def test_component(): from scipy import stats x = load_sparse_sample() c1,cs1 = bct.get_components(x) assert np.max(c1) == 19 assert np.max(cs1) == 72 try: import networkx c2,cs2 = bct.get_components(x, no_depend=True) assert np.max(c2) == 19 assert np.max(cs2) == 72 except ImportError: pass assert bct.number_of_components(x) == 19
def test_component():
from scipy import stats
x = load_sparse_sample()
c1, cs1 = bct.get_components(x)
assert np.max(c1) == 19
assert np.max(cs1) == 72
try:
import networkx
c2, cs2 = bct.get_components(x, no_depend=True)
assert np.max(c2) == 19
assert np.max(cs2) == 72
except ImportError:
pass
assert bct.number_of_components(x) == 19
def test_component():
from scipy import stats
x = load_sparse_sample()
c1, cs1 = bct.get_components(x)
print(np.max(c1), 19)
assert np.max(c1) == 19
print(np.max(cs1), 72)
assert np.max(cs1) == 72
def test_component():
from scipy import stats
x = load_sparse_sample()
c1, cs1 = bct.get_components(x)
print(np.max(c1), 19)
assert np.max(c1) == 19
print(np.max(cs1), 72)
assert np.max(cs1) == 72
def getBiggestComponent(pairwise_measure_matrix):
"""
Get the biggest component of the weighted adjacency matrix.
Arguments: pairwise_measure_matrix, numpy.ndarray
Returns: biggest_comp, the biggest component of the weighted adjacency matrix
keep_indices, the indices of the nodes in the biggest component
comp_assign, integers indicating to which component each node was designated
comp_size, the size of each component
Note: Requires bct, the python version of the brain connectivity toolbox
https://github.com/aestrivex/bctpy
"""
adjacency_matrix = (pairwise_measure_matrix > 0).astype(int)
comp_assign, comp_size = bct.get_components(adjacency_matrix)
keep_indices = np.nonzero(comp_assign == comp_size.argmax() + 1)[0]
biggest_comp = pairwise_measure_matrix[keep_indices][:, keep_indices]
np.fill_diagonal(biggest_comp, 0)
return biggest_comp, keep_indices, comp_assign, comp_size
def nbs_bct(x,y,thresh,k=1000,tail='both',paired=False,verbose=False):
'''
Performs the NBS for populations X and Y for a t-statistic threshold of
alpha.
Parameters
----------
x : NxNxP np.ndarray
matrix representing the first population with P subjects. must be
symmetric.
y : NxNxQ np.ndarray
matrix representing the second population with Q subjects. Q need not
equal P. must be symmetric.
thresh : float
minimum t-value used as threshold
k : int
number of permutations used to estimate the empirical null
distribution
tail : {'left', 'right', 'both'}
enables specification of particular alternative hypothesis
'left' : mean population of X < mean population of Y
'right' : mean population of Y < mean population of X
'both' : means are unequal (default)
paired : bool
use paired sample t-test instead of population t-test. requires both
subject populations to have equal N. default value = False
verbose : bool
print some extra information each iteration. defaults value = False
Returns
-------
pval : Cx1 np.ndarray
A vector of corrected p-values for each component of the networks
identified. If at least one p-value is less than alpha, the omnibus
null hypothesis can be rejected at alpha significance. The null
hypothesis is that the value of the connectivity from each edge has
equal mean across the two populations.
adj : IxIxC np.ndarray
an adjacency matrix identifying the edges comprising each component.
edges are assigned indexed values.
null : Kx1 np.ndarray
A vector of K sampled from the null distribution of maximal component
size.
Notes
-----
ALGORITHM DESCRIPTION
The NBS is a nonparametric statistical test used to isolate the
components of an N x N undirected connectivity matrix that differ
significantly between two distinct populations. Each element of the
connectivity matrix stores a connectivity value and each member of
the two populations possesses a distinct connectivity matrix. A
component of a connectivity matrix is defined as a set of
interconnected edges.
The NBS is essentially a procedure to control the family-wise error
rate, in the weak sense, when the null hypothesis is tested
independently at each of the N(N-1)/2 edges comprising the undirected
connectivity matrix. The NBS can provide greater statistical power
than conventional procedures for controlling the family-wise error
rate, such as the false discovery rate, if the set of edges at which
the null hypothesis is rejected constitues a large component or
components.
