def test_export(self, format):
jfile = datafile('R1347D_jacksheet.txt')
scheme = 'bipolar'
area = 0.001
ec = ElectrodeConfig.from_jacksheet(jfile, 'R1347D', scheme, area)
ec.name = '8DEC2017L0M0STIM'
anodes = ['LAD8', 'LPHCD8', 'LAHCD9', 'RAD8', 'LOFD8', 'RPHCD8']
cathodes = ['LAD9', 'LPHCD9', 'LAHCD10', 'RAD9', 'LOFD9', 'RPHCD9']
for args in zip(anodes, cathodes):
ec.add_stim_channel(*args)
if format == 'csv':
with open(datafile("R1347D_8DEC2017L0M0STIM.csv"), 'r') as f:
ref = f.read().split()
new = ec.to_csv().split()
for n, line in enumerate(ref):
assert line == new[n]
else:
with open(datafile('R1347D_8DEC2017L0M0STIM_bipolar.bin'),
'rb') as f:
ref = f.read().split(b'|')
new = ec.to_bin().split(b'|')
for n, line in enumerate(ref):
if len(line) == 0:
break
assert line == new[n]
def test_contacts_as_recarray(self):
ec = ElectrodeConfig.from_jacksheet(datafile("simple_jacksheet.txt"))
arr = ec.contacts_as_recarray()
for i, num in enumerate(range(1, 36)):
assert arr.jack_box_num[i] == num
assert len(arr.contact_name) == 37
assert len(arr.description) == 37
def test_no_mux_crossing():
pairs = create_pairs(datafile('mux_test_jacksheet.csv'))
for pair in pairs.pair:
if 'A' in pair:
assert 'B' not in pair
if 'B' in pair:
assert 'A' not in pair
def test_from_jacksheet(self, scheme, area):
jfile = datafile('simple_jacksheet.txt')
subject = "subject"
if scheme == 'invalid':
with pytest.raises(AssertionError):
ElectrodeConfig.from_jacksheet(jfile, subject, scheme)
return
ec = ElectrodeConfig.from_jacksheet(jfile, subject, scheme, area=area)
assert isinstance(ec.contacts[1].port, int)
assert ec.subject == subject
assert ec.num_contacts == 37
assert ec.num_sense_channels == 37 if scheme == 'monopolar' else 35
assert ec.num_stim_channels == 0
if area == 0.5:
for contact in ec.contacts.values():
assert contact.area == area
else:
areas = ElectrodeConfig.read_area_file(area)
regex = re.compile(r'(\d*[a-zA-Z]+)')
for contact in ec.contacts.values():
electrode = contact.label[:regex.match(contact.label).end()]
area_ = areas[areas.label == electrode].area
assert all(area_ == contact.area)
def test_write_pairs():
pairs = create_pairs(datafile('R1308T_jacksheet.txt'))
# Unsupported file type
with tempdir() as path:
filename = osp.join(path, "test.xyz")
with pytest.raises(ValueError):
write_pairs(pairs, filename)
# CSV files
with tempdir() as path:
filename = osp.join(path, 'test.csv')
write_pairs(pairs, filename)
df = pd.read_csv(filename)
for column in pairs.columns:
assert all(df[column] == pairs[column])
# JSON files
with tempdir() as path:
filename = osp.join(path, 'pairs.json')
# No subject
with pytest.raises(ValueError):
write_pairs(pairs, filename)
write_pairs(pairs, filename, subject='R0000X')
with open(filename, 'r') as f:
data = json.loads(f.read())
assert 'R0000X' in data
def test_create_pairs(filename):
pairs = create_pairs(datafile(filename))
assert 'pair' in pairs.columns
assert 'label1' in pairs.columns
assert 'label2' in pairs.columns
assert 'contact1' in pairs.columns
assert 'contact2' in pairs.columns
assert 'mux' in pairs.columns
combos = np.array([sorted(pair.split('-')) for pair in pairs.pair])
df = pd.DataFrame({'e1': combos[:, 0], 'e2': combos[:, 1]})
# No contact should be paired with itself
same = [df.loc[i, 'e1'] == df.loc[i, 'e2'] for i in df.index]
