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 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}")
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',
