def test_icoherence():
data = np.load("../examples/data/eeg_32chans_10secs.npy")
csdparams = {'NFFT': 256, 'noverlap': 256 / 2.0}
icoh = icoherence(data, [1.0, 4.0], 128.0, **csdparams)
expected = np.load("data/test_icoherence.npy")
np.testing.assert_array_equal(icoh, expected)
def _get_fc_graph(x, band_freq, sampling_freq, fc_measure='corr',
link_cutoff=0., band_freq_hi=(20., 45.), nfft=128,
n_overlap=64):
"""
Build a functional connectivity network from the given data stream.
:param x: numpy array of shape (n_channels, n_samples);
:param band_freq: list with two elements, the band in which to estimate FC;
:param sampling_freq: float, sampling frequency of the stream;
:param fc_measure: functional connectivity measure to use;
:param link_cutoff: links with absolute FC measure below this value will be
removed;
:param band_freq_hi: high band used to estimate FC when using 'aec';
:param nfft: TODO, affects 'wpli' and 'dwpli';
:param n_overlap: TODO, affects 'wpli' and 'dwpli';
:return: FC graph in numpy format (note that node features are all ones).
"""
if fc_measure == 'iplv':
_, ef = fc.iplv(x, band_freq, sampling_freq)
elif fc_measure == 'icoh':
ef = fc.icoherence(x, band_freq, sampling_freq)
elif fc_measure == 'corr':
ef = fc.corr(x, band_freq, sampling_freq)
elif fc_measure == 'aec':
ef = fc.aec(x, band_freq, band_freq_hi, sampling_freq)
elif fc_measure == 'wpli':
csdparams = {'NFFT': nfft, 'noverlap': n_overlap}
ef = fc.wpli(x, band_freq, sampling_freq, **csdparams)
ef = np.abs(ef)
elif fc_measure == 'dwpli':
csdparams = {'NFFT': nfft, 'noverlap': n_overlap}
ef = fc.dwpli(x, band_freq, sampling_freq, **csdparams)
ef = np.abs(ef)
elif fc_measure == 'dpli':
ef = fc.dpli(x, band_freq, sampling_freq)
else:
raise ValueError('Invalid fc_measure')
# Set the main diagonal to zero (no self-loops)
np.fill_diagonal(ef, 0.0)
# Compute adjacency matrix by rounding to 0 and 1 based on the cutoff
adj = ef.copy()
if link_cutoff != 0:
adj[np.abs(adj) >= link_cutoff] = 1
adj[np.abs(adj) < link_cutoff] = 0
else:
adj[...] = 1
# Dummy node features
# TODO: proper nf
nf = np.ones((ef.shape[0], 1))
# Edge features
ef = ef[..., None]
return adj, nf, ef
def _get_fc_graph(x,
fc_measure,
nf_mode,
band_freq=None,
band_freq_hi=None,
sampling_freq=None,
nfft=None,
n_overlap=None):
if fc_measure == 'iplv':
_, ef = fc.iplv(x, band_freq, sampling_freq)
elif fc_measure == 'icoh':
ef = fc.icoherence(x, band_freq, sampling_freq)
elif fc_measure == 'corr':
ef = fc.corr(x, band_freq, sampling_freq)
elif fc_measure == 'aec':
ef = fc.aec(x, band_freq, band_freq_hi, sampling_freq)
elif fc_measure == 'wpli':
csdparams = {'NFFT': nfft, 'noverlap': n_overlap}
ef = fc.wpli(x, band_freq, sampling_freq, **csdparams)
elif fc_measure == 'dwpli':
csdparams = {'NFFT': nfft, 'noverlap': n_overlap}
ef = fc.dwpli(x, band_freq, sampling_freq, **csdparams)
elif fc_measure == 'dpli':
ef = fc.dpli(x, band_freq, sampling_freq)
else:
raise ValueError('Invalid fc_measure ' + fc_measure)
# Dummy node features
if nf_mode == 'full':
nf = x.copy()
elif nf_mode == 'mean':
nf = np.mean(x, -1)
elif nf_mode == 'energy':
nf = np.sum(x**2, -1)
elif nf_mode == 'power':
nf = np.sum(x**2, -1) / x.shape[-1]
elif nf_mode == 'ones':
nf = np.ones((ef.shape[0], 1))
else:
raise ValueError('Invalid nf_mode' + nf_mode)
return nf, ef
def _get_fc_graph(x,
band_freq,
sampling_freq,
fc_measure='corr',
link_cutoff=0.,
band_freq_hi=(20., 45.),
nfft=128,
n_overlap=64,
nf_mode='mean',
self_loops=True):
"""
Build a functional connectivity network from the given data stream.
