Skip to content

Commit

Permalink
Update documentation
Browse files Browse the repository at this point in the history
  • Loading branch information
github-actions committed Jan 19, 2025
1 parent 2811aa0 commit 461e654
Show file tree
Hide file tree
Showing 86 changed files with 8,100 additions and 15,061 deletions.
22 changes: 11 additions & 11 deletions sed/develop/_modules/index.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,12 +2,12 @@
<!DOCTYPE html>


<html lang="en" data-content_root="" >
<html lang="en" data-content_root="../" >

<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Overview: module code &#8212; SED 0.4.0.dev0 documentation</title>
<title>Overview: module code &#8212; SED 0.4.1.dev383+g27234e0 documentation</title>



Expand All @@ -29,32 +29,32 @@
<link href="../_static/styles/theme.css?digest=8878045cc6db502f8baf" rel="stylesheet" />
<link href="../_static/styles/pydata-sphinx-theme.css?digest=8878045cc6db502f8baf" rel="stylesheet" />

<link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=a746c00c" />
<link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=8f2a1f02" />

<!-- So that users can add custom icons -->
<script src="../_static/scripts/fontawesome.js?digest=8878045cc6db502f8baf"></script>
<!-- Pre-loaded scripts that we'll load fully later -->
<link rel="preload" as="script" href="../_static/scripts/bootstrap.js?digest=8878045cc6db502f8baf" />
<link rel="preload" as="script" href="../_static/scripts/pydata-sphinx-theme.js?digest=8878045cc6db502f8baf" />

<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=57b8f4a9"></script>
<script src="../_static/doctools.js?v=888ff710"></script>
<script src="../_static/sphinx_highlight.js?v=4825356b"></script>
<script src="../_static/documentation_options.js?v=db21e222"></script>
<script src="../_static/doctools.js?v=9bcbadda"></script>
<script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="https://unpkg.com/@jupyter-widgets/html-manager@^0.20.1/dist/embed-amd.js"></script>
<script src="https://cdn.jsdelivr.net/npm/@jupyter-widgets/html-manager@^1.0.1/dist/embed-amd.js"></script>
<script>DOCUMENTATION_OPTIONS.pagename = '_modules/index';</script>
<script>
DOCUMENTATION_OPTIONS.theme_version = '0.16.1';
DOCUMENTATION_OPTIONS.theme_switcher_json_url = 'https://raw.githubusercontent.com/OpenCOMPES/docs/main/sed/switcher.json';
DOCUMENTATION_OPTIONS.theme_switcher_version_match = '0.4.0.dev0';
DOCUMENTATION_OPTIONS.theme_switcher_version_match = '0.4.1.dev383+g27234e0';
DOCUMENTATION_OPTIONS.show_version_warning_banner =
true;
</script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<meta name="viewport" content="width=device-width, initial-scale=1"/>
<meta name="docsearch:language" content="en"/>
<meta name="docsearch:version" content="0.4.0.dev0" />
<meta name="docsearch:version" content="0.4.1.dev383+g27234e0" />
</head>


Expand Down Expand Up @@ -116,7 +116,7 @@



<p class="title logo__title">SED 0.4.0.dev0 documentation</p>
<p class="title logo__title">SED 0.4.1.dev383+g27234e0 documentation</p>

</a></div>

Expand Down Expand Up @@ -485,7 +485,7 @@ <h1>All modules for which code is available</h1>
<div class="footer-item">

<p class="sphinx-version">
Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.1.2.
Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 8.1.3.
<br/>
</p>
</div>
Expand Down
151 changes: 72 additions & 79 deletions sed/develop/_modules/sed/binning/binning.html
View file

Large diffs are not rendered by default.

70 changes: 37 additions & 33 deletions sed/develop/_modules/sed/binning/numba_bin.html
View file

Large diffs are not rendered by default.

73 changes: 37 additions & 36 deletions sed/develop/_modules/sed/binning/utils.html
View file

Large diffs are not rendered by default.

291 changes: 167 additions & 124 deletions sed/develop/_modules/sed/calibrator/delay.html
View file

Large diffs are not rendered by default.

