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<p class="caption" role="heading"><span class="caption-text">Introduction</span></p>
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<li class="toctree-l1"><a class="reference internal" href="../installation/">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../overview/">Overview</a></li>
<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>
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<p class="caption" role="heading"><span class="caption-text">Developer Notes</span></p>
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<li class="toctree-l1"><a class="reference internal" href="../tfrecords/">TFRecords: Reading and Writing</a></li>
<li class="toctree-l1"><a class="reference internal" href="../dataloaders/">Dataloaders: Sampling and Augmentation</a></li>
<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>
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<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 current"><a class="current reference internal" href="#">slideflow.slide</a></li>
<li class="toctree-l1"><a class="reference internal" href="../slide_qc/">slideflow.slide.qc</a></li>
<li class="toctree-l1"><a class="reference internal" href="../stats/">slideflow.stats</a></li>
<li class="toctree-l1"><a class="reference internal" href="../util/">slideflow.util</a></li>
<li class="toctree-l1"><a class="reference internal" href="../studio_module/">slideflow.studio</a></li>
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<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 & 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-slide">
<h1>slideflow.slide<a class="headerlink" href="#slideflow-slide" title="Permalink to this heading">¶</a></h1>
<p>This module contains classes to load slides and extract tiles. For optimal performance, tile extraction should
generally not be performed by instancing these classes directly, but by calling either
<a class="reference internal" href="../project/#slideflow.Project.extract_tiles" title="slideflow.Project.extract_tiles"><code class="xref py py-func docutils literal notranslate"><span class="pre">slideflow.Project.extract_tiles()</span></code></a> or <a class="reference internal" href="../dataset/#slideflow.Dataset.extract_tiles" title="slideflow.Dataset.extract_tiles"><code class="xref py py-func docutils literal notranslate"><span class="pre">slideflow.Dataset.extract_tiles()</span></code></a>, which include performance
optimizations and additional functionality.</p>
<section id="slideflow-wsi">
<h2>slideflow.WSI<a class="headerlink" href="#slideflow-wsi" title="Permalink to this heading">¶</a></h2>
<dl class="py class">
<dt class="sig sig-object py" id="slideflow.slide.WSI">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">WSI</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">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">stride_div</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">enable_downsample</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">roi_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 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">rois</span></span><span class="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">roi_method</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'auto'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">roi_filter_method</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'center'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">origin</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Tuple" title="(in Python v3.12)"><span class="pre">Tuple</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">(0,</span> <span class="pre">0)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pb</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Progress</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbose</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_edge_tiles</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mpp</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">simplify_roi_tolerance</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">artifact_labels</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">reader_kwargs</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Any" title="(in Python v3.12)"><span class="pre">Any</span></a></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/slideflow/slide/wsi/#WSI"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.slide.WSI" title="Permalink to this definition">¶</a></dt>
<dd><p>Loads a slide and its annotated region of interest (ROI).</p>
<p>Loads slide and ROI(s).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>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 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>) – Size of tiles to extract, 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>) – Size of tiles to extract, in microns (int) or
magnification (str, e.g. “20x”).</p></li>
<li><p><strong>stride_div</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Stride divisor for tile extraction
(1 = no tile overlap; 2 = 50% overlap, etc). Defaults to 1.</p></li>
<li><p><strong>enable_downsample</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a><em>, </em><em>optional</em>) – Allow use of downsampled
intermediate layers in the slide image pyramid, which greatly
improves tile extraction speed. May result in artifacts for
slides with incompletely generated intermediates pyramids.
Defaults to True.</p></li>
<li><p><strong>roi_dir</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Directory in which to search for ROI CSV
files. Defaults to None.</p></li>
<li><p><strong>rois</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>(</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>)</em>) – Alternatively, a list of ROI paths can be
explicitly provided. Defaults to None.</p></li>
<li><p><strong>roi_method</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Either ‘inside’, ‘outside’, ‘auto’, or ‘ignore’.
Determines how ROIs are used to extract tiles.
If ‘inside’ or ‘outside’, will extract tiles in/out of an ROI,
and raise errors.MissingROIError if an ROI is not available.
If ‘auto’, will extract tiles inside an ROI if available,
and across the whole-slide if no ROI is found.
If ‘ignore’, will extract tiles across the whole-slide
regardless of whether an ROI is available.
Defaults to ‘auto’.</p></li>
<li><p><strong>roi_filter_method</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a>) – Method of filtering tiles with
ROIs. Either ‘center’ or float (0-1). If ‘center’, tiles are
filtered with ROIs based on the center of the tile. If float,
tiles are filtered based on the proportion of the tile inside
the ROI, and <code class="docutils literal notranslate"><span class="pre">roi_filter_method</span></code> is interpreted as a
threshold. If the proportion of a tile inside the ROI is
greater than this number, the tile is included. For example,
if <code class="docutils literal notranslate"><span class="pre">roi_filter_method=0.7</span></code>, a tile that is 80% inside of an
ROI will be included, and a tile that is 50% inside of an ROI
will be excluded. Defaults to ‘center’.</p></li>
<li><p><strong>origin</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.12)"><em>tuple</em></a><em>(</em><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>)</em>) – Offset the starting grid (x, y).
Either a tuple of ints or ‘random’. Defaults to (0, 0).</p></li>
<li><p><strong>pb</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">Progress</span></code>, optional) – Multiprocessing
capable Progress instance; will update progress bar during
tile extraction if provided.</p></li>
<li><p><strong>verbose</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a><em>, </em><em>optional</em>) – Controls verbosity of output. If False,
suppresses warnings about slide skipping when ROIs are missing.
Defaults to True.</p></li>
<li><p><strong>mpp</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a><em>, </em><em>optional</em>) – Override the microns-per-pixel value for
the slide. Defaults to None (auto-detects).</p></li>
<li><p><strong>ignore_missing_mpp</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a><em>, </em><em>optional</em>) – If a slide does not have
microns-per-pixel (MPP) information stored in EXIF data
(key 65326), set the MPP to a default value
(<code class="docutils literal notranslate"><span class="pre">sf.slide.DEFAULG_JPG_MPP</span></code>). If False and MPP data is
missing, raises <code class="docutils literal notranslate"><span class="pre">sf.errors.SlideMissingMPPError</span></code>.</p></li>
<li><p><strong>use_bounds</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – If True, use the slide bounds to determine
the slide dimensions. This will crop out unscanned white space.
