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@ -52,6 +52,9 @@
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<h2>API Documentation</h2>
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<ul class="memberlist">
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<li>
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<a class="function" href="#errorbar">errorbar</a>
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</li>
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<li>
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<a class="function" href="#dump_object">dump_object</a>
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</li>
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@ -87,141 +90,232 @@
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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="nn">pickle</span>
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</span><span id="L-2"><a href="#L-2"><span class="linenos"> 2</span></a><span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
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</span><span id="L-3"><a href="#L-3"><span class="linenos"> 3</span></a><span class="kn">from</span> <span class="nn">.obs</span> <span class="kn">import</span> <span class="n">Obs</span>
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</span><span id="L-4"><a href="#L-4"><span class="linenos"> 4</span></a>
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</span><span id="L-3"><a href="#L-3"><span class="linenos"> 3</span></a><span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
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</span><span id="L-4"><a href="#L-4"><span class="linenos"> 4</span></a><span class="kn">from</span> <span class="nn">.obs</span> <span class="kn">import</span> <span class="n">Obs</span>
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</span><span id="L-5"><a href="#L-5"><span class="linenos"> 5</span></a>
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</span><span id="L-6"><a href="#L-6"><span class="linenos"> 6</span></a><span class="k">def</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>
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</span><span id="L-7"><a href="#L-7"><span class="linenos"> 7</span></a><span class="w"> </span><span class="sd">"""Dump object into pickle file.</span>
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</span><span id="L-8"><a href="#L-8"><span class="linenos"> 8</span></a>
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</span><span id="L-9"><a href="#L-9"><span class="linenos"> 9</span></a><span class="sd"> Parameters</span>
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</span><span id="L-10"><a href="#L-10"><span class="linenos"> 10</span></a><span class="sd"> ----------</span>
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</span><span id="L-11"><a href="#L-11"><span class="linenos"> 11</span></a><span class="sd"> obj : object</span>
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</span><span id="L-12"><a href="#L-12"><span class="linenos"> 12</span></a><span class="sd"> object to be saved in the pickle file</span>
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</span><span id="L-13"><a href="#L-13"><span class="linenos"> 13</span></a><span class="sd"> name : str</span>
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</span><span id="L-14"><a href="#L-14"><span class="linenos"> 14</span></a><span class="sd"> name of the file</span>
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</span><span id="L-15"><a href="#L-15"><span class="linenos"> 15</span></a><span class="sd"> path : str</span>
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</span><span id="L-16"><a href="#L-16"><span class="linenos"> 16</span></a><span class="sd"> specifies a custom path for the file (default '.')</span>
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</span><span id="L-17"><a href="#L-17"><span class="linenos"> 17</span></a>
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</span><span id="L-18"><a href="#L-18"><span class="linenos"> 18</span></a><span class="sd"> Returns</span>
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</span><span id="L-19"><a href="#L-19"><span class="linenos"> 19</span></a><span class="sd"> -------</span>
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</span><span id="L-20"><a href="#L-20"><span class="linenos"> 20</span></a><span class="sd"> None</span>
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</span><span id="L-21"><a href="#L-21"><span class="linenos"> 21</span></a><span class="sd"> """</span>
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</span><span id="L-22"><a href="#L-22"><span class="linenos"> 22</span></a> <span class="k">if</span> <span class="s1">'path'</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
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</span><span id="L-23"><a href="#L-23"><span class="linenos"> 23</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">'path'</span><span class="p">)</span> <span class="o">+</span> <span class="s1">'/'</span> <span class="o">+</span> <span class="n">name</span> <span class="o">+</span> <span class="s1">'.p'</span>
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</span><span id="L-24"><a href="#L-24"><span class="linenos"> 24</span></a> <span class="k">else</span><span class="p">:</span>
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</span><span id="L-25"><a href="#L-25"><span class="linenos"> 25</span></a> <span class="n">file_name</span> <span class="o">=</span> <span class="n">name</span> <span class="o">+</span> <span class="s1">'.p'</span>
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</span><span id="L-26"><a href="#L-26"><span class="linenos"> 26</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">'wb'</span><span class="p">)</span> <span class="k">as</span> <span class="n">fb</span><span class="p">:</span>
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</span><span id="L-27"><a href="#L-27"><span class="linenos"> 27</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>
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</span><span id="L-28"><a href="#L-28"><span class="linenos"> 28</span></a>
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</span><span id="L-29"><a href="#L-29"><span class="linenos"> 29</span></a>
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</span><span id="L-30"><a href="#L-30"><span class="linenos"> 30</span></a><span class="k">def</span> <span class="nf">load_object</span><span class="p">(</span><span class="n">path</span><span class="p">):</span>
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</span><span id="L-31"><a href="#L-31"><span class="linenos"> 31</span></a><span class="w"> </span><span class="sd">"""Load object from pickle file.</span>
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</span><span id="L-32"><a href="#L-32"><span class="linenos"> 32</span></a>
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</span><span id="L-33"><a href="#L-33"><span class="linenos"> 33</span></a><span class="sd"> Parameters</span>
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</span><span id="L-34"><a href="#L-34"><span class="linenos"> 34</span></a><span class="sd"> ----------</span>
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</span><span id="L-35"><a href="#L-35"><span class="linenos"> 35</span></a><span class="sd"> path : str</span>
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</span><span id="L-36"><a href="#L-36"><span class="linenos"> 36</span></a><span class="sd"> path to the file</span>
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</span><span id="L-6"><a href="#L-6"><span class="linenos"> 6</span></a>
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</span><span id="L-7"><a href="#L-7"><span class="linenos"> 7</span></a><span class="k">def</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>
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</span><span id="L-8"><a href="#L-8"><span class="linenos"> 8</span></a><span class="w"> </span><span class="sd">"""pyerrors wrapper for the errorbars method of matplotlib</span>
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</span><span id="L-9"><a href="#L-9"><span class="linenos"> 9</span></a>
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</span><span id="L-10"><a href="#L-10"><span class="linenos"> 10</span></a><span class="sd"> Parameters</span>
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</span><span id="L-11"><a href="#L-11"><span class="linenos"> 11</span></a><span class="sd"> ----------</span>
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</span><span id="L-12"><a href="#L-12"><span class="linenos"> 12</span></a><span class="sd"> x : list</span>
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</span><span id="L-13"><a href="#L-13"><span class="linenos"> 13</span></a><span class="sd"> A list of x-values which can be Obs.</span>
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</span><span id="L-14"><a href="#L-14"><span class="linenos"> 14</span></a><span class="sd"> y : list</span>
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</span><span id="L-15"><a href="#L-15"><span class="linenos"> 15</span></a><span class="sd"> A list of y-values which can be Obs.</span>
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</span><span id="L-16"><a href="#L-16"><span class="linenos"> 16</span></a><span class="sd"> axes : (matplotlib.pyplot.axes)</span>
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</span><span id="L-17"><a href="#L-17"><span class="linenos"> 17</span></a><span class="sd"> The axes to plot on. default is plt.</span>
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</span><span id="L-18"><a href="#L-18"><span class="linenos"> 18</span></a><span class="sd"> """</span>
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</span><span id="L-19"><a href="#L-19"><span class="linenos"> 19</span></a> <span class="n">val</span> <span class="o">=</span> <span class="p">{}</span>
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</span><span id="L-20"><a href="#L-20"><span class="linenos"> 20</span></a> <span class="n">err</span> <span class="o">=</span> <span class="p">{}</span>
