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<li class="toctree-l1"><a class="reference internal" href="../dataset_features/">slideflow.DatasetFeatures</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">slideflow.Heatmap</a></li>
<li class="toctree-l1"><a class="reference internal" href="../model_params/">slideflow.ModelParams</a></li>
<li class="toctree-l1"><a class="reference internal" href="../mosaic/">slideflow.Mosaic</a></li>
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<li class="toctree-l1"><a class="reference internal" href="../tutorial4/">Tutorial 4: Model evaluation & heatmaps</a></li>
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<section id="slideflow-heatmap">
<h1>slideflow.Heatmap<a class="headerlink" href="#slideflow-heatmap" title="Permalink to this heading">¶</a></h1>
<dl class="py class">
<dt class="sig sig-object py" id="slideflow.Heatmap">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">Heatmap</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">slide</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 class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="../slide/#slideflow.slide.WSI" title="slideflow.slide.wsi.WSI"><span class="pre">WSI</span></a></span></em>, <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/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">stride_div</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 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">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">32</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_threads</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 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">num_processes</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 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">img_format</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">'auto'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">generate</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">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">generator_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.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><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 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">device</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">torch.device</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">load_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/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><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">wsi_kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/slideflow/heatmap/#Heatmap"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.Heatmap" title="Permalink to this definition">¶</a></dt>
<dd><p>Generate a heatmap of predictions across a whole-slide image.</p>
<p>This interface is designed to be used with tile-based models, and
does not support multiple-instance learning models. Attention heatmaps
of multiple-instance learning models can be generated using
<a class="reference internal" href="../mil_module/#slideflow.mil.predict_slide" title="slideflow.mil.predict_slide"><code class="xref py py-func docutils literal notranslate"><span class="pre">slideflow.mil.predict_slide()</span></code></a>.</p>
<p>Initialize a heatmap from a path to a slide or a <code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.WSI</span></code>.</p>
<dl>
<dt>Examples</dt><dd><p>Create a heatmap from a path to a slide.</p>
<blockquote>
<div><div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">model_path</span> <span class="o">=</span> <span class="s1">'path/to/saved_model'</span>
<span class="n">heatmap</span> <span class="o">=</span> <span class="n">sf</span><span class="o">.</span><span class="n">Heatmap</span><span class="p">(</span><span class="s1">'slide.svs'</span><span class="p">,</span> <span class="n">model_path</span><span class="p">)</span>
</pre></div>
</div>
</div></blockquote>
<p>Create a heatmap, with grayspace filtering disabled.</p>
<blockquote>
<div><div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">heatmap</span> <span class="o">=</span> <span class="n">sf</span><span class="o">.</span><span class="n">Heatmap</span><span class="p">(</span><span class="o">...</span><span class="p">,</span> <span class="n">grayspace_fraction</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
</pre></div>
</div>
</div></blockquote>
<p>Create a heatmap from a <code class="docutils literal notranslate"><span class="pre">sf.WSI</span></code> object.</p>
<blockquote>
<div><div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="c1"># Load a slide</span>
<span class="n">wsi</span> <span class="o">=</span> <span class="n">sf</span><span class="o">.</span><span class="n">WSI</span><span class="p">(</span><span class="n">tile_px</span><span class="o">=</span><span class="mi">299</span><span class="p">,</span> <span class="n">tile_um</span><span class="o">=</span><span class="mi">302</span><span class="p">)</span>
<span class="c1"># Apply Otsu's thresholding to the slide,</span>
<span class="c1"># so heatmap is only generated on areas with tissue.</span>
<span class="n">wsi</span><span class="o">.</span><span class="n">qc</span><span class="p">(</span><span class="s1">'otsu'</span><span class="p">)</span>
<span class="c1"># Generate the heatmap</span>
<span class="n">heatmap</span> <span class="o">=</span> <span class="n">sf</span><span class="o">.</span><span class="n">Heatmap</span><span class="p">(</span><span class="n">wsi</span><span class="p">,</span> <span class="n">model_path</span><span class="p">)</span>
</pre></div>
</div>
</div></blockquote>
</dd>
</dl>
<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>slide</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Path to slide.</p></li>
<li><p><strong>model</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Path to Tensorflow or PyTorch model.</p></li>
<li><p><strong>stride_div</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>) – Divisor for stride when convoluting
across slide. Defaults to 2.</p></li>
<li><p><strong>roi_dir</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>) – Directory in which slide ROI is contained.
