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b-heifets · Jun 24, 2024 · e1187bb · e1187bb
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diff --git a/unravel/docs/_build/doctrees/environment.pickle b/unravel/docs/_build/doctrees/environment.pickle
diff --git a/unravel/docs/_build/doctrees/installation.doctree b/unravel/docs/_build/doctrees/installation.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/segment/brain_mask.doctree b/unravel/docs/_build/doctrees/unravel/segment/brain_mask.doctree
diff --git a/unravel/docs/_build/doctrees/unravel/segment/copy_tifs.doctree b/unravel/docs/_build/doctrees/unravel/segment/copy_tifs.doctree
diff --git a/unravel/docs/_build/html/_modules/unravel/segment/brain_mask.html b/unravel/docs/_build/html/_modules/unravel/segment/brain_mask.html
@@ -356,7 +356,7 @@ <h1>Source code for unravel.segment.brain_mask</h1><div class="highlight"><pre>
 
 <span class="sd">Usage:</span>
 <span class="sd">------</span>
-<span class="sd">    seg_brain_mask -v </span>
+<span class="sd">    seg_brain_mask -ilp &lt;path/brain_mask.ilp&gt; [-i reg_inputs/autofl_50um.nii.gz] [-r 50] [-v] </span>
 
 <span class="sd">Prereqs: </span>
 <span class="sd">    - Train ilastik (tissue = label 1) w/ tifs from reg_inputs/autofl_&lt;asterisk&gt;um_tifs/&lt;asterisk&gt;.tif (from ``reg_prep``)</span>

diff --git a/unravel/docs/_build/html/_modules/unravel/segment/copy_tifs.html b/unravel/docs/_build/html/_modules/unravel/segment/copy_tifs.html
@@ -394,7 +394,7 @@ <h1>Source code for unravel.segment.copy_tifs</h1><div class="highlight"><pre>
 
 <div class="viewcode-block" id="copy_specific_slices">
 <a class="viewcode-back" href="../../../unravel/segment/copy_tifs.html#unravel.segment.copy_tifs.copy_specific_slices">[docs]</a>
-<span class="k">def</span> <span class="nf">copy_specific_slices</span><span class="p">(</span><span class="n">sample_path</span><span class="p">,</span> <span class="n">source_dir</span><span class="p">,</span> <span class="n">target_dir</span><span class="p">,</span> <span class="n">slice_numbers</span><span class="p">):</span>
+<span class="k">def</span> <span class="nf">copy_specific_slices</span><span class="p">(</span><span class="n">sample_path</span><span class="p">,</span> <span class="n">source_dir</span><span class="p">,</span> <span class="n">target_dir</span><span class="p">,</span> <span class="n">slice_numbers</span><span class="p">,</span> <span class="n">verbose</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Copy the specified slices to the target directory.</span>
 <span class="sd">    </span>
 <span class="sd">    Args:</span>
@@ -407,10 +407,10 @@ <h1>Source code for unravel.segment.copy_tifs</h1><div class="highlight"><pre>
         <span class="k">if</span> <span class="nb">any</span><span class="p">(</span><span class="n">file_path</span><span class="o">.</span><span class="n">stem</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="nb">slice</span><span class="si">:</span><span class="s2">04</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span> <span class="k">for</span> <span class="nb">slice</span> <span class="ow">in</span> <span class="nb">map</span><span class="p">(</span><span class="nb">int</span><span class="p">,</span> <span class="n">slice_numbers</span><span class="p">)):</span>
             <span class="n">dest_file</span> <span class="o">=</span> <span class="n">target_dir</span> <span class="o">/</span> <span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">sample_path</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s1">_</span><span class="si">{</span><span class="n">file_path</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s1">&#39;</span>
             <span class="n">shutil</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="n">file_path</span><span class="p">,</span> <span class="n">dest_file</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="k">if</span> <span class="n">verbose</span><span class="p">:</span>
                 <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Copied </span><span class="si">{</span><span class="n">file_path</span><span class="si">}</span><span class="s2"> to </span><span class="si">{</span><span class="n">dest_file</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
         <span class="k">else</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="k">if</span> <span class="n">verbose</span><span class="p">:</span>
                 <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;File </span><span class="si">{</span><span class="n">file_path</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s2"> does not match specified slices and was not copied.&quot;</span><span class="p">)</span></div>
 
