def test_do_subject_files_exist_template_for_existing_files_exist():
subjects_dir = os.path.join(TEST_DATA_DIR, 'empty_subjects')
subjects_file = os.path.join(subjects_dir, 'subjects_empty.txt')
subjects_list = nit.read_subjects_file(subjects_file)
assert len(subjects_list) == 3
missing = nit.do_subject_files_exist(subjects_list, subjects_dir, filename_template='${SUBJECT_ID}.txt')
assert len(missing) == 0
def test_do_subject_files_exist_raises_on_too_much_fileinfo():
subjects_dir = TEST_DATA_DIR
subjects_file = os.path.join(subjects_dir, 'subjects.txt')
subjects_list = nit.read_subjects_file(subjects_file)
assert len(subjects_list) == 5
with pytest.raises(ValueError) as exc_info:
missing = nit.do_subject_files_exist(subjects_list, subjects_dir, filename='not_there', filename_template='not_there')
assert 'Exactly one of' in str(exc_info.value)
def test_read_subjects_file_five_subjects():
subjects_file = os.path.join(TEST_DATA_DIR, 'subjects.txt')
subject_ids = nit.read_subjects_file(subjects_file)
assert len(subject_ids) == 5
assert 'subject1' in subject_ids
assert 'subject2' in subject_ids
assert 'subject3' in subject_ids
assert 'subject4' in subject_ids
assert 'subject5' in subject_ids
def test_read_subjects_file_csv_format_tab_separated_with_header():
subjects_file = os.path.join(TEST_DATA_DIR, 'subject_files_tab_separated', 'subjects_including_s6_tab_hdr.csv')
subject_ids = nit.read_subjects_file(subjects_file, has_header_line=True, delimiter='\t') # the name arg 'delimiter' should be passed on to csv.reader by the function. This is tested here.
assert len(subject_ids) == 6
assert 'subject1' in subject_ids
assert 'subject2' in subject_ids
assert 'subject3' in subject_ids
assert 'subject4' in subject_ids
assert 'subject5' in subject_ids
assert 'subject6' in subject_ids
def test_read_subjects_file_csv_format_comma_separated_no_header():
subjects_file = os.path.join(TEST_DATA_DIR, 'subjects_including_s6.csv')
subject_ids = nit.read_subjects_file(subjects_file)
assert len(subject_ids) == 6
assert 'subject1' in subject_ids
assert 'subject2' in subject_ids
assert 'subject3' in subject_ids
assert 'subject4' in subject_ids
assert 'subject5' in subject_ids
assert 'subject6' in subject_ids
def test_do_subject_files_exist_not_there():
subjects_dir = TEST_DATA_DIR
subjects_file = os.path.join(subjects_dir, 'subjects.txt')
subjects_list = nit.read_subjects_file(subjects_file)
assert len(subjects_list) == 5
missing = nit.do_subject_files_exist(subjects_list, subjects_dir, filename='not_there')
assert len(missing) == 5
assert 'subject1' in missing
assert 'subject2' in missing
assert 'subject3' in missing
assert 'subject4' in missing
assert 'subject5' in missing
def test_do_subject_files_exist_lh_area():
expected_subjects_dir = TEST_DATA_DIR
expected_fsaverage_surf_dir = os.path.join(TEST_DATA_DIR, 'fsaverage', 'surf')
if not os.path.isdir(expected_fsaverage_surf_dir):
pytest.skip("Test data missing: e.g., directory '%s' does not exist. You can get all test data by running './develop/get_test_data_all.bash' in the repo root." % expected_fsaverage_surf_dir)
subjects_dir = TEST_DATA_DIR
subjects_file = os.path.join(subjects_dir, 'subjects.txt')
subjects_list = nit.read_subjects_file(subjects_file)
assert len(subjects_list) == 5
missing = nit.do_subject_files_exist(subjects_list, subjects_dir, filename='lh.area')
assert len(missing) == 0
def test_do_subject_files_exist_template_for_existing_files():
subjects_dir = os.path.join(TEST_DATA_DIR, 'empty_subjects')
subjects_file = os.path.join(subjects_dir, 'subjects_empty.txt')
subjects_list = nit.read_subjects_file(subjects_file)
assert len(subjects_list) == 3
expected_missing_file1 = os.path.join(subjects_dir, 'empty1', 'surf', 'empty1_not_there.txt')
expected_missing_file2 = os.path.join(subjects_dir, 'empty2', 'surf', 'empty2_not_there.txt')
expected_missing_file3 = os.path.join(subjects_dir, 'empty3', 'surf', 'empty3_not_there.txt')
missing = nit.do_subject_files_exist(subjects_list, subjects_dir, filename_template='${SUBJECT_ID}_not_there.txt')
assert len(missing) == 3
assert missing['empty1'] == expected_missing_file1
assert missing['empty2'] == expected_missing_file2
assert missing['empty3'] == expected_missing_file3
def brain_consistency():
"""
Brain data consistency checks.
