def returnCenterline(fname, div):
if centerline.returnCenterline(fname, 1, div) == 1:#this save the centerline: centerline/file_name_div_centerline.nii.gz
div += 1
returnCenterline(fname, div)
else:
#print centerline.returnCenterline(fname, 1, div)
#print div
return div
def returnCenterline(fname, div):
if centerline.returnCenterline(
fname, 1, div
) == 1: #this save the centerline: centerline/file_name_div_centerline.nii.gz
div += 1
returnCenterline(fname, div)
else:
#print centerline.returnCenterline(fname, 1, div)
#print div
return div
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')
