def test_flash_bem():
"""Test mne flash_bem."""
check_usage(mne_flash_bem, force_help=True)
# Using the sample dataset
subjects_dir = op.join(sample.data_path(download=False), 'subjects')
# Copy necessary files to tempdir
tempdir = _TempDir()
mridata_path = op.join(subjects_dir, 'sample', 'mri')
subject_path_new = op.join(tempdir, 'sample')
mridata_path_new = op.join(subject_path_new, 'mri')
os.makedirs(op.join(mridata_path_new, 'flash'))
os.makedirs(op.join(subject_path_new, 'bem'))
shutil.copyfile(op.join(mridata_path, 'T1.mgz'),
op.join(mridata_path_new, 'T1.mgz'))
shutil.copyfile(op.join(mridata_path, 'brain.mgz'),
op.join(mridata_path_new, 'brain.mgz'))
# Copy the available mri/flash/mef*.mgz files from the dataset
flash_path = op.join(mridata_path_new, 'flash')
for kind in (5, 30):
in_fname = op.join(mridata_path, 'flash', 'mef%02d.mgz' % kind)
shutil.copyfile(in_fname, op.join(flash_path, op.basename(in_fname)))
# Test mne flash_bem with --noconvert option
# (since there are no DICOM Flash images in dataset)
out_fnames = list()
for kind in ('outer_skin', 'outer_skull', 'inner_skull'):
out_fnames.append(op.join(subject_path_new, 'bem', 'outer_skin.surf'))
assert not any(op.isfile(out_fname) for out_fname in out_fnames)
with ArgvSetter(('-d', tempdir, '-s', 'sample', '-n'),
disable_stdout=False, disable_stderr=False):
mne_flash_bem.run()
# do they exist and are expected size
for out_fname in out_fnames:
_, tris = read_surface(out_fname)
assert len(tris) == 5120
def test_flash_bem():
"""Test mne flash_bem."""
check_usage(mne_flash_bem, force_help=True)
# Using the sample dataset
subjects_dir = op.join(sample.data_path(download=False), 'subjects')
# Copy necessary files to tempdir
tempdir = _TempDir()
mridata_path = op.join(subjects_dir, 'sample', 'mri')
mridata_path_new = op.join(tempdir, 'sample', 'mri')
os.makedirs(op.join(mridata_path_new, 'flash'))
os.makedirs(op.join(tempdir, 'sample', 'bem'))
shutil.copyfile(op.join(mridata_path, 'T1.mgz'),
op.join(mridata_path_new, 'T1.mgz'))
shutil.copyfile(op.join(mridata_path, 'brain.mgz'),
op.join(mridata_path_new, 'brain.mgz'))
# Copy the available mri/flash/mef*.mgz files from the dataset
files = glob.glob(op.join(mridata_path, 'flash', 'mef*.mgz'))
for infile in files:
shutil.copyfile(infile, op.join(mridata_path_new, 'flash',
op.basename(infile)))
# Test mne flash_bem with --noconvert option
# (since there are no DICOM Flash images in dataset)
currdir = os.getcwd()
with ArgvSetter(('-d', tempdir, '-s', 'sample', '-n'),
disable_stdout=False, disable_stderr=False):
mne_flash_bem.run()
os.chdir(currdir)
def _assemble_forward_model_matrix(inverse_operator):
from mne.datasets import sample
warn('Currently info is read from the raw file. TODO: change to getting it from the stream')
data_path = sample.data_path()
fname_raw = data_path + '/MEG/sample/sample_audvis_raw.fif'
raw = mne.io.read_raw_fif(fname_raw, verbose='ERROR')
info = raw.info
channel_cnt = info['nchan']
I = np.identity(channel_cnt)
dummy_raw = mne.io.RawArray(data=I, info=info, verbose='ERROR')
dummy_raw.set_eeg_reference(verbose='ERROR');
# Applying inverse modelling to an identity matrix gives us the forward model matrix
snr = 1.0 # use smaller SNR for raw data
lambda2 = 1.0 / snr ** 2
method = "MNE" # use sLORETA method (could also be MNE or dSPM)
stc = mne.minimum_norm.apply_inverse_raw(dummy_raw, inverse_operator, lambda2, method)
return stc.data
def test_regression():
"""Test Ordinary Least Squares Regression
"""
data_path = sample.data_path()
raw_fname = data_path + '/MEG/sample/sample_audvis_filt-0-40_raw.fif'
event_fname = data_path + '/MEG/sample/sample_audvis_filt-0-40_raw-eve.fif'
tmin, tmax = -0.2, 0.5
event_id = dict(aud_l=1, aud_r=2)
# Setup for reading the raw data
raw = mne.io.Raw(raw_fname)
events = mne.read_events(event_fname)[:10]
epochs = mne.Epochs(raw, events, event_id, tmin, tmax, proj=True,
baseline=(None, 0))
picks = np.arange(len(epochs.ch_names))
evoked = epochs.average(picks=picks)
design_matrix = epochs.events[:, 1:].astype(np.float64)
# makes the intercept
design_matrix[:, 0] = 1
# creates contrast: aud_l=0, aud_r=1
design_matrix[:, 1] -= 1
with warnings.catch_warnings(record=True) as w:
lm = linear_regression(epochs, design_matrix, ['intercept', 'aud'])
assert_true(w[0].category == UserWarning)
assert_true('non-data' in '%s' % w[0].message)
for predictor, parameters in lm.items():
for value in parameters:
assert_equal(value.data.shape, evoked.data.shape)
assert_raises(ValueError, linear_regression, [epochs, epochs],
design_matrix)
stc = read_source_estimate(stc_fname).crop(0, 0.02)
stc_list = [stc, stc, stc]
stc_gen = (s for s in stc_list)
lm1 = linear_regression(stc_list, design_matrix[:len(stc_list)])
lm2 = linear_regression(stc_gen, design_matrix[:len(stc_list)])
for k in lm1:
for v1, v2 in zip(lm1[k], lm2[k]):
assert_array_equal(v1.data, v2.data)
def test_preload_memmap():
tmpdir = mkdtemp(dir="/Users/cjb/tmp")
mmap_fname = opj(tmpdir, "raw_data.dat")
# fname='ec_rest_before_tsss_mc_rsl.fif'
data_path = sample.data_path(download=False)
fname = data_path + "/MEG/sample/sample_audvis_raw.fif"
raw = Raw(fname, preload=False)
# """This function actually preloads the data"""
# data_buffer = mmap_fname
# raw._data = raw._read_segment(data_buffer=data_buffer)[0]
# assert len(raw._data) == raw.info['nchan']
# raw.preload = True
# raw.close()
raw.preload_data(data_buffer=mmap_fname)
data_shape = raw._data.shape
print("Contents of raw._data after reading from fif:")
print(type(raw._data))
print(raw._data[100][:5])
del raw._data
raw._data = np.memmap(mmap_fname, dtype="float64", mode="c", shape=data_shape)
print("Contents of raw._data after RE-loading:")
print(type(raw._data))
print(raw._data[100][:5])
raw.filter(None, 40)
print("Contents of raw._data after filtering:")
print(type(raw._data))
print(raw._data[100][:5])
