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Commit c30f1c74 authored by Paul McCarthy's avatar Paul McCarthy :mountain_bicyclist:
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RF: Push srcToRefMat up to the NonLinearTransform class, so it can also be 

used by the DisplacementField class.
parent 2de38f86
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fsl/transform/nonlinear.py
+ 76
− 53
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......@@ -53,6 +53,17 @@ class NonLinearTransform(fslimage.Image):
the corresponding location in the source image space. Therefore, these
non-linear transformation effectively encode a transformation *from* the
reference image *to* the source image.
A FNIRT nonlinear transformation often contains a *premat*, a global
affine transformation from the source space to the reference space, which
was calculated with FLIRT, and used as the starting point for the
non-linear optimisation performed by FNIRT.
This affine may be provided when creating a ``NonLinearTransform`` as the
``srcToRefMat`` argument to :meth:`__init__`, and is subsequently accessed
via the :meth:`srcToRefMat` attribute.
"""
......@@ -62,28 +73,40 @@ class NonLinearTransform(fslimage.Image):
ref,
srcSpace=None,
refSpace=None,
srcToRefMat=None,
**kwargs):
"""Create a ``NonLinearTransform``.
:arg image: A string containing the name of an image file to load,
or a :mod:`numpy` array, or a :mod:`nibabel` image
object.
:arg image: A string containing the name of an image file to
load, or a :mod:`numpy` array, or a :mod:`nibabel`
image object.
:arg src: :class:`.Nifti` representing the source image.
:arg src: :class:`.Nifti` representing the source image.
:arg ref: :class:`.Nifti` representing the reference image.
:arg ref: :class:`.Nifti` representing the reference image.
:arg srcSpace: Coordinate system in the source image that this
``NonLinearTransform`` maps to. Defaults to ``'fsl'``.
:arg srcSpace: Coordinate system in the source image that this
``NonLinearTransform`` maps to. Defaults to
``'fsl'``.
:arg refSpace: Coordinate system in the reference image that this
``NonLinearTransform`` maps from. Defaults to ``'fsl'``.
:arg refSpace: Coordinate system in the reference image that this
``NonLinearTransform`` maps from. Defaults to
``'fsl'``.
:arg srcToRefMat: Optional initial global affine transformation from
the source image to the reference image. This is
assumed to be a FLIRT-style matrix, i.e. it
transforms from source image ``srcSpace`` coordinates
into reference image ``srcSpace`` coordinates
(typically ``'fsl'`` coordinates, i.e. scaled voxels
potentially with a left-right flip).
All other arguments are passed through to :meth:`.Image.__init__`.
"""
if srcSpace is None: srcSpace = 'fsl'
if refSpace is None: refSpace = 'fsl'
if srcSpace is None: srcSpace = 'fsl'
if refSpace is None: refSpace = 'fsl'
if srcToRefMat is not None: srcToRefMat = np.copy(srcToRefMat)
if srcSpace not in ('fsl', 'voxel', 'world') or \
refSpace not in ('fsl', 'voxel', 'world'):
......@@ -92,10 +115,15 @@ class NonLinearTransform(fslimage.Image):
fslimage.Image.__init__(self, image, **kwargs)
self.__src = fslimage.Nifti(src.header.copy())
self.__ref = fslimage.Nifti(ref.header.copy())
self.__srcSpace = srcSpace
self.__refSpace = refSpace
self.__src = fslimage.Nifti(src.header.copy())
self.__ref = fslimage.Nifti(ref.header.copy())
self.__srcSpace = srcSpace
self.__refSpace = refSpace
self.__srcToRefMat = srcToRefMat
self.__refToSrcMat = None
if srcToRefMat is not None:
self.__refToSrcMat = affine.invert(srcToRefMat)
@property
......@@ -130,6 +158,22 @@ class NonLinearTransform(fslimage.Image):
return self.__refSpace
@property
def srcToRefMat(self):
"""Return the initial source-to-reference affine, or ``None`` if
there isn't one.
"""
return self.__srcToRefMat
@property
def refToSrcMat(self):
"""Return the inverse of the initial source-to-reference affine, or
``None`` if there isn't one.
