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IndirectFlatPlateAbsorption2.py
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IndirectFlatPlateAbsorption2.py
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# Mantid Repository : https://github.com/mantidproject/mantid
#
# Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
# NScD Oak Ridge National Laboratory, European Spallation Source,
# Institut Laue - Langevin & CSNS, Institute of High Energy Physics, CAS
# SPDX - License - Identifier: GPL - 3.0 +
from mantid.simpleapi import SetBeam, SetSample, MonteCarloAbsorption, GroupWorkspaces
from mantid.api import (DataProcessorAlgorithm, AlgorithmFactory, MatrixWorkspaceProperty,
PropertyMode, Progress, WorkspaceGroupProperty, mtd)
from mantid.kernel import (StringListValidator, StringMandatoryValidator, IntBoundedValidator,
Direction, logger, FloatBoundedValidator, FloatMandatoryValidator)
class IndirectFlatPlateAbsorption(DataProcessorAlgorithm):
# Sample variables
_sample_ws_name=None
_sample_chemical_formula=None
_sample_density_type=None
_sample_density=None
_sample_height=None
_sample_width=None
_sample_thickness=None
_sample_angle=None
# Container variables
_can_ws_name=None
_use_can_corrections=None
_can_chemical_formula=None
_can_density_type=None
_can_density=None
_can_front_thickness=None
_can_back_thickness=None
_can_scale=None
_output_ws=None
_abs_ws=None
_ass_ws=None
_acc_ws=None
def category(self):
return "Workflow\\Inelastic;CorrectionFunctions\\AbsorptionCorrections;Workflow\\MIDAS"
def summary(self):
return "Calculates indirect absorption corrections for a flat sample shape."
def version(self):
return 2
def PyInit(self):
# Sample
self.declareProperty(MatrixWorkspaceProperty('SampleWorkspace', '', direction=Direction.Input),
doc='Sample workspace')
self.declareProperty(name='SampleChemicalFormula', defaultValue='',
validator=StringMandatoryValidator(),
doc='Chemical formula for the sample')
self.declareProperty(name='SampleDensityType', defaultValue='Mass Density',
validator=StringListValidator(['Mass Density', 'Number Density']),
doc='Use of Mass density or Number density')
self.declareProperty(name='SampleDensity', defaultValue=0.1,
validator=FloatBoundedValidator(0.0),
doc='Mass density (g/cm^3) or Number density (atoms/Angstrom^3)')
self.declareProperty(name='SampleHeight', defaultValue=1.0,
validator=FloatBoundedValidator(0.0),
doc='Sample height')
self.declareProperty(name='SampleWidth', defaultValue=1.0,
validator=FloatBoundedValidator(0.0),
doc='Sample width')
self.declareProperty(name='SampleThickness', defaultValue=0.5,
validator=FloatBoundedValidator(0.0),
doc='Sample thickness')
self.declareProperty(name='SampleAngle', defaultValue=0.0,
validator=FloatMandatoryValidator(),
doc='Sample angle')
# Container
self.declareProperty(MatrixWorkspaceProperty('CanWorkspace', '', optional=PropertyMode.Optional,
direction=Direction.Input),
doc='Container workspace')
self.declareProperty(name='UseCanCorrections', defaultValue=False,
doc='Use can corrections in subtraction')
self.declareProperty(name='CanChemicalFormula', defaultValue='',
doc='Chemical formula for the Container')
self.declareProperty(name='CanDensityType', defaultValue='Mass Density',
validator=StringListValidator(['Mass Density', 'Number Density']),
doc='Use of Mass density or Number density')
self.declareProperty(name='CanDensity', defaultValue=0.1,
validator=FloatBoundedValidator(0.0),
doc='Mass density (g/cm^3) or Number density (atoms/Angstrom^3)')
self.declareProperty(name='CanFrontThickness', defaultValue=0.1,
validator=FloatBoundedValidator(0.0),
doc='Can front thickness')
self.declareProperty(name='CanBackThickness', defaultValue=0.1,
validator=FloatBoundedValidator(0.0),
doc='Can back thickness')
self.declareProperty(name='CanScaleFactor', defaultValue=1.0,
validator=FloatBoundedValidator(0.0),
doc='Scale factor to multiply can data')
# Beam size
self.declareProperty(name='BeamHeight', defaultValue=1.0,