# PROBLEM: Now the filtered data are IN MEMORY, but as a memmap
# What if I'd like to continue from here using it as an ndarray?
del raw._data
rmtree(tmpdir, ignore_errors=True)
from mne.datasets import sample
from mne.label import read_label, label_sign_flip
from mne.event import read_events
from mne.epochs import Epochs
from mne.source_estimate import read_source_estimate, VolSourceEstimate
from mne import fiff, read_cov, read_forward_solution
from mne.minimum_norm.inverse import (apply_inverse, read_inverse_operator,
apply_inverse_raw, apply_inverse_epochs,
make_inverse_operator,
write_inverse_operator,
compute_rank_inverse)
from mne.utils import _TempDir
from ...externals import six
s_path = op.join(sample.data_path(download=False), 'MEG', 'sample')
fname_inv = op.join(s_path, 'sample_audvis-meg-oct-6-meg-inv.fif')
fname_inv_fixed = op.join(s_path, 'sample_audvis-meg-oct-6-meg-fixed-inv.fif')
fname_inv_nodepth = op.join(s_path,
'sample_audvis-meg-oct-6-meg-nodepth'
'-fixed-inv.fif')
fname_inv_diag = op.join(s_path,
'sample_audvis-meg-oct-6-meg-diagnoise-inv.fif')
fname_vol_inv = op.join(s_path, 'sample_audvis-meg-vol-7-meg-inv.fif')
fname_data = op.join(s_path, 'sample_audvis-ave.fif')
fname_cov = op.join(s_path, 'sample_audvis-cov.fif')
fname_fwd = op.join(s_path, 'sample_audvis-meg-oct-6-fwd.fif')
fname_fwd_meeg = op.join(s_path, 'sample_audvis-meg-eeg-oct-6-fwd.fif')
fname_raw = op.join(s_path, 'sample_audvis_filt-0-40_raw.fif')
fname_event = op.join(s_path, 'sample_audvis_filt-0-40_raw-eve.fif')
fname_label = op.join(s_path, 'labels', '%s.label')
#
# License: BSD (3-clause)
import numpy as np
import pylab as pl
import mne
from mne.fiff.pick import pick_types_evoked, pick_types_forward
from mne.datasets import sample
from mne.time_frequency import iir_filter_raw, morlet
from mne.viz import plot_evoked, plot_sparse_source_estimates
from mne.simulation import generate_sparse_stc, generate_evoked
###############################################################################
# Load real data as templates
data_path = sample.data_path('/Users/sudregp/mne-python/examples/')
raw = mne.fiff.Raw(data_path + '/MEG/sample/sample_audvis_raw.fif')
proj = mne.read_proj(data_path + '/MEG/sample/sample_audvis_ecg_proj.fif')
raw.info['projs'] += proj
raw.info['bads'] = ['MEG 2443', 'EEG 053'] # mark bad channels
fwd_fname = data_path + '/MEG/sample/sample_audvis-meg-eeg-oct-6-fwd.fif'
ave_fname = data_path + '/MEG/sample/sample_audvis-no-filter-ave.fif'
cov_fname = data_path + '/MEG/sample/sample_audvis-cov.fif'
fwd = mne.read_forward_solution(fwd_fname, force_fixed=True, surf_ori=True)
fwd = pick_types_forward(fwd, meg=True, eeg=True, exclude=raw.info['bads'])
cov = mne.read_cov(cov_fname)
# -*- coding: utf-8 -*- """ ============================ Plot an estimate of data SNR ============================ This estimates the SNR as a function of time for a set of data. """ # Author: Eric Larson <*****@*****.**> # # License: BSD (3-clause) from os import path as op from mne.datasets.sample import data_path from mne.minimum_norm import read_inverse_operator from mne import read_evokeds from mne.viz import plot_snr_estimate print(__doc__) data_dir = op.join(data_path(), 'MEG', 'sample') fname_inv = op.join(data_dir, 'sample_audvis-meg-oct-6-meg-inv.fif') fname_evoked = op.join(data_dir, 'sample_audvis-ave.fif') inv = read_inverse_operator(fname_inv) evoked = read_evokeds(fname_evoked, baseline=(None, 0))[0] plot_snr_estimate(evoked, inv)
=========================
Find events from the stimulation/trigger channel in the raw data.
The plot them to get an idea of the paradigm.
"""
# Author: Alexandre Gramfort <*****@*****.**>
#
# License: BSD (3-clause)
import mne
from mne.datasets import sample
from mne.io import Raw
print(__doc__)
data_path = sample.data_path()
fname = data_path + '/MEG/sample/sample_audvis_raw.fif'
# Reading events
raw = Raw(fname)
events = mne.find_events(raw, stim_channel='STI 014')
# Writing events
mne.write_events('events.fif', events)
for ind, before, after in events[:5]:
print("At sample %d stim channel went from %d to %d"
% (ind, before, after))
# Plot the events to get an idea of the paradigm
def test_events_sampledata():
"""Test events."""
data_path = sample.data_path()
raw_fname = data_path + '/MEG/sample/sample_audvis_filt-0-40_raw.fif'
raw = read_raw_fif(raw_fname, preload=True)
raw_tmin, raw_tmax = 0, 90
tmin, tmax = -0.2, 0.5
event_id = dict(aud_l=1, vis_l=3)
# select gradiometers
picks = pick_types(raw.info,
meg='grad',
eeg=False,
eog=True,
stim=True,
exclude=raw.info['bads'])
# load data with usual Epochs for later verification
raw_cropped = raw.copy().crop(raw_tmin, raw_tmax)
events_offline = find_events(raw_cropped)
epochs_offline = Epochs(raw_cropped,
events_offline,
event_id=event_id,
tmin=tmin,
tmax=tmax,
picks=picks,
decim=1,
reject=dict(grad=4000e-13, eog=150e-6),
baseline=None)
epochs_offline.drop_bad()
# create the mock-client object
rt_client = MockRtClient(raw)
rt_epochs = RtEpochs(rt_client,
event_id,
tmin,
tmax,
picks=picks,
decim=1,
reject=dict(grad=4000e-13, eog=150e-6),
baseline=None,
isi_max=1.)
rt_epochs.start()
rt_client.send_data(rt_epochs,
picks,
tmin=raw_tmin,
tmax=raw_tmax,
buffer_size=1000)
expected_events = epochs_offline.events.copy()
expected_events[:, 0] = expected_events[:, 0] - raw_cropped.first_samp
assert np.all(
expected_events[:, 0] <= (raw_tmax - tmax) * raw.info['sfreq'])
assert_array_equal(rt_epochs.events, expected_events)
assert len(rt_epochs) == len(epochs_offline)
data_picks = pick_types(epochs_offline.info,
meg='grad',
eeg=False,
eog=True,
stim=False,
exclude=raw.info['bads'])
for ev_num, ev in enumerate(rt_epochs.iter_evoked()):
if ev_num == 0:
X_rt = ev.data[None, data_picks, :]
y_rt = int(ev.comment) # comment attribute contains the event_id
else:
X_rt = np.concatenate((X_rt, ev.data[None, data_picks, :]), axis=0)
y_rt = np.append(y_rt, int(ev.comment))
X_offline = epochs_offline.get_data()[:, data_picks, :]
y_offline = epochs_offline.events[:, 2]
assert_array_equal(X_rt, X_offline)
assert_array_equal(y_rt, y_offline)
"""
# Authors: Alexandre Gramfort <*****@*****.**>
# Martin Luessi <*****@*****.**>
# License: BSD (3-clause)
print __doc__
import numpy as np
from mne import fiff, read_proj, read_selection
from mne.time_frequency import compute_raw_psd
from mne.datasets import sample
###############################################################################
# Set parameters
data_path = sample.data_path("..")
raw_fname = data_path + "/MEG/sample/sample_audvis_raw.fif"
proj_fname = data_path + "/MEG/sample/sample_audvis_eog_proj.fif"
# Setup for reading the raw data
raw = fiff.Raw(raw_fname)
exclude = raw.info["bads"] + ["MEG 2443", "EEG 053"] # bads + 2 more
# Add SSP projection vectors to reduce EOG and ECG artifacts
projs = read_proj(proj_fname)
raw.add_proj(projs, remove_existing=True)
# Pick MEG magnetometers in the Left-temporal region
selection = read_selection("Left-temporal")
picks = fiff.pick_types(raw.info, meg="mag", eeg=False, eog=False, stim=False, exclude=exclude, selection=selection)
def _guess_surfaces_dir_based_on(mne_forward_model_file_path):
# If the forward model that was used is from the mne's sample dataset, then we can use curvatures from there
path_to_sample = os.path.realpath(sample.data_path(verbose='ERROR'))
if os.path.realpath(mne_forward_model_file_path).startswith(path_to_sample):
return os.path.join(path_to_sample, "subjects", "sample", "surf")
# -*- coding: utf-8 -*-
"""
======================
Configuring MNE python
======================
This tutorial gives a short introduction to MNE configurations.
"""
import os.path as op
import mne
from mne.datasets.sample import data_path
fname = op.join(data_path(), 'MEG', 'sample', 'sample_audvis_raw.fif')
raw = mne.io.read_raw_fif(fname).crop(0, 10)
original_level = mne.get_config('MNE_LOGGING_LEVEL', 'INFO')
###############################################################################
# MNE-python stores configurations to a folder called `.mne` in the user's
# home directory, or to AppData directory on Windows. The path to the config
# file can be found out by calling :func:`mne.get_config_path`.
print(mne.get_config_path())
###############################################################################
# These configurations include information like sample data paths and plotter
# window sizes. Files inside this folder should never be modified manually.
# Let's see what the configurations contain.
print(mne.get_config())
###############################################################################
# We see fields like "MNE_DATASETS_SAMPLE_PATH". As the name suggests, this is
Reading BEM surfaces from a forward solution
============================================
Plot BEM surfaces used for forward solution generation.
