def TotalScatteringReduction(config=None):
facility = config['Facility']
title = config['Title']
instr = config['Instrument']
# Get sample info
sample = config['Sample']
sam_mass_density = sample.get('MassDensity', None)
sam_packing_fraction = sample.get('PackingFraction', None)
sam_geometry = sample.get('Geometry', None)
sam_material = sample.get('Material', None)
# Get normalization info
van = config['Normalization']
van_mass_density = van.get('MassDensity', None)
van_packing_fraction = van.get('PackingFraction', 1.0)
van_geometry = van.get('Geometry', None)
van_material = van.get('Material', 'V')
# Get calibration, characterization, and other settings
merging = config['Merging']
binning = merging['QBinning']
# Grouping
grouping = merging.get('Grouping', None)
cache_dir = config.get("CacheDir", os.path.abspath('.'))
OutputDir = config.get("OutputDir", os.path.abspath('.'))
# Create Nexus file basenames
sample['Runs'] = expand_ints(sample['Runs'])
sample['Background']['Runs'] = expand_ints(sample['Background'].get(
'Runs', None))
'''
Currently not implemented:
# wkspIndices = merging.get('SumBanks', None)
# high_q_linear_fit_range = config['HighQLinearFitRange']
POWGEN options not used
#alignAndFocusArgs['RemovePromptPulseWidth'] = 50
# alignAndFocusArgs['CompressTolerance'] use defaults
# alignAndFocusArgs['UnwrapRef'] POWGEN option
# alignAndFocusArgs['LowResRef'] POWGEN option
# alignAndFocusArgs['LowResSpectrumOffset'] POWGEN option
How much of each bank gets merged has info here in the form of
# {"ID", "Qmin", "QMax"}
# alignAndFocusArgs['CropWavelengthMin'] from characterizations file
# alignAndFocusArgs['CropWavelengthMax'] from characterizations file
'''
if facility == 'SNS':
facility_file_format = '%s_%d'
else:
facility_file_format = '%s%d'
sam_scans = ','.join(
[facility_file_format % (instr, num) for num in sample['Runs']])
container_scans = ','.join([
facility_file_format % (instr, num)
for num in sample['Background']["Runs"]
])
container_bg = None
if "Background" in sample['Background']:
sample['Background']['Background']['Runs'] = expand_ints(
sample['Background']['Background']['Runs'])
container_bg = ','.join([
facility_file_format % (instr, num)
for num in sample['Background']['Background']['Runs']
])
if len(container_bg) == 0:
container_bg = None
van['Runs'] = expand_ints(van['Runs'])
van_scans = ','.join(
[facility_file_format % (instr, num) for num in van['Runs']])
van_bg_scans = None
if 'Background' in van:
van_bg_scans = van['Background']['Runs']
van_bg_scans = expand_ints(van_bg_scans)
van_bg_scans = ','.join(
[facility_file_format % (instr, num) for num in van_bg_scans])
# Override Nexus file basename with Filenames if present
if "Filenames" in sample:
sam_scans = ','.join(sample["Filenames"])
if "Filenames" in sample['Background']:
container_scans = ','.join(sample['Background']["Filenames"])
if "Background" in sample['Background']:
if "Filenames" in sample['Background']['Background']:
container_bg = ','.join(
sample['Background']['Background']['Filenames'])
if "Filenames" in van:
van_scans = ','.join(van["Filenames"])
if "Background" in van:
if "Filenames" in van['Background']:
van_bg_scans = ','.join(van['Background']["Filenames"])
# Output nexus filename
nexus_filename = title + '.nxs'
try:
os.remove(nexus_filename)
except OSError:
pass
# Get sample corrections
sam_abs_corr = sample.get("AbsorptionCorrection", None)
sam_ms_corr = sample.get("MultipleScatteringCorrection", None)
sam_inelastic_corr = SetInelasticCorrection(
sample.get('InelasticCorrection', None))
# Get vanadium corrections
van_mass_density = van.get('MassDensity', van_mass_density)
van_packing_fraction = van.get('PackingFraction', van_packing_fraction)
van_abs_corr = van.get("AbsorptionCorrection", {"Type": None})
van_ms_corr = van.get("MultipleScatteringCorrection", {"Type": None})
van_inelastic_corr = SetInelasticCorrection(
van.get('InelasticCorrection', None))
alignAndFocusArgs = dict()
alignAndFocusArgs['CalFilename'] = config['Calibration']['Filename']
