AnnularRingAbsorption.cpp

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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 +
#include "MantidAlgorithms/AnnularRingAbsorption.h"
 
#include "MantidAPI/InstrumentValidator.h"
#include "MantidAPI/WorkspaceUnitValidator.h"
 
#include "MantidGeometry/Instrument.h"
#include "MantidGeometry/Instrument/ObjComponent.h"
#include "MantidGeometry/Instrument/ReferenceFrame.h"
#include "MantidGeometry/Instrument/SampleEnvironment.h"
#include "MantidGeometry/Objects/CSGObject.h"
#include "MantidGeometry/Objects/ShapeFactory.h"
 
#include "MantidKernel/Atom.h"
#include "MantidKernel/BoundedValidator.h"
#include "MantidKernel/CompositeValidator.h"
#include "MantidKernel/MandatoryValidator.h"
#include "MantidKernel/Material.h"
#include "MantidKernel/NeutronAtom.h"
#include "MantidKernel/V3D.h"
 
#include <boost/format.hpp>
#include <memory>
 
namespace Mantid::Algorithms {
using namespace Mantid::API;
using namespace Mantid::Kernel;
 
// Register the algorithm into the AlgorithmFactory
DECLARE_ALGORITHM(AnnularRingAbsorption)
 
//----------------------------------------------------------------------------------------------
 
 
const std::string AnnularRingAbsorption::name() const { return "AnnularRingAbsorption"; }
 
int AnnularRingAbsorption::version() const { return 1; }
 
const std::string AnnularRingAbsorption::category() const { return "CorrectionFunctions\\AbsorptionCorrections"; }
 
const std::string AnnularRingAbsorption::summary() const {
  return "Calculates bin-by-bin correction factors for attenuation due to "
         "absorption "
         "in a cylindrical sample in the wall of a hollow can";
}
 
//----------------------------------------------------------------------------------------------
void AnnularRingAbsorption::init() {
  // The input workspace must have an instrument and units of wavelength
  auto wsValidator = std::make_shared<CompositeValidator>();
  wsValidator->add<WorkspaceUnitValidator>("Wavelength");
  wsValidator->add<InstrumentValidator>();
  declareProperty(std::make_unique<WorkspaceProperty<>>("InputWorkspace", "", Direction::Input, wsValidator),
                  "The input workspace in units of wavelength.");
 
  declareProperty(std::make_unique<WorkspaceProperty<>>("OutputWorkspace", "", Direction::Output),
                  "The name to use for the output workspace.");
 
  // -- can properties --
  auto mustBePositive = std::make_shared<BoundedValidator<double>>();
  mustBePositive->setLower(0.0);
  declareProperty("CanOuterRadius", -1.0, mustBePositive, "The outer radius of the can in centimetres");
  declareProperty("CanInnerRadius", -1.0, mustBePositive, "The inner radius of the can in centimetres");
 
  // -- sample properties --
  declareProperty("SampleHeight", -1.0, mustBePositive, "The height of the sample in centimetres");
  declareProperty("SampleThickness", -1.0, mustBePositive, "The thickness of the sample in centimetres");
  auto nonEmptyString = std::make_shared<MandatoryValidator<std::string>>();
  declareProperty("SampleChemicalFormula", "", "Chemical composition of the sample material", nonEmptyString);
  declareProperty("SampleNumberDensity", -1.0, mustBePositive,
                  "The number density of the sample in number of formulas per "
                  "cubic angstrom");
 
  // -- Monte Carlo properties --
  auto positiveInt = std::make_shared<Kernel::BoundedValidator<int>>();
  positiveInt->setLower(1);
  declareProperty("NumberOfWavelengthPoints", EMPTY_INT(), positiveInt,
                  "The number of wavelength points for which a simulation is "
                  "atttempted (default: all points)");
  declareProperty("EventsPerPoint", 300, positiveInt,
                  "The number of \"neutron\" events to generate per simulated point");
  declareProperty("SeedValue", 123456789, positiveInt, "Seed the random number generator with this value");
}
 
//----------------------------------------------------------------------------------------------
void AnnularRingAbsorption::exec() {
  MatrixWorkspace_sptr inputWS = getProperty("InputWorkspace");
  // We neglect any absorption in the can so the actual shape defined is a
  // hollow cylinder
  // where the sample is in the centre of the can wall
  attachSample(inputWS);
 
  MatrixWorkspace_sptr factors = runMonteCarloAbsorptionCorrection(inputWS);
  setProperty("OutputWorkspace", factors);
}
 
