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  <section id="slideflow-grad">
<h1>slideflow.grad<a class="headerlink" href="#slideflow-grad" title="Permalink to this heading">¶</a></h1>
<p>This submodule contains tools for calculating and display pixel attribution, or
saliency, maps. See <a class="reference internal" href="../saliency/#saliency"><span class="std std-ref">Saliency Maps</span></a> for more information.</p>
<dl class="py class">
<dt class="sig sig-object py" id="slideflow.grad.SaliencyMap">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">SaliencyMap</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">model</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Callable" title="(in Python v3.12)"><span class="pre">Callable</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">class_idx</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/slideflow/grad/#SaliencyMap"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.grad.SaliencyMap" title="Permalink to this definition">¶</a></dt>
<dd><p>Class to assist with calculation and display of saliency maps.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>model</strong> (<em>Callable</em>) – Differentiable model from which saliency is
calculated.</p></li>
<li><p><strong>class_idx</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Index of class for backpropagating gradients.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="slideflow.grad.SaliencyMap.__init__">
<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">model</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Callable" title="(in Python v3.12)"><span class="pre">Callable</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">class_idx</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="reference internal" href="../_modules/slideflow/grad/#SaliencyMap.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.grad.SaliencyMap.__init__" title="Permalink to this definition">¶</a></dt>
<dd><p>Class to assist with calculation and display of saliency maps.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>model</strong> (<em>Callable</em>) – Differentiable model from which saliency is
calculated.</p></li>
<li><p><strong>class_idx</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Index of class for backpropagating gradients.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="py method">
<dt class="sig sig-object py" id="slideflow.grad.SaliencyMap.all">
<span class="sig-name descname"><span class="pre">all</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">img</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Dict" title="(in Python v3.12)"><span class="pre">Dict</span></a></span></span><a class="reference internal" href="../_modules/slideflow/grad/#SaliencyMap.all"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.grad.SaliencyMap.all" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculate all saliency map methods.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>img</strong> (<em>np.ndarray</em>) – Pre-processed input image in W, H, C format.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Dictionary mapping name of saliency method to saliency map.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Dict</p>
</dd>
</dl>
</dd></dl>

<dl class="py method">
<dt class="sig sig-object py" id="slideflow.grad.SaliencyMap.blur_integrated_gradients">
<span class="sig-name descname"><span class="pre">blur_integrated_gradients</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">img</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">batch_size</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">20</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">smooth</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">ndarray</span></span></span><a class="reference internal" href="../_modules/slideflow/grad/#SaliencyMap.blur_integrated_gradients"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.grad.SaliencyMap.blur_integrated_gradients" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculate saliency map using blur integrated gradients.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>img</strong> (<em>np.ndarray</em>) – Pre-processed input image in W, H, C format.</p></li>
<li><p><strong>batch_size</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Batch size. Defaults to 20.</p></li>
<li><p><strong>smooth</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>) – Smooth gradients. Defaults to False.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Saliency map.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>np.ndarray</p>
</dd>
</dl>
</dd></dl>

<dl class="py method">
<dt class="sig sig-object py" id="slideflow.grad.SaliencyMap.gradcam">
<span class="sig-name descname"><span class="pre">gradcam</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">img</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">layer</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">smooth</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">ndarray</span></span></span><a class="reference internal" href="../_modules/slideflow/grad/#SaliencyMap.gradcam"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.grad.SaliencyMap.gradcam" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculate gradient-based saliency map.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>img</strong> (<em>np.ndarray</em>) – Pre-processed input image in W, H, C format.</p></li>
<li><p><strong>smooth</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>) – Smooth gradients. Defaults to False.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Saliency map.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>np.ndarray</p>
</dd>
</dl>
</dd></dl>

<dl class="py method">
<dt class="sig sig-object py" id="slideflow.grad.SaliencyMap.guided_integrated_gradients">
<span class="sig-name descname"><span class="pre">guided_integrated_gradients</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">img</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">x_steps</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">25</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_dist</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fraction</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.5</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">smooth</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">ndarray</span></span></span><a class="reference internal" href="../_modules/slideflow/grad/#SaliencyMap.guided_integrated_gradients"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.grad.SaliencyMap.guided_integrated_gradients" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculate saliency map using guided integrated gradients.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>img</strong> (<em>np.ndarray</em>) – Pre-processed input image in W, H, C format.</p></li>
<li><p><strong>x_steps</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Steps for gradient calculation.
Defaults to 25.</p></li>
<li><p><strong>max_dist</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>) – Maximum distance for gradient
calculation. Defaults to 1.0.</p></li>
<li><p><strong>fraction</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>) – Fraction for gradient calculation.
Defaults to 0.5.</p></li>
<li><p><strong>smooth</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>) – Smooth gradients. Defaults to False.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Saliency map.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>np.ndarray</p>
</dd>
</dl>
</dd></dl>

