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IntegratePeakTimeSlices.h
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IntegratePeakTimeSlices.h
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/*
* IntegratePeakTimeSlices.h
*
* Created on: May 5, 2011
* Author: ruth
*/
#ifndef INTEGRATEPEAKTIMESLICES_H_
#define INTEGRATEPEAKTIMESLICES_H_
#include "MantidAPI/Algorithm.h"
#include "MantidAPI/IAlgorithm.h"
#include "MantidAPI/ITableWorkspace_fwd.h"
#include "MantidAPI/MatrixWorkspace_fwd.h"
#include "MantidAPI/SpectraDetectorTypes.h"
#include "MantidDataObjects/PeaksWorkspace.h"
#include "MantidDataObjects/TableWorkspace.h"
#include "MantidGeometry/Crystal/IPeak.h"
#include "MantidGeometry/Instrument/RectangularDetector.h"
#include "MantidKernel/cow_ptr.h"
#include "MantidKernel/V3D.h"
#include <array>
// Forward Declarations
namespace Mantid {
namespace HistogramData {
class HistogramX;
}
}
namespace Mantid {
namespace Crystal {
/**
Integrates each time slice using the BivariateNormal formula, adding the
results to the
peak object
@author Ruth Mikkelson, SNS, ORNL
@date 06/06/2011
Copyright © 2009 ISIS Rutherford Appleton Laboratory, NScD Oak Ridge
National Laboratory & European Spallation Source
This file is part of Mantid.
Mantid is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 3 of the License, or
(at your option) any later version.
Mantid is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
File change history is stored at: <https://github.com/mantidproject/mantid>
Code Documentation is available at: <http://doxygen.mantidproject.org>
*/
class DataModeHandler {
public:
DataModeHandler() { init(); }
DataModeHandler(const DataModeHandler &handler);
DataModeHandler(double baseRCRadius, double lastRCRadius, double lastRow,
double lastCol, double CellWidth, double CellHeight,
bool CalcVariance, int MinCol, int MaxCol, int MinRow,
int MaxRow) {
init();
this->baseRCRadius = baseRCRadius;
this->lastRCRadius = lastRCRadius;
this->lastRow = lastRow;
this->lastCol = lastCol;
this->CellWidth = CellWidth;
this->CellHeight = CellHeight;
this->CalcVariance = CalcVariance;
this->MaxCol = MaxCol;
this->MaxRow = MaxRow;
this->MinCol = MinCol;
this->MinRow = MinRow;
}
void setTime(double time) { this->time = time; }
// Returns true if "Edge Peak" otherwise returns false
bool setStatBase(std::vector<double> const &StatBase);
bool isEdgePeak(const double *params, int nparams);
void setHeightHalfWidthInfo(const MantidVec &xvals, const MantidVec &yvals,
const MantidVec &counts);
void setCurrentRadius(double radius) { currentRadius = radius; }
void setCurrentCenter(const Kernel::V3D newCenter) {
Kernel::V3D XX(newCenter);
currentPosition = XX;
}
double getCurrentRadius() { return currentRadius; }
Kernel::V3D getCurrentCenter() { return currentPosition; }
void updateEdgeXsize(double newsize) {
if (EdgeX < 0)
EdgeX = newsize;
else if (newsize < EdgeX)
EdgeX = newsize;
}
void updateEdgeYsize(double newsize) {
if (EdgeY < 0)
EdgeY = newsize;
else if (newsize < EdgeY)
EdgeY = newsize;
}
void CalcVariancesFromData(double background, double meanx, double meany,
double &Varxx, double &Varxy, double &Varyy,
std::vector<double> &StatBase);
bool IsEnoughData(const double *ParameterValues, Kernel::Logger &);
double getNewRCRadius();
double getInitBackground() { return back_calc; }
double getInitRow() { return row_calc; }
double getInitCol() { return col_calc; }
double getInitIntensity() { return Intensity_calc; }
double getInitVarx() { return Vx_calc; }
double getInitVary() { return Vy_calc; }
double getInitVarxy() { return Vxy_calc; }
std::string CalcConstraints(std::vector<std::pair<double, double>> &Bounds,
bool CalcVariances);
std::string getTies() { return ""; }
bool CalcVariances();
std::vector<double> GetParams(double b);
double StatBaseVals(int index) {
if (index < 0 || index >= (int)StatBase.size())
return 0.0;
return StatBase[index];
}
double CalcISAWIntensity(const double *params);
double CalcISAWIntensityVariance(const double *params, const double *errs,
double chiSqOvDOF);
/**
* For Edge Peaks
*/
double CalcSampleIntensityMultiplier(const double *params) const;
/**
* Returns init values with background and variances replaced by arguments.
