def register_com(vol_a: Volume, vol_b: Volume) -> Tuple[Volume, Volume]:
"""
Perform center-of-mass registration on two volumes
:param vol_a: The fixed volume
:param vol_b: The moving volume
:return: The updated volumes
"""
from dipy.align.imaffine import transform_centers_of_mass
affine = transform_centers_of_mass(vol_a, vol_a.grid_to_world, vol_b,
vol_b.grid_to_world)
vol_b.world_transform[:] = np.array(affine.affine)
return vol_a, vol_b
def test_transform_centers_of_mass_3d():
np.random.seed(1246592)
shape = (64, 64, 64)
rm = 8
sp = vf.create_sphere(shape[0] // 2, shape[1] // 2, shape[2] // 2, rm)
moving = np.zeros(shape)
# The center of mass will be (16, 16, 16), in image coordinates
moving[:shape[0] // 2, :shape[1] // 2, :shape[2] // 2] = sp[...]
rs = 16
# The center of mass will be (32, 32, 32), in image coordinates
static = vf.create_sphere(shape[0], shape[1], shape[2], rs)
# Create arbitrary image-to-space transforms
axis = np.array([.5, 2.0, 1.5])
t = 0.15 # translation factor
trans = np.array([[1, 0, 0, -t * shape[0]],
[0, 1, 0, -t * shape[1]],
[0, 0, 1, -t * shape[2]],
[0, 0, 0, 1]])
trans_inv = npl.inv(trans)
for rotation_angle in [-1 * np.pi / 6.0, 0.0, np.pi / 5.0]:
for scale_factor in [0.83, 1.3, 2.07]: # scale
rot = np.zeros(shape=(4, 4))
rot[:3, :3] = geometry.rodrigues_axis_rotation(axis,
rotation_angle)
rot[3, 3] = 1.0
scale = np.array([[1 * scale_factor, 0, 0, 0],
[0, 1 * scale_factor, 0, 0],
[0, 0, 1 * scale_factor, 0],
[0, 0, 0, 1]])
static_grid2world = trans_inv.dot(scale.dot(rot.dot(trans)))
moving_grid2world = npl.inv(static_grid2world)
# Expected translation
c_static = static_grid2world.dot((32, 32, 32, 1))[:3]
c_moving = moving_grid2world.dot((16, 16, 16, 1))[:3]
expected = np.eye(4)
expected[:3, 3] = c_moving - c_static
# Implementation under test
actual = imaffine.transform_centers_of_mass(static,
static_grid2world,
moving,
moving_grid2world)
assert_array_almost_equal(actual.affine, expected)
def mutualInfo_dipy(img1, img2):
img1_grid2world = np.identity(3)
img2_grid2world = np.identity(3)
# compute center of mass
c_of_mass = transform_centers_of_mass(img1, img1_grid2world, img2,
img2_grid2world)
x_shift = c_of_mass.affine[1, -1]
y_shift = c_of_mass.affine[0, -1]
# prepare affine registration
nbins = 32
sampling_prop = None
metric = MutualInformationMetric(nbins, sampling_prop)
level_iters = [10000, 1000, 100]
sigmas = [3.0, 1.0, 0.0]
factors = [4, 2, 1]
affreg = AffineRegistration(metric=metric,
level_iters=level_iters,
sigmas=sigmas,
factors=factors)
# translation
translation = affreg.optimize(img1,
img2,
TranslationTransform2D(),
None,
img1_grid2world,
img2_grid2world,
starting_affine=c_of_mass.affine)
# rotation
# ~ rigid = affreg.optimize(im1, im2, RigidTransform2D(), None,
# ~ im1_grid2world, im2_grid2world,
# ~ starting_affine=translation.affine)
# ~ transformed = rigid.transform(im2)
# ~ # resize, shear
# ~ affine = affreg.optimize(im1, im2, AffineTransform2D(), None,
# ~ im1_grid2world, im2_grid2world,
# ~ starting_affine=rigid.affine)
x_shift = translation.affine[1, -1]
y_shift = translation.affine[0, -1]
return np.asarray([-x_shift, -y_shift])
def center_of_mass(self, static, static_grid2world,
moving, moving_grid2world):
""" Function for the center of mass based image registration.