If a tuple of int, interprets the bounds as <code class="docutils literal notranslate"><span class="pre">(top_left_x,</span>
<span class="pre">top_left_y,</span> <span class="pre">width,</span> <span class="pre">height)</span></code>. If False, use the full slide
dimensions. <strong>Only available when using Libvips</strong>
(<code class="docutils literal notranslate"><span class="pre">SF_SLIDE_BACKEND=libvips</span></code>). Defaults to False.</p></li>
<li><p><strong>transforms</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>(</em><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>)</em><em>, </em><em>optional</em>) – List of transforms to apply to
the slide before establishing coordinate grid. Options include
any combination of <code class="docutils literal notranslate"><span class="pre">ROTATE_90_CLOCKWISE</span></code>,
<code class="docutils literal notranslate"><span class="pre">ROTATE_180_CLOCKWISE</span></code>, <code class="docutils literal notranslate"><span class="pre">ROTATE_270_CLOCKWISE</span></code>,
<code class="docutils literal notranslate"><span class="pre">FLIP_HORIZONTAL</span></code>, and <code class="docutils literal notranslate"><span class="pre">FLIP_VERTICAL</span></code>. <strong>Only available
when using Libvips</strong> (<code class="docutils literal notranslate"><span class="pre">SF_SLIDE_BACKEND=libvips</span></code>).
Defaults to None.</p></li>
<li><p><strong>artifact_labels</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>(</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>)</em><em>, </em><em>optional</em>) – List of ROI issue labels
to treat as artifacts. Whenever this is not None, all the ROIs with
referred label will be inverted with ROI.invert().
Defaults to an empty list.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<section id="attributes">
<h3>Attributes<a class="headerlink" href="#attributes" title="Permalink to this heading">¶</a></h3>
<table class="autosummary longtable docutils align-default">
<tbody>
<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">WSI.dimensions</span></code></p></td>
<td><p>Dimensions of highest-magnification level (width, height)</p></td>
</tr>
<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">WSI.qc_mask</span></code></p></td>
<td><p>Returns union of all QC masks.</p></td>
</tr>
<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">WSI.levels</span></code></p></td>
<td><p>List of dict, with metadata for each level.</p></td>
</tr>
<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">WSI.level_dimensions</span></code></p></td>
<td><p>List of list, with dimensions for each slide level.</p></td>
</tr>
<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">WSI.level_downsamples</span></code></p></td>
<td><p>Downsample of each level (starts at 1, increases with lower mag).</p></td>
</tr>
<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">WSI.level_mpp</span></code></p></td>
<td><p>Microns-per-pixel (MPP) for each level.</p></td>
</tr>
<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">WSI.properties</span></code></p></td>
<td><p>Dictionary of metadata loaded from the slide.</p></td>
</tr>
<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">WSI.slide</span></code></p></td>
<td><p>Backend-specific slide object.</p></td>
</tr>
<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">WSI.vendor</span></code></p></td>
<td><p>Slide scanner vendor, if available.</p></td>
</tr>
</tbody>
</table>
</section>
<section id="methods">
<h3>Methods<a class="headerlink" href="#methods" title="Permalink to this heading">¶</a></h3>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.WSI.align_to">
<span class="sig-name descname"><span class="pre">align_to</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">slide</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#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">apply</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">finetune_depth</span></span><span class="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.Sequence" title="(in Python v3.12)"><span class="pre">Sequence</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a><span class="p"><span class="pre">]</span></span><span class="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">normalizer</span></span><span class="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">'reinhard_mask'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">allow_errors</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Tuple" title="(in Python v3.12)"><span class="pre">Tuple</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Tuple" title="(in Python v3.12)"><span class="pre">Tuple</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">,</span></span><span 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></span><a class="headerlink" href="#slideflow.WSI.align_to" title="Permalink to this definition">¶</a></dt>
<dd><p>Align this slide to another slide.</p>
<p>Alignment is performed by first aligning thumbnails at low magnification
(mpp = 8), then progressively fine-tuning alignment at increasing
magnification (mpp = 1, 0.5, 0.25), focused on a dense tissue region.
The densest tissue region is identified using the QC mask, if available,
otherwise via Otsu thresholding.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>slide</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.WSI</span></code>) – Slide to align to.</p></li>
<li><p><strong>apply</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Whether to apply the alignment to the slide.</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>finetune_depth</strong> (<em>Optional</em><em>[</em><em>List</em><em>[</em><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>]</em><em>]</em>) – List of magnifications at
which to fine-tune alignment. Defaults to [1, 0.5, 0.25].</p></li>
<li><p><strong>normalizer</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Stain normalization method to use.
Defaults to ‘reinhard_mask’.</p></li>
<li><p><strong>allow_errors</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Whether to allow and ignore alignment errors
when finetuning at higher magnification. Defaults to False.</p></li>
</ul>
</dd>
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Tuple of (x, y) offset and MSE of initial alignment.</p>
</dd>
<dt class="field-even">Raises<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#TypeError" title="(in Python v3.12)"><strong>TypeError</strong></a> – If <code class="docutils literal notranslate"><span class="pre">slide</span></code> is not a <code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.WSI</span></code> object.</p></li>
<li><p><strong>AlignmentError</strong> – If initial, thumbnail-based alignment fails, or
if finetuning alignment fails at any magnification and
<code class="docutils literal notranslate"><span class="pre">allow_errors</span></code> is False.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.WSI.align_tiles_to">
<span class="sig-name descname"><span class="pre">align_tiles_to</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">slide</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#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">normalizer</span></span><span class="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">'reinhard_mask'</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">allow_errors</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mask_on_fail</span></span><span class="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">align_by</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'fit'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ignore_outliers</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">num_workers</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">ndarray</span></span></span><a class="headerlink" href="#slideflow.WSI.align_tiles_to" title="Permalink to this definition">¶</a></dt>
<dd><p>Align tiles to another slide.</p>
<p>Differs from <a class="reference internal" href="#slideflow.WSI.align_to" title="slideflow.WSI.align_to"><code class="xref py py-meth docutils literal notranslate"><span class="pre">slideflow.WSI.align_to()</span></code></a> in that it aligns each
tile individually, rather than the slide as a whole. This is useful
when aligning slides with distortion, whose alignment may drift across
the 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>slide</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.WSI</span></code>) – Slide to align to.</p></li>
<li><p><strong>normalizer</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Stain normalization method to use.</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>allow_errors</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Whether to allow and ignore alignment errors
when finetuning alignment fails at any magnification and
<code class="docutils literal notranslate"><span class="pre">allow_errors</span></code> is False. Defaults to True.</p></li>
<li><p><strong>mask_on_fail</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Whether to mask tiles that fail alignment.
