Automatic Update

Wed Jun 26 17:09:59 UTC 2024

api.html

@@ -43,7 +43,7 @@ <h3>Navigation</h3>
 <span id="api"></span><h1>API<a class="headerlink" href="#module-pytools" title="Link to this heading">¶</a></h1>
 <dl class="py class">
 <dt class="sig sig-object py" id="pytools.HedwigZarrImage">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pytools.</span></span><span class="sig-name descname"><span class="pre">HedwigZarrImage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">zarr_grp</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Group</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">_ome_info</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">OMEInfo</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">_ome_idx</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</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><span class="sig-paren">)</span><a class="headerlink" href="#pytools.HedwigZarrImage" title="Link to this definition">¶</a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pytools.</span></span><span class="sig-name descname"><span class="pre">HedwigZarrImage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">zarr_grp</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Group</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">_ome_info</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">OMEInfo</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">_ome_idx</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</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="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">compute_args</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</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">None</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">mappingproxy({'scheduler':</span> <span class="pre">'threads'})</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.HedwigZarrImage" title="Link to this definition">¶</a></dt>
 <dd><p>Represents a OME-NGFF Zarr pyramidal image. The members provide information useful for the Hedwig imaging pipelines.</p>
 <dl class="py property">
 <dt class="sig sig-object py" id="pytools.HedwigZarrImage.dims">
@@ -184,7 +184,7 @@ <h3>Navigation</h3>
 
 <dl class="py class">
 <dt class="sig sig-object py" id="pytools.HedwigZarrImages">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pytools.</span></span><span class="sig-name descname"><span class="pre">HedwigZarrImages</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">zarr_path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Path</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">read_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.HedwigZarrImages" title="Link to this definition">¶</a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pytools.</span></span><span class="sig-name descname"><span class="pre">HedwigZarrImages</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">zarr_path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Path</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">read_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">compute_args</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</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">None</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">mappingproxy({'scheduler':</span> <span class="pre">'threads',</span> <span class="pre">'num_workers':</span> <span class="pre">4})</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.HedwigZarrImages" title="Link to this definition">¶</a></dt>
 <dd><p>Represents the set of images in a OME-NGFF ZARR structure.</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="pytools.HedwigZarrImages.get_series_keys">
@@ -331,7 +331,7 @@ <h3>Navigation</h3>
 
 <dl class="py function">
 <dt class="sig sig-object py" id="pytools.utils.zarr.build_pyramid">
-<span class="sig-prename descclassname"><span class="pre">pytools.utils.zarr.</span></span><span class="sig-name descname"><span class="pre">build_pyramid</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">zarr_path</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">components</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">chunks</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">shrink</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">[-1,</span> <span class="pre">-2]</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">overwrite</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.utils.zarr.build_pyramid" title="Link to this definition">¶</a></dt>
+<span class="sig-prename descclassname"><span class="pre">pytools.utils.zarr.</span></span><span class="sig-name descname"><span class="pre">build_pyramid</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">zarr_path</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">components</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">chunks</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">shrink</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">(-1,</span> <span class="pre">-2)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">overwrite</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.utils.zarr.build_pyramid" title="Link to this definition">¶</a></dt>
 <dd><p>Iteratively generate multiple resolutions of zarr arrays.</p>
 <p>The input array is named by the first items in the components. The remaining components are iteratively generated by
 reducing the resolution in the “shrink” dimensions, by a factor of 2.</p>
@@ -340,7 +340,24 @@ <h3>Navigation</h3>
 <dl class="py class" id="module-pytools.utils.histogram">
 <dt class="sig sig-object py" id="pytools.utils.histogram.DaskHistogramHelper">
 <em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pytools.utils.histogram.</span></span><span class="sig-name descname"><span class="pre">DaskHistogramHelper</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">arr:</span> <span class="pre">&lt;module</span> <span class="pre">'dask.array'</span> <span class="pre">from</span> <span class="pre">'/opt/hostedtoolcache/Python/3.9.19/x64/lib/python3.9/site-packages/dask/array/__init__.py'&gt;</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pytools.utils.histogram.DaskHistogramHelper" title="Link to this definition">¶</a></dt>
-<dd></dd></dl>
+<dd><dl class="py method">
+<dt class="sig sig-object py" id="pytools.utils.histogram.DaskHistogramHelper.compute_histogram">
+<span class="sig-name descname"><span class="pre">compute_histogram</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">histogram_bin_edges</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">density</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</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">compute_args</span></span><span class="o"><span class="pre">=</span></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"><span class="pre">Tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">array</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">array</span><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#pytools.utils.histogram.DaskHistogramHelper.compute_histogram" title="Link to this definition">¶</a></dt>
+<dd><p>Compute the histogram of the array.</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>histogram_bin_edges</strong> – The edges of the bins. If None, the edges are computed from the array, with integers
+of 16 bits or less, the edges are computed from the dtype for exact bins.</p></li>
+<li><p><strong>density</strong> – If True, the histogram is normalized to form a probability density, otherwise the count of
+samples in each bin.</p></li>
+<li><p><strong>compute_args</strong> – Additional arguments to pass to the dask compute method.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+</dd></dl>
 
