Updated documentation

Signed-off-by: Nicola VIGANO <[email protected]>

Author: Obi-Wan

docs/_modules/corrct/attenuation.html

@@ -86,13 +86,14 @@ <h1>Source code for corrct.attenuation</h1><div class="highlight"><pre>
 
 <span class="kn">from</span> <span class="nn">tqdm</span> <span class="kn">import</span> <span class="n">tqdm</span>
 
-<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Dict</span><span class="p">,</span> <span class="n">Optional</span><span class="p">,</span> <span class="n">Sequence</span><span class="p">,</span> <span class="n">Union</span>
+<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Dict</span><span class="p">,</span> <span class="n">Optional</span><span class="p">,</span> <span class="n">Sequence</span><span class="p">,</span> <span class="n">Union</span><span class="p">,</span> <span class="n">List</span>
 <span class="kn">from</span> <span class="nn">numpy.typing</span> <span class="kn">import</span> <span class="n">ArrayLike</span><span class="p">,</span> <span class="n">DTypeLike</span><span class="p">,</span> <span class="n">NDArray</span>
 
 
 <span class="n">num_threads</span> <span class="o">=</span> <span class="nb">round</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">log2</span><span class="p">(</span><span class="n">mp</span><span class="o">.</span><span class="n">cpu_count</span><span class="p">()</span> <span class="o">+</span> <span class="mi">1</span><span class="p">))</span>
 
 <span class="n">NDArrayFloat</span> <span class="o">=</span> <span class="n">NDArray</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">floating</span><span class="p">]</span>
+<span class="n">NDArrayInt</span> <span class="o">=</span> <span class="n">NDArray</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">integer</span><span class="p">]</span>
 
 
 <div class="viewcode-block" id="AttenuationVolume"><a class="viewcode-back" href="../../corrct.html#corrct.attenuation.AttenuationVolume">[docs]</a><span class="k">class</span> <span class="nc">AttenuationVolume</span><span class="p">:</span>
@@ -207,8 +208,8 @@ <h1>Source code for corrct.attenuation</h1><div class="highlight"><pre>
         <span class="n">rot_ind</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span>
         <span class="n">det_ind</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span>
         <span class="n">slice_ind</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">int</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
-        <span class="n">axes</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="n">Sequence</span><span class="p">[</span><span class="nb">int</span><span class="p">],</span> <span class="n">NDArray</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span><span class="o">-</span><span class="mi">2</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">),</span>
-    <span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+        <span class="n">axes</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="n">Sequence</span><span class="p">[</span><span class="nb">int</span><span class="p">],</span> <span class="n">NDArrayInt</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span><span class="o">-</span><span class="mi">2</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">),</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">List</span><span class="p">[</span><span class="nb">float</span><span class="p">]:</span>
         <span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Plot the requested attenuation map.</span>
 
@@ -225,6 +226,11 @@ <h1>Source code for corrct.attenuation</h1><div class="highlight"><pre>
 <span class="sd">        axes : Sequence[int] | NDArray, optional</span>
 <span class="sd">            Axes of the slice. The default is (-2, -1).</span>
 
+<span class="sd">        Returns</span>
+<span class="sd">        -------</span>
+<span class="sd">        List[float]</span>
+<span class="sd">            The extent of the axes plot (min-max coords).</span>
+
 <span class="sd">        Raises</span>
 <span class="sd">        ------</span>
 <span class="sd">        ValueError</span>
@@ -241,7 +247,8 @@ <h1>Source code for corrct.attenuation</h1><div class="highlight"><pre>
         <span class="n">slice_shape</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">vol_shape_zyx</span><span class="p">[</span><span class="nb">list</span><span class="p">(</span><span class="n">axes</span><span class="p">)]</span>
         <span class="n">coords</span> <span class="o">=</span> <span class="p">[(</span><span class="o">-</span><span class="p">(</span><span class="n">s</span> <span class="o">-</span> <span class="mi">1</span><span class="p">)</span> <span class="o">/</span> <span class="mi">2</span><span class="p">,</span> <span class="p">(</span><span class="n">s</span> <span class="o">-</span> <span class="mi">1</span><span class="p">)</span> <span class="o">/</span> <span class="mi">2</span><span class="p">)</span> <span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">slice_shape</span><span class="p">]</span>
 
-        <span class="n">ax</span><span class="o">.</span><span class="n">imshow</span><span class="p">(</span><span class="n">att_map</span><span class="p">,</span> <span class="n">extent</span><span class="o">=</span><span class="nb">list</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">concatenate</span><span class="p">(</span><span class="n">coords</span><span class="p">)))</span>
+        <span class="n">extent</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">concatenate</span><span class="p">(</span><span class="n">coords</span><span class="p">))</span>
+        <span class="n">ax</span><span class="o">.</span><span class="n">imshow</span><span class="p">(</span><span class="n">att_map</span><span class="p">,</span> <span class="n">extent</span><span class="o">=</span><span class="n">extent</span><span class="p">)</span>
 