The NBS comprises fours steps:
1. Perform a two-sample T-test at each edge indepedently to test the
hypothesis that the value of connectivity between the two
populations come from distributions with equal means.
2. Threshold the T-statistic available at each edge to form a set of
suprathreshold edges.
3. Identify any components in the adjacency matrix defined by the set
of suprathreshold edges. These are referred to as observed
components. Compute the size of each observed component
identified; that is, the number of edges it comprises.
4. Repeat K times steps 1-3, each time randomly permuting members of
the two populations and storing the size of the largest component
identified for each permuation. This yields an empirical estimate
of the null distribution of maximal component size. A corrected
p-value for each observed component is then calculated using this
null distribution.
[1] Zalesky A, Fornito A, Bullmore ET (2010) Network-based statistic:
Identifying differences in brain networks. NeuroImage.
10.1016/j.neuroimage.2010.06.041
'''
def ttest2_stat_only(x,y,tail):
t=np.mean(x)-np.mean(y)
n1,n2=len(x),len(y)
s=np.sqrt(((n1-1)*np.var(x,ddof=1)+(n2-1)*np.var(y,ddof=1))/(n1+n2-2))
denom=s*np.sqrt(1/n1+1/n2)
if denom==0: return 0
if tail=='both': return np.abs(t/denom)
if tail=='left': return -t/denom
else: return t/denom
def ttest_paired_stat_only(A,B,tail):
n = len(A-B)
df = n-1
sample_ss = np.sum((A-B)**2) - np.sum(A-B)**2/n
unbiased_std = np.sqrt(sample_ss/(n-1))
z = np.mean(A-B) / unbiased_std
t = z * np.sqrt(n)
if tail=='both': return np.abs(t)
if tail=='left': return -t
else: return t
if tail not in ('both','left','right'):
raise BCTParamError('Tail must be both, left, right')
ix,jx,nx=x.shape
iy,jy,ny=y.shape
if not ix==jx==iy==jy:
raise BCTParamError('Population matrices are of inconsistent size')
else:
n=ix
if paired and nx!=ny:
raise BCTParamError('Population matrices must be an equal size')
#only consider upper triangular edges
ixes=np.where(np.triu(np.ones((n,n)),1))
#number of edges
m=np.size(ixes,axis=1)
#vectorize connectivity matrices for speed
xmat,ymat=np.zeros((m,nx)),np.zeros((m,ny))
for i in xrange(nx):
xmat[:,i]=x[:,:,i][ixes].squeeze()
for i in xrange(ny):
ymat[:,i]=y[:,:,i][ixes].squeeze()
del x,y
#perform t-test at each edge
t_stat=np.zeros((m,))
for i in xrange(m):
if paired:
t_stat[i]=ttest_paired_stat_only(xmat[i,:],ymat[i,:],tail)
else:
t_stat[i]=ttest2_stat_only(xmat[i,:],ymat[i,:],tail)
#threshold
ind_t,=np.where(t_stat>thresh)
if len(ind_t) == 0:
raise BCTParamError("Unsuitable threshold")
#suprathreshold adjacency matrix
adj=np.zeros((n,n))
adj[(ixes[0][ind_t],ixes[1][ind_t])]=1
#adj[ixes][ind_t]=1
adj=adj+adj.T
a,sz=get_components(adj)
#convert size from nodes to number of edges
#only consider components comprising more than one node (e.g. a/l 1 edge)
ind_sz,=np.where(sz>1)
ind_sz+=1
nr_components=np.size(ind_sz)
sz_links=np.zeros((nr_components,))
for i in xrange(nr_components):
nodes,=np.where(ind_sz[i]==a)
sz_links[i]=np.sum(adj[np.ix_(nodes,nodes)])/2
adj[np.ix_(nodes,nodes)]*=(i+2)
#subtract 1 to delete any edges not comprising a component
adj[np.where(adj)]-=1
if np.size(sz_links):
max_sz=np.max(sz_links)
else:
#max_sz=0
raise BCTParamError('True matrix is degenerate')
print 'max component size is %i'%max_sz
#estimate empirical null distribution of maximum component size by
#generating k independent permutations
print 'estimating null distribution with %i permutations'%k
null=np.zeros((k,))
hit=0
for u in xrange(k):
#randomize
if paired:
indperm = np.sign(0.5 - np.random.rand(1, nx))
