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              <p class="caption" role="heading"><span class="caption-text">Introduction</span></p>
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  <section id="slideflow-io">
<h1>slideflow.io<a class="headerlink" href="#slideflow-io" title="Permalink to this heading">¶</a></h1>
<p>This module contains utility functions for working with TFRecords, cross-compatible
with both Tensorflow and PyTorch.</p>
<p>Functions included in this module assist with processing TFRecords, detecting image and data format,
extracting tiles, splitting and merging TFrecords, and a variety of other manipulations.</p>
<p>Additional Tensorflow-specific TFRecord reading/writing utility functions are
available in <a class="reference internal" href="../io_tensorflow/#module-slideflow.io.tensorflow" title="slideflow.io.tensorflow"><code class="xref py py-mod docutils literal notranslate"><span class="pre">slideflow.io.tensorflow</span></code></a>, and additional PyTorch-specific
functions are in <a class="reference internal" href="../io_torch/#module-slideflow.io.torch" title="slideflow.io.torch"><code class="xref py py-mod docutils literal notranslate"><span class="pre">slideflow.io.torch</span></code></a>.</p>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.io.convert_dtype">
<span class="sig-name descname"><span class="pre">convert_dtype</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">img</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Any" title="(in Python v3.12)"><span class="pre">Any</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">dtype</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dtype</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">tf.dtypes.DType</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">torch.dtype</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Any" title="(in Python v3.12)"><span class="pre">Any</span></a></span></span><a class="reference internal" href="../_modules/slideflow/io/io_utils/#convert_dtype"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.io.convert_dtype" title="Permalink to this definition">¶</a></dt>
<dd><p>Converts an image from one type to another.</p>
<p>Images can be converted to and from numpy arrays, Torch Tensors and
Tensorflow Tensors. Images can also be converted from standardized
float images to RGB uint8 images, and vice versa.</p>
<p>Supported formats for starting and ending dtype include:</p>
<table class="docutils align-default">
<colgroup>
<col style="width: 20%" />
<col style="width: 80%" />
</colgroup>
<tbody>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">np.uint8</span></code></p></td>
<td><p>Image in RGB (WHC) uint8 format.</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">np.float32</span></code></p></td>
<td><p>RGB (WHC) image. If the source image is a numpy uint8 or torch uint8,
it will be standardized with <code class="docutils literal notranslate"><span class="pre">(img</span> <span class="pre">/</span> <span class="pre">127.5)</span> <span class="pre">-</span> <span class="pre">1</span></code>.
If the source image is a tensorflow image,
standardization uses <code class="docutils literal notranslate"><span class="pre">tf.image.per_image_standardization()</span></code>.</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">torch.uint8</span></code></p></td>
<td><p>Image in RGB (CWH) uint8 format.</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">torch.float32</span></code></p></td>
<td><p>Image converted with <code class="docutils literal notranslate"><span class="pre">(img</span> <span class="pre">/</span> <span class="pre">127.5)</span> <span class="pre">-</span> <span class="pre">1</span></code> and WHC -&gt; CWH.</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">tf.uint8</span></code></p></td>
<td><p>Image in RGB (WHC) uint8 format.</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">tf.float32</span></code></p></td>
<td><p>Image converted with <code class="docutils literal notranslate"><span class="pre">tf.image.per_image_standardization()</span></code></p></td>
</tr>
</tbody>
</table>
<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>img</strong> (<em>Any</em>) – Input image or batch of images.</p></li>
<li><p><strong>start_dtype</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#type" title="(in Python v3.12)"><em>type</em></a>) – Starting dtype.</p></li>
<li><p><strong>end_dtype</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#type" title="(in Python v3.12)"><em>type</em></a>) – Target dtype for conversion.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Converted image or batch of images.</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.io.detect_tfrecord_format">
<span class="sig-name descname"><span class="pre">detect_tfrecord_format</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tfr</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Tuple" title="(in Python v3.12)"><span class="pre">Tuple</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span><span class="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 class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/slideflow/io/io_utils/#detect_tfrecord_format"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.io.detect_tfrecord_format" title="Permalink to this definition">¶</a></dt>
<dd><p>Detects tfrecord format.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>tfr</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Path to tfrecord.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><p>A tuple containing</p>
<blockquote>
<div><p>list(str): List of detected features.</p>
<p>str: Image file type (png/jpeg)</p>