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</span><span id="L-21"><a href="#L-21"><span class="linenos"> 21</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">"x"</span><span class="p">,</span> <span class="s2">"y"</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>
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</span><span id="L-22"><a href="#L-22"><span class="linenos"> 22</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>
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</span><span id="L-23"><a href="#L-23"><span class="linenos"> 23</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">'e_dvalue'</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>
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</span><span id="L-24"><a href="#L-24"><span class="linenos"> 24</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>
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</span><span id="L-25"><a href="#L-25"><span class="linenos"> 25</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>
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</span><span id="L-26"><a href="#L-26"><span class="linenos"> 26</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>
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</span><span id="L-27"><a href="#L-27"><span class="linenos"> 27</span></a> <span class="k">else</span><span class="p">:</span>
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</span><span id="L-28"><a href="#L-28"><span class="linenos"> 28</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>
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</span><span id="L-29"><a href="#L-29"><span class="linenos"> 29</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>
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</span><span id="L-30"><a href="#L-30"><span class="linenos"> 30</span></a>
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</span><span id="L-31"><a href="#L-31"><span class="linenos"> 31</span></a> <span class="k">if</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s2">err"</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
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</span><span id="L-32"><a href="#L-32"><span class="linenos"> 32</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">"</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s2">err"</span><span class="p">)</span>
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</span><span id="L-33"><a href="#L-33"><span class="linenos"> 33</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">"</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s2">err"</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
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</span><span id="L-34"><a href="#L-34"><span class="linenos"> 34</span></a>
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</span><span id="L-35"><a href="#L-35"><span class="linenos"> 35</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">"x"</span><span class="p">],</span> <span class="n">val</span><span class="p">[</span><span class="s2">"y"</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">"x"</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">"y"</span><span class="p">],</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
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</span><span id="L-36"><a href="#L-36"><span class="linenos"> 36</span></a>
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</span><span id="L-37"><a href="#L-37"><span class="linenos"> 37</span></a>
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</span><span id="L-38"><a href="#L-38"><span class="linenos"> 38</span></a><span class="sd"> Returns</span>
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</span><span id="L-39"><a href="#L-39"><span class="linenos"> 39</span></a><span class="sd"> -------</span>
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</span><span id="L-40"><a href="#L-40"><span class="linenos"> 40</span></a><span class="sd"> object : Obs</span>
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</span><span id="L-41"><a href="#L-41"><span class="linenos"> 41</span></a><span class="sd"> Loaded Object</span>
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</span><span id="L-42"><a href="#L-42"><span class="linenos"> 42</span></a><span class="sd"> """</span>
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</span><span id="L-43"><a href="#L-43"><span class="linenos"> 43</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">'rb'</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
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</span><span id="L-44"><a href="#L-44"><span class="linenos"> 44</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>
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</span><span id="L-45"><a href="#L-45"><span class="linenos"> 45</span></a>
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</span><span id="L-46"><a href="#L-46"><span class="linenos"> 46</span></a>
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</span><span id="L-47"><a href="#L-47"><span class="linenos"> 47</span></a><span class="k">def</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>
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</span><span id="L-48"><a href="#L-48"><span class="linenos"> 48</span></a><span class="w"> </span><span class="sd">"""Generate an Obs object with given value, dvalue and name for test purposes</span>
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</span><span id="L-38"><a href="#L-38"><span class="linenos"> 38</span></a><span class="k">def</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>
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</span><span id="L-39"><a href="#L-39"><span class="linenos"> 39</span></a><span class="w"> </span><span class="sd">"""Dump object into pickle file.</span>
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</span><span id="L-40"><a href="#L-40"><span class="linenos"> 40</span></a>
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</span><span id="L-41"><a href="#L-41"><span class="linenos"> 41</span></a><span class="sd"> Parameters</span>
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</span><span id="L-42"><a href="#L-42"><span class="linenos"> 42</span></a><span class="sd"> ----------</span>
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</span><span id="L-43"><a href="#L-43"><span class="linenos"> 43</span></a><span class="sd"> obj : object</span>
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</span><span id="L-44"><a href="#L-44"><span class="linenos"> 44</span></a><span class="sd"> object to be saved in the pickle file</span>
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</span><span id="L-45"><a href="#L-45"><span class="linenos"> 45</span></a><span class="sd"> name : str</span>
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</span><span id="L-46"><a href="#L-46"><span class="linenos"> 46</span></a><span class="sd"> name of the file</span>
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</span><span id="L-47"><a href="#L-47"><span class="linenos"> 47</span></a><span class="sd"> path : str</span>
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</span><span id="L-48"><a href="#L-48"><span class="linenos"> 48</span></a><span class="sd"> specifies a custom path for the file (default '.')</span>
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</span><span id="L-49"><a href="#L-49"><span class="linenos"> 49</span></a>
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</span><span id="L-50"><a href="#L-50"><span class="linenos"> 50</span></a><span class="sd"> Parameters</span>
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</span><span id="L-51"><a href="#L-51"><span class="linenos"> 51</span></a><span class="sd"> ----------</span>
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</span><span id="L-52"><a href="#L-52"><span class="linenos"> 52</span></a><span class="sd"> value : float</span>
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</span><span id="L-53"><a href="#L-53"><span class="linenos"> 53</span></a><span class="sd"> central value of the Obs to be generated.</span>
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</span><span id="L-54"><a href="#L-54"><span class="linenos"> 54</span></a><span class="sd"> dvalue : float</span>
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</span><span id="L-55"><a href="#L-55"><span class="linenos"> 55</span></a><span class="sd"> error of the Obs to be generated.</span>
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</span><span id="L-56"><a href="#L-56"><span class="linenos"> 56</span></a><span class="sd"> name : str</span>
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</span><span id="L-57"><a href="#L-57"><span class="linenos"> 57</span></a><span class="sd"> name of the ensemble for which the Obs is to be generated.</span>
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</span><span id="L-58"><a href="#L-58"><span class="linenos"> 58</span></a><span class="sd"> samples: int</span>
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</span><span id="L-59"><a href="#L-59"><span class="linenos"> 59</span></a><span class="sd"> number of samples for the Obs (default 1000).</span>
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</span><span id="L-50"><a href="#L-50"><span class="linenos"> 50</span></a><span class="sd"> Returns</span>
|
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</span><span id="L-51"><a href="#L-51"><span class="linenos"> 51</span></a><span class="sd"> -------</span>
|
||||
</span><span id="L-52"><a href="#L-52"><span class="linenos"> 52</span></a><span class="sd"> None</span>
|
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</span><span id="L-53"><a href="#L-53"><span class="linenos"> 53</span></a><span class="sd"> """</span>
|
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</span><span id="L-54"><a href="#L-54"><span class="linenos"> 54</span></a> <span class="k">if</span> <span class="s1">'path'</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
|
||||
</span><span id="L-55"><a href="#L-55"><span class="linenos"> 55</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">'path'</span><span class="p">)</span> <span class="o">+</span> <span class="s1">'/'</span> <span class="o">+</span> <span class="n">name</span> <span class="o">+</span> <span class="s1">'.p'</span>
