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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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<summary>View Source</summary>
<div class="codehilite"><pre><span></span><span class="ch">#!/usr/bin/env python</span>
<span class="c1"># coding: utf-8</span>
<span class="kn">import</span> <span class="nn">ctypes</span>
<span class="kn">import</span> <span class="nn">hashlib</span>
<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 class="kn">from</span> <span class="nn">..obs</span> <span class="kn">import</span> <span class="n">Obs</span>
<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">'./libbdio.so'</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
<span class="sd">""" Extract generic MCMC data from a bdio file</span>
<span class="sd"> read_ADerrors requires bdio to be compiled into a shared library. This can be achieved by</span>
<span class="sd"> adding the flag -fPIC to CC and changing the all target to</span>
<span class="sd"> all: bdio.o $(LIBDIR)</span>
<span class="sd"> gcc -shared -Wl,-soname,libbdio.so -o $(BUILDDIR)/libbdio.so $(BUILDDIR)/bdio.o</span>
<span class="sd"> cp $(BUILDDIR)/libbdio.so $(LIBDIR)/</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> file_path -- path to the bdio file</span>
<span class="sd"> bdio_path -- path to the shared bdio library libbdio.so (default ./libbdio.so)</span>
<span class="sd"> """</span>
<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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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">'utf-8'</span><span class="p">)</span>
<span class="n">read</span> <span class="o">=</span> <span class="s1">'r'</span>
<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">'utf-8'</span><span class="p">)</span>
<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 class="n">return_list</span> <span class="o">=</span> <span class="p">[]</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Reading of bdio file started'</span><span class="p">)</span>
<span class="k">while</span> <span class="mi">1</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
<span class="n">bdio_seek_record</span><span class="p">(</span><span class="n">fbdio</span><span class="p">)</span>
<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 class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">7</span><span class="p">:</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'MD5sum found'</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 class="k">continue</span>
<span class="k">if</span> <span class="n">ruinfo</span> <span class="o"><</span> <span class="mi">0</span><span class="p">:</span>
<span class="c1"># EOF reached</span>
<span class="k">break</span>
<span class="n">bdio_get_rlen</span><span class="p">(</span><span class="n">fbdio</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">read_c_double</span><span class="p">():</span>
<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="n">pd_buf</span> <span class="o">=</span> <span class="n">d_buf</span><span class="p">()</span>
<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 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 class="k">return</span> <span class="n">pd_buf</span><span class="o">.</span><span class="n">value</span>
<span class="n">mean</span> <span class="o">=</span> <span class="n">read_c_double</span><span class="p">()</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'mean'</span><span class="p">,</span> <span class="n">mean</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">read_c_size_t</span><span class="p">():</span>
<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 class="n">pd_buf</span> <span class="o">=</span> <span class="n">d_buf</span><span class="p">()</span>
<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 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 class="k">return</span> <span class="n">pd_buf</span><span class="o">.</span><span class="n">value</span>
<span class="n">neid</span> <span class="o">=</span> <span class="n">read_c_size_t</span><span class="p">()</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'neid'</span><span class="p">,</span> <span class="n">neid</span><span class="p">)</span>
<span class="n">ndata</span> <span class="o">=</span> <span class="p">[]</span>
<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 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 class="nb">print</span><span class="p">(</span><span class="s1">'ndata'</span><span class="p">,</span> <span class="n">ndata</span><span class="p">)</span>
<span class="n">nrep</span> <span class="o">=</span> <span class="p">[]</span>
<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 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 class="nb">print</span><span class="p">(</span><span class="s1">'nrep'</span><span class="p">,</span> <span class="n">nrep</span><span class="p">)</span>
<span class="n">vrep</span> <span class="o">=</span> <span class="p">[]</span>
<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 class="n">vrep</span><span class="o">.</span><span class="n">append</span><span class="p">([])</span>
<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 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 class="nb">print</span><span class="p">(</span><span class="s1">'vrep'</span><span class="p">,</span> <span class="n">vrep</span><span class="p">)</span>
<span class="n">ids</span> <span class="o">=</span> <span class="p">[]</span>
<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 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 class="nb">print</span><span class="p">(</span><span class="s1">'ids'</span><span class="p">,</span> <span class="n">ids</span><span class="p">)</span>
<span class="n">nt</span> <span class="o">=</span> <span class="p">[]</span>
<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 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 class="nb">print</span><span class="p">(</span><span class="s1">'nt'</span><span class="p">,</span> <span class="n">nt</span><span class="p">)</span>
<span class="n">zero</span> <span class="o">=</span> <span class="p">[]</span>
<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 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 class="nb">print</span><span class="p">(</span><span class="s1">'zero'</span><span class="p">,</span> <span class="n">zero</span><span class="p">)</span>
<span class="n">four</span> <span class="o">=</span> <span class="p">[]</span>
<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 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 class="nb">print</span><span class="p">(</span><span class="s1">'four'</span><span class="p">,</span> <span class="n">four</span><span class="p">)</span>
<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 class="n">pd_buf</span> <span class="o">=</span> <span class="n">d_buf</span><span class="p">()</span>
<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 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 class="n">delta</span> <span class="o">=</span> <span class="n">pd_buf</span><span class="p">[:]</span>
<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 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 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 class="n">tmp_names</span> <span class="o">=</span> <span class="p">[]</span>
<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 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 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 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 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">' '</span> <span class="o">*</span> <span class="n">missing_chars</span> <span class="o">+</span> <span class="s1">'|r'</span> <span class="o">+</span> <span class="s1">'</span><span class="si">{0:03d}</span><span class="s1">'</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">index</span><span class="p">))</span>
<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 class="n">bdio_close</span><span class="p">(</span><span class="n">fbdio</span><span class="p">)</span>
<span class="nb">print</span><span class="p">()</span>
<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">'observable(s) extracted.'</span><span class="p">)</span>
<span class="k">return</span> <span class="n">return_list</span>
<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">'./libbdio.so'</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
<span class="sd">""" Write Obs to a bdio file according to ADerrors conventions</span>
<span class="sd"> read_mesons requires bdio to be compiled into a shared library. This can be achieved by</span>
<span class="sd"> adding the flag -fPIC to CC and changing the all target to</span>
<span class="sd"> all: bdio.o $(LIBDIR)</span>
<span class="sd"> gcc -shared -Wl,-soname,libbdio.so -o $(BUILDDIR)/libbdio.so $(BUILDDIR)/bdio.o</span>
<span class="sd"> cp $(BUILDDIR)/libbdio.so $(LIBDIR)/</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> file_path -- path to the bdio file</span>
<span class="sd"> bdio_path -- path to the shared bdio library libbdio.so (default ./libbdio.so)</span>
<span class="sd"> """</span>
<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 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">'e_names'</span><span class="p">):</span>
<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">'Run the gamma method first for all obs.'</span><span class="p">)</span>
