Restructured toctrees and added rst files for each module so they can…

… be cross referenced
b-heifets · Jun 11, 2024 · 36439a3 · 36439a3
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diff --git a/unravel/docs/_build/doctrees/unravel/voxel_stats/vstats.doctree b/unravel/docs/_build/doctrees/unravel/voxel_stats/vstats.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/voxel_stats/whole_to_LR_avg.doctree b/unravel/docs/_build/doctrees/unravel/voxel_stats/whole_to_LR_avg.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/voxel_stats/z_score.doctree b/unravel/docs/_build/doctrees/unravel/voxel_stats/z_score.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/warp/to_atlas.doctree b/unravel/docs/_build/doctrees/unravel/warp/to_atlas.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/warp/to_native.doctree b/unravel/docs/_build/doctrees/unravel/warp/to_native.doctree
diff --git a/unravel/docs/_build/doctrees/modules.doctree → .../_build/doctrees/unravel/warp/toc.doctree b/unravel/docs/_build/doctrees/modules.doctree → .../_build/doctrees/unravel/warp/toc.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/warp/warp.doctree b/unravel/docs/_build/doctrees/unravel/warp/warp.doctree
diff --git a/unravel/docs/_build/html/.buildinfo b/unravel/docs/_build/html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 81ca74ad115bd8e1754d40bf3d5a748e
+config: c0f6dde0431a096ed7b659b352f11328
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/unravel/docs/_build/html/_images/batch_stitching_1.JPG b/unravel/docs/_build/html/_images/batch_stitching_1.JPG
diff --git a/unravel/docs/_build/html/_images/batch_stitching_2.JPG b/unravel/docs/_build/html/_images/batch_stitching_2.JPG
diff --git a/unravel/docs/_build/html/_modules/index.html b/unravel/docs/_build/html/_modules/index.html
@@ -28,6 +28,7 @@
 <link rel="preload" as="font" type="font/woff2" crossorigin href="../_static/vendor/fontawesome/6.5.2/webfonts/fa-regular-400.woff2" />
 
     <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=a746c00c" />
+    <link rel="stylesheet" type="text/css" href="../_static/togglebutton.css?v=13237357" />
     <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=165b5da3" />
 
   <!-- Pre-loaded scripts that we'll load fully later -->
@@ -38,6 +39,12 @@
     <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>let toggleHintShow = 'Click to show';</script>
+    <script>let toggleHintHide = 'Click to hide';</script>
+    <script>let toggleOpenOnPrint = 'true';</script>
+    <script src="../_static/togglebutton.js?v=4a39c7ea"></script>
+    <script>var togglebuttonSelector = '.toggle, .admonition.dropdown';</script>
+    <script>var togglebuttonSelector = '.toggle, .admonition.dropdown';</script>
     <script>DOCUMENTATION_OPTIONS.pagename = '_modules/index';</script>
     <link rel="icon" href="../_static/favicon.png"/>
     <link rel="index" title="Index" href="../genindex.html" />
@@ -151,8 +158,8 @@
 
 
 <li class="nav-item pst-header-nav-item">
-  <a class="nav-link nav-internal" href="../modules.html">
-    unravel
+  <a class="nav-link nav-internal" href="../unravel/toc.html">
+    unravel package
   </a>
 </li>
 
@@ -264,8 +271,8 @@
 
 
 <li class="nav-item pst-header-nav-item">
-  <a class="nav-link nav-internal" href="../modules.html">
-    unravel
+  <a class="nav-link nav-internal" href="../unravel/toc.html">
+    unravel package
   </a>
 </li>
 
@@ -423,6 +430,8 @@ <h1>All modules for which code is available</h1>
 <li><a href="unravel/voxel_stats/apply_mask.html">unravel.voxel_stats.apply_mask</a></li>
 <li><a href="unravel/voxel_stats/hemi_to_LR_avg.html">unravel.voxel_stats.hemi_to_LR_avg</a></li>
 <li><a href="unravel/voxel_stats/mirror.html">unravel.voxel_stats.mirror</a></li>
+<li><a href="unravel/voxel_stats/other/IF_outliers.html">unravel.voxel_stats.other.IF_outliers</a></li>
+<li><a href="unravel/voxel_stats/other/r_to_p.html">unravel.voxel_stats.other.r_to_p</a></li>
 <li><a href="unravel/voxel_stats/prep_vstats.html">unravel.voxel_stats.prep_vstats</a></li>
 <li><a href="unravel/voxel_stats/vstats.html">unravel.voxel_stats.vstats</a></li>
 <li><a href="unravel/voxel_stats/whole_to_LR_avg.html">unravel.voxel_stats.whole_to_LR_avg</a></li>