<dl class="py method">
<dt class="sig sig-object py" id="slideflow.grad.SaliencyMap.integrated_gradients">
<span class="sig-name descname"><span class="pre">integrated_gradients</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">img</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">x_steps</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">25</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">batch_size</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">20</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">smooth</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">ndarray</span></span></span><a class="reference internal" href="../_modules/slideflow/grad/#SaliencyMap.integrated_gradients"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.grad.SaliencyMap.integrated_gradients" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculate saliency map using integrated gradients.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>img</strong> (<em>np.ndarray</em>) – Pre-processed input image in W, H, C format.</p></li>
<li><p><strong>x_steps</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Steps for gradient calculation.
Defaults to 25.</p></li>
<li><p><strong>max_dist</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>) – Maximum distance for gradient
calculation. Defaults to 1.0.</p></li>
<li><p><strong>smooth</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>) – Smooth gradients. Defaults to False.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Saliency map.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>np.ndarray</p>
</dd>
</dl>
</dd></dl>

<dl class="py method">
<dt class="sig sig-object py" id="slideflow.grad.SaliencyMap.vanilla">
<span class="sig-name descname"><span class="pre">vanilla</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">img</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">smooth</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">ndarray</span></span></span><a class="reference internal" href="../_modules/slideflow/grad/#SaliencyMap.vanilla"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.grad.SaliencyMap.vanilla" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculate gradient-based saliency map.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>img</strong> (<em>np.ndarray</em>) – Pre-processed input image in W, H, C format.</p></li>
<li><p><strong>smooth</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>) – Smooth gradients. Defaults to False.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Saliency map.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>np.ndarray</p>
</dd>
</dl>
</dd></dl>

<dl class="py method">
<dt class="sig sig-object py" id="slideflow.grad.SaliencyMap.xrai">
<span class="sig-name descname"><span class="pre">xrai</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">img</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">batch_size</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">20</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">ndarray</span></span></span><a class="reference internal" href="../_modules/slideflow/grad/#SaliencyMap.xrai"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.grad.SaliencyMap.xrai" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculate saliency map using XRAI.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>img</strong> (<em>np.ndarray</em>) – Pre-processed input image in W, H, C format.</p></li>
<li><p><strong>batch_size</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Batch size. Defaults to 20.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Saliency map.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>np.ndarray</p>
</dd>
</dl>
</dd></dl>

<dl class="py method">
<dt class="sig sig-object py" id="slideflow.grad.SaliencyMap.xrai_fast">
<span class="sig-name descname"><span class="pre">xrai_fast</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">img</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">batch_size</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">20</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">ndarray</span></span></span><a class="reference internal" href="../_modules/slideflow/grad/#SaliencyMap.xrai_fast"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.grad.SaliencyMap.xrai_fast" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculate saliency map using XRAI (fast implementation).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>img</strong> (<em>np.ndarray</em>) – Pre-processed input image in W, H, C format.</p></li>
<li><p><strong>batch_size</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Batch size. Defaults to 20.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Saliency map.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>np.ndarray</p>
</dd>
</dl>
</dd></dl>

