lattice/pyerrors
1
0
Fork 0
mirror of https://github.com/fjosw/pyerrors.git synced 2025-05-15 12:03:42 +02:00
Code Issues Projects Releases Packages Wiki Activity

Documentation updated

Browse source
This commit is contained in:
fjosw 2022-02-08 13:38:36 +00:00
parent 8784d0a7e7
commit cfcb07d314
3 changed files with 268 additions and 252 deletions
Download patch file Download diff file Expand all files Collapse all files

6
docs/pyerrors/input/openQCD.html
View file

@ -297,8 +297,7 @@
<span class="k">return</span> <span class="n">result</span> <span class="k">return</span> <span class="n">result</span>
<span class="k">def</span> <span class="nf">extract_t0</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">prefix</span><span class="p">,</span> <span class="n">dtr_read</span><span class="p">,</span> <span class="n">xmin</span><span class="p">,</span> <span class="k">def</span> <span class="nf">extract_t0</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">prefix</span><span class="p">,</span> <span class="n">dtr_read</span><span class="p">,</span> <span class="n">xmin</span><span class="p">,</span> <span class="n">spatial_extent</span><span class="p">,</span> <span class="n">fit_range</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
<span class="n">spatial_extent</span><span class="p">,</span> <span class="n">fit_range</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;Extract t0 from given .ms.dat files. Returns t0 as Obs.</span> <span class="sd">&quot;&quot;&quot;Extract t0 from given .ms.dat files. Returns t0 as Obs.</span>
<span class="sd"> It is assumed that all boundary effects have</span> <span class="sd"> It is assumed that all boundary effects have</span>
@ -1094,8 +1093,7 @@ Print additional information that is useful for debugging.</li>
<details> <details>
<summary>View Source</summary> <summary>View Source</summary>
<div class="codehilite"><pre><span></span><span class="k">def</span> <span class="nf">extract_t0</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">prefix</span><span class="p">,</span> <span class="n">dtr_read</span><span class="p">,</span> <span class="n">xmin</span><span class="p">,</span> <div class="codehilite"><pre><span></span><span class="k">def</span> <span class="nf">extract_t0</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">prefix</span><span class="p">,</span> <span class="n">dtr_read</span><span class="p">,</span> <span class="n">xmin</span><span class="p">,</span> <span class="n">spatial_extent</span><span class="p">,</span> <span class="n">fit_range</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
<span class="n">spatial_extent</span><span class="p">,</span> <span class="n">fit_range</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;Extract t0 from given .ms.dat files. Returns t0 as Obs.</span> <span class="sd">&quot;&quot;&quot;Extract t0 from given .ms.dat files. Returns t0 as Obs.</span>
<span class="sd"> It is assumed that all boundary effects have</span> <span class="sd"> It is assumed that all boundary effects have</span>

512
docs/pyerrors/input/sfcf.html
View file

@ -80,57 +80,46 @@
<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">utils</span> <span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">utils</span>
<span class="k">def</span> <span class="nf">read_sfcf</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">prefix</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">quarks</span><span class="o">=</span><span class="s1">&#39;.*&#39;</span><span class="p">,</span> <span class="n">noffset</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">wf</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">wf2</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="k">def</span> <span class="nf">read_sfcf</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">prefix</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">quarks</span><span class="o">=</span><span class="s1">&#39;.*&#39;</span><span class="p">,</span> <span class="n">corr_type</span><span class="o">=</span><span class="s1">&#39;bi&#39;</span><span class="p">,</span> <span class="n">noffset</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">wf</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">wf2</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">version</span><span class="o">=</span><span class="s2">&quot;1.0c&quot;</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
<span class="n">version</span><span class="o">=</span><span class="s2">&quot;1.0c&quot;</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span> <span class="sd">&quot;&quot;&quot;Read sfcf c format from given folder structure.</span>
<span class="sd">&quot;&quot;&quot;Read sfcf format from given folder structure.</span>
<span class="sd"> Parameters</span> <span class="sd"> Parameters</span>
<span class="sd"> ----------</span> <span class="sd"> ----------</span>
<span class="sd"> path : str</span> <span class="sd"> quarks: str</span>
<span class="sd"> Path to the measurement files.</span>
<span class="sd"> prefix : str</span>
<span class="sd"> Ensemble prefix for which the data is to be extracted.</span>
<span class="sd"> name : str</span>
<span class="sd"> Name of the correlation function to be extracted from the file</span>
<span class="sd"> quarks: str, optional</span>
<span class="sd"> Label of the quarks used in the sfcf input file. e.g. &quot;quark quark&quot;</span> <span class="sd"> Label of the quarks used in the sfcf input file. e.g. &quot;quark quark&quot;</span>
<span class="sd"> for version 0.0 this does NOT need to be given with the typical &quot; - &quot;</span> <span class="sd"> for version 0.0 this does NOT need to be given with the typical &quot; - &quot;</span>
<span class="sd"> that is present in the output file,</span> <span class="sd"> that is present in the output file,</span>
<span class="sd"> this is done automatically for this version</span> <span class="sd"> this is done automatically for this version</span>
<span class="sd"> noffset: int, optional</span> <span class="sd"> noffset: int</span>
<span class="sd"> Offset of the source (only relevant when wavefunctions are used)</span> <span class="sd"> Offset of the source (only relevant when wavefunctions are used)</span>
<span class="sd"> wf: int, optional</span> <span class="sd"> wf: int</span>
<span class="sd"> ID of wave function</span> <span class="sd"> ID of wave function</span>
<span class="sd"> wf2: int, optional</span> <span class="sd"> wf2: int</span>
<span class="sd"> ID of the second wavefunction</span> <span class="sd"> ID of the second wavefunction</span>
<span class="sd"> (only relevant for boundary-to-boundary correlation functions)</span> <span class="sd"> (only relevant for boundary-to-boundary correlation functions)</span>
<span class="sd"> im: bool, optional</span> <span class="sd"> im: bool</span>
<span class="sd"> if True, read imaginary instead of real part</span> <span class="sd"> if True, read imaginary instead of real part</span>
<span class="sd"> of the correlation function.</span> <span class="sd"> of the correlation function.</span>
<span class="sd"> b2b: bool, optional</span> <span class="sd"> corr_type : str</span>
<span class="sd"> if True, read a time-dependent boundary-to-boundary</span> <span class="sd"> change between bi (boundary - inner) (default) bib (boundary - inner - boundary) and bb (boundary - boundary)</span>
<span class="sd"> correlation function</span> <span class="sd"> correlator types</span>
<span class="sd"> single: bool, optional</span> <span class="sd"> names : list</span>
<span class="sd"> if True, read time independent boundary to boundary</span>
<span class="sd"> correlation function</span>
<span class="sd"> names: list, optional</span>
<span class="sd"> Alternative labeling for replicas/ensembles.</span> <span class="sd"> Alternative labeling for replicas/ensembles.</span>
<span class="sd"> Has to have the appropriate length</span> <span class="sd"> Has to have the appropriate length</span>
<span class="sd"> ens_name : str, optional</span> <span class="sd"> ens_name : str</span>
<span class="sd"> replaces the name of the ensemble</span> <span class="sd"> replaces the name of the ensemble</span>
<span class="sd"> version: str, optional</span> <span class="sd"> version: str</span>
<span class="sd"> version of SFCF, with which the measurement was done.</span> <span class="sd"> version of SFCF, with which the measurement was done.</span>
<span class="sd"> if the compact output option (-c) was specified,</span> <span class="sd"> if the compact output option (-c) was spectified,</span>
<span class="sd"> append a &quot;c&quot; to the version (e.g. &quot;1.0c&quot;)</span> <span class="sd"> append a &quot;c&quot; to the version (e.g. &quot;1.0c&quot;)</span>
<span class="sd"> if the append output option (-a) was specified,</span> <span class="sd"> if the append output option (-a) was specified,</span>
<span class="sd"> append an &quot;a&quot; to the version. Currently supported versions</span> <span class="sd"> append an &quot;a&quot; to the version</span>
<span class="sd"> are &quot;0.0&quot;, &quot;1.0&quot;, &quot;2.0&quot;, &quot;1.0c&quot;, &quot;2.0c&quot;, &quot;1.0a&quot; and &quot;2.0a&quot;.</span> <span class="sd"> replica: list</span>
<span class="sd"> replica: list, optional</span>
<span class="sd"> list of replica to be read, default is all</span> <span class="sd"> list of replica to be read, default is all</span>
<span class="sd"> files: list, optional</span> <span class="sd"> files: list</span>
<span class="sd"> list of files to be read per replica, default is all.</span> <span class="sd"> list of files to be read per replica, default is all.</span>
<span class="sd"> for non-compact output format, hand the folders to be read here.</span> <span class="sd"> for non-conpact ouztput format, hand the folders to be read here.</span>
<span class="sd"> check_configs: list, optional</span> <span class="sd"> check_configs:</span>
<span class="sd"> list of list of supposed configs, eg. [range(1,1000)]</span> <span class="sd"> list of list of supposed configs, eg. [range(1,1000)]</span>
<span class="sd"> for one replicum with 1000 configs</span> <span class="sd"> for one replicum with 1000 configs</span>
<span class="sd"> &quot;&quot;&quot;</span> <span class="sd"> &quot;&quot;&quot;</span>
@ -140,25 +129,28 @@
<span class="k">else</span><span class="p">:</span> <span class="k">else</span><span class="p">:</span>
<span class="n">im</span> <span class="o">=</span> <span class="mi">0</span> <span class="n">im</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">part</span> <span class="o">=</span> <span class="s1">&#39;real&#39;</span> <span class="n">part</span> <span class="o">=</span> <span class="s1">&#39;real&#39;</span>
<span class="k">if</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;single&#39;</span><span class="p">):</span>
<span class="n">b2b</span> <span class="o">=</span> <span class="mi">1</span>
<span class="n">single</span> <span class="o">=</span> <span class="mi">1</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">if</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;b2b&#39;</span><span class="p">):</span>
<span class="n">b2b</span> <span class="o">=</span> <span class="mi">1</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">b2b</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">single</span> <span class="o">=</span> <span class="mi">0</span>
<span class="k">if</span> <span class="s2">&quot;replica&quot;</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span> <span class="k">if</span> <span class="s2">&quot;replica&quot;</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
<span class="n">reps</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="s2">&quot;replica&quot;</span><span class="p">)</span> <span class="n">reps</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="s2">&quot;replica&quot;</span><span class="p">)</span>
<span class="k">if</span> <span class="n">corr_type</span> <span class="o">==</span> <span class="s1">&#39;bb&#39;</span><span class="p">:</span>
<span class="n">b2b</span> <span class="o">=</span> <span class="kc">True</span>
<span class="n">single</span> <span class="o">=</span> <span class="kc">True</span>
<span class="k">elif</span> <span class="n">corr_type</span> <span class="o">==</span> <span class="s1">&#39;bib&#39;</span><span class="p">:</span>
<span class="n">b2b</span> <span class="o">=</span> <span class="kc">True</span>
<span class="n">single</span> <span class="o">=</span> <span class="kc">False</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">b2b</span> <span class="o">=</span> <span class="kc">False</span>
<span class="n">single</span> <span class="o">=</span> <span class="kc">False</span>
<span class="c1"># due to higher usage in current projects,</span>
<span class="c1"># compact file format is default</span>
<span class="n">compact</span> <span class="o">=</span> <span class="kc">True</span> <span class="n">compact</span> <span class="o">=</span> <span class="kc">True</span>
<span class="n">appended</span> <span class="o">=</span> <span class="kc">False</span> <span class="n">appended</span> <span class="o">=</span> <span class="kc">False</span>
<span class="c1"># get version string</span>
<span class="n">known_versions</span> <span class="o">=</span> <span class="p">[</span><span class="s2">&quot;0.0&quot;</span><span class="p">,</span> <span class="s2">&quot;1.0&quot;</span><span class="p">,</span> <span class="s2">&quot;2.0&quot;</span><span class="p">,</span> <span class="s2">&quot;1.0c&quot;</span><span class="p">,</span> <span class="s2">&quot;2.0c&quot;</span><span class="p">,</span> <span class="s2">&quot;1.0a&quot;</span><span class="p">,</span> <span class="s2">&quot;2.0a&quot;</span><span class="p">]</span> <span class="n">known_versions</span> <span class="o">=</span> <span class="p">[</span><span class="s2">&quot;0.0&quot;</span><span class="p">,</span> <span class="s2">&quot;1.0&quot;</span><span class="p">,</span> <span class="s2">&quot;2.0&quot;</span><span class="p">,</span> <span class="s2">&quot;1.0c&quot;</span><span class="p">,</span> <span class="s2">&quot;2.0c&quot;</span><span class="p">,</span> <span class="s2">&quot;1.0a&quot;</span><span class="p">,</span> <span class="s2">&quot;2.0a&quot;</span><span class="p">]</span>
<span class="k">if</span> <span class="n">version</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">known_versions</span><span class="p">:</span> <span class="k">if</span> <span class="n">version</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">known_versions</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">&quot;This version is not known!&quot;</span><span class="p">)</span> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">&quot;This version is not known!&quot;</span><span class="p">)</span>
<span class="c1"># if the letter c is appended to the version,</span>
<span class="c1"># the compact fileformat is used (former read_sfcf_c)</span>
<span class="k">if</span><span class="p">(</span><span class="n">version</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="o">==</span> <span class="s2">&quot;c&quot;</span><span class="p">):</span> <span class="k">if</span><span class="p">(</span><span class="n">version</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="o">==</span> <span class="s2">&quot;c&quot;</span><span class="p">):</span>
<span class="n">appended</span> <span class="o">=</span> <span class="kc">False</span> <span class="n">appended</span> <span class="o">=</span> <span class="kc">False</span>
<span class="n">compact</span> <span class="o">=</span> <span class="kc">True</span> <span class="n">compact</span> <span class="o">=</span> <span class="kc">True</span>
@ -183,20 +175,22 @@
<span class="k">else</span><span class="p">:</span> <span class="k">else</span><span class="p">:</span>
<span class="n">ls</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">filenames</span><span class="p">)</span> <span class="n">ls</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">filenames</span><span class="p">)</span>
<span class="k">break</span> <span class="k">break</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">ls</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Error, directory not found&#39;</span><span class="p">)</span>
<span class="c1"># Exclude folders with different names</span> <span class="c1"># Exclude folders with different names</span>
<span class="k">for</span> <span class="n">exc</span> <span class="ow">in</span> <span class="n">ls</span><span class="p">:</span> <span class="k">for</span> <span class="n">exc</span> <span class="ow">in</span> <span class="n">ls</span><span class="p">:</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">fnmatch</span><span class="o">.</span><span class="n">fnmatch</span><span class="p">(</span><span class="n">exc</span><span class="p">,</span> <span class="n">prefix</span> <span class="o">+</span> <span class="s1">&#39;*&#39;</span><span class="p">):</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">fnmatch</span><span class="o">.</span><span class="n">fnmatch</span><span class="p">(</span><span class="n">exc</span><span class="p">,</span> <span class="n">prefix</span> <span class="o">+</span> <span class="s1">&#39;*&#39;</span><span class="p">):</span>
<span class="n">ls</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">ls</span><span class="p">)</span> <span class="o">-</span> <span class="nb">set</span><span class="p">([</span><span class="n">exc</span><span class="p">]))</span> <span class="n">ls</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">ls</span><span class="p">)</span> <span class="o">-</span> <span class="nb">set</span><span class="p">([</span><span class="n">exc</span><span class="p">]))</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">ls</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;No matching directories found.&#39;</span><span class="p">)</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">ls</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
<span class="n">ls</span><span class="o">.</span><span class="n">sort</span><span class="p">(</span><span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="nb">int</span><span class="p">(</span><span class="n">re</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;\d+&#39;</span><span class="p">,</span> <span class="n">x</span><span class="p">[</span><span class="nb">len</span><span class="p">(</span><span class="n">prefix</span><span class="p">):])[</span><span class="mi">0</span><span class="p">]))</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">appended</span><span class="p">:</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">appended</span><span class="p">:</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">ls</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
<span class="c1"># New version, to cope with ids, etc.</span>
<span class="n">ls</span><span class="o">.</span><span class="n">sort</span><span class="p">(</span><span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="nb">int</span><span class="p">(</span><span class="n">re</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;\d+&#39;</span><span class="p">,</span> <span class="n">x</span><span class="p">[</span><span class="nb">len</span><span class="p">(</span><span class="n">prefix</span><span class="p">):])[</span><span class="mi">0</span><span class="p">]))</span>
<span class="n">replica</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">ls</span><span class="p">)</span> <span class="n">replica</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">ls</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span> <span class="k">else</span><span class="p">:</span>
