def test_HFIRCalculateGoniometer_HB3A_phi(self):
omega = np.deg2rad(42)
chi = np.deg2rad(-3)
phi = np.deg2rad(23)
R1 = np.array([
[np.cos(omega), 0, -np.sin(omega)], # omega 0,1,0,-1
[0, 1, 0],
[np.sin(omega), 0, np.cos(omega)]
])
R2 = np.array([
[np.cos(chi), np.sin(chi), 0], # chi 0,0,1,-1
[-np.sin(chi), np.cos(chi), 0],
[0, 0, 1]
])
R3 = np.array([
[np.cos(phi), 0, -np.sin(phi)], # phi 0,1,0,-1
[0, 1, 0],
[np.sin(phi), 0, np.cos(phi)]
])
R = np.dot(np.dot(R1, R2), R3)
wl = 1.54
k = 2 * np.pi / wl
theta = np.deg2rad(47)
phi = np.deg2rad(13)
q_lab = np.array([
-np.sin(theta) * np.cos(phi), -np.sin(theta) * np.sin(phi),
1 - np.cos(theta)
]) * k
q_sample = np.dot(np.linalg.inv(R), q_lab)
peaks = CreatePeaksWorkspace(OutputType="LeanElasticPeak",
NumberOfPeaks=0)
AddSampleLog(peaks, "Wavelength", str(wl), "Number")
SetGoniometer(peaks, Axis0='42,0,1,0,-1',
Axis1='-3,0,0,1,-1') # don't set phi
p = peaks.createPeakQSample(q_sample)
peaks.addPeak(p)
HFIRCalculateGoniometer(peaks,
OverrideProperty=True,
InnerGoniometer=True)
g = Goniometer()
g.setR(peaks.getPeak(0).getGoniometerMatrix())
YZY = g.getEulerAngles('YZY')
self.assertAlmostEqual(YZY[0], -42, delta=1e-10) # omega
self.assertAlmostEqual(YZY[1], 3, delta=1e-10) # chi
self.assertAlmostEqual(YZY[2], -23, delta=1e-1) # phi
self.assertAlmostEqual(peaks.getPeak(0).getWavelength(),
1.54,
delta=1e-10)
def PyExec(self):
peaks = self.getProperty('Workspace').value
wavelength = self.getProperty("Wavelength").value
if wavelength == Property.EMPTY_DBL:
wavelength = float(peaks.run()['wavelength'].value)
if self.getProperty("OverrideProperty").value:
flip_x = self.getProperty("FlipX").value
inner = self.getProperty("InnerGoniometer").value
else:
flip_x = peaks.getInstrument().getName() == "HB3A"
if peaks.getInstrument().getName() == "HB3A":
inner = math.isclose(peaks.run().getTimeAveragedStd("omega"),
0.0)
else:
inner = False
starting_goniometer = peaks.run().getGoniometer().getR()
for n in range(peaks.getNumberPeaks()):
p = peaks.getPeak(n)
g = Goniometer()
g.setR(starting_goniometer)
g.calcFromQSampleAndWavelength(V3D(*p.getQSampleFrame()),
wavelength, flip_x, inner)
self.log().information(
"Found goniometer omega={:.2f} chi={:.2f} phi={:.2f} for peak {} with Q_sample {}"
.format(*g.getEulerAngles('YZY'), n, p.getQSampleFrame()))
p.setWavelength(wavelength)
p.setGoniometerMatrix(g.getR())
def test_HFIRCalculateGoniometer_HB2C_omega(self):
omega = np.deg2rad(42)
R = np.array([[np.cos(omega), 0, np.sin(omega)], [0, 1, 0],
[-np.sin(omega), 0, np.cos(omega)]])
wl = 1.54
k = 2 * np.pi / wl
theta = np.deg2rad(47)
phi = np.deg2rad(13)
q_lab = np.array([
-np.sin(theta) * np.cos(phi), -np.sin(theta) * np.sin(phi),
1 - np.cos(theta)
]) * k
q_sample = np.dot(np.linalg.inv(R), q_lab)
peaks = CreatePeaksWorkspace(OutputType="LeanElasticPeak",
NumberOfPeaks=0)
p = peaks.createPeakQSample(q_sample)
peaks.addPeak(p)
HFIRCalculateGoniometer(peaks, wl)
g = Goniometer()
g.setR(peaks.getPeak(0).getGoniometerMatrix())
YZY = g.getEulerAngles('YZY')
