Merge branch 'rel/3.3.1' into 'v3.3'

Rel/3.3.1

See merge request fsl/fslpy!256

CHANGELOG.rst

 This document contains the ``fslpy`` release history in reverse chronological
 order.
 
+3.3.1 (Thursday 8th October 2020)
+---------------------------------
+
+
+Changed
+^^^^^^^
+
+
+* The :func:`.affine.decompose` and :func:`.affine.compose` functions now
+  have the ability to return/accept shear components.
+
+
+Fixed
+^^^^^
+
+
+* Fixed a bug in the :func:`.affine.decompose` function which was corrupting
+  the scale estimates when given an affine containing shears.
+
 
 3.3.0 (Tuesday 22nd September 2020)
 -----------------------------------

fsl/transform/affine.py

@@ -120,7 +120,7 @@ def scaleOffsetXform(scales, offsets):
     return xform
 
 
-def compose(scales, offsets, rotations, origin=None):
+def compose(scales, offsets, rotations, origin=None, shears=None):
     """Compose a transformation matrix out of the given scales, offsets
     and axis rotations.
 
@@ -133,6 +133,8 @@ def compose(scales, offsets, rotations, origin=None):
 
     :arg origin:    Origin of rotation - must be scaled by the ``scales``.
                     If not provided, the rotation origin is ``(0, 0, 0)``.
+
+    :arg shears:    Sequence of three shear values
     """
 
     preRotate  = np.eye(4)
@@ -154,6 +156,7 @@ def compose(scales, offsets, rotations, origin=None):
     scale  = np.eye(4, dtype=np.float64)
     offset = np.eye(4, dtype=np.float64)
     rotate = np.eye(4, dtype=np.float64)
+    shear  = np.eye(4, dtype=np.float64)
 
     scale[  0,  0] = scales[ 0]
     scale[  1,  1] = scales[ 1]
@@ -164,10 +167,15 @@ def compose(scales, offsets, rotations, origin=None):
 
     rotate[:3, :3] = rotations
 
-    return concat(offset, postRotate, rotate, preRotate, scale)
+    if shears is not None:
+        shear[0, 1] = shears[0]
+        shear[0, 2] = shears[1]
+        shear[1, 2] = shears[2]
+
+    return concat(offset, postRotate, rotate, preRotate, scale, shear)
 
 
-def decompose(xform, angles=True):
+def decompose(xform, angles=True, shears=False):
     """Decomposes the given transformation matrix into separate offsets,
     scales, and rotations, according to the algorithm described in:
 
@@ -175,8 +183,7 @@ def decompose(xform, angles=True):
     320-323 in *Graphics Gems II*, James Arvo (editor), Academic Press, 1991,
     ISBN: 0120644819.
 
-    It is assumed that the given transform has no perspective components. Any
-    shears in the affine are discarded.
+    It is assumed that the given transform has no perspective components.
 
     :arg xform:  A ``(3, 3)`` or ``(4, 4)`` affine transformation matrix.
 
@@ -184,6 +191,8 @@ def decompose(xform, angles=True):
                  as axis-angles, in radians. Otherwise, the rotation matrix
                  is returned.
 
+    :arg shears: Defaults to ``False``. If ``True``, shears are returned.
+
     :returns: The following:
 
                - A sequence of three scales
@@ -191,6 +200,7 @@ def decompose(xform, angles=True):
                  was a ``(3, 3)`` matrix)
                - A sequence of three rotations, in radians. Or, if
                  ``angles is False``, a rotation matrix.
+               - If ``shears is True``, a sequence of three shears.
     """
 
     # The inline comments in the code below are taken verbatim from
@@ -199,7 +209,7 @@ def decompose(xform, angles=True):
     # The next step is to extract the translations. This is trivial;
     # we find t_x = M_{4,1}, t_y = M_{4,2}, and t_z = M_{4,3}. At this
     # point we are left with a 3*3 matrix M' = M_{1..3,1..3}.
-    xform = xform.T
+    xform = np.array(xform).T
 
     if xform.shape == (4, 4):
         translations = xform[ 3, :3]
@@ -214,6 +224,7 @@ def decompose(xform, angles=True):
     # The process of finding the scaling factors and shear parameters
     # is interleaved. First, find s_x = |M'_1|.
     sx = np.sqrt(np.dot(M1, M1))
+    M1 = M1 / sx
 
     # Then, compute an initial value for the xy shear factor,
     # s_xy = M'_1 * M'_2. (this is too large by the y scaling factor).
@@ -230,7 +241,7 @@ def decompose(xform, angles=True):
     # The second row is normalized, and s_xy is divided by s_y to
     # get its final value.
     M2  = M2  / sy
-    sxy = sxy / sy
+    sxy = sxy / sx
 
