From d776e34a3abc6159c41b2777dfa5e061a93c8a6b Mon Sep 17 00:00:00 2001
From: Vickie Lynch <lynchve@ornl.gov>
Date: Fri, 23 Oct 2015 16:38:29 -0400
Subject: [PATCH] Refs #14072 use LatticeFunction not LatticeErrors
---
Framework/Crystal/CMakeLists.txt | 2 -
.../Crystal/inc/MantidCrystal/LatticeErrors.h | 75 ----
.../OptimizeLatticeForCellType.h | 17 +-
Framework/Crystal/src/LatticeErrors.cpp | 88 -----
.../src/OptimizeLatticeForCellType.cpp | 349 ++++++------------
.../test/OptimizeLatticeForCellTypeTest.h | 7 +-
6 files changed, 122 insertions(+), 416 deletions(-)
delete mode 100644 Framework/Crystal/inc/MantidCrystal/LatticeErrors.h
delete mode 100644 Framework/Crystal/src/LatticeErrors.cpp
diff --git a/Framework/Crystal/CMakeLists.txt b/Framework/Crystal/CMakeLists.txt
index 75e9b1fbbc7..23a4ae3ce45 100644
--- a/Framework/Crystal/CMakeLists.txt
+++ b/Framework/Crystal/CMakeLists.txt
@@ -28,7 +28,6 @@ set ( SRC_FILES
src/IntegratePeakTimeSlices.cpp
src/IntegratePeaksHybrid.cpp
src/IntegratePeaksUsingClusters.cpp
- src/LatticeErrors.cpp
src/LoadHKL.cpp
src/LoadIsawPeaks.cpp
src/LoadIsawSpectrum.cpp
@@ -102,7 +101,6 @@ set ( INC_FILES
inc/MantidCrystal/IntegratePeakTimeSlices.h
inc/MantidCrystal/IntegratePeaksHybrid.h
inc/MantidCrystal/IntegratePeaksUsingClusters.h
- inc/MantidCrystal/LatticeErrors.h
inc/MantidCrystal/LoadHKL.h
inc/MantidCrystal/LoadIsawPeaks.h
inc/MantidCrystal/LoadIsawSpectrum.h
diff --git a/Framework/Crystal/inc/MantidCrystal/LatticeErrors.h b/Framework/Crystal/inc/MantidCrystal/LatticeErrors.h
deleted file mode 100644
index eb4216b722c..00000000000
--- a/Framework/Crystal/inc/MantidCrystal/LatticeErrors.h
+++ /dev/null
@@ -1,75 +0,0 @@
-/*
- * LatticeErrors.h
- *
- * Created on: Jan 26, 2013
- * Author: ruth
- */
-
-#ifndef PEAKHKLERRORS_H_
-#define PEAKHKLERRORS_H_
-#include "MantidKernel/System.h"
-
-#include "MantidAPI/IFunction.h"
-#include "MantidGeometry/Instrument.h"
-#include "MantidAPI/ParamFunction.h"
-#include "MantidAPI/IFunction1D.h"
-#include "MantidDataObjects/PeaksWorkspace.h"
-#include "MantidAPI/IFunction.h"
-#include "MantidGeometry/Crystal/OrientedLattice.h"
-#include "MantidKernel/Matrix.h"
-
-namespace Mantid {
-namespace Crystal {
-
-/**
-
- @author Ruth Mikkelson, SNS,ORNL
- @date 01/26/2013
- Copyright © 2012 ISIS Rutherford Appleton Laboratory, NScD Oak Ridge
- National Laboratory & European Spallation Source
-
- This file is part of Mantid.
-
- Mantid is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 3 of the License, or
- (at your option) any later version.
-
- Mantid is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>.
