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@daniel-rijsketic
daniel-rijsketic committed Jul 1, 2024
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Binary file modified unravel/docs/_build/doctrees/environment.pickle
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1 change: 1 addition & 0 deletions unravel/docs/_build/html/_modules/unravel/image_io/nii_info.html
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Expand Up @@ -375,6 +375,7 @@ <h1>Source code for unravel.image_io.nii_info</h1><div class="highlight"><pre>
<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/img.nii.gz&#39;</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;-v&#39;</span><span class="p">,</span> <span class="s1">&#39;--verbose&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Increase verbosity.&#39;</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="n">default</span><span class="o">=</span><span class="kc">False</span><span class="p">)</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>

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2 changes: 1 addition & 1 deletion unravel/docs/_build/html/_modules/unravel/voxel_stats/z_score.html
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Expand Up @@ -412,7 +412,7 @@ <h1>Source code for unravel.voxel_stats.z_score</h1><div class="highlight"><pre>
<span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-amas&#39;</span><span class="p">,</span> <span class="s1">&#39;--atlas_mask&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;path/atlas_mask.nii.gz (can use tmas and/or amas)&#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="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;-n&#39;</span><span class="p">,</span> <span class="s1">&#39;--no_tmask&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Provide flag to avoid use of tmas&#39;</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="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-fri&#39;</span><span class="p">,</span> <span class="s1">&#39;--fixed_reg_in&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Reference nii header from ``reg``. Default: reg_outputs/autofl_50um_masked_fixed_reg_input.nii.gz&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s2">&quot;reg_outputs/autofl_50um_masked_fixed_reg_input.nii.gz&quot;</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;-a&#39;</span><span class="p">,</span> <span class="s1">&#39;--atlas&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;path/atlas.nii.gz for warping mask to atlas space (Default: path/gubra_ano_combined_25um.nii.gz)&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s1">&#39;/usr/local/unravel/atlases/gubra/gubra_ano_combined_25um.nii.gz&#39;</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;-a&#39;</span><span class="p">,</span> <span class="s1">&#39;--atlas&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;path/atlas.nii.gz. It is used as a fixed image for warping a brain mask to atlas space (Default: path/gubra_ano_combined_25um.nii.gz)&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s1">&#39;/usr/local/unravel/atlases/gubra/gubra_ano_combined_25um.nii.gz&#39;</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;-inp&#39;</span><span class="p">,</span> <span class="s1">&#39;--interpol&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Type of interpolation (nearestNeighbor, multiLabel [default]).&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s1">&#39;multiLabel&#39;</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;-v&#39;</span><span class="p">,</span> <span class="s1">&#39;--verbose&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Increase verbosity&#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="n">parser</span><span class="o">.</span><span class="n">epilog</span> <span class="o">=</span> <span class="vm">__doc__</span>
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2 changes: 1 addition & 1 deletion unravel/docs/_build/html/_modules/unravel/warp/to_atlas.html
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Expand Up @@ -399,7 +399,7 @@ <h1>Source code for unravel.warp.to_atlas</h1><div class="highlight"><pre>
<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>
<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;-a&#39;</span><span class="p">,</span> <span class="s1">&#39;--atlas&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;path/atlas.nii.gz (Default: /usr/local/unravel/atlases/gubra/gubra_ano_combined_25um.nii.gz)&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s1">&#39;/usr/local/unravel/atlases/gubra/gubra_ano_combined_25um.nii.gz&#39;</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;-a&#39;</span><span class="p">,</span> <span class="s1">&#39;--atlas&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;path/atlas.nii.gz for use as the fixed image (Default: /usr/local/unravel/atlases/gubra/gubra_ano_combined_25um.nii.gz)&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s1">&#39;/usr/local/unravel/atlases/gubra/gubra_ano_combined_25um.nii.gz&#39;</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;-dt&#39;</span><span class="p">,</span> <span class="s1">&#39;--dtype&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Desired dtype for output (e.g., uint8, uint16). Default: uint16&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s2">&quot;uint16&quot;</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;-fri&#39;</span><span class="p">,</span> <span class="s1">&#39;--fixed_reg_in&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Reference nii header from ``reg``. Default: reg_outputs/autofl_50um_masked_fixed_reg_input.nii.gz&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s2">&quot;reg_outputs/autofl_50um_masked_fixed_reg_input.nii.gz&quot;</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;-r&#39;</span><span class="p">,</span> <span class="s1">&#39;--reg_res&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Resolution of registration inputs in microns. Default: 50&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s1">&#39;50&#39;</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>
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