solve mask_path pb

aramis-lab · Jun 6, 2024 · 4819d0e · 4819d0e
1 parent e011574
commit 4819d0e
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Showing 2 changed files with 11 additions and 12 deletions.
diff --git a/clinicadl/caps_dataset/data.py b/clinicadl/caps_dataset/data.py
@@ -516,7 +516,9 @@ def __init__(
         self.roi_list = preprocessing_dict["roi_list"]
         self.uncropped_roi = preprocessing_dict["uncropped_roi"]
         self.prepare_dl = preprocessing_dict["prepare_dl"]
-
+        self.mask_paths, self.mask_arrays = self._get_mask_paths_and_tensors(
+            caps_directory, multi_cohort, preprocessing_dict
+        )
         super().__init__(
             caps_directory,
             data_file,
@@ -531,15 +533,12 @@ def __init__(
 
         self.config.preprocessing.roi_list = preprocessing_dict["roi_list"]
         self.config.preprocessing.uncropped_roi = preprocessing_dict["uncropped_roi"]
-        (
-            self.config.preprocessing.mask_paths,
-            self.config.preprocessing.mask_arrays,
-        ) = self._get_mask_paths_and_tensors(
-            caps_directory, multi_cohort, preprocessing_dict
-        )
-        self.mask_paths, self.mask_arrays = self._get_mask_paths_and_tensors(
-            self.config.data.caps_dict, multi_cohort, preprocessing_dict
-        )
+        # (
+        #     self.config.data.mask_path,
+        #     self.config.preprocessing.mask_arrays,
+        # ) = self._get_mask_paths_and_tensors(
+        #     caps_directory, multi_cohort, preprocessing_dict
+        # )
 
     @property
     def elem_index(self):

diff --git a/clinicadl/preprocessing/config.py b/clinicadl/preprocessing/config.py
@@ -4,7 +4,7 @@
 from typing import Annotated, Any, Dict, Optional, Union
 
 from pydantic import BaseModel, ConfigDict, field_validator
-from pydantic.types import PositiveInt
+from pydantic.types import NonNegativeInt
 
 from clinicadl.utils.enum import (
     ExtractionMethod,
@@ -56,7 +56,7 @@ class PreprocessingSliceConfig(PreprocessingConfig):
     extract_method: ExtractionMethod = ExtractionMethod.SLICE
     slice_direction: SliceDirection = SliceDirection.SAGITTAL
     slice_mode: SliceMode = SliceMode.RGB
-    discarded_slices: Annotated[list[PositiveInt], 2] = [0, 0]
+    discarded_slices: Annotated[list[NonNegativeInt], 2] = [0, 0]
 
 
 class PreprocessingROIConfig(PreprocessingConfig):