def test_evoked_resample():
"""Test for resampling of evoked data
"""
# upsample, write it out, read it in
ave = read_evoked(fname, 0)
sfreq_normal = ave.info['sfreq']
ave.resample(2 * sfreq_normal)
write_evoked(op.join(tempdir, 'evoked.fif'), ave)
ave_up = read_evoked(op.join(tempdir, 'evoked.fif'), 0)
# compare it to the original
ave_normal = read_evoked(fname, 0)
# and compare the original to the downsampled upsampled version
ave_new = read_evoked(op.join(tempdir, 'evoked.fif'), 0)
ave_new.resample(sfreq_normal)
assert_array_almost_equal(ave_normal.data, ave_new.data, 2)
assert_array_almost_equal(ave_normal.times, ave_new.times)
assert_equal(ave_normal.nave, ave_new.nave)
assert_equal(ave_normal._aspect_kind, ave_new._aspect_kind)
assert_equal(ave_normal.kind, ave_new.kind)
assert_equal(ave_normal.last, ave_new.last)
assert_equal(ave_normal.first, ave_new.first)
# for the above to work, the upsampling just about had to, but
# we'll add a couple extra checks anyway
assert_true(len(ave_up.times) == 2 * len(ave_normal.times))
assert_true(ave_up.data.shape[1] == 2 * ave_normal.data.shape[1])
def test_io_evoked():
"""Test IO for evoked data (fif + gz) with integer and str args
"""
ave = read_evoked(fname, 0)
write_evoked(op.join(tempdir, 'evoked.fif'), ave)
ave2 = read_evoked(op.join(tempdir, 'evoked.fif'))
# This not being assert_array_equal due to windows rounding
assert_true(np.allclose(ave.data, ave2.data, atol=1e-16, rtol=1e-3))
assert_array_almost_equal(ave.times, ave2.times)
assert_equal(ave.nave, ave2.nave)
assert_equal(ave._aspect_kind, ave2._aspect_kind)
assert_equal(ave.kind, ave2.kind)
assert_equal(ave.last, ave2.last)
assert_equal(ave.first, ave2.first)
# test compressed i/o
ave2 = read_evoked(fname_gz, 0)
assert_true(np.allclose(ave.data, ave2.data, atol=1e-16, rtol=1e-8))
# test str access
setno = 'Left Auditory'
assert_raises(ValueError, read_evoked, fname, setno, kind='stderr')
assert_raises(ValueError, read_evoked, fname, setno, kind='standard_error')
ave3 = read_evoked(fname, setno)
assert_array_almost_equal(ave.data, ave3.data, 19)
def test_evoked_standard_error():
"""Test calculation and read/write of standard error
"""
epochs = Epochs(raw, events[:4], event_id, tmin, tmax, picks=picks,
baseline=(None, 0))
evoked = [epochs.average(), epochs.standard_error()]
fiff.write_evoked(op.join(tempdir, 'evoked.fif'), evoked)
evoked2 = read_evoked(op.join(tempdir, 'evoked.fif'), [0, 1])
evoked3 = [read_evoked(op.join(tempdir, 'evoked.fif'), 'Unknown'),
read_evoked(op.join(tempdir, 'evoked.fif'), 'Unknown',
kind='standard_error')]
for evoked_new in [evoked2, evoked3]:
assert_true(evoked_new[0]._aspect_kind ==
fiff.FIFF.FIFFV_ASPECT_AVERAGE)
assert_true(evoked_new[0].kind == 'average')
assert_true(evoked_new[1]._aspect_kind ==
fiff.FIFF.FIFFV_ASPECT_STD_ERR)
assert_true(evoked_new[1].kind == 'standard_error')
for ave, ave2 in zip(evoked, evoked_new):
assert_array_almost_equal(ave.data, ave2.data)
assert_array_almost_equal(ave.times, ave2.times)
assert_equal(ave.nave, ave2.nave)
assert_equal(ave._aspect_kind, ave2._aspect_kind)
assert_equal(ave.kind, ave2.kind)
assert_equal(ave.last, ave2.last)
assert_equal(ave.first, ave2.first)
def test_io_evoked():
"""Test IO for evoked data (fif + gz) with integer and str args
"""
ave = read_evokeds(fname, 0)
write_evokeds(op.join(tempdir, 'evoked.fif'), ave)
ave2 = read_evokeds(op.join(tempdir, 'evoked.fif'))[0]