# alignAndFocusArgs['GroupFilename'] don't use
# alignAndFocusArgs['Params'] = "0.,0.02,40."
alignAndFocusArgs['ResampleX'] = -6000
alignAndFocusArgs['Dspacing'] = False
alignAndFocusArgs['PreserveEvents'] = False
alignAndFocusArgs['MaxChunkSize'] = 8
alignAndFocusArgs['CacheDir'] = os.path.abspath(cache_dir)
# Get any additional AlignAndFocusArgs from JSON input
if "AlignAndFocusArgs" in config:
otherArgs = config["AlignAndFocusArgs"]
alignAndFocusArgs.update(otherArgs)
print(alignAndFocusArgs)
# Setup grouping
output_grouping = False
grp_wksp = "wksp_output_group"
if grouping:
if 'Initial' in grouping:
if grouping['Initial'] and not grouping['Initial'] == u'':
alignAndFocusArgs['GroupFilename'] = grouping['Initial']
if 'Output' in grouping:
if grouping['Output'] and not grouping['Output'] == u'':
output_grouping = True
LoadDetectorsGroupingFile(InputFile=grouping['Output'],
OutputWorkspace=grp_wksp)
# If no output grouping specified, create it with Calibration Grouping
if not output_grouping:
LoadDiffCal(alignAndFocusArgs['CalFilename'],
InstrumentName=instr,
WorkspaceName=grp_wksp.replace('_group', ''),
MakeGroupingWorkspace=True,
MakeCalWorkspace=False,
MakeMaskWorkspace=False)
# Setup the 6 bank method if no grouping specified
if not grouping:
CreateGroupingWorkspace(InstrumentName=instr,
GroupDetectorsBy='Group',
OutputWorkspace=grp_wksp)
alignAndFocusArgs['GroupingWorkspace'] = grp_wksp
# TODO take out the RecalculatePCharge in the future once tested
# Load Sample
print("#-----------------------------------#")
print("# Sample")
print("#-----------------------------------#")
sam_wksp = load('sample', sam_scans, sam_geometry, sam_material,
sam_mass_density, **alignAndFocusArgs)
sample_title = "sample_and_container"
print(os.path.join(OutputDir, sample_title + ".dat"))
print("HERE:", mtd[sam_wksp].getNumberHistograms())
print(grp_wksp)
save_banks(InputWorkspace=sam_wksp,
Filename=nexus_filename,
Title=sample_title,
OutputDir=OutputDir,
GroupingWorkspace=grp_wksp,
Binning=binning)
sam_molecular_mass = mtd[sam_wksp].sample().getMaterial(
).relativeMolecularMass()
natoms = getNumberAtoms(sam_packing_fraction,
sam_mass_density,
sam_molecular_mass,
Geometry=sam_geometry)
# Load Sample Container
print("#-----------------------------------#")
print("# Sample Container")
print("#-----------------------------------#")
container = load('container', container_scans, **alignAndFocusArgs)
save_banks(InputWorkspace=container,
Filename=nexus_filename,
Title=container,
OutputDir=OutputDir,
GroupingWorkspace=grp_wksp,
Binning=binning)
# Load Sample Container Background
if container_bg is not None:
print("#-----------------------------------#")
print("# Sample Container's Background")
print("#-----------------------------------#")
container_bg = load('container_background', container_bg,
**alignAndFocusArgs)
save_banks(InputWorkspace=container_bg,
Filename=nexus_filename,
Title=container_bg,
OutputDir=OutputDir,
GroupingWorkspace=grp_wksp,
Binning=binning)
# Load Vanadium
print("#-----------------------------------#")
print("# Vanadium")
print("#-----------------------------------#")
van_wksp = load('vanadium', van_scans, van_geometry, van_material,
van_mass_density, **alignAndFocusArgs)
vanadium_title = "vanadium_and_background"
save_banks(InputWorkspace=van_wksp,
Filename=nexus_filename,
Title=vanadium_title,
OutputDir=OutputDir,
GroupingWorkspace=grp_wksp,
Binning=binning)
