make html

unravel/docs/_build/html/_modules/unravel/voxel_stats/vstats_prep.html

@@ -403,7 +403,7 @@ <h1>Source code for unravel.voxel_stats.vstats_prep</h1><div class="highlight"><
 
     <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;-sa&#39;</span><span class="p">,</span> <span class="s1">&#39;--spatial_avg&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Spatial averaging in 2D or 3D (2 or 3). Default: None&#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="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;-rb&#39;</span><span class="p">,</span> <span class="s1">&#39;--rb_radius&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Radius of rolling ball in pixels (Default: 4)&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="mi">4</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;-rb&#39;</span><span class="p">,</span> <span class="s1">&#39;--rb_radius&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Radius of rolling ball in pixels (Default: None)&#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="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;-x&#39;</span><span class="p">,</span> <span class="s1">&#39;--xy_res&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Native x/y voxel size in microns (Default: get via metadata)&#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="nb">type</span><span class="o">=</span><span class="nb">float</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;-z&#39;</span><span class="p">,</span> <span class="s1">&#39;--z_res&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Native z voxel size in microns (Default: get via metadata)&#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="nb">type</span><span class="o">=</span><span class="nb">float</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;-c&#39;</span><span class="p">,</span> <span class="s1">&#39;--chann_idx&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;.czi channel index. Default: 1&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="mi">1</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>
@@ -466,17 +466,18 @@ <h1>Source code for unravel.voxel_stats.vstats_prep</h1><div class="highlight"><
                 <span class="n">img</span> <span class="o">=</span> <span class="n">spatial_average_2D</span><span class="p">(</span><span class="n">img</span><span class="p">,</span> <span class="n">apply_2D_mean_filter</span><span class="p">,</span> <span class="n">kernel_size</span><span class="o">=</span><span class="p">(</span><span class="mi">3</span><span class="p">,</span> <span class="mi">3</span><span class="p">))</span>
 
             <span class="c1"># Rolling ball background subtraction</span>
-            <span class="n">rb_img</span> <span class="o">=</span> <span class="n">rolling_ball_subtraction_opencv_parallel</span><span class="p">(</span><span class="n">img</span><span class="p">,</span> <span class="n">radius</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">rb_radius</span><span class="p">,</span> <span class="n">threads</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">threads</span><span class="p">)</span>  
+            <span class="k">if</span> <span class="n">args</span><span class="o">.</span><span class="n">rb_radius</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+                <span class="n">img</span> <span class="o">=</span> <span class="n">rolling_ball_subtraction_opencv_parallel</span><span class="p">(</span><span class="n">img</span><span class="p">,</span> <span class="n">radius</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">rb_radius</span><span class="p">,</span> <span class="n">threads</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">threads</span><span class="p">)</span>  
 
             <span class="c1"># Resample the rb_img to the resolution of registration (and optionally reorient for compatibility with MIRACL)</span>
-            <span class="n">rb_img</span> <span class="o">=</span> <span class="n">reg_prep</span><span class="p">(</span><span class="n">rb_img</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">xy_res</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">z_res</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">reg_res</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">zoom_order</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">miracl</span><span class="p">)</span>
+            <span class="n">img</span> <span class="o">=</span> <span class="n">reg_prep</span><span class="p">(</span><span class="n">img</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">xy_res</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">z_res</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">reg_res</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">zoom_order</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">miracl</span><span class="p">)</span>
 
             <span class="c1"># Warp the image to atlas space</span>
             <span class="n">fixed_reg_input</span> <span class="o">=</span> <span class="n">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">fixed_reg_in</span><span class="p">)</span>    
             <span class="k">if</span> <span class="ow">not</span> <span class="n">fixed_reg_input</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
                 <span class="n">fixed_reg_input</span> <span class="o">=</span> <span class="n">sample_path</span> <span class="o">/</span> <span class="s2">&quot;reg_outputs&quot;</span> <span class="o">/</span> <span class="s2">&quot;autofl_50um_fixed_reg_input.nii.gz&quot;</span>
 
