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<!DOCTYPE html>

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              <p class="caption" role="heading"><span class="caption-text">Introduction</span></p>

<ul>

<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>

<li class="toctree-l1"><a class="reference internal" href="../quickstart/">Quickstart</a></li>

<li class="toctree-l1"><a class="reference internal" href="../project_setup/">Setting up a Project</a></li>

<li class="toctree-l1"><a class="reference internal" href="../datasets_and_val/">Datasets</a></li>

<li class="toctree-l1"><a class="reference internal" href="../slide_processing/">Slide Processing</a></li>

<li class="toctree-l1"><a class="reference internal" href="../training/">Training</a></li>

<li class="toctree-l1"><a class="reference internal" href="../evaluation/">Evaluation</a></li>

<li class="toctree-l1"><a class="reference internal" href="../posthoc/">Layer Activations</a></li>

<li class="toctree-l1"><a class="reference internal" href="../uq/">Uncertainty Quantification</a></li>

<li class="toctree-l1"><a class="reference internal" href="../features/">Generating Features</a></li>

<li class="toctree-l1"><a class="reference internal" href="../mil/">Multiple-Instance Learning (MIL)</a></li>

<li class="toctree-l1"><a class="reference internal" href="../ssl/">Self-Supervised Learning (SSL)</a></li>

<li class="toctree-l1"><a class="reference internal" href="../stylegan/">Generative Networks (GANs)</a></li>

<li class="toctree-l1"><a class="reference internal" href="../saliency/">Saliency Maps</a></li>

<li class="toctree-l1"><a class="reference internal" href="../segmentation/">Tissue Segmentation</a></li>

<li class="toctree-l1"><a class="reference internal" href="../cellseg/">Cell Segmentation</a></li>

<li class="toctree-l1"><a class="reference internal" href="../custom_loops/">Custom Training Loops</a></li>

<li class="toctree-l1"><a class="reference internal" href="../studio/">Slideflow Studio: Live Visualization</a></li>

<li class="toctree-l1"><a class="reference internal" href="../troubleshooting/">Troubleshooting</a></li>

</ul>

<p class="caption" role="heading"><span class="caption-text">Developer Notes</span></p>

<ul>

<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>

<li class="toctree-l1"><a class="reference internal" href="../custom_extractors/">Custom Feature Extractors</a></li>

<li class="toctree-l1"><a class="reference internal" href="../tile_labels/">Strong Supervision with Tile Labels</a></li>

<li class="toctree-l1"><a class="reference internal" href="../plugins/">Creating a Slideflow Plugin</a></li>

</ul>

<p class="caption" role="heading"><span class="caption-text">API</span></p>

<ul class="current">

<li class="toctree-l1"><a class="reference internal" href="../slideflow/">slideflow</a></li>

<li class="toctree-l1"><a class="reference internal" href="../project/">slideflow.Project</a></li>

<li class="toctree-l1"><a class="reference internal" href="../dataset/">slideflow.Dataset</a></li>

<li class="toctree-l1"><a class="reference internal" href="../dataset_features/">slideflow.DatasetFeatures</a></li>

<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>

<li class="toctree-l1"><a class="reference internal" href="../slidemap/">slideflow.SlideMap</a></li>

<li class="toctree-l1"><a class="reference internal" href="../biscuit/">slideflow.biscuit</a></li>

<li class="toctree-l1"><a class="reference internal" href="../slideflow_cellseg/">slideflow.cellseg</a></li>

<li class="toctree-l1"><a class="reference internal" href="../io/">slideflow.io</a></li>

<li class="toctree-l1"><a class="reference internal" href="../io_tensorflow/">slideflow.io.tensorflow</a></li>

<li class="toctree-l1"><a class="reference internal" href="../io_torch/">slideflow.io.torch</a></li>

<li class="toctree-l1"><a class="reference internal" href="../gan/">slideflow.gan</a></li>

<li class="toctree-l1"><a class="reference internal" href="../grad/">slideflow.grad</a></li>

<li class="toctree-l1"><a class="reference internal" href="../mil_module/">slideflow.mil</a></li>

<li class="toctree-l1"><a class="reference internal" href="../model/">slideflow.model</a></li>

<li class="toctree-l1"><a class="reference internal" href="../model_tensorflow/">slideflow.model.tensorflow</a></li>

<li class="toctree-l1"><a class="reference internal" href="../model_torch/">slideflow.model.torch</a></li>

<li class="toctree-l1"><a class="reference internal" href="../norm/">slideflow.norm</a></li>

<li class="toctree-l1"><a class="reference internal" href="../simclr/">slideflow.simclr</a></li>

<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 current"><a class="current reference internal" href="#">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>

<ul>

<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-util">

<h1>slideflow.util<a class="headerlink" href="#slideflow-util" title="Permalink to this heading"></a></h1>

<p>This module contains a variety of utility functions used throughout the package.</p>

<span class="target" id="module-slideflow.util"></span><dl class="py class">

<dt class="sig sig-object py" id="slideflow.util.EasyDict">

<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">EasyDict</span></span><a class="reference internal" href="../_modules/slideflow/util/#EasyDict"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.EasyDict" title="Permalink to this definition"></a></dt>

<dd><p>Convenience class that behaves like a dict but allows access

with the attribute syntax.</p>

</dd></dl>



<dl class="py class">

<dt class="sig sig-object py" id="slideflow.util.FeatureExtractionProgress">

<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">FeatureExtractionProgress</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">columns</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">ProgressColumn</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">console</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Console</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">auto_refresh</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">refresh_per_second</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">10</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">speed_estimate_period</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">30.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">transient</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">redirect_stdout</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">redirect_stderr</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">get_time</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Callable" title="(in Python v3.12)"><span class="pre">Callable</span></a><span class="p"><span class="pre">[</span></span><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/functions.html#float" title="(in Python v3.12)"><span class="pre">float</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">disable</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">expand</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><a class="reference internal" href="../_modules/slideflow/util/#FeatureExtractionProgress"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.FeatureExtractionProgress" title="Permalink to this definition"></a></dt>

<dd><dl class="py method">

<dt class="sig sig-object py" id="slideflow.util.FeatureExtractionProgress.get_renderables">

<span class="sig-name descname"><span class="pre">get_renderables</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/slideflow/util/#FeatureExtractionProgress.get_renderables"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.FeatureExtractionProgress.get_renderables" title="Permalink to this definition"></a></dt>

