def getTransform(self, from_, to):
"""Return a matrix which may be used to transform coordinates from
``from_`` to ``to``.
The following values are accepted for the ``from_`` and ``to``
parameters:
- ``'world'``: World coordinate system
- ``'display'`` Display coordinate system
- ``'mesh'`` The coordinate system of this mesh.
"""
nfrom_ = self.normaliseSpace(from_)
nto = self.normaliseSpace(to)
ref = self.refImage
if ref is None:
return np.eye(4)
opts = self.displayCtx.getOpts(ref)
xform = opts.getTransform(nfrom_, nto)
if from_ == 'mesh' and self.coordSpace == 'torig':
surfToVox = affine.invert(fslmgh.voxToSurfMat(ref))
xform = affine.concat(xform,
ref.getAffine('voxel', 'world'),
surfToVox)
if to == 'mesh' and self.coordSpace == 'torig':
voxToSurf = fslmgh.voxToSurfMat(ref)
xform = affine.concat(voxToSurf,
ref.getAffine('world', 'voxel'),
xform)
return xform
def transformCoords(self, coords, from_, to, *args, **kwargs):
"""Transforms the given ``coords`` from ``from_`` to ``to``.
:arg coords: Coordinates to transform.
:arg from_: Space that the coordinates are in
:arg to: Space to transform the coordinates to
All other parameters are passed through to the
:meth:`.NiftiOpts.transformCoords` method of the reference image
``DisplayOpts``.
The following values are accepted for the ``from_`` and ``to``
parameters:
- ``'world'``: World coordinate system
- ``'display'`` Display coordinate system
- ``'mesh'`` The coordinate system of this mesh.
- ``'voxel'``: The voxel coordinate system of the reference
image
- ``'id'``: Equivalent to ``'voxel'``.
"""
nfrom_ = self.normaliseSpace(from_)
nto = self.normaliseSpace(to)
ref = self.refImage
pre = None
post = None
if ref is None:
return coords
if from_ == 'mesh' and self.coordSpace == 'torig':
pre = affine.concat(ref.getAffine('voxel', 'world'),
affine.invert(fslmgh.voxToSurfMat(ref)))
if to == 'mesh' and self.coordSpace == 'torig':
post = affine.concat(fslmgh.voxToSurfMat(ref),
ref.getAffine('world', 'voxel'))
opts = self.displayCtx.getOpts(ref)
return opts.transformCoords(coords,
nfrom_,
nto,
pre=pre,
post=post,
**kwargs)
def test_voxToSurfMat():
testfile = op.join(datadir, 'example.mgz')
img = fslmgh.MGHImage(testfile)
assert np.all(np.isclose(img.voxToSurfMat, fslmgh.voxToSurfMat(img)))