963 changes: 548 additions & 415 deletions sed/develop/_modules/sed/calibrator/energy.html
View file

Large diffs are not rendered by default.

746 changes: 448 additions & 298 deletions sed/develop/_modules/sed/calibrator/momentum.html
View file

Large diffs are not rendered by default.

213 changes: 165 additions & 48 deletions sed/develop/_modules/sed/core/config.html
View file

Large diffs are not rendered by default.

225 changes: 111 additions & 114 deletions sed/develop/_modules/sed/core/dfops.html
View file

Large diffs are not rendered by default.

106 changes: 77 additions & 29 deletions sed/develop/_modules/sed/core/metadata.html
View file

Large diffs are not rendered by default.

1,099 changes: 617 additions & 482 deletions sed/develop/_modules/sed/core/processor.html
View file

Large diffs are not rendered by default.

123 changes: 74 additions & 49 deletions sed/develop/_modules/sed/dataset/dataset.html
View file

Large diffs are not rendered by default.

89 changes: 55 additions & 34 deletions sed/develop/_modules/sed/diagnostics.html
View file

Large diffs are not rendered by default.

54 changes: 30 additions & 24 deletions sed/develop/_modules/sed/io/hdf5.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,12 +2,12 @@
<!DOCTYPE html>


<html lang="en" data-content_root="" >
<html lang="en" data-content_root="../../../" >

<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>sed.io.hdf5 &#8212; SED 0.4.0.dev0 documentation</title>
<title>sed.io.hdf5 &#8212; SED 0.4.1.dev383+g27234e0 documentation</title>



Expand All @@ -29,32 +29,32 @@
<link href="../../../_static/styles/theme.css?digest=8878045cc6db502f8baf" rel="stylesheet" />
<link href="../../../_static/styles/pydata-sphinx-theme.css?digest=8878045cc6db502f8baf" rel="stylesheet" />

<link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=a746c00c" />
<link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=8f2a1f02" />

<!-- So that users can add custom icons -->
<script src="../../../_static/scripts/fontawesome.js?digest=8878045cc6db502f8baf"></script>
<!-- Pre-loaded scripts that we'll load fully later -->
<link rel="preload" as="script" href="../../../_static/scripts/bootstrap.js?digest=8878045cc6db502f8baf" />
<link rel="preload" as="script" href="../../../_static/scripts/pydata-sphinx-theme.js?digest=8878045cc6db502f8baf" />

<script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js?v=57b8f4a9"></script>
<script src="../../../_static/doctools.js?v=888ff710"></script>
<script src="../../../_static/sphinx_highlight.js?v=4825356b"></script>
<script src="../../../_static/documentation_options.js?v=db21e222"></script>
<script src="../../../_static/doctools.js?v=9bcbadda"></script>
<script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script src="https://unpkg.com/@jupyter-widgets/html-manager@^0.20.1/dist/embed-amd.js"></script>
<script src="https://cdn.jsdelivr.net/npm/@jupyter-widgets/html-manager@^1.0.1/dist/embed-amd.js"></script>
<script>DOCUMENTATION_OPTIONS.pagename = '_modules/sed/io/hdf5';</script>
<script>
DOCUMENTATION_OPTIONS.theme_version = '0.16.1';
DOCUMENTATION_OPTIONS.theme_switcher_json_url = 'https://raw.githubusercontent.com/OpenCOMPES/docs/main/sed/switcher.json';
DOCUMENTATION_OPTIONS.theme_switcher_version_match = '0.4.0.dev0';
DOCUMENTATION_OPTIONS.theme_switcher_version_match = '0.4.1.dev383+g27234e0';
DOCUMENTATION_OPTIONS.show_version_warning_banner =
true;
</script>
<link rel="index" title="Index" href="../../../genindex.html" />
<link rel="search" title="Search" href="../../../search.html" />
<meta name="viewport" content="width=device-width, initial-scale=1"/>
<meta name="docsearch:language" content="en"/>
<meta name="docsearch:version" content="0.4.0.dev0" />
<meta name="docsearch:version" content="0.4.1.dev383+g27234e0" />
</head>


