diff --git a/fsl/utils/transform/dispfield.py b/fsl/utils/transform/nonlinear.py
similarity index 67%
rename from fsl/utils/transform/dispfield.py
rename to fsl/utils/transform/nonlinear.py
index 4b73b00135970e943dc93143039ca7b6301e627e..4cd0da681187631090607d70f2b6c64da266b4f6 100644
--- a/fsl/utils/transform/dispfield.py
+++ b/fsl/utils/transform/nonlinear.py
@@ -1,75 +1,83 @@
#!/usr/bin/env python
#
-# dispfield.py - FNIRT displacement fields
+# nonlinear.py -
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
-"""
-
-
-FNIRT displacement field files may contain coordinates in one of two
-formats:
-
-"""
import numpy as np
-import fsl.data.image as fslimage
-from . import affine
+import fsl.data.image as fslimage
+from . import affine
-class DisplacementField(fslimage.Image):
- """
+
+class NonLinearTransform(fslimage.Image):
+ """Class which represents a FNIRT non-linear transformation
"""
def __init__(self, *args, **kwargs):
"""
"""
- source = kwargs.pop('source', None)
- reference = kwargs.pop('reference', None)
- dispType = kwargs.pop('dispType', None)
- sourceSpace = kwargs.pop('sourceSpace', 'fsl')
- referenceSpace = kwargs.pop('referenceSpace', 'fsl')
+ src = kwargs.pop('src', None)
+ ref = kwargs.pop('ref', None)
+ srcSpace = kwargs.pop('srceSpace', 'fsl')
+ refSpace = kwargs.pop('refSpace', 'fsl')
fslimage.Image.__init__(self, *args, **kwargs)
- if source is not None: source = source .header.copy()
- if reference is not None: reference = reference.header.copy()
- else: reference = self .header.copy()
+ if src is not None: src = src .header.copy()
+ if ref is not None: ref = ref .header.copy()
+ else: ref = self.header.copy()
- self.__dispType = dispType
- self.__source = source
- self.__reference = reference
- self.__sourceSpace = sourceSpace
- self.__referenceSpace = referenceSpace
+ self.__src = src
+ self.__ref = ref
+ self.__srcSpace = srcSpace
+ self.__refSpace = refSpace
@property
- def source(self):
- return self.__source
+ def src(self):
+ return self.__src
@property
- def reference(self):
- return self.__reference
+ def ref(self):
+ return self.__ref
@property
- def sourceSpace(self):
- return self.__sourceSpace
+ def srcSpace(self):
+ return self.__srcSpace
@property
- def referenceSpace(self):
- """irrelevant if absolute displacement"""
- return self.__referenceSpace
+ def refSpace(self):
+ return self.__refSpace
+
+
+class DisplacementField(NonLinearTransform):
+ """Class which represents a FNIRT displacement field which, at each voxel,
+ contains an absolute or relative displacement from a source space to a
+ reference space.
+ """
+
+ def __init__(self, *args, **kwargs):
+ """
+ """
+
+ dispType = kwargs.pop('dispType', None)
+
+ NonLinearTransform.__init__(self, *args, **kwargs)
+
+ self.__dispType = dispType
@property
def displacementType(self):
if self.__dispType is None:
- self.__dispType = detectType(self)
+ self.__dispType = detectDisplacementType(self)
return self.__dispType
@@ -83,7 +91,8 @@ class DisplacementField(fslimage.Image):
return self.displacementType == 'relative'
-def detectType(field):
+
+def detectDisplacementType(field):
"""Attempt to automatically determine whether a displacement field is
specified in absolute or relative coordinates.
@@ -99,7 +108,7 @@ def detectType(field):
# standard deviation than one which
# contains relative coordinates.
absdata = field[:]
- reldata = convertType(field, 'relative')
+ reldata = convertDisplacementType(field, 'relative')
stdabs = absdata.std(axis=(0, 1, 2)).sum()
stdrel = reldata.std(axis=(0, 1, 2)).sum()
@@ -107,7 +116,7 @@ def detectType(field):
else: return 'relative'
-def convertType(field, dispType=None):
+def convertDisplacementType(field, dispType=None):
"""Convert a displacement field between storing absolute and relative
displacements.
"""
@@ -120,7 +129,7 @@ def convertType(field, dispType=None):
# we need the coordinates of every voxel
# in the reference FSL coordinate system.
dx, dy, dz = field.shape[:3]
- v2fsl = field.getAffine('voxel', field.sourceSpace)
+ v2fsl = field.getAffine('voxel', field.srcSpace)
coords = np.meshgrid(np.arange(dx),
np.arange(dy),
np.arange(dz), indexing='ij')
@@ -137,7 +146,7 @@ def convertType(field, dispType=None):
elif dispType == 'relative': return field.data - coords
-def convertSpace(field, src, from_, to, ref=None, dispType=None):
+def convertDisplacementSpace(field, src, from_, to, ref=None, dispType=None):
"""Adjust the source and/or reference spaces of the given displacement
field.
"""
@@ -148,14 +157,14 @@ def convertSpace(field, src, from_, to, ref=None, dispType=None):
# Get the field in absolute
# coordinates if necessary
fieldcoords = field.data
- if field.relative: srccoords = convertType(field)
+ if field.relative: srccoords = convertDisplacementType(field)
else: srccoords = fieldcoords
# Now transform those source
# coordinates from the original
# source space to the source
# space specified by "from_"
- srcmat = src.getAffine(field.sourceSpace, from_)
+ srcmat = src.getAffine(field.srcSpace, from_)
srccoords = srccoords.reshape((-1, 3))
srccoords = affine.transform(srccoords, srcmat)
@@ -175,7 +184,7 @@ def convertSpace(field, src, from_, to, ref=None, dispType=None):
# displacements from source "from_"
# space into reference "to" space.
else:
- refmat = ref.getAffine(field.referenceSpace, to)
+ refmat = ref.getAffine(field.refSpace, to)
refcoords = fieldcoords.reshape((-1, 3))
refcoords = affine.transform(refcoords, refmat)
fieldcoords = srccoords - refcoords
@@ -183,8 +192,8 @@ def convertSpace(field, src, from_, to, ref=None, dispType=None):
return DisplacementField(
fieldcoords.reshape(field.shape),
header=field.header,
- source=src,
- reference=ref,
- sourceSpace=from_,
- referenceSpace=to,
+ src=src,
+ ref=ref,
+ srcSpace=from_,
+ refSpace=to,
dispType=dispType)
diff --git a/tests/test_transform_dispfield.py b/tests/test_transform_nonlinear.py
similarity index 100%
rename from tests/test_transform_dispfield.py
rename to tests/test_transform_nonlinear.py