<span class="n">replica</span> <span class="o">=</span> <span class="nb">len</span><span class="p">([</span><span class="n">file</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;.&quot;</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="k">for</span> <span class="n">file</span> <span class="ow">in</span> <span class="n">ls</span><span class="p">])</span> <span class="o">//</span> <span class="nb">len</span><span class="p">(</span><span class="nb">set</span><span class="p">([</span><span class="n">file</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;.&quot;</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="k">for</span> <span class="n">file</span> <span class="ow">in</span> <span class="n">ls</span><span class="p">]))</span> <span class="n">replica</span> <span class="o">=</span> <span class="nb">len</span><span class="p">([</span><span class="n">file</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;.&quot;</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="k">for</span> <span class="n">file</span> <span class="ow">in</span> <span class="n">ls</span><span class="p">])</span> <span class="o">//</span> <span class="nb">len</span><span class="p">(</span><span class="nb">set</span><span class="p">([</span><span class="n">file</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;.&quot;</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="k">for</span> <span class="n">file</span> <span class="ow">in</span> <span class="n">ls</span><span class="p">]))</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Read&quot;</span><span class="p">,</span> <span class="n">part</span><span class="p">,</span> <span class="s2">&quot;part of &#39;&quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">name</span><span class="p">)</span> <span class="o">+</span> <span class="s2">&quot;&#39; with prefix &#39;&quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">prefix</span><span class="p">)</span> <span class="o">+</span> <span class="s2">&quot;&#39; (&quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">replica</span><span class="p">)</span> <span class="o">+</span> <span class="s2">&quot; replica)&quot;</span><span class="p">)</span> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Read&#39;</span><span class="p">,</span> <span class="n">part</span><span class="p">,</span> <span class="s1">&#39;part of&#39;</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="s1">&#39;from&#39;</span><span class="p">,</span> <span class="n">prefix</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span>
<span class="s1">&#39;,&#39;</span><span class="p">,</span> <span class="n">replica</span><span class="p">,</span> <span class="s1">&#39;replica&#39;</span><span class="p">)</span>
<span class="k">if</span> <span class="s1">&#39;names&#39;</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span> <span class="k">if</span> <span class="s1">&#39;names&#39;</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
<span class="n">new_names</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;names&#39;</span><span class="p">)</span> <span class="n">new_names</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;names&#39;</span><span class="p">)</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">new_names</span><span class="p">)</span> <span class="o">!=</span> <span class="nb">len</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">new_names</span><span class="p">)):</span> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">new_names</span><span class="p">)</span> <span class="o">!=</span> <span class="nb">len</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">new_names</span><span class="p">)):</span>
@ -204,6 +198,8 @@
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">new_names</span><span class="p">)</span> <span class="o">!=</span> <span class="n">replica</span><span class="p">:</span> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">new_names</span><span class="p">)</span> <span class="o">!=</span> <span class="n">replica</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Names does not have the required length&#39;</span><span class="p">,</span> <span class="n">replica</span><span class="p">)</span> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Names does not have the required length&#39;</span><span class="p">,</span> <span class="n">replica</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span> <span class="k">else</span><span class="p">:</span>
<span class="c1"># Adjust replica names to new bookmarking system</span>
<span class="n">new_names</span> <span class="o">=</span> <span class="p">[]</span> <span class="n">new_names</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">appended</span><span class="p">:</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">appended</span><span class="p">:</span>
<span class="k">for</span> <span class="n">entry</span> <span class="ow">in</span> <span class="n">ls</span><span class="p">:</span> <span class="k">for</span> <span class="n">entry</span> <span class="ow">in</span> <span class="n">ls</span><span class="p">:</span>
@ -224,6 +220,7 @@
<span class="n">ls</span><span class="o">.</span><span class="n">sort</span><span class="p">(</span><span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="nb">int</span><span class="p">(</span><span class="n">re</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;\d+&#39;</span><span class="p">,</span> <span class="n">x</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]))</span> <span class="n">ls</span><span class="o">.</span><span class="n">sort</span><span class="p">(</span><span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="nb">int</span><span class="p">(</span><span class="n">re</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;\d+&#39;</span><span class="p">,</span> <span class="n">x</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]))</span>
<span class="k">for</span> <span class="n">entry</span> <span class="ow">in</span> <span class="n">ls</span><span class="p">:</span> <span class="k">for</span> <span class="n">entry</span> <span class="ow">in</span> <span class="n">ls</span><span class="p">:</span>
<span class="n">myentry</span> <span class="o">=</span> <span class="n">entry</span><span class="p">[:</span><span class="o">-</span><span class="nb">len</span><span class="p">(</span><span class="n">name</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span><span class="p">]</span> <span class="n">myentry</span> <span class="o">=</span> <span class="n">entry</span><span class="p">[:</span><span class="o">-</span><span class="nb">len</span><span class="p">(</span><span class="n">name</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span><span class="p">]</span>
<span class="c1"># print(myentry)</span>
<span class="k">try</span><span class="p">:</span> <span class="k">try</span><span class="p">:</span>
<span class="n">idx</span> <span class="o">=</span> <span class="n">myentry</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="s1">&#39;r&#39;</span><span class="p">)</span> <span class="n">idx</span> <span class="o">=</span> <span class="n">myentry</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="s1">&#39;r&#39;</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">Exception</span><span class="p">:</span> <span class="k">except</span> <span class="ne">Exception</span><span class="p">:</span>
@ -233,6 +230,7 @@
<span class="n">new_names</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;ens_name&#39;</span><span class="p">)</span> <span class="o">+</span> <span class="s1">&#39;|&#39;</span> <span class="o">+</span> <span class="n">myentry</span><span class="p">[</span><span class="n">idx</span><span class="p">:])</span> <span class="n">new_names</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;ens_name&#39;</span><span class="p">)</span> <span class="o">+</span> <span class="s1">&#39;|&#39;</span> <span class="o">+</span> <span class="n">myentry</span><span class="p">[</span><span class="n">idx</span><span class="p">:])</span>
<span class="k">else</span><span class="p">:</span> <span class="k">else</span><span class="p">:</span>
<span class="n">new_names</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">myentry</span><span class="p">[:</span><span class="n">idx</span><span class="p">]</span> <span class="o">+</span> <span class="s1">&#39;|&#39;</span> <span class="o">+</span> <span class="n">myentry</span><span class="p">[</span><span class="n">idx</span><span class="p">:])</span> <span class="n">new_names</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">myentry</span><span class="p">[:</span><span class="n">idx</span><span class="p">]</span> <span class="o">+</span> <span class="s1">&#39;|&#39;</span> <span class="o">+</span> <span class="n">myentry</span><span class="p">[</span><span class="n">idx</span><span class="p">:])</span>
<span class="c1"># print(new_names)</span>
<span class="n">idl</span> <span class="o">=</span> <span class="p">[]</span> <span class="n">idl</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">appended</span><span class="p">:</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">appended</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">ls</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">ls</span><span class="p">):</span>
@ -248,16 +246,18 @@
<span class="n">sub_ls</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">dirnames</span><span class="p">)</span> <span class="n">sub_ls</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">dirnames</span><span class="p">)</span>
<span class="k">break</span> <span class="k">break</span>
<span class="k">for</span> <span class="n">exc</span> <span class="ow">in</span> <span class="n">sub_ls</span><span class="p">:</span> <span class="c1"># print(sub_ls)</span>
<span class="k">if</span> <span class="n">compact</span><span class="p">:</span> <span class="k">if</span> <span class="n">compact</span><span class="p">:</span>
<span class="k">for</span> <span class="n">exc</span> <span class="ow">in</span> <span class="n">sub_ls</span><span class="p">:</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">fnmatch</span><span class="o">.</span><span class="n">fnmatch</span><span class="p">(</span><span class="n">exc</span><span class="p">,</span> <span class="n">prefix</span> <span class="o">+</span> <span class="s1">&#39;*&#39;</span><span class="p">):</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">fnmatch</span><span class="o">.</span><span class="n">fnmatch</span><span class="p">(</span><span class="n">exc</span><span class="p">,</span> <span class="n">prefix</span> <span class="o">+</span> <span class="s1">&#39;*&#39;</span><span class="p">):</span>
<span class="n">sub_ls</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">sub_ls</span><span class="p">)</span> <span class="o">-</span> <span class="nb">set</span><span class="p">([</span><span class="n">exc</span><span class="p">]))</span> <span class="n">sub_ls</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">sub_ls</span><span class="p">)</span> <span class="o">-</span> <span class="nb">set</span><span class="p">([</span><span class="n">exc</span><span class="p">]))</span>
<span class="n">sub_ls</span><span class="o">.</span><span class="n">sort</span><span class="p">(</span><span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">sub_ls</span><span class="o">.</span><span class="n">sort</span><span class="p">(</span><span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="nb">int</span><span class="p">(</span><span class="n">re</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;\d+&#39;</span><span class="p">,</span> <span class="n">x</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]))</span>
<span class="nb">int</span><span class="p">(</span><span class="n">re</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;\d+&#39;</span><span class="p">,</span> <span class="n">x</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]))</span> <span class="k">else</span><span class="p">:</span>
<span class="k">else</span><span class="p">:</span> <span class="k">for</span> <span class="n">exc</span> <span class="ow">in</span> <span class="n">sub_ls</span><span class="p">:</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">fnmatch</span><span class="o">.</span><span class="n">fnmatch</span><span class="p">(</span><span class="n">exc</span><span class="p">,</span> <span class="s1">&#39;cfg*&#39;</span><span class="p">):</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">fnmatch</span><span class="o">.</span><span class="n">fnmatch</span><span class="p">(</span><span class="n">exc</span><span class="p">,</span> <span class="s1">&#39;cfg*&#39;</span><span class="p">):</span>
<span class="n">sub_ls</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">sub_ls</span><span class="p">)</span> <span class="o">-</span> <span class="nb">set</span><span class="p">([</span><span class="n">exc</span><span class="p">]))</span> <span class="n">sub_ls</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">sub_ls</span><span class="p">)</span> <span class="o">-</span> <span class="nb">set</span><span class="p">([</span><span class="n">exc</span><span class="p">]))</span>
<span class="n">sub_ls</span><span class="o">.</span><span class="n">sort</span><span class="p">(</span><span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="nb">int</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">3</span><span class="p">:]))</span> <span class="n">sub_ls</span><span class="o">.</span><span class="n">sort</span><span class="p">(</span><span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="nb">int</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">3</span><span class="p">:]))</span>
<span class="c1"># print(sub_ls)</span>
<span class="n">rep_idl</span> <span class="o">=</span> <span class="p">[]</span> <span class="n">rep_idl</span> <span class="o">=</span> <span class="p">[]</span>
<span class="n">no_cfg</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">sub_ls</span><span class="p">)</span> <span class="n">no_cfg</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">sub_ls</span><span class="p">)</span>
<span class="k">for</span> <span class="n">cfg</span> <span class="ow">in</span> <span class="n">sub_ls</span><span class="p">:</span> <span class="k">for</span> <span class="n">cfg</span> <span class="ow">in</span> <span class="n">sub_ls</span><span class="p">:</span>
@ -269,88 +269,98 @@
<span class="k">except</span> <span class="ne">Exception</span><span class="p">:</span> <span class="k">except</span> <span class="ne">Exception</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">&quot;Couldn&#39;t parse idl from directroy, problem with file &quot;</span> <span class="o">+</span> <span class="n">cfg</span><span class="p">)</span> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">&quot;Couldn&#39;t parse idl from directroy, problem with file &quot;</span> <span class="o">+</span> <span class="n">cfg</span><span class="p">)</span>
<span class="n">rep_idl</span><span class="o">.</span><span class="n">sort</span><span class="p">()</span> <span class="n">rep_idl</span><span class="o">.</span><span class="n">sort</span><span class="p">()</span>
<span class="c1"># maybe there is a better way to print the idls</span>
<span class="nb">print</span><span class="p">(</span><span class="n">item</span><span class="p">,</span> <span class="s1">&#39;:&#39;</span><span class="p">,</span> <span class="n">no_cfg</span><span class="p">,</span> <span class="s1">&#39; configurations&#39;</span><span class="p">)</span> <span class="nb">print</span><span class="p">(</span><span class="n">item</span><span class="p">,</span> <span class="s1">&#39;:&#39;</span><span class="p">,</span> <span class="n">no_cfg</span><span class="p">,</span> <span class="s1">&#39; configurations&#39;</span><span class="p">)</span>
<span class="n">idl</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">rep_idl</span><span class="p">)</span> <span class="n">idl</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">rep_idl</span><span class="p">)</span>
<span class="c1"># here we have found all the files we need to look into.</span>
<span class="k">if</span> <span class="n">i</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span> <span class="k">if</span> <span class="n">i</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="k">if</span> <span class="n">compact</span><span class="p">:</span> <span class="c1"># here, we want to find the place within the file,</span>
<span class="c1"># where the correlator we need is stored.</span>
<span class="c1"># to do so, the pattern needed is put together</span>
<span class="c1"># from the input values</span>
<span class="k">if</span> <span class="n">version</span> <span class="o">==</span> <span class="s2">&quot;0.0&quot;</span><span class="p">:</span>
<span class="n">pattern</span> <span class="o">=</span> <span class="s2">&quot;# &quot;</span> <span class="o">+</span> <span class="n">name</span> <span class="o">+</span> <span class="s2">&quot; : offset &quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">noffset</span><span class="p">)</span> <span class="o">+</span> <span class="s2">&quot;, wf &quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">wf</span><span class="p">)</span>
<span class="c1"># if b2b, a second wf is needed</span>
<span class="k">if</span> <span class="n">b2b</span><span class="p">:</span>
<span class="n">pattern</span> <span class="o">+=</span> <span class="s2">&quot;, wf_2 &quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">wf2</span><span class="p">)</span>
<span class="n">qs</span> <span class="o">=</span> <span class="n">quarks</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot; &quot;</span><span class="p">)</span>
<span class="n">pattern</span> <span class="o">+=</span> <span class="s2">&quot; : &quot;</span> <span class="o">+</span> <span class="n">qs</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="s2">&quot; - &quot;</span> <span class="o">+</span> <span class="n">qs</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
<span class="n">file</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">path</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">item</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">sub_ls</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">name</span><span class="p">,</span> <span class="s2">&quot;r&quot;</span><span class="p">)</span>
<span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">file</span><span class="p">):</span>
<span class="k">if</span> <span class="n">read</span> <span class="o">==</span> <span class="mi">1</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="ow">and</span> <span class="n">k</span> <span class="o">&gt;</span> <span class="n">start</span> <span class="o">+</span> <span class="mi">1</span><span class="p">:</span>
<span class="k">break</span>
<span class="k">if</span> <span class="n">read</span> <span class="o">==</span> <span class="mi">1</span> <span class="ow">and</span> <span class="n">k</span> <span class="o">&gt;=</span> <span class="n">start</span><span class="p">:</span>
<span class="n">T</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="k">if</span> <span class="n">pattern</span> <span class="ow">in</span> <span class="n">line</span><span class="p">:</span>
<span class="n">read</span> <span class="o">=</span> <span class="mi">1</span>
<span class="n">start</span> <span class="o">=</span> <span class="n">k</span> <span class="o">+</span> <span class="mi">1</span>
<span class="nb">print</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">T</span><span class="p">)</span> <span class="o">+</span> <span class="s2">&quot; entries found.&quot;</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">pattern</span> <span class="o">=</span> <span class="s1">&#39;name &#39;</span> <span class="o">+</span> <span class="n">name</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">quarks &#39;</span> <span class="o">+</span> <span class="n">quarks</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">offset &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">noffset</span><span class="p">)</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">wf &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">wf</span><span class="p">)</span> <span class="n">pattern</span> <span class="o">=</span> <span class="s1">&#39;name &#39;</span> <span class="o">+</span> <span class="n">name</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">quarks &#39;</span> <span class="o">+</span> <span class="n">quarks</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">offset &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">noffset</span><span class="p">)</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">wf &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">wf</span><span class="p">)</span>
<span class="k">if</span> <span class="n">b2b</span><span class="p">:</span> <span class="k">if</span> <span class="n">b2b</span><span class="p">:</span>
<span class="n">pattern</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">wf_2 &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">wf2</span><span class="p">)</span> <span class="n">pattern</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">wf_2 &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">wf2</span><span class="p">)</span>
<span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">path</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">item</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">sub_ls</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s1">&#39;r&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span> <span class="c1"># and the file is parsed through to find the pattern</span>