van_molecular_mass = mtd[van_wksp].sample().getMaterial(
).relativeMolecularMass()
nvan_atoms = getNumberAtoms(1.0,
van_mass_density,
van_molecular_mass,
Geometry=van_geometry)
print("Sample natoms:", natoms)
print("Vanadium natoms:", nvan_atoms)
print("Vanadium natoms / Sample natoms:", nvan_atoms / natoms)
# Load Vanadium Background
van_bg = None
if van_bg_scans is not None:
print("#-----------------------------------#")
print("# Vanadium Background")
print("#-----------------------------------#")
van_bg = load('vanadium_background', van_bg_scans, **alignAndFocusArgs)
vanadium_bg_title = "vanadium_background"
save_banks(InputWorkspace=van_bg,
Filename=nexus_filename,
Title=vanadium_bg_title,
OutputDir=OutputDir,
GroupingWorkspace=grp_wksp,
Binning=binning)
# Load Instrument Characterizations
if "Characterizations" in merging:
PDDetermineCharacterizations(
InputWorkspace=sam_wksp,
Characterizations='characterizations',
ReductionProperties='__snspowderreduction')
propMan = PropertyManagerDataService.retrieve('__snspowderreduction')
qmax = 2. * np.pi / propMan['d_min'].value
qmin = 2. * np.pi / propMan['d_max'].value
for a, b in zip(qmin, qmax):
print('Qrange:', a, b)
# TODO: Add when we apply Qmin, Qmax cropping
# mask_info = generateCropingTable(qmin, qmax)
# STEP 1: Subtract Backgrounds
sam_raw = 'sam_raw'
CloneWorkspace(InputWorkspace=sam_wksp,
OutputWorkspace=sam_raw) # for later
container_raw = 'container_raw'
CloneWorkspace(InputWorkspace=container,
OutputWorkspace=container_raw) # for later
if van_bg is not None:
Minus(LHSWorkspace=van_wksp,
RHSWorkspace=van_bg,
OutputWorkspace=van_wksp)
Minus(LHSWorkspace=sam_wksp,
RHSWorkspace=container,
OutputWorkspace=sam_wksp)
if container_bg is not None:
Minus(LHSWorkspace=container,
RHSWorkspace=container_bg,
OutputWorkspace=container)
for wksp in [container, van_wksp, sam_wksp]:
ConvertUnits(InputWorkspace=wksp,
OutputWorkspace=wksp,
Target="MomentumTransfer",
EMode="Elastic")
container_title = "container_minus_back"
vanadium_title = "vanadium_minus_back"
sample_title = "sample_minus_back"
save_banks(InputWorkspace=container,
Filename=nexus_filename,
Title=container_title,
OutputDir=OutputDir,
GroupingWorkspace=grp_wksp,
Binning=binning)
save_banks(InputWorkspace=van_wksp,
Filename=nexus_filename,
Title=vanadium_title,
OutputDir=OutputDir,
GroupingWorkspace=grp_wksp,
Binning=binning)
save_banks(InputWorkspace=sam_wksp,
Filename=nexus_filename,
Title=sample_title,
OutputDir=OutputDir,
GroupingWorkspace=grp_wksp,
Binning=binning)
# STEP 2.0: Prepare vanadium as normalization calibrant
# Multiple-Scattering and Absorption (Steps 2-4) for Vanadium
van_corrected = 'van_corrected'
ConvertUnits(InputWorkspace=van_wksp,
OutputWorkspace=van_corrected,
Target="Wavelength",
EMode="Elastic")
if "Type" in van_abs_corr:
if van_abs_corr['Type'] == 'Carpenter' \
or van_ms_corr['Type'] == 'Carpenter':
CarpenterSampleCorrection(
InputWorkspace=van_corrected,
OutputWorkspace=van_corrected,
CylinderSampleRadius=van['Geometry']['Radius'])
elif van_abs_corr['Type'] == 'Mayers' \
or van_ms_corr['Type'] == 'Mayers':
if van_ms_corr['Type'] == 'Mayers':
MayersSampleCorrection(InputWorkspace=van_corrected,
OutputWorkspace=van_corrected,
MultipleScattering=True)
else:
MayersSampleCorrection(InputWorkspace=van_corrected,
OutputWorkspace=van_corrected,
MultipleScattering=False)
else:
print("NO VANADIUM absorption or multiple scattering!")
