Automatic Update

Mon Sep 25 17:44:28 UTC 2023

api.html

@@ -110,7 +110,9 @@ <h1>API<a class="headerlink" href="#api" title="Permalink to this heading"></
 </li>
 <li class="toctree-l2"><a class="reference internal" href="utils-module.html">UTILS</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="neuroglancer.html">neuroglancer module</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="neuroglancer.html#neuroglancer.gen_zarr"><code class="docutils literal notranslate"><span class="pre">gen_zarr()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="neuroglancer.html#neuroglancer.rechunk_zarr"><code class="docutils literal notranslate"><span class="pre">rechunk_zarr()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="neuroglancer.html#neuroglancer.bioformats_gen_zarr"><code class="docutils literal notranslate"><span class="pre">bioformats_gen_zarr()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="neuroglancer.html#neuroglancer.zarr_build_multiscales"><code class="docutils literal notranslate"><span class="pre">zarr_build_multiscales()</span></code></a></li>
 </ul>
 </li>
 <li class="toctree-l3"><a class="reference internal" href="utils.html">utils module</a><ul>

em_workflows.html

@@ -118,7 +118,9 @@ <h1>em_workflows<a class="headerlink" href="#em-workflows" title="Permalink to t
 </li>
 <li class="toctree-l1"><a class="reference internal" href="utils-module.html">UTILS</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="neuroglancer.html">neuroglancer module</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="neuroglancer.html#neuroglancer.gen_zarr"><code class="docutils literal notranslate"><span class="pre">gen_zarr()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="neuroglancer.html#neuroglancer.rechunk_zarr"><code class="docutils literal notranslate"><span class="pre">rechunk_zarr()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="neuroglancer.html#neuroglancer.bioformats_gen_zarr"><code class="docutils literal notranslate"><span class="pre">bioformats_gen_zarr()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="neuroglancer.html#neuroglancer.zarr_build_multiscales"><code class="docutils literal notranslate"><span class="pre">zarr_build_multiscales()</span></code></a></li>
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="utils.html">utils module</a><ul>

genindex.html

@@ -107,6 +107,10 @@ <h2 id="A">A</h2>
 
 <h2 id="B">B</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="neuroglancer.html#neuroglancer.bioformats_gen_zarr">bioformats_gen_zarr() (in module neuroglancer)</a>
+</li>
+  </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li>
     brt.flow
@@ -247,8 +251,6 @@ <h2 id="G">G</h2>
       <li><a href="brt_flow.html#brt.flow.gen_tilt_movie">gen_tilt_movie() (in module brt.flow)</a>
 </li>
       <li><a href="sem_flow.html#sem_tomo.flow.gen_xfalign_comand">gen_xfalign_comand() (in module sem_tomo.flow)</a>
-</li>
-      <li><a href="neuroglancer.html#neuroglancer.gen_zarr">gen_zarr() (in module neuroglancer)</a>
 </li>
       <li><a href="file_path.html#file_path.FilePath.get_environment">get_environment() (file_path.FilePath method)</a>
 
@@ -344,6 +346,8 @@ <h2 id="N">N</h2>
 <h2 id="R">R</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="neuroglancer.html#neuroglancer.rechunk_zarr">rechunk_zarr() (in module neuroglancer)</a>
+</li>
       <li><a href="file_path.html#file_path.FilePath.rm_workdir">rm_workdir() (file_path.FilePath method)</a>
 </li>
   </ul></td>
@@ -419,6 +423,10 @@ <h2 id="Z">Z</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="utils.html#utils.Header.z">z (utils.Header attribute)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="neuroglancer.html#neuroglancer.zarr_build_multiscales">zarr_build_multiscales() (in module neuroglancer)</a>
 </li>
   </ul></td>
 </tr></table>