Expand Down Expand Up @@ -116,7 +116,7 @@



<p class="title logo__title">SED 0.4.0.dev0 documentation</p>
<p class="title logo__title">SED 0.4.1.dev383+g27234e0 documentation</p>

</a></div>

Expand Down Expand Up @@ -417,14 +417,14 @@ <h1>Source code for sed.io.hdf5</h1><div class="highlight"><pre>
<span></span><span class="sd">&quot;&quot;&quot;This module contains hdf5 file input/output functions for the sed.io module</span>

<span class="sd">&quot;&quot;&quot;</span>
<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Union</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">__future__</span><span class="w"> </span><span class="kn">import</span> <span class="n">annotations</span>

<span class="kn">import</span> <span class="nn">h5py</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="kn">import</span> <span class="nn">xarray</span> <span class="k">as</span> <span class="nn">xr</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">h5py</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">xarray</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">xr</span>


<span class="k">def</span> <span class="nf">recursive_write_metadata</span><span class="p">(</span><span class="n">h5group</span><span class="p">:</span> <span class="n">h5py</span><span class="o">.</span><span class="n">Group</span><span class="p">,</span> <span class="n">node</span><span class="p">:</span> <span class="nb">dict</span><span class="p">):</span>
<span class="k">def</span><span class="w"> </span><span class="nf">recursive_write_metadata</span><span class="p">(</span><span class="n">h5group</span><span class="p">:</span> <span class="n">h5py</span><span class="o">.</span><span class="n">Group</span><span class="p">,</span> <span class="n">node</span><span class="p">:</span> <span class="nb">dict</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Recurses through a python dictionary and writes it into an hdf5 file.</span>

<span class="sd"> Args:</span>
Expand Down Expand Up @@ -465,16 +465,16 @@ <h1>Source code for sed.io.hdf5</h1><div class="highlight"><pre>
<span class="k">except</span> <span class="ne">BaseException</span> <span class="k">as</span> <span class="n">exc</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
<span class="sa">f</span><span class="s2">&quot;Unknown error occurred, cannot save </span><span class="si">{</span><span class="n">item</span><span class="si">}</span><span class="s2"> of type </span><span class="si">{</span><span class="nb">type</span><span class="p">(</span><span class="n">item</span><span class="p">)</span><span class="si">}</span><span class="s2">.&quot;</span><span class="p">,</span>
<span class="p">)</span> <span class="kn">from</span> <span class="nn">exc</span>
<span class="p">)</span> <span class="kn">from</span><span class="w"> </span><span class="nn">exc</span>


<span class="k">def</span> <span class="nf">recursive_parse_metadata</span><span class="p">(</span>
<span class="n">node</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="n">h5py</span><span class="o">.</span><span class="n">Group</span><span class="p">,</span> <span class="n">h5py</span><span class="o">.</span><span class="n">Dataset</span><span class="p">],</span>
<span class="k">def</span><span class="w"> </span><span class="nf">recursive_parse_metadata</span><span class="p">(</span>
<span class="n">node</span><span class="p">:</span> <span class="n">h5py</span><span class="o">.</span><span class="n">Group</span> <span class="o">|</span> <span class="n">h5py</span><span class="o">.</span><span class="n">Dataset</span><span class="p">,</span>
<span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">:</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Recurses through an hdf5 file, and parse it into a dictionary.</span>

<span class="sd"> Args:</span>
<span class="sd"> node (Union[h5py.Group, h5py.Dataset]): hdf5 group or dataset to parse into</span>
<span class="sd"> node (h5py.Group | h5py.Dataset): hdf5 group or dataset to parse into</span>
<span class="sd"> dictionary.</span>

<span class="sd"> Returns:</span>
Expand All @@ -497,7 +497,9 @@ <h1>Source code for sed.io.hdf5</h1><div class="highlight"><pre>
<span class="k">return</span> <span class="n">dictionary</span>


