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+medipt.org
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+<!DOCTYPE html>
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+  <title>Overview: module code &mdash; MedIPT</title>
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+  <h1>All modules for which code is available</h1>
+<ul><li><a href="medipt/crop_image/threshold_crop_background.html">medipt.crop_image.threshold_crop_background</a></li>
+<li><a href="medipt/resample_image/resample_image.html">medipt.resample_image.resample_image</a></li>
+<li><a href="medipt/transforms/intensity/change_image_gamma.html">medipt.transforms.intensity.change_image_gamma</a></li>
+<li><a href="medipt/transforms/intensity/clamp_intensity.html">medipt.transforms.intensity.clamp_intensity</a></li>
+<li><a href="medipt/transforms/intensity/gaussian_blur.html">medipt.transforms.intensity.gaussian_blur</a></li>
+<li><a href="medipt/transforms/intensity/gaussian_noise.html">medipt.transforms.intensity.gaussian_noise</a></li>
+<li><a href="medipt/transforms/intensity/intensity_utils_np.html">medipt.transforms.intensity.intensity_utils_np</a></li>
+<li><a href="medipt/transforms/intensity/intensity_utils_sitk.html">medipt.transforms.intensity.intensity_utils_sitk</a></li>
+<li><a href="medipt/transforms/intensity/rescale_intensity.html">medipt.transforms.intensity.rescale_intensity</a></li>
+<li><a href="medipt/transforms/intensity/shift_scale_intensity.html">medipt.transforms.intensity.shift_scale_intensity</a></li>
+<li><a href="medipt/transforms/spatial/composite_transform.html">medipt.transforms.spatial.composite_transform</a></li>
+<li><a href="medipt/transforms/spatial/elastic_deformation_transform.html">medipt.transforms.spatial.elastic_deformation_transform</a></li>
+<li><a href="medipt/transforms/spatial/flipping_transform.html">medipt.transforms.spatial.flipping_transform</a></li>
+<li><a href="medipt/transforms/spatial/random_affine_transform.html">medipt.transforms.spatial.random_affine_transform</a></li>
+<li><a href="medipt/transforms/spatial/rotation_transform.html">medipt.transforms.spatial.rotation_transform</a></li>
+<li><a href="medipt/transforms/spatial/scaling_transform.html">medipt.transforms.spatial.scaling_transform</a></li>
+<li><a href="medipt/transforms/spatial/spatial_transform.html">medipt.transforms.spatial.spatial_transform</a></li>
+<li><a href="medipt/transforms/spatial/spatial_transform_init.html">medipt.transforms.spatial.spatial_transform_init</a></li>
+<li><a href="medipt/transforms/spatial/translation_transform.html">medipt.transforms.spatial.translation_transform</a></li>
+<li><a href="medipt/transforms/transform_coordinate.html">medipt.transforms.transform_coordinate</a></li>
+<li><a href="medipt/utils.html">medipt.utils</a></li>
+<ul><li><a href="medipt/utils/image_input_output_space.html">medipt.utils.image_input_output_space</a></li>
+<li><a href="medipt/utils/random_float.html">medipt.utils.random_float</a></li>
+<li><a href="medipt/utils/spatial_utils.html">medipt.utils.spatial_utils</a></li>
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diff --git a/_modules/medipt/crop_image/threshold_crop_background.html b/_modules/medipt/crop_image/threshold_crop_background.html
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+<!DOCTYPE html>
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+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  <title>medipt.crop_image.threshold_crop_background &mdash; MedIPT</title>
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+                0.1.8
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+<p class="caption" role="heading"><span class="caption-text">Package References:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../../../documentation/medipt.html">medipt package</a></li>
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+
+  <h1>Source code for medipt.crop_image.threshold_crop_background</h1><div class="highlight"><pre>
+<span></span><span class="kn">import</span> <span class="nn">SimpleITK</span> <span class="k">as</span> <span class="nn">sitk</span>
+<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Union</span>
+
+<div class="viewcode-block" id="threshold_crop_background"><a class="viewcode-back" href="../../../documentation/medipt.crop_image.html#medipt.crop_image.threshold_crop_background.threshold_crop_background">[docs]</a><span class="k">def</span> <span class="nf">threshold_crop_background</span><span class="p">(</span><span class="n">image</span><span class="p">:</span> <span class="n">sitk</span><span class="o">.</span><span class="n">Image</span><span class="p">,</span>
+                              <span class="n">inside_value</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">float</span><span class="p">],</span>
+                              <span class="n">outside_value</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">float</span><span class="p">],</span>
+                              <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">sitk</span><span class="o">.</span><span class="n">Image</span><span class="p">:</span>
+
+
+    <span class="n">binary_image_filter</span> <span class="o">=</span> <span class="n">sitk</span><span class="o">.</span><span class="n">OtsuThresholdImageFilter</span><span class="p">()</span>
+    <span class="n">binary_image_filter</span><span class="o">.</span><span class="n">SetInsideValue</span><span class="p">(</span><span class="n">inside_value</span><span class="p">)</span>
+    <span class="n">binary_image_filter</span><span class="o">.</span><span class="n">SetOutsideValue</span><span class="p">(</span><span class="n">outside_value</span><span class="p">)</span>
+
+    <span class="n">binary_image</span> <span class="o">=</span> <span class="n">binary_image_filter</span><span class="o">.</span><span class="n">Execute</span><span class="p">(</span><span class="n">image</span><span class="p">)</span>
+
+    <span class="n">label_shape_filter</span> <span class="o">=</span> <span class="n">sitk</span><span class="o">.</span><span class="n">LabelShapeStatisticsImageFilter</span><span class="p">()</span>
+    <span class="n">label_shape_filter</span><span class="o">.</span><span class="n">Execute</span><span class="p">(</span><span class="n">binary_image</span><span class="p">)</span>
+    <span class="n">bounding_box</span> <span class="o">=</span> <span class="n">label_shape_filter</span><span class="o">.</span><span class="n">GetBoundingBox</span><span class="p">(</span><span class="n">outside_value</span><span class="p">)</span>
+    <span class="c1"># The bounding box&#39;s first &quot;dim&quot; entries are the starting index and last &quot;dim&quot; entries the size</span>
+
+    <span class="n">cropped_image</span> <span class="o">=</span> <span class="n">sitk</span><span class="o">.</span><span class="n">RegionOfInterest</span><span class="p">(</span><span class="n">image</span><span class="p">,</span> <span class="n">bounding_box</span><span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">bounding_box</span><span class="p">)</span><span class="o">/</span><span class="mi">2</span><span class="p">):],</span> <span class="n">bounding_box</span><span class="p">[</span><span class="mi">0</span><span class="p">:</span><span class="nb">int</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">bounding_box</span><span class="p">)</span><span class="o">/</span><span class="mi">2</span><span class="p">)])</span>
+
+    <span class="k">return</span> <span class="n">cropped_image</span></div>
+</pre></div>
+
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