|
||||
</span><span id="L-56"><a href="#L-56"><span class="linenos"> 56</span></a> <span class="k">else</span><span class="p">:</span>
|
||||
</span><span id="L-57"><a href="#L-57"><span class="linenos"> 57</span></a> <span class="n">file_name</span> <span class="o">=</span> <span class="n">name</span> <span class="o">+</span> <span class="s1">'.p'</span>
|
||||
</span><span id="L-58"><a href="#L-58"><span class="linenos"> 58</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">'wb'</span><span class="p">)</span> <span class="k">as</span> <span class="n">fb</span><span class="p">:</span>
|
||||
</span><span id="L-59"><a href="#L-59"><span class="linenos"> 59</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-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="sd"> Returns</span>
|
||||
</span><span id="L-62"><a href="#L-62"><span class="linenos"> 62</span></a><span class="sd"> -------</span>
|
||||
</span><span id="L-63"><a href="#L-63"><span class="linenos"> 63</span></a><span class="sd"> res : Obs</span>
|
||||
</span><span id="L-64"><a href="#L-64"><span class="linenos"> 64</span></a><span class="sd"> Generated Observable</span>
|
||||
</span><span id="L-65"><a href="#L-65"><span class="linenos"> 65</span></a><span class="sd"> """</span>
|
||||
</span><span id="L-66"><a href="#L-66"><span class="linenos"> 66</span></a> <span class="k">if</span> <span class="n">dvalue</span> <span class="o"><=</span> <span class="mf">0.0</span><span class="p">:</span>
|
||||
</span><span id="L-67"><a href="#L-67"><span class="linenos"> 67</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-68"><a href="#L-68"><span class="linenos"> 68</span></a> <span class="k">else</span><span class="p">:</span>
|
||||
</span><span id="L-69"><a href="#L-69"><span class="linenos"> 69</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-70"><a href="#L-70"><span class="linenos"> 70</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-71"><a href="#L-71"><span class="linenos"> 71</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-72"><a href="#L-72"><span class="linenos"> 72</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-73"><a href="#L-73"><span class="linenos"> 73</span></a> <span class="n">deltas</span> <span class="o">+=</span> <span class="n">value</span>
|
||||
</span><span id="L-74"><a href="#L-74"><span class="linenos"> 74</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-75"><a href="#L-75"><span class="linenos"> 75</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-76"><a href="#L-76"><span class="linenos"> 76</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"><</span> <span class="mf">1e-10</span> <span class="o">*</span> <span class="n">dvalue</span><span class="p">:</span>
|
||||
</span><span id="L-77"><a href="#L-77"><span class="linenos"> 77</span></a> <span class="k">break</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="k">def</span> <span class="nf">load_object</span><span class="p">(</span><span class="n">path</span><span class="p">):</span>
|
||||
</span><span id="L-63"><a href="#L-63"><span class="linenos"> 63</span></a><span class="w"> </span><span class="sd">"""Load object from pickle file.</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="sd"> Parameters</span>
|
||||
</span><span id="L-66"><a href="#L-66"><span class="linenos"> 66</span></a><span class="sd"> ----------</span>
|
||||
</span><span id="L-67"><a href="#L-67"><span class="linenos"> 67</span></a><span class="sd"> path : str</span>
|
||||
</span><span id="L-68"><a href="#L-68"><span class="linenos"> 68</span></a><span class="sd"> path to the file</span>
|
||||
</span><span id="L-69"><a href="#L-69"><span class="linenos"> 69</span></a>
|
||||
</span><span id="L-70"><a href="#L-70"><span class="linenos"> 70</span></a><span class="sd"> Returns</span>
|
||||
</span><span id="L-71"><a href="#L-71"><span class="linenos"> 71</span></a><span class="sd"> -------</span>
|
||||
</span><span id="L-72"><a href="#L-72"><span class="linenos"> 72</span></a><span class="sd"> object : Obs</span>
|
||||
</span><span id="L-73"><a href="#L-73"><span class="linenos"> 73</span></a><span class="sd"> Loaded Object</span>
|
||||
</span><span id="L-74"><a href="#L-74"><span class="linenos"> 74</span></a><span class="sd"> """</span>
|
||||
</span><span id="L-75"><a href="#L-75"><span class="linenos"> 75</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">'rb'</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
|
||||
</span><span id="L-76"><a href="#L-76"><span class="linenos"> 76</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-77"><a href="#L-77"><span class="linenos"> 77</span></a>
|
||||
</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="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-80"><a href="#L-80"><span class="linenos"> 80</span></a>
|
||||
</span><span id="L-81"><a href="#L-81"><span class="linenos"> 81</span></a> <span class="k">return</span> <span class="n">res</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-84"><a href="#L-84"><span class="linenos"> 84</span></a><span class="k">def</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-85"><a href="#L-85"><span class="linenos"> 85</span></a><span class="w"> </span><span class="sd">""" Generate observables with given covariance and autocorrelation times.</span>
|
||||
</span><span id="L-86"><a href="#L-86"><span class="linenos"> 86</span></a>
|
||||
</span><span id="L-87"><a href="#L-87"><span class="linenos"> 87</span></a><span class="sd"> Parameters</span>
|
||||
</span><span id="L-88"><a href="#L-88"><span class="linenos"> 88</span></a><span class="sd"> ----------</span>
|
||||
</span><span id="L-89"><a href="#L-89"><span class="linenos"> 89</span></a><span class="sd"> means : list</span>
|
||||
</span><span id="L-90"><a href="#L-90"><span class="linenos"> 90</span></a><span class="sd"> list containing the mean value of each observable.</span>
|
||||
</span><span id="L-91"><a href="#L-91"><span class="linenos"> 91</span></a><span class="sd"> cov : numpy.ndarray</span>
|
||||
</span><span id="L-92"><a href="#L-92"><span class="linenos"> 92</span></a><span class="sd"> covariance matrix for the data to be generated.</span>
|
||||
</span><span id="L-93"><a href="#L-93"><span class="linenos"> 93</span></a><span class="sd"> name : str</span>
|
||||
</span><span id="L-94"><a href="#L-94"><span class="linenos"> 94</span></a><span class="sd"> ensemble name for the data to be geneated.</span>
|
||||
</span><span id="L-95"><a href="#L-95"><span class="linenos"> 95</span></a><span class="sd"> tau : float or list</span>
|
||||
</span><span id="L-96"><a href="#L-96"><span class="linenos"> 96</span></a><span class="sd"> can either be a real number or a list with an entry for</span>
|
||||
</span><span id="L-97"><a href="#L-97"><span class="linenos"> 97</span></a><span class="sd"> every dataset.</span>
|
||||
</span><span id="L-98"><a href="#L-98"><span class="linenos"> 98</span></a><span class="sd"> samples : int</span>
|
||||
</span><span id="L-99"><a href="#L-99"><span class="linenos"> 99</span></a><span class="sd"> number of samples to be generated for each observable.</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="sd"> Returns</span>
|
||||
</span><span id="L-102"><a href="#L-102"><span class="linenos">102</span></a><span class="sd"> -------</span>
|
||||
</span><span id="L-103"><a href="#L-103"><span class="linenos">103</span></a><span class="sd"> corr_obs : list[Obs]</span>
|
||||
</span><span id="L-104"><a href="#L-104"><span class="linenos">104</span></a><span class="sd"> Generated observable list</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><span id="L-107"><a href="#L-107"><span class="linenos">107</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-108"><a href="#L-108"><span class="linenos">108</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-109"><a href="#L-109"><span class="linenos">109</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"><</span> <span class="mf">0.5</span><span class="p">:</span>
|
||||
</span><span id="L-110"><a href="#L-110"><span class="linenos">110</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">'All integrated autocorrelations have to be >= 0.5.'</span><span class="p">)</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="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-113"><a href="#L-113"><span class="linenos">113</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-79"><a href="#L-79"><span class="linenos"> 79</span></a><span class="k">def</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-80"><a href="#L-80"><span class="linenos"> 80</span></a><span class="w"> </span><span class="sd">"""Generate an Obs object with given value, dvalue and name for test purposes</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="sd"> Parameters</span>
|
||||
</span><span id="L-83"><a href="#L-83"><span class="linenos"> 83</span></a><span class="sd"> ----------</span>
|
||||
</span><span id="L-84"><a href="#L-84"><span class="linenos"> 84</span></a><span class="sd"> value : float</span>
|
||||
</span><span id="L-85"><a href="#L-85"><span class="linenos"> 85</span></a><span class="sd"> central value of the Obs to be generated.</span>
|
||||
</span><span id="L-86"><a href="#L-86"><span class="linenos"> 86</span></a><span class="sd"> dvalue : float</span>
|
||||
</span><span id="L-87"><a href="#L-87"><span class="linenos"> 87</span></a><span class="sd"> error of the Obs to be generated.</span>
|
||||
</span><span id="L-88"><a href="#L-88"><span class="linenos"> 88</span></a><span class="sd"> name : str</span>
|
||||
</span><span id="L-89"><a href="#L-89"><span class="linenos"> 89</span></a><span class="sd"> name of the ensemble for which the Obs is to be generated.</span>
|
||||
</span><span id="L-90"><a href="#L-90"><span class="linenos"> 90</span></a><span class="sd"> samples: int</span>
|
||||
</span><span id="L-91"><a href="#L-91"><span class="linenos"> 91</span></a><span class="sd"> number of samples for the Obs (default 1000).</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="sd"> Returns</span>
|
||||
</span><span id="L-94"><a href="#L-94"><span class="linenos"> 94</span></a><span class="sd"> -------</span>
|
||||
</span><span id="L-95"><a href="#L-95"><span class="linenos"> 95</span></a><span class="sd"> res : Obs</span>
|
||||
</span><span id="L-96"><a href="#L-96"><span class="linenos"> 96</span></a><span class="sd"> Generated Observable</span>
|
||||
</span><span id="L-97"><a href="#L-97"><span class="linenos"> 97</span></a><span class="sd"> """</span>
|
||||
</span><span id="L-98"><a href="#L-98"><span class="linenos"> 98</span></a> <span class="k">if</span> <span class="n">dvalue</span> <span class="o"><=</span> <span class="mf">0.0</span><span class="p">:</span>
|
||||
</span><span id="L-99"><a href="#L-99"><span class="linenos"> 99</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-100"><a href="#L-100"><span class="linenos">100</span></a> <span class="k">else</span><span class="p">:</span>
|
||||
</span><span id="L-101"><a href="#L-101"><span class="linenos">101</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-102"><a href="#L-102"><span class="linenos">102</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-103"><a href="#L-103"><span class="linenos">103</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-104"><a href="#L-104"><span class="linenos">104</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-105"><a href="#L-105"><span class="linenos">105</span></a> <span class="n">deltas</span> <span class="o">+=</span> <span class="n">value</span>
|
||||
</span><span id="L-106"><a href="#L-106"><span class="linenos">106</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-107"><a href="#L-107"><span class="linenos">107</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-108"><a href="#L-108"><span class="linenos">108</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"><</span> <span class="mf">1e-10</span> <span class="o">*</span> <span class="n">dvalue</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-110"><a href="#L-110"><span class="linenos">110</span></a>
|
||||
</span><span id="L-111"><a href="#L-111"><span class="linenos">111</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-112"><a href="#L-112"><span class="linenos">112</span></a>
|
||||
</span><span id="L-113"><a href="#L-113"><span class="linenos">113</span></a> <span class="k">return</span> <span class="n">res</span>
|
||||
</span><span id="L-114"><a href="#L-114"><span class="linenos">114</span></a>
|
||||
</span><span id="L-115"><a href="#L-115"><span class="linenos">115</span></a> <span class="c1"># Normalize samples such that sample variance matches input</span>
|
||||
</span><span id="L-116"><a href="#L-116"><span class="linenos">116</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-117"><a href="#L-117"><span class="linenos">117</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-115"><a href="#L-115"><span class="linenos">115</span></a>
|
||||
</span><span id="L-116"><a href="#L-116"><span class="linenos">116</span></a><span class="k">def</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-117"><a href="#L-117"><span class="linenos">117</span></a><span class="w"> </span><span class="sd">""" Generate observables with given covariance and autocorrelation times.</span>
|
||||
</span><span id="L-118"><a href="#L-118"><span class="linenos">118</span></a>
|
||||
</span><span id="L-119"><a href="#L-119"><span class="linenos">119</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-120"><a href="#L-120"><span class="linenos">120</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-121"><a href="#L-121"><span class="linenos">121</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-122"><a href="#L-122"><span class="linenos">122</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-123"><a href="#L-123"><span class="linenos">123</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-124"><a href="#L-124"><span class="linenos">124</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="k">def</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-127"><a href="#L-127"><span class="linenos">127</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-128"><a href="#L-128"><span class="linenos">128</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-129"><a href="#L-129"><span class="linenos">129</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-130"><a href="#L-130"><span class="linenos">130</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">"Wrong data type in list."</span><span class="p">)</span>
|
||||
</span><span id="L-131"><a href="#L-131"><span class="linenos">131</span></a> <span class="k">for</span> <span class="n">attr</span> <span class="ow">in</span> <span class="p">[</span><span class="s2">"reweighted"</span><span class="p">,</span> <span class="s2">"e_content"</span><span class="p">,</span> <span class="s2">"idl"</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="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-133"><a href="#L-133"><span class="linenos">133</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-134"><a href="#L-134"><span class="linenos">134</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="sa">f</span><span class="s2">"All Obs in list have to have the same state '</span><span class="si">{</span><span class="n">attr</span><span class="si">}</span><span class="s2">'."</span><span class="p">)</span>
|
||||
</span><span id="L-119"><a href="#L-119"><span class="linenos">119</span></a><span class="sd"> Parameters</span>
|
||||
</span><span id="L-120"><a href="#L-120"><span class="linenos">120</span></a><span class="sd"> ----------</span>
|
||||
</span><span id="L-121"><a href="#L-121"><span class="linenos">121</span></a><span class="sd"> means : list</span>
|
||||
</span><span id="L-122"><a href="#L-122"><span class="linenos">122</span></a><span class="sd"> list containing the mean value of each observable.</span>
|
||||
</span><span id="L-123"><a href="#L-123"><span class="linenos">123</span></a><span class="sd"> cov : numpy.ndarray</span>
|
||||
</span><span id="L-124"><a href="#L-124"><span class="linenos">124</span></a><span class="sd"> covariance matrix for the data to be generated.</span>
|
||||
</span><span id="L-125"><a href="#L-125"><span class="linenos">125</span></a><span class="sd"> name : str</span>
|
||||
</span><span id="L-126"><a href="#L-126"><span class="linenos">126</span></a><span class="sd"> ensemble name for the data to be geneated.</span>
|
||||
</span><span id="L-127"><a href="#L-127"><span class="linenos">127</span></a><span class="sd"> tau : float or list</span>
|
||||
</span><span id="L-128"><a href="#L-128"><span class="linenos">128</span></a><span class="sd"> can either be a real number or a list with an entry for</span>
|
||||
</span><span id="L-129"><a href="#L-129"><span class="linenos">129</span></a><span class="sd"> every dataset.</span>
|
||||
</span><span id="L-130"><a href="#L-130"><span class="linenos">130</span></a><span class="sd"> samples : int</span>
|
||||
</span><span id="L-131"><a href="#L-131"><span class="linenos">131</span></a><span class="sd"> number of samples to be generated for each observable.</span>
|
||||
</span><span id="L-132"><a href="#L-132"><span class="linenos">132</span></a>
|
||||
</span><span id="L-133"><a href="#L-133"><span class="linenos">133</span></a><span class="sd"> Returns</span>
|
||||
</span><span id="L-134"><a href="#L-134"><span class="linenos">134</span></a><span class="sd"> -------</span>
|
||||
</span><span id="L-135"><a href="#L-135"><span class="linenos">135</span></a><span class="sd"> corr_obs : list[Obs]</span>
|
||||
</span><span id="L-136"><a href="#L-136"><span class="linenos">136</span></a><span class="sd"> Generated observable list</span>
|
||||
</span><span id="L-137"><a href="#L-137"><span class="linenos">137</span></a><span class="sd"> """</span>
|
||||
</span><span id="L-138"><a href="#L-138"><span class="linenos">138</span></a>
|
||||
</span><span id="L-139"><a href="#L-139"><span class="linenos">139</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-140"><a href="#L-140"><span class="linenos">140</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-141"><a href="#L-141"><span class="linenos">141</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"><</span> <span class="mf">0.5</span><span class="p">:</span>
|
||||
</span><span id="L-142"><a href="#L-142"><span class="linenos">142</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">'All integrated autocorrelations have to be >= 0.5.'</span><span class="p">)</span>
|
||||
</span><span id="L-143"><a href="#L-143"><span class="linenos">143</span></a>
|
||||
</span><span id="L-144"><a href="#L-144"><span class="linenos">144</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-145"><a href="#L-145"><span class="linenos">145</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-146"><a href="#L-146"><span class="linenos">146</span></a>
|
||||
</span><span id="L-147"><a href="#L-147"><span class="linenos">147</span></a> <span class="c1"># Normalize samples such that sample variance matches input</span>
|
||||
</span><span id="L-148"><a href="#L-148"><span class="linenos">148</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-149"><a href="#L-149"><span class="linenos">149</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-150"><a href="#L-150"><span class="linenos">150</span></a>
|
||||
</span><span id="L-151"><a href="#L-151"><span class="linenos">151</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-152"><a href="#L-152"><span class="linenos">152</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-153"><a href="#L-153"><span class="linenos">153</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-154"><a href="#L-154"><span class="linenos">154</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-155"><a href="#L-155"><span class="linenos">155</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-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><span id="L-158"><a href="#L-158"><span class="linenos">158</span></a><span class="k">def</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-159"><a href="#L-159"><span class="linenos">159</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-160"><a href="#L-160"><span class="linenos">160</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-161"><a href="#L-161"><span class="linenos">161</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-162"><a href="#L-162"><span class="linenos">162</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">"Wrong data type in list."</span><span class="p">)</span>
|
