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meshfitting.py
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meshfitting.py
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import os
from multiprocessing import Pool
from functools import partial
def meshGeneration(subject_dir, template_dir, param_dir, tmps_dir, vtks_dir, dofs_dir):
os.system('rm {0}/*.txt'.format(subject_dir))
os.system('rm {0}/*'.format(vtks_dir))
os.system('rm {0}/*'.format(tmps_dir))
for fr in ['ED', 'ES']:
###########################################################################
# extract meshes of lvendo, lvepi, lvmyo, rv and rveip at ED and ES, respectively
os.system('binarize '
'{0}/PHsegmentation_{2}.gipl '
'{1}/vtk_RV_{2}.nii.gz '
'4 4 255 0'
.format(subject_dir, tmps_dir, fr))
os.system('mcubes '
'{0}/vtk_RV_{2}.nii.gz '
'{1}/RV_{2}.vtk '
'120 -blur 2'
.format(tmps_dir, vtks_dir, fr))
os.system('binarize '
'{0}/PHsegmentation_{2}.gipl '
'{1}/vtk_RVepi_{2}.nii.gz '
'3 4 255 0'
.format(subject_dir, tmps_dir, fr))
os.system('mcubes '
'{0}/vtk_RVepi_{2}.nii.gz '
'{1}/RVepi_{2}.vtk '
'120 -blur 2'
.format(tmps_dir, vtks_dir, fr))
os.system('padding '
'{0}/PHsegmentation_{2}.gipl '
'{0}/PHsegmentation_{2}.gipl '
'{1}/vtk_LV_{2}.nii.gz '
'4 0'
.format(subject_dir, tmps_dir, fr))
os.system('padding '
'{1}/vtk_LV_{2}.nii.gz '
'{0}/PHsegmentation_{2}.gipl '
'{1}/vtk_LV_{2}.nii.gz '
'3 0'
.format(subject_dir, tmps_dir, fr))
os.system('binarize '
'{0}/PHsegmentation_{2}.gipl '
'{1}/vtk_LVendo_{2}.nii.gz '
'1 1 255 0'
.format(subject_dir, tmps_dir, fr))
os.system('mcubes '
'{0}/vtk_LVendo_{2}.nii.gz '
'{1}/LVendo_{2}.vtk '
'120 -blur 2'
.format(tmps_dir, vtks_dir, fr))
os.system('binarize '
'{0}/PHsegmentation_{2}.gipl '
'{1}/vtk_LVepi_{2}.nii.gz '
'1 2 255 0'
.format(subject_dir, tmps_dir, fr))
os.system('mcubes '
'{0}/vtk_LVepi_{2}.nii.gz '
'{1}/LVepi_{2}.vtk '
'120 -blur 2'
.format(tmps_dir, vtks_dir, fr))
os.system('binarize '
'{0}/PHsegmentation_{2}.gipl '
'{1}/vtk_LVmyo_{2}.nii.gz '
'2 2 255 0'
.format(subject_dir, tmps_dir, fr))
os.system('mcubes '
'{0}/vtk_LVmyo_{2}.nii.gz '
'{1}/LVmyo_{2}.vtk '
'120 -blur 2'
.format(tmps_dir, vtks_dir, fr))
# os.system('binarize '
# '{0}/seg_lvsa_SR_{2}.nii.gz '
# '{1}/vtk_RV_{2}.nii.gz '
# '4 4 255 0'
# .format(subject_dir, tmps_dir, fr))
#
# os.system('mcubes '
# '{0}/vtk_RV_{2}.nii.gz '
# '{1}/RV_{2}.vtk '
# '120 -blur 2'
# .format(tmps_dir, vtks_dir, fr))
#
# os.system('binarize '
# '{0}/seg_lvsa_SR_{2}.nii.gz '
# '{1}/vtk_RVepi_{2}.nii.gz '
# '3 4 255 0'
# .format(subject_dir, tmps_dir, fr))
#
# os.system('mcubes '
# '{0}/vtk_RVepi_{2}.nii.gz '
# '{1}/RVepi_{2}.vtk '
# '120 -blur 2'
# .format(tmps_dir, vtks_dir, fr))
#