Parameters
----------
static : 2D or 3D array
the image to be used as reference during optimization.
static_grid2world : array, shape (dim+1, dim+1), optional
the voxel-to-space transformation associated with the static
image. The default is None, implying the transform is the
identity.
moving : 2D or 3D array
the image to be used as "moving" during optimization. It is
necessary to pre-align the moving image to ensure its domain
lies inside the domain of the deformation fields. This is assumed
to be accomplished by "pre-aligning" the moving image towards the
static using an affine transformation given by the
'starting_affine' matrix
moving_grid2world : array, shape (dim+1, dim+1), optional
the voxel-to-space transformation associated with the moving
image. The default is None, implying the transform is the
identity.
"""
img_registration = transform_centers_of_mass(static,
static_grid2world,
moving,
moving_grid2world)
transformed = img_registration.transform(moving)
return transformed, img_registration.affine
.. figure:: resampled_0.png
:align: center
.. figure:: resampled_1.png
:align: center
.. figure:: resampled_2.png
:align: center
Input images before alignment.
"""
"""
We can obtain a very rough (and fast) registration by just aligning the centers
of mass of the two images
"""
c_of_mass = transform_centers_of_mass(static, static_grid2world,
moving, moving_grid2world)
"""
We can now transform the moving image and draw it on top of the static image,
registration is not likely to be good, but at least they will occupy roughly
the same space
"""
transformed = c_of_mass.transform(moving)
regtools.overlay_slices(static, transformed, None, 0,
"Static", "Transformed", "transformed_com_0.png")
regtools.overlay_slices(static, transformed, None, 1,
"Static", "Transformed", "transformed_com_1.png")
regtools.overlay_slices(static, transformed, None, 2,
"Static", "Transformed", "transformed_com_2.png")
def _compute_morph_sdr(mri_from, mri_to, niter_affine=(100, 100, 10),
niter_sdr=(5, 5, 3), zooms=(5., 5., 5.)):
"""Get a matrix that morphs data from one subject to another."""
_check_dep(nibabel='2.1.0', dipy='0.10.1')
import nibabel as nib
with np.testing.suppress_warnings():
from dipy.align import imaffine, imwarp, metrics, transforms
from dipy.align.reslice import reslice
logger.info('Computing nonlinear Symmetric Diffeomorphic Registration...')
# use voxel size of mri_from
if zooms is None:
zooms = mri_from.header.get_zooms()[:3]
zooms = np.atleast_1d(zooms).astype(float)
if zooms.shape == (1,):
zooms = np.repeat(zooms, 3)
if zooms.shape != (3,):
raise ValueError('zooms must be None, a singleton, or have shape (3,),'
' got shape %s' % (zooms.shape,))
# reslice mri_from
mri_from_res, mri_from_res_affine = reslice(
mri_from.get_data(), mri_from.affine, mri_from.header.get_zooms()[:3],
zooms)
with warnings.catch_warnings(): # nibabel<->numpy warning
mri_from = nib.Nifti1Image(mri_from_res, mri_from_res_affine)
# reslice mri_to
mri_to_res, mri_to_res_affine = reslice(
mri_to.get_data(), mri_to.affine, mri_to.header.get_zooms()[:3],
zooms)
with warnings.catch_warnings(): # nibabel<->numpy warning
mri_to = nib.Nifti1Image(mri_to_res, mri_to_res_affine)
affine = mri_to.affine
mri_to = np.array(mri_to.dataobj, float) # to ndarray
mri_to /= mri_to.max()
mri_from_affine = mri_from.affine # get mri_from to world transform
mri_from = np.array(mri_from.dataobj, float) # to ndarray
mri_from /= mri_from.max() # normalize
# compute center of mass
c_of_mass = imaffine.transform_centers_of_mass(
mri_to, affine, mri_from, affine)
# set up Affine Registration
affreg = imaffine.AffineRegistration(
metric=imaffine.MutualInformationMetric(nbins=32),
level_iters=list(niter_affine),
sigmas=[3.0, 1.0, 0.0],
factors=[4, 2, 1])
# translation
translation = affreg.optimize(
mri_to, mri_from, transforms.TranslationTransform3D(), None, affine,
mri_from_affine, starting_affine=c_of_mass.affine)
# rigid body transform (translation + rotation)
rigid = affreg.optimize(
mri_to, mri_from, transforms.RigidTransform3D(), None,
affine, mri_from_affine, starting_affine=translation.affine)
# affine transform (translation + rotation + scaling)
pre_affine = affreg.optimize(
mri_to, mri_from, transforms.AffineTransform3D(), None,
affine, mri_from_affine, starting_affine=rigid.affine)
# compute mapping
sdr = imwarp.SymmetricDiffeomorphicRegistration(
metrics.CCMetric(3), list(niter_sdr))
sdr_morph = sdr.optimize(mri_to, pre_affine.transform(mri_from))
shape = tuple(sdr_morph.domain_shape) # should be tuple of int
logger.info('done.')
