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pyerrors/docs/pyerrors/input/bdio.html
fjosw 745f9a9bfb Documentation updated
2024-01-21 11:42:22 +00:00

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<h2>API Documentation</h2>
<ul class="memberlist">
<li>
<a class="function" href="#read_ADerrors">read_ADerrors</a>
</li>
<li>
<a class="function" href="#write_ADerrors">write_ADerrors</a>
</li>
<li>
<a class="function" href="#read_mesons">read_mesons</a>
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<h1 class="modulename">
<a href="./../../pyerrors.html">pyerrors</a><wbr>.<a href="./../input.html">input</a><wbr>.bdio </h1>
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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">ctypes</span>
</span><span id="L-2"><a href="#L-2"><span class="linenos"> 2</span></a><span class="kn">import</span> <span class="nn">hashlib</span>
</span><span id="L-3"><a href="#L-3"><span class="linenos"> 3</span></a><span class="kn">import</span> <span class="nn">autograd.numpy</span> <span class="k">as</span> <span class="nn">np</span> <span class="c1"># Thinly-wrapped numpy</span>
</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>
</span><span id="L-5"><a href="#L-5"><span class="linenos"> 5</span></a>
</span><span id="L-6"><a href="#L-6"><span class="linenos"> 6</span></a>
</span><span id="L-7"><a href="#L-7"><span class="linenos"> 7</span></a><span class="k">def</span> <span class="nf">read_ADerrors</span><span class="p">(</span><span class="n">file_path</span><span class="p">,</span> <span class="n">bdio_path</span><span class="o">=</span><span class="s1">&#39;./libbdio.so&#39;</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
</span><span id="L-8"><a href="#L-8"><span class="linenos"> 8</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot; Extract generic MCMC data from a bdio file</span>
</span><span id="L-9"><a href="#L-9"><span class="linenos"> 9</span></a>
</span><span id="L-10"><a href="#L-10"><span class="linenos"> 10</span></a><span class="sd"> read_ADerrors requires bdio to be compiled into a shared library. This can be achieved by</span>
</span><span id="L-11"><a href="#L-11"><span class="linenos"> 11</span></a><span class="sd"> adding the flag -fPIC to CC and changing the all target to</span>
</span><span id="L-12"><a href="#L-12"><span class="linenos"> 12</span></a>
</span><span id="L-13"><a href="#L-13"><span class="linenos"> 13</span></a><span class="sd"> all: bdio.o $(LIBDIR)</span>
</span><span id="L-14"><a href="#L-14"><span class="linenos"> 14</span></a><span class="sd"> gcc -shared -Wl,-soname,libbdio.so -o $(BUILDDIR)/libbdio.so $(BUILDDIR)/bdio.o</span>
</span><span id="L-15"><a href="#L-15"><span class="linenos"> 15</span></a><span class="sd"> cp $(BUILDDIR)/libbdio.so $(LIBDIR)/</span>
</span><span id="L-16"><a href="#L-16"><span class="linenos"> 16</span></a>
</span><span id="L-17"><a href="#L-17"><span class="linenos"> 17</span></a><span class="sd"> Parameters</span>
</span><span id="L-18"><a href="#L-18"><span class="linenos"> 18</span></a><span class="sd"> ----------</span>
</span><span id="L-19"><a href="#L-19"><span class="linenos"> 19</span></a><span class="sd"> file_path -- path to the bdio file</span>
</span><span id="L-20"><a href="#L-20"><span class="linenos"> 20</span></a><span class="sd"> bdio_path -- path to the shared bdio library libbdio.so (default ./libbdio.so)</span>
</span><span id="L-21"><a href="#L-21"><span class="linenos"> 21</span></a>
</span><span id="L-22"><a href="#L-22"><span class="linenos"> 22</span></a><span class="sd"> Returns</span>
</span><span id="L-23"><a href="#L-23"><span class="linenos"> 23</span></a><span class="sd"> -------</span>
</span><span id="L-24"><a href="#L-24"><span class="linenos"> 24</span></a><span class="sd"> data : List[Obs]</span>
</span><span id="L-25"><a href="#L-25"><span class="linenos"> 25</span></a><span class="sd"> Extracted data</span>
</span><span id="L-26"><a href="#L-26"><span class="linenos"> 26</span></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="L-27"><a href="#L-27"><span class="linenos"> 27</span></a> <span class="n">bdio</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">cdll</span><span class="o">.</span><span class="n">LoadLibrary</span><span class="p">(</span><span class="n">bdio_path</span><span class="p">)</span>
</span><span id="L-28"><a href="#L-28"><span class="linenos"> 28</span></a>
</span><span id="L-29"><a href="#L-29"><span class="linenos"> 29</span></a> <span class="n">bdio_open</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_open</span>
</span><span id="L-30"><a href="#L-30"><span class="linenos"> 30</span></a> <span class="n">bdio_open</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span>
</span><span id="L-31"><a href="#L-31"><span class="linenos"> 31</span></a>
</span><span id="L-32"><a href="#L-32"><span class="linenos"> 32</span></a> <span class="n">bdio_close</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_close</span>
</span><span id="L-33"><a href="#L-33"><span class="linenos"> 33</span></a> <span class="n">bdio_close</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_int</span>
</span><span id="L-34"><a href="#L-34"><span class="linenos"> 34</span></a> <span class="n">bdio_close</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="L-35"><a href="#L-35"><span class="linenos"> 35</span></a>
</span><span id="L-36"><a href="#L-36"><span class="linenos"> 36</span></a> <span class="n">bdio_seek_record</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_seek_record</span>
</span><span id="L-37"><a href="#L-37"><span class="linenos"> 37</span></a> <span class="n">bdio_seek_record</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_int</span>
</span><span id="L-38"><a href="#L-38"><span class="linenos"> 38</span></a> <span class="n">bdio_seek_record</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="L-39"><a href="#L-39"><span class="linenos"> 39</span></a>
</span><span id="L-40"><a href="#L-40"><span class="linenos"> 40</span></a> <span class="n">bdio_get_rlen</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_get_rlen</span>
</span><span id="L-41"><a href="#L-41"><span class="linenos"> 41</span></a> <span class="n">bdio_get_rlen</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_int</span>
</span><span id="L-42"><a href="#L-42"><span class="linenos"> 42</span></a> <span class="n">bdio_get_rlen</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="L-43"><a href="#L-43"><span class="linenos"> 43</span></a>
</span><span id="L-44"><a href="#L-44"><span class="linenos"> 44</span></a> <span class="n">bdio_get_ruinfo</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_get_ruinfo</span>
</span><span id="L-45"><a href="#L-45"><span class="linenos"> 45</span></a> <span class="n">bdio_get_ruinfo</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_int</span>
</span><span id="L-46"><a href="#L-46"><span class="linenos"> 46</span></a> <span class="n">bdio_get_ruinfo</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="L-47"><a href="#L-47"><span class="linenos"> 47</span></a>
</span><span id="L-48"><a href="#L-48"><span class="linenos"> 48</span></a> <span class="n">bdio_read</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_read</span>
</span><span id="L-49"><a href="#L-49"><span class="linenos"> 49</span></a> <span class="n">bdio_read</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span>
</span><span id="L-50"><a href="#L-50"><span class="linenos"> 50</span></a> <span class="n">bdio_read</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_char_p</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="L-51"><a href="#L-51"><span class="linenos"> 51</span></a>
</span><span id="L-52"><a href="#L-52"><span class="linenos"> 52</span></a> <span class="n">bdio_read_f64</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_read_f64</span>
</span><span id="L-53"><a href="#L-53"><span class="linenos"> 53</span></a> <span class="n">bdio_read_f64</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span>
</span><span id="L-54"><a href="#L-54"><span class="linenos"> 54</span></a> <span class="n">bdio_read_f64</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="L-55"><a href="#L-55"><span class="linenos"> 55</span></a>
</span><span id="L-56"><a href="#L-56"><span class="linenos"> 56</span></a> <span class="n">bdio_read_int32</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_read_int32</span>
</span><span id="L-57"><a href="#L-57"><span class="linenos"> 57</span></a> <span class="n">bdio_read_int32</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span>
</span><span id="L-58"><a href="#L-58"><span class="linenos"> 58</span></a> <span class="n">bdio_read_int32</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="L-59"><a href="#L-59"><span class="linenos"> 59</span></a>
</span><span id="L-60"><a href="#L-60"><span class="linenos"> 60</span></a> <span class="n">b_path</span> <span class="o">=</span> <span class="n">file_path</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span>
</span><span id="L-61"><a href="#L-61"><span class="linenos"> 61</span></a> <span class="n">read</span> <span class="o">=</span> <span class="s1">&#39;r&#39;</span>
</span><span id="L-62"><a href="#L-62"><span class="linenos"> 62</span></a> <span class="n">b_read</span> <span class="o">=</span> <span class="n">read</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span>
</span><span id="L-63"><a href="#L-63"><span class="linenos"> 63</span></a>
</span><span id="L-64"><a href="#L-64"><span class="linenos"> 64</span></a> <span class="n">fbdio</span> <span class="o">=</span> <span class="n">bdio_open</span><span class="p">(</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_char_p</span><span class="p">(</span><span class="n">b_path</span><span class="p">),</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_char_p</span><span class="p">(</span><span class="n">b_read</span><span class="p">),</span> <span class="kc">None</span><span class="p">)</span>
</span><span id="L-65"><a href="#L-65"><span class="linenos"> 65</span></a>
</span><span id="L-66"><a href="#L-66"><span class="linenos"> 66</span></a> <span class="n">return_list</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="L-67"><a href="#L-67"><span class="linenos"> 67</span></a>
</span><span id="L-68"><a href="#L-68"><span class="linenos"> 68</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Reading of bdio file started&#39;</span><span class="p">)</span>
</span><span id="L-69"><a href="#L-69"><span class="linenos"> 69</span></a> <span class="k">while</span> <span class="kc">True</span><span class="p">:</span>
</span><span id="L-70"><a href="#L-70"><span class="linenos"> 70</span></a> <span class="n">bdio_seek_record</span><span class="p">(</span><span class="n">fbdio</span><span class="p">)</span>
</span><span id="L-71"><a href="#L-71"><span class="linenos"> 71</span></a> <span class="n">ruinfo</span> <span class="o">=</span> <span class="n">bdio_get_ruinfo</span><span class="p">(</span><span class="n">fbdio</span><span class="p">)</span>
</span><span id="L-72"><a href="#L-72"><span class="linenos"> 72</span></a>
</span><span id="L-73"><a href="#L-73"><span class="linenos"> 73</span></a> <span class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">7</span><span class="p">:</span>
</span><span id="L-74"><a href="#L-74"><span class="linenos"> 74</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;MD5sum found&#39;</span><span class="p">)</span> <span class="c1"># For now we just ignore these entries and do not perform any checks on them</span>
</span><span id="L-75"><a href="#L-75"><span class="linenos"> 75</span></a> <span class="k">continue</span>
</span><span id="L-76"><a href="#L-76"><span class="linenos"> 76</span></a>
</span><span id="L-77"><a href="#L-77"><span class="linenos"> 77</span></a> <span class="k">if</span> <span class="n">ruinfo</span> <span class="o">&lt;</span> <span class="mi">0</span><span class="p">:</span>
</span><span id="L-78"><a href="#L-78"><span class="linenos"> 78</span></a> <span class="c1"># EOF reached</span>
</span><span id="L-79"><a href="#L-79"><span class="linenos"> 79</span></a> <span class="k">break</span>
</span><span id="L-80"><a href="#L-80"><span class="linenos"> 80</span></a> <span class="n">bdio_get_rlen</span><span class="p">(</span><span class="n">fbdio</span><span class="p">)</span>
</span><span id="L-81"><a href="#L-81"><span class="linenos"> 81</span></a>
</span><span id="L-82"><a href="#L-82"><span class="linenos"> 82</span></a> <span class="k">def</span> <span class="nf">read_c_double</span><span class="p">():</span>
</span><span id="L-83"><a href="#L-83"><span class="linenos"> 83</span></a> <span class="n">d_buf</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_double</span>
</span><span id="L-84"><a href="#L-84"><span class="linenos"> 84</span></a> <span class="n">pd_buf</span> <span class="o">=</span> <span class="n">d_buf</span><span class="p">()</span>
</span><span id="L-85"><a href="#L-85"><span class="linenos"> 85</span></a> <span class="n">ppd_buf</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">(</span><span class="n">ctypes</span><span class="o">.</span><span class="n">addressof</span><span class="p">(</span><span class="n">pd_buf</span><span class="p">))</span>
</span><span id="L-86"><a href="#L-86"><span class="linenos"> 86</span></a> <span class="n">bdio_read_f64</span><span class="p">(</span><span class="n">ppd_buf</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span><span class="p">(</span><span class="mi">8</span><span class="p">),</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">(</span><span class="n">fbdio</span><span class="p">))</span>
</span><span id="L-87"><a href="#L-87"><span class="linenos"> 87</span></a> <span class="k">return</span> <span class="n">pd_buf</span><span class="o">.</span><span class="n">value</span>
</span><span id="L-88"><a href="#L-88"><span class="linenos"> 88</span></a>
</span><span id="L-89"><a href="#L-89"><span class="linenos"> 89</span></a> <span class="n">mean</span> <span class="o">=</span> <span class="n">read_c_double</span><span class="p">()</span>
</span><span id="L-90"><a href="#L-90"><span class="linenos"> 90</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;mean&#39;</span><span class="p">,</span> <span class="n">mean</span><span class="p">)</span>
</span><span id="L-91"><a href="#L-91"><span class="linenos"> 91</span></a>
</span><span id="L-92"><a href="#L-92"><span class="linenos"> 92</span></a> <span class="k">def</span> <span class="nf">read_c_size_t</span><span class="p">():</span>
</span><span id="L-93"><a href="#L-93"><span class="linenos"> 93</span></a> <span class="n">d_buf</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span>
</span><span id="L-94"><a href="#L-94"><span class="linenos"> 94</span></a> <span class="n">pd_buf</span> <span class="o">=</span> <span class="n">d_buf</span><span class="p">()</span>
</span><span id="L-95"><a href="#L-95"><span class="linenos"> 95</span></a> <span class="n">ppd_buf</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">(</span><span class="n">ctypes</span><span class="o">.</span><span class="n">addressof</span><span class="p">(</span><span class="n">pd_buf</span><span class="p">))</span>
</span><span id="L-96"><a href="#L-96"><span class="linenos"> 96</span></a> <span class="n">bdio_read_int32</span><span class="p">(</span><span class="n">ppd_buf</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span><span class="p">(</span><span class="mi">4</span><span class="p">),</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">(</span><span class="n">fbdio</span><span class="p">))</span>
</span><span id="L-97"><a href="#L-97"><span class="linenos"> 97</span></a> <span class="k">return</span> <span class="n">pd_buf</span><span class="o">.</span><span class="n">value</span>
</span><span id="L-98"><a href="#L-98"><span class="linenos"> 98</span></a>
</span><span id="L-99"><a href="#L-99"><span class="linenos"> 99</span></a> <span class="n">neid</span> <span class="o">=</span> <span class="n">read_c_size_t</span><span class="p">()</span>
</span><span id="L-100"><a href="#L-100"><span class="linenos">100</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;neid&#39;</span><span class="p">,</span> <span class="n">neid</span><span class="p">)</span>
</span><span id="L-101"><a href="#L-101"><span class="linenos">101</span></a>
</span><span id="L-102"><a href="#L-102"><span class="linenos">102</span></a> <span class="n">ndata</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="L-103"><a href="#L-103"><span class="linenos">103</span></a> <span class="k">for</span> <span class="n">index</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">neid</span><span class="p">):</span>
</span><span id="L-104"><a href="#L-104"><span class="linenos">104</span></a> <span class="n">ndata</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">read_c_size_t</span><span class="p">())</span>
</span><span id="L-105"><a href="#L-105"><span class="linenos">105</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;ndata&#39;</span><span class="p">,</span> <span class="n">ndata</span><span class="p">)</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="n">nrep</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="L-108"><a href="#L-108"><span class="linenos">108</span></a> <span class="k">for</span> <span class="n">index</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">neid</span><span class="p">):</span>
</span><span id="L-109"><a href="#L-109"><span class="linenos">109</span></a> <span class="n">nrep</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">read_c_size_t</span><span class="p">())</span>
</span><span id="L-110"><a href="#L-110"><span class="linenos">110</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;nrep&#39;</span><span class="p">,</span> <span class="n">nrep</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">vrep</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="L-113"><a href="#L-113"><span class="linenos">113</span></a> <span class="k">for</span> <span class="n">index</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">neid</span><span class="p">):</span>
</span><span id="L-114"><a href="#L-114"><span class="linenos">114</span></a> <span class="n">vrep</span><span class="o">.</span><span class="n">append</span><span class="p">([])</span>
</span><span id="L-115"><a href="#L-115"><span class="linenos">115</span></a> <span class="k">for</span> <span class="n">jndex</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nrep</span><span class="p">[</span><span class="n">index</span><span class="p">]):</span>
</span><span id="L-116"><a href="#L-116"><span class="linenos">116</span></a> <span class="n">vrep</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">read_c_size_t</span><span class="p">())</span>
</span><span id="L-117"><a href="#L-117"><span class="linenos">117</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;vrep&#39;</span><span class="p">,</span> <span class="n">vrep</span><span class="p">)</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">ids</span> <span class="o">=</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">index</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">neid</span><span class="p">):</span>
</span><span id="L-121"><a href="#L-121"><span class="linenos">121</span></a> <span class="n">ids</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">read_c_size_t</span><span class="p">())</span>
</span><span id="L-122"><a href="#L-122"><span class="linenos">122</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;ids&#39;</span><span class="p">,</span> <span class="n">ids</span><span class="p">)</span>
</span><span id="L-123"><a href="#L-123"><span class="linenos">123</span></a>
</span><span id="L-124"><a href="#L-124"><span class="linenos">124</span></a> <span class="n">nt</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="L-125"><a href="#L-125"><span class="linenos">125</span></a> <span class="k">for</span> <span class="n">index</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">neid</span><span class="p">):</span>
</span><span id="L-126"><a href="#L-126"><span class="linenos">126</span></a> <span class="n">nt</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">read_c_size_t</span><span class="p">())</span>
</span><span id="L-127"><a href="#L-127"><span class="linenos">127</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;nt&#39;</span><span class="p">,</span> <span class="n">nt</span><span class="p">)</span>
</span><span id="L-128"><a href="#L-128"><span class="linenos">128</span></a>
</span><span id="L-129"><a href="#L-129"><span class="linenos">129</span></a> <span class="n">zero</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="L-130"><a href="#L-130"><span class="linenos">130</span></a> <span class="k">for</span> <span class="n">index</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">neid</span><span class="p">):</span>
</span><span id="L-131"><a href="#L-131"><span class="linenos">131</span></a> <span class="n">zero</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">read_c_double</span><span class="p">())</span>
</span><span id="L-132"><a href="#L-132"><span class="linenos">132</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;zero&#39;</span><span class="p">,</span> <span class="n">zero</span><span class="p">)</span>
</span><span id="L-133"><a href="#L-133"><span class="linenos">133</span></a>
</span><span id="L-134"><a href="#L-134"><span class="linenos">134</span></a> <span class="n">four</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="L-135"><a href="#L-135"><span class="linenos">135</span></a> <span class="k">for</span> <span class="n">index</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">neid</span><span class="p">):</span>
</span><span id="L-136"><a href="#L-136"><span class="linenos">136</span></a> <span class="n">four</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">read_c_double</span><span class="p">())</span>
</span><span id="L-137"><a href="#L-137"><span class="linenos">137</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;four&#39;</span><span class="p">,</span> <span class="n">four</span><span class="p">)</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="n">d_buf</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_double</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">ndata</span><span class="p">)</span>
</span><span id="L-140"><a href="#L-140"><span class="linenos">140</span></a> <span class="n">pd_buf</span> <span class="o">=</span> <span class="n">d_buf</span><span class="p">()</span>
</span><span id="L-141"><a href="#L-141"><span class="linenos">141</span></a> <span class="n">ppd_buf</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">(</span><span class="n">ctypes</span><span class="o">.</span><span class="n">addressof</span><span class="p">(</span><span class="n">pd_buf</span><span class="p">))</span>
</span><span id="L-142"><a href="#L-142"><span class="linenos">142</span></a> <span class="n">bdio_read_f64</span><span class="p">(</span><span class="n">ppd_buf</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span><span class="p">(</span><span class="mi">8</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">ndata</span><span class="p">)),</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">(</span><span class="n">fbdio</span><span class="p">))</span>
</span><span id="L-143"><a href="#L-143"><span class="linenos">143</span></a> <span class="n">delta</span> <span class="o">=</span> <span class="n">pd_buf</span><span class="p">[:]</span>
</span><span id="L-144"><a href="#L-144"><span class="linenos">144</span></a>
</span><span id="L-145"><a href="#L-145"><span class="linenos">145</span></a> <span class="n">samples</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">delta</span><span class="p">)</span> <span class="o">+</span> <span class="n">mean</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">cumsum</span><span class="p">([</span><span class="n">a</span> <span class="k">for</span> <span class="n">su</span> <span class="ow">in</span> <span class="n">vrep</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">su</span><span class="p">])[:</span><span class="o">-</span><span class="mi">1</span><span class="p">])</span>
</span><span id="L-146"><a href="#L-146"><span class="linenos">146</span></a> <span class="n">no_reps</span> <span class="o">=</span> <span class="p">[</span><span class="nb">len</span><span class="p">(</span><span class="n">o</span><span class="p">)</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">vrep</span><span class="p">]</span>
</span><span id="L-147"><a href="#L-147"><span class="linenos">147</span></a> <span class="k">assert</span> <span class="nb">len</span><span class="p">(</span><span class="n">ids</span><span class="p">)</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="n">no_reps</span><span class="p">)</span>
</span><span id="L-148"><a href="#L-148"><span class="linenos">148</span></a> <span class="n">tmp_names</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="L-149"><a href="#L-149"><span class="linenos">149</span></a> <span class="n">ens_length</span> <span class="o">=</span> <span class="nb">max</span><span class="p">([</span><span class="nb">len</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">o</span><span class="p">))</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">ids</span><span class="p">])</span>
</span><span id="L-150"><a href="#L-150"><span class="linenos">150</span></a> <span class="k">for</span> <span class="n">loc_id</span><span class="p">,</span> <span class="n">reps</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">ids</span><span class="p">,</span> <span class="n">no_reps</span><span class="p">):</span>
</span><span id="L-151"><a href="#L-151"><span class="linenos">151</span></a> <span class="k">for</span> <span class="n">index</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">reps</span><span class="p">):</span>
</span><span id="L-152"><a href="#L-152"><span class="linenos">152</span></a> <span class="n">missing_chars</span> <span class="o">=</span> <span class="n">ens_length</span> <span class="o">-</span> <span class="nb">len</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">loc_id</span><span class="p">))</span>
</span><span id="L-153"><a href="#L-153"><span class="linenos">153</span></a> <span class="n">tmp_names</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">loc_id</span><span class="p">)</span> <span class="o">+</span> <span class="s1">&#39; &#39;</span> <span class="o">*</span> <span class="n">missing_chars</span> <span class="o">+</span> <span class="s1">&#39;|r&#39;</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="si">{0:03d}</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">index</span><span class="p">))</span>
</span><span id="L-154"><a href="#L-154"><span class="linenos">154</span></a>
</span><span id="L-155"><a href="#L-155"><span class="linenos">155</span></a> <span class="n">return_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">Obs</span><span class="p">(</span><span class="n">samples</span><span class="p">,</span> <span class="n">tmp_names</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 class="n">bdio_close</span><span class="p">(</span><span class="n">fbdio</span><span class="p">)</span>
</span><span id="L-158"><a href="#L-158"><span class="linenos">158</span></a> <span class="nb">print</span><span class="p">()</span>
</span><span id="L-159"><a href="#L-159"><span class="linenos">159</span></a> <span class="nb">print</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">return_list</span><span class="p">),</span> <span class="s1">&#39;observable(s) extracted.&#39;</span><span class="p">)</span>
</span><span id="L-160"><a href="#L-160"><span class="linenos">160</span></a> <span class="k">return</span> <span class="n">return_list</span>
</span><span id="L-161"><a href="#L-161"><span class="linenos">161</span></a>
</span><span id="L-162"><a href="#L-162"><span class="linenos">162</span></a>
</span><span id="L-163"><a href="#L-163"><span class="linenos">163</span></a><span class="k">def</span> <span class="nf">write_ADerrors</span><span class="p">(</span><span class="n">obs_list</span><span class="p">,</span> <span class="n">file_path</span><span class="p">,</span> <span class="n">bdio_path</span><span class="o">=</span><span class="s1">&#39;./libbdio.so&#39;</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
</span><span id="L-164"><a href="#L-164"><span class="linenos">164</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot; Write Obs to a bdio file according to ADerrors conventions</span>
</span><span id="L-165"><a href="#L-165"><span class="linenos">165</span></a>
</span><span id="L-166"><a href="#L-166"><span class="linenos">166</span></a><span class="sd"> read_mesons requires bdio to be compiled into a shared library. This can be achieved by</span>
</span><span id="L-167"><a href="#L-167"><span class="linenos">167</span></a><span class="sd"> adding the flag -fPIC to CC and changing the all target to</span>
</span><span id="L-168"><a href="#L-168"><span class="linenos">168</span></a>
</span><span id="L-169"><a href="#L-169"><span class="linenos">169</span></a><span class="sd"> all: bdio.o $(LIBDIR)</span>
</span><span id="L-170"><a href="#L-170"><span class="linenos">170</span></a><span class="sd"> gcc -shared -Wl,-soname,libbdio.so -o $(BUILDDIR)/libbdio.so $(BUILDDIR)/bdio.o</span>
</span><span id="L-171"><a href="#L-171"><span class="linenos">171</span></a><span class="sd"> cp $(BUILDDIR)/libbdio.so $(LIBDIR)/</span>
</span><span id="L-172"><a href="#L-172"><span class="linenos">172</span></a>
</span><span id="L-173"><a href="#L-173"><span class="linenos">173</span></a><span class="sd"> Parameters</span>
</span><span id="L-174"><a href="#L-174"><span class="linenos">174</span></a><span class="sd"> ----------</span>
</span><span id="L-175"><a href="#L-175"><span class="linenos">175</span></a><span class="sd"> file_path -- path to the bdio file</span>
</span><span id="L-176"><a href="#L-176"><span class="linenos">176</span></a><span class="sd"> bdio_path -- path to the shared bdio library libbdio.so (default ./libbdio.so)</span>
</span><span id="L-177"><a href="#L-177"><span class="linenos">177</span></a>
</span><span id="L-178"><a href="#L-178"><span class="linenos">178</span></a><span class="sd"> Returns</span>
</span><span id="L-179"><a href="#L-179"><span class="linenos">179</span></a><span class="sd"> -------</span>
</span><span id="L-180"><a href="#L-180"><span class="linenos">180</span></a><span class="sd"> success : int</span>
</span><span id="L-181"><a href="#L-181"><span class="linenos">181</span></a><span class="sd"> returns 0 is successful</span>
</span><span id="L-182"><a href="#L-182"><span class="linenos">182</span></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="L-183"><a href="#L-183"><span class="linenos">183</span></a>
</span><span id="L-184"><a href="#L-184"><span class="linenos">184</span></a> <span class="k">for</span> <span class="n">obs</span> <span class="ow">in</span> <span class="n">obs_list</span><span class="p">:</span>
</span><span id="L-185"><a href="#L-185"><span class="linenos">185</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">obs</span><span class="p">,</span> <span class="s1">&#39;e_names&#39;</span><span class="p">):</span>
</span><span id="L-186"><a href="#L-186"><span class="linenos">186</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Run the gamma method first for all obs.&#39;</span><span class="p">)</span>
</span><span id="L-187"><a href="#L-187"><span class="linenos">187</span></a>
</span><span id="L-188"><a href="#L-188"><span class="linenos">188</span></a> <span class="n">bdio</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">cdll</span><span class="o">.</span><span class="n">LoadLibrary</span><span class="p">(</span><span class="n">bdio_path</span><span class="p">)</span>
</span><span id="L-189"><a href="#L-189"><span class="linenos">189</span></a>
</span><span id="L-190"><a href="#L-190"><span class="linenos">190</span></a> <span class="n">bdio_open</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_open</span>
</span><span id="L-191"><a href="#L-191"><span class="linenos">191</span></a> <span class="n">bdio_open</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span>
</span><span id="L-192"><a href="#L-192"><span class="linenos">192</span></a>
</span><span id="L-193"><a href="#L-193"><span class="linenos">193</span></a> <span class="n">bdio_close</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_close</span>
</span><span id="L-194"><a href="#L-194"><span class="linenos">194</span></a> <span class="n">bdio_close</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_int</span>
</span><span id="L-195"><a href="#L-195"><span class="linenos">195</span></a> <span class="n">bdio_close</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="L-196"><a href="#L-196"><span class="linenos">196</span></a>
</span><span id="L-197"><a href="#L-197"><span class="linenos">197</span></a> <span class="n">bdio_start_record</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_start_record</span>
</span><span id="L-198"><a href="#L-198"><span class="linenos">198</span></a> <span class="n">bdio_start_record</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_int</span>
</span><span id="L-199"><a href="#L-199"><span class="linenos">199</span></a> <span class="n">bdio_start_record</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="L-200"><a href="#L-200"><span class="linenos">200</span></a>
</span><span id="L-201"><a href="#L-201"><span class="linenos">201</span></a> <span class="n">bdio_flush_record</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_flush_record</span>
</span><span id="L-202"><a href="#L-202"><span class="linenos">202</span></a> <span class="n">bdio_flush_record</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_int</span>
</span><span id="L-203"><a href="#L-203"><span class="linenos">203</span></a> <span class="n">bdio_flush_record</span><span class="o">.</span><span class="n">argytpes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="L-204"><a href="#L-204"><span class="linenos">204</span></a>
</span><span id="L-205"><a href="#L-205"><span class="linenos">205</span></a> <span class="n">bdio_write_f64</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_write_f64</span>
</span><span id="L-206"><a href="#L-206"><span class="linenos">206</span></a> <span class="n">bdio_write_f64</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span>
</span><span id="L-207"><a href="#L-207"><span class="linenos">207</span></a> <span class="n">bdio_write_f64</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="L-208"><a href="#L-208"><span class="linenos">208</span></a>
