def test_qangle_NoGC_NoOC_right(self):
# No geometry constraints, no omega constraints, all parameters are arrays,
# except for sign=-1
test_case5 = array([[10, 0, 1, 0, 0, 0.72, 0, 0.12, -19, 0, 80.5, 0, 80.5, 0],
[10, 0, 0, 1, 0, 0.72, 0, 0.12, -19, 0, 80.5, 0, 20.5, 0],
[10, 0, -1, 0, 0, 0.72, 0, 0.12, -19, 0, 80.5, 0, -99.5, 0],
[10, 0, 0, -1, 0, 0.72, 0, 0.12, -19, 0, 80.5, 0, -159.5, 0],
[10, 0, 1, 1, 0, 1.2, 0, 0.36, -33.2, 0, 73.4, 0, 43.4, 0],
[10, 0, 0.2, 0, 0, 0.14, 0, 0, -3.8, 0, 88.1, 0, 88.1, 0],
[10, 0, 0.02, 0, 0, 0.015, 0, 5e-05, -0.4, 0, 89.8, 0, 89.8, 0],
[10, 5, 1, 0, 0, 0.28, 0, 0.67, -10.4, 0, 22.8, 0, 22.8, 0],
[10, -5, 1, 0, 0, 0.59, 0, -0.43, -12.6, 0, 126.3, 0, 126.3, 0],
[10, 0, 5, 0, 0, 2.05, 0, 3, -111.3, 0, 34.4, 0, 34.3, 0]])
a=10
b=10
c=10
alpha=90
beta=90
gamma=120
u=[1,0,0]
v=[0,1,0]
ol=OrientedLattice(a, b, c, alpha, beta, gamma)
ol.setUFromVectors(u,v)
sign=-1
(Ei, DE, H, K, L, expected_Qx, expected_Qy, expected_Qz, expected_in_plane_kf_angle,
expected_out_plane_kf_angle, expected_in_plane_Q_angle, expected_out_plane_Q_angle,
expected_omega, expected_error_code) = test_case5.T
HKL = vstack([H,K,L]).T
pars = {'Ei': Ei, 'hkl': HKL, 'DeltaE': DE, 'sign': sign}
expected_error_code = [ErrorCodes(ec) for ec in expected_error_code]
self.run_test(ol, expected_Qx, expected_Qy, expected_Qz, expected_in_plane_Q_angle, expected_out_plane_Q_angle,
expected_in_plane_kf_angle, expected_out_plane_kf_angle, expected_omega, expected_error_code, **pars)
def qe_para(self):
self.orien = OrientedLattice(*Alignment.para)
self.para = Alignment.para
self.hkl = [self.point.h, self.point.k, self.point.l]
self.len = self.orien.qFromHKL(self.hkl).norm()
self.mono = Monochromator(en=self.point.ei)
self.ana = Monochromator(en=self.point.ef)
def test_qFromHKL(self):
ol = OrientedLattice(1,1,1)
hkl = V3D(1,1,1)
qVec = ol.qFromHKL(hkl)
self.assertAlmostEqual(hkl.X() * 2 * np.pi, qVec.X(), 9)
self.assertAlmostEqual(hkl.Y() * 2 * np.pi, qVec.Y(), 9)
self.assertAlmostEqual(hkl.Z() * 2 * np.pi, qVec.Z(), 9)
def test_hklFromQ(self):
ol = OrientedLattice(1, 1, 1)
qVec = V3D(1, 1, 1)
hkl = ol.hklFromQ(qVec)
self.assertAlmostEqual(hkl.X() * 2 * np.pi, qVec.X(), 9)
self.assertAlmostEqual(hkl.Y() * 2 * np.pi, qVec.Y(), 9)
self.assertAlmostEqual(hkl.Z() * 2 * np.pi, qVec.Z(), 9)
def test_qFromHKL(self):
ol = OrientedLattice(1, 1, 1)
hkl = V3D(1, 1, 1)
qVec = ol.qFromHKL(hkl)
self.assertAlmostEqual(hkl.X() * 2 * np.pi, qVec.X(), 9)
self.assertAlmostEqual(hkl.Y() * 2 * np.pi, qVec.Y(), 9)
self.assertAlmostEqual(hkl.Z() * 2 * np.pi, qVec.Z(), 9)
def test_hklFromQ(self):
ol = OrientedLattice(1,1,1)
qVec = V3D(1,1,1)
hkl = ol.hklFromQ(qVec)
self.assertAlmostEqual(hkl.X() * 2 * np.pi, qVec.X(), 9)
self.assertAlmostEqual(hkl.Y() * 2 * np.pi, qVec.Y(), 9)
self.assertAlmostEqual(hkl.Z() * 2 * np.pi, qVec.Z(), 9)
def test_create_nonorthogonal_transform_with_nonorthogonal_lattice_and_nonorthogonal_projections(
self):
lattice = OrientedLattice(1, 1, 2, 90, 90, 120.)
x_proj, y_proj = (1, 0, 0), (1, 1, 0)
transform = NonOrthogonalTransform.from_lattice(
lattice, x_proj, y_proj)
self.assertAlmostEqual(transform.angle,
np.radians(lattice.recAngle(*x_proj, *y_proj)))
def test_hklFromQ_input_types(self):
'''
Test that you can provide input q values as different python types.
'''
ol = OrientedLattice(1,1,1)
self.assertTrue(isinstance( ol.hklFromQ(V3D(1,1,1)), V3D), "Should work with V3D input")
self.assertTrue(isinstance( ol.hklFromQ([1,1,1]), V3D), "Should work with python array input" )
self.assertTrue(isinstance( ol.hklFromQ(np.array([1,1,1])), V3D), "Should work with numpy array input" )
def test_simple_values(self):
u1 = OrientedLattice()
self.assertEquals(u1.a1(),1)
self.assertEquals(u1.alpha(),90)
u2 = OrientedLattice(3,4,5)
self.assertAlmostEqual(u2.b1(),1./3.,10)
self.assertAlmostEqual(u2.alphastar(),90,10)
u3 = u2;
self.assertAlmostEqual(u3.volume(),1./u2.recVolume(),10)
u2.seta(3);
self.assertAlmostEqual(u2.a(),3,10)
def test_qangle_NoGC_NoOC(self):
# No geometry constraints, no omega constraints, all parameters are arrays
test_case1 = array([[10, 0, 1, 0, 0, 1, -0.72, 0, 0.12, 19, 0, -80.5, 0, -80.5, 0],
[10, 0, 0, 1, 0, 1, -0.72, 0, 0.12, 19, 0, -80.5, 0, -140.5, 0],
[10, 0, -1, 0, 0, 1, -0.72, 0, 0.12, 19, 0, -80.5, 0, 99.5, 0],
[10, 0, 0, -1, 0, 1, -0.72, 0, 0.12, 19, 0, -80.5, 0, 39.5, 0],
[10, 0, 1, 1, 0, 1, -1.2, 0, 0.36, 33.2, 0, -73.4, 0, -103.4, 0],
[10, 0, 0.2, 0, 0, 1, -0.14, 0, 0, 3.8, 0, -88.1, 0, -88.1, 0],
[10, 0, 0.02, 0, 0, 1, -0.015, 0, 5e-05, 0.4, 0, -89.8, 0, -89.8, 0],
[10, 5, 1, 0, 0, 1, -0.28, 0, 0.67, 10.4, 0, -22.8, 0, -22.7, 0],
[10, -5, 1, 0, 0, 1, -0.59, 0, -0.43, 12.6, 0, -126.3, 0, -126.3, 0],
[10, 0, 5, 0, 0, 1, -2.05, 0, 3, 111.3, 0, -34.4, 0, -34.3, 0],
[10, 0, 1, -0.01, -0.18, 1, -0.71, -0.11, 0.12, 19, 3, -80.3, -9, -79.7, 0],
[10, 0, 1, 0, -0.6, 1, -0.72, -0.38, 0.15, 19.13, 10, -77.8, -27.5, -77.9, 0],
[10, 0, 1, 0, 0, -1, 0.72, 0, 0.12, -19, 0, 80.5, 0, 80.5, 0],
[10, 0, 0, 1, 0, -1, 0.72, 0, 0.12, -19, 0, 80.5, 0, 20.5, 0],
[10, 0, -1, 0, 0, -1, 0.72, 0, 0.12, -19, 0, 80.5, 0, -99.5, 0],
[10, 0, 0, -1, 0, -1, 0.72, 0, 0.12, -19, 0, 80.5, 0, -159.5, 0],
[10, 0, 1, 1, 0, -1, 1.2, 0, 0.36, -33.2, 0, 73.4, 0, 43.4, 0],
[10, 0, 0.2, 0, 0, -1, 0.14, 0, 0, -3.8, 0, 88.1, 0, 88.1, 0],
[10, 0, 0.02, 0, 0, -1, 0.015, 0, 5e-05, -0.4, 0, 89.8, 0, 89.8, 0],
[10, 5, 1, 0, 0, -1, 0.28, 0, 0.67, -10.4, 0, 22.8, 0, 22.8, 0],
[10, -5, 1, 0, 0, -1, 0.59, 0, -0.43, -12.6, 0, 126.3, 0, 126.3, 0],
[10, 0, 5, 0, 0, -1, 2.05, 0, 3, -111.3, 0, 34.4, 0, 34.3, 0],
[20, 0, 1, 0, 0, 1, -0.72, 0, 0.08, 13.4, 0, -83.3, 0, -83.3, 0],
[10, 0, 8, 0, 0, 1, nan, nan, nan, nan, nan, nan, nan, nan, 2],
[10, 20, 1, 0, 0, 1, nan, nan, nan, nan, nan, nan, nan, nan, 2],
[-10, 0, 1, 0, 0, 1, nan, nan, nan, nan, nan, nan, nan, nan, 1],
[10, 0, 1, 0, nan, 1, nan, nan, nan, nan, nan, nan, nan, nan, 1],
[10, 0, -1.3, 3.4, -3.5, -1, nan, nan, nan, nan, nan, nan, nan, nan, 3],
[10, 0, -1.3, 3.4, 3.5, -1, nan, nan, nan, nan, nan, nan, nan, nan, 3]])
a=10
b=10
c=10
alpha=90
beta=90
gamma=120
u=[1,0,0]
v=[0,1,0]
ol=OrientedLattice(a, b, c, alpha, beta, gamma)
ol.setUFromVectors(u,v)
(Ei, DE, H, K, L, sign, expected_Qx, expected_Qy, expected_Qz, expected_in_plane_kf_angle,
expected_out_plane_kf_angle, expected_in_plane_Q_angle, expected_out_plane_Q_angle,
expected_omega, expected_error_code) = test_case1.T
HKL = vstack([H,K,L]).T
pars = {'Ei': Ei, 'hkl': HKL, 'DeltaE': DE, 'sign': sign}
expected_error_code = [ErrorCodes(ec) for ec in expected_error_code]
self.run_test(ol, expected_Qx, expected_Qy, expected_Qz, expected_in_plane_Q_angle, expected_out_plane_Q_angle,
expected_in_plane_kf_angle, expected_out_plane_kf_angle, expected_omega, expected_error_code, **pars)
def test_hklFromQ_input_types(self):
'''
Test that you can provide input q values as different python types.
'''
ol = OrientedLattice(1, 1, 1)
self.assertTrue(isinstance(ol.hklFromQ(V3D(1, 1, 1)), V3D),
"Should work with V3D input")
self.assertTrue(isinstance(ol.hklFromQ([1, 1, 1]), V3D),
"Should work with python array input")
self.assertTrue(isinstance(ol.hklFromQ(np.array([1, 1, 1])), V3D),
"Should work with numpy array input")
def test_qangle_GC_OC(self):
# Geometry constraints, no omega constraints, all parameters are arrays
test_case8 = array([[10, 0, 1, 0, 0, 1, nan, nan, nan, nan, nan, nan, nan, nan, 6],
[10, 0, 0, 1, 0, 1, nan, nan, nan, nan, nan, nan, nan, nan, 6],
[10, 0, -1, 0, 0, 1, nan, nan, nan, nan, nan, nan, nan, nan, 6],
[10, 0, 0, -1, 0, 1, -0.72, 0, 0.12, 19, 0, -80.5, 0, 39.5, 0],
[10, 0, 1, 1, 0, 1, nan, nan, nan, nan, nan, nan, nan, nan, 6],
[10, 0, 0.2, 0, 0, 1, nan, nan, nan, nan, nan, nan, nan, nan, 4],
[10, 0, 0.02, 0, 0, 1, nan, nan, nan, nan, nan, nan, nan, nan, 4],
[10, 5, 1, 0, 0, 1, nan, nan, nan, nan, nan, nan, nan, nan, 6],
[10, -5, 1, 0, 0, 1, nan, nan, nan, nan, nan, nan, nan, nan, 6],
[10, 0, 5, 0, 0, 1, nan, nan, nan, nan, nan, nan, nan, nan, 4],
[10, 0, 1, -0.01, -0.18, 1, nan, nan, nan, nan, nan, nan, nan, nan, 6],
[10, 0, 1, 0, -0.6, 1, nan, nan, nan, nan, nan, nan, nan, nan, 4],
[10, 0, 1, 0, 0, -1, nan, nan, nan, nan, nan, nan, nan, nan, 4],
[10, 0, 0, 1, 0, -1, nan, nan, nan, nan, nan, nan, nan, nan, 4],
[10, 0, -1, 0, 0, -1, nan, nan, nan, nan, nan, nan, nan, nan, 4],
[10, 0, 0, -1, 0, -1, nan, nan, nan, nan, nan, nan, nan, nan, 4],
[10, 0, 1, 1, 0, -1, nan, nan, nan, nan, nan, nan, nan, nan, 4],
[10, 0, 0.2, 0, 0, -1, nan, nan, nan, nan, nan, nan, nan, nan, 4],
[10, 0, 0.02, 0, 0, -1, nan, nan, nan, nan, nan, nan, nan, nan, 4],
[10, 5, 1, 0, 0, -1, nan, nan, nan, nan, nan, nan, nan, nan, 4],
[10, -5, 1, 0, 0, -1, nan, nan, nan, nan, nan, nan, nan, nan, 4],
[10, 0, 5, 0, 0, -1, nan, nan, nan, nan, nan, nan, nan, nan, 4],
[20, 0, 1, 0, 0, 1, nan, nan, nan, nan, nan, nan, nan, nan, 6],
