def main(file_name, smooth=3):
div = [25]
#div = [13,15,19,23,25]
#div = [5,7,9,11,13,15,19,23,25]
#div = int(div)
path, fname, ext_fname = sct.extract_fname(file_name)
exit = 0
print 'file to be processed: ', file_name
print 'Applying propseg to get the centerline as a binary image...'
#fname_seg = fname+'_seg'
fname_centerline = fname + '_centerline'
cmd = 'sct_propseg -i ' + file_name + ' -o . -t t2 -centerline-binary'
sct.run(cmd)
print 'centerline smoothing...'
fname_smooth = fname_centerline + '_smooth'
print 'Gauss sigma: ', smooth
cmd = 'fslmaths ' + fname_centerline + ' -s ' + str(
smooth) + ' ' + fname_smooth + ext_fname
sct.run(cmd)
for d in div:
add = d - 1
e = 1
print 'generating the centerline...'
while e == 1:
add += 1
#e = centerline.returnCenterline(fname_smooth+ext_fname, 1, add)
e = centerline.check_nurbs(add, None, None,
fname_smooth + ext_fname)
if add > 30:
exit = 1
break
if exit == 1:
break
d = add
size = e
nurbs_ctl_points = int(size) / d
#d = returnCenterline(fname_smooth+ext_fname, d)
print 'straightening... d = ', str(d)
#fcenterline = './centerlines/'+fname_smooth+'_'+str(d)+'_centerline.nii.gz'
cmd = 'sct_straighten_spinalcord -i ' + file_name + ' -c ' + fname_smooth + ext_fname + ' -n ' + str(
nurbs_ctl_points)
sct.run(cmd)
'''
print 'applying propseg'
fname_straight = fname+'_straight'+ext_fname
final_file_name = fname+'_straight_seg'+ext_fname
cmd = 'sct_propseg -i '+fname_straight+' -t t2'
'''
print 'apply warp to segmentation'
#final_file_name = fname+'_straightttt_seg'+ext_fname
final_file_name = fname + '_straight_seg' + ext_fname
#cmd = 'sct_WarpImageMultiTransform 3 '+fname_seg+ext_fname+' '+final_file_name+' warp_curve2straight.nii.gz'
cmd = 'sct_WarpImageMultiTransform 3 ' + fname_smooth + ext_fname + ' ' + final_file_name + ' warp_curve2straight.nii.gz'
sct.run(cmd)
print 'annalyzing the straightened file'
linear_fitting.returnSquaredErrors(final_file_name, d, size)
os.remove(fname_centerline + ext_fname)
os.remove(fname_smooth + ext_fname)
os.remove('warp_curve2straight.nii.gz')
os.remove('warp_straight2curve.nii.gz')
def main(file_name, smooth = 3):
div = [25]
#div = [13,15,19,23,25]
#div = [5,7,9,11,13,15,19,23,25]
#div = int(div)
path, fname, ext_fname = sct.extract_fname(file_name)
exit = 0
print 'file to be processed: ',file_name
print 'Applying propseg to get the centerline as a binary image...'
#fname_seg = fname+'_seg'
fname_centerline = fname+'_centerline'
cmd = 'sct_propseg -i '+file_name+' -o . -t t2 -centerline-binary'
sct.run(cmd)
print 'centerline smoothing...'
fname_smooth = fname_centerline+'_smooth'
print 'Gauss sigma: ', smooth
cmd = 'fslmaths '+fname_centerline+' -s '+str(smooth)+' '+fname_smooth+ext_fname
sct.run(cmd)
for d in div:
add = d - 1
e = 1
print 'generating the centerline...'
