make html

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

@@ -634,7 +634,7 @@ <h1>Source code for unravel.core.img_io</h1><div class="highlight"><pre>
 <span class="sd">    save_metadata : str, optional</span>
 <span class="sd">        Path to save metadata file. Default is None.</span>
 <span class="sd">    xy_res : float, optional</span>
-<span class="sd">        The resolution in the xy-plane.</span>
+<span class="sd">        The resolution in the xy-plane (use if res is not specified in the metadata).</span>
 <span class="sd">    z_res : float, optional</span>
 <span class="sd">        The resolution in the z-plane.</span>
 
@@ -652,7 +652,18 @@ <h1>Source code for unravel.core.img_io</h1><div class="highlight"><pre>
     <span class="n">ndarray</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="o">.</span><span class="n">astype</span><span class="p">(</span><span class="n">data_type</span><span class="p">)</span>
     <span class="n">ndarray</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">squeeze</span><span class="p">(</span><span class="n">ndarray</span><span class="p">)</span>
     <span class="n">ndarray</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">transpose</span><span class="p">(</span><span class="n">ndarray</span><span class="p">,</span> <span class="p">(</span><span class="mi">2</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">))</span> <span class="k">if</span> <span class="n">desired_axis_order</span> <span class="o">==</span> <span class="s2">&quot;zyx&quot;</span> <span class="k">else</span> <span class="n">ndarray</span>
+
+    <span class="n">res_specified</span> <span class="o">=</span> <span class="kc">True</span> <span class="k">if</span> <span class="n">xy_res</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="k">else</span> <span class="kc">False</span>
+    <span class="k">if</span> <span class="n">res_specified</span><span class="p">:</span>
+        <span class="n">original_xy_res</span> <span class="o">=</span> <span class="n">xy_res</span>
+        <span class="n">original_z_res</span> <span class="o">=</span> <span class="n">z_res</span>
+
     <span class="n">xy_res</span><span class="p">,</span> <span class="n">z_res</span><span class="p">,</span> <span class="n">x_dim</span><span class="p">,</span> <span class="n">y_dim</span><span class="p">,</span> <span class="n">z_dim</span> <span class="o">=</span> <span class="n">metadata</span><span class="p">(</span><span class="n">nii_path</span><span class="p">,</span> <span class="n">ndarray</span><span class="p">,</span> <span class="n">return_res</span><span class="p">,</span> <span class="n">return_metadata</span><span class="p">,</span> <span class="n">save_metadata</span><span class="o">=</span><span class="n">save_metadata</span><span class="p">)</span>
+
+    <span class="k">if</span> <span class="n">res_specified</span><span class="p">:</span>
+        <span class="n">xy_res</span> <span class="o">=</span> <span class="n">original_xy_res</span>
+        <span class="n">z_res</span> <span class="o">=</span> <span class="n">original_z_res</span>
+
     <span class="k">return</span> <span class="n">return_3D_img</span><span class="p">(</span><span class="n">ndarray</span><span class="p">,</span> <span class="n">return_metadata</span><span class="p">,</span> <span class="n">return_res</span><span class="p">,</span> <span class="n">xy_res</span><span class="p">,</span> <span class="n">z_res</span><span class="p">,</span> <span class="n">x_dim</span><span class="p">,</span> <span class="n">y_dim</span><span class="p">,</span> <span class="n">z_dim</span><span class="p">)</span></div>
 
 

unravel/docs/_build/html/_modules/unravel/warp/to_atlas.html

@@ -490,7 +490,7 @@ <h1>Source code for unravel.warp.to_atlas</h1><div class="highlight"><pre>
             <span class="n">sample_path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">sample</span><span class="p">)</span><span class="o">.</span><span class="n">resolve</span><span class="p">()</span> <span class="k">if</span> <span class="n">sample</span> <span class="o">!=</span> <span class="n">Path</span><span class="o">.</span><span class="n">cwd</span><span class="p">()</span><span class="o">.</span><span class="n">name</span> <span class="k">else</span> <span class="n">Path</span><span class="o">.</span><span class="n">cwd</span><span class="p">()</span>
 
             <span class="n">output</span> <span class="o">=</span> <span class="n">sample_path</span> <span class="o">/</span> <span class="s2">&quot;atlas_space&quot;</span> <span class="o">/</span> <span class="n">args</span><span class="o">.</span><span class="n">output</span>
-            <span class="n">output</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">parents</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+            <span class="n">output</span><span class="o">.</span><span class="n">parent</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">parents</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
             <span class="k">if</span> <span class="n">output</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
                 <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="se">\n\n</span><span class="s2">    </span><span class="si">{</span><span class="n">output</span><span class="si">}</span><span class="s2"> already exists. Skipping.</span><span class="se">\n</span><span class="s2">&quot;</span><span class="p">)</span>
                 <span class="k">continue</span>

unravel/docs/_build/html/unravel/core/img_io.html

@@ -647,7 +647,7 @@ <h2>Helper Functions:<a class="headerlink" href="#helper-functions" title="Link
 <li><p><strong>return_res</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a><em>, </em><em>optional</em>) – Whether to return resolutions. Default is False.</p></li>
 <li><p><strong>return_metadata</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a><em>, </em><em>optional</em>) – Whether to return metadata. Default is False.</p></li>
 <li><p><strong>save_metadata</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Path to save metadata file. Default is None.</p></li>
-<li><p><strong>xy_res</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a><em>, </em><em>optional</em>) – The resolution in the xy-plane.</p></li>
+<li><p><strong>xy_res</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a><em>, </em><em>optional</em>) – The resolution in the xy-plane (use if res is not specified in the metadata).</p></li>
 <li><p><strong>z_res</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a><em>, </em><em>optional</em>) – The resolution in the z-plane.</p></li>
 </ul>
 </dd>