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actions-user committed Nov 26, 2024
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70 changes: 34 additions & 36 deletions main/reference/vision/utils/io/index.html
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Expand Up @@ -3427,8 +3427,7 @@ <h3 id="eva.vision.utils.io.nifti.save_array_as_nifti" class="doc doc-heading">
<span class="normal"><a href="#__codelineno-0-54">54</a></span>
<span class="normal"><a href="#__codelineno-0-55">55</a></span>
<span class="normal"><a href="#__codelineno-0-56">56</a></span>
<span class="normal"><a href="#__codelineno-0-57">57</a></span>
<span class="normal"><a href="#__codelineno-0-58">58</a></span></pre></div></td><td class="code"><div><pre><span></span><code><span id="__span-0-43"><a id="__codelineno-0-43" name="__codelineno-0-43"></a><span class="k">def</span> <span class="nf">save_array_as_nifti</span><span class="p">(</span>
<span class="normal"><a href="#__codelineno-0-57">57</a></span></pre></div></td><td class="code"><div><pre><span></span><code><span id="__span-0-43"><a id="__codelineno-0-43" name="__codelineno-0-43"></a><span class="k">def</span> <span class="nf">save_array_as_nifti</span><span class="p">(</span>
</span><span id="__span-0-44"><a id="__codelineno-0-44" name="__codelineno-0-44"></a> <span class="n">array</span><span class="p">:</span> <span class="n">npt</span><span class="o">.</span><span class="n">ArrayLike</span><span class="p">,</span>
</span><span id="__span-0-45"><a id="__codelineno-0-45" name="__codelineno-0-45"></a> <span class="n">filename</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
</span><span id="__span-0-46"><a id="__codelineno-0-46" name="__codelineno-0-46"></a> <span class="o">*</span><span class="p">,</span>
Expand All @@ -3442,8 +3441,7 @@ <h3 id="eva.vision.utils.io.nifti.save_array_as_nifti" class="doc doc-heading">
</span><span id="__span-0-54"><a id="__codelineno-0-54" name="__codelineno-0-54"></a><span class="sd"> dtype: The data type to save the image.</span>
</span><span id="__span-0-55"><a id="__codelineno-0-55" name="__codelineno-0-55"></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="__span-0-56"><a id="__codelineno-0-56" name="__codelineno-0-56"></a> <span class="n">nifti_image</span> <span class="o">=</span> <span class="n">nib</span><span class="o">.</span><span class="n">Nifti1Image</span><span class="p">(</span><span class="n">array</span><span class="p">,</span> <span class="n">affine</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">eye</span><span class="p">(</span><span class="mi">4</span><span class="p">),</span> <span class="n">dtype</span><span class="o">=</span><span class="n">dtype</span><span class="p">)</span> <span class="c1"># type: ignore</span>
</span><span id="__span-0-57"><a id="__codelineno-0-57" name="__codelineno-0-57"></a> <span class="n">nifti_image</span><span class="o">.</span><span class="n">header</span><span class="o">.</span><span class="n">get_xyzt_units</span><span class="p">()</span>
</span><span id="__span-0-58"><a id="__codelineno-0-58" name="__codelineno-0-58"></a> <span class="n">nifti_image</span><span class="o">.</span><span class="n">to_filename</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
</span><span id="__span-0-57"><a id="__codelineno-0-57" name="__codelineno-0-57"></a> <span class="n">nifti_image</span><span class="o">.</span><span class="n">to_filename</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
</span></code></pre></div></td></tr></table></div>
</details>
</div>
Expand Down Expand Up @@ -3550,7 +3548,8 @@ <h3 id="eva.vision.utils.io.nifti.fetch_nifti_shape" class="doc doc-heading">

<details class="quote">
<summary>Source code in <code>src/eva/vision/utils/io/nifti.py</code></summary>
<div class="language-python highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"><a href="#__codelineno-0-61">61</a></span>
<div class="language-python highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"><a href="#__codelineno-0-60">60</a></span>
<span class="normal"><a href="#__codelineno-0-61">61</a></span>
