en/latest/a00089_source.html

 /*  ObjCryst++ Object-Oriented Crystallographic Library

     (c) 2000-2002 Vincent Favre-Nicolin vincefn@users.sourceforge.net

         2000-2001 University of Geneva (Switzerland)


     This program 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 2 of the License, or

     (at your option) any later version.


     This program 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, write to the Free Software

     Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA

 */

 #ifndef _OBJCRYST_POWDERPATTERN_H_

 #define _OBJCRYST_POWDERPATTERN_H_


 #include <utility>

 #include <list>

 #include <string>


 #include "ObjCryst/CrystVector/CrystVector.h"

 #include "ObjCryst/ObjCryst/General.h"

 #include "ObjCryst/ObjCryst/Crystal.h"

 #include "ObjCryst/ObjCryst/ScatteringCorr.h"

 #include "ObjCryst/ObjCryst/ReflectionProfile.h"

 #include "ObjCryst/ObjCryst/CIF.h"

 #include "ObjCryst/ObjCryst/Indexing.h"

 #include "ObjCryst/ObjCryst/DiffractionDataSingleCrystal.h"


 namespace ObjCryst

 {

 class PeakList;

 class PowderPattern;

 class PowderPatternDiffraction;


 //######################################################################

 class CylinderAbsCorr:public ScatteringCorr

 {

 public:

    CylinderAbsCorr(const PowderPatternDiffraction &data);

    virtual ~CylinderAbsCorr();

    virtual const string & GetName() const;

    virtual const string & GetClassName() const;

 protected:

    virtual void CalcCorr() const;

    const PowderPatternDiffraction *mpPowderPatternDiff;

 };


 //######################################################################

 //######################################################################

 class PowderPatternComponent : virtual public RefinableObj

 {

    public:

       PowderPatternComponent();

       PowderPatternComponent(const PowderPatternComponent&);

       virtual ~PowderPatternComponent();

       virtual const string& GetClassName() const;


       const PowderPattern& GetParentPowderPattern()const;

       PowderPattern& GetParentPowderPattern();

       virtual void SetParentPowderPattern(PowderPattern&)=0;

       virtual const CrystVector_REAL& GetPowderPatternCalc()const=0;

       virtual std::map<RefinablePar*,CrystVector_REAL>& GetPowderPattern_FullDeriv(std::set<RefinablePar *> &vPar);

       virtual pair<const CrystVector_REAL*,const RefinableObjClock*> GetPowderPatternIntegratedCalc()const=0;

       virtual std::map<RefinablePar*,CrystVector_REAL>& GetPowderPatternIntegrated_FullDeriv(std::set<RefinablePar *> &vPar);

       bool IsScalable()const;

       virtual const CrystVector_REAL& GetPowderPatternCalcVariance()const=0;

       virtual pair<const CrystVector_REAL*,const RefinableObjClock*>

          GetPowderPatternIntegratedCalcVariance() const=0;

       virtual bool HasPowderPatternCalcVariance()const=0;

       const RefinableObjClock& GetClockPowderPatternCalc()const;

       const list<pair<const REAL ,const string > >& GetPatternLabelList() const;

    protected:

       const RefinableObjClock& GetClockPowderPatternCalcVariance()const;


       virtual void CalcPowderPattern() const=0;

       virtual void CalcPowderPattern_FullDeriv(std::set<RefinablePar *> &vPar);

       virtual void CalcPowderPatternIntegrated_FullDeriv(std::set<RefinablePar *> &vPar);


       virtual const CrystVector_long& GetBraggLimits()const=0;

       const RefinableObjClock& GetClockBraggLimits()const;


       virtual void SetMaxSinThetaOvLambda(const REAL max)=0;


       mutable CrystVector_REAL mPowderPatternCalc;

       mutable CrystVector_REAL mPowderPatternIntegratedCalc;


       mutable CrystVector_REAL mPowderPatternCalcVariance;

       mutable CrystVector_REAL mPowderPatternIntegratedCalcVariance;


       mutable CrystVector_long mIntegratedReflLimits;


       virtual void Prepare()=0;


       bool mIsScalable;


       //Clocks

          mutable RefinableObjClock mClockPowderPatternCalc;

          mutable RefinableObjClock mClockPowderPatternIntegratedCalc;

          mutable RefinableObjClock mClockPowderPatternVarianceCalc;

          mutable RefinableObjClock mClockPowderPatternIntegratedVarianceCalc;


       PowderPattern *mpParentPowderPattern;

       mutable RefinableObjClock mClockBraggLimits;


       mutable list<pair<const REAL ,const string > > mvLabel;


       mutable std::map<RefinablePar*,CrystVector_REAL> mPowderPattern_FullDeriv;

       mutable std::map<RefinablePar*,CrystVector_REAL> mPowderPatternIntegrated_FullDeriv;

       //Eventually this should be removed (?)

       friend class PowderPattern;

 };

 extern ObjRegistry<PowderPatternComponent> gPowderPatternComponentRegistry;


 //######################################################################

 //######################################################################

 class PowderPatternBackground : public PowderPatternComponent

 {

    public:

       PowderPatternBackground();

       PowderPatternBackground(const PowderPatternBackground&);

       virtual ~PowderPatternBackground();

       virtual const string& GetClassName() const;


       virtual void SetParentPowderPattern(PowderPattern&);

       virtual const CrystVector_REAL& GetPowderPatternCalc()const;

       virtual pair<const CrystVector_REAL*,const RefinableObjClock*>

          GetPowderPatternIntegratedCalc()const;

       void ImportUserBackground(const string &filename);

       void SetInterpPoints(const CrystVector_REAL tth, const CrystVector_REAL backgd);

       const std::pair<const CrystVector_REAL*,const CrystVector_REAL*> GetInterpPoints()const;

       virtual void XMLOutput(ostream &os,int indent=0)const;

       virtual void XMLInput(istream &is,const XMLCrystTag &tag);

