slideflow / Git / [78ef36] /docs/slide

Models:
DanielG/
slideflow
Downloads: 1
[78ef36]: / docs / slide_qc / index.html
History
Download this file
669 lines (502 with data), 46.5 kB

<!DOCTYPE html>
<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
<head>
  <meta charset="utf-8">
  <meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />

  <meta name="viewport" content="width=device-width, initial-scale=1.0">

  <title>slideflow.slide.qc &mdash; slideflow 3.0.0 documentation</title>















  <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
  <!-- <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> -->
  <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
  <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
    <link rel="index" title="Index" href="../genindex/" />
    <link rel="search" title="Search" href="../search/" />
    <link rel="next" title="slideflow.stats" href="../stats/" />
    <link rel="prev" title="slideflow.slide" href="../slide/" />




  <script src="../_static/js/modernizr.min.js"></script>

  <!-- Preload the theme fonts -->

<link rel="preload" href="../_static/fonts/FreightSans/freight-sans-book.woff2" as="font" type="font/woff2" crossorigin="anonymous">
<link rel="preload" href="../_static/fonts/FreightSans/freight-sans-medium.woff2" as="font" type="font/woff2" crossorigin="anonymous">
<link rel="preload" href="../_static/fonts/IBMPlexMono/IBMPlexMono-Medium.woff2" as="font" type="font/woff2" crossorigin="anonymous">
<link rel="preload" href="../_static/fonts/FreightSans/freight-sans-bold.woff2" as="font" type="font/woff2" crossorigin="anonymous">
<link rel="preload" href="../_static/fonts/FreightSans/freight-sans-medium-italic.woff2" as="font" type="font/woff2" crossorigin="anonymous">
<link rel="preload" href="../_static/fonts/IBMPlexMono/IBMPlexMono-SemiBold.woff2" as="font" type="font/woff2" crossorigin="anonymous">

<!-- Preload the katex fonts -->

<link rel="preload" href="https://cdn.jsdelivr.net/npm/katex@0.10.0/dist/fonts/KaTeX_Math-Italic.woff2" as="font" type="font/woff2" crossorigin="anonymous">
<link rel="preload" href="https://cdn.jsdelivr.net/npm/katex@0.10.0/dist/fonts/KaTeX_Main-Regular.woff2" as="font" type="font/woff2" crossorigin="anonymous">
<link rel="preload" href="https://cdn.jsdelivr.net/npm/katex@0.10.0/dist/fonts/KaTeX_Main-Bold.woff2" as="font" type="font/woff2" crossorigin="anonymous">
<link rel="preload" href="https://cdn.jsdelivr.net/npm/katex@0.10.0/dist/fonts/KaTeX_Size1-Regular.woff2" as="font" type="font/woff2" crossorigin="anonymous">
<link rel="preload" href="https://cdn.jsdelivr.net/npm/katex@0.10.0/dist/fonts/KaTeX_Size4-Regular.woff2" as="font" type="font/woff2" crossorigin="anonymous">
<link rel="preload" href="https://cdn.jsdelivr.net/npm/katex@0.10.0/dist/fonts/KaTeX_Size2-Regular.woff2" as="font" type="font/woff2" crossorigin="anonymous">
<link rel="preload" href="https://cdn.jsdelivr.net/npm/katex@0.10.0/dist/fonts/KaTeX_Size3-Regular.woff2" as="font" type="font/woff2" crossorigin="anonymous">
<link rel="preload" href="https://cdn.jsdelivr.net/npm/katex@0.10.0/dist/fonts/KaTeX_Caligraphic-Regular.woff2" as="font" type="font/woff2" crossorigin="anonymous">
  <link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.15.2/css/all.css" integrity="sha384-vSIIfh2YWi9wW0r9iZe7RJPrKwp6bG+s9QZMoITbCckVJqGCCRhc+ccxNcdpHuYu" crossorigin="anonymous">
  <script defer data-domain="slideflow.dev" src="https://plausible.io/js/script.js"></script>
</head>

