update paths

neuro/segmentation/paths.py

@@ -1,4 +1,4 @@
-from pathlib import Path
+from imlib.general.system import ensure_directory_exists
 
 from neuro.atlas_tools import paths as reg_paths
 
@@ -11,26 +11,35 @@ class Paths:
     """
 
     def __init__(self, registration_output_folder, downsampled_image):
-        self.registration_output_folder = Path(registration_output_folder)
-        self.downsampled_image = self.join(downsampled_image)
+        self.registration_output_folder = registration_output_folder
 
-        self.tmp__inverse_transformed_image = self.join(
+        self.segmentation_directory = (
+            self.registration_output_folder / "manual_segmentation"
+        )
+
+        ensure_directory_exists(self.segmentation_directory)
+        self.downsampled_image = self.join_seg_files(downsampled_image)
+
+        self.tmp__inverse_transformed_image = self.join_seg_files(
             "image_standard_space.nii"
         )
-        self.tmp__inverse_transform_log_path = self.join(
+        self.tmp__inverse_transform_log_path = self.join_seg_files(
             "inverse_transform_log.txt"
         )
-        self.tmp__inverse_transform_error_path = self.join(
+        self.tmp__inverse_transform_error_path = self.join_seg_files(
             "inverse_transform_error.txt"
         )
 
-        self.annotations = self.join(reg_paths.ANNOTATIONS)
-        self.hemispheres = self.join(reg_paths.HEMISPHERES)
+        self.annotations = self.join_reg_files(reg_paths.ANNOTATIONS)
+        self.hemispheres = self.join_reg_files(reg_paths.HEMISPHERES)
 
-        self.regions_directory = self.join("regions")
+        self.regions_directory = self.join_seg_files("regions")
         self.region_summary_csv = self.regions_directory / "summary.csv"
 
-        self.tracks_directory = self.join("tracks")
+        self.tracks_directory = self.join_seg_files("tracks")
 
-    def join(self, filename):
+    def join_reg_files(self, filename):
         return self.registration_output_folder / filename
+
+    def join_seg_files(self, filename):
+        return self.segmentation_directory / filename