diff --git a/fsl/data/atlases.py b/fsl/data/atlases.py
index b34499d17555a3386ea52da4198ce5e21d3b79ad..8d5dad9bd679b4bd8786de4a5a8e41c21db3d310 100644
--- a/fsl/data/atlases.py
+++ b/fsl/data/atlases.py
@@ -54,7 +54,7 @@ import fsl.data.image as fslimage
import fsl.data.constants as constants
from fsl.utils.platform import platform as platform
import fsl.utils.image.resample as resample
-import fsl.transform as transform
+import fsl.transform.affine as affine
import fsl.utils.notifier as notifier
import fsl.utils.settings as fslsettings
@@ -572,7 +572,7 @@ class AtlasDescription(object):
# Load the appropriate transformation matrix
# and transform all those voxel coordinates
# into world coordinates
- coords = transform.transform(coords, self.xforms[0])
+ coords = affine.transform(coords, self.xforms[0])
# Update the coordinates
# in our label objects
@@ -810,7 +810,7 @@ class LabelAtlas(Atlas):
"""
if not voxel:
- loc = transform.transform([loc], self.worldToVoxMat)[0]
+ loc = affine.transform([loc], self.worldToVoxMat)[0]
loc = [int(v) for v in loc.round()]
if loc[0] < 0 or \
@@ -983,7 +983,7 @@ class ProbabilisticAtlas(Atlas):
"""
if not voxel:
- loc = transform.transform([loc], self.worldToVoxMat)[0]
+ loc = affine.transform([loc], self.worldToVoxMat)[0]
loc = [int(v) for v in loc.round()]
if loc[0] < 0 or \
diff --git a/fsl/data/featanalysis.py b/fsl/data/featanalysis.py
index fbaaf694244c19045d37a45c2bc9ecd53038777a..718ef679b0502337ecf5aba68a481b336fedd0e6 100644
--- a/fsl/data/featanalysis.py
+++ b/fsl/data/featanalysis.py
@@ -47,11 +47,10 @@ import logging
import os.path as op
import numpy as np
-import fsl.utils.path as fslpath
-import fsl.transform as transform
-
-from . import image as fslimage
-from . import featdesign
+import fsl.utils.path as fslpath
+import fsl.transform.affine as affine
+from . import image as fslimage
+from . import featdesign
log = logging.getLogger(__name__)
@@ -467,9 +466,9 @@ def loadClusterResults(featdir, settings, contrast):
zcog = [c.zcogx, c.zcogy, c.zcogz]
copemax = [c.copemaxx, c.copemaxy, c.copemaxz]
- zmax = transform.transform([zmax], coordXform)[0].round()
- zcog = transform.transform([zcog], coordXform)[0].round()
- copemax = transform.transform([copemax], coordXform)[0].round()
+ zmax = affine.transform([zmax], coordXform)[0].round()
+ zcog = affine.transform([zcog], coordXform)[0].round()
+ copemax = affine.transform([copemax], coordXform)[0].round()
c.zmaxx, c.zmaxy, c.zmaxz = zmax
c.zcogx, c.zcogy, c.zcogz = zcog
diff --git a/fsl/data/image.py b/fsl/data/image.py
index 03dfc48a0aae0e91108861954f6d1bc6b61c629b..95aa3875dfbd547323336cd017700378aa75fd6a 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -46,7 +46,7 @@ import nibabel as nib
import nibabel.fileslice as fileslice
import fsl.utils.meta as meta
-import fsl.transform as transform
+import fsl.transform.affine as affine
import fsl.utils.notifier as notifier
import fsl.utils.memoize as memoize
import fsl.utils.path as fslpath
@@ -332,9 +332,9 @@ class Nifti(notifier.Notifier, meta.Meta):
refpix = (header.get('intent_p1', 1),
header.get('intent_p2', 1),
header.get('intent_p3', 1))
- voxToWorldMat = transform.concat(
- transform.scaleOffsetXform(refpix, 0),
- transform.scaleOffsetXform(knotpix, 0))
+ voxToWorldMat = affine.concat(
+ affine.scaleOffsetXform(refpix, 0),
+ affine.scaleOffsetXform(knotpix, 0))
# If the qform or sform codes are unknown,
# then we can't assume that the transform
@@ -348,7 +348,7 @@ class Nifti(notifier.Notifier, meta.Meta):
# should just be a straight scaling matrix.
elif qform == 0 and sform == 0:
pixdims = header.get_zooms()
- voxToWorldMat = transform.scaleOffsetXform(pixdims, 0)
+ voxToWorldMat = affine.scaleOffsetXform(pixdims, 0)
