diff --git a/fsl/transform/fnirt.py b/fsl/transform/fnirt.py
index 358269f9fc300e5c659928ef405b30339e611e20..2a2351a0ed8f7cd1aa5ff2d48b62626361845964 100644
--- a/fsl/transform/fnirt.py
+++ b/fsl/transform/fnirt.py
@@ -124,33 +124,40 @@ header of the coefficient field file.
import logging
-import numpy as np
import nibabel as nib
+import numpy as np
import fsl.data.constants as constants
+import fsl.data.image as fslimage
+from . import affine
+from . import nonlinear
log = logging.getLogger(__name__)
-def _readFnirtDisplacementField(fname, img, src, ref, dispType=None):
- """Loads ``fname``, assumed to be a FNIRT displacement field.
+def _readFnirtDeformationField(fname, img, src, ref, defType=None):
+ """Loads ``fname``, assumed to be a FNIRT deformation field.
- :arg fname: File name of FNIRT displacement field
- :arg img: ``fname`` loaded as an :class:`.Image`
- :arg src: Source image
- :arg ref: Reference image
- :arg dispType: Displacement type - either ``'absolute'`` or ``'relative'``.
- If not provided, is automatically inferred from the data.
- :return: A :class:`.DisplacementField`
+ :arg fname: File name of FNIRT deformation field
+
+ :arg img: ``fname`` loaded as an :class:`.Image`
+
+ :arg src: Source image
+
+ :arg ref: Reference image
+
+ :arg defType: Deformation type - either ``'absolute'`` or ``'relative'``.
+ If not provided, is automatically inferred from the data.
+
+ :return: A :class:`.DeformationField` object
"""
- from . import nonlinear
- return nonlinear.DisplacementField(fname,
- src,
- ref,
- srcSpace='fsl',
- refSpace='fsl',
- dispType=dispType)
+ return nonlinear.DeformationField(fname,
+ src,
+ ref,
+ srcSpace='fsl',
+ refSpace='fsl',
+ defType=defType)
def _readFnirtCoefficientField(fname, img, src, ref):
@@ -163,9 +170,6 @@ def _readFnirtCoefficientField(fname, img, src, ref):
:return: A :class:`.CoefficientField`
"""
- from . import affine
- from . import nonlinear
-
# FNIRT uses NIFTI header fields in
# non-standard ways to store some
# additional information about the
@@ -226,22 +230,22 @@ def _readFnirtCoefficientField(fname, img, src, ref):
fieldToRefMat=fieldToRefMat)
-def readFnirt(fname, src, ref, dispType=None):
+def readFnirt(fname, src, ref, defType=None):
"""Reads a non-linear FNIRT transformation image, returning
- a :class:`.DisplacementField` or :class:`.CoefficientField` depending
+ a :class:`.DeformationField` or :class:`.CoefficientField` depending
on the file type.
:arg fname: File name of FNIRT transformation
:arg src: Source image
:arg ref: Reference image
- :arg dispType: Displacement type - either ``'absolute'`` or ``'relative'``.
- If not provided, is automatically inferred from the data.
+ :arg defType: Deformation type - either ``'absolute'`` or ``'relative'``.
+ Only used if the file is a deformation field. If not
+ provided, is automatically inferred from the data.
"""
# Figure out whether the file
- # is a displacement field or
+ # is a deformation field or
# a coefficient field
- import fsl.data.image as fslimage
img = fslimage.Image(fname, loadData=False)
disps = (constants.FSL_FNIRT_DISPLACEMENT_FIELD,
@@ -253,7 +257,7 @@ def readFnirt(fname, src, ref, dispType=None):
constants.FSL_TOPUP_QUADRATIC_SPLINE_COEFFICIENTS)
if img.intent in disps:
- return _readFnirtDisplacementField(fname, img, src, ref, dispType)
+ return _readFnirtDeformationField(fname, img, src, ref, defType)
elif img.intent in coefs:
return _readFnirtCoefficientField(fname, img, src, ref)
else:
@@ -263,15 +267,13 @@ def readFnirt(fname, src, ref, dispType=None):
def toFnirt(field):
"""Convert a :class:`.NonLinearTransform` to a FNIRT-compatible
- :class:`.DisplacementField` or :class:`.CoefficientField`.
+ :class:`.DeformationField` or :class:`.CoefficientField`.
:arg field: :class:`.NonLinearTransform` to convert
- :return: A FNIRT-compatible :class:`.DisplacementField` or
+ :return: A FNIRT-compatible :class:`.DeformationField` or
:class:`.CoefficientField`.
"""
- from . import nonlinear
-
# If we have a coefficient field
# which transforms between fsl
# space, we can just create a copy.
@@ -330,36 +332,35 @@ def toFnirt(field):
srcToRefMat=field.srcToRefMat)
# Otherwise we have a non-FSL coefficient
- # field, or a displacement field.
- #
- # We can't convert a CoefficientField
- # which doesn't transform in FSL
- # coordinates, because the coefficients
- # will have been calculated between some
- # other source/reference coordinate
- # systems, and we can't adjust the
- # coefficients to encode an FSL->FSL
- # deformation.
+ # field, or a deformation field.
else:
+ # We can't convert a CoefficientField
+ # which doesn't transform in FSL
+ # coordinates, because the coefficients
+ # will have been calculated between some
+ # other source/reference coordinate
+ # systems, and we can't adjust the
+ # coefficients to encode an FSL->FSL
+ # deformation.
if isinstance(field, nonlinear.CoefficientField):
- field = nonlinear.coefficientFieldToDisplacementField(field)
+ field = nonlinear.coefficientFieldToDeformationField(field)
# Again, if we have a displacement
# field which transforms between
# fsl spaces, we can just take a copy
if field.srcSpace == 'fsl' and field.refSpace == 'fsl':
- field = nonlinear.DisplacementField(
+ field = nonlinear.DeformationField(
field.data,
+ header=field.header,
src=field.src,
ref=field.ref,
- xform=field.voxToWorldMat,
- dispType=field.displacementType)
+ defType=field.deformationType)
# Otherwise we have to adjust the
# displacements so they transform
# between fsl coordinates.
- field = nonlinear.convertDisplacementSpace(
+ field = nonlinear.convertDeformationSpace(
field, from_='fsl', to='fsl')
field.header['intent_code'] = constants.FSL_FNIRT_DISPLACEMENT_FIELD
@@ -369,23 +370,19 @@ def toFnirt(field):
def fromFnirt(field, from_='world', to='world'):
"""Convert a FNIRT-style :class:`.NonLinearTransform` to a generic
- :class:`.DisplacementField`.
+ :class:`.DeformationField`.
:arg field: A FNIRT-style :class:`.CoefficientField` or
- :class:`.DisplacementField`
+ :class:`.DeformationField`
:arg from_: Desired reference image coordinate system
:arg to: Desired source image coordinate system
- :return: A :class:`.DisplacementField` which contains displacements
+ :return: A :class:`.DeformationField` which contains displacements
from the reference image ``from_`` cordinate system to the
source image ``to`` coordinate syste.
"""
- from . import nonlinear
-
- # see comments in toFnirt
if isinstance(field, nonlinear.CoefficientField):
- field = nonlinear.coefficientFieldToDisplacementField(field)
-
- return nonlinear.convertDisplacementSpace(field, from_=from_, to=to)
+ field = nonlinear.coefficientFieldToDeformationField(field)
+ return nonlinear.convertDeformationSpace(field, from_=from_, to=to)
diff --git a/fsl/transform/x5.py b/fsl/transform/x5.py
index 9b819ab6d56af8a22dd8f553cdd2795a244fd8ef..5d25dced4f0380ade7a1fb5e3c03cc416d1b57ae 100644
--- a/fsl/transform/x5.py
+++ b/fsl/transform/x5.py
@@ -397,16 +397,17 @@ def readNonLinearX5(fname):
_readMetadata(f)
- ref = _readSpace( f['/A'])
- src = _readSpace( f['/B'])
- field, space = _readDeformation(f['/Transform'])
+ ref = _readSpace( f['/A'])
+ src = _readSpace( f['/B'])
+ field, xform, defType = _readDeformation(f['/Transform'])
return nonlinear.DeformationField(field,
- header=space.header,
+ xform=xform,
src=src,
ref=ref,
srcSpace='world',
- refSpace='world')
+ refSpace='world',
+ defType=defType)
def writeNonLinearX5(fname, field):
@@ -421,8 +422,8 @@ def writeNonLinearX5(fname, field):
f.attrs['Type'] = 'nonlinear'
_writeMetadata(f)
- _writeSpace( f.create_group('/A'), f.ref)
- _writeSpace( f.create_group('/B'), f.src)
+ _writeSpace( f.create_group('/A'), field.ref)
+ _writeSpace( f.create_group('/B'), field.src)
_writeDeformation(f.create_group('/Transform'), field)
@@ -538,8 +539,8 @@ def _readDeformation(group):
- A ``numpy.arrayThe`` containing the deformation field
- - A :class:`.Nifti` object representing the deformation
- field space
+ - A ``numpy.array`` of shape ``(4, 4) `` containing the
+ voxel to world affine for the deformation field
- The deformation type - either ``'absolute'`` or
``'relative'``
@@ -554,7 +555,7 @@ def _readDeformation(group):
if subtype not in ('absolute', 'relative'):
raise X5Error('Unknown deformation type: {}'.format(subtype))
- mapping = _readSpace(group['Mapping'])
+ mapping = _readAffine(group['Mapping'])
field = group['Matrix']
if len(field.shape) != 4 or field.shape[3] != 3:
@@ -570,10 +571,15 @@ def _writeDeformation(group, field):
:arg field: A :class:`.DeformationField` object
"""
+ if field.srcSpace != 'world' or \
+ field.refSpace != 'world':
+ raise X5Error('Deformation field must encode a '
+ 'world<->world transformation')
+
group.attrs['Type'] = 'deformation'
group.attrs['SubType'] = field.deformationType
mapping = group.create_group('Mapping')
group.create_dataset('Matrix', data=field.data)
- _writeSpace(mapping, field)
+ _writeAffine(mapping, field.getAffine('voxel', 'world'))