# os.system('padding '
# '{0}/seg_lvsa_SR_{2}.nii.gz '
# '{0}/seg_lvsa_SR_{2}.nii.gz '
# '{1}/vtk_LV_{2}.nii.gz '
# '4 0'
# .format(subject_dir, tmps_dir, fr))
#
# os.system('padding '
# '{1}/vtk_LV_{2}.nii.gz '
# '{0}/seg_lvsa_SR_{2}.nii.gz '
# '{1}/vtk_LV_{2}.nii.gz '
# '3 0'
# .format(subject_dir, tmps_dir, fr))
#
# os.system('binarize '
# '{0}/seg_lvsa_SR_{2}.nii.gz '
# '{1}/vtk_LVendo_{2}.nii.gz '
# '1 1 255 0'
# .format(subject_dir, tmps_dir, fr))
#
# os.system('mcubes '
# '{0}/vtk_LVendo_{2}.nii.gz '
# '{1}/LVendo_{2}.vtk '
# '120 -blur 2'
# .format(tmps_dir, vtks_dir, fr))
#
# os.system('binarize '
# '{0}/seg_lvsa_SR_{2}.nii.gz '
# '{1}/vtk_LVepi_{2}.nii.gz '
# '1 2 255 0'
# .format(subject_dir, tmps_dir, fr))
#
# os.system('mcubes '
# '{0}/vtk_LVepi_{2}.nii.gz '
# '{1}/LVepi_{2}.vtk '
# '120 -blur 2'
# .format(tmps_dir, vtks_dir, fr))
#
# os.system('binarize '
# '{0}/seg_lvsa_SR_{2}.nii.gz '
# '{1}/vtk_LVmyo_{2}.nii.gz '
# '2 2 255 0'
# .format(subject_dir, tmps_dir, fr))
#
# os.system('mcubes '
# '{0}/vtk_LVmyo_{2}.nii.gz '
# '{1}/LVmyo_{2}.vtk '
# '120 -blur 2'
# .format(tmps_dir, vtks_dir, fr))
###############################################################################
#use landmark to initialise the registration
# os.system('prreg '
# '{0}/landmarks.vtk '
# '{1}/landmarks.vtk '
# '-dofout {2}/landmarks.dof.gz'
# .format(subject_dir, template_dir, dofs_dir))
###############################################################################
for fr in ['ED', 'ES']:
# os.system('msrreg 3 '
# '{0}/RV_{4}.vtk '
# '{0}/LVendo_{4}.vtk '
# '{0}/LVepi_{4}.vtk '
# '{1}/RV_{4}.vtk '
# '{1}/LVendo_{4}.vtk '
# '{1}/LVepi_{4}.vtk '
# '-dofin {2}/landmarks.dof.gz '
# '-dofout {3}/{4}.dof.gz '
# '-symmetric'
# .format(vtks_dir, template_dir, dofs_dir, tmps_dir, fr))
os.system('msrreg 3 '
'{0}/RV_{3}.vtk '
'{0}/LVendo_{3}.vtk '
'{0}/LVepi_{3}.vtk '
'{1}/RV_{3}.vtk '
'{1}/LVendo_{3}.vtk '
'{1}/LVepi_{3}.vtk '
'-dofout {2}/{3}.dof.gz '
'-symmetric'
.format(vtks_dir, template_dir, tmps_dir, fr))
os.system('msrreg 2 '
'{0}/LVendo_{3}.vtk '
'{0}/LVepi_{3}.vtk '
'{1}/LVendo_{3}.vtk '
'{1}/LVepi_{3}.vtk '
'-dofin {2}/{3}.dof.gz '
'-dofout {2}/lv_{3}_rreg.dof.gz '
'-symmetric'
.format(vtks_dir, template_dir, tmps_dir, fr))
os.system('srreg '
'{0}/RV_{3}.vtk '
'{1}/RV_{3}.vtk '
'-dofin {2}/{3}.dof.gz '
'-dofout {2}/rv_{3}_rreg.dof.gz '
'-symmetric'
.format(vtks_dir, template_dir, tmps_dir, fr))
###########################################################################
os.system('ptransformation '
'{0}/RV_{2}.vtk '
'{0}/N_RV_{2}.vtk '
'-dofin {1}/rv_{2}_rreg.dof.gz'
.format(vtks_dir, tmps_dir, fr))
os.system('ptransformation '
'{0}/RVepi_{2}.vtk '
'{0}/N_RVepi_{2}.vtk '