Defaults to True.</p></li>
<li><p><strong>align_by</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Either ‘tile’ or ‘fit’. If ‘tile’, tiles are
aligned individually. If ‘fit’, tiles are aligned by fitting
a plane to the alignment of all tiles. Defaults to ‘tile’.</p></li>
<li><p><strong>ignore_outliers</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Whether to ignore outliers when fitting
a plane to tile alignment. Defaults to True.</p></li>
<li><p><strong>**kwargs</strong> – Keyword arguments passed to <a class="reference internal" href="#slideflow.WSI.align_to" title="slideflow.WSI.align_to"><code class="xref py py-meth docutils literal notranslate"><span class="pre">slideflow.WSI.align_to()</span></code></a>.</p></li>
</ul>
</dd>
<dt class="field-odd">Raises<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.12)"><strong>ValueError</strong></a> – If <code class="docutils literal notranslate"><span class="pre">align_by</span></code> is not ‘tile’ or ‘fit’.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Alignment grid, with shape = (grid_x, grid_y, 2).</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>np.ndarray</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.WSI.apply_qc_mask">
<span class="sig-name descname"><span class="pre">apply_qc_mask</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mask</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">QCMask</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">filter_threshold</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a><span 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">is_roi</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Image</span></span></span><a class="headerlink" href="#slideflow.WSI.apply_qc_mask" title="Permalink to this definition">¶</a></dt>
<dd><p>Apply custom slide-level QC by filtering grid coordinates.</p>
<p>The mask should have a shape (height, width) proportional to the
slide’s dimensions.</p>
<p>If the mask is numerical, the mask is thresholded at filter_threshold,
with values above the threshold indicating a region to discard.</p>
<p>If the mask is a boolean array, True indicates a region to
discard and False indicates a region to keep.</p>
<p>If the mask is a QCMask, the filter_threshold is ignored.</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>mask</strong> (np.ndarray or <code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.slide.QCMask</span></code>, optional) – Boolean QC mask array or <code class="docutils literal notranslate"><span class="pre">QCMask</span></code> object. If None, will
re-apply the current masks. Defaults to None.</p></li>
<li><p><strong>filter_threshold</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a>) – Percent of a tile detected as
background that will trigger a tile to be discarded.
Only used if <code class="docutils literal notranslate"><span class="pre">mask</span></code> is an np.ndarray.
Defaults to 0.6.</p></li>
</ul>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><p><strong>is_roi</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Whether the mask is an ROI mask. Only used if <code class="docutils literal notranslate"><span class="pre">mask</span></code>
is an <code class="docutils literal notranslate"><span class="pre">np.ndarray</span></code>. Defaults to False.</p>
</dd>
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Image of applied QC mask.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>Image</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.WSI.apply_segmentation">
<span class="sig-name descname"><span class="pre">apply_segmentation</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">segmentation</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">sf.cellseg.Segmentation</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="headerlink" href="#slideflow.WSI.apply_segmentation" title="Permalink to this definition">¶</a></dt>
<dd><p>Apply cell segmentation to the slide.</p>
<p>This sets the coordinates to the centroids of the segmentation.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>segmentation</strong> (<a class="reference internal" href="../slideflow_cellseg/#slideflow.cellseg.Segmentation" title="slideflow.cellseg.Segmentation"><em>slideflow.cellseg.Segmentation</em></a>) – Segmentation object
to apply.</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.WSI.area">
<span class="sig-name descname"><span class="pre">area</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a></span></span><a class="headerlink" href="#slideflow.WSI.area" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculate area (mm^2) of slide that passes QC masking.</p>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.WSI.build_generator">
<span class="sig-name descname"><span class="pre">build_generator</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">shuffle</span></span><span class="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">whitespace_fraction</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">whitespace_threshold</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a><span 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">grayspace_fraction</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">grayspace_threshold</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a><span 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">normalizer</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="../norm/#slideflow.norm.StainNormalizer" title="slideflow.norm.StainNormalizer"><span class="pre">StainNormalizer</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">normalizer_source</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">context_normalize</span></span><span class="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">num_threads</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_processes</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">show_progress</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">img_format</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'numpy'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">full_core</span></span><span class="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">yolo</span></span><span class="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">draw_roi</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pool</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/multiprocessing.html#multiprocessing.pool.Pool" title="(in Python v3.12)"><span class="pre">Pool</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">dry_run</span></span><span class="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">lazy_iter</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#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">shard</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Tuple" title="(in Python v3.12)"><span class="pre">Tuple</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_tiles</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">from_centroids</span></span><span class="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">apply_masks</span></span><span class="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">deterministic</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><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/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="headerlink" href="#slideflow.WSI.build_generator" title="Permalink to this definition">¶</a></dt>
<dd><p>Builds a tile generator to extract tiles from this slide.</p>
<dl class="field-list simple">
<dt class="field-odd">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>shuffle</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Shuffle images during extraction.</p></li>
<li><p><strong>whitespace_fraction</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a><em>, </em><em>optional</em>) – Range 0-1. Defaults to 1.
Discard tiles with this fraction of whitespace. If 1, will not
perform whitespace filtering.</p></li>
<li><p><strong>whitespace_threshold</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Range 0-255. Defaults to 230.
Threshold above which a pixel (RGB average) is whitespace.</p></li>
<li><p><strong>grayspace_fraction</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a><em>, </em><em>optional</em>) – Range 0-1. Defaults to 0.6.
Discard tiles with this fraction of grayspace. If 1, will not
perform grayspace filtering.</p></li>
<li><p><strong>grayspace_threshold</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a><em>, </em><em>optional</em>) – Range 0-1. Defaults to 0.05.
Pixels in HSV format with saturation below this threshold are
considered grayspace.</p></li>
<li><p><strong>normalizer</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Normalization strategy to use on image
tiles. Defaults to None.</p></li>
<li><p><strong>normalizer_source</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Stain normalization preset or
path to a source image. Valid presets include ‘v1’, ‘v2’, and
‘v3’. If None, will use the default present (‘v3’).
Defaults to None.</p></li>
<li><p><strong>context_normalize</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – If normalizing, use context from
the rest of the slide when calculating stain matrix
concentrations. Defaults to False (normalize each image tile
as separate images).</p></li>
<li><p><strong>num_threads</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – If specified, will extract tiles with a
ThreadPool using the specified number of threads. Cannot
supply both <cite>num_threads</cite> and <cite>num_processes</cite>. Libvips is
particularly slow with ThreadPools. Defaults to None in the
Libvips backend, and the number of CPU cores when using cuCIM.</p></li>
<li><p><strong>num_processes</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – If specified, will extract tiles with a
multiprocessing pool using the specified number of processes.
Cannot supply both <cite>num_threads</cite> and <cite>num_processes</cite>.
With the libvips backend, this defaults to half the number of
CPU cores, and with cuCIM, this defaults to None.</p></li>
<li><p><strong>show_progress</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a><em>, </em><em>optional</em>) – Show a progress bar.</p></li>
<li><p><strong>img_format</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Image format. Either ‘numpy’, ‘jpg’,
or ‘png’. Defaults to ‘numpy’.</p></li>
<li><p><strong>yolo</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a><em>, </em><em>optional</em>) – Include yolo-formatted tile-level ROI
annotations in the return dictionary, under the key ‘yolo’.
Defaults to False.</p></li>
<li><p><strong>draw_roi</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a><em>, </em><em>optional</em>) – Draws ROIs onto extracted tiles.