</dd></dl>

<span class="target" id="module-slideflow.grad"></span><p>Submodule for calculating/displaying pixel attribution (saliency maps).</p>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.grad.grayscale">
<span class="sig-name descname"><span class="pre">grayscale</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">image_3d</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vmax</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vmin</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">percentile</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">99</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/slideflow/grad/#grayscale"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.grad.grayscale" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns a 3D tensor as a grayscale 2D tensor.
This method sums a 3D tensor across the absolute value of axis=2, and then
clips values at a given percentile.</p>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.grad.comparison_plot">
<span class="sig-name descname"><span class="pre">comparison_plot</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">original</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">maps</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Dict" title="(in Python v3.12)"><span class="pre">Dict</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">ndarray</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cmap</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Any" title="(in Python v3.12)"><span class="pre">Any</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'plt.cm.gray'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">n_rows</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">3</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">n_cols</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">3</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="reference internal" href="../_modules/slideflow/grad/plot_utils/#comparison_plot"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.grad.comparison_plot" title="Permalink to this definition">¶</a></dt>
<dd><p>Plots comparison of many saliency maps for a single image in a grid.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>original</strong> (<em>np.ndarray</em>) – Original (unprocessed) image.</p></li>
<li><p><strong>maps</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.12)"><em>dict</em></a><em>(</em><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>np.ndarray</em><em>)</em>) – Dictionary mapping saliency map names
to the numpy array maps.</p></li>
<li><p><strong>cmap</strong> (<em>matplotlib colormap</em><em>, </em><em>optional</em>) – Colormap for maps.
Defaults to plt.cm.gray.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.grad.inferno">
<span class="sig-name descname"><span class="pre">inferno</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">img</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/slideflow/grad/plot_utils/#inferno"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.grad.inferno" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.grad.multi_plot">
<span class="sig-name descname"><span class="pre">multi_plot</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">raw_imgs</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><span class="pre">ndarray</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">processed_imgs</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><span class="pre">ndarray</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Callable" title="(in Python v3.12)"><span class="pre">Callable</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">cmap</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'inferno'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">xlabels</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ylabels</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="reference internal" href="../_modules/slideflow/grad/plot_utils/#multi_plot"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.grad.multi_plot" title="Permalink to this definition">¶</a></dt>
<dd><p>Creates a plot of saliency maps and overlays for a given set of images.</p>
<p>The first row will be the raw images.
The second row will be an overlay of the saliency map and the raw image.
The third row will be the saliency maps.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>raw_imgs</strong> (<em>List</em><em>[</em><em>np.ndarray</em><em>]</em>) – Raw, unprocessed images.</p></li>
<li><p><strong>processed_imgs</strong> (<em>List</em><em>[</em><em>np.ndarray</em><em>]</em>) – Processed images.</p></li>
<li><p><strong>method</strong> (<em>Callable</em>) – Saliency method.</p></li>
<li><p><strong>cmap</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>) – Colormap. Defaults to ‘inferno’.</p></li>
<li><p><strong>xlabels</strong> (<em>Optional</em><em>[</em><em>List</em><em>[</em><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>]</em><em>, </em><em>optional</em>) – Labels for x-axis.
Defaults to None.</p></li>
<li><p><strong>ylabels</strong> (<em>Optional</em><em>[</em><em>List</em><em>[</em><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>]</em><em>, </em><em>optional</em>) – Labels for y-axis.
Defaults to None.</p></li>
</ul>
</dd>
<dt class="field-even">Raises<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.12)"><strong>ValueError</strong></a> – If length of raw_imgs, processed_imgs are not equal.</p></li>
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.12)"><strong>ValueError</strong></a> – If xlabels is provided and not a list.</p></li>
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.12)"><strong>ValueError</strong></a> – If ylabels is provided and not a list.</p></li>
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.12)"><strong>ValueError</strong></a> – If xlabels is provided and length does not equal raw_imgs.</p></li>
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.12)"><strong>ValueError</strong></a> – If ylabels is provided and length does not equal raw_imgs.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.grad.oranges">
<span class="sig-name descname"><span class="pre">oranges</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">img</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/slideflow/grad/plot_utils/#oranges"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.grad.oranges" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.grad.overlay">
<span class="sig-name descname"><span class="pre">overlay</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">image</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mask</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/slideflow/grad/plot_utils/#overlay"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.grad.overlay" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.grad.saliency_map_comparison">
<span class="sig-name descname"><span class="pre">saliency_map_comparison</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">orig_imgs</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><span class="pre">ndarray</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">saliency_fn</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Callable" title="(in Python v3.12)"><span class="pre">Callable</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">process_fn</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Callable" title="(in Python v3.12)"><span class="pre">Callable</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">saliency_labels</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cmap</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'inferno'</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Any" title="(in Python v3.12)"><span class="pre">Any</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="reference internal" href="../_modules/slideflow/grad/plot_utils/#saliency_map_comparison"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.grad.saliency_map_comparison" title="Permalink to this definition">¶</a></dt>
<dd><p>Plots several saliency maps for a list of images.</p>
<p>Each row is a unique image.
The first column is the original image. Each column after is a saliency
map generated each of the functions provided to <cite>saliency_fn</cite>.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>orig_imgs</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>(</em><em>np.ndarray</em><em>)</em>) – Original (unprocessed) images for
which to generate saliency maps.</p></li>
<li><p><strong>saliency_fn</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>(</em><em>Callable</em><em>)</em>) – List of saliency map functions.</p></li>
<li><p><strong>process_fn</strong> (<em>Callable</em>) – Function for processing images. This function
will be applied to images before images are passed to the
saliency map function.</p></li>
<li><p><strong>saliency_labels</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>(</em><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>, </em><em>optional</em>) – Labels for provided saliency
maps. Defaults to None.</p></li>
<li><p><strong>cmap</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>) – Colormap for saliency maps.
Defaults to ‘inferno’.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

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<li><a class="reference internal" href="#slideflow.grad.SaliencyMap"><code class="docutils literal notranslate"><span class="pre">SaliencyMap</span></code></a><ul>
<li><a class="reference internal" href="#slideflow.grad.SaliencyMap.__init__"><code class="docutils literal notranslate"><span class="pre">SaliencyMap.__init__()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.grad.SaliencyMap.all"><code class="docutils literal notranslate"><span class="pre">SaliencyMap.all()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.grad.SaliencyMap.blur_integrated_gradients"><code class="docutils literal notranslate"><span class="pre">SaliencyMap.blur_integrated_gradients()</span></code></a></li>
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<li><a class="reference internal" href="#slideflow.grad.comparison_plot"><code class="docutils literal notranslate"><span class="pre">comparison_plot()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.grad.inferno"><code class="docutils literal notranslate"><span class="pre">inferno()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.grad.multi_plot"><code class="docutils literal notranslate"><span class="pre">multi_plot()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.grad.oranges"><code class="docutils literal notranslate"><span class="pre">oranges()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.grad.overlay"><code class="docutils literal notranslate"><span class="pre">overlay()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.grad.saliency_map_comparison"><code class="docutils literal notranslate"><span class="pre">saliency_map_comparison()</span></code></a></li>
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