def test_io_complex():
"""Test IO with complex data types
"""
dtypes = [np.complex64, np.complex128]
raw = Raw(fif_fname, preload=True)
picks = np.arange(5)
start, stop = raw.time_as_index([0, 5])
data_orig, _ = raw[picks, start:stop]
for di, dtype in enumerate(dtypes):
imag_rand = np.array(1j * np.random.randn(data_orig.shape[0],
data_orig.shape[1]), dtype)
raw_cp = raw.copy()
raw_cp._data = np.array(raw_cp._data, dtype)
raw_cp._data[picks, start:stop] += imag_rand
# this should throw an error because it's complex
with warnings.catch_warnings(record=True) as w:
raw_cp.save(op.join(tempdir, 'raw.fif'), picks, tmin=0, tmax=5)
# warning only gets thrown on first instance
assert_equal(len(w), 1 if di == 0 else 0)
raw2 = Raw(op.join(tempdir, 'raw.fif'))
raw2_data, _ = raw2[picks, :]
n_samp = raw2_data.shape[1]
assert_array_almost_equal(raw2_data[:, :n_samp],
raw_cp._data[picks, :n_samp])
# with preloading
raw2 = Raw(op.join(tempdir, 'raw.fif'), preload=True)
raw2_data, _ = raw2[picks, :]
n_samp = raw2_data.shape[1]
assert_array_almost_equal(raw2_data[:, :n_samp],
raw_cp._data[picks, :n_samp])
def test_io_raw():
"""Test IO for raw data (Neuromag + CTF + gz)
"""
fnames_in = [fif_fname, fif_gz_fname, ctf_fname]
fnames_out = ["raw.fif", "raw.fif.gz", "raw.fif"]
for fname_in, fname_out in zip(fnames_in, fnames_out):
raw = Raw(fname_in)
nchan = raw.info["nchan"]
ch_names = raw.info["ch_names"]
meg_channels_idx = [k for k in range(nchan) if ch_names[k][0] == "M"]
n_channels = 100
meg_channels_idx = meg_channels_idx[:n_channels]
start, stop = raw.time_as_index([0, 5])
data, times = raw[meg_channels_idx, start : (stop + 1)]
meg_ch_names = [ch_names[k] for k in meg_channels_idx]
# Set up pick list: MEG + STI 014 - bad channels
include = ["STI 014"]
include += meg_ch_names
picks = pick_types(
raw.info, meg=True, eeg=False, stim=True, misc=True, include=include, exclude=raw.info["bads"]
)
print "Number of picked channels : %d" % len(picks)
# Writing with drop_small_buffer True
raw.save(fname_out, picks, tmin=0, tmax=4, buffer_size_sec=3, drop_small_buffer=True)
raw2 = Raw(fname_out, preload=True)
sel = pick_channels(raw2.ch_names, meg_ch_names)
data2, times2 = raw2[sel, :]
assert_true(times2.max() <= 3)
# Writing
raw.save(fname_out, picks, tmin=0, tmax=5)
if fname_in == fif_fname or fname_in == fif_fname + ".gz":
assert_true(len(raw.info["dig"]) == 146)
raw2 = Raw(fname_out)
sel = pick_channels(raw2.ch_names, meg_ch_names)
data2, times2 = raw2[sel, :]
assert_array_almost_equal(data, data2)
assert_array_almost_equal(times, times2)
assert_array_almost_equal(raw.info["dev_head_t"]["trans"], raw2.info["dev_head_t"]["trans"])
assert_array_almost_equal(raw.info["sfreq"], raw2.info["sfreq"])
if fname_in == fif_fname or fname_in == fif_fname + ".gz":
assert_array_almost_equal(raw.info["dig"][0]["r"], raw2.info["dig"][0]["r"])
def test_io_complex():
"""Test IO with complex data types
"""
dtypes = [np.complex64, np.complex128]
raw = Raw(fif_fname, preload=True)
picks = np.arange(5)
start, stop = raw.time_as_index([0, 5])
data_orig, _ = raw[picks, start:stop]
for di, dtype in enumerate(dtypes):
imag_rand = np.array(
1j * np.random.randn(data_orig.shape[0], data_orig.shape[1]),
dtype)
raw_cp = raw.copy()
raw_cp._data = np.array(raw_cp._data, dtype)
raw_cp._data[picks, start:stop] += imag_rand
# this should throw an error because it's complex
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
raw_cp.save(op.join(tempdir, 'raw.fif'),
picks,
tmin=0,
tmax=5,
overwrite=True)
# warning gets thrown on every instance b/c simplifilter('always')
assert_equal(len(w), 1)
raw2 = Raw(op.join(tempdir, 'raw.fif'))
raw2_data, _ = raw2[picks, :]
n_samp = raw2_data.shape[1]
assert_allclose(raw2_data[:, :n_samp], raw_cp._data[picks, :n_samp])
# with preloading
raw2 = Raw(op.join(tempdir, 'raw.fif'), preload=True)
raw2_data, _ = raw2[picks, :]
n_samp = raw2_data.shape[1]
