debugging

SPIDER.py

@@ -44,15 +44,16 @@ def subset_file_list(all_files: List[str], subset_ids: Set[int]):
 
 def standardize_3D_image(
     image: np.ndarray,
-    resize_shape: Tuple[int, int, int]
+    resize_shape: Tuple[int, int]
 ) -> np.ndarray:
     """Aligns dimensions of image to be (height, width, channels) and resizes
-    images to values specified in resize_shape."""
+    images to values specified in resize_shape (note that original channels
+    are preserved)."""
     # Align height, width, channel dims
     if image.shape[0] < image.shape[2]:
         image = np.transpose(image, axes=[1, 2, 0])
     # Resize image
-    image = skimage.transform.resize(image, resize_shape)
+    image = skimage.transform.resize(image, resize_shape) # Preserves original channels
     # Rescale to UInt8 type
     image = skimage.img_as_ubyte(image)
     return image
@@ -63,7 +64,7 @@ N_PATIENTS = 218
 MIN_IVD = 0
 MAX_IVD = 9
 DEFAULT_SCAN_TYPES = ['t1', 't2', 't2_SPACE']
-DEFAULT_RESIZE = (512, 512, 30)
+DEFAULT_RESIZE = (512, 512)
 
 _CITATION = """\
 @misc{vandergraaf2023lumbar,
@@ -193,8 +194,8 @@ class SPIDER(datasets.GeneratorBasedBuilder):
         features = datasets.Features({
             "patient_id": datasets.Value("string"),
             "scan_type": datasets.Value("string"),
-            "image": datasets.Image("uint8"),
-            "mask": datasets.Image("uint8"),
+            "image": datasets.Array3D(dtype='uint8'),
+            "mask": datasets.Array3D(dtype='uint8'),
             # "image": datasets.Array3D(shape=self.config.resize_shape, dtype='uint8'),
             # "mask": datasets.Array3D(shape=self.config.resize_shape, dtype='uint8'),
             "image_path": datasets.Value("string"),
@@ -519,8 +520,8 @@ class SPIDER(datasets.GeneratorBasedBuilder):
             return_dict = {
                 'patient_id':patient_id,
                 'scan_type':scan_type,
-                'image':datasets.Image().encode_example(image_array_standardized),
-                'mask':datasets.Image().encode_example(mask_array_standardized),
+                'image_array':image_array_standardized,
+                'mask_array':mask_array_standardized,
                 'image_path':image_path, 
                 'mask_path':mask_path, 
                 'metadata':image_overview,