def test_parse_bids_filename_with_full_path():
ident = scanid.parse_bids_filename(
"/some/folder/sub-CMH0001_ses-01_run-1_T1w.nii.gz")
assert ident.subject == 'CMH0001'
assert ident.session == '01'
assert ident.run == '1'
assert ident.suffix == 'T1w'
def test_optional_entities_dont_get_parsed_as_suffix():
optional_entities = "sub-CMH0001_ses-01_{}_T1w.nii.gz"
for entity in ['run', 'acq', 'ce', 'rec', 'echo', 'ce', 'mod', 'task']:
optional_field = '{}-11'.format(entity)
bids_name = optional_entities.format(optional_field)
parsed = scanid.parse_bids_filename(bids_name)
assert optional_field not in parsed.suffix
def test_parse_bids_filename_without_ext():
ident = scanid.parse_bids_filename(
"/some/folder/sub-CMH0001_ses-02_run-3_T1w")
assert ident.subject == 'CMH0001'
assert ident.session == '02'
assert ident.run == '3'
assert ident.suffix == 'T1w'
def test_bids_file_correctly_parses_when_all_task_entities_given():
task_bids = "sub-CMH0001_ses-01_task-abcd_acq-efgh_" + \
"rec-ijkl_run-1_echo-11_imi"
parsed = scanid.parse_bids_filename(task_bids)
assert str(parsed) == task_bids
def test_bids_file_correctly_parses_when_all_anat_entities_given():
anat_bids = "sub-CMH0001_ses-01_acq-abcd_ce-efgh_rec-ijkl_" + \
"run-1_mod-mnop_somesuffix"
parsed = scanid.parse_bids_filename(anat_bids)
assert str(parsed) == anat_bids
def test_bids_file_equals_itself_with_path_and_ext():
bids_name = "sub-CMH0001_ses-01_run-1_T1w"
bids_full_path = "/some/folder/somewhere/{}.nii.gz".format(bids_name)
ident = scanid.parse_bids_filename(bids_name)
assert ident == bids_full_path
def test_bids_file_equals_string_of_itself_minus_run():
bids_name = "sub-CMH0001_ses-01_run-1_T1w"
ident = scanid.parse_bids_filename(bids_name)
assert ident == bids_name.replace("run-1_", "")
def test_bids_file_equals_string_of_itself():
bids_name = "sub-CMH0001_ses-01_run-1_T1w"
ident = scanid.parse_bids_filename(bids_name)
assert ident == bids_name
def test_empty_entity_name_and_label_does_not_get_set_as_suffix():
with pytest.raises(scanid.ParseException):
scanid.parse_bids_filename("sub-CMH_ses-01_-_T1w.nii.gz")
def test_unknown_entity_does_not_get_set_as_suffix():
with pytest.raises(scanid.ParseException):
scanid.parse_bids_filename("sub-CMH_ses-01_new-FIELD_T1w.nii.gz")
def test_parse_bids_filename_missing_suffix_and_run():
with pytest.raises(scanid.ParseException):
scanid.parse_bids_filename("sub-CMH0001_ses-01.nii.gz")
def test_parse_bids_filename_malformed_session():
with pytest.raises(scanid.ParseException):
scanid.parse_bids_filename("sub-CMH0001_ses-_run-1_T1w")
def test_parse_bids_filename_missing_subject():
with pytest.raises(scanid.ParseException):
scanid.parse_bids_filename("ses-01_run-1_T1w")
def test_parse_bids_filename_without_run():
scanid.parse_bids_filename("sub-CMH0001_ses-01_T1w.nii.gz")
def test_bids_file_correctly_parses_when_all_fmap_entities_given():
fmap_bids = "sub-CMH0001_ses-01_acq-abcd_dir-efgh_run-1_fmap"
parsed = scanid.parse_bids_filename(fmap_bids)
assert str(parsed) == fmap_bids
def test_bids_file_raises_exception_when_wrong_entities_used_for_fmap():
with pytest.raises(scanid.ParseException):
scanid.parse_bids_filename("sub-CMH0001_ses-01_dir-somedir_"
"rec-somefield_run-1_T1w.nii.gz")
def test_bids_file_handles_prelapse_session_strings():
prelapse_file = "sub-BRG33006_ses-01R_run-1_something"
parsed = scanid.parse_bids_filename(prelapse_file)
assert str(parsed) == prelapse_file
def test_parse_bids_filename():
ident = scanid.parse_bids_filename("sub-CMH0001_ses-01_run-1_T1w.nii.gz")
assert ident.subject == 'CMH0001'
assert ident.session == '01'
assert ident.run == '1'
assert ident.suffix == 'T1w'