Merge pull request #11 from avnishks/dev

Check if LTA is RAS-to-RAS

samseg/cli/run_samseg_long.py

@@ -104,10 +104,54 @@ def main():
     else:
         savePosteriors = args.save_posteriors
 
+    # define LTA type - reused from transform.h
+    type_descriptions = {
+        0: "LINEAR_VOX_TO_VOX",
+        1: "LINEAR_RAS_TO_RAS",
+        2: "LINEAR_PHYSVOX_TO_PHYSVOX",
+        10: "TRANSFORM_ARRAY_TYPE",
+        11: "MORPH_3D_TYPE",
+        12: "MNI_TRANSFORM_TYPE",
+        13: "MATLAB_ASCII_TYPE",
+        14: "REGISTER_DAT",
+        15: "FSLREG_TYPE",
+        21: "LINEAR_CORONAL_RAS_TO_CORONAL_RAS",
+        "LINEAR_VOX_TO_VOX": "LINEAR_VOXEL_TO_VOXEL",
+        "LINEAR_CORONAL_RAS_TO_CORONAL_RAS": "LINEAR_COR_TO_COR",
+    }
+
+    def check_lta_file(filepath):
+        try:
+            with open(filepath, 'r') as file:
+                for line in file:
+                    if "type" in line.lower():
+                        # Extract the type value, accounting for variable spacing around '='
+                        type_value = line.split('=')[-1].strip()
+                        try:
+                            type_value = int(type_value)
+                        except ValueError:
+                            pass  # Keep as string if conversion fails, to handle descriptive keys
+
+                        if type_value == 1:
+                            return True, "LTA is of type RAS-to-RAS, proceeding as before."
+                        elif type_value in type_descriptions:
+                            error_message = f"Error: LTA file type is {type_descriptions[type_value]}. Convert to RAS-to-RAS and try again."
+                            return False, error_message
+                        else:
+                            return False, "Error: LTA file type is of an unknown type."
+            return False, "Error: 'Type' line not found in the file - unable to determine if LTA is of type RAS-to-RAS."
+        except Exception as e:
+            return False, f"An error occurred: {str(e)}"
+
     tpToBaseTransforms = []
     if args.tp_to_base_transform:
         for tpTobase in args.tp_to_base_transform:
-            tpToBaseTransforms.append(sf.load_affine(tpTobase))
+            should_continue, message = check_lta_file(tpTobase)
+            if should_continue:
+                tpToBaseTransforms.append(sf.load_affine(tpTobase))
+            else:
+                print(message)
+                sys.exit(1)
     else:
         print("Assuming an identity transformation between base and each time point")
         for tp in args.timepoint: