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commit 7a5434f08a361e19df8997496fd4d6cac400ee66 Author: Fernando Cervantes Sanchez <[email protected]> Date: Wed May 8 10:50:25 2024 -0400 Created documentation from source commit 6ff5f6239ddb89b5ff8228a956e3ca646fe34465 Merge: dd6a056 4afb0bd Author: Fernando Cervantes Sanchez <[email protected]> Date: Wed May 8 10:47:32 2024 -0400 Merge branch 'main' into gh-pages-dev commit dd6a0562351c8554ad7d31dcf41f16eb9ad5e6c7 Author: Fernando Cervantes Sanchez <[email protected]> Date: Wed May 8 10:46:43 2024 -0400 Added example for PatchSampler for inference commit 77311f42a0c7e74345f6a743ae4e1d5f5e5c16b6 Merge: 861fe51 fb57026 Author: Fernando Cervantes Sanchez <[email protected]> Date: Tue May 7 17:21:45 2024 -0400 Merge branch 'main' into gh-pages-dev commit 4afb0bd Author: Fernando Cervantes Sanchez <[email protected]> Date: Tue May 7 17:01:57 2024 -0400 Added example notebook to documentation commit 0f1d718 Author: Fernando Cervantes Sanchez <[email protected]> Date: Tue May 7 16:32:16 2024 -0400 Standardized patch sampling method to handle smaller and bigger mask scales than image scale commit 61995e2 Author: Fernando Cervantes Sanchez <[email protected]> Date: Thu May 2 15:59:57 2024 -0400 Fixed patch slices generation in PatchSampler to always retrieve patches of the defined shape commit 784906f Author: Fernando Cervantes Sanchez <[email protected]> Date: Thu May 2 10:38:54 2024 -0400 Added tests for stride and pad parameters of PatchSampler class commit 149cfc2 Author: Fernando Cervantes Sanchez <[email protected]> Date: Wed May 1 16:26:04 2024 -0400 Padding and stride added to PatchSampler and ImageBase classes to allow overlapping patches extraction commit 0de4ad1 Author: Fernando Cervantes Sanchez <[email protected]> Date: Tue Apr 30 10:51:24 2024 -0400 Fixed missing patches from chunks smaller than the input image chunk size commit bf8aae6 Author: Fernando Cervantes Sanchez <[email protected]> Date: Fri Apr 5 11:55:35 2024 -0400 Fixed spatial chunk size computation when patch sizes are grater than the chunk size commit 3a53ef5 Author: Fernando Cervantes Sanchez <[email protected]> Date: Fri Mar 29 16:46:02 2024 -0400 Reverted change in the computation when masks elements are relative smaller than patch sizes commit 43c2942 Author: Fernando Cervantes Sanchez <[email protected]> Date: Fri Mar 29 14:46:38 2024 -0400 Changed PatchSampler to take as base the patche size instead of the input image's chunk sizes commit fb57026 Author: Fernando Cervantes Sanchez <[email protected]> Date: Fri Oct 6 14:04:50 2023 -0400 Integration of CI/CD practices (#2) * Integration CI/CD pipeline to this project * Corrected github actions test workflow * Install the package before test it * Created empty __init__.py inside tests to record coverage * Changed name of sample_images_generator.py to utils.py for clarity * Updated test workflow to use a non-supported workaround for the multiple OpenMP runtime library issue * Updated test workflow to report coverage * Moved non-pytorch compatibility test to last position * Added test for datasets with zero expected samples
TheJacksonLaboratory · May 8, 2024 · 03df904 · 03df904
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diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
@@ -0,0 +1,31 @@
+name: Run Tests on push
+on: [push, pull_request, workflow_dispatch]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
+
+      - name: Install ependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install torch==1.13.1+cpu torchvision==0.14.1+cpu --extra-index-url https://download.pytorch.org/whl/cpu
+          pip install tqdm==4.66.1
+          pip install tifffile==2023.9.26
+          pip install .
+
+      - name: Test with pytest
+        run: |
+          pip install pytest pytest-cov
+          # When using pytest and pytorch at the same time, an error of multiple copied of OpenMP runtime library will rise.
+          # This is a well known issue and is the reason of why pytorch uses unitest for testing and not pytest.
+          # This is a non-recomended, non-supported, and therefore non-elegant solution for that problem, but at least let run the test suite.
+          export KMP_DUPLICATE_LIB_OK=TRUE
+          pytest tests --cov=zarrdataset
+          coverage report -m
diff --git a/.gitignore b/.gitignore
@@ -50,6 +50,7 @@ coverage.xml
 *.py,cover
 .hypothesis/
 .pytest_cache/
+example.py
 
