><span class="o">.</span><span class="n">get_ylim</span><span class="p">()</span> </span><span id="L-75"><a href="#L-75"><span class="linenos"> 75</span></a> <span class="n">retval</span> <span class="o">=</span> <span class="p">(</span><span class="o">-</span><span class="n">fit_result</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">/</span> <span class="n">fit_result</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
</span><span id="L-76"><a href="#L-76"><span class="linenos"> 76</span></a> <span class="n">ax0</span><span class="o">.</span><span class="n">fill_betweenx</span><span class="p">(</span><span class="n">ylim</span><span class="p">,</span> <span class="n">x1</span><span class="o">=</span><span class="n">retval</span><span class="o">.</span><span class="n">value</span> <span class="o">-</span> <span class="n">retval</span><span class="o">.</span><span class="n">dvalue</span><span class="p">,</span> <span class="n">x2</span><span class="o">=</span><span class="n">retval</span><span class="o">.</span><span class="n">value</span> <span class="o">+</span> <span class="n">retval</span><span class="o">.</span><span class="n">dvalue</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="s1">&#39;gray&#39;</span><span class="p">,</span> <span class="n">alpha</span><span class="o">=</span><span class="mf">0.4</span><span class="p">)</span> </span><span id="L-76"><a href="#L-76"><span class="linenos"> 76</span></a> <span class="n">retval</span><span class="o">.</span><span class="n">gamma_method</span><span class="p">()</span>
</span><span id="L-77"><a href="#L-77"><span class="linenos"> 77</span></a> <span class="n">ax0</span><span class="o">.</span><span class="n">set_ylim</span><span class="p">(</span><span class="n">ylim</span><span class="p">)</span> </span><span id="L-77"><a href="#L-77"><span class="linenos"> 77</span></a> <span class="n">ylim</span> <span class="o">=</span> <span class="n">ax0</span><span class="o">.</span><span class="n">get_ylim</span><span class="p">()</span>
</span><span id="L-78"><a href="#L-78"><span class="linenos"> 78</span></a> <span class="k">if</span> <span class="n">observable</span> <span class="o">==</span> <span class="s1">&#39;t0&#39;</span><span class="p">:</span> </span><span id="L-78"><a href="#L-78"><span class="linenos"> 78</span></a> <span class="n">ax0</span><span class="o">.</span><span class="n">fill_betweenx</span><span class="p">(</span><span class="n">ylim</span><span class="p">,</span> <span class="n">x1</span><span class="o">=</span><span class="n">retval</span><span class="o">.</span><span class="n">value</span> <span class="o">-</span> <span class="n">retval</span><span class="o">.</span><span class="n">dvalue</span><span class="p">,</span> <span class="n">x2</span><span class="o">=</span><span class="n">retval</span><span class="o">.</span><span class="n">value</span> <span class="o">+</span> <span class="n">retval</span><span class="o">.</span><span class="n">dvalue</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="s1">&#39;gray&#39;</span><span class="p">,</span> <span class="n">alpha</span><span class="o">=</span><span class="mf">0.4</span><span class="p">)</span>
</span><span id="L-79"><a href="#L-79"><span class="linenos"> 79</span></a> <span class="n">ax0</span><span class="o">.</span><span class="n">set_ylabel</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;$t^2 \langle E(t) \rangle - 0.3 $&#39;</span><span class="p">)</span> </span><span id="L-79"><a href="#L-79"><span class="linenos"> 79</span></a> <span class="n">ax0</span><span class="o">.</span><span class="n">set_ylim</span><span class="p">(</span><span class="n">ylim</span><span class="p">)</span>
</span><span id="L-80"><a href="#L-80"><span class="linenos"> 80</span></a> <span class="k">elif</span> <span class="n">observable</span> <span class="o">==</span> <span class="s1">&#39;w0&#39;</span><span class="p">:</span> </span><span id="L-80"><a href="#L-80"><span class="linenos"> 80</span></a> <span class="k">if</span> <span class="n">observable</span> <span class="o">==</span> <span class="s1">&#39;t0&#39;</span><span class="p">:</span>
</span><span id="L-81"><a href="#L-81"><span class="linenos"> 81</span></a> <span class="n">ax0</span><span class="o">.</span><span class="n">set_ylabel</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;$t d(t^2 \langle E(t) \rangle)/dt - 0.3 $&#39;</span><span class="p">)</span> </span><span id="L-81"><a href="#L-81"><span class="linenos"> 81</span></a> <span class="n">ax0</span><span class="o">.</span><span class="n">set_ylabel</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;$t^2 \langle E(t) \rangle - 0.3 $&#39;</span><span class="p">)</span>
</span><span id="L-82"><a href="#L-82"><span class="linenos"> 82</span></a> <span class="n">xlim</span> <span class="o">=</span> <span class="n">ax0</span><span class="o">.</span><span class="n">get_xlim</span><span class="p">()</span> </span><span id="L-82"><a href="#L-82"><span class="linenos"> 82</span></a> <span class="k">elif</span> <span class="n">observable</span> <span class="o">==</span> <span class="s1">&#39;w0&#39;</span><span class="p">:</span>
</span><span id="L-83"><a href="#L-83"><span class="linenos"> 83</span></a> </span><span id="L-83"><a href="#L-83"><span class="linenos"> 83</span></a> <span class="n">ax0</span><span class="o">.</span><span class="n">set_ylabel</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;$t d(t^2 \langle E(t) \rangle)/dt - 0.3 $&#39;</span><span class="p">)</span>
</span><span id="L-84"><a href="#L-84"><span class="linenos"> 84</span></a> <span class="n">fit_res</span> <span class="o">=</span> <span class="p">[</span><span class="n">fit_result</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="n">fit_result</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">*</span> <span class="n">xi</span> <span class="k">for</span> <span class="n">xi</span> <span class="ow">in</span> <span class="n">x</span><span class="p">]</span> </span><span id="L-84"><a href="#L-84"><span class="linenos"> 84</span></a> <span class="n">xlim</span> <span class="o">=</span> <span class="n">ax0</span><span class="o">.</span><span class="n">get_xlim</span><span class="p">()</span>
</span><span id="L-85"><a href="#L-85"><span class="linenos"> 85</span></a> <span class="n">residuals</span> <span class="o">=</span> <span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">([</span><span class="n">o</span><span class="o">.</span><span class="n">value</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">y</span><span class="p">])</span> <span class="o">-</span> <span class="p">[</span><span class="n">o</span><span class="o">.</span><span class="n">value</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">fit_res</span><span class="p">])</span> <span class="o">/</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">([</span><span class="n">o</span><span class="o">.</span><span class="n">dvalue</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">y</span><span class="p">])</span> </span><span id="L-85"><a href="#L-85"><span class="linenos"> 85</span></a>
</span><span id="L-86"><a href="#L-86"><span class="linenos"> 86</span></a> <span class="n">ax1</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">subplot</span><span class="p">(</span><span class="n">gs</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> </span><span id="L-86"><a href="#L-86"><span class="linenos"> 86</span></a> <span class="n">fit_res</span> <span class="o">=</span> <span class="p">[</span><span class="n">fit_result</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="n">fit_result</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">*</span> <span class="n">xi</span> <span class="k">for</span> <span class="n">xi</span> <span class="ow">in</span> <span class="n">x</span><span class="p">]</span>
</span><span id="L-87"><a href="#L-87"><span class="linenos"> 87</span></a> <span class="n">ax1</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">residuals</span><span class="p">,</span> <span class="s1">&#39;ko&#39;</span><span class="p">,</span> <span class="n">ls</span><span class="o">=</span><span class="s1">&#39;none&#39;</span><span class="p">,</span> <span class="n">markersize</span><span class="o">=</span><span class="mi">5</span><span class="p">)</span> </span><span id="L-87"><a href="#L-87"><span class="linenos"> 87</span></a> <span class="n">residuals</span> <span class="o">=</span> <span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">([</span><span class="n">o</span><span class="o">.</span><span class="n">value</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">y</span><span class="p">])</span> <span class="o">-</span> <span class="p">[</span><span class="n">o</span><span class="o">.</span><span class="n">value</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">fit_res</span><span class="p">])</span> <span class="o">/</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">([</span><span class="n">o</span><span class="o">.</span><span class="n">dvalue</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">y</span><span class="p">])</span>
</span><span id="L-88"><a href="#L-88"><span class="linenos"> 88</span></a> <span class="n">ax1</span><span class="o">.</span><span class="n">tick_params</span><span class="p">(</span><span class="n">direction</span><span class="o">=</span><span class="s1">&#39;out&#39;</span><span class="p">)</span> </span><span id="L-88"><a href="#L-88"><span class="linenos"> 88</span></a> <span class="n">ax1</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">subplot</span><span class="p">(</span><span class="n">gs</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
</span><span id="L-89"><a href="#L-89"><span class="linenos"> 89</span></a> <span class="n">ax1</span><span class="o">.</span><span class="n">tick_params</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="s2">&quot;x&quot;</span><span class="p">,</span> <span class="n">bottom</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">top</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">labelbottom</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span> </span><span id="L-89"><a href="#L-89"><span class="linenos"> 89</span></a> <span class="n">ax1</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">residuals</span><span class="p">,</span> <span class="s1">&#39;ko&#39;</span><span class="p">,</span> <span class="n">ls</span><span class="o">=</span><span class="s1">&#39;none&#39;</span><span class="p">,</span> <span class="n">markersize</span><span class="o">=</span><span class="mi">5</span><span class="p">)</span>
</span><span id="L-90"><a href="#L-90"><span class="linenos"> 90</span></a> <span class="n">ax1</span><span class="o">.</span><span class="n">axhline</span><span class="p">(</span><span class="n">y</span><span class="o">=</span><span class="mf">0.0</span><span class="p">,</span> <span class="n">ls</span><span class="o">=</span><span class="s1">&#39;--&#39;</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="s1">&#39;k&#39;</span><span class="p">)</span> </span><span id="L-90"><a href="#L-90"><span class="linenos"> 90</span></a> <span class="n">ax1</span><span class="o">.</span><span class="n">tick_params</span><span class="p">(</span><span class="n">direction</span><span class="o">=</span><span class="s1">&#39;out&#39;</span><span class="p">)</span>
</span><span id="L-91"><a href="#L-91"><span class="linenos"> 91</span></a> <span class="n">ax1</span><span class="o">.</span><span class="n">fill_between</span><span class="p">(</span><span class="n">xlim</span><span class="p">,</span> <span class="o">-</span><span class="mf">1.0</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">,</span> <span class="n">alpha</span><span class="o">=</span><span class="mf">0.1</span><span class="p">,</span> <span class="n">facecolor</span><span class="o">=</span><span class="s1">&#39;k&#39;</span><span class="p">)</span> </span><span id="L-91"><a href="#L-91"><span class="linenos"> 91</span></a> <span class="n">ax1</span><span class="o">.</span><span class="n">tick_params</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="s2">&quot;x&quot;</span><span class="p">,</span> <span class="n">bottom</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">top</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">labelbottom</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
</span><span id="L-92"><a href="#L-92"><span class="linenos"> 92</span></a> <span class="n">ax1</span><span class="o">.</span><span class="n">set_xlim</span><span class="p">(</span><span class="n">xlim</span><span class="p">)</span> </span><span id="L-92"><a href="#L-92"><span class="linenos"> 92</span></a> <span class="n">ax1</span><span class="o">.</span><span class="n">axhline</span><span class="p">(</span><span class="n">y</span><span class="o">=</span><span class="mf">0.0</span><span class="p">,</span> <span class="n">ls</span><span class="o">=</span><span class="s1">&#39;--&#39;</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="s1">&#39;k&#39;</span><span class="p">)</span>
</span><span id="L-93"><a href="#L-93"><span class="linenos"> 93</span></a> <span class="n">ax1</span><span class="o">.</span><span class="n">set_ylabel</span><span class="p">(</span><span class="s1">&#39;Residuals&#39;</span><span class="p">)</span> </span><span id="L-93"><a href="#L-93"><span class="linenos"> 93</span></a> <span class="n">ax1</span><span class="o">.</span><span class="n">fill_between</span><span class="p">(</span><span class="n">xlim</span><span class="p">,</span> <span class="o">-</span><span class="mf">1.0</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">,</span> <span class="n">alpha</span><span class="o">=</span><span class="mf">0.1</span><span class="p">,</span> <span class="n">facecolor</span><span class="o">=</span><span class="s1">&#39;k&#39;</span><span class="p">)</span>
</span><span id="L-94"><a href="#L-94"><span class="linenos"> 94</span></a> <span class="n">ax1</span><span class="o">.</span><span class="n">set_xlabel</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;$t/a^2$&#39;</span><span class="p">)</span> </span><span id="L-94"><a href="#L-94"><span class="linenos"> 94</span></a> <span class="n">ax1</span><span class="o">.</span><span class="n">set_xlim</span><span class="p">(</span><span class="n">xlim</span><span class="p">)</span>
</span><span id="L-95"><a href="#L-95"><span class="linenos"> 95</span></a> </span><span id="L-95"><a href="#L-95"><span class="linenos"> 95</span></a> <span class="n">ax1</span><span class="o">.</span><span class="n">set_ylabel</span><span class="p">(</span><span class="s1">&#39;Residuals&#39;</span><span class="p">)</span>
</span><span id="L-96"><a href="#L-96"><span class="linenos"> 96</span></a> <span class="n">plt</span><span class="o">.</span><span class="n">draw</span><span class="p">()</span> </span><span id="L-96"><a href="#L-96"><span class="linenos"> 96</span></a> <span class="n">ax1</span><span class="o">.</span><span class="n">set_xlabel</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;$t/a^2$&#39;</span><span class="p">)</span>
</span><span id="L-97"><a href="#L-97"><span class="linenos"> 97</span></a> <span class="k">return</span> <span class="o">-</span><span class="n">fit_result</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">/</span> <span class="n">fit_result</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> </span><span id="L-97"><a href="#L-97"><span class="linenos"> 97</span></a>
</span><span id="L-98"><a href="#L-98"><span class="linenos"> 98</span></a> </span><span id="L-98"><a href="#L-98"><span class="linenos"> 98</span></a> <span class="n">plt</span><span class="o">.</span><span class="n">draw</span><span class="p">()</span>
</span><span id="L-99"><a href="#L-99"><span class="linenos"> 99</span></a> </span><span id="L-99"><a href="#L-99"><span class="linenos"> 99</span></a> <span class="k">return</span> <span class="o">-</span><span class="n">fit_result</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">/</span> <span class="n">fit_result</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
</span><span id="L-100"><a href="#L-100"><span class="linenos">100</span></a><span class="k">def</span><span class="w"> </span><span class="nf">read_pbp</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">prefix</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span> </span><span id="L-100"><a href="#L-100"><span class="linenos">100</span></a>
</span><span id="L-101"><a href="#L-101"><span class="linenos">101</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Read pbp format from given folder structure.</span> </span><span id="L-101"><a href="#L-101"><span class="linenos">101</span></a>
</span><span id="L-102"><a href="#L-102"><span class="linenos">102</span></a> </span><span id="L-102"><a href="#L-102"><span class="linenos">102</span></a><span class="k">def</span><span class="w"> </span><span class="nf">read_pbp</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">prefix</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
</span><span id="L-103"><a href="#L-103"><span class="linenos">103</span></a><span class="sd"> Parameters</span> </span><span id="L-103"><a href="#L-103"><span class="linenos">103</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Read pbp format from given folder structure.</span>
</span><span id="L-104"><a href="#L-104"><span class="linenos">104</span></a><span class="sd"> ----------</span> </span><span id="L-104"><a href="#L-104"><span class="linenos">104</span></a>
</span><span id="L-105"><a href="#L-105"><span class="linenos">105</span></a><span class="sd"> r_start : list</span> </span><span id="L-105"><a href="#L-105"><span class="linenos">105</span></a><span class="sd"> Parameters</span>
</span><span id="L-106"><a href="#L-106"><span class="linenos">106</span></a><span class="sd"> list which contains the first config to be read for each replicum</span> </span><span id="L-106"><a href="#L-106"><span class="linenos">106</span></a><span class="sd"> ----------</span>
</span><span id="L-107"><a href="#L-107"><span class="linenos">107</span></a><span class="sd"> r_stop : list</span> </span><span id="L-107"><a href="#L-107"><span class="linenos">107</span></a><span class="sd"> r_start : list</span>
</span><span id="L-108"><a href="#L-108"><span class="linenos">108</span></a><span class="sd"> list which contains the last config to be read for each replicum</span> </span><span id="L-108"><a href="#L-108"><span class="linenos">108</span></a><span class="sd"> list which contains the first config to be read for each replicum</span>
</span><span id="L-109"><a href="#L-109"><span class="linenos">109</span></a> </span><span id="L-109"><a href="#L-109"><span class="linenos">109</span></a><span class="sd"> r_stop : list</span>
</span><span id="L-110"><a href="#L-110"><span class="linenos">110</span></a><span class="sd"> Returns</span> </span><span id="L-110"><a href="#L-110"><span class="linenos">110</span></a><span class="sd"> list which contains the last config to be read for each replicum</span>
</span><span id="L-111"><a href="#L-111"><span class="linenos">111</span></a><span class="sd"> -------</span> </span><span id="L-111"><a href="#L-111"><span class="linenos">111</span></a>
</span><span id="L-112"><a href="#L-112"><span class="linenos">112</span></a><span class="sd"> result : list[Obs]</span> </span><span id="L-112"><a href="#L-112"><span class="linenos">112</span></a><span class="sd"> Returns</span>
</span><span id="L-113"><a href="#L-113"><span class="linenos">113</span></a><span class="sd"> list of observables read</span> </span><span id="L-113"><a href="#L-113"><span class="linenos">113</span></a><span class="sd"> -------</span>
</span><span id="L-114"><a href="#L-114"><span class="linenos">114</span></a><span class="sd"> &quot;&quot;&quot;</span> </span><span id="L-114"><a href="#L-114"><span class="linenos">114</span></a><span class="sd"> result : list[Obs]</span>
</span><span id="L-115"><a href="#L-115"><span class="linenos">115</span></a> </span><span id="L-115"><a href="#L-115"><span class="linenos">115</span></a><span class="sd"> list of observables read</span>
</span><span id="L-116"><a href="#L-116"><span class="linenos">116</span></a> <span class="n">ls</span> <span class="o">=</span> <span class="p">[]</span> </span><span id="L-116"><a href="#L-116"><span class="linenos">116</span></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="L-117"><a href="#L-117"><span class="linenos">117</span></a> <span class="k">for</span> <span class="p">(</span><span class="n">dirpath</span><span class="p">,</span> <span class="n">dirnames</span><span class="p">,</span> <span class="n">filenames</span><span class="p">)</span> <span class="ow">in</span> <span class="n">os</span><span class="o">.</span><span class="n">walk</span><span class="p">(</span><span class="n">path</span><span class="p">):</span> </span><span id="L-117"><a href="#L-117"><span class="linenos">117</span></a>
</span><span id="L-118"><a href="#L-118"><span class="linenos">118</span></a> <span class="n">ls</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">filenames</span><span class="p">)</span> </span><span id="L-118"><a href="#L-118"><span class="linenos">118</span></a> <span class="n">ls</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="L-119"><a href="#L-119"><span class="linenos">119</span></a> <span class="k">break</span> </span><span id="L-119"><a href="#L-119"><span class="linenos">119</span></a> <span class="k">for</span> <span class="p">(</span><span class="n">_dirpath</span><span class="p">,</span> <span class="n">_dirnames</span><span class="p">,</span> <span class="n">filenames</span><span class="p">)</span> <span class="ow">in</span> <span class="n">os</span><span class="o">.</span><span class="n">walk</span><span class="p">(</span><span class="n">path</span><span class="p">):</span>
</span><span id="L-120"><a href="#L-120"><span class="linenos">120</span></a> </span><span id="L-120"><a href="#L-120"><span class="linenos">120</span></a> <span class="n">ls</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">filenames</span><span class="p">)</span>
</span><span id="L-121"><a href="#L-121"><span class="linenos">121</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">ls</span><span class="p">:</span> </span><span id="L-121"><a href="#L-121"><span class="linenos">121</span></a> <span class="k">break</span>
</span><span id="L-122"><a href="#L-122"><span class="linenos">122</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Error, directory not found&#39;</span><span class="p">)</span> </span><span id="L-122"><a href="#L-122"><span class="linenos">122</span></a>
</span><span id="L-123"><a href="#L-123"><span class="linenos">123</span></a> </span><span id="L-123"><a href="#L-123"><span class="linenos">123</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">ls</span><span class="p">:</span>
</span><span id="L-124"><a href="#L-124"><span class="linenos">124</span></a> <span class="c1"># Exclude files with different names</span> </span><span id="L-124"><a href="#L-124"><span class="linenos">124</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Error, directory not found&#39;</span><span class="p">)</span>
</span><span id="L-125"><a href="#L-125"><span class="linenos">125</span></a> <span class="k">for</span> <span class="n">exc</span> <span class="ow">in</span> <span class="n">ls</span><span class="p">:</span> </span><span id="L-125"><a href="#L-125"><span class="linenos">125</span></a>
</span><span id="L-126"><a href="#L-126"><span class="linenos">126</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">fnmatch</span><span class="o">.</span><span class="n">fnmatch</span><span class="p">(</span><span class="n">exc</span><span class="p">,</span> <span class="n">prefix</span> <span class="o">+</span> <span class="s1">&#39;*.dat&#39;</span><span class="p">):</span> </span><span id="L-126"><a href="#L-126"><span class="linenos">126</span></a> <span class="c1"># Exclude files with different names</span>
</span><span id="L-127"><a href="#L-127"><span class="linenos">127</span></a> <span class="n">ls</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">ls</span><span class="p">)</span> <span class="o">-</span> <span class="nb">set</span><span class="p">([</span><span class="n">exc</span><span class="p">]))</span> </span><span id="L-127"><a href="#L-127"><span class="linenos">127</span></a> <span class="k">for</span> <span class="n">exc</span> <span class="ow">in</span> <span class="n">ls</span><span class="p">:</span>
</span><span id="L-128"><a href="#L-128"><span class="linenos">128</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">ls</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span> </span><span id="L-128"><a href="#L-128"><span class="linenos">128</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">fnmatch</span><span class="o">.</span><span class="n">fnmatch</span><span class="p">(</span><span class="n">exc</span><span class="p">,</span> <span class="n">prefix</span> <span class="o">+</span> <span class="s1">&#39;*.dat&#39;</span><span class="p">):</span>
</span><span id="L-129"><a href="#L-129"><span class="linenos">129</span></a> <span class="n">ls</span><span class="o">.</span><span class="n">sort</span><span class="p">(</span><span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="nb">int</span><span class="p">(</span><span class="n">re</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;\d+&#39;</span><span class="p">,</span> <span class="n">x</span><span class="p">[</span><span class="nb">len</span><span class="p">(</span><span class="n">prefix</span><span class="p">):])[</span><span class="mi">0</span><span class="p">]))</span> </span><span id="L-129"><a href="#L-129"><span class="linenos">129</span></a> <span class="n">ls</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">ls</span><span class="p">)</span> <span class="o">-</span> <span class="nb">set</span><span class="p">([</span><span class="n">exc</span><span class="p">]))</span>
</span><span id="L-130"><a href="#L-130"><span class="linenos">130</span></a> <span class="n">replica</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">ls</span><span class="p">)</span> </span><span id="L-130"><a href="#L-130"><span class="linenos">130</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">ls</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
</span><span id="L-131"><a href="#L-131"><span class="linenos">131</span></a> </span><span id="L-131"><a href="#L-131"><span class="linenos">131</span></a> <span class="n">ls</span><span class="o">.</span><span class="n">sort</span><span class="p">(</span><span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="nb">int</span><span class="p">(</span><span class="n">re</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;\d+&#39;</span><span class="p">,</span> <span class="n">x</span><span class="p">[</span><span class="nb">len</span><span class="p">(</span><span class="n">prefix</span><span class="p">):])[</span><span class="mi">0</span><span class="p">]))</span>
</span><span id="L-132"><a href="#L-132"><span class="linenos">132</span></a> <span class="k">if</span> <span class="s1">&#39;r_start&#39;</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span> </span><span id="L-132"><a href="#L-132"><span class="linenos">132</span></a> <span class="n">replica</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">ls</span><span class="p">)</span>
</span><span id="L-133"><a href="#L-133"><span class="linenos">133</span></a> <span class="n">r_start</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;r_start&#39;</span><span class="p">)</span> </span><span id="L-133"><a href="#L-133"><span class="linenos">133</span></a>
</span><span id="L-134"><a href="#L-134"><span class="linenos">134</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">r_start</span><span class="p">)</span> <span class="o">!=</span> <span class="n">replica</span><span class="p">:</span> </span><span id="L-134"><a href="#L-134"><span class="linenos">134</span></a> <span class="k">if</span> <span class="s1">&#39;r_start&#39;</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
</span><span id="L-135"><a href="#L-135"><span class="linenos">135</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;r_start does not match number of replicas&#39;</span><span class="p">)</span> </span><span id="L-135"><a href="#L-135"><span class="linenos">135</span></a> <span class="n">r_start</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;r_start&#39;</span><span class="p">)</span>
</span><span id="L-136"><a href="#L-136"><span class="linenos">136</span></a> <span class="c1"># Adjust Configuration numbering to python index</span> </span><span id="L-136"><a href="#L-136"><span class="linenos">136</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">r_start</span><span class="p">)</span> <span class="o">!=</span> <span class="n">replica</span><span class="p">:</span>
</span><span id="L-137"><a href="#L-137"><span class="linenos">137</span></a> <span class="n">r_start</span> <span class="o">=</span> <span class="p">[</span><span class="n">o</span> <span class="o">-</span> <span class="mi">1</span> <span class="k">if</span> <span class="n">o</span> <span class="k">else</span> <span class="kc">None</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">r_start</span><span class="p">]</span> </span><span id="L-137"><a href="#L-137"><span class="linenos">137</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;r_start does not match number of replicas&#39;</span><span class="p">)</span>
</span><span id="L-138"><a href="#L-138"><span class="linenos">138</span></a> <span class="k">else</span><span class="p">:</span> </span><span id="L-138"><a href="#L-138"><span class="linenos">138</span></a> <span class="c1"># Adjust Configuration numbering to python index</span>
</span><span id="L-139"><a href="#L-139"><span class="linenos">139</span></a> <span class="n">r_start</span> <span class="o">=</span> <span class="p">[</span><span class="kc">None</span><span class="p">]</span> <span class="o">*</span> <span class="n">replica</span> </span><span id="L-139"><a href="#L-139"><span class="linenos">139</span></a> <span class="n">r_start</span> <span class="o">=</span> <span class="p">[</span><span class="n">o</span> <span class="o">-</span> <span class="mi">1</span> <span class="k">if</span> <span class="n">o</span> <span class="k">else</span> <span class="kc">None</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">r_start</span><span class="p">]</span>
</span><span id="L-140"><a href="#L-140"><span class="linenos">140</span></a> </span><span id="L-140"><a href="#L-140"><span class="linenos">140</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="L-141"><a href="#L-141"><span class="linenos">141</span></a> <span class="k">if</span> <span class="s1">&#39;r_stop&#39;</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span> </span><span id="L-141"><a href="#L-141"><span class="linenos">141</span></a> <span class="n">r_start</span> <span class="o">=</span> <span class="p">[</span><span class="kc">None</span><span class="p">]</span> <span class="o">*</span> <span class="n">replica</span>
</span><span id="L-142"><a href="#L-142"><span class="linenos">142</span></a> <span class="n">r_stop</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;r_stop&#39;</span><span class="p">)</span> </span><span id="L-142"><a href="#L-142"><span class="linenos">142</span></a>
</span><span id="L-143"><a href="#L-143"><span class="linenos">143</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">r_stop</span><span class="p">)</span> <span class="o">!=</span> <span class="n">replica</span><span class="p">:</span> </span><span id="L-143"><a href="#L-143"><span class="linenos">143</span></a> <span class="k">if</span> <span class="s1">&#39;r_stop&#39;</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
</span><span id="L-144"><a href="#L-144"><span class="linenos">144</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;r_stop does not match number of replicas&#39;</span><span class="p">)</span> </span><span id="L-144"><a href="#L-144"><span class="linenos">144</span></a> <span class="n">r_stop</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;r_stop&#39;</span><span class="p">)</span>
</span><span id="L-145"><a href="#L-145"><span class="linenos">145</span></a> <span class="k">else</span><span class="p">:</span> </span><span id="L-145"><a href="#L-145"><span class="linenos">145</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">r_stop</span><span class="p">)</span> <span class="o">!=</span> <span class="n">replica</span><span class="p">:</span>
</span><span id="L-146"><a href="#L-146"><span class="linenos">146</span></a> <span class="n">r_stop</span> <span class="o">=</span> <span class="p">[</span><span class="kc">None</span><span class="p">]</span> <span class="o">*</span> <span class="n">replica</span> </span><span id="L-146"><a href="#L-146"><span class="linenos">146</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;r_stop does not match number of replicas&#39;</span><span class="p">)</span>
</span><span id="L-147"><a href="#L-147"><span class="linenos">147</span></a> </span><span id="L-147"><a href="#L-147"><span class="linenos">147</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="L-148"><a href="#L-148"><span class="linenos">148</span></a> <span class="nb">print</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;Read &lt;bar</span><span class="si">{psi}</span><span class="s1">\psi&gt; from&#39;</span><span class="p">,</span> <span class="n">prefix</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span> <span class="s1">&#39;,&#39;</span><span class="p">,</span> <span class="n">replica</span><span class="p">,</span> <span class="s1">&#39;replica&#39;</span><span class="p">,</span> <span class="n">end</span><span class="o">=</span><span class="s1">&#39;&#39;</span><span class="p">)</span> </span><span id="L-148"><a href="#L-148"><span class="linenos">148</span></a> <span class="n">r_stop</span> <span class="o">=</span> <span class="p">[</span><span class="kc">None</span><span class="p">]</span> <span class="o">*</span> <span class="n">replica</span>
</span><span id="L-149"><a href="#L-149"><span class="linenos">149</span></a> </span><span id="L-149"><a href="#L-149"><span class="linenos">149</span></a>
</span><span id="L-150"><a href="#L-150"><span class="linenos">150</span></a> <span class="n">print_err</span> <span class="o">=</span> <span class="mi">0</span> </span><span id="L-150"><a href="#L-150"><span class="linenos">150</span></a> <span class="nb">print</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;Read &lt;bar</span><span class="si">{psi}</span><span class="s1">\psi&gt; from&#39;</span><span class="p">,</span> <span class="n">prefix</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span> <span class="s1">&#39;,&#39;</span><span class="p">,</span> <span class="n">replica</span><span class="p">,</span> <span class="s1">&#39;replica&#39;</span><span class="p">,</span> <span class="n">end</span><span class="o">=</span><span class="s1">&#39;&#39;</span><span class="p">)</span>
</span><span id="L-151"><a href="#L-151"><span class="linenos">151</span></a> <span class="k">if</span> <span class="s1">&#39;print_err&#39;</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span> </span><span id="L-151"><a href="#L-151"><span class="linenos">151</span></a>
</span><span id="L-152"><a href="#L-152"><span class="linenos">152</span></a> <span class="n">print_err</span> <span class="o">=</span> <span class="mi">1</span> </span><span id="L-152"><a href="#L-152"><span class="linenos">152</span></a> <span class="n">print_err</span> <span class="o">=</span> <span class="mi">0</span>
</span><span id="L-153"><a href="#L-153"><span class="linenos">153</span></a> <span class="nb">print</span><span class="p">()</span> </span><span id="L-153"><a href="#L-153"><span class="linenos">153</span></a> <span class="k">if</span> <span class="s1">&#39;print_err&#39;</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
</span><span id="L-154"><a href="#L-154"><span class="linenos">154</span></a> </span><span id="L-154"><a href="#L-154"><span class="linenos">154</span></a> <span class="n">print_err</span> <span class="o">=</span> <span class="mi">1</span>
</span><span id="L-155"><a href="#L-155"><span class="linenos">155</span></a> <span class="n">deltas</span> <span class="o">=</span> <span class="p">[]</span> </span><span id="L-155"><a href="#L-155"><span class="linenos">155</span></a> <span class="nb">print</span><span class="p">()</span>
</span><span id="L-156"><a href="#L-156"><span class="linenos">156</span></a> </span><span id="L-156"><a href="#L-156"><span class="linenos">156</span></a>
</span><span id="L-157"><a href="#L-157"><span class="linenos">157</span></a> <span class="k">for</span> <span class="n">rep</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">replica</span><span class="p">):</span> </span><span id="L-157"><a href="#L-157"><span class="linenos">157</span></a> <span class="n">deltas</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="L-158"><a href="#L-158"><span class="linenos">158</span></a> <span class="n">tmp_array</span> <span class="o">=</span> <span class="p">[]</span> </span><span id="L-158"><a href="#L-158"><span class="linenos">158</span></a>
</span><span id="L-159"><a href="#L-159"><span class="linenos">159</span></a> <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">path</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">ls</span><span class="p">[</span><span class="n">rep</span><span class="p">],</span> <span class="s1">&#39;rb&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span> </span><span id="L-159"><a href="#L-159"><span class="linenos">159</span></a> <span class="k">for</span> <span class="n">rep</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">replica</span><span class="p">):</span>
</span><span id="L-160"><a href="#L-160"><span class="linenos">160</span></a> </span><span id="L-160"><a href="#L-160"><span class="linenos">160</span></a> <span class="n">tmp_array</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="L-161"><a href="#L-161"><span class="linenos">161</span></a> <span class="n">t</span> <span class="o">=</span> <span class="n">fp</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="mi">4</span><span class="p">)</span> <span class="c1"># number of reweighting factors</span> </span><span id="L-161"><a href="#L-161"><span class="linenos">161</span></a> <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">path</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">ls</span><span class="p">[</span><span class="n">rep</span><span class="p">],</span> <span class="s1">&#39;rb&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span>
</span><span id="L-162"><a href="#L-162"><span class="linenos">162</span></a> <span class="k">if</span> <span class="n">rep</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span> </span><span id="L-162"><a href="#L-162"><span class="linenos">162</span></a>
</span><span id="L-163"><a href="#L-163"><span class="linenos">163</span></a> <span class="n">nrw</span> <span class="o">=</span> <span class="n">struct</span><span class="o">.</span><span class="n">unpack</span><span class="p">(</span><span class="s1">&#39;i&#39;</span><span class="p">,</span> <span class="n">t</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> </span><span id="L-163"><a href="#L-163"><span class="linenos">163</span></a> <span class="n">t</span> <span class="o">=</span> <span class="n">fp</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="mi">4</span><span class="p">)</span> <span class="c1"># number of reweighting factors</span>
</span><span id="L-164"><a href="#L-164"><span class="linenos">164</span></a> <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nrw</span><span class="p">):</span> </span><span id="L-164"><a href="#L-164"><span class="linenos">164</span></a> <span class="k">if</span> <span class="n">rep</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
</span><span id="L-165"><a href="#L-165"><span class="linenos">165</span></a> <span class="n">deltas</span><span class="o">.</span><span class="n">append</span><span class="p">([])</span> </span><span id="L-165"><a href="#L-165"><span class="linenos">165</span></a> <span class="n">nrw</span> <span class="o">=</span> <span class="n">struct</span><span class="o">.</span><span class="n">unpack</span><span class="p">(</span><span class="s1">&#39;i&#39;</span><span class="p">,</span> <span class="n">t</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
</span><span id="L-166"><a href="#L-166"><span class="linenos">166</span></a> <span class="k">else</span><span class="p">:</span> </span><span id="L-166"><a href="#L-166"><span class="linenos">166</span></a> <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nrw</span><span class="p">):</span>
</span><span id="L-167"><a href="#L-167"><span class="linenos">167</span></a> <span class="k">if</span> <span class="n">nrw</span> <span class="o">!=</span> <span class="n">struct</span><span class="o">.</span><span class="n">unpack</span><span class="p">(</span><span class="s1">&#39;i&#39;</span><span class="p">,</span> <span class="n">t</span><span class="p">)[</span><span class="mi">0</span><span class="p">]:</span> </span><span id="L-167"><a href="#L-167"><span class="linenos">167</span></a> <span class="n">deltas</span><span class="o">.</span><span class="n">append</span><span class="p">([])</span>
</span><span id="L-168"><a href="#L-168"><span class="linenos">168</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Error: different number of factors for replicum&#39;</span><span class="p">,</span> <span class="n">rep</span><span class="p">)</span> </span><span id="L-168"><a href="#L-168"><span class="linenos">168</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="L-169"><a href="#L-169"><span class="linenos">169</span></a> </span><span id="L-169"><a href="#L-169"><span class="linenos">169</span></a> <span class="k">if</span> <span class="n">nrw</span> <span class="o">!=</span> <span class="n">struct</span><span class="o">.</span><span class="n">unpack</span><span class="p">(</span><span class="s1">&#39;i&#39;</span><span class="p">,</span> <span class="n">t</span><span class="p">)[</span><span class="mi">0</span><span class="p">]:</span>
</span><span id="L-170"><a href="#L-170"><span class="linenos">170</span></a> <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nrw</span><span class="p">):</span> </span><span id="L-170"><a href="#L-170"><span class="linenos">170</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Error: different number of factors for replicum&#39;</span><span class="p">,</span> <span class="n">rep</span><span class="p">)</span>
</span><span id="L-171"><a href="#L-171"><span class="linenos">171</span></a> <span class="n">tmp_array</span><span class="o">.</span><span class="n">append</span><span class="p">([])</span> </span><span id="L-171"><a href="#L-171"><span class="linenos">171</span></a>
</span><span id="L-172"><a href="#L-172"><span class="linenos">172</span></a> </span><span id="L-172"><a href="#L-172"><span class="linenos">172</span></a> <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nrw</span><span class="p">):</span>
</span><span id="L-173"><a href="#L-173"><span class="linenos">173</span></a> <span class="c1"># This block is necessary for openQCD1.6 ms1 files</span> </span><span id="L-173"><a href="#L-173"><span class="linenos">173</span></a> <span class="n">tmp_array</span><span class="o">.</span><span class="n">append</span><span class="p">([])</span>
</span><span id="L-174"><a href="#L-174"><span class="linenos">174</span></a> <span class="n">nfct</span> <span class="o">=</span> <span class="p">[]</span> </span><span id="L-174"><a href="#L-174"><span class="linenos">174</span></a>
</span><span id="L-175"><a href="#L-175"><span class="linenos">175</span></a> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nrw</span><span class="p">):</span> </span><span id="L-175"><a href="#L-175"><span class="linenos">175</span></a> <span class="c1"># This block is necessary for openQCD1.6 ms1 files</span>
</span><span id="L-176"><a href="#L-176"><span class="linenos">176</span></a> <span class="n">t</span> <span class="o">=</span> <span class="n">fp</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="mi">4</span><span class="p">)</span> </span><span id="L-176"><a href="#L-176"><span class="linenos">176</span></a> <span class="n">nfct</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="L-177"><a href="#L-177"><span class="linenos">177</span></a> <span class="n">nfct</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">struct</span><span class="o">.</span><span class="n">unpack</span><span class="p">(</span><span class="s1">&#39;i&#39;</span><span class="p">,</span> <span class="n">t</span><span class="p">)[</span><span class="mi">0</span><span class="p">])</span> </span><span id="L-177"><a href="#L-177"><span class="linenos">177</span></a> <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nrw</span><span class="p">):</span>
</span><span id="L-178"><a href="#L-178"><span class="linenos">178</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;nfct: &#39;</span><span class="p">,</span> <span class="n">nfct</span><span class="p">)</span> <span class="c1"># Hasenbusch factor, 1 for rat reweighting</span> </span><span id="L-178"><a href="#L-178"><span class="linenos">178</span></a> <span class="n">t</span> <span class="o">=</span> <span class="n">fp</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="mi">4</span><span class="p">)</span>
</span><span id="L-179"><a href="#L-179"><span class="linenos">179</span></a> </span><span id="L-179"><a href="#L-179"><span class="linenos">179</span></a> <span class="n">nfct</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">struct</span><span class="o">.</span><span class="n">unpack</span><span class="p">(</span><span class="s1">&#39;i&#39;</span><span class="p">,</span> <span class="n">t</span><span class="p">)[</span><span class="mi">0</span><span class="p">])</span>
</span><span id="L-180"><a href="#L-180"><span class="linenos">180</span></a> <span class="n">nsrc</span> <span class="o">=</span> <span class="p">[]</span> </span><span id="L-180"><a href="#L-180"><span class="linenos">180</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;nfct: &#39;</span><span class="p">,</span> <span class="n">nfct</span><span class="p">)</span> <span class="c1"># Hasenbusch factor, 1 for rat reweighting</span>
</span><span id="L-181"><a href="#L-181"><span class="linenos">181</span></a> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nrw</span><span class="p">):</span> </span><span id="L-181"><a href="#L-181"><span class="linenos">181</span></a>
</span><span id="L-182"><a href="#L-182"><span class="linenos">182</span></a> <span class="n">t</span> <span class="o">=</span> <span class="n">fp</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="mi">4</span><span class="p">)</span> </span><span id="L-182"><a href="#L-182"><span class="linenos">182</span></a> <span class="n">nsrc</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="L-183"><a href="#L-183"><span class="linenos">183</span></a> <span class="n">nsrc</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">struct</span><span class="o">.</span><span class="n">unpack</span><span class="p">(</span><span class="s1">&#39;i&#39;</span><span class="p">,</span> <span class="n">t</span><span class="p">)[</span><span class="mi">0</span><span class="p">])</span> </span><span id="L-183"><a href="#L-183"><span class="linenos">183</span></a> <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nrw</span><span class="p">):</span>
</span><span id="L-184"><a href="#L-184"><span class="linenos">184</span></a> </span><span id="L-184"><a href="#L-184"><span class="linenos">184</span></a> <span class="n">t</span> <span class="o">=</span> <span class="n">fp</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="mi">4</span><span class="p">)</span>
</span><span id="L-185"><a href="#L-185"><span class="linenos">185</span></a> <span class="c1"># body</span> </span><span id="L-185"><a href="#L-185"><span class="linenos">185</span></a> <span class="n">nsrc</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">struct</span><span class="o">.</span><span class="n">unpack</span><span class="p">(</span><span class="s1">&#39;i&#39;</span><span class="p">,</span> <span class="n">t</span><span class="p">)[</span><span class="mi">0</span><span class="p">])</span>
</span><span id="L-186"><a href="#L-186"><span class="linenos">186</span></a> <span class="k">while</span> <span class="kc">True</span><span class="p">:</span> </span><span id="L-186"><a href="#L-186"><span class="linenos">186</span></a>
</span><span id="L-187"><a href="#L-187"><span class="linenos">187</span></a> <span class="n">t</span> <span class="o">=</span> <span class="n">fp</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="mi">4</span><span class="p">)</span> </span><span id="L-187"><a href="#L-187"><span class="linenos">187</span></a> <span class="c1"># body</span>
</span><span id="L-188"><a href="#L-188"><span class="linenos">188</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">t</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mi">4</span><span class="p">:</span> </span><span id="L-188"><a href="#L-188"><span class="linenos">188</span></a> <span class="k">while</span> <span class="kc">True</span><span class="p">:</span>
</span><span id="L-189"><a href="#L-189"><span class="linenos">189</span></a> <span class="k">break</span> </span><span id="L-189"><a href="#L-189"><span class="linenos">189</span></a> <span class="n">t</span> <span class="o">=</span> <span class="n">fp</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="mi">4</span><span class="p">)</span>
</span><span id="L-190"><a href="#L-190"><span class="linenos">190</span></a> <span class="k">if</span> <span class="n">print_err</span><span class="p">:</span> </span><span id="L-190"><a href="#L-190"><span class="linenos">190</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">t</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mi">4</span><span class="p">:</span>
</span><span id="L-191"><a href="#L-191"><span class="linenos">191</span></a> <span class="n">config_no</span> <span class="o">=</span> <span class="n">struct</span><span class="o">.</span><span class="n">unpack</span><span class="p">(</span><span class="s1">&#39;i&#39;</span><span class="p">,</span> <span class="n">t</span><span class="p">)</span> </span><span id="L-191"><a href="#L-191"><span class="linenos">191</span></a> <span class="k">break</span>
</span><span id="L-192"><a href="#L-192"><span class="linenos">192</span></a> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nrw</span><span class="p">):</span> </span><span id="L-192"><a href="#L-192"><span class="linenos">192</span></a> <span class="k">if</span> <span class="n">print_err</span><span class="p">:</span>
</span><span id="L-193"><a href="#L-193"><span class="linenos">193</span></a> <span class="n">tmp_nfct</span> <span class="o">=</span> <span class="mf">1.0</span> </span><span id="L-193"><a href="#L-193"><span class="linenos">193</span></a> <span class="n">config_no</span> <span class="o">=</span> <span class="n">struct</span><span class="o">.</span><span class="n">unpack</span><span class="p">(</span><span class="s1">&#39;i&#39;</span><span class="p">,</span> <span class="n">t</span><span class="p">)</span>
</span><span id="L-194"><a href="#L-194"><span class="linenos">194</span></a> <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nfct</span><span class="p">[</span><span class="n">i</span><span class="p">]):</span> </span><span id="L-194"><a href="#L-194"><span class="linenos">194</span></a> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nrw</span><span class="p">):</span>
</span><span id="L-195"><a href="#L-195"><span class="linenos">195</span></a> <span class="n">t</span> <span class="o">=</span> <span class="n">fp</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="mi">8</span> <span class="o">*</span> <span class="n">nsrc</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> </span><span id="L-195"><a href="#L-195"><span class="linenos">195</span></a> <span class="n">tmp_nfct</span> <span class="o">=</span> <span class="mf">1.0</span>
</span><span id="L-196"><a href="#L-196"><span class="linenos">196</span></a> <span class="n">t</span> <span class="o">=</span> <span class="n">fp</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="mi">8</span> <span class="o">*</span> <span class="n">nsrc</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> </span><span id="L-196"><a href="#L-196"><span class="linenos">196</span></a> <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nfct</span><span class="p">[</span><span class="n">i</span><span class="p">]):</span>
</span><span id="L-197"><a href="#L-197"><span class="linenos">197</span></a> <span class="n">tmp_rw</span> <span class="o">=</span> <span class="n">struct</span><span class="o">.</span><span class="n">unpack</span><span class="p">(</span><span class="s1">&#39;d&#39;</span> <span class="o">*</span> <span class="n">nsrc</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">t</span><span class="p">)</span> </span><span id="L-197"><a href="#L-197"><span class="linenos">197</span></a> <span class="n">t</span> <span class="o">=</span> <span class="n">fp</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="mi">8</span> <span class="o">*</span> <span class="n">nsrc</span><span class="p">[</span><span class="n">i</span><span class="p">])</span>
</span><span id="L-198"><a href="#L-198"><span class="linenos">198</span></a> <span class="n">tmp_nfct</span> <span class="o">*=</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">tmp_rw</span><span class="p">))</span> </span><span id="L-198"><a href="#L-198"><span class="linenos">198</span></a> <span class="n">t</span> <span class="o">=</span> <span class="n">fp</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="mi">8</span> <span class="o">*</span> <span class="n">nsrc</span><span class="p">[</span><span class="n">i</span><span class="p">])</span>
</span><span id="L-199"><a href="#L-199"><span class="linenos">199</span></a> <span class="k">if</span> <span class="n">print_err</span><span class="p">:</span> </span><span id="L-199"><a href="#L-199"><span class="linenos">199</span></a> <span class="n">tmp_rw</span> <span class="o">=</span> <span class="n">struct</span><span class="o">.</span><span class="n">unpack</span><span class="p">(</span><span class="s1">&#39;d&#39;</span> <span class="o">*</span> <span class="n">nsrc</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">t</span><span class="p">)</span>
</span><span id="L-200"><a href="#L-200"><span class="linenos">200</span></a> <span class="nb">print</span><span class="p">(</span><span class="n">config_no</span><span class="p">,</span> <span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">tmp_rw</span><span class="p">)),</span> <span class="n">np</span><span class="o">.</span><span class="n">std</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">tmp_rw</span><span class="p">)))</span> </span><span id="L-200"><a href="#L-200"><span class="linenos">200</span></a> <span class="n">tmp_nfct</span> <span class="o">*=</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">tmp_rw</span><span class="p">))</span>
</span><span id="L-201"><a href="#L-201"><span class="linenos">201</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Sources:&#39;</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">tmp_rw</span><span class="p">))</span> </span><span id="L-201"><a href="#L-201"><span class="linenos">201</span></a> <span class="k">if</span> <span class="n">print_err</span><span class="p">:</span>
</span><span id="L-202"><a href="#L-202"><span class="linenos">202</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Partial factor:&#39;</span><span class="p">,</span> <span class="n">tmp_nfct</span><span class="p">)</span> </span><span id="L-202"><a href="#L-202"><span class="linenos">202</span></a> <span class="nb">print</span><span class="p">(</span><span class="n">config_no</span><span class="p">,</span> <span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">tmp_rw</span><span class="p">)),</span> <span class="n">np</span><span class="o">.</span><span class="n">std</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">tmp_rw</span><span class="p">)))</span>
</span><span id="L-203"><a href="#L-203"><span class="linenos">203</span></a> <span class="n">tmp_array</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">tmp_nfct</span><span class="p">)</span> </span><span id="L-203"><a href="#L-203"><span class="linenos">203</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Sources:&#39;</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">tmp_rw</span><span class="p">))</span>
</span><span id="L-204"><a href="#L-204"><span class="linenos">204</span></a> </span><span id="L-204"><a href="#L-204"><span class="linenos">204</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Partial factor:&#39;</span><span class="p">,</span> <span class="n">tmp_nfct</span><span class="p">)</span>
</span><span id="L-205"><a href="#L-205"><span class="linenos">205</span></a> <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nrw</span><span class="p">):</span> </span><span id="L-205"><a href="#L-205"><span class="linenos">205</span></a> <span class="n">tmp_array</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">tmp_nfct</span><span class="p">)</span>
</span><span id="L-206"><a href="#L-206"><span class="linenos">206</span></a> <span class="n">deltas</span><span class="p">[</span><span class="n">k</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">tmp_array</span><span class="p">[</span><span class="n">k</span><span class="p">][</span><span class="n">r_start</span><span class="p">[</span><span class="n">rep</span><span class="p">]:</span><span class="n">r_stop</span><span class="p">[</span><span class="n">rep</span><span class="p">]])</span> </span><span id="L-206"><a href="#L-206"><span class="linenos">206</span></a>
</span><span id="L-207"><a href="#L-207"><span class="linenos">207</span></a> </span><span id="L-207"><a href="#L-207"><span class="linenos">207</span></a> <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nrw</span><span class="p">):</span>
</span><span id="L-208"><a href="#L-208"><span class="linenos">208</span></a> <span class="n">rep_names</span> <span class="o">=</span> <span class="p">[]</span> </span><span id="L-208"><a href="#L-208"><span class="linenos">208</span></a> <span class="n">deltas</span><span class="p">[</span><span class="n">k</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">tmp_array</span><span class="p">[</span><span class="n">k</span><span class="p">][</span><span class="n">r_start</span><span class="p">[</span><span class="n">rep</span><span class="p">]:</span><span class="n">r_stop</span><span class="p">[</span><span class="n">rep</span><span class="p">]])</span>
</span><span id="L-209"><a href="#L-209"><span class="linenos">209</span></a> <span class="k">for</span> <span class="n">entry</span> <span class="ow">in</span> <span class="n">ls</span><span class="p">:</span> </span><span id="L-209"><a href="#L-209"><span class="linenos">209</span></a>
</span><span id="L-210"><a href="#L-210"><span class="linenos">210</span></a> <span class="n">truncated_entry</span> <span class="o">=</span> <span class="n">entry</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> </span><span id="L-210"><a href="#L-210"><span class="linenos">210</span></a> <span class="n">rep_names</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="L-211"><a href="#L-211"><span class="linenos">211</span></a> <span class="n">idx</span> <span class="o">=</span> <span class="n">truncated_entry</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="s1">&#39;r&#39;</span><span class="p">)</span> </span><span id="L-211"><a href="#L-211"><span class="linenos">211</span></a> <span class="k">for</span> <span class="n">entry</span> <span class="ow">in</span> <span class="n">ls</span><span class="p">:</span>
</span><span id="L-212"><a href="#L-212"><span class="linenos">212</span></a> <span class="n">rep_names</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">truncated_entry</span><span class="p">[:</span><span class="n">idx</span><span class="p">]</span> <span class="o">+</span> <span class="s1">&#39;|&#39;</span> <span class="o">+</span> <span class="n">truncated_entry</span><span class="p">[</span><span class="n">idx</span><span class="p">:])</span> </span><span id="L-212"><a href="#L-212"><span class="linenos">212</span></a> <span class="n">truncated_entry</span> <span class="o">=</span> <span class="n">entry</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
</span><span id="L-213"><a href="#L-213"><span class="linenos">213</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">,</span> <span class="n">nrw</span><span class="p">,</span> <span class="sa">r</span><span class="s1">&#39;&lt;bar</span><span class="si">{psi}</span><span class="s1">\psi&gt; with&#39;</span><span class="p">,</span> <span class="n">nsrc</span><span class="p">,</span> <span class="s1">&#39;sources&#39;</span><span class="p">)</span> </span><span id="L-213"><a href="#L-213"><span class="linenos">213</span></a> <span class="n">idx</span> <span class="o">=</span> <span class="n">truncated_entry</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="s1">&#39;r&#39;</span><span class="p">)</span>
</span><span id="L-214"><a href="#L-214"><span class="linenos">214</span></a> <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span> </span><span id="L-214"><a href="#L-214"><span class="linenos">214</span></a> <span class="n">rep_names</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">truncated_entry</span><span class="p">[:</span><span class="n">idx</span><span class="p">]</span> <span class="o">+</span> <span class="s1">&#39;|&#39;</span> <span class="o">+</span> <span class="n">truncated_entry</span><span class="p">[</span><span class="n">idx</span><span class="p">:])</span>
</span><span id="L-215"><a href="#L-215"><span class="linenos">215</span></a> <span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nrw</span><span class="p">):</span> </span><span id="L-215"><a href="#L-215"><span class="linenos">215</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">,</span> <span class="n">nrw</span><span class="p">,</span> <span class="sa">r</span><span class="s1">&#39;&lt;bar</span><span class="si">{psi}</span><span class="s1">\psi&gt; with&#39;</span><span class="p">,</span> <span class="n">nsrc</span><span class="p">,</span> <span class="s1">&#39;sources&#39;</span><span class="p">)</span>
</span><span id="L-216"><a href="#L-216"><span class="linenos">216</span></a> <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">Obs</span><span class="p">(</span><span class="n">deltas</span><span class="p">[</span><span class="n">t</span><span class="p">],</span> <span class="n">rep_names</span><span class="p">))</span> </span><span id="L-216"><a href="#L-216"><span class="linenos">216</span></a> <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="L-217"><a href="#L-217"><span class="linenos">217</span></a> </span><span id="L-217"><a href="#L-217"><span class="linenos">217</span></a> <span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nrw</span><span class="p">):</span>
</span><span id="L-218"><a href="#L-218"><span class="linenos">218</span></a> <span class="k">return</span> <span class="n">result</span> </span><span id="L-218"><a href="#L-218"><span class="linenos">218</span></a> <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">Obs</span><span class="p">(</span><span class="n">deltas</span><span class="p">[</span><span class="n">t</span><span class="p">],</span> <span class="n">rep_names</span><span class="p">))</span>
</span><span id="L-219"><a href="#L-219"><span class="linenos">219</span></a>
</span><span id="L-220"><a href="#L-220"><span class="linenos">220</span></a> <span class="k">return</span> <span class="n">result</span>
</span></pre></div> </span></pre></div>
@ -312,91 +314,91 @@
</div> </div>
<a class="headerlink" href="#fit_t0"></a> <a class="headerlink" href="#fit_t0"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="fit_t0-14"><a href="#fit_t0-14"><span class="linenos">14</span></a><span class="k">def</span><span class="w"> </span><span class="nf">fit_t0</span><span class="p">(</span><span class="n">t2E_dict</span><span class="p">,</span> <span class="n">fit_range</span><span class="p">,</span> <span class="n">plot_fit</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">observable</span><span class="o">=</span><span class="s1">&#39;t0&#39;</span><span class="p">):</span> <div class="pdoc-code codehilite"><pre><span></span><span id="fit_t0-16"><a href="#fit_t0-16"><span class="linenos"> 16</span></a><span class="k">def</span><span class="w"> </span><span class="nf">fit_t0</span><span class="p">(</span><span class="n">t2E_dict</span><span class="p">,</span> <span class="n">fit_range</span><span class="p">,</span> <span class="n">plot_fit</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">observable</span><span class="o">=</span><span class="s1">&#39;t0&#39;</span><span class="p">):</span>
</span><span id="fit_t0-15"><a href="#fit_t0-15"><span class="linenos">15</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Compute the root of (flow-based) data based on a dictionary that contains</span> </span><span id="fit_t0-17"><a href="#fit_t0-17"><span class="linenos"> 17</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Compute the root of (flow-based) data based on a dictionary that contains</span>
</span><span id="fit_t0-16"><a href="#fit_t0-16"><span class="linenos">16</span></a><span class="sd"> the necessary information in key-value pairs a la (flow time: observable at flow time).</span> </span><span id="fit_t0-18"><a href="#fit_t0-18"><span class="linenos"> 18</span></a><span class="sd"> the necessary information in key-value pairs a la (flow time: observable at flow time).</span>
</span><span id="fit_t0-17"><a href="#fit_t0-17"><span class="linenos">17</span></a> </span><span id="fit_t0-19"><a href="#fit_t0-19"><span class="linenos"> 19</span></a>
</span><span id="fit_t0-18"><a href="#fit_t0-18"><span class="linenos">18</span></a><span class="sd"> It is assumed that the data is monotonically increasing and passes zero from below.</span> </span><span id="fit_t0-20"><a href="#fit_t0-20"><span class="linenos"> 20</span></a><span class="sd"> It is assumed that the data is monotonically increasing and passes zero from below.</span>
</span><span id="fit_t0-19"><a href="#fit_t0-19"><span class="linenos">19</span></a><span class="sd"> No exception is thrown if this is not the case (several roots, no monotonic increase).</span> </span><span id="fit_t0-21"><a href="#fit_t0-21"><span class="linenos"> 21</span></a><span class="sd"> No exception is thrown if this is not the case (several roots, no monotonic increase).</span>
</span><span id="fit_t0-20"><a href="#fit_t0-20"><span class="linenos">20</span></a><span class="sd"> An exception is thrown if no root can be found in the data.</span> </span><span id="fit_t0-22"><a href="#fit_t0-22"><span class="linenos"> 22</span></a><span class="sd"> An exception is thrown if no root can be found in the data.</span>
</span><span id="fit_t0-21"><a href="#fit_t0-21"><span class="linenos">21</span></a> </span><span id="fit_t0-23"><a href="#fit_t0-23"><span class="linenos"> 23</span></a>
</span><span id="fit_t0-22"><a href="#fit_t0-22"><span class="linenos">22</span></a><span class="sd"> A linear fit in the vicinity of the root is performed to exctract the root from the</span> </span><span id="fit_t0-24"><a href="#fit_t0-24"><span class="linenos"> 24</span></a><span class="sd"> A linear fit in the vicinity of the root is performed to exctract the root from the</span>
</span><span id="fit_t0-23"><a href="#fit_t0-23"><span class="linenos">23</span></a><span class="sd"> two fit parameters.</span> </span><span id="fit_t0-25"><a href="#fit_t0-25"><span class="linenos"> 25</span></a><span class="sd"> two fit parameters.</span>
</span><span id="fit_t0-24"><a href="#fit_t0-24"><span class="linenos">24</span></a> </span><span id="fit_t0-26"><a href="#fit_t0-26"><span class="linenos"> 26</span></a>
</span><span id="fit_t0-25"><a href="#fit_t0-25"><span class="linenos">25</span></a><span class="sd"> Parameters</span> </span><span id="fit_t0-27"><a href="#fit_t0-27"><span class="linenos"> 27</span></a><span class="sd"> Parameters</span>
</span><span id="fit_t0-26"><a href="#fit_t0-26"><span class="linenos">26</span></a><span class="sd"> ----------</span> </span><span id="fit_t0-28"><a href="#fit_t0-28"><span class="linenos"> 28</span></a><span class="sd"> ----------</span>
</span><span id="fit_t0-27"><a href="#fit_t0-27"><span class="linenos">27</span></a><span class="sd"> t2E_dict : dict</span> </span><span id="fit_t0-29"><a href="#fit_t0-29"><span class="linenos"> 29</span></a><span class="sd"> t2E_dict : dict</span>
</span><span id="fit_t0-28"><a href="#fit_t0-28"><span class="linenos">28</span></a><span class="sd"> Dictionary with pairs of (flow time: observable at flow time) where the flow times</span> </span><span id="fit_t0-30"><a href="#fit_t0-30"><span class="linenos"> 30</span></a><span class="sd"> Dictionary with pairs of (flow time: observable at flow time) where the flow times</span>
</span><span id="fit_t0-29"><a href="#fit_t0-29"><span class="linenos">29</span></a><span class="sd"> are of type float and the observables of type Obs.</span> </span><span id="fit_t0-31"><a href="#fit_t0-31"><span class="linenos"> 31</span></a><span class="sd"> are of type float and the observables of type Obs.</span>
</span><span id="fit_t0-30"><a href="#fit_t0-30"><span class="linenos">30</span></a><span class="sd"> fit_range : int</span> </span><span id="fit_t0-32"><a href="#fit_t0-32"><span class="linenos"> 32</span></a><span class="sd"> fit_range : int</span>
</span><span id="fit_t0-31"><a href="#fit_t0-31"><span class="linenos">31</span></a><span class="sd"> Number of data points left and right of the zero</span> </span><span id="fit_t0-33"><a href="#fit_t0-33"><span class="linenos"> 33</span></a><span class="sd"> Number of data points left and right of the zero</span>
</span><span id="fit_t0-32"><a href="#fit_t0-32"><span class="linenos">32</span></a><span class="sd"> crossing to be included in the linear fit.</span> </span><span id="fit_t0-34"><a href="#fit_t0-34"><span class="linenos"> 34</span></a><span class="sd"> crossing to be included in the linear fit.</span>
</span><span id="fit_t0-33"><a href="#fit_t0-33"><span class="linenos">33</span></a><span class="sd"> plot_fit : bool</span> </span><span id="fit_t0-35"><a href="#fit_t0-35"><span class="linenos"> 35</span></a><span class="sd"> plot_fit : bool</span>
</span><span id="fit_t0-34"><a href="#fit_t0-34"><span class="linenos">34</span></a><span class="sd"> If true, the fit for the extraction of t0 is shown together with the data. (Default: False)</span> </span><span id="fit_t0-36"><a href="#fit_t0-36"><span class="linenos"> 36</span></a><span class="sd"> If true, the fit for the extraction of t0 is shown together with the data. (Default: False)</span>
</span><span id="fit_t0-35"><a href="#fit_t0-35"><span class="linenos">35</span></a><span class="sd"> observable: str</span> </span><span id="fit_t0-37"><a href="#fit_t0-37"><span class="linenos"> 37</span></a><span class="sd"> observable: str</span>
</span><span id="fit_t0-36"><a href="#fit_t0-36"><span class="linenos">36</span></a><span class="sd"> Keyword to identify the observable to print the correct ylabel (if plot_fit is True)</span> </span><span id="fit_t0-38"><a href="#fit_t0-38"><span class="linenos"> 38</span></a><span class="sd"> Keyword to identify the observable to print the correct ylabel (if plot_fit is True)</span>
</span><span id="fit_t0-37"><a href="#fit_t0-37"><span class="linenos">37</span></a><span class="sd"> for the observables &#39;t0&#39; and &#39;w0&#39;. No y label is printed otherwise. (Default: &#39;t0&#39;)</span> </span><span id="fit_t0-39"><a href="#fit_t0-39"><span class="linenos"> 39</span></a><span class="sd"> for the observables &#39;t0&#39; and &#39;w0&#39;. No y label is printed otherwise. (Default: &#39;t0&#39;)</span>
</span><span id="fit_t0-38"><a href="#fit_t0-38"><span class="linenos">38</span></a> </span><span id="fit_t0-40"><a href="#fit_t0-40"><span class="linenos"> 40</span></a>
</span><span id="fit_t0-39"><a href="#fit_t0-39"><span class="linenos">39</span></a><span class="sd"> Returns</span> </span><span id="fit_t0-41"><a href="#fit_t0-41"><span class="linenos"> 41</span></a><span class="sd"> Returns</span>
</span><span id="fit_t0-40"><a href="#fit_t0-40"><span class="linenos">40</span></a><span class="sd"> -------</span> </span><span id="fit_t0-42"><a href="#fit_t0-42"><span class="linenos"> 42</span></a><span class="sd"> -------</span>
</span><span id="fit_t0-41"><a href="#fit_t0-41"><span class="linenos">41</span></a><span class="sd"> root : Obs</span> </span><span id="fit_t0-43"><a href="#fit_t0-43"><span class="linenos"> 43</span></a><span class="sd"> root : Obs</span>
</span><span id="fit_t0-42"><a href="#fit_t0-42"><span class="linenos">42</span></a><span class="sd"> The root of the data series.</span> </span><span id="fit_t0-44"><a href="#fit_t0-44"><span class="linenos"> 44</span></a><span class="sd"> The root of the data series.</span>
</span><span id="fit_t0-43"><a href="#fit_t0-43"><span class="linenos">43</span></a><span class="sd"> &quot;&quot;&quot;</span> </span><span id="fit_t0-45"><a href="#fit_t0-45"><span class="linenos"> 45</span></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="fit_t0-44"><a href="#fit_t0-44"><span class="linenos">44</span></a> </span><span id="fit_t0-46"><a href="#fit_t0-46"><span class="linenos"> 46</span></a>
</span><span id="fit_t0-45"><a href="#fit_t0-45"><span class="linenos">45</span></a> <span class="n">zero_crossing</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">argmax</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span> </span><span id="fit_t0-47"><a href="#fit_t0-47"><span class="linenos"> 47</span></a> <span class="n">zero_crossing</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">argmax</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span>
</span><span id="fit_t0-46"><a href="#fit_t0-46"><span class="linenos">46</span></a> <span class="p">[</span><span class="n">o</span><span class="o">.</span><span class="n">value</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">t2E_dict</span><span class="o">.</span><span class="n">values</span><span class="p">()])</span> <span class="o">&gt;</span> <span class="mf">0.0</span><span class="p">)</span> </span><span id="fit_t0-48"><a href="#fit_t0-48"><span class="linenos"> 48</span></a> <span class="p">[</span><span class="n">o</span><span class="o">.</span><span class="n">value</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">t2E_dict</span><span class="o">.</span><span class="n">values</span><span class="p">()])</span> <span class="o">&gt;</span> <span class="mf">0.0</span><span class="p">)</span>
</span><span id="fit_t0-47"><a href="#fit_t0-47"><span class="linenos">47</span></a> </span><span id="fit_t0-49"><a href="#fit_t0-49"><span class="linenos"> 49</span></a>
</span><span id="fit_t0-48"><a href="#fit_t0-48"><span class="linenos">48</span></a> <span class="k">if</span> <span class="n">zero_crossing</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span> </span><span id="fit_t0-50"><a href="#fit_t0-50"><span class="linenos"> 50</span></a> <span class="k">if</span> <span class="n">zero_crossing</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
