Add an option to specif the orientation to show the image in the viewer

manual_correction.py

@@ -258,6 +258,21 @@ def get_parser():
              }\n
              """),
     )
+    parser.add_argument(
+        '-change-orient',
+        type=str,
+        help=
+        " R| Orientation to show the image in the viewer. If provided, the image and label will be reoriented before "
+        "opening the viewer. After manual correction, the image and label will be reoriented back to the original "
+        "orientation. "
+        "Possible options: LAS,LAI,LPS,LPI,LSA,LSP,LIA,LIP,RAS,RAI,RPS,RPI,RSA,RSP,RIA,RIP,ALS,ALI,ARS,ARI,ASL,ASR,"
+        "AIL,AIR,PLS,PLI,PRS,PRI,PSL,PSR,PIL,PIR,SLA,SLP,SRA,SRP,SAL,SAR,SPL,SPR,ILA,ILP,IRA,IRP,IAL,IAR,IPL,IPR}",
+        choices=['LAS', 'LAI', 'LPS', 'LPI', 'LSA', 'LSP', 'LIA', 'LIP', 'RAS', 'RAI', 'RPS', 'RPI', 'RSA', 'RSP',
+                 'RIA', 'RIP', 'ALS', 'ALI', 'ARS', 'ARI', 'ASL', 'ASR', 'AIL', 'AIR', 'PLS', 'PLI', 'PRS', 'PRI',
+                 'PSL', 'PSR', 'PIL', 'PIR', 'SLA', 'SLP', 'SRA', 'SRP', 'SAL', 'SAR', 'SPL', 'SPR', 'ILA', 'ILP',
+                 'IRA', 'IRP', 'IAL', 'IAR', 'IPL', 'IPR'],
+        default=''
+    )
     parser.add_argument(
         '-v', '--verbose',
         help="Full verbose (for debugging)",
@@ -862,6 +877,16 @@ def main():
                     # For example: '/Users/user/dataset/derivatives/labels/sub-001/anat/sub-001_T2w_seg.nii.gz'
                     # The information regarding the modified data will be stored within the sidecar .json file
                     fname_out = utils.add_suffix(os.path.join(path_out, subject, ses, contrast, filename), suffix_dict[task])
+
+                    # Change orientation of the input image (if different from the original orientation)
+                    if args.change_orient:
+                        # Get image and label orientation
+                        image_orig_orient = utils.get_orientation(fname)
+                        label_orig_orient = utils.get_orientation(fname_label)
+                        # Change orientation of the input image for better visualization
+                        if image_orig_orient != args.change_orient or label_orig_orient != args.change_orient:
+                            utils.change_orientation(fname, args.change_orient)
+                            utils.change_orientation(fname_label, args.change_orient)
 
                     # Create subject folder in output if they do not exist
                     os.makedirs(os.path.join(path_out, subject, ses, contrast), exist_ok=True)
@@ -924,6 +949,14 @@ def main():
                     # Keep track of corrected files in YAML.
                     dict_yml = utils.track_corrections(files_dict=dict_yml.copy(), config_path=args.config, file_path=fname, task=task)
 
+                    # Change orientation of the input image back to the original orientation
+                    if args.change_orient:
+                        image_current_orientation = utils.get_orientation(fname)
+                        label_current_orientation = utils.get_orientation(fname_label)
+                        if image_current_orientation != image_orig_orient or label_current_orientation != label_orig_orient:
+                            utils.change_orientation(fname, image_orig_orient)
+                            utils.change_orientation(fname_out, label_orig_orient)
+
             else:
                 sys.exit("ERROR: The list of files to correct is empty. \nMaybe, you have already corrected all the "
                          "files? Please, check the YAML file: {}".format(args.config))

utils.py

@@ -332,3 +332,43 @@ def track_corrections(files_dict, config_path, file_path, task):
     return files_dict
 
 
+def get_orientation(file_path):
+    """
+    Get the orientation of the input nifti file
+    :param file_path: path to the nifti file
+    :return: actual orientation of the nifti file, e.g., 'RPI'
+    """
+
+    def _parse_orientation(output_bytes: bytes) -> str:
+        """
+        Parse the image orientation from the provided output bytes.
+        Args: output_bytes (bytes): The input bytes containing the output from sct_image command.
+        Returns:
+        str: The parsed image orientation.
+        """
+
+        output_string = output_bytes.decode('utf-8')
+        lines = output_string.strip().split('\n')
+        # Get only the string containing the orientation, e.g., 'RPI'
+        orientation = lines[-1].strip()
+        return orientation
+
+    # Note: we use bash command 'sct_image' to get the orientation instead of SCT's Image class because this would
+    # introduce dependency on SCT conda environment
+    output = subprocess.run(['sct_image', '-i', file_path, '-getorient'], capture_output=True)
+    orientation = _parse_orientation(output.stdout)  # e.g., 'RPI'
+
+    return orientation
+
+
+def change_orientation(file_path, orientation):
+    """
+    Change the orientation of the input nifti file
+    :param file_path: path to the nifti file
+    :param orientation: desired orientation of the nifti file, e.g., 'RPI'
+    """
+
+    # Change the orientation of the input nifti file
+    # Note: The image is currently being overwritten
+    subprocess.run(['sct_image', '-i', file_path, '-setorient', orientation, '-o', file_path], capture_output=True)
+    print(f"Orientation of {file_path} has been changed to {orientation}")