'-dofin {1}/rv_{2}_rreg.dof.gz'
.format(vtks_dir, tmps_dir, fr))
os.system('ptransformation '
'{0}/LVendo_{2}.vtk '
'{0}/N_LVendo_{2}.vtk '
'-dofin {1}/lv_{2}_rreg.dof.gz'
.format(vtks_dir, tmps_dir, fr))
os.system('ptransformation '
'{0}/LVepi_{2}.vtk '
'{0}/N_LVepi_{2}.vtk '
'-dofin {1}/lv_{2}_rreg.dof.gz'
.format(vtks_dir, tmps_dir, fr))
os.system('ptransformation '
'{0}/LVmyo_{2}.vtk '
'{0}/N_LVmyo_{2}.vtk '
'-dofin {1}/lv_{2}_rreg.dof.gz'
.format(vtks_dir, tmps_dir, fr))
os.system('transformation '
'{0}/vtk_RV_{1}.nii.gz '
'{0}/N_vtk_RV_{1}.nii.gz '
'-dofin {0}/lv_{1}_rreg.dof.gz '
'-invert'
.format(tmps_dir, fr))
os.system('transformation '
'{0}/vtk_LV_{1}.nii.gz '
'{0}/N_vtk_LV_{1}.nii.gz '
'-dofin {0}/lv_{1}_rreg.dof.gz '
'-invert'
.format(tmps_dir, fr))
###########################################################################
#affine
os.system('areg '
'{0}/vtk_RV_{3}.nii.gz '
'{1}/N_vtk_RV_{3}.nii.gz '
'-dofout {1}/rv_{3}_areg.dof.gz '
'-parin {2}/segareg.txt'
.format(template_dir, tmps_dir, param_dir, fr))
os.system('areg '
'{0}/vtk_LV_{3}.nii.gz '
'{1}/N_vtk_LV_{3}.nii.gz '
'-dofout {1}/lv_{3}_areg.dof.gz '
'-parin {2}/segareg.txt'
.format(template_dir, tmps_dir, param_dir, fr))
#non-rigid
os.system('nreg '
'{0}/vtk_RV_{3}.nii.gz '
'{1}/N_vtk_RV_{3}.nii.gz '
'-dofin {1}/rv_{3}_areg.dof.gz '
'-dofout {1}/rv_{3}_nreg.dof.gz '
'-parin {2}/segreg.txt'
.format(template_dir, tmps_dir, param_dir, fr))
os.system('snreg '
'{0}/RV_{3}.vtk '
'{1}/N_RV_{3}.vtk '
'-dofin {2}/rv_{3}_nreg.dof.gz '
'-dofout {2}/rv{3}ds8.dof.gz '
'-ds 8 -symmetric'
.format(template_dir, vtks_dir, tmps_dir, fr))
os.system('nreg '
'{0}/vtk_LV_{3}.nii.gz '
'{1}/N_vtk_LV_{3}.nii.gz '
'-dofin {1}/lv_{3}_areg.dof.gz '
'-dofout {1}/lv_{3}_nreg.dof.gz '
'-parin {2}/segreg.txt'
.format(template_dir, tmps_dir, param_dir, fr))
os.system('msnreg 2 '
'{0}/LVendo_{3}.vtk '
'{0}/LVepi_{3}.vtk '
'{1}/N_LVendo_{3}.vtk '
'{1}/N_LVepi_{3}.vtk '
'-dofin {2}/lv_{3}_nreg.dof.gz '
'-dofout {2}/lv{3}final.dof.gz '
'-ds 4 -symmetric'
.format(template_dir, vtks_dir, tmps_dir, fr))
# same number of points
os.system('cardiacsurfacemap '
'{0}/LVendo_{3}.vtk '
'{1}/N_LVendo_{3}.vtk '
'{2}/lv{3}final.dof.gz '
'{1}/F_LVendo_{3}.vtk'
.format(template_dir, vtks_dir, tmps_dir, fr))
os.system('cardiacsurfacemap '
'{0}/LVepi_{3}.vtk '
'{1}/N_LVepi_{3}.vtk '
'{2}/lv{3}final.dof.gz '
'{1}/F_LVepi_{3}.vtk'
.format(template_dir, vtks_dir, tmps_dir, fr))
os.system('ptransformation '
'{0}/LVmyo_{3}.vtk '
'{1}/F_LVmyo_{3}.vtk '
'-dofin {2}/lv{3}final.dof.gz'
.format(template_dir, vtks_dir, tmps_dir, fr))
os.system('cardiacsurfacemap '
'{0}/RV_{3}.vtk '
'{1}/N_RV_{3}.vtk '
'{2}/rv{3}ds8.dof.gz '
'{1}/C_RV_{3}.vtk'
