make html

unravel/docs/_build/html/_modules/unravel/image_tools/atlas/relabel_nii.html

@@ -410,7 +410,7 @@ <h1>Source code for unravel.image_tools.atlas.relabel_nii</h1><div class="highli
 
     <span class="c1"># Load the NIfTI image</span>
     <span class="n">nii</span> <span class="o">=</span> <span class="n">nib</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">args</span><span class="o">.</span><span class="n">input</span><span class="p">)</span>
-    <span class="n">img</span> <span class="o">=</span> <span class="n">nii</span><span class="o">.</span><span class="n">get_fdata</span><span class="p">(</span><span class="n">dtye</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">float32</span><span class="p">)</span>
+    <span class="n">img</span> <span class="o">=</span> <span class="n">nii</span><span class="o">.</span><span class="n">get_fdata</span><span class="p">(</span><span class="n">dtype</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">float32</span><span class="p">)</span>
 
     <span class="c1"># Initialize an empty ndarray with the same shape as img and data type uint16</span>
     <span class="k">if</span> <span class="n">args</span><span class="o">.</span><span class="n">data_type</span><span class="p">:</span> 

unravel/docs/_build/html/_modules/unravel/image_tools/unique_intensities.html

@@ -360,10 +360,10 @@ <h1>Source code for unravel.image_tools.unique_intensities</h1><div class="highl
 
 <span class="sd">Usage for printing the number of voxels for each intensity that is present:</span>
 <span class="sd">---------------------------------------------------------------------------</span>
-<span class="sd">    img_unique -i path/input_img.nii.gz</span>
+<span class="sd">    img_unique -i path/input_img.nii.gz -s</span>
 
-<span class="sd">Usage for checking which clusters are present if the min cluster size was 100 voxels:</span>
-<span class="sd">-------------------------------------------------------------------------------------</span>
+<span class="sd">Usage for printing unique intensities w/ a min cluster size &gt; 100 voxels:</span>
+<span class="sd">-------------------------------------------------------------------------</span>
 <span class="sd">    img_unique -i path/input_img.nii.gz -m 100</span>
 <span class="sd">&quot;&quot;&quot;</span>
 

unravel/docs/_build/html/_modules/unravel/register/reg.html

@@ -406,7 +406,6 @@ <h1>Source code for unravel.register.reg</h1><div class="highlight"><pre>
 
     <span class="c1"># Optional arguments:</span>
     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-f&#39;</span><span class="p">,</span> <span class="s1">&#39;--fixed_img&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;reg_inputs/autofl_50um_masked.nii.gz (from ``reg_prep``)&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s2">&quot;reg_inputs/autofl_50um_masked.nii.gz&quot;</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;Warped moving image aligned with the fixed image. Default: &lt;moving_img&gt;__warped_moving_img.nii.gz&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</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;-mas&#39;</span><span class="p">,</span> <span class="s1">&#39;--mask&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">&quot;Brain mask for bias correction. Default: reg_inputs/autofl_50um_brain_mask.nii.gz. or pass in None&quot;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s2">&quot;reg_inputs/autofl_50um_brain_mask.nii.gz&quot;</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;-ro&#39;</span><span class="p">,</span> <span class="s1">&#39;--reg_outputs&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">&quot;Name of folder w/ outputs from ``reg`` (e.g., transforms). Default: reg_outputs&quot;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s2">&quot;reg_outputs&quot;</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;-tp&#39;</span><span class="p">,</span> <span class="s1">&#39;--tform_prefix&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Prefix of transforms output from ants.registration. Default: ANTsPy_&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s2">&quot;ANTsPy_&quot;</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>
@@ -416,7 +415,7 @@ <h1>Source code for unravel.register.reg</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;-ort&#39;</span><span class="p">,</span> <span class="s1">&#39;--ort_code&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;3 letter orientation code of fixed image if not set in fixed_img (e.g., RAS)&#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;-ia&#39;</span><span class="p">,</span> <span class="s1">&#39;--init_align&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Name of initially aligned image (moving reg input). Default: &lt;moving_img&gt;__initial_alignment_to_fixed_img.nii.gz&#39;</span> <span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</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;-it&#39;</span><span class="p">,</span> <span class="s1">&#39;--init_time&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Time in seconds allowed for ``reg_affine_initializer`` to run. Default: 30&#39;</span> <span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s1">&#39;30&#39;</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="nb">str</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: /usr/local/unravel/atlases/gubra/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;-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 (outputs &lt;reg_outputs&gt;/&lt;atlas&gt;_in_tissue_space.nii.gz for checking reg; Default: /usr/local/unravel/atlases/gubra/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;-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.&#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>
@@ -507,7 +506,7 @@ <h1>Source code for unravel.register.reg</h1><div class="highlight"><pre>
                 <span class="n">reg_inputs_fixed_img_nii</span> <span class="o">=</span> <span class="n">nib</span><span class="o">.</span><span class="n">Nifti1Image</span><span class="p">(</span><span class="n">fixed_img</span><span class="p">,</span> <span class="n">fixed_img_nii</span><span class="o">.</span><span class="n">affine</span><span class="o">.</span><span class="n">copy</span><span class="p">(),</span> <span class="n">fixed_img_nii</span><span class="o">.</span><span class="n">header</span><span class="p">)</span>
                 <span class="n">reg_inputs_fixed_img_nii</span><span class="o">.</span><span class="n">set_data_dtype</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">float32</span><span class="p">)</span>
 