-
- File change history is stored at: <https://github.com/mantidproject/mantid>
- Code Documentation is available at: <http://doxygen.mantidproject.org>
- */
-class DLLExport LatticeErrors : public API::ParamFunction,
- public API::IFunction1D {
-public:
- LatticeErrors();
- virtual ~LatticeErrors();
-
- std::string name() const { return std::string("LatticeErrors"); };
-
- virtual int version() const { return 1; };
-
- const std::string category() const { return "Crystal"; };
-
- void function1D(double *out, const double *xValues, const size_t nData) const;
-
- // void functionDeriv1D(Mantid::API::Jacobian* out, const double *xValues,
- // const size_t nData);
-
- void functionDerivLocal(API::Jacobian *, const double *, const size_t);
- void functionDeriv(const API::FunctionDomain &domain,
- API::Jacobian &jacobian);
-
- void init();
-};
-}
-}
-
-#endif /* PEAKHKLERRORS_H_ */
diff --git a/Framework/Crystal/inc/MantidCrystal/OptimizeLatticeForCellType.h b/Framework/Crystal/inc/MantidCrystal/OptimizeLatticeForCellType.h
index 75747b2ce28..36f90a39c66 100644
--- a/Framework/Crystal/inc/MantidCrystal/OptimizeLatticeForCellType.h
+++ b/Framework/Crystal/inc/MantidCrystal/OptimizeLatticeForCellType.h
@@ -41,7 +41,7 @@ namespace Crystal {
Code Documentation is available at: <http://doxygen.mantidproject.org>
*/
class DLLExport OptimizeLatticeForCellType : public API::Algorithm {
- public:
+public:
/// Default constructorMatrix
OptimizeLatticeForCellType();
/// Destructor
@@ -59,22 +59,21 @@ class DLLExport OptimizeLatticeForCellType : public API::Algorithm {
virtual int version() const { return 1; }
/// Algorithm's category for identification overriding a virtual method
virtual const std::string category() const { return "Crystal"; }
- /// Call TOFLattice as a Child Algorithm to get statistics of the peaks
- double optLatticeSum(std::string inname, std::string cell_type,
- std::vector<double> ¶ms);
- void optLattice(std::string inname, std::vector<double> ¶ms, double *out);
- private:
+ std::vector<double> outParams(std::string cell_type, int icol,
+ API::ITableWorkspace_sptr ParamTable);
+ std::string inParams(std::string cell_type, std::vector<double> &lat);
+
+private:
// Overridden Algorithm methods
void init();
void exec();
/// Function to find peaks near detector edge
bool edgePixel(DataObjects::PeaksWorkspace_sptr ws, std::string bankName,
int col, int row, int Edge);
- Kernel::DblMatrix aMatrix(std::vector<double> lattice);
};
-} // namespace Algorithm
-} // namespace Mantid
+} // namespace Algorithm
+} // namespace Mantid
#endif /*MANTID_CRYSTAL_OptimizeLatticeForCellType_H_*/
diff --git a/Framework/Crystal/src/LatticeErrors.cpp b/Framework/Crystal/src/LatticeErrors.cpp
deleted file mode 100644
index a0a5306a38b..00000000000
--- a/Framework/Crystal/src/LatticeErrors.cpp
+++ /dev/null
@@ -1,88 +0,0 @@
-/*
- * LatticeErrors.cpp
- *
-
- */
-#include "MantidAPI/FunctionFactory.h"
-#include "MantidAPI/IConstraint.h"
-#include "MantidAPI/IFunction1D.h"
-#include "MantidGeometry/Crystal/IPeak.h"
-#include "MantidAPI/ParamFunction.h"
-#include "MantidCrystal/LatticeErrors.h"
-#include "MantidCrystal/SCDPanelErrors.h"
-#include "MantidCrystal/OptimizeLatticeForCellType.h"
-
-using namespace Mantid::DataObjects;
-using namespace Mantid::API;
-using namespace Mantid::Kernel;
-using namespace Mantid::Geometry;
-using Mantid::Geometry::CompAssembly;
-using Mantid::Geometry::IObjComponent_const_sptr;
-
-namespace Mantid {
-
-namespace Crystal {
-namespace {
-/// static logger
-Kernel::Logger g_log("LatticeErrors");
-}
-
-DECLARE_FUNCTION(LatticeErrors)
-
-LatticeErrors::LatticeErrors() : ParamFunction(), IFunction1D() {}
-
-LatticeErrors::~LatticeErrors() {}
-
-void LatticeErrors::init() {
- declareParameter("p0", 0.0, "a lattice param");
- declareParameter("p1", 0.0, "b lattice param");
- declareParameter("p2", 0.0, "c lattice param");
- declareParameter("p3", 0.0, "alpha lattice param");
- declareParameter("p4", 0.0, "beta lattice param");
- declareParameter("p5", 0.0, "gamma lattice param");
-}
-
-/**
- * Calculates the h,k, and l offsets from an integer for (some of )the peaks,
- *given the parameter values.
