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              <p class="caption" role="heading"><span class="caption-text">Introduction</span></p>
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<p class="caption" role="heading"><span class="caption-text">Tutorials</span></p>
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<li class="toctree-l1"><a class="reference internal" href="../tutorial5/">Tutorial 5: Creating a mosaic map</a></li>
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  <section id="slideflow-datasetfeatures">
<h1>slideflow.DatasetFeatures<a class="headerlink" href="#slideflow-datasetfeatures" title="Permalink to this heading">¶</a></h1>
<dl class="py class">
<dt class="sig sig-object py" id="slideflow.DatasetFeatures">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">DatasetFeatures</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/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><span class="pre">tf.keras.models.Model</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">torch.nn.Module</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dataset</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">sf.Dataset</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">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.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/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/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/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><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="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.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/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a><span class="p"><span class="pre">]</span></span><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">cache</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="n"><span class="pre">annotations</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/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/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/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><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="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.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/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a><span class="p"><span class="pre">]</span></span><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><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><a class="reference internal" href="../_modules/slideflow/model/features/#DatasetFeatures"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.DatasetFeatures" title="Permalink to this definition">¶</a></dt>
<dd><p>Loads annotations, saved layer activations / features, and prepares
output saving directories. Will also read/write processed features to a
PKL cache file to save time in future iterations.</p>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>Storing predictions along with layer features is optional, to offer the user
reduced memory footprint. For example, saving predictions for a 10,000 slide
dataset with 1000 categorical outcomes would require:</p>
<p>4 bytes/float32-logit
* 1000 predictions/slide
* 3000 tiles/slide
* 10000 slides
~= 112 GB</p>
</div>
<p>Calculate features / layer activations from model, storing to
internal parameters <code class="docutils literal notranslate"><span class="pre">self.activations</span></code>, and <code class="docutils literal notranslate"><span class="pre">self.predictions</span></code>,
<code class="docutils literal notranslate"><span class="pre">self.locations</span></code>, dictionaries mapping slides to arrays of activations,
predictions, and locations for each tiles’ constituent tiles.</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> (<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 model from which to calculate activations.</p></li>
<li><p><strong>dataset</strong> (<a class="reference internal" href="../dataset/#slideflow.Dataset" title="slideflow.Dataset"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.Dataset</span></code></a>) – Dataset from which to
generate activations.</p></li>
<li><p><strong>labels</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>) – Dict mapping slide names to outcome
categories.</p></li>
<li><p><strong>cache</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>) – File for PKL cache.</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>augment</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><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>) – Whether to use data augmentation
during feature extraction. If True, will use default
augmentation. If str, will use augmentation specified by the
string. Defaults to None.</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>) – Batch size for activations calculations.
Defaults to 32.</p></li>
<li><p><strong>device</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>) – Device to use for feature extraction.
Only used for PyTorch feature extractors. Defaults to None.</p></li>
<li><p><strong>include_preds</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Calculate and store predictions.
Defaults to True.</p></li>
<li><p><strong>include_uncertainty</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>) – Whether to include model
uncertainty in the output. Only used if the feature generator
is a UQ-enabled model. Defaults to True.</p></li>
<li><p><strong>layers</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><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>) – Layers to extract features from. May be
the name of a single layer (str) or a list of layers (list).
Only used if model is a str. Defaults to ‘postconv’.</p></li>
<li><p><strong>normalizer</strong> ((str or <a class="reference internal" href="../norm/#slideflow.norm.StainNormalizer" title="slideflow.norm.StainNormalizer"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.norm.StainNormalizer</span></code></a>), optional) – Stain normalization strategy to use on image tiles prior to
feature extraction. This argument is invalid if <code class="docutils literal notranslate"><span class="pre">model</span></code> is a
feature extractor built from a trained model, as stain
normalization will be specified by the model configuration.
Defaults to None.</p></li>
<li><p><strong>normalizer_source</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>) – Stain normalization preset
or path to a source image. Valid presets include ‘v1’, ‘v2’,
and ‘v3’. If None, will use the default present (‘v3’).
This argument is invalid if <code class="docutils literal notranslate"><span class="pre">model</span></code> is a feature extractor
built from a trained model. Defaults to None.</p></li>
<li><p><strong>num_workers</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 workers to use for feature
extraction. Only used for PyTorch feature extractors. Defaults
to None.</p></li>
<li><p><strong>pool_sort</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Use multiprocessing pools to perform final
sorting. Defaults to True.</p></li>
<li><p><strong>progress</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Show a progress bar during feature calculation.
