def call_calc_centrality():
import time
datafile = "/data/Projects/ABIDE_Initiative/CPAC/test_qp/Centrality_Working/resting_preproc_0051466_session_1/_mask_mask_abide_90percent_gm_3mm/_scan_rest_1_rest/resample_functional_to_template_0/residual_wtsimt_flirt.nii.gz"
template = "/home2/data/Projects/ABIDE_Initiative/CPAC/abide/templates/masks/mask_abide_90percent_gm_3mm.nii.gz"
method_options = [True, False]
weight_options = [True, True]
option = 0
threshold = 0.266037302736
allocated_memory = 12
start = time.clock()
calc_centrality(datafile, template, method_options, weight_options, option, threshold, allocated_memory)
end = time.clock()
print (end-start)
def test_calc_centrality():
infile = "/home2/data/Projects/ABIDE_Initiative/CPAC/test_qp/All_Output/sym_links/pipeline_MerrittIsland/_compcor_ncomponents_5_linear1.global1.motion1.quadratic1.compcor1.CSF_0.96_GM_0.7_WM_0.96/0051466_session_1/scan_rest_1_rest/func/functional_mni.nii.gz"
maskfile = "/home2/data/Projects/ABIDE_Initiative/CPAC/abide/templates/masks/mask_abide_90percent_gm.nii.gz"
tmp1 = calc_centrality(infile, maskfile, [1,0], [1,1], 0, 0.01, 12)
# datafile : string (nifti file)
# path to subject data file
# template : string (nifti file)
# path to mask/parcellation unit
# method_options : list (boolean)
# list of two booleans for binarize and weighted options respectively
# weight_options : list (boolean)
# list of two booleans for binarize and weighted options respectively
# option : an integer
# 0 for probability p_value, 1 for sparsity threshold,
# any other for threshold value
# threshold : a float
# pvalue/sparsity_threshold/threshold value
# allocated_memory : string
# amount of memory allocated to degree centrality
config_file = "files/config_fsl.yml"
subject_infos = common.gen_file_map(CPAC_OUTPUT)
curdir = os.getcwd()
os.chdir(__file__)
conf = common.load_configuration(config_file)
old_subject_file = common.load_subject_list(conf.subjectListFile)
new_subject_file = setup_group_subject_list(config_file, subject_infos)
os.chdir(curdir)
# All should be right here
assert_equal(np.array(old_subject_file), np.array(new_subject_file))
# Case where only one path is correct
"""
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.")
###
# Call on the Big Guy/Gal (CPAC)
###
curdir = os.getcwd()
os.chdir(args.outdir)
out_list = calc_centrality(args.input, args.mask, method_options, weight_options, option,
threshold, args.memlimit)
os.chdir(curdir)
###
# Z-Score
###
def zscore_image(infile, mask, outfile):
import os, commands
cmd = "fslstats %s -k %s -m" % (infile, mask)
print cmd
mean = commands.getstatusoutput(cmd)
mean = float(mean[1])
import sys
sys.path.insert(0, '/home2/data/Projects/CPAC_Regression_Test/nipype-installs/fcp-indi-nipype/running-install/lib/python2.7/site-packages')
sys.path.insert(1, "/home2/data/Projects/CPAC_Regression_Test/2013-05-30_cwas/C-PAC")
sys.path.append("/home/data/PublicProgram/epd-7.2-2-rh5-x86_64/lib/python2.7/site-packages")
from CPAC.network_centrality import calc_centrality
datafile = "/data/Projects/ABIDE_Initiative/CPAC/test_qp/Centrality_Working/resting_preproc_0051466_session_1/_mask_mask_abide_90percent_gm_3mm/_scan_rest_1_rest/resample_functional_to_template_0/residual_wtsimt_flirt.nii.gz"
template = "/home2/data/Projects/ABIDE_Initiative/CPAC/abide/templates/masks/mask_abide_90percent_gm_3mm.nii.gz"
method_options = [True, False]
weight_options = [True, True]
option = 0
threshold = 0.001
allocated_memory = 1
calc_centrality(datafile, template, method_options, weight_options, option, threshold, allocated_memory)
#datafile = "/data/Projects/ABIDE_Initiative/CPAC/test_qp/Centrality_Working/resting_preproc_0051466_session_1/_mask_mask_abide_90percent_gm_4mm/_scan_rest_1_rest/resample_functional_to_template_0/residual_wtsimt_flirt.nii.gz"
#template = "/home2/data/Projects/ABIDE_Initiative/CPAC/abide/templates/masks/mask_abide_90percent_gm_4mm.nii.gz"
#method_options = [True, False]
#weight_options = [True, True]
#option = 0
#threshold = 0.266037302736
#allocated_memory = 12
#
#calc_centrality(datafile, template, method_options, weight_options, option, threshold, allocated_memory)
elif args.no_threshold:
option = 3
threshold = None
else:
raise SystemExit(
"You must specify one threshold option: --pvalue, --sparsity, --rho, or --no-threshold."
)
###
# Call on the Big Guy/Gal (CPAC)
###
curdir = os.getcwd()
os.chdir(args.outdir)
out_list = calc_centrality(args.input, args.mask, method_options,
weight_options, option, threshold, args.memlimit)
os.chdir(curdir)
###
# Z-Score
###
def zscore_image(infile, mask, outfile):
import os, commands
cmd = "fslstats %s -k %s -m" % (infile, mask)
print cmd
mean = commands.getstatusoutput(cmd)
mean = float(mean[1])