[10, 0, 8, 0, 0, 1, nan, nan, nan, nan, nan, nan, nan, nan, 2],
[10, 20, 1, 0, 0, 1, nan, nan, nan, nan, nan, nan, nan, nan, 2]])
a=10
b=10
c=10
alpha=90
beta=90
gamma=120
u=[1,0,0]
v=[0,1,0]
ol=OrientedLattice(a, b, c, alpha, beta, gamma)
ol.setUFromVectors(u,v)
(Ei, DE, H, K, L, sign, expected_Qx, expected_Qy, expected_Qz, expected_in_plane_kf_angle,
expected_out_plane_kf_angle, expected_in_plane_Q_angle, expected_out_plane_Q_angle,
expected_omega, expected_error_code) = test_case8.T
HKL = vstack([H,K,L]).T
pars = {'Ei': Ei, 'hkl': HKL, 'DeltaE': DE, 'sign': sign, 'detector_constraints': True, 'horizontal_extent': [5.,65.],
'vertical_extent': [-7.5, 7.5], 'horizontal_extent_low': [-1,1.], 'vertical_extent_low': [-1.,1.],
'goniometer_constraints': True, 'goniometer_range': [-20., 50]}
expected_error_code = [ErrorCodes(ec) for ec in expected_error_code]
self.run_test(ol, expected_Qx, expected_Qy, expected_Qz, expected_in_plane_Q_angle, expected_out_plane_Q_angle,
expected_in_plane_kf_angle, expected_out_plane_kf_angle, expected_omega, expected_error_code, **pars)
def test_qangle_NoGC_OC(self):
# Geometry constraints, no omega constraints, all parameters are arrays
test_case7 = array([[10, 0, 1, 0, 0, 1, nan, nan, nan, nan, nan, nan, nan, nan, 6],
[10, 0, 0, 1, 0, 1, nan, nan, nan, nan, nan, nan, nan, nan, 6],
[10, 0, -1, 0, 0, 1, nan, nan, nan, nan, nan, nan, nan, nan, 6],
[10, 0, 0, -1, 0, 1, -0.72, 0, 0.12, 19, 0, -80.5, 0, 39.5, 0],
[10, 0, 1, 1, 0, 1, nan, nan, nan, nan, nan, nan, nan, nan, 6],
[10, 0, 0.2, 0, 0, 1, nan, nan, nan, nan, nan, nan, nan, nan, 6],
[10, 0, 0.02, 0, 0, 1, nan, nan, nan, nan, nan, nan, nan, nan, 6],
[10, 5, 1, 0, 0, 1, nan, nan, nan, nan, nan, nan, nan, nan, 6],
[10, -5, 1, 0, 0, 1, nan, nan, nan, nan, nan, nan, nan, nan, 6],
[10, 0, 5, 0, 0, 1, nan, nan, nan, nan, nan, nan, nan, nan, 6],
[10, 0, 1, -0.01, -0.18, 1, nan, nan, nan, nan, nan, nan, nan, nan, 6],
[10, 0, 1, 0, -0.6, 1, nan, nan, nan, nan, nan, nan, nan, nan, 6],
[10, 0, 1, 0, 0, -1, nan, nan, nan, nan, nan, nan, nan, nan, 6],
[10, 0, 0, 1, 0, -1, 0.72, 0, 0.12, -19, 0, 80.5, 0, 20.5, 0],
[10, 0, -1, 0, 0, -1, nan, nan, nan, nan, nan, nan, nan, nan, 6],
[10, 0, 0, -1, 0, -1, nan, nan, nan, nan, nan, nan, nan, nan, 6],
[10, 0, 1, 1, 0, -1, 1.2, 0, 0.36, -33.2, 0, 73.4, 0, 43.4, 0],
[10, 0, 0.2, 0, 0, -1, nan, nan, nan, nan, nan, nan, nan, nan, 6],
[10, 0, 0.02, 0, 0, -1, nan, nan, nan, nan, nan, nan, nan, nan, 6],
[10, 5, 1, 0, 0, -1, 0.28, 0, 0.67, -10.4, 0, 22.8, 0, 22.8, 0],
[10, -5, 1, 0, 0, -1, nan, nan, nan, nan, nan, nan, nan, nan, 6],
[10, 0, 5, 0, 0, -1, 2.05, 0, 3, -111.3, 0, 34.4, 0, 34.3, 0],
[20, 0, 1, 0, 0, 1, nan, nan, nan, nan, nan, nan, nan, nan, 6],
[10, 0, 8, 0, 0, 1, nan, nan, nan, nan, nan, nan, nan, nan, 2],
[10, 20, 1, 0, 0, 1, nan, nan, nan, nan, nan, nan, nan, nan, 2]])
a=10
b=10
c=10
alpha=90
beta=90
gamma=120
u=[1,0,0]
v=[0,1,0]
ol=OrientedLattice(a, b, c, alpha, beta, gamma)
ol.setUFromVectors(u,v)
(Ei, DE, H, K, L, sign, expected_Qx, expected_Qy, expected_Qz, expected_in_plane_kf_angle,
expected_out_plane_kf_angle, expected_in_plane_Q_angle, expected_out_plane_Q_angle,
expected_omega, expected_error_code) = test_case7.T
HKL = vstack([H,K,L]).T
pars = {'Ei': Ei, 'hkl': HKL, 'DeltaE': DE, 'sign': sign, 'goniometer_constraints': True, 'goniometer_range': [-20., 50]}
expected_error_code = [ErrorCodes(ec) for ec in expected_error_code]
self.run_test(ol, expected_Qx, expected_Qy, expected_Qz, expected_in_plane_Q_angle, expected_out_plane_Q_angle,
expected_in_plane_kf_angle, expected_out_plane_kf_angle, expected_omega, expected_error_code, **pars)
class Monochromator():
# only for PG
__slots__ = ['lambdan', 'tth', 'en']
def __init__(self, reflect=[0, 0, 2], **kargs):
self.kargs = kargs
self.pgo = OrientedLattice(2.461, 2.461, 6.708, 90, 90, 60)
self.q = self.pgo.qFromHKL(reflect).norm()
if 'lambdan' in self.kargs.keys():
self.lambdan = self.kargs['lambdan']
self.en = (9.045 / self.lambdan)**2
self.k = 2 * math.pi / self.lambdan
self.lambda2m2()
if 'tth' in self.kargs.keys():
self.tth = abs(self.kargs['tth'])
self.monolambda()
if 'en' in self.kargs.keys():
self.en = self.kargs['en']
self.lambdan = 9.045 / (math.sqrt(self.en))
self.k = 2 * math.pi / self.lambdan
self.lambda2m2()
def lambda2m2(self):
stth = self.q / 2.0 / self.k
self.tth = math.asin(stth) * 360 / math.pi
def monolambda(self):
self.k = self.q / 2 / math.sin(self.tth * math.pi / 360)
self.lambdan = 2 * math.pi / self.k
self.en = (9.045 / self.lambdan)**2
def from_lattice(cls, lattice: OrientedLattice, x_proj: Sequence, y_proj: Sequence):
"""
:param lattice: An OrientedLattice object defining the unit cell
:param x_proj: Projection vector of dimension associated with X coordinate
:param y_proj: Projection vector of dimension associated with Y coordinate
"""
return cls(np.radians(lattice.recAngle(*x_proj, *y_proj)))
def test_qangle_NoGC_NoOC_newOL(self):
# No geometry constraints, no omega constraints, all parameters are arrays
test_case9 = array([[10, 0, 1, 0, 0, 1, -2.02, 0, 1.33, 66.8, 0, -56.6, 0, -56.6, 0],
[10, 0, 0, 1, 0, 1, -1.01, 0, 0.24, 27.3, 0, -76.4, 0, -136.4, 0],
[10, 0, -1, 0, 0, 1, -2.02, 0, 1.33, 66.8, 0, -56.6, 0, 123.4, 0],
[10, 0, 0, -1, 0, 1, -1.01, 0, 0.24, 27.3, 0, -76.4, 0, 43.6, 0],
[10, 0, 1, 1, 0, 1, -2.2, 0, 2.15, 88.7, 0, -45.7, 0, -62.7, 0],
[10, 0, 0.2, 0, 0, 1, -0.48, 0, 0.05, 12.6, 0, -83.7, 0, -83.7, 0],
[10, 0, 0.02, 0, 0, 1, -0.04984, 0, 0.00057, 1.3, 0, -89.4, 0, -89.4, 0],