else:
CloneWorkspace(InputWorkspace=van_corrected,
OutputWorkspace=van_corrected)
ConvertUnits(InputWorkspace=van_corrected,
OutputWorkspace=van_corrected,
Target='MomentumTransfer',
EMode='Elastic')
vanadium_title += "_ms_abs_corrected"
save_banks(InputWorkspace=van_corrected,
Filename=nexus_filename,
Title=vanadium_title,
OutputDir=OutputDir,
GroupingWorkspace=grp_wksp,
Binning=binning)
save_banks(InputWorkspace=van_corrected,
Filename=nexus_filename,
Title=vanadium_title + "_with_peaks",
OutputDir=OutputDir,
GroupingWorkspace=grp_wksp,
Binning=binning)
# TODO subtract self-scattering of vanadium (According to Eq. 7 of Howe,
# McGreevey, and Howells, JPCM, 1989)
# Smooth Vanadium (strip peaks plus smooth)
ConvertUnits(InputWorkspace=van_corrected,
OutputWorkspace=van_corrected,
Target='dSpacing',
EMode='Elastic')
# After StripVanadiumPeaks, the workspace goes from EventWorkspace ->
# Workspace2D
StripVanadiumPeaks(InputWorkspace=van_corrected,
OutputWorkspace=van_corrected,
BackgroundType='Quadratic')
ConvertUnits(InputWorkspace=van_corrected,
OutputWorkspace=van_corrected,
Target='MomentumTransfer',
EMode='Elastic')
vanadium_title += '_peaks_stripped'
save_banks(InputWorkspace=van_corrected,
Filename=nexus_filename,
Title=vanadium_title,
OutputDir=OutputDir,
GroupingWorkspace=grp_wksp,
Binning=binning)
ConvertUnits(InputWorkspace=van_corrected,
OutputWorkspace=van_corrected,
Target='TOF',
EMode='Elastic')
FFTSmooth(InputWorkspace=van_corrected,
OutputWorkspace=van_corrected,
Filter="Butterworth",
Params='20,2',
IgnoreXBins=True,
AllSpectra=True)
ConvertUnits(InputWorkspace=van_corrected,
OutputWorkspace=van_corrected,
Target='MomentumTransfer',
EMode='Elastic')
vanadium_title += '_smoothed'
save_banks(InputWorkspace=van_corrected,
Filename=nexus_filename,
Title=vanadium_title,
OutputDir=OutputDir,
GroupingWorkspace=grp_wksp,
Binning=binning)
# Inelastic correction
if van_inelastic_corr['Type'] == "Placzek":
van_scan = van['Runs'][0]
van_incident_wksp = 'van_incident_wksp'
van_inelastic_opts = van['InelasticCorrection']
lambda_binning_fit = van_inelastic_opts['LambdaBinningForFit']
lambda_binning_calc = van_inelastic_opts['LambdaBinningForCalc']
print('van_scan:', van_scan)
GetIncidentSpectrumFromMonitor(Filename=facility_file_format %
(instr, van_scan),
OutputWorkspace=van_incident_wksp)
fit_type = van['InelasticCorrection']['FitSpectrumWith']
FitIncidentSpectrum(InputWorkspace=van_incident_wksp,
OutputWorkspace=van_incident_wksp,
FitSpectrumWith=fit_type,
BinningForFit=lambda_binning_fit,
BinningForCalc=lambda_binning_calc,
PlotDiagnostics=False)
van_placzek = 'van_placzek'
SetSample(InputWorkspace=van_incident_wksp,
Material={
'ChemicalFormula': str(van_material),
'SampleMassDensity': str(van_mass_density)
})
CalculatePlaczekSelfScattering(IncidentWorkspace=van_incident_wksp,
ParentWorkspace=van_corrected,
OutputWorkspace=van_placzek,
L1=19.5,
L2=alignAndFocusArgs['L2'],
Polar=alignAndFocusArgs['Polar'])
ConvertToHistogram(InputWorkspace=van_placzek,
OutputWorkspace=van_placzek)
# Save before rebin in Q
for wksp in [van_placzek, van_corrected]:
ConvertUnits(InputWorkspace=wksp,
OutputWorkspace=wksp,
Target='MomentumTransfer',
EMode='Elastic')
Rebin(InputWorkspace=wksp,
OutputWorkspace=wksp,
Params=binning,
PreserveEvents=True)
save_banks(InputWorkspace=van_placzek,
Filename=nexus_filename,
Title="vanadium_placzek",
OutputDir=OutputDir,
GroupingWorkspace=grp_wksp,
Binning=binning)
# Rebin in Wavelength
for wksp in [van_placzek, van_corrected]:
ConvertUnits(InputWorkspace=wksp,
OutputWorkspace=wksp,
Target='Wavelength',
EMode='Elastic')
