Merge pull request #1182 from effigies/enh/qform_calculation

ENH: Set symmetric threshold for identifying unit quaternions in qform calculation

Author: matthew-brett

doc/source/nifti_images.rst

@@ -273,8 +273,8 @@ You can get and set the qform affine using the equivalent methods to those for
 the sform: ``get_qform()``, ``set_qform()``.
 
 >>> n1_header.get_qform(coded=True)
-(array([[ -2.  ,   0.  ,   0.  , 117.86],
-       [ -0.  ,   1.97,  -0.36, -35.72],
+(array([[ -2.  ,   0.  ,  -0.  , 117.86],
+       [  0.  ,   1.97,  -0.36, -35.72],
        [  0.  ,   0.32,   2.17,  -7.25],
        [  0.  ,   0.  ,   0.  ,   1.  ]]), 1)
 

nibabel/nifti1.py

@@ -688,7 +688,7 @@ class Nifti1Header(SpmAnalyzeHeader):
     single_magic = b'n+1'
 
     # Quaternion threshold near 0, based on float32 precision
-    quaternion_threshold = -np.finfo(np.float32).eps * 3
+    quaternion_threshold = np.finfo(np.float32).eps * 3
 
     def __init__(self, binaryblock=None, endianness=None, check=True, extensions=()):
         """Initialize header from binary data block and extensions"""

nibabel/quaternions.py

@@ -42,10 +42,10 @@ def fillpositive(xyz, w2_thresh=None):
     xyz : iterable
        iterable containing 3 values, corresponding to quaternion x, y, z
     w2_thresh : None or float, optional
-       threshold to determine if w squared is really negative.
+       threshold to determine if w squared is non-zero.
        If None (default) then w2_thresh set equal to
-       ``-np.finfo(xyz.dtype).eps``, if possible, otherwise
-       ``-np.finfo(np.float64).eps``
+       3 * ``np.finfo(xyz.dtype).eps``, if possible, otherwise
+       3 * ``np.finfo(np.float64).eps``
 
     Returns
     -------
@@ -89,17 +89,17 @@ def fillpositive(xyz, w2_thresh=None):
     # If necessary, guess precision of input
     if w2_thresh is None:
         try:  # trap errors for non-array, integer array
-            w2_thresh = -np.finfo(xyz.dtype).eps * 3
+            w2_thresh = np.finfo(xyz.dtype).eps * 3
         except (AttributeError, ValueError):
-            w2_thresh = -FLOAT_EPS * 3
+            w2_thresh = FLOAT_EPS * 3
     # Use maximum precision
     xyz = np.asarray(xyz, dtype=MAX_FLOAT)
     # Calculate w
-    w2 = 1.0 - np.dot(xyz, xyz)
-    if w2 < 0:
-        if w2 < w2_thresh:
-            raise ValueError(f'w2 should be positive, but is {w2:e}')
+    w2 = 1.0 - xyz @ xyz
+    if np.abs(w2) < np.abs(w2_thresh):
         w = 0
+    elif w2 < 0:
+        raise ValueError(f'w2 should be positive, but is {w2:e}')
     else:
         w = np.sqrt(w2)
     return np.r_[w, xyz]

nibabel/tests/test_quaternions.py

@@ -16,35 +16,40 @@
 from .. import eulerangles as nea
 from .. import quaternions as nq
 
+
+def norm(vec):
+    # Return unit vector with same orientation as input vector
+    return vec / np.sqrt(vec @ vec)
+
+
+def gen_vec(dtype):
+    # Generate random 3-vector in [-1, 1]^3
+    rand = np.random.default_rng()
+    return rand.uniform(low=-1.0, high=1.0, size=(3,)).astype(dtype)
+
+
 # Example rotations
-eg_rots = []
-params = (-pi, pi, pi / 2)
-zs = np.arange(*params)
-ys = np.arange(*params)
-xs = np.arange(*params)
-for z in zs:
-    for y in ys:
-        for x in xs:
-            eg_rots.append(nea.euler2mat(z, y, x))
+eg_rots = [
+    nea.euler2mat(z, y, x)
+    for z in np.arange(-pi, pi, pi / 2)
+    for y in np.arange(-pi, pi, pi / 2)
+    for x in np.arange(-pi, pi, pi / 2)
+]
+
 # Example quaternions (from rotations)
-eg_quats = []
-for M in eg_rots:
-    eg_quats.append(nq.mat2quat(M))
+eg_quats = [nq.mat2quat(M) for M in eg_rots]
 # M, quaternion pairs
 eg_pairs = list(zip(eg_rots, eg_quats))
 