</div></blockquote>
</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.io.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">tfrecord</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">destination</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="reference internal" href="../_modules/slideflow/io/#extract_tiles"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.io.extract_tiles" title="Permalink to this definition">¶</a></dt>
<dd><p>Extracts images within a TFRecord to a destination folder.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>tfrecord</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Path to tfrecord.</p></li>
<li><p><strong>destination</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Destination path to write loose images.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.io.get_locations_from_tfrecord">
<span class="sig-name descname"><span class="pre">get_locations_from_tfrecord</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Tuple" title="(in Python v3.12)"><span class="pre">Tuple</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/slideflow/io/#get_locations_from_tfrecord"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.io.get_locations_from_tfrecord" title="Permalink to this definition">¶</a></dt>
<dd><p>Return list of tile locations (X, Y) for all items in the TFRecord.</p>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.io.get_tfrecord_by_index">
<span class="sig-name descname"><span class="pre">get_tfrecord_by_index</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tfrecord</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">index</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#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">compression_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">index_array</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><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Dict" title="(in Python v3.12)"><span class="pre">Dict</span></a></span></span><a class="reference internal" href="../_modules/slideflow/util/tfrecord2idx/#get_tfrecord_by_index"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.io.get_tfrecord_by_index" title="Permalink to this definition">¶</a></dt>
<dd><p>Read a specific record in a TFRecord file.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>tfrecord</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – TFRecord file to read.</p></li>
<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 record to read from the file.</p></li>
<li><p><strong>compression_type</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Type of compression in the TFRecord file.
Either ‘gzip’ or None. Defaults to None.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>A dictionary mapping record names (e.g., <code class="docutils literal notranslate"><span class="pre">'slide'</span></code>, <code class="docutils literal notranslate"><span class="pre">'image_raw'</span></code>,
<code class="docutils literal notranslate"><span class="pre">'loc_x'</span></code>, and <code class="docutils literal notranslate"><span class="pre">'loc_y'</span></code>) to their values. <code class="docutils literal notranslate"><span class="pre">'slide'</span></code> will be a
string, <code class="docutils literal notranslate"><span class="pre">image_raw</span></code> will be bytes, and <code class="docutils literal notranslate"><span class="pre">'loc_x'</span></code> and <code class="docutils literal notranslate"><span class="pre">'loc_y'</span></code>
will be <cite>int</cite>.</p>
</dd>
<dt class="field-odd">Raises<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>slideflow.error.EmptyTFRecordsError</strong> – If the file is empty.</p></li>
<li><p><strong>slideflow.error.InvalidTFRecordIndex</strong> – If the given index cannot be found.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.io.get_tfrecord_by_location">
<span class="sig-name descname"><span class="pre">get_tfrecord_by_location</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tfrecord</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">location</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Tuple" title="(in Python v3.12)"><span class="pre">Tuple</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">decode</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><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">locations_array</span></span><span class="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/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><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">index_array</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><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Any" title="(in Python v3.12)"><span class="pre">Any</span></a></span></span><a class="reference internal" href="../_modules/slideflow/io/#get_tfrecord_by_location"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.io.get_tfrecord_by_location" title="Permalink to this definition">¶</a></dt>
<dd><p>Reads and returns an individual record from a tfrecord by index,
including slide name and processed image data.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>tfrecord</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Path to TFRecord file.</p></li>
<li><p><strong>location</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>) – <code class="docutils literal notranslate"><span class="pre">(x,</span> <span class="pre">y)</span></code> tile location.
Searches the TFRecord for the tile that corresponds to this
location.</p></li>
<li><p><strong>decode</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Decode the associated record, returning Tensors.
