debugging

SPIDER.py

@@ -170,8 +170,8 @@ class SPIDER(datasets.GeneratorBasedBuilder):
         features = datasets.Features({
             "patient_id": datasets.Value("string"),
             "scan_type": datasets.Value("string"),
-            "raw_image": datasets.Image(decode=False),
-            "raw_mask": datasets.Image(decode=False),
+            "image_path": datasets.Value("string"),
+            "mask_path": datasets.Value("string"),
             "image_array": datasets.Array3D(shape=image_size, dtype='float64'),
             "mask_array": datasets.Array3D(shape=image_size, dtype='float64'),
             "metadata": {
@@ -479,8 +479,8 @@ class SPIDER(datasets.GeneratorBasedBuilder):
             image_path = os.path.join(paths_dict['images'], 'images', example)
             image = sitk.ReadImage(image_path)
             
-            # Rescale image intensities to [0, 255] and cast as UInt8 type
-            image = sitk.Cast(sitk.RescaleIntensity(image), sitk.sitkUInt8)
+            # # Rescale image intensities to [0, 255] and cast as UInt8 type
+            # image = sitk.Cast(sitk.RescaleIntensity(image), sitk.sitkUInt8)
         
             # Convert .mha image to original size numeric array
             image_array_original = sitk.GetArrayFromImage(image)
@@ -491,15 +491,14 @@ class SPIDER(datasets.GeneratorBasedBuilder):
                 resize_shape,
             )
 
-            # Create PIL image object of original image
-            # PIL_original_image = PIL.Image.fromarray(image_array_original)
-
+            # NOTE: since the original array shape is not standardized, cannot return in dataset
+            
             # Load .mha mask file
             mask_path = os.path.join(paths_dict['masks'], 'masks', example)
             mask = sitk.ReadImage(mask_path)
             
-            # Rescale mask intensities to [0, 255] and cast as UInt8 type
-            mask = sitk.Cast(sitk.RescaleIntensity(mask), sitk.sitkUInt8)
+            # # Rescale mask intensities to [0, 255] and cast as UInt8 type
+            # mask = sitk.Cast(sitk.RescaleIntensity(mask), sitk.sitkUInt8)
 
             # Convert .mha mask to original size numeric array
             mask_array_original = sitk.GetArrayFromImage(mask)
@@ -510,9 +509,6 @@ class SPIDER(datasets.GeneratorBasedBuilder):
                 resize_shape,
             )
 
-            # Create PIL image object of original mask
-            # PIL_original_mask = PIL.Image.fromarray(mask_array_original)
-
             # Extract overview data corresponding to image
             image_overview = overview_dict[scan_id]
 
@@ -523,8 +519,8 @@ class SPIDER(datasets.GeneratorBasedBuilder):
             return_dict = {
                 'patient_id':patient_id,
                 'scan_type':scan_type,
-                'raw_image':image_array_original, 
-                'raw_mask':mask_array_original, 
+                'image_path':image_path, 
+                'mask_path':mask_path, 
                 'image_array':image_array_standardized,
                 'mask_array':mask_array_standardized,
                 'metadata':image_overview,