PyPI - spacr - Versions diffs - 0.4.60__tar.gz → 0.9.0__tar.gz - Mend

spacr 0.4.60tar.gz → 0.9.0tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (469) hide show

{spacr-0.4.60/spacr.egg-info → spacr-0.9.0}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.4.60
+Version: 0.9.0
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson
@@ -41,6 +41,8 @@ Requires-Dist: pillow<11.0,>=10.2.0
 Requires-Dist: tifffile>=2023.4.12
 Requires-Dist: nd2reader<4.0,>=3.3.0
 Requires-Dist: czifile
+Requires-Dist: pylibCZIrw<6.0,>=5.0.0
+Requires-Dist: aicspylibczi
 Requires-Dist: readlif
 Requires-Dist: imageio<3.0,>=2.34.0
 Requires-Dist: pingouin<1.0,>=0.5.5
@@ -79,7 +81,7 @@ Provides-Extra: full
 Requires-Dist: opencv-python; extra == "full"
 .. |Documentation Status| image:: https://readthedocs.org/projects/spacr/badge/?version=latest
-   :target: https://spacr.readthedocs.io/en/latest/?badge=latest
+   :target: https://einarolafsson.github.io/spacr
 .. |PyPI version| image:: https://badge.fury.io/py/spacr.svg
    :target: https://badge.fury.io/py/spacr
 .. |Python version| image:: https://img.shields.io/pypi/pyversions/spacr

{spacr-0.4.60 → spacr-0.9.0}/README.rst RENAMED Viewed

@@ -1,5 +1,5 @@
 .. |Documentation Status| image:: https://readthedocs.org/projects/spacr/badge/?version=latest
-   :target: https://spacr.readthedocs.io/en/latest/?badge=latest
+   :target: https://einarolafsson.github.io/spacr
 .. |PyPI version| image:: https://badge.fury.io/py/spacr.svg
    :target: https://badge.fury.io/py/spacr
 .. |Python version| image:: https://img.shields.io/pypi/pyversions/spacr

spacr-0.9.0/docs/.doctrees/environment.pickle ADDED Viewed

Binary file

spacr-0.9.0/docs/_modules/SetupDict.html ADDED Viewed

@@ -0,0 +1,256 @@
+<!DOCTYPE html>
+<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>SetupDict &mdash; spacr 0.5.0 documentation</title>
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=80d5e7a1" />
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+</head>
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+        <div class="wy-side-nav-search"  style="background: #005f73" >
+          <a href="../index.html">
+              <img src="../_static/logo_spacr.png" class="logo" alt="Logo"/>
+          </a>
+<div role="search">
+  <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
+    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
+    <input type="hidden" name="check_keywords" value="yes" />
+    <input type="hidden" name="area" value="default" />
+  </form>
+</div>
+        </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="../api/index.html">API Reference</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="../api/main/index.html">main</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="../api/main/index.html#module-contents">Module Contents</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="../api/main/index.html#main.main"><code class="docutils literal notranslate"><span class="pre">main()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/main/index.html#main.parser"><code class="docutils literal notranslate"><span class="pre">parser</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/main/index.html#main.args"><code class="docutils literal notranslate"><span class="pre">args</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/main/index.html#main.opt"><code class="docutils literal notranslate"><span class="pre">opt</span></code></a></li>
+</ul>
+</li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="../api/core/index.html">core</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="../api/core/index.html#submodules">Submodules</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="../api/core/BasePredictor/index.html">core.BasePredictor</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/core/BaseTrainer/index.html">core.BaseTrainer</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/core/Baseline/index.html">core.Baseline</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/core/MEDIAR/index.html">core.MEDIAR</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/core/utils/index.html">core.utils</a></li>
+</ul>
+</li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="../api/spacr/index.html">spacr</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="../api/spacr/index.html#submodules">Submodules</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/app_annotate/index.html">spacr.app_annotate</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/app_classify/index.html">spacr.app_classify</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/app_make_masks/index.html">spacr.app_make_masks</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/app_mask/index.html">spacr.app_mask</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/app_measure/index.html">spacr.app_measure</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/app_sequencing/index.html">spacr.app_sequencing</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/app_umap/index.html">spacr.app_umap</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/chat_bot/index.html">spacr.chat_bot</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/core/index.html">spacr.core</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/deep_spacr/index.html">spacr.deep_spacr</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/gui/index.html">spacr.gui</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/gui_core/index.html">spacr.gui_core</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/gui_elements/index.html">spacr.gui_elements</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/gui_utils/index.html">spacr.gui_utils</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/io/index.html">spacr.io</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/logger/index.html">spacr.logger</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/measure/index.html">spacr.measure</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/mediar/index.html">spacr.mediar</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/ml/index.html">spacr.ml</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/openai/index.html">spacr.openai</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/plot/index.html">spacr.plot</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/sequencing/index.html">spacr.sequencing</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/settings/index.html">spacr.settings</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/sim/index.html">spacr.sim</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/sp_stats/index.html">spacr.sp_stats</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/spacr_cellpose/index.html">spacr.spacr_cellpose</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/submodules/index.html">spacr.submodules</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/timelapse/index.html">spacr.timelapse</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/toxo/index.html">spacr.toxo</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/utils/index.html">spacr.utils</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/version/index.html">spacr.version</a></li>
+</ul>
+</li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="../api/predict/index.html">predict</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="../api/predict/index.html#module-contents">Module Contents</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="../api/predict/index.html#predict.main"><code class="docutils literal notranslate"><span class="pre">main()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/predict/index.html#predict.parser"><code class="docutils literal notranslate"><span class="pre">parser</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/predict/index.html#predict.args"><code class="docutils literal notranslate"><span class="pre">args</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/predict/index.html#predict.opt"><code class="docutils literal notranslate"><span class="pre">opt</span></code></a></li>
+</ul>
+</li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="../api/evaluate/index.html">evaluate</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="../api/evaluate/index.html#module-contents">Module Contents</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="../api/evaluate/index.html#evaluate.main"><code class="docutils literal notranslate"><span class="pre">main()</span></code></a></li>
+</ul>
+</li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="../api/SetupDict/index.html">SetupDict</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="../api/SetupDict/index.html#module-contents">Module Contents</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="../api/SetupDict/index.html#SetupDict.TRAINER"><code class="docutils literal notranslate"><span class="pre">TRAINER</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/SetupDict/index.html#SetupDict.OPTIMIZER"><code class="docutils literal notranslate"><span class="pre">OPTIMIZER</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/SetupDict/index.html#SetupDict.SCHEDULER"><code class="docutils literal notranslate"><span class="pre">SCHEDULER</span></code></a></li>
+</ul>
+</li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="../api/train_tools/index.html">train_tools</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="../api/train_tools/index.html#submodules">Submodules</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="../api/train_tools/data_utils/index.html">train_tools.data_utils</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/train_tools/measures/index.html">train_tools.measures</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/train_tools/models/index.html">train_tools.models</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/train_tools/utils/index.html">train_tools.utils</a></li>
+</ul>
+</li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="../api/generate_mapping/index.html">generate_mapping</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="../api/generate_mapping/index.html#module-contents">Module Contents</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="../api/generate_mapping/index.html#generate_mapping.public_paths_labeled"><code class="docutils literal notranslate"><span class="pre">public_paths_labeled()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/generate_mapping/index.html#generate_mapping.official_paths_labeled"><code class="docutils literal notranslate"><span class="pre">official_paths_labeled()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/generate_mapping/index.html#generate_mapping.official_paths_tuning"><code class="docutils literal notranslate"><span class="pre">official_paths_tuning()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/generate_mapping/index.html#generate_mapping.add_mapping_to_json"><code class="docutils literal notranslate"><span class="pre">add_mapping_to_json()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/generate_mapping/index.html#generate_mapping.parser"><code class="docutils literal notranslate"><span class="pre">parser</span></code></a></li>
+</ul>
+</li>
+</ul>
+</li>
+</ul>
+</li>
+</ul>
+        </div>
+      </div>
+    </nav>
+    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu"  style="background: #005f73" >
+          <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+          <a href="../index.html">spacr</a>
+      </nav>
+      <div class="wy-nav-content">
+        <div class="rst-content">
+          <div role="navigation" aria-label="Page navigation">
+  <ul class="wy-breadcrumbs">
+      <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
+          <li class="breadcrumb-item"><a href="index.html">Module code</a></li>
+      <li class="breadcrumb-item active">SetupDict</li>
+      <li class="wy-breadcrumbs-aside">
+      </li>
+  </ul>
+  <hr/>
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+  <h1>Source code for SetupDict</h1><div class="highlight"><pre>
+<span></span><span class="kn">import</span> <span class="nn">torch.optim</span> <span class="k">as</span> <span class="nn">optim</span>
+<span class="kn">import</span> <span class="nn">torch.optim.lr_scheduler</span> <span class="k">as</span> <span class="nn">lr_scheduler</span>
+<span class="kn">import</span> <span class="nn">monai</span>
+<span class="kn">import</span> <span class="nn">core</span>
+<span class="kn">from</span> <span class="nn">train_tools</span> <span class="kn">import</span> <span class="n">models</span>
+<span class="kn">from</span> <span class="nn">train_tools.models</span> <span class="kn">import</span> <span class="o">*</span>
+<span class="n">__all__</span> <span class="o">=</span> <span class="p">[</span><span class="s2">&quot;TRAINER&quot;</span><span class="p">,</span> <span class="s2">&quot;OPTIMIZER&quot;</span><span class="p">,</span> <span class="s2">&quot;SCHEDULER&quot;</span><span class="p">]</span>
+<div class="viewcode-block" id="TRAINER">
+<a class="viewcode-back" href="../api/SetupDict/index.html#SetupDict.TRAINER">[docs]</a>
+<span class="n">TRAINER</span> <span class="o">=</span> <span class="p">{</span>
+    <span class="s2">&quot;baseline&quot;</span><span class="p">:</span> <span class="n">core</span><span class="o">.</span><span class="n">Baseline</span><span class="o">.</span><span class="n">Trainer</span><span class="p">,</span>
+    <span class="s2">&quot;mediar&quot;</span><span class="p">:</span> <span class="n">core</span><span class="o">.</span><span class="n">MEDIAR</span><span class="o">.</span><span class="n">Trainer</span><span class="p">,</span>
+<span class="p">}</span></div>
+<span class="n">PREDICTOR</span> <span class="o">=</span> <span class="p">{</span>
+    <span class="s2">&quot;baseline&quot;</span><span class="p">:</span> <span class="n">core</span><span class="o">.</span><span class="n">Baseline</span><span class="o">.</span><span class="n">Predictor</span><span class="p">,</span>
+    <span class="s2">&quot;mediar&quot;</span><span class="p">:</span> <span class="n">core</span><span class="o">.</span><span class="n">MEDIAR</span><span class="o">.</span><span class="n">Predictor</span><span class="p">,</span>
+    <span class="s2">&quot;ensemble_mediar&quot;</span><span class="p">:</span> <span class="n">core</span><span class="o">.</span><span class="n">MEDIAR</span><span class="o">.</span><span class="n">EnsemblePredictor</span><span class="p">,</span>
+<span class="p">}</span>
+<span class="n">MODELS</span> <span class="o">=</span> <span class="p">{</span>
+    <span class="s2">&quot;unet&quot;</span><span class="p">:</span> <span class="n">monai</span><span class="o">.</span><span class="n">networks</span><span class="o">.</span><span class="n">nets</span><span class="o">.</span><span class="n">UNet</span><span class="p">,</span>
+    <span class="s2">&quot;unetr&quot;</span><span class="p">:</span> <span class="n">monai</span><span class="o">.</span><span class="n">networks</span><span class="o">.</span><span class="n">nets</span><span class="o">.</span><span class="n">unetr</span><span class="o">.</span><span class="n">UNETR</span><span class="p">,</span>
+    <span class="s2">&quot;swinunetr&quot;</span><span class="p">:</span> <span class="n">monai</span><span class="o">.</span><span class="n">networks</span><span class="o">.</span><span class="n">nets</span><span class="o">.</span><span class="n">SwinUNETR</span><span class="p">,</span>
+    <span class="s2">&quot;mediar-former&quot;</span><span class="p">:</span> <span class="n">models</span><span class="o">.</span><span class="n">MEDIARFormer</span><span class="p">,</span>
+<span class="p">}</span>
+<div class="viewcode-block" id="OPTIMIZER">
+<a class="viewcode-back" href="../api/SetupDict/index.html#SetupDict.OPTIMIZER">[docs]</a>
+<span class="n">OPTIMIZER</span> <span class="o">=</span> <span class="p">{</span>
+    <span class="s2">&quot;sgd&quot;</span><span class="p">:</span> <span class="n">optim</span><span class="o">.</span><span class="n">SGD</span><span class="p">,</span>
+    <span class="s2">&quot;adam&quot;</span><span class="p">:</span> <span class="n">optim</span><span class="o">.</span><span class="n">Adam</span><span class="p">,</span>
+    <span class="s2">&quot;adamw&quot;</span><span class="p">:</span> <span class="n">optim</span><span class="o">.</span><span class="n">AdamW</span><span class="p">,</span>
+<span class="p">}</span></div>
+<div class="viewcode-block" id="SCHEDULER">
+<a class="viewcode-back" href="../api/SetupDict/index.html#SetupDict.SCHEDULER">[docs]</a>
+<span class="n">SCHEDULER</span> <span class="o">=</span> <span class="p">{</span>
+    <span class="s2">&quot;step&quot;</span><span class="p">:</span> <span class="n">lr_scheduler</span><span class="o">.</span><span class="n">StepLR</span><span class="p">,</span>
+    <span class="s2">&quot;multistep&quot;</span><span class="p">:</span> <span class="n">lr_scheduler</span><span class="o">.</span><span class="n">MultiStepLR</span><span class="p">,</span>
+    <span class="s2">&quot;cosine&quot;</span><span class="p">:</span> <span class="n">lr_scheduler</span><span class="o">.</span><span class="n">CosineAnnealingLR</span><span class="p">,</span>
+<span class="p">}</span></div>
+</pre></div>
+           </div>
+          </div>
+          <footer>
+  <hr/>
+  <div role="contentinfo">
+    <p>&#169; Copyright .</p>
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spacr 0.4.60__tar.gz → 0.9.0__tar.gz

spacr 0.4.60tar.gz → 0.9.0tar.gz