Defaults to True.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Unprocessed raw TFRecord bytes if <code class="docutils literal notranslate"><span class="pre">decode=False</span></code>, otherwise a
tuple containing <code class="docutils literal notranslate"><span class="pre">(slide,</span> <span class="pre">image)</span></code>, where <code class="docutils literal notranslate"><span class="pre">image</span></code> is a
uint8 Tensor.</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.io.get_tfrecord_parser">
<span class="sig-name descname"><span class="pre">get_tfrecord_parser</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tfrecord_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">features_to_return</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Iterable" title="(in Python v3.12)"><span class="pre">Iterable</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span></span><span 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">decode_images</span></span><span class="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">standardize</span></span><span class="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">normalizer</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="../norm/#slideflow.norm.StainNormalizer" title="slideflow.norm.StainNormalizer"><span class="pre">StainNormalizer</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">augment</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Callable" title="(in Python v3.12)"><span class="pre">Callable</span></a></span></span><a class="reference internal" href="../_modules/slideflow/io/torch/data_utils/#get_tfrecord_parser"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.io.get_tfrecord_parser" title="Permalink to this definition">¶</a></dt>
<dd><p>Gets tfrecord parser using dareblopy reader. Torch implementation;
different than sf.io.tensorflow</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_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 tfrecord to parse.</p></li>
<li><p><strong>features_to_return</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> or </em><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>) – Designates format for how
features should be returned from parser. If a list of feature names
is provided, the parsing function will return tfrecord features as
a list in the order provided. If a dictionary of labels (keys)
mapping to feature names (values) is provided, features will be
returned from the parser as a dictionary matching the same format.
If None, will return all features as a list.</p></li>
<li><p><strong>decode_images</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>) – Decode raw image strings into image
arrays. Defaults to True.</p></li>
<li><p><strong>standardize</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a><em>, </em><em>optional</em>) – Standardize images into the range (0,1).
Defaults to False.</p></li>
<li><p><strong>normalizer</strong> (<a class="reference internal" href="../norm/#slideflow.norm.StainNormalizer" title="slideflow.norm.StainNormalizer"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.norm.StainNormalizer</span></code></a>) – Stain normalizer
to use on images. Defaults to None.</p></li>
<li><p><strong>augment</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – <p>Image augmentations to perform. Augmentations include:</p>
<ul>
<li><p><code class="docutils literal notranslate"><span class="pre">'x'</span></code>: Random horizontal flip</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">'y'</span></code>: Random vertical flip</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">'r'</span></code>: Random 90-degree rotation</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">'j'</span></code>: Random JPEG compression (50% chance to compress with quality between 50-100)</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">'b'</span></code>: Random Gaussian blur (10% chance to blur with sigma between 0.5-2.0)</p></li>
</ul>
<p>Combine letters to define augmentations, such as <code class="docutils literal notranslate"><span class="pre">'xyrjn'</span></code>.
A value of True will use <code class="docutils literal notranslate"><span class="pre">'xyrjb'</span></code>.
Note: this function does not support stain augmentation.</p>
</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><p>A tuple containing</p>
<blockquote>
<div><p>func: Parsing function</p>
<p>dict: Detected feature description for the tfrecord</p>
</div></blockquote>
</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.io.get_tfrecord_length">
<span class="sig-name descname"><span class="pre">get_tfrecord_length</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tfrecord</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span></span><a class="reference internal" href="../_modules/slideflow/util/tfrecord2idx/#get_tfrecord_length"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.io.get_tfrecord_length" title="Permalink to this definition">¶</a></dt>
<dd><p>Return the number of records in a TFRecord file.</p>
<p>Uses an index file if available, otherwise iterates through
the file to find the total record length.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>tfrecord</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Path to TFRecord.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Number of records.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)">int</a></p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.io.read_and_return_record">
<span class="sig-name descname"><span class="pre">read_and_return_record</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">record</span></span><span class="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#bytes" title="(in Python v3.12)"><span class="pre">bytes</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">parser</span></span><span class="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">assign_slide</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Dict" title="(in Python v3.12)"><span class="pre">Dict</span></a></span></span><a class="reference internal" href="../_modules/slideflow/io/torch/data_utils/#read_and_return_record"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.io.read_and_return_record" title="Permalink to this definition">¶</a></dt>
<dd><p>Process raw TFRecord bytes into a format that can be written with
<code class="docutils literal notranslate"><span class="pre">tf.io.TFRecordWriter</span></code>.</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>record</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#bytes" title="(in Python v3.12)"><em>bytes</em></a>) – Raw TFRecord bytes (unparsed)</p></li>
<li><p><strong>parser</strong> (<em>Callable</em>) – TFRecord parser, as returned by
<code class="xref py py-func docutils literal notranslate"><span class="pre">sf.io.get_tfrecord_parser()</span></code></p></li>
<li><p><strong>assign_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><em>, </em><em>optional</em>) – Slide name to override the record with.
