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<p class="caption" role="heading"><span class="caption-text">Introduction</span></p>
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<section id="slideflow-io-tensorflow">
<h1>slideflow.io.tensorflow<a class="headerlink" href="#slideflow-io-tensorflow" title="Permalink to this heading">¶</a></h1>
<p>TFRecord interleaving in the Tensorflow backend is accomplished with <a class="reference internal" href="#slideflow.io.tensorflow.interleave" title="slideflow.io.tensorflow.interleave"><code class="xref py py-func docutils literal notranslate"><span class="pre">slideflow.io.tensorflow.interleave()</span></code></a>, which interleaves a set of tfrecords together into a <code class="xref py py-class docutils literal notranslate"><span class="pre">tf.data.Datasets</span></code> object that can be used for training. This interleaving can include patient or category-level balancing for returned batches (see <a class="reference internal" href="../dataloaders/#balancing"><span class="std std-ref">Oversampling with balancing</span></a>).</p>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>The TFRecord reading and interleaving implemented in this module is only compatible with Tensorflow models. The <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> module includes a PyTorch-specific TFRecord reader.</p>
</div>
<span class="target" id="module-slideflow.io.tensorflow"></span><dl class="py function">
<dt class="sig sig-object py" id="slideflow.io.tensorflow.checkpoint_to_tf_model">
<span class="sig-name descname"><span class="pre">checkpoint_to_tf_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">models_dir</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">model_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="reference internal" href="../_modules/slideflow/io/tensorflow/#checkpoint_to_tf_model"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.io.tensorflow.checkpoint_to_tf_model" title="Permalink to this definition">¶</a></dt>
<dd><p>Convert a checkpoint file into a saved model.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>models_dir</strong> – Directory containing the model.</p></li>
<li><p><strong>model_name</strong> – Name of the model to convert.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.io.tensorflow.decode_image">
<span class="sig-name descname"><span class="pre">decode_image</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">img_string</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#bytes" title="(in Python v3.12)"><span class="pre">bytes</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">img_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></em>, <em class="sig-param"><span class="n"><span class="pre">crop_left</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">crop_width</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resize_target</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resize_method</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'lanczos3'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resize_aa</span></span><span class="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">size</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Tensor</span></span></span><a class="reference internal" href="../_modules/slideflow/io/tensorflow/#decode_image"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.io.tensorflow.decode_image" title="Permalink to this definition">¶</a></dt>
<dd><p>Decodes an image.</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>img_string</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#bytes" title="(in Python v3.12)"><em>bytes</em></a>) – Image bytes (JPG/PNG).</p></li>
<li><p><strong>img_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 image data; ‘jpg’, ‘jpeg’, or ‘png’.</p></li>
<li><p><strong>crop_left</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Crop image starting at this top-left
coordinate. Defaults to None.</p></li>
<li><p><strong>crop_width</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Crop image to this width.
Defaults to None.</p></li>
<li><p><strong>resize_target</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Resize image, post-crop, to this target
size in pixels. Defaults to None.</p></li>
<li><p><strong>resize_method</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Resizing method, if applicable.
Defaults to ‘lanczos3’.</p></li>
<li><p><strong>resize_aa</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a><em>, </em><em>optional</em>) – If resizing, use antialiasing.
Defaults to True.</p></li>
<li><p><strong>size</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Set the image size/width (pixels).
Defaults to None.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Processed image (uint8).</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>tf.Tensor</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.io.tensorflow.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 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">to_numpy</span></span><span class="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">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">img_size</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">error_if_invalid</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">decode_kwargs</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Any" title="(in Python v3.12)"><span class="pre">Any</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Callable" title="(in Python v3.12)"><span class="pre">Callable</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="reference internal" href="../_modules/slideflow/io/tensorflow/#get_tfrecord_parser"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.io.tensorflow.get_tfrecord_parser" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns a tfrecord parsing function based on the specified parameters.</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>to_numpy</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>) – Convert records from tensors->numpy arrays.
Defaults to False.</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 image strings into 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>img_size</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Width of images in pixels. Will call tf.set_shape(…)
if provided. 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>
<li><p><code class="docutils literal notranslate"><span class="pre">'n'</span></code>: Random <a class="reference internal" href="../norm/#stain-augmentation"><span class="std std-ref">Stain Augmentation</span></a> (requires stain normalizer)</p></li>
</ul>
<p>Combine letters to define augmentations, such as <code class="docutils literal notranslate"><span class="pre">'xyrjn'</span></code>.