"""
# Author: Jaakko Leppakangas <*****@*****.**>
#
# License: BSD (3-clause)
import os.path as op
from mayavi import mlab
import mne
from mne.datasets.sample import data_path
print(__doc__)
data_path = data_path()
fname = op.join(data_path, 'MEG', 'sample', 'sample_audvis_raw.fif')
raw = mne.io.read_raw_fif(fname)
subjects_dir = op.join(data_path, 'subjects')
###############################################################################
# Here we use :func:`mne.viz.plot_trans` with ``trans=None`` to plot only the
# surfaces without any transformations. For plotting transformation, see
# :ref:`tut_forward`.
mne.viz.plot_trans(raw.info, trans=None, subject='sample',
subjects_dir=subjects_dir, meg_sensors=[], eeg_sensors=[],
head='outer_skin', skull=['inner_skull', 'outer_skull'])
mlab.view(40, 60)
from nose.tools import assert_true
import nose
import copy
from mne.datasets import sample
from mne.label import read_label, label_sign_flip
from mne.event import read_events
from mne.epochs import Epochs
from mne.source_estimate import read_source_estimate
from mne import fiff, read_cov, read_forward_solution
from mne.minimum_norm.inverse import apply_inverse, read_inverse_operator, \
apply_inverse_raw, apply_inverse_epochs, make_inverse_operator, \
write_inverse_operator
examples_folder = op.join(op.dirname(__file__), '..', '..', '..', 'examples')
s_path = op.join(sample.data_path(examples_folder), 'MEG', 'sample')
fname_inv = op.join(s_path, 'sample_audvis-meg-oct-6-meg-inv.fif')
fname_inv_fixed = op.join(s_path, 'sample_audvis-meg-oct-6-meg-fixed-inv.fif')
fname_vol_inv = op.join(s_path, 'sample_audvis-meg-vol-7-meg-inv.fif')
fname_data = op.join(s_path, 'sample_audvis-ave.fif')
fname_cov = op.join(s_path, 'sample_audvis-cov.fif')
fname_fwd = op.join(s_path, 'sample_audvis-meg-oct-6-fwd.fif')
fname_raw = op.join(s_path, 'sample_audvis_filt-0-40_raw.fif')
fname_event = op.join(s_path, 'sample_audvis_filt-0-40_raw-eve.fif')
fname_label = op.join(s_path, 'labels', '%s.label')
inverse_operator = read_inverse_operator(fname_inv)
inverse_operator_fixed = read_inverse_operator(fname_inv_fixed)
inverse_operator_vol = read_inverse_operator(fname_vol_inv)
label_lh = read_label(fname_label % 'Aud-lh')
label_rh = read_label(fname_label % 'Aud-rh')
WEIGHT_PATH = join(NETWORK_PATH, 'weights')
NETWORK_VALIDATION_PATH = join(NETWORK_PATH, 'validation')
UTILS_PATH = join(ROOT, 'utils')
PREDICTION_PATH = join(ROOT, 'epoch_validation')
##############
# DATA MODEL #
##############
if not os.environ.get("FREESURFER_HOME"):
print("FREESURFER_HOME environment variable not found. Have you installed Freesurfer properly?")
SPACING = 'ico3' # Source space grid spacing. Options: ico3, ico4, ico5, oct4, oct5 or oct6
DATA_PATH = None
#SUBJECTS_DIR = os.environ.get("SUBJECTS_DIR") or join(sample.data_path(), 'subjects')
SUBJECTS_DIR = join(sample.data_path(), 'subjects')
os.environ["SUBJECTS_DIR"] = SUBJECTS_DIR
SUBJECT_NAME = None
RAW_PATH = None
BEM_PATH = None
COV_PATH = None
TRANS_PATH = None
SRC_PATH = None
RAW_EMPTY_ROOM_PATH = None
EMPTY_SIGNAL = 0.5 # Proportion of empty signal in addition to simulated data
SNR = 1.0
N_DIPOLES = 1 # If N_DIPOLES = 1
# then only one hemisphere (left hemisphere) gets simulated.
SIMULATION_MODEL_KWARGS = get_simulation_model_kwargs(N_DIPOLES, SNR)
"""Find number of examples in MNE-Python.
"""
# Author: Mainak Jas <*****@*****.**>
import os
import os.path as op
import fnmatch
from mne.datasets import sample
def recursive_search(path, pattern):
"""Auxiliary function for recursive_search of the directory.
"""
filtered_files = list()
for dirpath, dirnames, files in os.walk(path):
for f in fnmatch.filter(files, pattern):
filtered_files.append(op.realpath(op.join(dirpath, f)))
return filtered_files
# assuming sample data is in examples dir
example_path = op.dirname(sample.data_path())
tutorial_path = op.join(op.split(example_path)[0], 'tutorials')
tutorial_files = recursive_search(tutorial_path, '*.py')
example_files = recursive_search(example_path, '*.py')
print('Number of examples is %d' % len(example_files))
print('Number of tutorials is %d' % len(tutorial_files))
:ref:`ch_morph`. """ # Author: Tommy Clausner <*****@*****.**> # # License: BSD (3-clause) import os import mne from mne.datasets import sample print(__doc__) ############################################################################### # Setup paths sample_dir_raw = sample.data_path() sample_dir = os.path.join(sample_dir_raw, 'MEG', 'sample') subjects_dir = os.path.join(sample_dir_raw, 'subjects') fname_stc = os.path.join(sample_dir, 'sample_audvis-meg') ############################################################################### # Load example data # Read stc from file stc = mne.read_source_estimate(fname_stc, subject='sample') ############################################################################### # Setting up SourceMorph for SourceEstimate # ----------------------------------------- #
import os.path as op
# from numpy.testing import assert_array_almost_equal
import mne
from mne.datasets import sample
examples_folder = op.join(op.dirname(__file__), '..', '..', 'examples')
data_path = sample.data_path(examples_folder)
fname = op.join(data_path, 'subjects', 'sample', 'bem',
'sample-5120-5120-5120-bem-sol.fif')
def test_io_bem_surfaces():
"""Testing reading of bem surfaces
"""
surf = mne.read_bem_surfaces(fname, add_geom=False)
surf = mne.read_bem_surfaces(fname, add_geom=True)
print "Number of surfaces : %d" % len(surf)
import os.path as op
from mayavi import mlab
import mne
from mne.io import read_raw_fif, read_raw_ctf, read_raw_bti, read_raw_kit
from mne.io import read_raw_artemis123
from mne.datasets import sample, spm_face, testing
from mne.viz import plot_trans
print(__doc__)
bti_path = op.abspath(op.dirname(mne.__file__)) + '/io/bti/tests/data/'
kit_path = op.abspath(op.dirname(mne.__file__)) + '/io/kit/tests/data/'
raws = dict(
Neuromag=read_raw_fif(sample.data_path() +
'/MEG/sample/sample_audvis_raw.fif'),
CTF_275=read_raw_ctf(spm_face.data_path() +
'/MEG/spm/SPM_CTF_MEG_example_faces1_3D.ds'),
Magnes_3600wh=read_raw_bti(op.join(bti_path, 'test_pdf_linux'),
op.join(bti_path, 'test_config_linux'),
op.join(bti_path, 'test_hs_linux')),
KIT=read_raw_kit(op.join(kit_path, 'test.sqd')),
Artemis123=read_raw_artemis123(op.join(testing.data_path(), 'ARTEMIS123',
'Artemis_Data_2016-11-03-15h-58m_test.bin'))
)
for system, raw in raws.items():
# We don't have coil definitions for KIT refs, so exclude them
ref_meg = False if system == 'KIT' else True
fig = plot_trans(raw.info, trans=None, dig=False, eeg_sensors=False,
# Authors: Richard Höchenberger <*****@*****.**>
# License: BSD (3-clause)
###############################################################################
# Load the ``sample`` dataset, and create a concatenated raw data object.
from pathlib import Path
from tempfile import NamedTemporaryFile
import mne
from mne.datasets import sample
from mne_bids import write_raw_bids, BIDSPath
data_path = Path(sample.data_path())
raw_fname = data_path / 'MEG' / 'sample' / 'sample_audvis_raw.fif'
output_path = data_path / '..' / 'MNE-sample-data-bids'
bids_path = BIDSPath(subject='01', task='audiovisual', root=output_path)
raw = mne.io.read_raw_fif(raw_fname)
raw.info['line_freq'] = 60
raw_concat = mne.concatenate_raws([raw.copy(), raw])
###############################################################################
# Trying to write these data will fail.
try:
write_raw_bids(raw=raw_concat, bids_path=bids_path, overwrite=True)
except ValueError as e:
print(f'Data cannot be written. Exception message was: {e}')
Configuration parameters for the study. This should be in a folder called ``library/`` inside the ``processing/`` directory. """ import os import numpy as np from mne.datasets import sample ############################################################################### # DIRECTORIES # ----------- # Let's set the `study path`` where the data is stored on your system # study_path = '/Users/sophie/Dropbox/CBD_Hackaton_PreProc/MNE-sample-data/' # study_path = '../MNE-sample-data/' study_path = sample.data_path() # The ``subjects_dir`` and ``meg_dir`` for reading anatomical and MEG files. subjects_dir = os.path.join(study_path, 'subjects') meg_dir = os.path.join(study_path, 'MEG') ############################################################################### # DEFINE SUBJECTS # --------------- # # A list of ``subject names`` # These are the ``nips`` in neurospin lingo # To define the subjects, we use a list with all the subject names. Even if its # a single subject, it needs to be set up as a list with a single element.
