make html

unravel/docs/_build/html/_modules/unravel/cluster_stats/brain_model.html

@@ -354,14 +354,24 @@ <h1>Source code for unravel.cluster_stats.brain_model</h1><div class="highlight"
 <span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">Use ``cluster_brain_model`` from UNRAVEL to prep .nii.gz and RGBA .txt for vizualization in dsi_studio.</span>
 
-<span class="sd">Usage</span>
-<span class="sd">-----</span>
-<span class="sd">    cluster_brain_model -i input.csv -m -sa path/gubra_ano_split_25um.nii.gz -v</span>
+<span class="sd">Usage with CCFv3:</span>
+<span class="sd">-----------------</span>
+<span class="sd">    cluster_brain_model -i input.nii.gz -m -sa path/atlas_CCFv3_2020_30um_split.nii.gz -v </span>
 
-<span class="sd">The input image will be binarized and multiplied by the split atlas to apply region IDs.</span>
+<span class="sd">Usage with gubra atlas:</span>
+<span class="sd">-----------------------</span>
+<span class="sd">    cluster_brain_model -i input.nii.gz -m -sa path/gubra_ano_split_25um.nii.gz -v -ax 0 -s 2</span>
 
 <span class="sd">Outputs: </span>
-<span class="sd">    img_WB.nii.gz (bilateral version of cluster index w/ ABA colors)</span>
+<span class="sd">    - img_WB.nii.gz (bilateral version of cluster index w/ ABA colors)</span>
+<span class="sd">    - rgba.txt (RGBA values for each region in the cluster index)</span>
+
+<span class="sd">Note: </span>
+<span class="sd">    - The input image will be binarized and multiplied by the split atlas to apply region IDs.</span>
+<span class="sd">    - regional_summary_CCFv3-2020.csv is in UNRAVEL/unravel/core/csvs/</span>
+<span class="sd">    - It has columns: Region_ID, ID_Path, Region, Abbr, General_Region, R, G, B</span>
+<span class="sd">    - Alternatively, use regional_summary.csv or provide a custom CSV with the same columns.</span>
+<span class="sd">    - Use DSI Studio to visualize the cluster index with the RGBA values.</span>
 <span class="sd">&quot;&quot;&quot;</span>
 
 <span class="kn">import</span> <span class="nn">argparse</span>
@@ -384,9 +394,10 @@ <h1>Source code for unravel.cluster_stats.brain_model</h1><div class="highlight"
     <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="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>
     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-m&#39;</span><span class="p">,</span> <span class="s1">&#39;--mirror&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Mirror the image in the x-axis for a bilateral representation. 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;-ax&#39;</span><span class="p">,</span> <span class="s1">&#39;--axis&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Axis to flip the image along. Default: 0&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="nb">int</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;-s&#39;</span><span class="p">,</span> <span class="s1">&#39;--shift&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Number of voxels to shift content after flipping. Default: 2&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="nb">int</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;-ax&#39;</span><span class="p">,</span> <span class="s1">&#39;--axis&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Axis to flip the image along if mirroing. Default: 2&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="nb">int</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;-s&#39;</span><span class="p">,</span> <span class="s1">&#39;--shift&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Number of voxels to shift content after flipping. Default: 0&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="nb">int</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;-sa&#39;</span><span class="p">,</span> <span class="s1">&#39;--split_atlas&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;path/gubra_ano_split_25um.nii.gz. Default: gubra_ano_split_25um.nii.gz&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s1">&#39;gubra_ano_split_25um.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;-csv&#39;</span><span class="p">,</span> <span class="s1">&#39;--csv_path&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;CSV name or path/name.csv. Default: regional_summary_CCFv3-2020.csv&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s1">&#39;regional_summary_CCFv3-2020.csv&#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;-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="k">return</span> <span class="n">parser</span><span class="o">.</span><span class="n">parse_args</span><span class="p">()</span></div>
@@ -449,10 +460,12 @@ <h1>Source code for unravel.cluster_stats.brain_model</h1><div class="highlight"
     <span class="n">present_regions</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="n">histogram</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="mi">1</span> <span class="c1"># Add 1 to account for the background</span>
 
