PyPI - spacr - Versions diffs - 0.3.81__tar.gz → 0.4.15__tar.gz - Mend

spacr 0.3.81tar.gz → 0.4.15tar.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 (341) hide show

{spacr-0.3.81 → spacr-0.4.15}/.readthedocs.yaml RENAMED Viewed

@@ -1,7 +1,7 @@
 version: 2
 build:
-  os: ubuntu-20.04
+  os: ubuntu-22.04
   tools:
     python: "3.9"

{spacr-0.3.81 → spacr-0.4.15}/MANIFEST.in RENAMED Viewed

@@ -13,7 +13,6 @@ 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
@@ -31,4 +30,8 @@ global-exclude .gitmodules
 global-exclude docs-env/
 # Exclude model files from distribution
-exclude spacr/resources/models/cp/*
+exclude spacr/resources/models/cp/*
+prune notebooks
+prune spacr/notebooks
+prune spacr/datasets

{spacr-0.3.81/spacr.egg-info → spacr-0.4.15}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.3.81
+Version: 0.4.15
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson
@@ -32,6 +32,7 @@ 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: matplotlib_venn<2.0,>=1.1
 Requires-Dist: adjustText<2.0,>=1.2.0
 Requires-Dist: bottleneck<2.0,>=1.3.6
 Requires-Dist: numexpr<3.0,>=2.8.4

spacr-0.4.15/docs/source/_build/doctrees/environment.pickle ADDED Viewed

Binary file

{spacr-0.3.81 → spacr-0.4.15}/docs/source/_build/html/_sources/index.rst.txt RENAMED Viewed

@@ -1,5 +1,5 @@
 .. spacr documentation master file, created by
-   sphinx-quickstart on Sat Dec 21 02:09:20 PM EST 2024.
+   sphinx-quickstart on Fri Feb 21 01:21:55 PM EST 2025.
 Welcome to spacr's documentation!
 =================================

{spacr-0.3.81 → spacr-0.4.15}/docs/source/_build/html/_static/documentation_options.js RENAMED Viewed

@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: 'Models already downloaded to: /home/carruthers/anaconda3/envs/spacr/lib/python3.9/site-packages/spacr/resources/models0.3.80',
+    VERSION: 'Models already downloaded to: /home/olafsson/anaconda3/envs/spacr/lib/python3.9/site-packages/spacr/resources/models0.4.0',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

spacr-0.4.15/docs/source/_build/html/genindex.html ADDED Viewed

@@ -0,0 +1,103 @@
+<!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>Index &mdash; spacr Models already downloaded to: /home/olafsson/anaconda3/envs/spacr/lib/python3.9/site-packages/spacr/resources/models
+0.4.0 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" />
+      <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=f27469d6"></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="#" />
+    <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 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">
+              <!-- Local TOC -->
+              <div class="local-toc"></div>
+        </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 active">Index</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 id="index">Index</h1>
+<div class="genindex-jumpbox">
+</div>
+           </div>
+          </div>
+          <footer>
+  <hr/>
+  <div role="contentinfo">
+    <p>&#169; Copyright 2025, Einar Olafsson.</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>
+      </div>
+    </section>
+  </div>
+  <script>
+      jQuery(function () {
+          SphinxRtdTheme.Navigation.enable(true);
+      });
+  </script>
+</body>
+</html>

{spacr-0.3.81 → spacr-0.4.15}/docs/source/_build/html/index.html RENAMED Viewed

@@ -6,21 +6,20 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Welcome to spacr’s documentation! &mdash; spacr Models already downloaded to: /home/carruthers/anaconda3/envs/spacr/lib/python3.9/site-packages/spacr/resources/models
-0.3.80 documentation</title>
+  <title>Welcome to spacr’s documentation! &mdash; spacr Models already downloaded to: /home/olafsson/anaconda3/envs/spacr/lib/python3.9/site-packages/spacr/resources/models
+0.4.0 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" />
       <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=8ad38ec3"></script>
+      <script src="_static/documentation_options.js?v=f27469d6"></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" />
-    <link rel="next" title="spacr" href="modules.html" />
+    <link rel="search" title="Search" href="search.html" />
 </head>
 <body class="wy-body-for-nav">
@@ -42,11 +41,12 @@
   </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>
+              <!-- Local TOC -->
+              <div class="local-toc"><ul>
+<li><a class="reference internal" href="#">Welcome to spacr’s documentation!</a></li>
+<li><a class="reference internal" href="#indices-and-tables">Indices and tables</a></li>
 </ul>
+</div>
         </div>
       </div>
     </nav>
@@ -74,13 +74,6 @@
   <section id="welcome-to-spacr-s-documentation">
 <h1>Welcome to spacr’s documentation!<a class="headerlink" href="#welcome-to-spacr-s-documentation" title="Link to this heading"></a></h1>
 <div class="toctree-wrapper compound">
-<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><ul>
-<li class="toctree-l2"><a class="reference internal" href="spacr.html">spacr package</a></li>
-</ul>
-</li>
-</ul>
 </div>
 </section>
 <section id="indices-and-tables">
@@ -95,14 +88,12 @@
            </div>
           </div>
-          <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="modules.html" class="btn btn-neutral float-right" title="spacr" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
-    </div>
+          <footer>
   <hr/>
   <div role="contentinfo">
-    <p>&#169; Copyright 2024, Your Name.</p>
+    <p>&#169; Copyright 2025, Einar Olafsson.</p>
   </div>
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a

spacr-0.4.15/docs/source/_build/html/objects.inv ADDED Viewed

Binary file

{spacr-0.3.81 → spacr-0.4.15}/docs/source/_build/html/search.html RENAMED Viewed

@@ -5,8 +5,8 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Search &mdash; spacr Models already downloaded to: /home/carruthers/anaconda3/envs/spacr/lib/python3.9/site-packages/spacr/resources/models
-0.3.80 documentation</title>
+  <title>Search &mdash; spacr Models already downloaded to: /home/olafsson/anaconda3/envs/spacr/lib/python3.9/site-packages/spacr/resources/models
+0.4.0 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" />
@@ -14,7 +14,7 @@
       <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=8ad38ec3"></script>
+      <script src="_static/documentation_options.js?v=f27469d6"></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>
@@ -43,11 +43,8 @@
   </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>
+              <!-- Local TOC -->
+              <div class="local-toc"></div>
         </div>
       </div>
     </nav>
@@ -91,7 +88,7 @@
   <hr/>
   <div role="contentinfo">
-    <p>&#169; Copyright 2024, Your Name.</p>
+    <p>&#169; Copyright 2025, Einar Olafsson.</p>
   </div>
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a

spacr-0.4.15/docs/source/_build/html/searchindex.js ADDED Viewed

@@ -0,0 +1 @@

+ Search.setIndex({"alltitles": {"Indices and tables": [[0, "indices-and-tables"]], "Welcome to spacr\u2019s documentation!": [[0, null]]}, "docnames": ["index"], "envversion": {"sphinx": 62, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.todo": 2, "sphinx.ext.viewcode": 1}, "filenames": ["index.rst"], "indexentries": {}, "objects": {}, "objnames": {}, "objtypes": {}, "terms": {"index": 0, "modul": 0, "page": 0, "search": 0}, "titles": ["Welcome to spacr\u2019s documentation!"], "titleterms": {"": 0, "document": 0, "indic": 0, "spacr": 0, "tabl": 0, "welcom": 0}})

{spacr-0.3.81 → spacr-0.4.15}/docs/source/conf.py RENAMED Viewed

@@ -7,11 +7,11 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 project = 'spacr'
-copyright = '2024, Your Name'
-author = 'Your Name'
+copyright = '2025, Einar Olafsson'
+author = 'Einar Olafsson'
-version = 'Models already downloaded to: /home/carruthers/anaconda3/envs/spacr/lib/python3.9/site-packages/spacr/resources/models\n0.3.80'
-release = 'Models already downloaded to: /home/carruthers/anaconda3/envs/spacr/lib/python3.9/site-packages/spacr/resources/models\n0.3.80'
+version = 'Models already downloaded to: /home/olafsson/anaconda3/envs/spacr/lib/python3.9/site-packages/spacr/resources/models\n0.4.0'
+release = 'Models already downloaded to: /home/olafsson/anaconda3/envs/spacr/lib/python3.9/site-packages/spacr/resources/models\n0.4.0'
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration

{spacr-0.3.81 → spacr-0.4.15}/docs/source/index.rst RENAMED Viewed

@@ -1,5 +1,5 @@
 .. spacr documentation master file, created by
-   sphinx-quickstart on Sat Dec 21 02:09:20 PM EST 2024.
+   sphinx-quickstart on Fri Feb 21 01:21:55 PM EST 2025.
 Welcome to spacr's documentation!
 =================================

{spacr-0.3.81 → spacr-0.4.15}/setup.py RENAMED Viewed

@@ -28,6 +28,7 @@ dependencies = [
     'captum>=0.7.0, <1.0',
     'seaborn>=0.13.2,<1.0',
     'matplotlib>=3.8.3,<4.0',
+    'matplotlib_venn>=1.1,<2.0',
     'adjustText>=1.2.0,<2.0',
     'bottleneck>=1.3.6,<2.0',
     'numexpr>=2.8.4,<3.0',
@@ -69,7 +70,7 @@ dependencies = [
 setup(
     name="spacr",
-    version="0.3.81",
+    version="0.4.15",
     author="Einar Birnir Olafsson",
     author_email="olafsson@med.umich.com",
     description="Spatial phenotype analysis of crisp screens (SpaCr)",

{spacr-0.3.81 → spacr-0.4.15}/setup_docs.sh RENAMED Viewed

@@ -22,7 +22,7 @@ cat <<EOL > ../.readthedocs.yaml
 version: 2
 build:
-  os: ubuntu-20.04
+  os: ubuntu-22.04
   tools:
     python: "3.9"
@@ -40,7 +40,7 @@ EOL
 VERSION=$(python -c "from spacr.version import version; print(version)")
 # Run sphinx-quickstart with necessary configurations in the source directory
-sphinx-quickstart source -q -p "spacr" -a "Your Name" -v "$VERSION" --ext-autodoc --ext-viewcode --ext-todo
+sphinx-quickstart source -q -p "spacr" -a "Einar Olafsson" -v "$VERSION" --ext-autodoc --ext-viewcode --ext-todo
 # Update conf.py with additional configurations
 cat <<EOT >> source/conf.py

{spacr-0.3.81 → spacr-0.4.15}/spacr/__init__.py RENAMED Viewed

@@ -27,7 +27,7 @@ from . import openai
 from . import ml
 from . import toxo
 from . import cellpose
-from . import stats
+from . import sp_stats
 from . import logger
 __all__ = [
@@ -58,7 +58,7 @@ __all__ = [
     "ml",
     "toxo",
     "cellpose",
-    "stats",
+    "sp_stats",
     "logger"
 ]
@@ -67,8 +67,4 @@ logging.basicConfig(filename='spacr.log', level=logging.INFO,
 from .utils import download_models
-# Check if models already exist
-#models_dir = os.path.join(os.path.dirname(__file__), 'resources', 'models', 'cp')
-#if not os.path.exists(models_dir) or not os.listdir(models_dir):
-#    print("Models not found, downloading...")
 download_models()

{spacr-0.3.81 → spacr-0.4.15}/spacr/core.py RENAMED Viewed

@@ -7,17 +7,24 @@ from IPython.display import display
 import warnings
 warnings.filterwarnings("ignore", message="3D stack used, but stitch_threshold=0 and do_3D=False, so masks are made per plane only")
-def preprocess_generate_masks(src, settings={}):
+def preprocess_generate_masks(settings):
     from .io import preprocess_img_data, _load_and_concatenate_arrays
     from .plot import plot_image_mask_overlay, plot_arrays
-    from .utils import _pivot_counts_table, check_mask_folder, adjust_cell_masks, print_progress, save_settings
+    from .utils import _pivot_counts_table, check_mask_folder, adjust_cell_masks, print_progress, save_settings, delete_intermedeate_files, format_path_for_system, normalize_src_path
     from .settings import set_default_settings_preprocess_generate_masks
-    if not isinstance(settings['src'], (str, list)):
-        ValueError(f'src must be a string or a list of strings')
+    if 'src' in settings:
+        if not isinstance(settings['src'], (str, list)):
+            ValueError(f'src must be a string or a list of strings')
+            return
+    else:
+        ValueError(f'src is a required parameter')
         return
+    settings['src'] = normalize_src_path(settings['src'])
     if isinstance(settings['src'], str):
         settings['src'] = [settings['src']]
@@ -25,11 +32,11 @@ def preprocess_generate_masks(src, settings={}):
         source_folders = settings['src']
         for source_folder in source_folders:
             print(f'Processing folder: {source_folder}')
+            source_folder = format_path_for_system(source_folder)
             settings['src'] = source_folder
             src = source_folder
-            settings = set_default_settings_preprocess_generate_masks(src, settings)
-            save_settings(settings, name='gen_mask')
+            settings = set_default_settings_preprocess_generate_masks(settings)
+            save_settings(settings, name='gen_mask_settings')
             if not settings['pathogen_channel'] is None:
                 custom_model_ls = ['toxo_pv_lumen','toxo_cyto']
@@ -158,6 +165,10 @@ def preprocess_generate_masks(src, settings={}):
             torch.cuda.empty_cache()
             gc.collect()
+            if settings['delete_intermediate']:
+                delete_intermedeate_files(settings)
             print("Successfully completed run")
     return
@@ -172,8 +183,10 @@ def generate_cellpose_masks(src, settings, object_type):
     gc.collect()
     if not torch.cuda.is_available():
         print(f'Torch CUDA is not available, using CPU')
-    settings = set_default_settings_preprocess_generate_masks(src, settings)
+    settings['src'] = src
+    settings = set_default_settings_preprocess_generate_masks(settings)
     if settings['verbose']:
         settings_df = pd.DataFrame(list(settings.items()), columns=['setting_key', 'setting_value'])
@@ -192,11 +205,13 @@ def generate_cellpose_masks(src, settings, object_type):
         timelapse_objects = settings['timelapse_objects']
     batch_size = settings['batch_size']
     cellprob_threshold = settings[f'{object_type}_CP_prob']
     flow_threshold = settings[f'{object_type}_FT']
     object_settings = _get_object_settings(object_type, settings)
     model_name = object_settings['model_name']
     cellpose_channels = _get_cellpose_channels(src, settings['nucleus_channel'], settings['pathogen_channel'], settings['cell_channel'])
@@ -473,7 +488,7 @@ def generate_image_umap(settings={}):
         df, image_paths_tmp = correct_paths(df, settings['src'][i])
         all_df = pd.concat([all_df, df], axis=0)
         #image_paths.extend(image_paths_tmp)
     all_df['cond'] = all_df['column_name'].apply(map_condition, neg=settings['neg'], pos=settings['pos'], mix=settings['mix'])
     if settings['exclude_conditions']:
@@ -493,7 +508,7 @@ def generate_image_umap(settings={}):
         # Extract and reset the index for the column to compare
         col_to_compare = all_df[settings['col_to_compare']].reset_index(drop=True)
+        print(col_to_compare)
         #if settings['only_top_features']:
         #    column_list = None
@@ -781,8 +796,10 @@ def generate_mediar_masks(src, settings, object_type):
     if not torch.cuda.is_available():
         print(f'Torch CUDA is not available, using CPU')
+    settings['src'] = src
     # Preprocess settings
-    settings = set_default_settings_preprocess_generate_masks(src, settings)
+    settings = set_default_settings_preprocess_generate_masks(settings)
     if settings['verbose']:
         settings_df = pd.DataFrame(list(settings.items()), columns=['setting_key', 'setting_value'])

spacr 0.3.81__tar.gz → 0.4.15__tar.gz

spacr 0.3.81tar.gz → 0.4.15tar.gz