Updated documentation and built doc website

2024-12-02 16:31:03 +01:00
parent 23e0ced190
commit f3bb82a937
21 changed files with 1657 additions and 60 deletions
--- a/docs/build/doctrees/environment.pickle
+++ b/docs/build/doctrees/environment.pickle
--- a/docs/build/doctrees/index.doctree
+++ b/docs/build/doctrees/index.doctree
--- a/docs/build/doctrees/modules/src.doctree
+++ b/docs/build/doctrees/modules/src.doctree
--- a/docs/build/doctrees/modules/vis.doctree
+++ b/docs/build/doctrees/modules/vis.doctree
--- a/docs/build/html/_modules/index.html
+++ b/docs/build/html/_modules/index.html
@ -46,8 +46,8 @@
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="../modules/src.html">HDF5 Data Operations</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../modules/src.html#module-src.hdf5_writer">HDF5 Writer</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../modules/src.html#module-src.hdf5_vis">Data Visualization</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../modules/pipelines.html">Pipelines and workflows</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../modules/vis.html">Data Visualization</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../modules/utils.html">Data Structure Conversion</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../modules/notebooks.html">Notebooks</a></li>
 </ul>
@ -79,9 +79,9 @@
 <ul><li><a href="pipelines/data_integration.html">pipelines.data_integration</a></li>
 <li><a href="pipelines/metadata_revision.html">pipelines.metadata_revision</a></li>
 <li><a href="src/hdf5_ops.html">src.hdf5_ops</a></li>
-<li><a href="src/hdf5_vis.html">src.hdf5_vis</a></li>
 <li><a href="src/hdf5_writer.html">src.hdf5_writer</a></li>
 <li><a href="utils/g5505_utils.html">utils.g5505_utils</a></li>
+<li><a href="visualization/hdf5_vis.html">visualization.hdf5_vis</a></li>
 </ul>