||||
</span><span id="L-163"><a href="#L-163"><span class="linenos">163</span></a> <span class="k">for</span> <span class="n">attr</span> <span class="ow">in</span> <span class="p">[</span><span class="s2">"reweighted"</span><span class="p">,</span> <span class="s2">"e_content"</span><span class="p">,</span> <span class="s2">"idl"</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="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-165"><a href="#L-165"><span class="linenos">165</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-166"><a href="#L-166"><span class="linenos">166</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="sa">f</span><span class="s2">"All Obs in list have to have the same state '</span><span class="si">{</span><span class="n">attr</span><span class="si">}</span><span class="s2">'."</span><span class="p">)</span>
|
||||
</span></pre></div>
|
||||
|
||||
|
||||
</section>
|
||||
<section id="errorbar">
|
||||
<input id="errorbar-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
|
||||
<div class="attr function">
|
||||
|
||||
<span class="def">def</span>
|
||||
<span class="name">errorbar</span><span class="signature pdoc-code multiline">(<span class="param"> <span class="n">x</span>,</span><span class="param"> <span class="n">y</span>,</span><span class="param"> <span class="n">axes</span><span class="o">=<</span><span class="n">module</span> <span class="s1">'matplotlib.pyplot'</span> <span class="kn">from</span> <span class="s1">'/opt/hostedtoolcache/Python/3.10.9/x64/lib/python3.10/site-packages/matplotlib/pyplot.py'</span><span class="o">></span>,</span><span class="param"> <span class="o">**</span><span class="n">kwargs</span></span><span class="return-annotation">):</span></span>
|
||||
|
||||
<label class="view-source-button" for="errorbar-view-source"><span>View Source</span></label>
|
||||
|
||||
</div>
|
||||
<a class="headerlink" href="#errorbar"></a>
|
||||
<div class="pdoc-code codehilite"><pre><span></span><span id="errorbar-8"><a href="#errorbar-8"><span class="linenos"> 8</span></a><span class="k">def</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-9"><a href="#errorbar-9"><span class="linenos"> 9</span></a><span class="w"> </span><span class="sd">"""pyerrors wrapper for the errorbars method of matplotlib</span>
|
||||
</span><span id="errorbar-10"><a href="#errorbar-10"><span class="linenos">10</span></a>
|
||||
</span><span id="errorbar-11"><a href="#errorbar-11"><span class="linenos">11</span></a><span class="sd"> Parameters</span>
|
||||
</span><span id="errorbar-12"><a href="#errorbar-12"><span class="linenos">12</span></a><span class="sd"> ----------</span>
|
||||
</span><span id="errorbar-13"><a href="#errorbar-13"><span class="linenos">13</span></a><span class="sd"> x : list</span>
|
||||
</span><span id="errorbar-14"><a href="#errorbar-14"><span class="linenos">14</span></a><span class="sd"> A list of x-values which can be Obs.</span>
|
||||
</span><span id="errorbar-15"><a href="#errorbar-15"><span class="linenos">15</span></a><span class="sd"> y : list</span>
|
||||
</span><span id="errorbar-16"><a href="#errorbar-16"><span class="linenos">16</span></a><span class="sd"> A list of y-values which can be Obs.</span>
|
||||
</span><span id="errorbar-17"><a href="#errorbar-17"><span class="linenos">17</span></a><span class="sd"> axes : (matplotlib.pyplot.axes)</span>
|
||||
</span><span id="errorbar-18"><a href="#errorbar-18"><span class="linenos">18</span></a><span class="sd"> The axes to plot on. default is plt.</span>
|
||||
</span><span id="errorbar-19"><a href="#errorbar-19"><span class="linenos">19</span></a><span class="sd"> """</span>
|
||||
</span><span id="errorbar-20"><a href="#errorbar-20"><span class="linenos">20</span></a> <span class="n">val</span> <span class="o">=</span> <span class="p">{}</span>
|
||||
</span><span id="errorbar-21"><a href="#errorbar-21"><span class="linenos">21</span></a> <span class="n">err</span> <span class="o">=</span> <span class="p">{}</span>
|
||||
</span><span id="errorbar-22"><a href="#errorbar-22"><span class="linenos">22</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">"x"</span><span class="p">,</span> <span class="s2">"y"</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-23"><a href="#errorbar-23"><span class="linenos">23</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-24"><a href="#errorbar-24"><span class="linenos">24</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">'e_dvalue'</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-25"><a href="#errorbar-25"><span class="linenos">25</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-26"><a href="#errorbar-26"><span class="linenos">26</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-27"><a href="#errorbar-27"><span class="linenos">27</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-28"><a href="#errorbar-28"><span class="linenos">28</span></a> <span class="k">else</span><span class="p">:</span>
|
||||
</span><span id="errorbar-29"><a href="#errorbar-29"><span class="linenos">29</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-30"><a href="#errorbar-30"><span class="linenos">30</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-31"><a href="#errorbar-31"><span class="linenos">31</span></a>
|
||||
</span><span id="errorbar-32"><a href="#errorbar-32"><span class="linenos">32</span></a> <span class="k">if</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s2">err"</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
|
||||
</span><span id="errorbar-33"><a href="#errorbar-33"><span class="linenos">33</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">"</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s2">err"</span><span class="p">)</span>
|
||||
</span><span id="errorbar-34"><a href="#errorbar-34"><span class="linenos">34</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">"</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s2">err"</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
|
||||
</span><span id="errorbar-35"><a href="#errorbar-35"><span class="linenos">35</span></a>
|
||||
</span><span id="errorbar-36"><a href="#errorbar-36"><span class="linenos">36</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">"x"</span><span class="p">],</span> <span class="n">val</span><span class="p">[</span><span class="s2">"y"</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">"x"</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">"y"</span><span class="p">],</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
|
||||
</span></pre></div>
|
||||
|
||||
|
||||
<div class="docstring"><p>pyerrors wrapper for the errorbars method of matplotlib</p>
|
||||
|
||||
<h6 id="parameters">Parameters</h6>
|
||||
|
||||
<ul>
|
||||
<li><strong>x</strong> (list):
|
||||
A list of x-values which can be Obs.</li>
|
||||
<li><strong>y</strong> (list):
|
||||
A list of y-values which can be Obs.</li>
|
||||
<li><strong>axes</strong> ((matplotlib.pyplot.axes)):
|
||||
The axes to plot on. default is plt.</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
</section>
|
||||
<section id="dump_object">
|
||||
<input id="dump_object-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
|
||||
|
|
@ -234,28 +328,28 @@
|
|||
|
||||
</div>
|
||||
<a class="headerlink" href="#dump_object"></a>
|
||||
<div class="pdoc-code codehilite"><pre><span></span><span id="dump_object-7"><a href="#dump_object-7"><span class="linenos"> 7</span></a><span class="k">def</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-8"><a href="#dump_object-8"><span class="linenos"> 8</span></a><span class="w"> </span><span class="sd">"""Dump object into pickle file.</span>
|
||||
</span><span id="dump_object-9"><a href="#dump_object-9"><span class="linenos"> 9</span></a>
|
||||
</span><span id="dump_object-10"><a href="#dump_object-10"><span class="linenos">10</span></a><span class="sd"> Parameters</span>
|
||||
</span><span id="dump_object-11"><a href="#dump_object-11"><span class="linenos">11</span></a><span class="sd"> ----------</span>
|
||||
</span><span id="dump_object-12"><a href="#dump_object-12"><span class="linenos">12</span></a><span class="sd"> obj : object</span>
|
||||
</span><span id="dump_object-13"><a href="#dump_object-13"><span class="linenos">13</span></a><span class="sd"> object to be saved in the pickle file</span>
|
||||
</span><span id="dump_object-14"><a href="#dump_object-14"><span class="linenos">14</span></a><span class="sd"> name : str</span>
|
||||
</span><span id="dump_object-15"><a href="#dump_object-15"><span class="linenos">15</span></a><span class="sd"> name of the file</span>
|
||||
</span><span id="dump_object-16"><a href="#dump_object-16"><span class="linenos">16</span></a><span class="sd"> path : str</span>
|
||||
</span><span id="dump_object-17"><a href="#dump_object-17"><span class="linenos">17</span></a><span class="sd"> specifies a custom path for the file (default '.')</span>
|
||||
</span><span id="dump_object-18"><a href="#dump_object-18"><span class="linenos">18</span></a>
|
||||
</span><span id="dump_object-19"><a href="#dump_object-19"><span class="linenos">19</span></a><span class="sd"> Returns</span>
|
||||
</span><span id="dump_object-20"><a href="#dump_object-20"><span class="linenos">20</span></a><span class="sd"> -------</span>
|
||||
</span><span id="dump_object-21"><a href="#dump_object-21"><span class="linenos">21</span></a><span class="sd"> None</span>
|
||||
</span><span id="dump_object-22"><a href="#dump_object-22"><span class="linenos">22</span></a><span class="sd"> """</span>
|
||||
</span><span id="dump_object-23"><a href="#dump_object-23"><span class="linenos">23</span></a> <span class="k">if</span> <span class="s1">'path'</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
|
||||
</span><span id="dump_object-24"><a href="#dump_object-24"><span class="linenos">24</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">'path'</span><span class="p">)</span> <span class="o">+</span> <span class="s1">'/'</span> <span class="o">+</span> <span class="n">name</span> <span class="o">+</span> <span class="s1">'.p'</span>
|
||||
</span><span id="dump_object-25"><a href="#dump_object-25"><span class="linenos">25</span></a> <span class="k">else</span><span class="p">:</span>
|
||||
