RF: Moved affine.identify to staticmethod Nifti.identifyAffine

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

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')

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')