# This not being assert_array_equal due to windows rounding
assert_true(np.allclose(ave.data, ave2.data, atol=1e-16, rtol=1e-3))
assert_array_almost_equal(ave.times, ave2.times)
assert_equal(ave.nave, ave2.nave)
assert_equal(ave._aspect_kind, ave2._aspect_kind)
assert_equal(ave.kind, ave2.kind)
assert_equal(ave.last, ave2.last)
assert_equal(ave.first, ave2.first)
# test compressed i/o
ave2 = read_evokeds(fname_gz, 0)
assert_true(np.allclose(ave.data, ave2.data, atol=1e-16, rtol=1e-8))
# test str access
condition = 'Left Auditory'
assert_raises(ValueError, read_evokeds, fname, condition, kind='stderr')
assert_raises(ValueError,
read_evokeds,
fname,
condition,
kind='standard_error')
ave3 = read_evokeds(fname, condition)
assert_array_almost_equal(ave.data, ave3.data, 19)
# test deprecation warning for read_evoked and write_evoked
# XXX should be deleted for 0.9 release
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
ave = read_evoked(fname, setno=0)
assert_true(w[0].category == DeprecationWarning)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
write_evoked(op.join(tempdir, 'evoked.fif'), ave)
assert_true(w[0].category == DeprecationWarning)
# test read_evokeds and write_evokeds
types = ['Left Auditory', 'Right Auditory', 'Left visual', 'Right visual']
aves1 = read_evokeds(fname)
aves2 = read_evokeds(fname, [0, 1, 2, 3])
aves3 = read_evokeds(fname, types)
write_evokeds(op.join(tempdir, 'evoked.fif'), aves1)
aves4 = read_evokeds(op.join(tempdir, 'evoked.fif'))
for aves in [aves2, aves3, aves4]:
for [av1, av2] in zip(aves1, aves):
assert_array_almost_equal(av1.data, av2.data)
assert_array_almost_equal(av1.times, av2.times)
assert_equal(av1.nave, av2.nave)
assert_equal(av1.kind, av2.kind)
assert_equal(av1._aspect_kind, av2._aspect_kind)
assert_equal(av1.last, av2.last)
assert_equal(av1.first, av2.first)
assert_equal(av1.comment, av2.comment)
def test_io_evoked():
"""Test IO for evoked data (fif + gz) with integer and str args
"""
ave = read_evoked(fname, 0)
write_evoked(op.join(tempdir, 'evoked.fif'), ave)
ave2 = read_evoked(op.join(tempdir, 'evoked.fif'))
# This not being assert_array_equal due to windows rounding
assert_true(np.allclose(ave.data, ave2.data, atol=1e-16, rtol=1e-3))
assert_array_almost_equal(ave.times, ave2.times)
assert_equal(ave.nave, ave2.nave)
assert_equal(ave._aspect_kind, ave2._aspect_kind)
assert_equal(ave.kind, ave2.kind)
assert_equal(ave.last, ave2.last)
assert_equal(ave.first, ave2.first)
# test compressed i/o
ave2 = read_evoked(fname_gz, 0)
assert_true(np.allclose(ave.data, ave2.data, atol=1e-16, rtol=1e-8))
# test str access
setno = 'Left Auditory'
assert_raises(ValueError, read_evoked, fname, setno, kind='stderr')
assert_raises(ValueError, read_evoked, fname, setno, kind='standard_error')
ave3 = read_evoked(fname, setno)
assert_array_almost_equal(ave.data, ave3.data, 19)
def test_evoked_resample():
"""Test for resampling of evoked data
"""
# upsample, write it out, read it in
ave = read_evoked(fname, 0)
sfreq_normal = ave.info['sfreq']
ave.resample(2 * sfreq_normal)
write_evoked(op.join(tempdir, 'evoked.fif'), ave)
ave_up = read_evoked(op.join(tempdir, 'evoked.fif'), 0)
# compare it to the original
ave_normal = read_evoked(fname, 0)
# and compare the original to the downsampled upsampled version
ave_new = read_evoked(op.join(tempdir, 'evoked.fif'), 0)
ave_new.resample(sfreq_normal)
assert_array_almost_equal(ave_normal.data, ave_new.data, 2)
assert_array_almost_equal(ave_normal.times, ave_new.times)
assert_equal(ave_normal.nave, ave_new.nave)
assert_equal(ave_normal._aspect_kind, ave_new._aspect_kind)
assert_equal(ave_normal.kind, ave_new.kind)
assert_equal(ave_normal.last, ave_new.last)
assert_equal(ave_normal.first, ave_new.first)
# for the above to work, the upsampling just about had to, but
# we'll add a couple extra checks anyway
assert_true(len(ave_up.times) == 2 * len(ave_normal.times))
assert_true(ave_up.data.shape[1] == 2 * ave_normal.data.shape[1])
def test_evoked_standard_error():
"""Test calculation and read/write of standard error
"""
epochs = Epochs(raw,
events[:4],
event_id,
tmin,
tmax,
picks=picks,
baseline=(None, 0))
evoked = [epochs.average(), epochs.standard_error()]
fiff.write_evoked(op.join(tempdir, 'evoked.fif'), evoked)
evoked2 = read_evoked(op.join(tempdir, 'evoked.fif'), [0, 1])
evoked3 = [
read_evoked(op.join(tempdir, 'evoked.fif'), 'Unknown'),
read_evoked(op.join(tempdir, 'evoked.fif'),
'Unknown',
kind='standard_error')
]
for evoked_new in [evoked2, evoked3]:
assert_true(
evoked_new[0]._aspect_kind == fiff.FIFF.FIFFV_ASPECT_AVERAGE)
assert_true(evoked_new[0].kind == 'average')
assert_true(
evoked_new[1]._aspect_kind == fiff.FIFF.FIFFV_ASPECT_STD_ERR)
assert_true(evoked_new[1].kind == 'standard_error')
for ave, ave2 in zip(evoked, evoked_new):
assert_array_almost_equal(ave.data, ave2.data)
assert_array_almost_equal(ave.times, ave2.times)
assert_equal(ave.nave, ave2.nave)
assert_equal(ave._aspect_kind, ave2._aspect_kind)
assert_equal(ave.kind, ave2.kind)
assert_equal(ave.last, ave2.last)
assert_equal(ave.first, ave2.first)
def test_io_evoked():
"""Test IO for evoked data (fif + gz) with integer and str args
"""
ave = read_evokeds(fname, 0)
write_evokeds(op.join(tempdir, 'evoked.fif'), ave)
ave2 = read_evokeds(op.join(tempdir, 'evoked.fif'))[0]
# This not being assert_array_equal due to windows rounding
assert_true(np.allclose(ave.data, ave2.data, atol=1e-16, rtol=1e-3))
assert_array_almost_equal(ave.times, ave2.times)
assert_equal(ave.nave, ave2.nave)
assert_equal(ave._aspect_kind, ave2._aspect_kind)
assert_equal(ave.kind, ave2.kind)
assert_equal(ave.last, ave2.last)
assert_equal(ave.first, ave2.first)
# test compressed i/o
ave2 = read_evokeds(fname_gz, 0)
assert_true(np.allclose(ave.data, ave2.data, atol=1e-16, rtol=1e-8))
# test str access
condition = 'Left Auditory'
assert_raises(ValueError, read_evokeds, fname, condition, kind='stderr')
assert_raises(ValueError, read_evokeds, fname, condition,
kind='standard_error')
ave3 = read_evokeds(fname, condition)
assert_array_almost_equal(ave.data, ave3.data, 19)
# test deprecation warning for read_evoked and write_evoked
# XXX should be deleted for 0.9 release
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
ave = read_evoked(fname, setno=0)
assert_true(w[0].category == DeprecationWarning)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
write_evoked(op.join(tempdir, 'evoked.fif'), ave)
assert_true(w[0].category == DeprecationWarning)
# test read_evokeds and write_evokeds
types = ['Left Auditory', 'Right Auditory', 'Left visual', 'Right visual']
aves1 = read_evokeds(fname)
aves2 = read_evokeds(fname, [0, 1, 2, 3])
aves3 = read_evokeds(fname, types)
write_evokeds(op.join(tempdir, 'evoked.fif'), aves1)
aves4 = read_evokeds(op.join(tempdir, 'evoked.fif'))
for aves in [aves2, aves3, aves4]:
for [av1, av2] in zip(aves1, aves):
assert_array_almost_equal(av1.data, av2.data)