Defaults to True.</p></li>
<li><p><strong>transform</strong> (<em>Callable</em><em>, </em><em>optional</em>) – Custom transform to apply to
images. Applied before standardization. If the feature extractor
is a PyTorch model, the transform should be a torchvision
transform.</p></li>
<li><p><strong>verbose</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Show verbose logging output. Defaults to True.</p></li>
</ul>
</dd>
</dl>
<dl>
<dt>Examples</dt><dd><p>Calculate features using a feature extractor.</p>
<blockquote>
<div><div class="highlight-python 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="c1"># Create a feature extractor</span>
<span class="n">retccl</span> <span class="o">=</span> <span class="n">sf</span><span class="o">.</span><span class="n">build_feature_extractor</span><span class="p">(</span><span class="s1">&#39;retccl&#39;</span><span class="p">,</span> <span class="n">resize</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>

<span class="c1"># Load a dataset</span>
<span class="n">P</span> <span class="o">=</span> <span class="n">sf</span><span class="o">.</span><span class="n">load_project</span><span class="p">(</span><span class="o">...</span><span class="p">)</span>
<span class="n">dataset</span> <span class="o">=</span> <span class="n">P</span><span class="o">.</span><span class="n">dataset</span><span class="p">(</span><span class="o">...</span><span class="p">)</span>

<span class="c1"># Calculate features</span>
<span class="n">dts_ftrs</span> <span class="o">=</span> <span class="n">sf</span><span class="o">.</span><span class="n">DatasetFeatures</span><span class="p">(</span><span class="n">retccl</span><span class="p">,</span> <span class="n">dataset</span><span class="p">)</span>
</pre></div>
</div>
</div></blockquote>
<p>Calculate features using a trained model (preferred).</p>
<blockquote>
<div><div class="highlight-python 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="c1"># Create a feature extractor from the saved model.</span>
<span class="n">extractor</span> <span class="o">=</span> <span class="n">sf</span><span class="o">.</span><span class="n">build_feature_extractor</span><span class="p">(</span>
    <span class="s1">&#39;/path/to/trained_model.zip&#39;</span><span class="p">,</span>
    <span class="n">layers</span><span class="o">=</span><span class="p">[</span><span class="s1">&#39;postconv&#39;</span><span class="p">]</span>
<span class="p">)</span>

<span class="c1"># Calculate features across the dataset</span>
<span class="n">dts_ftrs</span> <span class="o">=</span> <span class="n">sf</span><span class="o">.</span><span class="n">DatasetFeatures</span><span class="p">(</span><span class="n">extractor</span><span class="p">,</span> <span class="n">dataset</span><span class="p">)</span>
</pre></div>
</div>
</div></blockquote>
<p>Calculate features using a trained model (legacy).</p>
<blockquote>
<div><div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="c1"># This method is deprecated, and will be removed in a</span>
<span class="c1"># future release. Please use the method above instead.</span>
<span class="n">dts_ftrs</span> <span class="o">=</span> <span class="n">sf</span><span class="o">.</span><span class="n">DatasetFeatures</span><span class="p">(</span>
    <span class="s1">&#39;/path/to/trained_model.zip&#39;</span><span class="p">,</span>
    <span class="n">dataset</span><span class="o">=</span><span class="n">dataset</span><span class="p">,</span>
    <span class="n">layers</span><span class="o">=</span><span class="p">[</span><span class="s1">&#39;postconv&#39;</span><span class="p">]</span>
<span class="p">)</span>
</pre></div>
</div>
</div></blockquote>
<p>Calculate features from a loaded model.</p>
<blockquote>
<div><div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">tensorflow</span> <span class="k">as</span> <span class="nn">tf</span>
<span class="kn">import</span> <span class="nn">slideflow</span> <span class="k">as</span> <span class="nn">sf</span>

<span class="c1"># Load a model</span>
<span class="n">model</span> <span class="o">=</span> <span class="n">tf</span><span class="o">.</span><span class="n">keras</span><span class="o">.</span><span class="n">models</span><span class="o">.</span><span class="n">load_model</span><span class="p">(</span><span class="s1">&#39;/path/to/model.h5&#39;</span><span class="p">)</span>