</span><span id="dump_object-26"><a href="#dump_object-26"><span class="linenos">26</span></a> <span class="n">file_name</span> <span class="o">=</span> <span class="n">name</span> <span class="o">+</span> <span class="s1">'.p'</span>
|
||||
</span><span id="dump_object-27"><a href="#dump_object-27"><span class="linenos">27</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">'wb'</span><span class="p">)</span> <span class="k">as</span> <span class="n">fb</span><span class="p">:</span>
|
||||
</span><span id="dump_object-28"><a href="#dump_object-28"><span class="linenos">28</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>
|
||||
<div class="pdoc-code codehilite"><pre><span></span><span id="dump_object-39"><a href="#dump_object-39"><span class="linenos">39</span></a><span class="k">def</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-40"><a href="#dump_object-40"><span class="linenos">40</span></a><span class="w"> </span><span class="sd">"""Dump object into pickle file.</span>
|
||||
</span><span id="dump_object-41"><a href="#dump_object-41"><span class="linenos">41</span></a>
|
||||
</span><span id="dump_object-42"><a href="#dump_object-42"><span class="linenos">42</span></a><span class="sd"> Parameters</span>
|
||||
</span><span id="dump_object-43"><a href="#dump_object-43"><span class="linenos">43</span></a><span class="sd"> ----------</span>
|
||||
</span><span id="dump_object-44"><a href="#dump_object-44"><span class="linenos">44</span></a><span class="sd"> obj : object</span>
|
||||
</span><span id="dump_object-45"><a href="#dump_object-45"><span class="linenos">45</span></a><span class="sd"> object to be saved in the pickle file</span>
|
||||
</span><span id="dump_object-46"><a href="#dump_object-46"><span class="linenos">46</span></a><span class="sd"> name : str</span>
|
||||
</span><span id="dump_object-47"><a href="#dump_object-47"><span class="linenos">47</span></a><span class="sd"> name of the file</span>
|
||||
</span><span id="dump_object-48"><a href="#dump_object-48"><span class="linenos">48</span></a><span class="sd"> path : str</span>
|
||||
</span><span id="dump_object-49"><a href="#dump_object-49"><span class="linenos">49</span></a><span class="sd"> specifies a custom path for the file (default '.')</span>
|
||||
</span><span id="dump_object-50"><a href="#dump_object-50"><span class="linenos">50</span></a>
|
||||
</span><span id="dump_object-51"><a href="#dump_object-51"><span class="linenos">51</span></a><span class="sd"> Returns</span>
|
||||
</span><span id="dump_object-52"><a href="#dump_object-52"><span class="linenos">52</span></a><span class="sd"> -------</span>
|
||||
</span><span id="dump_object-53"><a href="#dump_object-53"><span class="linenos">53</span></a><span class="sd"> None</span>
|
||||
</span><span id="dump_object-54"><a href="#dump_object-54"><span class="linenos">54</span></a><span class="sd"> """</span>
|
||||
</span><span id="dump_object-55"><a href="#dump_object-55"><span class="linenos">55</span></a> <span class="k">if</span> <span class="s1">'path'</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
|
||||
</span><span id="dump_object-56"><a href="#dump_object-56"><span class="linenos">56</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">'path'</span><span class="p">)</span> <span class="o">+</span> <span class="s1">'/'</span> <span class="o">+</span> <span class="n">name</span> <span class="o">+</span> <span class="s1">'.p'</span>
|
||||
</span><span id="dump_object-57"><a href="#dump_object-57"><span class="linenos">57</span></a> <span class="k">else</span><span class="p">:</span>
|
||||
</span><span id="dump_object-58"><a href="#dump_object-58"><span class="linenos">58</span></a> <span class="n">file_name</span> <span class="o">=</span> <span class="n">name</span> <span class="o">+</span> <span class="s1">'.p'</span>
|
||||
</span><span id="dump_object-59"><a href="#dump_object-59"><span class="linenos">59</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">'wb'</span><span class="p">)</span> <span class="k">as</span> <span class="n">fb</span><span class="p">:</span>
|
||||
</span><span id="dump_object-60"><a href="#dump_object-60"><span class="linenos">60</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>
|
||||
|
||||
|
||||
|
|
@ -292,21 +386,21 @@ specifies a custom path for the file (default '.')</li>
|
|||
|
||||
</div>
|
||||
<a class="headerlink" href="#load_object"></a>
|
||||
<div class="pdoc-code codehilite"><pre><span></span><span id="load_object-31"><a href="#load_object-31"><span class="linenos">31</span></a><span class="k">def</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-32"><a href="#load_object-32"><span class="linenos">32</span></a><span class="w"> </span><span class="sd">"""Load object from pickle file.</span>
|
||||
</span><span id="load_object-33"><a href="#load_object-33"><span class="linenos">33</span></a>
|
||||
</span><span id="load_object-34"><a href="#load_object-34"><span class="linenos">34</span></a><span class="sd"> Parameters</span>
|
||||
</span><span id="load_object-35"><a href="#load_object-35"><span class="linenos">35</span></a><span class="sd"> ----------</span>
|
||||
</span><span id="load_object-36"><a href="#load_object-36"><span class="linenos">36</span></a><span class="sd"> path : str</span>
|
||||
</span><span id="load_object-37"><a href="#load_object-37"><span class="linenos">37</span></a><span class="sd"> path to the file</span>
|
||||
</span><span id="load_object-38"><a href="#load_object-38"><span class="linenos">38</span></a>
|
||||
</span><span id="load_object-39"><a href="#load_object-39"><span class="linenos">39</span></a><span class="sd"> Returns</span>
|
||||
</span><span id="load_object-40"><a href="#load_object-40"><span class="linenos">40</span></a><span class="sd"> -------</span>
|
||||
</span><span id="load_object-41"><a href="#load_object-41"><span class="linenos">41</span></a><span class="sd"> object : Obs</span>
|
||||
</span><span id="load_object-42"><a href="#load_object-42"><span class="linenos">42</span></a><span class="sd"> Loaded Object</span>
|
||||
</span><span id="load_object-43"><a href="#load_object-43"><span class="linenos">43</span></a><span class="sd"> """</span>
|
||||
</span><span id="load_object-44"><a href="#load_object-44"><span class="linenos">44</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">'rb'</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
|
||||
</span><span id="load_object-45"><a href="#load_object-45"><span class="linenos">45</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>
|
||||
<div class="pdoc-code codehilite"><pre><span></span><span id="load_object-63"><a href="#load_object-63"><span class="linenos">63</span></a><span class="k">def</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-64"><a href="#load_object-64"><span class="linenos">64</span></a><span class="w"> </span><span class="sd">"""Load object from pickle file.</span>
|
||||
</span><span id="load_object-65"><a href="#load_object-65"><span class="linenos">65</span></a>
|
||||
</span><span id="load_object-66"><a href="#load_object-66"><span class="linenos">66</span></a><span class="sd"> Parameters</span>
|
||||
</span><span id="load_object-67"><a href="#load_object-67"><span class="linenos">67</span></a><span class="sd"> ----------</span>
|
||||
</span><span id="load_object-68"><a href="#load_object-68"><span class="linenos">68</span></a><span class="sd"> path : str</span>
|
||||
</span><span id="load_object-69"><a href="#load_object-69"><span class="linenos">69</span></a><span class="sd"> path to the file</span>
|
||||
</span><span id="load_object-70"><a href="#load_object-70"><span class="linenos">70</span></a>
|
||||
</span><span id="load_object-71"><a href="#load_object-71"><span class="linenos">71</span></a><span class="sd"> Returns</span>
|
||||
</span><span id="load_object-72"><a href="#load_object-72"><span class="linenos">72</span></a><span class="sd"> -------</span>
|
||||
</span><span id="load_object-73"><a href="#load_object-73"><span class="linenos">73</span></a><span class="sd"> object : Obs</span>
|
||||
</span><span id="load_object-74"><a href="#load_object-74"><span class="linenos">74</span></a><span class="sd"> Loaded Object</span>
|
||||
</span><span id="load_object-75"><a href="#load_object-75"><span class="linenos">75</span></a><span class="sd"> """</span>
|
||||
</span><span id="load_object-76"><a href="#load_object-76"><span class="linenos">76</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">'rb'</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
|
||||
</span><span id="load_object-77"><a href="#load_object-77"><span class="linenos">77</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>
|
||||
|
||||
|
||||
|
|
@ -340,41 +434,41 @@ Loaded Object</li>
|
|||
|
||||
</div>
|
||||
<a class="headerlink" href="#pseudo_Obs"></a>
|
||||
<div class="pdoc-code codehilite"><pre><span></span><span id="pseudo_Obs-48"><a href="#pseudo_Obs-48"><span class="linenos">48</span></a><span class="k">def</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-49"><a href="#pseudo_Obs-49"><span class="linenos">49</span></a><span class="w"> </span><span class="sd">"""Generate an Obs object with given value, dvalue and name for test purposes</span>
|
||||
</span><span id="pseudo_Obs-50"><a href="#pseudo_Obs-50"><span class="linenos">50</span></a>
|
||||
</span><span id="pseudo_Obs-51"><a href="#pseudo_Obs-51"><span class="linenos">51</span></a><span class="sd"> Parameters</span>
|
||||
</span><span id="pseudo_Obs-52"><a href="#pseudo_Obs-52"><span class="linenos">52</span></a><span class="sd"> ----------</span>
|
||||
</span><span id="pseudo_Obs-53"><a href="#pseudo_Obs-53"><span class="linenos">53</span></a><span class="sd"> value : float</span>
|
||||
</span><span id="pseudo_Obs-54"><a href="#pseudo_Obs-54"><span class="linenos">54</span></a><span class="sd"> central value of the Obs to be generated.</span>
|
||||
</span><span id="pseudo_Obs-55"><a href="#pseudo_Obs-55"><span class="linenos">55</span></a><span class="sd"> dvalue : float</span>
|
||||
</span><span id="pseudo_Obs-56"><a href="#pseudo_Obs-56"><span class="linenos">56</span></a><span class="sd"> error of the Obs to be generated.</span>
|
||||
</span><span id="pseudo_Obs-57"><a href="#pseudo_Obs-57"><span class="linenos">57</span></a><span class="sd"> name : str</span>
|
||||