assert_array_almost_equal(av1.times, av2.times)
assert_equal(av1.nave, av2.nave)
assert_equal(av1.kind, av2.kind)
assert_equal(av1._aspect_kind, av2._aspect_kind)
assert_equal(av1.last, av2.last)
assert_equal(av1.first, av2.first)
assert_equal(av1.comment, av2.comment)
def test_io_multi_evoked():
"""Test IO for multiple evoked datasets
"""
aves = read_evoked(fname, [0, 1, 2, 3])
write_evoked('evoked.fif', aves)
aves2 = read_evoked('evoked.fif', [0, 1, 2, 3])
for [ave, ave2] in zip(aves, aves2):
assert_array_almost_equal(ave.data, ave2.data)
assert_array_almost_equal(ave.times, ave2.times)
assert_equal(ave.nave, ave2.nave)
assert_equal(ave.aspect_kind, ave2.aspect_kind)
assert_equal(ave.last, ave2.last)
assert_equal(ave.first, ave2.first)
def test_io_evoked():
"""Test IO for evoked data
"""
ave = read_evoked(fname)
ave.crop(tmin=0)
write_evoked('evoked.fif', ave)
ave2 = read_evoked('evoked.fif')
assert_array_almost_equal(ave.data, ave2.data)
assert_array_almost_equal(ave.times, ave2.times)
assert_equal(ave.nave, ave2.nave)
assert_equal(ave.aspect_kind, ave2.aspect_kind)
assert_equal(ave.last, ave2.last)
assert_equal(ave.first, ave2.first)
def test_evoked_standard_error():
"""Test calculation and read/write of standard error
"""
epochs = Epochs(raw, events[:4], event_id, tmin, tmax, picks=picks,
baseline=(None, 0))
evoked = [epochs.average(), epochs.standard_error()]
fiff.write_evoked('evoked.fif', evoked)
evoked2 = fiff.read_evoked('evoked.fif', [0, 1])
assert_true(evoked2[0].aspect_kind == fiff.FIFF.FIFFV_ASPECT_AVERAGE)
assert_true(evoked2[1].aspect_kind == fiff.FIFF.FIFFV_ASPECT_STD_ERR)
for ave, ave2 in zip(evoked, evoked2):
assert_array_almost_equal(ave.data, ave2.data)
assert_array_almost_equal(ave.times, ave2.times)
assert_equal(ave.nave, ave2.nave)
assert_equal(ave.aspect_kind, ave2.aspect_kind)
assert_equal(ave.last, ave2.last)
assert_equal(ave.first, ave2.first)
def test_io_multi_evoked():
"""Test IO for multiple evoked datasets
"""
aves = read_evoked(fname, [0, 1, 2, 3])
write_evoked(op.join(tempdir, 'evoked.fif'), aves)
aves2 = read_evoked(op.join(tempdir, 'evoked.fif'), [0, 1, 2, 3])
types = ['Left Auditory', 'Right Auditory', 'Left visual', 'Right visual']
aves3 = read_evoked(op.join(tempdir, 'evoked.fif'), types)
for aves_new in [aves2, aves3]:
for [ave, ave_new] in zip(aves, aves_new):
assert_array_almost_equal(ave.data, ave_new.data)
assert_array_almost_equal(ave.times, ave_new.times)
assert_equal(ave.nave, ave_new.nave)
assert_equal(ave.kind, ave_new.kind)
assert_equal(ave._aspect_kind, ave_new._aspect_kind)
assert_equal(ave.last, ave_new.last)
assert_equal(ave.first, ave_new.first)
# this should throw an error since there are mulitple datasets
assert_raises(ValueError, read_evoked, fname)
def test_io_multi_evoked():
"""Test IO for multiple evoked datasets
"""
aves = read_evoked(fname, [0, 1, 2, 3])
write_evoked(op.join(tempdir, 'evoked.fif'), aves)
aves2 = read_evoked(op.join(tempdir, 'evoked.fif'), [0, 1, 2, 3])
types = ['Left Auditory', 'Right Auditory', 'Left visual', 'Right visual']
aves3 = read_evoked(op.join(tempdir, 'evoked.fif'), types)
for aves_new in [aves2, aves3]:
for [ave, ave_new] in zip(aves, aves_new):
assert_array_almost_equal(ave.data, ave_new.data)
assert_array_almost_equal(ave.times, ave_new.times)
assert_equal(ave.nave, ave_new.nave)
assert_equal(ave.kind, ave_new.kind)
assert_equal(ave._aspect_kind, ave_new._aspect_kind)
assert_equal(ave.last, ave_new.last)
