TEST(FunctionFactoryTest, CreateCompositeFunctionTest)
{
std::string ini = "CompositeFunction("
"FunctionFactoryTestFunction(A=10,B=20),"
"FunctionFactoryTestFunction(A=30,B=40)"
")";
IFunction_sptr fun = FunctionFactory::instance().createFitFunction(ini);
EXPECT_TRUE( fun.get() != nullptr );
CompositeFunction_sptr cf = boost::dynamic_pointer_cast<CompositeFunction>(fun);
EXPECT_TRUE( cf.get() != nullptr );
EXPECT_EQ( cf->nFunctions(), 2 );
auto f1 = cf->getFunction(0);
auto f2 = cf->getFunction(1);
EXPECT_EQ(f1->getParameter("A"),10);
EXPECT_EQ(f1->getParameter("B"),20);
EXPECT_EQ(f2->getParameter("A"),30);
EXPECT_EQ(f2->getParameter("B"),40);
EXPECT_EQ(cf->getParameter("f0.A"),10);
EXPECT_EQ(cf->getParameter("f0.B"),20);
EXPECT_EQ(cf->getParameter("f1.A"),30);
EXPECT_EQ(cf->getParameter("f1.B"),40);
std::cerr << '\n' << fun->asString(true) << '\n' << std::endl;
IFunction_sptr fun1 = FunctionFactory::instance().createFitFunction(ini);
EXPECT_TRUE( fun1.get() != nullptr );
cf = boost::dynamic_pointer_cast<CompositeFunction>(fun1);
EXPECT_TRUE( cf.get() != nullptr );
EXPECT_EQ( cf->nFunctions(), 2 );
EXPECT_EQ(cf->getParameter("f0.A"),10);
EXPECT_EQ(cf->getParameter("f0.B"),20);
EXPECT_EQ(cf->getParameter("f1.A"),30);
EXPECT_EQ(cf->getParameter("f1.B"),40);
}
void IqtFit::plotGuess(QtProperty *) {
// Do nothing if there is no sample data curve
if (!m_uiForm.ppPlot->hasCurve("Sample"))
return;
CompositeFunction_sptr function = createFunction(true);
// Create the double* array from the input workspace
const size_t binIndxLow =
m_ffInputWS->binIndexOf(m_ffRangeManager->value(m_properties["StartX"]));
const size_t binIndxHigh =
m_ffInputWS->binIndexOf(m_ffRangeManager->value(m_properties["EndX"]));
const size_t nData = binIndxHigh - binIndxLow;
std::vector<double> inputXData(nData);
const Mantid::MantidVec &XValues = m_ffInputWS->readX(0);
const bool isHistogram = m_ffInputWS->isHistogramData();
for (size_t i = 0; i < nData; i++) {
if (isHistogram)
inputXData[i] =
0.5 * (XValues[binIndxLow + i] + XValues[binIndxLow + i + 1]);
else
inputXData[i] = XValues[binIndxLow + i];
}
FunctionDomain1DVector domain(inputXData);
FunctionValues outputData(domain);
function->function(domain, outputData);
QVector<double> dataX;
QVector<double> dataY;
for (size_t i = 0; i < nData; i++) {
dataX.append(inputXData[i]);
dataY.append(outputData.getCalculated(i));
}
IAlgorithm_sptr createWsAlg =
AlgorithmManager::Instance().create("CreateWorkspace");
createWsAlg->initialize();
createWsAlg->setChild(true);
createWsAlg->setLogging(false);
createWsAlg->setProperty("OutputWorkspace", "__GuessAnon");
createWsAlg->setProperty("NSpec", 1);
createWsAlg->setProperty("DataX", dataX.toStdVector());
createWsAlg->setProperty("DataY", dataY.toStdVector());
createWsAlg->execute();
MatrixWorkspace_sptr guessWs = createWsAlg->getProperty("OutputWorkspace");
m_uiForm.ppPlot->addSpectrum("Guess", guessWs, 0, Qt::green);
}
/// Returns a TableWorkspace with refined cell parameters and error.
