mirror of
https://github.com/fjosw/pyerrors.git
synced 2025-05-15 20:13:41 +02:00
Documentation updated
This commit is contained in:
fjosw
parent
ab22af5d54
commit
53df2a5d81
4 changed files with 47 additions and 26 deletions
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@ -87,17 +87,14 @@
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<details>
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<summary>View Source</summary>
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<div class="codehilite"><pre><span></span><span class="ch">#!/usr/bin/env python</span>
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<span class="c1"># coding: utf-8</span>
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<span class="kn">import</span> <span class="nn">os</span>
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<div class="codehilite"><pre><span></span><span class="kn">import</span> <span class="nn">os</span>
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<span class="kn">import</span> <span class="nn">h5py</span>
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<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
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<span class="kn">from</span> <span class="nn">..obs</span> <span class="kn">import</span> <span class="n">Obs</span><span class="p">,</span> <span class="n">CObs</span>
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<span class="kn">from</span> <span class="nn">..correlators</span> <span class="kn">import</span> <span class="n">Corr</span>
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<span class="k">def</span> <span class="nf">_get_files</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">filestem</span><span class="p">):</span>
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<span class="k">def</span> <span class="nf">_get_files</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">filestem</span><span class="p">,</span> <span class="n">idl</span><span class="p">):</span>
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<span class="n">ls</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">listdir</span><span class="p">(</span><span class="n">path</span><span class="p">)</span>
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<span class="c1"># Clean up file list</span>
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@ -112,11 +109,19 @@
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<span class="c1"># Sort according to configuration number</span>
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<span class="n">files</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="n">get_cnfg_number</span><span class="p">)</span>
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<span class="c1"># Check that configurations are evenly spaced</span>
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<span class="n">cnfg_numbers</span> <span class="o">=</span> <span class="p">[]</span>
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<span class="n">filtered_files</span> <span class="o">=</span> <span class="p">[]</span>
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<span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">files</span><span class="p">:</span>
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<span class="n">cnfg_numbers</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">get_cnfg_number</span><span class="p">(</span><span class="n">line</span><span class="p">))</span>
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<span class="n">no</span> <span class="o">=</span> <span class="n">get_cnfg_number</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
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<span class="k">if</span> <span class="n">idl</span><span class="p">:</span>
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<span class="k">if</span> <span class="n">no</span> <span class="ow">in</span> <span class="nb">list</span><span class="p">(</span><span class="n">idl</span><span class="p">):</span>
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<span class="n">filtered_files</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
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<span class="n">cnfg_numbers</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">no</span><span class="p">)</span>
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<span class="k">else</span><span class="p">:</span>
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<span class="n">filtered_files</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
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<span class="n">cnfg_numbers</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">no</span><span class="p">)</span>
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<span class="c1"># Check that configurations are evenly spaced</span>
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<span class="n">dc</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">unique</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">diff</span><span class="p">(</span><span class="n">cnfg_numbers</span><span class="p">))</span>
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<span class="k">if</span> <span class="n">np</span><span class="o">.</span><span class="n">any</span><span class="p">(</span><span class="n">dc</span> <span class="o"><</span> <span class="mi">0</span><span class="p">):</span>
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<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">"Unsorted files"</span><span class="p">)</span>
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@ -125,10 +130,10 @@
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<span class="k">else</span><span class="p">:</span>
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<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">'Configurations are not evenly spaced.'</span><span class="p">)</span>
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<span class="k">return</span> <span class="n">files</span><span class="p">,</span> <span class="n">idx</span>
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<span class="k">return</span> <span class="n">filtered_files</span><span class="p">,</span> <span class="n">idx</span>
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<span class="k">def</span> <span class="nf">read_meson_hd5</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">filestem</span><span class="p">,</span> <span class="n">ens_id</span><span class="p">,</span> <span class="n">meson</span><span class="o">=</span><span class="s1">'meson_0'</span><span class="p">,</span> <span class="n">tree</span><span class="o">=</span><span class="s1">'meson'</span><span class="p">):</span>
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<span class="k">def</span> <span class="nf">read_meson_hd5</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">filestem</span><span class="p">,</span> <span class="n">ens_id</span><span class="p">,</span> <span class="n">meson</span><span class="o">=</span><span class="s1">'meson_0'</span><span class="p">,</span> <span class="n">tree</span><span class="o">=</span><span class="s1">'meson'</span><span class="p">,</span> <span class="n">idl</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
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<span class="sd">"""Read hadrons meson hdf5 file and extract the meson labeled 'meson'</span>
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<span class="sd"> Parameters</span>
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@ -146,9 +151,11 @@
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<span class="sd"> Label of the upmost directory in the hdf5 file, default 'meson'</span>
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<span class="sd"> for outputs of the Meson module. Can be altered to read input</span>
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<span class="sd"> from other modules with similar structures.</span>
