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              <p class="caption" role="heading"><span class="caption-text">Introduction</span></p>
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<li class="toctree-l1"><a class="reference internal" href="../tutorial5/">Tutorial 5: Creating a mosaic map</a></li>
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  <section id="slideflow-mosaic">
<span id="mosaic"></span><h1>slideflow.Mosaic<a class="headerlink" href="#slideflow-mosaic" title="Permalink to this heading">¶</a></h1>
<p><a class="reference internal" href="#slideflow.Mosaic" title="slideflow.Mosaic"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.Mosaic</span></code></a> plots tile images onto a map of slides, generating a mosaic map.</p>
<p>The idea of a mosaic map is to visualize image feature variation across slides and among categories, in an attempt
to better understand the kinds of image features discriminative models might be using to generate class predictions.
They are created by first generating whole-dataset layer features (using
<a class="reference internal" href="../dataset_features/#slideflow.DatasetFeatures" title="slideflow.DatasetFeatures"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.DatasetFeatures</span></code></a>), which are then mapped into two-dimensional space using UMAP
dimensionality reduction (<a class="reference internal" href="../slidemap/#slideflow.SlideMap" title="slideflow.SlideMap"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.SlideMap</span></code></a>). This resulting SlideMap is then passed to
<a class="reference internal" href="#slideflow.Mosaic" title="slideflow.Mosaic"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.Mosaic</span></code></a>, which overlays tile images onto the dimensionality-reduced slide map.</p>
<p>An example of a mosaic map can be found in Figure 4 of <a class="reference external" href="https://doi.org/10.1038/s41379-020-00724-3">this paper</a>.
It bears some resemblence to the Activation Atlases created by
<a class="reference external" href="https://distill.pub/2019/activation-atlas/">Google and OpenAI</a>, without the use of feature inversion.</p>
<p>See <a class="reference internal" href="../posthoc/#mosaic-map"><span class="std std-ref">Mosaic Maps</span></a> for an example of how a mosaic map can be used in the context of a project.</p>
<dl class="py class">
<dt class="sig sig-object py" id="slideflow.Mosaic">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">Mosaic</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">images</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="../slidemap/#slideflow.SlideMap" title="slideflow.stats.slidemap.SlideMap"><span class="pre">SlideMap</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><span class="pre">ndarray</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><span class="pre">ndarray</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Tuple" title="(in Python v3.12)"><span class="pre">Tuple</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/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="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">coords</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Tuple" title="(in Python v3.12)"><span class="pre">Tuple</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">ndarray</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tfrecords</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">normalizer</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="../norm/#slideflow.norm.StainNormalizer" title="slideflow.norm.StainNormalizer"><span class="pre">StainNormalizer</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">normalizer_source</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">grid_kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/slideflow/mosaic/#Mosaic"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.Mosaic" title="Permalink to this definition">¶</a></dt>
<dd><p>Visualization of plotted image tiles.</p>
<p>Generate a mosaic map, which visualizes plotted image tiles.</p>
<p>Creating a mosaic map requires two components: a set of images and
corresponding coordinates. Images and coordinates can either be manually
provided, or the mosaic can dynamically read images from TFRecords as
needed, reducing memory requirements.</p>
<p>The first argument provides the images, and may be any of the following:</p>
<ul class="simple">
<li><p>A list or array of images (np.ndarray, HxWxC)</p></li>
<li><p>A list of tuples, containing <code class="docutils literal notranslate"><span class="pre">(slide_name,</span> <span class="pre">tfrecord_index)</span></code></p></li>