d=np.hstack((xmat,ymat))*np.hstack((indperm,indperm))
else:
d=np.hstack((xmat,ymat))[:,np.random.permutation(nx+ny)]
t_stat_perm=np.zeros((m,))
for i in xrange(m):
if paired:
t_stat_perm[i]=ttest_paired_stat_only(d[i,:nx],d[i,-nx:],tail)
else:
t_stat_perm[i]=ttest2_stat_only(d[i,:nx],d[i,-ny:],tail)
ind_t,=np.where(t_stat_perm>thresh)
adj_perm=np.zeros((n,n))
adj_perm[(ixes[0][ind_t],ixes[1][ind_t])]=1
adj_perm=adj_perm+adj_perm.T
a,sz=get_components(adj_perm)
ind_sz,=np.where(sz>1)
ind_sz+=1
nr_components_perm=np.size(ind_sz)
sz_links_perm=np.zeros((nr_components_perm))
for i in xrange(nr_components_perm):
nodes,=np.where(ind_sz[i]==a)
sz_links_perm[i]=np.sum(adj_perm[np.ix_(nodes,nodes)])/2
if np.size(sz_links_perm):
null[u]=np.max(sz_links_perm)
else:
null[u]=0
#compare to the true dataset
if null[u] >= max_sz: hit+=1
if verbose:
print ('permutation %i of %i. Permutation max is %s. Observed max'
' is %s. P-val estimate is %.3f')%(
u,k,null[u],max_sz,hit/(u+1))
elif (u%(k/10) == 0 or u==k-1):
print 'permutation %i of %i. p-value so far is %.3f'%(u,k,
hit/(u+1))
pvals=np.zeros((nr_components,))
#calculate p-vals
for i in xrange(nr_components):
pvals[i]=np.size(np.where(null>=sz_links[i]))/k
return pvals,adj,null
def nbs_bct(x,y,thresh,k=1000,tail='both'):
'''
PVAL = NBS(X,Y,THRESH)
Performs the NBS for populations X and Y for a t-statistic threshold of
alpha.
inputs: x,y, matrices representing the two populations being compared.
x and y are of size NxNxP, where N is the number of nodes
in the network and P is the number of subjects within the
population. P need not be equal for both X and Y.
X[i,j,k] stores the connectivity value corresponding to
the edge between i and j for the kth member of the
population. x and y must be symmetric.
thresh, the minimum t-value used as threshold
k, the number of permutations to be generated to estimate the
empirical null distribution (default 1000)
tail, enables specification of the type of alternative hypothesis
to test.
'left': mean of population X < mean of population Y
'right': mean of population Y < mean of population X
'both': means are unequal (default)
outputs:
pval, a vector of corrected p-values for each component of the
network that is identified. If at least one p-value is
less than alpha, then the omnibus null hypothesis can be
rejected at alpha significance. The null hypothesis is that
the value of connectivity at each edge comes from
distributions of equal mean between the two populations.
adj, an adjacency matrix identifying the edges comprising each
component. Edges are assigned indexed values.
null, A vector of k samples from the null distribution of maximal
component size
ALGORITHM DESCRIPTION
The NBS is a nonparametric statistical test used to isolate the
components of an N x N undirected connectivity matrix that differ
significantly between two distinct populations. Each element of the
connectivity matrix stores a connectivity value and each member of
the two populations possesses a distinct connectivity matrix. A
component of a connectivity matrix is defined as a set of
interconnected edges.
The NBS is essentially a procedure to control the family-wise error
rate, in the weak sense, when the null hypothesis is tested
independently at each of the N(N-1)/2 edges comprising the undirected
connectivity matrix. The NBS can provide greater statistical power
than conventional procedures for controlling the family-wise error
rate, such as the false discovery rate, if the set of edges at which
the null hypothesis is rejected constitues a large component or
components.