</span><span id="L-209"><a href="#L-209"><span class="linenos">209</span></a> <span class="n">bdio_write_int32</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_write_int32</span>
</span><span id="L-210"><a href="#L-210"><span class="linenos">210</span></a> <span class="n">bdio_write_int32</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span>
</span><span id="L-211"><a href="#L-211"><span class="linenos">211</span></a> <span class="n">bdio_write_int32</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="L-212"><a href="#L-212"><span class="linenos">212</span></a>
</span><span id="L-213"><a href="#L-213"><span class="linenos">213</span></a> <span class="n">b_path</span> <span class="o">=</span> <span class="n">file_path</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span>
</span><span id="L-214"><a href="#L-214"><span class="linenos">214</span></a> <span class="n">write</span> <span class="o">=</span> <span class="s1">&#39;w&#39;</span>
</span><span id="L-215"><a href="#L-215"><span class="linenos">215</span></a> <span class="n">b_write</span> <span class="o">=</span> <span class="n">write</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span>
</span><span id="L-216"><a href="#L-216"><span class="linenos">216</span></a> <span class="n">form</span> <span class="o">=</span> <span class="s1">&#39;pyerrors ADerror export&#39;</span>
</span><span id="L-217"><a href="#L-217"><span class="linenos">217</span></a> <span class="n">b_form</span> <span class="o">=</span> <span class="n">form</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span>
</span><span id="L-218"><a href="#L-218"><span class="linenos">218</span></a>
</span><span id="L-219"><a href="#L-219"><span class="linenos">219</span></a> <span class="n">fbdio</span> <span class="o">=</span> <span class="n">bdio_open</span><span class="p">(</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_char_p</span><span class="p">(</span><span class="n">b_path</span><span class="p">),</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_char_p</span><span class="p">(</span><span class="n">b_write</span><span class="p">),</span> <span class="n">b_form</span><span class="p">)</span>
</span><span id="L-220"><a href="#L-220"><span class="linenos">220</span></a>
</span><span id="L-221"><a href="#L-221"><span class="linenos">221</span></a> <span class="k">for</span> <span class="n">obs</span> <span class="ow">in</span> <span class="n">obs_list</span><span class="p">:</span>
</span><span id="L-222"><a href="#L-222"><span class="linenos">222</span></a> <span class="c1"># mean = obs.value</span>
</span><span id="L-223"><a href="#L-223"><span class="linenos">223</span></a> <span class="n">neid</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">obs</span><span class="o">.</span><span class="n">e_names</span><span class="p">)</span>
</span><span id="L-224"><a href="#L-224"><span class="linenos">224</span></a> <span class="n">vrep</span> <span class="o">=</span> <span class="p">[[</span><span class="n">obs</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="n">o</span><span class="p">]</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">sl</span><span class="p">]</span> <span class="k">for</span> <span class="n">sl</span> <span class="ow">in</span> <span class="nb">list</span><span class="p">(</span><span class="n">obs</span><span class="o">.</span><span class="n">e_content</span><span class="o">.</span><span class="n">values</span><span class="p">())]</span>
</span><span id="L-225"><a href="#L-225"><span class="linenos">225</span></a> <span class="n">vrep_write</span> <span class="o">=</span> <span class="p">[</span><span class="n">item</span> <span class="k">for</span> <span class="n">sublist</span> <span class="ow">in</span> <span class="n">vrep</span> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">sublist</span><span class="p">]</span>
</span><span id="L-226"><a href="#L-226"><span class="linenos">226</span></a> <span class="n">ndata</span> <span class="o">=</span> <span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">o</span><span class="p">)</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">vrep</span><span class="p">]</span>
</span><span id="L-227"><a href="#L-227"><span class="linenos">227</span></a> <span class="n">nrep</span> <span class="o">=</span> <span class="p">[</span><span class="nb">len</span><span class="p">(</span><span class="n">o</span><span class="p">)</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">vrep</span><span class="p">]</span>
</span><span id="L-228"><a href="#L-228"><span class="linenos">228</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;ndata&#39;</span><span class="p">,</span> <span class="n">ndata</span><span class="p">)</span>
</span><span id="L-229"><a href="#L-229"><span class="linenos">229</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;nrep&#39;</span><span class="p">,</span> <span class="n">nrep</span><span class="p">)</span>
</span><span id="L-230"><a href="#L-230"><span class="linenos">230</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;vrep&#39;</span><span class="p">,</span> <span class="n">vrep</span><span class="p">)</span>
</span><span id="L-231"><a href="#L-231"><span class="linenos">231</span></a> <span class="n">keys</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">obs</span><span class="o">.</span><span class="n">e_content</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
</span><span id="L-232"><a href="#L-232"><span class="linenos">232</span></a> <span class="n">ids</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="L-233"><a href="#L-233"><span class="linenos">233</span></a> <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">keys</span><span class="p">:</span>
</span><span id="L-234"><a href="#L-234"><span class="linenos">234</span></a> <span class="k">try</span><span class="p">:</span> <span class="c1"># Try to convert key to integer</span>
</span><span id="L-235"><a href="#L-235"><span class="linenos">235</span></a> <span class="n">ids</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">key</span><span class="p">))</span>
</span><span id="L-236"><a href="#L-236"><span class="linenos">236</span></a> <span class="k">except</span> <span class="ne">Exception</span><span class="p">:</span> <span class="c1"># If not possible construct a hash</span>
</span><span id="L-237"><a href="#L-237"><span class="linenos">237</span></a> <span class="n">ids</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">hashlib</span><span class="o">.</span><span class="n">sha256</span><span class="p">(</span><span class="n">key</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">))</span><span class="o">.</span><span class="n">hexdigest</span><span class="p">(),</span> <span class="mi">16</span><span class="p">)</span> <span class="o">%</span> <span class="mi">10</span> <span class="o">**</span> <span class="mi">8</span><span class="p">)</span>
</span><span id="L-238"><a href="#L-238"><span class="linenos">238</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;ids&#39;</span><span class="p">,</span> <span class="n">ids</span><span class="p">)</span>
</span><span id="L-239"><a href="#L-239"><span class="linenos">239</span></a> <span class="n">nt</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="L-240"><a href="#L-240"><span class="linenos">240</span></a> <span class="k">for</span> <span class="n">e</span><span class="p">,</span> <span class="n">e_name</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">obs</span><span class="o">.</span><span class="n">e_names</span><span class="p">):</span>
</span><span id="L-241"><a href="#L-241"><span class="linenos">241</span></a>
</span><span id="L-242"><a href="#L-242"><span class="linenos">242</span></a> <span class="n">r_length</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="L-243"><a href="#L-243"><span class="linenos">243</span></a> <span class="k">for</span> <span class="n">r_name</span> <span class="ow">in</span> <span class="n">obs</span><span class="o">.</span><span class="n">e_content</span><span class="p">[</span><span class="n">e_name</span><span class="p">]:</span>
</span><span id="L-244"><a href="#L-244"><span class="linenos">244</span></a> <span class="n">r_length</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">obs</span><span class="o">.</span><span class="n">deltas</span><span class="p">[</span><span class="n">r_name</span><span class="p">]))</span>
</span><span id="L-245"><a href="#L-245"><span class="linenos">245</span></a>
</span><span id="L-246"><a href="#L-246"><span class="linenos">246</span></a> <span class="c1"># e_N = np.sum(r_length)</span>
</span><span id="L-247"><a href="#L-247"><span class="linenos">247</span></a> <span class="n">nt</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">max</span><span class="p">(</span><span class="n">r_length</span><span class="p">)</span> <span class="o">//</span> <span class="mi">2</span><span class="p">)</span>
</span><span id="L-248"><a href="#L-248"><span class="linenos">248</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;nt&#39;</span><span class="p">,</span> <span class="n">nt</span><span class="p">)</span>
</span><span id="L-249"><a href="#L-249"><span class="linenos">249</span></a> <span class="n">zero</span> <span class="o">=</span> <span class="n">neid</span> <span class="o">*</span> <span class="p">[</span><span class="mf">0.0</span><span class="p">]</span>
</span><span id="L-250"><a href="#L-250"><span class="linenos">250</span></a> <span class="n">four</span> <span class="o">=</span> <span class="n">neid</span> <span class="o">*</span> <span class="p">[</span><span class="mf">4.0</span><span class="p">]</span>
</span><span id="L-251"><a href="#L-251"><span class="linenos">251</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;zero&#39;</span><span class="p">,</span> <span class="n">zero</span><span class="p">)</span>
</span><span id="L-252"><a href="#L-252"><span class="linenos">252</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;four&#39;</span><span class="p">,</span> <span class="n">four</span><span class="p">)</span>
</span><span id="L-253"><a href="#L-253"><span class="linenos">253</span></a> <span class="n">delta</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">concatenate</span><span class="p">([</span><span class="n">item</span> <span class="k">for</span> <span class="n">sublist</span> <span class="ow">in</span> <span class="p">[[</span><span class="n">obs</span><span class="o">.</span><span class="n">deltas</span><span class="p">[</span><span class="n">o</span><span class="p">]</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">sl</span><span class="p">]</span> <span class="k">for</span> <span class="n">sl</span> <span class="ow">in</span> <span class="nb">list</span><span class="p">(</span><span class="n">obs</span><span class="o">.</span><span class="n">e_content</span><span class="o">.</span><span class="n">values</span><span class="p">())]</span> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">sublist</span><span class="p">])</span>
</span><span id="L-254"><a href="#L-254"><span class="linenos">254</span></a>
</span><span id="L-255"><a href="#L-255"><span class="linenos">255</span></a> <span class="n">bdio_start_record</span><span class="p">(</span><span class="mh">0x00</span><span class="p">,</span> <span class="mi">8</span><span class="p">,</span> <span class="n">fbdio</span><span class="p">)</span>
</span><span id="L-256"><a href="#L-256"><span class="linenos">256</span></a>
</span><span id="L-257"><a href="#L-257"><span class="linenos">257</span></a> <span class="k">def</span> <span class="nf">write_c_double</span><span class="p">(</span><span class="n">double</span><span class="p">):</span>
</span><span id="L-258"><a href="#L-258"><span class="linenos">258</span></a> <span class="n">pd_buf</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_double</span><span class="p">(</span><span class="n">double</span><span class="p">)</span>
</span><span id="L-259"><a href="#L-259"><span class="linenos">259</span></a> <span class="n">ppd_buf</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">(</span><span class="n">ctypes</span><span class="o">.</span><span class="n">addressof</span><span class="p">(</span><span class="n">pd_buf</span><span class="p">))</span>
</span><span id="L-260"><a href="#L-260"><span class="linenos">260</span></a> <span class="n">bdio_write_f64</span><span class="p">(</span><span class="n">ppd_buf</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span><span class="p">(</span><span class="mi">8</span><span class="p">),</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">(</span><span class="n">fbdio</span><span class="p">))</span>
</span><span id="L-261"><a href="#L-261"><span class="linenos">261</span></a>
</span><span id="L-262"><a href="#L-262"><span class="linenos">262</span></a> <span class="k">def</span> <span class="nf">write_c_size_t</span><span class="p">(</span><span class="n">int32</span><span class="p">):</span>
</span><span id="L-263"><a href="#L-263"><span class="linenos">263</span></a> <span class="n">pd_buf</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span><span class="p">(</span><span class="n">int32</span><span class="p">)</span>
</span><span id="L-264"><a href="#L-264"><span class="linenos">264</span></a> <span class="n">ppd_buf</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">(</span><span class="n">ctypes</span><span class="o">.</span><span class="n">addressof</span><span class="p">(</span><span class="n">pd_buf</span><span class="p">))</span>
</span><span id="L-265"><a href="#L-265"><span class="linenos">265</span></a> <span class="n">bdio_write_int32</span><span class="p">(</span><span class="n">ppd_buf</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span><span class="p">(</span><span class="mi">4</span><span class="p">),</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">(</span><span class="n">fbdio</span><span class="p">))</span>
</span><span id="L-266"><a href="#L-266"><span class="linenos">266</span></a>
</span><span id="L-267"><a href="#L-267"><span class="linenos">267</span></a> <span class="n">write_c_double</span><span class="p">(</span><span class="n">obs</span><span class="o">.</span><span class="n">value</span><span class="p">)</span>
</span><span id="L-268"><a href="#L-268"><span class="linenos">268</span></a> <span class="n">write_c_size_t</span><span class="p">(</span><span class="n">neid</span><span class="p">)</span>
</span><span id="L-269"><a href="#L-269"><span class="linenos">269</span></a>
</span><span id="L-270"><a href="#L-270"><span class="linenos">270</span></a> <span class="k">for</span> <span class="n">element</span> <span class="ow">in</span> <span class="n">ndata</span><span class="p">:</span>
</span><span id="L-271"><a href="#L-271"><span class="linenos">271</span></a> <span class="n">write_c_size_t</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
</span><span id="L-272"><a href="#L-272"><span class="linenos">272</span></a> <span class="k">for</span> <span class="n">element</span> <span class="ow">in</span> <span class="n">nrep</span><span class="p">:</span>
</span><span id="L-273"><a href="#L-273"><span class="linenos">273</span></a> <span class="n">write_c_size_t</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
</span><span id="L-274"><a href="#L-274"><span class="linenos">274</span></a> <span class="k">for</span> <span class="n">element</span> <span class="ow">in</span> <span class="n">vrep_write</span><span class="p">:</span>
</span><span id="L-275"><a href="#L-275"><span class="linenos">275</span></a> <span class="n">write_c_size_t</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
</span><span id="L-276"><a href="#L-276"><span class="linenos">276</span></a> <span class="k">for</span> <span class="n">element</span> <span class="ow">in</span> <span class="n">ids</span><span class="p">:</span>
</span><span id="L-277"><a href="#L-277"><span class="linenos">277</span></a> <span class="n">write_c_size_t</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
</span><span id="L-278"><a href="#L-278"><span class="linenos">278</span></a> <span class="k">for</span> <span class="n">element</span> <span class="ow">in</span> <span class="n">nt</span><span class="p">:</span>
</span><span id="L-279"><a href="#L-279"><span class="linenos">279</span></a> <span class="n">write_c_size_t</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
</span><span id="L-280"><a href="#L-280"><span class="linenos">280</span></a>
</span><span id="L-281"><a href="#L-281"><span class="linenos">281</span></a> <span class="k">for</span> <span class="n">element</span> <span class="ow">in</span> <span class="n">zero</span><span class="p">:</span>
</span><span id="L-282"><a href="#L-282"><span class="linenos">282</span></a> <span class="n">write_c_double</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
</span><span id="L-283"><a href="#L-283"><span class="linenos">283</span></a> <span class="k">for</span> <span class="n">element</span> <span class="ow">in</span> <span class="n">four</span><span class="p">:</span>
</span><span id="L-284"><a href="#L-284"><span class="linenos">284</span></a> <span class="n">write_c_double</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
</span><span id="L-285"><a href="#L-285"><span class="linenos">285</span></a>
</span><span id="L-286"><a href="#L-286"><span class="linenos">286</span></a> <span class="k">for</span> <span class="n">element</span> <span class="ow">in</span> <span class="n">delta</span><span class="p">:</span>
</span><span id="L-287"><a href="#L-287"><span class="linenos">287</span></a> <span class="n">write_c_double</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
</span><span id="L-288"><a href="#L-288"><span class="linenos">288</span></a>
</span><span id="L-289"><a href="#L-289"><span class="linenos">289</span></a> <span class="n">bdio_close</span><span class="p">(</span><span class="n">fbdio</span><span class="p">)</span>
</span><span id="L-290"><a href="#L-290"><span class="linenos">290</span></a> <span class="k">return</span> <span class="mi">0</span>
</span><span id="L-291"><a href="#L-291"><span class="linenos">291</span></a>
</span><span id="L-292"><a href="#L-292"><span class="linenos">292</span></a>
</span><span id="L-293"><a href="#L-293"><span class="linenos">293</span></a><span class="k">def</span> <span class="nf">_get_kwd</span><span class="p">(</span><span class="n">string</span><span class="p">,</span> <span class="n">key</span><span class="p">):</span>
</span><span id="L-294"><a href="#L-294"><span class="linenos">294</span></a> <span class="k">return</span> <span class="p">(</span><span class="n">string</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">key</span><span class="p">,</span> <span class="mi">1</span><span class="p">)[</span><span class="mi">1</span><span class="p">])</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot; &quot;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
</span><span id="L-295"><a href="#L-295"><span class="linenos">295</span></a>
</span><span id="L-296"><a href="#L-296"><span class="linenos">296</span></a>
</span><span id="L-297"><a href="#L-297"><span class="linenos">297</span></a><span class="k">def</span> <span class="nf">_get_corr_name</span><span class="p">(</span><span class="n">string</span><span class="p">,</span> <span class="n">key</span><span class="p">):</span>
</span><span id="L-298"><a href="#L-298"><span class="linenos">298</span></a> <span class="k">return</span> <span class="p">(</span><span class="n">string</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">key</span><span class="p">,</span> <span class="mi">1</span><span class="p">)[</span><span class="mi">1</span><span class="p">])</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39; NDIM=&#39;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
</span><span id="L-299"><a href="#L-299"><span class="linenos">299</span></a>
</span><span id="L-300"><a href="#L-300"><span class="linenos">300</span></a>
</span><span id="L-301"><a href="#L-301"><span class="linenos">301</span></a><span class="k">def</span> <span class="nf">read_mesons</span><span class="p">(</span><span class="n">file_path</span><span class="p">,</span> <span class="n">bdio_path</span><span class="o">=</span><span class="s1">&#39;./libbdio.so&#39;</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
</span><span id="L-302"><a href="#L-302"><span class="linenos">302</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot; Extract mesons data from a bdio file and return it as a dictionary</span>
</span><span id="L-303"><a href="#L-303"><span class="linenos">303</span></a>
</span><span id="L-304"><a href="#L-304"><span class="linenos">304</span></a><span class="sd"> The dictionary can be accessed with a tuple consisting of (type, source_position, kappa1, kappa2)</span>
</span><span id="L-305"><a href="#L-305"><span class="linenos">305</span></a>
</span><span id="L-306"><a href="#L-306"><span class="linenos">306</span></a><span class="sd"> read_mesons requires bdio to be compiled into a shared library. This can be achieved by</span>
</span><span id="L-307"><a href="#L-307"><span class="linenos">307</span></a><span class="sd"> adding the flag -fPIC to CC and changing the all target to</span>
</span><span id="L-308"><a href="#L-308"><span class="linenos">308</span></a>
</span><span id="L-309"><a href="#L-309"><span class="linenos">309</span></a><span class="sd"> all: bdio.o $(LIBDIR)</span>
</span><span id="L-310"><a href="#L-310"><span class="linenos">310</span></a><span class="sd"> gcc -shared -Wl,-soname,libbdio.so -o $(BUILDDIR)/libbdio.so $(BUILDDIR)/bdio.o</span>
</span><span id="L-311"><a href="#L-311"><span class="linenos">311</span></a><span class="sd"> cp $(BUILDDIR)/libbdio.so $(LIBDIR)/</span>
</span><span id="L-312"><a href="#L-312"><span class="linenos">312</span></a>
</span><span id="L-313"><a href="#L-313"><span class="linenos">313</span></a><span class="sd"> Parameters</span>
</span><span id="L-314"><a href="#L-314"><span class="linenos">314</span></a><span class="sd"> ----------</span>
</span><span id="L-315"><a href="#L-315"><span class="linenos">315</span></a><span class="sd"> file_path : str</span>
</span><span id="L-316"><a href="#L-316"><span class="linenos">316</span></a><span class="sd"> path to the bdio file</span>
</span><span id="L-317"><a href="#L-317"><span class="linenos">317</span></a><span class="sd"> bdio_path : str</span>
</span><span id="L-318"><a href="#L-318"><span class="linenos">318</span></a><span class="sd"> path to the shared bdio library libbdio.so (default ./libbdio.so)</span>
</span><span id="L-319"><a href="#L-319"><span class="linenos">319</span></a><span class="sd"> start : int</span>
</span><span id="L-320"><a href="#L-320"><span class="linenos">320</span></a><span class="sd"> The first configuration to be read (default 1)</span>
</span><span id="L-321"><a href="#L-321"><span class="linenos">321</span></a><span class="sd"> stop : int</span>
</span><span id="L-322"><a href="#L-322"><span class="linenos">322</span></a><span class="sd"> The last configuration to be read (default None)</span>
</span><span id="L-323"><a href="#L-323"><span class="linenos">323</span></a><span class="sd"> step : int</span>
</span><span id="L-324"><a href="#L-324"><span class="linenos">324</span></a><span class="sd"> Fixed step size between two measurements (default 1)</span>
</span><span id="L-325"><a href="#L-325"><span class="linenos">325</span></a><span class="sd"> alternative_ensemble_name : str</span>
</span><span id="L-326"><a href="#L-326"><span class="linenos">326</span></a><span class="sd"> Manually overwrite ensemble name</span>
</span><span id="L-327"><a href="#L-327"><span class="linenos">327</span></a>
</span><span id="L-328"><a href="#L-328"><span class="linenos">328</span></a><span class="sd"> Returns</span>
</span><span id="L-329"><a href="#L-329"><span class="linenos">329</span></a><span class="sd"> -------</span>
</span><span id="L-330"><a href="#L-330"><span class="linenos">330</span></a><span class="sd"> data : dict</span>
</span><span id="L-331"><a href="#L-331"><span class="linenos">331</span></a><span class="sd"> Extracted meson data</span>
</span><span id="L-332"><a href="#L-332"><span class="linenos">332</span></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="L-333"><a href="#L-333"><span class="linenos">333</span></a>
</span><span id="L-334"><a href="#L-334"><span class="linenos">334</span></a> <span class="n">start</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;start&#39;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
</span><span id="L-335"><a href="#L-335"><span class="linenos">335</span></a> <span class="n">stop</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;stop&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
</span><span id="L-336"><a href="#L-336"><span class="linenos">336</span></a> <span class="n">step</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;step&#39;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
</span><span id="L-337"><a href="#L-337"><span class="linenos">337</span></a>
</span><span id="L-338"><a href="#L-338"><span class="linenos">338</span></a> <span class="n">bdio</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">cdll</span><span class="o">.</span><span class="n">LoadLibrary</span><span class="p">(</span><span class="n">bdio_path</span><span class="p">)</span>
</span><span id="L-339"><a href="#L-339"><span class="linenos">339</span></a>
</span><span id="L-340"><a href="#L-340"><span class="linenos">340</span></a> <span class="n">bdio_open</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_open</span>
</span><span id="L-341"><a href="#L-341"><span class="linenos">341</span></a> <span class="n">bdio_open</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span>
</span><span id="L-342"><a href="#L-342"><span class="linenos">342</span></a>
</span><span id="L-343"><a href="#L-343"><span class="linenos">343</span></a> <span class="n">bdio_close</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_close</span>
</span><span id="L-344"><a href="#L-344"><span class="linenos">344</span></a> <span class="n">bdio_close</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_int</span>
</span><span id="L-345"><a href="#L-345"><span class="linenos">345</span></a> <span class="n">bdio_close</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="L-346"><a href="#L-346"><span class="linenos">346</span></a>
</span><span id="L-347"><a href="#L-347"><span class="linenos">347</span></a> <span class="n">bdio_seek_record</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_seek_record</span>
</span><span id="L-348"><a href="#L-348"><span class="linenos">348</span></a> <span class="n">bdio_seek_record</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_int</span>
</span><span id="L-349"><a href="#L-349"><span class="linenos">349</span></a> <span class="n">bdio_seek_record</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="L-350"><a href="#L-350"><span class="linenos">350</span></a>
</span><span id="L-351"><a href="#L-351"><span class="linenos">351</span></a> <span class="n">bdio_get_rlen</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_get_rlen</span>
</span><span id="L-352"><a href="#L-352"><span class="linenos">352</span></a> <span class="n">bdio_get_rlen</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_int</span>
</span><span id="L-353"><a href="#L-353"><span class="linenos">353</span></a> <span class="n">bdio_get_rlen</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="L-354"><a href="#L-354"><span class="linenos">354</span></a>
</span><span id="L-355"><a href="#L-355"><span class="linenos">355</span></a> <span class="n">bdio_get_ruinfo</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_get_ruinfo</span>
</span><span id="L-356"><a href="#L-356"><span class="linenos">356</span></a> <span class="n">bdio_get_ruinfo</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_int</span>
</span><span id="L-357"><a href="#L-357"><span class="linenos">357</span></a> <span class="n">bdio_get_ruinfo</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="L-358"><a href="#L-358"><span class="linenos">358</span></a>
</span><span id="L-359"><a href="#L-359"><span class="linenos">359</span></a> <span class="n">bdio_read</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_read</span>
</span><span id="L-360"><a href="#L-360"><span class="linenos">360</span></a> <span class="n">bdio_read</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span>
</span><span id="L-361"><a href="#L-361"><span class="linenos">361</span></a> <span class="n">bdio_read</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_char_p</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="L-362"><a href="#L-362"><span class="linenos">362</span></a>
</span><span id="L-363"><a href="#L-363"><span class="linenos">363</span></a> <span class="n">bdio_read_f64</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_read_f64</span>
</span><span id="L-364"><a href="#L-364"><span class="linenos">364</span></a> <span class="n">bdio_read_f64</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span>
</span><span id="L-365"><a href="#L-365"><span class="linenos">365</span></a> <span class="n">bdio_read_f64</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="L-366"><a href="#L-366"><span class="linenos">366</span></a>
</span><span id="L-367"><a href="#L-367"><span class="linenos">367</span></a> <span class="n">b_path</span> <span class="o">=</span> <span class="n">file_path</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span>
</span><span id="L-368"><a href="#L-368"><span class="linenos">368</span></a> <span class="n">read</span> <span class="o">=</span> <span class="s1">&#39;r&#39;</span>
</span><span id="L-369"><a href="#L-369"><span class="linenos">369</span></a> <span class="n">b_read</span> <span class="o">=</span> <span class="n">read</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span>
</span><span id="L-370"><a href="#L-370"><span class="linenos">370</span></a> <span class="n">form</span> <span class="o">=</span> <span class="s1">&#39;Generic Correlator Format 1.0&#39;</span>
</span><span id="L-371"><a href="#L-371"><span class="linenos">371</span></a> <span class="n">b_form</span> <span class="o">=</span> <span class="n">form</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span>
</span><span id="L-372"><a href="#L-372"><span class="linenos">372</span></a>
</span><span id="L-373"><a href="#L-373"><span class="linenos">373</span></a> <span class="n">ensemble_name</span> <span class="o">=</span> <span class="s1">&#39;&#39;</span>
</span><span id="L-374"><a href="#L-374"><span class="linenos">374</span></a> <span class="n">volume</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># lattice volume</span>
</span><span id="L-375"><a href="#L-375"><span class="linenos">375</span></a> <span class="n">boundary_conditions</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="L-376"><a href="#L-376"><span class="linenos">376</span></a> <span class="n">corr_name</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># Contains correlator names</span>
</span><span id="L-377"><a href="#L-377"><span class="linenos">377</span></a> <span class="n">corr_type</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># Contains correlator data type (important for reading out numerical data)</span>
</span><span id="L-378"><a href="#L-378"><span class="linenos">378</span></a> <span class="n">corr_props</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># Contanis propagator types (Component of corr_kappa)</span>
</span><span id="L-379"><a href="#L-379"><span class="linenos">379</span></a> <span class="n">d0</span> <span class="o">=</span> <span class="mi">0</span> <span class="c1"># tvals</span>
</span><span id="L-380"><a href="#L-380"><span class="linenos">380</span></a> <span class="n">d1</span> <span class="o">=</span> <span class="mi">0</span> <span class="c1"># nnoise</span>
</span><span id="L-381"><a href="#L-381"><span class="linenos">381</span></a> <span class="n">prop_kappa</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># Contains propagator kappas (Component of corr_kappa)</span>
</span><span id="L-382"><a href="#L-382"><span class="linenos">382</span></a> <span class="n">prop_source</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># Contains propagator source positions</span>
</span><span id="L-383"><a href="#L-383"><span class="linenos">383</span></a> <span class="c1"># Check noise type for multiple replica?</span>
</span><span id="L-384"><a href="#L-384"><span class="linenos">384</span></a> <span class="n">corr_no</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
</span><span id="L-385"><a href="#L-385"><span class="linenos">385</span></a> <span class="n">data</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="L-386"><a href="#L-386"><span class="linenos">386</span></a> <span class="n">idl</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="L-387"><a href="#L-387"><span class="linenos">387</span></a>
</span><span id="L-388"><a href="#L-388"><span class="linenos">388</span></a> <span class="n">fbdio</span> <span class="o">=</span> <span class="n">bdio_open</span><span class="p">(</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_char_p</span><span class="p">(</span><span class="n">b_path</span><span class="p">),</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_char_p</span><span class="p">(</span><span class="n">b_read</span><span class="p">),</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_char_p</span><span class="p">(</span><span class="n">b_form</span><span class="p">))</span>
</span><span id="L-389"><a href="#L-389"><span class="linenos">389</span></a>
</span><span id="L-390"><a href="#L-390"><span class="linenos">390</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Reading of bdio file started&#39;</span><span class="p">)</span>
</span><span id="L-391"><a href="#L-391"><span class="linenos">391</span></a> <span class="k">while</span> <span class="kc">True</span><span class="p">:</span>
</span><span id="L-392"><a href="#L-392"><span class="linenos">392</span></a> <span class="n">bdio_seek_record</span><span class="p">(</span><span class="n">fbdio</span><span class="p">)</span>
</span><span id="L-393"><a href="#L-393"><span class="linenos">393</span></a> <span class="n">ruinfo</span> <span class="o">=</span> <span class="n">bdio_get_ruinfo</span><span class="p">(</span><span class="n">fbdio</span><span class="p">)</span>
</span><span id="L-394"><a href="#L-394"><span class="linenos">394</span></a> <span class="k">if</span> <span class="n">ruinfo</span> <span class="o">&lt;</span> <span class="mi">0</span><span class="p">:</span>
</span><span id="L-395"><a href="#L-395"><span class="linenos">395</span></a> <span class="c1"># EOF reached</span>