<dd><p>Get a number of renderables for the progress display.</p>

</dd></dl>



</dd></dl>



<dl class="py class">

<dt class="sig sig-object py" id="slideflow.util.ImgBatchSpeedColumn">

<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">ImgBatchSpeedColumn</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">batch_size</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</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><a class="reference internal" href="../_modules/slideflow/util/#ImgBatchSpeedColumn"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.ImgBatchSpeedColumn" title="Permalink to this definition"></a></dt>

<dd><p>Renders human readable transfer speed.</p>

<dl class="py method">

<dt class="sig sig-object py" id="slideflow.util.ImgBatchSpeedColumn.__init__">

<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">batch_size</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</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><a class="reference internal" href="../_modules/slideflow/util/#ImgBatchSpeedColumn.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.ImgBatchSpeedColumn.__init__" title="Permalink to this definition"></a></dt>

<dd></dd></dl>



<dl class="py method">

<dt class="sig sig-object py" id="slideflow.util.ImgBatchSpeedColumn.render">

<span class="sig-name descname"><span class="pre">render</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">task</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Task</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">Text</span></span></span><a class="reference internal" href="../_modules/slideflow/util/#ImgBatchSpeedColumn.render"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.ImgBatchSpeedColumn.render" title="Permalink to this definition"></a></dt>

<dd><p>Show data transfer speed.</p>

</dd></dl>



</dd></dl>



<dl class="py class">

<dt class="sig sig-object py" id="slideflow.util.LabeledMofNCompleteColumn">

<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">LabeledMofNCompleteColumn</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">unit</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">args</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><a class="reference internal" href="../_modules/slideflow/util/#LabeledMofNCompleteColumn"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.LabeledMofNCompleteColumn" title="Permalink to this definition"></a></dt>

<dd><p>Renders a completion column with labels.</p>

<dl class="py method">

<dt class="sig sig-object py" id="slideflow.util.LabeledMofNCompleteColumn.__init__">

<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">unit</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">args</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><a class="reference internal" href="../_modules/slideflow/util/#LabeledMofNCompleteColumn.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.LabeledMofNCompleteColumn.__init__" title="Permalink to this definition"></a></dt>

<dd></dd></dl>



<dl class="py method">

<dt class="sig sig-object py" id="slideflow.util.LabeledMofNCompleteColumn.render">

<span class="sig-name descname"><span class="pre">render</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">task</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Task</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">Text</span></span></span><a class="reference internal" href="../_modules/slideflow/util/#LabeledMofNCompleteColumn.render"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.LabeledMofNCompleteColumn.render" title="Permalink to this definition"></a></dt>

<dd><p>Show completion status with labels.</p>

</dd></dl>



</dd></dl>



<dl class="py class">

<dt class="sig sig-object py" id="slideflow.util.MultiprocessProgress">

<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">MultiprocessProgress</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pb</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/slideflow/util/#MultiprocessProgress"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.MultiprocessProgress" title="Permalink to this definition"></a></dt>

<dd><p>Wrapper for a rich.progress bar that can be shared across processes.</p>

<dl class="py method">

<dt class="sig sig-object py" id="slideflow.util.MultiprocessProgress.__init__">

<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pb</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/slideflow/util/#MultiprocessProgress.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.MultiprocessProgress.__init__" title="Permalink to this definition"></a></dt>

<dd></dd></dl>



</dd></dl>



<dl class="py class">

<dt class="sig sig-object py" id="slideflow.util.MultiprocessProgressTracker">

<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">MultiprocessProgressTracker</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tasks</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/slideflow/util/#MultiprocessProgressTracker"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.MultiprocessProgressTracker" title="Permalink to this definition"></a></dt>

<dd><p>Wrapper for a rich.progress tracker that can be shared across processes.</p>

<dl class="py method">

<dt class="sig sig-object py" id="slideflow.util.MultiprocessProgressTracker.__init__">

<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tasks</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/slideflow/util/#MultiprocessProgressTracker.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.MultiprocessProgressTracker.__init__" title="Permalink to this definition"></a></dt>

<dd></dd></dl>



</dd></dl>



<dl class="py class">

<dt class="sig sig-object py" id="slideflow.util.TileExtractionProgress">

<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">TileExtractionProgress</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">columns</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">ProgressColumn</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">console</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Console</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">auto_refresh</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">refresh_per_second</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">10</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">speed_estimate_period</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">30.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">transient</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">redirect_stdout</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">redirect_stderr</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">get_time</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Callable" title="(in Python v3.12)"><span class="pre">Callable</span></a><span class="p"><span class="pre">[</span></span><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/functions.html#float" title="(in Python v3.12)"><span class="pre">float</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">disable</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">expand</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><a class="reference internal" href="../_modules/slideflow/util/#TileExtractionProgress"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.TileExtractionProgress" title="Permalink to this definition"></a></dt>

<dd><dl class="py method">

<dt class="sig sig-object py" id="slideflow.util.TileExtractionProgress.get_renderables">

<span class="sig-name descname"><span class="pre">get_renderables</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/slideflow/util/#TileExtractionProgress.get_renderables"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.TileExtractionProgress.get_renderables" title="Permalink to this definition"></a></dt>

<dd><p>Get a number of renderables for the progress display.</p>

</dd></dl>



</dd></dl>



<dl class="py class">

<dt class="sig sig-object py" id="slideflow.util.TileExtractionSpeedColumn">

<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">TileExtractionSpeedColumn</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">table_column</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Column</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/slideflow/util/#TileExtractionSpeedColumn"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.TileExtractionSpeedColumn" title="Permalink to this definition"></a></dt>

<dd><p>Renders human readable transfer speed.</p>

<dl class="py method">

<dt class="sig sig-object py" id="slideflow.util.TileExtractionSpeedColumn.render">

<span class="sig-name descname"><span class="pre">render</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">task</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Task</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">Text</span></span></span><a class="reference internal" href="../_modules/slideflow/util/#TileExtractionSpeedColumn.render"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.TileExtractionSpeedColumn.render" title="Permalink to this definition"></a></dt>

<dd><p>Show data transfer speed.</p>

</dd></dl>



</dd></dl>



<dl class="py class">

<dt class="sig sig-object py" id="slideflow.util.ValidJSONEncoder">

<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">ValidJSONEncoder</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">skipkeys</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ensure_ascii</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">check_circular</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">allow_nan</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sort_keys</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">indent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">separators</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">default</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/slideflow/util/#ValidJSONEncoder"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.ValidJSONEncoder" title="Permalink to this definition"></a></dt>

<dd><p>Constructor for JSONEncoder, with sensible defaults.</p>

<p>If skipkeys is false, then it is a TypeError to attempt

encoding of keys that are not str, int, float or None.  If

skipkeys is True, such items are simply skipped.</p>

<p>If ensure_ascii is true, the output is guaranteed to be str

objects with all incoming non-ASCII characters escaped.  If

ensure_ascii is false, the output can contain non-ASCII characters.</p>

<p>If check_circular is true, then lists, dicts, and custom encoded

objects will be checked for circular references during encoding to

prevent an infinite recursion (which would cause an RecursionError).

