def warpANTSAffine(targetName, referenceName, affineName, oname, interpolationType='trilinear'):
baseName=rcommon.getBaseFileName(targetName)
nib_target=nib.load(targetName)
nib_reference=nib.load(referenceName)
M=nib_target.get_affine()
F=nib_reference.get_affine()
referenceShape=np.array(nib_reference.shape, dtype=np.int32)
######Load and compose affine#####
if not affineName:
T=np.eye(4)
else:
T=rcommon.readAntsAffine(affineName)
affineComposition=np.linalg.inv(M).dot(T.dot(F))
######################
if interpolationType=='NN':
target=nib_target.get_data().squeeze().astype(np.int32)
target=np.copy(target, order='C')
warped=np.array(tf.warp_discrete_volumeNNAffine(target, referenceShape, affineComposition)).astype(np.int16)
else:
target=nib_target.get_data().squeeze().astype(np.float64)
target=np.copy(target, order='C')
warped=np.array(tf.warp_volume_affine(target, referenceShape, affineComposition)).astype(np.int16)
warped=nib.Nifti1Image(warped, F)
if not oname:
oname="warped"+baseName+"nii.gz"
warped.to_filename(oname)
def save_registration_results(init_affine, displacement, inverse, params):
r'''
Warp the target image using the obtained deformation field
'''
fixed = nib.load(params.reference)
fixed_affine = fixed.get_affine()
reference_shape = np.array(fixed.shape, dtype=np.int32)
warp_dir = params.warp_dir
base_moving = rcommon.getBaseFileName(params.target)
base_fixed = rcommon.getBaseFileName(params.reference)
moving = nib.load(params.target).get_data().squeeze().astype(np.float64)
moving = moving.copy(order='C')
warped = np.array(tf.warp_volume(moving, displacement)).astype(np.int16)
img_warped = nib.Nifti1Image(warped, fixed_affine)
img_warped.to_filename('warpedDiff_'+base_moving+'_'+base_fixed+'.nii.gz')
#---warp the target image using the affine transformation only---
moving = nib.load(params.target).get_data().squeeze().astype(np.float64)
moving = moving.copy(order='C')
warped = np.array(
tf.warp_volume_affine(moving, reference_shape, init_affine)
).astype(np.int16)
img_warped = nib.Nifti1Image(warped, fixed_affine)
img_warped.to_filename('warpedAffine_'+base_moving+'_'+base_fixed+'.nii.gz')
#---warp all volumes in the warp directory using NN interpolation
names = [os.path.join(warp_dir, name) for name in os.listdir(warp_dir)]
for name in names:
to_warp = nib.load(name).get_data().squeeze().astype(np.int32)
to_warp = to_warp.copy(order='C')
base_warp = rcommon.getBaseFileName(name)
warped = np.array(
tf.warp_discrete_volumeNN(to_warp, displacement)).astype(np.int16)
img_warped = nib.Nifti1Image(warped, fixed_affine)
img_warped.to_filename('warpedDiff_'+base_warp+'_'+base_fixed+'.nii.gz')
#---finally, the optional output
if params.output_list == None:
return
if 'lattice' in params.output_list:
save_deformed_lattice_3d(
displacement,
'latticeDispDiff_'+base_moving+'_'+base_fixed+'.nii.gz')
if 'inv_lattice' in params.output_list:
save_deformed_lattice_3d(
inverse, 'invLatticeDispDiff_'+base_moving+'_'+base_fixed+'.nii.gz')
if 'displacement' in params.output_list:
np.save('dispDiff_'+base_moving+'_'+base_fixed+'.npy', displacement)
if 'inverse' in params.output_list:
np.save('invDispDiff_'+base_moving+'_'+base_fixed+'.npy', inverse)
def showRegistrationResultMidSlices(fnameMoving, fnameFixed, fnameAffine=None):
'''
showRegistrationResultMidSlices('IBSR_01_ana_strip.nii.gz', 't1_icbm_normal_1mm_pn0_rf0_peeled.nii.gz', 'IBSR_01_ana_strip_t1_icbm_normal_1mm_pn0_rf0_peeledAffine.txt')