 
@@ -437,7 +437,7 @@ <h1>Source code for unravel.segment.copy_tifs</h1><div class="highlight"><pre>
             <span class="n">source_path</span> <span class="o">=</span> <span class="n">resolve_path</span><span class="p">(</span><span class="n">sample_path</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="c1"># Copy the selected slices to the target directory</span>
-            <span class="n">copy_specific_slices</span><span class="p">(</span><span class="n">sample_path</span><span class="p">,</span> <span class="n">source_path</span><span class="p">,</span> <span class="n">target_dir</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">slices</span><span class="p">)</span>
+            <span class="n">copy_specific_slices</span><span class="p">(</span><span class="n">sample_path</span><span class="p">,</span> <span class="n">source_path</span><span class="p">,</span> <span class="n">target_dir</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">slices</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">verbose</span><span class="p">)</span>
 
             <span class="n">progress</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">task_id</span><span class="p">,</span> <span class="n">advance</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span></div>
 

diff --git a/unravel/docs/_build/html/_sources/installation.md.txt b/unravel/docs/_build/html/_sources/installation.md.txt
@@ -119,8 +119,14 @@ pip install unravel
     ```
 
 12. **Update scripts periodically:**
+    :::{hint}
+    * Make a backup of the code that you used for analysis before updating
+    :::
+
     ```bash
-    git pull
+    cd <path/to/repo/clone>
+
+    git pull  # This will update the local repo
     ```
 
 ## Editing .bashrc or .zshrc

diff --git a/unravel/docs/_build/html/installation.html b/unravel/docs/_build/html/installation.html
@@ -483,7 +483,15 @@ <h2>Installing UNRAVEL on Linux or WSL<a class="headerlink" href="#installing-un
 </div>
 </li>
 <li><p><strong>Update scripts periodically:</strong></p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>git<span class="w"> </span>pull
+<div class="admonition hint">
+<p class="admonition-title">Hint</p>
+<ul class="simple">
+<li><p>Make a backup of the code that you used for analysis before updating</p></li>
+</ul>
+</div>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">cd</span><span class="w"> </span>&lt;path/to/repo/clone&gt;
+
+git<span class="w"> </span>pull<span class="w">  </span><span class="c1"># This will update the local repo</span>
 </pre></div>
 </div>
 </li>

diff --git a/unravel/docs/_build/html/searchindex.js b/unravel/docs/_build/html/searchindex.js
diff --git a/unravel/docs/_build/html/unravel/segment/brain_mask.html b/unravel/docs/_build/html/unravel/segment/brain_mask.html
@@ -492,7 +492,7 @@
 <section id="usage">
 <h2>Usage:<a class="headerlink" href="#usage" title="Link to this heading">#</a></h2>
 <blockquote>
-<div><p>seg_brain_mask -v</p>
+<div><p>seg_brain_mask -ilp &lt;path/brain_mask.ilp&gt; [-i reg_inputs/autofl_50um.nii.gz] [-r 50] [-v]</p>
 </div></blockquote>
 <dl class="simple">
 <dt>Prereqs:</dt><dd><ul class="simple">

diff --git a/unravel/docs/_build/html/unravel/segment/copy_tifs.html b/unravel/docs/_build/html/unravel/segment/copy_tifs.html
@@ -508,7 +508,7 @@ <h2>Usage to prep for <code class="docutils literal notranslate"><span class="pr
 
 <dl class="py function">
 <dt class="sig sig-object py" id="unravel.segment.copy_tifs.copy_specific_slices">
-<span class="sig-prename descclassname"><span class="pre">unravel.segment.copy_tifs.</span></span><span class="sig-name descname"><span class="pre">copy_specific_slices</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">sample_path</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source_dir</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target_dir</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">slice_numbers</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/unravel/segment/copy_tifs.html#copy_specific_slices"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#unravel.segment.copy_tifs.copy_specific_slices" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">unravel.segment.copy_tifs.</span></span><span class="sig-name descname"><span class="pre">copy_specific_slices</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">sample_path</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source_dir</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target_dir</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">slice_numbers</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbose</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/unravel/segment/copy_tifs.html#copy_specific_slices"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#unravel.segment.copy_tifs.copy_specific_slices" title="Link to this definition">#</a></dt>
 <dd><p>Copy the specified slices to the target directory.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>

diff --git a/unravel/docs/installation.md b/unravel/docs/installation.md
@@ -119,8 +119,14 @@ pip install unravel
     ```
 
 12. **Update scripts periodically:**
+    :::{hint}
+    * Make a backup of the code that you used for analysis before updating
+    :::
+
     ```bash
-    git pull
+    cd <path/to/repo/clone>
+
+    git pull  # This will update the local repo
     ```
 
 ## Editing .bashrc or .zshrc