 # Translations
 *.mo

diff --git a/docs/.buildinfo b/docs/.buildinfo
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diff --git a/docs/_modules/index.html b/docs/_modules/index.html
@@ -1,23 +1,24 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Overview: module code &mdash; ZarrDataset  documentation</title>
-      <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/graphviz.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=80d5e7a1" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
+      <link rel="stylesheet" type="text/css" href="../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=fd3f3429" />
+
+
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-        <script src="../_static/doctools.js"></script>
-        <script src="../_static/sphinx_highlight.js"></script>
+        <script src="../_static/jquery.js?v=5d32c60e"></script>
+        <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+        <script src="../_static/documentation_options.js?v=5929fcd5"></script>
+        <script src="../_static/doctools.js?v=9a2dae69"></script>
+        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" /> 
@@ -55,6 +56,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../examples/advanced_masked_datasets_example.html">Custom masks for sampling specific regions from images with ZarrDataset</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../examples/basic_labeled_datasets_example.html">Labeled dataset loading with ZarrDataset</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../examples/advanced_example_pytorch.html">Integration of ZarrDataset with PyTorch’s DataLoader (Advanced)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../examples/advanced_example_pytorch_inference.html">Integration of ZarrDataset with PyTorch’s DataLoader for inference (Advanced)</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
 <ul>

diff --git a/docs/_modules/zarrdataset/_augs.html b/docs/_modules/zarrdataset/_augs.html
@@ -1,23 +1,24 @@
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@@ -55,6 +56,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../examples/advanced_masked_datasets_example.html">Custom masks for sampling specific regions from images with ZarrDataset</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../examples/basic_labeled_datasets_example.html">Labeled dataset loading with ZarrDataset</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../examples/advanced_example_pytorch.html">Integration of ZarrDataset with PyTorch’s DataLoader (Advanced)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../examples/advanced_example_pytorch_inference.html">Integration of ZarrDataset with PyTorch’s DataLoader for inference (Advanced)</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
 <ul>
@@ -92,7 +94,9 @@ <h1>Source code for zarrdataset._augs</h1><div class="highlight"><pre>
 <span></span><span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
 
 
-<div class="viewcode-block" id="ToDtype"><a class="viewcode-back" href="../../autoapi/zarrdataset/index.html#zarrdataset._augs.ToDtype">[docs]</a><span class="k">class</span> <span class="nc">ToDtype</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+<div class="viewcode-block" id="ToDtype">
+<a class="viewcode-back" href="../../autoapi/zarrdataset/index.html#zarrdataset._augs.ToDtype">[docs]</a>
+<span class="k">class</span> <span class="nc">ToDtype</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Converted a numpy NDArray to the specified data type.</span>
 
 <span class="sd">    Parameters</span>
@@ -103,7 +107,9 @@ <h1>Source code for zarrdataset._augs</h1><div class="highlight"><pre>
     <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">dtype</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">dtype</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_dtype</span> <span class="o">=</span> <span class="n">dtype</span>
 
-<div class="viewcode-block" id="ToDtype.__call__"><a class="viewcode-back" href="../../autoapi/zarrdataset/index.html#zarrdataset._augs.ToDtype.__call__">[docs]</a>    <span class="k">def</span> <span class="fm">__call__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">image</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">-&gt;</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">:</span>
+<div class="viewcode-block" id="ToDtype.__call__">
+<a class="viewcode-back" href="../../autoapi/zarrdataset/index.html#zarrdataset._augs.ToDtype.__call__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__call__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">image</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">-&gt;</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">:</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;Casts the type of `image` to the data type specified with `dtype`.</span>
 
 <span class="sd">        Parameters</span>
@@ -119,8 +125,13 @@ <h1>Source code for zarrdataset._augs</h1><div class="highlight"><pre>
         <span class="n">casted_image</span> <span class="o">=</span> <span class="n">image</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_dtype</span><span class="p">)</span>
         <span class="k">return</span> <span class="n">casted_image</span></div>
 
-<div class="viewcode-block" id="ToDtype.__repr__"><a class="viewcode-back" href="../../autoapi/zarrdataset/index.html#zarrdataset._augs.ToDtype.__repr__">[docs]</a>    <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
-        <span class="k">return</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="si">}</span><span class="s2">(dtype=</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">_dtype</span><span class="si">}</span><span class="s2">)&quot;</span></div></div>
+
+<div class="viewcode-block" id="ToDtype.__repr__">
+<a class="viewcode-back" href="../../autoapi/zarrdataset/index.html#zarrdataset._augs.ToDtype.__repr__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
+        <span class="k">return</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="si">}</span><span class="s2">(dtype=</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">_dtype</span><span class="si">}</span><span class="s2">)&quot;</span></div>
+</div>
+
 </pre></div>
 
            </div>