[10, 5, 1, 0, 0, 1, -1.52, 0, 1.88, 78.2, 0, -39, 0, -39, 0],
[10, -5, 1, 0, 0, 1, -2.29, 0, 0.78, 58.3, 0, -71.1, 0, -71.1, 0],
[10, 0, 1.5, 0, 0, 1, -2.05, 0, 3, 111.3, 0, -34.4, 0, -34.3, 0],
[10, 0, 1, 0, -0.2, 1, -2.02, -0.13, 1.33, 66.8, 3.3, -56.5, -3, -56.6, 0],
[10, 0, 1, 0, -0.6, 1, -1.99, -0.38, 1.36, 67.4, 10, -55.7, -9, -55.7, 0], #Qz
[10, 0, 1, 0, 0, -1, 2.02, 0, 1.33, -66.8, 0, 56.6, 0, 56.6, 0],
[10, 0, 0, 1, 0, -1, 1.01, 0, 0.24, -27.3, 0, 76.4, 0, 16.4, 0],
[10, 0, -1, 0, 0, -1, 2.02, 0, 1.33, -66.8, 0, 56.6, 0, -123.4, 0],
[10, 0, 0, -1, 0, -1, 1.01, 0, 0.24, -27.3, 0, 76.4, 0, -163.6, 0],
[10, 0, 1, 1, 0, -1, 2.2, 0, 2.15, -88.7, 0, 45.7, 0, 28.7, 0],
[10, 0, 0.2, 0, 0, -1, 0.48, 0, 0.05, -12.6, 0, 83.7, 0, 83.7, 0],
[10, 0, 0.02, 0, 0, -1, 0.04984, 0, 0.00057, -1.3, 0, 89.4, 0, 89.4, 0],
[10, 5, 1, 0, 0, -1, 1.52, 0, 1.88, -78.2, 0, 39, 0, 39, 0],
[10, -5, 1, 0, 0, -1, 2.29, 0, 0.78, -58.3, 0, 71.1, 0, 71.1, 0],
[20, 0, 1, 0, 0, 1, -2.23, 0, 0.94, 45.8, 0, -67.1, 0, -67.1, 0],
[10, 0, 8, 0, 0, 1, nan, nan, nan, nan, nan, nan, nan, nan, 2],
[10, 20, 1, 0, 0, 1, nan, nan, nan, nan, nan, nan, nan, nan, 2]])
a=3
b=7
c=10
alpha=90
beta=90
gamma=120
u=[1,0,0]
v=[0,1,0]
ol=OrientedLattice(a, b, c, alpha, beta, gamma)
ol.setUFromVectors(u,v)
(Ei, DE, H, K, L, sign, expected_Qx, expected_Qy, expected_Qz, expected_in_plane_kf_angle,
expected_out_plane_kf_angle, expected_in_plane_Q_angle, expected_out_plane_Q_angle,
expected_omega, expected_error_code) = test_case9.T
HKL = vstack([H,K,L]).T
pars = {'Ei': Ei, 'hkl': HKL, 'DeltaE': DE, 'sign': sign}
expected_error_code = [ErrorCodes(ec) for ec in expected_error_code]
self.run_test(ol, expected_Qx, expected_Qy, expected_Qz, expected_in_plane_Q_angle, expected_out_plane_Q_angle,
expected_in_plane_kf_angle, expected_out_plane_kf_angle, expected_omega, expected_error_code, **pars)
def __init__(self, reflect=[0, 0, 2], **kargs):
self.kargs = kargs
self.pgo = OrientedLattice(2.461, 2.461, 6.708, 90, 90, 60)
self.q = self.pgo.qFromHKL(reflect).norm()
if 'lambdan' in self.kargs.keys():
self.lambdan = self.kargs['lambdan']
self.en = (9.045 / self.lambdan)**2
self.k = 2 * math.pi / self.lambdan
self.lambda2m2()
if 'tth' in self.kargs.keys():
self.tth = abs(self.kargs['tth'])
self.monolambda()
if 'en' in self.kargs.keys():
self.en = self.kargs['en']
self.lambdan = 9.045 / (math.sqrt(self.en))
self.k = 2 * math.pi / self.lambdan
self.lambda2m2()
def test_create_nonorthogonal_transform_with_orthogonal_lattice_and_nonorthogonal_projections(
self):
lattice = OrientedLattice() # default angle=90 degrees
transform = NonOrthogonalTransform.from_lattice(lattice,
x_proj=(1, 0, 0),
y_proj=(1, 1, 0))
self.assertAlmostEqual(transform.angle, 0.25 * np.pi)
def convertQSampleToHKL(ws,
OutputWorkspace='__md_hkl',
norm=None,
UB=None,
Extents=[-10, 10, -10, 10, -10, 10],
Bins=[101, 101, 101],
Append=False):
ol = OrientedLattice()
ol.setUB(UB)
q1 = ol.qFromHKL([1, 0, 0])
q2 = ol.qFromHKL([0, 1, 0])
q3 = ol.qFromHKL([0, 0, 1])
BinMD(InputWorkspace=ws,
AxisAligned=False,
NormalizeBasisVectors=False,
BasisVector0='[H,0,0],A^-1,{},{},{}'.format(q1.X(), q1.Y(), q1.Z()),
BasisVector1='[0,K,0],A^-1,{},{},{}'.format(q2.X(), q2.Y(), q2.Z()),
BasisVector2='[0,0,L],A^-1,{},{},{}'.format(q3.X(), q3.Y(), q3.Z()),
OutputExtents=Extents,
OutputBins=Bins,
TemporaryDataWorkspace=OutputWorkspace
if Append and mtd.doesExist(OutputWorkspace) else None,
OutputWorkspace=OutputWorkspace)
if norm is not None:
mtd[str(norm)].run().getGoniometer().setR(
mtd[str(ws)].getExperimentInfo(0).run().getGoniometer().getR())
convertToHKL(norm,
OutputWorkspace=str(OutputWorkspace) + '_norm',
UB=UB,
Extents=Extents,
Bins=Bins,
Append=Append)
return OutputWorkspace
def _create_mock_workspace(ws_type,
coords: SpecialCoordinateSystem = None,
has_oriented_lattice: bool = None,
ndims: int = 2):
"""
:param ws_type: Used this as spec for Mock
:param coords: MD coordinate system for MD workspaces
:param has_oriented_lattice: If the mock should claim to have an attached a lattice
:param ndims: The number of dimensions
"""
ws = MagicMock(spec=ws_type)
if hasattr(ws, 'getExperimentInfo'):
ws.getNumDims.return_value = ndims
ws.getNumNonIntegratedDims.return_value = ndims
if ws_type == IMDHistoWorkspace:
ws.isMDHistoWorkspace.return_value = True
ws.getNonIntegratedDimensions.return_value = [
MagicMock(), MagicMock()
]
ws.hasOriginalWorkspace.return_value = False
basis_mat = np.eye(ndims)
ws.getBasisVector.side_effect = lambda idim: basis_mat[:, idim]
else:
ws.isMDHistoWorkspace.return_value = False
ws.getSpecialCoordinateSystem.return_value = coords
run = MagicMock()
run.get.return_value = MagicMock()
run.get().value = np.eye(3).flatten() # proj matrix is always 3x3
expt_info = MagicMock()
sample = MagicMock()
sample.hasOrientedLattice.return_value = has_oriented_lattice
if has_oriented_lattice:
lattice = OrientedLattice(1, 1, 1, 90, 90, 90)
sample.getOrientedLattice.return_value = lattice
expt_info.sample.return_value = sample
expt_info.run.return_value = run
ws.getExperimentInfo.return_value = expt_info
ws.getExperimentInfo().sample()
elif hasattr(ws, 'getNumberHistograms'):
ws.getNumDims.return_value = 2
ws.getNumberHistograms.return_value = 3
mock_dimension = MagicMock()
mock_dimension.getNBins.return_value = 3
ws.getDimension.return_value = mock_dimension
return ws
def run_test(v1, v2):
cell = OrientedLattice()
testhelpers.assertRaisesNothing(self, cell.setUFromVectors, v1, v2)
rot = cell.getUB();
expected = np.array([(0,1.,0.), (0.,0.,1.), (1.,0.,0.)])
