def PyExec(self):
self._setup()
if not self.getProperty("InputWorkspace").isDefault:
self._output_ws = CloneWorkspace(Inputworkspace=self._input_ws,
OutputWorkspace=self._output_ws,
StoreInADS=False)
else:
self._output_ws = CreateWorkspace(NSpec=1, DataX=[0], DataY=[0],
UnitX='Wavelength', Distribution=False,
StoreInADS=False)
self._output_ws = Rebin(InputWorkspace=self._output_ws,
Params=self._bin_params,
StoreInADS=False)
if self._output_ws.isDistribution():
ConvertFromDistribution(Workspace=self._output_ws,
StoreInADS=False)
self._output_ws = ConvertToPointData(InputWorkspace=self._output_ws,
StoreInADS=False)
self._output_ws = ConvertUnits(InputWorkspace=self._output_ws,
Target='Wavelength',
EMode='Elastic',
StoreInADS=False)
if self.getProperty('Alpha').isDefault:
if self._density_type == 'Mass Density':
SetSampleMaterial(
InputWorkspace=self._output_ws,
ChemicalFormula=self._chemical_formula,
SampleMassDensity=self._density,
StoreInADS=False)
self._density = self._output_ws.sample().getMaterial().numberDensityEffective
elif self._density_type == 'Number Density':
SetSampleMaterial(
InputWorkspace=self._output_ws,
ChemicalFormula=self._chemical_formula,
SampleNumberDensity=self._density,
StoreInADS=False)
else:
raise RuntimeError(f'Unknown "DensityType": {self._density_type}')
if self.getProperty('MeasuredEfficiency').isDefault:
self._calculate_area_density_from_density()
else:
self._calculate_area_density_from_efficiency()
self._calculate_alpha_absXS_term()
if self._xsection_type == "TotalXSection":
self._calculate_alpha_scatXS_term()
wavelengths = self._output_ws.readX(0)
efficiency = self._calculate_efficiency(wavelengths)
for histo in range(self._output_ws.getNumberHistograms()):
self._output_ws.setY(histo, efficiency)
self.setProperty('OutputWorkspace', self._output_ws)
def test_simple(self):
input_x = np.array([0.1, 0.2, 0.3, 0.4, 0.5])
input_y = np.array([1., 2, 3, 2, 1])
input_e = np.array([0.1, 0.14, 0.17, 0.14, 0.1])
sq = CreateWorkspace(DataX=input_x,
DataY=input_y,
DataE=input_e,
UnitX='MomentumTransfer')
SetSampleMaterial(InputWorkspace=sq, ChemicalFormula='Ar')
fq = PDConvertReciprocalSpace(InputWorkspace=sq,
To='F(Q)',
From='S(Q)')
x = fq.readX(0)
y = fq.readY(0)
e = fq.readE(0)
self.assertTrue(np.array_equal(x, input_x))
self.assertTrue(np.array_equal(y, input_x * (input_y - 1)))
self.assertTrue(np.array_equal(e, input_x * input_e))
fkq = PDConvertReciprocalSpace(InputWorkspace=sq,
To='FK(Q)',
From='S(Q)')
x = fkq.readX(0)
y = fkq.readY(0)
e = fkq.readE(0)
bsq = sq.sample().getMaterial().cohScatterLengthSqrd()
self.assertTrue(np.array_equal(x, input_x))
self.assertTrue(np.allclose(y, bsq * (input_y - 1)))
self.assertTrue(np.allclose(e, bsq * input_e))
def runTest(self):
# load data for bank 1 (incl. monitor spectra 1-5)
van = load_data_and_normalise('WISH/input/11_4/WISH00019612.raw',
outputWorkspace="van")
# create Abs Correction for V
shape = '''<sphere id="V-sphere">
<centre x="0.0" y="0.0" z="0.0" />
<radius val="0.0025"/>
</sphere>'''
CreateSampleShape(InputWorkspace=van, ShapeXML=shape)
SetSampleMaterial(InputWorkspace=van,
SampleNumberDensity=0.0119,
ScatteringXSection=5.197,
AttenuationXSection=4.739,
ChemicalFormula='V0.95 Nb0.05')
abs_cor = AbsorptionCorrection(InputWorkspace=van, ElementSize=0.5)
