def test_read_dig_hpts():
"""Test reading .hpts file (from MNE legacy)."""
fname = op.join(op.dirname(_BRAINVISON_FILE), 'tests', 'data', 'test.hpts')
montage = read_dig_hpts(fname)
assert repr(montage) == (
'<DigMontage | '
'0 extras (headshape), 5 HPIs, 3 fiducials, 34 channels>')
def importbdf(bdfname,
nchans=34,
refchans=['EXG1', 'EXG2'],
hptsname=None,
mask=255,
extrachans=[],
exclude=[],
verbose=None):
"""Wrapper around mne-python to import BDF files
Parameters
----------
bdfname - Name of the biosemi .bdf filename with full path
nchans - Number of EEG channels (including references)
(Optional) By default, 34 (32 + 2 references)
refchans - list of strings with reference channel names
(Optional) By default ['EXG1','EXG2'].
Use None for average reference.
hptsname - Name of the electrode position file in .hpts format with path
(Optional) By default a 32 channel Biosemi layout is used. If
the nchans is >= 64 and < 96, a 64 channel Biosemi layout is
used. If nchans >= 96, a 96 channel biosemi layout is used.
Formats other than .hpts will also likely work, but behavior
may vary.
mask - Integer mask to use for trigger channel (Default is 255).
extrachans - Additional channels other than EEG and EXG that may be in the
bdf file. These will be marked as MISC in mne-python.
Specify as list of names.
exclude - List of channel names to exclude from importing
verbose - bool, str, int, or None (Optional)
The verbosity of messages to print. If a str, it can be either DEBUG,
INFO, WARNING, ERROR, or CRITICAL.
Returns
-------
raw - MNE raw data object of rereferences and preloaded data
eves - Event list (3 column array as required by mne.Epochs)
Requires
--------
mne-python module > release 0.7
"""
# Default HPTS file
if (hptsname is None):
anlffr_root = os.path.dirname(sys.modules['anlffr'].__file__)
if nchans >= 64 and nchans < 96:
logger.info('Number of channels is greater than 64.'
' Hence loading a 64 channel montage.')
hptspath = os.path.join(anlffr_root, 'helper/sysfiles/')
hptsname = 'biosemi64.hpts'
montage = read_dig_hpts(hptspath + hptsname)
misc = ['EXG3', 'EXG4', 'EXG5', 'EXG6', 'EXG7', 'EXG8']
else:
if nchans >= 96:
logger.info('Number of channels is greater than 96.'
' Hence loading a 96 channel montage.')
hptspath = os.path.join(anlffr_root, 'helper/sysfiles/')
hptsname = 'biosemi96.hpts'
montage = read_dig_hpts(hptspath + hptsname)
misc = ['EXG3', 'EXG4', 'EXG5', 'EXG6', 'EXG7', 'EXG8']
else:
if nchans == 2:
logger.info('Number of channels is 2.'
'Guessing ABR montage or saccades.')
montage = None
misc = []
else:
logger.info('Loading a default 32 channel montage.')
hptspath = os.path.join(anlffr_root, 'helper/sysfiles/')
hptsname = 'biosemi32.hpts'
montage = read_dig_hpts(hptspath + hptsname)
misc = ['EXG3', 'EXG4', 'EXG5', 'EXG6', 'EXG7', 'EXG8']
else:
montage = read_dig_hpts(hptsname) # User-supplied
misc = ['EXG3', 'EXG4', 'EXG5', 'EXG6', 'EXG7', 'EXG8']
misc += extrachans
raw = read_raw_bdf(bdfname,
preload=True,
misc=misc,
exclude=exclude,
stim_channel='auto')
raw.set_montage(montage, on_missing='warn')
# Rereference
if refchans is not None:
sys.stdout.write('Re-referencing data to: ' + ' '.join(refchans))
(raw, ref_data) = set_eeg_reference(raw, refchans, copy=False)
raw.info['bads'] += refchans
else:
# Add average reference operator for possible use later
ave_ref_operator = make_eeg_average_ref_proj(raw.info, activate=False)
raw = raw.add_proj(ave_ref_operator)
eves = find_events(raw, shortest_event=1, mask=mask)
return (raw, eves)