deploy: ad207ae

_sources/reference/api/colabseg.ColabSegData.load_pickle.rst.txt

@@ -0,0 +1,6 @@
+ColabSegData.load\_pickle
+=================================
+
+.. currentmodule:: colabseg
+
+.. automethod:: ColabSegData.load_pickle

_sources/reference/api/colabseg.ColabSegData.rst.txt

@@ -82,6 +82,9 @@
            ColabSegData.load_hdf
 
 
+           ColabSegData.load_pickle
+
+
            ColabSegData.load_point_cloud
 
 
@@ -112,6 +115,9 @@
            ColabSegData.save_hdf
 
 
+           ColabSegData.save_pickle
+
+
            ColabSegData.save_values_txt
 
 

_sources/reference/api/colabseg.ColabSegData.save_pickle.rst.txt

@@ -0,0 +1,6 @@
+ColabSegData.save\_pickle
+=================================
+
+.. currentmodule:: colabseg
+
+.. automethod:: ColabSegData.save_pickle

_sources/reference/api/colabseg.segmentation_gui.JupyterFramework.load_pickle.rst.txt

@@ -0,0 +1,6 @@
+JupyterFramework.load\_pickle
+======================================================
+
+.. currentmodule:: colabseg.segmentation_gui
+
+.. automethod:: JupyterFramework.load_pickle

_sources/reference/api/colabseg.segmentation_gui.JupyterFramework.rst.txt

@@ -103,6 +103,9 @@
            JupyterFramework.load_mrc_file
 
 
+           JupyterFramework.load_pickle
+
+
            JupyterFramework.load_raw_image
 
 
@@ -136,6 +139,9 @@
            JupyterFramework.rotate_flat
 
 
+           JupyterFramework.sample_fit
+
+
            JupyterFramework.save_clusters_mrc
 
 
@@ -151,6 +157,9 @@
            JupyterFramework.save_normals_file
 
 
+           JupyterFramework.save_pickle
+
+
            JupyterFramework.save_radii_file
 
 

_sources/reference/api/colabseg.segmentation_gui.JupyterFramework.sample_fit.rst.txt

@@ -0,0 +1,6 @@
+JupyterFramework.sample\_fit
+=====================================================
+
+.. currentmodule:: colabseg.segmentation_gui
+
+.. automethod:: JupyterFramework.sample_fit

_sources/reference/api/colabseg.segmentation_gui.JupyterFramework.save_pickle.rst.txt

@@ -0,0 +1,6 @@
+JupyterFramework.save\_pickle
+======================================================
+
+.. currentmodule:: colabseg.segmentation_gui
+
+.. automethod:: JupyterFramework.save_pickle

