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Enable to make small peaks visible in calculation mode. Refs #6747.
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@wdzhou
wdzhou committed Apr 11, 2013
1 parent ce7b09d commit 2d2dbf7
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Showing 2 changed files with 66 additions and 14 deletions.
4 changes: 3 additions & 1 deletion Code/Mantid/Framework/CurveFitting/inc/MantidCurveFitting/LeBailFit.h
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Original file line number Diff line number Diff line change
Expand Up @@ -340,6 +340,8 @@ namespace CurveFitting
/// Fit mode
FunctionMode m_fitMode;

double m_indicatePeakHeight;

//-------------------------- Monte Carlo Variables--------------------------
map<int, vector<string> > m_MCGroups;
size_t m_numMCGroups;
Expand All @@ -364,7 +366,7 @@ namespace CurveFitting
enum {RANDOMWALK, DRUNKENWALK} m_walkStyle;

/// Minimum height of a peak to be counted in smoothing background
double m_minimumHeight;
double m_minimumPeakHeight;

/// Flag to allow peaks with duplicated (HKL)^2 in input .hkl file
bool m_tolerateInputDupHKL2Peaks;
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76 changes: 63 additions & 13 deletions Code/Mantid/Framework/CurveFitting/src/LeBailFit.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@
#include "MantidAPI/IFunction.h"
#include "MantidKernel/ArrayProperty.h"
#include "MantidKernel/Statistics.h"
#include "MantidKernel/VisibleWhenProperty.h"
#include "MantidCurveFitting/BackgroundFunction.h"
#include "MantidAPI/FunctionFactory.h"
#include "MantidAPI/TextAxis.h"
Expand Down Expand Up @@ -131,13 +132,13 @@ namespace CurveFitting
auto validator = boost::make_shared<Kernel::StringListValidator>(functions);
this->declareProperty("Function", "LeBailFit", validator, "Functionality");

//------------------ Background Related Properties -------------------------
/*------------------------ Background Related Properties ---------------------------------*/
// About background: Background type, input (table workspace or array)
std::vector<std::string> bkgdtype;
bkgdtype.push_back("Polynomial");
bkgdtype.push_back("Chebyshev");
auto bkgdvalidator = boost::make_shared<Kernel::StringListValidator>(bkgdtype);
this->declareProperty("BackgroundType", "Polynomial", bkgdvalidator, "Background type");
declareProperty("BackgroundType", "Polynomial", bkgdvalidator, "Background type");

// Background function order
// this->declareProperty("BackgroundFunctionOrder", 12, "Order of background function.");
Expand All @@ -151,41 +152,76 @@ namespace CurveFitting
API::PropertyMode::Optional);
this->declareProperty(tablewsprop3, "Optional table workspace containing the fit result for background.");

// UseInputPeakHeights
this->declareProperty("UseInputPeakHeights", true,
"For 'Calculation' mode only, use peak heights specified in ReflectionWorkspace. "
"Otherwise, calcualte peaks' heights. ");

// Peak Radius
this->declareProperty("PeakRadius", 5, "Range (multiplier relative to FWHM) for a full peak. ");

// Pattern calcualtion
this->declareProperty("PlotIndividualPeaks", false, "Option to output each individual peak in mode Calculation.");
/*------------------------ Properties for Calculation Mode --------------------------------*/
// Output option to plot each individual peak
declareProperty("PlotIndividualPeaks", false,
"Option to output each individual peak in mode Calculation.");
setPropertySettings("PlotIndividualPeaks",
new VisibleWhenProperty("Function", IS_EQUAL_TO, "Calculation"));

// Make each reflection visible
declareProperty("IndicationPeakHeight", 0.0,
"Heigh of peaks (reflections) if its calculated height is smaller than user-defined minimum.");
setPropertySettings("IndicationPeakHeight",
new VisibleWhenProperty("Function", IS_EQUAL_TO, "Calculation"));

// UseInputPeakHeights
declareProperty("UseInputPeakHeights", true,
"For 'Calculation' mode only, use peak heights specified in ReflectionWorkspace. "
"Otherwise, calcualte peaks' heights. ");
setPropertySettings("UseInputPeakHeights",
new VisibleWhenProperty("Function", IS_EQUAL_TO, "Calculation"));