<div class="container-fluid header-holder tutorials-header" id="header-holder">
  <div class="container">
    <div class="header-container">
      <a class="header-logo" href="https://slideflow.dev" aria-label="Slideflow"></a>

      <div class="main-menu">
        <ul>
          <li class="active">
            <a href="https://slideflow.dev">Docs</a>
          </li>

          <li>
            <a href="https://slideflow.dev/tutorial1/">Tutorials</a>
          </li>

          <li>
            <a href="https://github.com/slideflow/slideflow">GitHub</a>
          </li>
        </ul>
      </div>

      <a class="main-menu-open-button" href="#" data-behavior="open-mobile-menu"></a>
    </div>
  </div>
</div>

<body class="pytorch-body">





    <div class="table-of-contents-link-wrapper">
      <span>Table of Contents</span>
      <a href="#" class="toggle-table-of-contents" data-behavior="toggle-table-of-contents"></a>
    </div>

    <nav data-toggle="wy-nav-shift" class="pytorch-left-menu" id="pytorch-left-menu">
      <div class="pytorch-side-scroll">
        <div class="pytorch-menu pytorch-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
          <div class="pytorch-left-menu-search">





                <div class="version">
                  3.0
                </div>









<div role="search">
  <form id="rtd-search-form" class="wy-form" action="../search/" method="get">
    <input type="text" name="q" placeholder="Search Docs" />
    <input type="hidden" name="check_keywords" value="yes" />
    <input type="hidden" name="area" value="default" />
  </form>
</div>