diff --git a/unravel/docs/_build/html/_modules/unravel/cluster_stats/brain_model.html b/unravel/docs/_build/html/_modules/unravel/cluster_stats/brain_model.html
@@ -28,6 +28,7 @@
 <link rel="preload" as="font" type="font/woff2" crossorigin href="../../../_static/vendor/fontawesome/6.5.2/webfonts/fa-regular-400.woff2" />
 
     <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=a746c00c" />
+    <link rel="stylesheet" type="text/css" href="../../../_static/togglebutton.css?v=13237357" />
     <link rel="stylesheet" type="text/css" href="../../../_static/custom.css?v=165b5da3" />
 
   <!-- Pre-loaded scripts that we'll load fully later -->
@@ -38,6 +39,12 @@
     <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>let toggleHintShow = 'Click to show';</script>
+    <script>let toggleHintHide = 'Click to hide';</script>
+    <script>let toggleOpenOnPrint = 'true';</script>
+    <script src="../../../_static/togglebutton.js?v=4a39c7ea"></script>
+    <script>var togglebuttonSelector = '.toggle, .admonition.dropdown';</script>
+    <script>var togglebuttonSelector = '.toggle, .admonition.dropdown';</script>
     <script>DOCUMENTATION_OPTIONS.pagename = '_modules/unravel/cluster_stats/brain_model';</script>
     <link rel="icon" href="../../../_static/favicon.png"/>
     <link rel="index" title="Index" href="../../../genindex.html" />
@@ -151,8 +158,8 @@
 
 
 <li class="nav-item pst-header-nav-item">
-  <a class="nav-link nav-internal" href="../../../modules.html">
-    unravel
+  <a class="nav-link nav-internal" href="../../../unravel/toc.html">
+    unravel package
   </a>
 </li>
 
@@ -264,8 +271,8 @@
 
 
 <li class="nav-item pst-header-nav-item">
-  <a class="nav-link nav-internal" href="../../../modules.html">
-    unravel
+  <a class="nav-link nav-internal" href="../../../unravel/toc.html">
+    unravel package
   </a>
 </li>
 
@@ -369,7 +376,7 @@ <h1>Source code for unravel.cluster_stats.brain_model</h1><div class="highlight"
 
 
 <div class="viewcode-block" id="parse_args">
-<a class="viewcode-back" href="../../../unravel.cluster_stats.html#unravel.cluster_stats.brain_model.parse_args">[docs]</a>
+<a class="viewcode-back" href="../../../unravel/cluster_stats/brain_model.html#unravel.cluster_stats.brain_model.parse_args">[docs]</a>
 <span class="k">def</span> <span class="nf">parse_args</span><span class="p">():</span>
     <span class="n">parser</span> <span class="o">=</span> <span class="n">argparse</span><span class="o">.</span><span class="n">ArgumentParser</span><span class="p">(</span><span class="n">description</span><span class="o">=</span><span class="s1">&#39;Prep .nii.gz and RGBA .txt for vizualization in dsi_studio&#39;</span><span class="p">,</span> <span class="n">formatter_class</span><span class="o">=</span><span class="n">SuppressMetavar</span><span class="p">)</span>
     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-i&#39;</span><span class="p">,</span> <span class="s1">&#39;--input&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">&quot;path/img.nii.gz (e.g., valid cluster index)&quot;</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>
@@ -392,7 +399,7 @@ <h1>Source code for unravel.cluster_stats.brain_model</h1><div class="highlight"
 
 
 <div class="viewcode-block" id="main">
-<a class="viewcode-back" href="../../../unravel.cluster_stats.html#unravel.cluster_stats.brain_model.main">[docs]</a>
+<a class="viewcode-back" href="../../../unravel/cluster_stats/brain_model.html#unravel.cluster_stats.brain_model.main">[docs]</a>
 <span class="k">def</span> <span class="nf">main</span><span class="p">():</span>
     <span class="n">args</span> <span class="o">=</span> <span class="n">parse_args</span><span class="p">()</span>
 

diff --git a/unravel/docs/_build/html/_modules/unravel/cluster_stats/crop_clusters.html b/unravel/docs/_build/html/_modules/unravel/cluster_stats/crop_clusters.html
@@ -28,6 +28,7 @@
 <link rel="preload" as="font" type="font/woff2" crossorigin href="../../../_static/vendor/fontawesome/6.5.2/webfonts/fa-regular-400.woff2" />
 
