def calc_centrality(in_file, template, method_option, threshold_option,
threshold, allocated_memory):
'''
Function to calculate centrality and map them to a nifti file
Parameters
----------
in_file : string (nifti file)
path to subject data file
template : string (nifti file)
path to mask/parcellation unit
method_option : string
accepted values are 'degree centrality', 'eigenvector centrality', and
'lfcd'
threshold_option : string
accepted values are: 'significance', 'sparsity', and 'correlation'
threshold : float
pvalue/sparsity_threshold/threshold value
allocated_memory : string
amount of memory allocated to degree centrality
Returns
-------
out_list : list
list containing out mapped centrality images
'''
# Import packages
from CPAC.network_centrality import load,\
get_centrality_by_rvalue,\
get_centrality_by_sparsity,\
get_centrality_fast,\
map_centrality_matrix,\
calc_blocksize,\
convert_pvalue_to_r
from CPAC.network_centrality.utils import check_centrality_params
from CPAC.cwas.subdist import norm_cols
# First check input parameters and get proper formatted method/thr options
method_option, threshold_option = \
check_centrality_params(method_option, threshold_option, threshold)
# Init variables
out_list = []
ts, aff, mask, t_type, scans = load(in_file, template)
# If we're doing degree sparsity
if method_option == 'degree' and threshold_option == 'sparsity':
block_size = calc_blocksize(ts, memory_allocated=allocated_memory,
sparsity_thresh=threshold)
# Otherwise
elif method_option == 'eigenvector':
block_size = calc_blocksize(ts, memory_allocated=allocated_memory,
include_full_matrix=True)
# Otherwise, compute blocksize with regards to available memory
else:
block_size = calc_blocksize(ts, memory_allocated=allocated_memory,
include_full_matrix=False)
# Normalize the timeseries for easy dot-product correlation calc.
ts_normd = norm_cols(ts.T)
# P-value threshold centrality
if threshold_option == 'significance':
r_value = convert_pvalue_to_r(in_file, threshold, two_tailed=False)
centrality_matrix = get_centrality_by_rvalue(ts_normd,
mask,
method_option,
r_value,
block_size)
# Sparsity threshold
elif threshold_option == 'sparsity':
centrality_matrix = get_centrality_by_sparsity(ts_normd,
method_option,
threshold,
block_size)
# R-value threshold centrality
elif threshold_option == 'correlation':
centrality_matrix = get_centrality_by_rvalue(ts_normd,
mask,
method_option,
threshold,
block_size)
# For fast approach (no thresholding)
elif threshold_option == 3:
centrality_matrix = get_centrality_fast(ts, method_option)
# Otherwise, incorrect input for threshold_option
else:
err_msg = 'Threshold option: %s not supported for network centrality '\
'measure: %s; fix this in the pipeline config'\
% (str(threshold_option), str(method_option))
raise Exception(err_msg)
# Map the arrays back to images
for mat in centrality_matrix:
centrality_image = map_centrality_matrix(mat, aff, mask, t_type)
out_list.append(centrality_image)
# Finally return
return out_list
def calc_centrality(datafile,
template,
method_option,
threshold_option,
threshold,
weight_options,
allocated_memory):
'''
Method to calculate centrality and map them to a nifti file
Parameters
----------
datafile : string (nifti file)
path to subject data file
template : string (nifti file)
path to mask/parcellation unit
method_option : integer
0 - degree centrality calculation, 1 - eigenvector centrality calculation, 2 - lFCD calculation
threshold_option : an integer
0 for probability p_value, 1 for sparsity threshold,
2 for actual threshold value, and 3 for no threshold and fast approach
threshold : a float
pvalue/sparsity_threshold/threshold value
weight_options : list (boolean)
list of booleans, where, weight_options[0] corresponds to binary counting
and weight_options[1] corresponds to weighted counting (e.g. [True,False])
allocated_memory : string
amount of memory allocated to degree centrality
Returns
-------
out_list : list
list containing out mapped centrality images
'''
# Import packages
from CPAC.network_centrality import load,\
get_centrality_by_rvalue,\
get_centrality_by_sparsity,\
get_centrality_fast,\
map_centrality_matrix,\
calc_blocksize,\
convert_pvalue_to_r
from CPAC.cwas.subdist import norm_cols
# Check for input errors
if weight_options.count(True) == 0:
raise Exception("Invalid values in weight options" \
"At least one True value is required")
# If it's sparsity thresholding, check for (0,1]
if threshold_option == 1:
if threshold <= 0 or threshold > 1:
raise Exception('Threshold value must be a positive number'\
'greater than 0 and less than or equal to 1.'\
'\nCurrently it is set at %d' % threshold)
if method_option == 2 and threshold_option != 2:
raise Exception('lFCD must use correlation-type thresholding.'\
'Check the pipline configuration has this setting')
import time
start = time.clock()
# Init variables
out_list = []
ts, aff, mask, t_type, scans = load(datafile, template)
# If we're doing eigenvectory centrality, need entire correlation matrix
if method_option == 0 and threshold_option == 1:
block_size = calc_blocksize(ts, memory_allocated=allocated_memory,
sparsity_thresh=threshold)
elif method_option == 1:
block_size = calc_blocksize(ts, memory_allocated=allocated_memory,
include_full_matrix=True)
# Otherwise, compute blocksize with regards to available memory
else:
block_size = calc_blocksize(ts, memory_allocated=allocated_memory,
include_full_matrix=False)