     <span class="c1"># Get R, G, B values for each region</span>
-    <span class="n">color_map</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">Path</span><span class="p">(</span><span class="vm">__file__</span><span class="p">)</span><span class="o">.</span><span class="n">parent</span><span class="o">.</span><span class="n">parent</span> <span class="o">/</span> <span class="s1">&#39;core&#39;</span> <span class="o">/</span> <span class="s1">&#39;csvs&#39;</span> <span class="o">/</span> <span class="s1">&#39;regional_summary.csv&#39;</span><span class="p">)</span> <span class="c1">#(Region_ID,ID_Path,Region,Abbr,General_Region,R,G,B)</span>
+    <span class="k">if</span> <span class="n">args</span><span class="o">.</span><span class="n">csv_path</span> <span class="o">==</span> <span class="s1">&#39;regional_summary.csv&#39;</span> <span class="ow">or</span> <span class="n">args</span><span class="o">.</span><span class="n">csv_path</span> <span class="o">==</span> <span class="s1">&#39;regional_summary_CCFv3-2020.csv&#39;</span><span class="p">:</span> 
+        <span class="n">color_map</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">Path</span><span class="p">(</span><span class="vm">__file__</span><span class="p">)</span><span class="o">.</span><span class="n">parent</span><span class="o">.</span><span class="n">parent</span> <span class="o">/</span> <span class="s1">&#39;core&#39;</span> <span class="o">/</span> <span class="s1">&#39;csvs&#39;</span> <span class="o">/</span> <span class="n">args</span><span class="o">.</span><span class="n">csv_path</span><span class="p">)</span> <span class="c1">#(Region_ID,ID_Path,Region,Abbr,General_Region,R,G,B)</span>
+    <span class="k">else</span><span class="p">:</span>
+        <span class="n">color_map</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">args</span><span class="o">.</span><span class="n">csv_path</span><span class="p">)</span>
 
     <span class="c1"># Delete rgba.txt if it exists (used for coloring the regions in DSI Studio)</span>
-
     <span class="k">if</span> <span class="n">Path</span><span class="p">(</span><span class="n">txt_output</span><span class="p">)</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
         <span class="n">Path</span><span class="p">(</span><span class="n">txt_output</span><span class="p">)</span><span class="o">.</span><span class="n">unlink</span><span class="p">()</span>
 