assert_allclose(raw2_data[:, :n_samp], raw_cp._data[picks, :n_samp])
def test_io_complex():
"""Test IO with complex data types
"""
dtypes = [np.complex64, np.complex128]
raw = Raw(fif_fname, preload=True)
picks = np.arange(5)
start, stop = raw.time_as_index([0, 5])
data_orig, _ = raw[picks, start:stop]
for di, dtype in enumerate(dtypes):
imag_rand = np.array(
1j * np.random.randn(data_orig.shape[0], data_orig.shape[1]),
dtype)
raw_cp = deepcopy(raw)
raw_cp._data = np.array(raw_cp._data, dtype)
raw_cp._data[picks, start:stop] += imag_rand
# this should throw an error because it's complex
with warnings.catch_warnings(record=True) as w:
raw_cp.save('raw.fif', picks, tmin=0, tmax=5)
# warning only gets thrown on first instance
assert_equal(len(w), 1 if di == 0 else 0)
raw2 = Raw('raw.fif')
raw2_data, _ = raw2[picks, :]
n_samp = raw2_data.shape[1]
assert_array_almost_equal(raw2_data[:, :n_samp],
raw_cp._data[picks, :n_samp])
# with preloading
raw2 = Raw('raw.fif', preload=True)
raw2_data, _ = raw2[picks, :]
n_samp = raw2_data.shape[1]
assert_array_almost_equal(raw2_data[:, :n_samp],
raw_cp._data[picks, :n_samp])
def test_raw_index_as_time():
""" Test index as time conversion"""
raw = Raw(fif_fname, preload=True)
t0 = raw.index_as_time([0], True)[0]
t1 = raw.index_as_time([100], False)[0]
t2 = raw.index_as_time([100], True)[0]
assert_true((t2 - t1) == t0)
# ensure we can go back and forth
t3 = raw.index_as_time(raw.time_as_index([0], True), True)
assert_array_almost_equal(t3, [0.0], 2)
t3 = raw.index_as_time(raw.time_as_index(raw.info['sfreq'], True), True)
assert_array_almost_equal(t3, [raw.info['sfreq']], 2)
t3 = raw.index_as_time(raw.time_as_index(raw.info['sfreq'], False), False)
assert_array_almost_equal(t3, [raw.info['sfreq']], 2)
i0 = raw.time_as_index(raw.index_as_time([0], True), True)
assert_true(i0[0] == 0)
i1 = raw.time_as_index(raw.index_as_time([100], True), True)
assert_true(i1[0] == 100)
# Have to add small amount of time because we truncate via int casting
i1 = raw.time_as_index(raw.index_as_time([100.0001], False), False)
assert_true(i1[0] == 100)
def test_raw_index_as_time():
""" Test index as time conversion"""
raw = Raw(fif_fname, preload=True)
t0 = raw.index_as_time([0], True)[0]
t1 = raw.index_as_time([100], False)[0]
t2 = raw.index_as_time([100], True)[0]
assert_true((t2 - t1) == t0)
# ensure we can go back and forth
t3 = raw.index_as_time(raw.time_as_index([0], True), True)
assert_array_almost_equal(t3, [0.0], 2)
t3 = raw.index_as_time(raw.time_as_index(raw.info['sfreq'], True), True)
assert_array_almost_equal(t3, [raw.info['sfreq']], 2)
t3 = raw.index_as_time(raw.time_as_index(raw.info['sfreq'], False), False)
assert_array_almost_equal(t3, [raw.info['sfreq']], 2)
i0 = raw.time_as_index(raw.index_as_time([0], True), True)
assert_true(i0[0] == 0)
i1 = raw.time_as_index(raw.index_as_time([100], True), True)
assert_true(i1[0] == 100)
# Have to add small amount of time because we truncate via int casting
i1 = raw.time_as_index(raw.index_as_time([100.0001], False), False)
assert_true(i1[0] == 100)
def test_io_raw():
"""Test IO for raw data (Neuromag + CTF + gz)
"""
# Let's construct a simple test for IO first
raw = Raw(fif_fname, preload=True)
raw.crop(0, 3.5)
# put in some data that we know the values of
data = np.random.randn(raw._data.shape[0], raw._data.shape[1])
raw._data[:, :] = data
# save it somewhere
fname = op.join(tempdir, 'test_copy_raw.fif')
raw.save(fname, buffer_size_sec=1.0)
# read it in, make sure the whole thing matches
raw = Raw(fname)
assert_true(np.allclose(data, raw[:, :][0], 1e-6, 1e-20))
# let's read portions across the 1-sec tag boundary, too
inds = raw.time_as_index([1.75, 2.25])
sl = slice(inds[0], inds[1])
assert_true(np.allclose(data[:, sl], raw[:, sl][0], 1e-6, 1e-20))
# now let's do some real I/O
fnames_in = [fif_fname, fif_gz_fname, ctf_fname]