</span><span id="L-396"><a href="#L-396"><span class="linenos">396</span></a> <span class="k">break</span>
</span><span id="L-397"><a href="#L-397"><span class="linenos">397</span></a> <span class="n">rlen</span> <span class="o">=</span> <span class="n">bdio_get_rlen</span><span class="p">(</span><span class="n">fbdio</span><span class="p">)</span>
</span><span id="L-398"><a href="#L-398"><span class="linenos">398</span></a> <span class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">5</span><span class="p">:</span>
</span><span id="L-399"><a href="#L-399"><span class="linenos">399</span></a> <span class="n">d_buf</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_double</span> <span class="o">*</span> <span class="p">(</span><span class="mi">2</span> <span class="o">+</span> <span class="n">d0</span> <span class="o">*</span> <span class="n">d1</span> <span class="o">*</span> <span class="mi">2</span><span class="p">)</span>
</span><span id="L-400"><a href="#L-400"><span class="linenos">400</span></a> <span class="n">pd_buf</span> <span class="o">=</span> <span class="n">d_buf</span><span class="p">()</span>
</span><span id="L-401"><a href="#L-401"><span class="linenos">401</span></a> <span class="n">ppd_buf</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">(</span><span class="n">ctypes</span><span class="o">.</span><span class="n">addressof</span><span class="p">(</span><span class="n">pd_buf</span><span class="p">))</span>
</span><span id="L-402"><a href="#L-402"><span class="linenos">402</span></a> <span class="n">bdio_read_f64</span><span class="p">(</span><span class="n">ppd_buf</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span><span class="p">(</span><span class="n">rlen</span><span class="p">),</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">(</span><span class="n">fbdio</span><span class="p">))</span>
</span><span id="L-403"><a href="#L-403"><span class="linenos">403</span></a> <span class="k">if</span> <span class="n">corr_type</span><span class="p">[</span><span class="n">corr_no</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;complex&#39;</span><span class="p">:</span>
</span><span id="L-404"><a href="#L-404"><span class="linenos">404</span></a> <span class="n">tmp_mean</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">pd_buf</span><span class="p">[</span><span class="mi">2</span> <span class="o">+</span> <span class="mi">2</span> <span class="o">*</span> <span class="n">d1</span><span class="p">:</span><span class="o">-</span><span class="mi">2</span> <span class="o">*</span> <span class="n">d1</span><span class="p">:</span><span class="mi">2</span><span class="p">]),</span> <span class="n">d0</span> <span class="o">-</span> <span class="mi">2</span><span class="p">)),</span> <span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
</span><span id="L-405"><a href="#L-405"><span class="linenos">405</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="L-406"><a href="#L-406"><span class="linenos">406</span></a> <span class="n">tmp_mean</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">pd_buf</span><span class="p">[</span><span class="mi">2</span> <span class="o">+</span> <span class="n">d1</span><span class="p">:</span><span class="o">-</span><span class="n">d0</span> <span class="o">*</span> <span class="n">d1</span> <span class="o">-</span> <span class="n">d1</span><span class="p">]),</span> <span class="n">d0</span> <span class="o">-</span> <span class="mi">2</span><span class="p">)),</span> <span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
</span><span id="L-407"><a href="#L-407"><span class="linenos">407</span></a>
</span><span id="L-408"><a href="#L-408"><span class="linenos">408</span></a> <span class="n">data</span><span class="p">[</span><span class="n">corr_no</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">tmp_mean</span><span class="p">)</span>
</span><span id="L-409"><a href="#L-409"><span class="linenos">409</span></a> <span class="n">corr_no</span> <span class="o">+=</span> <span class="mi">1</span>
</span><span id="L-410"><a href="#L-410"><span class="linenos">410</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="L-411"><a href="#L-411"><span class="linenos">411</span></a> <span class="n">alt_buf</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">create_string_buffer</span><span class="p">(</span><span class="mi">1024</span><span class="p">)</span>
</span><span id="L-412"><a href="#L-412"><span class="linenos">412</span></a> <span class="n">palt_buf</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_char_p</span><span class="p">(</span><span class="n">ctypes</span><span class="o">.</span><span class="n">addressof</span><span class="p">(</span><span class="n">alt_buf</span><span class="p">))</span>
</span><span id="L-413"><a href="#L-413"><span class="linenos">413</span></a> <span class="n">iread</span> <span class="o">=</span> <span class="n">bdio_read</span><span class="p">(</span><span class="n">palt_buf</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span><span class="p">(</span><span class="n">rlen</span><span class="p">),</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">(</span><span class="n">fbdio</span><span class="p">))</span>
</span><span id="L-414"><a href="#L-414"><span class="linenos">414</span></a> <span class="k">if</span> <span class="n">rlen</span> <span class="o">!=</span> <span class="n">iread</span><span class="p">:</span>
</span><span id="L-415"><a href="#L-415"><span class="linenos">415</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Error&#39;</span><span class="p">)</span>
</span><span id="L-416"><a href="#L-416"><span class="linenos">416</span></a> <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">item</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">alt_buf</span><span class="p">):</span>
</span><span id="L-417"><a href="#L-417"><span class="linenos">417</span></a> <span class="k">if</span> <span class="n">item</span> <span class="o">==</span> <span class="sa">b</span><span class="s1">&#39;</span><span class="se">\x00</span><span class="s1">&#39;</span><span class="p">:</span>
</span><span id="L-418"><a href="#L-418"><span class="linenos">418</span></a> <span class="n">alt_buf</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="sa">b</span><span class="s1">&#39; &#39;</span>
</span><span id="L-419"><a href="#L-419"><span class="linenos">419</span></a> <span class="n">tmp_string</span> <span class="o">=</span> <span class="p">(</span><span class="n">alt_buf</span><span class="p">[:]</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s2">&quot;utf-8&quot;</span><span class="p">))</span><span class="o">.</span><span class="n">rstrip</span><span class="p">()</span>
</span><span id="L-420"><a href="#L-420"><span class="linenos">420</span></a> <span class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
</span><span id="L-421"><a href="#L-421"><span class="linenos">421</span></a> <span class="n">ensemble_name</span> <span class="o">=</span> <span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;ENSEMBLE=&#39;</span><span class="p">)</span>
</span><span id="L-422"><a href="#L-422"><span class="linenos">422</span></a> <span class="n">volume</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;L0=&#39;</span><span class="p">)))</span>
</span><span id="L-423"><a href="#L-423"><span class="linenos">423</span></a> <span class="n">volume</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;L1=&#39;</span><span class="p">)))</span>
</span><span id="L-424"><a href="#L-424"><span class="linenos">424</span></a> <span class="n">volume</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;L2=&#39;</span><span class="p">)))</span>
</span><span id="L-425"><a href="#L-425"><span class="linenos">425</span></a> <span class="n">volume</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;L3=&#39;</span><span class="p">)))</span>
</span><span id="L-426"><a href="#L-426"><span class="linenos">426</span></a> <span class="n">boundary_conditions</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;BC0=&#39;</span><span class="p">))</span>
</span><span id="L-427"><a href="#L-427"><span class="linenos">427</span></a> <span class="n">boundary_conditions</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;BC1=&#39;</span><span class="p">))</span>
</span><span id="L-428"><a href="#L-428"><span class="linenos">428</span></a> <span class="n">boundary_conditions</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;BC2=&#39;</span><span class="p">))</span>
</span><span id="L-429"><a href="#L-429"><span class="linenos">429</span></a> <span class="n">boundary_conditions</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;BC3=&#39;</span><span class="p">))</span>
</span><span id="L-430"><a href="#L-430"><span class="linenos">430</span></a>
</span><span id="L-431"><a href="#L-431"><span class="linenos">431</span></a> <span class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
</span><span id="L-432"><a href="#L-432"><span class="linenos">432</span></a> <span class="n">corr_name</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">_get_corr_name</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;CORR_NAME=&#39;</span><span class="p">))</span>
</span><span id="L-433"><a href="#L-433"><span class="linenos">433</span></a> <span class="n">corr_type</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;DATATYPE=&#39;</span><span class="p">))</span>
</span><span id="L-434"><a href="#L-434"><span class="linenos">434</span></a> <span class="n">corr_props</span><span class="o">.</span><span class="n">append</span><span class="p">([</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;PROP0=&#39;</span><span class="p">),</span> <span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;PROP1=&#39;</span><span class="p">)])</span>
</span><span id="L-435"><a href="#L-435"><span class="linenos">435</span></a> <span class="k">if</span> <span class="n">d0</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
</span><span id="L-436"><a href="#L-436"><span class="linenos">436</span></a> <span class="n">d0</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;D0=&#39;</span><span class="p">))</span>
</span><span id="L-437"><a href="#L-437"><span class="linenos">437</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="L-438"><a href="#L-438"><span class="linenos">438</span></a> <span class="k">if</span> <span class="n">d0</span> <span class="o">!=</span> <span class="nb">int</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;D0=&#39;</span><span class="p">)):</span>
</span><span id="L-439"><a href="#L-439"><span class="linenos">439</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Error: Varying number of time values&#39;</span><span class="p">)</span>
</span><span id="L-440"><a href="#L-440"><span class="linenos">440</span></a> <span class="k">if</span> <span class="n">d1</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
</span><span id="L-441"><a href="#L-441"><span class="linenos">441</span></a> <span class="n">d1</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;D1=&#39;</span><span class="p">))</span>
</span><span id="L-442"><a href="#L-442"><span class="linenos">442</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="L-443"><a href="#L-443"><span class="linenos">443</span></a> <span class="k">if</span> <span class="n">d1</span> <span class="o">!=</span> <span class="nb">int</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;D1=&#39;</span><span class="p">)):</span>
</span><span id="L-444"><a href="#L-444"><span class="linenos">444</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Error: Varying number of random sources&#39;</span><span class="p">)</span>
</span><span id="L-445"><a href="#L-445"><span class="linenos">445</span></a> <span class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span>
</span><span id="L-446"><a href="#L-446"><span class="linenos">446</span></a> <span class="n">prop_kappa</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;KAPPA=&#39;</span><span class="p">))</span>
</span><span id="L-447"><a href="#L-447"><span class="linenos">447</span></a> <span class="n">prop_source</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;x0=&#39;</span><span class="p">))</span>
</span><span id="L-448"><a href="#L-448"><span class="linenos">448</span></a> <span class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">4</span><span class="p">:</span>
</span><span id="L-449"><a href="#L-449"><span class="linenos">449</span></a> <span class="n">cnfg_no</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;CNFG_ID=&#39;</span><span class="p">))</span>
</span><span id="L-450"><a href="#L-450"><span class="linenos">450</span></a> <span class="k">if</span> <span class="n">stop</span><span class="p">:</span>
</span><span id="L-451"><a href="#L-451"><span class="linenos">451</span></a> <span class="k">if</span> <span class="n">cnfg_no</span> <span class="o">&gt;</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;stop&#39;</span><span class="p">):</span>
</span><span id="L-452"><a href="#L-452"><span class="linenos">452</span></a> <span class="k">break</span>
</span><span id="L-453"><a href="#L-453"><span class="linenos">453</span></a> <span class="n">idl</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">cnfg_no</span><span class="p">)</span>
</span><span id="L-454"><a href="#L-454"><span class="linenos">454</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\r</span><span class="si">%s</span><span class="s1"> </span><span class="si">%i</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="s1">&#39;Reading configuration&#39;</span><span class="p">,</span> <span class="n">cnfg_no</span><span class="p">),</span> <span class="n">end</span><span class="o">=</span><span class="s1">&#39;</span><span class="se">\r</span><span class="s1">&#39;</span><span class="p">)</span>
</span><span id="L-455"><a href="#L-455"><span class="linenos">455</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">idl</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
</span><span id="L-456"><a href="#L-456"><span class="linenos">456</span></a> <span class="n">no_corrs</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">corr_name</span><span class="p">)</span>
</span><span id="L-457"><a href="#L-457"><span class="linenos">457</span></a> <span class="n">data</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="L-458"><a href="#L-458"><span class="linenos">458</span></a> <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">no_corrs</span><span class="p">):</span>
</span><span id="L-459"><a href="#L-459"><span class="linenos">459</span></a> <span class="n">data</span><span class="o">.</span><span class="n">append</span><span class="p">([])</span>
</span><span id="L-460"><a href="#L-460"><span class="linenos">460</span></a>
</span><span id="L-461"><a href="#L-461"><span class="linenos">461</span></a> <span class="n">corr_no</span> <span class="o">=</span> <span class="mi">0</span>
</span><span id="L-462"><a href="#L-462"><span class="linenos">462</span></a>
</span><span id="L-463"><a href="#L-463"><span class="linenos">463</span></a> <span class="n">bdio_close</span><span class="p">(</span><span class="n">fbdio</span><span class="p">)</span>
</span><span id="L-464"><a href="#L-464"><span class="linenos">464</span></a>
</span><span id="L-465"><a href="#L-465"><span class="linenos">465</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">Ensemble: &#39;</span><span class="p">,</span> <span class="n">ensemble_name</span><span class="p">)</span>
</span><span id="L-466"><a href="#L-466"><span class="linenos">466</span></a> <span class="k">if</span> <span class="s1">&#39;alternative_ensemble_name&#39;</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
</span><span id="L-467"><a href="#L-467"><span class="linenos">467</span></a> <span class="n">ensemble_name</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;alternative_ensemble_name&#39;</span><span class="p">)</span>
</span><span id="L-468"><a href="#L-468"><span class="linenos">468</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Ensemble name overwritten to&#39;</span><span class="p">,</span> <span class="n">ensemble_name</span><span class="p">)</span>
</span><span id="L-469"><a href="#L-469"><span class="linenos">469</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Lattice volume: &#39;</span><span class="p">,</span> <span class="n">volume</span><span class="p">)</span>
</span><span id="L-470"><a href="#L-470"><span class="linenos">470</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Boundary conditions: &#39;</span><span class="p">,</span> <span class="n">boundary_conditions</span><span class="p">)</span>
</span><span id="L-471"><a href="#L-471"><span class="linenos">471</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Number of time values: &#39;</span><span class="p">,</span> <span class="n">d0</span><span class="p">)</span>
</span><span id="L-472"><a href="#L-472"><span class="linenos">472</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Number of random sources: &#39;</span><span class="p">,</span> <span class="n">d1</span><span class="p">)</span>
</span><span id="L-473"><a href="#L-473"><span class="linenos">473</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Number of corrs: &#39;</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">corr_name</span><span class="p">))</span>
</span><span id="L-474"><a href="#L-474"><span class="linenos">474</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Number of configurations: &#39;</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">idl</span><span class="p">))</span>
</span><span id="L-475"><a href="#L-475"><span class="linenos">475</span></a>
</span><span id="L-476"><a href="#L-476"><span class="linenos">476</span></a> <span class="n">corr_kappa</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># Contains kappa values for both propagators of given correlation function</span>
</span><span id="L-477"><a href="#L-477"><span class="linenos">477</span></a> <span class="n">corr_source</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="L-478"><a href="#L-478"><span class="linenos">478</span></a> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">corr_props</span><span class="p">:</span>
</span><span id="L-479"><a href="#L-479"><span class="linenos">479</span></a> <span class="n">corr_kappa</span><span class="o">.</span><span class="n">append</span><span class="p">([</span><span class="nb">float</span><span class="p">(</span><span class="n">prop_kappa</span><span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">item</span><span class="p">[</span><span class="mi">0</span><span class="p">])]),</span> <span class="nb">float</span><span class="p">(</span><span class="n">prop_kappa</span><span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">item</span><span class="p">[</span><span class="mi">1</span><span class="p">])])])</span>
</span><span id="L-480"><a href="#L-480"><span class="linenos">480</span></a> <span class="k">if</span> <span class="n">prop_source</span><span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">item</span><span class="p">[</span><span class="mi">0</span><span class="p">])]</span> <span class="o">!=</span> <span class="n">prop_source</span><span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">item</span><span class="p">[</span><span class="mi">1</span><span class="p">])]:</span>
</span><span id="L-481"><a href="#L-481"><span class="linenos">481</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Source position do not match for correlator&#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">item</span><span class="p">))</span>
</span><span id="L-482"><a href="#L-482"><span class="linenos">482</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="L-483"><a href="#L-483"><span class="linenos">483</span></a> <span class="n">corr_source</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">prop_source</span><span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">item</span><span class="p">[</span><span class="mi">0</span><span class="p">])]))</span>
</span><span id="L-484"><a href="#L-484"><span class="linenos">484</span></a>
</span><span id="L-485"><a href="#L-485"><span class="linenos">485</span></a> <span class="k">if</span> <span class="n">stop</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
</span><span id="L-486"><a href="#L-486"><span class="linenos">486</span></a> <span class="n">stop</span> <span class="o">=</span> <span class="n">idl</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
</span><span id="L-487"><a href="#L-487"><span class="linenos">487</span></a> <span class="n">idl_target</span> <span class="o">=</span> <span class="nb">range</span><span class="p">(</span><span class="n">start</span><span class="p">,</span> <span class="n">stop</span> <span class="o">+</span> <span class="mi">1</span><span class="p">,</span> <span class="n">step</span><span class="p">)</span>
</span><span id="L-488"><a href="#L-488"><span class="linenos">488</span></a>
</span><span id="L-489"><a href="#L-489"><span class="linenos">489</span></a> <span class="k">if</span> <span class="nb">set</span><span class="p">(</span><span class="n">idl</span><span class="p">)</span> <span class="o">!=</span> <span class="nb">set</span><span class="p">(</span><span class="n">idl_target</span><span class="p">):</span>
</span><span id="L-490"><a href="#L-490"><span class="linenos">490</span></a> <span class="k">try</span><span class="p">:</span>
</span><span id="L-491"><a href="#L-491"><span class="linenos">491</span></a> <span class="n">indices</span> <span class="o">=</span> <span class="p">[</span><span class="n">idl</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">idl_target</span><span class="p">]</span>
</span><span id="L-492"><a href="#L-492"><span class="linenos">492</span></a> <span class="k">except</span> <span class="ne">ValueError</span> <span class="k">as</span> <span class="n">err</span><span class="p">:</span>
</span><span id="L-493"><a href="#L-493"><span class="linenos">493</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Configurations in file do no match target list!&#39;</span><span class="p">,</span> <span class="n">err</span><span class="p">)</span>
</span><span id="L-494"><a href="#L-494"><span class="linenos">494</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="L-495"><a href="#L-495"><span class="linenos">495</span></a> <span class="n">indices</span> <span class="o">=</span> <span class="kc">None</span>
</span><span id="L-496"><a href="#L-496"><span class="linenos">496</span></a>
</span><span id="L-497"><a href="#L-497"><span class="linenos">497</span></a> <span class="n">result</span> <span class="o">=</span> <span class="p">{}</span>
</span><span id="L-498"><a href="#L-498"><span class="linenos">498</span></a> <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">no_corrs</span><span class="p">):</span>
</span><span id="L-499"><a href="#L-499"><span class="linenos">499</span></a> <span class="n">tmp_corr</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="L-500"><a href="#L-500"><span class="linenos">500</span></a> <span class="n">tmp_data</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">data</span><span class="p">[</span><span class="n">c</span><span class="p">])</span>
</span><span id="L-501"><a href="#L-501"><span class="linenos">501</span></a> <span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">d0</span> <span class="o">-</span> <span class="mi">2</span><span class="p">):</span>
</span><span id="L-502"><a href="#L-502"><span class="linenos">502</span></a> <span class="k">if</span> <span class="n">indices</span><span class="p">:</span>
</span><span id="L-503"><a href="#L-503"><span class="linenos">503</span></a> <span class="n">deltas</span> <span class="o">=</span> <span class="p">[</span><span class="n">tmp_data</span><span class="p">[:,</span> <span class="n">t</span><span class="p">][</span><span class="n">index</span><span class="p">]</span> <span class="k">for</span> <span class="n">index</span> <span class="ow">in</span> <span class="n">indices</span><span class="p">]</span>
</span><span id="L-504"><a href="#L-504"><span class="linenos">504</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="L-505"><a href="#L-505"><span class="linenos">505</span></a> <span class="n">deltas</span> <span class="o">=</span> <span class="n">tmp_data</span><span class="p">[:,</span> <span class="n">t</span><span class="p">]</span>
</span><span id="L-506"><a href="#L-506"><span class="linenos">506</span></a> <span class="n">tmp_corr</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">Obs</span><span class="p">([</span><span class="n">deltas</span><span class="p">],</span> <span class="p">[</span><span class="n">ensemble_name</span><span class="p">],</span> <span class="n">idl</span><span class="o">=</span><span class="p">[</span><span class="n">idl_target</span><span class="p">]))</span>
</span><span id="L-507"><a href="#L-507"><span class="linenos">507</span></a> <span class="n">result</span><span class="p">[(</span><span class="n">corr_name</span><span class="p">[</span><span class="n">c</span><span class="p">],</span> <span class="n">corr_source</span><span class="p">[</span><span class="n">c</span><span class="p">])</span> <span class="o">+</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">corr_kappa</span><span class="p">[</span><span class="n">c</span><span class="p">])]</span> <span class="o">=</span> <span class="n">tmp_corr</span>
</span><span id="L-508"><a href="#L-508"><span class="linenos">508</span></a>
</span><span id="L-509"><a href="#L-509"><span class="linenos">509</span></a> <span class="c1"># Check that all data entries have the same number of configurations</span>
</span><span id="L-510"><a href="#L-510"><span class="linenos">510</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="nb">set</span><span class="p">([</span><span class="n">o</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">N</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="nb">list</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">values</span><span class="p">())]))</span> <span class="o">!=</span> <span class="mi">1</span><span class="p">:</span>
</span><span id="L-511"><a href="#L-511"><span class="linenos">511</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Error: Not all correlators have the same number of configurations. bdio file is possibly corrupted.&#39;</span><span class="p">)</span>
</span><span id="L-512"><a href="#L-512"><span class="linenos">512</span></a>
</span><span id="L-513"><a href="#L-513"><span class="linenos">513</span></a> <span class="k">return</span> <span class="n">result</span>
</span><span id="L-514"><a href="#L-514"><span class="linenos">514</span></a>
</span><span id="L-515"><a href="#L-515"><span class="linenos">515</span></a>
</span><span id="L-516"><a href="#L-516"><span class="linenos">516</span></a><span class="k">def</span> <span class="nf">read_dSdm</span><span class="p">(</span><span class="n">file_path</span><span class="p">,</span> <span class="n">bdio_path</span><span class="o">=</span><span class="s1">&#39;./libbdio.so&#39;</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
</span><span id="L-517"><a href="#L-517"><span class="linenos">517</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot; Extract dSdm data from a bdio file and return it as a dictionary</span>
</span><span id="L-518"><a href="#L-518"><span class="linenos">518</span></a>
</span><span id="L-519"><a href="#L-519"><span class="linenos">519</span></a><span class="sd"> The dictionary can be accessed with a tuple consisting of (type, kappa)</span>
</span><span id="L-520"><a href="#L-520"><span class="linenos">520</span></a>
</span><span id="L-521"><a href="#L-521"><span class="linenos">521</span></a><span class="sd"> read_dSdm requires bdio to be compiled into a shared library. This can be achieved by</span>
</span><span id="L-522"><a href="#L-522"><span class="linenos">522</span></a><span class="sd"> adding the flag -fPIC to CC and changing the all target to</span>
</span><span id="L-523"><a href="#L-523"><span class="linenos">523</span></a>
</span><span id="L-524"><a href="#L-524"><span class="linenos">524</span></a><span class="sd"> all: bdio.o $(LIBDIR)</span>
</span><span id="L-525"><a href="#L-525"><span class="linenos">525</span></a><span class="sd"> gcc -shared -Wl,-soname,libbdio.so -o $(BUILDDIR)/libbdio.so $(BUILDDIR)/bdio.o</span>
</span><span id="L-526"><a href="#L-526"><span class="linenos">526</span></a><span class="sd"> cp $(BUILDDIR)/libbdio.so $(LIBDIR)/</span>
</span><span id="L-527"><a href="#L-527"><span class="linenos">527</span></a>
</span><span id="L-528"><a href="#L-528"><span class="linenos">528</span></a><span class="sd"> Parameters</span>
</span><span id="L-529"><a href="#L-529"><span class="linenos">529</span></a><span class="sd"> ----------</span>
</span><span id="L-530"><a href="#L-530"><span class="linenos">530</span></a><span class="sd"> file_path : str</span>
</span><span id="L-531"><a href="#L-531"><span class="linenos">531</span></a><span class="sd"> path to the bdio file</span>
</span><span id="L-532"><a href="#L-532"><span class="linenos">532</span></a><span class="sd"> bdio_path : str</span>
</span><span id="L-533"><a href="#L-533"><span class="linenos">533</span></a><span class="sd"> path to the shared bdio library libbdio.so (default ./libbdio.so)</span>
</span><span id="L-534"><a href="#L-534"><span class="linenos">534</span></a><span class="sd"> start : int</span>
</span><span id="L-535"><a href="#L-535"><span class="linenos">535</span></a><span class="sd"> The first configuration to be read (default 1)</span>
</span><span id="L-536"><a href="#L-536"><span class="linenos">536</span></a><span class="sd"> stop : int</span>
</span><span id="L-537"><a href="#L-537"><span class="linenos">537</span></a><span class="sd"> The last configuration to be read (default None)</span>
</span><span id="L-538"><a href="#L-538"><span class="linenos">538</span></a><span class="sd"> step : int</span>
</span><span id="L-539"><a href="#L-539"><span class="linenos">539</span></a><span class="sd"> Fixed step size between two measurements (default 1)</span>
</span><span id="L-540"><a href="#L-540"><span class="linenos">540</span></a><span class="sd"> alternative_ensemble_name : str</span>
</span><span id="L-541"><a href="#L-541"><span class="linenos">541</span></a><span class="sd"> Manually overwrite ensemble name</span>
</span><span id="L-542"><a href="#L-542"><span class="linenos">542</span></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="L-543"><a href="#L-543"><span class="linenos">543</span></a>
</span><span id="L-544"><a href="#L-544"><span class="linenos">544</span></a> <span class="n">start</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;start&#39;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
</span><span id="L-545"><a href="#L-545"><span class="linenos">545</span></a> <span class="n">stop</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;stop&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
</span><span id="L-546"><a href="#L-546"><span class="linenos">546</span></a> <span class="n">step</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;step&#39;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
</span><span id="L-547"><a href="#L-547"><span class="linenos">547</span></a>
</span><span id="L-548"><a href="#L-548"><span class="linenos">548</span></a> <span class="n">bdio</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">cdll</span><span class="o">.</span><span class="n">LoadLibrary</span><span class="p">(</span><span class="n">bdio_path</span><span class="p">)</span>
</span><span id="L-549"><a href="#L-549"><span class="linenos">549</span></a>
</span><span id="L-550"><a href="#L-550"><span class="linenos">550</span></a> <span class="n">bdio_open</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_open</span>
</span><span id="L-551"><a href="#L-551"><span class="linenos">551</span></a> <span class="n">bdio_open</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span>
</span><span id="L-552"><a href="#L-552"><span class="linenos">552</span></a>
</span><span id="L-553"><a href="#L-553"><span class="linenos">553</span></a> <span class="n">bdio_close</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_close</span>
</span><span id="L-554"><a href="#L-554"><span class="linenos">554</span></a> <span class="n">bdio_close</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_int</span>
</span><span id="L-555"><a href="#L-555"><span class="linenos">555</span></a> <span class="n">bdio_close</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="L-556"><a href="#L-556"><span class="linenos">556</span></a>
</span><span id="L-557"><a href="#L-557"><span class="linenos">557</span></a> <span class="n">bdio_seek_record</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_seek_record</span>
</span><span id="L-558"><a href="#L-558"><span class="linenos">558</span></a> <span class="n">bdio_seek_record</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_int</span>
</span><span id="L-559"><a href="#L-559"><span class="linenos">559</span></a> <span class="n">bdio_seek_record</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="L-560"><a href="#L-560"><span class="linenos">560</span></a>
</span><span id="L-561"><a href="#L-561"><span class="linenos">561</span></a> <span class="n">bdio_get_rlen</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_get_rlen</span>
</span><span id="L-562"><a href="#L-562"><span class="linenos">562</span></a> <span class="n">bdio_get_rlen</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_int</span>
</span><span id="L-563"><a href="#L-563"><span class="linenos">563</span></a> <span class="n">bdio_get_rlen</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="L-564"><a href="#L-564"><span class="linenos">564</span></a>
</span><span id="L-565"><a href="#L-565"><span class="linenos">565</span></a> <span class="n">bdio_get_ruinfo</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_get_ruinfo</span>
</span><span id="L-566"><a href="#L-566"><span class="linenos">566</span></a> <span class="n">bdio_get_ruinfo</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_int</span>
</span><span id="L-567"><a href="#L-567"><span class="linenos">567</span></a> <span class="n">bdio_get_ruinfo</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="L-568"><a href="#L-568"><span class="linenos">568</span></a>
</span><span id="L-569"><a href="#L-569"><span class="linenos">569</span></a> <span class="n">bdio_read</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_read</span>
</span><span id="L-570"><a href="#L-570"><span class="linenos">570</span></a> <span class="n">bdio_read</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span>