while e == 1:
add += 1
#e = centerline.returnCenterline(fname_smooth+ext_fname, 1, add)
e = centerline.check_nurbs(add, None, None, fname_smooth+ext_fname)
if add > 30:
exit = 1
break
if exit == 1:
break
d = add
size = e
nurbs_ctl_points = int(size)/d
#d = returnCenterline(fname_smooth+ext_fname, d)
print 'straightening... d = ', str(d)
#fcenterline = './centerlines/'+fname_smooth+'_'+str(d)+'_centerline.nii.gz'
cmd = 'sct_straighten_spinalcord -i '+file_name+' -c '+fname_smooth+ext_fname+' -n '+str(nurbs_ctl_points)
sct.run(cmd)
'''
print 'applying propseg'
fname_straight = fname+'_straight'+ext_fname
final_file_name = fname+'_straight_seg'+ext_fname
cmd = 'sct_propseg -i '+fname_straight+' -t t2'
'''
print 'apply warp to segmentation'
#final_file_name = fname+'_straightttt_seg'+ext_fname
final_file_name = fname+'_straight_seg'+ext_fname
#cmd = 'sct_WarpImageMultiTransform 3 '+fname_seg+ext_fname+' '+final_file_name+' warp_curve2straight.nii.gz'
cmd = 'sct_WarpImageMultiTransform 3 '+fname_smooth+ext_fname+' '+final_file_name+' warp_curve2straight.nii.gz'
sct.run(cmd)
print 'annalyzing the straightened file'
linear_fitting.returnSquaredErrors(final_file_name, d, size)
os.remove(fname_centerline+ext_fname)
os.remove(fname_smooth+ext_fname)
os.remove('warp_curve2straight.nii.gz')
os.remove('warp_straight2curve.nii.gz')
def main():
div = [3,5,7,9,11,13,15,19,23,25]
nurbs_ctl_points = param.nurbs_ctl_points
fitting_method = param.fitting_method
sigma = param.sigma
centerline = param.centerline
s = 0
d = 0
exit = 0
file_name = ''
warp = param.warp
try:
opts, args = getopt.getopt(sys.argv[1:],'hi:M:n:d:s:c:v:w:r:h:')
except getopt.GetoptError as err:
print str(err)
usage()
for opt, arg in opts:
if opt == '-h':
usage()
elif opt in ('-i'):
file_name = arg
elif opt in ('-M'):
fitting_method = arg
elif opt in ('-n'):
nurbs_ctl_points = int(arg)
elif opt in ('-d'):
d = 1
div = int(arg)
elif opt in ('-s'):
s = 1
sigma = str(arg)
elif opt in ('-c'):
centerline = str(arg)
fname_centerline = centerline
elif opt in ('-v'):
verbose = int(arg)
elif opt in ('-w'):
write = arg
elif opt in ('-r'):
remove = arg
print 'file to be processed: ',file_name
path, fname, ext_fname = sct.extract_fname(file_name)
if not fitting_method == 'NURBS' and not fitting_method == 'polynomial' and not fitting_method == 'non_parametrique' and not fitting_method == 'smooth':
usage()
if centerline == None:
# Generating centerline using propseg (Warning: be sure propseg work well with the input file)
print 'Applying propseg to get the centerline as a binary image...'
fname_centerline = fname+'_centerline'
cmd = 'sct_propseg -i ' + file_name + ' -o . -t t2 -centerline-binary'
sct.run(cmd)
else:
path, fname_centerline, ext_fname = sct.extract_fname(centerline)
if s is not 0:
print 'centerline smoothing...'
fname_smooth = fname_centerline+'_smooth'
print 'Gauss sigma: ', s
cmd = 'fslmaths ' + fname_centerline + ' -s ' + str(s) + ' ' + fname_smooth + ext_fname
sct.run(cmd)
fname_centerline = fname_smooth+ext_fname
else:
fname_centerline = centerline
if fitting_method == 'NURBS':
if not d and not nurbs_ctl_points:
for d in div:
add = d - 1
e = 1
print 'generating the centerline...'
