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              <p class="caption" role="heading"><span class="caption-text">Introduction</span></p>
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<li class="toctree-l1"><a class="reference internal" href="../installation/">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../overview/">Overview</a></li>
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<li class="toctree-l1"><a class="reference internal" href="../datasets_and_val/">Datasets</a></li>
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<li class="toctree-l1"><a class="reference internal" href="../tfrecords/">TFRecords: Reading and Writing</a></li>
<li class="toctree-l1"><a class="reference internal" href="../dataloaders/">Dataloaders: Sampling and Augmentation</a></li>
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<li class="toctree-l1"><a class="reference internal" href="../heatmap/">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="../gan/">slideflow.gan</a></li>
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<li class="toctree-l1"><a class="reference internal" href="../mil_module/">slideflow.mil</a></li>
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<li class="toctree-l1"><a class="reference internal" href="../model_tensorflow/">slideflow.model.tensorflow</a></li>
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<li class="toctree-l1"><a class="reference internal" href="../norm/">slideflow.norm</a></li>
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<li class="toctree-l1"><a class="reference internal" href="../slide/">slideflow.slide</a></li>
<li class="toctree-l1"><a class="reference internal" href="../slide_qc/">slideflow.slide.qc</a></li>
<li class="toctree-l1"><a class="reference internal" href="../stats/">slideflow.stats</a></li>
<li class="toctree-l1"><a class="reference internal" href="../util/">slideflow.util</a></li>
<li class="toctree-l1"><a class="reference internal" href="../studio_module/">slideflow.studio</a></li>
</ul>
<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="../tutorial1/">Tutorial 1: Model training (simple)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tutorial2/">Tutorial 2: Model training (advanced)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tutorial3/">Tutorial 3: Using a custom architecture</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tutorial4/">Tutorial 4: Model evaluation &amp; heatmaps</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tutorial5/">Tutorial 5: Creating a mosaic map</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tutorial6/">Tutorial 6: Custom slide filtering</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tutorial7/">Tutorial 7: Training with custom augmentations</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tutorial8/">Tutorial 8: Multiple-Instance Learning</a></li>
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  <section id="slideflow-dataset">
<span id="dataset"></span><h1>slideflow.Dataset<a class="headerlink" href="#slideflow-dataset" title="Permalink to this heading">¶</a></h1>
<dl class="py class">
<dt class="sig sig-object py" id="slideflow.Dataset">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">Dataset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">config</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/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.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="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">sources</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/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">tile_px</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">tile_um</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/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="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tfrecords</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">tiles</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">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/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">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/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">filters</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="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">filter_blank</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/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">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/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">DataFrame</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">min_tiles</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><span class="sig-paren">)</span><a class="reference internal" href="../_modules/slideflow/dataset/#Dataset"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.Dataset" title="Permalink to this definition">¶</a></dt>
<dd><p>Supervises organization and processing of slides, tfrecords, and tiles.</p>
<p>Datasets can be comprised of one or more sources, where a source is a
combination of slides and any associated regions of interest (ROI) and
extracted image tiles (stored as TFRecords or loose images).</p>
<p>Datasets can be created in two ways: either by loading one dataset source,
or by loading a dataset configuration that contains information about
multiple dataset sources.</p>
<p>For the first approach, the dataset source configuration is provided via
keyword arguments (<code class="docutils literal notranslate"><span class="pre">tiles</span></code>, <code class="docutils literal notranslate"><span class="pre">tfrecords</span></code>, <code class="docutils literal notranslate"><span class="pre">slides</span></code>, and <code class="docutils literal notranslate"><span class="pre">roi</span></code>).
Each is a path to a directory containing the respective data.</p>
<p>For the second approach, the first argument <code class="docutils literal notranslate"><span class="pre">config</span></code> is either a nested
dictionary containing the configuration for multiple dataset sources, or
a path to a JSON file with this information. The second argument is a list
of dataset sources to load (keys from the <code class="docutils literal notranslate"><span class="pre">config</span></code> dictionary).</p>
<p>With either approach, slide/patient-level annotations are provided through
the <code class="docutils literal notranslate"><span class="pre">annotations</span></code> keyword argument, which can either be a path to a CSV
file, or a pandas DataFrame, which must contain at minimum the column
‘<cite>patient</cite>’.</p>
<p>Initialize a Dataset to organize processed images.</p>
<dl>
<dt>Examples</dt><dd><p>Load a dataset via keyword arguments.</p>
<blockquote>
<div><div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">dataset</span> <span class="o">=</span> <span class="n">Dataset</span><span class="p">(</span>
    <span class="n">tfrecords</span><span class="o">=</span><span class="s1">&#39;../path&#39;</span><span class="p">,</span>
    <span class="n">slides</span><span class="o">=</span><span class="s1">&#39;../path&#39;</span><span class="p">,</span>
    <span class="n">annotations</span><span class="o">=</span><span class="s1">&#39;../file.csv&#39;</span>
<span class="p">)</span>
</pre></div>
</div>
</div></blockquote>
<p>Load a dataset configuration file and specify dataset source(s).</p>
<blockquote>
<div><div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">dataset</span> <span class="o">=</span> <span class="n">Dataset</span><span class="p">(</span>
    <span class="n">config</span><span class="o">=</span><span class="s1">&#39;../path/to/config.json&#39;</span><span class="p">,</span>
    <span class="n">sources</span><span class="o">=</span><span class="p">[</span><span class="s1">&#39;Lung_Adeno&#39;</span><span class="p">,</span> <span class="s1">&#39;Lung_Squam&#39;</span><span class="p">],</span>
    <span class="n">annotations</span><span class="o">=</span><span class="s1">&#39;../file.csv</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>config</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#dict" title="(in Python v3.12)"><em>dict</em></a>) – Either a dictionary or a path to a JSON file.
If a dictionary, keys should be dataset source names, and
values should be dictionaries containing the keys ‘tiles’,
‘tfrecords’, ‘roi’, and/or ‘slides’, specifying directories for
each dataset source. If <cite>config</cite> is a str, it should be a path
to a JSON file containing a dictionary with the same
formatting. If None, tiles, tfrecords, roi and/or slides should
be manually provided via keyword arguments. Defaults to None.</p></li>
<li><p><strong>sources</strong> (<em>List</em><em>[</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>]</em>) – List of dataset sources to include from
configuration. If not provided, will use all sources in the
provided configuration. Defaults to None.</p></li>
<li><p><strong>tile_px</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Tile size in pixels.</p></li>
<li><p><strong>tile_um</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> or </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Tile size in microns (int) or magnification
(str, e.g. “20x”).</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>filters</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>) – Dataset filters to use for
selecting slides. See <a class="reference internal" href="#slideflow.Dataset.filter" title="slideflow.Dataset.filter"><code class="xref py py-meth docutils literal notranslate"><span class="pre">slideflow.Dataset.filter()</span></code></a> for
more information. Defaults to None.</p></li>
<li><p><strong>filter_blank</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>) or </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>) – Skip slides that have
blank values in these patient annotation columns.
Defaults to None.</p></li>
<li><p><strong>min_tiles</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>) – Only include slides with this
many tiles at minimum. Defaults to 0.</p></li>
<li><p><strong>annotations</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> or </em><em>pd.DataFrame</em><em>, </em><em>optional</em>) – Path
to annotations file or pandas DataFrame with slide-level
annotations. Defaults to None.</p></li>
</ul>
</dd>
<dt class="field-odd">Raises<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>errors.SourceNotFoundError</strong> – If provided source does not exist
    in the dataset config.</p>
</dd>
</dl>
</dd></dl>

<section id="attributes">
<h2>Attributes<a class="headerlink" href="#attributes" title="Permalink to this heading">¶</a></h2>
<table class="autosummary longtable docutils align-default">
<tbody>
<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">Dataset.annotations</span></code></p></td>
<td><p>Pandas DataFrame of all loaded clinical annotations.</p></td>
</tr>
<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">Dataset.filters</span></code></p></td>
<td><p>Returns the active filters, if any.</p></td>
</tr>
<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">Dataset.filter_blank</span></code></p></td>
<td><p>Returns the active filter_blank filter, if any.</p></td>
</tr>
<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">Dataset.filtered_annotations</span></code></p></td>
<td><p>Pandas DataFrame of clinical annotations, after filtering.</p></td>
</tr>
<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">Dataset.img_format</span></code></p></td>
<td><p>Format of images stored in TFRecords (jpg/png).</p></td>
</tr>
<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">Dataset.min_tiles</span></code></p></td>
<td><p>Returns the active min_tiles filter, if any (defaults to 0).</p></td>
</tr>
<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">Dataset.num_tiles</span></code></p></td>
<td><p>Number of tiles in tfrecords after filtering/clipping.</p></td>
</tr>
</tbody>
</table>
</section>
<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.Dataset.balance">
<span class="sig-name descname"><span class="pre">balance</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">headers</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/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">strategy</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">'category'</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">force</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><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.Dataset" title="slideflow.dataset.Dataset"><span class="pre">Dataset</span></a></span></span><a class="headerlink" href="#slideflow.Dataset.balance" title="Permalink to this definition">¶</a></dt>
<dd><p>Return a dataset with mini-batch balancing configured.</p>
<p>Mini-batch balancing can be configured at tile, slide, patient, or
category levels.</p>
<p>Balancing information is saved to the attribute <code class="docutils literal notranslate"><span class="pre">prob_weights</span></code>, which
is used by the interleaving dataloaders when sampling from tfrecords
to create a batch.</p>
<p>Tile level balancing will create prob_weights reflective of the number
of tiles per slide, thus causing the batch sampling to mirror random
sampling from the entire population of  tiles (rather than randomly
sampling from slides).</p>
<p>Slide level balancing is the default behavior, where batches are
assembled by randomly sampling from each slide/tfrecord with equal
probability. This balancing behavior would be the same as no balancing.</p>
<p>Patient level balancing is used to randomly sample from individual
patients with equal probability. This is distinct from slide level
balancing, as some patients may have multiple slides per patient.</p>
<p>Category level balancing takes a list of annotation header(s) and
generates prob_weights such that each category is sampled equally.
