def methods( t1full, t2full, t2flair, options, verbose=False, debug=False, nohup=False):
print('\nRunnning ants_lct.py\n')
if qa.qa_input_files( input_files, False):
if not os.path.exists( out_directory ):
os.makedirs( out_directory )
# bash $0 -d 3 -e brainWithSkullTemplate.nii.gz -m brainPrior.nii.gz -p segmentationPriors%d.nii.gz -o output \${anatomicalImages[@]}
callCommand = ['antsLongitudinalCorticalThickness.sh', '-d', '3', '-t', options['t_option'], '-w', '0.25',
'-e', options['e_option'], '-m', options['m_option'], '-f', options['f_option'], '-p', options['p_option'],
'-o', options['o_option'], t1full
]
callCommand = callCommand + [ '-a', t1full ]
if not t2full == None:
callCommand = callCommand + [ '-a', t2full ]
if not inArgs.t2flair == None:
callCommand = callCommand + [ '-a', t2flair ]
util.iw_subprocess( callCommand, verbose, debug, nohup )
else:
print('\nUnable to run iwAntsCT.py. Failed input QA.')
qa.qa_exist( input_files, True )
print('\n')
def methods(t1full,
t2full,
t2flair,
options,
verbose=False,
debug=False,
nohup=False):
print('\nRunnning ants_ct.py\n')
if qa.qa_input_files(input_files, False):
if not os.path.exists(out_directory):
os.makedirs(out_directory)
callCommand = [
'antsCorticalThickness.sh', '-d', '3', '-t', options['t_option'],
'-w', '0.25', '-e', options['e_option'], '-m', options['m_option'],
'-f', options['f_option'], '-p', options['p_option'], '-o',
options['o_option']
]
callCommand = callCommand + ['-a', t1full]
if not t2full == None:
callCommand = callCommand + ['-a', t2full]
if not inArgs.t2flair == None:
callCommand = callCommand + ['-a', t2flair]
util.iw_subprocess(callCommand, verbose, debug, nohup)
else:
print('\nUnable to run iwAntsCT.py. Failed input QA.')
qa.qa_exist(input_files, True)
print('\n')
m_option,
'f_option':
f_option,
'p_option':
p_option,
'p_options':
[p1_option, p2_option, p3_option, p4_option, p5_option, p6_option],
'o_option':
inArgs.outdir + '/' + inArgs.outprefix
}
# QA inputs
#
if 'input' in inArgs.qa:
qa.qa_input_files(input_files, True, False)
qa.freeview(input_files[:2], True, inArgs.verbose)
qa.freeview(input_files[2:], True, inArgs.verbose)
# Archive/Clean Directory
if inArgs.archive:
archive(out_directory, 'archive')
if inArgs.clean:
clean(out_directory)
# Replace Mask
if inArgs.mask is not None:
def main():
usage = "usage: %prog [options] arg1 arg2"
parser = argparse.ArgumentParser(prog='create_sphere')
parser.add_argument("in_image", help="Image")
parser.add_argument("in_csv", help="CSV file containing coordinates")
parser.add_argument("out_image", help="Image")
parser.add_argument("--label", help="Label number", type=int, default=1000)
parser.add_argument("--radius", help="Radius of ROI", type=int, default=5)
parser.add_argument("--roi_prefix", help="ROI prefix added to --image", default="roi.")
parser.add_argument("--roi_add", help="Display Results", action="store_true", default=False)
parser.add_argument("--roi_type", help="ROI Type (sphere, point)", choices=['sphere', 'point'], default='sphere')
parser.add_argument("--merge", help="Merge ROIs", action="store_true", default=True)
parser.add_argument("--collapse", help="Collapse ROIs", action="store_true", default=True)
parser.add_argument("-d", "--display", help="Display Results", action="store_true", default=False)
parser.add_argument("-v", "--verbose", help="Verbose flag", action="store_true", default=False)
parser.add_argument("--debug", help="Debug flag", action="store_true", default=False)
parser.add_argument("--method", help="Method ( 'equation', 'convolution')", choices = ('convolution, equation'),
default='convolution')
parser.add_argument("--qi", help="QA inputs", action="store_true", default=False)
parser.add_argument("--qo", help="QA outputs", action="store_true", default=False)
parser.add_argument("-r", "--run", help="Run processing pipeline", action="store_true", default=False)
# group = parser.add_mutually_exclusive_group(required=True)
parser.add_argument("--point", help="Input a single point", nargs=3, type=float, default=None)
inArgs = parser.parse_args()
input_files = [[inArgs.in_image, ':colormap=grayscale']]
# output_files = [[ inArgs.image, ':colormap=grayscale'],
# [ roiImage, ':colormap=jet']]
if inArgs.roi_type == 'sphere':
radius = inArgs.radius
else:
radius = 0
if inArgs.debug:
print ("inArgs.in_image = " + str(inArgs.in_image))
print ("inArgs.in_csv = " + str(inArgs.in_csv))
print ("inArgs.out_image = " + str(inArgs.out_image))
print ("inArgs.radius = " + str(inArgs.radius))
print
print ("radius = " + str(radius))
print
print ("inArgs.display = " + str(inArgs.display))
print ("inArgs.debug = " + str(inArgs.debug))
print ("inArgs.verbose = " + str(inArgs.verbose))
print
# print ("ROI image = " + roiImage)
print
if inArgs.qi:
_qa_utilities.qa_input_files(input_files, inArgs.verbose, False)
in_points = pd.read_csv(inArgs.in_csv)
create_roi(inArgs.out_image, inArgs.in_image, in_points, inArgs.radius, inArgs.method, inArgs.verbose, inArgs.debug)