def check_angle(self, name, expected, mu=-99, delta=99, nu=99,
eta=99, chi=99, phi=99):
"""All in degrees"""
pos = YouPosition(mu, delta, nu, eta, chi, phi)
pos.changeToRadians()
calculated = self.calc._anglesToVirtualAngles(pos, None)[name] * TODEG
assert_almost_equal(calculated, expected)
def check_angle(self,
name,
expected,
mu=-99,
delta=99,
nu=99,
eta=99,
chi=99,
phi=99):
"""All in degrees"""
pos = YouPosition(mu, delta, nu, eta, chi, phi, unit='DEG')
pos.changeToRadians()
calculated = self.calc._anglesToVirtualAngles(pos, None)[name] * TODEG
assert_almost_equal(calculated, expected)
def decode_reflection(ref_dict, geometry):
h, k, l = eval(ref_dict['hkl'])
time = ref_dict['time'] and gt(ref_dict['time'])
pos_tuple = eval(ref_dict['pos'])
try:
position = geometry.create_position(*pos_tuple)
except AttributeError:
position = YouPosition(*pos_tuple)
return _Reflection(h, k, l, position, ref_dict['energy'], str(ref_dict['tag']), repr(time))
def physical_angles_to_internal_position(self, physical_angle_tuple):
# i16: phi, chi, eta, mu, delta, gam
# H. You: mu, delta, nu, eta, chi, phi
phi_phys, chi_phys, eta_phys, mu_phys, delta_phys, gam_phys = physical_angle_tuple
return YouPosition(mu_phys,
delta_phys,
gam_phys,
eta_phys,
chi_phys,
phi_phys,
unit='DEG')
def edit_orientation(self, idx, h, k, l, x, y, z, position, tag, time):
"""num starts at 1"""
try:
num = self.get_tag_index(idx)
except IndexError:
raise DiffcalcException("There is no orientation " + repr(idx) +
" to edit.")
if type(position) in (list, tuple):
position = YouPosition(*position)
self._orientlist[num] = _Orientation(h, k, l, x, y, z, position, tag,
time.__repr__())
def add_orientation(self, h, k, l, x, y, z, position, tag, time):
"""adds a crystal orientation
"""
if type(position) in (list, tuple):
try:
position = self._geometry.create_position(*position)
except AttributeError:
position = YouPosition(*position)
self._orientlist += [
_Orientation(h, k, l, x, y, z, position, tag, time.__repr__())
]
def add_reflection(self, h, k, l, position, energy, tag, time):
"""adds a reflection, position in degrees
"""
if type(position) in (list, tuple):
try:
position = self._geometry.create_position(*position)
except AttributeError:
position = YouPosition(*position)
self._reflist += [
_Reflection(h, k, l, position, energy, tag, time.__repr__())
]
def _create_position_pseudo_angles_pair(self, wavelength, mu, delta, nu, eta, chi, phi):
# Create position
position = YouPosition(mu, delta, nu, eta, chi, phi)
position = _tidy_degenerate_solutions(position, self.constraints)
if position.phi <= -pi + SMALL:
position.phi += 2 * pi
# pseudo angles calculated along the way were for the initial solution
# and may be invalid for the chosen solution TODO: anglesToHkl need no
# longer check the pseudo_angles as they will be generated with the
# same function and it will prove nothing
pseudo_angles = self._anglesToVirtualAngles(position, wavelength)
return position, pseudo_angles
def _filter_valid_sample_solutions(
self, delta, nu, possible_mu_eta_chi_phi_tuples, wavelength, hkl,
ref_constraint_name, ref_constraint_value):
mu_eta_chi_phi_tuples = []
if logger.isEnabledFor(logging.DEBUG):
msg = 'Checking all sample solutions (found to be within limits)\n'
for mu, eta, chi, phi in possible_mu_eta_chi_phi_tuples:
pos = YouPosition(mu, delta, nu, eta, chi, phi)
hkl_actual = self._anglesToHkl(pos, wavelength)
hkl_okay = sequence_ne(hkl, hkl_actual)
if hkl_okay:
virtual_angles = self._anglesToVirtualAngles(pos, wavelength)
if not ref_constraint_name:
virtual_okay = True;
elif ref_constraint_name == 'a_eq_b':
virtual_okay = ne(virtual_angles['alpha'],
virtual_angles['beta'])
else:
virtual_okay = ne(ref_constraint_value,
virtual_angles[ref_constraint_name])
else:
virtual_okay = False
if hkl_okay and virtual_okay:
mu_eta_chi_phi_tuples.append((mu, eta, chi, phi))
if logger.isEnabledFor(logging.DEBUG):
msg += '*' if virtual_okay else '.'
msg += '*' if hkl_okay else '.'
msg += ('mu=% 7.10f, eta=% 7.10f, chi=% 7.10f, phi=% 7.10f' %
(mu * TODEG, eta * TODEG, chi * TODEG, phi * TODEG))
if hkl_okay:
virtual_angles_in_deg = {}
for k in virtual_angles:
virtual_angles_in_deg[k] = virtual_angles[k] * TODEG
msg += (' --- psi=%(psi) 7.3f, tau=%(tau) 7.3f, '
'naz=%(naz) 7.3f, qaz=%(qaz) 7.3f, alpha=%(alpha) '
'7.3f, beta=%(beta) 7.3f' % virtual_angles_in_deg)
msg += 'hkl= ' + str(hkl_actual)
msg += '\n'
if logger.isEnabledFor(logging.DEBUG):
logger.debug(msg)
return mu_eta_chi_phi_tuples
def physical_angles_to_internal_position(self, physical_angle_tuple):
# mu, delta, nu, eta, chi, phi
delta_phys, gam_phys, eta_phys, chi_phys, phi_phys = physical_angle_tuple
return YouPosition(0, delta_phys, gam_phys, -eta_phys, -chi_phys,
-phi_phys, 'DEG')
def physical_angles_to_internal_position(self, physical_angle_tuple):
delta_phys, gam_phys, eta_phys, phi_phys = physical_angle_tuple
return YouPosition(0, delta_phys, gam_phys, eta_phys, -90, phi_phys,
'DEG')
def posFromI16sEuler(phi, chi, eta, mu, delta, gamma):
return YouPosition(mu, delta, gamma, eta, chi, phi, unit='DEG')
def test_psi5(self):
#self.check_angle('psi', 0, mu=10, delta=.00000001,
#nu=0, eta=0, chi=90, phi=0)
pos = YouPosition(0, .00000001, 0, 0, 90, 0)
pos.changeToRadians()
assert isnan(self.calc._anglesToVirtualAngles(pos, None)['psi'])
def test_psi5(self):
#self.check_angle('psi', 0, mu=10, delta=.00000001,
#nu=0, eta=0, chi=90, phi=0)
pos = YouPosition(0, 0, 0, 0, 90, 0, 'DEG')
pos.changeToRadians()
assert isnan(self.calc._anglesToVirtualAngles(pos, None)['psi'])
def test_psi0(self):
pos = YouPosition(0, 0, 0, 0, 0, 0, 'DEG')
assert isnan(self.calc._anglesToVirtualAngles(pos, None)['psi'])
def physical_angles_to_internal_position(self, physical_angle_tuple):
# i16: phi, chi, eta, mu, delta, gam
# H. You: mu, delta, nu, eta, chi, phi
phi, chi, eta, mu, delta, gam = physical_angle_tuple
return YouPosition(mu, delta, gam, eta, chi, phi)