-                <span class="c1"># Set the orientation of the image (use if not already set correctly in the header; check with ``io_nii``)</span>
+                <span class="c1"># Set the orientation of the image (use if not already set correctly in the header; check with ``io_nii_info``)</span>
                 <span class="k">if</span> <span class="n">args</span><span class="o">.</span><span class="n">ort_code</span><span class="p">:</span> 
                     <span class="n">reg_inputs_fixed_img_nii</span> <span class="o">=</span> <span class="n">reorient_nii</span><span class="p">(</span><span class="n">reg_inputs_fixed_img_nii</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">ort_code</span><span class="p">,</span> <span class="n">zero_origin</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">apply</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">form_code</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
 
@@ -562,10 +561,10 @@ <h1>Source code for unravel.register.reg</h1><div class="highlight"><pre>
                 <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">    Running registration </span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>
                 <span class="n">output_prefix</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">Path</span><span class="p">(</span><span class="n">reg_outputs_path</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">tform_prefix</span><span class="p">))</span>
                 <span class="n">reg</span> <span class="o">=</span> <span class="n">ants</span><span class="o">.</span><span class="n">registration</span><span class="p">(</span>
-                    <span class="n">fixed</span><span class="o">=</span><span class="n">fixed_image</span><span class="p">,</span> <span class="c1"># e.g., fixed autofluo image</span>
-                    <span class="n">moving</span><span class="o">=</span><span class="n">transformed_image</span><span class="p">,</span> <span class="c1"># e.g., the initially aligned moving image (e.g., template)</span>
+                    <span class="n">fixed</span><span class="o">=</span><span class="n">fixed_image</span><span class="p">,</span>  <span class="c1"># e.g., fixed autofluo image</span>
+                    <span class="n">moving</span><span class="o">=</span><span class="n">transformed_image</span><span class="p">,</span>  <span class="c1"># e.g., the initially aligned moving image (e.g., template)</span>
                     <span class="n">type_of_transform</span><span class="o">=</span><span class="s1">&#39;SyN&#39;</span><span class="p">,</span>  <span class="c1"># SyN = symmetric normalization</span>
-                    <span class="n">grad_step</span><span class="o">=</span><span class="mf">0.1</span><span class="p">,</span> <span class="c1"># Gradient step size</span>
+                    <span class="n">grad_step</span><span class="o">=</span><span class="mf">0.1</span><span class="p">,</span>  <span class="c1"># Gradient step size</span>
                     <span class="n">syn_metric</span><span class="o">=</span><span class="s1">&#39;CC&#39;</span><span class="p">,</span>  <span class="c1"># Cross-correlation</span>
                     <span class="n">syn_sampling</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span>  <span class="c1"># Corresponds to CC radius</span>
                     <span class="n">reg_iterations</span><span class="o">=</span><span class="p">(</span><span class="mi">100</span><span class="p">,</span> <span class="mi">70</span><span class="p">,</span> <span class="mi">50</span><span class="p">,</span> <span class="mi">20</span><span class="p">),</span>  <span class="c1"># Convergence criteria</span>

