def test_ward_spatial_scikit_with_mask(self):
from pyhrf.parcellation import parcellation_dist, parcellation_ward_spatial
from pyhrf.graph import graph_from_lattice, kerMask2D_4n
from pyhrf.ndarray import expand_array_in_mask
if debug:
print 'data:'
print self.p1
print ''
mask = self.p1 != 0
graph = graph_from_lattice(mask, kerMask2D_4n)
X = self.p1[np.where(mask)].reshape(-1,1)
labels = parcellation_ward_spatial(X, n_clusters=4, graph=graph)
labels = expand_array_in_mask(labels, mask)
# print 'labels:'
# print labels
#+1 because parcellation_dist sees 0 as background:
dist = parcellation_dist(self.p1+1, labels+1)[0]
self.assertEqual(dist, 0)
def create_3Dlabels_Potts(condition_defs, beta, dims, mask):
labels = []
graph = graph_from_lattice(mask, kerMask=kerMask3D_6n, toroidal=True)
for c in condition_defs:
tmp = genPotts(graph, beta, 2)
tmp = np.reshape(tmp, dims)
labels.append(tmp)
return np.array(labels)
def create_3Dlabels_Potts(condition_defs, beta, dims, mask):
labels = []
graph = graph_from_lattice(mask, kerMask=kerMask3D_6n, toroidal=True)
for c in condition_defs:
tmp = genPotts(graph, beta, 2)
tmp = np.reshape(tmp, dims)
labels.append(tmp)
return np.array(labels)
def test_split_parcel(self):
shape = (5, 5, 5)
mask = np.zeros(shape, dtype=int)
mask[1:-1, 1:-1, 1:-1] = 1
mask_labels = mask[np.where(mask)]
g = graph_from_lattice(mask, kerMask3D_6n)
nparcels = 2
pm.split_parcel(mask_labels, {1: g}, 1, nparcels, inplace=True,
verbosity=0)
def create_labels_Potts(condition_defs, beta, nb_voxels):
labels = []
nb_voxels = nb_voxels**.5 # assume square shape
shape = (nb_voxels, nb_voxels)
mask = np.ones(shape, dtype=int)
graph = graph_from_lattice(mask, kerMask=kerMask2D_4n, toroidal=True)
shape = (1, nb_voxels, nb_voxels)
for c in condition_defs:
tmp = genPotts(graph, beta, 2)
tmp = np.reshape(tmp, shape)
labels.append(tmp)
return np.array(labels)
def create_labels_Potts(condition_defs, beta, nb_voxels):
labels = []
nb_voxels = nb_voxels ** 0.5 # assume square shape
shape = (nb_voxels, nb_voxels)
mask = np.ones(shape, dtype=int)
graph = graph_from_lattice(mask, kerMask=kerMask2D_4n, toroidal=True)
shape = (1, nb_voxels, nb_voxels)
for c in condition_defs:
tmp = genPotts(graph, beta, 2)
tmp = np.reshape(tmp, shape)
labels.append(tmp)
return np.array(labels)
def test_ward_spatial_scikit(self):
from pyhrf.parcellation import parcellation_dist, \
parcellation_ward_spatial
from pyhrf.graph import graph_from_lattice, kerMask2D_4n
X = np.reshape(self.p1, (-1, 1))
graph = graph_from_lattice(np.ones(self.p1.shape), kerMask2D_4n)
labels = parcellation_ward_spatial(X, n_clusters=5, graph=graph)
labels = np.reshape(labels, self.p1.shape)
# +1 because parcellation_dist sees 0 as background
dist = parcellation_dist(self.p1 + 1, labels + 1)[0]
self.assertEqual(dist, 0)
def parcellate_balanced_vol(mask, nb_parcels):
"""
Performs a balanced partitioning on the input mask using a balloon patroling
algorithm [Eurol 2009]. Values with 0 are discarded position in the mask.