return shape, zooms, affine, pre_affine, sdr_morph
def quick_check():
img1_fname = "/home/omar/data/DATA_NeoBrainS12/T1.nii.gz"
img2_fname = "/home/omar/data/DATA_NeoBrainS12/set2_i1_t1.nii.gz"
img1_nib = nib.load(img1_fname)
img1 = img1_nib.get_data().squeeze()
img1_affine = img1_nib.get_affine()
img2_nib = nib.load(img2_fname)
img2 = img2_nib.get_data().squeeze()
img2_affine = img2_nib.get_affine()
# nib.aff2axcodes(img1_affine)
#aff = AffineMap(None, img1.shape, img1_affine, img2.shape, img2_affine)
#aff = transform_centers_of_mass(img1, img1_affine, img2, img2_affine)
aff = dipy_align(img1, img1_affine, img2, img2_affine, np.eye(4))
img2_resampled = aff.transform(img2)
rt.overlay_slices(img1, img2_resampled, slice_type=0)
rt.overlay_slices(img1, img2_resampled, slice_type=1)
rt.overlay_slices(img1, img2_resampled, slice_type=2)
# Verify that original and RAS versions of neo1 describe the same object
# Load original data
neo1_fname = get_neobrain('train', 1, 'T1')
neo1_old, neo1_old_affine, neo1_old_spacing, neo1_old_ori = load_from_raw(neo1_fname)
# Load RAS version
neo1_nib = nib.load(neo1_fname)
neo1 = neo1_nib.get_data()
neo1_affine = neo1_nib.get_affine()
# Resample RAS on top of original
aff = AffineMap(None, neo1_old.shape, neo1_old_affine, neo1.shape, neo1_affine)
neo1_resampled = aff.transform(neo1)
rt.overlay_slices(neo1_old, neo1_resampled, slice_type=0)
rt.overlay_slices(neo1_old, neo1_resampled, slice_type=1)
rt.overlay_slices(neo1_old, neo1_resampled, slice_type=2)
# Attempt to resample a test volume on top of training
neo2_fname = get_neobrain('test', 1, 'i1_t1')
neo2_nib = nib.load(neo2_fname)
neo2 = neo2_nib.get_data()
neo2_affine = neo2_nib.get_affine()
aff = transform_centers_of_mass(neo1, neo1_affine, neo2, neo2_affine)
#aff = dipy_align(neo1, neo1_affine, neo2, neo2_affine)
neo2_resampled = aff.transform(neo2)
rt.overlay_slices(neo1, neo2_resampled, slice_type=0)
rt.overlay_slices(neo1, neo2_resampled, slice_type=1)
rt.overlay_slices(neo1, neo2_resampled, slice_type=2)
# Load atlas
atlas_fname = get_neobrain('atlas', 'neo-withSkull', None)
atlas_nib = nib.load(atlas_fname)
atlas_affine = atlas_nib.get_affine()
atlas = atlas_nib.get_data()
rt.plot_slices(atlas)
# Resample atlas on top of neo1
aff = AffineMap(None, neo1.shape, neo1_affine, atlas.shape, atlas_affine)
atlas_resampled = aff.transform(atlas)
rt.overlay_slices(neo1, atlas_resampled)
def c_of_mass(moving, static, static_affine, moving_affine,
reg, starting_affine, params0=None):
transform = transform_centers_of_mass(static, static_affine,
moving, moving_affine)
transformed = transform.transform(moving)
return transformed, transform.affine
brainweb_nib = nib.load(brainweb_name)
brainweb = brainweb_nib.get_data().squeeze()
brainweb_affine = brainweb_nib.get_affine()
brainweb = brainweb.transpose([0, 2, 1])[::-1, :, :]
rt.plot_slices(brainweb)
brainweb_affine = ibsr1_affine.copy()
brainweb_affine[brainweb_affine != 0] = 1
brainweb_affine[0, 0] = -1
# Reslice Brainweb on IBSR1
ibsr_to_bw = AffineMap(None, ibsr1.shape, ibsr1_affine, brainweb.shape, brainweb_affine)
bw_on_ibsr1 = ibsr_to_bw.transform(brainweb)
rt.overlay_slices(ibsr1, bw_on_ibsr1) # misaligned
c_of_mass = transform_centers_of_mass(ibsr1, ibsr1_affine, brainweb, brainweb_affine)