Defaults to False.</p></li>
<li><p><strong>dry_run</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a><em>, </em><em>optional</em>) – Determine tiles that would be extracted,
but do not export any images. Defaults to None.</p></li>
<li><p><strong>max_tiles</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Only extract this many tiles per slide.
Defaults to None.</p></li>
<li><p><strong>from_centroids</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Extract tiles from cell segmentation
centroids, rather than in a grid-wise pattern. Requires that
cell segmentation has already been applied with
<cite>WSI.apply_segmentation()</cite>. Defaults to False.</p></li>
<li><p><strong>apply_masks</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Apply cell segmentation masks to tiles. Ignored
if cell segmentation has been applied to the slide.
Defaults to True.</p></li>
<li><p><strong>deterministic</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Return tile images in reproducible,
deterministic order. May slightly decrease iteration time.
Defaults to True.</p></li>
<li><p><strong>shard</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.12)"><em>tuple</em></a><em>(</em><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>)</em><em>, </em><em>optional</em>) – If provided, will only extract
tiles from the shard with index <cite>shard[0]</cite> out of <cite>shard[1]</cite>
shards. Defaults to None.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><ul class="simple">
<li><p><code class="docutils literal notranslate"><span class="pre">"image"</span></code>: image data.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">"yolo"</span></code>: yolo-formatted annotations, (x_center, y_center, width, height), optional.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">"grid"</span></code>: (x, y) grid coordinates of the tile.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">"loc"</span></code>: (x, y) coordinates of tile center, in base (level=0) dimension.</p></li>
</ul>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>A generator that yields a dictionary with the keys</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.WSI.dim_to_mpp">
<span class="sig-name descname"><span class="pre">dim_to_mpp</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dimensions</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Tuple" title="(in Python v3.12)"><span class="pre">Tuple</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</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><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a></span></span><a class="headerlink" href="#slideflow.WSI.dim_to_mpp" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.WSI.get_tile_mask">
<span class="sig-name descname"><span class="pre">get_tile_mask</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">index</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sparse_mask</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">ndarray</span></span></span><a class="headerlink" href="#slideflow.WSI.get_tile_mask" title="Permalink to this definition">¶</a></dt>
<dd><p>Get a mask for a tile, given a sparse mask.</p>
<dl>
<dt>Examples</dt><dd><p>Get a mask for a tile, given a sparse mask.</p>
<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="kn">from</span> <span class="nn">slideflow.cellseg</span> <span class="kn">import</span> <span class="n">seg_utils</span><span class="p">,</span> <span class="n">Segmentation</span>
<span class="gp">>>> </span><span class="n">segmentation</span> <span class="o">=</span> <span class="n">Segmentation</span><span class="p">(</span><span class="o">...</span><span class="p">)</span>
<span class="gp">>>> </span><span class="n">wsi</span> <span class="o">=</span> <span class="n">sf</span><span class="o">.</span><span class="n">WSI</span><span class="p">(</span><span class="o">...</span><span class="p">)</span>
<span class="gp">>>> </span><span class="n">wsi</span><span class="o">.</span><span class="n">apply_segmentation</span><span class="p">(</span><span class="n">segmentation</span><span class="p">)</span>
<span class="gp">>>> </span><span class="n">sparse_mask</span> <span class="o">=</span> <span class="n">seg_utils</span><span class="o">.</span><span class="n">sparse_mask</span><span class="p">(</span><span class="n">segmentation</span><span class="o">.</span><span class="n">masks</span><span class="p">)</span>
<span class="gp">>>> </span><span class="n">wsi</span><span class="o">.</span><span class="n">get_tile_mask</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">sparse_mask</span><span class="p">)</span>
<span class="go"><numpy.ndarray></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"><ul class="simple">
<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Index of tile.</p></li>
<li><p><strong>sparse_mask</strong> (<em>scipy.sparse.csr_matrix</em>) – Sparse mask.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Mask for tile.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>numpy.ndarray</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.WSI.get_tile_dataframe">
<span class="sig-name descname"><span class="pre">get_tile_dataframe</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">DataFrame</span></span></span><a class="headerlink" href="#slideflow.WSI.get_tile_dataframe" title="Permalink to this definition">¶</a></dt>
<dd><p>Build a dataframe of tiles and associated ROI labels.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p><ul class="simple">
<li><p><code class="docutils literal notranslate"><span class="pre">loc_x</span></code>: X-coordinate of tile center</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">loc_y</span></code>: Y-coordinate of tile center</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">grid_x</span></code>: X grid index of the tile</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">grid_y</span></code>: Y grid index of the tile</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">roi_name</span></code>: Name of the ROI if tile is in an ROI, else None</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">roi_desc</span></code>: Description of the ROI if tile is in ROI, else None</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">label</span></code>: ROI label, if present.</p></li>
</ul>
</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>Pandas dataframe of all tiles, with the following columns</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.WSI.extract_cells">
<span class="sig-name descname"><span class="pre">extract_cells</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tfrecord_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 class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tiles_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 class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">img_format</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'jpg'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">report</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">apply_masks</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">SlideReport</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="headerlink" href="#slideflow.WSI.extract_cells" title="Permalink to this definition">¶</a></dt>
<dd><p>Extract tiles from cell segmentation centroids.</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_dir</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – If provided, saves tiles into a TFRecord file
(named according to slide name) here.</p></li>
<li><p><strong>tiles_dir</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – If provided, saves loose images into a
subdirectory (per slide name) here.</p></li>
<li><p><strong>img_format</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – ‘png’ or ‘jpg’. Format of images for internal
storage in tfrecords. PNG (lossless) format recommended for
fidelity, JPG (lossy) for efficiency. Defaults to ‘jpg’.</p></li>
<li><p><strong>report</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Generate and return PDF report of tile extraction.</p></li>
<li><p><strong>apply_masks</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Apply cell segmentation masks to the extracted
tiles. Defaults to True.</p></li>
</ul>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><p><strong>**kwargs</strong> – All keyword arguments are passed to <code class="xref py py-meth docutils literal notranslate"><span class="pre">WSI.extract_tiles()</span></code>.</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.WSI.extract_tiles">
<span class="sig-name descname"><span class="pre">extract_tiles</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tfrecord_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 class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tiles_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 class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">img_format</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'jpg'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">report</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">SlideReport</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="headerlink" href="#slideflow.WSI.extract_tiles" title="Permalink to this definition">¶</a></dt>
<dd><p>Extracts tiles from slide using the build_generator() method,
saving tiles into a TFRecord file or as loose JPG tiles in a directory.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>tfrecord_dir</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – If provided, saves tiles into a TFRecord file
(named according to slide name) here.</p></li>
<li><p><strong>tiles_dir</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – If provided, saves loose images in a subdirectory
(per slide name) here.</p></li>
<li><p><strong>img_format</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – ‘png’ or ‘jpg’. Format of images for internal
storage in tfrecords. PNG (lossless) format recommended for
fidelity, JPG (lossy) for efficiency. Defaults to ‘jpg’.</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>whitespace_fraction</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a><em>, </em><em>optional</em>) – Range 0-1. Defaults to 1.