A value of True will use <code class="docutils literal notranslate"><span class="pre">'xyrjb'</span></code>.</p>
</p></li>
<li><p><strong>error_if_invalid</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>) – Raise an error if a tfrecord cannot
be read. Defaults to True.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.io.tensorflow.interleave">
<span class="sig-name descname"><span class="pre">interleave</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">paths</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</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="n"><span class="pre">batch_size</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">clip</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Dict" title="(in Python v3.12)"><span class="pre">Dict</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">deterministic</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">drop_last</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">from_wsi</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">incl_loc</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">incl_slidenames</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">infinite</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">img_size</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">labels</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Dict" title="(in Python v3.12)"><span class="pre">Dict</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Dict" title="(in Python v3.12)"><span class="pre">Dict</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Dict" title="(in Python v3.12)"><span class="pre">Dict</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">normalizer</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference 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">num_parallel_reads</span></span><span class="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">4</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_shards</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pool</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">mp.pool.Pool</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">prob_weights</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Dict" title="(in Python v3.12)"><span class="pre">Dict</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rois</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">roi_method</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'auto'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">shard_idx</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/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">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">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tile_um</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tfrecord_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 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">transform</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Callable" title="(in Python v3.12)"><span class="pre">Callable</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">decode_kwargs</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Any" title="(in Python v3.12)"><span class="pre">Any</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Iterable" title="(in Python v3.12)"><span class="pre">Iterable</span></a></span></span><a class="reference internal" href="../_modules/slideflow/io/tensorflow/#interleave"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.io.tensorflow.interleave" title="Permalink to this definition">¶</a></dt>
<dd><p>Generate an interleaved dataset from a collection of tfrecord files.</p>
<p>The interleaved dataset samples from tfrecord files randomly according to
balancing, if provided. Requires manifest for balancing. Assumes TFRecord
files are named by slide.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>paths</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>(</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>)</em>) – List of paths to TFRecord files or whole-slide
images.</p>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><strong>augment</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – <p>Image augmentations to perform. Augmentations include:</p>
<ul>
<li><p><code class="docutils literal notranslate"><span class="pre">'x'</span></code>: Random horizontal flip</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">'y'</span></code>: Random vertical flip</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">'r'</span></code>: Random 90-degree rotation</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">'j'</span></code>: Random JPEG compression (50% chance to compress with quality between 50-100)</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">'b'</span></code>: Random Gaussian blur (10% chance to blur with sigma between 0.5-2.0)</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">'n'</span></code>: Random <a class="reference internal" href="../norm/#stain-augmentation"><span class="std std-ref">Stain Augmentation</span></a> (requires stain normalizer)</p></li>
</ul>
<p>Combine letters to define augmentations, such as <code class="docutils literal notranslate"><span class="pre">'xyrjn'</span></code>.
A value of True will use <code class="docutils literal notranslate"><span class="pre">'xyrjb'</span></code>.</p>
</p></li>
<li><p><strong>batch_size</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Batch size.</p></li>
<li><p><strong>clip</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.12)"><em>dict</em></a><em>, </em><em>optional</em>) – Dict mapping tfrecords to number of tiles to
take per tfrecord. Defaults to None.</p></li>
<li><p><strong>deterministic</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a><em>, </em><em>optional</em>) – When num_parallel_calls is specified,
if this boolean is specified, it controls the order in which the
transformation produces elements. If set to False, the
transformation is allowed to yield elements out of order to trade
determinism for performance. Defaults to False.</p></li>
<li><p><strong>drop_last</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a><em>, </em><em>optional</em>) – Drop the last non-full batch.
Defaults to False.</p></li>
<li><p><strong>from_wsi</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Generate predictions from tiles dynamically
extracted from whole-slide images, rather than TFRecords.
Defaults to False (use TFRecords).</p></li>
<li><p><strong>incl_loc</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – ‘coord’, ‘grid’, or None. Return (x,y)
coordinates (‘coord’) for each tile center along with tile
images, or the (x,y) grid coordinates for each tile.
Defaults to ‘coord’.</p></li>
<li><p><strong>incl_slidenames</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a><em>, </em><em>optional</em>) – Include slidenames as third returned
variable. Defaults to False.</p></li>
<li><p><strong>infinite</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a><em>, </em><em>optional</em>) – Create an finite dataset. WARNING: If
infinite is False && balancing is used, some tiles will be skipped.