           </div>
--- a/docs/build/html/_modules/visualization/hdf5_vis.html
+++ b/docs/build/html/_modules/visualization/hdf5_vis.html
@ -0,0 +1,182 @@
+<!DOCTYPE html>
+<html class="writer-html5" lang="en" data-content_root="../../">
+<head>
+  <meta charset="utf-8" />
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  <title>visualization.hdf5_vis &mdash; DIMA 1.0.0 documentation</title>
+      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=80d5e7a1" />
+      <link rel="stylesheet" type="text/css" href="../../_static/css/theme.css?v=19f00094" />
+
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+        <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+        <script src="../../_static/documentation_options.js?v=8d563738"></script>
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+        <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
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+    <script src="../../_static/js/theme.js"></script>
+    <link rel="index" title="Index" href="../../genindex.html" />
+    <link rel="search" title="Search" href="../../search.html" /> 
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+<body class="wy-body-for-nav"> 
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+<div role="search">
+  <form id="rtd-search-form" class="wy-form" action="../../search.html" method="get">
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+        </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+              <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../../modules/src.html">HDF5 Data Operations</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../modules/src.html#module-src.hdf5_writer">HDF5 Writer</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../modules/src.html#data-visualization">Data Visualization</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../modules/pipelines.html">Pipelines and workflows</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../modules/vis.html">Data Visualization</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../modules/utils.html">Data Structure Conversion</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../modules/notebooks.html">Notebooks</a></li>
+</ul>
+
+        </div>
+      </div>
+    </nav>
+
+    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
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+          <a href="../../index.html">DIMA</a>
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+        <div class="rst-content">
+          <div role="navigation" aria-label="Page navigation">
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+      <li><a href="../../index.html" class="icon icon-home" aria-label="Home"></a></li>
+          <li class="breadcrumb-item"><a href="../index.html">Module code</a></li>
+      <li class="breadcrumb-item active">visualization.hdf5_vis</li>
+      <li class="wy-breadcrumbs-aside">
+      </li>
+  </ul>
+  <hr/>
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+             
+  <h1>Source code for visualization.hdf5_vis</h1><div class="highlight"><pre>
+<span></span><span class="kn">import</span> <span class="nn">sys</span>
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="n">root_dir</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">curdir</span><span class="p">)</span>
+<span class="n">sys</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">root_dir</span><span class="p">)</span>
+
+<span class="kn">import</span> <span class="nn">h5py</span>
+<span class="kn">import</span> <span class="nn">yaml</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">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
+
+<span class="kn">from</span> <span class="nn">plotly.subplots</span> <span class="kn">import</span> <span class="n">make_subplots</span>
+<span class="kn">import</span> <span class="nn">plotly.graph_objects</span> <span class="k">as</span> <span class="nn">go</span>
+<span class="kn">import</span> <span class="nn">plotly.express</span> <span class="k">as</span> <span class="nn">px</span>
+<span class="c1">#import plotly.io as pio</span>
+<span class="kn">from</span> <span class="nn">src.hdf5_ops</span> <span class="kn">import</span> <span class="n">get_parent_child_relationships</span>
+
+ 
+
+<div class="viewcode-block" id="display_group_hierarchy_on_a_treemap">
+<a class="viewcode-back" href="../../modules/vis.html#visualization.hdf5_vis.display_group_hierarchy_on_a_treemap">[docs]</a>
+<span class="k">def</span> <span class="nf">display_group_hierarchy_on_a_treemap</span><span class="p">(</span><span class="n">filename</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
+
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    filename (str): hdf5 file&#39;s filename&quot;&quot;&quot;</span>
+
+    <span class="k">with</span> <span class="n">h5py</span><span class="o">.</span><span class="n">File</span><span class="p">(</span><span class="n">filename</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="n">nodes</span><span class="p">,</span> <span class="n">parents</span><span class="p">,</span> <span class="n">values</span> <span class="o">=</span> <span class="n">get_parent_child_relationships</span><span class="p">(</span><span class="n">file</span><span class="p">)</span>
+
+        <span class="n">metadata_list</span> <span class="o">=</span> <span class="p">[]</span>
+        <span class="n">metadata_dict</span><span class="o">=</span><span class="p">{}</span>
+        <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">file</span><span class="o">.</span><span class="n">attrs</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>            
+            <span class="c1">#if &#39;metadata&#39; in key:</span>
+            <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">file</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="n">key</span><span class="p">],</span> <span class="nb">str</span><span class="p">):</span>  <span class="c1"># Check if the attribute is a string</span>
