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# -*- coding: utf-8 -*-
"""
.. _ex-sim-source:
==============================
Generate simulated source data
==============================
This example illustrates how to use the :class:`mne.simulation.SourceSimulator`
class to generate source estimates and raw data. It is meant to be a brief
introduction and only highlights the simplest use case.
"""
# Author: Kostiantyn Maksymenko <kostiantyn.maksymenko@gmail.com>
# Samuel Deslauriers-Gauthier <sam.deslauriers@gmail.com>
#
# License: BSD-3-Clause
# %%
import numpy as np
import mne
from mne.datasets import sample
print(__doc__)
# %%
# For this example, we will be using the information of the sample subject.
# This will download the data if it not already on your machine. We also set
# the subjects directory so we don't need to give it to functions.
data_path = sample.data_path()
subjects_dir = data_path / 'subjects'
subject = 'sample'
# %%
# First, we get an info structure from the test subject.
evoked_fname = data_path / 'MEG' / subject / 'sample_audvis-ave.fif'
info = mne.io.read_info(evoked_fname)
tstep = 1. / info['sfreq']
# %%
# To simulate sources, we also need a source space. It can be obtained from the
# forward solution of the sample subject.
fwd_fname = data_path / 'MEG' / subject / 'sample_audvis-meg-eeg-oct-6-fwd.fif'
fwd = mne.read_forward_solution(fwd_fname)
src = fwd['src']
# %%
# To select a region to activate, we use the caudal middle frontal to grow
# a region of interest.
selected_label = mne.read_labels_from_annot(
subject, regexp='caudalmiddlefrontal-lh', subjects_dir=subjects_dir)[0]
location = 'center' # Use the center of the region as a seed.
extent = 10. # Extent in mm of the region.
label = mne.label.select_sources(
subject, selected_label, location=location, extent=extent,
subjects_dir=subjects_dir)
# %%
# Define the time course of the activity for each source of the region to
# activate. Here we use a sine wave at 18 Hz with a peak amplitude
# of 10 nAm.
source_time_series = np.sin(2. * np.pi * 18. * np.arange(100) * tstep) * 10e-9
# %%
# Define when the activity occurs using events. The first column is the sample
# of the event, the second is not used, and the third is the event id. Here the
# events occur every 200 samples.
n_events = 50
events = np.zeros((n_events, 3), int)
events[:, 0] = 100 + 200 * np.arange(n_events) # Events sample.
events[:, 2] = 1 # All events have the sample id.
# %%
# Create simulated source activity. Here we use a SourceSimulator whose
# add_data method is key. It specified where (label), what
# (source_time_series), and when (events) an event type will occur.
source_simulator = mne.simulation.SourceSimulator(src, tstep=tstep)
source_simulator.add_data(label, source_time_series, events)
# %%
# Project the source time series to sensor space and add some noise. The source
# simulator can be given directly to the simulate_raw function.
raw = mne.simulation.simulate_raw(info, source_simulator, forward=fwd)
cov = mne.make_ad_hoc_cov(raw.info)
mne.simulation.add_noise(raw, cov, iir_filter=[0.2, -0.2, 0.04])
raw.plot()
# %%
# Plot evoked data to get another view of the simulated raw data.
events = mne.find_events(raw)
epochs = mne.Epochs(raw, events, 1, tmin=-0.05, tmax=0.2)
evoked = epochs.average()
evoked.plot()
|
