From a4f06be4ffc63d79af7d342516503231fd2a67d8 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Mon, 22 Jul 2019 14:05:51 +0100
Subject: [PATCH] BF: Call existent parseVersionString function, as opposed to
non-existent variant. applyDeformation/convertDeformationType/Space were
assuming voxel alignment between deformation field and reference image.
---
fsl/transform/nonlinear.py | 36 +++++++++++++++++++++++++-----------
fsl/transform/x5.py | 4 ++--
2 files changed, 27 insertions(+), 13 deletions(-)
diff --git a/fsl/transform/nonlinear.py b/fsl/transform/nonlinear.py
index 520c5b7a5..82776bfe6 100644
--- a/fsl/transform/nonlinear.py
+++ b/fsl/transform/nonlinear.py
@@ -584,7 +584,8 @@ def convertDeformationType(field, defType=None):
# we need the coordinates of every voxel
# in the reference coordinate system.
dx, dy, dz = field.shape[:3]
- xform = field.getAffine('voxel', field.refSpace)
+ xform = affine.concat(field.ref.getAffine('world', field.refSpace),
+ field .getAffine('voxel', 'world'))
coords = np.meshgrid(np.arange(dx),
np.arange(dy),
@@ -659,9 +660,12 @@ def convertDeformationSpace(field, from_, to):
refcoords = np.array(refcoords)
refcoords = refcoords.transpose((1, 2, 3, 0)).reshape((-1, 3))
- if from_ != 'voxel':
- refmat = field.ref.getAffine('voxel', from_)
- refcoords = affine.transform(refcoords, refmat)
+ xform = affine.concat(
+ field.ref.getAffine('world', from_),
+ field .getAffine('voxel', 'world'))
+
+ if not np.all(np.isclose(xform, np.eye(4))):
+ refcoords = affine.transform(refcoords, xform)
fieldcoords = srccoords - refcoords
@@ -711,6 +715,7 @@ def applyDeformation(image, field, ref=None, order=1, mode=None, cval=None):
if order is None: order = 1
if mode is None: mode = 'nearest'
if cval is None: cval = 0
+ if ref is None: ref = field.ref
# We need the field to contain
# absolute source image voxel
@@ -725,13 +730,22 @@ def applyDeformation(image, field, ref=None, order=1, mode=None, cval=None):
refSpace='voxel',
defType='absolute')
- # Resample to alternate reference image
- # space if provided - regions of the
- # field outside of the reference image
- # space will contain -1s, so will be
- # detected as out of bounds by
- # map_coordinates
- if ref is not None:
+ # If the field is not voxel-aligned
+ # to the reference, we need to
+ # resample the field itself into the
+ # reference image space (assumed to
+ # be world-aligned). If field and ref
+ # are not not world aligned, regions
+ # of the field outside of the
+ # reference image space will contain
+ # -1s, so will be detected as out of
+ # bounds by map_coordinates below.
+ #
+ # This will potentially result in
+ # truncation at the field boundaries,
+ # but there's nothing we can do about
+ # that.
+ if not field.sameSpace(ref):
field = resample.resampleToReference(field,
ref,
order=1,
diff --git a/fsl/transform/x5.py b/fsl/transform/x5.py
index 4f14413ed..1ffe03282 100644
--- a/fsl/transform/x5.py
+++ b/fsl/transform/x5.py
@@ -458,8 +458,8 @@ def _readMetadata(group):
version = group.attrs.get('Version')
meta = group.attrs.get('Metadata')
- parserver = fslversion.parseVersion(X5_VERSION)
- filever = fslversion.parseVersion(version)
+ parserver = fslversion.parseVersionString(X5_VERSION)
+ filever = fslversion.parseVersionString(version)
if (format != X5_FORMAT) or (filever[0] != parserver[0]):
raise X5Error('Incompatible format/version (required: {}/{}, '
--
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