validator=FloatBoundedValidator(0.0),
doc='Height of the beam (cm)')
self.declareProperty(name='BeamWidth', defaultValue=1.0,
validator=FloatBoundedValidator(0.0),
doc='Width of the beam (cm)')
# General
self.declareProperty(name='NumberWavelengths', defaultValue=10,
validator=IntBoundedValidator(1),
doc='Number of wavelengths for calculation')
self.declareProperty(name='Events', defaultValue=1000,
validator=IntBoundedValidator(0),
doc='Number of neutron events')
# Output
self.declareProperty(MatrixWorkspaceProperty('OutputWorkspace', '', direction=Direction.Output),
doc='The output corrected workspace')
self.declareProperty(WorkspaceGroupProperty('CorrectionsWorkspace', '', direction=Direction.Output,
optional=PropertyMode.Optional),
doc='The workspace group to save correction factors')
def PyExec(self):
# Set up progress reporting
n_prog_reports = 2
if self._can_ws_name is not None:
n_prog_reports += 1
prog = Progress(self, 0.0, 1.0, n_prog_reports)
sample_wave_ws = '__sam_wave'
convert_unit_alg = self.createChildAlgorithm("ConvertUnits", enableLogging=False)
convert_unit_alg.setProperty("InputWorkspace", self._sample_ws_name)
convert_unit_alg.setProperty("OutputWorkspace", sample_wave_ws)
convert_unit_alg.setProperty("Target", 'Wavelength')
convert_unit_alg.setProperty("EMode", self._emode)
convert_unit_alg.setProperty("EFixed", self._efixed)
convert_unit_alg.execute()
mtd.addOrReplace(sample_wave_ws, convert_unit_alg.getProperty("OutputWorkspace").value)
SetBeam(sample_wave_ws,
Geometry={'Shape': 'Slit',
'Width': self._beam_width,
'Height': self._beam_height})
if self._sample_density_type == 'Mass Density':
sample_mat_list = {'ChemicalFormula': self._sample_chemical_formula,
'SampleMassDensity': self._sample_density}
if self._sample_density_type == 'Number Density':
sample_mat_list = {'ChemicalFormula': self._sample_chemical_formula,
'SampleNumberDensity': self._sample_density}
SetSample(sample_wave_ws,
Geometry={'Shape': 'FlatPlate',
'Width': self._sample_width,
'Height': self._sample_height,
'Thick': self._sample_thickness,
'Center': [0., 0., 0.],
'Angle': self._sample_angle},
Material=sample_mat_list)
prog.report('Calculating sample corrections')
MonteCarloAbsorption(InputWorkspace=sample_wave_ws,
OutputWorkspace=self._ass_ws,
EventsPerPoint=self._events,
NumberOfWavelengthPoints=self._number_wavelengths,
Interpolation='CSpline')
group = self._ass_ws
delete_alg = self.createChildAlgorithm("DeleteWorkspace", enableLogging=False)
multiply_alg = self.createChildAlgorithm("Multiply", enableLogging=False)
divide_alg = self.createChildAlgorithm("Divide", enableLogging=False)
minus_alg = self.createChildAlgorithm("Minus", enableLogging=False)
if self._can_ws_name is not None:
can1_wave_ws = '__can1_wave'
can2_wave_ws = '__can2_wave'
convert_unit_alg.setProperty("InputWorkspace", self._can_ws_name)
convert_unit_alg.setProperty("OutputWorkspace", can1_wave_ws)
convert_unit_alg.setProperty("Target", 'Wavelength')
convert_unit_alg.setProperty("EMode", self._emode)
convert_unit_alg.setProperty("EFixed", self._efixed)
convert_unit_alg.execute()
mtd.addOrReplace(can1_wave_ws, convert_unit_alg.getProperty("OutputWorkspace").value)
if self._can_scale != 1.0:
logger.information('Scaling container by: %s' % self._can_scale)
scale_alg = self.createChildAlgorithm("Scale", enableLogging=False)
scale_alg.setProperty("InputWorkspace", can1_wave_ws)
scale_alg.setProperty("OutputWorkspace", can1_wave_ws)
scale_alg.setProperty("Factor", self._can_scale)
scale_alg.setProperty("Operation", 'Multiply')
scale_alg.execute()
clone_alg = self.createChildAlgorithm("CloneWorkspace", enableLogging=False)
clone_alg.setProperty("InputWorkspace", can1_wave_ws)
clone_alg.setProperty("OutputWorkspace", can2_wave_ws)
clone_alg.execute()
mtd.addOrReplace(can2_wave_ws, clone_alg.getProperty("OutputWorkspace").value)
if self._use_can_corrections:
prog.report('Calculating container corrections')
divide_alg.setProperty("LHSWorkspace", sample_wave_ws)
