diff --git a/.clang-format b/.clang-format
index 5bead5f39dd3c5841f615beb6472c4c504d407af..8aa6b1a8549d79d51b23df2f66a019a477927489 100644
--- a/.clang-format
+++ b/.clang-format
@@ -1,2 +1,47 @@
-BasedOnStyle: LLVM
+---
+# BasedOnStyle: Google
+AccessModifierOffset: -1
+ConstructorInitializerIndentWidth: 4
+AlignEscapedNewlinesLeft: true
+AlignTrailingComments: true
+AllowAllParametersOfDeclarationOnNextLine: true
+AllowShortIfStatementsOnASingleLine: true
+AllowShortLoopsOnASingleLine: true
+AlwaysBreakTemplateDeclarations: true
+AlwaysBreakBeforeMultilineStrings: true
+BreakBeforeBinaryOperators: false
+BreakBeforeTernaryOperators: true
+BreakConstructorInitializersBeforeComma: false
+BinPackParameters: true
+ColumnLimit: 80
+ConstructorInitializerAllOnOneLineOrOnePerLine: true
+DerivePointerBinding: true
+ExperimentalAutoDetectBinPacking: false
+IndentCaseLabels: true
+MaxEmptyLinesToKeep: 1
+NamespaceIndentation: None
+ObjCSpaceBeforeProtocolList: false
+PenaltyBreakBeforeFirstCallParameter: 1
+PenaltyBreakComment: 60
+PenaltyBreakString: 1000
+PenaltyBreakFirstLessLess: 120
+PenaltyExcessCharacter: 1000000
+PenaltyReturnTypeOnItsOwnLine: 200
+PointerBindsToType: true
+SpacesBeforeTrailingComments: 2
+Cpp11BracedListStyle: true
+Standard: Auto
+IndentWidth: 2
+TabWidth: 8
+UseTab: Never
+BreakBeforeBraces: Attach
+IndentFunctionDeclarationAfterType: true
+SpacesInParentheses: false
+SpacesInAngles: false
+SpaceInEmptyParentheses: false
+SpacesInCStyleCastParentheses: false
+SpaceAfterControlStatementKeyword: true
+SpaceBeforeAssignmentOperators: true
+ContinuationIndentWidth: 4
+...
diff --git a/Framework/Crystal/inc/MantidCrystal/OptimizeLatticeForCellType.h b/Framework/Crystal/inc/MantidCrystal/OptimizeLatticeForCellType.h
index fb4caa904d1bfea75159d75fc22fc504a83b1879..75747b2ce2850d253cff857c26fab336af3855dd 100644
--- a/Framework/Crystal/inc/MantidCrystal/OptimizeLatticeForCellType.h
+++ b/Framework/Crystal/inc/MantidCrystal/OptimizeLatticeForCellType.h
@@ -5,6 +5,7 @@
#include "MantidKernel/System.h"
#include "MantidDataObjects/OffsetsWorkspace.h"
#include "MantidDataObjects/PeaksWorkspace.h"
+#include "MantidAPI/IFunction.h"
#include <gsl/gsl_blas.h>
#include <gsl/gsl_multifit_nlin.h>
#include <gsl/gsl_multimin.h>
@@ -40,7 +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
@@ -63,7 +64,7 @@ public:
std::vector<double> ¶ms);
void optLattice(std::string inname, std::vector<double> ¶ms, double *out);
-private:
+ private:
// Overridden Algorithm methods
void init();
void exec();
@@ -71,12 +72,9 @@ private:
bool edgePixel(DataObjects::PeaksWorkspace_sptr ws, std::string bankName,
int col, int row, int Edge);
Kernel::DblMatrix aMatrix(std::vector<double> lattice);
- void calculateErrors(std::string inname, std::string cell_type,
- std::vector<double> &Params, std::vector<double> &sigabc,
- double chisq);
};
-} // namespace Algorithm
-} // namespace Mantid
+} // namespace Algorithm
+} // namespace Mantid
#endif /*MANTID_CRYSTAL_OptimizeLatticeForCellType_H_*/
diff --git a/Framework/Crystal/src/OptimizeLatticeForCellType.cpp b/Framework/Crystal/src/OptimizeLatticeForCellType.cpp
index a426f3b0196904774cd85526ef02ca5bc7e181a1..f580bdbd8e08bfffdff3dfe92f2d824432ca760a 100644
--- a/Framework/Crystal/src/OptimizeLatticeForCellType.cpp
+++ b/Framework/Crystal/src/OptimizeLatticeForCellType.cpp
@@ -95,7 +95,7 @@ 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 +104,7 @@ 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());