# correct Vanadium run for absorption
van = Divide(LHSWorkspace=van,
RHSWorkspace=abs_cor,
OutputWorkspace=van)
# smooth data
SmoothNeighbours(InputWorkspace=van,
OutputWorkspace=van,
Radius=3,
NumberOfNeighbours=6)
SmoothData(InputWorkspace=van, OutputWorkspace=van, NPoints=300)
def test_material(self):
ws = CreateWorkspace(DataX=[1], DataY=[1], StoreInADS=False)
sample = ws.sample()
SetSampleMaterial(ws, "Al2 O3", SampleMassDensity=4, StoreInADS=False)
material = sample.getMaterial()
self.assertAlmostEqual(material.numberDensity, 0.1181, places=4)
self.assertAlmostEqual(material.relativeMolecularMass(),
101.961,
places=3)
atoms, numatoms = material.chemicalFormula()
self.assertEqual(len(atoms), len(numatoms))
self.assertEqual(len(atoms), 2)
self.assertEqual(numatoms[0], 2)
self.assertEqual(numatoms[1], 3)
xs0 = atoms[0].neutron()
xs1 = atoms[1].neutron()
# the correct way to calculate for coherent cross section
# is to average the scattering lengths then convert to a cross section
b_real = (xs0['coh_scatt_length_real'] * 2 +
xs1['coh_scatt_length_real'] * 3) / 5
b_imag = (xs0['coh_scatt_length_img'] * 2 +
xs1['coh_scatt_length_img'] * 3) / 5
xs = .04 * pi * (b_real * b_real + b_imag * b_imag)
self.assertAlmostEquals(material.cohScatterXSection(), xs, places=4)
def test_computeincoherentdos(self):
ws = CreateSampleWorkspace()
# Will fail unless the input workspace has Q and DeltaE axes.
with self.assertRaises(RuntimeError):
ws_DOS = ComputeIncoherentDOS(ws)
ws = CreateSampleWorkspace(XUnit = 'DeltaE')
with self.assertRaises(RuntimeError):
ws_DOS = ComputeIncoherentDOS(ws)
# Creates a workspace with two optic phonon modes at +E and -E with Q^2 dependence and population correct for T=300K
ws = self.createPhononWS(300, 5, 'DeltaE')
# This should work!
ws_DOS = ComputeIncoherentDOS(ws)
self.assertEqual(ws_DOS.getAxis(0).getUnit().unitID(), 'DeltaE')
self.assertEqual(ws_DOS.getNumberHistograms(), 1)
# Checks that it works if the workspace has |Q| along x instead of y, and converts energy to wavenumber
ws = Transpose(ws)
ws_DOS = ComputeIncoherentDOS(ws, Temperature = 300, EnergyBinning = '-20, 0.2, 20', Wavenumbers = True)
self.assertEqual(ws_DOS.getAxis(0).getUnit().unitID(), 'DeltaE_inWavenumber')
self.assertEqual(ws_DOS.blocksize(), 200)
# Checks that the Bose factor correction is ok.
dos_eplus = np.max(ws_DOS.readY(0)[100:200])
dos_eminus = np.max(ws_DOS.readY(0)[:100])
self.assertAlmostEqual(dos_eplus / dos_eminus, 1., places=1)
# Check that unit conversion from cm^-1 to meV works and also that conversion to states/meV is done
ws = self.convertToWavenumber(ws)
SetSampleMaterial(ws, 'Al')
ws_DOSn = ComputeIncoherentDOS(ws, EnergyBinning = '-160, 1.6, 160', StatesPerEnergy = True)
self.assertTrue('states' in ws_DOSn.YUnitLabel())
self.assertEqual(ws_DOSn.getAxis(0).getUnit().unitID(), 'DeltaE')
material = ws.sample().getMaterial()
factor = material.relativeMolecularMass() / (material.totalScatterXSection() * 1000) * 4 * np.pi
self.assertAlmostEqual(np.max(ws_DOSn.readY(0)) / (np.max(ws_DOS.readY(0))*factor), 1., places=1)
def test_simple(self):
input_x = np.array([0.1, 0.2, 0.3, 0.4, 0.5])
input_y = np.array([1., 2, 3, 2, 1])
input_e = np.array([0.1, 0.14, 0.17, 0.14, 0.1])
Gr = CreateWorkspace(DataX=input_x, DataY=input_y, DataE=input_e)