*Varxy=0
*
*/
std::vector<double> InitValues(double Varx, double Vary, double b);
double baseRCRadius;
double lastRCRadius;
double HalfWidthAtHalfHeightRadius;
double calcNewRCRadius;
double lastRow;
int MinRow, MaxRow;
double lastCol;
int MinCol, MaxCol;
double time;
double CellWidth;
double CellHeight;
double VarxHW, VaryHW;
double currentRadius;
Kernel::V3D currentPosition;
std::vector<double> StatBase;
double EdgeX, EdgeY;
double lastISAWIntensity, lastISAWVariance;
bool CalcVariance;
bool case4; // if true result of successful merge of dir =1 chan=0 and chan=1
double back_calc, Intensity_calc, row_calc, col_calc, Vx_calc, Vy_calc,
Vxy_calc;
private:
void init() {
baseRCRadius = -1;
lastRCRadius = -1;
lastRow = -1;
lastCol = -1;
EdgeX = EdgeY = -1;
calcNewRCRadius = -1;
MaxRow = -1;
MaxCol = -1;
MinRow = -1;
MinCol = -1;
time = -1;
CalcVariance = true;
CellWidth = CellHeight = 0;
currentRadius = -1;
lastISAWIntensity = -1;
lastISAWVariance = -1;
currentPosition = Kernel::V3D();
HalfWidthAtHalfHeightRadius = -1;
case4 = false;
VarxHW = -1;
VaryHW = -1;
back_calc = Intensity_calc = row_calc = col_calc = Vx_calc = Vy_calc =
Vxy_calc = -1;
}
};
class DLLExport IntegratePeakTimeSlices : public Mantid::API::Algorithm {
public:
/// Default constructor
IntegratePeakTimeSlices();
/// Destructor
~IntegratePeakTimeSlices() override;
/// Algorithm's name for identification overriding a virtual method
const std::string name() const override { return "IntegratePeakTimeSlices"; }
/// Summary of algorithms purpose
const std::string summary() const override {
return "The algorithm uses CurveFitting::BivariateNormal for fitting a "
"time slice";
}
/// Algorithm's version for identification overriding a virtual method
int version() const override { return 1; }
/// Algorithm's category for identification overriding a virtual method
const std::string category() const override { return "Crystal\\Integration"; }
private:
void init() override;
void exec() override;
bool m_EdgePeak;
std::string m_AttributeNames[20];
std::string m_ParameterNames[7];
boost::shared_ptr<DataModeHandler> m_AttributeValues;
std::array<double, 7> m_ParameterValues;
Mantid::detid2index_map m_wi_to_detid_map;
int *m_NeighborIDs; // Stores IDs of nearest neighbors
double m_R0; ///<for Weak Peaks, these can be set using info from close
Kernel::V3D m_center; ///< for Describing the Plane at the Peak
Kernel::V3D m_xvec; ///< for Describing the Plane at the Peak
Kernel::V3D m_yvec; ///< for Describing the Plane at the Peak
double
m_ROW; ///< for Describing the Row(or 0) describing the center of the Peak
double
m_COL; ///< for Describing the Column(or 0) describing the center of the
/// Peak
double m_cellWidth; ///< for Describing the Plane at the Peak
double m_cellHeight; ///< for Describing the Plane at the Peak
int m_NROWS;
int m_NCOLS;
void SetUpData(API::MatrixWorkspace_sptr &Data,
API::MatrixWorkspace_const_sptr const &inpWkSpace,
boost::shared_ptr<Geometry::IComponent> comp,
const int chanMin, const int chanMax, double CentX,
double CentY, Kernel::V3D &CentNghbr,