This requires categorical outcomes.</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>headers</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> of </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>) – List of annotation headers if
balancing by category. Defaults to None.</p></li>
<li><p><strong>strategy</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>) – ‘tile’, ‘slide’, ‘patient’ or ‘category’.
Create prob_weights used to balance dataset batches to evenly
distribute slides, patients, or categories in a given batch.
Tile-level balancing generates prob_weights reflective of the
total number of tiles in a slide. Defaults to ‘category.’</p></li>
<li><p><strong>force</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>) – If using category-level balancing,
interpret all headers as categorical variables, even if the
header appears to be a float.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>balanced <a class="reference internal" href="#slideflow.Dataset" title="slideflow.Dataset"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.Dataset</span></code></a> object.</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.build_index">
<span class="sig-name descname"><span class="pre">build_index</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">force</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="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_workers</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><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.Dataset.build_index" title="Permalink to this definition">¶</a></dt>
<dd><p>Build index files for TFRecords.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>force</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Force re-build existing indices.</p>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><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
building indices. Defaults to num_cpus, up to maximum of 16.</p>
</dd>
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>None</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.cell_segmentation">
<span class="sig-name descname"><span class="pre">cell_segmentation</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">diam_um</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></em>, <em class="sig-param"><span class="n"><span class="pre">dest</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="o"><span class="pre">*</span></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"><span class="pre">cellpose.models.Cellpose</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/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">'cyto2'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">window_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">256</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">diam_mean</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">qc</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">qc_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/stdtypes.html#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">buffer</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">q_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">2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">force</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">save_centroid</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">save_flow</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><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.Dataset.cell_segmentation" title="Permalink to this definition">¶</a></dt>
<dd><p>Perform cell segmentation on slides, saving segmentation masks.</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>diam_um</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>) – Cell segmentation diameter, in microns.</p></li>
<li><p><strong>dest</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Destination in which to save cell segmentation masks.</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>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 cell segmentation. Defaults to 8.</p></li>
<li><p><strong>cp_thresh</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a>) – Cell probability threshold. All pixels with
value above threshold kept for masks, decrease to find more and
larger masks. Defaults to 0.</p></li>
<li><p><strong>diam_mean</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>) – Cell diameter to detect, in pixels
(without image resizing). If None, uses Cellpose defaults (17
for the ‘nuclei’ model, 30 for all others).</p></li>
<li><p><strong>downscale</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a>) – Factor by which to downscale generated masks
after calculation. Defaults to None (keep masks at original
size).</p></li>
<li><p><strong>flow_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>) – Flow error threshold (all cells with errors
below threshold are kept). Defaults to 0.4.</p></li>
<li><p><strong>gpus</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><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>) – GPUs to use for cell segmentation.
Defaults to 0 (first GPU).</p></li>
<li><p><strong>interp</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Interpolate during 2D dynamics. Defaults to True.</p></li>
<li><p><strong>qc</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Slide-level quality control method to use before
performing cell segmentation. Defaults to “Otsu”.</p></li>
<li><p><strong>model</strong> (str, <code class="xref py py-class docutils literal notranslate"><span class="pre">cellpose.models.Cellpose</span></code>) – Cellpose model to
use for cell segmentation. May be any valid cellpose model.
Defaults to ‘cyto2’.</p></li>
<li><p><strong>mpp</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a>) – Microns-per-pixel at which cells should be segmented.
Defaults to 0.5.</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.
Defaults to 2 * num_gpus.</p></li>
<li><p><strong>save_centroid</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Save mask centroids. Increases memory
utilization slightly. Defaults to True.</p></li>
<li><p><strong>save_flow</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Save flow values for the whole-slide image.
Increases memory utilization. Defaults to False.</p></li>
<li><p><strong>sources</strong> (<em>List</em><em>[</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>]</em>) – List of dataset sources to include from
configuration file.</p></li>
<li><p><strong>tile</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Tiles image to decrease GPU/CPU memory usage.
Defaults to True.</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 log output at the INFO level.
Defaults to True.</p></li>
<li><p><strong>window_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>) – Window size at which to segment cells across
a whole-slide image. Defaults to 256.</p></li>
</ul>
</dd>
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>None</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.check_duplicates">
<span class="sig-name descname"><span class="pre">check_duplicates</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">dataset</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#slideflow.Dataset" title="slideflow.dataset.Dataset"><span class="pre">Dataset</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">px</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">64</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mse_thresh</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/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.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/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="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#slideflow.Dataset.check_duplicates" title="Permalink to this definition">¶</a></dt>
<dd><p>Check for duplicate slides by comparing slide thumbnails.</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>dataset</strong> (<cite>slideflow.Dataset</cite>, optional) – Also check for
duplicate slides between this dataset and the provided dataset.</p></li>
<li><p><strong>px</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Pixel size at which to compare thumbnails.
Defaults to 64.</p></li>
<li><p><strong>mse_thresh</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – MSE threshold below which an image pair is
considered duplicate. Defaults to 100.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>List of path pairs of potential duplicates.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>List[<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)">str</a>], optional</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.clear_filters">
<span class="sig-name descname"><span class="pre">clear_filters</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 internal" href="#slideflow.Dataset" title="slideflow.dataset.Dataset"><span class="pre">Dataset</span></a></span></span><a class="headerlink" href="#slideflow.Dataset.clear_filters" title="Permalink to this definition">¶</a></dt>
<dd><p>Return a dataset with all filters cleared.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference internal" href="#slideflow.Dataset" title="slideflow.Dataset"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.Dataset</span></code></a> object.</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.clip">
<span class="sig-name descname"><span class="pre">clip</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">max_tiles</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">strategy</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">headers</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> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="#slideflow.Dataset" title="slideflow.dataset.Dataset"><span class="pre">Dataset</span></a></span></span><a class="headerlink" href="#slideflow.Dataset.clip" title="Permalink to this definition">¶</a></dt>
<dd><p>Return a dataset with TFRecords clipped to a max number of tiles.</p>
<p>Clip the number of tiles per tfrecord to a given maximum value and/or
to the min number of tiles per patient or category.</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>max_tiles</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>) – Clip the maximum number of tiles per
tfrecord to this number. Defaults to 0 (do not perform
tfrecord-level clipping).</p></li>
<li><p><strong>strategy</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>) – ‘slide’, ‘patient’, or ‘category’.
Clip the maximum number of tiles to the minimum tiles seen
across slides, patients, or categories. If ‘category’, headers
must be provided. Defaults to None (do not perform group-level
clipping).</p></li>
<li><p><strong>headers</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> of </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>) – List of annotation headers to use
if clipping by minimum category count (strategy=’category’).
