def get_centrality_by_rvalue(ts_normd,
template,
method_option,
weight_options,
r_value,
block_size):
'''
Method to calculate degree/eigenvector centrality and lFCD
via correlation (r-value) threshold
Parameters
----------
ts_normd : ndarray (float)
timeseries of shape (ntpts x nvoxs) that is normalized; i.e. the data
is demeaned and divided by its L2-norm
template : ndarray
three dimensional array with non-zero elements corresponding to the
indices at which the lFCD metric is analyzed
method_option : integer
0 - degree centrality calculation,
1 - eigenvector centrality calculation,
2 - lFCD calculation
weight_options : list (boolean)
weight_options[0] - True or False to perform binary counting
weight_options[1] - True or False to perform weighted counting
threshold : a float
threshold (as correlation r) value
block_size : an integer
the number of rows (voxels) to compute timeseries correlation over
at any one time
Returns
-------
out_list : list (string, ndarray)
list of (string,ndarray) elements corresponding to:
string - the name of the metric
ndarray - the array of values to be mapped for that metric
'''
# Import packages
from CPAC.network_centrality.utils import cluster_data
# Init variables
out_list = []
nvoxs = ts_normd.shape[1]
# ntpts = timeseries.shape[0]
calc_degree = False
calc_eigen = False
calc_lfcd = False
# Select which method we're going to perform
if method_option == 0:
calc_degree = True
elif method_option == 1:
calc_eigen = True
elif method_option == 2:
calc_lfcd = True
# Weighting
out_binarize = weight_options[0]
out_weighted = weight_options[1]
# Init degree centrality outputs
if calc_degree:
# If binary weighting, init output map
if out_binarize:
degree_binarize = np.zeros(nvoxs, dtype=ts_normd.dtype)
out_list.append(('degree_centrality_binarize', degree_binarize))
# If connection weighting, init output map
if out_weighted:
degree_weighted = np.zeros(nvoxs, dtype=ts_normd.dtype)
out_list.append(('degree_centrality_weighted', degree_weighted))
# Init eigenvector centrality outputs
if calc_eigen:
r_matrix = np.zeros((nvoxs,nvoxs), dtype=ts_normd.dtype)
# If binary weighting, init output map
if out_binarize:
eigen_binarize = np.zeros(nvoxs, dtype=ts_normd.dtype)
out_list.append(('eigenvector_centrality_binarize', eigen_binarize))
# If connection weighting, init output map
if out_weighted:
eigen_weighted = np.zeros(nvoxs, dtype=ts_normd.dtype)
out_list.append(('eigenvector_centrality_weighted', eigen_weighted))
# Init lFCD outputs
if calc_lfcd:
# If binary weighting, init output map
if out_binarize:
lfcd_binarize = np.zeros(nvoxs, dtype=ts_normd.dtype)
out_list.append(('lfcd_binarize', lfcd_binarize))
# If connection weighting, init output map
if out_weighted:
lfcd_weighted = np.zeros(nvoxs, dtype=ts_normd.dtype)
out_list.append(('lfcd_weighted', lfcd_weighted))
# Prepare to loop through and calculate correlation matrix
n = 0
m = block_size
block_no = 1
# Run as long as our last row index is <= nvoxs
while m <= nvoxs:
# First, compute block of correlation matrix
print 'running block %d: rows %d thru %d' % (block_no, n, m)
rmat_block = np.dot(ts_normd[:,n:m].T, ts_normd)
# Degree centrality calculation
if calc_degree:
if weight_options[0]:
degree_centrality(rmat_block, r_value, method='binarize',
out=degree_binarize[n:m])
if weight_options[1]:
degree_centrality(rmat_block, r_value, method='weighted',
out=degree_weighted[n:m])
# Eigenvector centrality - append global corr. matrix
if calc_eigen:
r_matrix[n:m] = rmat_block
# lFCD - perform lFCD algorithm
if calc_lfcd:
xyz_a = np.argwhere(template)
krange = rmat_block.shape[0]
print '...iterating through seeds in block - lfcd'
for k in range (0,krange):
corr_seed = rmat_block[k,:]
labels = cluster_data(corr_seed,r_value,xyz_a)
seed_label = labels[n+k]
if out_binarize:
if seed_label > 0:
lfcd = np.sum(labels==seed_label)
else:
lfcd = 1
lfcd_binarize[n+k] = lfcd
if out_weighted:
if seed_label > 0:
lfcd = np.sum(corr_seed*(labels==seed_label))
else:
lfcd = 1
lfcd_weighted[n+k] = lfcd
# Delete block of corr matrix and increment indices
del rmat_block
# Move next block start point up to last block finish point
n = m
# If we finished at nvoxs last time, break the loop
if n == nvoxs:
break
# Else, if our next block runs over nvoxs, limit it to nvoxs
elif (m+block_size) > nvoxs:
m = nvoxs
# Else, just increment end of next block by block_size
else:
m += block_size
# Increment block number
block_no += 1
# Correct for self-correlation in degree centrality
if calc_degree:
if out_binarize:
idx = np.where(degree_binarize)
degree_binarize[idx] = degree_binarize[idx]-1
if out_weighted:
idx = np.where(degree_weighted)
degree_weighted[idx] = degree_weighted[idx]-1
# Perform eigenvector measures
try:
if calc_eigen:
if out_binarize:
print '...calculating binarize eigenvector'
eigen_binarize[:] = eigenvector_centrality(r_matrix,
r_value,
method='binarize').squeeze()
if out_weighted:
print '...calculating weighted eigenvector'
eigen_weighted[:] = eigenvector_centrality(r_matrix,
r_value,
method='weighted').squeeze()
del r_matrix
except Exception:
print 'Error in calcuating eigen vector centrality'
raise
# Return list of outputs
return out_list
def get_centrality_by_rvalue(ts_normd, template, method_option, r_value, block_size):
'''
Method to calculate degree/eigenvector centrality and lFCD
via correlation (r-value) threshold
Parameters
----------
ts_normd : ndarray (float)
timeseries of shape (ntpts x nvoxs) that is normalized; i.e. the data
is demeaned and divided by its L2-norm
template : ndarray
three dimensional array with non-zero elements corresponding to the
indices at which the lFCD metric is analyzed
method_option : integer
0 - degree centrality calculation,
1 - eigenvector centrality calculation,
2 - lFCD calculation
threshold : a float
threshold (as correlation r) value
block_size : an integer
the number of rows (voxels) to compute timeseries correlation over
at any one time
Returns
-------
out_list : list (string, ndarray)
list of (string,ndarray) elements corresponding to:
string - the name of the metric
ndarray - the array of values to be mapped for that metric
'''
# Import packages
import copy
import numpy as np
import copy
from nipype import logging
from CPAC.network_centrality.utils import cluster_data
import CPAC.network_centrality.core as core
# Init variables
logger = logging.getLogger('workflow')
out_list = []
nvoxs = ts_normd.shape[1]
# Init degree centrality outputs
if method_option == 'degree':
# Init output map
degree_binarize = np.zeros(nvoxs, dtype=ts_normd.dtype)
out_list.append(('degree_centrality_binarize', degree_binarize))
# Init output map
degree_weighted = np.zeros(nvoxs, dtype=ts_normd.dtype)
out_list.append(('degree_centrality_weighted', degree_weighted))
# Init eigenvector centrality outputs
if method_option == 'eigenvector':
r_matrix = np.zeros((nvoxs,nvoxs), dtype=ts_normd.dtype)
# Init output map
eigen_binarize = np.zeros(nvoxs, dtype=ts_normd.dtype)
out_list.append(('eigenvector_centrality_binarize', eigen_binarize))
# Init output map
eigen_weighted = np.zeros(nvoxs, dtype=ts_normd.dtype)
out_list.append(('eigenvector_centrality_weighted', eigen_weighted))
# Init lFCD outputs
if method_option == 'lfcd':
# Init output map
lfcd_binarize = np.zeros(nvoxs, dtype=ts_normd.dtype)
out_list.append(('lfcd_binarize', lfcd_binarize))
# Init output map
lfcd_weighted = np.zeros(nvoxs, dtype=ts_normd.dtype)
out_list.append(('lfcd_weighted', lfcd_weighted))
# Prepare to loop through and calculate correlation matrix
n = 0
m = block_size
block_no = 1
# Run as long as our last row index is <= nvoxs
while m <= nvoxs:
# First, compute block of correlation matrix
logger.info('running block %d: rows %d thru %d' % (block_no, n, m))
rmat_block = np.dot(ts_normd[:,n:m].T, ts_normd)
# Degree centrality calculation
if method_option == 'degree':
core.degree_centrality(rmat_block, r_value, method='binarize',
out=degree_binarize[n:m])
core.degree_centrality(rmat_block, r_value, method='weighted',
out=degree_weighted[n:m])
# Eigenvector centrality - append global corr. matrix
if method_option == 'eigenvector':
r_matrix[n:m] = rmat_block
# lFCD - perform lFCD algorithm
if method_option == 'lfcd':
xyz_a = np.argwhere(template)
krange = rmat_block.shape[0]
logger.info('...iterating through seeds in block - lfcd')
for k in range (0,krange):
corr_seed = rmat_block[k,:]
labels = cluster_data(corr_seed,r_value,xyz_a)
seed_label = labels[n+k]
# Binarized lFCD
if seed_label > 0:
lfcd_bin = np.sum(labels==seed_label)
lfcd_wght = np.sum(corr_seed*(labels==seed_label))
else:
lfcd_bin = lfcd_wght = 1
lfcd_binarize[n+k] = lfcd_bin
lfcd_weighted[n+k] = lfcd_wght
# Delete block of corr matrix and increment indices
del rmat_block
# Move next block start point up to last block finish point
n = m
# If we finished at nvoxs last time, break the loop
if n == nvoxs:
break
# Else, if our next block runs over nvoxs, limit it to nvoxs
elif (m+block_size) > nvoxs:
m = nvoxs
# Else, just increment end of next block by block_size
else:
m += block_size
# Increment block number
block_no += 1
# Correct for self-correlation in degree centrality
if method_option == 'degree':
idx = np.where(degree_binarize)
degree_binarize[idx] = degree_binarize[idx]-1
idx = np.where(degree_weighted)
degree_weighted[idx] = degree_weighted[idx]-1
# Perform eigenvector measures
if method_option == 'eigenvector':
logger.info('...calculating binarize eigenvector')
# Have to deepcopy the r_matrix because thresh and sum overwrites
# its values via pass-by-reference
eigen_binarize[:] = \
core.eigenvector_centrality(copy.deepcopy(r_matrix), r_value,
method='binarize').squeeze()
logger.info('...calculating weighted eigenvector')
eigen_weighted[:] = \
core.eigenvector_centrality(r_matrix, r_value,
method='weighted').squeeze()
del r_matrix
# Return list of outputs
return out_list