unravel/docs/_build/html/_modules/unravel/cluster_stats/cluster_summary.html

@@ -552,7 +552,9 @@ <h1>Source code for unravel.cluster_stats.cluster_summary</h1><div class="highli
             <span class="s1">&#39;-ci&#39;</span><span class="p">,</span> <span class="n">rev_cluster_index_path</span><span class="p">,</span>
             <span class="s1">&#39;-ids&#39;</span><span class="p">,</span> <span class="o">*</span><span class="n">valid_cluster_ids</span><span class="p">,</span>
             <span class="s1">&#39;-vcd&#39;</span><span class="p">,</span> <span class="n">valid_clusters_index_dir</span><span class="p">,</span>
-            <span class="s1">&#39;-a&#39;</span><span class="p">,</span> <span class="n">cfg</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">atlas</span>
+            <span class="s1">&#39;-a&#39;</span><span class="p">,</span> <span class="n">cfg</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">atlas</span><span class="p">,</span>
+            <span class="s1">&#39;-scsv&#39;</span><span class="p">,</span> <span class="n">cfg</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">sunburst_csv_path</span><span class="p">,</span>
+            <span class="s1">&#39;-icsv&#39;</span><span class="p">,</span> <span class="n">cfg</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">info_csv_path</span>
         <span class="p">]</span>
         <span class="k">if</span> <span class="n">cfg</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">output_rgb_lut</span><span class="p">:</span>
             <span class="n">index_args</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s1">&#39;-rgb&#39;</span><span class="p">)</span>
@@ -566,7 +568,8 @@ <h1>Source code for unravel.cluster_stats.cluster_summary</h1><div class="highli
             <span class="s1">&#39;-i&#39;</span><span class="p">,</span> <span class="n">valid_cluster_index_path</span><span class="p">,</span>
             <span class="s1">&#39;-ax&#39;</span><span class="p">,</span> <span class="n">cfg</span><span class="o">.</span><span class="n">brain</span><span class="o">.</span><span class="n">axis</span><span class="p">,</span>
             <span class="s1">&#39;-s&#39;</span><span class="p">,</span> <span class="n">cfg</span><span class="o">.</span><span class="n">brain</span><span class="o">.</span><span class="n">shift</span><span class="p">,</span>
-            <span class="s1">&#39;-sa&#39;</span><span class="p">,</span> <span class="n">cfg</span><span class="o">.</span><span class="n">brain</span><span class="o">.</span><span class="n">split_atlas</span>
+            <span class="s1">&#39;-sa&#39;</span><span class="p">,</span> <span class="n">cfg</span><span class="o">.</span><span class="n">brain</span><span class="o">.</span><span class="n">split_atlas</span><span class="p">,</span>
+            <span class="s1">&#39;-csv&#39;</span><span class="p">,</span> <span class="n">cfg</span><span class="o">.</span><span class="n">brain</span><span class="o">.</span><span class="n">csv_path</span>
         <span class="p">]</span>
         <span class="k">if</span> <span class="n">cfg</span><span class="o">.</span><span class="n">brain</span><span class="o">.</span><span class="n">mirror</span><span class="p">:</span> 
             <span class="n">brain_args</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s1">&#39;-m&#39;</span><span class="p">)</span>
@@ -585,7 +588,8 @@ <h1>Source code for unravel.cluster_stats.cluster_summary</h1><div class="highli
         <span class="n">table_args</span> <span class="o">=</span> <span class="p">[</span>
             <span class="s1">&#39;-vcd&#39;</span><span class="p">,</span> <span class="n">valid_clusters_index_dir</span><span class="p">,</span>
             <span class="s1">&#39;-t&#39;</span><span class="p">,</span> <span class="n">cfg</span><span class="o">.</span><span class="n">table</span><span class="o">.</span><span class="n">top_regions</span><span class="p">,</span>
-            <span class="s1">&#39;-pv&#39;</span><span class="p">,</span> <span class="n">cfg</span><span class="o">.</span><span class="n">table</span><span class="o">.</span><span class="n">percent_vol</span>
+            <span class="s1">&#39;-pv&#39;</span><span class="p">,</span> <span class="n">cfg</span><span class="o">.</span><span class="n">table</span><span class="o">.</span><span class="n">percent_vol</span><span class="p">,</span>
+            <span class="s1">&#39;-csv&#39;</span><span class="p">,</span> <span class="n">cfg</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">info_csv_path</span>
         <span class="p">]</span>
         <span class="k">if</span> <span class="n">args</span><span class="o">.</span><span class="n">verbose</span><span class="p">:</span>
             <span class="n">table_args</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s1">&#39;-v&#39;</span><span class="p">)</span>
@@ -629,7 +633,8 @@ <h1>Source code for unravel.cluster_stats.cluster_summary</h1><div class="highli
         <span class="c1"># Run cluster_legend</span>
         <span class="k">if</span> <span class="n">Path</span><span class="p">(</span><span class="s1">&#39;valid_clusters_tables_and_legend&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
             <span class="n">legend_args</span> <span class="o">=</span> <span class="p">[</span>
-                <span class="s1">&#39;-p&#39;</span><span class="p">,</span> <span class="s1">&#39;valid_clusters_tables_and_legend&#39;</span>
+                <span class="s1">&#39;-p&#39;</span><span class="p">,</span> <span class="s1">&#39;valid_clusters_tables_and_legend&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;-csv&#39;</span><span class="p">,</span> <span class="n">cfg</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">info_csv_path</span>
             <span class="p">]</span>
             <span class="n">run_script</span><span class="p">(</span><span class="s1">&#39;cluster_legend&#39;</span><span class="p">,</span> <span class="n">legend_args</span><span class="p">)</span>