<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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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">'utf-8'</span><span class="p">)</span>
<span class="n">write</span> <span class="o">=</span> <span class="s1">'w'</span>
<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">'utf-8'</span><span class="p">)</span>
<span class="n">form</span> <span class="o">=</span> <span class="s1">'pyerrors ADerror export'</span>
<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">'utf-8'</span><span class="p">)</span>
<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 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 class="c1"># mean = obs.value</span>
<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 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 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 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 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 class="nb">print</span><span class="p">(</span><span class="s1">'ndata'</span><span class="p">,</span> <span class="n">ndata</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'nrep'</span><span class="p">,</span> <span class="n">nrep</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'vrep'</span><span class="p">,</span> <span class="n">vrep</span><span class="p">)</span>
<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 class="n">ids</span> <span class="o">=</span> <span class="p">[]</span>
<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 class="k">try</span><span class="p">:</span> <span class="c1"># Try to convert key to integer</span>
<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 class="k">except</span> <span class="ne">Exception</span><span class="p">:</span> <span class="c1"># If not possible construct a hash</span>
<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">'utf-8'</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 class="nb">print</span><span class="p">(</span><span class="s1">'ids'</span><span class="p">,</span> <span class="n">ids</span><span class="p">)</span>
<span class="n">nt</span> <span class="o">=</span> <span class="p">[]</span>
<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 class="n">r_length</span> <span class="o">=</span> <span class="p">[]</span>
<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 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 class="c1"># e_N = np.sum(r_length)</span>
<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 class="nb">print</span><span class="p">(</span><span class="s1">'nt'</span><span class="p">,</span> <span class="n">nt</span><span class="p">)</span>
<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 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 class="nb">print</span><span class="p">(</span><span class="s1">'zero'</span><span class="p">,</span> <span class="n">zero</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'four'</span><span class="p">,</span> <span class="n">four</span><span class="p">)</span>
<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 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 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 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 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 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 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 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 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 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 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 class="n">write_c_size_t</span><span class="p">(</span><span class="n">neid</span><span class="p">)</span>
<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 class="n">write_c_size_t</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
<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 class="n">write_c_size_t</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
<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 class="n">write_c_size_t</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
<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 class="n">write_c_size_t</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
<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 class="n">write_c_size_t</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
<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 class="n">write_c_double</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
<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 class="n">write_c_double</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
<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 class="n">write_c_double</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
<span class="n">bdio_close</span><span class="p">(</span><span class="n">fbdio</span><span class="p">)</span>
<span class="k">return</span> <span class="mi">0</span>
<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 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">" "</span><span class="p">,</span> <span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
<span class="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 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">' NDIM='</span><span class="p">,</span> <span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
<span class="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">'./libbdio.so'</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
<span class="sd">""" Extract mesons data from a bdio file and return it as a dictionary</span>
<span class="sd"> The dictionary can be accessed with a tuple consisting of (type, source_position, kappa1, kappa2)</span>
<span class="sd"> read_mesons requires bdio to be compiled into a shared library. This can be achieved by</span>
<span class="sd"> adding the flag -fPIC to CC and changing the all target to</span>
<span class="sd"> all: bdio.o $(LIBDIR)</span>
<span class="sd"> gcc -shared -Wl,-soname,libbdio.so -o $(BUILDDIR)/libbdio.so $(BUILDDIR)/bdio.o</span>
<span class="sd"> cp $(BUILDDIR)/libbdio.so $(LIBDIR)/</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> file_path -- path to the bdio file</span>
<span class="sd"> bdio_path -- path to the shared bdio library libbdio.so (default ./libbdio.so)</span>
<span class="sd"> stop -- stops reading at given configuration number (default None)</span>
<span class="sd"> alternative_ensemble_name -- Manually overwrite ensemble name</span>
<span class="sd"> """</span>
<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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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">'utf-8'</span><span class="p">)</span>
<span class="n">read</span> <span class="o">=</span> <span class="s1">'r'</span>
<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">'utf-8'</span><span class="p">)</span>
<span class="n">form</span> <span class="o">=</span> <span class="s1">'Generic Correlator Format 1.0'</span>
<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">'utf-8'</span><span class="p">)</span>
<span class="n">ensemble_name</span> <span class="o">=</span> <span class="s1">''</span>
<span class="n">volume</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># lattice volume</span>
<span class="n">boundary_conditions</span> <span class="o">=</span> <span class="p">[]</span>
<span class="n">corr_name</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># Contains correlator names</span>
<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 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 class="n">d0</span> <span class="o">=</span> <span class="mi">0</span> <span class="c1"># tvals</span>
<span class="n">d1</span> <span class="o">=</span> <span class="mi">0</span> <span class="c1"># nnoise</span>
<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 class="n">prop_source</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># Contains propagator source positions</span>
<span class="c1"># Check noise type for multiple replica?</span>
<span class="n">cnfg_no</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
<span class="n">corr_no</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
<span class="n">data</span> <span class="o">=</span> <span class="p">[]</span>
<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 class="nb">print</span><span class="p">(</span><span class="s1">'Reading of bdio file started'</span><span class="p">)</span>
<span class="k">while</span> <span class="mi">1</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
<span class="n">bdio_seek_record</span><span class="p">(</span><span class="n">fbdio</span><span class="p">)</span>
<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 class="k">if</span> <span class="n">ruinfo</span> <span class="o"><</span> <span class="mi">0</span><span class="p">:</span>
<span class="c1"># EOF reached</span>
<span class="k">break</span>
<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 class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">5</span><span class="p">:</span>
<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 class="n">pd_buf</span> <span class="o">=</span> <span class="n">d_buf</span><span class="p">()</span>
<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 class="n">iread</span> <span class="o">=</span> <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 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">'complex'</span><span class="p">:</span>