Rebin(InputWorkspace=wksp,
OutputWorkspace=wksp,
Params=lambda_binning_calc,
PreserveEvents=True)
# Save after rebin in Q
for wksp in [van_placzek, van_corrected]:
ConvertUnits(InputWorkspace=wksp,
OutputWorkspace=wksp,
Target='MomentumTransfer',
EMode='Elastic')
# Subtract correction in Wavelength
for wksp in [van_placzek, van_corrected]:
ConvertUnits(InputWorkspace=wksp,
OutputWorkspace=wksp,
Target='Wavelength',
EMode='Elastic')
if not mtd[wksp].isDistribution():
ConvertToDistribution(wksp)
Minus(LHSWorkspace=van_corrected,
RHSWorkspace=van_placzek,
OutputWorkspace=van_corrected)
# Save after subtraction
for wksp in [van_placzek, van_corrected]:
ConvertUnits(InputWorkspace=wksp,
OutputWorkspace=wksp,
Target='MomentumTransfer',
EMode='Elastic')
vanadium_title += '_placzek_corrected'
save_banks(InputWorkspace=van_corrected,
Filename=nexus_filename,
Title=vanadium_title,
OutputDir=OutputDir,
GroupingWorkspace=grp_wksp,
Binning=binning)
ConvertUnits(InputWorkspace=van_corrected,
OutputWorkspace=van_corrected,
Target='MomentumTransfer',
EMode='Elastic')
SetUncertainties(InputWorkspace=van_corrected,
OutputWorkspace=van_corrected,
SetError='zero')
# STEP 2.1: Normalize by Vanadium
for name in [sam_wksp, van_corrected]:
ConvertUnits(InputWorkspace=name,
OutputWorkspace=name,
Target='MomentumTransfer',
EMode='Elastic',
ConvertFromPointData=False)
Rebin(InputWorkspace=name,
OutputWorkspace=name,
Params=binning,
PreserveEvents=True)
# if not mtd[name].isDistribution():
# ConvertToDistribution(name)
Divide(LHSWorkspace=sam_wksp,
RHSWorkspace=van_corrected,
OutputWorkspace=sam_wksp)
# Divide(
# LHSWorkspace=sam_raw,
# RHSWorkspace=van_corrected,
# OutputWorkspace=sam_raw)
sample_title += "_normalized"
save_banks(InputWorkspace=sam_wksp,
Filename=nexus_filename,
Title=sample_title,
OutputDir=OutputDir,
GroupingWorkspace=grp_wksp,
Binning=binning)
save_banks(InputWorkspace=sam_raw,
Filename=nexus_filename,
Title="sample_normalized",
OutputDir=OutputDir,
GroupingWorkspace=grp_wksp,
Binning=binning)
# Output an initial I(Q) for sample
iq_filename = title + '_initial_iofq_banks.nxs'
save_banks(InputWorkspace=sam_wksp,
Filename=iq_filename,
Title="IQ_banks",
OutputDir=OutputDir,
GroupingWorkspace=grp_wksp,
Binning=binning)
for name in [container, van_corrected]:
ConvertUnits(InputWorkspace=name,
OutputWorkspace=name,
Target='MomentumTransfer',
EMode='Elastic',
ConvertFromPointData=False)
Rebin(InputWorkspace=name,
OutputWorkspace=name,
Params=binning,
PreserveEvents=True)
# if not mtd[name].isDistribution():
# ConvertToDistribution(name)
print()
print("## Container ##")
print("YUnit:", mtd[container].YUnit(), "|", mtd[van_corrected].YUnit())
print("blocksize:", mtd[container].blocksize(),
mtd[van_corrected].blocksize())
print("dist:", mtd[container].isDistribution(),
mtd[van_corrected].isDistribution())
print("Do bins match?:", myMatchingBins(container, van_corrected))
print("Distributions?", mtd[container].isDistribution(),
mtd[van_corrected].isDistribution())
print()
Divide(LHSWorkspace=container,
RHSWorkspace=van_corrected,
OutputWorkspace=container)
# Divide(
# LHSWorkspace=container_raw,
# RHSWorkspace=van_corrected,
# OutputWorkspace=container_raw)
# if van_bg is not None:
# Divide(
# LHSWorkspace=van_bg,
# RHSWorkspace=van_corrected,
# OutputWorkspace=van_bg)
# if container_bg is not None:
# Divide(
# LHSWorkspace=container_bg,
# RHSWorkspace=van_corrected,
# OutputWorkspace=container_bg)
print()
print("## Container After Divide##")
print("YUnit:", mtd[container].YUnit(), "|", mtd[van_corrected].YUnit())
print("blocksize:", mtd[container].blocksize(),