fnames_out = ['raw.fif', 'raw.fif.gz', 'raw.fif']
for fname_in, fname_out in zip(fnames_in, fnames_out):
fname_out = op.join(tempdir, fname_out)
raw = Raw(fname_in)
nchan = raw.info['nchan']
ch_names = raw.info['ch_names']
meg_channels_idx = [k for k in range(nchan)
if ch_names[k][0] == 'M']
n_channels = 100
meg_channels_idx = meg_channels_idx[:n_channels]
start, stop = raw.time_as_index([0, 5])
data, times = raw[meg_channels_idx, start:(stop + 1)]
meg_ch_names = [ch_names[k] for k in meg_channels_idx]
# Set up pick list: MEG + STI 014 - bad channels
include = ['STI 014']
include += meg_ch_names
picks = pick_types(raw.info, meg=True, eeg=False, stim=True,
misc=True, ref_meg=True, include=include,
exclude='bads')
# Writing with drop_small_buffer True
raw.save(fname_out, picks, tmin=0, tmax=4, buffer_size_sec=3,
drop_small_buffer=True, overwrite=True)
raw2 = Raw(fname_out, preload=True)
sel = pick_channels(raw2.ch_names, meg_ch_names)
data2, times2 = raw2[sel, :]
assert_true(times2.max() <= 3)
# Writing
raw.save(fname_out, picks, tmin=0, tmax=5, overwrite=True)
if fname_in == fif_fname or fname_in == fif_fname + '.gz':
assert_true(len(raw.info['dig']) == 146)
raw2 = Raw(fname_out)
sel = pick_channels(raw2.ch_names, meg_ch_names)
data2, times2 = raw2[sel, :]
assert_true(np.allclose(data, data2, 1e-6, 1e-20))
assert_allclose(times, times2)
assert_allclose(raw.info['sfreq'], raw2.info['sfreq'], rtol=1e-5)
# check transformations
for trans in ['dev_head_t', 'dev_ctf_t', 'ctf_head_t']:
if raw.info[trans] is None:
assert_true(raw2.info[trans] is None)
else:
assert_array_equal(raw.info[trans]['trans'],
raw2.info[trans]['trans'])
# check transformation 'from' and 'to'
if trans.startswith('dev'):
from_id = FIFF.FIFFV_COORD_DEVICE
else:
from_id = FIFF.FIFFV_MNE_COORD_CTF_HEAD
if trans[4:8] == 'head':
to_id = FIFF.FIFFV_COORD_HEAD
else:
to_id = FIFF.FIFFV_MNE_COORD_CTF_HEAD
for raw_ in [raw, raw2]:
assert_true(raw_.info[trans]['from'] == from_id)
assert_true(raw_.info[trans]['to'] == to_id)
if fname_in == fif_fname or fname_in == fif_fname + '.gz':
assert_allclose(raw.info['dig'][0]['r'], raw2.info['dig'][0]['r'])
raw_fname = data_path + '/MEG/sample/sample_audvis_filt-0-40_raw.fif'
###############################################################################
# get raw data
raw = Raw(raw_fname)
# set picks
picks = mne.fiff.pick_types(raw.info,
meg=True,
eeg=False,
eog=False,
stim=False,
exclude='bads')
# pick times relative to the onset of the MEG measurement.
start, stop = raw.time_as_index([100, 115], use_first_samp=False)
# export to nitime using a copy of the data
raw_ts = raw.to_nitime(start=start, stop=stop, picks=picks, copy=True)
###############################################################################
# explore some nitime timeseries features
# get start
print raw_ts.t0
# get duration
print raw_ts.duration
# get sample duration (sampling interval)
print raw_ts.sampling_interval
# plot spatial sensitivities of EOG and ECG ICA components
title = 'Spatial patterns of ICA components for ECG+EOG (Magnetometers)'
source_idx = range(15)
ica.plot_topomap([ecg_source_idx, eog_source_idx], ch_type='mag')
plt.suptitle(title, fontsize=12)
###############################################################################
# Show MEG data before and after ICA cleaning.
# We now add the eog artifacts to the ica.exclusion list
ica.exclude += [eog_source_idx]
# Restore sensor space data
raw_ica = ica.pick_sources_raw(raw, include=None)
start_compare, stop_compare = raw.time_as_index([100, 106])
data, times = raw[picks, start_compare:stop_compare]
data_clean, _ = raw_ica[picks, start_compare:stop_compare]
plt.figure()
plt.plot(times, data.T)
plt.xlabel('time (s)')
plt.xlim(100, 106)
plt.ylabel('Raw MEG data (T)')
y0, y1 = plt.ylim()
plt.figure()
plt.plot(times, data_clean.T)
plt.xlabel('time (s)')
plt.xlim(100, 106)
data_path = sample.data_path('..')