Defaults to None.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>clipped <a class="reference internal" href="#slideflow.Dataset" title="slideflow.Dataset"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.Dataset</span></code></a> object.</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.convert_xml_rois">
<span class="sig-name descname"><span class="pre">convert_xml_rois</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.Dataset.convert_xml_rois" title="Permalink to this definition">¶</a></dt>
<dd><p>Convert ImageScope XML ROI files to QuPath format CSV ROI files.</p>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.extract_cells">
<span class="sig-name descname"><span class="pre">extract_cells</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">masks_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>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/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">SlideReport</span><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#slideflow.Dataset.extract_cells" title="Permalink to this definition">¶</a></dt>
<dd><p>Extract cell images from slides, with a tile at each cell centroid.</p>
<p>Requires that cells have already been segmented with
<code class="docutils literal notranslate"><span class="pre">Dataset.cell_segmentation()</span></code>.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>masks_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>) – Location of saved segmentation masks.</p>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><strong>apply_masks</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Apply cell segmentation masks to the extracted
tiles. Defaults to True.</p></li>
<li><p><strong>**kwargs</strong> – All other keyword arguments for
<code class="xref py py-meth docutils literal notranslate"><span class="pre">Dataset.extract_tiles()</span></code>.</p></li>
</ul>
</dd>
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Dictionary mapping slide paths to each slide’s SlideReport
(<code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.slide.report.SlideReport</span></code>)</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.extract_tiles">
<span class="sig-name descname"><span class="pre">extract_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="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">save_tiles</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">save_tfrecords</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">source</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">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><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">enable_downsample</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">roi_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">'auto'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">roi_filter_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/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">'center'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">skip_extracted</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">tma</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">randomize_origin</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">buffer</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">q_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">2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">qc</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/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.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Callable" title="(in Python v3.12)"><span class="pre">Callable</span></a><span class="p"><span class="pre">]</span></span><span 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">report</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">use_edge_tiles</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">artifact_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/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/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">[]</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mpp_override</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="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Any" title="(in Python v3.12)"><span class="pre">Any</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/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">SlideReport</span><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#slideflow.Dataset.extract_tiles" title="Permalink to this definition">¶</a></dt>
<dd><p>Extract tiles from a group of slides.</p>
<p>Extracted tiles are saved either loose image or in TFRecord format.</p>
<p>Extracted tiles are either saved in TFRecord format
(<code class="docutils literal notranslate"><span class="pre">save_tfrecords=True</span></code>, default) or as loose *.jpg / *.png images
(<code class="docutils literal notranslate"><span class="pre">save_tiles=True</span></code>). TFRecords or image tiles are saved in the
the tfrecord and tile directories configured by
<a class="reference internal" href="#slideflow.Dataset" title="slideflow.Dataset"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.Dataset</span></code></a>.</p>
<dl class="field-list simple">
<dt class="field-odd">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>save_tiles</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>) – Save tile images in loose format.
Defaults to False.</p></li>
<li><p><strong>save_tfrecords</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Save compressed image data from
extracted tiles into TFRecords in the corresponding TFRecord
directory. Defaults to True.</p></li>
<li><p><strong>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>) – Name of dataset source from which to select
slides for extraction. Defaults to None. If not provided, will
default to all sources in project.</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>) – Stride divisor for tile extraction.
A stride of 1 will extract non-overlapping tiles.
A stride_div of 2 will extract overlapping tiles, with a stride
equal to 50% of the tile width. Defaults to 1.</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>) – Enable downsampling for slides.
This may result in corrupted image tiles if downsampled slide
layers are corrupted or incomplete. Defaults to True.</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 skip the slide 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>roi_filter_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> or </em><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a>) – Method of filtering tiles with
ROIs. Either ‘center’ or float (0-1). If ‘center’, tiles are
filtered with ROIs based on the center of the tile. If float,
tiles are filtered based on the proportion of the tile inside
the ROI, and <code class="docutils literal notranslate"><span class="pre">roi_filter_method</span></code> is interpreted as a
threshold. If the proportion of a tile inside the ROI is
greater than this number, the tile is included. For example,
if <code class="docutils literal notranslate"><span class="pre">roi_filter_method=0.7</span></code>, a tile that is 80% inside of an
ROI will be included, and a tile that is 50% inside of an ROI
will be excluded. Defaults to ‘center’.</p></li>
<li><p><strong>skip_extracted</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Skip slides that have already
been extracted. Defaults to True.</p></li>
<li><p><strong>tma</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Reads slides as Tumor Micro-Arrays (TMAs).
Deprecated argument; all slides are now read as standard WSIs.</p></li>
<li><p><strong>randomize_origin</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Randomize pixel starting
position during extraction. Defaults to False.</p></li>
<li><p><strong>buffer</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>) – Slides will be copied to this directory
before extraction. Defaults to None. Using an SSD or ramdisk
buffer vastly improves tile extraction speed.</p></li>
<li><p><strong>q_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>) – Size of queue when using a buffer.
Defaults to 2.</p></li>
<li><p><strong>qc</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>) – ‘otsu’, ‘blur’, ‘both’, or None. Perform blur
detection quality control - discarding tiles with detected
out-of-focus regions or artifact - and/or otsu’s method.
Increases tile extraction time. Defaults to None.</p></li>
<li><p><strong>report</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Save a PDF report of tile extraction.
Defaults to True.</p></li>
<li><p><strong>normalizer</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>) – Normalization strategy.
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’).
Defaults to None.</p></li>
<li><p><strong>whitespace_fraction</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a><em>, </em><em>optional</em>) – Range 0-1. Discard tiles
with this fraction of whitespace. If 1, will not perform
whitespace filtering. Defaults to 1.</p></li>
<li><p><strong>whitespace_threshold</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>) – Range 0-255. Defaults to 230.
Threshold above which a pixel (RGB average) is whitespace.</p></li>
<li><p><strong>grayspace_fraction</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a><em>, </em><em>optional</em>) – Range 0-1. Defaults to 0.6.
Discard tiles with this fraction of grayspace.
If 1, will not perform grayspace filtering.</p></li>
<li><p><strong>grayspace_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>) – Range 0-1. Defaults to 0.05.
Pixels in HSV format with saturation below this threshold are
considered grayspace.</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>) – ‘png’ or ‘jpg’. Defaults to ‘jpg’.
Image format to use in tfrecords. PNG (lossless) for fidelity,
JPG (lossy) for efficiency.</p></li>
<li><p><strong>shuffle</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>) – Shuffle tiles prior to storage in
tfrecords. Defaults to True.</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 worker processes for each
tile extractor. When using cuCIM slide reading backend,
defaults to the total number of available CPU cores, using the
‘fork’ multiprocessing method. With Libvips, this defaults to
the total number of available CPU cores or 32, whichever is
lower, using ‘spawn’ multiprocessing.</p></li>
<li><p><strong>qc_blur_radius</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>) – Quality control blur radius for
out-of-focus area detection. Used if qc=True. Defaults to 3.</p></li>
<li><p><strong>qc_blur_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>) – Quality control blur threshold
for detecting out-of-focus areas. Only used if qc=True.
Defaults to 0.1</p></li>
<li><p><strong>qc_filter_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>) – Float between 0-1. Tiles
with more than this proportion of blur will be discarded.
Only used if qc=True. Defaults to 0.6.</p></li>
<li><p><strong>qc_mpp</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>) – Microns-per-pixel indicating image
magnification level at which quality control is performed.
Defaults to mpp=4 (effective magnification 2.5 X)</p></li>
<li><p><strong>dry_run</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>) – Determine tiles that would be extracted,
but do not export any images. Defaults to None.</p></li>
<li><p><strong>max_tiles</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>) – Only extract this many tiles per slide.
Defaults to None.</p></li>
<li><p><strong>use_edge_tiles</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 edge tiles in extraction. Areas
outside the slide will be padded white. Defaults to False.</p></li>
<li><p><strong>artifact_labels</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>(</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>) or </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>) – List of ROI issue labels
to treat as artifacts. Whenever this is not None, all the ROIs with
referred label will be inverted with ROI.invert().
Defaults to an empty list.</p></li>
<li><p><strong>mpp_override</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>) – Override the microns-per-pixel
for each slide. If None, will auto-detect microns-per-pixel
for all slides and raise an error if MPP is not found.
Defaults to None.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Dictionary mapping slide paths to each slide’s SlideReport
(<code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.slide.report.SlideReport</span></code>)</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.extract_tiles_from_tfrecords">
<span class="sig-name descname"><span class="pre">extract_tiles_from_tfrecords</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">dest</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.Dataset.extract_tiles_from_tfrecords" title="Permalink to this definition">¶</a></dt>
<dd><p>Extract tiles from a set of TFRecords.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>dest</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 tile images.
If None, uses dataset default. Defaults to None.</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.filter">
<span class="sig-name descname"><span class="pre">filter</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">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.Any" title="(in Python v3.12)"><span class="pre">Any</span></a></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Any" title="(in Python v3.12)"><span class="pre">Any</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="#slideflow.Dataset" title="slideflow.dataset.Dataset"><span class="pre">Dataset</span></a></span></span><a class="headerlink" href="#slideflow.Dataset.filter" title="Permalink to this definition">¶</a></dt>
<dd><p>Return a filtered dataset.</p>
<p>This method can either accept a single argument (<code class="docutils literal notranslate"><span class="pre">filters</span></code>) or any
combination of keyword arguments (<code class="docutils literal notranslate"><span class="pre">filters</span></code>, <code class="docutils literal notranslate"><span class="pre">filter_blank</span></code>, or
<code class="docutils literal notranslate"><span class="pre">min_tiles</span></code>).</p>
<dl class="field-list simple">
<dt class="field-odd">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>filters</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>) – Dictionary used for filtering
the dataset. Dictionary keys should be column headers in the
patient annotations, and the values should be the variable
states to be included in the dataset. For example,
<code class="docutils literal notranslate"><span class="pre">filters={'HPV_status':</span> <span class="pre">['negative',</span> <span class="pre">'positive']}</span></code>
would filter the dataset by the column <code class="docutils literal notranslate"><span class="pre">HPV_status</span></code> and only
include slides with values of either <code class="docutils literal notranslate"><span class="pre">'negative'</span></code> or
<code class="docutils literal notranslate"><span class="pre">'positive'</span></code> in this column.
