diff --git a/fsl/data/image.py b/fsl/data/image.py
index 95aa3875dfbd547323336cd017700378aa75fd6a..d4edf9690ddf30a10c8ac22d673814c77a35d360 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -34,6 +34,7 @@ and file names:
import os
import os.path as op
+import itertools as it
import string
import logging
import tempfile
@@ -408,6 +409,54 @@ class Nifti(notifier.Notifier, meta.Meta):
return affines, isneuro
+ @staticmethod
+ def identifyAffine(image, xform, from_=None, to=None):
+ """Attempt to identify the source or destination space for the given
+ affine.
+
+ ``xform`` is assumed to be an affine transformation which can be used
+ to transform coordinates between two coordinate systems associated with
+ ``image``.
+
+ If one of ``from_`` or ``to`` is provided, the other will be derived.
+ If neither are provided, both will be derived. See the
+ :meth:`.Nifti.getAffine` method for details on the valild values that
+ ``from_`` and ``to`` may take.
+
+ :arg image: :class:`.Nifti` instance associated with the affine.
+
+ :arg xform: ``(4, 4)`` ``numpy`` array encoding an affine
+ transformation
+
+ :arg from_: Label specifying the coordinate system which ``xform``
+ takes as input
+
+ :arg to: Label specifying the coordinate system which ``xform``
+ produces as output
+
+ :returns: A tuple containing:
+ - A label for the ``from_`` coordinate system
+ - A label for the ``to`` coordinate system
+ """
+
+ if (from_ is not None) and (to is not None):
+ return from_, to
+
+ if from_ is not None: froms = [from_]
+ else: froms = ['voxel', 'fsl', 'world']
+ if to is not None: tos = [to]
+ else: tos = ['voxel', 'fsl', 'world']
+
+ for from_, to in it.product(froms, tos):
+
+ candidate = image.getAffine(from_, to)
+
+ if np.all(np.isclose(candidate, xform)):
+ return from_, to
+
+ raise ValueError('Could not identify affine')
+
+
def strval(self, key):
"""Returns the specified NIFTI header field, converted to a python
string, correctly null-terminated, and with non-printable characters
diff --git a/fsl/transform/affine.py b/fsl/transform/affine.py
index 5aaa66f35abe812c061c10e0de92c48fc996fac8..e0364bf94030c76d6df99a5222ce6439bed8df38 100644
--- a/fsl/transform/affine.py
+++ b/fsl/transform/affine.py
@@ -21,7 +21,6 @@ transformations. The following functions are available:
axisAnglesToRotMat
axisBounds
rmsdev
- identify
And a few more functions are provided for working with vectors:
@@ -34,9 +33,9 @@ And a few more functions are provided for working with vectors:
"""
+import collections.abc as abc
import numpy as np
import numpy.linalg as linalg
-import collections.abc as abc
def invert(x):
@@ -583,57 +582,3 @@ def rmsdev(T1, T2, R=None, xc=None):
erms = np.sqrt(erms)
return erms
-
-
-def identify(image, xform, from_=None, to=None):
- """Attempt to identify the source or destination space for the given
- affine.
-
- ``xform`` is assumed to be an affine transformation which can be used
- to transform coordinates between two coordinate systems associated with
- ``image``.
-
- One of ``from_`` or ``to`` must be provided. Whichever is not provided
- will be derived. See the :meth:`.Nifti.getAffine` method for details on
- the valild values that ``from_`` and ``to`` may take.
-
- :arg image: :class:`.Nifti` instance associated with the affine.
-
- :arg xform: ``(4, 4)`` ``numpy`` array encoding an affine transformation
-
- :arg from_: Label specifying the coordinate system which ``xform``
- takes as input
-
- :arg to: Label specifying the coordinate system which ``xform``
- produces as output
-
- :returns: A tuple containing:
- - A label for the ``from_`` coordinate system
- - A label for the ``to`` coordinate system
- """
-
- if (from_ is None) and (to is None):
- raise ValueError('One of from_ or to must be provided')
-
- if (from_ is not None) and (to is not None):
- return from_, to
-
- if from_ is None:
- voxel = image.getAffine('voxel', to)
- fsl = image.getAffine('fsl', to)
- world = image.getAffine('world', to)
-
- if np.all(np.isclose(voxel, xform)): return 'voxel', to
- if np.all(np.isclose(fsl, xform)): return 'fsl', to
- if np.all(np.isclose(world, xform)): return 'world', to
-
- if to is None:
- voxel = image.getAffine(from_, 'voxel')
- fsl = image.getAffine(from_, 'fsl')
- world = image.getAffine(from_, 'world')
-
- if np.all(np.isclose(voxel, xform)): return 'voxel', to
- if np.all(np.isclose(fsl, xform)): return 'fsl', to
- if np.all(np.isclose(world, xform)): return 'world', to
-
- raise ValueError('Could not identify affine')
diff --git a/fsl/transform/x5.py b/fsl/transform/x5.py
index 5e3162f4529c42e39eaffd922769abc232e5f934..1d29a5777663d2b9c6f88cfac2648a7266636e8f 100644
--- a/fsl/transform/x5.py
+++ b/fsl/transform/x5.py
@@ -335,9 +335,10 @@ import numpy as np
import nibabel as nib
import h5py
-import fsl.version as version
-from . import affine
-from . import nonlinear
+import fsl.version as version
+import fsl.data.image as fslimage
+from . import affine
+from . import nonlinear
X5_FORMAT = 'X5'
@@ -593,9 +594,11 @@ def _readNonLinearCommon(group):
try:
if pre is not None:
- refSpace = affine.identify(ref, pre, from_='world')[1]
+ refSpace = fslimage.Nifti.identifyAffine(
+ ref, pre, from_='world')[1]
if post is not None:
- srcSpace = affine.identify(src, post, to='world')[ 0]
+ srcSpace = fslimage.Nifti.identifyAffine(
+ src, post, to='world')[ 0]
except ValueError:
raise X5Error('Invalid pre/post affine')