Add Transforms Testcases and fix some stuff (#696)

* Add transforms testcases

* Transforms updates and testcases

* Replace all old usages of xfcapi to the new versions

Author: kevindlewis23

hexrd/cli/find_orientations.py

@@ -85,7 +85,7 @@ def write_results(results, cfg):
     )
     for gid, q in enumerate(results['qbar'].T):
         phi = 2*np.arccos(q[0])
-        n = xfcapi.unitRowVector(q[1:])
+        n = xfcapi.unit_vector(q[1:])
         grain_params = np.hstack([phi*n, const.zeros_3, const.identity_6x1])
         gw.dump_grain(gid, 1., 0., grain_params)
     gw.close()

hexrd/cli/fit_grains.py

@@ -77,7 +77,7 @@ def rotation_matrices(self):
             n = len(self.expmap)
             rmats = np.zeros((n, 3, 3))
             for i in range(n):
-                rmats[i] = xfcapi.makeRotMatOfExpMap(self.expmap[i])
+                rmats[i] = xfcapi.make_rmat_of_expmap(self.expmap[i])
             self._rotation_matrices = rmats
         return self._rotation_matrices
 
@@ -307,7 +307,7 @@ def execute(args, parser):
                 gw = instrument.GrainDataWriter(grains_filename)
                 for i_g, q in enumerate(qbar.T):
                     phi = 2*np.arccos(q[0])
-                    n = xfcapi.unitRowVector(q[1:])
+                    n = xfcapi.unit_vector(q[1:])
                     grain_params = np.hstack(
                         [phi*n, cnst.zeros_3, cnst.identity_6x1]
                     )

hexrd/fitgrains.py

@@ -14,6 +14,7 @@
 
 from hexrd import instrument
 from hexrd.transforms import xfcapi
+from hexrd import rotations
 from hexrd.fitting import fitGrain, objFuncFitGrain, gFlag_ref
 
 logger = logging.getLogger(__name__)
@@ -258,7 +259,7 @@ def fit_grain_FF_reduced(grain_id):
             x_diff = abs(xyo_det[:, 0] - xyo_det_fit['calc_xy'][:, 0])
             y_diff = abs(xyo_det[:, 1] - xyo_det_fit['calc_xy'][:, 1])
             ome_diff = np.degrees(
-                xfcapi.angularDifference(xyo_det[:, 2],
+                rotations.angularDifference(xyo_det[:, 2],
                                          xyo_det_fit['calc_omes'])
                 )
 

hexrd/fitting/calibration/laue.py

@@ -69,7 +69,7 @@ def grain_params_euler(self):
 
         grain_params = self.grain_params.copy()
         rme = RotMatEuler(np.zeros(3), **self.euler_convention)
-        rme.rmat = xfcapi.makeRotMatOfExpMap(grain_params[:3])
+        rme.rmat = xfcapi.make_rmat_of_expmap(grain_params[:3])
         grain_params[:3] = np.degrees(rme.angles)
         return grain_params
 
@@ -171,7 +171,7 @@ def autopick_points(self, raw_img_dict, tth_tol=5., eta_tol=5.,
         rmat_s = np.eye(3)  # !!! forcing to identity
         omega = 0.  # !!! same ^^^
 
-        rmat_c = xfcapi.makeRotMatOfExpMap(self.grain_params[:3])
+        rmat_c = xfcapi.make_rmat_of_expmap(self.grain_params[:3])
         tvec_c = self.grain_params[3:6]
         # vinv_s = self.grain_params[6:12]  # !!!: patches don't take this yet
 
