def test_braindataconsistency_init_invalid_hemi():
subjects_list = ['subject1', 'subject2']
with pytest.raises(ValueError) as exc_info:
bdc = bqa.BrainDataConsistency(TEST_DATA_DIR,
subjects_list,
hemi='invalid_hemi')
assert 'hemi must be one of' in str(exc_info.value)
assert 'invalid_hemi' in str(exc_info.value)
def test_braindataconsistency_init():
subjects_list = ['subject1', 'subject2']
bdc = bqa.BrainDataConsistency(TEST_DATA_DIR, subjects_list)
assert bdc.hemis == ['lh', 'rh']
assert len(bdc.subject_issues) == 2
assert 'subject1' in bdc.subject_issues
assert 'subject2' in bdc.subject_issues
assert len(bdc.subject_issues['subject1']) == 0
assert len(bdc.subject_issues['subject2']) == 0
def test_braindataconsistency_check_custom_runs():
expected_subject2_testdata_dir = os.path.join(TEST_DATA_DIR, 'subject2')
if not os.path.isdir(expected_subject2_testdata_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_subject2_testdata_dir)
subjects_list = ['subject1', 'subject2']
bdc = bqa.BrainDataConsistency(TEST_DATA_DIR, subjects_list, hemi='lh')
bdc.check_file_modification_times = False
bdc.check_custom(['area'], ['area'])
def test_braindataconsistency_check_essentials_runs():
expected_subject2_testdata_dir = os.path.join(TEST_DATA_DIR, 'subject2')
if not os.path.isdir(expected_subject2_testdata_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_subject2_testdata_dir)
subjects_list = ['subject1', 'subject2']
bdc = bqa.BrainDataConsistency(TEST_DATA_DIR, subjects_list)
bdc.check_essentials()
bdc.check_essentials(
) # run again, this time no vertices should be counted
def test_braindataconsistency_ptd():
subjects_list = ['subject1', 'subject2']
bdc = bqa.BrainDataConsistency(TEST_DATA_DIR, subjects_list)
assert bdc._ptd(25) == "0:00:25 later"
assert bdc._ptd(-70) == "0:01:10 earlier"
def test_braindataconsistency_pts():
subjects_list = ['subject1', 'subject2']
bdc = bqa.BrainDataConsistency(TEST_DATA_DIR, subjects_list)
assert bdc._pts(1235235455) == "2009-02-21 16:57:35"
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)