def setup_logging(script_name):
"""Save mne-python log to a file in logs folder"""
log_basename = Path(script_name).stem
log_fname = log_basename + ".log"
log_savepath = (paths.dirs.logs) / log_fname
logger = getLogger(log_basename)
logger.setLevel(logging.INFO)
if not logger.hasHandlers():
stderr_handler = StreamHandler()
file_handler = FileHandler(log_savepath)
stderr_handler.setLevel(logging.WARNING)
file_handler.setLevel(logging.INFO)
fmt = Formatter("%(asctime)s - %(name)s - %(levelname)s - %(message)s")
stderr_handler.setFormatter(fmt)
file_handler.setFormatter(fmt)
logger.addHandler(stderr_handler)
logger.addHandler(file_handler)
write_log_header(log_savepath)
set_log_file(log_savepath, overwrite=False)
return logger
def test_cuda():
"""Test CUDA-based filtering
"""
Fs = 500
sig_len_secs = 20
a = np.random.randn(sig_len_secs * Fs)
set_log_file(log_file, overwrite=True)
for fl in [None, 2048]:
bp = band_pass_filter(a, Fs, 4, 8, n_jobs=1, filter_length=fl)
bs = band_stop_filter(a, Fs, 4 - 0.5, 8 + 0.5, n_jobs=1,
filter_length=fl)
lp = low_pass_filter(a, Fs, 8, n_jobs=1, filter_length=fl)
hp = high_pass_filter(lp, Fs, 4, n_jobs=1, filter_length=fl)
bp_c = band_pass_filter(a, Fs, 4, 8, n_jobs='cuda', filter_length=fl,
verbose='INFO')
bs_c = band_stop_filter(a, Fs, 4 - 0.5, 8 + 0.5, n_jobs='cuda',
filter_length=fl, verbose='INFO')
lp_c = low_pass_filter(a, Fs, 8, n_jobs='cuda', filter_length=fl,
verbose='INFO')
hp_c = high_pass_filter(lp, Fs, 4, n_jobs='cuda', filter_length=fl,
verbose='INFO')
assert_array_almost_equal(bp, bp_c, 12)
assert_array_almost_equal(bs, bs_c, 12)
assert_array_almost_equal(lp, lp_c, 12)
assert_array_almost_equal(hp, hp_c, 12)
# check to make sure we actually used CUDA
set_log_file()
out = open(log_file).readlines()
assert_true(sum(['Using CUDA for FFT FIR filtering' in o
for o in out]) == 8)
def test_cuda():
"""Test CUDA-based filtering
"""
# NOTE: don't make test_cuda() the last test, or pycuda might spew
# some warnings about clean-up failing
# Also, using `n_jobs='cuda'` on a non-CUDA system should be fine,
# as it should fall back to using n_jobs=1.
tempdir = _TempDir()
log_file = op.join(tempdir, 'temp_log.txt')
sfreq = 500
sig_len_secs = 20
a = np.random.randn(sig_len_secs * sfreq)
set_log_file(log_file, overwrite=True)
for fl in ['10s', None, 2048]:
bp = band_pass_filter(a, sfreq, 4, 8, n_jobs=1, filter_length=fl)
bs = band_stop_filter(a, sfreq, 4 - 0.5, 8 + 0.5, n_jobs=1,
filter_length=fl)
lp = low_pass_filter(a, sfreq, 8, n_jobs=1, filter_length=fl)
hp = high_pass_filter(lp, sfreq, 4, n_jobs=1, filter_length=fl)
bp_c = band_pass_filter(a, sfreq, 4, 8, n_jobs='cuda',
filter_length=fl, verbose='INFO')
bs_c = band_stop_filter(a, sfreq, 4 - 0.5, 8 + 0.5, n_jobs='cuda',
filter_length=fl, verbose='INFO')
lp_c = low_pass_filter(a, sfreq, 8, n_jobs='cuda', filter_length=fl,
verbose='INFO')
hp_c = high_pass_filter(lp, sfreq, 4, n_jobs='cuda', filter_length=fl,
verbose='INFO')
assert_array_almost_equal(bp, bp_c, 12)
assert_array_almost_equal(bs, bs_c, 12)
assert_array_almost_equal(lp, lp_c, 12)
assert_array_almost_equal(hp, hp_c, 12)
# check to make sure we actually used CUDA
set_log_file()
with open(log_file) as fid:
out = fid.readlines()
# triage based on whether or not we actually expected to use CUDA
from mne.cuda import _cuda_capable # allow above funs to set it
tot = 12 if _cuda_capable else 0
assert_true(sum(['Using CUDA for FFT FIR filtering' in o
for o in out]) == tot)
# check resampling
a = np.random.RandomState(0).randn(3, sig_len_secs * sfreq)
a1 = resample(a, 1, 2, n_jobs=2, npad=0)
a2 = resample(a, 1, 2, n_jobs='cuda', npad=0)
a3 = resample(a, 2, 1, n_jobs=2, npad=0)
a4 = resample(a, 2, 1, n_jobs='cuda', npad=0)
assert_array_almost_equal(a3, a4, 14)
assert_array_almost_equal(a1, a2, 14)
assert_array_equal(resample([0, 0], 2, 1, n_jobs='cuda'), [0., 0., 0., 0.])
