Calculates degree centrality using CPAC code

cpac_centrality.py

#!/usr/bin/env python

import argparse
import os
from os import path

from CPAC.network_centrality import calc_centrality


###
# Load command-line argument
###

parser = argparse.ArgumentParser(description='Compute centrality for a given timeseries.')

# Inputs
parser.add_argument('-i', '--input', help='Input timeseries data file', 
                    required=True)
parser.add_argument('-m', '--mask', help='Brain mask (by default the program will create a mask where voxels have non-zero variance regardeless of the user specified mask).')

# Option: Method
parser.add_argument('--degree', help='Calculate degree centrality', 
                    action="store_true")
parser.add_argument('--eigen', help='Calculate eigenvector centrality', 
                    action="store_true")
parser.add_argument('--lfcd', help='Calculate lFCD (local functional connectivity density)', 
                    action="store_true")

# Option: Outputs
parser.add_argument('--binarize', action="store_true", 
                    help='For a given voxel, save the number of connections that pass a threshold')
parser.add_argument('--weighted', action="store_true", 
                    help='For a given voxel, save the sum of all connection weights that pass a threshold.')

# Option: Threshold
# TODO: explicitly check that only one is specified.
parser.add_argument('--no-threshold', action='store_true', 
                    help="The raw correlations will be used and the approach will be very fast and low memory usage.")
parser.add_argument('--sparsity', type=float, 
                    help="Sparsity based threshold. (Only one threshold option can be specified.)")
parser.add_argument('--pvalue', type=float, 
                    help='P-value threshold for each connection. (Only one threshold option can be specified.)')
parser.add_argument('--rho', type=float, 
                    help="Regular correlation threshold. (Only one threshold option can be specified.)")

# Option: Memory
parser.add_argument('--memlimit', type=float, 
                    help="Memory limit that should be set.")

# Option: Threads
parser.add_argument('--nthreads', type=int, default=1, 
                    help="Number of threads to parallel processes for Intel MKL")

# Output
parser.add_argument('-o', '--outdir', default=os.getcwd(), help="Output directory")



###
# Parse and Read User Args
###

args = parser.parse_args()

try:
    import mkl
    mkl.set_num_threads(args.nthreads)
except ImportError:
    pass
 
method_options  = [args.degree, args.eigen, args.lfcd]
if method_options.count(True) != 1:
    raise SystemExit("either --degree, --eigen, or --lfcd must be specified")
method_option   = [ i for i,opt in enumerate(method_options) if opt is True ][0] # 0=degree, 1=eigen, 2=lfcd

if not args.binarize and not args.weighted:
    raise SystemExit("--binarize and/or --weighted must be specified")
weight_options = [args.binarize, args.weighted]

# 0 = probability p-value
# 1 = sparsity threshold
# 2 = actual threshold value
# 3 = no threshold and fast approach
if args.pvalue is not None:
    option = 0
    threshold = args.pvalue
elif args.sparsity is not None:
    option = 1
    threshold = args.sparsity
elif args.rho is not None:
    option = 2
    threshold = args.rho
elif args.no_threshold:
    option = 3
    threshold = None
else:
    raise SystemExit("You must specify one threshold option: --pvalue, --sparsity, --rho, or --no-threshold.")
  
outdir      = os.path.abspath(args.outdir)
infile      = os.path.abspath(args.input)
maskfile    = os.path.abspath(args.mask)


###
# Call on the Big Guy/Gal (CPAC)
###

curdir = os.getcwd()
#args.outdir = os.path.abspath(args.outdir)
os.chdir(outdir)

res = calc_centrality(infile, maskfile, method_option, option, threshold, 
                      weight_options, args.memlimit)

print(res)

os.chdir(curdir)

sample_run.bash

#!/usr/bin/env bash

# Sample run using the script above.

func_file="/data/Projects/ABIDE_Initiative/CCS/processed/Pitt_50003/func/rest_1/rest.sm0.mni152.nii.gz"
mask_file="/home2/data/Projects/ABIDE_Initiative/CPAC/abide/templates/masks/mask_ccs_90percent_gm.nii.gz"

./cpac_centrality.py \
    -i ${func_file} \
    -m ${mask_file} \
    --degree \
    --binarize --weighted \
    --pvalue 0.001 \
    --memlimit 8 \
    -o $(pwd)/tmp2