<span class="n">content</span> <span class="o">=</span> <span class="n">file</span><span class="o">.</span><span class="n">read</span><span class="p">()</span> <span class="k">if</span> <span class="n">compact</span><span class="p">:</span>
<span class="n">match</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="n">pattern</span><span class="p">,</span> <span class="n">content</span><span class="p">)</span> <span class="n">file</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">path</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">item</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">sub_ls</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s2">&quot;r&quot;</span><span class="p">)</span>
<span class="k">if</span> <span class="n">match</span><span class="p">:</span> <span class="k">else</span><span class="p">:</span>
<span class="c1"># the start and end point of the correlator</span> <span class="c1"># for non-compactified versions of the files</span>
<span class="c1"># in question is extracted for later use in</span> <span class="n">file</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">path</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">item</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">sub_ls</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">name</span><span class="p">,</span> <span class="s2">&quot;r&quot;</span><span class="p">)</span>
<span class="c1"># the other files</span>
<span class="n">start_read</span> <span class="o">=</span> <span class="n">content</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="n">match</span><span class="o">.</span><span class="n">start</span><span class="p">())</span> <span class="o">+</span> <span class="mi">5</span> <span class="o">+</span> <span class="n">b2b</span>
<span class="n">end_match</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;\n\s*\n&#39;</span><span class="p">,</span> <span class="n">content</span><span class="p">[</span><span class="n">match</span><span class="o">.</span><span class="n">start</span><span class="p">():])</span>
<span class="n">T</span> <span class="o">=</span> <span class="n">content</span><span class="p">[</span><span class="n">match</span><span class="o">.</span><span class="n">start</span><span class="p">():]</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="n">end_match</span><span class="o">.</span><span class="n">start</span><span class="p">())</span> <span class="o">-</span> <span class="mi">4</span> <span class="o">-</span> <span class="n">b2b</span>
<span class="k">assert</span> <span class="n">T</span> <span class="o">&gt;</span> <span class="mi">0</span>
<span class="nb">print</span><span class="p">(</span><span class="n">T</span><span class="p">,</span> <span class="s1">&#39;entries, starting to read in line&#39;</span><span class="p">,</span> <span class="n">start_read</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Correlator with pattern</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">+</span> <span class="n">pattern</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">not found.&#39;</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="c1"># this part does the same as above,</span>
<span class="c1"># but for non-compactified versions of the files</span>
<span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">path</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">item</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">sub_ls</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">name</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span>
<span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">fp</span><span class="p">):</span>
<span class="k">if</span> <span class="n">version</span> <span class="o">==</span> <span class="s2">&quot;0.0&quot;</span><span class="p">:</span>
<span class="c1"># check if this is really the right file</span>
<span class="c1"># by matching pattern similar to above</span>
<span class="n">pattern</span> <span class="o">=</span> <span class="s2">&quot;# &quot;</span> <span class="o">+</span> <span class="n">name</span> <span class="o">+</span> <span class="s2">&quot; : offset &quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">noffset</span><span class="p">)</span> <span class="o">+</span> <span class="s2">&quot;, wf &quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">wf</span><span class="p">)</span>
<span class="c1"># if b2b, a second wf is needed</span>
<span class="k">if</span> <span class="n">b2b</span><span class="p">:</span>
<span class="n">pattern</span> <span class="o">+=</span> <span class="s2">&quot;, wf_2 &quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">wf2</span><span class="p">)</span>
<span class="n">qs</span> <span class="o">=</span> <span class="n">quarks</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot; &quot;</span><span class="p">)</span>
<span class="n">pattern</span> <span class="o">+=</span> <span class="s2">&quot; : &quot;</span> <span class="o">+</span> <span class="n">qs</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="s2">&quot; - &quot;</span> <span class="o">+</span> <span class="n">qs</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
<span class="k">if</span> <span class="n">read</span> <span class="o">==</span> <span class="mi">1</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="ow">and</span> <span class="n">k</span> <span class="o">&gt;</span> <span class="n">start</span> <span class="o">+</span> <span class="mi">1</span><span class="p">:</span>
<span class="k">break</span>
<span class="k">if</span> <span class="n">read</span> <span class="o">==</span> <span class="mi">1</span> <span class="ow">and</span> <span class="n">k</span> <span class="o">&gt;=</span> <span class="n">start</span><span class="p">:</span>
<span class="n">T</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="k">if</span> <span class="n">version</span> <span class="o">==</span> <span class="s2">&quot;0.0&quot;</span><span class="p">:</span> <span class="n">content</span> <span class="o">=</span> <span class="n">file</span><span class="o">.</span><span class="n">read</span><span class="p">()</span>
<span class="k">if</span> <span class="n">pattern</span> <span class="ow">in</span> <span class="n">line</span><span class="p">:</span> <span class="n">match</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="n">pattern</span><span class="p">,</span> <span class="n">content</span><span class="p">)</span>
<span class="c1"># print(line)</span> <span class="k">if</span> <span class="n">match</span><span class="p">:</span>
<span class="n">read</span> <span class="o">=</span> <span class="mi">1</span> <span class="n">start_read</span> <span class="o">=</span> <span class="n">content</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="n">match</span><span class="o">.</span><span class="n">start</span><span class="p">())</span> <span class="o">+</span> <span class="mi">5</span> <span class="o">+</span> <span class="n">b2b</span>
<span class="n">start</span> <span class="o">=</span> <span class="n">k</span> <span class="o">+</span> <span class="mi">1</span> <span class="n">end_match</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;\n\s*\n&#39;</span><span class="p">,</span> <span class="n">content</span><span class="p">[</span><span class="n">match</span><span class="o">.</span><span class="n">start</span><span class="p">():])</span>
<span class="k">else</span><span class="p">:</span> <span class="n">T</span> <span class="o">=</span> <span class="n">content</span><span class="p">[</span><span class="n">match</span><span class="o">.</span><span class="n">start</span><span class="p">():]</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="n">end_match</span><span class="o">.</span><span class="n">start</span><span class="p">())</span> <span class="o">-</span> <span class="mi">4</span> <span class="o">-</span> <span class="n">b2b</span>
<span class="k">if</span> <span class="s1">&#39;[correlator]&#39;</span> <span class="ow">in</span> <span class="n">line</span><span class="p">:</span> <span class="k">assert</span> <span class="n">T</span> <span class="o">&gt;</span> <span class="mi">0</span>
<span class="n">read</span> <span class="o">=</span> <span class="mi">1</span> <span class="nb">print</span><span class="p">(</span><span class="n">T</span><span class="p">,</span> <span class="s1">&#39;entries, starting to read in line&#39;</span><span class="p">,</span> <span class="n">start_read</span><span class="p">)</span>
<span class="n">start</span> <span class="o">=</span> <span class="n">k</span> <span class="o">+</span> <span class="mi">7</span> <span class="o">+</span> <span class="n">b2b</span> <span class="k">else</span><span class="p">:</span>
<span class="n">T</span> <span class="o">-=</span> <span class="n">b2b</span> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Correlator with pattern</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">+</span> <span class="n">pattern</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">not found.&#39;</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">T</span><span class="p">)</span> <span class="o">+</span> <span class="s2">&quot; entries found.&quot;</span><span class="p">)</span> <span class="c1"># we found where the correlator</span>
<span class="c1"># that is to be read is in the files</span>
<span class="c1"># after preparing the datastructure</span>
<span class="c1"># the correlators get parsed into...</span>
<span class="n">deltas</span> <span class="o">=</span> <span class="p">[]</span> <span class="n">deltas</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">T</span><span class="p">):</span> <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">T</span><span class="p">):</span>
<span class="n">deltas</span><span class="o">.</span><span class="n">append</span><span class="p">([])</span> <span class="n">deltas</span><span class="o">.</span><span class="n">append</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">T</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">T</span><span class="p">):</span>
<span class="n">deltas</span><span class="p">[</span><span class="n">t</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="n">no_cfg</span><span class="p">))</span> <span class="n">deltas</span><span class="p">[</span><span class="n">t</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="n">no_cfg</span><span class="p">))</span>
<span class="c1"># ...the actual parsing can start.</span>
<span class="c1"># we iterate through all measurement files in the path given...</span> <span class="c1"># we iterate through all measurement files in the path given...</span>
<span class="k">if</span> <span class="n">compact</span><span class="p">:</span> <span class="k">if</span> <span class="n">compact</span><span class="p">:</span>
<span class="k">for</span> <span class="n">cfg</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">no_cfg</span><span class="p">):</span> <span class="k">for</span> <span class="n">cfg</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">no_cfg</span><span class="p">):</span>
<span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">path</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">item</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">sub_ls</span><span class="p">[</span><span class="n">cfg</span><span class="p">])</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span> <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">path</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">item</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">sub_ls</span><span class="p">[</span><span class="n">cfg</span><span class="p">])</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span>
<span class="n">lines</span> <span class="o">=</span> <span class="n">fp</span><span class="o">.</span><span class="n">readlines</span><span class="p">()</span> <span class="n">lines</span> <span class="o">=</span> <span class="n">fp</span><span class="o">.</span><span class="n">readlines</span><span class="p">()</span>
<span class="c1"># check, if the correlator is in fact</span>
<span class="c1"># printed completely</span>
<span class="k">if</span><span class="p">(</span><span class="n">start_read</span> <span class="o">+</span> <span class="n">T</span> <span class="o">&gt;</span> <span class="nb">len</span><span class="p">(</span><span class="n">lines</span><span class="p">)):</span> <span class="k">if</span><span class="p">(</span><span class="n">start_read</span> <span class="o">+</span> <span class="n">T</span> <span class="o">&gt;</span> <span class="nb">len</span><span class="p">(</span><span class="n">lines</span><span class="p">)):</span>
<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">&quot;EOF before end of correlator data! Maybe &quot;</span> <span class="o">+</span> <span class="n">path</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">item</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">sub_ls</span><span class="p">[</span><span class="n">cfg</span><span class="p">]</span> <span class="o">+</span> <span class="s2">&quot; is corrupted?&quot;</span><span class="p">)</span> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">&quot;EOF before end of correlator data! Maybe &quot;</span> <span class="o">+</span> <span class="n">path</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">item</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">sub_ls</span><span class="p">[</span><span class="n">cfg</span><span class="p">]</span> <span class="o">+</span> <span class="s2">&quot; is corrupted?&quot;</span><span class="p">)</span>
<span class="c1"># and start to read the correlator.</span>
<span class="c1"># the range here is chosen like this,</span>
<span class="c1"># since this allows for implementing</span>
<span class="c1"># a security check for every read correlator later...</span>
<span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">start_read</span> <span class="o">-</span> <span class="mi">6</span><span class="p">,</span> <span class="n">start_read</span> <span class="o">+</span> <span class="n">T</span><span class="p">):</span> <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">start_read</span> <span class="o">-</span> <span class="mi">6</span><span class="p">,</span> <span class="n">start_read</span> <span class="o">+</span> <span class="n">T</span><span class="p">):</span>
<span class="k">if</span> <span class="n">k</span> <span class="o">==</span> <span class="n">start_read</span> <span class="o">-</span> <span class="mi">5</span> <span class="o">-</span> <span class="n">b2b</span><span class="p">:</span> <span class="k">if</span> <span class="n">k</span> <span class="o">==</span> <span class="n">start_read</span> <span class="o">-</span> <span class="mi">5</span> <span class="o">-</span> <span class="n">b2b</span><span class="p">:</span>
<span class="k">if</span> <span class="n">lines</span><span class="p">[</span><span class="n">k</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="o">!=</span> <span class="s1">&#39;name &#39;</span> <span class="o">+</span> <span class="n">name</span><span class="p">:</span> <span class="k">if</span> <span class="n">lines</span><span class="p">[</span><span class="n">k</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="o">!=</span> <span class="s1">&#39;name &#39;</span> <span class="o">+</span> <span class="n">name</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Wrong format&#39;</span><span class="p">,</span> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Wrong format&#39;</span><span class="p">,</span> <span class="n">sub_ls</span><span class="p">[</span><span class="n">cfg</span><span class="p">])</span>
<span class="n">sub_ls</span><span class="p">[</span><span class="n">cfg</span><span class="p">])</span>
<span class="k">if</span><span class="p">(</span><span class="n">k</span> <span class="o">&gt;=</span> <span class="n">start_read</span> <span class="ow">and</span> <span class="n">k</span> <span class="o">&lt;</span> <span class="n">start_read</span> <span class="o">+</span> <span class="n">T</span><span class="p">):</span> <span class="k">if</span><span class="p">(</span><span class="n">k</span> <span class="o">&gt;=</span> <span class="n">start_read</span> <span class="ow">and</span> <span class="n">k</span> <span class="o">&lt;</span> <span class="n">start_read</span> <span class="o">+</span> <span class="n">T</span><span class="p">):</span>
<span class="n">floats</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="nb">float</span><span class="p">,</span> <span class="n">lines</span><span class="p">[</span><span class="n">k</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">()))</span> <span class="n">floats</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="nb">float</span><span class="p">,</span> <span class="n">lines</span><span class="p">[</span><span class="n">k</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">()))</span>
<span class="n">deltas</span><span class="p">[</span><span class="n">k</span> <span class="o">-</span> <span class="n">start_read</span><span class="p">][</span><span class="n">i</span><span class="p">][</span><span class="n">cfg</span><span class="p">]</span> <span class="o">=</span> <span class="n">floats</span><span class="p">[</span><span class="o">-</span><span class="mi">2</span><span class="p">:][</span><span class="n">im</span><span class="p">]</span> <span class="n">deltas</span><span class="p">[</span><span class="n">k</span> <span class="o">-</span> <span class="n">start_read</span><span class="p">][</span><span class="n">i</span><span class="p">][</span><span class="n">cfg</span><span class="p">]</span> <span class="o">=</span> <span class="n">floats</span><span class="p">[</span><span class="o">-</span><span class="mi">2</span><span class="p">:][</span><span class="n">im</span><span class="p">]</span>
<span class="k">else</span><span class="p">:</span> <span class="k">else</span><span class="p">:</span>
<span class="k">for</span> <span class="n">cnfg</span><span class="p">,</span> <span class="n">subitem</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">sub_ls</span><span class="p">):</span> <span class="k">for</span> <span class="n">cnfg</span><span class="p">,</span> <span class="n">subitem</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">sub_ls</span><span class="p">):</span>
<span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">path</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">item</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">subitem</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">name</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span> <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">path</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">item</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">subitem</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">name</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span>
<span class="c1"># since the non-compatified files</span>
<span class="c1"># are typically not so long,</span>
<span class="c1"># we can iterate over the whole file.</span>
<span class="c1"># here one can also implement the chekc from above.</span>
<span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">fp</span><span class="p">):</span> <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">fp</span><span class="p">):</span>
<span class="k">if</span><span class="p">(</span><span class="n">k</span> <span class="o">&gt;=</span> <span class="n">start</span> <span class="ow">and</span> <span class="n">k</span> <span class="o">&lt;</span> <span class="n">start</span> <span class="o">+</span> <span class="n">T</span><span class="p">):</span> <span class="k">if</span><span class="p">(</span><span class="n">k</span> <span class="o">&gt;=</span> <span class="n">start_read</span> <span class="ow">and</span> <span class="n">k</span> <span class="o">&lt;</span> <span class="n">start_read</span> <span class="o">+</span> <span class="n">T</span><span class="p">):</span>
<span class="n">floats</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="nb">float</span><span class="p">,</span> <span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">()))</span> <span class="n">floats</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="nb">float</span><span class="p">,</span> <span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">()))</span>
<span class="k">if</span> <span class="n">version</span> <span class="o">==</span> <span class="s2">&quot;0.0&quot;</span><span class="p">:</span> <span class="k">if</span> <span class="n">version</span> <span class="o">==</span> <span class="s2">&quot;0.0&quot;</span><span class="p">:</span>