mtd[van_corrected].blocksize())
print("dist:", mtd[container].isDistribution(),
mtd[van_corrected].isDistribution())
print("Do bins match?:", myMatchingBins(container, van_corrected))
print("Distributions?", mtd[container].isDistribution(),
mtd[van_corrected].isDistribution())
print()
container_title += '_normalized'
save_banks(InputWorkspace=container,
Filename=nexus_filename,
Title=container_title,
OutputDir=OutputDir,
GroupingWorkspace=grp_wksp,
Binning=binning)
save_banks(InputWorkspace=container_raw,
Filename=nexus_filename,
Title="container_normalized",
OutputDir=OutputDir,
GroupingWorkspace=grp_wksp,
Binning=binning)
# if container_bg is not None:
# container_bg_title += "_normalised"
# save_banks(InputWorkspace=container_bg,
# Filename=nexus_filename,
# Title=container_bg_title,
# OutputDir=OutputDir,
# GroupingWorkspace=grp_wksp,
# Binning=binning)
# if van_bg is not None:
# vanadium_bg_title += "_normalized"
# save_banks(InputWorkspace=van_bg,
# Filename=nexus_filename,
# Title=vanadium_bg_title,
# OutputDir=OutputDir,
# GroupingWorkspace=grp_wksp,
# Binning=binning)
# STEP 3 & 4: Subtract multiple scattering and apply absorption correction
ConvertUnits(InputWorkspace=sam_wksp,
OutputWorkspace=sam_wksp,
Target="Wavelength",
EMode="Elastic")
sam_corrected = 'sam_corrected'
if sam_abs_corr:
if sam_abs_corr['Type'] == 'Carpenter' \
or sam_ms_corr['Type'] == 'Carpenter':
CarpenterSampleCorrection(
InputWorkspace=sam_wksp,
OutputWorkspace=sam_corrected,
CylinderSampleRadius=sample['Geometry']['Radius'])
elif sam_abs_corr['Type'] == 'Mayers' \
or sam_ms_corr['Type'] == 'Mayers':
if sam_ms_corr['Type'] == 'Mayers':
MayersSampleCorrection(InputWorkspace=sam_wksp,
OutputWorkspace=sam_corrected,
MultipleScattering=True)
else:
MayersSampleCorrection(InputWorkspace=sam_wksp,
OutputWorkspace=sam_corrected,
MultipleScattering=False)
else:
print("NO SAMPLE absorption or multiple scattering!")
CloneWorkspace(InputWorkspace=sam_wksp,
OutputWorkspace=sam_corrected)
ConvertUnits(InputWorkspace=sam_corrected,
OutputWorkspace=sam_corrected,
Target='MomentumTransfer',
EMode='Elastic')
sample_title += "_ms_abs_corrected"
save_banks(InputWorkspace=sam_corrected,
Filename=nexus_filename,
Title=sample_title,
OutputDir=OutputDir,
GroupingWorkspace=grp_wksp,
Binning=binning)
else:
CloneWorkspace(InputWorkspace=sam_wksp, OutputWorkspace=sam_corrected)
# STEP 5: Divide by number of atoms in sample
mtd[sam_corrected] = (nvan_atoms / natoms) * mtd[sam_corrected]
ConvertUnits(InputWorkspace=sam_corrected,
OutputWorkspace=sam_corrected,
Target='MomentumTransfer',
EMode='Elastic')
sample_title += "_norm_by_atoms"
save_banks(InputWorkspace=sam_corrected,
Filename=nexus_filename,
Title=sample_title,
OutputDir=OutputDir,
GroupingWorkspace=grp_wksp,
Binning=binning)
# STEP 6: Divide by total scattering length squared = total scattering
# cross-section over 4 * pi
sigma_v = mtd[van_corrected].sample().getMaterial().totalScatterXSection()
prefactor = (sigma_v / (4. * np.pi))
print("Total scattering cross-section of Vanadium:", sigma_v,
" sigma_v / 4*pi:", prefactor)
mtd[sam_corrected] = prefactor * mtd[sam_corrected]
sample_title += '_multiply_by_vanSelfScat'
save_banks(InputWorkspace=sam_corrected,
Filename=nexus_filename,
Title=sample_title,
OutputDir=OutputDir,
GroupingWorkspace=grp_wksp,
Binning=binning)
# STEP 7: Inelastic correction
ConvertUnits(InputWorkspace=sam_corrected,
OutputWorkspace=sam_corrected,
Target='Wavelength',
EMode='Elastic')
if sam_inelastic_corr['Type'] == "Placzek":
if sam_material is None:
error = "For Placzek correction, must specifiy a sample material."