# This loops stands for checking if nurbs will work with d
while e == 1:
add += 1
e = centerline.check_nurbs(add, None, None, fname_smooth+ext_fname)
if add > 30:
exit = 1
break
if exit == 1:
break
d = add
size = e
nurbs_ctl_points = int(size)/d
elif not nurbs_ctl_points:
nurbs_ctl_points = int(size)/d
print 'straightening... d = ', str(d)
# STRAIGHTEN USING NURBS
cmd = 'sct_straighten_spinalcord -i ' + file_name + ' -c ' + fname_centerline + ' -n ' + str(nurbs_ctl_points)
sct.run(cmd)
print 'apply warp to segmentation'
#final_file_name = fname+'_straightttt_seg'+ext_fname
final_file_name = fname + '_straight_seg' + ext_fname
#cmd = 'sct_WarpImageMultiTransform 3 '+fname_seg+ext_fname+' '+final_file_name+' warp_curve2straight.nii.gz'
cmd = 'sct_WarpImageMultiTransform 3 ' + fname_centerline + ' ' + final_file_name + ' warp_curve2straight.nii.gz'
sct.run(cmd)
print 'annalyzing the straightened file'
linear_fitting.returnSquaredErrors(final_file_name, d, size)
elif fitting_method == 'polynomial':
# STRAIGHTEN USING POLYNOMIAL FITTING
cmd = 'sct_straighten_spinalcord -i ' + file_name + ' -c ' + fname_smooth + ext_fname + ' -f polynomial -v 2'
d = 'polynomial'
size = 13
# STRAIGHTEN USING 'non_parametric'
sct.run(cmd)
print 'apply warp to segmentation'
#final_file_name = fname+'_straightttt_seg'+ext_fname
final_file_name = fname+'_straight_seg'+ext_fname
#cmd = 'sct_WarpImageMultiTransform 3 '+fname_seg+ext_fname+' '+final_file_name+' warp_curve2straight.nii.gz'
cmd = 'sct_WarpImageMultiTransform 3 '+fname_smooth+ext_fname+' '+final_file_name+' warp_curve2straight.nii.gz'
sct.run(cmd)
elif fitting_method == 'smooth':
# STRAIGHTEN USING POLYNOMIAL FITTING
cmd = 'sct_straighten_spinalcord -i ' + file_name + ' -c ' + fname_centerline + ' -f smooth -v 2'
d = 'smooth'
size = 13
# STRAIGHTEN USING 'non_parametric'
sct.run(cmd)
if warp == 1:
print 'apply warp to segmentation'
#final_file_name = fname+'_straightttt_seg'+ext_fname
final_file_name = fname+'_straight_seg'+ext_fname
#cmd = 'sct_WarpImageMultiTransform 3 '+fname_seg+ext_fname+' '+final_file_name+' warp_curve2straight.nii.gz'
cmd = 'sct_WarpImageMultiTransform 3 '+fname_centerline+' '+final_file_name+' warp_curve2straight.nii.gz'
else:
print 'Applying propseg to the straightened volume...'
fname_straightened = fname+'_straight'
cmd = 'sct_propseg -i ' + fname_straightened + ext_fname +' -o . -t t2 -centerline-binary'
final_file_name = fname_straightened + '_centerline' + ext_fname
sct.run(cmd)
elif fitting_method == 'non-parametric':
cmd = 'sct_straighten_spinalcord -i '+file_name+' -c '+fname_smooth+ext_fname+' -f non_parametrique -v 2'
d = 'polynomial'
size = 13
# STRAIGHTEN USING 'non_parametric'
sct.run(cmd)
print 'apply warp to segmentation'
#final_file_name = fname+'_straightttt_seg'+ext_fname
final_file_name = fname+'_straight_seg'+ext_fname
#cmd = 'sct_WarpImageMultiTransform 3 '+fname_seg+ext_fname+' '+final_file_name+' warp_curve2straight.nii.gz'
cmd = 'sct_WarpImageMultiTransform 3 '+fname_smooth+ext_fname+' '+final_file_name+' warp_curve2straight.nii.gz'
sct.run(cmd)
print 'annalyzing the straightened file'
linear_fitting.returnSquaredErrors(final_file_name, d, size)
os.remove(fname_centerline+ext_fname)
os.remove(fname_smooth+ext_fname)
os.remove('warp_curve2straight.nii.gz')
os.remove('warp_straight2curve.nii.gz')
def main():
div = [3, 5, 7, 9, 11, 13, 15, 19, 23, 25]
nurbs_ctl_points = param.nurbs_ctl_points
fitting_method = param.fitting_method
sigma = param.sigma
centerline = param.centerline
s = 0
d = 0
exit = 0
file_name = ''
warp = param.warp
try:
opts, args = getopt.getopt(sys.argv[1:], 'hi:M:n:d:s:c:v:w:r:h:')
except getopt.GetoptError as err:
print str(err)
usage()
for opt, arg in opts:
if opt == '-h':
usage()
elif opt in ('-i'):
file_name = arg
elif opt in ('-M'):
fitting_method = arg
elif opt in ('-n'):
nurbs_ctl_points = int(arg)
elif opt in ('-d'):
d = 1
div = int(arg)
elif opt in ('-s'):
s = 1
sigma = str(arg)
elif opt in ('-c'):
centerline = str(arg)
fname_centerline = centerline
elif opt in ('-v'):
verbose = int(arg)
elif opt in ('-w'):
write = arg
elif opt in ('-r'):
remove = arg
print 'file to be processed: ', file_name
path, fname, ext_fname = sct.extract_fname(file_name)
if not fitting_method == 'NURBS' and not fitting_method == 'polynomial' and not fitting_method == 'non_parametrique' and not fitting_method == 'smooth':
usage()
if centerline == None:
# Generating centerline using propseg (Warning: be sure propseg work well with the input file)
print 'Applying propseg to get the centerline as a binary image...'