assert_array_equal(resample(np.zeros(2, np.float32), 2, 1, n_jobs='cuda'),
[0., 0., 0., 0.])
def test_cuda():
"""Test CUDA-based filtering
"""
# NOTE: don't make test_cuda() the last test, or pycuda might spew
# some warnings about clean-up failing
# Also, using `n_jobs='cuda'` on a non-CUDA system should be fine,
# as it should fall back to using n_jobs=1.
tempdir = _TempDir()
log_file = op.join(tempdir, 'temp_log.txt')
sfreq = 500
sig_len_secs = 20
a = np.random.randn(sig_len_secs * sfreq)
set_log_file(log_file, overwrite=True)
for fl in ['10s', None, 2048]:
bp = band_pass_filter(a, sfreq, 4, 8, n_jobs=1, filter_length=fl)
bs = band_stop_filter(a, sfreq, 4 - 0.5, 8 + 0.5, n_jobs=1,
filter_length=fl)
lp = low_pass_filter(a, sfreq, 8, n_jobs=1, filter_length=fl)
hp = high_pass_filter(lp, sfreq, 4, n_jobs=1, filter_length=fl)
bp_c = band_pass_filter(a, sfreq, 4, 8, n_jobs='cuda',
filter_length=fl, verbose='INFO')
bs_c = band_stop_filter(a, sfreq, 4 - 0.5, 8 + 0.5, n_jobs='cuda',
filter_length=fl, verbose='INFO')
lp_c = low_pass_filter(a, sfreq, 8, n_jobs='cuda', filter_length=fl,
verbose='INFO')
hp_c = high_pass_filter(lp, sfreq, 4, n_jobs='cuda', filter_length=fl,
verbose='INFO')
assert_array_almost_equal(bp, bp_c, 12)
assert_array_almost_equal(bs, bs_c, 12)
assert_array_almost_equal(lp, lp_c, 12)
assert_array_almost_equal(hp, hp_c, 12)
# check to make sure we actually used CUDA
set_log_file()
with open(log_file) as fid:
out = fid.readlines()
# triage based on whether or not we actually expected to use CUDA
tot = 12 if cuda_capable else 0
assert_true(sum(['Using CUDA for FFT FIR filtering' in o
for o in out]) == tot)
# check resampling
a = np.random.RandomState(0).randn(3, sig_len_secs * sfreq)
a1 = resample(a, 1, 2, n_jobs=2, npad=0)
a2 = resample(a, 1, 2, n_jobs='cuda', npad=0)
a3 = resample(a, 2, 1, n_jobs=2, npad=0)
a4 = resample(a, 2, 1, n_jobs='cuda', npad=0)
assert_array_almost_equal(a3, a4, 14)
assert_array_almost_equal(a1, a2, 14)
def __init__(self,
db: str,
path: str,
include_extensions: List[str] = ['edf'],
exclude_events: List[str] = None) -> None:
logging.debug('Create index at %s', db)
logging.debug('Load index at %s', db)
engine = create_engine(db)
BaseTable.metadata.create_all(engine)
self.db = sessionmaker(bind=engine)()
self.path = path
self.include_extensions = include_extensions
self.exclude_events = exclude_events
logging.debug('Redirect MNE logging interface to file')
set_log_file(join(path, 'mne.log'), overwrite=False)
def test_notch_filters():
"""Test notch filters
"""
tempdir = _TempDir()
log_file = op.join(tempdir, 'temp_log.txt')
# let's use an ugly, prime sfreq for fun
sfreq = 487.0
sig_len_secs = 20
t = np.arange(0, int(sig_len_secs * sfreq)) / sfreq
freqs = np.arange(60, 241, 60)
# make a "signal"
rng = np.random.RandomState(0)
a = rng.randn(int(sig_len_secs * sfreq))
orig_power = np.sqrt(np.mean(a**2))
# make line noise
a += np.sum([np.sin(2 * np.pi * f * t) for f in freqs], axis=0)
# only allow None line_freqs with 'spectrum_fit' mode
assert_raises(ValueError, notch_filter, a, sfreq, None, 'fft')