Args:
- mask (numpy.ndarray): binary 3D array of valid position to parcellate
- nb_parcels (int): the required number of parcels
Return:
- the parcellation (numpy.ndarray): a 3D array of integers
"""
parcellation = np.zeros(mask.shape, dtype=int)
nvox = (mask != 0).sum()
# Iterate over connected components in the input mask
for cc_mask in mg.split_mask_into_cc_iter(mask != 0):
logger.info('Treating a connected component (CC) of %d positions',
cc_mask.sum())
g = mg.graph_from_lattice(cc_mask)
size_cc = cc_mask.sum()
# compute the required number of parcels within the current CC:
cc_np = max(int(np.round(nb_parcels * size_cc / (nvox * 1.))), 1)
logger.info('Split (CC) into %d parcels', cc_np)
cc_labels = np.ones(cc_mask.sum(), dtype=int)
if cc_np > 1:
split_parcel(cc_labels, {1: g},
1,
cc_np,
inplace=True,
verbosity=2,
balance_tolerance='draft')
else: # only one parcel expected, CC must be too small to be splited
cc_labels[:] = 1
logger.info('Split done!')
# accumulate parcellation result
maxp = parcellation.max()
parcellation += expand_array_in_mask(cc_labels + maxp, cc_mask > 0)
return parcellation
def test_ward_spatial_scikit_with_mask(self):
from pyhrf.parcellation import parcellation_dist, parcellation_ward_spatial
from pyhrf.graph import graph_from_lattice, kerMask2D_4n
from pyhrf.ndarray import expand_array_in_mask
if debug:
print 'data:'
print self.p1
print ''
mask = self.p1 != 0
graph = graph_from_lattice(mask, kerMask2D_4n)
X = self.p1[np.where(mask)].reshape(-1, 1)
labels = parcellation_ward_spatial(X, n_clusters=4, graph=graph)
labels = expand_array_in_mask(labels, mask)
#+1 because parcellation_dist sees 0 as background:
dist = parcellation_dist(self.p1 + 1, labels + 1)[0]
self.assertEqual(dist, 0)
def parcellate_balanced_vol(mask, nb_parcels):
"""
Performs a balanced partitioning on the input mask using a balloon patroling
algorithm [Eurol 2009]. Values with 0 are discarded position in the mask.
Args:
- mask (numpy.ndarray): binary 3D array of valid position to parcellate
- nb_parcels (int): the required number of parcels
Return:
- the parcellation (numpy.ndarray): a 3D array of integers
"""
parcellation = np.zeros(mask.shape, dtype=int)
nvox = (mask != 0).sum()
# Iterate over connected components in the input mask
for cc_mask in mg.split_mask_into_cc_iter(mask != 0):
pyhrf.verbose(2, 'Treating a connected component (CC) of %d positions' \
%cc_mask.sum())
g = mg.graph_from_lattice(cc_mask)
size_cc = cc_mask.sum()
# compute the required number of parcels within the current CC:
cc_np = max(int(np.round(nb_parcels * size_cc / (nvox*1.))), 1)
pyhrf.verbose(2, 'Split (CC) into %d parcels' %cc_np)
cc_labels = np.ones(cc_mask.sum(), dtype=int)
if cc_np > 1:
split_parcel(cc_labels, {1:g}, 1, cc_np, inplace=True,
verbosity=2, balance_tolerance='draft')
else: #only one parcel expected, CC must be too small to be splited
cc_labels[:] = 1
pyhrf.verbose(2, 'Split done!')