Defaults to None.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Dictionary mapping record key to a tuple containing (bytes, dtype).</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.io.serialized_record">
<span class="sig-name descname"><span class="pre">serialized_record</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#bytes" title="(in Python v3.12)"><span class="pre">bytes</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">image_raw</span></span><span class="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#bytes" title="(in Python v3.12)"><span class="pre">bytes</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">loc_x</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">loc_y</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/slideflow/io/torch/data_utils/#serialized_record"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.io.serialized_record" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns a serialized example for TFRecord storage, ready to be written
by a TFRecordWriter.</p>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.io.tfrecord_has_locations">
<span class="sig-name descname"><span class="pre">tfrecord_has_locations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">check_x</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">check_y</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span></span><a class="reference internal" href="../_modules/slideflow/io/#tfrecord_has_locations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.io.tfrecord_has_locations" title="Permalink to this definition">¶</a></dt>
<dd><p>Check if a given TFRecord has location information stored.</p>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.io.update_manifest_at_dir">
<span class="sig-name descname"><span class="pre">update_manifest_at_dir</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">directory</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">force_update</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Dict" title="(in Python v3.12)"><span class="pre">Dict</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="reference internal" href="../_modules/slideflow/io/#update_manifest_at_dir"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.io.update_manifest_at_dir" title="Permalink to this definition">¶</a></dt>
<dd><p>Log number of tiles in each TFRecord file present in the given
directory and all subdirectories, saving manifest to file within
the parent directory.</p>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.io.write_tfrecords_multi">
<span class="sig-name descname"><span class="pre">write_tfrecords_multi</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_directory</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_directory</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="reference internal" href="../_modules/slideflow/io/#write_tfrecords_multi"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.io.write_tfrecords_multi" title="Permalink to this definition">¶</a></dt>
<dd><p>Write multiple tfrecords, one for each slide, from a directory of images.</p>
<p>Scans a folder for subfolders, assumes subfolders are slide names.
Assembles all image tiles within subfolders, assuming the subfolder is the
slide name. Collects all image tiles and exports into multiple tfrecord
files, one for each slide.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>input_directory</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Directory of images.</p></li>
<li><p><strong>output_directory</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Directory in which to write TFRecord files.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.io.write_tfrecords_single">
<span class="sig-name descname"><span class="pre">write_tfrecords_single</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_directory</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_directory</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">slide</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span></span><a class="reference internal" href="../_modules/slideflow/io/#write_tfrecords_single"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.io.write_tfrecords_single" title="Permalink to this definition">¶</a></dt>
<dd><p>Scans a folder for image tiles, annotates using the provided slide,
exports into a single tfrecord file.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>input_directory</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Directory of images.</p></li>
<li><p><strong>output_directory</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Directory in which to write TFRecord file.</p></li>
<li><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – TFRecord filename (without path).</p></li>
<li><p><strong>slide</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Slide name to assign to records inside TFRecord.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Number of records written.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)">int</a></p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.io.write_tfrecords_merge">
<span class="sig-name descname"><span class="pre">write_tfrecords_merge</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_directory</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_directory</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span></span><a class="reference internal" href="../_modules/slideflow/io/#write_tfrecords_merge"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.io.write_tfrecords_merge" title="Permalink to this definition">¶</a></dt>
<dd><p>Scans a folder for subfolders, assumes subfolders are slide names.