<span class="n">deltas</span><span class="p">[</span><span class="n">k</span> <span class="o">-</span> <span class="n">start</span><span class="p">][</span><span class="n">i</span><span class="p">][</span><span class="n">cnfg</span><span class="p">]</span> <span class="o">=</span> <span class="n">floats</span><span class="p">[</span><span class="n">im</span><span class="p">]</span> <span class="n">deltas</span><span class="p">[</span><span class="n">k</span> <span class="o">-</span> <span class="n">start</span><span class="p">][</span><span class="n">i</span><span class="p">][</span><span class="n">cnfg</span><span class="p">]</span> <span class="o">=</span> <span class="n">floats</span><span class="p">[</span><span class="n">im</span> <span class="o">-</span> <span class="n">single</span><span class="p">]</span>
<span class="k">else</span><span class="p">:</span> <span class="k">else</span><span class="p">:</span>
<span class="n">deltas</span><span class="p">[</span><span class="n">k</span> <span class="o">-</span> <span class="n">start</span><span class="p">][</span><span class="n">i</span><span class="p">][</span><span class="n">cnfg</span><span class="p">]</span> <span class="o">=</span> <span class="n">floats</span><span class="p">[</span><span class="mi">1</span> <span class="o">+</span> <span class="n">im</span> <span class="o">-</span> <span class="n">single</span><span class="p">]</span> <span class="n">deltas</span><span class="p">[</span><span class="n">k</span> <span class="o">-</span> <span class="n">start_read</span><span class="p">][</span><span class="n">i</span><span class="p">][</span><span class="n">cnfg</span><span class="p">]</span> <span class="o">=</span> <span class="n">floats</span><span class="p">[</span><span class="mi">1</span> <span class="o">+</span> <span class="n">im</span> <span class="o">-</span> <span class="n">single</span><span class="p">]</span>
<span class="k">else</span><span class="p">:</span> <span class="k">else</span><span class="p">:</span>
<span class="k">if</span> <span class="s2">&quot;files&quot;</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span> <span class="k">if</span> <span class="s2">&quot;files&quot;</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
@ -360,8 +370,6 @@
<span class="k">if</span> <span class="ow">not</span> <span class="n">fnmatch</span><span class="o">.</span><span class="n">fnmatch</span><span class="p">(</span><span class="n">exc</span><span class="p">,</span> <span class="n">prefix</span> <span class="o">+</span> <span class="s1">&#39;*.&#39;</span> <span class="o">+</span> <span class="n">name</span><span class="p">):</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">fnmatch</span><span class="o">.</span><span class="n">fnmatch</span><span class="p">(</span><span class="n">exc</span><span class="p">,</span> <span class="n">prefix</span> <span class="o">+</span> <span class="s1">&#39;*.&#39;</span> <span class="o">+</span> <span class="n">name</span><span class="p">):</span>
<span class="n">ls</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">ls</span><span class="p">)</span> <span class="o">-</span> <span class="nb">set</span><span class="p">([</span><span class="n">exc</span><span class="p">]))</span> <span class="n">ls</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">ls</span><span class="p">)</span> <span class="o">-</span> <span class="nb">set</span><span class="p">([</span><span class="n">exc</span><span class="p">]))</span>
<span class="n">ls</span><span class="o">.</span><span class="n">sort</span><span class="p">(</span><span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="nb">int</span><span class="p">(</span><span class="n">re</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;\d+&#39;</span><span class="p">,</span> <span class="n">x</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]))</span> <span class="n">ls</span><span class="o">.</span><span class="n">sort</span><span class="p">(</span><span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="nb">int</span><span class="p">(</span><span class="n">re</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;\d+&#39;</span><span class="p">,</span> <span class="n">x</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]))</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">ls</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;File(s) for correlator &#39;</span> <span class="o">+</span> <span class="n">name</span> <span class="o">+</span> <span class="s1">&#39; not found.&#39;</span><span class="p">)</span>
<span class="n">pattern</span> <span class="o">=</span> <span class="s1">&#39;name &#39;</span> <span class="o">+</span> <span class="n">name</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">quarks &#39;</span> <span class="o">+</span> <span class="n">quarks</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">offset &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">noffset</span><span class="p">)</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">wf &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">wf</span><span class="p">)</span> <span class="n">pattern</span> <span class="o">=</span> <span class="s1">&#39;name &#39;</span> <span class="o">+</span> <span class="n">name</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">quarks &#39;</span> <span class="o">+</span> <span class="n">quarks</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">offset &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">noffset</span><span class="p">)</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">wf &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">wf</span><span class="p">)</span>
<span class="k">if</span> <span class="n">b2b</span><span class="p">:</span> <span class="k">if</span> <span class="n">b2b</span><span class="p">:</span>
<span class="n">pattern</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">wf_2 &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">wf2</span><span class="p">)</span> <span class="n">pattern</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">wf_2 &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">wf2</span><span class="p">)</span>
@ -373,9 +381,9 @@
<span class="k">for</span> <span class="n">linenumber</span><span class="p">,</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">content</span><span class="p">):</span> <span class="k">for</span> <span class="n">linenumber</span><span class="p">,</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">content</span><span class="p">):</span>
<span class="k">if</span> <span class="s2">&quot;[run]&quot;</span> <span class="ow">in</span> <span class="n">line</span><span class="p">:</span> <span class="k">if</span> <span class="s2">&quot;[run]&quot;</span> <span class="ow">in</span> <span class="n">line</span><span class="p">:</span>
<span class="n">data_starts</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">linenumber</span><span class="p">)</span> <span class="n">data_starts</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">linenumber</span><span class="p">)</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">data_starts</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">-</span> <span class="n">data_starts</span><span class="p">[</span><span class="n">i</span> <span class="o">-</span> <span class="mi">1</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</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">data_starts</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">-</span> <span class="n">data_starts</span><span class="p">[</span><span class="n">i</span> <span class="o">-</span> <span class="mi">1</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">data_starts</span><span class="p">))]))</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
<span class="nb">range</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">data_starts</span><span class="p">))]))</span> <span class="o">&gt;</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="s2">&quot;Irregularities in file structure found, not all runs have the same output length&quot;</span><span class="p">)</span> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">&quot;Irregularities in file structure found, not all runs have the same output length&quot;</span><span class="p">)</span>
<span class="c1"># first chunk of data</span>
<span class="n">chunk</span> <span class="o">=</span> <span class="n">content</span><span class="p">[:</span><span class="n">data_starts</span><span class="p">[</span><span class="mi">1</span><span class="p">]]</span> <span class="n">chunk</span> <span class="o">=</span> <span class="n">content</span><span class="p">[:</span><span class="n">data_starts</span><span class="p">[</span><span class="mi">1</span><span class="p">]]</span>
<span class="k">for</span> <span class="n">linenumber</span><span class="p">,</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">chunk</span><span class="p">):</span> <span class="k">for</span> <span class="n">linenumber</span><span class="p">,</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">chunk</span><span class="p">):</span>
<span class="k">if</span> <span class="n">line</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">&quot;gauge_name&quot;</span><span class="p">):</span> <span class="k">if</span> <span class="n">line</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">&quot;gauge_name&quot;</span><span class="p">):</span>
@ -383,25 +391,31 @@
<span class="k">elif</span> <span class="n">line</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">&quot;[correlator]&quot;</span><span class="p">):</span> <span class="k">elif</span> <span class="n">line</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">&quot;[correlator]&quot;</span><span class="p">):</span>
<span class="n">corr_line</span> <span class="o">=</span> <span class="n">linenumber</span> <span class="n">corr_line</span> <span class="o">=</span> <span class="n">linenumber</span>
<span class="n">found_pat</span> <span class="o">=</span> <span class="s2">&quot;&quot;</span> <span class="n">found_pat</span> <span class="o">=</span> <span class="s2">&quot;&quot;</span>
<span class="k">for</span> <span class="n">li</span> <span class="ow">in</span> <span class="n">chunk</span><span class="p">[</span><span class="n">corr_line</span> <span class="o">+</span> <span class="mi">1</span><span class="p">:</span><span class="n">corr_line</span> <span class="o">+</span> <span class="mi">6</span> <span class="o">+</span> <span class="n">b2b</span><span class="p">]:</span> <span class="k">for</span> <span class="n">li</span> <span class="ow">in</span> <span class="n">chunk</span><span class="p">[</span><span class="n">corr_line</span> <span class="o">+</span> <span class="mi">1</span><span class="p">:</span> <span class="n">corr_line</span> <span class="o">+</span> <span class="mi">6</span> <span class="o">+</span> <span class="n">b2b</span><span class="p">]:</span>
<span class="n">found_pat</span> <span class="o">+=</span> <span class="n">li</span> <span class="n">found_pat</span> <span class="o">+=</span> <span class="n">li</span>
<span class="k">if</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="n">pattern</span><span class="p">,</span> <span class="n">found_pat</span><span class="p">):</span> <span class="k">if</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="n">pattern</span><span class="p">,</span> <span class="n">found_pat</span><span class="p">):</span>
<span class="n">start_read</span> <span class="o">=</span> <span class="n">corr_line</span> <span class="o">+</span> <span class="mi">7</span> <span class="o">+</span> <span class="n">b2b</span> <span class="n">start_read</span> <span class="o">=</span> <span class="n">corr_line</span> <span class="o">+</span> <span class="mi">7</span> <span class="o">+</span> <span class="n">b2b</span>
<span class="n">T</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">chunk</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span> <span class="o">-</span> <span class="n">start_read</span> <span class="k">break</span>
<span class="n">endline</span> <span class="o">=</span> <span class="n">corr_line</span> <span class="o">+</span> <span class="mi">6</span> <span class="o">+</span> <span class="n">b2b</span>
<span class="k">while</span> <span class="ow">not</span> <span class="n">chunk</span><span class="p">[</span><span class="n">endline</span><span class="p">]</span> <span class="o">==</span> <span class="s2">&quot;</span><span class="se">\n</span><span class="s2">&quot;</span><span class="p">:</span>
<span class="n">endline</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="n">T</span> <span class="o">=</span> <span class="n">endline</span> <span class="o">-</span> <span class="n">start_read</span>
<span class="k">if</span> <span class="n">rep</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span> <span class="k">if</span> <span class="n">rep</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="n">deltas</span> <span class="o">=</span> <span class="p">[]</span> <span class="n">deltas</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">T</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">T</span><span class="p">):</span>
<span class="n">deltas</span><span class="o">.</span><span class="n">append</span><span class="p">([])</span> <span class="n">deltas</span><span class="o">.</span><span class="n">append</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">T</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">T</span><span class="p">):</span>
<span class="n">deltas</span><span class="p">[</span><span class="n">t</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">data_starts</span><span class="p">)))</span> <span class="n">deltas</span><span class="p">[</span><span class="n">t</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">data_starts</span><span class="p">)))</span>
<span class="c1"># all other chunks should follow the same structure</span>
<span class="k">for</span> <span class="n">cnfg</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">data_starts</span><span class="p">)):</span> <span class="k">for</span> <span class="n">cnfg</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">data_starts</span><span class="p">)):</span>
<span class="n">start</span> <span class="o">=</span> <span class="n">data_starts</span><span class="p">[</span><span class="n">cnfg</span><span class="p">]</span> <span class="n">start</span> <span class="o">=</span> <span class="n">data_starts</span><span class="p">[</span><span class="n">cnfg</span><span class="p">]</span>
<span class="n">stop</span> <span class="o">=</span> <span class="n">start</span> <span class="o">+</span> <span class="n">data_starts</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">stop</span> <span class="o">=</span> <span class="n">start</span> <span class="o">+</span> <span class="n">data_starts</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
<span class="n">chunk</span> <span class="o">=</span> <span class="n">content</span><span class="p">[</span><span class="n">start</span><span class="p">:</span><span class="n">stop</span><span class="p">]</span> <span class="n">chunk</span> <span class="o">=</span> <span class="n">content</span><span class="p">[</span><span class="n">start</span><span class="p">:</span><span class="n">stop</span><span class="p">]</span>
<span class="c1"># meta_data = {}</span>
<span class="k">try</span><span class="p">:</span> <span class="k">try</span><span class="p">:</span>
<span class="n">rep_idl</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">chunk</span><span class="p">[</span><span class="n">gauge_line</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;n&quot;</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]))</span> <span class="n">rep_idl</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">chunk</span><span class="p">[</span><span class="n">gauge_line</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;n&quot;</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]))</span>
<span class="k">except</span> <span class="ne">Exception</span><span class="p">:</span> <span class="k">except</span> <span class="ne">Exception</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">&quot;Couldn&#39;t parse idl from directroy, problem with chunk around line &quot;</span> <span class="o">+</span> <span class="n">gauge_line</span><span class="p">)</span> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">&quot;Couldn&#39;t parse idl from directory, problem with chunk around line &quot;</span><span class="p">,</span> <span class="n">gauge_line</span><span class="p">)</span>
<span class="n">found_pat</span> <span class="o">=</span> <span class="s2">&quot;&quot;</span> <span class="n">found_pat</span> <span class="o">=</span> <span class="s2">&quot;&quot;</span>
<span class="k">for</span> <span class="n">li</span> <span class="ow">in</span> <span class="n">chunk</span><span class="p">[</span><span class="n">corr_line</span> <span class="o">+</span> <span class="mi">1</span><span class="p">:</span><span class="n">corr_line</span> <span class="o">+</span> <span class="mi">6</span> <span class="o">+</span> <span class="n">b2b</span><span class="p">]:</span> <span class="k">for</span> <span class="n">li</span> <span class="ow">in</span> <span class="n">chunk</span><span class="p">[</span><span class="n">corr_line</span> <span class="o">+</span> <span class="mi">1</span><span class="p">:</span><span class="n">corr_line</span> <span class="o">+</span> <span class="mi">6</span> <span class="o">+</span> <span class="n">b2b</span><span class="p">]:</span>
@ -409,7 +423,7 @@
<span class="k">if</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="n">pattern</span><span class="p">,</span> <span class="n">found_pat</span><span class="p">):</span> <span class="k">if</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="n">pattern</span><span class="p">,</span> <span class="n">found_pat</span><span class="p">):</span>
<span class="k">for</span> <span class="n">t</span><span class="p">,</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">chunk</span><span class="p">[</span><span class="n">start_read</span><span class="p">:</span><span class="n">start_read</span> <span class="o">+</span> <span class="n">T</span><span class="p">]):</span> <span class="k">for</span> <span class="n">t</span><span class="p">,</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">chunk</span><span class="p">[</span><span class="n">start_read</span><span class="p">:</span><span class="n">start_read</span> <span class="o">+</span> <span class="n">T</span><span class="p">]):</span>
<span class="n">floats</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="nb">float</span><span class="p">,</span> <span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">()))</span> <span class="n">floats</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="nb">float</span><span class="p">,</span> <span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">()))</span>
<span class="n">deltas</span><span class="p">[</span><span class="n">t</span><span class="p">][</span><span class="n">rep</span><span class="p">][</span><span class="n">cnfg</span><span class="p">]</span> <span class="o">=</span> <span class="n">floats</span><span class="p">[</span><span class="o">-</span><span class="mi">2</span><span class="p">:][</span><span class="n">im</span><span class="p">]</span> <span class="n">deltas</span><span class="p">[</span><span class="n">t</span><span class="p">][</span><span class="n">rep</span><span class="p">][</span><span class="n">cnfg</span><span class="p">]</span> <span class="o">=</span> <span class="n">floats</span><span class="p">[</span><span class="n">im</span> <span class="o">+</span> <span class="mi">1</span> <span class="o">-</span> <span class="n">single</span><span class="p">]</span>
<span class="n">idl</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">rep_idl</span><span class="p">)</span> <span class="n">idl</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">rep_idl</span><span class="p">)</span>
<span class="k">if</span> <span class="s2">&quot;check_configs&quot;</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span> <span class="k">if</span> <span class="s2">&quot;check_configs&quot;</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
@ -440,6 +454,7 @@
prefix, prefix,
name, name,
quarks=&#39;.*&#39;, quarks=&#39;.*&#39;,
corr_type=&#39;bi&#39;,
noffset=0, noffset=0,
wf=0, wf=0,
wf2=0, wf2=0,
@ -450,57 +465,46 @@
<details> <details>
<summary>View Source</summary> <summary>View Source</summary>
