Merge pull request #2 from TIO-IKIM/setup

Adding build

.gitignore

@@ -12,11 +12,9 @@ notebooks
 
 # local configs
 .vscode
-Tissue-Classifier-Data
-tests_backup
-tests/static_test_files/preprocessing/basic
-tests/static_test_files/preprocessing/complex_annotation
-tests/static_test_files/preprocessing/custom
-tests/static_test_files/preprocessing/overlap
 tests/tmp_results_folder/*
-output
+
+# Build
+pathopatch.egg-info/
+dist
+build

LICENSE.md

@@ -0,0 +1 @@
+<p xmlns:cc="http://creativecommons.org/ns#" xmlns:dct="http://purl.org/dc/terms/"><a property="dct:title" rel="cc:attributionURL" href="https://github.com/TIO-IKIM/PathoPatcher">PathoPatcher</a> by <a rel="cc:attributionURL dct:creator" property="cc:attributionName" href="https://github.com/FabianHoerst">Fabian Hörst, University Hospital Essen,</a> is licensed under <a href="http://creativecommons.org/licenses/by-nc-sa/4.0/?ref=chooser-v1" target="_blank" rel="license noopener noreferrer" style="display:inline-block;">CC BY-NC-SA 4.0<img style="height:22px!important;margin-left:3px;vertical-align:text-bottom;" src="https://mirrors.creativecommons.org/presskit/icons/cc.svg?ref=chooser-v1"><img style="height:22px!important;margin-left:3px;vertical-align:text-bottom;" src="https://mirrors.creativecommons.org/presskit/icons/by.svg?ref=chooser-v1"><img style="height:22px!important;margin-left:3px;vertical-align:text-bottom;" src="https://mirrors.creativecommons.org/presskit/icons/nc.svg?ref=chooser-v1"><img style="height:22px!important;margin-left:3px;vertical-align:text-bottom;" src="https://mirrors.creativecommons.org/presskit/icons/sa.svg?ref=chooser-v1"></a></p>

README.md

@@ -275,3 +275,6 @@ TBD
 
 ## Citation
 TBD
+
+## License
+<p xmlns:cc="http://creativecommons.org/ns#" xmlns:dct="http://purl.org/dc/terms/"><a property="dct:title" rel="cc:attributionURL" href="https://github.com/TIO-IKIM/PathoPatcher">PathoPatcher</a> by <a rel="cc:attributionURL dct:creator" property="cc:attributionName" href="https://github.com/FabianHoerst">Fabian Hörst, University Hospital Essen,</a> is licensed under <a href="http://creativecommons.org/licenses/by-nc-sa/4.0/?ref=chooser-v1" target="_blank" rel="license noopener noreferrer" style="display:inline-block;">CC BY-NC-SA 4.0<img style="height:22px!important;margin-left:3px;vertical-align:text-bottom;" src="https://mirrors.creativecommons.org/presskit/icons/cc.svg?ref=chooser-v1"><img style="height:22px!important;margin-left:3px;vertical-align:text-bottom;" src="https://mirrors.creativecommons.org/presskit/icons/by.svg?ref=chooser-v1"><img style="height:22px!important;margin-left:3px;vertical-align:text-bottom;" src="https://mirrors.creativecommons.org/presskit/icons/nc.svg?ref=chooser-v1"><img style="height:22px!important;margin-left:3px;vertical-align:text-bottom;" src="https://mirrors.creativecommons.org/presskit/icons/sa.svg?ref=chooser-v1"></a></p>