Simple script to check brain data consistency.
"""
# Parse command line arguments
parser = argparse.ArgumentParser(
description="Check brain data consistency.")
parser.add_argument(
"subjects_dir",
help=
"The directory that contains your subjects. Note: in most cases you can pass the environment variable SUBJECTS_DIR."
)
parser.add_argument(
"subjects_file",
help=
"Text file containing all subjects that should be checked, one subject per line."
)
parser.add_argument(
"-m",
"--measures-native",
help=
"Which vertex-wise native space measure data to check (e.g., 'area' to check files 'surf/lh.area' and similar). Colon-separated string or 'None'. Defaults to 'area:volume:thickness'.",
default="area:volume:thickness")
parser.add_argument(
"-s",
"--measures-standard",
help=
"Which vertex-wise standard space measure data to check (e.g., 'area' to check files 'surf/lh.area.fwhmX.fsaverage.mgh' and similar). Colon-separated string or 'None'. Defaults to 'area:volume:thickness'.",
default="area:volume:thickness")
parser.add_argument(
"-a",
"--average-subject",
help=
"Name of the average subject (template) for standard space data (see '-s'). Defaults to 'fsaverage'.",
default="fsaverage")
parser.add_argument(
"-f",
"--fwhm-list",
help=
"The list of fwhm files to check for standard space data (see '-s'). Defaults to '0:5:10:15:20:25'.",
default="0:5:10:15:20:25")
parser.add_argument(
"-r",
"--report",
help=
"File name for the report in HTML format. If not given, no HTML report is written.",
default=None)
verb_group = parser.add_mutually_exclusive_group(required=False)
verb_group.add_argument("-v",
"--verbose",
help="Increase output verbosity to INFO.",
action="store_true")
verb_group.add_argument(
"-w",
"--verbosity",
help=
"Set verbosity level. One of 'WARN', 'INFO', or 'DEBUG'. Defaults to 'WARN'",
default="WARN")
args = parser.parse_args()
log_level = logging.WARN # Default
if args.verbose:
log_level = logging.INFO
elif args.verbosity:
if args.verbosity == 'INFO':
log_level = logging.INFO
elif args.verbosity == 'DEBUG':
log_level = logging.DEBUG
logging.basicConfig(level=log_level)
logger.info("---Brain Data Consistency Checks---")
logger.info("Using subjects_dir '%s' and subjects file '%s'." %
(args.subjects_dir, args.subjects_file))
native_measures = args.measures_native.split(":")
if args.measures_native == "None":
native_measures = []
standard_measures = args.measures_standard.split(":")
if args.measures_standard == "None":
standard_measures = []
standard_fwhm_list = args.fwhm_list.split(":")
subjects_list = nit.read_subjects_file(args.subjects_file)
logger.info("Handling %d subjects." % (len(subjects_list)))
if len(native_measures):
logger.info("Handling %d native space measures: %s" %
(len(native_measures), ", ".join(native_measures)))
else:
logger.info("Not handling any native space measures.")
if len(standard_measures):
logger.info(
"Handling %d standard space measures using template subject '%s': %s"
% (len(standard_measures), args.average_subject,
", ".join(standard_measures)))
logger.info(
"Handling standard space measures at %d fwhm settings: %s" %
(len(standard_fwhm_list), ", ".join(standard_fwhm_list)))
else:
logger.info("Not handling any standard space measures.")
bdc = brainqa.BrainDataConsistency(args.subjects_dir,
subjects_list,
log_level=log_level)
bdc.average_subject = args.average_subject
bdc.fwhm_list = standard_fwhm_list
bdc.check_custom(native_measures, standard_measures)
if args.report:
bdc.save_html_report(args.report)
sys.exit(0)
def test_read_subjects_file_one_subject():
subjects_file = os.path.join(TEST_DATA_DIR, 'subjects_only1.txt')
subject_ids = nit.read_subjects_file(subjects_file)
assert len(subject_ids) == 1
assert 'subject1' in subject_ids