fname_inv = data_path + '/MEG/sample/sample_audvis-meg-oct-6-meg-inv.fif'
fname_raw = data_path + '/MEG/sample/sample_audvis_raw.fif'
label_name = 'Aud-lh'
fname_label = data_path + '/MEG/sample/labels/%s.label' % label_name
snr = 1.0 # use smaller SNR for raw data
lambda2 = 1.0 / snr ** 2
method = "sLORETA" # use sLORETA method (could also be MNE or dSPM)
# Load data
raw = Raw(fname_raw)
inverse_operator = read_inverse_operator(fname_inv)
label = mne.read_label(fname_label)
start, stop = raw.time_as_index([0, 15]) # read the first 15s of data
# Compute inverse solution
stc = apply_inverse_raw(raw, inverse_operator, lambda2, method, label,
start, stop, pick_normal=False)
# Save result in stc files
stc.save('mne_%s_raw_inverse_%s' % (method, label_name))
###############################################################################
# View activation time-series
pl.plot(1e3 * stc.times, stc.data[::100, :].T)
pl.xlabel('time (ms)')
pl.ylabel('%s value' % method)
pl.show()
def test_raw_time_as_index():
""" Test time as index conversion"""
raw = Raw(fif_fname, preload=True)
first_samp = raw.time_as_index([0], True)[0]
assert_true(raw.first_samp == -first_samp)
# explained variance. Also we decide to use 64 PCA components before mixing
# back to sensor space. These include the PCA components supplied to ICA plus
# additional PCA components up to rank 64 of the MEG data.
# This allows to control the trade-off between denoising and preserving signal.
ica = ICA(n_components=0.90,
n_pca_components=64,
max_pca_components=100,
noise_cov=None,
random_state=0)
print ica
# 1 minute exposure should be sufficient for artifact detection.
# However, rejection performance may significantly improve when using
# the entire data range
start, stop = raw.time_as_index([100, 160])
# decompose sources for raw data
ica.decompose_raw(raw, start=start, stop=stop, picks=picks)
print ica
sources = ica.get_sources_raw(raw, start=start, stop=stop)
# setup reasonable time window for inspection
start_plot, stop_plot = raw.time_as_index([100, 103])
# plot components
ica.plot_sources_raw(raw, start=start_plot, stop=stop_plot)
###############################################################################
# Automatically find the ECG component using correlation with ECG signal.
def test_io_raw():
"""Test IO for raw data (Neuromag + CTF + gz)
"""
fnames_in = [fif_fname, fif_gz_fname, ctf_fname]
fnames_out = ['raw.fif', 'raw.fif.gz', 'raw.fif']
for fname_in, fname_out in zip(fnames_in, fnames_out):
fname_out = op.join(tempdir, fname_out)
raw = Raw(fname_in)
nchan = raw.info['nchan']
ch_names = raw.info['ch_names']
meg_channels_idx = [k for k in range(nchan)
if ch_names[k][0] == 'M']
n_channels = 100
meg_channels_idx = meg_channels_idx[:n_channels]
start, stop = raw.time_as_index([0, 5])
data, times = raw[meg_channels_idx, start:(stop + 1)]
meg_ch_names = [ch_names[k] for k in meg_channels_idx]
# Set up pick list: MEG + STI 014 - bad channels
include = ['STI 014']
include += meg_ch_names
picks = pick_types(raw.info, meg=True, eeg=False, stim=True,
misc=True, include=include, exclude='bads')
# Writing with drop_small_buffer True
raw.save(fname_out, picks, tmin=0, tmax=4, buffer_size_sec=3,
drop_small_buffer=True)
raw2 = Raw(fname_out, preload=True)
sel = pick_channels(raw2.ch_names, meg_ch_names)
data2, times2 = raw2[sel, :]
assert_true(times2.max() <= 3)
# Writing
raw.save(fname_out, picks, tmin=0, tmax=5)
if fname_in == fif_fname or fname_in == fif_fname + '.gz':
assert_true(len(raw.info['dig']) == 146)
raw2 = Raw(fname_out)
sel = pick_channels(raw2.ch_names, meg_ch_names)
data2, times2 = raw2[sel, :]
assert_array_almost_equal(data, data2)
assert_array_almost_equal(times, times2)
assert_array_almost_equal(raw.info['sfreq'], raw2.info['sfreq'])
# check transformations
for trans in ['dev_head_t', 'dev_ctf_t', 'ctf_head_t']:
if raw.info[trans] is None:
assert_true(raw2.info[trans] is None)
else:
assert_array_equal(raw.info[trans]['trans'],
raw2.info[trans]['trans'])
# check transformation 'from' and 'to'
if trans.startswith('dev'):
from_id = FIFF.FIFFV_COORD_DEVICE
else:
from_id = FIFF.FIFFV_MNE_COORD_CTF_HEAD
if trans[4:8] == 'head':
to_id = FIFF.FIFFV_COORD_HEAD
else:
to_id = FIFF.FIFFV_MNE_COORD_CTF_HEAD
for raw_ in [raw, raw2]:
assert_true(raw_.info[trans]['from'] == from_id)
assert_true(raw_.info[trans]['to'] == to_id)
if fname_in == fif_fname or fname_in == fif_fname + '.gz':
assert_array_almost_equal(raw.info['dig'][0]['r'],
raw2.info['dig'][0]['r'])
def test_io_raw():
"""Test IO for raw data (Neuromag + CTF + gz)
"""
fnames_in = [fif_fname, fif_gz_fname, ctf_fname]
fnames_out = ['raw.fif', 'raw.fif.gz', 'raw.fif']
for fname_in, fname_out in zip(fnames_in, fnames_out):
raw = Raw(fname_in)
nchan = raw.info['nchan']
ch_names = raw.info['ch_names']
meg_channels_idx = [k for k in range(nchan) if ch_names[k][0] == 'M']
n_channels = 100
meg_channels_idx = meg_channels_idx[:n_channels]
start, stop = raw.time_as_index([0, 5])
data, times = raw[meg_channels_idx, start:(stop + 1)]
meg_ch_names = [ch_names[k] for k in meg_channels_idx]
# Set up pick list: MEG + STI 014 - bad channels
include = ['STI 014']
include += meg_ch_names
picks = pick_types(raw.info,
meg=True,
eeg=False,
stim=True,
misc=True,
include=include,
exclude=raw.info['bads'])
print "Number of picked channels : %d" % len(picks)
# Writing with drop_small_buffer True
raw.save(fname_out,
picks,
tmin=0,
tmax=4,
buffer_size_sec=3,
drop_small_buffer=True)
raw2 = Raw(fname_out, preload=True)
sel = pick_channels(raw2.ch_names, meg_ch_names)
data2, times2 = raw2[sel, :]
assert_true(times2.max() <= 3)
# Writing
raw.save(fname_out, picks, tmin=0, tmax=5)
if fname_in == fif_fname or fname_in == fif_fname + '.gz':
assert_true(len(raw.info['dig']) == 146)
raw2 = Raw(fname_out)
sel = pick_channels(raw2.ch_names, meg_ch_names)
data2, times2 = raw2[sel, :]
assert_array_almost_equal(data, data2)
assert_array_almost_equal(times, times2)
assert_array_almost_equal(raw.info['dev_head_t']['trans'],
raw2.info['dev_head_t']['trans'])
assert_array_almost_equal(raw.info['sfreq'], raw2.info['sfreq'])
if fname_in == fif_fname or fname_in == fif_fname + '.gz':
assert_array_almost_equal(raw.info['dig'][0]['r'],
raw2.info['dig'][0]['r'])
# explained variance.
ica = ICA(n_components=0.90, max_pca_components=100, noise_cov=None,
random_state=0)
# For maximum rejection performance we will compute the decomposition on
# the entire time range
# decompose sources for raw data, select n_components by explained variance
ica.decompose_raw(raw, start=None, stop=None, picks=picks)
print ica
sources = ica.get_sources_raw(raw)
# setup reasonable time window for inspection
start_plot, stop_plot = raw.time_as_index([100, 103])
# plot components
ica.plot_sources_raw(raw, start=start_plot, stop=stop_plot)
###############################################################################
# Automatically find the ECG component using correlation with ECG signal
# As we don't have an ECG channel we use one that correlates a lot with heart
# beats: 'MEG 1531'. We can directly pass the name to the find_sources method.
# We select the pearson correlation from scipy stats via string label.
# The function is internally modified to be applicable to 2D arrays and,
# hence, returns product-moment correlation scores for each ICA source.
eog_scores = ica.find_sources_raw(raw, target='EOG 061',
score_func='pearsonr')
def __call__(self, sender, **kwargs):
"""post save callback entry point.
logger.debug('MNE-init()')
:param sender: The model class.
:param instance: The actual instance being saved.
:param created: A boolean; True if a new record was created.