<span class="normal"><a href="#__codelineno-0-62">62</a></span>
<span class="normal"><a href="#__codelineno-0-63">63</a></span>
<span class="normal"><a href="#__codelineno-0-64">64</a></span>
Expand All @@ -3564,23 +3563,22 @@ <h3 id="eva.vision.utils.io.nifti.fetch_nifti_shape" class="doc doc-heading">
<span class="normal"><a href="#__codelineno-0-72">72</a></span>
<span class="normal"><a href="#__codelineno-0-73">73</a></span>
<span class="normal"><a href="#__codelineno-0-74">74</a></span>
<span class="normal"><a href="#__codelineno-0-75">75</a></span>
<span class="normal"><a href="#__codelineno-0-76">76</a></span></pre></div></td><td class="code"><div><pre><span></span><code><span id="__span-0-61"><a id="__codelineno-0-61" name="__codelineno-0-61"></a><span class="k">def</span> <span class="nf">fetch_nifti_shape</span><span class="p">(</span><span class="n">path</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Tuple</span><span class="p">[</span><span class="nb">int</span><span class="p">]:</span>
</span><span id="__span-0-62"><a id="__codelineno-0-62" name="__codelineno-0-62"></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Fetches the NIfTI image shape from a file.</span>
</span><span id="__span-0-63"><a id="__codelineno-0-63" name="__codelineno-0-63"></a>
</span><span id="__span-0-64"><a id="__codelineno-0-64" name="__codelineno-0-64"></a><span class="sd"> Args:</span>
</span><span id="__span-0-65"><a id="__codelineno-0-65" name="__codelineno-0-65"></a><span class="sd"> path: The path to the NIfTI file.</span>
</span><span id="__span-0-66"><a id="__codelineno-0-66" name="__codelineno-0-66"></a>
</span><span id="__span-0-67"><a id="__codelineno-0-67" name="__codelineno-0-67"></a><span class="sd"> Returns:</span>
</span><span id="__span-0-68"><a id="__codelineno-0-68" name="__codelineno-0-68"></a><span class="sd"> The image shape.</span>
</span><span id="__span-0-69"><a id="__codelineno-0-69" name="__codelineno-0-69"></a>
</span><span id="__span-0-70"><a id="__codelineno-0-70" name="__codelineno-0-70"></a><span class="sd"> Raises:</span>
</span><span id="__span-0-71"><a id="__codelineno-0-71" name="__codelineno-0-71"></a><span class="sd"> FileExistsError: If the path does not exist or it is unreachable.</span>
</span><span id="__span-0-72"><a id="__codelineno-0-72" name="__codelineno-0-72"></a><span class="sd"> ValueError: If the input channel is invalid for the image.</span>
</span><span id="__span-0-73"><a id="__codelineno-0-73" name="__codelineno-0-73"></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="__span-0-74"><a id="__codelineno-0-74" name="__codelineno-0-74"></a> <span class="n">_utils</span><span class="o">.</span><span class="n">check_file</span><span class="p">(</span><span class="n">path</span><span class="p">)</span>
</span><span id="__span-0-75"><a id="__codelineno-0-75" name="__codelineno-0-75"></a> <span class="n">image</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">path</span><span class="p">)</span> <span class="c1"># type: ignore</span>
</span><span id="__span-0-76"><a id="__codelineno-0-76" name="__codelineno-0-76"></a> <span class="k">return</span> <span class="n">image</span><span class="o">.</span><span class="n">header</span><span class="o">.</span><span class="n">get_data_shape</span><span class="p">()</span> <span class="c1"># type: ignore</span>
<span class="normal"><a href="#__codelineno-0-75">75</a></span></pre></div></td><td class="code"><div><pre><span></span><code><span id="__span-0-60"><a id="__codelineno-0-60" name="__codelineno-0-60"></a><span class="k">def</span> <span class="nf">fetch_nifti_shape</span><span class="p">(</span><span class="n">path</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Tuple</span><span class="p">[</span><span class="nb">int</span><span class="p">]:</span>
</span><span id="__span-0-61"><a id="__codelineno-0-61" name="__codelineno-0-61"></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Fetches the NIfTI image shape from a file.</span>
</span><span id="__span-0-62"><a id="__codelineno-0-62" name="__codelineno-0-62"></a>