assert_equal(ave.first, ave_new.first)
# this should throw an error since there are mulitple datasets
assert_raises(ValueError, read_evoked, fname)
def test_io_evoked():
"""Test IO for evoked data (fif + gz)
"""
ave = read_evoked(fname)
ave.crop(tmin=0)
write_evoked('evoked.fif', ave)
ave2 = read_evoked('evoked.fif')
assert_array_almost_equal(ave.data, ave2.data)
assert_array_almost_equal(ave.times, ave2.times)
assert_equal(ave.nave, ave2.nave)
assert_equal(ave.aspect_kind, ave2.aspect_kind)
assert_equal(ave.last, ave2.last)
assert_equal(ave.first, ave2.first)
# test compressed i/o
ave2 = read_evoked(fname_gz)
ave2.crop(tmin=0)
assert_array_equal(ave.data, ave2.data)
def test_shift_time_evoked():
""" Test for shifting of time scale
"""
# Shift backward
ave = read_evoked(fname, 0)
ave.shift_time(-0.1, relative=True)
write_evoked(op.join(tempdir, 'evoked.fif'), ave)
# Shift forward twice the amount
ave_bshift = read_evoked(op.join(tempdir, 'evoked.fif'), 0)
ave_bshift.shift_time(0.2, relative=True)
write_evoked(op.join(tempdir, 'evoked.fif'), ave_bshift)
# Shift backward again
ave_fshift = read_evoked(op.join(tempdir, 'evoked.fif'), 0)
ave_fshift.shift_time(-0.1, relative=True)
write_evoked(op.join(tempdir, 'evoked.fif'), ave_fshift)
ave_normal = read_evoked(fname, 0)
ave_relative = read_evoked(op.join(tempdir, 'evoked.fif'), 0)
assert_true(np.allclose(ave_normal.data, ave_relative.data,
atol=1e-16, rtol=1e-3))
assert_array_almost_equal(ave_normal.times, ave_relative.times, 10)
assert_equal(ave_normal.last, ave_relative.last)
assert_equal(ave_normal.first, ave_relative.first)
# Absolute time shift
ave = read_evoked(fname, 0)
ave.shift_time(-0.3, relative=False)
write_evoked(op.join(tempdir, 'evoked.fif'), ave)
ave_absolute = read_evoked(op.join(tempdir, 'evoked.fif'), 0)
assert_true(np.allclose(ave_normal.data, ave_absolute.data,
atol=1e-16, rtol=1e-3))
assert_equal(ave_absolute.first, int(-0.3 * ave.info['sfreq']))
def test_shift_time_evoked():
""" Test for shifting of time scale
"""
# Shift backward
ave = read_evoked(fname, 0)
ave.shift_time(-0.1, relative=True)
write_evoked(op.join(tempdir, 'evoked.fif'), ave)
# Shift forward twice the amount
ave_bshift = read_evoked(op.join(tempdir, 'evoked.fif'), 0)
ave_bshift.shift_time(0.2, relative=True)
write_evoked(op.join(tempdir, 'evoked.fif'), ave_bshift)
# Shift backward again
ave_fshift = read_evoked(op.join(tempdir, 'evoked.fif'), 0)
ave_fshift.shift_time(-0.1, relative=True)
write_evoked(op.join(tempdir, 'evoked.fif'), ave_fshift)
ave_normal = read_evoked(fname, 0)
ave_relative = read_evoked(op.join(tempdir, 'evoked.fif'), 0)
assert_true(
np.allclose(ave_normal.data, ave_relative.data, atol=1e-16, rtol=1e-3))
assert_array_almost_equal(ave_normal.times, ave_relative.times, 10)
assert_equal(ave_normal.last, ave_relative.last)
assert_equal(ave_normal.first, ave_relative.first)
# Absolute time shift
ave = read_evoked(fname, 0)
ave.shift_time(-0.3, relative=False)
write_evoked(op.join(tempdir, 'evoked.fif'), ave)
ave_absolute = read_evoked(op.join(tempdir, 'evoked.fif'), 0)
assert_true(
np.allclose(ave_normal.data, ave_absolute.data, atol=1e-16, rtol=1e-3))
assert_equal(ave_absolute.first, int(-0.3 * ave.info['sfreq']))
fiff.Raw.filter(raw, l_freq = hp_cutoff, h_freq = lp_cutoff)
##Pick all channels
picks = []
for i in range(raw.info['nchan']):
picks.append(i)
##Read Epochs and compute Evoked :)
print 'Reading Epochs from raw file...'
epochs = mne.Epochs(raw, events, event_id, tmin, tmax, baseline = (None,0), picks = picks, proj = True, name = condName, preload = True, flat = dict(mag = magFlat, grad= gradFlat), reject=dict(mag=magRej, grad=gradRej))
print epochs
evoked = [epochs[cond].average(picks =picks) for cond in event_id]
##Write Evoked
print 'Writing Evoked data to -ave.fif file...'
fiff.write_evoked(data_path + '/ave_projon/'+subjID+'_' + par + run +'-ave.fif', evoked)
evokedRuns.append(evoked)
print 'Completed! See ave.fif result in folder', data_path + '/ave_projon/'
##Show the Result - Plotting the evoked data
#mne.viz.plot_evoked(evoked, exclude = [])
#print len(evokedRuns)
##Make the Final Grand average of all the runs
runData = []
runNave = []
newEvokeds = []
newEvoked = copy.deepcopy(evoked)
count = 0
numCond = len(newEvoked)
for i in range(raw_ssp.info['nchan']):
picks.append(i)
###Read epochs
epochs = mne.Epochs(raw_ssp, events, event_id, tmin, tmax, picks=picks, baseline=(None, 0),add_eeg_ref=avgRefVal, proj=projVal,reject=dict(eeg=eegRej,mag=magRej,grad=gradRej),flat=dict(mag=magFlat, grad=gradFlat))
print epochs
evokeds = [epochs[cond].average(picks=picks) for cond in event_id]
###Add the 120 conditions for BaleenHP
if exp == 'BaleenHP':
evoked_Rel = evokeds[4]+evokeds[5]
evoked_Unrel = evokeds[6]+evokeds[7]
evokeds.append(evoked_Rel)
evokeds.append(evoked_Unrel)
fiff.write_evoked(data_path + 'ave_projon/'+args.subj+'_'+exp+evRun+'-ave.fif',evokeds)
evokedRuns.append(evokeds)
##############################
############Make grand-average
runData = []
runNave = []
newEvoked = copy.deepcopy(evokedRuns[0])
print newEvoked
count = 0
numCond = len(newEvoked)
for c in range(numCond):
def mnepy_avg(subjID,run):
import mne
from mne import fiff
from mne import viz
#from mne.viz import evoked
import argparse
import copy
import numpy
#######Get Input ##
print subjID
########Analysis Parameters##
###Projection and Average Reference and Filtering
projVal = True
avgRefVal = False
hp_cutoff = 0.7
lp_cutoff = 40
event_id = 2
#######Experiment specific parameters
###TimeWindow
tmin = 0
tmax = 2.0 ##float(cc.epMax[eve])
if run == 'CRM':
tmax = 1.0
elif run == 'DFNAM':
tmax = 2.0
########Artifact rejection parameters
###General
gradRej = 2000e-13
magRej = 3000e-15
magFlat = 1e-14
gradFlat = 1000e-15
####################################
#######Compute averages for each run
# # evoked=[]
# if subjID == 'EP2':
# runs = ['run1', 'run2', 'run3']
evokedRuns =[]
# for run in runs:
###Event file suffix
eveSuffix = '.eve'
eve_file = run + eveSuffix #eve + eveSuffix
print "You have chosen the event file " + eve_file
##Setup Subject Speciifc Information
data_path = '/home/custine/MEG/data/epi_conn/' +subjID
event_file = data_path + '/eve/' + eve_file
print event_file
raw_file = data_path + '/' + run +'_raw.fif' ##Change this suffix if you are using SSP
avgLog_file = data_path + '/logs/' +run+ '_py-ave.log'
print raw_file, avgLog_file
#
##Setup Reading fiff data structure
print 'Reading Raw data... '
raw = fiff.Raw(raw_file, preload = True)
events = mne.read_events(event_file)
#print events
mne.set_log_file(fname = avgLog_file, overwrite = True)
##Filter raw data
fiff.Raw.filter(raw, l_freq = hp_cutoff, h_freq = lp_cutoff)
#Pick all channels
picks = []
for i in range(raw.info['nchan']):
picks.append(i)
##Read Epochs and compute Evoked :)
print 'Reading Epochs from evoked file...'