       //virtual void XMLInputOld(istream &is,const IOCrystTag &tag);

       virtual void GetGeneGroup(const RefinableObj &obj,

                                 CrystVector_uint & groupIndex,

                                 unsigned int &firstGroup) const;

       virtual void BeginOptimization(const bool allowApproximations=false,

                                      const bool enableRestraints=false);

       virtual const CrystVector_REAL& GetPowderPatternCalcVariance()const;

       virtual pair<const CrystVector_REAL*,const RefinableObjClock*>

          GetPowderPatternIntegratedCalcVariance() const;

       virtual bool HasPowderPatternCalcVariance()const;

       virtual void TagNewBestConfig()const;

       void OptimizeBayesianBackground();

       void FixParametersBeyondMaxresolution(RefinableObj &obj);

    protected:

       virtual void CalcPowderPattern() const;

       virtual void CalcPowderPattern_FullDeriv(std::set<RefinablePar *> &vPar);

       virtual void CalcPowderPatternIntegrated() const;

       virtual void CalcPowderPatternIntegrated_FullDeriv(std::set<RefinablePar *> &vPar);

       virtual void Prepare();

       virtual const CrystVector_long& GetBraggLimits()const;

       virtual void SetMaxSinThetaOvLambda(const REAL max);

       void InitRefParList();

       void InitOptions();

       void InitSpline()const;

       int mBackgroundNbPoint;

       CrystVector_REAL mBackgroundInterpPointX;

       CrystVector_REAL mBackgroundInterpPointIntensity;

       mutable CrystVector_long mPointOrder;

       mutable CrystVector_REAL mvSplinePixel;

       mutable CubicSpline mvSpline;

       // Clocks

          RefinableObjClock mClockBackgroundPoint;

          mutable RefinableObjClock mClockSpline;


       REAL mMaxSinThetaOvLambda;


       REAL mModelVariance;


       RefObjOpt mInterpolationModel;

       //To be removed

       friend class PowderPattern;

    #ifdef __WX__CRYST__

    public:

       virtual WXCrystObjBasic* WXCreate(wxWindow*);

       friend class WXPowderPatternBackground;

    #endif

 };


 //######################################################################

 //######################################################################

 class PowderPatternDiffraction : virtual public PowderPatternComponent,public ScatteringData

 {

    public:

       PowderPatternDiffraction();

       PowderPatternDiffraction(const PowderPatternDiffraction&);

       virtual ~PowderPatternDiffraction();

       virtual PowderPatternDiffraction* CreateCopy()const;

       virtual const string& GetClassName() const;


       virtual void SetParentPowderPattern(PowderPattern&);

       virtual const CrystVector_REAL& GetPowderPatternCalc()const;

       virtual pair<const CrystVector_REAL*,const RefinableObjClock*>

          GetPowderPatternIntegratedCalc()const;


       void SetReflectionProfilePar(const ReflectionProfileType prof,

                                    const REAL fwhmCagliotiW,

                                    const REAL fwhmCagliotiU=0,

                                    const REAL fwhmCagliotiV=0,

                                    const REAL eta0=0.5,

                                    const REAL eta1=0.);

       void SetProfile(ReflectionProfile *prof);

       const ReflectionProfile& GetProfile()const;

       ReflectionProfile& GetProfile();

       virtual void GenHKLFullSpace()const;

       virtual void XMLOutput(ostream &os,int indent=0)const;

       virtual void XMLInput(istream &is,const XMLCrystTag &tag);

       //virtual void XMLInputOld(istream &is,const IOCrystTag &tag);

       virtual void GetGeneGroup(const RefinableObj &obj,

                                 CrystVector_uint & groupIndex,

                                 unsigned int &firstGroup) const;

       virtual void BeginOptimization(const bool allowApproximations=false,

                                      const bool enableRestraints=false);

       virtual void EndOptimization();

       virtual void SetApproximationFlag(const bool allow);

       virtual const Radiation& GetRadiation()const;

       virtual const CrystVector_REAL& GetPowderPatternCalcVariance()const;

       virtual pair<const CrystVector_REAL*,const RefinableObjClock*>

          GetPowderPatternIntegratedCalcVariance() const;

       virtual bool HasPowderPatternCalcVariance()const;

       virtual void SetCrystal(Crystal &crystal);

       void SetExtractionMode(const bool extract=true,const bool init=false);

       bool GetExtractionMode()const;

       void ExtractLeBail(unsigned int nbcycle=1);

       virtual long GetNbReflBelowMaxSinThetaOvLambda()const;

       void SetFrozenLatticePar(const unsigned int i, REAL v);

       REAL GetFrozenLatticePar(const unsigned int i) const;

       void FreezeLatticePar(const bool use);

       bool FreezeLatticePar() const;

       unsigned int GetProfileFitNetNbObs()const;

       bool HasFhklObsSq() const;

       const CrystVector_REAL& GetFhklObsSq() const;

    protected:

       virtual void CalcPowderPattern() const;

       virtual void CalcPowderPattern_FullDeriv(std::set<RefinablePar *> &vPar);

       virtual void CalcPowderPatternIntegrated() const;

       virtual void CalcPowderPatternIntegrated_FullDeriv(std::set<RefinablePar *> &vPar);


       void CalcPowderReflProfile()const;

       void CalcPowderReflProfile_FullDeriv(std::set<RefinablePar *> &vPar);

       void CalcIntensityCorr()const;

       virtual void CalcIhkl() const;

       virtual void CalcIhkl_FullDeriv(std::set<RefinablePar*> &vPar);

       virtual void Prepare();

       virtual void InitOptions();

       virtual const CrystVector_long& GetBraggLimits()const;

       virtual void SetMaxSinThetaOvLambda(const REAL max);

       virtual const CrystMatrix_REAL& GetBMatrix()const;

       void CalcFrozenBMatrix()const;

       void PrepareIntegratedProfile()const;

       //Clocks

          RefinableObjClock mClockProfilePar;

          RefinableObjClock mClockLorentzPolarSlitCorrPar;

       //Clocks (internal, mutable)

          mutable RefinableObjClock mClockIntensityCorr;

          mutable RefinableObjClock mClockProfileCalc;

          mutable RefinableObjClock mClockIhklCalc;

          ReflectionProfile *mpReflectionProfile;

       // Corrections

          mutable CrystVector_REAL mIntensityCorr;

          LorentzCorr mCorrLorentz;

          PolarizationCorr mCorrPolar;

          PowderSlitApertureCorr mCorrSlitAperture;

          TextureMarchDollase mCorrTextureMarchDollase;

          TextureEllipsoid mCorrTextureEllipsoid;

          TOFCorr mCorrTOF;