-            <span class="n">to_atlas</span><span class="p">(</span><span class="n">sample_path</span><span class="p">,</span> <span class="n">rb_img</span><span class="p">,</span> <span class="n">fixed_reg_input</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">atlas</span><span class="p">,</span> <span class="n">output</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">interpol</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="s1">&#39;uint16&#39;</span><span class="p">)</span>
+            <span class="n">to_atlas</span><span class="p">(</span><span class="n">sample_path</span><span class="p">,</span> <span class="n">img</span><span class="p">,</span> <span class="n">fixed_reg_input</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">atlas</span><span class="p">,</span> <span class="n">output</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">interpol</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="s1">&#39;uint16&#39;</span><span class="p">)</span>
 
             <span class="c1"># Copy the atlas to atlas_space</span>
             <span class="n">atlas_space</span> <span class="o">=</span> <span class="n">sample_path</span> <span class="o">/</span> <span class="s2">&quot;atlas_space&quot;</span>

unravel/docs/_build/html/_sources/guide.md.txt

@@ -150,6 +150,7 @@ unravel_commands -m
 - [**seg_copy_tifs**](unravel.segment.copy_tifs): Copy TIF images (copy select tifs to target dir for training ilastik).
 - [**seg_brain_mask**](unravel.segment.brain_mask): Create brain mask (segment resampled autofluo tifs).
 - [**seg_ilastik**](unravel.segment.ilastik_pixel_classification): Perform pixel classification w/ Ilastik to segment features of interest.
+- [**seg_labels_to_masks**](unravel.segment.labels_to_masks): Convert each label to a binary .nii.gz. 
 :::
 
 :::{tab-item} Voxel-wise stats

unravel/docs/_build/html/_sources/installation.md.txt

@@ -74,7 +74,11 @@ For more detailed information, you can view the commit history:
     - 
 
 :::{note}
+After WSL is installed, you may open and use the WSL app. 
+
 To enable copy/paste in the PowerShell or WSL, click the icon in the upper left --> Properties --> Edit Options -> check "Use Ctrl+Shift+C/V as Copy/Paste --> OK. 
+
+[Video tutorial](https://www.youtube.com/watch?v=i547sSXhq0E) on navigating to your files (either the WSL file system or your C and D drives).
 :::
 
 For detailed instructions, visit the [WSL Installation Guide](https://docs.microsoft.com/en-us/windows/wsl/install).
@@ -87,6 +91,12 @@ For detailed instructions, visit the [WSL Installation Guide](https://docs.micro
 
     ### Option A: Using pyenv
 
+    :::{note}
+    Pyenv can work on Windows, but this is not recommended (e.g., see notes [here](https://github.com/pyenv/pyenv))
+
+    Alternatively, use [pyenv-win](https://github.com/pyenv-win/pyenv-win), [venv](https://docs.python.org/3/library/venv.html), or [conda](https://conda.io/projects/conda/en/latest/user-guide/install/index.html).
+    :::
+
     **a. Install dependencies:**
     ```bash
     sudo apt-get update
@@ -104,11 +114,14 @@ For detailed instructions, visit the [WSL Installation Guide](https://docs.micro
 
     **c. Add pyenv to your shell startup file (.bashrc or .zshrc):**
     ```bash
+    (
+    echo '' >> ~/.bashrc
     echo 'export PYENV_ROOT="$HOME/.pyenv"' >> ~/.bashrc
     echo 'export PATH="$PYENV_ROOT/bin:$PATH"' >> ~/.bashrc
-    echo -e 'if command -v pyenv 1>/dev/null 2>&1; then\n  eval "$(pyenv init --path)"\nfi' >> ~/.bashrc
-    echo -e 'if command -v pyenv 1>/dev/null 2>&1; then\n  eval "$(pyenv init -)"\nfi' >> ~/.bashrc
-    exec "$SHELL"
+    echo 'eval "$(pyenv init --path)"' >> ~/.bashrc
+    echo 'eval "$(pyenv init -)"' >> ~/.bashrc
+    echo 'eval "$(pyenv virtualenv-init -)"' >> ~/.bashrc
+    )
     ```
 
     **d. Install Python 3.11:**
@@ -150,14 +163,7 @@ For detailed instructions, visit the [WSL Installation Guide](https://docs.micro
 :::
 