Defaults to None.</p></li>
<li><p><strong>rois</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>optional</em>) – List of paths to slide ROIs. Alternative to
providing roi_dir. Defaults to None.</p></li>
<li><p><strong>roi_method</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Either ‘inside’, ‘outside’, ‘auto’, or ‘ignore’.
Determines how ROIs are used to extract tiles.
If ‘inside’ or ‘outside’, will extract tiles in/out of an ROI,
and raise errors.MissingROIError if an ROI is not available.
If ‘auto’, will extract tiles inside an ROI if available,
and across the whole-slide if no ROI is found.
If ‘ignore’, will extract tiles across the whole-slide
regardless of whether an ROI is available.
Defaults to ‘auto’.</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 for calculating predictions.
Defaults to 32.</p></li>
<li><p><strong>num_threads</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>) – Number of tile worker threads. Cannot
supply both <code class="docutils literal notranslate"><span class="pre">num_threads</span></code> (uses thread pool) and
<code class="docutils literal notranslate"><span class="pre">num_processes</span></code> (uses multiprocessing pool). Defaults to
CPU core count.</p></li>
<li><p><strong>num_processes</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>) – Number of child processes to spawn
for multiprocessing pool. Defaults to None (does not use
multiprocessing).</p></li>
<li><p><strong>enable_downsample</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>) – Enable the use of downsampled
slide image layers. Defaults to True.</p></li>
<li><p><strong>img_format</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>) – Image format (png, jpg) to use when
extracting tiles from slide. Must match the image format
the model was trained on. If ‘auto’, will use the format
logged in the model params.json. Defaults to ‘auto’.</p></li>
<li><p><strong>generate</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Generate the heatmap after initialization.
If False, heatmap will need to be manually generated by
calling :meth:<code class="docutils literal notranslate"><span class="pre">Heatmap.generate()</span></code>.</p></li>
<li><p><strong>generator_kwargs</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><em>optional</em>) – Keyword arguments passed to
the <a class="reference internal" href="../slide/#slideflow.WSI.build_generator" title="slideflow.WSI.build_generator"><code class="xref py py-meth docutils literal notranslate"><span class="pre">slideflow.WSI.build_generator()</span></code></a>.</p></li>
<li><p><strong>device</strong> (<em>torch.device</em><em>, </em><em>optional</em>) – PyTorch device. Defaults to
initializing a new CUDA device.</p></li>
</ul>
</dd>
</dl>
<p>:keyword Any keyword argument accepted by <code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.WSI</span></code>.:</p>
</dd></dl>
<section id="methods">
<h2>Methods<a class="headerlink" href="#methods" title="Permalink to this heading">¶</a></h2>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Heatmap.add_inset">
<span class="sig-name descname"><span class="pre">add_inset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">x</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.Tuple" title="(in Python v3.12)"><span class="pre">Tuple</span></a><span class="p"><span class="pre">[</span></span><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 class="p"><span class="pre">,</span></span><span class="w"> </span><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 class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">y</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.Tuple" title="(in Python v3.12)"><span class="pre">Tuple</span></a><span class="p"><span class="pre">[</span></span><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 class="p"><span class="pre">,</span></span><span class="w"> </span><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 class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">zoom</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">5</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">loc</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">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mark1</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">2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mark2</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">4</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axes</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">True</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Inset</span></span></span><a class="headerlink" href="#slideflow.Heatmap.add_inset" title="Permalink to this definition">¶</a></dt>
<dd><p>Adds a zoom inset to the heatmap.</p>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Heatmap.clear_insets">
<span class="sig-name descname"><span class="pre">clear_insets</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</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="headerlink" href="#slideflow.Heatmap.clear_insets" title="Permalink to this definition">¶</a></dt>
<dd><p>Removes zoom insets.</p>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Heatmap.generate">
<span class="sig-name descname"><span class="pre">generate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">asynchronous</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">→</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Tuple" title="(in Python v3.12)"><span class="pre">Tuple</span></a><span class="p"><span class="pre">[</span></span><span class="pre">ndarray</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/threading.html#threading.Thread" title="(in Python v3.12)"><span class="pre">Thread</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><a class="headerlink" href="#slideflow.Heatmap.generate" title="Permalink to this definition">¶</a></dt>
<dd><p>Manually generate the heatmap.</p>