+                <span class="n">metadata_key</span> <span class="o">=</span> <span class="n">key</span><span class="p">[</span><span class="n">key</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">)</span> <span class="o">+</span> <span class="mi">1</span><span class="p">:]</span>
+                <span class="n">metadata_value</span> <span class="o">=</span> <span class="n">file</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="n">key</span><span class="p">]</span>
+                <span class="n">metadata_dict</span><span class="p">[</span><span class="n">metadata_key</span><span class="p">]</span> <span class="o">=</span> <span class="n">metadata_value</span>
+                <span class="n">metadata_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">metadata_key</span><span class="si">}</span><span class="s1">: </span><span class="si">{</span><span class="n">metadata_value</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
+            
+            <span class="c1">#metadata_dict[key[key.find(&#39;_&#39;)+1::]]= file.attrs[key]</span>
+            <span class="c1">#metadata_list.append(key[key.find(&#39;_&#39;)+1::]+&#39;:&#39;+file.attrs[key])</span>
+
+        <span class="n">metadata</span> <span class="o">=</span> <span class="s1">&#39;&lt;br&gt;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s1">&#39;&lt;br&gt;&#39;</span><span class="p">]</span> <span class="o">+</span> <span class="n">metadata_list</span><span class="p">)</span>
+
+    <span class="n">customdata_series</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">Series</span><span class="p">(</span><span class="n">nodes</span><span class="p">)</span>
+    <span class="n">customdata_series</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="n">metadata</span>
+
+    <span class="n">fig</span> <span class="o">=</span> <span class="n">make_subplots</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="n">specs</span><span class="o">=</span><span class="p">[[{</span><span class="s2">&quot;type&quot;</span><span class="p">:</span> <span class="s2">&quot;domain&quot;</span><span class="p">}]],)</span>
+    <span class="n">fig</span><span class="o">.</span><span class="n">add_trace</span><span class="p">(</span><span class="n">go</span><span class="o">.</span><span class="n">Treemap</span><span class="p">(</span>
+        <span class="n">labels</span><span class="o">=</span><span class="n">nodes</span><span class="p">,</span> <span class="c1">#formating_df[&#39;formated_names&#39;][nodes],</span>
+        <span class="n">parents</span><span class="o">=</span><span class="n">parents</span><span class="p">,</span><span class="c1">#formating_df[&#39;formated_names&#39;][parents],</span>
+        <span class="n">values</span><span class="o">=</span><span class="n">values</span><span class="p">,</span>
+        <span class="n">branchvalues</span><span class="o">=</span><span class="s1">&#39;remainder&#39;</span><span class="p">,</span>
+        <span class="n">customdata</span><span class="o">=</span> <span class="n">customdata_series</span><span class="p">,</span>
+        <span class="c1">#marker=dict(</span>
+        <span class="c1">#    colors=df_all_trees[&#39;color&#39;],</span>
+        <span class="c1">#    colorscale=&#39;RdBu&#39;,</span>
+        <span class="c1">#    cmid=average_score),</span>
+        <span class="c1">#hovertemplate=&#39;&lt;b&gt;%{label} &lt;/b&gt; &lt;br&gt; Number of files: %{value}&lt;br&gt; Success rate: %{color:.2f}&#39;,</span>
+        <span class="n">hovertemplate</span><span class="o">=</span><span class="s1">&#39;&lt;b&gt;%</span><span class="si">{label}</span><span class="s1"> &lt;/b&gt; &lt;br&gt; Count: %</span><span class="si">{value}</span><span class="s1"> &lt;br&gt; Path: %</span><span class="si">{customdata}</span><span class="s1">&#39;</span><span class="p">,</span>
+        <span class="n">name</span><span class="o">=</span><span class="s1">&#39;&#39;</span><span class="p">,</span>
+        <span class="n">root_color</span><span class="o">=</span><span class="s2">&quot;lightgrey&quot;</span>
+        <span class="p">))</span>
+    <span class="n">fig</span><span class="o">.</span><span class="n">update_layout</span><span class="p">(</span><span class="n">width</span> <span class="o">=</span> <span class="mi">800</span><span class="p">,</span> <span class="n">height</span><span class="o">=</span> <span class="mi">600</span><span class="p">,</span> <span class="n">margin</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="n">t</span><span class="o">=</span><span class="mi">50</span><span class="p">,</span> <span class="n">l</span><span class="o">=</span><span class="mi">25</span><span class="p">,</span> <span class="n">r</span><span class="o">=</span><span class="mi">25</span><span class="p">,</span> <span class="n">b</span><span class="o">=</span><span class="mi">25</span><span class="p">))</span>
+    <span class="n">fig</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
+    <span class="n">file_name</span><span class="p">,</span> <span class="n">file_ext</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
+    <span class="n">fig</span><span class="o">.</span><span class="n">write_html</span><span class="p">(</span><span class="n">file_name</span> <span class="o">+</span> <span class="s2">&quot;.html&quot;</span><span class="p">)</span></div>
+
+   
+    <span class="c1">#pio.write_image(fig,file_name + &quot;.png&quot;,width=800,height=600,format=&#39;png&#39;)</span>
+
+<span class="c1">#</span>
+</pre></div>
+
+           </div>
+          </div>
+          <footer>
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>&#169; Copyright 2024, JFFO.</p>
+  </div>
+
+  Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
+    <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
+    provided by <a href="https://readthedocs.org">Read the Docs</a>.
+   
+
+</footer>
+        </div>
+      </div>
+    </section>
+  </div>
+  <script>
+      jQuery(function () {
+          SphinxRtdTheme.Navigation.enable(true);
+      });
+  </script> 
+
+</body>
+</html>
--- a/docs/build/html/_sources/index.rst.txt
+++ b/docs/build/html/_sources/index.rst.txt
@ -14,6 +14,8 @@ Welcome to DIMA's documentation!

