Update

src/utils/config_manager.py

@@ -54,7 +54,7 @@ class ConfigManager:
                 "models_directory": "data/models",
                 "base_model_choices": [
                     "yolov8s-seg.pt",
-                    "yolov11s-seg.pt",
+                    "yolo11s-seg.pt",
                 ],
             },
             "training": {
@@ -225,6 +225,4 @@ class ConfigManager:
 
     def get_allowed_extensions(self) -> list:
         """Get list of allowed image file extensions."""
-        return self.get(
-            "image_repository.allowed_extensions", Image.SUPPORTED_EXTENSIONS
-        )
+        return self.get("image_repository.allowed_extensions", Image.SUPPORTED_EXTENSIONS)

src/utils/image.py

@@ -46,9 +46,9 @@ def get_pseudo_rgb(arr: np.ndarray, gamma: float = 0.3) -> np.ndarray:
     a3[a3 > p9999] = p9999
     a3 /= a3.max()
 
-    # return np.stack([a1, np.zeros(a1.shape), np.zeros(a1.shape)], axis=0)
+    return np.stack([a1, np.zeros(a1.shape), np.zeros(a1.shape)], axis=0)
     return np.stack([a2, np.zeros(a1.shape), np.zeros(a1.shape)], axis=0)
-    return np.stack([a1, a2, a3], axis=0)
+    # return np.stack([a1, a2, a3], axis=0)
 
 
 class ImageLoadError(Exception):
@@ -114,8 +114,7 @@ class Image:
         if not is_image_file(str(self.path), self.SUPPORTED_EXTENSIONS):
             ext = self.path.suffix.lower()
             raise ImageLoadError(
-                f"Unsupported image format: {ext}. "
-                f"Supported formats: {', '.join(self.SUPPORTED_EXTENSIONS)}"
+                f"Unsupported image format: {ext}. " f"Supported formats: {', '.join(self.SUPPORTED_EXTENSIONS)}"
             )
 
         try:

src/utils/image_converters.py

@@ -18,7 +18,13 @@ class UT:
         self.rois = None
         if no_labels:
             self.rois = ImagejRoi.fromfile(self.roifile_fn)
-            self.stem = self.roifile_fn.stem.split("Roi-")[1]
+            print(self.roifile_fn.stem)
+            print(self.roifile_fn.parent.parts[-1])
+            if "Roi-" in self.roifile_fn.stem:
+                self.stem = self.roifile_fn.stem.split("Roi-")[1]
+            else:
+                self.stem = self.roifile_fn.parent.parts[-1]
+
         else:
             self.roifile_fn = roifile_fn / roifile_fn.parts[-1]
             self.stem = self.roifile_fn.stem
@@ -95,9 +101,7 @@ class UT:
             for i, roi in enumerate(self.rois):
                 rc = roi.subpixel_coordinates
                 if rc is None:
-                    print(
-                        f"No coordinates: {self.roifile_fn}, element {i}, out of {len(self.rois)}"
-                    )
+                    print(f"No coordinates: {self.roifile_fn}, element {i}, out of {len(self.rois)}")
                     continue
                 xmn, ymn = rc.min(axis=0)
                 xmx, ymx = rc.max(axis=0)
@@ -143,6 +147,9 @@ if __name__ == "__main__":
     )
     args = parser.parse_args()
 
+    # print(args)
+    # aa
+
     for path in args.input:
         print("Path:", path)
         if not args.no_labels:
@@ -152,6 +159,7 @@ if __name__ == "__main__":
 
         else:
             for rfn in Path(path).glob("*.zip"):
+                # if Path(path).suffix == ".zip":
                 print("Roi FN:", rfn)
                 ut = UT(rfn, args.no_labels)
                 ut.export_rois(args.output, class_index=0)