<p>This function is automatically called when creating the heatmap if the
heatmap was initialized with <code class="docutils literal notranslate"><span class="pre">generate=True</span></code> (default behavior).</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>asynchronous</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>) – Generate heatmap in a separate thread,
returning the numpy array which is updated in realtime with
heatmap predictions and the heatmap thread. Defaults to False,
returning None.</p></li>
<li><p><strong>callback</strong> (<em>Callable</em><em>, </em><em>optional</em>) – Callback function to call each time
the heatmap grid updated. The callback function should accept
a single argument: a list of nested (x_idx, y_idx) lists,
indicating the grid indices updated. Defaults to None.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><p><code class="docutils literal notranslate"><span class="pre">None</span></code> if <code class="docutils literal notranslate"><span class="pre">threaded=False</span></code>, otherwise returns a tuple containing</p>
<blockquote>
<div><p><strong>grid</strong>: Numpy array containing updated in realtime
with heatmap predictions as they are calculated.</p>
<p><strong>Thread</strong>: Thread in which heatmap is generated.</p>
</div></blockquote>
</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Heatmap.load">
<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">path</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><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</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="headerlink" href="#slideflow.Heatmap.load" title="Permalink to this definition">¶</a></dt>
<dd><p>Load heatmap predictions and uncertainty from .npz file.</p>
<p>This function is an alias for <a class="reference internal" href="#slideflow.Heatmap.load_npz" title="slideflow.Heatmap.load_npz"><code class="xref py py-meth docutils literal notranslate"><span class="pre">slideflow.Heatmap.load_npz()</span></code></a>.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>path</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>) – Source .npz file. Must have ‘predictions’ key
and optionally ‘uncertainty’.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>None</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Heatmap.load_npz">
<span class="sig-name descname"><span class="pre">load_npz</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">path</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><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</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="headerlink" href="#slideflow.Heatmap.load_npz" title="Permalink to this definition">¶</a></dt>
<dd><p>Load heatmap predictions and uncertainty from .npz file.</p>
<p>Loads predictions from <code class="docutils literal notranslate"><span class="pre">'predictions'</span></code> in .npz file, and uncertainty from
<code class="docutils literal notranslate"><span class="pre">'uncertainty'</span></code> if present, as generated from
<code class="xref py py-meth docutils literal notranslate"><span class="pre">slideflow.Heatmap.save_npz()`()</span></code>. This function is the same as
calling <code class="docutils literal notranslate"><span class="pre">heatmap.load()</span></code>.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>path</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>) – Source .npz file. Must have ‘predictions’ key
and optionally ‘uncertainty’.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>None</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Heatmap.plot">
<span class="sig-name descname"><span class="pre">plot</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></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>, <em class="sig-param"><span class="n"><span class="pre">heatmap_alpha</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">0.6</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">'coolwarm'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interpolation</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">'none'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vmin</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</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vmax</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</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vcenter</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">ax</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Axes</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">thumb_kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</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="headerlink" href="#slideflow.Heatmap.plot" title="Permalink to this definition">¶</a></dt>
<dd><p>Plot a predictive heatmap.</p>
<p>If in a Jupyter notebook, the heatmap will be displayed in the cell
output. If running via script or shell, the heatmap can then be
shown on screen using matplotlib <code class="docutils literal notranslate"><span class="pre">plt.show()</span></code>:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">slideflow</span> <span class="k">as</span> <span class="nn">sf</span>
<span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
<span class="n">heatmap</span> <span class="o">=</span> <span class="n">sf</span><span class="o">.</span><span class="n">Heatmap</span><span class="p">(</span><span class="o">...</span><span class="p">)</span>
<span class="n">heatmap</span><span class="o">.</span><span class="n">plot</span><span class="p">()</span>
<span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
</pre></div>
</div>
<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>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>) – Class index to plot.</p></li>
<li><p><strong>heatmap_alpha</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>) – Alpha of heatmap overlay.