<div class="viewcode-block" id="to_h5"><a class="viewcode-back" href="../../../sed/io.html#sed.io.to_h5">[docs]</a><span class="k">def</span> <span class="nf">to_h5</span><span class="p">(</span><span class="n">data</span><span class="p">:</span> <span class="n">xr</span><span class="o">.</span><span class="n">DataArray</span><span class="p">,</span> <span class="n">faddr</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">mode</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s2">&quot;w&quot;</span><span class="p">):</span>
<div class="viewcode-block" id="to_h5">
<a class="viewcode-back" href="../../../sed/io.html#sed.io.to_h5">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">to_h5</span><span class="p">(</span><span class="n">data</span><span class="p">:</span> <span class="n">xr</span><span class="o">.</span><span class="n">DataArray</span><span class="p">,</span> <span class="n">faddr</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">mode</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s2">&quot;w&quot;</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Save xarray formatted data to hdf5</span>

<span class="sd"> Args:</span>
Expand Down Expand Up @@ -546,7 +548,10 @@ <h1>Source code for sed.io.hdf5</h1><div class="highlight"><pre>
<span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Saving complete!&quot;</span><span class="p">)</span></div>


<div class="viewcode-block" id="load_h5"><a class="viewcode-back" href="../../../sed/io.html#sed.io.load_h5">[docs]</a><span class="k">def</span> <span class="nf">load_h5</span><span class="p">(</span><span class="n">faddr</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">mode</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s2">&quot;r&quot;</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">xr</span><span class="o">.</span><span class="n">DataArray</span><span class="p">:</span>

<div class="viewcode-block" id="load_h5">
<a class="viewcode-back" href="../../../sed/io.html#sed.io.load_h5">[docs]</a>
<span class="k">def</span><span class="w"> </span><span class="nf">load_h5</span><span class="p">(</span><span class="n">faddr</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">mode</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s2">&quot;r&quot;</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">xr</span><span class="o">.</span><span class="n">DataArray</span><span class="p">:</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Read xarray data from formatted hdf5 file</span>

<span class="sd"> Args:</span>
Expand All @@ -566,7 +571,7 @@ <h1>Source code for sed.io.hdf5</h1><div class="highlight"><pre>
<span class="k">except</span> <span class="ne">KeyError</span> <span class="k">as</span> <span class="n">exc</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
<span class="sa">f</span><span class="s2">&quot;Wrong Data Format, the BinnedData were not found. The error was</span><span class="si">{</span><span class="n">exc</span><span class="si">}</span><span class="s2">.&quot;</span><span class="p">,</span>
<span class="p">)</span> <span class="kn">from</span> <span class="nn">exc</span>
<span class="p">)</span> <span class="kn">from</span><span class="w"> </span><span class="nn">exc</span>

<span class="c1"># Reading the axes</span>
<span class="n">bin_axes</span> <span class="o">=</span> <span class="p">[]</span>
Expand All @@ -579,7 +584,7 @@ <h1>Source code for sed.io.hdf5</h1><div class="highlight"><pre>
<span class="k">except</span> <span class="ne">KeyError</span> <span class="k">as</span> <span class="n">exc</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
<span class="sa">f</span><span class="s2">&quot;Wrong Data Format, the axes were not found. The error was </span><span class="si">{</span><span class="n">exc</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">,</span>
<span class="p">)</span> <span class="kn">from</span> <span class="nn">exc</span>
<span class="p">)</span> <span class="kn">from</span><span class="w"> </span><span class="nn">exc</span>

<span class="c1"># load metadata</span>
<span class="n">metadata</span> <span class="o">=</span> <span class="kc">None</span>
Expand All @@ -604,6 +609,7 @@ <h1>Source code for sed.io.hdf5</h1><div class="highlight"><pre>
<span class="n">xarray</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="s2">&quot;metadata&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">metadata</span>

<span class="k">return</span> <span class="n">xarray</span></div>

</pre></div>

</article>
Expand Down Expand Up @@ -654,7 +660,7 @@ <h1>Source code for sed.io.hdf5</h1><div class="highlight"><pre>
<div class="footer-item">

<p class="sphinx-version">
Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.1.2.
Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 8.1.3.
<br/>
</p>
</div>
Expand Down
Loading

0 comments on commit 461e654

Please sign in to comment.