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aramis-lab · Jun 10, 2024 · 15be72f · 15be72f
1 parent 72130d1
commit 15be72f
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Showing 2 changed files with 4 additions and 7 deletions.
diff --git a/clinicadl/quality_check/t1_linear/quality_check.py b/clinicadl/quality_check/t1_linear/quality_check.py
@@ -10,7 +10,7 @@
 from torch.cuda.amp import autocast
 from torch.utils.data import DataLoader
 
-from clinicadl.caps_dataset.data import CapsDataset
+from clinicadl.caps_dataset.caps_dataset_config import CapsDatasetConfig
 from clinicadl.generate.generate_utils import load_and_check_tsv
 from clinicadl.utils.clinica_utils import RemoteFileStructure, fetch_file
 from clinicadl.utils.enum import ExtractionMethod, Preprocessing
@@ -68,6 +68,7 @@ def quality_check(
     logger = getLogger("clinicadl.quality_check")
     config = CapsDatasetConfig.from_preprocessing_and_extraction_method(
         caps_directory=caps_dir,
+        extraction=ExtractionMethod.IMAGE,
         preprocessing_type=Preprocessing.T1_LINEAR,
         preprocessing=Preprocessing.T1_LINEAR,
         use_uncropped_image=use_uncropped_image,

diff --git a/clinicadl/quality_check/t1_linear/utils.py b/clinicadl/quality_check/t1_linear/utils.py
@@ -12,6 +12,7 @@
 from clinicadl.caps_dataset.caps_dataset_utils import compute_folder_and_file_type
 from clinicadl.utils.clinica_utils import clinicadl_file_reader, linear_nii
 from clinicadl.utils.enum import LinearModality, Preprocessing
+from clinicadl.utils.exceptions import ClinicaDLException
 
 
 class QCDataset(Dataset):
@@ -39,7 +40,7 @@ def __init__(
         if ("session_id" not in list(self.df.columns.values)) or (
             "participant_id" not in list(self.df.columns.values)
         ):
-            raise Exception(
+            raise ClinicaDLException(
                 "The data file is not in the correct format."
                 "Columns should include ['participant_id', 'session_id']"
             )
@@ -53,11 +54,6 @@ def __init__(
             "file_type": linear_nii(LinearModality.T1W, self.use_uncropped_image),
             "use_tensor": self.use_extracted_tensors,
         }
-        self.config = PrepareDataImageConfig(
-            caps_directory=Path(""),
-            preprocessing_cls=Preprocessing.T1_LINEAR,
-            use_uncropped_image=use_uncropped_image,
-        )
 
     def __len__(self):
         return len(self.df)