     <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=a746c00c" />
+    <link rel="stylesheet" type="text/css" href="../../../_static/togglebutton.css?v=13237357" />
     <link rel="stylesheet" type="text/css" href="../../../_static/custom.css?v=165b5da3" />
 
   <!-- Pre-loaded scripts that we'll load fully later -->
@@ -38,6 +39,12 @@
     <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>let toggleHintShow = 'Click to show';</script>
+    <script>let toggleHintHide = 'Click to hide';</script>
+    <script>let toggleOpenOnPrint = 'true';</script>
+    <script src="../../../_static/togglebutton.js?v=4a39c7ea"></script>
+    <script>var togglebuttonSelector = '.toggle, .admonition.dropdown';</script>
+    <script>var togglebuttonSelector = '.toggle, .admonition.dropdown';</script>
     <script>DOCUMENTATION_OPTIONS.pagename = '_modules/unravel/cluster_stats/crop_clusters';</script>
     <link rel="icon" href="../../../_static/favicon.png"/>
     <link rel="index" title="Index" href="../../../genindex.html" />
@@ -151,8 +158,8 @@
 
 
 <li class="nav-item pst-header-nav-item">
-  <a class="nav-link nav-internal" href="../../../modules.html">
-    unravel
+  <a class="nav-link nav-internal" href="../../../unravel/toc.html">
+    unravel package
   </a>
 </li>
 
@@ -264,8 +271,8 @@
 
 
 <li class="nav-item pst-header-nav-item">
-  <a class="nav-link nav-internal" href="../../../modules.html">
-    unravel
+  <a class="nav-link nav-internal" href="../../../unravel/toc.html">
+    unravel package
   </a>
 </li>
 
@@ -366,7 +373,7 @@ <h1>Source code for unravel.cluster_stats.crop_clusters</h1><div class="highligh
 
 
 <div class="viewcode-block" id="parse_args">
-<a class="viewcode-back" href="../../../unravel.cluster_stats.html#unravel.cluster_stats.crop_clusters.parse_args">[docs]</a>
+<a class="viewcode-back" href="../../../unravel/cluster_stats/crop_clusters.html#unravel.cluster_stats.crop_clusters.parse_args">[docs]</a>
 <span class="k">def</span> <span class="nf">parse_args</span><span class="p">():</span>
     <span class="n">parser</span> <span class="o">=</span> <span class="n">argparse</span><span class="o">.</span><span class="n">ArgumentParser</span><span class="p">(</span><span class="n">description</span><span class="o">=</span><span class="s1">&#39;Load image, crop cluster, and save as .nii.gz&#39;</span><span class="p">,</span> <span class="n">formatter_class</span><span class="o">=</span><span class="n">SuppressMetavar</span><span class="p">)</span>
     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-i&#39;</span><span class="p">,</span> <span class="s1">&#39;--input&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;path/img.czi, path/img.nii.gz, or path/tif_dir&#39;</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>
@@ -381,7 +388,7 @@ <h1>Source code for unravel.cluster_stats.crop_clusters</h1><div class="highligh
 
 
 <div class="viewcode-block" id="save_cropped_img">
-<a class="viewcode-back" href="../../../unravel.cluster_stats.html#unravel.cluster_stats.crop_clusters.save_cropped_img">[docs]</a>
+<a class="viewcode-back" href="../../../unravel/cluster_stats/crop_clusters.html#unravel.cluster_stats.crop_clusters.save_cropped_img">[docs]</a>
 <span class="k">def</span> <span class="nf">save_cropped_img</span><span class="p">(</span><span class="n">img_cropped</span><span class="p">,</span> <span class="n">xy_res</span><span class="p">,</span> <span class="n">z_res</span><span class="p">,</span> <span class="n">args</span><span class="p">,</span> <span class="n">cluster</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
     <span class="k">if</span> <span class="n">args</span><span class="o">.</span><span class="n">output</span><span class="p">:</span>
         <span class="n">save_path</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">output</span>
@@ -400,7 +407,7 @@ <h1>Source code for unravel.cluster_stats.crop_clusters</h1><div class="highligh
 
