def writeList(filename, data):
myFile = open(filename, "w")
myFile.close()
myFile = open(filename, "a")
for row in data:
myFile.write(str(row))
myFile.write("\n")
myFile.close()
make_lingua(filename)
def writeTable(filename, data):
myFile = open(filename, "w")
myFile.close()
myFile = open(filename, "a")
for row in data:
for item in row:
myFile.write(str(item))
myFile.write("\t")
myFile.write("\n")
myFile.close()
make_lingua(filename)
def compute_proj_ecgeog(in_path, in_fif_fname):
if in_fif_fname.endswith('_raw.fif') or in_fif_fname.endswith('-raw.fif'):
prefix = in_fif_fname[:-8]
else:
prefix = in_fif_fname[:-4]
if average:
ecg_proj_fname = in_path + 'ssp/' +prefix + '_ecg_avg_proj.fif'
eog_proj_fname = in_path + 'ssp/' +prefix + '_eog_avg_proj.fif'
out_fif_fname = in_path + 'ssp/' +prefix + '_ecgeog_avg_proj_raw.fif'
else:
ecg_proj_fname = in_path + 'ssp/' + prefix + '_ecg_proj.fif'
eog_proj_fname = in_path + 'ssp/' + prefix + '_eog_proj.fif'
out_fif_fname = in_path + 'ssp/' + prefix + '_ecgeog_proj_raw.fif'
##Reading raw file
in_fif_fname = in_path + in_fif_fname
raw = mne.fiff.Raw(in_fif_fname) #, preload=preload)
print 'Applying ECG and EOG projector'
command = ('mne_process_raw --cd %s --raw %s --proj %s --proj %s --proj %s '
'--projoff --save %s --filteroff'
% (in_path, in_fif_fname, eog_proj_fname, ecg_proj_fname, in_fif_fname,
out_fif_fname))
make_lingua(out_fif_fname)
print 'Command executed: %s' % command
print 'Running : %s' % command
st = os.system(command)
if st != 0:
raise ValueError('Problem while running : %s' % command)
else:
print 'Done'
print ('Computed ECG EOG Rejection fif file. Saved result as %s' % out_fif_fname)
def compute_proj_ecgeog(in_path, in_fif_fname):
if in_fif_fname.endswith('_raw.fif') or in_fif_fname.endswith('-raw.fif'):
prefix = in_fif_fname[:-8]
else:
prefix = in_fif_fname[:-4]
if average:
ecg_proj_fname = in_path + 'ssp/' + prefix + '_ecg_avg_proj.fif'
eog_proj_fname = in_path + 'ssp/' + prefix + '_eog_avg_proj.fif'
out_fif_fname = in_path + 'ssp/' + prefix + '_ecgeog_avg_proj_raw.fif'
else:
ecg_proj_fname = in_path + 'ssp/' + prefix + '_ecg_proj.fif'
eog_proj_fname = in_path + 'ssp/' + prefix + '_eog_proj.fif'
out_fif_fname = in_path + 'ssp/' + prefix + '_ecgeog_proj_raw.fif'
##Reading raw file
in_fif_fname = in_path + in_fif_fname
raw = mne.fiff.Raw(in_fif_fname) #, preload=preload)
print 'Applying ECG and EOG projector'
command = (
'mne_process_raw --cd %s --raw %s --proj %s --proj %s --proj %s '
'--projoff --save %s --filteroff' %
(in_path, in_fif_fname, eog_proj_fname, ecg_proj_fname, in_fif_fname,
out_fif_fname))
make_lingua(out_fif_fname)
print 'Command executed: %s' % command
print 'Running : %s' % command
st = os.system(command)
if st != 0:
raise ValueError('Problem while running : %s' % command)
else:
print 'Done'
print('Computed ECG EOG Rejection fif file. Saved result as %s' %
out_fif_fname)
def compute_proj_ecg(in_path, in_fif_fname, tmin, tmax, n_grad, n_mag, n_eeg,
l_freq, h_freq, average, filter_length, n_jobs, ch_name,
reject, avg_ref, bads, preload, flat):
"""Compute SSP/PCA projections for ECG/EOG artifacts
Parameters
----------
in_fif_fname: string
Raw fif File
XXX
"""
if in_fif_fname.endswith('_raw.fif') or in_fif_fname.endswith('-raw.fif'):
prefix = in_fif_fname[:-8]
else:
prefix = in_fif_fname[:-4]
ecg_event_fname = in_path + 'ssp/' + prefix + '_ecg-eve.fif'
if average:
ecg_proj_fname = in_path + 'ssp/' + prefix + '_ecg_avg_proj.fif'
out_fif_fname = in_path + 'ssp/' + prefix + '_ecg_avg_proj_raw.fif'
else:
ecg_proj_fname = in_path + 'ssp/' + prefix + '_ecg_proj.fif'
out_fif_fname = in_path + 'ssp/' + prefix + '_ecg_proj_raw.fif'
print 'Reading fif File'
in_fif_fname = in_path + in_fif_fname
raw = mne.fiff.Raw(in_fif_fname, preload=preload)
# if (in_path == '/cluster/kuperberg/SemPrMM/MEG/data/ya30/'):
# save after 84s of MEG data in FIF file
# raw = raw[: , 84:]
#raw.save('sample_audvis_meg_raw.fif', tmin=84)
print 'Running ECG SSP computation'
ecg_events, _, _ = mne.artifacts.find_ecg_events(raw, ch_name=ch_name)
print "Writing ECG events in %s" % ecg_event_fname
mne.write_events(ecg_event_fname, ecg_events)
make_lingua(ecg_event_fname)
if avg_ref:
print "Adding average EEG reference projection."
eeg_proj = mne.fiff.proj.make_eeg_average_ref_proj(raw.info)
raw.info['projs'].append(eeg_proj)
print 'Computing ECG projector'
# Handler rejection parameters
if len(mne.fiff.pick_types(raw.info, meg='grad', eeg=False,
eog=False)) == 0:
del reject['grad']
if len(mne.fiff.pick_types(raw.info, meg='mag', eeg=False,
eog=False)) == 0:
del reject['mag']
if len(mne.fiff.pick_types(raw.info, meg=False, eeg=True, eog=False)) == 0:
del reject['eeg']
if len(mne.fiff.pick_types(raw.info, meg=False, eeg=False, eog=True)) == 0:
del reject['eog']
picks = mne.fiff.pick_types(raw.info,
meg=True,
eeg=True,
eog=True,
exclude=raw.info['bads'] + bads)
if l_freq is None and h_freq is not None:
raw.high_pass_filter(picks, h_freq, filter_length, n_jobs)
if l_freq is not None and h_freq is None:
raw.low_pass_filter(picks, h_freq, filter_length, n_jobs)
if l_freq is not None and h_freq is not None:
raw.band_pass_filter(picks, l_freq, h_freq, filter_length, n_jobs)
epochs_ecg = mne.Epochs(raw,
ecg_events,
None,
tmin,
tmax,
baseline=None,
picks=picks,
reject=reject,
proj=True)
print epochs_ecg
projs_init = raw.info['projs']
if average:
evoked_ecg = epochs_ecg.average()
projs_ecg = mne.compute_proj_evoked(evoked_ecg,
n_grad=n_grad,
n_mag=n_mag,
n_eeg=n_eeg)
else:
print epochs_ecg, n_grad, n_mag, n_eeg
projs_ecg = mne.compute_proj_epochs(epochs_ecg,
n_grad=n_grad,
n_mag=n_mag,
n_eeg=n_eeg)
print "Writing ECG projections in %s" % ecg_proj_fname
mne.write_proj(
ecg_proj_fname, projs_ecg + projs_init
) ## Original Projections written along with the ecg projections.
print "Writing ECG projections in %s" % ecg_proj_fname
mne.write_proj(ecg_proj_fname, projs_ecg)
return in_fif_fname, ecg_proj_fname, out_fif_fname
def compute_proj_eog(in_path, in_fif_fname, tmin, tmax, n_grad, n_mag, n_eeg,
l_freq, h_freq, average, filter_length, n_jobs, ch_name,
reject, avg_ref, bads, preload):
#####Defining filenames
if in_fif_fname.endswith('_raw.fif') or in_fif_fname.endswith('-raw.fif'):
prefix = in_fif_fname[:-8]
else:
prefix = in_fif_fname[:-4]
eog_event_fname = in_path + 'ssp/' + prefix + '_PYeog-eve.fif'
if average:
eog_proj_fname = in_path + 'ssp/' + prefix + '_eog_avg_proj.fif'
out_fif_fname = in_path + 'ssp/' + prefix + '_eog_avg_proj_raw.fif'
else:
eog_proj_fname = in_path + 'ssp/' + prefix + '_PYeog_proj.fif'
out_fif_fname = in_path + 'ssp/' + prefix + '_PYeog_proj_raw.fif'
####Reading in raw data
in_fif_fname = in_path + in_fif_fname
raw = mne.fiff.Raw(in_fif_fname, preload=preload)
print 'Running EOG SSP computation'
eog_events, _ = mne.artifacts.find_eog_events(
raw
) # since our copy of the mne.artifacts.events.py script returns two parameters.
print "Writing EOG events in %s" % eog_event_fname
mne.write_events(eog_event_fname, eog_events)
make_lingua(eog_event_fname)
print 'Computing EOG projector'
# Handler rejection parameters
if len(mne.fiff.pick_types(raw.info, meg='grad', eeg=False,
ecg=False)) == 0:
del reject['grad']
if len(mne.fiff.pick_types(raw.info, meg='mag', eeg=False,
ecg=False)) == 0:
del reject['mag']
if len(mne.fiff.pick_types(raw.info, meg=False, eeg=True, ecg=False)) == 0:
del reject['eeg']
if len(mne.fiff.pick_types(raw.info, meg=False, eeg=False, ecg=True)) == 0:
del reject['ecg']
picks_eog = mne.fiff.pick_types(raw.info,
meg=True,
eeg=True,
ecg=True,
exclude=raw.info['bads'] + bads)
if l_freq is None and h_freq is not None:
raw.high_pass_filter(picks, h_freq, filter_length, n_jobs)
if l_freq is not None and h_freq is None:
raw.low_pass_filter(picks, h_freq, filter_length, n_jobs)
if l_freq is not None and h_freq is not None:
raw.band_pass_filter(picks_eog, l_freq, h_freq, filter_length, n_jobs)
epochs_eog = mne.Epochs(raw,
eog_events,
None,
tmin,
tmax,
baseline=None,
picks=picks_eog,
reject=reject,
proj=True)
projs_init = raw.info['projs']
if average:
evoked_eog = epochs_eog.average()
projs_eog = mne.compute_proj_evoked(evoked_eog,
n_grad=n_grad,
n_mag=n_mag,
n_eeg=n_eeg)
else:
print epochs_eog, n_grad, n_mag, n_eeg
projs_eog = mne.compute_proj_epochs(epochs_eog,
n_grad=n_grad,
n_mag=n_mag,
n_eeg=n_eeg)
print "Writing EOG projections in %s" % eog_proj_fname
mne.write_proj(eog_proj_fname, projs_eog)
return in_fif_fname, eog_proj_fname, out_fif_fname
bad_fname = in_path + bad_fname
print bad_fname
if bad_fname is not None:
bads = [w.rstrip().split() for w in open(bad_fname).readlines()]
print 'Bad channels read : %s' % bads
else:
bads = []
print type(tmin)
if tag == 'ecg':
in_fif_fname, ecg_proj_fname, out_fif_fname = compute_proj_ecg(
in_path, raw_in, tmin, tmax, n_grad, n_mag, n_eeg, l_freq, h_freq,
average, filter_length, n_jobs, ch_name, reject, avg_ref, bads,
preload, flat)
make_lingua(in_fif_fname)
make_lingua(ecg_proj_fname)
print 'Applying ECG projector'
command = ('mne_process_raw --cd %s --raw %s --proj %s --proj %s '
'--projoff --save %s --filteroff' %
(in_path, in_fif_fname, ecg_proj_fname, in_fif_fname,
out_fif_fname))
st = os.system(command)
if st != 0:
raise ValueError('Problem while running : %s' % command)
else:
print 'Command executed: %s' % command
