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fjosw 2022-02-08 13:50:07 +00:00
parent 6d3a4164f9
commit 41ee866cd0
4 changed files with 11 additions and 51 deletions
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5
docs/pyerrors/input/bdio.html
View file

@ -78,10 +78,7 @@
<details>
<summary>View Source</summary>
<div class="codehilite"><pre><span></span><span class="ch">#!/usr/bin/env python</span>
<span class="c1"># coding: utf-8</span>
<span class="kn">import</span> <span class="nn">ctypes</span>
<div class="codehilite"><pre><span></span><span class="kn">import</span> <span class="nn">ctypes</span>
<span class="kn">import</span> <span class="nn">hashlib</span>
<span class="kn">import</span> <span class="nn">autograd.numpy</span> <span class="k">as</span> <span class="nn">np</span> <span class="c1"># Thinly-wrapped numpy</span>
<span class="kn">from</span> <span class="nn">..obs</span> <span class="kn">import</span> <span class="n">Obs</span>

2
docs/pyerrors/input/openQCD.html
View file

@ -653,7 +653,6 @@
<span class="n">found</span> <span class="o">=</span> <span class="p">[]</span>
<span class="n">files</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="p">(</span><span class="n">dirpath</span><span class="p">,</span> <span class="n">dirnames</span><span class="p">,</span> <span class="n">filenames</span><span class="p">)</span> <span class="ow">in</span> <span class="n">os</span><span class="o">.</span><span class="n">walk</span><span class="p">(</span><span class="n">path</span> <span class="o">+</span> <span class="s2">&quot;/&quot;</span><span class="p">):</span>
<span class="c1"># print(filenames)</span>
<span class="n">found</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">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">found</span><span class="p">:</span>
@ -1476,7 +1475,6 @@ If False: The config numbers are assumed to be traj_number // difference</li>
<span class="n">found</span> <span class="o">=</span> <span class="p">[]</span>
<span class="n">files</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="p">(</span><span class="n">dirpath</span><span class="p">,</span> <span class="n">dirnames</span><span class="p">,</span> <span class="n">filenames</span><span class="p">)</span> <span class="ow">in</span> <span class="n">os</span><span class="o">.</span><span class="n">walk</span><span class="p">(</span><span class="n">path</span> <span class="o">+</span> <span class="s2">&quot;/&quot;</span><span class="p">):</span>
<span class="c1"># print(filenames)</span>
<span class="n">found</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">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">found</span><span class="p">:</span>

53
docs/pyerrors/input/sfcf.html
View file

@ -69,10 +69,7 @@
<details>
<summary>View Source</summary>
<div class="codehilite"><pre><span></span><span class="ch">#!/usr/bin/env python</span>
<span class="c1"># coding: utf-8</span>
<span class="kn">import</span> <span class="nn">os</span>
<div class="codehilite"><pre><span></span><span class="kn">import</span> <span class="nn">os</span>
<span class="kn">import</span> <span class="nn">fnmatch</span>
<span class="kn">import</span> <span class="nn">re</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span> <span class="c1"># Thinly-wrapped numpy</span>
@ -110,7 +107,7 @@
<span class="sd"> replaces the name of the ensemble</span>
<span class="sd"> version: str</span>
<span class="sd"> version of SFCF, with which the measurement was done.</span>
<span class="sd"> if the compact output option (-c) was spectified,</span>
<span class="sd"> if the compact output option (-c) was specified,</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"> append an &quot;a&quot; to the version</span>
@ -118,7 +115,7 @@
<span class="sd"> list of replica to be read, default is all</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"> for non-conpact ouztput format, hand the folders to be read here.</span>
<span class="sd"> for non-compact output format, hand the folders to be read here.</span>
<span class="sd"> check_configs:</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>
@ -140,17 +137,12 @@
<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">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="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="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="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>
@ -198,8 +190,6 @@
<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">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="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>
@ -220,7 +210,6 @@
<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="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="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>
@ -230,7 +219,6 @@
<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="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="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>
@ -245,8 +233,6 @@
<span class="k">else</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="c1"># print(sub_ls)</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>
@ -257,7 +243,6 @@
<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="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="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">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>
@ -272,7 +257,7 @@
<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="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="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="c1"># here, we want to find the place within the file,</span>
<span class="c1"># where the correlator we need is stored.</span>
@ -326,8 +311,6 @@
<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="c1"># ...the actual parsing can start.</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">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>
@ -383,7 +366,6 @@
<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="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="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="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>
@ -411,7 +393,6 @@
<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">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="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>
@ -495,7 +476,7 @@
<span class="sd"> replaces the name of the ensemble</span>
<span class="sd"> version: str</span>
<span class="sd"> version of SFCF, with which the measurement was done.</span>
<span class="sd"> if the compact output option (-c) was spectified,</span>
<span class="sd"> if the compact output option (-c) was specified,</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"> append an &quot;a&quot; to the version</span>
@ -503,7 +484,7 @@
<span class="sd"> list of replica to be read, default is all</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"> for non-conpact ouztput format, hand the folders to be read here.</span>
<span class="sd"> for non-compact output format, hand the folders to be read here.</span>
<span class="sd"> check_configs:</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>
@ -525,17 +506,12 @@
<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">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="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="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="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>
@ -583,8 +559,6 @@
<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">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="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>
@ -605,7 +579,6 @@
<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="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="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>
@ -615,7 +588,6 @@
<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="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="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>
@ -630,8 +602,6 @@
<span class="k">else</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="c1"># print(sub_ls)</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>
@ -642,7 +612,6 @@
<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="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="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">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>
@ -657,7 +626,7 @@
<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="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="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="c1"># here, we want to find the place within the file,</span>
<span class="c1"># where the correlator we need is stored.</span>
@ -711,8 +680,6 @@
<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="c1"># ...the actual parsing can start.</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">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>
@ -768,7 +735,6 @@
<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="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="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="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>
@ -796,7 +762,6 @@
<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">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="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>
@ -858,7 +823,7 @@ Has to have the appropriate length</li>
replaces the name of the ensemble</li>
<li><strong>version</strong> (str):
version of SFCF, with which the measurement was done.
if the compact output option (-c) was spectified,
if the compact output option (-c) was specified,
append a "c" to the version (e.g. "1.0c")
if the append output option (-a) was specified,
append an "a" to the version</li>
@ -866,7 +831,7 @@ append an "a" to the version</li>
list of replica to be read, default is all</li>
<li><strong>files</strong> (list):
list of files to be read per replica, default is all.
for non-conpact ouztput format, hand the folders to be read here.</li>
for non-compact output format, hand the folders to be read here.</li>
<li><strong>check_configs:</strong>: list of list of supposed configs, eg. [range(1,1000)]
for one replicum with 1000 configs</li>
</ul>

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