deploy: 953b0ae

b-heifets · Aug 29, 2024 · 36df6fd · 36df6fd
1 parent 680240c
commit 36df6fd
Show file tree

Hide file tree

Showing 210 changed files with 4,696 additions and 4,782 deletions.
diff --git a/_modules/index.html b/_modules/index.html
@@ -370,9 +370,8 @@ <h1>All modules for which code is available</h1>
 <li><a href="unravel/cluster_stats/sunburst.html">unravel.cluster_stats.sunburst</a></li>
 <li><a href="unravel/cluster_stats/table.html">unravel.cluster_stats.table</a></li>
 <li><a href="unravel/cluster_stats/validation.html">unravel.cluster_stats.validation</a></li>
-<li><a href="unravel/core/argparse_utils.html">unravel.core.argparse_utils</a></li>
-<li><a href="unravel/core/argparse_utils_rich.html">unravel.core.argparse_utils_rich</a></li>
 <li><a href="unravel/core/config.html">unravel.core.config</a></li>
+<li><a href="unravel/core/help_formatter.html">unravel.core.help_formatter</a></li>
 <li><a href="unravel/core/img_io.html">unravel.core.img_io</a></li>
 <li><a href="unravel/core/img_tools.html">unravel.core.img_tools</a></li>
 <li><a href="unravel/core/utils.html">unravel.core.utils</a></li>

diff --git a/_modules/unravel/cluster_stats/brain_model.html b/_modules/unravel/cluster_stats/brain_model.html
diff --git a/_modules/unravel/cluster_stats/crop.html b/_modules/unravel/cluster_stats/crop.html
@@ -354,16 +354,28 @@ <h1>Source code for unravel.cluster_stats.crop</h1><div class="highlight"><pre>
 <span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">Use ``cstats_crop`` from UNRAVEL to load image, load bounding box, crop cluster, and save as .nii.gz.</span>
 
-<span class="sd">Usage</span>
-<span class="sd">-----</span>
-<span class="sd">    cstats_crop -i path/img.nii.gz -b path/bbox.txt -o path/output_img.nii.gz -a -x $XY -z $Z -v</span>
+<span class="sd">Note:</span>
+<span class="sd">    - -x and -z need to be provided if the resolution is not extracted from the image metadata.</span>
+<span class="sd">    - Use -a, -b, or -c to specify the crop method.</span>
+
+<span class="sd">Usage with all clusters:</span>
+<span class="sd">------------------------</span>
+<span class="sd">    cstats_crop -i path/img.nii.gz -o path/output_img.nii.gz -a [-x $XY] [-z $Z] [-v]</span>
+
+<span class="sd">Usage with a bounding box:</span>
+<span class="sd">--------------------------</span>
+<span class="sd">    cstats_crop -i path/img.nii.gz -o path/output_img.nii.gz -b path/bbox.txt [-x $XY] [-z $Z] [-v]</span>
+<span class="sd">    </span>
+<span class="sd">Usage with a cluster ID:</span>
+<span class="sd">------------------------</span>
+<span class="sd">    cstats_crop -i path/img.nii.gz -o path/output_img.nii.gz -c 1 [-x $XY] [-z $Z] [-v]</span>
 <span class="sd">&quot;&quot;&quot;</span>
 
-<span class="kn">import</span> <span class="nn">argparse</span>
 <span class="kn">from</span> <span class="nn">rich.traceback</span> <span class="kn">import</span> <span class="n">install</span>
 <span class="kn">from</span> <span class="nn">rich</span> <span class="kn">import</span> <span class="nb">print</span>
 