# Normalize the timeseries for easy dot-product correlation calc.
ts_normd = norm_cols(ts.T)
# P-value threshold centrality
if threshold_option == 0:
r_value = convert_pvalue_to_r(scans, threshold)
centrality_matrix = get_centrality_by_rvalue(ts_normd,
mask,
method_option,
weight_options,
r_value,
block_size)
# Sparsity threshold
elif threshold_option == 1:
centrality_matrix = get_centrality_by_sparsity(ts_normd,
method_option,
weight_options,
threshold,
block_size)
# R-value threshold centrality
elif threshold_option == 2:
centrality_matrix = get_centrality_by_rvalue(ts_normd,
mask,
method_option,
weight_options,
threshold,
block_size)
# For fast approach (no thresholding)
elif threshold_option == 3:
centrality_matrix = get_centrality_fast(ts, method_option)
# Otherwise, incorrect input for threshold_option
else:
raise Exception('Option must be between 0-3 and not %s, check your '\
'pipeline config file' % str(threshold_option))
# Print timing info
print 'Timing:', time.clock() - start
# Map the arrays back to images
for mat in centrality_matrix:
centrality_image = map_centrality_matrix(mat, aff, mask, t_type)
out_list.append(centrality_image)
# Finally return
return out_list
def calc_centrality(datafile,
template,
method_option,
threshold_option,
threshold,
weight_options,
allocated_memory):
"""
Method to calculate centrality and map them to a nifti file
Parameters
----------
datafile : string (nifti file)
path to subject data file
template : string (nifti file)
path to mask/parcellation unit
method_option : integer
0 - degree centrality calculation, 1 - eigenvector centrality calculation, 2 - lFCD calculation
weight_options : list (boolean)
list of two booleans for binarize and weighted options respectively
threshold_option : an integer
0 for probability p_value, 1 for sparsity threshold,
2 for actual threshold value, and 3 for no threshold and fast approach
threshold : a float
pvalue/sparsity_threshold/threshold value
weight_options : list (boolean)
list of booleans, where, weight_options[0] corresponds to binary counting
and weight_options[1] corresponds to weighted counting (e.g. [True,False])
allocated_memory : string
amount of memory allocated to degree centrality
Returns
-------
out_list : list
list containing out mapped centrality images
"""
from CPAC.network_centrality import load,\
get_centrality_by_thresh,\
get_centrality_by_sparsity,\
get_centrality_fast,\
map_centrality_matrix
out_list = []
# if method_options.count(True) == 0:
# raise Exception("Invalid values in method_options " \
# "At least one True value is required")
if weight_options.count(True) == 0:
raise Exception("Invalid values in weight options" \
"At least one True value is required")
ts, aff, mask, t_type, scans = load(datafile, template)
import time
start = time.clock()
#p-value threshold centrality
if threshold_option == 0:
centrality_matrix = get_centrality_by_thresh(ts,
mask,
method_option,
weight_options,
threshold,
None,
allocated_memory)
#for sparsity threshold
elif threshold_option == 1:
centrality_matrix = get_centrality_by_sparsity(ts,
method_option,
weight_options,
threshold,
allocated_memory)
#r-value threshold centrality
elif threshold_option == 2:
centrality_matrix = get_centrality_by_thresh(ts,
mask,
method_option,
weight_options,
threshold,
threshold,
allocated_memory)
#for fast approach (no thresholding)
elif threshold_option == 3:
centrality_matrix = get_centrality_fast(ts, method_option)
else:
raise Exception("option must be between 0-3 and not %s" % str(method_option))
print "timing:", (time.clock() - start)
def get_image(matrix, template_type):
centrality_image = map_centrality_matrix(matrix,
aff,
mask,
template_type)
out_list.append(centrality_image)
for mat in centrality_matrix:
get_image(mat, t_type)
return out_list