 5. **Install Ilastik:**
-    - Download the Ilastik installer from the [Ilastik website](https://www.ilastik.org/download.html).
-    - Follow the installation instructions specific to your operating system.
-    - Example for Linux:
-        ```bash
-        wget https://files.ilastik.org/ilastik-1.3.3post3-Linux.tar.bz2
-        tar -xjf ilastik-1.3.3post3-Linux.tar.bz2
-        sudo mv ilastik-1.3.3post3-Linux /usr/local/
-        ```
+    - [Ilastik installation website](https://www.ilastik.org/download.html).
 
 6. **Install FSL:**
     - Follow the installation instructions from the [FSL website](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation).

unravel/docs/_build/html/guide.html

@@ -543,6 +543,7 @@ <h2>Common commands<a class="headerlink" href="#common-commands" title="Link to
 <li><p><a class="reference internal" href="unravel/segment/copy_tifs.html#unravel-segment-copy-tifs"><span class="std std-ref"><strong>seg_copy_tifs</strong></span></a>: Copy TIF images (copy select tifs to target dir for training ilastik).</p></li>
 <li><p><a class="reference internal" href="unravel/segment/brain_mask.html#unravel-segment-brain-mask"><span class="std std-ref"><strong>seg_brain_mask</strong></span></a>: Create brain mask (segment resampled autofluo tifs).</p></li>
 <li><p><a class="reference internal" href="unravel/segment/ilastik_pixel_classification.html#unravel-segment-ilastik-pixel-classification"><span class="std std-ref"><strong>seg_ilastik</strong></span></a>: Perform pixel classification w/ Ilastik to segment features of interest.</p></li>
+<li><p><a class="reference internal" href="unravel/segment/labels_to_masks.html#unravel-segment-labels-to-masks"><span class="std std-ref"><strong>seg_labels_to_masks</strong></span></a>: Convert each label to a binary .nii.gz.</p></li>
 </ul>
 </div>
 <input id="sd-tab-item-12" name="sd-tab-set-1" type="radio">

unravel/docs/_build/html/installation.html

@@ -433,7 +433,9 @@ <h2>Setting Up Windows Subsystem for Linux (WSL)<a class="headerlink" href="#set
 </ol>
 <div class="admonition note">
 <p class="admonition-title">Note</p>
+<p>After WSL is installed, you may open and use the WSL app.</p>
 <p>To enable copy/paste in the PowerShell or WSL, click the icon in the upper left –&gt; Properties –&gt; Edit Options -&gt; check “Use Ctrl+Shift+C/V as Copy/Paste –&gt; OK.</p>
+<p><a class="reference external" href="https://www.youtube.com/watch?v=i547sSXhq0E">Video tutorial</a> on navigating to your files (either the WSL file system or your C and D drives).</p>
 </div>
 <p>For detailed instructions, visit the <a class="reference external" href="https://docs.microsoft.com/en-us/windows/wsl/install">WSL Installation Guide</a>.</p>
 </section>
@@ -443,6 +445,11 @@ <h2>Installing UNRAVEL on Linux or WSL<a class="headerlink" href="#installing-un
 <li><p><strong>Open a terminal</strong></p></li>
 <li><p><strong>Install pyenv, venv, or other tool(s) to manage Python versions and create a virtual environment:</strong></p>
 <h3 class="rubric" id="option-a-using-pyenv">Option A: Using pyenv</h3>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<p>Pyenv can work on Windows, but this is not recommended (e.g., see notes <a class="reference external" href="https://github.com/pyenv/pyenv">here</a>)</p>
+<p>Alternatively, use <a class="reference external" href="https://github.com/pyenv-win/pyenv-win">pyenv-win</a>, <a class="reference external" href="https://docs.python.org/3/library/venv.html">venv</a>, or <a class="reference external" href="https://conda.io/projects/conda/en/latest/user-guide/install/index.html">conda</a>.</p>
+</div>
 <p><strong>a. Install dependencies:</strong></p>
 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>sudo<span class="w"> </span>apt-get<span class="w"> </span>update
 
