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Added some properties. Refs #9358.
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@wdzhou
wdzhou committed May 1, 2014
1 parent e0794ce commit 959be2b
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Showing 2 changed files with 74 additions and 45 deletions.
3 changes: 3 additions & 0 deletions Code/Mantid/Framework/Algorithms/inc/MantidAlgorithms/GeneratePeaks.h
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Expand Up @@ -78,6 +78,9 @@ namespace Algorithms
API::IPeakFunction_sptr getPeakFunction(API::IFunction_sptr infunction);

std::map<specid_t, specid_t> mSpectrumMap;

/// Flag to use automatic background (???)
bool m_useAutoBkgd;
};


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116 changes: 71 additions & 45 deletions Code/Mantid/Framework/Algorithms/src/GeneratePeaks.cpp
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Expand Up @@ -36,6 +36,7 @@ Peak parameters must have the following parameters, which are case sensitive in
#include "MantidAPI/WorkspaceProperty.h"
#include "MantidAPI/WorkspaceFactory.h"
#include "MantidAPI/FunctionFactory.h"
#include "MantidAPI/IBackgroundFunction.h"
#include "MantidKernel/ListValidator.h"
#include "MantidAPI/Column.h"
#include "MantidAPI/FunctionDomain1D.h"
Expand Down Expand Up @@ -83,33 +84,41 @@ namespace Algorithms
*/
void GeneratePeaks::init()
{
this->declareProperty(new API::WorkspaceProperty<DataObjects::TableWorkspace>("PeakParametersWorkspace", "", Direction::Input),
"Input TableWorkspace for peak's parameters.");
declareProperty(new API::WorkspaceProperty<DataObjects::TableWorkspace>("PeakParametersWorkspace", "", Direction::Input),
"Input TableWorkspace for peak's parameters.");

this->declareProperty("PeakFunction", "Gaussian", boost::make_shared<StringListValidator>(FunctionFactory::Instance().getFunctionNames<API::IPeakFunction>()),
"Peak function to calculate.");
declareProperty("PeakFunction", "Gaussian", boost::make_shared<StringListValidator>(
FunctionFactory::Instance().getFunctionNames<API::IPeakFunction>()),
"Peak function to calculate.");

this->declareProperty(new API::WorkspaceProperty<API::MatrixWorkspace>("InputWorkspace", "", Direction::Input, PropertyMode::Optional),
"InputWorkspace (optional) to take information for the instrument, and where to evaluate the x-axis.");
std::vector<std::string> bkgdnames = FunctionFactory::Instance().getFunctionNames<API::IBackgroundFunction>();
bkgdnames.push_back("Auto");
declareProperty("BackgroundFunction", "Flat", boost::make_shared<StringListValidator>(bkgdnames),
"Background function to calculate. ");

this->declareProperty(
new Kernel::ArrayProperty<double>("BinningParameters", boost::make_shared<Kernel::RebinParamsValidator>(true)),
"A comma separated list of first bin boundary, width, last bin boundary. Optionally\n"
"this can be followed by a comma and more widths and last boundary pairs.\n"
"Negative width values indicate logarithmic binning.");
declareProperty(new API::WorkspaceProperty<API::MatrixWorkspace>("InputWorkspace", "", Direction::Input, PropertyMode::Optional),
"InputWorkspace (optional) to take information for the instrument, and where to evaluate the x-axis.");

declareProperty(
new Kernel::ArrayProperty<double>("BinningParameters", boost::make_shared<Kernel::RebinParamsValidator>(true)),
"A comma separated list of first bin boundary, width, last bin boundary. Optionally\n"
"this can be followed by a comma and more widths and last boundary pairs.\n"
"Negative width values indicate logarithmic binning.");

this->declareProperty("NumberWidths", 2., "Number of peak width to evaluate each peak for. Default=2.");
this->declareProperty(new API::WorkspaceProperty<API::MatrixWorkspace>("OutputWorkspace", "", Direction::Output),
"Output Workspace to put the calculated data.");

this->declareProperty("GenerateBackground", true, "Whether or not to generate the background");
declareProperty("NumberWidths", 2., "Number of peak width to evaluate each peak for. Default=2.");
declareProperty(new API::WorkspaceProperty<API::MatrixWorkspace>("OutputWorkspace", "", Direction::Output),
"Output Workspace to put the calculated data.");

this->declareProperty("MaxAllowedChi2", 100.0, "Maximum chi^2 of the peak allowed to calculate. Default 100.");
declareProperty("GenerateBackground", true, "Whether or not to generate the background");

declareProperty("MaxAllowedChi2", 100.0, "Maximum chi^2 of the peak allowed to calculate. Default 100.");

declareProperty("IgnoreWidePeaks", false, "If selected, the peaks that are wider than fit window "
"(denoted by negative chi^2) are ignored.");

declareProperty("IsRawParameterTable", true, "Flag to show whether the parameter table contains raw parameters. ");