unravel/docs/_build/html/unravel/image_tools/toc.html

@@ -555,7 +555,7 @@ <h1>unravel.image_tools package<a class="headerlink" href="#unravel-image-tools-
 <li class="toctree-l1"><a class="reference internal" href="unique_intensities.html">unravel.image_tools.unique_intensities module</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="unique_intensities.html#usage-for-printing-all-non-zero-intensities">Usage for printing all non-zero intensities:</a></li>
 <li class="toctree-l2"><a class="reference internal" href="unique_intensities.html#usage-for-printing-the-number-of-voxels-for-each-intensity-that-is-present">Usage for printing the number of voxels for each intensity that is present:</a></li>
-<li class="toctree-l2"><a class="reference internal" href="unique_intensities.html#usage-for-checking-which-clusters-are-present-if-the-min-cluster-size-was-100-voxels">Usage for checking which clusters are present if the min cluster size was 100 voxels:</a></li>
+<li class="toctree-l2"><a class="reference internal" href="unique_intensities.html#usage-for-printing-unique-intensities-w-a-min-cluster-size-100-voxels">Usage for printing unique intensities w/ a min cluster size &gt; 100 voxels:</a></li>
 <li class="toctree-l2"><a class="reference internal" href="unique_intensities.html#unravel.image_tools.unique_intensities.parse_args"><code class="docutils literal notranslate"><span class="pre">parse_args()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="unique_intensities.html#unravel.image_tools.unique_intensities.uniq_intensities"><code class="docutils literal notranslate"><span class="pre">uniq_intensities()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="unique_intensities.html#unravel.image_tools.unique_intensities.main"><code class="docutils literal notranslate"><span class="pre">main()</span></code></a></li>

unravel/docs/_build/html/unravel/image_tools/unique_intensities.html

@@ -498,11 +498,11 @@ <h2>Usage for printing all non-zero intensities:<a class="headerlink" href="#usa
 <section id="usage-for-printing-the-number-of-voxels-for-each-intensity-that-is-present">
 <h2>Usage for printing the number of voxels for each intensity that is present:<a class="headerlink" href="#usage-for-printing-the-number-of-voxels-for-each-intensity-that-is-present" title="Link to this heading">#</a></h2>
 <blockquote>
-<div><p>img_unique -i path/input_img.nii.gz</p>
+<div><p>img_unique -i path/input_img.nii.gz -s</p>
 </div></blockquote>
 </section>
-<section id="usage-for-checking-which-clusters-are-present-if-the-min-cluster-size-was-100-voxels">
-<h2>Usage for checking which clusters are present if the min cluster size was 100 voxels:<a class="headerlink" href="#usage-for-checking-which-clusters-are-present-if-the-min-cluster-size-was-100-voxels" title="Link to this heading">#</a></h2>
+<section id="usage-for-printing-unique-intensities-w-a-min-cluster-size-100-voxels">
+<h2>Usage for printing unique intensities w/ a min cluster size &gt; 100 voxels:<a class="headerlink" href="#usage-for-printing-unique-intensities-w-a-min-cluster-size-100-voxels" title="Link to this heading">#</a></h2>
 <blockquote>
 <div><p>img_unique -i path/input_img.nii.gz -m 100</p>
 </div></blockquote>
@@ -588,7 +588,7 @@ <h2>Usage for checking which clusters are present if the min cluster size was 10
     <ul class="visible nav section-nav flex-column">
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#usage-for-printing-all-non-zero-intensities">Usage for printing all non-zero intensities:</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#usage-for-printing-the-number-of-voxels-for-each-intensity-that-is-present">Usage for printing the number of voxels for each intensity that is present:</a></li>
-<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#usage-for-checking-which-clusters-are-present-if-the-min-cluster-size-was-100-voxels">Usage for checking which clusters are present if the min cluster size was 100 voxels:</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#usage-for-printing-unique-intensities-w-a-min-cluster-size-100-voxels">Usage for printing unique intensities w/ a min cluster size &gt; 100 voxels:</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#unravel.image_tools.unique_intensities.parse_args"><code class="docutils literal notranslate"><span class="pre">parse_args()</span></code></a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#unravel.image_tools.unique_intensities.uniq_intensities"><code class="docutils literal notranslate"><span class="pre">uniq_intensities()</span></code></a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#unravel.image_tools.unique_intensities.main"><code class="docutils literal notranslate"><span class="pre">main()</span></code></a></li>