</span><span id="fit_t0-49"><a href="#fit_t0-49"><span class="linenos">49</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Desired flow time not in data&#39;</span><span class="p">)</span> </span><span id="fit_t0-51"><a href="#fit_t0-51"><span class="linenos"> 51</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Desired flow time not in data&#39;</span><span class="p">)</span>
</span><span id="fit_t0-50"><a href="#fit_t0-50"><span class="linenos">50</span></a> </span><span id="fit_t0-52"><a href="#fit_t0-52"><span class="linenos"> 52</span></a>
</span><span id="fit_t0-51"><a href="#fit_t0-51"><span class="linenos">51</span></a> <span class="n">x</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">t2E_dict</span><span class="o">.</span><span class="n">keys</span><span class="p">())[</span><span class="n">zero_crossing</span> <span class="o">-</span> <span class="n">fit_range</span><span class="p">:</span> </span><span id="fit_t0-53"><a href="#fit_t0-53"><span class="linenos"> 53</span></a> <span class="n">x</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">t2E_dict</span><span class="o">.</span><span class="n">keys</span><span class="p">())[</span><span class="n">zero_crossing</span> <span class="o">-</span> <span class="n">fit_range</span><span class="p">:</span>
</span><span id="fit_t0-52"><a href="#fit_t0-52"><span class="linenos">52</span></a> <span class="n">zero_crossing</span> <span class="o">+</span> <span class="n">fit_range</span><span class="p">]</span> </span><span id="fit_t0-54"><a href="#fit_t0-54"><span class="linenos"> 54</span></a> <span class="n">zero_crossing</span> <span class="o">+</span> <span class="n">fit_range</span><span class="p">]</span>
</span><span id="fit_t0-53"><a href="#fit_t0-53"><span class="linenos">53</span></a> <span class="n">y</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">t2E_dict</span><span class="o">.</span><span class="n">values</span><span class="p">())[</span><span class="n">zero_crossing</span> <span class="o">-</span> <span class="n">fit_range</span><span class="p">:</span> </span><span id="fit_t0-55"><a href="#fit_t0-55"><span class="linenos"> 55</span></a> <span class="n">y</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">t2E_dict</span><span class="o">.</span><span class="n">values</span><span class="p">())[</span><span class="n">zero_crossing</span> <span class="o">-</span> <span class="n">fit_range</span><span class="p">:</span>
</span><span id="fit_t0-54"><a href="#fit_t0-54"><span class="linenos">54</span></a> <span class="n">zero_crossing</span> <span class="o">+</span> <span class="n">fit_range</span><span class="p">]</span> </span><span id="fit_t0-56"><a href="#fit_t0-56"><span class="linenos"> 56</span></a> <span class="n">zero_crossing</span> <span class="o">+</span> <span class="n">fit_range</span><span class="p">]</span>
</span><span id="fit_t0-55"><a href="#fit_t0-55"><span class="linenos">55</span></a> <span class="p">[</span><span class="n">o</span><span class="o">.</span><span class="n">gamma_method</span><span class="p">()</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">y</span><span class="p">]</span> </span><span id="fit_t0-57"><a href="#fit_t0-57"><span class="linenos"> 57</span></a> <span class="p">[</span><span class="n">o</span><span class="o">.</span><span class="n">gamma_method</span><span class="p">()</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">y</span><span class="p">]</span>
</span><span id="fit_t0-56"><a href="#fit_t0-56"><span class="linenos">56</span></a> </span><span id="fit_t0-58"><a href="#fit_t0-58"><span class="linenos"> 58</span></a>
</span><span id="fit_t0-57"><a href="#fit_t0-57"><span class="linenos">57</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mi">2</span> <span class="o">*</span> <span class="n">fit_range</span><span class="p">:</span> </span><span id="fit_t0-59"><a href="#fit_t0-59"><span class="linenos"> 59</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mi">2</span> <span class="o">*</span> <span class="n">fit_range</span><span class="p">:</span>
</span><span id="fit_t0-58"><a href="#fit_t0-58"><span class="linenos">58</span></a> <span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span><span class="s1">&#39;Fit range smaller than expected! Fitting from </span><span class="si">%1.2e</span><span class="s1"> to </span><span class="si">%1.2e</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">x</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]))</span> </span><span id="fit_t0-60"><a href="#fit_t0-60"><span class="linenos"> 60</span></a> <span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;Fit range smaller than expected! Fitting from </span><span class="si">{</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="si">:</span><span class="s1">1.2e</span><span class="si">}</span><span class="s1"> to </span><span class="si">{</span><span class="n">x</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="si">:</span><span class="s1">1.2e</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">,</span> <span class="n">stacklevel</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span>
</span><span id="fit_t0-59"><a href="#fit_t0-59"><span class="linenos">59</span></a> </span><span id="fit_t0-61"><a href="#fit_t0-61"><span class="linenos"> 61</span></a>
</span><span id="fit_t0-60"><a href="#fit_t0-60"><span class="linenos">60</span></a> <span class="n">fit_result</span> <span class="o">=</span> <span class="n">fit_lin</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">)</span> </span><span id="fit_t0-62"><a href="#fit_t0-62"><span class="linenos"> 62</span></a> <span class="n">fit_result</span> <span class="o">=</span> <span class="n">fit_lin</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">)</span>
</span><span id="fit_t0-61"><a href="#fit_t0-61"><span class="linenos">61</span></a> </span><span id="fit_t0-63"><a href="#fit_t0-63"><span class="linenos"> 63</span></a>
</span><span id="fit_t0-62"><a href="#fit_t0-62"><span class="linenos">62</span></a> <span class="k">if</span> <span class="n">plot_fit</span> <span class="ow">is</span> <span class="kc">True</span><span class="p">:</span> </span><span id="fit_t0-64"><a href="#fit_t0-64"><span class="linenos"> 64</span></a> <span class="k">if</span> <span class="n">plot_fit</span> <span class="ow">is</span> <span class="kc">True</span><span class="p">:</span>
</span><span id="fit_t0-63"><a href="#fit_t0-63"><span class="linenos">63</span></a> <span class="n">plt</span><span class="o">.</span><span class="n">figure</span><span class="p">()</span> </span><span id="fit_t0-65"><a href="#fit_t0-65"><span class="linenos"> 65</span></a> <span class="n">plt</span><span class="o">.</span><span class="n">figure</span><span class="p">()</span>
</span><span id="fit_t0-64"><a href="#fit_t0-64"><span class="linenos">64</span></a> <span class="n">gs</span> <span class="o">=</span> <span class="n">gridspec</span><span class="o">.</span><span class="n">GridSpec</span><span class="p">(</span><span class="mi">2</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="n">height_ratios</span><span class="o">=</span><span class="p">[</span><span class="mi">3</span><span class="p">,</span> <span class="mi">1</span><span class="p">],</span> <span class="n">wspace</span><span class="o">=</span><span class="mf">0.0</span><span class="p">,</span> <span class="n">hspace</span><span class="o">=</span><span class="mf">0.0</span><span class="p">)</span> </span><span id="fit_t0-66"><a href="#fit_t0-66"><span class="linenos"> 66</span></a> <span class="n">gs</span> <span class="o">=</span> <span class="n">gridspec</span><span class="o">.</span><span class="n">GridSpec</span><span class="p">(</span><span class="mi">2</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="n">height_ratios</span><span class="o">=</span><span class="p">[</span><span class="mi">3</span><span class="p">,</span> <span class="mi">1</span><span class="p">],</span> <span class="n">wspace</span><span class="o">=</span><span class="mf">0.0</span><span class="p">,</span> <span class="n">hspace</span><span class="o">=</span><span class="mf">0.0</span><span class="p">)</span>
</span><span id="fit_t0-65"><a href="#fit_t0-65"><span class="linenos">65</span></a> <span class="n">ax0</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">subplot</span><span class="p">(</span><span class="n">gs</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> </span><span id="fit_t0-67"><a href="#fit_t0-67"><span class="linenos"> 67</span></a> <span class="n">ax0</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">subplot</span><span class="p">(</span><span class="n">gs</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
</span><span id="fit_t0-66"><a href="#fit_t0-66"><span class="linenos">66</span></a> <span class="n">xmore</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">t2E_dict</span><span class="o">.</span><span class="n">keys</span><span class="p">())[</span><span class="n">zero_crossing</span> <span class="o">-</span> <span class="n">fit_range</span> <span class="o">-</span> <span class="mi">2</span><span class="p">:</span> <span class="n">zero_crossing</span> <span class="o">+</span> <span class="n">fit_range</span> <span class="o">+</span> <span class="mi">2</span><span class="p">]</span> </span><span id="fit_t0-68"><a href="#fit_t0-68"><span class="linenos"> 68</span></a> <span class="n">xmore</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">t2E_dict</span><span class="o">.</span><span class="n">keys</span><span class="p">())[</span><span class="n">zero_crossing</span> <span class="o">-</span> <span class="n">fit_range</span> <span class="o">-</span> <span class="mi">2</span><span class="p">:</span> <span class="n">zero_crossing</span> <span class="o">+</span> <span class="n">fit_range</span> <span class="o">+</span> <span class="mi">2</span><span class="p">]</span>
</span><span id="fit_t0-67"><a href="#fit_t0-67"><span class="linenos">67</span></a> <span class="n">ymore</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">t2E_dict</span><span class="o">.</span><span class="n">values</span><span class="p">())[</span><span class="n">zero_crossing</span> <span class="o">-</span> <span class="n">fit_range</span> <span class="o">-</span> <span class="mi">2</span><span class="p">:</span> <span class="n">zero_crossing</span> <span class="o">+</span> <span class="n">fit_range</span> <span class="o">+</span> <span class="mi">2</span><span class="p">]</span> </span><span id="fit_t0-69"><a href="#fit_t0-69"><span class="linenos"> 69</span></a> <span class="n">ymore</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">t2E_dict</span><span class="o">.</span><span class="n">values</span><span class="p">())[</span><span class="n">zero_crossing</span> <span class="o">-</span> <span class="n">fit_range</span> <span class="o">-</span> <span class="mi">2</span><span class="p">:</span> <span class="n">zero_crossing</span> <span class="o">+</span> <span class="n">fit_range</span> <span class="o">+</span> <span class="mi">2</span><span class="p">]</span>
</span><span id="fit_t0-68"><a href="#fit_t0-68"><span class="linenos">68</span></a> <span class="p">[</span><span class="n">o</span><span class="o">.</span><span class="n">gamma_method</span><span class="p">()</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">ymore</span><span class="p">]</span> </span><span id="fit_t0-70"><a href="#fit_t0-70"><span class="linenos"> 70</span></a> <span class="p">[</span><span class="n">o</span><span class="o">.</span><span class="n">gamma_method</span><span class="p">()</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">ymore</span><span class="p">]</span>
</span><span id="fit_t0-69"><a href="#fit_t0-69"><span class="linenos">69</span></a> <span class="n">ax0</span><span class="o">.</span><span class="n">errorbar</span><span class="p">(</span><span class="n">xmore</span><span class="p">,</span> <span class="p">[</span><span class="n">yi</span><span class="o">.</span><span class="n">value</span> <span class="k">for</span> <span class="n">yi</span> <span class="ow">in</span> <span class="n">ymore</span><span class="p">],</span> <span class="n">yerr</span><span class="o">=</span><span class="p">[</span><span class="n">yi</span><span class="o">.</span><span class="n">dvalue</span> <span class="k">for</span> <span class="n">yi</span> <span class="ow">in</span> <span class="n">ymore</span><span class="p">],</span> <span class="n">fmt</span><span class="o">=</span><span class="s1">&#39;x&#39;</span><span class="p">)</span> </span><span id="fit_t0-71"><a href="#fit_t0-71"><span class="linenos"> 71</span></a> <span class="n">ax0</span><span class="o">.</span><span class="n">errorbar</span><span class="p">(</span><span class="n">xmore</span><span class="p">,</span> <span class="p">[</span><span class="n">yi</span><span class="o">.</span><span class="n">value</span> <span class="k">for</span> <span class="n">yi</span> <span class="ow">in</span> <span class="n">ymore</span><span class="p">],</span> <span class="n">yerr</span><span class="o">=</span><span class="p">[</span><span class="n">yi</span><span class="o">.</span><span class="n">dvalue</span> <span class="k">for</span> <span class="n">yi</span> <span class="ow">in</span> <span class="n">ymore</span><span class="p">],</span> <span class="n">fmt</span><span class="o">=</span><span class="s1">&#39;x&#39;</span><span class="p">)</span>
</span><span id="fit_t0-70"><a href="#fit_t0-70"><span class="linenos">70</span></a> <span class="n">xplot</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="n">x</span><span class="p">),</span> <span class="n">np</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="n">x</span><span class="p">))</span> </span><span id="fit_t0-72"><a href="#fit_t0-72"><span class="linenos"> 72</span></a> <span class="n">xplot</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="n">x</span><span class="p">),</span> <span class="n">np</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="n">x</span><span class="p">))</span>
</span><span id="fit_t0-71"><a href="#fit_t0-71"><span class="linenos">71</span></a> <span class="n">yplot</span> <span class="o">=</span> <span class="p">[</span><span class="n">fit_result</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="n">fit_result</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">*</span> <span class="n">xi</span> <span class="k">for</span> <span class="n">xi</span> <span class="ow">in</span> <span class="n">xplot</span><span class="p">]</span> </span><span id="fit_t0-73"><a href="#fit_t0-73"><span class="linenos"> 73</span></a> <span class="n">yplot</span> <span class="o">=</span> <span class="p">[</span><span class="n">fit_result</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="n">fit_result</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">*</span> <span class="n">xi</span> <span class="k">for</span> <span class="n">xi</span> <span class="ow">in</span> <span class="n">xplot</span><span class="p">]</span>
</span><span id="fit_t0-72"><a href="#fit_t0-72"><span class="linenos">72</span></a> <span class="p">[</span><span class="n">yi</span><span class="o">.</span><span class="n">gamma_method</span><span class="p">()</span> <span class="k">for</span> <span class="n">yi</span> <span class="ow">in</span> <span class="n">yplot</span><span class="p">]</span> </span><span id="fit_t0-74"><a href="#fit_t0-74"><span class="linenos"> 74</span></a> <span class="p">[</span><span class="n">yi</span><span class="o">.</span><span class="n">gamma_method</span><span class="p">()</span> <span class="k">for</span> <span class="n">yi</span> <span class="ow">in</span> <span class="n">yplot</span><span class="p">]</span>
</span><span id="fit_t0-73"><a href="#fit_t0-73"><span class="linenos">73</span></a> <span class="n">ax0</span><span class="o">.</span><span class="n">fill_between</span><span class="p">(</span><span class="n">xplot</span><span class="p">,</span> <span class="n">y1</span><span class="o">=</span><span class="p">[</span><span class="n">yi</span><span class="o">.</span><span class="n">value</span> <span class="o">-</span> <span class="n">yi</span><span class="o">.</span><span class="n">dvalue</span> <span class="k">for</span> <span class="n">yi</span> <span class="ow">in</span> <span class="n">yplot</span><span class="p">],</span> <span class="n">y2</span><span class="o">=</span><span class="p">[</span><span class="n">yi</span><span class="o">.</span><span class="n">value</span> <span class="o">+</span> <span class="n">yi</span><span class="o">.</span><span class="n">dvalue</span> <span class="k">for</span> <span class="n">yi</span> <span class="ow">in</span> <span class="n">yplot</span><span class="p">])</span> </span><span id="fit_t0-75"><a href="#fit_t0-75"><span class="linenos"> 75</span></a> <span class="n">ax0</span><span class="o">.</span><span class="n">fill_between</span><span class="p">(</span><span class="n">xplot</span><span class="p">,</span> <span class="n">y1</span><span class="o">=</span><span class="p">[</span><span class="n">yi</span><span class="o">.</span><span class="n">value</span> <span class="o">-</span> <span class="n">yi</span><span class="o">.</span><span class="n">dvalue</span> <span class="k">for</span> <span class="n">yi</span> <span class="ow">in</span> <span class="n">yplot</span><span class="p">],</span> <span class="n">y2</span><span class="o">=</span><span class="p">[</span><span class="n">yi</span><span class="o">.</span><span class="n">value</span> <span class="o">+</span> <span class="n">yi</span><span class="o">.</span><span class="n">dvalue</span> <span class="k">for</span> <span class="n">yi</span> <span class="ow">in</span> <span class="n">yplot</span><span class="p">])</span>
</span><span id="fit_t0-74"><a href="#fit_t0-74"><span class="linenos">74</span></a> <span class="n">retval</span> <span class="o">=</span> <span class="p">(</span><span class="o">-</span><span class="n">fit_result</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">/</span> <span class="n">fit_result</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> </span><span id="fit_t0-76"><a href="#fit_t0-76"><span class="linenos"> 76</span></a> <span class="n">retval</span> <span class="o">=</span> <span class="p">(</span><span class="o">-</span><span class="n">fit_result</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">/</span> <span class="n">fit_result</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
</span><span id="fit_t0-75"><a href="#fit_t0-75"><span class="linenos">75</span></a> <span class="n">retval</span><span class="o">.</span><span class="n">gamma_method</span><span class="p">()</span> </span><span id="fit_t0-77"><a href="#fit_t0-77"><span class="linenos"> 77</span></a> <span class="n">retval</span><span class="o">.</span><span class="n">gamma_method</span><span class="p">()</span>
</span><span id="fit_t0-76"><a href="#fit_t0-76"><span class="linenos">76</span></a> <span class="n">ylim</span> <span class="o">=</span> <span class="n">ax0</span><span class="o">.</span><span class="n">get_ylim</span><span class="p">()</span> </span><span id="fit_t0-78"><a href="#fit_t0-78"><span class="linenos"> 78</span></a> <span class="n">ylim</span> <span class="o">=</span> <span class="n">ax0</span><span class="o">.</span><span class="n">get_ylim</span><span class="p">()</span>
</span><span id="fit_t0-77"><a href="#fit_t0-77"><span class="linenos">77</span></a> <span class="n">ax0</span><span class="o">.</span><span class="n">fill_betweenx</span><span class="p">(</span><span class="n">ylim</span><span class="p">,</span> <span class="n">x1</span><span class="o">=</span><span class="n">retval</span><span class="o">.</span><span class="n">value</span> <span class="o">-</span> <span class="n">retval</span><span class="o">.</span><span class="n">dvalue</span><span class="p">,</span> <span class="n">x2</span><span class="o">=</span><span class="n">retval</span><span class="o">.</span><span class="n">value</span> <span class="o">+</span> <span class="n">retval</span><span class="o">.</span><span class="n">dvalue</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="s1">&#39;gray&#39;</span><span class="p">,</span> <span class="n">alpha</span><span class="o">=</span><span class="mf">0.4</span><span class="p">)</span> </span><span id="fit_t0-79"><a href="#fit_t0-79"><span class="linenos"> 79</span></a> <span class="n">ax0</span><span class="o">.</span><span class="n">fill_betweenx</span><span class="p">(</span><span class="n">ylim</span><span class="p">,</span> <span class="n">x1</span><span class="o">=</span><span class="n">retval</span><span class="o">.</span><span class="n">value</span> <span class="o">-</span> <span class="n">retval</span><span class="o">.</span><span class="n">dvalue</span><span class="p">,</span> <span class="n">x2</span><span class="o">=</span><span class="n">retval</span><span class="o">.</span><span class="n">value</span> <span class="o">+</span> <span class="n">retval</span><span class="o">.</span><span class="n">dvalue</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="s1">&#39;gray&#39;</span><span class="p">,</span> <span class="n">alpha</span><span class="o">=</span><span class="mf">0.4</span><span class="p">)</span>
</span><span id="fit_t0-78"><a href="#fit_t0-78"><span class="linenos">78</span></a> <span class="n">ax0</span><span class="o">.</span><span class="n">set_ylim</span><span class="p">(</span><span class="n">ylim</span><span class="p">)</span> </span><span id="fit_t0-80"><a href="#fit_t0-80"><span class="linenos"> 80</span></a> <span class="n">ax0</span><span class="o">.</span><span class="n">set_ylim</span><span class="p">(</span><span class="n">ylim</span><span class="p">)</span>
</span><span id="fit_t0-79"><a href="#fit_t0-79"><span class="linenos">79</span></a> <span class="k">if</span> <span class="n">observable</span> <span class="o">==</span> <span class="s1">&#39;t0&#39;</span><span class="p">:</span> </span><span id="fit_t0-81"><a href="#fit_t0-81"><span class="linenos"> 81</span></a> <span class="k">if</span> <span class="n">observable</span> <span class="o">==</span> <span class="s1">&#39;t0&#39;</span><span class="p">:</span>
</span><span id="fit_t0-80"><a href="#fit_t0-80"><span class="linenos">80</span></a> <span class="n">ax0</span><span class="o">.</span><span class="n">set_ylabel</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;$t^2 \langle E(t) \rangle - 0.3 $&#39;</span><span class="p">)</span> </span><span id="fit_t0-82"><a href="#fit_t0-82"><span class="linenos"> 82</span></a> <span class="n">ax0</span><span class="o">.</span><span class="n">set_ylabel</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;$t^2 \langle E(t) \rangle - 0.3 $&#39;</span><span class="p">)</span>
</span><span id="fit_t0-81"><a href="#fit_t0-81"><span class="linenos">81</span></a> <span class="k">elif</span> <span class="n">observable</span> <span class="o">==</span> <span class="s1">&#39;w0&#39;</span><span class="p">:</span> </span><span id="fit_t0-83"><a href="#fit_t0-83"><span class="linenos"> 83</span></a> <span class="k">elif</span> <span class="n">observable</span> <span class="o">==</span> <span class="s1">&#39;w0&#39;</span><span class="p">:</span>
</span><span id="fit_t0-82"><a href="#fit_t0-82"><span class="linenos">82</span></a> <span class="n">ax0</span><span class="o">.</span><span class="n">set_ylabel</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;$t d(t^2 \langle E(t) \rangle)/dt - 0.3 $&#39;</span><span class="p">)</span> </span><span id="fit_t0-84"><a href="#fit_t0-84"><span class="linenos"> 84</span></a> <span class="n">ax0</span><span class="o">.</span><span class="n">set_ylabel</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;$t d(t^2 \langle E(t) \rangle)/dt - 0.3 $&#39;</span><span class="p">)</span>
</span><span id="fit_t0-83"><a href="#fit_t0-83"><span class="linenos">83</span></a> <span class="n">xlim</span> <span class="o">=</span> <span class="n">ax0</span><span class="o">.</span><span class="n">get_xlim</span><span class="p">()</span> </span><span id="fit_t0-85"><a href="#fit_t0-85"><span class="linenos"> 85</span></a> <span class="n">xlim</span> <span class="o">=</span> <span class="n">ax0</span><span class="o">.</span><span class="n">get_xlim</span><span class="p">()</span>
</span><span id="fit_t0-84"><a href="#fit_t0-84"><span class="linenos">84</span></a> </span><span id="fit_t0-86"><a href="#fit_t0-86"><span class="linenos"> 86</span></a>
</span><span id="fit_t0-85"><a href="#fit_t0-85"><span class="linenos">85</span></a> <span class="n">fit_res</span> <span class="o">=</span> <span class="p">[</span><span class="n">fit_result</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="n">fit_result</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">*</span> <span class="n">xi</span> <span class="k">for</span> <span class="n">xi</span> <span class="ow">in</span> <span class="n">x</span><span class="p">]</span> </span><span id="fit_t0-87"><a href="#fit_t0-87"><span class="linenos"> 87</span></a> <span class="n">fit_res</span> <span class="o">=</span> <span class="p">[</span><span class="n">fit_result</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="n">fit_result</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">*</span> <span class="n">xi</span> <span class="k">for</span> <span class="n">xi</span> <span class="ow">in</span> <span class="n">x</span><span class="p">]</span>
</span><span id="fit_t0-86"><a href="#fit_t0-86"><span class="linenos">86</span></a> <span class="n">residuals</span> <span class="o">=</span> <span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">([</span><span class="n">o</span><span class="o">.</span><span class="n">value</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">y</span><span class="p">])</span> <span class="o">-</span> <span class="p">[</span><span class="n">o</span><span class="o">.</span><span class="n">value</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">fit_res</span><span class="p">])</span> <span class="o">/</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">([</span><span class="n">o</span><span class="o">.</span><span class="n">dvalue</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">y</span><span class="p">])</span> </span><span id="fit_t0-88"><a href="#fit_t0-88"><span class="linenos"> 88</span></a> <span class="n">residuals</span> <span class="o">=</span> <span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">([</span><span class="n">o</span><span class="o">.</span><span class="n">value</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">y</span><span class="p">])</span> <span class="o">-</span> <span class="p">[</span><span class="n">o</span><span class="o">.</span><span class="n">value</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">fit_res</span><span class="p">])</span> <span class="o">/</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">([</span><span class="n">o</span><span class="o">.</span><span class="n">dvalue</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">y</span><span class="p">])</span>
</span><span id="fit_t0-87"><a href="#fit_t0-87"><span class="linenos">87</span></a> <span class="n">ax1</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">subplot</span><span class="p">(</span><span class="n">gs</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> </span><span id="fit_t0-89"><a href="#fit_t0-89"><span class="linenos"> 89</span></a> <span class="n">ax1</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">subplot</span><span class="p">(</span><span class="n">gs</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
</span><span id="fit_t0-88"><a href="#fit_t0-88"><span class="linenos">88</span></a> <span class="n">ax1</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">residuals</span><span class="p">,</span> <span class="s1">&#39;ko&#39;</span><span class="p">,</span> <span class="n">ls</span><span class="o">=</span><span class="s1">&#39;none&#39;</span><span class="p">,</span> <span class="n">markersize</span><span class="o">=</span><span class="mi">5</span><span class="p">)</span> </span><span id="fit_t0-90"><a href="#fit_t0-90"><span class="linenos"> 90</span></a> <span class="n">ax1</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">residuals</span><span class="p">,</span> <span class="s1">&#39;ko&#39;</span><span class="p">,</span> <span class="n">ls</span><span class="o">=</span><span class="s1">&#39;none&#39;</span><span class="p">,</span> <span class="n">markersize</span><span class="o">=</span><span class="mi">5</span><span class="p">)</span>
</span><span id="fit_t0-89"><a href="#fit_t0-89"><span class="linenos">89</span></a> <span class="n">ax1</span><span class="o">.</span><span class="n">tick_params</span><span class="p">(</span><span class="n">direction</span><span class="o">=</span><span class="s1">&#39;out&#39;</span><span class="p">)</span> </span><span id="fit_t0-91"><a href="#fit_t0-91"><span class="linenos"> 91</span></a> <span class="n">ax1</span><span class="o">.</span><span class="n">tick_params</span><span class="p">(</span><span class="n">direction</span><span class="o">=</span><span class="s1">&#39;out&#39;</span><span class="p">)</span>
</span><span id="fit_t0-90"><a href="#fit_t0-90"><span class="linenos">90</span></a> <span class="n">ax1</span><span class="o">.</span><span class="n">tick_params</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="s2">&quot;x&quot;</span><span class="p">,</span> <span class="n">bottom</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">top</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">labelbottom</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span> </span><span id="fit_t0-92"><a href="#fit_t0-92"><span class="linenos"> 92</span></a> <span class="n">ax1</span><span class="o">.</span><span class="n">tick_params</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="s2">&quot;x&quot;</span><span class="p">,</span> <span class="n">bottom</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">top</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">labelbottom</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
</span><span id="fit_t0-91"><a href="#fit_t0-91"><span class="linenos">91</span></a> <span class="n">ax1</span><span class="o">.</span><span class="n">axhline</span><span class="p">(</span><span class="n">y</span><span class="o">=</span><span class="mf">0.0</span><span class="p">,</span> <span class="n">ls</span><span class="o">=</span><span class="s1">&#39;--&#39;</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="s1">&#39;k&#39;</span><span class="p">)</span> </span><span id="fit_t0-93"><a href="#fit_t0-93"><span class="linenos"> 93</span></a> <span class="n">ax1</span><span class="o">.</span><span class="n">axhline</span><span class="p">(</span><span class="n">y</span><span class="o">=</span><span class="mf">0.0</span><span class="p">,</span> <span class="n">ls</span><span class="o">=</span><span class="s1">&#39;--&#39;</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="s1">&#39;k&#39;</span><span class="p">)</span>
</span><span id="fit_t0-92"><a href="#fit_t0-92"><span class="linenos">92</span></a> <span class="n">ax1</span><span class="o">.</span><span class="n">fill_between</span><span class="p">(</span><span class="n">xlim</span><span class="p">,</span> <span class="o">-</span><span class="mf">1.0</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">,</span> <span class="n">alpha</span><span class="o">=</span><span class="mf">0.1</span><span class="p">,</span> <span class="n">facecolor</span><span class="o">=</span><span class="s1">&#39;k&#39;</span><span class="p">)</span> </span><span id="fit_t0-94"><a href="#fit_t0-94"><span class="linenos"> 94</span></a> <span class="n">ax1</span><span class="o">.</span><span class="n">fill_between</span><span class="p">(</span><span class="n">xlim</span><span class="p">,</span> <span class="o">-</span><span class="mf">1.0</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">,</span> <span class="n">alpha</span><span class="o">=</span><span class="mf">0.1</span><span class="p">,</span> <span class="n">facecolor</span><span class="o">=</span><span class="s1">&#39;k&#39;</span><span class="p">)</span>
</span><span id="fit_t0-93"><a href="#fit_t0-93"><span class="linenos">93</span></a> <span class="n">ax1</span><span class="o">.</span><span class="n">set_xlim</span><span class="p">(</span><span class="n">xlim</span><span class="p">)</span> </span><span id="fit_t0-95"><a href="#fit_t0-95"><span class="linenos"> 95</span></a> <span class="n">ax1</span><span class="o">.</span><span class="n">set_xlim</span><span class="p">(</span><span class="n">xlim</span><span class="p">)</span>
</span><span id="fit_t0-94"><a href="#fit_t0-94"><span class="linenos">94</span></a> <span class="n">ax1</span><span class="o">.</span><span class="n">set_ylabel</span><span class="p">(</span><span class="s1">&#39;Residuals&#39;</span><span class="p">)</span> </span><span id="fit_t0-96"><a href="#fit_t0-96"><span class="linenos"> 96</span></a> <span class="n">ax1</span><span class="o">.</span><span class="n">set_ylabel</span><span class="p">(</span><span class="s1">&#39;Residuals&#39;</span><span class="p">)</span>
</span><span id="fit_t0-95"><a href="#fit_t0-95"><span class="linenos">95</span></a> <span class="n">ax1</span><span class="o">.</span><span class="n">set_xlabel</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;$t/a^2$&#39;</span><span class="p">)</span> </span><span id="fit_t0-97"><a href="#fit_t0-97"><span class="linenos"> 97</span></a> <span class="n">ax1</span><span class="o">.</span><span class="n">set_xlabel</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;$t/a^2$&#39;</span><span class="p">)</span>
</span><span id="fit_t0-96"><a href="#fit_t0-96"><span class="linenos">96</span></a> </span><span id="fit_t0-98"><a href="#fit_t0-98"><span class="linenos"> 98</span></a>
</span><span id="fit_t0-97"><a href="#fit_t0-97"><span class="linenos">97</span></a> <span class="n">plt</span><span class="o">.</span><span class="n">draw</span><span class="p">()</span> </span><span id="fit_t0-99"><a href="#fit_t0-99"><span class="linenos"> 99</span></a> <span class="n">plt</span><span class="o">.</span><span class="n">draw</span><span class="p">()</span>
</span><span id="fit_t0-98"><a href="#fit_t0-98"><span class="linenos">98</span></a> <span class="k">return</span> <span class="o">-</span><span class="n">fit_result</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">/</span> <span class="n">fit_result</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> </span><span id="fit_t0-100"><a href="#fit_t0-100"><span class="linenos">100</span></a> <span class="k">return</span> <span class="o">-</span><span class="n">fit_result</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">/</span> <span class="n">fit_result</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
</span></pre></div> </span></pre></div>
@ -447,125 +449,125 @@ The root of the data series.</li>
</div> </div>
<a class="headerlink" href="#read_pbp"></a> <a class="headerlink" href="#read_pbp"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="read_pbp-101"><a href="#read_pbp-101"><span class="linenos">101</span></a><span class="k">def</span><span class="w"> </span><span class="nf">read_pbp</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">prefix</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span> <div class="pdoc-code codehilite"><pre><span></span><span id="read_pbp-103"><a href="#read_pbp-103"><span class="linenos">103</span></a><span class="k">def</span><span class="w"> </span><span class="nf">read_pbp</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">prefix</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
</span><span id="read_pbp-102"><a href="#read_pbp-102"><span class="linenos">102</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Read pbp format from given folder structure.</span> </span><span id="read_pbp-104"><a href="#read_pbp-104"><span class="linenos">104</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Read pbp format from given folder structure.</span>
</span><span id="read_pbp-103"><a href="#read_pbp-103"><span class="linenos">103</span></a> </span><span id="read_pbp-105"><a href="#read_pbp-105"><span class="linenos">105</span></a>
</span><span id="read_pbp-104"><a href="#read_pbp-104"><span class="linenos">104</span></a><span class="sd"> Parameters</span> </span><span id="read_pbp-106"><a href="#read_pbp-106"><span class="linenos">106</span></a><span class="sd"> Parameters</span>
</span><span id="read_pbp-105"><a href="#read_pbp-105"><span class="linenos">105</span></a><span class="sd"> ----------</span> </span><span id="read_pbp-107"><a href="#read_pbp-107"><span class="linenos">107</span></a><span class="sd"> ----------</span>
</span><span id="read_pbp-106"><a href="#read_pbp-106"><span class="linenos">106</span></a><span class="sd"> r_start : list</span> </span><span id="read_pbp-108"><a href="#read_pbp-108"><span class="linenos">108</span></a><span class="sd"> r_start : list</span>
</span><span id="read_pbp-107"><a href="#read_pbp-107"><span class="linenos">107</span></a><span class="sd"> list which contains the first config to be read for each replicum</span> </span><span id="read_pbp-109"><a href="#read_pbp-109"><span class="linenos">109</span></a><span class="sd"> list which contains the first config to be read for each replicum</span>
</span><span id="read_pbp-108"><a href="#read_pbp-108"><span class="linenos">108</span></a><span class="sd"> r_stop : list</span> </span><span id="read_pbp-110"><a href="#read_pbp-110"><span class="linenos">110</span></a><span class="sd"> r_stop : list</span>
</span><span id="read_pbp-109"><a href="#read_pbp-109"><span class="linenos">109</span></a><span class="sd"> list which contains the last config to be read for each replicum</span> </span><span id="read_pbp-111"><a href="#read_pbp-111"><span class="linenos">111</span></a><span class="sd"> list which contains the last config to be read for each replicum</span>
</span><span id="read_pbp-110"><a href="#read_pbp-110"><span class="linenos">110</span></a> </span><span id="read_pbp-112"><a href="#read_pbp-112"><span class="linenos">112</span></a>
</span><span id="read_pbp-111"><a href="#read_pbp-111"><span class="linenos">111</span></a><span class="sd"> Returns</span> </span><span id="read_pbp-113"><a href="#read_pbp-113"><span class="linenos">113</span></a><span class="sd"> Returns</span>
</span><span id="read_pbp-112"><a href="#read_pbp-112"><span class="linenos">112</span></a><span class="sd"> -------</span> </span><span id="read_pbp-114"><a href="#read_pbp-114"><span class="linenos">114</span></a><span class="sd"> -------</span>
</span><span id="read_pbp-113"><a href="#read_pbp-113"><span class="linenos">113</span></a><span class="sd"> result : list[Obs]</span> </span><span id="read_pbp-115"><a href="#read_pbp-115"><span class="linenos">115</span></a><span class="sd"> result : list[Obs]</span>
</span><span id="read_pbp-114"><a href="#read_pbp-114"><span class="linenos">114</span></a><span class="sd"> list of observables read</span> </span><span id="read_pbp-116"><a href="#read_pbp-116"><span class="linenos">116</span></a><span class="sd"> list of observables read</span>
</span><span id="read_pbp-115"><a href="#read_pbp-115"><span class="linenos">115</span></a><span class="sd"> &quot;&quot;&quot;</span> </span><span id="read_pbp-117"><a href="#read_pbp-117"><span class="linenos">117</span></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="read_pbp-116"><a href="#read_pbp-116"><span class="linenos">116</span></a> </span><span id="read_pbp-118"><a href="#read_pbp-118"><span class="linenos">118</span></a>
</span><span id="read_pbp-117"><a href="#read_pbp-117"><span class="linenos">117</span></a> <span class="n">ls</span> <span class="o">=</span> <span class="p">[]</span> </span><span id="read_pbp-119"><a href="#read_pbp-119"><span class="linenos">119</span></a> <span class="n">ls</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="read_pbp-118"><a href="#read_pbp-118"><span class="linenos">118</span></a> <span class="k">for</span> <span class="p">(</span><span class="n">dirpath</span><span class="p">,</span> <span class="n">dirnames</span><span class="p">,</span> <span class="n">filenames</span><span class="p">)</span> <span class="ow">in</span> <span class="n">os</span><span class="o">.</span><span class="n">walk</span><span class="p">(</span><span class="n">path</span><span class="p">):</span> </span><span id="read_pbp-120"><a href="#read_pbp-120"><span class="linenos">120</span></a> <span class="k">for</span> <span class="p">(</span><span class="n">_dirpath</span><span class="p">,</span> <span class="n">_dirnames</span><span class="p">,</span> <span class="n">filenames</span><span class="p">)</span> <span class="ow">in</span> <span class="n">os</span><span class="o">.</span><span class="n">walk</span><span class="p">(</span><span class="n">path</span><span class="p">):</span>
</span><span id="read_pbp-119"><a href="#read_pbp-119"><span class="linenos">119</span></a> <span class="n">ls</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">filenames</span><span class="p">)</span> </span><span id="read_pbp-121"><a href="#read_pbp-121"><span class="linenos">121</span></a> <span class="n">ls</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">filenames</span><span class="p">)</span>
</span><span id="read_pbp-120"><a href="#read_pbp-120"><span class="linenos">120</span></a> <span class="k">break</span> </span><span id="read_pbp-122"><a href="#read_pbp-122"><span class="linenos">122</span></a> <span class="k">break</span>
</span><span id="read_pbp-121"><a href="#read_pbp-121"><span class="linenos">121</span></a> </span><span id="read_pbp-123"><a href="#read_pbp-123"><span class="linenos">123</span></a>
</span><span id="read_pbp-122"><a href="#read_pbp-122"><span class="linenos">122</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">ls</span><span class="p">:</span> </span><span id="read_pbp-124"><a href="#read_pbp-124"><span class="linenos">124</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">ls</span><span class="p">:</span>
</span><span id="read_pbp-123"><a href="#read_pbp-123"><span class="linenos">123</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Error, directory not found&#39;</span><span class="p">)</span> </span><span id="read_pbp-125"><a href="#read_pbp-125"><span class="linenos">125</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Error, directory not found&#39;</span><span class="p">)</span>
</span><span id="read_pbp-124"><a href="#read_pbp-124"><span class="linenos">124</span></a> </span><span id="read_pbp-126"><a href="#read_pbp-126"><span class="linenos">126</span></a>
</span><span id="read_pbp-125"><a href="#read_pbp-125"><span class="linenos">125</span></a> <span class="c1"># Exclude files with different names</span> </span><span id="read_pbp-127"><a href="#read_pbp-127"><span class="linenos">127</span></a> <span class="c1"># Exclude files with different names</span>
</span><span id="read_pbp-126"><a href="#read_pbp-126"><span class="linenos">126</span></a> <span class="k">for</span> <span class="n">exc</span> <span class="ow">in</span> <span class="n">ls</span><span class="p">:</span> </span><span id="read_pbp-128"><a href="#read_pbp-128"><span class="linenos">128</span></a> <span class="k">for</span> <span class="n">exc</span> <span class="ow">in</span> <span class="n">ls</span><span class="p">:</span>
</span><span id="read_pbp-127"><a href="#read_pbp-127"><span class="linenos">127</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">fnmatch</span><span class="o">.</span><span class="n">fnmatch</span><span class="p">(</span><span class="n">exc</span><span class="p">,</span> <span class="n">prefix</span> <span class="o">+</span> <span class="s1">&#39;*.dat&#39;</span><span class="p">):</span> </span><span id="read_pbp-129"><a href="#read_pbp-129"><span class="linenos">129</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">fnmatch</span><span class="o">.</span><span class="n">fnmatch</span><span class="p">(</span><span class="n">exc</span><span class="p">,</span> <span class="n">prefix</span> <span class="o">+</span> <span class="s1">&#39;*.dat&#39;</span><span class="p">):</span>
</span><span id="read_pbp-128"><a href="#read_pbp-128"><span class="linenos">128</span></a> <span class="n">ls</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">ls</span><span class="p">)</span> <span class="o">-</span> <span class="nb">set</span><span class="p">([</span><span class="n">exc</span><span class="p">]))</span> </span><span id="read_pbp-130"><a href="#read_pbp-130"><span class="linenos">130</span></a> <span class="n">ls</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">ls</span><span class="p">)</span> <span class="o">-</span> <span class="nb">set</span><span class="p">([</span><span class="n">exc</span><span class="p">]))</span>
</span><span id="read_pbp-129"><a href="#read_pbp-129"><span class="linenos">129</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">ls</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span> </span><span id="read_pbp-131"><a href="#read_pbp-131"><span class="linenos">131</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">ls</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
</span><span id="read_pbp-130"><a href="#read_pbp-130"><span class="linenos">130</span></a> <span class="n">ls</span><span class="o">.</span><span class="n">sort</span><span class="p">(</span><span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="nb">int</span><span class="p">(</span><span class="n">re</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;\d+&#39;</span><span class="p">,</span> <span class="n">x</span><span class="p">[</span><span class="nb">len</span><span class="p">(</span><span class="n">prefix</span><span class="p">):])[</span><span class="mi">0</span><span class="p">]))</span> </span><span id="read_pbp-132"><a href="#read_pbp-132"><span class="linenos">132</span></a> <span class="n">ls</span><span class="o">.</span><span class="n">sort</span><span class="p">(</span><span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="nb">int</span><span class="p">(</span><span class="n">re</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;\d+&#39;</span><span class="p">,</span> <span class="n">x</span><span class="p">[</span><span class="nb">len</span><span class="p">(</span><span class="n">prefix</span><span class="p">):])[</span><span class="mi">0</span><span class="p">]))</span>
</span><span id="read_pbp-131"><a href="#read_pbp-131"><span class="linenos">131</span></a> <span class="n">replica</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">ls</span><span class="p">)</span> </span><span id="read_pbp-133"><a href="#read_pbp-133"><span class="linenos">133</span></a> <span class="n">replica</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">ls</span><span class="p">)</span>
</span><span id="read_pbp-132"><a href="#read_pbp-132"><span class="linenos">132</span></a> </span><span id="read_pbp-134"><a href="#read_pbp-134"><span class="linenos">134</span></a>
</span><span id="read_pbp-133"><a href="#read_pbp-133"><span class="linenos">133</span></a> <span class="k">if</span> <span class="s1">&#39;r_start&#39;</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span> </span><span id="read_pbp-135"><a href="#read_pbp-135"><span class="linenos">135</span></a> <span class="k">if</span> <span class="s1">&#39;r_start&#39;</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
</span><span id="read_pbp-134"><a href="#read_pbp-134"><span class="linenos">134</span></a> <span class="n">r_start</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;r_start&#39;</span><span class="p">)</span> </span><span id="read_pbp-136"><a href="#read_pbp-136"><span class="linenos">136</span></a> <span class="n">r_start</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;r_start&#39;</span><span class="p">)</span>
</span><span id="read_pbp-135"><a href="#read_pbp-135"><span class="linenos">135</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">r_start</span><span class="p">)</span> <span class="o">!=</span> <span class="n">replica</span><span class="p">:</span> </span><span id="read_pbp-137"><a href="#read_pbp-137"><span class="linenos">137</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">r_start</span><span class="p">)</span> <span class="o">!=</span> <span class="n">replica</span><span class="p">:</span>
</span><span id="read_pbp-136"><a href="#read_pbp-136"><span class="linenos">136</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;r_start does not match number of replicas&#39;</span><span class="p">)</span> </span><span id="read_pbp-138"><a href="#read_pbp-138"><span class="linenos">138</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;r_start does not match number of replicas&#39;</span><span class="p">)</span>
</span><span id="read_pbp-137"><a href="#read_pbp-137"><span class="linenos">137</span></a> <span class="c1"># Adjust Configuration numbering to python index</span> </span><span id="read_pbp-139"><a href="#read_pbp-139"><span class="linenos">139</span></a> <span class="c1"># Adjust Configuration numbering to python index</span>
</span><span id="read_pbp-138"><a href="#read_pbp-138"><span class="linenos">138</span></a> <span class="n">r_start</span> <span class="o">=</span> <span class="p">[</span><span class="n">o</span> <span class="o">-</span> <span class="mi">1</span> <span class="k">if</span> <span class="n">o</span> <span class="k">else</span> <span class="kc">None</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">r_start</span><span class="p">]</span> </span><span id="read_pbp-140"><a href="#read_pbp-140"><span class="linenos">140</span></a> <span class="n">r_start</span> <span class="o">=</span> <span class="p">[</span><span class="n">o</span> <span class="o">-</span> <span class="mi">1</span> <span class="k">if</span> <span class="n">o</span> <span class="k">else</span> <span class="kc">None</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">r_start</span><span class="p">]</span>
</span><span id="read_pbp-139"><a href="#read_pbp-139"><span class="linenos">139</span></a> <span class="k">else</span><span class="p">:</span> </span><span id="read_pbp-141"><a href="#read_pbp-141"><span class="linenos">141</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="read_pbp-140"><a href="#read_pbp-140"><span class="linenos">140</span></a> <span class="n">r_start</span> <span class="o">=</span> <span class="p">[</span><span class="kc">None</span><span class="p">]</span> <span class="o">*</span> <span class="n">replica</span> </span><span id="read_pbp-142"><a href="#read_pbp-142"><span class="linenos">142</span></a> <span class="n">r_start</span> <span class="o">=</span> <span class="p">[</span><span class="kc">None</span><span class="p">]</span> <span class="o">*</span> <span class="n">replica</span>
</span><span id="read_pbp-141"><a href="#read_pbp-141"><span class="linenos">141</span></a> </span><span id="read_pbp-143"><a href="#read_pbp-143"><span class="linenos">143</span></a>
</span><span id="read_pbp-142"><a href="#read_pbp-142"><span class="linenos">142</span></a> <span class="k">if</span> <span class="s1">&#39;r_stop&#39;</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span> </span><span id="read_pbp-144"><a href="#read_pbp-144"><span class="linenos">144</span></a> <span class="k">if</span> <span class="s1">&#39;r_stop&#39;</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
</span><span id="read_pbp-143"><a href="#read_pbp-143"><span class="linenos">143</span></a> <span class="n">r_stop</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;r_stop&#39;</span><span class="p">)</span> </span><span id="read_pbp-145"><a href="#read_pbp-145"><span class="linenos">145</span></a> <span class="n">r_stop</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;r_stop&#39;</span><span class="p">)</span>
</span><span id="read_pbp-144"><a href="#read_pbp-144"><span class="linenos">144</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">r_stop</span><span class="p">)</span> <span class="o">!=</span> <span class="n">replica</span><span class="p">:</span> </span><span id="read_pbp-146"><a href="#read_pbp-146"><span class="linenos">146</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">r_stop</span><span class="p">)</span> <span class="o">!=</span> <span class="n">replica</span><span class="p">:</span>
</span><span id="read_pbp-145"><a href="#read_pbp-145"><span class="linenos">145</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;r_stop does not match number of replicas&#39;</span><span class="p">)</span> </span><span id="read_pbp-147"><a href="#read_pbp-147"><span class="linenos">147</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;r_stop does not match number of replicas&#39;</span><span class="p">)</span>
</span><span id="read_pbp-146"><a href="#read_pbp-146"><span class="linenos">146</span></a> <span class="k">else</span><span class="p">:</span> </span><span id="read_pbp-148"><a href="#read_pbp-148"><span class="linenos">148</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="read_pbp-147"><a href="#read_pbp-147"><span class="linenos">147</span></a> <span class="n">r_stop</span> <span class="o">=</span> <span class="p">[</span><span class="kc">None</span><span class="p">]</span> <span class="o">*</span> <span class="n">replica</span> </span><span id="read_pbp-149"><a href="#read_pbp-149"><span class="linenos">149</span></a> <span class="n">r_stop</span> <span class="o">=</span> <span class="p">[</span><span class="kc">None</span><span class="p">]</span> <span class="o">*</span> <span class="n">replica</span>
</span><span id="read_pbp-148"><a href="#read_pbp-148"><span class="linenos">148</span></a>
</span><span id="read_pbp-149"><a href="#read_pbp-149"><span class="linenos">149</span></a> <span class="nb">print</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;Read &lt;bar</span><span class="si">{psi}</span><span class="s1">\psi&gt; from&#39;</span><span class="p">,</span> <span class="n">prefix</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span> <span class="s1">&#39;,&#39;</span><span class="p">,</span> <span class="n">replica</span><span class="p">,</span> <span class="s1">&#39;replica&#39;</span><span class="p">,</span> <span class="n">end</span><span class="o">=</span><span class="s1">&#39;&#39;</span><span class="p">)</span>
</span><span id="read_pbp-150"><a href="#read_pbp-150"><span class="linenos">150</span></a> </span><span id="read_pbp-150"><a href="#read_pbp-150"><span class="linenos">150</span></a>
</span><span id="read_pbp-151"><a href="#read_pbp-151"><span class="linenos">151</span></a> <span class="n">print_err</span> <span class="o">=</span> <span class="mi">0</span> </span><span id="read_pbp-151"><a href="#read_pbp-151"><span class="linenos">151</span></a> <span class="nb">print</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;Read &lt;bar</span><span class="si">{psi}</span><span class="s1">\psi&gt; from&#39;</span><span class="p">,</span> <span class="n">prefix</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span> <span class="s1">&#39;,&#39;</span><span class="p">,</span> <span class="n">replica</span><span class="p">,</span> <span class="s1">&#39;replica&#39;</span><span class="p">,</span> <span class="n">end</span><span class="o">=</span><span class="s1">&#39;&#39;</span><span class="p">)</span>
</span><span id="read_pbp-152"><a href="#read_pbp-152"><span class="linenos">152</span></a> <span class="k">if</span> <span class="s1">&#39;print_err&#39;</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span> </span><span id="read_pbp-152"><a href="#read_pbp-152"><span class="linenos">152</span></a>
</span><span id="read_pbp-153"><a href="#read_pbp-153"><span class="linenos">153</span></a> <span class="n">print_err</span> <span class="o">=</span> <span class="mi">1</span> </span><span id="read_pbp-153"><a href="#read_pbp-153"><span class="linenos">153</span></a> <span class="n">print_err</span> <span class="o">=</span> <span class="mi">0</span>
</span><span id="read_pbp-154"><a href="#read_pbp-154"><span class="linenos">154</span></a> <span class="nb">print</span><span class="p">()</span> </span><span id="read_pbp-154"><a href="#read_pbp-154"><span class="linenos">154</span></a> <span class="k">if</span> <span class="s1">&#39;print_err&#39;</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
</span><span id="read_pbp-155"><a href="#read_pbp-155"><span class="linenos">155</span></a> </span><span id="read_pbp-155"><a href="#read_pbp-155"><span class="linenos">155</span></a> <span class="n">print_err</span> <span class="o">=</span> <span class="mi">1</span>
</span><span id="read_pbp-156"><a href="#read_pbp-156"><span class="linenos">156</span></a> <span class="n">deltas</span> <span class="o">=</span> <span class="p">[]</span> </span><span id="read_pbp-156"><a href="#read_pbp-156"><span class="linenos">156</span></a> <span class="nb">print</span><span class="p">()</span>
</span><span id="read_pbp-157"><a href="#read_pbp-157"><span class="linenos">157</span></a> </span><span id="read_pbp-157"><a href="#read_pbp-157"><span class="linenos">157</span></a>
</span><span id="read_pbp-158"><a href="#read_pbp-158"><span class="linenos">158</span></a> <span class="k">for</span> <span class="n">rep</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">replica</span><span class="p">):</span> </span><span id="read_pbp-158"><a href="#read_pbp-158"><span class="linenos">158</span></a> <span class="n">deltas</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="read_pbp-159"><a href="#read_pbp-159"><span class="linenos">159</span></a> <span class="n">tmp_array</span> <span class="o">=</span> <span class="p">[]</span> </span><span id="read_pbp-159"><a href="#read_pbp-159"><span class="linenos">159</span></a>
</span><span id="read_pbp-160"><a href="#read_pbp-160"><span class="linenos">160</span></a> <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">path</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">ls</span><span class="p">[</span><span class="n">rep</span><span class="p">],</span> <span class="s1">&#39;rb&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span> </span><span id="read_pbp-160"><a href="#read_pbp-160"><span class="linenos">160</span></a> <span class="k">for</span> <span class="n">rep</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">replica</span><span class="p">):</span>
</span><span id="read_pbp-161"><a href="#read_pbp-161"><span class="linenos">161</span></a> </span><span id="read_pbp-161"><a href="#read_pbp-161"><span class="linenos">161</span></a> <span class="n">tmp_array</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="read_pbp-162"><a href="#read_pbp-162"><span class="linenos">162</span></a> <span class="n">t</span> <span class="o">=</span> <span class="n">fp</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="mi">4</span><span class="p">)</span> <span class="c1"># number of reweighting factors</span> </span><span id="read_pbp-162"><a href="#read_pbp-162"><span class="linenos">162</span></a> <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">path</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">ls</span><span class="p">[</span><span class="n">rep</span><span class="p">],</span> <span class="s1">&#39;rb&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span>
</span><span id="read_pbp-163"><a href="#read_pbp-163"><span class="linenos">163</span></a> <span class="k">if</span> <span class="n">rep</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span> </span><span id="read_pbp-163"><a href="#read_pbp-163"><span class="linenos">163</span></a>
</span><span id="read_pbp-164"><a href="#read_pbp-164"><span class="linenos">164</span></a> <span class="n">nrw</span> <span class="o">=</span> <span class="n">struct</span><span class="o">.</span><span class="n">unpack</span><span class="p">(</span><span class="s1">&#39;i&#39;</span><span class="p">,</span> <span class="n">t</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> </span><span id="read_pbp-164"><a href="#read_pbp-164"><span class="linenos">164</span></a> <span class="n">t</span> <span class="o">=</span> <span class="n">fp</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="mi">4</span><span class="p">)</span> <span class="c1"># number of reweighting factors</span>
</span><span id="read_pbp-165"><a href="#read_pbp-165"><span class="linenos">165</span></a> <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nrw</span><span class="p">):</span> </span><span id="read_pbp-165"><a href="#read_pbp-165"><span class="linenos">165</span></a> <span class="k">if</span> <span class="n">rep</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
</span><span id="read_pbp-166"><a href="#read_pbp-166"><span class="linenos">166</span></a> <span class="n">deltas</span><span class="o">.</span><span class="n">append</span><span class="p">([])</span> </span><span id="read_pbp-166"><a href="#read_pbp-166"><span class="linenos">166</span></a> <span class="n">nrw</span> <span class="o">=</span> <span class="n">struct</span><span class="o">.</span><span class="n">unpack</span><span class="p">(</span><span class="s1">&#39;i&#39;</span><span class="p">,</span> <span class="n">t</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
</span><span id="read_pbp-167"><a href="#read_pbp-167"><span class="linenos">167</span></a> <span class="k">else</span><span class="p">:</span> </span><span id="read_pbp-167"><a href="#read_pbp-167"><span class="linenos">167</span></a> <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nrw</span><span class="p">):</span>
</span><span id="read_pbp-168"><a href="#read_pbp-168"><span class="linenos">168</span></a> <span class="k">if</span> <span class="n">nrw</span> <span class="o">!=</span> <span class="n">struct</span><span class="o">.</span><span class="n">unpack</span><span class="p">(</span><span class="s1">&#39;i&#39;</span><span class="p">,</span> <span class="n">t</span><span class="p">)[</span><span class="mi">0</span><span class="p">]:</span> </span><span id="read_pbp-168"><a href="#read_pbp-168"><span class="linenos">168</span></a> <span class="n">deltas</span><span class="o">.</span><span class="n">append</span><span class="p">([])</span>
</span><span id="read_pbp-169"><a href="#read_pbp-169"><span class="linenos">169</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Error: different number of factors for replicum&#39;</span><span class="p">,</span> <span class="n">rep</span><span class="p">)</span> </span><span id="read_pbp-169"><a href="#read_pbp-169"><span class="linenos">169</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="read_pbp-170"><a href="#read_pbp-170"><span class="linenos">170</span></a> </span><span id="read_pbp-170"><a href="#read_pbp-170"><span class="linenos">170</span></a> <span class="k">if</span> <span class="n">nrw</span> <span class="o">!=</span> <span class="n">struct</span><span class="o">.</span><span class="n">unpack</span><span class="p">(</span><span class="s1">&#39;i&#39;</span><span class="p">,</span> <span class="n">t</span><span class="p">)[</span><span class="mi">0</span><span class="p">]:</span>
</span><span id="read_pbp-171"><a href="#read_pbp-171"><span class="linenos">171</span></a> <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nrw</span><span class="p">):</span> </span><span id="read_pbp-171"><a href="#read_pbp-171"><span class="linenos">171</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Error: different number of factors for replicum&#39;</span><span class="p">,</span> <span class="n">rep</span><span class="p">)</span>
</span><span id="read_pbp-172"><a href="#read_pbp-172"><span class="linenos">172</span></a> <span class="n">tmp_array</span><span class="o">.</span><span class="n">append</span><span class="p">([])</span> </span><span id="read_pbp-172"><a href="#read_pbp-172"><span class="linenos">172</span></a>
</span><span id="read_pbp-173"><a href="#read_pbp-173"><span class="linenos">173</span></a> </span><span id="read_pbp-173"><a href="#read_pbp-173"><span class="linenos">173</span></a> <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nrw</span><span class="p">):</span>
</span><span id="read_pbp-174"><a href="#read_pbp-174"><span class="linenos">174</span></a> <span class="c1"># This block is necessary for openQCD1.6 ms1 files</span> </span><span id="read_pbp-174"><a href="#read_pbp-174"><span class="linenos">174</span></a> <span class="n">tmp_array</span><span class="o">.</span><span class="n">append</span><span class="p">([])</span>
</span><span id="read_pbp-175"><a href="#read_pbp-175"><span class="linenos">175</span></a> <span class="n">nfct</span> <span class="o">=</span> <span class="p">[]</span> </span><span id="read_pbp-175"><a href="#read_pbp-175"><span class="linenos">175</span></a>
</span><span id="read_pbp-176"><a href="#read_pbp-176"><span class="linenos">176</span></a> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nrw</span><span class="p">):</span> </span><span id="read_pbp-176"><a href="#read_pbp-176"><span class="linenos">176</span></a> <span class="c1"># This block is necessary for openQCD1.6 ms1 files</span>
</span><span id="read_pbp-177"><a href="#read_pbp-177"><span class="linenos">177</span></a> <span class="n">t</span> <span class="o">=</span> <span class="n">fp</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="mi">4</span><span class="p">)</span> </span><span id="read_pbp-177"><a href="#read_pbp-177"><span class="linenos">177</span></a> <span class="n">nfct</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="read_pbp-178"><a href="#read_pbp-178"><span class="linenos">178</span></a> <span class="n">nfct</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">struct</span><span class="o">.</span><span class="n">unpack</span><span class="p">(</span><span class="s1">&#39;i&#39;</span><span class="p">,</span> <span class="n">t</span><span class="p">)[</span><span class="mi">0</span><span class="p">])</span> </span><span id="read_pbp-178"><a href="#read_pbp-178"><span class="linenos">178</span></a> <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nrw</span><span class="p">):</span>
</span><span id="read_pbp-179"><a href="#read_pbp-179"><span class="linenos">179</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;nfct: &#39;</span><span class="p">,</span> <span class="n">nfct</span><span class="p">)</span> <span class="c1"># Hasenbusch factor, 1 for rat reweighting</span> </span><span id="read_pbp-179"><a href="#read_pbp-179"><span class="linenos">179</span></a> <span class="n">t</span> <span class="o">=</span> <span class="n">fp</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="mi">4</span><span class="p">)</span>
</span><span id="read_pbp-180"><a href="#read_pbp-180"><span class="linenos">180</span></a> </span><span id="read_pbp-180"><a href="#read_pbp-180"><span class="linenos">180</span></a> <span class="n">nfct</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">struct</span><span class="o">.</span><span class="n">unpack</span><span class="p">(</span><span class="s1">&#39;i&#39;</span><span class="p">,</span> <span class="n">t</span><span class="p">)[</span><span class="mi">0</span><span class="p">])</span>
</span><span id="read_pbp-181"><a href="#read_pbp-181"><span class="linenos">181</span></a> <span class="n">nsrc</span> <span class="o">=</span> <span class="p">[]</span> </span><span id="read_pbp-181"><a href="#read_pbp-181"><span class="linenos">181</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;nfct: &#39;</span><span class="p">,</span> <span class="n">nfct</span><span class="p">)</span> <span class="c1"># Hasenbusch factor, 1 for rat reweighting</span>
</span><span id="read_pbp-182"><a href="#read_pbp-182"><span class="linenos">182</span></a> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nrw</span><span class="p">):</span> </span><span id="read_pbp-182"><a href="#read_pbp-182"><span class="linenos">182</span></a>
</span><span id="read_pbp-183"><a href="#read_pbp-183"><span class="linenos">183</span></a> <span class="n">t</span> <span class="o">=</span> <span class="n">fp</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="mi">4</span><span class="p">)</span> </span><span id="read_pbp-183"><a href="#read_pbp-183"><span class="linenos">183</span></a> <span class="n">nsrc</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="read_pbp-184"><a href="#read_pbp-184"><span class="linenos">184</span></a> <span class="n">nsrc</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">struct</span><span class="o">.</span><span class="n">unpack</span><span class="p">(</span><span class="s1">&#39;i&#39;</span><span class="p">,</span> <span class="n">t</span><span class="p">)[</span><span class="mi">0</span><span class="p">])</span> </span><span id="read_pbp-184"><a href="#read_pbp-184"><span class="linenos">184</span></a> <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nrw</span><span class="p">):</span>
</span><span id="read_pbp-185"><a href="#read_pbp-185"><span class="linenos">185</span></a> </span><span id="read_pbp-185"><a href="#read_pbp-185"><span class="linenos">185</span></a> <span class="n">t</span> <span class="o">=</span> <span class="n">fp</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="mi">4</span><span class="p">)</span>
</span><span id="read_pbp-186"><a href="#read_pbp-186"><span class="linenos">186</span></a> <span class="c1"># body</span> </span><span id="read_pbp-186"><a href="#read_pbp-186"><span class="linenos">186</span></a> <span class="n">nsrc</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">struct</span><span class="o">.</span><span class="n">unpack</span><span class="p">(</span><span class="s1">&#39;i&#39;</span><span class="p">,</span> <span class="n">t</span><span class="p">)[</span><span class="mi">0</span><span class="p">])</span>
</span><span id="read_pbp-187"><a href="#read_pbp-187"><span class="linenos">187</span></a> <span class="k">while</span> <span class="kc">True</span><span class="p">:</span> </span><span id="read_pbp-187"><a href="#read_pbp-187"><span class="linenos">187</span></a>
</span><span id="read_pbp-188"><a href="#read_pbp-188"><span class="linenos">188</span></a> <span class="n">t</span> <span class="o">=</span> <span class="n">fp</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="mi">4</span><span class="p">)</span> </span><span id="read_pbp-188"><a href="#read_pbp-188"><span class="linenos">188</span></a> <span class="c1"># body</span>
</span><span id="read_pbp-189"><a href="#read_pbp-189"><span class="linenos">189</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">t</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mi">4</span><span class="p">:</span> </span><span id="read_pbp-189"><a href="#read_pbp-189"><span class="linenos">189</span></a> <span class="k">while</span> <span class="kc">True</span><span class="p">:</span>
</span><span id="read_pbp-190"><a href="#read_pbp-190"><span class="linenos">190</span></a> <span class="k">break</span> </span><span id="read_pbp-190"><a href="#read_pbp-190"><span class="linenos">190</span></a> <span class="n">t</span> <span class="o">=</span> <span class="n">fp</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="mi">4</span><span class="p">)</span>
</span><span id="read_pbp-191"><a href="#read_pbp-191"><span class="linenos">191</span></a> <span class="k">if</span> <span class="n">print_err</span><span class="p">:</span> </span><span id="read_pbp-191"><a href="#read_pbp-191"><span class="linenos">191</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">t</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mi">4</span><span class="p">:</span>
</span><span id="read_pbp-192"><a href="#read_pbp-192"><span class="linenos">192</span></a> <span class="n">config_no</span> <span class="o">=</span> <span class="n">struct</span><span class="o">.</span><span class="n">unpack</span><span class="p">(</span><span class="s1">&#39;i&#39;</span><span class="p">,</span> <span class="n">t</span><span class="p">)</span> </span><span id="read_pbp-192"><a href="#read_pbp-192"><span class="linenos">192</span></a> <span class="k">break</span>
</span><span id="read_pbp-193"><a href="#read_pbp-193"><span class="linenos">193</span></a> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nrw</span><span class="p">):</span> </span><span id="read_pbp-193"><a href="#read_pbp-193"><span class="linenos">193</span></a> <span class="k">if</span> <span class="n">print_err</span><span class="p">:</span>
</span><span id="read_pbp-194"><a href="#read_pbp-194"><span class="linenos">194</span></a> <span class="n">tmp_nfct</span> <span class="o">=</span> <span class="mf">1.0</span> </span><span id="read_pbp-194"><a href="#read_pbp-194"><span class="linenos">194</span></a> <span class="n">config_no</span> <span class="o">=</span> <span class="n">struct</span><span class="o">.</span><span class="n">unpack</span><span class="p">(</span><span class="s1">&#39;i&#39;</span><span class="p">,</span> <span class="n">t</span><span class="p">)</span>
</span><span id="read_pbp-195"><a href="#read_pbp-195"><span class="linenos">195</span></a> <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nfct</span><span class="p">[</span><span class="n">i</span><span class="p">]):</span> </span><span id="read_pbp-195"><a href="#read_pbp-195"><span class="linenos">195</span></a> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nrw</span><span class="p">):</span>
</span><span id="read_pbp-196"><a href="#read_pbp-196"><span class="linenos">196</span></a> <span class="n">t</span> <span class="o">=</span> <span class="n">fp</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="mi">8</span> <span class="o">*</span> <span class="n">nsrc</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> </span><span id="read_pbp-196"><a href="#read_pbp-196"><span class="linenos">196</span></a> <span class="n">tmp_nfct</span> <span class="o">=</span> <span class="mf">1.0</span>
</span><span id="read_pbp-197"><a href="#read_pbp-197"><span class="linenos">197</span></a> <span class="n">t</span> <span class="o">=</span> <span class="n">fp</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="mi">8</span> <span class="o">*</span> <span class="n">nsrc</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> </span><span id="read_pbp-197"><a href="#read_pbp-197"><span class="linenos">197</span></a> <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nfct</span><span class="p">[</span><span class="n">i</span><span class="p">]):</span>
</span><span id="read_pbp-198"><a href="#read_pbp-198"><span class="linenos">198</span></a> <span class="n">tmp_rw</span> <span class="o">=</span> <span class="n">struct</span><span class="o">.</span><span class="n">unpack</span><span class="p">(</span><span class="s1">&#39;d&#39;</span> <span class="o">*</span> <span class="n">nsrc</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">t</span><span class="p">)</span> </span><span id="read_pbp-198"><a href="#read_pbp-198"><span class="linenos">198</span></a> <span class="n">t</span> <span class="o">=</span> <span class="n">fp</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="mi">8</span> <span class="o">*</span> <span class="n">nsrc</span><span class="p">[</span><span class="n">i</span><span class="p">])</span>
</span><span id="read_pbp-199"><a href="#read_pbp-199"><span class="linenos">199</span></a> <span class="n">tmp_nfct</span> <span class="o">*=</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">tmp_rw</span><span class="p">))</span> </span><span id="read_pbp-199"><a href="#read_pbp-199"><span class="linenos">199</span></a> <span class="n">t</span> <span class="o">=</span> <span class="n">fp</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="mi">8</span> <span class="o">*</span> <span class="n">nsrc</span><span class="p">[</span><span class="n">i</span><span class="p">])</span>