Otherwise, no such check takes place.</p>

<p>If allow_nan is true, then NaN, Infinity, and -Infinity will be

encoded as such.  This behavior is not JSON specification compliant,

but is consistent with most JavaScript based encoders and decoders.

Otherwise, it will be a ValueError to encode such floats.</p>

<p>If sort_keys is true, then the output of dictionaries will be

sorted by key; this is useful for regression tests to ensure

that JSON serializations can be compared on a day-to-day basis.</p>

<p>If indent is a non-negative integer, then JSON array

elements and object members will be pretty-printed with that

indent level.  An indent level of 0 will only insert newlines.

None is the most compact representation.</p>

<p>If specified, separators should be an (item_separator, key_separator)

tuple.  The default is (’, ‘, ‘: ‘) if <em>indent</em> is <code class="docutils literal notranslate"><span class="pre">None</span></code> and

(‘,’, ‘: ‘) otherwise.  To get the most compact JSON representation,

you should specify (‘,’, ‘:’) to eliminate whitespace.</p>

<p>If specified, default is a function that gets called for objects

that can’t otherwise be serialized.  It should return a JSON encodable

version of the object or raise a <code class="docutils literal notranslate"><span class="pre">TypeError</span></code>.</p>

<dl class="py method">

<dt class="sig sig-object py" id="slideflow.util.ValidJSONEncoder.default">

<span class="sig-name descname"><span class="pre">default</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">obj</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/slideflow/util/#ValidJSONEncoder.default"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.ValidJSONEncoder.default" title="Permalink to this definition"></a></dt>

<dd><p>Implement this method in a subclass such that it returns

a serializable object for <code class="docutils literal notranslate"><span class="pre">o</span></code>, or calls the base implementation

(to raise a <code class="docutils literal notranslate"><span class="pre">TypeError</span></code>).</p>

<p>For example, to support arbitrary iterators, you could

implement default like this:</p>

<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="k">def</span> <span class="nf">default</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">o</span><span class="p">):</span>

    <span class="k">try</span><span class="p">:</span>

        <span class="n">iterable</span> <span class="o">=</span> <span class="nb">iter</span><span class="p">(</span><span class="n">o</span><span class="p">)</span>

    <span class="k">except</span> <span class="ne">TypeError</span><span class="p">:</span>

        <span class="k">pass</span>

    <span class="k">else</span><span class="p">:</span>

        <span class="k">return</span> <span class="nb">list</span><span class="p">(</span><span class="n">iterable</span><span class="p">)</span>

    <span class="c1"># Let the base class default method raise the TypeError</span>

    <span class="k">return</span> <span class="n">JSONEncoder</span><span class="o">.</span><span class="n">default</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">o</span><span class="p">)</span>

</pre></div>

</div>

</dd></dl>



</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.about">

<span class="sig-name descname"><span class="pre">about</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">console</span></span><span class="o"><span class="pre">=</span></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="reference internal" href="../_modules/slideflow/util/#about"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.about" title="Permalink to this definition"></a></dt>

<dd><p>Print a summary of the slideflow version and active backends.</p>

<dl>

<dt>Example</dt><dd><div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">sf</span><span class="o">.</span><span class="n">about</span><span class="p">()</span>

<span class="go">╭=======================╮</span>

<span class="go">│       Slideflow       │</span>

<span class="go">│    Version: 3.0.0     │</span>

<span class="go">│  Backend: torch       │</span>

<span class="go">│ Slide Backend: cucim  │</span>

<span class="go">│ https://slideflow.dev │</span>

<span class="go">╰=======================╯</span>

</pre></div>

</div>

</dd>

</dl>

<dl class="field-list simple">

<dt class="field-odd">Parameters<span class="colon">:</span></dt>

<dd class="field-odd"><p><strong>console</strong> (<em>rich.console.Console</em><em>, </em><em>optional</em>) – Active console, if one exists.

Defaults to None.</p>

</dd>

</dl>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.batch">

<span class="sig-name descname"><span class="pre">batch</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">iterable</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></em>, <em class="sig-param"><span class="n"><span class="pre">n</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"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Iterable" title="(in Python v3.12)"><span class="pre">Iterable</span></a></span></span><a class="reference internal" href="../_modules/slideflow/util/#batch"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.batch" title="Permalink to this definition"></a></dt>

<dd><p>Separates an interable into batches of maximum size <cite>n</cite>.</p>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.batch_generator">

<span class="sig-name descname"><span class="pre">batch_generator</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">iterable</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Iterable" title="(in Python v3.12)"><span class="pre">Iterable</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">n</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"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Iterable" title="(in Python v3.12)"><span class="pre">Iterable</span></a></span></span><a class="reference internal" href="../_modules/slideflow/util/#batch_generator"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.batch_generator" title="Permalink to this definition"></a></dt>

<dd><p>Separates an interable into batches of maximum size <cite>n</cite>.</p>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.bin_values_to_slide_grid">

<span class="sig-name descname"><span class="pre">bin_values_to_slide_grid</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">locations</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">values</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">wsi</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="../slide/#slideflow.slide.WSI" title="slideflow.slide.wsi.WSI"><span class="pre">WSI</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">background</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">'min'</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">ndarray</span></span></span><a class="reference internal" href="../_modules/slideflow/util/#bin_values_to_slide_grid"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.bin_values_to_slide_grid" title="Permalink to this definition"></a></dt>

<dd><p>Bin heatmap values to a slide grid, using tile location information.</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>locations</strong> (<em>np.ndarray</em>) – Array of shape <code class="docutils literal notranslate"><span class="pre">(n_tiles,</span> <span class="pre">2)</span></code> containing x, y

coordinates for all image tiles. Coordinates represent the center

for an associated tile, and must be in a grid.</p></li>

<li><p><strong>values</strong> (<em>np.ndarray</em>) – Array of shape <code class="docutils literal notranslate"><span class="pre">(n_tiles,)</span></code> containing heatmap

values for each tile.</p></li>

<li><p><strong>wsi</strong> (<em>slideflow.wsi.WSI</em>) – WSI object.</p></li>

</ul>

</dd>

<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>

<dd class="field-even"><p><strong>background</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>) – Background strategy for heatmap. Can be