assert_raises(ValueError, notch_filter, a, sfreq, None, 'iir')
methods = ['spectrum_fit', 'spectrum_fit', 'fft', 'fft', 'iir']
filter_lengths = [None, None, None, 8192, None]
line_freqs = [None, freqs, freqs, freqs, freqs]
tols = [2, 1, 1, 1]
for meth, lf, fl, tol in zip(methods, line_freqs, filter_lengths, tols):
if lf is None:
set_log_file(log_file, overwrite=True)
b = notch_filter(a,
sfreq,
lf,
filter_length=fl,
method=meth,
verbose='INFO')
if lf is None:
set_log_file()
with open(log_file) as fid:
out = fid.readlines()
if len(out) != 2:
raise ValueError('Detected frequencies not logged properly')
out = np.fromstring(out[1], sep=', ')
assert_array_almost_equal(out, freqs)
new_power = np.sqrt(sum_squared(b) / b.size)
assert_almost_equal(new_power, orig_power, tol)
def test_cuda():
"""Test CUDA-based filtering
"""
# NOTE: don't make test_cuda() the last test, or pycuda might spew
# some warnings about clean-up failing
Fs = 500
sig_len_secs = 20
a = np.random.randn(sig_len_secs * Fs)
set_log_file(log_file, overwrite=True)
for fl in ['10s', None, 2048]:
bp = band_pass_filter(a, Fs, 4, 8, n_jobs=1, filter_length=fl)
bs = band_stop_filter(a, Fs, 4 - 0.5, 8 + 0.5, n_jobs=1,
filter_length=fl)
lp = low_pass_filter(a, Fs, 8, n_jobs=1, filter_length=fl)
hp = high_pass_filter(lp, Fs, 4, n_jobs=1, filter_length=fl)
bp_c = band_pass_filter(a, Fs, 4, 8, n_jobs='cuda', filter_length=fl,
verbose='INFO')
bs_c = band_stop_filter(a, Fs, 4 - 0.5, 8 + 0.5, n_jobs='cuda',
filter_length=fl, verbose='INFO')
lp_c = low_pass_filter(a, Fs, 8, n_jobs='cuda', filter_length=fl,
verbose='INFO')
hp_c = high_pass_filter(lp, Fs, 4, n_jobs='cuda', filter_length=fl,
verbose='INFO')
assert_array_almost_equal(bp, bp_c, 12)
assert_array_almost_equal(bs, bs_c, 12)
assert_array_almost_equal(lp, lp_c, 12)
assert_array_almost_equal(hp, hp_c, 12)
# check to make sure we actually used CUDA
set_log_file()
with open(log_file) as fid:
out = fid.readlines()
assert_true(sum(['Using CUDA for FFT FIR filtering' in o
for o in out]) == 12)
# check resampling
a = np.random.RandomState(0).randn(3, sig_len_secs * Fs)
a1 = resample(a, 1, 2, n_jobs=2, npad=0)
a2 = resample(a, 1, 2, n_jobs='cuda', npad=0)
a3 = resample(a, 2, 1, n_jobs=2, npad=0)
a4 = resample(a, 2, 1, n_jobs='cuda', npad=0)
assert_array_almost_equal(a3, a4, 14)
assert_array_almost_equal(a1, a2, 14)
def test_cuda():
"""Test CUDA-based filtering
"""
# NOTE: don't make test_cuda() the last test, or pycuda might spew
# some warnings about clean-up failing
Fs = 500
sig_len_secs = 20
a = np.random.randn(sig_len_secs * Fs)
set_log_file(log_file, overwrite=True)
for fl in ['10s', None, 2048]:
bp = band_pass_filter(a, Fs, 4, 8, n_jobs=1, filter_length=fl)
bs = band_stop_filter(a, Fs, 4 - 0.5, 8 + 0.5, n_jobs=1,
filter_length=fl)
lp = low_pass_filter(a, Fs, 8, n_jobs=1, filter_length=fl)
hp = high_pass_filter(lp, Fs, 4, n_jobs=1, filter_length=fl)
bp_c = band_pass_filter(a, Fs, 4, 8, n_jobs='cuda', filter_length=fl,
verbose='INFO')
bs_c = band_stop_filter(a, Fs, 4 - 0.5, 8 + 0.5, n_jobs='cuda',
filter_length=fl, verbose='INFO')
lp_c = low_pass_filter(a, Fs, 8, n_jobs='cuda', filter_length=fl,