<div class="codehilite"><pre><span></span><span class="k">def</span> <span class="nf">read_sfcf</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">prefix</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">quarks</span><span class="o">=</span><span class="s1">&#39;.*&#39;</span><span class="p">,</span> <span class="n">noffset</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">wf</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">wf2</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <div class="codehilite"><pre><span></span><span class="k">def</span> <span class="nf">read_sfcf</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">prefix</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">quarks</span><span class="o">=</span><span class="s1">&#39;.*&#39;</span><span class="p">,</span> <span class="n">corr_type</span><span class="o">=</span><span class="s1">&#39;bi&#39;</span><span class="p">,</span> <span class="n">noffset</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">wf</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">wf2</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">version</span><span class="o">=</span><span class="s2">&quot;1.0c&quot;</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
<span class="n">version</span><span class="o">=</span><span class="s2">&quot;1.0c&quot;</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span> <span class="sd">&quot;&quot;&quot;Read sfcf c format from given folder structure.</span>
<span class="sd">&quot;&quot;&quot;Read sfcf format from given folder structure.</span>
<span class="sd"> Parameters</span> <span class="sd"> Parameters</span>
<span class="sd"> ----------</span> <span class="sd"> ----------</span>
<span class="sd"> path : str</span> <span class="sd"> quarks: str</span>
<span class="sd"> Path to the measurement files.</span>
<span class="sd"> prefix : str</span>
<span class="sd"> Ensemble prefix for which the data is to be extracted.</span>
<span class="sd"> name : str</span>
<span class="sd"> Name of the correlation function to be extracted from the file</span>
<span class="sd"> quarks: str, optional</span>
<span class="sd"> Label of the quarks used in the sfcf input file. e.g. &quot;quark quark&quot;</span> <span class="sd"> Label of the quarks used in the sfcf input file. e.g. &quot;quark quark&quot;</span>
<span class="sd"> for version 0.0 this does NOT need to be given with the typical &quot; - &quot;</span> <span class="sd"> for version 0.0 this does NOT need to be given with the typical &quot; - &quot;</span>
<span class="sd"> that is present in the output file,</span> <span class="sd"> that is present in the output file,</span>
<span class="sd"> this is done automatically for this version</span> <span class="sd"> this is done automatically for this version</span>
<span class="sd"> noffset: int, optional</span> <span class="sd"> noffset: int</span>
<span class="sd"> Offset of the source (only relevant when wavefunctions are used)</span> <span class="sd"> Offset of the source (only relevant when wavefunctions are used)</span>
<span class="sd"> wf: int, optional</span> <span class="sd"> wf: int</span>
<span class="sd"> ID of wave function</span> <span class="sd"> ID of wave function</span>
<span class="sd"> wf2: int, optional</span> <span class="sd"> wf2: int</span>
<span class="sd"> ID of the second wavefunction</span> <span class="sd"> ID of the second wavefunction</span>
<span class="sd"> (only relevant for boundary-to-boundary correlation functions)</span> <span class="sd"> (only relevant for boundary-to-boundary correlation functions)</span>
<span class="sd"> im: bool, optional</span> <span class="sd"> im: bool</span>
<span class="sd"> if True, read imaginary instead of real part</span> <span class="sd"> if True, read imaginary instead of real part</span>
<span class="sd"> of the correlation function.</span> <span class="sd"> of the correlation function.</span>
<span class="sd"> b2b: bool, optional</span> <span class="sd"> corr_type : str</span>
<span class="sd"> if True, read a time-dependent boundary-to-boundary</span> <span class="sd"> change between bi (boundary - inner) (default) bib (boundary - inner - boundary) and bb (boundary - boundary)</span>
<span class="sd"> correlation function</span> <span class="sd"> correlator types</span>
<span class="sd"> single: bool, optional</span> <span class="sd"> names : list</span>
<span class="sd"> if True, read time independent boundary to boundary</span>
<span class="sd"> correlation function</span>
<span class="sd"> names: list, optional</span>
<span class="sd"> Alternative labeling for replicas/ensembles.</span> <span class="sd"> Alternative labeling for replicas/ensembles.</span>
<span class="sd"> Has to have the appropriate length</span> <span class="sd"> Has to have the appropriate length</span>
<span class="sd"> ens_name : str, optional</span> <span class="sd"> ens_name : str</span>
<span class="sd"> replaces the name of the ensemble</span> <span class="sd"> replaces the name of the ensemble</span>
<span class="sd"> version: str, optional</span> <span class="sd"> version: str</span>
<span class="sd"> version of SFCF, with which the measurement was done.</span> <span class="sd"> version of SFCF, with which the measurement was done.</span>
<span class="sd"> if the compact output option (-c) was specified,</span> <span class="sd"> if the compact output option (-c) was spectified,</span>
<span class="sd"> append a &quot;c&quot; to the version (e.g. &quot;1.0c&quot;)</span> <span class="sd"> append a &quot;c&quot; to the version (e.g. &quot;1.0c&quot;)</span>
<span class="sd"> if the append output option (-a) was specified,</span> <span class="sd"> if the append output option (-a) was specified,</span>
<span class="sd"> append an &quot;a&quot; to the version. Currently supported versions</span> <span class="sd"> append an &quot;a&quot; to the version</span>
<span class="sd"> are &quot;0.0&quot;, &quot;1.0&quot;, &quot;2.0&quot;, &quot;1.0c&quot;, &quot;2.0c&quot;, &quot;1.0a&quot; and &quot;2.0a&quot;.</span> <span class="sd"> replica: list</span>
<span class="sd"> replica: list, optional</span>
<span class="sd"> list of replica to be read, default is all</span> <span class="sd"> list of replica to be read, default is all</span>
<span class="sd"> files: list, optional</span> <span class="sd"> files: list</span>
<span class="sd"> list of files to be read per replica, default is all.</span> <span class="sd"> list of files to be read per replica, default is all.</span>
<span class="sd"> for non-compact output format, hand the folders to be read here.</span> <span class="sd"> for non-conpact ouztput format, hand the folders to be read here.</span>
<span class="sd"> check_configs: list, optional</span> <span class="sd"> check_configs:</span>
<span class="sd"> list of list of supposed configs, eg. [range(1,1000)]</span> <span class="sd"> list of list of supposed configs, eg. [range(1,1000)]</span>
<span class="sd"> for one replicum with 1000 configs</span> <span class="sd"> for one replicum with 1000 configs</span>
<span class="sd"> &quot;&quot;&quot;</span> <span class="sd"> &quot;&quot;&quot;</span>
@ -510,25 +514,28 @@
<span class="k">else</span><span class="p">:</span> <span class="k">else</span><span class="p">:</span>
<span class="n">im</span> <span class="o">=</span> <span class="mi">0</span> <span class="n">im</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">part</span> <span class="o">=</span> <span class="s1">&#39;real&#39;</span> <span class="n">part</span> <span class="o">=</span> <span class="s1">&#39;real&#39;</span>
<span class="k">if</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;single&#39;</span><span class="p">):</span>
<span class="n">b2b</span> <span class="o">=</span> <span class="mi">1</span>
<span class="n">single</span> <span class="o">=</span> <span class="mi">1</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">if</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;b2b&#39;</span><span class="p">):</span>
<span class="n">b2b</span> <span class="o">=</span> <span class="mi">1</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">b2b</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">single</span> <span class="o">=</span> <span class="mi">0</span>
<span class="k">if</span> <span class="s2">&quot;replica&quot;</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span> <span class="k">if</span> <span class="s2">&quot;replica&quot;</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
<span class="n">reps</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="s2">&quot;replica&quot;</span><span class="p">)</span> <span class="n">reps</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="s2">&quot;replica&quot;</span><span class="p">)</span>
<span class="k">if</span> <span class="n">corr_type</span> <span class="o">==</span> <span class="s1">&#39;bb&#39;</span><span class="p">:</span>
<span class="n">b2b</span> <span class="o">=</span> <span class="kc">True</span>
<span class="n">single</span> <span class="o">=</span> <span class="kc">True</span>
<span class="k">elif</span> <span class="n">corr_type</span> <span class="o">==</span> <span class="s1">&#39;bib&#39;</span><span class="p">:</span>
<span class="n">b2b</span> <span class="o">=</span> <span class="kc">True</span>
<span class="n">single</span> <span class="o">=</span> <span class="kc">False</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">b2b</span> <span class="o">=</span> <span class="kc">False</span>
<span class="n">single</span> <span class="o">=</span> <span class="kc">False</span>
<span class="c1"># due to higher usage in current projects,</span>
<span class="c1"># compact file format is default</span>
<span class="n">compact</span> <span class="o">=</span> <span class="kc">True</span> <span class="n">compact</span> <span class="o">=</span> <span class="kc">True</span>
<span class="n">appended</span> <span class="o">=</span> <span class="kc">False</span> <span class="n">appended</span> <span class="o">=</span> <span class="kc">False</span>
<span class="c1"># get version string</span>
<span class="n">known_versions</span> <span class="o">=</span> <span class="p">[</span><span class="s2">&quot;0.0&quot;</span><span class="p">,</span> <span class="s2">&quot;1.0&quot;</span><span class="p">,</span> <span class="s2">&quot;2.0&quot;</span><span class="p">,</span> <span class="s2">&quot;1.0c&quot;</span><span class="p">,</span> <span class="s2">&quot;2.0c&quot;</span><span class="p">,</span> <span class="s2">&quot;1.0a&quot;</span><span class="p">,</span> <span class="s2">&quot;2.0a&quot;</span><span class="p">]</span> <span class="n">known_versions</span> <span class="o">=</span> <span class="p">[</span><span class="s2">&quot;0.0&quot;</span><span class="p">,</span> <span class="s2">&quot;1.0&quot;</span><span class="p">,</span> <span class="s2">&quot;2.0&quot;</span><span class="p">,</span> <span class="s2">&quot;1.0c&quot;</span><span class="p">,</span> <span class="s2">&quot;2.0c&quot;</span><span class="p">,</span> <span class="s2">&quot;1.0a&quot;</span><span class="p">,</span> <span class="s2">&quot;2.0a&quot;</span><span class="p">]</span>
<span class="k">if</span> <span class="n">version</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">known_versions</span><span class="p">:</span> <span class="k">if</span> <span class="n">version</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">known_versions</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">&quot;This version is not known!&quot;</span><span class="p">)</span> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">&quot;This version is not known!&quot;</span><span class="p">)</span>
<span class="c1"># if the letter c is appended to the version,</span>
<span class="c1"># the compact fileformat is used (former read_sfcf_c)</span>
<span class="k">if</span><span class="p">(</span><span class="n">version</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="o">==</span> <span class="s2">&quot;c&quot;</span><span class="p">):</span> <span class="k">if</span><span class="p">(</span><span class="n">version</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="o">==</span> <span class="s2">&quot;c&quot;</span><span class="p">):</span>
<span class="n">appended</span> <span class="o">=</span> <span class="kc">False</span> <span class="n">appended</span> <span class="o">=</span> <span class="kc">False</span>
<span class="n">compact</span> <span class="o">=</span> <span class="kc">True</span> <span class="n">compact</span> <span class="o">=</span> <span class="kc">True</span>
@ -553,20 +560,22 @@
<span class="k">else</span><span class="p">:</span> <span class="k">else</span><span class="p">:</span>
<span class="n">ls</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">filenames</span><span class="p">)</span> <span class="n">ls</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">filenames</span><span class="p">)</span>
<span class="k">break</span> <span class="k">break</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">ls</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Error, directory not found&#39;</span><span class="p">)</span>
<span class="c1"># Exclude folders with different names</span> <span class="c1"># Exclude folders with different names</span>
<span class="k">for</span> <span class="n">exc</span> <span class="ow">in</span> <span class="n">ls</span><span class="p">:</span> <span class="k">for</span> <span class="n">exc</span> <span class="ow">in</span> <span class="n">ls</span><span class="p">:</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">fnmatch</span><span class="o">.</span><span class="n">fnmatch</span><span class="p">(</span><span class="n">exc</span><span class="p">,</span> <span class="n">prefix</span> <span class="o">+</span> <span class="s1">&#39;*&#39;</span><span class="p">):</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">fnmatch</span><span class="o">.</span><span class="n">fnmatch</span><span class="p">(</span><span class="n">exc</span><span class="p">,</span> <span class="n">prefix</span> <span class="o">+</span> <span class="s1">&#39;*&#39;</span><span class="p">):</span>
<span class="n">ls</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">ls</span><span class="p">)</span> <span class="o">-</span> <span class="nb">set</span><span class="p">([</span><span class="n">exc</span><span class="p">]))</span> <span class="n">ls</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">ls</span><span class="p">)</span> <span class="o">-</span> <span class="nb">set</span><span class="p">([</span><span class="n">exc</span><span class="p">]))</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">ls</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;No matching directories found.&#39;</span><span class="p">)</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">ls</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
<span class="n">ls</span><span class="o">.</span><span class="n">sort</span><span class="p">(</span><span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="nb">int</span><span class="p">(</span><span class="n">re</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;\d+&#39;</span><span class="p">,</span> <span class="n">x</span><span class="p">[</span><span class="nb">len</span><span class="p">(</span><span class="n">prefix</span><span class="p">):])[</span><span class="mi">0</span><span class="p">]))</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">appended</span><span class="p">:</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">appended</span><span class="p">:</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">ls</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
<span class="c1"># New version, to cope with ids, etc.</span>
<span class="n">ls</span><span class="o">.</span><span class="n">sort</span><span class="p">(</span><span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="nb">int</span><span class="p">(</span><span class="n">re</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;\d+&#39;</span><span class="p">,</span> <span class="n">x</span><span class="p">[</span><span class="nb">len</span><span class="p">(</span><span class="n">prefix</span><span class="p">):])[</span><span class="mi">0</span><span class="p">]))</span>
<span class="n">replica</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">ls</span><span class="p">)</span> <span class="n">replica</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">ls</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span> <span class="k">else</span><span class="p">:</span>
<span class="n">replica</span> <span class="o">=</span> <span class="nb">len</span><span class="p">([</span><span class="n">file</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;.&quot;</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="k">for</span> <span class="n">file</span> <span class="ow">in</span> <span class="n">ls</span><span class="p">])</span> <span class="o">//</span> <span class="nb">len</span><span class="p">(</span><span class="nb">set</span><span class="p">([</span><span class="n">file</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;.&quot;</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="k">for</span> <span class="n">file</span> <span class="ow">in</span> <span class="n">ls</span><span class="p">]))</span> <span class="n">replica</span> <span class="o">=</span> <span class="nb">len</span><span class="p">([</span><span class="n">file</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;.&quot;</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="k">for</span> <span class="n">file</span> <span class="ow">in</span> <span class="n">ls</span><span class="p">])</span> <span class="o">//</span> <span class="nb">len</span><span class="p">(</span><span class="nb">set</span><span class="p">([</span><span class="n">file</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;.&quot;</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="k">for</span> <span class="n">file</span> <span class="ow">in</span> <span class="n">ls</span><span class="p">]))</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Read&quot;</span><span class="p">,</span> <span class="n">part</span><span class="p">,</span> <span class="s2">&quot;part of &#39;&quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">name</span><span class="p">)</span> <span class="o">+</span> <span class="s2">&quot;&#39; with prefix &#39;&quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">prefix</span><span class="p">)</span> <span class="o">+</span> <span class="s2">&quot;&#39; (&quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">replica</span><span class="p">)</span> <span class="o">+</span> <span class="s2">&quot; replica)&quot;</span><span class="p">)</span> <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Read&#39;</span><span class="p">,</span> <span class="n">part</span><span class="p">,</span> <span class="s1">&#39;part of&#39;</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="s1">&#39;from&#39;</span><span class="p">,</span> <span class="n">prefix</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span>
<span class="s1">&#39;,&#39;</span><span class="p">,</span> <span class="n">replica</span><span class="p">,</span> <span class="s1">&#39;replica&#39;</span><span class="p">)</span>
<span class="k">if</span> <span class="s1">&#39;names&#39;</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span> <span class="k">if</span> <span class="s1">&#39;names&#39;</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
<span class="n">new_names</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;names&#39;</span><span class="p">)</span> <span class="n">new_names</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;names&#39;</span><span class="p">)</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">new_names</span><span class="p">)</span> <span class="o">!=</span> <span class="nb">len</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">new_names</span><span class="p">)):</span> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">new_names</span><span class="p">)</span> <span class="o">!=</span> <span class="nb">len</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">new_names</span><span class="p">)):</span>
@ -574,6 +583,8 @@
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">new_names</span><span class="p">)</span> <span class="o">!=</span> <span class="n">replica</span><span class="p">:</span> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">new_names</span><span class="p">)</span> <span class="o">!=</span> <span class="n">replica</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Names does not have the required length&#39;</span><span class="p">,</span> <span class="n">replica</span><span class="p">)</span> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Names does not have the required length&#39;</span><span class="p">,</span> <span class="n">replica</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span> <span class="k">else</span><span class="p">:</span>
<span class="c1"># Adjust replica names to new bookmarking system</span>