<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 class="k">else</span><span class="p">:</span>
<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 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 class="n">corr_no</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="k">else</span><span class="p">:</span>
<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 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 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 class="k">if</span> <span class="n">rlen</span> <span class="o">!=</span> <span class="n">iread</span><span class="p">:</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Error'</span><span class="p">)</span>
<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 class="k">if</span> <span class="n">item</span> <span class="o">==</span> <span class="sa">b</span><span class="s1">'</span><span class="se">\x00</span><span class="s1">'</span><span class="p">:</span>
<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">' '</span>
<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">"utf-8"</span><span class="p">))</span><span class="o">.</span><span class="n">rstrip</span><span class="p">()</span>
<span class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<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">'ENSEMBLE='</span><span class="p">)</span>
<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">'L0='</span><span class="p">)))</span>
<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">'L1='</span><span class="p">)))</span>
<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">'L2='</span><span class="p">)))</span>
<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">'L3='</span><span class="p">)))</span>
<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">'BC0='</span><span class="p">))</span>
<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">'BC1='</span><span class="p">))</span>
<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">'BC2='</span><span class="p">))</span>
<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">'BC3='</span><span class="p">))</span>
<span class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
<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">'CORR_NAME='</span><span class="p">))</span>
<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">'DATATYPE='</span><span class="p">))</span>
<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">'PROP0='</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">'PROP1='</span><span class="p">)])</span>
<span class="k">if</span> <span class="n">d0</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</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">'D0='</span><span class="p">))</span>
<span class="k">else</span><span class="p">:</span>
<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">'D0='</span><span class="p">)):</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Error: Varying number of time values'</span><span class="p">)</span>
<span class="k">if</span> <span class="n">d1</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</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">'D1='</span><span class="p">))</span>
<span class="k">else</span><span class="p">:</span>
<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">'D1='</span><span class="p">)):</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Error: Varying number of random sources'</span><span class="p">)</span>
<span class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span>
<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">'KAPPA='</span><span class="p">))</span>
<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">'x0='</span><span class="p">))</span>
<span class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">4</span><span class="p">:</span>
<span class="k">if</span> <span class="s1">'stop'</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
<span class="k">if</span> <span class="n">cnfg_no</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">'stop'</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span><span class="p">:</span>
<span class="k">break</span>
<span class="n">cnfg_no</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'</span><span class="se">\r</span><span class="si">%s</span><span class="s1"> </span><span class="si">%i</span><span class="s1">'</span> <span class="o">%</span> <span class="p">(</span><span class="s1">'Reading configuration'</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 class="n">end</span><span class="o">=</span><span class="s1">'</span><span class="se">\r</span><span class="s1">'</span><span class="p">)</span>
<span class="k">if</span> <span class="n">cnfg_no</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<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 class="n">data</span> <span class="o">=</span> <span class="p">[]</span>
<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 class="n">data</span><span class="o">.</span><span class="n">append</span><span class="p">([])</span>
<span class="n">corr_no</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">bdio_close</span><span class="p">(</span><span class="n">fbdio</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'</span><span class="se">\n</span><span class="s1">Ensemble: '</span><span class="p">,</span> <span class="n">ensemble_name</span><span class="p">)</span>
<span class="k">if</span> <span class="s1">'alternative_ensemble_name'</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
<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">'alternative_ensemble_name'</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Ensemble name overwritten to'</span><span class="p">,</span> <span class="n">ensemble_name</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Lattice volume: '</span><span class="p">,</span> <span class="n">volume</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Boundary conditions: '</span><span class="p">,</span> <span class="n">boundary_conditions</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Number of time values: '</span><span class="p">,</span> <span class="n">d0</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Number of random sources: '</span><span class="p">,</span> <span class="n">d1</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Number of corrs: '</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 class="nb">print</span><span class="p">(</span><span class="s1">'Number of configurations: '</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 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 class="n">corr_source</span> <span class="o">=</span> <span class="p">[]</span>
<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 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 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 class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">'Source position do not match for correlator'</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">item</span><span class="p">))</span>
<span class="k">else</span><span class="p">:</span>
<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 class="n">result</span> <span class="o">=</span> <span class="p">{}</span>
<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 class="n">tmp_corr</span> <span class="o">=</span> <span class="p">[]</span>
<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 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">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">t</span><span class="p">]],</span> <span class="p">[</span><span class="n">ensemble_name</span><span class="p">]))</span>
<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="nb">sorted</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 class="c1"># Check that all data entries have the same number of configurations</span>
<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 class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">'Error: Not all correlators have the same number of configurations. bdio file is possibly corrupted.'</span><span class="p">)</span>
<span class="k">return</span> <span class="n">result</span>
<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">'./libbdio.so'</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
<span class="sd">""" Extract dSdm data from a bdio file and return it as a dictionary</span>
<span class="sd"> The dictionary can be accessed with a tuple consisting of (type, kappa)</span>
<span class="sd"> read_dSdm requires bdio to be compiled into a shared library. This can be achieved by</span>
<span class="sd"> adding the flag -fPIC to CC and changing the all target to</span>
<span class="sd"> all: bdio.o $(LIBDIR)</span>
<span class="sd"> gcc -shared -Wl,-soname,libbdio.so -o $(BUILDDIR)/libbdio.so $(BUILDDIR)/bdio.o</span>
<span class="sd"> cp $(BUILDDIR)/libbdio.so $(LIBDIR)/</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> file_path -- path to the bdio file</span>
<span class="sd"> bdio_path -- path to the shared bdio library libbdio.so (default ./libbdio.so)</span>
<span class="sd"> stop -- stops reading at given configuration number (default None)</span>
<span class="sd"> """</span>
<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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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">'utf-8'</span><span class="p">)</span>
<span class="n">read</span> <span class="o">=</span> <span class="s1">'r'</span>