</span><span id="read_pbp-200"><a href="#read_pbp-200"><span class="linenos">200</span></a> <span class="k">if</span> <span class="n">print_err</span><span class="p">:</span> </span><span id="read_pbp-200"><a href="#read_pbp-200"><span class="linenos">200</span></a> <span class="n">tmp_rw</span> <span class="o">=</span> <span class="n">struct</span><span class="o">.</span><span class="n">unpack</span><span class="p">(</span><span class="s1">&#39;d&#39;</span> <span class="o">*</span> <span class="n">nsrc</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">t</span><span class="p">)</span>
</span><span id="read_pbp-201"><a href="#read_pbp-201"><span class="linenos">201</span></a> <span class="nb">print</span><span class="p">(</span><span class="n">config_no</span><span class="p">,</span> <span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">tmp_rw</span><span class="p">)),</span> <span class="n">np</span><span class="o">.</span><span class="n">std</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">tmp_rw</span><span class="p">)))</span> </span><span id="read_pbp-201"><a href="#read_pbp-201"><span class="linenos">201</span></a> <span class="n">tmp_nfct</span> <span class="o">*=</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">tmp_rw</span><span class="p">))</span>
</span><span id="read_pbp-202"><a href="#read_pbp-202"><span class="linenos">202</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Sources:&#39;</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">tmp_rw</span><span class="p">))</span> </span><span id="read_pbp-202"><a href="#read_pbp-202"><span class="linenos">202</span></a> <span class="k">if</span> <span class="n">print_err</span><span class="p">:</span>
</span><span id="read_pbp-203"><a href="#read_pbp-203"><span class="linenos">203</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Partial factor:&#39;</span><span class="p">,</span> <span class="n">tmp_nfct</span><span class="p">)</span> </span><span id="read_pbp-203"><a href="#read_pbp-203"><span class="linenos">203</span></a> <span class="nb">print</span><span class="p">(</span><span class="n">config_no</span><span class="p">,</span> <span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">tmp_rw</span><span class="p">)),</span> <span class="n">np</span><span class="o">.</span><span class="n">std</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">tmp_rw</span><span class="p">)))</span>
</span><span id="read_pbp-204"><a href="#read_pbp-204"><span class="linenos">204</span></a> <span class="n">tmp_array</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">tmp_nfct</span><span class="p">)</span> </span><span id="read_pbp-204"><a href="#read_pbp-204"><span class="linenos">204</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Sources:&#39;</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">tmp_rw</span><span class="p">))</span>
</span><span id="read_pbp-205"><a href="#read_pbp-205"><span class="linenos">205</span></a> </span><span id="read_pbp-205"><a href="#read_pbp-205"><span class="linenos">205</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Partial factor:&#39;</span><span class="p">,</span> <span class="n">tmp_nfct</span><span class="p">)</span>
</span><span id="read_pbp-206"><a href="#read_pbp-206"><span class="linenos">206</span></a> <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nrw</span><span class="p">):</span> </span><span id="read_pbp-206"><a href="#read_pbp-206"><span class="linenos">206</span></a> <span class="n">tmp_array</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">tmp_nfct</span><span class="p">)</span>
</span><span id="read_pbp-207"><a href="#read_pbp-207"><span class="linenos">207</span></a> <span class="n">deltas</span><span class="p">[</span><span class="n">k</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">tmp_array</span><span class="p">[</span><span class="n">k</span><span class="p">][</span><span class="n">r_start</span><span class="p">[</span><span class="n">rep</span><span class="p">]:</span><span class="n">r_stop</span><span class="p">[</span><span class="n">rep</span><span class="p">]])</span> </span><span id="read_pbp-207"><a href="#read_pbp-207"><span class="linenos">207</span></a>
</span><span id="read_pbp-208"><a href="#read_pbp-208"><span class="linenos">208</span></a> </span><span id="read_pbp-208"><a href="#read_pbp-208"><span class="linenos">208</span></a> <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nrw</span><span class="p">):</span>
</span><span id="read_pbp-209"><a href="#read_pbp-209"><span class="linenos">209</span></a> <span class="n">rep_names</span> <span class="o">=</span> <span class="p">[]</span> </span><span id="read_pbp-209"><a href="#read_pbp-209"><span class="linenos">209</span></a> <span class="n">deltas</span><span class="p">[</span><span class="n">k</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">tmp_array</span><span class="p">[</span><span class="n">k</span><span class="p">][</span><span class="n">r_start</span><span class="p">[</span><span class="n">rep</span><span class="p">]:</span><span class="n">r_stop</span><span class="p">[</span><span class="n">rep</span><span class="p">]])</span>
</span><span id="read_pbp-210"><a href="#read_pbp-210"><span class="linenos">210</span></a> <span class="k">for</span> <span class="n">entry</span> <span class="ow">in</span> <span class="n">ls</span><span class="p">:</span> </span><span id="read_pbp-210"><a href="#read_pbp-210"><span class="linenos">210</span></a>
</span><span id="read_pbp-211"><a href="#read_pbp-211"><span class="linenos">211</span></a> <span class="n">truncated_entry</span> <span class="o">=</span> <span class="n">entry</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> </span><span id="read_pbp-211"><a href="#read_pbp-211"><span class="linenos">211</span></a> <span class="n">rep_names</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="read_pbp-212"><a href="#read_pbp-212"><span class="linenos">212</span></a> <span class="n">idx</span> <span class="o">=</span> <span class="n">truncated_entry</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="s1">&#39;r&#39;</span><span class="p">)</span> </span><span id="read_pbp-212"><a href="#read_pbp-212"><span class="linenos">212</span></a> <span class="k">for</span> <span class="n">entry</span> <span class="ow">in</span> <span class="n">ls</span><span class="p">:</span>
</span><span id="read_pbp-213"><a href="#read_pbp-213"><span class="linenos">213</span></a> <span class="n">rep_names</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">truncated_entry</span><span class="p">[:</span><span class="n">idx</span><span class="p">]</span> <span class="o">+</span> <span class="s1">&#39;|&#39;</span> <span class="o">+</span> <span class="n">truncated_entry</span><span class="p">[</span><span class="n">idx</span><span class="p">:])</span> </span><span id="read_pbp-213"><a href="#read_pbp-213"><span class="linenos">213</span></a> <span class="n">truncated_entry</span> <span class="o">=</span> <span class="n">entry</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
</span><span id="read_pbp-214"><a href="#read_pbp-214"><span class="linenos">214</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">,</span> <span class="n">nrw</span><span class="p">,</span> <span class="sa">r</span><span class="s1">&#39;&lt;bar</span><span class="si">{psi}</span><span class="s1">\psi&gt; with&#39;</span><span class="p">,</span> <span class="n">nsrc</span><span class="p">,</span> <span class="s1">&#39;sources&#39;</span><span class="p">)</span> </span><span id="read_pbp-214"><a href="#read_pbp-214"><span class="linenos">214</span></a> <span class="n">idx</span> <span class="o">=</span> <span class="n">truncated_entry</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="s1">&#39;r&#39;</span><span class="p">)</span>
</span><span id="read_pbp-215"><a href="#read_pbp-215"><span class="linenos">215</span></a> <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span> </span><span id="read_pbp-215"><a href="#read_pbp-215"><span class="linenos">215</span></a> <span class="n">rep_names</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">truncated_entry</span><span class="p">[:</span><span class="n">idx</span><span class="p">]</span> <span class="o">+</span> <span class="s1">&#39;|&#39;</span> <span class="o">+</span> <span class="n">truncated_entry</span><span class="p">[</span><span class="n">idx</span><span class="p">:])</span>
</span><span id="read_pbp-216"><a href="#read_pbp-216"><span class="linenos">216</span></a> <span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nrw</span><span class="p">):</span> </span><span id="read_pbp-216"><a href="#read_pbp-216"><span class="linenos">216</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">,</span> <span class="n">nrw</span><span class="p">,</span> <span class="sa">r</span><span class="s1">&#39;&lt;bar</span><span class="si">{psi}</span><span class="s1">\psi&gt; with&#39;</span><span class="p">,</span> <span class="n">nsrc</span><span class="p">,</span> <span class="s1">&#39;sources&#39;</span><span class="p">)</span>
</span><span id="read_pbp-217"><a href="#read_pbp-217"><span class="linenos">217</span></a> <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">Obs</span><span class="p">(</span><span class="n">deltas</span><span class="p">[</span><span class="n">t</span><span class="p">],</span> <span class="n">rep_names</span><span class="p">))</span> </span><span id="read_pbp-217"><a href="#read_pbp-217"><span class="linenos">217</span></a> <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="read_pbp-218"><a href="#read_pbp-218"><span class="linenos">218</span></a> </span><span id="read_pbp-218"><a href="#read_pbp-218"><span class="linenos">218</span></a> <span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nrw</span><span class="p">):</span>
</span><span id="read_pbp-219"><a href="#read_pbp-219"><span class="linenos">219</span></a> <span class="k">return</span> <span class="n">result</span> </span><span id="read_pbp-219"><a href="#read_pbp-219"><span class="linenos">219</span></a> <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">Obs</span><span class="p">(</span><span class="n">deltas</span><span class="p">[</span><span class="n">t</span><span class="p">],</span> <span class="n">rep_names</span><span class="p">))</span>
</span><span id="read_pbp-220"><a href="#read_pbp-220"><span class="linenos">220</span></a>
</span><span id="read_pbp-221"><a href="#read_pbp-221"><span class="linenos">221</span></a> <span class="k">return</span> <span class="n">result</span>
</span></pre></div> </span></pre></div>

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<label class="view-source-button" for="mod-pandas-view-source"><span>View Source</span></label> <label class="view-source-button" for="mod-pandas-view-source"><span>View Source</span></label>
<div class="pdoc-code codehilite"><pre><span></span><span id="L-1"><a href="#L-1"><span class="linenos"> 1</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">warnings</span> <div class="pdoc-code codehilite"><pre><span></span><span id="L-1"><a href="#L-1"><span class="linenos"> 1</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">gzip</span>
</span><span id="L-2"><a href="#L-2"><span class="linenos"> 2</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">gzip</span> </span><span id="L-2"><a href="#L-2"><span class="linenos"> 2</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">sqlite3</span>
</span><span id="L-3"><a href="#L-3"><span class="linenos"> 3</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">sqlite3</span> </span><span id="L-3"><a href="#L-3"><span class="linenos"> 3</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">warnings</span>
</span><span id="L-4"><a href="#L-4"><span class="linenos"> 4</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">contextlib</span><span class="w"> </span><span class="kn">import</span> <span class="n">closing</span> </span><span id="L-4"><a href="#L-4"><span class="linenos"> 4</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">contextlib</span><span class="w"> </span><span class="kn">import</span> <span class="n">closing</span>
</span><span id="L-5"><a href="#L-5"><span class="linenos"> 5</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">pandas</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">pd</span> </span><span id="L-5"><a href="#L-5"><span class="linenos"> 5</span></a>
</span><span id="L-6"><a href="#L-6"><span class="linenos"> 6</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">..obs</span><span class="w"> </span><span class="kn">import</span> <span class="n">Obs</span> </span><span id="L-6"><a href="#L-6"><span class="linenos"> 6</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
</span><span id="L-7"><a href="#L-7"><span class="linenos"> 7</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">..correlators</span><span class="w"> </span><span class="kn">import</span> <span class="n">Corr</span> </span><span id="L-7"><a href="#L-7"><span class="linenos"> 7</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">pandas</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">pd</span>
</span><span id="L-8"><a href="#L-8"><span class="linenos"> 8</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">.json</span><span class="w"> </span><span class="kn">import</span> <span class="n">create_json_string</span><span class="p">,</span> <span class="n">import_json_string</span> </span><span id="L-8"><a href="#L-8"><span class="linenos"> 8</span></a>
</span><span id="L-9"><a href="#L-9"><span class="linenos"> 9</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span> </span><span id="L-9"><a href="#L-9"><span class="linenos"> 9</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">..correlators</span><span class="w"> </span><span class="kn">import</span> <span class="n">Corr</span>
</span><span id="L-10"><a href="#L-10"><span class="linenos"> 10</span></a> </span><span id="L-10"><a href="#L-10"><span class="linenos"> 10</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">..obs</span><span class="w"> </span><span class="kn">import</span> <span class="n">Obs</span>
</span><span id="L-11"><a href="#L-11"><span class="linenos"> 11</span></a> </span><span id="L-11"><a href="#L-11"><span class="linenos"> 11</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">.json</span><span class="w"> </span><span class="kn">import</span> <span class="n">create_json_string</span><span class="p">,</span> <span class="n">import_json_string</span>
</span><span id="L-12"><a href="#L-12"><span class="linenos"> 12</span></a><span class="k">def</span><span class="w"> </span><span class="nf">to_sql</span><span class="p">(</span><span class="n">df</span><span class="p">,</span> <span class="n">table_name</span><span class="p">,</span> <span class="n">db</span><span class="p">,</span> <span class="n">if_exists</span><span class="o">=</span><span class="s1">&#39;fail&#39;</span><span class="p">,</span> <span class="n">gz</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span> </span><span id="L-12"><a href="#L-12"><span class="linenos"> 12</span></a>
</span><span id="L-13"><a href="#L-13"><span class="linenos"> 13</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Write DataFrame including Obs or Corr valued columns to sqlite database.</span> </span><span id="L-13"><a href="#L-13"><span class="linenos"> 13</span></a>
</span><span id="L-14"><a href="#L-14"><span class="linenos"> 14</span></a> </span><span id="L-14"><a href="#L-14"><span class="linenos"> 14</span></a><span class="k">def</span><span class="w"> </span><span class="nf">to_sql</span><span class="p">(</span><span class="n">df</span><span class="p">,</span> <span class="n">table_name</span><span class="p">,</span> <span class="n">db</span><span class="p">,</span> <span class="n">if_exists</span><span class="o">=</span><span class="s1">&#39;fail&#39;</span><span class="p">,</span> <span class="n">gz</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
</span><span id="L-15"><a href="#L-15"><span class="linenos"> 15</span></a><span class="sd"> Parameters</span> </span><span id="L-15"><a href="#L-15"><span class="linenos"> 15</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Write DataFrame including Obs or Corr valued columns to sqlite database.</span>
</span><span id="L-16"><a href="#L-16"><span class="linenos"> 16</span></a><span class="sd"> ----------</span> </span><span id="L-16"><a href="#L-16"><span class="linenos"> 16</span></a>
</span><span id="L-17"><a href="#L-17"><span class="linenos"> 17</span></a><span class="sd"> df : pandas.DataFrame</span> </span><span id="L-17"><a href="#L-17"><span class="linenos"> 17</span></a><span class="sd"> Parameters</span>
</span><span id="L-18"><a href="#L-18"><span class="linenos"> 18</span></a><span class="sd"> Dataframe to be written to the database.</span> </span><span id="L-18"><a href="#L-18"><span class="linenos"> 18</span></a><span class="sd"> ----------</span>
</span><span id="L-19"><a href="#L-19"><span class="linenos"> 19</span></a><span class="sd"> table_name : str</span> </span><span id="L-19"><a href="#L-19"><span class="linenos"> 19</span></a><span class="sd"> df : pandas.DataFrame</span>
</span><span id="L-20"><a href="#L-20"><span class="linenos"> 20</span></a><span class="sd"> Name of the table in the database.</span> </span><span id="L-20"><a href="#L-20"><span class="linenos"> 20</span></a><span class="sd"> Dataframe to be written to the database.</span>
</span><span id="L-21"><a href="#L-21"><span class="linenos"> 21</span></a><span class="sd"> db : str</span> </span><span id="L-21"><a href="#L-21"><span class="linenos"> 21</span></a><span class="sd"> table_name : str</span>
</span><span id="L-22"><a href="#L-22"><span class="linenos"> 22</span></a><span class="sd"> Path to the sqlite database.</span> </span><span id="L-22"><a href="#L-22"><span class="linenos"> 22</span></a><span class="sd"> Name of the table in the database.</span>
</span><span id="L-23"><a href="#L-23"><span class="linenos"> 23</span></a><span class="sd"> if exists : str</span> </span><span id="L-23"><a href="#L-23"><span class="linenos"> 23</span></a><span class="sd"> db : str</span>
</span><span id="L-24"><a href="#L-24"><span class="linenos"> 24</span></a><span class="sd"> How to behave if table already exists. Options &#39;fail&#39;, &#39;replace&#39;, &#39;append&#39;.</span> </span><span id="L-24"><a href="#L-24"><span class="linenos"> 24</span></a><span class="sd"> Path to the sqlite database.</span>
</span><span id="L-25"><a href="#L-25"><span class="linenos"> 25</span></a><span class="sd"> gz : bool</span> </span><span id="L-25"><a href="#L-25"><span class="linenos"> 25</span></a><span class="sd"> if exists : str</span>
</span><span id="L-26"><a href="#L-26"><span class="linenos"> 26</span></a><span class="sd"> If True the json strings are gzipped.</span> </span><span id="L-26"><a href="#L-26"><span class="linenos"> 26</span></a><span class="sd"> How to behave if table already exists. Options &#39;fail&#39;, &#39;replace&#39;, &#39;append&#39;.</span>
</span><span id="L-27"><a href="#L-27"><span class="linenos"> 27</span></a> </span><span id="L-27"><a href="#L-27"><span class="linenos"> 27</span></a><span class="sd"> gz : bool</span>
</span><span id="L-28"><a href="#L-28"><span class="linenos"> 28</span></a><span class="sd"> Returns</span> </span><span id="L-28"><a href="#L-28"><span class="linenos"> 28</span></a><span class="sd"> If True the json strings are gzipped.</span>
</span><span id="L-29"><a href="#L-29"><span class="linenos"> 29</span></a><span class="sd"> -------</span> </span><span id="L-29"><a href="#L-29"><span class="linenos"> 29</span></a>
</span><span id="L-30"><a href="#L-30"><span class="linenos"> 30</span></a><span class="sd"> None</span> </span><span id="L-30"><a href="#L-30"><span class="linenos"> 30</span></a><span class="sd"> Returns</span>
</span><span id="L-31"><a href="#L-31"><span class="linenos"> 31</span></a><span class="sd"> &quot;&quot;&quot;</span> </span><span id="L-31"><a href="#L-31"><span class="linenos"> 31</span></a><span class="sd"> -------</span>
</span><span id="L-32"><a href="#L-32"><span class="linenos"> 32</span></a> <span class="n">se_df</span> <span class="o">=</span> <span class="n">_serialize_df</span><span class="p">(</span><span class="n">df</span><span class="p">,</span> <span class="n">gz</span><span class="o">=</span><span class="n">gz</span><span class="p">)</span> </span><span id="L-32"><a href="#L-32"><span class="linenos"> 32</span></a><span class="sd"> None</span>
</span><span id="L-33"><a href="#L-33"><span class="linenos"> 33</span></a> <span class="k">with</span> <span class="n">closing</span><span class="p">(</span><span class="n">sqlite3</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="n">db</span><span class="p">))</span> <span class="k">as</span> <span class="n">con</span><span class="p">:</span> </span><span id="L-33"><a href="#L-33"><span class="linenos"> 33</span></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="L-34"><a href="#L-34"><span class="linenos"> 34</span></a> <span class="n">se_df</span><span class="o">.</span><span class="n">to_sql</span><span class="p">(</span><span class="n">table_name</span><span class="p">,</span> <span class="n">con</span><span class="o">=</span><span class="n">con</span><span class="p">,</span> <span class="n">if_exists</span><span class="o">=</span><span class="n">if_exists</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span> </span><span id="L-34"><a href="#L-34"><span class="linenos"> 34</span></a> <span class="n">se_df</span> <span class="o">=</span> <span class="n">_serialize_df</span><span class="p">(</span><span class="n">df</span><span class="p">,</span> <span class="n">gz</span><span class="o">=</span><span class="n">gz</span><span class="p">)</span>
</span><span id="L-35"><a href="#L-35"><span class="linenos"> 35</span></a> </span><span id="L-35"><a href="#L-35"><span class="linenos"> 35</span></a> <span class="k">with</span> <span class="n">closing</span><span class="p">(</span><span class="n">sqlite3</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="n">db</span><span class="p">))</span> <span class="k">as</span> <span class="n">con</span><span class="p">:</span>
</span><span id="L-36"><a href="#L-36"><span class="linenos"> 36</span></a> </span><span id="L-36"><a href="#L-36"><span class="linenos"> 36</span></a> <span class="n">se_df</span><span class="o">.</span><span class="n">to_sql</span><span class="p">(</span><span class="n">table_name</span><span class="p">,</span> <span class="n">con</span><span class="o">=</span><span class="n">con</span><span class="p">,</span> <span class="n">if_exists</span><span class="o">=</span><span class="n">if_exists</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
</span><span id="L-37"><a href="#L-37"><span class="linenos"> 37</span></a><span class="k">def</span><span class="w"> </span><span class="nf">read_sql</span><span class="p">(</span><span class="n">sql</span><span class="p">,</span> <span class="n">db</span><span class="p">,</span> <span class="n">auto_gamma</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span> </span><span id="L-37"><a href="#L-37"><span class="linenos"> 37</span></a>
</span><span id="L-38"><a href="#L-38"><span class="linenos"> 38</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Execute SQL query on sqlite database and obtain DataFrame including Obs or Corr valued columns.</span> </span><span id="L-38"><a href="#L-38"><span class="linenos"> 38</span></a>
</span><span id="L-39"><a href="#L-39"><span class="linenos"> 39</span></a> </span><span id="L-39"><a href="#L-39"><span class="linenos"> 39</span></a><span class="k">def</span><span class="w"> </span><span class="nf">read_sql</span><span class="p">(</span><span class="n">sql</span><span class="p">,</span> <span class="n">db</span><span class="p">,</span> <span class="n">auto_gamma</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
</span><span id="L-40"><a href="#L-40"><span class="linenos"> 40</span></a><span class="sd"> Parameters</span> </span><span id="L-40"><a href="#L-40"><span class="linenos"> 40</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Execute SQL query on sqlite database and obtain DataFrame including Obs or Corr valued columns.</span>
</span><span id="L-41"><a href="#L-41"><span class="linenos"> 41</span></a><span class="sd"> ----------</span> </span><span id="L-41"><a href="#L-41"><span class="linenos"> 41</span></a>
</span><span id="L-42"><a href="#L-42"><span class="linenos"> 42</span></a><span class="sd"> sql : str</span> </span><span id="L-42"><a href="#L-42"><span class="linenos"> 42</span></a><span class="sd"> Parameters</span>
</span><span id="L-43"><a href="#L-43"><span class="linenos"> 43</span></a><span class="sd"> SQL query to be executed.</span> </span><span id="L-43"><a href="#L-43"><span class="linenos"> 43</span></a><span class="sd"> ----------</span>
</span><span id="L-44"><a href="#L-44"><span class="linenos"> 44</span></a><span class="sd"> db : str</span> </span><span id="L-44"><a href="#L-44"><span class="linenos"> 44</span></a><span class="sd"> sql : str</span>
</span><span id="L-45"><a href="#L-45"><span class="linenos"> 45</span></a><span class="sd"> Path to the sqlite database.</span> </span><span id="L-45"><a href="#L-45"><span class="linenos"> 45</span></a><span class="sd"> SQL query to be executed.</span>
</span><span id="L-46"><a href="#L-46"><span class="linenos"> 46</span></a><span class="sd"> auto_gamma : bool</span> </span><span id="L-46"><a href="#L-46"><span class="linenos"> 46</span></a><span class="sd"> db : str</span>
</span><span id="L-47"><a href="#L-47"><span class="linenos"> 47</span></a><span class="sd"> If True applies the gamma_method to all imported Obs objects with the default parameters for</span> </span><span id="L-47"><a href="#L-47"><span class="linenos"> 47</span></a><span class="sd"> Path to the sqlite database.</span>
</span><span id="L-48"><a href="#L-48"><span class="linenos"> 48</span></a><span class="sd"> the error analysis. Default False.</span> </span><span id="L-48"><a href="#L-48"><span class="linenos"> 48</span></a><span class="sd"> auto_gamma : bool</span>
</span><span id="L-49"><a href="#L-49"><span class="linenos"> 49</span></a> </span><span id="L-49"><a href="#L-49"><span class="linenos"> 49</span></a><span class="sd"> If True applies the gamma_method to all imported Obs objects with the default parameters for</span>
</span><span id="L-50"><a href="#L-50"><span class="linenos"> 50</span></a><span class="sd"> Returns</span> </span><span id="L-50"><a href="#L-50"><span class="linenos"> 50</span></a><span class="sd"> the error analysis. Default False.</span>
</span><span id="L-51"><a href="#L-51"><span class="linenos"> 51</span></a><span class="sd"> -------</span> </span><span id="L-51"><a href="#L-51"><span class="linenos"> 51</span></a>
</span><span id="L-52"><a href="#L-52"><span class="linenos"> 52</span></a><span class="sd"> data : pandas.DataFrame</span> </span><span id="L-52"><a href="#L-52"><span class="linenos"> 52</span></a><span class="sd"> Returns</span>
</span><span id="L-53"><a href="#L-53"><span class="linenos"> 53</span></a><span class="sd"> Dataframe with the content of the sqlite database.</span> </span><span id="L-53"><a href="#L-53"><span class="linenos"> 53</span></a><span class="sd"> -------</span>
</span><span id="L-54"><a href="#L-54"><span class="linenos"> 54</span></a><span class="sd"> &quot;&quot;&quot;</span> </span><span id="L-54"><a href="#L-54"><span class="linenos"> 54</span></a><span class="sd"> data : pandas.DataFrame</span>
</span><span id="L-55"><a href="#L-55"><span class="linenos"> 55</span></a> <span class="k">with</span> <span class="n">closing</span><span class="p">(</span><span class="n">sqlite3</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="n">db</span><span class="p">))</span> <span class="k">as</span> <span class="n">con</span><span class="p">:</span> </span><span id="L-55"><a href="#L-55"><span class="linenos"> 55</span></a><span class="sd"> Dataframe with the content of the sqlite database.</span>
</span><span id="L-56"><a href="#L-56"><span class="linenos"> 56</span></a> <span class="n">extract_df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_sql</span><span class="p">(</span><span class="n">sql</span><span class="p">,</span> <span class="n">con</span><span class="o">=</span><span class="n">con</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span> </span><span id="L-56"><a href="#L-56"><span class="linenos"> 56</span></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="L-57"><a href="#L-57"><span class="linenos"> 57</span></a> <span class="k">return</span> <span class="n">_deserialize_df</span><span class="p">(</span><span class="n">extract_df</span><span class="p">,</span> <span class="n">auto_gamma</span><span class="o">=</span><span class="n">auto_gamma</span><span class="p">)</span> </span><span id="L-57"><a href="#L-57"><span class="linenos"> 57</span></a> <span class="k">with</span> <span class="n">closing</span><span class="p">(</span><span class="n">sqlite3</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="n">db</span><span class="p">))</span> <span class="k">as</span> <span class="n">con</span><span class="p">:</span>
</span><span id="L-58"><a href="#L-58"><span class="linenos"> 58</span></a> </span><span id="L-58"><a href="#L-58"><span class="linenos"> 58</span></a> <span class="n">extract_df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_sql</span><span class="p">(</span><span class="n">sql</span><span class="p">,</span> <span class="n">con</span><span class="o">=</span><span class="n">con</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
</span><span id="L-59"><a href="#L-59"><span class="linenos"> 59</span></a> </span><span id="L-59"><a href="#L-59"><span class="linenos"> 59</span></a> <span class="k">return</span> <span class="n">_deserialize_df</span><span class="p">(</span><span class="n">extract_df</span><span class="p">,</span> <span class="n">auto_gamma</span><span class="o">=</span><span class="n">auto_gamma</span><span class="p">)</span>
</span><span id="L-60"><a href="#L-60"><span class="linenos"> 60</span></a><span class="k">def</span><span class="w"> </span><span class="nf">dump_df</span><span class="p">(</span><span class="n">df</span><span class="p">,</span> <span class="n">fname</span><span class="p">,</span> <span class="n">gz</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span> </span><span id="L-60"><a href="#L-60"><span class="linenos"> 60</span></a>
</span><span id="L-61"><a href="#L-61"><span class="linenos"> 61</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Exports a pandas DataFrame containing Obs valued columns to a (gzipped) csv file.</span> </span><span id="L-61"><a href="#L-61"><span class="linenos"> 61</span></a>
</span><span id="L-62"><a href="#L-62"><span class="linenos"> 62</span></a> </span><span id="L-62"><a href="#L-62"><span class="linenos"> 62</span></a><span class="k">def</span><span class="w"> </span><span class="nf">dump_df</span><span class="p">(</span><span class="n">df</span><span class="p">,</span> <span class="n">fname</span><span class="p">,</span> <span class="n">gz</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
</span><span id="L-63"><a href="#L-63"><span class="linenos"> 63</span></a><span class="sd"> Before making use of pandas to_csv functionality Obs objects are serialized via the standardized</span> </span><span id="L-63"><a href="#L-63"><span class="linenos"> 63</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Exports a pandas DataFrame containing Obs valued columns to a (gzipped) csv file.</span>
</span><span id="L-64"><a href="#L-64"><span class="linenos"> 64</span></a><span class="sd"> json format of pyerrors.</span> </span><span id="L-64"><a href="#L-64"><span class="linenos"> 64</span></a>
</span><span id="L-65"><a href="#L-65"><span class="linenos"> 65</span></a> </span><span id="L-65"><a href="#L-65"><span class="linenos"> 65</span></a><span class="sd"> Before making use of pandas to_csv functionality Obs objects are serialized via the standardized</span>
</span><span id="L-66"><a href="#L-66"><span class="linenos"> 66</span></a><span class="sd"> Parameters</span> </span><span id="L-66"><a href="#L-66"><span class="linenos"> 66</span></a><span class="sd"> json format of pyerrors.</span>
</span><span id="L-67"><a href="#L-67"><span class="linenos"> 67</span></a><span class="sd"> ----------</span> </span><span id="L-67"><a href="#L-67"><span class="linenos"> 67</span></a>
</span><span id="L-68"><a href="#L-68"><span class="linenos"> 68</span></a><span class="sd"> df : pandas.DataFrame</span> </span><span id="L-68"><a href="#L-68"><span class="linenos"> 68</span></a><span class="sd"> Parameters</span>
</span><span id="L-69"><a href="#L-69"><span class="linenos"> 69</span></a><span class="sd"> Dataframe to be dumped to a file.</span> </span><span id="L-69"><a href="#L-69"><span class="linenos"> 69</span></a><span class="sd"> ----------</span>
</span><span id="L-70"><a href="#L-70"><span class="linenos"> 70</span></a><span class="sd"> fname : str</span> </span><span id="L-70"><a href="#L-70"><span class="linenos"> 70</span></a><span class="sd"> df : pandas.DataFrame</span>
</span><span id="L-71"><a href="#L-71"><span class="linenos"> 71</span></a><span class="sd"> Filename of the output file.</span> </span><span id="L-71"><a href="#L-71"><span class="linenos"> 71</span></a><span class="sd"> Dataframe to be dumped to a file.</span>
</span><span id="L-72"><a href="#L-72"><span class="linenos"> 72</span></a><span class="sd"> gz : bool</span> </span><span id="L-72"><a href="#L-72"><span class="linenos"> 72</span></a><span class="sd"> fname : str</span>
</span><span id="L-73"><a href="#L-73"><span class="linenos"> 73</span></a><span class="sd"> If True, the output is a gzipped csv file. If False, the output is a csv file.</span> </span><span id="L-73"><a href="#L-73"><span class="linenos"> 73</span></a><span class="sd"> Filename of the output file.</span>
</span><span id="L-74"><a href="#L-74"><span class="linenos"> 74</span></a> </span><span id="L-74"><a href="#L-74"><span class="linenos"> 74</span></a><span class="sd"> gz : bool</span>
</span><span id="L-75"><a href="#L-75"><span class="linenos"> 75</span></a><span class="sd"> Returns</span> </span><span id="L-75"><a href="#L-75"><span class="linenos"> 75</span></a><span class="sd"> If True, the output is a gzipped csv file. If False, the output is a csv file.</span>
</span><span id="L-76"><a href="#L-76"><span class="linenos"> 76</span></a><span class="sd"> -------</span> </span><span id="L-76"><a href="#L-76"><span class="linenos"> 76</span></a>
</span><span id="L-77"><a href="#L-77"><span class="linenos"> 77</span></a><span class="sd"> None</span> </span><span id="L-77"><a href="#L-77"><span class="linenos"> 77</span></a><span class="sd"> Returns</span>
</span><span id="L-78"><a href="#L-78"><span class="linenos"> 78</span></a><span class="sd"> &quot;&quot;&quot;</span> </span><span id="L-78"><a href="#L-78"><span class="linenos"> 78</span></a><span class="sd"> -------</span>
</span><span id="L-79"><a href="#L-79"><span class="linenos"> 79</span></a> <span class="k">for</span> <span class="n">column</span> <span class="ow">in</span> <span class="n">df</span><span class="p">:</span> </span><span id="L-79"><a href="#L-79"><span class="linenos"> 79</span></a><span class="sd"> None</span>
</span><span id="L-80"><a href="#L-80"><span class="linenos"> 80</span></a> <span class="n">serialize</span> <span class="o">=</span> <span class="n">_need_to_serialize</span><span class="p">(</span><span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">])</span> </span><span id="L-80"><a href="#L-80"><span class="linenos"> 80</span></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="L-81"><a href="#L-81"><span class="linenos"> 81</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">serialize</span><span class="p">:</span> </span><span id="L-81"><a href="#L-81"><span class="linenos"> 81</span></a> <span class="k">for</span> <span class="n">column</span> <span class="ow">in</span> <span class="n">df</span><span class="p">:</span>
</span><span id="L-82"><a href="#L-82"><span class="linenos"> 82</span></a> <span class="k">if</span> <span class="nb">all</span><span class="p">(</span><span class="nb">isinstance</span><span class="p">(</span><span class="n">entry</span><span class="p">,</span> <span class="p">(</span><span class="nb">int</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">integer</span><span class="p">,</span> <span class="nb">float</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">floating</span><span class="p">))</span> <span class="k">for</span> <span class="n">entry</span> <span class="ow">in</span> <span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]):</span> </span><span id="L-82"><a href="#L-82"><span class="linenos"> 82</span></a> <span class="n">serialize</span> <span class="o">=</span> <span class="n">_need_to_serialize</span><span class="p">(</span><span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">])</span>
</span><span id="L-83"><a href="#L-83"><span class="linenos"> 83</span></a> <span class="k">if</span> <span class="nb">any</span><span class="p">([</span><span class="n">np</span><span class="o">.</span><span class="n">isnan</span><span class="p">(</span><span class="n">entry</span><span class="p">)</span> <span class="k">for</span> <span class="n">entry</span> <span class="ow">in</span> <span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]]):</span> </span><span id="L-83"><a href="#L-83"><span class="linenos"> 83</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">serialize</span><span class="p">:</span>
</span><span id="L-84"><a href="#L-84"><span class="linenos"> 84</span></a> <span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span><span class="s2">&quot;nan value in column &quot;</span> <span class="o">+</span> <span class="n">column</span> <span class="o">+</span> <span class="s2">&quot; will be replaced by None&quot;</span><span class="p">,</span> <span class="ne">UserWarning</span><span class="p">)</span> </span><span id="L-84"><a href="#L-84"><span class="linenos"> 84</span></a> <span class="k">if</span> <span class="nb">all</span><span class="p">(</span><span class="nb">isinstance</span><span class="p">(</span><span class="n">entry</span><span class="p">,</span> <span class="p">(</span><span class="nb">int</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">integer</span><span class="p">,</span> <span class="nb">float</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">floating</span><span class="p">))</span> <span class="k">for</span> <span class="n">entry</span> <span class="ow">in</span> <span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]):</span>
</span><span id="L-85"><a href="#L-85"><span class="linenos"> 85</span></a> </span><span id="L-85"><a href="#L-85"><span class="linenos"> 85</span></a> <span class="k">if</span> <span class="nb">any</span><span class="p">([</span><span class="n">np</span><span class="o">.</span><span class="n">isnan</span><span class="p">(</span><span class="n">entry</span><span class="p">)</span> <span class="k">for</span> <span class="n">entry</span> <span class="ow">in</span> <span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]]):</span>
</span><span id="L-86"><a href="#L-86"><span class="linenos"> 86</span></a> <span class="n">out</span> <span class="o">=</span> <span class="n">_serialize_df</span><span class="p">(</span><span class="n">df</span><span class="p">,</span> <span class="n">gz</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span> </span><span id="L-86"><a href="#L-86"><span class="linenos"> 86</span></a> <span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span><span class="s2">&quot;nan value in column &quot;</span> <span class="o">+</span> <span class="n">column</span> <span class="o">+</span> <span class="s2">&quot; will be replaced by None&quot;</span><span class="p">,</span> <span class="ne">UserWarning</span><span class="p">,</span> <span class="n">stacklevel</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span>
</span><span id="L-87"><a href="#L-87"><span class="linenos"> 87</span></a> </span><span id="L-87"><a href="#L-87"><span class="linenos"> 87</span></a>
</span><span id="L-88"><a href="#L-88"><span class="linenos"> 88</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">fname</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s1">&#39;.csv&#39;</span><span class="p">):</span> </span><span id="L-88"><a href="#L-88"><span class="linenos"> 88</span></a> <span class="n">out</span> <span class="o">=</span> <span class="n">_serialize_df</span><span class="p">(</span><span class="n">df</span><span class="p">,</span> <span class="n">gz</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
</span><span id="L-89"><a href="#L-89"><span class="linenos"> 89</span></a> <span class="n">fname</span> <span class="o">+=</span> <span class="s1">&#39;.csv&#39;</span> </span><span id="L-89"><a href="#L-89"><span class="linenos"> 89</span></a>
</span><span id="L-90"><a href="#L-90"><span class="linenos"> 90</span></a> </span><span id="L-90"><a href="#L-90"><span class="linenos"> 90</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">fname</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s1">&#39;.csv&#39;</span><span class="p">):</span>
</span><span id="L-91"><a href="#L-91"><span class="linenos"> 91</span></a> <span class="k">if</span> <span class="n">gz</span> <span class="ow">is</span> <span class="kc">True</span><span class="p">:</span> </span><span id="L-91"><a href="#L-91"><span class="linenos"> 91</span></a> <span class="n">fname</span> <span class="o">+=</span> <span class="s1">&#39;.csv&#39;</span>
</span><span id="L-92"><a href="#L-92"><span class="linenos"> 92</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">fname</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s1">&#39;.gz&#39;</span><span class="p">):</span> </span><span id="L-92"><a href="#L-92"><span class="linenos"> 92</span></a>
</span><span id="L-93"><a href="#L-93"><span class="linenos"> 93</span></a> <span class="n">fname</span> <span class="o">+=</span> <span class="s1">&#39;.gz&#39;</span> </span><span id="L-93"><a href="#L-93"><span class="linenos"> 93</span></a> <span class="k">if</span> <span class="n">gz</span> <span class="ow">is</span> <span class="kc">True</span><span class="p">:</span>
</span><span id="L-94"><a href="#L-94"><span class="linenos"> 94</span></a> <span class="n">out</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="n">fname</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">compression</span><span class="o">=</span><span class="s1">&#39;gzip&#39;</span><span class="p">)</span> </span><span id="L-94"><a href="#L-94"><span class="linenos"> 94</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">fname</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s1">&#39;.gz&#39;</span><span class="p">):</span>
</span><span id="L-95"><a href="#L-95"><span class="linenos"> 95</span></a> <span class="k">else</span><span class="p">:</span> </span><span id="L-95"><a href="#L-95"><span class="linenos"> 95</span></a> <span class="n">fname</span> <span class="o">+=</span> <span class="s1">&#39;.gz&#39;</span>
</span><span id="L-96"><a href="#L-96"><span class="linenos"> 96</span></a> <span class="n">out</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="n">fname</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span> </span><span id="L-96"><a href="#L-96"><span class="linenos"> 96</span></a> <span class="n">out</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="n">fname</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">compression</span><span class="o">=</span><span class="s1">&#39;gzip&#39;</span><span class="p">)</span>
</span><span id="L-97"><a href="#L-97"><span class="linenos"> 97</span></a> </span><span id="L-97"><a href="#L-97"><span class="linenos"> 97</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="L-98"><a href="#L-98"><span class="linenos"> 98</span></a> </span><span id="L-98"><a href="#L-98"><span class="linenos"> 98</span></a> <span class="n">out</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="n">fname</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
</span><span id="L-99"><a href="#L-99"><span class="linenos"> 99</span></a><span class="k">def</span><span class="w"> </span><span class="nf">load_df</span><span class="p">(</span><span class="n">fname</span><span class="p">,</span> <span class="n">auto_gamma</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">gz</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span> </span><span id="L-99"><a href="#L-99"><span class="linenos"> 99</span></a>
</span><span id="L-100"><a href="#L-100"><span class="linenos">100</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Imports a pandas DataFrame from a csv.(gz) file in which Obs objects are serialized as json strings.</span> </span><span id="L-100"><a href="#L-100"><span class="linenos">100</span></a>
</span><span id="L-101"><a href="#L-101"><span class="linenos">101</span></a> </span><span id="L-101"><a href="#L-101"><span class="linenos">101</span></a><span class="k">def</span><span class="w"> </span><span class="nf">load_df</span><span class="p">(</span><span class="n">fname</span><span class="p">,</span> <span class="n">auto_gamma</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">gz</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
</span><span id="L-102"><a href="#L-102"><span class="linenos">102</span></a><span class="sd"> Parameters</span> </span><span id="L-102"><a href="#L-102"><span class="linenos">102</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Imports a pandas DataFrame from a csv.(gz) file in which Obs objects are serialized as json strings.</span>
</span><span id="L-103"><a href="#L-103"><span class="linenos">103</span></a><span class="sd"> ----------</span> </span><span id="L-103"><a href="#L-103"><span class="linenos">103</span></a>
</span><span id="L-104"><a href="#L-104"><span class="linenos">104</span></a><span class="sd"> fname : str</span> </span><span id="L-104"><a href="#L-104"><span class="linenos">104</span></a><span class="sd"> Parameters</span>
</span><span id="L-105"><a href="#L-105"><span class="linenos">105</span></a><span class="sd"> Filename of the input file.</span> </span><span id="L-105"><a href="#L-105"><span class="linenos">105</span></a><span class="sd"> ----------</span>
</span><span id="L-106"><a href="#L-106"><span class="linenos">106</span></a><span class="sd"> auto_gamma : bool</span> </span><span id="L-106"><a href="#L-106"><span class="linenos">106</span></a><span class="sd"> fname : str</span>
</span><span id="L-107"><a href="#L-107"><span class="linenos">107</span></a><span class="sd"> If True applies the gamma_method to all imported Obs objects with the default parameters for</span> </span><span id="L-107"><a href="#L-107"><span class="linenos">107</span></a><span class="sd"> Filename of the input file.</span>
</span><span id="L-108"><a href="#L-108"><span class="linenos">108</span></a><span class="sd"> the error analysis. Default False.</span> </span><span id="L-108"><a href="#L-108"><span class="linenos">108</span></a><span class="sd"> auto_gamma : bool</span>
</span><span id="L-109"><a href="#L-109"><span class="linenos">109</span></a><span class="sd"> gz : bool</span> </span><span id="L-109"><a href="#L-109"><span class="linenos">109</span></a><span class="sd"> If True applies the gamma_method to all imported Obs objects with the default parameters for</span>
</span><span id="L-110"><a href="#L-110"><span class="linenos">110</span></a><span class="sd"> If True, assumes that data is gzipped. If False, assumes JSON file.</span> </span><span id="L-110"><a href="#L-110"><span class="linenos">110</span></a><span class="sd"> the error analysis. Default False.</span>
</span><span id="L-111"><a href="#L-111"><span class="linenos">111</span></a> </span><span id="L-111"><a href="#L-111"><span class="linenos">111</span></a><span class="sd"> gz : bool</span>
</span><span id="L-112"><a href="#L-112"><span class="linenos">112</span></a><span class="sd"> Returns</span> </span><span id="L-112"><a href="#L-112"><span class="linenos">112</span></a><span class="sd"> If True, assumes that data is gzipped. If False, assumes JSON file.</span>
</span><span id="L-113"><a href="#L-113"><span class="linenos">113</span></a><span class="sd"> -------</span> </span><span id="L-113"><a href="#L-113"><span class="linenos">113</span></a>
</span><span id="L-114"><a href="#L-114"><span class="linenos">114</span></a><span class="sd"> data : pandas.DataFrame</span> </span><span id="L-114"><a href="#L-114"><span class="linenos">114</span></a><span class="sd"> Returns</span>
</span><span id="L-115"><a href="#L-115"><span class="linenos">115</span></a><span class="sd"> Dataframe with the content of the sqlite database.</span> </span><span id="L-115"><a href="#L-115"><span class="linenos">115</span></a><span class="sd"> -------</span>
</span><span id="L-116"><a href="#L-116"><span class="linenos">116</span></a><span class="sd"> &quot;&quot;&quot;</span> </span><span id="L-116"><a href="#L-116"><span class="linenos">116</span></a><span class="sd"> data : pandas.DataFrame</span>
</span><span id="L-117"><a href="#L-117"><span class="linenos">117</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">fname</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s1">&#39;.csv&#39;</span><span class="p">)</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">fname</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s1">&#39;.gz&#39;</span><span class="p">):</span> </span><span id="L-117"><a href="#L-117"><span class="linenos">117</span></a><span class="sd"> Dataframe with the content of the sqlite database.</span>
</span><span id="L-118"><a href="#L-118"><span class="linenos">118</span></a> <span class="n">fname</span> <span class="o">+=</span> <span class="s1">&#39;.csv&#39;</span> </span><span id="L-118"><a href="#L-118"><span class="linenos">118</span></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="L-119"><a href="#L-119"><span class="linenos">119</span></a> </span><span id="L-119"><a href="#L-119"><span class="linenos">119</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">fname</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s1">&#39;.csv&#39;</span><span class="p">)</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">fname</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s1">&#39;.gz&#39;</span><span class="p">):</span>
</span><span id="L-120"><a href="#L-120"><span class="linenos">120</span></a> <span class="k">if</span> <span class="n">gz</span> <span class="ow">is</span> <span class="kc">True</span><span class="p">:</span> </span><span id="L-120"><a href="#L-120"><span class="linenos">120</span></a> <span class="n">fname</span> <span class="o">+=</span> <span class="s1">&#39;.csv&#39;</span>
</span><span id="L-121"><a href="#L-121"><span class="linenos">121</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">fname</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s1">&#39;.gz&#39;</span><span class="p">):</span> </span><span id="L-121"><a href="#L-121"><span class="linenos">121</span></a>
</span><span id="L-122"><a href="#L-122"><span class="linenos">122</span></a> <span class="n">fname</span> <span class="o">+=</span> <span class="s1">&#39;.gz&#39;</span> </span><span id="L-122"><a href="#L-122"><span class="linenos">122</span></a> <span class="k">if</span> <span class="n">gz</span> <span class="ow">is</span> <span class="kc">True</span><span class="p">:</span>
</span><span id="L-123"><a href="#L-123"><span class="linenos">123</span></a> <span class="k">with</span> <span class="n">gzip</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="n">fname</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span> </span><span id="L-123"><a href="#L-123"><span class="linenos">123</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">fname</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s1">&#39;.gz&#39;</span><span class="p">):</span>
</span><span id="L-124"><a href="#L-124"><span class="linenos">124</span></a> <span class="n">re_import</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">f</span><span class="p">,</span> <span class="n">keep_default_na</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span> </span><span id="L-124"><a href="#L-124"><span class="linenos">124</span></a> <span class="n">fname</span> <span class="o">+=</span> <span class="s1">&#39;.gz&#39;</span>
</span><span id="L-125"><a href="#L-125"><span class="linenos">125</span></a> <span class="k">else</span><span class="p">:</span> </span><span id="L-125"><a href="#L-125"><span class="linenos">125</span></a> <span class="k">with</span> <span class="n">gzip</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="n">fname</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
</span><span id="L-126"><a href="#L-126"><span class="linenos">126</span></a> <span class="k">if</span> <span class="n">fname</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s1">&#39;.gz&#39;</span><span class="p">):</span> </span><span id="L-126"><a href="#L-126"><span class="linenos">126</span></a> <span class="n">re_import</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">f</span><span class="p">,</span> <span class="n">keep_default_na</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
</span><span id="L-127"><a href="#L-127"><span class="linenos">127</span></a> <span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span><span class="s2">&quot;Trying to read from </span><span class="si">%s</span><span class="s2"> without unzipping!&quot;</span> <span class="o">%</span> <span class="n">fname</span><span class="p">,</span> <span class="ne">UserWarning</span><span class="p">)</span> </span><span id="L-127"><a href="#L-127"><span class="linenos">127</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="L-128"><a href="#L-128"><span class="linenos">128</span></a> <span class="n">re_import</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">fname</span><span class="p">,</span> <span class="n">keep_default_na</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span> </span><span id="L-128"><a href="#L-128"><span class="linenos">128</span></a> <span class="k">if</span> <span class="n">fname</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s1">&#39;.gz&#39;</span><span class="p">):</span>
</span><span id="L-129"><a href="#L-129"><span class="linenos">129</span></a> </span><span id="L-129"><a href="#L-129"><span class="linenos">129</span></a> <span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Trying to read from </span><span class="si">{</span><span class="n">fname</span><span class="si">}</span><span class="s2"> without unzipping!&quot;</span><span class="p">,</span> <span class="ne">UserWarning</span><span class="p">,</span> <span class="n">stacklevel</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span>
</span><span id="L-130"><a href="#L-130"><span class="linenos">130</span></a> <span class="k">return</span> <span class="n">_deserialize_df</span><span class="p">(</span><span class="n">re_import</span><span class="p">,</span> <span class="n">auto_gamma</span><span class="o">=</span><span class="n">auto_gamma</span><span class="p">)</span> </span><span id="L-130"><a href="#L-130"><span class="linenos">130</span></a> <span class="n">re_import</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">fname</span><span class="p">,</span> <span class="n">keep_default_na</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
</span><span id="L-131"><a href="#L-131"><span class="linenos">131</span></a> </span><span id="L-131"><a href="#L-131"><span class="linenos">131</span></a>
</span><span id="L-132"><a href="#L-132"><span class="linenos">132</span></a> </span><span id="L-132"><a href="#L-132"><span class="linenos">132</span></a> <span class="k">return</span> <span class="n">_deserialize_df</span><span class="p">(</span><span class="n">re_import</span><span class="p">,</span> <span class="n">auto_gamma</span><span class="o">=</span><span class="n">auto_gamma</span><span class="p">)</span>
</span><span id="L-133"><a href="#L-133"><span class="linenos">133</span></a><span class="k">def</span><span class="w"> </span><span class="nf">_serialize_df</span><span class="p">(</span><span class="n">df</span><span class="p">,</span> <span class="n">gz</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span> </span><span id="L-133"><a href="#L-133"><span class="linenos">133</span></a>
</span><span id="L-134"><a href="#L-134"><span class="linenos">134</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Serializes all Obs or Corr valued columns into json strings according to the pyerrors json specification.</span> </span><span id="L-134"><a href="#L-134"><span class="linenos">134</span></a>
</span><span id="L-135"><a href="#L-135"><span class="linenos">135</span></a> </span><span id="L-135"><a href="#L-135"><span class="linenos">135</span></a><span class="k">def</span><span class="w"> </span><span class="nf">_serialize_df</span><span class="p">(</span><span class="n">df</span><span class="p">,</span> <span class="n">gz</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
</span><span id="L-136"><a href="#L-136"><span class="linenos">136</span></a><span class="sd"> Parameters</span> </span><span id="L-136"><a href="#L-136"><span class="linenos">136</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Serializes all Obs or Corr valued columns into json strings according to the pyerrors json specification.</span>
</span><span id="L-137"><a href="#L-137"><span class="linenos">137</span></a><span class="sd"> ----------</span> </span><span id="L-137"><a href="#L-137"><span class="linenos">137</span></a>
</span><span id="L-138"><a href="#L-138"><span class="linenos">138</span></a><span class="sd"> df : pandas.DataFrame</span> </span><span id="L-138"><a href="#L-138"><span class="linenos">138</span></a><span class="sd"> Parameters</span>
</span><span id="L-139"><a href="#L-139"><span class="linenos">139</span></a><span class="sd"> DataFrame to be serilized.</span> </span><span id="L-139"><a href="#L-139"><span class="linenos">139</span></a><span class="sd"> ----------</span>
</span><span id="L-140"><a href="#L-140"><span class="linenos">140</span></a><span class="sd"> gz: bool</span> </span><span id="L-140"><a href="#L-140"><span class="linenos">140</span></a><span class="sd"> df : pandas.DataFrame</span>
</span><span id="L-141"><a href="#L-141"><span class="linenos">141</span></a><span class="sd"> gzip the json string representation. Default False.</span> </span><span id="L-141"><a href="#L-141"><span class="linenos">141</span></a><span class="sd"> DataFrame to be serilized.</span>
</span><span id="L-142"><a href="#L-142"><span class="linenos">142</span></a><span class="sd"> &quot;&quot;&quot;</span> </span><span id="L-142"><a href="#L-142"><span class="linenos">142</span></a><span class="sd"> gz: bool</span>
</span><span id="L-143"><a href="#L-143"><span class="linenos">143</span></a> <span class="n">out</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span> </span><span id="L-143"><a href="#L-143"><span class="linenos">143</span></a><span class="sd"> gzip the json string representation. Default False.</span>
</span><span id="L-144"><a href="#L-144"><span class="linenos">144</span></a> <span class="k">for</span> <span class="n">column</span> <span class="ow">in</span> <span class="n">out</span><span class="p">:</span> </span><span id="L-144"><a href="#L-144"><span class="linenos">144</span></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="L-145"><a href="#L-145"><span class="linenos">145</span></a> <span class="n">serialize</span> <span class="o">=</span> <span class="n">_need_to_serialize</span><span class="p">(</span><span class="n">out</span><span class="p">[</span><span class="n">column</span><span class="p">])</span> </span><span id="L-145"><a href="#L-145"><span class="linenos">145</span></a> <span class="n">out</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
</span><span id="L-146"><a href="#L-146"><span class="linenos">146</span></a> </span><span id="L-146"><a href="#L-146"><span class="linenos">146</span></a> <span class="k">for</span> <span class="n">column</span> <span class="ow">in</span> <span class="n">out</span><span class="p">:</span>
</span><span id="L-147"><a href="#L-147"><span class="linenos">147</span></a> <span class="k">if</span> <span class="n">serialize</span> <span class="ow">is</span> <span class="kc">True</span><span class="p">:</span> </span><span id="L-147"><a href="#L-147"><span class="linenos">147</span></a> <span class="n">serialize</span> <span class="o">=</span> <span class="n">_need_to_serialize</span><span class="p">(</span><span class="n">out</span><span class="p">[</span><span class="n">column</span><span class="p">])</span>
</span><span id="L-148"><a href="#L-148"><span class="linenos">148</span></a> <span class="n">out</span><span class="p">[</span><span class="n">column</span><span class="p">]</span> <span class="o">=</span> <span class="n">out</span><span class="p">[</span><span class="n">column</span><span class="p">]</span><span class="o">.</span><span class="n">transform</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">create_json_string</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">indent</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">_is_null</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">else</span> <span class="kc">None</span><span class="p">)</span> </span><span id="L-148"><a href="#L-148"><span class="linenos">148</span></a>
</span><span id="L-149"><a href="#L-149"><span class="linenos">149</span></a> <span class="k">if</span> <span class="n">gz</span> <span class="ow">is</span> <span class="kc">True</span><span class="p">:</span> </span><span id="L-149"><a href="#L-149"><span class="linenos">149</span></a> <span class="k">if</span> <span class="n">serialize</span> <span class="ow">is</span> <span class="kc">True</span><span class="p">:</span>
</span><span id="L-150"><a href="#L-150"><span class="linenos">150</span></a> <span class="n">out</span><span class="p">[</span><span class="n">column</span><span class="p">]</span> <span class="o">=</span> <span class="n">out</span><span class="p">[</span><span class="n">column</span><span class="p">]</span><span class="o">.</span><span class="n">transform</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">gzip</span><span class="o">.</span><span class="n">compress</span><span class="p">(</span><span class="n">x</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">))</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">_is_null</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">else</span> <span class="n">gzip</span><span class="o">.</span><span class="n">compress</span><span class="p">(</span><span class="sa">b</span><span class="s1">&#39;&#39;</span><span class="p">))</span> </span><span id="L-150"><a href="#L-150"><span class="linenos">150</span></a> <span class="n">out</span><span class="p">[</span><span class="n">column</span><span class="p">]</span> <span class="o">=</span> <span class="n">out</span><span class="p">[</span><span class="n">column</span><span class="p">]</span><span class="o">.</span><span class="n">transform</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">create_json_string</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">indent</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">_is_null</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">else</span> <span class="kc">None</span><span class="p">)</span>
</span><span id="L-151"><a href="#L-151"><span class="linenos">151</span></a> <span class="k">return</span> <span class="n">out</span> </span><span id="L-151"><a href="#L-151"><span class="linenos">151</span></a> <span class="k">if</span> <span class="n">gz</span> <span class="ow">is</span> <span class="kc">True</span><span class="p">:</span>
</span><span id="L-152"><a href="#L-152"><span class="linenos">152</span></a> </span><span id="L-152"><a href="#L-152"><span class="linenos">152</span></a> <span class="n">out</span><span class="p">[</span><span class="n">column</span><span class="p">]</span> <span class="o">=</span> <span class="n">out</span><span class="p">[</span><span class="n">column</span><span class="p">]</span><span class="o">.</span><span class="n">transform</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">gzip</span><span class="o">.</span><span class="n">compress</span><span class="p">(</span><span class="n">x</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">))</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">_is_null</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">else</span> <span class="n">gzip</span><span class="o">.</span><span class="n">compress</span><span class="p">(</span><span class="sa">b</span><span class="s1">&#39;&#39;</span><span class="p">))</span>
</span><span id="L-153"><a href="#L-153"><span class="linenos">153</span></a> </span><span id="L-153"><a href="#L-153"><span class="linenos">153</span></a> <span class="k">return</span> <span class="n">out</span>
</span><span id="L-154"><a href="#L-154"><span class="linenos">154</span></a><span class="k">def</span><span class="w"> </span><span class="nf">_deserialize_df</span><span class="p">(</span><span class="n">df</span><span class="p">,</span> <span class="n">auto_gamma</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span> </span><span id="L-154"><a href="#L-154"><span class="linenos">154</span></a>
</span><span id="L-155"><a href="#L-155"><span class="linenos">155</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Deserializes all pyerrors json strings into Obs or Corr objects according to the pyerrors json specification.</span> </span><span id="L-155"><a href="#L-155"><span class="linenos">155</span></a>
</span><span id="L-156"><a href="#L-156"><span class="linenos">156</span></a> </span><span id="L-156"><a href="#L-156"><span class="linenos">156</span></a><span class="k">def</span><span class="w"> </span><span class="nf">_deserialize_df</span><span class="p">(</span><span class="n">df</span><span class="p">,</span> <span class="n">auto_gamma</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
</span><span id="L-157"><a href="#L-157"><span class="linenos">157</span></a><span class="sd"> Parameters</span> </span><span id="L-157"><a href="#L-157"><span class="linenos">157</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Deserializes all pyerrors json strings into Obs or Corr objects according to the pyerrors json specification.</span>
</span><span id="L-158"><a href="#L-158"><span class="linenos">158</span></a><span class="sd"> ----------</span> </span><span id="L-158"><a href="#L-158"><span class="linenos">158</span></a>
</span><span id="L-159"><a href="#L-159"><span class="linenos">159</span></a><span class="sd"> df : pandas.DataFrame</span> </span><span id="L-159"><a href="#L-159"><span class="linenos">159</span></a><span class="sd"> Parameters</span>
</span><span id="L-160"><a href="#L-160"><span class="linenos">160</span></a><span class="sd"> DataFrame to be deserilized.</span> </span><span id="L-160"><a href="#L-160"><span class="linenos">160</span></a><span class="sd"> ----------</span>
</span><span id="L-161"><a href="#L-161"><span class="linenos">161</span></a><span class="sd"> auto_gamma : bool</span> </span><span id="L-161"><a href="#L-161"><span class="linenos">161</span></a><span class="sd"> df : pandas.DataFrame</span>
</span><span id="L-162"><a href="#L-162"><span class="linenos">162</span></a><span class="sd"> If True applies the gamma_method to all imported Obs objects with the default parameters for</span> </span><span id="L-162"><a href="#L-162"><span class="linenos">162</span></a><span class="sd"> DataFrame to be deserilized.</span>
</span><span id="L-163"><a href="#L-163"><span class="linenos">163</span></a><span class="sd"> the error analysis. Default False.</span> </span><span id="L-163"><a href="#L-163"><span class="linenos">163</span></a><span class="sd"> auto_gamma : bool</span>
</span><span id="L-164"><a href="#L-164"><span class="linenos">164</span></a> </span><span id="L-164"><a href="#L-164"><span class="linenos">164</span></a><span class="sd"> If True applies the gamma_method to all imported Obs objects with the default parameters for</span>
</span><span id="L-165"><a href="#L-165"><span class="linenos">165</span></a><span class="sd"> Notes:</span> </span><span id="L-165"><a href="#L-165"><span class="linenos">165</span></a><span class="sd"> the error analysis. Default False.</span>
</span><span id="L-166"><a href="#L-166"><span class="linenos">166</span></a><span class="sd"> ------</span> </span><span id="L-166"><a href="#L-166"><span class="linenos">166</span></a>
</span><span id="L-167"><a href="#L-167"><span class="linenos">167</span></a><span class="sd"> In case any column of the DataFrame is gzipped it is gunzipped in the process.</span> </span><span id="L-167"><a href="#L-167"><span class="linenos">167</span></a><span class="sd"> Notes:</span>
</span><span id="L-168"><a href="#L-168"><span class="linenos">168</span></a><span class="sd"> &quot;&quot;&quot;</span> </span><span id="L-168"><a href="#L-168"><span class="linenos">168</span></a><span class="sd"> ------</span>
</span><span id="L-169"><a href="#L-169"><span class="linenos">169</span></a> <span class="c1"># In pandas 3+, string columns use &#39;str&#39; dtype instead of &#39;object&#39;</span> </span><span id="L-169"><a href="#L-169"><span class="linenos">169</span></a><span class="sd"> In case any column of the DataFrame is gzipped it is gunzipped in the process.</span>
</span><span id="L-170"><a href="#L-170"><span class="linenos">170</span></a> <span class="n">string_like_dtypes</span> <span class="o">=</span> <span class="p">[</span><span class="s2">&quot;object&quot;</span><span class="p">,</span> <span class="s2">&quot;str&quot;</span><span class="p">]</span> <span class="k">if</span> <span class="nb">int</span><span class="p">(</span><span class="n">pd</span><span class="o">.</span><span class="n">__version__</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;.&quot;</span><span class="p">)[</span><span class="mi">0</span><span class="p">])</span> <span class="o">&gt;=</span> <span class="mi">3</span> <span class="k">else</span> <span class="p">[</span><span class="s2">&quot;object&quot;</span><span class="p">]</span> </span><span id="L-170"><a href="#L-170"><span class="linenos">170</span></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="L-171"><a href="#L-171"><span class="linenos">171</span></a> <span class="k">for</span> <span class="n">column</span> <span class="ow">in</span> <span class="n">df</span><span class="o">.</span><span class="n">select_dtypes</span><span class="p">(</span><span class="n">include</span><span class="o">=</span><span class="n">string_like_dtypes</span><span class="p">):</span> </span><span id="L-171"><a href="#L-171"><span class="linenos">171</span></a> <span class="c1"># In pandas 3+, string columns use &#39;str&#39; dtype instead of &#39;object&#39;</span>
</span><span id="L-172"><a href="#L-172"><span class="linenos">172</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">])</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span> </span><span id="L-172"><a href="#L-172"><span class="linenos">172</span></a> <span class="n">string_like_dtypes</span> <span class="o">=</span> <span class="p">[</span><span class="s2">&quot;object&quot;</span><span class="p">,</span> <span class="s2">&quot;str&quot;</span><span class="p">]</span> <span class="k">if</span> <span class="nb">int</span><span class="p">(</span><span class="n">pd</span><span class="o">.</span><span class="n">__version__</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;.&quot;</span><span class="p">)[</span><span class="mi">0</span><span class="p">])</span> <span class="o">&gt;=</span> <span class="mi">3</span> <span class="k">else</span> <span class="p">[</span><span class="s2">&quot;object&quot;</span><span class="p">]</span>
</span><span id="L-173"><a href="#L-173"><span class="linenos">173</span></a> <span class="k">continue</span> </span><span id="L-173"><a href="#L-173"><span class="linenos">173</span></a> <span class="k">for</span> <span class="n">column</span> <span class="ow">in</span> <span class="n">df</span><span class="o">.</span><span class="n">select_dtypes</span><span class="p">(</span><span class="n">include</span><span class="o">=</span><span class="n">string_like_dtypes</span><span class="p">):</span>
</span><span id="L-174"><a href="#L-174"><span class="linenos">174</span></a> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]</span><span class="o">.</span><span class="n">iloc</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="nb">bytes</span><span class="p">):</span> </span><span id="L-174"><a href="#L-174"><span class="linenos">174</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">])</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
</span><span id="L-175"><a href="#L-175"><span class="linenos">175</span></a> <span class="k">if</span> <span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]</span><span class="o">.</span><span class="n">iloc</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="sa">b</span><span class="s2">&quot;</span><span class="se">\x1f\x8b\x08\x00</span><span class="s2">&quot;</span><span class="p">):</span> </span><span id="L-175"><a href="#L-175"><span class="linenos">175</span></a> <span class="k">continue</span>
</span><span id="L-176"><a href="#L-176"><span class="linenos">176</span></a> <span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]</span><span class="o">.</span><span class="n">transform</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">gzip</span><span class="o">.</span><span class="n">decompress</span><span class="p">(</span><span class="n">x</span><span class="p">)</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">pd</span><span class="o">.</span><span class="n">isna</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">)</span> </span><span id="L-176"><a href="#L-176"><span class="linenos">176</span></a> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]</span><span class="o">.</span><span class="n">iloc</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="nb">bytes</span><span class="p">):</span>
</span><span id="L-177"><a href="#L-177"><span class="linenos">177</span></a> </span><span id="L-177"><a href="#L-177"><span class="linenos">177</span></a> <span class="k">if</span> <span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]</span><span class="o">.</span><span class="n">iloc</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="sa">b</span><span class="s2">&quot;</span><span class="se">\x1f\x8b\x08\x00</span><span class="s2">&quot;</span><span class="p">):</span>
</span><span id="L-178"><a href="#L-178"><span class="linenos">178</span></a> <span class="k">if</span> <span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]</span><span class="o">.</span><span class="n">notna</span><span class="p">()</span><span class="o">.</span><span class="n">any</span><span class="p">():</span> </span><span id="L-178"><a href="#L-178"><span class="linenos">178</span></a> <span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]</span><span class="o">.</span><span class="n">transform</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">gzip</span><span class="o">.</span><span class="n">decompress</span><span class="p">(</span><span class="n">x</span><span class="p">)</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">pd</span><span class="o">.</span><span class="n">isna</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">)</span>
