def get_PDC(var_coef): #the var_coef has a shape of 16 x 16*lag order
'''
Takes in the concatenated 16x80 VAR coefficient array and
apply the pdc function from SCoT library with a sampling rate of 128/2hz.
@return: 5x16x16 array, where each of the 5 array represents a frequency band,
eg: Alpha, Beta, Gamma, Theta, Delta
'''
no_of_bands = 5
patient_pdc = []
for x in range(no_of_bands):
PDC_output = [None] * 16
for i in range(len(PDC_output)):
PDC_output[i] = [None] * 16
patient_pdc.append(PDC_output)
c = cn.connectivity(['PDC'], var_coef, nfft=64)
patient = c['PDC']
for row in range(16):
for column in range(16):
bandwidths = [(0, 4), (4, 8), (8, 14), (14, 31), (31, 64)]
for b in range(
len(bandwidths)): #get the average value of the bandwidths
lower_band = bandwidths[b][0]
upper_band = bandwidths[b][1]
patient_pdc[b][row][column] = average(
patient[row][column][lower_band:upper_band])
return patient_pdc #returns 5x16x16
def testFunction(self):
# Three sources: a <- b <- c
# simply test if connectivity measures are 0 where expected
b0 = np.array([[0, 0.9, 0], [0, 0, 0.9], [0, 0, 0]])
identity = np.eye(3)
nfft = 5
measures = ['A', 'H', 'COH', 'DTF', 'PDC']
C = connectivity.Connectivity(b=b0, c=identity, nfft=nfft)
c = connectivity.connectivity(measures, b=b0, c=identity, nfft=nfft)
for m in measures:
self.assertTrue(np.all(c[m] == getattr(C, m)()))
def testFunction(self):
# Three sources: a <- b <-c
# simply test if connectivity measures are 0 where expected to be so
b0 = np.array([[0, 0.9, 0], [0, 0, 0.9], [0, 0, 0]])
identity = np.eye(3)
nfft = 5
measures = ['A', 'H', 'COH', 'DTF', 'PDC']
C = connectivity.Connectivity(b=b0, c=identity, nfft=nfft)
c = connectivity.connectivity(measures, b=b0, c=identity, nfft=nfft)
for m in measures:
self.assertTrue(np.all(c[m] == getattr(C, m)()))
print('computing GPDC connectivity...')
mvar = scot.var.VAR(morder)
# result : array, shape (`repeats`, n_channels, n_channels, nfft)
surr = scs.surrogate_connectivity(gcmethod,
label_ts,
mvar,
nfft=nfft,
n_jobs=njobs,
repeats=n_surr)
mvar.fit(label_ts)
# mvar coefficients (n_channels, n_channels * model_order)
# mvar covariance matrix (n_channels, n_channels)
# result : array, shape (n_channels, n_channels, `nfft`)
cau = connectivity(gcmethod, mvar.coef, mvar.rescov, nfft=nfft)
# get the band averaged, thresholded connectivity matrix
caus, max_cons, max_surrs = prepare_causality_matrix(
cau,
surr,
freqs,
nfft=nfft,
sfreq=epochs.info['sfreq'],
surr_thresh=surr_thresh)
print('Shape of causality matrix: ', caus.shape)
# get label names used for plotting
labels_fname = get_jumeg_path() + '/examples/label_names.list'
yaml_fname = get_jumeg_path() + '/examples/aparc_cortex_based_grouping.yaml'
def causal_analysis(fn_norm, method='GPDC', morder=None, repeats=1000,
msave=True, per=99.99,
sfreq=678,
freqs=[(4, 8), (8, 12), (12, 18), (18, 30), (30, 40)]):
'''
Calculate causality matrices of real data and surrogates. And calculate
the significant causal matrix for each frequency band.
Parameters
----------
fnnorm: string
The file name of model order estimation.
morder: int
The optimized model order.
method: string
causality measures.
repeats: int
Shuffling times for surrogates.
msave: bool
Save the causal matrix of the whole frequency domain or not.
per: float or int
Percentile of the surrogates.
sfreq: float
The sampling rate.
freqs: list
The list of interest frequency bands.
'''
import scot.connectivity_statistics as scs
from scot.connectivity import connectivity
import scot
path_list = get_files_from_list(fn_norm)
# loop across all filenames
for fnnorm in path_list:
cau_path = os.path.split(fnnorm)[0]
name = os.path.basename(fnnorm)
condition = name.split('_')[0]
sig_path = cau_path + '/sig_cau_%d/' % morder
set_directory(sig_path)
fncau = fnnorm[:fnnorm.rfind('.npy')] + ',morder%d,cau.npy' % morder
fnsurr = fnnorm[:fnnorm.rfind('.npy')] + ',morder%d,surrcau.npy' % morder
X = np.load(fnnorm)
X = X.transpose(2, 0, 1)
mvar = scot.var.VAR(morder)
surr = scs.surrogate_connectivity(method, X, mvar,
repeats=repeats)
mvar.fit(X)
cau = connectivity(method, mvar.coef, mvar.rescov)
if msave:
np.save(fncau, cau)
np.save(fnsurr, surr)
nfft = cau.shape[-1]
delta_F = sfreq / float(2 * nfft)
sig_freqs = []
nfreq = len(freqs)
#surr_bands = []
#cau_bands = []
for ifreq in range(nfreq):
print 'Frequency index used..', ifreq
fmin, fmax = int(freqs[ifreq][0] / delta_F), int(freqs[ifreq][1] /
delta_F)
con_band = np.mean(cau[:, :, fmin:fmax + 1], axis=-1)
np.fill_diagonal(con_band, 0)
surr_band = np.mean(surr[:, :, :, fmin:fmax + 1], axis=-1)
r, s, _ = surr_band.shape
for i in xrange(r):
ts = surr_band[i]
np.fill_diagonal(ts, 0)
#surr_bands.append(surr_band)
#cau_bands.append(con_band)
con_b = con_band.flatten()
con_b = con_b[con_b > 0]
surr_b = surr_band.reshape(r, s * s)
surr_b = surr_b[surr_b > 0]
thr = np.percentile(surr_band, per)
print 'max surrogates %.4f' % thr
con_band[con_band < thr] = 0
con_band[con_band >= thr] = 1
histout = sig_path + '%s,%d-%d,distribution.png'\
% (condition, freqs[ifreq][0], freqs[ifreq][1])
throut = sig_path + '%s,%d-%d,threshold.png'\
% (condition, freqs[ifreq][0], freqs[ifreq][1])
_plot_hist(con_b, surr_b, histout)
# _plot_thr(con_b, thr, surr_band.max(), alpha, throut)
_plot_thr(con_b, thr, surr_band.max(), per, throut)
# con_band[con_band < z_thre] = 0
# con_band[con_band >= z_thre] = 1
sig_freqs.append(con_band)
sig_freqs = np.array(sig_freqs)
print 'Saving computed arrays..'
np.save(sig_path + '%s_sig_con_band.npy' % condition, sig_freqs)
#cau_bands = np.array(cau_bands)
#np.save(fncau, cau_bands)
#surr_bands = np.array(surr_bands)
#np.save(fnsurr, surr_bands)
return