   modules/pipelines

+   modules/vis
+
   modules/utils

   modules/notebooks
--- a/docs/build/html/_sources/modules/src.rst.txt
+++ b/docs/build/html/_sources/modules/src.rst.txt
@ -14,14 +14,5 @@ HDF5 Writer
   :undoc-members:
   :show-inheritance:

-Data Visualization 
-==================
-
-.. automodule:: src.hdf5_vis
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-


--- a/docs/build/html/_sources/modules/vis.rst.txt
+++ b/docs/build/html/_sources/modules/vis.rst.txt
@ -0,0 +1,7 @@
+Data Visualization 
+==================
+
+.. automodule:: visualization.hdf5_vis
+   :members:
+   :undoc-members:
+   :show-inheritance:
--- a/docs/build/html/genindex.html
+++ b/docs/build/html/genindex.html
@ -46,8 +46,8 @@
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="modules/src.html">HDF5 Data Operations</a></li>
 <li class="toctree-l1"><a class="reference internal" href="modules/src.html#module-src.hdf5_writer">HDF5 Writer</a></li>
-<li class="toctree-l1"><a class="reference internal" href="modules/src.html#module-src.hdf5_vis">Data Visualization</a></li>
 <li class="toctree-l1"><a class="reference internal" href="modules/pipelines.html">Pipelines and workflows</a></li>
+<li class="toctree-l1"><a class="reference internal" href="modules/vis.html">Data Visualization</a></li>
 <li class="toctree-l1"><a class="reference internal" href="modules/utils.html">Data Structure Conversion</a></li>
 <li class="toctree-l1"><a class="reference internal" href="modules/notebooks.html">Notebooks</a></li>
 </ul>
@ -146,7 +146,7 @@
 </li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="modules/src.html#src.hdf5_vis.display_group_hierarchy_on_a_treemap">display_group_hierarchy_on_a_treemap() (in module src.hdf5_vis)</a>
+      <li><a href="modules/vis.html#visualization.hdf5_vis.display_group_hierarchy_on_a_treemap">display_group_hierarchy_on_a_treemap() (in module visualization.hdf5_vis)</a>
 </li>
  </ul></td>
 </tr></table>
@ -233,12 +233,12 @@
        <li><a href="modules/pipelines.html#module-pipelines.metadata_revision">pipelines.metadata_revision</a>
 </li>
        <li><a href="modules/src.html#module-src.hdf5_ops">src.hdf5_ops</a>
-</li>
-        <li><a href="modules/src.html#module-src.hdf5_vis">src.hdf5_vis</a>
 </li>
        <li><a href="modules/src.html#module-src.hdf5_writer">src.hdf5_writer</a>
 </li>
        <li><a href="modules/utils.html#module-utils.g5505_utils">utils.g5505_utils</a>
+</li>
+        <li><a href="modules/vis.html#module-visualization.hdf5_vis">visualization.hdf5_vis</a>
 </li>
      </ul></li>
  </ul></td>
@ -307,23 +307,16 @@
      <li><a href="modules/src.html#src.hdf5_ops.serialize_metadata">serialize_metadata() (in module src.hdf5_ops)</a>
 </li>
      <li><a href="modules/utils.html#utils.g5505_utils.setup_logging">setup_logging() (in module utils.g5505_utils)</a>
-</li>
-      <li><a href="modules/utils.html#utils.g5505_utils.split_sample_col_into_sample_and_data_quality_cols">split_sample_col_into_sample_and_data_quality_cols() (in module utils.g5505_utils)</a>
 </li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="modules/utils.html#utils.g5505_utils.split_sample_col_into_sample_and_data_quality_cols">split_sample_col_into_sample_and_data_quality_cols() (in module utils.g5505_utils)</a>
+</li>
      <li>
    src.hdf5_ops

      <ul>
        <li><a href="modules/src.html#module-src.hdf5_ops">module</a>
-</li>
-      </ul></li>
-      <li>
-    src.hdf5_vis
-
-      <ul>
-        <li><a href="modules/src.html#module-src.hdf5_vis">module</a>
 </li>
      </ul></li>
      <li>
@ -373,6 +366,15 @@
      <li><a href="modules/pipelines.html#pipelines.metadata_revision.validate_yaml_dict">validate_yaml_dict() (in module pipelines.metadata_revision)</a>
 </li>
  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li>
+    visualization.hdf5_vis
+
+      <ul>
+        <li><a href="modules/vis.html#module-visualization.hdf5_vis">module</a>
+</li>
+      </ul></li>
+  </ul></td>
 </tr></table>