print 'Done'
print('Computed ECG Rejection fif file. Saved result as %s' %
out_fif_fname)
make_lingua(out_fif_fname)
subject_lines = []
for sub in subjects:
if sub in v:
if len(sub) > 3: ##This makes the tabbing pretty for the table; different for longer subject names
beg = '%s\t' % sub
else:
beg = '%s\t\t' % sub
results = '\t\t'.join(['%i' % ( v[sub][code][1]) for code in codes])
subject_lines.append('%s%s' % (beg, results))
#write out dat for each paradigm
f = open(fname, 'w')
f.write(code_line + '\n')
f.write('\n'.join(subject_lines))
f.close()
print("Saved total table to %s" % fname)
make_lingua(fname)
##make combined rejTable
for k,v in all_data.items():
if k == 'BaleenHP':
fname = '/%s/kuperberg/SemPrMM/MEG/results/artifact_rejection/combined_rejection/ssp/%s_%s_remaining_events_ecgeog.txt' % (pre, subjType, k)
codes = sorted(v[subjType+'8'].keys(), cmp=lambda x,y: cmp(int(x), int(y))) ##This is the codes for the events for the paradigm
code_line = '\t\t%s' % '\t\t'.join(codes) ##This just puts them together to head the table
subject_lines = []
for sub in subjects:
subjLine = []
if sub in v:
if len(sub) > 3: ##This makes the tabbing pretty for the table; different for longer subject names
beg = '%s\t' % sub
else:
beg = '%s\t\t' % sub
print subjects
study_results = parse_study(study, subjects)
logf = '/cluster/kuperberg/SemPrMM/MEG/results/behavioral_accuracy/R/MEG_%s_%s_accuracy.log' % (
listPrefix, study)
with open(logf, 'w') as f:
f.write('sub:\t\t')
good_keys = sorted([key for key in codes[study].keys()],
lambda x, y: cmp(int(x), int(y)))
#write out header
f.write('CondCode\t\tAccuracy\tUnknown\n')
for sub in sorted(study_results.keys()):
results = study_results[sub]
total_num = 0
total_den = 0
for key in good_keys:
v = results[key]
total_num += v['c']
total_den += v['t']
if v['rts']:
avg_rt = sum(v['rts']) / float(len(v['rts']))
else:
avg_rt = 0
f.write(sub + '\t\t')
f.write(codes[study][key][0] + '\t\t')
f.write(
"%1.3f\t\t%1.3f\t\n" %
(round(float(v['c']) / v['t'], 3), round(avg_rt, 3)))
## f.write('ALL TASKS\n')
## f.write("{0}\n".format(round(float(total_num)/total_den,3)))
make_lingua(logf)
def compute_proj_ecg(in_path, in_fif_fname, tmin, tmax, n_grad, n_mag, n_eeg, l_freq, h_freq, average, filter_length, n_jobs, ch_name, reject, avg_ref, bads, preload, flat):
"""Compute SSP/PCA projections for ECG/EOG artifacts
Parameters
----------
in_fif_fname: string
Raw fif File
XXX
"""
if in_fif_fname.endswith('_raw.fif') or in_fif_fname.endswith('-raw.fif'):
prefix = in_fif_fname[:-8]
else:
prefix = in_fif_fname[:-4]
ecg_event_fname = in_path + 'ssp/' + prefix + '_ecg-eve.fif'
if average:
ecg_proj_fname = in_path + 'ssp/' + prefix + '_ecg_avg_proj.fif'
out_fif_fname = in_path + 'ssp/' + prefix + '_ecg_avg_proj_raw.fif'
else:
ecg_proj_fname = in_path + 'ssp/' + prefix + '_ecg_proj.fif'
out_fif_fname = in_path + 'ssp/' + prefix + '_ecg_proj_raw.fif'
print 'Reading fif File'
in_fif_fname = in_path + in_fif_fname
raw = mne.fiff.Raw(in_fif_fname, preload=preload)
# if (in_path == '/cluster/kuperberg/SemPrMM/MEG/data/ya30/'):
# save after 84s of MEG data in FIF file
# raw = raw[: , 84:]
#raw.save('sample_audvis_meg_raw.fif', tmin=84)
print 'Running ECG SSP computation'
ecg_events, _, _ = mne.artifacts.find_ecg_events(raw, ch_name=ch_name)
print "Writing ECG events in %s" % ecg_event_fname
mne.write_events(ecg_event_fname, ecg_events)
make_lingua(ecg_event_fname)
if avg_ref:
print "Adding average EEG reference projection."
