rebuild documentation

- fix error message in example notebook - add stitching and parsing example notebooks
MannLabs · Sep 11, 2024 · 5a38d8e · 5a38d8e
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diff --git a/docs/doctrees/environment.pickle b/docs/doctrees/environment.pickle
diff --git a/docs/doctrees/nbsphinx/pages/tools/parsing/example_parsing_notebook.ipynb b/docs/doctrees/nbsphinx/pages/tools/parsing/example_parsing_notebook.ipynb
@@ -1,5 +1,13 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "6fc618c5",
+   "metadata": {},
+   "source": [
+    "# Example Parsing Notebook to rename phenix experiments"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 2,

diff --git a/docs/doctrees/pages/notebooks/example_scPortrait_project.doctree b/docs/doctrees/pages/notebooks/example_scPortrait_project.doctree
diff --git a/docs/doctrees/pages/tools/parsing/example_parsing_notebook.doctree b/docs/doctrees/pages/tools/parsing/example_parsing_notebook.doctree
diff --git a/docs/doctrees/pages/tools/parsing/parsing.doctree b/docs/doctrees/pages/tools/parsing/parsing.doctree
diff --git a/docs/doctrees/pages/tools/stitching/stitching.doctree b/docs/doctrees/pages/tools/stitching/stitching.doctree
diff --git a/docs/html/_sources/pages/pipeline/stitching.rst.txt b/docs/html/_sources/pages/pipeline/stitching.rst.txt
@@ -1,2 +1,3 @@
 stitching
-=========
+=========
+
diff --git a/docs/html/_sources/pages/tools/parsing/example_parsing_notebook.ipynb.txt b/docs/html/_sources/pages/tools/parsing/example_parsing_notebook.ipynb.txt
@@ -1,5 +1,13 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "6fc618c5",
+   "metadata": {},
+   "source": [
+    "# Example Parsing Notebook to rename phenix experiments"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 2,

diff --git a/docs/html/_sources/pages/tools/parsing/parsing.rst.txt b/docs/html/_sources/pages/tools/parsing/parsing.rst.txt
@@ -1,2 +1,9 @@
 parsing
-=======
+=======
+
+Example notebook showing the use of the parsing module.
+
+.. toctree::
+   :maxdepth: 2
+
+   example_parsing_notebook.ipynb
diff --git a/docs/html/_sources/pages/tools/stitching/stitching.rst.txt b/docs/html/_sources/pages/tools/stitching/stitching.rst.txt
@@ -1,2 +1,9 @@
 stitching
 =========
+
+Example notebook showing how to use the stitching module.
+
+.. toctree::
+   :maxdepth: 2
+
+   example_stitching_notebook.ipynb
diff --git a/docs/html/genindex.html b/docs/html/genindex.html
@@ -152,8 +152,29 @@
 </ul>
 <p class="caption" role="heading"><span class="caption-text">scPortrait tools</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="pages/tools/parsing/parsing.html">parsing</a></li>
-<li class="toctree-l1"><a class="reference internal" href="pages/tools/stitching/stitching.html">stitching</a></li>
+<li class="toctree-l1"><a class="reference internal" href="pages/tools/parsing/parsing.html">parsing</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="pages/tools/parsing/example_parsing_notebook.html">Example Parsing Notebook to rename phenix experiments</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="pages/tools/stitching/stitching.html">stitching</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="pages/tools/stitching/example_stitching_notebook.html">Example Stitching Notebook</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="pages/tools/stitching/example_stitching_notebook.html#Single-threaded-Stitching">Single-threaded Stitching</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="pages/tools/stitching/example_stitching_notebook.html#initializing-the-stitcher-object">initializing the stitcher object</a></li>
+<li class="toctree-l4"><a class="reference internal" href="pages/tools/stitching/example_stitching_notebook.html#Generating-thumbnails">Generating thumbnails</a></li>
+<li class="toctree-l4"><a class="reference internal" href="pages/tools/stitching/example_stitching_notebook.html#Generating-full-scale-stitched-image">Generating full-scale stitched image</a></li>
+</ul>
+</li>
+<li class="toctree-l3"><a class="reference internal" href="pages/tools/stitching/example_stitching_notebook.html#Multi-threaded-Stitching">Multi-threaded Stitching</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="pages/tools/stitching/example_stitching_notebook.html#id1">initializing the stitcher object</a></li>
+<li class="toctree-l4"><a class="reference internal" href="pages/tools/stitching/example_stitching_notebook.html#id2">Generating thumbnails</a></li>
+<li class="toctree-l4"><a class="reference internal" href="pages/tools/stitching/example_stitching_notebook.html#id3">Generating full-scale stitched image</a></li>
+</ul>
+</li>
