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Commit 66c008d5 authored by Paul McCarthy's avatar Paul McCarthy :mountain_bicyclist:
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RF,BF: Refactored x5/fnirt modules for new specs - I think the refactoring is 

complete?
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fsl/transform/fnirt.py
+ 52
− 55
View file @ 66c008d5
......@@ -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)
fsl/transform/x5.py
+ 17
− 11
View file @ 66c008d5
......@@ -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'))
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