     # The xz and yz shear factors are computed as in the preceding,
     sxz = np.dot(M1, M3)
@@ -245,8 +256,8 @@ def decompose(xform, angles=True):
     # the third row is normalized, and the xz and yz shear factors are
     # rescaled.
     M3  = M3  / sz
-    sxz = sxz / sz
-    syz = sxz / sz
+    sxz = sxz / sx
+    syz = syz / sy
 
     # The resulting matrix now is a pure rotation matrix, except that it
     # might still include a scale factor of -1. If the determinant of the
@@ -266,7 +277,13 @@ def decompose(xform, angles=True):
     if angles: rotations = rotMatToAxisAngles(R.T)
     else:      rotations = R.T
 
-    return np.array([sx, sy, sz]), translations, rotations
+    retval = [np.array([sx, sy, sz]), translations, rotations]
+
+    if shears:
+        retval.append(np.array((sxy, sxz, syz)))
+
+    return tuple(retval)
+
 
 
 def rotMatToAffine(rotmat, origin=None):

fsl/version.py

@@ -47,7 +47,7 @@ import            re
 import            string
 
 
-__version__ = '3.3.0'
+__version__ = '3.3.1'
 """Current version number, as a string. """
 
 

tests/test_transform/test_affine.py

@@ -226,8 +226,10 @@ def test_compose_and_decompose():
         xform                      = lines[i * 4: i * 4 + 4]
         xform                      = np.genfromtxt(xform)
 
-        scales, offsets, rotations = affine.decompose(xform)
-        result = affine.compose(scales, offsets, rotations)
+        scales, offsets, rotations, shears = affine.decompose(
+            xform, shears=True)
+
+        result = affine.compose(scales, offsets, rotations, shears=shears)
 
         assert np.all(np.isclose(xform, result, atol=1e-5))
 
@@ -235,8 +237,10 @@ def test_compose_and_decompose():
         # different rotation origin, but we test
         # explicitly passing the origin for
         # completeness
-        scales, offsets, rotations = affine.decompose(xform)
-        result = affine.compose(scales, offsets, rotations, [0, 0, 0])
+        scales, offsets, rotations, shears = affine.decompose(
+            xform, shears=True)
+        result = affine.compose(
+            scales, offsets, rotations, origin=[0, 0, 0], shears=shears)
 
         assert np.all(np.isclose(xform, result, atol=1e-5))
 

tests/test_transform/testdata/test_transform_test_compose.txt

@@ -23,7 +23,7 @@
 1.0  0.0   0.0  0.0
 0.0  1.0   0.0  0.0
 0.0  0.0  -1.0  0.0
-0.0  0.0   0.0  1.0 
+0.0  0.0   0.0  1.0
 
 0.5   0.0  0.0   0.0
 0.0   2.4  0.0   0.0
@@ -35,22 +35,22 @@
 0.0   0.0   1.6  53.0
 0.0   0.0   0.0   1.0
 
-0.5            0.0            0.0           10.0         
+0.5            0.0            0.0           10.0
 0.0            0.0           -1.6           -6.7877502441
 0.0            2.4            0.0           29.7931518555
-0.0            0.0            0.0            1.0         
+0.0            0.0            0.0            1.0
 
 0.0           -2.4           -0.0           30.6160888672
 0.0            0.0           -1.6           -6.7877502441
 0.5            0.0            0.0           50.5961608887
-0.0            0.0            0.0            1.0         
+0.0            0.0            0.0            1.0
 
 -0.0            1.3765834472   1.3106432709   0.0736983719
  0.0           -1.9659649063   0.9177222982  14.1062102814
  0.5            0.0            0.0           50.5961608887
  0.0            0.0            0.0            1.0
 
- 0.453766452   -0.7004337463   0.4832135801  16.789591468 
+ 0.453766452   -0.7004337463   0.4832135801  16.789591468
 -0.0159784155   1.6056689296   1.1880787388 -16.2943532298
 -0.2093817023  -1.640493784    0.9565424959  66.1123321137
  0.0            0.0            0.0            1.0
@@ -109,3 +109,8 @@
  0.041017  -0.081580  -6.319922   72.090378
 -0.000000   0.381914  -1.365036  -41.159451
  0.000000   0.000000   0.000000    1.000000
+
+1.1441229   0.833406   3.765340    3
+0.8312539   2.459607  -0.804545    4
+1.4142136   1.554275   1.724796    5
+0.0         0.0        0.0         1