make html

unravel/docs/_build/html/_modules/index.html

@@ -412,6 +412,7 @@ <h1>All modules for which code is available</h1>
 <li><a href="unravel/segment/brain_mask.html">unravel.segment.brain_mask</a></li>
 <li><a href="unravel/segment/copy_tifs.html">unravel.segment.copy_tifs</a></li>
 <li><a href="unravel/segment/ilastik_pixel_classification.html">unravel.segment.ilastik_pixel_classification</a></li>
+<li><a href="unravel/segment/labels_to_masks.html">unravel.segment.labels_to_masks</a></li>
 <li><a href="unravel/unravel_commands.html">unravel.unravel_commands</a></li>
 <li><a href="unravel/utilities/aggregate_files_from_sample_dirs.html">unravel.utilities.aggregate_files_from_sample_dirs</a></li>
 <li><a href="unravel/utilities/aggregate_files_recursively.html">unravel.utilities.aggregate_files_recursively</a></li>

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

@@ -554,7 +554,7 @@ <h1>Source code for unravel.cluster_stats.cluster_summary</h1><div class="highli
             <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="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="s1">&#39;-in&#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>

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

@@ -391,8 +391,8 @@ <h1>Source code for unravel.cluster_stats.index</h1><div class="highlight"><pre>
     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-vcd&#39;</span><span class="p">,</span> <span class="s1">&#39;--valid_clusters_dir&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;path/name_of_the_output_directory. Default: valid_clusters&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s1">&#39;_valid_clusters&#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;--atlas&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;path/atlas.nii.gz (Default: path/gubra_ano_combined_25um.nii.gz)&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s1">&#39;/usr/local/unravel/atlases/gubra/gubra_ano_combined_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;-rgb&#39;</span><span class="p">,</span> <span class="s1">&#39;--output_rgb_lut&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Output sunburst_RGBs.csv if flag provided (for Allen brain atlas coloring)&#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">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-scsv&#39;</span><span class="p">,</span> <span class="s1">&#39;--sunburst_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: sunburst_IDPath_Abbrv_CCFv3-2020.csv&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s1">&#39;sunburst_IDPath_Abbrv_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;-icsv&#39;</span><span class="p">,</span> <span class="s1">&#39;--info_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: CCFv3-2020_info.csv&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s1">&#39;CCFv3-2020_info.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;-scsv&#39;</span><span class="p">,</span> <span class="s1">&#39;--sunburst_csv&#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: sunburst_IDPath_Abbrv_CCFv3-2020.csv&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s1">&#39;sunburst_IDPath_Abbrv_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;-in&#39;</span><span class="p">,</span> <span class="s1">&#39;--info&#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: CCFv3-2020_info.csv&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s1">&#39;CCFv3-2020_info.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>
@@ -462,15 +462,15 @@ <h1>Source code for unravel.cluster_stats.index</h1><div class="highlight"><pre>
 
     <span class="c1"># Parallel processing of sunburst plots</span>
     <span class="k">with</span> <span class="n">ThreadPoolExecutor</span><span class="p">()</span> <span class="k">as</span> <span class="n">executor</span><span class="p">:</span>
-        <span class="n">futures</span> <span class="o">=</span> <span class="p">[</span><span class="n">executor</span><span class="o">.</span><span class="n">submit</span><span class="p">(</span><span class="n">generate_sunburst</span><span class="p">,</span> <span class="n">cluster</span><span class="p">,</span> <span class="n">img</span><span class="p">,</span> <span class="n">atlas</span><span class="p">,</span> <span class="n">xyz_res_in_um</span><span class="p">,</span> <span class="n">data_type</span><span class="p">,</span> <span class="n">output_dir</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">sunburst_csv_path</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">info_csv_path</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">output_rgb_lut</span><span class="p">)</span> <span class="k">for</span> <span class="n">cluster</span> <span class="ow">in</span> <span class="n">args</span><span class="o">.</span><span class="n">valid_cluster_ids</span><span class="p">]</span>
+        <span class="n">futures</span> <span class="o">=</span> <span class="p">[</span><span class="n">executor</span><span class="o">.</span><span class="n">submit</span><span class="p">(</span><span class="n">generate_sunburst</span><span class="p">,</span> <span class="n">cluster</span><span class="p">,</span> <span class="n">img</span><span class="p">,</span> <span class="n">atlas</span><span class="p">,</span> <span class="n">xyz_res_in_um</span><span class="p">,</span> <span class="n">data_type</span><span class="p">,</span> <span class="n">output_dir</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">sunburst_csv</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">info</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">output_rgb_lut</span><span class="p">)</span> <span class="k">for</span> <span class="n">cluster</span> <span class="ow">in</span> <span class="n">args</span><span class="o">.</span><span class="n">valid_cluster_ids</span><span class="p">]</span>
         <span class="k">for</span> <span class="n">future</span> <span class="ow">in</span> <span class="n">futures</span><span class="p">:</span>
             <span class="n">future</span><span class="o">.</span><span class="n">result</span><span class="p">()</span>  <span class="c1"># Wait for all threads to complete</span>
 
     <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;    Saved valid cluster index: </span><span class="si">{</span><span class="n">output_image_path</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
     <span class="n">nib</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="n">nib</span><span class="o">.</span><span class="n">Nifti1Image</span><span class="p">(</span><span class="n">valid_cluster_index</span><span class="p">,</span> <span class="n">nii</span><span class="o">.</span><span class="n">affine</span><span class="p">,</span> <span class="n">nii</span><span class="o">.</span><span class="n">header</span><span class="p">),</span> <span class="n">output_image_path</span><span class="p">)</span>
 