‘min’, ‘mean’, ‘median’, ‘max’, or ‘mask’. Defaults to ‘min’.</p>

</dd>

</dl>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.choice_input">

<span class="sig-name descname"><span class="pre">choice_input</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">prompt</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">valid_choices</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">default=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">multi_choice=False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">input_type=&lt;class</span> <span class="pre">'str'&gt;</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/slideflow/util/#choice_input"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.choice_input" title="Permalink to this definition"></a></dt>

<dd><p>Prompts user for multi-choice input.</p>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.create_triangles">

<span class="sig-name descname"><span class="pre">create_triangles</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vertices</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">hole_vertices</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">hole_points</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/slideflow/util/#create_triangles"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.create_triangles" title="Permalink to this definition"></a></dt>

<dd><p>Tessellate a complex polygon, possibly with holes.</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>vertices</strong> – A list of vertices [(x1, y1), (x2, y2), …] defining the polygon boundary.</p></li>

<li><p><strong>holes</strong> – An optional list of points [(hx1, hy1), (hx2, hy2), …] inside each hole in the polygon.</p></li>

</ul>

</dd>

<dt class="field-even">Returns<span class="colon">:</span></dt>

<dd class="field-even"><p>A numpy array of vertices for the tessellated triangles.</p>

</dd>

</dl>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.download_from_tcga">

<span class="sig-name descname"><span class="pre">download_from_tcga</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uuid</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">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">message</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">'Downloading...'</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="reference internal" href="../_modules/slideflow/util/#download_from_tcga"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.download_from_tcga" title="Permalink to this definition"></a></dt>

<dd><p>Download a file from TCGA (GDC) by UUID.</p>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.getLoggingLevel">

<span class="sig-name descname"><span class="pre">getLoggingLevel</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/slideflow/util/#getLoggingLevel"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.getLoggingLevel" title="Permalink to this definition"></a></dt>

<dd><p>Return the current logging level.</p>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.get_ensemble_model_config">

<span class="sig-name descname"><span class="pre">get_ensemble_model_config</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">model_path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Dict" title="(in Python v3.12)"><span class="pre">Dict</span></a></span></span><a class="reference internal" href="../_modules/slideflow/util/#get_ensemble_model_config"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.get_ensemble_model_config" title="Permalink to this definition"></a></dt>

<dd><p>Loads ensemble model configuration JSON file.</p>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.get_gan_config">

<span class="sig-name descname"><span class="pre">get_gan_config</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">model_path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Dict" title="(in Python v3.12)"><span class="pre">Dict</span></a></span></span><a class="reference internal" href="../_modules/slideflow/util/#get_gan_config"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.get_gan_config" title="Permalink to this definition"></a></dt>

<dd><p>Loads a GAN training_options.json for an associated network PKL.</p>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.get_model_config">

<span class="sig-name descname"><span class="pre">get_model_config</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">model_path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Dict" title="(in Python v3.12)"><span class="pre">Dict</span></a></span></span><a class="reference internal" href="../_modules/slideflow/util/#get_model_config"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.get_model_config" title="Permalink to this definition"></a></dt>

<dd><p>Loads model configuration JSON file.</p>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.get_model_normalizer">

<span class="sig-name descname"><span class="pre">get_model_normalizer</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">model_path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><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><a class="reference internal" href="../_modules/slideflow/util/#get_model_normalizer"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.get_model_normalizer" title="Permalink to this definition"></a></dt>

<dd><p>Loads and fits normalizer using configuration at a model path.</p>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.get_preprocess_fn">

<span class="sig-name descname"><span class="pre">get_preprocess_fn</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">model_path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/slideflow/util/#get_preprocess_fn"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.get_preprocess_fn" title="Permalink to this definition"></a></dt>

<dd><p>Returns a function which preprocesses a uint8 image for a model.</p>

<dl class="field-list simple">

<dt class="field-odd">Parameters<span class="colon">:</span></dt>

<dd class="field-odd"><p><strong>model_path</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Path to a saved Slideflow model.</p>

</dd>

<dt class="field-even">Returns<span class="colon">:</span></dt>

<dd class="field-even"><p>A function which accepts a single image or batch of uint8 images,

and returns preprocessed (and stain normalized) float32 images.</p>

</dd>

</dl>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.get_relative_tfrecord_paths">

<span class="sig-name descname"><span class="pre">get_relative_tfrecord_paths</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">root</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">directory</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">''</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="reference internal" href="../_modules/slideflow/util/#get_relative_tfrecord_paths"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.get_relative_tfrecord_paths" title="Permalink to this definition"></a></dt>

<dd><p>Returns relative tfrecord paths with respect to the given directory.</p>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.get_slide_paths">

<span class="sig-name descname"><span class="pre">get_slide_paths</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">slides_dir</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="reference internal" href="../_modules/slideflow/util/#get_slide_paths"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.get_slide_paths" title="Permalink to this definition"></a></dt>

<dd><p>Get all slide paths from a given directory containing slides.</p>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.get_slides_from_model_manifest">

<span class="sig-name descname"><span class="pre">get_slides_from_model_manifest</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">model_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="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 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="reference internal" href="../_modules/slideflow/util/#get_slides_from_model_manifest"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.get_slides_from_model_manifest" title="Permalink to this definition"></a></dt>

<dd><p>Get list of slides from a model manifest.</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_path</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Path to model from which to load the model manifest.</p></li>

<li><p><strong>dataset</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – ‘training’ or ‘validation’. Will return only slides

from this dataset. Defaults to None (all).</p></li>

</ul>

</dd>

<dt class="field-even">Returns<span class="colon">:</span></dt>

<dd class="field-even"><p>List of slide names.</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.util.get_valid_model_dir">

<span class="sig-name descname"><span class="pre">get_valid_model_dir</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">root</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></span><a class="reference internal" href="../_modules/slideflow/util/#get_valid_model_dir"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.get_valid_model_dir" title="Permalink to this definition"></a></dt>

<dd><p>This function returns the path of the first indented directory from root.