.format(template_dir, vtks_dir, tmps_dir, fr))
###########################################################################
os.system('cp {0}/F_LVendo_{1}.vtk {0}/S_LVendo_{1}.vtk'.format(vtks_dir, fr))
os.system('cp {0}/F_LVepi_{1}.vtk {0}/S_LVepi_{1}.vtk'.format(vtks_dir, fr))
os.system('cp {0}/F_LVmyo_{1}.vtk {0}/S_LVmyo_{1}.vtk'.format(vtks_dir, fr))
os.system('cp {0}/F_LVmyo_{1}.vtk {0}/C_LVmyo_{1}.vtk'.format(vtks_dir, fr))
os.system('cp {0}/F_LVmyo_{1}.vtk {0}/W_LVmyo_{1}.vtk'.format(vtks_dir, fr))
os.system('cp {0}/C_RV_{1}.vtk {0}/S_RV_{1}.vtk'.format(vtks_dir, fr))
os.system('cp {0}/C_RV_{1}.vtk {0}/W_RV_{1}.vtk'.format(vtks_dir, fr))
###########################################################################
# compute the quantities of the heart with respect to template
os.system('cardiacwallthickness '
'{0}/F_LVendo_{1}.vtk '
'{0}/F_LVepi_{1}.vtk '
'-myocardium '
'{0}/W_LVmyo_{1}.vtk'
.format(vtks_dir, fr))
os.system('cardiacenlargedistance '
'{0}/S_LVendo_{2}.vtk '
'{0}/S_LVepi_{2}.vtk '
'{1}/LVendo_{2}.vtk '
'{1}/LVepi_{2}.vtk '
'-myocardium '
'{0}/S_LVmyo_{2}.vtk'
.format(vtks_dir, template_dir, fr))
os.system('DiscreteCurvatureEstimator '
'{0}/C_LVmyo_{1}.vtk '
'{0}/FC_LVmyo_{1}.vtk'
.format(vtks_dir, fr))
os.system('cardiaccurvature '
'{0}/FC_LVmyo_{1}.vtk '
'{0}/C_LVmyo_{1}.vtk '
'-smooth 64'
.format(vtks_dir, fr))
os.system('DiscreteCurvatureEstimator '
'{0}/C_RV_{1}.vtk '
'{0}/FC_RV_{1}.vtk'
.format(vtks_dir, fr))
os.system('cardiaccurvature '
'{0}/FC_RV_{1}.vtk '
'{0}/C_RV_{1}.vtk '
'-smooth 64'
.format(vtks_dir, fr))
os.system('sevaluation '
'{0}/S_RV_{2}.vtk '
'{1}/RV_{2}.vtk '
'-scalar '
'-signed'
.format(vtks_dir, template_dir, fr))
os.system('cardiacwallthickness '
'{0}/W_RV_{1}.vtk '
'{0}/N_RVepi_{1}.vtk'
.format(vtks_dir, fr))
###########################################################################
# os.system('vtk2txt {0}/C_RV_{1}.vtk {2}/rv_{1}_curvature.txt'.format(vtks_dir, fr, subject_dir))
# os.system('vtk2txt {0}/W_RV_{1}.vtk {2}/rv_{1}_wallthickness.txt'.format(vtks_dir, fr, subject_dir))
# os.system('vtk2txt {0}/S_RV_{1}.vtk {2}/rv_{1}_signeddistances.txt'.format(vtks_dir, fr, subject_dir))
# os.system('vtk2txt {0}/W_LVmyo_{1}.vtk {2}/lv_myo{1}_wallthickness.txt'.format(vtks_dir, fr, subject_dir))
# os.system('vtk2txt {0}/C_LVmyo_{1}.vtk {2}/lv_myo{1}_curvature.txt'.format(vtks_dir, fr, subject_dir))
# os.system('vtk2txt {0}/S_LVmyo_{1}.vtk {2}/lv_myo{1}_signeddistances.txt'.format(vtks_dir, fr, subject_dir))
if fr == 'ED':
fr_ = 'ed'
os.system('vtk2txt {0}/C_RV_{1}.vtk {2}/rv_{3}_curvature.txt'.format(vtks_dir, fr, subject_dir, fr_))
os.system('vtk2txt {0}/W_RV_{1}.vtk {2}/rv_{3}_wallthickness.txt'.format(vtks_dir, fr, subject_dir, fr_))