<span class="c1"># Calculate features</span>
<span class="n">dts_ftrs</span> <span class="o">=</span> <span class="n">sf</span><span class="o">.</span><span class="n">DatasetFeatures</span><span class="p">(</span>
    <span class="n">model</span><span class="p">,</span>
    <span class="n">layers</span><span class="o">=</span><span class="p">[</span><span class="s1">&#39;postconv&#39;</span><span class="p">],</span>
    <span class="n">dataset</span>
<span class="p">)</span>
</pre></div>
</div>
</div></blockquote>
</dd>
</dl>
</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.DatasetFeatures.activations_by_category">
<span class="sig-name descname"><span class="pre">activations_by_category</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">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/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="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/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/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/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a><span class="p"><span class="pre">]</span></span><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></span><a class="headerlink" href="#slideflow.DatasetFeatures.activations_by_category" title="Permalink to this definition">¶</a></dt>
<dd><p>For each outcome category, calculates activations of a given
feature across all tiles in the category. Requires annotations to
have been provided.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>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 activations layer to return, stratified by
outcome category.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Dict mapping categories to feature activations for all
tiles in the category.</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#dict" title="(in Python v3.12)">dict</a></p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.DatasetFeatures.box_plots">
<span class="sig-name descname"><span class="pre">box_plots</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">features</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/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">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><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="headerlink" href="#slideflow.DatasetFeatures.box_plots" title="Permalink to this definition">¶</a></dt>
<dd><p>Generates plots comparing node activations at slide- and tile-level.</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>features</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/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>)</em>) – List of feature indices for which to
generate box plots.</p></li>
<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 box plots.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.DatasetFeatures.concat">
<span class="sig-name descname"><span class="pre">concat</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">args</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.Iterable" title="(in Python v3.12)"><span class="pre">Iterable</span></a><span class="p"><span class="pre">[</span></span><a class="reference internal" href="#slideflow.DatasetFeatures" title="slideflow.model.features.DatasetFeatures"><span class="pre">DatasetFeatures</span></a><span class="p"><span class="pre">]</span></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 internal" href="#slideflow.DatasetFeatures" title="slideflow.model.features.DatasetFeatures"><span class="pre">DatasetFeatures</span></a></span></span><a class="headerlink" href="#slideflow.DatasetFeatures.concat" title="Permalink to this definition">¶</a></dt>
<dd><p>Concatenate activations from multiple DatasetFeatures together.</p>
<p>For example, if <code class="docutils literal notranslate"><span class="pre">df1</span></code> is a DatasetFeatures object with 2048 features
and <code class="docutils literal notranslate"><span class="pre">df2</span></code> is a DatasetFeatures object with 1024 features,
then <code class="docutils literal notranslate"><span class="pre">sf.DatasetFeatures.concat([df1,</span> <span class="pre">df2])</span></code> would return an object
with 3072.</p>
<p>Vectors from DatasetFeatures objects are concatenated in the given order.