eeg_proj = mne.fiff.proj.make_eeg_average_ref_proj(raw.info)
raw.info['projs'].append(eeg_proj)
print 'Computing ECG projector'
# Handler rejection parameters
if len(mne.fiff.pick_types(raw.info, meg='grad', eeg=False, eog=False)) == 0:
del reject['grad']
if len(mne.fiff.pick_types(raw.info, meg='mag', eeg=False, eog=False)) == 0:
del reject['mag']
if len(mne.fiff.pick_types(raw.info, meg=False, eeg=True, eog=False)) == 0:
del reject['eeg']
if len(mne.fiff.pick_types(raw.info, meg=False, eeg=False, eog=True)) == 0:
del reject['eog']
picks = mne.fiff.pick_types(raw.info, meg=True, eeg=True, eog=True,
exclude=raw.info['bads'] + bads)
if l_freq is None and h_freq is not None:
raw.high_pass_filter(picks, h_freq, filter_length, n_jobs)
if l_freq is not None and h_freq is None:
raw.low_pass_filter(picks, h_freq, filter_length, n_jobs)
if l_freq is not None and h_freq is not None:
raw.band_pass_filter(picks, l_freq, h_freq, filter_length, n_jobs)
epochs_ecg = mne.Epochs(raw, ecg_events, None, tmin, tmax, baseline=None,
picks=picks, reject=reject, proj=True)
print epochs_ecg
projs_init = raw.info['projs']
if average:
evoked_ecg = epochs_ecg.average()
projs_ecg = mne.compute_proj_evoked(evoked_ecg, n_grad=n_grad, n_mag=n_mag,
n_eeg=n_eeg)
else:
print epochs_ecg, n_grad, n_mag, n_eeg
projs_ecg = mne.compute_proj_epochs(epochs_ecg, n_grad=n_grad, n_mag=n_mag,
n_eeg=n_eeg)
print "Writing ECG projections in %s" % ecg_proj_fname
mne.write_proj(ecg_proj_fname, projs_ecg + projs_init) ## Original Projections written along with the ecg projections.
print "Writing ECG projections in %s" % ecg_proj_fname
mne.write_proj(ecg_proj_fname, projs_ecg)
return in_fif_fname, ecg_proj_fname, out_fif_fname
def compute_proj_eog(in_path, in_fif_fname, tmin, tmax, n_grad, n_mag, n_eeg, l_freq, h_freq, average, filter_length, n_jobs, ch_name, reject, avg_ref, bads, preload):
#####Defining filenames
if in_fif_fname.endswith('_raw.fif') or in_fif_fname.endswith('-raw.fif'):
prefix = in_fif_fname[:-8]
else:
prefix = in_fif_fname[:-4]
eog_event_fname = in_path + 'ssp/'+ prefix + '_PYeog-eve.fif'
if average:
eog_proj_fname = in_path + 'ssp/' + prefix + '_eog_avg_proj.fif'
out_fif_fname = in_path + 'ssp/' + prefix + '_eog_avg_proj_raw.fif'
else:
eog_proj_fname = in_path + 'ssp/' + prefix + '_PYeog_proj.fif'
out_fif_fname = in_path + 'ssp/' + prefix + '_PYeog_proj_raw.fif'
####Reading in raw data
in_fif_fname = in_path + in_fif_fname
raw = mne.fiff.Raw(in_fif_fname, preload=preload)
print 'Running EOG SSP computation'
eog_events, _= mne.artifacts.find_eog_events(raw) # since our copy of the mne.artifacts.events.py script returns two parameters.