raise Exception(error)
for sam_scan in sample['Runs']:
sam_incident_wksp = 'sam_incident_wksp'
sam_inelastic_opts = sample['InelasticCorrection']
lambda_binning_fit = sam_inelastic_opts['LambdaBinningForFit']
lambda_binning_calc = sam_inelastic_opts['LambdaBinningForCalc']
GetIncidentSpectrumFromMonitor(Filename=facility_file_format %
(instr, sam_scan),
OutputWorkspace=sam_incident_wksp)
fit_type = sample['InelasticCorrection']['FitSpectrumWith']
FitIncidentSpectrum(InputWorkspace=sam_incident_wksp,
OutputWorkspace=sam_incident_wksp,
FitSpectrumWith=fit_type,
BinningForFit=lambda_binning_fit,
BinningForCalc=lambda_binning_calc)
sam_placzek = 'sam_placzek'
SetSample(InputWorkspace=sam_incident_wksp,
Material={
'ChemicalFormula': str(sam_material),
'SampleMassDensity': str(sam_mass_density)
})
CalculatePlaczekSelfScattering(IncidentWorkspace=sam_incident_wksp,
ParentWorkspace=sam_corrected,
OutputWorkspace=sam_placzek,
L1=19.5,
L2=alignAndFocusArgs['L2'],
Polar=alignAndFocusArgs['Polar'])
ConvertToHistogram(InputWorkspace=sam_placzek,
OutputWorkspace=sam_placzek)
# Save before rebin in Q
for wksp in [sam_placzek, sam_corrected]:
ConvertUnits(InputWorkspace=wksp,
OutputWorkspace=wksp,
Target='MomentumTransfer',
EMode='Elastic')
Rebin(InputWorkspace=wksp,
OutputWorkspace=wksp,
Params=binning,
PreserveEvents=True)
save_banks(InputWorkspace=sam_placzek,
Filename=nexus_filename,
Title="sample_placzek",
OutputDir=OutputDir,
GroupingWorkspace=grp_wksp,
Binning=binning)
# Save after rebin in Q
for wksp in [sam_placzek, sam_corrected]:
ConvertUnits(InputWorkspace=wksp,
OutputWorkspace=wksp,
Target='MomentumTransfer',
EMode='Elastic')
Minus(LHSWorkspace=sam_corrected,
RHSWorkspace=sam_placzek,
OutputWorkspace=sam_corrected)
# Save after subtraction
for wksp in [sam_placzek, sam_corrected]:
ConvertUnits(InputWorkspace=wksp,
OutputWorkspace=wksp,
Target='MomentumTransfer',
EMode='Elastic')
sample_title += '_placzek_corrected'
save_banks(InputWorkspace=sam_corrected,
Filename=nexus_filename,
Title=sample_title,
OutputDir=OutputDir,
GroupingWorkspace=grp_wksp,
Binning=binning)
# STEP 7: Output spectrum
# TODO Since we already went from Event -> 2D workspace, can't use this
# anymore
print('sam:', mtd[sam_corrected].id())
print('van:', mtd[van_corrected].id())
if alignAndFocusArgs['PreserveEvents']:
CompressEvents(InputWorkspace=sam_corrected,
OutputWorkspace=sam_corrected)
# F(Q) bank-by-bank Section
CloneWorkspace(InputWorkspace=sam_corrected, OutputWorkspace='FQ_banks_ws')
# TODO: Add the following when implemented - FQ_banks = 'FQ_banks'
# S(Q) bank-by-bank Section
material = mtd[sam_corrected].sample().getMaterial()
if material.name() is None or len(material.name().strip()) == 0:
raise RuntimeError('Sample material was not set')
bcoh_avg_sqrd = material.cohScatterLength() * material.cohScatterLength()
btot_sqrd_avg = material.totalScatterLengthSqrd()
laue_monotonic_diffuse_scat = btot_sqrd_avg / bcoh_avg_sqrd
CloneWorkspace(InputWorkspace=sam_corrected, OutputWorkspace='SQ_banks_ws')
# TODO: Add the following when implemented
'''
SQ_banks = (1. / bcoh_avg_sqrd) * \
mtd['SQ_banks_ws'] - laue_monotonic_diffuse_scat + 1.