- *
- * @param out For each peak element in this array.
- * @param xValues xValues give the index in the PeaksWorkspace for the peak.
- *For each peak considered there are
- * three consecutive entries all with the same index
- * @param nData The size of the xValues and out arrays
- */
-void LatticeErrors::function1D(double *out, const double *xValues,
- const size_t nData) const {
- UNUSED_ARG(xValues);
- std::string PeakWorkspaceName = "_peaks";
- std::vector<double> Params;
- Params.push_back(getParameter("p0"));
- Params.push_back(getParameter("p1"));
- Params.push_back(getParameter("p2"));
- Params.push_back(getParameter("p3"));
- Params.push_back(getParameter("p4"));
- Params.push_back(getParameter("p5"));
-
- Mantid::Crystal::OptimizeLatticeForCellType u;
- u.optLattice(PeakWorkspaceName, Params, out);
- double ChiSqTot = 0;
- for (size_t i = 0; i < nData; i++) {
- ChiSqTot += out[i];
- }
-
- g_log.debug() << " Chi**2 = " << ChiSqTot << " nData = " << nData
- << std::endl;
-}
-void LatticeErrors::functionDerivLocal(API::Jacobian *, const double *,
- const size_t) {
- throw Mantid::Kernel::Exception::NotImplementedError(
- "functionDerivLocal is not implemented for LatticeErrors.");
-}
-
-void LatticeErrors::functionDeriv(const API::FunctionDomain &domain,
- API::Jacobian &jacobian) {
- calNumericalDeriv(domain, jacobian);
-}
-}
-}
diff --git a/Framework/Crystal/src/OptimizeLatticeForCellType.cpp b/Framework/Crystal/src/OptimizeLatticeForCellType.cpp
index f580bdbd8e0..83f7bb62841 100644
--- a/Framework/Crystal/src/OptimizeLatticeForCellType.cpp
+++ b/Framework/Crystal/src/OptimizeLatticeForCellType.cpp
@@ -45,9 +45,6 @@ void OptimizeLatticeForCellType::init() {
cellTypes.push_back(ReducedCell::HEXAGONAL());
cellTypes.push_back(ReducedCell::RHOMBOHEDRAL());
cellTypes.push_back(ReducedCell::MONOCLINIC());
- cellTypes.push_back("Monoclinic ( a unique )");
- cellTypes.push_back("Monoclinic ( b unique )");
- cellTypes.push_back("Monoclinic ( c unique )");
cellTypes.push_back(ReducedCell::TRICLINIC());
declareProperty("CellType", cellTypes[0],
boost::make_shared<StringListValidator>(cellTypes),
@@ -95,7 +92,7 @@ void OptimizeLatticeForCellType::exec() {
runWS.push_back(ws);
if (perRun) {
- std::vector<std::pair<std::string, bool>> criteria;
+ std::vector<std::pair<std::string, bool> > criteria;
// Sort by run number
criteria.push_back(std::pair<std::string, bool>("runnumber", true));
ws->sort(criteria);
@@ -104,7 +101,7 @@ void OptimizeLatticeForCellType::exec() {
int count = 0;
for (size_t i = 0; i < peaks_all.size(); i++) {
if (peaks_all[i].getRunNumber() != run) {
- count++; // first entry in runWS is input workspace
+ count++; // first entry in runWS is input workspace
DataObjects::PeaksWorkspace_sptr cloneWS(new PeaksWorkspace());
cloneWS->setInstrument(ws->getInstrument());
cloneWS->copyExperimentInfoFrom(ws.get());
@@ -126,19 +123,8 @@ void OptimizeLatticeForCellType::exec() {
const DblMatrix UB = peakWS->sample().getOrientedLattice().getUB();
std::vector<double> lat(6);
IndexingUtils::GetLatticeParameters(UB, lat);
- // initialize parameters for optimization
- size_t n_peaks = peakWS->getNumberPeaks();
- MatrixWorkspace_sptr data = WorkspaceFactory::Instance().create(
- std::string("Workspace2D"), 1, n_peaks, n_peaks);
- for (size_t i = 0; i < data->blocksize(); i++) {
- data->dataX(0)[i] = static_cast<double>(i);
- data->dataY(0)[i] = 0.0;
- data->dataE(0)[i] = 1.0;
- }
- std::ostringstream fun_str;
- fun_str << "name=LatticeErrors";
- for (size_t i = 0; i < 6; i++) fun_str << ",p" << i << "=" << lat[i];
+ std::string fun_str = inParams(cell_type, lat);
IAlgorithm_sptr fit_alg;
try {
@@ -149,43 +135,9 @@ void OptimizeLatticeForCellType::exec() {
throw;
}
- fit_alg->setPropertyValue("Function", fun_str.str());
- if (cell_type == ReducedCell::CUBIC()) {
- std::ostringstream tie_str;
- tie_str << "p1=p0,p2=p0,p3=90,p4=90,p5=90";
- fit_alg->setProperty("Ties", tie_str.str());
- } else if (cell_type == ReducedCell::TETRAGONAL()) {
- std::ostringstream tie_str;
- tie_str << "p1=p0,p3=90,p4=90,p5=90";
- fit_alg->setProperty("Ties", tie_str.str());
- } else if (cell_type == ReducedCell::ORTHORHOMBIC()) {
- std::ostringstream tie_str;
- tie_str << "p3=90,p4=90,p5=90";
- fit_alg->setProperty("Ties", tie_str.str());
- } else if (cell_type == ReducedCell::RHOMBOHEDRAL()) {
- std::ostringstream tie_str;
- tie_str << "p1=p0,p2=p0,p4=p3,p5=p3";
- fit_alg->setProperty("Ties", tie_str.str());
- } else if (cell_type == ReducedCell::HEXAGONAL()) {
- std::ostringstream tie_str;
- tie_str << "p1=p0,p3=90,p4=90,p5=120";
- fit_alg->setProperty("Ties", tie_str.str());
- } else if (cell_type == "Monoclinic ( a unique )") {
- std::ostringstream tie_str;
- tie_str << "p4=90,p5=90";
- fit_alg->setProperty("Ties", tie_str.str());
- } else if (cell_type == ReducedCell::MONOCLINIC() ||
- cell_type == "Monoclinic ( b unique )") {
- std::ostringstream tie_str;
- tie_str << "p3=90,p5=90";
- fit_alg->setProperty("Ties", tie_str.str());
- } else if (cell_type == "Monoclinic ( c unique )") {
- std::ostringstream tie_str;
- tie_str << "p3=90,p4=90";
- fit_alg->setProperty("Ties", tie_str.str());
- }
- fit_alg->setProperty("InputWorkspace", data);
- fit_alg->setProperty("WorkspaceIndex", 0);
+ fit_alg->setPropertyValue("Function", fun_str);
+ fit_alg->setProperty("Ties", "ZeroShift=0.0");
+ fit_alg->setProperty("InputWorkspace", peakWS);
fit_alg->setProperty("CostFunction", "Unweighted least squares");
fit_alg->setProperty("CreateOutput", true);
fit_alg->setProperty("Output", "fit");
@@ -193,26 +145,13 @@ void OptimizeLatticeForCellType::exec() {
double chisq = fit_alg->getProperty("OutputChi2overDoF");
ITableWorkspace_sptr ParamTable = fit_alg->getProperty("OutputParameters");
+ std::vector<double> Params = outParams(cell_type, 1, ParamTable);
- std::vector<double> Params;
- IFunction_sptr out = fit_alg->getProperty("Function");
-
- Params.push_back(out->getParameter("p0"));
- Params.push_back(out->getParameter("p1"));
- Params.push_back(out->getParameter("p2"));
- Params.push_back(out->getParameter("p3"));
- Params.push_back(out->getParameter("p4"));
- Params.push_back(out->getParameter("p5"));
-
- std::vector<double> sigabc(Params.size());
- OrientedLattice latt = peakWS->mutableSample().getOrientedLattice();
- DblMatrix UBnew = latt.getUB();
-
- for (size_t i = 0; i < 6; i++) sigabc[i] = ParamTable->Double(i, 2);
+ std::vector<double> sigabc = outParams(cell_type, 2, ParamTable);
OrientedLattice o_lattice;
- o_lattice.setUB(UBnew);
-
+ o_lattice.set(Params[0], Params[1], Params[2], Params[3], Params[4],
+ Params[5]);
o_lattice.setError(sigabc[0], sigabc[1], sigabc[2], sigabc[3], sigabc[4],
sigabc[5]);
@@ -233,14 +172,15 @@ void OptimizeLatticeForCellType::exec() {
AnalysisDataService::Instance().remove("_peaks");
if (perRun) {
std::string outputdir = getProperty("OutputDirectory");
- if (outputdir[outputdir.size() - 1] != '/') outputdir += "/";
+ if (outputdir[outputdir.size() - 1] != '/')
+ outputdir += "/";
// Save Peaks
Mantid::API::IAlgorithm_sptr savePks_alg =
createChildAlgorithm("SaveIsawPeaks");
savePks_alg->setPropertyValue("InputWorkspace", runWS[i_run]->getName());
- savePks_alg->setProperty(
- "Filename",
- outputdir + "ls" + runWS[i_run]->getName() + ".integrate");
+ savePks_alg->setProperty("Filename", outputdir + "ls" +
+ runWS[i_run]->getName() +
+ ".integrate");
savePks_alg->executeAsChildAlg();
g_log.notice() << "See output file: " << outputdir + "ls" +
runWS[i_run]->getName() +
@@ -250,8 +190,8 @@ void OptimizeLatticeForCellType::exec() {
Mantid::API::IAlgorithm_sptr saveUB_alg =
createChildAlgorithm("SaveIsawUB");
saveUB_alg->setPropertyValue("InputWorkspace", runWS[i_run]->getName());
- saveUB_alg->setProperty(
- "Filename", outputdir + "ls" + runWS[i_run]->getName() + ".mat");
+ saveUB_alg->setProperty("Filename", outputdir + "ls" +
+ runWS[i_run]->getName() + ".mat");
saveUB_alg->executeAsChildAlg();
// Show the names of files written
g_log.notice() << "See output file: "
@@ -262,151 +202,123 @@ void OptimizeLatticeForCellType::exec() {
}
//-----------------------------------------------------------------------------------------
/**
- @param inname Name of Filename containing peaks
@param cell_type cell type to optimize
- @param params optimized cell parameters
- @return chisq of optimization
+ @param lat optimized cell parameters
+ @return fun_str string of parameters for fitting
*/
-double OptimizeLatticeForCellType::optLatticeSum(std::string inname,
- std::string cell_type,
- std::vector<double> ¶ms) {
+std::string OptimizeLatticeForCellType::inParams(std::string cell_type,
+ std::vector<double> &lat) {
+ std::ostringstream fun_str;
+ fun_str << "name=LatticeFunction,CrystalSystem=" << cell_type;
+
std::vector<double> lattice_parameters;
lattice_parameters.assign(6, 0);
if (cell_type == ReducedCell::CUBIC()) {
- lattice_parameters[0] = params[0];
- lattice_parameters[1] = params[0];
- lattice_parameters[2] = params[0];
+ fun_str << ",a=" << lat[0];
+ } else if (cell_type == ReducedCell::TETRAGONAL()) {
+ fun_str << ",a=" << lat[0];
+ fun_str << ",c=" << lat[2];
+ } else if (cell_type == ReducedCell::ORTHORHOMBIC()) {
+ fun_str << ",a=" << lat[0];
+ fun_str << ",b=" << lat[1];
+ fun_str << ",c=" << lat[2];
+ } else if (cell_type == ReducedCell::RHOMBOHEDRAL()) {
+ fun_str << ",a=" << lat[0];
+ fun_str << ",Alpha=" << lat[3];
+ } else if (cell_type == ReducedCell::HEXAGONAL()) {
+ fun_str << ",a=" << lat[0];
+ fun_str << ",c=" << lat[2];
+ } else if (cell_type == ReducedCell::MONOCLINIC()) {
+ fun_str << ",a=" << lat[0];
+ fun_str << ",b=" << lat[1];
+ fun_str << ",c=" << lat[2];
+ fun_str << ",Beta=" << lat[4];
+ } else if (cell_type == ReducedCell::TRICLINIC()) {
+ fun_str << ",a=" << lat[0];
+ fun_str << ",b=" << lat[1];
+ fun_str << ",c=" << lat[2];
+ fun_str << ",Alpha=" << lat[3];
+ fun_str << ",Beta=" << lat[4];
+ fun_str << ",Gamma=" << lat[5];
+ }
+ return fun_str.str();
+}
+//-----------------------------------------------------------------------------------------
+/**
+ @param cell_type cell type to optimize
+ @param col 1 for parameter 2 for error
+ @param ParamTable optimized cell parameters
+ @return chisq of optimization
+*/
+std::vector<double>
+OptimizeLatticeForCellType::outParams(std::string cell_type, int icol,
+ ITableWorkspace_sptr ParamTable) {
+ std::vector<double> lattice_parameters;
+ lattice_parameters.assign(6, 0);
+
+ if (cell_type == ReducedCell::CUBIC()) {
+ lattice_parameters[0] = ParamTable->Double(0, icol);
+ lattice_parameters[1] = ParamTable->Double(0, icol);
+ lattice_parameters[2] = ParamTable->Double(0, icol);
+ if (icol == 2)
+ return lattice_parameters;
lattice_parameters[3] = 90;
lattice_parameters[4] = 90;
lattice_parameters[5] = 90;
} else if (cell_type == ReducedCell::TETRAGONAL()) {
- lattice_parameters[0] = params[0];
- lattice_parameters[1] = params[0];
- lattice_parameters[2] = params[1];
-
+ lattice_parameters[0] = ParamTable->Double(0, icol);
+ lattice_parameters[1] = ParamTable->Double(0, icol);
+ lattice_parameters[2] = ParamTable->Double(1, icol);
+ if (icol == 2)
+ return lattice_parameters;
lattice_parameters[3] = 90;
lattice_parameters[4] = 90;
lattice_parameters[5] = 90;
} else if (cell_type == ReducedCell::ORTHORHOMBIC()) {
- lattice_parameters[0] = params[0];
- lattice_parameters[1] = params[1];
- lattice_parameters[2] = params[2];
-
+ lattice_parameters[0] = ParamTable->Double(0, icol);
+ lattice_parameters[1] = ParamTable->Double(1, icol);
+ lattice_parameters[2] = ParamTable->Double(2, icol);
+ if (icol == 2)
+ return lattice_parameters;
lattice_parameters[3] = 90;
lattice_parameters[4] = 90;
lattice_parameters[5] = 90;
} else if (cell_type == ReducedCell::RHOMBOHEDRAL()) {
- lattice_parameters[0] = params[0];
- lattice_parameters[1] = params[0];
- lattice_parameters[2] = params[0];
-
- lattice_parameters[3] = params[1];
- lattice_parameters[4] = params[1];
- lattice_parameters[5] = params[1];
+ lattice_parameters[0] = ParamTable->Double(0, icol);
+ lattice_parameters[1] = ParamTable->Double(0, icol);
+ lattice_parameters[2] = ParamTable->Double(0, icol);
+ lattice_parameters[3] = ParamTable->Double(1, icol);
+ lattice_parameters[4] = ParamTable->Double(1, icol);
+ lattice_parameters[5] = ParamTable->Double(1, icol);
} else if (cell_type == ReducedCell::HEXAGONAL()) {
- lattice_parameters[0] = params[0];
- lattice_parameters[1] = params[0];
- lattice_parameters[2] = params[1];
-
+ lattice_parameters[0] = ParamTable->Double(0, icol);
+ lattice_parameters[1] = ParamTable->Double(0, icol);
+ lattice_parameters[2] = ParamTable->Double(1, icol);
+ if (icol == 2)
+ return lattice_parameters;
lattice_parameters[3] = 90;
lattice_parameters[4] = 90;
lattice_parameters[5] = 120;
- } else if (cell_type == "Monoclinic ( a unique )") {
- lattice_parameters[0] = params[0];
- lattice_parameters[1] = params[1];
- lattice_parameters[2] = params[2];
-
- lattice_parameters[3] = params[3];
- lattice_parameters[4] = 90;
- lattice_parameters[5] = 90;
- } else if (cell_type == ReducedCell::MONOCLINIC() ||
- cell_type == "Monoclinic ( b unique )") {
- lattice_parameters[0] = params[0];
- lattice_parameters[1] = params[1];
- lattice_parameters[2] = params[2];
-
+ } else if (cell_type == ReducedCell::MONOCLINIC()) {
+ lattice_parameters[0] = ParamTable->Double(0, icol);
+ lattice_parameters[1] = ParamTable->Double(1, icol);
+ lattice_parameters[2] = ParamTable->Double(2, icol);
+ lattice_parameters[4] = ParamTable->Double(3, icol);
+ if (icol == 2)
+ return lattice_parameters;
lattice_parameters[3] = 90;
- lattice_parameters[4] = params[3];
lattice_parameters[5] = 90;
- } else if (cell_type == "Monoclinic ( c unique )") {
- lattice_parameters[0] = params[0];
- lattice_parameters[1] = params[1];
- lattice_parameters[2] = params[2];
-
- lattice_parameters[3] = 90;
- lattice_parameters[4] = 90;
- lattice_parameters[5] = params[3];
} else if (cell_type == ReducedCell::TRICLINIC()) {
- lattice_parameters[0] = params[0];
- lattice_parameters[1] = params[1];
- lattice_parameters[2] = params[2];
-
- lattice_parameters[3] = params[3];
- lattice_parameters[4] = params[4];
- lattice_parameters[5] = params[5];
+ lattice_parameters[0] = ParamTable->Double(0, icol);
+ lattice_parameters[1] = ParamTable->Double(1, icol);
+ lattice_parameters[2] = ParamTable->Double(2, icol);
+ lattice_parameters[3] = ParamTable->Double(3, icol);
+ lattice_parameters[4] = ParamTable->Double(4, icol);
+ lattice_parameters[5] = ParamTable->Double(5, icol);
}
- PeaksWorkspace_sptr ws = boost::dynamic_pointer_cast<PeaksWorkspace>(
- AnalysisDataService::Instance().retrieve(inname));
- size_t n_peaks = ws->getNumberPeaks();
- double *out = new double[n_peaks];
- optLattice(inname, lattice_parameters, out);
- double ChiSqTot = 0;
- for (size_t i = 0; i < n_peaks; i++) ChiSqTot += out[i];
- delete[] out;
- return ChiSqTot;
-}
-//-----------------------------------------------------------------------------------------
-/**
- @param inname Name of workspace containing peaks
- @param params optimized cell parameters
- @param out residuals from optimization
-*/
-void OptimizeLatticeForCellType::optLattice(std::string inname,
- std::vector<double> ¶ms,
- double *out) {
- PeaksWorkspace_sptr ws = boost::dynamic_pointer_cast<PeaksWorkspace>(
- AnalysisDataService::Instance().retrieve(inname));
- const std::vector<Peak> &peaks = ws->getPeaks();
- size_t n_peaks = ws->getNumberPeaks();
- std::vector<V3D> q_vector;
- std::vector<V3D> hkl_vector;
-
- for (size_t i = 0; i < params.size(); i++) params[i] = std::abs(params[i]);
- for (size_t i = 0; i < n_peaks; i++) {
- q_vector.push_back(peaks[i].getQSampleFrame());
- hkl_vector.push_back(peaks[i].getHKL());
- }
-
- Mantid::API::IAlgorithm_sptr alg = createChildAlgorithm("CalculateUMatrix");
- alg->setPropertyValue("PeaksWorkspace", inname);
- alg->setProperty("a", params[0]);
- alg->setProperty("b", params[1]);
- alg->setProperty("c", params[2]);
- alg->setProperty("alpha", params[3]);
- alg->setProperty("beta", params[4]);
- alg->setProperty("gamma", params[5]);
- alg->executeAsChildAlg();
-
- ws = alg->getProperty("PeaksWorkspace");
- OrientedLattice latt = ws->mutableSample().getOrientedLattice();
- DblMatrix UB = latt.getUB();
- DblMatrix A = aMatrix(params);
- DblMatrix Bc = A;
- Bc.Invert();
- DblMatrix U1_B1 = UB * A;
- OrientedLattice o_lattice;
- o_lattice.setUB(U1_B1);
- DblMatrix U1 = o_lattice.getU();
- DblMatrix U1_Bc = U1 * Bc;
-
- for (size_t i = 0; i < hkl_vector.size(); i++) {
- V3D error = U1_Bc * hkl_vector[i] - q_vector[i] / (2.0 * M_PI);
- out[i] = error.norm2();
- }
-
- return;
+ return lattice_parameters;
}
//-----------------------------------------------------------------------------------------
/**
@@ -420,7 +332,8 @@ void OptimizeLatticeForCellType::optLattice(std::string inname,
bool OptimizeLatticeForCellType::edgePixel(PeaksWorkspace_sptr ws,
std::string bankName, int col,
int row, int Edge) {
- if (bankName.compare("None") == 0) return false;
+ if (bankName.compare("None") == 0)
+ return false;
Geometry::Instrument_const_sptr Iptr = ws->getInstrument();
boost::shared_ptr<const IComponent> parent =
Iptr->getComponentByName(bankName);
@@ -453,46 +366,6 @@ bool OptimizeLatticeForCellType::edgePixel(PeaksWorkspace_sptr ws,
}
return false;
}
-//-----------------------------------------------------------------------------------------
-/**
- @param lattice lattice parameters
- @return the A matrix calculated
-*/
-DblMatrix OptimizeLatticeForCellType::aMatrix(std::vector<double> lattice) {
- double degrees_to_radians = M_PI / 180;
- double alpha = lattice[3] * degrees_to_radians;
- double beta = lattice[4] * degrees_to_radians;
- double gamma = lattice[5] * degrees_to_radians;
-
- double l1 = lattice[0];
- double l2 = 0;
- double l3 = 0;
-
- double m1 = lattice[1] * std::cos(gamma);
- double m2 = lattice[1] * std::sin(gamma);
- double m3 = 0;
-
- double n1 = std::cos(beta);
- double n2 =
- (std::cos(alpha) - std::cos(beta) * std::cos(gamma)) / std::sin(gamma);
- double n3 = std::sqrt(1 - n1 * n1 - n2 * n2);
- n1 *= lattice[2];
- n2 *= lattice[2];
- n3 *= lattice[2];
-
- DblMatrix result(3, 3);
- result[0][0] = l1;
- result[0][1] = l2;
- result[0][2] = l3;
- result[1][0] = m1;
- result[1][1] = m2;
- result[1][2] = m3;
- result[2][0] = n1;
- result[2][1] = n2;
- result[2][2] = n3;
-
- return result;
-}
-} // namespace Algorithm
-} // namespace Mantid
+} // namespace Algorithm
+} // namespace Mantid
diff --git a/Framework/Crystal/test/OptimizeLatticeForCellTypeTest.h b/Framework/Crystal/test/OptimizeLatticeForCellTypeTest.h
index cfb87881032..b6a3c5a0b7f 100644
--- a/Framework/Crystal/test/OptimizeLatticeForCellTypeTest.h
+++ b/Framework/Crystal/test/OptimizeLatticeForCellTypeTest.h
@@ -59,8 +59,7 @@ public:
TS_ASSERT_THROWS_NOTHING(alg.initialize())
TS_ASSERT(alg.isInitialized())
TS_ASSERT_THROWS_NOTHING(alg.setPropertyValue("PeaksWorkspace", WSName));
- TS_ASSERT_THROWS_NOTHING(
- alg.setPropertyValue("CellType", "Monoclinic ( a unique )"));
+ TS_ASSERT_THROWS_NOTHING(alg.setPropertyValue("CellType", "Monoclinic"));
TS_ASSERT_THROWS_NOTHING(alg.execute(););
TS_ASSERT(alg.isExecuted());
@@ -69,8 +68,8 @@ public:
// Check that the UB matrix is the same as in TOPAZ_3007.mat
OrientedLattice latt = ws->mutableSample().getOrientedLattice();
- double correct_UB[] = {-0.0477, 0.0413, -0.0005, -0.0055, -0.0090,
- 0.1250, 0.0610, 0.0314, 0.0110};
+ double correct_UB[] = { -0.0477, 0.0413, -0.0005, -0.0055, -0.0090,
+ 0.1250, 0.0610, 0.0314, 0.0110 };
std::vector<double> UB_calculated = latt.getUB().getVector();
--
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