//---------------------------------------------------------------------------------------------
// Private members
//---------------------------------------------------------------------------------------------
 
void AnnularRingAbsorption::attachSample(const MatrixWorkspace_sptr &workspace) {
  runCreateSampleShape(workspace);
  runSetSampleMaterial(workspace);
}
 
void AnnularRingAbsorption::runCreateSampleShape(const API::MatrixWorkspace_sptr &workspace) {
  auto inst = workspace->getInstrument();
  auto refFrame = inst->getReferenceFrame();
 
  bool childLog = g_log.is(Logger::Priority::PRIO_DEBUG);
  auto alg = this->createChildAlgorithm("CreateSampleShape", -1, -1, childLog);
  alg->setProperty("InputWorkspace", workspace);
  alg->setPropertyValue("ShapeXML", createSampleShapeXML(refFrame->vecPointingUp()));
  try {
    alg->executeAsChildAlg();
  } catch (const std::exception &exc) {
    throw std::invalid_argument(std::string("Unable to create sample shape: '") + exc.what() + "'");
  }
}
 
std::string AnnularRingAbsorption::createSampleShapeXML(const V3D &upAxis) const {
  // User input
  const double canLowRadiusCM = getProperty("CanInnerRadius");
  const double canUppRadiusCM = getProperty("CanOuterRadius");
  const double sampleHeightCM = getProperty("SampleHeight");
  const double sampleThickCM = getProperty("SampleThickness");
  // Sample dimensions for approximation (converted to metres)
  const double wallMidPtCM = canLowRadiusCM + 0.5 * (canUppRadiusCM - canLowRadiusCM);
  const double lowRadiusMtr = (wallMidPtCM - 0.5 * sampleThickCM) / 100.;
  const double uppRadiusMtr = (wallMidPtCM + 0.5 * sampleThickCM) / 100.;
 
  // Cylinders oriented along Y, with origin at the centre as expected by
  // the MonteCarloAbsorption algorithm.
  const V3D bottomCentre{0.0, -sampleHeightCM / 2.0 / 100.0, 0.0}; // in metres.
  const std::string innerCylID = std::string("inner-cyl");
  const std::string innerCyl = cylinderXML(innerCylID, bottomCentre, lowRadiusMtr, upAxis, sampleHeightCM / 100.0);
  const std::string outerCylID = std::string("outer-cyl");
  const std::string outerCyl = cylinderXML(outerCylID, bottomCentre, uppRadiusMtr, upAxis, sampleHeightCM / 100.0);
 
  // Combine shapes
  boost::format algebra("<algebra val=\"(%1% (# %2%))\" />");
  algebra % outerCylID % innerCylID;
  auto xml = outerCyl + "\n" + innerCyl + "\n" + algebra.str();
  g_log.debug() << "Sample shape XML:\n" << xml << "\n";
  return xml;
}
 
const std::string AnnularRingAbsorption::cylinderXML(const std::string &id, const V3D &bottomCentre,
                                                     const double radius, const V3D &axis, const double height) const {
  // The newline characters are not necessary for the XML but they make it
  // easier to read for debugging
  static const char *CYL_TEMPLATE = "<cylinder id=\"%1%\">\n"
                                    "<centre-of-bottom-base x=\"%2%\" y=\"%3%\" z=\"%4%\" />\n"
                                    " <axis x=\"%5%\" y=\"%6%\" z=\"%7%\" />\n"
                                    " <radius val=\"%8%\" />\n"
                                    " <height val=\"%9%\" />\n"
                                    "</cylinder>";
 
  boost::format xml(CYL_TEMPLATE);
  xml % id % bottomCentre.X() % bottomCentre.Y() % bottomCentre.Z() % axis.X() % axis.Y() % axis.Z() % radius % height;
  return xml.str();
}
 
void AnnularRingAbsorption::runSetSampleMaterial(const API::MatrixWorkspace_sptr &workspace) {
  bool childLog = g_log.is(Logger::Priority::PRIO_DEBUG);
  auto alg = this->createChildAlgorithm("SetSampleMaterial", -1, -1, childLog);
  alg->setProperty("InputWorkspace", workspace);
  alg->setProperty("ChemicalFormula", getPropertyValue("SampleChemicalFormula"));
  alg->setProperty<double>("SampleNumberDensity", getProperty("SampleNumberDensity"));
  try {
    alg->executeAsChildAlg();
  } catch (std::exception &exc) {
    throw std::invalid_argument(std::string("Unable to set sample material: '") + exc.what() + "'");
  }
}
 
MatrixWorkspace_sptr AnnularRingAbsorption::runMonteCarloAbsorptionCorrection(const MatrixWorkspace_sptr &workspace) {
  bool childLog = g_log.is(Logger::Priority::PRIO_DEBUG);
  auto alg = this->createChildAlgorithm("MonteCarloAbsorption", 0.1, 1.0, childLog);
  alg->setProperty("InputWorkspace", workspace);
  alg->setProperty<int>("NumberOfWavelengthPoints", getProperty("NumberOfWavelengthPoints"));
  alg->setProperty<int>("EventsPerPoint", getProperty("EventsPerPoint"));
  alg->setProperty<int>("SeedValue", getProperty("SeedValue"));
  try {
    alg->executeAsChildAlg();
  } catch (std::exception &exc) {
    throw std::invalid_argument(std::string("Error running absorption correction: '") + exc.what() + "'");
  }
 
  return alg->getProperty("OutputWorkspace");
}
 
} // namespace Mantid::Algorithms