fname_centerline = fname + '_centerline'
cmd = 'sct_propseg -i ' + file_name + ' -o . -t t2 -centerline-binary'
sct.run(cmd)
else:
path, fname_centerline, ext_fname = sct.extract_fname(centerline)
if s is not 0:
print 'centerline smoothing...'
fname_smooth = fname_centerline + '_smooth'
print 'Gauss sigma: ', s
cmd = 'fslmaths ' + fname_centerline + ' -s ' + str(
s) + ' ' + fname_smooth + ext_fname
sct.run(cmd)
fname_centerline = fname_smooth + ext_fname
else:
fname_centerline = centerline
if fitting_method == 'NURBS':
if not d and not nurbs_ctl_points:
for d in div:
add = d - 1
e = 1
print 'generating the centerline...'
# This loops stands for checking if nurbs will work with d
while e == 1:
add += 1
e = centerline.check_nurbs(add, None, None,
fname_smooth + ext_fname)
if add > 30:
exit = 1
break
if exit == 1:
break
d = add
size = e
nurbs_ctl_points = int(size) / d
elif not nurbs_ctl_points:
nurbs_ctl_points = int(size) / d
print 'straightening... d = ', str(d)
# STRAIGHTEN USING NURBS
cmd = 'sct_straighten_spinalcord -i ' + file_name + ' -c ' + fname_centerline + ' -n ' + str(
nurbs_ctl_points)
sct.run(cmd)
print 'apply warp to segmentation'
#final_file_name = fname+'_straightttt_seg'+ext_fname
final_file_name = fname + '_straight_seg' + ext_fname
#cmd = 'sct_WarpImageMultiTransform 3 '+fname_seg+ext_fname+' '+final_file_name+' warp_curve2straight.nii.gz'
cmd = 'sct_WarpImageMultiTransform 3 ' + fname_centerline + ' ' + final_file_name + ' warp_curve2straight.nii.gz'
sct.run(cmd)
print 'annalyzing the straightened file'
linear_fitting.returnSquaredErrors(final_file_name, d, size)
elif fitting_method == 'polynomial':
# STRAIGHTEN USING POLYNOMIAL FITTING
cmd = 'sct_straighten_spinalcord -i ' + file_name + ' -c ' + fname_smooth + ext_fname + ' -f polynomial -v 2'
d = 'polynomial'
size = 13
# STRAIGHTEN USING 'non_parametric'
sct.run(cmd)
print 'apply warp to segmentation'
#final_file_name = fname+'_straightttt_seg'+ext_fname
final_file_name = fname + '_straight_seg' + ext_fname
#cmd = 'sct_WarpImageMultiTransform 3 '+fname_seg+ext_fname+' '+final_file_name+' warp_curve2straight.nii.gz'
cmd = 'sct_WarpImageMultiTransform 3 ' + fname_smooth + ext_fname + ' ' + final_file_name + ' warp_curve2straight.nii.gz'
sct.run(cmd)
elif fitting_method == 'smooth':
# STRAIGHTEN USING POLYNOMIAL FITTING
cmd = 'sct_straighten_spinalcord -i ' + file_name + ' -c ' + fname_centerline + ' -f smooth -v 2'
d = 'smooth'
size = 13
# STRAIGHTEN USING 'non_parametric'
sct.run(cmd)
if warp == 1:
print 'apply warp to segmentation'
#final_file_name = fname+'_straightttt_seg'+ext_fname
final_file_name = fname + '_straight_seg' + ext_fname
#cmd = 'sct_WarpImageMultiTransform 3 '+fname_seg+ext_fname+' '+final_file_name+' warp_curve2straight.nii.gz'
cmd = 'sct_WarpImageMultiTransform 3 ' + fname_centerline + ' ' + final_file_name + ' warp_curve2straight.nii.gz'
else:
print 'Applying propseg to the straightened volume...'