The NBS comprises fours steps:
1. Perform a two-sample T-test at each edge indepedently to test the
hypothesis that the value of connectivity between the two
populations come from distributions with equal means.
2. Threshold the T-statistic available at each edge to form a set of
suprathreshold edges.
3. Identify any components in the adjacency matrix defined by the set
of suprathreshold edges. These are referred to as observed
components. Compute the size of each observed component
identified; that is, the number of edges it comprises.
4. Repeat K times steps 1-3, each time randomly permuting members of
the two populations and storing the size of the largest component
identified for each permuation. This yields an empirical estimate
of the null distribution of maximal component size. A corrected
p-value for each observed component is then calculated using this
null distribution.
[1] Zalesky A, Fornito A, Bullmore ET (2010) Network-based statistic:
Identifying differences in brain networks. NeuroImage.
10.1016/j.neuroimage.2010.06.041
DEPENDENCIES
Please note that nbs_bct depends on networkx
'''
def ttest2_stat_only(x,y,tail):
t=np.mean(x)-np.mean(y)
n1,n2=len(x),len(y)
s=np.sqrt(((n1-1)*np.var(x)+(n2-1)*np.var(y))/(n1+n2-2))
denom=s*np.sqrt(1/n1+1/n2)
if denom==0: return 0
if tail=='both': return np.abs(t/denom)
if tail=='left': return -t/denom
else: return t/denom
if tail not in ('both','left','right'):
raise BCTParamError('Tail must be both, left, right')
ix,jx,nx=x.shape
iy,jy,ny=y.shape
if not ix==jx==iy==jy:
raise BCTParamError('Population matrices are of inconsistent size')
else:
n=ix
#only consider upper triangular edges
ixes=np.where(np.triu(np.ones((n,n)),1))
#number of edges
m=np.size(ixes,axis=1)
#vectorize connectivity matrices for speed
xmat,ymat=np.zeros((m,nx)),np.zeros((m,ny))
for i in xrange(nx):
xmat[:,i]=x[:,:,i][ixes].squeeze()
for i in xrange(ny):
ymat[:,i]=y[:,:,i][ixes].squeeze()
del x,y
#perform t-test at each edge
t_stat=np.zeros((m,))
for i in xrange(m):
t_stat[i]=ttest2_stat_only(xmat[i,:],ymat[i,:],tail)
#threshold
ind_t,=np.where(t_stat>thresh)
#suprathreshold adjacency matrix
adj=np.zeros((n,n))
adj[np.ix_(ixes[0][ind_t],ixes[1][ind_t])]=1
#adj[ixes][ind_t]=1
adj=adj+adj.T
a,sz=get_components(adj)
#convert size from nodes to number of edges
#only consider components comprising more than one node (e.g. a/l 1 edge)
ind_sz,=np.where(sz>1)
ind_sz+=1
nr_components=np.size(ind_sz)
sz_links=np.zeros((nr_components,))
for i in xrange(nr_components):
nodes,=np.where(ind_sz[i]==a)
sz_links[i]=np.sum(adj[np.ix_(nodes,nodes)])/2
for i in xrange(nr_components):
adj[np.ix_(nodes,nodes)]*=(i+2)
#subtract 1 to delete any edges not comprising a component
adj[np.where(adj)]-=1
if np.size(sz_links):
max_sz=np.max(sz_links)
else:
max_sz=0
print 'max component size is %i'%max_sz
#estimate empirical null distribution of maximum component size by
#generating k independent permutations
print 'estimating null distribution with %i permutations'%k
null=np.zeros((k,))
hit=0
for u in xrange(k):
#randomize
d=np.hstack((xmat,ymat))[:,np.random.permutation(nx+ny)]
t_stat_perm=np.zeros((m,))
for i in xrange(m):
t_stat_perm[i]=ttest2_stat_only(d[i,:nx],d[i,-ny:],tail)
ind_t,=np.where(t_stat_perm>thresh)
adj_perm=np.zeros((n,n))
adj_perm[np.ix_(ixes[0][ind_t],ixes[1][ind_t])]=1
adj_perm=adj_perm+adj_perm.T
a,sz=get_components(adj_perm)
ind_sz,=np.where(sz>1)
ind_sz+=1
nr_components_perm=np.size(ind_sz)
sz_links_perm=np.zeros((nr_components_perm))
for i in xrange(nr_components_perm):
nodes,=np.where(ind_sz[i]==a)
sz_links_perm[i]=np.sum(adj_perm[np.ix_(nodes,nodes)])/2
if np.size(sz_links_perm):
null[u]=np.max(sz_links_perm)
else:
null[u]=0
#compare to the true dataset
if null[u] >= max_sz: hit+=1
