spacr 0.3.1__tar.gz → 0.3.22__tar.gz

spacr-0.3.22/.readthedocs.yaml

@@ -0,0 +1,15 @@
+version: 2
+
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.9"
+
+sphinx:
+  configuration: docs/source/conf.py
+
+python:
+  install:
+    - requirements: docs/requirements.txt
+    - method: pip
+      path: .

spacr-0.3.22/MANIFEST.in

@@ -0,0 +1,34 @@
+recursive-include spacr/resources/models/cp *
+recursive-include spacr/resources/icons *
+recursive-include spacr/resources/font *
+recursive-include spacr/resources/MEDIAR *
+recursive-include spacr/resources/MEDIAR_weights *
+
+# Include essential files
+include *.py
+include *.sh
+include *.txt
+include *.yaml
+include requirements.txt
+
+# Recursively include specific folders and file types
+recursive-include docs *.rst *.py *.html *.css *.js *.inv *.pickle *.png *.svg *.ttf *.woff *.woff2 *.eot *.txt *.bat Makefile
+recursive-include notebooks *.ipynb
+recursive-include path *.csv *.db
+recursive-include settings *.csv
+recursive-include source *.py *.rst
+
+# Recursively include fonts
+recursive-include fonts *.ttf
+
+# Exclude unnecessary files
+global-exclude *.pyc
+global-exclude *.pyo
+global-exclude __pycache__/
+global-exclude .DS_Store
+global-exclude .git
+global-exclude .gitmodules
+global-exclude docs-env/
+
+# Exclude model files from distribution
+exclude spacr/resources/models/cp/*

{spacr-0.3.1/spacr.egg-info → spacr-0.3.22}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.3.1
+Version: 0.3.22
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson
@@ -8,35 +8,43 @@ Author-email: olafsson@med.umich.com
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
+Description-Content-Type: text/x-rst
 License-File: LICENSE
-Requires-Dist: torch<3.0,>=2.0
-Requires-Dist: torchvision<1.0,>=0.1
-Requires-Dist: torch-geometric<3.0,>=2.5
 Requires-Dist: numpy<2.0,>=1.26.4
-Requires-Dist: bottleneck<2.0,>=1.3.6
-Requires-Dist: numexpr<3.0,>=2.8.4
 Requires-Dist: pandas<3.0,>=2.2.1
-Requires-Dist: statsmodels<1.0,>=0.14.1
+Requires-Dist: scipy<2.0,>=1.12.0
+Requires-Dist: cellpose<4.0,>=3.0.6
 Requires-Dist: scikit-image<1.0,>=0.22.0
 Requires-Dist: scikit-learn<2.0,>=1.4.1
-Requires-Dist: seaborn<1.0,>=0.13.2
-Requires-Dist: matplotlib<4.0,>=3.8.3
-Requires-Dist: shap<1.0,>=0.45.0
-Requires-Dist: pillow<11.0,>=10.2.0
-Requires-Dist: imageio<3.0,>=2.34.0
-Requires-Dist: scipy<2.0,>=1.12.0
-Requires-Dist: ipywidgets<9.0,>=8.1.2
 Requires-Dist: mahotas<2.0,>=1.4.13
 Requires-Dist: btrack<1.0,>=0.6.5
 Requires-Dist: trackpy<1.0,>=0.6.2
-Requires-Dist: cellpose<4.0,>=3.0.6
-Requires-Dist: IPython<9.0,>=8.18.1
+Requires-Dist: statsmodels<1.0,>=0.14.1
+Requires-Dist: shap<1.0,>=0.45.0
+Requires-Dist: torch<3.0,>=2.0
+Requires-Dist: torchvision<1.0,>=0.1
+Requires-Dist: torch-geometric<3.0,>=2.5
+Requires-Dist: torchcam<1.0,>=0.4.0
+Requires-Dist: transformers<5.0,>=4.45.2
+Requires-Dist: segmentation_models_pytorch>=0.3.3
+Requires-Dist: monai>=1.3.0
+Requires-Dist: captum<1.0,>=0.7.0
+Requires-Dist: seaborn<1.0,>=0.13.2
+Requires-Dist: matplotlib<4.0,>=3.8.3
+Requires-Dist: adjustText<2.0,>=1.2.0
+Requires-Dist: bottleneck<2.0,>=1.3.6
+Requires-Dist: numexpr<3.0,>=2.8.4
 Requires-Dist: opencv-python-headless<5.0,>=4.9.0.80
+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: imageio<3.0,>=2.34.0
+Requires-Dist: pingouin<1.0,>=0.5.5
 Requires-Dist: umap-learn<1.0,>=0.5.6
 Requires-Dist: ttkthemes<4.0,>=3.2.2
 Requires-Dist: xgboost<3.0,>=2.0.3
 Requires-Dist: PyWavelets<2.0,>=1.6.0
-Requires-Dist: torchcam<1.0,>=0.4.0
 Requires-Dist: ttf_opensans>=2020.10.30
 Requires-Dist: customtkinter<6.0,>=5.2.2
 Requires-Dist: biopython<2.0,>=1.80
@@ -49,15 +57,15 @@ Requires-Dist: tables<4.0,>=3.8.0
 Requires-Dist: rapidfuzz<4.0,>=3.9
 Requires-Dist: keyring<16.0,>=15.1
 Requires-Dist: screeninfo<1.0,>=0.8.1
-Requires-Dist: ipykernel
-Requires-Dist: gdown
 Requires-Dist: fastremap>=1.14.1
-Requires-Dist: monai>=1.3.0
 Requires-Dist: pytz>=2023.3.post1
-Requires-Dist: segmentation_models_pytorch>=0.3.3
-Requires-Dist: tifffile>=2023.4.12
 Requires-Dist: tqdm>=4.65.0
 Requires-Dist: wandb>=0.16.2
+Requires-Dist: openai<2.0,>=1.50.2
+Requires-Dist: gdown
+Requires-Dist: IPython<9.0,>=8.18.1
+Requires-Dist: ipykernel
+Requires-Dist: ipywidgets<9.0,>=8.1.2
 Requires-Dist: huggingface-hub<0.25,>=0.24.0
 Provides-Extra: dev
 Requires-Dist: pytest<3.11,>=3.9; extra == "dev"
@@ -115,6 +123,7 @@ If using Windows, switch to Linux—it's free, open-source, and better.
 Before installing SpaCr on OSX ensure OpenMP is installed::
 
    brew install libomp
+   brew install hdf5
 
 SpaCr GUI requires Tkinter. On Linux, ensure Tkinter is installed. (Tkinter is included with the standard Python installation on macOS and Windows)::
 

{spacr-0.3.1 → spacr-0.3.22}/README.rst

@@ -47,6 +47,7 @@ If using Windows, switch to Linux—it's free, open-source, and better.
 Before installing SpaCr on OSX ensure OpenMP is installed::
 
    brew install libomp
+   brew install hdf5
 
 SpaCr GUI requires Tkinter. On Linux, ensure Tkinter is installed. (Tkinter is included with the standard Python installation on macOS and Windows)::
 

spacr-0.3.22/deploy_docs.sh

@@ -0,0 +1,18 @@
+#!/bin/bash
+
+# Exit if any subcommand fails
+set -e
+
+# Build the documentation
+cd docs
+make clean
+make html
+
+# Copy the generated files to the root of the docs directory
+cp -r build/html/* .
+
+# Add and commit the changes
+git add .
+git commit -m "Update documentation"
+git push origin main
+

spacr-0.3.22/docs/requirements.txt

@@ -0,0 +1,3 @@
+sphinx
+sphinx_rtd_theme
+sphinx-autodoc-typehints

spacr-0.3.22/docs/source/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

spacr-0.3.22/docs/source/_build/html/_modules/index.html

@@ -0,0 +1,128 @@
+<!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 0.2.65 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=19f00094" />
+
+  
+  <!--[if lt IE 9]>
+    <script src="../_static/js/html5shiv.min.js"></script>
+  <![endif]-->
+  
+        <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=30a7333d"></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" >
+
+          
+          
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+            spacr
+          </a>
+              <div class="version">
+                0.2.65
+              </div>
+<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">
+              <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../modules.html">spacr</a></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" >
+          <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+          <a href="../index.html">spacr</a>
+      </nav>
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+        <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/graph_learning.html">spacr.graph_learning</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/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/timelapse.html">spacr.timelapse</a></li>
+<li><a href="spacr/utils.html">spacr.utils</a></li>
+</ul>
+
+           </div>
+          </div>
+          <footer>
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>&#169; Copyright 2024, Your Name.</p>
+  </div>
+
+  Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
+    <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
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+  </script> 
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spacr-0.3.22/docs/source/_build/html/_modules/spacr/app_annotate.html

@@ -0,0 +1,164 @@
+<!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>spacr.app_annotate &mdash; spacr 0.2.65 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=19f00094" />
+
+  
+  <!--[if lt IE 9]>
+    <script src="../../_static/js/html5shiv.min.js"></script>
+  <![endif]-->
+  
+        <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=30a7333d"></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" >
+
+          
+          
+          <a href="../../index.html" class="icon icon-home">
+            spacr
+          </a>
+              <div class="version">
+                0.2.65
+              </div>
+<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">
+              <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../../modules.html">spacr</a></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" >
+          <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">spacr.app_annotate</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 spacr.app_annotate</h1><div class="highlight"><pre>
+<span></span><span class="kn">import</span> <span class="nn">tkinter</span> <span class="k">as</span> <span class="nn">tk</span>
+<span class="kn">from</span> <span class="nn">tkinter</span> <span class="kn">import</span> <span class="n">ttk</span>
+<span class="kn">from</span> <span class="nn">.gui</span> <span class="kn">import</span> <span class="n">MainApp</span>
+<span class="kn">from</span> <span class="nn">.gui_elements</span> <span class="kn">import</span> <span class="n">set_dark_style</span><span class="p">,</span> <span class="n">spacrButton</span>
+
+<div class="viewcode-block" id="initiate_annotation_app">
+<a class="viewcode-back" href="../../spacr.html#spacr.app_annotate.initiate_annotation_app">[docs]</a>
+<span class="k">def</span> <span class="nf">initiate_annotation_app</span><span class="p">(</span><span class="n">parent_frame</span><span class="p">):</span>
+    <span class="kn">from</span> <span class="nn">.gui_utils</span> <span class="kn">import</span> <span class="n">generate_annotate_fields</span><span class="p">,</span> <span class="n">annotate_app</span>
+    <span class="c1"># Set up the settings window</span>
+    <span class="n">settings_window</span> <span class="o">=</span> <span class="n">tk</span><span class="o">.</span><span class="n">Toplevel</span><span class="p">(</span><span class="n">parent_frame</span><span class="p">)</span>
+    <span class="n">settings_window</span><span class="o">.</span><span class="n">title</span><span class="p">(</span><span class="s2">&quot;Annotation Settings&quot;</span><span class="p">)</span>
+    <span class="n">style_out</span> <span class="o">=</span> <span class="n">set_dark_style</span><span class="p">(</span><span class="n">ttk</span><span class="o">.</span><span class="n">Style</span><span class="p">())</span>
+    <span class="n">settings_window</span><span class="o">.</span><span class="n">configure</span><span class="p">(</span><span class="n">bg</span><span class="o">=</span><span class="n">style_out</span><span class="p">[</span><span class="s1">&#39;bg_color&#39;</span><span class="p">])</span>
+    <span class="n">settings_frame</span> <span class="o">=</span> <span class="n">tk</span><span class="o">.</span><span class="n">Frame</span><span class="p">(</span><span class="n">settings_window</span><span class="p">,</span> <span class="n">bg</span><span class="o">=</span><span class="n">style_out</span><span class="p">[</span><span class="s1">&#39;bg_color&#39;</span><span class="p">])</span>
+    <span class="n">settings_frame</span><span class="o">.</span><span class="n">pack</span><span class="p">(</span><span class="n">fill</span><span class="o">=</span><span class="n">tk</span><span class="o">.</span><span class="n">BOTH</span><span class="p">,</span> <span class="n">expand</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+    <span class="n">vars_dict</span> <span class="o">=</span> <span class="n">generate_annotate_fields</span><span class="p">(</span><span class="n">settings_frame</span><span class="p">)</span>
+    
+    <span class="k">def</span> <span class="nf">start_annotation_app</span><span class="p">():</span>
+        <span class="n">settings</span> <span class="o">=</span> <span class="p">{</span><span class="n">key</span><span class="p">:</span> <span class="n">data</span><span class="p">[</span><span class="s1">&#39;entry&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">()</span> <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">data</span> <span class="ow">in</span> <span class="n">vars_dict</span><span class="o">.</span><span class="n">items</span><span class="p">()}</span>
+        <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;channels&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;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;img_size&#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="nb">int</span><span class="p">,</span> <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;img_size&#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="c1"># Convert string to list of integers</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="nb">list</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="nb">int</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="c1"># Convert string to list of integers</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="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>
+        <span class="k">except</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="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="n">settings</span><span class="p">[</span><span class="s1">&#39;db&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;db&#39;</span><span class="p">,</span> <span class="s1">&#39;default.db&#39;</span><span class="p">)</span>
+
+        <span class="c1"># Convert empty strings to None</span>
+        <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">value</span> <span class="ow">in</span> <span class="n">settings</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
+            <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">value</span><span class="p">,</span> <span class="nb">list</span><span class="p">):</span>
+                <span class="n">settings</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="n">v</span> <span class="k">if</span> <span class="n">v</span> <span class="o">!=</span> <span class="s1">&#39;&#39;</span> <span class="k">else</span> <span class="kc">None</span> <span class="k">for</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">value</span><span class="p">]</span>
+            <span class="k">elif</span> <span class="n">value</span> <span class="o">==</span> <span class="s1">&#39;&#39;</span><span class="p">:</span>
+                <span class="n">settings</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span>
+
+        <span class="n">settings_window</span><span class="o">.</span><span class="n">destroy</span><span class="p">()</span>
+
+        <span class="n">annotate_app</span><span class="p">(</span><span class="n">parent_frame</span><span class="p">,</span> <span class="n">settings</span><span class="p">)</span>
+    
+    <span class="n">start_button</span> <span class="o">=</span> <span class="n">spacrButton</span><span class="p">(</span><span class="n">settings_window</span><span class="p">,</span> <span class="n">text</span><span class="o">=</span><span class="s2">&quot;annotate&quot;</span><span class="p">,</span> <span class="n">command</span><span class="o">=</span><span class="n">start_annotation_app</span><span class="p">,</span> <span class="n">show_text</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+    <span class="n">start_button</span><span class="o">.</span><span class="n">pack</span><span class="p">(</span><span class="n">pady</span><span class="o">=</span><span class="mi">10</span><span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="start_annotate_app">
+<a class="viewcode-back" href="../../spacr.html#spacr.app_annotate.start_annotate_app">[docs]</a>
+<span class="k">def</span> <span class="nf">start_annotate_app</span><span class="p">():</span>
+    <span class="n">app</span> <span class="o">=</span> <span class="n">MainApp</span><span class="p">(</span><span class="n">default_app</span><span class="o">=</span><span class="s2">&quot;Annotate&quot;</span><span class="p">)</span>
+    <span class="n">app</span><span class="o">.</span><span class="n">mainloop</span><span class="p">()</span></div>
+
+
+<span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s2">&quot;__main__&quot;</span><span class="p">:</span>
+    <span class="n">start_annotate_app</span><span class="p">()</span>
+</pre></div>
+
+           </div>
+          </div>
+          <footer>
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>&#169; Copyright 2024, Your Name.</p>
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spacr-0.3.22/docs/source/_build/html/_modules/spacr/app_classify.html

@@ -0,0 +1,117 @@
+<!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>spacr.app_classify &mdash; spacr 0.2.65 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=19f00094" />
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+  <!--[if lt IE 9]>
+    <script src="../../_static/js/html5shiv.min.js"></script>
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+        <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
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+        <script src="../../_static/doctools.js?v=9a2dae69"></script>
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+    <script src="../../_static/js/theme.js"></script>
+    <link rel="index" title="Index" href="../../genindex.html" />
+    <link rel="search" title="Search" href="../../search.html" /> 
+</head>
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+<body class="wy-body-for-nav"> 
+  <div class="wy-grid-for-nav">
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+      <div class="wy-side-scroll">
+        <div class="wy-side-nav-search" >
+
+          
+          
+          <a href="../../index.html" class="icon icon-home">
+            spacr
+          </a>
+              <div class="version">
+                0.2.65
+              </div>
+<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">
+              <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../../modules.html">spacr</a></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" >
+          <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">spacr.app_classify</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 spacr.app_classify</h1><div class="highlight"><pre>
+<span></span><span class="kn">from</span> <span class="nn">.gui</span> <span class="kn">import</span> <span class="n">MainApp</span>
+
+<div class="viewcode-block" id="start_classify_app">
+<a class="viewcode-back" href="../../spacr.html#spacr.app_classify.start_classify_app">[docs]</a>
+<span class="k">def</span> <span class="nf">start_classify_app</span><span class="p">():</span>
+    <span class="n">app</span> <span class="o">=</span> <span class="n">MainApp</span><span class="p">(</span><span class="n">default_app</span><span class="o">=</span><span class="s2">&quot;Classify&quot;</span><span class="p">)</span>
+    <span class="n">app</span><span class="o">.</span><span class="n">mainloop</span><span class="p">()</span></div>
+
+
+<span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s2">&quot;__main__&quot;</span><span class="p">:</span>
+    <span class="n">start_classify_app</span><span class="p">()</span>
+</pre></div>
+
+           </div>
+          </div>
+          <footer>
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>&#169; Copyright 2024, Your Name.</p>
+  </div>
+
+  Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
+    <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
+    provided by <a href="https://readthedocs.org">Read the Docs</a>.
+   
+
+</footer>
+        </div>
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+    </section>
+  </div>
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+      jQuery(function () {
+          SphinxRtdTheme.Navigation.enable(true);
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+</html>