"""
Registration tools
"""
import nibabel as nib
import numpy as np
from dipy.align.imaffine import AffineMap
from dipy.align.imwarp import DiffeomorphicMap
__all__ = [
"read_affine_mapping",
"read_syn_mapping",
"read_old_mapping",
]
def reduce_shape(shape):
"""
Reduce dimension in shape to 3 if possible
"""
try:
return shape[:3]
except TypeError:
return shape
[docs]
def read_syn_mapping(disp, codisp):
"""
Read a syn registration mapping from a nifti file
Parameters
----------
disp : str or Nifti1Image
If string, file must of an image or ndarray.
If image, contains the mapping displacement field in each voxel
from subject to template
codisp : str or Nifti1Image
If string, file must of an image or ndarray.
If image, contains the mapping displacement field in each voxel
from template to subject
Returns
-------
A :class:`DiffeomorphicMap` object
"""
if isinstance(disp, str):
disp = nib.load(disp)
if isinstance(codisp, str):
codisp = nib.load(codisp)
mapping = DiffeomorphicMap(
dim=3,
disp_shape=codisp.get_fdata().shape[:3],
disp_grid2world=None,
domain_shape=disp.get_fdata().shape[:3],
domain_grid2world=None,
codomain_shape=codisp.get_fdata().shape[:3],
codomain_grid2world=None,
)
mapping.forward = disp.get_fdata().astype(np.float32)
mapping.backward = codisp.get_fdata().astype(np.float32)
return mapping
[docs]
def read_affine_mapping(affine, domain_img, codomain_img):
"""
Read a syn registration mapping from a nifti file
Parameters
----------
affine : str or ndarray
If string, file must of an ndarray.
If ndarray, contains affine transformation used for mapping
domain_img : str or Nifti1Image
codomain_img : str or Nifti1Image
Returns
-------
A :class:`AffineMap` object
"""
if isinstance(affine, str):
affine = np.load(affine)
if isinstance(domain_img, str):
domain_img = nib.load(domain_img)
if isinstance(codomain_img, str):
codomain_img = nib.load(codomain_img)
mapping = AffineMap(
affine,
domain_grid_shape=reduce_shape(domain_img.shape),
domain_grid2world=domain_img.affine,
codomain_grid_shape=reduce_shape(codomain_img.shape),
codomain_grid2world=codomain_img.affine,
)
return mapping
[docs]
def read_old_mapping(disp, domain_img, codomain_img, prealign=None):
"""
Warning: This is only used for pyAFQ tests and backwards compatibility.
Read old-style registration mapping from a nifti file.
Parameters
----------
disp : str or Nifti1Image
If string, file must of an image or ndarray.
If image, contains the mapping displacement field in each voxel
Shape (x, y, z, 3, 2)
domain_img : str or Nifti1Image
codomain_img : str or Nifti1Image
Returns
-------
A :class:`DiffeomorphicMap` object
"""
if isinstance(disp, str):
disp = nib.load(disp)
if isinstance(domain_img, str):
domain_img = nib.load(domain_img)
if isinstance(codomain_img, str):
codomain_img = nib.load(codomain_img)
mapping = DiffeomorphicMap(
3,
disp.shape[:3],
disp_grid2world=np.linalg.inv(disp.affine),
domain_shape=domain_img.shape[:3],
domain_grid2world=domain_img.affine,
codomain_shape=codomain_img.shape,
codomain_grid2world=codomain_img.affine,
prealign=prealign,
)
disp_data = disp.get_fdata().astype(np.float32)
mapping.forward = disp_data[..., 0]
mapping.backward = disp_data[..., 1]
mapping.is_inverse = False
return mapping