epochs = mne.Epochs(raw, events, event_id, tmin, tmax, baseline = (None,0), proj = True, picks = picks, preload = True, flat = dict(mag = magFlat, grad= gradFlat), reject=dict(mag=magRej, grad=gradRej))
print epochs
evoked = [epochs.average(picks =None)]
# # epochs.plot()
##Write Evoked
print 'Writing Evoked data to -ave.fif file...'
fiff.write_evoked(data_path + '/ave_projon/' + run +'-noise-ave.fif', evoked)
evokedRuns.append(evoked)
print 'Completed! See ave.fif result in folder', data_path + '/ave_projon/'
#
## # ###############################################################################
## # #Show the Result - Plotting the evoked data
## # mne.viz.evoked.plot_evoked(evoked, exclude = [])
#
print len(evokedRuns)
picks = fiff.pick_types(raw.info, meg=False, eeg=True, stim=False, eog=True,
include=include, exclude='bads')
# Read epochs
epochs = mne.Epochs(raw, events, event_ids, tmin, tmax, picks=picks,
baseline=(None, 0), reject=dict(eeg=80e-6, eog=150e-6))
# Let's equalize the trial counts in each condition
epochs.equalize_event_counts(['AudL', 'AudR', 'VisL', 'VisR'], copy=False)
# Now let's combine some conditions
combine_event_ids(epochs, ['AudL', 'AudR'], {'Auditory': 12}, copy=False)
combine_event_ids(epochs, ['VisL', 'VisR'], {'Visual': 34}, copy=False)
# average epochs and get Evoked datasets
evokeds = [epochs[cond].average() for cond in ['Auditory', 'Visual']]
# save evoked data to disk
fiff.write_evoked('sample_auditory_and_visual_eeg-ave.fif', evokeds)
###############################################################################
# View evoked response
import matplotlib.pyplot as plt
plt.clf()
ax = plt.subplot(2, 1, 1)
evokeds[0].plot(axes=ax)
plt.title('EEG evoked potential, auditory trials')
plt.ylabel('Potential (uV)')
ax = plt.subplot(2, 1, 2)
evokeds[1].plot(axes=ax)
plt.title('EEG evoked potential, visual trials')
plt.ylabel('Potential (uV)')
plt.show()
mne.epochs.equalize_epoch_counts([epochsAPrime, epochsBPrime],
method="mintime")
print "Epochs after equalising"
print epochsAPrime
print epochsBPrime
###Averaging Epochs#######
evokedAPrime = epochsAPrime.average(picks=picks)
evokedBPrime = epochsBPrime.average(picks=picks)
for ep in [evokedAPrime, evokedBPrime]:
evokeds.append(ep)
###Computing Evoked Potentials#######
fiff.write_evoked(
data_path + '/' + ave_dest + '/' + args.subj + '_' + expName + evRun +
'-equalisedPri-ave.fif', evokeds)
evokedRuns.append(evokeds)
#######################################
##########Make grand-average###########
runData = []
runNave = []
newEvoked = copy.deepcopy(evokedRuns[0])
count = 0
numCond = len(newEvoked)
for c in range(numCond):
for evRun in evokedRuns:
runData.append(evRun[c].data)
runNave.append(evRun[c].nave)
print "Epochs After equalising"
print epochsAX
print epochsBX
print epochsAY
print epochsBY
###Averaging Epochs#######
evokedAY =epochsAY.average(picks = picks)
evokedBX =epochsBX.average(picks = picks)
evokedBY =epochsBY.average(picks = picks)
evokedAX =epochsAX.average(picks = picks)
for ep in [evokedAY, evokedBX, evokedBY, evokedAX]:
evokeds.append(ep)
fiff.write_evoked(data_path +'/' + ave_dest +'/'+ args.subj+'_'+expName+evRun+'-equalisedTar-ave.fif',evokeds)
evokedRuns.append(evokeds)
##
####################################
############Make grand-average######
runData = []
runNave = []
newEvoked = copy.deepcopy(evokedRuns[0])
#print newEvoked
count = 0
numCond = len(newEvoked)
for c in range(numCond):
for evRun in evokedRuns:
runData.append(evRun[c].data)
def mnepy_avg(subjID, sessID, eve, ssp_type):
import mne
from mne import fiff
from mne import viz
from mne.viz import evoked
import argparse
import condCodes as cc
import copy
import numpy