# accumulate parcellation result
maxp = parcellation.max()
parcellation += expand_array_in_mask(cc_labels + maxp, cc_mask>0)
return parcellation
def trait(self):
areas = ['ra']
labelFields = {}
cNames = ['inactiv', 'activ']
height = self.data.getheight()
width = self.data.getwidth()
spConf = RegularLatticeMapping((height, width, 1))
graph = graph_from_lattice(ones((height, width, 1), dtype=int))
Y = self.data.post_lecture()
J = Y.shape[0]
l = int(sqrt(J))
FlagZ = 1
q_Z0 = zeros((self.scen.M, self.scen.K, J), dtype=float64)
if not FlagZ:
q_Z0 = q_Z
FlagH = 1
TT, m_h = getCanoHRF(self.scen.Thrf - self.scen.dt, self.scen.dt)
hrf0 = hrf0 = array(m_h).astype(float64)
Sigma_H0 = eye(hrf0.shape[0])
if not FlagH:
hrf0 = h_H
Sigma_H0 = Sigma_H
return Y, graph, hrf0, Sigma_H0, q_Z0, width, height, FlagZ, FlagH
def gen_hrf(self,
nItMin=30,
nItMax=30,
estimateSigmaH=0,
estimateBeta=0,
Onsets={'nuages': array([0])},
scale=1,
):
"""
allow to generate figures
:param nItMin: Minimum number of iteration
:type nItMin: int
:param nItMax: Maximum number of iteration
:type nItMax: int
:param estimateSigmaH: estimation of sigmaH
:type estimateSigmaH: int
:param estimateBeta: estimation of Beta
:type estimateBeta: int
:param scale: scale factor
:type scale: int
"""
# estimationSigmah = 0 sans estimation de sigmh , estimationSigmah=1 estimation de sigmah
# estimateBeta = 0 sans estimation de beta , estimateBeta=1 estimation de beta
# construction Onsets
# Onsets = {'nuages' : array([1,6,7])}
areas = ['ra']
labelFields = {}
cNames = ['inactiv', 'activ']
spConf = RegularLatticeMapping((self.height, self.width, 1))
graph = graph_from_lattice(
ones((self.height, self.width, 1), dtype=int))
J = self.Y.shape[0]
l = int(sqrt(J))
# NbIter, nrls_mean, hrf_mean, hrf_covar, labels_proba, noise_var, \
# nrls_class_mean, nrls_class_var, beta, drift_coeffs, drift,CONTRAST, CONTRASTVAR, \
# nrls_criteria, hrf_criteria,labels_criteria, nrls_hrf_criteria, compute_time,compute_time_mean, \
# nrls_covar, stimulus_induced_signal, density_ratio,density_ratio_cano, density_ratio_diff, density_ratio_prod, \
# ppm_a_nrl,ppm_g_nrl, ppm_a_contrasts, ppm_g_contrasts, variation_coeff = \
# jde_vem_bold_fast_python(pl,graph, Y, Onsets, Thrf, K,TR, beta, dt, estimateSigmaH, sigmaH,nItMax,nItMin,estimateBeta)
# FlagZ = 1
# q_Z = zeros((M,K,J),dtype=float64)
# NbIter,m_A, m_H, q_Z, sigma_epsilone, mu_k, sigma_k,Beta,L,PL,CONTRAST, CONTRASTVAR,cA,cH,cZ,cAH,cTime,cTimeMean,Sigma_A,XX = \
# Main_vbjde_Extension_TD(height,width,q_Z,FlagZ,pl,graph,Y,Onsets,Thrf,K,TR,beta,dt,scale,estimateSigmaH,sigmaH,nItMax,nItMin,estimateBeta)
# facteur = 1.0
# Y,height,width,bande = lecture_data(dataDir,2660,2730,2600,2680,bande,start,facteur,end)
# FlagZ = 0
# NbIter_f,m_A_f, m_H_f, q_Z_f, sigma_epsilone_f, mu_k_f, sigma_k_f,Beta_f,L_f,PL,CONTRAST, CONTRASTVAR,cA,cH,cZ,cAH,cTime,cTimeMean,Sigma_A,XX = \
# Main_vbjde_Extension_TD(height,width,q_Z,FlagZ,pl,graph,Y,Onsets,Thrf,K,TR,beta,dt,scale,estimateSigmaH,sigmaH,nItMax,nItMin,estimateBeta)
# ytild=PL
# matshow(reshape(m_A_f[:,0],(height,width)) - reshape(m_A[:,0],(height,width)),cmap=get_cmap('gray'))
# colorbar()
FlagZ = 1