 
 <div class="viewcode-block" id="main">
-<a class="viewcode-back" href="../../../unravel.cluster_stats.html#unravel.cluster_stats.crop_clusters.main">[docs]</a>
+<a class="viewcode-back" href="../../../unravel/cluster_stats/crop_clusters.html#unravel.cluster_stats.crop_clusters.main">[docs]</a>
 <span class="k">def</span> <span class="nf">main</span><span class="p">():</span> 
     <span class="n">args</span> <span class="o">=</span> <span class="n">parse_args</span><span class="p">()</span>
 

diff --git a/unravel/docs/_build/html/_modules/unravel/cluster_stats/effect_sizes/effect_sizes.html b/unravel/docs/_build/html/_modules/unravel/cluster_stats/effect_sizes/effect_sizes.html
@@ -28,6 +28,7 @@
 <link rel="preload" as="font" type="font/woff2" crossorigin href="../../../../_static/vendor/fontawesome/6.5.2/webfonts/fa-regular-400.woff2" />
 
     <link rel="stylesheet" type="text/css" href="../../../../_static/pygments.css?v=a746c00c" />
+    <link rel="stylesheet" type="text/css" href="../../../../_static/togglebutton.css?v=13237357" />
     <link rel="stylesheet" type="text/css" href="../../../../_static/custom.css?v=165b5da3" />
 
   <!-- Pre-loaded scripts that we'll load fully later -->
@@ -38,6 +39,12 @@
     <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>let toggleHintShow = 'Click to show';</script>
+    <script>let toggleHintHide = 'Click to hide';</script>
+    <script>let toggleOpenOnPrint = 'true';</script>
+    <script src="../../../../_static/togglebutton.js?v=4a39c7ea"></script>
+    <script>var togglebuttonSelector = '.toggle, .admonition.dropdown';</script>
+    <script>var togglebuttonSelector = '.toggle, .admonition.dropdown';</script>
     <script>DOCUMENTATION_OPTIONS.pagename = '_modules/unravel/cluster_stats/effect_sizes/effect_sizes';</script>
     <link rel="icon" href="../../../../_static/favicon.png"/>
     <link rel="index" title="Index" href="../../../../genindex.html" />
@@ -151,8 +158,8 @@
 
 
 <li class="nav-item pst-header-nav-item">
-  <a class="nav-link nav-internal" href="../../../../modules.html">
-    unravel
+  <a class="nav-link nav-internal" href="../../../../unravel/toc.html">
+    unravel package
   </a>
 </li>
 
@@ -264,8 +271,8 @@
 
 
 <li class="nav-item pst-header-nav-item">
-  <a class="nav-link nav-internal" href="../../../../modules.html">
-    unravel
+  <a class="nav-link nav-internal" href="../../../../unravel/toc.html">
+    unravel package
   </a>
 </li>
 
@@ -363,7 +370,7 @@ <h1>Source code for unravel.cluster_stats.effect_sizes.effect_sizes</h1><div cla
 <span class="kn">from</span> <span class="nn">unravel.core.argparse_utils</span> <span class="kn">import</span> <span class="n">SuppressMetavar</span><span class="p">,</span> <span class="n">SM</span>
 
 <div class="viewcode-block" id="parse_args">
-<a class="viewcode-back" href="../../../../unravel.cluster_stats.effect_sizes.html#unravel.cluster_stats.effect_sizes.effect_sizes.parse_args">[docs]</a>
+<a class="viewcode-back" href="../../../../unravel/cluster_stats/effect_sizes/effect_sizes.html#unravel.cluster_stats.effect_sizes.effect_sizes.parse_args">[docs]</a>
 <span class="k">def</span> <span class="nf">parse_args</span><span class="p">():</span>
     <span class="n">parser</span> <span class="o">=</span> <span class="n">argparse</span><span class="o">.</span><span class="n">ArgumentParser</span><span class="p">(</span><span class="n">description</span><span class="o">=</span><span class="s1">&#39;&#39;&#39;Calculates the effect size for a comparison between two groups for each cluster [or a valid cluster list]&#39;&#39;&#39;</span><span class="p">,</span> <span class="n">formatter_class</span><span class="o">=</span><span class="n">SuppressMetavar</span><span class="p">)</span>
     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-i&#39;</span><span class="p">,</span> <span class="s1">&#39;--input_csv&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;CSV with densities (Columns: Samples, Conditions, Cluster_1, Cluster_2, ...)&#39;</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>
@@ -391,7 +398,7 @@ <h1>Source code for unravel.cluster_stats.effect_sizes.effect_sizes</h1><div cla
 
