def test_read_sample_one(self):
"""Read the third extra_data sample (i.e. having index = 2). """
filename = os.path.join(os.path.dirname(os.path.realpath(__file__)),
"..", "tests", "testdata",
"bidsmap_example_new.yaml")
bidsmap_yaml = read_yaml_as_string(filename)
bidsmap = read_bidsmap(bidsmap_yaml)
index = 2
modality = 'extra_data'
yaml = ruamel.yaml.YAML()
sample = read_sample(bidsmap, modality, index)
sample_yaml = yaml.dump(sample, sys.stdout)
yaml = ruamel.yaml.YAML()
filename = os.path.join(os.path.dirname(os.path.realpath(__file__)),
"..", "tests", "testdata",
"bidsmap_example_new_sample2.yaml")
with open(filename) as fp:
test_sample_yaml = fp.read()
test_sample = yaml.load(test_sample_yaml)
test_sample_yaml = yaml.dump(test_sample, sys.stdout)
self.assertEqual(test_sample_yaml, sample_yaml)
def test_get_list_summary(self):
test_list_summary = [{
"modality":
"extra_data",
"provenance_file":
"M109.MR.WUR_BRAIN_ADHD.0002.0001.2018.03.01.13.05.10.140625.104357083.IMA",
"provenance_path":
"M:\\bidscoin\\raw\\sub-P002\\ses-mri01\\02_localizer AANGEPAST 11 SLICES",
"bids_name":
"sub-*_ses-*_acq-localizerAANGEPAST11SLICES_run-<<1>>"
}, {
"modality":
"extra_data",
"provenance_file":
"M109.MR.WUR_BRAIN_ADHD.0003.0001.2018.03.01.13.05.10.140625.104359017.IMA",
"provenance_path":
"M:\\bidscoin\\raw\\sub-P002\\ses-mri01\\03_Stoptaak_ep2d_bold_nomoco",
"bids_name":
"sub-*_ses-*_acq-Stoptaakep2dboldnomoco_run-<<1>>"
}, {
"modality":
"extra_data",
"provenance_file":
"M109.MR.WUR_BRAIN_ADHD.0004.0001.2018.03.01.13.05.10.140625.104364139.IMA",
"provenance_path":
"M:\\bidscoin\\raw\\sub-P002\\ses-mri01\\04_t1_mpr_sag_p2_iso_1",
"bids_name":
"sub-*_ses-*_acq-t1mprsagp2iso1_run-<<1>>"
}, {
"modality":
"extra_data",
"provenance_file":
"M109.MR.WUR_BRAIN_ADHD.0005.0001.2018.03.01.13.05.10.140625.104368237.IMA",
"provenance_path":
"M:\\bidscoin\\raw\\sub-P002\\ses-mri01\\05_Flanker_ep2d_bold_nomoco",
"bids_name":
"sub-*_ses-*_acq-Flankerep2dboldnomoco_run-<<1>>"
}, {
"modality":
"extra_data",
"provenance_file":
"M005.MR.WUR_BRAIN_ADHD.0007.0001.2018.04.12.13.00.48.734375.108749947.IMA",
"provenance_path":
"M:\\bidscoin\\raw\\sub-P002\\ses-mri02\\07_t1_fl3d_sag_p3_iso_1",
"bids_name":
"sub-*_ses-*_acq-t1fl3dsagp3iso1_run-<<1>>"
}]
filename = os.path.join(os.path.dirname(os.path.realpath(__file__)),
"..", "tests", "testdata",
"bidsmap_example_new.yaml")
bidsmap_yaml = read_yaml_as_string(filename)
bidsmap = read_bidsmap(bidsmap_yaml)
list_summary = get_list_summary(bidsmap)
self.assertEqual(list_summary, test_list_summary)
def test_get_num_samples(self):
"""Determine the number of extra_data samples."""