+<li class="toctree-l3"><a class="reference internal" href="pages/tools/stitching/example_stitching_notebook.html#Visualize-Stitching-Output">Visualize Stitching Output</a></li>
+</ul>
+</li>
+</ul>
+</li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Module API</span></p>
 <ul>

diff --git a/docs/html/index.html b/docs/html/index.html
@@ -156,8 +156,29 @@
 </ul>
 <p class="caption" role="heading"><span class="caption-text">scPortrait tools</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="pages/tools/parsing/parsing.html">parsing</a></li>
-<li class="toctree-l1"><a class="reference internal" href="pages/tools/stitching/stitching.html">stitching</a></li>
+<li class="toctree-l1"><a class="reference internal" href="pages/tools/parsing/parsing.html">parsing</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="pages/tools/parsing/example_parsing_notebook.html">Example Parsing Notebook to rename phenix experiments</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="pages/tools/stitching/stitching.html">stitching</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="pages/tools/stitching/example_stitching_notebook.html">Example Stitching Notebook</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="pages/tools/stitching/example_stitching_notebook.html#Single-threaded-Stitching">Single-threaded Stitching</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="pages/tools/stitching/example_stitching_notebook.html#initializing-the-stitcher-object">initializing the stitcher object</a></li>
+<li class="toctree-l4"><a class="reference internal" href="pages/tools/stitching/example_stitching_notebook.html#Generating-thumbnails">Generating thumbnails</a></li>
+<li class="toctree-l4"><a class="reference internal" href="pages/tools/stitching/example_stitching_notebook.html#Generating-full-scale-stitched-image">Generating full-scale stitched image</a></li>
+</ul>
+</li>
+<li class="toctree-l3"><a class="reference internal" href="pages/tools/stitching/example_stitching_notebook.html#Multi-threaded-Stitching">Multi-threaded Stitching</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="pages/tools/stitching/example_stitching_notebook.html#id1">initializing the stitcher object</a></li>
+<li class="toctree-l4"><a class="reference internal" href="pages/tools/stitching/example_stitching_notebook.html#id2">Generating thumbnails</a></li>
+<li class="toctree-l4"><a class="reference internal" href="pages/tools/stitching/example_stitching_notebook.html#id3">Generating full-scale stitched image</a></li>
+</ul>
+</li>
+<li class="toctree-l3"><a class="reference internal" href="pages/tools/stitching/example_stitching_notebook.html#Visualize-Stitching-Output">Visualize Stitching Output</a></li>
+</ul>
+</li>
+</ul>
+</li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Module API</span></p>
 <ul>
@@ -322,8 +343,14 @@ <h1>Documentation<a class="headerlink" href="#documentation" title="Link to this
 <div class="toctree-wrapper compound">
 <p class="caption" role="heading"><span class="caption-text">scPortrait tools</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="pages/tools/parsing/parsing.html">parsing</a></li>
-<li class="toctree-l1"><a class="reference internal" href="pages/tools/stitching/stitching.html">stitching</a></li>
+<li class="toctree-l1"><a class="reference internal" href="pages/tools/parsing/parsing.html">parsing</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="pages/tools/parsing/example_parsing_notebook.html">Example Parsing Notebook to rename phenix experiments</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="pages/tools/stitching/stitching.html">stitching</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="pages/tools/stitching/example_stitching_notebook.html">Example Stitching Notebook</a></li>
+</ul>
+</li>
 </ul>
 </div>
 <div class="toctree-wrapper compound">

diff --git a/docs/html/objects.inv b/docs/html/objects.inv
diff --git a/docs/html/pages/example_notebooks.html b/docs/html/pages/example_notebooks.html
@@ -157,8 +157,28 @@
 </ul>
 <p class="caption" role="heading"><span class="caption-text">scPortrait tools</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="tools/parsing/parsing.html">parsing</a></li>
-<li class="toctree-l1"><a class="reference internal" href="tools/stitching/stitching.html">stitching</a></li>
+<li class="toctree-l1"><a class="reference internal" href="tools/parsing/parsing.html">parsing</a><ul class="simple">