<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">'utf-8'</span><span class="p">)</span>
<span class="n">form</span> <span class="o">=</span> <span class="s1">'Generic Correlator Format 1.0'</span>
<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">'utf-8'</span><span class="p">)</span>
<span class="n">ensemble_name</span> <span class="o">=</span> <span class="s1">''</span>
<span class="n">volume</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># lattice volume</span>
<span class="n">boundary_conditions</span> <span class="o">=</span> <span class="p">[]</span>
<span class="n">corr_name</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># Contains correlator names</span>
<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 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 class="n">d0</span> <span class="o">=</span> <span class="mi">0</span> <span class="c1"># tvals</span>
<span class="c1"># d1 = 0 # nnoise</span>
<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 class="c1"># Check noise type for multiple replica?</span>
<span class="n">cnfg_no</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
<span class="n">corr_no</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
<span class="n">data</span> <span class="o">=</span> <span class="p">[]</span>
<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 class="nb">print</span><span class="p">(</span><span class="s1">'Reading of bdio file started'</span><span class="p">)</span>
<span class="k">while</span> <span class="mi">1</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
<span class="n">bdio_seek_record</span><span class="p">(</span><span class="n">fbdio</span><span class="p">)</span>
<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 class="k">if</span> <span class="n">ruinfo</span> <span class="o"><</span> <span class="mi">0</span><span class="p">:</span>
<span class="c1"># EOF reached</span>
<span class="k">break</span>
<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 class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">5</span><span class="p">:</span>
<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 class="n">pd_buf</span> <span class="o">=</span> <span class="n">d_buf</span><span class="p">()</span>
<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 class="n">iread</span> <span class="o">=</span> <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 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 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 class="n">corr_no</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="k">else</span><span class="p">:</span>
<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 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 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 class="k">if</span> <span class="n">rlen</span> <span class="o">!=</span> <span class="n">iread</span><span class="p">:</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Error'</span><span class="p">)</span>
<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 class="k">if</span> <span class="n">item</span> <span class="o">==</span> <span class="sa">b</span><span class="s1">'</span><span class="se">\x00</span><span class="s1">'</span><span class="p">:</span>
<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">' '</span>
<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">"utf-8"</span><span class="p">))</span><span class="o">.</span><span class="n">rstrip</span><span class="p">()</span>
<span class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<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">'CREATOR='</span><span class="p">)</span>
<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">'ENSEMBLE='</span><span class="p">)</span>
<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">'L0='</span><span class="p">)))</span>
<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">'L1='</span><span class="p">)))</span>
<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">'L2='</span><span class="p">)))</span>
<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">'L3='</span><span class="p">)))</span>
<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">'BC0='</span><span class="p">))</span>
<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">'BC1='</span><span class="p">))</span>
<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">'BC2='</span><span class="p">))</span>
<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">'BC3='</span><span class="p">))</span>
<span class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
<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">'CORR_NAME='</span><span class="p">))</span>
<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">'DATATYPE='</span><span class="p">))</span>
<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">'PROP0='</span><span class="p">))</span>
<span class="k">if</span> <span class="n">d0</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</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">'D0='</span><span class="p">))</span>
<span class="k">else</span><span class="p">:</span>
<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">'D0='</span><span class="p">)):</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Error: Varying number of time values'</span><span class="p">)</span>
<span class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span>
<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">'KAPPA='</span><span class="p">))</span>
<span class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">4</span><span class="p">:</span>
<span class="k">if</span> <span class="s1">'stop'</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
<span class="k">if</span> <span class="n">cnfg_no</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">'stop'</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span><span class="p">:</span>
<span class="k">break</span>
<span class="n">cnfg_no</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'</span><span class="se">\r</span><span class="si">%s</span><span class="s1"> </span><span class="si">%i</span><span class="s1">'</span> <span class="o">%</span> <span class="p">(</span><span class="s1">'Reading configuration'</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 class="n">end</span><span class="o">=</span><span class="s1">'</span><span class="se">\r</span><span class="s1">'</span><span class="p">)</span>
<span class="k">if</span> <span class="n">cnfg_no</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<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 class="n">data</span> <span class="o">=</span> <span class="p">[]</span>
<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 class="n">data</span><span class="o">.</span><span class="n">append</span><span class="p">([])</span>
<span class="n">corr_no</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">bdio_close</span><span class="p">(</span><span class="n">fbdio</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'</span><span class="se">\n</span><span class="s1">Creator: '</span><span class="p">,</span> <span class="n">creator</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Ensemble: '</span><span class="p">,</span> <span class="n">ensemble_name</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Lattice volume: '</span><span class="p">,</span> <span class="n">volume</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Boundary conditions: '</span><span class="p">,</span> <span class="n">boundary_conditions</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Number of random sources: '</span><span class="p">,</span> <span class="n">d0</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Number of corrs: '</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 class="nb">print</span><span class="p">(</span><span class="s1">'Number of configurations: '</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 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 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 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="n">result</span> <span class="o">=</span> <span class="p">{}</span>
<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 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">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="p">[</span><span class="n">ensemble_name</span><span class="p">])</span>
<span class="c1"># Check that all data entries have the same number of configurations</span>
<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 class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">'Error: Not all correlators have the same number of configurations. bdio file is possibly corrupted.'</span><span class="p">)</span>
<span class="k">return</span> <span class="n">result</span>
</pre></div>
</details>
</section>
<section id="read_ADerrors">
<div class="attr function"><a class="headerlink" href="#read_ADerrors">#  </a>
<span class="def">def</span>
<span class="name">read_ADerrors</span><span class="signature">(file_path, bdio_path='./libbdio.so', **kwargs)</span>:
</div>
<details>
<summary>View Source</summary>
<div class="codehilite"><pre><span></span><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">'./libbdio.so'</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
<span class="sd">""" Extract generic MCMC data from a bdio file</span>
<span class="sd"> read_ADerrors requires bdio to be compiled into a shared library. This can be achieved by</span>