double &neighborRadius, // from CentDet
double Radius, std::string &spec_idList);
bool getNeighborPixIDs(boost::shared_ptr<Geometry::IComponent> comp,
Kernel::V3D &Center, double &Radius, int *&ArryofID);
int CalculateTimeChannelSpan(Geometry::IPeak const &peak, const double dQ,
const Mantid::HistogramData::HistogramX &X,
const int specNum, int &Centerchan);
double CalculatePositionSpan(Geometry::IPeak const &peak, const double dQ);
void InitializeColumnNamesInTableWorkspace(
DataObjects::TableWorkspace_sptr &TabWS);
/// Prepares the data for futher analysis adding meta data and marking data on
/// the edges of detectors
void SetUpData1(API::MatrixWorkspace_sptr &Data,
API::MatrixWorkspace_const_sptr const &inpWkSpace,
const int chanMin, const int chanMax, double Radius,
Kernel::V3D CentPos, std::string &spec_idList
);
/**
* Tests several starting points in the Marquardt algorithm then calls Fit.
*/
void PreFit(API::MatrixWorkspace_sptr &Data, double &chisqOverDOF, bool &done,
std::vector<std::string> &names, std::vector<double> ¶ms,
std::vector<double> &errs, double lastRow, double lastCol,
double neighborRadius);
void Fit(API::MatrixWorkspace_sptr &Data, double &chisqOverDOF, bool &done,
std::vector<std::string> &names, std::vector<double> ¶ms,
std::vector<double> &errs, double lastRow, double lastCol,
double neighborRadius);
std::string CalculateFunctionProperty_Fit();
bool isGoodFit(std::vector<double> const ¶ms,
std::vector<double> const &errs,
std::vector<std::string> const &names, double chisqOverDOF);
// returns last row added
int UpdateOutputWS(DataObjects::TableWorkspace_sptr &TabWS, const int dir,
const double chan, std::vector<double> const ¶ms,
std::vector<double> const &errs,
std::vector<std::string> const &names, const double Chisq,
const double time, std::string spec_idList);
void updatePeakInformation(std::vector<double> const ¶ms,
std::vector<double> const &errs,
std::vector<std::string> const &names,
double &TotVariance, double &TotIntensity,
double const TotSliceIntensity,
double const TotSliceVariance,
double const chisqdivDOF, const int ncells);
void updateStats(const double intensity, const double variance,
const double row, const double col,
std::vector<double> &StatBase);
int findNameInVector(std::string const &oneName,
std::vector<std::string> const &nameList);
double CalculateIsawIntegrateError(const double background,
const double backError,
const double ChiSqOverDOF,
const double TotVariance,
const int ncells);
void FindPlane(Kernel::V3D ¢er, Kernel::V3D &xvec, Kernel::V3D &yvec,
double &ROW, double &COL, int &NROWS, int &NCOLS,
double &pixWidthx, double &pixHeighty,
Geometry::IPeak const &peak) const;
int findTimeChannel(const Mantid::HistogramData::HistogramX &X,
const double time);
// returns true if Neighborhood list is changed
bool updateNeighbors(boost::shared_ptr<Geometry::IComponent> &comp,
Kernel::V3D CentPos, Kernel::V3D oldCenter,
double NewRadius, double &neighborRadius);
bool m_debug;
};
} // namespace Crystal
} // namespace Mantid
#endif /* INTEGRATEPEAKTIMESLICES_H_ */