divide_alg.setProperty("RHSWorkspace", self._ass_ws)
divide_alg.setProperty("OutputWorkspace", sample_wave_ws)
divide_alg.execute()
if self._sample_density_type == 'Mass Density':
container_mat_list = {'ChemicalFormula': self._can_chemical_formula,
'SampleMassDensity': self._can_density}
if self._sample_density_type == 'Number Density':
container_mat_list = {'ChemicalFormula': self._can_chemical_formula,
'SampleNumberDensity': self._can_density}
SetBeam(can1_wave_ws,
Geometry={'Shape': 'Slit',
'Width': self._beam_width,
'Height': self._beam_height})
offset_front = 0.5 * (self._can_front_thickness + self._sample_thickness)
SetSample(can1_wave_ws,
Geometry={'Shape': 'FlatPlate',
'Width': self._sample_width,
'Height': self._sample_height,
'Thick': self._can_front_thickness,
'Center': [0., 0., -offset_front],
'Angle': self._sample_angle},
Material=container_mat_list)
MonteCarloAbsorption(InputWorkspace=can1_wave_ws,
OutputWorkspace='__Acc1',
EventsPerPoint=self._events,
NumberOfWavelengthPoints=self._number_wavelengths,
Interpolation='CSpline')
SetBeam(can2_wave_ws,
Geometry={'Shape': 'Slit',
'Width': self._beam_width,
'Height': self._beam_height})
offset_back = 0.5 * (self._can_back_thickness + self._sample_thickness)
SetSample(can2_wave_ws,
Geometry={'Shape': 'FlatPlate',
'Width': self._sample_width,
'Height': self._sample_height,
'Thick': self._can_back_thickness,
'Center': [0., 0., offset_back],
'Angle': self._sample_angle},
Material=container_mat_list)
MonteCarloAbsorption(InputWorkspace=can2_wave_ws,
OutputWorkspace='__Acc2',
EventsPerPoint=self._events,
NumberOfWavelengthPoints=self._number_wavelengths,
Interpolation='CSpline')
multiply_alg.setProperty("LHSWorkspace", '__Acc1')
multiply_alg.setProperty("RHSWorkspace", '__Acc2')
multiply_alg.setProperty("OutputWorkspace", self._acc_ws)
multiply_alg.execute()
mtd.addOrReplace(self._acc_ws, multiply_alg.getProperty("OutputWorkspace").value)
delete_alg.setProperty("Workspace", '__Acc1')
delete_alg.execute()
delete_alg.setProperty("Workspace", '__Acc2')
delete_alg.execute()
divide_alg.setProperty("LHSWorkspace", can1_wave_ws)
divide_alg.setProperty("RHSWorkspace", self._acc_ws)
divide_alg.setProperty("OutputWorkspace", can1_wave_ws)
divide_alg.execute()
minus_alg.setProperty("LHSWorkspace", sample_wave_ws)
minus_alg.setProperty("RHSWorkspace", can1_wave_ws)
minus_alg.setProperty("OutputWorkspace", sample_wave_ws)
minus_alg.execute()
group += ',' + self._acc_ws
else:
prog.report('Calculating container scaling')
minus_alg.setProperty("LHSWorkspace", sample_wave_ws)
minus_alg.setProperty("RHSWorkspace", can1_wave_ws)
minus_alg.setProperty("OutputWorkspace", sample_wave_ws)
minus_alg.execute()
divide_alg.setProperty("LHSWorkspace", sample_wave_ws)
divide_alg.setProperty("RHSWorkspace", self._ass_ws)
divide_alg.setProperty("OutputWorkspace", sample_wave_ws)
divide_alg.execute()
delete_alg.setProperty("Workspace", can1_wave_ws)
delete_alg.execute()
delete_alg.setProperty("Workspace", can2_wave_ws)
delete_alg.execute()
else:
divide_alg.setProperty("LHSWorkspace", sample_wave_ws)
divide_alg.setProperty("RHSWorkspace", self._ass_ws)
divide_alg.setProperty("OutputWorkspace", sample_wave_ws)
divide_alg.execute()
convert_unit_alg.setProperty("InputWorkspace", sample_wave_ws)
convert_unit_alg.setProperty("OutputWorkspace", self._output_ws)
convert_unit_alg.setProperty("Target", 'DeltaE')
convert_unit_alg.setProperty("EMode", self._emode)
convert_unit_alg.setProperty("EFixed", self._efixed)
convert_unit_alg.execute()
mtd.addOrReplace(self._output_ws, convert_unit_alg.getProperty("OutputWorkspace").value)
delete_alg.setProperty("Workspace", sample_wave_ws)
delete_alg.execute()
prog.report('Recording sample logs')
sample_log_workspaces = [self._output_ws, self._ass_ws]
sample_logs = [('sample_shape', 'flatplate'),
('sample_filename', self._sample_ws_name),
('sample_height', self._sample_height),
('sample_width', self._sample_width),
('sample_thickness', self._sample_thickness),
