diff --git a/Code/Mantid/Framework/CurveFitting/src/PawleyFunction.cpp b/Code/Mantid/Framework/CurveFitting/src/PawleyFunction.cpp
index b54db9de6e7ba28d3e7084d05b49d98d24f0f134..bfaa272e26cac04350802bbfdb9d207d433671e6 100644
--- a/Code/Mantid/Framework/CurveFitting/src/PawleyFunction.cpp
+++ b/Code/Mantid/Framework/CurveFitting/src/PawleyFunction.cpp
@@ -267,9 +267,8 @@ DECLARE_FUNCTION(PawleyFunction)
/// Constructor
PawleyFunction::PawleyFunction()
- : IPawleyFunction(), m_compositeFunction(),
- m_pawleyParameterFunction(), m_peakProfileComposite(), m_hkls(),
- m_dUnit(), m_wsUnit() {}
+ : IPawleyFunction(), m_compositeFunction(), m_pawleyParameterFunction(),
+ m_peakProfileComposite(), m_hkls(), m_dUnit(), m_wsUnit() {}
void PawleyFunction::setMatrixWorkspace(
boost::shared_ptr<const MatrixWorkspace> workspace, size_t wi,
@@ -366,16 +365,24 @@ void PawleyFunction::function(const FunctionDomain &domain,
FunctionValues &values) const {
UnitCell cell = m_pawleyParameterFunction->getUnitCellFromParameters();
double zeroShift = m_pawleyParameterFunction->getParameter("ZeroShift");
+ std::string centreName =
+ m_pawleyParameterFunction->getProfileFunctionCenterParameterName();
for (size_t i = 0; i < m_hkls.size(); ++i) {
double centre = getTransformedCenter(cell.d(m_hkls[i]));
- m_peakProfileComposite->getFunction(i)->setParameter(
- m_pawleyParameterFunction->getProfileFunctionCenterParameterName(),
- centre + zeroShift);
+ m_peakProfileComposite->getFunction(i)
+ ->setParameter(centreName, centre + zeroShift);
}
m_peakProfileComposite->function(domain, values);
+
+ for (size_t i = 0; i < m_hkls.size(); ++i) {
+ m_peakProfileComposite->getFunction(i)
+ ->setParameter(centreName, m_peakProfileComposite->getFunction(i)
+ ->getParameter(centreName) -
+ zeroShift);
+ }
}
/// Removes all peaks from the function.
diff --git a/Code/Mantid/Framework/SINQ/inc/MantidSINQ/PoldiFitPeaks2D.h b/Code/Mantid/Framework/SINQ/inc/MantidSINQ/PoldiFitPeaks2D.h
index dc2d381822e324b24fffd5f45d4f864a9865e578..343d2e7476482b480979cfff1660826e083029a0 100644
--- a/Code/Mantid/Framework/SINQ/inc/MantidSINQ/PoldiFitPeaks2D.h
+++ b/Code/Mantid/Framework/SINQ/inc/MantidSINQ/PoldiFitPeaks2D.h
@@ -5,6 +5,7 @@
#include "MantidSINQ/DllConfig.h"
#include "MantidAPI/Algorithm.h"
#include "MantidAPI/IFunction.h"
+#include "MantidAPI/IPeakFunction.h"
#include "MantidDataObjects/TableWorkspace.h"
#include "MantidSINQ/PoldiUtilities/PoldiPeakCollection.h"
#include "MantidSINQ/PoldiUtilities/PoldiTimeTransformer.h"
@@ -58,6 +59,18 @@ public:
virtual const std::string summary() const;
+ Poldi2DFunction_sptr getFunctionIndividualPeaks(
+ std::string profileFunctionName,
+ const PoldiPeakCollection_sptr &peakCollection) const;
+
+ Poldi2DFunction_sptr
+ getFunctionPawley(std::string profileFunctionName,
+ const PoldiPeakCollection_sptr &peakCollection) const;
+
+ PoldiPeak_sptr
+ getPeakFromPeakFunction(API::IPeakFunction_sptr profileFunction,
+ const Kernel::V3D &hkl) const;
+
protected:
PoldiPeakCollection_sptr
getPeakCollection(const DataObjects::TableWorkspace_sptr &peakTable) const;
diff --git a/Code/Mantid/Framework/SINQ/src/PoldiFitPeaks2D.cpp b/Code/Mantid/Framework/SINQ/src/PoldiFitPeaks2D.cpp
index 735094834f0288d4e726c83a446d37d785719773..24023846edad6fd6e7e3c8b527919f1c4ae85119 100644
--- a/Code/Mantid/Framework/SINQ/src/PoldiFitPeaks2D.cpp
+++ b/Code/Mantid/Framework/SINQ/src/PoldiFitPeaks2D.cpp
@@ -12,6 +12,7 @@ use the Build/wiki_maker.py script to generate your full wiki page.