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="tools/stitching/stitching.html">stitching</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="tools/stitching/example_stitching_notebook.html">Example Stitching Notebook</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="tools/stitching/example_stitching_notebook.html#Single-threaded-Stitching">Single-threaded Stitching</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="tools/stitching/example_stitching_notebook.html#initializing-the-stitcher-object">initializing the stitcher object</a></li>
+<li class="toctree-l4"><a class="reference internal" href="tools/stitching/example_stitching_notebook.html#Generating-thumbnails">Generating thumbnails</a></li>
+<li class="toctree-l4"><a class="reference internal" href="tools/stitching/example_stitching_notebook.html#Generating-full-scale-stitched-image">Generating full-scale stitched image</a></li>
+</ul>
+</li>
+<li class="toctree-l3"><a class="reference internal" href="tools/stitching/example_stitching_notebook.html#Multi-threaded-Stitching">Multi-threaded Stitching</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="tools/stitching/example_stitching_notebook.html#id1">initializing the stitcher object</a></li>
+<li class="toctree-l4"><a class="reference internal" href="tools/stitching/example_stitching_notebook.html#id2">Generating thumbnails</a></li>
+<li class="toctree-l4"><a class="reference internal" href="tools/stitching/example_stitching_notebook.html#id3">Generating full-scale stitched image</a></li>
+</ul>
+</li>
+<li class="toctree-l3"><a class="reference internal" href="tools/stitching/example_stitching_notebook.html#Visualize-Stitching-Output">Visualize Stitching Output</a></li>
+</ul>
+</li>
+</ul>
+</li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Module API</span></p>
 <ul>
@@ -173,23 +193,7 @@
 <li class="toctree-l4"><a class="reference internal" href="module/pipeline.html#shardedsegmentation">ShardedSegmentation</a></li>
 </ul>
 </li>
-<li class="toctree-l3"><a class="reference internal" href="module/pipeline.html#module-scportrait.pipeline.segmentation.workflows">segmentation workflows</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="module/pipeline.html#scportrait.pipeline.segmentation.workflows.WGASegmentation"><code class="docutils literal notranslate"><span class="pre">WGASegmentation</span></code></a></li>
-<li class="toctree-l4"><a class="reference internal" href="module/pipeline.html#scportrait.pipeline.segmentation.workflows.ShardedWGASegmentation"><code class="docutils literal notranslate"><span class="pre">ShardedWGASegmentation</span></code></a></li>
-<li class="toctree-l4"><a class="reference internal" href="module/pipeline.html#scportrait.pipeline.segmentation.workflows.DAPISegmentation"><code class="docutils literal notranslate"><span class="pre">DAPISegmentation</span></code></a></li>
-<li class="toctree-l4"><a class="reference internal" href="module/pipeline.html#scportrait.pipeline.segmentation.workflows.ShardedDAPISegmentation"><code class="docutils literal notranslate"><span class="pre">ShardedDAPISegmentation</span></code></a></li>
-<li class="toctree-l4"><a class="reference internal" href="module/pipeline.html#scportrait.pipeline.segmentation.workflows.DAPISegmentationCellpose"><code class="docutils literal notranslate"><span class="pre">DAPISegmentationCellpose</span></code></a></li>
-<li class="toctree-l4"><a class="reference internal" href="module/pipeline.html#scportrait.pipeline.segmentation.workflows.ShardedDAPISegmentationCellpose"><code class="docutils literal notranslate"><span class="pre">ShardedDAPISegmentationCellpose</span></code></a></li>
-<li class="toctree-l4"><a class="reference internal" href="module/pipeline.html#scportrait.pipeline.segmentation.workflows.CytosolSegmentationCellpose"><code class="docutils literal notranslate"><span class="pre">CytosolSegmentationCellpose</span></code></a></li>
-<li class="toctree-l4"><a class="reference internal" href="module/pipeline.html#scportrait.pipeline.segmentation.workflows.ShardedCytosolSegmentationCellpose"><code class="docutils literal notranslate"><span class="pre">ShardedCytosolSegmentationCellpose</span></code></a></li>
-<li class="toctree-l4"><a class="reference internal" href="module/pipeline.html#scportrait.pipeline.segmentation.workflows.CytosolSegmentationDownsamplingCellpose"><code class="docutils literal notranslate"><span class="pre">CytosolSegmentationDownsamplingCellpose</span></code></a></li>
-<li class="toctree-l4"><a class="reference internal" href="module/pipeline.html#scportrait.pipeline.segmentation.workflows.ShardedCytosolSegmentationDownsamplingCellpose"><code class="docutils literal notranslate"><span class="pre">ShardedCytosolSegmentationDownsamplingCellpose</span></code></a></li>
