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_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_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_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 from_jacksheet(cls,
filename,
subject="",
scheme='bipolar',
area=0.5,
ignore_labels=['ECG', 'EKG']):
"""Create a new :class:`ElectrodeConfig` instance from a jacksheet.
Parameters
----------
filename : str
Path to jacksheet file.
subject : str
Subject ID
scheme : str
Referencing scheme to use (``bipolar`` or ``monopolar``).
area : float or str
Default surface area to use in mm^2 when a float or a file that
maps electrode labels to surface areas (see :meth:`read_area_file`
for file format details).
ignore_labels: list or tuple
Labels to ignore within the jacksheet
Returns
-------
config : ElectrodeConfig
"""
js = read_jacksheet(filename, ignore_labels=ignore_labels)
config = ElectrodeConfig()
config.subject = subject
config._jacksheet = js
if isinstance(area, str):
area_map = cls.read_area_file(area)
try:
areas = [
area_map[area_map.label == row.electrode].area.values[0]
for _, row in js.iterrows()
]
except IndexError as e:
raise IndexError(
str(e) + " HINT: check for typos in area file")
else:
areas = [area] * len(js)
jsdf = pd.DataFrame({
'label':
js.label,
'port':
js.index,
'area':
areas,
'description': ['Jackbox number {}'.format(n) for n in js.index]
})
contacts = [Contact.from_series(s) for _, s in jsdf.iterrows()]
for c in contacts:
config.contacts[c.port] = c
if scheme == 'bipolar':
pairs = create_pairs(filename, ignore_labels=ignore_labels)
elif scheme == 'monopolar':
pairs = create_monopolar_pairs(filename,
ignore_labels=ignore_labels)
else:
raise AssertionError("Unrecognized referencing scheme")
config.sense_channels = [
SenseChannel.from_series(s) for _, s in pd.DataFrame({
'name':
pairs.label1 +
"CR" if scheme == 'monopolar' else pairs.label1 + pairs.label2,
'contact':
pairs.contact1,
'ref':
pairs.contact2,
'description':
pairs.pair
}).iterrows()
]
return config
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')))