#include "MantidAPI/MultiDomainFunction.h"
#include "MantidSINQ/PoldiUtilities/PoldiSpectrumDomainFunction.h"
#include "MantidSINQ/PoldiUtilities/PoldiSpectrumLinearBackground.h"
+#include "MantidSINQ/PoldiUtilities/PoldiSpectrumPawleyFunction.h"
#include "MantidAPI/FunctionDomain1D.h"
#include "MantidSINQ/PoldiUtilities/IPoldiFunction1D.h"
@@ -19,6 +20,7 @@ use the Build/wiki_maker.py script to generate your full wiki page.
#include "MantidSINQ/PoldiUtilities/PoldiInstrumentAdapter.h"
#include "MantidSINQ/PoldiUtilities/PoldiDeadWireDecorator.h"
#include "MantidAPI/IPeakFunction.h"
+#include "MantidAPI/IPawleyFunction.h"
#include "MantidSINQ/PoldiUtilities/Poldi2DFunction.h"
@@ -50,9 +52,7 @@ const std::string PoldiFitPeaks2D::name() const { return "PoldiFitPeaks2D"; }
int PoldiFitPeaks2D::version() const { return 1; }
/// Algorithm's category for identification. @see Algorithm::category
-const std::string PoldiFitPeaks2D::category() const {
- return "SINQ\\Poldi";
-}
+const std::string PoldiFitPeaks2D::category() const { return "SINQ\\Poldi"; }
/// Very short algorithm summary. @see Algorith::summary
const std::string PoldiFitPeaks2D::summary() const {
@@ -71,6 +71,17 @@ void PoldiFitPeaks2D::init() {
"Profile function to use for integrating the peak profiles "
"before calculating the spectrum.");
+ declareProperty("PawleyFit", false, "Instead of refining individual peaks, "
+ "refine a unit cell. Peaks must be "
+ "indexed, an initial cell must be "
+ "provided, as well as a crystal system.");
+ declareProperty("InitialCell", "", "Initial unit cell parameters as 6 "
+ "space-separated numbers. Only used when "
+ "PawleyFit is checked.");
+ declareProperty("CrystalSystem", "", "Crystal system to use for constraining "
+ "unit cell parameters. Only used when "
+ "PawleyFit is checked.");
+
declareProperty("FitConstantBackground", true,
"Add a constant background term to the fit.");
declareProperty("ConstantBackgroundParameter", 0.0,
@@ -102,6 +113,47 @@ void PoldiFitPeaks2D::init() {
"Table workspace with fitted peaks.");
}
+PoldiPeak_sptr
+PoldiFitPeaks2D::getPeakFromPeakFunction(IPeakFunction_sptr profileFunction,
+ const V3D &hkl) const {
+ double centre = profileFunction->centre();
+ double height = profileFunction->height();
+
+ size_t dIndex = 0;
+ size_t iIndex = 0;
+ size_t fIndex = 0;
+
+ for (size_t j = 0; j < profileFunction->nParams(); ++j) {
+ if (profileFunction->getParameter(j) == centre) {
+ dIndex = j;
+ } else if (profileFunction->getParameter(j) == height) {
+ iIndex = j;
+ } else {
+ fIndex = j;
+ }
+ }
+
+ // size_t dIndex = peakFunction->parameterIndex("Centre");
+ UncertainValue d(profileFunction->getParameter(dIndex),
+ profileFunction->getError(dIndex));
+
+ // size_t iIndex = peakFunction->parameterIndex("Area");
+ UncertainValue intensity(profileFunction->getParameter(iIndex),
+ profileFunction->getError(iIndex));
+
+ // size_t fIndex = peakFunction->parameterIndex("Sigma");
+ double fwhmValue = profileFunction->fwhm();
+ UncertainValue fwhm(fwhmValue, fwhmValue /
+ profileFunction->getParameter(fIndex) *
+ profileFunction->getError(fIndex));
+
+ PoldiPeak_sptr peak =
+ PoldiPeak::create(MillerIndices(hkl), d, intensity, UncertainValue(1.0));
+ peak->setFwhm(fwhm, PoldiPeak::FwhmRelation::AbsoluteD);
+
+ return peak;
+}
+
/**
* Construct a PoldiPeakCollection from a Poldi2DFunction
*