@@ -457,11 +464,14 @@ <h3 class="rubric" id="option-a-using-pyenv">Option A: Using pyenv</h3>
 </pre></div>
 </div>
 <p><strong>c. Add pyenv to your shell startup file (.bashrc or .zshrc):</strong></p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">echo</span><span class="w"> </span><span class="s1">&#39;export PYENV_ROOT=&quot;$HOME/.pyenv&quot;&#39;</span><span class="w"> </span>&gt;&gt;<span class="w"> </span>~/.bashrc
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="o">(</span>
+<span class="nb">echo</span><span class="w"> </span><span class="s1">&#39;&#39;</span><span class="w"> </span>&gt;&gt;<span class="w"> </span>~/.bashrc
+<span class="nb">echo</span><span class="w"> </span><span class="s1">&#39;export PYENV_ROOT=&quot;$HOME/.pyenv&quot;&#39;</span><span class="w"> </span>&gt;&gt;<span class="w"> </span>~/.bashrc
 <span class="nb">echo</span><span class="w"> </span><span class="s1">&#39;export PATH=&quot;$PYENV_ROOT/bin:$PATH&quot;&#39;</span><span class="w"> </span>&gt;&gt;<span class="w"> </span>~/.bashrc
-<span class="nb">echo</span><span class="w"> </span>-e<span class="w"> </span><span class="s1">&#39;if command -v pyenv 1&gt;/dev/null 2&gt;&amp;1; then\n  eval &quot;$(pyenv init --path)&quot;\nfi&#39;</span><span class="w"> </span>&gt;&gt;<span class="w"> </span>~/.bashrc
-<span class="nb">echo</span><span class="w"> </span>-e<span class="w"> </span><span class="s1">&#39;if command -v pyenv 1&gt;/dev/null 2&gt;&amp;1; then\n  eval &quot;$(pyenv init -)&quot;\nfi&#39;</span><span class="w"> </span>&gt;&gt;<span class="w"> </span>~/.bashrc
-<span class="nb">exec</span><span class="w"> </span><span class="s2">&quot;</span><span class="nv">$SHELL</span><span class="s2">&quot;</span>
+<span class="nb">echo</span><span class="w"> </span><span class="s1">&#39;eval &quot;$(pyenv init --path)&quot;&#39;</span><span class="w"> </span>&gt;&gt;<span class="w"> </span>~/.bashrc
+<span class="nb">echo</span><span class="w"> </span><span class="s1">&#39;eval &quot;$(pyenv init -)&quot;&#39;</span><span class="w"> </span>&gt;&gt;<span class="w"> </span>~/.bashrc
+<span class="nb">echo</span><span class="w"> </span><span class="s1">&#39;eval &quot;$(pyenv virtualenv-init -)&quot;&#39;</span><span class="w"> </span>&gt;&gt;<span class="w"> </span>~/.bashrc
+<span class="o">)</span>
 </pre></div>
 </div>
 <p><strong>d. Install Python 3.11:</strong></p>
@@ -501,16 +511,8 @@ <h3 class="rubric" id="option-b-using-venv">Option B: Using venv</h3>
 </div>
 <ol class="arabic" start="5">
 <li><p><strong>Install Ilastik:</strong></p>
-<ul>
-<li><p>Download the Ilastik installer from the <a class="reference external" href="https://www.ilastik.org/download.html">Ilastik website</a>.</p></li>
-<li><p>Follow the installation instructions specific to your operating system.</p></li>
-<li><p>Example for Linux:</p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>wget<span class="w"> </span>https://files.ilastik.org/ilastik-1.3.3post3-Linux.tar.bz2
-tar<span class="w"> </span>-xjf<span class="w"> </span>ilastik-1.3.3post3-Linux.tar.bz2
-sudo<span class="w"> </span>mv<span class="w"> </span>ilastik-1.3.3post3-Linux<span class="w"> </span>/usr/local/
-</pre></div>
-</div>
-</li>
+<ul class="simple">
+<li><p><a class="reference external" href="https://www.ilastik.org/download.html">Ilastik installation website</a>.</p></li>
 </ul>
 </li>
 <li><p><strong>Install FSL:</strong></p>