environment.yaml

@@ -4,59 +4,31 @@ channels:
   - defaults
 dependencies:
   - python=3.10.12
-  - openslide=3.4.1
+  - openslide=4.0.0
   - pip=23.0
   - python-javabridge
   - pip:
     - Pillow==9.5.0
     - PyYAML==6.0
     - Shapely==1.8.5.post1
-    - SimpleITK==2.2.1
-    - albumentations==1.3.0
     - black==23.1.0
-    - csbdeep==0.7.4
     - colorama==0.4.6
-    - einops==0.6.1
     - flake8-html==0.4.3
     - flake8==6.0.0
-    - future==0.18.2
     - genbadge==1.1.0
     - geojson==3.0.0
-    - h5py==3.9.0
     - histolab==0.6.0
-    - imageio==2.31.1
-    - ipython-genutils==0.2.0
-    - jupyterlab==4.0.2
-    - kaleido==0.2.1
-    - keras==2.12.0
-    - keras==2.12.0
-    - mako==1.2.4
     - matplotlib==3.7.1
     - natsort==8.4.0
     - numpy>1.22,<1.24
     - opencv_python_headless==4.5.4.58
     - openslide_python==1.2.0
-    - pandarallel==1.6.5
     - pandas==1.5.3
     - pre-commit==3.0.3
     - pydantic==1.10.4
-    - pyjwt==2.6.0
     - pytest==7.4.4
     - pytest-sugar==0.9.7
     - rasterio==1.3.5.post1
-    - schema==0.7.5
     - scikit-image==0.19.3
-    - scikit-learn==1.2.1
-    - scikit-survival==0.21.0
-    - scipy>1.5.0,<=1.8.2
-    - seaborn==0.12.2
-    - sqlalchemy==2.0.17
-    - stardist==0.8.5
-    - tabulate==0.9.0
-    - tensorflow==2.12.0
-    - torchinfo==1.8.0
-    - torchmetrics==0.11.4
     - torchvision==0.16.2
     - tqdm==4.65.0
-    - ujson==5.8.0
-    - wandb==0.15.4

pathopatcher/annotation_conversion.py → pathopatch/annotation_conversion.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python
+
 # -*- coding: utf-8 -*-
 # Geojson annotation preprocessing
 #

pathopatcher/cli.py → pathopatch/cli.py

@@ -16,9 +16,9 @@
 import yaml
 from pydantic import BaseModel, validator
 
-from pathopatcher.base_ml.base_cli import ABCParser
-from pathopatcher.config.config import ANNOTATION_EXT, LOGGING_EXT, WSI_EXT
-from pathopatcher.utils.logger import Logger
+from pathopatch.base_ml.base_cli import ABCParser
+from pathopatch.config.config import ANNOTATION_EXT, LOGGING_EXT, WSI_EXT
+from pathopatch.utils.logger import Logger
 
 
 class PreProcessingYamlConfig(BaseModel):

pathopatcher/macenko.py → pathopatch/macenko_vector_generation.py

@@ -1,4 +1,12 @@
+#!/usr/bin/env python
+
 # -*- coding: utf-8 -*-
+# Main entry point for Macenko
+#
+# @ Fabian Hörst, [email protected]
+# Institute for Artifical Intelligence in Medicine,
+# University Medicine Essen
+
 import inspect
 import logging
 import os
@@ -15,10 +23,11 @@
 parentdir = os.path.dirname(parentdir)
 sys.path.insert(0, parentdir)
 
-from pathopatcher.cli import MacenkoParser
-from pathopatcher.patch_extraction.patch_extraction import PreProcessor
+from pathopatch.cli import MacenkoParser
+from pathopatch.patch_extraction.patch_extraction import PreProcessor
 
-if __name__ == "__main__":
+
+def main():
     configuration_parser = MacenkoParser()
     configuration, logger = configuration_parser.get_config()
 
@@ -28,3 +37,7 @@
     )
 
     logger.info("Finished Macenko Vector Calculation!")
+
+
+if __name__ == "__main__":
+    main()

pathopatcher/patch_extraction/patch_extraction.py → pathopatch/patch_extraction/patch_extraction.py

@@ -31,15 +31,15 @@
 from shapely.geometry import Polygon
 from tqdm import tqdm
 
-from pathopatcher import logger
-from pathopatcher.cli import PreProcessingConfig
-from pathopatcher.patch_extraction.storage import Storage
-from pathopatcher.utils.exceptions import (
+from pathopatch import logger
+from pathopatch.cli import PreProcessingConfig
+from pathopatch.patch_extraction.storage import Storage
+from pathopatch.utils.exceptions import (
     UnalignedDataException,
     WrongParameterException,
 )
-from pathopatcher.utils.patch_dataset import load_tissue_detection_dl
-from pathopatcher.utils.patch_util import (
+from pathopatch.utils.patch_dataset import load_tissue_detection_dl
+from pathopatch.utils.patch_util import (
     DeepZoomGeneratorOS,
     calculate_background_ratio,
     compute_interesting_patches,
@@ -55,7 +55,7 @@
     target_mag_to_downsample,
     target_mpp_to_downsample,
 )
-from pathopatcher.utils.tools import end_timer, module_exists, start_timer
+from pathopatch.utils.tools import end_timer, module_exists, start_timer
 
 warnings.filterwarnings("ignore", category=DeprecationWarning)
 warnings.filterwarnings("ignore", category=UserWarning)
@@ -414,7 +414,7 @@ def _set_hardware(self, hardware_selection: str = "cucim") -> None:
             logger.info("Using CuCIM")
             from cucim import CuImage
 
-            from pathopatcher.patch_extraction.cucim_deepzoom import (
+            from pathopatch.patch_extraction.cucim_deepzoom import (
                 DeepZoomGeneratorCucim,
             )
 
@@ -458,7 +458,7 @@ def _set_tissue_detector(self) -> None:
         model = mobilenet_v3_small().to(device=self.detector_device)
         model.classifier[-1] = nn.Linear(1024, 4)
         checkpoint = torch.load(
-            "./pathopatcher/data/tissue_detector.pt",
+            "./pathopatch/data/tissue_detector.pt", # this causes errors
             map_location=self.detector_device,
         )
         model.load_state_dict(checkpoint["model_state_dict"])

pathopatcher/patch_extraction/process_batch.py → pathopatch/patch_extraction/process_batch.py

@@ -15,7 +15,7 @@
 from PIL import Image
 from shapely.geometry import Polygon
 
-from pathopatcher.utils.patch_util import (
+from pathopatch.utils.patch_util import (
     DeepZoomGeneratorOS,
     calculate_background_ratio,
     get_intersected_labels,
@@ -24,9 +24,9 @@
     patch_to_tile_size,
     standardize_brightness,
 )
-from pathopatcher.utils.tools import module_exists
+from pathopatch.utils.tools import module_exists
 
-from pathopatcher import logger
+from pathopatch import logger
 
 
 def process_batch(
@@ -107,7 +107,7 @@ def process_batch(
     if module_exists("cucim", error="ignore"):
         from cucim import CuImage
 
-        from pathopatcher.deepzoom.cucim_deepzoom import DeepZoomGeneratorCucim
+        from pathopatch.deepzoom.cucim_deepzoom import DeepZoomGeneratorCucim
 
         generator_module = DeepZoomGeneratorCucim
         image_loader = CuImage

pathopatcher/utils/logger.py → pathopatch/utils/logger.py

@@ -14,7 +14,7 @@
 import sys
 
 from colorama import init
-from pathopatcher.config.config import COLOR_CODES_LOGGING
+from pathopatch.config.config import COLOR_CODES_LOGGING
 
 init(autoreset=True)
 

pathopatcher/utils/masking.py → pathopatch/utils/masking.py

@@ -22,7 +22,7 @@
 from shapely.affinity import scale
 from shapely.geometry import Polygon
 
-from pathopatcher import logger
+from pathopatch import logger
 
 
 def generate_tissue_mask(

pathopatcher/utils/patch_util.py → pathopatch/utils/patch_util.py

@@ -24,13 +24,13 @@
 from shapely.geometry import Polygon, shape
 from shapely.validation import make_valid
 
-from pathopatcher import logger
-from pathopatcher.utils.exceptions import WrongParameterException
-from pathopatcher.utils.masking import (
+from pathopatch import logger
+from pathopatch.utils.exceptions import WrongParameterException
+from pathopatch.utils.masking import (
     convert_polygons_to_mask,
     generate_tissue_mask,
 )
-from pathopatcher.utils.plotting import generate_polygon_overview
+from pathopatch.utils.plotting import generate_polygon_overview
 
 
 def get_files_from_dir(

pathopatcher/utils/plotting.py → pathopatch/utils/plotting.py

@@ -16,8 +16,8 @@
 from rasterio.mask import mask as rasterio_mask
 from shapely.geometry import Polygon
 
-from pathopatcher.config.config import COLOR_DEFINITIONS
-from pathopatcher.utils.masking import get_filtered_polygons
+from pathopatch.config.config import COLOR_DEFINITIONS
+from pathopatch.utils.masking import get_filtered_polygons
 
 
 def generate_polygon_overview(

pathopatcher/utils/tools.py → pathopatch/utils/tools.py

@@ -13,7 +13,7 @@
 from timeit import default_timer as timer
 from typing import Dict, List, Optional, Tuple, Union
 
-from pathopatcher import logger
+from pathopatch import logger
 
 
 # Helper timing functions

pathopatcher/main_extraction.py → pathopatch/wsi_extraction.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python
+
 # -*- coding: utf-8 -*-
 # Main entry point for patch-preprocessing
 #
@@ -8,21 +10,22 @@
 import sys
 import os
 
-project_root = os.path.dirname(os.path.abspath(__file__))
-sys.path.append(project_root)
-project_root = os.path.dirname(os.path.abspath(project_root))
-sys.path.append(project_root)
+# project_root = os.path.dirname(os.path.abspath(__file__))
+# sys.path.append(project_root)
+# project_root = os.path.dirname(os.path.abspath(project_root))
+# sys.path.append(project_root)
 
 import logging
 
 logger = logging.getLogger()
 logger.addHandler(logging.NullHandler())
 
-from pathopatcher.cli import PreProcessingParser
-from pathopatcher.patch_extraction.patch_extraction import PreProcessor
-from pathopatcher.utils.tools import close_logger
+from pathopatch.cli import PreProcessingParser
+from pathopatch.patch_extraction.patch_extraction import PreProcessor
+from pathopatch.utils.tools import close_logger
 
-if __name__ == "__main__":
+
+def main():
     configuration_parser = PreProcessingParser()
     configuration, logger = configuration_parser.get_config()
     configuration_parser.store_config()
@@ -32,3 +35,7 @@
 
     logger.info("Finished Preprocessing.")
     close_logger(logger)
+
+
+if __name__ == "__main__":
+    main()

requirements.txt

@@ -0,0 +1,21 @@
+Pillow>=9.5.0
+PyYAML
+Shapely==1.8.5.post1
+colorama
+future
+geojson==3.0.0
+histolab==0.6.0
+matplotlib
+natsort
+numpy>1.22,<1.24
+opencv_python_headless
+openslide_python
+pandas
+pydantic==1.10.4
+rasterio==1.3.5.post1
+requests
+scikit-image
+setuptools<=65.6.3
+tqdm
+torchvision
+torch

requirements_develop.txt

@@ -0,0 +1,27 @@
+Pillow>=9.5.0
+PyYAML
+Shapely==1.8.5.post1
+black
+colorama
+flake8
+flake8-html
+genbadge
+geojson==3.0.0
+histolab==0.6.0
+matplotlib
+natsort
+numpy>1.22,<1.24
+opencv_python_headless
+openslide_python
+pandas
+pre-commit
+pydantic==1.10.4
+pytest
+pytest-sugar
+rasterio==1.3.5.post1
+requests
+scikit-image
+setuptools<=65.6.3
+tqdm
+torchvision
+torch