self.assertAlmostEqual(YZY[0], 42, delta=1e-10) # omega
self.assertAlmostEqual(YZY[1], 0, delta=1e-10) # chi
self.assertAlmostEqual(YZY[2], 0, delta=1e-10) # phi
self.assertAlmostEqual(peaks.getPeak(0).getWavelength(),
1.54,
delta=1e-10)
InputWorkspace='ConvertHFIRSCDtoMDETest_data', Wavelength=1.488)
ConvertHFIRSCDtoMDETest_peaks = FindPeaksMD(
InputWorkspace=ConvertHFIRSCDtoMDETest_Q,
PeakDistanceThreshold=2.2,
CalculateGoniometerForCW=True,
Wavelength=1.488)
ConvertHFIRSCDtoMDETest_leanpeaks = FindPeaksMD(
InputWorkspace=ConvertHFIRSCDtoMDETest_Q,
PeakDistanceThreshold=2.2,
OutputType='LeanElasticPeak')
LoadMD('./ExternalData/Testing/Data/SystemTest/HB2C_WANDSCD_norm.nxs',
OutputWorkspace='ConvertWANDSCDtoQTest_norm')
ConvertWANDSCDtoQTest_Q = ConvertWANDSCDtoQ(
InputWorkspace='ConvertHFIRSCDtoMDETest_data',
NormalisationWorkspace='ConvertWANDSCDtoQTest_norm')
ConvertWANDSCDtoQTest_peaks = FindPeaksMD(
InputWorkspace=ConvertWANDSCDtoQTest_Q,
PeakDistanceThreshold=2,
CalculateGoniometerForCW=True,
Wavelength=1.488)
from mantid.geometry import Goniometer
wavelength = 1.488
for n in range(ConvertHFIRSCDtoMDETest_leanpeaks.getNumberPeaks()):
p = ConvertHFIRSCDtoMDETest_leanpeaks.getPeak(n)
g = Goniometer()
g.calcFromQSampleAndWavelength(p.getQSampleFrame(), wavelength)
p.setWavelength(wavelength)
p.setGoniometerMatrix(g.getR())
print(g.getEulerAngles('YZY'))
q_lab = np.array([
-np.sin(theta) * np.cos(phi), -np.sin(theta) * np.sin(phi),
1 - np.cos(theta)
]) * k
q_sample = np.dot(np.linalg.inv(R), q_lab)
peaks = CreatePeaksWorkspace(OutputType="LeanElasticPeak", NumberOfPeaks=0)
p = peaks.createPeakQSample(q_sample)
peaks.addPeak(p)
HFIRCalculateGoniometer(peaks, wl, OverrideProperty=True, InnerGoniometer=True)
g = Goniometer()
g.setR(peaks.getPeak(0).getGoniometerMatrix())
print(g.getEulerAngles('YZY'))
assert np.isclose(g.getEulerAngles('YZY')[0], 42)
chi = np.deg2rad(-3)
phi = np.deg2rad(23)
R1 = np.array([
[np.cos(omega), 0, -np.sin(omega)], # omega 0,1,0,-1
[0, 1, 0],
[np.sin(omega), 0, np.cos(omega)]
])
R2 = np.array([
[np.cos(chi), np.sin(chi), 0], # chi 0,0,1,-1
[-np.sin(chi), np.cos(chi), 0],
HFIRCalculateGoniometer(filter_int_peaks2)
leanelasticpeaks3 = PredictPeaks("data",
ReflectionCondition='B-face centred',
OutputType='LeanElasticPeak')
ws = CreatePeaksWorkspace()
SetUB(ws, a=2, b=2, c=2)
p = PredictPeaks(ws, OutputType='LeanElasticPeak', CalculateWavelength=False)
peaks = leanelasticpeaks3
wavelength = peaks.run()['wavelength'].value
flip_x = peaks.getInstrument().getName() == "HB3A"
if peaks.getInstrument().getName() == "HB3A":
inner = math.isclose(peaks.run().getTimeAveragedStd("omega"), 0.0)
else:
inner = False
for n in range(peaks.getNumberPeaks()):
p = peaks.getPeak(n)
g = Goniometer()
g.calcFromQSampleAndWavelength(V3D(*p.getQSampleFrame()), wavelength,
flip_x, inner)
p.setWavelength(wavelength)
p.setGoniometerMatrix(g.getR())
print(g.getEulerAngles('YZY'))
def test_setR_getR(self):
g = Goniometer()
r = np.array([(1., 0., 0.), (0., 0., 1.), (0., -1., 0.)])