np.testing.assert_array_almost_equal(expected, rot, 8)
def plot_Qpeaks(self):
proj3d.persp_transformation = self.orthogonal_proj
try:
# Find size of screen
import curses
stdscr = curses.initscr()
self.screen_x, self.screen_y = stdscr.getmaxyx()
self.screen_x = min(self.screen_x, self.screen_y)
self.screen_y = self.screen_x
except:
self.screen_x = 40
self.screen_y = 40
plt.rcParams.update({'font.size': 10})
if len(self.mod) == 0:
IndexPeaks(PeaksWorkspace=self.peaks_ws,
Tolerance=self.tolerance,
RoundHKLs=False,
CommonUBForAll=True)
elif len(self.mod) > 0:
IndexPeaksWithSatellites(PeaksWorkspace=self.peaks_ws,
RoundHKLs=False,
ModVector1=self.mod,
MaxOrder=1)
npeaksTotal = self.peaks_ws.getNumberPeaks()
self.c = []
self.x = []
self.y = []
self.z = []
self.s = []
for i in range(npeaksTotal):
peak = self.peaks_ws.getPeak(i)
hklp = V3D(peak.getH() - math.floor(peak.getH()),
peak.getK() - math.floor(peak.getK()),
peak.getL() - math.floor(peak.getL()))
if peak.getSigmaIntensity() != 0.0:
IsigI = peak.getIntensity() / peak.getSigmaIntensity()
else:
IsigI = 0.0
#if IsigI < 50:
#continue
intensity = max(self.minIntensity, peak.getIntensity())
for i in range(-1, 1):
for j in range(-1, 1):
for k in range(-1, 1):
if (abs(hklp[0] + i) < 1.0 and abs(hklp[1] + j) < 1.0
and abs(hklp[2] + k) < 1.0):
self.x.append(hklp[0] + i)
self.y.append(hklp[1] + j)
self.z.append(hklp[2] + k)
self.c.append(intensity)
self.s.append(5)
nPts = 100
x_grid = np.linspace(-1, 1, nPts + 1)
x_half = np.zeros(nPts)
for j in range(nPts):
x_half[j] = 0.5 * (x_grid[j] + x_grid[j + 1])
sumIntensityX = np.zeros(nPts)
for i in range(len(self.x)):
for j in range(nPts):
if self.x[i] > x_grid[j] and self.x[i] < x_grid[j + 1]:
sumIntensityX[j] = sumIntensityX[j] + self.c[i]
sumIntensityY = np.zeros(nPts)
for i in range(len(self.y)):
for j in range(nPts):
if self.y[i] > x_grid[j] and self.y[i] < x_grid[j + 1]:
sumIntensityY[j] = sumIntensityY[j] + self.c[i]
sumIntensityZ = np.zeros(nPts)
for i in range(len(self.z)):
for j in range(nPts):
if self.z[i] > x_grid[j] and self.z[i] < x_grid[j + 1]:
sumIntensityZ[j] = sumIntensityZ[j] + self.c[i]
# Plot figure with subplots of different sizes
fig = plt.figure("Modulated Structures",
figsize=(self.screen_x, self.screen_y))
# set up subplot grid
gridspec.GridSpec(3, 3)
ax = plt.subplot2grid((3, 3), (0, 2))
plt.plot(x_half, sumIntensityX)
maxGrid = "max\n"
for i in range(2, nPts - 2):
if abs(x_half[i]) > 0.55 or abs(x_half[i]) < 0.05:
continue
if sumIntensityX[i] > sumIntensityX[
i - 1] and sumIntensityX[i] > sumIntensityX[
i + 1] and sumIntensityX[i - 1] > sumIntensityX[
i - 2] and sumIntensityX[i + 1] > sumIntensityX[i +
2]:
maxGrid += "{:f}\n".format(x_half[i])
ax.text(0.05, 0.60, maxGrid, fontsize=10, transform=ax.transAxes)
ax.set_yscale('log')
ax.set_xlabel('H')
ax.set_ylabel(r'$\Sigma$I')
ax = plt.subplot2grid((3, 3), (1, 2))
plt.plot(x_half, sumIntensityY)
maxGrid = "max\n"
for i in range(2, nPts - 2):
if abs(x_half[i]) > 0.5 or abs(x_half[i]) < 0.05:
continue
if sumIntensityY[i] > sumIntensityY[
i - 1] and sumIntensityY[i] > sumIntensityY[
i + 1] and sumIntensityY[i - 1] > sumIntensityY[
i - 2] and sumIntensityY[i + 1] > sumIntensityY[i +
2]:
maxGrid += "{:f}\n".format(x_half[i])
ax.text(0.05, 0.60, maxGrid, fontsize=10, transform=ax.transAxes)
ax.set_yscale('log')
ax.set_xlabel('K')
ax.set_ylabel(r'$\Sigma$I')
ax = plt.subplot2grid((3, 3), (2, 2))
plt.plot(x_half, sumIntensityZ)
maxGrid = "max\n"
for i in range(2, nPts - 2):
if abs(x_half[i]) > 0.5 or abs(x_half[i]) < 0.05:
continue
if sumIntensityZ[i] > sumIntensityZ[
i - 1] and sumIntensityZ[i] > sumIntensityZ[
i + 1] and sumIntensityZ[i - 1] > sumIntensityZ[
i - 2] and sumIntensityZ[i + 1] > sumIntensityZ[i +
2]:
maxGrid += "{:f}\n".format(x_half[i])
ax.text(0.05, 0.60, maxGrid, fontsize=10, transform=ax.transAxes)
ax.set_yscale('log')
ax.set_xlabel('L')
ax.set_ylabel(r'$\Sigma$I')
vmin = min(self.c)
vmax = max(self.c)
logNorm = colors.LogNorm(vmin=vmin, vmax=vmax)
self.axP = plt.subplot2grid((3, 3), (0, 0),
colspan=2,
rowspan=3,
projection='3d')
sp = self.axP.scatter(self.x,
self.y,
self.z,
c=self.c,
vmin=vmin,
vmax=vmax,
norm=logNorm,
s=self.s,
cmap='rainbow',
picker=True,
alpha=0.2)
self.props = dict(boxstyle='round', facecolor='wheat', alpha=1.0)
#cid = fig.canvas.mpl_connect('pick_event', self.onpick3)
pid = fig.canvas.mpl_connect('key_press_event', self.onpress)
try:
lattice = self.peaks_ws.sample().getOrientedLattice()
except:
lattice = OrientedLattice(1, 1, 1)
astar = V3D(0.5, 0, 0)
bstar = V3D(0, 0.5, 0)
cstar = V3D(0, 0, 0.5)
hkls = np.array(
[np.array([x, y, z]) for x, y, z in zip(self.x, self.y, self.z)])
labels, centroids = self.dbscan(hkls, eps=.0425, min_points=6)
i = 0
modTest = str(self.peaks_ws.getPeak(0).getRunNumber())
lastRun = str(self.peaks_ws.getPeak(npeaksTotal - 1).getRunNumber())
if lastRun != modTest:
modTest = modTest + "-" + lastRun
modTest = modTest + " Type a, b, or c for axis alignment"
for x in centroids:
self.axP.plot([x[0]], [x[1]], [x[2]],
'wo',
ms=40,
markerfacecolor="None",
markeredgecolor='red',
markeredgewidth=3)
if x[0] * x[0] + x[1] * x[1] + x[2] * x[2] > 0.01 and x[
0] >= -0.5 and x[1] >= -0.5 and x[2] >= -0.5 and x[
0] <= 0.5 and x[1] <= 0.5 and x[2] <= 0.5:
modTest += "\nModulation Vector = " + "{:.3f}".format(
x[0]) + ", " + "{:.3f}".format(
x[1]) + ", " + "{:.3f}".format(x[2])
if len(self.mod) == 0:
self.mod = "{:.3f}".format(x[0]) + "," + "{:.3f}".format(
x[1]) + "," + "{:.3f}".format(x[2])
IndexPeaksWithSatellites(PeaksWorkspace=self.peaks_ws,
RoundHKLs=False,
ModVector1=self.mod,
MaxOrder=1)
self.axP.plot([0, astar[0]], [0, astar[1]], [0, astar[2]], color='r')
self.axP.text(astar[0],
astar[1],
astar[2],
'%s' % ('a*'),
size=20,
zorder=1,
color='r')
self.axP.plot([0, bstar[0]], [0, bstar[1]], [0, bstar[2]], color='b')
self.axP.text(bstar[0],
bstar[1],
bstar[2],
'%s' % ('b*'),
size=20,
zorder=1,
color='b')
self.axP.plot([0, cstar[0]], [0, cstar[1]], [0, cstar[2]], color='g')
self.axP.text(cstar[0],
cstar[1],
cstar[2],
'%s' % ('c*'),
size=20,
zorder=1,
color='g')
self.axP.text2D(0.05,
0.80,
modTest + "\nLattice = " + " " +
"{:.3f}".format(lattice.a()) + " " +
"{:.3f}".format(lattice.b()) + " " +
"{:.3f}".format(lattice.c()) + " " +
"{:.3f}".format(lattice.alpha()) + " " +
"{:.3f}".format(lattice.beta()) + " " +
"{:.3f}".format(lattice.gamma()) + "\nError = " + " " +
"{:.3E}".format(lattice.errora()) + " " +
"{:.3E}".format(lattice.errorb()) + " " +
"{:.3E}".format(lattice.errorc()) + " " +
"{:.3E}".format(lattice.erroralpha()) + " " +
"{:.3E}".format(lattice.errorbeta()) + " " +
"{:.3E}".format(lattice.errorgamma()),
fontsize=10,
transform=self.axP.transAxes)
self.axP.set_xlabel('H')
self.axP.set_ylabel('K')
self.axP.set_zlabel('L')
# Create cubic bounding box to simulate equal aspect ratio
max_range = max([
max(self.x) - min(self.x),
max(self.y) - min(self.y),
max(self.z) - min(self.z)
])
Xb = 0.5 * max_range * np.mgrid[-1:2:2, -1:2:2, -1:2:2][0].flatten(
) + 0.5 * (max(self.x) + min(self.x))
Yb = 0.5 * max_range * np.mgrid[-1:2:2, -1:2:2, -1:2:2][1].flatten(
) + 0.5 * (max(self.y) + min(self.y))
Zb = 0.5 * max_range * np.mgrid[-1:2:2, -1:2:2, -1:2:2][2].flatten(
) + 0.5 * (max(self.z) + min(self.z))
# Comment or uncomment following both lines to test the fake bounding box:
for xb, yb, zb in zip(Xb, Yb, Zb):
self.axP.plot([xb], [yb], [zb], 'w')
plt.show()
#fig.canvas.mpl_disconnect(cid)
fig.canvas.mpl_disconnect(pid)
def _qangle_validate_inputs(
hkl: np.array, Ei: float or np.array, DeltaE: float or np.array,
sign: float or np.array, lattice: OrientedLattice,
detector_constraints: bool, horizontal_extent: np.array,
vertical_extent: np.array, horizontal_extent_low: np.array,
vertical_extent_low: np.array, goniometer_constraints: bool,
goniometer_range):
"""
Validate inputs for qangle function, according to the rules for
that function
"""
try:
len_hkl = len(hkl)
if len(hkl[0]) != 3:
raise ValueError()
except (TypeError, ValueError):
raise ValueError('hkl is not an array of triplets')
try:
# check if float
Ei = float(Ei)
Ei = np.full(len_hkl, Ei)
except ValueError:
raise ValueError('Ei is not a float or numpy array')
except TypeError:
if len(Ei) != len_hkl:
raise ValueError('Ei has different length than hkl')
try:
# check if float
DeltaE = float(DeltaE)
DeltaE = np.full(len_hkl, DeltaE)
except ValueError:
raise ValueError('DeltaE is not a float or numpy array')
except TypeError:
if len(DeltaE) != len_hkl:
raise ValueError('DeltaE has different length than hkl')
try:
# check if int
sign = int(sign)
sign = np.full(len_hkl, sign)
except ValueError:
raise ValueError('sign is not an int or numpy array')
except TypeError:
if len(sign) != len_hkl:
raise ValueError('sign has different length than hkl')
try:
UB = lattice.getUB() * 2. * np.pi
except:
raise ValueError("Can't get the UB matrix from the lattice object")
# inputs for geometry and goniometer constraints
if detector_constraints:
if horizontal_extent[0] < -180 or horizontal_extent[
1] < horizontal_extent[0] or horizontal_extent[1] > 180:
raise ValueError(
f"Horizontal constraints must obey -180 <= horizontal_extent[0]"
f" ({horizontal_extent[0]}) <= horizontal_extent[1] ({horizontal_extent[1]})<=180"
)
if vertical_extent[0] < -180 or vertical_extent[1] < vertical_extent[
0] or vertical_extent[1] > 180:
raise ValueError(
f"Vertical constraints must obey -180 <= vertical_extent[0] ({vertical_extent[0]}) "
f"<= vertical_extent[1] ({vertical_extent[1]}) <=180")
if horizontal_extent_low[0] < -180 or horizontal_extent_low[
1] < horizontal_extent_low[0] or horizontal_extent_low[1] > 180:
raise ValueError(
f"Horizontal constraints must obey -180 <= horizontal_extent_low[0]"
f" ({horizontal_extent_low[0]}) <= horizontal_extent_low[1] ({horizontal_extent_low[1]}) <=180"
)
if vertical_extent_low[0] < -180 or vertical_extent_low[
1] < vertical_extent_low[0] or vertical_extent_low[1] > 180:
raise ValueError(
f"Vertical constraints must obey -180 <= vertical_extent_low[0] ({vertical_extent_low[0]}) "
f"<= vertical_extent_low[1] ({vertical_extent_low[1]}) <=180")
if goniometer_constraints:
if goniometer_range[1]<goniometer_range[0] or \
goniometer_range[0]<-180. or goniometer_range[1]>180.:
raise ValueError("goniometer_range must be an increasing array, "
"with both limits between -180 and 180 degrees")
return (Ei, DeltaE, sign, UB)
def run_test(v1, v2):
cell = OrientedLattice()
testhelpers.assertRaisesNothing(self, cell.setUFromVectors, v1, v2)
rot = cell.getUB()
expected = np.array([(0, 1., 0.), (0., 0., 1.), (1., 0., 0.)])