<li><p>A <code class="docutils literal notranslate"><span class="pre">slideflow.SlideMap</span></code> object</p></li>
</ul>
<p>The second argument provides the coordinates, and may be any of:</p>
<ul class="simple">
<li><p>A list or array of (x, y) coordinates for each image</p></li>
<li><p>None (if the first argument is a <code class="docutils literal notranslate"><span class="pre">SlideMap</span></code>, which has coordinates)</p></li>
</ul>
<p>If images are to be read dynamically from tfrecords (with a <code class="docutils literal notranslate"><span class="pre">SlideMap</span></code>,
or by providing tfrecord indices directly), the keyword argument
<code class="docutils literal notranslate"><span class="pre">tfrecords</span></code> must be specified with paths to tfrecords.</p>
<p>Published examples:</p>
<ul class="simple">
<li><p>Figure 4: <a class="reference external" href="https://doi.org/10.1038/s41379-020-00724-3">https://doi.org/10.1038/s41379-020-00724-3</a></p></li>
<li><p>Figure 6: <a class="reference external" href="https://doi.org/10.1038/s41467-022-34025-x">https://doi.org/10.1038/s41467-022-34025-x</a></p></li>
</ul>
<dl>
<dt>Examples</dt><dd><p>Generate a mosaic map from a list of images and coordinates.</p>
<blockquote>
<div><div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="c1"># Example data (images are HxWxC, np.ndarray)</span>
<span class="n">images</span> <span class="o">=</span> <span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">(</span><span class="o">...</span><span class="p">),</span> <span class="o">...</span><span class="p">]</span>
<span class="n">coords</span> <span class="o">=</span> <span class="p">[(</span><span class="mf">0.2</span><span class="p">,</span> <span class="mf">0.9</span><span class="p">),</span> <span class="o">...</span><span class="p">]</span>

<span class="c1"># Generate the mosaic</span>
<span class="n">mosaic</span> <span class="o">=</span> <span class="n">Mosaic</span><span class="p">(</span><span class="n">images</span><span class="p">,</span> <span class="n">coordinates</span><span class="p">)</span>
</pre></div>
</div>
</div></blockquote>
<p>Generate a mosaic map from tuples of TFRecord paths and indices.</p>
<blockquote>
<div><div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="c1"># Example data</span>
<span class="n">paths</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;/path/to/tfrecord.tfrecords&#39;</span><span class="p">,</span> <span class="o">...</span><span class="p">]</span>
<span class="n">idx</span> <span class="o">=</span> <span class="p">[</span><span class="mi">253</span><span class="p">,</span> <span class="mi">112</span><span class="p">,</span> <span class="o">...</span><span class="p">]</span>
<span class="n">coords</span> <span class="o">=</span> <span class="p">[(</span><span class="mf">0.2</span><span class="p">,</span> <span class="mf">0.9</span><span class="p">),</span> <span class="o">...</span><span class="p">]</span>
<span class="n">tuples</span> <span class="o">=</span> <span class="p">[(</span><span class="n">tfr</span><span class="p">,</span> <span class="n">idx</span><span class="p">)</span> <span class="k">for</span> <span class="n">tfr</span><span class="p">,</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">paths</span><span class="p">,</span> <span class="n">idx</span><span class="p">)]</span>

<span class="c1"># Generate mosaic map</span>
<span class="n">mosaic</span> <span class="o">=</span> <span class="n">sf</span><span class="o">.</span><span class="n">Mosaic</span><span class="p">(</span><span class="n">tuples</span><span class="p">,</span> <span class="n">coords</span><span class="p">)</span>
</pre></div>
</div>
</div></blockquote>
<p>Generate a mosaic map from a SlideMap and list of TFRecord paths.</p>
<blockquote>
<div><div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="c1"># Prepare a SlideMap from a project</span>
<span class="n">P</span> <span class="o">=</span> <span class="n">sf</span><span class="o">.</span><span class="n">Project</span><span class="p">(</span><span class="s1">&#39;/project/path&#39;</span><span class="p">)</span>
<span class="n">ftrs</span> <span class="o">=</span> <span class="n">P</span><span class="o">.</span><span class="n">generate_features</span><span class="p">(</span><span class="s1">&#39;/path/to/model&#39;</span><span class="p">)</span>
<span class="n">slide_map</span> <span class="o">=</span> <span class="n">sf</span><span class="o">.</span><span class="n">SlideMap</span><span class="o">.</span><span class="n">from_features</span><span class="p">(</span><span class="n">ftrs</span><span class="p">)</span>

<span class="c1"># Generate mosaic</span>