<span class="sd"> adding the flag -fPIC to CC and changing the all target to</span>
<span class="sd"> all: bdio.o $(LIBDIR)</span>
<span class="sd"> gcc -shared -Wl,-soname,libbdio.so -o $(BUILDDIR)/libbdio.so $(BUILDDIR)/bdio.o</span>
<span class="sd"> cp $(BUILDDIR)/libbdio.so $(LIBDIR)/</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> file_path -- path to the bdio file</span>
<span class="sd"> bdio_path -- path to the shared bdio library libbdio.so (default ./libbdio.so)</span>
<span class="sd"> """</span>
<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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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">'utf-8'</span><span class="p">)</span>
<span class="n">read</span> <span class="o">=</span> <span class="s1">'r'</span>
<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">'utf-8'</span><span class="p">)</span>
<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 class="n">return_list</span> <span class="o">=</span> <span class="p">[]</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Reading of bdio file started'</span><span class="p">)</span>
<span class="k">while</span> <span class="mi">1</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
<span class="n">bdio_seek_record</span><span class="p">(</span><span class="n">fbdio</span><span class="p">)</span>
<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 class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">7</span><span class="p">:</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'MD5sum found'</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 class="k">continue</span>
<span class="k">if</span> <span class="n">ruinfo</span> <span class="o"><</span> <span class="mi">0</span><span class="p">:</span>
<span class="c1"># EOF reached</span>
<span class="k">break</span>
<span class="n">bdio_get_rlen</span><span class="p">(</span><span class="n">fbdio</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">read_c_double</span><span class="p">():</span>
<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="n">pd_buf</span> <span class="o">=</span> <span class="n">d_buf</span><span class="p">()</span>
<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 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 class="k">return</span> <span class="n">pd_buf</span><span class="o">.</span><span class="n">value</span>
<span class="n">mean</span> <span class="o">=</span> <span class="n">read_c_double</span><span class="p">()</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'mean'</span><span class="p">,</span> <span class="n">mean</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">read_c_size_t</span><span class="p">():</span>
<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 class="n">pd_buf</span> <span class="o">=</span> <span class="n">d_buf</span><span class="p">()</span>
<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 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 class="k">return</span> <span class="n">pd_buf</span><span class="o">.</span><span class="n">value</span>
<span class="n">neid</span> <span class="o">=</span> <span class="n">read_c_size_t</span><span class="p">()</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'neid'</span><span class="p">,</span> <span class="n">neid</span><span class="p">)</span>
<span class="n">ndata</span> <span class="o">=</span> <span class="p">[]</span>
<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 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 class="nb">print</span><span class="p">(</span><span class="s1">'ndata'</span><span class="p">,</span> <span class="n">ndata</span><span class="p">)</span>
<span class="n">nrep</span> <span class="o">=</span> <span class="p">[]</span>
<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 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 class="nb">print</span><span class="p">(</span><span class="s1">'nrep'</span><span class="p">,</span> <span class="n">nrep</span><span class="p">)</span>
<span class="n">vrep</span> <span class="o">=</span> <span class="p">[]</span>
<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 class="n">vrep</span><span class="o">.</span><span class="n">append</span><span class="p">([])</span>
<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 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 class="nb">print</span><span class="p">(</span><span class="s1">'vrep'</span><span class="p">,</span> <span class="n">vrep</span><span class="p">)</span>
<span class="n">ids</span> <span class="o">=</span> <span class="p">[]</span>
<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 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 class="nb">print</span><span class="p">(</span><span class="s1">'ids'</span><span class="p">,</span> <span class="n">ids</span><span class="p">)</span>
<span class="n">nt</span> <span class="o">=</span> <span class="p">[]</span>
<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 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 class="nb">print</span><span class="p">(</span><span class="s1">'nt'</span><span class="p">,</span> <span class="n">nt</span><span class="p">)</span>
<span class="n">zero</span> <span class="o">=</span> <span class="p">[]</span>
<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 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 class="nb">print</span><span class="p">(</span><span class="s1">'zero'</span><span class="p">,</span> <span class="n">zero</span><span class="p">)</span>
<span class="n">four</span> <span class="o">=</span> <span class="p">[]</span>
<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 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 class="nb">print</span><span class="p">(</span><span class="s1">'four'</span><span class="p">,</span> <span class="n">four</span><span class="p">)</span>
<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 class="n">pd_buf</span> <span class="o">=</span> <span class="n">d_buf</span><span class="p">()</span>
<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 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 class="n">delta</span> <span class="o">=</span> <span class="n">pd_buf</span><span class="p">[:]</span>
<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 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 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 class="n">tmp_names</span> <span class="o">=</span> <span class="p">[]</span>
<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 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 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 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 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">' '</span> <span class="o">*</span> <span class="n">missing_chars</span> <span class="o">+</span> <span class="s1">'|r'</span> <span class="o">+</span> <span class="s1">'</span><span class="si">{0:03d}</span><span class="s1">'</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">index</span><span class="p">))</span>
<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 class="n">bdio_close</span><span class="p">(</span><span class="n">fbdio</span><span class="p">)</span>
<span class="nb">print</span><span class="p">()</span>
<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">'observable(s) extracted.'</span><span class="p">)</span>
<span class="k">return</span> <span class="n">return_list</span>
</pre></div>
</details>
<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>
</div>
</section>
<section id="write_ADerrors">
<div class="attr function"><a class="headerlink" href="#write_ADerrors">#  </a>
<span class="def">def</span>
<span class="name">write_ADerrors</span><span class="signature">(obs_list, file_path, bdio_path='./libbdio.so', **kwargs)</span>:
</div>
<details>
<summary>View Source</summary>
<div class="codehilite"><pre><span></span><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">'./libbdio.so'</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
<span class="sd">""" Write Obs to a bdio file according to ADerrors conventions</span>
<span class="sd"> read_mesons requires bdio to be compiled into a shared library. This can be achieved by</span>
<span class="sd"> adding the flag -fPIC to CC and changing the all target to</span>
<span class="sd"> all: bdio.o $(LIBDIR)</span>
<span class="sd"> gcc -shared -Wl,-soname,libbdio.so -o $(BUILDDIR)/libbdio.so $(BUILDDIR)/bdio.o</span>
<span class="sd"> cp $(BUILDDIR)/libbdio.so $(LIBDIR)/</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> file_path -- path to the bdio file</span>
<span class="sd"> bdio_path -- path to the shared bdio library libbdio.so (default ./libbdio.so)</span>
<span class="sd"> """</span>
<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 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">'e_names'</span><span class="p">):</span>
<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">'Run the gamma method first for all obs.'</span><span class="p">)</span>
<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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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">'utf-8'</span><span class="p">)</span>
<span class="n">write</span> <span class="o">=</span> <span class="s1">'w'</span>
<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">'utf-8'</span><span class="p">)</span>
<span class="n">form</span> <span class="o">=</span> <span class="s1">'pyerrors ADerror export'</span>