@@ -358,16 +358,16 @@ def autopick_points(self, raw_img_dict, tth_tol=5., eta_tol=5.,
                     # need xy coords
                     # !!! forcing ome = 0. -- could be inconsistent with rmat_s
                     cmv = np.atleast_2d(np.hstack([com_angs, omega]))
-                    gvec_c = xfcapi.anglesToGVec(
+                    gvec_c = xfcapi.angles_to_gvec(
                         cmv,
                         chi=self.instr.chi,
-                        rMat_c=rmat_c,
-                        bHat_l=self.instr.beam_vector)
-                    new_xy = xfcapi.gvecToDetectorXY(
+                        rmat_c=rmat_c,
+                        beam_vec=self.instr.beam_vector)
+                    new_xy = xfcapi.gvec_to_xy(
                         gvec_c,
                         det.rmat, rmat_s, rmat_c,
                         det.tvec, self.instr.tvec, tvec_c,
-                        beamVec=self.instr.beam_vector)
+                        beam_vec=self.instr.beam_vector)
                     meas_xy[iRefl, :] = new_xy
                     if det.distortion is not None:
                         meas_xy[iRefl, :] = det.distortion.apply_inverse(

hexrd/fitting/calibration/multigrain.py

@@ -6,6 +6,7 @@
 
 from hexrd import constants as cnst
 from hexrd import matrixutil as mutil
+from hexrd import rotations
 from hexrd.transforms import xfcapi
 
 from .. import grains as grainutil
@@ -49,7 +50,7 @@ def calibrate_instrument_from_sx(
     if ome_period is not None:
         for det_key in instr.detectors:
             for ig in range(ngrains):
-                xyo_det[det_key][ig][:, 2] = xfcapi.mapAngle(
+                xyo_det[det_key][ig][:, 2] = rotations.mapAngle(
                         xyo_det[det_key][ig][:, 2],
                         ome_period
                 )
@@ -257,7 +258,7 @@ def sxcal_obj_func(plist_fit, plist_full,
             # 3) apply stretch tensor
             # 4) normalize reciprocal lattice vectors in SAMPLE frame
             # 5) transform unit reciprocal lattice vetors back to CRYSAL frame
-            rmat_c = xfcapi.makeRotMatOfExpMap(grain[:3])
+            rmat_c = xfcapi.make_rmat_of_expmap(grain[:3])
             tvec_c = grain[3:6]
             vinv_s = grain[6:]
             gvec_c = np.dot(bmat, ghkls.T)
@@ -314,7 +315,7 @@ def sxcal_obj_func(plist_fit, plist_full,
         calc_omes_all = np.hstack(calc_omes_all)
 
         diff_vecs_xy = calc_xy_all - meas_xy_all
-        diff_ome = xfcapi.angularDifference(calc_omes_all, meas_omes_all)
+        diff_ome = rotations.angularDifference(calc_omes_all, meas_omes_all)
         retval = np.hstack(
             [diff_vecs_xy,
              diff_ome.reshape(npts_tot, 1)]
@@ -359,8 +360,8 @@ def parse_reflection_tables(cfg, instr, grain_ids, refit_idx=None):
             valid_reflections = gtable[:, 0] >= 0  # is indexed
             not_saturated = gtable[:, 6] < panel.saturation_level
             # throw away extremem etas
-            p90 = xfcapi.angularDifference(gtable[:, 8], cnst.piby2)
-            m90 = xfcapi.angularDifference(gtable[:, 8], -cnst.piby2)
+            p90 = rotations.angularDifference(gtable[:, 8], cnst.piby2)
+            m90 = rotations.angularDifference(gtable[:, 8], -cnst.piby2)
             accept_etas = np.logical_or(p90 > ext_eta_tol,
                                         m90 > ext_eta_tol)
             logger.info(f"panel '{det_key}', grain {grain_id}")

hexrd/fitting/grains.py

@@ -7,6 +7,8 @@
 from hexrd import matrixutil as mutil
 
 from hexrd.transforms import xfcapi
+from hexrd import constants
+from hexrd import rotations
 
 from hexrd.xrdutil import extract_detector_transformation
 
@@ -15,8 +17,8 @@
 epsf = np.finfo(float).eps  # ~2.2e-16
 sqrt_epsf = np.sqrt(epsf)  # ~1.5e-8
 
-bVec_ref = xfcapi.bVec_ref
-eta_ref = xfcapi.eta_ref
+bVec_ref = constants.beam_vec
+eta_ref = constants.eta_vec
 vInv_ref = np.r_[1., 1., 1., 0., 0., 0.]
 
