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@daniel-rijsketic
daniel-rijsketic committed Jul 2, 2024
1 parent 55c5c09 commit d7c0d29
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9 changes: 6 additions & 3 deletions unravel/docs/_build/html/_modules/unravel/image_tools/pad.html
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Expand Up @@ -380,6 +380,7 @@ <h1>Source code for unravel.image_tools.pad</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;-ort&#39;</span><span class="p">,</span> <span class="s1">&#39;--ort_code&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;3 letter orientation code of fixed image if not set in fixed_img (e.g., RAS)&#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;-r&#39;</span><span class="p">,</span> <span class="s1">&#39;--ref_nii&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Reference image for setting the orientation code&#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;-o&#39;</span><span class="p">,</span> <span class="s1">&#39;--output&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;path/img.nii.gz. Default: None (saves as path/img_pad.nii.gz) &#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;-zero&#39;</span><span class="p">,</span> <span class="s1">&#39;--zero_origin&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Set the origin to zero in the affine matrix. Default: False&#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">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. Default: False&#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>
Expand Down Expand Up @@ -409,11 +410,13 @@ <h1>Source code for unravel.image_tools.pad</h1><div class="highlight"><pre>

<span class="c1"># Set the orientation of the image (use if not already set correctly in the header; check with ``io_reorient_nii``)</span>
<span class="k">if</span> <span class="n">args</span><span class="o">.</span><span class="n">ort_code</span><span class="p">:</span>
<span class="n">fixed_img_padded_nii</span> <span class="o">=</span> <span class="n">reorient_nii</span><span class="p">(</span><span class="n">fixed_img_padded_nii</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">ort_code</span><span class="p">,</span> <span class="n">zero_origin</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">apply</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">form_code</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">fixed_img_padded_nii</span> <span class="o">=</span> <span class="n">reorient_nii</span><span class="p">(</span><span class="n">fixed_img_padded_nii</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">ort_code</span><span class="p">,</span> <span class="n">zero_origin</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">zero_origin</span><span class="p">,</span> <span class="n">apply</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">form_code</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="k">elif</span> <span class="n">args</span><span class="o">.</span><span class="n">ref_nii</span><span class="p">:</span>
<span class="n">ref_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">ref_nii</span><span class="p">)</span>
<span class="n">ort_code</span> <span class="o">=</span> <span class="n">nii_axis_codes</span><span class="p">(</span><span class="n">ref_nii</span><span class="p">)</span>
<span class="n">fixed_img_padded_nii</span> <span class="o">=</span> <span class="n">reorient_nii</span><span class="p">(</span><span class="n">fixed_img_padded_nii</span><span class="p">,</span> <span class="n">ort_code</span><span class="p">,</span> <span class="n">zero_origin</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">apply</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">form_code</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="n">fixed_img_padded_nii</span> <span class="o">=</span> <span class="n">reorient_nii</span><span class="p">(</span><span class="n">fixed_img_padded_nii</span><span class="p">,</span> <span class="n">ort_code</span><span class="p">,</span> <span class="n">zero_origin</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">zero_origin</span><span class="p">,</span> <span class="n">apply</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">form_code</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">fixed_img_padded_nii</span> <span class="o">=</span> <span class="n">reorient_nii</span><span class="p">(</span><span class="n">fixed_img_padded_nii</span><span class="p">,</span> <span class="n">nii_axis_codes</span><span class="p">(</span><span class="n">nii</span><span class="p">),</span> <span class="n">zero_origin</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">apply</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">form_code</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>

<span class="k">if</span> <span class="n">args</span><span class="o">.</span><span class="n">output</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">padded_img_path</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">input</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;.nii.gz&#39;</span><span class="p">,</span> <span class="s1">&#39;_pad.nii.gz&#39;</span><span class="p">)</span>
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