Discard tiles with this fraction of whitespace. If 1, will not
perform whitespace filtering.</p></li>
<li><p><strong>whitespace_threshold</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Range 0-255. Defaults to 230.
Threshold above which a pixel (RGB average) is whitespace.</p></li>
<li><p><strong>grayspace_fraction</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a><em>, </em><em>optional</em>) – Range 0-1. Defaults to 0.6.
Discard tiles with this fraction of grayspace. If 1, will not
perform grayspace filtering.</p></li>
<li><p><strong>grayspace_threshold</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a><em>, </em><em>optional</em>) – Range 0-1. Defaults to 0.05.
Pixels in HSV format with saturation below this threshold are
considered grayspace.</p></li>
<li><p><strong>normalizer</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Normalization to use on image tiles.
Defaults to None.</p></li>
<li><p><strong>normalizer_source</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Stain normalization preset or
path to a source image. Valid presets include ‘v1’, ‘v2’, and
‘v3’. If None, will use the default present (‘v3’).
Defaults to None.</p></li>
<li><p><strong>full_core</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>) – Extract an entire detected core, rather
than subdividing into image tiles. Defaults to False.</p></li>
<li><p><strong>shuffle</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Shuffle images during extraction.</p></li>
<li><p><strong>num_threads</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Number of threads to allocate to workers.</p></li>
<li><p><strong>yolo</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>) – Export yolo-formatted tile-level ROI
annotations (.txt) in the tile directory. Requires that
tiles_dir is set. Defaults to False.</p></li>
<li><p><strong>draw_roi</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a><em>, </em><em>optional</em>) – Draws ROIs onto extracted tiles.
Defaults to False.</p></li>
<li><p><strong>dry_run</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a><em>, </em><em>optional</em>) – Determine tiles that would be extracted,
but do not export any images. Defaults to None.</p></li>
<li><p><strong>num_threads</strong> – If specified, will extract tiles with a
ThreadPool using the specified number of threads. Cannot
supply both <cite>num_threads</cite> and <cite>num_processes</cite>. Libvips is
particularly slow with ThreadPools. Defaults to None in the
Libvips backend, and the number of CPU cores when using cuCIM.</p></li>
<li><p><strong>num_processes</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – If specified, will extract tiles with a
multiprocessing pool using the specified number of processes.
Cannot supply both <cite>num_threads</cite> and <cite>num_processes</cite>.
With the libvips backend, this defaults to half the number of
CPU cores, and with cuCIM, this defaults to None.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.WSI.export_rois">
<span class="sig-name descname"><span class="pre">export_rois</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dest</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></span><a class="headerlink" href="#slideflow.WSI.export_rois" title="Permalink to this definition">¶</a></dt>
<dd><p>Export loaded ROIs to a given destination, in CSV format.</p>
<p>ROIs are exported with the columns ‘roi_name’, ‘x_base’, and ‘y_base’.
Coordinates are in base dimension (level 0) of the slide.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>dest</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Path to destination folder. If not provided, will
export ROIs in the current folder. Defaults to None.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>None</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.WSI.has_rois">
<span class="sig-name descname"><span class="pre">has_rois</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span></span><a class="headerlink" href="#slideflow.WSI.has_rois" title="Permalink to this definition">¶</a></dt>
<dd><p>Checks if the slide has loaded ROIs and they are not being ignored.</p>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.WSI.load_csv_roi">
<span class="sig-name descname"><span class="pre">load_csv_roi</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">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></em>, <em class="sig-param"><span class="n"><span class="pre">process</span></span><span class="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">scale</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">skip_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">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">simplify_tolerance</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span></span><a class="headerlink" href="#slideflow.WSI.load_csv_roi" title="Permalink to this definition">¶</a></dt>
<dd><p>Load ROIs from a CSV file.</p>
<p>CSV file must contain headers ‘ROI_name’, ‘X_base’, and ‘Y_base’.</p>
<p>Any previously loaded ROIs are cleared prior to loading.</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 CSV file.</p>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><strong>process</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Process ROIs after loading. Defaults to True.</p></li>
<li><p><strong>scale</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Scale factor to apply to ROI coordinates. Defaults to 1.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.WSI.load_json_roi">
<span class="sig-name descname"><span class="pre">load_json_roi</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">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></em>, <em class="sig-param"><span class="n"><span class="pre">scale</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">process</span></span><span class="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">skip_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">True</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span></span><a class="headerlink" href="#slideflow.WSI.load_json_roi" title="Permalink to this definition">¶</a></dt>
<dd><p>Load ROIs from a JSON file.</p>
<p>JSON file must contain a ‘shapes’ key, with a list of dictionaries
containing a ‘points’ key, whose value is a list of (x, y) coordinates.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>path</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Path to JSON file.</p></li>
<li><p><strong>scale</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Scale factor to apply to ROI coordinates. Defaults to 1.</p></li>
<li><p><strong>process</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Process ROIs after loading. Defaults to True.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.WSI.load_roi_array">
<span class="sig-name descname"><span class="pre">load_roi_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">array</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="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">process</span></span><span class="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">label</span></span><span class="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">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 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">allow_errors</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">simplify_tolerance</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span></span><a class="headerlink" href="#slideflow.WSI.load_roi_array" title="Permalink to this definition">¶</a></dt>
<dd><p>Load an ROI from a numpy array.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>array</strong> (<em>np.ndarray</em>) – Array of shape (n_points, 2) containing
the coordinates of the ROI shape, in base (level=0) dimension.</p>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><p><strong>process</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Process ROIs after loading. Defaults to True.</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.WSI.mpp_to_dim">
<span class="sig-name descname"><span class="pre">mpp_to_dim</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mpp</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Tuple" title="(in Python v3.12)"><span class="pre">Tuple</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#slideflow.WSI.mpp_to_dim" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.WSI.predict">
<span class="sig-name descname"><span class="pre">predict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">model</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Tuple" title="(in Python v3.12)"><span class="pre">Tuple</span></a><span class="p"><span class="pre">[</span></span><span class="pre">ndarray</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">ndarray</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 class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#slideflow.WSI.predict" title="Permalink to this definition">¶</a></dt>
<dd><p>Generate a whole-slide prediction from a saved model.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>model</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Path to saved model trained in Slideflow.</p>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><strong>batch_size</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Batch size for calculating predictions.