assert not any(same)
# No pairs should be repeated
df = pd.DataFrame({'pair': ['-'.join(combo) for combo in combos]})
assert len(df.pair.unique()) == len(df)
# Labels should match pairs
for n, row in pairs.iterrows():
assert row.label1 in row.pair
assert row.label2 in row.pair
def test_creation_methods(self, odin, jacksheet, scheme):
ec = ElectrodeConfig(filename=datafile(odin))
ec2 = ElectrodeConfig.from_jacksheet(datafile(jacksheet),
scheme=scheme)
assert len(ec.contacts) == len(ec2.contacts)
assert len(ec.sense_channels) == len(ec2.sense_channels)
# n.b., stim channels shouldn't be defined for ec2
assert len(ec2.stim_channels) == 0
for i, _ in enumerate(ec.contacts):
assert ec.contacts[i].label == ec2.contacts[i].label
assert ec.contacts[i].port == ec2.contacts[i].port
for i, _ in enumerate(ec.sense_channels):
assert ec.sense_channels[i].name == ec2.sense_channels[i].name
assert ec.sense_channels[i].contact == ec2.sense_channels[
i].contact
assert ec.sense_channels[i].ref == ec2.sense_channels[i].ref
def test_read_jacksheet(filename, ignore_labels, standardize_labels):
jacksheet = datafile(filename)
js = read_jacksheet(jacksheet, ignore_labels=ignore_labels, standardize_labels=standardize_labels)
if filename.startswith('simple'):
assert len(js) == 37
elif filename.startswith('R1308T'):
assert len(js) == 128 if not ignore_labels else 126
elif filename.startswith('R1306E'):
assert len(js) == 122 if not ignore_labels else 120
labels = js.label.values
assert ('2RD1' in labels) if standardize_labels else ('2Rd1' in labels)
assert 'electrode' in js.columns
def test_read_config_file(self, extension):
ec = ElectrodeConfig()
filename = 'R1308T_14JUN2017L0M0STIM' + extension
if extension == '.txt':
with pytest.raises(RuntimeError):
ec.read_config_file(datafile(filename))
return
ec.read_config_file(datafile(filename))
assert ec.subject == 'R1308T'
assert ec.version == '1.2'
assert ec.name == '14JUN2017L0M0STIM'
assert all([ch.name == ch.label for ch in ec.sense_channels])
assert all([ch.name == ch.label for ch in ec.stim_channels])
assert len(ec.contacts) == 126
assert len(ec.sense_channels) == 126
assert len(ec.stim_channels) == 3
ec2 = ElectrodeConfig(datafile(filename))
assert ec.subject == ec2.subject
assert ec.version == ec2.version
assert ec.name == ec2.name
assert all(
[ec.contacts[i] == ec2.contacts[i] for i in ec.contacts.keys()])
assert all([
ec.sense_channels[i] == ec2.sense_channels[i]
for i in range(len(ec.sense_channels))
])
assert all([
ec.stim_channels[i] == ec2.stim_channels[i]
for i in range(len(ec.stim_channels))
])
def test_pairs_to_json():
pairs = create_pairs(datafile('R1308T_jacksheet.txt'))
with tempdir() as path:
pairs_to_json(pairs, 'R1308T', path)
pair_list = pairs.pair.tolist()
outfile = osp.join(path, 'pairs.json')
assert osp.exists(outfile)
with open(outfile, 'r') as f:
result = json.loads(f.read())
assert 'R1308T' in result.keys()
assert 'pairs' in result['R1308T'].keys()
for key in result['R1308T']['pairs']:
assert key in pair_list
def test_add_stim_channel(self):
ec = ElectrodeConfig.from_jacksheet(datafile('simple_jacksheet.txt'))
assert len(ec.stim_channels) == 0
ec.add_stim_channel('A1', 'A2')
assert len(ec.stim_channels) == 1
stim = ec.stim_channels[0]
assert stim.name == 'A1_A2'
assert stim.anode == 1