:type created: bool
"""
logger.error('MNE-call()')
instance = kwargs.get('instance')
schema = self.getSchema()
filepath = instance.get_absolute_filepath()
raw_fname = filepath
""":only process MNE fif files"""
if not filepath.endswith('.fif'):
return None
try:
logger.error('MNE-fif image found')
#handle MNE files
#get raw data
raw = Raw(raw_fname)
metadata_dump = dict()
###############################################################################
# explore some nitime timeseries features
logger.error('step 1')
# get start
#metadata_dump['start'] = raw.t0
logger.error('step 1.0')
# get sampling frequnecy
metadata_dump['sampling_frequency'] = raw.info['sfreq']
logger.error('step 1.1')
# get bad channel lists
metadata_dump['bads'] = raw.info['bads']
logger.error('step 1.2')
# get projects
metadata_dump['projects'] = raw.info['projs']
# get measure date
metadata_dump['measure_date'] = raw.info['meas_date']
# get measure id
metadata_dump['measure_id'] = raw.info['meas_id']
# get file id logger.error('image_information ' + raw.info['file_id'])
#metadata_dump['image_information'] = 'Some fixed value'
#metadata_dump['image_information'] = raw.info['comps']
logger.error('step 1.2.1')
metadata_dump['experimenter'] = raw.info['experimenter']
logger.error(metadata_dump['experimenter'])
logger.error('step 1.2.2')
metadata_dump['description'] = raw.info['description']
logger.error(metadata_dump['description'])
#logger.error('step 1.2.3')
#metadata_dump['proj_id'] = raw.info['proj_id']
#logger.error(metadata_dump['proj_id'])
logger.error('step 1.2.3')
metadata_dump['proj_name'] = raw.info['proj_name']
logger.error(metadata_dump['proj_name'])
#logger.error('step 1.2.5')
#metadata_dump['chs'] = raw.info['chs']
#logger.error(metadata_dump['chs'])
#logger.error('step 1.2.6')
#metadata_dump['secs'] = raw.info['meas_id']['secs']
#logger.error('step 1.2.7')
#metadata_dump['usecs'] = raw.info['meas_id']['usecs']
#logger.error('step 1.2.8')
#metadata_dump['comps'] = raw.info['comps']
#logger.error(metadata_dump['comps'])
#logger.error('step 1.2.9')
#metadata_dump['acq_pars'] = raw.info['acq_pars']
#logger.error(metadata_dump['acq_pars'])
logger.error('step 1.2.4')
metadata_dump['acq_stim'] = raw.info['acq_stim']
logger.error(metadata_dump['acq_stim'])
#logger.error('step 1.2.11')
#metadata_dump['dig'] = raw.info['dig']
#logger.error(metadata_dump['dig'])
logger.error('step 1.2.5')
metadata_dump['number_of_channels'] = raw.info['nchan']
logger.error(raw.info['nchan'])
logger.error('step 1.2.6')
metadata_dump['number_of_timepoints'] = raw.n_times
logger.error(metadata_dump['number_of_timepoints'])
logger.error('step 1.2.7')
metadata_dump['channel_names'] = "".join(raw.ch_names)
#STI
numberOfSTI = 0
for term in raw.ch_names:
if term.startswith('STI'):
numberOfSTI += 1
metadata_dump['numberOfSTI'] = numberOfSTI
#EOG
numberOfEOG = 0
for term2 in raw.ch_names:
if term2.startswith('EOG'):
numberOfEOG += 1
metadata_dump['numberOfEOG'] = numberOfEOG
#EEG
numberOfEEG = 0
for term3 in raw.ch_names:
if term3.startswith('EEG'):
numberOfEEG += 1
metadata_dump['numberOfEEG'] = numberOfEEG
#MEG
numberOfMEG = 0
for term4 in raw.ch_names:
if term4.startswith('MEG'):
numberOfMEG += 1
metadata_dump['numberOfMEG'] = numberOfMEG
# get duration
#metadata_dump['duration'] = raw.duration
# get sample duration (sampling interval)
#metadata_dump['sampling_interval'] = raw.info['sampling_interval']
# get exported raw information
#metadata_dump['raw_info'] = raw.metadata.keys()
# get channel names (attribute added during export)
#logger.error('step 1.2.10')
#metadata_dump['channel_names'] = raw.ch_names
#logger.error(raw.ch_names)
#metadata_dump['channel_names'] = raw_ts.ch_names[:3]
# get The width of the transition band of the highpass filter
metadata_dump['highpass'] = raw.info['highpass']