<span class="n">new_names</span> <span class="o">=</span> <span class="p">[]</span> <span class="n">new_names</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">appended</span><span class="p">:</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">appended</span><span class="p">:</span>
<span class="k">for</span> <span class="n">entry</span> <span class="ow">in</span> <span class="n">ls</span><span class="p">:</span> <span class="k">for</span> <span class="n">entry</span> <span class="ow">in</span> <span class="n">ls</span><span class="p">:</span>
@ -594,6 +605,7 @@
<span class="n">ls</span><span class="o">.</span><span class="n">sort</span><span class="p">(</span><span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="nb">int</span><span class="p">(</span><span class="n">re</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;\d+&#39;</span><span class="p">,</span> <span class="n">x</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]))</span> <span class="n">ls</span><span class="o">.</span><span class="n">sort</span><span class="p">(</span><span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="nb">int</span><span class="p">(</span><span class="n">re</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;\d+&#39;</span><span class="p">,</span> <span class="n">x</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]))</span>
<span class="k">for</span> <span class="n">entry</span> <span class="ow">in</span> <span class="n">ls</span><span class="p">:</span> <span class="k">for</span> <span class="n">entry</span> <span class="ow">in</span> <span class="n">ls</span><span class="p">:</span>
<span class="n">myentry</span> <span class="o">=</span> <span class="n">entry</span><span class="p">[:</span><span class="o">-</span><span class="nb">len</span><span class="p">(</span><span class="n">name</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span><span class="p">]</span> <span class="n">myentry</span> <span class="o">=</span> <span class="n">entry</span><span class="p">[:</span><span class="o">-</span><span class="nb">len</span><span class="p">(</span><span class="n">name</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span><span class="p">]</span>
<span class="c1"># print(myentry)</span>
<span class="k">try</span><span class="p">:</span> <span class="k">try</span><span class="p">:</span>
<span class="n">idx</span> <span class="o">=</span> <span class="n">myentry</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="s1">&#39;r&#39;</span><span class="p">)</span> <span class="n">idx</span> <span class="o">=</span> <span class="n">myentry</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="s1">&#39;r&#39;</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">Exception</span><span class="p">:</span> <span class="k">except</span> <span class="ne">Exception</span><span class="p">:</span>
@ -603,6 +615,7 @@
<span class="n">new_names</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;ens_name&#39;</span><span class="p">)</span> <span class="o">+</span> <span class="s1">&#39;|&#39;</span> <span class="o">+</span> <span class="n">myentry</span><span class="p">[</span><span class="n">idx</span><span class="p">:])</span> <span class="n">new_names</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;ens_name&#39;</span><span class="p">)</span> <span class="o">+</span> <span class="s1">&#39;|&#39;</span> <span class="o">+</span> <span class="n">myentry</span><span class="p">[</span><span class="n">idx</span><span class="p">:])</span>
<span class="k">else</span><span class="p">:</span> <span class="k">else</span><span class="p">:</span>
<span class="n">new_names</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">myentry</span><span class="p">[:</span><span class="n">idx</span><span class="p">]</span> <span class="o">+</span> <span class="s1">&#39;|&#39;</span> <span class="o">+</span> <span class="n">myentry</span><span class="p">[</span><span class="n">idx</span><span class="p">:])</span> <span class="n">new_names</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">myentry</span><span class="p">[:</span><span class="n">idx</span><span class="p">]</span> <span class="o">+</span> <span class="s1">&#39;|&#39;</span> <span class="o">+</span> <span class="n">myentry</span><span class="p">[</span><span class="n">idx</span><span class="p">:])</span>
<span class="c1"># print(new_names)</span>
<span class="n">idl</span> <span class="o">=</span> <span class="p">[]</span> <span class="n">idl</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">appended</span><span class="p">:</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">appended</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">ls</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">ls</span><span class="p">):</span>
@ -618,16 +631,18 @@
<span class="n">sub_ls</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">dirnames</span><span class="p">)</span> <span class="n">sub_ls</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">dirnames</span><span class="p">)</span>
<span class="k">break</span> <span class="k">break</span>
<span class="k">for</span> <span class="n">exc</span> <span class="ow">in</span> <span class="n">sub_ls</span><span class="p">:</span> <span class="c1"># print(sub_ls)</span>
<span class="k">if</span> <span class="n">compact</span><span class="p">:</span> <span class="k">if</span> <span class="n">compact</span><span class="p">:</span>
<span class="k">for</span> <span class="n">exc</span> <span class="ow">in</span> <span class="n">sub_ls</span><span class="p">:</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">fnmatch</span><span class="o">.</span><span class="n">fnmatch</span><span class="p">(</span><span class="n">exc</span><span class="p">,</span> <span class="n">prefix</span> <span class="o">+</span> <span class="s1">&#39;*&#39;</span><span class="p">):</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">fnmatch</span><span class="o">.</span><span class="n">fnmatch</span><span class="p">(</span><span class="n">exc</span><span class="p">,</span> <span class="n">prefix</span> <span class="o">+</span> <span class="s1">&#39;*&#39;</span><span class="p">):</span>
<span class="n">sub_ls</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">sub_ls</span><span class="p">)</span> <span class="o">-</span> <span class="nb">set</span><span class="p">([</span><span class="n">exc</span><span class="p">]))</span> <span class="n">sub_ls</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">sub_ls</span><span class="p">)</span> <span class="o">-</span> <span class="nb">set</span><span class="p">([</span><span class="n">exc</span><span class="p">]))</span>
<span class="n">sub_ls</span><span class="o">.</span><span class="n">sort</span><span class="p">(</span><span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">sub_ls</span><span class="o">.</span><span class="n">sort</span><span class="p">(</span><span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="nb">int</span><span class="p">(</span><span class="n">re</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;\d+&#39;</span><span class="p">,</span> <span class="n">x</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]))</span>
<span class="nb">int</span><span class="p">(</span><span class="n">re</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;\d+&#39;</span><span class="p">,</span> <span class="n">x</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]))</span> <span class="k">else</span><span class="p">:</span>
<span class="k">else</span><span class="p">:</span> <span class="k">for</span> <span class="n">exc</span> <span class="ow">in</span> <span class="n">sub_ls</span><span class="p">:</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">fnmatch</span><span class="o">.</span><span class="n">fnmatch</span><span class="p">(</span><span class="n">exc</span><span class="p">,</span> <span class="s1">&#39;cfg*&#39;</span><span class="p">):</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">fnmatch</span><span class="o">.</span><span class="n">fnmatch</span><span class="p">(</span><span class="n">exc</span><span class="p">,</span> <span class="s1">&#39;cfg*&#39;</span><span class="p">):</span>
<span class="n">sub_ls</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">sub_ls</span><span class="p">)</span> <span class="o">-</span> <span class="nb">set</span><span class="p">([</span><span class="n">exc</span><span class="p">]))</span> <span class="n">sub_ls</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">sub_ls</span><span class="p">)</span> <span class="o">-</span> <span class="nb">set</span><span class="p">([</span><span class="n">exc</span><span class="p">]))</span>
<span class="n">sub_ls</span><span class="o">.</span><span class="n">sort</span><span class="p">(</span><span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="nb">int</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">3</span><span class="p">:]))</span> <span class="n">sub_ls</span><span class="o">.</span><span class="n">sort</span><span class="p">(</span><span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="nb">int</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">3</span><span class="p">:]))</span>
<span class="c1"># print(sub_ls)</span>
<span class="n">rep_idl</span> <span class="o">=</span> <span class="p">[]</span> <span class="n">rep_idl</span> <span class="o">=</span> <span class="p">[]</span>
<span class="n">no_cfg</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">sub_ls</span><span class="p">)</span> <span class="n">no_cfg</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">sub_ls</span><span class="p">)</span>
<span class="k">for</span> <span class="n">cfg</span> <span class="ow">in</span> <span class="n">sub_ls</span><span class="p">:</span> <span class="k">for</span> <span class="n">cfg</span> <span class="ow">in</span> <span class="n">sub_ls</span><span class="p">:</span>
@ -639,88 +654,98 @@
<span class="k">except</span> <span class="ne">Exception</span><span class="p">:</span> <span class="k">except</span> <span class="ne">Exception</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">&quot;Couldn&#39;t parse idl from directroy, problem with file &quot;</span> <span class="o">+</span> <span class="n">cfg</span><span class="p">)</span> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">&quot;Couldn&#39;t parse idl from directroy, problem with file &quot;</span> <span class="o">+</span> <span class="n">cfg</span><span class="p">)</span>
<span class="n">rep_idl</span><span class="o">.</span><span class="n">sort</span><span class="p">()</span> <span class="n">rep_idl</span><span class="o">.</span><span class="n">sort</span><span class="p">()</span>
<span class="c1"># maybe there is a better way to print the idls</span>
<span class="nb">print</span><span class="p">(</span><span class="n">item</span><span class="p">,</span> <span class="s1">&#39;:&#39;</span><span class="p">,</span> <span class="n">no_cfg</span><span class="p">,</span> <span class="s1">&#39; configurations&#39;</span><span class="p">)</span> <span class="nb">print</span><span class="p">(</span><span class="n">item</span><span class="p">,</span> <span class="s1">&#39;:&#39;</span><span class="p">,</span> <span class="n">no_cfg</span><span class="p">,</span> <span class="s1">&#39; configurations&#39;</span><span class="p">)</span>
<span class="n">idl</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">rep_idl</span><span class="p">)</span> <span class="n">idl</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">rep_idl</span><span class="p">)</span>
<span class="c1"># here we have found all the files we need to look into.</span>
<span class="k">if</span> <span class="n">i</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span> <span class="k">if</span> <span class="n">i</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="k">if</span> <span class="n">compact</span><span class="p">:</span> <span class="c1"># here, we want to find the place within the file,</span>
<span class="c1"># where the correlator we need is stored.</span>
<span class="c1"># to do so, the pattern needed is put together</span>
<span class="c1"># from the input values</span>
<span class="k">if</span> <span class="n">version</span> <span class="o">==</span> <span class="s2">&quot;0.0&quot;</span><span class="p">:</span>
<span class="n">pattern</span> <span class="o">=</span> <span class="s2">&quot;# &quot;</span> <span class="o">+</span> <span class="n">name</span> <span class="o">+</span> <span class="s2">&quot; : offset &quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">noffset</span><span class="p">)</span> <span class="o">+</span> <span class="s2">&quot;, wf &quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">wf</span><span class="p">)</span>
<span class="c1"># if b2b, a second wf is needed</span>
<span class="k">if</span> <span class="n">b2b</span><span class="p">:</span>
<span class="n">pattern</span> <span class="o">+=</span> <span class="s2">&quot;, wf_2 &quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">wf2</span><span class="p">)</span>
<span class="n">qs</span> <span class="o">=</span> <span class="n">quarks</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot; &quot;</span><span class="p">)</span>
<span class="n">pattern</span> <span class="o">+=</span> <span class="s2">&quot; : &quot;</span> <span class="o">+</span> <span class="n">qs</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="s2">&quot; - &quot;</span> <span class="o">+</span> <span class="n">qs</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
<span class="n">file</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">path</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">item</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">sub_ls</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">name</span><span class="p">,</span> <span class="s2">&quot;r&quot;</span><span class="p">)</span>
<span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">file</span><span class="p">):</span>
<span class="k">if</span> <span class="n">read</span> <span class="o">==</span> <span class="mi">1</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="ow">and</span> <span class="n">k</span> <span class="o">&gt;</span> <span class="n">start</span> <span class="o">+</span> <span class="mi">1</span><span class="p">:</span>
<span class="k">break</span>
<span class="k">if</span> <span class="n">read</span> <span class="o">==</span> <span class="mi">1</span> <span class="ow">and</span> <span class="n">k</span> <span class="o">&gt;=</span> <span class="n">start</span><span class="p">:</span>
<span class="n">T</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="k">if</span> <span class="n">pattern</span> <span class="ow">in</span> <span class="n">line</span><span class="p">:</span>
<span class="n">read</span> <span class="o">=</span> <span class="mi">1</span>
<span class="n">start</span> <span class="o">=</span> <span class="n">k</span> <span class="o">+</span> <span class="mi">1</span>
<span class="nb">print</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">T</span><span class="p">)</span> <span class="o">+</span> <span class="s2">&quot; entries found.&quot;</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">pattern</span> <span class="o">=</span> <span class="s1">&#39;name &#39;</span> <span class="o">+</span> <span class="n">name</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">quarks &#39;</span> <span class="o">+</span> <span class="n">quarks</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">offset &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">noffset</span><span class="p">)</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">wf &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">wf</span><span class="p">)</span> <span class="n">pattern</span> <span class="o">=</span> <span class="s1">&#39;name &#39;</span> <span class="o">+</span> <span class="n">name</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">quarks &#39;</span> <span class="o">+</span> <span class="n">quarks</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">offset &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">noffset</span><span class="p">)</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">wf &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">wf</span><span class="p">)</span>
<span class="k">if</span> <span class="n">b2b</span><span class="p">:</span> <span class="k">if</span> <span class="n">b2b</span><span class="p">:</span>
<span class="n">pattern</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">wf_2 &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">wf2</span><span class="p">)</span> <span class="n">pattern</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">wf_2 &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">wf2</span><span class="p">)</span>
<span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">path</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">item</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">sub_ls</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s1">&#39;r&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span> <span class="c1"># and the file is parsed through to find the pattern</span>
<span class="n">content</span> <span class="o">=</span> <span class="n">file</span><span class="o">.</span><span class="n">read</span><span class="p">()</span> <span class="k">if</span> <span class="n">compact</span><span class="p">:</span>
<span class="n">match</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="n">pattern</span><span class="p">,</span> <span class="n">content</span><span class="p">)</span> <span class="n">file</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">path</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">item</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">sub_ls</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s2">&quot;r&quot;</span><span class="p">)</span>
<span class="k">if</span> <span class="n">match</span><span class="p">:</span> <span class="k">else</span><span class="p">:</span>
<span class="c1"># the start and end point of the correlator</span> <span class="c1"># for non-compactified versions of the files</span>
<span class="c1"># in question is extracted for later use in</span> <span class="n">file</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">path</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">item</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">sub_ls</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">name</span><span class="p">,</span> <span class="s2">&quot;r&quot;</span><span class="p">)</span>
<span class="c1"># the other files</span>
<span class="n">start_read</span> <span class="o">=</span> <span class="n">content</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="n">match</span><span class="o">.</span><span class="n">start</span><span class="p">())</span> <span class="o">+</span> <span class="mi">5</span> <span class="o">+</span> <span class="n">b2b</span>
<span class="n">end_match</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;\n\s*\n&#39;</span><span class="p">,</span> <span class="n">content</span><span class="p">[</span><span class="n">match</span><span class="o">.</span><span class="n">start</span><span class="p">():])</span>
<span class="n">T</span> <span class="o">=</span> <span class="n">content</span><span class="p">[</span><span class="n">match</span><span class="o">.</span><span class="n">start</span><span class="p">():]</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="n">end_match</span><span class="o">.</span><span class="n">start</span><span class="p">())</span> <span class="o">-</span> <span class="mi">4</span> <span class="o">-</span> <span class="n">b2b</span>
<span class="k">assert</span> <span class="n">T</span> <span class="o">&gt;</span> <span class="mi">0</span>
<span class="nb">print</span><span class="p">(</span><span class="n">T</span><span class="p">,</span> <span class="s1">&#39;entries, starting to read in line&#39;</span><span class="p">,</span> <span class="n">start_read</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Correlator with pattern</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">+</span> <span class="n">pattern</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">not found.&#39;</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="c1"># this part does the same as above,</span>
<span class="c1"># but for non-compactified versions of the files</span>
<span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">path</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">item</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">sub_ls</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">name</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span>
<span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">fp</span><span class="p">):</span>
