def calc_offset_for_hkl(self, hkl_offset, hkl_ref):
"""
Calculate polar and azimuthal angles and scaling factor
relating offset and reference hkl values
"""
d_ref = self._state.crystal.get_hkl_plane_distance(hkl_ref)
hklref_nphi = self._UB * matrix([[hkl_ref[0]], [hkl_ref[1]],
[hkl_ref[2]]])
d_offset = self._state.crystal.get_hkl_plane_distance(hkl_offset)
hkloff_nphi = self._UB * matrix([[hkl_offset[0]], [hkl_offset[1]],
[hkl_offset[2]]])
sc = d_ref / d_offset
par_ref_off = cross3(hklref_nphi, hkloff_nphi)
if norm3(par_ref_off) < SMALL:
return 0, float('nan'), sc
y_axis = cross3(hklref_nphi, matrix('0; 1; 0'))
if norm3(y_axis) < SMALL:
y_axis = cross3(hklref_nphi, matrix('0; 0; 1'))
x_axis = cross3(y_axis, hklref_nphi)
x_coord = cos(angle_between_vectors(hkloff_nphi, x_axis))
y_coord = cos(angle_between_vectors(hkloff_nphi, y_axis))
pol = angle_between_vectors(hklref_nphi, hkloff_nphi)
if abs(y_coord) < SMALL and abs(x_coord) < SMALL:
# Set azimuthal rotation matrix to identity
az = 0
else:
az = atan2(y_coord, x_coord)
return pol, az, sc
def get_hkl_plane_angle(self, hkl1, hkl2):
'''Calculates and returns the angle between [hkl1] and [hkl2] planes'''
hkl1 = matrix([hkl1]).T
hkl2 = matrix([hkl2]).T
nphi1 = self._bMatrix * hkl1
nphi2 = self._bMatrix * hkl2
angle = angle_between_vectors(nphi1, nphi2)
return angle
def _calc_N(Q, n):
"""Return N as described by Equation 31"""
Q = normalised(Q)
n = normalised(n)
if is_small(angle_between_vectors(Q, n)):
raise ValueError('Q and n are parallel and cannot be used to create '
'an orthonormal matrix')
Qxn = cross3(Q, n)
QxnxQ = cross3(Qxn, Q)
QxnxQ = normalised(QxnxQ)
Qxn = normalised(Qxn)
return matrix([[Q[0, 0], QxnxQ[0, 0], Qxn[0, 0]],
[Q[1, 0], QxnxQ[1, 0], Qxn[1, 0]],
[Q[2, 0], QxnxQ[2, 0], Qxn[2, 0]]])
def _calc_N(Q, n):
"""Return N as described by Equation 31"""
Q = normalised(Q)
n = normalised(n)
if is_small(angle_between_vectors(Q, n)):
raise ValueError('Q and n are parallel and cannot be used to create '
'an orthonormal matrix')
Qxn = cross3(Q, n)
QxnxQ = cross3(Qxn, Q)
QxnxQ = normalised(QxnxQ)
Qxn = normalised(Qxn)
return matrix([[Q[0, 0], QxnxQ[0, 0], Qxn[0, 0]],
[Q[1, 0], QxnxQ[1, 0], Qxn[1, 0]],
[Q[2, 0], QxnxQ[2, 0], Qxn[2, 0]]])
def _func_orient(vals, crystal, ref_data):
quat = _get_quat_from_u123(*vals)
trial_u = _get_rot_matrix(*quat)
tmp_ub = trial_u * crystal.B
res = 0
I = matrix('1 0 0; 0 1 0; 0 0 1')
for (hkl_vals, pos_vals, en) in ref_data:
wl = 12.3984 / en
[MU, DELTA, NU, ETA, CHI,
PHI] = create_you_matrices(*pos_vals.totuple())
q_del = (NU * DELTA - I) * matrix([[0], [2 * pi / wl], [0]])
q_vals = PHI.I * CHI.I * ETA.I * MU.I * q_del
q_hkl = tmp_ub * hkl_vals
res += angle_between_vectors(q_hkl, q_vals)
return res
def _hklToAngles(self, h, k, l, wavelength, return_all_solutions=False):
"""(pos, virtualAngles) = hklToAngles(h, k, l, wavelength) --- with
Position object pos and the virtual angles returned in degrees. Some
modes may not calculate all virtual angles.