          CylinderAbsCorr mCorrCylAbs;


          mutable CrystVector_REAL mIhklCalc;

          mutable std::map<RefinablePar*,CrystVector_REAL> mIhkl_FullDeriv;

          mutable CrystVector_REAL mIhklCalcVariance;


       // Saved arrays to speed-up computations

          struct ReflProfile

          {

             long first;

             long last;

             CrystVector_REAL profile;

          };

          mutable vector<ReflProfile> mvReflProfile;

          mutable std::map<RefinablePar*,vector<CrystVector_REAL> > mvReflProfile_FullDeriv;


       // When using integrated profiles

          mutable vector< pair<unsigned long, CrystVector_REAL> > mIntegratedProfileFactor;

          mutable RefinableObjClock mClockIntegratedProfileFactor;

       bool mExtractionMode;

       DiffractionDataSingleCrystal *mpLeBailData;

       mutable CrystVector_REAL mFrozenLatticePar;

       bool mFreezeLatticePar;

       mutable CrystMatrix_REAL mFrozenBMatrix;

       mutable CrystMatrix_REAL mGenHKLBMatrix;

   #ifdef __WX__CRYST__

    public:

       virtual WXCrystObjBasic* WXCreate(wxWindow*);

       friend class WXPowderPatternDiffraction;

    #endif

    private:

       // Avoid compiler warnings.  Explicitly hide the base-class method.

       void GenHKLFullSpace(const REAL, const bool) const;

 };


 //######################################################################

 //######################################################################

 class PowderPattern : public RefinableObj

 {

     public:

       PowderPattern();

       PowderPattern(const PowderPattern&);

       ~PowderPattern();

       virtual const string& GetClassName() const;

       void AddPowderPatternComponent(PowderPatternComponent &);

       void RemovePowderPatternComponent(PowderPatternComponent &);

       void RemovePowderPatternComponent(const int i);

       unsigned int GetNbPowderPatternComponent()const;

       const PowderPatternComponent& GetPowderPatternComponent(const string &name)const;

       const PowderPatternComponent& GetPowderPatternComponent(const int)const;

       PowderPatternComponent& GetPowderPatternComponent(const string &name);

       PowderPatternComponent& GetPowderPatternComponent(const int);

       REAL GetScaleFactor(const int i)const;

       REAL GetScaleFactor(const PowderPatternComponent &comp)const;

       void SetScaleFactor(const int i, REAL s);

       void SetScaleFactor(const PowderPatternComponent &comp, REAL s);


       // Pattern parameters (2theta range, wavelength, radiation)

          void SetPowderPatternPar(const REAL min,

                                   const REAL step,

                                   unsigned long nbPoint);

          void SetPowderPatternX(const CrystVector_REAL &x);

          unsigned long GetNbPoint()const;

          unsigned long GetNbPointUsed()const;

          const RefinableObjClock& GetClockNbPointUsed()const;


          void SetRadiation(const Radiation &radiation);

          const Radiation& GetRadiation()const;

          Radiation& GetRadiation();


          void SetRadiationType(const RadiationType radiation);

          RadiationType GetRadiationType()const;

          void SetWavelength(const REAL lambda);


          void SetWavelength(const string &XRayTubeElementName,const REAL alpha12ratio=0.5);


          void SetEnergy(const REAL energy);

          REAL GetWavelength()const;


       //Access to pattern data

          const CrystVector_REAL& GetPowderPatternCalc()const;

          std::map<RefinablePar*,CrystVector_REAL>& GetPowderPattern_FullDeriv(std::set<RefinablePar *> &vPar);

          const CrystVector_REAL& GetPowderPatternObs()const;

          const CrystVector_REAL& GetPowderPatternObsSigma()const;

          const CrystVector_REAL& GetPowderPatternVariance()const;

          const CrystVector_REAL& GetPowderPatternWeight()const;

          REAL GetPowderPatternXMin()const;

          REAL GetPowderPatternXStep()const;

          REAL GetPowderPatternXMax()const;

          const CrystVector_REAL& GetPowderPatternX()const;

          const CrystVector_REAL& GetChi2Cumul(const int mode=-1)const;


       // Clocks

          const RefinableObjClock& GetClockPowderPatternCalc()const;

          const RefinableObjClock& GetClockPowderPatternPar()const;

          const RefinableObjClock& GetClockPowderPatternRadiation()const;

          const RefinableObjClock& GetClockPowderPatternXCorr()const;

          const RefinableObjClock& GetClockPowderPatternAbsCorr() const;


       // Corrections to the x (2theta, tof) coordinate

          void SetXZero(const REAL newZero);

          void Set2ThetaDisplacement(const REAL displacement);

          void Set2ThetaTransparency(const REAL transparency);


       // Import & export powder pattern

          void ImportPowderPatternFullprof(const string &fullprofFileName);

          void ImportPowderPatternPSI_DMC(const string &filename);

          void ImportPowderPatternILL_D1A5(const string &filename);

          void ImportPowderPatternXdd(const string &fileName);

          void ImportPowderPatternSietronicsCPI(const string &fileName);

          void ImportPowderPattern2ThetaObsSigma(const string &fileName,const int nbSkip=0);

          void ImportPowderPatternFullprof4(const string &fileName);

          void ImportPowderPatternMultiDetectorLLBG42(const string &fileName);

          void ImportPowderPattern2ThetaObs(const string &fileName,const int nbSkip=0);

          void ImportPowderPatternTOF_ISIS_XYSigma(const string &fileName);

          void ImportPowderPatternGSAS(const string &fileName);

          void ImportPowderPatternCIF(const CIF &cif);

          void SetPowderPatternObs(const CrystVector_REAL& obs);

          void SetPowderPatternObsSigma(const CrystVector_REAL& sigma);


          void SavePowderPattern(const string &filename="powderPattern.out") const;

          void PrintObsCalcData(ostream&os=cout)const;


       // Statistics..

