PyPI - spacr - Versions diffs - 1.0.1__tar.gz → 1.0.5__tar.gz - Mend

spacr 1.0.1tar.gz → 1.0.5tar.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 (701) hide show

{spacr-1.0.1/spacr.egg-info → spacr-1.0.5}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 1.0.1
+Version: 1.0.5
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson
@@ -75,7 +75,7 @@ Requires-Dist: ipywidgets<9.0,>=8.1.2
 Requires-Dist: brokenaxes<1.0,>=0.6.2
 Requires-Dist: huggingface-hub<0.25,>=0.24.0
 Provides-Extra: dev
-Requires-Dist: pytest<3.11,>=3.9; extra == "dev"
+Requires-Dist: pytest<3.12,>=3.9; extra == "dev"
 Provides-Extra: headless
 Requires-Dist: opencv-python-headless; extra == "headless"
 Provides-Extra: full
@@ -164,16 +164,6 @@ SpaCr GUI requires Tkinter.
    spacr
-Data Availability
------------------
-- **Raw sequencing data** are available from NCBI BioProject `PRJNA1261935 <https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1261935>`_ and SRA accessions: `SRR33531217 <https://www.ncbi.nlm.nih.gov/sra/SRR33531217>`_, `SRR33531218 <https://www.ncbi.nlm.nih.gov/sra/SRR33531218>`_, `SRR33531219 <https://www.ncbi.nlm.nih.gov/sra/SRR33531219>`_, `SRR33531220 <https://www.ncbi.nlm.nih.gov/sra/SRR33531220>`_
-- **Image data** is deposited at EBI BioStudies under accession:
-  `S-BIAD2076 <https://www.ebi.ac.uk/biostudies/studies/S-BIAD2076>`_
-  *(If the link redirects to the main BioStudies portal, copy and paste it directly into your browser.)*
 Example Notebooks
 -----------------
@@ -204,6 +194,25 @@ Click below to explore the step-by-step GUI and Notebook tutorials for spaCR:
 |Tutorial|
+spaCRPower
+----------
+Power analasys of pooled perterbation spaCR screens.
+`spaCRPower <https://github.com/maomlab/spaCRPower>`_
+Data Availability
+-----------------
+- **Full microscopy image dataset:**
+  `EMBL-EBI BioStudies S-BIAD2135 <https://doi.org/10.6019/S-BIAD2135>`_
+- **Testing dataset:**
+  `Hugging Face toxo_mito <https://huggingface.co/datasets/einarolafsson/toxo_mito>`_
+- **Sequencing data:**
+  `NCBI BioProject PRJNA1261935 <https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA1261935>`_
 License
 -------
 spaCR is distributed under the terms of the MIT License.

{spacr-1.0.1 → spacr-1.0.5}/README.rst RENAMED Viewed

@@ -81,16 +81,6 @@ SpaCr GUI requires Tkinter.
    spacr
-Data Availability
------------------
-- **Raw sequencing data** are available from NCBI BioProject `PRJNA1261935 <https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1261935>`_ and SRA accessions: `SRR33531217 <https://www.ncbi.nlm.nih.gov/sra/SRR33531217>`_, `SRR33531218 <https://www.ncbi.nlm.nih.gov/sra/SRR33531218>`_, `SRR33531219 <https://www.ncbi.nlm.nih.gov/sra/SRR33531219>`_, `SRR33531220 <https://www.ncbi.nlm.nih.gov/sra/SRR33531220>`_
-- **Image data** is deposited at EBI BioStudies under accession:
-  `S-BIAD2076 <https://www.ebi.ac.uk/biostudies/studies/S-BIAD2076>`_
-  *(If the link redirects to the main BioStudies portal, copy and paste it directly into your browser.)*
 Example Notebooks
 -----------------
@@ -121,6 +111,25 @@ Click below to explore the step-by-step GUI and Notebook tutorials for spaCR:
 |Tutorial|
+spaCRPower
+----------
+Power analasys of pooled perterbation spaCR screens.
+`spaCRPower <https://github.com/maomlab/spaCRPower>`_
+Data Availability
+-----------------
+- **Full microscopy image dataset:**
+  `EMBL-EBI BioStudies S-BIAD2135 <https://doi.org/10.6019/S-BIAD2135>`_
+- **Testing dataset:**
+  `Hugging Face toxo_mito <https://huggingface.co/datasets/einarolafsson/toxo_mito>`_
+- **Sequencing data:**
+  `NCBI BioProject PRJNA1261935 <https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA1261935>`_
 License
 -------
 spaCR is distributed under the terms of the MIT License.

spacr-1.0.5/docs/_build/html/.doctrees/environment.pickle ADDED Viewed

Binary file

spacr-1.0.5/docs/_build/html/_modules/index.html ADDED Viewed

@@ -0,0 +1,166 @@
+<!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>Overview: module code &mdash; spacr 1.0.1 documentation</title>
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=80d5e7a1" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=e59714d7" />
+      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=45a07ac9" />
+      <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=292eb321"></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" />
+</head>
+<body class="wy-body-for-nav">
+  <div class="wy-grid-for-nav">
+    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+      <div class="wy-side-scroll">
+        <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/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/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/ml/index.html">spacr.ml</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>
+</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 active">Overview: module code</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>All modules for which code is available</h1>
+<ul><li><a href="spacr/app_annotate.html">spacr.app_annotate</a></li>
+<li><a href="spacr/app_classify.html">spacr.app_classify</a></li>
+<li><a href="spacr/app_make_masks.html">spacr.app_make_masks</a></li>
+<li><a href="spacr/app_mask.html">spacr.app_mask</a></li>
+<li><a href="spacr/app_measure.html">spacr.app_measure</a></li>
+<li><a href="spacr/app_sequencing.html">spacr.app_sequencing</a></li>
+<li><a href="spacr/app_umap.html">spacr.app_umap</a></li>
+<li><a href="spacr/core.html">spacr.core</a></li>
+<li><a href="spacr/deep_spacr.html">spacr.deep_spacr</a></li>
+<li><a href="spacr/gui.html">spacr.gui</a></li>
+<li><a href="spacr/gui_core.html">spacr.gui_core</a></li>
+<li><a href="spacr/gui_elements.html">spacr.gui_elements</a></li>
+<li><a href="spacr/gui_utils.html">spacr.gui_utils</a></li>
+<li><a href="spacr/io.html">spacr.io</a></li>
+<li><a href="spacr/logger.html">spacr.logger</a></li>
+<li><a href="spacr/measure.html">spacr.measure</a></li>
+<li><a href="spacr/ml.html">spacr.ml</a></li>
+<li><a href="spacr/plot.html">spacr.plot</a></li>
+<li><a href="spacr/sequencing.html">spacr.sequencing</a></li>
+<li><a href="spacr/settings.html">spacr.settings</a></li>
+<li><a href="spacr/sim.html">spacr.sim</a></li>
+<li><a href="spacr/sp_stats.html">spacr.sp_stats</a></li>
+<li><a href="spacr/spacr_cellpose.html">spacr.spacr_cellpose</a></li>
+<li><a href="spacr/submodules.html">spacr.submodules</a></li>
+<li><a href="spacr/timelapse.html">spacr.timelapse</a></li>
+<li><a href="spacr/toxo.html">spacr.toxo</a></li>
+<li><a href="spacr/utils.html">spacr.utils</a></li>
+<li><a href="spacr/version.html">spacr.version</a></li>
+</ul>
+           </div>
+          </div>
+          <footer>
+  <hr/>
+  <div role="contentinfo">
+    <p>&#169; Copyright .</p>
+  </div>
+  Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
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+    provided by <a href="https://readthedocs.org">Read the Docs</a>.
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+      jQuery(function () {
+          SphinxRtdTheme.Navigation.enable(true);
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+</body>
+</html>

{spacr-1.0.1/docs → spacr-1.0.5/docs/_build/html}/_modules/spacr/app_annotate.html RENAMED Viewed

@@ -5,14 +5,16 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>spacr.app_annotate &mdash; spacr 0.5.0 documentation</title>
+  <title>spacr.app_annotate &mdash; spacr 1.0.1 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=80d5e7a1" />
       <link rel="stylesheet" type="text/css" href="../../_static/css/theme.css?v=e59714d7" />
       <link rel="stylesheet" type="text/css" href="../../_static/graphviz.css?v=fd3f3429" />
-      <link rel="stylesheet" type="text/css" href="../../_static/custom.css" />
+      <link rel="stylesheet" type="text/css" href="../../_static/custom.css?v=45a07ac9" />
-      <script src="../../_static/documentation_options.js?v=1dd76d02"></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=292eb321"></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>
@@ -42,27 +44,6 @@
         </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>
@@ -72,7 +53,6 @@
 <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>
@@ -82,9 +62,7 @@
 <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>
@@ -100,53 +78,6 @@
 </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>
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-</li>
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-</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>
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-</li>
-</ul>
-</li>
 </ul>
 </li>
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@@ -213,6 +144,10 @@
         <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;percentiles&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="n">convert_to_number</span><span class="p">,</span> <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;percentiles&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)))</span> <span class="k">if</span> <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;percentiles&#39;</span><span class="p">]</span> <span class="k">else</span> <span class="p">[</span><span class="mi">2</span><span class="p">,</span> <span class="mi">98</span><span class="p">]</span>
         <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;normalize&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;normalize&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="s1">&#39;true&#39;</span>
         <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;normalize_channels&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;normalize_channels&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)</span>
+        <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;outline&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;outline&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)</span> <span class="k">if</span> <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;outline&#39;</span><span class="p">]</span> <span class="k">else</span> <span class="kc">None</span>
+        <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;outline_threshold_factor&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">settings</span><span class="p">[</span><span class="s1">&#39;outline_threshold_factor&#39;</span><span class="p">])</span> <span class="k">if</span> <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;outline_threshold_factor&#39;</span><span class="p">]</span> <span class="k">else</span> <span class="mf">1.0</span>
+        <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;outline_sigma&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">settings</span><span class="p">[</span><span class="s1">&#39;outline_threshold_factor&#39;</span><span class="p">])</span> <span class="k">if</span> <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;outline_threshold_factor&#39;</span><span class="p">]</span> <span class="k">else</span> <span class="mf">1.0</span>
         <span class="k">try</span><span class="p">:</span>
             <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;measurement&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;measurement&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)</span> <span class="k">if</span> <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;measurement&#39;</span><span class="p">]</span> <span class="k">else</span> <span class="kc">None</span>
             <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;threshold&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span> <span class="k">if</span> <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;threshold&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="s1">&#39;none&#39;</span> <span class="k">else</span> <span class="nb">int</span><span class="p">(</span><span class="n">settings</span><span class="p">[</span><span class="s1">&#39;threshold&#39;</span><span class="p">])</span>

{spacr-1.0.1/docs → spacr-1.0.5/docs/_build/html}/_modules/spacr/app_classify.html RENAMED Viewed

@@ -5,14 +5,16 @@
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   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>spacr.app_classify &mdash; spacr 0.5.0 documentation</title>
+  <title>spacr.app_classify &mdash; spacr 1.0.1 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=80d5e7a1" />
       <link rel="stylesheet" type="text/css" href="../../_static/css/theme.css?v=e59714d7" />
       <link rel="stylesheet" type="text/css" href="../../_static/graphviz.css?v=fd3f3429" />
-      <link rel="stylesheet" type="text/css" href="../../_static/custom.css" />
+      <link rel="stylesheet" type="text/css" href="../../_static/custom.css?v=45a07ac9" />
-      <script src="../../_static/documentation_options.js?v=1dd76d02"></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=292eb321"></script>
       <script src="../../_static/doctools.js?v=9a2dae69"></script>
       <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
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@@ -42,27 +44,6 @@
         </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>
@@ -72,7 +53,6 @@
 <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>
@@ -82,9 +62,7 @@
 <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>
@@ -100,53 +78,6 @@
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 </ul>
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-<li class="toctree-l2"><a class="reference internal" href="../../api/predict/index.html">predict</a><ul>
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-<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>
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-</li>
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-<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>
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-</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>
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-</li>
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-<li class="toctree-l4"><a class="reference internal" href="../../api/train_tools/measures/index.html">train_tools.measures</a></li>
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-</li>
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-<li class="toctree-l3"><a class="reference internal" href="../../api/generate_mapping/index.html#module-contents">Module Contents</a><ul>
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-<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>
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-</ul>
-</li>
-</ul>
-</li>
 </ul>
 </li>
 </ul>

spacr 1.0.1__tar.gz → 1.0.5__tar.gz

spacr 1.0.1tar.gz → 1.0.5tar.gz