showRegistrationResultMidSlices('warpedDiff_IBSR_01_ana_strip_t1_icbm_normal_1mm_pn0_rf0_peeled.nii.gz', 't1_icbm_normal_1mm_pn0_rf0_peeled.nii.gz', None)
showRegistrationResultMidSlices('warpedDiff_IBSR_01_ana_strip_IBSR_02_ana_strip.nii.gz', '/opt/registration/data/t1/IBSR18/IBSR_02/IBSR_02_ana_strip.nii.gz', None)
showRegistrationResultMidSlices('warpedDiff_IBSR_01_segTRI_ana_IBSR_02_ana_strip.nii.gz', '/opt/registration/data/t1/IBSR18/IBSR_02/IBSR_02_segTRI_ana.nii.gz', None)
##Worst pair:
showRegistrationResultMidSlices('warpedDiff_IBSR_16_segTRI_ana_IBSR_12_ana_strip.nii.gz', '/opt/registration/data/t1/IBSR18/IBSR_12/IBSR_12_segTRI_ana.nii.gz', None)
showRegistrationResultMidSlices('/opt/registration/data/t1/IBSR18/IBSR_16/IBSR_16_segTRI_ana.nii.gz', '/opt/registration/data/t1/IBSR18/IBSR_12/IBSR_12_segTRI_ana.nii.gz', None)
showRegistrationResultMidSlices('/opt/registration/data/t1/IBSR18/IBSR_16/IBSR_16_ana_strip.nii.gz', '/opt/registration/data/t1/IBSR18/IBSR_12/IBSR_12_ana_strip.nii.gz', None)
showRegistrationResultMidSlices('warpedAffine_IBSR_16_segTRI_ana_IBSR_12_ana_strip.nii.gz', '/opt/registration/data/t1/IBSR18/IBSR_12/IBSR_12_segTRI_ana.nii.gz', None)
showRegistrationResultMidSlices('warpedDiff_IBSR_16_ana_strip_IBSR_12_ana_strip.nii.gz', '/opt/registration/data/t1/IBSR18/IBSR_12/IBSR_12_ana_strip.nii.gz', None)
showRegistrationResultMidSlices('warpedAffine_IBSR_16_ana_strip_IBSR_12_ana_strip.nii.gz', '/opt/registration/data/t1/IBSR18/IBSR_12/IBSR_12_ana_strip.nii.gz', None)
showRegistrationResultMidSlices('/opt/registration/data/t1/IBSR18/IBSR_10/IBSR_10_ana_strip.nii.gz', '/opt/registration/data/t1/IBSR18/IBSR_16/IBSR_16_ana_strip.nii.gz', None)
showRegistrationResultMidSlices('warpedAffine_IBSR_10_ana_strip_IBSR_16_ana_strip.nii.gz', '/opt/registration/data/t1/IBSR18/IBSR_16/IBSR_16_ana_strip.nii.gz', None)
showRegistrationResultMidSlices('warpedAffine_IBSR_16_ana_strip_IBSR_10_ana_strip.nii.gz', '/opt/registration/data/t1/IBSR18/IBSR_10/IBSR_10_ana_strip.nii.gz', None)
showRegistrationResultMidSlices('warpedDiff_IBSR_16_ana_strip_IBSR_10_ana_strip.nii.gz', '/opt/registration/data/t1/IBSR18/IBSR_10/IBSR_10_ana_strip.nii.gz', None)
showRegistrationResultMidSlices('warpedDiff_IBSR_01_ana_strip_IBSR_08_ana_strip.nii.gz', '/opt/registration/data/t1/IBSR18/IBSR_08/IBSR_08_ana_strip.nii.gz', None)
showRegistrationResultMidSlices('/opt/registration/data/t1/IBSR18/IBSR_01/IBSR_01_ana_strip.nii.gz', '/opt/registration/data/t1/IBSR18/IBSR_08/IBSR_08_ana_strip.nii.gz', None)
showRegistrationResultMidSlices('warpedDiff_IBSR_13_ana_strip_IBSR_10_ana_strip.nii.gz', '/opt/registration/data/t1/IBSR18/IBSR_10/IBSR_10_ana_strip.nii.gz', None)
showRegistrationResultMidSlices('warpedAffine_IBSR_13_ana_strip_IBSR_10_ana_strip.nii.gz', '/opt/registration/data/t1/IBSR18/IBSR_10/IBSR_10_ana_strip.nii.gz', None)
showRegistrationResultMidSlices('/opt/registration/data/t1/IBSR18/IBSR_13/IBSR_13_ana_strip.nii.gz', '/opt/registration/data/t1/IBSR18/IBSR_10/IBSR_10_ana_strip.nii.gz', None)
showRegistrationResultMidSlices('warpedDiff_IBSR_01_ana_strip_IBSR_02_ana_strip.nii.gz', '/opt/registration/data/t1/IBSR18/IBSR_10/IBSR_10_ana_strip.nii.gz', None)
showRegistrationResultMidSlices('warpedAffine_IBSR_16_seg_ana_IBSR_10_ana_strip.nii.gz', '/opt/registration/data/t1/IBSR18/IBSR_10/IBSR_10_seg_ana.nii.gz', None)
showRegistrationResultMidSlices('/opt/registration/data/t1/IBSR18/IBSR_16/IBSR_16_seg_ana.nii.gz', '/opt/registration/data/t1/IBSR18/IBSR_10/IBSR_10_seg_ana.nii.gz', None)
