roi_size moved to common section; added multi image extentions support

README.md

@@ -52,33 +52,36 @@ Your data directory must follow this hierarchy:
 
 ```
 path_to_data_folder/
-├── images/        # Input images
+├── images/        # Input images (any supported format)
 │   ├── img1.tif
-│   ├── img2.tif
+│   ├── img2.png
-│   └── ...
+│   └── …
-└── masks/         # Ground-truth instance masks
+└── masks/         # Ground-truth instance masks (any supported format)
     ├── mask1.tif
-    ├── mask2.tif
+    ├── mask2.jpg
-    └── ...
+    └── …
 ```
 
 If your dataset contains multiple classes (e.g., class A and B) and you prefer not to duplicate images, you can organize masks into class-specific subdirectories:
 
 ```
 path_to_data_folder/
-├── images/
+├── images/        # Input images (any supported format)
-│   └── img1.tif
+│   └── img1.bmp
 └── masks/
-    ├── A/      # Masks for class A
+    ├── A/         # Masks for class A (any supported format)
-    │   ├── img1_mask.tif
+    │   ├── img1_mask.png
-    │   └── ...
+    │   └── …
-    └── B/      # Masks for class B
+    └── B/         # Masks for class B (any supported format)
-        ├── img1_mask.tif
+        ├── img1_mask.jpeg
-        └── ...
+        └── …
 ```
 
 In this case, set the `masks_subdir` field in your dataset configuration to the name of the mask subdirectory (e.g., `"A"` or `"B"`).
 
+**Supported file formats**: Image and mask files can have any of these extensions:
+`tif`, `tiff`, `png`, `jpg`, `bmp`, `jpeg`.
+
 **Mask format**: Instance masks should be provided for multi-label segmentation with channel-last ordering, i.e., each mask array must have shape `(H, W, C)`.
 
 ---

config/dataset_config.py

@@ -10,6 +10,7 @@ class DatasetCommonConfig(BaseModel):
     seed: Optional[int] = 0         # Seed for splitting if data is not pre-split (and all random operations)
     device: str = "cuda:0"          # Device used for training/testing (e.g., 'cpu' or 'cuda')
     use_amp: bool = False           # Flag to use Automatic Mixed Precision (AMP)
+    roi_size: int = 512             # The size of the square window for cropping
     masks_subdir: str = ""          # Subdirectory where the required masks are located, e.g. 'masks/cars'
     predictions_dir: str = "."      # Directory to save predictions
     pretrained_weights: str = ""    # Path to pretrained weights
@@ -21,6 +22,8 @@ class DatasetCommonConfig(BaseModel):
         """
         if not self.device:
             raise ValueError("device must be provided and non-empty")
+        if self.roi_size <= 0:
+            raise ValueError("roi_size must be > 0")
         return self
 
 
@@ -70,7 +73,6 @@ class DatasetTrainingConfig(BaseModel):
     test_offset: int = 0            # Offset for testing data 
 
     batch_size: int = 1             # Batch size for training
-    roi_size: int = 512             # The size of the square window for cropping
     num_epochs: int = 100           # Number of training epochs
     val_freq: int = 1               # Frequency of validation during training
 
@@ -124,14 +126,11 @@ class DatasetTrainingConfig(BaseModel):
         """
         Validates numeric fields:
         - batch_size and num_epochs must be > 0.
-        - roi_size must be > 0.
         - val_freq must be >= 0.
         - offsets must be >= 0.
         """
         if self.batch_size <= 0:
             raise ValueError("batch_size must be > 0")
-        if self.roi_size <= 0:
-            raise ValueError("roi_size must be > 0")
         if self.num_epochs <= 0:
             raise ValueError("num_epochs must be > 0")
         if self.val_freq < 0:

core/data/transforms/load_image.py

@@ -1,7 +1,7 @@
 import numpy as np
 import tifffile as tif
 import skimage.io as io
-from typing import List, Optional, Sequence, Type, Union
+from typing import Final, List, Optional, Sequence, Type, Union
 
 from monai.utils.enums import PostFix
 from monai.utils.module import optional_import
@@ -24,8 +24,11 @@ __all__ = [
     "CustomLoadImaged",        # Dictionary-based image loader
     "CustomLoadImageD",        # Dictionary-based image loader
     "CustomLoadImageDict",     # Dictionary-based image loader
+    "SUPPORTED_IMAGE_FORMATS"
 ]
 
+SUPPORTED_IMAGE_FORMATS: Final[Sequence[str]] = ["tif", "tiff", "png", "jpg", "bmp", "jpeg"]
+
 
 class CustomLoadImage(LoadImage):
     """
@@ -150,8 +153,7 @@ class UniversalImageReader(NumpyReader):
         
         Supported extensions: tif, tiff, png, jpg, bmp, jpeg.
         """
-        suffixes: Sequence[str] = ["tif", "tiff", "png", "jpg", "bmp", "jpeg"]
+        return has_itk or is_supported_format(filename, SUPPORTED_IMAGE_FORMATS)
-        return has_itk or is_supported_format(filename, suffixes)
 
     def read(self, data: Union[Sequence[PathLike], PathLike], **kwargs):
         """

core/segmentator.py

@@ -38,6 +38,7 @@ import csv
 import copy
 import time
 import tifffile as tiff
+from itertools import chain
 
 from pprint import pformat
 from tabulate import tabulate
@@ -56,6 +57,7 @@ from core.utils import (
     compute_f1_score,
     compute_average_precision_score
 )
+from core.data.transforms.load_image import SUPPORTED_IMAGE_FORMATS
 
 from core.logger import get_logger
 
@@ -749,8 +751,9 @@ class CellSegmentator:
         """
         # Collect sorted list of image paths
         images = sorted(
-            glob.glob(os.path.join(images_dir, '*.tif')) +
+            chain(glob.glob(
-            glob.glob(os.path.join(images_dir, '*.tiff'))
+                os.path.join(images_dir, f'*.{ext}')) for ext in SUPPORTED_IMAGE_FORMATS
+            )
         )
         if not images:
             raise FileNotFoundError(f"No images found in path or pattern: '{images_dir}'")
@@ -758,8 +761,9 @@ class CellSegmentator:
         if masks_dir is not None:
             # Collect and validate sorted list of mask paths
             masks = sorted(
-                glob.glob(os.path.join(masks_dir, '*.tif')) +
+                chain(glob.glob(
-                glob.glob(os.path.join(masks_dir, '*.tiff'))
+                    os.path.join(masks_dir, f'*.{ext}')) for ext in SUPPORTED_IMAGE_FORMATS
+                )
             )
             if len(images) != len(masks):
                 raise ValueError(f"Number of masks ({len(masks)}) does not match number of images ({len(images)})")
@@ -1031,7 +1035,7 @@ class CellSegmentator:
             # Use sliding window inference for non-training phases
             outputs = sliding_window_inference(
                 inputs,
-                roi_size=512,
+                roi_size=self._dataset_setup.common.roi_size,
                 sw_batch_size=4,
                 predictor=self._model,
                 padding_mode="constant",

main.py

@@ -60,7 +60,7 @@ def main():
     segmentator = CellSegmentator(config)
     segmentator.create_dataloaders(
         train_transforms=get_train_transforms(
-            roi_size=config.dataset_config.training.roi_size) if mode == "train" else None,
+            roi_size=config.dataset_config.common.roi_size) if mode == "train" else None,
         valid_transforms=get_valid_transforms() if mode == "train" else None,
         test_transforms=get_test_transforms() if mode in ("train", "test") else None,
         predict_transforms=get_predict_transforms() if mode == "predict" else None