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<!DOCTYPE html>
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<h1>Source code for src.hdf5_data_extraction</h1><div class="highlight"><pre>
<span></span><span class="kn">import</span> <span class="nn">h5py</span>
<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</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">os</span>
<span class="kn">import</span> <span class="nn">src.hdf5_vis</span> <span class="k">as</span> <span class="nn">hdf5_vis</span>
<div class="viewcode-block" id="read_dataset_from_hdf5file">
<a class="viewcode-back" href="../../modules/src.html#src.hdf5_data_extraction.read_dataset_from_hdf5file">[docs]</a>
<span class="k">def</span> <span class="nf">read_dataset_from_hdf5file</span><span class="p">(</span><span class="n">hdf5_file_path</span><span class="p">,</span> <span class="n">dataset_path</span><span class="p">):</span>
<span class="c1"># Open the HDF5 file</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">hdf5_file_path</span><span class="p">,</span> <span class="s1">&#39;r&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">hdf</span><span class="p">:</span>
<span class="c1"># Load the dataset</span>
<span class="n">dataset</span> <span class="o">=</span> <span class="n">hdf</span><span class="p">[</span><span class="n">dataset_path</span><span class="p">]</span>
<span class="n">data</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">empty</span><span class="p">(</span><span class="n">dataset</span><span class="o">.</span><span class="n">shape</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="n">dataset</span><span class="o">.</span><span class="n">dtype</span><span class="p">)</span>
<span class="n">dataset</span><span class="o">.</span><span class="n">read_direct</span><span class="p">(</span><span class="n">data</span><span class="p">)</span>
<span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">data</span><span class="p">)</span>
<span class="k">for</span> <span class="n">col_name</span> <span class="ow">in</span> <span class="n">df</span><span class="o">.</span><span class="n">select_dtypes</span><span class="p">(</span><span class="n">exclude</span><span class="o">=</span><span class="s1">&#39;number&#39;</span><span class="p">):</span>
<span class="n">df</span><span class="p">[</span><span class="n">col_name</span><span class="p">]</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="n">col_name</span><span class="p">]</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span> <span class="c1">#apply(lambda x: x.decode(&#39;utf-8&#39;) if isinstance(x,bytes) else x)</span>
<span class="c1">## Extract metadata (attributes) and convert to a dictionary</span>
<span class="c1">#metadata = hdf5_vis.construct_attributes_dict(hdf[dataset_name].attrs)</span>
<span class="c1">## Create a one-row DataFrame with the metadata</span>
<span class="c1">#metadata_df = pd.DataFrame.from_dict(data, orient=&#39;columns&#39;) </span>
<span class="k">return</span> <span class="n">df</span></div>
<div class="viewcode-block" id="read_metadata_from_hdf5obj">
<a class="viewcode-back" href="../../modules/src.html#src.hdf5_data_extraction.read_metadata_from_hdf5obj">[docs]</a>
<span class="k">def</span> <span class="nf">read_metadata_from_hdf5obj</span><span class="p">(</span><span class="n">hdf5_file_path</span><span class="p">,</span> <span class="n">obj_path</span><span class="p">):</span>
<span class="c1"># TODO: Complete this function</span>
<span class="n">metadata_df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="o">.</span><span class="n">empty</span><span class="p">()</span>
<span class="k">return</span> <span class="n">metadata_df</span></div>
<div class="viewcode-block" id="list_datasets_in_hdf5file">
<a class="viewcode-back" href="../../modules/src.html#src.hdf5_data_extraction.list_datasets_in_hdf5file">[docs]</a>
<span class="k">def</span> <span class="nf">list_datasets_in_hdf5file</span><span class="p">(</span><span class="n">hdf5_file_path</span><span class="p">):</span>
<span class="k">def</span> <span class="nf">get_datasets</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">obj</span><span class="p">,</span> <span class="n">list_of_datasets</span><span class="p">):</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">obj</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="n">list_of_datasets</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">name</span><span class="p">)</span>
<span class="c1">#print(f&#39;Adding dataset: {name}&#39;) #tail: {head} head: {tail}&#39;)</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">hdf5_file_path</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">list_of_datasets</span> <span class="o">=</span> <span class="p">[]</span>
<span class="n">file</span><span class="o">.</span><span class="n">visititems</span><span class="p">(</span><span class="k">lambda</span> <span class="n">name</span><span class="p">,</span> <span class="n">obj</span><span class="p">:</span> <span class="n">get_datasets</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">obj</span><span class="p">,</span> <span class="n">list_of_datasets</span><span class="p">))</span>
<span class="n">dataset_df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">({</span><span class="s1">&#39;dataset_name&#39;</span><span class="p">:</span><span class="n">list_of_datasets</span><span class="p">})</span>
<span class="n">dataset_df</span><span class="p">[</span><span class="s1">&#39;parent_instrument&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">dataset_df</span><span class="p">[</span><span class="s1">&#39;dataset_name&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">apply</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;/&#39;</span><span class="p">)[</span><span class="o">-</span><span class="mi">3</span><span class="p">])</span>
<span class="n">dataset_df</span><span class="p">[</span><span class="s1">&#39;parent_file&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">dataset_df</span><span class="p">[</span><span class="s1">&#39;dataset_name&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">apply</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;/&#39;</span><span class="p">)[</span><span class="o">-</span><span class="mi">2</span><span class="p">])</span>
<span class="k">return</span> <span class="n">dataset_df</span></div>
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<h1>Source code for src.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/src.html#src.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>
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