         <span class="k">if</span> <span class="n">other_dim</span> <span class="o">==</span> <span class="o">-</span><span class="mi">3</span><span class="p">:</span>
             <span class="n">arrow_length</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linalg</span><span class="o">.</span><span class="n">norm</span><span class="p">(</span><span class="n">slice_shape</span><span class="p">)</span> <span class="o">/</span> <span class="n">np</span><span class="o">.</span><span class="n">pi</span>
@@ -262,13 +269,15 @@ <h1>Source code for corrct.attenuation</h1><div class="highlight"><pre>
             <span class="n">beam_e_orig</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">])</span>
 
             <span class="n">ax</span><span class="o">.</span><span class="n">arrow</span><span class="p">(</span><span class="o">*</span><span class="n">beam_i_orig</span><span class="p">,</span> <span class="o">*</span><span class="n">beam_i_dir</span><span class="p">,</span> <span class="o">**</span><span class="n">arrow_args</span><span class="p">,</span> <span class="n">fc</span><span class="o">=</span><span class="s2">&quot;r&quot;</span><span class="p">,</span> <span class="n">ec</span><span class="o">=</span><span class="s2">&quot;r&quot;</span><span class="p">)</span>
-            <span class="n">ax</span><span class="o">.</span><span class="n">arrow</span><span class="p">(</span><span class="o">*</span><span class="n">beam_e_orig</span><span class="p">,</span> <span class="o">*</span><span class="n">beam_e_dir</span><span class="p">,</span> <span class="o">**</span><span class="n">arrow_args</span><span class="p">,</span> <span class="n">fc</span><span class="o">=</span><span class="s2">&quot;k&quot;</span><span class="p">,</span> <span class="n">ec</span><span class="o">=</span><span class="s2">&quot;k&quot;</span><span class="p">)</span></div>
+            <span class="n">ax</span><span class="o">.</span><span class="n">arrow</span><span class="p">(</span><span class="o">*</span><span class="n">beam_e_orig</span><span class="p">,</span> <span class="o">*</span><span class="n">beam_e_dir</span><span class="p">,</span> <span class="o">**</span><span class="n">arrow_args</span><span class="p">,</span> <span class="n">fc</span><span class="o">=</span><span class="s2">&quot;k&quot;</span><span class="p">,</span> <span class="n">ec</span><span class="o">=</span><span class="s2">&quot;k&quot;</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">extent</span></div>
 
 <div class="viewcode-block" id="AttenuationVolume.get_maps"><a class="viewcode-back" href="../../corrct.html#corrct.attenuation.AttenuationVolume.get_maps">[docs]</a>    <span class="k">def</span> <span class="nf">get_maps</span><span class="p">(</span>
         <span class="bp">self</span><span class="p">,</span>
         <span class="n">roi</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">ArrayLike</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
-        <span class="n">rot_ind</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">slice</span><span class="p">,</span> <span class="n">Sequence</span><span class="p">[</span><span class="nb">int</span><span class="p">],</span> <span class="kc">None</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
-        <span class="n">det_ind</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">slice</span><span class="p">,</span> <span class="n">Sequence</span><span class="p">[</span><span class="nb">int</span><span class="p">],</span> <span class="kc">None</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">rot_ind</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">slice</span><span class="p">,</span> <span class="n">Sequence</span><span class="p">[</span><span class="nb">int</span><span class="p">],</span> <span class="n">NDArrayInt</span><span class="p">,</span> <span class="kc">None</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">det_ind</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">slice</span><span class="p">,</span> <span class="n">Sequence</span><span class="p">[</span><span class="nb">int</span><span class="p">],</span> <span class="n">NDArrayInt</span><span class="p">,</span> <span class="kc">None</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
     <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">NDArray</span><span class="p">:</span>
         <span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Return the attenuation maps.</span>
@@ -307,8 +316,8 @@ <h1>Source code for corrct.attenuation</h1><div class="highlight"><pre>
 <div class="viewcode-block" id="AttenuationVolume.get_projector_args"><a class="viewcode-back" href="../../corrct.html#corrct.attenuation.AttenuationVolume.get_projector_args">[docs]</a>    <span class="k">def</span> <span class="nf">get_projector_args</span><span class="p">(</span>
         <span class="bp">self</span><span class="p">,</span>
         <span class="n">roi</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">ArrayLike</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
-        <span class="n">rot_ind</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">slice</span><span class="p">,</span> <span class="n">Sequence</span><span class="p">[</span><span class="nb">int</span><span class="p">],</span> <span class="kc">None</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
-        <span class="n">det_ind</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">slice</span><span class="p">,</span> <span class="n">Sequence</span><span class="p">[</span><span class="nb">int</span><span class="p">],</span> <span class="kc">None</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">rot_ind</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">slice</span><span class="p">,</span> <span class="n">Sequence</span><span class="p">[</span><span class="nb">int</span><span class="p">],</span> <span class="n">NDArrayInt</span><span class="p">,</span> <span class="kc">None</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">det_ind</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">slice</span><span class="p">,</span> <span class="n">Sequence</span><span class="p">[</span><span class="nb">int</span><span class="p">],</span> <span class="n">NDArrayInt</span><span class="p">,</span> <span class="kc">None</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
     <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">NDArray</span><span class="p">]:</span>
         <span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Return the projector arguments.</span>