<span class="k">if</span> <span class="n">version</span> <span class="o">==</span> <span class="s2">&quot;0.0&quot;</span><span class="p">:</span>
<span class="c1"># check if this is really the right file</span>
<span class="c1"># by matching pattern similar to above</span>
<span class="n">pattern</span> <span class="o">=</span> <span class="s2">&quot;# &quot;</span> <span class="o">+</span> <span class="n">name</span> <span class="o">+</span> <span class="s2">&quot; : offset &quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">noffset</span><span class="p">)</span> <span class="o">+</span> <span class="s2">&quot;, wf &quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">wf</span><span class="p">)</span>
<span class="c1"># if b2b, a second wf is needed</span>
<span class="k">if</span> <span class="n">b2b</span><span class="p">:</span>
<span class="n">pattern</span> <span class="o">+=</span> <span class="s2">&quot;, wf_2 &quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">wf2</span><span class="p">)</span>
<span class="n">qs</span> <span class="o">=</span> <span class="n">quarks</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot; &quot;</span><span class="p">)</span>
<span class="n">pattern</span> <span class="o">+=</span> <span class="s2">&quot; : &quot;</span> <span class="o">+</span> <span class="n">qs</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="s2">&quot; - &quot;</span> <span class="o">+</span> <span class="n">qs</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
<span class="k">if</span> <span class="n">read</span> <span class="o">==</span> <span class="mi">1</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="ow">and</span> <span class="n">k</span> <span class="o">&gt;</span> <span class="n">start</span> <span class="o">+</span> <span class="mi">1</span><span class="p">:</span>
<span class="k">break</span>
<span class="k">if</span> <span class="n">read</span> <span class="o">==</span> <span class="mi">1</span> <span class="ow">and</span> <span class="n">k</span> <span class="o">&gt;=</span> <span class="n">start</span><span class="p">:</span>
<span class="n">T</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="k">if</span> <span class="n">version</span> <span class="o">==</span> <span class="s2">&quot;0.0&quot;</span><span class="p">:</span> <span class="n">content</span> <span class="o">=</span> <span class="n">file</span><span class="o">.</span><span class="n">read</span><span class="p">()</span>
<span class="k">if</span> <span class="n">pattern</span> <span class="ow">in</span> <span class="n">line</span><span class="p">:</span> <span class="n">match</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="n">pattern</span><span class="p">,</span> <span class="n">content</span><span class="p">)</span>
<span class="c1"># print(line)</span> <span class="k">if</span> <span class="n">match</span><span class="p">:</span>
<span class="n">read</span> <span class="o">=</span> <span class="mi">1</span> <span class="n">start_read</span> <span class="o">=</span> <span class="n">content</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="n">match</span><span class="o">.</span><span class="n">start</span><span class="p">())</span> <span class="o">+</span> <span class="mi">5</span> <span class="o">+</span> <span class="n">b2b</span>
<span class="n">start</span> <span class="o">=</span> <span class="n">k</span> <span class="o">+</span> <span class="mi">1</span> <span class="n">end_match</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;\n\s*\n&#39;</span><span class="p">,</span> <span class="n">content</span><span class="p">[</span><span class="n">match</span><span class="o">.</span><span class="n">start</span><span class="p">():])</span>
<span class="k">else</span><span class="p">:</span> <span class="n">T</span> <span class="o">=</span> <span class="n">content</span><span class="p">[</span><span class="n">match</span><span class="o">.</span><span class="n">start</span><span class="p">():]</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="n">end_match</span><span class="o">.</span><span class="n">start</span><span class="p">())</span> <span class="o">-</span> <span class="mi">4</span> <span class="o">-</span> <span class="n">b2b</span>
<span class="k">if</span> <span class="s1">&#39;[correlator]&#39;</span> <span class="ow">in</span> <span class="n">line</span><span class="p">:</span> <span class="k">assert</span> <span class="n">T</span> <span class="o">&gt;</span> <span class="mi">0</span>
<span class="n">read</span> <span class="o">=</span> <span class="mi">1</span> <span class="nb">print</span><span class="p">(</span><span class="n">T</span><span class="p">,</span> <span class="s1">&#39;entries, starting to read in line&#39;</span><span class="p">,</span> <span class="n">start_read</span><span class="p">)</span>
<span class="n">start</span> <span class="o">=</span> <span class="n">k</span> <span class="o">+</span> <span class="mi">7</span> <span class="o">+</span> <span class="n">b2b</span> <span class="k">else</span><span class="p">:</span>
<span class="n">T</span> <span class="o">-=</span> <span class="n">b2b</span> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Correlator with pattern</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">+</span> <span class="n">pattern</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">not found.&#39;</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">T</span><span class="p">)</span> <span class="o">+</span> <span class="s2">&quot; entries found.&quot;</span><span class="p">)</span> <span class="c1"># we found where the correlator</span>
<span class="c1"># that is to be read is in the files</span>
<span class="c1"># after preparing the datastructure</span>
<span class="c1"># the correlators get parsed into...</span>
<span class="n">deltas</span> <span class="o">=</span> <span class="p">[]</span> <span class="n">deltas</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">T</span><span class="p">):</span> <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">T</span><span class="p">):</span>
<span class="n">deltas</span><span class="o">.</span><span class="n">append</span><span class="p">([])</span> <span class="n">deltas</span><span class="o">.</span><span class="n">append</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">T</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">T</span><span class="p">):</span>
<span class="n">deltas</span><span class="p">[</span><span class="n">t</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="n">no_cfg</span><span class="p">))</span> <span class="n">deltas</span><span class="p">[</span><span class="n">t</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="n">no_cfg</span><span class="p">))</span>
<span class="c1"># ...the actual parsing can start.</span>
<span class="c1"># we iterate through all measurement files in the path given...</span> <span class="c1"># we iterate through all measurement files in the path given...</span>
<span class="k">if</span> <span class="n">compact</span><span class="p">:</span> <span class="k">if</span> <span class="n">compact</span><span class="p">:</span>
<span class="k">for</span> <span class="n">cfg</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">no_cfg</span><span class="p">):</span> <span class="k">for</span> <span class="n">cfg</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">no_cfg</span><span class="p">):</span>
<span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">path</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">item</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">sub_ls</span><span class="p">[</span><span class="n">cfg</span><span class="p">])</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span> <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">path</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">item</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">sub_ls</span><span class="p">[</span><span class="n">cfg</span><span class="p">])</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span>
<span class="n">lines</span> <span class="o">=</span> <span class="n">fp</span><span class="o">.</span><span class="n">readlines</span><span class="p">()</span> <span class="n">lines</span> <span class="o">=</span> <span class="n">fp</span><span class="o">.</span><span class="n">readlines</span><span class="p">()</span>
<span class="c1"># check, if the correlator is in fact</span>
<span class="c1"># printed completely</span>
<span class="k">if</span><span class="p">(</span><span class="n">start_read</span> <span class="o">+</span> <span class="n">T</span> <span class="o">&gt;</span> <span class="nb">len</span><span class="p">(</span><span class="n">lines</span><span class="p">)):</span> <span class="k">if</span><span class="p">(</span><span class="n">start_read</span> <span class="o">+</span> <span class="n">T</span> <span class="o">&gt;</span> <span class="nb">len</span><span class="p">(</span><span class="n">lines</span><span class="p">)):</span>
<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">&quot;EOF before end of correlator data! Maybe &quot;</span> <span class="o">+</span> <span class="n">path</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">item</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">sub_ls</span><span class="p">[</span><span class="n">cfg</span><span class="p">]</span> <span class="o">+</span> <span class="s2">&quot; is corrupted?&quot;</span><span class="p">)</span> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">&quot;EOF before end of correlator data! Maybe &quot;</span> <span class="o">+</span> <span class="n">path</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">item</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">sub_ls</span><span class="p">[</span><span class="n">cfg</span><span class="p">]</span> <span class="o">+</span> <span class="s2">&quot; is corrupted?&quot;</span><span class="p">)</span>
<span class="c1"># and start to read the correlator.</span>
<span class="c1"># the range here is chosen like this,</span>
<span class="c1"># since this allows for implementing</span>
<span class="c1"># a security check for every read correlator later...</span>
<span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">start_read</span> <span class="o">-</span> <span class="mi">6</span><span class="p">,</span> <span class="n">start_read</span> <span class="o">+</span> <span class="n">T</span><span class="p">):</span> <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">start_read</span> <span class="o">-</span> <span class="mi">6</span><span class="p">,</span> <span class="n">start_read</span> <span class="o">+</span> <span class="n">T</span><span class="p">):</span>
<span class="k">if</span> <span class="n">k</span> <span class="o">==</span> <span class="n">start_read</span> <span class="o">-</span> <span class="mi">5</span> <span class="o">-</span> <span class="n">b2b</span><span class="p">:</span> <span class="k">if</span> <span class="n">k</span> <span class="o">==</span> <span class="n">start_read</span> <span class="o">-</span> <span class="mi">5</span> <span class="o">-</span> <span class="n">b2b</span><span class="p">:</span>
<span class="k">if</span> <span class="n">lines</span><span class="p">[</span><span class="n">k</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="o">!=</span> <span class="s1">&#39;name &#39;</span> <span class="o">+</span> <span class="n">name</span><span class="p">:</span> <span class="k">if</span> <span class="n">lines</span><span class="p">[</span><span class="n">k</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="o">!=</span> <span class="s1">&#39;name &#39;</span> <span class="o">+</span> <span class="n">name</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Wrong format&#39;</span><span class="p">,</span> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;Wrong format&#39;</span><span class="p">,</span> <span class="n">sub_ls</span><span class="p">[</span><span class="n">cfg</span><span class="p">])</span>
<span class="n">sub_ls</span><span class="p">[</span><span class="n">cfg</span><span class="p">])</span>
<span class="k">if</span><span class="p">(</span><span class="n">k</span> <span class="o">&gt;=</span> <span class="n">start_read</span> <span class="ow">and</span> <span class="n">k</span> <span class="o">&lt;</span> <span class="n">start_read</span> <span class="o">+</span> <span class="n">T</span><span class="p">):</span> <span class="k">if</span><span class="p">(</span><span class="n">k</span> <span class="o">&gt;=</span> <span class="n">start_read</span> <span class="ow">and</span> <span class="n">k</span> <span class="o">&lt;</span> <span class="n">start_read</span> <span class="o">+</span> <span class="n">T</span><span class="p">):</span>
<span class="n">floats</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="nb">float</span><span class="p">,</span> <span class="n">lines</span><span class="p">[</span><span class="n">k</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">()))</span> <span class="n">floats</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="nb">float</span><span class="p">,</span> <span class="n">lines</span><span class="p">[</span><span class="n">k</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">()))</span>
<span class="n">deltas</span><span class="p">[</span><span class="n">k</span> <span class="o">-</span> <span class="n">start_read</span><span class="p">][</span><span class="n">i</span><span class="p">][</span><span class="n">cfg</span><span class="p">]</span> <span class="o">=</span> <span class="n">floats</span><span class="p">[</span><span class="o">-</span><span class="mi">2</span><span class="p">:][</span><span class="n">im</span><span class="p">]</span> <span class="n">deltas</span><span class="p">[</span><span class="n">k</span> <span class="o">-</span> <span class="n">start_read</span><span class="p">][</span><span class="n">i</span><span class="p">][</span><span class="n">cfg</span><span class="p">]</span> <span class="o">=</span> <span class="n">floats</span><span class="p">[</span><span class="o">-</span><span class="mi">2</span><span class="p">:][</span><span class="n">im</span><span class="p">]</span>
<span class="k">else</span><span class="p">:</span> <span class="k">else</span><span class="p">:</span>
<span class="k">for</span> <span class="n">cnfg</span><span class="p">,</span> <span class="n">subitem</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">sub_ls</span><span class="p">):</span> <span class="k">for</span> <span class="n">cnfg</span><span class="p">,</span> <span class="n">subitem</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">sub_ls</span><span class="p">):</span>
<span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">path</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">item</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">subitem</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">name</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span> <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">path</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">item</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">subitem</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">name</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span>
<span class="c1"># since the non-compatified files</span>
<span class="c1"># are typically not so long,</span>
<span class="c1"># we can iterate over the whole file.</span>
<span class="c1"># here one can also implement the chekc from above.</span>
<span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">fp</span><span class="p">):</span> <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">fp</span><span class="p">):</span>
<span class="k">if</span><span class="p">(</span><span class="n">k</span> <span class="o">&gt;=</span> <span class="n">start</span> <span class="ow">and</span> <span class="n">k</span> <span class="o">&lt;</span> <span class="n">start</span> <span class="o">+</span> <span class="n">T</span><span class="p">):</span> <span class="k">if</span><span class="p">(</span><span class="n">k</span> <span class="o">&gt;=</span> <span class="n">start_read</span> <span class="ow">and</span> <span class="n">k</span> <span class="o">&lt;</span> <span class="n">start_read</span> <span class="o">+</span> <span class="n">T</span><span class="p">):</span>
<span class="n">floats</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="nb">float</span><span class="p">,</span> <span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">()))</span> <span class="n">floats</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="nb">float</span><span class="p">,</span> <span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">()))</span>
<span class="k">if</span> <span class="n">version</span> <span class="o">==</span> <span class="s2">&quot;0.0&quot;</span><span class="p">:</span> <span class="k">if</span> <span class="n">version</span> <span class="o">==</span> <span class="s2">&quot;0.0&quot;</span><span class="p">:</span>
<span class="n">deltas</span><span class="p">[</span><span class="n">k</span> <span class="o">-</span> <span class="n">start</span><span class="p">][</span><span class="n">i</span><span class="p">][</span><span class="n">cnfg</span><span class="p">]</span> <span class="o">=</span> <span class="n">floats</span><span class="p">[</span><span class="n">im</span><span class="p">]</span> <span class="n">deltas</span><span class="p">[</span><span class="n">k</span> <span class="o">-</span> <span class="n">start</span><span class="p">][</span><span class="n">i</span><span class="p">][</span><span class="n">cnfg</span><span class="p">]</span> <span class="o">=</span> <span class="n">floats</span><span class="p">[</span><span class="n">im</span> <span class="o">-</span> <span class="n">single</span><span class="p">]</span>
<span class="k">else</span><span class="p">:</span> <span class="k">else</span><span class="p">:</span>
<span class="n">deltas</span><span class="p">[</span><span class="n">k</span> <span class="o">-</span> <span class="n">start</span><span class="p">][</span><span class="n">i</span><span class="p">][</span><span class="n">cnfg</span><span class="p">]</span> <span class="o">=</span> <span class="n">floats</span><span class="p">[</span><span class="mi">1</span> <span class="o">+</span> <span class="n">im</span> <span class="o">-</span> <span class="n">single</span><span class="p">]</span> <span class="n">deltas</span><span class="p">[</span><span class="n">k</span> <span class="o">-</span> <span class="n">start_read</span><span class="p">][</span><span class="n">i</span><span class="p">][</span><span class="n">cnfg</span><span class="p">]</span> <span class="o">=</span> <span class="n">floats</span><span class="p">[</span><span class="mi">1</span> <span class="o">+</span> <span class="n">im</span> <span class="o">-</span> <span class="n">single</span><span class="p">]</span>
<span class="k">else</span><span class="p">:</span> <span class="k">else</span><span class="p">:</span>
<span class="k">if</span> <span class="s2">&quot;files&quot;</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span> <span class="k">if</span> <span class="s2">&quot;files&quot;</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
@ -730,8 +755,6 @@
<span class="k">if</span> <span class="ow">not</span> <span class="n">fnmatch</span><span class="o">.</span><span class="n">fnmatch</span><span class="p">(</span><span class="n">exc</span><span class="p">,</span> <span class="n">prefix</span> <span class="o">+</span> <span class="s1">&#39;*.&#39;</span> <span class="o">+</span> <span class="n">name</span><span class="p">):</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">fnmatch</span><span class="o">.</span><span class="n">fnmatch</span><span class="p">(</span><span class="n">exc</span><span class="p">,</span> <span class="n">prefix</span> <span class="o">+</span> <span class="s1">&#39;*.&#39;</span> <span class="o">+</span> <span class="n">name</span><span class="p">):</span>
<span class="n">ls</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">ls</span><span class="p">)</span> <span class="o">-</span> <span class="nb">set</span><span class="p">([</span><span class="n">exc</span><span class="p">]))</span> <span class="n">ls</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">ls</span><span class="p">)</span> <span class="o">-</span> <span class="nb">set</span><span class="p">([</span><span class="n">exc</span><span class="p">]))</span>