During concatenation, predictions and uncertainty are dropped.</p>
<p>If there are any tiles that do not have calculated features in both
dataframes, these will be dropped.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>args</strong> (Iterable[<code class="xref py py-class docutils literal notranslate"><span class="pre">DatasetFeatures</span></code>]) – DatasetFeatures objects
to concatenate.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>DatasetFeatures object with concatenated
features.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p><code class="xref py py-class docutils literal notranslate"><span class="pre">DatasetFeatures</span></code></p>
</dd>
</dl>
<dl>
<dt>Examples</dt><dd><p>Concatenate two DatasetFeatures objects.</p>
<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">df1</span> <span class="o">=</span> <span class="n">DatasetFeatures</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="n">dataset</span><span class="p">,</span> <span class="n">layers</span><span class="o">=</span><span class="s1">&#39;postconv&#39;</span><span class="p">)</span>
<span class="gp">&gt;&gt;&gt; </span><span class="n">df2</span> <span class="o">=</span> <span class="n">DatasetFeatures</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="n">dataset</span><span class="p">,</span> <span class="n">layers</span><span class="o">=</span><span class="s1">&#39;sepconv_3&#39;</span><span class="p">)</span>
<span class="gp">&gt;&gt;&gt; </span><span class="n">df</span> <span class="o">=</span> <span class="n">DatasetFeatures</span><span class="o">.</span><span class="n">concat</span><span class="p">([</span><span class="n">df1</span><span class="p">,</span> <span class="n">df2</span><span class="p">])</span>
</pre></div>
</div>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.DatasetFeatures.from_df">
<span class="sig-name descname"><span class="pre">from_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">df</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">DataFrame</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 internal" href="#slideflow.DatasetFeatures" title="slideflow.model.features.DatasetFeatures"><span class="pre">DatasetFeatures</span></a></span></span><a class="headerlink" href="#slideflow.DatasetFeatures.from_df" title="Permalink to this definition">¶</a></dt>
<dd><p>Load DataFrame of features, as exported by <code class="xref py py-meth docutils literal notranslate"><span class="pre">DatasetFeatures.to_df()</span></code></p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>df</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code>) – DataFrame of features, as exported by
<code class="xref py py-meth docutils literal notranslate"><span class="pre">DatasetFeatures.to_df()</span></code></p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>DatasetFeatures object</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p><code class="xref py py-class docutils literal notranslate"><span class="pre">DatasetFeatures</span></code></p>
</dd>
</dl>
<dl>
<dt>Examples</dt><dd><p>Recreate DatasetFeatures after export to a DataFrame.</p>
<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">df</span> <span class="o">=</span> <span class="n">features</span><span class="o">.</span><span class="n">to_df</span><span class="p">()</span>
<span class="gp">&gt;&gt;&gt; </span><span class="n">new_features</span> <span class="o">=</span> <span class="n">DatasetFeatures</span><span class="o">.</span><span class="n">from_df</span><span class="p">(</span><span class="n">df</span><span class="p">)</span>
</pre></div>
</div>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.DatasetFeatures.load_cache">
<span class="sig-name descname"><span class="pre">load_cache</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><a class="headerlink" href="#slideflow.DatasetFeatures.load_cache" title="Permalink to this definition">¶</a></dt>
<dd><p>Load cached activations from PKL.</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>) – Path to pkl cache.</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.DatasetFeatures.map_activations">
<span class="sig-name descname"><span class="pre">map_activations</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="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 internal" href="../slidemap/#slideflow.SlideMap" title="slideflow.stats.slidemap.SlideMap"><span class="pre">SlideMap</span></a></span></span><a class="headerlink" href="#slideflow.DatasetFeatures.map_activations" title="Permalink to this definition">¶</a></dt>
<dd><p>Map activations with UMAP.</p>
<dl class="field-list simple">
<dt class="field-odd">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>...</strong> – </p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>sf.SlideMap</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.DatasetFeatures.map_predictions">
<span class="sig-name descname"><span class="pre">map_predictions</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/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">0</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/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">0</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 internal" href="../slidemap/#slideflow.SlideMap" title="slideflow.stats.slidemap.SlideMap"><span class="pre">SlideMap</span></a></span></span><a class="headerlink" href="#slideflow.DatasetFeatures.map_predictions" title="Permalink to this definition">¶</a></dt>
<dd><p>Map tile predictions onto x/y coordinate space.</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>x</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>) – Outcome category id for which predictions will
be mapped to the X-axis. Defaults to 0.</p></li>
<li><p><strong>y</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>) – Outcome category id for which predictions will
be mapped to the Y-axis. Defaults to 0.</p></li>
</ul>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><p><strong>cache</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>) – Path to parquet file to cache coordinates.