ITableWorkspace_sptr PoldiFitPeaks2D::getRefinedCellParameters(
const IFunction_sptr &fitFunction) const {
Poldi2DFunction_sptr poldi2DFunction =
boost::dynamic_pointer_cast<Poldi2DFunction>(fitFunction);
if (!poldi2DFunction || poldi2DFunction->nFunctions() < 1) {
throw std::invalid_argument(
"Cannot process function that is not a Poldi2DFunction.");
}
// Create a new table for lattice parameters
ITableWorkspace_sptr latticeParameterTable =
WorkspaceFactory::Instance().createTable();
latticeParameterTable->addColumn("str", "Parameter");
latticeParameterTable->addColumn("double", "Value");
latticeParameterTable->addColumn("double", "Error");
// The first function should be PoldiSpectrumPawleyFunction
boost::shared_ptr<PoldiSpectrumPawleyFunction> poldiPawleyFunction =
boost::dynamic_pointer_cast<PoldiSpectrumPawleyFunction>(
poldi2DFunction->getFunction(0));
if (!poldiPawleyFunction) {
throw std::invalid_argument("First function in Poldi2DFunction is not "
"PoldiSpectrumPawleyFunction.");
}
// Get the actual PawleyFunction to extract parameters.
IPawleyFunction_sptr pawleyFunction =
boost::dynamic_pointer_cast<IPawleyFunction>(
poldiPawleyFunction->getDecoratedFunction());
if (pawleyFunction) {
CompositeFunction_sptr pawleyParts =
boost::dynamic_pointer_cast<CompositeFunction>(
pawleyFunction->getDecoratedFunction());
// The first function in PawleyFunction contains the parameters
IFunction_sptr pawleyParameters = pawleyParts->getFunction(0);
for (size_t i = 0; i < pawleyParameters->nParams(); ++i) {
TableRow newRow = latticeParameterTable->appendRow();
newRow << pawleyParameters->parameterName(i)
<< pawleyParameters->getParameter(i)
<< pawleyParameters->getError(i);
}
}
return latticeParameterTable;
}
/** Makes sure that the function is consistent.
*/
void CompositeFunction::checkFunction() {
m_nParams = 0;
m_paramOffsets.clear();
m_IFunction.clear();
std::vector<IFunction_sptr> functions(m_functions.begin(), m_functions.end());
m_functions.clear();
for (auto &f : functions) {
CompositeFunction_sptr cf =
boost::dynamic_pointer_cast<CompositeFunction>(f);
if (cf)
cf->checkFunction();
addFunction(f);
}
}
void PoldiFitPeaks1D::setValuesFromProfileFunction(
PoldiPeak_sptr poldiPeak, const IFunction_sptr &fittedFunction) const {
CompositeFunction_sptr totalFunction =
boost::dynamic_pointer_cast<CompositeFunction>(fittedFunction);
if (totalFunction) {
IPeakFunction_sptr peakFunction =
boost::dynamic_pointer_cast<IPeakFunction>(
totalFunction->getFunction(0));
if (peakFunction) {
poldiPeak->setIntensity(
UncertainValue(peakFunction->height(), peakFunction->getError(0)));
poldiPeak->setQ(
UncertainValue(peakFunction->centre(), peakFunction->getError(1)));
poldiPeak->setFwhm(UncertainValue(peakFunction->fwhm(),
getFwhmWidthRelation(peakFunction) *
peakFunction->getError(2)));
}
}
}
/**
* Split this function into independent functions. The number of functions in
* the
* returned vector must be equal to the number
* of domains. The result of evaluation of the i-th function on the i-th domain
* must be
* the same as if this MultiDomainFunction was evaluated.