</span><span id="pseudo_Obs-58"><a href="#pseudo_Obs-58"><span class="linenos">58</span></a><span class="sd"> name of the ensemble for which the Obs is to be generated.</span>
|
||||
</span><span id="pseudo_Obs-59"><a href="#pseudo_Obs-59"><span class="linenos">59</span></a><span class="sd"> samples: int</span>
|
||||
</span><span id="pseudo_Obs-60"><a href="#pseudo_Obs-60"><span class="linenos">60</span></a><span class="sd"> number of samples for the Obs (default 1000).</span>
|
||||
</span><span id="pseudo_Obs-61"><a href="#pseudo_Obs-61"><span class="linenos">61</span></a>
|
||||
</span><span id="pseudo_Obs-62"><a href="#pseudo_Obs-62"><span class="linenos">62</span></a><span class="sd"> Returns</span>
|
||||
</span><span id="pseudo_Obs-63"><a href="#pseudo_Obs-63"><span class="linenos">63</span></a><span class="sd"> -------</span>
|
||||
</span><span id="pseudo_Obs-64"><a href="#pseudo_Obs-64"><span class="linenos">64</span></a><span class="sd"> res : Obs</span>
|
||||
</span><span id="pseudo_Obs-65"><a href="#pseudo_Obs-65"><span class="linenos">65</span></a><span class="sd"> Generated Observable</span>
|
||||
</span><span id="pseudo_Obs-66"><a href="#pseudo_Obs-66"><span class="linenos">66</span></a><span class="sd"> """</span>
|
||||
</span><span id="pseudo_Obs-67"><a href="#pseudo_Obs-67"><span class="linenos">67</span></a> <span class="k">if</span> <span class="n">dvalue</span> <span class="o"><=</span> <span class="mf">0.0</span><span class="p">:</span>
|
||||
</span><span id="pseudo_Obs-68"><a href="#pseudo_Obs-68"><span class="linenos">68</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-69"><a href="#pseudo_Obs-69"><span class="linenos">69</span></a> <span class="k">else</span><span class="p">:</span>
|
||||
</span><span id="pseudo_Obs-70"><a href="#pseudo_Obs-70"><span class="linenos">70</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-71"><a href="#pseudo_Obs-71"><span class="linenos">71</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-72"><a href="#pseudo_Obs-72"><span class="linenos">72</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-73"><a href="#pseudo_Obs-73"><span class="linenos">73</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-74"><a href="#pseudo_Obs-74"><span class="linenos">74</span></a> <span class="n">deltas</span> <span class="o">+=</span> <span class="n">value</span>
|
||||
</span><span id="pseudo_Obs-75"><a href="#pseudo_Obs-75"><span class="linenos">75</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-76"><a href="#pseudo_Obs-76"><span class="linenos">76</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-77"><a href="#pseudo_Obs-77"><span class="linenos">77</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"><</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-78"><a href="#pseudo_Obs-78"><span class="linenos">78</span></a> <span class="k">break</span>
|
||||
</span><span id="pseudo_Obs-79"><a href="#pseudo_Obs-79"><span class="linenos">79</span></a>
|
||||
</span><span id="pseudo_Obs-80"><a href="#pseudo_Obs-80"><span class="linenos">80</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-81"><a href="#pseudo_Obs-81"><span class="linenos">81</span></a>
|
||||
</span><span id="pseudo_Obs-82"><a href="#pseudo_Obs-82"><span class="linenos">82</span></a> <span class="k">return</span> <span class="n">res</span>
|
||||
<div class="pdoc-code codehilite"><pre><span></span><span id="pseudo_Obs-80"><a href="#pseudo_Obs-80"><span class="linenos"> 80</span></a><span class="k">def</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-81"><a href="#pseudo_Obs-81"><span class="linenos"> 81</span></a><span class="w"> </span><span class="sd">"""Generate an Obs object with given value, dvalue and name for test purposes</span>
|
||||
</span><span id="pseudo_Obs-82"><a href="#pseudo_Obs-82"><span class="linenos"> 82</span></a>
|
||||
</span><span id="pseudo_Obs-83"><a href="#pseudo_Obs-83"><span class="linenos"> 83</span></a><span class="sd"> Parameters</span>
|
||||
</span><span id="pseudo_Obs-84"><a href="#pseudo_Obs-84"><span class="linenos"> 84</span></a><span class="sd"> ----------</span>
|
||||
</span><span id="pseudo_Obs-85"><a href="#pseudo_Obs-85"><span class="linenos"> 85</span></a><span class="sd"> value : float</span>
|
||||
</span><span id="pseudo_Obs-86"><a href="#pseudo_Obs-86"><span class="linenos"> 86</span></a><span class="sd"> central value of the Obs to be generated.</span>
|
||||
</span><span id="pseudo_Obs-87"><a href="#pseudo_Obs-87"><span class="linenos"> 87</span></a><span class="sd"> dvalue : float</span>
|
||||
</span><span id="pseudo_Obs-88"><a href="#pseudo_Obs-88"><span class="linenos"> 88</span></a><span class="sd"> error of the Obs to be generated.</span>
|
||||
</span><span id="pseudo_Obs-89"><a href="#pseudo_Obs-89"><span class="linenos"> 89</span></a><span class="sd"> name : str</span>
|
||||
</span><span id="pseudo_Obs-90"><a href="#pseudo_Obs-90"><span class="linenos"> 90</span></a><span class="sd"> name of the ensemble for which the Obs is to be generated.</span>
|
||||
</span><span id="pseudo_Obs-91"><a href="#pseudo_Obs-91"><span class="linenos"> 91</span></a><span class="sd"> samples: int</span>
|
||||
</span><span id="pseudo_Obs-92"><a href="#pseudo_Obs-92"><span class="linenos"> 92</span></a><span class="sd"> number of samples for the Obs (default 1000).</span>
|
||||
</span><span id="pseudo_Obs-93"><a href="#pseudo_Obs-93"><span class="linenos"> 93</span></a>
|
||||
</span><span id="pseudo_Obs-94"><a href="#pseudo_Obs-94"><span class="linenos"> 94</span></a><span class="sd"> Returns</span>
|
||||
</span><span id="pseudo_Obs-95"><a href="#pseudo_Obs-95"><span class="linenos"> 95</span></a><span class="sd"> -------</span>
|
||||
</span><span id="pseudo_Obs-96"><a href="#pseudo_Obs-96"><span class="linenos"> 96</span></a><span class="sd"> res : Obs</span>
|
||||
</span><span id="pseudo_Obs-97"><a href="#pseudo_Obs-97"><span class="linenos"> 97</span></a><span class="sd"> Generated Observable</span>
|
||||
</span><span id="pseudo_Obs-98"><a href="#pseudo_Obs-98"><span class="linenos"> 98</span></a><span class="sd"> """</span>
|
||||
</span><span id="pseudo_Obs-99"><a href="#pseudo_Obs-99"><span class="linenos"> 99</span></a> <span class="k">if</span> <span class="n">dvalue</span> <span class="o"><=</span> <span class="mf">0.0</span><span class="p">:</span>
|
||||
</span><span id="pseudo_Obs-100"><a href="#pseudo_Obs-100"><span class="linenos">100</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-101"><a href="#pseudo_Obs-101"><span class="linenos">101</span></a> <span class="k">else</span><span class="p">:</span>
|
||||
</span><span id="pseudo_Obs-102"><a href="#pseudo_Obs-102"><span class="linenos">102</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-103"><a href="#pseudo_Obs-103"><span class="linenos">103</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-104"><a href="#pseudo_Obs-104"><span class="linenos">104</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-105"><a href="#pseudo_Obs-105"><span class="linenos">105</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-106"><a href="#pseudo_Obs-106"><span class="linenos">106</span></a> <span class="n">deltas</span> <span class="o">+=</span> <span class="n">value</span>
|
||||
</span><span id="pseudo_Obs-107"><a href="#pseudo_Obs-107"><span class="linenos">107</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-108"><a href="#pseudo_Obs-108"><span class="linenos">108</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-109"><a href="#pseudo_Obs-109"><span class="linenos">109</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"><</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-110"><a href="#pseudo_Obs-110"><span class="linenos">110</span></a> <span class="k">break</span>
|
||||
</span><span id="pseudo_Obs-111"><a href="#pseudo_Obs-111"><span class="linenos">111</span></a>
|
||||
</span><span id="pseudo_Obs-112"><a href="#pseudo_Obs-112"><span class="linenos">112</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-113"><a href="#pseudo_Obs-113"><span class="linenos">113</span></a>
|
||||
</span><span id="pseudo_Obs-114"><a href="#pseudo_Obs-114"><span class="linenos">114</span></a> <span class="k">return</span> <span class="n">res</span>
|
||||
</span></pre></div>
|
||||
|
||||
|
||||
|
|
@ -414,46 +508,46 @@ Generated Observable</li>
|
|||
|
||||
</div>
|
||||
<a class="headerlink" href="#gen_correlated_data"></a>
|
||||
<div class="pdoc-code codehilite"><pre><span></span><span id="gen_correlated_data-85"><a href="#gen_correlated_data-85"><span class="linenos"> 85</span></a><span class="k">def</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-86"><a href="#gen_correlated_data-86"><span class="linenos"> 86</span></a><span class="w"> </span><span class="sd">""" Generate observables with given covariance and autocorrelation times.</span>
|
||||
</span><span id="gen_correlated_data-87"><a href="#gen_correlated_data-87"><span class="linenos"> 87</span></a>
|
||||
</span><span id="gen_correlated_data-88"><a href="#gen_correlated_data-88"><span class="linenos"> 88</span></a><span class="sd"> Parameters</span>
|
||||
</span><span id="gen_correlated_data-89"><a href="#gen_correlated_data-89"><span class="linenos"> 89</span></a><span class="sd"> ----------</span>
|
||||
</span><span id="gen_correlated_data-90"><a href="#gen_correlated_data-90"><span class="linenos"> 90</span></a><span class="sd"> means : list</span>
|
||||
</span><span id="gen_correlated_data-91"><a href="#gen_correlated_data-91"><span class="linenos"> 91</span></a><span class="sd"> list containing the mean value of each observable.</span>
|
||||
</span><span id="gen_correlated_data-92"><a href="#gen_correlated_data-92"><span class="linenos"> 92</span></a><span class="sd"> cov : numpy.ndarray</span>
|
||||
</span><span id="gen_correlated_data-93"><a href="#gen_correlated_data-93"><span class="linenos"> 93</span></a><span class="sd"> covariance matrix for the data to be generated.</span>
|
||||
</span><span id="gen_correlated_data-94"><a href="#gen_correlated_data-94"><span class="linenos"> 94</span></a><span class="sd"> name : str</span>
|
||||
</span><span id="gen_correlated_data-95"><a href="#gen_correlated_data-95"><span class="linenos"> 95</span></a><span class="sd"> ensemble name for the data to be geneated.</span>
|
||||
</span><span id="gen_correlated_data-96"><a href="#gen_correlated_data-96"><span class="linenos"> 96</span></a><span class="sd"> tau : float or list</span>