# Otherwise we let nibabel decide
# which transform to use.
@@ -389,21 +389,21 @@ class Nifti(notifier.Notifier, meta.Meta):
if isneuro:
x = (shape[0] - 1) * pixdim[0]
- flip = transform.scaleOffsetXform([-1, 1, 1],
- [ x, 0, 0])
- voxToScaledVoxMat = transform.concat(flip, voxToScaledVoxMat)
+ flip = affine.scaleOffsetXform([-1, 1, 1],
+ [ x, 0, 0])
+ voxToScaledVoxMat = affine.concat(flip, voxToScaledVoxMat)
affines['fsl', 'fsl'] = np.eye(4)
affines['voxel', 'voxel'] = np.eye(4)
affines['world', 'world'] = np.eye(4)
affines['voxel', 'world'] = voxToWorldMat
- affines['world', 'voxel'] = transform.invert(voxToWorldMat)
+ affines['world', 'voxel'] = affine.invert(voxToWorldMat)
affines['voxel', 'fsl'] = voxToScaledVoxMat
- affines['fsl', 'voxel'] = transform.invert(voxToScaledVoxMat)
- affines['fsl', 'world'] = transform.concat(affines['voxel', 'world'],
- affines['fsl', 'voxel'])
- affines['world', 'fsl'] = transform.concat(affines['voxel', 'fsl'],
- affines['world', 'voxel'])
+ affines['fsl', 'voxel'] = affine.invert(voxToScaledVoxMat)
+ affines['fsl', 'world'] = affine.concat(affines['voxel', 'world'],
+ affines['fsl', 'voxel'])
+ affines['world', 'fsl'] = affine.concat(affines['voxel', 'fsl'],
+ affines['world', 'voxel'])
return affines, isneuro
diff --git a/fsl/data/mesh.py b/fsl/data/mesh.py
index d512972d11904703d8db062815e2cb4b94dc4bd4..c15e49ced5f972e39e01af4c520053ecdb6b809a 100644
--- a/fsl/data/mesh.py
+++ b/fsl/data/mesh.py
@@ -33,9 +33,9 @@ import collections
import os.path as op
import numpy as np
-import fsl.utils.meta as meta
-import fsl.utils.notifier as notifier
-import fsl.transform as transform
+import fsl.utils.meta as meta
+import fsl.utils.notifier as notifier
+import fsl.transform.affine as affine
log = logging.getLogger(__name__)
@@ -693,7 +693,7 @@ def calcFaceNormals(vertices, indices):
v2 = vertices[indices[:, 2]]
fnormals = np.cross((v1 - v0), (v2 - v0))
- fnormals = transform.normalise(fnormals)
+ fnormals = affine.normalise(fnormals)
return fnormals
@@ -724,7 +724,7 @@ def calcVertexNormals(vertices, indices, fnormals):
vnormals[v2, :] += fnormals[i]
# normalise to unit length
- return transform.normalise(vnormals)
+ return affine.normalise(vnormals)
def needsFixing(vertices, indices, fnormals, loBounds, hiBounds):
@@ -769,4 +769,4 @@ def needsFixing(vertices, indices, fnormals, loBounds, hiBounds):
# vertex to the camera is positive
# If it isn't, we need to flip the
# triangle winding order.
- return np.dot(n, transform.normalise(camera - vert)) < 0
+ return np.dot(n, affine.normalise(camera - vert)) < 0
diff --git a/fsl/data/mghimage.py b/fsl/data/mghimage.py
index 9693d21fab84f09e00163736fc4344600d834dc4..fea4c9970ecae56ec84f2274f656f11e3e6df2e8 100644
--- a/fsl/data/mghimage.py
+++ b/fsl/data/mghimage.py
@@ -14,9 +14,9 @@ import os.path as op
import six
import nibabel as nib
-import fsl.utils.path as fslpath
-import fsl.transform as transform
-import fsl.data.image as fslimage
+import fsl.utils.path as fslpath
+import fsl.transform.affine as affine
+import fsl.data.image as fslimage
ALLOWED_EXTENSIONS = ['.mgz', '.mgh']
@@ -55,12 +55,12 @@ class MGHImage(fslimage.Image):
filename = None
data = image.get_data()
- affine = image.affine
+ xform = image.affine
vox2surf = image.header.get_vox2ras_tkr()
fslimage.Image.__init__(self,
data,
- xform=affine,
+ xform=xform,
name=name,
dataSource=filename)
@@ -68,9 +68,9 @@ class MGHImage(fslimage.Image):
self.setMeta('mghImageFile', filename)
self.__voxToSurfMat = vox2surf
- self.__surfToVoxMat = transform.invert(vox2surf)
- self.__surfToWorldMat = transform.concat(affine, self.__surfToVoxMat)
- self.__worldToSurfMat = transform.invert(self.__surfToWorldMat)
+ self.__surfToVoxMat = affine.invert(vox2surf)
+ self.__surfToWorldMat = affine.concat(affine, self.__surfToVoxMat)
+ self.__worldToSurfMat = affine.invert(self.__surfToWorldMat)
def save(self, filename=None):
diff --git a/fsl/transform/__init__.py b/fsl/transform/__init__.py
index 8961c518224a444e79e68bd3bc54df2f63acd626..2c86ce512aeda3a909c8cae11e2a11a06796cb70 100644
--- a/fsl/transform/__init__.py
+++ b/fsl/transform/__init__.py
@@ -6,41 +6,14 @@
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
"""This module contains functions for working with linear and non-linear FSL
-transformations.
-"""
-
-
-from .affine import ( # noqa
- invert,
- concat,
- veclength,
- normalise,
- scaleOffsetXform,
- compose,
- decompose,
- rotMatToAffine,
- rotMatToAxisAngles,
- axisAnglesToRotMat,
- axisBounds,
- transform,
- transformNormal,
- rmsdev)
+transformations. Functionality is split across the following modules:
-from .flirt import ( # noqa
- readFlirt,
- writeFlirt,
- fromFlirt,
- toFlirt,
- flirtMatrixToSform,
- sformToFlirtMatrix)
+.. autosummary::
+ :nosignatures:
-from .fnirt import ( # noqa
- readFnirt,
- toFnirt,
- fromFnirt)
-
-from .x5 import ( # noqa
- readLinearX5,
- writeLinearX5,
- readNonLinearX5,
- writeNonLinearX5)
+ .affine
+ .flirt
+ .fnirt
+ .nonlinear
+ .x5
+"""