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janelia-cellmap · Jan 10, 2025 · 0f2083a · 0f2083a
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diff --git a/_modules/cellmap_data/dataloader.html b/_modules/cellmap_data/dataloader.html
@@ -29,7 +29,7 @@
   <link href="../../_static/styles/theme.css?digest=8878045cc6db502f8baf" rel="stylesheet" />
 <link href="../../_static/styles/pydata-sphinx-theme.css?digest=8878045cc6db502f8baf" rel="stylesheet" />
 
-    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=a746c00c" />
+    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=8f2a1f02" />
     <link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-book-theme.css?v=a3416100" />
 
   <!-- So that users can add custom icons -->
@@ -250,17 +250,17 @@ <h1></h1>
                 <article class="bd-article">
 
   <h1>Source code for cellmap_data.dataloader</h1><div class="highlight"><pre>
-<span></span><span class="kn">import</span> <span class="nn">torch</span>
-<span class="kn">from</span> <span class="nn">torch.utils.data</span> <span class="kn">import</span> <span class="n">DataLoader</span><span class="p">,</span> <span class="n">Sampler</span><span class="p">,</span> <span class="n">Subset</span>
-<span class="kn">from</span> <span class="nn">.dataset</span> <span class="kn">import</span> <span class="n">CellMapDataset</span>
-<span class="kn">from</span> <span class="nn">.multidataset</span> <span class="kn">import</span> <span class="n">CellMapMultiDataset</span>
-<span class="kn">from</span> <span class="nn">.dataset_writer</span> <span class="kn">import</span> <span class="n">CellMapDatasetWriter</span>
-<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Callable</span><span class="p">,</span> <span class="n">Iterable</span><span class="p">,</span> <span class="n">Optional</span><span class="p">,</span> <span class="n">Sequence</span>
+<span></span><span class="kn">import</span><span class="w"> </span><span class="nn">torch</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">torch.utils.data</span><span class="w"> </span><span class="kn">import</span> <span class="n">DataLoader</span><span class="p">,</span> <span class="n">Sampler</span><span class="p">,</span> <span class="n">Subset</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.dataset</span><span class="w"> </span><span class="kn">import</span> <span class="n">CellMapDataset</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.multidataset</span><span class="w"> </span><span class="kn">import</span> <span class="n">CellMapMultiDataset</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.dataset_writer</span><span class="w"> </span><span class="kn">import</span> <span class="n">CellMapDatasetWriter</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">typing</span><span class="w"> </span><span class="kn">import</span> <span class="n">Callable</span><span class="p">,</span> <span class="n">Iterable</span><span class="p">,</span> <span class="n">Optional</span><span class="p">,</span> <span class="n">Sequence</span>
 
 
 <div class="viewcode-block" id="CellMapDataLoader">
 <a class="viewcode-back" href="../../cellmap_data.dataloader.html#cellmap_data.CellMapDataLoader">[docs]</a>
-<span class="k">class</span> <span class="nc">CellMapDataLoader</span><span class="p">:</span>
+<span class="k">class</span><span class="w"> </span><span class="nc">CellMapDataLoader</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Utility class to create a DataLoader for a CellMapDataset or CellMapMultiDataset.</span>
 
@@ -284,7 +284,7 @@ <h1>Source code for cellmap_data.dataloader</h1><div class="highlight"><pre>
 
 <div class="viewcode-block" id="CellMapDataLoader.__init__">
 <a class="viewcode-back" href="../../cellmap_data.CellMapDataLoader.html#cellmap_data.CellMapDataLoader.__init__">[docs]</a>
-    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+    <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span>
         <span class="bp">self</span><span class="p">,</span>
         <span class="n">dataset</span><span class="p">:</span> <span class="n">CellMapMultiDataset</span> <span class="o">|</span> <span class="n">CellMapDataset</span> <span class="o">|</span> <span class="n">Subset</span> <span class="o">|</span> <span class="n">CellMapDatasetWriter</span><span class="p">,</span>
         <span class="n">classes</span><span class="p">:</span> <span class="n">Iterable</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span>
@@ -358,14 +358,14 @@ <h1>Source code for cellmap_data.dataloader</h1><div class="highlight"><pre>
 
 <div class="viewcode-block" id="CellMapDataLoader.__getitem__">
 <a class="viewcode-back" href="../../cellmap_data.dataloader.html#cellmap_data.CellMapDataLoader.__getitem__">[docs]</a>
-    <span class="k">def</span> <span class="fm">__getitem__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">indices</span><span class="p">:</span> <span class="n">Sequence</span><span class="p">[</span><span class="nb">int</span><span class="p">])</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">:</span>
+    <span class="k">def</span><span class="w"> </span><span class="fm">__getitem__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">indices</span><span class="p">:</span> <span class="n">Sequence</span><span class="p">[</span><span class="nb">int</span><span class="p">])</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">:</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;Get an item from the DataLoader.&quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">collate_fn</span><span class="p">([</span><span class="bp">self</span><span class="o">.</span><span class="n">loader</span><span class="o">.</span><span class="n">dataset</span><span class="p">[</span><span class="n">index</span><span class="p">]</span> <span class="k">for</span> <span class="n">index</span> <span class="ow">in</span> <span class="n">indices</span><span class="p">])</span></div>
 
 
 <div class="viewcode-block" id="CellMapDataLoader.refresh">
 <a class="viewcode-back" href="../../cellmap_data.dataloader.html#cellmap_data.CellMapDataLoader.refresh">[docs]</a>
-    <span class="k">def</span> <span class="nf">refresh</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+    <span class="k">def</span><span class="w"> </span><span class="nf">refresh</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;If the sampler is a Callable, refresh the DataLoader with the current sampler.&quot;&quot;&quot;</span>
         <span class="n">kwargs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">default_kwargs</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
         <span class="n">kwargs</span><span class="o">.</span><span class="n">update</span><span class="p">(</span>
@@ -390,7 +390,7 @@ <h1>Source code for cellmap_data.dataloader</h1><div class="highlight"><pre>
 
 <div class="viewcode-block" id="CellMapDataLoader.collate_fn">
 <a class="viewcode-back" href="../../cellmap_data.dataloader.html#cellmap_data.CellMapDataLoader.collate_fn">[docs]</a>
-    <span class="k">def</span> <span class="nf">collate_fn</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">batch</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">dict</span><span class="p">])</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">torch</span><span class="o">.</span><span class="n">Tensor</span><span class="p">]:</span>
+    <span class="k">def</span><span class="w"> </span><span class="nf">collate_fn</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">batch</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">dict</span><span class="p">])</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">torch</span><span class="o">.</span><span class="n">Tensor</span><span class="p">]:</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;Combine a list of dictionaries from different sources into a single dictionary for output.&quot;&quot;&quot;</span>
         <span class="n">outputs</span> <span class="o">=</span> <span class="p">{}</span>
         <span class="k">for</span> <span class="n">b</span> <span class="ow">in</span> <span class="n">batch</span><span class="p">:</span>