fname_straightened = fname + '_straight'
cmd = 'sct_propseg -i ' + fname_straightened + ext_fname + ' -o . -t t2 -centerline-binary'
final_file_name = fname_straightened + '_centerline' + ext_fname
sct.run(cmd)
elif fitting_method == 'non-parametric':
cmd = 'sct_straighten_spinalcord -i ' + file_name + ' -c ' + fname_smooth + ext_fname + ' -f non_parametrique -v 2'
d = 'polynomial'
size = 13
# STRAIGHTEN USING 'non_parametric'
sct.run(cmd)
print 'apply warp to segmentation'
#final_file_name = fname+'_straightttt_seg'+ext_fname
final_file_name = fname + '_straight_seg' + ext_fname
#cmd = 'sct_WarpImageMultiTransform 3 '+fname_seg+ext_fname+' '+final_file_name+' warp_curve2straight.nii.gz'
cmd = 'sct_WarpImageMultiTransform 3 ' + fname_smooth + ext_fname + ' ' + final_file_name + ' warp_curve2straight.nii.gz'
sct.run(cmd)
print 'annalyzing the straightened file'
linear_fitting.returnSquaredErrors(final_file_name, d, size)
os.remove(fname_centerline + ext_fname)
os.remove(fname_smooth + ext_fname)
os.remove('warp_curve2straight.nii.gz')
os.remove('warp_straight2curve.nii.gz')
def main(file_name, smooth = 3):
div = [5]
#,7,9,11,13,15,19,23,25]
#div = int(div)
path, fname, ext_fname = sct.extract_fname(file_name)
print 'file to be processed: ',file_name
print 'Applying propseg...'
fname_seg = fname+'_seg'
cmd = 'sct_propseg -i '+file_name+' -o . -t t2'
sct.run(cmd)
print 'image smoothing...'
fname_smooth = fname_seg+'_smooth'
print 'Gauss sigma: ', smooth
cmd = 'fslmaths '+fname_seg+' -s '+str(smooth)+' '+fname_smooth+ext_fname
sct.run(cmd)
for d in div:
add = d - 1
e = 1
print 'generating the centerline...'
while e == 1:
add += 1
e = centerline.returnCenterline(fname_smooth+ext_fname, 1, add)
d = add
#d = returnCenterline(fname_smooth+ext_fname, d)
print 'straightening... d = ', str(d)
fcenterline = './centerlines/'+fname_smooth+'_'+str(d)+'_centerline.nii.gz'
cmd = 'sct_straighten_spinalcord -i '+file_name+' -c '+fcenterline
sct.run(cmd)
'''
print 'applying propseg'
fname_straight = fname+'_straight'+ext_fname
final_file_name = fname+'_straight_seg'+ext_fname
cmd = 'sct_propseg -i '+fname_straight+' -t t2'
'''
print 'apply warp to segmentation'
#final_file_name = fname+'_straightttt_seg'+ext_fname
final_file_name = fname+'_straight_seg'+ext_fname
#cmd = 'sct_WarpImageMultiTransform 3 '+fname_seg+ext_fname+' '+final_file_name+' warp_curve2straight.nii.gz'
cmd = 'sct_WarpImageMultiTransform 3 '+fname_smooth+ext_fname+' '+final_file_name+' warp_curve2straight.nii.gz'
sct.run(cmd)
print 'annalyzing the straightened file'
linear_fitting.returnSquaredErrors(final_file_name, d)
os.remove(fname_seg+ext_fname)
os.remove(fname_smooth+ext_fname)
os.remove('warp_curve2straight.nii.gz')
os.remove('warp_straight2curve.nii.gz')