added orientation setting function

utils/data_utils.py

@@ -248,7 +248,7 @@ def load_and_preprocess(file_paths, orientation):
 
     return volume, label_map, header
 
-def load():
+def load(file_paths, orientation):
     """Load Data Function
 
     This function loads the required data files and extracts relevant information from it.
@@ -266,7 +266,15 @@ def load():
         None
     """
 
-    return pass
+    nifty_volume, label_map = nb.load(file_paths[0]), nb.load(file_paths[1])
+    volume, label_map = nifty_volume.get_fdata(), nift_labeled_volume.ged_fdata()
+
+    # Do we need min-max normalization here? Will need to check when debuggint and testing
+    volume = (volume - np.min(volume)) / (np.max(volume) - np.min(volume))
+
+    volume, label_map = 
+
+    return volume, label_map, nifty_volume.header
 
 def preprocess():
 
@@ -281,6 +289,36 @@ def preprocess():
 
     return pass
 
+def set_orientation(volume, label_map, orientation):
+    """Load Data Orientation
+
+    This function modifies the orientation of the input and output data depending on the required orientation.
+
+    Args:
+        volume (np.array): Array of training image data of data type dtype.
+        label_map (np.array): Array of labelled image data of data type dtype.
+        orientation (str): String detailing the current view (COR, SAG, AXL)
+    
+    Returns:
+        volume (np.array): Array of training image data of data type dtype.
+        label_map (np.array): Array of labelled image data of data type dtype.
+    
+    Raises:
+        ValueError: Orientation value is invalid. It must be either >>coronal<<, >>axial<< or >>sagital<<
+    """
+
+    # TODO: will need to check if these alignments correpond with our data.
+    # These alignments work for ADNI
+
+    if orientation == "sagittal":
+        return volume, label_map # This is assumed to be the default orientation
+    elif orientation == "axial":
+        return volume.transpose((1, 2, 0)), label_map.transpose((2, 0, 1))
+    elif orientation == "coronal":
+        return
+    else:
+        raise ValueError("Orientation value is invalid. It must be either >>coronal<<, >>axial<< or >>sagital<< ")
+
 if __name__ == "__main__":
 
     folder_location = '/well/win-biobank/projects/imaging/data/data3/subjectsAll/'