Transforms Testcases

.gitignore

@@ -128,3 +128,6 @@ dmypy.json
 
 # MacOSX dir index files
 .DS_Store
+
+
+.vscode/

hexrd/transforms/new_capi/transforms_definitions.py

@@ -221,9 +221,11 @@ class DEF_xy_to_gvec(DEF_Func):
         (3, ) translation vector connecting LAB FRAME to SAMPLE FRAME
     tvec_c : array_like
         (3, ) translation vector connecting SAMPLE FRAME to CRYSTAL FRAME
-    rmat_b : array_like, optional
-        (3, 3) COB matrix taking components in the BEAM FRAME to the LAB FRAME;
-        defaults to None, which implies the standard setting of identity.
+    beam_vec : ndarray, optional
+        Unit vector pointing towards the X-ray source in the lab frame.
+        Defaults to [0,0,-1]
+    eta_vec : ndarray, optional
+        Vector defining eta=0 in the lab frame.  Defaults to [1,0,0]
     distortion : distortion class, optional
         Default is None
     output_ref : bool, optional
@@ -245,12 +247,12 @@ class DEF_xy_to_gvec(DEF_Func):
     -----
     ???: is there a need to flatten the tvec inputs?
     ???: include optional wavelength input for returning G with magnitude?
-    ???: is there a need to check that rmat_b is orthogonal if spec'd?
     """
     def _signature(xy_d,
                    rmat_d, rmat_s,
                    tvec_d, tvec_s, tvec_c,
-                   rmat_b=None,
+                   beam_vec=None,
+                   eta_vec=None,
                    distortion=None,
                    output_ref=False):
         pass
@@ -516,7 +518,7 @@ def _signature(vec_in):
 class DEF_make_sample_rmat(DEF_Func):
     """
     Make SAMPLE frame rotation matrices as composition of
-    rotation of ome about the axis
+    rotation of omega about the axis
 
     [0., cos(chi), sin(chi)]
 
@@ -526,16 +528,16 @@ class DEF_make_sample_rmat(DEF_Func):
     ----------
     chi : float
         The inclination angle of the goniometer axis (standard coords)
-    ome : array_like
+    omega : array_like
         (n) angles to generate rotation matrices from.
 
     Returns
     -------
     array_like
         (n, 3, 3) a vector of the n rotation matrices along the
-        axis defined by chi, one for each ome.
+        axis defined by chi, one for each omega.
     """
-    def _signature(chi, ome):
+    def _signature(chi, omega):
         pass
 
 

hexrd/transforms/new_capi/xf_new_capi.py

@@ -34,7 +34,7 @@
 def angles_to_gvec(angs, beam_vec=None, eta_vec=None, chi=None, rmat_c=None):
     """
 
-    Takes triplets of angles in the beam frame (2*theta, eta, optional omega)
+    Takes triplets of angles in the beam frame (2*theta, eta[, omega])
     to components of unit G-vectors in the LAB frame.  If the omega
     values are not trivial (i.e. angs[:, 2] = 0.), then the components
     are in the SAMPLE frame.  If the crystal rmat is specified and
@@ -46,12 +46,12 @@ def angles_to_gvec(angs, beam_vec=None, eta_vec=None, chi=None, rmat_c=None):
     ----------
     angs : ndarray
         The euler angles of diffraction. The last dimension must be 2 or 3.  In
-        (2*theta, eta, omega) or (2*theta, eta) format.
+        (2*theta, eta[, omega]) format. omega is optional.
     beam_vec : ndarray, optional
         Unit vector pointing towards the X-ray source in the lab frame.
         Defaults to [0,0,-1]
     eta_vec : ndarray, optional
-        Vector defining eta=0 in the lab frame.  Defaults to [1,0,0]
+        Unit vector defining eta=0 in the lab frame.  Defaults to [1,0,0]
     chi : float, optional
         The inclination angle of the sample frame about the lab frame X.
     rmat_c : ndarray, optional
@@ -91,7 +91,7 @@ def angles_to_gvec(angs, beam_vec=None, eta_vec=None, chi=None, rmat_c=None):
 def angles_to_dvec(angs, beam_vec=None, eta_vec=None, chi=None, rmat_c=None):
     """
 