This only works when the indented folder name starts with a 5 digit number,

like “00000%”.</p>

<dl>

<dt>Examples</dt><dd><p>If the root has 3 files:

root/00000-foldername/

root/00001-foldername/

root/00002-foldername/</p>

<p>The function returns “root/00000-foldername/”</p>

</dd>

</dl>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.global_path">

<span class="sig-name descname"><span class="pre">global_path</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">root</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">path_string</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/slideflow/util/#global_path"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.global_path" title="Permalink to this definition"></a></dt>

<dd><p>Returns global path from a local path.</p>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.infer_stride">

<span class="sig-name descname"><span class="pre">infer_stride</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">locations</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">wsi</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/slideflow/util/#infer_stride"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.infer_stride" title="Permalink to this definition"></a></dt>

<dd><p>Infer the stride of a grid of locations from a set of locations.</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>locations</strong> (<em>np.ndarray</em>) – Nx2 array of locations</p></li>

<li><p><strong>wsi</strong> (<em>slideflow.wsi.WSI</em>) – WSI object</p></li>

</ul>

</dd>

<dt class="field-even">Returns<span class="colon">:</span></dt>

<dd class="field-even"><p>inferred stride divisor in pixels</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#float" title="(in Python v3.12)">float</a></p>

</dd>

</dl>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.is_model">

<span class="sig-name descname"><span class="pre">is_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#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="reference internal" href="../_modules/slideflow/util/#is_model"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.is_model" title="Permalink to this definition"></a></dt>

<dd><p>Checks if the given path is a valid Slideflow model.</p>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.is_project">

<span class="sig-name descname"><span class="pre">is_project</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#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="reference internal" href="../_modules/slideflow/util/#is_project"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.is_project" title="Permalink to this definition"></a></dt>

<dd><p>Checks if the given path is a valid Slideflow project.</p>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.is_simclr_model_path">

<span class="sig-name descname"><span class="pre">is_simclr_model_path</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/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/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span></span><a class="reference internal" href="../_modules/slideflow/util/#is_simclr_model_path"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.is_simclr_model_path" title="Permalink to this definition"></a></dt>

<dd><p>Checks if the given path is a valid SimCLR model or checkpoint.</p>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.is_slide">

<span class="sig-name descname"><span class="pre">is_slide</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#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="reference internal" href="../_modules/slideflow/util/#is_slide"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.is_slide" title="Permalink to this definition"></a></dt>

<dd><p>Checks if the given path is a supported slide.</p>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.is_tensorflow_model_path">

<span class="sig-name descname"><span class="pre">is_tensorflow_model_path</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#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="reference internal" href="../_modules/slideflow/util/#is_tensorflow_model_path"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.is_tensorflow_model_path" title="Permalink to this definition"></a></dt>

<dd><p>Checks if the given path is a valid Slideflow/Tensorflow model.</p>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.is_tile_size_compatible">

<span class="sig-name descname"><span class="pre">is_tile_size_compatible</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tile_px1</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">tile_um1</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></em>, <em class="sig-param"><span class="n"><span class="pre">tile_px2</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">tile_um2</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></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="reference internal" href="../_modules/slideflow/util/#is_tile_size_compatible"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.is_tile_size_compatible" title="Permalink to this definition"></a></dt>

<dd><p>Check whether tile sizes are compatible.</p>

<dl class="simple">

<dt>Compatibility is defined as:</dt><dd><ul class="simple">

<li><p>Equal size in pixels</p></li>

<li><p>If tile width (tile_um) is defined in microns (int) for both, these must be equal</p></li>

<li><p>If tile width (tile_um) is defined as a magnification (str) for both, these must be equal</p></li>

<li><p>If one is defined in microns and the other as a magnification, the calculated magnification must be +/- 2.</p></li>

</ul>

</dd>

</dl>

<p>Example 1:

- tile_px1=299, tile_um1=302

- tile_px2=299, tile_um2=304

- Incompatible (unequal micron width)</p>

<p>Example 2:

- tile_px1=299, tile_um1=10x

- tile_px2=299, tile_um2=9x

- Incompatible (unequal magnification)</p>

<p>Example 3:

- tile_px1=299, tile_um1=302

- tile_px2=299, tile_um2=10x

- Compatible (first has an equivalent magnification of 9.9x, which is +/- 2 compared to 10x)</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>tile_px1</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) of first slide.</p></li>

<li><p><strong>tile_um1</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) of first slide.

Can also be expressed as a magnification level, e.g. <code class="docutils literal notranslate"><span class="pre">'10x'</span></code></p></li>

<li><p><strong>tile_px2</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) of second slide.</p></li>

<li><p><strong>tile_um2</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) of second slide.

Can also be expressed as a magnification level, e.g. <code class="docutils literal notranslate"><span class="pre">'10x'</span></code></p></li>

</ul>

</dd>

<dt class="field-even">Returns<span class="colon">:</span></dt>

<dd class="field-even"><p>Whether the tile sizes are compatible.</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.util.is_torch_model_path">

<span class="sig-name descname"><span class="pre">is_torch_model_path</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#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="reference internal" href="../_modules/slideflow/util/#is_torch_model_path"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.is_torch_model_path" title="Permalink to this definition"></a></dt>

<dd><p>Checks if the given path is a valid Slideflow/PyTorch model.</p>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.is_uq_model">

<span class="sig-name descname"><span class="pre">is_uq_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">model_path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#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="reference internal" href="../_modules/slideflow/util/#is_uq_model"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.is_uq_model" title="Permalink to this definition"></a></dt>

<dd><p>Checks if the given model path points to a UQ-enabled model.</p>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.isnumeric">

<span class="sig-name descname"><span class="pre">isnumeric</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">val</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/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span></span><a class="reference internal" href="../_modules/slideflow/util/#isnumeric"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.isnumeric" title="Permalink to this definition"></a></dt>

<dd><p>Check if the given value is numeric (numpy or python).</p>

<p>Tensors will return False.</p>

<p>Specifically checks if the value is a python int or float,

or if the value is a numpy array with a numeric dtype (int or float).</p>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.load_json">

<span class="sig-name descname"><span class="pre">load_json</span></span><span class="sig-paren">(</span><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><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="reference internal" href="../_modules/slideflow/util/#load_json"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.load_json" title="Permalink to this definition"></a></dt>

<dd><p>Reads JSON data from file.</p>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.load_predictions">

<span class="sig-name descname"><span class="pre">load_predictions</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">DataFrame</span></span></span><a class="reference internal" href="../_modules/slideflow/util/#load_predictions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.load_predictions" title="Permalink to this definition"></a></dt>

<dd><p>Loads a ‘csv’, ‘parquet’ or ‘feather’ file to a pandas dataframe.</p>

<dl class="field-list simple">

<dt class="field-odd">Parameters<span class="colon">:</span></dt>

<dd class="field-odd"><p><strong>path</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Path to the file to be read.</p>

</dd>

<dt class="field-even">Returns<span class="colon">:</span></dt>

<dd class="field-even"><p>The dataframe read from the path.</p>

</dd>

<dt class="field-odd">Return type<span class="colon">:</span></dt>

<dd class="field-odd"><p>df (pd.DataFrame)</p>

</dd>

</dl>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.location_heatmap">

<span class="sig-name descname"><span class="pre">location_heatmap</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">locations</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">values</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">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">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>, <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/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/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">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></em>, <em class="sig-param"><span class="n"><span class="pre">interpolation</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span 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">'bicubic'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cmap</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'inferno'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">norm</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">background</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">'min'</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="reference internal" href="../_modules/slideflow/util/#location_heatmap"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.location_heatmap" title="Permalink to this definition"></a></dt>