See <a class="reference external" href="https://slideflow.dev/datasets_and_val/#filtering">Filtering</a>
for further discussion. Defaults to None.</p></li>
<li><p><strong>filter_blank</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>) or </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>) – Skip slides that have
blank values in these patient annotation columns.
Defaults to None.</p></li>
<li><p><strong>min_tiles</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Filter out tfrecords that have less than this
minimum number of tiles. Defaults to 0.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Dataset with filter added.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference internal" href="#slideflow.Dataset" title="slideflow.Dataset"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.Dataset</span></code></a></p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.find_slide">
<span class="sig-name descname"><span class="pre">find_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="o"><span class="pre">*</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 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">patient</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">&#x2192;</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 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.Dataset.find_slide" title="Permalink to this definition">¶</a></dt>
<dd><p>Find a slide path from a given slide or patient.</p>
<dl class="field-list simple">
<dt class="field-odd">Keyword Arguments<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>) – Find a tfrecord associated with this slide name.</p></li>
<li><p><strong>patient</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Find a tfrecord associated with this patient.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Matching path to slide, if found. If not found, returns None</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.Dataset.find_tfrecord">
<span class="sig-name descname"><span class="pre">find_tfrecord</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></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 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">patient</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">&#x2192;</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 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.Dataset.find_tfrecord" title="Permalink to this definition">¶</a></dt>
<dd><p>Find a TFRecord path from a given slide or patient.</p>
<dl class="field-list simple">
<dt class="field-odd">Keyword Arguments<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>) – Find a tfrecord associated with this slide name.</p></li>
<li><p><strong>patient</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Find a tfrecord associated with this patient.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Matching path to tfrecord, if found. Otherwise, returns None</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.Dataset.generate_feature_bags">
<span class="sig-name descname"><span class="pre">generate_feature_bags</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">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">BaseFeatureExtractor</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="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">force_regenerate</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">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">slide_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">16</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_gpus</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><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Any" title="(in Python v3.12)"><span class="pre">Any</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="headerlink" href="#slideflow.Dataset.generate_feature_bags" title="Permalink to this definition">¶</a></dt>
<dd><p>Generate bags of tile-level features for slides for use with 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>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 generate activations.
May provide either this or “pt_files”</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><em>, </em><em>optional</em>) – Save exported activations in .pt format.</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>layers</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a>) – Which model layer(s) generate activations.
If <code class="docutils literal notranslate"><span class="pre">model</span></code> is a saved model, this defaults to ‘postconv’.
Not used if <code class="docutils literal notranslate"><span class="pre">model</span></code> is pretrained feature extractor.
Defaults to None.</p></li>
<li><p><strong>force_regenerate</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Forcibly regenerate activations
for all slides even if .pt file exists. Defaults to False.</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 during feature calculation.
Defaults to 32.</p></li>
<li><p><strong>slide_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>) – Interleave feature calculation across
this many slides. Higher values may improve performance
but require more memory. Defaults to 16.</p></li>
<li><p><strong>num_gpus</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Number of GPUs to use for feature extraction.
Defaults to 0.</p></li>
<li><p><strong>**kwargs</strong> – Additional keyword arguments are passed to
<a class="reference internal" href="../dataset_features/#slideflow.DatasetFeatures" title="slideflow.DatasetFeatures"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.DatasetFeatures</span></code></a>.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.get_tfrecord_locations">
<span class="sig-name descname"><span class="pre">get_tfrecord_locations</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/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.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 class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#slideflow.Dataset.get_tfrecord_locations" title="Permalink to this definition">¶</a></dt>
<dd><p>Return a list of locations stored in an associated TFRecord.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><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>) – Slide name.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>List of tuples of (x, y) coordinates.</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.get_tile_dataframe">
<span class="sig-name descname"><span class="pre">get_tile_dataframe</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">roi_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">'auto'</span></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><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><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.Dataset.get_tile_dataframe" title="Permalink to this definition">¶</a></dt>
<dd><p>Generate a pandas dataframe with tile-level ROI labels.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p><ul class="simple">
<li><p><code class="docutils literal notranslate"><span class="pre">loc_x</span></code>: X-coordinate of tile center</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">loc_y</span></code>: Y-coordinate of tile center</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">grid_x</span></code>: X grid index of the tile</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">grid_y</span></code>: Y grid index of the tile</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">roi_name</span></code>: Name of the ROI if tile is in an ROI, else None</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">roi_desc</span></code>: Description of the ROI if tile is in ROI, else None</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">label</span></code>: ROI label, if present.</p></li>
</ul>
</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>Pandas dataframe of all tiles, with the following columns</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.harmonize_labels">
<span class="sig-name descname"><span class="pre">harmonize_labels</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">args</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#slideflow.Dataset" title="slideflow.dataset.Dataset"><span class="pre">Dataset</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">header</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">&#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.Dataset.harmonize_labels" title="Permalink to this definition">¶</a></dt>
<dd><p>Harmonize labels with another dataset.</p>
<p>Returns categorical label assignments converted to int, harmonized with
another dataset to ensure label consistency between datasets.</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>*args</strong> (<a class="reference internal" href="#slideflow.Dataset" title="slideflow.Dataset"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.Dataset</span></code></a>) – Any number of Datasets.</p></li>
<li><p><strong>header</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Categorical annotation header.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Dict mapping slide names to categories.</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.is_float">
<span class="sig-name descname"><span class="pre">is_float</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">header</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/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span></span><a class="headerlink" href="#slideflow.Dataset.is_float" title="Permalink to this definition">¶</a></dt>
<dd><p>Check if labels in the given header can all be converted to float.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>header</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Annotations column header.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>If all values from header can be converted to float.</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/functions.html#bool" title="(in Python v3.12)">bool</a></p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.kfold_split">
<span class="sig-name descname"><span class="pre">kfold_split</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">k</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="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="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/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">preserved_site</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">site_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/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/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/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">'site'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">splits</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">read_only</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><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.Tuple" title="(in Python v3.12)"><span class="pre">Tuple</span></a><span class="p"><span class="pre">[</span></span><a class="reference internal" href="#slideflow.Dataset" title="slideflow.dataset.Dataset"><span class="pre">Dataset</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference internal" href="#slideflow.Dataset" title="slideflow.dataset.Dataset"><span class="pre">Dataset</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="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#slideflow.Dataset.kfold_split" title="Permalink to this definition">¶</a></dt>
<dd><p>Split the dataset into k cross-folds.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>k</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Number of cross-folds.</p>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<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> or </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>) – Either a dictionary mapping slides
to labels, or an outcome label (<code class="docutils literal notranslate"><span class="pre">str</span></code>). Used for balancing
outcome labels in training and validation cohorts. If None,
will not balance k-fold splits by outcome labels. Defaults
to None.</p></li>
<li><p><strong>preserved_site</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Split with site-preserved cross-validation.
Defaults to False.</p></li>
<li><p><strong>site_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 patients to site labels,
or an outcome column with site labels. Only used for site
preserved cross validation. Defaults to ‘site’.</p></li>
<li><p><strong>splits</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 JSON file containing validation
splits. Defaults to None.</p></li>
<li><p><strong>read_only</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Prevents writing validation splits to file.
Defaults to False.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.labels">
<span class="sig-name descname"><span class="pre">labels</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">headers</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/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></em>, <em class="sig-param"><span class="n"><span class="pre">use_float</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 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/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">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">assign</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.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="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">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">'index'</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/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="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/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.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/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/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></span><a class="headerlink" href="#slideflow.Dataset.labels" title="Permalink to this definition">¶</a></dt>
<dd><p>Return a dict of slide names mapped to patient id and label(s).</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>headers</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>(</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>)</em><em>) </em><em>Annotation header</em><em>(</em><em>s</em>) – May be a list or string.</p></li>
<li><p><strong>use_float</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>) – If true, convert data into float; if unable, raise TypeError.
If false, interpret all data as categorical.
If a dict(bool), look up each header to determine type.
If ‘auto’, will try to convert all data into float. For each
header in which this fails, will interpret as categorical.</p></li>
<li><p><strong>assign</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>) – Dictionary mapping label ids to
label names. If not provided, will map ids to names by sorting
alphabetically.</p></li>
<li><p><strong>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>) – Either ‘index’ or ‘name.’ Indicates which
format should be used for categorical outcomes when returning
the label dictionary. If ‘name’, uses the string label name.