Defaults to True.</p></li>
<li><p><strong>img_size</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Image width in pixels.</p></li>
<li><p><strong>labels</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.12)"><em>dict</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Dict or function. If dict, must map
slide names to outcome labels. If function, function must accept an
image (tensor) and slide name (str), and return a dict
{‘image_raw’: image (tensor)} and label (int or float). If not
provided, all labels will be None.</p></li>
<li><p><strong>normalizer</strong> (<a class="reference internal" href="../norm/#slideflow.norm.StainNormalizer" title="slideflow.norm.StainNormalizer"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.norm.StainNormalizer</span></code></a>, optional) – Normalizer to use on images. Defaults to None.</p></li>
<li><p><strong>num_parallel_reads</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Number of parallel reads for each
TFRecordDataset. Defaults to 4.</p></li>
<li><p><strong>num_shards</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Shard the tfrecord datasets, used for
multiprocessing datasets. Defaults to None.</p></li>
<li><p><strong>pool</strong> (<em>multiprocessing.Pool</em>) – Shared multiprocessing pool. Useful
if <code class="docutils literal notranslate"><span class="pre">from_wsi=True</span></code>, for sharing a unified processing pool between
dataloaders. Defaults to None.</p></li>
<li><p><strong>prob_weights</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.12)"><em>dict</em></a><em>, </em><em>optional</em>) – Dict mapping tfrecords to probability of
including in batch. Defaults to None.</p></li>
<li><p><strong>rois</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>(</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>)</em><em>, </em><em>optional</em>) – List of ROI paths. Only used if
from_wsi=True. Defaults to None.</p></li>
<li><p><strong>roi_method</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Method for extracting ROIs. Only used if
from_wsi=True. Defaults to ‘auto’.</p></li>
<li><p><strong>shard_idx</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Index of the tfrecord shard to use.
Defaults to None.</p></li>
<li><p><strong>standardize</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a><em>, </em><em>optional</em>) – Standardize images to (0,1).
Defaults to True.</p></li>
<li><p><strong>tile_um</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Size of tiles to extract from WSI, in
microns. Only used if from_wsi=True. Defaults to None.</p></li>
<li><p><strong>tfrecord_parser</strong> (<em>Callable</em><em>, </em><em>optional</em>) – Custom parser for TFRecords.
Defaults to None.</p></li>
<li><p><strong>transform</strong> (<em>Callable</em><em>, </em><em>optional</em>) – Arbitrary transform function.
Performs transformation after augmentations but before
standardization. Defaults to None.</p></li>
<li><p><strong>**decode_kwargs</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.12)"><em>dict</em></a>) – Keyword arguments to pass to
<a class="reference internal" href="#slideflow.io.tensorflow.decode_image" title="slideflow.io.tensorflow.decode_image"><code class="xref py py-func docutils literal notranslate"><span class="pre">slideflow.io.tensorflow.decode_image()</span></code></a>.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.io.tensorflow.join_tfrecord">
<span class="sig-name descname"><span class="pre">join_tfrecord</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_folder</span></span><span class="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_file</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <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">→</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/tensorflow/#join_tfrecord"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.io.tensorflow.join_tfrecord" title="Permalink to this definition">¶</a></dt>
<dd><p>Randomly sample from tfrecords in the input folder with shuffling,
and combine 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_folder</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Folder containing tfrecord files.</p></li>
<li><p><strong>output_file</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Output tfrecord file.</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>) – Assign a slide name to all images.