('sample_angle', self._sample_angle)]
if self._can_ws_name is not None:
sample_logs.append(('container_filename', self._can_ws_name))
sample_logs.append(('container_scale', self._can_scale))
if self._use_can_corrections:
sample_log_workspaces.append(self._acc_ws)
sample_logs.append(('container_front_thickness', self._can_front_thickness))
sample_logs.append(('container_back_thickness', self._can_back_thickness))
log_names = [item[0] for item in sample_logs]
log_values = [item[1] for item in sample_logs]
add_sample_log_alg = self.createChildAlgorithm("AddSampleLogMultiple", enableLogging=False)
for ws_name in sample_log_workspaces:
add_sample_log_alg.setProperty("Workspace", ws_name)
add_sample_log_alg.setProperty("LogNames", log_names)
add_sample_log_alg.setProperty("LogValues", log_values)
add_sample_log_alg.execute()
self.setProperty('OutputWorkspace', self._output_ws)
# Output the Ass workspace if it is wanted, delete if not
if self._abs_ws == '':
delete_alg.setProperty("Workspace", self._ass_ws)
delete_alg.execute()
if self._can_ws_name is not None and self._use_can_corrections:
delete_alg.setProperty("Workspace", self._acc_ws)
delete_alg.execute()
else:
GroupWorkspaces(InputWorkspaces=group,
OutputWorkspace=self._abs_ws,
EnableLogging=False)
self.setProperty('CorrectionsWorkspace', self._abs_ws)
def _setup(self):
"""
Get algorithm properties.
"""
self._sample_ws_name = self.getPropertyValue('SampleWorkspace')
self._sample_chemical_formula = self.getPropertyValue('SampleChemicalFormula')
self._sample_density_type = self.getPropertyValue('SampleDensityType')
self._sample_density = self.getProperty('SampleDensity').value
self._sample_height = self.getProperty('SampleHeight').value
self._sample_width = self.getProperty('SampleWidth').value
self._sample_thickness = self.getProperty('SampleThickness').value
self._sample_angle = self.getProperty('SampleAngle').value
self._can_ws_name = self.getPropertyValue('CanWorkspace')
if self._can_ws_name == '':
self._can_ws_name = None
self._use_can_corrections = self.getProperty('UseCanCorrections').value
self._can_chemical_formula = self.getPropertyValue('CanChemicalFormula')
self._can_density_type = self.getPropertyValue('CanDensityType')
self._can_density = self.getProperty('CanDensity').value
self._can_front_thickness = self.getProperty('CanFrontThickness').value
self._can_back_thickness = self.getProperty('CanBackThickness').value
self._can_scale = self.getProperty('CanScaleFactor').value
self._emode = 'Indirect'
self._efixed = self._getEfixed()
self._number_wavelengths = self.getProperty('NumberWavelengths').value
self._events = self.getProperty('Events').value
self._beam_height = self.getProperty('BeamHeight').value
self._beam_width = self.getProperty('BeamWidth').value
self._output_ws = self.getPropertyValue('OutputWorkspace')
self._abs_ws = self.getPropertyValue('CorrectionsWorkspace')
if self._abs_ws == '':
self._ass_ws = '__ass'
self._acc_ws = '__acc'
else:
self._ass_ws = self._abs_ws + '_ass'
self._acc_ws = self._abs_ws + '_acc'
def validateInputs(self):
"""
Validate algorithm options.
"""
self._setup()
issues = dict()
if self._use_can_corrections and self._can_chemical_formula == '':
issues['CanChemicalFormula'] = 'Must be set to use can corrections'
if self._use_can_corrections and self._can_ws_name is None:
issues['CanWorkspace'] = 'Must specify a can workspace to use can corrections'
return issues
def _getEfixed(self):
inst = mtd[self._sample_ws_name].getInstrument()
if inst.hasParameter('Efixed'):
return inst.getNumberParameter('EFixed')[0]
if inst.hasParameter('analyser'):
analyser_name = inst.getStringParameter('analyser')[0]
analyser_comp = inst.getComponentByName(analyser_name)
if analyser_comp is not None and analyser_comp.hasParameter('Efixed'):
return analyser_comp.getNumberParameter('EFixed')[0]
raise ValueError('No Efixed parameter found')
# Register algorithm with Mantid
AlgorithmFactory.subscribe(IndirectFlatPlateAbsorption)