@@ -138,8 +138,7 @@ void OptimizeLatticeForCellType::exec() {
std::ostringstream fun_str;
fun_str << "name=LatticeErrors";
- for (size_t i = 0; i < 6; i++)
- fun_str << ",p" << i << "=" << lat[i];
+ for (size_t i = 0; i < 6; i++) fun_str << ",p" << i << "=" << lat[i];
IAlgorithm_sptr fit_alg;
try {
@@ -187,13 +186,14 @@ void OptimizeLatticeForCellType::exec() {
}
fit_alg->setProperty("InputWorkspace", data);
fit_alg->setProperty("WorkspaceIndex", 0);
- fit_alg->setProperty("MaxIterations", 5000);
+ fit_alg->setProperty("CostFunction", "Unweighted least squares");
fit_alg->setProperty("CreateOutput", true);
fit_alg->setProperty("Output", "fit");
fit_alg->executeAsChildAlg();
- MatrixWorkspace_sptr fitWS = fit_alg->getProperty("OutputWorkspace");
double chisq = fit_alg->getProperty("OutputChi2overDoF");
+ ITableWorkspace_sptr ParamTable = fit_alg->getProperty("OutputParameters");
+
std::vector<double> Params;
IFunction_sptr out = fit_alg->getProperty("Function");
@@ -208,33 +208,13 @@ void OptimizeLatticeForCellType::exec() {
OrientedLattice latt = peakWS->mutableSample().getOrientedLattice();
DblMatrix UBnew = latt.getUB();
- calculateErrors(runWS[i_run]->getName(), cell_type, Params, sigabc, chisq);
+ for (size_t i = 0; i < 6; i++) sigabc[i] = ParamTable->Double(i, 2);
+
OrientedLattice o_lattice;
o_lattice.setUB(UBnew);
- if (cell_type == ReducedCell::CUBIC()) {
- o_lattice.setError(sigabc[0], sigabc[0], sigabc[0], 0, 0, 0);
- } else if (cell_type == ReducedCell::TETRAGONAL()) {
- o_lattice.setError(sigabc[0], sigabc[0], sigabc[1], 0, 0, 0);
- } else if (cell_type == ReducedCell::ORTHORHOMBIC()) {
- o_lattice.setError(sigabc[0], sigabc[1], sigabc[2], 0, 0, 0);
- } else if (cell_type == ReducedCell::RHOMBOHEDRAL()) {
- o_lattice.setError(sigabc[0], sigabc[0], sigabc[0], sigabc[1], sigabc[1],
- sigabc[1]);
- } else if (cell_type == ReducedCell::HEXAGONAL()) {
- o_lattice.setError(sigabc[0], sigabc[0], sigabc[1], 0, 0, 0);
- } else if (cell_type == "Monoclinic ( a unique )") {
- o_lattice.setError(sigabc[0], sigabc[1], sigabc[2], sigabc[3], 0, 0);
- } else if (cell_type == ReducedCell::MONOCLINIC() ||
- cell_type == "Monoclinic ( b unique )") {
- o_lattice.setError(sigabc[0], sigabc[1], sigabc[2], 0, sigabc[3], 0);
-
- } else if (cell_type == "Monoclinic ( c unique )") {
- o_lattice.setError(sigabc[0], sigabc[1], sigabc[2], 0, 0, sigabc[3]);
- } else if (cell_type == ReducedCell::TRICLINIC()) {
- o_lattice.setError(sigabc[0], sigabc[1], sigabc[2], sigabc[3], sigabc[4],
- sigabc[5]);
- }
+ o_lattice.setError(sigabc[0], sigabc[1], sigabc[2], sigabc[3], sigabc[4],
+ sigabc[5]);
// Show the modified lattice parameters
g_log.notice() << runWS[i_run]->getName() << " " << o_lattice << "\n";
@@ -253,15 +233,14 @@ 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() +
@@ -271,8 +250,8 @@ 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: "
@@ -374,8 +353,7 @@ double OptimizeLatticeForCellType::optLatticeSum(std::string inname,
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];
+ for (size_t i = 0; i < n_peaks; i++) ChiSqTot += out[i];
delete[] out;
return ChiSqTot;
}
@@ -395,8 +373,7 @@ void OptimizeLatticeForCellType::optLattice(std::string inname,
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 < 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());
@@ -443,8 +420,7 @@ 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);
@@ -517,118 +493,6 @@ DblMatrix OptimizeLatticeForCellType::aMatrix(std::vector<double> lattice) {
return result;
}
-//-----------------------------------------------------------------------------------------
-/**
- @param npeaks Number of peaks
- @param inname Name of workspace containing peaks
- @param cell_type cell type to optimize
- @param Params optimized cell parameters
- @param sigabc errors of optimized parameters
- @param chisq chisq from optimization
-*/
-void OptimizeLatticeForCellType::calculateErrors(std::string inname,
- std::string cell_type,
- std::vector<double> &Params,
- std::vector<double> &sigabc,
- double chisq) {
-
- for (size_t i = 0; i < sigabc.size(); i++)
- sigabc[i] = 0.0;
-
- int MAX_STEPS = 10; // evaluate approximation using deltas
- // ranging over 10 orders of magnitudue
- double START_DELTA = 1.0e-2; // start with change of 1%
- std::vector<double> approx; // save list of approximations
-
- double delta;
- size_t nopt = 1;
- if (cell_type.compare(0, 2, "Te") == 0)
- nopt = 2;
- else if (cell_type.compare(0, 2, "Or") == 0)
- nopt = 3;
- else if (cell_type.compare(0, 2, "Rh") == 0)
- nopt = 2;
- else if (cell_type.compare(0, 2, "He") == 0)
- nopt = 2;
- else if (cell_type.compare(0, 2, "Mo") == 0)
- nopt = 4;
- else if (cell_type.compare(0, 2, "Tr") == 0)
- nopt = 6;
-
- std::vector<double> x;
- x.push_back(Params[0]);
- if (cell_type.compare(0, 2, "Te") == 0)
- x.push_back(Params[2]);
- else if (cell_type.compare(0, 2, "Or") == 0) {
- x.push_back(Params[1]);
- x.push_back(Params[2]);
- } else if (cell_type.compare(0, 2, "Rh") == 0)
- x.push_back(Params[3]);
- else if (cell_type.compare(0, 2, "He") == 0)
- x.push_back(Params[2]);
- else if (cell_type.compare(0, 2, "Mo") == 0) {
- x.push_back(Params[1]);
- x.push_back(Params[2]);
- if (cell_type.length() < 13)
- x.push_back(Params[4]); // default is b
- else if (cell_type.compare(13, 1, "a") == 0)
- x.push_back(Params[3]);
- else if (cell_type.compare(13, 1, "b") == 0)
- x.push_back(Params[4]);
- else if (cell_type.compare(13, 1, "c") == 0)
- x.push_back(Params[5]);
- } else if (cell_type.compare(0, 2, "Tr") == 0)
- for (size_t i = 1; i < nopt; i++)
- x.push_back(Params[i]);
-
- for (size_t k = 0; k < nopt; k++) {
- double diff = 0.0;
-
- double x_save = x[k];
-
- if (x_save < 1.0e-8) // if parameter essentially 0, use
- delta = 1.0e-8; // a "small" step
- else
- delta = START_DELTA * x_save;
-
- for (int count = 0; count < MAX_STEPS; count++) {
- x[k] = x_save + delta;
- double chi_3 = optLatticeSum(inname, cell_type, x);
-
- x[k] = x_save - delta;
- double chi_1 = optLatticeSum(inname, cell_type, x);
-
- x[k] = x_save;
- double chi_2 = optLatticeSum(inname, cell_type, x);
-
- diff = chi_1 - 2 * chi_2 + chi_3;
- if (diff > 0) {
- approx.push_back(std::abs(delta) * std::sqrt(2.0 / std::abs(diff)));
- }
- delta = delta / 10;
- }
- if (approx.size() == 0)
- sigabc[k] = Mantid::EMPTY_DBL(); // no reasonable value
-
- else if (approx.size() == 1)
- sigabc[k] = approx[0]; // only one possible value
-
- else // use one with smallest diff
- {
- double min_diff = Mantid::EMPTY_DBL();
- for (size_t i = 0; i < approx.size() - 1; i++) {
- diff = std::abs((approx[i + 1] - approx[i]) / approx[i]);
- if (diff < min_diff) {
- sigabc[k] = approx[i + 1];
- min_diff = diff;
- }
- }
- }
- }
-
- for (size_t i = 0; i < std::min<size_t>(7, sigabc.size()); i++)
- sigabc[i] = sqrt(chisq) * sigabc[i];
-}
-} // namespace Algorithm
-} // namespace Mantid
+} // namespace Algorithm
+} // namespace Mantid