# print ('permutation %i of %i. Permutation max is %s. Observed max is '
# '%s. P-val estimate is %.3f')%(u,k,null[u],max_sz,hit/(u+1))
print 'permutation %i of %i. p-value so far is %.3f'%(u,k,hit/(u+1))
pvals=np.zeros((nr_components,))
#calculate p-vals
for i in xrange(nr_components):
pvals[i]=np.size(np.where(null>=sz_links[i]))/k
return pvals,adj,null
skewness = 1
while abs(skewness) > 0.3:
w = bct.threshold_proportional(corrmat, kappa)
skewness = skew(bct.degrees_und(w))
kappa += 0.01
df.at[(subject, sessions[i], task, conds[j], mask),
"k_scale-free", ] = kappa
# reset kappa starting point
# calculate proportion of connections that need to be retained
# for node connectedness
kappa = 0.01
num = 2
while num > 1:
w = bct.threshold_proportional(corrmat, kappa)
[comp, num] = bct.get_components(w)
num = np.unique(comp).shape[0]
kappa += 0.01
df.at[(subject, sessions[i], task, conds[j], mask),
"k_connected", ] = kappa
else:
pass
# df.at[(subject, sessions[i], task, conds[j], mask),'k_connected'] = kappa
except Exception as e:
print(subject, "didn't run, because", e)
df.to_csv(
join(
data_dir,
"phys-learn-fci_kappa_{0}-{1}.csv".format(
connectivity_metric, str(datetime.datetime.now())),
def create_feature_matrix(structure_matrix_file):
# Feature matrix with each element containing an NxN array
feature_matrix = []
# EDGE WEIGHT (Depth 0)
# weighted & undirected network
structural_connectivity_array = np.array(
pd.DataFrame(loadmat(structure_matrix_file)['connectivity']))
feature_matrix.append(structural_connectivity_array)
# DEGREE (Depth 1 & 2)
# Node degree is the number of links connected to the node.
deg = bct.degrees_und(structural_connectivity_array)
fill_array_2D(feature_matrix, deg)
# *** Conversion of connection weights to connection lengths ***
connection_length_matrix = bct.weight_conversion(
structural_connectivity_array, 'lengths')
# print(connection_length_matrix)
# SHORTEST PATH LENGTH (Depth 3 & 4)
'''
The distance matrix contains lengths of shortest paths between all pairs of nodes.
An entry (u,v) represents the length of shortest path from node u to node v.
The average shortest path length is the characteristic path length of the network.
'''
shortest_path = bct.distance_wei(connection_length_matrix)
feature_matrix.append(
shortest_path[0]) # distance (shortest weighted path) matrix
feature_matrix.append(
shortest_path[1]
) # matrix of number of edges in shortest weighted path
# BETWEENNESS CENTRALITY (Depth 5 & 6)
'''
Node betweenness centrality is the fraction of all shortest paths in
the network that contain a given node. Nodes with high values of
betweenness centrality participate in a large number of shortest paths.
'''
bc = bct.betweenness_wei(connection_length_matrix)
fill_array_2D(feature_matrix, bc)
# CLUSTERING COEFFICIENTS (Depth 7 & 8)
'''
The weighted clustering coefficient is the average "intensity" of
triangles around a node.
'''
cl = bct.clustering_coef_wu(connection_length_matrix)
fill_array_2D(feature_matrix, cl)
# Find disconnected nodes - component size set to 1
new_array = structural_connectivity_array
W_bin = bct.weight_conversion(structural_connectivity_array, 'binarize')
[comps, comp_sizes] = bct.get_components(W_bin)
print('comp: ', comps)
print('sizes: ', comp_sizes)
for i in range(len(comps)):
if (comps[i] != statistics.mode(comps)):
new_array = np.delete(new_array, new_array[i])
return feature_matrix
def nbs_bct(x, y, thresh, k=1000, tail='both', paired=False, verbose=False):
'''
PVAL = NBS(X,Y,THRESH)
Performs the NBS for populations X and Y for a t-statistic threshold of
alpha.
inputs: x,y, matrices representing the two populations being compared.
x and y are of size NxNxP, where N is the number of nodes
in the network and P is the number of subjects within the
population. P need not be equal for both X and Y.