'''
save_banks(InputWorkspace="FQ_banks_ws",
Filename=nexus_filename,
Title="FQ_banks",
OutputDir=OutputDir,
GroupingWorkspace=grp_wksp,
Binning=binning)
save_banks(InputWorkspace="SQ_banks_ws",
Filename=nexus_filename,
Title="SQ_banks",
OutputDir=OutputDir,
GroupingWorkspace=grp_wksp,
Binning=binning)
# Output a main S(Q) and F(Q) file
fq_filename = title + '_fofq_banks_corrected.nxs'
save_banks(InputWorkspace="FQ_banks_ws",
Filename=fq_filename,
Title="FQ_banks",
OutputDir=OutputDir,
GroupingWorkspace=grp_wksp,
Binning=binning)
sq_filename = title + '_sofq_banks_corrected.nxs'
save_banks(InputWorkspace="SQ_banks_ws",
Filename=sq_filename,
Title="SQ_banks",
OutputDir=OutputDir,
GroupingWorkspace=grp_wksp,
Binning=binning)
# STOP HERE FOR NOW
print("<b>^2:", bcoh_avg_sqrd)
print("<b^2>:", btot_sqrd_avg)
print("Laue term:", laue_monotonic_diffuse_scat)
print("sample total xsection:",
mtd[sam_corrected].sample().getMaterial().totalScatterXSection())
print("vanadium total xsection:",
mtd[van_corrected].sample().getMaterial().totalScatterXSection())
# Output Bragg Diffraction
ConvertUnits(InputWorkspace=sam_corrected,
OutputWorkspace=sam_corrected,
Target="TOF",
EMode="Elastic")
ConvertToHistogram(InputWorkspace=sam_corrected,
OutputWorkspace=sam_corrected)
Rebin(InputWorkspace=sam_corrected,
OutputWorkspace=sam_corrected,
Params="350.0,-0.0001,26233.0")
xmin = "450.0,1100.0,2050.0,3400.0,4500.0"
xmax = "11000.0,11000.0,11000.0,11000.0,11000.0"
CropWorkspaceRagged(InputWorkspace=sam_corrected,
OutputWorkspace=sam_corrected,
Xmin=xmin,
Xmax=xmax)
return mtd[sam_corrected]
# ResampleX(InputWorkspace=sam_corrected,
# OutputWorkspace=sam_corrected,
# NumberBins=3000,
# LogBinning=True)
# SaveGSS(InputWorkspace=sam_corrected,
# Filename=os.path.join(OutputDir,title+".gsa"),
# SplitFiles=False,
# Append=False,
# MultiplyByBinWidth=True,
# Format="SLOG",
# ExtendedHeader=True)
# process the run
'''
def PyExec(self):
self._loadCharacterizations()
charac = ""
if mtd.doesExist("characterizations"):
charac = "characterizations"
# arguments for both AlignAndFocusPowder and AlignAndFocusPowderFromFiles
self._alignArgs['OutputWorkspace'] = self.getPropertyValue(
"OutputWorkspace")
self._alignArgs['RemovePromptPulseWidth'] = self.getProperty(
"RemovePromptPulseWidth").value
self._alignArgs['CompressTolerance'] = COMPRESS_TOL_TOF
self._alignArgs['PreserveEvents'] = True
self._alignArgs['CalFileName'] = self.getProperty(
"CalibrationFile").value
self._alignArgs['Params'] = self.getProperty("Binning").value
self._alignArgs['ResampleX'] = self.getProperty("ResampleX").value
self._alignArgs['Dspacing'] = True
self._alignArgs['CropWavelengthMin'] = self.getProperty(
'CropWavelengthMin').value
self._alignArgs['CropWavelengthMax'] = self.getProperty(
'CropWavelengthMax').value
self._alignArgs['ReductionProperties'] = '__snspowderreduction'
wksp = self.getProperty("InputWorkspace").value
if wksp is None: # run from file with caching
wksp = AlignAndFocusPowderFromFiles(
Filename=self.getProperty("Filename").value,
CacheDir=self.getProperty("CacheDir").value,
MaxChunkSize=self.getProperty("MaxChunkSize").value,
FilterBadPulses=self.getProperty("FilterBadPulses").value,
Characterizations=charac,
FrequencyLogNames=self.getProperty("FrequencyLogNames").value,
WaveLengthLogNames=self.getProperty(
"WaveLengthLogNames").value,
**(self._alignArgs))
else: # process the input workspace
self.log().information(
"Using input workspace. Ignoring properties 'Filename', " +
"'OutputWorkspace', 'MaxChunkSize', and 'FilterBadPulses'")
# get the correct row of the table
PDDetermineCharacterizations(
InputWorkspace=wksp,
Characterizations=charac,
ReductionProperties="__snspowderreduction",
FrequencyLogNames=self.getProperty("FrequencyLogNames").value,
WaveLengthLogNames=self.getProperty(
"WaveLengthLogNames").value)
wksp = AlignAndFocusPowder(InputWorkspace=wksp,
**(self._alignArgs))
wksp = NormaliseByCurrent(InputWorkspace=wksp, OutputWorkspace=wksp)
wksp.getRun()['gsas_monitor'] = 1
if self._iparmFile is not None:
wksp.getRun()['iparm_file'] = self._iparmFile
wksp = SetUncertainties(InputWorkspace=wksp,
OutputWorkspace=wksp,
SetError="sqrtOrOne")
SaveGSS(InputWorkspace=wksp,
Filename=self.getProperty("PDFgetNFile").value,
SplitFiles=False,
Append=False,
MultiplyByBinWidth=False,
Bank=mantid.pmds["__snspowderreduction"]["bank"].value,
Format="SLOG",
ExtendedHeader=True)
self.setProperty("OutputWorkspace", wksp)