@@ -127,77 +179,72 @@ PoldiPeakCollection_sptr PoldiFitPeaks2D::getPeakCollectionFromFunction(
boost::make_shared<PoldiPeakCollection>(PoldiPeakCollection::Integral);
for (size_t i = 0; i < poldi2DFunction->nFunctions(); ++i) {
- boost::shared_ptr<PoldiSpectrumDomainFunction> peakFunction =
- boost::dynamic_pointer_cast<PoldiSpectrumDomainFunction>(
+ boost::shared_ptr<PoldiSpectrumPawleyFunction> poldiPawleyFunction =
+ boost::dynamic_pointer_cast<PoldiSpectrumPawleyFunction>(
poldi2DFunction->getFunction(i));
- if (peakFunction) {
- IPeakFunction_sptr profileFunction =
- boost::dynamic_pointer_cast<IPeakFunction>(
- peakFunction->getProfileFunction());
+ if (poldiPawleyFunction) {
+ IPawleyFunction_sptr pawleyFunction =
+ poldiPawleyFunction->getPawleyFunction();
+ if (pawleyFunction) {
+ CompositeFunction_sptr wrappedFn =
+ boost::dynamic_pointer_cast<CompositeFunction>(
+ pawleyFunction->getDecoratedFunction());
+ IFunction_sptr pawleyParamFn = wrappedFn->getFunction(0);
+ for (size_t j = 0; j < pawleyParamFn->nParams(); ++j) {
+ std::cout << j << " " << pawleyParamFn->parameterName(j) << " "
+ << pawleyParamFn->getParameter(j) << " "
+ << pawleyParamFn->getError(j) << std::endl;
+ }
+
+ for (size_t j = 0; j < pawleyFunction->getPeakCount(); ++j) {
+ IPeakFunction_sptr profileFunction =
+ pawleyFunction->getPeakFunction(j);
+ V3D peakHKL = pawleyFunction->getPeakHKL(j);
- double centre = profileFunction->centre();
- double height = profileFunction->height();
+ PoldiPeak_sptr peak =
+ getPeakFromPeakFunction(profileFunction, peakHKL);
- size_t dIndex = 0;
- size_t iIndex = 0;
- size_t fIndex = 0;
+ normalizedPeaks->addPeak(peak);
- for (size_t j = 0; j < profileFunction->nParams(); ++j) {
- if (profileFunction->getParameter(j) == centre) {
- dIndex = j;
- } else if (profileFunction->getParameter(j) == height) {
- iIndex = j;
- } else {
- fIndex = j;
+ for (size_t p = 0; p < profileFunction->nParams(); ++p) {
+ std::cout << j << " " << p << " "
+ << profileFunction->parameterName(p) << " "
+ << profileFunction->getParameter(p) << std::endl;
+ }
}
}
+ break;
+ }
- // size_t dIndex = peakFunction->parameterIndex("Centre");
- UncertainValue d(peakFunction->getParameter(dIndex),
- peakFunction->getError(dIndex));
-
- // size_t iIndex = peakFunction->parameterIndex("Area");
- UncertainValue intensity(peakFunction->getParameter(iIndex),
- peakFunction->getError(iIndex));
+ boost::shared_ptr<PoldiSpectrumDomainFunction> peakFunction =
+ boost::dynamic_pointer_cast<PoldiSpectrumDomainFunction>(
+ poldi2DFunction->getFunction(i));
- // size_t fIndex = peakFunction->parameterIndex("Sigma");
- double fwhmValue = profileFunction->fwhm();
- UncertainValue fwhm(fwhmValue, fwhmValue /
- peakFunction->getParameter(fIndex) *
- peakFunction->getError(fIndex));
+ if (peakFunction) {
+ IPeakFunction_sptr profileFunction =
+ boost::dynamic_pointer_cast<IPeakFunction>(
+ peakFunction->getProfileFunction());
PoldiPeak_sptr peak =
- PoldiPeak::create(MillerIndices(), d, intensity, UncertainValue(1.0));
- peak->setFwhm(fwhm, PoldiPeak::FwhmRelation::AbsoluteD);
+ getPeakFromPeakFunction(profileFunction, V3D(0, 0, 0));
normalizedPeaks->addPeak(peak);
+ continue;
}
}
return normalizedPeaks;
}
-/**
- * Constructs a proper function from a peak collection
- *
- * This method constructs a Poldi2DFunction and assigns one
- *PoldiSpectrumDomainFunction to it for
- * each peak contained in the peak collection.
- *
- * @param peakCollection :: PoldiPeakCollection containing peaks with integral
- *intensities
- * @return Poldi2DFunction with one PoldiSpectrumDomainFunction per peak
- */
-Poldi2DFunction_sptr PoldiFitPeaks2D::getFunctionFromPeakCollection(
+Poldi2DFunction_sptr PoldiFitPeaks2D::getFunctionIndividualPeaks(
+ std::string profileFunctionName,
const PoldiPeakCollection_sptr &peakCollection) const {
Poldi2DFunction_sptr mdFunction(new Poldi2DFunction);
for (size_t i = 0; i < peakCollection->peakCount(); ++i) {
PoldiPeak_sptr peak = peakCollection->peak(i);
- std::string profileFunctionName = getProperty("PeakProfileFunction");
-
boost::shared_ptr<PoldiSpectrumDomainFunction> peakFunction =
boost::dynamic_pointer_cast<PoldiSpectrumDomainFunction>(
FunctionFactory::Instance().createFunction(
@@ -226,6 +273,86 @@ Poldi2DFunction_sptr PoldiFitPeaks2D::getFunctionFromPeakCollection(
return mdFunction;
}
+Poldi2DFunction_sptr PoldiFitPeaks2D::getFunctionPawley(
+ std::string profileFunctionName,
+ const PoldiPeakCollection_sptr &peakCollection) const {
+ Poldi2DFunction_sptr mdFunction(new Poldi2DFunction);
+
+ boost::shared_ptr<PoldiSpectrumPawleyFunction> poldiPawleyFunction =
+ boost::dynamic_pointer_cast<PoldiSpectrumPawleyFunction>(
+ FunctionFactory::Instance().createFunction(
+ "PoldiSpectrumPawleyFunction"));
+
+ if (!poldiPawleyFunction) {
+ throw std::invalid_argument("Could not create pawley function.");
+ }
+
+ poldiPawleyFunction->setDecoratedFunction("PawleyFunction");
+
+ IPawleyFunction_sptr pawleyFunction =
+ poldiPawleyFunction->getPawleyFunction();
+ pawleyFunction->setProfileFunction(profileFunctionName);
+
+ std::string crystalSystem = getProperty("CrystalSystem");
+ pawleyFunction->setCrystalSystem(crystalSystem);
+
+ std::string initialCell = getProperty("InitialCell");
+ pawleyFunction->setUnitCell(initialCell);
+
+ IPeakFunction_sptr pFun = boost::dynamic_pointer_cast<IPeakFunction>(
+ FunctionFactory::Instance().createFunction(profileFunctionName));
+
+ for (size_t i = 0; i < peakCollection->peakCount(); ++i) {
+ PoldiPeak_sptr peak = peakCollection->peak(i);
+
+ pFun->setCentre(peak->d());
+ pFun->setFwhm(peak->fwhm(PoldiPeak::AbsoluteD));
+ pFun->setIntensity(peak->intensity());
+
+ pawleyFunction->addPeak(peak->hkl().asV3D(),
+ peak->fwhm(PoldiPeak::AbsoluteD),
+ pFun->height());
+
+ IPeakFunction_sptr p = pawleyFunction->getPeakFunction(i);
+ V3D h = pawleyFunction->getPeakHKL(i);
+ std::cout << p->centre() << " " << p->fwhm() << " " << h << std::endl;
+ }
+
+ pawleyFunction->fix(pawleyFunction->parameterIndex("f0.ZeroShift"));
+
+ mdFunction->addFunction(poldiPawleyFunction);
+
+ for (size_t i = 0; i < mdFunction->nParams(); ++i) {
+ std::cout << i << " " << mdFunction->parameterName(i) << " "
+ << mdFunction->getParameter(i) << std::endl;
+ }
+
+ return mdFunction;
+}
+
+/**
+ * Constructs a proper function from a peak collection
+ *
+ * This method constructs a Poldi2DFunction and assigns one
+ *PoldiSpectrumDomainFunction to it for
+ * each peak contained in the peak collection.