<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">'utf-8'</span><span class="p">)</span>
<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 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 class="c1"># mean = obs.value</span>
<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 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 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 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 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 class="nb">print</span><span class="p">(</span><span class="s1">'ndata'</span><span class="p">,</span> <span class="n">ndata</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'nrep'</span><span class="p">,</span> <span class="n">nrep</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'vrep'</span><span class="p">,</span> <span class="n">vrep</span><span class="p">)</span>
<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 class="n">ids</span> <span class="o">=</span> <span class="p">[]</span>
<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 class="k">try</span><span class="p">:</span> <span class="c1"># Try to convert key to integer</span>
<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 class="k">except</span> <span class="ne">Exception</span><span class="p">:</span> <span class="c1"># If not possible construct a hash</span>
<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">'utf-8'</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 class="nb">print</span><span class="p">(</span><span class="s1">'ids'</span><span class="p">,</span> <span class="n">ids</span><span class="p">)</span>
<span class="n">nt</span> <span class="o">=</span> <span class="p">[]</span>
<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 class="n">r_length</span> <span class="o">=</span> <span class="p">[]</span>
<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 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 class="c1"># e_N = np.sum(r_length)</span>
<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 class="nb">print</span><span class="p">(</span><span class="s1">'nt'</span><span class="p">,</span> <span class="n">nt</span><span class="p">)</span>
<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 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 class="nb">print</span><span class="p">(</span><span class="s1">'zero'</span><span class="p">,</span> <span class="n">zero</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'four'</span><span class="p">,</span> <span class="n">four</span><span class="p">)</span>
<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 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 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 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 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 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 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 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 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 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 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 class="n">write_c_size_t</span><span class="p">(</span><span class="n">neid</span><span class="p">)</span>
<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 class="n">write_c_size_t</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
<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 class="n">write_c_size_t</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
<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 class="n">write_c_size_t</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
<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 class="n">write_c_size_t</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
<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 class="n">write_c_size_t</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
<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 class="n">write_c_double</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
<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 class="n">write_c_double</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
<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 class="n">write_c_double</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
<span class="n">bdio_close</span><span class="p">(</span><span class="n">fbdio</span><span class="p">)</span>
<span class="k">return</span> <span class="mi">0</span>
</pre></div>
</details>
<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>
</div>
</section>
<section id="read_mesons">
<div class="attr function"><a class="headerlink" href="#read_mesons">#  </a>
<span class="def">def</span>
<span class="name">read_mesons</span><span class="signature">(file_path, bdio_path='./libbdio.so', **kwargs)</span>:
</div>
<details>
<summary>View Source</summary>
<div class="codehilite"><pre><span></span><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">'./libbdio.so'</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
<span class="sd">""" Extract mesons data from a bdio file and return it as a dictionary</span>
<span class="sd"> The dictionary can be accessed with a tuple consisting of (type, source_position, kappa1, kappa2)</span>
<span class="sd"> read_mesons requires bdio to be compiled into a shared library. This can be achieved by</span>
<span class="sd"> adding the flag -fPIC to CC and changing the all target to</span>
<span class="sd"> all: bdio.o $(LIBDIR)</span>
<span class="sd"> gcc -shared -Wl,-soname,libbdio.so -o $(BUILDDIR)/libbdio.so $(BUILDDIR)/bdio.o</span>
<span class="sd"> cp $(BUILDDIR)/libbdio.so $(LIBDIR)/</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> file_path -- path to the bdio file</span>
<span class="sd"> bdio_path -- path to the shared bdio library libbdio.so (default ./libbdio.so)</span>
<span class="sd"> stop -- stops reading at given configuration number (default None)</span>
<span class="sd"> alternative_ensemble_name -- Manually overwrite ensemble name</span>
<span class="sd"> """</span>
<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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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">'utf-8'</span><span class="p">)</span>
<span class="n">read</span> <span class="o">=</span> <span class="s1">'r'</span>
<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">'utf-8'</span><span class="p">)</span>
<span class="n">form</span> <span class="o">=</span> <span class="s1">'Generic Correlator Format 1.0'</span>
<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">'utf-8'</span><span class="p">)</span>
<span class="n">ensemble_name</span> <span class="o">=</span> <span class="s1">''</span>
<span class="n">volume</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># lattice volume</span>
<span class="n">boundary_conditions</span> <span class="o">=</span> <span class="p">[]</span>
<span class="n">corr_name</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># Contains correlator names</span>
<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 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 class="n">d0</span> <span class="o">=</span> <span class="mi">0</span> <span class="c1"># tvals</span>
<span class="n">d1</span> <span class="o">=</span> <span class="mi">0</span> <span class="c1"># nnoise</span>
<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 class="n">prop_source</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># Contains propagator source positions</span>
<span class="c1"># Check noise type for multiple replica?</span>
<span class="n">cnfg_no</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
<span class="n">corr_no</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
<span class="n">data</span> <span class="o">=</span> <span class="p">[]</span>
<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 class="nb">print</span><span class="p">(</span><span class="s1">'Reading of bdio file started'</span><span class="p">)</span>
<span class="k">while</span> <span class="mi">1</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
<span class="n">bdio_seek_record</span><span class="p">(</span><span class="n">fbdio</span><span class="p">)</span>
<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 class="k">if</span> <span class="n">ruinfo</span> <span class="o"><</span> <span class="mi">0</span><span class="p">:</span>
<span class="c1"># EOF reached</span>
<span class="k">break</span>
<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 class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">5</span><span class="p">:</span>
<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 class="n">pd_buf</span> <span class="o">=</span> <span class="n">d_buf</span><span class="p">()</span>
<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 class="n">iread</span> <span class="o">=</span> <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 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">'complex'</span><span class="p">:</span>
<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 class="k">else</span><span class="p">:</span>
<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 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 class="n">corr_no</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="k">else</span><span class="p">:</span>
