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409 lines
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HTML
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DIMA
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<li class="toctree-l1"><a class="reference internal" href="modules/src.html">HDF5 Data Operations</a></li>
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<li class="toctree-l1"><a class="reference internal" href="modules/src.html#module-src.hdf5_writer">HDF5 Writer</a></li>
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<li class="toctree-l1"><a class="reference internal" href="modules/pipelines.html">Pipelines and workflows</a></li>
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<li class="toctree-l1"><a class="reference internal" href="modules/vis.html">Data Visualization</a></li>
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<li class="toctree-l1"><a class="reference internal" href="modules/utils.html">Data Structure Conversion</a></li>
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<h1 id="index">Index</h1>
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<div class="genindex-jumpbox">
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<a href="#A"><strong>A</strong></a>
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| <a href="#C"><strong>C</strong></a>
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| <a href="#D"><strong>D</strong></a>
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| <a href="#E"><strong>E</strong></a>
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| <a href="#G"><strong>G</strong></a>
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| <a href="#H"><strong>H</strong></a>
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| <a href="#I"><strong>I</strong></a>
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| <a href="#L"><strong>L</strong></a>
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| <a href="#M"><strong>M</strong></a>
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| <a href="#N"><strong>N</strong></a>
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| <a href="#P"><strong>P</strong></a>
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| <a href="#R"><strong>R</strong></a>
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| <a href="#S"><strong>S</strong></a>
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| <a href="#T"><strong>T</strong></a>
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| <a href="#U"><strong>U</strong></a>
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| <a href="#V"><strong>V</strong></a>
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</div>
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<h2 id="A">A</h2>
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<table style="width: 100%" class="indextable genindextable"><tr>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="modules/src.html#src.hdf5_ops.HDF5DataOpsManager.append_dataset">append_dataset() (src.hdf5_ops.HDF5DataOpsManager method)</a>
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</li>
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<li><a href="modules/src.html#src.hdf5_ops.HDF5DataOpsManager.append_metadata">append_metadata() (src.hdf5_ops.HDF5DataOpsManager method)</a>
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</li>
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</ul></td>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="modules/utils.html#utils.g5505_utils.augment_with_filenumber">augment_with_filenumber() (in module utils.g5505_utils)</a>
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</li>
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<li><a href="modules/utils.html#utils.g5505_utils.augment_with_filetype">augment_with_filetype() (in module utils.g5505_utils)</a>
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</li>
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</ul></td>
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</tr></table>
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<h2 id="C">C</h2>
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<table style="width: 100%" class="indextable genindextable"><tr>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="modules/utils.html#utils.g5505_utils.convert_attrdict_to_np_structured_array">convert_attrdict_to_np_structured_array() (in module utils.g5505_utils)</a>
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</li>
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<li><a href="modules/utils.html#utils.g5505_utils.convert_dataframe_to_np_structured_array">convert_dataframe_to_np_structured_array() (in module utils.g5505_utils)</a>
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</li>
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<li><a href="modules/utils.html#utils.g5505_utils.convert_string_to_bytes">convert_string_to_bytes() (in module utils.g5505_utils)</a>
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</li>
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<li><a href="modules/utils.html#utils.g5505_utils.copy_directory_with_contraints">copy_directory_with_contraints() (in module utils.g5505_utils)</a>
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</li>
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</ul></td>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="modules/pipelines.html#pipelines.data_integration.copy_subtree_and_create_hdf5">copy_subtree_and_create_hdf5() (in module pipelines.data_integration)</a>
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</li>
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<li><a href="modules/pipelines.html#pipelines.metadata_revision.count">count() (in module pipelines.metadata_revision)</a>
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</li>
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<li><a href="modules/src.html#src.hdf5_writer.create_hdf5_file_from_dataframe">create_hdf5_file_from_dataframe() (in module src.hdf5_writer)</a>
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</li>
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<li><a href="modules/src.html#src.hdf5_writer.create_hdf5_file_from_filesystem_path">create_hdf5_file_from_filesystem_path() (in module src.hdf5_writer)</a>
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</li>
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<li><a href="modules/utils.html#utils.g5505_utils.created_at">created_at() (in module utils.g5505_utils)</a>
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</li>
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</ul></td>
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</tr></table>
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<h2 id="D">D</h2>
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<table style="width: 100%" class="indextable genindextable"><tr>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="modules/src.html#src.hdf5_ops.HDF5DataOpsManager.delete_metadata">delete_metadata() (src.hdf5_ops.HDF5DataOpsManager method)</a>
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</li>
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</ul></td>
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<td style="width: 33%; vertical-align: top;"><ul>
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<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>
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</li>
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</ul></td>
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</tr></table>