 <span class="c1"># Create a condition selector to handle pooling of data</span>
 <div class="viewcode-block" id="condition_selector">
-<a class="viewcode-back" href="../../../../unravel.cluster_stats.effect_sizes.html#unravel.cluster_stats.effect_sizes.effect_sizes.condition_selector">[docs]</a>
+<a class="viewcode-back" href="../../../../unravel/cluster_stats/effect_sizes/effect_sizes.html#unravel.cluster_stats.effect_sizes.effect_sizes.condition_selector">[docs]</a>
 <span class="k">def</span> <span class="nf">condition_selector</span><span class="p">(</span><span class="n">df</span><span class="p">,</span> <span class="n">condition</span><span class="p">,</span> <span class="n">unique_conditions</span><span class="p">,</span> <span class="n">condition_column</span><span class="o">=</span><span class="s1">&#39;Conditions&#39;</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Create a condition selector to handle pooling of data in a DataFrame based on specified conditions.</span>
 <span class="sd">    This function checks if the &#39;condition&#39; is exactly present in the &#39;Conditions&#39; column or is a prefix of any condition in this column. </span>
@@ -417,7 +424,7 @@ <h1>Source code for unravel.cluster_stats.effect_sizes.effect_sizes</h1><div cla
 
 <span class="c1"># Calculate the effect size for each cluster and sex</span>
 <div class="viewcode-block" id="hedges_g">
-<a class="viewcode-back" href="../../../../unravel.cluster_stats.effect_sizes.html#unravel.cluster_stats.effect_sizes.effect_sizes.hedges_g">[docs]</a>
+<a class="viewcode-back" href="../../../../unravel/cluster_stats/effect_sizes/effect_sizes.html#unravel.cluster_stats.effect_sizes.effect_sizes.hedges_g">[docs]</a>
 <span class="k">def</span> <span class="nf">hedges_g</span><span class="p">(</span><span class="n">df</span><span class="p">,</span> <span class="n">condition_1</span><span class="p">,</span> <span class="n">condition_2</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">read_csv</span><span class="p">(</span><span class="n">df</span><span class="p">)</span>
@@ -487,7 +494,7 @@ <h1>Source code for unravel.cluster_stats.effect_sizes.effect_sizes</h1><div cla
 
 
 <div class="viewcode-block" id="filter_dataframe">
-<a class="viewcode-back" href="../../../../unravel.cluster_stats.effect_sizes.html#unravel.cluster_stats.effect_sizes.effect_sizes.filter_dataframe">[docs]</a>
+<a class="viewcode-back" href="../../../../unravel/cluster_stats/effect_sizes/effect_sizes.html#unravel.cluster_stats.effect_sizes.effect_sizes.filter_dataframe">[docs]</a>
 <span class="k">def</span> <span class="nf">filter_dataframe</span><span class="p">(</span><span class="n">df</span><span class="p">,</span> <span class="n">cluster_list</span><span class="p">):</span>
     <span class="c1"># If no clusters provided, return the original DataFrame</span>
     <span class="k">if</span> <span class="n">cluster_list</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
@@ -499,7 +506,7 @@ <h1>Source code for unravel.cluster_stats.effect_sizes.effect_sizes</h1><div cla
 
 
 <div class="viewcode-block" id="main">
-<a class="viewcode-back" href="../../../../unravel.cluster_stats.effect_sizes.html#unravel.cluster_stats.effect_sizes.effect_sizes.main">[docs]</a>
+<a class="viewcode-back" href="../../../../unravel/cluster_stats/effect_sizes/effect_sizes.html#unravel.cluster_stats.effect_sizes.effect_sizes.main">[docs]</a>
 <span class="k">def</span> <span class="nf">main</span><span class="p">():</span>
     <span class="n">args</span> <span class="o">=</span> <span class="n">parse_args</span><span class="p">()</span>