/*--------------------------- Properties for Fitting Mode ---------------------------------*/
// Minimizer
std::vector<std::string> minimizerOptions = API::FuncMinimizerFactory::Instance().getKeys(); // :Instance().getKeys();
declareProperty("Minimizer","Levenberg-MarquardtMD",
Kernel::IValidator_sptr(new Kernel::ListValidator<std::string>(minimizerOptions)),
"The minimizer method applied to do the fit, default is Levenberg-Marquardt", Kernel::Direction::InOut);
setPropertySettings("Minimizer",
new VisibleWhenProperty("Function", IS_EQUAL_TO, "LeBailFit"));

declareProperty("Damping", 1.0, "Damping factor if minizer is 'Damping'");
setPropertySettings("Damping",
new VisibleWhenProperty("Function", IS_EQUAL_TO, "LeBailFit"));
setPropertySettings("Damping",
new VisibleWhenProperty("Function", IS_EQUAL_TO, "MonteCarlo"));

declareProperty("NumberMinimizeSteps", 100, "Number of Monte Carlo random walk steps.");
setPropertySettings("NumberMinimizeSteps",
new VisibleWhenProperty("Function", IS_EQUAL_TO, "LeBailFit"));
setPropertySettings("NumberMinimizeSteps",
new VisibleWhenProperty("Function", IS_EQUAL_TO, "MonteCarlo"));

//----------------- Parameters for Monte Carlo Simulated Annealing --------------------------
auto mcwsprop = new WorkspaceProperty<TableWorkspace>("MCSetupWorkspace", "", Direction::Input,
PropertyMode::Optional);
declareProperty(mcwsprop, "Name of table workspace containing parameters' setup for Monte Carlo simualted annearling. ");
declareProperty(mcwsprop,
"Name of table workspace containing parameters' setup for Monte Carlo simualted annearling. ");
setPropertySettings("MCSetupWorkspace",
new VisibleWhenProperty("Function", IS_EQUAL_TO, "MonteCarlo"));


declareProperty("RandomSeed", 1, "Randum number seed.");
setPropertySettings("RandomSeed",
new VisibleWhenProperty("Function", IS_EQUAL_TO, "MonteCarlo"));

declareProperty("AnnealingTemperature", 1.0, "Temperature used Monte Carlo. "
"Negative temperature is for simulated annealing. ");
setPropertySettings("AnnealingTemperature",
new VisibleWhenProperty("Function", IS_EQUAL_TO, "MonteCarlo"));

declareProperty("UseAnnealing", true, "Allow annealing temperature adjusted automatically.");
setPropertySettings("UseAnnealing",
new VisibleWhenProperty("Function", IS_EQUAL_TO, "MonteCarlo"));

declareProperty("DrunkenWalk", false, "Flag to use drunken walk algorithm. "
"Otherwise, random walk algorithm is used. ");
setPropertySettings("DrunkenWalk",
new VisibleWhenProperty("Function", IS_EQUAL_TO, "MonteCarlo"));

declareProperty("MinimumPeakHeight", 0.01, "Minimum height of a peak to be counted "
"during smoothing background by exponential smooth algorithm. ");
Expand Down Expand Up @@ -445,7 +481,8 @@ namespace CurveFitting
throw invalid_argument(errss.str());
}

m_minimumHeight = getProperty("MinimumPeakHeight");
m_minimumPeakHeight = getProperty("MinimumPeakHeight");
m_indicatePeakHeight = getProperty("IndicationPeakHeight");

// Tolerate duplicated input peak or not?
m_tolerateInputDupHKL2Peaks = getProperty("AllowDegeneratedPeaks");
Expand Down Expand Up @@ -600,7 +637,20 @@ namespace CurveFitting
calculatePeaksIntensities(dataws, workspaceindex, zerobackground, peaksvalues);
}

// 3. Calcualte model pattern
// 3. (Optionally) set peak intensities to a large value if their height is not large enough
if (m_indicatePeakHeight > 1.0E-10)
{
for (size_t i = 0; i < m_dspPeaks.size(); ++i)
{
ThermalNeutronBk2BkExpConvPVoigt_sptr thispeak = m_dspPeaks[i].second;
if (thispeak->height() < m_minimumPeakHeight)
{
thispeak->setHeight(m_indicatePeakHeight);
}
}
}

// 4. Calcualte model pattern
m_lebailFunction->function(domain, values);

return allpeaksvalid;
Expand Down Expand Up @@ -3511,7 +3561,7 @@ namespace CurveFitting
{
ThermalNeutronBk2BkExpConvPVoigt_sptr thispeak = m_dspPeaks[ipk].second;
double height = thispeak->height();
if (height > m_minimumHeight)
if (height > m_minimumPeakHeight)
{
// a) Calculate boundary
double fwhm = thispeak->fwhm();
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