Updated docs

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

@@ -388,7 +388,7 @@ <h1>Source code for unravel.cluster_stats.cluster_validation</h1><div class="hig
 <span class="kn">from</span> <span class="nn">unravel.core.img_io</span> <span class="kn">import</span> <span class="n">load_3D_img</span><span class="p">,</span> <span class="n">load_image_metadata_from_txt</span><span class="p">,</span> <span class="n">load_nii_subset</span><span class="p">,</span> <span class="n">resolve_path</span>
 <span class="kn">from</span> <span class="nn">unravel.core.img_tools</span> <span class="kn">import</span> <span class="n">cluster_IDs</span>
 <span class="kn">from</span> <span class="nn">unravel.core.utils</span> <span class="kn">import</span> <span class="n">print_cmd_and_times</span><span class="p">,</span> <span class="n">initialize_progress_bar</span><span class="p">,</span> <span class="n">get_samples</span><span class="p">,</span> <span class="n">print_func_name_args_times</span>
-<span class="kn">from</span> <span class="nn">warp.to_native</span> <span class="kn">import</span> <span class="n">to_native</span>
+<span class="kn">from</span> <span class="nn">unravel.warp.to_native</span> <span class="kn">import</span> <span class="n">to_native</span>
 
 
 <div class="viewcode-block" id="parse_args">

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

@@ -372,7 +372,7 @@ <h1>Source code for unravel.cluster_stats.recursively_mirror_rev_cluster_indices
 <span class="kn">from</span> <span class="nn">unravel.core.argparse_utils</span> <span class="kn">import</span> <span class="n">SM</span><span class="p">,</span> <span class="n">SuppressMetavar</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">print_cmd_and_times</span>
-<span class="kn">from</span> <span class="nn">voxel_stats.mirror</span> <span class="kn">import</span> <span class="n">mirror</span>
+<span class="kn">from</span> <span class="nn">unravel.voxel_stats.mirror</span> <span class="kn">import</span> <span class="n">mirror</span>
 
 <div class="viewcode-block" id="parse_args">
 <a class="viewcode-back" href="../../../unravel/cluster_stats/recursively_mirror_rev_cluster_indices.html#unravel.cluster_stats.recursively_mirror_rev_cluster_indices.parse_args">[docs]</a>

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

@@ -582,7 +582,17 @@ <h1>Source code for unravel.core.img_tools</h1><div class="highlight"><pre>
 <div class="viewcode-block" id="cluster_IDs">
 <a class="viewcode-back" href="../../../unravel/core/img_tools.html#unravel.core.img_tools.cluster_IDs">[docs]</a>
 <span class="k">def</span> <span class="nf">cluster_IDs</span><span class="p">(</span><span class="n">ndarray</span><span class="p">,</span> <span class="n">min_extent</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">print_IDs</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">print_sizes</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
-<span class="w">    </span><span class="sd">&quot;&quot;&quot;Prints cluster IDs [and sizes] for clusters &gt; minextent voxels&quot;&quot;&quot;</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Gets unique intensities [and sizes] for regions/clusters &gt; minextent voxels and prints them in a string-separated list. </span>
+
+<span class="sd">    Args:</span>
+<span class="sd">        ndarray</span>
+<span class="sd">        min_extent (int, optional): _description_. Defaults to 1.</span>
+<span class="sd">        print_IDs (bool, optional): _description_. Defaults to False.</span>
+<span class="sd">        print_sizes (bool, optional): _description_. Defaults to False.</span>
+
+<span class="sd">    Returns:</span>
+<span class="sd">        list of ints: list of unique intensities</span>
+<span class="sd">    &quot;&quot;&quot;</span>
 
     <span class="c1"># Get unique intensities and their counts</span>
     <span class="n">unique_intensities</span><span class="p">,</span> <span class="n">counts</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">unique</span><span class="p">(</span><span class="n">ndarray</span><span class="p">[</span><span class="n">ndarray</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">],</span> <span class="n">return_counts</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>

unravel/docs/_build/html/_modules/unravel/image_io/io_img.html

@@ -390,7 +390,7 @@ <h1>Source code for unravel.image_io.io_img</h1><div class="highlight"><pre>
     <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: Test if other scripts in image_io are redundant and can be removed</span>
+<span class="c1"># TODO: Test if other scripts in image_io are redundant and can be removed. If not, consolidate them into this script.</span>
 