-    Takes triplets of angles in the beam frame (2*theta, eta, omega)
+    Takes triplets of angles in the beam frame (2*theta, eta[, omega])
     to components of unit diffraction vectors in the LAB frame.  If the omega
     values are not trivial (i.e. angs[:, 2] = 0.), then the components
     are in the SAMPLE frame.  If the crystal rmat is specified and
@@ -101,13 +101,13 @@ def angles_to_dvec(angs, beam_vec=None, eta_vec=None, chi=None, rmat_c=None):
     Parameters
     ----------
     angs : ndarray
-        The euler angles of diffraction. The last dimension must be 3.  In
-        (2*theta, eta, omega) format.
+        The euler angles of diffraction. The last dimension must be 2 or 3.  In
+        (2*theta, eta[, omega]) format. omega is optional.
     beam_vec : ndarray, optional
         Unit vector pointing towards the X-ray source in the lab frame.
         Defaults to [0,0,-1]
     eta_vec : ndarray, optional
-        Vector defining eta=0 in the lab frame.  Defaults to [1,0,0]
+        Unit vector defining eta=0 in the lab frame.  Defaults to [1,0,0]
     chi : float, optional
         The inclination angle of the sample frame about the lab frame X.
     rmat_c : ndarray, optional
@@ -124,6 +124,10 @@ def angles_to_dvec(angs, beam_vec=None, eta_vec=None, chi=None, rmat_c=None):
     beam_vec = beam_vec if beam_vec is not None else cnst.beam_vec
     eta_vec = eta_vec if eta_vec is not None else cnst.eta_vec
 
+    # if only a pair is provided... convert to a triplet with omegas == 0
+    # so that behavior is preserved.
+    if angs.shape[-1] == 2:
+        angs = np.hstack((angs, np.zeros(angs.shape[:-1] + (1,))))
     angs = np.ascontiguousarray(np.atleast_2d(angs))
     beam_vec = np.ascontiguousarray(beam_vec.flatten())
     eta_vec = np.ascontiguousarray(eta_vec.flatten())
@@ -160,7 +164,7 @@ def makeGVector(hkl, bMat):
 
     """
     assert hkl.shape[0] == 3, 'hkl input must be (3, n)'
-    return unitVector(np.dot(bMat, hkl))
+    return unit_vector(np.dot(bMat, hkl))
 
 
 @xf_api
@@ -268,7 +272,8 @@ def xy_to_gvec(
     tvec_d,
     tvec_s,
     tvec_c,
-    rmat_b=None,
+    beam_vec=None,
+    eta_vec=None,
     distortion=None,
     output_ref=False,
 ):
@@ -294,9 +299,11 @@ def xy_to_gvec(
         (3, ) translation vector connecting LAB FRAME to SAMPLE FRAME
     tvec_c : array_like
         (3, ) translation vector connecting SAMPLE FRAME to CRYSTAL FRAME
-    rmat_b : array_like, optional
-        (3, 3) COB matrix taking components in the BEAM FRAME to the LAB FRAME;
-        defaults to None, which implies the standard setting of identity.
+    beam_vec : ndarray, optional
+        Unit vector pointing towards the X-ray source in the lab frame.
+        Defaults to [0,0,-1]
+    eta_vec : ndarray, optional
+        Unit vector defining eta=0 in the lab frame.  Defaults to [1,0,0]
     distortion : distortion class, optional
         Default is None
     output_ref : bool, optional
@@ -306,21 +313,14 @@ def xy_to_gvec(
     Returns
     -------
     array_like
-        (n, 2) ndarray containing the (tth, eta) pairs associated with each
+        (n, 2) ndarray containing the (2th, eta) pairs associated with each
         (x, y) associated with gVecs
     array_like
         (n, 3) ndarray containing the associated G vector directions in the
         LAB FRAME
     array_like, optional
         if output_ref is True
     """
-    # TODO: in the C library beam vector and eta vector are expected. However
-    # we receive rmat_b. Please check this!
-    #
-    # It also seems that the output_ref version is not present as the argument
-    # gets ignored
-
-    rmat_b = rmat_b if rmat_b is not None else cnst.identity_3x3
 