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<h2 id="E">E</h2>
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<table style="width: 100%" class="indextable genindextable"><tr>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="modules/src.html#src.hdf5_ops.HDF5DataOpsManager.extract_and_load_dataset_metadata">extract_and_load_dataset_metadata() (src.hdf5_ops.HDF5DataOpsManager method)</a>
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</li>
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</ul></td>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="modules/src.html#src.hdf5_ops.HDF5DataOpsManager.extract_dataset_as_dataframe">extract_dataset_as_dataframe() (src.hdf5_ops.HDF5DataOpsManager method)</a>
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</li>
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</ul></td>
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</tr></table>
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<h2 id="G">G</h2>
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<table style="width: 100%" class="indextable genindextable"><tr>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="modules/src.html#src.hdf5_ops.get_groups_at_a_level">get_groups_at_a_level() (in module src.hdf5_ops)</a>
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</li>
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<li><a href="modules/src.html#src.hdf5_ops.HDF5DataOpsManager.get_metadata">get_metadata() (src.hdf5_ops.HDF5DataOpsManager method)</a>
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</li>
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</ul></td>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="modules/src.html#src.hdf5_ops.get_parent_child_relationships">get_parent_child_relationships() (in module src.hdf5_ops)</a>
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</li>
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<li><a href="modules/utils.html#utils.g5505_utils.group_by_df_column">group_by_df_column() (in module utils.g5505_utils)</a>
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</li>
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</ul></td>
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</tr></table>
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<h2 id="H">H</h2>
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<table style="width: 100%" class="indextable genindextable"><tr>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="modules/src.html#src.hdf5_ops.HDF5DataOpsManager">HDF5DataOpsManager (class in src.hdf5_ops)</a>
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</li>
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</ul></td>
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</tr></table>
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<h2 id="I">I</h2>
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<table style="width: 100%" class="indextable genindextable"><tr>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="modules/utils.html#utils.g5505_utils.infer_units">infer_units() (in module utils.g5505_utils)</a>
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</li>
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<li><a href="modules/utils.html#utils.g5505_utils.is_callable_list">is_callable_list() (in module utils.g5505_utils)</a>
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</li>
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</ul></td>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="modules/utils.html#utils.g5505_utils.is_str_list">is_str_list() (in module utils.g5505_utils)</a>
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</li>
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<li><a href="modules/utils.html#utils.g5505_utils.is_structured_array">is_structured_array() (in module utils.g5505_utils)</a>
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</li>
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</ul></td>
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</tr></table>
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<h2 id="L">L</h2>
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<table style="width: 100%" class="indextable genindextable"><tr>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="modules/pipelines.html#pipelines.data_integration.load_config_and_setup_logging">load_config_and_setup_logging() (in module pipelines.data_integration)</a>
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</li>
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</ul></td>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="modules/src.html#src.hdf5_ops.HDF5DataOpsManager.load_file_obj">load_file_obj() (src.hdf5_ops.HDF5DataOpsManager method)</a>
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</li>
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<li><a href="modules/pipelines.html#pipelines.metadata_revision.load_yaml">load_yaml() (in module pipelines.metadata_revision)</a>
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</li>
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</ul></td>
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</tr></table>
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<h2 id="M">M</h2>
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<table style="width: 100%" class="indextable genindextable"><tr>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="modules/utils.html#utils.g5505_utils.make_file_copy">make_file_copy() (in module utils.g5505_utils)</a>
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</li>
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<li>
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module
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<ul>
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<li><a href="modules/notebooks.html#module-notebooks">notebooks</a>
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</li>
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<li><a href="modules/pipelines.html#module-pipelines.data_integration">pipelines.data_integration</a>
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</li>
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<li><a href="modules/pipelines.html#module-pipelines.metadata_revision">pipelines.metadata_revision</a>
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</li>
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<li><a href="modules/src.html#module-src.hdf5_ops">src.hdf5_ops</a>
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</li>
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<li><a href="modules/src.html#module-src.hdf5_writer">src.hdf5_writer</a>
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</li>
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<li><a href="modules/utils.html#module-utils.g5505_utils">utils.g5505_utils</a>
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</li>
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<li><a href="modules/vis.html#module-visualization.hdf5_vis">visualization.hdf5_vis</a>
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</li>
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</ul></li>
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</ul></td>
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</tr></table>
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<h2 id="N">N</h2>
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<table style="width: 100%" class="indextable genindextable"><tr>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li>