X[i,j,k] stores the connectivity value corresponding to
the edge between i and j for the kth member of the
population. x and y must be symmetric.
thresh, the minimum t-value used as threshold
k, the number of permutations to be generated to estimate the
empirical null distribution (default 1000)
tail, enables specification of the type of alternative hypothesis
to test.
'left': mean of population X < mean of population Y
'right': mean of population Y < mean of population X
'both': means are unequal (default)
paired, use paired sample t-test instead of population t-test.
defaults to False.
verbose, print extra information. default False
outputs:
pval, a vector of corrected p-values for each component of the
network that is identified. If at least one p-value is
less than alpha, then the omnibus null hypothesis can be
rejected at alpha significance. The null hypothesis is that
the value of connectivity at each edge comes from
distributions of equal mean between the two populations.
adj, an adjacency matrix identifying the edges comprising each
component. Edges are assigned indexed values.
null, A vector of k samples from the null distribution of maximal
component size
ALGORITHM DESCRIPTION
The NBS is a nonparametric statistical test used to isolate the
components of an N x N undirected connectivity matrix that differ
significantly between two distinct populations. Each element of the
connectivity matrix stores a connectivity value and each member of
the two populations possesses a distinct connectivity matrix. A
component of a connectivity matrix is defined as a set of
interconnected edges.
The NBS is essentially a procedure to control the family-wise error
rate, in the weak sense, when the null hypothesis is tested
independently at each of the N(N-1)/2 edges comprising the undirected
connectivity matrix. The NBS can provide greater statistical power
than conventional procedures for controlling the family-wise error
rate, such as the false discovery rate, if the set of edges at which
the null hypothesis is rejected constitues a large component or
components.
The NBS comprises fours steps:
1. Perform a two-sample T-test at each edge indepedently to test the
hypothesis that the value of connectivity between the two
populations come from distributions with equal means.
2. Threshold the T-statistic available at each edge to form a set of
suprathreshold edges.
3. Identify any components in the adjacency matrix defined by the set
of suprathreshold edges. These are referred to as observed
components. Compute the size of each observed component
identified; that is, the number of edges it comprises.
4. Repeat K times steps 1-3, each time randomly permuting members of
the two populations and storing the size of the largest component
identified for each permuation. This yields an empirical estimate
of the null distribution of maximal component size. A corrected
p-value for each observed component is then calculated using this
null distribution.
[1] Zalesky A, Fornito A, Bullmore ET (2010) Network-based statistic:
Identifying differences in brain networks. NeuroImage.