Defaults to None.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.io.tensorflow.multi_image_example">
<span class="sig-name descname"><span class="pre">multi_image_example</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_dict</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Dict" title="(in Python v3.12)"><span class="pre">Dict</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Example</span></span></span><a class="reference internal" href="../_modules/slideflow/io/tensorflow/#multi_image_example"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.io.tensorflow.multi_image_example" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns a Tensorflow Data example for storage with multiple images.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>slide</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#bytes" title="(in Python v3.12)"><em>bytes</em></a>) – Slide name.</p></li>
<li><p><strong>image_dict</strong> (<em>Dict</em>) – Dictionary of image names and image bytes.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Tensorflow Data example.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Example</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.io.tensorflow.parser_from_labels">
<span class="sig-name descname"><span class="pre">parser_from_labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">labels</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Dict" title="(in Python v3.12)"><span class="pre">Dict</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Dict" title="(in Python v3.12)"><span class="pre">Dict</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Dict" title="(in Python v3.12)"><span class="pre">Dict</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Callable" title="(in Python v3.12)"><span class="pre">Callable</span></a></span></span><a class="reference internal" href="../_modules/slideflow/io/tensorflow/#parser_from_labels"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.io.tensorflow.parser_from_labels" title="Permalink to this definition">¶</a></dt>
<dd><p>Create a label parsing function used for parsing slides into single
or multi-outcome labels.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>labels</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.12)"><em>dict</em></a>) – Dictionary mapping slide names to outcome labels.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Label parsing function.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Callable</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.io.tensorflow.preprocess_uint8">
<span class="sig-name descname"><span class="pre">preprocess_uint8</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"><span class="pre">Tensor</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">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">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resize_px</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resize_method</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'lanczos3'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resize_aa</span></span><span class="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">as_dict</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Dict" title="(in Python v3.12)"><span class="pre">Dict</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">Tensor</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/slideflow/io/tensorflow/#preprocess_uint8"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.io.tensorflow.preprocess_uint8" title="Permalink to this definition">¶</a></dt>
<dd><p>Process batch of tensorflow images, resizing, normalizing,
and standardizing.</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>img</strong> (<em>tf.Tensor</em>) – Batch of tensorflow images (uint8).</p></li>
<li><p><strong>normalizer</strong> (<em>sf.norm.StainNormalizer</em><em>, </em><em>optional</em>) – Normalizer.
Defaults to None.</p></li>
<li><p><strong>standardize</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a><em>, </em><em>optional</em>) – Standardize images. Defaults to True.</p></li>
<li><p><strong>resize_px</strong> (<em>Optional</em><em>[</em><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>]</em><em>, </em><em>optional</em>) – Resize images. Defaults to None.</p></li>
<li><p><strong>resize_method</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Resize method. Defaults to ‘lanczos3’.</p></li>
<li><p><strong>resize_aa</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>) – Apply antialiasing during resizing.
Defaults to True.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Processed image.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Dict[<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)">str</a>, tf.Tensor]</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.io.tensorflow.print_tfrecord">
<span class="sig-name descname"><span class="pre">print_tfrecord</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">target</span></span><span class="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">→</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/tensorflow/#print_tfrecord"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.io.tensorflow.print_tfrecord" title="Permalink to this definition">¶</a></dt>
<dd><p>Print the slide names (and locations, if present) for records
in the given tfrecord file.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>target</strong> – Path to the tfrecord file or folder containing tfrecord files.</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.io.tensorflow.process_image">
<span class="sig-name descname"><span class="pre">process_image</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"><span class="pre">Tensor</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Dict" title="(in Python v3.12)"><span class="pre">Dict</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">Tensor</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Any" title="(in Python v3.12)"><span class="pre">Any</span></a></span></em>, <em class="sig-param"><span class="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">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 class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">transform</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Callable" title="(in Python v3.12)"><span class="pre">Callable</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/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">size</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Tuple" title="(in Python v3.12)"><span class="pre">Tuple</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.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><span class="pre">Tensor</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="p"><span class="pre">...</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/slideflow/io/tensorflow/#process_image"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.io.tensorflow.process_image" title="Permalink to this definition">¶</a></dt>
<dd><p>Applies augmentations and/or standardization to an image Tensor.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>record</strong> (<em>Union</em><em>[</em><em>tf.Tensor</em><em>, </em><em>Dict</em><em>[</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>tf.Tensor</em><em>]</em><em>]</em>) – Image Tensor.</p>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<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. Defaults to False.</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">'xyrj'</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>
<li><p><strong>transform</strong> (<em>Callable</em><em>, </em><em>optional</em>) – Arbitrary transform function.
Performs transformation after augmentations but before standardization.