<span class="n">mosaic</span> <span class="o">=</span> <span class="n">Mosaic</span><span class="p">(</span><span class="n">slide_map</span><span class="p">,</span> <span class="n">tfrecords</span><span class="o">=</span><span class="n">ftrs</span><span class="o">.</span><span class="n">tfrecords</span><span class="p">)</span>
</pre></div>
</div>
</div></blockquote>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>images</strong> (list(np.ndarray), tuple, <a class="reference internal" href="../slidemap/#slideflow.SlideMap" title="slideflow.SlideMap"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.SlideMap</span></code></a>) – Images from which to generate the mosaic. May be a list or
array of images (np.ndarray, HxWxC), a list of tuples,
containing <code class="docutils literal notranslate"><span class="pre">(slide_name,</span> <span class="pre">tfrecord_index)</span></code>, or a
<code class="docutils literal notranslate"><span class="pre">slideflow.SlideMap</span></code> object.</p></li>
<li><p><strong>coords</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>(</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>)</em>) – Coordinates for images. May be a list or array
of (x, y) coordinates for each image (of same length
as <code class="docutils literal notranslate"><span class="pre">images</span></code>), or None (if <code class="docutils literal notranslate"><span class="pre">images</span></code> is a <code class="docutils literal notranslate"><span class="pre">SlideMap</span></code> object).</p></li>
</ul>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><strong>tfrecords</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>(</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>)</em><em>, </em><em>optional</em>) – TFRecord paths. Required if
<code class="docutils literal notranslate"><span class="pre">images</span></code> is either a <code class="docutils literal notranslate"><span class="pre">SlideMap</span></code> object or a list of tuples
containing <code class="docutils literal notranslate"><span class="pre">(slide_name,</span> <span class="pre">tfrecord_index)</span></code>. Defaults to None.</p></li>
<li><p><strong>num_tiles_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>) – Mosaic map grid size. Defaults to 50.</p></li>
<li><p><strong>tile_select</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>) – ‘first’, ‘nearest’, or ‘centroid’.
Determines how to choose a tile for display on each grid space.
If ‘first’, will display the first valid tile in a grid space
(fastest; recommended). If ‘nearest’, will display tile nearest
to center of grid space. If ‘centroid’, for each grid, will
calculate which tile is nearest to centroid tile_meta.
Defaults to ‘nearest’.</p></li>
<li><p><strong>tile_meta</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>) – Tile metadata, used for tile_select.
Dictionary should have slide names as keys, mapped to list of
metadata (length of list = number of tiles in slide).
Defaults to None.</p></li>
<li><p><strong>normalizer</strong> ((str or <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) – Normalization strategy to use on image tiles. Defaults to None.</p></li>
<li><p><strong>normalizer_source</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Stain normalization preset or
path to a source image. Valid presets include ‘v1’, ‘v2’, and
‘v3’. If None, will use the default present (‘v3’).
Defaults to None.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<section id="methods">
<h2>Methods<a class="headerlink" href="#methods" title="Permalink to this heading">¶</a></h2>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Mosaic.generate_grid">
<span class="sig-name descname"><span class="pre">generate_grid</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_tiles_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">50</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tile_meta</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Dict" title="(in Python v3.12)"><span class="pre">Dict</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tile_select</span></span><span class="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">'first'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_dist</span></span><span class="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><a class="headerlink" href="#slideflow.Mosaic.generate_grid" title="Permalink to this definition">¶</a></dt>
<dd><p>Generate the mosaic map grid.</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>num_tiles_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>) – Mosaic map grid size. Defaults to 50.</p></li>
<li><p><strong>tile_meta</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>) – Tile metadata, used for tile_select.