filename = os.path.join(os.path.dirname(os.path.realpath(__file__)),
"..", "tests", "testdata",
"bidsmap_example_new.yaml")
bidsmap_yaml = read_yaml_as_string(filename)
bidsmap = read_bidsmap(bidsmap_yaml)
modality = 'extra_data'
num_samples = get_num_samples(bidsmap, modality)
self.assertEqual(num_samples, 5)
def test_read_bidsmap(self):
filename = os.path.join(os.path.dirname(os.path.realpath(__file__)),
"..", "tests", "testdata",
"bidsmap_example_new.yaml")
bidsmap_yaml = read_yaml_as_string(filename)
bidsmap = read_bidsmap(bidsmap_yaml)
yaml = ruamel.yaml.YAML()
with open(filename) as fp:
test_bidsmap_yaml = fp.read()
test_bidsmap = yaml.load(test_bidsmap_yaml)
self.assertEqual(bidsmap_yaml, test_bidsmap_yaml)
self.assertEqual(bidsmap, test_bidsmap)
def test_read_sample_all(self):
"""Loop over all extra_data samples and read them. """
filename = os.path.join(os.path.dirname(os.path.realpath(__file__)),
"..", "tests", "testdata",
"bidsmap_example_new.yaml")
bidsmap_yaml = read_yaml_as_string(filename)
bidsmap = read_bidsmap(bidsmap_yaml)
modality = 'extra_data'
num_samples = get_num_samples(bidsmap, modality)
self.assertEqual(num_samples, 5)
for i in range(num_samples):
sample = read_sample(bidsmap, modality, i)
def test_update_bidsmap(self):
filename = os.path.join(os.path.dirname(os.path.realpath(__file__)),
"..", "tests", "testdata",
"bidsmap_example_new.yaml")
source_bidsmap_yaml = read_yaml_as_string(filename)
source_bidsmap = read_bidsmap(source_bidsmap_yaml)
source_modality = 'extra_data'
source_index = 2
yaml = ruamel.yaml.YAML()
filename = os.path.join(os.path.dirname(os.path.realpath(__file__)),
"..", "tests", "testdata",
"bidsmap_example_new_sample2.yaml")
with open(filename) as fp:
test_sample_yaml = fp.read()
test_sample = yaml.load(test_sample_yaml)
target_modality = 'anat'
target_sample = copy.deepcopy(test_sample)
target_bidsmap = update_bidsmap(source_bidsmap, source_modality,
source_index, target_modality,
target_sample)
self.assertNotEqual(target_bidsmap, source_bidsmap)
self.assertNotEqual(target_bidsmap['DICOM'][target_modality],
source_bidsmap['DICOM'][target_modality])
self.assertNotEqual(target_bidsmap['DICOM'][source_modality],
source_bidsmap['DICOM'][source_modality])
self.assertEqual(len(target_bidsmap['DICOM'][target_modality]), 1)
self.assertEqual(len(target_bidsmap['DICOM'][source_modality]), 4)
target_filename = os.path.join(
os.path.dirname(os.path.realpath(__file__)), "..", "tests",
"testdata", "bidsmap_example_out.yaml")
reference_filename = os.path.join(
os.path.dirname(os.path.realpath(__file__)), "..", "tests",
"testdata", "bidsmap_example_new_out.yaml")
save_bidsmap(target_filename, target_bidsmap)
text1 = open(target_filename).readlines()
text2 = open(reference_filename).readlines()
lines = list(difflib.unified_diff(text1, text2))
logger.info(''.join(lines))
self.assertEqual(len(lines), 0) # Difference must be zero
logdir = os.path.dirname(os.path.abspath(args.logfile))
if not os.path.exists(logdir):
os.makedirs(logdir)
setup_logging(args.logfile)
logger.info('Started BIDS editor')
# Validate the arguments
if not os.path.exists(args.rawfolder):
raise Exception("Raw folder not found: {}".format(args.rawfolder))
if not os.path.exists(args.inputbidsmap):
raise Exception("Input BIDS map not found: {}".format(
args.inputbidsmap))
# Obtain the initial bidsmap info
input_bidsmap_yaml = bidsutils.read_yaml_as_string(args.inputbidsmap)
input_bidsmap = bidsutils.read_bidsmap(input_bidsmap_yaml)
output_bidsmap = copy.deepcopy(input_bidsmap)
logger.info('Input raw data folder: {}'.format(args.rawfolder))
logger.info('Input BIDS map: {}'.format(args.inputbidsmap))
logger.info('Output log file: {}'.format(args.logfile))
# Start the application
app = QApplication(sys.argv)
app.setApplicationName("BIDS editor")
mainwin = QMainWindow()
gui = Ui_MainWindow()
gui.setupUi(mainwin, args.rawfolder, args.inputbidsmap, input_bidsmap,
output_bidsmap)