*/
std::vector<IFunction_sptr>
MultiDomainFunction::createEquivalentFunctions() const {
size_t nDomains = m_maxIndex + 1;
std::vector<CompositeFunction_sptr> compositeFunctions(nDomains);
for (size_t iFun = 0; iFun < nFunctions(); ++iFun) {
// find the domains member function must be applied to
std::vector<size_t> domains;
getDomainIndices(iFun, nDomains, domains);
for (auto i = domains.begin(); i != domains.end(); ++i) {
size_t j = *i;
CompositeFunction_sptr cf = compositeFunctions[j];
if (!cf) {
// create a composite function for each domain
cf = CompositeFunction_sptr(new CompositeFunction());
compositeFunctions[j] = cf;
}
// add copies of all functions applied to j-th domain to a single
// compositefunction
cf->addFunction(FunctionFactory::Instance().createInitialized(
getFunction(iFun)->asString()));
}
}
std::vector<IFunction_sptr> outFunctions(nDomains);
// fill in the output vector
// check functions containing a single member and take it out of the composite
for (size_t i = 0; i < compositeFunctions.size(); ++i) {
auto fun = compositeFunctions[i];
if (!fun || fun->nFunctions() == 0) {
throw std::runtime_error("There is no function for domain " +
boost::lexical_cast<std::string>(i));
}
if (fun->nFunctions() > 1) {
outFunctions[i] = fun;
} else {
outFunctions[i] = fun->getFunction(0);
}
}
return outFunctions;
}
PoldiPeakCollection_sptr
PoldiFitPeaks1D2::fitPeaks(const PoldiPeakCollection_sptr &peaks) {
g_log.information() << "Peaks to fit: " << peaks->peakCount() << std::endl;
std::vector<RefinedRange_sptr> rawRanges = getRefinedRanges(peaks);
std::vector<RefinedRange_sptr> reducedRanges = getReducedRanges(rawRanges);
g_log.information() << "Ranges used for fitting: " << reducedRanges.size()
<< std::endl;
Workspace2D_sptr dataWorkspace = getProperty("InputWorkspace");
m_fitplots->removeAll();
for (size_t i = 0; i < reducedRanges.size(); ++i) {
RefinedRange_sptr currentRange = reducedRanges[i];
int nMin = getBestChebyshevPolynomialDegree(dataWorkspace, currentRange);
if (nMin > -1) {
IAlgorithm_sptr fit = getFitAlgorithm(dataWorkspace, currentRange, nMin);
fit->execute();
IFunction_sptr fitFunction = fit->getProperty("Function");
CompositeFunction_sptr composite =
boost::dynamic_pointer_cast<CompositeFunction>(fitFunction);
if (!composite) {
throw std::runtime_error("Not a composite function!");
}
std::vector<PoldiPeak_sptr> peaks = currentRange->getPeaks();
for (size_t i = 0; i < peaks.size(); ++i) {
setValuesFromProfileFunction(peaks[i], composite->getFunction(i));
MatrixWorkspace_sptr fpg = fit->getProperty("OutputWorkspace");
m_fitplots->addWorkspace(fpg);
}
}
}
return getReducedPeakCollection(peaks);
}
/**
* Construct a PoldiPeakCollection from a Poldi2DFunction
*
* This method performs the opposite operation of
*getFunctionFromPeakCollection.
* It takes a function, checks if it's of the proper type and turns the
* information into a PoldiPeakCollection.
*
* @param Poldi2DFunction with one PoldiSpectrumDomainFunction per peak
* @return PoldiPeakCollection containing peaks with normalized intensities
*/
PoldiPeakCollection_sptr PoldiFitPeaks2D::getPeakCollectionFromFunction(
const IFunction_sptr &fitFunction) {
Poldi2DFunction_sptr poldi2DFunction =
boost::dynamic_pointer_cast<Poldi2DFunction>(fitFunction);
if (!poldi2DFunction) {
throw std::invalid_argument(
"Cannot process function that is not a Poldi2DFunction.");
}
PoldiPeakCollection_sptr normalizedPeaks =
boost::make_shared<PoldiPeakCollection>(PoldiPeakCollection::Integral);
boost::shared_ptr<const Kernel::DblMatrix> covarianceMatrix =
poldi2DFunction->getCovarianceMatrix();
size_t offset = 0;
for (size_t i = 0; i < poldi2DFunction->nFunctions(); ++i) {
boost::shared_ptr<PoldiSpectrumPawleyFunction> poldiPawleyFunction =
boost::dynamic_pointer_cast<PoldiSpectrumPawleyFunction>(
poldi2DFunction->getFunction(i));
// If it's a Pawley function, there are several peaks in one function.
