pdnl-process 0.1__tar.gz

pdnl_process-0.1/.github/publish.yml

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+name: Upload Python Package to PyPI when a Release is Created
+
+# build the documentation whenever there are new commits on main
+on:
+  push:
+
+jobs:
+  pypi-publish:
+    name: Publish release to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/pdnl_wildcat
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build
+      - name: Build package
+        run: python -m build
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

pdnl_process-0.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: pdnl_process
+Version: 0.1
+Summary: PDNL Process
+Project-URL: Homepage, https://github.com/PennCompPathology/pdnl_process
+Author-email: Noah Capp <noahmcapp@gmail.com>
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: >=3.9
+Requires-Dist: pdnl-sana

pdnl_process-0.1/pdnl_process/__init__.py

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+from .main import main

pdnl_process-0.1/pdnl_process/main.py

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+#!/usr/bin/env python3
+
+import os
+import sys
+import argparse
+import json
+
+import numpy as np
+import pdnl_sana.image
+import pdnl_sana.process
+import pdnl_sana.logging
+import pdnl_sana.filter
+
+from matplotlib import pyplot as plt
+
+def main():
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-i', '--input_file', help="path to image file to process", required=True)
+    parser.add_argument('-o', '--output_file', help="path to write outputs to", required=True)
+    parser.add_argument('-m', '--mask_file', help="path to mask file to apply to the image", default=None)
+    parser.add_argument('-s', '--staining_code', help="stain protocol used to stain the input image", default='H-DAB')
+    parser.add_argument('-p', '--parameters_file', help=".json file containing processing parameters", default=None)
+    parser.add_argument('--debug', action='store_true', help="plots an output image to analyze")
+    args = parser.parse_args()
+
+    frame = pdnl_sana.image.Frame(args.input_file)
+    if args.mask_file:
+        mask = pdnl_sana.image.Frame(args.mask_file)
+    else:
+        mask = None
+    if args.parameters_file:
+        params = json.load(open(args.parameters_file))
+    else:
+        params = {}
+    print(params)
+
+    file_name = os.path.splitext(os.path.basename(args.input_file))[0]
+    debug_level = 'full' if args.debug else 'normal'
+    logger = pdnl_sana.logging.Logger(debug_level, os.path.splitext(args.output_file)[0]+'.pkl')
+    print(debug_level)
+    
+    if args.staining_code == 'H-DAB':
+        processor = pdnl_sana.process.HDABProcessor(
+            logger, frame, main_mask=mask, 
+            apply_smoothing=params.get('apply_smoothing', False),
+            normalize_background=params.get('normalize_background', False),
+            stain_vector=params.get('stain_vector', None)
+        )
+
+    out = processor.run(
+        triangular_strictness=params.get('triangular_strictness', 0.0),
+        minimum_threshold=params.get('minimum_threshold', 0),
+        od_threshold=params.get('od_threshold', None),
+        morphology_filters=[pdnl_sana.filter.MorphologyFilter(**filter_params) for filter_params in params.get('morphology_filters', [])],
+    )['positive_dab']
+
+    plt.show()
+
+    out.save(args.output_file)
+    
+if __name__ == "__main__":
+    main()

pdnl_process-0.1/pyproject.toml

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+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "pdnl_process"
+version = "0.1"
+authors = [
+  { name="Noah Capp", email="noahmcapp@gmail.com" },
+]
+description = "PDNL Process"
+dependencies = [
+    "pdnl_sana"
+]
+readme = "README.md"
+requires-python = ">=3.9"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Intended Audience :: Science/Research",
+    "Development Status :: 4 - Beta",
+    "Topic :: Scientific/Engineering :: Medical Science Apps."
+]
+
+[project.urls]
+Homepage = "https://github.com/PennCompPathology/pdnl_process"
+
+[project.scripts]
+pdnl_process = "pdnl_process:main"