genindex.html

@@ -717,14 +717,20 @@ <h2 id="L">L</h2>
 </li>
       <li><a href="reference/api/colabseg.ColabSegData.load_hdf.html#colabseg.ColabSegData.load_hdf">load_hdf() (ColabSegData method)</a>
 </li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="reference/api/colabseg.py3dmol_controls.seg_visualization.load_model_from_file.html#colabseg.py3dmol_controls.seg_visualization.load_model_from_file">load_model_from_file() (seg_visualization method)</a>
 </li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="reference/api/colabseg.segmentation_gui.JupyterFramework.load_mrc_file.html#colabseg.segmentation_gui.JupyterFramework.load_mrc_file">load_mrc_file() (JupyterFramework method)</a>
 </li>
       <li><a href="reference/api/colabseg.py3dmol_controls.seg_visualization.load_normal_positions.html#colabseg.py3dmol_controls.seg_visualization.load_normal_positions">load_normal_positions() (seg_visualization method)</a>
 </li>
+      <li><a href="reference/api/colabseg.ColabSegData.load_pickle.html#colabseg.ColabSegData.load_pickle">load_pickle() (ColabSegData class method)</a>
+
+      <ul>
+        <li><a href="reference/api/colabseg.segmentation_gui.JupyterFramework.load_pickle.html#colabseg.segmentation_gui.JupyterFramework.load_pickle">(JupyterFramework method)</a>
+</li>
+      </ul></li>
       <li><a href="reference/api/colabseg.ColabSegData.load_point_cloud.html#colabseg.ColabSegData.load_point_cloud">load_point_cloud() (ColabSegData method)</a>
 </li>
       <li><a href="reference/api/colabseg.ColabSegData.load_protein_position.html#colabseg.ColabSegData.load_protein_position">load_protein_position() (ColabSegData method)</a>
@@ -944,6 +950,8 @@ <h2 id="S">S</h2>
         <li><a href="reference/api/colabseg.parametrization.Sphere.sample.html#colabseg.parametrization.Sphere.sample">(Sphere method)</a>
 </li>
       </ul></li>
+      <li><a href="reference/api/colabseg.segmentation_gui.JupyterFramework.sample_fit.html#colabseg.segmentation_gui.JupyterFramework.sample_fit">sample_fit() (JupyterFramework method)</a>
+</li>
       <li><a href="reference/api/colabseg.segmentation_gui.JupyterFramework.save_clusters_mrc.html#colabseg.segmentation_gui.JupyterFramework.save_clusters_mrc">save_clusters_mrc() (JupyterFramework method)</a>
 </li>
       <li><a href="reference/api/colabseg.segmentation_gui.JupyterFramework.save_clusters_txt.html#colabseg.segmentation_gui.JupyterFramework.save_clusters_txt">save_clusters_txt() (JupyterFramework method)</a>
@@ -956,12 +964,18 @@ <h2 id="S">S</h2>
 </li>
       <li><a href="reference/api/colabseg.segmentation_gui.JupyterFramework.save_normals_file.html#colabseg.segmentation_gui.JupyterFramework.save_normals_file">save_normals_file() (JupyterFramework method)</a>
 </li>
+      <li><a href="reference/api/colabseg.ColabSegData.save_pickle.html#colabseg.ColabSegData.save_pickle">save_pickle() (ColabSegData method)</a>
+
+      <ul>
+        <li><a href="reference/api/colabseg.segmentation_gui.JupyterFramework.save_pickle.html#colabseg.segmentation_gui.JupyterFramework.save_pickle">(JupyterFramework method)</a>
+</li>
+      </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="reference/api/colabseg.segmentation_gui.JupyterFramework.save_radii_file.html#colabseg.segmentation_gui.JupyterFramework.save_radii_file">save_radii_file() (JupyterFramework method)</a>
 </li>
       <li><a href="reference/api/colabseg.segmentation_gui.JupyterFramework.save_radii_plot.html#colabseg.segmentation_gui.JupyterFramework.save_radii_plot">save_radii_plot() (JupyterFramework method)</a>
 </li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="reference/api/colabseg.segmentation_gui.JupyterFramework.save_state_hdf.html#colabseg.segmentation_gui.JupyterFramework.save_state_hdf">save_state_hdf() (JupyterFramework method)</a>
 </li>
       <li><a href="reference/api/colabseg.ColabSegData.save_values_txt.html#colabseg.ColabSegData.save_values_txt">save_values_txt() (ColabSegData static method)</a>

index.html

@@ -348,7 +348,7 @@
 
   <span class="target" id="module-project"></span><section id="project-documentation">
 <h1>colabseg documentation<a class="headerlink" href="#project-documentation" title="Permalink to this heading">#</a></h1>
-<p><strong>Date</strong>: Mar 30, 2024 <strong>Version</strong>: 0.1</p>
+<p><strong>Date</strong>: Apr 20, 2024 <strong>Version</strong>: 0.1</p>
 <p>colabseg is an open source library for interactive editing, processing, and visualizing membrane segmentations from cryo-ET data.</p>
 <div class="sd-container-fluid sd-sphinx-override sd-mb-4 docutils">
 <div class="sd-row sd-row-cols-2 sd-row-cols-xs-2 sd-row-cols-sm-2 sd-row-cols-md-2 sd-row-cols-lg-2 docutils">