neuroglancer.html

@@ -95,15 +95,33 @@
   <section id="module-neuroglancer">
 <span id="neuroglancer-module"></span><h1>neuroglancer module<a class="headerlink" href="#module-neuroglancer" title="Permalink to this heading"></a></h1>
 <dl class="py function">
-<dt class="sig sig-object py" id="neuroglancer.gen_zarr">
-<span class="sig-prename descclassname"><span class="pre">neuroglancer.</span></span><span class="sig-name descname"><span class="pre">gen_zarr</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fp_in</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="file_path.html#file_path.FilePath" title="file_path.FilePath"><span class="pre">FilePath</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">width</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">height</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">depth</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</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> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">Dict:</span></span></span><a class="headerlink" href="#neuroglancer.gen_zarr" title="Permalink to this definition"></a></dt>
-<dd><div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">bioformats2raw</span> <span class="o">--</span><span class="n">scale</span><span class="o">-</span><span class="nb">format</span><span class="o">-</span><span class="n">string</span> <span class="s1">&#39;%2$d&#39;</span> <span class="o">--</span><span class="n">compression</span><span class="o">=</span><span class="n">blosc</span> <span class="o">--</span><span class="n">compression</span><span class="o">-</span><span class="n">properties</span> <span class="n">cname</span><span class="o">=</span><span class="n">zstd</span>
-               <span class="o">--</span><span class="n">compression</span><span class="o">-</span><span class="n">properties</span> <span class="n">clevel</span><span class="o">=</span><span class="mi">5</span> <span class="o">--</span><span class="n">compression</span><span class="o">-</span><span class="n">properties</span> <span class="n">shuffle</span><span class="o">=</span><span class="mi">1</span>  <span class="o">--</span><span class="n">resolutions</span> <span class="mi">1</span>
-               <span class="o">--</span><span class="n">chunk_depth</span> <span class="mi">128</span> <span class="o">--</span><span class="n">tile_width</span> <span class="mi">128</span> <span class="o">--</span><span class="n">tile_height</span> <span class="mi">128</span> <span class="nb">input</span><span class="o">.</span><span class="n">mrc</span> <span class="n">output</span><span class="o">.</span><span class="n">zarr</span>
-</pre></div>
-</div>
+<dt class="sig sig-object py" id="neuroglancer.rechunk_zarr">
+<span class="sig-prename descclassname"><span class="pre">neuroglancer.</span></span><span class="sig-name descname"><span class="pre">rechunk_zarr</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">zarr_fp</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Path</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">None</span></span></span><a class="headerlink" href="#neuroglancer.rechunk_zarr" title="Permalink to this definition"></a></dt>
+<dd></dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="neuroglancer.bioformats_gen_zarr">
+<span class="sig-prename descclassname"><span class="pre">neuroglancer.</span></span><span class="sig-name descname"><span class="pre">bioformats_gen_zarr</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">file_path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">FilePath</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">input_fname</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rechunk</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</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">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">width</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="n"><span class="pre">height</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="n"><span class="pre">resolutions</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="n"><span class="pre">depth</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="#neuroglancer.bioformats_gen_zarr" title="Permalink to this definition"></a></dt>
+<dd><p>Following params alter based on what kind of flow is running…</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_fname</strong> – Depending on the flow, input fname might be different</p></li>
+<li><p><strong>rechunk</strong> – Rechunk zarrs if required</p></li>
+<li><p><strong>width</strong> – </p></li>
+<li><p><strong>height</strong> – </p></li>
+<li><p><strong>resolutions</strong> – </p></li>
+<li><p><strong>depth</strong> – These arguments are only used by BRT and SEM flows</p></li>
+</ul>
+</dd>
+</dl>
 </dd></dl>
 
+<dl class="py function">
+<dt class="sig sig-object py" id="neuroglancer.zarr_build_multiscales">
+<span class="sig-prename descclassname"><span class="pre">neuroglancer.</span></span><span class="sig-name descname"><span class="pre">zarr_build_multiscales</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">file_path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">FilePath</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">None</span></span></span><a class="headerlink" href="#neuroglancer.zarr_build_multiscales" title="Permalink to this definition"></a></dt>
+<dd></dd></dl>
+
 </section>
 
 

utils-module.html

@@ -96,7 +96,9 @@ <h1>UTILS<a class="headerlink" href="#utils" title="Permalink to this heading">
 <div class="toctree-wrapper compound">
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="neuroglancer.html">neuroglancer module</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="neuroglancer.html#neuroglancer.gen_zarr"><code class="docutils literal notranslate"><span class="pre">gen_zarr()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="neuroglancer.html#neuroglancer.rechunk_zarr"><code class="docutils literal notranslate"><span class="pre">rechunk_zarr()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="neuroglancer.html#neuroglancer.bioformats_gen_zarr"><code class="docutils literal notranslate"><span class="pre">bioformats_gen_zarr()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="neuroglancer.html#neuroglancer.zarr_build_multiscales"><code class="docutils literal notranslate"><span class="pre">zarr_build_multiscales()</span></code></a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="utils.html">utils module</a><ul>