</span><span id="L-571"><a href="#L-571"><span class="linenos">571</span></a> <span class="n">bdio_read</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_char_p</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="L-572"><a href="#L-572"><span class="linenos">572</span></a>
</span><span id="L-573"><a href="#L-573"><span class="linenos">573</span></a> <span class="n">bdio_read_f64</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_read_f64</span>
</span><span id="L-574"><a href="#L-574"><span class="linenos">574</span></a> <span class="n">bdio_read_f64</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span>
</span><span id="L-575"><a href="#L-575"><span class="linenos">575</span></a> <span class="n">bdio_read_f64</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="L-576"><a href="#L-576"><span class="linenos">576</span></a>
</span><span id="L-577"><a href="#L-577"><span class="linenos">577</span></a> <span class="n">b_path</span> <span class="o">=</span> <span class="n">file_path</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span>
</span><span id="L-578"><a href="#L-578"><span class="linenos">578</span></a> <span class="n">read</span> <span class="o">=</span> <span class="s1">&#39;r&#39;</span>
</span><span id="L-579"><a href="#L-579"><span class="linenos">579</span></a> <span class="n">b_read</span> <span class="o">=</span> <span class="n">read</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span>
</span><span id="L-580"><a href="#L-580"><span class="linenos">580</span></a> <span class="n">form</span> <span class="o">=</span> <span class="s1">&#39;Generic Correlator Format 1.0&#39;</span>
</span><span id="L-581"><a href="#L-581"><span class="linenos">581</span></a> <span class="n">b_form</span> <span class="o">=</span> <span class="n">form</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span>
</span><span id="L-582"><a href="#L-582"><span class="linenos">582</span></a>
</span><span id="L-583"><a href="#L-583"><span class="linenos">583</span></a> <span class="n">ensemble_name</span> <span class="o">=</span> <span class="s1">&#39;&#39;</span>
</span><span id="L-584"><a href="#L-584"><span class="linenos">584</span></a> <span class="n">volume</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># lattice volume</span>
</span><span id="L-585"><a href="#L-585"><span class="linenos">585</span></a> <span class="n">boundary_conditions</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="L-586"><a href="#L-586"><span class="linenos">586</span></a> <span class="n">corr_name</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># Contains correlator names</span>
</span><span id="L-587"><a href="#L-587"><span class="linenos">587</span></a> <span class="n">corr_type</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># Contains correlator data type (important for reading out numerical data)</span>
</span><span id="L-588"><a href="#L-588"><span class="linenos">588</span></a> <span class="n">corr_props</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># Contains propagator types (Component of corr_kappa)</span>
</span><span id="L-589"><a href="#L-589"><span class="linenos">589</span></a> <span class="n">d0</span> <span class="o">=</span> <span class="mi">0</span> <span class="c1"># tvals</span>
</span><span id="L-590"><a href="#L-590"><span class="linenos">590</span></a> <span class="c1"># d1 = 0 # nnoise</span>
</span><span id="L-591"><a href="#L-591"><span class="linenos">591</span></a> <span class="n">prop_kappa</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># Contains propagator kappas (Component of corr_kappa)</span>
</span><span id="L-592"><a href="#L-592"><span class="linenos">592</span></a> <span class="c1"># Check noise type for multiple replica?</span>
</span><span id="L-593"><a href="#L-593"><span class="linenos">593</span></a> <span class="n">corr_no</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
</span><span id="L-594"><a href="#L-594"><span class="linenos">594</span></a> <span class="n">data</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="L-595"><a href="#L-595"><span class="linenos">595</span></a> <span class="n">idl</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="L-596"><a href="#L-596"><span class="linenos">596</span></a>
</span><span id="L-597"><a href="#L-597"><span class="linenos">597</span></a> <span class="n">fbdio</span> <span class="o">=</span> <span class="n">bdio_open</span><span class="p">(</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_char_p</span><span class="p">(</span><span class="n">b_path</span><span class="p">),</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_char_p</span><span class="p">(</span><span class="n">b_read</span><span class="p">),</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_char_p</span><span class="p">(</span><span class="n">b_form</span><span class="p">))</span>
</span><span id="L-598"><a href="#L-598"><span class="linenos">598</span></a>
</span><span id="L-599"><a href="#L-599"><span class="linenos">599</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Reading of bdio file started&#39;</span><span class="p">)</span>
</span><span id="L-600"><a href="#L-600"><span class="linenos">600</span></a> <span class="k">while</span> <span class="kc">True</span><span class="p">:</span>
</span><span id="L-601"><a href="#L-601"><span class="linenos">601</span></a> <span class="n">bdio_seek_record</span><span class="p">(</span><span class="n">fbdio</span><span class="p">)</span>
</span><span id="L-602"><a href="#L-602"><span class="linenos">602</span></a> <span class="n">ruinfo</span> <span class="o">=</span> <span class="n">bdio_get_ruinfo</span><span class="p">(</span><span class="n">fbdio</span><span class="p">)</span>
</span><span id="L-603"><a href="#L-603"><span class="linenos">603</span></a> <span class="k">if</span> <span class="n">ruinfo</span> <span class="o">&lt;</span> <span class="mi">0</span><span class="p">:</span>
</span><span id="L-604"><a href="#L-604"><span class="linenos">604</span></a> <span class="c1"># EOF reached</span>
</span><span id="L-605"><a href="#L-605"><span class="linenos">605</span></a> <span class="k">break</span>
</span><span id="L-606"><a href="#L-606"><span class="linenos">606</span></a> <span class="n">rlen</span> <span class="o">=</span> <span class="n">bdio_get_rlen</span><span class="p">(</span><span class="n">fbdio</span><span class="p">)</span>
</span><span id="L-607"><a href="#L-607"><span class="linenos">607</span></a> <span class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">5</span><span class="p">:</span>
</span><span id="L-608"><a href="#L-608"><span class="linenos">608</span></a> <span class="n">d_buf</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_double</span> <span class="o">*</span> <span class="p">(</span><span class="mi">2</span> <span class="o">+</span> <span class="n">d0</span><span class="p">)</span>
</span><span id="L-609"><a href="#L-609"><span class="linenos">609</span></a> <span class="n">pd_buf</span> <span class="o">=</span> <span class="n">d_buf</span><span class="p">()</span>
</span><span id="L-610"><a href="#L-610"><span class="linenos">610</span></a> <span class="n">ppd_buf</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">(</span><span class="n">ctypes</span><span class="o">.</span><span class="n">addressof</span><span class="p">(</span><span class="n">pd_buf</span><span class="p">))</span>
</span><span id="L-611"><a href="#L-611"><span class="linenos">611</span></a> <span class="n">bdio_read_f64</span><span class="p">(</span><span class="n">ppd_buf</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span><span class="p">(</span><span class="n">rlen</span><span class="p">),</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">(</span><span class="n">fbdio</span><span class="p">))</span>
</span><span id="L-612"><a href="#L-612"><span class="linenos">612</span></a> <span class="n">tmp_mean</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">pd_buf</span><span class="p">[</span><span class="mi">2</span><span class="p">:]))</span>
</span><span id="L-613"><a href="#L-613"><span class="linenos">613</span></a>
</span><span id="L-614"><a href="#L-614"><span class="linenos">614</span></a> <span class="n">data</span><span class="p">[</span><span class="n">corr_no</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">tmp_mean</span><span class="p">)</span>
</span><span id="L-615"><a href="#L-615"><span class="linenos">615</span></a> <span class="n">corr_no</span> <span class="o">+=</span> <span class="mi">1</span>
</span><span id="L-616"><a href="#L-616"><span class="linenos">616</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="L-617"><a href="#L-617"><span class="linenos">617</span></a> <span class="n">alt_buf</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">create_string_buffer</span><span class="p">(</span><span class="mi">1024</span><span class="p">)</span>
</span><span id="L-618"><a href="#L-618"><span class="linenos">618</span></a> <span class="n">palt_buf</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_char_p</span><span class="p">(</span><span class="n">ctypes</span><span class="o">.</span><span class="n">addressof</span><span class="p">(</span><span class="n">alt_buf</span><span class="p">))</span>
</span><span id="L-619"><a href="#L-619"><span class="linenos">619</span></a> <span class="n">iread</span> <span class="o">=</span> <span class="n">bdio_read</span><span class="p">(</span><span class="n">palt_buf</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span><span class="p">(</span><span class="n">rlen</span><span class="p">),</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">(</span><span class="n">fbdio</span><span class="p">))</span>
</span><span id="L-620"><a href="#L-620"><span class="linenos">620</span></a> <span class="k">if</span> <span class="n">rlen</span> <span class="o">!=</span> <span class="n">iread</span><span class="p">:</span>
</span><span id="L-621"><a href="#L-621"><span class="linenos">621</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Error&#39;</span><span class="p">)</span>
</span><span id="L-622"><a href="#L-622"><span class="linenos">622</span></a> <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">item</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">alt_buf</span><span class="p">):</span>
</span><span id="L-623"><a href="#L-623"><span class="linenos">623</span></a> <span class="k">if</span> <span class="n">item</span> <span class="o">==</span> <span class="sa">b</span><span class="s1">&#39;</span><span class="se">\x00</span><span class="s1">&#39;</span><span class="p">:</span>
</span><span id="L-624"><a href="#L-624"><span class="linenos">624</span></a> <span class="n">alt_buf</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="sa">b</span><span class="s1">&#39; &#39;</span>
</span><span id="L-625"><a href="#L-625"><span class="linenos">625</span></a> <span class="n">tmp_string</span> <span class="o">=</span> <span class="p">(</span><span class="n">alt_buf</span><span class="p">[:]</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s2">&quot;utf-8&quot;</span><span class="p">))</span><span class="o">.</span><span class="n">rstrip</span><span class="p">()</span>
</span><span id="L-626"><a href="#L-626"><span class="linenos">626</span></a> <span class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
</span><span id="L-627"><a href="#L-627"><span class="linenos">627</span></a> <span class="n">creator</span> <span class="o">=</span> <span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;CREATOR=&#39;</span><span class="p">)</span>
</span><span id="L-628"><a href="#L-628"><span class="linenos">628</span></a> <span class="n">ensemble_name</span> <span class="o">=</span> <span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;ENSEMBLE=&#39;</span><span class="p">)</span>
</span><span id="L-629"><a href="#L-629"><span class="linenos">629</span></a> <span class="n">volume</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;L0=&#39;</span><span class="p">)))</span>
</span><span id="L-630"><a href="#L-630"><span class="linenos">630</span></a> <span class="n">volume</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;L1=&#39;</span><span class="p">)))</span>
</span><span id="L-631"><a href="#L-631"><span class="linenos">631</span></a> <span class="n">volume</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;L2=&#39;</span><span class="p">)))</span>
</span><span id="L-632"><a href="#L-632"><span class="linenos">632</span></a> <span class="n">volume</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;L3=&#39;</span><span class="p">)))</span>
</span><span id="L-633"><a href="#L-633"><span class="linenos">633</span></a> <span class="n">boundary_conditions</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;BC0=&#39;</span><span class="p">))</span>
</span><span id="L-634"><a href="#L-634"><span class="linenos">634</span></a> <span class="n">boundary_conditions</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;BC1=&#39;</span><span class="p">))</span>
</span><span id="L-635"><a href="#L-635"><span class="linenos">635</span></a> <span class="n">boundary_conditions</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;BC2=&#39;</span><span class="p">))</span>
</span><span id="L-636"><a href="#L-636"><span class="linenos">636</span></a> <span class="n">boundary_conditions</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;BC3=&#39;</span><span class="p">))</span>
</span><span id="L-637"><a href="#L-637"><span class="linenos">637</span></a>
</span><span id="L-638"><a href="#L-638"><span class="linenos">638</span></a> <span class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
</span><span id="L-639"><a href="#L-639"><span class="linenos">639</span></a> <span class="n">corr_name</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">_get_corr_name</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;CORR_NAME=&#39;</span><span class="p">))</span>
</span><span id="L-640"><a href="#L-640"><span class="linenos">640</span></a> <span class="n">corr_type</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;DATATYPE=&#39;</span><span class="p">))</span>
</span><span id="L-641"><a href="#L-641"><span class="linenos">641</span></a> <span class="n">corr_props</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;PROP0=&#39;</span><span class="p">))</span>
</span><span id="L-642"><a href="#L-642"><span class="linenos">642</span></a> <span class="k">if</span> <span class="n">d0</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
</span><span id="L-643"><a href="#L-643"><span class="linenos">643</span></a> <span class="n">d0</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;D0=&#39;</span><span class="p">))</span>
</span><span id="L-644"><a href="#L-644"><span class="linenos">644</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="L-645"><a href="#L-645"><span class="linenos">645</span></a> <span class="k">if</span> <span class="n">d0</span> <span class="o">!=</span> <span class="nb">int</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;D0=&#39;</span><span class="p">)):</span>
</span><span id="L-646"><a href="#L-646"><span class="linenos">646</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Error: Varying number of time values&#39;</span><span class="p">)</span>
</span><span id="L-647"><a href="#L-647"><span class="linenos">647</span></a> <span class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span>
</span><span id="L-648"><a href="#L-648"><span class="linenos">648</span></a> <span class="n">prop_kappa</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;KAPPA=&#39;</span><span class="p">))</span>
</span><span id="L-649"><a href="#L-649"><span class="linenos">649</span></a> <span class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">4</span><span class="p">:</span>
</span><span id="L-650"><a href="#L-650"><span class="linenos">650</span></a> <span class="n">cnfg_no</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;CNFG_ID=&#39;</span><span class="p">))</span>
</span><span id="L-651"><a href="#L-651"><span class="linenos">651</span></a> <span class="k">if</span> <span class="n">stop</span><span class="p">:</span>
</span><span id="L-652"><a href="#L-652"><span class="linenos">652</span></a> <span class="k">if</span> <span class="n">cnfg_no</span> <span class="o">&gt;</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;stop&#39;</span><span class="p">):</span>
</span><span id="L-653"><a href="#L-653"><span class="linenos">653</span></a> <span class="k">break</span>
</span><span id="L-654"><a href="#L-654"><span class="linenos">654</span></a> <span class="n">idl</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">cnfg_no</span><span class="p">)</span>
</span><span id="L-655"><a href="#L-655"><span class="linenos">655</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\r</span><span class="si">%s</span><span class="s1"> </span><span class="si">%i</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="s1">&#39;Reading configuration&#39;</span><span class="p">,</span> <span class="n">cnfg_no</span><span class="p">),</span> <span class="n">end</span><span class="o">=</span><span class="s1">&#39;</span><span class="se">\r</span><span class="s1">&#39;</span><span class="p">)</span>
</span><span id="L-656"><a href="#L-656"><span class="linenos">656</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">idl</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
</span><span id="L-657"><a href="#L-657"><span class="linenos">657</span></a> <span class="n">no_corrs</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">corr_name</span><span class="p">)</span>
</span><span id="L-658"><a href="#L-658"><span class="linenos">658</span></a> <span class="n">data</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="L-659"><a href="#L-659"><span class="linenos">659</span></a> <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">no_corrs</span><span class="p">):</span>
</span><span id="L-660"><a href="#L-660"><span class="linenos">660</span></a> <span class="n">data</span><span class="o">.</span><span class="n">append</span><span class="p">([])</span>
</span><span id="L-661"><a href="#L-661"><span class="linenos">661</span></a>
</span><span id="L-662"><a href="#L-662"><span class="linenos">662</span></a> <span class="n">corr_no</span> <span class="o">=</span> <span class="mi">0</span>
</span><span id="L-663"><a href="#L-663"><span class="linenos">663</span></a> <span class="n">bdio_close</span><span class="p">(</span><span class="n">fbdio</span><span class="p">)</span>
</span><span id="L-664"><a href="#L-664"><span class="linenos">664</span></a>
</span><span id="L-665"><a href="#L-665"><span class="linenos">665</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">Creator: &#39;</span><span class="p">,</span> <span class="n">creator</span><span class="p">)</span>
</span><span id="L-666"><a href="#L-666"><span class="linenos">666</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Ensemble: &#39;</span><span class="p">,</span> <span class="n">ensemble_name</span><span class="p">)</span>
</span><span id="L-667"><a href="#L-667"><span class="linenos">667</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Lattice volume: &#39;</span><span class="p">,</span> <span class="n">volume</span><span class="p">)</span>
</span><span id="L-668"><a href="#L-668"><span class="linenos">668</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Boundary conditions: &#39;</span><span class="p">,</span> <span class="n">boundary_conditions</span><span class="p">)</span>
</span><span id="L-669"><a href="#L-669"><span class="linenos">669</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Number of random sources: &#39;</span><span class="p">,</span> <span class="n">d0</span><span class="p">)</span>
</span><span id="L-670"><a href="#L-670"><span class="linenos">670</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Number of corrs: &#39;</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">corr_name</span><span class="p">))</span>
</span><span id="L-671"><a href="#L-671"><span class="linenos">671</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Number of configurations: &#39;</span><span class="p">,</span> <span class="n">cnfg_no</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
</span><span id="L-672"><a href="#L-672"><span class="linenos">672</span></a>
</span><span id="L-673"><a href="#L-673"><span class="linenos">673</span></a> <span class="n">corr_kappa</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># Contains kappa values for both propagators of given correlation function</span>
</span><span id="L-674"><a href="#L-674"><span class="linenos">674</span></a> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">corr_props</span><span class="p">:</span>
</span><span id="L-675"><a href="#L-675"><span class="linenos">675</span></a> <span class="n">corr_kappa</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="n">prop_kappa</span><span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">item</span><span class="p">)]))</span>
</span><span id="L-676"><a href="#L-676"><span class="linenos">676</span></a>
</span><span id="L-677"><a href="#L-677"><span class="linenos">677</span></a> <span class="k">if</span> <span class="n">stop</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
</span><span id="L-678"><a href="#L-678"><span class="linenos">678</span></a> <span class="n">stop</span> <span class="o">=</span> <span class="n">idl</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
</span><span id="L-679"><a href="#L-679"><span class="linenos">679</span></a> <span class="n">idl_target</span> <span class="o">=</span> <span class="nb">range</span><span class="p">(</span><span class="n">start</span><span class="p">,</span> <span class="n">stop</span> <span class="o">+</span> <span class="mi">1</span><span class="p">,</span> <span class="n">step</span><span class="p">)</span>
</span><span id="L-680"><a href="#L-680"><span class="linenos">680</span></a> <span class="k">try</span><span class="p">:</span>
</span><span id="L-681"><a href="#L-681"><span class="linenos">681</span></a> <span class="n">indices</span> <span class="o">=</span> <span class="p">[</span><span class="n">idl</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">idl_target</span><span class="p">]</span>
</span><span id="L-682"><a href="#L-682"><span class="linenos">682</span></a> <span class="k">except</span> <span class="ne">ValueError</span> <span class="k">as</span> <span class="n">err</span><span class="p">:</span>
</span><span id="L-683"><a href="#L-683"><span class="linenos">683</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Configurations in file do no match target list!&#39;</span><span class="p">,</span> <span class="n">err</span><span class="p">)</span>
</span><span id="L-684"><a href="#L-684"><span class="linenos">684</span></a>
</span><span id="L-685"><a href="#L-685"><span class="linenos">685</span></a> <span class="n">result</span> <span class="o">=</span> <span class="p">{}</span>
</span><span id="L-686"><a href="#L-686"><span class="linenos">686</span></a> <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">no_corrs</span><span class="p">):</span>
</span><span id="L-687"><a href="#L-687"><span class="linenos">687</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">asarray</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">c</span><span class="p">])[</span><span class="n">index</span><span class="p">]</span> <span class="k">for</span> <span class="n">index</span> <span class="ow">in</span> <span class="n">indices</span><span class="p">]</span>
</span><span id="L-688"><a href="#L-688"><span class="linenos">688</span></a> <span class="n">result</span><span class="p">[(</span><span class="n">corr_name</span><span class="p">[</span><span class="n">c</span><span class="p">],</span> <span class="nb">str</span><span class="p">(</span><span class="n">corr_kappa</span><span class="p">[</span><span class="n">c</span><span class="p">]))]</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">ensemble_name</span><span class="p">],</span> <span class="n">idl</span><span class="o">=</span><span class="p">[</span><span class="n">idl_target</span><span class="p">])</span>
</span><span id="L-689"><a href="#L-689"><span class="linenos">689</span></a>
</span><span id="L-690"><a href="#L-690"><span class="linenos">690</span></a> <span class="c1"># Check that all data entries have the same number of configurations</span>
</span><span id="L-691"><a href="#L-691"><span class="linenos">691</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="nb">set</span><span class="p">([</span><span class="n">o</span><span class="o">.</span><span class="n">N</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="nb">list</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">values</span><span class="p">())]))</span> <span class="o">!=</span> <span class="mi">1</span><span class="p">:</span>
</span><span id="L-692"><a href="#L-692"><span class="linenos">692</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Error: Not all correlators have the same number of configurations. bdio file is possibly corrupted.&#39;</span><span class="p">)</span>
</span><span id="L-693"><a href="#L-693"><span class="linenos">693</span></a>
</span><span id="L-694"><a href="#L-694"><span class="linenos">694</span></a> <span class="k">return</span> <span class="n">result</span>
</span></pre></div>
</section>
<section id="read_ADerrors">
<input id="read_ADerrors-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">read_ADerrors</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">file_path</span>, </span><span class="param"><span class="n">bdio_path</span><span class="o">=</span><span class="s1">&#39;./libbdio.so&#39;</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="read_ADerrors-view-source"><span>View Source</span></label>
</div>
<a class="headerlink" href="#read_ADerrors"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="read_ADerrors-8"><a href="#read_ADerrors-8"><span class="linenos"> 8</span></a><span class="k">def</span> <span class="nf">read_ADerrors</span><span class="p">(</span><span class="n">file_path</span><span class="p">,</span> <span class="n">bdio_path</span><span class="o">=</span><span class="s1">&#39;./libbdio.so&#39;</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
</span><span id="read_ADerrors-9"><a href="#read_ADerrors-9"><span class="linenos"> 9</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot; Extract generic MCMC data from a bdio file</span>
</span><span id="read_ADerrors-10"><a href="#read_ADerrors-10"><span class="linenos"> 10</span></a>
</span><span id="read_ADerrors-11"><a href="#read_ADerrors-11"><span class="linenos"> 11</span></a><span class="sd"> read_ADerrors requires bdio to be compiled into a shared library. This can be achieved by</span>
</span><span id="read_ADerrors-12"><a href="#read_ADerrors-12"><span class="linenos"> 12</span></a><span class="sd"> adding the flag -fPIC to CC and changing the all target to</span>
</span><span id="read_ADerrors-13"><a href="#read_ADerrors-13"><span class="linenos"> 13</span></a>
</span><span id="read_ADerrors-14"><a href="#read_ADerrors-14"><span class="linenos"> 14</span></a><span class="sd"> all: bdio.o $(LIBDIR)</span>
</span><span id="read_ADerrors-15"><a href="#read_ADerrors-15"><span class="linenos"> 15</span></a><span class="sd"> gcc -shared -Wl,-soname,libbdio.so -o $(BUILDDIR)/libbdio.so $(BUILDDIR)/bdio.o</span>
</span><span id="read_ADerrors-16"><a href="#read_ADerrors-16"><span class="linenos"> 16</span></a><span class="sd"> cp $(BUILDDIR)/libbdio.so $(LIBDIR)/</span>
</span><span id="read_ADerrors-17"><a href="#read_ADerrors-17"><span class="linenos"> 17</span></a>
</span><span id="read_ADerrors-18"><a href="#read_ADerrors-18"><span class="linenos"> 18</span></a><span class="sd"> Parameters</span>
</span><span id="read_ADerrors-19"><a href="#read_ADerrors-19"><span class="linenos"> 19</span></a><span class="sd"> ----------</span>
</span><span id="read_ADerrors-20"><a href="#read_ADerrors-20"><span class="linenos"> 20</span></a><span class="sd"> file_path -- path to the bdio file</span>
</span><span id="read_ADerrors-21"><a href="#read_ADerrors-21"><span class="linenos"> 21</span></a><span class="sd"> bdio_path -- path to the shared bdio library libbdio.so (default ./libbdio.so)</span>
</span><span id="read_ADerrors-22"><a href="#read_ADerrors-22"><span class="linenos"> 22</span></a>
</span><span id="read_ADerrors-23"><a href="#read_ADerrors-23"><span class="linenos"> 23</span></a><span class="sd"> Returns</span>
</span><span id="read_ADerrors-24"><a href="#read_ADerrors-24"><span class="linenos"> 24</span></a><span class="sd"> -------</span>
</span><span id="read_ADerrors-25"><a href="#read_ADerrors-25"><span class="linenos"> 25</span></a><span class="sd"> data : List[Obs]</span>
</span><span id="read_ADerrors-26"><a href="#read_ADerrors-26"><span class="linenos"> 26</span></a><span class="sd"> Extracted data</span>
</span><span id="read_ADerrors-27"><a href="#read_ADerrors-27"><span class="linenos"> 27</span></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="read_ADerrors-28"><a href="#read_ADerrors-28"><span class="linenos"> 28</span></a> <span class="n">bdio</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">cdll</span><span class="o">.</span><span class="n">LoadLibrary</span><span class="p">(</span><span class="n">bdio_path</span><span class="p">)</span>
</span><span id="read_ADerrors-29"><a href="#read_ADerrors-29"><span class="linenos"> 29</span></a>
</span><span id="read_ADerrors-30"><a href="#read_ADerrors-30"><span class="linenos"> 30</span></a> <span class="n">bdio_open</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_open</span>
</span><span id="read_ADerrors-31"><a href="#read_ADerrors-31"><span class="linenos"> 31</span></a> <span class="n">bdio_open</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span>
</span><span id="read_ADerrors-32"><a href="#read_ADerrors-32"><span class="linenos"> 32</span></a>
</span><span id="read_ADerrors-33"><a href="#read_ADerrors-33"><span class="linenos"> 33</span></a> <span class="n">bdio_close</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_close</span>
</span><span id="read_ADerrors-34"><a href="#read_ADerrors-34"><span class="linenos"> 34</span></a> <span class="n">bdio_close</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_int</span>
</span><span id="read_ADerrors-35"><a href="#read_ADerrors-35"><span class="linenos"> 35</span></a> <span class="n">bdio_close</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="read_ADerrors-36"><a href="#read_ADerrors-36"><span class="linenos"> 36</span></a>
</span><span id="read_ADerrors-37"><a href="#read_ADerrors-37"><span class="linenos"> 37</span></a> <span class="n">bdio_seek_record</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_seek_record</span>
</span><span id="read_ADerrors-38"><a href="#read_ADerrors-38"><span class="linenos"> 38</span></a> <span class="n">bdio_seek_record</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_int</span>
</span><span id="read_ADerrors-39"><a href="#read_ADerrors-39"><span class="linenos"> 39</span></a> <span class="n">bdio_seek_record</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="read_ADerrors-40"><a href="#read_ADerrors-40"><span class="linenos"> 40</span></a>
</span><span id="read_ADerrors-41"><a href="#read_ADerrors-41"><span class="linenos"> 41</span></a> <span class="n">bdio_get_rlen</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_get_rlen</span>
</span><span id="read_ADerrors-42"><a href="#read_ADerrors-42"><span class="linenos"> 42</span></a> <span class="n">bdio_get_rlen</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_int</span>
</span><span id="read_ADerrors-43"><a href="#read_ADerrors-43"><span class="linenos"> 43</span></a> <span class="n">bdio_get_rlen</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="read_ADerrors-44"><a href="#read_ADerrors-44"><span class="linenos"> 44</span></a>
</span><span id="read_ADerrors-45"><a href="#read_ADerrors-45"><span class="linenos"> 45</span></a> <span class="n">bdio_get_ruinfo</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_get_ruinfo</span>
</span><span id="read_ADerrors-46"><a href="#read_ADerrors-46"><span class="linenos"> 46</span></a> <span class="n">bdio_get_ruinfo</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_int</span>
</span><span id="read_ADerrors-47"><a href="#read_ADerrors-47"><span class="linenos"> 47</span></a> <span class="n">bdio_get_ruinfo</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="read_ADerrors-48"><a href="#read_ADerrors-48"><span class="linenos"> 48</span></a>
</span><span id="read_ADerrors-49"><a href="#read_ADerrors-49"><span class="linenos"> 49</span></a> <span class="n">bdio_read</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_read</span>
</span><span id="read_ADerrors-50"><a href="#read_ADerrors-50"><span class="linenos"> 50</span></a> <span class="n">bdio_read</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span>
</span><span id="read_ADerrors-51"><a href="#read_ADerrors-51"><span class="linenos"> 51</span></a> <span class="n">bdio_read</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_char_p</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="read_ADerrors-52"><a href="#read_ADerrors-52"><span class="linenos"> 52</span></a>
</span><span id="read_ADerrors-53"><a href="#read_ADerrors-53"><span class="linenos"> 53</span></a> <span class="n">bdio_read_f64</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_read_f64</span>
</span><span id="read_ADerrors-54"><a href="#read_ADerrors-54"><span class="linenos"> 54</span></a> <span class="n">bdio_read_f64</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span>
</span><span id="read_ADerrors-55"><a href="#read_ADerrors-55"><span class="linenos"> 55</span></a> <span class="n">bdio_read_f64</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="read_ADerrors-56"><a href="#read_ADerrors-56"><span class="linenos"> 56</span></a>
</span><span id="read_ADerrors-57"><a href="#read_ADerrors-57"><span class="linenos"> 57</span></a> <span class="n">bdio_read_int32</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_read_int32</span>
</span><span id="read_ADerrors-58"><a href="#read_ADerrors-58"><span class="linenos"> 58</span></a> <span class="n">bdio_read_int32</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span>
</span><span id="read_ADerrors-59"><a href="#read_ADerrors-59"><span class="linenos"> 59</span></a> <span class="n">bdio_read_int32</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="read_ADerrors-60"><a href="#read_ADerrors-60"><span class="linenos"> 60</span></a>
</span><span id="read_ADerrors-61"><a href="#read_ADerrors-61"><span class="linenos"> 61</span></a> <span class="n">b_path</span> <span class="o">=</span> <span class="n">file_path</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span>