 # Set of arbitrary unit quaternions
-unit_quats = set()
-params = range(-2, 3)
-for w in params:
-    for x in params:
-        for y in params:
-            for z in params:
-                q = (w, x, y, z)
-                Nq = np.sqrt(np.dot(q, q))
-                if not Nq == 0:
-                    q = tuple([e / Nq for e in q])
-                    unit_quats.add(q)
+unit_quats = set(
+    tuple(norm(np.r_[w, x, y, z]))
+    for w in range(-2, 3)
+    for x in range(-2, 3)
+    for y in range(-2, 3)
+    for z in range(-2, 3)
+    if (w, x, y, z) != (0, 0, 0, 0)
+)
 
 
 def test_fillpos():
@@ -69,6 +74,51 @@ def test_fillpos():
     assert wxyz[0] == 0.0
 
 
+@pytest.mark.parametrize('dtype', ('f4', 'f8'))
+def test_fillpositive_plus_minus_epsilon(dtype):
+    # Deterministic test for fillpositive threshold
+    # We are trying to fill (x, y, z) with a w such that |(w, x, y, z)| == 1
+    # If |(x, y, z)| is slightly off one, w should still be 0
+    nptype = np.dtype(dtype).type
+
+    # Obviously, |(x, y, z)| == 1
+    baseline = np.array([0, 0, 1], dtype=dtype)
+
+    # Obviously, |(x, y, z)| ~ 1
+    plus = baseline * nptype(1 + np.finfo(dtype).eps)
+    minus = baseline * nptype(1 - np.finfo(dtype).eps)
+
+    assert nq.fillpositive(plus)[0] == 0.0
+    assert nq.fillpositive(minus)[0] == 0.0
+
+    # |(x, y, z)| > 1, no real solutions
+    plus = baseline * nptype(1 + 2 * np.finfo(dtype).eps)
+    with pytest.raises(ValueError):
+        nq.fillpositive(plus)
+
+    # |(x, y, z)| < 1, two real solutions, we choose positive
+    minus = baseline * nptype(1 - 2 * np.finfo(dtype).eps)
+    assert nq.fillpositive(minus)[0] > 0.0
+
+
+@pytest.mark.parametrize('dtype', ('f4', 'f8'))
+def test_fillpositive_simulated_error(dtype):
+    # Nondeterministic test for fillpositive threshold
+    # Create random vectors, normalize to unit length, and count on floating point
+    # error to result in magnitudes larger/smaller than one
+    # This is to simulate cases where a unit quaternion with w == 0 would be encoded
+    # as xyz with small error, and we want to recover the w of 0
+
+    # Permit 1 epsilon per value (default, but make explicit here)
+    w2_thresh = 3 * np.finfo(dtype).eps
+
+    pos_error = neg_error = False
+    for _ in range(50):
+        xyz = norm(gen_vec(dtype))
+
+        assert nq.fillpositive(xyz, w2_thresh)[0] == 0.0
+
+
 def test_conjugate():
     # Takes sequence
     cq = nq.conjugate((1, 0, 0, 0))
@@ -125,7 +175,7 @@ def test_norm():
 def test_mult(M1, q1, M2, q2):
     # Test that quaternion * same as matrix *
     q21 = nq.mult(q2, q1)
-    assert_array_almost_equal, np.dot(M2, M1), nq.quat2mat(q21)
+    assert_array_almost_equal, M2 @ M1, nq.quat2mat(q21)
 
 
 @pytest.mark.parametrize('M, q', eg_pairs)
@@ -146,7 +196,7 @@ def test_eye():
 @pytest.mark.parametrize('M, q', eg_pairs)
 def test_qrotate(vec, M, q):
     vdash = nq.rotate_vector(vec, q)
-    vM = np.dot(M, vec)
+    vM = M @ vec
     assert_array_almost_equal(vdash, vM)
 
 
@@ -179,6 +229,6 @@ def test_angle_axis():
         nq.nearly_equivalent(q, q2)
         aa_mat = nq.angle_axis2mat(theta, vec)
         assert_array_almost_equal(aa_mat, M)
-        unit_vec = vec / np.sqrt(vec.dot(vec))
+        unit_vec = norm(vec)
         aa_mat2 = nq.angle_axis2mat(theta, unit_vec, is_normalized=True)
         assert_array_almost_equal(aa_mat2, M)