bw_on_ibsr1 = c_of_mass.transform(brainweb)
rt.overlay_slices(ibsr1, bw_on_ibsr1) # roughly aligned
# Start affine alignment
aff_name = "ibsr1_to_brainweb.p"
if os.path.isfile(aff_name):
ibsr_bw_affmap = pickle.load(open(aff_name, "r"))
else:
ibsr_bw_affmap = dipy_align(ibsr1, ibsr1_affine, brainweb, brainweb_affine)
pickle.dump(ibsr_bw_affmap, open(aff_name, "w"))
bw_on_ibsr1 = ibsr_bw_affmap.transform(brainweb)
rt.overlay_slices(ibsr1, bw_on_ibsr1, slice_type=0) # aligned (sagital view)
rt.overlay_slices(ibsr1, bw_on_ibsr1, slice_type=1) # aligned (axial view)
rt.overlay_slices(ibsr1, bw_on_ibsr1, slice_type=2) # aligned (coronal view)
brainweb_nib = nib.load(brainweb_name)
brainweb = brainweb_nib.get_data().squeeze()
brainweb_affine = brainweb_nib.get_affine()
brainweb = brainweb.transpose([0, 2, 1])[::-1, :, :]
rt.plot_slices(brainweb)
brainweb_affine = ibsr1_affine.copy()
brainweb_affine[brainweb_affine != 0] = 1
brainweb_affine[0, 0] = -1
# Reslice Brainweb on IBSR1
ibsr_to_bw = AffineMap(None, ibsr1.shape, ibsr1_affine, brainweb.shape,
brainweb_affine)
bw_on_ibsr1 = ibsr_to_bw.transform(brainweb)
rt.overlay_slices(ibsr1, bw_on_ibsr1) # misaligned
c_of_mass = transform_centers_of_mass(ibsr1, ibsr1_affine, brainweb,
brainweb_affine)
bw_on_ibsr1 = c_of_mass.transform(brainweb)
rt.overlay_slices(ibsr1, bw_on_ibsr1) # roughly aligned
# Start affine alignment
aff_name = 'ibsr1_to_brainweb.p'
if os.path.isfile(aff_name):
ibsr_bw_affmap = pickle.load(open(aff_name, 'r'))
else:
ibsr_bw_affmap = dipy_align(ibsr1, ibsr1_affine, brainweb, brainweb_affine)
pickle.dump(ibsr_bw_affmap, open(aff_name, 'w'))
bw_on_ibsr1 = ibsr_bw_affmap.transform(brainweb)
rt.overlay_slices(ibsr1, bw_on_ibsr1, slice_type=0) # aligned (sagital view)
rt.overlay_slices(ibsr1, bw_on_ibsr1, slice_type=1) # aligned (axial view)
rt.overlay_slices(ibsr1, bw_on_ibsr1, slice_type=2) # aligned (coronal view)
def quick_check():
img1_fname = "/home/omar/data/DATA_NeoBrainS12/T1.nii.gz"
img2_fname = "/home/omar/data/DATA_NeoBrainS12/set2_i1_t1.nii.gz"
img1_nib = nib.load(img1_fname)
img1 = img1_nib.get_data().squeeze()
img1_affine = img1_nib.get_affine()
img2_nib = nib.load(img2_fname)
img2 = img2_nib.get_data().squeeze()
img2_affine = img2_nib.get_affine()
# nib.aff2axcodes(img1_affine)
#aff = AffineMap(None, img1.shape, img1_affine, img2.shape, img2_affine)
#aff = transform_centers_of_mass(img1, img1_affine, img2, img2_affine)
aff = dipy_align(img1, img1_affine, img2, img2_affine, np.eye(4))
img2_resampled = aff.transform(img2)
rt.overlay_slices(img1, img2_resampled, slice_type=0)
rt.overlay_slices(img1, img2_resampled, slice_type=1)
rt.overlay_slices(img1, img2_resampled, slice_type=2)
# Verify that original and RAS versions of neo1 describe the same object
# Load original data
neo1_fname = get_neobrain('train', 1, 'T1')
neo1_old, neo1_old_affine, neo1_old_spacing, neo1_old_ori = load_from_raw(
neo1_fname)
# Load RAS version
neo1_nib = nib.load(neo1_fname)
neo1 = neo1_nib.get_data()
neo1_affine = neo1_nib.get_affine()
# Resample RAS on top of original
aff = AffineMap(None, neo1_old.shape, neo1_old_affine, neo1.shape,
neo1_affine)
neo1_resampled = aff.transform(neo1)
rt.overlay_slices(neo1_old, neo1_resampled, slice_type=0)
rt.overlay_slices(neo1_old, neo1_resampled, slice_type=1)