          REAL GetR()const ;

          REAL GetIntegratedR()const ;

          REAL GetRw()const;

          REAL GetIntegratedRw()const;

          REAL GetChi2()const;

          REAL GetIntegratedChi2()const;

          REAL GetChi2_Option()const;

          void FitScaleFactorForR()const;

          void FitScaleFactorForIntegratedR()const;

          void FitScaleFactorForRw()const;

          void FitScaleFactorForIntegratedRw()const;

          void SetSigmaToSqrtIobs();

          void SetWeightToInvSigmaSq(const REAL minRelatSigma=1e-3);

          void SetWeightToUnit();

          void SetWeightPolynomial(const REAL a, const REAL b, const REAL c,

                                      const REAL minRelatIobs=1e-3);


          void AddExcludedRegion(const REAL min2Theta,const REAL max2theta);


       virtual void BeginOptimization(const bool allowApproximations=false,

                                      const bool enableRestraints=false);

       //virtual void SetApproximationFlag(const bool allow);

       virtual void GlobalOptRandomMove(const REAL mutationAmplitude,

                                        const RefParType *type=gpRefParTypeObjCryst);

       virtual REAL GetLogLikelihood()const;

       //LSQ functions

          virtual unsigned int GetNbLSQFunction()const;

          virtual const CrystVector_REAL& GetLSQCalc(const unsigned int) const;

          virtual const CrystVector_REAL& GetLSQObs(const unsigned int) const;

          virtual const CrystVector_REAL& GetLSQWeight(const unsigned int) const;

          virtual std::map<RefinablePar*, CrystVector_REAL>& GetLSQ_FullDeriv(const unsigned int,std::set<RefinablePar *> &vPar);

       // I/O

          virtual void XMLOutput(ostream &os,int indent=0)const;

          virtual void XMLInput(istream &is,const XMLCrystTag &tag);

          //virtual void XMLInputOld(istream &is,const IOCrystTag &tag);

          void Prepare();

       virtual void GetGeneGroup(const RefinableObj &obj,

                                 CrystVector_uint & groupIndex,

                                 unsigned int &firstGroup) const;

       virtual void SetMaxSinThetaOvLambda(const REAL max);

       REAL GetMaxSinThetaOvLambda()const;


       // For integrated pattern calculations

          const CrystVector_long& GetIntegratedProfileMin()const;

          const CrystVector_long& GetIntegratedProfileMax()const;

          const RefinableObjClock& GetIntegratedProfileLimitsClock()const;

       REAL X2XCorr(const REAL x)const;

       REAL X2PixelCorr(const REAL x)const;

       REAL X2Pixel(const REAL x)const;


          REAL STOL2X(const REAL stol)const;

          REAL X2STOL(const REAL x)const;

          REAL STOL2Pixel(const REAL stol)const;

       PeakList FindPeaks(const float dmin=2.0,const float maxratio=0.01,const unsigned int maxpeak=100);

       const CrystVector_REAL &GetScaleFactor() const;

       CrystVector_REAL &GetScaleFactor();

       void ExportFullprof(const std::string &prefix)const;

       void SetMuR(const REAL muR);

       REAL GetMuR() const;

    protected:

       void CalcPowderPattern() const;

       void CalcPowderPattern_FullDeriv(std::set<RefinablePar *> &vPar);

       void CalcPowderPatternIntegrated() const;

       void CalcPowderPatternIntegrated_FullDeriv(std::set<RefinablePar *> &vPar);

       virtual void Init();

       void PrepareIntegratedRfactor()const;

       void CalcNbPointUsed()const;

       virtual void InitOptions();


       mutable CrystVector_REAL mPowderPatternCalc;

       mutable std::map<RefinablePar*,CrystVector_REAL> mPowderPattern_FullDeriv;

       mutable CrystVector_REAL mPowderPatternIntegratedCalc;

       mutable std::map<RefinablePar*,CrystVector_REAL> mPowderPatternIntegrated_FullDeriv;

       mutable CrystVector_REAL mPowderPatternBackgroundCalc;

       mutable CrystVector_REAL mPowderPatternBackgroundIntegratedCalc;

       CrystVector_REAL mPowderPatternObs;

       CrystVector_REAL mPowderPatternObsSigma;

       mutable CrystVector_REAL mPowderPatternWeight;

       mutable CrystVector_REAL mPowderPatternVariance;

       mutable CrystVector_REAL mPowderPatternVarianceIntegrated;

       mutable CrystVector_REAL mChi2Cumul;


       mutable CrystVector_REAL mPowderPatternUsedCalc;

       mutable std::map<RefinablePar*,CrystVector_REAL> mPowderPatternUsed_FullDeriv;

       mutable CrystVector_REAL mPowderPatternUsedObs;

       mutable CrystVector_REAL mPowderPatternUsedWeight;


       CrystVector_REAL mX;

       bool mIsXAscending;

       unsigned long mNbPoint;


       Radiation mRadiation;


       // Clocks

          RefinableObjClock mClockPowderPatternPar;

          RefinableObjClock mClockPowderPatternRadiation;

          mutable RefinableObjClock mClockPowderPatternCalc;

          mutable RefinableObjClock mClockPowderPatternIntegratedCalc;

          RefinableObjClock mClockPowderPatternXCorr;

          mutable RefinableObjClock mClockScaleFactor;

          mutable RefinableObjClock mClockCorrAbs;


       //Excluded regions in the powder pattern, for statistics.

          CrystVector_REAL mExcludedRegionMinX;

          CrystVector_REAL mExcludedRegionMaxX;


       //Various corrections to 2theta-to be used by the components

          REAL mXZero;

          REAL m2ThetaDisplacement;

          REAL m2ThetaTransparency;

          REAL mDIFC,mDIFA;

       // Components of the powder pattern

          ObjRegistry<PowderPatternComponent> mPowderPatternComponentRegistry;

          mutable CrystVector_REAL mScaleFactor;


       REAL mMuR;


       bool mUseFastLessPreciseFunc;


       // For statistics

          bool mStatisticsExcludeBackground;

          mutable CrystVector_int mScalableComponentIndex;

          mutable CrystMatrix_REAL mFitScaleFactorM,mFitScaleFactorB,mFitScaleFactorX;


          RefObjOpt mOptProfileIntegration;


       // Integrated R-factors

          mutable CrystVector_long mIntegratedPatternMin,mIntegratedPatternMax;

          mutable CrystVector_REAL mIntegratedObs;

          mutable CrystVector_REAL mIntegratedWeight;

          mutable CrystVector_REAL mIntegratedWeightObs;

          mutable CrystVector_REAL mIntegratedVarianceObs;

          mutable RefinableObjClock mClockIntegratedFactorsPrep;