return;
}

Expand All @@ -121,6 +130,12 @@ namespace Algorithms
// Get properties
DataObjects::TableWorkspace_sptr peakParamWS = this->getProperty("PeakParametersWorkspace");
std::string peakFunction = this->getProperty("PeakFunction");
std::string bkgdFunction = getProperty("BackgroundFunction");
if (bkgdFunction.compare("Auto") == 0)
{
m_useAutoBkgd = true;
bkgdFunction = "Quardratic";
}

const std::vector<double> binParameters = this->getProperty("BinningParameters");
MatrixWorkspace_const_sptr inputWS = this->getProperty("InputWorkspace");
Expand Down Expand Up @@ -168,36 +183,37 @@ namespace Algorithms

this->setProperty("OutputWorkspace", outputWS);

// 4. Generate peaks
// Generate peaks
generatePeaks(outputWS, peakParamWS, peakFunction, newWSFromParent);

return;
}

namespace { // anonymous name space
/**
namespace
{ // anonymous name space
/**
* Determine if the table contains raw parameters.
*/
bool isRawTable(const std::vector<std::string> & colNames)
{
if (colNames.size() != 6)
return true;
if (colNames[0].compare("centre") != 0)
return true;
if (colNames[1].compare("width") != 0)
return true;
if (colNames[2].compare("height") != 0)
return true;
if (colNames[3].compare("backgroundintercept") != 0)
return true;
if (colNames[4].compare("backgroundslope") != 0)
return true;
if (colNames[5].compare("A2") != 0)
return true;
return false;
}
bool isRawTable(const std::vector<std::string> & colNames)
{
if (colNames.size() != 6)
return true;
if (colNames[0].compare("centre") != 0)
return true;
if (colNames[1].compare("width") != 0)
return true;
if (colNames[2].compare("height") != 0)
return true;
if (colNames[3].compare("backgroundintercept") != 0)
return true;
if (colNames[4].compare("backgroundslope") != 0)
return true;
if (colNames[5].compare("A2") != 0)
return true;
return false;
}

/**
/**
* Determine how many parameters are in the peak function.
*/
std::size_t getBkgOffset(const std::vector<std::string> & colNames, const bool isRaw)
Expand Down Expand Up @@ -245,7 +261,9 @@ namespace Algorithms
}
columnNames.erase(columnNames.begin()+(columnNames.size()-1)); // don't need to know that name either
const bool isRaw = isRawTable(columnNames);
const std::size_t bkgOffset = getBkgOffset(columnNames, isRaw);
// const std::size_t bkgOffset = getBkgOffset(columnNames, isRaw);
// FIXME - This should be more flexible/smart
const std::size_t bkgOffset = 3;
g_log.information() << "isRaw=" << isRaw << " bkgOffset=" << bkgOffset << "\n";

// Create data structure for all peaks functions
Expand Down Expand Up @@ -378,7 +396,8 @@ namespace Algorithms
std::string paramName;
for (std::size_t i = 0; i < bkg_offset; i++)
{
paramName = colNames[i].substr(3);
// paramName = colNames[i].substr(3);
paramName = colNames[i];
peakFunc->setParameter(paramName, getTableValue(peakParmsWS, colNames[i], rowNum));
}
}
Expand All @@ -404,7 +423,8 @@ namespace Algorithms
std::string paramName;
for (std::size_t i = bkg_offset; i < colNames.size(); i++)
{
paramName = colNames[i].substr(3);
// paramName = colNames[i].substr(3);
paramName = colNames[i];
backFunc->setParameter(paramName, getTableValue(peakParmsWS, colNames[i], rowNum));
}
}
Expand Down Expand Up @@ -489,24 +509,30 @@ namespace Algorithms

//----------------------------------------------------------------------------------------------
/** Get set of spectra of the input table workspace
*/
* Spectra is set to the column named 'spectrum'.
* Algorithm supports multiple peaks in multiple spectra
*/
void GeneratePeaks::getSpectraSet(DataObjects::TableWorkspace_const_sptr peakParmsWS, std::set<specid_t>& spectra)
{
size_t numpeaks = peakParmsWS->rowCount();
API::Column_const_sptr col = peakParmsWS->getColumn("spectrum");

for (size_t ipk = 0; ipk < numpeaks; ipk ++)
{
API::Column_const_sptr col = peakParmsWS->getColumn("spectrum");
specid_t specid = static_cast<specid_t>((*col)[ipk]);
spectra.insert(specid);
g_log.debug() << "Peak " << ipk << ": specid = " << specid << std::endl;

std::stringstream outss;
outss << "Peak " << ipk << ": specid = " << specid;
g_log.debug(outss.str());
}

std::set<specid_t>::iterator pit;
specid_t icount = 0;
for (pit = spectra.begin(); pit != spectra.end(); ++pit)
{
mSpectrumMap.insert(std::make_pair(*pit, icount));
++icount;
++ icount;
}

return;
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