if (poldiPawleyFunction) {
IPawleyFunction_sptr pawleyFunction =
poldiPawleyFunction->getPawleyFunction();
if (pawleyFunction) {
CompositeFunction_sptr decoratedFunction =
boost::dynamic_pointer_cast<CompositeFunction>(
pawleyFunction->getDecoratedFunction());
offset = decoratedFunction->getFunction(0)->nParams();
for (size_t j = 0; j < pawleyFunction->getPeakCount(); ++j) {
IPeakFunction_sptr profileFunction =
pawleyFunction->getPeakFunction(j);
size_t nLocalParams = profileFunction->nParams();
boost::shared_ptr<Kernel::DblMatrix> localCov =
getLocalCovarianceMatrix(covarianceMatrix, offset, nLocalParams);
profileFunction->setCovarianceMatrix(localCov);
// Increment offset for next function
offset += nLocalParams;
V3D peakHKL = pawleyFunction->getPeakHKL(j);
PoldiPeak_sptr peak =
getPeakFromPeakFunction(profileFunction, peakHKL);
normalizedPeaks->addPeak(peak);
}
}
break;
}
// Otherwise, it's just one peak in this function.
boost::shared_ptr<PoldiSpectrumDomainFunction> peakFunction =
boost::dynamic_pointer_cast<PoldiSpectrumDomainFunction>(
poldi2DFunction->getFunction(i));
if (peakFunction) {
IPeakFunction_sptr profileFunction =
boost::dynamic_pointer_cast<IPeakFunction>(
peakFunction->getProfileFunction());
// Get local covariance matrix
size_t nLocalParams = profileFunction->nParams();
boost::shared_ptr<Kernel::DblMatrix> localCov =
getLocalCovarianceMatrix(covarianceMatrix, offset, nLocalParams);
profileFunction->setCovarianceMatrix(localCov);
// Increment offset for next function
offset += nLocalParams;
PoldiPeak_sptr peak =
getPeakFromPeakFunction(profileFunction, V3D(0, 0, 0));
normalizedPeaks->addPeak(peak);
}
}
return normalizedPeaks;
}
/**
* Create a composite function from an expression.
* @param expr :: The input expression
* @param parentAttributes :: An output map filled with the attribute name &
* values of the parent function
* @return A pointer to the created function
*/
CompositeFunction_sptr FunctionFactoryImpl::createComposite(
const Expression &expr,
std::map<std::string, std::string> &parentAttributes) const {
if (expr.name() != ";")
inputError(expr.str());
if (expr.size() == 0) {
return CompositeFunction_sptr();
}
const std::vector<Expression> &terms = expr.terms();
auto it = terms.cbegin();
const Expression &term = it->bracketsRemoved();
CompositeFunction_sptr cfun;
if (term.name() == "=") {
if (term.terms()[0].name() == "composite") {
cfun = boost::dynamic_pointer_cast<CompositeFunction>(
createFunction(term.terms()[1].name()));
if (!cfun)
inputError(expr.str());
++it;
} else if (term.terms()[0].name() == "name") {
cfun = boost::dynamic_pointer_cast<CompositeFunction>(
createFunction("CompositeFunction"));
if (!cfun)
inputError(expr.str());
} else {
inputError(expr.str());
}
} else if (term.name() == ",") {
auto firstTerm = term.terms().cbegin();
if (firstTerm->name() == "=") {
if (firstTerm->terms()[0].name() == "composite") {
cfun = boost::dynamic_pointer_cast<CompositeFunction>(
createSimple(term, parentAttributes));
if (!cfun)
inputError(expr.str());
++it;
} else if (firstTerm->terms()[0].name() == "name") {
cfun = boost::dynamic_pointer_cast<CompositeFunction>(
createFunction("CompositeFunction"));
if (!cfun)
inputError(expr.str());
} else {
inputError(expr.str());
}
}
} else if (term.name() == ";") {
cfun = boost::dynamic_pointer_cast<CompositeFunction>(
createFunction("CompositeFunction"));
if (!cfun)
inputError(expr.str());
} else {
inputError(expr.str());
}
if (!cfun)
inputError(expr.str());
for (; it != terms.end(); ++it) {
const Expression &term = it->bracketsRemoved();
IFunction_sptr fun;
std::map<std::string, std::string> pAttributes;
if (term.name() == ";") {
fun = createComposite(term, pAttributes);
if (!fun)
continue;
} else {
std::string parName = term[0].name();
if (parName.size() >= 10 && parName.substr(0, 10) == "constraint") {
addConstraints(cfun, term[1]);
continue;
} else if (parName == "ties") {
addTies(cfun, term[1]);
continue;
} else {
fun = createSimple(term, pAttributes);
}
}
cfun->addFunction(fun);
size_t i = cfun->nFunctions() - 1;
for (auto &pAttribute : pAttributes) {
// Apply parent attributes of the child function to this function. If this
// function doesn't have those attributes, they get passed up the chain to
// this function's parent.