<span class="n">ls</span><span class="o">.</span><span class="n">sort</span><span class="p">(</span><span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="nb">int</span><span class="p">(</span><span class="n">re</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;\d+&#39;</span><span class="p">,</span> <span class="n">x</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]))</span> <span class="n">ls</span><span class="o">.</span><span class="n">sort</span><span class="p">(</span><span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="nb">int</span><span class="p">(</span><span class="n">re</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;\d+&#39;</span><span class="p">,</span> <span class="n">x</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]))</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">ls</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;File(s) for correlator &#39;</span> <span class="o">+</span> <span class="n">name</span> <span class="o">+</span> <span class="s1">&#39; not found.&#39;</span><span class="p">)</span>
<span class="n">pattern</span> <span class="o">=</span> <span class="s1">&#39;name &#39;</span> <span class="o">+</span> <span class="n">name</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">quarks &#39;</span> <span class="o">+</span> <span class="n">quarks</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">offset &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">noffset</span><span class="p">)</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">wf &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">wf</span><span class="p">)</span> <span class="n">pattern</span> <span class="o">=</span> <span class="s1">&#39;name &#39;</span> <span class="o">+</span> <span class="n">name</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">quarks &#39;</span> <span class="o">+</span> <span class="n">quarks</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">offset &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">noffset</span><span class="p">)</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">wf &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">wf</span><span class="p">)</span>
<span class="k">if</span> <span class="n">b2b</span><span class="p">:</span> <span class="k">if</span> <span class="n">b2b</span><span class="p">:</span>
<span class="n">pattern</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">wf_2 &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">wf2</span><span class="p">)</span> <span class="n">pattern</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">wf_2 &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">wf2</span><span class="p">)</span>
@ -743,9 +766,9 @@
<span class="k">for</span> <span class="n">linenumber</span><span class="p">,</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">content</span><span class="p">):</span> <span class="k">for</span> <span class="n">linenumber</span><span class="p">,</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">content</span><span class="p">):</span>
<span class="k">if</span> <span class="s2">&quot;[run]&quot;</span> <span class="ow">in</span> <span class="n">line</span><span class="p">:</span> <span class="k">if</span> <span class="s2">&quot;[run]&quot;</span> <span class="ow">in</span> <span class="n">line</span><span class="p">:</span>
<span class="n">data_starts</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">linenumber</span><span class="p">)</span> <span class="n">data_starts</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">linenumber</span><span class="p">)</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">data_starts</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">-</span> <span class="n">data_starts</span><span class="p">[</span><span class="n">i</span> <span class="o">-</span> <span class="mi">1</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</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">data_starts</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">-</span> <span class="n">data_starts</span><span class="p">[</span><span class="n">i</span> <span class="o">-</span> <span class="mi">1</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">data_starts</span><span class="p">))]))</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
<span class="nb">range</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">data_starts</span><span class="p">))]))</span> <span class="o">&gt;</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="s2">&quot;Irregularities in file structure found, not all runs have the same output length&quot;</span><span class="p">)</span> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">&quot;Irregularities in file structure found, not all runs have the same output length&quot;</span><span class="p">)</span>
<span class="c1"># first chunk of data</span>
<span class="n">chunk</span> <span class="o">=</span> <span class="n">content</span><span class="p">[:</span><span class="n">data_starts</span><span class="p">[</span><span class="mi">1</span><span class="p">]]</span> <span class="n">chunk</span> <span class="o">=</span> <span class="n">content</span><span class="p">[:</span><span class="n">data_starts</span><span class="p">[</span><span class="mi">1</span><span class="p">]]</span>
<span class="k">for</span> <span class="n">linenumber</span><span class="p">,</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">chunk</span><span class="p">):</span> <span class="k">for</span> <span class="n">linenumber</span><span class="p">,</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">chunk</span><span class="p">):</span>
<span class="k">if</span> <span class="n">line</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">&quot;gauge_name&quot;</span><span class="p">):</span> <span class="k">if</span> <span class="n">line</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">&quot;gauge_name&quot;</span><span class="p">):</span>
@ -753,25 +776,31 @@
<span class="k">elif</span> <span class="n">line</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">&quot;[correlator]&quot;</span><span class="p">):</span> <span class="k">elif</span> <span class="n">line</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">&quot;[correlator]&quot;</span><span class="p">):</span>
<span class="n">corr_line</span> <span class="o">=</span> <span class="n">linenumber</span> <span class="n">corr_line</span> <span class="o">=</span> <span class="n">linenumber</span>
<span class="n">found_pat</span> <span class="o">=</span> <span class="s2">&quot;&quot;</span> <span class="n">found_pat</span> <span class="o">=</span> <span class="s2">&quot;&quot;</span>
<span class="k">for</span> <span class="n">li</span> <span class="ow">in</span> <span class="n">chunk</span><span class="p">[</span><span class="n">corr_line</span> <span class="o">+</span> <span class="mi">1</span><span class="p">:</span><span class="n">corr_line</span> <span class="o">+</span> <span class="mi">6</span> <span class="o">+</span> <span class="n">b2b</span><span class="p">]:</span> <span class="k">for</span> <span class="n">li</span> <span class="ow">in</span> <span class="n">chunk</span><span class="p">[</span><span class="n">corr_line</span> <span class="o">+</span> <span class="mi">1</span><span class="p">:</span> <span class="n">corr_line</span> <span class="o">+</span> <span class="mi">6</span> <span class="o">+</span> <span class="n">b2b</span><span class="p">]:</span>
<span class="n">found_pat</span> <span class="o">+=</span> <span class="n">li</span> <span class="n">found_pat</span> <span class="o">+=</span> <span class="n">li</span>
<span class="k">if</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="n">pattern</span><span class="p">,</span> <span class="n">found_pat</span><span class="p">):</span> <span class="k">if</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="n">pattern</span><span class="p">,</span> <span class="n">found_pat</span><span class="p">):</span>
<span class="n">start_read</span> <span class="o">=</span> <span class="n">corr_line</span> <span class="o">+</span> <span class="mi">7</span> <span class="o">+</span> <span class="n">b2b</span> <span class="n">start_read</span> <span class="o">=</span> <span class="n">corr_line</span> <span class="o">+</span> <span class="mi">7</span> <span class="o">+</span> <span class="n">b2b</span>
<span class="n">T</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">chunk</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span> <span class="o">-</span> <span class="n">start_read</span> <span class="k">break</span>
<span class="n">endline</span> <span class="o">=</span> <span class="n">corr_line</span> <span class="o">+</span> <span class="mi">6</span> <span class="o">+</span> <span class="n">b2b</span>
<span class="k">while</span> <span class="ow">not</span> <span class="n">chunk</span><span class="p">[</span><span class="n">endline</span><span class="p">]</span> <span class="o">==</span> <span class="s2">&quot;</span><span class="se">\n</span><span class="s2">&quot;</span><span class="p">:</span>
<span class="n">endline</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="n">T</span> <span class="o">=</span> <span class="n">endline</span> <span class="o">-</span> <span class="n">start_read</span>
<span class="k">if</span> <span class="n">rep</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span> <span class="k">if</span> <span class="n">rep</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="n">deltas</span> <span class="o">=</span> <span class="p">[]</span> <span class="n">deltas</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">T</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">T</span><span class="p">):</span>
<span class="n">deltas</span><span class="o">.</span><span class="n">append</span><span class="p">([])</span> <span class="n">deltas</span><span class="o">.</span><span class="n">append</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">T</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">T</span><span class="p">):</span>
<span class="n">deltas</span><span class="p">[</span><span class="n">t</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">data_starts</span><span class="p">)))</span> <span class="n">deltas</span><span class="p">[</span><span class="n">t</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">data_starts</span><span class="p">)))</span>
<span class="c1"># all other chunks should follow the same structure</span>
<span class="k">for</span> <span class="n">cnfg</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">data_starts</span><span class="p">)):</span> <span class="k">for</span> <span class="n">cnfg</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">data_starts</span><span class="p">)):</span>
<span class="n">start</span> <span class="o">=</span> <span class="n">data_starts</span><span class="p">[</span><span class="n">cnfg</span><span class="p">]</span> <span class="n">start</span> <span class="o">=</span> <span class="n">data_starts</span><span class="p">[</span><span class="n">cnfg</span><span class="p">]</span>
<span class="n">stop</span> <span class="o">=</span> <span class="n">start</span> <span class="o">+</span> <span class="n">data_starts</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">stop</span> <span class="o">=</span> <span class="n">start</span> <span class="o">+</span> <span class="n">data_starts</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
<span class="n">chunk</span> <span class="o">=</span> <span class="n">content</span><span class="p">[</span><span class="n">start</span><span class="p">:</span><span class="n">stop</span><span class="p">]</span> <span class="n">chunk</span> <span class="o">=</span> <span class="n">content</span><span class="p">[</span><span class="n">start</span><span class="p">:</span><span class="n">stop</span><span class="p">]</span>
<span class="c1"># meta_data = {}</span>
<span class="k">try</span><span class="p">:</span> <span class="k">try</span><span class="p">:</span>
<span class="n">rep_idl</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">chunk</span><span class="p">[</span><span class="n">gauge_line</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;n&quot;</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]))</span> <span class="n">rep_idl</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">chunk</span><span class="p">[</span><span class="n">gauge_line</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;n&quot;</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]))</span>
<span class="k">except</span> <span class="ne">Exception</span><span class="p">:</span> <span class="k">except</span> <span class="ne">Exception</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">&quot;Couldn&#39;t parse idl from directroy, problem with chunk around line &quot;</span> <span class="o">+</span> <span class="n">gauge_line</span><span class="p">)</span> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">&quot;Couldn&#39;t parse idl from directory, problem with chunk around line &quot;</span><span class="p">,</span> <span class="n">gauge_line</span><span class="p">)</span>
<span class="n">found_pat</span> <span class="o">=</span> <span class="s2">&quot;&quot;</span> <span class="n">found_pat</span> <span class="o">=</span> <span class="s2">&quot;&quot;</span>
<span class="k">for</span> <span class="n">li</span> <span class="ow">in</span> <span class="n">chunk</span><span class="p">[</span><span class="n">corr_line</span> <span class="o">+</span> <span class="mi">1</span><span class="p">:</span><span class="n">corr_line</span> <span class="o">+</span> <span class="mi">6</span> <span class="o">+</span> <span class="n">b2b</span><span class="p">]:</span> <span class="k">for</span> <span class="n">li</span> <span class="ow">in</span> <span class="n">chunk</span><span class="p">[</span><span class="n">corr_line</span> <span class="o">+</span> <span class="mi">1</span><span class="p">:</span><span class="n">corr_line</span> <span class="o">+</span> <span class="mi">6</span> <span class="o">+</span> <span class="n">b2b</span><span class="p">]:</span>
@ -779,7 +808,7 @@
<span class="k">if</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="n">pattern</span><span class="p">,</span> <span class="n">found_pat</span><span class="p">):</span> <span class="k">if</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="n">pattern</span><span class="p">,</span> <span class="n">found_pat</span><span class="p">):</span>
<span class="k">for</span> <span class="n">t</span><span class="p">,</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">chunk</span><span class="p">[</span><span class="n">start_read</span><span class="p">:</span><span class="n">start_read</span> <span class="o">+</span> <span class="n">T</span><span class="p">]):</span> <span class="k">for</span> <span class="n">t</span><span class="p">,</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">chunk</span><span class="p">[</span><span class="n">start_read</span><span class="p">:</span><span class="n">start_read</span> <span class="o">+</span> <span class="n">T</span><span class="p">]):</span>
<span class="n">floats</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="nb">float</span><span class="p">,</span> <span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">()))</span> <span class="n">floats</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="nb">float</span><span class="p">,</span> <span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">()))</span>
<span class="n">deltas</span><span class="p">[</span><span class="n">t</span><span class="p">][</span><span class="n">rep</span><span class="p">][</span><span class="n">cnfg</span><span class="p">]</span> <span class="o">=</span> <span class="n">floats</span><span class="p">[</span><span class="o">-</span><span class="mi">2</span><span class="p">:][</span><span class="n">im</span><span class="p">]</span> <span class="n">deltas</span><span class="p">[</span><span class="n">t</span><span class="p">][</span><span class="n">rep</span><span class="p">][</span><span class="n">cnfg</span><span class="p">]</span> <span class="o">=</span> <span class="n">floats</span><span class="p">[</span><span class="n">im</span> <span class="o">+</span> <span class="mi">1</span> <span class="o">-</span> <span class="n">single</span><span class="p">]</span>
<span class="n">idl</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">rep_idl</span><span class="p">)</span> <span class="n">idl</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">rep_idl</span><span class="p">)</span>
<span class="k">if</span> <span class="s2">&quot;check_configs&quot;</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span> <span class="k">if</span> <span class="s2">&quot;check_configs&quot;</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
@ -799,57 +828,46 @@
</details> </details>
<div class="docstring"><p>Read sfcf format from given folder structure.</p> <div class="docstring"><p>Read sfcf c format from given folder structure.</p>
<h6 id="parameters">Parameters</h6> <h6 id="parameters">Parameters</h6>
<ul> <ul>
<li><strong>path</strong> (str): <li><strong>quarks</strong> (str):
Path to the measurement files.</li>
<li><strong>prefix</strong> (str):
Ensemble prefix for which the data is to be extracted.</li>
<li><strong>name</strong> (str):
Name of the correlation function to be extracted from the file</li>
<li><strong>quarks</strong> (str, optional):
Label of the quarks used in the sfcf input file. e.g. "quark quark" Label of the quarks used in the sfcf input file. e.g. "quark quark"
for version 0.0 this does NOT need to be given with the typical " - " for version 0.0 this does NOT need to be given with the typical " - "
that is present in the output file, that is present in the output file,
this is done automatically for this version</li> this is done automatically for this version</li>
<li><strong>noffset</strong> (int, optional): <li><strong>noffset</strong> (int):
Offset of the source (only relevant when wavefunctions are used)</li> Offset of the source (only relevant when wavefunctions are used)</li>
<li><strong>wf</strong> (int, optional): <li><strong>wf</strong> (int):
ID of wave function</li> ID of wave function</li>
<li><strong>wf2</strong> (int, optional): <li><strong>wf2</strong> (int):
ID of the second wavefunction ID of the second wavefunction
(only relevant for boundary-to-boundary correlation functions)</li> (only relevant for boundary-to-boundary correlation functions)</li>
<li><strong>im</strong> (bool, optional): <li><strong>im</strong> (bool):
if True, read imaginary instead of real part if True, read imaginary instead of real part
of the correlation function.</li> of the correlation function.</li>
<li><strong>b2b</strong> (bool, optional): <li><strong>corr_type</strong> (str):
if True, read a time-dependent boundary-to-boundary change between bi (boundary - inner) (default) bib (boundary - inner - boundary) and bb (boundary - boundary)
correlation function</li> correlator types</li>
<li><strong>single</strong> (bool, optional): <li><strong>names</strong> (list):
if True, read time independent boundary to boundary
correlation function</li>
<li><strong>names</strong> (list, optional):
Alternative labeling for replicas/ensembles. Alternative labeling for replicas/ensembles.
Has to have the appropriate length</li> Has to have the appropriate length</li>
<li><strong>ens_name</strong> (str, optional): <li><strong>ens_name</strong> (str):
replaces the name of the ensemble</li> replaces the name of the ensemble</li>
<li><strong>version</strong> (str, optional): <li><strong>version</strong> (str):
version of SFCF, with which the measurement was done. version of SFCF, with which the measurement was done.
if the compact output option (-c) was specified, if the compact output option (-c) was spectified,
append a "c" to the version (e.g. "1.0c") append a "c" to the version (e.g. "1.0c")
if the append output option (-a) was specified, if the append output option (-a) was specified,
append an "a" to the version. Currently supported versions append an "a" to the version</li>
are "0.0", "1.0", "2.0", "1.0c", "2.0c", "1.0a" and "2.0a".</li> <li><strong>replica</strong> (list):
<li><strong>replica</strong> (list, optional):
list of replica to be read, default is all</li> list of replica to be read, default is all</li>
<li><strong>files</strong> (list, optional): <li><strong>files</strong> (list):
list of files to be read per replica, default is all. list of files to be read per replica, default is all.
for non-compact output format, hand the folders to be read here.</li> for non-conpact ouztput format, hand the folders to be read here.</li>
<li><strong>check_configs</strong> (list, optional): <li><strong>check_configs:</strong>: list of list of supposed configs, eg. [range(1,1000)]
list of list of supposed configs, eg. [range(1,1000)]
for one replicum with 1000 configs</li> for one replicum with 1000 configs</li>
</ul> </ul>
</div> </div>

2
docs/search.js
View file

File diff suppressed because one or more lines are too long