       // Statistical indicators

          mutable REAL mChi2,mIntegratedChi2;

          mutable REAL mChi2LikeNorm,mIntegratedChi2LikeNorm;

          mutable REAL mR;

          mutable REAL mRw;

          mutable RefinableObjClock mClockChi2,mClockIntegratedChi2;

       REAL mMaxSinThetaOvLambda;

       mutable unsigned long mNbPointUsed;

       mutable unsigned long mNbIntegrationUsed;

       mutable RefinableObjClock mClockNbPointUsed;

    #ifdef __WX__CRYST__

    public:

       virtual WXCrystObjBasic* WXCreate(wxWindow*);

       friend class WXPowderPattern;

       // This should be removed

       friend class WXPowderPatternGraph;

    #endif

 };

 extern ObjRegistry<PowderPattern> gPowderPatternRegistry;

 //######################################################################

 //    PROFILE FUNCTIONS (for powder diffraction)

 //######################################################################


 CrystVector_REAL PowderProfileGauss  (const CrystVector_REAL theta,

                                       const REAL fwhm,

                                       const REAL asymmetryPar=1.);

 CrystVector_REAL PowderProfileLorentz(const CrystVector_REAL theta,

                                       const REAL fwhm,

                                       const REAL asymmetryPar=1.);


 //######################################################################

 //    Spacegroup explorer

 //######################################################################

 struct SPGScore

 {

    SPGScore(const string &s, const REAL r, const REAL g, const unsigned int nbextinct, const REAL ngof=0, const unsigned int nbrefl=0);

    string hm;

    REAL rw;

    REAL gof;

    REAL ngof;

    unsigned int nbextinct446;

    unsigned int nbreflused;

 };


 bool compareSPGScore(const SPGScore &s1, const SPGScore &s2);


 std::vector<bool> spgExtinctionFingerprint(Crystal &c, const cctbx::sgtbx::space_group &spg);


 class SpaceGroupExplorer

 {

 public:

    SpaceGroupExplorer(PowderPatternDiffraction *pd);

    SPGScore Run(const string &spg, const bool fitprofile=false, const bool verbose=false,

                 const bool restore_orig=false, const bool update_display=true,

                 const REAL relative_length_tolerance=0.01, const REAL absolute_angle_tolerance_degree=0.5);

    SPGScore Run(const cctbx::sgtbx::space_group &spg, const bool fitprofile=false,

                 const bool verbose=false, const bool restore_orig=false, const bool update_display=true,

                 const REAL relative_length_tolerance=0.01, const REAL absolute_angle_tolerance_degree=0.5);

    void RunAll(const bool fitprofile_all=false, const bool verbose=true, const bool keep_best=false,

                const bool update_display=true, const bool fitprofile_p1=true,

                const REAL relative_length_tolerance=0.01, const REAL absolute_angle_tolerance_degree=0.5);

    const list<SPGScore>& GetScores() const;

 private:

    REAL GetP1IntegratedGoF();

    PowderPatternDiffraction *mpDiff;

    CrystVector_REAL mP1IntegratedProfileMin,mP1IntegratedProfileMax;

    list<SPGScore> mvSPG;

    std::map<std::vector<bool>,SPGScore> mvSPGExtinctionFingerprint;

 };


 }//namespace ObjCryst

 #endif // _OBJCRYST_POWDERPATTERN_H_

ObjCryst
The namespace which includes all objects (crystallographic and algorithmic) in ObjCryst++.
Definition: doc-main.h:25

ObjCryst::ReflectionProfileType
ReflectionProfileType
Profile type for powder (could it be used fopr single crystals on 2D detectors ?)
Definition: General.h:105

ObjCryst::spgExtinctionFingerprint
std::vector< bool > spgExtinctionFingerprint(Crystal &c, const cctbx::sgtbx::space_group &spg)
Function which determines the unique extinction fingerprint of a spacegroup, by calculating all prese...
Definition: PowderPattern.cpp:6888

ObjCryst::gPowderPatternComponentRegistry
ObjRegistry< PowderPatternComponent > gPowderPatternComponentRegistry("List of all PowderPattern Components")
Global registry for all PowderPatternComponent objects.
Definition: PowderPattern.h:214

ObjCryst::RadiationType
RadiationType
Type of radiation used.
Definition: General.h:96

ObjCryst::gpRefParTypeObjCryst
const RefParType * gpRefParTypeObjCryst
Top RefParType for the ObjCryst++ library.
Definition: RefinableObj.cpp:78

ObjCryst::CIF
Main CIF class - parses the stream and separates data blocks, comments, items, loops.
Definition: CIF.h:170

ObjCryst::Crystal
Crystal class: Unit cell, spacegroup, scatterers.
Definition: Crystal.h:98

ObjCryst::DiffractionDataSingleCrystal
DiffractionData object for Single Crystal analysis.
Definition: DiffractionDataSingleCrystal.h:51

ObjCryst::PeakList
Class to store positions of observed reflections.
Definition: Indexing.h:117

ObjCryst::CylinderAbsCorr
Cylinder absorption correction.
Definition: PowderPattern.h:50

ObjCryst::CylinderAbsCorr::GetName
virtual const string & GetName() const
Get the name of this object.
Definition: PowderPattern.cpp:71

ObjCryst::CylinderAbsCorr::CalcCorr
virtual void CalcCorr() const
Do the computation of corrected intensities.
Definition: PowderPattern.cpp:84

ObjCryst::CylinderAbsCorr::CylinderAbsCorr
CylinderAbsCorr(const PowderPatternDiffraction &data)
Constructor.
Definition: PowderPattern.cpp:64

ObjCryst::CylinderAbsCorr::GetClassName
virtual const string & GetClassName() const
Get the name of the class.
Definition: PowderPattern.cpp:78

ObjCryst::PowderPatternComponent
Generic class to compute components (eg the contribution of a given phase, or background) of a powder...
Definition: PowderPattern.h:73

ObjCryst::PowderPatternComponent::mPowderPatternCalcVariance
CrystVector_REAL mPowderPatternCalcVariance
The variance associated to each point of the calculated powder pattern.
Definition: PowderPattern.h:174

ObjCryst::PowderPatternComponent::GetClassName
virtual const string & GetClassName() const
Name for this class ("RefinableObj", "Crystal",...).
Definition: PowderPattern.cpp:156

ObjCryst::PowderPatternComponent::IsScalable
bool IsScalable() const
Is this component scalable ?
Definition: PowderPattern.cpp:184

ObjCryst::PowderPatternComponent::GetPowderPatternCalc
virtual const CrystVector_REAL & GetPowderPatternCalc() const =0
Get the calculated powder pattern for this component.

