def set_miscut(self, xyz, angle, add_miscut=False):
"""Calculate U matrix using a miscut axis and an angle"""
if xyz is None:
rot_matrix = xyz_rotation([0, 1, 0], angle)
else:
rot_matrix = self._tobj.transform(xyz_rotation(xyz, angle))
if self.is_ub_calculated() and add_miscut:
new_U = rot_matrix * self._U
else:
new_U = rot_matrix
self.set_U_manually(new_U, False)
self.print_surface()
self.save()
def testSetub(self):
self.ub.newub('testsetub_custom')
self.ub.setlat('NaCl', 1.1)
zrot = xyz_rotation([0, 0, 1], self.t_hand * 30. * TORAD)
self.ub.setu(zrot.tolist())
mneq_(self.ub.ubcalc.UB, self.xrot * self.ub.ubcalc._state.crystal.B)
def setup_method(self):
TestUBCommandsYou.setup_method(self)
inv = matrix([[0, 0, 1], [0, 1, 0], [1, 0, 0]])
self.xrot = xyz_rotation([1, 0, 0], 30. * TORAD)
self.t_matrix = inv * self.xrot
self.t_hand = -1
settings.geometry = SixCircle(beamline_axes_transform=self.t_matrix.I)
def calc_hkl_offset(self, h, k, l, pol, az):
"""
Calculate hkl orientation values that are related to
the input hkl values by rotation with a given polar
and azimuthal angles
"""
hkl_nphi = self._UB * matrix([[h], [k], [l]])
y_axis = cross3(hkl_nphi, matrix('0; 1; 0'))
if norm3(y_axis) < SMALL:
y_axis = cross3(hkl_nphi, matrix('0; 0; 1'))
rot_polar = xyz_rotation(y_axis.T.tolist()[0], pol)
rot_azimuthal = xyz_rotation(hkl_nphi.T.tolist()[0], az)
hklrot_nphi = rot_azimuthal * rot_polar * hkl_nphi
hklrot = self._UB.I * hklrot_nphi
hkl_list = hklrot.T.tolist()[0]
return hkl_list
def testSetub(self):
self.ub.newub('testsetub_custom')
self.ub.setlat('NaCl', 1.1)
zrot = xyz_rotation([0, 0 , 1], 30. * TORAD)
self.ub.setu(zrot.tolist())
mneq_(self.ub.ubcalc.UB, self.conv.transform(self.zrot) * self.ub.ubcalc._state.crystal.B)
def setup_method(self):
settings.ubcalc_persister = UbCalculationNonPersister()
inv = matrix([[0, 0, -1], [0, 1, 0], [1, 0, 0]])
self.zrot = xyz_rotation([0, 0 ,1], 30. * TORAD)
self.t_matrix = inv * self.zrot
self.t_hand = 1
settings.geometry = SixCircle(beamline_axes_transform=self.t_matrix)
settings.ubcalc_strategy = YouUbCalcStrategy()
settings.angles_to_hkl_function = youAnglesToHkl
settings.Pos = YouPositionScenario
_UBCommandsBase.setup_method(self)
def set_miscut(self, xyz, angle, add_miscut=False):
"""Calculate U matrix using a miscut axis and an angle"""
if xyz is None:
rot_matrix = xyz_rotation([0, 1, 0], angle)
if self.is_ub_calculated() and add_miscut:
self._U = rot_matrix * self._U
else:
self._U = rot_matrix
else:
rot_matrix = xyz_rotation(xyz, angle)
try:
rot_matrix = self._ROT * rot_matrix * self._ROT.I
except TypeError:
pass
if self.is_ub_calculated() and add_miscut:
self._U = rot_matrix * self._U
else:
self._U = rot_matrix
self._state.configure_calc_type(manual_U=self._U)
self._UB = self._U * self._state.crystal.B
self.print_reference()
self.save()