-<li class="toctree-l4"><a class="reference internal" href="module/pipeline.html#scportrait.pipeline.segmentation.workflows.CytosolOnlySegmentationCellpose"><code class="docutils literal notranslate"><span class="pre">CytosolOnlySegmentationCellpose</span></code></a></li>
-<li class="toctree-l4"><a class="reference internal" href="module/pipeline.html#scportrait.pipeline.segmentation.workflows.Sharded_CytosolOnly_Cellpose_Segmentation"><code class="docutils literal notranslate"><span class="pre">Sharded_CytosolOnly_Cellpose_Segmentation</span></code></a></li>
-<li class="toctree-l4"><a class="reference internal" href="module/pipeline.html#scportrait.pipeline.segmentation.workflows.CytosolOnly_Segmentation_Downsampling_Cellpose"><code class="docutils literal notranslate"><span class="pre">CytosolOnly_Segmentation_Downsampling_Cellpose</span></code></a></li>
-<li class="toctree-l4"><a class="reference internal" href="module/pipeline.html#scportrait.pipeline.segmentation.workflows.Sharded_CytosolOnly_Segmentation_Downsampling_Cellpose"><code class="docutils literal notranslate"><span class="pre">Sharded_CytosolOnly_Segmentation_Downsampling_Cellpose</span></code></a></li>
-</ul>
-</li>
+<li class="toctree-l3"><a class="reference internal" href="module/pipeline.html#segmentation-workflows">segmentation workflows</a></li>
 <li class="toctree-l3"><a class="reference internal" href="module/pipeline.html#extraction">extraction</a><ul>
 <li class="toctree-l4"><a class="reference internal" href="module/pipeline.html#hdf5cellextraction">HDF5CellExtraction</a></li>
 </ul>
@@ -206,29 +210,26 @@
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="module/processing.html">processing</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="module/processing.html#module-scportrait.processing.images">images</a></li>
-<li class="toctree-l3"><a class="reference internal" href="module/processing.html#module-scportrait.processing.masks">masks</a></li>
+<li class="toctree-l3"><a class="reference internal" href="module/processing.html#images">images</a></li>
+<li class="toctree-l3"><a class="reference internal" href="module/processing.html#masks">masks</a></li>
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="module/io.html">processing</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="module/io.html#module-scportrait.processing.images">images</a></li>
-<li class="toctree-l3"><a class="reference internal" href="module/io.html#module-scportrait.processing.masks">masks</a></li>
+<li class="toctree-l3"><a class="reference internal" href="module/io.html#images">images</a></li>
+<li class="toctree-l3"><a class="reference internal" href="module/io.html#masks">masks</a></li>
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="module/tools.html">tools</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="module/tools/parsing.html">parsing</a></li>
-<li class="toctree-l3"><a class="reference internal" href="module/tools/stitching.html">stitching</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="module/tools/stitching.html#parameters">Parameters:</a></li>
-</ul>
-</li>
+<li class="toctree-l3"><a class="reference internal" href="module/tools/stitching.html">stitching</a></li>
 <li class="toctree-l3"><a class="reference internal" href="module/tools/ml.html">ml</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="module/tools/ml.html#module-scportrait.tools.ml.datasets">datasets</a></li>
-<li class="toctree-l4"><a class="reference internal" href="module/tools/ml.html#module-scportrait.tools.ml.metrics">metrics</a></li>
+<li class="toctree-l4"><a class="reference internal" href="module/tools/ml.html#datasets">datasets</a></li>
+<li class="toctree-l4"><a class="reference internal" href="module/tools/ml.html#metrics">metrics</a></li>
 <li class="toctree-l4"><a class="reference internal" href="module/tools/ml.html#models">models</a></li>
 <li class="toctree-l4"><a class="reference internal" href="module/tools/ml.html#plmodels">plmodels</a></li>
-<li class="toctree-l4"><a class="reference internal" href="module/tools/ml.html#module-scportrait.tools.ml.pretrained_models">pretrained_models</a></li>
-<li class="toctree-l4"><a class="reference internal" href="module/tools/ml.html#module-scportrait.tools.ml.transforms">transforms</a></li>
-<li class="toctree-l4"><a class="reference internal" href="module/tools/ml.html#module-scportrait.tools.ml.utils">utils</a></li>
+<li class="toctree-l4"><a class="reference internal" href="module/tools/ml.html#pretrained-models">pretrained_models</a></li>
+<li class="toctree-l4"><a class="reference internal" href="module/tools/ml.html#transforms">transforms</a></li>
+<li class="toctree-l4"><a class="reference internal" href="module/tools/ml.html#utils">utils</a></li>
 </ul>
 </li>
 </ul>