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IndirectAnnulusAbsorption2.py
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IndirectAnnulusAbsorption2.py
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from __future__ import (absolute_import, division, print_function)
from mantid.simpleapi import SetBeam, SetSample, MonteCarloAbsorption, GroupWorkspaces
from mantid.api import (DataProcessorAlgorithm, AlgorithmFactory, MatrixWorkspaceProperty,
PropertyMode, Progress, WorkspaceGroupProperty, mtd)
from mantid.kernel import (StringMandatoryValidator, Direction, logger, IntBoundedValidator,
FloatBoundedValidator, StringListValidator)
class IndirectAnnulusAbsorption(DataProcessorAlgorithm):
# Sample variables
_sample_ws_name=''
_sample_chemical_formula=''
_sample_density_type=None
_sample_density=0.0
_sample_inner_radius=0.0
_sample_outer_radius=0.0
# Container variables
_can_ws_name=''
_can_chemical_formula=''
_can_density_type=None
_can_density=0.0
_can_inner_radius=0.0
_can_outer_radius=0.0
_use_can_corrections=False
_can_scale=0.0
_output_ws=None
_ass_ws=None
_abs_ws=None
_acc_ws=None
_events=0
def category(self):
return "Workflow\\Inelastic;CorrectionFunctions\\AbsorptionCorrections;Workflow\\MIDAS"
def summary(self):
return "Calculates indirect absorption corrections for an annulus sample shape."
def version(self):
return 2
def PyInit(self):
# Sample options
self.declareProperty(MatrixWorkspaceProperty('SampleWorkspace', '', direction=Direction.Input),
doc='Sample workspace.')
self.declareProperty(name='SampleChemicalFormula', defaultValue='', validator=StringMandatoryValidator(),
doc='Sample chemical formula')
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,
doc='Mass density (g/cm^3) or Number density (atoms/Angstrom^3)')
self.declareProperty(name='SampleInnerRadius', defaultValue=0.23,
validator=FloatBoundedValidator(0.0),
doc='Sample radius')
self.declareProperty(name='SampleOuterRadius', defaultValue=0.27,
validator=FloatBoundedValidator(0.0),
doc='Sample radius')
self.declareProperty(name='SampleHeight', defaultValue=1.0,
validator=FloatBoundedValidator(0.0),
doc='Sample height')
# Container options
self.declareProperty(MatrixWorkspaceProperty('CanWorkspace', '', optional=PropertyMode.Optional,
direction=Direction.Input),
doc='Container workspace.')
self.declareProperty(name='UseCanCorrections', defaultValue=False,
doc='Use Container 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='Container density type.')
self.declareProperty(name='CanDensity', defaultValue=1.0,
validator=FloatBoundedValidator(0.0),
doc='Container number density')
self.declareProperty(name='CanInnerRadius', defaultValue=0.19,
validator=FloatBoundedValidator(0.0),
doc='Container inner radius')
self.declareProperty(name='CanOuterRadius', defaultValue=0.35,
validator=FloatBoundedValidator(0.0),
doc='Container outer radius')
self.declareProperty(name='CanScaleFactor', defaultValue=1.0,
validator=FloatBoundedValidator(0.0),
doc='Scale factor to multiply Container data')
# Beam size
self.declareProperty('DefaultBeamSize', defaultValue=True,
doc='Override beam size with instrument defaults')
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 options
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 options
self.declareProperty(MatrixWorkspaceProperty('OutputWorkspace', '', direction=Direction.Output),
doc='The output corrected workspace.')
self.declareProperty(WorkspaceGroupProperty('CorrectionsWorkspace', '', direction=Direction.Output,
optional=PropertyMode.Optional),
doc='The corrections workspace for scattering and absorptions in sample.')
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)
sample_thickness = self._sample_outer_radius - self._sample_inner_radius
logger.information('Sample thickness: ' + str(sample_thickness))
prog.report('Calculating sample corrections')
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': 'HollowCylinder',
'Height': self._sample_height,
'InnerRadius': self._sample_inner_radius,
'OuterRadius': self._sample_outer_radius,
'Center': [0., 0., 0.],
'Axis': 1},
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)
divide_alg = self.createChildAlgorithm("Divide", enableLogging=False)
minus_alg = self.createChildAlgorithm("Minus", enableLogging=False)
multiply_alg = self.createChildAlgorithm("Multiply", 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)
can_thickness_1 = self._sample_inner_radius - self._can_inner_radius
can_thickness_2 = self._can_outer_radius - self._sample_outer_radius
logger.information('Container thickness: %f & %f' % (can_thickness_1, can_thickness_2))
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})
SetSample(can1_wave_ws,
Geometry={'Shape': 'HollowCylinder',
'Height': float(self._sample_height),
'InnerRadius': float(self._can_inner_radius),
'OuterRadius': float(self._sample_inner_radius),
'Center': [0., 0., 0.],
'Axis': 1},
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})
SetSample(can2_wave_ws,
Geometry={'Shape': 'HollowCylinder',
'Height': float(self._sample_height),
'InnerRadius': float(self._sample_outer_radius),
'OuterRadius': float(self._can_outer_radius),
'Center': [0., 0., 0.],
'Axis': 1},
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 can 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', 'annulus'),
('sample_filename', self._sample_ws_name),
('sample_inner', self._sample_inner_radius),
('sample_outer', self._sample_outer_radius),
('can_inner', self._can_inner_radius),
('can_outer', self._can_outer_radius)]
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_thickness_1', can_thickness_1))
sample_logs.append(('container_thickness_2', can_thickness_2))
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_inner_radius = self.getProperty('SampleInnerRadius').value
self._sample_outer_radius = self.getProperty('SampleOuterRadius').value
self._sample_height = self.getProperty('SampleHeight').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_inner_radius = self.getProperty('CanInnerRadius').value
self._can_outer_radius = self.getProperty('CanOuterRadius').value
self._can_scale = self.getProperty('CanScaleFactor').value
self._beam_height = float(self.getProperty('BeamHeight').value)
self._beam_width = float(self.getProperty('BeamWidth').value)
self._emode = 'Indirect'
self._efixed = self._getEfixed()
self._number_wavelengths = self.getProperty('NumberWavelengths').value
self._events = self.getPropertyValue('Events')
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'
# Get beam size defaults
inst = mtd[self._sample_ws_name].getInstrument()
has_beam = inst.hasParameter('Workflow.beam-height')
default = self.getProperty('DefaultBeamSize').value
if default and not has_beam:
default = False
logger.warning("Instrument has no default beam size; will use inputs")
if default:
self._beam_height = float(inst.getStringParameter('Workflow.beam-height')[0])
self._beam_width = float(inst.getStringParameter('Workflow.beam-width')[0])
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['UseCanCorrections'] = 'Must specify a can workspace to use can corrections'
# Geometry validation: can inner < sample inner < sample outer < can outer
if self._sample_outer_radius <= self._sample_inner_radius:
issues['SampleOuterRadius'] = 'Must be greater than SampleInnerRadius'
if self._can_ws_name is not None:
if self._sample_inner_radius <= self._can_inner_radius:
issues['SampleInnerRadius'] = 'Must be greater than CanInnerRadius'
if self._can_outer_radius <= self._sample_outer_radius:
issues['CanOuterRadius'] = 'Must be greater than SampleOuterRadius'
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(IndirectAnnulusAbsorption)