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PredictSatellitePeaks.cpp
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PredictSatellitePeaks.cpp
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// Mantid Repository : https://github.com/mantidproject/mantid
//
// Copyright © 2020 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 +
/*
* PredictSatellitePeaks.cpp
*
* Created on: July 15, 2018
* Author: Vickie Lynch
*/
#include "MantidCrystal/PredictSatellitePeaks.h"
#include "MantidAPI/OrientedLatticeValidator.h"
#include "MantidAPI/Run.h"
#include "MantidAPI/Sample.h"
#include "MantidAPI/WorkspaceFactory.h"
#include "MantidCrystal/PeakAlgorithmHelpers.h"
#include "MantidDataObjects/PeaksWorkspace.h"
#include "MantidGeometry/Crystal/BasicHKLFilters.h"
#include "MantidGeometry/Crystal/HKLGenerator.h"
#include "MantidGeometry/Crystal/OrientedLattice.h"
#include "MantidGeometry/Objects/InstrumentRayTracer.h"
#include "MantidKernel/EnabledWhenProperty.h"
#include <boost/math/special_functions/round.hpp>
namespace Mantid {
using namespace Mantid::DataObjects;
using namespace Mantid::API;
using namespace std;
using namespace Mantid::Geometry;
using namespace Mantid::Kernel;
namespace Crystal {
// handy shortcuts
DECLARE_ALGORITHM(PredictSatellitePeaks)
/** Constructor
*/
PredictSatellitePeaks::PredictSatellitePeaks() : m_qConventionFactor(qConventionFactor()) {}
/// Initialise the properties
void PredictSatellitePeaks::init() {
auto latticeValidator = std::make_shared<OrientedLatticeValidator>();
declareProperty(std::make_unique<WorkspaceProperty<IPeaksWorkspace>>("Peaks", "", Direction::Input, latticeValidator),
"Workspace of Peaks with orientation matrix that indexed the peaks and "
"instrument loaded");
declareProperty(std::make_unique<WorkspaceProperty<IPeaksWorkspace>>("SatellitePeaks", "", Direction::Output),
"Workspace of Peaks with peaks with fractional h,k, and/or l values");
ModulationProperties::appendTo(this);
declareProperty("GetModVectorsFromUB", false, "If false Modulation Vectors will be read from input");
declareProperty("IncludeIntegerHKL", true, "If false order 0 peaks are not included in workspace (integer HKL)");
declareProperty("IncludeAllPeaksInRange", false,
"If false only offsets from "
"peaks from Peaks workspace "
"in input are used");
declareProperty(std::make_unique<PropertyWithValue<double>>("WavelengthMin", 0.1, Direction::Input),
"Minimum wavelength limit at which to start looking for "
"single-crystal peaks.");
declareProperty(std::make_unique<PropertyWithValue<double>>("WavelengthMax", 100.0, Direction::Input),
"Maximum wavelength limit at which to start looking for "
"single-crystal peaks.");
declareProperty(std::make_unique<PropertyWithValue<double>>("MinDSpacing", 0.1, Direction::Input),
"Minimum d-spacing of peaks to consider. Default = 0.1");
declareProperty(std::make_unique<PropertyWithValue<double>>("MaxDSpacing", 100.0, Direction::Input),
"Maximum d-spacing of peaks to consider");
setPropertySettings("WavelengthMin", std::make_unique<Kernel::EnabledWhenProperty>(string("IncludeAllPeaksInRange"),
Kernel::IS_EQUAL_TO, "1"));
setPropertySettings("WavelengthMax", std::make_unique<Kernel::EnabledWhenProperty>(string("IncludeAllPeaksInRange"),
Kernel::IS_EQUAL_TO, "1"));
setPropertySettings("MinDSpacing", std::make_unique<Kernel::EnabledWhenProperty>(string("IncludeAllPeaksInRange"),