def make_inverse_operator():
from mne.datasets import sample
from mne.minimum_norm import read_inverse_operator
data_path = sample.data_path()
filename_inv = data_path + '/MEG/sample/sample_audvis-meg-oct-6-meg-inv.fif'
return read_inverse_operator(filename_inv, verbose='ERROR')
# License: BSD (3-clause)
import numpy as np
import pylab as pl
import mne
from mne.fiff.pick import pick_types_evoked, pick_types_forward
from mne.datasets import sample
from mne.time_frequency import iir_filter_raw, morlet
from mne.viz import plot_evoked, plot_sparse_source_estimates
from mne.simulation import generate_sparse_stc, generate_evoked
import virtual_electrode as ve
###############################################################################
# Load real data as templates
data_path = sample.data_path('/Users/sudregp/mne-python/examples/')
raw = mne.fiff.Raw(data_path + '/MEG/sample/sample_audvis_raw.fif', preload=True)
fwd_fname = data_path + '/MEG/sample/sample_audvis-meg-eeg-oct-6-fwd.fif'
ave_fname = data_path + '/MEG/sample/sample_audvis-no-filter-ave.fif'
cov_fname = data_path + '/MEG/sample/sample_audvis-cov.fif'
fwd = mne.read_forward_solution(fwd_fname, force_fixed=True, surf_ori=True)
fwd = pick_types_forward(fwd, meg=True)
cov = mne.read_cov(cov_fname)
evoked_template = mne.fiff.read_evoked(ave_fname, setno=0, baseline=None)
label_names = ['Aud-lh', 'Aud-lh', 'Aud-lh', 'Aud-lh', 'Aud-lh']
# -*- coding: utf-8 -*-
"""
======================
Configuring MNE python
======================
This tutorial gives a short introduction to MNE configurations.
"""
import os.path as op
import mne
from mne.datasets.sample import data_path
fname = op.join(data_path(), 'MEG', 'sample', 'sample_audvis_raw.fif')
raw = mne.io.read_raw_fif(fname).crop(0, 10)
original_level = mne.get_config('MNE_LOGGING_LEVEL', 'INFO')
###############################################################################
# MNE-python stores configurations to a folder called `.mne` in the user's
# home directory, or to AppData directory on Windows. The path to the config
# file can be found out by calling :func:`mne.get_config_path`.
print(mne.get_config_path())
###############################################################################
# These configurations include information like sample data paths and plotter
# window sizes. Files inside this folder should never be modified manually.
# Let's see what the configurations contain.
print(mne.get_config())
###############################################################################
# We see fields like "MNE_DATASETS_SAMPLE_PATH". As the name suggests, this is
import os.path as op
# from numpy.testing import assert_array_almost_equal
import mne
from mne.datasets import sample
examples_folder = op.join(op.dirname(__file__), '..', '..', 'examples')
data_path = sample.data_path(examples_folder)
fname = op.join(data_path, 'subjects', 'sample', 'bem',
'sample-5120-5120-5120-bem-sol.fif')
def test_io_bem_surfaces():
"""Testing reading of bem surfaces
"""
surf = mne.read_bem_surfaces(fname, add_geom=False)
surf = mne.read_bem_surfaces(fname, add_geom=True)
print "Number of surfaces : %d" % len(surf)
import os
import numpy as np
import mne
from mne.datasets import sample
from mne.minimum_norm import read_inverse_operator
from .. import MISC_CHANNEL_TYPE
from ..helpers.misc import all_upper
data_path = sample.data_path(verbose='ERROR')
sample_dir = os.path.join(data_path, 'MEG', 'sample')
neuromag_forward_file_path = os.path.join(sample_dir,
'sample_audvis-meg-oct-6-fwd.fif')
standard_1005_forward_file_path = os.path.join(
sample_dir, 'sample_1005-eeg-oct-6-fwd.fif')
def _pick_columns_from_matrix(matrix: np.ndarray, output_column_labels: list,
input_column_labels: list) -> np.ndarray:
"""
From matrix take only the columns that correspond to output_column_labels - in the order of the latter.
:param matrix: each column in matrix has a label (eg. EEG channel name)
:param output_column_labels: labels that we need
:param input_column_labels: labels that we have
:return: np.ndarray with len(output_column_labels) columns and the same number of rows as matrix has.
"""
# Choose the right columns, put zeros where label is missing
row_count = matrix.shape[0]
output_matrix = np.zeros((row_count, len(output_column_labels)))
from mne.datasets import sample
from mne.label import read_label, label_sign_flip
from mne.event import read_events
from mne.epochs import Epochs
from mne.source_estimate import read_source_estimate, VolSourceEstimate
from mne import read_cov, read_forward_solution
from mne.fiff import read_evokeds, Raw, pick_types
from mne.minimum_norm.inverse import (apply_inverse, read_inverse_operator,
apply_inverse_raw, apply_inverse_epochs,
make_inverse_operator,
write_inverse_operator,
compute_rank_inverse)
from mne.utils import _TempDir
from ...externals import six
s_path = op.join(sample.data_path(download=False), 'MEG', 'sample')
fname_inv = op.join(s_path, 'sample_audvis-meg-oct-6-meg-inv.fif')
fname_inv_fixed = op.join(s_path, 'sample_audvis-meg-oct-6-meg-fixed-inv.fif')
fname_inv_nodepth = op.join(
s_path, 'sample_audvis-meg-oct-6-meg-nodepth'
'-fixed-inv.fif')
fname_inv_diag = op.join(s_path,
'sample_audvis-meg-oct-6-meg-diagnoise-inv.fif')
fname_vol_inv = op.join(s_path, 'sample_audvis-meg-vol-7-meg-inv.fif')
fname_data = op.join(s_path, 'sample_audvis-ave.fif')
fname_cov = op.join(s_path, 'sample_audvis-cov.fif')
fname_fwd = op.join(s_path, 'sample_audvis-meg-oct-6-fwd.fif')
fname_fwd_meeg = op.join(s_path, 'sample_audvis-meg-eeg-oct-6-fwd.fif')
fname_raw = op.join(s_path, 'sample_audvis_filt-0-40_raw.fif')
fname_event = op.join(s_path, 'sample_audvis_filt-0-40_raw-eve.fif')
fname_label = op.join(s_path, 'labels', '%s.label')
import os.path as op
from mayavi import mlab
import mne
from mne.io import read_raw_fif, read_raw_ctf, read_raw_bti, read_raw_kit
from mne.datasets import sample, spm_face
from mne.viz import plot_trans
print(__doc__)
bti_path = op.abspath(op.dirname(mne.__file__)) + "/io/bti/tests/data/"
kit_path = op.abspath(op.dirname(mne.__file__)) + "/io/kit/tests/data/"
raws = dict(
Neuromag=read_raw_fif(sample.data_path() + "/MEG/sample/sample_audvis_raw.fif"),
CTF_275=read_raw_ctf(spm_face.data_path() + "/MEG/spm/SPM_CTF_MEG_example_faces1_3D.ds"),
Magnes_3600wh=read_raw_bti(
op.join(bti_path, "test_pdf_linux"), op.join(bti_path, "test_config_linux"), op.join(bti_path, "test_hs_linux")
),
KIT=read_raw_kit(op.join(kit_path, "test.sqd")),
)
for system, raw in raws.items():
# We don't have coil definitions for KIT refs, so exclude them
ref_meg = False if system == "KIT" else True
fig = plot_trans(
raw.info, trans=None, dig=False, eeg_sensors=False, meg_sensors=True, coord_frame="meg", ref_meg=ref_meg
)
mlab.title(system)
from scipy import sparse
from nose.tools import assert_true, assert_raises
import copy
from mne.datasets import sample
from mne.label import read_label, label_sign_flip
from mne.event import read_events
from mne.epochs import Epochs
from mne.source_estimate import read_source_estimate
from mne import fiff, read_cov, read_forward_solution
from mne.minimum_norm.inverse import apply_inverse, read_inverse_operator, \
apply_inverse_raw, apply_inverse_epochs, make_inverse_operator, \
write_inverse_operator, compute_rank_inverse
from mne.utils import _TempDir
s_path = op.join(sample.data_path(), 'MEG', 'sample')
fname_inv = op.join(s_path, 'sample_audvis-meg-oct-6-meg-inv.fif')
fname_inv_fixed = op.join(s_path, 'sample_audvis-meg-oct-6-meg-fixed-inv.fif')
fname_inv_nodepth = op.join(s_path,
'sample_audvis-meg-oct-6-meg-nodepth-fixed-inv.fif')
fname_inv_diag = op.join(s_path,
'sample_audvis-meg-oct-6-meg-diagnoise-inv.fif')
fname_vol_inv = op.join(s_path, 'sample_audvis-meg-vol-7-meg-inv.fif')
fname_data = op.join(s_path, 'sample_audvis-ave.fif')
fname_cov = op.join(s_path, 'sample_audvis-cov.fif')
fname_fwd = op.join(s_path, 'sample_audvis-meg-oct-6-fwd.fif')
fname_raw = op.join(s_path, 'sample_audvis_filt-0-40_raw.fif')
fname_event = op.join(s_path, 'sample_audvis_filt-0-40_raw-eve.fif')
fname_label = op.join(s_path, 'labels', '%s.label')
inverse_operator = read_inverse_operator(fname_inv)
"""Find number of examples in MNE-Python.