</span><span id="read_ADerrors-62"><a href="#read_ADerrors-62"><span class="linenos"> 62</span></a> <span class="n">read</span> <span class="o">=</span> <span class="s1">&#39;r&#39;</span>
</span><span id="read_ADerrors-63"><a href="#read_ADerrors-63"><span class="linenos"> 63</span></a> <span class="n">b_read</span> <span class="o">=</span> <span class="n">read</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span>
</span><span id="read_ADerrors-64"><a href="#read_ADerrors-64"><span class="linenos"> 64</span></a>
</span><span id="read_ADerrors-65"><a href="#read_ADerrors-65"><span class="linenos"> 65</span></a> <span class="n">fbdio</span> <span class="o">=</span> <span class="n">bdio_open</span><span class="p">(</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_char_p</span><span class="p">(</span><span class="n">b_path</span><span class="p">),</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_char_p</span><span class="p">(</span><span class="n">b_read</span><span class="p">),</span> <span class="kc">None</span><span class="p">)</span>
</span><span id="read_ADerrors-66"><a href="#read_ADerrors-66"><span class="linenos"> 66</span></a>
</span><span id="read_ADerrors-67"><a href="#read_ADerrors-67"><span class="linenos"> 67</span></a> <span class="n">return_list</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="read_ADerrors-68"><a href="#read_ADerrors-68"><span class="linenos"> 68</span></a>
</span><span id="read_ADerrors-69"><a href="#read_ADerrors-69"><span class="linenos"> 69</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Reading of bdio file started&#39;</span><span class="p">)</span>
</span><span id="read_ADerrors-70"><a href="#read_ADerrors-70"><span class="linenos"> 70</span></a> <span class="k">while</span> <span class="kc">True</span><span class="p">:</span>
</span><span id="read_ADerrors-71"><a href="#read_ADerrors-71"><span class="linenos"> 71</span></a> <span class="n">bdio_seek_record</span><span class="p">(</span><span class="n">fbdio</span><span class="p">)</span>
</span><span id="read_ADerrors-72"><a href="#read_ADerrors-72"><span class="linenos"> 72</span></a> <span class="n">ruinfo</span> <span class="o">=</span> <span class="n">bdio_get_ruinfo</span><span class="p">(</span><span class="n">fbdio</span><span class="p">)</span>
</span><span id="read_ADerrors-73"><a href="#read_ADerrors-73"><span class="linenos"> 73</span></a>
</span><span id="read_ADerrors-74"><a href="#read_ADerrors-74"><span class="linenos"> 74</span></a> <span class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">7</span><span class="p">:</span>
</span><span id="read_ADerrors-75"><a href="#read_ADerrors-75"><span class="linenos"> 75</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;MD5sum found&#39;</span><span class="p">)</span> <span class="c1"># For now we just ignore these entries and do not perform any checks on them</span>
</span><span id="read_ADerrors-76"><a href="#read_ADerrors-76"><span class="linenos"> 76</span></a> <span class="k">continue</span>
</span><span id="read_ADerrors-77"><a href="#read_ADerrors-77"><span class="linenos"> 77</span></a>
</span><span id="read_ADerrors-78"><a href="#read_ADerrors-78"><span class="linenos"> 78</span></a> <span class="k">if</span> <span class="n">ruinfo</span> <span class="o">&lt;</span> <span class="mi">0</span><span class="p">:</span>
</span><span id="read_ADerrors-79"><a href="#read_ADerrors-79"><span class="linenos"> 79</span></a> <span class="c1"># EOF reached</span>
</span><span id="read_ADerrors-80"><a href="#read_ADerrors-80"><span class="linenos"> 80</span></a> <span class="k">break</span>
</span><span id="read_ADerrors-81"><a href="#read_ADerrors-81"><span class="linenos"> 81</span></a> <span class="n">bdio_get_rlen</span><span class="p">(</span><span class="n">fbdio</span><span class="p">)</span>
</span><span id="read_ADerrors-82"><a href="#read_ADerrors-82"><span class="linenos"> 82</span></a>
</span><span id="read_ADerrors-83"><a href="#read_ADerrors-83"><span class="linenos"> 83</span></a> <span class="k">def</span> <span class="nf">read_c_double</span><span class="p">():</span>
</span><span id="read_ADerrors-84"><a href="#read_ADerrors-84"><span class="linenos"> 84</span></a> <span class="n">d_buf</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_double</span>
</span><span id="read_ADerrors-85"><a href="#read_ADerrors-85"><span class="linenos"> 85</span></a> <span class="n">pd_buf</span> <span class="o">=</span> <span class="n">d_buf</span><span class="p">()</span>
</span><span id="read_ADerrors-86"><a href="#read_ADerrors-86"><span class="linenos"> 86</span></a> <span class="n">ppd_buf</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">(</span><span class="n">ctypes</span><span class="o">.</span><span class="n">addressof</span><span class="p">(</span><span class="n">pd_buf</span><span class="p">))</span>
</span><span id="read_ADerrors-87"><a href="#read_ADerrors-87"><span class="linenos"> 87</span></a> <span class="n">bdio_read_f64</span><span class="p">(</span><span class="n">ppd_buf</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span><span class="p">(</span><span class="mi">8</span><span class="p">),</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">(</span><span class="n">fbdio</span><span class="p">))</span>
</span><span id="read_ADerrors-88"><a href="#read_ADerrors-88"><span class="linenos"> 88</span></a> <span class="k">return</span> <span class="n">pd_buf</span><span class="o">.</span><span class="n">value</span>
</span><span id="read_ADerrors-89"><a href="#read_ADerrors-89"><span class="linenos"> 89</span></a>
</span><span id="read_ADerrors-90"><a href="#read_ADerrors-90"><span class="linenos"> 90</span></a> <span class="n">mean</span> <span class="o">=</span> <span class="n">read_c_double</span><span class="p">()</span>
</span><span id="read_ADerrors-91"><a href="#read_ADerrors-91"><span class="linenos"> 91</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;mean&#39;</span><span class="p">,</span> <span class="n">mean</span><span class="p">)</span>
</span><span id="read_ADerrors-92"><a href="#read_ADerrors-92"><span class="linenos"> 92</span></a>
</span><span id="read_ADerrors-93"><a href="#read_ADerrors-93"><span class="linenos"> 93</span></a> <span class="k">def</span> <span class="nf">read_c_size_t</span><span class="p">():</span>
</span><span id="read_ADerrors-94"><a href="#read_ADerrors-94"><span class="linenos"> 94</span></a> <span class="n">d_buf</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span>
</span><span id="read_ADerrors-95"><a href="#read_ADerrors-95"><span class="linenos"> 95</span></a> <span class="n">pd_buf</span> <span class="o">=</span> <span class="n">d_buf</span><span class="p">()</span>
</span><span id="read_ADerrors-96"><a href="#read_ADerrors-96"><span class="linenos"> 96</span></a> <span class="n">ppd_buf</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">(</span><span class="n">ctypes</span><span class="o">.</span><span class="n">addressof</span><span class="p">(</span><span class="n">pd_buf</span><span class="p">))</span>
</span><span id="read_ADerrors-97"><a href="#read_ADerrors-97"><span class="linenos"> 97</span></a> <span class="n">bdio_read_int32</span><span class="p">(</span><span class="n">ppd_buf</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span><span class="p">(</span><span class="mi">4</span><span class="p">),</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">(</span><span class="n">fbdio</span><span class="p">))</span>
</span><span id="read_ADerrors-98"><a href="#read_ADerrors-98"><span class="linenos"> 98</span></a> <span class="k">return</span> <span class="n">pd_buf</span><span class="o">.</span><span class="n">value</span>
</span><span id="read_ADerrors-99"><a href="#read_ADerrors-99"><span class="linenos"> 99</span></a>
</span><span id="read_ADerrors-100"><a href="#read_ADerrors-100"><span class="linenos">100</span></a> <span class="n">neid</span> <span class="o">=</span> <span class="n">read_c_size_t</span><span class="p">()</span>
</span><span id="read_ADerrors-101"><a href="#read_ADerrors-101"><span class="linenos">101</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;neid&#39;</span><span class="p">,</span> <span class="n">neid</span><span class="p">)</span>
</span><span id="read_ADerrors-102"><a href="#read_ADerrors-102"><span class="linenos">102</span></a>
</span><span id="read_ADerrors-103"><a href="#read_ADerrors-103"><span class="linenos">103</span></a> <span class="n">ndata</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="read_ADerrors-104"><a href="#read_ADerrors-104"><span class="linenos">104</span></a> <span class="k">for</span> <span class="n">index</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">neid</span><span class="p">):</span>
</span><span id="read_ADerrors-105"><a href="#read_ADerrors-105"><span class="linenos">105</span></a> <span class="n">ndata</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">read_c_size_t</span><span class="p">())</span>
</span><span id="read_ADerrors-106"><a href="#read_ADerrors-106"><span class="linenos">106</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;ndata&#39;</span><span class="p">,</span> <span class="n">ndata</span><span class="p">)</span>
</span><span id="read_ADerrors-107"><a href="#read_ADerrors-107"><span class="linenos">107</span></a>
</span><span id="read_ADerrors-108"><a href="#read_ADerrors-108"><span class="linenos">108</span></a> <span class="n">nrep</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="read_ADerrors-109"><a href="#read_ADerrors-109"><span class="linenos">109</span></a> <span class="k">for</span> <span class="n">index</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">neid</span><span class="p">):</span>
</span><span id="read_ADerrors-110"><a href="#read_ADerrors-110"><span class="linenos">110</span></a> <span class="n">nrep</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">read_c_size_t</span><span class="p">())</span>
</span><span id="read_ADerrors-111"><a href="#read_ADerrors-111"><span class="linenos">111</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;nrep&#39;</span><span class="p">,</span> <span class="n">nrep</span><span class="p">)</span>
</span><span id="read_ADerrors-112"><a href="#read_ADerrors-112"><span class="linenos">112</span></a>
</span><span id="read_ADerrors-113"><a href="#read_ADerrors-113"><span class="linenos">113</span></a> <span class="n">vrep</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="read_ADerrors-114"><a href="#read_ADerrors-114"><span class="linenos">114</span></a> <span class="k">for</span> <span class="n">index</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">neid</span><span class="p">):</span>
</span><span id="read_ADerrors-115"><a href="#read_ADerrors-115"><span class="linenos">115</span></a> <span class="n">vrep</span><span class="o">.</span><span class="n">append</span><span class="p">([])</span>
</span><span id="read_ADerrors-116"><a href="#read_ADerrors-116"><span class="linenos">116</span></a> <span class="k">for</span> <span class="n">jndex</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nrep</span><span class="p">[</span><span class="n">index</span><span class="p">]):</span>
</span><span id="read_ADerrors-117"><a href="#read_ADerrors-117"><span class="linenos">117</span></a> <span class="n">vrep</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">read_c_size_t</span><span class="p">())</span>
</span><span id="read_ADerrors-118"><a href="#read_ADerrors-118"><span class="linenos">118</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;vrep&#39;</span><span class="p">,</span> <span class="n">vrep</span><span class="p">)</span>
</span><span id="read_ADerrors-119"><a href="#read_ADerrors-119"><span class="linenos">119</span></a>
</span><span id="read_ADerrors-120"><a href="#read_ADerrors-120"><span class="linenos">120</span></a> <span class="n">ids</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="read_ADerrors-121"><a href="#read_ADerrors-121"><span class="linenos">121</span></a> <span class="k">for</span> <span class="n">index</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">neid</span><span class="p">):</span>
</span><span id="read_ADerrors-122"><a href="#read_ADerrors-122"><span class="linenos">122</span></a> <span class="n">ids</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">read_c_size_t</span><span class="p">())</span>
</span><span id="read_ADerrors-123"><a href="#read_ADerrors-123"><span class="linenos">123</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;ids&#39;</span><span class="p">,</span> <span class="n">ids</span><span class="p">)</span>
</span><span id="read_ADerrors-124"><a href="#read_ADerrors-124"><span class="linenos">124</span></a>
</span><span id="read_ADerrors-125"><a href="#read_ADerrors-125"><span class="linenos">125</span></a> <span class="n">nt</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="read_ADerrors-126"><a href="#read_ADerrors-126"><span class="linenos">126</span></a> <span class="k">for</span> <span class="n">index</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">neid</span><span class="p">):</span>
</span><span id="read_ADerrors-127"><a href="#read_ADerrors-127"><span class="linenos">127</span></a> <span class="n">nt</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">read_c_size_t</span><span class="p">())</span>
</span><span id="read_ADerrors-128"><a href="#read_ADerrors-128"><span class="linenos">128</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;nt&#39;</span><span class="p">,</span> <span class="n">nt</span><span class="p">)</span>
</span><span id="read_ADerrors-129"><a href="#read_ADerrors-129"><span class="linenos">129</span></a>
</span><span id="read_ADerrors-130"><a href="#read_ADerrors-130"><span class="linenos">130</span></a> <span class="n">zero</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="read_ADerrors-131"><a href="#read_ADerrors-131"><span class="linenos">131</span></a> <span class="k">for</span> <span class="n">index</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">neid</span><span class="p">):</span>
</span><span id="read_ADerrors-132"><a href="#read_ADerrors-132"><span class="linenos">132</span></a> <span class="n">zero</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">read_c_double</span><span class="p">())</span>
</span><span id="read_ADerrors-133"><a href="#read_ADerrors-133"><span class="linenos">133</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;zero&#39;</span><span class="p">,</span> <span class="n">zero</span><span class="p">)</span>
</span><span id="read_ADerrors-134"><a href="#read_ADerrors-134"><span class="linenos">134</span></a>
</span><span id="read_ADerrors-135"><a href="#read_ADerrors-135"><span class="linenos">135</span></a> <span class="n">four</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="read_ADerrors-136"><a href="#read_ADerrors-136"><span class="linenos">136</span></a> <span class="k">for</span> <span class="n">index</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">neid</span><span class="p">):</span>
</span><span id="read_ADerrors-137"><a href="#read_ADerrors-137"><span class="linenos">137</span></a> <span class="n">four</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">read_c_double</span><span class="p">())</span>
</span><span id="read_ADerrors-138"><a href="#read_ADerrors-138"><span class="linenos">138</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;four&#39;</span><span class="p">,</span> <span class="n">four</span><span class="p">)</span>
</span><span id="read_ADerrors-139"><a href="#read_ADerrors-139"><span class="linenos">139</span></a>
</span><span id="read_ADerrors-140"><a href="#read_ADerrors-140"><span class="linenos">140</span></a> <span class="n">d_buf</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_double</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">ndata</span><span class="p">)</span>
</span><span id="read_ADerrors-141"><a href="#read_ADerrors-141"><span class="linenos">141</span></a> <span class="n">pd_buf</span> <span class="o">=</span> <span class="n">d_buf</span><span class="p">()</span>
</span><span id="read_ADerrors-142"><a href="#read_ADerrors-142"><span class="linenos">142</span></a> <span class="n">ppd_buf</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">(</span><span class="n">ctypes</span><span class="o">.</span><span class="n">addressof</span><span class="p">(</span><span class="n">pd_buf</span><span class="p">))</span>
</span><span id="read_ADerrors-143"><a href="#read_ADerrors-143"><span class="linenos">143</span></a> <span class="n">bdio_read_f64</span><span class="p">(</span><span class="n">ppd_buf</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span><span class="p">(</span><span class="mi">8</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">ndata</span><span class="p">)),</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">(</span><span class="n">fbdio</span><span class="p">))</span>
</span><span id="read_ADerrors-144"><a href="#read_ADerrors-144"><span class="linenos">144</span></a> <span class="n">delta</span> <span class="o">=</span> <span class="n">pd_buf</span><span class="p">[:]</span>
</span><span id="read_ADerrors-145"><a href="#read_ADerrors-145"><span class="linenos">145</span></a>
</span><span id="read_ADerrors-146"><a href="#read_ADerrors-146"><span class="linenos">146</span></a> <span class="n">samples</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">delta</span><span class="p">)</span> <span class="o">+</span> <span class="n">mean</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">cumsum</span><span class="p">([</span><span class="n">a</span> <span class="k">for</span> <span class="n">su</span> <span class="ow">in</span> <span class="n">vrep</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">su</span><span class="p">])[:</span><span class="o">-</span><span class="mi">1</span><span class="p">])</span>
</span><span id="read_ADerrors-147"><a href="#read_ADerrors-147"><span class="linenos">147</span></a> <span class="n">no_reps</span> <span class="o">=</span> <span class="p">[</span><span class="nb">len</span><span class="p">(</span><span class="n">o</span><span class="p">)</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">vrep</span><span class="p">]</span>
</span><span id="read_ADerrors-148"><a href="#read_ADerrors-148"><span class="linenos">148</span></a> <span class="k">assert</span> <span class="nb">len</span><span class="p">(</span><span class="n">ids</span><span class="p">)</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="n">no_reps</span><span class="p">)</span>
</span><span id="read_ADerrors-149"><a href="#read_ADerrors-149"><span class="linenos">149</span></a> <span class="n">tmp_names</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="read_ADerrors-150"><a href="#read_ADerrors-150"><span class="linenos">150</span></a> <span class="n">ens_length</span> <span class="o">=</span> <span class="nb">max</span><span class="p">([</span><span class="nb">len</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">o</span><span class="p">))</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">ids</span><span class="p">])</span>
</span><span id="read_ADerrors-151"><a href="#read_ADerrors-151"><span class="linenos">151</span></a> <span class="k">for</span> <span class="n">loc_id</span><span class="p">,</span> <span class="n">reps</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">ids</span><span class="p">,</span> <span class="n">no_reps</span><span class="p">):</span>
</span><span id="read_ADerrors-152"><a href="#read_ADerrors-152"><span class="linenos">152</span></a> <span class="k">for</span> <span class="n">index</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">reps</span><span class="p">):</span>
</span><span id="read_ADerrors-153"><a href="#read_ADerrors-153"><span class="linenos">153</span></a> <span class="n">missing_chars</span> <span class="o">=</span> <span class="n">ens_length</span> <span class="o">-</span> <span class="nb">len</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">loc_id</span><span class="p">))</span>
</span><span id="read_ADerrors-154"><a href="#read_ADerrors-154"><span class="linenos">154</span></a> <span class="n">tmp_names</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">loc_id</span><span class="p">)</span> <span class="o">+</span> <span class="s1">&#39; &#39;</span> <span class="o">*</span> <span class="n">missing_chars</span> <span class="o">+</span> <span class="s1">&#39;|r&#39;</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="si">{0:03d}</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">index</span><span class="p">))</span>
</span><span id="read_ADerrors-155"><a href="#read_ADerrors-155"><span class="linenos">155</span></a>
</span><span id="read_ADerrors-156"><a href="#read_ADerrors-156"><span class="linenos">156</span></a> <span class="n">return_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">Obs</span><span class="p">(</span><span class="n">samples</span><span class="p">,</span> <span class="n">tmp_names</span><span class="p">))</span>
</span><span id="read_ADerrors-157"><a href="#read_ADerrors-157"><span class="linenos">157</span></a>
</span><span id="read_ADerrors-158"><a href="#read_ADerrors-158"><span class="linenos">158</span></a> <span class="n">bdio_close</span><span class="p">(</span><span class="n">fbdio</span><span class="p">)</span>
</span><span id="read_ADerrors-159"><a href="#read_ADerrors-159"><span class="linenos">159</span></a> <span class="nb">print</span><span class="p">()</span>
</span><span id="read_ADerrors-160"><a href="#read_ADerrors-160"><span class="linenos">160</span></a> <span class="nb">print</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">return_list</span><span class="p">),</span> <span class="s1">&#39;observable(s) extracted.&#39;</span><span class="p">)</span>
</span><span id="read_ADerrors-161"><a href="#read_ADerrors-161"><span class="linenos">161</span></a> <span class="k">return</span> <span class="n">return_list</span>
</span></pre></div>
<div class="docstring"><p>Extract generic MCMC data from a bdio file</p>
<p>read_ADerrors requires bdio to be compiled into a shared library. This can be achieved by
adding the flag -fPIC to CC and changing the all target to</p>
<p>all: bdio.o $(LIBDIR)
gcc -shared -Wl,-soname,libbdio.so -o $(BUILDDIR)/libbdio.so $(BUILDDIR)/bdio.o
cp $(BUILDDIR)/libbdio.so $(LIBDIR)/</p>
<h6 id="parameters">Parameters</h6>
<ul>
<li><strong>file_path -- path to the bdio file</strong></li>
<li><strong>bdio_path -- path to the shared bdio library libbdio.so (default ./libbdio.so)</strong></li>
</ul>
<h6 id="returns">Returns</h6>
<ul>
<li><strong>data</strong> (List[Obs]):
Extracted data</li>
</ul>
</div>
</section>
<section id="write_ADerrors">
<input id="write_ADerrors-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">write_ADerrors</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">obs_list</span>, </span><span class="param"><span class="n">file_path</span>, </span><span class="param"><span class="n">bdio_path</span><span class="o">=</span><span class="s1">&#39;./libbdio.so&#39;</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="write_ADerrors-view-source"><span>View Source</span></label>
</div>
<a class="headerlink" href="#write_ADerrors"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="write_ADerrors-164"><a href="#write_ADerrors-164"><span class="linenos">164</span></a><span class="k">def</span> <span class="nf">write_ADerrors</span><span class="p">(</span><span class="n">obs_list</span><span class="p">,</span> <span class="n">file_path</span><span class="p">,</span> <span class="n">bdio_path</span><span class="o">=</span><span class="s1">&#39;./libbdio.so&#39;</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
</span><span id="write_ADerrors-165"><a href="#write_ADerrors-165"><span class="linenos">165</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot; Write Obs to a bdio file according to ADerrors conventions</span>
</span><span id="write_ADerrors-166"><a href="#write_ADerrors-166"><span class="linenos">166</span></a>
</span><span id="write_ADerrors-167"><a href="#write_ADerrors-167"><span class="linenos">167</span></a><span class="sd"> read_mesons requires bdio to be compiled into a shared library. This can be achieved by</span>
</span><span id="write_ADerrors-168"><a href="#write_ADerrors-168"><span class="linenos">168</span></a><span class="sd"> adding the flag -fPIC to CC and changing the all target to</span>
</span><span id="write_ADerrors-169"><a href="#write_ADerrors-169"><span class="linenos">169</span></a>
</span><span id="write_ADerrors-170"><a href="#write_ADerrors-170"><span class="linenos">170</span></a><span class="sd"> all: bdio.o $(LIBDIR)</span>
</span><span id="write_ADerrors-171"><a href="#write_ADerrors-171"><span class="linenos">171</span></a><span class="sd"> gcc -shared -Wl,-soname,libbdio.so -o $(BUILDDIR)/libbdio.so $(BUILDDIR)/bdio.o</span>
</span><span id="write_ADerrors-172"><a href="#write_ADerrors-172"><span class="linenos">172</span></a><span class="sd"> cp $(BUILDDIR)/libbdio.so $(LIBDIR)/</span>
</span><span id="write_ADerrors-173"><a href="#write_ADerrors-173"><span class="linenos">173</span></a>
</span><span id="write_ADerrors-174"><a href="#write_ADerrors-174"><span class="linenos">174</span></a><span class="sd"> Parameters</span>
</span><span id="write_ADerrors-175"><a href="#write_ADerrors-175"><span class="linenos">175</span></a><span class="sd"> ----------</span>
</span><span id="write_ADerrors-176"><a href="#write_ADerrors-176"><span class="linenos">176</span></a><span class="sd"> file_path -- path to the bdio file</span>
</span><span id="write_ADerrors-177"><a href="#write_ADerrors-177"><span class="linenos">177</span></a><span class="sd"> bdio_path -- path to the shared bdio library libbdio.so (default ./libbdio.so)</span>
</span><span id="write_ADerrors-178"><a href="#write_ADerrors-178"><span class="linenos">178</span></a>
</span><span id="write_ADerrors-179"><a href="#write_ADerrors-179"><span class="linenos">179</span></a><span class="sd"> Returns</span>
</span><span id="write_ADerrors-180"><a href="#write_ADerrors-180"><span class="linenos">180</span></a><span class="sd"> -------</span>
</span><span id="write_ADerrors-181"><a href="#write_ADerrors-181"><span class="linenos">181</span></a><span class="sd"> success : int</span>
</span><span id="write_ADerrors-182"><a href="#write_ADerrors-182"><span class="linenos">182</span></a><span class="sd"> returns 0 is successful</span>
</span><span id="write_ADerrors-183"><a href="#write_ADerrors-183"><span class="linenos">183</span></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="write_ADerrors-184"><a href="#write_ADerrors-184"><span class="linenos">184</span></a>
</span><span id="write_ADerrors-185"><a href="#write_ADerrors-185"><span class="linenos">185</span></a> <span class="k">for</span> <span class="n">obs</span> <span class="ow">in</span> <span class="n">obs_list</span><span class="p">:</span>
</span><span id="write_ADerrors-186"><a href="#write_ADerrors-186"><span class="linenos">186</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">obs</span><span class="p">,</span> <span class="s1">&#39;e_names&#39;</span><span class="p">):</span>
</span><span id="write_ADerrors-187"><a href="#write_ADerrors-187"><span class="linenos">187</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Run the gamma method first for all obs.&#39;</span><span class="p">)</span>
</span><span id="write_ADerrors-188"><a href="#write_ADerrors-188"><span class="linenos">188</span></a>
</span><span id="write_ADerrors-189"><a href="#write_ADerrors-189"><span class="linenos">189</span></a> <span class="n">bdio</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">cdll</span><span class="o">.</span><span class="n">LoadLibrary</span><span class="p">(</span><span class="n">bdio_path</span><span class="p">)</span>
</span><span id="write_ADerrors-190"><a href="#write_ADerrors-190"><span class="linenos">190</span></a>
</span><span id="write_ADerrors-191"><a href="#write_ADerrors-191"><span class="linenos">191</span></a> <span class="n">bdio_open</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_open</span>
</span><span id="write_ADerrors-192"><a href="#write_ADerrors-192"><span class="linenos">192</span></a> <span class="n">bdio_open</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span>
</span><span id="write_ADerrors-193"><a href="#write_ADerrors-193"><span class="linenos">193</span></a>
</span><span id="write_ADerrors-194"><a href="#write_ADerrors-194"><span class="linenos">194</span></a> <span class="n">bdio_close</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_close</span>
</span><span id="write_ADerrors-195"><a href="#write_ADerrors-195"><span class="linenos">195</span></a> <span class="n">bdio_close</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_int</span>
</span><span id="write_ADerrors-196"><a href="#write_ADerrors-196"><span class="linenos">196</span></a> <span class="n">bdio_close</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="write_ADerrors-197"><a href="#write_ADerrors-197"><span class="linenos">197</span></a>
</span><span id="write_ADerrors-198"><a href="#write_ADerrors-198"><span class="linenos">198</span></a> <span class="n">bdio_start_record</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_start_record</span>
</span><span id="write_ADerrors-199"><a href="#write_ADerrors-199"><span class="linenos">199</span></a> <span class="n">bdio_start_record</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_int</span>
</span><span id="write_ADerrors-200"><a href="#write_ADerrors-200"><span class="linenos">200</span></a> <span class="n">bdio_start_record</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="write_ADerrors-201"><a href="#write_ADerrors-201"><span class="linenos">201</span></a>
</span><span id="write_ADerrors-202"><a href="#write_ADerrors-202"><span class="linenos">202</span></a> <span class="n">bdio_flush_record</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_flush_record</span>
</span><span id="write_ADerrors-203"><a href="#write_ADerrors-203"><span class="linenos">203</span></a> <span class="n">bdio_flush_record</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_int</span>
</span><span id="write_ADerrors-204"><a href="#write_ADerrors-204"><span class="linenos">204</span></a> <span class="n">bdio_flush_record</span><span class="o">.</span><span class="n">argytpes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="write_ADerrors-205"><a href="#write_ADerrors-205"><span class="linenos">205</span></a>
</span><span id="write_ADerrors-206"><a href="#write_ADerrors-206"><span class="linenos">206</span></a> <span class="n">bdio_write_f64</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_write_f64</span>
</span><span id="write_ADerrors-207"><a href="#write_ADerrors-207"><span class="linenos">207</span></a> <span class="n">bdio_write_f64</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span>
</span><span id="write_ADerrors-208"><a href="#write_ADerrors-208"><span class="linenos">208</span></a> <span class="n">bdio_write_f64</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="write_ADerrors-209"><a href="#write_ADerrors-209"><span class="linenos">209</span></a>
</span><span id="write_ADerrors-210"><a href="#write_ADerrors-210"><span class="linenos">210</span></a> <span class="n">bdio_write_int32</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_write_int32</span>
</span><span id="write_ADerrors-211"><a href="#write_ADerrors-211"><span class="linenos">211</span></a> <span class="n">bdio_write_int32</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span>
</span><span id="write_ADerrors-212"><a href="#write_ADerrors-212"><span class="linenos">212</span></a> <span class="n">bdio_write_int32</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="write_ADerrors-213"><a href="#write_ADerrors-213"><span class="linenos">213</span></a>
</span><span id="write_ADerrors-214"><a href="#write_ADerrors-214"><span class="linenos">214</span></a> <span class="n">b_path</span> <span class="o">=</span> <span class="n">file_path</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span>
</span><span id="write_ADerrors-215"><a href="#write_ADerrors-215"><span class="linenos">215</span></a> <span class="n">write</span> <span class="o">=</span> <span class="s1">&#39;w&#39;</span>
</span><span id="write_ADerrors-216"><a href="#write_ADerrors-216"><span class="linenos">216</span></a> <span class="n">b_write</span> <span class="o">=</span> <span class="n">write</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span>
</span><span id="write_ADerrors-217"><a href="#write_ADerrors-217"><span class="linenos">217</span></a> <span class="n">form</span> <span class="o">=</span> <span class="s1">&#39;pyerrors ADerror export&#39;</span>
</span><span id="write_ADerrors-218"><a href="#write_ADerrors-218"><span class="linenos">218</span></a> <span class="n">b_form</span> <span class="o">=</span> <span class="n">form</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span>
</span><span id="write_ADerrors-219"><a href="#write_ADerrors-219"><span class="linenos">219</span></a>
</span><span id="write_ADerrors-220"><a href="#write_ADerrors-220"><span class="linenos">220</span></a> <span class="n">fbdio</span> <span class="o">=</span> <span class="n">bdio_open</span><span class="p">(</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_char_p</span><span class="p">(</span><span class="n">b_path</span><span class="p">),</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_char_p</span><span class="p">(</span><span class="n">b_write</span><span class="p">),</span> <span class="n">b_form</span><span class="p">)</span>
</span><span id="write_ADerrors-221"><a href="#write_ADerrors-221"><span class="linenos">221</span></a>
</span><span id="write_ADerrors-222"><a href="#write_ADerrors-222"><span class="linenos">222</span></a> <span class="k">for</span> <span class="n">obs</span> <span class="ow">in</span> <span class="n">obs_list</span><span class="p">:</span>
</span><span id="write_ADerrors-223"><a href="#write_ADerrors-223"><span class="linenos">223</span></a> <span class="c1"># mean = obs.value</span>
</span><span id="write_ADerrors-224"><a href="#write_ADerrors-224"><span class="linenos">224</span></a> <span class="n">neid</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">obs</span><span class="o">.</span><span class="n">e_names</span><span class="p">)</span>