If ‘index’, returns an int (index corresponding with the
returned list of unique outcomes as str). Defaults to ‘index’.</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><strong>dict</strong>: Dictionary mapping slides to outcome labels in
numerical format (float for continuous outcomes, int of outcome
label id for categorical outcomes).</p>
<p><strong>list</strong>: List of unique labels. For categorical outcomes,
this will be a list of str; indices correspond with the outcome
label id.</p>
</div></blockquote>
</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.load_annotations">
<span class="sig-name descname"><span class="pre">load_annotations</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">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/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">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 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.Dataset.load_annotations" title="Permalink to this definition">¶</a></dt>
<dd><p>Load annotations.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>annotations</strong> (<em>Union</em><em>[</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>pd.DataFrame</em><em>]</em>) – Either path to annotations
in CSV format, or a pandas DataFrame.</p>
</dd>
<dt class="field-even">Raises<span class="colon">:</span></dt>
<dd class="field-even"><p><strong>errors.AnnotationsError</strong> – If annotations are incorrectly formatted.</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.load_indices">
<span class="sig-name descname"><span class="pre">load_indices</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">verbose</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</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.Dataset.load_indices" title="Permalink to this definition">¶</a></dt>
<dd><p>Return TFRecord indices.</p>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.manifest">
<span class="sig-name descname"><span class="pre">manifest</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">key</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">'path'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">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/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/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.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="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#slideflow.Dataset.manifest" title="Permalink to this definition">¶</a></dt>
<dd><p>Generate a manifest of all tfrecords.</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>key</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 ‘path’ (default) or ‘name’. Determines key format
in the manifest dictionary.</p></li>
<li><p><strong>filter</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Apply active filters to manifest.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Dict mapping key (path or slide name) to number of tiles.</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.Dataset.manifest_histogram">
<span class="sig-name descname"><span class="pre">manifest_histogram</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">by</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">binrange</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 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/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="headerlink" href="#slideflow.Dataset.manifest_histogram" title="Permalink to this definition">¶</a></dt>
<dd><p>Plot histograms of tiles-per-slide.</p>
<dl>
<dt>Example</dt><dd><p>Create histograms of tiles-per-slide, stratified by site.</p>
<blockquote>
<div><div class="highlight-python notranslate"><div class="highlight"><pre><span></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">dataset</span><span class="o">.</span><span class="n">manifest_histogram</span><span class="p">(</span><span class="n">by</span><span class="o">=</span><span class="s1">&#39;site&#39;</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>
</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>by</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>) – Stratify histograms by this annotation column
header. Defaults to None.</p></li>
<li><p><strong>binrange</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.12)"><em>tuple</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><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>) – Histogram bin ranges. If None, uses
full range. Defaults to None.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.patients">
<span class="sig-name descname"><span class="pre">patients</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><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></span><a class="headerlink" href="#slideflow.Dataset.patients" title="Permalink to this definition">¶</a></dt>
<dd><p>Return a list of patient IDs from this dataset.</p>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.get_bags">
<span class="sig-name descname"><span class="pre">get_bags</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></em>, <em class="sig-param"><span class="n"><span class="pre">warn_missing</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#slideflow.Dataset.get_bags" title="Permalink to this definition">¶</a></dt>
<dd><p>Return list of all *.pt files with slide names in this dataset.</p>
<p>May return more than one *.pt file for each slide.</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>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><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>) – Directory(ies) to search for *.pt files.</p></li>
<li><p><strong>warn_missing</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Raise a warning if any slides in this dataset
do not have a *.pt file.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.read_tfrecord_by_location">
<span class="sig-name descname"><span class="pre">read_tfrecord_by_location</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>, <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/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">decode</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 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.Any" title="(in Python v3.12)"><span class="pre">Any</span></a></span></span><a class="headerlink" href="#slideflow.Dataset.read_tfrecord_by_location" title="Permalink to this definition">¶</a></dt>
<dd><p>Read a record from a TFRecord, indexed by location.</p>
<p>Finds the associated TFRecord for a slide, and returns the record
inside which corresponds to a given tile location.</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>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>) – Name of slide. Will search for the slide’s associated
TFRecord.</p></li>
<li><p><strong>loc</strong> (<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><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>) – <code class="docutils literal notranslate"><span class="pre">(x,</span> <span class="pre">y)</span></code> tile location. Searches the TFRecord
for the tile that corresponds to this location.</p></li>
<li><p><strong>decode</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Decode the associated record, returning Tensors.
Defaults to True.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Unprocessed raw TFRecord bytes if <code class="docutils literal notranslate"><span class="pre">decode=False</span></code>, otherwise a
tuple containing <code class="docutils literal notranslate"><span class="pre">(slide,</span> <span class="pre">image)</span></code>, where <code class="docutils literal notranslate"><span class="pre">image</span></code> is a
uint8 Tensor.</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.remove_filter">
<span class="sig-name descname"><span class="pre">remove_filter</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><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Any" title="(in Python v3.12)"><span class="pre">Any</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="#slideflow.Dataset" title="slideflow.dataset.Dataset"><span class="pre">Dataset</span></a></span></span><a class="headerlink" href="#slideflow.Dataset.remove_filter" title="Permalink to this definition">¶</a></dt>
<dd><p>Remove a specific filter from the active filters.</p>
<dl class="field-list simple">
<dt class="field-odd">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>filters</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> of </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Filter keys. Will remove filters with
these keys.</p></li>
<li><p><strong>filter_blank</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> of </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Will remove these headers stored in
filter_blank.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Dataset with filter removed.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference internal" href="#slideflow.Dataset" title="slideflow.Dataset"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.Dataset</span></code></a></p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.rebuild_index">
<span class="sig-name descname"><span class="pre">rebuild_index</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/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="headerlink" href="#slideflow.Dataset.rebuild_index" title="Permalink to this definition">¶</a></dt>
<dd><p>Rebuild index files for TFRecords.</p>
<p>Equivalent to <code class="docutils literal notranslate"><span class="pre">Dataset.build_index(force=True)</span></code>.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>None</strong> – </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.Dataset.resize_tfrecords">
<span class="sig-name descname"><span class="pre">resize_tfrecords</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">tile_px</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="headerlink" href="#slideflow.Dataset.resize_tfrecords" title="Permalink to this definition">¶</a></dt>
<dd><p>Resize images in a set of TFRecords to a given pixel size.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>tile_px</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Target pixel size for resizing TFRecord images.</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.rois">
<span class="sig-name descname"><span class="pre">rois</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.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></span><a class="headerlink" href="#slideflow.Dataset.rois" title="Permalink to this definition">¶</a></dt>
<dd><p>Return a list of all ROIs.</p>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.slide_manifest">
<span class="sig-name descname"><span class="pre">slide_manifest</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">roi_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">'auto'</span></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><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">tma</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">source</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">low_memory</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><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.Dataset.slide_manifest" title="Permalink to this definition">¶</a></dt>
<dd><p>Return a dictionary of slide names and estimated number of tiles.</p>
<p>Uses Otsu thresholding for background filtering, and the ROI strategy.</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>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 skip a slide 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>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>) – Stride divisor for tile extraction.
A stride of 1 will extract non-overlapping tiles.
A stride_div of 2 will extract overlapping tiles, with a stride
equal to 50% of the tile width. Defaults to 1.</p></li>
<li><p><strong>tma</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Deprecated argument. Tumor micro-arrays are read as
standard slides. Defaults to False.</p></li>
<li><p><strong>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>) – Dataset source name.
Defaults to None (using all sources).</p></li>
<li><p><strong>low_memory</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Operate in low-memory mode at the cost of
worse performance.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Dictionary mapping slide names to number of
estimated non-background tiles in the slide.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Dict[<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)">str</a>, <a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)">int</a>]</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.slide_paths">
<span class="sig-name descname"><span class="pre">slide_paths</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">source</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">apply_filters</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/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></span><a class="headerlink" href="#slideflow.Dataset.slide_paths" title="Permalink to this definition">¶</a></dt>
<dd><p>Return a list of paths to slides.</p>
<p>Either returns a list of paths to all slides, or slides only matching
dataset filters.</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>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>) – Dataset source name.
Defaults to None (using all sources).</p></li>
<li><p><strong>filter</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>) – Return only slide paths meeting filter
criteria. If False, return all slides. Defaults to True.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>List of slide paths.</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#list" title="(in Python v3.12)">list</a>(<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.Dataset.slides">
<span class="sig-name descname"><span class="pre">slides</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.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></span><a class="headerlink" href="#slideflow.Dataset.slides" title="Permalink to this definition">¶</a></dt>
<dd><p>Return a list of slide names in this dataset.</p>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.split">
<span class="sig-name descname"><span class="pre">split</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">model_type</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">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="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/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">val_strategy</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">'fixed'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">splits</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">val_fraction</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a><span 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">val_k_fold</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">k_fold_iter</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">site_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/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/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/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">'site'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">read_only</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">from_wsi</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><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 internal" href="#slideflow.Dataset" title="slideflow.dataset.Dataset"><span class="pre">Dataset</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference internal" href="#slideflow.Dataset" title="slideflow.dataset.Dataset"><span class="pre">Dataset</span></a><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#slideflow.Dataset.split" title="Permalink to this definition">¶</a></dt>
<dd><p>Split this dataset into a training and validation dataset.</p>
<p>If a validation split has already been prepared (e.g. K-fold iterations
were already determined), the previously generated split will be used.