print "Writing EOG events in %s" % eog_event_fname
mne.write_events(eog_event_fname, eog_events)
make_lingua(eog_event_fname)
print 'Computing EOG projector'
# Handler rejection parameters
if len(mne.fiff.pick_types(raw.info, meg='grad', eeg=False, ecg=False)) == 0:
del reject['grad']
if len(mne.fiff.pick_types(raw.info, meg='mag', eeg=False, ecg=False)) == 0:
del reject['mag']
if len(mne.fiff.pick_types(raw.info, meg=False, eeg=True, ecg=False)) == 0:
del reject['eeg']
if len(mne.fiff.pick_types(raw.info, meg=False, eeg=False, ecg=True)) == 0:
del reject['ecg']
picks_eog = mne.fiff.pick_types(raw.info, meg=True, eeg=True, ecg=True,
exclude=raw.info['bads'] + bads)
if l_freq is None and h_freq is not None:
raw.high_pass_filter(picks, h_freq, filter_length, n_jobs)
if l_freq is not None and h_freq is None:
raw.low_pass_filter(picks, h_freq, filter_length, n_jobs)
if l_freq is not None and h_freq is not None:
raw.band_pass_filter(picks_eog, l_freq, h_freq, filter_length, n_jobs)
epochs_eog = mne.Epochs(raw, eog_events, None, tmin, tmax, baseline=None,
picks=picks_eog, reject=reject, proj=True)
projs_init = raw.info['projs']
if average:
evoked_eog = epochs_eog.average()
projs_eog = mne.compute_proj_evoked(evoked_eog, n_grad=n_grad, n_mag=n_mag,
n_eeg=n_eeg)
else:
print epochs_eog, n_grad, n_mag, n_eeg
projs_eog = mne.compute_proj_epochs(epochs_eog, n_grad=n_grad, n_mag=n_mag,
n_eeg=n_eeg)
print "Writing EOG projections in %s" % eog_proj_fname
mne.write_proj(eog_proj_fname, projs_eog)
return in_fif_fname, eog_proj_fname, out_fif_fname
bad_fname = options.bad_fname
bad_fname = in_path + bad_fname
print bad_fname
if bad_fname is not None:
bads = [w.rstrip().split() for w in open(bad_fname).readlines()]
print 'Bad channels read : %s' % bads
else:
bads = []
print type(tmin)
if tag == 'ecg':
in_fif_fname, ecg_proj_fname, out_fif_fname = compute_proj_ecg(in_path, raw_in, tmin, tmax, n_grad, n_mag, n_eeg, l_freq, h_freq,
average, filter_length, n_jobs, ch_name, reject,
avg_ref, bads, preload, flat)
make_lingua(in_fif_fname)
make_lingua(ecg_proj_fname)
print 'Applying ECG projector'
command = ('mne_process_raw --cd %s --raw %s --proj %s --proj %s '
'--projoff --save %s --filteroff'
% (in_path, in_fif_fname, ecg_proj_fname, in_fif_fname,
out_fif_fname))
st = os.system(command)
if st != 0:
raise ValueError('Problem while running : %s' % command)
else:
print 'Command executed: %s' % command
print 'Done'
print ('Computed ECG Rejection fif file. Saved result as %s' % out_fif_fname)
make_lingua(out_fif_fname)
if len(
sub
) > 3: ##This makes the tabbing pretty for the table; different for longer subject names
beg = '%s\t' % sub
else:
beg = '%s\t\t' % sub
results = '\t\t'.join(
['%i' % (v[sub][code][1]) for code in codes])
subject_lines.append('%s%s' % (beg, results))
#write out dat for each paradigm
f = open(fname, 'w')
f.write(code_line + '\n')
f.write('\n'.join(subject_lines))
f.close()
print("Saved total table to %s" % fname)
make_lingua(fname)
##make combined rejTable
for k, v in all_data.items():
if k == 'BaleenHP':
fname = '/%s/kuperberg/SemPrMM/MEG/results/artifact_rejection/combined_rejection/ssp/%s_%s_remaining_events_ecgeog.txt' % (
pre, subjType, k)
codes = sorted(
v[subjType + '8'].keys(), cmp=lambda x, y: cmp(int(x), int(
y))) ##This is the codes for the events for the paradigm
code_line = '\t\t%s' % '\t\t'.join(
codes) ##This just puts them together to head the table
subject_lines = []
for sub in subjects:
subjLine = []
if sub in v: