Fixing dependencies

Author: FabianHoerst

.gitignore

@@ -33,3 +33,5 @@ test_database/dicom_leica_anonymized
 test_database/dicom_wsidicomizer
 mask_ihc.ipynb
 test_output
+debug*
+idc*

pathopatch/cli.py

@@ -683,9 +683,9 @@ def store_config(self) -> None:
         for k, v in config_repr_str.items():
             config_repr[k] = v
         # convert the string to Path
-        log_path = Path(self.preprocessing.log_path)
+        log_path = Path(self.preprocessconfig.log_path)
 
-        #using the / to join paths
+        # using the / to join paths
         config_file_path = log_path / "config.yaml"
 
         # store in log directory

pathopatch/patch_extraction/patch_extraction.py

@@ -1211,6 +1211,7 @@ def process_queue(
                 patch_mask = np.zeros(
                     (tile_size, tile_size), dtype=np.uint8
                 )  # TODO: continue missing?
+                continue
             else:
                 intersected_labels, ratio, patch_mask = get_intersected_labels(
                     tile_size=tile_size,

pathopatch/utils/masking.py

@@ -238,8 +238,12 @@ def apply_otsu_thresholding(tile: np.ndarray) -> np.ndarray:
     otsu_masking = masked_image_gray < thresh
     # improving mask
     otsu_masking = sk_morphology.remove_small_objects(otsu_masking, 60)
-    otsu_masking = sk_morphology.dilation(otsu_masking, sk_morphology.square(12))
-    otsu_masking = sk_morphology.closing(otsu_masking, sk_morphology.square(5))
+    with warnings.catch_warnings():
+        warnings.filterwarnings(
+            "ignore", category=FutureWarning, message=".*square.*deprecated.*"
+        )
+        otsu_masking = sk_morphology.dilation(otsu_masking, sk_morphology.square(12))
+        otsu_masking = sk_morphology.closing(otsu_masking, sk_morphology.square(5))
     otsu_masking = sk_morphology.remove_small_holes(otsu_masking, 250)
     tile = mask_rgb(tile, otsu_masking).astype(np.uint8)
 

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pathopatch"
-version = "1.0.6"
+version = "1.0.8"
 authors = [
     {name = "Fabian Hörst", email = "[email protected]"},
 ]
@@ -25,26 +25,26 @@ license = { text = "CC-BY-ND-4.0" }
 dependencies = [
     "Pillow>=9.5.0",
     "PyYAML",
-    "Shapely==1.8.5.post1",
+    "Shapely>=1.8.5.post1,<=2.0.5",
     "colorama",
     "future",
     "geojson>=3.0.0",
     "matplotlib",
     "natsort",
-    "numpy>1.22,<1.24",
+    "numpy<2.0.0",
     "opencv_python_headless",
     "openslide_python",
     "pandas",
     "pydantic==1.10.4",
     "rasterio==1.3.5.post1",
     "requests",
-    "scikit-image",
+    "scikit-image<0.27",
     "setuptools<=65.6.3",
     "tqdm",
     "torchvision",
     "torch",
-    "wsidicom==0.20.4",
-    "wsidicomizer==0.14.1",
+    "wsidicom",
+    "wsidicomizer",
     "pydicom==2.4.4",
 ]
 

requirements.txt

@@ -15,7 +15,7 @@ pandas
 pydantic==1.10.4
 rasterio==1.3.5.post1
 requests
-scikit-image
+scikit-image<0.27
 setuptools<=65.6.3
 tqdm
 torchvision