showRegistrationResultMidSlices('/opt/registration/data/t1/IBSR18/IBSR_01/IBSR_01_segTRI_fill_ana.nii.gz', 'warpedAffine_IBSR_10_segTRI_fill_ana_IBSR_01_ana_strip.nii.gz', None)
showRegistrationResultMidSlices('warpedDiff_IBSR_07_ana_strip_IBSR_17_ana_strip.nii.gz', '/opt/registration/data/t1/IBSR18/IBSR_17/IBSR_17_ana_strip.nii.gz', None)
showRegistrationResultMidSlices('/opt/registration/data/t1/IBSR18/IBSR_07/IBSR_07_ana_strip.nii.gz', '/opt/registration/data/t1/IBSR18/IBSR_17/IBSR_17_ana_strip.nii.gz', None)
showRegistrationResultMidSlices('warpedDiff_IBSR_06_ana_strip_IBSR_17_ana_strip.nii.gz', '/opt/registration/data/t1/IBSR18/IBSR_17/IBSR_17_ana_strip.nii.gz', None)
showRegistrationResultMidSlices('warpedDiff_IBSR_07_ana_strip_IBSR_12_ana_strip.nii.gz', '/opt/registration/data/t1/IBSR18/IBSR_12/IBSR_12_ana_strip.nii.gz', None)
showRegistrationResultMidSlices('warpedDiff_IBSR_15_ana_strip_IBSR_10_ana_strip.nii.gz', '/opt/registration/data/t1/IBSR18/IBSR_10/IBSR_10_ana_strip.nii.gz', None)
showRegistrationResultMidSlices('warpedDiff_IBSR_01_ana_strip_t1_icbm_normal_1mm_pn0_rf0_peeled.nii.gz', 't1_icbm_normal_1mm_pn0_rf0_peeled.nii.gz', None)
showRegistrationResultMidSlices('warpedDiff_IBSR_01_segTRI_fill_ana_t1_icbm_normal_1mm_pn0_rf0_peeled.nii.gz', 'data/phantom_1.0mm_normal_crisp.rawb.nii.gz', None)
showRegistrationResultMidSlices('data/t1/t1_icbm_normal_1mm_pn0_rf0_peeled.nii.gz', 'data/phantom_1.0mm_normal_crisp_peeled.nii.gz', None)
showRegistrationResultMidSlices('data/t2/t2_icbm_normal_1mm_pn0_rf0_peeled.nii.gz', 'data/phantom_1.0mm_normal_crisp_peeled.nii.gz', None)
showRegistrationResultMidSlices('warpedDiff_IBSR_16_ana_strip_t1_icbm_normal_1mm_pn0_rf0_peeled.nii.gz', 'data/t1/t1_icbm_normal_1mm_pn0_rf0_peeled.nii.gz', None)
showRegistrationResultMidSlices('warpedAffine_IBSR_16_ana_strip_t1_icbm_normal_1mm_pn0_rf0_peeled.nii.gz', 'data/t1/t1_icbm_normal_1mm_pn0_rf0_peeled.nii.gz', None)
showRegistrationResultMidSlices('test16.nii.gz', 'data/t1/t1_icbm_normal_1mm_pn0_rf0_peeled.nii.gz', None)
showRegistrationResultMidSlices('data/t1/t1_icbm_normal_1mm_pn0_rf0.rawb_peeled.nii.gz', 'data/t1/t1_icbm_normal_1mm_pn0_rf0.rawb_peeled.nii.gz', None)
showRegistrationResultMidSlices('warpedAffine_IBSR_15_ana_strip_t1_icbm_normal_1mm_pn0_rf0_peeled.nii.gz', 'data/t1/t1_icbm_normal_1mm_pn0_rf0_peeled.nii.gz', None)
showRegistrationResultMidSlices('warpedDiff_IBSR_15_ana_strip_t1_icbm_normal_1mm_pn0_rf0_peeled.nii.gz', 'data/t1/t1_icbm_normal_1mm_pn0_rf0_peeled.nii.gz', None)
showRegistrationResultMidSlices('warpedAffine_IBSR_01_ana_strip_t1_icbm_normal_1mm_pn0_rf0_peeled.nii.gz', 'data/t1/t1_icbm_normal_1mm_pn0_rf0_peeled.nii.gz', None)
showRegistrationResultMidSlices('warpedDiff_IBSR_01_ana_strip_t1_icbm_normal_1mm_pn0_rf0_peeled.nii.gz', 'data/t1/t1_icbm_normal_1mm_pn0_rf0_peeled.nii.gz', None)
'''
if(fnameAffine==None):
T=np.eye(4)
else:
T=rcommon.readAntsAffine(fnameAffine)
print 'T:',T
fixed=nib.load(fnameFixed)
F=fixed.get_affine()
print 'F:',F
fixed=fixed.get_data().squeeze().astype(np.float64)
moving=nib.load(fnameMoving)
M=moving.get_affine()
print 'M:',M
moving=moving.get_data().squeeze().astype(np.float64)
initAffine=np.linalg.inv(M).dot(T.dot(F))
fixed=np.copy(fixed, order='C')
moving=np.copy(moving, order='C')
warped=np.array(tf.warp_volume_affine(moving, np.array(fixed.shape).astype(np.int32), initAffine))
sh=warped.shape
rcommon.overlayImages(warped[sh[0]//2,:,:], fixed[sh[0]//2,:,:])
rcommon.overlayImages(warped[:,sh[1]//2,:], fixed[:,sh[1]//2,:])
rcommon.overlayImages(warped[:,:,sh[2]//2], fixed[:,:,sh[2]//2])