</span><span id="write_ADerrors-225"><a href="#write_ADerrors-225"><span class="linenos">225</span></a> <span class="n">vrep</span> <span class="o">=</span> <span class="p">[[</span><span class="n">obs</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="n">o</span><span class="p">]</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">sl</span><span class="p">]</span> <span class="k">for</span> <span class="n">sl</span> <span class="ow">in</span> <span class="nb">list</span><span class="p">(</span><span class="n">obs</span><span class="o">.</span><span class="n">e_content</span><span class="o">.</span><span class="n">values</span><span class="p">())]</span>
</span><span id="write_ADerrors-226"><a href="#write_ADerrors-226"><span class="linenos">226</span></a> <span class="n">vrep_write</span> <span class="o">=</span> <span class="p">[</span><span class="n">item</span> <span class="k">for</span> <span class="n">sublist</span> <span class="ow">in</span> <span class="n">vrep</span> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">sublist</span><span class="p">]</span>
</span><span id="write_ADerrors-227"><a href="#write_ADerrors-227"><span class="linenos">227</span></a> <span class="n">ndata</span> <span class="o">=</span> <span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">o</span><span class="p">)</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">vrep</span><span class="p">]</span>
</span><span id="write_ADerrors-228"><a href="#write_ADerrors-228"><span class="linenos">228</span></a> <span class="n">nrep</span> <span class="o">=</span> <span class="p">[</span><span class="nb">len</span><span class="p">(</span><span class="n">o</span><span class="p">)</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">vrep</span><span class="p">]</span>
</span><span id="write_ADerrors-229"><a href="#write_ADerrors-229"><span class="linenos">229</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;ndata&#39;</span><span class="p">,</span> <span class="n">ndata</span><span class="p">)</span>
</span><span id="write_ADerrors-230"><a href="#write_ADerrors-230"><span class="linenos">230</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;nrep&#39;</span><span class="p">,</span> <span class="n">nrep</span><span class="p">)</span>
</span><span id="write_ADerrors-231"><a href="#write_ADerrors-231"><span class="linenos">231</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;vrep&#39;</span><span class="p">,</span> <span class="n">vrep</span><span class="p">)</span>
</span><span id="write_ADerrors-232"><a href="#write_ADerrors-232"><span class="linenos">232</span></a> <span class="n">keys</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">obs</span><span class="o">.</span><span class="n">e_content</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
</span><span id="write_ADerrors-233"><a href="#write_ADerrors-233"><span class="linenos">233</span></a> <span class="n">ids</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="write_ADerrors-234"><a href="#write_ADerrors-234"><span class="linenos">234</span></a> <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">keys</span><span class="p">:</span>
</span><span id="write_ADerrors-235"><a href="#write_ADerrors-235"><span class="linenos">235</span></a> <span class="k">try</span><span class="p">:</span> <span class="c1"># Try to convert key to integer</span>
</span><span id="write_ADerrors-236"><a href="#write_ADerrors-236"><span class="linenos">236</span></a> <span class="n">ids</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">key</span><span class="p">))</span>
</span><span id="write_ADerrors-237"><a href="#write_ADerrors-237"><span class="linenos">237</span></a> <span class="k">except</span> <span class="ne">Exception</span><span class="p">:</span> <span class="c1"># If not possible construct a hash</span>
</span><span id="write_ADerrors-238"><a href="#write_ADerrors-238"><span class="linenos">238</span></a> <span class="n">ids</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">hashlib</span><span class="o">.</span><span class="n">sha256</span><span class="p">(</span><span class="n">key</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">))</span><span class="o">.</span><span class="n">hexdigest</span><span class="p">(),</span> <span class="mi">16</span><span class="p">)</span> <span class="o">%</span> <span class="mi">10</span> <span class="o">**</span> <span class="mi">8</span><span class="p">)</span>
</span><span id="write_ADerrors-239"><a href="#write_ADerrors-239"><span class="linenos">239</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;ids&#39;</span><span class="p">,</span> <span class="n">ids</span><span class="p">)</span>
</span><span id="write_ADerrors-240"><a href="#write_ADerrors-240"><span class="linenos">240</span></a> <span class="n">nt</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="write_ADerrors-241"><a href="#write_ADerrors-241"><span class="linenos">241</span></a> <span class="k">for</span> <span class="n">e</span><span class="p">,</span> <span class="n">e_name</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">obs</span><span class="o">.</span><span class="n">e_names</span><span class="p">):</span>
</span><span id="write_ADerrors-242"><a href="#write_ADerrors-242"><span class="linenos">242</span></a>
</span><span id="write_ADerrors-243"><a href="#write_ADerrors-243"><span class="linenos">243</span></a> <span class="n">r_length</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="write_ADerrors-244"><a href="#write_ADerrors-244"><span class="linenos">244</span></a> <span class="k">for</span> <span class="n">r_name</span> <span class="ow">in</span> <span class="n">obs</span><span class="o">.</span><span class="n">e_content</span><span class="p">[</span><span class="n">e_name</span><span class="p">]:</span>
</span><span id="write_ADerrors-245"><a href="#write_ADerrors-245"><span class="linenos">245</span></a> <span class="n">r_length</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">obs</span><span class="o">.</span><span class="n">deltas</span><span class="p">[</span><span class="n">r_name</span><span class="p">]))</span>
</span><span id="write_ADerrors-246"><a href="#write_ADerrors-246"><span class="linenos">246</span></a>
</span><span id="write_ADerrors-247"><a href="#write_ADerrors-247"><span class="linenos">247</span></a> <span class="c1"># e_N = np.sum(r_length)</span>
</span><span id="write_ADerrors-248"><a href="#write_ADerrors-248"><span class="linenos">248</span></a> <span class="n">nt</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">max</span><span class="p">(</span><span class="n">r_length</span><span class="p">)</span> <span class="o">//</span> <span class="mi">2</span><span class="p">)</span>
</span><span id="write_ADerrors-249"><a href="#write_ADerrors-249"><span class="linenos">249</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;nt&#39;</span><span class="p">,</span> <span class="n">nt</span><span class="p">)</span>
</span><span id="write_ADerrors-250"><a href="#write_ADerrors-250"><span class="linenos">250</span></a> <span class="n">zero</span> <span class="o">=</span> <span class="n">neid</span> <span class="o">*</span> <span class="p">[</span><span class="mf">0.0</span><span class="p">]</span>
</span><span id="write_ADerrors-251"><a href="#write_ADerrors-251"><span class="linenos">251</span></a> <span class="n">four</span> <span class="o">=</span> <span class="n">neid</span> <span class="o">*</span> <span class="p">[</span><span class="mf">4.0</span><span class="p">]</span>
</span><span id="write_ADerrors-252"><a href="#write_ADerrors-252"><span class="linenos">252</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;zero&#39;</span><span class="p">,</span> <span class="n">zero</span><span class="p">)</span>
</span><span id="write_ADerrors-253"><a href="#write_ADerrors-253"><span class="linenos">253</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;four&#39;</span><span class="p">,</span> <span class="n">four</span><span class="p">)</span>
</span><span id="write_ADerrors-254"><a href="#write_ADerrors-254"><span class="linenos">254</span></a> <span class="n">delta</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">concatenate</span><span class="p">([</span><span class="n">item</span> <span class="k">for</span> <span class="n">sublist</span> <span class="ow">in</span> <span class="p">[[</span><span class="n">obs</span><span class="o">.</span><span class="n">deltas</span><span class="p">[</span><span class="n">o</span><span class="p">]</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">sl</span><span class="p">]</span> <span class="k">for</span> <span class="n">sl</span> <span class="ow">in</span> <span class="nb">list</span><span class="p">(</span><span class="n">obs</span><span class="o">.</span><span class="n">e_content</span><span class="o">.</span><span class="n">values</span><span class="p">())]</span> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">sublist</span><span class="p">])</span>
</span><span id="write_ADerrors-255"><a href="#write_ADerrors-255"><span class="linenos">255</span></a>
</span><span id="write_ADerrors-256"><a href="#write_ADerrors-256"><span class="linenos">256</span></a> <span class="n">bdio_start_record</span><span class="p">(</span><span class="mh">0x00</span><span class="p">,</span> <span class="mi">8</span><span class="p">,</span> <span class="n">fbdio</span><span class="p">)</span>
</span><span id="write_ADerrors-257"><a href="#write_ADerrors-257"><span class="linenos">257</span></a>
</span><span id="write_ADerrors-258"><a href="#write_ADerrors-258"><span class="linenos">258</span></a> <span class="k">def</span> <span class="nf">write_c_double</span><span class="p">(</span><span class="n">double</span><span class="p">):</span>
</span><span id="write_ADerrors-259"><a href="#write_ADerrors-259"><span class="linenos">259</span></a> <span class="n">pd_buf</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_double</span><span class="p">(</span><span class="n">double</span><span class="p">)</span>
</span><span id="write_ADerrors-260"><a href="#write_ADerrors-260"><span class="linenos">260</span></a> <span class="n">ppd_buf</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">(</span><span class="n">ctypes</span><span class="o">.</span><span class="n">addressof</span><span class="p">(</span><span class="n">pd_buf</span><span class="p">))</span>
</span><span id="write_ADerrors-261"><a href="#write_ADerrors-261"><span class="linenos">261</span></a> <span class="n">bdio_write_f64</span><span class="p">(</span><span class="n">ppd_buf</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span><span class="p">(</span><span class="mi">8</span><span class="p">),</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">(</span><span class="n">fbdio</span><span class="p">))</span>
</span><span id="write_ADerrors-262"><a href="#write_ADerrors-262"><span class="linenos">262</span></a>
</span><span id="write_ADerrors-263"><a href="#write_ADerrors-263"><span class="linenos">263</span></a> <span class="k">def</span> <span class="nf">write_c_size_t</span><span class="p">(</span><span class="n">int32</span><span class="p">):</span>
</span><span id="write_ADerrors-264"><a href="#write_ADerrors-264"><span class="linenos">264</span></a> <span class="n">pd_buf</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span><span class="p">(</span><span class="n">int32</span><span class="p">)</span>
</span><span id="write_ADerrors-265"><a href="#write_ADerrors-265"><span class="linenos">265</span></a> <span class="n">ppd_buf</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">(</span><span class="n">ctypes</span><span class="o">.</span><span class="n">addressof</span><span class="p">(</span><span class="n">pd_buf</span><span class="p">))</span>
</span><span id="write_ADerrors-266"><a href="#write_ADerrors-266"><span class="linenos">266</span></a> <span class="n">bdio_write_int32</span><span class="p">(</span><span class="n">ppd_buf</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span><span class="p">(</span><span class="mi">4</span><span class="p">),</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">(</span><span class="n">fbdio</span><span class="p">))</span>
</span><span id="write_ADerrors-267"><a href="#write_ADerrors-267"><span class="linenos">267</span></a>
</span><span id="write_ADerrors-268"><a href="#write_ADerrors-268"><span class="linenos">268</span></a> <span class="n">write_c_double</span><span class="p">(</span><span class="n">obs</span><span class="o">.</span><span class="n">value</span><span class="p">)</span>
</span><span id="write_ADerrors-269"><a href="#write_ADerrors-269"><span class="linenos">269</span></a> <span class="n">write_c_size_t</span><span class="p">(</span><span class="n">neid</span><span class="p">)</span>
</span><span id="write_ADerrors-270"><a href="#write_ADerrors-270"><span class="linenos">270</span></a>
</span><span id="write_ADerrors-271"><a href="#write_ADerrors-271"><span class="linenos">271</span></a> <span class="k">for</span> <span class="n">element</span> <span class="ow">in</span> <span class="n">ndata</span><span class="p">:</span>
</span><span id="write_ADerrors-272"><a href="#write_ADerrors-272"><span class="linenos">272</span></a> <span class="n">write_c_size_t</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
</span><span id="write_ADerrors-273"><a href="#write_ADerrors-273"><span class="linenos">273</span></a> <span class="k">for</span> <span class="n">element</span> <span class="ow">in</span> <span class="n">nrep</span><span class="p">:</span>
</span><span id="write_ADerrors-274"><a href="#write_ADerrors-274"><span class="linenos">274</span></a> <span class="n">write_c_size_t</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
</span><span id="write_ADerrors-275"><a href="#write_ADerrors-275"><span class="linenos">275</span></a> <span class="k">for</span> <span class="n">element</span> <span class="ow">in</span> <span class="n">vrep_write</span><span class="p">:</span>
</span><span id="write_ADerrors-276"><a href="#write_ADerrors-276"><span class="linenos">276</span></a> <span class="n">write_c_size_t</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
</span><span id="write_ADerrors-277"><a href="#write_ADerrors-277"><span class="linenos">277</span></a> <span class="k">for</span> <span class="n">element</span> <span class="ow">in</span> <span class="n">ids</span><span class="p">:</span>
</span><span id="write_ADerrors-278"><a href="#write_ADerrors-278"><span class="linenos">278</span></a> <span class="n">write_c_size_t</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
</span><span id="write_ADerrors-279"><a href="#write_ADerrors-279"><span class="linenos">279</span></a> <span class="k">for</span> <span class="n">element</span> <span class="ow">in</span> <span class="n">nt</span><span class="p">:</span>
</span><span id="write_ADerrors-280"><a href="#write_ADerrors-280"><span class="linenos">280</span></a> <span class="n">write_c_size_t</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
</span><span id="write_ADerrors-281"><a href="#write_ADerrors-281"><span class="linenos">281</span></a>
</span><span id="write_ADerrors-282"><a href="#write_ADerrors-282"><span class="linenos">282</span></a> <span class="k">for</span> <span class="n">element</span> <span class="ow">in</span> <span class="n">zero</span><span class="p">:</span>
</span><span id="write_ADerrors-283"><a href="#write_ADerrors-283"><span class="linenos">283</span></a> <span class="n">write_c_double</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
</span><span id="write_ADerrors-284"><a href="#write_ADerrors-284"><span class="linenos">284</span></a> <span class="k">for</span> <span class="n">element</span> <span class="ow">in</span> <span class="n">four</span><span class="p">:</span>
</span><span id="write_ADerrors-285"><a href="#write_ADerrors-285"><span class="linenos">285</span></a> <span class="n">write_c_double</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
</span><span id="write_ADerrors-286"><a href="#write_ADerrors-286"><span class="linenos">286</span></a>
</span><span id="write_ADerrors-287"><a href="#write_ADerrors-287"><span class="linenos">287</span></a> <span class="k">for</span> <span class="n">element</span> <span class="ow">in</span> <span class="n">delta</span><span class="p">:</span>
</span><span id="write_ADerrors-288"><a href="#write_ADerrors-288"><span class="linenos">288</span></a> <span class="n">write_c_double</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
</span><span id="write_ADerrors-289"><a href="#write_ADerrors-289"><span class="linenos">289</span></a>
</span><span id="write_ADerrors-290"><a href="#write_ADerrors-290"><span class="linenos">290</span></a> <span class="n">bdio_close</span><span class="p">(</span><span class="n">fbdio</span><span class="p">)</span>
</span><span id="write_ADerrors-291"><a href="#write_ADerrors-291"><span class="linenos">291</span></a> <span class="k">return</span> <span class="mi">0</span>
</span></pre></div>
<div class="docstring"><p>Write Obs to a bdio file according to ADerrors conventions</p>
<p>read_mesons requires bdio to be compiled into a shared library. This can be achieved by
adding the flag -fPIC to CC and changing the all target to</p>
<p>all: bdio.o $(LIBDIR)
gcc -shared -Wl,-soname,libbdio.so -o $(BUILDDIR)/libbdio.so $(BUILDDIR)/bdio.o
cp $(BUILDDIR)/libbdio.so $(LIBDIR)/</p>
<h6 id="parameters">Parameters</h6>
<ul>
<li><strong>file_path -- path to the bdio file</strong></li>
<li><strong>bdio_path -- path to the shared bdio library libbdio.so (default ./libbdio.so)</strong></li>
</ul>
<h6 id="returns">Returns</h6>
<ul>
<li><strong>success</strong> (int):
returns 0 is successful</li>
</ul>
</div>
</section>
<section id="read_mesons">
<input id="read_mesons-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">read_mesons</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">file_path</span>, </span><span class="param"><span class="n">bdio_path</span><span class="o">=</span><span class="s1">&#39;./libbdio.so&#39;</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="read_mesons-view-source"><span>View Source</span></label>
</div>
<a class="headerlink" href="#read_mesons"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="read_mesons-302"><a href="#read_mesons-302"><span class="linenos">302</span></a><span class="k">def</span> <span class="nf">read_mesons</span><span class="p">(</span><span class="n">file_path</span><span class="p">,</span> <span class="n">bdio_path</span><span class="o">=</span><span class="s1">&#39;./libbdio.so&#39;</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
</span><span id="read_mesons-303"><a href="#read_mesons-303"><span class="linenos">303</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot; Extract mesons data from a bdio file and return it as a dictionary</span>
</span><span id="read_mesons-304"><a href="#read_mesons-304"><span class="linenos">304</span></a>
</span><span id="read_mesons-305"><a href="#read_mesons-305"><span class="linenos">305</span></a><span class="sd"> The dictionary can be accessed with a tuple consisting of (type, source_position, kappa1, kappa2)</span>
</span><span id="read_mesons-306"><a href="#read_mesons-306"><span class="linenos">306</span></a>
</span><span id="read_mesons-307"><a href="#read_mesons-307"><span class="linenos">307</span></a><span class="sd"> read_mesons requires bdio to be compiled into a shared library. This can be achieved by</span>
</span><span id="read_mesons-308"><a href="#read_mesons-308"><span class="linenos">308</span></a><span class="sd"> adding the flag -fPIC to CC and changing the all target to</span>
</span><span id="read_mesons-309"><a href="#read_mesons-309"><span class="linenos">309</span></a>
</span><span id="read_mesons-310"><a href="#read_mesons-310"><span class="linenos">310</span></a><span class="sd"> all: bdio.o $(LIBDIR)</span>
</span><span id="read_mesons-311"><a href="#read_mesons-311"><span class="linenos">311</span></a><span class="sd"> gcc -shared -Wl,-soname,libbdio.so -o $(BUILDDIR)/libbdio.so $(BUILDDIR)/bdio.o</span>
</span><span id="read_mesons-312"><a href="#read_mesons-312"><span class="linenos">312</span></a><span class="sd"> cp $(BUILDDIR)/libbdio.so $(LIBDIR)/</span>
</span><span id="read_mesons-313"><a href="#read_mesons-313"><span class="linenos">313</span></a>
</span><span id="read_mesons-314"><a href="#read_mesons-314"><span class="linenos">314</span></a><span class="sd"> Parameters</span>
</span><span id="read_mesons-315"><a href="#read_mesons-315"><span class="linenos">315</span></a><span class="sd"> ----------</span>
</span><span id="read_mesons-316"><a href="#read_mesons-316"><span class="linenos">316</span></a><span class="sd"> file_path : str</span>
</span><span id="read_mesons-317"><a href="#read_mesons-317"><span class="linenos">317</span></a><span class="sd"> path to the bdio file</span>
</span><span id="read_mesons-318"><a href="#read_mesons-318"><span class="linenos">318</span></a><span class="sd"> bdio_path : str</span>
</span><span id="read_mesons-319"><a href="#read_mesons-319"><span class="linenos">319</span></a><span class="sd"> path to the shared bdio library libbdio.so (default ./libbdio.so)</span>
</span><span id="read_mesons-320"><a href="#read_mesons-320"><span class="linenos">320</span></a><span class="sd"> start : int</span>
</span><span id="read_mesons-321"><a href="#read_mesons-321"><span class="linenos">321</span></a><span class="sd"> The first configuration to be read (default 1)</span>
</span><span id="read_mesons-322"><a href="#read_mesons-322"><span class="linenos">322</span></a><span class="sd"> stop : int</span>
</span><span id="read_mesons-323"><a href="#read_mesons-323"><span class="linenos">323</span></a><span class="sd"> The last configuration to be read (default None)</span>
</span><span id="read_mesons-324"><a href="#read_mesons-324"><span class="linenos">324</span></a><span class="sd"> step : int</span>
</span><span id="read_mesons-325"><a href="#read_mesons-325"><span class="linenos">325</span></a><span class="sd"> Fixed step size between two measurements (default 1)</span>
</span><span id="read_mesons-326"><a href="#read_mesons-326"><span class="linenos">326</span></a><span class="sd"> alternative_ensemble_name : str</span>
</span><span id="read_mesons-327"><a href="#read_mesons-327"><span class="linenos">327</span></a><span class="sd"> Manually overwrite ensemble name</span>
</span><span id="read_mesons-328"><a href="#read_mesons-328"><span class="linenos">328</span></a>
</span><span id="read_mesons-329"><a href="#read_mesons-329"><span class="linenos">329</span></a><span class="sd"> Returns</span>
</span><span id="read_mesons-330"><a href="#read_mesons-330"><span class="linenos">330</span></a><span class="sd"> -------</span>
</span><span id="read_mesons-331"><a href="#read_mesons-331"><span class="linenos">331</span></a><span class="sd"> data : dict</span>
</span><span id="read_mesons-332"><a href="#read_mesons-332"><span class="linenos">332</span></a><span class="sd"> Extracted meson data</span>
</span><span id="read_mesons-333"><a href="#read_mesons-333"><span class="linenos">333</span></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="read_mesons-334"><a href="#read_mesons-334"><span class="linenos">334</span></a>
</span><span id="read_mesons-335"><a href="#read_mesons-335"><span class="linenos">335</span></a> <span class="n">start</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;start&#39;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
</span><span id="read_mesons-336"><a href="#read_mesons-336"><span class="linenos">336</span></a> <span class="n">stop</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;stop&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
</span><span id="read_mesons-337"><a href="#read_mesons-337"><span class="linenos">337</span></a> <span class="n">step</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;step&#39;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
</span><span id="read_mesons-338"><a href="#read_mesons-338"><span class="linenos">338</span></a>
</span><span id="read_mesons-339"><a href="#read_mesons-339"><span class="linenos">339</span></a> <span class="n">bdio</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">cdll</span><span class="o">.</span><span class="n">LoadLibrary</span><span class="p">(</span><span class="n">bdio_path</span><span class="p">)</span>
</span><span id="read_mesons-340"><a href="#read_mesons-340"><span class="linenos">340</span></a>
</span><span id="read_mesons-341"><a href="#read_mesons-341"><span class="linenos">341</span></a> <span class="n">bdio_open</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_open</span>
</span><span id="read_mesons-342"><a href="#read_mesons-342"><span class="linenos">342</span></a> <span class="n">bdio_open</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span>
</span><span id="read_mesons-343"><a href="#read_mesons-343"><span class="linenos">343</span></a>
</span><span id="read_mesons-344"><a href="#read_mesons-344"><span class="linenos">344</span></a> <span class="n">bdio_close</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_close</span>
</span><span id="read_mesons-345"><a href="#read_mesons-345"><span class="linenos">345</span></a> <span class="n">bdio_close</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_int</span>
</span><span id="read_mesons-346"><a href="#read_mesons-346"><span class="linenos">346</span></a> <span class="n">bdio_close</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="read_mesons-347"><a href="#read_mesons-347"><span class="linenos">347</span></a>
</span><span id="read_mesons-348"><a href="#read_mesons-348"><span class="linenos">348</span></a> <span class="n">bdio_seek_record</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_seek_record</span>
</span><span id="read_mesons-349"><a href="#read_mesons-349"><span class="linenos">349</span></a> <span class="n">bdio_seek_record</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_int</span>
</span><span id="read_mesons-350"><a href="#read_mesons-350"><span class="linenos">350</span></a> <span class="n">bdio_seek_record</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="read_mesons-351"><a href="#read_mesons-351"><span class="linenos">351</span></a>
</span><span id="read_mesons-352"><a href="#read_mesons-352"><span class="linenos">352</span></a> <span class="n">bdio_get_rlen</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_get_rlen</span>
</span><span id="read_mesons-353"><a href="#read_mesons-353"><span class="linenos">353</span></a> <span class="n">bdio_get_rlen</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_int</span>
</span><span id="read_mesons-354"><a href="#read_mesons-354"><span class="linenos">354</span></a> <span class="n">bdio_get_rlen</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="read_mesons-355"><a href="#read_mesons-355"><span class="linenos">355</span></a>
</span><span id="read_mesons-356"><a href="#read_mesons-356"><span class="linenos">356</span></a> <span class="n">bdio_get_ruinfo</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_get_ruinfo</span>
</span><span id="read_mesons-357"><a href="#read_mesons-357"><span class="linenos">357</span></a> <span class="n">bdio_get_ruinfo</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_int</span>
</span><span id="read_mesons-358"><a href="#read_mesons-358"><span class="linenos">358</span></a> <span class="n">bdio_get_ruinfo</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="read_mesons-359"><a href="#read_mesons-359"><span class="linenos">359</span></a>
</span><span id="read_mesons-360"><a href="#read_mesons-360"><span class="linenos">360</span></a> <span class="n">bdio_read</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_read</span>
</span><span id="read_mesons-361"><a href="#read_mesons-361"><span class="linenos">361</span></a> <span class="n">bdio_read</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span>
</span><span id="read_mesons-362"><a href="#read_mesons-362"><span class="linenos">362</span></a> <span class="n">bdio_read</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_char_p</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="read_mesons-363"><a href="#read_mesons-363"><span class="linenos">363</span></a>
</span><span id="read_mesons-364"><a href="#read_mesons-364"><span class="linenos">364</span></a> <span class="n">bdio_read_f64</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_read_f64</span>
</span><span id="read_mesons-365"><a href="#read_mesons-365"><span class="linenos">365</span></a> <span class="n">bdio_read_f64</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span>
</span><span id="read_mesons-366"><a href="#read_mesons-366"><span class="linenos">366</span></a> <span class="n">bdio_read_f64</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="read_mesons-367"><a href="#read_mesons-367"><span class="linenos">367</span></a>
</span><span id="read_mesons-368"><a href="#read_mesons-368"><span class="linenos">368</span></a> <span class="n">b_path</span> <span class="o">=</span> <span class="n">file_path</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span>
</span><span id="read_mesons-369"><a href="#read_mesons-369"><span class="linenos">369</span></a> <span class="n">read</span> <span class="o">=</span> <span class="s1">&#39;r&#39;</span>
</span><span id="read_mesons-370"><a href="#read_mesons-370"><span class="linenos">370</span></a> <span class="n">b_read</span> <span class="o">=</span> <span class="n">read</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span>
</span><span id="read_mesons-371"><a href="#read_mesons-371"><span class="linenos">371</span></a> <span class="n">form</span> <span class="o">=</span> <span class="s1">&#39;Generic Correlator Format 1.0&#39;</span>
</span><span id="read_mesons-372"><a href="#read_mesons-372"><span class="linenos">372</span></a> <span class="n">b_form</span> <span class="o">=</span> <span class="n">form</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span>
</span><span id="read_mesons-373"><a href="#read_mesons-373"><span class="linenos">373</span></a>
</span><span id="read_mesons-374"><a href="#read_mesons-374"><span class="linenos">374</span></a> <span class="n">ensemble_name</span> <span class="o">=</span> <span class="s1">&#39;&#39;</span>
</span><span id="read_mesons-375"><a href="#read_mesons-375"><span class="linenos">375</span></a> <span class="n">volume</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># lattice volume</span>
</span><span id="read_mesons-376"><a href="#read_mesons-376"><span class="linenos">376</span></a> <span class="n">boundary_conditions</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="read_mesons-377"><a href="#read_mesons-377"><span class="linenos">377</span></a> <span class="n">corr_name</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># Contains correlator names</span>
</span><span id="read_mesons-378"><a href="#read_mesons-378"><span class="linenos">378</span></a> <span class="n">corr_type</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># Contains correlator data type (important for reading out numerical data)</span>
</span><span id="read_mesons-379"><a href="#read_mesons-379"><span class="linenos">379</span></a> <span class="n">corr_props</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># Contanis propagator types (Component of corr_kappa)</span>
</span><span id="read_mesons-380"><a href="#read_mesons-380"><span class="linenos">380</span></a> <span class="n">d0</span> <span class="o">=</span> <span class="mi">0</span> <span class="c1"># tvals</span>
</span><span id="read_mesons-381"><a href="#read_mesons-381"><span class="linenos">381</span></a> <span class="n">d1</span> <span class="o">=</span> <span class="mi">0</span> <span class="c1"># nnoise</span>
</span><span id="read_mesons-382"><a href="#read_mesons-382"><span class="linenos">382</span></a> <span class="n">prop_kappa</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># Contains propagator kappas (Component of corr_kappa)</span>
</span><span id="read_mesons-383"><a href="#read_mesons-383"><span class="linenos">383</span></a> <span class="n">prop_source</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># Contains propagator source positions</span>
</span><span id="read_mesons-384"><a href="#read_mesons-384"><span class="linenos">384</span></a> <span class="c1"># Check noise type for multiple replica?</span>
</span><span id="read_mesons-385"><a href="#read_mesons-385"><span class="linenos">385</span></a> <span class="n">corr_no</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
</span><span id="read_mesons-386"><a href="#read_mesons-386"><span class="linenos">386</span></a> <span class="n">data</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="read_mesons-387"><a href="#read_mesons-387"><span class="linenos">387</span></a> <span class="n">idl</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="read_mesons-388"><a href="#read_mesons-388"><span class="linenos">388</span></a>
</span><span id="read_mesons-389"><a href="#read_mesons-389"><span class="linenos">389</span></a> <span class="n">fbdio</span> <span class="o">=</span> <span class="n">bdio_open</span><span class="p">(</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_char_p</span><span class="p">(</span><span class="n">b_path</span><span class="p">),</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_char_p</span><span class="p">(</span><span class="n">b_read</span><span class="p">),</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_char_p</span><span class="p">(</span><span class="n">b_form</span><span class="p">))</span>
</span><span id="read_mesons-390"><a href="#read_mesons-390"><span class="linenos">390</span></a>
</span><span id="read_mesons-391"><a href="#read_mesons-391"><span class="linenos">391</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Reading of bdio file started&#39;</span><span class="p">)</span>
</span><span id="read_mesons-392"><a href="#read_mesons-392"><span class="linenos">392</span></a> <span class="k">while</span> <span class="kc">True</span><span class="p">:</span>
</span><span id="read_mesons-393"><a href="#read_mesons-393"><span class="linenos">393</span></a> <span class="n">bdio_seek_record</span><span class="p">(</span><span class="n">fbdio</span><span class="p">)</span>
</span><span id="read_mesons-394"><a href="#read_mesons-394"><span class="linenos">394</span></a> <span class="n">ruinfo</span> <span class="o">=</span> <span class="n">bdio_get_ruinfo</span><span class="p">(</span><span class="n">fbdio</span><span class="p">)</span>
</span><span id="read_mesons-395"><a href="#read_mesons-395"><span class="linenos">395</span></a> <span class="k">if</span> <span class="n">ruinfo</span> <span class="o">&lt;</span> <span class="mi">0</span><span class="p">:</span>
</span><span id="read_mesons-396"><a href="#read_mesons-396"><span class="linenos">396</span></a> <span class="c1"># EOF reached</span>
</span><span id="read_mesons-397"><a href="#read_mesons-397"><span class="linenos">397</span></a> <span class="k">break</span>