+ *
+ * @param peakCollection :: PoldiPeakCollection containing peaks with integral
+ *intensities
+ * @return Poldi2DFunction with one PoldiSpectrumDomainFunction per peak
+ */
+Poldi2DFunction_sptr PoldiFitPeaks2D::getFunctionFromPeakCollection(
+ const PoldiPeakCollection_sptr &peakCollection) const {
+ std::string profileFunctionName = getProperty("PeakProfileFunction");
+
+ bool pawleyFit = getProperty("PawleyFit");
+ if (pawleyFit) {
+ return getFunctionPawley(profileFunctionName, peakCollection);
+ }
+
+ return getFunctionIndividualPeaks(profileFunctionName, peakCollection);
+}
+
/// Executes the algorithm
void PoldiFitPeaks2D::exec() {
TableWorkspace_sptr peakTable = getProperty("PoldiPeakWorkspace");
diff --git a/Code/Mantid/Framework/SINQ/src/PoldiUtilities/PoldiSpectrumPawleyFunction.cpp b/Code/Mantid/Framework/SINQ/src/PoldiUtilities/PoldiSpectrumPawleyFunction.cpp
index ef2d24267fff9ffc053cba2ee1c943348cadb9f5..32094fb95ae044c7e2fe711ed145c182729373f2 100644
--- a/Code/Mantid/Framework/SINQ/src/PoldiUtilities/PoldiSpectrumPawleyFunction.cpp
+++ b/Code/Mantid/Framework/SINQ/src/PoldiUtilities/PoldiSpectrumPawleyFunction.cpp
@@ -34,13 +34,16 @@ void PoldiSpectrumPawleyFunction::function1DSpectrum(
FunctionValues localValues(*helper->domain);
for (size_t i = 0; i < helper->dOffsets.size(); ++i) {
- double newDOffset = helper->dOffsets[i];
+ double newDOffset =
+ helper->dOffsets[i] * helper->deltaD + helper->dFractionalOffsets[i];
m_pawleyFunction->setParameter("f0.ZeroShift", newDOffset);
+ size_t baseOffset = helper->minTOFN;
+
m_pawleyFunction->function(*(helper->domain), localValues);
for (size_t j = 0; j < localValues.size(); ++j) {
- values.addToCalculated(j % domainSize,
+ values.addToCalculated((j + baseOffset) % domainSize,
localValues[j] * helper->factors[j]);
}
}
@@ -60,18 +63,23 @@ void PoldiSpectrumPawleyFunction::functionDeriv1DSpectrum(
if (helper) {
for (size_t i = 0; i < helper->dOffsets.size(); ++i) {
- double newDOffset = helper->dOffsets[i];
+ double newDOffset =
+ helper->dOffsets[i] * helper->deltaD + helper->dFractionalOffsets[i];
m_pawleyFunction->setParameter("f0.ZeroShift", newDOffset);
+ size_t baseOffset = helper->minTOFN;
+
LocalJacobian localJacobian(ny, nParams);
m_pawleyFunction->functionDeriv(*(helper->domain), localJacobian);
for (size_t j = 0; j < ny; ++j) {
- size_t wrapped = j % domainSize;
+ size_t wrapped = (j + baseOffset) % domainSize;
for (size_t p = 0; p < nParams; ++p) {
- jacobian.set(wrapped, p,
- jacobian.get(wrapped, p) +
- localJacobian.getRaw(j, p) * helper->factors[j]);
+ if (m_pawleyFunction->isActive(p)) {
+ jacobian.set(wrapped, p,
+ jacobian.get(wrapped, p) +
+ localJacobian.getRaw(j, p) * helper->factors[j]);
+ }
}
}
}
@@ -86,19 +94,20 @@ PoldiSpectrumPawleyFunction::poldiFunction1D(const std::vector<int> &indices,
FunctionValues &values) const {}
IPawleyFunction_sptr PoldiSpectrumPawleyFunction::getPawleyFunction() const {
- return m_pawleyFunction;
+ return m_pawleyFunction;
}
-void PoldiSpectrumPawleyFunction::beforeDecoratedFunctionSet(const IFunction_sptr &fn)
-{
- IPawleyFunction_sptr pawleyFunction =
- boost::dynamic_pointer_cast<IPawleyFunction>(fn);
+void PoldiSpectrumPawleyFunction::beforeDecoratedFunctionSet(
+ const IFunction_sptr &fn) {
+ IPawleyFunction_sptr pawleyFunction =
+ boost::dynamic_pointer_cast<IPawleyFunction>(fn);
- if (!pawleyFunction) {
- throw std::invalid_argument("Function is not a pawley function.");
- }
+ if (!pawleyFunction) {
+ throw std::invalid_argument("Function is not a pawley function.");
+ }
- m_pawleyFunction = pawleyFunction;
+ m_pawleyFunction = pawleyFunction;
+ m_pawleyFunction->fix(m_pawleyFunction->parameterIndex("f0.ZeroShift"));
}
DECLARE_FUNCTION(PoldiSpectrumPawleyFunction)
diff --git a/Code/Mantid/Framework/SINQ/test/PoldiSpectrumPawleyFunctionTest.h b/Code/Mantid/Framework/SINQ/test/PoldiSpectrumPawleyFunctionTest.h
index 5c61783146da7d191be00e7d24a4d63395f5eb57..aebc73942545167053f24ad199ee8069523f089e 100644
--- a/Code/Mantid/Framework/SINQ/test/PoldiSpectrumPawleyFunctionTest.h
+++ b/Code/Mantid/Framework/SINQ/test/PoldiSpectrumPawleyFunctionTest.h
@@ -5,7 +5,7 @@
#include "MantidSINQ/PoldiUtilities/PoldiSpectrumPawleyFunction.h"
-using Mantid::SINQ::PoldiSpectrumPawleyFunction;
+using namespace Mantid::Poldi;
using namespace Mantid::API;
class PoldiSpectrumPawleyFunctionTest : public CxxTest::TestSuite
@@ -26,4 +26,4 @@ public:
};
-#endif /* MANTID_SINQ_POLDISPECTRUMPAWLEYFUNCTIONTEST_H_ */
\ No newline at end of file
+#endif /* MANTID_SINQ_POLDISPECTRUMPAWLEYFUNCTIONTEST_H_ */
diff --git a/Code/Mantid/instrument/POLDI_Parameters_2014b.xml b/Code/Mantid/instrument/POLDI_Parameters_2014b.xml
index e7c318fa2fec41be006d7b9b9e5e1365a4f41bdf..4867cd326c1a49022812bc68dac0e4697ca39e43 100644
--- a/Code/Mantid/instrument/POLDI_Parameters_2014b.xml
+++ b/Code/Mantid/instrument/POLDI_Parameters_2014b.xml
@@ -3,22 +3,22 @@
<component-link name="chopper">
<parameter name="t0" type="number">
- <value val="-0.00801" />
+ <value val="-0.0069" />
</parameter>
<parameter name="t0_const" type="number">
- <value val="-18.3" />
+ <value val="-6.9" />
</parameter>
</component-link>
<component-link name="detector">
<parameter name="two_theta" type="number">
- <value val="90.95" />
+ <value val="91.12" />
</parameter>
<parameter name="x">
- <value val="-1.000" />
+ <value val="-0.8322" />
</parameter>
<parameter name="y">
- <value val="-0.900" />
+ <value val="-0.910" />
</parameter>
</component-link>