ObjCryst::PowderPatternComponent::SetMaxSinThetaOvLambda
virtual void SetMaxSinThetaOvLambda(const REAL max)=0
Set the maximum value for sin(theta)/lambda.

ObjCryst::PowderPatternComponent::mClockPowderPatternIntegratedVarianceCalc
RefinableObjClock mClockPowderPatternIntegratedVarianceCalc
When was the 'integrated' powder pattern variance last computed ?
Definition: PowderPattern.h:198

ObjCryst::PowderPatternComponent::mClockPowderPatternVarianceCalc
RefinableObjClock mClockPowderPatternVarianceCalc
When was the powder pattern variance last computed ?
Definition: PowderPattern.h:196

ObjCryst::PowderPatternComponent::Prepare
virtual void Prepare()=0

ObjCryst::PowderPatternComponent::SetParentPowderPattern
virtual void SetParentPowderPattern(PowderPattern &)=0
Set the PowderPattern object which uses this component.

ObjCryst::PowderPatternComponent::GetBraggLimits
virtual const CrystVector_long & GetBraggLimits() const =0
Get the pixel positions separating the integration intervals around reflections.

ObjCryst::PowderPatternComponent::mClockBraggLimits
RefinableObjClock mClockBraggLimits
Get last time the Bragg Limits were changed.
Definition: PowderPattern.h:203

ObjCryst::PowderPatternComponent::GetParentPowderPattern
const PowderPattern & GetParentPowderPattern() const
Get the PowderPattern object which uses this component.
Definition: PowderPattern.cpp:162

ObjCryst::PowderPatternComponent::HasPowderPatternCalcVariance
virtual bool HasPowderPatternCalcVariance() const =0
Does this component have a variance associated with each calculated point ? i.e., do we use maximum l...

ObjCryst::PowderPatternComponent::CalcPowderPatternIntegrated_FullDeriv
virtual void CalcPowderPatternIntegrated_FullDeriv(std::set< RefinablePar * > &vPar)
Calc the integrated powder pattern.
Definition: PowderPattern.cpp:223

ObjCryst::PowderPatternComponent::CalcPowderPattern
virtual void CalcPowderPattern() const =0
Calc the powder pattern.

ObjCryst::PowderPatternComponent::mPowderPatternIntegratedCalc
CrystVector_REAL mPowderPatternIntegratedCalc
The calculated powder pattern, integrated.
Definition: PowderPattern.h:171

ObjCryst::PowderPatternComponent::mIsScalable
bool mIsScalable
Scalable ? (crystal phase = scalable, background= not scalable)
Definition: PowderPattern.h:188

ObjCryst::PowderPatternComponent::mClockPowderPatternCalc
RefinableObjClock mClockPowderPatternCalc
When was the powder pattern last computed ?
Definition: PowderPattern.h:192

ObjCryst::PowderPatternComponent::GetClockPowderPatternCalcVariance
const RefinableObjClock & GetClockPowderPatternCalcVariance() const
Last time the variance on the pattern was actually calculated.

ObjCryst::PowderPatternComponent::mvLabel
list< pair< const REAL,const string > > mvLabel
The labels associated to different points of the pattern.
Definition: PowderPattern.h:206

ObjCryst::PowderPatternComponent::GetPowderPatternIntegratedCalc
virtual pair< const CrystVector_REAL *, const RefinableObjClock * > GetPowderPatternIntegratedCalc() const =0
Get the integrated values of the powder pattern.

ObjCryst::PowderPatternComponent::mIntegratedReflLimits
CrystVector_long mIntegratedReflLimits
Interval limits around each reflection, for integrated R-factors.
Definition: PowderPattern.h:179

ObjCryst::PowderPatternComponent::GetClockPowderPatternCalc
const RefinableObjClock & GetClockPowderPatternCalc() const
Last time the powder pattern was calculated.
Definition: PowderPattern.cpp:186

ObjCryst::PowderPatternComponent::mpParentPowderPattern
PowderPattern * mpParentPowderPattern
The PowderPattern object in which this component is included.
Definition: PowderPattern.h:201

ObjCryst::PowderPatternComponent::GetPowderPatternCalcVariance
virtual const CrystVector_REAL & GetPowderPatternCalcVariance() const =0
Get the variance associated to each point of the calculated powder pattern, for this component.

ObjCryst::PowderPatternComponent::mClockPowderPatternIntegratedCalc
RefinableObjClock mClockPowderPatternIntegratedCalc
When was the 'integrated' powder pattern last computed ?
Definition: PowderPattern.h:194

ObjCryst::PowderPatternComponent::mPowderPatternCalc
CrystVector_REAL mPowderPatternCalc
The calculated component of a powder pattern.
Definition: PowderPattern.h:169

ObjCryst::PowderPatternComponent::GetPowderPatternIntegratedCalcVariance
virtual pair< const CrystVector_REAL *, const RefinableObjClock * > GetPowderPatternIntegratedCalcVariance() const =0
Get the variance associated to each point of the calculated powder pattern, for this component (integ...