"""
return self.__refToSrcMat
def transform(self, coords, from_=None, to=None):
"""Transform coordinates from the reference image space to the source
image space. Implemented by sub-classes.
......@@ -254,11 +298,18 @@ class DisplacementField(NonLinearTransform):
if self.absolute: disps = self.data[xs, ys, zs, :]
else: disps = self.data[xs, ys, zs, :] + coords[voxmask]
# Make sure the coordinates
# are in the requested
# source image space
# Make sure the coordinates are
# in the requested source image
# space, and apply the initial
# inv(srcToRefMat) if it there
# is one
postmat = self.refToSrcMat
if to != self.srcSpace:
xform = self.src.getAffine(self.srcSpace, to)
if postmat is not None: postmat = affine.concat(xform, postmat)
else: postmat = xform
if postmat is not None:
disps = affine.transform(disps, xform)
# Nans for input coordinates
......@@ -276,16 +327,6 @@ class CoefficientField(NonLinearTransform):
The :meth:`displacements` method can be used to calculate relative
displacements for a set of reference space voxel coordinates.
A FNIRT coefficient field typically contains a *premat*, a global affine
transformation from the source space to the reference space, which was
used as the starting point for the non-linear optimisation performed by
FNIRT.
This affine must be provided when creating a ``CoefficientField``, and is
subsequently accessed via the :meth:`srcToRefMat` or :meth:`premat`
attributes.
"""
......@@ -297,7 +338,6 @@ class CoefficientField(NonLinearTransform):
refSpace,
fieldType,
knotSpacing,
srcToRefMat,
fieldToRefMat,
**kwargs):
"""Create a ``CoefficientField``.
......@@ -307,13 +347,6 @@ class CoefficientField(NonLinearTransform):
:arg knotSpacing: A tuple containing the spline knot spacings along
each axis.
:arg srcToRefMat: Initial global affine transformation from the
source image to the reference image. This is
assumed to be a FLIRT-style matrix, i.e. it
transforms from source image FSL coordinates
into reference image FSL coordinates (scaled
voxels).
:arg fieldToRefMat: Affine transformation which can transform reference
image voxel coordinates into coefficient field
voxel coordinates.
......@@ -335,7 +368,6 @@ class CoefficientField(NonLinearTransform):
self.__fieldType = fieldType
self.__knotSpacing = tuple(knotSpacing)
self.__srcToRefMat = np.copy(srcToRefMat)
self.__fieldToRefMat = np.copy(fieldToRefMat)
self.__refToFieldMat = affine.invert(self.__fieldToRefMat)
......@@ -348,14 +380,6 @@ class CoefficientField(NonLinearTransform):
return self.__fieldType
@property
def srcToRefMat(self):
"""Return an initial global affine transformation from the source
image to the reference image.
"""
return np.copy(self.__srcToRefMat)
@property
def knotSpacing(self):
"""Return a tuple containing spline knot spacings along the x, y, and
......@@ -688,20 +712,19 @@ def coefficientFieldToDisplacementField(field,
# Apply the premat if requested -
# this will transform the coordinates
# from aligned-src to orig-src space.
if premat:
if premat and field.srcToRefMat is not None:
# We apply the premat in the same way
# that fnirtfileutils does - applying
# the inverse affine to every ref space
# voxel coordinate, then adding it to
# the existing displacements.
shape = disps.shape
disps = disps.reshape(-1, 3)
refToSrc = affine.invert(field.srcToRefMat)
premat = affine.concat(refToSrc - np.eye(4),
field.ref.getAffine('voxel', 'fsl'))
disps = disps + affine.transform(xyz, premat)
disps = disps.reshape(shape)
shape = disps.shape
disps = disps.reshape(-1, 3)
premat = affine.concat(field.refToSrcMat - np.eye(4),
field.ref.getAffine('voxel', 'fsl'))
disps = disps + affine.transform(xyz, premat)
disps = disps.reshape(shape)
# note that convertwarp applies a premat
# differently - its method is equivalent
......
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