verbose='INFO')
hp_c = high_pass_filter(lp, Fs, 4, n_jobs='cuda', filter_length=fl,
verbose='INFO')
assert_array_almost_equal(bp, bp_c, 12)
assert_array_almost_equal(bs, bs_c, 12)
assert_array_almost_equal(lp, lp_c, 12)
assert_array_almost_equal(hp, hp_c, 12)
# check to make sure we actually used CUDA
set_log_file()
out = open(log_file).readlines()
assert_true(sum(['Using CUDA for FFT FIR filtering' in o
for o in out]) == 12)
# check resampling
a = np.random.RandomState(0).randn(3, sig_len_secs * Fs)
a1 = resample(a, 1, 2, n_jobs=2, npad=0)
a2 = resample(a, 1, 2, n_jobs='cuda', npad=0)
a3 = resample(a, 2, 1, n_jobs=2, npad=0)
a4 = resample(a, 2, 1, n_jobs='cuda', npad=0)
assert_array_almost_equal(a3, a4, 14)
assert_array_almost_equal(a1, a2, 14)
def test_notch_filters():
"""Test notch filters
"""
tempdir = _TempDir()
log_file = op.join(tempdir, 'temp_log.txt')
# let's use an ugly, prime sfreq for fun
sfreq = 487.0
sig_len_secs = 20
t = np.arange(0, int(sig_len_secs * sfreq)) / sfreq
freqs = np.arange(60, 241, 60)
# make a "signal"
rng = np.random.RandomState(0)
a = rng.randn(int(sig_len_secs * sfreq))
orig_power = np.sqrt(np.mean(a ** 2))
# make line noise
a += np.sum([np.sin(2 * np.pi * f * t) for f in freqs], axis=0)
# only allow None line_freqs with 'spectrum_fit' mode
assert_raises(ValueError, notch_filter, a, sfreq, None, 'fft')
assert_raises(ValueError, notch_filter, a, sfreq, None, 'iir')
methods = ['spectrum_fit', 'spectrum_fit', 'fft', 'fft', 'iir']
filter_lengths = [None, None, None, 8192, None]
line_freqs = [None, freqs, freqs, freqs, freqs]
tols = [2, 1, 1, 1]
for meth, lf, fl, tol in zip(methods, line_freqs, filter_lengths, tols):
if lf is None:
set_log_file(log_file, overwrite=True)
b = notch_filter(a, sfreq, lf, filter_length=fl, method=meth,
verbose='INFO')
if lf is None:
set_log_file()
with open(log_file) as fid:
out = fid.readlines()
if len(out) != 2:
raise ValueError('Detected frequencies not logged properly')
out = np.fromstring(out[1], sep=', ')
assert_array_almost_equal(out, freqs)
new_power = np.sqrt(sum_squared(b) / b.size)
assert_almost_equal(new_power, orig_power, tol)
def test_notch_filters():
"""Test notch filters
"""
# let's use an ugly, prime Fs for fun
Fs = 487.0
sig_len_secs = 20
t = np.arange(0, sig_len_secs * Fs) / Fs
freqs = np.arange(60, 241, 60)
# make a "signal"
rng = np.random.RandomState(0)
a = rng.randn(sig_len_secs * Fs)
orig_power = np.sqrt(np.mean(a ** 2))
# make line noise
a += np.sum([np.sin(2 * np.pi * f * t) for f in freqs], axis=0)
# only allow None line_freqs with 'spectrum_fit' mode
assert_raises(ValueError, notch_filter, a, Fs, None, 'fft')
assert_raises(ValueError, notch_filter, a, Fs, None, 'iir')
methods = ['spectrum_fit', 'spectrum_fit', 'fft', 'fft', 'iir']
filter_lengths = [None, None, None, 8192, None]
line_freqs = [None, freqs, freqs, freqs, freqs]
tols = [2, 1, 1, 1]
for meth, lf, fl, tol in zip(methods, line_freqs, filter_lengths, tols):
if lf is None:
set_log_file(log_file)
b = notch_filter(a, Fs, lf, filter_length=fl, method=meth,
verbose='INFO')