ObjCryst::PowderPatternComponent::mPowderPatternIntegratedCalcVariance
CrystVector_REAL mPowderPatternIntegratedCalcVariance
The variance associated to each point of the calculated powder pattern, integrated.
Definition: PowderPattern.h:176

ObjCryst::PowderPatternComponent::GetClockBraggLimits
const RefinableObjClock & GetClockBraggLimits() const
Get last time the Bragg Limits were changed.
Definition: PowderPattern.cpp:190

ObjCryst::PowderPatternComponent::GetPatternLabelList
const list< pair< const REAL,const string > > & GetPatternLabelList() const
Get a list of labels for the pattern (usually reflection indexes).
Definition: PowderPattern.cpp:195

ObjCryst::PowderPatternBackground
Phase to compute a background contribution to a powder pattern using an interpolation.
Definition: PowderPattern.h:223

ObjCryst::PowderPatternBackground::CalcPowderPatternIntegrated_FullDeriv
virtual void CalcPowderPatternIntegrated_FullDeriv(std::set< RefinablePar * > &vPar)
Calc the integrated powder pattern.
Definition: PowderPattern.cpp:632

ObjCryst::PowderPatternBackground::OptimizeBayesianBackground
void OptimizeBayesianBackground()
Optimize the background using a Bayesian approach.
Definition: PowderPattern.cpp:430

ObjCryst::PowderPatternBackground::HasPowderPatternCalcVariance
virtual bool HasPowderPatternCalcVariance() const
Does this component have a variance associated with each calculated point ? i.e., do we use maximum l...
Definition: PowderPattern.cpp:417

ObjCryst::PowderPatternBackground::mPointOrder
CrystVector_long mPointOrder
Subscript of the points, sorted the correct order, taking into account the type of radiation (monochr...
Definition: PowderPattern.h:288

ObjCryst::PowderPatternBackground::mvSplinePixel
CrystVector_REAL mvSplinePixel
Vector of pixel values between each interval, for faster CubicSpline calculations.
Definition: PowderPattern.h:291

ObjCryst::PowderPatternBackground::mBackgroundNbPoint
int mBackgroundNbPoint
Number of fitting points for background.
Definition: PowderPattern.h:281

ObjCryst::PowderPatternBackground::TagNewBestConfig
virtual void TagNewBestConfig() const
During a global optimization, tells the object that the current config is the latest "best" config.
Definition: PowderPattern.cpp:426

ObjCryst::PowderPatternBackground::SetMaxSinThetaOvLambda
virtual void SetMaxSinThetaOvLambda(const REAL max)
Set the maximum value for sin(theta)/lambda.
Definition: PowderPattern.cpp:685

ObjCryst::PowderPatternBackground::BeginOptimization
virtual void BeginOptimization(const bool allowApproximations=false, const bool enableRestraints=false)
This should be called by any optimization class at the begining of an optimization.
Definition: PowderPattern.cpp:397

ObjCryst::PowderPatternBackground::XMLOutput
virtual void XMLOutput(ostream &os, int indent=0) const
Output to stream in well-formed XML.
Definition: ObjCryst/IO.cpp:1665

ObjCryst::PowderPatternBackground::mvSpline
CubicSpline mvSpline
Spline used for interpolation.
Definition: PowderPattern.h:295

ObjCryst::PowderPatternBackground::mBackgroundInterpPointX
CrystVector_REAL mBackgroundInterpPointX
Vector of 2theta values for the fitting points of the background.
Definition: PowderPattern.h:283

ObjCryst::PowderPatternBackground::GetGeneGroup
virtual void GetGeneGroup(const RefinableObj &obj, CrystVector_uint &groupIndex, unsigned int &firstGroup) const
Get the gene group assigned to each parameter.
Definition: PowderPattern.cpp:381

ObjCryst::PowderPatternBackground::CalcPowderPattern
virtual void CalcPowderPattern() const
Calc the powder pattern.
Definition: PowderPattern.cpp:486

ObjCryst::PowderPatternBackground::SetParentPowderPattern
virtual void SetParentPowderPattern(PowderPattern &)
Set the PowderPattern object which uses this component.
Definition: PowderPattern.cpp:277

ObjCryst::PowderPatternBackground::GetPowderPatternCalcVariance
virtual const CrystVector_REAL & GetPowderPatternCalcVariance() const
Get the variance associated to each point of the calculated powder pattern, for this component.
Definition: PowderPattern.cpp:403

ObjCryst::PowderPatternBackground::FixParametersBeyondMaxresolution
void FixParametersBeyondMaxresolution(RefinableObj &obj)
Fix parameters corresponding to points of the pattern that are not actually calculated.
Definition: PowderPattern.cpp:474

ObjCryst::PowderPatternBackground::GetClassName
virtual const string & GetClassName() const
Name for this class ("RefinableObj", "Crystal",...).
Definition: PowderPattern.cpp:271

ObjCryst::PowderPatternBackground::GetPowderPatternIntegratedCalcVariance
virtual pair< const CrystVector_REAL *, const RefinableObjClock * > GetPowderPatternIntegratedCalcVariance() const
Get the variance associated to each point of the calculated powder pattern, for this component (integ...
Definition: PowderPattern.cpp:410

ObjCryst::PowderPatternBackground::mInterpolationModel
RefObjOpt mInterpolationModel
Type of interpolation performed: linear or cubic spline.
Definition: PowderPattern.h:314

ObjCryst::PowderPatternBackground::mBackgroundInterpPointIntensity
CrystVector_REAL mBackgroundInterpPointIntensity
Values of background at interpolating points.
Definition: PowderPattern.h:285

ObjCryst::PowderPatternBackground::mMaxSinThetaOvLambda
REAL mMaxSinThetaOvLambda
Maximum sin(theta)/lambda for all calculations (10 by default).
Definition: PowderPattern.h:307

ObjCryst::PowderPatternBackground::Prepare
virtual void Prepare()
Definition: PowderPattern.cpp:675

ObjCryst::PowderPatternBackground::GetPowderPatternIntegratedCalc
virtual pair< const CrystVector_REAL *, const RefinableObjClock * > GetPowderPatternIntegratedCalc() const
Get the integrated values of the powder pattern.
Definition: PowderPattern.cpp:294

ObjCryst::PowderPatternBackground::mClockBackgroundPoint
RefinableObjClock mClockBackgroundPoint
Modification of the interpolated points.
Definition: PowderPattern.h:298

ObjCryst::PowderPatternBackground::ImportUserBackground
void ImportUserBackground(const string &filename)
Import background points from a file (with two columns 2theta (or tof), intensity)
Definition: PowderPattern.cpp:301

ObjCryst::PowderPatternBackground::GetBraggLimits
virtual const CrystVector_long & GetBraggLimits() const
Get the pixel positions separating the integration intervals around reflections.
Definition: PowderPattern.cpp:678

ObjCryst::PowderPatternBackground::GetPowderPatternCalc
virtual const CrystVector_REAL & GetPowderPatternCalc() const
Get the calculated powder pattern for this component.
Definition: PowderPattern.cpp:287