-<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>
+<span class="kn">from</span> <span class="nn">unravel.core.help_formatter</span> <span class="kn">import</span> <span class="n">RichArgumentParser</span><span class="p">,</span> <span class="n">SuppressMetavar</span><span class="p">,</span> <span class="n">SM</span>
+
 <span class="kn">from</span> <span class="nn">unravel.core.config</span> <span class="kn">import</span> <span class="n">Configuration</span>
 <span class="kn">from</span> <span class="nn">unravel.core.img_io</span> <span class="kn">import</span> <span class="n">load_3D_img</span><span class="p">,</span> <span class="n">save_as_nii</span>
 <span class="kn">from</span> <span class="nn">unravel.core.img_tools</span> <span class="kn">import</span> <span class="n">find_bounding_box</span><span class="p">,</span> <span class="n">cluster_IDs</span><span class="p">,</span> <span class="n">crop</span>
@@ -373,16 +385,22 @@ <h1>Source code for unravel.cluster_stats.crop</h1><div class="highlight"><pre>
 <div class="viewcode-block" id="parse_args">
 <a class="viewcode-back" href="../../../unravel/cluster_stats/crop.html#unravel.cluster_stats.crop.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">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>
-    <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-o&#39;</span><span class="p">,</span> <span class="s1">&#39;--output&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;path/output_img.nii.gz&#39;</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</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;-b&#39;</span><span class="p">,</span> <span class="s1">&#39;--bbox&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;path/bbox.txt&#39;</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</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;-c&#39;</span><span class="p">,</span> <span class="s1">&#39;--cluster&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Cluster intensity to get bbox and crop&#39;</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</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;-a&#39;</span><span class="p">,</span> <span class="s1">&#39;--all_clusters&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Crop each cluster. Default: False&#39;</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s1">&#39;store_true&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">False</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;-x&#39;</span><span class="p">,</span> <span class="s1">&#39;--xy_res&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;xy voxel size in microns for the raw data&#39;</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="nb">float</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</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;-z&#39;</span><span class="p">,</span> <span class="s1">&#39;--z_res&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;z voxel size in microns for the raw data&#39;</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="nb">float</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</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;-v&#39;</span><span class="p">,</span> <span class="s1">&#39;--verbose&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Increase verbosity. Default: False&#39;</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s1">&#39;store_true&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
-    <span class="n">parser</span><span class="o">.</span><span class="n">epilog</span> <span class="o">=</span> <span class="vm">__doc__</span>
+    <span class="n">parser</span> <span class="o">=</span> <span class="n">RichArgumentParser</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">add_help</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">docstring</span><span class="o">=</span><span class="vm">__doc__</span><span class="p">)</span>
+
+    <span class="n">reqs</span> <span class="o">=</span> <span class="n">parser</span><span class="o">.</span><span class="n">add_argument_group</span><span class="p">(</span><span class="s1">&#39;Required arguments&#39;</span><span class="p">)</span>
+    <span class="n">reqs</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>
+
+    <span class="n">opts</span> <span class="o">=</span> <span class="n">parser</span><span class="o">.</span><span class="n">add_argument_group</span><span class="p">(</span><span class="s1">&#39;Optional args&#39;</span><span class="p">)</span>
+    <span class="n">opts</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-o&#39;</span><span class="p">,</span> <span class="s1">&#39;--output&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;path/output_img.nii.gz&#39;</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>
+    <span class="n">opts</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-b&#39;</span><span class="p">,</span> <span class="s1">&#39;--bbox&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;path/bbox.txt&#39;</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>
+    <span class="n">opts</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-c&#39;</span><span class="p">,</span> <span class="s1">&#39;--cluster&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Cluster ID/intensity to get bbox and crop&#39;</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>
+    <span class="n">opts</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-a&#39;</span><span class="p">,</span> <span class="s1">&#39;--all_clusters&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Crop each cluster. Default: False&#39;</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s1">&#39;store_true&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+    <span class="n">opts</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-x&#39;</span><span class="p">,</span> <span class="s1">&#39;--xy_res&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;xy voxel size in microns for the raw data&#39;</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="nb">float</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>
+    <span class="n">opts</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-z&#39;</span><span class="p">,</span> <span class="s1">&#39;--z_res&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;z voxel size in microns for the raw data&#39;</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="nb">float</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>
+
+    <span class="n">general</span> <span class="o">=</span> <span class="n">parser</span><span class="o">.</span><span class="n">add_argument_group</span><span class="p">(</span><span class="s1">&#39;General arguments&#39;</span><span class="p">)</span>
+    <span class="n">general</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-v&#39;</span><span class="p">,</span> <span class="s1">&#39;--verbose&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Increase verbosity. Default: False&#39;</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s1">&#39;store_true&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+
     <span class="k">return</span> <span class="n">parser</span><span class="o">.</span><span class="n">parse_args</span><span class="p">()</span></div>