</span><span id="L-179"><a href="#L-179"><span class="linenos">179</span></a> <span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">({</span><span class="sa">r</span><span class="s1">&#39;^$&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">},</span> <span class="n">regex</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span> </span><span id="L-179"><a href="#L-179"><span class="linenos">179</span></a>
</span><span id="L-180"><a href="#L-180"><span class="linenos">180</span></a> <span class="n">i</span> <span class="o">=</span> <span class="mi">0</span> </span><span id="L-180"><a href="#L-180"><span class="linenos">180</span></a> <span class="k">if</span> <span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]</span><span class="o">.</span><span class="n">notna</span><span class="p">()</span><span class="o">.</span><span class="n">any</span><span class="p">():</span>
</span><span id="L-181"><a href="#L-181"><span class="linenos">181</span></a> <span class="k">while</span> <span class="n">i</span> <span class="o">&lt;</span> <span class="nb">len</span><span class="p">(</span><span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">])</span> <span class="ow">and</span> <span class="n">pd</span><span class="o">.</span><span class="n">isna</span><span class="p">(</span><span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]</span><span class="o">.</span><span class="n">iloc</span><span class="p">[</span><span class="n">i</span><span class="p">]):</span> </span><span id="L-181"><a href="#L-181"><span class="linenos">181</span></a> <span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">({</span><span class="sa">r</span><span class="s1">&#39;^$&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">},</span> <span class="n">regex</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
</span><span id="L-182"><a href="#L-182"><span class="linenos">182</span></a> <span class="n">i</span> <span class="o">+=</span> <span class="mi">1</span> </span><span id="L-182"><a href="#L-182"><span class="linenos">182</span></a> <span class="n">i</span> <span class="o">=</span> <span class="mi">0</span>
</span><span id="L-183"><a href="#L-183"><span class="linenos">183</span></a> <span class="k">if</span> <span class="n">i</span> <span class="o">&lt;</span> <span class="nb">len</span><span class="p">(</span><span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">])</span> <span class="ow">and</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]</span><span class="o">.</span><span class="n">iloc</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="nb">str</span><span class="p">):</span> </span><span id="L-183"><a href="#L-183"><span class="linenos">183</span></a> <span class="k">while</span> <span class="n">i</span> <span class="o">&lt;</span> <span class="nb">len</span><span class="p">(</span><span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">])</span> <span class="ow">and</span> <span class="n">pd</span><span class="o">.</span><span class="n">isna</span><span class="p">(</span><span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]</span><span class="o">.</span><span class="n">iloc</span><span class="p">[</span><span class="n">i</span><span class="p">]):</span>
</span><span id="L-184"><a href="#L-184"><span class="linenos">184</span></a> <span class="k">if</span> <span class="s1">&#39;&quot;program&quot;:&#39;</span> <span class="ow">in</span> <span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]</span><span class="o">.</span><span class="n">iloc</span><span class="p">[</span><span class="n">i</span><span class="p">][:</span><span class="mi">20</span><span class="p">]:</span> </span><span id="L-184"><a href="#L-184"><span class="linenos">184</span></a> <span class="n">i</span> <span class="o">+=</span> <span class="mi">1</span>
</span><span id="L-185"><a href="#L-185"><span class="linenos">185</span></a> <span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]</span><span class="o">.</span><span class="n">transform</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">import_json_string</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">verbose</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">pd</span><span class="o">.</span><span class="n">isna</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">else</span> <span class="kc">None</span><span class="p">)</span> </span><span id="L-185"><a href="#L-185"><span class="linenos">185</span></a> <span class="k">if</span> <span class="n">i</span> <span class="o">&lt;</span> <span class="nb">len</span><span class="p">(</span><span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">])</span> <span class="ow">and</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]</span><span class="o">.</span><span class="n">iloc</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="nb">str</span><span class="p">):</span>
</span><span id="L-186"><a href="#L-186"><span class="linenos">186</span></a> <span class="k">if</span> <span class="n">auto_gamma</span> <span class="ow">is</span> <span class="kc">True</span><span class="p">:</span> </span><span id="L-186"><a href="#L-186"><span class="linenos">186</span></a> <span class="k">if</span> <span class="s1">&#39;&quot;program&quot;:&#39;</span> <span class="ow">in</span> <span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]</span><span class="o">.</span><span class="n">iloc</span><span class="p">[</span><span class="n">i</span><span class="p">][:</span><span class="mi">20</span><span class="p">]:</span>
</span><span id="L-187"><a href="#L-187"><span class="linenos">187</span></a> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]</span><span class="o">.</span><span class="n">iloc</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="nb">list</span><span class="p">):</span> </span><span id="L-187"><a href="#L-187"><span class="linenos">187</span></a> <span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]</span><span class="o">.</span><span class="n">transform</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">import_json_string</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">verbose</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">pd</span><span class="o">.</span><span class="n">isna</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">else</span> <span class="kc">None</span><span class="p">)</span>
</span><span id="L-188"><a href="#L-188"><span class="linenos">188</span></a> <span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]</span><span class="o">.</span><span class="n">apply</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="p">[</span><span class="n">o</span><span class="o">.</span><span class="n">gm</span><span class="p">()</span> <span class="k">if</span> <span class="n">o</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="k">else</span> <span class="n">x</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">x</span><span class="p">]</span> <span class="k">if</span> <span class="n">x</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="k">else</span> <span class="n">x</span><span class="p">)</span> </span><span id="L-188"><a href="#L-188"><span class="linenos">188</span></a> <span class="k">if</span> <span class="n">auto_gamma</span> <span class="ow">is</span> <span class="kc">True</span><span class="p">:</span>
</span><span id="L-189"><a href="#L-189"><span class="linenos">189</span></a> <span class="k">else</span><span class="p">:</span> </span><span id="L-189"><a href="#L-189"><span class="linenos">189</span></a> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]</span><span class="o">.</span><span class="n">iloc</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="nb">list</span><span class="p">):</span>
</span><span id="L-190"><a href="#L-190"><span class="linenos">190</span></a> <span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]</span><span class="o">.</span><span class="n">apply</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span><span class="o">.</span><span class="n">gm</span><span class="p">()</span> <span class="k">if</span> <span class="n">x</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="k">else</span> <span class="n">x</span><span class="p">)</span> </span><span id="L-190"><a href="#L-190"><span class="linenos">190</span></a> <span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]</span><span class="o">.</span><span class="n">apply</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="p">[</span><span class="n">o</span><span class="o">.</span><span class="n">gm</span><span class="p">()</span> <span class="k">if</span> <span class="n">o</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="k">else</span> <span class="n">x</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">x</span><span class="p">]</span> <span class="k">if</span> <span class="n">x</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="k">else</span> <span class="n">x</span><span class="p">)</span>
</span><span id="L-191"><a href="#L-191"><span class="linenos">191</span></a> <span class="c1"># Convert NA values back to Python None for compatibility with `x is None` checks</span> </span><span id="L-191"><a href="#L-191"><span class="linenos">191</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="L-192"><a href="#L-192"><span class="linenos">192</span></a> <span class="k">if</span> <span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]</span><span class="o">.</span><span class="n">isna</span><span class="p">()</span><span class="o">.</span><span class="n">any</span><span class="p">():</span> </span><span id="L-192"><a href="#L-192"><span class="linenos">192</span></a> <span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]</span><span class="o">.</span><span class="n">apply</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span><span class="o">.</span><span class="n">gm</span><span class="p">()</span> <span class="k">if</span> <span class="n">x</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="k">else</span> <span class="n">x</span><span class="p">)</span>
</span><span id="L-193"><a href="#L-193"><span class="linenos">193</span></a> <span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">object</span><span class="p">)</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]</span><span class="o">.</span><span class="n">notna</span><span class="p">(),</span> <span class="kc">None</span><span class="p">)</span> </span><span id="L-193"><a href="#L-193"><span class="linenos">193</span></a> <span class="c1"># Convert NA values back to Python None for compatibility with `x is None` checks</span>
</span><span id="L-194"><a href="#L-194"><span class="linenos">194</span></a> <span class="k">return</span> <span class="n">df</span> </span><span id="L-194"><a href="#L-194"><span class="linenos">194</span></a> <span class="k">if</span> <span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]</span><span class="o">.</span><span class="n">isna</span><span class="p">()</span><span class="o">.</span><span class="n">any</span><span class="p">():</span>
</span><span id="L-195"><a href="#L-195"><span class="linenos">195</span></a> </span><span id="L-195"><a href="#L-195"><span class="linenos">195</span></a> <span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">object</span><span class="p">)</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]</span><span class="o">.</span><span class="n">notna</span><span class="p">(),</span> <span class="kc">None</span><span class="p">)</span>
</span><span id="L-196"><a href="#L-196"><span class="linenos">196</span></a> </span><span id="L-196"><a href="#L-196"><span class="linenos">196</span></a> <span class="k">return</span> <span class="n">df</span>
</span><span id="L-197"><a href="#L-197"><span class="linenos">197</span></a><span class="k">def</span><span class="w"> </span><span class="nf">_need_to_serialize</span><span class="p">(</span><span class="n">col</span><span class="p">):</span> </span><span id="L-197"><a href="#L-197"><span class="linenos">197</span></a>
</span><span id="L-198"><a href="#L-198"><span class="linenos">198</span></a> <span class="n">serialize</span> <span class="o">=</span> <span class="kc">False</span> </span><span id="L-198"><a href="#L-198"><span class="linenos">198</span></a>
</span><span id="L-199"><a href="#L-199"><span class="linenos">199</span></a> <span class="n">i</span> <span class="o">=</span> <span class="mi">0</span> </span><span id="L-199"><a href="#L-199"><span class="linenos">199</span></a><span class="k">def</span><span class="w"> </span><span class="nf">_need_to_serialize</span><span class="p">(</span><span class="n">col</span><span class="p">):</span>
</span><span id="L-200"><a href="#L-200"><span class="linenos">200</span></a> <span class="k">while</span> <span class="n">i</span> <span class="o">&lt;</span> <span class="nb">len</span><span class="p">(</span><span class="n">col</span><span class="p">)</span> <span class="ow">and</span> <span class="n">_is_null</span><span class="p">(</span><span class="n">col</span><span class="o">.</span><span class="n">iloc</span><span class="p">[</span><span class="n">i</span><span class="p">]):</span> </span><span id="L-200"><a href="#L-200"><span class="linenos">200</span></a> <span class="n">serialize</span> <span class="o">=</span> <span class="kc">False</span>
</span><span id="L-201"><a href="#L-201"><span class="linenos">201</span></a> <span class="n">i</span> <span class="o">+=</span> <span class="mi">1</span> </span><span id="L-201"><a href="#L-201"><span class="linenos">201</span></a> <span class="n">i</span> <span class="o">=</span> <span class="mi">0</span>
</span><span id="L-202"><a href="#L-202"><span class="linenos">202</span></a> <span class="k">if</span> <span class="n">i</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="n">col</span><span class="p">):</span> </span><span id="L-202"><a href="#L-202"><span class="linenos">202</span></a> <span class="k">while</span> <span class="n">i</span> <span class="o">&lt;</span> <span class="nb">len</span><span class="p">(</span><span class="n">col</span><span class="p">)</span> <span class="ow">and</span> <span class="n">_is_null</span><span class="p">(</span><span class="n">col</span><span class="o">.</span><span class="n">iloc</span><span class="p">[</span><span class="n">i</span><span class="p">]):</span>
</span><span id="L-203"><a href="#L-203"><span class="linenos">203</span></a> <span class="k">return</span> <span class="n">serialize</span> </span><span id="L-203"><a href="#L-203"><span class="linenos">203</span></a> <span class="n">i</span> <span class="o">+=</span> <span class="mi">1</span>
</span><span id="L-204"><a href="#L-204"><span class="linenos">204</span></a> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">col</span><span class="o">.</span><span class="n">iloc</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="p">(</span><span class="n">Obs</span><span class="p">,</span> <span class="n">Corr</span><span class="p">)):</span> </span><span id="L-204"><a href="#L-204"><span class="linenos">204</span></a> <span class="k">if</span> <span class="n">i</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="n">col</span><span class="p">):</span>
</span><span id="L-205"><a href="#L-205"><span class="linenos">205</span></a> <span class="n">serialize</span> <span class="o">=</span> <span class="kc">True</span> </span><span id="L-205"><a href="#L-205"><span class="linenos">205</span></a> <span class="k">return</span> <span class="n">serialize</span>
</span><span id="L-206"><a href="#L-206"><span class="linenos">206</span></a> <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">col</span><span class="o">.</span><span class="n">iloc</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="nb">list</span><span class="p">):</span> </span><span id="L-206"><a href="#L-206"><span class="linenos">206</span></a> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">col</span><span class="o">.</span><span class="n">iloc</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="p">(</span><span class="n">Obs</span><span class="p">,</span> <span class="n">Corr</span><span class="p">)):</span>
</span><span id="L-207"><a href="#L-207"><span class="linenos">207</span></a> <span class="k">if</span> <span class="nb">all</span><span class="p">(</span><span class="nb">isinstance</span><span class="p">(</span><span class="n">o</span><span class="p">,</span> <span class="n">Obs</span><span class="p">)</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">col</span><span class="o">.</span><span class="n">iloc</span><span class="p">[</span><span class="n">i</span><span class="p">]):</span> </span><span id="L-207"><a href="#L-207"><span class="linenos">207</span></a> <span class="n">serialize</span> <span class="o">=</span> <span class="kc">True</span>
</span><span id="L-208"><a href="#L-208"><span class="linenos">208</span></a> <span class="n">serialize</span> <span class="o">=</span> <span class="kc">True</span> </span><span id="L-208"><a href="#L-208"><span class="linenos">208</span></a> <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">col</span><span class="o">.</span><span class="n">iloc</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="nb">list</span><span class="p">):</span>
</span><span id="L-209"><a href="#L-209"><span class="linenos">209</span></a> <span class="k">return</span> <span class="n">serialize</span> </span><span id="L-209"><a href="#L-209"><span class="linenos">209</span></a> <span class="k">if</span> <span class="nb">all</span><span class="p">(</span><span class="nb">isinstance</span><span class="p">(</span><span class="n">o</span><span class="p">,</span> <span class="n">Obs</span><span class="p">)</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">col</span><span class="o">.</span><span class="n">iloc</span><span class="p">[</span><span class="n">i</span><span class="p">]):</span>
</span><span id="L-210"><a href="#L-210"><span class="linenos">210</span></a> </span><span id="L-210"><a href="#L-210"><span class="linenos">210</span></a> <span class="n">serialize</span> <span class="o">=</span> <span class="kc">True</span>
</span><span id="L-211"><a href="#L-211"><span class="linenos">211</span></a> </span><span id="L-211"><a href="#L-211"><span class="linenos">211</span></a> <span class="k">return</span> <span class="n">serialize</span>
</span><span id="L-212"><a href="#L-212"><span class="linenos">212</span></a><span class="k">def</span><span class="w"> </span><span class="nf">_is_null</span><span class="p">(</span><span class="n">val</span><span class="p">):</span> </span><span id="L-212"><a href="#L-212"><span class="linenos">212</span></a>
</span><span id="L-213"><a href="#L-213"><span class="linenos">213</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Check if a value is null (None or NA), handling list/array values.&quot;&quot;&quot;</span> </span><span id="L-213"><a href="#L-213"><span class="linenos">213</span></a>
</span><span id="L-214"><a href="#L-214"><span class="linenos">214</span></a> <span class="k">return</span> <span class="kc">False</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">val</span><span class="p">,</span> <span class="p">(</span><span class="nb">list</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">))</span> <span class="k">else</span> <span class="n">pd</span><span class="o">.</span><span class="n">isna</span><span class="p">(</span><span class="n">val</span><span class="p">)</span> </span><span id="L-214"><a href="#L-214"><span class="linenos">214</span></a><span class="k">def</span><span class="w"> </span><span class="nf">_is_null</span><span class="p">(</span><span class="n">val</span><span class="p">):</span>
</span><span id="L-215"><a href="#L-215"><span class="linenos">215</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Check if a value is null (None or NA), handling list/array values.&quot;&quot;&quot;</span>
</span><span id="L-216"><a href="#L-216"><span class="linenos">216</span></a> <span class="k">return</span> <span class="kc">False</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">val</span><span class="p">,</span> <span class="p">(</span><span class="nb">list</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">))</span> <span class="k">else</span> <span class="n">pd</span><span class="o">.</span><span class="n">isna</span><span class="p">(</span><span class="n">val</span><span class="p">)</span>
</span></pre></div> </span></pre></div>
@ -314,29 +316,29 @@
</div> </div>
<a class="headerlink" href="#to_sql"></a> <a class="headerlink" href="#to_sql"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="to_sql-13"><a href="#to_sql-13"><span class="linenos">13</span></a><span class="k">def</span><span class="w"> </span><span class="nf">to_sql</span><span class="p">(</span><span class="n">df</span><span class="p">,</span> <span class="n">table_name</span><span class="p">,</span> <span class="n">db</span><span class="p">,</span> <span class="n">if_exists</span><span class="o">=</span><span class="s1">&#39;fail&#39;</span><span class="p">,</span> <span class="n">gz</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span> <div class="pdoc-code codehilite"><pre><span></span><span id="to_sql-15"><a href="#to_sql-15"><span class="linenos">15</span></a><span class="k">def</span><span class="w"> </span><span class="nf">to_sql</span><span class="p">(</span><span class="n">df</span><span class="p">,</span> <span class="n">table_name</span><span class="p">,</span> <span class="n">db</span><span class="p">,</span> <span class="n">if_exists</span><span class="o">=</span><span class="s1">&#39;fail&#39;</span><span class="p">,</span> <span class="n">gz</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
</span><span id="to_sql-14"><a href="#to_sql-14"><span class="linenos">14</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Write DataFrame including Obs or Corr valued columns to sqlite database.</span> </span><span id="to_sql-16"><a href="#to_sql-16"><span class="linenos">16</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Write DataFrame including Obs or Corr valued columns to sqlite database.</span>
</span><span id="to_sql-15"><a href="#to_sql-15"><span class="linenos">15</span></a> </span><span id="to_sql-17"><a href="#to_sql-17"><span class="linenos">17</span></a>
</span><span id="to_sql-16"><a href="#to_sql-16"><span class="linenos">16</span></a><span class="sd"> Parameters</span> </span><span id="to_sql-18"><a href="#to_sql-18"><span class="linenos">18</span></a><span class="sd"> Parameters</span>
</span><span id="to_sql-17"><a href="#to_sql-17"><span class="linenos">17</span></a><span class="sd"> ----------</span> </span><span id="to_sql-19"><a href="#to_sql-19"><span class="linenos">19</span></a><span class="sd"> ----------</span>
</span><span id="to_sql-18"><a href="#to_sql-18"><span class="linenos">18</span></a><span class="sd"> df : pandas.DataFrame</span> </span><span id="to_sql-20"><a href="#to_sql-20"><span class="linenos">20</span></a><span class="sd"> df : pandas.DataFrame</span>
</span><span id="to_sql-19"><a href="#to_sql-19"><span class="linenos">19</span></a><span class="sd"> Dataframe to be written to the database.</span> </span><span id="to_sql-21"><a href="#to_sql-21"><span class="linenos">21</span></a><span class="sd"> Dataframe to be written to the database.</span>
</span><span id="to_sql-20"><a href="#to_sql-20"><span class="linenos">20</span></a><span class="sd"> table_name : str</span> </span><span id="to_sql-22"><a href="#to_sql-22"><span class="linenos">22</span></a><span class="sd"> table_name : str</span>
</span><span id="to_sql-21"><a href="#to_sql-21"><span class="linenos">21</span></a><span class="sd"> Name of the table in the database.</span> </span><span id="to_sql-23"><a href="#to_sql-23"><span class="linenos">23</span></a><span class="sd"> Name of the table in the database.</span>
</span><span id="to_sql-22"><a href="#to_sql-22"><span class="linenos">22</span></a><span class="sd"> db : str</span> </span><span id="to_sql-24"><a href="#to_sql-24"><span class="linenos">24</span></a><span class="sd"> db : str</span>
</span><span id="to_sql-23"><a href="#to_sql-23"><span class="linenos">23</span></a><span class="sd"> Path to the sqlite database.</span> </span><span id="to_sql-25"><a href="#to_sql-25"><span class="linenos">25</span></a><span class="sd"> Path to the sqlite database.</span>
</span><span id="to_sql-24"><a href="#to_sql-24"><span class="linenos">24</span></a><span class="sd"> if exists : str</span> </span><span id="to_sql-26"><a href="#to_sql-26"><span class="linenos">26</span></a><span class="sd"> if exists : str</span>
</span><span id="to_sql-25"><a href="#to_sql-25"><span class="linenos">25</span></a><span class="sd"> How to behave if table already exists. Options &#39;fail&#39;, &#39;replace&#39;, &#39;append&#39;.</span> </span><span id="to_sql-27"><a href="#to_sql-27"><span class="linenos">27</span></a><span class="sd"> How to behave if table already exists. Options &#39;fail&#39;, &#39;replace&#39;, &#39;append&#39;.</span>
</span><span id="to_sql-26"><a href="#to_sql-26"><span class="linenos">26</span></a><span class="sd"> gz : bool</span> </span><span id="to_sql-28"><a href="#to_sql-28"><span class="linenos">28</span></a><span class="sd"> gz : bool</span>
</span><span id="to_sql-27"><a href="#to_sql-27"><span class="linenos">27</span></a><span class="sd"> If True the json strings are gzipped.</span> </span><span id="to_sql-29"><a href="#to_sql-29"><span class="linenos">29</span></a><span class="sd"> If True the json strings are gzipped.</span>
</span><span id="to_sql-28"><a href="#to_sql-28"><span class="linenos">28</span></a> </span><span id="to_sql-30"><a href="#to_sql-30"><span class="linenos">30</span></a>
</span><span id="to_sql-29"><a href="#to_sql-29"><span class="linenos">29</span></a><span class="sd"> Returns</span> </span><span id="to_sql-31"><a href="#to_sql-31"><span class="linenos">31</span></a><span class="sd"> Returns</span>
</span><span id="to_sql-30"><a href="#to_sql-30"><span class="linenos">30</span></a><span class="sd"> -------</span> </span><span id="to_sql-32"><a href="#to_sql-32"><span class="linenos">32</span></a><span class="sd"> -------</span>
</span><span id="to_sql-31"><a href="#to_sql-31"><span class="linenos">31</span></a><span class="sd"> None</span> </span><span id="to_sql-33"><a href="#to_sql-33"><span class="linenos">33</span></a><span class="sd"> None</span>
</span><span id="to_sql-32"><a href="#to_sql-32"><span class="linenos">32</span></a><span class="sd"> &quot;&quot;&quot;</span> </span><span id="to_sql-34"><a href="#to_sql-34"><span class="linenos">34</span></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="to_sql-33"><a href="#to_sql-33"><span class="linenos">33</span></a> <span class="n">se_df</span> <span class="o">=</span> <span class="n">_serialize_df</span><span class="p">(</span><span class="n">df</span><span class="p">,</span> <span class="n">gz</span><span class="o">=</span><span class="n">gz</span><span class="p">)</span> </span><span id="to_sql-35"><a href="#to_sql-35"><span class="linenos">35</span></a> <span class="n">se_df</span> <span class="o">=</span> <span class="n">_serialize_df</span><span class="p">(</span><span class="n">df</span><span class="p">,</span> <span class="n">gz</span><span class="o">=</span><span class="n">gz</span><span class="p">)</span>
</span><span id="to_sql-34"><a href="#to_sql-34"><span class="linenos">34</span></a> <span class="k">with</span> <span class="n">closing</span><span class="p">(</span><span class="n">sqlite3</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="n">db</span><span class="p">))</span> <span class="k">as</span> <span class="n">con</span><span class="p">:</span> </span><span id="to_sql-36"><a href="#to_sql-36"><span class="linenos">36</span></a> <span class="k">with</span> <span class="n">closing</span><span class="p">(</span><span class="n">sqlite3</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="n">db</span><span class="p">))</span> <span class="k">as</span> <span class="n">con</span><span class="p">:</span>
</span><span id="to_sql-35"><a href="#to_sql-35"><span class="linenos">35</span></a> <span class="n">se_df</span><span class="o">.</span><span class="n">to_sql</span><span class="p">(</span><span class="n">table_name</span><span class="p">,</span> <span class="n">con</span><span class="o">=</span><span class="n">con</span><span class="p">,</span> <span class="n">if_exists</span><span class="o">=</span><span class="n">if_exists</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span> </span><span id="to_sql-37"><a href="#to_sql-37"><span class="linenos">37</span></a> <span class="n">se_df</span><span class="o">.</span><span class="n">to_sql</span><span class="p">(</span><span class="n">table_name</span><span class="p">,</span> <span class="n">con</span><span class="o">=</span><span class="n">con</span><span class="p">,</span> <span class="n">if_exists</span><span class="o">=</span><span class="n">if_exists</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
</span></pre></div> </span></pre></div>
@ -377,27 +379,27 @@ If True the json strings are gzipped.</li>
</div> </div>
<a class="headerlink" href="#read_sql"></a> <a class="headerlink" href="#read_sql"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="read_sql-38"><a href="#read_sql-38"><span class="linenos">38</span></a><span class="k">def</span><span class="w"> </span><span class="nf">read_sql</span><span class="p">(</span><span class="n">sql</span><span class="p">,</span> <span class="n">db</span><span class="p">,</span> <span class="n">auto_gamma</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span> <div class="pdoc-code codehilite"><pre><span></span><span id="read_sql-40"><a href="#read_sql-40"><span class="linenos">40</span></a><span class="k">def</span><span class="w"> </span><span class="nf">read_sql</span><span class="p">(</span><span class="n">sql</span><span class="p">,</span> <span class="n">db</span><span class="p">,</span> <span class="n">auto_gamma</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
</span><span id="read_sql-39"><a href="#read_sql-39"><span class="linenos">39</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Execute SQL query on sqlite database and obtain DataFrame including Obs or Corr valued columns.</span> </span><span id="read_sql-41"><a href="#read_sql-41"><span class="linenos">41</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Execute SQL query on sqlite database and obtain DataFrame including Obs or Corr valued columns.</span>
</span><span id="read_sql-40"><a href="#read_sql-40"><span class="linenos">40</span></a> </span><span id="read_sql-42"><a href="#read_sql-42"><span class="linenos">42</span></a>
</span><span id="read_sql-41"><a href="#read_sql-41"><span class="linenos">41</span></a><span class="sd"> Parameters</span> </span><span id="read_sql-43"><a href="#read_sql-43"><span class="linenos">43</span></a><span class="sd"> Parameters</span>
</span><span id="read_sql-42"><a href="#read_sql-42"><span class="linenos">42</span></a><span class="sd"> ----------</span> </span><span id="read_sql-44"><a href="#read_sql-44"><span class="linenos">44</span></a><span class="sd"> ----------</span>
</span><span id="read_sql-43"><a href="#read_sql-43"><span class="linenos">43</span></a><span class="sd"> sql : str</span> </span><span id="read_sql-45"><a href="#read_sql-45"><span class="linenos">45</span></a><span class="sd"> sql : str</span>
</span><span id="read_sql-44"><a href="#read_sql-44"><span class="linenos">44</span></a><span class="sd"> SQL query to be executed.</span> </span><span id="read_sql-46"><a href="#read_sql-46"><span class="linenos">46</span></a><span class="sd"> SQL query to be executed.</span>
</span><span id="read_sql-45"><a href="#read_sql-45"><span class="linenos">45</span></a><span class="sd"> db : str</span> </span><span id="read_sql-47"><a href="#read_sql-47"><span class="linenos">47</span></a><span class="sd"> db : str</span>
</span><span id="read_sql-46"><a href="#read_sql-46"><span class="linenos">46</span></a><span class="sd"> Path to the sqlite database.</span> </span><span id="read_sql-48"><a href="#read_sql-48"><span class="linenos">48</span></a><span class="sd"> Path to the sqlite database.</span>
</span><span id="read_sql-47"><a href="#read_sql-47"><span class="linenos">47</span></a><span class="sd"> auto_gamma : bool</span> </span><span id="read_sql-49"><a href="#read_sql-49"><span class="linenos">49</span></a><span class="sd"> auto_gamma : bool</span>
</span><span id="read_sql-48"><a href="#read_sql-48"><span class="linenos">48</span></a><span class="sd"> If True applies the gamma_method to all imported Obs objects with the default parameters for</span> </span><span id="read_sql-50"><a href="#read_sql-50"><span class="linenos">50</span></a><span class="sd"> If True applies the gamma_method to all imported Obs objects with the default parameters for</span>
</span><span id="read_sql-49"><a href="#read_sql-49"><span class="linenos">49</span></a><span class="sd"> the error analysis. Default False.</span> </span><span id="read_sql-51"><a href="#read_sql-51"><span class="linenos">51</span></a><span class="sd"> the error analysis. Default False.</span>
</span><span id="read_sql-50"><a href="#read_sql-50"><span class="linenos">50</span></a> </span><span id="read_sql-52"><a href="#read_sql-52"><span class="linenos">52</span></a>
</span><span id="read_sql-51"><a href="#read_sql-51"><span class="linenos">51</span></a><span class="sd"> Returns</span> </span><span id="read_sql-53"><a href="#read_sql-53"><span class="linenos">53</span></a><span class="sd"> Returns</span>
</span><span id="read_sql-52"><a href="#read_sql-52"><span class="linenos">52</span></a><span class="sd"> -------</span> </span><span id="read_sql-54"><a href="#read_sql-54"><span class="linenos">54</span></a><span class="sd"> -------</span>
</span><span id="read_sql-53"><a href="#read_sql-53"><span class="linenos">53</span></a><span class="sd"> data : pandas.DataFrame</span> </span><span id="read_sql-55"><a href="#read_sql-55"><span class="linenos">55</span></a><span class="sd"> data : pandas.DataFrame</span>
</span><span id="read_sql-54"><a href="#read_sql-54"><span class="linenos">54</span></a><span class="sd"> Dataframe with the content of the sqlite database.</span> </span><span id="read_sql-56"><a href="#read_sql-56"><span class="linenos">56</span></a><span class="sd"> Dataframe with the content of the sqlite database.</span>
</span><span id="read_sql-55"><a href="#read_sql-55"><span class="linenos">55</span></a><span class="sd"> &quot;&quot;&quot;</span> </span><span id="read_sql-57"><a href="#read_sql-57"><span class="linenos">57</span></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="read_sql-56"><a href="#read_sql-56"><span class="linenos">56</span></a> <span class="k">with</span> <span class="n">closing</span><span class="p">(</span><span class="n">sqlite3</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="n">db</span><span class="p">))</span> <span class="k">as</span> <span class="n">con</span><span class="p">:</span> </span><span id="read_sql-58"><a href="#read_sql-58"><span class="linenos">58</span></a> <span class="k">with</span> <span class="n">closing</span><span class="p">(</span><span class="n">sqlite3</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="n">db</span><span class="p">))</span> <span class="k">as</span> <span class="n">con</span><span class="p">:</span>
</span><span id="read_sql-57"><a href="#read_sql-57"><span class="linenos">57</span></a> <span class="n">extract_df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_sql</span><span class="p">(</span><span class="n">sql</span><span class="p">,</span> <span class="n">con</span><span class="o">=</span><span class="n">con</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span> </span><span id="read_sql-59"><a href="#read_sql-59"><span class="linenos">59</span></a> <span class="n">extract_df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_sql</span><span class="p">(</span><span class="n">sql</span><span class="p">,</span> <span class="n">con</span><span class="o">=</span><span class="n">con</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
</span><span id="read_sql-58"><a href="#read_sql-58"><span class="linenos">58</span></a> <span class="k">return</span> <span class="n">_deserialize_df</span><span class="p">(</span><span class="n">extract_df</span><span class="p">,</span> <span class="n">auto_gamma</span><span class="o">=</span><span class="n">auto_gamma</span><span class="p">)</span> </span><span id="read_sql-60"><a href="#read_sql-60"><span class="linenos">60</span></a> <span class="k">return</span> <span class="n">_deserialize_df</span><span class="p">(</span><span class="n">extract_df</span><span class="p">,</span> <span class="n">auto_gamma</span><span class="o">=</span><span class="n">auto_gamma</span><span class="p">)</span>
</span></pre></div> </span></pre></div>
@ -436,43 +438,43 @@ Dataframe with the content of the sqlite database.</li>
</div> </div>
<a class="headerlink" href="#dump_df"></a> <a class="headerlink" href="#dump_df"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="dump_df-61"><a href="#dump_df-61"><span class="linenos">61</span></a><span class="k">def</span><span class="w"> </span><span class="nf">dump_df</span><span class="p">(</span><span class="n">df</span><span class="p">,</span> <span class="n">fname</span><span class="p">,</span> <span class="n">gz</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span> <div class="pdoc-code codehilite"><pre><span></span><span id="dump_df-63"><a href="#dump_df-63"><span class="linenos">63</span></a><span class="k">def</span><span class="w"> </span><span class="nf">dump_df</span><span class="p">(</span><span class="n">df</span><span class="p">,</span> <span class="n">fname</span><span class="p">,</span> <span class="n">gz</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
</span><span id="dump_df-62"><a href="#dump_df-62"><span class="linenos">62</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Exports a pandas DataFrame containing Obs valued columns to a (gzipped) csv file.</span> </span><span id="dump_df-64"><a href="#dump_df-64"><span class="linenos">64</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Exports a pandas DataFrame containing Obs valued columns to a (gzipped) csv file.</span>
</span><span id="dump_df-63"><a href="#dump_df-63"><span class="linenos">63</span></a> </span><span id="dump_df-65"><a href="#dump_df-65"><span class="linenos">65</span></a>
</span><span id="dump_df-64"><a href="#dump_df-64"><span class="linenos">64</span></a><span class="sd"> Before making use of pandas to_csv functionality Obs objects are serialized via the standardized</span> </span><span id="dump_df-66"><a href="#dump_df-66"><span class="linenos">66</span></a><span class="sd"> Before making use of pandas to_csv functionality Obs objects are serialized via the standardized</span>
</span><span id="dump_df-65"><a href="#dump_df-65"><span class="linenos">65</span></a><span class="sd"> json format of pyerrors.</span> </span><span id="dump_df-67"><a href="#dump_df-67"><span class="linenos">67</span></a><span class="sd"> json format of pyerrors.</span>
</span><span id="dump_df-66"><a href="#dump_df-66"><span class="linenos">66</span></a> </span><span id="dump_df-68"><a href="#dump_df-68"><span class="linenos">68</span></a>
</span><span id="dump_df-67"><a href="#dump_df-67"><span class="linenos">67</span></a><span class="sd"> Parameters</span> </span><span id="dump_df-69"><a href="#dump_df-69"><span class="linenos">69</span></a><span class="sd"> Parameters</span>
</span><span id="dump_df-68"><a href="#dump_df-68"><span class="linenos">68</span></a><span class="sd"> ----------</span> </span><span id="dump_df-70"><a href="#dump_df-70"><span class="linenos">70</span></a><span class="sd"> ----------</span>
</span><span id="dump_df-69"><a href="#dump_df-69"><span class="linenos">69</span></a><span class="sd"> df : pandas.DataFrame</span> </span><span id="dump_df-71"><a href="#dump_df-71"><span class="linenos">71</span></a><span class="sd"> df : pandas.DataFrame</span>
</span><span id="dump_df-70"><a href="#dump_df-70"><span class="linenos">70</span></a><span class="sd"> Dataframe to be dumped to a file.</span> </span><span id="dump_df-72"><a href="#dump_df-72"><span class="linenos">72</span></a><span class="sd"> Dataframe to be dumped to a file.</span>
</span><span id="dump_df-71"><a href="#dump_df-71"><span class="linenos">71</span></a><span class="sd"> fname : str</span> </span><span id="dump_df-73"><a href="#dump_df-73"><span class="linenos">73</span></a><span class="sd"> fname : str</span>
</span><span id="dump_df-72"><a href="#dump_df-72"><span class="linenos">72</span></a><span class="sd"> Filename of the output file.</span> </span><span id="dump_df-74"><a href="#dump_df-74"><span class="linenos">74</span></a><span class="sd"> Filename of the output file.</span>
</span><span id="dump_df-73"><a href="#dump_df-73"><span class="linenos">73</span></a><span class="sd"> gz : bool</span> </span><span id="dump_df-75"><a href="#dump_df-75"><span class="linenos">75</span></a><span class="sd"> gz : bool</span>
</span><span id="dump_df-74"><a href="#dump_df-74"><span class="linenos">74</span></a><span class="sd"> If True, the output is a gzipped csv file. If False, the output is a csv file.</span> </span><span id="dump_df-76"><a href="#dump_df-76"><span class="linenos">76</span></a><span class="sd"> If True, the output is a gzipped csv file. If False, the output is a csv file.</span>
</span><span id="dump_df-75"><a href="#dump_df-75"><span class="linenos">75</span></a> </span><span id="dump_df-77"><a href="#dump_df-77"><span class="linenos">77</span></a>
</span><span id="dump_df-76"><a href="#dump_df-76"><span class="linenos">76</span></a><span class="sd"> Returns</span> </span><span id="dump_df-78"><a href="#dump_df-78"><span class="linenos">78</span></a><span class="sd"> Returns</span>
</span><span id="dump_df-77"><a href="#dump_df-77"><span class="linenos">77</span></a><span class="sd"> -------</span> </span><span id="dump_df-79"><a href="#dump_df-79"><span class="linenos">79</span></a><span class="sd"> -------</span>
</span><span id="dump_df-78"><a href="#dump_df-78"><span class="linenos">78</span></a><span class="sd"> None</span> </span><span id="dump_df-80"><a href="#dump_df-80"><span class="linenos">80</span></a><span class="sd"> None</span>
</span><span id="dump_df-79"><a href="#dump_df-79"><span class="linenos">79</span></a><span class="sd"> &quot;&quot;&quot;</span> </span><span id="dump_df-81"><a href="#dump_df-81"><span class="linenos">81</span></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="dump_df-80"><a href="#dump_df-80"><span class="linenos">80</span></a> <span class="k">for</span> <span class="n">column</span> <span class="ow">in</span> <span class="n">df</span><span class="p">:</span> </span><span id="dump_df-82"><a href="#dump_df-82"><span class="linenos">82</span></a> <span class="k">for</span> <span class="n">column</span> <span class="ow">in</span> <span class="n">df</span><span class="p">:</span>
</span><span id="dump_df-81"><a href="#dump_df-81"><span class="linenos">81</span></a> <span class="n">serialize</span> <span class="o">=</span> <span class="n">_need_to_serialize</span><span class="p">(</span><span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">])</span> </span><span id="dump_df-83"><a href="#dump_df-83"><span class="linenos">83</span></a> <span class="n">serialize</span> <span class="o">=</span> <span class="n">_need_to_serialize</span><span class="p">(</span><span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">])</span>
</span><span id="dump_df-82"><a href="#dump_df-82"><span class="linenos">82</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">serialize</span><span class="p">:</span> </span><span id="dump_df-84"><a href="#dump_df-84"><span class="linenos">84</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">serialize</span><span class="p">:</span>
</span><span id="dump_df-83"><a href="#dump_df-83"><span class="linenos">83</span></a> <span class="k">if</span> <span class="nb">all</span><span class="p">(</span><span class="nb">isinstance</span><span class="p">(</span><span class="n">entry</span><span class="p">,</span> <span class="p">(</span><span class="nb">int</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">integer</span><span class="p">,</span> <span class="nb">float</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">floating</span><span class="p">))</span> <span class="k">for</span> <span class="n">entry</span> <span class="ow">in</span> <span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]):</span> </span><span id="dump_df-85"><a href="#dump_df-85"><span class="linenos">85</span></a> <span class="k">if</span> <span class="nb">all</span><span class="p">(</span><span class="nb">isinstance</span><span class="p">(</span><span class="n">entry</span><span class="p">,</span> <span class="p">(</span><span class="nb">int</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">integer</span><span class="p">,</span> <span class="nb">float</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">floating</span><span class="p">))</span> <span class="k">for</span> <span class="n">entry</span> <span class="ow">in</span> <span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]):</span>
</span><span id="dump_df-84"><a href="#dump_df-84"><span class="linenos">84</span></a> <span class="k">if</span> <span class="nb">any</span><span class="p">([</span><span class="n">np</span><span class="o">.</span><span class="n">isnan</span><span class="p">(</span><span class="n">entry</span><span class="p">)</span> <span class="k">for</span> <span class="n">entry</span> <span class="ow">in</span> <span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]]):</span> </span><span id="dump_df-86"><a href="#dump_df-86"><span class="linenos">86</span></a> <span class="k">if</span> <span class="nb">any</span><span class="p">([</span><span class="n">np</span><span class="o">.</span><span class="n">isnan</span><span class="p">(</span><span class="n">entry</span><span class="p">)</span> <span class="k">for</span> <span class="n">entry</span> <span class="ow">in</span> <span class="n">df</span><span class="p">[</span><span class="n">column</span><span class="p">]]):</span>
</span><span id="dump_df-85"><a href="#dump_df-85"><span class="linenos">85</span></a> <span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span><span class="s2">&quot;nan value in column &quot;</span> <span class="o">+</span> <span class="n">column</span> <span class="o">+</span> <span class="s2">&quot; will be replaced by None&quot;</span><span class="p">,</span> <span class="ne">UserWarning</span><span class="p">)</span> </span><span id="dump_df-87"><a href="#dump_df-87"><span class="linenos">87</span></a> <span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span><span class="s2">&quot;nan value in column &quot;</span> <span class="o">+</span> <span class="n">column</span> <span class="o">+</span> <span class="s2">&quot; will be replaced by None&quot;</span><span class="p">,</span> <span class="ne">UserWarning</span><span class="p">,</span> <span class="n">stacklevel</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span>
</span><span id="dump_df-86"><a href="#dump_df-86"><span class="linenos">86</span></a>
</span><span id="dump_df-87"><a href="#dump_df-87"><span class="linenos">87</span></a> <span class="n">out</span> <span class="o">=</span> <span class="n">_serialize_df</span><span class="p">(</span><span class="n">df</span><span class="p">,</span> <span class="n">gz</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
</span><span id="dump_df-88"><a href="#dump_df-88"><span class="linenos">88</span></a> </span><span id="dump_df-88"><a href="#dump_df-88"><span class="linenos">88</span></a>
</span><span id="dump_df-89"><a href="#dump_df-89"><span class="linenos">89</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">fname</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s1">&#39;.csv&#39;</span><span class="p">):</span> </span><span id="dump_df-89"><a href="#dump_df-89"><span class="linenos">89</span></a> <span class="n">out</span> <span class="o">=</span> <span class="n">_serialize_df</span><span class="p">(</span><span class="n">df</span><span class="p">,</span> <span class="n">gz</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
</span><span id="dump_df-90"><a href="#dump_df-90"><span class="linenos">90</span></a> <span class="n">fname</span> <span class="o">+=</span> <span class="s1">&#39;.csv&#39;</span> </span><span id="dump_df-90"><a href="#dump_df-90"><span class="linenos">90</span></a>
</span><span id="dump_df-91"><a href="#dump_df-91"><span class="linenos">91</span></a> </span><span id="dump_df-91"><a href="#dump_df-91"><span class="linenos">91</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">fname</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s1">&#39;.csv&#39;</span><span class="p">):</span>
</span><span id="dump_df-92"><a href="#dump_df-92"><span class="linenos">92</span></a> <span class="k">if</span> <span class="n">gz</span> <span class="ow">is</span> <span class="kc">True</span><span class="p">:</span> </span><span id="dump_df-92"><a href="#dump_df-92"><span class="linenos">92</span></a> <span class="n">fname</span> <span class="o">+=</span> <span class="s1">&#39;.csv&#39;</span>
</span><span id="dump_df-93"><a href="#dump_df-93"><span class="linenos">93</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">fname</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s1">&#39;.gz&#39;</span><span class="p">):</span> </span><span id="dump_df-93"><a href="#dump_df-93"><span class="linenos">93</span></a>
</span><span id="dump_df-94"><a href="#dump_df-94"><span class="linenos">94</span></a> <span class="n">fname</span> <span class="o">+=</span> <span class="s1">&#39;.gz&#39;</span> </span><span id="dump_df-94"><a href="#dump_df-94"><span class="linenos">94</span></a> <span class="k">if</span> <span class="n">gz</span> <span class="ow">is</span> <span class="kc">True</span><span class="p">:</span>
</span><span id="dump_df-95"><a href="#dump_df-95"><span class="linenos">95</span></a> <span class="n">out</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="n">fname</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">compression</span><span class="o">=</span><span class="s1">&#39;gzip&#39;</span><span class="p">)</span> </span><span id="dump_df-95"><a href="#dump_df-95"><span class="linenos">95</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">fname</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s1">&#39;.gz&#39;</span><span class="p">):</span>
</span><span id="dump_df-96"><a href="#dump_df-96"><span class="linenos">96</span></a> <span class="k">else</span><span class="p">:</span> </span><span id="dump_df-96"><a href="#dump_df-96"><span class="linenos">96</span></a> <span class="n">fname</span> <span class="o">+=</span> <span class="s1">&#39;.gz&#39;</span>
</span><span id="dump_df-97"><a href="#dump_df-97"><span class="linenos">97</span></a> <span class="n">out</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="n">fname</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span> </span><span id="dump_df-97"><a href="#dump_df-97"><span class="linenos">97</span></a> <span class="n">out</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="n">fname</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">compression</span><span class="o">=</span><span class="s1">&#39;gzip&#39;</span><span class="p">)</span>
</span><span id="dump_df-98"><a href="#dump_df-98"><span class="linenos">98</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="dump_df-99"><a href="#dump_df-99"><span class="linenos">99</span></a> <span class="n">out</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="n">fname</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
</span></pre></div> </span></pre></div>
@ -512,38 +514,38 @@ If True, the output is a gzipped csv file. If False, the output is a csv file.</
</div> </div>
<a class="headerlink" href="#load_df"></a> <a class="headerlink" href="#load_df"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="load_df-100"><a href="#load_df-100"><span class="linenos">100</span></a><span class="k">def</span><span class="w"> </span><span class="nf">load_df</span><span class="p">(</span><span class="n">fname</span><span class="p">,</span> <span class="n">auto_gamma</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">gz</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span> <div class="pdoc-code codehilite"><pre><span></span><span id="load_df-102"><a href="#load_df-102"><span class="linenos">102</span></a><span class="k">def</span><span class="w"> </span><span class="nf">load_df</span><span class="p">(</span><span class="n">fname</span><span class="p">,</span> <span class="n">auto_gamma</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">gz</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
</span><span id="load_df-101"><a href="#load_df-101"><span class="linenos">101</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Imports a pandas DataFrame from a csv.(gz) file in which Obs objects are serialized as json strings.</span> </span><span id="load_df-103"><a href="#load_df-103"><span class="linenos">103</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Imports a pandas DataFrame from a csv.(gz) file in which Obs objects are serialized as json strings.</span>
</span><span id="load_df-102"><a href="#load_df-102"><span class="linenos">102</span></a> </span><span id="load_df-104"><a href="#load_df-104"><span class="linenos">104</span></a>
</span><span id="load_df-103"><a href="#load_df-103"><span class="linenos">103</span></a><span class="sd"> Parameters</span> </span><span id="load_df-105"><a href="#load_df-105"><span class="linenos">105</span></a><span class="sd"> Parameters</span>
</span><span id="load_df-104"><a href="#load_df-104"><span class="linenos">104</span></a><span class="sd"> ----------</span> </span><span id="load_df-106"><a href="#load_df-106"><span class="linenos">106</span></a><span class="sd"> ----------</span>
</span><span id="load_df-105"><a href="#load_df-105"><span class="linenos">105</span></a><span class="sd"> fname : str</span> </span><span id="load_df-107"><a href="#load_df-107"><span class="linenos">107</span></a><span class="sd"> fname : str</span>
</span><span id="load_df-106"><a href="#load_df-106"><span class="linenos">106</span></a><span class="sd"> Filename of the input file.</span> </span><span id="load_df-108"><a href="#load_df-108"><span class="linenos">108</span></a><span class="sd"> Filename of the input file.</span>
</span><span id="load_df-107"><a href="#load_df-107"><span class="linenos">107</span></a><span class="sd"> auto_gamma : bool</span> </span><span id="load_df-109"><a href="#load_df-109"><span class="linenos">109</span></a><span class="sd"> auto_gamma : bool</span>
</span><span id="load_df-108"><a href="#load_df-108"><span class="linenos">108</span></a><span class="sd"> If True applies the gamma_method to all imported Obs objects with the default parameters for</span> </span><span id="load_df-110"><a href="#load_df-110"><span class="linenos">110</span></a><span class="sd"> If True applies the gamma_method to all imported Obs objects with the default parameters for</span>
</span><span id="load_df-109"><a href="#load_df-109"><span class="linenos">109</span></a><span class="sd"> the error analysis. Default False.</span> </span><span id="load_df-111"><a href="#load_df-111"><span class="linenos">111</span></a><span class="sd"> the error analysis. Default False.</span>
</span><span id="load_df-110"><a href="#load_df-110"><span class="linenos">110</span></a><span class="sd"> gz : bool</span> </span><span id="load_df-112"><a href="#load_df-112"><span class="linenos">112</span></a><span class="sd"> gz : bool</span>
</span><span id="load_df-111"><a href="#load_df-111"><span class="linenos">111</span></a><span class="sd"> If True, assumes that data is gzipped. If False, assumes JSON file.</span> </span><span id="load_df-113"><a href="#load_df-113"><span class="linenos">113</span></a><span class="sd"> If True, assumes that data is gzipped. If False, assumes JSON file.</span>
</span><span id="load_df-112"><a href="#load_df-112"><span class="linenos">112</span></a> </span><span id="load_df-114"><a href="#load_df-114"><span class="linenos">114</span></a>
</span><span id="load_df-113"><a href="#load_df-113"><span class="linenos">113</span></a><span class="sd"> Returns</span> </span><span id="load_df-115"><a href="#load_df-115"><span class="linenos">115</span></a><span class="sd"> Returns</span>
</span><span id="load_df-114"><a href="#load_df-114"><span class="linenos">114</span></a><span class="sd"> -------</span> </span><span id="load_df-116"><a href="#load_df-116"><span class="linenos">116</span></a><span class="sd"> -------</span>
</span><span id="load_df-115"><a href="#load_df-115"><span class="linenos">115</span></a><span class="sd"> data : pandas.DataFrame</span> </span><span id="load_df-117"><a href="#load_df-117"><span class="linenos">117</span></a><span class="sd"> data : pandas.DataFrame</span>
</span><span id="load_df-116"><a href="#load_df-116"><span class="linenos">116</span></a><span class="sd"> Dataframe with the content of the sqlite database.</span> </span><span id="load_df-118"><a href="#load_df-118"><span class="linenos">118</span></a><span class="sd"> Dataframe with the content of the sqlite database.</span>
</span><span id="load_df-117"><a href="#load_df-117"><span class="linenos">117</span></a><span class="sd"> &quot;&quot;&quot;</span> </span><span id="load_df-119"><a href="#load_df-119"><span class="linenos">119</span></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="load_df-118"><a href="#load_df-118"><span class="linenos">118</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">fname</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s1">&#39;.csv&#39;</span><span class="p">)</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">fname</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s1">&#39;.gz&#39;</span><span class="p">):</span> </span><span id="load_df-120"><a href="#load_df-120"><span class="linenos">120</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">fname</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s1">&#39;.csv&#39;</span><span class="p">)</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">fname</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s1">&#39;.gz&#39;</span><span class="p">):</span>
</span><span id="load_df-119"><a href="#load_df-119"><span class="linenos">119</span></a> <span class="n">fname</span> <span class="o">+=</span> <span class="s1">&#39;.csv&#39;</span> </span><span id="load_df-121"><a href="#load_df-121"><span class="linenos">121</span></a> <span class="n">fname</span> <span class="o">+=</span> <span class="s1">&#39;.csv&#39;</span>
</span><span id="load_df-120"><a href="#load_df-120"><span class="linenos">120</span></a> </span><span id="load_df-122"><a href="#load_df-122"><span class="linenos">122</span></a>
</span><span id="load_df-121"><a href="#load_df-121"><span class="linenos">121</span></a> <span class="k">if</span> <span class="n">gz</span> <span class="ow">is</span> <span class="kc">True</span><span class="p">:</span> </span><span id="load_df-123"><a href="#load_df-123"><span class="linenos">123</span></a> <span class="k">if</span> <span class="n">gz</span> <span class="ow">is</span> <span class="kc">True</span><span class="p">:</span>
</span><span id="load_df-122"><a href="#load_df-122"><span class="linenos">122</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">fname</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s1">&#39;.gz&#39;</span><span class="p">):</span> </span><span id="load_df-124"><a href="#load_df-124"><span class="linenos">124</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">fname</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s1">&#39;.gz&#39;</span><span class="p">):</span>
</span><span id="load_df-123"><a href="#load_df-123"><span class="linenos">123</span></a> <span class="n">fname</span> <span class="o">+=</span> <span class="s1">&#39;.gz&#39;</span> </span><span id="load_df-125"><a href="#load_df-125"><span class="linenos">125</span></a> <span class="n">fname</span> <span class="o">+=</span> <span class="s1">&#39;.gz&#39;</span>
</span><span id="load_df-124"><a href="#load_df-124"><span class="linenos">124</span></a> <span class="k">with</span> <span class="n">gzip</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="n">fname</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span> </span><span id="load_df-126"><a href="#load_df-126"><span class="linenos">126</span></a> <span class="k">with</span> <span class="n">gzip</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="n">fname</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
</span><span id="load_df-125"><a href="#load_df-125"><span class="linenos">125</span></a> <span class="n">re_import</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">f</span><span class="p">,</span> <span class="n">keep_default_na</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span> </span><span id="load_df-127"><a href="#load_df-127"><span class="linenos">127</span></a> <span class="n">re_import</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">f</span><span class="p">,</span> <span class="n">keep_default_na</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
</span><span id="load_df-126"><a href="#load_df-126"><span class="linenos">126</span></a> <span class="k">else</span><span class="p">:</span> </span><span id="load_df-128"><a href="#load_df-128"><span class="linenos">128</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="load_df-127"><a href="#load_df-127"><span class="linenos">127</span></a> <span class="k">if</span> <span class="n">fname</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s1">&#39;.gz&#39;</span><span class="p">):</span> </span><span id="load_df-129"><a href="#load_df-129"><span class="linenos">129</span></a> <span class="k">if</span> <span class="n">fname</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s1">&#39;.gz&#39;</span><span class="p">):</span>
</span><span id="load_df-128"><a href="#load_df-128"><span class="linenos">128</span></a> <span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span><span class="s2">&quot;Trying to read from </span><span class="si">%s</span><span class="s2"> without unzipping!&quot;</span> <span class="o">%</span> <span class="n">fname</span><span class="p">,</span> <span class="ne">UserWarning</span><span class="p">)</span> </span><span id="load_df-130"><a href="#load_df-130"><span class="linenos">130</span></a> <span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Trying to read from </span><span class="si">{</span><span class="n">fname</span><span class="si">}</span><span class="s2"> without unzipping!&quot;</span><span class="p">,</span> <span class="ne">UserWarning</span><span class="p">,</span> <span class="n">stacklevel</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span>
</span><span id="load_df-129"><a href="#load_df-129"><span class="linenos">129</span></a> <span class="n">re_import</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">fname</span><span class="p">,</span> <span class="n">keep_default_na</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span> </span><span id="load_df-131"><a href="#load_df-131"><span class="linenos">131</span></a> <span class="n">re_import</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">fname</span><span class="p">,</span> <span class="n">keep_default_na</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
</span><span id="load_df-130"><a href="#load_df-130"><span class="linenos">130</span></a> </span><span id="load_df-132"><a href="#load_df-132"><span class="linenos">132</span></a>
</span><span id="load_df-131"><a href="#load_df-131"><span class="linenos">131</span></a> <span class="k">return</span> <span class="n">_deserialize_df</span><span class="p">(</span><span class="n">re_import</span><span class="p">,</span> <span class="n">auto_gamma</span><span class="o">=</span><span class="n">auto_gamma</span><span class="p">)</span> </span><span id="load_df-133"><a href="#load_df-133"><span class="linenos">133</span></a> <span class="k">return</span> <span class="n">_deserialize_df</span><span class="p">(</span><span class="n">re_import</span><span class="p">,</span> <span class="n">auto_gamma</span><span class="o">=</span><span class="n">auto_gamma</span><span class="p">)</span>
</span></pre></div> </span></pre></div>

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@ -86,9 +86,9 @@
<div class="pdoc-code codehilite"><pre><span></span><span id="L-1"><a href="#L-1"><span class="linenos"> 1</span></a><span class="sd">&quot;&quot;&quot;Utilities for the input&quot;&quot;&quot;</span> <div class="pdoc-code codehilite"><pre><span></span><span id="L-1"><a href="#L-1"><span class="linenos"> 1</span></a><span class="sd">&quot;&quot;&quot;Utilities for the input&quot;&quot;&quot;</span>
</span><span id="L-2"><a href="#L-2"><span class="linenos"> 2</span></a> </span><span id="L-2"><a href="#L-2"><span class="linenos"> 2</span></a>
</span><span id="L-3"><a href="#L-3"><span class="linenos"> 3</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">re</span> </span><span id="L-3"><a href="#L-3"><span class="linenos"> 3</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">fnmatch</span>
</span><span id="L-4"><a href="#L-4"><span class="linenos"> 4</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">fnmatch</span> </span><span id="L-4"><a href="#L-4"><span class="linenos"> 4</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">os</span>
</span><span id="L-5"><a href="#L-5"><span class="linenos"> 5</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">os</span> </span><span id="L-5"><a href="#L-5"><span class="linenos"> 5</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">re</span>
</span><span id="L-6"><a href="#L-6"><span class="linenos"> 6</span></a> </span><span id="L-6"><a href="#L-6"><span class="linenos"> 6</span></a>
</span><span id="L-7"><a href="#L-7"><span class="linenos"> 7</span></a> </span><span id="L-7"><a href="#L-7"><span class="linenos"> 7</span></a>
</span><span id="L-8"><a href="#L-8"><span class="linenos"> 8</span></a><span class="k">def</span><span class="w"> </span><span class="nf">sort_names</span><span class="p">(</span><span class="n">ll</span><span class="p">):</span> </span><span id="L-8"><a href="#L-8"><span class="linenos"> 8</span></a><span class="k">def</span><span class="w"> </span><span class="nf">sort_names</span><span class="p">(</span><span class="n">ll</span><span class="p">):</span>
@ -190,7 +190,7 @@
</span><span id="L-104"><a href="#L-104"><span class="linenos">104</span></a><span class="sd"> &quot;&quot;&quot;</span> </span><span id="L-104"><a href="#L-104"><span class="linenos">104</span></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="L-105"><a href="#L-105"><span class="linenos">105</span></a> </span><span id="L-105"><a href="#L-105"><span class="linenos">105</span></a>
</span><span id="L-106"><a href="#L-106"><span class="linenos">106</span></a> <span class="n">ls</span> <span class="o">=</span> <span class="p">[]</span> </span><span id="L-106"><a href="#L-106"><span class="linenos">106</span></a> <span class="n">ls</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="L-107"><a href="#L-107"><span class="linenos">107</span></a> <span class="k">for</span> <span class="p">(</span><span class="n">dirpath</span><span class="p">,</span> <span class="n">dirnames</span><span class="p">,</span> <span class="n">filenames</span><span class="p">)</span> <span class="ow">in</span> <span class="n">os</span><span class="o">.</span><span class="n">walk</span><span class="p">(</span><span class="n">path</span><span class="p">):</span> </span><span id="L-107"><a href="#L-107"><span class="linenos">107</span></a> <span class="k">for</span> <span class="p">(</span><span class="n">_dirpath</span><span class="p">,</span> <span class="n">dirnames</span><span class="p">,</span> <span class="n">_filenames</span><span class="p">)</span> <span class="ow">in</span> <span class="n">os</span><span class="o">.</span><span class="n">walk</span><span class="p">(</span><span class="n">path</span><span class="p">):</span>
</span><span id="L-108"><a href="#L-108"><span class="linenos">108</span></a> <span class="n">ls</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">dirnames</span><span class="p">)</span> </span><span id="L-108"><a href="#L-108"><span class="linenos">108</span></a> <span class="n">ls</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">dirnames</span><span class="p">)</span>
</span><span id="L-109"><a href="#L-109"><span class="linenos">109</span></a> <span class="k">break</span> </span><span id="L-109"><a href="#L-109"><span class="linenos">109</span></a> <span class="k">break</span>
</span><span id="L-110"><a href="#L-110"><span class="linenos">110</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">ls</span><span class="p">:</span> </span><span id="L-110"><a href="#L-110"><span class="linenos">110</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">ls</span><span class="p">:</span>
@ -206,7 +206,7 @@
</span><span id="L-120"><a href="#L-120"><span class="linenos">120</span></a> <span class="n">rep_path</span> <span class="o">=</span> <span class="n">path</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">rep</span> </span><span id="L-120"><a href="#L-120"><span class="linenos">120</span></a> <span class="n">rep_path</span> <span class="o">=</span> <span class="n">path</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">rep</span>
</span><span id="L-121"><a href="#L-121"><span class="linenos">121</span></a> <span class="c1"># files of replicum</span> </span><span id="L-121"><a href="#L-121"><span class="linenos">121</span></a> <span class="c1"># files of replicum</span>
</span><span id="L-122"><a href="#L-122"><span class="linenos">122</span></a> <span class="n">sub_ls</span> <span class="o">=</span> <span class="p">[]</span> </span><span id="L-122"><a href="#L-122"><span class="linenos">122</span></a> <span class="n">sub_ls</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="L-123"><a href="#L-123"><span class="linenos">123</span></a> <span class="k">for</span> <span class="p">(</span><span class="n">dirpath</span><span class="p">,</span> <span class="n">dirnames</span><span class="p">,</span> <span class="n">filenames</span><span class="p">)</span> <span class="ow">in</span> <span class="n">os</span><span class="o">.</span><span class="n">walk</span><span class="p">(</span><span class="n">rep_path</span><span class="p">):</span> </span><span id="L-123"><a href="#L-123"><span class="linenos">123</span></a> <span class="k">for</span> <span class="p">(</span><span class="n">_dirpath</span><span class="p">,</span> <span class="n">_dirnames</span><span class="p">,</span> <span class="n">filenames</span><span class="p">)</span> <span class="ow">in</span> <span class="n">os</span><span class="o">.</span><span class="n">walk</span><span class="p">(</span><span class="n">rep_path</span><span class="p">):</span>
</span><span id="L-124"><a href="#L-124"><span class="linenos">124</span></a> <span class="n">sub_ls</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">filenames</span><span class="p">)</span> </span><span id="L-124"><a href="#L-124"><span class="linenos">124</span></a> <span class="n">sub_ls</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">filenames</span><span class="p">)</span>
</span><span id="L-125"><a href="#L-125"><span class="linenos">125</span></a> </span><span id="L-125"><a href="#L-125"><span class="linenos">125</span></a>
</span><span id="L-126"><a href="#L-126"><span class="linenos">126</span></a> <span class="c1"># filter</span> </span><span id="L-126"><a href="#L-126"><span class="linenos">126</span></a> <span class="c1"># filter</span>
@ -218,9 +218,9 @@
</span><span id="L-132"><a href="#L-132"><span class="linenos">132</span></a> <span class="n">rep_nums</span> <span class="o">=</span> <span class="s1">&#39;&#39;</span> </span><span id="L-132"><a href="#L-132"><span class="linenos">132</span></a> <span class="n">rep_nums</span> <span class="o">=</span> <span class="s1">&#39;&#39;</span>
</span><span id="L-133"><a href="#L-133"><span class="linenos">133</span></a> <span class="k">for</span> <span class="n">file</span> <span class="ow">in</span> <span class="n">param_files</span><span class="p">:</span> </span><span id="L-133"><a href="#L-133"><span class="linenos">133</span></a> <span class="k">for</span> <span class="n">file</span> <span class="ow">in</span> <span class="n">param_files</span><span class="p">:</span>
</span><span id="L-134"><a href="#L-134"><span class="linenos">134</span></a> <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">rep_path</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">file</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span> </span><span id="L-134"><a href="#L-134"><span class="linenos">134</span></a> <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">rep_path</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">file</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span>
</span><span id="L-135"><a href="#L-135"><span class="linenos">135</span></a> <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">fp</span><span class="p">:</span> </span><span id="L-135"><a href="#L-135"><span class="linenos">135</span></a> <span class="n">last_line</span> <span class="o">=</span> <span class="s1">&#39;&#39;</span>
</span><span id="L-136"><a href="#L-136"><span class="linenos">136</span></a> <span class="k">pass</span> </span><span id="L-136"><a href="#L-136"><span class="linenos">136</span></a> <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">fp</span><span class="p">:</span>
</span><span id="L-137"><a href="#L-137"><span class="linenos">137</span></a> <span class="n">last_line</span> <span class="o">=</span> <span class="n">line</span> </span><span id="L-137"><a href="#L-137"><span class="linenos">137</span></a> <span class="n">last_line</span> <span class="o">=</span> <span class="n">line</span>
</span><span id="L-138"><a href="#L-138"><span class="linenos">138</span></a> <span class="k">if</span> <span class="n">last_line</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">2</span><span class="p">]</span> <span class="o">!=</span> <span class="n">param_hash</span><span class="p">:</span> </span><span id="L-138"><a href="#L-138"><span class="linenos">138</span></a> <span class="k">if</span> <span class="n">last_line</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">2</span><span class="p">]</span> <span class="o">!=</span> <span class="n">param_hash</span><span class="p">:</span>
</span><span id="L-139"><a href="#L-139"><span class="linenos">139</span></a> <span class="n">rep_nums</span> <span class="o">+=</span> <span class="n">file</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;_&quot;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span> <span class="o">+</span> <span class="s1">&#39;,&#39;</span> </span><span id="L-139"><a href="#L-139"><span class="linenos">139</span></a> <span class="n">rep_nums</span> <span class="o">+=</span> <span class="n">file</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;_&quot;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span> <span class="o">+</span> <span class="s1">&#39;,&#39;</span>
</span><span id="L-140"><a href="#L-140"><span class="linenos">140</span></a> <span class="n">nums</span><span class="p">[</span><span class="n">rep_path</span><span class="p">]</span> <span class="o">=</span> <span class="n">rep_nums</span> </span><span id="L-140"><a href="#L-140"><span class="linenos">140</span></a> <span class="n">nums</span><span class="p">[</span><span class="n">rep_path</span><span class="p">]</span> <span class="o">=</span> <span class="n">rep_nums</span>