"""
# Author: Mainak Jas <*****@*****.**>
import os
import os.path as op
import fnmatch
from mne.datasets import sample
def recursive_search(path, pattern):
"""Auxiliary function for recursive_search of the directory.
"""
filtered_files = list()
for dirpath, dirnames, files in os.walk(path):
for f in fnmatch.filter(files, pattern):
filtered_files.append(op.realpath(op.join(dirpath, f)))
return filtered_files
# assuming sample data is in examples dir
example_path = op.dirname(sample.data_path())
example_files = recursive_search(example_path, '*.py')
print('Number of examples is %d' % len(example_files))
from sklearn.linear_model import LogisticRegression # Logistic Regression classifier. ''' - TransformerMixin : Mixin class for all transformers in scikit-learn. 이 클래스는 fit(),transform()메서드를 나만의 변환기에 생성하였을 경우 마지막 메서드인 fit_transform()를 자동으로 생성 - Pipeline : 여러가지의 변환기들을 하나로 연결 - Logistic Regression (로지스틱 회귀) : 변수를 입력할 경우 이를 0~1의 범위로 변환 후 이를 통해서 확률값을 계산하고 마지막으로 분류(어떤 클래스에 대한 확률이 가장 높은지 계산)하는 지도 학습 알고리즘. ''' # tools for plotting confusion matrices (confusion matrix : 지도 학습으로 훈련된 분류 알고리즘의 성능을 시각화한 표 / 행과 열은 각각 예측 된 클래스의 인스턴스와 실제 클래스의 인스턴스를 나타냄) from matplotlib import pyplot as plt # matplotlib : 파이썬 기반의 시각화 라이브러리. 여러 가지 그래프를 그려주는 함수들 내장. # while the default tensorflow ordering is 'channels_last' we set it here # to be explicit in case if the user has changed the default ordering K.set_image_data_format(‘channels_last’) # Sets the value of the image data format convention. ## Process, filter and epoch the data ## data_path = sample.data_path() # mne.datasets.sample.data_path : 샘플 데이터셋의 복사본의 로컬 경로를 가져오는 함수 # Set parameters and read data raw_fname = data_path + ‘/MEG/sample/sample_audvis_filt_0-40_raw.fif’ event_fname = data_path + ‘/MEG/sample/sample_audvis_filt_0-40_raw-eve.fif’ tmin, tmax = -0., 1 event_id = dict(aud_l=1, aud_r=2, vis_l=3, vis_r=4) # Setup for reading the raw data raw = io.Raw(raw_fname, preload=False, verbose=False) raw.filter(2, None, method=’iir’) # replace baselining with high-pass events = mne.read_events(event_fname) ''' mne.io.Raw : FIF 파일 형식의 raw data. - raw_fname (str) : load할 raw file 파일명. 파일명이 raw.fif, raw_sss.fif, raw_tsss.fif, _meg.fif, _eeg.fif, _ieeg.fif로 끝나야 오류 발생 안 함
from main import get_data
from mne.channels import read_ch_connectivity
from mne.stats import permutation_cluster_test
import numpy as np
from mne.io import read_raw_fif
from mne.datasets import sample
from mne.channels import find_layout
from mne.viz import plot_topomap
import os
import matplotlib.pyplot as plt
from scipy.signal import butter, lfilter
info = read_raw_fif(sample.data_path() + '/MEG/sample/sample_audvis_raw.fif',verbose=False).info
connectivity = read_ch_connectivity('neuromag306planar_neighb.mat', picks=None)
def butter_lowpass(cutoff, fs, order=5):
nyq = 0.5 * fs
normal_cutoff = cutoff / nyq
b, a = butter(order, normal_cutoff, btype='low', analog=False)
return b, a
def butter_lowpass_filter(data, cutoff, fs, order=5):
b, a = butter_lowpass(cutoff, fs, order=order)
y=np.zeros(data.shape)
for tr in range(data.shape[0]):
for ch in range(data.shape[2]):
y[tr,:,ch] = lfilter(b, a, data[tr,:,ch])
return y
# First, we will load the example dataset from MNE, and have a quick look at the data. # # The MNE sample dataset is a combined MEG/EEG recording with an audiovisual task, as # described `here <https://mne.tools/stable/overview/datasets_index.html?#sample>`_. # # For the current example, we are going to sub-select only the EEG data, # and analyze it as continuous (non-epoched) data. # # Note that if you don't already have the data, the ``sample.data_path`` method # will download the MNE sample dataset. # ################################################################################################### # Get the data path for the MNE example data raw_fname = sample.data_path() + '/MEG/sample/sample_audvis_filt-0-40_raw.fif' # Load the file of example MNE data raw = io.read_raw_fif(raw_fname, preload=True, verbose=False) ################################################################################################### # Select EEG channels from the dataset raw = raw.pick_types(meg=False, eeg=True, eog=False, exclude='bads') # Grab the sampling rate from the data fs = raw.info['sfreq'] ################################################################################################### # Settings for exploring an example channel of data
from nose.tools import assert_true
import nose
import copy
from mne.datasets import sample
from mne.label import read_label, label_sign_flip
from mne.event import read_events
from mne.epochs import Epochs
from mne.source_estimate import read_source_estimate
from mne import fiff, read_cov, read_forward_solution
from mne.minimum_norm.inverse import apply_inverse, read_inverse_operator, \
apply_inverse_raw, apply_inverse_epochs, make_inverse_operator, \
write_inverse_operator
examples_folder = op.join(op.dirname(__file__), '..', '..', '..', 'examples')
s_path = op.join(sample.data_path(examples_folder), 'MEG', 'sample')
fname_inv = op.join(s_path, 'sample_audvis-meg-oct-6-meg-inv.fif')
fname_inv_fixed = op.join(s_path, 'sample_audvis-meg-oct-6-meg-fixed-inv.fif')
fname_vol_inv = op.join(s_path, 'sample_audvis-meg-vol-7-meg-inv.fif')
fname_data = op.join(s_path, 'sample_audvis-ave.fif')
fname_cov = op.join(s_path, 'sample_audvis-cov.fif')
fname_fwd = op.join(s_path, 'sample_audvis-meg-oct-6-fwd.fif')
fname_raw = op.join(s_path, 'sample_audvis_filt-0-40_raw.fif')
fname_event = op.join(s_path, 'sample_audvis_filt-0-40_raw-eve.fif')
fname_label = op.join(s_path, 'labels', '%s.label')
inverse_operator = read_inverse_operator(fname_inv)
inverse_operator_fixed = read_inverse_operator(fname_inv_fixed)
inverse_operator_vol = read_inverse_operator(fname_vol_inv)
label_lh = read_label(fname_label % 'Aud-lh')
label_rh = read_label(fname_label % 'Aud-rh')
def test_volume_source_morph():
"""Test volume source estimate morph, special cases and exceptions."""