</span><span id="__span-0-63"><a id="__codelineno-0-63" name="__codelineno-0-63"></a><span class="sd"> Args:</span>
</span><span id="__span-0-64"><a id="__codelineno-0-64" name="__codelineno-0-64"></a><span class="sd"> path: The path to the NIfTI file.</span>
</span><span id="__span-0-65"><a id="__codelineno-0-65" name="__codelineno-0-65"></a>
</span><span id="__span-0-66"><a id="__codelineno-0-66" name="__codelineno-0-66"></a><span class="sd"> Returns:</span>
</span><span id="__span-0-67"><a id="__codelineno-0-67" name="__codelineno-0-67"></a><span class="sd"> The image shape.</span>
</span><span id="__span-0-68"><a id="__codelineno-0-68" name="__codelineno-0-68"></a>
</span><span id="__span-0-69"><a id="__codelineno-0-69" name="__codelineno-0-69"></a><span class="sd"> Raises:</span>
</span><span id="__span-0-70"><a id="__codelineno-0-70" name="__codelineno-0-70"></a><span class="sd"> FileExistsError: If the path does not exist or it is unreachable.</span>
</span><span id="__span-0-71"><a id="__codelineno-0-71" name="__codelineno-0-71"></a><span class="sd"> ValueError: If the input channel is invalid for the image.</span>
</span><span id="__span-0-72"><a id="__codelineno-0-72" name="__codelineno-0-72"></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="__span-0-73"><a id="__codelineno-0-73" name="__codelineno-0-73"></a> <span class="n">_utils</span><span class="o">.</span><span class="n">check_file</span><span class="p">(</span><span class="n">path</span><span class="p">)</span>
</span><span id="__span-0-74"><a id="__codelineno-0-74" name="__codelineno-0-74"></a> <span class="n">image</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">path</span><span class="p">)</span> <span class="c1"># type: ignore</span>
</span><span id="__span-0-75"><a id="__codelineno-0-75" name="__codelineno-0-75"></a> <span class="k">return</span> <span class="n">image</span><span class="o">.</span><span class="n">header</span><span class="o">.</span><span class="n">get_data_shape</span><span class="p">()</span> <span class="c1"># type: ignore</span>
</span></code></pre></div></td></tr></table></div>
</details>
</div>
Expand Down Expand Up @@ -3654,7 +3652,8 @@ <h3 id="eva.vision.utils.io.nifti.fetch_nifti_axis_direction_code" class="doc do

<details class="quote">
<summary>Source code in <code>src/eva/vision/utils/io/nifti.py</code></summary>
<div class="language-python highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"><a href="#__codelineno-0-79">79</a></span>
<div class="language-python highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"><a href="#__codelineno-0-78">78</a></span>
<span class="normal"><a href="#__codelineno-0-79">79</a></span>
<span class="normal"><a href="#__codelineno-0-80">80</a></span>
<span class="normal"><a href="#__codelineno-0-81">81</a></span>
<span class="normal"><a href="#__codelineno-0-82">82</a></span>
Expand All @@ -3664,19 +3663,18 @@ <h3 id="eva.vision.utils.io.nifti.fetch_nifti_axis_direction_code" class="doc do
<span class="normal"><a href="#__codelineno-0-86">86</a></span>
<span class="normal"><a href="#__codelineno-0-87">87</a></span>
<span class="normal"><a href="#__codelineno-0-88">88</a></span>
<span class="normal"><a href="#__codelineno-0-89">89</a></span>
<span class="normal"><a href="#__codelineno-0-90">90</a></span></pre></div></td><td class="code"><div><pre><span></span><code><span id="__span-0-79"><a id="__codelineno-0-79" name="__codelineno-0-79"></a><span class="k">def</span> <span class="nf">fetch_nifti_axis_direction_code</span><span class="p">(</span><span class="n">path</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
</span><span id="__span-0-80"><a id="__codelineno-0-80" name="__codelineno-0-80"></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Fetches the NIfTI axis direction code from a file.</span>
</span><span id="__span-0-81"><a id="__codelineno-0-81" name="__codelineno-0-81"></a>
</span><span id="__span-0-82"><a id="__codelineno-0-82" name="__codelineno-0-82"></a><span class="sd"> Args:</span>
</span><span id="__span-0-83"><a id="__codelineno-0-83" name="__codelineno-0-83"></a><span class="sd"> path: The path to the NIfTI file.</span>