os.system('vtk2txt {0}/S_RV_{1}.vtk {2}/rv_{3}_signeddistances.txt'.format(vtks_dir, fr, subject_dir, fr_))
os.system('vtk2txt {0}/W_LVmyo_{1}.vtk {2}/lv_myo{3}_wallthickness.txt'.format(vtks_dir, fr, subject_dir, fr_))
os.system('vtk2txt {0}/C_LVmyo_{1}.vtk {2}/lv_myo{3}_curvature.txt'.format(vtks_dir, fr, subject_dir, fr_))
os.system('vtk2txt {0}/S_LVmyo_{1}.vtk {2}/lv_myo{3}_signeddistances.txt'.format(vtks_dir, fr, subject_dir, fr_))
if fr == 'ES':
fr_ = 'es'
os.system('vtk2txt {0}/C_RV_{1}.vtk {2}/rv_{3}_curvature.txt'.format(vtks_dir, fr, subject_dir, fr_))
os.system('vtk2txt {0}/W_RV_{1}.vtk {2}/rv_{3}_wallthickness.txt'.format(vtks_dir, fr, subject_dir, fr_))
os.system('vtk2txt {0}/S_RV_{1}.vtk {2}/rv_{3}_signeddistances.txt'.format(vtks_dir, fr, subject_dir, fr_))
os.system('vtk2txt {0}/W_LVmyo_{1}.vtk {2}/lv_myo{3}_wallthickness.txt'.format(vtks_dir, fr, subject_dir, fr_))
os.system('vtk2txt {0}/C_LVmyo_{1}.vtk {2}/lv_myo{3}_curvature.txt'.format(vtks_dir, fr, subject_dir, fr_))
os.system('vtk2txt {0}/S_LVmyo_{1}.vtk {2}/lv_myo{3}_signeddistances.txt'.format(vtks_dir, fr, subject_dir, fr_))
def apply_PC(subject, data_dir, param_dir, template_dir, mirtk):
print(' co-registering {0}'.format(subject))
subject_dir = os.path.join(data_dir, subject)
if os.path.isdir(subject_dir):
tmps_dir = '{0}/tmps'.format(subject_dir)
vtks_dir = '{0}/vtks'.format(subject_dir)
dofs_dir = '{0}/dofs'.format(subject_dir)
meshGeneration(subject_dir, template_dir, param_dir, tmps_dir, vtks_dir, dofs_dir)
print(' finish generating meshes from segmentations in {0}'.format(subject))
else:
print(' {0} is not a valid directory, do nothing'.format(subject_dir))
def meshCoregstration(dir_0, dir_2, dir_3, coreNo, parallel, mirtk):
if parallel:
print('Generate meshes from segmentations running on {0} cores'.format(coreNo))
pool = Pool(processes = coreNo)
# partial only in Python 2.7+
pool.map(partial(apply_PC,
data_dir=dir_0,
param_dir=dir_2,
template_dir=dir_3,
mirtk=mirtk),
sorted(os.listdir(dir_0)))
else:
print('Generate meshes from segmentations running subsequently')
data_dir, param_dir, template_dir = dir_0, dir_2, dir_3
for subject in sorted(os.listdir(data_dir)):
print(' co-registering {0}'.format(subject))
subject_dir = os.path.join(data_dir, subject)
if not os.path.isdir(subject_dir):
print(' {0} is not a valid folder, Skip'.format(subject_dir))
continue
tmps_dir = '{0}/tmps'.format(subject_dir)
vtks_dir = '{0}/vtks'.format(subject_dir)
dofs_dir = '{0}/dofs'.format(subject_dir)
meshGeneration(subject_dir, template_dir, param_dir, tmps_dir, vtks_dir, dofs_dir)
print(' finish generating meshes from segmentations in {0}'.format(subject))