import nibabel as nib
data_path = sample.data_path(
download=False) # because testing data has no brain.mgz
subjects_dir = os.path.join(data_path, 'subjects')
sample_dir = os.path.join(data_path, 'MEG', 'sample')
fname_inv_vol = os.path.join(sample_dir,
'sample_audvis-meg-vol-7-meg-inv.fif')
inverse_operator_vol = read_inverse_operator(fname_inv_vol)
stc_vol = read_source_estimate(fname_vol, 'sample')
# check for invalid input type
with pytest.raises(ValueError, match='src must be an instance of'):
SourceMorph(src=42)
# check for raising an error if neither
# inverse_operator_vol['src'][0]['subject_his_id'] nor subject_from is set,
# but attempting to perform a volume morph
src = inverse_operator_vol['src']
src[0]['subject_his_id'] = None
with pytest.raises(ValueError, match='subject_from is None.'):
SourceMorph(src=src, subjects_dir=subjects_dir)
# check infer subject_from from src[0]['subject_his_id']
src[0]['subject_his_id'] = 'sample'
with pytest.raises(ValueError, match='Inter-hemispheric morphing'):
SourceMorph(src=src, subjects_dir=subjects_dir, xhemi=True)
with pytest.raises(ValueError, match='Only surface'):
SourceMorph(src=src, sparse=True)
source_morph_vol = SourceMorph(subjects_dir=subjects_dir,
src=inverse_operator_vol['src'],
niter_affine=(1, ),
niter_sdr=(1, ),
spacing=7)
assert source_morph_vol.subject_from == 'sample'
# the brain used in sample data has shape (255, 255, 255)
assert (tuple(
source_morph_vol.params['DiffeomorphicMap']['domain_shape']) == (37,
37,
37))
assert (tuple(
source_morph_vol.params['AffineMap']['domain_shape']) == (37, 37, 37))
# proofs the above
assert source_morph_vol.spacing == 7
# assure proper src shape
assert source_morph_vol.params['src_shape_full'] == (src[0]['mri_height'],
src[0]['mri_depth'],
src[0]['mri_width'])
fwd = read_forward_solution(
os.path.join(sample_dir, 'sample_audvis-meg-vol-7-fwd.fif'))
# check input via path to src and path to subject_to
source_morph_vol = SourceMorph(subject_from='sample',
subject_to=os.path.join(
data_path, 'subjects', 'fsaverage',
'mri', 'brain.mgz'),
subjects_dir=subjects_dir,
niter_affine=(1, ),
src=fwd['src'],
niter_sdr=(1, ),
spacing=7)
# check wrong subject_to
with pytest.raises(IOError, match='cannot read file'):
SourceMorph(subject_from='sample',
subject_to='42',
subjects_dir=subjects_dir,
src=fwd['src'])
# two different ways of saving
source_morph_vol.save(os.path.join(tempdir, 'vol'))
# check loading
source_morph_vol_r = read_source_morph(
os.path.join(tempdir, 'vol-morph.h5'))
# check for invalid file name handling ()
with pytest.raises(IOError, match='not found'):
read_source_morph(os.path.join(tempdir, '42'))
# check morph
stc_vol_morphed = source_morph_vol(stc_vol)
# check as_volume=True
assert isinstance(source_morph_vol(stc_vol, as_volume=True),
nib.Nifti1Image)
# check for subject_from mismatch
source_morph_vol_r.subject_from = '42'
with pytest.raises(ValueError, match='subject_from must match'):
source_morph_vol_r(stc_vol_morphed)
# check if nifti is in grid morph space with voxel_size == spacing
img_morph_res = source_morph_vol.as_volume(stc_vol_morphed,
mri_resolution=False)
# assure morph spacing
assert isinstance(img_morph_res, nib.Nifti1Image)
assert img_morph_res.header.get_zooms()[:3] == (7., 7., 7.)
# assure src shape
img_mri_res = source_morph_vol.as_volume(stc_vol_morphed,
mri_resolution=True)
assert isinstance(img_mri_res, nib.Nifti1Image)
assert (img_mri_res.shape == (src[0]['mri_height'], src[0]['mri_depth'],
src[0]['mri_width']) +
(img_mri_res.shape[3], ))
# check if nifti is defined resolution with voxel_size == (5., 5., 5.)
img_any_res = source_morph_vol.as_volume(stc_vol_morphed,
mri_resolution=(5., 5., 5.),
fname=os.path.join(tempdir, '42'))
assert isinstance(img_any_res, nib.Nifti1Image)
assert img_any_res.header.get_zooms()[:3] == (5., 5., 5.)
# check if morph outputs correct data
assert isinstance(stc_vol_morphed, VolSourceEstimate)
# check if loaded and saved objects contain the same
assert (all([
read == saved
for read, saved in zip(sorted(source_morph_vol_r.__dict__),
sorted(source_morph_vol.__dict__))
]))
# check __repr__
assert isinstance(source_morph_vol.__repr__(), string_types)
# check Nifti2Image
assert isinstance(
source_morph_vol.as_volume(stc_vol_morphed,
mri_resolution=True,
mri_space=True,
format='nifti2'), nib.Nifti2Image)
with pytest.raises(ValueError, match='subject_from does not match'):
SourceMorph(src=src, subject_from='42')
# check wrong format
with pytest.raises(ValueError, match='invalid format specifier'):
source_morph_vol.as_volume(stc_vol_morphed, format='42')
with pytest.raises(ValueError, match='invalid format specifier'):
stc_vol_morphed.as_volume(inverse_operator_vol['src'], format='42')
import os.path as op
from mayavi import mlab
import mne
from mne.io import read_raw_fif, read_raw_ctf, read_raw_bti, read_raw_kit
from mne.io import read_raw_artemis123
from mne.datasets import sample, spm_face, testing
from mne.viz import plot_alignment
print(__doc__)
bti_path = op.abspath(op.dirname(mne.__file__)) + '/io/bti/tests/data/'
kit_path = op.abspath(op.dirname(mne.__file__)) + '/io/kit/tests/data/'
raws = {
'Neuromag': read_raw_fif(sample.data_path() +
'/MEG/sample/sample_audvis_raw.fif'),
'CTF 275': read_raw_ctf(spm_face.data_path() +
'/MEG/spm/SPM_CTF_MEG_example_faces1_3D.ds'),
'Magnes 3600wh': read_raw_bti(op.join(bti_path, 'test_pdf_linux'),
op.join(bti_path, 'test_config_linux'),
op.join(bti_path, 'test_hs_linux')),
'KIT': read_raw_kit(op.join(kit_path, 'test.sqd')),
'Artemis123': read_raw_artemis123(op.join(
testing.data_path(), 'ARTEMIS123',
'Artemis_Data_2017-04-14-10h-38m-59s_Phantom_1k_HPI_1s.bin')),
}
for system, raw in sorted(raws.items()):
meg = ['helmet', 'sensors']
# We don't have coil definitions for KIT refs, so exclude them
import mne
import numpy as np
import pylab as plt
from mne.datasets import sample
# create data
fs = 500
ch_names = ['Fp1','Fp2','F7','F3','Fz','F4','F8','Ft9','Fc5','Fc1','Fc2','Fc6','Ft10','T7','C3','Cz','C4','T8','Tp9',
'Cp5','Cp1','Cp2','Cp6','Tp10','P7','P3','Pz','P4','P8','O1','Oz','O2']
info = mne.create_info(ch_names=ch_names, sfreq=fs, montage=mne.channels.read_montage(kind='standard_1005'), ch_types=['eeg' for ch in ch_names])
data = np.random.normal(loc=0, scale=0.00001, size=(5000, len(info["ch_names"])))
raw = mne.io.RawArray(data.T, info)
#raw.plot()
#plt.show()
# create cov matrix
noise_cov = mne.compute_raw_covariance(raw)
mne.viz.plot_cov(noise_cov, raw.info)
# forward solution
fname_fwd = sample.data_path() + '/MEG/sample/sample_audvis-meg-oct-6-fwd.fif'
fwd = mne.read_forward_solution(fname_fwd, surf_ori=True)
import os.path as op