 
 <div class="viewcode-block" id="main">

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

@@ -385,25 +385,45 @@ <h1>Source code for unravel.image_tools.unique_intensities</h1><div class="highl
 <span class="k">def</span> <span class="nf">parse_args</span><span class="p">():</span>
     <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;-i&#39;</span><span class="p">,</span> <span class="s1">&#39;--input&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;path/input_img.nii.gz&#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;-m&#39;</span><span class="p">,</span> <span class="s1">&#39;--minextent&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Min cluster size in voxels (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="n">action</span><span class="o">=</span><span class="n">SM</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">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;--min_extent&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Min cluster size in voxels (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="n">action</span><span class="o">=</span><span class="n">SM</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">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;--print_sizes&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Print cluster IDs and sizes. Default: False&#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">action</span><span class="o">=</span><span class="s1">&#39;store_true&#39;</span><span class="p">)</span>
     <span class="c1"># parser.add_argument(&#39;-v&#39;, &#39;--verbose&#39;, help=&#39;Increase verbosity. Default: False&#39;, action=&#39;store_true&#39;, default=False)</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>
 
 
+<div class="viewcode-block" id="uniq_intensities">
+<a class="viewcode-back" href="../../../unravel/image_tools/unique_intensities.html#unravel.image_tools.unique_intensities.uniq_intensities">[docs]</a>
+<span class="k">def</span> <span class="nf">uniq_intensities</span><span class="p">(</span><span class="nb">input</span><span class="p">,</span> <span class="n">min_extent</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">print_sizes</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Loads a 3D image and prints non-zero unique intensity values in a space-separated list.</span>
+
+<span class="sd">    Args:</span>
+<span class="sd">        input (_type_): _description_</span>
+<span class="sd">        min_extent (int, optional): _description_. Defaults to 1.</span>
+<span class="sd">        print_sizes (bool, optional): _description_. Defaults to False.</span>
+
+<span class="sd">    Returns:</span>
+<span class="sd">        list of ints: list of unique intensities</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="k">if</span> <span class="nb">str</span><span class="p">(</span><span class="nb">input</span><span class="p">)</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s2">&quot;.nii.gz&quot;</span><span class="p">):</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="nb">input</span><span class="p">)</span>
+        <span class="n">img</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asanyarray</span><span class="p">(</span><span class="n">nii</span><span class="o">.</span><span class="n">dataobj</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">uint16</span><span class="p">)</span><span class="o">.</span><span class="n">squeeze</span><span class="p">()</span>
+    <span class="k">else</span><span class="p">:</span> 
+        <span class="n">img</span> <span class="o">=</span> <span class="n">load_3D_img</span><span class="p">(</span><span class="nb">input</span><span class="p">)</span>
+
+    <span class="n">uniq_intensities</span> <span class="o">=</span> <span class="n">cluster_IDs</span><span class="p">(</span><span class="n">img</span><span class="p">,</span> <span class="n">min_extent</span><span class="o">=</span><span class="n">min_extent</span><span class="p">,</span> <span class="n">print_IDs</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">print_sizes</span><span class="o">=</span><span class="n">print_sizes</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">uniq_intensities</span></div>
+
+
 <div class="viewcode-block" id="main">
 <a class="viewcode-back" href="../../../unravel/image_tools/unique_intensities.html#unravel.image_tools.unique_intensities.main">[docs]</a>
 <span class="k">def</span> <span class="nf">main</span><span class="p">():</span>
     <span class="n">args</span> <span class="o">=</span> <span class="n">parse_args</span><span class="p">()</span>
 
-    <span class="k">if</span> <span class="nb">str</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="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s2">&quot;.nii.gz&quot;</span><span class="p">):</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">np</span><span class="o">.</span><span class="n">asanyarray</span><span class="p">(</span><span class="n">nii</span><span class="o">.</span><span class="n">dataobj</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">uint16</span><span class="p">)</span><span class="o">.</span><span class="n">squeeze</span><span class="p">()</span>
-    <span class="k">else</span><span class="p">:</span> 
-        <span class="n">img</span> <span class="o">=</span> <span class="n">load_3D_img</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"># Print unique intensities in image</span>
+    <span class="n">uniq_intensities</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">args</span><span class="o">.</span><span class="n">min_extent</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">print_sizes</span><span class="p">)</span></div>
 
-    <span class="n">cluster_IDs</span><span class="p">(</span><span class="n">img</span><span class="p">,</span> <span class="n">min_extent</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">minextent</span><span class="p">,</span> <span class="n">print_IDs</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">print_sizes</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">print_sizes</span><span class="p">)</span></div>
 
 
 <span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s1">&#39;__main__&#39;</span><span class="p">:</span>