Defaults to None (caching disabled).</p>
</dd>
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>sf.SlideMap</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.DatasetFeatures.merge">
<span class="sig-name descname"><span class="pre">merge</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">df</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#slideflow.DatasetFeatures" title="slideflow.model.features.DatasetFeatures"><span class="pre">DatasetFeatures</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="headerlink" href="#slideflow.DatasetFeatures.merge" title="Permalink to this definition">¶</a></dt>
<dd><p>Merges with another DatasetFeatures.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>df</strong> (<a class="reference internal" href="#slideflow.DatasetFeatures" title="slideflow.DatasetFeatures"><em>slideflow.DatasetFeatures</em></a>) – TargetDatasetFeatures
to merge with.</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.DatasetFeatures.remove_slide">
<span class="sig-name descname"><span class="pre">remove_slide</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">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></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="headerlink" href="#slideflow.DatasetFeatures.remove_slide" title="Permalink to this definition">¶</a></dt>
<dd><p>Removes slide from calculated features.</p>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.DatasetFeatures.save_cache">
<span class="sig-name descname"><span class="pre">save_cache</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><a class="headerlink" href="#slideflow.DatasetFeatures.save_cache" title="Permalink to this definition">¶</a></dt>
<dd><p>Cache calculated activations to file.</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>) – Path to pkl.</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.DatasetFeatures.save_example_tiles">
<span class="sig-name descname"><span class="pre">save_example_tiles</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">features</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/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">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">slides</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">tiles_per_feature</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">100</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="headerlink" href="#slideflow.DatasetFeatures.save_example_tiles" title="Permalink to this definition">¶</a></dt>
<dd><p>For a set of activation features, saves image tiles named according
to their corresponding activations.</p>
<p>Duplicate image tiles will be saved for each feature, organized into
subfolders named according to feature.</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>features</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/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>)</em>) – Features to evaluate.</p></li>
<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 folder in which to save examples tiles.</p></li>
<li><p><strong>slides</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 slide names. If provided, will
only include tiles from these slides. Defaults to None.</p></li>
<li><p><strong>tiles_per_feature</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 tiles to include as
examples for each feature. Defaults to 100. Will evenly sample
this many tiles across the activation gradient.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.DatasetFeatures.softmax_mean">
<span class="sig-name descname"><span class="pre">softmax_mean</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">&#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 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></span><a class="headerlink" href="#slideflow.DatasetFeatures.softmax_mean" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculates the mean prediction vector (post-softmax) across
all tiles in each slide.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>This is a dictionary mapping slides to the mean logits
array for all tiles in each slide.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.12)">dict</a></p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.DatasetFeatures.softmax_percent">
<span class="sig-name descname"><span class="pre">softmax_percent</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">prediction_filter</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/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><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">&#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 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></span><a class="headerlink" href="#slideflow.DatasetFeatures.softmax_percent" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns dictionary mapping slides to a vector of length num_classes
with the percent of tiles in each slide predicted to be each outcome.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>prediction_filter</strong> – (optional) List of int. If provided, will
restrict predictions to only these categories, with final
prediction being based based on highest logit among these
categories.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>This is a dictionary mapping slides to an array of
percentages for each logit, of length num_classes</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#dict" title="(in Python v3.12)">dict</a></p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.DatasetFeatures.softmax_predict">
<span class="sig-name descname"><span class="pre">softmax_predict</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">prediction_filter</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/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><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">&#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 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/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#slideflow.DatasetFeatures.softmax_predict" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns slide-level predictions, assuming the model is predicting a
categorical outcome, by generating a prediction for each individual
tile, and making a slide-level prediction by finding the most
frequently predicted outcome among its constituent tiles.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>prediction_filter</strong> – (optional) List of int. If provided, will
restrict predictions to only these categories, with final
prediction based based on highest logit among these categories.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Dictionary mapping slide names to slide-level predictions.</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#dict" title="(in Python v3.12)">dict</a></p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.DatasetFeatures.stats">
<span class="sig-name descname"><span class="pre">stats</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 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">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><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'mean'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">threshold</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><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.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/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/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/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/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></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="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/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/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></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.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 class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#slideflow.DatasetFeatures.stats" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculates activation averages across categories, as well as
tile-level and patient-level statistics, using ANOVA, exporting to
CSV if desired.</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><em>, </em><em>optional</em>) – Path to directory in which CSV file will
be saved. Defaults to None.</p></li>
<li><p><strong>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><em>, </em><em>optional</em>) – Indicates method of aggregating tile-level
data into slide-level data. Either ‘mean’ (default) or
‘threshold’. If mean, slide-level feature data is calculated by
averaging feature activations across all tiles. If threshold,
slide-level feature data is calculated by counting the number
of tiles with feature activations &gt; threshold and dividing by
the total number of tiles. Defaults to ‘mean’.</p></li>
<li><p><strong>threshold</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>) – Threshold if using ‘threshold’ method.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><p>A tuple containing</p>
<blockquote>
<div><p>dict: Dict mapping slides to dict of slide-level features;</p>
<p>dict: Dict mapping features to tile-level statistics (‘p’, ‘f’);</p>
<p>dict: Dict mapping features to slide-level statistics (‘p’, ‘f’);</p>
</div></blockquote>
</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.DatasetFeatures.to_csv">
<span class="sig-name descname"><span class="pre">to_csv</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">filename</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">level</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">'tile'</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/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">'mean'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">slides</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><span class="sig-paren">)</span><a class="headerlink" href="#slideflow.DatasetFeatures.to_csv" title="Permalink to this definition">¶</a></dt>
<dd><p>Exports calculated activations to csv.</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>filename</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 CSV file for export.</p></li>
<li><p><strong>level</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – ‘tile’ or ‘slide’. Indicates whether tile or
slide-level activations are saved. Defaults to ‘tile’.</p></li>
<li><p><strong>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>) – Method of summarizing slide-level results. Either
‘mean’ or ‘median’. Defaults to ‘mean’.</p></li>
<li><p><strong>slides</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>) – Slides to export. If None, exports all slides.