"""
if not self.constraints.is_fully_constrained():
raise DiffcalcException(
"Diffcalc is not fully constrained.\n"
"Type 'help con' for instructions")
if not self.constraints.is_current_mode_implemented():
raise DiffcalcException(
"Sorry, the selected constraint combination is valid but "
"is not implemented. Type 'help con' for implemented combinations")
# constraints are dictionaries
ref_constraint = self.constraints.reference
if ref_constraint:
ref_constraint_name, ref_constraint_value = ref_constraint.items()[0]
det_constraint = self.constraints.detector
naz_constraint = self.constraints.naz
samp_constraints = self.constraints.sample
assert not (det_constraint and naz_constraint), (
"Two 'detector' constraints given")
h_phi = self._get_ubmatrix() * matrix([[h], [k], [l]])
theta = self._calc_theta(h_phi, wavelength)
tau = angle_between_vectors(h_phi, self._get_n_phi())
### Reference constraint column ###
if ref_constraint:
# An angle for the reference vector (n) is given (Section 5.2)
psi, alpha, _ = self._calc_remaining_reference_angles(
ref_constraint_name, ref_constraint_value, theta, tau)
### Detector constraint column ###
if det_constraint or naz_constraint:
qaz, naz, delta, nu = self._calc_det_angles_given_det_or_naz_constraint(
det_constraint, naz_constraint, theta, tau, alpha)
### Sample constraint column ###
if len(samp_constraints) == 1:
# a detector and reference constraint will have been given
mu, eta, chi, phi = self._calc_sample_angles_from_one_sample_constraint(
h, k, l, wavelength, samp_constraints, h_phi, theta,
ref_constraint_name, ref_constraint_value, alpha, qaz, naz,
delta, nu)
solution_tuples = [(mu, delta, nu, eta, chi, phi)]
elif len(samp_constraints) == 2:
assert ref_constraint, ('No code yet to handle 2 sample '
'without a reference constraint!')
angles = self._calc_sample_given_two_sample_and_reference(
h, k, l, wavelength, samp_constraints, h_phi, theta,
ref_constraint_name, ref_constraint_value, psi)
solution_tuples = [angles]
elif len(samp_constraints) == 3:
solution_tuples = self._calc_angles_given_three_sample_constraints(
h, k, l, wavelength, return_all_solutions, samp_constraints,
h_phi, theta)
position_pseudo_angles_pairs = []
for mu, delta, nu, eta, chi, phi in solution_tuples:
pair = self._create_position_pseudo_angles_pair(
wavelength, mu, delta, nu, eta, chi, phi)
position_pseudo_angles_pairs.append(pair)
return position_pseudo_angles_pairs
def _hklToAngles(self, h, k, l, wavelength, return_all_solutions=False):
"""(pos, virtualAngles) = hklToAngles(h, k, l, wavelength) --- with
Position object pos and the virtual angles returned in degrees. Some
modes may not calculate all virtual angles.
"""
if not self.constraints.is_fully_constrained():
raise DiffcalcException(
"Diffcalc is not fully constrained.\n"
"Type 'help con' for instructions")
if not self.constraints.is_current_mode_implemented():
raise DiffcalcException(
"Sorry, the selected constraint combination is valid but "
"is not implemented. Type 'help con' for implemented combinations")
# constraints are dictionaries
ref_constraint = self.constraints.reference
if ref_constraint:
ref_constraint_name, ref_constraint_value = ref_constraint.items()[0]
det_constraint = self.constraints.detector
naz_constraint = self.constraints.naz
samp_constraints = self.constraints.sample
assert not (det_constraint and naz_constraint), (
"Two 'detector' constraints given")
h_phi = self._get_ubmatrix() * matrix([[h], [k], [l]])
theta = self._calc_theta(h_phi, wavelength)
tau = angle_between_vectors(h_phi, self._get_n_phi())
### Reference constraint column ###
if ref_constraint:
# An angle for the reference vector (n) is given (Section 5.2)
psi, alpha, _ = self._calc_remaining_reference_angles(
ref_constraint_name, ref_constraint_value, theta, tau)
# IMPORTNANT: other psi solutions are possibly valid.
# TODO: ensure this is handled consistently in all paths below
# currently only handled in
# self._calc_sample_given_two_sample_and_reference(...)
### Detector constraint column ###
if det_constraint or naz_constraint:
qaz, naz, delta, nu = self._calc_det_angles_given_det_or_naz_constraint(
det_constraint, naz_constraint, theta, tau, alpha)
### Sample constraint column ###
if len(samp_constraints) == 1:
# a detector and reference constraint will have been given
mu, eta, chi, phi = self._calc_sample_angles_from_one_sample_constraint(
h, k, l, wavelength, samp_constraints, h_phi, theta,
ref_constraint_name, ref_constraint_value, alpha, qaz, naz,
delta, nu)
solution_tuples = [(mu, delta, nu, eta, chi, phi)]
elif len(samp_constraints) == 2:
assert ref_constraint, ('No code yet to handle 2 sample '
'without a reference constraint!')
angles = self._calc_sample_given_two_sample_and_reference(
h, k, l, wavelength, samp_constraints, h_phi, theta,
ref_constraint_name, ref_constraint_value, psi)
solution_tuples = [angles]
elif len(samp_constraints) == 3:
solution_tuples = self._calc_angles_given_three_sample_constraints(
h, k, l, wavelength, return_all_solutions, samp_constraints,
h_phi, theta)
position_pseudo_angles_pairs = []
for mu, delta, nu, eta, chi, phi in solution_tuples:
pair = self._create_position_pseudo_angles_pair(
wavelength, mu, delta, nu, eta, chi, phi)
position_pseudo_angles_pairs.append(pair)
return position_pseudo_angles_pairs