napari plugin, QOL and refactors

ucsdmanorlab · Jun 1, 2024 · 20415cf · 20415cf
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diff --git a/.gitignore b/.gitignore
@@ -4,6 +4,7 @@ preds/
 trained/
 imports/
 model_testing/
+testnapari/
 
 *.pth
 *.lock

diff --git a/.napari-hub/DESCRIPTION.md b/.napari-hub/DESCRIPTION.md
@@ -0,0 +1,2 @@
+**PSSR** is a standardized PyTorch-based workflow for super-resolution tasks using microscopy images.
+The **PSSR** User Guide and full API Reference is available in the [PSSR Documentation](https://ucsdmanorlab.github.io/PSSR).
diff --git a/README.md b/README.md
@@ -9,5 +9,5 @@ The **PSSR** User Guide and full API Reference is available in the [PSSR Documen
 If you have never used **PSSR** before, [Getting Started](https://ucsdmanorlab.github.io/PSSR/guide/start.html) outlines installation and basic usage.
 Full reference and explanations of all **PSSR** tools is available in [API Reference](https://ucsdmanorlab.github.io/PSSR/reference/api.html).
 
-The package is still in development. All code can be found at [https://github.com/ucsdmanorlab/PSSR](https://github.com/ucsdmanorlab/PSSR).
+This package is under continuous development. All code can be found at [https://github.com/ucsdmanorlab/PSSR](https://github.com/ucsdmanorlab/PSSR).
 If you experience any bugs, unexpected behaviors, or have any suggestions, make sure to [open a ticket](https://github.com/ucsdmanorlab/PSSR/issues).
diff --git a/dist/pssr-2.0.0-py3-none-any.whl b/dist/pssr-2.0.0-py3-none-any.whl
diff --git a/dist/pssr-2.0.0.tar.gz b/dist/pssr-2.0.0.tar.gz
diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle
diff --git a/docs/build/doctrees/guide/start.doctree b/docs/build/doctrees/guide/start.doctree
diff --git a/docs/build/doctrees/guide/workflow.doctree b/docs/build/doctrees/guide/workflow.doctree
diff --git a/docs/build/doctrees/index.doctree b/docs/build/doctrees/index.doctree
diff --git a/docs/build/doctrees/reference/CLI.doctree b/docs/build/doctrees/reference/CLI.doctree
diff --git a/docs/build/doctrees/reference/api.doctree b/docs/build/doctrees/reference/api.doctree
diff --git a/docs/build/doctrees/reference/crappifiers/MultiCrappifier.doctree b/docs/build/doctrees/reference/crappifiers/MultiCrappifier.doctree
diff --git a/docs/build/doctrees/reference/data/ImageDataset.doctree b/docs/build/doctrees/reference/data/ImageDataset.doctree
diff --git a/docs/build/doctrees/reference/data/PairedImageDataset.doctree b/docs/build/doctrees/reference/data/PairedImageDataset.doctree
diff --git a/docs/build/doctrees/reference/data/PairedSlidingDataset.doctree b/docs/build/doctrees/reference/data/PairedSlidingDataset.doctree
diff --git a/docs/build/doctrees/reference/data/SlidingDataset.doctree b/docs/build/doctrees/reference/data/SlidingDataset.doctree
diff --git a/docs/build/doctrees/reference/models/RDResUNet.doctree b/docs/build/doctrees/reference/models/RDResUNet.doctree
diff --git a/docs/build/doctrees/reference/models/ResUNet.doctree b/docs/build/doctrees/reference/models/ResUNet.doctree
diff --git a/docs/build/doctrees/reference/models/SwinIR.doctree b/docs/build/doctrees/reference/models/SwinIR.doctree
diff --git a/docs/build/doctrees/reference/predict/predict_collage.doctree b/docs/build/doctrees/reference/predict/predict_collage.doctree
diff --git a/docs/build/doctrees/reference/predict/predict_images.doctree b/docs/build/doctrees/reference/predict/predict_images.doctree
diff --git a/docs/build/doctrees/reference/predict/test_metrics.doctree b/docs/build/doctrees/reference/predict/test_metrics.doctree
diff --git a/docs/build/doctrees/reference/train/train_crappifier.doctree b/docs/build/doctrees/reference/train/train_crappifier.doctree
diff --git a/docs/build/doctrees/reference/train/train_paired.doctree b/docs/build/doctrees/reference/train/train_paired.doctree
diff --git a/docs/build/doctrees/reference/loss.doctree → docs/build/doctrees/reference/util.doctree b/docs/build/doctrees/reference/loss.doctree → docs/build/doctrees/reference/util.doctree
diff --git a/.../doctrees/reference/loss/SSIMLoss.doctree → .../doctrees/reference/util/SSIMLoss.doctree b/.../doctrees/reference/loss/SSIMLoss.doctree → .../doctrees/reference/util/SSIMLoss.doctree
diff --git a/...trees/reference/loss/pixel_metric.doctree → ...trees/reference/util/pixel_metric.doctree b/...trees/reference/loss/pixel_metric.doctree → ...trees/reference/util/pixel_metric.doctree
diff --git a/docs/build/html/.buildinfo b/docs/build/html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: bc6c4eaf27447939c9b4e682dd233c06
+config: 5c492d92e36c65983af02d00b702c744
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/build/html/_sources/guide/start.rst.txt b/docs/build/html/_sources/guide/start.rst.txt
@@ -23,7 +23,7 @@ You can easily install **PSSR** via the ``pip`` package manager:
 