Assembles all image tiles within subfolders and labels using the provided
annotation_dict, assuming the subfolder is the slide name. Collects all
image tiles and exports into a single tfrecord file.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>input_directory</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Directory of images.</p></li>
<li><p><strong>output_directory</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Directory in which to write TFRecord file.</p></li>
<li><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – TFRecord filename (without path).</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Number of records written.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)">int</a></p>
</dd>
</dl>
</dd></dl>

<section id="slideflow-io-preservedsite">
<h2>slideflow.io.preservedsite<a class="headerlink" href="#slideflow-io-preservedsite" title="Permalink to this heading">¶</a></h2>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.io.preservedsite.generate_crossfolds">
<span class="sig-name descname"><span class="pre">generate_crossfolds</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'auto'</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#slideflow.io.preservedsite.generate_crossfolds" title="Permalink to this definition">¶</a></dt>
<dd><p>Generates site preserved cross-folds, balanced on a given category.</p>
<p>Preserved-site cross-validation is performed as described in the manuscript
<a class="reference external" href="https://doi.org/10.1038/s41467-021-24698-1">https://doi.org/10.1038/s41467-021-24698-1</a>.</p>
<p>Available solvers include Bonmin and CPLEX. The solver can be manually set
with <code class="docutils literal notranslate"><span class="pre">method</span></code>.  If not provided, the solver will default to CPLEX if
available, and Bonmin as a fallback.</p>
<p>CPLEX is properitary software by IBM.</p>
<p>Bonmin can be installed with:</p>
<blockquote>
<div><div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>conda<span class="w"> </span>install<span class="w"> </span>-c<span class="w"> </span>conda-forge<span class="w"> </span>coinbonmin
</pre></div>
</div>
</div></blockquote>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>data</strong> (<em>pandas.DataFrame</em>) – Dataframe with slides that must be split into
crossfolds.</p></li>
<li><p><strong>category</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – The column in data to stratify by.</p></li>
<li><p><strong>k</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Number of crossfolds for splitting. Defaults to 3.</p></li>
<li><p><strong>target_column</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Name for target column to contain the assigned
crossfolds for each patient in the output dataframe.</p></li>
<li><p><strong>timelimit</strong> – maximum time to spend solving</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>dataframe with a new column, ‘CV3’ that contains values 1 - 3,
indicating the assigned crossfold</p>
</dd>
</dl>
</dd></dl>

</section>
</section>


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<li><a class="reference internal" href="#">slideflow.io</a><ul>
<li><a class="reference internal" href="#slideflow.io.convert_dtype"><code class="docutils literal notranslate"><span class="pre">convert_dtype()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.io.detect_tfrecord_format"><code class="docutils literal notranslate"><span class="pre">detect_tfrecord_format()</span></code></a></li>
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<li><a class="reference internal" href="#slideflow.io.get_locations_from_tfrecord"><code class="docutils literal notranslate"><span class="pre">get_locations_from_tfrecord()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.io.get_tfrecord_by_index"><code class="docutils literal notranslate"><span class="pre">get_tfrecord_by_index()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.io.get_tfrecord_by_location"><code class="docutils literal notranslate"><span class="pre">get_tfrecord_by_location()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.io.get_tfrecord_parser"><code class="docutils literal notranslate"><span class="pre">get_tfrecord_parser()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.io.get_tfrecord_length"><code class="docutils literal notranslate"><span class="pre">get_tfrecord_length()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.io.read_and_return_record"><code class="docutils literal notranslate"><span class="pre">read_and_return_record()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.io.serialized_record"><code class="docutils literal notranslate"><span class="pre">serialized_record()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.io.tfrecord_has_locations"><code class="docutils literal notranslate"><span class="pre">tfrecord_has_locations()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.io.update_manifest_at_dir"><code class="docutils literal notranslate"><span class="pre">update_manifest_at_dir()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.io.write_tfrecords_multi"><code class="docutils literal notranslate"><span class="pre">write_tfrecords_multi()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.io.write_tfrecords_single"><code class="docutils literal notranslate"><span class="pre">write_tfrecords_single()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.io.write_tfrecords_merge"><code class="docutils literal notranslate"><span class="pre">write_tfrecords_merge()</span></code></a></li>
<li><a class="reference internal" href="#slideflow-io-preservedsite">slideflow.io.preservedsite</a><ul>
<li><a class="reference internal" href="#slideflow.io.preservedsite.generate_crossfolds"><code class="docutils literal notranslate"><span class="pre">generate_crossfolds()</span></code></a></li>
</ul>
</li>
</ul>
</li>
</ul>

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