Limit warnings raised by check_files_exist when running another round…

… of corrections. (#39)

- the check_files_exist function now also checks for labels under the derivatives
- we are doing this because if labels exist under derivatives, we do not want raise warnings

Fixes: #38

manual_correction.py

@@ -572,14 +572,14 @@ def main():
         'FILES_CENTERLINE': args.suffix_files_centerline    # e.g., _centerline or _label-centerline
     }
 
-    # Check for missing files before starting the whole process
-    if not args.add_seg_only:
-        utils.check_files_exist(dict_yml, utils.get_full_path(args.path_in), suffix_dict)
-
     path_out = utils.get_full_path(args.path_out)
     # check that output folder exists and has write permission
     path_out_deriv = utils.check_output_folder(path_out, args.path_derivatives)
 
+    # Check for missing files before starting the whole process
+    if not args.add_seg_only:
+        utils.check_files_exist(dict_yml, utils.get_full_path(args.path_in), suffix_dict, path_out_deriv)
+
     # Fetch parameters for FSLeyes
     param_fsleyes = ParamFSLeyes(cm=args.fsleyes_cm, dr=args.fsleyes_dr, second_orthoview=args.fsleyes_second_orthoview)
 

utils.py

@@ -195,12 +195,13 @@ def get_full_path(path):
     return os.path.abspath(os.path.expanduser(path))
 
 
-def check_files_exist(dict_files, path_data, suffix_dict):
+def check_files_exist(dict_files, path_data, suffix_dict, path_derivatives=None):
     """
     Check if all files listed in the input dictionary exist
     :param dict_files:
     :param path_data: folder where BIDS dataset is located
     :param suffix_dict: dictionary with label file suffixes
+    :param path_derivatives: folder where derivatives are located
     :return:
     """
     missing_files = []
@@ -216,8 +217,20 @@ def check_files_exist(dict_files, path_data, suffix_dict):
                 # Construct absolute path to the input label (segmentation, labeling etc.) file
                 # For example: '/Users/user/dataset/data_processed/sub-001/anat/sub-001_T2w_seg.nii.gz'
                 fname_label = add_suffix(fname, suffix_dict[task])
-                if not os.path.exists(fname_label):
-                    missing_files_labels.append(fname_label)
+                # If path_derivatives exists, check also labels under the derivatives folder
+                # Note: we are doing this because if labels exist under derivatives, we do not want raise warnings
+                if path_derivatives is not None:
+                    # Construct absolute path to the label under derivatives folder
+                    fname_label_derivatives = os.path.join(path_derivatives, subject, ses, contrast,
+                                                           add_suffix(filename, suffix_dict[task] + '-manual'))
+                    # Check if there is no label (i.e., no file under path_data and no label under path_derivatives)
+                    # If no label is in either directory, add the file to the list of missing files.
+                    if not os.path.exists(fname_label) and not os.path.exists(fname_label_derivatives):
+                        missing_files_labels.append(fname_label)
+                # No derivatives folder
+                else:
+                    if not os.path.exists(fname_label):
+                        missing_files_labels.append(fname_label)
     if missing_files:
         logging.warning("The following files are missing: \n{}".format(missing_files))
         logging.warning("\nPlease check that the files listed in the yaml file and the input path are correct.\n")