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IndirectTransmission.py
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IndirectTransmission.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 +
#pylint: disable=no-init
from mantid.simpleapi import *
from mantid.api import *
from mantid.kernel import *
from mantid import config
import math
def _get_instrument_property_list(instrument, property_name):
"""
Gets a list of properties from an instrument string property.
@param instrument Instrument object
@param property_name Name of property
@return A list of string values
"""
raw_property_list = instrument.getStringParameter(property_name)
if raw_property_list is None or len(raw_property_list) == 0:
raise RuntimeError('Got empty list for parameter %s' % property_name)
property_list = raw_property_list[0].split(',')
return property_list
class IndirectTransmission(PythonAlgorithm):
def category(self):
return "Workflow\\MIDAS"
def summary(self):
return "Calculates the scattering & transmission for Indirect Geometry spectrometers."
def PyInit(self):
self.declareProperty(name='Instrument', defaultValue='IRIS',
validator=StringListValidator(['IRIS', 'OSIRIS', 'TOSCA', 'BASIS', 'VISION', 'IN16B']),
doc='Instrument')
self.declareProperty(name='Analyser', defaultValue='graphite',
validator=StringListValidator(['graphite', 'mica', 'fmica', 'silicon']),
doc='Analyser')
self.declareProperty(name='Reflection', defaultValue='002',
validator=StringListValidator(['002', '004', '006', '111', '311']),
doc='Reflection')
self.declareProperty(name='ChemicalFormula', defaultValue='', validator=StringMandatoryValidator(),
doc='Sample chemical formula')
self.declareProperty(name='DensityType', defaultValue = 'Mass Density',
validator=StringListValidator(['Mass Density', 'Number Density']),
doc = 'Use of Mass density or Number density')
self.declareProperty(name='Density', defaultValue=0.1,
doc='Mass density (g/cm^3) or Number density (atoms/Angstrom^3). Default=0.1')
self.declareProperty(name='Thickness', defaultValue=0.1,
doc='Sample thickness (cm). Default=0.1')
self.declareProperty(WorkspaceProperty('OutputWorkspace', "", Direction.Output),
doc="The name of the output workspace.")
#pylint: disable=too-many-locals
def PyExec(self):
instrument_name = self.getPropertyValue('Instrument')
analyser = self.getPropertyValue('Analyser')
reflection = self.getPropertyValue('Reflection')
formula = self.getPropertyValue('ChemicalFormula')
densityType = self.getPropertyValue('DensityType')
density = self.getProperty('Density').value
thickness = self.getPropertyValue('Thickness')
# Create an empty instrument workspace
workspace = '__empty_' + instrument_name
CreateSimulationWorkspace(OutputWorkspace=workspace,
Instrument=instrument_name,
BinParams='0,0.5,1')
# Do some validation on the analyser and reflection
instrument = mtd[workspace].getInstrument()
valid_analysers = _get_instrument_property_list(instrument, 'analysers')
logger.debug('Valid analysers for instrument %s: %s' % (instrument_name, str(valid_analysers)))
# Check the analyser is valid for the instrument
if analyser not in valid_analysers:
# Remove idf/ipf workspace
DeleteWorkspace(workspace)
raise RuntimeError('Analyser %s not valid for instrument %s' % (analyser, instrument_name))
else:
# If the analyser was valid then we can check the reflection
reflections_param_name = 'refl-%s' % analyser
valid_reflections = _get_instrument_property_list(instrument, reflections_param_name)
logger.debug('Valid reflections for analyser %s: %s' % (analyser, str(valid_reflections)))
if reflection not in valid_reflections:
# Remove idf/ipf workspace
DeleteWorkspace(workspace)
raise RuntimeError('Reflection %s not valid for analyser %s on instrument %s' % (reflection, analyser, instrument_name))
# Load instrument parameter file
idf_directory = config['instrumentDefinition.directory']
name_stem = instrument_name + '_' + analyser + '_' + reflection
ipf_filename = idf_directory + name_stem + '_Parameters.xml'
LoadParameterFile(Workspace=workspace, Filename=ipf_filename)
# Get efixed value
efixed = self._get_efixed(workspace)
logger.notice('Analyser : ' + analyser + reflection + ' with energy = ' + str(efixed))
if densityType == 'Mass Density':
SetSampleMaterial(InputWorkspace=workspace, ChemicalFormula=formula, SampleMassDensity=density)
else:
SetSampleMaterial(InputWorkspace=workspace, ChemicalFormula=formula, SampleNumberDensity=density)
# Elastic wavelength
wave = 1.8 * math.sqrt(25.2429 / efixed)
material = mtd[str(workspace)].sample().getMaterial()
number_density = material.numberDensityEffective
absorption_x_section = material.absorbXSection(wave)
coherent_x_section = material.cohScatterXSection()
incoherent_x_section = material.incohScatterXSection()
scattering_s_section = incoherent_x_section + coherent_x_section
thickness = float(thickness)
total_x_section = absorption_x_section + scattering_s_section
transmission = math.exp(-number_density * total_x_section * thickness)
scattering = 1.0 - math.exp(-number_density * scattering_s_section * thickness)
# Create table workspace to store calculations
table_ws = self.getPropertyValue('OutputWorkspace')
table_ws = CreateEmptyTableWorkspace(OutputWorkspace=table_ws)
table_ws.addColumn("str", "Name")
table_ws.addColumn("double", "Value")
# Names for each of the output values
output_names = ['Wavelength', 'Absorption Xsection', 'Coherent Xsection', 'Incoherent Xsection',
'Total scattering Xsection', 'Number density', 'Thickness', 'Transmission (abs+scatt)', 'Total scattering']
# List of the calculated values
output_values = [wave, absorption_x_section, coherent_x_section, incoherent_x_section,
scattering_s_section, number_density, thickness, transmission, scattering]
# Build table of values
for data in zip(output_names, output_values):
table_ws.addRow(list(data))
logger.information(': '.join([str(d) for d in data]))
# Remove idf/ipf workspace
DeleteWorkspace(workspace)
self.setProperty("OutputWorkspace", table_ws)
def _get_efixed(self, workspace):
"""
Gets an efixed value form a workspace.
@param workspace Name of workspace to extract from
@return Fixed energy value
"""
from IndirectCommon import getEfixed
try:
# Try to get efixed from the parameters first
efixed = getEfixed(workspace)
except ValueError:
# If that fails then get it by taking from group of all detectors
wsHandle = mtd[workspace]
spectra_list = list(range(0, wsHandle.getNumberHistograms()))
GroupDetectors(InputWorkspace=workspace,
OutputWorkspace=workspace,
SpectraList=spectra_list)
wsHandle = mtd[workspace]
det = wsHandle.getDetector(0)
efixed = wsHandle.getEFixed(det.getID())
return efixed
# Register algorithm with Mantid
AlgorithmFactory.subscribe(IndirectTransmission)