Defaults to None.</p></li>
<li><p><strong>size</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Set the image shape. Defaults to None.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.io.tensorflow.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#bytes" title="(in Python v3.12)"><span class="pre">bytes</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Example</span></span></span><a class="reference internal" href="../_modules/slideflow/io/tensorflow/#read_and_return_record"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.io.tensorflow.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.tensorflow.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> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#bytes" title="(in Python v3.12)"><span class="pre">bytes</span></a></span></span><a class="reference internal" href="../_modules/slideflow/io/tensorflow/#serialized_record"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.io.tensorflow.serialized_record" title="Permalink to this definition">¶</a></dt>
<dd><p>Serialize a record for TFRecord storage.</p>
<p>The serialized record will be in a data format ready to be written
by a TFRecordWriter.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>slide</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#bytes" title="(in Python v3.12)"><em>bytes</em></a>) – Slide name.</p></li>
<li><p><strong>image_raw</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#bytes" title="(in Python v3.12)"><em>bytes</em></a>) – Image bytes.</p></li>
<li><p><strong>loc_x</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – X coordinate of image. Defaults to 0.</p></li>
<li><p><strong>loc_y</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Y coordinate of image. Defaults to 0.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Serialized record.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#bytes" title="(in Python v3.12)">bytes</a></p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.io.tensorflow.shuffle_tfrecord">
<span class="sig-name descname"><span class="pre">shuffle_tfrecord</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">target</span></span><span class="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">→</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/tensorflow/#shuffle_tfrecord"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.io.tensorflow.shuffle_tfrecord" title="Permalink to this definition">¶</a></dt>
<dd><p>Shuffle records in a TFRecord, saving the original to a .old file.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>target</strong> – Path to the tfrecord file.</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.io.tensorflow.shuffle_tfrecords_by_dir">
<span class="sig-name descname"><span class="pre">shuffle_tfrecords_by_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><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="reference internal" href="../_modules/slideflow/io/tensorflow/#shuffle_tfrecords_by_dir"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.io.tensorflow.shuffle_tfrecords_by_dir" title="Permalink to this definition">¶</a></dt>
<dd><p>For each TFRecord in a directory, shuffle records in the TFRecord,
saving the original to a .old file.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>directory</strong> – Path to the directory containing tfrecord files.</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.io.tensorflow.split_tfrecord">
<span class="sig-name descname"><span class="pre">split_tfrecord</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tfrecord_file</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_folder</span></span><span class="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">→</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/tensorflow/#split_tfrecord"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.io.tensorflow.split_tfrecord" title="Permalink to this definition">¶</a></dt>
<dd><p>Split records from a single tfrecord into individual tfrecord
files, stratified by 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>tfrecord_file</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Path to tfrecord file.</p></li>
<li><p><strong>output_folder</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 output folder.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.io.tensorflow.tfrecord_example">
<span class="sig-name descname"><span class="pre">tfrecord_example</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 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">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 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">0</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Example</span></span></span><a class="reference internal" href="../_modules/slideflow/io/tensorflow/#tfrecord_example"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.io.tensorflow.tfrecord_example" title="Permalink to this definition">¶</a></dt>
<dd><p>Return a Tensorflow Data example for TFRecord storage.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>slide</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#bytes" title="(in Python v3.12)"><em>bytes</em></a>) – Slide name.</p></li>
<li><p><strong>image_raw</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#bytes" title="(in Python v3.12)"><em>bytes</em></a>) – Image bytes.</p></li>
<li><p><strong>loc_x</strong> (<em>Optional</em><em>[</em><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>]</em><em>, </em><em>optional</em>) – X coordinate of image. Defaults to 0.</p></li>
<li><p><strong>loc_y</strong> (<em>Optional</em><em>[</em><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>]</em><em>, </em><em>optional</em>) – Y coordinate of image. Defaults to 0.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Tensorflow Data example.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Example</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.io.tensorflow.transform_tfrecord">
<span class="sig-name descname"><span class="pre">transform_tfrecord</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">origin</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">target</span></span><span class="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">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>, <em class="sig-param"><span class="n"><span class="pre">hue_shift</span></span><span class="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">resize</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="reference internal" href="../_modules/slideflow/io/tensorflow/#transform_tfrecord"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.io.tensorflow.transform_tfrecord" title="Permalink to this definition">¶</a></dt>
<dd><p>Transform images in a single tfrecord.</p>
<p>Can perform hue shifting, resizing, or re-assigning slide label.</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>origin</strong> – Path to the original tfrecord file.</p></li>
<li><p><strong>target</strong> – Path to the new tfrecord file.</p></li>
<li><p><strong>assign_slide</strong> – If provided, will assign this slide name to all
records in the new tfrecord.</p></li>
<li><p><strong>hue_shift</strong> – If provided, will shift the hue of all images by
this amount.</p></li>
<li><p><strong>resize</strong> – If provided, will resize all images to this size.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
</section>
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Datasets
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