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<span class="sd"> idl : range</span>
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<span class="sd"> If specified only conifgurations in the given range are read in.</span>
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<span class="sd"> """</span>
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<span class="n">files</span><span class="p">,</span> <span class="n">idx</span> <span class="o">=</span> <span class="n">_get_files</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">filestem</span><span class="p">)</span>
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<span class="n">files</span><span class="p">,</span> <span class="n">idx</span> <span class="o">=</span> <span class="n">_get_files</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">filestem</span><span class="p">,</span> <span class="n">idl</span><span class="p">)</span>
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<span class="n">corr_data</span> <span class="o">=</span> <span class="p">[]</span>
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<span class="n">infos</span> <span class="o">=</span> <span class="p">[]</span>
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@ -212,7 +219,7 @@
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<span class="bp">self</span><span class="o">.</span><span class="n">mom_out</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">obj</span><span class="p">,</span> <span class="s1">'mom_out'</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
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<span class="k">def</span> <span class="nf">read_ExternalLeg_hd5</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">filestem</span><span class="p">,</span> <span class="n">ens_id</span><span class="p">,</span> <span class="n">order</span><span class="o">=</span><span class="s1">'F'</span><span class="p">):</span>
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<span class="k">def</span> <span class="nf">read_ExternalLeg_hd5</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">filestem</span><span class="p">,</span> <span class="n">ens_id</span><span class="p">,</span> <span class="n">order</span><span class="o">=</span><span class="s1">'F'</span><span class="p">,</span> <span class="n">idl</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
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<span class="sd">"""Read hadrons ExternalLeg hdf5 file and output an array of CObs</span>
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<span class="sd"> Parameters</span>
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@ -223,9 +230,11 @@
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<span class="sd"> order -- order in which the array is to be reshaped,</span>
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<span class="sd"> 'F' for the first index changing fastest (9 4x4 matrices) default.</span>
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<span class="sd"> 'C' for the last index changing fastest (16 3x3 matrices),</span>
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<span class="sd"> idl : range</span>
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<span class="sd"> If specified only conifgurations in the given range are read in.</span>
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<span class="sd"> """</span>
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<span class="n">files</span><span class="p">,</span> <span class="n">idx</span> <span class="o">=</span> <span class="n">_get_files</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">filestem</span><span class="p">)</span>
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<span class="n">files</span><span class="p">,</span> <span class="n">idx</span> <span class="o">=</span> <span class="n">_get_files</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">filestem</span><span class="p">,</span> <span class="n">idl</span><span class="p">)</span>
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<span class="n">mom</span> <span class="o">=</span> <span class="kc">None</span>
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@ -250,7 +259,7 @@
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<span class="k">return</span> <span class="n">Npr_matrix</span><span class="p">(</span><span class="n">matrix</span><span class="o">.</span><span class="n">swapaxes</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span><span class="o">.</span><span class="n">reshape</span><span class="p">((</span><span class="mi">12</span><span class="p">,</span> <span class="mi">12</span><span class="p">),</span> <span class="n">order</span><span class="o">=</span><span class="n">order</span><span class="p">),</span> <span class="n">mom_in</span><span class="o">=</span><span class="n">mom</span><span class="p">)</span>
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<span class="k">def</span> <span class="nf">read_Bilinear_hd5</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">filestem</span><span class="p">,</span> <span class="n">ens_id</span><span class="p">,</span> <span class="n">order</span><span class="o">=</span><span class="s1">'F'</span><span class="p">):</span>
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<span class="k">def</span> <span class="nf">read_Bilinear_hd5</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">filestem</span><span class="p">,</span> <span class="n">ens_id</span><span class="p">,</span> <span class="n">order</span><span class="o">=</span><span class="s1">'F'</span><span class="p">,</span> <span class="n">idl</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
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<span class="sd">"""Read hadrons Bilinear hdf5 file and output an array of CObs</span>
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<span class="sd"> Parameters</span>
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@ -261,9 +270,11 @@
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<span class="sd"> order -- order in which the array is to be reshaped,</span>
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<span class="sd"> 'F' for the first index changing fastest (9 4x4 matrices) default.</span>
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<span class="sd"> 'C' for the last index changing fastest (16 3x3 matrices),</span>
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<span class="sd"> idl : range</span>
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<span class="sd"> If specified only conifgurations in the given range are read in.</span>
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<span class="sd"> """</span>
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<span class="n">files</span><span class="p">,</span> <span class="n">idx</span> <span class="o">=</span> <span class="n">_get_files</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">filestem</span><span class="p">)</span>
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<span class="n">files</span><span class="p">,</span> <span class="n">idx</span> <span class="o">=</span> <span class="n">_get_files</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">filestem</span><span class="p">,</span> <span class="n">idl</span><span class="p">)</span>
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<span class="n">mom_in</span> <span class="o">=</span> <span class="kc">None</span>
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<span class="n">mom_out</span> <span class="o">=</span> <span class="kc">None</span>
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@ -310,12 +321,12 @@
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<span class="def">def</span>
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<span class="name">read_meson_hd5</span><span class="signature">(path, filestem, ens_id, meson='meson_0', tree='meson')</span>:
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<span class="name">read_meson_hd5</span><span class="signature">(path, filestem, ens_id, meson='meson_0', tree='meson', idl=None)</span>:
