Fixing detector path

.github/workflows/test_build.yml

@@ -40,7 +40,5 @@ jobs:
       run: python -m pytest -vv -s ./tests/test_macenko_module
     - name : Run Core Tests
       run: python -m pytest -vv -s ./tests/test_core_modules
-    - name : Run Dicom Tests
-      run: python -m pytest -vv -s ./tests/test_dicom_module
     - name : Run Dataset and Dataloader Tests
       run: python -m pytest -vv -s ./tests/test_pytorch_dataset

pathopatch/patch_extraction/dataset.py

@@ -325,7 +325,7 @@ 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(
-            "./pathopatch/data/tissue_detector.pt",  # this causes errors
+            "/pathopatch/data/tissue_detector.pt",  # this causes errors
             map_location=self.detector_device,
         )
         model.load_state_dict(checkpoint["model_state_dict"])

pathopatch/patch_extraction/patch_extraction.py

@@ -478,7 +478,9 @@ 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(
-            "./pathopatch/data/tissue_detector.pt",  # this causes errors
+            (
+                Path(os.path.dirname(__file__)).parent / "data" / "tissue_detector.pt"
+            ).resolve(),
             map_location=self.detector_device,
         )
         model.load_state_dict(checkpoint["model_state_dict"])

pathopatch/wsi_interfaces/wsidicomizer_openslide.py

@@ -17,7 +17,14 @@ def __init__(self, dcm_folder: Union[Path, str]) -> None:
         self.level_count: int
         self.level_downsamples: List[float]
 
-        source = WsiDicomFileSource.open(dcm_folder)
+        # iterate through the folder to check if a DICOMDIR file exists
+        dcm_folder = Path(dcm_folder)
+        files = [f for f in dcm_folder.iterdir() if f.is_file()]
+        if not any(f.name == "DICOMDIR" for f in files):
+            source = WsiDicomFileSource.open(dcm_folder)
+        else:
+            source = WsiDicomFileSource.open_dicomdir(dcm_folder / "DICOMDIR")
+
         super().__init__(source, True)
 
         # information and properties to make this compatible with OpenSlide

setup.py

@@ -1,6 +1,6 @@
 from setuptools import find_packages, setup
 
-VERSION = "1.0.1b"
+VERSION = "1.0.4b"
 DESCRIPTION = "PathoPatch - Accelerating Artificial Intelligence Based Whole Slide Image Analysis with an Optimized Preprocessing Pipeline"
 with open("docs/README_pypi.md", "r") as fh:
     LONG_DESCRIPTION = fh.read()
@@ -39,8 +39,8 @@
         "tqdm",
         "torchvision",
         "torch",
-        "wsidicom=0.20.4",
-        "wsidicomizer=0.13.2",
+        "wsidicom==0.20.4",
+        "wsidicomizer==0.13.2",
     ],
     scripts=[
         "pathopatch/wsi_extraction.py",
@@ -64,4 +64,6 @@
         "Operating System :: Microsoft :: Windows",
         "Operating System :: POSIX :: Other",
     ],
+    include_package_data=True,
+    package_data={"pathopatch": ["data/*"]},
 )

test.sh

@@ -0,0 +1,6 @@
+python -m pytest -vv -s ./tests/test_cli
+python -m pytest -vv -s ./tests/test_utils
+python -m pytest -vv -s ./tests/test_macenko_module
+python -m pytest -vv -s ./tests/test_core_modules
+python -m pytest -vv -s ./tests/test_dicom_module
+python -m pytest -vv -s ./tests/test_pytorch_dataset

test_database/download_links.txt

@@ -1,3 +1,4 @@
 https://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/CMU-1.svs
 https://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/CMU-1-Small-Region.svs
 https://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/JP2K-33003-1.svs
+https://drive.google.com/uc?export=download&id=15EjjYxtWf3_o_H4REckK1A0A8JGbpWC6

tests/static_test_files/preprocessing/baseline/config.yaml

@@ -10,3 +10,6 @@ processes: 8
 # other
 log_level: debug
 overwrite: True
+
+apply_prefilter: True
+filter_patches: True