Dictionary should have slide names as keys, mapped to list of
metadata (length of list = number of tiles in slide).
Defaults to None.</p></li>
<li><p><strong>tile_select</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>) – ‘first’, ‘nearest’, or ‘centroid’.
Determines how to choose a tile for display on each grid space.
If ‘first’, will display the first valid tile in a grid space
(fastest; recommended). If ‘nearest’, will display tile nearest
to center of grid space. If ‘centroid’, for each grid, will
calculate which tile is nearest to centroid tile_meta.
Defaults to ‘nearest’.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Mosaic.plot">
<span class="sig-name descname"><span class="pre">plot</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">figsize</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Tuple" title="(in Python v3.12)"><span class="pre">Tuple</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">(200,</span> <span class="pre">200)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">focus</span></span><span class="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">focus_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">background</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'#dfdfdf'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pool</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Any" title="(in Python v3.12)"><span class="pre">Any</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="headerlink" href="#slideflow.Mosaic.plot" title="Permalink to this definition">¶</a></dt>
<dd><p>Initializes figures and places image tiles.</p>
<p>If in a Jupyter notebook, the heatmap will be displayed in the cell
output. If running via script or shell, the heatmap can then be
shown on screen using matplotlib <code class="docutils literal notranslate"><span class="pre">plt.show()</span></code>:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">slideflow</span> <span class="k">as</span> <span class="nn">sf</span>
<span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>

<span class="n">heatmap</span> <span class="o">=</span> <span class="n">sf</span><span class="o">.</span><span class="n">Heatmap</span><span class="p">(</span><span class="o">...</span><span class="p">)</span>
<span class="n">heatmap</span><span class="o">.</span><span class="n">plot</span><span class="p">()</span>
<span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
</pre></div>
</div>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>figsize</strong> (<em>Tuple</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><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>) – Figure size. Defaults to
(200, 200).</p></li>
<li><p><strong>focus</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>, </em><em>optional</em>) – List of tfrecords (paths) to highlight
on the mosaic. Defaults to None.</p></li>
<li><p><strong>focus_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>) – Highlight tiles from this slide.
Defaults to None.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Mosaic.points_at_grid_index">
<span class="sig-name descname"><span class="pre">points_at_grid_index</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">x</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">y</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#slideflow.Mosaic.points_at_grid_index" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Mosaic.save">
<span class="sig-name descname"><span class="pre">save</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Any" title="(in Python v3.12)"><span class="pre">Any</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="headerlink" href="#slideflow.Mosaic.save" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves the mosaic map figure to the given filename.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Path at which to save the mosiac image.</p>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><strong>figsize</strong> (<em>Tuple</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><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>) – Figure size. Defaults to
(200, 200).</p></li>
<li><p><strong>focus</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>, </em><em>optional</em>) – List of tfrecords (paths) to highlight on
the mosaic.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Mosaic.save_report">
<span class="sig-name descname"><span class="pre">save_report</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="headerlink" href="#slideflow.Mosaic.save_report" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a report of which tiles (and their corresponding slide)
were displayed on the Mosaic map, in CSV format.</p>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.Mosaic.view">
<span class="sig-name descname"><span class="pre">view</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">slides</span></span><span class="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><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="headerlink" href="#slideflow.Mosaic.view" title="Permalink to this definition">¶</a></dt>
<dd><p>Open Mosaic in Slideflow Studio.</p>
<p>See <a class="reference internal" href="../studio/#studio"><span class="std std-ref">Slideflow Studio: Live Visualization</span></a> for more information.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>slides</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>) – Path to whole-slide images. Used for
displaying image tile context when hovering over a mosaic grid.
Defaults to None.</p>
</dd>
</dl>
</dd></dl>

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