np.testing.assert_array_almost_equal(expected, rot, 8)
from mantid.simpleapi import *
from mantid.geometry import OrientedLattice
van = LoadNexus(
'/HFIR/HB2C/IPTS-7776/shared/autoreduce/HB2C_{}.nxs'.format(6558))
LoadIsawUB('van', '/SNS/users/rwp/wand/single5/PNO_T.mat')
ub = mtd['van'].sample().getOrientedLattice().getUB().copy()
ol = OrientedLattice()
ol.setUB(ub)
q1 = ol.qFromHKL([1, 0, 0])
q2 = ol.qFromHKL([0, 1, 0])
q3 = ol.qFromHKL([0, 0, 1])
if 'data' in mtd:
mtd.remove('data')
if 'norm' in mtd:
mtd.remove('norm')
for run in range(4756, 6558, 1):
print(run)
md = LoadMD(
Filename='/HFIR/HB2C/IPTS-7776/shared/autoreduce/HB2C_{}_MDE.nxs'.
format(run))
mtd['van'].run().getGoniometer().setR(
mtd['md'].getExperimentInfo(0).run().getGoniometer().getR())
#BinMD(InputWorkspace='md', OutputWorkspace='mdh', AlignedDim0='Q_sample_x,-10,10,401', AlignedDim1='Q_sample_y,-1,1,41', AlignedDim2='Q_sample_z,-10,10,401')
BinMD(InputWorkspace='md',
OutputWorkspace='mdh',
def test_simple_values(self):
u1 = OrientedLattice()
self.assertEquals(u1.a1(), 1)
self.assertEquals(u1.alpha(), 90)
u2 = OrientedLattice(3, 4, 5)
self.assertAlmostEqual(u2.b1(), 1. / 3., 10)
self.assertAlmostEqual(u2.alphastar(), 90, 10)
u3 = u2
self.assertAlmostEqual(u3.volume(), 1. / u2.recVolume(), 10)
u2.seta(3)
self.assertAlmostEqual(u2.a(), 3, 10)
OutputWorkspace='tzero2D',
Params='0.1,-0.005,20')
DiffractionFocussing('tzero2D',
OutputWorkspace='tzero2D',
GroupingWorkspace='group')
DReference = [
0.9179, 0.9600, 1.0451, 1.1085, 1.2458, 1.3576, 1.6374, 1.9200, 3.1353
] # Si
def get_d(ol, h, k, l):
return 2 * np.pi / np.linalg.norm(ol.qFromHKL([h, k, l]))
ol = OrientedLattice(3.905044, 3.905044, 11.166629, 90, 90, 90)
DReference = [
get_d(ol, 0, 0, 1),
get_d(ol, 0, 0, 2),
get_d(ol, 1, 0, 0),
get_d(ol, 0, 0, 3),
#get_d(ol, 1, 0, 1), #0
get_d(ol, 1, 0, 2),
#get_d(ol, 0, 0, 4), #0
get_d(ol, 1, 1, 0),
get_d(ol, 1, 0, 3),
get_d(ol, 1, 1, 1),
get_d(ol, 1, 1, 2),
get_d(ol, 1, 0, 4),
get_d(ol, 0, 0, 5),
from mantid.simpleapi import * from mantid.geometry import OrientedLattice from itertools import permutations import numpy as np ol = OrientedLattice(5, 7, 12, 90, 90, 120) ub = ol.getUB() print(ub) peaks = CreatePeaksWorkspace(NumberOfPeaks=0) peaks.addPeak(peaks.createPeakQSample(2 * np.pi * np.dot(ub, [1, 1, 1]))) peaks.addPeak(peaks.createPeakQSample(2 * np.pi * np.dot(ub, [1, 1, 0]))) peaks.addPeak(peaks.createPeakQSample(2 * np.pi * np.dot(ub, [1, 2, 0]))) peaks2 = CreatePeaksWorkspace(NumberOfPeaks=0) peaks2.addPeak(peaks2.createPeakQSample(2 * np.pi * np.dot(ub, [1, 1, 1]))) peaks2.addPeak(peaks2.createPeakQSample(2 * np.pi * np.dot(ub, [1, 1, 0]))) peaks2.addPeak(peaks2.createPeakQSample(2 * np.pi * np.dot(ub, [1, 2, 0]))) CompareWorkspaces(peaks, peaks2, Tolerance=1e-4) ws = CreateSampleWorkspace() peaks = CreatePeaksWorkspace(InstrumentWorkspace='ws') peaks2 = CreatePeaksWorkspace(InstrumentWorkspace='ws') peaks.getPeak(0).setRunNumber(123) CompareWorkspaces(peaks, peaks2, Tolerance=1e-4)
class Scisoft():
def __init__(self, point):
# input : qe
# output : qe+tas
self.point = point
self.qe_para()
self.qe_limit()
if self.limit_qe == 1:
self.scisoft()
if tp.ModeChoice.mode == 3:
# add sample stick rotation s0
self.scisoft_premium()
self.tas = tl.TasLimit(self.tas).point
else:
self.tas = tl.TasLimit(self.tas).point
else:
self.tas = pd.Series(data=None,
index=tp.TasStatus.tas_status.index.drop(
['mts', 'sta', 'dtx']).copy())
self.tas['s1s2_limit'] = 1
self.tas['soft_limit'] = 1
self.tas['qe_limit'] = self.limit_qe
# raise Exception as
def qe_para(self):
self.orien = OrientedLattice(*Alignment.para)
self.para = Alignment.para
self.hkl = [self.point.h, self.point.k, self.point.l]
self.len = self.orien.qFromHKL(self.hkl).norm()
self.mono = Monochromator(en=self.point.ei)
self.ana = Monochromator(en=self.point.ef)
def qe_limit(self):
if self.mono.k + self.ana.k < self.len:
self.limit_qe = tp.LimitNumb.Modenumb[tp.LimitNumb.mode]
else:
self.limit_qe = 1
def angdif(self):
# angle between point and refa
p0 = self.hkl
p1 = Alignment.refa
p2 = Alignment.refb
theta1 = self.orien.recAngle(p0[0], p0[1], p0[2], p1.h, p1.k, p1.l)
valcos1 = math.cos(math.radians(theta1))
theta2 = self.orien.recAngle(p0[0], p0[1], p0[2], p2.h, p2.k, p2.l)
valcos2 = math.cos(math.radians(theta2))
if valcos1 * valcos2 == 0:
self.angdiff = theta1 * (valcos1 + valcos2)
else:
self.angdiff = theta1 * abs(valcos2) / valcos2
def scisoft(self):
s2_value = (self.mono.k**2 + self.ana.k**2 -
self.len**2) / 2.0 / self.mono.k / self.ana.k
self.tth = math.degrees(math.acos(s2_value))
self.angdif()
s2 = self.tth * tp.TasConfig.tas_config.s
s1dif = (self.mono.k**2 - self.ana.k**2 +
self.len**2) / 2.0 / self.mono.k / self.len
s1dif = math.acos(s1dif)
s1dif = s1dif * 180 / math.pi
s1 = -1 * Alignment.delta - self.angdiff - s1dif * tp.TasConfig.tas_config.s
index = ['m1', 'm2', 's1', 's2', 'a1', 'a2']
self.tas = pd.Series(data=[
self.mono.tth / 2, self.mono.tth, s1, s2, self.ana.tth / 2,
self.ana.tth
],
index=index)
def s1p_split(self):
# s0 first : magnet
# s1 first : crystat
s1p = self.tas.s1
delta_s1p = s1p - (tp.TasStatus.tas_status.s1 +
tp.TasStatus.tas_status.s0)
if tp.SplitMode.mode == 0:
s0 = tp.TasStatus.tas_status.s0 + delta_s1p
s1 = tp.TasStatus.tas_status.s1
elif tp.SplitMode.mode == 1:
s1 = tp.TasStatus.tas_status.s1 + delta_s1p
s0 = tp.TasStatus.tas_status.s0
return pd.Series(data=[s0, s1], index=['s0', 's1'])
def scisoft_premium(self):
junk = self.tas
addition = self.s1p_split()
junk.pop('s1')
self.tas = junk.append(addition)
def runTest(self):
# Na Mn Cl3
# R -3 H (148)
# 6.592 6.592 18.585177 90 90 120
# UB/wavelength from /HFIR/HB3A/IPTS-25470/shared/autoreduce/HB3A_exp0769_scan0040.nxs
ub = np.array([[1.20297e-01, 1.70416e-01, 1.43000e-04],
[8.16000e-04, -8.16000e-04, 5.38040e-02],
[1.27324e-01, -4.05110e-02, -4.81000e-04]])
wavelength = 1.553
# create fake MDEventWorkspace, similar to what is expected from exp769 after loading with HB3AAdjustSampleNorm
MD_Q_sample = CreateMDWorkspace(
Dimensions='3',
Extents='-5,5,-5,5,-5,5',
Names='Q_sample_x,Q_sample_y,Q_sample_z',
Units='rlu,rlu,rlu',
Frames='QSample,QSample,QSample')
inst = LoadEmptyInstrument(InstrumentName='HB3A')
AddTimeSeriesLog(inst, 'omega', '2010-01-01T00:00:00', 0.)
AddTimeSeriesLog(inst, 'phi', '2010-01-01T00:00:00', 0.)
AddTimeSeriesLog(inst, 'chi', '2010-01-01T00:00:00', 0.)
MD_Q_sample.addExperimentInfo(inst)
SetUB(MD_Q_sample, UB=ub)
ol = OrientedLattice()
ol.setUB(ub)
sg = SpaceGroupFactory.createSpaceGroup("R -3")
hkl = []
sat_hkl = []
for h in range(0, 6):
for k in range(0, 6):
for l in range(0, 11):
if sg.isAllowedReflection([h, k, l]):
if h == k == l == 0:
continue
q = V3D(h, k, l)
q_sample = ol.qFromHKL(q)
if not np.any(np.array(q_sample) > 5):
hkl.append(q)
FakeMDEventData(
MD_Q_sample,
PeakParams='1000,{},{},{},0.05'.format(
*q_sample))
# satellite peaks at 0,0,+1.5
q = V3D(h, k, l + 1.5)
q_sample = ol.qFromHKL(q)
if not np.any(np.array(q_sample) > 5):
sat_hkl.append(q)
FakeMDEventData(
MD_Q_sample,
PeakParams='100,{},{},{},0.02'.format(
*q_sample))
# satellite peaks at 0,0,-1.5
q = V3D(h, k, l - 1.5)
q_sample = ol.qFromHKL(q)
if not np.any(np.array(q_sample) > 5):
sat_hkl.append(q)
FakeMDEventData(
MD_Q_sample,
PeakParams='100,{},{},{},0.02'.format(
*q_sample))
# Check that this fake workpsace gives us the expected UB
peaks = FindPeaksMD(MD_Q_sample,
PeakDistanceThreshold=1,
OutputType='LeanElasticPeak')
FindUBUsingFFT(peaks, MinD=5, MaxD=20)
ShowPossibleCells(peaks)
SelectCellOfType(peaks,
CellType='Rhombohedral',
Centering='R',
Apply=True)
OptimizeLatticeForCellType(peaks, CellType='Hexagonal', Apply=True)
found_ol = peaks.sample().getOrientedLattice()
self.assertAlmostEqual(found_ol.a(), 6.592, places=2)
self.assertAlmostEqual(found_ol.b(), 6.592, places=2)
self.assertAlmostEqual(found_ol.c(), 18.585177, places=2)
self.assertAlmostEqual(found_ol.alpha(), 90)
self.assertAlmostEqual(found_ol.beta(), 90)
self.assertAlmostEqual(found_ol.gamma(), 120)
# nuclear peaks
predict = HB3APredictPeaks(
MD_Q_sample,
Wavelength=wavelength,
ReflectionCondition='Rhombohedrally centred, obverse',
SatellitePeaks=True,
IncludeIntegerHKL=True)
predict = HB3AIntegratePeaks(MD_Q_sample, predict, 0.25)
self.assertEqual(predict.getNumberPeaks(), 66)
# check that the found peaks are expected
for n in range(predict.getNumberPeaks()):
HKL = predict.getPeak(n).getHKL()
self.assertTrue(HKL in hkl, msg=f"Peak {n} with HKL={HKL}")
# magnetic peaks
satellites = HB3APredictPeaks(
MD_Q_sample,
Wavelength=wavelength,
ReflectionCondition='Rhombohedrally centred, obverse',
SatellitePeaks=True,
ModVector1='0,0,1.5',
MaxOrder=1,
IncludeIntegerHKL=False)
satellites = HB3AIntegratePeaks(MD_Q_sample, satellites, 0.1)
self.assertEqual(satellites.getNumberPeaks(), 80)
# check that the found peaks are expected
for n in range(satellites.getNumberPeaks()):
HKL = satellites.getPeak(n).getHKL()
self.assertTrue(HKL in sat_hkl, msg=f"Peak {n} with HKL={HKL}")