rt.overlay_slices(neo1_old, neo1_resampled, slice_type=2)
# Attempt to resample a test volume on top of training
neo2_fname = get_neobrain('test', 1, 'i1_t1')
neo2_nib = nib.load(neo2_fname)
neo2 = neo2_nib.get_data()
neo2_affine = neo2_nib.get_affine()
aff = transform_centers_of_mass(neo1, neo1_affine, neo2, neo2_affine)
#aff = dipy_align(neo1, neo1_affine, neo2, neo2_affine)
neo2_resampled = aff.transform(neo2)
rt.overlay_slices(neo1, neo2_resampled, slice_type=0)
rt.overlay_slices(neo1, neo2_resampled, slice_type=1)
rt.overlay_slices(neo1, neo2_resampled, slice_type=2)
# Load atlas
atlas_fname = get_neobrain('atlas', 'neo-withSkull', None)
atlas_nib = nib.load(atlas_fname)
atlas_affine = atlas_nib.get_affine()
atlas = atlas_nib.get_data()
rt.plot_slices(atlas)
# Resample atlas on top of neo1
aff = AffineMap(None, neo1.shape, neo1_affine, atlas.shape, atlas_affine)
atlas_resampled = aff.transform(atlas)
rt.overlay_slices(neo1, atlas_resampled)
def warp_syn_dipy(static_fname, moving_fname):
import os
import numpy as np
import nibabel as nb
from dipy.align.metrics import CCMetric
from dipy.align.imaffine import (transform_centers_of_mass,
AffineMap,
MutualInformationMetric,
AffineRegistration)
from dipy.align.transforms import (TranslationTransform3D,
RigidTransform3D,
AffineTransform3D)
from dipy.align.imwarp import (DiffeomorphicMap,
SymmetricDiffeomorphicRegistration)
from nipype.utils.filemanip import fname_presuffix
static = nb.load(static_fname)
moving = nb.load(moving_fname)
c_of_mass = transform_centers_of_mass(static.get_data(), static.affine,
moving.get_data(), moving.affine)
nbins = 32
sampling_prop = None
metric = MutualInformationMetric(nbins, sampling_prop)
level_iters = [10000, 1000, 100]
sigmas = [3.0, 1.0, 0.0]
factors = [4, 2, 1]
affreg = AffineRegistration(metric=metric,
level_iters=level_iters,
sigmas=sigmas,
factors=factors)
transform = TranslationTransform3D()
params0 = None
starting_affine = c_of_mass.affine
translation = affreg.optimize(static.get_data(), moving.get_data(),
transform, params0,
static.affine, moving.affine,
starting_affine=starting_affine)
transform = RigidTransform3D()
params0 = None
starting_affine = translation.affine
rigid = affreg.optimize(static.get_data(), moving.get_data(), transform, params0,
static.affine, moving.affine,
starting_affine=starting_affine)
transform = AffineTransform3D()
params0 = None
starting_affine = rigid.affine
affine = affreg.optimize(static.get_data(), moving.get_data(), transform, params0,
static.affine, moving.affine,
starting_affine=starting_affine)
metric = CCMetric(3, sigma_diff=3.)
level_iters = [25, 10, 5]
sdr = SymmetricDiffeomorphicRegistration(metric, level_iters)
starting_affine = affine.affine
mapping = sdr.optimize(
static.get_data(), moving.get_data(),
static.affine, moving.affine,
starting_affine)
warped_filename = os.path.abspath(fname_presuffix(moving_fname, newpath='./', suffix='_warped', use_ext=True))
warped = nb.Nifti1Image(mapping.transform(moving.get_data()), static.affine)
warped.to_filename(warped_filename)
warp_filename = os.path.abspath(fname_presuffix(moving_fname, newpath='./', suffix='_warp.npz', use_ext=False))
np.savez(warp_filename,prealign=mapping.prealign,forward=mapping.forward,backward=mapping.backward)
return warp_filename, warped_filename