          </div>







              <p class="caption" role="heading"><span class="caption-text">Introduction</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../installation/">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../overview/">Overview</a></li>
<li class="toctree-l1"><a class="reference internal" href="../quickstart/">Quickstart</a></li>
<li class="toctree-l1"><a class="reference internal" href="../project_setup/">Setting up a Project</a></li>
<li class="toctree-l1"><a class="reference internal" href="../datasets_and_val/">Datasets</a></li>
<li class="toctree-l1"><a class="reference internal" href="../slide_processing/">Slide Processing</a></li>
<li class="toctree-l1"><a class="reference internal" href="../training/">Training</a></li>
<li class="toctree-l1"><a class="reference internal" href="../evaluation/">Evaluation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../posthoc/">Layer Activations</a></li>
<li class="toctree-l1"><a class="reference internal" href="../uq/">Uncertainty Quantification</a></li>
<li class="toctree-l1"><a class="reference internal" href="../features/">Generating Features</a></li>
<li class="toctree-l1"><a class="reference internal" href="../mil/">Multiple-Instance Learning (MIL)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../ssl/">Self-Supervised Learning (SSL)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../stylegan/">Generative Networks (GANs)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../saliency/">Saliency Maps</a></li>
<li class="toctree-l1"><a class="reference internal" href="../segmentation/">Tissue Segmentation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../cellseg/">Cell Segmentation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../custom_loops/">Custom Training Loops</a></li>
<li class="toctree-l1"><a class="reference internal" href="../studio/">Slideflow Studio: Live Visualization</a></li>
<li class="toctree-l1"><a class="reference internal" href="../troubleshooting/">Troubleshooting</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Developer Notes</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../tfrecords/">TFRecords: Reading and Writing</a></li>
<li class="toctree-l1"><a class="reference internal" href="../dataloaders/">Dataloaders: Sampling and Augmentation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../custom_extractors/">Custom Feature Extractors</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tile_labels/">Strong Supervision with Tile Labels</a></li>
<li class="toctree-l1"><a class="reference internal" href="../plugins/">Creating a Slideflow Plugin</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">API</span></p>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="../slideflow/">slideflow</a></li>
<li class="toctree-l1"><a class="reference internal" href="../project/">slideflow.Project</a></li>
<li class="toctree-l1"><a class="reference internal" href="../dataset/">slideflow.Dataset</a></li>
<li class="toctree-l1"><a class="reference internal" href="../dataset_features/">slideflow.DatasetFeatures</a></li>
<li class="toctree-l1"><a class="reference internal" href="../heatmap/">slideflow.Heatmap</a></li>
<li class="toctree-l1"><a class="reference internal" href="../model_params/">slideflow.ModelParams</a></li>
<li class="toctree-l1"><a class="reference internal" href="../mosaic/">slideflow.Mosaic</a></li>
<li class="toctree-l1"><a class="reference internal" href="../slidemap/">slideflow.SlideMap</a></li>
<li class="toctree-l1"><a class="reference internal" href="../biscuit/">slideflow.biscuit</a></li>
<li class="toctree-l1"><a class="reference internal" href="../slideflow_cellseg/">slideflow.cellseg</a></li>
<li class="toctree-l1"><a class="reference internal" href="../io/">slideflow.io</a></li>
<li class="toctree-l1"><a class="reference internal" href="../io_tensorflow/">slideflow.io.tensorflow</a></li>
<li class="toctree-l1"><a class="reference internal" href="../io_torch/">slideflow.io.torch</a></li>
<li class="toctree-l1"><a class="reference internal" href="../gan/">slideflow.gan</a></li>
<li class="toctree-l1"><a class="reference internal" href="../grad/">slideflow.grad</a></li>
<li class="toctree-l1"><a class="reference internal" href="../mil_module/">slideflow.mil</a></li>
<li class="toctree-l1"><a class="reference internal" href="../model/">slideflow.model</a></li>
<li class="toctree-l1"><a class="reference internal" href="../model_tensorflow/">slideflow.model.tensorflow</a></li>
<li class="toctree-l1"><a class="reference internal" href="../model_torch/">slideflow.model.torch</a></li>
<li class="toctree-l1"><a class="reference internal" href="../norm/">slideflow.norm</a></li>
<li class="toctree-l1"><a class="reference internal" href="../simclr/">slideflow.simclr</a></li>
<li class="toctree-l1"><a class="reference internal" href="../slide/">slideflow.slide</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">slideflow.slide.qc</a></li>
<li class="toctree-l1"><a class="reference internal" href="../stats/">slideflow.stats</a></li>
<li class="toctree-l1"><a class="reference internal" href="../util/">slideflow.util</a></li>
<li class="toctree-l1"><a class="reference internal" href="../studio_module/">slideflow.studio</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Tutorials</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../tutorial1/">Tutorial 1: Model training (simple)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tutorial2/">Tutorial 2: Model training (advanced)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tutorial3/">Tutorial 3: Using a custom architecture</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tutorial4/">Tutorial 4: Model evaluation &amp; heatmaps</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tutorial5/">Tutorial 5: Creating a mosaic map</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tutorial6/">Tutorial 6: Custom slide filtering</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tutorial7/">Tutorial 7: Training with custom augmentations</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tutorial8/">Tutorial 8: Multiple-Instance Learning</a></li>
</ul>



        </div>
      </div>
    </nav>

    <div class="pytorch-container">
      <div class="pytorch-page-level-bar" id="pytorch-page-level-bar">
        <div class="pytorch-breadcrumbs-wrapper">
















<div role="navigation" aria-label="breadcrumbs navigation">

  <ul class="pytorch-breadcrumbs">

      <li>
        <a href="../">

            Docs

        </a> &gt;
      </li>


      <li>slideflow.slide.qc</li>


      <li class="pytorch-breadcrumbs-aside">


            <a href="../_sources/slide_qc.rst.txt" rel="nofollow"><img src="../_static/images/view-page-source-icon.svg"></a>


      </li>

  </ul>


</div>
        </div>

        <div class="pytorch-shortcuts-wrapper" id="pytorch-shortcuts-wrapper">
          Shortcuts
        </div>
      </div>

      <section data-toggle="wy-nav-shift" id="pytorch-content-wrap" class="pytorch-content-wrap">
        <div class="pytorch-content-left">



          <div class="rst-content">

            <div role="main" class="main-content" itemscope="itemscope" itemtype="http://schema.org/Article">
             <article itemprop="articleBody" id="pytorch-article" class="pytorch-article">

  <section id="slideflow-slide-qc">
<span id="qc"></span><h1>slideflow.slide.qc<a class="headerlink" href="#slideflow-slide-qc" title="Permalink to this heading">¶</a></h1>
<p>This module contains functions for slide-level quality control, including Otsu’s thresholding and Gaussian blur filtering. Quality control methods are used by passing a list of callables to the <code class="docutils literal notranslate"><span class="pre">qc</span></code> argument of <code class="docutils literal notranslate"><span class="pre">.extract_tiles()</span></code>. They can also be directly applied to a slide with <a class="reference internal" href="../slide/#slideflow.WSI.qc" title="slideflow.WSI.qc"><code class="xref py py-meth docutils literal notranslate"><span class="pre">slideflow.WSI.qc()</span></code></a>.</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">slideflow</span> <span class="k">as</span> <span class="nn">sf</span>
<span class="kn">from</span> <span class="nn">slideflow.slide</span> <span class="kn">import</span> <span class="n">qc</span>

<span class="c1"># Define custom QC options</span>
<span class="n">qc</span> <span class="o">=</span> <span class="p">[</span>
  <span class="n">qc</span><span class="o">.</span><span class="n">Otsu</span><span class="p">(),</span>
  <span class="n">qc</span><span class="o">.</span><span class="n">Gaussian</span><span class="p">(</span><span class="n">sigma</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span>
<span class="p">]</span>

<span class="c1"># Use this QC during tile extraction</span>
<span class="n">P</span><span class="o">.</span><span class="n">extract_tiles</span><span class="p">(</span><span class="n">qc</span><span class="o">=</span><span class="n">qc</span><span class="p">)</span>

<span class="c1"># Alternatively, you can use the same QC directly on a WSI object</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="n">wsi</span><span class="o">.</span><span class="n">qc</span><span class="p">(</span><span class="n">qc</span><span class="p">)</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
</pre></div>
</div>
<dl class="py class">
<dt class="sig sig-object py" id="slideflow.slide.qc.Otsu">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">Otsu</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">slide_level</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/slideflow/slide/qc/otsu/#Otsu"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.slide.qc.Otsu" title="Permalink to this definition">¶</a></dt>
<dd><p>Prepare Otsu’s thresholding algorithm for filtering a slide.</p>
<p>This method is used to detect areas of tissue and remove background.</p>
<p>This QC method works by obtaining a thumbnail of a slide, and converting
the image into the HSV color space. The HSV image undergoes a median blur
using OpenCV with a kernel size of 7, and the image is thresholded
using <code class="docutils literal notranslate"><span class="pre">cv2.THRESH_OTSU</span></code>. This results in a binary mask, which
is then applied to the slide for filtering.</p>
<p>Original paper: <a class="reference external" href="https://ieeexplore.ieee.org/document/4310076">https://ieeexplore.ieee.org/document/4310076</a></p>
<div class="admonition warning">
<p class="admonition-title">Warning</p>
<p>Otsu’s thresholding may give unexpected results with slides
that have many large pen marks, erroneously identifying pen marks
as tissue and removing the actual tissue as background.
This behavior can be circumvented by applying a Gaussian filter
before Otsu’s thresholding.</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">slideflow</span> <span class="k">as</span> <span class="nn">sf</span>
<span class="kn">from</span> <span class="nn">slideflow.slide</span> <span class="kn">import</span> <span class="n">qc</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="n">gaussian</span> <span class="o">=</span> <span class="n">qc</span><span class="o">.</span><span class="n">GaussianV2</span><span class="p">()</span>
<span class="n">otsu</span> <span class="o">=</span> <span class="n">qc</span><span class="o">.</span><span class="n">Otsu</span><span class="p">()</span>
<span class="n">wsi</span><span class="o">.</span><span class="n">qc</span><span class="p">([</span><span class="n">gaussian</span><span class="p">,</span> <span class="n">otsu</span><span class="p">])</span>
</pre></div>
</div>
</div>
<dl>
<dt>Examples</dt><dd><p>Apply Otsu’s thresholding to a slide.</p>
<blockquote>
<div><div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">slideflow</span> <span class="k">as</span> <span class="nn">sf</span>
<span class="kn">from</span> <span class="nn">slideflow.slide</span> <span class="kn">import</span> <span class="n">qc</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="n">otsu</span> <span class="o">=</span> <span class="n">qc</span><span class="o">.</span><span class="n">Otsu</span><span class="p">()</span>
<span class="n">wsi</span><span class="o">.</span><span class="n">qc</span><span class="p">(</span><span class="n">otsu</span><span class="p">)</span>
</pre></div>
</div>
</div></blockquote>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>level</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Slide pyramid level at which to perform filtering.
Defaults to second-lowest available level.</p>
</dd>
</dl>
</dd></dl>

<dl class="py class">
<dt class="sig sig-object py" id="slideflow.slide.qc.Gaussian">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">Gaussian</span></span><span class="sig-paren">(</span><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">sigma</span></span><span class="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">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><span class="sig-paren">)</span><a class="reference internal" href="../_modules/slideflow/slide/qc/gaussian/#Gaussian"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.slide.qc.Gaussian" title="Permalink to this definition">¶</a></dt>
<dd><p>Prepare Gaussian filtering algorithm for filtering a slide.</p>
<p>This method is used to remove out-of-focus areas and pen marks.</p>
<p>This QC method works by obtaining a thumbnail of a slide, and converting
the image into grayspace. A gaussian filter with a given sigma
(default=3) is calculated using scikit-image. Areas with blur below
the given threshold (default=0.02) are filtered out.</p>
<dl>
<dt>Examples</dt><dd><p>Apply Gaussian filtering to a slide.</p>
<blockquote>
<div><div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">slideflow</span> <span class="k">as</span> <span class="nn">sf</span>
<span class="kn">from</span> <span class="nn">slideflow.slide</span> <span class="kn">import</span> <span class="n">qc</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="n">gaussian</span> <span class="o">=</span> <span class="n">qc</span><span class="o">.</span><span class="n">Gaussian</span><span class="p">()</span>
<span class="n">wsi</span><span class="o">.</span><span class="n">qc</span><span class="p">(</span><span class="n">gaussian</span><span class="p">)</span>
</pre></div>
</div>
</div></blockquote>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>mpp</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a>) – Microns-per-pixel at which to perform filtering.
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).</p></li>
<li><p><strong>sigma</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Sigma (radius) for Gaussian filter. Defaults to 3.</p></li>
<li><p><strong>threshold</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a>) – Gaussian threshold. Defaults to 0.02.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="py class">
<dt class="sig sig-object py" id="slideflow.slide.qc.Save">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">Save</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">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><a class="reference internal" href="../_modules/slideflow/slide/qc/saver/#Save"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.slide.qc.Save" title="Permalink to this definition">¶</a></dt>
<dd><p>QC function which saves the mask to a numpy file.</p>
<p>When this QC method is applied to a slide, the current QC masks
(e.g., as applied by the Otsu or Gaussian filtering methods) are saved
to a numpy file. These saved masks can be loaded in the future
using <a class="reference internal" href="#slideflow.slide.qc.Load" title="slideflow.slide.qc.Load"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.slide.qc.Load</span></code></a>. Saving/loading masks saves time
by allowing to avoid regenerating masks repeatedly.</p>
<p>By default, masks are saved in the same folder as whole-slide images.</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">slideflow.slide</span> <span class="kn">import</span> <span class="n">qc</span>

<span class="c1"># Define a QC approach that auto-saves masks</span>
<span class="n">qc</span> <span class="o">=</span> <span class="p">[</span>
    <span class="n">qc</span><span class="o">.</span><span class="n">Otsu</span><span class="p">(),</span>
    <span class="n">qc</span><span class="o">.</span><span class="n">Save</span><span class="p">()</span>
<span class="p">]</span>
<span class="n">P</span><span class="o">.</span><span class="n">extract_tiles</span><span class="p">(</span><span class="n">qc</span><span class="o">=</span><span class="n">qc</span><span class="p">)</span>

<span class="o">...</span>
<span class="c1"># Auto-load previously saved masks</span>
<span class="n">qc</span> <span class="o">=</span> <span class="p">[</span>
    <span class="n">qc</span><span class="o">.</span><span class="n">Load</span><span class="p">()</span>
<span class="p">]</span>
<span class="n">P</span><span class="o">.</span><span class="n">extract_tiles</span><span class="p">(</span><span class="n">qc</span><span class="o">=</span><span class="n">qc</span><span class="p">)</span>
</pre></div>
</div>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><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><em>, </em><em>optional</em>) – Path in which to save the qc mask.
If None, will save in the same directory as the slide.
Defaults to None.</p>
</dd>
</dl>
</dd></dl>

<dl class="py class">
<dt class="sig sig-object py" id="slideflow.slide.qc.Load">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">Load</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">source</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/slideflow/slide/qc/saver/#Load"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.slide.qc.Load" title="Permalink to this definition">¶</a></dt>
<dd><p>QC function which loads a saved numpy mask.</p>
<p>Loads and applies a QC mask which was saved by
<a class="reference internal" href="#slideflow.slide.qc.Save" title="slideflow.slide.qc.Save"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.slide.qc.Save</span></code></a></p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>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>) – Path to search for qc mask.
If None, will search in the same directory as the slide.
Defaults to None.</p>
</dd>
</dl>
</dd></dl>

<dl class="py class">
<dt class="sig sig-object py" id="slideflow.slide.qc.StridedDL">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">StridedDL</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">model</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Callable" title="(in Python v3.12)"><span class="pre">Callable</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">pred_idx</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">tile_px</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">tile_um</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">buffer</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/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">8</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">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pred_threshold</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.5</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">wsi_kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/slideflow/slide/qc/strided_dl/#StridedDL"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.slide.qc.StridedDL" title="Permalink to this definition">¶</a></dt>
<dd><p>QC function which uses a deep learning model to generate a QC mask.</p>
<p>When this QC method is applied to a slide, the given deep learning model
generates predictions across the whole-slide image (using the class index
specified by <code class="docutils literal notranslate"><span class="pre">pred_idx</span></code>). Areas with a prediction above
<code class="docutils literal notranslate"><span class="pre">pred_threshold</span></code> are masked, to be discarded.</p>
<dl>
<dt>Examples</dt><dd><p>Create a DeepFocus module that filters out-of-focus tiles.</p>
<blockquote>
<div><div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">slideflow</span> <span class="k">as</span> <span class="nn">sf</span>
<span class="kn">from</span> <span class="nn">slideflow.slide.qc</span> <span class="kn">import</span> <span class="n">strided_dl</span>
<span class="kn">from</span> <span class="nn">deepfocus</span> <span class="kn">import</span> <span class="n">deepfocus_v3</span>

<span class="n">deepfocus</span> <span class="o">=</span> <span class="n">strided_dl</span><span class="o">.</span><span class="n">StridedDL</span><span class="p">(</span>
    <span class="n">model</span><span class="o">=</span><span class="n">deepfocus_v3</span><span class="p">(),</span>
    <span class="n">pred_idx</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
    <span class="n">tile_px</span><span class="o">=</span><span class="mi">64</span><span class="p">,</span>
    <span class="n">tile_um</span><span class="o">=</span><span class="s1">&#39;40x&#39;</span>
<span class="p">)</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="n">wsi</span><span class="o">.</span><span class="n">qc</span><span class="p">(</span><span class="n">deepfocus</span><span class="p">)</span>
</pre></div>
</div>
</div></blockquote>
<p>Do the same, but using class inheritance.</p>
<blockquote>
<div><div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">slideflow</span> <span class="k">as</span> <span class="nn">sf</span>
<span class="kn">from</span> <span class="nn">slideflow.slide.qc</span> <span class="kn">import</span> <span class="n">strided_dl</span>
<span class="kn">from</span> <span class="nn">deepfocus</span> <span class="kn">import</span> <span class="n">deepfocus_v3</span>

<span class="k">class</span> <span class="nc">DeepFocus</span><span class="p">(</span><span class="n">strided_dl</span><span class="o">.</span><span class="n">StridedDL</span><span class="p">):</span>

    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
        <span class="n">model</span> <span class="o">=</span> <span class="n">deepfocus_v3</span><span class="p">()</span>
        <span class="n">checkpoint</span> <span class="o">=</span> <span class="s1">&#39;/path/to/checkpoint-ver5&#39;</span>
        <span class="n">load_checkpoint</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="n">checkpoint</span><span class="p">)</span>
        <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
            <span class="n">model</span><span class="o">=</span><span class="n">model</span><span class="p">,</span>
            <span class="n">pred_idx</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
            <span class="n">tile_px</span><span class="o">=</span><span class="mi">64</span><span class="p">,</span>
            <span class="n">tile_um</span><span class="o">=</span><span class="s1">&#39;40x&#39;</span>
        <span class="p">)</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="n">deepfocus</span> <span class="o">=</span> <span class="n">DeepFocus</span><span class="p">()</span>
<span class="n">wsi</span><span class="o">.</span><span class="n">qc</span><span class="p">(</span><span class="n">deepfocus</span><span class="p">)</span>
</pre></div>
</div>
</div></blockquote>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>model</strong> (<em>callable</em>) – Deep learning model.</p></li>
<li><p><strong>pred_idx</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Index of the model output to interpret as the
final prediction.</p></li>
<li><p><strong>tile_px</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Tile size.</p></li>
<li><p><strong>tile_um</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>) – Tile size, in microns (int) or
magnification (str).</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>verbose</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Show a progress bar during calculation.</p></li>
<li><p><strong>buffer</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 tiles (width and height) to extract and
process simultaneously. Extracted tile size (width/height)
will be  <code class="docutils literal notranslate"><span class="pre">tile_px</span> <span class="pre">*</span> <span class="pre">buffer</span></code>. Defaults to 8.</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>) – Grayspace fraction when extracting
tiles from slides. Defaults to 1 (disables).</p></li>
<li><p><strong>pred_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>) – Predictions below this value are masked.</p></li>
<li><p><strong>kwargs</strong> (<em>Any</em>) – All remaining keyword arguments are passed to
<a class="reference internal" href="../slide/#slideflow.WSI.build_generator" title="slideflow.WSI.build_generator"><code class="xref py py-meth docutils literal notranslate"><span class="pre">slideflow.WSI.build_generator()</span></code></a>.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

</section>


             </article>

            </div>
            <footer>

    <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">

        <a href="../stats/" class="btn btn-neutral float-right" title="slideflow.stats" accesskey="n" rel="next">Next <img src="../_static/images/chevron-right-orange.svg" class="next-page"></a>


        <a href="../slide/" class="btn btn-neutral" title="slideflow.slide" accesskey="p" rel="prev"><img src="../_static/images/chevron-right-orange.svg" class="previous-page"> Previous</a>

    </div>




    <hr>



  <div role="contentinfo">
    <p>
        &copy; Copyright 2023, James M Dolezal.