<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 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 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 class="k">if</span> <span class="n">rlen</span> <span class="o">!=</span> <span class="n">iread</span><span class="p">:</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Error'</span><span class="p">)</span>
<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 class="k">if</span> <span class="n">item</span> <span class="o">==</span> <span class="sa">b</span><span class="s1">'</span><span class="se">\x00</span><span class="s1">'</span><span class="p">:</span>
<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">' '</span>
<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">"utf-8"</span><span class="p">))</span><span class="o">.</span><span class="n">rstrip</span><span class="p">()</span>
<span class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<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">'ENSEMBLE='</span><span class="p">)</span>
<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">'L0='</span><span class="p">)))</span>
<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">'L1='</span><span class="p">)))</span>
<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">'L2='</span><span class="p">)))</span>
<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">'L3='</span><span class="p">)))</span>
<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">'BC0='</span><span class="p">))</span>
<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">'BC1='</span><span class="p">))</span>
<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">'BC2='</span><span class="p">))</span>
<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">'BC3='</span><span class="p">))</span>
<span class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
<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">'CORR_NAME='</span><span class="p">))</span>
<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">'DATATYPE='</span><span class="p">))</span>
<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">'PROP0='</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">'PROP1='</span><span class="p">)])</span>
<span class="k">if</span> <span class="n">d0</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</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">'D0='</span><span class="p">))</span>
<span class="k">else</span><span class="p">:</span>
<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">'D0='</span><span class="p">)):</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Error: Varying number of time values'</span><span class="p">)</span>
<span class="k">if</span> <span class="n">d1</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</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">'D1='</span><span class="p">))</span>
<span class="k">else</span><span class="p">:</span>
<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">'D1='</span><span class="p">)):</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Error: Varying number of random sources'</span><span class="p">)</span>
<span class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span>
<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">'KAPPA='</span><span class="p">))</span>
<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">'x0='</span><span class="p">))</span>
<span class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">4</span><span class="p">:</span>
<span class="k">if</span> <span class="s1">'stop'</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
<span class="k">if</span> <span class="n">cnfg_no</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">'stop'</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span><span class="p">:</span>
<span class="k">break</span>
<span class="n">cnfg_no</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'</span><span class="se">\r</span><span class="si">%s</span><span class="s1"> </span><span class="si">%i</span><span class="s1">'</span> <span class="o">%</span> <span class="p">(</span><span class="s1">'Reading configuration'</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 class="n">end</span><span class="o">=</span><span class="s1">'</span><span class="se">\r</span><span class="s1">'</span><span class="p">)</span>
<span class="k">if</span> <span class="n">cnfg_no</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<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 class="n">data</span> <span class="o">=</span> <span class="p">[]</span>
<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 class="n">data</span><span class="o">.</span><span class="n">append</span><span class="p">([])</span>
<span class="n">corr_no</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">bdio_close</span><span class="p">(</span><span class="n">fbdio</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'</span><span class="se">\n</span><span class="s1">Ensemble: '</span><span class="p">,</span> <span class="n">ensemble_name</span><span class="p">)</span>
<span class="k">if</span> <span class="s1">'alternative_ensemble_name'</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
<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">'alternative_ensemble_name'</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Ensemble name overwritten to'</span><span class="p">,</span> <span class="n">ensemble_name</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Lattice volume: '</span><span class="p">,</span> <span class="n">volume</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Boundary conditions: '</span><span class="p">,</span> <span class="n">boundary_conditions</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Number of time values: '</span><span class="p">,</span> <span class="n">d0</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Number of random sources: '</span><span class="p">,</span> <span class="n">d1</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Number of corrs: '</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 class="nb">print</span><span class="p">(</span><span class="s1">'Number of configurations: '</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 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 class="n">corr_source</span> <span class="o">=</span> <span class="p">[]</span>
<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 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 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 class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">'Source position do not match for correlator'</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">item</span><span class="p">))</span>
<span class="k">else</span><span class="p">:</span>
<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 class="n">result</span> <span class="o">=</span> <span class="p">{}</span>
<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 class="n">tmp_corr</span> <span class="o">=</span> <span class="p">[]</span>
<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 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">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">t</span><span class="p">]],</span> <span class="p">[</span><span class="n">ensemble_name</span><span class="p">]))</span>
<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="nb">sorted</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 class="c1"># Check that all data entries have the same number of configurations</span>
<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 class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">'Error: Not all correlators have the same number of configurations. bdio file is possibly corrupted.'</span><span class="p">)</span>
<span class="k">return</span> <span class="n">result</span>
</pre></div>
</details>
<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 -- path to the bdio file</strong></li>
<li><strong>bdio_path -- path to the shared bdio library libbdio.so (default ./libbdio.so)</strong></li>
<li><strong>stop -- stops reading at given configuration number (default None)</strong></li>
<li><strong>alternative_ensemble_name -- Manually overwrite ensemble name</strong></li>
</ul>
</div>
</section>
<section id="read_dSdm">
<div class="attr function"><a class="headerlink" href="#read_dSdm">#  </a>
<span class="def">def</span>
<span class="name">read_dSdm</span><span class="signature">(file_path, bdio_path='./libbdio.so', **kwargs)</span>:
</div>
<details>
<summary>View Source</summary>
<div class="codehilite"><pre><span></span><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">'./libbdio.so'</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
<span class="sd">""" Extract dSdm data from a bdio file and return it as a dictionary</span>
<span class="sd"> The dictionary can be accessed with a tuple consisting of (type, kappa)</span>
<span class="sd"> read_dSdm requires bdio to be compiled into a shared library. This can be achieved by</span>
<span class="sd"> adding the flag -fPIC to CC and changing the all target to</span>
<span class="sd"> all: bdio.o $(LIBDIR)</span>
<span class="sd"> gcc -shared -Wl,-soname,libbdio.so -o $(BUILDDIR)/libbdio.so $(BUILDDIR)/bdio.o</span>
<span class="sd"> cp $(BUILDDIR)/libbdio.so $(LIBDIR)/</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> file_path -- path to the bdio file</span>
<span class="sd"> bdio_path -- path to the shared bdio library libbdio.so (default ./libbdio.so)</span>
<span class="sd"> stop -- stops reading at given configuration number (default None)</span>