from mayavi import mlab
import mne
from mne.io import Raw, read_raw_ctf, read_raw_bti, read_raw_kit
from mne.datasets import sample, spm_face
from mne.viz import plot_trans
print(__doc__)
bti_path = op.abspath(op.dirname(mne.__file__)) + '/io/bti/tests/data/'
kit_path = op.abspath(op.dirname(mne.__file__)) + '/io/kit/tests/data/'
raws = dict(
Neuromag=Raw(sample.data_path() + '/MEG/sample/sample_audvis_raw.fif'),
CTF_275=read_raw_ctf(spm_face.data_path() +
'/MEG/spm/SPM_CTF_MEG_example_faces1_3D.ds'),
Magnes_3600wh=read_raw_bti(bti_path + 'test_pdf_linux',
bti_path + 'test_config_linux',
bti_path + 'test_hs_linux'),
KIT=read_raw_kit(kit_path + 'test.sqd'),
)
for system, raw in raws.items():
# We don't have coil definitions for KIT refs, so exclude them
ref_meg = False if system == 'KIT' else True
fig = plot_trans(raw.info, trans=None, dig=False, eeg_sensors=False,
meg_sensors=True, coord_frame='meg', ref_meg=ref_meg)
mlab.title(system)
# License: BSD (3-clause)
import os
import matplotlib.pyplot as plt
import nibabel as nib
import mne
from mne.datasets import sample
from mne.minimum_norm import apply_inverse, read_inverse_operator
from nilearn.plotting import plot_glass_brain
print(__doc__)
###############################################################################
# Setup paths
sample_dir_raw = sample.data_path()
sample_dir = os.path.join(sample_dir_raw, 'MEG', 'sample')
subjects_dir = os.path.join(sample_dir_raw, 'subjects')
fname_evoked = os.path.join(sample_dir, 'sample_audvis-ave.fif')
fname_inv = os.path.join(sample_dir, 'sample_audvis-meg-vol-7-meg-inv.fif')
fname_t1_fsaverage = os.path.join(subjects_dir, 'fsaverage', 'mri',
'brain.mgz')
###############################################################################
# Compute example data. For reference see
# :ref:`sphx_glr_auto_examples_inverse_plot_compute_mne_inverse_volume.py`
#
# Load data:
evoked = mne.read_evokeds(fname_evoked, condition=0, baseline=(None, 0))
"""Decorator to skip test if scikit-learn >= 0.12 is not available"""
@wraps(function)
def dec(*args, **kwargs):
if not check_sklearn_version(min_version='0.12'):
from nose.plugins.skip import SkipTest
raise SkipTest('Test %s skipped, requires scikit-learn >= 0.12'
% function.__name__)
ret = function(*args, **kwargs)
return ret
return dec
if not lacks_mayavi:
mlab.options.backend = 'test'
data_dir = data_path()
subjects_dir = op.join(data_dir, 'subjects')
sample_src = read_source_spaces(op.join(data_dir, 'subjects', 'sample',
'bem', 'sample-oct-6-src.fif'))
ecg_fname = op.join(data_dir, 'MEG', 'sample', 'sample_audvis_ecg_proj.fif')
evoked_fname = op.join(data_dir, 'MEG', 'sample', 'sample_audvis-ave.fif')
base_dir = op.join(op.dirname(__file__), '..', 'fiff', 'tests', 'data')
fname = op.join(base_dir, 'test-ave.fif')
raw_fname = op.join(base_dir, 'test_raw.fif')
cov_fname = op.join(base_dir, 'test-cov.fif')
event_name = op.join(base_dir, 'test-eve.fif')
event_id, tmin, tmax = 1, -0.2, 0.5
n_chan = 15
raw = fiff.Raw(raw_fname, preload=False)
events = read_events(event_name)
import mne
from mne.io import read_raw_fif, read_raw_ctf, read_raw_bti, read_raw_kit
from mne.io import read_raw_artemis123
from mne.datasets import sample, spm_face, testing
from mne.viz import plot_alignment, set_3d_title
print(__doc__)
###############################################################################
# Neuromag
# --------
kwargs = dict(eeg=False, coord_frame='meg', show_axes=True, verbose=True)
raw = read_raw_fif(sample.data_path() + '/MEG/sample/sample_audvis_raw.fif')
fig = plot_alignment(raw.info, meg=('helmet', 'sensors'), **kwargs)
set_3d_title(figure=fig, title='Neuromag')
###############################################################################
# CTF
# ---
raw = read_raw_ctf(spm_face.data_path() +
'/MEG/spm/SPM_CTF_MEG_example_faces1_3D.ds')
fig = plot_alignment(raw.info, meg=('helmet', 'sensors', 'ref'), **kwargs)
set_3d_title(figure=fig, title='CTF 275')
###############################################################################
# BTi
# ---
from scipy import sparse
from nose.tools import assert_true, assert_raises
import copy
from mne.datasets import sample
from mne.label import read_label, label_sign_flip
from mne.event import read_events
from mne.epochs import Epochs
from mne.source_estimate import read_source_estimate
from mne import fiff, read_cov, read_forward_solution
from mne.minimum_norm.inverse import apply_inverse, read_inverse_operator, \
apply_inverse_raw, apply_inverse_epochs, make_inverse_operator, \
write_inverse_operator, compute_rank_inverse
from mne.utils import _TempDir
s_path = op.join(sample.data_path(), 'MEG', 'sample')
fname_inv = op.join(s_path, 'sample_audvis-meg-oct-6-meg-inv.fif')
fname_inv_fixed = op.join(s_path, 'sample_audvis-meg-oct-6-meg-fixed-inv.fif')
fname_inv_nodepth = op.join(s_path,
'sample_audvis-meg-oct-6-meg-nodepth-fixed-inv.fif')
fname_inv_diag = op.join(s_path,
'sample_audvis-meg-oct-6-meg-diagnoise-inv.fif')
fname_vol_inv = op.join(s_path, 'sample_audvis-meg-vol-7-meg-inv.fif')
fname_data = op.join(s_path, 'sample_audvis-ave.fif')
fname_cov = op.join(s_path, 'sample_audvis-cov.fif')
fname_fwd = op.join(s_path, 'sample_audvis-meg-oct-6-fwd.fif')
fname_raw = op.join(s_path, 'sample_audvis_filt-0-40_raw.fif')
fname_event = op.join(s_path, 'sample_audvis_filt-0-40_raw-eve.fif')
fname_label = op.join(s_path, 'labels', '%s.label')
label_lh = read_label(fname_label % 'Aud-lh')
def SimulateRaw(amp1=50, amp2=100, freq=1., batch=1):
"""Create simulated raw data and events of two kinds
Keyword Args:
amp1 (float): amplitude of first condition effect
amp2 (float): ampltiude of second condition effect,
null hypothesis amp1=amp2
freq (float): Frequency of simulated signal 1. for ERP 10. for alpha
batch (int): number of groups of 255 trials in each condition
Returns:
raw: simulated EEG MNE raw object with two event types
event_id: dict of the two events for input to PreProcess()
"""
data_path = sample.data_path()
raw_fname = data_path + '/MEG/sample/sample_audvis_raw.fif'
trans_fname = data_path + '/MEG/sample/sample_audvis_raw-trans.fif'
src_fname = data_path + '/subjects/sample/bem/sample-oct-6-src.fif'
bem_fname = (data_path +
'/subjects/sample/bem/sample-5120-5120-5120-bem-sol.fif')
raw_single = mne.io.read_raw_fif(raw_fname, preload=True)
raw_single.set_eeg_reference(projection=True)
raw_single = raw_single.crop(0., 255.)
raw_single = raw_single.copy().pick_types(meg=False,
eeg=True,
eog=True,
stim=True)
#concatenate 4 raws together to make 1000 trials
raw = []
for i in range(batch):
raw.append(raw_single)
raw = concatenate_raws(raw)
epoch_duration = 1.