</span><span id="read_mesons-398"><a href="#read_mesons-398"><span class="linenos">398</span></a> <span class="n">rlen</span> <span class="o">=</span> <span class="n">bdio_get_rlen</span><span class="p">(</span><span class="n">fbdio</span><span class="p">)</span>
</span><span id="read_mesons-399"><a href="#read_mesons-399"><span class="linenos">399</span></a> <span class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">5</span><span class="p">:</span>
</span><span id="read_mesons-400"><a href="#read_mesons-400"><span class="linenos">400</span></a> <span class="n">d_buf</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_double</span> <span class="o">*</span> <span class="p">(</span><span class="mi">2</span> <span class="o">+</span> <span class="n">d0</span> <span class="o">*</span> <span class="n">d1</span> <span class="o">*</span> <span class="mi">2</span><span class="p">)</span>
</span><span id="read_mesons-401"><a href="#read_mesons-401"><span class="linenos">401</span></a> <span class="n">pd_buf</span> <span class="o">=</span> <span class="n">d_buf</span><span class="p">()</span>
</span><span id="read_mesons-402"><a href="#read_mesons-402"><span class="linenos">402</span></a> <span class="n">ppd_buf</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">(</span><span class="n">ctypes</span><span class="o">.</span><span class="n">addressof</span><span class="p">(</span><span class="n">pd_buf</span><span class="p">))</span>
</span><span id="read_mesons-403"><a href="#read_mesons-403"><span class="linenos">403</span></a> <span class="n">bdio_read_f64</span><span class="p">(</span><span class="n">ppd_buf</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span><span class="p">(</span><span class="n">rlen</span><span class="p">),</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">(</span><span class="n">fbdio</span><span class="p">))</span>
</span><span id="read_mesons-404"><a href="#read_mesons-404"><span class="linenos">404</span></a> <span class="k">if</span> <span class="n">corr_type</span><span class="p">[</span><span class="n">corr_no</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;complex&#39;</span><span class="p">:</span>
</span><span id="read_mesons-405"><a href="#read_mesons-405"><span class="linenos">405</span></a> <span class="n">tmp_mean</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">pd_buf</span><span class="p">[</span><span class="mi">2</span> <span class="o">+</span> <span class="mi">2</span> <span class="o">*</span> <span class="n">d1</span><span class="p">:</span><span class="o">-</span><span class="mi">2</span> <span class="o">*</span> <span class="n">d1</span><span class="p">:</span><span class="mi">2</span><span class="p">]),</span> <span class="n">d0</span> <span class="o">-</span> <span class="mi">2</span><span class="p">)),</span> <span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
</span><span id="read_mesons-406"><a href="#read_mesons-406"><span class="linenos">406</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="read_mesons-407"><a href="#read_mesons-407"><span class="linenos">407</span></a> <span class="n">tmp_mean</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">pd_buf</span><span class="p">[</span><span class="mi">2</span> <span class="o">+</span> <span class="n">d1</span><span class="p">:</span><span class="o">-</span><span class="n">d0</span> <span class="o">*</span> <span class="n">d1</span> <span class="o">-</span> <span class="n">d1</span><span class="p">]),</span> <span class="n">d0</span> <span class="o">-</span> <span class="mi">2</span><span class="p">)),</span> <span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
</span><span id="read_mesons-408"><a href="#read_mesons-408"><span class="linenos">408</span></a>
</span><span id="read_mesons-409"><a href="#read_mesons-409"><span class="linenos">409</span></a> <span class="n">data</span><span class="p">[</span><span class="n">corr_no</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">tmp_mean</span><span class="p">)</span>
</span><span id="read_mesons-410"><a href="#read_mesons-410"><span class="linenos">410</span></a> <span class="n">corr_no</span> <span class="o">+=</span> <span class="mi">1</span>
</span><span id="read_mesons-411"><a href="#read_mesons-411"><span class="linenos">411</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="read_mesons-412"><a href="#read_mesons-412"><span class="linenos">412</span></a> <span class="n">alt_buf</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">create_string_buffer</span><span class="p">(</span><span class="mi">1024</span><span class="p">)</span>
</span><span id="read_mesons-413"><a href="#read_mesons-413"><span class="linenos">413</span></a> <span class="n">palt_buf</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_char_p</span><span class="p">(</span><span class="n">ctypes</span><span class="o">.</span><span class="n">addressof</span><span class="p">(</span><span class="n">alt_buf</span><span class="p">))</span>
</span><span id="read_mesons-414"><a href="#read_mesons-414"><span class="linenos">414</span></a> <span class="n">iread</span> <span class="o">=</span> <span class="n">bdio_read</span><span class="p">(</span><span class="n">palt_buf</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span><span class="p">(</span><span class="n">rlen</span><span class="p">),</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">(</span><span class="n">fbdio</span><span class="p">))</span>
</span><span id="read_mesons-415"><a href="#read_mesons-415"><span class="linenos">415</span></a> <span class="k">if</span> <span class="n">rlen</span> <span class="o">!=</span> <span class="n">iread</span><span class="p">:</span>
</span><span id="read_mesons-416"><a href="#read_mesons-416"><span class="linenos">416</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Error&#39;</span><span class="p">)</span>
</span><span id="read_mesons-417"><a href="#read_mesons-417"><span class="linenos">417</span></a> <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">item</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">alt_buf</span><span class="p">):</span>
</span><span id="read_mesons-418"><a href="#read_mesons-418"><span class="linenos">418</span></a> <span class="k">if</span> <span class="n">item</span> <span class="o">==</span> <span class="sa">b</span><span class="s1">&#39;</span><span class="se">\x00</span><span class="s1">&#39;</span><span class="p">:</span>
</span><span id="read_mesons-419"><a href="#read_mesons-419"><span class="linenos">419</span></a> <span class="n">alt_buf</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="sa">b</span><span class="s1">&#39; &#39;</span>
</span><span id="read_mesons-420"><a href="#read_mesons-420"><span class="linenos">420</span></a> <span class="n">tmp_string</span> <span class="o">=</span> <span class="p">(</span><span class="n">alt_buf</span><span class="p">[:]</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s2">&quot;utf-8&quot;</span><span class="p">))</span><span class="o">.</span><span class="n">rstrip</span><span class="p">()</span>
</span><span id="read_mesons-421"><a href="#read_mesons-421"><span class="linenos">421</span></a> <span class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
</span><span id="read_mesons-422"><a href="#read_mesons-422"><span class="linenos">422</span></a> <span class="n">ensemble_name</span> <span class="o">=</span> <span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;ENSEMBLE=&#39;</span><span class="p">)</span>
</span><span id="read_mesons-423"><a href="#read_mesons-423"><span class="linenos">423</span></a> <span class="n">volume</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;L0=&#39;</span><span class="p">)))</span>
</span><span id="read_mesons-424"><a href="#read_mesons-424"><span class="linenos">424</span></a> <span class="n">volume</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;L1=&#39;</span><span class="p">)))</span>
</span><span id="read_mesons-425"><a href="#read_mesons-425"><span class="linenos">425</span></a> <span class="n">volume</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;L2=&#39;</span><span class="p">)))</span>
</span><span id="read_mesons-426"><a href="#read_mesons-426"><span class="linenos">426</span></a> <span class="n">volume</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;L3=&#39;</span><span class="p">)))</span>
</span><span id="read_mesons-427"><a href="#read_mesons-427"><span class="linenos">427</span></a> <span class="n">boundary_conditions</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;BC0=&#39;</span><span class="p">))</span>
</span><span id="read_mesons-428"><a href="#read_mesons-428"><span class="linenos">428</span></a> <span class="n">boundary_conditions</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;BC1=&#39;</span><span class="p">))</span>
</span><span id="read_mesons-429"><a href="#read_mesons-429"><span class="linenos">429</span></a> <span class="n">boundary_conditions</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;BC2=&#39;</span><span class="p">))</span>
</span><span id="read_mesons-430"><a href="#read_mesons-430"><span class="linenos">430</span></a> <span class="n">boundary_conditions</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;BC3=&#39;</span><span class="p">))</span>
</span><span id="read_mesons-431"><a href="#read_mesons-431"><span class="linenos">431</span></a>
</span><span id="read_mesons-432"><a href="#read_mesons-432"><span class="linenos">432</span></a> <span class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
</span><span id="read_mesons-433"><a href="#read_mesons-433"><span class="linenos">433</span></a> <span class="n">corr_name</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">_get_corr_name</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;CORR_NAME=&#39;</span><span class="p">))</span>
</span><span id="read_mesons-434"><a href="#read_mesons-434"><span class="linenos">434</span></a> <span class="n">corr_type</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;DATATYPE=&#39;</span><span class="p">))</span>
</span><span id="read_mesons-435"><a href="#read_mesons-435"><span class="linenos">435</span></a> <span class="n">corr_props</span><span class="o">.</span><span class="n">append</span><span class="p">([</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;PROP0=&#39;</span><span class="p">),</span> <span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;PROP1=&#39;</span><span class="p">)])</span>
</span><span id="read_mesons-436"><a href="#read_mesons-436"><span class="linenos">436</span></a> <span class="k">if</span> <span class="n">d0</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
</span><span id="read_mesons-437"><a href="#read_mesons-437"><span class="linenos">437</span></a> <span class="n">d0</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;D0=&#39;</span><span class="p">))</span>
</span><span id="read_mesons-438"><a href="#read_mesons-438"><span class="linenos">438</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="read_mesons-439"><a href="#read_mesons-439"><span class="linenos">439</span></a> <span class="k">if</span> <span class="n">d0</span> <span class="o">!=</span> <span class="nb">int</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;D0=&#39;</span><span class="p">)):</span>
</span><span id="read_mesons-440"><a href="#read_mesons-440"><span class="linenos">440</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Error: Varying number of time values&#39;</span><span class="p">)</span>
</span><span id="read_mesons-441"><a href="#read_mesons-441"><span class="linenos">441</span></a> <span class="k">if</span> <span class="n">d1</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
</span><span id="read_mesons-442"><a href="#read_mesons-442"><span class="linenos">442</span></a> <span class="n">d1</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;D1=&#39;</span><span class="p">))</span>
</span><span id="read_mesons-443"><a href="#read_mesons-443"><span class="linenos">443</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="read_mesons-444"><a href="#read_mesons-444"><span class="linenos">444</span></a> <span class="k">if</span> <span class="n">d1</span> <span class="o">!=</span> <span class="nb">int</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;D1=&#39;</span><span class="p">)):</span>
</span><span id="read_mesons-445"><a href="#read_mesons-445"><span class="linenos">445</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Error: Varying number of random sources&#39;</span><span class="p">)</span>
</span><span id="read_mesons-446"><a href="#read_mesons-446"><span class="linenos">446</span></a> <span class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span>
</span><span id="read_mesons-447"><a href="#read_mesons-447"><span class="linenos">447</span></a> <span class="n">prop_kappa</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;KAPPA=&#39;</span><span class="p">))</span>
</span><span id="read_mesons-448"><a href="#read_mesons-448"><span class="linenos">448</span></a> <span class="n">prop_source</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;x0=&#39;</span><span class="p">))</span>
</span><span id="read_mesons-449"><a href="#read_mesons-449"><span class="linenos">449</span></a> <span class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">4</span><span class="p">:</span>
</span><span id="read_mesons-450"><a href="#read_mesons-450"><span class="linenos">450</span></a> <span class="n">cnfg_no</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;CNFG_ID=&#39;</span><span class="p">))</span>
</span><span id="read_mesons-451"><a href="#read_mesons-451"><span class="linenos">451</span></a> <span class="k">if</span> <span class="n">stop</span><span class="p">:</span>
</span><span id="read_mesons-452"><a href="#read_mesons-452"><span class="linenos">452</span></a> <span class="k">if</span> <span class="n">cnfg_no</span> <span class="o">&gt;</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;stop&#39;</span><span class="p">):</span>
</span><span id="read_mesons-453"><a href="#read_mesons-453"><span class="linenos">453</span></a> <span class="k">break</span>
</span><span id="read_mesons-454"><a href="#read_mesons-454"><span class="linenos">454</span></a> <span class="n">idl</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">cnfg_no</span><span class="p">)</span>
</span><span id="read_mesons-455"><a href="#read_mesons-455"><span class="linenos">455</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\r</span><span class="si">%s</span><span class="s1"> </span><span class="si">%i</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="s1">&#39;Reading configuration&#39;</span><span class="p">,</span> <span class="n">cnfg_no</span><span class="p">),</span> <span class="n">end</span><span class="o">=</span><span class="s1">&#39;</span><span class="se">\r</span><span class="s1">&#39;</span><span class="p">)</span>
</span><span id="read_mesons-456"><a href="#read_mesons-456"><span class="linenos">456</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">idl</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
</span><span id="read_mesons-457"><a href="#read_mesons-457"><span class="linenos">457</span></a> <span class="n">no_corrs</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">corr_name</span><span class="p">)</span>
</span><span id="read_mesons-458"><a href="#read_mesons-458"><span class="linenos">458</span></a> <span class="n">data</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="read_mesons-459"><a href="#read_mesons-459"><span class="linenos">459</span></a> <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">no_corrs</span><span class="p">):</span>
</span><span id="read_mesons-460"><a href="#read_mesons-460"><span class="linenos">460</span></a> <span class="n">data</span><span class="o">.</span><span class="n">append</span><span class="p">([])</span>
</span><span id="read_mesons-461"><a href="#read_mesons-461"><span class="linenos">461</span></a>
</span><span id="read_mesons-462"><a href="#read_mesons-462"><span class="linenos">462</span></a> <span class="n">corr_no</span> <span class="o">=</span> <span class="mi">0</span>
</span><span id="read_mesons-463"><a href="#read_mesons-463"><span class="linenos">463</span></a>
</span><span id="read_mesons-464"><a href="#read_mesons-464"><span class="linenos">464</span></a> <span class="n">bdio_close</span><span class="p">(</span><span class="n">fbdio</span><span class="p">)</span>
</span><span id="read_mesons-465"><a href="#read_mesons-465"><span class="linenos">465</span></a>
</span><span id="read_mesons-466"><a href="#read_mesons-466"><span class="linenos">466</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">Ensemble: &#39;</span><span class="p">,</span> <span class="n">ensemble_name</span><span class="p">)</span>
</span><span id="read_mesons-467"><a href="#read_mesons-467"><span class="linenos">467</span></a> <span class="k">if</span> <span class="s1">&#39;alternative_ensemble_name&#39;</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
</span><span id="read_mesons-468"><a href="#read_mesons-468"><span class="linenos">468</span></a> <span class="n">ensemble_name</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;alternative_ensemble_name&#39;</span><span class="p">)</span>
</span><span id="read_mesons-469"><a href="#read_mesons-469"><span class="linenos">469</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Ensemble name overwritten to&#39;</span><span class="p">,</span> <span class="n">ensemble_name</span><span class="p">)</span>
</span><span id="read_mesons-470"><a href="#read_mesons-470"><span class="linenos">470</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Lattice volume: &#39;</span><span class="p">,</span> <span class="n">volume</span><span class="p">)</span>
</span><span id="read_mesons-471"><a href="#read_mesons-471"><span class="linenos">471</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Boundary conditions: &#39;</span><span class="p">,</span> <span class="n">boundary_conditions</span><span class="p">)</span>
</span><span id="read_mesons-472"><a href="#read_mesons-472"><span class="linenos">472</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Number of time values: &#39;</span><span class="p">,</span> <span class="n">d0</span><span class="p">)</span>
</span><span id="read_mesons-473"><a href="#read_mesons-473"><span class="linenos">473</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Number of random sources: &#39;</span><span class="p">,</span> <span class="n">d1</span><span class="p">)</span>
</span><span id="read_mesons-474"><a href="#read_mesons-474"><span class="linenos">474</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Number of corrs: &#39;</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">corr_name</span><span class="p">))</span>
</span><span id="read_mesons-475"><a href="#read_mesons-475"><span class="linenos">475</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Number of configurations: &#39;</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">idl</span><span class="p">))</span>
</span><span id="read_mesons-476"><a href="#read_mesons-476"><span class="linenos">476</span></a>
</span><span id="read_mesons-477"><a href="#read_mesons-477"><span class="linenos">477</span></a> <span class="n">corr_kappa</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># Contains kappa values for both propagators of given correlation function</span>
</span><span id="read_mesons-478"><a href="#read_mesons-478"><span class="linenos">478</span></a> <span class="n">corr_source</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="read_mesons-479"><a href="#read_mesons-479"><span class="linenos">479</span></a> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">corr_props</span><span class="p">:</span>
</span><span id="read_mesons-480"><a href="#read_mesons-480"><span class="linenos">480</span></a> <span class="n">corr_kappa</span><span class="o">.</span><span class="n">append</span><span class="p">([</span><span class="nb">float</span><span class="p">(</span><span class="n">prop_kappa</span><span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">item</span><span class="p">[</span><span class="mi">0</span><span class="p">])]),</span> <span class="nb">float</span><span class="p">(</span><span class="n">prop_kappa</span><span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">item</span><span class="p">[</span><span class="mi">1</span><span class="p">])])])</span>
</span><span id="read_mesons-481"><a href="#read_mesons-481"><span class="linenos">481</span></a> <span class="k">if</span> <span class="n">prop_source</span><span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">item</span><span class="p">[</span><span class="mi">0</span><span class="p">])]</span> <span class="o">!=</span> <span class="n">prop_source</span><span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">item</span><span class="p">[</span><span class="mi">1</span><span class="p">])]:</span>
</span><span id="read_mesons-482"><a href="#read_mesons-482"><span class="linenos">482</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Source position do not match for correlator&#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">item</span><span class="p">))</span>
</span><span id="read_mesons-483"><a href="#read_mesons-483"><span class="linenos">483</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="read_mesons-484"><a href="#read_mesons-484"><span class="linenos">484</span></a> <span class="n">corr_source</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">prop_source</span><span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">item</span><span class="p">[</span><span class="mi">0</span><span class="p">])]))</span>
</span><span id="read_mesons-485"><a href="#read_mesons-485"><span class="linenos">485</span></a>
</span><span id="read_mesons-486"><a href="#read_mesons-486"><span class="linenos">486</span></a> <span class="k">if</span> <span class="n">stop</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
</span><span id="read_mesons-487"><a href="#read_mesons-487"><span class="linenos">487</span></a> <span class="n">stop</span> <span class="o">=</span> <span class="n">idl</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
</span><span id="read_mesons-488"><a href="#read_mesons-488"><span class="linenos">488</span></a> <span class="n">idl_target</span> <span class="o">=</span> <span class="nb">range</span><span class="p">(</span><span class="n">start</span><span class="p">,</span> <span class="n">stop</span> <span class="o">+</span> <span class="mi">1</span><span class="p">,</span> <span class="n">step</span><span class="p">)</span>
</span><span id="read_mesons-489"><a href="#read_mesons-489"><span class="linenos">489</span></a>
</span><span id="read_mesons-490"><a href="#read_mesons-490"><span class="linenos">490</span></a> <span class="k">if</span> <span class="nb">set</span><span class="p">(</span><span class="n">idl</span><span class="p">)</span> <span class="o">!=</span> <span class="nb">set</span><span class="p">(</span><span class="n">idl_target</span><span class="p">):</span>
</span><span id="read_mesons-491"><a href="#read_mesons-491"><span class="linenos">491</span></a> <span class="k">try</span><span class="p">:</span>
</span><span id="read_mesons-492"><a href="#read_mesons-492"><span class="linenos">492</span></a> <span class="n">indices</span> <span class="o">=</span> <span class="p">[</span><span class="n">idl</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">idl_target</span><span class="p">]</span>
</span><span id="read_mesons-493"><a href="#read_mesons-493"><span class="linenos">493</span></a> <span class="k">except</span> <span class="ne">ValueError</span> <span class="k">as</span> <span class="n">err</span><span class="p">:</span>
</span><span id="read_mesons-494"><a href="#read_mesons-494"><span class="linenos">494</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Configurations in file do no match target list!&#39;</span><span class="p">,</span> <span class="n">err</span><span class="p">)</span>
</span><span id="read_mesons-495"><a href="#read_mesons-495"><span class="linenos">495</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="read_mesons-496"><a href="#read_mesons-496"><span class="linenos">496</span></a> <span class="n">indices</span> <span class="o">=</span> <span class="kc">None</span>
</span><span id="read_mesons-497"><a href="#read_mesons-497"><span class="linenos">497</span></a>
</span><span id="read_mesons-498"><a href="#read_mesons-498"><span class="linenos">498</span></a> <span class="n">result</span> <span class="o">=</span> <span class="p">{}</span>
</span><span id="read_mesons-499"><a href="#read_mesons-499"><span class="linenos">499</span></a> <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">no_corrs</span><span class="p">):</span>
</span><span id="read_mesons-500"><a href="#read_mesons-500"><span class="linenos">500</span></a> <span class="n">tmp_corr</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="read_mesons-501"><a href="#read_mesons-501"><span class="linenos">501</span></a> <span class="n">tmp_data</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">data</span><span class="p">[</span><span class="n">c</span><span class="p">])</span>
</span><span id="read_mesons-502"><a href="#read_mesons-502"><span class="linenos">502</span></a> <span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">d0</span> <span class="o">-</span> <span class="mi">2</span><span class="p">):</span>
</span><span id="read_mesons-503"><a href="#read_mesons-503"><span class="linenos">503</span></a> <span class="k">if</span> <span class="n">indices</span><span class="p">:</span>
</span><span id="read_mesons-504"><a href="#read_mesons-504"><span class="linenos">504</span></a> <span class="n">deltas</span> <span class="o">=</span> <span class="p">[</span><span class="n">tmp_data</span><span class="p">[:,</span> <span class="n">t</span><span class="p">][</span><span class="n">index</span><span class="p">]</span> <span class="k">for</span> <span class="n">index</span> <span class="ow">in</span> <span class="n">indices</span><span class="p">]</span>
</span><span id="read_mesons-505"><a href="#read_mesons-505"><span class="linenos">505</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="read_mesons-506"><a href="#read_mesons-506"><span class="linenos">506</span></a> <span class="n">deltas</span> <span class="o">=</span> <span class="n">tmp_data</span><span class="p">[:,</span> <span class="n">t</span><span class="p">]</span>
</span><span id="read_mesons-507"><a href="#read_mesons-507"><span class="linenos">507</span></a> <span class="n">tmp_corr</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">Obs</span><span class="p">([</span><span class="n">deltas</span><span class="p">],</span> <span class="p">[</span><span class="n">ensemble_name</span><span class="p">],</span> <span class="n">idl</span><span class="o">=</span><span class="p">[</span><span class="n">idl_target</span><span class="p">]))</span>
</span><span id="read_mesons-508"><a href="#read_mesons-508"><span class="linenos">508</span></a> <span class="n">result</span><span class="p">[(</span><span class="n">corr_name</span><span class="p">[</span><span class="n">c</span><span class="p">],</span> <span class="n">corr_source</span><span class="p">[</span><span class="n">c</span><span class="p">])</span> <span class="o">+</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">corr_kappa</span><span class="p">[</span><span class="n">c</span><span class="p">])]</span> <span class="o">=</span> <span class="n">tmp_corr</span>
</span><span id="read_mesons-509"><a href="#read_mesons-509"><span class="linenos">509</span></a>
</span><span id="read_mesons-510"><a href="#read_mesons-510"><span class="linenos">510</span></a> <span class="c1"># Check that all data entries have the same number of configurations</span>
</span><span id="read_mesons-511"><a href="#read_mesons-511"><span class="linenos">511</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="nb">set</span><span class="p">([</span><span class="n">o</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">N</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="nb">list</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">values</span><span class="p">())]))</span> <span class="o">!=</span> <span class="mi">1</span><span class="p">:</span>
</span><span id="read_mesons-512"><a href="#read_mesons-512"><span class="linenos">512</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Error: Not all correlators have the same number of configurations. bdio file is possibly corrupted.&#39;</span><span class="p">)</span>
</span><span id="read_mesons-513"><a href="#read_mesons-513"><span class="linenos">513</span></a>
</span><span id="read_mesons-514"><a href="#read_mesons-514"><span class="linenos">514</span></a> <span class="k">return</span> <span class="n">result</span>
</span></pre></div>
<div class="docstring"><p>Extract mesons data from a bdio file and return it as a dictionary</p>
<p>The dictionary can be accessed with a tuple consisting of (type, source_position, kappa1, kappa2)</p>
<p>read_mesons requires bdio to be compiled into a shared library. This can be achieved by
adding the flag -fPIC to CC and changing the all target to</p>
<p>all: bdio.o $(LIBDIR)
gcc -shared -Wl,-soname,libbdio.so -o $(BUILDDIR)/libbdio.so $(BUILDDIR)/bdio.o
cp $(BUILDDIR)/libbdio.so $(LIBDIR)/</p>
<h6 id="parameters">Parameters</h6>
<ul>
<li><strong>file_path</strong> (str):
path to the bdio file</li>
<li><strong>bdio_path</strong> (str):
path to the shared bdio library libbdio.so (default ./libbdio.so)</li>
<li><strong>start</strong> (int):
The first configuration to be read (default 1)</li>
<li><strong>stop</strong> (int):
The last configuration to be read (default None)</li>
<li><strong>step</strong> (int):
Fixed step size between two measurements (default 1)</li>
<li><strong>alternative_ensemble_name</strong> (str):
Manually overwrite ensemble name</li>
</ul>
<h6 id="returns">Returns</h6>
<ul>
<li><strong>data</strong> (dict):
Extracted meson data</li>
</ul>
</div>
</section>
<section id="read_dSdm">
<input id="read_dSdm-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">read_dSdm</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">file_path</span>, </span><span class="param"><span class="n">bdio_path</span><span class="o">=</span><span class="s1">&#39;./libbdio.so&#39;</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="read_dSdm-view-source"><span>View Source</span></label>
</div>
<a class="headerlink" href="#read_dSdm"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="read_dSdm-517"><a href="#read_dSdm-517"><span class="linenos">517</span></a><span class="k">def</span> <span class="nf">read_dSdm</span><span class="p">(</span><span class="n">file_path</span><span class="p">,</span> <span class="n">bdio_path</span><span class="o">=</span><span class="s1">&#39;./libbdio.so&#39;</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
</span><span id="read_dSdm-518"><a href="#read_dSdm-518"><span class="linenos">518</span></a><span class="w"> </span><span class="sd">&quot;&quot;&quot; Extract dSdm data from a bdio file and return it as a dictionary</span>
</span><span id="read_dSdm-519"><a href="#read_dSdm-519"><span class="linenos">519</span></a>
</span><span id="read_dSdm-520"><a href="#read_dSdm-520"><span class="linenos">520</span></a><span class="sd"> The dictionary can be accessed with a tuple consisting of (type, kappa)</span>
</span><span id="read_dSdm-521"><a href="#read_dSdm-521"><span class="linenos">521</span></a>
</span><span id="read_dSdm-522"><a href="#read_dSdm-522"><span class="linenos">522</span></a><span class="sd"> read_dSdm requires bdio to be compiled into a shared library. This can be achieved by</span>
</span><span id="read_dSdm-523"><a href="#read_dSdm-523"><span class="linenos">523</span></a><span class="sd"> adding the flag -fPIC to CC and changing the all target to</span>
</span><span id="read_dSdm-524"><a href="#read_dSdm-524"><span class="linenos">524</span></a>
</span><span id="read_dSdm-525"><a href="#read_dSdm-525"><span class="linenos">525</span></a><span class="sd"> all: bdio.o $(LIBDIR)</span>
</span><span id="read_dSdm-526"><a href="#read_dSdm-526"><span class="linenos">526</span></a><span class="sd"> gcc -shared -Wl,-soname,libbdio.so -o $(BUILDDIR)/libbdio.so $(BUILDDIR)/bdio.o</span>
</span><span id="read_dSdm-527"><a href="#read_dSdm-527"><span class="linenos">527</span></a><span class="sd"> cp $(BUILDDIR)/libbdio.so $(LIBDIR)/</span>
</span><span id="read_dSdm-528"><a href="#read_dSdm-528"><span class="linenos">528</span></a>
</span><span id="read_dSdm-529"><a href="#read_dSdm-529"><span class="linenos">529</span></a><span class="sd"> Parameters</span>
</span><span id="read_dSdm-530"><a href="#read_dSdm-530"><span class="linenos">530</span></a><span class="sd"> ----------</span>
</span><span id="read_dSdm-531"><a href="#read_dSdm-531"><span class="linenos">531</span></a><span class="sd"> file_path : str</span>
</span><span id="read_dSdm-532"><a href="#read_dSdm-532"><span class="linenos">532</span></a><span class="sd"> path to the bdio file</span>
</span><span id="read_dSdm-533"><a href="#read_dSdm-533"><span class="linenos">533</span></a><span class="sd"> bdio_path : str</span>
</span><span id="read_dSdm-534"><a href="#read_dSdm-534"><span class="linenos">534</span></a><span class="sd"> path to the shared bdio library libbdio.so (default ./libbdio.so)</span>
</span><span id="read_dSdm-535"><a href="#read_dSdm-535"><span class="linenos">535</span></a><span class="sd"> start : int</span>
</span><span id="read_dSdm-536"><a href="#read_dSdm-536"><span class="linenos">536</span></a><span class="sd"> The first configuration to be read (default 1)</span>
</span><span id="read_dSdm-537"><a href="#read_dSdm-537"><span class="linenos">537</span></a><span class="sd"> stop : int</span>
</span><span id="read_dSdm-538"><a href="#read_dSdm-538"><span class="linenos">538</span></a><span class="sd"> The last configuration to be read (default None)</span>
</span><span id="read_dSdm-539"><a href="#read_dSdm-539"><span class="linenos">539</span></a><span class="sd"> step : int</span>
</span><span id="read_dSdm-540"><a href="#read_dSdm-540"><span class="linenos">540</span></a><span class="sd"> Fixed step size between two measurements (default 1)</span>
</span><span id="read_dSdm-541"><a href="#read_dSdm-541"><span class="linenos">541</span></a><span class="sd"> alternative_ensemble_name : str</span>
</span><span id="read_dSdm-542"><a href="#read_dSdm-542"><span class="linenos">542</span></a><span class="sd"> Manually overwrite ensemble name</span>
</span><span id="read_dSdm-543"><a href="#read_dSdm-543"><span class="linenos">543</span></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="read_dSdm-544"><a href="#read_dSdm-544"><span class="linenos">544</span></a>