10.1016/j.neuroimage.2010.06.041
'''
def ttest2_stat_only(x, y, tail):
t = np.mean(x) - np.mean(y)
n1, n2 = len(x), len(y)
s = np.sqrt(((n1 - 1) * np.var(x, ddof=1) +
(n2 - 1) * np.var(y, ddof=1)) / (n1 + n2 - 2))
denom = s * np.sqrt(1 / n1 + 1 / n2)
if denom == 0: return 0
if tail == 'both': return np.abs(t / denom)
if tail == 'left': return -t / denom
else: return t / denom
def ttest_paired_stat_only(A, B, tail):
n = len(A - B)
df = n - 1
sample_ss = np.sum((A - B)**2) - np.sum(A - B)**2 / n
unbiased_std = np.sqrt(sample_ss / (n - 1))
z = np.mean(A - B) / unbiased_std
t = z * np.sqrt(n)
if tail == 'both': return np.abs(t)
if tail == 'left': return -t
else: return t
if tail not in ('both', 'left', 'right'):
raise BCTParamError('Tail must be both, left, right')
ix, jx, nx = x.shape
iy, jy, ny = y.shape
if not ix == jx == iy == jy:
raise BCTParamError('Population matrices are of inconsistent size')
else:
n = ix
if paired and nx != ny:
raise BCTParamError('Population matrices must be an equal size')
#only consider upper triangular edges
ixes = np.where(np.triu(np.ones((n, n)), 1))
#number of edges
m = np.size(ixes, axis=1)
#vectorize connectivity matrices for speed
xmat, ymat = np.zeros((m, nx)), np.zeros((m, ny))
for i in xrange(nx):
xmat[:, i] = x[:, :, i][ixes].squeeze()
for i in xrange(ny):
ymat[:, i] = y[:, :, i][ixes].squeeze()
del x, y
#perform t-test at each edge
t_stat = np.zeros((m, ))
for i in xrange(m):
if paired:
t_stat[i] = ttest_paired_stat_only(xmat[i, :], ymat[i, :], tail)
else:
t_stat[i] = ttest2_stat_only(xmat[i, :], ymat[i, :], tail)
#threshold
ind_t, = np.where(t_stat > thresh)
#suprathreshold adjacency matrix
adj = np.zeros((n, n))
adj[(ixes[0][ind_t], ixes[1][ind_t])] = 1
#adj[ixes][ind_t]=1
adj = adj + adj.T
a, sz = get_components(adj)
#convert size from nodes to number of edges
#only consider components comprising more than one node (e.g. a/l 1 edge)
ind_sz, = np.where(sz > 1)
ind_sz += 1
nr_components = np.size(ind_sz)
sz_links = np.zeros((nr_components, ))
for i in xrange(nr_components):
nodes, = np.where(ind_sz[i] == a)
sz_links[i] = np.sum(adj[np.ix_(nodes, nodes)]) / 2
adj[np.ix_(nodes, nodes)] *= (i + 2)
#subtract 1 to delete any edges not comprising a component
adj[np.where(adj)] -= 1
if np.size(sz_links):
max_sz = np.max(sz_links)
else:
#max_sz=0
raise BCTParamError('True matrix is degenerate')
print 'max component size is %i' % max_sz
#estimate empirical null distribution of maximum component size by
#generating k independent permutations
print 'estimating null distribution with %i permutations' % k
null = np.zeros((k, ))
hit = 0
for u in xrange(k):
#randomize
if paired:
indperm = np.sign(0.5 - np.random.rand(1, nx))
d = np.hstack((xmat, ymat)) * np.hstack((indperm, indperm))
else:
d = np.hstack((xmat, ymat))[:, np.random.permutation(nx + ny)]
t_stat_perm = np.zeros((m, ))
for i in xrange(m):
if paired:
t_stat_perm[i] = ttest_paired_stat_only(
d[i, :nx], d[i, -nx:], tail)
else:
t_stat_perm[i] = ttest2_stat_only(d[i, :nx], d[i, -ny:], tail)
ind_t, = np.where(t_stat_perm > thresh)
adj_perm = np.zeros((n, n))
adj_perm[(ixes[0][ind_t], ixes[1][ind_t])] = 1
adj_perm = adj_perm + adj_perm.T
a, sz = get_components(adj_perm)
ind_sz, = np.where(sz > 1)
ind_sz += 1
nr_components_perm = np.size(ind_sz)
sz_links_perm = np.zeros((nr_components_perm))
for i in xrange(nr_components_perm):
nodes, = np.where(ind_sz[i] == a)
sz_links_perm[i] = np.sum(adj_perm[np.ix_(nodes, nodes)]) / 2
if np.size(sz_links_perm):
null[u] = np.max(sz_links_perm)
else:
null[u] = 0
#compare to the true dataset
if null[u] >= max_sz: hit += 1
if verbose:
print(
'permutation %i of %i. Permutation max is %s. Observed max'
' is %s. P-val estimate is %.3f') % (u, k, null[u], max_sz,
hit / (u + 1))
elif (u % (k / 10) == 0 or u == k - 1):
print 'permutation %i of %i. p-value so far is %.3f' % (u, k,
hit /
(u + 1))
pvals = np.zeros((nr_components, ))
#calculate p-vals
for i in xrange(nr_components):
pvals[i] = np.size(np.where(null >= sz_links[i])) / k
return pvals, adj, null