if lf is None:
set_log_file()
out = open(log_file).readlines()
if len(out) != 2:
raise ValueError('Detected frequencies not logged properly')
out = np.fromstring(out[1], sep=', ')
assert_array_almost_equal(out, freqs)
new_power = np.sqrt(np.mean(b ** 2))
assert_almost_equal(new_power, orig_power, tol)
def __init__(self,
path: str,
name: str,
version: str = None,
extensions: List[str] = [".edf"],
exclude_file: List[str] = None,
exclude_channels_set: List[str] = None,
exclude_channels_reference: List[str] = None,
exclude_sampling_frequency: List[str] = None,
minimum_annotation_duration: float = None) -> None:
# Set basic attributes
self.path = os.path.abspath(os.path.join(path, version))
self.name = name
self.version = version
# Set data set filter attributes
self.extensions = extensions if extensions else []
self.exclude_file = exclude_file if exclude_file else []
self.exclude_channels_set = exclude_channels_set if exclude_channels_set else []
self.exclude_channels_reference = exclude_channels_reference if exclude_channels_reference else []
self.exclude_sampling_frequency = exclude_sampling_frequency if exclude_sampling_frequency else []
self.minimum_annotation_duration = minimum_annotation_duration if minimum_annotation_duration else 0
logging.info("Init dataset '%s'@'%s' at '%s'", self.name, self.version,
self.path)
# Make workspace directory
logging.debug("Make .pyeeglab directory")
workspace = os.path.join(self.path, ".pyeeglab")
os.makedirs(workspace, exist_ok=True)
logging.debug("Make .pyeeglab/cache directory")
os.makedirs(os.path.join(workspace, "cache"), exist_ok=True)
logging.debug("Set MNE log .pyeeglab/mne.log")
mne.set_log_file(os.path.join(workspace, "mne.log"), overwrite=False)
# Index data set files
self.index()
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)
logger.setLevel(LOG_LEVEL)
logger.handlers = []
# add file print_handler
msg_format = (
"[%(asctime)s] %(levelname)s [%(name)s.%(funcName)s:%(lineno)d] %(message)s"
)
formatter = logging.Formatter(msg_format)
logname = os.path.join(LOGDIR, "eztrack.log")
file_handler = RotatingFileHandler(logname, maxBytes=200000, backupCount=10)
file_handler.setFormatter(formatter)
logger.addHandler(file_handler)
# set logging level for submodules: mne, mne-bids
mne.set_log_level(LOG_LEVEL)
mne.set_log_file(logname, msg_format, overwrite=False)
# add stream print_handler to stdout
# print_handler = logging.StreamHandler(sys.stdout)
# print_handler.setLevel(logging.DEBUG)
# logger.addHandler(print_handler)
logger.propagate = False
# Help message settings
help_colors = {
"cls": HelpColorsCommand,
"help_headers_color": "yellow",
"help_options_color": "green",
}
import pylab
import matplotlib.pyplot as plt
import mne
import numpy as np
import glob
import os.path
import pandas as pd
import warnings
import logging
mne.set_log_level('Warning')
mne.set_log_file('abraxas_erp.log', overwrite=True)
layout = mne.channels.read_layout("EEG1005.lay")
montage = mne.channels.read_montage(kind="standard_1020")
raw = {}
epochs = {}
evoked = {}
# event trigger and conditions
event_id = {
'iien': 182,
'iiev': 181,