Kernel::IS_EQUAL_TO, "1"));
setPropertySettings("MaxDSpacing", std::make_unique<Kernel::EnabledWhenProperty>(string("IncludeAllPeaksInRange"),
Kernel::IS_EQUAL_TO, "1"));
}
/// Run the algorithm
void PredictSatellitePeaks::exec() {
bool includePeaksInRange = getProperty("IncludeAllPeaksInRange");
Peaks = getProperty("Peaks");
if (!Peaks)
throw std::invalid_argument("Input workspace is not a IPeaksWorkspace. Type=" + Peaks->id());
if (!includePeaksInRange) {
exec_peaks();
return;
}
V3D offsets1 = getOffsetVector(ModulationProperties::ModVector1);
V3D offsets2 = getOffsetVector(ModulationProperties::ModVector2);
V3D offsets3 = getOffsetVector(ModulationProperties::ModVector3);
int maxOrder = getProperty(ModulationProperties::MaxOrder);
bool crossTerms = getProperty(ModulationProperties::CrossTerms);
bool includeOrderZero = getProperty("IncludeIntegerHKL");
// boolean for only including order zero once
bool notOrderZero = false;
API::Sample sample = Peaks->mutableSample();
auto lattice = std::make_unique<OrientedLattice>(sample.getOrientedLattice());
bool fromUB = getProperty("GetModVectorsFromUB");
if (fromUB) {
offsets1 = lattice->getModVec(0);
offsets2 = lattice->getModVec(1);
offsets3 = lattice->getModVec(2);
if (maxOrder == 0)
maxOrder = lattice->getMaxOrder();
crossTerms = lattice->getCrossTerm();
} else {
lattice->setModVec1(offsets1);
lattice->setModVec2(offsets2);
lattice->setModVec3(offsets3);
lattice->setMaxOrder(maxOrder);
lattice->setCrossTerm(crossTerms);
}
outPeaks = std::dynamic_pointer_cast<IPeaksWorkspace>(WorkspaceFactory::Instance().createPeaks(Peaks->id()));
outPeaks->copyExperimentInfoFrom(Peaks.get());
outPeaks->mutableSample().setOrientedLattice(std::move(lattice));
Kernel::Matrix<double> goniometer;
goniometer.identityMatrix();
const double lambdaMin = getProperty("WavelengthMin");
const double lambdaMax = getProperty("WavelengthMax");
std::vector<V3D> possibleHKLs;
const double dMin = getProperty("MinDSpacing");
const double dMax = getProperty("MaxDSpacing");
Geometry::HKLGenerator gen(outPeaks->sample().getOrientedLattice(), dMin);
auto dSpacingFilter = std::make_shared<HKLFilterDRange>(outPeaks->sample().getOrientedLattice(), dMin, dMax);
V3D hkl_begin = *(gen.begin());
g_log.information() << "HKL range for d_min of " << dMin << " to d_max of " << dMax << " is from " << hkl_begin
<< " to " << hkl_begin * -1.0 << ", a total of " << gen.size() << " possible HKL's\n";
if (gen.size() > MAX_NUMBER_HKLS)
throw std::invalid_argument("More than 10 billion HKLs to search. Is "
"your d_min value too small?");
possibleHKLs.clear();
possibleHKLs.reserve(gen.size());
std::remove_copy_if(gen.begin(), gen.end(), std::back_inserter(possibleHKLs), (~dSpacingFilter)->fn());
size_t N = possibleHKLs.size();
N = max<size_t>(100, N);
const auto &UB = outPeaks->sample().getOrientedLattice().getUB();
goniometer = Peaks->run().getGoniometerMatrix();
int runNumber = Peaks->getRunNumber();
Progress prog(this, 0.0, 1.0, N);
vector<vector<int>> alreadyDonePeaks;
auto orientedUB = goniometer * UB;
HKLFilterWavelength lambdaFilter(orientedUB, lambdaMin, lambdaMax);
outPeaks->mutableRun().addProperty<std::vector<double>>("Offset1", offsets1, true);
outPeaks->mutableRun().addProperty<std::vector<double>>("Offset2", offsets2, true);