# get The width of the transition band of the lowpass filter
metadata_dump['lowpass'] = raw.info['lowpass']
logger.error('step 2')
###############################################################################
#Plot graph
want_meg = True
want_eeg = False
want_stim = False
include = []
exclude = raw.info['bads']
logger.error('step 2.1')
picks = mne.fiff.pick_types(raw.info, meg=want_meg, eeg=want_eeg,stim=want_stim, include=include, exclude=exclude)
some_picks = picks[:5] # take 5 first
start, stop = raw.time_as_index([0, 15]) # read the first 15s of data
data, times = raw[some_picks, start:(stop + 1)]
logger.error('step 2.2')
import matplotlib.pyplot as pl
pl.close('all')
pl.plot(times, data.T)
pl.xlabel('time (s)')
pl.ylabel('MEG data (T)')
logger.error('step 2.3')
#outputextension = "png"
#tf = tempfile.TemporaryFile(delete=False)
#outputfilename = tf.name
pl.savefig('/opt/mytardis/data/staging/test1.png')
#tf.close()
logger.error('step 2.4')
previewImage64 = self.base64_encode_file('/opt/mytardis/data/staging/test1.png')
#os.remove(outputfilename)
logger.error('step 2.5')
if previewImage64:
metadata_dump['previewImage'] = previewImage64
self.saveMetadata(instance, schema, metadata_dump)
except Exception, e:
logger.debug(e)
return None
from mne.fiff import Raw
from mne.datasets import sample
data_path = sample.data_path()
raw_fname = data_path + '/MEG/sample/sample_audvis_filt-0-40_raw.fif'
###############################################################################
# get raw data
raw = Raw(raw_fname)
# set picks
picks = mne.fiff.pick_types(raw.info, meg=True, eeg=False, eog=False,
stim=False, exclude='bads')
# pick times relative to the onset of the MEG measurement.
start, stop = raw.time_as_index([100, 115], use_first_samp=False)
# export to nitime using a copy of the data
raw_ts = raw.to_nitime(start=start, stop=stop, picks=picks, copy=True)
###############################################################################
# explore some nitime timeseries features
# get start
print raw_ts.t0
# get duration
print raw_ts.duration
# get sample duration (sampling interval)
print raw_ts.sampling_interval
# Instead of the actual number of components here we pass a float value
# between 0 and 1 to select n_components by a percentage of
# explained variance. Also we decide to use 64 PCA components before mixing
# back to sensor space. These include the PCA components supplied to ICA plus
# additional PCA components up to rank 64 of the MEG data.
# This allows to control the trade-off between denoising and preserving signal.
ica = ICA(n_components=0.90, n_pca_components=64, max_pca_components=100,
noise_cov=None, random_state=0)
print ica
# 1 minute exposure should be sufficient for artifact detection.
# However, rejection performance may significantly improve when using
# the entire data range
start, stop = raw.time_as_index([100, 160])
# decompose sources for raw data
ica.decompose_raw(raw, start=start, stop=stop, picks=picks)
print ica
sources = ica.get_sources_raw(raw, start=start, stop=stop)
# setup reasonable time window for inspection
start_plot, stop_plot = raw.time_as_index([100, 103])
# plot components
ica.plot_sources_raw(raw, start=start_plot, stop=stop_plot)
###############################################################################
# Automatically find the ECG component using correlation with ECG signal.
title = 'Spatial patterns of ICA components for ECG+EOG (Magnetometers)'
source_idx = range(15)
ica.plot_topomap([ecg_source_idx, eog_source_idx], ch_type='mag')
plt.suptitle(title, fontsize=12)
###############################################################################
# Show MEG data before and after ICA cleaning.
# We now add the eog artifacts to the ica.exclusion list
ica.exclude += [eog_source_idx]
# Restore sensor space data and keep all PCA components
raw_ica = ica.pick_sources_raw(raw, include=None, n_pca_components=1.0)