    $ pip install pssr
 
-However, specific versions can also be installed directly from the `GitHub <https://github.com/ucsdmanorlab/PSSR>`_ repository:
+All package versions are also available on the `GitHub <https://github.com/ucsdmanorlab/PSSR>`_ repository:
 
 .. code-block:: console
 

diff --git a/docs/build/html/_sources/guide/workflow.rst.txt b/docs/build/html/_sources/guide/workflow.rst.txt
@@ -18,7 +18,7 @@ Before diving into the code, we will first specify our imports.
     from pssr.data import ImageDataset
     from pssr.crappifiers import Poisson
     from pssr.models import ResUNet
-    from pssr.loss import SSIMLoss
+    from pssr.util import SSIMLoss
     from pssr.train import train_paired
     from torch.optim.lr_scheduler import ReduceLROnPlateau
 
@@ -91,7 +91,7 @@ We will first define our loss function.
 
     loss_fn = SSIMLoss(mix=.8, ms=True)
 
-While MSE loss can also be used to good results, we will instead use :doc:`../reference/loss/SSIMLoss` here, which will optimize visually significant elements our predictions.
+While MSE loss can also be used to good results, we will instead use :doc:`../reference/util/SSIMLoss` here, which will optimize visually significant elements our predictions.
 The ``mix`` argument controls the inverse contribution of corrected L1 loss, while the ``ms`` argument enables MS-SSIM, a more robust version of SSIM.
 
 |

diff --git a/docs/build/html/_sources/index.rst.txt b/docs/build/html/_sources/index.rst.txt
@@ -8,7 +8,7 @@ containing various improvements and new features.
 If you have never used **PSSR** before, :doc:`guide/start` outlines installation and basic usage.
 Full reference and explanations of all **PSSR** tools is available in :doc:`API Reference <reference/api>`.
 
-The package is still in development. All code can be found at `https://github.com/ucsdmanorlab/PSSR <https://github.com/ucsdmanorlab/PSSR>`_.
+This package is under continuous development. All code can be found at `https://github.com/ucsdmanorlab/PSSR <https://github.com/ucsdmanorlab/PSSR>`_.
 If you experience any bugs, unexpected behaviors, or have any suggestions, make sure to `open a ticket <https://github.com/ucsdmanorlab/PSSR/issues>`_.
 
 

diff --git a/docs/build/html/_sources/reference/api.rst.txt b/docs/build/html/_sources/reference/api.rst.txt
@@ -11,5 +11,5 @@ pssr
    data
    crappifiers
    models
-   loss
+   util
    CLI
diff --git a/docs/build/html/_sources/reference/loss.rst.txt b/docs/build/html/_sources/reference/loss.rst.txt
diff --git a/docs/build/html/_sources/reference/loss/SSIMLoss.rst.txt b/docs/build/html/_sources/reference/loss/SSIMLoss.rst.txt
diff --git a/docs/build/html/_sources/reference/loss/pixel_metric.rst.txt b/docs/build/html/_sources/reference/loss/pixel_metric.rst.txt
diff --git a/docs/build/html/_static/documentation_options.js b/docs/build/html/_static/documentation_options.js
@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '1.2.2',
+    VERSION: '2.0.0',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

diff --git a/docs/build/html/genindex.html b/docs/build/html/genindex.html
@@ -4,7 +4,7 @@
     <meta name="viewport" content="width=device-width,initial-scale=1"/>
     <meta name="color-scheme" content="light dark"><link rel="index" title="Index" href="#" /><link rel="search" title="Search" href="search.html" />
 
-    <!-- Generated with Sphinx 7.2.6 and Furo 2024.01.29 --><title>Index - PSSR 1.2.2 documentation</title>
+    <!-- Generated with Sphinx 7.2.6 and Furo 2024.01.29 --><title>Index - PSSR 2.0.0 documentation</title>
 <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=362ab14a" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo.css?v=135e06be" />
     <link rel="stylesheet" type="text/css" href="_static/design-style.1e8bd061cd6da7fc9cf755528e8ffc24.min.css?v=0a3b3ea7" />
@@ -122,7 +122,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="index.html"><div class="brand">PSSR 1.2.2 documentation</div></a>
+      <a href="index.html"><div class="brand">PSSR 2.0.0 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -145,7 +145,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand" href="index.html">
 
 
-  <span class="sidebar-brand-text">PSSR 1.2.2 documentation</span>
+  <span class="sidebar-brand-text">PSSR 2.0.0 documentation</span>
 
 </a><form class="sidebar-search-container" method="get" action="search.html" role="search">
   <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
@@ -197,9 +197,9 @@
 <li class="toctree-l3"><a class="reference internal" href="reference/models/SwinIR.html">SwinIR</a></li>
 </ul>
 </li>
-<li class="toctree-l2 has-children"><a class="reference internal" href="reference/loss.html">loss</a><input class="toctree-checkbox" id="toctree-checkbox-7" name="toctree-checkbox-7" role="switch" type="checkbox"/><label for="toctree-checkbox-7"><div class="visually-hidden">Toggle navigation of loss</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
-<li class="toctree-l3"><a class="reference internal" href="reference/loss/SSIMLoss.html">SSIMLoss</a></li>
-<li class="toctree-l3"><a class="reference internal" href="reference/loss/pixel_metric.html">pixel_metric</a></li>
+<li class="toctree-l2 has-children"><a class="reference internal" href="reference/util.html">util</a><input class="toctree-checkbox" id="toctree-checkbox-7" name="toctree-checkbox-7" role="switch" type="checkbox"/><label for="toctree-checkbox-7"><div class="visually-hidden">Toggle navigation of util</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l3"><a class="reference internal" href="reference/util/SSIMLoss.html">SSIMLoss</a></li>
+<li class="toctree-l3"><a class="reference internal" href="reference/util/pixel_metric.html">pixel_metric</a></li>
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="reference/CLI.html">CLI</a></li>
@@ -263,14 +263,14 @@ <h2>_</h2>
           <li><a href="reference/data/PairedSlidingDataset.html#pssr.data.PairedSlidingDataset.__init__">(in module pssr.data.PairedSlidingDataset)</a>
 </li>
           <li><a href="reference/data/SlidingDataset.html#pssr.data.SlidingDataset.__init__">(in module pssr.data.SlidingDataset)</a>
-</li>
-          <li><a href="reference/loss/SSIMLoss.html#pssr.loss.SSIMLoss.__init__">(in module pssr.loss.SSIMLoss)</a>
 </li>
           <li><a href="reference/models/RDResUNet.html#pssr.models.RDResUNet.__init__">(in module pssr.models.RDResUNet)</a>
 </li>
           <li><a href="reference/models/ResUNet.html#pssr.models.ResUNet.__init__">(in module pssr.models.ResUNet)</a>
 </li>
           <li><a href="reference/models/SwinIR.html#pssr.models.SwinIR.__init__">(in module pssr.models.SwinIR)</a>
+</li>
+          <li><a href="reference/util/SSIMLoss.html#pssr.util.SSIMLoss.__init__">(in module pssr.util.SSIMLoss)</a>
 </li>
         </ul></li>
     </ul></td>
@@ -323,7 +323,7 @@ <h2>N</h2>
   <h2>P</h2>
   <table style="width: 100%" class="indextable genindextable"><tr>
     <td style="width: 33%; vertical-align: top;"><ul>
-        <li><a href="reference/loss/pixel_metric.html#pssr.loss.pixel_metric">pixel_metric() (in module pssr.loss)</a>
+        <li><a href="reference/util/pixel_metric.html#pssr.util.pixel_metric">pixel_metric() (in module pssr.util)</a>
 </li>
         <li><a href="reference/predict/predict_collage.html#pssr.predict.predict_collage">predict_collage() (in module pssr.predict)</a>
 </li>
@@ -385,7 +385,7 @@ <h2>T</h2>
 
     </aside>
   </div>
-</div><script src="_static/documentation_options.js?v=fd7cadf9"></script>
+</div><script src="_static/documentation_options.js?v=51b770b3"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/furo.js?v=32e29ea5"></script>

diff --git a/docs/build/html/guide/principles.html b/docs/build/html/guide/principles.html
@@ -6,7 +6,7 @@
 <link rel="index" title="Index" href="../genindex.html" /><link rel="search" title="Search" href="../search.html" /><link rel="next" title="Workflow" href="workflow.html" /><link rel="prev" title="Getting Started" href="start.html" />
 
     <!-- Generated with Sphinx 7.2.6 and Furo 2024.01.29 -->
-        <title>Principles of PSSR - PSSR 1.2.2 documentation</title>
+        <title>Principles of PSSR - PSSR 2.0.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=362ab14a" />
     <link rel="stylesheet" type="text/css" href="../_static/styles/furo.css?v=135e06be" />
     <link rel="stylesheet" type="text/css" href="../_static/design-style.1e8bd061cd6da7fc9cf755528e8ffc24.min.css?v=0a3b3ea7" />
@@ -124,7 +124,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../index.html"><div class="brand">PSSR 1.2.2 documentation</div></a>
+      <a href="../index.html"><div class="brand">PSSR 2.0.0 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -147,7 +147,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand" href="../index.html">
 
 
-  <span class="sidebar-brand-text">PSSR 1.2.2 documentation</span>
+  <span class="sidebar-brand-text">PSSR 2.0.0 documentation</span>
 
 </a><form class="sidebar-search-container" method="get" action="../search.html" role="search">
   <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
@@ -199,9 +199,9 @@
 <li class="toctree-l3"><a class="reference internal" href="../reference/models/SwinIR.html">SwinIR</a></li>
 </ul>
 </li>
-<li class="toctree-l2 has-children"><a class="reference internal" href="../reference/loss.html">loss</a><input class="toctree-checkbox" id="toctree-checkbox-7" name="toctree-checkbox-7" role="switch" type="checkbox"/><label for="toctree-checkbox-7"><div class="visually-hidden">Toggle navigation of loss</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
-<li class="toctree-l3"><a class="reference internal" href="../reference/loss/SSIMLoss.html">SSIMLoss</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../reference/loss/pixel_metric.html">pixel_metric</a></li>
+<li class="toctree-l2 has-children"><a class="reference internal" href="../reference/util.html">util</a><input class="toctree-checkbox" id="toctree-checkbox-7" name="toctree-checkbox-7" role="switch" type="checkbox"/><label for="toctree-checkbox-7"><div class="visually-hidden">Toggle navigation of util</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l3"><a class="reference internal" href="../reference/util/SSIMLoss.html">SSIMLoss</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../reference/util/pixel_metric.html">pixel_metric</a></li>
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="../reference/CLI.html">CLI</a></li>
@@ -352,7 +352,7 @@ <h2>The Crappifier<a class="headerlink" href="#the-crappifier" title="Link to th
 
     </aside>
   </div>
-</div><script src="../_static/documentation_options.js?v=fd7cadf9"></script>
+</div><script src="../_static/documentation_options.js?v=51b770b3"></script>
     <script src="../_static/doctools.js?v=888ff710"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/scripts/furo.js?v=32e29ea5"></script>

diff --git a/docs/build/html/guide/start.html b/docs/build/html/guide/start.html
@@ -6,7 +6,7 @@
 <link rel="index" title="Index" href="../genindex.html" /><link rel="search" title="Search" href="../search.html" /><link rel="next" title="Principles of PSSR" href="principles.html" /><link rel="prev" title="PSSR Documentation" href="../index.html" />
 
     <!-- Generated with Sphinx 7.2.6 and Furo 2024.01.29 -->
-        <title>Getting Started - PSSR 1.2.2 documentation</title>
+        <title>Getting Started - PSSR 2.0.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=362ab14a" />
     <link rel="stylesheet" type="text/css" href="../_static/styles/furo.css?v=135e06be" />
     <link rel="stylesheet" type="text/css" href="../_static/design-style.1e8bd061cd6da7fc9cf755528e8ffc24.min.css?v=0a3b3ea7" />
@@ -124,7 +124,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../index.html"><div class="brand">PSSR 1.2.2 documentation</div></a>
+      <a href="../index.html"><div class="brand">PSSR 2.0.0 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -147,7 +147,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand" href="../index.html">
 
 
-  <span class="sidebar-brand-text">PSSR 1.2.2 documentation</span>
+  <span class="sidebar-brand-text">PSSR 2.0.0 documentation</span>
 
 </a><form class="sidebar-search-container" method="get" action="../search.html" role="search">
   <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
@@ -199,9 +199,9 @@
 <li class="toctree-l3"><a class="reference internal" href="../reference/models/SwinIR.html">SwinIR</a></li>
 </ul>
 </li>
-<li class="toctree-l2 has-children"><a class="reference internal" href="../reference/loss.html">loss</a><input class="toctree-checkbox" id="toctree-checkbox-7" name="toctree-checkbox-7" role="switch" type="checkbox"/><label for="toctree-checkbox-7"><div class="visually-hidden">Toggle navigation of loss</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
-<li class="toctree-l3"><a class="reference internal" href="../reference/loss/SSIMLoss.html">SSIMLoss</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../reference/loss/pixel_metric.html">pixel_metric</a></li>
+<li class="toctree-l2 has-children"><a class="reference internal" href="../reference/util.html">util</a><input class="toctree-checkbox" id="toctree-checkbox-7" name="toctree-checkbox-7" role="switch" type="checkbox"/><label for="toctree-checkbox-7"><div class="visually-hidden">Toggle navigation of util</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l3"><a class="reference internal" href="../reference/util/SSIMLoss.html">SSIMLoss</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../reference/util/pixel_metric.html">pixel_metric</a></li>
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="../reference/CLI.html">CLI</a></li>
@@ -259,7 +259,7 @@ <h2>Installation<a class="headerlink" href="#installation" title="Link to this h
 <div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$ </span>pip<span class="w"> </span>install<span class="w"> </span>pssr
 </pre></div>
 </div>
-<p>However, specific versions can also be installed directly from the <a class="reference external" href="https://github.com/ucsdmanorlab/PSSR">GitHub</a> repository:</p>
+<p>All package versions are also available on the <a class="reference external" href="https://github.com/ucsdmanorlab/PSSR">GitHub</a> repository:</p>
 <div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$ </span>pip<span class="w"> </span>install<span class="w"> </span>git+https://github.com/ucsdmanorlab/PSSR/dist/pssr-x.x.x-py3-none-any.whl
 </pre></div>
 </div>
@@ -321,7 +321,7 @@ <h3>Named Arguments<a class="headerlink" href="#named-arguments" title="Link to
 <p class="sd-card-text">Default: 3</p>
 </dd>
 <dt><kbd>-mse, --mse</kbd></dt>
-<dd><p class="sd-card-text">use MSE loss instead of SSIM loss</p>
+<dd><p class="sd-card-text">use MSE loss instead of MS-SSIM loss</p>
 <p class="sd-card-text">Default: False</p>
 </dd>
 <dt><kbd>-cp, --checkpoint</kbd></dt>
@@ -476,7 +476,7 @@ <h2>Next Steps<a class="headerlink" href="#next-steps" title="Link to this headi
 
     </aside>
   </div>
-</div><script src="../_static/documentation_options.js?v=fd7cadf9"></script>
+</div><script src="../_static/documentation_options.js?v=51b770b3"></script>
     <script src="../_static/doctools.js?v=888ff710"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/scripts/furo.js?v=32e29ea5"></script>
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		PSSR is a standardized PyTorch-based workflow for super-resolution tasks using microscopy images.
		The PSSR User Guide and full API Reference is available in the [PSSR Documentation](https://ucsdmanorlab.github.io/PSSR).
-Original file line number
+Diff line change
@@ Expand Up / @@ -11,5 +11,5 @@ pssr @@
        data
        crappifiers
        models
-       loss
+       util
        CLI