outPeaks->mutableRun().addProperty<std::vector<double>>("Offset3", offsets3, true);
for (auto &hkl : possibleHKLs) {
if (crossTerms) {
predictOffsetsWithCrossTerms(offsets1, offsets2, offsets3, maxOrder, runNumber, goniometer, hkl, lambdaFilter,
includePeaksInRange, includeOrderZero, alreadyDonePeaks);
} else {
predictOffsets(0, offsets1, maxOrder, runNumber, goniometer, hkl, lambdaFilter, includePeaksInRange,
includeOrderZero, alreadyDonePeaks);
predictOffsets(1, offsets2, maxOrder, runNumber, goniometer, hkl, lambdaFilter, includePeaksInRange, notOrderZero,
alreadyDonePeaks);
predictOffsets(2, offsets3, maxOrder, runNumber, goniometer, hkl, lambdaFilter, includePeaksInRange, notOrderZero,
alreadyDonePeaks);
}
}
// Sort peaks by run number so that peaks with equal goniometer matrices are
// adjacent
std::vector<std::pair<std::string, bool>> criteria;
criteria.emplace_back("RunNumber", true);
auto isPeaksWorkspace = std::dynamic_pointer_cast<PeaksWorkspace>(outPeaks);
if (isPeaksWorkspace)
criteria.emplace_back("BankName", true);
criteria.emplace_back("h", true);
criteria.emplace_back("k", true);
criteria.emplace_back("l", true);
outPeaks->sort(criteria);
for (int i = 0; i < static_cast<int>(outPeaks->getNumberPeaks()); ++i) {
outPeaks->getPeak(i).setPeakNumber(i);
}
setProperty("SatellitePeaks", outPeaks);
}
void PredictSatellitePeaks::exec_peaks() {
V3D offsets1 = getOffsetVector(ModulationProperties::ModVector1);
V3D offsets2 = getOffsetVector(ModulationProperties::ModVector2);
V3D offsets3 = getOffsetVector(ModulationProperties::ModVector3);
int maxOrder = getProperty(ModulationProperties::MaxOrder);
bool crossTerms = getProperty(ModulationProperties::CrossTerms);
API::Sample sample = Peaks->mutableSample();
auto lattice = std::make_unique<OrientedLattice>(sample.getOrientedLattice());
bool fromUB = getProperty("GetModVectorsFromUB");
if (fromUB) {
offsets1 = lattice->getModVec(0);
offsets2 = lattice->getModVec(1);
offsets3 = lattice->getModVec(2);
if (maxOrder == 0)
maxOrder = lattice->getMaxOrder();
crossTerms = lattice->getCrossTerm();
} else {
lattice->setModVec1(offsets1);
lattice->setModVec2(offsets2);
lattice->setModVec3(offsets3);
lattice->setMaxOrder(maxOrder);
lattice->setCrossTerm(crossTerms);
}
bool includePeaksInRange = false;
bool includeOrderZero = getProperty("IncludeIntegerHKL");
// boolean for only including order zero once
bool notOrderZero = false;
if (Peaks->getNumberPeaks() <= 0) {
g_log.error() << "There are No peaks in the input PeaksWorkspace\n";
return;
}
outPeaks = std::dynamic_pointer_cast<IPeaksWorkspace>(WorkspaceFactory::Instance().createPeaks(Peaks->id()));
outPeaks->copyExperimentInfoFrom(Peaks.get());
outPeaks->mutableSample().setOrientedLattice(std::move(lattice));
vector<vector<int>> alreadyDonePeaks;
HKLFilterWavelength lambdaFilter(DblMatrix(3, 3, true), 0.1, 100.);
outPeaks->mutableRun().addProperty<std::vector<double>>("Offset1", offsets1, true);
outPeaks->mutableRun().addProperty<std::vector<double>>("Offset2", offsets2, true);
outPeaks->mutableRun().addProperty<std::vector<double>>("Offset3", offsets3, true);
for (int i = 0; i < static_cast<int>(Peaks->getNumberPeaks()); ++i) {
const Kernel::Matrix<double> peakGoniometerMatrix = Peaks->getPeak(i).getGoniometerMatrix();
int runNumber = Peaks->getPeak(i).getRunNumber();
V3D hkl = Peaks->getPeak(i).getHKL();