Otherwise, create a new split and log the result in the TFRecord
directory so future models may use the same split for consistency.</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_type</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 ‘classification’ or ‘regression’. Defaults
to ‘classification’ if <code class="docutils literal notranslate"><span class="pre">labels</span></code> is provided.</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> or </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Either a dictionary of slides: labels,
or an outcome label (<code class="docutils literal notranslate"><span class="pre">str</span></code>). Used for balancing outcome
labels in training and validation cohorts. Defaults to None.</p></li>
<li><p><strong>val_strategy</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 ‘k-fold’, ‘k-fold-preserved-site’,
‘bootstrap’, or ‘fixed’. Defaults to ‘fixed’.</p></li>
<li><p><strong>splits</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 JSON file containing validation
splits. Defaults to None.</p></li>
<li><p><strong>outcome_key</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>) – Key indicating outcome label in
slide_labels_dict. Defaults to ‘outcome_label’.</p></li>
<li><p><strong>val_fraction</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a><em>, </em><em>optional</em>) – Proportion of data for validation.
Not used if strategy is k-fold. Defaults to None.</p></li>
<li><p><strong>val_k_fold</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – K, required if using K-fold validation.
Defaults to None.</p></li>
<li><p><strong>k_fold_iter</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>) – Which K-fold iteration to generate
starting at 1. Fequired if using K-fold validation.
Defaults to None.</p></li>
<li><p><strong>site_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 patients to site labels,
or an outcome column with site labels. Only used for site
preserved cross validation. Defaults to ‘site’.</p></li>
<li><p><strong>read_only</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Prevents writing validation splits to file.
Defaults to False.</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><a class="reference internal" href="#slideflow.Dataset" title="slideflow.Dataset"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.Dataset</span></code></a>: Training dataset.</p>
<p><a class="reference internal" href="#slideflow.Dataset" title="slideflow.Dataset"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.Dataset</span></code></a>: Validation dataset.</p>
</div></blockquote>
</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.split_tfrecords_by_roi">
<span class="sig-name descname"><span class="pre">split_tfrecords_by_roi</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">destination</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">roi_filter_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/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">'center'</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.Dataset.split_tfrecords_by_roi" title="Permalink to this definition">¶</a></dt>
<dd><p>Split dataset tfrecords into separate tfrecords according to ROI.</p>
<p>Will generate two sets of tfrecords, with identical names: one with
tiles inside the ROIs, one with tiles outside the ROIs. Will skip any
tfrecords that are missing ROIs. Requires slides to be available.</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>destination</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Destination path.</p></li>
<li><p><strong>roi_filter_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> or </em><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a>) – Method of filtering tiles with
ROIs. Either ‘center’ or float (0-1). If ‘center’, tiles are
filtered with ROIs based on the center of the tile. If float,
tiles are filtered based on the proportion of the tile inside
the ROI, and <code class="docutils literal notranslate"><span class="pre">roi_filter_method</span></code> is interpreted as a
threshold. If the proportion of a tile inside the ROI is
greater than this number, the tile is included. For example,
if <code class="docutils literal notranslate"><span class="pre">roi_filter_method=0.7</span></code>, a tile that is 80% inside of an
ROI will be included, and a tile that is 50% inside of an ROI
will be excluded. Defaults to ‘center’.</p></li>
</ul>
</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.Dataset.summary">
<span class="sig-name descname"><span class="pre">summary</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/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="headerlink" href="#slideflow.Dataset.summary" title="Permalink to this definition">¶</a></dt>
<dd><p>Print a summary of this dataset.</p>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.tensorflow">
<span class="sig-name descname"><span class="pre">tensorflow</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">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><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 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">from_wsi</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><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Any" title="(in Python v3.12)"><span class="pre">Any</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">tf.data.Dataset</span></span></span><a class="headerlink" href="#slideflow.Dataset.tensorflow" title="Permalink to this definition">¶</a></dt>
<dd><p>Return a Tensorflow Dataset object that interleaves tfrecords.</p>
<p>The returned dataset yields a batch of (image, label) for each tile.
Labels may be specified either via a dict mapping slide names to
outcomes, or a parsing function which accept and image and slide name,
returning a dict {‘image_raw’: image(tensor)} and label (int or float).</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>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> or </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>) – Dict or function. If dict, must
map slide names to outcome labels. If function, function must
accept an image (tensor) and slide name (str), and return a
dict {‘image_raw’: image (tensor)} and label (int or float).
If not provided, all labels will be 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.</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/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – <p>Image augmentations to perform. Augmentations include:</p>
<ul>
<li><p><code class="docutils literal notranslate"><span class="pre">'x'</span></code>: Random horizontal flip</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">'y'</span></code>: Random vertical flip</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">'r'</span></code>: Random 90-degree rotation</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">'j'</span></code>: Random JPEG compression (50% chance to compress with quality between 50-100)</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">'b'</span></code>: Random Gaussian blur (10% chance to blur with sigma between 0.5-2.0)</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">'n'</span></code>: Random <a class="reference internal" href="../norm/#stain-augmentation"><span class="std std-ref">Stain Augmentation</span></a> (requires stain normalizer)</p></li>
</ul>
<p>Combine letters to define augmentations, such as <code class="docutils literal notranslate"><span class="pre">'xyrjn'</span></code>.
A value of True will use <code class="docutils literal notranslate"><span class="pre">'xyrjb'</span></code>.</p>
</p></li>
<li><p><strong>deterministic</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>) – When num_parallel_calls is specified,
if this boolean is specified, it controls the order in which the
transformation produces elements. If set to False, the
transformation is allowed to yield elements out of order to trade
determinism for performance. Defaults to False.</p></li>
<li><p><strong>drop_last</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>) – Drop the last non-full batch.
Defaults to False.</p></li>
<li><p><strong>from_wsi</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 predictions from tiles dynamically
extracted from whole-slide images, rather than TFRecords.
Defaults to False (use TFRecords).</p></li>
<li><p><strong>incl_loc</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>) – ‘coord’, ‘grid’, or None. Return (x,y)
origin coordinates (‘coord’) for each tile center along with tile
images, or the (x,y) grid coordinates for each tile.
Defaults to ‘coord’.</p></li>
<li><p><strong>incl_slidenames</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>) – Include slidenames as third returned
variable. Defaults to False.</p></li>
<li><p><strong>infinite</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>) – Create an finite dataset. WARNING: If
infinite is False &amp;&amp; balancing is used, some tiles will be skipped.
Defaults to True.</p></li>
<li><p><strong>img_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>) – Image width in pixels.</p></li>
<li><p><strong>normalizer</strong> (<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) – Normalizer to use on images. Defaults to None.</p></li>
<li><p><strong>num_parallel_reads</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 parallel reads for each
TFRecordDataset. Defaults to 4.</p></li>
<li><p><strong>num_shards</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>) – Shard the tfrecord datasets, used for
multiprocessing datasets. Defaults to None.</p></li>
<li><p><strong>pool</strong> (<em>multiprocessing.Pool</em>) – Shared multiprocessing pool. Useful
if <code class="docutils literal notranslate"><span class="pre">from_wsi=True</span></code>, for sharing a unified processing pool between
dataloaders. 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><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>)</em><em>, </em><em>optional</em>) – List of ROI paths. Only used if
from_wsi=True.  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><em>, </em><em>optional</em>) – Method for extracting ROIs. Only used if
from_wsi=True. Defaults to ‘auto’.</p></li>
<li><p><strong>shard_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><em>, </em><em>optional</em>) – Index of the tfrecord shard to use.
Defaults to None.</p></li>
<li><p><strong>standardize</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>) – Standardize images to (0,1).
Defaults to True.</p></li>
<li><p><strong>tile_um</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>) – Size of tiles to extract from WSI, in
microns. Only used if from_wsi=True. Defaults to None.</p></li>
<li><p><strong>tfrecord_parser</strong> (<em>Callable</em><em>, </em><em>optional</em>) – Custom parser for TFRecords.
Defaults to None.</p></li>
<li><p><strong>transform</strong> (<em>Callable</em><em>, </em><em>optional</em>) – Arbitrary transform function.