Defaults to 32.</p></li>
<li><p><strong>num_threads</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Number of tile worker threads. Cannot
supply both <code class="docutils literal notranslate"><span class="pre">num_threads</span></code> (uses thread pool) and
<code class="docutils literal notranslate"><span class="pre">num_processes</span></code> (uses multiprocessing pool). Defaults to
CPU core count.</p></li>
<li><p><strong>num_processes</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Number of child processes to spawn
for multiprocessing pool. Defaults to None (does not use
multiprocessing).</p></li>
<li><p><strong>img_format</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Image format (png, jpg) to use when
extracting tiles from slide. Must match the image format
the model was trained on. If ‘auto’, will use the format
logged in the model params.json. Defaults to ‘auto’.</p></li>
<li><p><strong>device</strong> (<em>torch.device</em><em>, </em><em>optional</em>) – PyTorch device. Defaults to
initializing a new CUDA device.</p></li>
<li><p><strong>generator_kwargs</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.12)"><em>dict</em></a><em>, </em><em>optional</em>) – Keyword arguments passed to
the <a class="reference internal" href="#slideflow.WSI.build_generator" title="slideflow.WSI.build_generator"><code class="xref py py-meth docutils literal notranslate"><span class="pre">slideflow.WSI.build_generator()</span></code></a>.</p></li>
</ul>
</dd>
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p><p>Predictions for each outcome, with shape = (num_classes, )</p>
<p>np.ndarray, optional: Uncertainty for each outcome, if the model was
trained with uncertainty, with shape = (num_classes,)</p>
</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>np.ndarray</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.WSI.preview">
<span class="sig-name descname"><span class="pre">preview</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rois</span></span><span class="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">thumb_kwargs</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Dict" title="(in Python v3.12)"><span class="pre">Dict</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">low_res</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Image</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="headerlink" href="#slideflow.WSI.preview" title="Permalink to this definition">¶</a></dt>
<dd><p>Performs a dry run of tile extraction without saving any images,
returning a PIL image of the slide thumbnail annotated with a grid of
tiles that were marked for extraction.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>rois</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>) – Draw ROI annotation(s) onto the image.
Defaults to True.</p>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><strong>whitespace_fraction</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a><em>, </em><em>optional</em>) – Range 0-1. Defaults to 1.
Discard tiles with this fraction of whitespace. If 1, will not
perform whitespace filtering.</p></li>
<li><p><strong>whitespace_threshold</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Range 0-255. Defaults to 230.
Threshold above which a pixel (RGB average) is considered
whitespace.</p></li>
<li><p><strong>grayspace_fraction</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a><em>, </em><em>optional</em>) – Range 0-1. Defaults to 0.6.
Discard tiles with this fraction of grayspace. If 1, will not
perform grayspace filtering.</p></li>
<li><p><strong>grayspace_threshold</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a><em>, </em><em>optional</em>) – Range 0-1. Defaults to 0.05.
Pixels in HSV format with saturation below this threshold are
considered grayspace.</p></li>
<li><p><strong>full_core</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>) – Extract an entire detected core, rather
than subdividing into image tiles. Defaults to False.</p></li>
<li><p><strong>num_threads</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Number of threads to allocate to workers.</p></li>
<li><p><strong>yolo</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>) – Export yolo-formatted tile-level ROI
annotations (.txt) in the tile directory. Requires that
tiles_dir is set. Defaults to False.</p></li>
<li><p><strong>thumb_kwargs</strong> (<em>Optional</em><em>[</em><em>Dict</em><em>]</em><em>, </em><em>optional</em>) – Keyword arguments to pass
to the thumb method. Defaults to None.</p></li>
<li><p><strong>low_res</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>) – Use low resolution thumbnail. Defaults to
True.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.WSI.process_rois">
<span class="sig-name descname"><span class="pre">process_rois</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#slideflow.WSI.process_rois" title="Permalink to this definition">¶</a></dt>
<dd><p>Process loaded ROIs and apply to the slide grid.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Number of ROIs processed.</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/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.WSI.show_alignment">
<span class="sig-name descname"><span class="pre">show_alignment</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">slide</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#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">mpp</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">4</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Image</span></span></span><a class="headerlink" href="#slideflow.WSI.show_alignment" title="Permalink to this definition">¶</a></dt>
<dd><p>Show aligned thumbnail of another slide.</p>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.WSI.square_thumb">
<span class="sig-name descname"><span class="pre">square_thumb</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">width</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">512</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_associated_image</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Image</span></span></span><a class="headerlink" href="#slideflow.WSI.square_thumb" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns a square thumbnail of the slide, with black bar borders.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>width</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Width/height of thumbnail in pixels.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>PIL image</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.WSI.qc">
<span class="sig-name descname"><span class="pre">qc</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Callable" title="(in Python v3.12)"><span class="pre">Callable</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Callable" title="(in Python v3.12)"><span class="pre">Callable</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">blur_radius</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">3</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">blur_threshold</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.02</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filter_threshold</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.6</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">blur_mpp</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pool</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/multiprocessing.html#multiprocessing.pool.Pool" title="(in Python v3.12)"><span class="pre">Pool</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Image</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="headerlink" href="#slideflow.WSI.qc" title="Permalink to this definition">¶</a></dt>
<dd><p>Applies quality control to a slide, performing filtering based on
a whole-slide image thumbnail.</p>
<p>‘blur’ method filters out blurry or out-of-focus slide sections.
‘otsu’ method filters out background based on automatic saturation
thresholding in the HSV colorspace.
‘both’ applies both methods of filtering.</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>method</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>Callable</em><em>, </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>(</em><em>Callable</em><em>)</em>) – Quality control method(s).
If a string, may be ‘blur’, ‘otsu’, or ‘both’.
If a callable (or list of callables), each must accept a sf.WSI
object and return a np.ndarray (dtype=np.bool).</p></li>
<li><p><strong>blur_radius</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Blur radius. Only used if method is
‘blur’ or ‘both’.</p></li>
<li><p><strong>blur_threshold</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a><em>, </em><em>optional</em>) – Blur threshold. Only used if
method is ‘blur’ or ‘both.’</p></li>
<li><p><strong>filter_threshold</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a>) – Percent of a tile detected as
background that will trigger a tile to be discarded.
Defaults to 0.6.</p></li>
<li><p><strong>blur_mpp</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a><em>, </em><em>optional</em>) – Size of WSI thumbnail on which to
perform blur QC, in microns-per-pixel. Defaults to 4 times the
tile extraction MPP (e.g. for a tile_px/tile_um combination
at 10X effective magnification, where tile_px=tile_um, the
default blur_mpp would be 4, or effective magnification 2.5x).