q_Z0 = zeros((self.M, self.K, J), dtype=float64)
if not FlagZ:
q_Z0 = q_Z
FlagH = 1
TT, m_h = getCanoHRF(self.Thrf - self.dt, self.dt)
hrf0 = array(m_h).astype(float64)
Sigma_H0 = eye(hrf0.shape[0])
if not FlagH:
hrf0 = h_H
Sigma_H0 = Sigma_H
self.m_A, self.m_H, self.q_Z, sigma_epsilone, mu_k, sigma_k, Beta, PL, Sigma_A, XX, Sigma_H = \
Main_vbjde_Extension_TD(
FlagH, hrf0, Sigma_H0, self.height, self.width, q_Z0, FlagZ,
self.pl, graph, self.Y, Onsets, self.Thrf, self.K, self.TR,
self.beta, self.dt, scale,
estimateSigmaH, self.sigmaH, nItMin, estimateBeta)
fgs = self.ConditionalNRLHist(self.m_A, self.q_Z)
MMin = -1.0 # Y.min()
MMax = 1.0 # Y.max()
pas = (MMax - MMin) / 100
xx = arange(MMin, MMax, pas)
g0 = self.gaussian(xx, mu_k[0][0], sigma_k[0][0])
g1 = self.gaussian(xx, mu_k[0][1], sigma_k[0][1])
#
# figure(77)
# plot(xx,g0*pas, label='m=%.2f;v=%.2f' % (mu_k[0][0],sigma_k[0][0]))
# hold(True)
# plot(xx,g1*pas, label='m=%.2f;v=%.2f' % (mu_k[0][1],sigma_k[0][1]))
# legend()
# savgarde des PLs #
# if ((pl != 0 )and (savepl !=0 )) :
# for i in range (0,ytild.shape[0]) :
# figure(nf)
# PL_img =reshape(ytild[i,:],(height,width))
# matshow(PL_img,cmap=get_cmap('gray'))
# colorbar()
# nf=nf+1
# savefig(outDir+'PL'+str(i)+'bande=' +str(bande)+'.png')
# savefig(outDir+'PL'+str(i)+'bande=' +str(bande)+'beta='+str(beta)+'sigma='+str(sigmaH)+'pl='+str(pl)+'dt='+str(dt)+'thrf'+str(Thrf)+'.png')
#
# figure Hrf #######
fgs.insert(0, figure((self.nf + 1) * 123))
title("Fonction de reponse", fontsize='xx-large')
figtext(0.2, 0.04,
'bande = ' + str(self.bande) +
' beta =' + str(self.beta) +
' sigma = ' + str(self.sigmaH) +
' pl = ' + str(self.pl) +
' dt = ' + str(self.dt) +
' thrf = ' + str(self.Thrf),
fontsize='x-large')
plot(self.m_H)
if self.shower == 1:
show()
return fgs
def gen_hrf(
self,
nItMin=30,
nItMax=30,
estimateSigmaH=0,
estimateBeta=0,
Onsets={'nuages': array([0])},
scale=1,
):
"""
allow to generate figures
:param nItMin: Minimum number of iteration
:type nItMin: int
:param nItMax: Maximum number of iteration
:type nItMax: int
:param estimateSigmaH: estimation of sigmaH
:type estimateSigmaH: int
:param estimateBeta: estimation of Beta
:type estimateBeta: int
:param scale: scale factor
:type scale: int
"""
# estimationSigmah = 0 sans estimation de sigmh , estimationSigmah=1 estimation de sigmah
# estimateBeta = 0 sans estimation de beta , estimateBeta=1 estimation de beta
# construction Onsets
# Onsets = {'nuages' : array([1,6,7])}
areas = ['ra']
labelFields = {}
cNames = ['inactiv', 'activ']
spConf = RegularLatticeMapping((self.height, self.width, 1))
graph = graph_from_lattice(
ones((self.height, self.width, 1), dtype=int))
J = self.Y.shape[0]
l = int(sqrt(J))
# NbIter, nrls_mean, hrf_mean, hrf_covar, labels_proba, noise_var, \
# nrls_class_mean, nrls_class_var, beta, drift_coeffs, drift,CONTRAST, CONTRASTVAR, \
# nrls_criteria, hrf_criteria,labels_criteria, nrls_hrf_criteria, compute_time,compute_time_mean, \
# nrls_covar, stimulus_induced_signal, density_ratio,density_ratio_cano, density_ratio_diff, density_ratio_prod, \
# ppm_a_nrl,ppm_g_nrl, ppm_a_contrasts, ppm_g_contrasts, variation_coeff = \
# jde_vem_bold_fast_python(pl,graph, Y, Onsets, Thrf, K,TR, beta, dt, estimateSigmaH, sigmaH,nItMax,nItMin,estimateBeta)
# FlagZ = 1
# q_Z = zeros((M,K,J),dtype=float64)
# NbIter,m_A, m_H, q_Z, sigma_epsilone, mu_k, sigma_k,Beta,L,PL,CONTRAST, CONTRASTVAR,cA,cH,cZ,cAH,cTime,cTimeMean,Sigma_A,XX = \
# Main_vbjde_Extension_TD(height,width,q_Z,FlagZ,pl,graph,Y,Onsets,Thrf,K,TR,beta,dt,scale,estimateSigmaH,sigmaH,nItMax,nItMin,estimateBeta)
# facteur = 1.0
# Y,height,width,bande = lecture_data(dataDir,2660,2730,2600,2680,bande,start,facteur,end)
# FlagZ = 0
# NbIter_f,m_A_f, m_H_f, q_Z_f, sigma_epsilone_f, mu_k_f, sigma_k_f,Beta_f,L_f,PL,CONTRAST, CONTRASTVAR,cA,cH,cZ,cAH,cTime,cTimeMean,Sigma_A,XX = \
# Main_vbjde_Extension_TD(height,width,q_Z,FlagZ,pl,graph,Y,Onsets,Thrf,K,TR,beta,dt,scale,estimateSigmaH,sigmaH,nItMax,nItMin,estimateBeta)
# ytild=PL
# matshow(reshape(m_A_f[:,0],(height,width)) - reshape(m_A[:,0],(height,width)),cmap=get_cmap('gray'))
# colorbar()
FlagZ = 1
q_Z0 = zeros((self.M, self.K, J), dtype=float64)
if not FlagZ:
q_Z0 = q_Z
FlagH = 1
TT, m_h = getCanoHRF(self.Thrf - self.dt, self.dt)
self.hrf0 = hrf0 = array(m_h).astype(float64)
Sigma_H0 = eye(hrf0.shape[0])
if not FlagH:
hrf0 = h_H
Sigma_H0 = Sigma_H
self.m_A, self.m_H, self.q_Z, sigma_epsilone, mu_k, sigma_k, Beta, PL, Sigma_A, XX, Sigma_H = \
Main_vbjde_Extension_TD(
FlagH, hrf0, Sigma_H0, self.height, self.width, q_Z0, FlagZ,
self.pl, graph, self.Y, Onsets, self.Thrf, self.K, self.TR,
self.beta, self.dt, scale,
estimateSigmaH, self.sigmaH, nItMin, estimateBeta)
fgs = self.ConditionalNRLHist(self.m_A, self.q_Z)
MMin = -1.0 # Y.min()
MMax = 1.0 # Y.max()
pas = (MMax - MMin) / 100
xx = arange(MMin, MMax, pas)
g0 = self.gaussian(xx, mu_k[0][0], sigma_k[0][0])
g1 = self.gaussian(xx, mu_k[0][1], sigma_k[0][1])
#
# figure(77)
# plot(xx,g0*pas, label='m=%.2f;v=%.2f' % (mu_k[0][0],sigma_k[0][0]))
# hold(True)
# plot(xx,g1*pas, label='m=%.2f;v=%.2f' % (mu_k[0][1],sigma_k[0][1]))
# legend()
# savgarde des PLs #
# if ((pl != 0 )and (savepl !=0 )) :
# for i in range (0,ytild.shape[0]) :
# figure(nf)
# PL_img =reshape(ytild[i,:],(height,width))
# matshow(PL_img,cmap=get_cmap('gray'))
# colorbar()
# nf=nf+1
# savefig(outDir+'PL'+str(i)+'bande=' +str(bande)+'.png')
# savefig(outDir+'PL'+str(i)+'bande=' +str(bande)+'beta='+str(beta)+'sigma='+str(sigmaH)+'pl='+str(pl)+'dt='+str(dt)+'thrf'+str(Thrf)+'.png')
#
# figure Hrf #######
fgs.insert(0, figure((self.nf + 1) * 123))
title("Fonction de reponse", fontsize='xx-large')
figtext(0.2,
0.04,
'bande = ' + str(self.bande) + ' beta =' + str(self.beta) +
' sigma = ' + str(self.sigmaH) + ' pl = ' + str(self.pl) +
' dt = ' + str(self.dt) + ' thrf = ' + str(self.Thrf),
fontsize='x-large')
plot(self.m_H)
if self.shower == 1:
show()
return fgs