assert stim.cathode == 2
with pytest.raises(ContactNotFoundError):
ec.add_stim_channel('C1', 'A2')
with pytest.raises(ContactNotFoundError):
ec.add_stim_channel('A1', 'C2')
with pytest.raises(ContactNotFoundError):
ec.add_stim_channel('C1', 'C3')
def test_make_odin_config(scheme, format):
subject = 'R1308T' if scheme == 'monopolar' else 'R1347D'
filename = '{:s}_jacksheet.txt'.format(subject)
prefix = 'R1308T_14JUN2017L0M0STIM' if subject == 'R1308T' else 'R1347D_8DEC2017L0M0STIM'
output_filename = prefix + '.' + format
jfile = datafile(filename)
if scheme == 'monopolar':
stim_channels = [('LB6', 'LB7'), ('LC7', 'LC8'), ('LB5', 'LB6')]
else:
stim_channels = [('LAD8', 'LAD9'), ('LPHCD8', 'LPHCD9'),
('LAHCD9', 'LAHCD10'), ('RAD8', 'RAD9'),
('LOFD8', 'LOFD9'), ('RPHCD8', 'RPHCD9')]
makeconf = partial(make_odin_config,
jfile,
prefix,
0.001,
stim_channels=stim_channels,
scheme=scheme,
format=format)
# Printing to stdout
makeconf()
# Saving to a directory
with tempdir() as path:
makeconf(path=path)
outfile = osp.join(path, output_filename)
assert osp.exists(outfile)
# Verify that each primary sense channel is only listed once
if format == 'csv':
config = read_sense_config(outfile)
assert len(config.c1) == len(config.c1.unique())
assert all(config.c1 == config.c1.unique())
elif format == 'bin':
reffile = '{}_{}.bin'.format(prefix, scheme)
with open(resource_filename('bptools.test.data', reffile),
'rb') as ref:
with open(outfile, 'rb') as gen:
rlines = ref.read()
glines = gen.read()
rlines = rlines.split(b'|')
glines = glines.split(b'|')
for i, line in enumerate(rlines):
if not len(line):
break
# We don't really care if the comment section differs
assert line.split(b'#')[0] == glines[i].split(b'#')[0]
# Explicitly specifiying leads to include
good_leads = [n for n in range(1, 4)]
with tempdir() as path:
outfile = osp.join(path, output_filename)
makeconf(path=path, good_leads=good_leads)
if format == 'csv':
config = read_sense_config(outfile)
if scheme == 'bipolar':
assert len(config) == 2
else:
assert len(config) == 3
elif format == 'bin':
pass # FIXME
def test_create_monopolar_pairs():
pairs = create_monopolar_pairs(datafile('simple_jacksheet.txt'))
assert all(pairs.contact2 == 0)
print(pairs)
assert all(pairs.pair[i] == "{}-CR".format(pairs.label1[i])
for i in range(len(pairs)))
def test_muxes():
"""Test that muxes are labeled properly."""
pairs = create_monopolar_pairs(datafile("simple_jacksheet.txt"))
assert all(pairs.mux[:32] == 0)
assert all(pairs.mux[32:] == 1)
write_pairs(pairs, filename)
df = pd.read_csv(filename)
for column in pairs.columns:
assert all(df[column] == pairs[column])
# JSON files
with tempdir() as path:
filename = osp.join(path, 'pairs.json')
# No subject
with pytest.raises(ValueError):
write_pairs(pairs, filename)
write_pairs(pairs, filename, subject='R0000X')
with open(filename, 'r') as f:
data = json.loads(f.read())
assert 'R0000X' in data
# Not testing remainder since covered in test_pairs_to_json
if __name__ == "__main__":
from bptools.jacksheet import read_jacksheet
from bptools.pairs import create_monopolar_pairs
js = read_jacksheet(datafile('simple_jacksheet.txt'))
print(create_monopolar_pairs(datafile('simple_jacksheet.txt')))
print(create_pairs(datafile('simple_jacksheet.txt')))
# print(create_pairs(datafile('R1306E_jacksheet.txt')))