:param x: numpy array of shape (n_channels, n_samples);
:param band_freq: list with two elements, the band in which to estimate FC;
:param sampling_freq: float, sampling frequency of the stream;
:param fc_measure: functional connectivity measure to use. Possible measures
are: iplv, icoh, corr, aec, wpli, dwpli, dpli (see documentation of
Dyfunconn);
:param link_cutoff: links with absolute FC measure below this value will be
removed;
:param band_freq_hi: high band used to estimate FC when using 'aec';
:param nfft: TODO, affects 'wpli' and 'dwpli';
:param n_overlap: TODO, affects 'wpli' and 'dwpli';
:param nf_mode: how to compute node features. Possible modes are: full,
mean, energy, ones.
:param self_loops: add self loops to FC network;
:return: FC graph in numpy format (note that node features are all ones).
"""
if fc_measure == 'iplv':
_, ef = fc.iplv(x, band_freq, sampling_freq)
elif fc_measure == 'icoh':
ef = fc.icoherence(x, band_freq, sampling_freq)
elif fc_measure == 'corr':
ef = fc.corr(x, band_freq, sampling_freq)
elif fc_measure == 'aec':
ef = fc.aec(x, band_freq, band_freq_hi, sampling_freq)
elif fc_measure == 'wpli':
csdparams = {'NFFT': nfft, 'noverlap': n_overlap}
ef = fc.wpli(x, band_freq, sampling_freq, **csdparams)
ef = np.abs(ef)
elif fc_measure == 'dwpli':
csdparams = {'NFFT': nfft, 'noverlap': n_overlap}
ef = fc.dwpli(x, band_freq, sampling_freq, **csdparams)
ef = np.abs(ef)
elif fc_measure == 'dpli':
ef = fc.dpli(x, band_freq, sampling_freq)
else:
raise ValueError('Invalid fc_measure {}'.format(fc_measure))
# Compute adjacency matrix by rounding to 0 and 1 based on the cutoff
adj = ef.copy()
if link_cutoff != 0:
adj[np.abs(adj) >= link_cutoff] = 1
adj[np.abs(adj) < link_cutoff] = 0
else:
adj[...] = 1
if self_loops:
# Set the main diagonal to zero
np.fill_diagonal(adj, 1.0)
else:
np.fill_diagonal(ef, 0.0)
np.fill_diagonal(adj, 1.0)
# Dummy node features
if nf_mode == 'full':
nf = x.copy()
elif nf_mode == 'mean':
nf = np.mean(x, -1)
elif nf_mode == 'energy':
nf = np.sum(x**2, -1)
elif nf_mode == 'ones':
nf = np.ones((ef.shape[0], 1))
else:
raise ValueError('Invalid nf_mode {}'.format(nf_mode))
# Edge features
ef = ef[..., None]
return adj, nf, ef
# -*- coding: utf-8 -*-
# Author: Avraam Marimpis <*****@*****.**>
import numpy as np
np.set_printoptions(precision=3, linewidth=256)
from dyfunconn.fc import coherence, icoherence
if __name__ == "__main__":
data = np.load(
"/home/makism/Github/dyfunconn/examples/data/eeg_32chans_10secs.npy")
data = data[0:5, :]
csdparams = {'NFFT': 256, 'noverlap': 256 / 2.0}
coh = coherence(data, [1.0, 4.0], 128.0, **csdparams)
icoh = icoherence(data, [1.0, 4.0], 128.0)
print "Coherence: \n", coh
print "Imagenary Coherence: \n", icoh