@ -408,7 +408,7 @@ string with integers of which idls are missing</li>
</span><span id="check_params-105"><a href="#check_params-105"><span class="linenos">105</span></a><span class="sd"> &quot;&quot;&quot;</span> </span><span id="check_params-105"><a href="#check_params-105"><span class="linenos">105</span></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="check_params-106"><a href="#check_params-106"><span class="linenos">106</span></a> </span><span id="check_params-106"><a href="#check_params-106"><span class="linenos">106</span></a>
</span><span id="check_params-107"><a href="#check_params-107"><span class="linenos">107</span></a> <span class="n">ls</span> <span class="o">=</span> <span class="p">[]</span> </span><span id="check_params-107"><a href="#check_params-107"><span class="linenos">107</span></a> <span class="n">ls</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="check_params-108"><a href="#check_params-108"><span class="linenos">108</span></a> <span class="k">for</span> <span class="p">(</span><span class="n">dirpath</span><span class="p">,</span> <span class="n">dirnames</span><span class="p">,</span> <span class="n">filenames</span><span class="p">)</span> <span class="ow">in</span> <span class="n">os</span><span class="o">.</span><span class="n">walk</span><span class="p">(</span><span class="n">path</span><span class="p">):</span> </span><span id="check_params-108"><a href="#check_params-108"><span class="linenos">108</span></a> <span class="k">for</span> <span class="p">(</span><span class="n">_dirpath</span><span class="p">,</span> <span class="n">dirnames</span><span class="p">,</span> <span class="n">_filenames</span><span class="p">)</span> <span class="ow">in</span> <span class="n">os</span><span class="o">.</span><span class="n">walk</span><span class="p">(</span><span class="n">path</span><span class="p">):</span>
</span><span id="check_params-109"><a href="#check_params-109"><span class="linenos">109</span></a> <span class="n">ls</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">dirnames</span><span class="p">)</span> </span><span id="check_params-109"><a href="#check_params-109"><span class="linenos">109</span></a> <span class="n">ls</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">dirnames</span><span class="p">)</span>
</span><span id="check_params-110"><a href="#check_params-110"><span class="linenos">110</span></a> <span class="k">break</span> </span><span id="check_params-110"><a href="#check_params-110"><span class="linenos">110</span></a> <span class="k">break</span>
</span><span id="check_params-111"><a href="#check_params-111"><span class="linenos">111</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">ls</span><span class="p">:</span> </span><span id="check_params-111"><a href="#check_params-111"><span class="linenos">111</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">ls</span><span class="p">:</span>
@ -424,7 +424,7 @@ string with integers of which idls are missing</li>
</span><span id="check_params-121"><a href="#check_params-121"><span class="linenos">121</span></a> <span class="n">rep_path</span> <span class="o">=</span> <span class="n">path</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">rep</span> </span><span id="check_params-121"><a href="#check_params-121"><span class="linenos">121</span></a> <span class="n">rep_path</span> <span class="o">=</span> <span class="n">path</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">rep</span>
</span><span id="check_params-122"><a href="#check_params-122"><span class="linenos">122</span></a> <span class="c1"># files of replicum</span> </span><span id="check_params-122"><a href="#check_params-122"><span class="linenos">122</span></a> <span class="c1"># files of replicum</span>
</span><span id="check_params-123"><a href="#check_params-123"><span class="linenos">123</span></a> <span class="n">sub_ls</span> <span class="o">=</span> <span class="p">[]</span> </span><span id="check_params-123"><a href="#check_params-123"><span class="linenos">123</span></a> <span class="n">sub_ls</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="check_params-124"><a href="#check_params-124"><span class="linenos">124</span></a> <span class="k">for</span> <span class="p">(</span><span class="n">dirpath</span><span class="p">,</span> <span class="n">dirnames</span><span class="p">,</span> <span class="n">filenames</span><span class="p">)</span> <span class="ow">in</span> <span class="n">os</span><span class="o">.</span><span class="n">walk</span><span class="p">(</span><span class="n">rep_path</span><span class="p">):</span> </span><span id="check_params-124"><a href="#check_params-124"><span class="linenos">124</span></a> <span class="k">for</span> <span class="p">(</span><span class="n">_dirpath</span><span class="p">,</span> <span class="n">_dirnames</span><span class="p">,</span> <span class="n">filenames</span><span class="p">)</span> <span class="ow">in</span> <span class="n">os</span><span class="o">.</span><span class="n">walk</span><span class="p">(</span><span class="n">rep_path</span><span class="p">):</span>
</span><span id="check_params-125"><a href="#check_params-125"><span class="linenos">125</span></a> <span class="n">sub_ls</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">filenames</span><span class="p">)</span> </span><span id="check_params-125"><a href="#check_params-125"><span class="linenos">125</span></a> <span class="n">sub_ls</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">filenames</span><span class="p">)</span>
</span><span id="check_params-126"><a href="#check_params-126"><span class="linenos">126</span></a> </span><span id="check_params-126"><a href="#check_params-126"><span class="linenos">126</span></a>
</span><span id="check_params-127"><a href="#check_params-127"><span class="linenos">127</span></a> <span class="c1"># filter</span> </span><span id="check_params-127"><a href="#check_params-127"><span class="linenos">127</span></a> <span class="c1"># filter</span>
@ -436,9 +436,9 @@ string with integers of which idls are missing</li>
</span><span id="check_params-133"><a href="#check_params-133"><span class="linenos">133</span></a> <span class="n">rep_nums</span> <span class="o">=</span> <span class="s1">&#39;&#39;</span> </span><span id="check_params-133"><a href="#check_params-133"><span class="linenos">133</span></a> <span class="n">rep_nums</span> <span class="o">=</span> <span class="s1">&#39;&#39;</span>
</span><span id="check_params-134"><a href="#check_params-134"><span class="linenos">134</span></a> <span class="k">for</span> <span class="n">file</span> <span class="ow">in</span> <span class="n">param_files</span><span class="p">:</span> </span><span id="check_params-134"><a href="#check_params-134"><span class="linenos">134</span></a> <span class="k">for</span> <span class="n">file</span> <span class="ow">in</span> <span class="n">param_files</span><span class="p">:</span>
</span><span id="check_params-135"><a href="#check_params-135"><span class="linenos">135</span></a> <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">rep_path</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">file</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span> </span><span id="check_params-135"><a href="#check_params-135"><span class="linenos">135</span></a> <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">rep_path</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">file</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span>
</span><span id="check_params-136"><a href="#check_params-136"><span class="linenos">136</span></a> <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">fp</span><span class="p">:</span> </span><span id="check_params-136"><a href="#check_params-136"><span class="linenos">136</span></a> <span class="n">last_line</span> <span class="o">=</span> <span class="s1">&#39;&#39;</span>
</span><span id="check_params-137"><a href="#check_params-137"><span class="linenos">137</span></a> <span class="k">pass</span> </span><span id="check_params-137"><a href="#check_params-137"><span class="linenos">137</span></a> <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">fp</span><span class="p">:</span>
</span><span id="check_params-138"><a href="#check_params-138"><span class="linenos">138</span></a> <span class="n">last_line</span> <span class="o">=</span> <span class="n">line</span> </span><span id="check_params-138"><a href="#check_params-138"><span class="linenos">138</span></a> <span class="n">last_line</span> <span class="o">=</span> <span class="n">line</span>
</span><span id="check_params-139"><a href="#check_params-139"><span class="linenos">139</span></a> <span class="k">if</span> <span class="n">last_line</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">2</span><span class="p">]</span> <span class="o">!=</span> <span class="n">param_hash</span><span class="p">:</span> </span><span id="check_params-139"><a href="#check_params-139"><span class="linenos">139</span></a> <span class="k">if</span> <span class="n">last_line</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">2</span><span class="p">]</span> <span class="o">!=</span> <span class="n">param_hash</span><span class="p">:</span>
</span><span id="check_params-140"><a href="#check_params-140"><span class="linenos">140</span></a> <span class="n">rep_nums</span> <span class="o">+=</span> <span class="n">file</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;_&quot;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span> <span class="o">+</span> <span class="s1">&#39;,&#39;</span> </span><span id="check_params-140"><a href="#check_params-140"><span class="linenos">140</span></a> <span class="n">rep_nums</span> <span class="o">+=</span> <span class="n">file</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;_&quot;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span> <span class="o">+</span> <span class="s1">&#39;,&#39;</span>
</span><span id="check_params-141"><a href="#check_params-141"><span class="linenos">141</span></a> <span class="n">nums</span><span class="p">[</span><span class="n">rep_path</span><span class="p">]</span> <span class="o">=</span> <span class="n">rep_nums</span> </span><span id="check_params-141"><a href="#check_params-141"><span class="linenos">141</span></a> <span class="n">nums</span><span class="p">[</span><span class="n">rep_path</span><span class="p">]</span> <span class="o">=</span> <span class="n">rep_nums</span>

333
docs/pyerrors/integrate.html
View file

@ -77,92 +77,93 @@
<label class="view-source-button" for="mod-integrate-view-source"><span>View Source</span></label> <label class="view-source-button" for="mod-integrate-view-source"><span>View Source</span></label>
<div class="pdoc-code codehilite"><pre><span></span><span id="L-1"><a href="#L-1"><span class="linenos"> 1</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span> <div class="pdoc-code codehilite"><pre><span></span><span id="L-1"><a href="#L-1"><span class="linenos"> 1</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
</span><span id="L-2"><a href="#L-2"><span class="linenos"> 2</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">.obs</span><span class="w"> </span><span class="kn">import</span> <span class="n">derived_observable</span><span class="p">,</span> <span class="n">Obs</span> </span><span id="L-2"><a href="#L-2"><span class="linenos"> 2</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">autograd</span><span class="w"> </span><span class="kn">import</span> <span class="n">jacobian</span>
</span><span id="L-3"><a href="#L-3"><span class="linenos"> 3</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">autograd</span><span class="w"> </span><span class="kn">import</span> <span class="n">jacobian</span> </span><span id="L-3"><a href="#L-3"><span class="linenos"> 3</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">scipy.integrate</span><span class="w"> </span><span class="kn">import</span> <span class="n">quad</span> <span class="k">as</span> <span class="n">squad</span>
</span><span id="L-4"><a href="#L-4"><span class="linenos"> 4</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">scipy.integrate</span><span class="w"> </span><span class="kn">import</span> <span class="n">quad</span> <span class="k">as</span> <span class="n">squad</span> </span><span id="L-4"><a href="#L-4"><span class="linenos"> 4</span></a>
</span><span id="L-5"><a href="#L-5"><span class="linenos"> 5</span></a> </span><span id="L-5"><a href="#L-5"><span class="linenos"> 5</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">.obs</span><span class="w"> </span><span class="kn">import</span> <span class="n">Obs</span><span class="p">,</span> <span class="n">derived_observable</span>
</span><span id="L-6"><a href="#L-6"><span class="linenos"> 6</span></a> </span><span id="L-6"><a href="#L-6"><span class="linenos"> 6</span></a>
</span><span id="L-7"><a href="#L-7"><span class="linenos"> 7</span></a><span class="k">def</span><span class="w"> </span><span class="nf">quad</span><span class="p">(</span><span class="n">func</span><span class="p">,</span> <span class="n">p</span><span class="p">,</span> <span class="n">a</span><span class="p">,</span> <span class="n">b</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span> </span><span id="L-7"><a href="#L-7"><span class="linenos"> 7</span></a>
</span><span id="L-8"><a href="#L-8"><span class="linenos"> 8</span></a><span class="w"> </span><span class="sd">&#39;&#39;&#39;Performs a (one-dimensional) numeric integration of f(p, x) from a to b.</span> </span><span id="L-8"><a href="#L-8"><span class="linenos"> 8</span></a><span class="k">def</span><span class="w"> </span><span class="nf">quad</span><span class="p">(</span><span class="n">func</span><span class="p">,</span> <span class="n">p</span><span class="p">,</span> <span class="n">a</span><span class="p">,</span> <span class="n">b</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
</span><span id="L-9"><a href="#L-9"><span class="linenos"> 9</span></a> </span><span id="L-9"><a href="#L-9"><span class="linenos"> 9</span></a><span class="w"> </span><span class="sd">&#39;&#39;&#39;Performs a (one-dimensional) numeric integration of f(p, x) from a to b.</span>
</span><span id="L-10"><a href="#L-10"><span class="linenos">10</span></a><span class="sd"> The integration is performed using scipy.integrate.quad().</span> </span><span id="L-10"><a href="#L-10"><span class="linenos">10</span></a>
</span><span id="L-11"><a href="#L-11"><span class="linenos">11</span></a><span class="sd"> All parameters that can be passed to scipy.integrate.quad may also be passed to this function.</span> </span><span id="L-11"><a href="#L-11"><span class="linenos">11</span></a><span class="sd"> The integration is performed using scipy.integrate.quad().</span>
</span><span id="L-12"><a href="#L-12"><span class="linenos">12</span></a><span class="sd"> The output is the same as for scipy.integrate.quad, the first element being an Obs.</span> </span><span id="L-12"><a href="#L-12"><span class="linenos">12</span></a><span class="sd"> All parameters that can be passed to scipy.integrate.quad may also be passed to this function.</span>
</span><span id="L-13"><a href="#L-13"><span class="linenos">13</span></a> </span><span id="L-13"><a href="#L-13"><span class="linenos">13</span></a><span class="sd"> The output is the same as for scipy.integrate.quad, the first element being an Obs.</span>
</span><span id="L-14"><a href="#L-14"><span class="linenos">14</span></a><span class="sd"> Parameters</span> </span><span id="L-14"><a href="#L-14"><span class="linenos">14</span></a>
</span><span id="L-15"><a href="#L-15"><span class="linenos">15</span></a><span class="sd"> ----------</span> </span><span id="L-15"><a href="#L-15"><span class="linenos">15</span></a><span class="sd"> Parameters</span>
</span><span id="L-16"><a href="#L-16"><span class="linenos">16</span></a><span class="sd"> func : object</span> </span><span id="L-16"><a href="#L-16"><span class="linenos">16</span></a><span class="sd"> ----------</span>
</span><span id="L-17"><a href="#L-17"><span class="linenos">17</span></a><span class="sd"> function to integrate, has to be of the form</span> </span><span id="L-17"><a href="#L-17"><span class="linenos">17</span></a><span class="sd"> func : object</span>
</span><span id="L-18"><a href="#L-18"><span class="linenos">18</span></a> </span><span id="L-18"><a href="#L-18"><span class="linenos">18</span></a><span class="sd"> function to integrate, has to be of the form</span>
</span><span id="L-19"><a href="#L-19"><span class="linenos">19</span></a><span class="sd"> ```python</span> </span><span id="L-19"><a href="#L-19"><span class="linenos">19</span></a>
</span><span id="L-20"><a href="#L-20"><span class="linenos">20</span></a><span class="sd"> import autograd.numpy as anp</span> </span><span id="L-20"><a href="#L-20"><span class="linenos">20</span></a><span class="sd"> ```python</span>
</span><span id="L-21"><a href="#L-21"><span class="linenos">21</span></a> </span><span id="L-21"><a href="#L-21"><span class="linenos">21</span></a><span class="sd"> import autograd.numpy as anp</span>
</span><span id="L-22"><a href="#L-22"><span class="linenos">22</span></a><span class="sd"> def func(p, x):</span> </span><span id="L-22"><a href="#L-22"><span class="linenos">22</span></a>
</span><span id="L-23"><a href="#L-23"><span class="linenos">23</span></a><span class="sd"> return p[0] + p[1] * x + p[2] * anp.sinh(x)</span> </span><span id="L-23"><a href="#L-23"><span class="linenos">23</span></a><span class="sd"> def func(p, x):</span>
</span><span id="L-24"><a href="#L-24"><span class="linenos">24</span></a><span class="sd"> ```</span> </span><span id="L-24"><a href="#L-24"><span class="linenos">24</span></a><span class="sd"> return p[0] + p[1] * x + p[2] * anp.sinh(x)</span>
</span><span id="L-25"><a href="#L-25"><span class="linenos">25</span></a><span class="sd"> where x is the integration variable.</span> </span><span id="L-25"><a href="#L-25"><span class="linenos">25</span></a><span class="sd"> ```</span>
</span><span id="L-26"><a href="#L-26"><span class="linenos">26</span></a><span class="sd"> p : list of floats or Obs</span> </span><span id="L-26"><a href="#L-26"><span class="linenos">26</span></a><span class="sd"> where x is the integration variable.</span>
</span><span id="L-27"><a href="#L-27"><span class="linenos">27</span></a><span class="sd"> parameters of the function func.</span> </span><span id="L-27"><a href="#L-27"><span class="linenos">27</span></a><span class="sd"> p : list of floats or Obs</span>
</span><span id="L-28"><a href="#L-28"><span class="linenos">28</span></a><span class="sd"> a: float or Obs</span> </span><span id="L-28"><a href="#L-28"><span class="linenos">28</span></a><span class="sd"> parameters of the function func.</span>
</span><span id="L-29"><a href="#L-29"><span class="linenos">29</span></a><span class="sd"> Lower limit of integration (use -numpy.inf for -infinity).</span> </span><span id="L-29"><a href="#L-29"><span class="linenos">29</span></a><span class="sd"> a: float or Obs</span>
</span><span id="L-30"><a href="#L-30"><span class="linenos">30</span></a><span class="sd"> b: float or Obs</span> </span><span id="L-30"><a href="#L-30"><span class="linenos">30</span></a><span class="sd"> Lower limit of integration (use -numpy.inf for -infinity).</span>
</span><span id="L-31"><a href="#L-31"><span class="linenos">31</span></a><span class="sd"> Upper limit of integration (use -numpy.inf for -infinity).</span> </span><span id="L-31"><a href="#L-31"><span class="linenos">31</span></a><span class="sd"> b: float or Obs</span>
</span><span id="L-32"><a href="#L-32"><span class="linenos">32</span></a><span class="sd"> All parameters of scipy.integrate.quad</span> </span><span id="L-32"><a href="#L-32"><span class="linenos">32</span></a><span class="sd"> Upper limit of integration (use -numpy.inf for -infinity).</span>
</span><span id="L-33"><a href="#L-33"><span class="linenos">33</span></a> </span><span id="L-33"><a href="#L-33"><span class="linenos">33</span></a><span class="sd"> All parameters of scipy.integrate.quad</span>
</span><span id="L-34"><a href="#L-34"><span class="linenos">34</span></a><span class="sd"> Returns</span> </span><span id="L-34"><a href="#L-34"><span class="linenos">34</span></a>
</span><span id="L-35"><a href="#L-35"><span class="linenos">35</span></a><span class="sd"> -------</span> </span><span id="L-35"><a href="#L-35"><span class="linenos">35</span></a><span class="sd"> Returns</span>
</span><span id="L-36"><a href="#L-36"><span class="linenos">36</span></a><span class="sd"> y : Obs</span> </span><span id="L-36"><a href="#L-36"><span class="linenos">36</span></a><span class="sd"> -------</span>
</span><span id="L-37"><a href="#L-37"><span class="linenos">37</span></a><span class="sd"> The integral of func from `a` to `b`.</span> </span><span id="L-37"><a href="#L-37"><span class="linenos">37</span></a><span class="sd"> y : Obs</span>
</span><span id="L-38"><a href="#L-38"><span class="linenos">38</span></a><span class="sd"> abserr : float</span> </span><span id="L-38"><a href="#L-38"><span class="linenos">38</span></a><span class="sd"> The integral of func from `a` to `b`.</span>
</span><span id="L-39"><a href="#L-39"><span class="linenos">39</span></a><span class="sd"> An estimate of the absolute error in the result.</span> </span><span id="L-39"><a href="#L-39"><span class="linenos">39</span></a><span class="sd"> abserr : float</span>
</span><span id="L-40"><a href="#L-40"><span class="linenos">40</span></a><span class="sd"> infodict : dict</span> </span><span id="L-40"><a href="#L-40"><span class="linenos">40</span></a><span class="sd"> An estimate of the absolute error in the result.</span>
</span><span id="L-41"><a href="#L-41"><span class="linenos">41</span></a><span class="sd"> A dictionary containing additional information.</span> </span><span id="L-41"><a href="#L-41"><span class="linenos">41</span></a><span class="sd"> infodict : dict</span>
</span><span id="L-42"><a href="#L-42"><span class="linenos">42</span></a><span class="sd"> Run scipy.integrate.quad_explain() for more information.</span> </span><span id="L-42"><a href="#L-42"><span class="linenos">42</span></a><span class="sd"> A dictionary containing additional information.</span>
</span><span id="L-43"><a href="#L-43"><span class="linenos">43</span></a><span class="sd"> message</span> </span><span id="L-43"><a href="#L-43"><span class="linenos">43</span></a><span class="sd"> Run scipy.integrate.quad_explain() for more information.</span>
</span><span id="L-44"><a href="#L-44"><span class="linenos">44</span></a><span class="sd"> A convergence message.</span> </span><span id="L-44"><a href="#L-44"><span class="linenos">44</span></a><span class="sd"> message</span>
</span><span id="L-45"><a href="#L-45"><span class="linenos">45</span></a><span class="sd"> explain</span> </span><span id="L-45"><a href="#L-45"><span class="linenos">45</span></a><span class="sd"> A convergence message.</span>
</span><span id="L-46"><a href="#L-46"><span class="linenos">46</span></a><span class="sd"> Appended only with &#39;cos&#39; or &#39;sin&#39; weighting and infinite</span> </span><span id="L-46"><a href="#L-46"><span class="linenos">46</span></a><span class="sd"> explain</span>
</span><span id="L-47"><a href="#L-47"><span class="linenos">47</span></a><span class="sd"> integration limits, it contains an explanation of the codes in</span> </span><span id="L-47"><a href="#L-47"><span class="linenos">47</span></a><span class="sd"> Appended only with &#39;cos&#39; or &#39;sin&#39; weighting and infinite</span>
</span><span id="L-48"><a href="#L-48"><span class="linenos">48</span></a><span class="sd"> infodict[&#39;ierlst&#39;]</span> </span><span id="L-48"><a href="#L-48"><span class="linenos">48</span></a><span class="sd"> integration limits, it contains an explanation of the codes in</span>
</span><span id="L-49"><a href="#L-49"><span class="linenos">49</span></a><span class="sd"> &#39;&#39;&#39;</span> </span><span id="L-49"><a href="#L-49"><span class="linenos">49</span></a><span class="sd"> infodict[&#39;ierlst&#39;]</span>
</span><span id="L-50"><a href="#L-50"><span class="linenos">50</span></a> </span><span id="L-50"><a href="#L-50"><span class="linenos">50</span></a><span class="sd"> &#39;&#39;&#39;</span>
</span><span id="L-51"><a href="#L-51"><span class="linenos">51</span></a> <span class="n">Np</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">p</span><span class="p">)</span> </span><span id="L-51"><a href="#L-51"><span class="linenos">51</span></a>
</span><span id="L-52"><a href="#L-52"><span class="linenos">52</span></a> <span class="n">isobs</span> <span class="o">=</span> <span class="p">[</span><span class="kc">True</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">pi</span><span class="p">,</span> <span class="n">Obs</span><span class="p">)</span> <span class="k">else</span> <span class="kc">False</span> <span class="k">for</span> <span class="n">pi</span> <span class="ow">in</span> <span class="n">p</span><span class="p">]</span> </span><span id="L-52"><a href="#L-52"><span class="linenos">52</span></a> <span class="n">Np</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
</span><span id="L-53"><a href="#L-53"><span class="linenos">53</span></a> <span class="n">pval</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">p</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">value</span> <span class="k">if</span> <span class="n">isobs</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="k">else</span> <span class="n">p</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">Np</span><span class="p">)],)</span> </span><span id="L-53"><a href="#L-53"><span class="linenos">53</span></a> <span class="n">isobs</span> <span class="o">=</span> <span class="p">[</span><span class="kc">True</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">pi</span><span class="p">,</span> <span class="n">Obs</span><span class="p">)</span> <span class="k">else</span> <span class="kc">False</span> <span class="k">for</span> <span class="n">pi</span> <span class="ow">in</span> <span class="n">p</span><span class="p">]</span>
</span><span id="L-54"><a href="#L-54"><span class="linenos">54</span></a> <span class="n">pobs</span> <span class="o">=</span> <span class="p">[</span><span class="n">p</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">Np</span><span class="p">)</span> <span class="k">if</span> <span class="n">isobs</span><span class="p">[</span><span class="n">i</span><span class="p">]]</span> </span><span id="L-54"><a href="#L-54"><span class="linenos">54</span></a> <span class="n">pval</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">p</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">value</span> <span class="k">if</span> <span class="n">isobs</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="k">else</span> <span class="n">p</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">Np</span><span class="p">)],)</span>
</span><span id="L-55"><a href="#L-55"><span class="linenos">55</span></a> </span><span id="L-55"><a href="#L-55"><span class="linenos">55</span></a> <span class="n">pobs</span> <span class="o">=</span> <span class="p">[</span><span class="n">p</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">Np</span><span class="p">)</span> <span class="k">if</span> <span class="n">isobs</span><span class="p">[</span><span class="n">i</span><span class="p">]]</span>
</span><span id="L-56"><a href="#L-56"><span class="linenos">56</span></a> <span class="n">bounds</span> <span class="o">=</span> <span class="p">[</span><span class="n">a</span><span class="p">,</span> <span class="n">b</span><span class="p">]</span> </span><span id="L-56"><a href="#L-56"><span class="linenos">56</span></a>
</span><span id="L-57"><a href="#L-57"><span class="linenos">57</span></a> <span class="n">isobs_b</span> <span class="o">=</span> <span class="p">[</span><span class="kc">True</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">bi</span><span class="p">,</span> <span class="n">Obs</span><span class="p">)</span> <span class="k">else</span> <span class="kc">False</span> <span class="k">for</span> <span class="n">bi</span> <span class="ow">in</span> <span class="n">bounds</span><span class="p">]</span> </span><span id="L-57"><a href="#L-57"><span class="linenos">57</span></a> <span class="n">bounds</span> <span class="o">=</span> <span class="p">[</span><span class="n">a</span><span class="p">,</span> <span class="n">b</span><span class="p">]</span>
</span><span id="L-58"><a href="#L-58"><span class="linenos">58</span></a> <span class="n">bval</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">bounds</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">value</span> <span class="k">if</span> <span class="n">isobs_b</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="k">else</span> <span class="n">bounds</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">2</span><span class="p">)])</span> </span><span id="L-58"><a href="#L-58"><span class="linenos">58</span></a> <span class="n">isobs_b</span> <span class="o">=</span> <span class="p">[</span><span class="kc">True</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">bi</span><span class="p">,</span> <span class="n">Obs</span><span class="p">)</span> <span class="k">else</span> <span class="kc">False</span> <span class="k">for</span> <span class="n">bi</span> <span class="ow">in</span> <span class="n">bounds</span><span class="p">]</span>
</span><span id="L-59"><a href="#L-59"><span class="linenos">59</span></a> <span class="n">bobs</span> <span class="o">=</span> <span class="p">[</span><span class="n">bounds</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">2</span><span class="p">)</span> <span class="k">if</span> <span class="n">isobs_b</span><span class="p">[</span><span class="n">i</span><span class="p">]]</span> </span><span id="L-59"><a href="#L-59"><span class="linenos">59</span></a> <span class="n">bval</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">bounds</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">value</span> <span class="k">if</span> <span class="n">isobs_b</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="k">else</span> <span class="n">bounds</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">2</span><span class="p">)])</span>
</span><span id="L-60"><a href="#L-60"><span class="linenos">60</span></a> <span class="n">bsign</span> <span class="o">=</span> <span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">]</span> </span><span id="L-60"><a href="#L-60"><span class="linenos">60</span></a> <span class="n">bobs</span> <span class="o">=</span> <span class="p">[</span><span class="n">bounds</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">2</span><span class="p">)</span> <span class="k">if</span> <span class="n">isobs_b</span><span class="p">[</span><span class="n">i</span><span class="p">]]</span>
</span><span id="L-61"><a href="#L-61"><span class="linenos">61</span></a> </span><span id="L-61"><a href="#L-61"><span class="linenos">61</span></a> <span class="n">bsign</span> <span class="o">=</span> <span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">]</span>
</span><span id="L-62"><a href="#L-62"><span class="linenos">62</span></a> <span class="n">ifunc</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">vectorize</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">func</span><span class="p">(</span><span class="n">pval</span><span class="p">,</span> <span class="n">x</span><span class="p">))</span> </span><span id="L-62"><a href="#L-62"><span class="linenos">62</span></a>
</span><span id="L-63"><a href="#L-63"><span class="linenos">63</span></a> </span><span id="L-63"><a href="#L-63"><span class="linenos">63</span></a> <span class="n">ifunc</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">vectorize</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">func</span><span class="p">(</span><span class="n">pval</span><span class="p">,</span> <span class="n">x</span><span class="p">))</span>
</span><span id="L-64"><a href="#L-64"><span class="linenos">64</span></a> <span class="n">intpars</span> <span class="o">=</span> <span class="n">squad</span><span class="o">.</span><span class="vm">__code__</span><span class="o">.</span><span class="n">co_varnames</span><span class="p">[</span><span class="mi">3</span><span class="p">:</span><span class="mi">3</span> <span class="o">+</span> <span class="nb">len</span><span class="p">(</span><span class="n">squad</span><span class="o">.</span><span class="vm">__defaults__</span><span class="p">)]</span> </span><span id="L-64"><a href="#L-64"><span class="linenos">64</span></a>
</span><span id="L-65"><a href="#L-65"><span class="linenos">65</span></a> <span class="n">ikwargs</span> <span class="o">=</span> <span class="p">{</span><span class="n">k</span><span class="p">:</span> <span class="n">kwargs</span><span class="p">[</span><span class="n">k</span><span class="p">]</span> <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="n">intpars</span> <span class="k">if</span> <span class="n">k</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">}</span> </span><span id="L-65"><a href="#L-65"><span class="linenos">65</span></a> <span class="n">intpars</span> <span class="o">=</span> <span class="n">squad</span><span class="o">.</span><span class="vm">__code__</span><span class="o">.</span><span class="n">co_varnames</span><span class="p">[</span><span class="mi">3</span><span class="p">:</span><span class="mi">3</span> <span class="o">+</span> <span class="nb">len</span><span class="p">(</span><span class="n">squad</span><span class="o">.</span><span class="vm">__defaults__</span><span class="p">)]</span>
</span><span id="L-66"><a href="#L-66"><span class="linenos">66</span></a> </span><span id="L-66"><a href="#L-66"><span class="linenos">66</span></a> <span class="n">ikwargs</span> <span class="o">=</span> <span class="p">{</span><span class="n">k</span><span class="p">:</span> <span class="n">kwargs</span><span class="p">[</span><span class="n">k</span><span class="p">]</span> <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="n">intpars</span> <span class="k">if</span> <span class="n">k</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">}</span>
</span><span id="L-67"><a href="#L-67"><span class="linenos">67</span></a> <span class="n">integration_result</span> <span class="o">=</span> <span class="n">squad</span><span class="p">(</span><span class="n">ifunc</span><span class="p">,</span> <span class="n">bval</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">bval</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="o">**</span><span class="n">ikwargs</span><span class="p">)</span> </span><span id="L-67"><a href="#L-67"><span class="linenos">67</span></a>
</span><span id="L-68"><a href="#L-68"><span class="linenos">68</span></a> <span class="n">val</span> <span class="o">=</span> <span class="n">integration_result</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> </span><span id="L-68"><a href="#L-68"><span class="linenos">68</span></a> <span class="n">integration_result</span> <span class="o">=</span> <span class="n">squad</span><span class="p">(</span><span class="n">ifunc</span><span class="p">,</span> <span class="n">bval</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">bval</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="o">**</span><span class="n">ikwargs</span><span class="p">)</span>
</span><span id="L-69"><a href="#L-69"><span class="linenos">69</span></a> </span><span id="L-69"><a href="#L-69"><span class="linenos">69</span></a> <span class="n">val</span> <span class="o">=</span> <span class="n">integration_result</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
</span><span id="L-70"><a href="#L-70"><span class="linenos">70</span></a> <span class="n">jac</span> <span class="o">=</span> <span class="n">jacobian</span><span class="p">(</span><span class="n">func</span><span class="p">)</span> </span><span id="L-70"><a href="#L-70"><span class="linenos">70</span></a>
</span><span id="L-71"><a href="#L-71"><span class="linenos">71</span></a> </span><span id="L-71"><a href="#L-71"><span class="linenos">71</span></a> <span class="n">jac</span> <span class="o">=</span> <span class="n">jacobian</span><span class="p">(</span><span class="n">func</span><span class="p">)</span>
</span><span id="L-72"><a href="#L-72"><span class="linenos">72</span></a> <span class="n">derivint</span> <span class="o">=</span> <span class="p">[]</span> </span><span id="L-72"><a href="#L-72"><span class="linenos">72</span></a>
</span><span id="L-73"><a href="#L-73"><span class="linenos">73</span></a> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">Np</span><span class="p">):</span> </span><span id="L-73"><a href="#L-73"><span class="linenos">73</span></a> <span class="n">derivint</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="L-74"><a href="#L-74"><span class="linenos">74</span></a> <span class="k">if</span> <span class="n">isobs</span><span class="p">[</span><span class="n">i</span><span class="p">]:</span> </span><span id="L-74"><a href="#L-74"><span class="linenos">74</span></a> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">Np</span><span class="p">):</span>
</span><span id="L-75"><a href="#L-75"><span class="linenos">75</span></a> <span class="n">ifunc</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">vectorize</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">jac</span><span class="p">(</span><span class="n">pval</span><span class="p">,</span> <span class="n">x</span><span class="p">)[</span><span class="n">i</span><span class="p">])</span> </span><span id="L-75"><a href="#L-75"><span class="linenos">75</span></a> <span class="k">if</span> <span class="n">isobs</span><span class="p">[</span><span class="n">i</span><span class="p">]:</span>
</span><span id="L-76"><a href="#L-76"><span class="linenos">76</span></a> <span class="n">derivint</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">squad</span><span class="p">(</span><span class="n">ifunc</span><span class="p">,</span> <span class="n">bounds</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">bounds</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="o">**</span><span class="n">ikwargs</span><span class="p">)[</span><span class="mi">0</span><span class="p">])</span> </span><span id="L-76"><a href="#L-76"><span class="linenos">76</span></a> <span class="n">ifunc</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">vectorize</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">,</span> <span class="n">i</span><span class="o">=</span><span class="n">i</span><span class="p">:</span> <span class="n">jac</span><span class="p">(</span><span class="n">pval</span><span class="p">,</span> <span class="n">x</span><span class="p">)[</span><span class="n">i</span><span class="p">])</span>
</span><span id="L-77"><a href="#L-77"><span class="linenos">77</span></a> </span><span id="L-77"><a href="#L-77"><span class="linenos">77</span></a> <span class="n">derivint</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">squad</span><span class="p">(</span><span class="n">ifunc</span><span class="p">,</span> <span class="n">bounds</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">bounds</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="o">**</span><span class="n">ikwargs</span><span class="p">)[</span><span class="mi">0</span><span class="p">])</span>
</span><span id="L-78"><a href="#L-78"><span class="linenos">78</span></a> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">2</span><span class="p">):</span> </span><span id="L-78"><a href="#L-78"><span class="linenos">78</span></a>
</span><span id="L-79"><a href="#L-79"><span class="linenos">79</span></a> <span class="k">if</span> <span class="n">isobs_b</span><span class="p">[</span><span class="n">i</span><span class="p">]:</span> </span><span id="L-79"><a href="#L-79"><span class="linenos">79</span></a> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">2</span><span class="p">):</span>
</span><span id="L-80"><a href="#L-80"><span class="linenos">80</span></a> <span class="n">derivint</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">bsign</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">*</span> <span class="n">func</span><span class="p">(</span><span class="n">pval</span><span class="p">,</span> <span class="n">bval</span><span class="p">[</span><span class="n">i</span><span class="p">]))</span> </span><span id="L-80"><a href="#L-80"><span class="linenos">80</span></a> <span class="k">if</span> <span class="n">isobs_b</span><span class="p">[</span><span class="n">i</span><span class="p">]:</span>
</span><span id="L-81"><a href="#L-81"><span class="linenos">81</span></a> </span><span id="L-81"><a href="#L-81"><span class="linenos">81</span></a> <span class="n">derivint</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">bsign</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">*</span> <span class="n">func</span><span class="p">(</span><span class="n">pval</span><span class="p">,</span> <span class="n">bval</span><span class="p">[</span><span class="n">i</span><span class="p">]))</span>
</span><span id="L-82"><a href="#L-82"><span class="linenos">82</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">derivint</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span> </span><span id="L-82"><a href="#L-82"><span class="linenos">82</span></a>
</span><span id="L-83"><a href="#L-83"><span class="linenos">83</span></a> <span class="k">return</span> <span class="n">integration_result</span> </span><span id="L-83"><a href="#L-83"><span class="linenos">83</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">derivint</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
</span><span id="L-84"><a href="#L-84"><span class="linenos">84</span></a> </span><span id="L-84"><a href="#L-84"><span class="linenos">84</span></a> <span class="k">return</span> <span class="n">integration_result</span>
</span><span id="L-85"><a href="#L-85"><span class="linenos">85</span></a> <span class="n">res</span> <span class="o">=</span> <span class="n">derived_observable</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">:</span> <span class="mi">0</span> <span class="o">*</span> <span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="n">np</span><span class="o">.</span><span class="n">finfo</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">float64</span><span class="p">)</span><span class="o">.</span><span class="n">eps</span><span class="p">)</span> <span class="o">*</span> <span class="p">(</span><span class="n">pval</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="n">np</span><span class="o">.</span><span class="n">finfo</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">float64</span><span class="p">)</span><span class="o">.</span><span class="n">eps</span><span class="p">)</span> <span class="o">+</span> <span class="n">val</span><span class="p">,</span> <span class="n">pobs</span> <span class="o">+</span> <span class="n">bobs</span><span class="p">,</span> <span class="n">man_grad</span><span class="o">=</span><span class="n">derivint</span><span class="p">)</span> </span><span id="L-85"><a href="#L-85"><span class="linenos">85</span></a>
</span><span id="L-86"><a href="#L-86"><span class="linenos">86</span></a> </span><span id="L-86"><a href="#L-86"><span class="linenos">86</span></a> <span class="n">res</span> <span class="o">=</span> <span class="n">derived_observable</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">:</span> <span class="mi">0</span> <span class="o">*</span> <span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="n">np</span><span class="o">.</span><span class="n">finfo</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">float64</span><span class="p">)</span><span class="o">.</span><span class="n">eps</span><span class="p">)</span> <span class="o">*</span> <span class="p">(</span><span class="n">pval</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="n">np</span><span class="o">.</span><span class="n">finfo</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">float64</span><span class="p">)</span><span class="o">.</span><span class="n">eps</span><span class="p">)</span> <span class="o">+</span> <span class="n">val</span><span class="p">,</span> <span class="n">pobs</span> <span class="o">+</span> <span class="n">bobs</span><span class="p">,</span> <span class="n">man_grad</span><span class="o">=</span><span class="n">derivint</span><span class="p">)</span>
</span><span id="L-87"><a href="#L-87"><span class="linenos">87</span></a> <span class="k">return</span> <span class="p">(</span><span class="n">res</span><span class="p">,</span> <span class="o">*</span><span class="n">integration_result</span><span class="p">[</span><span class="mi">1</span><span class="p">:])</span> </span><span id="L-87"><a href="#L-87"><span class="linenos">87</span></a>
</span><span id="L-88"><a href="#L-88"><span class="linenos">88</span></a> <span class="k">return</span> <span class="p">(</span><span class="n">res</span><span class="p">,</span> <span class="o">*</span><span class="n">integration_result</span><span class="p">[</span><span class="mi">1</span><span class="p">:])</span>
</span></pre></div> </span></pre></div>
@ -178,87 +179,87 @@
</div> </div>
<a class="headerlink" href="#quad"></a> <a class="headerlink" href="#quad"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="quad-8"><a href="#quad-8"><span class="linenos"> 8</span></a><span class="k">def</span><span class="w"> </span><span class="nf">quad</span><span class="p">(</span><span class="n">func</span><span class="p">,</span> <span class="n">p</span><span class="p">,</span> <span class="n">a</span><span class="p">,</span> <span class="n">b</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span> <div class="pdoc-code codehilite"><pre><span></span><span id="quad-9"><a href="#quad-9"><span class="linenos"> 9</span></a><span class="k">def</span><span class="w"> </span><span class="nf">quad</span><span class="p">(</span><span class="n">func</span><span class="p">,</span> <span class="n">p</span><span class="p">,</span> <span class="n">a</span><span class="p">,</span> <span class="n">b</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
</span><span id="quad-9"><a href="#quad-9"><span class="linenos"> 9</span></a><span class="w"> </span><span class="sd">&#39;&#39;&#39;Performs a (one-dimensional) numeric integration of f(p, x) from a to b.</span> </span><span id="quad-10"><a href="#quad-10"><span class="linenos">10</span></a><span class="w"> </span><span class="sd">&#39;&#39;&#39;Performs a (one-dimensional) numeric integration of f(p, x) from a to b.</span>
</span><span id="quad-10"><a href="#quad-10"><span class="linenos">10</span></a> </span><span id="quad-11"><a href="#quad-11"><span class="linenos">11</span></a>
</span><span id="quad-11"><a href="#quad-11"><span class="linenos">11</span></a><span class="sd"> The integration is performed using scipy.integrate.quad().</span> </span><span id="quad-12"><a href="#quad-12"><span class="linenos">12</span></a><span class="sd"> The integration is performed using scipy.integrate.quad().</span>
</span><span id="quad-12"><a href="#quad-12"><span class="linenos">12</span></a><span class="sd"> All parameters that can be passed to scipy.integrate.quad may also be passed to this function.</span> </span><span id="quad-13"><a href="#quad-13"><span class="linenos">13</span></a><span class="sd"> All parameters that can be passed to scipy.integrate.quad may also be passed to this function.</span>
</span><span id="quad-13"><a href="#quad-13"><span class="linenos">13</span></a><span class="sd"> The output is the same as for scipy.integrate.quad, the first element being an Obs.</span> </span><span id="quad-14"><a href="#quad-14"><span class="linenos">14</span></a><span class="sd"> The output is the same as for scipy.integrate.quad, the first element being an Obs.</span>
</span><span id="quad-14"><a href="#quad-14"><span class="linenos">14</span></a> </span><span id="quad-15"><a href="#quad-15"><span class="linenos">15</span></a>
</span><span id="quad-15"><a href="#quad-15"><span class="linenos">15</span></a><span class="sd"> Parameters</span> </span><span id="quad-16"><a href="#quad-16"><span class="linenos">16</span></a><span class="sd"> Parameters</span>
</span><span id="quad-16"><a href="#quad-16"><span class="linenos">16</span></a><span class="sd"> ----------</span> </span><span id="quad-17"><a href="#quad-17"><span class="linenos">17</span></a><span class="sd"> ----------</span>
</span><span id="quad-17"><a href="#quad-17"><span class="linenos">17</span></a><span class="sd"> func : object</span> </span><span id="quad-18"><a href="#quad-18"><span class="linenos">18</span></a><span class="sd"> func : object</span>
</span><span id="quad-18"><a href="#quad-18"><span class="linenos">18</span></a><span class="sd"> function to integrate, has to be of the form</span> </span><span id="quad-19"><a href="#quad-19"><span class="linenos">19</span></a><span class="sd"> function to integrate, has to be of the form</span>
</span><span id="quad-19"><a href="#quad-19"><span class="linenos">19</span></a> </span><span id="quad-20"><a href="#quad-20"><span class="linenos">20</span></a>
</span><span id="quad-20"><a href="#quad-20"><span class="linenos">20</span></a><span class="sd"> ```python</span> </span><span id="quad-21"><a href="#quad-21"><span class="linenos">21</span></a><span class="sd"> ```python</span>
</span><span id="quad-21"><a href="#quad-21"><span class="linenos">21</span></a><span class="sd"> import autograd.numpy as anp</span> </span><span id="quad-22"><a href="#quad-22"><span class="linenos">22</span></a><span class="sd"> import autograd.numpy as anp</span>
</span><span id="quad-22"><a href="#quad-22"><span class="linenos">22</span></a> </span><span id="quad-23"><a href="#quad-23"><span class="linenos">23</span></a>
</span><span id="quad-23"><a href="#quad-23"><span class="linenos">23</span></a><span class="sd"> def func(p, x):</span> </span><span id="quad-24"><a href="#quad-24"><span class="linenos">24</span></a><span class="sd"> def func(p, x):</span>
</span><span id="quad-24"><a href="#quad-24"><span class="linenos">24</span></a><span class="sd"> return p[0] + p[1] * x + p[2] * anp.sinh(x)</span> </span><span id="quad-25"><a href="#quad-25"><span class="linenos">25</span></a><span class="sd"> return p[0] + p[1] * x + p[2] * anp.sinh(x)</span>
</span><span id="quad-25"><a href="#quad-25"><span class="linenos">25</span></a><span class="sd"> ```</span> </span><span id="quad-26"><a href="#quad-26"><span class="linenos">26</span></a><span class="sd"> ```</span>
</span><span id="quad-26"><a href="#quad-26"><span class="linenos">26</span></a><span class="sd"> where x is the integration variable.</span> </span><span id="quad-27"><a href="#quad-27"><span class="linenos">27</span></a><span class="sd"> where x is the integration variable.</span>
</span><span id="quad-27"><a href="#quad-27"><span class="linenos">27</span></a><span class="sd"> p : list of floats or Obs</span> </span><span id="quad-28"><a href="#quad-28"><span class="linenos">28</span></a><span class="sd"> p : list of floats or Obs</span>
</span><span id="quad-28"><a href="#quad-28"><span class="linenos">28</span></a><span class="sd"> parameters of the function func.</span> </span><span id="quad-29"><a href="#quad-29"><span class="linenos">29</span></a><span class="sd"> parameters of the function func.</span>
</span><span id="quad-29"><a href="#quad-29"><span class="linenos">29</span></a><span class="sd"> a: float or Obs</span> </span><span id="quad-30"><a href="#quad-30"><span class="linenos">30</span></a><span class="sd"> a: float or Obs</span>
</span><span id="quad-30"><a href="#quad-30"><span class="linenos">30</span></a><span class="sd"> Lower limit of integration (use -numpy.inf for -infinity).</span> </span><span id="quad-31"><a href="#quad-31"><span class="linenos">31</span></a><span class="sd"> Lower limit of integration (use -numpy.inf for -infinity).</span>
</span><span id="quad-31"><a href="#quad-31"><span class="linenos">31</span></a><span class="sd"> b: float or Obs</span> </span><span id="quad-32"><a href="#quad-32"><span class="linenos">32</span></a><span class="sd"> b: float or Obs</span>
</span><span id="quad-32"><a href="#quad-32"><span class="linenos">32</span></a><span class="sd"> Upper limit of integration (use -numpy.inf for -infinity).</span> </span><span id="quad-33"><a href="#quad-33"><span class="linenos">33</span></a><span class="sd"> Upper limit of integration (use -numpy.inf for -infinity).</span>
</span><span id="quad-33"><a href="#quad-33"><span class="linenos">33</span></a><span class="sd"> All parameters of scipy.integrate.quad</span> </span><span id="quad-34"><a href="#quad-34"><span class="linenos">34</span></a><span class="sd"> All parameters of scipy.integrate.quad</span>
</span><span id="quad-34"><a href="#quad-34"><span class="linenos">34</span></a> </span><span id="quad-35"><a href="#quad-35"><span class="linenos">35</span></a>
</span><span id="quad-35"><a href="#quad-35"><span class="linenos">35</span></a><span class="sd"> Returns</span> </span><span id="quad-36"><a href="#quad-36"><span class="linenos">36</span></a><span class="sd"> Returns</span>
</span><span id="quad-36"><a href="#quad-36"><span class="linenos">36</span></a><span class="sd"> -------</span> </span><span id="quad-37"><a href="#quad-37"><span class="linenos">37</span></a><span class="sd"> -------</span>
</span><span id="quad-37"><a href="#quad-37"><span class="linenos">37</span></a><span class="sd"> y : Obs</span> </span><span id="quad-38"><a href="#quad-38"><span class="linenos">38</span></a><span class="sd"> y : Obs</span>
</span><span id="quad-38"><a href="#quad-38"><span class="linenos">38</span></a><span class="sd"> The integral of func from `a` to `b`.</span> </span><span id="quad-39"><a href="#quad-39"><span class="linenos">39</span></a><span class="sd"> The integral of func from `a` to `b`.</span>
</span><span id="quad-39"><a href="#quad-39"><span class="linenos">39</span></a><span class="sd"> abserr : float</span> </span><span id="quad-40"><a href="#quad-40"><span class="linenos">40</span></a><span class="sd"> abserr : float</span>
</span><span id="quad-40"><a href="#quad-40"><span class="linenos">40</span></a><span class="sd"> An estimate of the absolute error in the result.</span> </span><span id="quad-41"><a href="#quad-41"><span class="linenos">41</span></a><span class="sd"> An estimate of the absolute error in the result.</span>
</span><span id="quad-41"><a href="#quad-41"><span class="linenos">41</span></a><span class="sd"> infodict : dict</span> </span><span id="quad-42"><a href="#quad-42"><span class="linenos">42</span></a><span class="sd"> infodict : dict</span>
</span><span id="quad-42"><a href="#quad-42"><span class="linenos">42</span></a><span class="sd"> A dictionary containing additional information.</span> </span><span id="quad-43"><a href="#quad-43"><span class="linenos">43</span></a><span class="sd"> A dictionary containing additional information.</span>
</span><span id="quad-43"><a href="#quad-43"><span class="linenos">43</span></a><span class="sd"> Run scipy.integrate.quad_explain() for more information.</span> </span><span id="quad-44"><a href="#quad-44"><span class="linenos">44</span></a><span class="sd"> Run scipy.integrate.quad_explain() for more information.</span>
</span><span id="quad-44"><a href="#quad-44"><span class="linenos">44</span></a><span class="sd"> message</span> </span><span id="quad-45"><a href="#quad-45"><span class="linenos">45</span></a><span class="sd"> message</span>
</span><span id="quad-45"><a href="#quad-45"><span class="linenos">45</span></a><span class="sd"> A convergence message.</span> </span><span id="quad-46"><a href="#quad-46"><span class="linenos">46</span></a><span class="sd"> A convergence message.</span>
</span><span id="quad-46"><a href="#quad-46"><span class="linenos">46</span></a><span class="sd"> explain</span> </span><span id="quad-47"><a href="#quad-47"><span class="linenos">47</span></a><span class="sd"> explain</span>
</span><span id="quad-47"><a href="#quad-47"><span class="linenos">47</span></a><span class="sd"> Appended only with &#39;cos&#39; or &#39;sin&#39; weighting and infinite</span> </span><span id="quad-48"><a href="#quad-48"><span class="linenos">48</span></a><span class="sd"> Appended only with &#39;cos&#39; or &#39;sin&#39; weighting and infinite</span>
</span><span id="quad-48"><a href="#quad-48"><span class="linenos">48</span></a><span class="sd"> integration limits, it contains an explanation of the codes in</span> </span><span id="quad-49"><a href="#quad-49"><span class="linenos">49</span></a><span class="sd"> integration limits, it contains an explanation of the codes in</span>
</span><span id="quad-49"><a href="#quad-49"><span class="linenos">49</span></a><span class="sd"> infodict[&#39;ierlst&#39;]</span> </span><span id="quad-50"><a href="#quad-50"><span class="linenos">50</span></a><span class="sd"> infodict[&#39;ierlst&#39;]</span>
</span><span id="quad-50"><a href="#quad-50"><span class="linenos">50</span></a><span class="sd"> &#39;&#39;&#39;</span> </span><span id="quad-51"><a href="#quad-51"><span class="linenos">51</span></a><span class="sd"> &#39;&#39;&#39;</span>
</span><span id="quad-51"><a href="#quad-51"><span class="linenos">51</span></a> </span><span id="quad-52"><a href="#quad-52"><span class="linenos">52</span></a>
</span><span id="quad-52"><a href="#quad-52"><span class="linenos">52</span></a> <span class="n">Np</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">p</span><span class="p">)</span> </span><span id="quad-53"><a href="#quad-53"><span class="linenos">53</span></a> <span class="n">Np</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
</span><span id="quad-53"><a href="#quad-53"><span class="linenos">53</span></a> <span class="n">isobs</span> <span class="o">=</span> <span class="p">[</span><span class="kc">True</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">pi</span><span class="p">,</span> <span class="n">Obs</span><span class="p">)</span> <span class="k">else</span> <span class="kc">False</span> <span class="k">for</span> <span class="n">pi</span> <span class="ow">in</span> <span class="n">p</span><span class="p">]</span> </span><span id="quad-54"><a href="#quad-54"><span class="linenos">54</span></a> <span class="n">isobs</span> <span class="o">=</span> <span class="p">[</span><span class="kc">True</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">pi</span><span class="p">,</span> <span class="n">Obs</span><span class="p">)</span> <span class="k">else</span> <span class="kc">False</span> <span class="k">for</span> <span class="n">pi</span> <span class="ow">in</span> <span class="n">p</span><span class="p">]</span>
</span><span id="quad-54"><a href="#quad-54"><span class="linenos">54</span></a> <span class="n">pval</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">p</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">value</span> <span class="k">if</span> <span class="n">isobs</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="k">else</span> <span class="n">p</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">Np</span><span class="p">)],)</span> </span><span id="quad-55"><a href="#quad-55"><span class="linenos">55</span></a> <span class="n">pval</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">p</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">value</span> <span class="k">if</span> <span class="n">isobs</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="k">else</span> <span class="n">p</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">Np</span><span class="p">)],)</span>
</span><span id="quad-55"><a href="#quad-55"><span class="linenos">55</span></a> <span class="n">pobs</span> <span class="o">=</span> <span class="p">[</span><span class="n">p</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">Np</span><span class="p">)</span> <span class="k">if</span> <span class="n">isobs</span><span class="p">[</span><span class="n">i</span><span class="p">]]</span> </span><span id="quad-56"><a href="#quad-56"><span class="linenos">56</span></a> <span class="n">pobs</span> <span class="o">=</span> <span class="p">[</span><span class="n">p</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">Np</span><span class="p">)</span> <span class="k">if</span> <span class="n">isobs</span><span class="p">[</span><span class="n">i</span><span class="p">]]</span>
</span><span id="quad-56"><a href="#quad-56"><span class="linenos">56</span></a> </span><span id="quad-57"><a href="#quad-57"><span class="linenos">57</span></a>
</span><span id="quad-57"><a href="#quad-57"><span class="linenos">57</span></a> <span class="n">bounds</span> <span class="o">=</span> <span class="p">[</span><span class="n">a</span><span class="p">,</span> <span class="n">b</span><span class="p">]</span> </span><span id="quad-58"><a href="#quad-58"><span class="linenos">58</span></a> <span class="n">bounds</span> <span class="o">=</span> <span class="p">[</span><span class="n">a</span><span class="p">,</span> <span class="n">b</span><span class="p">]</span>
</span><span id="quad-58"><a href="#quad-58"><span class="linenos">58</span></a> <span class="n">isobs_b</span> <span class="o">=</span> <span class="p">[</span><span class="kc">True</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">bi</span><span class="p">,</span> <span class="n">Obs</span><span class="p">)</span> <span class="k">else</span> <span class="kc">False</span> <span class="k">for</span> <span class="n">bi</span> <span class="ow">in</span> <span class="n">bounds</span><span class="p">]</span> </span><span id="quad-59"><a href="#quad-59"><span class="linenos">59</span></a> <span class="n">isobs_b</span> <span class="o">=</span> <span class="p">[</span><span class="kc">True</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">bi</span><span class="p">,</span> <span class="n">Obs</span><span class="p">)</span> <span class="k">else</span> <span class="kc">False</span> <span class="k">for</span> <span class="n">bi</span> <span class="ow">in</span> <span class="n">bounds</span><span class="p">]</span>
</span><span id="quad-59"><a href="#quad-59"><span class="linenos">59</span></a> <span class="n">bval</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">bounds</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">value</span> <span class="k">if</span> <span class="n">isobs_b</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="k">else</span> <span class="n">bounds</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">2</span><span class="p">)])</span> </span><span id="quad-60"><a href="#quad-60"><span class="linenos">60</span></a> <span class="n">bval</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">bounds</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">value</span> <span class="k">if</span> <span class="n">isobs_b</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="k">else</span> <span class="n">bounds</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">2</span><span class="p">)])</span>
</span><span id="quad-60"><a href="#quad-60"><span class="linenos">60</span></a> <span class="n">bobs</span> <span class="o">=</span> <span class="p">[</span><span class="n">bounds</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">2</span><span class="p">)</span> <span class="k">if</span> <span class="n">isobs_b</span><span class="p">[</span><span class="n">i</span><span class="p">]]</span> </span><span id="quad-61"><a href="#quad-61"><span class="linenos">61</span></a> <span class="n">bobs</span> <span class="o">=</span> <span class="p">[</span><span class="n">bounds</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">2</span><span class="p">)</span> <span class="k">if</span> <span class="n">isobs_b</span><span class="p">[</span><span class="n">i</span><span class="p">]]</span>
</span><span id="quad-61"><a href="#quad-61"><span class="linenos">61</span></a> <span class="n">bsign</span> <span class="o">=</span> <span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">]</span> </span><span id="quad-62"><a href="#quad-62"><span class="linenos">62</span></a> <span class="n">bsign</span> <span class="o">=</span> <span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">]</span>
</span><span id="quad-62"><a href="#quad-62"><span class="linenos">62</span></a> </span><span id="quad-63"><a href="#quad-63"><span class="linenos">63</span></a>
</span><span id="quad-63"><a href="#quad-63"><span class="linenos">63</span></a> <span class="n">ifunc</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">vectorize</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">func</span><span class="p">(</span><span class="n">pval</span><span class="p">,</span> <span class="n">x</span><span class="p">))</span> </span><span id="quad-64"><a href="#quad-64"><span class="linenos">64</span></a> <span class="n">ifunc</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">vectorize</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">func</span><span class="p">(</span><span class="n">pval</span><span class="p">,</span> <span class="n">x</span><span class="p">))</span>
</span><span id="quad-64"><a href="#quad-64"><span class="linenos">64</span></a> </span><span id="quad-65"><a href="#quad-65"><span class="linenos">65</span></a>
</span><span id="quad-65"><a href="#quad-65"><span class="linenos">65</span></a> <span class="n">intpars</span> <span class="o">=</span> <span class="n">squad</span><span class="o">.</span><span class="vm">__code__</span><span class="o">.</span><span class="n">co_varnames</span><span class="p">[</span><span class="mi">3</span><span class="p">:</span><span class="mi">3</span> <span class="o">+</span> <span class="nb">len</span><span class="p">(</span><span class="n">squad</span><span class="o">.</span><span class="vm">__defaults__</span><span class="p">)]</span> </span><span id="quad-66"><a href="#quad-66"><span class="linenos">66</span></a> <span class="n">intpars</span> <span class="o">=</span> <span class="n">squad</span><span class="o">.</span><span class="vm">__code__</span><span class="o">.</span><span class="n">co_varnames</span><span class="p">[</span><span class="mi">3</span><span class="p">:</span><span class="mi">3</span> <span class="o">+</span> <span class="nb">len</span><span class="p">(</span><span class="n">squad</span><span class="o">.</span><span class="vm">__defaults__</span><span class="p">)]</span>
</span><span id="quad-66"><a href="#quad-66"><span class="linenos">66</span></a> <span class="n">ikwargs</span> <span class="o">=</span> <span class="p">{</span><span class="n">k</span><span class="p">:</span> <span class="n">kwargs</span><span class="p">[</span><span class="n">k</span><span class="p">]</span> <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="n">intpars</span> <span class="k">if</span> <span class="n">k</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">}</span> </span><span id="quad-67"><a href="#quad-67"><span class="linenos">67</span></a> <span class="n">ikwargs</span> <span class="o">=</span> <span class="p">{</span><span class="n">k</span><span class="p">:</span> <span class="n">kwargs</span><span class="p">[</span><span class="n">k</span><span class="p">]</span> <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="n">intpars</span> <span class="k">if</span> <span class="n">k</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">}</span>
</span><span id="quad-67"><a href="#quad-67"><span class="linenos">67</span></a> </span><span id="quad-68"><a href="#quad-68"><span class="linenos">68</span></a>
</span><span id="quad-68"><a href="#quad-68"><span class="linenos">68</span></a> <span class="n">integration_result</span> <span class="o">=</span> <span class="n">squad</span><span class="p">(</span><span class="n">ifunc</span><span class="p">,</span> <span class="n">bval</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">bval</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="o">**</span><span class="n">ikwargs</span><span class="p">)</span> </span><span id="quad-69"><a href="#quad-69"><span class="linenos">69</span></a> <span class="n">integration_result</span> <span class="o">=</span> <span class="n">squad</span><span class="p">(</span><span class="n">ifunc</span><span class="p">,</span> <span class="n">bval</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">bval</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="o">**</span><span class="n">ikwargs</span><span class="p">)</span>
</span><span id="quad-69"><a href="#quad-69"><span class="linenos">69</span></a> <span class="n">val</span> <span class="o">=</span> <span class="n">integration_result</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> </span><span id="quad-70"><a href="#quad-70"><span class="linenos">70</span></a> <span class="n">val</span> <span class="o">=</span> <span class="n">integration_result</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
</span><span id="quad-70"><a href="#quad-70"><span class="linenos">70</span></a> </span><span id="quad-71"><a href="#quad-71"><span class="linenos">71</span></a>
</span><span id="quad-71"><a href="#quad-71"><span class="linenos">71</span></a> <span class="n">jac</span> <span class="o">=</span> <span class="n">jacobian</span><span class="p">(</span><span class="n">func</span><span class="p">)</span> </span><span id="quad-72"><a href="#quad-72"><span class="linenos">72</span></a> <span class="n">jac</span> <span class="o">=</span> <span class="n">jacobian</span><span class="p">(</span><span class="n">func</span><span class="p">)</span>
</span><span id="quad-72"><a href="#quad-72"><span class="linenos">72</span></a> </span><span id="quad-73"><a href="#quad-73"><span class="linenos">73</span></a>
</span><span id="quad-73"><a href="#quad-73"><span class="linenos">73</span></a> <span class="n">derivint</span> <span class="o">=</span> <span class="p">[]</span> </span><span id="quad-74"><a href="#quad-74"><span class="linenos">74</span></a> <span class="n">derivint</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="quad-74"><a href="#quad-74"><span class="linenos">74</span></a> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">Np</span><span class="p">):</span> </span><span id="quad-75"><a href="#quad-75"><span class="linenos">75</span></a> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">Np</span><span class="p">):</span>
</span><span id="quad-75"><a href="#quad-75"><span class="linenos">75</span></a> <span class="k">if</span> <span class="n">isobs</span><span class="p">[</span><span class="n">i</span><span class="p">]:</span> </span><span id="quad-76"><a href="#quad-76"><span class="linenos">76</span></a> <span class="k">if</span> <span class="n">isobs</span><span class="p">[</span><span class="n">i</span><span class="p">]:</span>
</span><span id="quad-76"><a href="#quad-76"><span class="linenos">76</span></a> <span class="n">ifunc</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">vectorize</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">jac</span><span class="p">(</span><span class="n">pval</span><span class="p">,</span> <span class="n">x</span><span class="p">)[</span><span class="n">i</span><span class="p">])</span> </span><span id="quad-77"><a href="#quad-77"><span class="linenos">77</span></a> <span class="n">ifunc</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">vectorize</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">,</span> <span class="n">i</span><span class="o">=</span><span class="n">i</span><span class="p">:</span> <span class="n">jac</span><span class="p">(</span><span class="n">pval</span><span class="p">,</span> <span class="n">x</span><span class="p">)[</span><span class="n">i</span><span class="p">])</span>
</span><span id="quad-77"><a href="#quad-77"><span class="linenos">77</span></a> <span class="n">derivint</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">squad</span><span class="p">(</span><span class="n">ifunc</span><span class="p">,</span> <span class="n">bounds</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">bounds</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="o">**</span><span class="n">ikwargs</span><span class="p">)[</span><span class="mi">0</span><span class="p">])</span> </span><span id="quad-78"><a href="#quad-78"><span class="linenos">78</span></a> <span class="n">derivint</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">squad</span><span class="p">(</span><span class="n">ifunc</span><span class="p">,</span> <span class="n">bounds</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">bounds</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="o">**</span><span class="n">ikwargs</span><span class="p">)[</span><span class="mi">0</span><span class="p">])</span>
</span><span id="quad-78"><a href="#quad-78"><span class="linenos">78</span></a> </span><span id="quad-79"><a href="#quad-79"><span class="linenos">79</span></a>
</span><span id="quad-79"><a href="#quad-79"><span class="linenos">79</span></a> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">2</span><span class="p">):</span> </span><span id="quad-80"><a href="#quad-80"><span class="linenos">80</span></a> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">2</span><span class="p">):</span>
</span><span id="quad-80"><a href="#quad-80"><span class="linenos">80</span></a> <span class="k">if</span> <span class="n">isobs_b</span><span class="p">[</span><span class="n">i</span><span class="p">]:</span> </span><span id="quad-81"><a href="#quad-81"><span class="linenos">81</span></a> <span class="k">if</span> <span class="n">isobs_b</span><span class="p">[</span><span class="n">i</span><span class="p">]:</span>
</span><span id="quad-81"><a href="#quad-81"><span class="linenos">81</span></a> <span class="n">derivint</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">bsign</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">*</span> <span class="n">func</span><span class="p">(</span><span class="n">pval</span><span class="p">,</span> <span class="n">bval</span><span class="p">[</span><span class="n">i</span><span class="p">]))</span> </span><span id="quad-82"><a href="#quad-82"><span class="linenos">82</span></a> <span class="n">derivint</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">bsign</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">*</span> <span class="n">func</span><span class="p">(</span><span class="n">pval</span><span class="p">,</span> <span class="n">bval</span><span class="p">[</span><span class="n">i</span><span class="p">]))</span>
</span><span id="quad-82"><a href="#quad-82"><span class="linenos">82</span></a> </span><span id="quad-83"><a href="#quad-83"><span class="linenos">83</span></a>
</span><span id="quad-83"><a href="#quad-83"><span class="linenos">83</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">derivint</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span> </span><span id="quad-84"><a href="#quad-84"><span class="linenos">84</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">derivint</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
</span><span id="quad-84"><a href="#quad-84"><span class="linenos">84</span></a> <span class="k">return</span> <span class="n">integration_result</span> </span><span id="quad-85"><a href="#quad-85"><span class="linenos">85</span></a> <span class="k">return</span> <span class="n">integration_result</span>
</span><span id="quad-85"><a href="#quad-85"><span class="linenos">85</span></a> </span><span id="quad-86"><a href="#quad-86"><span class="linenos">86</span></a>
</span><span id="quad-86"><a href="#quad-86"><span class="linenos">86</span></a> <span class="n">res</span> <span class="o">=</span> <span class="n">derived_observable</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">:</span> <span class="mi">0</span> <span class="o">*</span> <span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="n">np</span><span class="o">.</span><span class="n">finfo</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">float64</span><span class="p">)</span><span class="o">.</span><span class="n">eps</span><span class="p">)</span> <span class="o">*</span> <span class="p">(</span><span class="n">pval</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="n">np</span><span class="o">.</span><span class="n">finfo</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">float64</span><span class="p">)</span><span class="o">.</span><span class="n">eps</span><span class="p">)</span> <span class="o">+</span> <span class="n">val</span><span class="p">,</span> <span class="n">pobs</span> <span class="o">+</span> <span class="n">bobs</span><span class="p">,</span> <span class="n">man_grad</span><span class="o">=</span><span class="n">derivint</span><span class="p">)</span> </span><span id="quad-87"><a href="#quad-87"><span class="linenos">87</span></a> <span class="n">res</span> <span class="o">=</span> <span class="n">derived_observable</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">:</span> <span class="mi">0</span> <span class="o">*</span> <span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="n">np</span><span class="o">.</span><span class="n">finfo</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">float64</span><span class="p">)</span><span class="o">.</span><span class="n">eps</span><span class="p">)</span> <span class="o">*</span> <span class="p">(</span><span class="n">pval</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="n">np</span><span class="o">.</span><span class="n">finfo</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">float64</span><span class="p">)</span><span class="o">.</span><span class="n">eps</span><span class="p">)</span> <span class="o">+</span> <span class="n">val</span><span class="p">,</span> <span class="n">pobs</span> <span class="o">+</span> <span class="n">bobs</span><span class="p">,</span> <span class="n">man_grad</span><span class="o">=</span><span class="n">derivint</span><span class="p">)</span>
</span><span id="quad-87"><a href="#quad-87"><span class="linenos">87</span></a> </span><span id="quad-88"><a href="#quad-88"><span class="linenos">88</span></a>
</span><span id="quad-88"><a href="#quad-88"><span class="linenos">88</span></a> <span class="k">return</span> <span class="p">(</span><span class="n">res</span><span class="p">,</span> <span class="o">*</span><span class="n">integration_result</span><span class="p">[</span><span class="mi">1</span><span class="p">:])</span> </span><span id="quad-89"><a href="#quad-89"><span class="linenos">89</span></a> <span class="k">return</span> <span class="p">(</span><span class="n">res</span><span class="p">,</span> <span class="o">*</span><span class="n">integration_result</span><span class="p">[</span><span class="mi">1</span><span class="p">:])</span>
</span></pre></div> </span></pre></div>

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<label class="view-source-button" for="mod-misc-view-source"><span>View Source</span></label> <label class="view-source-button" for="mod-misc-view-source"><span>View Source</span></label>
<div class="pdoc-code codehilite"><pre><span></span><span id="L-1"><a href="#L-1"><span class="linenos"> 1</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">platform</span> <div class="pdoc-code codehilite"><pre><span></span><span id="L-1"><a href="#L-1"><span class="linenos"> 1</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">pickle</span>
</span><span id="L-2"><a href="#L-2"><span class="linenos"> 2</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span> </span><span id="L-2"><a href="#L-2"><span class="linenos"> 2</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">platform</span>
</span><span id="L-3"><a href="#L-3"><span class="linenos"> 3</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">scipy</span> </span><span id="L-3"><a href="#L-3"><span class="linenos"> 3</span></a>
</span><span id="L-4"><a href="#L-4"><span class="linenos"> 4</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">matplotlib</span> </span><span id="L-4"><a href="#L-4"><span class="linenos"> 4</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">matplotlib</span>
</span><span id="L-5"><a href="#L-5"><span class="linenos"> 5</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">matplotlib.pyplot</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">plt</span> </span><span id="L-5"><a href="#L-5"><span class="linenos"> 5</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">matplotlib.pyplot</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">plt</span>
</span><span id="L-6"><a href="#L-6"><span class="linenos"> 6</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">pandas</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">pd</span> </span><span id="L-6"><a href="#L-6"><span class="linenos"> 6</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
</span><span id="L-7"><a href="#L-7"><span class="linenos"> 7</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">pickle</span> </span><span id="L-7"><a href="#L-7"><span class="linenos"> 7</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">pandas</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">pd</span>
</span><span id="L-8"><a href="#L-8"><span class="linenos"> 8</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">.obs</span><span class="w"> </span><span class="kn">import</span> <span class="n">Obs</span> </span><span id="L-8"><a href="#L-8"><span class="linenos"> 8</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">scipy</span>
</span><span id="L-9"><a href="#L-9"><span class="linenos"> 9</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">.version</span><span class="w"> </span><span class="kn">import</span> <span class="n">__version__</span> </span><span id="L-9"><a href="#L-9"><span class="linenos"> 9</span></a>
</span><span id="L-10"><a href="#L-10"><span class="linenos"> 10</span></a> </span><span id="L-10"><a href="#L-10"><span class="linenos"> 10</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">.obs</span><span class="w"> </span><span class="kn">import</span> <span class="n">Obs</span>
</span><span id="L-11"><a href="#L-11"><span class="linenos"> 11</span></a> </span><span id="L-11"><a href="#L-11"><span class="linenos"> 11</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">.version</span><span class="w"> </span><span class="kn">import</span> <span class="n">__version__</span>
</span><span id="L-12"><a href="#L-12"><span class="linenos"> 12</span></a><span class="k">def</span><span class="w"> </span><span class="nf">print_config</span><span class="p">():</span> </span><span id="L-12"><a href="#L-12"><span class="linenos"> 12</span></a>
</span><span id="L-13"><a href="#L-13"><span class="linenos"> 13</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Print information about version of python, pyerrors and dependencies.&quot;&quot;&quot;</span> </span><span id="L-13"><a href="#L-13"><span class="linenos"> 13</span></a>
</span><span id="L-14"><a href="#L-14"><span class="linenos"> 14</span></a> <span class="n">config</span> <span class="o">=</span> <span class="p">{</span><span class="s2">&quot;system&quot;</span><span class="p">:</span> <span class="n">platform</span><span class="o">.</span><span class="n">system</span><span class="p">(),</span> </span><span id="L-14"><a href="#L-14"><span class="linenos"> 14</span></a><span class="k">def</span><span class="w"> </span><span class="nf">print_config</span><span class="p">():</span>
</span><span id="L-15"><a href="#L-15"><span class="linenos"> 15</span></a> <span class="s2">&quot;python&quot;</span><span class="p">:</span> <span class="n">platform</span><span class="o">.</span><span class="n">python_version</span><span class="p">(),</span> </span><span id="L-15"><a href="#L-15"><span class="linenos"> 15</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Print information about version of python, pyerrors and dependencies.&quot;&quot;&quot;</span>
</span><span id="L-16"><a href="#L-16"><span class="linenos"> 16</span></a> <span class="s2">&quot;pyerrors&quot;</span><span class="p">:</span> <span class="n">__version__</span><span class="p">,</span> </span><span id="L-16"><a href="#L-16"><span class="linenos"> 16</span></a> <span class="n">config</span> <span class="o">=</span> <span class="p">{</span><span class="s2">&quot;system&quot;</span><span class="p">:</span> <span class="n">platform</span><span class="o">.</span><span class="n">system</span><span class="p">(),</span>
</span><span id="L-17"><a href="#L-17"><span class="linenos"> 17</span></a> <span class="s2">&quot;numpy&quot;</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">__version__</span><span class="p">,</span> </span><span id="L-17"><a href="#L-17"><span class="linenos"> 17</span></a> <span class="s2">&quot;python&quot;</span><span class="p">:</span> <span class="n">platform</span><span class="o">.</span><span class="n">python_version</span><span class="p">(),</span>
</span><span id="L-18"><a href="#L-18"><span class="linenos"> 18</span></a> <span class="s2">&quot;scipy&quot;</span><span class="p">:</span> <span class="n">scipy</span><span class="o">.</span><span class="n">__version__</span><span class="p">,</span> </span><span id="L-18"><a href="#L-18"><span class="linenos"> 18</span></a> <span class="s2">&quot;pyerrors&quot;</span><span class="p">:</span> <span class="n">__version__</span><span class="p">,</span>
</span><span id="L-19"><a href="#L-19"><span class="linenos"> 19</span></a> <span class="s2">&quot;matplotlib&quot;</span><span class="p">:</span> <span class="n">matplotlib</span><span class="o">.</span><span class="n">__version__</span><span class="p">,</span> </span><span id="L-19"><a href="#L-19"><span class="linenos"> 19</span></a> <span class="s2">&quot;numpy&quot;</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">__version__</span><span class="p">,</span>
</span><span id="L-20"><a href="#L-20"><span class="linenos"> 20</span></a> <span class="s2">&quot;pandas&quot;</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">__version__</span><span class="p">}</span> </span><span id="L-20"><a href="#L-20"><span class="linenos"> 20</span></a> <span class="s2">&quot;scipy&quot;</span><span class="p">:</span> <span class="n">scipy</span><span class="o">.</span><span class="n">__version__</span><span class="p">,</span>
</span><span id="L-21"><a href="#L-21"><span class="linenos"> 21</span></a> </span><span id="L-21"><a href="#L-21"><span class="linenos"> 21</span></a> <span class="s2">&quot;matplotlib&quot;</span><span class="p">:</span> <span class="n">matplotlib</span><span class="o">.</span><span class="n">__version__</span><span class="p">,</span>
</span><span id="L-22"><a href="#L-22"><span class="linenos"> 22</span></a> <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">value</span> <span class="ow">in</span> <span class="n">config</span><span class="o">.</span><span class="n">items</span><span class="p">():</span> </span><span id="L-22"><a href="#L-22"><span class="linenos"> 22</span></a> <span class="s2">&quot;pandas&quot;</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">__version__</span><span class="p">}</span>
</span><span id="L-23"><a href="#L-23"><span class="linenos"> 23</span></a> <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">key</span><span class="si">:</span><span class="s2"> &lt;10</span><span class="si">}</span><span class="se">\t</span><span class="s2"> </span><span class="si">{</span><span class="n">value</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span> </span><span id="L-23"><a href="#L-23"><span class="linenos"> 23</span></a>
</span><span id="L-24"><a href="#L-24"><span class="linenos"> 24</span></a> </span><span id="L-24"><a href="#L-24"><span class="linenos"> 24</span></a> <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">value</span> <span class="ow">in</span> <span class="n">config</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
</span><span id="L-25"><a href="#L-25"><span class="linenos"> 25</span></a> </span><span id="L-25"><a href="#L-25"><span class="linenos"> 25</span></a> <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">key</span><span class="si">:</span><span class="s2"> &lt;10</span><span class="si">}</span><span class="se">\t</span><span class="s2"> </span><span class="si">{</span><span class="n">value</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
</span><span id="L-26"><a href="#L-26"><span class="linenos"> 26</span></a><span class="k">def</span><span class="w"> </span><span class="nf">errorbar</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">axes</span><span class="o">=</span><span class="n">plt</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span> </span><span id="L-26"><a href="#L-26"><span class="linenos"> 26</span></a>
</span><span id="L-27"><a href="#L-27"><span class="linenos"> 27</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;pyerrors wrapper for the errorbars method of matplotlib</span> </span><span id="L-27"><a href="#L-27"><span class="linenos"> 27</span></a>
</span><span id="L-28"><a href="#L-28"><span class="linenos"> 28</span></a> </span><span id="L-28"><a href="#L-28"><span class="linenos"> 28</span></a><span class="k">def</span><span class="w"> </span><span class="nf">errorbar</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">axes</span><span class="o">=</span><span class="n">plt</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
</span><span id="L-29"><a href="#L-29"><span class="linenos"> 29</span></a><span class="sd"> Parameters</span> </span><span id="L-29"><a href="#L-29"><span class="linenos"> 29</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;pyerrors wrapper for the errorbars method of matplotlib</span>
</span><span id="L-30"><a href="#L-30"><span class="linenos"> 30</span></a><span class="sd"> ----------</span> </span><span id="L-30"><a href="#L-30"><span class="linenos"> 30</span></a>
</span><span id="L-31"><a href="#L-31"><span class="linenos"> 31</span></a><span class="sd"> x : list</span> </span><span id="L-31"><a href="#L-31"><span class="linenos"> 31</span></a><span class="sd"> Parameters</span>
</span><span id="L-32"><a href="#L-32"><span class="linenos"> 32</span></a><span class="sd"> A list of x-values which can be Obs.</span> </span><span id="L-32"><a href="#L-32"><span class="linenos"> 32</span></a><span class="sd"> ----------</span>
</span><span id="L-33"><a href="#L-33"><span class="linenos"> 33</span></a><span class="sd"> y : list</span> </span><span id="L-33"><a href="#L-33"><span class="linenos"> 33</span></a><span class="sd"> x : list</span>
</span><span id="L-34"><a href="#L-34"><span class="linenos"> 34</span></a><span class="sd"> A list of y-values which can be Obs.</span> </span><span id="L-34"><a href="#L-34"><span class="linenos"> 34</span></a><span class="sd"> A list of x-values which can be Obs.</span>
</span><span id="L-35"><a href="#L-35"><span class="linenos"> 35</span></a><span class="sd"> axes : (matplotlib.pyplot.axes)</span> </span><span id="L-35"><a href="#L-35"><span class="linenos"> 35</span></a><span class="sd"> y : list</span>
</span><span id="L-36"><a href="#L-36"><span class="linenos"> 36</span></a><span class="sd"> The axes to plot on. default is plt.</span> </span><span id="L-36"><a href="#L-36"><span class="linenos"> 36</span></a><span class="sd"> A list of y-values which can be Obs.</span>
</span><span id="L-37"><a href="#L-37"><span class="linenos"> 37</span></a><span class="sd"> &quot;&quot;&quot;</span> </span><span id="L-37"><a href="#L-37"><span class="linenos"> 37</span></a><span class="sd"> axes : (matplotlib.pyplot.axes)</span>
</span><span id="L-38"><a href="#L-38"><span class="linenos"> 38</span></a> <span class="n">val</span> <span class="o">=</span> <span class="p">{}</span> </span><span id="L-38"><a href="#L-38"><span class="linenos"> 38</span></a><span class="sd"> The axes to plot on. default is plt.</span>
</span><span id="L-39"><a href="#L-39"><span class="linenos"> 39</span></a> <span class="n">err</span> <span class="o">=</span> <span class="p">{}</span> </span><span id="L-39"><a href="#L-39"><span class="linenos"> 39</span></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="L-40"><a href="#L-40"><span class="linenos"> 40</span></a> <span class="k">for</span> <span class="n">name</span><span class="p">,</span> <span class="n">comp</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">([</span><span class="s2">&quot;x&quot;</span><span class="p">,</span> <span class="s2">&quot;y&quot;</span><span class="p">],</span> <span class="p">[</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">]):</span> </span><span id="L-40"><a href="#L-40"><span class="linenos"> 40</span></a> <span class="n">val</span> <span class="o">=</span> <span class="p">{}</span>
</span><span id="L-41"><a href="#L-41"><span class="linenos"> 41</span></a> <span class="k">if</span> <span class="nb">all</span><span class="p">(</span><span class="nb">isinstance</span><span class="p">(</span><span class="n">o</span><span class="p">,</span> <span class="n">Obs</span><span class="p">)</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">comp</span><span class="p">):</span> </span><span id="L-41"><a href="#L-41"><span class="linenos"> 41</span></a> <span class="n">err</span> <span class="o">=</span> <span class="p">{}</span>
</span><span id="L-42"><a href="#L-42"><span class="linenos"> 42</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="nb">all</span><span class="p">(</span><span class="nb">hasattr</span><span class="p">(</span><span class="n">o</span><span class="p">,</span> <span class="s1">&#39;e_dvalue&#39;</span><span class="p">)</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">comp</span><span class="p">):</span> </span><span id="L-42"><a href="#L-42"><span class="linenos"> 42</span></a> <span class="k">for</span> <span class="n">name</span><span class="p">,</span> <span class="n">comp</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">([</span><span class="s2">&quot;x&quot;</span><span class="p">,</span> <span class="s2">&quot;y&quot;</span><span class="p">],</span> <span class="p">[</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">],</span> <span class="n">strict</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
</span><span id="L-43"><a href="#L-43"><span class="linenos"> 43</span></a> <span class="p">[</span><span class="n">o</span><span class="o">.</span><span class="n">gamma_method</span><span class="p">()</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">comp</span><span class="p">]</span> </span><span id="L-43"><a href="#L-43"><span class="linenos"> 43</span></a> <span class="k">if</span> <span class="nb">all</span><span class="p">(</span><span class="nb">isinstance</span><span class="p">(</span><span class="n">o</span><span class="p">,</span> <span class="n">Obs</span><span class="p">)</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">comp</span><span class="p">):</span>
</span><span id="L-44"><a href="#L-44"><span class="linenos"> 44</span></a> <span class="n">val</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="n">o</span><span class="o">.</span><span class="n">value</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">comp</span><span class="p">]</span> </span><span id="L-44"><a href="#L-44"><span class="linenos"> 44</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="nb">all</span><span class="p">(</span><span class="nb">hasattr</span><span class="p">(</span><span class="n">o</span><span class="p">,</span> <span class="s1">&#39;e_dvalue&#39;</span><span class="p">)</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">comp</span><span class="p">):</span>
</span><span id="L-45"><a href="#L-45"><span class="linenos"> 45</span></a> <span class="n">err</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="n">o</span><span class="o">.</span><span class="n">dvalue</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">comp</span><span class="p">]</span> </span><span id="L-45"><a href="#L-45"><span class="linenos"> 45</span></a> <span class="p">[</span><span class="n">o</span><span class="o">.</span><span class="n">gamma_method</span><span class="p">()</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">comp</span><span class="p">]</span>
</span><span id="L-46"><a href="#L-46"><span class="linenos"> 46</span></a> <span class="k">else</span><span class="p">:</span> </span><span id="L-46"><a href="#L-46"><span class="linenos"> 46</span></a> <span class="n">val</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="n">o</span><span class="o">.</span><span class="n">value</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">comp</span><span class="p">]</span>
</span><span id="L-47"><a href="#L-47"><span class="linenos"> 47</span></a> <span class="n">val</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="n">comp</span> </span><span id="L-47"><a href="#L-47"><span class="linenos"> 47</span></a> <span class="n">err</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="n">o</span><span class="o">.</span><span class="n">dvalue</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">comp</span><span class="p">]</span>
</span><span id="L-48"><a href="#L-48"><span class="linenos"> 48</span></a> <span class="n">err</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span> </span><span id="L-48"><a href="#L-48"><span class="linenos"> 48</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="L-49"><a href="#L-49"><span class="linenos"> 49</span></a> </span><span id="L-49"><a href="#L-49"><span class="linenos"> 49</span></a> <span class="n">val</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="n">comp</span>
</span><span id="L-50"><a href="#L-50"><span class="linenos"> 50</span></a> <span class="k">if</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s2">err&quot;</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span> </span><span id="L-50"><a href="#L-50"><span class="linenos"> 50</span></a> <span class="n">err</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span>
</span><span id="L-51"><a href="#L-51"><span class="linenos"> 51</span></a> <span class="n">err</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s2">err&quot;</span><span class="p">)</span> </span><span id="L-51"><a href="#L-51"><span class="linenos"> 51</span></a>
</span><span id="L-52"><a href="#L-52"><span class="linenos"> 52</span></a> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s2">err&quot;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span> </span><span id="L-52"><a href="#L-52"><span class="linenos"> 52</span></a> <span class="k">if</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s2">err&quot;</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
</span><span id="L-53"><a href="#L-53"><span class="linenos"> 53</span></a> </span><span id="L-53"><a href="#L-53"><span class="linenos"> 53</span></a> <span class="n">err</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s2">err&quot;</span><span class="p">)</span>
</span><span id="L-54"><a href="#L-54"><span class="linenos"> 54</span></a> <span class="n">axes</span><span class="o">.</span><span class="n">errorbar</span><span class="p">(</span><span class="n">val</span><span class="p">[</span><span class="s2">&quot;x&quot;</span><span class="p">],</span> <span class="n">val</span><span class="p">[</span><span class="s2">&quot;y&quot;</span><span class="p">],</span> <span class="n">xerr</span><span class="o">=</span><span class="n">err</span><span class="p">[</span><span class="s2">&quot;x&quot;</span><span class="p">],</span> <span class="n">yerr</span><span class="o">=</span><span class="n">err</span><span class="p">[</span><span class="s2">&quot;y&quot;</span><span class="p">],</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span> </span><span id="L-54"><a href="#L-54"><span class="linenos"> 54</span></a> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s2">err&quot;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
</span><span id="L-55"><a href="#L-55"><span class="linenos"> 55</span></a> </span><span id="L-55"><a href="#L-55"><span class="linenos"> 55</span></a>
</span><span id="L-56"><a href="#L-56"><span class="linenos"> 56</span></a> </span><span id="L-56"><a href="#L-56"><span class="linenos"> 56</span></a> <span class="n">axes</span><span class="o">.</span><span class="n">errorbar</span><span class="p">(</span><span class="n">val</span><span class="p">[</span><span class="s2">&quot;x&quot;</span><span class="p">],</span> <span class="n">val</span><span class="p">[</span><span class="s2">&quot;y&quot;</span><span class="p">],</span> <span class="n">xerr</span><span class="o">=</span><span class="n">err</span><span class="p">[</span><span class="s2">&quot;x&quot;</span><span class="p">],</span> <span class="n">yerr</span><span class="o">=</span><span class="n">err</span><span class="p">[</span><span class="s2">&quot;y&quot;</span><span class="p">],</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
</span><span id="L-57"><a href="#L-57"><span class="linenos"> 57</span></a><span class="k">def</span><span class="w"> </span><span class="nf">dump_object</span><span class="p">(</span><span class="n">obj</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span> </span><span id="L-57"><a href="#L-57"><span class="linenos"> 57</span></a>
</span><span id="L-58"><a href="#L-58"><span class="linenos"> 58</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Dump object into pickle file.</span> </span><span id="L-58"><a href="#L-58"><span class="linenos"> 58</span></a>
</span><span id="L-59"><a href="#L-59"><span class="linenos"> 59</span></a> </span><span id="L-59"><a href="#L-59"><span class="linenos"> 59</span></a><span class="k">def</span><span class="w"> </span><span class="nf">dump_object</span><span class="p">(</span><span class="n">obj</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
</span><span id="L-60"><a href="#L-60"><span class="linenos"> 60</span></a><span class="sd"> Parameters</span> </span><span id="L-60"><a href="#L-60"><span class="linenos"> 60</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Dump object into pickle file.</span>
</span><span id="L-61"><a href="#L-61"><span class="linenos"> 61</span></a><span class="sd"> ----------</span> </span><span id="L-61"><a href="#L-61"><span class="linenos"> 61</span></a>
</span><span id="L-62"><a href="#L-62"><span class="linenos"> 62</span></a><span class="sd"> obj : object</span> </span><span id="L-62"><a href="#L-62"><span class="linenos"> 62</span></a><span class="sd"> Parameters</span>
</span><span id="L-63"><a href="#L-63"><span class="linenos"> 63</span></a><span class="sd"> object to be saved in the pickle file</span> </span><span id="L-63"><a href="#L-63"><span class="linenos"> 63</span></a><span class="sd"> ----------</span>
</span><span id="L-64"><a href="#L-64"><span class="linenos"> 64</span></a><span class="sd"> name : str</span> </span><span id="L-64"><a href="#L-64"><span class="linenos"> 64</span></a><span class="sd"> obj : object</span>
</span><span id="L-65"><a href="#L-65"><span class="linenos"> 65</span></a><span class="sd"> name of the file</span> </span><span id="L-65"><a href="#L-65"><span class="linenos"> 65</span></a><span class="sd"> object to be saved in the pickle file</span>
</span><span id="L-66"><a href="#L-66"><span class="linenos"> 66</span></a><span class="sd"> path : str</span> </span><span id="L-66"><a href="#L-66"><span class="linenos"> 66</span></a><span class="sd"> name : str</span>
</span><span id="L-67"><a href="#L-67"><span class="linenos"> 67</span></a><span class="sd"> specifies a custom path for the file (default &#39;.&#39;)</span> </span><span id="L-67"><a href="#L-67"><span class="linenos"> 67</span></a><span class="sd"> name of the file</span>
</span><span id="L-68"><a href="#L-68"><span class="linenos"> 68</span></a> </span><span id="L-68"><a href="#L-68"><span class="linenos"> 68</span></a><span class="sd"> path : str</span>
</span><span id="L-69"><a href="#L-69"><span class="linenos"> 69</span></a><span class="sd"> Returns</span> </span><span id="L-69"><a href="#L-69"><span class="linenos"> 69</span></a><span class="sd"> specifies a custom path for the file (default &#39;.&#39;)</span>
</span><span id="L-70"><a href="#L-70"><span class="linenos"> 70</span></a><span class="sd"> -------</span> </span><span id="L-70"><a href="#L-70"><span class="linenos"> 70</span></a>
</span><span id="L-71"><a href="#L-71"><span class="linenos"> 71</span></a><span class="sd"> None</span> </span><span id="L-71"><a href="#L-71"><span class="linenos"> 71</span></a><span class="sd"> Returns</span>
</span><span id="L-72"><a href="#L-72"><span class="linenos"> 72</span></a><span class="sd"> &quot;&quot;&quot;</span> </span><span id="L-72"><a href="#L-72"><span class="linenos"> 72</span></a><span class="sd"> -------</span>
</span><span id="L-73"><a href="#L-73"><span class="linenos"> 73</span></a> <span class="k">if</span> <span class="s1">&#39;path&#39;</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span> </span><span id="L-73"><a href="#L-73"><span class="linenos"> 73</span></a><span class="sd"> None</span>
</span><span id="L-74"><a href="#L-74"><span class="linenos"> 74</span></a> <span class="n">file_name</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;path&#39;</span><span class="p">)</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">name</span> <span class="o">+</span> <span class="s1">&#39;.p&#39;</span> </span><span id="L-74"><a href="#L-74"><span class="linenos"> 74</span></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="L-75"><a href="#L-75"><span class="linenos"> 75</span></a> <span class="k">else</span><span class="p">:</span> </span><span id="L-75"><a href="#L-75"><span class="linenos"> 75</span></a> <span class="k">if</span> <span class="s1">&#39;path&#39;</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
</span><span id="L-76"><a href="#L-76"><span class="linenos"> 76</span></a> <span class="n">file_name</span> <span class="o">=</span> <span class="n">name</span> <span class="o">+</span> <span class="s1">&#39;.p&#39;</span> </span><span id="L-76"><a href="#L-76"><span class="linenos"> 76</span></a> <span class="n">file_name</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;path&#39;</span><span class="p">)</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">name</span> <span class="o">+</span> <span class="s1">&#39;.p&#39;</span>
</span><span id="L-77"><a href="#L-77"><span class="linenos"> 77</span></a> <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">file_name</span><span class="p">,</span> <span class="s1">&#39;wb&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fb</span><span class="p">:</span> </span><span id="L-77"><a href="#L-77"><span class="linenos"> 77</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="L-78"><a href="#L-78"><span class="linenos"> 78</span></a> <span class="n">pickle</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="n">obj</span><span class="p">,</span> <span class="n">fb</span><span class="p">)</span> </span><span id="L-78"><a href="#L-78"><span class="linenos"> 78</span></a> <span class="n">file_name</span> <span class="o">=</span> <span class="n">name</span> <span class="o">+</span> <span class="s1">&#39;.p&#39;</span>
</span><span id="L-79"><a href="#L-79"><span class="linenos"> 79</span></a> </span><span id="L-79"><a href="#L-79"><span class="linenos"> 79</span></a> <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">file_name</span><span class="p">,</span> <span class="s1">&#39;wb&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fb</span><span class="p">:</span>
</span><span id="L-80"><a href="#L-80"><span class="linenos"> 80</span></a> </span><span id="L-80"><a href="#L-80"><span class="linenos"> 80</span></a> <span class="n">pickle</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="n">obj</span><span class="p">,</span> <span class="n">fb</span><span class="p">)</span>
</span><span id="L-81"><a href="#L-81"><span class="linenos"> 81</span></a><span class="k">def</span><span class="w"> </span><span class="nf">load_object</span><span class="p">(</span><span class="n">path</span><span class="p">):</span> </span><span id="L-81"><a href="#L-81"><span class="linenos"> 81</span></a>
</span><span id="L-82"><a href="#L-82"><span class="linenos"> 82</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Load object from pickle file.</span> </span><span id="L-82"><a href="#L-82"><span class="linenos"> 82</span></a>
</span><span id="L-83"><a href="#L-83"><span class="linenos"> 83</span></a> </span><span id="L-83"><a href="#L-83"><span class="linenos"> 83</span></a><span class="k">def</span><span class="w"> </span><span class="nf">load_object</span><span class="p">(</span><span class="n">path</span><span class="p">):</span>
</span><span id="L-84"><a href="#L-84"><span class="linenos"> 84</span></a><span class="sd"> Parameters</span> </span><span id="L-84"><a href="#L-84"><span class="linenos"> 84</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Load object from pickle file.</span>
</span><span id="L-85"><a href="#L-85"><span class="linenos"> 85</span></a><span class="sd"> ----------</span> </span><span id="L-85"><a href="#L-85"><span class="linenos"> 85</span></a>
</span><span id="L-86"><a href="#L-86"><span class="linenos"> 86</span></a><span class="sd"> path : str</span> </span><span id="L-86"><a href="#L-86"><span class="linenos"> 86</span></a><span class="sd"> Parameters</span>
</span><span id="L-87"><a href="#L-87"><span class="linenos"> 87</span></a><span class="sd"> path to the file</span> </span><span id="L-87"><a href="#L-87"><span class="linenos"> 87</span></a><span class="sd"> ----------</span>
</span><span id="L-88"><a href="#L-88"><span class="linenos"> 88</span></a> </span><span id="L-88"><a href="#L-88"><span class="linenos"> 88</span></a><span class="sd"> path : str</span>
</span><span id="L-89"><a href="#L-89"><span class="linenos"> 89</span></a><span class="sd"> Returns</span> </span><span id="L-89"><a href="#L-89"><span class="linenos"> 89</span></a><span class="sd"> path to the file</span>
</span><span id="L-90"><a href="#L-90"><span class="linenos"> 90</span></a><span class="sd"> -------</span> </span><span id="L-90"><a href="#L-90"><span class="linenos"> 90</span></a>
</span><span id="L-91"><a href="#L-91"><span class="linenos"> 91</span></a><span class="sd"> object : Obs</span> </span><span id="L-91"><a href="#L-91"><span class="linenos"> 91</span></a><span class="sd"> Returns</span>
</span><span id="L-92"><a href="#L-92"><span class="linenos"> 92</span></a><span class="sd"> Loaded Object</span> </span><span id="L-92"><a href="#L-92"><span class="linenos"> 92</span></a><span class="sd"> -------</span>
</span><span id="L-93"><a href="#L-93"><span class="linenos"> 93</span></a><span class="sd"> &quot;&quot;&quot;</span> </span><span id="L-93"><a href="#L-93"><span class="linenos"> 93</span></a><span class="sd"> object : Obs</span>
</span><span id="L-94"><a href="#L-94"><span class="linenos"> 94</span></a> <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="s1">&#39;rb&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span> </span><span id="L-94"><a href="#L-94"><span class="linenos"> 94</span></a><span class="sd"> Loaded Object</span>
</span><span id="L-95"><a href="#L-95"><span class="linenos"> 95</span></a> <span class="k">return</span> <span class="n">pickle</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">file</span><span class="p">)</span> </span><span id="L-95"><a href="#L-95"><span class="linenos"> 95</span></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="L-96"><a href="#L-96"><span class="linenos"> 96</span></a> </span><span id="L-96"><a href="#L-96"><span class="linenos"> 96</span></a> <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="s1">&#39;rb&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
</span><span id="L-97"><a href="#L-97"><span class="linenos"> 97</span></a> </span><span id="L-97"><a href="#L-97"><span class="linenos"> 97</span></a> <span class="k">return</span> <span class="n">pickle</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">file</span><span class="p">)</span>
</span><span id="L-98"><a href="#L-98"><span class="linenos"> 98</span></a><span class="k">def</span><span class="w"> </span><span class="nf">pseudo_Obs</span><span class="p">(</span><span class="n">value</span><span class="p">,</span> <span class="n">dvalue</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">samples</span><span class="o">=</span><span class="mi">1000</span><span class="p">):</span> </span><span id="L-98"><a href="#L-98"><span class="linenos"> 98</span></a>
</span><span id="L-99"><a href="#L-99"><span class="linenos"> 99</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Generate an Obs object with given value, dvalue and name for test purposes</span> </span><span id="L-99"><a href="#L-99"><span class="linenos"> 99</span></a>
</span><span id="L-100"><a href="#L-100"><span class="linenos">100</span></a> </span><span id="L-100"><a href="#L-100"><span class="linenos">100</span></a><span class="k">def</span><span class="w"> </span><span class="nf">pseudo_Obs</span><span class="p">(</span><span class="n">value</span><span class="p">,</span> <span class="n">dvalue</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">samples</span><span class="o">=</span><span class="mi">1000</span><span class="p">):</span>
</span><span id="L-101"><a href="#L-101"><span class="linenos">101</span></a><span class="sd"> Parameters</span> </span><span id="L-101"><a href="#L-101"><span class="linenos">101</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Generate an Obs object with given value, dvalue and name for test purposes</span>
</span><span id="L-102"><a href="#L-102"><span class="linenos">102</span></a><span class="sd"> ----------</span> </span><span id="L-102"><a href="#L-102"><span class="linenos">102</span></a>
</span><span id="L-103"><a href="#L-103"><span class="linenos">103</span></a><span class="sd"> value : float</span> </span><span id="L-103"><a href="#L-103"><span class="linenos">103</span></a><span class="sd"> Parameters</span>
</span><span id="L-104"><a href="#L-104"><span class="linenos">104</span></a><span class="sd"> central value of the Obs to be generated.</span> </span><span id="L-104"><a href="#L-104"><span class="linenos">104</span></a><span class="sd"> ----------</span>
</span><span id="L-105"><a href="#L-105"><span class="linenos">105</span></a><span class="sd"> dvalue : float</span> </span><span id="L-105"><a href="#L-105"><span class="linenos">105</span></a><span class="sd"> value : float</span>
</span><span id="L-106"><a href="#L-106"><span class="linenos">106</span></a><span class="sd"> error of the Obs to be generated.</span> </span><span id="L-106"><a href="#L-106"><span class="linenos">106</span></a><span class="sd"> central value of the Obs to be generated.</span>
</span><span id="L-107"><a href="#L-107"><span class="linenos">107</span></a><span class="sd"> name : str</span> </span><span id="L-107"><a href="#L-107"><span class="linenos">107</span></a><span class="sd"> dvalue : float</span>
</span><span id="L-108"><a href="#L-108"><span class="linenos">108</span></a><span class="sd"> name of the ensemble for which the Obs is to be generated.</span> </span><span id="L-108"><a href="#L-108"><span class="linenos">108</span></a><span class="sd"> error of the Obs to be generated.</span>
</span><span id="L-109"><a href="#L-109"><span class="linenos">109</span></a><span class="sd"> samples: int</span> </span><span id="L-109"><a href="#L-109"><span class="linenos">109</span></a><span class="sd"> name : str</span>
</span><span id="L-110"><a href="#L-110"><span class="linenos">110</span></a><span class="sd"> number of samples for the Obs (default 1000).</span> </span><span id="L-110"><a href="#L-110"><span class="linenos">110</span></a><span class="sd"> name of the ensemble for which the Obs is to be generated.</span>
</span><span id="L-111"><a href="#L-111"><span class="linenos">111</span></a> </span><span id="L-111"><a href="#L-111"><span class="linenos">111</span></a><span class="sd"> samples: int</span>
</span><span id="L-112"><a href="#L-112"><span class="linenos">112</span></a><span class="sd"> Returns</span> </span><span id="L-112"><a href="#L-112"><span class="linenos">112</span></a><span class="sd"> number of samples for the Obs (default 1000).</span>
</span><span id="L-113"><a href="#L-113"><span class="linenos">113</span></a><span class="sd"> -------</span> </span><span id="L-113"><a href="#L-113"><span class="linenos">113</span></a>
</span><span id="L-114"><a href="#L-114"><span class="linenos">114</span></a><span class="sd"> res : Obs</span> </span><span id="L-114"><a href="#L-114"><span class="linenos">114</span></a><span class="sd"> Returns</span>
</span><span id="L-115"><a href="#L-115"><span class="linenos">115</span></a><span class="sd"> Generated Observable</span> </span><span id="L-115"><a href="#L-115"><span class="linenos">115</span></a><span class="sd"> -------</span>
</span><span id="L-116"><a href="#L-116"><span class="linenos">116</span></a><span class="sd"> &quot;&quot;&quot;</span> </span><span id="L-116"><a href="#L-116"><span class="linenos">116</span></a><span class="sd"> res : Obs</span>
</span><span id="L-117"><a href="#L-117"><span class="linenos">117</span></a> <span class="k">if</span> <span class="n">dvalue</span> <span class="o">&lt;=</span> <span class="mf">0.0</span><span class="p">:</span> </span><span id="L-117"><a href="#L-117"><span class="linenos">117</span></a><span class="sd"> Generated Observable</span>
</span><span id="L-118"><a href="#L-118"><span class="linenos">118</span></a> <span class="k">return</span> <span class="n">Obs</span><span class="p">([</span><span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="n">samples</span><span class="p">)</span> <span class="o">+</span> <span class="n">value</span><span class="p">],</span> <span class="p">[</span><span class="n">name</span><span class="p">])</span> </span><span id="L-118"><a href="#L-118"><span class="linenos">118</span></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="L-119"><a href="#L-119"><span class="linenos">119</span></a> <span class="k">else</span><span class="p">:</span> </span><span id="L-119"><a href="#L-119"><span class="linenos">119</span></a> <span class="k">if</span> <span class="n">dvalue</span> <span class="o">&lt;=</span> <span class="mf">0.0</span><span class="p">:</span>
</span><span id="L-120"><a href="#L-120"><span class="linenos">120</span></a> <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">100</span><span class="p">):</span> </span><span id="L-120"><a href="#L-120"><span class="linenos">120</span></a> <span class="k">return</span> <span class="n">Obs</span><span class="p">([</span><span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="n">samples</span><span class="p">)</span> <span class="o">+</span> <span class="n">value</span><span class="p">],</span> <span class="p">[</span><span class="n">name</span><span class="p">])</span>
</span><span id="L-121"><a href="#L-121"><span class="linenos">121</span></a> <span class="n">deltas</span> <span class="o">=</span> <span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">normal</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span> <span class="n">dvalue</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="n">samples</span><span class="p">),</span> <span class="n">samples</span><span class="p">)]</span> </span><span id="L-121"><a href="#L-121"><span class="linenos">121</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="L-122"><a href="#L-122"><span class="linenos">122</span></a> <span class="n">deltas</span> <span class="o">-=</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">deltas</span><span class="p">)</span> </span><span id="L-122"><a href="#L-122"><span class="linenos">122</span></a> <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">100</span><span class="p">):</span>
</span><span id="L-123"><a href="#L-123"><span class="linenos">123</span></a> <span class="n">deltas</span> <span class="o">*=</span> <span class="n">dvalue</span> <span class="o">/</span> <span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">((</span><span class="n">np</span><span class="o">.</span><span class="n">var</span><span class="p">(</span><span class="n">deltas</span><span class="p">)</span> <span class="o">/</span> <span class="n">samples</span><span class="p">))</span> <span class="o">/</span> <span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="mi">1</span> <span class="o">+</span> <span class="mi">3</span> <span class="o">/</span> <span class="n">samples</span><span class="p">)</span> </span><span id="L-123"><a href="#L-123"><span class="linenos">123</span></a> <span class="n">deltas</span> <span class="o">=</span> <span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">normal</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span> <span class="n">dvalue</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="n">samples</span><span class="p">),</span> <span class="n">samples</span><span class="p">)]</span> <span class="c1"># noqa: NPY002</span>
</span><span id="L-124"><a href="#L-124"><span class="linenos">124</span></a> <span class="n">deltas</span> <span class="o">+=</span> <span class="n">value</span> </span><span id="L-124"><a href="#L-124"><span class="linenos">124</span></a> <span class="n">deltas</span> <span class="o">-=</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">deltas</span><span class="p">)</span>
</span><span id="L-125"><a href="#L-125"><span class="linenos">125</span></a> <span class="n">res</span> <span class="o">=</span> <span class="n">Obs</span><span class="p">(</span><span class="n">deltas</span><span class="p">,</span> <span class="p">[</span><span class="n">name</span><span class="p">])</span> </span><span id="L-125"><a href="#L-125"><span class="linenos">125</span></a> <span class="n">deltas</span> <span class="o">*=</span> <span class="n">dvalue</span> <span class="o">/</span> <span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">var</span><span class="p">(</span><span class="n">deltas</span><span class="p">)</span> <span class="o">/</span> <span class="n">samples</span><span class="p">)</span> <span class="o">/</span> <span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="mi">1</span> <span class="o">+</span> <span class="mi">3</span> <span class="o">/</span> <span class="n">samples</span><span class="p">)</span>
</span><span id="L-126"><a href="#L-126"><span class="linenos">126</span></a> <span class="n">res</span><span class="o">.</span><span class="n">gamma_method</span><span class="p">(</span><span class="n">S</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">tau_exp</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span> </span><span id="L-126"><a href="#L-126"><span class="linenos">126</span></a> <span class="n">deltas</span> <span class="o">+=</span> <span class="n">value</span>
</span><span id="L-127"><a href="#L-127"><span class="linenos">127</span></a> <span class="k">if</span> <span class="nb">abs</span><span class="p">(</span><span class="n">res</span><span class="o">.</span><span class="n">dvalue</span> <span class="o">-</span> <span class="n">dvalue</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mf">1e-10</span> <span class="o">*</span> <span class="n">dvalue</span><span class="p">:</span> </span><span id="L-127"><a href="#L-127"><span class="linenos">127</span></a> <span class="n">res</span> <span class="o">=</span> <span class="n">Obs</span><span class="p">(</span><span class="n">deltas</span><span class="p">,</span> <span class="p">[</span><span class="n">name</span><span class="p">])</span>
</span><span id="L-128"><a href="#L-128"><span class="linenos">128</span></a> <span class="k">break</span> </span><span id="L-128"><a href="#L-128"><span class="linenos">128</span></a> <span class="n">res</span><span class="o">.</span><span class="n">gamma_method</span><span class="p">(</span><span class="n">S</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">tau_exp</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
</span><span id="L-129"><a href="#L-129"><span class="linenos">129</span></a> </span><span id="L-129"><a href="#L-129"><span class="linenos">129</span></a> <span class="k">if</span> <span class="nb">abs</span><span class="p">(</span><span class="n">res</span><span class="o">.</span><span class="n">dvalue</span> <span class="o">-</span> <span class="n">dvalue</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mf">1e-10</span> <span class="o">*</span> <span class="n">dvalue</span><span class="p">:</span>
</span><span id="L-130"><a href="#L-130"><span class="linenos">130</span></a> <span class="n">res</span><span class="o">.</span><span class="n">_value</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">value</span><span class="p">)</span> </span><span id="L-130"><a href="#L-130"><span class="linenos">130</span></a> <span class="k">break</span>
</span><span id="L-131"><a href="#L-131"><span class="linenos">131</span></a> </span><span id="L-131"><a href="#L-131"><span class="linenos">131</span></a>
</span><span id="L-132"><a href="#L-132"><span class="linenos">132</span></a> <span class="k">return</span> <span class="n">res</span> </span><span id="L-132"><a href="#L-132"><span class="linenos">132</span></a> <span class="n">res</span><span class="o">.</span><span class="n">_value</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">value</span><span class="p">)</span>
</span><span id="L-133"><a href="#L-133"><span class="linenos">133</span></a> </span><span id="L-133"><a href="#L-133"><span class="linenos">133</span></a>
</span><span id="L-134"><a href="#L-134"><span class="linenos">134</span></a> </span><span id="L-134"><a href="#L-134"><span class="linenos">134</span></a> <span class="k">return</span> <span class="n">res</span>
</span><span id="L-135"><a href="#L-135"><span class="linenos">135</span></a><span class="k">def</span><span class="w"> </span><span class="nf">gen_correlated_data</span><span class="p">(</span><span class="n">means</span><span class="p">,</span> <span class="n">cov</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">tau</span><span class="o">=</span><span class="mf">0.5</span><span class="p">,</span> <span class="n">samples</span><span class="o">=</span><span class="mi">1000</span><span class="p">):</span> </span><span id="L-135"><a href="#L-135"><span class="linenos">135</span></a>
</span><span id="L-136"><a href="#L-136"><span class="linenos">136</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot; Generate observables with given covariance and autocorrelation times.</span> </span><span id="L-136"><a href="#L-136"><span class="linenos">136</span></a>
</span><span id="L-137"><a href="#L-137"><span class="linenos">137</span></a> </span><span id="L-137"><a href="#L-137"><span class="linenos">137</span></a><span class="k">def</span><span class="w"> </span><span class="nf">gen_correlated_data</span><span class="p">(</span><span class="n">means</span><span class="p">,</span> <span class="n">cov</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">tau</span><span class="o">=</span><span class="mf">0.5</span><span class="p">,</span> <span class="n">samples</span><span class="o">=</span><span class="mi">1000</span><span class="p">):</span>
</span><span id="L-138"><a href="#L-138"><span class="linenos">138</span></a><span class="sd"> Parameters</span> </span><span id="L-138"><a href="#L-138"><span class="linenos">138</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot; Generate observables with given covariance and autocorrelation times.</span>
</span><span id="L-139"><a href="#L-139"><span class="linenos">139</span></a><span class="sd"> ----------</span> </span><span id="L-139"><a href="#L-139"><span class="linenos">139</span></a>
</span><span id="L-140"><a href="#L-140"><span class="linenos">140</span></a><span class="sd"> means : list</span> </span><span id="L-140"><a href="#L-140"><span class="linenos">140</span></a><span class="sd"> Parameters</span>
</span><span id="L-141"><a href="#L-141"><span class="linenos">141</span></a><span class="sd"> list containing the mean value of each observable.</span> </span><span id="L-141"><a href="#L-141"><span class="linenos">141</span></a><span class="sd"> ----------</span>
</span><span id="L-142"><a href="#L-142"><span class="linenos">142</span></a><span class="sd"> cov : numpy.ndarray</span> </span><span id="L-142"><a href="#L-142"><span class="linenos">142</span></a><span class="sd"> means : list</span>
</span><span id="L-143"><a href="#L-143"><span class="linenos">143</span></a><span class="sd"> covariance matrix for the data to be generated.</span> </span><span id="L-143"><a href="#L-143"><span class="linenos">143</span></a><span class="sd"> list containing the mean value of each observable.</span>
</span><span id="L-144"><a href="#L-144"><span class="linenos">144</span></a><span class="sd"> name : str</span> </span><span id="L-144"><a href="#L-144"><span class="linenos">144</span></a><span class="sd"> cov : numpy.ndarray</span>
</span><span id="L-145"><a href="#L-145"><span class="linenos">145</span></a><span class="sd"> ensemble name for the data to be geneated.</span> </span><span id="L-145"><a href="#L-145"><span class="linenos">145</span></a><span class="sd"> covariance matrix for the data to be generated.</span>
</span><span id="L-146"><a href="#L-146"><span class="linenos">146</span></a><span class="sd"> tau : float or list</span> </span><span id="L-146"><a href="#L-146"><span class="linenos">146</span></a><span class="sd"> name : str</span>
</span><span id="L-147"><a href="#L-147"><span class="linenos">147</span></a><span class="sd"> can either be a real number or a list with an entry for</span> </span><span id="L-147"><a href="#L-147"><span class="linenos">147</span></a><span class="sd"> ensemble name for the data to be geneated.</span>
</span><span id="L-148"><a href="#L-148"><span class="linenos">148</span></a><span class="sd"> every dataset.</span> </span><span id="L-148"><a href="#L-148"><span class="linenos">148</span></a><span class="sd"> tau : float or list</span>
</span><span id="L-149"><a href="#L-149"><span class="linenos">149</span></a><span class="sd"> samples : int</span> </span><span id="L-149"><a href="#L-149"><span class="linenos">149</span></a><span class="sd"> can either be a real number or a list with an entry for</span>
</span><span id="L-150"><a href="#L-150"><span class="linenos">150</span></a><span class="sd"> number of samples to be generated for each observable.</span> </span><span id="L-150"><a href="#L-150"><span class="linenos">150</span></a><span class="sd"> every dataset.</span>
</span><span id="L-151"><a href="#L-151"><span class="linenos">151</span></a> </span><span id="L-151"><a href="#L-151"><span class="linenos">151</span></a><span class="sd"> samples : int</span>
</span><span id="L-152"><a href="#L-152"><span class="linenos">152</span></a><span class="sd"> Returns</span> </span><span id="L-152"><a href="#L-152"><span class="linenos">152</span></a><span class="sd"> number of samples to be generated for each observable.</span>
</span><span id="L-153"><a href="#L-153"><span class="linenos">153</span></a><span class="sd"> -------</span> </span><span id="L-153"><a href="#L-153"><span class="linenos">153</span></a>
</span><span id="L-154"><a href="#L-154"><span class="linenos">154</span></a><span class="sd"> corr_obs : list[Obs]</span> </span><span id="L-154"><a href="#L-154"><span class="linenos">154</span></a><span class="sd"> Returns</span>
</span><span id="L-155"><a href="#L-155"><span class="linenos">155</span></a><span class="sd"> Generated observable list</span> </span><span id="L-155"><a href="#L-155"><span class="linenos">155</span></a><span class="sd"> -------</span>
</span><span id="L-156"><a href="#L-156"><span class="linenos">156</span></a><span class="sd"> &quot;&quot;&quot;</span> </span><span id="L-156"><a href="#L-156"><span class="linenos">156</span></a><span class="sd"> corr_obs : list[Obs]</span>
</span><span id="L-157"><a href="#L-157"><span class="linenos">157</span></a> </span><span id="L-157"><a href="#L-157"><span class="linenos">157</span></a><span class="sd"> Generated observable list</span>
</span><span id="L-158"><a href="#L-158"><span class="linenos">158</span></a> <span class="k">assert</span> <span class="nb">len</span><span class="p">(</span><span class="n">means</span><span class="p">)</span> <span class="o">==</span> <span class="n">cov</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> </span><span id="L-158"><a href="#L-158"><span class="linenos">158</span></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="L-159"><a href="#L-159"><span class="linenos">159</span></a> <span class="n">tau</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">tau</span><span class="p">)</span> </span><span id="L-159"><a href="#L-159"><span class="linenos">159</span></a>
</span><span id="L-160"><a href="#L-160"><span class="linenos">160</span></a> <span class="k">if</span> <span class="n">np</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="n">tau</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mf">0.5</span><span class="p">:</span> </span><span id="L-160"><a href="#L-160"><span class="linenos">160</span></a> <span class="k">assert</span> <span class="nb">len</span><span class="p">(</span><span class="n">means</span><span class="p">)</span> <span class="o">==</span> <span class="n">cov</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
</span><span id="L-161"><a href="#L-161"><span class="linenos">161</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;All integrated autocorrelations have to be &gt;= 0.5.&#39;</span><span class="p">)</span> </span><span id="L-161"><a href="#L-161"><span class="linenos">161</span></a> <span class="n">tau</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">tau</span><span class="p">)</span>
</span><span id="L-162"><a href="#L-162"><span class="linenos">162</span></a> </span><span id="L-162"><a href="#L-162"><span class="linenos">162</span></a> <span class="k">if</span> <span class="n">np</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="n">tau</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mf">0.5</span><span class="p">:</span>
</span><span id="L-163"><a href="#L-163"><span class="linenos">163</span></a> <span class="n">a</span> <span class="o">=</span> <span class="p">(</span><span class="mi">2</span> <span class="o">*</span> <span class="n">tau</span> <span class="o">-</span> <span class="mi">1</span><span class="p">)</span> <span class="o">/</span> <span class="p">(</span><span class="mi">2</span> <span class="o">*</span> <span class="n">tau</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span> </span><span id="L-163"><a href="#L-163"><span class="linenos">163</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;All integrated autocorrelations have to be &gt;= 0.5.&#39;</span><span class="p">)</span>
</span><span id="L-164"><a href="#L-164"><span class="linenos">164</span></a> <span class="n">rand</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">multivariate_normal</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">zeros_like</span><span class="p">(</span><span class="n">means</span><span class="p">),</span> <span class="n">cov</span> <span class="o">*</span> <span class="n">samples</span><span class="p">,</span> <span class="n">samples</span><span class="p">)</span> </span><span id="L-164"><a href="#L-164"><span class="linenos">164</span></a>
</span><span id="L-165"><a href="#L-165"><span class="linenos">165</span></a> </span><span id="L-165"><a href="#L-165"><span class="linenos">165</span></a> <span class="n">a</span> <span class="o">=</span> <span class="p">(</span><span class="mi">2</span> <span class="o">*</span> <span class="n">tau</span> <span class="o">-</span> <span class="mi">1</span><span class="p">)</span> <span class="o">/</span> <span class="p">(</span><span class="mi">2</span> <span class="o">*</span> <span class="n">tau</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
</span><span id="L-166"><a href="#L-166"><span class="linenos">166</span></a> <span class="c1"># Normalize samples such that sample variance matches input</span> </span><span id="L-166"><a href="#L-166"><span class="linenos">166</span></a> <span class="n">rand</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">multivariate_normal</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">zeros_like</span><span class="p">(</span><span class="n">means</span><span class="p">),</span> <span class="n">cov</span> <span class="o">*</span> <span class="n">samples</span><span class="p">,</span> <span class="n">samples</span><span class="p">)</span> <span class="c1"># noqa: NPY002</span>
</span><span id="L-167"><a href="#L-167"><span class="linenos">167</span></a> <span class="n">norm</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">np</span><span class="o">.</span><span class="n">var</span><span class="p">(</span><span class="n">o</span><span class="p">,</span> <span class="n">ddof</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span> <span class="o">/</span> <span class="n">samples</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">rand</span><span class="o">.</span><span class="n">T</span><span class="p">])</span> </span><span id="L-167"><a href="#L-167"><span class="linenos">167</span></a>
</span><span id="L-168"><a href="#L-168"><span class="linenos">168</span></a> <span class="n">rand</span> <span class="o">=</span> <span class="n">rand</span> <span class="o">@</span> <span class="n">np</span><span class="o">.</span><span class="n">diag</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">diag</span><span class="p">(</span><span class="n">cov</span><span class="p">)))</span> <span class="o">@</span> <span class="n">np</span><span class="o">.</span><span class="n">diag</span><span class="p">(</span><span class="mi">1</span> <span class="o">/</span> <span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="n">norm</span><span class="p">))</span> </span><span id="L-168"><a href="#L-168"><span class="linenos">168</span></a> <span class="c1"># Normalize samples such that sample variance matches input</span>
</span><span id="L-169"><a href="#L-169"><span class="linenos">169</span></a> </span><span id="L-169"><a href="#L-169"><span class="linenos">169</span></a> <span class="n">norm</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">np</span><span class="o">.</span><span class="n">var</span><span class="p">(</span><span class="n">o</span><span class="p">,</span> <span class="n">ddof</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span> <span class="o">/</span> <span class="n">samples</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">rand</span><span class="o">.</span><span class="n">T</span><span class="p">])</span>
</span><span id="L-170"><a href="#L-170"><span class="linenos">170</span></a> <span class="n">data</span> <span class="o">=</span> <span class="p">[</span><span class="n">rand</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> </span><span id="L-170"><a href="#L-170"><span class="linenos">170</span></a> <span class="n">rand</span> <span class="o">=</span> <span class="n">rand</span> <span class="o">@</span> <span class="n">np</span><span class="o">.</span><span class="n">diag</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">diag</span><span class="p">(</span><span class="n">cov</span><span class="p">)))</span> <span class="o">@</span> <span class="n">np</span><span class="o">.</span><span class="n">diag</span><span class="p">(</span><span class="mi">1</span> <span class="o">/</span> <span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="n">norm</span><span class="p">))</span>
</span><span id="L-171"><a href="#L-171"><span class="linenos">171</span></a> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="n">samples</span><span class="p">):</span> </span><span id="L-171"><a href="#L-171"><span class="linenos">171</span></a>
</span><span id="L-172"><a href="#L-172"><span class="linenos">172</span></a> <span class="n">data</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="mi">1</span> <span class="o">-</span> <span class="n">a</span> <span class="o">**</span> <span class="mi">2</span><span class="p">)</span> <span class="o">*</span> <span class="n">rand</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">+</span> <span class="n">a</span> <span class="o">*</span> <span class="n">data</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">])</span> </span><span id="L-172"><a href="#L-172"><span class="linenos">172</span></a> <span class="n">data</span> <span class="o">=</span> <span class="p">[</span><span class="n">rand</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span>
</span><span id="L-173"><a href="#L-173"><span class="linenos">173</span></a> <span class="n">corr_data</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">data</span><span class="p">)</span> <span class="o">-</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span> <span class="o">+</span> <span class="n">means</span> </span><span id="L-173"><a href="#L-173"><span class="linenos">173</span></a> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="n">samples</span><span class="p">):</span>
</span><span id="L-174"><a href="#L-174"><span class="linenos">174</span></a> <span class="k">return</span> <span class="p">[</span><span class="n">Obs</span><span class="p">([</span><span class="n">dat</span><span class="p">],</span> <span class="p">[</span><span class="n">name</span><span class="p">])</span> <span class="k">for</span> <span class="n">dat</span> <span class="ow">in</span> <span class="n">corr_data</span><span class="o">.</span><span class="n">T</span><span class="p">]</span> </span><span id="L-174"><a href="#L-174"><span class="linenos">174</span></a> <span class="n">data</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="mi">1</span> <span class="o">-</span> <span class="n">a</span> <span class="o">**</span> <span class="mi">2</span><span class="p">)</span> <span class="o">*</span> <span class="n">rand</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">+</span> <span class="n">a</span> <span class="o">*</span> <span class="n">data</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">])</span>
</span><span id="L-175"><a href="#L-175"><span class="linenos">175</span></a> </span><span id="L-175"><a href="#L-175"><span class="linenos">175</span></a> <span class="n">corr_data</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">data</span><span class="p">)</span> <span class="o">-</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span> <span class="o">+</span> <span class="n">means</span>
</span><span id="L-176"><a href="#L-176"><span class="linenos">176</span></a> </span><span id="L-176"><a href="#L-176"><span class="linenos">176</span></a> <span class="k">return</span> <span class="p">[</span><span class="n">Obs</span><span class="p">([</span><span class="n">dat</span><span class="p">],</span> <span class="p">[</span><span class="n">name</span><span class="p">])</span> <span class="k">for</span> <span class="n">dat</span> <span class="ow">in</span> <span class="n">corr_data</span><span class="o">.</span><span class="n">T</span><span class="p">]</span>
</span><span id="L-177"><a href="#L-177"><span class="linenos">177</span></a><span class="k">def</span><span class="w"> </span><span class="nf">_assert_equal_properties</span><span class="p">(</span><span class="n">ol</span><span class="p">,</span> <span class="n">otype</span><span class="o">=</span><span class="n">Obs</span><span class="p">):</span> </span><span id="L-177"><a href="#L-177"><span class="linenos">177</span></a>
</span><span id="L-178"><a href="#L-178"><span class="linenos">178</span></a> <span class="n">otype</span> <span class="o">=</span> <span class="nb">type</span><span class="p">(</span><span class="n">ol</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> </span><span id="L-178"><a href="#L-178"><span class="linenos">178</span></a>
</span><span id="L-179"><a href="#L-179"><span class="linenos">179</span></a> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">ol</span><span class="p">[</span><span class="mi">1</span><span class="p">:]:</span> </span><span id="L-179"><a href="#L-179"><span class="linenos">179</span></a><span class="k">def</span><span class="w"> </span><span class="nf">_assert_equal_properties</span><span class="p">(</span><span class="n">ol</span><span class="p">,</span> <span class="n">otype</span><span class="o">=</span><span class="n">Obs</span><span class="p">):</span>
</span><span id="L-180"><a href="#L-180"><span class="linenos">180</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">o</span><span class="p">,</span> <span class="n">otype</span><span class="p">):</span> </span><span id="L-180"><a href="#L-180"><span class="linenos">180</span></a> <span class="n">otype</span> <span class="o">=</span> <span class="nb">type</span><span class="p">(</span><span class="n">ol</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
</span><span id="L-181"><a href="#L-181"><span class="linenos">181</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">&quot;Wrong data type in list.&quot;</span><span class="p">)</span> </span><span id="L-181"><a href="#L-181"><span class="linenos">181</span></a> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">ol</span><span class="p">[</span><span class="mi">1</span><span class="p">:]:</span>
</span><span id="L-182"><a href="#L-182"><span class="linenos">182</span></a> <span class="k">for</span> <span class="n">attr</span> <span class="ow">in</span> <span class="p">[</span><span class="s2">&quot;reweighted&quot;</span><span class="p">,</span> <span class="s2">&quot;e_content&quot;</span><span class="p">,</span> <span class="s2">&quot;idl&quot;</span><span class="p">]:</span> </span><span id="L-182"><a href="#L-182"><span class="linenos">182</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">o</span><span class="p">,</span> <span class="n">otype</span><span class="p">):</span>
</span><span id="L-183"><a href="#L-183"><span class="linenos">183</span></a> <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">ol</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">attr</span><span class="p">):</span> </span><span id="L-183"><a href="#L-183"><span class="linenos">183</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">&quot;Wrong data type in list.&quot;</span><span class="p">)</span>
</span><span id="L-184"><a href="#L-184"><span class="linenos">184</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">ol</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">attr</span><span class="p">)</span> <span class="o">==</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">o</span><span class="p">,</span> <span class="n">attr</span><span class="p">):</span> </span><span id="L-184"><a href="#L-184"><span class="linenos">184</span></a> <span class="k">for</span> <span class="n">attr</span> <span class="ow">in</span> <span class="p">[</span><span class="s2">&quot;reweighted&quot;</span><span class="p">,</span> <span class="s2">&quot;e_content&quot;</span><span class="p">,</span> <span class="s2">&quot;idl&quot;</span><span class="p">]:</span>
</span><span id="L-185"><a href="#L-185"><span class="linenos">185</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;All Obs in list have to have the same state &#39;</span><span class="si">{</span><span class="n">attr</span><span class="si">}</span><span class="s2">&#39;.&quot;</span><span class="p">)</span> </span><span id="L-185"><a href="#L-185"><span class="linenos">185</span></a> <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">ol</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">attr</span><span class="p">):</span>
</span><span id="L-186"><a href="#L-186"><span class="linenos">186</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">ol</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">attr</span><span class="p">)</span> <span class="o">==</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">o</span><span class="p">,</span> <span class="n">attr</span><span class="p">):</span>
</span><span id="L-187"><a href="#L-187"><span class="linenos">187</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;All Obs in list have to have the same state &#39;</span><span class="si">{</span><span class="n">attr</span><span class="si">}</span><span class="s2">&#39;.&quot;</span><span class="p">)</span>
</span></pre></div> </span></pre></div>
@ -291,18 +293,18 @@
</div> </div>
<a class="headerlink" href="#print_config"></a> <a class="headerlink" href="#print_config"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="print_config-13"><a href="#print_config-13"><span class="linenos">13</span></a><span class="k">def</span><span class="w"> </span><span class="nf">print_config</span><span class="p">():</span> <div class="pdoc-code codehilite"><pre><span></span><span id="print_config-15"><a href="#print_config-15"><span class="linenos">15</span></a><span class="k">def</span><span class="w"> </span><span class="nf">print_config</span><span class="p">():</span>
</span><span id="print_config-14"><a href="#print_config-14"><span class="linenos">14</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Print information about version of python, pyerrors and dependencies.&quot;&quot;&quot;</span> </span><span id="print_config-16"><a href="#print_config-16"><span class="linenos">16</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Print information about version of python, pyerrors and dependencies.&quot;&quot;&quot;</span>
</span><span id="print_config-15"><a href="#print_config-15"><span class="linenos">15</span></a> <span class="n">config</span> <span class="o">=</span> <span class="p">{</span><span class="s2">&quot;system&quot;</span><span class="p">:</span> <span class="n">platform</span><span class="o">.</span><span class="n">system</span><span class="p">(),</span> </span><span id="print_config-17"><a href="#print_config-17"><span class="linenos">17</span></a> <span class="n">config</span> <span class="o">=</span> <span class="p">{</span><span class="s2">&quot;system&quot;</span><span class="p">:</span> <span class="n">platform</span><span class="o">.</span><span class="n">system</span><span class="p">(),</span>
</span><span id="print_config-16"><a href="#print_config-16"><span class="linenos">16</span></a> <span class="s2">&quot;python&quot;</span><span class="p">:</span> <span class="n">platform</span><span class="o">.</span><span class="n">python_version</span><span class="p">(),</span> </span><span id="print_config-18"><a href="#print_config-18"><span class="linenos">18</span></a> <span class="s2">&quot;python&quot;</span><span class="p">:</span> <span class="n">platform</span><span class="o">.</span><span class="n">python_version</span><span class="p">(),</span>
</span><span id="print_config-17"><a href="#print_config-17"><span class="linenos">17</span></a> <span class="s2">&quot;pyerrors&quot;</span><span class="p">:</span> <span class="n">__version__</span><span class="p">,</span> </span><span id="print_config-19"><a href="#print_config-19"><span class="linenos">19</span></a> <span class="s2">&quot;pyerrors&quot;</span><span class="p">:</span> <span class="n">__version__</span><span class="p">,</span>
</span><span id="print_config-18"><a href="#print_config-18"><span class="linenos">18</span></a> <span class="s2">&quot;numpy&quot;</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">__version__</span><span class="p">,</span> </span><span id="print_config-20"><a href="#print_config-20"><span class="linenos">20</span></a> <span class="s2">&quot;numpy&quot;</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">__version__</span><span class="p">,</span>
</span><span id="print_config-19"><a href="#print_config-19"><span class="linenos">19</span></a> <span class="s2">&quot;scipy&quot;</span><span class="p">:</span> <span class="n">scipy</span><span class="o">.</span><span class="n">__version__</span><span class="p">,</span> </span><span id="print_config-21"><a href="#print_config-21"><span class="linenos">21</span></a> <span class="s2">&quot;scipy&quot;</span><span class="p">:</span> <span class="n">scipy</span><span class="o">.</span><span class="n">__version__</span><span class="p">,</span>
</span><span id="print_config-20"><a href="#print_config-20"><span class="linenos">20</span></a> <span class="s2">&quot;matplotlib&quot;</span><span class="p">:</span> <span class="n">matplotlib</span><span class="o">.</span><span class="n">__version__</span><span class="p">,</span> </span><span id="print_config-22"><a href="#print_config-22"><span class="linenos">22</span></a> <span class="s2">&quot;matplotlib&quot;</span><span class="p">:</span> <span class="n">matplotlib</span><span class="o">.</span><span class="n">__version__</span><span class="p">,</span>
</span><span id="print_config-21"><a href="#print_config-21"><span class="linenos">21</span></a> <span class="s2">&quot;pandas&quot;</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">__version__</span><span class="p">}</span> </span><span id="print_config-23"><a href="#print_config-23"><span class="linenos">23</span></a> <span class="s2">&quot;pandas&quot;</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">__version__</span><span class="p">}</span>
</span><span id="print_config-22"><a href="#print_config-22"><span class="linenos">22</span></a> </span><span id="print_config-24"><a href="#print_config-24"><span class="linenos">24</span></a>
</span><span id="print_config-23"><a href="#print_config-23"><span class="linenos">23</span></a> <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">value</span> <span class="ow">in</span> <span class="n">config</span><span class="o">.</span><span class="n">items</span><span class="p">():</span> </span><span id="print_config-25"><a href="#print_config-25"><span class="linenos">25</span></a> <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">value</span> <span class="ow">in</span> <span class="n">config</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
</span><span id="print_config-24"><a href="#print_config-24"><span class="linenos">24</span></a> <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">key</span><span class="si">:</span><span class="s2"> &lt;10</span><span class="si">}</span><span class="se">\t</span><span class="s2"> </span><span class="si">{</span><span class="n">value</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span> </span><span id="print_config-26"><a href="#print_config-26"><span class="linenos">26</span></a> <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">key</span><span class="si">:</span><span class="s2"> &lt;10</span><span class="si">}</span><span class="se">\t</span><span class="s2"> </span><span class="si">{</span><span class="n">value</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
</span></pre></div> </span></pre></div>
@ -322,35 +324,35 @@
</div> </div>
<a class="headerlink" href="#errorbar"></a> <a class="headerlink" href="#errorbar"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="errorbar-27"><a href="#errorbar-27"><span class="linenos">27</span></a><span class="k">def</span><span class="w"> </span><span class="nf">errorbar</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">axes</span><span class="o">=</span><span class="n">plt</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span> <div class="pdoc-code codehilite"><pre><span></span><span id="errorbar-29"><a href="#errorbar-29"><span class="linenos">29</span></a><span class="k">def</span><span class="w"> </span><span class="nf">errorbar</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">axes</span><span class="o">=</span><span class="n">plt</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
</span><span id="errorbar-28"><a href="#errorbar-28"><span class="linenos">28</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;pyerrors wrapper for the errorbars method of matplotlib</span> </span><span id="errorbar-30"><a href="#errorbar-30"><span class="linenos">30</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;pyerrors wrapper for the errorbars method of matplotlib</span>
</span><span id="errorbar-29"><a href="#errorbar-29"><span class="linenos">29</span></a> </span><span id="errorbar-31"><a href="#errorbar-31"><span class="linenos">31</span></a>
</span><span id="errorbar-30"><a href="#errorbar-30"><span class="linenos">30</span></a><span class="sd"> Parameters</span> </span><span id="errorbar-32"><a href="#errorbar-32"><span class="linenos">32</span></a><span class="sd"> Parameters</span>
</span><span id="errorbar-31"><a href="#errorbar-31"><span class="linenos">31</span></a><span class="sd"> ----------</span> </span><span id="errorbar-33"><a href="#errorbar-33"><span class="linenos">33</span></a><span class="sd"> ----------</span>
</span><span id="errorbar-32"><a href="#errorbar-32"><span class="linenos">32</span></a><span class="sd"> x : list</span> </span><span id="errorbar-34"><a href="#errorbar-34"><span class="linenos">34</span></a><span class="sd"> x : list</span>
</span><span id="errorbar-33"><a href="#errorbar-33"><span class="linenos">33</span></a><span class="sd"> A list of x-values which can be Obs.</span> </span><span id="errorbar-35"><a href="#errorbar-35"><span class="linenos">35</span></a><span class="sd"> A list of x-values which can be Obs.</span>
</span><span id="errorbar-34"><a href="#errorbar-34"><span class="linenos">34</span></a><span class="sd"> y : list</span> </span><span id="errorbar-36"><a href="#errorbar-36"><span class="linenos">36</span></a><span class="sd"> y : list</span>
</span><span id="errorbar-35"><a href="#errorbar-35"><span class="linenos">35</span></a><span class="sd"> A list of y-values which can be Obs.</span> </span><span id="errorbar-37"><a href="#errorbar-37"><span class="linenos">37</span></a><span class="sd"> A list of y-values which can be Obs.</span>
</span><span id="errorbar-36"><a href="#errorbar-36"><span class="linenos">36</span></a><span class="sd"> axes : (matplotlib.pyplot.axes)</span> </span><span id="errorbar-38"><a href="#errorbar-38"><span class="linenos">38</span></a><span class="sd"> axes : (matplotlib.pyplot.axes)</span>
</span><span id="errorbar-37"><a href="#errorbar-37"><span class="linenos">37</span></a><span class="sd"> The axes to plot on. default is plt.</span> </span><span id="errorbar-39"><a href="#errorbar-39"><span class="linenos">39</span></a><span class="sd"> The axes to plot on. default is plt.</span>
</span><span id="errorbar-38"><a href="#errorbar-38"><span class="linenos">38</span></a><span class="sd"> &quot;&quot;&quot;</span> </span><span id="errorbar-40"><a href="#errorbar-40"><span class="linenos">40</span></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="errorbar-39"><a href="#errorbar-39"><span class="linenos">39</span></a> <span class="n">val</span> <span class="o">=</span> <span class="p">{}</span> </span><span id="errorbar-41"><a href="#errorbar-41"><span class="linenos">41</span></a> <span class="n">val</span> <span class="o">=</span> <span class="p">{}</span>
</span><span id="errorbar-40"><a href="#errorbar-40"><span class="linenos">40</span></a> <span class="n">err</span> <span class="o">=</span> <span class="p">{}</span> </span><span id="errorbar-42"><a href="#errorbar-42"><span class="linenos">42</span></a> <span class="n">err</span> <span class="o">=</span> <span class="p">{}</span>
</span><span id="errorbar-41"><a href="#errorbar-41"><span class="linenos">41</span></a> <span class="k">for</span> <span class="n">name</span><span class="p">,</span> <span class="n">comp</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">([</span><span class="s2">&quot;x&quot;</span><span class="p">,</span> <span class="s2">&quot;y&quot;</span><span class="p">],</span> <span class="p">[</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">]):</span> </span><span id="errorbar-43"><a href="#errorbar-43"><span class="linenos">43</span></a> <span class="k">for</span> <span class="n">name</span><span class="p">,</span> <span class="n">comp</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">([</span><span class="s2">&quot;x&quot;</span><span class="p">,</span> <span class="s2">&quot;y&quot;</span><span class="p">],</span> <span class="p">[</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">],</span> <span class="n">strict</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
</span><span id="errorbar-42"><a href="#errorbar-42"><span class="linenos">42</span></a> <span class="k">if</span> <span class="nb">all</span><span class="p">(</span><span class="nb">isinstance</span><span class="p">(</span><span class="n">o</span><span class="p">,</span> <span class="n">Obs</span><span class="p">)</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">comp</span><span class="p">):</span> </span><span id="errorbar-44"><a href="#errorbar-44"><span class="linenos">44</span></a> <span class="k">if</span> <span class="nb">all</span><span class="p">(</span><span class="nb">isinstance</span><span class="p">(</span><span class="n">o</span><span class="p">,</span> <span class="n">Obs</span><span class="p">)</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">comp</span><span class="p">):</span>
</span><span id="errorbar-43"><a href="#errorbar-43"><span class="linenos">43</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="nb">all</span><span class="p">(</span><span class="nb">hasattr</span><span class="p">(</span><span class="n">o</span><span class="p">,</span> <span class="s1">&#39;e_dvalue&#39;</span><span class="p">)</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">comp</span><span class="p">):</span> </span><span id="errorbar-45"><a href="#errorbar-45"><span class="linenos">45</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="nb">all</span><span class="p">(</span><span class="nb">hasattr</span><span class="p">(</span><span class="n">o</span><span class="p">,</span> <span class="s1">&#39;e_dvalue&#39;</span><span class="p">)</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">comp</span><span class="p">):</span>
</span><span id="errorbar-44"><a href="#errorbar-44"><span class="linenos">44</span></a> <span class="p">[</span><span class="n">o</span><span class="o">.</span><span class="n">gamma_method</span><span class="p">()</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">comp</span><span class="p">]</span> </span><span id="errorbar-46"><a href="#errorbar-46"><span class="linenos">46</span></a> <span class="p">[</span><span class="n">o</span><span class="o">.</span><span class="n">gamma_method</span><span class="p">()</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">comp</span><span class="p">]</span>
</span><span id="errorbar-45"><a href="#errorbar-45"><span class="linenos">45</span></a> <span class="n">val</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="n">o</span><span class="o">.</span><span class="n">value</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">comp</span><span class="p">]</span> </span><span id="errorbar-47"><a href="#errorbar-47"><span class="linenos">47</span></a> <span class="n">val</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="n">o</span><span class="o">.</span><span class="n">value</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">comp</span><span class="p">]</span>
</span><span id="errorbar-46"><a href="#errorbar-46"><span class="linenos">46</span></a> <span class="n">err</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="n">o</span><span class="o">.</span><span class="n">dvalue</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">comp</span><span class="p">]</span> </span><span id="errorbar-48"><a href="#errorbar-48"><span class="linenos">48</span></a> <span class="n">err</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="n">o</span><span class="o">.</span><span class="n">dvalue</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">comp</span><span class="p">]</span>
</span><span id="errorbar-47"><a href="#errorbar-47"><span class="linenos">47</span></a> <span class="k">else</span><span class="p">:</span> </span><span id="errorbar-49"><a href="#errorbar-49"><span class="linenos">49</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="errorbar-48"><a href="#errorbar-48"><span class="linenos">48</span></a> <span class="n">val</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="n">comp</span> </span><span id="errorbar-50"><a href="#errorbar-50"><span class="linenos">50</span></a> <span class="n">val</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="n">comp</span>
</span><span id="errorbar-49"><a href="#errorbar-49"><span class="linenos">49</span></a> <span class="n">err</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span> </span><span id="errorbar-51"><a href="#errorbar-51"><span class="linenos">51</span></a> <span class="n">err</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span>
</span><span id="errorbar-50"><a href="#errorbar-50"><span class="linenos">50</span></a> </span><span id="errorbar-52"><a href="#errorbar-52"><span class="linenos">52</span></a>
</span><span id="errorbar-51"><a href="#errorbar-51"><span class="linenos">51</span></a> <span class="k">if</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s2">err&quot;</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span> </span><span id="errorbar-53"><a href="#errorbar-53"><span class="linenos">53</span></a> <span class="k">if</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s2">err&quot;</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
</span><span id="errorbar-52"><a href="#errorbar-52"><span class="linenos">52</span></a> <span class="n">err</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s2">err&quot;</span><span class="p">)</span> </span><span id="errorbar-54"><a href="#errorbar-54"><span class="linenos">54</span></a> <span class="n">err</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s2">err&quot;</span><span class="p">)</span>
</span><span id="errorbar-53"><a href="#errorbar-53"><span class="linenos">53</span></a> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s2">err&quot;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span> </span><span id="errorbar-55"><a href="#errorbar-55"><span class="linenos">55</span></a> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s2">err&quot;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
</span><span id="errorbar-54"><a href="#errorbar-54"><span class="linenos">54</span></a> </span><span id="errorbar-56"><a href="#errorbar-56"><span class="linenos">56</span></a>
</span><span id="errorbar-55"><a href="#errorbar-55"><span class="linenos">55</span></a> <span class="n">axes</span><span class="o">.</span><span class="n">errorbar</span><span class="p">(</span><span class="n">val</span><span class="p">[</span><span class="s2">&quot;x&quot;</span><span class="p">],</span> <span class="n">val</span><span class="p">[</span><span class="s2">&quot;y&quot;</span><span class="p">],</span> <span class="n">xerr</span><span class="o">=</span><span class="n">err</span><span class="p">[</span><span class="s2">&quot;x&quot;</span><span class="p">],</span> <span class="n">yerr</span><span class="o">=</span><span class="n">err</span><span class="p">[</span><span class="s2">&quot;y&quot;</span><span class="p">],</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span> </span><span id="errorbar-57"><a href="#errorbar-57"><span class="linenos">57</span></a> <span class="n">axes</span><span class="o">.</span><span class="n">errorbar</span><span class="p">(</span><span class="n">val</span><span class="p">[</span><span class="s2">&quot;x&quot;</span><span class="p">],</span> <span class="n">val</span><span class="p">[</span><span class="s2">&quot;y&quot;</span><span class="p">],</span> <span class="n">xerr</span><span class="o">=</span><span class="n">err</span><span class="p">[</span><span class="s2">&quot;x&quot;</span><span class="p">],</span> <span class="n">yerr</span><span class="o">=</span><span class="n">err</span><span class="p">[</span><span class="s2">&quot;y&quot;</span><span class="p">],</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
</span></pre></div> </span></pre></div>
@ -381,28 +383,28 @@ The axes to plot on. default is plt.</li>
</div> </div>
<a class="headerlink" href="#dump_object"></a> <a class="headerlink" href="#dump_object"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="dump_object-58"><a href="#dump_object-58"><span class="linenos">58</span></a><span class="k">def</span><span class="w"> </span><span class="nf">dump_object</span><span class="p">(</span><span class="n">obj</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span> <div class="pdoc-code codehilite"><pre><span></span><span id="dump_object-60"><a href="#dump_object-60"><span class="linenos">60</span></a><span class="k">def</span><span class="w"> </span><span class="nf">dump_object</span><span class="p">(</span><span class="n">obj</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
</span><span id="dump_object-59"><a href="#dump_object-59"><span class="linenos">59</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Dump object into pickle file.</span> </span><span id="dump_object-61"><a href="#dump_object-61"><span class="linenos">61</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Dump object into pickle file.</span>
</span><span id="dump_object-60"><a href="#dump_object-60"><span class="linenos">60</span></a> </span><span id="dump_object-62"><a href="#dump_object-62"><span class="linenos">62</span></a>
</span><span id="dump_object-61"><a href="#dump_object-61"><span class="linenos">61</span></a><span class="sd"> Parameters</span> </span><span id="dump_object-63"><a href="#dump_object-63"><span class="linenos">63</span></a><span class="sd"> Parameters</span>
</span><span id="dump_object-62"><a href="#dump_object-62"><span class="linenos">62</span></a><span class="sd"> ----------</span> </span><span id="dump_object-64"><a href="#dump_object-64"><span class="linenos">64</span></a><span class="sd"> ----------</span>
</span><span id="dump_object-63"><a href="#dump_object-63"><span class="linenos">63</span></a><span class="sd"> obj : object</span> </span><span id="dump_object-65"><a href="#dump_object-65"><span class="linenos">65</span></a><span class="sd"> obj : object</span>
</span><span id="dump_object-64"><a href="#dump_object-64"><span class="linenos">64</span></a><span class="sd"> object to be saved in the pickle file</span> </span><span id="dump_object-66"><a href="#dump_object-66"><span class="linenos">66</span></a><span class="sd"> object to be saved in the pickle file</span>
</span><span id="dump_object-65"><a href="#dump_object-65"><span class="linenos">65</span></a><span class="sd"> name : str</span> </span><span id="dump_object-67"><a href="#dump_object-67"><span class="linenos">67</span></a><span class="sd"> name : str</span>
</span><span id="dump_object-66"><a href="#dump_object-66"><span class="linenos">66</span></a><span class="sd"> name of the file</span> </span><span id="dump_object-68"><a href="#dump_object-68"><span class="linenos">68</span></a><span class="sd"> name of the file</span>
</span><span id="dump_object-67"><a href="#dump_object-67"><span class="linenos">67</span></a><span class="sd"> path : str</span> </span><span id="dump_object-69"><a href="#dump_object-69"><span class="linenos">69</span></a><span class="sd"> path : str</span>
</span><span id="dump_object-68"><a href="#dump_object-68"><span class="linenos">68</span></a><span class="sd"> specifies a custom path for the file (default &#39;.&#39;)</span> </span><span id="dump_object-70"><a href="#dump_object-70"><span class="linenos">70</span></a><span class="sd"> specifies a custom path for the file (default &#39;.&#39;)</span>
</span><span id="dump_object-69"><a href="#dump_object-69"><span class="linenos">69</span></a> </span><span id="dump_object-71"><a href="#dump_object-71"><span class="linenos">71</span></a>
</span><span id="dump_object-70"><a href="#dump_object-70"><span class="linenos">70</span></a><span class="sd"> Returns</span> </span><span id="dump_object-72"><a href="#dump_object-72"><span class="linenos">72</span></a><span class="sd"> Returns</span>
</span><span id="dump_object-71"><a href="#dump_object-71"><span class="linenos">71</span></a><span class="sd"> -------</span> </span><span id="dump_object-73"><a href="#dump_object-73"><span class="linenos">73</span></a><span class="sd"> -------</span>
</span><span id="dump_object-72"><a href="#dump_object-72"><span class="linenos">72</span></a><span class="sd"> None</span> </span><span id="dump_object-74"><a href="#dump_object-74"><span class="linenos">74</span></a><span class="sd"> None</span>
</span><span id="dump_object-73"><a href="#dump_object-73"><span class="linenos">73</span></a><span class="sd"> &quot;&quot;&quot;</span> </span><span id="dump_object-75"><a href="#dump_object-75"><span class="linenos">75</span></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="dump_object-74"><a href="#dump_object-74"><span class="linenos">74</span></a> <span class="k">if</span> <span class="s1">&#39;path&#39;</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span> </span><span id="dump_object-76"><a href="#dump_object-76"><span class="linenos">76</span></a> <span class="k">if</span> <span class="s1">&#39;path&#39;</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
</span><span id="dump_object-75"><a href="#dump_object-75"><span class="linenos">75</span></a> <span class="n">file_name</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;path&#39;</span><span class="p">)</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">name</span> <span class="o">+</span> <span class="s1">&#39;.p&#39;</span> </span><span id="dump_object-77"><a href="#dump_object-77"><span class="linenos">77</span></a> <span class="n">file_name</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;path&#39;</span><span class="p">)</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">name</span> <span class="o">+</span> <span class="s1">&#39;.p&#39;</span>
</span><span id="dump_object-76"><a href="#dump_object-76"><span class="linenos">76</span></a> <span class="k">else</span><span class="p">:</span> </span><span id="dump_object-78"><a href="#dump_object-78"><span class="linenos">78</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="dump_object-77"><a href="#dump_object-77"><span class="linenos">77</span></a> <span class="n">file_name</span> <span class="o">=</span> <span class="n">name</span> <span class="o">+</span> <span class="s1">&#39;.p&#39;</span> </span><span id="dump_object-79"><a href="#dump_object-79"><span class="linenos">79</span></a> <span class="n">file_name</span> <span class="o">=</span> <span class="n">name</span> <span class="o">+</span> <span class="s1">&#39;.p&#39;</span>
</span><span id="dump_object-78"><a href="#dump_object-78"><span class="linenos">78</span></a> <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">file_name</span><span class="p">,</span> <span class="s1">&#39;wb&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fb</span><span class="p">:</span> </span><span id="dump_object-80"><a href="#dump_object-80"><span class="linenos">80</span></a> <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">file_name</span><span class="p">,</span> <span class="s1">&#39;wb&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fb</span><span class="p">:</span>
</span><span id="dump_object-79"><a href="#dump_object-79"><span class="linenos">79</span></a> <span class="n">pickle</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="n">obj</span><span class="p">,</span> <span class="n">fb</span><span class="p">)</span> </span><span id="dump_object-81"><a href="#dump_object-81"><span class="linenos">81</span></a> <span class="n">pickle</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="n">obj</span><span class="p">,</span> <span class="n">fb</span><span class="p">)</span>
</span></pre></div> </span></pre></div>
@ -439,21 +441,21 @@ specifies a custom path for the file (default '.')</li>
</div> </div>
<a class="headerlink" href="#load_object"></a> <a class="headerlink" href="#load_object"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="load_object-82"><a href="#load_object-82"><span class="linenos">82</span></a><span class="k">def</span><span class="w"> </span><span class="nf">load_object</span><span class="p">(</span><span class="n">path</span><span class="p">):</span> <div class="pdoc-code codehilite"><pre><span></span><span id="load_object-84"><a href="#load_object-84"><span class="linenos">84</span></a><span class="k">def</span><span class="w"> </span><span class="nf">load_object</span><span class="p">(</span><span class="n">path</span><span class="p">):</span>
</span><span id="load_object-83"><a href="#load_object-83"><span class="linenos">83</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Load object from pickle file.</span> </span><span id="load_object-85"><a href="#load_object-85"><span class="linenos">85</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Load object from pickle file.</span>
</span><span id="load_object-84"><a href="#load_object-84"><span class="linenos">84</span></a> </span><span id="load_object-86"><a href="#load_object-86"><span class="linenos">86</span></a>
</span><span id="load_object-85"><a href="#load_object-85"><span class="linenos">85</span></a><span class="sd"> Parameters</span> </span><span id="load_object-87"><a href="#load_object-87"><span class="linenos">87</span></a><span class="sd"> Parameters</span>
</span><span id="load_object-86"><a href="#load_object-86"><span class="linenos">86</span></a><span class="sd"> ----------</span> </span><span id="load_object-88"><a href="#load_object-88"><span class="linenos">88</span></a><span class="sd"> ----------</span>
</span><span id="load_object-87"><a href="#load_object-87"><span class="linenos">87</span></a><span class="sd"> path : str</span> </span><span id="load_object-89"><a href="#load_object-89"><span class="linenos">89</span></a><span class="sd"> path : str</span>
</span><span id="load_object-88"><a href="#load_object-88"><span class="linenos">88</span></a><span class="sd"> path to the file</span> </span><span id="load_object-90"><a href="#load_object-90"><span class="linenos">90</span></a><span class="sd"> path to the file</span>
</span><span id="load_object-89"><a href="#load_object-89"><span class="linenos">89</span></a> </span><span id="load_object-91"><a href="#load_object-91"><span class="linenos">91</span></a>
</span><span id="load_object-90"><a href="#load_object-90"><span class="linenos">90</span></a><span class="sd"> Returns</span> </span><span id="load_object-92"><a href="#load_object-92"><span class="linenos">92</span></a><span class="sd"> Returns</span>
</span><span id="load_object-91"><a href="#load_object-91"><span class="linenos">91</span></a><span class="sd"> -------</span> </span><span id="load_object-93"><a href="#load_object-93"><span class="linenos">93</span></a><span class="sd"> -------</span>
</span><span id="load_object-92"><a href="#load_object-92"><span class="linenos">92</span></a><span class="sd"> object : Obs</span> </span><span id="load_object-94"><a href="#load_object-94"><span class="linenos">94</span></a><span class="sd"> object : Obs</span>
</span><span id="load_object-93"><a href="#load_object-93"><span class="linenos">93</span></a><span class="sd"> Loaded Object</span> </span><span id="load_object-95"><a href="#load_object-95"><span class="linenos">95</span></a><span class="sd"> Loaded Object</span>
</span><span id="load_object-94"><a href="#load_object-94"><span class="linenos">94</span></a><span class="sd"> &quot;&quot;&quot;</span> </span><span id="load_object-96"><a href="#load_object-96"><span class="linenos">96</span></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="load_object-95"><a href="#load_object-95"><span class="linenos">95</span></a> <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="s1">&#39;rb&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span> </span><span id="load_object-97"><a href="#load_object-97"><span class="linenos">97</span></a> <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="s1">&#39;rb&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
</span><span id="load_object-96"><a href="#load_object-96"><span class="linenos">96</span></a> <span class="k">return</span> <span class="n">pickle</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">file</span><span class="p">)</span> </span><span id="load_object-98"><a href="#load_object-98"><span class="linenos">98</span></a> <span class="k">return</span> <span class="n">pickle</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">file</span><span class="p">)</span>
</span></pre></div> </span></pre></div>
@ -487,41 +489,41 @@ Loaded Object</li>
</div> </div>
<a class="headerlink" href="#pseudo_Obs"></a> <a class="headerlink" href="#pseudo_Obs"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="pseudo_Obs-99"><a href="#pseudo_Obs-99"><span class="linenos"> 99</span></a><span class="k">def</span><span class="w"> </span><span class="nf">pseudo_Obs</span><span class="p">(</span><span class="n">value</span><span class="p">,</span> <span class="n">dvalue</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">samples</span><span class="o">=</span><span class="mi">1000</span><span class="p">):</span> <div class="pdoc-code codehilite"><pre><span></span><span id="pseudo_Obs-101"><a href="#pseudo_Obs-101"><span class="linenos">101</span></a><span class="k">def</span><span class="w"> </span><span class="nf">pseudo_Obs</span><span class="p">(</span><span class="n">value</span><span class="p">,</span> <span class="n">dvalue</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">samples</span><span class="o">=</span><span class="mi">1000</span><span class="p">):</span>
</span><span id="pseudo_Obs-100"><a href="#pseudo_Obs-100"><span class="linenos">100</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Generate an Obs object with given value, dvalue and name for test purposes</span> </span><span id="pseudo_Obs-102"><a href="#pseudo_Obs-102"><span class="linenos">102</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Generate an Obs object with given value, dvalue and name for test purposes</span>
</span><span id="pseudo_Obs-101"><a href="#pseudo_Obs-101"><span class="linenos">101</span></a> </span><span id="pseudo_Obs-103"><a href="#pseudo_Obs-103"><span class="linenos">103</span></a>
</span><span id="pseudo_Obs-102"><a href="#pseudo_Obs-102"><span class="linenos">102</span></a><span class="sd"> Parameters</span> </span><span id="pseudo_Obs-104"><a href="#pseudo_Obs-104"><span class="linenos">104</span></a><span class="sd"> Parameters</span>
</span><span id="pseudo_Obs-103"><a href="#pseudo_Obs-103"><span class="linenos">103</span></a><span class="sd"> ----------</span> </span><span id="pseudo_Obs-105"><a href="#pseudo_Obs-105"><span class="linenos">105</span></a><span class="sd"> ----------</span>
</span><span id="pseudo_Obs-104"><a href="#pseudo_Obs-104"><span class="linenos">104</span></a><span class="sd"> value : float</span> </span><span id="pseudo_Obs-106"><a href="#pseudo_Obs-106"><span class="linenos">106</span></a><span class="sd"> value : float</span>
</span><span id="pseudo_Obs-105"><a href="#pseudo_Obs-105"><span class="linenos">105</span></a><span class="sd"> central value of the Obs to be generated.</span> </span><span id="pseudo_Obs-107"><a href="#pseudo_Obs-107"><span class="linenos">107</span></a><span class="sd"> central value of the Obs to be generated.</span>
</span><span id="pseudo_Obs-106"><a href="#pseudo_Obs-106"><span class="linenos">106</span></a><span class="sd"> dvalue : float</span> </span><span id="pseudo_Obs-108"><a href="#pseudo_Obs-108"><span class="linenos">108</span></a><span class="sd"> dvalue : float</span>
</span><span id="pseudo_Obs-107"><a href="#pseudo_Obs-107"><span class="linenos">107</span></a><span class="sd"> error of the Obs to be generated.</span> </span><span id="pseudo_Obs-109"><a href="#pseudo_Obs-109"><span class="linenos">109</span></a><span class="sd"> error of the Obs to be generated.</span>
</span><span id="pseudo_Obs-108"><a href="#pseudo_Obs-108"><span class="linenos">108</span></a><span class="sd"> name : str</span> </span><span id="pseudo_Obs-110"><a href="#pseudo_Obs-110"><span class="linenos">110</span></a><span class="sd"> name : str</span>
</span><span id="pseudo_Obs-109"><a href="#pseudo_Obs-109"><span class="linenos">109</span></a><span class="sd"> name of the ensemble for which the Obs is to be generated.</span> </span><span id="pseudo_Obs-111"><a href="#pseudo_Obs-111"><span class="linenos">111</span></a><span class="sd"> name of the ensemble for which the Obs is to be generated.</span>
</span><span id="pseudo_Obs-110"><a href="#pseudo_Obs-110"><span class="linenos">110</span></a><span class="sd"> samples: int</span> </span><span id="pseudo_Obs-112"><a href="#pseudo_Obs-112"><span class="linenos">112</span></a><span class="sd"> samples: int</span>
</span><span id="pseudo_Obs-111"><a href="#pseudo_Obs-111"><span class="linenos">111</span></a><span class="sd"> number of samples for the Obs (default 1000).</span> </span><span id="pseudo_Obs-113"><a href="#pseudo_Obs-113"><span class="linenos">113</span></a><span class="sd"> number of samples for the Obs (default 1000).</span>
</span><span id="pseudo_Obs-112"><a href="#pseudo_Obs-112"><span class="linenos">112</span></a> </span><span id="pseudo_Obs-114"><a href="#pseudo_Obs-114"><span class="linenos">114</span></a>
</span><span id="pseudo_Obs-113"><a href="#pseudo_Obs-113"><span class="linenos">113</span></a><span class="sd"> Returns</span> </span><span id="pseudo_Obs-115"><a href="#pseudo_Obs-115"><span class="linenos">115</span></a><span class="sd"> Returns</span>
</span><span id="pseudo_Obs-114"><a href="#pseudo_Obs-114"><span class="linenos">114</span></a><span class="sd"> -------</span> </span><span id="pseudo_Obs-116"><a href="#pseudo_Obs-116"><span class="linenos">116</span></a><span class="sd"> -------</span>
</span><span id="pseudo_Obs-115"><a href="#pseudo_Obs-115"><span class="linenos">115</span></a><span class="sd"> res : Obs</span> </span><span id="pseudo_Obs-117"><a href="#pseudo_Obs-117"><span class="linenos">117</span></a><span class="sd"> res : Obs</span>
</span><span id="pseudo_Obs-116"><a href="#pseudo_Obs-116"><span class="linenos">116</span></a><span class="sd"> Generated Observable</span> </span><span id="pseudo_Obs-118"><a href="#pseudo_Obs-118"><span class="linenos">118</span></a><span class="sd"> Generated Observable</span>
</span><span id="pseudo_Obs-117"><a href="#pseudo_Obs-117"><span class="linenos">117</span></a><span class="sd"> &quot;&quot;&quot;</span> </span><span id="pseudo_Obs-119"><a href="#pseudo_Obs-119"><span class="linenos">119</span></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="pseudo_Obs-118"><a href="#pseudo_Obs-118"><span class="linenos">118</span></a> <span class="k">if</span> <span class="n">dvalue</span> <span class="o">&lt;=</span> <span class="mf">0.0</span><span class="p">:</span> </span><span id="pseudo_Obs-120"><a href="#pseudo_Obs-120"><span class="linenos">120</span></a> <span class="k">if</span> <span class="n">dvalue</span> <span class="o">&lt;=</span> <span class="mf">0.0</span><span class="p">:</span>
</span><span id="pseudo_Obs-119"><a href="#pseudo_Obs-119"><span class="linenos">119</span></a> <span class="k">return</span> <span class="n">Obs</span><span class="p">([</span><span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="n">samples</span><span class="p">)</span> <span class="o">+</span> <span class="n">value</span><span class="p">],</span> <span class="p">[</span><span class="n">name</span><span class="p">])</span> </span><span id="pseudo_Obs-121"><a href="#pseudo_Obs-121"><span class="linenos">121</span></a> <span class="k">return</span> <span class="n">Obs</span><span class="p">([</span><span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="n">samples</span><span class="p">)</span> <span class="o">+</span> <span class="n">value</span><span class="p">],</span> <span class="p">[</span><span class="n">name</span><span class="p">])</span>
</span><span id="pseudo_Obs-120"><a href="#pseudo_Obs-120"><span class="linenos">120</span></a> <span class="k">else</span><span class="p">:</span> </span><span id="pseudo_Obs-122"><a href="#pseudo_Obs-122"><span class="linenos">122</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="pseudo_Obs-121"><a href="#pseudo_Obs-121"><span class="linenos">121</span></a> <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">100</span><span class="p">):</span> </span><span id="pseudo_Obs-123"><a href="#pseudo_Obs-123"><span class="linenos">123</span></a> <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">100</span><span class="p">):</span>
</span><span id="pseudo_Obs-122"><a href="#pseudo_Obs-122"><span class="linenos">122</span></a> <span class="n">deltas</span> <span class="o">=</span> <span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">normal</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span> <span class="n">dvalue</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="n">samples</span><span class="p">),</span> <span class="n">samples</span><span class="p">)]</span> </span><span id="pseudo_Obs-124"><a href="#pseudo_Obs-124"><span class="linenos">124</span></a> <span class="n">deltas</span> <span class="o">=</span> <span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">normal</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span> <span class="n">dvalue</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="n">samples</span><span class="p">),</span> <span class="n">samples</span><span class="p">)]</span> <span class="c1"># noqa: NPY002</span>
</span><span id="pseudo_Obs-123"><a href="#pseudo_Obs-123"><span class="linenos">123</span></a> <span class="n">deltas</span> <span class="o">-=</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">deltas</span><span class="p">)</span> </span><span id="pseudo_Obs-125"><a href="#pseudo_Obs-125"><span class="linenos">125</span></a> <span class="n">deltas</span> <span class="o">-=</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">deltas</span><span class="p">)</span>
</span><span id="pseudo_Obs-124"><a href="#pseudo_Obs-124"><span class="linenos">124</span></a> <span class="n">deltas</span> <span class="o">*=</span> <span class="n">dvalue</span> <span class="o">/</span> <span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">((</span><span class="n">np</span><span class="o">.</span><span class="n">var</span><span class="p">(</span><span class="n">deltas</span><span class="p">)</span> <span class="o">/</span> <span class="n">samples</span><span class="p">))</span> <span class="o">/</span> <span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="mi">1</span> <span class="o">+</span> <span class="mi">3</span> <span class="o">/</span> <span class="n">samples</span><span class="p">)</span> </span><span id="pseudo_Obs-126"><a href="#pseudo_Obs-126"><span class="linenos">126</span></a> <span class="n">deltas</span> <span class="o">*=</span> <span class="n">dvalue</span> <span class="o">/</span> <span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">var</span><span class="p">(</span><span class="n">deltas</span><span class="p">)</span> <span class="o">/</span> <span class="n">samples</span><span class="p">)</span> <span class="o">/</span> <span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="mi">1</span> <span class="o">+</span> <span class="mi">3</span> <span class="o">/</span> <span class="n">samples</span><span class="p">)</span>
</span><span id="pseudo_Obs-125"><a href="#pseudo_Obs-125"><span class="linenos">125</span></a> <span class="n">deltas</span> <span class="o">+=</span> <span class="n">value</span> </span><span id="pseudo_Obs-127"><a href="#pseudo_Obs-127"><span class="linenos">127</span></a> <span class="n">deltas</span> <span class="o">+=</span> <span class="n">value</span>
</span><span id="pseudo_Obs-126"><a href="#pseudo_Obs-126"><span class="linenos">126</span></a> <span class="n">res</span> <span class="o">=</span> <span class="n">Obs</span><span class="p">(</span><span class="n">deltas</span><span class="p">,</span> <span class="p">[</span><span class="n">name</span><span class="p">])</span> </span><span id="pseudo_Obs-128"><a href="#pseudo_Obs-128"><span class="linenos">128</span></a> <span class="n">res</span> <span class="o">=</span> <span class="n">Obs</span><span class="p">(</span><span class="n">deltas</span><span class="p">,</span> <span class="p">[</span><span class="n">name</span><span class="p">])</span>
</span><span id="pseudo_Obs-127"><a href="#pseudo_Obs-127"><span class="linenos">127</span></a> <span class="n">res</span><span class="o">.</span><span class="n">gamma_method</span><span class="p">(</span><span class="n">S</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">tau_exp</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span> </span><span id="pseudo_Obs-129"><a href="#pseudo_Obs-129"><span class="linenos">129</span></a> <span class="n">res</span><span class="o">.</span><span class="n">gamma_method</span><span class="p">(</span><span class="n">S</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">tau_exp</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
</span><span id="pseudo_Obs-128"><a href="#pseudo_Obs-128"><span class="linenos">128</span></a> <span class="k">if</span> <span class="nb">abs</span><span class="p">(</span><span class="n">res</span><span class="o">.</span><span class="n">dvalue</span> <span class="o">-</span> <span class="n">dvalue</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mf">1e-10</span> <span class="o">*</span> <span class="n">dvalue</span><span class="p">:</span> </span><span id="pseudo_Obs-130"><a href="#pseudo_Obs-130"><span class="linenos">130</span></a> <span class="k">if</span> <span class="nb">abs</span><span class="p">(</span><span class="n">res</span><span class="o">.</span><span class="n">dvalue</span> <span class="o">-</span> <span class="n">dvalue</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mf">1e-10</span> <span class="o">*</span> <span class="n">dvalue</span><span class="p">:</span>
</span><span id="pseudo_Obs-129"><a href="#pseudo_Obs-129"><span class="linenos">129</span></a> <span class="k">break</span> </span><span id="pseudo_Obs-131"><a href="#pseudo_Obs-131"><span class="linenos">131</span></a> <span class="k">break</span>
</span><span id="pseudo_Obs-130"><a href="#pseudo_Obs-130"><span class="linenos">130</span></a>
</span><span id="pseudo_Obs-131"><a href="#pseudo_Obs-131"><span class="linenos">131</span></a> <span class="n">res</span><span class="o">.</span><span class="n">_value</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">value</span><span class="p">)</span>
</span><span id="pseudo_Obs-132"><a href="#pseudo_Obs-132"><span class="linenos">132</span></a> </span><span id="pseudo_Obs-132"><a href="#pseudo_Obs-132"><span class="linenos">132</span></a>
</span><span id="pseudo_Obs-133"><a href="#pseudo_Obs-133"><span class="linenos">133</span></a> <span class="k">return</span> <span class="n">res</span> </span><span id="pseudo_Obs-133"><a href="#pseudo_Obs-133"><span class="linenos">133</span></a> <span class="n">res</span><span class="o">.</span><span class="n">_value</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">value</span><span class="p">)</span>
</span><span id="pseudo_Obs-134"><a href="#pseudo_Obs-134"><span class="linenos">134</span></a>
</span><span id="pseudo_Obs-135"><a href="#pseudo_Obs-135"><span class="linenos">135</span></a> <span class="k">return</span> <span class="n">res</span>
</span></pre></div> </span></pre></div>
@ -561,46 +563,46 @@ Generated Observable</li>
</div> </div>
<a class="headerlink" href="#gen_correlated_data"></a> <a class="headerlink" href="#gen_correlated_data"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="gen_correlated_data-136"><a href="#gen_correlated_data-136"><span class="linenos">136</span></a><span class="k">def</span><span class="w"> </span><span class="nf">gen_correlated_data</span><span class="p">(</span><span class="n">means</span><span class="p">,</span> <span class="n">cov</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">tau</span><span class="o">=</span><span class="mf">0.5</span><span class="p">,</span> <span class="n">samples</span><span class="o">=</span><span class="mi">1000</span><span class="p">):</span> <div class="pdoc-code codehilite"><pre><span></span><span id="gen_correlated_data-138"><a href="#gen_correlated_data-138"><span class="linenos">138</span></a><span class="k">def</span><span class="w"> </span><span class="nf">gen_correlated_data</span><span class="p">(</span><span class="n">means</span><span class="p">,</span> <span class="n">cov</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">tau</span><span class="o">=</span><span class="mf">0.5</span><span class="p">,</span> <span class="n">samples</span><span class="o">=</span><span class="mi">1000</span><span class="p">):</span>
</span><span id="gen_correlated_data-137"><a href="#gen_correlated_data-137"><span class="linenos">137</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot; Generate observables with given covariance and autocorrelation times.</span> </span><span id="gen_correlated_data-139"><a href="#gen_correlated_data-139"><span class="linenos">139</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot; Generate observables with given covariance and autocorrelation times.</span>
</span><span id="gen_correlated_data-138"><a href="#gen_correlated_data-138"><span class="linenos">138</span></a> </span><span id="gen_correlated_data-140"><a href="#gen_correlated_data-140"><span class="linenos">140</span></a>
</span><span id="gen_correlated_data-139"><a href="#gen_correlated_data-139"><span class="linenos">139</span></a><span class="sd"> Parameters</span> </span><span id="gen_correlated_data-141"><a href="#gen_correlated_data-141"><span class="linenos">141</span></a><span class="sd"> Parameters</span>
</span><span id="gen_correlated_data-140"><a href="#gen_correlated_data-140"><span class="linenos">140</span></a><span class="sd"> ----------</span> </span><span id="gen_correlated_data-142"><a href="#gen_correlated_data-142"><span class="linenos">142</span></a><span class="sd"> ----------</span>
</span><span id="gen_correlated_data-141"><a href="#gen_correlated_data-141"><span class="linenos">141</span></a><span class="sd"> means : list</span> </span><span id="gen_correlated_data-143"><a href="#gen_correlated_data-143"><span class="linenos">143</span></a><span class="sd"> means : list</span>
</span><span id="gen_correlated_data-142"><a href="#gen_correlated_data-142"><span class="linenos">142</span></a><span class="sd"> list containing the mean value of each observable.</span> </span><span id="gen_correlated_data-144"><a href="#gen_correlated_data-144"><span class="linenos">144</span></a><span class="sd"> list containing the mean value of each observable.</span>
</span><span id="gen_correlated_data-143"><a href="#gen_correlated_data-143"><span class="linenos">143</span></a><span class="sd"> cov : numpy.ndarray</span> </span><span id="gen_correlated_data-145"><a href="#gen_correlated_data-145"><span class="linenos">145</span></a><span class="sd"> cov : numpy.ndarray</span>
</span><span id="gen_correlated_data-144"><a href="#gen_correlated_data-144"><span class="linenos">144</span></a><span class="sd"> covariance matrix for the data to be generated.</span> </span><span id="gen_correlated_data-146"><a href="#gen_correlated_data-146"><span class="linenos">146</span></a><span class="sd"> covariance matrix for the data to be generated.</span>
</span><span id="gen_correlated_data-145"><a href="#gen_correlated_data-145"><span class="linenos">145</span></a><span class="sd"> name : str</span> </span><span id="gen_correlated_data-147"><a href="#gen_correlated_data-147"><span class="linenos">147</span></a><span class="sd"> name : str</span>
</span><span id="gen_correlated_data-146"><a href="#gen_correlated_data-146"><span class="linenos">146</span></a><span class="sd"> ensemble name for the data to be geneated.</span> </span><span id="gen_correlated_data-148"><a href="#gen_correlated_data-148"><span class="linenos">148</span></a><span class="sd"> ensemble name for the data to be geneated.</span>
</span><span id="gen_correlated_data-147"><a href="#gen_correlated_data-147"><span class="linenos">147</span></a><span class="sd"> tau : float or list</span> </span><span id="gen_correlated_data-149"><a href="#gen_correlated_data-149"><span class="linenos">149</span></a><span class="sd"> tau : float or list</span>
</span><span id="gen_correlated_data-148"><a href="#gen_correlated_data-148"><span class="linenos">148</span></a><span class="sd"> can either be a real number or a list with an entry for</span> </span><span id="gen_correlated_data-150"><a href="#gen_correlated_data-150"><span class="linenos">150</span></a><span class="sd"> can either be a real number or a list with an entry for</span>
</span><span id="gen_correlated_data-149"><a href="#gen_correlated_data-149"><span class="linenos">149</span></a><span class="sd"> every dataset.</span> </span><span id="gen_correlated_data-151"><a href="#gen_correlated_data-151"><span class="linenos">151</span></a><span class="sd"> every dataset.</span>
</span><span id="gen_correlated_data-150"><a href="#gen_correlated_data-150"><span class="linenos">150</span></a><span class="sd"> samples : int</span> </span><span id="gen_correlated_data-152"><a href="#gen_correlated_data-152"><span class="linenos">152</span></a><span class="sd"> samples : int</span>
</span><span id="gen_correlated_data-151"><a href="#gen_correlated_data-151"><span class="linenos">151</span></a><span class="sd"> number of samples to be generated for each observable.</span> </span><span id="gen_correlated_data-153"><a href="#gen_correlated_data-153"><span class="linenos">153</span></a><span class="sd"> number of samples to be generated for each observable.</span>
</span><span id="gen_correlated_data-152"><a href="#gen_correlated_data-152"><span class="linenos">152</span></a> </span><span id="gen_correlated_data-154"><a href="#gen_correlated_data-154"><span class="linenos">154</span></a>
</span><span id="gen_correlated_data-153"><a href="#gen_correlated_data-153"><span class="linenos">153</span></a><span class="sd"> Returns</span> </span><span id="gen_correlated_data-155"><a href="#gen_correlated_data-155"><span class="linenos">155</span></a><span class="sd"> Returns</span>
</span><span id="gen_correlated_data-154"><a href="#gen_correlated_data-154"><span class="linenos">154</span></a><span class="sd"> -------</span> </span><span id="gen_correlated_data-156"><a href="#gen_correlated_data-156"><span class="linenos">156</span></a><span class="sd"> -------</span>
</span><span id="gen_correlated_data-155"><a href="#gen_correlated_data-155"><span class="linenos">155</span></a><span class="sd"> corr_obs : list[Obs]</span> </span><span id="gen_correlated_data-157"><a href="#gen_correlated_data-157"><span class="linenos">157</span></a><span class="sd"> corr_obs : list[Obs]</span>
</span><span id="gen_correlated_data-156"><a href="#gen_correlated_data-156"><span class="linenos">156</span></a><span class="sd"> Generated observable list</span> </span><span id="gen_correlated_data-158"><a href="#gen_correlated_data-158"><span class="linenos">158</span></a><span class="sd"> Generated observable list</span>
</span><span id="gen_correlated_data-157"><a href="#gen_correlated_data-157"><span class="linenos">157</span></a><span class="sd"> &quot;&quot;&quot;</span> </span><span id="gen_correlated_data-159"><a href="#gen_correlated_data-159"><span class="linenos">159</span></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="gen_correlated_data-158"><a href="#gen_correlated_data-158"><span class="linenos">158</span></a> </span><span id="gen_correlated_data-160"><a href="#gen_correlated_data-160"><span class="linenos">160</span></a>
</span><span id="gen_correlated_data-159"><a href="#gen_correlated_data-159"><span class="linenos">159</span></a> <span class="k">assert</span> <span class="nb">len</span><span class="p">(</span><span class="n">means</span><span class="p">)</span> <span class="o">==</span> <span class="n">cov</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> </span><span id="gen_correlated_data-161"><a href="#gen_correlated_data-161"><span class="linenos">161</span></a> <span class="k">assert</span> <span class="nb">len</span><span class="p">(</span><span class="n">means</span><span class="p">)</span> <span class="o">==</span> <span class="n">cov</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
</span><span id="gen_correlated_data-160"><a href="#gen_correlated_data-160"><span class="linenos">160</span></a> <span class="n">tau</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">tau</span><span class="p">)</span> </span><span id="gen_correlated_data-162"><a href="#gen_correlated_data-162"><span class="linenos">162</span></a> <span class="n">tau</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">tau</span><span class="p">)</span>
</span><span id="gen_correlated_data-161"><a href="#gen_correlated_data-161"><span class="linenos">161</span></a> <span class="k">if</span> <span class="n">np</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="n">tau</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mf">0.5</span><span class="p">:</span> </span><span id="gen_correlated_data-163"><a href="#gen_correlated_data-163"><span class="linenos">163</span></a> <span class="k">if</span> <span class="n">np</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="n">tau</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mf">0.5</span><span class="p">:</span>
</span><span id="gen_correlated_data-162"><a href="#gen_correlated_data-162"><span class="linenos">162</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;All integrated autocorrelations have to be &gt;= 0.5.&#39;</span><span class="p">)</span> </span><span id="gen_correlated_data-164"><a href="#gen_correlated_data-164"><span class="linenos">164</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;All integrated autocorrelations have to be &gt;= 0.5.&#39;</span><span class="p">)</span>
</span><span id="gen_correlated_data-163"><a href="#gen_correlated_data-163"><span class="linenos">163</span></a> </span><span id="gen_correlated_data-165"><a href="#gen_correlated_data-165"><span class="linenos">165</span></a>
</span><span id="gen_correlated_data-164"><a href="#gen_correlated_data-164"><span class="linenos">164</span></a> <span class="n">a</span> <span class="o">=</span> <span class="p">(</span><span class="mi">2</span> <span class="o">*</span> <span class="n">tau</span> <span class="o">-</span> <span class="mi">1</span><span class="p">)</span> <span class="o">/</span> <span class="p">(</span><span class="mi">2</span> <span class="o">*</span> <span class="n">tau</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span> </span><span id="gen_correlated_data-166"><a href="#gen_correlated_data-166"><span class="linenos">166</span></a> <span class="n">a</span> <span class="o">=</span> <span class="p">(</span><span class="mi">2</span> <span class="o">*</span> <span class="n">tau</span> <span class="o">-</span> <span class="mi">1</span><span class="p">)</span> <span class="o">/</span> <span class="p">(</span><span class="mi">2</span> <span class="o">*</span> <span class="n">tau</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
</span><span id="gen_correlated_data-165"><a href="#gen_correlated_data-165"><span class="linenos">165</span></a> <span class="n">rand</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">multivariate_normal</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">zeros_like</span><span class="p">(</span><span class="n">means</span><span class="p">),</span> <span class="n">cov</span> <span class="o">*</span> <span class="n">samples</span><span class="p">,</span> <span class="n">samples</span><span class="p">)</span> </span><span id="gen_correlated_data-167"><a href="#gen_correlated_data-167"><span class="linenos">167</span></a> <span class="n">rand</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">multivariate_normal</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">zeros_like</span><span class="p">(</span><span class="n">means</span><span class="p">),</span> <span class="n">cov</span> <span class="o">*</span> <span class="n">samples</span><span class="p">,</span> <span class="n">samples</span><span class="p">)</span> <span class="c1"># noqa: NPY002</span>
</span><span id="gen_correlated_data-166"><a href="#gen_correlated_data-166"><span class="linenos">166</span></a> </span><span id="gen_correlated_data-168"><a href="#gen_correlated_data-168"><span class="linenos">168</span></a>
</span><span id="gen_correlated_data-167"><a href="#gen_correlated_data-167"><span class="linenos">167</span></a> <span class="c1"># Normalize samples such that sample variance matches input</span> </span><span id="gen_correlated_data-169"><a href="#gen_correlated_data-169"><span class="linenos">169</span></a> <span class="c1"># Normalize samples such that sample variance matches input</span>
</span><span id="gen_correlated_data-168"><a href="#gen_correlated_data-168"><span class="linenos">168</span></a> <span class="n">norm</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">np</span><span class="o">.</span><span class="n">var</span><span class="p">(</span><span class="n">o</span><span class="p">,</span> <span class="n">ddof</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span> <span class="o">/</span> <span class="n">samples</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">rand</span><span class="o">.</span><span class="n">T</span><span class="p">])</span> </span><span id="gen_correlated_data-170"><a href="#gen_correlated_data-170"><span class="linenos">170</span></a> <span class="n">norm</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">np</span><span class="o">.</span><span class="n">var</span><span class="p">(</span><span class="n">o</span><span class="p">,</span> <span class="n">ddof</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span> <span class="o">/</span> <span class="n">samples</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">rand</span><span class="o">.</span><span class="n">T</span><span class="p">])</span>
</span><span id="gen_correlated_data-169"><a href="#gen_correlated_data-169"><span class="linenos">169</span></a> <span class="n">rand</span> <span class="o">=</span> <span class="n">rand</span> <span class="o">@</span> <span class="n">np</span><span class="o">.</span><span class="n">diag</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">diag</span><span class="p">(</span><span class="n">cov</span><span class="p">)))</span> <span class="o">@</span> <span class="n">np</span><span class="o">.</span><span class="n">diag</span><span class="p">(</span><span class="mi">1</span> <span class="o">/</span> <span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="n">norm</span><span class="p">))</span> </span><span id="gen_correlated_data-171"><a href="#gen_correlated_data-171"><span class="linenos">171</span></a> <span class="n">rand</span> <span class="o">=</span> <span class="n">rand</span> <span class="o">@</span> <span class="n">np</span><span class="o">.</span><span class="n">diag</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">diag</span><span class="p">(</span><span class="n">cov</span><span class="p">)))</span> <span class="o">@</span> <span class="n">np</span><span class="o">.</span><span class="n">diag</span><span class="p">(</span><span class="mi">1</span> <span class="o">/</span> <span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="n">norm</span><span class="p">))</span>
</span><span id="gen_correlated_data-170"><a href="#gen_correlated_data-170"><span class="linenos">170</span></a> </span><span id="gen_correlated_data-172"><a href="#gen_correlated_data-172"><span class="linenos">172</span></a>
</span><span id="gen_correlated_data-171"><a href="#gen_correlated_data-171"><span class="linenos">171</span></a> <span class="n">data</span> <span class="o">=</span> <span class="p">[</span><span class="n">rand</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> </span><span id="gen_correlated_data-173"><a href="#gen_correlated_data-173"><span class="linenos">173</span></a> <span class="n">data</span> <span class="o">=</span> <span class="p">[</span><span class="n">rand</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span>
</span><span id="gen_correlated_data-172"><a href="#gen_correlated_data-172"><span class="linenos">172</span></a> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="n">samples</span><span class="p">):</span> </span><span id="gen_correlated_data-174"><a href="#gen_correlated_data-174"><span class="linenos">174</span></a> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="n">samples</span><span class="p">):</span>
</span><span id="gen_correlated_data-173"><a href="#gen_correlated_data-173"><span class="linenos">173</span></a> <span class="n">data</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="mi">1</span> <span class="o">-</span> <span class="n">a</span> <span class="o">**</span> <span class="mi">2</span><span class="p">)</span> <span class="o">*</span> <span class="n">rand</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">+</span> <span class="n">a</span> <span class="o">*</span> <span class="n">data</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">])</span> </span><span id="gen_correlated_data-175"><a href="#gen_correlated_data-175"><span class="linenos">175</span></a> <span class="n">data</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="mi">1</span> <span class="o">-</span> <span class="n">a</span> <span class="o">**</span> <span class="mi">2</span><span class="p">)</span> <span class="o">*</span> <span class="n">rand</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">+</span> <span class="n">a</span> <span class="o">*</span> <span class="n">data</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">])</span>
</span><span id="gen_correlated_data-174"><a href="#gen_correlated_data-174"><span class="linenos">174</span></a> <span class="n">corr_data</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">data</span><span class="p">)</span> <span class="o">-</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span> <span class="o">+</span> <span class="n">means</span> </span><span id="gen_correlated_data-176"><a href="#gen_correlated_data-176"><span class="linenos">176</span></a> <span class="n">corr_data</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">data</span><span class="p">)</span> <span class="o">-</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span> <span class="o">+</span> <span class="n">means</span>
</span><span id="gen_correlated_data-175"><a href="#gen_correlated_data-175"><span class="linenos">175</span></a> <span class="k">return</span> <span class="p">[</span><span class="n">Obs</span><span class="p">([</span><span class="n">dat</span><span class="p">],</span> <span class="p">[</span><span class="n">name</span><span class="p">])</span> <span class="k">for</span> <span class="n">dat</span> <span class="ow">in</span> <span class="n">corr_data</span><span class="o">.</span><span class="n">T</span><span class="p">]</span> </span><span id="gen_correlated_data-177"><a href="#gen_correlated_data-177"><span class="linenos">177</span></a> <span class="k">return</span> <span class="p">[</span><span class="n">Obs</span><span class="p">([</span><span class="n">dat</span><span class="p">],</span> <span class="p">[</span><span class="n">name</span><span class="p">])</span> <span class="k">for</span> <span class="n">dat</span> <span class="ow">in</span> <span class="n">corr_data</span><span class="o">.</span><span class="n">T</span><span class="p">]</span>
</span></pre></div> </span></pre></div>

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docs/pyerrors/mpm.html
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@ -78,67 +78,68 @@
<div class="pdoc-code codehilite"><pre><span></span><span id="L-1"><a href="#L-1"><span class="linenos"> 1</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span> <div class="pdoc-code codehilite"><pre><span></span><span id="L-1"><a href="#L-1"><span class="linenos"> 1</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
</span><span id="L-2"><a href="#L-2"><span class="linenos"> 2</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">scipy.linalg</span> </span><span id="L-2"><a href="#L-2"><span class="linenos"> 2</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">scipy.linalg</span>
</span><span id="L-3"><a href="#L-3"><span class="linenos"> 3</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">.obs</span><span class="w"> </span><span class="kn">import</span> <span class="n">Obs</span> </span><span id="L-3"><a href="#L-3"><span class="linenos"> 3</span></a>
</span><span id="L-4"><a href="#L-4"><span class="linenos"> 4</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">.linalg</span><span class="w"> </span><span class="kn">import</span> <span class="n">svd</span><span class="p">,</span> <span class="n">eig</span> </span><span id="L-4"><a href="#L-4"><span class="linenos"> 4</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">.linalg</span><span class="w"> </span><span class="kn">import</span> <span class="n">eig</span><span class="p">,</span> <span class="n">svd</span>
</span><span id="L-5"><a href="#L-5"><span class="linenos"> 5</span></a> </span><span id="L-5"><a href="#L-5"><span class="linenos"> 5</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">.obs</span><span class="w"> </span><span class="kn">import</span> <span class="n">Obs</span>
</span><span id="L-6"><a href="#L-6"><span class="linenos"> 6</span></a> </span><span id="L-6"><a href="#L-6"><span class="linenos"> 6</span></a>
</span><span id="L-7"><a href="#L-7"><span class="linenos"> 7</span></a><span class="k">def</span><span class="w"> </span><span class="nf">matrix_pencil_method</span><span class="p">(</span><span class="n">corrs</span><span class="p">,</span> <span class="n">k</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">p</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span> </span><span id="L-7"><a href="#L-7"><span class="linenos"> 7</span></a>
</span><span id="L-8"><a href="#L-8"><span class="linenos"> 8</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Matrix pencil method to extract k energy levels from data</span> </span><span id="L-8"><a href="#L-8"><span class="linenos"> 8</span></a><span class="k">def</span><span class="w"> </span><span class="nf">matrix_pencil_method</span><span class="p">(</span><span class="n">corrs</span><span class="p">,</span> <span class="n">k</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">p</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
</span><span id="L-9"><a href="#L-9"><span class="linenos"> 9</span></a> </span><span id="L-9"><a href="#L-9"><span class="linenos"> 9</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Matrix pencil method to extract k energy levels from data</span>
</span><span id="L-10"><a href="#L-10"><span class="linenos">10</span></a><span class="sd"> Implementation of the matrix pencil method based on</span> </span><span id="L-10"><a href="#L-10"><span class="linenos">10</span></a>
</span><span id="L-11"><a href="#L-11"><span class="linenos">11</span></a><span class="sd"> eq. (2.17) of Y. Hua, T. K. Sarkar, IEEE Trans. Acoust. 38, 814-824 (1990)</span> </span><span id="L-11"><a href="#L-11"><span class="linenos">11</span></a><span class="sd"> Implementation of the matrix pencil method based on</span>
</span><span id="L-12"><a href="#L-12"><span class="linenos">12</span></a> </span><span id="L-12"><a href="#L-12"><span class="linenos">12</span></a><span class="sd"> eq. (2.17) of Y. Hua, T. K. Sarkar, IEEE Trans. Acoust. 38, 814-824 (1990)</span>
</span><span id="L-13"><a href="#L-13"><span class="linenos">13</span></a><span class="sd"> Parameters</span> </span><span id="L-13"><a href="#L-13"><span class="linenos">13</span></a>
</span><span id="L-14"><a href="#L-14"><span class="linenos">14</span></a><span class="sd"> ----------</span> </span><span id="L-14"><a href="#L-14"><span class="linenos">14</span></a><span class="sd"> Parameters</span>
</span><span id="L-15"><a href="#L-15"><span class="linenos">15</span></a><span class="sd"> data : list</span> </span><span id="L-15"><a href="#L-15"><span class="linenos">15</span></a><span class="sd"> ----------</span>
</span><span id="L-16"><a href="#L-16"><span class="linenos">16</span></a><span class="sd"> can be a list of Obs for the analysis of a single correlator, or a list of lists</span> </span><span id="L-16"><a href="#L-16"><span class="linenos">16</span></a><span class="sd"> data : list</span>
</span><span id="L-17"><a href="#L-17"><span class="linenos">17</span></a><span class="sd"> of Obs if several correlators are to analyzed at once.</span> </span><span id="L-17"><a href="#L-17"><span class="linenos">17</span></a><span class="sd"> can be a list of Obs for the analysis of a single correlator, or a list of lists</span>
</span><span id="L-18"><a href="#L-18"><span class="linenos">18</span></a><span class="sd"> k : int</span> </span><span id="L-18"><a href="#L-18"><span class="linenos">18</span></a><span class="sd"> of Obs if several correlators are to analyzed at once.</span>
</span><span id="L-19"><a href="#L-19"><span class="linenos">19</span></a><span class="sd"> Number of states to extract (default 1).</span> </span><span id="L-19"><a href="#L-19"><span class="linenos">19</span></a><span class="sd"> k : int</span>
</span><span id="L-20"><a href="#L-20"><span class="linenos">20</span></a><span class="sd"> p : int</span> </span><span id="L-20"><a href="#L-20"><span class="linenos">20</span></a><span class="sd"> Number of states to extract (default 1).</span>
</span><span id="L-21"><a href="#L-21"><span class="linenos">21</span></a><span class="sd"> matrix pencil parameter which filters noise. The optimal value is expected between</span> </span><span id="L-21"><a href="#L-21"><span class="linenos">21</span></a><span class="sd"> p : int</span>
</span><span id="L-22"><a href="#L-22"><span class="linenos">22</span></a><span class="sd"> len(data)/3 and 2*len(data)/3. The computation is more expensive the closer p is</span> </span><span id="L-22"><a href="#L-22"><span class="linenos">22</span></a><span class="sd"> matrix pencil parameter which filters noise. The optimal value is expected between</span>
</span><span id="L-23"><a href="#L-23"><span class="linenos">23</span></a><span class="sd"> to len(data)/2 but could possibly suppress more noise (default len(data)//2).</span> </span><span id="L-23"><a href="#L-23"><span class="linenos">23</span></a><span class="sd"> len(data)/3 and 2*len(data)/3. The computation is more expensive the closer p is</span>
</span><span id="L-24"><a href="#L-24"><span class="linenos">24</span></a> </span><span id="L-24"><a href="#L-24"><span class="linenos">24</span></a><span class="sd"> to len(data)/2 but could possibly suppress more noise (default len(data)//2).</span>
</span><span id="L-25"><a href="#L-25"><span class="linenos">25</span></a><span class="sd"> Returns</span> </span><span id="L-25"><a href="#L-25"><span class="linenos">25</span></a>
</span><span id="L-26"><a href="#L-26"><span class="linenos">26</span></a><span class="sd"> -------</span> </span><span id="L-26"><a href="#L-26"><span class="linenos">26</span></a><span class="sd"> Returns</span>
</span><span id="L-27"><a href="#L-27"><span class="linenos">27</span></a><span class="sd"> energy_levels : list[Obs]</span> </span><span id="L-27"><a href="#L-27"><span class="linenos">27</span></a><span class="sd"> -------</span>
</span><span id="L-28"><a href="#L-28"><span class="linenos">28</span></a><span class="sd"> Extracted energy levels</span> </span><span id="L-28"><a href="#L-28"><span class="linenos">28</span></a><span class="sd"> energy_levels : list[Obs]</span>
</span><span id="L-29"><a href="#L-29"><span class="linenos">29</span></a><span class="sd"> &quot;&quot;&quot;</span> </span><span id="L-29"><a href="#L-29"><span class="linenos">29</span></a><span class="sd"> Extracted energy levels</span>
</span><span id="L-30"><a href="#L-30"><span class="linenos">30</span></a> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">corrs</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">Obs</span><span class="p">):</span> </span><span id="L-30"><a href="#L-30"><span class="linenos">30</span></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="L-31"><a href="#L-31"><span class="linenos">31</span></a> <span class="n">data</span> <span class="o">=</span> <span class="p">[</span><span class="n">corrs</span><span class="p">]</span> </span><span id="L-31"><a href="#L-31"><span class="linenos">31</span></a> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">corrs</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">Obs</span><span class="p">):</span>
</span><span id="L-32"><a href="#L-32"><span class="linenos">32</span></a> <span class="k">else</span><span class="p">:</span> </span><span id="L-32"><a href="#L-32"><span class="linenos">32</span></a> <span class="n">data</span> <span class="o">=</span> <span class="p">[</span><span class="n">corrs</span><span class="p">]</span>
</span><span id="L-33"><a href="#L-33"><span class="linenos">33</span></a> <span class="n">data</span> <span class="o">=</span> <span class="n">corrs</span> </span><span id="L-33"><a href="#L-33"><span class="linenos">33</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="L-34"><a href="#L-34"><span class="linenos">34</span></a> </span><span id="L-34"><a href="#L-34"><span class="linenos">34</span></a> <span class="n">data</span> <span class="o">=</span> <span class="n">corrs</span>
</span><span id="L-35"><a href="#L-35"><span class="linenos">35</span></a> <span class="n">lengths</span> <span class="o">=</span> <span class="p">[</span><span class="nb">len</span><span class="p">(</span><span class="n">d</span><span class="p">)</span> <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="n">data</span><span class="p">]</span> </span><span id="L-35"><a href="#L-35"><span class="linenos">35</span></a>
</span><span id="L-36"><a href="#L-36"><span class="linenos">36</span></a> <span class="k">if</span> <span class="n">lengths</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="n">lengths</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="o">!=</span> <span class="nb">len</span><span class="p">(</span><span class="n">lengths</span><span class="p">):</span> </span><span id="L-36"><a href="#L-36"><span class="linenos">36</span></a> <span class="n">lengths</span> <span class="o">=</span> <span class="p">[</span><span class="nb">len</span><span class="p">(</span><span class="n">d</span><span class="p">)</span> <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="n">data</span><span class="p">]</span>
</span><span id="L-37"><a href="#L-37"><span class="linenos">37</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;All datasets have to have the same length.&#39;</span><span class="p">)</span> </span><span id="L-37"><a href="#L-37"><span class="linenos">37</span></a> <span class="k">if</span> <span class="n">lengths</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="n">lengths</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="o">!=</span> <span class="nb">len</span><span class="p">(</span><span class="n">lengths</span><span class="p">):</span>
</span><span id="L-38"><a href="#L-38"><span class="linenos">38</span></a> </span><span id="L-38"><a href="#L-38"><span class="linenos">38</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;All datasets have to have the same length.&#39;</span><span class="p">)</span>
</span><span id="L-39"><a href="#L-39"><span class="linenos">39</span></a> <span class="n">data_sets</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">data</span><span class="p">)</span> </span><span id="L-39"><a href="#L-39"><span class="linenos">39</span></a>
</span><span id="L-40"><a href="#L-40"><span class="linenos">40</span></a> <span class="n">n_data</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> </span><span id="L-40"><a href="#L-40"><span class="linenos">40</span></a> <span class="n">data_sets</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">data</span><span class="p">)</span>
</span><span id="L-41"><a href="#L-41"><span class="linenos">41</span></a> </span><span id="L-41"><a href="#L-41"><span class="linenos">41</span></a> <span class="n">n_data</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
</span><span id="L-42"><a href="#L-42"><span class="linenos">42</span></a> <span class="k">if</span> <span class="n">p</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span> </span><span id="L-42"><a href="#L-42"><span class="linenos">42</span></a>
</span><span id="L-43"><a href="#L-43"><span class="linenos">43</span></a> <span class="n">p</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="n">n_data</span> <span class="o">//</span> <span class="mi">2</span><span class="p">,</span> <span class="n">k</span><span class="p">)</span> </span><span id="L-43"><a href="#L-43"><span class="linenos">43</span></a> <span class="k">if</span> <span class="n">p</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
</span><span id="L-44"><a href="#L-44"><span class="linenos">44</span></a> <span class="k">if</span> <span class="n">n_data</span> <span class="o">&lt;=</span> <span class="n">p</span><span class="p">:</span> </span><span id="L-44"><a href="#L-44"><span class="linenos">44</span></a> <span class="n">p</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="n">n_data</span> <span class="o">//</span> <span class="mi">2</span><span class="p">,</span> <span class="n">k</span><span class="p">)</span>
</span><span id="L-45"><a href="#L-45"><span class="linenos">45</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;The pencil p has to be smaller than the number of data samples.&#39;</span><span class="p">)</span> </span><span id="L-45"><a href="#L-45"><span class="linenos">45</span></a> <span class="k">if</span> <span class="n">n_data</span> <span class="o">&lt;=</span> <span class="n">p</span><span class="p">:</span>
</span><span id="L-46"><a href="#L-46"><span class="linenos">46</span></a> <span class="k">if</span> <span class="n">p</span> <span class="o">&lt;</span> <span class="n">k</span> <span class="ow">or</span> <span class="n">n_data</span> <span class="o">-</span> <span class="n">p</span> <span class="o">&lt;</span> <span class="n">k</span><span class="p">:</span> </span><span id="L-46"><a href="#L-46"><span class="linenos">46</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;The pencil p has to be smaller than the number of data samples.&#39;</span><span class="p">)</span>
</span><span id="L-47"><a href="#L-47"><span class="linenos">47</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Cannot extract&#39;</span><span class="p">,</span> <span class="n">k</span><span class="p">,</span> <span class="s1">&#39;energy levels with p=&#39;</span><span class="p">,</span> <span class="n">p</span><span class="p">,</span> <span class="s1">&#39;and N-p=&#39;</span><span class="p">,</span> <span class="n">n_data</span> <span class="o">-</span> <span class="n">p</span><span class="p">)</span> </span><span id="L-47"><a href="#L-47"><span class="linenos">47</span></a> <span class="k">if</span> <span class="n">p</span> <span class="o">&lt;</span> <span class="n">k</span> <span class="ow">or</span> <span class="n">n_data</span> <span class="o">-</span> <span class="n">p</span> <span class="o">&lt;</span> <span class="n">k</span><span class="p">:</span>
</span><span id="L-48"><a href="#L-48"><span class="linenos">48</span></a> </span><span id="L-48"><a href="#L-48"><span class="linenos">48</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Cannot extract&#39;</span><span class="p">,</span> <span class="n">k</span><span class="p">,</span> <span class="s1">&#39;energy levels with p=&#39;</span><span class="p">,</span> <span class="n">p</span><span class="p">,</span> <span class="s1">&#39;and N-p=&#39;</span><span class="p">,</span> <span class="n">n_data</span> <span class="o">-</span> <span class="n">p</span><span class="p">)</span>
</span><span id="L-49"><a href="#L-49"><span class="linenos">49</span></a> <span class="c1"># Construct the hankel matrices</span> </span><span id="L-49"><a href="#L-49"><span class="linenos">49</span></a>
</span><span id="L-50"><a href="#L-50"><span class="linenos">50</span></a> <span class="n">matrix</span> <span class="o">=</span> <span class="p">[]</span> </span><span id="L-50"><a href="#L-50"><span class="linenos">50</span></a> <span class="c1"># Construct the hankel matrices</span>
</span><span id="L-51"><a href="#L-51"><span class="linenos">51</span></a> <span class="k">for</span> <span class="n">n</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">data_sets</span><span class="p">):</span> </span><span id="L-51"><a href="#L-51"><span class="linenos">51</span></a> <span class="n">matrix</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="L-52"><a href="#L-52"><span class="linenos">52</span></a> <span class="n">matrix</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">scipy</span><span class="o">.</span><span class="n">linalg</span><span class="o">.</span><span class="n">hankel</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">n</span><span class="p">][:</span><span class="n">n_data</span> <span class="o">-</span> <span class="n">p</span><span class="p">],</span> <span class="n">data</span><span class="p">[</span><span class="n">n</span><span class="p">][</span><span class="n">n_data</span> <span class="o">-</span> <span class="n">p</span> <span class="o">-</span> <span class="mi">1</span><span class="p">:]))</span> </span><span id="L-52"><a href="#L-52"><span class="linenos">52</span></a> <span class="k">for</span> <span class="n">n</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">data_sets</span><span class="p">):</span>
</span><span id="L-53"><a href="#L-53"><span class="linenos">53</span></a> <span class="n">matrix</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">matrix</span><span class="p">)</span> </span><span id="L-53"><a href="#L-53"><span class="linenos">53</span></a> <span class="n">matrix</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">scipy</span><span class="o">.</span><span class="n">linalg</span><span class="o">.</span><span class="n">hankel</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">n</span><span class="p">][:</span><span class="n">n_data</span> <span class="o">-</span> <span class="n">p</span><span class="p">],</span> <span class="n">data</span><span class="p">[</span><span class="n">n</span><span class="p">][</span><span class="n">n_data</span> <span class="o">-</span> <span class="n">p</span> <span class="o">-</span> <span class="mi">1</span><span class="p">:]))</span>
</span><span id="L-54"><a href="#L-54"><span class="linenos">54</span></a> <span class="c1"># Construct y1 and y2</span> </span><span id="L-54"><a href="#L-54"><span class="linenos">54</span></a> <span class="n">matrix</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">matrix</span><span class="p">)</span>
</span><span id="L-55"><a href="#L-55"><span class="linenos">55</span></a> <span class="n">y1</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">concatenate</span><span class="p">(</span><span class="n">matrix</span><span class="p">[:,</span> <span class="p">:,</span> <span class="p">:</span><span class="n">p</span><span class="p">])</span> </span><span id="L-55"><a href="#L-55"><span class="linenos">55</span></a> <span class="c1"># Construct y1 and y2</span>
</span><span id="L-56"><a href="#L-56"><span class="linenos">56</span></a> <span class="n">y2</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">concatenate</span><span class="p">(</span><span class="n">matrix</span><span class="p">[:,</span> <span class="p">:,</span> <span class="mi">1</span><span class="p">:])</span> </span><span id="L-56"><a href="#L-56"><span class="linenos">56</span></a> <span class="n">y1</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">concatenate</span><span class="p">(</span><span class="n">matrix</span><span class="p">[:,</span> <span class="p">:,</span> <span class="p">:</span><span class="n">p</span><span class="p">])</span>
</span><span id="L-57"><a href="#L-57"><span class="linenos">57</span></a> <span class="c1"># Apply SVD to y2</span> </span><span id="L-57"><a href="#L-57"><span class="linenos">57</span></a> <span class="n">y2</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">concatenate</span><span class="p">(</span><span class="n">matrix</span><span class="p">[:,</span> <span class="p">:,</span> <span class="mi">1</span><span class="p">:])</span>
</span><span id="L-58"><a href="#L-58"><span class="linenos">58</span></a> <span class="n">u</span><span class="p">,</span> <span class="n">s</span><span class="p">,</span> <span class="n">vh</span> <span class="o">=</span> <span class="n">svd</span><span class="p">(</span><span class="n">y2</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span> </span><span id="L-58"><a href="#L-58"><span class="linenos">58</span></a> <span class="c1"># Apply SVD to y2</span>
</span><span id="L-59"><a href="#L-59"><span class="linenos">59</span></a> <span class="c1"># Construct z from y1 and SVD of y2, setting all singular values beyond the kth to zero</span> </span><span id="L-59"><a href="#L-59"><span class="linenos">59</span></a> <span class="n">u</span><span class="p">,</span> <span class="n">s</span><span class="p">,</span> <span class="n">vh</span> <span class="o">=</span> <span class="n">svd</span><span class="p">(</span><span class="n">y2</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
</span><span id="L-60"><a href="#L-60"><span class="linenos">60</span></a> <span class="n">z</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">diag</span><span class="p">(</span><span class="mf">1.</span> <span class="o">/</span> <span class="n">s</span><span class="p">[:</span><span class="n">k</span><span class="p">])</span> <span class="o">@</span> <span class="n">u</span><span class="p">[:,</span> <span class="p">:</span><span class="n">k</span><span class="p">]</span><span class="o">.</span><span class="n">T</span> <span class="o">@</span> <span class="n">y1</span> <span class="o">@</span> <span class="n">vh</span><span class="o">.</span><span class="n">T</span><span class="p">[:,</span> <span class="p">:</span><span class="n">k</span><span class="p">]</span> </span><span id="L-60"><a href="#L-60"><span class="linenos">60</span></a> <span class="c1"># Construct z from y1 and SVD of y2, setting all singular values beyond the kth to zero</span>
</span><span id="L-61"><a href="#L-61"><span class="linenos">61</span></a> <span class="c1"># Return the sorted logarithms of the real eigenvalues as Obs</span> </span><span id="L-61"><a href="#L-61"><span class="linenos">61</span></a> <span class="n">z</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">diag</span><span class="p">(</span><span class="mf">1.</span> <span class="o">/</span> <span class="n">s</span><span class="p">[:</span><span class="n">k</span><span class="p">])</span> <span class="o">@</span> <span class="n">u</span><span class="p">[:,</span> <span class="p">:</span><span class="n">k</span><span class="p">]</span><span class="o">.</span><span class="n">T</span> <span class="o">@</span> <span class="n">y1</span> <span class="o">@</span> <span class="n">vh</span><span class="o">.</span><span class="n">T</span><span class="p">[:,</span> <span class="p">:</span><span class="n">k</span><span class="p">]</span>
</span><span id="L-62"><a href="#L-62"><span class="linenos">62</span></a> <span class="n">energy_levels</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">abs</span><span class="p">(</span><span class="n">eig</span><span class="p">(</span><span class="n">z</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)))</span> </span><span id="L-62"><a href="#L-62"><span class="linenos">62</span></a> <span class="c1"># Return the sorted logarithms of the real eigenvalues as Obs</span>
</span><span id="L-63"><a href="#L-63"><span class="linenos">63</span></a> <span class="k">return</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">energy_levels</span><span class="p">,</span> <span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="nb">abs</span><span class="p">(</span><span class="n">x</span><span class="o">.</span><span class="n">value</span><span class="p">))</span> </span><span id="L-63"><a href="#L-63"><span class="linenos">63</span></a> <span class="n">energy_levels</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">abs</span><span class="p">(</span><span class="n">eig</span><span class="p">(</span><span class="n">z</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)))</span>
</span><span id="L-64"><a href="#L-64"><span class="linenos">64</span></a> <span class="k">return</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">energy_levels</span><span class="p">,</span> <span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="nb">abs</span><span class="p">(</span><span class="n">x</span><span class="o">.</span><span class="n">value</span><span class="p">))</span>
</span></pre></div> </span></pre></div>
@ -154,63 +155,63 @@
</div> </div>
<a class="headerlink" href="#matrix_pencil_method"></a> <a class="headerlink" href="#matrix_pencil_method"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="matrix_pencil_method-8"><a href="#matrix_pencil_method-8"><span class="linenos"> 8</span></a><span class="k">def</span><span class="w"> </span><span class="nf">matrix_pencil_method</span><span class="p">(</span><span class="n">corrs</span><span class="p">,</span> <span class="n">k</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">p</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span> <div class="pdoc-code codehilite"><pre><span></span><span id="matrix_pencil_method-9"><a href="#matrix_pencil_method-9"><span class="linenos"> 9</span></a><span class="k">def</span><span class="w"> </span><span class="nf">matrix_pencil_method</span><span class="p">(</span><span class="n">corrs</span><span class="p">,</span> <span class="n">k</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">p</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
</span><span id="matrix_pencil_method-9"><a href="#matrix_pencil_method-9"><span class="linenos"> 9</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Matrix pencil method to extract k energy levels from data</span> </span><span id="matrix_pencil_method-10"><a href="#matrix_pencil_method-10"><span class="linenos">10</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Matrix pencil method to extract k energy levels from data</span>
</span><span id="matrix_pencil_method-10"><a href="#matrix_pencil_method-10"><span class="linenos">10</span></a> </span><span id="matrix_pencil_method-11"><a href="#matrix_pencil_method-11"><span class="linenos">11</span></a>
</span><span id="matrix_pencil_method-11"><a href="#matrix_pencil_method-11"><span class="linenos">11</span></a><span class="sd"> Implementation of the matrix pencil method based on</span> </span><span id="matrix_pencil_method-12"><a href="#matrix_pencil_method-12"><span class="linenos">12</span></a><span class="sd"> Implementation of the matrix pencil method based on</span>
</span><span id="matrix_pencil_method-12"><a href="#matrix_pencil_method-12"><span class="linenos">12</span></a><span class="sd"> eq. (2.17) of Y. Hua, T. K. Sarkar, IEEE Trans. Acoust. 38, 814-824 (1990)</span> </span><span id="matrix_pencil_method-13"><a href="#matrix_pencil_method-13"><span class="linenos">13</span></a><span class="sd"> eq. (2.17) of Y. Hua, T. K. Sarkar, IEEE Trans. Acoust. 38, 814-824 (1990)</span>
</span><span id="matrix_pencil_method-13"><a href="#matrix_pencil_method-13"><span class="linenos">13</span></a> </span><span id="matrix_pencil_method-14"><a href="#matrix_pencil_method-14"><span class="linenos">14</span></a>
</span><span id="matrix_pencil_method-14"><a href="#matrix_pencil_method-14"><span class="linenos">14</span></a><span class="sd"> Parameters</span> </span><span id="matrix_pencil_method-15"><a href="#matrix_pencil_method-15"><span class="linenos">15</span></a><span class="sd"> Parameters</span>
</span><span id="matrix_pencil_method-15"><a href="#matrix_pencil_method-15"><span class="linenos">15</span></a><span class="sd"> ----------</span> </span><span id="matrix_pencil_method-16"><a href="#matrix_pencil_method-16"><span class="linenos">16</span></a><span class="sd"> ----------</span>
</span><span id="matrix_pencil_method-16"><a href="#matrix_pencil_method-16"><span class="linenos">16</span></a><span class="sd"> data : list</span> </span><span id="matrix_pencil_method-17"><a href="#matrix_pencil_method-17"><span class="linenos">17</span></a><span class="sd"> data : list</span>
</span><span id="matrix_pencil_method-17"><a href="#matrix_pencil_method-17"><span class="linenos">17</span></a><span class="sd"> can be a list of Obs for the analysis of a single correlator, or a list of lists</span> </span><span id="matrix_pencil_method-18"><a href="#matrix_pencil_method-18"><span class="linenos">18</span></a><span class="sd"> can be a list of Obs for the analysis of a single correlator, or a list of lists</span>
</span><span id="matrix_pencil_method-18"><a href="#matrix_pencil_method-18"><span class="linenos">18</span></a><span class="sd"> of Obs if several correlators are to analyzed at once.</span> </span><span id="matrix_pencil_method-19"><a href="#matrix_pencil_method-19"><span class="linenos">19</span></a><span class="sd"> of Obs if several correlators are to analyzed at once.</span>
</span><span id="matrix_pencil_method-19"><a href="#matrix_pencil_method-19"><span class="linenos">19</span></a><span class="sd"> k : int</span> </span><span id="matrix_pencil_method-20"><a href="#matrix_pencil_method-20"><span class="linenos">20</span></a><span class="sd"> k : int</span>
</span><span id="matrix_pencil_method-20"><a href="#matrix_pencil_method-20"><span class="linenos">20</span></a><span class="sd"> Number of states to extract (default 1).</span> </span><span id="matrix_pencil_method-21"><a href="#matrix_pencil_method-21"><span class="linenos">21</span></a><span class="sd"> Number of states to extract (default 1).</span>
</span><span id="matrix_pencil_method-21"><a href="#matrix_pencil_method-21"><span class="linenos">21</span></a><span class="sd"> p : int</span> </span><span id="matrix_pencil_method-22"><a href="#matrix_pencil_method-22"><span class="linenos">22</span></a><span class="sd"> p : int</span>
</span><span id="matrix_pencil_method-22"><a href="#matrix_pencil_method-22"><span class="linenos">22</span></a><span class="sd"> matrix pencil parameter which filters noise. The optimal value is expected between</span> </span><span id="matrix_pencil_method-23"><a href="#matrix_pencil_method-23"><span class="linenos">23</span></a><span class="sd"> matrix pencil parameter which filters noise. The optimal value is expected between</span>
</span><span id="matrix_pencil_method-23"><a href="#matrix_pencil_method-23"><span class="linenos">23</span></a><span class="sd"> len(data)/3 and 2*len(data)/3. The computation is more expensive the closer p is</span> </span><span id="matrix_pencil_method-24"><a href="#matrix_pencil_method-24"><span class="linenos">24</span></a><span class="sd"> len(data)/3 and 2*len(data)/3. The computation is more expensive the closer p is</span>
</span><span id="matrix_pencil_method-24"><a href="#matrix_pencil_method-24"><span class="linenos">24</span></a><span class="sd"> to len(data)/2 but could possibly suppress more noise (default len(data)//2).</span> </span><span id="matrix_pencil_method-25"><a href="#matrix_pencil_method-25"><span class="linenos">25</span></a><span class="sd"> to len(data)/2 but could possibly suppress more noise (default len(data)//2).</span>
</span><span id="matrix_pencil_method-25"><a href="#matrix_pencil_method-25"><span class="linenos">25</span></a> </span><span id="matrix_pencil_method-26"><a href="#matrix_pencil_method-26"><span class="linenos">26</span></a>
</span><span id="matrix_pencil_method-26"><a href="#matrix_pencil_method-26"><span class="linenos">26</span></a><span class="sd"> Returns</span> </span><span id="matrix_pencil_method-27"><a href="#matrix_pencil_method-27"><span class="linenos">27</span></a><span class="sd"> Returns</span>
</span><span id="matrix_pencil_method-27"><a href="#matrix_pencil_method-27"><span class="linenos">27</span></a><span class="sd"> -------</span> </span><span id="matrix_pencil_method-28"><a href="#matrix_pencil_method-28"><span class="linenos">28</span></a><span class="sd"> -------</span>
</span><span id="matrix_pencil_method-28"><a href="#matrix_pencil_method-28"><span class="linenos">28</span></a><span class="sd"> energy_levels : list[Obs]</span> </span><span id="matrix_pencil_method-29"><a href="#matrix_pencil_method-29"><span class="linenos">29</span></a><span class="sd"> energy_levels : list[Obs]</span>
</span><span id="matrix_pencil_method-29"><a href="#matrix_pencil_method-29"><span class="linenos">29</span></a><span class="sd"> Extracted energy levels</span> </span><span id="matrix_pencil_method-30"><a href="#matrix_pencil_method-30"><span class="linenos">30</span></a><span class="sd"> Extracted energy levels</span>
</span><span id="matrix_pencil_method-30"><a href="#matrix_pencil_method-30"><span class="linenos">30</span></a><span class="sd"> &quot;&quot;&quot;</span> </span><span id="matrix_pencil_method-31"><a href="#matrix_pencil_method-31"><span class="linenos">31</span></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="matrix_pencil_method-31"><a href="#matrix_pencil_method-31"><span class="linenos">31</span></a> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">corrs</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">Obs</span><span class="p">):</span> </span><span id="matrix_pencil_method-32"><a href="#matrix_pencil_method-32"><span class="linenos">32</span></a> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">corrs</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">Obs</span><span class="p">):</span>
</span><span id="matrix_pencil_method-32"><a href="#matrix_pencil_method-32"><span class="linenos">32</span></a> <span class="n">data</span> <span class="o">=</span> <span class="p">[</span><span class="n">corrs</span><span class="p">]</span> </span><span id="matrix_pencil_method-33"><a href="#matrix_pencil_method-33"><span class="linenos">33</span></a> <span class="n">data</span> <span class="o">=</span> <span class="p">[</span><span class="n">corrs</span><span class="p">]</span>
</span><span id="matrix_pencil_method-33"><a href="#matrix_pencil_method-33"><span class="linenos">33</span></a> <span class="k">else</span><span class="p">:</span> </span><span id="matrix_pencil_method-34"><a href="#matrix_pencil_method-34"><span class="linenos">34</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="matrix_pencil_method-34"><a href="#matrix_pencil_method-34"><span class="linenos">34</span></a> <span class="n">data</span> <span class="o">=</span> <span class="n">corrs</span> </span><span id="matrix_pencil_method-35"><a href="#matrix_pencil_method-35"><span class="linenos">35</span></a> <span class="n">data</span> <span class="o">=</span> <span class="n">corrs</span>
</span><span id="matrix_pencil_method-35"><a href="#matrix_pencil_method-35"><span class="linenos">35</span></a> </span><span id="matrix_pencil_method-36"><a href="#matrix_pencil_method-36"><span class="linenos">36</span></a>
</span><span id="matrix_pencil_method-36"><a href="#matrix_pencil_method-36"><span class="linenos">36</span></a> <span class="n">lengths</span> <span class="o">=</span> <span class="p">[</span><span class="nb">len</span><span class="p">(</span><span class="n">d</span><span class="p">)</span> <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="n">data</span><span class="p">]</span> </span><span id="matrix_pencil_method-37"><a href="#matrix_pencil_method-37"><span class="linenos">37</span></a> <span class="n">lengths</span> <span class="o">=</span> <span class="p">[</span><span class="nb">len</span><span class="p">(</span><span class="n">d</span><span class="p">)</span> <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="n">data</span><span class="p">]</span>
</span><span id="matrix_pencil_method-37"><a href="#matrix_pencil_method-37"><span class="linenos">37</span></a> <span class="k">if</span> <span class="n">lengths</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="n">lengths</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="o">!=</span> <span class="nb">len</span><span class="p">(</span><span class="n">lengths</span><span class="p">):</span> </span><span id="matrix_pencil_method-38"><a href="#matrix_pencil_method-38"><span class="linenos">38</span></a> <span class="k">if</span> <span class="n">lengths</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="n">lengths</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="o">!=</span> <span class="nb">len</span><span class="p">(</span><span class="n">lengths</span><span class="p">):</span>
</span><span id="matrix_pencil_method-38"><a href="#matrix_pencil_method-38"><span class="linenos">38</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;All datasets have to have the same length.&#39;</span><span class="p">)</span> </span><span id="matrix_pencil_method-39"><a href="#matrix_pencil_method-39"><span class="linenos">39</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;All datasets have to have the same length.&#39;</span><span class="p">)</span>
</span><span id="matrix_pencil_method-39"><a href="#matrix_pencil_method-39"><span class="linenos">39</span></a> </span><span id="matrix_pencil_method-40"><a href="#matrix_pencil_method-40"><span class="linenos">40</span></a>
</span><span id="matrix_pencil_method-40"><a href="#matrix_pencil_method-40"><span class="linenos">40</span></a> <span class="n">data_sets</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">data</span><span class="p">)</span> </span><span id="matrix_pencil_method-41"><a href="#matrix_pencil_method-41"><span class="linenos">41</span></a> <span class="n">data_sets</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">data</span><span class="p">)</span>
</span><span id="matrix_pencil_method-41"><a href="#matrix_pencil_method-41"><span class="linenos">41</span></a> <span class="n">n_data</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> </span><span id="matrix_pencil_method-42"><a href="#matrix_pencil_method-42"><span class="linenos">42</span></a> <span class="n">n_data</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
</span><span id="matrix_pencil_method-42"><a href="#matrix_pencil_method-42"><span class="linenos">42</span></a> </span><span id="matrix_pencil_method-43"><a href="#matrix_pencil_method-43"><span class="linenos">43</span></a>
</span><span id="matrix_pencil_method-43"><a href="#matrix_pencil_method-43"><span class="linenos">43</span></a> <span class="k">if</span> <span class="n">p</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span> </span><span id="matrix_pencil_method-44"><a href="#matrix_pencil_method-44"><span class="linenos">44</span></a> <span class="k">if</span> <span class="n">p</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
</span><span id="matrix_pencil_method-44"><a href="#matrix_pencil_method-44"><span class="linenos">44</span></a> <span class="n">p</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="n">n_data</span> <span class="o">//</span> <span class="mi">2</span><span class="p">,</span> <span class="n">k</span><span class="p">)</span> </span><span id="matrix_pencil_method-45"><a href="#matrix_pencil_method-45"><span class="linenos">45</span></a> <span class="n">p</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="n">n_data</span> <span class="o">//</span> <span class="mi">2</span><span class="p">,</span> <span class="n">k</span><span class="p">)</span>
</span><span id="matrix_pencil_method-45"><a href="#matrix_pencil_method-45"><span class="linenos">45</span></a> <span class="k">if</span> <span class="n">n_data</span> <span class="o">&lt;=</span> <span class="n">p</span><span class="p">:</span> </span><span id="matrix_pencil_method-46"><a href="#matrix_pencil_method-46"><span class="linenos">46</span></a> <span class="k">if</span> <span class="n">n_data</span> <span class="o">&lt;=</span> <span class="n">p</span><span class="p">:</span>
</span><span id="matrix_pencil_method-46"><a href="#matrix_pencil_method-46"><span class="linenos">46</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;The pencil p has to be smaller than the number of data samples.&#39;</span><span class="p">)</span> </span><span id="matrix_pencil_method-47"><a href="#matrix_pencil_method-47"><span class="linenos">47</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;The pencil p has to be smaller than the number of data samples.&#39;</span><span class="p">)</span>
</span><span id="matrix_pencil_method-47"><a href="#matrix_pencil_method-47"><span class="linenos">47</span></a> <span class="k">if</span> <span class="n">p</span> <span class="o">&lt;</span> <span class="n">k</span> <span class="ow">or</span> <span class="n">n_data</span> <span class="o">-</span> <span class="n">p</span> <span class="o">&lt;</span> <span class="n">k</span><span class="p">:</span> </span><span id="matrix_pencil_method-48"><a href="#matrix_pencil_method-48"><span class="linenos">48</span></a> <span class="k">if</span> <span class="n">p</span> <span class="o">&lt;</span> <span class="n">k</span> <span class="ow">or</span> <span class="n">n_data</span> <span class="o">-</span> <span class="n">p</span> <span class="o">&lt;</span> <span class="n">k</span><span class="p">:</span>
</span><span id="matrix_pencil_method-48"><a href="#matrix_pencil_method-48"><span class="linenos">48</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Cannot extract&#39;</span><span class="p">,</span> <span class="n">k</span><span class="p">,</span> <span class="s1">&#39;energy levels with p=&#39;</span><span class="p">,</span> <span class="n">p</span><span class="p">,</span> <span class="s1">&#39;and N-p=&#39;</span><span class="p">,</span> <span class="n">n_data</span> <span class="o">-</span> <span class="n">p</span><span class="p">)</span> </span><span id="matrix_pencil_method-49"><a href="#matrix_pencil_method-49"><span class="linenos">49</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Cannot extract&#39;</span><span class="p">,</span> <span class="n">k</span><span class="p">,</span> <span class="s1">&#39;energy levels with p=&#39;</span><span class="p">,</span> <span class="n">p</span><span class="p">,</span> <span class="s1">&#39;and N-p=&#39;</span><span class="p">,</span> <span class="n">n_data</span> <span class="o">-</span> <span class="n">p</span><span class="p">)</span>
</span><span id="matrix_pencil_method-49"><a href="#matrix_pencil_method-49"><span class="linenos">49</span></a> </span><span id="matrix_pencil_method-50"><a href="#matrix_pencil_method-50"><span class="linenos">50</span></a>
</span><span id="matrix_pencil_method-50"><a href="#matrix_pencil_method-50"><span class="linenos">50</span></a> <span class="c1"># Construct the hankel matrices</span> </span><span id="matrix_pencil_method-51"><a href="#matrix_pencil_method-51"><span class="linenos">51</span></a> <span class="c1"># Construct the hankel matrices</span>
</span><span id="matrix_pencil_method-51"><a href="#matrix_pencil_method-51"><span class="linenos">51</span></a> <span class="n">matrix</span> <span class="o">=</span> <span class="p">[]</span> </span><span id="matrix_pencil_method-52"><a href="#matrix_pencil_method-52"><span class="linenos">52</span></a> <span class="n">matrix</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="matrix_pencil_method-52"><a href="#matrix_pencil_method-52"><span class="linenos">52</span></a> <span class="k">for</span> <span class="n">n</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">data_sets</span><span class="p">):</span> </span><span id="matrix_pencil_method-53"><a href="#matrix_pencil_method-53"><span class="linenos">53</span></a> <span class="k">for</span> <span class="n">n</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">data_sets</span><span class="p">):</span>
</span><span id="matrix_pencil_method-53"><a href="#matrix_pencil_method-53"><span class="linenos">53</span></a> <span class="n">matrix</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">scipy</span><span class="o">.</span><span class="n">linalg</span><span class="o">.</span><span class="n">hankel</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">n</span><span class="p">][:</span><span class="n">n_data</span> <span class="o">-</span> <span class="n">p</span><span class="p">],</span> <span class="n">data</span><span class="p">[</span><span class="n">n</span><span class="p">][</span><span class="n">n_data</span> <span class="o">-</span> <span class="n">p</span> <span class="o">-</span> <span class="mi">1</span><span class="p">:]))</span> </span><span id="matrix_pencil_method-54"><a href="#matrix_pencil_method-54"><span class="linenos">54</span></a> <span class="n">matrix</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">scipy</span><span class="o">.</span><span class="n">linalg</span><span class="o">.</span><span class="n">hankel</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">n</span><span class="p">][:</span><span class="n">n_data</span> <span class="o">-</span> <span class="n">p</span><span class="p">],</span> <span class="n">data</span><span class="p">[</span><span class="n">n</span><span class="p">][</span><span class="n">n_data</span> <span class="o">-</span> <span class="n">p</span> <span class="o">-</span> <span class="mi">1</span><span class="p">:]))</span>
</span><span id="matrix_pencil_method-54"><a href="#matrix_pencil_method-54"><span class="linenos">54</span></a> <span class="n">matrix</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">matrix</span><span class="p">)</span> </span><span id="matrix_pencil_method-55"><a href="#matrix_pencil_method-55"><span class="linenos">55</span></a> <span class="n">matrix</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">matrix</span><span class="p">)</span>
</span><span id="matrix_pencil_method-55"><a href="#matrix_pencil_method-55"><span class="linenos">55</span></a> <span class="c1"># Construct y1 and y2</span> </span><span id="matrix_pencil_method-56"><a href="#matrix_pencil_method-56"><span class="linenos">56</span></a> <span class="c1"># Construct y1 and y2</span>
</span><span id="matrix_pencil_method-56"><a href="#matrix_pencil_method-56"><span class="linenos">56</span></a> <span class="n">y1</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">concatenate</span><span class="p">(</span><span class="n">matrix</span><span class="p">[:,</span> <span class="p">:,</span> <span class="p">:</span><span class="n">p</span><span class="p">])</span> </span><span id="matrix_pencil_method-57"><a href="#matrix_pencil_method-57"><span class="linenos">57</span></a> <span class="n">y1</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">concatenate</span><span class="p">(</span><span class="n">matrix</span><span class="p">[:,</span> <span class="p">:,</span> <span class="p">:</span><span class="n">p</span><span class="p">])</span>
</span><span id="matrix_pencil_method-57"><a href="#matrix_pencil_method-57"><span class="linenos">57</span></a> <span class="n">y2</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">concatenate</span><span class="p">(</span><span class="n">matrix</span><span class="p">[:,</span> <span class="p">:,</span> <span class="mi">1</span><span class="p">:])</span> </span><span id="matrix_pencil_method-58"><a href="#matrix_pencil_method-58"><span class="linenos">58</span></a> <span class="n">y2</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">concatenate</span><span class="p">(</span><span class="n">matrix</span><span class="p">[:,</span> <span class="p">:,</span> <span class="mi">1</span><span class="p">:])</span>
</span><span id="matrix_pencil_method-58"><a href="#matrix_pencil_method-58"><span class="linenos">58</span></a> <span class="c1"># Apply SVD to y2</span> </span><span id="matrix_pencil_method-59"><a href="#matrix_pencil_method-59"><span class="linenos">59</span></a> <span class="c1"># Apply SVD to y2</span>
</span><span id="matrix_pencil_method-59"><a href="#matrix_pencil_method-59"><span class="linenos">59</span></a> <span class="n">u</span><span class="p">,</span> <span class="n">s</span><span class="p">,</span> <span class="n">vh</span> <span class="o">=</span> <span class="n">svd</span><span class="p">(</span><span class="n">y2</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span> </span><span id="matrix_pencil_method-60"><a href="#matrix_pencil_method-60"><span class="linenos">60</span></a> <span class="n">u</span><span class="p">,</span> <span class="n">s</span><span class="p">,</span> <span class="n">vh</span> <span class="o">=</span> <span class="n">svd</span><span class="p">(</span><span class="n">y2</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
</span><span id="matrix_pencil_method-60"><a href="#matrix_pencil_method-60"><span class="linenos">60</span></a> <span class="c1"># Construct z from y1 and SVD of y2, setting all singular values beyond the kth to zero</span> </span><span id="matrix_pencil_method-61"><a href="#matrix_pencil_method-61"><span class="linenos">61</span></a> <span class="c1"># Construct z from y1 and SVD of y2, setting all singular values beyond the kth to zero</span>
</span><span id="matrix_pencil_method-61"><a href="#matrix_pencil_method-61"><span class="linenos">61</span></a> <span class="n">z</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">diag</span><span class="p">(</span><span class="mf">1.</span> <span class="o">/</span> <span class="n">s</span><span class="p">[:</span><span class="n">k</span><span class="p">])</span> <span class="o">@</span> <span class="n">u</span><span class="p">[:,</span> <span class="p">:</span><span class="n">k</span><span class="p">]</span><span class="o">.</span><span class="n">T</span> <span class="o">@</span> <span class="n">y1</span> <span class="o">@</span> <span class="n">vh</span><span class="o">.</span><span class="n">T</span><span class="p">[:,</span> <span class="p">:</span><span class="n">k</span><span class="p">]</span> </span><span id="matrix_pencil_method-62"><a href="#matrix_pencil_method-62"><span class="linenos">62</span></a> <span class="n">z</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">diag</span><span class="p">(</span><span class="mf">1.</span> <span class="o">/</span> <span class="n">s</span><span class="p">[:</span><span class="n">k</span><span class="p">])</span> <span class="o">@</span> <span class="n">u</span><span class="p">[:,</span> <span class="p">:</span><span class="n">k</span><span class="p">]</span><span class="o">.</span><span class="n">T</span> <span class="o">@</span> <span class="n">y1</span> <span class="o">@</span> <span class="n">vh</span><span class="o">.</span><span class="n">T</span><span class="p">[:,</span> <span class="p">:</span><span class="n">k</span><span class="p">]</span>
</span><span id="matrix_pencil_method-62"><a href="#matrix_pencil_method-62"><span class="linenos">62</span></a> <span class="c1"># Return the sorted logarithms of the real eigenvalues as Obs</span> </span><span id="matrix_pencil_method-63"><a href="#matrix_pencil_method-63"><span class="linenos">63</span></a> <span class="c1"># Return the sorted logarithms of the real eigenvalues as Obs</span>
</span><span id="matrix_pencil_method-63"><a href="#matrix_pencil_method-63"><span class="linenos">63</span></a> <span class="n">energy_levels</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">abs</span><span class="p">(</span><span class="n">eig</span><span class="p">(</span><span class="n">z</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)))</span> </span><span id="matrix_pencil_method-64"><a href="#matrix_pencil_method-64"><span class="linenos">64</span></a> <span class="n">energy_levels</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">abs</span><span class="p">(</span><span class="n">eig</span><span class="p">(</span><span class="n">z</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)))</span>
</span><span id="matrix_pencil_method-64"><a href="#matrix_pencil_method-64"><span class="linenos">64</span></a> <span class="k">return</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">energy_levels</span><span class="p">,</span> <span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="nb">abs</span><span class="p">(</span><span class="n">x</span><span class="o">.</span><span class="n">value</span><span class="p">))</span> </span><span id="matrix_pencil_method-65"><a href="#matrix_pencil_method-65"><span class="linenos">65</span></a> <span class="k">return</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">energy_levels</span><span class="p">,</span> <span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="nb">abs</span><span class="p">(</span><span class="n">x</span><span class="o">.</span><span class="n">value</span><span class="p">))</span>
</span></pre></div> </span></pre></div>

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<div class="pdoc-code codehilite"><pre><span></span><span id="L-1"><a href="#L-1"><span class="linenos"> 1</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span> <div class="pdoc-code codehilite"><pre><span></span><span id="L-1"><a href="#L-1"><span class="linenos"> 1</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
</span><span id="L-2"><a href="#L-2"><span class="linenos"> 2</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">scipy.optimize</span> </span><span id="L-2"><a href="#L-2"><span class="linenos"> 2</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">scipy.optimize</span>
</span><span id="L-3"><a href="#L-3"><span class="linenos"> 3</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">autograd</span><span class="w"> </span><span class="kn">import</span> <span class="n">jacobian</span> </span><span id="L-3"><a href="#L-3"><span class="linenos"> 3</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">autograd</span><span class="w"> </span><span class="kn">import</span> <span class="n">jacobian</span>
</span><span id="L-4"><a href="#L-4"><span class="linenos"> 4</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">.obs</span><span class="w"> </span><span class="kn">import</span> <span class="n">derived_observable</span> </span><span id="L-4"><a href="#L-4"><span class="linenos"> 4</span></a>
</span><span id="L-5"><a href="#L-5"><span class="linenos"> 5</span></a> </span><span id="L-5"><a href="#L-5"><span class="linenos"> 5</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">.obs</span><span class="w"> </span><span class="kn">import</span> <span class="n">derived_observable</span>
</span><span id="L-6"><a href="#L-6"><span class="linenos"> 6</span></a> </span><span id="L-6"><a href="#L-6"><span class="linenos"> 6</span></a>
</span><span id="L-7"><a href="#L-7"><span class="linenos"> 7</span></a><span class="k">def</span><span class="w"> </span><span class="nf">find_root</span><span class="p">(</span><span class="n">d</span><span class="p">,</span> <span class="n">func</span><span class="p">,</span> <span class="n">guess</span><span class="o">=</span><span class="mf">1.0</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span> </span><span id="L-7"><a href="#L-7"><span class="linenos"> 7</span></a>
</span><span id="L-8"><a href="#L-8"><span class="linenos"> 8</span></a><span class="w"> </span><span class="sa">r</span><span class="sd">&#39;&#39;&#39;Finds the root of the function func(x, d) where d is an `Obs`.</span> </span><span id="L-8"><a href="#L-8"><span class="linenos"> 8</span></a><span class="k">def</span><span class="w"> </span><span class="nf">find_root</span><span class="p">(</span><span class="n">d</span><span class="p">,</span> <span class="n">func</span><span class="p">,</span> <span class="n">guess</span><span class="o">=</span><span class="mf">1.0</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
</span><span id="L-9"><a href="#L-9"><span class="linenos"> 9</span></a> </span><span id="L-9"><a href="#L-9"><span class="linenos"> 9</span></a><span class="w"> </span><span class="sa">r</span><span class="sd">&#39;&#39;&#39;Finds the root of the function func(x, d) where d is an `Obs`.</span>
</span><span id="L-10"><a href="#L-10"><span class="linenos">10</span></a><span class="sd"> Parameters</span> </span><span id="L-10"><a href="#L-10"><span class="linenos">10</span></a>
</span><span id="L-11"><a href="#L-11"><span class="linenos">11</span></a><span class="sd"> -----------------</span> </span><span id="L-11"><a href="#L-11"><span class="linenos">11</span></a><span class="sd"> Parameters</span>
</span><span id="L-12"><a href="#L-12"><span class="linenos">12</span></a><span class="sd"> d : Obs</span> </span><span id="L-12"><a href="#L-12"><span class="linenos">12</span></a><span class="sd"> -----------------</span>
</span><span id="L-13"><a href="#L-13"><span class="linenos">13</span></a><span class="sd"> Obs passed to the function.</span> </span><span id="L-13"><a href="#L-13"><span class="linenos">13</span></a><span class="sd"> d : Obs</span>
</span><span id="L-14"><a href="#L-14"><span class="linenos">14</span></a><span class="sd"> func : object</span> </span><span id="L-14"><a href="#L-14"><span class="linenos">14</span></a><span class="sd"> Obs passed to the function.</span>
</span><span id="L-15"><a href="#L-15"><span class="linenos">15</span></a><span class="sd"> Function to be minimized. Any numpy functions have to use the autograd.numpy wrapper.</span> </span><span id="L-15"><a href="#L-15"><span class="linenos">15</span></a><span class="sd"> func : object</span>
</span><span id="L-16"><a href="#L-16"><span class="linenos">16</span></a><span class="sd"> Example:</span> </span><span id="L-16"><a href="#L-16"><span class="linenos">16</span></a><span class="sd"> Function to be minimized. Any numpy functions have to use the autograd.numpy wrapper.</span>
</span><span id="L-17"><a href="#L-17"><span class="linenos">17</span></a><span class="sd"> ```python</span> </span><span id="L-17"><a href="#L-17"><span class="linenos">17</span></a><span class="sd"> Example:</span>
</span><span id="L-18"><a href="#L-18"><span class="linenos">18</span></a><span class="sd"> import autograd.numpy as anp</span> </span><span id="L-18"><a href="#L-18"><span class="linenos">18</span></a><span class="sd"> ```python</span>
</span><span id="L-19"><a href="#L-19"><span class="linenos">19</span></a><span class="sd"> def root_func(x, d):</span> </span><span id="L-19"><a href="#L-19"><span class="linenos">19</span></a><span class="sd"> import autograd.numpy as anp</span>
</span><span id="L-20"><a href="#L-20"><span class="linenos">20</span></a><span class="sd"> return anp.exp(-x ** 2) - d</span> </span><span id="L-20"><a href="#L-20"><span class="linenos">20</span></a><span class="sd"> def root_func(x, d):</span>
</span><span id="L-21"><a href="#L-21"><span class="linenos">21</span></a><span class="sd"> ```</span> </span><span id="L-21"><a href="#L-21"><span class="linenos">21</span></a><span class="sd"> return anp.exp(-x ** 2) - d</span>
</span><span id="L-22"><a href="#L-22"><span class="linenos">22</span></a><span class="sd"> guess : float</span> </span><span id="L-22"><a href="#L-22"><span class="linenos">22</span></a><span class="sd"> ```</span>
</span><span id="L-23"><a href="#L-23"><span class="linenos">23</span></a><span class="sd"> Initial guess for the minimization.</span> </span><span id="L-23"><a href="#L-23"><span class="linenos">23</span></a><span class="sd"> guess : float</span>
</span><span id="L-24"><a href="#L-24"><span class="linenos">24</span></a> </span><span id="L-24"><a href="#L-24"><span class="linenos">24</span></a><span class="sd"> Initial guess for the minimization.</span>
</span><span id="L-25"><a href="#L-25"><span class="linenos">25</span></a><span class="sd"> Returns</span> </span><span id="L-25"><a href="#L-25"><span class="linenos">25</span></a>
</span><span id="L-26"><a href="#L-26"><span class="linenos">26</span></a><span class="sd"> -------</span> </span><span id="L-26"><a href="#L-26"><span class="linenos">26</span></a><span class="sd"> Returns</span>
</span><span id="L-27"><a href="#L-27"><span class="linenos">27</span></a><span class="sd"> res : Obs</span> </span><span id="L-27"><a href="#L-27"><span class="linenos">27</span></a><span class="sd"> -------</span>
</span><span id="L-28"><a href="#L-28"><span class="linenos">28</span></a><span class="sd"> `Obs` valued root of the function.</span> </span><span id="L-28"><a href="#L-28"><span class="linenos">28</span></a><span class="sd"> res : Obs</span>
</span><span id="L-29"><a href="#L-29"><span class="linenos">29</span></a><span class="sd"> &#39;&#39;&#39;</span> </span><span id="L-29"><a href="#L-29"><span class="linenos">29</span></a><span class="sd"> `Obs` valued root of the function.</span>
</span><span id="L-30"><a href="#L-30"><span class="linenos">30</span></a> <span class="n">d_val</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">vectorize</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span><span class="o">.</span><span class="n">value</span><span class="p">)(</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">d</span><span class="p">))</span> </span><span id="L-30"><a href="#L-30"><span class="linenos">30</span></a><span class="sd"> &#39;&#39;&#39;</span>
</span><span id="L-31"><a href="#L-31"><span class="linenos">31</span></a> </span><span id="L-31"><a href="#L-31"><span class="linenos">31</span></a> <span class="n">d_val</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">vectorize</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span><span class="o">.</span><span class="n">value</span><span class="p">)(</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">d</span><span class="p">))</span>
</span><span id="L-32"><a href="#L-32"><span class="linenos">32</span></a> <span class="n">root</span> <span class="o">=</span> <span class="n">scipy</span><span class="o">.</span><span class="n">optimize</span><span class="o">.</span><span class="n">fsolve</span><span class="p">(</span><span class="n">func</span><span class="p">,</span> <span class="n">guess</span><span class="p">,</span> <span class="n">d_val</span><span class="p">)</span> </span><span id="L-32"><a href="#L-32"><span class="linenos">32</span></a>
</span><span id="L-33"><a href="#L-33"><span class="linenos">33</span></a> </span><span id="L-33"><a href="#L-33"><span class="linenos">33</span></a> <span class="n">root</span> <span class="o">=</span> <span class="n">scipy</span><span class="o">.</span><span class="n">optimize</span><span class="o">.</span><span class="n">fsolve</span><span class="p">(</span><span class="n">func</span><span class="p">,</span> <span class="n">guess</span><span class="p">,</span> <span class="n">d_val</span><span class="p">)</span>
</span><span id="L-34"><a href="#L-34"><span class="linenos">34</span></a> <span class="c1"># Error propagation as detailed in arXiv:1809.01289</span> </span><span id="L-34"><a href="#L-34"><span class="linenos">34</span></a>
</span><span id="L-35"><a href="#L-35"><span class="linenos">35</span></a> <span class="k">try</span><span class="p">:</span> </span><span id="L-35"><a href="#L-35"><span class="linenos">35</span></a> <span class="c1"># Error propagation as detailed in arXiv:1809.01289</span>
</span><span id="L-36"><a href="#L-36"><span class="linenos">36</span></a> <span class="n">dx</span> <span class="o">=</span> <span class="n">jacobian</span><span class="p">(</span><span class="n">func</span><span class="p">)(</span><span class="n">root</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">d_val</span><span class="p">)</span> </span><span id="L-36"><a href="#L-36"><span class="linenos">36</span></a> <span class="k">try</span><span class="p">:</span>
</span><span id="L-37"><a href="#L-37"><span class="linenos">37</span></a> <span class="n">da</span> <span class="o">=</span> <span class="n">jacobian</span><span class="p">(</span><span class="k">lambda</span> <span class="n">u</span><span class="p">,</span> <span class="n">v</span><span class="p">:</span> <span class="n">func</span><span class="p">(</span><span class="n">v</span><span class="p">,</span> <span class="n">u</span><span class="p">))(</span><span class="n">d_val</span><span class="p">,</span> <span class="n">root</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> </span><span id="L-37"><a href="#L-37"><span class="linenos">37</span></a> <span class="n">dx</span> <span class="o">=</span> <span class="n">jacobian</span><span class="p">(</span><span class="n">func</span><span class="p">)(</span><span class="n">root</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">d_val</span><span class="p">)</span>
</span><span id="L-38"><a href="#L-38"><span class="linenos">38</span></a> <span class="k">except</span> <span class="p">(</span><span class="ne">TypeError</span><span class="p">,</span> <span class="ne">ValueError</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">linalg</span><span class="o">.</span><span class="n">LinAlgError</span><span class="p">):</span> </span><span id="L-38"><a href="#L-38"><span class="linenos">38</span></a> <span class="n">da</span> <span class="o">=</span> <span class="n">jacobian</span><span class="p">(</span><span class="k">lambda</span> <span class="n">u</span><span class="p">,</span> <span class="n">v</span><span class="p">:</span> <span class="n">func</span><span class="p">(</span><span class="n">v</span><span class="p">,</span> <span class="n">u</span><span class="p">))(</span><span class="n">d_val</span><span class="p">,</span> <span class="n">root</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
</span><span id="L-39"><a href="#L-39"><span class="linenos">39</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">&quot;It is required to use autograd.numpy instead of numpy within root functions, see the documentation for details.&quot;</span><span class="p">)</span> <span class="kn">from</span><span class="w"> </span><span class="kc">None</span> </span><span id="L-39"><a href="#L-39"><span class="linenos">39</span></a> <span class="k">except</span> <span class="p">(</span><span class="ne">TypeError</span><span class="p">,</span> <span class="ne">ValueError</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">linalg</span><span class="o">.</span><span class="n">LinAlgError</span><span class="p">):</span>
</span><span id="L-40"><a href="#L-40"><span class="linenos">40</span></a> <span class="n">deriv</span> <span class="o">=</span> <span class="o">-</span> <span class="n">da</span> <span class="o">/</span> <span class="n">dx</span> </span><span id="L-40"><a href="#L-40"><span class="linenos">40</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">&quot;It is required to use autograd.numpy instead of numpy within root functions, see the documentation for details.&quot;</span><span class="p">)</span> <span class="kn">from</span><span class="w"> </span><span class="kc">None</span>
</span><span id="L-41"><a href="#L-41"><span class="linenos">41</span></a> <span class="n">res</span> <span class="o">=</span> <span class="n">derived_observable</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">:</span> <span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="n">np</span><span class="o">.</span><span class="n">finfo</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">float64</span><span class="p">)</span><span class="o">.</span><span class="n">eps</span><span class="p">)</span> <span class="o">/</span> <span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">d</span><span class="p">)</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">value</span> <span class="o">+</span> <span class="n">np</span><span class="o">.</span><span class="n">finfo</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">float64</span><span class="p">)</span><span class="o">.</span><span class="n">eps</span><span class="p">)</span> <span class="o">*</span> <span class="n">root</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> </span><span id="L-41"><a href="#L-41"><span class="linenos">41</span></a> <span class="n">deriv</span> <span class="o">=</span> <span class="o">-</span> <span class="n">da</span> <span class="o">/</span> <span class="n">dx</span>
</span><span id="L-42"><a href="#L-42"><span class="linenos">42</span></a> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">d</span><span class="p">)</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">),</span> <span class="n">man_grad</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">deriv</span><span class="p">)</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">))</span> </span><span id="L-42"><a href="#L-42"><span class="linenos">42</span></a> <span class="n">res</span> <span class="o">=</span> <span class="n">derived_observable</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">:</span> <span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="n">np</span><span class="o">.</span><span class="n">finfo</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">float64</span><span class="p">)</span><span class="o">.</span><span class="n">eps</span><span class="p">)</span> <span class="o">/</span> <span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">d</span><span class="p">)</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">value</span> <span class="o">+</span> <span class="n">np</span><span class="o">.</span><span class="n">finfo</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">float64</span><span class="p">)</span><span class="o">.</span><span class="n">eps</span><span class="p">)</span> <span class="o">*</span> <span class="n">root</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
</span><span id="L-43"><a href="#L-43"><span class="linenos">43</span></a> <span class="k">return</span> <span class="n">res</span> </span><span id="L-43"><a href="#L-43"><span class="linenos">43</span></a> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">d</span><span class="p">)</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">),</span> <span class="n">man_grad</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">deriv</span><span class="p">)</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">))</span>
</span><span id="L-44"><a href="#L-44"><span class="linenos">44</span></a> <span class="k">return</span> <span class="n">res</span>
</span></pre></div> </span></pre></div>
@ -134,43 +135,43 @@
</div> </div>
<a class="headerlink" href="#find_root"></a> <a class="headerlink" href="#find_root"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="find_root-8"><a href="#find_root-8"><span class="linenos"> 8</span></a><span class="k">def</span><span class="w"> </span><span class="nf">find_root</span><span class="p">(</span><span class="n">d</span><span class="p">,</span> <span class="n">func</span><span class="p">,</span> <span class="n">guess</span><span class="o">=</span><span class="mf">1.0</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span> <div class="pdoc-code codehilite"><pre><span></span><span id="find_root-9"><a href="#find_root-9"><span class="linenos"> 9</span></a><span class="k">def</span><span class="w"> </span><span class="nf">find_root</span><span class="p">(</span><span class="n">d</span><span class="p">,</span> <span class="n">func</span><span class="p">,</span> <span class="n">guess</span><span class="o">=</span><span class="mf">1.0</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
</span><span id="find_root-9"><a href="#find_root-9"><span class="linenos"> 9</span></a><span class="w"> </span><span class="sa">r</span><span class="sd">&#39;&#39;&#39;Finds the root of the function func(x, d) where d is an `Obs`.</span> </span><span id="find_root-10"><a href="#find_root-10"><span class="linenos">10</span></a><span class="w"> </span><span class="sa">r</span><span class="sd">&#39;&#39;&#39;Finds the root of the function func(x, d) where d is an `Obs`.</span>
</span><span id="find_root-10"><a href="#find_root-10"><span class="linenos">10</span></a> </span><span id="find_root-11"><a href="#find_root-11"><span class="linenos">11</span></a>
</span><span id="find_root-11"><a href="#find_root-11"><span class="linenos">11</span></a><span class="sd"> Parameters</span> </span><span id="find_root-12"><a href="#find_root-12"><span class="linenos">12</span></a><span class="sd"> Parameters</span>
</span><span id="find_root-12"><a href="#find_root-12"><span class="linenos">12</span></a><span class="sd"> -----------------</span> </span><span id="find_root-13"><a href="#find_root-13"><span class="linenos">13</span></a><span class="sd"> -----------------</span>
</span><span id="find_root-13"><a href="#find_root-13"><span class="linenos">13</span></a><span class="sd"> d : Obs</span> </span><span id="find_root-14"><a href="#find_root-14"><span class="linenos">14</span></a><span class="sd"> d : Obs</span>
</span><span id="find_root-14"><a href="#find_root-14"><span class="linenos">14</span></a><span class="sd"> Obs passed to the function.</span> </span><span id="find_root-15"><a href="#find_root-15"><span class="linenos">15</span></a><span class="sd"> Obs passed to the function.</span>
</span><span id="find_root-15"><a href="#find_root-15"><span class="linenos">15</span></a><span class="sd"> func : object</span> </span><span id="find_root-16"><a href="#find_root-16"><span class="linenos">16</span></a><span class="sd"> func : object</span>
</span><span id="find_root-16"><a href="#find_root-16"><span class="linenos">16</span></a><span class="sd"> Function to be minimized. Any numpy functions have to use the autograd.numpy wrapper.</span> </span><span id="find_root-17"><a href="#find_root-17"><span class="linenos">17</span></a><span class="sd"> Function to be minimized. Any numpy functions have to use the autograd.numpy wrapper.</span>
</span><span id="find_root-17"><a href="#find_root-17"><span class="linenos">17</span></a><span class="sd"> Example:</span> </span><span id="find_root-18"><a href="#find_root-18"><span class="linenos">18</span></a><span class="sd"> Example:</span>
</span><span id="find_root-18"><a href="#find_root-18"><span class="linenos">18</span></a><span class="sd"> ```python</span> </span><span id="find_root-19"><a href="#find_root-19"><span class="linenos">19</span></a><span class="sd"> ```python</span>
</span><span id="find_root-19"><a href="#find_root-19"><span class="linenos">19</span></a><span class="sd"> import autograd.numpy as anp</span> </span><span id="find_root-20"><a href="#find_root-20"><span class="linenos">20</span></a><span class="sd"> import autograd.numpy as anp</span>
</span><span id="find_root-20"><a href="#find_root-20"><span class="linenos">20</span></a><span class="sd"> def root_func(x, d):</span> </span><span id="find_root-21"><a href="#find_root-21"><span class="linenos">21</span></a><span class="sd"> def root_func(x, d):</span>
</span><span id="find_root-21"><a href="#find_root-21"><span class="linenos">21</span></a><span class="sd"> return anp.exp(-x ** 2) - d</span> </span><span id="find_root-22"><a href="#find_root-22"><span class="linenos">22</span></a><span class="sd"> return anp.exp(-x ** 2) - d</span>
</span><span id="find_root-22"><a href="#find_root-22"><span class="linenos">22</span></a><span class="sd"> ```</span> </span><span id="find_root-23"><a href="#find_root-23"><span class="linenos">23</span></a><span class="sd"> ```</span>
</span><span id="find_root-23"><a href="#find_root-23"><span class="linenos">23</span></a><span class="sd"> guess : float</span> </span><span id="find_root-24"><a href="#find_root-24"><span class="linenos">24</span></a><span class="sd"> guess : float</span>
</span><span id="find_root-24"><a href="#find_root-24"><span class="linenos">24</span></a><span class="sd"> Initial guess for the minimization.</span> </span><span id="find_root-25"><a href="#find_root-25"><span class="linenos">25</span></a><span class="sd"> Initial guess for the minimization.</span>
</span><span id="find_root-25"><a href="#find_root-25"><span class="linenos">25</span></a> </span><span id="find_root-26"><a href="#find_root-26"><span class="linenos">26</span></a>
</span><span id="find_root-26"><a href="#find_root-26"><span class="linenos">26</span></a><span class="sd"> Returns</span> </span><span id="find_root-27"><a href="#find_root-27"><span class="linenos">27</span></a><span class="sd"> Returns</span>
</span><span id="find_root-27"><a href="#find_root-27"><span class="linenos">27</span></a><span class="sd"> -------</span> </span><span id="find_root-28"><a href="#find_root-28"><span class="linenos">28</span></a><span class="sd"> -------</span>
</span><span id="find_root-28"><a href="#find_root-28"><span class="linenos">28</span></a><span class="sd"> res : Obs</span> </span><span id="find_root-29"><a href="#find_root-29"><span class="linenos">29</span></a><span class="sd"> res : Obs</span>
</span><span id="find_root-29"><a href="#find_root-29"><span class="linenos">29</span></a><span class="sd"> `Obs` valued root of the function.</span> </span><span id="find_root-30"><a href="#find_root-30"><span class="linenos">30</span></a><span class="sd"> `Obs` valued root of the function.</span>
</span><span id="find_root-30"><a href="#find_root-30"><span class="linenos">30</span></a><span class="sd"> &#39;&#39;&#39;</span> </span><span id="find_root-31"><a href="#find_root-31"><span class="linenos">31</span></a><span class="sd"> &#39;&#39;&#39;</span>
</span><span id="find_root-31"><a href="#find_root-31"><span class="linenos">31</span></a> <span class="n">d_val</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">vectorize</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span><span class="o">.</span><span class="n">value</span><span class="p">)(</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">d</span><span class="p">))</span> </span><span id="find_root-32"><a href="#find_root-32"><span class="linenos">32</span></a> <span class="n">d_val</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">vectorize</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span><span class="o">.</span><span class="n">value</span><span class="p">)(</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">d</span><span class="p">))</span>
</span><span id="find_root-32"><a href="#find_root-32"><span class="linenos">32</span></a> </span><span id="find_root-33"><a href="#find_root-33"><span class="linenos">33</span></a>
</span><span id="find_root-33"><a href="#find_root-33"><span class="linenos">33</span></a> <span class="n">root</span> <span class="o">=</span> <span class="n">scipy</span><span class="o">.</span><span class="n">optimize</span><span class="o">.</span><span class="n">fsolve</span><span class="p">(</span><span class="n">func</span><span class="p">,</span> <span class="n">guess</span><span class="p">,</span> <span class="n">d_val</span><span class="p">)</span> </span><span id="find_root-34"><a href="#find_root-34"><span class="linenos">34</span></a> <span class="n">root</span> <span class="o">=</span> <span class="n">scipy</span><span class="o">.</span><span class="n">optimize</span><span class="o">.</span><span class="n">fsolve</span><span class="p">(</span><span class="n">func</span><span class="p">,</span> <span class="n">guess</span><span class="p">,</span> <span class="n">d_val</span><span class="p">)</span>
</span><span id="find_root-34"><a href="#find_root-34"><span class="linenos">34</span></a> </span><span id="find_root-35"><a href="#find_root-35"><span class="linenos">35</span></a>
</span><span id="find_root-35"><a href="#find_root-35"><span class="linenos">35</span></a> <span class="c1"># Error propagation as detailed in arXiv:1809.01289</span> </span><span id="find_root-36"><a href="#find_root-36"><span class="linenos">36</span></a> <span class="c1"># Error propagation as detailed in arXiv:1809.01289</span>
</span><span id="find_root-36"><a href="#find_root-36"><span class="linenos">36</span></a> <span class="k">try</span><span class="p">:</span> </span><span id="find_root-37"><a href="#find_root-37"><span class="linenos">37</span></a> <span class="k">try</span><span class="p">:</span>
</span><span id="find_root-37"><a href="#find_root-37"><span class="linenos">37</span></a> <span class="n">dx</span> <span class="o">=</span> <span class="n">jacobian</span><span class="p">(</span><span class="n">func</span><span class="p">)(</span><span class="n">root</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">d_val</span><span class="p">)</span> </span><span id="find_root-38"><a href="#find_root-38"><span class="linenos">38</span></a> <span class="n">dx</span> <span class="o">=</span> <span class="n">jacobian</span><span class="p">(</span><span class="n">func</span><span class="p">)(</span><span class="n">root</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">d_val</span><span class="p">)</span>
</span><span id="find_root-38"><a href="#find_root-38"><span class="linenos">38</span></a> <span class="n">da</span> <span class="o">=</span> <span class="n">jacobian</span><span class="p">(</span><span class="k">lambda</span> <span class="n">u</span><span class="p">,</span> <span class="n">v</span><span class="p">:</span> <span class="n">func</span><span class="p">(</span><span class="n">v</span><span class="p">,</span> <span class="n">u</span><span class="p">))(</span><span class="n">d_val</span><span class="p">,</span> <span class="n">root</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> </span><span id="find_root-39"><a href="#find_root-39"><span class="linenos">39</span></a> <span class="n">da</span> <span class="o">=</span> <span class="n">jacobian</span><span class="p">(</span><span class="k">lambda</span> <span class="n">u</span><span class="p">,</span> <span class="n">v</span><span class="p">:</span> <span class="n">func</span><span class="p">(</span><span class="n">v</span><span class="p">,</span> <span class="n">u</span><span class="p">))(</span><span class="n">d_val</span><span class="p">,</span> <span class="n">root</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
</span><span id="find_root-39"><a href="#find_root-39"><span class="linenos">39</span></a> <span class="k">except</span> <span class="p">(</span><span class="ne">TypeError</span><span class="p">,</span> <span class="ne">ValueError</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">linalg</span><span class="o">.</span><span class="n">LinAlgError</span><span class="p">):</span> </span><span id="find_root-40"><a href="#find_root-40"><span class="linenos">40</span></a> <span class="k">except</span> <span class="p">(</span><span class="ne">TypeError</span><span class="p">,</span> <span class="ne">ValueError</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">linalg</span><span class="o">.</span><span class="n">LinAlgError</span><span class="p">):</span>
</span><span id="find_root-40"><a href="#find_root-40"><span class="linenos">40</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">&quot;It is required to use autograd.numpy instead of numpy within root functions, see the documentation for details.&quot;</span><span class="p">)</span> <span class="kn">from</span><span class="w"> </span><span class="kc">None</span> </span><span id="find_root-41"><a href="#find_root-41"><span class="linenos">41</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">&quot;It is required to use autograd.numpy instead of numpy within root functions, see the documentation for details.&quot;</span><span class="p">)</span> <span class="kn">from</span><span class="w"> </span><span class="kc">None</span>
</span><span id="find_root-41"><a href="#find_root-41"><span class="linenos">41</span></a> <span class="n">deriv</span> <span class="o">=</span> <span class="o">-</span> <span class="n">da</span> <span class="o">/</span> <span class="n">dx</span> </span><span id="find_root-42"><a href="#find_root-42"><span class="linenos">42</span></a> <span class="n">deriv</span> <span class="o">=</span> <span class="o">-</span> <span class="n">da</span> <span class="o">/</span> <span class="n">dx</span>
</span><span id="find_root-42"><a href="#find_root-42"><span class="linenos">42</span></a> <span class="n">res</span> <span class="o">=</span> <span class="n">derived_observable</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">:</span> <span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="n">np</span><span class="o">.</span><span class="n">finfo</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">float64</span><span class="p">)</span><span class="o">.</span><span class="n">eps</span><span class="p">)</span> <span class="o">/</span> <span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">d</span><span class="p">)</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">value</span> <span class="o">+</span> <span class="n">np</span><span class="o">.</span><span class="n">finfo</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">float64</span><span class="p">)</span><span class="o">.</span><span class="n">eps</span><span class="p">)</span> <span class="o">*</span> <span class="n">root</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> </span><span id="find_root-43"><a href="#find_root-43"><span class="linenos">43</span></a> <span class="n">res</span> <span class="o">=</span> <span class="n">derived_observable</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">:</span> <span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="n">np</span><span class="o">.</span><span class="n">finfo</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">float64</span><span class="p">)</span><span class="o">.</span><span class="n">eps</span><span class="p">)</span> <span class="o">/</span> <span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">d</span><span class="p">)</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">value</span> <span class="o">+</span> <span class="n">np</span><span class="o">.</span><span class="n">finfo</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">float64</span><span class="p">)</span><span class="o">.</span><span class="n">eps</span><span class="p">)</span> <span class="o">*</span> <span class="n">root</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
</span><span id="find_root-43"><a href="#find_root-43"><span class="linenos">43</span></a> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">d</span><span class="p">)</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">),</span> <span class="n">man_grad</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">deriv</span><span class="p">)</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">))</span> </span><span id="find_root-44"><a href="#find_root-44"><span class="linenos">44</span></a> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">d</span><span class="p">)</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">),</span> <span class="n">man_grad</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">deriv</span><span class="p">)</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">))</span>
</span><span id="find_root-44"><a href="#find_root-44"><span class="linenos">44</span></a> <span class="k">return</span> <span class="n">res</span> </span><span id="find_root-45"><a href="#find_root-45"><span class="linenos">45</span></a> <span class="k">return</span> <span class="n">res</span>
</span></pre></div> </span></pre></div>

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