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</div>
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<details>
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<summary>View Source</summary>
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<div class="codehilite"><pre><span></span><span class="k">def</span> <span class="nf">read_meson_hd5</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">filestem</span><span class="p">,</span> <span class="n">ens_id</span><span class="p">,</span> <span class="n">meson</span><span class="o">=</span><span class="s1">'meson_0'</span><span class="p">,</span> <span class="n">tree</span><span class="o">=</span><span class="s1">'meson'</span><span class="p">):</span>
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<div class="codehilite"><pre><span></span><span class="k">def</span> <span class="nf">read_meson_hd5</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">filestem</span><span class="p">,</span> <span class="n">ens_id</span><span class="p">,</span> <span class="n">meson</span><span class="o">=</span><span class="s1">'meson_0'</span><span class="p">,</span> <span class="n">tree</span><span class="o">=</span><span class="s1">'meson'</span><span class="p">,</span> <span class="n">idl</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
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<span class="sd">"""Read hadrons meson hdf5 file and extract the meson labeled 'meson'</span>
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<span class="sd"> Parameters</span>
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@ -333,9 +344,11 @@
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<span class="sd"> Label of the upmost directory in the hdf5 file, default 'meson'</span>
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<span class="sd"> for outputs of the Meson module. Can be altered to read input</span>
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<span class="sd"> from other modules with similar structures.</span>
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<span class="sd"> idl : range</span>
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<span class="sd"> If specified only conifgurations in the given range are read in.</span>
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<span class="sd"> """</span>
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<span class="n">files</span><span class="p">,</span> <span class="n">idx</span> <span class="o">=</span> <span class="n">_get_files</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">filestem</span><span class="p">)</span>
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<span class="n">files</span><span class="p">,</span> <span class="n">idx</span> <span class="o">=</span> <span class="n">_get_files</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">filestem</span><span class="p">,</span> <span class="n">idl</span><span class="p">)</span>
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<span class="n">corr_data</span> <span class="o">=</span> <span class="p">[]</span>
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<span class="n">infos</span> <span class="o">=</span> <span class="p">[]</span>
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@ -379,6 +392,8 @@ corresponds to the pseudoscalar pseudoscalar two-point function.</li>
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Label of the upmost directory in the hdf5 file, default 'meson'
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for outputs of the Meson module. Can be altered to read input
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from other modules with similar structures.</li>
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<li><strong>idl</strong> (range):
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If specified only conifgurations in the given range are read in.</li>
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</ul>
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</div>
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@ -675,12 +690,12 @@ in and out momenta of the propagator are exchanged.</p>
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<span class="def">def</span>
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<span class="name">read_ExternalLeg_hd5</span><span class="signature">(path, filestem, ens_id, order='F')</span>:
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<span class="name">read_ExternalLeg_hd5</span><span class="signature">(path, filestem, ens_id, order='F', idl=None)</span>:
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</div>
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<details>
|
||||
<summary>View Source</summary>
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<div class="codehilite"><pre><span></span><span class="k">def</span> <span class="nf">read_ExternalLeg_hd5</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">filestem</span><span class="p">,</span> <span class="n">ens_id</span><span class="p">,</span> <span class="n">order</span><span class="o">=</span><span class="s1">'F'</span><span class="p">):</span>
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<div class="codehilite"><pre><span></span><span class="k">def</span> <span class="nf">read_ExternalLeg_hd5</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">filestem</span><span class="p">,</span> <span class="n">ens_id</span><span class="p">,</span> <span class="n">order</span><span class="o">=</span><span class="s1">'F'</span><span class="p">,</span> <span class="n">idl</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
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<span class="sd">"""Read hadrons ExternalLeg hdf5 file and output an array of CObs</span>
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<span class="sd"> Parameters</span>
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@ -691,9 +706,11 @@ in and out momenta of the propagator are exchanged.</p>
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<span class="sd"> order -- order in which the array is to be reshaped,</span>
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<span class="sd"> 'F' for the first index changing fastest (9 4x4 matrices) default.</span>
|
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<span class="sd"> 'C' for the last index changing fastest (16 3x3 matrices),</span>
|
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<span class="sd"> idl : range</span>
|
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<span class="sd"> If specified only conifgurations in the given range are read in.</span>
|
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<span class="sd"> """</span>
|
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|
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<span class="n">files</span><span class="p">,</span> <span class="n">idx</span> <span class="o">=</span> <span class="n">_get_files</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">filestem</span><span class="p">)</span>
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<span class="n">files</span><span class="p">,</span> <span class="n">idx</span> <span class="o">=</span> <span class="n">_get_files</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">filestem</span><span class="p">,</span> <span class="n">idl</span><span class="p">)</span>
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<span class="n">mom</span> <span class="o">=</span> <span class="kc">None</span>
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@ -730,6 +747,8 @@ in and out momenta of the propagator are exchanged.</p>
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<li><strong>ens_id -- name of the ensemble, required for internal bookkeeping</strong></li>
|
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<li><strong>order -- order in which the array is to be reshaped,</strong>: 'F' for the first index changing fastest (9 4x4 matrices) default.
