def saveDeformedLattice3D(displacement, oname):
minVal, maxVal=tf.get_displacement_range(displacement, None)
sh=np.array([np.ceil(maxVal[0]),np.ceil(maxVal[1]),np.ceil(maxVal[2])], dtype=np.int32)
L=np.array(rcommon.drawLattice3D(sh, 10))
warped=np.array(tf.warp_volume(L, displacement, np.eye(4))).astype(np.int16)
img=nib.Nifti1Image(warped, np.eye(4))
img.to_filename(oname)
def saveDeformedLattice3D(displacement, oname):
minVal, maxVal = tf.get_displacement_range(displacement, None)
sh = np.array([np.ceil(maxVal[0]),
np.ceil(maxVal[1]),
np.ceil(maxVal[2])],
dtype=np.int32)
L = np.array(rcommon.drawLattice3D(sh, 10))
warped = np.array(tf.warp_volume(L, displacement,
np.eye(4))).astype(np.int16)
img = nib.Nifti1Image(warped, np.eye(4))
img.to_filename(oname)
def save_deformed_lattice_3d(displacement, oname):
r'''
Applies the given displacement to a regular lattice and saves the resulting
image to a Nifti file with the given name
'''
min_val, max_val = tf.get_displacement_range(displacement, None)
shape = np.array([np.ceil(max_val[0]), np.ceil(max_val[1]),
np.ceil(max_val[2])], dtype = np.int32)
lattice = np.array(rcommon.drawLattice3D(shape, 10))
warped = np.array(tf.warp_volume(lattice, displacement)).astype(np.int16)
img = nib.Nifti1Image(warped, np.eye(4))
img.to_filename(oname)
def saveDeformedLattice3D(dname, oname='deformed_lattice.nii.gz'):
'''
saveDeformedLattice3D('displacement_templateT1ToIBSR01T1_diff.npy')
saveDeformedLattice3D('displacement_templateT1ToIBSR01T1_diffMulti.npy')
'''
print 'Loading displacement...'
displacement=np.load(dname)
minVal, maxVal=tf.get_displacement_range(displacement, None)
sh=np.array([np.ceil(maxVal[0]),np.ceil(maxVal[1]),np.ceil(maxVal[2])], dtype=np.int32)
print sh.dtype
print sh
L=np.array(drawLattice3D(sh, 10))
print 'Warping lattice...'
warped=np.array(tf.warp_volume(L, displacement, np.eye(4))).astype(np.int16)
print 'Transforming to Nifti...'
img=nib.Nifti1Image(warped, np.eye(4))
print 'Saving warped lattice as:',oname
img.to_filename(oname)
print 'done.'