# let's now compare the date before and after cleaning.
start_compare, stop_compare = raw.time_as_index([100, 106])
data, times = raw[picks, start_compare:stop_compare]
data_clean, _ = raw_ica[picks, start_compare:stop_compare]
# first the raw data
plt.figure()
plt.plot(times, data.T, color='r')
plt.plot(times, data_clean.T, color='k')
plt.xlabel('time (s)')
plt.xlim(100, 106)
plt.show()
# now the affected channel
affected_idx = raw.ch_names.index('MEG 1531')
plt.figure()
plt.plot(times, data[affected_idx], color='r')
def test_io_raw():
"""Test IO for raw data (Neuromag + CTF + gz)
"""
# Let's construct a simple test for IO first
raw = Raw(fif_fname, preload=True)
raw.crop(0, 3.5)
# put in some data that we know the values of
data = np.random.randn(raw._data.shape[0], raw._data.shape[1])
raw._data[:, :] = data
# save it somewhere
fname = op.join(tempdir, 'test_copy_raw.fif')
raw.save(fname, buffer_size_sec=1.0)
# read it in, make sure the whole thing matches
raw = Raw(fname)
assert_true(np.allclose(data, raw[:, :][0], 1e-6, 1e-20))
# let's read portions across the 1-sec tag boundary, too
inds = raw.time_as_index([1.75, 2.25])
sl = slice(inds[0], inds[1])
assert_true(np.allclose(data[:, sl], raw[:, sl][0], 1e-6, 1e-20))
# now let's do some real I/O
fnames_in = [fif_fname, fif_gz_fname, ctf_fname]
fnames_out = ['raw.fif', 'raw.fif.gz', 'raw.fif']
for fname_in, fname_out in zip(fnames_in, fnames_out):
fname_out = op.join(tempdir, fname_out)
raw = Raw(fname_in)
nchan = raw.info['nchan']
ch_names = raw.info['ch_names']
meg_channels_idx = [k for k in range(nchan) if ch_names[k][0] == 'M']
n_channels = 100
meg_channels_idx = meg_channels_idx[:n_channels]
start, stop = raw.time_as_index([0, 5])
data, times = raw[meg_channels_idx, start:(stop + 1)]
meg_ch_names = [ch_names[k] for k in meg_channels_idx]
# Set up pick list: MEG + STI 014 - bad channels
include = ['STI 014']
include += meg_ch_names
picks = pick_types(raw.info,
meg=True,
eeg=False,
stim=True,
misc=True,
ref_meg=True,
include=include,
exclude='bads')
# Writing with drop_small_buffer True
raw.save(fname_out,
picks,
tmin=0,
tmax=4,
buffer_size_sec=3,
drop_small_buffer=True,
overwrite=True)
raw2 = Raw(fname_out, preload=True)
sel = pick_channels(raw2.ch_names, meg_ch_names)
data2, times2 = raw2[sel, :]
assert_true(times2.max() <= 3)
# Writing
raw.save(fname_out, picks, tmin=0, tmax=5, overwrite=True)
if fname_in == fif_fname or fname_in == fif_fname + '.gz':
assert_true(len(raw.info['dig']) == 146)
raw2 = Raw(fname_out)
sel = pick_channels(raw2.ch_names, meg_ch_names)
data2, times2 = raw2[sel, :]
assert_true(np.allclose(data, data2, 1e-6, 1e-20))
assert_allclose(times, times2)
assert_allclose(raw.info['sfreq'], raw2.info['sfreq'], rtol=1e-5)
# check transformations
for trans in ['dev_head_t', 'dev_ctf_t', 'ctf_head_t']:
if raw.info[trans] is None:
assert_true(raw2.info[trans] is None)
else:
assert_array_equal(raw.info[trans]['trans'],
raw2.info[trans]['trans'])
# check transformation 'from' and 'to'
if trans.startswith('dev'):
from_id = FIFF.FIFFV_COORD_DEVICE
else:
from_id = FIFF.FIFFV_MNE_COORD_CTF_HEAD
if trans[4:8] == 'head':
to_id = FIFF.FIFFV_COORD_HEAD
else:
to_id = FIFF.FIFFV_MNE_COORD_CTF_HEAD
for raw_ in [raw, raw2]:
assert_true(raw_.info[trans]['from'] == from_id)
assert_true(raw_.info[trans]['to'] == to_id)
if fname_in == fif_fname or fname_in == fif_fname + '.gz':
assert_allclose(raw.info['dig'][0]['r'], raw2.info['dig'][0]['r'])
def test_raw_time_as_index():
""" Test index as time conversion"""
raw = Raw(fif_fname, preload=True)
first_samp = raw.time_as_index([0], True)[0]
assert_true(raw.first_samp == -first_samp)
data_path = sample.data_path()
fname_inv = data_path + '/MEG/sample/sample_audvis-meg-oct-6-meg-inv.fif'
fname_raw = data_path + '/MEG/sample/sample_audvis_raw.fif'
label_name = 'Aud-lh'
fname_label = data_path + '/MEG/sample/labels/%s.label' % label_name
snr = 1.0 # use smaller SNR for raw data
lambda2 = 1.0 / snr ** 2
method = "sLORETA" # use sLORETA method (could also be MNE or dSPM)
# Load data
raw = Raw(fname_raw)
inverse_operator = read_inverse_operator(fname_inv)
label = mne.read_label(fname_label)
start, stop = raw.time_as_index([0, 15]) # read the first 15s of data
# Compute inverse solution
stc = apply_inverse_raw(raw, inverse_operator, lambda2, method, label,
start, stop, pick_ori=None)
# Save result in stc files
stc.save('mne_%s_raw_inverse_%s' % (method, label_name))
###############################################################################
# View activation time-series
plt.plot(1e3 * stc.times, stc.data[::100, :].T)
plt.xlabel('time (ms)')
plt.ylabel('%s value' % method)
plt.show()
