added image standardization

SPIDER.py

@@ -24,6 +24,7 @@ import numpy as np
 import pandas as pd
 
 import datasets
+import skimage
 import SimpleITK as sitk
 
 # Define functions
@@ -36,12 +37,20 @@ def import_csv_data(filepath: str) -> List[Dict[str, str]]:
             results.append(line)
     return results
 
-def standardize_3D_image(image: np.ndarray) -> np.ndarray:
-    """TODO"""
+def standardize_3D_image(
+    image: np.ndarray,
+    resize_shape: Tuple[int, int, int]
+) -> np.ndarray:
+    """Aligns dimensions of image to be (height, width, channels) and resizes
+    images to values specified in resize_shape."""
+    # 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)
     return image
 
+
 # Define constants
 N_PATIENTS = 218
 MIN_IVD = 0
@@ -91,11 +100,11 @@ class CustomBuilderConfig(datasets.BuilderConfig):
         data_files: Optional[Union[str, Sequence, Mapping]] = None,
         description: Optional[str] = None,
         scan_types: List[str] = DEFAULT_SCAN_TYPES,
-        resize_dims: Tuple[int, int, int] = DEFAULT_RESIZE,
+        resize_shape: Tuple[int, int, int] = DEFAULT_RESIZE,
     ):
         super().__init__(name, version, data_dir, data_files, description)
         self.scan_types = scan_types
-        self.resize_dims = resize_dims
+        self.resize_shape = resize_shape
 
 
 class SPIDER(datasets.GeneratorBasedBuilder):
@@ -111,28 +120,28 @@ class SPIDER(datasets.GeneratorBasedBuilder):
     #         version=VERSION,
     #         description="Use images of all scan types (t1, t2, t2 SPACE)",
     #         scan_types=['t1', 't2', 't2_SPACE'],
-    #         resize_dims=DEFAULT_RESIZE,
+    #         resize_shape=DEFAULT_RESIZE,
     #     ),
     #     CustomBuilderConfig(
     #         name="t1_scan_types",
     #         version=VERSION,
     #         description="Use images of t1 scan types only",
     #         scan_types=['t1'],
-    #         resize_dims=DEFAULT_RESIZE,
+    #         resize_shape=DEFAULT_RESIZE,
     #     ),
     #     CustomBuilderConfig(
     #         name="t2_scan_types",
     #         version=VERSION,
     #         description="Use images of t2 scan types only",
     #         scan_types=['t2'],
-    #         resize_dims=DEFAULT_RESIZE,
+    #         resize_shape=DEFAULT_RESIZE,
     #     ),
     #     CustomBuilderConfig(
     #         name="t2_SPACE_scan_types",
     #         version=VERSION,
     #         description="Use images of t2 SPACE scan types only",
     #         scan_types=['t2_SPACE'],
-    #         resize_dims=DEFAULT_RESIZE,
+    #         resize_shape=DEFAULT_RESIZE,
     #     ),
     # ]
 
@@ -142,12 +151,12 @@ class SPIDER(datasets.GeneratorBasedBuilder):
         self,
         *args,
         scan_types: List[str] = DEFAULT_SCAN_TYPES,
-        resize_dims: Tuple[int, int, int] = DEFAULT_RESIZE,
+        resize_shape: Tuple[int, int, int] = DEFAULT_RESIZE,
         **kwargs,
     ):
         super().__init__(*args, **kwargs)
         self.scan_types = scan_types
-        self.resize_dims = resize_dims
+        self.resize_shape = resize_shape
 
     def _info(self):
         """
@@ -158,7 +167,7 @@ class SPIDER(datasets.GeneratorBasedBuilder):
             "patient_id": datasets.Value("string"),
             "scan_type": datasets.Value("string"),
             # "raw_image": datasets.Image(),
-            "numeric_array": datasets.Array3D(shape=self.resize_dims, dtype='int16'),
+            "numeric_array": datasets.Array3D(shape=self.resize_shape, dtype='int16'),
             "metadata": {
                 "num_vertebrae": datasets.Value(dtype="string"),
                 "num_discs": datasets.Value(dtype="string"),
@@ -246,7 +255,7 @@ class SPIDER(datasets.GeneratorBasedBuilder):
                     "paths_dict": paths_dict,
                     "split": "train",
                     "scan_types": self.scan_types,
-                    "resize_dims": self.resize_dims,
+                    "resize_shape": self.resize_shape,
                 },
             ),
             datasets.SplitGenerator(
@@ -255,7 +264,7 @@ class SPIDER(datasets.GeneratorBasedBuilder):
                     "paths_dict": paths_dict,
                     "split": "validate",
                     "scan_types": self.scan_types,
-                    "resize_dims": self.resize_dims,
+                    "resize_shape": self.resize_shape,
                 },
             ),
             datasets.SplitGenerator(
@@ -264,7 +273,7 @@ class SPIDER(datasets.GeneratorBasedBuilder):
                     "paths_dict": paths_dict,
                     "split": "test",
                     "scan_types": self.scan_types,
-                    "resize_dims": self.resize_dims,
+                    "resize_shape": self.resize_shape,
                 },
             ),
         ]
@@ -274,7 +283,7 @@ class SPIDER(datasets.GeneratorBasedBuilder):
         paths_dict: Dict[str, str],
         split: str,
         scan_types: List[str],
-        resize_dims: Tuple[int, int, int],
+        resize_shape: Tuple[int, int, int],
         validate_share: float = 0.3,
         test_share: float = 0.2,
         raw_image: bool = True,
@@ -475,9 +484,11 @@ class SPIDER(datasets.GeneratorBasedBuilder):
             image_path = os.path.join(paths_dict['images'], 'images', example)
             image = sitk.ReadImage(image_path)
             
-            # Convert .mha image to numeric array
-            image_array = sitk.GetArrayFromImage(image)
-            
+            # Convert .mha image to standardized numeric array
+            image_array = standardize_3D_image(
+                sitk.GetArrayFromImage(image), resize_shape
+            )
+
             #TODO: load mask file and numeric array
             
             # Extract overview data corresponding to image