Defaults to 0.6.</p></li>
<li><p><strong>show_roi</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>) – Overlay ROIs onto heatmap image.
Defaults to True.</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>) – Matplotlib heatmap colormap.
Defaults to ‘coolwarm’.</p></li>
<li><p><strong>interpolation</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>) – Interpolation strategy to use for
smoothing heatmap. Defaults to ‘none’.</p></li>
<li><p><strong>vmin</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a>) – Minimimum value to display on heatmap.
Defaults to 0.</p></li>
<li><p><strong>vcenter</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a>) – Center value for color display on heatmap.
Defaults to 0.5.</p></li>
<li><p><strong>vmax</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a>) – Maximum value to display on heatmap.
Defaults to 1.</p></li>
<li><p><strong>ax</strong> (<em>matplotlib.axes.Axes</em><em>, </em><em>optional</em>) – Figure axis. If not supplied,
will prepare a new figure axis.</p></li>
</ul>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><strong>show_roi</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>) – Overlay ROIs onto heatmap image.
Defaults to True.</p></li>
<li><p><strong>roi_color</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – ROI line color. Defaults to ‘k’ (black).</p></li>
<li><p><strong>linewidth</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Width of ROI line. Defaults to 5.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Heatmap.plot_thumbnail">
<span class="sig-name descname"><span class="pre">plot_thumbnail</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">show_roi</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="n"><span class="pre">roi_color</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">'k'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">linewidth</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">5</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">width</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 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">mpp</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 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">ax</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Axes</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><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">plt.image.AxesImage</span></span></span><a class="headerlink" href="#slideflow.Heatmap.plot_thumbnail" title="Permalink to this definition">¶</a></dt>
<dd><p>Plot a thumbnail of the slide, with or without ROI.</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>show_roi</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>) – Overlay ROIs onto heatmap image.
Defaults to True.</p></li>
<li><p><strong>roi_color</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – ROI line color. Defaults to ‘k’ (black).</p></li>
<li><p><strong>linewidth</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Width of ROI line. Defaults to 5.</p></li>
<li><p><strong>ax</strong> (<em>matplotlib.axes.Axes</em><em>, </em><em>optional</em>) – Figure axis. If not supplied,
will prepare a new figure axis.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Result from ax.imshow().</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>plt.image.AxesImage</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Heatmap.plot_with_logit_cmap">
<span class="sig-name descname"><span class="pre">plot_with_logit_cmap</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">logit_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.Callable" title="(in Python v3.12)"><span class="pre">Callable</span></a><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/typing.html#typing.Dict" title="(in Python v3.12)"><span class="pre">Dict</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">interpolation</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">'none'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ax</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Axes</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">thumb_kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</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="headerlink" href="#slideflow.Heatmap.plot_with_logit_cmap" title="Permalink to this definition">¶</a></dt>
<dd><p>Plot a heatmap using a specified logit colormap.</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>logit_cmap</strong> (<em>obj</em><em>, </em><em>optional</em>) – Either function or a dictionary use to
create heatmap colormap. Each image tile will generate a list
of predictions of length O, where O is the number of outcomes.