<span class="sd"> """</span>
<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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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">'utf-8'</span><span class="p">)</span>
<span class="n">read</span> <span class="o">=</span> <span class="s1">'r'</span>
<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">'utf-8'</span><span class="p">)</span>
<span class="n">form</span> <span class="o">=</span> <span class="s1">'Generic Correlator Format 1.0'</span>
<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">'utf-8'</span><span class="p">)</span>
<span class="n">ensemble_name</span> <span class="o">=</span> <span class="s1">''</span>
<span class="n">volume</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># lattice volume</span>
<span class="n">boundary_conditions</span> <span class="o">=</span> <span class="p">[]</span>
<span class="n">corr_name</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># Contains correlator names</span>
<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 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 class="n">d0</span> <span class="o">=</span> <span class="mi">0</span> <span class="c1"># tvals</span>
<span class="c1"># d1 = 0 # nnoise</span>
<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 class="c1"># Check noise type for multiple replica?</span>
<span class="n">cnfg_no</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
<span class="n">corr_no</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
<span class="n">data</span> <span class="o">=</span> <span class="p">[]</span>
<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 class="nb">print</span><span class="p">(</span><span class="s1">'Reading of bdio file started'</span><span class="p">)</span>
<span class="k">while</span> <span class="mi">1</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
<span class="n">bdio_seek_record</span><span class="p">(</span><span class="n">fbdio</span><span class="p">)</span>
<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 class="k">if</span> <span class="n">ruinfo</span> <span class="o"><</span> <span class="mi">0</span><span class="p">:</span>
<span class="c1"># EOF reached</span>
<span class="k">break</span>
<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 class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">5</span><span class="p">:</span>
<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 class="n">pd_buf</span> <span class="o">=</span> <span class="n">d_buf</span><span class="p">()</span>
<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 class="n">iread</span> <span class="o">=</span> <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 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 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 class="n">corr_no</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="k">else</span><span class="p">:</span>
<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 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 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 class="k">if</span> <span class="n">rlen</span> <span class="o">!=</span> <span class="n">iread</span><span class="p">:</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Error'</span><span class="p">)</span>
<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 class="k">if</span> <span class="n">item</span> <span class="o">==</span> <span class="sa">b</span><span class="s1">'</span><span class="se">\x00</span><span class="s1">'</span><span class="p">:</span>
<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">' '</span>
<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">"utf-8"</span><span class="p">))</span><span class="o">.</span><span class="n">rstrip</span><span class="p">()</span>
<span class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<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">'CREATOR='</span><span class="p">)</span>
<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">'ENSEMBLE='</span><span class="p">)</span>
<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">'L0='</span><span class="p">)))</span>
<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">'L1='</span><span class="p">)))</span>
<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">'L2='</span><span class="p">)))</span>
<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">'L3='</span><span class="p">)))</span>
<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">'BC0='</span><span class="p">))</span>
<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">'BC1='</span><span class="p">))</span>
<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">'BC2='</span><span class="p">))</span>
<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">'BC3='</span><span class="p">))</span>
<span class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
<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">'CORR_NAME='</span><span class="p">))</span>
<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">'DATATYPE='</span><span class="p">))</span>
<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">'PROP0='</span><span class="p">))</span>
<span class="k">if</span> <span class="n">d0</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</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">'D0='</span><span class="p">))</span>
<span class="k">else</span><span class="p">:</span>
<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">'D0='</span><span class="p">)):</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Error: Varying number of time values'</span><span class="p">)</span>
<span class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span>
<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">'KAPPA='</span><span class="p">))</span>
<span class="k">if</span> <span class="n">ruinfo</span> <span class="o">==</span> <span class="mi">4</span><span class="p">:</span>
<span class="k">if</span> <span class="s1">'stop'</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
<span class="k">if</span> <span class="n">cnfg_no</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">'stop'</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span><span class="p">:</span>
<span class="k">break</span>
<span class="n">cnfg_no</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'</span><span class="se">\r</span><span class="si">%s</span><span class="s1"> </span><span class="si">%i</span><span class="s1">'</span> <span class="o">%</span> <span class="p">(</span><span class="s1">'Reading configuration'</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 class="n">end</span><span class="o">=</span><span class="s1">'</span><span class="se">\r</span><span class="s1">'</span><span class="p">)</span>
<span class="k">if</span> <span class="n">cnfg_no</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<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 class="n">data</span> <span class="o">=</span> <span class="p">[]</span>
<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 class="n">data</span><span class="o">.</span><span class="n">append</span><span class="p">([])</span>
<span class="n">corr_no</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">bdio_close</span><span class="p">(</span><span class="n">fbdio</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'</span><span class="se">\n</span><span class="s1">Creator: '</span><span class="p">,</span> <span class="n">creator</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Ensemble: '</span><span class="p">,</span> <span class="n">ensemble_name</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Lattice volume: '</span><span class="p">,</span> <span class="n">volume</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Boundary conditions: '</span><span class="p">,</span> <span class="n">boundary_conditions</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Number of random sources: '</span><span class="p">,</span> <span class="n">d0</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Number of corrs: '</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 class="nb">print</span><span class="p">(</span><span class="s1">'Number of configurations: '</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 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 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 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="n">result</span> <span class="o">=</span> <span class="p">{}</span>
<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 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">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="p">[</span><span class="n">ensemble_name</span><span class="p">])</span>
<span class="c1"># Check that all data entries have the same number of configurations</span>
<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 class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">'Error: Not all correlators have the same number of configurations. bdio file is possibly corrupted.'</span><span class="p">)</span>
<span class="k">return</span> <span class="n">result</span>
</pre></div>
</details>
<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 -- path to the bdio file</strong></li>
<li><strong>bdio_path -- path to the shared bdio library libbdio.so (default ./libbdio.so)</strong></li>
<li><strong>stop -- stops reading at given configuration number (default None)</strong></li>
</ul>
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