     # the code seems to ignore this argument, assume output_ref == True not
     # implemented
@@ -335,8 +335,9 @@ def xy_to_gvec(
     tvec_d = np.ascontiguousarray(tvec_d.flatten())
     tvec_s = np.ascontiguousarray(tvec_s.flatten())
     tvec_c = np.ascontiguousarray(tvec_c.flatten())
-    beam_vec = np.ascontiguousarray((-rmat_b[:, 2]).flatten())
-    eta_vec = np.ascontiguousarray(rmat_b[:, 0].flatten())  # check this!
+    beam_vec = beam_vec if beam_vec is not None else cnst.beam_vec
+    eta_vec = eta_vec if eta_vec is not None else cnst.eta_vec
+
     return _impl.detectorXYToGvec(
         xy_d, rmat_d, rmat_s, tvec_d, tvec_s, tvec_c, beam_vec, eta_vec
     )
@@ -425,27 +426,28 @@ def make_oscill_rot_mat_array(chi, omeArray):
 
 
 @xf_api
-def make_sample_rmat(chi, ome):
+def make_sample_rmat(chi, omega):
     # TODO: Check this docstring
     """
     Make a rotation matrix representing the COB from sample frame to the lab
-    frame.
+    frame, or multiple at the same time.
 
     Parameters
     ----------
     chi : float
         The inclination angle of the sample frame about the lab frame Y.
-    ome : float or ndarray
+    omega : float or ndarray
         The oscillation angle(s) about the sample frame Y.
 
     Returns
     -------
     ndarray
-        A 3x3 rotation matrix representing the input oscillation angles.
+        A 3x3 rotation matrix representing the input oscillation angles if
+        omega is one value, or N 3x3 rotation matrices if omega is a list.
 
     """
-    ome_array = np.atleast_1d(ome)
-    if ome is ome_array:
+    ome_array = np.atleast_1d(omega)
+    if omega is ome_array:
         ome_array = np.ascontiguousarray(ome_array)
         result = _impl.makeOscillRotMat(chi, ome_array)
     else:
@@ -498,7 +500,7 @@ def make_beam_rmat(bvec_l, evec_l):
         vector components in the lab frame.
         the default is [0, 0, -1], which is the standard setting.
     evec_l : ndarray
-        Vector defining eta=0 in the lab frame.  Defaults to [1,0,0]
+        Unit vector defining eta=0 in the lab frame.  Defaults to [1,0,0]
     """
     arg1 = np.ascontiguousarray(bvec_l.flatten())
     arg2 = np.ascontiguousarray(evec_l.flatten())
@@ -508,7 +510,8 @@ def make_beam_rmat(bvec_l, evec_l):
 @xf_api
 def validate_angle_ranges(ang_list, start_angs, stop_angs, ccw=True):
     """
-    Find out if angles are in the CCW or CW range from start to stop
+    Find out if angles are in the CCW or CW range any of the start to stop
+    ranges
 
     Parameters
     ----------
@@ -525,7 +528,7 @@ def validate_angle_ranges(ang_list, start_angs, stop_angs, ccw=True):
     Returns
     -------
     ndarray
-        List of bools indicating if the angles are in the correct range
+        List of bools indicating if the angles are in any of the correct ranges
 
     """
     ang_list = ang_list.astype(np.double, order="C")

hexrd/transforms/xfcapi.py

@@ -4,24 +4,24 @@
 # and hexrdgui. This is so that we can see clearly what is in use.
 from .old_xfcapi import (
     # Old transform functions still in use
-    anglesToDVec,
+    anglesToDVec,  # new version provided below
     anglesToGVec,  # new version provided below
-    detectorXYToGvec,
+    detectorXYToGvec,  # new version provided below
     gvecToDetectorXY,  # new version provided below
     gvecToDetectorXYArray,  # new version provided below
     oscillAnglesOfHKLs,
     # Utility functions
     angularDifference,
-    quat_distance,
+    # quat_distance, # new version provided below
     makeDetectorRotMat,
-    makeEtaFrameRotMat,
-    makeOscillRotMat,  # new version provided below
-    makeOscillRotMatArray,  # new version provided below
-    makeRotMatOfExpMap,
+    makeEtaFrameRotMat,  # new version provided below (make_beam_rmat)
+    makeOscillRotMat,  # new version provided below (make_sample_rmat)
+    makeOscillRotMatArray,  # new version provided below (make_sample_rmat)
+    makeRotMatOfExpMap,  # new version provided below
     makeRotMatOfQuat,
     mapAngle,
     rowNorm,
-    unitRowVector,
+    unitRowVector,  # new version provided below (unit_vector)
     # Constants,
     bVec_ref,
     eta_ref,
@@ -35,5 +35,9 @@
     angles_to_gvec,
     angles_to_dvec,
     gvec_to_xy,  # this is gvecToDetectorXY and gvecToDetectorXYArray
+    xy_to_gvec,
     make_sample_rmat,  # this is makeOscillRotMat and makeOscillRotMatArray
+    make_beam_rmat,
+    unit_vector,
+    quat_distance
 )