Only used if method is ‘blur’ or ‘both’.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Image of applied QC mask.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Image</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.WSI.remove_qc">
<span class="sig-name descname"><span class="pre">remove_qc</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="headerlink" href="#slideflow.WSI.remove_qc" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.WSI.remove_roi">
<span class="sig-name descname"><span class="pre">remove_roi</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">idx</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">process</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="headerlink" href="#slideflow.WSI.remove_roi" title="Permalink to this definition">¶</a></dt>
<dd><p>Remove an ROI from the slide.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>(</em><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>)</em>) – Index or indices of the ROI(s) to remove.</p>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><p><strong>process</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Process ROIs after removing. Defaults to True.</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.WSI.tensorflow">
<span class="sig-name descname"><span class="pre">tensorflow</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">img_format</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'numpy'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">incl_slidenames</span></span><span class="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">incl_loc</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/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">shuffle</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Any" title="(in Python v3.12)"><span class="pre">Any</span></a></span></span><a class="headerlink" href="#slideflow.WSI.tensorflow" title="Permalink to this definition">¶</a></dt>
<dd><p>Create a Tensorflow Dataset which extractes tiles from this slide.</p>
<dl class="field-list">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>img_format</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Image format for returned image tiles.
Options include ‘png’, ‘jpg’, and ‘numpy’. Defaults to ‘numpy’.</p></li>
<li><p><strong>incl_slidenames</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a><em>, </em><em>optional</em>) – Yield slide names for each
image tile. Defaults to False.</p></li>
<li><p><strong>incl_loc</strong> (<em>Optional</em><em>[</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>]</em><em>, </em><em>optional</em>) – Yield image tile location
with each image tile. Options include True, ‘coord’, or ‘grid’.
If True or ‘coord’, will return X/Y coordinates of the tile center
in the slide’s highest magnification layer. If ‘grid’, returns
the grid indices for the tile. Defaults to None.</p></li>
<li><p><strong>shuffle</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a><em>, </em><em>optional</em>) – Shuffle image tiles. Defaults to True.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>tf.data.Dataset</p>
</dd>
<dt class="field-odd">Yields<span class="colon">:</span></dt>
<dd class="field-odd"><p><em>Iterator[Any]</em> – Items yielded by the Dataset are in dictionary
format, with the keys:</p>
<p>‘image_raw’: Contains the image (jpg, png, or numpy)
‘slide’: Slide name (if <code class="docutils literal notranslate"><span class="pre">incl_slidenames=True</span></code>)
‘loc_x’ Image tile center x location (if <code class="docutils literal notranslate"><span class="pre">incl_loc</span></code> provided)
‘loc_y’ Image tile center y location (if <code class="docutils literal notranslate"><span class="pre">incl_loc</span></code> provided)</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.WSI.torch">
<span class="sig-name descname"><span class="pre">torch</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">img_format</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'numpy'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">incl_slidenames</span></span><span class="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">incl_loc</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/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">shuffle</span></span><span class="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">infinite</span></span><span class="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">to_tensor</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Any" title="(in Python v3.12)"><span class="pre">Any</span></a></span></span><a class="headerlink" href="#slideflow.WSI.torch" title="Permalink to this definition">¶</a></dt>
<dd><p>Create a PyTorch iterator which extractes tiles from this slide.</p>
<dl class="field-list">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>img_format</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Image format for returned image tiles.
Options include ‘png’, ‘jpg’, and ‘numpy’. Defaults to ‘numpy’.</p></li>
<li><p><strong>incl_slidenames</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a><em>, </em><em>optional</em>) – Yield slide names for each
image tile. Defaults to False.</p></li>
<li><p><strong>incl_loc</strong> (<em>Optional</em><em>[</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>]</em><em>, </em><em>optional</em>) – Yield image tile location
with each image tile. Options include True, ‘coord’, or ‘grid’.
If True or ‘coord’, will return X/Y coordinates of the tile center
in the slide’s highest magnification layer. If ‘grid’, returns
the grid indices for the tile. Defaults to None.</p></li>
<li><p><strong>shuffle</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a><em>, </em><em>optional</em>) – Shuffle image tiles. Defaults to True.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>An iterator which yields image tiles as Torch tensors.</p>
</dd>
<dt class="field-odd">Yields<span class="colon">:</span></dt>
<dd class="field-odd"><p><em>Iterator[Any]</em> – Items yielded by the Dataset are in dictionary
format, with the keys:</p>
<p>‘image_raw’: Contains the image as a Tensor (jpg, png, or numpy)
‘slide’: Slide name (if <code class="docutils literal notranslate"><span class="pre">incl_slidenames=True</span></code>)
‘loc_x’ Image tile center x location (if <code class="docutils literal notranslate"><span class="pre">incl_loc</span></code> provided)
‘loc_y’ Image tile center y location (if <code class="docutils literal notranslate"><span class="pre">incl_loc</span></code> provided)</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.WSI.thumb">
<span class="sig-name descname"><span class="pre">thumb</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mpp</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">width</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">coords</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rect_linewidth</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rect_color</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'black'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rois</span></span><span class="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">linewidth</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">color</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'black'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_associated_image</span></span><span class="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">low_res</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Image</span></span></span><a class="headerlink" href="#slideflow.WSI.thumb" title="Permalink to this definition">¶</a></dt>
<dd><p>Generate a PIL Image of the slide thumbnail, with ROI overlay.</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>mpp</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a><em>, </em><em>optional</em>) – Microns-per-pixel, used to determine
thumbnail size.</p></li>
<li><p><strong>width</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Goal thumbnail width (alternative to mpp).</p></li>
<li><p><strong>coords</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>(</em><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>)</em><em>, </em><em>optional</em>) – List of tile extraction coordinates
to show as rectangles on the thumbnail, in [(x_center,
y_center), …] format. Defaults to None.</p></li>
<li><p><strong>rois</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>) – Draw ROIs onto thumbnail. Defaults to False.</p></li>
<li><p><strong>linewidth</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Width of ROI line. Defaults to 2.</p></li>
<li><p><strong>color</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Color of ROI. Defaults to black.</p></li>
<li><p><strong>use_associated_image</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Use the associated thumbnail image
in the slide, rather than reading from a pyramid layer.</p></li>
<li><p><strong>low_res</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Create thumbnail from the lowest-mangnification
pyramid layer. Defaults to False.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>PIL image</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.WSI.verify_alignment">
<span class="sig-name descname"><span class="pre">verify_alignment</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">slide</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#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">mpp</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">4</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a></span></span><a class="headerlink" href="#slideflow.WSI.verify_alignment" title="Permalink to this definition">¶</a></dt>
<dd><p>Verify alignment to another slide by calculating MSE.</p>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.WSI.view">
<span class="sig-name descname"><span class="pre">view</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#slideflow.WSI.view" title="Permalink to this definition">¶</a></dt>
<dd><p>Open the slide in Slideflow Studio for interactive display.</p>
<p>See <a class="reference internal" href="../studio/#studio"><span class="std std-ref">Slideflow Studio: Live Visualization</span></a> for more information.</p>
</dd></dl>
</section>
</section>
<section id="other-functions">
<h2>Other functions<a class="headerlink" href="#other-functions" title="Permalink to this heading">¶</a></h2>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.slide.predict">
<span class="sig-name descname"><span class="pre">predict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">slide</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">model</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stride_div</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Tuple" title="(in Python v3.12)"><span class="pre">Tuple</span></a><span class="p"><span class="pre">[</span></span><span class="pre">ndarray</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">ndarray</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 class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/slideflow/slide/utils/#predict"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.slide.predict" title="Permalink to this definition">¶</a></dt>
<dd><p>Generate a whole-slide prediction from a saved model.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>slide</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Path to slide.</p></li>
<li><p><strong>model</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Path to saved model trained in Slideflow.</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>stride_div</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Divisor for stride when convoluting
across slide. Defaults to 1.</p></li>
<li><p><strong>roi_dir</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Directory in which slide ROI is contained.
