From 358891a5fe62d075ac9393b1897a5875dfe9dbba Mon Sep 17 00:00:00 2001
From: neuronflow <florian.kofler@tum.de>
Date: Sat, 23 Dec 2023 00:57:35 +0100
Subject: [PATCH] clean coreg

Signed-off-by: neuronflow <florian.kofler@tum.de>
---
 brainles_preprocessing/preprocessor.py | 34 +++++++++-----------------
 1 file changed, 11 insertions(+), 23 deletions(-)

diff --git a/brainles_preprocessing/preprocessor.py b/brainles_preprocessing/preprocessor.py
index f11fb8a..c581a2e 100644
--- a/brainles_preprocessing/preprocessor.py
+++ b/brainles_preprocessing/preprocessor.py
@@ -82,9 +82,17 @@ def run(
                 registration_dir=coregistration_dir,
                 moving_image_name=file_name,
             )
-        self._save_coregistration(
-            coregistration_dir=coregistration_dir,
-            save_dir_coregistration=save_dir_coregistration,
+
+        shutil.copyfile(
+                src=self.center_modality.input_path,
+                dst=os.path.join(
+                coregistration_dir,
+                f"native__{self.center_modality.modality_name}.nii.gz",
+            )
+
+        self._save_output(
+            src=coregistration_dir,
+            save_dir=save_dir_coregistration,
         )
 
         # Register center modality to atlas
@@ -195,27 +203,7 @@ def _save_output(
                 dirs_exist_ok=True,
             )
 
-    def _save_coregistration(
-        self,
-        coregistration_dir: str,
-        save_dir_coregistration: Optional[str],
-    ):
-        if save_dir_coregistration:
-            save_dir_coregistration = turbopath(save_dir_coregistration)
-            native_cm = os.path.join(
-                coregistration_dir,
-                f"native__{self.center_modality.modality_name}.nii.gz",
-            )
 
-            shutil.copyfile(
-                src=self.center_modality.input_path,
-                dst=native_cm,
-            )
-            shutil.copytree(
-                src=coregistration_dir,
-                dst=save_dir_coregistration,
-                dirs_exist_ok=True,
-            )
 
 
 class PreprocessorGPU(Preprocessor):