reference/api/colabseg.ColabSegData.analyze_protein_membrane_min_distance.html

@@ -353,6 +353,7 @@
 <li class="toctree-l3"><a class="reference internal" href="colabseg.ColabSegData.interpolate_membrane_closed_surface.html">ColabSegData.interpolate_membrane_closed_surface</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.ColabSegData.interpolate_membrane_rbf.html">ColabSegData.interpolate_membrane_rbf</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.ColabSegData.load_hdf.html">ColabSegData.load_hdf</a></li>
+<li class="toctree-l3"><a class="reference internal" href="colabseg.ColabSegData.load_pickle.html">ColabSegData.load_pickle</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.ColabSegData.load_point_cloud.html">ColabSegData.load_point_cloud</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.ColabSegData.load_protein_position.html">ColabSegData.load_protein_position</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.ColabSegData.load_stl_file.html">ColabSegData.load_stl_file</a></li>
@@ -363,6 +364,7 @@
 <li class="toctree-l3"><a class="reference internal" href="colabseg.ColabSegData.reload_original_values.html">ColabSegData.reload_original_values</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.ColabSegData.reload_previous_step.html">ColabSegData.reload_previous_step</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.ColabSegData.save_hdf.html">ColabSegData.save_hdf</a></li>
+<li class="toctree-l3"><a class="reference internal" href="colabseg.ColabSegData.save_pickle.html">ColabSegData.save_pickle</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.ColabSegData.save_values_txt.html">ColabSegData.save_values_txt</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.ColabSegData.split_clusters.html">ColabSegData.split_clusters</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.ColabSegData.statistical_outlier_removal.html">ColabSegData.statistical_outlier_removal</a></li>
@@ -454,6 +456,7 @@
 <li class="toctree-l3"><a class="reference internal" href="colabseg.segmentation_gui.JupyterFramework.load_from_point_cloud.html">JupyterFramework.load_from_point_cloud</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.segmentation_gui.JupyterFramework.load_from_stl_file.html">JupyterFramework.load_from_stl_file</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.segmentation_gui.JupyterFramework.load_mrc_file.html">JupyterFramework.load_mrc_file</a></li>
+<li class="toctree-l3"><a class="reference internal" href="colabseg.segmentation_gui.JupyterFramework.load_pickle.html">JupyterFramework.load_pickle</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.segmentation_gui.JupyterFramework.load_raw_image.html">JupyterFramework.load_raw_image</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.segmentation_gui.JupyterFramework.load_state_hdf.html">JupyterFramework.load_state_hdf</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.segmentation_gui.JupyterFramework.load_viz.html">JupyterFramework.load_viz</a></li>
@@ -465,11 +468,13 @@
 <li class="toctree-l3"><a class="reference internal" href="colabseg.segmentation_gui.JupyterFramework.reset_input.html">JupyterFramework.reset_input</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.segmentation_gui.JupyterFramework.rotate_back.html">JupyterFramework.rotate_back</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.segmentation_gui.JupyterFramework.rotate_flat.html">JupyterFramework.rotate_flat</a></li>
+<li class="toctree-l3"><a class="reference internal" href="colabseg.segmentation_gui.JupyterFramework.sample_fit.html">JupyterFramework.sample_fit</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.segmentation_gui.JupyterFramework.save_clusters_mrc.html">JupyterFramework.save_clusters_mrc</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.segmentation_gui.JupyterFramework.save_clusters_txt.html">JupyterFramework.save_clusters_txt</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.segmentation_gui.JupyterFramework.save_distance_file.html">JupyterFramework.save_distance_file</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.segmentation_gui.JupyterFramework.save_distance_plot.html">JupyterFramework.save_distance_plot</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.segmentation_gui.JupyterFramework.save_normals_file.html">JupyterFramework.save_normals_file</a></li>
+<li class="toctree-l3"><a class="reference internal" href="colabseg.segmentation_gui.JupyterFramework.save_pickle.html">JupyterFramework.save_pickle</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.segmentation_gui.JupyterFramework.save_radii_file.html">JupyterFramework.save_radii_file</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.segmentation_gui.JupyterFramework.save_radii_plot.html">JupyterFramework.save_radii_plot</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.segmentation_gui.JupyterFramework.save_state_hdf.html">JupyterFramework.save_state_hdf</a></li>

reference/api/colabseg.ColabSegData.backup_step_to_previous.html

@@ -353,6 +353,7 @@
 <li class="toctree-l3"><a class="reference internal" href="colabseg.ColabSegData.interpolate_membrane_closed_surface.html">ColabSegData.interpolate_membrane_closed_surface</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.ColabSegData.interpolate_membrane_rbf.html">ColabSegData.interpolate_membrane_rbf</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.ColabSegData.load_hdf.html">ColabSegData.load_hdf</a></li>
+<li class="toctree-l3"><a class="reference internal" href="colabseg.ColabSegData.load_pickle.html">ColabSegData.load_pickle</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.ColabSegData.load_point_cloud.html">ColabSegData.load_point_cloud</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.ColabSegData.load_protein_position.html">ColabSegData.load_protein_position</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.ColabSegData.load_stl_file.html">ColabSegData.load_stl_file</a></li>
@@ -363,6 +364,7 @@
 <li class="toctree-l3"><a class="reference internal" href="colabseg.ColabSegData.reload_original_values.html">ColabSegData.reload_original_values</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.ColabSegData.reload_previous_step.html">ColabSegData.reload_previous_step</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.ColabSegData.save_hdf.html">ColabSegData.save_hdf</a></li>
+<li class="toctree-l3"><a class="reference internal" href="colabseg.ColabSegData.save_pickle.html">ColabSegData.save_pickle</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.ColabSegData.save_values_txt.html">ColabSegData.save_values_txt</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.ColabSegData.split_clusters.html">ColabSegData.split_clusters</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.ColabSegData.statistical_outlier_removal.html">ColabSegData.statistical_outlier_removal</a></li>
@@ -454,6 +456,7 @@
 <li class="toctree-l3"><a class="reference internal" href="colabseg.segmentation_gui.JupyterFramework.load_from_point_cloud.html">JupyterFramework.load_from_point_cloud</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.segmentation_gui.JupyterFramework.load_from_stl_file.html">JupyterFramework.load_from_stl_file</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.segmentation_gui.JupyterFramework.load_mrc_file.html">JupyterFramework.load_mrc_file</a></li>
+<li class="toctree-l3"><a class="reference internal" href="colabseg.segmentation_gui.JupyterFramework.load_pickle.html">JupyterFramework.load_pickle</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.segmentation_gui.JupyterFramework.load_raw_image.html">JupyterFramework.load_raw_image</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.segmentation_gui.JupyterFramework.load_state_hdf.html">JupyterFramework.load_state_hdf</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.segmentation_gui.JupyterFramework.load_viz.html">JupyterFramework.load_viz</a></li>
@@ -465,11 +468,13 @@
 <li class="toctree-l3"><a class="reference internal" href="colabseg.segmentation_gui.JupyterFramework.reset_input.html">JupyterFramework.reset_input</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.segmentation_gui.JupyterFramework.rotate_back.html">JupyterFramework.rotate_back</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.segmentation_gui.JupyterFramework.rotate_flat.html">JupyterFramework.rotate_flat</a></li>
+<li class="toctree-l3"><a class="reference internal" href="colabseg.segmentation_gui.JupyterFramework.sample_fit.html">JupyterFramework.sample_fit</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.segmentation_gui.JupyterFramework.save_clusters_mrc.html">JupyterFramework.save_clusters_mrc</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.segmentation_gui.JupyterFramework.save_clusters_txt.html">JupyterFramework.save_clusters_txt</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.segmentation_gui.JupyterFramework.save_distance_file.html">JupyterFramework.save_distance_file</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.segmentation_gui.JupyterFramework.save_distance_plot.html">JupyterFramework.save_distance_plot</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.segmentation_gui.JupyterFramework.save_normals_file.html">JupyterFramework.save_normals_file</a></li>
+<li class="toctree-l3"><a class="reference internal" href="colabseg.segmentation_gui.JupyterFramework.save_pickle.html">JupyterFramework.save_pickle</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.segmentation_gui.JupyterFramework.save_radii_file.html">JupyterFramework.save_radii_file</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.segmentation_gui.JupyterFramework.save_radii_plot.html">JupyterFramework.save_radii_plot</a></li>
 <li class="toctree-l3"><a class="reference internal" href="colabseg.segmentation_gui.JupyterFramework.save_state_hdf.html">JupyterFramework.save_state_hdf</a></li>