#######Get Input ##
print subjID
print sessID
print eve
data_path = '/home/custine/MEG/data/krns_kr3/' +subjID+'/'+sessID
if ssp_type == 'run':
raw_data_path = '/home/custine/MEG/data/krns_kr3/' +subjID+'/'+sessID
runSuffix = '_raw.fif'
elif ssp_type == 'ecg' or ssp_type == 'eog':
raw_data_path = '/home/custine/MEG/data/krns_kr3/' +subjID+'/'+sessID + '/ssp/mne'
runSuffix = '_clean_' + ssp_type + '_raw.fif'
########Analysis Parameters##
###Event file suffix
eveSuffix = '-Triggers.eve'
eve_file = eve + eveSuffix #eve + eveSuffix
print "You have chosen the event file " + eve_file
###Projection and Average Reference and Filtering
projVal = True
avgRefVal = False
hp_cutoff = 0.7
lp_cutoff = 50
#######Experiment specific parameters
###EventLabels and Runs
runs = cc.runDict[eve] ##TESTING################################################
print runs
labelList = cc.condLabels[eve]
event_id = {}
condName = {}
for row in labelList:
event_id[row[1]] = int(row[0])
condName[row[1]] = row[1]
print event_id
###TimeWindow
tmin = -.5
tmax = float(cc.epMax[eve])
# tmax = 3.00 #4Words Category
########Artifact rejection parameters
###General
gradRej = 4000e-13
magRej = 4000e-12
magFlat = 1e-14
gradFlat = 1000e-15
####################################
######Compute averages for each run
evoked=[]
evokedRuns =[]
for runID in runs:
print runID
##Setup Subject Speciifc Information
event_file = data_path + '/eve/triggers/' + subjID + '_'+ sessID +'_'+runID +'_' + eve_file
print event_file
raw_file = raw_data_path + '/' + subjID + '_' + sessID+ '_' + runID + runSuffix ##Change this suffix if you are using SSP ##_clean_ecg_
avgLog_file = data_path + '/ave_projon/logs/' +subjID + '_' + sessID+ '_'+runID + '_'+eve+'_' + ssp_type +'-ave.log'
print raw_file, avgLog_file
##Setup Reading fiff data structure
print 'Reading Raw data... '
raw = fiff.Raw(raw_file, preload = True)
events = mne.read_events(event_file)
print events
mne.set_log_file(fname = avgLog_file, overwrite = True)
##Filter raw data
fiff.Raw.filter(raw, l_freq = hp_cutoff, h_freq = lp_cutoff)
##Pick all channels
picks = []
for i in range(raw.info['nchan']):
picks.append(i)
##Read Epochs and compute Evoked :)
print 'Reading Epochs from evoked raw file...'
epochs = mne.Epochs(raw, events, event_id, tmin, tmax, baseline = (-0.5,0), picks = picks, proj = True, name = condName, preload = True, flat = dict(mag = magFlat, grad= gradFlat), reject=dict(mag=magRej, grad=gradRej))
print epochs
evoked = [epochs[cond].average(picks =picks) for cond in event_id]
# # epochs.plot()
##Write Evoked
print 'Writing Evoked data to -ave.fif file...'
fiff.write_evoked(data_path + '/ave_projon/' + subjID+'_' + sessID+'_'+runID+'_' + eve +'_' + ssp_type+'-ave.fif', evoked)
evokedRuns.append(evoked)
print 'Completed! See ave.fif result in folder', data_path + '/ave_projon/'
###############################################################################
##Show the Result - Plotting the evoked data
#mne.viz.evoked.plot_evoked(evoked, exclude = [])
print len(evokedRuns)
##Make the Final Grand average of all the runs
runData = []
runNave = []
newEvoked = copy.deepcopy(evoked)
print newEvoked
numCond = len(newEvoked)
print 'Length', numCond
for c in range(numCond):
for evRun in evokedRuns:
runData.append(evRun[c].data)
runNave.append(evRun[c].nave)
print 'Jane Here', c, runNave
gaveData = numpy.mean(runData,0)
gaveNave = numpy.sum(runNave)
print 'Sum', sum(runNave)
newEvoked[c].data = gaveData
newEvoked[c].nave = gaveNave
# runData = []
# runNave = []
print newEvoked[0].nave
##Write Grand average Evoked
fiff.write_evoked(data_path + '/ave_projon/'+subjID+'_' + sessID+'_' + eve +'_' + ssp_type+'_All-ave.fif', newEvoked)