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Handle KeyErrors more gracefully if user marks FILES_REG as a qc_fail.yml #72

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merged 4 commits into from
Nov 7, 2023
Merged

Handle KeyErrors more gracefully if user marks FILES_REG as a qc_fail.yml #72

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84e9d47
Check if task is in suffix_dict.keys(), if not, skip it
valosekj Nov 6, 2023
78f5cfc
Keep track of which tasks have possibly-bad suffixes
mguaypaq Nov 7, 2023
eb7c184
Fix test
mguaypaq Nov 7, 2023
93a38b2
Add comment why `if task not in suffix_dict.keys()` check is done aft…
valosekj Nov 7, 2023
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4 changes: 4 additions & 0 deletions manual_correction.py
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Original file line number Diff line number Diff line change
Expand Up @@ -756,6 +756,10 @@ def main():
# Perform manual corrections
for task, files in dict_yml.items():
if task.startswith('FILES'):
# Check if task is in suffix_dict.keys(), if not, skip it
if task not in suffix_dict.keys():
logging.warning("WARNING: {} is not a valid task. Skipping it.".format(task))
continue
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# Get the list of segmentation files to add to derivatives, excluding the manually corrected files in -config.
# TODO: probably extend also for other tasks (such as FILES_GMSEG)
if args.add_seg_only and task == 'FILES_SEG':
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10 changes: 8 additions & 2 deletions utils.py
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Expand Up @@ -209,8 +209,13 @@ def check_files_exist(dict_yml, path_img, path_label, suffix_dict):
"""
missing_files = []
missing_files_labels = []
missing_suffixes = set()
for task, files in dict_yml.items():
if task.startswith('FILES') and files:
# Check if task is in suffix_dict.keys(), if not, skip it
if task not in suffix_dict.keys():
logging.warning("WARNING: {} is not a valid task. Skipping it.".format(task))
continue
# Do no check if key is empty or if regex is used
if files is not None and '*' not in files[0]:
for file in files:
Expand All @@ -223,14 +228,15 @@ def check_files_exist(dict_yml, path_img, path_label, suffix_dict):
fname_label = add_suffix(os.path.join(path_label, subject, ses, contrast, filename), suffix_dict[task])
if not os.path.exists(fname_label):
missing_files_labels.append(fname_label)
missing_suffixes.add(suffix_dict[task])
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")
if missing_files_labels:
logging.warning("If you are creating label(s) from scratch, ignore the following message.")
logging.warning("\nThe following label files are missing: \n{}".format(missing_files_labels))
logging.warning("\nPlease check that the used suffix '{}' is correct. "
"If not, you can provide custom suffix using '-suffix-files-' flags.\n".format(suffix_dict[task]))
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"If not, you can provide custom suffix using '-suffix-files-' flags.\n".format(sorted(missing_suffixes)))


def check_output_folder(path_bids):
Expand Down Expand Up @@ -323,4 +329,4 @@ def track_corrections(files_dict, config_path, file_path, task):

return files_dict


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