--- a/docs/build/html/index.html
+++ b/docs/build/html/index.html
@ -48,8 +48,8 @@
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="modules/src.html">HDF5 Data Operations</a></li>
 <li class="toctree-l1"><a class="reference internal" href="modules/src.html#module-src.hdf5_writer">HDF5 Writer</a></li>
-<li class="toctree-l1"><a class="reference internal" href="modules/src.html#module-src.hdf5_vis">Data Visualization</a></li>
 <li class="toctree-l1"><a class="reference internal" href="modules/pipelines.html">Pipelines and workflows</a></li>
+<li class="toctree-l1"><a class="reference internal" href="modules/vis.html">Data Visualization</a></li>
 <li class="toctree-l1"><a class="reference internal" href="modules/utils.html">Data Structure Conversion</a></li>
 <li class="toctree-l1"><a class="reference internal" href="modules/notebooks.html">Notebooks</a></li>
 </ul>
@ -97,10 +97,6 @@
 <li class="toctree-l2"><a class="reference internal" href="modules/src.html#src.hdf5_writer.save_processed_dataframe_to_hdf5"><code class="docutils literal notranslate"><span class="pre">save_processed_dataframe_to_hdf5()</span></code></a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="modules/src.html#module-src.hdf5_vis">Data Visualization</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="modules/src.html#src.hdf5_vis.display_group_hierarchy_on_a_treemap"><code class="docutils literal notranslate"><span class="pre">display_group_hierarchy_on_a_treemap()</span></code></a></li>
-</ul>
-</li>
 <li class="toctree-l1"><a class="reference internal" href="modules/pipelines.html">Pipelines and workflows</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="modules/pipelines.html#pipelines.data_integration.copy_subtree_and_create_hdf5"><code class="docutils literal notranslate"><span class="pre">copy_subtree_and_create_hdf5()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="modules/pipelines.html#pipelines.data_integration.load_config_and_setup_logging"><code class="docutils literal notranslate"><span class="pre">load_config_and_setup_logging()</span></code></a></li>
@ -111,6 +107,10 @@
 <li class="toctree-l2"><a class="reference internal" href="modules/pipelines.html#pipelines.metadata_revision.validate_yaml_dict"><code class="docutils literal notranslate"><span class="pre">validate_yaml_dict()</span></code></a></li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="modules/vis.html">Data Visualization</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="modules/vis.html#visualization.hdf5_vis.display_group_hierarchy_on_a_treemap"><code class="docutils literal notranslate"><span class="pre">display_group_hierarchy_on_a_treemap()</span></code></a></li>
+</ul>
+</li>
 <li class="toctree-l1"><a class="reference internal" href="modules/utils.html">Data Structure Conversion</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="modules/utils.html#utils.g5505_utils.augment_with_filenumber"><code class="docutils literal notranslate"><span class="pre">augment_with_filenumber()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="modules/utils.html#utils.g5505_utils.augment_with_filetype"><code class="docutils literal notranslate"><span class="pre">augment_with_filetype()</span></code></a></li>
--- a/docs/build/html/modules/src.html
+++ b/docs/build/html/modules/src.html
@ -75,11 +75,8 @@
 <li class="toctree-l2"><a class="reference internal" href="#src.hdf5_writer.save_processed_dataframe_to_hdf5"><code class="docutils literal notranslate"><span class="pre">save_processed_dataframe_to_hdf5()</span></code></a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="#module-src.hdf5_vis">Data Visualization</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="#src.hdf5_vis.display_group_hierarchy_on_a_treemap"><code class="docutils literal notranslate"><span class="pre">display_group_hierarchy_on_a_treemap()</span></code></a></li>
-</ul>
-</li>
 <li class="toctree-l1"><a class="reference internal" href="pipelines.html">Pipelines and workflows</a></li>
+<li class="toctree-l1"><a class="reference internal" href="vis.html">Data Visualization</a></li>
 <li class="toctree-l1"><a class="reference internal" href="utils.html">Data Structure Conversion</a></li>
 <li class="toctree-l1"><a class="reference internal" href="notebooks.html">Notebooks</a></li>
 </ul>
@ -427,15 +424,6 @@ output_filename  (str): Path to the source HDF5 file.</p>
 </dl>
 </dd></dl>

-</section>
-<section id="module-src.hdf5_vis">
-<span id="data-visualization"></span><h1>Data Visualization<a class="headerlink" href="#module-src.hdf5_vis" title="Link to this heading"></a></h1>
-<dl class="py function">
-<dt class="sig sig-object py" id="src.hdf5_vis.display_group_hierarchy_on_a_treemap">
-<span class="sig-prename descclassname"><span class="pre">src.hdf5_vis.</span></span><span class="sig-name descname"><span class="pre">display_group_hierarchy_on_a_treemap</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/src/hdf5_vis.html#display_group_hierarchy_on_a_treemap"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#src.hdf5_vis.display_group_hierarchy_on_a_treemap" title="Link to this definition"></a></dt>
-<dd><p>filename (str): hdf5 file’s filename</p>
-</dd></dl>
-
 </section>


--- a/docs/build/html/modules/vis.html
+++ b/docs/build/html/modules/vis.html
@ -0,0 +1,127 @@
+<!DOCTYPE html>
+<html class="writer-html5" lang="en" data-content_root="../">
+<head>
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
+
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  <title>Data Visualization &mdash; DIMA 1.0.0 documentation</title>
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=80d5e7a1" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
+
+  
+  <!--[if lt IE 9]>
+    <script src="../_static/js/html5shiv.min.js"></script>
+  <![endif]-->
+  
+        <script src="../_static/jquery.js?v=5d32c60e"></script>
+        <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+        <script src="../_static/documentation_options.js?v=8d563738"></script>
+        <script src="../_static/doctools.js?v=9a2dae69"></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="../_static/js/theme.js"></script>
+    <link rel="index" title="Index" href="../genindex.html" />
+    <link rel="search" title="Search" href="../search.html" />
+    <link rel="next" title="Data Structure Conversion" href="utils.html" />
+    <link rel="prev" title="Pipelines and workflows" href="pipelines.html" /> 
+</head>
+
+<body class="wy-body-for-nav"> 
+  <div class="wy-grid-for-nav">
+    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+      <div class="wy-side-scroll">
+        <div class="wy-side-nav-search" >
+
+          
+          
+          <a href="../index.html" class="icon icon-home">
+            DIMA
+          </a>
+<div role="search">
+  <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
+    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
+    <input type="hidden" name="check_keywords" value="yes" />
+    <input type="hidden" name="area" value="default" />
+  </form>
+</div>
+        </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+              <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+<ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="src.html">HDF5 Data Operations</a></li>
+<li class="toctree-l1"><a class="reference internal" href="src.html#module-src.hdf5_writer">HDF5 Writer</a></li>
+<li class="toctree-l1"><a class="reference internal" href="src.html#data-visualization">Data Visualization</a></li>
+<li class="toctree-l1"><a class="reference internal" href="pipelines.html">Pipelines and workflows</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="#">Data Visualization</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#visualization.hdf5_vis.display_group_hierarchy_on_a_treemap"><code class="docutils literal notranslate"><span class="pre">display_group_hierarchy_on_a_treemap()</span></code></a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="utils.html">Data Structure Conversion</a></li>
+<li class="toctree-l1"><a class="reference internal" href="notebooks.html">Notebooks</a></li>
+</ul>
+
+        </div>
+      </div>
+    </nav>
+
+    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
+          <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+          <a href="../index.html">DIMA</a>
+      </nav>
+
+      <div class="wy-nav-content">
+        <div class="rst-content">
+          <div role="navigation" aria-label="Page navigation">
+  <ul class="wy-breadcrumbs">
+      <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
+      <li class="breadcrumb-item active">Data Visualization</li>
+      <li class="wy-breadcrumbs-aside">
+            <a href="../_sources/modules/vis.rst.txt" rel="nofollow"> View page source</a>
+      </li>
+  </ul>
+  <hr/>
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+             
+  <section id="module-visualization.hdf5_vis">
+<span id="data-visualization"></span><h1>Data Visualization<a class="headerlink" href="#module-visualization.hdf5_vis" title="Link to this heading"></a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="visualization.hdf5_vis.display_group_hierarchy_on_a_treemap">
+<span class="sig-prename descclassname"><span class="pre">visualization.hdf5_vis.</span></span><span class="sig-name descname"><span class="pre">display_group_hierarchy_on_a_treemap</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/visualization/hdf5_vis.html#display_group_hierarchy_on_a_treemap"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#visualization.hdf5_vis.display_group_hierarchy_on_a_treemap" title="Link to this definition"></a></dt>
+<dd><p>filename (str): hdf5 file’s filename</p>
+</dd></dl>
+
+</section>
+
+
+           </div>
+          </div>
+          <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
+        <a href="pipelines.html" class="btn btn-neutral float-left" title="Pipelines and workflows" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+        <a href="utils.html" class="btn btn-neutral float-right" title="Data Structure Conversion" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
+    </div>
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>&#169; Copyright 2024, JFFO.</p>
+  </div>
+
+  Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
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+      jQuery(function () {
+          SphinxRtdTheme.Navigation.enable(true);
+      });
+  </script> 
+
+</body>
+</html>
--- a/docs/build/html/objects.inv
+++ b/docs/build/html/objects.inv
--- a/docs/build/html/py-modindex.html
+++ b/docs/build/html/py-modindex.html
@ -49,8 +49,8 @@
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="modules/src.html">HDF5 Data Operations</a></li>
 <li class="toctree-l1"><a class="reference internal" href="modules/src.html#module-src.hdf5_writer">HDF5 Writer</a></li>
-<li class="toctree-l1"><a class="reference internal" href="modules/src.html#module-src.hdf5_vis">Data Visualization</a></li>
 <li class="toctree-l1"><a class="reference internal" href="modules/pipelines.html">Pipelines and workflows</a></li>
+<li class="toctree-l1"><a class="reference internal" href="modules/vis.html">Data Visualization</a></li>
 <li class="toctree-l1"><a class="reference internal" href="modules/utils.html">Data Structure Conversion</a></li>
 <li class="toctree-l1"><a class="reference internal" href="modules/notebooks.html">Notebooks</a></li>
 </ul>
@ -85,7 +85,8 @@
   <a href="#cap-n"><strong>n</strong></a> | 
   <a href="#cap-p"><strong>p</strong></a> | 
   <a href="#cap-s"><strong>s</strong></a> | 
-   <a href="#cap-u"><strong>u</strong></a>
+   <a href="#cap-u"><strong>u</strong></a> | 
+   <a href="#cap-v"><strong>v</strong></a>
   </div>