</span><span id="read_dSdm-545"><a href="#read_dSdm-545"><span class="linenos">545</span></a> <span class="n">start</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;start&#39;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
</span><span id="read_dSdm-546"><a href="#read_dSdm-546"><span class="linenos">546</span></a> <span class="n">stop</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;stop&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
</span><span id="read_dSdm-547"><a href="#read_dSdm-547"><span class="linenos">547</span></a> <span class="n">step</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;step&#39;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
</span><span id="read_dSdm-548"><a href="#read_dSdm-548"><span class="linenos">548</span></a>
</span><span id="read_dSdm-549"><a href="#read_dSdm-549"><span class="linenos">549</span></a> <span class="n">bdio</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">cdll</span><span class="o">.</span><span class="n">LoadLibrary</span><span class="p">(</span><span class="n">bdio_path</span><span class="p">)</span>
</span><span id="read_dSdm-550"><a href="#read_dSdm-550"><span class="linenos">550</span></a>
</span><span id="read_dSdm-551"><a href="#read_dSdm-551"><span class="linenos">551</span></a> <span class="n">bdio_open</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_open</span>
</span><span id="read_dSdm-552"><a href="#read_dSdm-552"><span class="linenos">552</span></a> <span class="n">bdio_open</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span>
</span><span id="read_dSdm-553"><a href="#read_dSdm-553"><span class="linenos">553</span></a>
</span><span id="read_dSdm-554"><a href="#read_dSdm-554"><span class="linenos">554</span></a> <span class="n">bdio_close</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_close</span>
</span><span id="read_dSdm-555"><a href="#read_dSdm-555"><span class="linenos">555</span></a> <span class="n">bdio_close</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_int</span>
</span><span id="read_dSdm-556"><a href="#read_dSdm-556"><span class="linenos">556</span></a> <span class="n">bdio_close</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="read_dSdm-557"><a href="#read_dSdm-557"><span class="linenos">557</span></a>
</span><span id="read_dSdm-558"><a href="#read_dSdm-558"><span class="linenos">558</span></a> <span class="n">bdio_seek_record</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_seek_record</span>
</span><span id="read_dSdm-559"><a href="#read_dSdm-559"><span class="linenos">559</span></a> <span class="n">bdio_seek_record</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_int</span>
</span><span id="read_dSdm-560"><a href="#read_dSdm-560"><span class="linenos">560</span></a> <span class="n">bdio_seek_record</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="read_dSdm-561"><a href="#read_dSdm-561"><span class="linenos">561</span></a>
</span><span id="read_dSdm-562"><a href="#read_dSdm-562"><span class="linenos">562</span></a> <span class="n">bdio_get_rlen</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_get_rlen</span>
</span><span id="read_dSdm-563"><a href="#read_dSdm-563"><span class="linenos">563</span></a> <span class="n">bdio_get_rlen</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_int</span>
</span><span id="read_dSdm-564"><a href="#read_dSdm-564"><span class="linenos">564</span></a> <span class="n">bdio_get_rlen</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="read_dSdm-565"><a href="#read_dSdm-565"><span class="linenos">565</span></a>
</span><span id="read_dSdm-566"><a href="#read_dSdm-566"><span class="linenos">566</span></a> <span class="n">bdio_get_ruinfo</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_get_ruinfo</span>
</span><span id="read_dSdm-567"><a href="#read_dSdm-567"><span class="linenos">567</span></a> <span class="n">bdio_get_ruinfo</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_int</span>
</span><span id="read_dSdm-568"><a href="#read_dSdm-568"><span class="linenos">568</span></a> <span class="n">bdio_get_ruinfo</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="read_dSdm-569"><a href="#read_dSdm-569"><span class="linenos">569</span></a>
</span><span id="read_dSdm-570"><a href="#read_dSdm-570"><span class="linenos">570</span></a> <span class="n">bdio_read</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_read</span>
</span><span id="read_dSdm-571"><a href="#read_dSdm-571"><span class="linenos">571</span></a> <span class="n">bdio_read</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span>
</span><span id="read_dSdm-572"><a href="#read_dSdm-572"><span class="linenos">572</span></a> <span class="n">bdio_read</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_char_p</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="read_dSdm-573"><a href="#read_dSdm-573"><span class="linenos">573</span></a>
</span><span id="read_dSdm-574"><a href="#read_dSdm-574"><span class="linenos">574</span></a> <span class="n">bdio_read_f64</span> <span class="o">=</span> <span class="n">bdio</span><span class="o">.</span><span class="n">bdio_read_f64</span>
</span><span id="read_dSdm-575"><a href="#read_dSdm-575"><span class="linenos">575</span></a> <span class="n">bdio_read_f64</span><span class="o">.</span><span class="n">restype</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span>
</span><span id="read_dSdm-576"><a href="#read_dSdm-576"><span class="linenos">576</span></a> <span class="n">bdio_read_f64</span><span class="o">.</span><span class="n">argtypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">]</span>
</span><span id="read_dSdm-577"><a href="#read_dSdm-577"><span class="linenos">577</span></a>
</span><span id="read_dSdm-578"><a href="#read_dSdm-578"><span class="linenos">578</span></a> <span class="n">b_path</span> <span class="o">=</span> <span class="n">file_path</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span>
</span><span id="read_dSdm-579"><a href="#read_dSdm-579"><span class="linenos">579</span></a> <span class="n">read</span> <span class="o">=</span> <span class="s1">&#39;r&#39;</span>
</span><span id="read_dSdm-580"><a href="#read_dSdm-580"><span class="linenos">580</span></a> <span class="n">b_read</span> <span class="o">=</span> <span class="n">read</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span>
</span><span id="read_dSdm-581"><a href="#read_dSdm-581"><span class="linenos">581</span></a> <span class="n">form</span> <span class="o">=</span> <span class="s1">&#39;Generic Correlator Format 1.0&#39;</span>
</span><span id="read_dSdm-582"><a href="#read_dSdm-582"><span class="linenos">582</span></a> <span class="n">b_form</span> <span class="o">=</span> <span class="n">form</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span>
</span><span id="read_dSdm-583"><a href="#read_dSdm-583"><span class="linenos">583</span></a>
</span><span id="read_dSdm-584"><a href="#read_dSdm-584"><span class="linenos">584</span></a> <span class="n">ensemble_name</span> <span class="o">=</span> <span class="s1">&#39;&#39;</span>
</span><span id="read_dSdm-585"><a href="#read_dSdm-585"><span class="linenos">585</span></a> <span class="n">volume</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># lattice volume</span>
</span><span id="read_dSdm-586"><a href="#read_dSdm-586"><span class="linenos">586</span></a> <span class="n">boundary_conditions</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="read_dSdm-587"><a href="#read_dSdm-587"><span class="linenos">587</span></a> <span class="n">corr_name</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># Contains correlator names</span>
</span><span id="read_dSdm-588"><a href="#read_dSdm-588"><span class="linenos">588</span></a> <span class="n">corr_type</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># Contains correlator data type (important for reading out numerical data)</span>
</span><span id="read_dSdm-589"><a href="#read_dSdm-589"><span class="linenos">589</span></a> <span class="n">corr_props</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># Contains propagator types (Component of corr_kappa)</span>
</span><span id="read_dSdm-590"><a href="#read_dSdm-590"><span class="linenos">590</span></a> <span class="n">d0</span> <span class="o">=</span> <span class="mi">0</span> <span class="c1"># tvals</span>
</span><span id="read_dSdm-591"><a href="#read_dSdm-591"><span class="linenos">591</span></a> <span class="c1"># d1 = 0 # nnoise</span>
</span><span id="read_dSdm-592"><a href="#read_dSdm-592"><span class="linenos">592</span></a> <span class="n">prop_kappa</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># Contains propagator kappas (Component of corr_kappa)</span>
</span><span id="read_dSdm-593"><a href="#read_dSdm-593"><span class="linenos">593</span></a> <span class="c1"># Check noise type for multiple replica?</span>
</span><span id="read_dSdm-594"><a href="#read_dSdm-594"><span class="linenos">594</span></a> <span class="n">corr_no</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
</span><span id="read_dSdm-595"><a href="#read_dSdm-595"><span class="linenos">595</span></a> <span class="n">data</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="read_dSdm-596"><a href="#read_dSdm-596"><span class="linenos">596</span></a> <span class="n">idl</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="read_dSdm-597"><a href="#read_dSdm-597"><span class="linenos">597</span></a>
</span><span id="read_dSdm-598"><a href="#read_dSdm-598"><span class="linenos">598</span></a> <span class="n">fbdio</span> <span class="o">=</span> <span class="n">bdio_open</span><span class="p">(</span><span class="n">ctypes</span><span class="o">.</span><span class="n">c_char_p</span><span class="p">(</span><span class="n">b_path</span><span class="p">),</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_char_p</span><span class="p">(</span><span class="n">b_read</span><span class="p">),</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_char_p</span><span class="p">(</span><span class="n">b_form</span><span class="p">))</span>
</span><span id="read_dSdm-599"><a href="#read_dSdm-599"><span class="linenos">599</span></a>
</span><span id="read_dSdm-600"><a href="#read_dSdm-600"><span class="linenos">600</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Reading of bdio file started&#39;</span><span class="p">)</span>
</span><span id="read_dSdm-601"><a href="#read_dSdm-601"><span class="linenos">601</span></a> <span class="k">while</span> <span class="kc">True</span><span class="p">:</span>
</span><span id="read_dSdm-602"><a href="#read_dSdm-602"><span class="linenos">602</span></a> <span class="n">bdio_seek_record</span><span class="p">(</span><span class="n">fbdio</span><span class="p">)</span>
</span><span id="read_dSdm-603"><a href="#read_dSdm-603"><span class="linenos">603</span></a> <span class="n">ruinfo</span> <span class="o">=</span> <span class="n">bdio_get_ruinfo</span><span class="p">(</span><span class="n">fbdio</span><span class="p">)</span>
</span><span id="read_dSdm-604"><a href="#read_dSdm-604"><span class="linenos">604</span></a> <span class="k">if</span> <span class="n">ruinfo</span> <span class="o">&lt;</span> <span class="mi">0</span><span class="p">:</span>
</span><span id="read_dSdm-605"><a href="#read_dSdm-605"><span class="linenos">605</span></a> <span class="c1"># EOF reached</span>
</span><span id="read_dSdm-606"><a href="#read_dSdm-606"><span class="linenos">606</span></a> <span class="k">break</span>
</span><span id="read_dSdm-607"><a href="#read_dSdm-607"><span class="linenos">607</span></a> <span class="n">rlen</span> <span class="o">=</span> <span class="n">bdio_get_rlen</span><span class="p">(</span><span class="n">fbdio</span><span class="p">)</span>
</span><span id="read_dSdm-608"><a href="#read_dSdm-608"><span class="linenos">608</span></a> <span class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">5</span><span class="p">:</span>
</span><span id="read_dSdm-609"><a href="#read_dSdm-609"><span class="linenos">609</span></a> <span class="n">d_buf</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_double</span> <span class="o">*</span> <span class="p">(</span><span class="mi">2</span> <span class="o">+</span> <span class="n">d0</span><span class="p">)</span>
</span><span id="read_dSdm-610"><a href="#read_dSdm-610"><span class="linenos">610</span></a> <span class="n">pd_buf</span> <span class="o">=</span> <span class="n">d_buf</span><span class="p">()</span>
</span><span id="read_dSdm-611"><a href="#read_dSdm-611"><span class="linenos">611</span></a> <span class="n">ppd_buf</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">(</span><span class="n">ctypes</span><span class="o">.</span><span class="n">addressof</span><span class="p">(</span><span class="n">pd_buf</span><span class="p">))</span>
</span><span id="read_dSdm-612"><a href="#read_dSdm-612"><span class="linenos">612</span></a> <span class="n">bdio_read_f64</span><span class="p">(</span><span class="n">ppd_buf</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span><span class="p">(</span><span class="n">rlen</span><span class="p">),</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">(</span><span class="n">fbdio</span><span class="p">))</span>
</span><span id="read_dSdm-613"><a href="#read_dSdm-613"><span class="linenos">613</span></a> <span class="n">tmp_mean</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">pd_buf</span><span class="p">[</span><span class="mi">2</span><span class="p">:]))</span>
</span><span id="read_dSdm-614"><a href="#read_dSdm-614"><span class="linenos">614</span></a>
</span><span id="read_dSdm-615"><a href="#read_dSdm-615"><span class="linenos">615</span></a> <span class="n">data</span><span class="p">[</span><span class="n">corr_no</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">tmp_mean</span><span class="p">)</span>
</span><span id="read_dSdm-616"><a href="#read_dSdm-616"><span class="linenos">616</span></a> <span class="n">corr_no</span> <span class="o">+=</span> <span class="mi">1</span>
</span><span id="read_dSdm-617"><a href="#read_dSdm-617"><span class="linenos">617</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="read_dSdm-618"><a href="#read_dSdm-618"><span class="linenos">618</span></a> <span class="n">alt_buf</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">create_string_buffer</span><span class="p">(</span><span class="mi">1024</span><span class="p">)</span>
</span><span id="read_dSdm-619"><a href="#read_dSdm-619"><span class="linenos">619</span></a> <span class="n">palt_buf</span> <span class="o">=</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_char_p</span><span class="p">(</span><span class="n">ctypes</span><span class="o">.</span><span class="n">addressof</span><span class="p">(</span><span class="n">alt_buf</span><span class="p">))</span>
</span><span id="read_dSdm-620"><a href="#read_dSdm-620"><span class="linenos">620</span></a> <span class="n">iread</span> <span class="o">=</span> <span class="n">bdio_read</span><span class="p">(</span><span class="n">palt_buf</span><span class="p">,</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_size_t</span><span class="p">(</span><span class="n">rlen</span><span class="p">),</span> <span class="n">ctypes</span><span class="o">.</span><span class="n">c_void_p</span><span class="p">(</span><span class="n">fbdio</span><span class="p">))</span>
</span><span id="read_dSdm-621"><a href="#read_dSdm-621"><span class="linenos">621</span></a> <span class="k">if</span> <span class="n">rlen</span> <span class="o">!=</span> <span class="n">iread</span><span class="p">:</span>
</span><span id="read_dSdm-622"><a href="#read_dSdm-622"><span class="linenos">622</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Error&#39;</span><span class="p">)</span>
</span><span id="read_dSdm-623"><a href="#read_dSdm-623"><span class="linenos">623</span></a> <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">item</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">alt_buf</span><span class="p">):</span>
</span><span id="read_dSdm-624"><a href="#read_dSdm-624"><span class="linenos">624</span></a> <span class="k">if</span> <span class="n">item</span> <span class="o">==</span> <span class="sa">b</span><span class="s1">&#39;</span><span class="se">\x00</span><span class="s1">&#39;</span><span class="p">:</span>
</span><span id="read_dSdm-625"><a href="#read_dSdm-625"><span class="linenos">625</span></a> <span class="n">alt_buf</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="sa">b</span><span class="s1">&#39; &#39;</span>
</span><span id="read_dSdm-626"><a href="#read_dSdm-626"><span class="linenos">626</span></a> <span class="n">tmp_string</span> <span class="o">=</span> <span class="p">(</span><span class="n">alt_buf</span><span class="p">[:]</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s2">&quot;utf-8&quot;</span><span class="p">))</span><span class="o">.</span><span class="n">rstrip</span><span class="p">()</span>
</span><span id="read_dSdm-627"><a href="#read_dSdm-627"><span class="linenos">627</span></a> <span class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
</span><span id="read_dSdm-628"><a href="#read_dSdm-628"><span class="linenos">628</span></a> <span class="n">creator</span> <span class="o">=</span> <span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;CREATOR=&#39;</span><span class="p">)</span>
</span><span id="read_dSdm-629"><a href="#read_dSdm-629"><span class="linenos">629</span></a> <span class="n">ensemble_name</span> <span class="o">=</span> <span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;ENSEMBLE=&#39;</span><span class="p">)</span>
</span><span id="read_dSdm-630"><a href="#read_dSdm-630"><span class="linenos">630</span></a> <span class="n">volume</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;L0=&#39;</span><span class="p">)))</span>
</span><span id="read_dSdm-631"><a href="#read_dSdm-631"><span class="linenos">631</span></a> <span class="n">volume</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;L1=&#39;</span><span class="p">)))</span>
</span><span id="read_dSdm-632"><a href="#read_dSdm-632"><span class="linenos">632</span></a> <span class="n">volume</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;L2=&#39;</span><span class="p">)))</span>
</span><span id="read_dSdm-633"><a href="#read_dSdm-633"><span class="linenos">633</span></a> <span class="n">volume</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;L3=&#39;</span><span class="p">)))</span>
</span><span id="read_dSdm-634"><a href="#read_dSdm-634"><span class="linenos">634</span></a> <span class="n">boundary_conditions</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;BC0=&#39;</span><span class="p">))</span>
</span><span id="read_dSdm-635"><a href="#read_dSdm-635"><span class="linenos">635</span></a> <span class="n">boundary_conditions</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;BC1=&#39;</span><span class="p">))</span>
</span><span id="read_dSdm-636"><a href="#read_dSdm-636"><span class="linenos">636</span></a> <span class="n">boundary_conditions</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;BC2=&#39;</span><span class="p">))</span>
</span><span id="read_dSdm-637"><a href="#read_dSdm-637"><span class="linenos">637</span></a> <span class="n">boundary_conditions</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;BC3=&#39;</span><span class="p">))</span>
</span><span id="read_dSdm-638"><a href="#read_dSdm-638"><span class="linenos">638</span></a>
</span><span id="read_dSdm-639"><a href="#read_dSdm-639"><span class="linenos">639</span></a> <span class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
</span><span id="read_dSdm-640"><a href="#read_dSdm-640"><span class="linenos">640</span></a> <span class="n">corr_name</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">_get_corr_name</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;CORR_NAME=&#39;</span><span class="p">))</span>
</span><span id="read_dSdm-641"><a href="#read_dSdm-641"><span class="linenos">641</span></a> <span class="n">corr_type</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;DATATYPE=&#39;</span><span class="p">))</span>
</span><span id="read_dSdm-642"><a href="#read_dSdm-642"><span class="linenos">642</span></a> <span class="n">corr_props</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;PROP0=&#39;</span><span class="p">))</span>
</span><span id="read_dSdm-643"><a href="#read_dSdm-643"><span class="linenos">643</span></a> <span class="k">if</span> <span class="n">d0</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
</span><span id="read_dSdm-644"><a href="#read_dSdm-644"><span class="linenos">644</span></a> <span class="n">d0</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;D0=&#39;</span><span class="p">))</span>
</span><span id="read_dSdm-645"><a href="#read_dSdm-645"><span class="linenos">645</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="read_dSdm-646"><a href="#read_dSdm-646"><span class="linenos">646</span></a> <span class="k">if</span> <span class="n">d0</span> <span class="o">!=</span> <span class="nb">int</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;D0=&#39;</span><span class="p">)):</span>
</span><span id="read_dSdm-647"><a href="#read_dSdm-647"><span class="linenos">647</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Error: Varying number of time values&#39;</span><span class="p">)</span>
</span><span id="read_dSdm-648"><a href="#read_dSdm-648"><span class="linenos">648</span></a> <span class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span>
</span><span id="read_dSdm-649"><a href="#read_dSdm-649"><span class="linenos">649</span></a> <span class="n">prop_kappa</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;KAPPA=&#39;</span><span class="p">))</span>
</span><span id="read_dSdm-650"><a href="#read_dSdm-650"><span class="linenos">650</span></a> <span class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">4</span><span class="p">:</span>
</span><span id="read_dSdm-651"><a href="#read_dSdm-651"><span class="linenos">651</span></a> <span class="n">cnfg_no</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">_get_kwd</span><span class="p">(</span><span class="n">tmp_string</span><span class="p">,</span> <span class="s1">&#39;CNFG_ID=&#39;</span><span class="p">))</span>
</span><span id="read_dSdm-652"><a href="#read_dSdm-652"><span class="linenos">652</span></a> <span class="k">if</span> <span class="n">stop</span><span class="p">:</span>
</span><span id="read_dSdm-653"><a href="#read_dSdm-653"><span class="linenos">653</span></a> <span class="k">if</span> <span class="n">cnfg_no</span> <span class="o">&gt;</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;stop&#39;</span><span class="p">):</span>
</span><span id="read_dSdm-654"><a href="#read_dSdm-654"><span class="linenos">654</span></a> <span class="k">break</span>
</span><span id="read_dSdm-655"><a href="#read_dSdm-655"><span class="linenos">655</span></a> <span class="n">idl</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">cnfg_no</span><span class="p">)</span>
</span><span id="read_dSdm-656"><a href="#read_dSdm-656"><span class="linenos">656</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\r</span><span class="si">%s</span><span class="s1"> </span><span class="si">%i</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="s1">&#39;Reading configuration&#39;</span><span class="p">,</span> <span class="n">cnfg_no</span><span class="p">),</span> <span class="n">end</span><span class="o">=</span><span class="s1">&#39;</span><span class="se">\r</span><span class="s1">&#39;</span><span class="p">)</span>
</span><span id="read_dSdm-657"><a href="#read_dSdm-657"><span class="linenos">657</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">idl</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
</span><span id="read_dSdm-658"><a href="#read_dSdm-658"><span class="linenos">658</span></a> <span class="n">no_corrs</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">corr_name</span><span class="p">)</span>
</span><span id="read_dSdm-659"><a href="#read_dSdm-659"><span class="linenos">659</span></a> <span class="n">data</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="read_dSdm-660"><a href="#read_dSdm-660"><span class="linenos">660</span></a> <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">no_corrs</span><span class="p">):</span>
</span><span id="read_dSdm-661"><a href="#read_dSdm-661"><span class="linenos">661</span></a> <span class="n">data</span><span class="o">.</span><span class="n">append</span><span class="p">([])</span>
</span><span id="read_dSdm-662"><a href="#read_dSdm-662"><span class="linenos">662</span></a>
</span><span id="read_dSdm-663"><a href="#read_dSdm-663"><span class="linenos">663</span></a> <span class="n">corr_no</span> <span class="o">=</span> <span class="mi">0</span>
</span><span id="read_dSdm-664"><a href="#read_dSdm-664"><span class="linenos">664</span></a> <span class="n">bdio_close</span><span class="p">(</span><span class="n">fbdio</span><span class="p">)</span>
</span><span id="read_dSdm-665"><a href="#read_dSdm-665"><span class="linenos">665</span></a>
</span><span id="read_dSdm-666"><a href="#read_dSdm-666"><span class="linenos">666</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">Creator: &#39;</span><span class="p">,</span> <span class="n">creator</span><span class="p">)</span>
</span><span id="read_dSdm-667"><a href="#read_dSdm-667"><span class="linenos">667</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Ensemble: &#39;</span><span class="p">,</span> <span class="n">ensemble_name</span><span class="p">)</span>
</span><span id="read_dSdm-668"><a href="#read_dSdm-668"><span class="linenos">668</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Lattice volume: &#39;</span><span class="p">,</span> <span class="n">volume</span><span class="p">)</span>
</span><span id="read_dSdm-669"><a href="#read_dSdm-669"><span class="linenos">669</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Boundary conditions: &#39;</span><span class="p">,</span> <span class="n">boundary_conditions</span><span class="p">)</span>
</span><span id="read_dSdm-670"><a href="#read_dSdm-670"><span class="linenos">670</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Number of random sources: &#39;</span><span class="p">,</span> <span class="n">d0</span><span class="p">)</span>
</span><span id="read_dSdm-671"><a href="#read_dSdm-671"><span class="linenos">671</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Number of corrs: &#39;</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">corr_name</span><span class="p">))</span>
</span><span id="read_dSdm-672"><a href="#read_dSdm-672"><span class="linenos">672</span></a> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Number of configurations: &#39;</span><span class="p">,</span> <span class="n">cnfg_no</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
</span><span id="read_dSdm-673"><a href="#read_dSdm-673"><span class="linenos">673</span></a>
</span><span id="read_dSdm-674"><a href="#read_dSdm-674"><span class="linenos">674</span></a> <span class="n">corr_kappa</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># Contains kappa values for both propagators of given correlation function</span>
</span><span id="read_dSdm-675"><a href="#read_dSdm-675"><span class="linenos">675</span></a> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">corr_props</span><span class="p">:</span>
</span><span id="read_dSdm-676"><a href="#read_dSdm-676"><span class="linenos">676</span></a> <span class="n">corr_kappa</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="n">prop_kappa</span><span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">item</span><span class="p">)]))</span>
</span><span id="read_dSdm-677"><a href="#read_dSdm-677"><span class="linenos">677</span></a>
</span><span id="read_dSdm-678"><a href="#read_dSdm-678"><span class="linenos">678</span></a> <span class="k">if</span> <span class="n">stop</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
</span><span id="read_dSdm-679"><a href="#read_dSdm-679"><span class="linenos">679</span></a> <span class="n">stop</span> <span class="o">=</span> <span class="n">idl</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
</span><span id="read_dSdm-680"><a href="#read_dSdm-680"><span class="linenos">680</span></a> <span class="n">idl_target</span> <span class="o">=</span> <span class="nb">range</span><span class="p">(</span><span class="n">start</span><span class="p">,</span> <span class="n">stop</span> <span class="o">+</span> <span class="mi">1</span><span class="p">,</span> <span class="n">step</span><span class="p">)</span>
</span><span id="read_dSdm-681"><a href="#read_dSdm-681"><span class="linenos">681</span></a> <span class="k">try</span><span class="p">:</span>
</span><span id="read_dSdm-682"><a href="#read_dSdm-682"><span class="linenos">682</span></a> <span class="n">indices</span> <span class="o">=</span> <span class="p">[</span><span class="n">idl</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">idl_target</span><span class="p">]</span>
</span><span id="read_dSdm-683"><a href="#read_dSdm-683"><span class="linenos">683</span></a> <span class="k">except</span> <span class="ne">ValueError</span> <span class="k">as</span> <span class="n">err</span><span class="p">:</span>
</span><span id="read_dSdm-684"><a href="#read_dSdm-684"><span class="linenos">684</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Configurations in file do no match target list!&#39;</span><span class="p">,</span> <span class="n">err</span><span class="p">)</span>
</span><span id="read_dSdm-685"><a href="#read_dSdm-685"><span class="linenos">685</span></a>
</span><span id="read_dSdm-686"><a href="#read_dSdm-686"><span class="linenos">686</span></a> <span class="n">result</span> <span class="o">=</span> <span class="p">{}</span>
</span><span id="read_dSdm-687"><a href="#read_dSdm-687"><span class="linenos">687</span></a> <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">no_corrs</span><span class="p">):</span>
</span><span id="read_dSdm-688"><a href="#read_dSdm-688"><span class="linenos">688</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">asarray</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">c</span><span class="p">])[</span><span class="n">index</span><span class="p">]</span> <span class="k">for</span> <span class="n">index</span> <span class="ow">in</span> <span class="n">indices</span><span class="p">]</span>
</span><span id="read_dSdm-689"><a href="#read_dSdm-689"><span class="linenos">689</span></a> <span class="n">result</span><span class="p">[(</span><span class="n">corr_name</span><span class="p">[</span><span class="n">c</span><span class="p">],</span> <span class="nb">str</span><span class="p">(</span><span class="n">corr_kappa</span><span class="p">[</span><span class="n">c</span><span class="p">]))]</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">ensemble_name</span><span class="p">],</span> <span class="n">idl</span><span class="o">=</span><span class="p">[</span><span class="n">idl_target</span><span class="p">])</span>
</span><span id="read_dSdm-690"><a href="#read_dSdm-690"><span class="linenos">690</span></a>
</span><span id="read_dSdm-691"><a href="#read_dSdm-691"><span class="linenos">691</span></a> <span class="c1"># Check that all data entries have the same number of configurations</span>
</span><span id="read_dSdm-692"><a href="#read_dSdm-692"><span class="linenos">692</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="nb">set</span><span class="p">([</span><span class="n">o</span><span class="o">.</span><span class="n">N</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="nb">list</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">values</span><span class="p">())]))</span> <span class="o">!=</span> <span class="mi">1</span><span class="p">:</span>
</span><span id="read_dSdm-693"><a href="#read_dSdm-693"><span class="linenos">693</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Error: Not all correlators have the same number of configurations. bdio file is possibly corrupted.&#39;</span><span class="p">)</span>
</span><span id="read_dSdm-694"><a href="#read_dSdm-694"><span class="linenos">694</span></a>
</span><span id="read_dSdm-695"><a href="#read_dSdm-695"><span class="linenos">695</span></a> <span class="k">return</span> <span class="n">result</span>
</span></pre></div>
<div class="docstring"><p>Extract dSdm data from a bdio file and return it as a dictionary</p>
<p>The dictionary can be accessed with a tuple consisting of (type, kappa)</p>
<p>read_dSdm requires bdio to be compiled into a shared library. This can be achieved by
adding the flag -fPIC to CC and changing the all target to</p>
<p>all: bdio.o $(LIBDIR)
gcc -shared -Wl,-soname,libbdio.so -o $(BUILDDIR)/libbdio.so $(BUILDDIR)/bdio.o
cp $(BUILDDIR)/libbdio.so $(LIBDIR)/</p>
<h6 id="parameters">Parameters</h6>
<ul>
<li><strong>file_path</strong> (str):
path to the bdio file</li>
<li><strong>bdio_path</strong> (str):
path to the shared bdio library libbdio.so (default ./libbdio.so)</li>
<li><strong>start</strong> (int):
The first configuration to be read (default 1)</li>
<li><strong>stop</strong> (int):
The last configuration to be read (default None)</li>
<li><strong>step</strong> (int):
Fixed step size between two measurements (default 1)</li>
<li><strong>alternative_ensemble_name</strong> (str):
Manually overwrite ensemble name</li>
</ul>
</div>
</section>
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<a href="${url}" class="attr ${doc.kind}">${heading}</a>
<div class="docstring">${doc.doc}</div>
</section>
`;
}
return html;
})());
}
if (getSearchTerm()) {
initialize();
searchBox.value = getSearchTerm();
onInput();
} else {
searchBox.addEventListener("focus", initialize, {once: true});
}
searchBox.addEventListener("keydown", e => {
if (["ArrowDown", "ArrowUp", "Enter"].includes(e.key)) {
let focused = currentContent.querySelector(".search-result.focused");
if (!focused) {
currentContent.querySelector(".search-result").classList.add("focused");
} else if (
e.key === "ArrowDown"
&& focused.nextElementSibling
&& focused.nextElementSibling.classList.contains("search-result")
) {
focused.classList.remove("focused");
focused.nextElementSibling.classList.add("focused");
focused.nextElementSibling.scrollIntoView({
behavior: "smooth",
block: "nearest",
inline: "nearest"
});
} else if (
e.key === "ArrowUp"
&& focused.previousElementSibling
&& focused.previousElementSibling.classList.contains("search-result")
) {
focused.classList.remove("focused");
focused.previousElementSibling.classList.add("focused");
focused.previousElementSibling.scrollIntoView({
behavior: "smooth",
block: "nearest",
inline: "nearest"
});
} else if (
e.key === "Enter"
) {
focused.querySelector("a").click();
}
}
});
</script></body>
</html>
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