If logit_cmap is a function, then the logit prediction list
will be passed to the function, and the function is expected
to return [R, G, B] values for display. If logit_cmap is a
dictionary, it should map ‘r’, ‘g’, and ‘b’ to indices; the
prediction for these outcome indices will be mapped to the RGB
colors. Thus, the corresponding color will only reflect up to
three outcomes. Example mapping prediction for outcome 0 to the
red colorspace, 3 to green, etc: {‘r’: 0, ‘g’: 3, ‘b’: 1}</p></li>
<li><p><strong>interpolation</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>) – Interpolation strategy to use for
smoothing heatmap. Defaults to ‘none’.</p></li>
<li><p><strong>ax</strong> (<em>matplotlib.axes.Axes</em><em>, </em><em>optional</em>) – Figure axis. If not supplied,
will prepare a new figure axis.</p></li>
</ul>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><strong>show_roi</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>) – Overlay ROIs onto heatmap image.
Defaults to True.</p></li>
<li><p><strong>roi_color</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – ROI line color. Defaults to ‘k’ (black).</p></li>
<li><p><strong>linewidth</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Width of ROI line. Defaults to 5.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Heatmap.plot_uncertainty">
<span class="sig-name descname"><span class="pre">plot_uncertainty</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">heatmap_alpha</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">0.6</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">'coolwarm'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interpolation</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">'none'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ax</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Axes</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">thumb_kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#slideflow.Heatmap.plot_uncertainty" title="Permalink to this definition">¶</a></dt>
<dd><p>Plot heatmap of uncertainty.</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>heatmap_alpha</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>) – Alpha of heatmap overlay.
Defaults to 0.6.</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>) – Matplotlib heatmap colormap.
Defaults to ‘coolwarm’.</p></li>
<li><p><strong>interpolation</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>) – Interpolation strategy to use for
smoothing heatmap. Defaults to ‘none’.</p></li>
<li><p><strong>ax</strong> (<em>matplotlib.axes.Axes</em><em>, </em><em>optional</em>) – Figure axis. If not supplied,
will prepare a new figure axis.</p></li>
</ul>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><strong>show_roi</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>) – Overlay ROIs onto heatmap image.
Defaults to True.</p></li>
<li><p><strong>roi_color</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – ROI line color. Defaults to ‘k’ (black).</p></li>
<li><p><strong>linewidth</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Width of ROI line. Defaults to 5.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Heatmap.save">
<span class="sig-name descname"><span class="pre">save</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outdir</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">show_roi</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">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interpolation</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">'none'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">logit_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.Callable" title="(in Python v3.12)"><span class="pre">Callable</span></a><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/typing.html#typing.Dict" title="(in Python v3.12)"><span class="pre">Dict</span></a><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">roi_color</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">'k'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">linewidth</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">5</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">→</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="headerlink" href="#slideflow.Heatmap.save" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves calculated predictions as heatmap overlays.</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>outdir</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Path to directory in which to save heatmap images.</p></li>
<li><p><strong>show_roi</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>) – Overlay ROIs onto heatmap image.
Defaults to True.</p></li>
<li><p><strong>interpolation</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>) – Interpolation strategy to use for
smoothing heatmap. Defaults to ‘none’.</p></li>
<li><p><strong>logit_cmap</strong> (<em>obj</em><em>, </em><em>optional</em>) – Either function or a dictionary use to
create heatmap colormap. Each image tile will generate a list
of predictions of length O, where O is the number of outcomes.