 
@@ -71,7 +73,7 @@ def fitGrain(gFull, instrument, reflections_dict,
     """
     # FIXME: will currently fail if omePeriod is specifed
     if omePeriod is not None:
-        # xyo_det[:, 2] = xfcapi.mapAngle(xyo_det[:, 2], omePeriod)
+        # xyo_det[:, 2] = rotations.mapAngle(xyo_det[:, 2], omePeriod)
         raise RuntimeError
 
     gFit = gFull[gFlag]
@@ -162,7 +164,7 @@ def objFuncFitGrain(gFit, gFull, gFlag,
     gFull[gFlag] = gFit
 
     # map parameters to functional arrays
-    rMat_c = xfcapi.makeRotMatOfExpMap(gFull[:3])
+    rMat_c = xfcapi.make_rmat_of_expmap(gFull[:3])
     tVec_c = gFull[3:6].reshape(3, 1)
     vInv_s = gFull[6:]
     vMat_s = mutil.vecMVToSymm(vInv_s)  # NOTE: Inverse of V from F = V * R
@@ -281,7 +283,9 @@ def objFuncFitGrain(gFit, gFull, gFlag,
         # return residual vector
         # IDEA: try angles instead of xys?
         diff_vecs_xy = calc_xy_all - meas_xyo_all[:, :2]
-        diff_ome = xfcapi.angularDifference(calc_omes_all, meas_xyo_all[:, 2])
+        diff_ome = rotations.angularDifference(
+            calc_omes_all, meas_xyo_all[:, 2]
+        )
         retval = np.hstack([diff_vecs_xy,
                             diff_ome.reshape(npts, 1)
                             ]).flatten()
@@ -309,15 +313,15 @@ def matchOmegas(xyo_det, hkls_idx, chi, rMat_c, bMat, wavelength,
     """
     # get omegas for rMat_s calculation
     if omePeriod is not None:
-        meas_omes = xfcapi.mapAngle(xyo_det[:, 2], omePeriod)
+        meas_omes = rotations.mapAngle(xyo_det[:, 2], omePeriod)
     else:
         meas_omes = xyo_det[:, 2]
 
-    oangs0, oangs1 = xfcapi.oscillAnglesOfHKLs(
+    oangs0, oangs1 = xfcapi.oscill_angles_of_hkls(
             hkls_idx.T, chi, rMat_c, bMat, wavelength,
-            vInv=vInv,
-            beamVec=beamVec,
-            etaVec=etaVec)
+            v_inv=vInv,
+            beam_vec=beamVec,
+            eta_vec=etaVec)
     if np.any(np.isnan(oangs0)):
         # debugging
         # TODO: remove this
@@ -333,10 +337,12 @@ def matchOmegas(xyo_det, hkls_idx, chi, rMat_c, bMat, wavelength,
         # CAPI version gives vstacked angles... must be (2, nhkls)
         calc_omes = np.vstack([oangs0[:, 2], oangs1[:, 2]])
     if omePeriod is not None:
-        calc_omes = np.vstack([xfcapi.mapAngle(oangs0[:, 2], omePeriod),
-                               xfcapi.mapAngle(oangs1[:, 2], omePeriod)])
+        calc_omes = np.vstack([rotations.mapAngle(oangs0[:, 2], omePeriod),
+                               rotations.mapAngle(oangs1[:, 2], omePeriod)])
     # do angular difference
-    diff_omes = xfcapi.angularDifference(np.tile(meas_omes, (2, 1)), calc_omes)
+    diff_omes = rotations.angularDifference(
+        np.tile(meas_omes, (2, 1)), calc_omes
+    )
     match_omes = np.argsort(diff_omes, axis=0) == 0
     calc_omes = calc_omes.T.flatten()[match_omes.T.flatten()]