def test_parse_file_entities():
filename = '/sub-03_ses-07_run-4_desc-bleargh_sekret.nii.gz'
# Test with entities taken from bids config
target = {'subject': '03', 'session': '07', 'run': 4, 'suffix': 'sekret'}
assert target == parse_file_entities(filename, config='bids')
config = Config.load('bids')
assert target == parse_file_entities(filename, config=[config])
# Test with entities taken from bids and derivatives config
target = {
'subject': '03',
'session': '07',
'run': 4,
'suffix': 'sekret',
'desc': 'bleargh'
}
assert target == parse_file_entities(filename)
assert target == parse_file_entities(filename,
config=['bids', 'derivatives'])
# Test with list of Entities
entities = [
Entity('subject', "[/\\\\]sub-([a-zA-Z0-9]+)"),
Entity('run', "[_/\\\\]run-0*(\\d+)", dtype=int),
Entity('suffix', "[._]*([a-zA-Z0-9]*?)\\.[^/\\\\]+$"),
Entity('desc', "desc-([a-zA-Z0-9]+)"),
]
# Leave out session to distinguish from previous test target
target = {'subject': '03', 'run': 4, 'suffix': 'sekret', 'desc': 'bleargh'}
assert target == parse_file_entities(filename, entities=entities)
def test_entity_matches(tmpdir):
filename = "aardvark-4-reporting-for-duty.txt"
tmpdir.mkdir("tmp").join(filename).write("###")
f = BIDSFile(os.path.join(str(tmpdir), filename))
e = Entity('avaricious', r'aardvark-(\d+)')
result = e.match_file(f)
assert result == '4'
def test_entity_matches(tmpdir):
filename = "aardvark-4-reporting-for-duty.txt"
tmpdir.mkdir("tmp").join(filename).write("###")
f = BIDSFile(os.path.join(str(tmpdir), filename))
e = Entity('avaricious', r'aardvark-(\d+)')
result = e.match_file(f)
assert result == '4'
def test_entity_unique_and_count():
e = Entity('prop', r'-(\d+)')
e.files = {
'test1-10.txt': '10',
'test2-7.txt': '7',
'test3-7.txt': '7'
}
assert sorted(e.unique()) == ['10', '7']
assert e.count() == 2
assert e.count(files=True) == 3
def test_entity_init_minimal():
e = Entity('avaricious', r'aardvark-(\d+)')
assert e.name == 'avaricious'
assert e.pattern == r'aardvark-(\d+)'
assert not e.mandatory
assert e.directory is None
assert e.files == {}
def subject_entity():
return Entity('subject',
"[/\\\\]sub-([a-zA-Z0-9]+)",
False,
"{{root}}{subject}",
None,
bleargh=True)
def test_entity_add_file():
e = Entity('prop', r'-(\d+)')
e.add_file('a', '1')
assert e.files['a'] == '1'
def test_entity_matches_with_map_func(sample_bidsfile):
bf = sample_bidsfile
e = Entity('test', map_func=lambda x: x.filename.split('-')[1])
assert e.match_file(bf) == '03_ses'
def test_entity_init_with_bad_dtype():
with pytest.raises(ValueError) as exc:
ent = Entity('test', dtype='superfloat')
msg = exc.value.message
assert msg.startswith("Invalid dtype")
def test_entity_add_file():
e = Entity('prop', r'-(\d+)')
e.add_file('a', '1')
assert e.files['a'] == '1'
def test_entity_unique_and_count():
e = Entity('prop', r'-(\d+)')
e.files = {'test1-10.txt': '10', 'test2-7.txt': '7', 'test3-7.txt': '7'}
assert sorted(e.unique()) == ['10', '7']
assert e.count() == 2
assert e.count(files=True) == 3
def test_entity_matches_with_map_func(sample_bidsfile):
bf = sample_bidsfile
e = Entity('test', map_func=lambda x: x.filename.split('-')[1])
assert e.match_file(bf) == '03_ses'