def data_fun(amp, freq):
"""Create function to create fake signal"""
def data_fun_inner(times):
"""Create fake signal with no noise"""
n_samp = len(times)
window = np.zeros(n_samp)
start, stop = [int(ii * float(n_samp) / 2) for ii in (0, 1)]
window[start:stop] = np.hamming(stop - start)
data = amp * 1e-9 * np.sin(2. * np.pi * freq * times)
data *= window
return data
return data_fun_inner
times = raw.times[:int(raw.info['sfreq'] * epoch_duration)]
src = read_source_spaces(src_fname)
stc_zero = simulate_sparse_stc(src,
n_dipoles=1,
times=times,
data_fun=data_fun(amp1, freq),
random_state=0)
stc_one = simulate_sparse_stc(src,
n_dipoles=1,
times=times,
data_fun=data_fun(amp2, freq),
random_state=0)
raw_sim_zero = simulate_raw(raw,
stc_zero,
trans_fname,
src,
bem_fname,
cov='simple',
blink=True,
n_jobs=1,
verbose=True)
raw_sim_one = simulate_raw(raw,
stc_one,
trans_fname,
src,
bem_fname,
cov='simple',
blink=True,
n_jobs=1,
verbose=True)
stim_pick = raw_sim_one.info['ch_names'].index('STI 014')
raw_sim_one._data[stim_pick][np.where(
raw_sim_one._data[stim_pick] == 1)] = 2
raw = concatenate_raws([raw_sim_zero, raw_sim_one])
event_id = {'CondZero': 1, 'CondOne': 2}
return raw, event_id
# House funcs here so PertInv is just scripting
import mne
from _make_perturbed_forward import make_pert_forward_solution, make_pert_forward_dipole
from mne.datasets import sample
import numpy as np # noqa
from mne.transforms import (_ensure_trans, transform_surface_to, apply_trans,
_get_trans, invert_transform, _print_coord_trans, _coord_frame_name,
Transform)
# local_data_path = 'C:\MEG\Local_mne_data'
data_path = sample.data_path() # local copy of mne sample data
raw_fname = data_path + '/MEG/sample/sample_audvis_raw.fif'
cov_fname = data_path + '/MEG/sample/sample_audvis-cov.fif'
subjects_dir = data_path + '/subjects'
subject = 'sample'
trans = data_path + '\MEG\sample/sample_audvis_raw-trans.fif'
mri_head_t, trans = _get_trans(trans)
head_mri_t = invert_transform(mri_head_t)
cov = mne.read_cov(cov_fname)
info = mne.io.read_info(raw_fname)
def fit_dips(min_rad, max_rad, nn, sphere, perts, sourcenorm):
testsources = dict(rr=[], nn=[])
nsources = max_rad - min_rad + 1
vertices = np.zeros((nsources, 1))
for i in range(min_rad, max_rad + 1):
ex, ey, ez = sourcenorm[0], sourcenorm[1], sourcenorm[2]
source = [.001*i*ex, .001*i*ey, .001*i*ez]
normal = [nn[0], nn[1], nn[2]]
testsources['rr'].append(source)
testsources['nn'].append(normal)
## does run with jupyter notebook but then # In[3]: # %load plotforward.py # going through https://martinos.org/mne/dev/auto_tutorials/plot_forward.html # conda activate mne # the sample data relies upon environment variable # MNE_DATASETS_SAMPLE_PATH -> # downloading sample data now import mne from mne.datasets import sample data_path = sample.data_path() # original version # MNE_DATASETS_SAMPLE_PATH = os.environ['MNE_DATASETS_SAMPLE_PATH'] #MNE_DATASETS_SAMPLE_PATH = '/usr/local/MNE-C/data' #data_path = MNE_DATA_ROOT + '/MNE-sample-data' # In[4]: # the raw file containing the channel location + types raw_fname = data_path + '/MEG/sample/sample_audvis_raw.fif' # The paths to Freesurfer reconstructions # subjects_dir = data_path + '/subjects' # subjects_dir = '/usr/local/freesurfer/stable5/subjects' freesurfer_path = '/usr/local/freesurfer/stable5' subjects_dir = data_path + '/subjects' # use the sample data as a source # subjects_dir = freesurfer_path + '/subjects'
the selected channels.
"""
print __doc__
# Authors: Alexandre Gramfort <*****@*****.**>
# Denis Engemann <*****@*****.**>
#
# License: BSD (3-clause)
import pylab as pl
import mne
from mne import fiff
from mne.datasets import sample
from mne.layouts import read_layout
data_path = sample.data_path('.')
###############################################################################
# Set parameters
raw_fname = data_path + '/MEG/sample/sample_audvis_filt-0-40_raw.fif'
event_fname = data_path + '/MEG/sample/sample_audvis_filt-0-40_raw-eve.fif'
event_id, tmin, tmax = 1, -0.2, 0.5
# Setup for reading the raw data
raw = fiff.Raw(raw_fname)
events = mne.read_events(event_fname)
# Set up pick list: EEG + MEG - bad channels (modify to your needs)
raw.info['bads'] = ['MEG 2443', 'EEG 053']
picks = fiff.pick_types(raw.info, meg='grad', eeg=False, stim=True, eog=True,
exclude=raw.info['bads'])
"""
# Authors: Alexandre Gramfort <*****@*****.**>
#
# License: BSD (3-clause)
print __doc__
import mne
from mne import fiff
from mne.datasets import sample
from mne.minimum_norm import read_inverse_operator, source_band_induced_power
###############################################################################
# Set parameters
data_path = sample.data_path('..')
raw_fname = data_path + '/MEG/sample/sample_audvis_raw.fif'
fname_inv = data_path + '/MEG/sample/sample_audvis-meg-oct-6-meg-inv.fif'
tmin, tmax, event_id = -0.2, 0.5, 1
# Setup for reading the raw data
raw = fiff.Raw(raw_fname)
events = mne.find_events(raw)
inverse_operator = read_inverse_operator(fname_inv)
include = []
exclude = raw.info['bads'] + ['MEG 2443', 'EEG 053'] # bads + 2 more
# picks MEG gradiometers
picks = fiff.pick_types(raw.info,
meg=True,
import os.path as op
import numpy as np
from numpy.testing import assert_array_almost_equal
from nose.tools import assert_true, assert_raises
from mne.datasets import sample
from mne import read_label, read_forward_solution
from mne.time_frequency import morlet
from mne.simulation import generate_sparse_stc, generate_evoked
from mne import read_cov
from mne.fiff import Raw, read_evokeds
from mne.fiff.pick import pick_types_evoked, pick_types_forward
data_path = sample.data_path(download=False)
fwd_fname = op.join(data_path, 'MEG', 'sample',
'sample_audvis-meg-eeg-oct-6-fwd.fif')
raw_fname = op.join(op.dirname(__file__), '..', '..', 'fiff', 'tests',
'data', 'test_raw.fif')
ave_fname = op.join(op.dirname(__file__), '..', '..', 'fiff', 'tests',
'data', 'test-ave.fif')
cov_fname = op.join(op.dirname(__file__), '..', '..', 'fiff', 'tests',
'data', 'test-cov.fif')
@sample.requires_sample_data
def test_simulate_evoked():
""" Test simulation of evoked data """
raw = Raw(raw_fname)
from ...externals.six import string_types
import os
import numpy as np
from numpy.testing import assert_allclose
from nose.tools import (assert_equal, assert_almost_equal, assert_false,
assert_raises, assert_true)
import warnings
import mne
from mne.datasets import sample
from mne.io.kit.tests import data_dir as kit_data_dir
from mne.utils import _TempDir, requires_traits, requires_mne_fs_in_env
data_path = sample.data_path(download=False)
raw_path = os.path.join(data_path, 'MEG', 'sample', 'sample_audvis_raw.fif')
kit_raw_path = os.path.join(kit_data_dir, 'test_bin_raw.fif')
subjects_dir = os.path.join(data_path, 'subjects')
warnings.simplefilter('always')
tempdir = _TempDir()
trans_dst = os.path.join(tempdir, 'test-trans.fif')
@sample.requires_sample_data
@requires_traits
def test_coreg_model():
"""Test CoregModel"""
from mne.gui._coreg_gui import CoregModel
""" # Author: Roman Goj <*****@*****.**> # # License: BSD (3-clause) import mne from mne import compute_covariance from mne.io import Raw from mne.datasets import sample from mne.event import make_fixed_length_events from mne.beamformer import tf_lcmv from mne.viz import plot_source_spectrogram print(__doc__) data_path = sample.data_path() raw_fname = data_path + '/MEG/sample/sample_audvis_raw.fif' noise_fname = data_path + '/MEG/sample/ernoise_raw.fif' event_fname = data_path + '/MEG/sample/sample_audvis_raw-eve.fif' fname_fwd = data_path + '/MEG/sample/sample_audvis-meg-eeg-oct-6-fwd.fif' subjects_dir = data_path + '/subjects' label_name = 'Aud-lh' fname_label = data_path + '/MEG/sample/labels/%s.label' % label_name ############################################################################### # Read raw data, preload to allow filtering raw = Raw(raw_fname, preload=True) raw.info['bads'] = ['MEG 2443'] # 1 bad MEG channel # Pick a selection of magnetometer channels. A subset of all channels was used # to speed up the example. For a solution based on all MEG channels use
xmin=-test_time_start / (test_time_end - test_time_start),
xmax=(duration - test_time_start) /
(test_time_end - test_time_start))
return pl
def add_alpha(p_cols, alphas):
cols = [to_rgb(c) for c in p_cols]
return [(c[0], c[1], c[2], a) for c, a in zip(cols, alphas[-len(p_cols):])]
###############################################################################
# Load EEG data
# -------------
raw_fname = os.path.join(sample.data_path(), 'MEG', 'sample',
'sample_audvis_filt-0-40_raw.fif')
raw = read_raw_fif(raw_fname, preload=True, verbose=False)
sfreq = int(raw.info['sfreq']) # 150 Hz
###############################################################################
# Offline processing of EEG data
# ------------------------------
# Apply common average reference on EEG channels
raw.pick_types(meg=False, eeg=True).apply_proj()
# Select two EEG channels for the example, preferably without artifact at the
# beginning, to have a reliable calibration
ch_names = ['EEG 010', 'EEG 015']