<dd><p>Generate a heatmap for a 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>locations</strong> (<em>np.ndarray</em>) – Array of shape <code class="docutils literal notranslate"><span class="pre">(n_tiles,</span> <span class="pre">2)</span></code> containing x, y

coordinates for all image tiles. Coordinates represent the center

for an associated tile, and must be in a grid.</p></li>

<li><p><strong>values</strong> (<em>np.ndarray</em>) – Array of shape <code class="docutils literal notranslate"><span class="pre">(n_tiles,)</span></code> containing heatmap

values for each tile.</p></li>

<li><p><strong>slide</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Path to corresponding slide.</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 pixel size.</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><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Tile micron or magnification size.</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>

<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>

<dd class="field-even"><ul class="simple">

<li><p><strong>interpolation</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Interpolation strategy for smoothing

heatmap. Defaults to ‘bicubic’.</p></li>

<li><p><strong>cmap</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Matplotlib colormap for heatmap. Can be any

valid matplotlib colormap. Defaults to ‘inferno’.</p></li>

<li><p><strong>norm</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 for assigning heatmap

values to colors. Either ‘two_slope’, or any other valid value

for the <code class="docutils literal notranslate"><span class="pre">norm</span></code> argument of <code class="docutils literal notranslate"><span class="pre">matplotlib.pyplot.imshow</span></code>.

If ‘two_slope’, normalizes values less than 0 and greater than 0

separately. Defaults to None.</p></li>

</ul>

</dd>

</dl>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.log_manifest">

<span class="sig-name descname"><span class="pre">log_manifest</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">train_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/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">val_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/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span></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/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">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 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">remove_extension</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></span><a class="reference internal" href="../_modules/slideflow/util/#log_manifest"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.log_manifest" title="Permalink to this definition"></a></dt>

<dd><p>Saves the training manifest in CSV format and returns as a string.</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>train_tfrecords</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>, </em><em>optional</em>) – List of training TFRecords.

Defaults to None.</p></li>

<li><p><strong>val_tfrecords</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>, </em><em>optional</em>) – List of validation TFRecords.

Defaults to None.</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>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>) – TFRecord outcome labels. Defaults to None.</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><em>, </em><em>optional</em>) – Path to CSV file to save. Defaults to None.</p></li>

<li><p><strong>remove_extension</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>) – Remove file extension from slide

names. Defaults to True.</p></li>

</ul>

</dd>

<dt class="field-odd">Returns<span class="colon">:</span></dt>

<dd class="field-odd"><p>Saved manifest in str format.</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.util.make_dir">

<span class="sig-name descname"><span class="pre">make_dir</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">_dir</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="reference internal" href="../_modules/slideflow/util/#make_dir"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.make_dir" title="Permalink to this definition"></a></dt>

<dd><p>Makes a directory if one does not already exist,

in a manner compatible with multithreading.</p>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.map_values_to_slide_grid">

<span class="sig-name descname"><span class="pre">map_values_to_slide_grid</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">locations</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">values</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">wsi</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="../slide/#slideflow.slide.WSI" title="slideflow.slide.wsi.WSI"><span class="pre">WSI</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">background</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">'min'</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">interpolation</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span 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">'bicubic'</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">ndarray</span></span></span><a class="reference internal" href="../_modules/slideflow/util/#map_values_to_slide_grid"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.map_values_to_slide_grid" title="Permalink to this definition"></a></dt>

<dd><p>Map heatmap values to a slide grid, using tile location information.</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>locations</strong> (<em>np.ndarray</em>) – Array of shape <code class="docutils literal notranslate"><span class="pre">(n_tiles,</span> <span class="pre">2)</span></code> containing x, y

coordinates for all image tiles. Coordinates represent the center

for an associated tile, and must be in a grid.</p></li>

<li><p><strong>values</strong> (<em>np.ndarray</em>) – Array of shape <code class="docutils literal notranslate"><span class="pre">(n_tiles,)</span></code> containing heatmap

values for each tile.</p></li>

<li><p><strong>wsi</strong> (<em>slideflow.wsi.WSI</em>) – WSI object.</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>background</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>) – Background strategy for heatmap. Can be

‘min’, ‘mean’, ‘median’, ‘max’, or ‘mask’. Defaults to ‘min’.</p></li>

<li><p><strong>interpolation</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Interpolation strategy for smoothing

heatmap. Defaults to ‘bicubic’.</p></li>

</ul>

</dd>

</dl>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.md5">

<span class="sig-name descname"><span class="pre">md5</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#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></span><a class="reference internal" href="../_modules/slideflow/util/#md5"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.md5" title="Permalink to this definition"></a></dt>

<dd><p>Calculate and return MD5 checksum for a file.</p>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.multi_warn">

<span class="sig-name descname"><span class="pre">multi_warn</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">arr</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></em>, <em class="sig-param"><span class="n"><span class="pre">compare</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Callable" title="(in Python v3.12)"><span class="pre">Callable</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">msg</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Callable" title="(in Python v3.12)"><span class="pre">Callable</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/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#int" title="(in Python v3.12)"><span class="pre">int</span></a></span></span><a class="reference internal" href="../_modules/slideflow/util/#multi_warn"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.multi_warn" title="Permalink to this definition"></a></dt>

<dd><p>Logs multiple warning</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>arr</strong> (<em>List</em>) – Array to compare.</p></li>

<li><p><strong>compare</strong> (<em>Callable</em>) – Comparison to perform on array. If True, will warn.</p></li>

<li><p><strong>msg</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Warning message.</p></li>

</ul>

</dd>

<dt class="field-even">Returns<span class="colon">:</span></dt>

<dd class="field-even"><p>Number of warnings.</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#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.util.path_input">

<span class="sig-name descname"><span class="pre">path_input</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">prompt</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">root</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">default</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">create_on_invalid</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">filetype</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">verify</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></span><a class="reference internal" href="../_modules/slideflow/util/#path_input"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.path_input" title="Permalink to this definition"></a></dt>

<dd><p>Prompts user for directory input.</p>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.path_to_ext">

<span class="sig-name descname"><span class="pre">path_to_ext</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#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></span><a class="reference internal" href="../_modules/slideflow/util/#path_to_ext"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.path_to_ext" title="Permalink to this definition"></a></dt>

<dd><p>Returns extension of a file path string.</p>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.path_to_name">

<span class="sig-name descname"><span class="pre">path_to_name</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#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></span><a class="reference internal" href="../_modules/slideflow/util/#path_to_name"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.path_to_name" title="Permalink to this definition"></a></dt>

<dd><p>Returns name of a file, without extension,

from a given full path string.</p>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.read_annotations">

<span class="sig-name descname"><span class="pre">read_annotations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#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.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="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.Dict" title="(in Python v3.12)"><span class="pre">Dict</span></a><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/slideflow/util/#read_annotations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.read_annotations" title="Permalink to this definition"></a></dt>

<dd><p>Read an annotations file.</p>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.relative_path">

<span class="sig-name descname"><span class="pre">relative_path</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">root</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/slideflow/util/#relative_path"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.relative_path" title="Permalink to this definition"></a></dt>

<dd><p>Returns a relative path, from a given root directory.</p>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.setLoggingLevel">

<span class="sig-name descname"><span class="pre">setLoggingLevel</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">level</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/slideflow/util/#setLoggingLevel"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.setLoggingLevel" title="Permalink to this definition"></a></dt>

<dd><p>Set the logging level.</p>

<p>Uses standard python logging levels:</p>

<ul class="simple">

<li><p>50: CRITICAL</p></li>

<li><p>40: ERROR</p></li>

<li><p>30: WARNING</p></li>

<li><p>20: INFO</p></li>

<li><p>10: DEBUG</p></li>

<li><p>0:  NOTSET</p></li>

</ul>

<dl class="field-list simple">

<dt class="field-odd">Parameters<span class="colon">:</span></dt>

<dd class="field-odd"><p><strong>level</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Logging level numeric value.</p>

</dd>

</dl>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.set_ignore_sigint">

<span class="sig-name descname"><span class="pre">set_ignore_sigint</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/slideflow/util/#set_ignore_sigint"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.set_ignore_sigint" title="Permalink to this definition"></a></dt>

<dd><p>Ignore keyboard interrupts.</p>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.split_list">

<span class="sig-name descname"><span class="pre">split_list</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">a</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></em>, <em class="sig-param"><span class="n"><span class="pre">n</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.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.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/slideflow/util/#split_list"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.split_list" title="Permalink to this definition"></a></dt>

<dd><p>Function to split a list into n components</p>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.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">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></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">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>, <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/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/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">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="reference internal" href="../_modules/slideflow/util/#tfrecord_heatmap"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.tfrecord_heatmap" title="Permalink to this definition"></a></dt>

<dd><p>Creates a tfrecord-based WSI heatmap using a dictionary of tile values

for heatmap display.</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>) – Path to tfrecord.</p></li>

<li><p><strong>slide</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Path to whole-slide image.</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>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 width 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 width in microns (int) or magnification

(str, e.g. “20x”).</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.util.tile_size_label">

<span class="sig-name descname"><span class="pre">tile_size_label</span></span><span class="sig-paren">(</span><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>, <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></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></span><a class="reference internal" href="../_modules/slideflow/util/#tile_size_label"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.tile_size_label" title="Permalink to this definition"></a></dt>

<dd><p>Return the string label of the given tile size.</p>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.to_onehot">

<span class="sig-name descname"><span class="pre">to_onehot</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">val</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">max</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"><span class="pre">ndarray</span></span></span><a class="reference internal" href="../_modules/slideflow/util/#to_onehot"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.to_onehot" title="Permalink to this definition"></a></dt>

<dd><p>Converts value to one-hot encoding</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>val</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Value to encode</p></li>

<li><p><strong>max</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Maximum value (length of onehot encoding)</p></li>

</ul>

</dd>

</dl>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.update_results_log">

<span class="sig-name descname"><span class="pre">update_results_log</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">results_log_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="n"><span class="pre">model_name</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">results_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></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="reference internal" href="../_modules/slideflow/util/#update_results_log"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.update_results_log" title="Permalink to this definition"></a></dt>

<dd><p>Dynamically update results_log when recording training metrics.</p>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.write_json">

<span class="sig-name descname"><span class="pre">write_json</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data</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="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><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="reference internal" href="../_modules/slideflow/util/#write_json"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.write_json" title="Permalink to this definition"></a></dt>

<dd><p>Write data to JSON file.</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>data</strong> (<em>Any</em>) – Data to write.</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>) – Path to JSON file.</p></li>

</ul>

</dd>

</dl>

</dd></dl>



<dl class="py function">

<dt class="sig sig-object py" id="slideflow.util.yes_no_input">

<span class="sig-name descname"><span class="pre">yes_no_input</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">prompt</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">default</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">'no'</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="reference internal" href="../_modules/slideflow/util/#yes_no_input"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.util.yes_no_input" title="Permalink to this definition"></a></dt>

<dd><p>Prompts user for yes/no input.</p>

</dd></dl>



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<li><a class="reference internal" href="#">slideflow.util</a><ul>

<li><a class="reference internal" href="#slideflow.util.EasyDict"><code class="docutils literal notranslate"><span class="pre">EasyDict</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.FeatureExtractionProgress"><code class="docutils literal notranslate"><span class="pre">FeatureExtractionProgress</span></code></a><ul>

<li><a class="reference internal" href="#slideflow.util.FeatureExtractionProgress.get_renderables"><code class="docutils literal notranslate"><span class="pre">FeatureExtractionProgress.get_renderables()</span></code></a></li>

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<li><a class="reference internal" href="#slideflow.util.ImgBatchSpeedColumn"><code class="docutils literal notranslate"><span class="pre">ImgBatchSpeedColumn</span></code></a><ul>

<li><a class="reference internal" href="#slideflow.util.ImgBatchSpeedColumn.__init__"><code class="docutils literal notranslate"><span class="pre">ImgBatchSpeedColumn.__init__()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.ImgBatchSpeedColumn.render"><code class="docutils literal notranslate"><span class="pre">ImgBatchSpeedColumn.render()</span></code></a></li>

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<li><a class="reference internal" href="#slideflow.util.LabeledMofNCompleteColumn"><code class="docutils literal notranslate"><span class="pre">LabeledMofNCompleteColumn</span></code></a><ul>

<li><a class="reference internal" href="#slideflow.util.LabeledMofNCompleteColumn.__init__"><code class="docutils literal notranslate"><span class="pre">LabeledMofNCompleteColumn.__init__()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.LabeledMofNCompleteColumn.render"><code class="docutils literal notranslate"><span class="pre">LabeledMofNCompleteColumn.render()</span></code></a></li>

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<li><a class="reference internal" href="#slideflow.util.MultiprocessProgress.__init__"><code class="docutils literal notranslate"><span class="pre">MultiprocessProgress.__init__()</span></code></a></li>

</ul>

</li>

<li><a class="reference internal" href="#slideflow.util.MultiprocessProgressTracker"><code class="docutils literal notranslate"><span class="pre">MultiprocessProgressTracker</span></code></a><ul>

<li><a class="reference internal" href="#slideflow.util.MultiprocessProgressTracker.__init__"><code class="docutils literal notranslate"><span class="pre">MultiprocessProgressTracker.__init__()</span></code></a></li>

</ul>

</li>

<li><a class="reference internal" href="#slideflow.util.TileExtractionProgress"><code class="docutils literal notranslate"><span class="pre">TileExtractionProgress</span></code></a><ul>

<li><a class="reference internal" href="#slideflow.util.TileExtractionProgress.get_renderables"><code class="docutils literal notranslate"><span class="pre">TileExtractionProgress.get_renderables()</span></code></a></li>

</ul>

</li>

<li><a class="reference internal" href="#slideflow.util.TileExtractionSpeedColumn"><code class="docutils literal notranslate"><span class="pre">TileExtractionSpeedColumn</span></code></a><ul>

<li><a class="reference internal" href="#slideflow.util.TileExtractionSpeedColumn.render"><code class="docutils literal notranslate"><span class="pre">TileExtractionSpeedColumn.render()</span></code></a></li>

</ul>

</li>

<li><a class="reference internal" href="#slideflow.util.ValidJSONEncoder"><code class="docutils literal notranslate"><span class="pre">ValidJSONEncoder</span></code></a><ul>

<li><a class="reference internal" href="#slideflow.util.ValidJSONEncoder.default"><code class="docutils literal notranslate"><span class="pre">ValidJSONEncoder.default()</span></code></a></li>

</ul>

</li>

<li><a class="reference internal" href="#slideflow.util.about"><code class="docutils literal notranslate"><span class="pre">about()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.batch"><code class="docutils literal notranslate"><span class="pre">batch()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.batch_generator"><code class="docutils literal notranslate"><span class="pre">batch_generator()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.bin_values_to_slide_grid"><code class="docutils literal notranslate"><span class="pre">bin_values_to_slide_grid()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.choice_input"><code class="docutils literal notranslate"><span class="pre">choice_input()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.create_triangles"><code class="docutils literal notranslate"><span class="pre">create_triangles()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.download_from_tcga"><code class="docutils literal notranslate"><span class="pre">download_from_tcga()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.getLoggingLevel"><code class="docutils literal notranslate"><span class="pre">getLoggingLevel()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.get_ensemble_model_config"><code class="docutils literal notranslate"><span class="pre">get_ensemble_model_config()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.get_gan_config"><code class="docutils literal notranslate"><span class="pre">get_gan_config()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.get_model_config"><code class="docutils literal notranslate"><span class="pre">get_model_config()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.get_model_normalizer"><code class="docutils literal notranslate"><span class="pre">get_model_normalizer()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.get_preprocess_fn"><code class="docutils literal notranslate"><span class="pre">get_preprocess_fn()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.get_relative_tfrecord_paths"><code class="docutils literal notranslate"><span class="pre">get_relative_tfrecord_paths()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.get_slide_paths"><code class="docutils literal notranslate"><span class="pre">get_slide_paths()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.get_slides_from_model_manifest"><code class="docutils literal notranslate"><span class="pre">get_slides_from_model_manifest()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.get_valid_model_dir"><code class="docutils literal notranslate"><span class="pre">get_valid_model_dir()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.global_path"><code class="docutils literal notranslate"><span class="pre">global_path()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.infer_stride"><code class="docutils literal notranslate"><span class="pre">infer_stride()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.is_model"><code class="docutils literal notranslate"><span class="pre">is_model()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.is_project"><code class="docutils literal notranslate"><span class="pre">is_project()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.is_simclr_model_path"><code class="docutils literal notranslate"><span class="pre">is_simclr_model_path()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.is_slide"><code class="docutils literal notranslate"><span class="pre">is_slide()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.is_tensorflow_model_path"><code class="docutils literal notranslate"><span class="pre">is_tensorflow_model_path()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.is_tile_size_compatible"><code class="docutils literal notranslate"><span class="pre">is_tile_size_compatible()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.is_torch_model_path"><code class="docutils literal notranslate"><span class="pre">is_torch_model_path()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.is_uq_model"><code class="docutils literal notranslate"><span class="pre">is_uq_model()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.isnumeric"><code class="docutils literal notranslate"><span class="pre">isnumeric()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.load_json"><code class="docutils literal notranslate"><span class="pre">load_json()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.load_predictions"><code class="docutils literal notranslate"><span class="pre">load_predictions()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.location_heatmap"><code class="docutils literal notranslate"><span class="pre">location_heatmap()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.log_manifest"><code class="docutils literal notranslate"><span class="pre">log_manifest()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.make_dir"><code class="docutils literal notranslate"><span class="pre">make_dir()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.map_values_to_slide_grid"><code class="docutils literal notranslate"><span class="pre">map_values_to_slide_grid()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.md5"><code class="docutils literal notranslate"><span class="pre">md5()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.multi_warn"><code class="docutils literal notranslate"><span class="pre">multi_warn()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.path_input"><code class="docutils literal notranslate"><span class="pre">path_input()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.path_to_ext"><code class="docutils literal notranslate"><span class="pre">path_to_ext()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.path_to_name"><code class="docutils literal notranslate"><span class="pre">path_to_name()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.read_annotations"><code class="docutils literal notranslate"><span class="pre">read_annotations()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.relative_path"><code class="docutils literal notranslate"><span class="pre">relative_path()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.setLoggingLevel"><code class="docutils literal notranslate"><span class="pre">setLoggingLevel()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.set_ignore_sigint"><code class="docutils literal notranslate"><span class="pre">set_ignore_sigint()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.split_list"><code class="docutils literal notranslate"><span class="pre">split_list()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.tfrecord_heatmap"><code class="docutils literal notranslate"><span class="pre">tfrecord_heatmap()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.tile_size_label"><code class="docutils literal notranslate"><span class="pre">tile_size_label()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.to_onehot"><code class="docutils literal notranslate"><span class="pre">to_onehot()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.update_results_log"><code class="docutils literal notranslate"><span class="pre">update_results_log()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.write_json"><code class="docutils literal notranslate"><span class="pre">write_json()</span></code></a></li>

<li><a class="reference internal" href="#slideflow.util.yes_no_input"><code class="docutils literal notranslate"><span class="pre">yes_no_input()</span></code></a></li>

</ul>

</li>

</ul>



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