   <table class="indextable modindextable">
@ -130,11 +131,6 @@
       <td>&#160;&#160;&#160;
       <a href="modules/src.html#module-src.hdf5_ops"><code class="xref">src.hdf5_ops</code></a></td><td>
       <em></em></td></tr>
-     <tr class="cg-2">
-       <td></td>
-       <td>&#160;&#160;&#160;
-       <a href="modules/src.html#module-src.hdf5_vis"><code class="xref">src.hdf5_vis</code></a></td><td>
-       <em></em></td></tr>
     <tr class="cg-2">
       <td></td>
       <td>&#160;&#160;&#160;
@ -154,6 +150,20 @@
       <td>&#160;&#160;&#160;
       <a href="modules/utils.html#module-utils.g5505_utils"><code class="xref">utils.g5505_utils</code></a></td><td>
       <em></em></td></tr>
+     <tr class="pcap"><td></td><td>&#160;</td><td></td></tr>
+     <tr class="cap" id="cap-v"><td></td><td>
+       <strong>v</strong></td><td></td></tr>
+     <tr>
+       <td><img src="_static/minus.png" class="toggler"
+              id="toggle-4" style="display: none" alt="-" /></td>
+       <td>
+       <code class="xref">visualization</code></td><td>
+       <em></em></td></tr>
+     <tr class="cg-4">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="modules/vis.html#module-visualization.hdf5_vis"><code class="xref">visualization.hdf5_vis</code></a></td><td>
+       <em></em></td></tr>
   </table>


--- a/docs/build/html/search.html
+++ b/docs/build/html/search.html
@ -49,8 +49,8 @@
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="modules/src.html">HDF5 Data Operations</a></li>
 <li class="toctree-l1"><a class="reference internal" href="modules/src.html#module-src.hdf5_writer">HDF5 Writer</a></li>
-<li class="toctree-l1"><a class="reference internal" href="modules/src.html#module-src.hdf5_vis">Data Visualization</a></li>
 <li class="toctree-l1"><a class="reference internal" href="modules/pipelines.html">Pipelines and workflows</a></li>
+<li class="toctree-l1"><a class="reference internal" href="modules/vis.html">Data Visualization</a></li>
 <li class="toctree-l1"><a class="reference internal" href="modules/utils.html">Data Structure Conversion</a></li>
 <li class="toctree-l1"><a class="reference internal" href="modules/notebooks.html">Notebooks</a></li>
 </ul>
--- a/docs/build/html/searchindex.js
+++ b/docs/build/html/searchindex.js