Defaults to None.</p></li>
<li><p><strong>rois</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>, </em><em>optional</em>) – List of paths to slide ROIs. Alternative to
providing roi_dir. Defaults to None.</p></li>
<li><p><strong>roi_method</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Either ‘inside’, ‘outside’, ‘auto’, or ‘ignore’.
Determines how ROIs are used to extract tiles.
If ‘inside’ or ‘outside’, will extract tiles in/out of an ROI,
and raise errors.MissingROIError if an ROI is not available.
If ‘auto’, will extract tiles inside an ROI if available,
and across the whole-slide if no ROI is found.
If ‘ignore’, will extract tiles across the whole-slide
regardless of whether an ROI is available.
Defaults to ‘auto’.</p></li>
<li><p><strong>batch_size</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Batch size for calculating predictions.
Defaults to 32.</p></li>
<li><p><strong>num_threads</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Number of tile worker threads. Cannot
supply both <code class="docutils literal notranslate"><span class="pre">num_threads</span></code> (uses thread pool) and
<code class="docutils literal notranslate"><span class="pre">num_processes</span></code> (uses multiprocessing pool). Defaults to
CPU core count.</p></li>
<li><p><strong>num_processes</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Number of child processes to spawn
for multiprocessing pool. Defaults to None (does not use
multiprocessing).</p></li>
<li><p><strong>enable_downsample</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a><em>, </em><em>optional</em>) – Enable the use of downsampled
slide image layers. Defaults to True.</p></li>
<li><p><strong>img_format</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Image format (png, jpg) to use when
extracting tiles from slide. Must match the image format
the model was trained on. If ‘auto’, will use the format
logged in the model params.json. Defaults to ‘auto’.</p></li>
<li><p><strong>generator_kwargs</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.12)"><em>dict</em></a><em>, </em><em>optional</em>) – Keyword arguments passed to
the <a class="reference internal" href="#slideflow.WSI.build_generator" title="slideflow.WSI.build_generator"><code class="xref py py-meth docutils literal notranslate"><span class="pre">slideflow.WSI.build_generator()</span></code></a>.</p></li>
<li><p><strong>device</strong> (<em>torch.device</em><em>, </em><em>optional</em>) – PyTorch device. Defaults to
initializing a new CUDA device.</p></li>
</ul>
</dd>
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p><p>Predictions for each outcome, with shape = (num_classes, )</p>
<p>np.ndarray, optional: Uncertainty for each outcome, if the model was
trained with uncertainty, with shape = (num_classes,)</p>
</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>np.ndarray</p>
</dd>
</dl>
</dd></dl>
</section>
</section>
</article>
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<div class="pytorch-side-scroll" id="pytorch-side-scroll-right">
<ul>
<li><a class="reference internal" href="#">slideflow.slide</a><ul>
<li><a class="reference internal" href="#slideflow-wsi">slideflow.WSI</a><ul>
<li><a class="reference internal" href="#slideflow.slide.WSI"><code class="docutils literal notranslate"><span class="pre">WSI</span></code></a></li>
<li><a class="reference internal" href="#attributes">Attributes</a></li>
<li><a class="reference internal" href="#methods">Methods</a><ul>
<li><a class="reference internal" href="#slideflow.WSI.align_to"><code class="docutils literal notranslate"><span class="pre">align_to()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.WSI.align_tiles_to"><code class="docutils literal notranslate"><span class="pre">align_tiles_to()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.WSI.apply_qc_mask"><code class="docutils literal notranslate"><span class="pre">apply_qc_mask()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.WSI.apply_segmentation"><code class="docutils literal notranslate"><span class="pre">apply_segmentation()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.WSI.area"><code class="docutils literal notranslate"><span class="pre">area()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.WSI.build_generator"><code class="docutils literal notranslate"><span class="pre">build_generator()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.WSI.dim_to_mpp"><code class="docutils literal notranslate"><span class="pre">dim_to_mpp()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.WSI.get_tile_mask"><code class="docutils literal notranslate"><span class="pre">get_tile_mask()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.WSI.get_tile_dataframe"><code class="docutils literal notranslate"><span class="pre">get_tile_dataframe()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.WSI.extract_cells"><code class="docutils literal notranslate"><span class="pre">extract_cells()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.WSI.extract_tiles"><code class="docutils literal notranslate"><span class="pre">extract_tiles()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.WSI.export_rois"><code class="docutils literal notranslate"><span class="pre">export_rois()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.WSI.has_rois"><code class="docutils literal notranslate"><span class="pre">has_rois()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.WSI.load_csv_roi"><code class="docutils literal notranslate"><span class="pre">load_csv_roi()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.WSI.load_json_roi"><code class="docutils literal notranslate"><span class="pre">load_json_roi()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.WSI.load_roi_array"><code class="docutils literal notranslate"><span class="pre">load_roi_array()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.WSI.mpp_to_dim"><code class="docutils literal notranslate"><span class="pre">mpp_to_dim()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.WSI.predict"><code class="docutils literal notranslate"><span class="pre">predict()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.WSI.preview"><code class="docutils literal notranslate"><span class="pre">preview()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.WSI.process_rois"><code class="docutils literal notranslate"><span class="pre">process_rois()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.WSI.show_alignment"><code class="docutils literal notranslate"><span class="pre">show_alignment()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.WSI.square_thumb"><code class="docutils literal notranslate"><span class="pre">square_thumb()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.WSI.qc"><code class="docutils literal notranslate"><span class="pre">qc()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.WSI.remove_qc"><code class="docutils literal notranslate"><span class="pre">remove_qc()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.WSI.remove_roi"><code class="docutils literal notranslate"><span class="pre">remove_roi()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.WSI.tensorflow"><code class="docutils literal notranslate"><span class="pre">tensorflow()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.WSI.torch"><code class="docutils literal notranslate"><span class="pre">torch()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.WSI.thumb"><code class="docutils literal notranslate"><span class="pre">thumb()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.WSI.verify_alignment"><code class="docutils literal notranslate"><span class="pre">verify_alignment()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.WSI.view"><code class="docutils literal notranslate"><span class="pre">view()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li><a class="reference internal" href="#other-functions">Other functions</a><ul>
<li><a class="reference internal" href="#slideflow.slide.predict"><code class="docutils literal notranslate"><span class="pre">predict()</span></code></a></li>
</ul>
</li>
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