if (crossTerms) {
predictOffsetsWithCrossTerms(offsets1, offsets2, offsets3, maxOrder, runNumber, peakGoniometerMatrix, hkl,
lambdaFilter, includePeaksInRange, includeOrderZero, alreadyDonePeaks);
} else {
predictOffsets(0, offsets1, maxOrder, runNumber, peakGoniometerMatrix, hkl, lambdaFilter, includePeaksInRange,
includeOrderZero, alreadyDonePeaks);
predictOffsets(1, offsets2, maxOrder, runNumber, peakGoniometerMatrix, hkl, lambdaFilter, includePeaksInRange,
notOrderZero, alreadyDonePeaks);
predictOffsets(2, offsets3, maxOrder, runNumber, peakGoniometerMatrix, hkl, lambdaFilter, includePeaksInRange,
notOrderZero, alreadyDonePeaks);
}
}
// Sort peaks by run number so that peaks with equal goniometer matrices are
// adjacent
std::vector<std::pair<std::string, bool>> criteria;
criteria.emplace_back("RunNumber", true);
workspace_type_enum const workspace_type = determineWorkspaceType(Peaks);
if (workspace_type == workspace_type_enum::regular_peaks) {
criteria.emplace_back("BankName", true);
}
criteria.emplace_back("h", true);
criteria.emplace_back("k", true);
criteria.emplace_back("l", true);
outPeaks->sort(criteria);
for (int i = 0; i < static_cast<int>(outPeaks->getNumberPeaks()); ++i) {
outPeaks->getPeak(i).setPeakNumber(i);
}
setProperty("SatellitePeaks", outPeaks);
}
PredictSatellitePeaks::workspace_type_enum
PredictSatellitePeaks::determineWorkspaceType(API::IPeaksWorkspace_sptr const &iPeaksWorkspace) const {
if (std::dynamic_pointer_cast<PeaksWorkspace>(iPeaksWorkspace) != nullptr) {
return workspace_type_enum::regular_peaks;
}
else if (std::dynamic_pointer_cast<LeanElasticPeaksWorkspace>(iPeaksWorkspace) != nullptr) {
return workspace_type_enum::lean_elastic_peaks;
}
else {
return workspace_type_enum::invalid;
}
}
void PredictSatellitePeaks::predictOffsets(const int indexModulatedVector, const V3D &offsets, const int maxOrder,
const int runNumber, const Kernel::Matrix<double> &goniometer,
const V3D &hkl, const HKLFilterWavelength &lambdaFilter,
const bool includePeaksInRange, const bool includeOrderZero,
vector<vector<int>> &alreadyDonePeaks) {
if (offsets == V3D(0, 0, 0) && !includeOrderZero)
return;
for (int order = -maxOrder; order <= maxOrder; order++) {
if (order == 0 && !includeOrderZero)
continue; // exclude order 0
V3D satelliteHKL(hkl);
satelliteHKL += offsets * order;
if (!lambdaFilter.isAllowed(satelliteHKL) && includePeaksInRange)
continue;
std::shared_ptr<IPeak> satellite_iPeak = createPeakForOutputWorkspace(goniometer, satelliteHKL);
V3D mnp;
mnp[indexModulatedVector] = order;
addPeakToOutputWorkspace(satellite_iPeak, goniometer, hkl, satelliteHKL, runNumber, alreadyDonePeaks, mnp);
}
}
void PredictSatellitePeaks::predictOffsetsWithCrossTerms(V3D offsets1, V3D offsets2, V3D offsets3, const int maxOrder,
const int runNumber,
Kernel::Matrix<double> const &peakGoniometerMatrix, V3D &hkl,
const HKLFilterWavelength &lambdaFilter,
const bool includePeaksInRange, const bool includeOrderZero,
vector<vector<int>> &alreadyDonePeaks) {
if (offsets1 == V3D(0, 0, 0) && offsets2 == V3D(0, 0, 0) && offsets3 == V3D(0, 0, 0) && !includeOrderZero)
return;
DblMatrix offsetsMat(3, 3);
offsetsMat.setColumn(0, offsets1);
offsetsMat.setColumn(1, offsets2);
offsetsMat.setColumn(2, offsets3);
int maxOrder1 = maxOrder;
if (offsets1 == V3D(0, 0, 0))
maxOrder1 = 0;
int maxOrder2 = maxOrder;
if (offsets2 == V3D(0, 0, 0))
maxOrder2 = 0;
int maxOrder3 = maxOrder;
if (offsets3 == V3D(0, 0, 0))
maxOrder3 = 0;
for (int m = -maxOrder1; m <= maxOrder1; m++)
for (int n = -maxOrder2; n <= maxOrder2; n++)
for (int p = -maxOrder3; p <= maxOrder3; p++) {
if (m == 0 && n == 0 && p == 0 && !includeOrderZero)
continue; // exclude 0,0,0
V3D satelliteHKL(hkl);
V3D mnp = V3D(m, n, p);
satelliteHKL -= offsetsMat * mnp;
if (!lambdaFilter.isAllowed(satelliteHKL) && includePeaksInRange)
continue;
std::shared_ptr<IPeak> satellite_iPeak = createPeakForOutputWorkspace(peakGoniometerMatrix, satelliteHKL);
addPeakToOutputWorkspace(satellite_iPeak, peakGoniometerMatrix, hkl, satelliteHKL, runNumber, alreadyDonePeaks,
mnp);
}
}
std::shared_ptr<Geometry::IPeak>
PredictSatellitePeaks::createPeakForOutputWorkspace(const Kernel::Matrix<double> &peakGoniometerMatrix,
const Kernel::V3D &satelliteHKL) {
workspace_type_enum workspace_type = determineWorkspaceType(Peaks);
const Kernel::DblMatrix &UB = Peaks->sample().getOrientedLattice().getUB();
if (workspace_type == workspace_type_enum::regular_peaks) {
Kernel::V3D const Qs = peakGoniometerMatrix * UB * satelliteHKL * 2.0 * M_PI * m_qConventionFactor;
// Check if Q is non-physical
if (Qs.Z() * m_qConventionFactor <= 0)
return nullptr;
std::shared_ptr<IPeak> satellite_iPeak = Peaks->createPeak(Qs, 1);
return satellite_iPeak;
}
else if (workspace_type == workspace_type_enum::lean_elastic_peaks) {
Kernel::V3D const Qs = UB * satelliteHKL * 2.0 * M_PI * m_qConventionFactor;
std::shared_ptr<IPeak> satellite_iPeak = Peaks->createPeakQSample(Qs);
return satellite_iPeak;
}
else
return nullptr;
}
void PredictSatellitePeaks::addPeakToOutputWorkspace(const std::shared_ptr<IPeak> &satellite_iPeak,
const Kernel::Matrix<double> &peak_goniometer_matrix,
const Kernel::V3D &hkl, const Kernel::V3D &satelliteHKL,
const int runNumber,
std::vector<std::vector<int>> &alreadyDonePeaks,
const Kernel::V3D &mnp) {
if (satellite_iPeak == nullptr)
return;
const workspace_type_enum workspace_type = determineWorkspaceType(Peaks);
if (workspace_type == workspace_type_enum::regular_peaks) {
const Geometry::InstrumentRayTracer tracer(Peaks->getInstrument());
const std::shared_ptr<Peak> peak = std::dynamic_pointer_cast<Peak>(satellite_iPeak);
if (!peak->findDetector(tracer))
return;
}
const std::vector<int> savPk{runNumber, boost::math::iround(1000.0 * satelliteHKL[0]),
boost::math::iround(1000.0 * satelliteHKL[1]),
boost::math::iround(1000.0 * satelliteHKL[2])};
const bool foundPeak = binary_search(alreadyDonePeaks.begin(), alreadyDonePeaks.end(), savPk);
if (!foundPeak) {
alreadyDonePeaks.emplace_back(savPk);
}
else
return;
satellite_iPeak->setGoniometerMatrix(peak_goniometer_matrix);
satellite_iPeak->setHKL(satelliteHKL * m_qConventionFactor);
satellite_iPeak->setIntHKL(hkl * m_qConventionFactor);
satellite_iPeak->setRunNumber(runNumber);
satellite_iPeak->setIntMNP(mnp * m_qConventionFactor);
outPeaks->addPeak(*satellite_iPeak);
return;
}
V3D PredictSatellitePeaks::getOffsetVector(const std::string &label) {
vector<double> offsets = getProperty(label);
if (offsets.empty()) {
offsets.emplace_back(0.0);
offsets.emplace_back(0.0);
offsets.emplace_back(0.0);
}
V3D offsets1 = V3D(offsets[0], offsets[1], offsets[2]);
return offsets1;
}
} // namespace Crystal
} // namespace Mantid