    </p>
  </div>

      <div>
        Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
      </div>


</footer>

          </div>
        </div>

        <div class="pytorch-content-right" id="pytorch-content-right">
          <div class="pytorch-right-menu" id="pytorch-right-menu">
            <div class="pytorch-side-scroll" id="pytorch-side-scroll-right">
              <ul>
<li><a class="reference internal" href="#">slideflow.slide.qc</a><ul>
<li><a class="reference internal" href="#slideflow.slide.qc.Otsu"><code class="docutils literal notranslate"><span class="pre">Otsu</span></code></a></li>
<li><a class="reference internal" href="#slideflow.slide.qc.Gaussian"><code class="docutils literal notranslate"><span class="pre">Gaussian</span></code></a></li>
<li><a class="reference internal" href="#slideflow.slide.qc.Save"><code class="docutils literal notranslate"><span class="pre">Save</span></code></a></li>
<li><a class="reference internal" href="#slideflow.slide.qc.Load"><code class="docutils literal notranslate"><span class="pre">Load</span></code></a></li>
<li><a class="reference internal" href="#slideflow.slide.qc.StridedDL"><code class="docutils literal notranslate"><span class="pre">StridedDL</span></code></a></li>
</ul>
</li>
</ul>

            </div>
          </div>
        </div>
      </section>
    </div>







       <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
         <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
         <script src="../_static/doctools.js"></script>
         <script src="../_static/sphinx_highlight.js"></script>



  <script type="text/javascript" src="../_static/js/vendor/jquery-3.6.3.min.js"></script>
  <script type="text/javascript" src="../_static/js/vendor/popper.min.js"></script>
  <script type="text/javascript" src="../_static/js/vendor/bootstrap.min.js"></script>
  <script src="https://cdnjs.cloudflare.com/ajax/libs/list.js/1.5.0/list.min.js"></script>
  <script type="text/javascript" src="../_static/js/theme.js"></script>

  <script type="text/javascript">
      jQuery(function () {
          SphinxRtdTheme.Navigation.enable(true);
      });
  </script>

  <!-- Begin Footer -->

  <!-- End Footer -->

  <!-- Begin Mobile Menu -->

  <div class="mobile-main-menu">
    <div class="container-fluid">
      <div class="container">
        <div class="mobile-main-menu-header-container">
          <a class="header-logo" href="https://pytorch.org/" aria-label="PyTorch"></a>
          <a class="main-menu-close-button" href="#" data-behavior="close-mobile-menu"></a>
        </div>
      </div>
    </div>

    <div class="mobile-main-menu-links-container">
      <div class="main-menu">
        <ul>
          <li>
            <a href="https://slideflow.dev">Docs</a>
          </li>

          <li>
            <a href="https://slideflow.dev/tutorial1/">Tutorials</a>
          </li>

          <li>
            <a href="https://github.com/slideflow/slideflow">Github</a>
          </li>
        </ul>
      </div>
    </div>
  </div>

  <!-- End Mobile Menu -->

  <script script type="text/javascript">
    var collapsedSections = [];
  </script>

  <script type="text/javascript" src="../_static/js/vendor/anchor.min.js"></script>

  <script type="text/javascript">
    $(document).ready(function() {
      mobileMenu.bind();
      mobileTOC.bind();
      pytorchAnchors.bind();
      sideMenus.bind();
      scrollToAnchor.bind();
      highlightNavigation.bind();
      mainMenuDropdown.bind();
      filterTags.bind();

      // Add class to links that have code blocks, since we cannot create links in code blocks
      $("article.pytorch-article a span.pre").each(function(e) {
        $(this).closest("a").addClass("has-code");
      });
    })
  </script>
</body>
</html>