Performs transformation after augmentations but before
standardization. Defaults to None.</p></li>
<li><p><strong>**decode_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>) – Keyword arguments to pass to
<a class="reference internal" href="../io_tensorflow/#slideflow.io.tensorflow.decode_image" title="slideflow.io.tensorflow.decode_image"><code class="xref py py-func docutils literal notranslate"><span class="pre">slideflow.io.tensorflow.decode_image()</span></code></a>.</p></li>
</ul>
</dd>
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>tf.data.Dataset</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.tfrecord_report">
<span class="sig-name descname"><span class="pre">tfrecord_report</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">dest</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">normalizer</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="../norm/#slideflow.norm.StainNormalizer" title="slideflow.norm.StainNormalizer"><span class="pre">StainNormalizer</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">&#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.Dataset.tfrecord_report" title="Permalink to this definition">¶</a></dt>
<dd><p>Create a PDF report of TFRecords.</p>
<p>Reports include 10 example tiles per TFRecord. Report is saved
in the target destination.</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>dest</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Directory in which to save the PDF report.</p></li>
<li><p><strong>normalizer</strong> (<cite>slideflow.norm.StainNormalizer</cite>, optional) – Normalizer to use on image tiles. Defaults to None.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.tfrecord_heatmap">
<span class="sig-name descname"><span class="pre">tfrecord_heatmap</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">tfrecord</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/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></em>, <em class="sig-param"><span class="n"><span class="pre">tile_dict</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/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#float" title="(in Python v3.12)"><span class="pre">float</span></a><span class="p"><span class="pre">]</span></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="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="headerlink" href="#slideflow.Dataset.tfrecord_heatmap" title="Permalink to this definition">¶</a></dt>
<dd><p>Create a tfrecord-based WSI heatmap.</p>
<p>Uses a dictionary of tile values for heatmap display, and saves to
the specified directory.</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>tfrecord</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> or </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>) – Path(s) to tfrecord(s).</p></li>
<li><p><strong>tile_dict</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.12)"><em>dict</em></a>) – Dictionary mapping tfrecord indices to a
tile-level value for display in heatmap format</p></li>
<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>) – Destination filename for heatmap.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.tfrecords">
<span class="sig-name descname"><span class="pre">tfrecords</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">source</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">&#x2192;</span> <span class="sig-return-typehint"><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></span><a class="headerlink" href="#slideflow.Dataset.tfrecords" title="Permalink to this definition">¶</a></dt>
<dd><p>Return a list of all tfrecords.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>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>) – Only return tfrecords from this dataset
source. Defaults to None (return all tfrecords in dataset).</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>List of tfrecords paths.</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.tfrecords_by_subfolder">
<span class="sig-name descname"><span class="pre">tfrecords_by_subfolder</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">subfolder</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/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></span><a class="headerlink" href="#slideflow.Dataset.tfrecords_by_subfolder" title="Permalink to this definition">¶</a></dt>
<dd><p>Return a list of all tfrecords in a specific subfolder.</p>
<p>Ignores any dataset filters.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>subfolder</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 subfolder to check for tfrecords.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>List of tfrecords paths.</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.tfrecords_folders">
<span class="sig-name descname"><span class="pre">tfrecords_folders</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.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></span><a class="headerlink" href="#slideflow.Dataset.tfrecords_folders" title="Permalink to this definition">¶</a></dt>
<dd><p>Return folders containing tfrecords.</p>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.tfrecords_from_tiles">
<span class="sig-name descname"><span class="pre">tfrecords_from_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">delete_tiles</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><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.Dataset.tfrecords_from_tiles" title="Permalink to this definition">¶</a></dt>
<dd><p>Create tfrecord files from a collection of raw images.</p>
<p>Images must be stored in the dataset source(s) tiles directory.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>delete_tiles</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Remove tiles after storing in tfrecords.</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.Dataset.tfrecords_have_locations">
<span class="sig-name descname"><span class="pre">tfrecords_have_locations</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/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span></span><a class="headerlink" href="#slideflow.Dataset.tfrecords_have_locations" title="Permalink to this definition">¶</a></dt>
<dd><p>Check if TFRecords have associated tile location information.</p>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.transform_tfrecords">
<span class="sig-name descname"><span class="pre">transform_tfrecords</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">dest</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="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="headerlink" href="#slideflow.Dataset.transform_tfrecords" title="Permalink to this definition">¶</a></dt>
<dd><p>Transform TFRecords, saving to a target path.</p>
<p>Tfrecords will be saved in the output directory nested by source name.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>dest</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Destination.</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.thumbnails">
<span class="sig-name descname"><span class="pre">thumbnails</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">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">512</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">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">enable_downsample</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.Dataset.thumbnails" title="Permalink to this definition">¶</a></dt>
<dd><p>Generate square slide thumbnails with black borders of fixed size.</p>
<p>Saves thumbnails to the specified directory.</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>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>) – Width/height of thumbnail in pixels.
Defaults to 512.</p></li>
<li><p><strong>dataset</strong> (<a class="reference internal" href="#slideflow.Dataset" title="slideflow.Dataset"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.Dataset</span></code></a>, optional) – Dataset
from which to generate activations. If not supplied, will
calculate activations for all tfrecords at the tile_px/tile_um
matching the supplied model, optionally using provided filters
and filter_blank.</p></li>
<li><p><strong>filters</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>) – Dataset filters to use for
selecting slides. See <a class="reference internal" href="#slideflow.Dataset.filter" title="slideflow.Dataset.filter"><code class="xref py py-meth docutils literal notranslate"><span class="pre">slideflow.Dataset.filter()</span></code></a> for
more information. Defaults to None.</p></li>
<li><p><strong>filter_blank</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>) or </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>) – Skip slides that have
blank values in these patient annotation columns.
Defaults to None.</p></li>
<li><p><strong>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>) – Include ROI in the thumbnail images.
Defaults to False.</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>) – If True and a thumbnail is not
embedded in the slide file, downsampling is permitted to
accelerate thumbnail calculation.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.torch">
<span class="sig-name descname"><span class="pre">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">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/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/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">DataFrame</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">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 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">rebuild_index</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">from_wsi</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><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Any" title="(in Python v3.12)"><span class="pre">Any</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">DataLoader</span></span></span><a class="headerlink" href="#slideflow.Dataset.torch" title="Permalink to this definition">¶</a></dt>
<dd><p>Return a PyTorch DataLoader object that interleaves tfrecords.</p>
<p>The returned dataloader yields a batch of (image, label) for each tile.</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>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><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, or </em><em>pd.DataFrame</em><em>, </em><em>optional</em>) – If a dict is provided,
expect a dict mapping slide names to outcome labels. If a str,
will intepret as categorical annotation header. For regression
tasks, or outcomes with manually assigned labels, pass the
first result of dataset.labels(…). If None, returns slide
instead of label.</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.</p></li>
<li><p><strong>rebuild_index</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Re-build index files even if already present.
Defaults to True.</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/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – <p>Image augmentations to perform. Augmentations include:</p>
<ul>
<li><p><code class="docutils literal notranslate"><span class="pre">'x'</span></code>: Random horizontal flip</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">'y'</span></code>: Random vertical flip</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">'r'</span></code>: Random 90-degree rotation</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">'j'</span></code>: Random JPEG compression (50% chance to compress with quality between 50-100)</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">'b'</span></code>: Random Gaussian blur (10% chance to blur with sigma between 0.5-2.0)</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">'n'</span></code>: Random <a class="reference internal" href="../norm/#stain-augmentation"><span class="std std-ref">Stain Augmentation</span></a> (requires stain normalizer)</p></li>
</ul>
<p>Combine letters to define augmentations, such as <code class="docutils literal notranslate"><span class="pre">'xyrjn'</span></code>.
A value of True will use <code class="docutils literal notranslate"><span class="pre">'xyrjb'</span></code>.</p>
</p></li>
<li><p><strong>chunk_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>) – Chunk size for image decoding.
Defaults to 1.</p></li>
<li><p><strong>drop_last</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>) – Drop the last non-full batch.
Defaults to False.</p></li>
<li><p><strong>from_wsi</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 predictions from tiles dynamically
extracted from whole-slide images, rather than TFRecords.
Defaults to False (use TFRecords).</p></li>
<li><p><strong>incl_loc</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>) – Include loc_x and loc_y (image tile
center coordinates, in base / level=0 dimension) as additional
returned variables. Defaults to False.</p></li>
<li><p><strong>incl_slidenames</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>) – Include slidenames as third returned
variable. Defaults to False.</p></li>
<li><p><strong>infinite</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>) – Infinitely repeat data. Defaults to True.</p></li>
<li><p><strong>max_size</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>) – Unused argument present for legacy
compatibility; will be removed.</p></li>
<li><p><strong>model_type</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>) – Used to generate random labels
(for StyleGAN2). Not required. Defaults to ‘classification’.</p></li>
<li><p><strong>num_replicas</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 GPUs or unique instances which
will have their own DataLoader. Used to interleave results among
workers without duplications. Defaults to 1.</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 DataLoader workers.
Defaults to 2.</p></li>
<li><p><strong>normalizer</strong> (<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) – Normalizer. Defaults to None.</p></li>
<li><p><strong>onehot</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>) – Onehot encode labels. Defaults to False.</p></li>
<li><p><strong>persistent_workers</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>) – Sets the DataLoader
persistent_workers flag. Defaults toNone (4 if not using a SPAMS
normalizer, 1 if using SPAMS).</p></li>
<li><p><strong>pin_memory</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>) – Pin memory to GPU. Defaults to True.</p></li>
<li><p><strong>pool</strong> (<em>multiprocessing.Pool</em>) – Shared multiprocessing pool. Useful
if from_wsi=True, for sharing a unified processing pool between
dataloaders. Defaults to None.</p></li>
<li><p><strong>prefetch_factor</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 batches to prefetch in each
SlideflowIterator. Defaults to 1.</p></li>
<li><p><strong>rank</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>) – Worker ID to identify this worker.