SetSampleMaterial(InputWorkspace=Gr, ChemicalFormula='Ar')
GKr = PDConvertRealSpace(InputWorkspace=Gr, To='GK(r)', From='G(r)')
x = GKr.readX(0)
y = GKr.readY(0)
e = GKr.readE(0)
bsq = Gr.sample().getMaterial().cohScatterLengthSqrd()
rho = Gr.sample().getMaterial().numberDensity
factor = bsq / (4. * np.pi * rho)
self.assertTrue(np.array_equal(x, input_x))
self.assertTrue(np.allclose(y, factor * input_y / input_x))
self.assertTrue(np.allclose(e, factor * input_e / input_x))
def test_material(self):
SetSampleMaterial(self._ws,"Al2 O3",SampleMassDensity=4)
material = self._ws.sample().getMaterial()
self.assertAlmostEqual(material.numberDensity, 0.1181, places=4)
self.assertAlmostEqual(material.relativeMolecularMass(), 101.961, places=3)
atoms, numatoms = material.chemicalFormula()
self.assertEquals(len(atoms), len(numatoms))
self.assertEquals(len(atoms), 2)
self.assertEquals(numatoms[0], 2)
self.assertEquals(numatoms[1], 3)
xs0 = atoms[0].neutron()
xs1 = atoms[1].neutron()
xs = ( xs0['coh_scatt_xs']*2 + xs1['coh_scatt_xs']*3 ) / 5
self.assertAlmostEquals(material.cohScatterXSection(), xs, places=4)
def test_material_already_defined(self):
SetSampleMaterial(InputWorkspace=self._red_ws,
ChemicalFormula='H2-O',
SampleMassDensity=1.0)
corrected = SimpleShapeMonteCarloAbsorption(
InputWorkspace=self._red_ws,
MaterialAlreadyDefined=True,
EventsPerPoint=200,
BeamHeight=3.5,
BeamWidth=4.0,
Height=2.0,
Shape='FlatPlate',
Width=2.0,
Thickness=2.0)
self._test_corrections_workspace(corrected)
CompareWorkspaces(self._corrected_flat_plate,
corrected,
Tolerance=1e-6)
def setUp(self):
# Create a workspace and change the sample material to non-trivial values.
workspace_name = "testWS"
CreateSampleWorkspace(OutputWorkspace=workspace_name)
self.ws = AnalysisDataService.retrieve(workspace_name)
self.formula = "C"
self.number_density = 3.4e21
self.absorption_xs = 3.5
self.scattering_xs = 6.7
self.coherent_xs = 3.2
self.incoherent_xs = 3.4
SetSampleMaterial(InputWorkspace=self.ws,
ChemicalFormula=self.formula,
SampleNumberDensity=self.number_density,
AttenuationXSection=self.absorption_xs,
ScatteringXSection=self.scattering_xs,
CoherentXSection=self.coherent_xs,
IncoherentXSection=self.incoherent_xs)
self.presenter = SampleMaterialDialogPresenter(self.ws)
incident_ws = 'incident_ws'
GetIncidentSpectrumFromMonitor(runs[0], OutputWorkspace=incident_ws)
# Fit incident spectrum
incident_fit = 'incident_fit'
fit_type = opts['FitSpectrumWith']
FitIncidentSpectrum(InputWorkspace=incident_ws,
OutputWorkspace=incident_fit,
FitSpectrumWith=fit_type,
BinningForFit=opts['LambdaBinningForFit'],
BinningForCalc=opts['LambdaBinningForCalc'],
PlotDiagnostics=opts['PlotFittingDiagnostics'])
# Set sample info
SetSampleMaterial(incident_fit, ChemicalFormula=str(sample['Material']))
CalculateElasticSelfScattering(InputWorkspace=incident_fit)
atom_species = GetSampleSpeciesInfo(incident_fit)
# Parameters for NOMAD detectors by bank
L1 = 19.5
banks = collections.OrderedDict()
banks[0] = {'L2': 2.01, 'theta': 15.10}
banks[1] = {'L2': 1.68, 'theta': 31.00}
banks[2] = {'L2': 1.14, 'theta': 65.00}
banks[3] = {'L2': 1.11, 'theta': 120.40}
banks[4] = {'L2': 0.79, 'theta': 150.10}
banks[5] = {'L2': 2.06, 'theta': 8.60}
L2 = [x['L2'] for bank, x in banks.iteritems()]
Polar = [x['theta'] for bank, x in banks.iteritems()]