'iaen': 172,
'iaev': 171,
'aien': 162,
'aiev': 161,
'aaen': 152,
'aaev': 151,
'iipn': 142,
'iipv': 141,
'iapn': 132,
from multiprocessing import Pool
import sleep_study as ss
channels = [
'EEG C3-M2',
'EEG O1-M2',
'EEG O2-M1',
'EEG CZ-O1',
'EEG C4-M1',
'EEG F4-M1',
]
out_dir = '~/preprocessed'
out_dir = os.path.expanduser(out_dir)
mne.set_log_file('log.txt')
existing = [x[:-4] for x in os.listdir('preprocessed')]
def preprocess(i):
# Potential problem: the order of channels are not considered
print('Processing %d' % i)
import sleep_study as ss
ss.init()
study = ss.data.study_list[i]
if study in existing:
return
try:
raw = ss.data.load_study(study, verbose=False)
if not all([name in raw.ch_names for name in channels]):
return
from mayavi import mlab # noqa
from surfer import Brain # noqa
import mne
## get analysis parameters from config file
if len(sys.argv) > 1:
print sys.argv[1]
module_name = sys.argv[1]
else:
module_name = 'WH_config'
C = importlib.import_module(module_name)
reload(C)
mne.set_log_file(fname=C.bem_log_file, overwrite=False)
# plt.ion() # interactive plotting
# subject numbers
subjs = C.subjs
###
n_sbs = len(subjs)
# for qsub
if len(sys.argv) > 2: # if in parallel mode
print "Running subject(s) {0} now in PARALLEL mode".format(sys.argv)
ss_idx = map(int, sys.argv[2:])
subjs_new = []
def test_logging():
"""Test logging (to file)
"""
old_log_file = open(fname_log, 'r')
old_lines = clean_lines(old_log_file.readlines())
old_log_file.close()
old_log_file_2 = open(fname_log_2, 'r')
old_lines_2 = clean_lines(old_log_file_2.readlines())
old_log_file_2.close()
if op.isfile(test_name):
os.remove(test_name)
# test it one way (printing default off)
set_log_file(test_name)
set_log_level('WARNING')
# should NOT print
evoked = Evoked(fname_evoked, setno=1)
assert_true(open(test_name).readlines() == [])
# should NOT print
evoked = Evoked(fname_evoked, setno=1, verbose=False)
assert_true(open(test_name).readlines() == [])
# should NOT print
evoked = Evoked(fname_evoked, setno=1, verbose='WARNING')
assert_true(open(test_name).readlines() == [])
# SHOULD print
evoked = Evoked(fname_evoked, setno=1, verbose=True)
new_log_file = open(test_name, 'r')
new_lines = clean_lines(new_log_file.readlines())
assert_equal(new_lines, old_lines)
# now go the other way (printing default on)
os.remove(test_name)
set_log_file(test_name)
set_log_level('INFO')
# should NOT print
evoked = Evoked(fname_evoked, setno=1, verbose='WARNING')
assert_true(open(test_name).readlines() == [])
# should NOT print
evoked = Evoked(fname_evoked, setno=1, verbose=False)
assert_true(open(test_name).readlines() == [])
# SHOULD print
evoked = Evoked(fname_evoked, setno=1)
new_log_file = open(test_name, 'r')
old_log_file = open(fname_log, 'r')
new_lines = clean_lines(new_log_file.readlines())
assert_equal(new_lines, old_lines)
# check to make sure appending works (and as default, raises a warning)
with warnings.catch_warnings(True) as w:
set_log_file(test_name, overwrite=False)
assert len(w) == 0
set_log_file(test_name)
assert len(w) == 1
evoked = Evoked(fname_evoked, setno=1)
new_log_file = open(test_name, 'r')
new_lines = clean_lines(new_log_file.readlines())
assert_equal(new_lines, old_lines_2)
# make sure overwriting works
set_log_file(test_name, overwrite=True)
# this line needs to be called to actually do some logging
evoked = Evoked(fname_evoked, setno=1)
new_log_file = open(test_name, 'r')
new_lines = clean_lines(new_log_file.readlines())
assert_equal(new_lines, old_lines)
###Get Subject and run-specific parameters
print evRun
data_path = '/cluster/kuperberg/SemPrMM/MEG/data/'+args.subj+'/'
event_fname = data_path + 'eve/' + args.subj + '_' + expName+evRun + evSuffix
#event_fname = data_path + args.subj + '_' + expName+evRun + evSuffix
print event_fname
raw_fname = data_path + args.subj+'_'+ expName +evRun+'_ssp_raw.fif' ##Using ssp because for only for ya12, ya27, ya31 AXCPT- ecg SSP has been perfrmed, rest have been sym-linked to the raw file.
avg_log_fname = data_path + 'ave_projon/logs/' +args.subj+ '_'+expName + evRun +'-equaliseTar-test-ave.log' ##CHANGE THIS
###Setup for reading the original raw data and events
raw = fiff.Raw(raw_fname, preload=True)
events = mne.read_events(event_fname)
raw_skip = raw.first_samp
mne.set_log_file(fname = avg_log_fname, overwrite = True)
###Correct events for the fact that ssp data has the skip removed
if (args.subj == "ya12") or (args.subj == 'ya27') or (args.subj == 'ya31'):
print "Adjusting events for SSP raw.fif files"
for row in events:
row[0] = row[0]-raw_skip
###Filter raw data
fiff.Raw.filter(raw,l_freq=hp_cutoff,h_freq=lp_cutoff)
###Pick all channels, including stimulus triggers
picks = []
for i in range(raw.info['nchan']):
picks.append(i)
from PyQt5.QtCore import QTimer
from cognigraph.pipeline import Pipeline
from cognigraph.nodes import sources, processors, outputs
from cognigraph.gui.window import GUIWindow
from cognigraph.gui.async_pipeline_update import AsyncUpdater
from cognigraph.gui.forward_dialog import FwdSetupDialog
np.warnings.filterwarnings('ignore') # noqa
# ----------------------------- setup logging ----------------------------- #
logfile = None
format = '%(asctime)s:%(name)-17s:%(levelname)s:%(message)s'
logging.basicConfig(level=logging.INFO, filename=logfile, format=format)
logger = logging.getLogger(__name__)
mne.set_log_level('ERROR')
mne.set_log_file(fname=logfile, output_format=format)
# -------------------------------------------------------------------------- #
# ----------------------------- setup argparse ----------------------------- #
parser = argparse.ArgumentParser()
parser.add_argument('-d',
'--data',
type=argparse.FileType('r'),
help='data path')
parser.add_argument('-f',
'--forward',
type=argparse.FileType('r'),
help='forward model path')
args = parser.parse_args()
# -------------------------------------------------------------------------- #
import scipy.io as sio
import numpy as np
import pandas as pd
import mne
import random
mne.set_log_file('./mne_output', overwrite=True)
srate = 1024
factor = 1. / 1000000.
interval = 5
start_time = 0
n_pnts = 1024
n_channels = 28
data_standardization = True
raw_plot = False
l_freq, h_freq = 5., 30.
channels = [
'C5', 'C3', 'C1', 'C2', 'C4', 'C6', 'CP5', 'CP3', 'CP1', 'CP2', 'CP4',
'CP6', 'P7', 'P5', 'P3', 'P1', 'P2', 'P4', 'P6', 'P8', 'F7', 'F5', 'F3',
'F1', 'F2', 'F4', 'F6', 'F8'
]
lab_index = 3
subjects = [
'ckm', 'clx', 'csb', 'fy', 'lw', 'ly', 'phl', 'szl', 'xwt', 'yfw', 'zjh'
]
subjects_num = 11
# subject = [1]
ch_names = [
'Fp1', 'Fpz', 'Fp2', 'F7', 'F3', 'Fz', 'F4', 'F8', 'FC5', 'FC1', 'FC2',
'FC6', 'M1', 'T7', 'C3', 'Cz', 'C4', 'T8', 'M2', 'CP5', 'CP1', 'CP2',
print avg_log_fname
###Setup for reading the original raw data and events#######
raw = fiff.Raw(raw_fname, preload=True)
events = mne.read_events(event_fname)
raw_skip = raw.first_samp
###Correct events for the fact that ssp data has the skip removed
if (args.subj == "ya12") or (args.subj == 'ya27') or (
args.subj == 'ya31'
): #############################Change back 0-- testing with ssp for all subjects CU 12/26/13
print "Adjusting events for SSP raw.fif files"
for row in events:
row[0] = row[0] - raw_skip
mne.set_log_file(fname=avg_log_fname, overwrite=True)
###Filter SSP raw data#######
fiff.Raw.filter(raw, l_freq=hp_cutoff, h_freq=lp_cutoff)
###Pick all channels, including stimulus triggers#######
picks = []
for i in range(raw.info['nchan']):
picks.append(i)
###Read Prime Epochs#######
###Include catch for subjects where ssp-ecg was performed###
epochsAPrime = mne.Epochs(raw,
events,
event_id['APrime'],
tmin,
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)
print event_id
tmin, tmax = -0.2, 0.5
#runs = cc.runDict['Word']
runs = ['emptyroom'] #, 'run1', 'run2'] ###For other runs use the baseline and set tmin/tmax using epoched data.
#print runs
covRuns = []
for runID in runs:
print runID
data_path = '/home/custine/MEG/data/krns_kr3/' +subjID+'/'+sessID
fname = data_path +'/'+ subjID + '_'+ sessID +'_'+runID +'_raw.fif'
print fname
cname = data_path +'/cov/'+ subjID + '_'+ sessID +'_' + runID + '-cov.fif'
covLog_file = data_path + '/logs/' +subjID + '_' + sessID+ '_'+runID + '_cov.log'
event_file = data_path + '/eve/triggers/' + subjID + '_'+ sessID +'_'+runID +'_' + eve_file
mne.set_log_file(fname = covLog_file, overwrite = True)
print covLog_file
print 'Reading Raw data... '
raw = io.Raw(fname)
if runID == "emptyroom":
tmin = 0
tmax = 2
cov = mne.compute_raw_data_covariance(raw, tmin = tmin, tmax = tmax) #, tmin = None, tmax = 0) #, reject = None, picks = picks)
print cov
else:
events = mne.read_events(event_file)
include = [] # or stim channels ['STI 014']
# #raw.info['bads'] += ['EEG 053'] # bads + 1 more
# # pick EEG channels
picks = mne.pick_types(raw.info, meg=True, eeg=False, stim=False, eog=True, include=include, exclude='bads')
logger = logging.getLogger()
logger.addHandler(logging.StreamHandler())
import mne
## get analysis parameters from config file
if len(sys.argv) > 1:
print sys.argv[1]
module_name = sys.argv[1]
else:
module_name = 'WH_config'
C = importlib.import_module(module_name)
reload(C)
mne.set_log_file(fname=C.bem_log_file, overwrite=True)
# plt.ion() # interactive plotting
# subject numbers
subjs = C.subjs
###
n_sbs = len(subjs)
# for qsub
if len(sys.argv) > 2: # if in parallel mode
print "Running subject(s) {0} now in PARALLEL mode".format(sys.argv)
ss_idx = map(int, sys.argv[2:])
subjs_new = []