if (cfun->hasLocalAttribute(pAttribute.first)) {
cfun->setLocalAttributeValue(i, pAttribute.first, pAttribute.second);
} else {
parentAttributes[pAttribute.first] = pAttribute.second;
}
}
}
if (cfun) {
cfun->applyTies();
}
return cfun;
}
void IqtFit::constrainIntensities(CompositeFunction_sptr func) {
std::string paramName = "f1.Intensity";
size_t index = func->parameterIndex(paramName);
switch (m_uiForm.cbFitType->currentIndex()) {
case 0: // 1 Exp
case 2: // 1 Str
if (!func->isFixed(index)) {
func->tie(paramName, "1-f0.A0");
} else {
std::string paramValue =
boost::lexical_cast<std::string>(func->getParameter(paramName));
func->tie(paramName, paramValue);
func->tie("f0.A0", "1-" + paramName);
}
break;
case 1: // 2 Exp
case 3: // 1 Exp & 1 Str
if (!func->isFixed(index)) {
func->tie(paramName, "1-f2.Intensity-f0.A0");
} else {
std::string paramValue =
boost::lexical_cast<std::string>(func->getParameter(paramName));
func->tie(paramName, "1-f2.Intensity-f0.A0");
func->tie(paramName, paramValue);
}
break;
}
}
/**
* Create a composite function from an expression.
* @param expr :: The input expression
* @param parentAttributes :: An output map filled with the attribute name & values of the parent function
* @return A pointer to the created function
*/
CompositeFunction_sptr FunctionFactoryImpl::createComposite(const Expression& expr, std::map<std::string,std::string>& parentAttributes)const
{
if (expr.name() != ";") inputError(expr.str());
if (expr.size() == 0)
{
return CompositeFunction_sptr();
}
const std::vector<Expression>& terms = expr.terms();
std::vector<Expression>::const_iterator it = terms.begin();
const Expression& term = it->bracketsRemoved();
CompositeFunction_sptr cfun;
if (term.name() == "=")
{
if (term.terms()[0].name() == "composite")
{
cfun = boost::dynamic_pointer_cast<CompositeFunction>(createFunction(term.terms()[1].name()));
if (!cfun) inputError(expr.str());
++it;
}
else if (term.terms()[0].name() == "name")
{
cfun = boost::dynamic_pointer_cast<CompositeFunction>(createFunction("CompositeFunction"));
if (!cfun) inputError(expr.str());
}
else
{
inputError(expr.str());
}
}
else if (term.name() == ",")
{
std::vector<Expression>::const_iterator firstTerm = term.terms().begin();
if (firstTerm->name() == "=")
{
if (firstTerm->terms()[0].name() == "composite")
{
cfun = boost::dynamic_pointer_cast<CompositeFunction>(createSimple(term,parentAttributes));
if (!cfun) inputError(expr.str());
++it;
}
else if (firstTerm->terms()[0].name() == "name")
{
cfun = boost::dynamic_pointer_cast<CompositeFunction>(createFunction("CompositeFunction"));
if (!cfun) inputError(expr.str());
}
else
{
inputError(expr.str());
}
}
}
else if (term.name() == ";")
{
cfun = boost::dynamic_pointer_cast<CompositeFunction>(createFunction("CompositeFunction"));
if (!cfun) inputError(expr.str());
}
else
{
inputError(expr.str());
}
for(;it!=terms.end();++it)
{
const Expression& term = it->bracketsRemoved();
IFunction_sptr fun;
std::map<std::string,std::string> pAttributes;
if (term.name() == ";")
{
fun = createComposite(term,pAttributes);
if (!fun) continue;
}
else
{
std::string parName = term[0].name();
if (parName.size() >= 10 && parName.substr(0,10) == "constraint")
{
addConstraints(cfun,term[1]);
continue;
}
else if (parName == "ties")
{
addTies(cfun,term[1]);
continue;
}
else
{
fun = createSimple(term,pAttributes);
}
}
cfun->addFunction(fun);
size_t i = cfun->nFunctions() - 1;
for(auto att = pAttributes.begin(); att != pAttributes.end(); ++att)
{
cfun->setLocalAttributeValue(i,att->first,att->second);
}
}
cfun->applyTies();
return cfun;
}