 <dl class="py class">
 <dt class="sig sig-object py" id="pytools.utils.histogram.HistogramBase">
@@ -470,7 +487,10 @@ <h3><a href="index.html">Table of Contents</a></h3>
 <li><a class="reference internal" href="#pytools.meta.is_int16"><code class="docutils literal notranslate"><span class="pre">is_int16()</span></code></a></li>
 <li><a class="reference internal" href="#pytools.utils.zarr.bin_shrink"><code class="docutils literal notranslate"><span class="pre">bin_shrink()</span></code></a></li>
 <li><a class="reference internal" href="#pytools.utils.zarr.build_pyramid"><code class="docutils literal notranslate"><span class="pre">build_pyramid()</span></code></a></li>
-<li><a class="reference internal" href="#pytools.utils.histogram.DaskHistogramHelper"><code class="docutils literal notranslate"><span class="pre">DaskHistogramHelper</span></code></a></li>
+<li><a class="reference internal" href="#pytools.utils.histogram.DaskHistogramHelper"><code class="docutils literal notranslate"><span class="pre">DaskHistogramHelper</span></code></a><ul>
+<li><a class="reference internal" href="#pytools.utils.histogram.DaskHistogramHelper.compute_histogram"><code class="docutils literal notranslate"><span class="pre">DaskHistogramHelper.compute_histogram()</span></code></a></li>
+</ul>
+</li>
 <li><a class="reference internal" href="#pytools.utils.histogram.HistogramBase"><code class="docutils literal notranslate"><span class="pre">HistogramBase</span></code></a></li>
 <li><a class="reference internal" href="#pytools.utils.histogram.ZARRHistogramHelper"><code class="docutils literal notranslate"><span class="pre">ZARRHistogramHelper</span></code></a></li>
 <li><a class="reference internal" href="#pytools.utils.histogram.histogram_robust_stats"><code class="docutils literal notranslate"><span class="pre">histogram_robust_stats()</span></code></a></li>

genindex.html

@@ -40,6 +40,7 @@ <h1 id="index">Index</h1>
 <div class="genindex-jumpbox">
  <a href="#Symbols"><strong>Symbols</strong></a>
  | <a href="#B"><strong>B</strong></a>
+ | <a href="#C"><strong>C</strong></a>
  | <a href="#D"><strong>D</strong></a>
  | <a href="#E"><strong>E</strong></a>
  | <a href="#F"><strong>F</strong></a>
@@ -124,6 +125,14 @@ <h2 id="B">B</h2>
   </ul></td>
 </tr></table>
 
+<h2 id="C">C</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api.html#pytools.utils.histogram.DaskHistogramHelper.compute_histogram">compute_histogram() (pytools.utils.histogram.DaskHistogramHelper method)</a>
+</li>
+  </ul></td>
+</tr></table>
+
 <h2 id="D">D</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>