Defaults to None.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.DatasetFeatures.to_df">
<span class="sig-name descname"><span class="pre">to_df</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">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">DataFrame</span></span></span><a class="headerlink" href="#slideflow.DatasetFeatures.to_df" title="Permalink to this definition">¶</a></dt>
<dd><p>Export activations, predictions, uncertainty, and locations to
a pandas DataFrame.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Dataframe with columns ‘activations’,
‘predictions’, ‘uncertainty’, and ‘locations’.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>pd.core.frame.DataFrame</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.DatasetFeatures.to_torch">
<span class="sig-name descname"><span class="pre">to_torch</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">slides</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">verbose</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">&#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="headerlink" href="#slideflow.DatasetFeatures.to_torch" title="Permalink to this definition">¶</a></dt>
<dd><p>Export activations in torch format to .pt files in the directory.</p>
<p>Used for training MIL models.</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 .pt files.</p></li>
<li><p><strong>verbose</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Verbose logging output. Defaults to True.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

</section>
</section>


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              <ul>
<li><a class="reference internal" href="#">slideflow.DatasetFeatures</a><ul>
<li><a class="reference internal" href="#slideflow.DatasetFeatures"><code class="docutils literal notranslate"><span class="pre">DatasetFeatures</span></code></a></li>
<li><a class="reference internal" href="#methods">Methods</a><ul>
<li><a class="reference internal" href="#slideflow.DatasetFeatures.activations_by_category"><code class="docutils literal notranslate"><span class="pre">activations_by_category()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.DatasetFeatures.box_plots"><code class="docutils literal notranslate"><span class="pre">box_plots()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.DatasetFeatures.concat"><code class="docutils literal notranslate"><span class="pre">concat()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.DatasetFeatures.from_df"><code class="docutils literal notranslate"><span class="pre">from_df()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.DatasetFeatures.load_cache"><code class="docutils literal notranslate"><span class="pre">load_cache()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.DatasetFeatures.map_activations"><code class="docutils literal notranslate"><span class="pre">map_activations()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.DatasetFeatures.map_predictions"><code class="docutils literal notranslate"><span class="pre">map_predictions()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.DatasetFeatures.merge"><code class="docutils literal notranslate"><span class="pre">merge()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.DatasetFeatures.remove_slide"><code class="docutils literal notranslate"><span class="pre">remove_slide()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.DatasetFeatures.save_cache"><code class="docutils literal notranslate"><span class="pre">save_cache()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.DatasetFeatures.save_example_tiles"><code class="docutils literal notranslate"><span class="pre">save_example_tiles()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.DatasetFeatures.softmax_mean"><code class="docutils literal notranslate"><span class="pre">softmax_mean()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.DatasetFeatures.softmax_percent"><code class="docutils literal notranslate"><span class="pre">softmax_percent()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.DatasetFeatures.softmax_predict"><code class="docutils literal notranslate"><span class="pre">softmax_predict()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.DatasetFeatures.stats"><code class="docutils literal notranslate"><span class="pre">stats()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.DatasetFeatures.to_csv"><code class="docutils literal notranslate"><span class="pre">to_csv()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.DatasetFeatures.to_df"><code class="docutils literal notranslate"><span class="pre">to_df()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.DatasetFeatures.to_torch"><code class="docutils literal notranslate"><span class="pre">to_torch()</span></code></a></li>
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