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notebooks
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<ul>
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<li><a href="modules/notebooks.html#module-notebooks">module</a>
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</li>
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</ul></li>
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</ul></td>
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</tr></table>
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<h2 id="P">P</h2>
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<table style="width: 100%" class="indextable genindextable"><tr>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li>
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pipelines.data_integration
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<ul>
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<li><a href="modules/pipelines.html#module-pipelines.data_integration">module</a>
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</li>
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</ul></li>
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</ul></td>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li>
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pipelines.metadata_revision
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<ul>
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<li><a href="modules/pipelines.html#module-pipelines.metadata_revision">module</a>
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</li>
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</ul></li>
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<li><a href="modules/utils.html#utils.g5505_utils.progressBar">progressBar() (in module utils.g5505_utils)</a>
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</li>
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</ul></td>
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</tr></table>
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<h2 id="R">R</h2>
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<table style="width: 100%" class="indextable genindextable"><tr>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="modules/src.html#src.hdf5_ops.read_mtable_as_dataframe">read_mtable_as_dataframe() (in module src.hdf5_ops)</a>
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</li>
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<li><a href="modules/src.html#src.hdf5_ops.HDF5DataOpsManager.reformat_datetime_column">reformat_datetime_column() (src.hdf5_ops.HDF5DataOpsManager method)</a>
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</li>
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</ul></td>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="modules/src.html#src.hdf5_ops.HDF5DataOpsManager.rename_metadata">rename_metadata() (src.hdf5_ops.HDF5DataOpsManager method)</a>
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</li>
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<li><a href="modules/pipelines.html#pipelines.data_integration.run_pipeline">run_pipeline() (in module pipelines.data_integration)</a>
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</li>
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</ul></td>
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</tr></table>
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<h2 id="S">S</h2>
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<table style="width: 100%" class="indextable genindextable"><tr>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="modules/utils.html#utils.g5505_utils.sanitize_dataframe">sanitize_dataframe() (in module utils.g5505_utils)</a>
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</li>
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<li><a href="modules/src.html#src.hdf5_writer.save_processed_dataframe_to_hdf5">save_processed_dataframe_to_hdf5() (in module src.hdf5_writer)</a>
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</li>
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<li><a href="modules/src.html#src.hdf5_ops.serialize_metadata">serialize_metadata() (in module src.hdf5_ops)</a>
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</li>
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<li><a href="modules/utils.html#utils.g5505_utils.setup_logging">setup_logging() (in module utils.g5505_utils)</a>
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</li>
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</ul></td>
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<td style="width: 33%; vertical-align: top;"><ul>
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<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>
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</li>
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<li>
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src.hdf5_ops
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<ul>
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<li><a href="modules/src.html#module-src.hdf5_ops">module</a>
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</li>
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</ul></li>
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<li>
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src.hdf5_writer
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<ul>
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<li><a href="modules/src.html#module-src.hdf5_writer">module</a>
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</li>
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</ul></li>
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</ul></td>
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</tr></table>
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<h2 id="T">T</h2>
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<table style="width: 100%" class="indextable genindextable"><tr>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="modules/utils.html#utils.g5505_utils.to_serializable_dtype">to_serializable_dtype() (in module utils.g5505_utils)</a>
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</li>
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</ul></td>
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</tr></table>
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<h2 id="U">U</h2>
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<table style="width: 100%" class="indextable genindextable"><tr>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="modules/src.html#src.hdf5_ops.HDF5DataOpsManager.unload_file_obj">unload_file_obj() (src.hdf5_ops.HDF5DataOpsManager method)</a>
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</li>
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<li><a href="modules/src.html#src.hdf5_ops.HDF5DataOpsManager.update_file">update_file() (src.hdf5_ops.HDF5DataOpsManager method)</a>
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</li>
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<li><a href="modules/pipelines.html#pipelines.metadata_revision.update_hdf5_file_with_review">update_hdf5_file_with_review() (in module pipelines.metadata_revision)</a>
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</li>
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</ul></td>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="modules/src.html#src.hdf5_ops.HDF5DataOpsManager.update_metadata">update_metadata() (src.hdf5_ops.HDF5DataOpsManager method)</a>
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