g.setR(r)
self.assertTrue((g.getR() == r).all())
def test_getEulerAngles(self):
g = Goniometer()
self.assertEquals(g.getEulerAngles()[0], 0)
self.assertEquals(g.getEulerAngles()[1], 0)
self.assertEquals(g.getEulerAngles()[2], 0)
def runTest(self):
HB3AAdjustSampleNorm(Filename="HB3A_exp0724_scan0183.nxs",
OutputWorkspace='data')
peaks = PredictPeaks("data",
ReflectionCondition='B-face centred',
CalculateGoniometerForCW=True,
Wavelength=1.008,
InnerGoniometer=True,
FlipX=True,
MinAngle=-2,
MaxAngle=90)
self.assertEqual(peaks.getNumberPeaks(), 57)
peak0 = peaks.getPeak(0)
self.assertDelta(peak0.getWavelength(), 1.008, 1e-5)
self.assertEqual(peak0.getH(), 0)
self.assertEqual(peak0.getK(), 0)
self.assertEqual(peak0.getL(), -14)
q_sample = peak0.getQSampleFrame()
self.assertDelta(q_sample[0], 4.45402, 1e-5)
self.assertDelta(q_sample[1], -0.419157, 1e-5)
self.assertDelta(q_sample[2], 0.0906594, 1e-5)
# test predicting with LeanElasticPeak, filter any peak with 0 intensity
PredictPeaks("data",
ReflectionCondition='B-face centred',
OutputType='LeanElasticPeak',
CalculateWavelength=False,
OutputWorkspace="leanelasticpeaks")
IntegratePeaksMD("data",
"leanelasticpeaks",
PeakRadius=0.1,
OutputWorkspace="integrated_peaks")
filtered_peaks = FilterPeaks("integrated_peaks",
FilterVariable='Intensity',
FilterValue=0,
Operator='>')
self.assertEqual(filtered_peaks.getNumberPeaks(), 66)
peak0 = filtered_peaks.getPeak(0)
self.assertDelta(peak0.getWavelength(), 0, 1e-5)
self.assertEqual(peak0.getH(), 0)
self.assertEqual(peak0.getK(), 0)
self.assertEqual(peak0.getL(), -14)
q_sample = peak0.getQSampleFrame()
self.assertDelta(q_sample[0], 4.45541, 1e-5)
self.assertDelta(q_sample[1], -0.420383, 1e-5)
self.assertDelta(q_sample[2], 0.0913072, 1e-5)
g = Goniometer()
g.setR(peak0.getGoniometerMatrix())
YZY = g.getEulerAngles('YZY')
self.assertDelta(YZY[0], 0, 1e-7)
self.assertDelta(YZY[1], 0, 1e-7)
self.assertDelta(YZY[2], 0, 1e-7)
self.assertDelta(peak0.getWavelength(), 0, 1e-9)
HFIRCalculateGoniometer(filtered_peaks)
peak0 = filtered_peaks.getPeak(0)
g = Goniometer()
g.setR(peak0.getGoniometerMatrix())
YZY = g.getEulerAngles('YZY')
self.assertDelta(YZY[0], -20.4997, 1e-7)
self.assertDelta(YZY[1], 0.0003, 1e-7)
self.assertDelta(YZY[2], 0.5340761720854811, 1e-7)
self.assertDelta(peak0.getWavelength(), 1.008, 1e-9)
def test_setR_getR(self):
g = Goniometer()
r = np.array([(1., 0., 0.), (0., 0., 1.), (0., -1., 0.)])
g.setR(r)
self.assertTrue((g.getR() == r).all())
def test_getEulerAngles(self):
g = Goniometer()
self.assertEqual(g.getEulerAngles()[0], 0)
self.assertEqual(g.getEulerAngles()[1], 0)
self.assertEqual(g.getEulerAngles()[2], 0)