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'C' for the last index changing fastest (16 3x3 matrices),</li>
|
||||
<li><strong>idl</strong> (range):
|
||||
If specified only conifgurations in the given range are read in.</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
|
@ -740,12 +759,12 @@ in and out momenta of the propagator are exchanged.</p>
|
|||
|
||||
|
||||
<span class="def">def</span>
|
||||
<span class="name">read_Bilinear_hd5</span><span class="signature">(path, filestem, ens_id, order='F')</span>:
|
||||
<span class="name">read_Bilinear_hd5</span><span class="signature">(path, filestem, ens_id, order='F', idl=None)</span>:
|
||||
</div>
|
||||
|
||||
<details>
|
||||
<summary>View Source</summary>
|
||||
<div class="codehilite"><pre><span></span><span class="k">def</span> <span class="nf">read_Bilinear_hd5</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">filestem</span><span class="p">,</span> <span class="n">ens_id</span><span class="p">,</span> <span class="n">order</span><span class="o">=</span><span class="s1">'F'</span><span class="p">):</span>
|
||||
<div class="codehilite"><pre><span></span><span class="k">def</span> <span class="nf">read_Bilinear_hd5</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">filestem</span><span class="p">,</span> <span class="n">ens_id</span><span class="p">,</span> <span class="n">order</span><span class="o">=</span><span class="s1">'F'</span><span class="p">,</span> <span class="n">idl</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
|
||||
<span class="sd">"""Read hadrons Bilinear hdf5 file and output an array of CObs</span>
|
||||
|
||||
<span class="sd"> Parameters</span>
|
||||
|
|
@ -756,9 +775,11 @@ in and out momenta of the propagator are exchanged.</p>
|
|||
<span class="sd"> order -- order in which the array is to be reshaped,</span>
|
||||
<span class="sd"> 'F' for the first index changing fastest (9 4x4 matrices) default.</span>
|
||||
<span class="sd"> 'C' for the last index changing fastest (16 3x3 matrices),</span>
|
||||
<span class="sd"> idl : range</span>
|
||||
<span class="sd"> If specified only conifgurations in the given range are read in.</span>
|
||||
<span class="sd"> """</span>
|
||||
|
||||
<span class="n">files</span><span class="p">,</span> <span class="n">idx</span> <span class="o">=</span> <span class="n">_get_files</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">filestem</span><span class="p">)</span>
|
||||
<span class="n">files</span><span class="p">,</span> <span class="n">idx</span> <span class="o">=</span> <span class="n">_get_files</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">filestem</span><span class="p">,</span> <span class="n">idl</span><span class="p">)</span>
|
||||
|
||||
<span class="n">mom_in</span> <span class="o">=</span> <span class="kc">None</span>
|
||||
<span class="n">mom_out</span> <span class="o">=</span> <span class="kc">None</span>
|
||||
|
|
@ -809,6 +830,8 @@ in and out momenta of the propagator are exchanged.</p>
|
|||
<li><strong>ens_id -- name of the ensemble, required for internal bookkeeping</strong></li>
|
||||
<li><strong>order -- order in which the array is to be reshaped,</strong>: 'F' for the first index changing fastest (9 4x4 matrices) default.
|
||||
'C' for the last index changing fastest (16 3x3 matrices),</li>
|
||||
<li><strong>idl</strong> (range):
|
||||
If specified only conifgurations in the given range are read in.</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue