spacr 0.0.1__tar.gz → 0.0.2__tar.gz

spacr-0.0.2/PKG-INFO

@@ -0,0 +1,130 @@
+Metadata-Version: 2.1
+Name: spacr
+Version: 0.0.2
+Summary: Spatial phenotype analysis of crisp screens (SpaCr)
+Home-page: https://github.com/EinarOlafsson/spacr
+Author: Einar Birnir Olafsson
+Author-email: olafsson@med.umich.com
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+License-File: LICENSE
+Requires-Dist: torch>=2.2.1
+Requires-Dist: torchvision>=0.17.1
+Requires-Dist: torch-geometric>=2.5.1
+Requires-Dist: numpy>=1.26.4
+Requires-Dist: pandas>=2.2.1
+Requires-Dist: statsmodels>=0.14.1
+Requires-Dist: scikit-image>=0.22.0
+Requires-Dist: scikit-learn>=1.4.1
+Requires-Dist: seaborn>=0.13.2
+Requires-Dist: matplotlib>=3.8.3
+Requires-Dist: pillow>=10.2.0
+Requires-Dist: imageio>=2.34.0
+Requires-Dist: scipy>=1.12.0
+Requires-Dist: ipywidgets>=8.1.2
+Requires-Dist: mahotas>=1.4.13
+Requires-Dist: btrack>=0.6.5
+Requires-Dist: trackpy>=0.6.2
+Requires-Dist: cellpose>=3.0.6
+Requires-Dist: IPython>=8.18.1
+Requires-Dist: opencv-python-headless>=4.9.0.80
+Requires-Dist: umap>=0.1.1
+Requires-Dist: ttkthemes>=3.2.2
+Requires-Dist: lxml>=5.1.0
+Provides-Extra: dev
+Requires-Dist: pytest>=3.9; extra == "dev"
+Provides-Extra: headless
+Requires-Dist: opencv-python-headless; extra == "headless"
+Provides-Extra: full
+Requires-Dist: opencv-python; extra == "full"
+
+[![PyPI version](https://badge.fury.io/py/spacr.svg)](https://badge.fury.io/py/spacr)
+[![Python version](https://img.shields.io/pypi/pyversions/spacr)](https://pypistats.org/packages/spacr)
+[![Licence: GPL v3](https://img.shields.io/github/license/EinarOlafsson/spacr)](https://github.com/EinarOlafsson/spacr/blob/master/LICENSE)
+[![repo size](https://img.shields.io/github/repo-size/EinarOlafsson/spacr)](https://github.com/EinarOlafsson/spacr/)
+
+# SpaCr
+<table>
+<tr>
+<td>
+  
+Spatial phenotype analysis of crisp screens (SpaCr). A collection of functions for generating cellpose masks -> single object images and measurements -> annotation and classification of single object images. Spacr uses batch normalization to facilitate accurate segmentation of objects with low foreground representation.
+
+</td>
+<td>
+
+<img src="spacr/logo_spacr.png" alt="SPACR Logo" title="SPACR Logo" width="600"/>
+
+</td>
+</tr>
+</table>
+
+## Features
+
+- **Generate Masks:** Generate cellpose masks for cells, nuclei and pathogen images.
+
+- **Object Measurements:** Measurements for each object including scikit-image-regionprops, intensity quantiles, shannon-entropy, pearsons and manders correlation, homogenicity and radial distribution. Measurements are saved to a sql database in object level tables.
+
+- **Crop Images:** Objects (e.g. cells) can be saved as PNGs from the object area or bounding box area of each object. Object paths are saved in an sql database that can be annotated and used to train CNNs/Transformer models for classefication tasks.
+
+- **Train CNNs or Transformers:** Train Torch Convolutional Neural Networks (CNNs) or Transformers to classify single object images. Train Torch models with IRM/ERM, checkpointing.
+
+- **Manual Annotation:** Supports manual annotation of single cell images and segmentation to refine training datasets for training CNNs/Transformers or cellpose, respectively.
+
+- **Finetune Cellpose Models:** Adjust pre-existing Cellpose models to your specific dataset for improved performance.
+
+- **Timelapse Data Support:** Track objects in timelapse image data.
+
+- **Simulations:** Simulate spatial phenotype screens.
+
+- **Misc:** Analyze Ca oscillation, recruitment, infection rate, plaque size/count.
+
+## Installation
+
+spacr requires Tkinter for its graphical user interface features.
+
+### Ubuntu
+
+Before installing spacr, ensure Tkinter is installed:
+
+(Tkinter is included with the standard Python installation on macOS, and Windows)
+
+On Linux:
+
+```
+sudo apt-get install python3-tk
+```
+
+install spacr with pip
+
+```
+pip install spacr
+```
+
+To run spacr GUIs after installing spacr:
+
+To generate masks:
+```
+gui_mask
+```
+To generate measurements and cropped images:
+```
+gui_measure
+```
+To curate masks for finetuning cellpose models:
+```
+gui_make_masks
+```
+To annotate paths to images in sql database created in gui_measure:
+```
+gui_annotate
+```
+Train torch CNNs/Transformers to classify single object images.
+```
+gui_classify
+```
+Simulate spatial phenotype screens.
+```
+gui_sim
+```

spacr-0.0.2/README.md

@@ -0,0 +1,89 @@
+[![PyPI version](https://badge.fury.io/py/spacr.svg)](https://badge.fury.io/py/spacr)
+[![Python version](https://img.shields.io/pypi/pyversions/spacr)](https://pypistats.org/packages/spacr)
+[![Licence: GPL v3](https://img.shields.io/github/license/EinarOlafsson/spacr)](https://github.com/EinarOlafsson/spacr/blob/master/LICENSE)
+[![repo size](https://img.shields.io/github/repo-size/EinarOlafsson/spacr)](https://github.com/EinarOlafsson/spacr/)
+
+# SpaCr
+<table>
+<tr>
+<td>
+  
+Spatial phenotype analysis of crisp screens (SpaCr). A collection of functions for generating cellpose masks -> single object images and measurements -> annotation and classification of single object images. Spacr uses batch normalization to facilitate accurate segmentation of objects with low foreground representation.
+
+</td>
+<td>
+
+<img src="spacr/logo_spacr.png" alt="SPACR Logo" title="SPACR Logo" width="600"/>
+
+</td>
+</tr>
+</table>
+
+## Features
+
+- **Generate Masks:** Generate cellpose masks for cells, nuclei and pathogen images.
+
+- **Object Measurements:** Measurements for each object including scikit-image-regionprops, intensity quantiles, shannon-entropy, pearsons and manders correlation, homogenicity and radial distribution. Measurements are saved to a sql database in object level tables.
+
+- **Crop Images:** Objects (e.g. cells) can be saved as PNGs from the object area or bounding box area of each object. Object paths are saved in an sql database that can be annotated and used to train CNNs/Transformer models for classefication tasks.
+
+- **Train CNNs or Transformers:** Train Torch Convolutional Neural Networks (CNNs) or Transformers to classify single object images. Train Torch models with IRM/ERM, checkpointing.
+
+- **Manual Annotation:** Supports manual annotation of single cell images and segmentation to refine training datasets for training CNNs/Transformers or cellpose, respectively.
+
+- **Finetune Cellpose Models:** Adjust pre-existing Cellpose models to your specific dataset for improved performance.
+
+- **Timelapse Data Support:** Track objects in timelapse image data.
+
+- **Simulations:** Simulate spatial phenotype screens.
+
+- **Misc:** Analyze Ca oscillation, recruitment, infection rate, plaque size/count.
+
+## Installation
+
+spacr requires Tkinter for its graphical user interface features.
+
+### Ubuntu
+
+Before installing spacr, ensure Tkinter is installed:
+
+(Tkinter is included with the standard Python installation on macOS, and Windows)
+
+On Linux:
+
+```
+sudo apt-get install python3-tk
+```
+
+install spacr with pip
+
+```
+pip install spacr
+```
+
+To run spacr GUIs after installing spacr:
+
+To generate masks:
+```
+gui_mask
+```
+To generate measurements and cropped images:
+```
+gui_measure
+```
+To curate masks for finetuning cellpose models:
+```
+gui_make_masks
+```
+To annotate paths to images in sql database created in gui_measure:
+```
+gui_annotate
+```
+Train torch CNNs/Transformers to classify single object images.
+```
+gui_classify
+```
+Simulate spatial phenotype screens.
+```
+gui_sim
+```

spacr-0.0.2/setup.py

@@ -0,0 +1,63 @@
+from setuptools import setup, find_packages
+
+# Ensure you have read the README.md content into a variable, e.g., `long_description`
+with open("README.md", "r", encoding="utf-8") as fh:
+    long_description = fh.read()
+
+dependencies = [
+    'torch>=2.2.1',
+    'torchvision>=0.17.1',
+    'torch-geometric>=2.5.1',
+    'numpy>=1.26.4',
+    'pandas>=2.2.1',
+    'statsmodels>=0.14.1',
+    'scikit-image>=0.22.0',
+    'scikit-learn>=1.4.1',
+    'seaborn>=0.13.2',
+    'matplotlib>=3.8.3',
+    'pillow>=10.2.0',
+    'imageio>=2.34.0',
+    'scipy>=1.12.0',
+    'ipywidgets>=8.1.2',
+    'mahotas>=1.4.13',
+    'btrack>=0.6.5',
+    'trackpy>=0.6.2',
+    'cellpose>=3.0.6',
+    'IPython>=8.18.1',
+    'opencv-python-headless>=4.9.0.80',
+    'umap>=0.1.1',
+    'ttkthemes>=3.2.2',
+    'lxml>=5.1.0'
+]
+
+setup(
+    name="spacr",
+    version="0.0.2",
+    author="Einar Birnir Olafsson",
+    author_email="olafsson@med.umich.com",
+    description="Spatial phenotype analysis of crisp screens (SpaCr)",
+    long_description=long_description,
+    url="https://github.com/EinarOlafsson/spacr",
+    packages=find_packages(exclude=["tests.*", "tests"]),
+    install_requires=dependencies,
+    entry_points={
+        'console_scripts': [
+            'gui_mask=spacr.gui_mask_app:gui_mask',
+            'gui_measure=spacr.gui_measure_app:gui_measure',
+            'gui_make_masks=spacr.mask_app:gui_make_masks',
+            'gui_annotation=spacr.annotate_app:gui_annotation',
+            'gui_classify=spacr.gui_classify_app:gui_classify',
+            'gui_sim=spacr.gui_sim_app:gui_sim',
+        ],
+    },
+    extras_require={
+        'dev': ['pytest>=3.9'],
+        'headless': ['opencv-python-headless'],
+        'full': ['opencv-python'],
+    },
+    classifiers=[
+        "Programming Language :: Python :: 3",
+        "License :: OSI Approved :: MIT License",
+        "Operating System :: OS Independent",
+    ]
+)

{spacr-0.0.1 → spacr-0.0.2}/spacr/__init__.py

@@ -11,9 +11,11 @@ from . import timelapse
 from . import train
 from . import mask_app
 from . import annotate_app
+from . import graph_learning
 from . import gui_utils
 from . import gui_mask_app
 from . import gui_measure_app
+from . import gui_classify_app
 from . import logger
 
 __all__ = [
@@ -26,10 +28,12 @@ __all__ = [
     "timelapse",
     "train",
     "annotate_app",
+    "graph_learning",
     "gui_utils",
     "mask_app",
     "gui_mask_app",
     "gui_measure_app",
+    "gui_classify_app",
     "logger"
 ]
 

spacr-0.0.2/spacr/alpha.py

@@ -0,0 +1,18 @@
+def gui_mask():
+    from .cli import get_arg_parser
+    from .version import version_str
+
+    args = get_arg_parser().parse_args()
+    
+    if args.version:
+        print(version_str)
+        return
+
+    if args.headless:
+        settings = {}
+        spacr.core.preprocess_generate_masks(settings['src'], settings=settings, advanced_settings={})
+        return
+
+    global vars_dict, root
+    root, vars_dict = initiate_mask_root(1000, 1500)
+    root.mainloop()

spacr-0.0.2/spacr/cli.py

@@ -0,0 +1,41 @@
+"""
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu and Michael Rariden.
+"""
+
+import argparse
+
+import argparse
+
+
+def get_arg_parser():
+    """ Parses command line arguments for spacr main functions
+
+    Note: this function has to be in a separate file to allow autodoc to work for CLI.
+    The autodoc_mock_imports in conf.py does not work for sphinx-argparse sometimes,
+    see https://github.com/ashb/sphinx-argparse/issues/9#issue-1097057823
+    """
+    
+    parser = argparse.ArgumentParser(description="SPACR Mask App Command Line Parameters")
+    hardware_args = parser.add_argument_group("Hardware Arguments")
+    input_img_args = parser.add_argument_group("Input Image Arguments")
+    #model_args = parser.add_argument_group("Model Arguments")
+    #algorithm_args = parser.add_argument_group("Algorithm Arguments")
+    #training_args = parser.add_argument_group("Training Arguments")
+    #output_args = parser.add_argument_group("Output Arguments")
+    
+    # misc settings
+    parser.add_argument("--version", action="store_true",
+                        help="show version info")
+    # misc settings
+    parser.add_argument("--headless", action="store_true",
+                        help="run the app without the gui")
+    
+    parser.add_argument("--verbose", action="store_true",
+                        help="show information about running and settings and save to log")
+    
+    hardware_args.add_argument("--gpu_device", required=False, default="0", type=str,
+                               help="which gpu device to use, use an integer for torch, or mps for M1")
+    
+    input_img_args.add_argument("--src", default=[], type=str,
+                                help="folder containing data to run or train on.")
+    return parser