|
||||
</span><span id="gen_correlated_data-97"><a href="#gen_correlated_data-97"><span class="linenos"> 97</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-98"><a href="#gen_correlated_data-98"><span class="linenos"> 98</span></a><span class="sd"> every dataset.</span>
|
||||
</span><span id="gen_correlated_data-99"><a href="#gen_correlated_data-99"><span class="linenos"> 99</span></a><span class="sd"> samples : int</span>
|
||||
</span><span id="gen_correlated_data-100"><a href="#gen_correlated_data-100"><span class="linenos">100</span></a><span class="sd"> number of samples to be generated for each observable.</span>
|
||||
</span><span id="gen_correlated_data-101"><a href="#gen_correlated_data-101"><span class="linenos">101</span></a>
|
||||
</span><span id="gen_correlated_data-102"><a href="#gen_correlated_data-102"><span class="linenos">102</span></a><span class="sd"> Returns</span>
|
||||
</span><span id="gen_correlated_data-103"><a href="#gen_correlated_data-103"><span class="linenos">103</span></a><span class="sd"> -------</span>
|
||||
</span><span id="gen_correlated_data-104"><a href="#gen_correlated_data-104"><span class="linenos">104</span></a><span class="sd"> corr_obs : list[Obs]</span>
|
||||
</span><span id="gen_correlated_data-105"><a href="#gen_correlated_data-105"><span class="linenos">105</span></a><span class="sd"> Generated observable list</span>
|
||||
</span><span id="gen_correlated_data-106"><a href="#gen_correlated_data-106"><span class="linenos">106</span></a><span class="sd"> """</span>
|
||||
</span><span id="gen_correlated_data-107"><a href="#gen_correlated_data-107"><span class="linenos">107</span></a>
|
||||
</span><span id="gen_correlated_data-108"><a href="#gen_correlated_data-108"><span class="linenos">108</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-109"><a href="#gen_correlated_data-109"><span class="linenos">109</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-110"><a href="#gen_correlated_data-110"><span class="linenos">110</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"><</span> <span class="mf">0.5</span><span class="p">:</span>
|
||||
</span><span id="gen_correlated_data-111"><a href="#gen_correlated_data-111"><span class="linenos">111</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">'All integrated autocorrelations have to be >= 0.5.'</span><span class="p">)</span>
|
||||
</span><span id="gen_correlated_data-112"><a href="#gen_correlated_data-112"><span class="linenos">112</span></a>
|
||||
</span><span id="gen_correlated_data-113"><a href="#gen_correlated_data-113"><span class="linenos">113</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-114"><a href="#gen_correlated_data-114"><span class="linenos">114</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-115"><a href="#gen_correlated_data-115"><span class="linenos">115</span></a>
|
||||
</span><span id="gen_correlated_data-116"><a href="#gen_correlated_data-116"><span class="linenos">116</span></a> <span class="c1"># Normalize samples such that sample variance matches input</span>
|
||||
</span><span id="gen_correlated_data-117"><a href="#gen_correlated_data-117"><span class="linenos">117</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-118"><a href="#gen_correlated_data-118"><span class="linenos">118</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>
|
||||
<div class="pdoc-code codehilite"><pre><span></span><span id="gen_correlated_data-117"><a href="#gen_correlated_data-117"><span class="linenos">117</span></a><span class="k">def</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-118"><a href="#gen_correlated_data-118"><span class="linenos">118</span></a><span class="w"> </span><span class="sd">""" Generate observables with given covariance and autocorrelation times.</span>
|
||||
</span><span id="gen_correlated_data-119"><a href="#gen_correlated_data-119"><span class="linenos">119</span></a>
|
||||
</span><span id="gen_correlated_data-120"><a href="#gen_correlated_data-120"><span class="linenos">120</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-121"><a href="#gen_correlated_data-121"><span class="linenos">121</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-122"><a href="#gen_correlated_data-122"><span class="linenos">122</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-123"><a href="#gen_correlated_data-123"><span class="linenos">123</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-124"><a href="#gen_correlated_data-124"><span class="linenos">124</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-120"><a href="#gen_correlated_data-120"><span class="linenos">120</span></a><span class="sd"> Parameters</span>
|
||||
</span><span id="gen_correlated_data-121"><a href="#gen_correlated_data-121"><span class="linenos">121</span></a><span class="sd"> ----------</span>
|
||||
</span><span id="gen_correlated_data-122"><a href="#gen_correlated_data-122"><span class="linenos">122</span></a><span class="sd"> means : list</span>
|
||||
</span><span id="gen_correlated_data-123"><a href="#gen_correlated_data-123"><span class="linenos">123</span></a><span class="sd"> list containing the mean value of each observable.</span>
|
||||
</span><span id="gen_correlated_data-124"><a href="#gen_correlated_data-124"><span class="linenos">124</span></a><span class="sd"> cov : numpy.ndarray</span>
|
||||
</span><span id="gen_correlated_data-125"><a href="#gen_correlated_data-125"><span class="linenos">125</span></a><span class="sd"> covariance matrix for the data to be generated.</span>
|
||||
</span><span id="gen_correlated_data-126"><a href="#gen_correlated_data-126"><span class="linenos">126</span></a><span class="sd"> name : str</span>
|
||||
</span><span id="gen_correlated_data-127"><a href="#gen_correlated_data-127"><span class="linenos">127</span></a><span class="sd"> ensemble name for the data to be geneated.</span>
|
||||
</span><span id="gen_correlated_data-128"><a href="#gen_correlated_data-128"><span class="linenos">128</span></a><span class="sd"> tau : float or list</span>
|
||||
</span><span id="gen_correlated_data-129"><a href="#gen_correlated_data-129"><span class="linenos">129</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-130"><a href="#gen_correlated_data-130"><span class="linenos">130</span></a><span class="sd"> every dataset.</span>
|
||||
</span><span id="gen_correlated_data-131"><a href="#gen_correlated_data-131"><span class="linenos">131</span></a><span class="sd"> samples : int</span>
|
||||
</span><span id="gen_correlated_data-132"><a href="#gen_correlated_data-132"><span class="linenos">132</span></a><span class="sd"> number of samples to be generated for each observable.</span>
|
||||
</span><span id="gen_correlated_data-133"><a href="#gen_correlated_data-133"><span class="linenos">133</span></a>
|
||||
</span><span id="gen_correlated_data-134"><a href="#gen_correlated_data-134"><span class="linenos">134</span></a><span class="sd"> Returns</span>
|
||||
</span><span id="gen_correlated_data-135"><a href="#gen_correlated_data-135"><span class="linenos">135</span></a><span class="sd"> -------</span>
|
||||
</span><span id="gen_correlated_data-136"><a href="#gen_correlated_data-136"><span class="linenos">136</span></a><span class="sd"> corr_obs : list[Obs]</span>
|
||||
</span><span id="gen_correlated_data-137"><a href="#gen_correlated_data-137"><span class="linenos">137</span></a><span class="sd"> Generated observable list</span>
|
||||
</span><span id="gen_correlated_data-138"><a href="#gen_correlated_data-138"><span class="linenos">138</span></a><span class="sd"> """</span>
|
||||
</span><span id="gen_correlated_data-139"><a href="#gen_correlated_data-139"><span class="linenos">139</span></a>
|
||||
</span><span id="gen_correlated_data-140"><a href="#gen_correlated_data-140"><span class="linenos">140</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-141"><a href="#gen_correlated_data-141"><span class="linenos">141</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-142"><a href="#gen_correlated_data-142"><span class="linenos">142</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"><</span> <span class="mf">0.5</span><span class="p">:</span>
|
||||
</span><span id="gen_correlated_data-143"><a href="#gen_correlated_data-143"><span class="linenos">143</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">'All integrated autocorrelations have to be >= 0.5.'</span><span class="p">)</span>
|
||||
</span><span id="gen_correlated_data-144"><a href="#gen_correlated_data-144"><span class="linenos">144</span></a>
|
||||
</span><span id="gen_correlated_data-145"><a href="#gen_correlated_data-145"><span class="linenos">145</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-146"><a href="#gen_correlated_data-146"><span class="linenos">146</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-147"><a href="#gen_correlated_data-147"><span class="linenos">147</span></a>
|
||||
</span><span id="gen_correlated_data-148"><a href="#gen_correlated_data-148"><span class="linenos">148</span></a> <span class="c1"># Normalize samples such that sample variance matches input</span>
|
||||
</span><span id="gen_correlated_data-149"><a href="#gen_correlated_data-149"><span class="linenos">149</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-150"><a href="#gen_correlated_data-150"><span class="linenos">150</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-151"><a href="#gen_correlated_data-151"><span class="linenos">151</span></a>
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</span><span id="gen_correlated_data-152"><a href="#gen_correlated_data-152"><span class="linenos">152</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>
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||||
</span><span id="gen_correlated_data-153"><a href="#gen_correlated_data-153"><span class="linenos">153</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-154"><a href="#gen_correlated_data-154"><span class="linenos">154</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-155"><a href="#gen_correlated_data-155"><span class="linenos">155</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-156"><a href="#gen_correlated_data-156"><span class="linenos">156</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>
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