</span><span id="__span-0-84"><a id="__codelineno-0-84" name="__codelineno-0-84"></a>
</span><span id="__span-0-85"><a id="__codelineno-0-85" name="__codelineno-0-85"></a><span class="sd"> Returns:</span>
</span><span id="__span-0-86"><a id="__codelineno-0-86" name="__codelineno-0-86"></a><span class="sd"> The axis direction codes as string (e.g. &quot;LAS&quot;).</span>
</span><span id="__span-0-87"><a id="__codelineno-0-87" name="__codelineno-0-87"></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="__span-0-88"><a id="__codelineno-0-88" name="__codelineno-0-88"></a> <span class="n">_utils</span><span class="o">.</span><span class="n">check_file</span><span class="p">(</span><span class="n">path</span><span class="p">)</span>
</span><span id="__span-0-89"><a id="__codelineno-0-89" name="__codelineno-0-89"></a> <span class="n">image_data</span><span class="p">:</span> <span class="n">nib</span><span class="o">.</span><span class="n">Nifti1Image</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">path</span><span class="p">)</span> <span class="c1"># type: ignore</span>
</span><span id="__span-0-90"><a id="__codelineno-0-90" name="__codelineno-0-90"></a> <span class="k">return</span> <span class="s2">&quot;&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">orientations</span><span class="o">.</span><span class="n">aff2axcodes</span><span class="p">(</span><span class="n">image_data</span><span class="o">.</span><span class="n">affine</span><span class="p">))</span>
<span class="normal"><a href="#__codelineno-0-89">89</a></span></pre></div></td><td class="code"><div><pre><span></span><code><span id="__span-0-78"><a id="__codelineno-0-78" name="__codelineno-0-78"></a><span class="k">def</span> <span class="nf">fetch_nifti_axis_direction_code</span><span class="p">(</span><span class="n">path</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
</span><span id="__span-0-79"><a id="__codelineno-0-79" name="__codelineno-0-79"></a><span class="w"> </span><span class="sd">&quot;&quot;&quot;Fetches the NIfTI axis direction code from a file.</span>
</span><span id="__span-0-80"><a id="__codelineno-0-80" name="__codelineno-0-80"></a>
</span><span id="__span-0-81"><a id="__codelineno-0-81" name="__codelineno-0-81"></a><span class="sd"> Args:</span>
</span><span id="__span-0-82"><a id="__codelineno-0-82" name="__codelineno-0-82"></a><span class="sd"> path: The path to the NIfTI file.</span>
</span><span id="__span-0-83"><a id="__codelineno-0-83" name="__codelineno-0-83"></a>
</span><span id="__span-0-84"><a id="__codelineno-0-84" name="__codelineno-0-84"></a><span class="sd"> Returns:</span>
</span><span id="__span-0-85"><a id="__codelineno-0-85" name="__codelineno-0-85"></a><span class="sd"> The axis direction codes as string (e.g. &quot;LAS&quot;).</span>
</span><span id="__span-0-86"><a id="__codelineno-0-86" name="__codelineno-0-86"></a><span class="sd"> &quot;&quot;&quot;</span>
</span><span id="__span-0-87"><a id="__codelineno-0-87" name="__codelineno-0-87"></a> <span class="n">_utils</span><span class="o">.</span><span class="n">check_file</span><span class="p">(</span><span class="n">path</span><span class="p">)</span>
</span><span id="__span-0-88"><a id="__codelineno-0-88" name="__codelineno-0-88"></a> <span class="n">image_data</span><span class="p">:</span> <span class="n">nib</span><span class="o">.</span><span class="n">Nifti1Image</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">path</span><span class="p">)</span> <span class="c1"># type: ignore</span>
</span><span id="__span-0-89"><a id="__codelineno-0-89" name="__codelineno-0-89"></a> <span class="k">return</span> <span class="s2">&quot;&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">orientations</span><span class="o">.</span><span class="n">aff2axcodes</span><span class="p">(</span><span class="n">image_data</span><span class="o">.</span><span class="n">affine</span><span class="p">))</span>
</span></code></pre></div></td></tr></table></div>
</details>
</div>
Expand Down
2 changes: 1 addition & 1 deletion main/search/search_index.json
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