     <span class="c1"># Generate the sunburst plot for the valid cluster index</span>
-    <span class="n">sunburst_df</span> <span class="o">=</span> <span class="n">sunburst</span><span class="p">(</span><span class="n">valid_cluster_index</span><span class="p">,</span> <span class="n">atlas</span><span class="p">,</span> <span class="n">xyz_res_in_um</span><span class="p">,</span> <span class="n">output_dir</span> <span class="o">/</span> <span class="s1">&#39;valid_clusters_sunburst.csv&#39;</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">sunburst_csv_path</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">info_csv_path</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">output_rgb_lut</span><span class="p">)</span>
+    <span class="n">sunburst_df</span> <span class="o">=</span> <span class="n">sunburst</span><span class="p">(</span><span class="n">valid_cluster_index</span><span class="p">,</span> <span class="n">atlas</span><span class="p">,</span> <span class="n">xyz_res_in_um</span><span class="p">,</span> <span class="n">output_dir</span> <span class="o">/</span> <span class="s1">&#39;valid_clusters_sunburst.csv&#39;</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">sunburst_csv</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">info</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">output_rgb_lut</span><span class="p">)</span>
 
     <span class="nb">print</span><span class="p">(</span><span class="n">sunburst_df</span><span class="p">)</span>
 

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

@@ -453,6 +453,14 @@ <h1>Source code for unravel.cluster_stats.legend</h1><div class="highlight"><pre
     <span class="c1"># Filter out files that start with legend</span>
     <span class="n">xlsx_files</span> <span class="o">=</span> <span class="p">[</span><span class="n">f</span> <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">xlsx_files</span> <span class="k">if</span> <span class="ow">not</span> <span class="nb">str</span><span class="p">(</span><span class="n">f</span><span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;/&#39;</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;legend&#39;</span><span class="p">)]</span>
 
+    <span class="k">if</span> <span class="n">xlsx_files</span> <span class="o">==</span> <span class="p">[]:</span>
+        <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;</span><span class="se">\n</span><span class="s2">    [red1]No *_valid_clusters_table.xlsx files found in the specified directory. Exiting...</span><span class="se">\n</span><span class="s2">&quot;</span><span class="p">)</span>
+        <span class="kn">import</span> <span class="nn">sys</span> <span class="p">;</span> <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">()</span>
+    <span class="k">else</span><span class="p">:</span>
+        <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">Processing:&#39;</span><span class="p">)</span>
+        <span class="k">for</span> <span class="n">file</span> <span class="ow">in</span> <span class="n">xlsx_files</span><span class="p">:</span>
+            <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;    </span><span class="si">{</span><span class="n">file</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
+
     <span class="c1"># Initialize a set to store unique regions from all files, accounting for headers in the second row</span>
     <span class="n">all_unique_regions</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span> <span class="c1"># Using a set to avoid duplicates</span>
 
@@ -463,7 +471,12 @@ <h1>Source code for unravel.cluster_stats.legend</h1><div class="highlight"><pre
 
     <span class="c1"># Convert the set to a sorted list for easier reading</span>
     <span class="n">all_unique_regions</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="n">all_unique_regions</span><span class="p">))</span>
-    <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;</span><span class="se">\n</span><span class="si">{</span><span class="n">all_unique_regions</span><span class="si">=}</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>
+
+    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">all_unique_regions</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+        <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;</span><span class="se">\n</span><span class="s2">    [red1]No regions found in the xlsx files. Headers expected in the second row. Exiting...</span><span class="se">\n</span><span class="s2">&quot;</span><span class="p">)</span>
+        <span class="kn">import</span> <span class="nn">sys</span> <span class="p">;</span> <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">()</span>
+
+    <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">Regions: </span><span class="si">{</span><span class="n">all_unique_regions</span><span class="si">}</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>
 
     <span class="c1"># Specify the column names you want to load</span>
     <span class="n">columns_to_load</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;structure_id_path&#39;</span><span class="p">,</span> <span class="s1">&#39;very_general_region&#39;</span><span class="p">,</span>  <span class="s1">&#39;collapsed_region_name&#39;</span><span class="p">,</span> <span class="s1">&#39;abbreviation&#39;</span><span class="p">,</span> <span class="s1">&#39;collapsed_region&#39;</span><span class="p">,</span> <span class="s1">&#39;other_abbreviation&#39;</span><span class="p">,</span> <span class="s1">&#39;other_abbreviation_defined&#39;</span><span class="p">,</span> <span class="s1">&#39;layer&#39;</span><span class="p">,</span> <span class="s1">&#39;sunburst&#39;</span><span class="p">]</span>

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

@@ -402,6 +402,7 @@ <h1>Source code for unravel.cluster_stats.mean_IF</h1><div class="highlight"><pr
     <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>
 
 
+<span class="c1"># TODO: process each cluster in parallel</span>
 
 <div class="viewcode-block" id="calculate_mean_intensity_in_clusters">
 <a class="viewcode-back" href="../../../unravel/cluster_stats/index.html#unravel.cluster_stats.mean_IF.calculate_mean_intensity_in_clusters">[docs]</a>

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

@@ -379,6 +379,7 @@ <h1>Source code for unravel.cluster_stats.mean_IF_summary</h1><div class="highli
 
 <span class="kn">import</span> <span class="nn">argparse</span>
 <span class="kn">import</span> <span class="nn">matplotlib</span> <span class="k">as</span> <span class="nn">mpl</span>
+<span class="n">mpl</span><span class="o">.</span><span class="n">use</span><span class="p">(</span><span class="s1">&#39;Agg&#39;</span><span class="p">)</span>
 <span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
 <span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
 <span class="kn">import</span> <span class="nn">os</span>