tests/transforms/common.py

@@ -0,0 +1,80 @@
+import math
+
+import numpy as np
+
+import hexrd.constants as ct
+from hexrd.transforms.new_capi.xf_new_capi import unit_vector
+
+
+def convert_axis_angle_to_rmat(axis, angle):
+    # Copied from: https://github.com/ovillellas/xrd-transforms/blob/b94f8b2d7839d883829d00a2adc5bec9c80e0116/test_xrd_transforms/common.py#L59  # noqa
+    # This is based on
+    # https://www.euclideanspace.com/maths/geometry/rotations/conversions/angleToMatrix/ # noqa
+
+    angle = float(angle)
+    axis = np.array(axis, dtype=float)
+    assert axis.shape == (3,)
+
+    if abs(angle) < ct.epsf:
+        return ct.identity_3x3
+
+    axis_norm = np.linalg.norm(axis)
+    if axis_norm < ct.epsf:
+        raise ValueError("axis is zero")
+
+    axis /= axis_norm
+
+    m = np.empty((3, 3), dtype=float)
+
+    c = math.cos(angle)
+    s = math.sin(angle)
+    t = 1.0 - c
+
+    m[0, 0] = c + axis[0]*axis[0]*t
+    m[0, 1] = axis[0]*axis[1]*t - axis[2]*s
+    m[0, 2] = axis[0]*axis[2]*t + axis[1]*s
+    m[1, 0] = axis[0]*axis[1]*t + axis[2]*s
+    m[1, 1] = c + axis[1]*axis[1]*t
+    m[1, 2] = axis[1]*axis[2]*t - axis[0]*s
+    m[2, 0] = axis[0]*axis[2]*t - axis[1]*s
+    m[2, 1] = axis[1]*axis[2]*t + axis[0]*s
+    m[2, 2] = c + axis[2]*axis[2]*t
+
+    return m
+
+
+def random_rotation_matrix():
+    # Generate a random unit quaternion
+    q = np.random.rand(4) * 2 - 1
+    q /= np.linalg.norm(q)
+    q0 = q[0]
+    q1 = q[1]
+    q2 = q[2]
+    q3 = q[3]
+
+    # First row of the rotation matrix
+    r00 = 2 * (q0 * q0 + q1 * q1) - 1
+    r01 = 2 * (q1 * q2 - q0 * q3)
+    r02 = 2 * (q1 * q3 + q0 * q2)
+
+    # Second row of the rotation matrix
+    r10 = 2 * (q1 * q2 + q0 * q3)
+    r11 = 2 * (q0 * q0 + q2 * q2) - 1
+    r12 = 2 * (q2 * q3 - q0 * q1)
+
+    # Third row of the rotation matrix
+    r20 = 2 * (q1 * q3 - q0 * q2)
+    r21 = 2 * (q2 * q3 + q0 * q1)
+    r22 = 2 * (q0 * q0 + q3 * q3) - 1
+
+    # 3x3 rotation matrix
+    rot_matrix = np.array([[r00, r01, r02],
+                           [r10, r11, r12],
+                           [r20, r21, r22]])
+    return rot_matrix
+
+
+def random_unit_vectors(shape1=3, shape2=None):
+    if shape2 is None:
+        return unit_vector(np.random.rand(shape1) * 2 - 1)
+    return unit_vector(np.random.rand(shape1, shape2) * 2 - 1)