make html

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

@@ -372,7 +372,7 @@ <h1>Source code for unravel.cluster_stats.brain_model</h1><div class="highlight"
 <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">rich.traceback</span> <span class="kn">import</span> <span class="n">install</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.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.config</span> <span class="kn">import</span> <span class="n">Configuration</span> 
 <span class="kn">from</span> <span class="nn">unravel.core.utils</span> <span class="kn">import</span> <span class="n">log_command</span><span class="p">,</span> <span class="n">verbose_start_msg</span><span class="p">,</span> <span class="n">verbose_end_msg</span>
 <span class="kn">from</span> <span class="nn">unravel.voxel_stats.mirror</span> <span class="kn">import</span> <span class="n">mirror</span>
@@ -392,6 +392,8 @@ <h1>Source code for unravel.cluster_stats.brain_model</h1><div class="highlight"
     <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: Consider consolidating regional_summary.csv (regional_summary_CCFv3-2017.csv) and regional_summary_CCFv3-2020.csv and ideally add logic to match usage automatic (i.e., no extra arg needed)</span>
+
 
 <div class="viewcode-block" id="main">
 <a class="viewcode-back" href="../../../unravel/cluster_stats/brain_model.html#unravel.cluster_stats.brain_model.main">[docs]</a>

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

@@ -443,11 +443,11 @@ <h1>Source code for unravel.cluster_stats.org_data</h1><div class="highlight"><p
             <span class="n">cluster_correction_dir</span> <span class="o">=</span> <span class="n">validation_dir_name</span>
 
         <span class="c1"># Regular expression to match the part before and after &#39;q*&#39; to remove any suffix added to the rev_cluster_index&lt;suffix&gt;.nii.gz</span>
-        <span class="n">pattern</span> <span class="o">=</span> <span class="sa">r</span><span class="s1">&#39;(.*q\d+\.\d+)(_.*)&#39;</span>
+        <span class="n">pattern</span> <span class="o">=</span> <span class="sa">r</span><span class="s1">&#39;(.*q\d+\.\d+)(_.+)?&#39;</span>  <span class="c1"># This also works when there is no &quot;suffix&quot;</span>
         <span class="n">match</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">pattern</span><span class="p">,</span> <span class="n">cluster_correction_dir</span><span class="p">)</span>
         <span class="k">if</span> <span class="n">match</span><span class="p">:</span>
             <span class="n">cluster_correction_dir</span> <span class="o">=</span> <span class="n">match</span><span class="o">.</span><span class="n">group</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
-            <span class="n">suffix</span> <span class="o">=</span> <span class="n">match</span><span class="o">.</span><span class="n">group</span><span class="p">(</span><span class="mi">2</span><span class="p">)[</span><span class="mi">1</span><span class="p">:]</span>  <span class="c1"># Remove the leading underscore</span>
+            <span class="n">suffix</span> <span class="o">=</span> <span class="n">match</span><span class="o">.</span><span class="n">group</span><span class="p">(</span><span class="mi">2</span><span class="p">)[</span><span class="mi">1</span><span class="p">:]</span> <span class="k">if</span> <span class="n">match</span><span class="o">.</span><span class="n">group</span><span class="p">(</span><span class="mi">2</span><span class="p">)</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span>  <span class="c1"># This gets the string after the q value if there is one</span>
         <span class="k">else</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 match found in cluster_org_data</span><span class="se">\n</span><span class="s2">&quot;</span><span class="p">)</span>
 

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

@@ -359,6 +359,10 @@ <h1>Source code for unravel.cluster_stats.recursively_mirror_rev_cluster_indices
 <span class="sd">    cluster_mirror_indices -m RH -v</span>
 <span class="sd">    </span>
 <span class="sd">Use this command after ``cluster_fdr`` to mirror the cluster indices for the other side of the brain before running ``cluster_validation``.  </span>
+
+<span class="sd">Note:</span>
+<span class="sd">    - Use -ax 2 and -s 0 for the CCFv3 2020 atlas.</span>
+<span class="sd">    - Use -ax 0 and -s 2 for the 25 um Gubra atlas</span>
 <span class="sd">&quot;&quot;&quot;</span>
 
 <span class="kn">import</span> <span class="nn">argparse</span>
@@ -380,15 +384,13 @@ <h1>Source code for unravel.cluster_stats.recursively_mirror_rev_cluster_indices
     <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;-m&#39;</span><span class="p">,</span> <span class="s1">&#39;--mas_side&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Side of the brain corresponding to the mask used for ``vstats`` and ``cluster_fdr`` (RH or LH)&#39;</span><span class="p">,</span> <span class="n">choices</span><span class="o">=</span><span class="p">[</span><span class="s1">&#39;RH&#39;</span><span class="p">,</span> <span class="s1">&#39;LH&#39;</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;-p&#39;</span><span class="p">,</span> <span class="s1">&#39;--pattern&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Glob pattern to match files. Default: **/*rev_cluster_index.nii.gz&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s1">&#39;**/*rev_cluster_index.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;-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. 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;-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>
 
 
-<span class="c1"># TODO: adapt to work with CCFv3 images if needed </span>
-
 
 <div class="viewcode-block" id="process_file">
 <a class="viewcode-back" href="../../../unravel/cluster_stats/recursively_mirror_rev_cluster_indices.html#unravel.cluster_stats.recursively_mirror_rev_cluster_indices.process_file">[docs]</a>

unravel/docs/_build/html/_modules/unravel/core/img_io.html

@@ -597,6 +597,8 @@ <h1>Source code for unravel.core.img_io</h1><div class="highlight"><pre>
     <span class="k">def</span> <span class="nf">load_single_tif</span><span class="p">(</span><span class="n">tif_file</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;Load a single .tif file using OpenCV and return the ndarray.&quot;&quot;&quot;</span>
         <span class="n">img</span> <span class="o">=</span> <span class="n">cv2</span><span class="o">.</span><span class="n">imread</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">tif_file</span><span class="p">),</span> <span class="n">cv2</span><span class="o">.</span><span class="n">IMREAD_UNCHANGED</span><span class="p">)</span>
+        <span class="k">if</span> <span class="n">img</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Failed to load image: </span><span class="si">{</span><span class="n">tif_file</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
         <span class="k">return</span> <span class="n">img</span>
     <span class="n">tif_files</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">Path</span><span class="p">(</span><span class="n">tif_path</span><span class="p">)</span><span class="o">.</span><span class="n">parent</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="s2">&quot;*.tif&quot;</span><span class="p">))</span>
     <span class="k">if</span> <span class="n">parallel_loading</span><span class="p">:</span>