If logit_cmap is a function, then the logit prediction list
will be passed to the function, and the function is expected
to return [R, G, B] values for display. If logit_cmap is a
dictionary, it should map ‘r’, ‘g’, and ‘b’ to indices; the
prediction for these outcome indices will be mapped to the RGB
colors. Thus, the corresponding color will only reflect up to
three outcomes. Example mapping prediction for outcome 0 to the
red colorspace, 3 to green, etc: {‘r’: 0, ‘g’: 3, ‘b’: 1}</p></li>
<li><p><strong>roi_color</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – ROI line color. Defaults to ‘k’ (black).</p></li>
<li><p><strong>linewidth</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Width of ROI line. Defaults to 5.</p></li>
</ul>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<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>) – Matplotlib heatmap colormap.
Defaults to ‘coolwarm’.</p></li>
<li><p><strong>vmin</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a>) – Minimimum value to display on heatmap.
Defaults to 0.</p></li>
<li><p><strong>vcenter</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a>) – Center value for color display on heatmap.
Defaults to 0.5.</p></li>
<li><p><strong>vmax</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a>) – Maximum value to display on heatmap.
Defaults to 1.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Heatmap.save_npz">
<span class="sig-name descname"><span class="pre">save_npz</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">path</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 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><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><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><a class="headerlink" href="#slideflow.Heatmap.save_npz" title="Permalink to this definition">¶</a></dt>
<dd><p>Save heatmap predictions and uncertainty in .npz format.</p>
<p>Saves heatmap predictions to <code class="docutils literal notranslate"><span class="pre">'predictions'</span></code> in the .npz file. If uncertainty
was calculated, this is saved to <code class="docutils literal notranslate"><span class="pre">'uncertainty'</span></code>. A Heatmap instance can
load a saved .npz file with <a class="reference internal" href="#slideflow.Heatmap.load" title="slideflow.Heatmap.load"><code class="xref py py-meth docutils literal notranslate"><span class="pre">slideflow.Heatmap.load()</span></code></a>.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>path</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>) – Destination filename for .npz file. Defaults
to {slidename}.npz</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Path to .npz file.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)">str</a></p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Heatmap.view">
<span class="sig-name descname"><span class="pre">view</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#slideflow.Heatmap.view" title="Permalink to this definition">¶</a></dt>
<dd><p>Load the Heatmap into Slideflow Studio for interactive view.</p>
<p>See <a class="reference internal" href="../studio/#studio"><span class="std std-ref">Slideflow Studio: Live Visualization</span></a> for more information.</p>
</dd></dl>
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<li><a class="reference internal" href="#">slideflow.Heatmap</a><ul>
<li><a class="reference internal" href="#slideflow.Heatmap"><code class="docutils literal notranslate"><span class="pre">Heatmap</span></code></a></li>
<li><a class="reference internal" href="#methods">Methods</a><ul>
<li><a class="reference internal" href="#slideflow.Heatmap.add_inset"><code class="docutils literal notranslate"><span class="pre">add_inset()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Heatmap.clear_insets"><code class="docutils literal notranslate"><span class="pre">clear_insets()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Heatmap.generate"><code class="docutils literal notranslate"><span class="pre">generate()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Heatmap.load"><code class="docutils literal notranslate"><span class="pre">load()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Heatmap.load_npz"><code class="docutils literal notranslate"><span class="pre">load_npz()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Heatmap.plot"><code class="docutils literal notranslate"><span class="pre">plot()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Heatmap.plot_thumbnail"><code class="docutils literal notranslate"><span class="pre">plot_thumbnail()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Heatmap.plot_with_logit_cmap"><code class="docutils literal notranslate"><span class="pre">plot_with_logit_cmap()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Heatmap.plot_uncertainty"><code class="docutils literal notranslate"><span class="pre">plot_uncertainty()</span></code></a></li>
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<li><a class="reference internal" href="#slideflow.Heatmap.save_npz"><code class="docutils literal notranslate"><span class="pre">save_npz()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Heatmap.view"><code class="docutils literal notranslate"><span class="pre">view()</span></code></a></li>
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