Used to interleave results.
among workers without duplications. Defaults to 0 (first worker).</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><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>)</em><em>, </em><em>optional</em>) – List of ROI paths. Only used if
from_wsi=True.  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><em>, </em><em>optional</em>) – Method for extracting ROIs. Only used if
from_wsi=True. Defaults to ‘auto’.</p></li>
<li><p><strong>standardize</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>) – Standardize images to mean 0 and
variance of 1. Defaults to True.</p></li>
<li><p><strong>tile_um</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>) – Size of tiles to extract from WSI, in
microns. Only used if from_wsi=True. Defaults to None.</p></li>
<li><p><strong>transform</strong> (<em>Callable</em><em>, </em><em>optional</em>) – Arbitrary torchvision transform
function. Performs transformation after augmentations but
before standardization. Defaults to None.</p></li>
<li><p><strong>tfrecord_parser</strong> (<em>Callable</em><em>, </em><em>optional</em>) – Custom parser for TFRecords.
Defaults to None.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.unclip">
<span class="sig-name descname"><span class="pre">unclip</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 internal" href="#slideflow.Dataset" title="slideflow.dataset.Dataset"><span class="pre">Dataset</span></a></span></span><a class="headerlink" href="#slideflow.Dataset.unclip" title="Permalink to this definition">¶</a></dt>
<dd><p>Return a dataset object with all clips removed.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Dataset with clips removed.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p><a class="reference internal" href="#slideflow.Dataset" title="slideflow.Dataset"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.Dataset</span></code></a></p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.update_manifest">
<span class="sig-name descname"><span class="pre">update_manifest</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">force_update</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><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.Dataset.update_manifest" title="Permalink to this definition">¶</a></dt>
<dd><p>Update tfrecord manifests.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>forced_update</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>) – Force regeneration of the
manifests from scratch.</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.update_annotations_with_slidenames">
<span class="sig-name descname"><span class="pre">update_annotations_with_slidenames</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">annotations_file</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.Dataset.update_annotations_with_slidenames" title="Permalink to this definition">¶</a></dt>
<dd><p>Automatically associated slide names and paths in the annotations.</p>
<p>Attempts to automatically associate slide names from a directory
with patients in a given annotations file, skipping any slide names
that are already present in the annotations file.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>annotations_file</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 annotations file.</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.verify_annotations_slides">
<span class="sig-name descname"><span class="pre">verify_annotations_slides</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/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="headerlink" href="#slideflow.Dataset.verify_annotations_slides" title="Permalink to this definition">¶</a></dt>
<dd><p>Verify that annotations are correctly loaded.</p>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Dataset.verify_img_format">
<span class="sig-name descname"><span class="pre">verify_img_format</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></em>, <em class="sig-param"><span class="n"><span class="pre">progress</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/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><a class="headerlink" href="#slideflow.Dataset.verify_img_format" title="Permalink to this definition">¶</a></dt>
<dd><p>Verify that all tfrecords have the same image format (PNG/JPG).</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>image format (png or jpeg)</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#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.Dataset.verify_slide_names">
<span class="sig-name descname"><span class="pre">verify_slide_names</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">allow_errors</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><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/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span></span><a class="headerlink" href="#slideflow.Dataset.verify_slide_names" title="Permalink to this definition">¶</a></dt>
<dd><p>Verify that slide names inside TFRecords match the file names.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>allow_errors</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Do not raise an error if there is a mismatch.
Defaults to False.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>If all slide names inside TFRecords match the TFRecord</dt><dd><p>file names.</p>
</dd>
</dl>
</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/functions.html#bool" title="(in Python v3.12)">bool</a></p>
</dd>
<dt class="field-even">Raises<span class="colon">:</span></dt>
<dd class="field-even"><p><strong>sf.errors.MismatchedSlideNamesError</strong> – If any slide names inside
    TFRecords do not match the TFRecord file names,
    and allow_errors=False.</p>
</dd>
</dl>
</dd></dl>

</section>
</section>


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              <ul>
<li><a class="reference internal" href="#">slideflow.Dataset</a><ul>
<li><a class="reference internal" href="#slideflow.Dataset"><code class="docutils literal notranslate"><span class="pre">Dataset</span></code></a></li>
<li><a class="reference internal" href="#attributes">Attributes</a></li>
<li><a class="reference internal" href="#methods">Methods</a><ul>
<li><a class="reference internal" href="#slideflow.Dataset.balance"><code class="docutils literal notranslate"><span class="pre">balance()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.build_index"><code class="docutils literal notranslate"><span class="pre">build_index()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.cell_segmentation"><code class="docutils literal notranslate"><span class="pre">cell_segmentation()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.check_duplicates"><code class="docutils literal notranslate"><span class="pre">check_duplicates()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.clear_filters"><code class="docutils literal notranslate"><span class="pre">clear_filters()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.clip"><code class="docutils literal notranslate"><span class="pre">clip()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.convert_xml_rois"><code class="docutils literal notranslate"><span class="pre">convert_xml_rois()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.extract_cells"><code class="docutils literal notranslate"><span class="pre">extract_cells()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.extract_tiles"><code class="docutils literal notranslate"><span class="pre">extract_tiles()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.extract_tiles_from_tfrecords"><code class="docutils literal notranslate"><span class="pre">extract_tiles_from_tfrecords()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.filter"><code class="docutils literal notranslate"><span class="pre">filter()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.find_slide"><code class="docutils literal notranslate"><span class="pre">find_slide()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.find_tfrecord"><code class="docutils literal notranslate"><span class="pre">find_tfrecord()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.generate_feature_bags"><code class="docutils literal notranslate"><span class="pre">generate_feature_bags()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.get_tfrecord_locations"><code class="docutils literal notranslate"><span class="pre">get_tfrecord_locations()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.get_tile_dataframe"><code class="docutils literal notranslate"><span class="pre">get_tile_dataframe()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.harmonize_labels"><code class="docutils literal notranslate"><span class="pre">harmonize_labels()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.is_float"><code class="docutils literal notranslate"><span class="pre">is_float()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.kfold_split"><code class="docutils literal notranslate"><span class="pre">kfold_split()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.labels"><code class="docutils literal notranslate"><span class="pre">labels()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.load_annotations"><code class="docutils literal notranslate"><span class="pre">load_annotations()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.load_indices"><code class="docutils literal notranslate"><span class="pre">load_indices()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.manifest"><code class="docutils literal notranslate"><span class="pre">manifest()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.manifest_histogram"><code class="docutils literal notranslate"><span class="pre">manifest_histogram()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.patients"><code class="docutils literal notranslate"><span class="pre">patients()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.get_bags"><code class="docutils literal notranslate"><span class="pre">get_bags()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.read_tfrecord_by_location"><code class="docutils literal notranslate"><span class="pre">read_tfrecord_by_location()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.remove_filter"><code class="docutils literal notranslate"><span class="pre">remove_filter()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.rebuild_index"><code class="docutils literal notranslate"><span class="pre">rebuild_index()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.resize_tfrecords"><code class="docutils literal notranslate"><span class="pre">resize_tfrecords()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.rois"><code class="docutils literal notranslate"><span class="pre">rois()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.slide_manifest"><code class="docutils literal notranslate"><span class="pre">slide_manifest()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.slide_paths"><code class="docutils literal notranslate"><span class="pre">slide_paths()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.slides"><code class="docutils literal notranslate"><span class="pre">slides()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.split"><code class="docutils literal notranslate"><span class="pre">split()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.split_tfrecords_by_roi"><code class="docutils literal notranslate"><span class="pre">split_tfrecords_by_roi()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.summary"><code class="docutils literal notranslate"><span class="pre">summary()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.tensorflow"><code class="docutils literal notranslate"><span class="pre">tensorflow()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.tfrecord_report"><code class="docutils literal notranslate"><span class="pre">tfrecord_report()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.tfrecord_heatmap"><code class="docutils literal notranslate"><span class="pre">tfrecord_heatmap()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.tfrecords"><code class="docutils literal notranslate"><span class="pre">tfrecords()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.tfrecords_by_subfolder"><code class="docutils literal notranslate"><span class="pre">tfrecords_by_subfolder()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.tfrecords_folders"><code class="docutils literal notranslate"><span class="pre">tfrecords_folders()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.tfrecords_from_tiles"><code class="docutils literal notranslate"><span class="pre">tfrecords_from_tiles()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.tfrecords_have_locations"><code class="docutils literal notranslate"><span class="pre">tfrecords_have_locations()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.transform_tfrecords"><code class="docutils literal notranslate"><span class="pre">transform_tfrecords()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.thumbnails"><code class="docutils literal notranslate"><span class="pre">thumbnails()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.torch"><code class="docutils literal notranslate"><span class="pre">torch()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.unclip"><code class="docutils literal notranslate"><span class="pre">unclip()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.update_manifest"><code class="docutils literal notranslate"><span class="pre">update_manifest()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.update_annotations_with_slidenames"><code class="docutils literal notranslate"><span class="pre">update_annotations_with_slidenames()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.verify_annotations_slides"><code class="docutils literal notranslate"><span class="pre">verify_annotations_slides()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.verify_img_format"><code class="docutils literal notranslate"><span class="pre">verify_img_format()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.Dataset.verify_slide_names"><code class="docutils literal notranslate"><span class="pre">verify_slide_names()</span></code></a></li>
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