ObjCryst::PowderPatternBackground::mClockSpline
RefinableObjClock mClockSpline
Initialization of the spline.
Definition: PowderPattern.h:300

ObjCryst::PowderPatternBackground::XMLInput
virtual void XMLInput(istream &is, const XMLCrystTag &tag)
Input From stream.
Definition: ObjCryst/IO.cpp:1711

ObjCryst::PowderPatternBackground::mModelVariance
REAL mModelVariance
Constant error (sigma) on the calculated pattern, due to an incomplete model.
Definition: PowderPattern.h:311

ObjCryst::PowderPatternDiffraction
Class to compute the contribution to a powder pattern from a crystalline phase.
Definition: PowderPattern.h:331

ObjCryst::PowderPatternDiffraction::SetExtractionMode
void SetExtractionMode(const bool extract=true, const bool init=false)
Prepare intensity extraction (Le Bail or Pawley)
Definition: PowderPattern.cpp:1047

ObjCryst::PowderPatternDiffraction::GetProfile
const ReflectionProfile & GetProfile() const
Get reflection profile.
Definition: PowderPattern.cpp:905

ObjCryst::PowderPatternDiffraction::GetPowderPatternIntegratedCalcVariance
virtual pair< const CrystVector_REAL *, const RefinableObjClock * > GetPowderPatternIntegratedCalcVariance() const
Get the variance associated to each point of the calculated powder pattern, for this component (integ...
Definition: PowderPattern.cpp:1016

ObjCryst::PowderPatternDiffraction::GetProfileFitNetNbObs
unsigned int GetProfileFitNetNbObs() const
Get the 'net' number of observed intensities, minus the number of reflections, for a profile fit.
Definition: PowderPattern.cpp:1276

ObjCryst::PowderPatternDiffraction::mClockLorentzPolarSlitCorrPar
RefinableObjClock mClockLorentzPolarSlitCorrPar
Last time the Lorentz-Polarization and slit parameters were changed.
Definition: PowderPattern.h:464

ObjCryst::PowderPatternDiffraction::SetFrozenLatticePar
void SetFrozenLatticePar(const unsigned int i, REAL v)
Change one parameter in mFrozenLatticePar. This triggers a call to CalcLocalBMatrix() if the paramete...
Definition: PowderPattern.cpp:1252

ObjCryst::PowderPatternDiffraction::mCorrCylAbs
CylinderAbsCorr mCorrCylAbs
Cylinder absorption correction.
Definition: PowderPattern.h:509

ObjCryst::PowderPatternDiffraction::XMLInput
virtual void XMLInput(istream &is, const XMLCrystTag &tag)
Input From stream.
Definition: ObjCryst/IO.cpp:1866

ObjCryst::PowderPatternDiffraction::GetFrozenLatticePar
REAL GetFrozenLatticePar(const unsigned int i) const
Access to one parameter in mFrozenLatticePar.
Definition: PowderPattern.cpp:1261

ObjCryst::PowderPatternDiffraction::GetPowderPatternCalc
virtual const CrystVector_REAL & GetPowderPatternCalc() const
Get the calculated powder pattern for this component.
Definition: PowderPattern.cpp:869

ObjCryst::PowderPatternDiffraction::GetPowderPatternIntegratedCalc
virtual pair< const CrystVector_REAL *, const RefinableObjClock * > GetPowderPatternIntegratedCalc() const
Get the integrated values of the powder pattern.
Definition: PowderPattern.cpp:876

ObjCryst::PowderPatternDiffraction::mFreezeLatticePar
bool mFreezeLatticePar
If true, use local cell parameters from mFrozenLatticePar rather than the Crystal.
Definition: PowderPattern.h:556

ObjCryst::PowderPatternDiffraction::mCorrPolar
PolarizationCorr mCorrPolar
Polarization correction.
Definition: PowderPattern.h:499

ObjCryst::PowderPatternDiffraction::mClockProfileCalc
RefinableObjClock mClockProfileCalc
Last time the reflection profiles were computed.
Definition: PowderPattern.h:469

ObjCryst::PowderPatternDiffraction::GetFhklObsSq
const CrystVector_REAL & GetFhklObsSq() const
Get the extracted structure factors modulus (squared), e.g.
Definition: PowderPattern.cpp:1310

ObjCryst::PowderPatternDiffraction::mExtractionMode
bool mExtractionMode
Extraction mode (Le Bail, Pawley)
Definition: PowderPattern.h:547

ObjCryst::PowderPatternDiffraction::mvReflProfile_FullDeriv
std::map< RefinablePar *, vector< CrystVector_REAL > > mvReflProfile_FullDeriv
Derivatives of reflection profiles versus a list of parameters.
Definition: PowderPattern.h:533

ObjCryst::PowderPatternDiffraction::CalcPowderPatternIntegrated_FullDeriv
virtual void CalcPowderPatternIntegrated_FullDeriv(std::set< RefinablePar * > &vPar)
Calc the integrated powder pattern.
Definition: PowderPattern.cpp:1666

ObjCryst::PowderPatternDiffraction::mClockIntegratedProfileFactor
RefinableObjClock mClockIntegratedProfileFactor
Last time the integrated values of normalized profiles was calculated.
Definition: PowderPattern.h:545

ObjCryst::PowderPatternDiffraction::mClockIhklCalc
RefinableObjClock mClockIhklCalc
Last time intensities were computed.
Definition: PowderPattern.h:471

ObjCryst::PowderPatternDiffraction::CalcPowderPattern
virtual void CalcPowderPattern() const
Calc the powder pattern.
Definition: PowderPattern.cpp:1317

ObjCryst::PowderPatternDiffraction::Prepare
virtual void Prepare()
Definition: PowderPattern.cpp:2339

ObjCryst::PowderPatternDiffraction::mClockProfilePar
RefinableObjClock mClockProfilePar
Last time the reflection parameters were changed.
Definition: PowderPattern.h:462

ObjCryst::PowderPatternDiffraction::mIntegratedProfileFactor
vector< pair< unsigned long, CrystVector_REAL > > mIntegratedProfileFactor
For each reflection, store the integrated value of the normalized profile over all integration interv...
Definition: PowderPattern.h:543

ObjCryst::PowderPatternDiffraction::SetCrystal
virtual void SetCrystal(Crystal &crystal)
Set the crystal for this experiment.
Definition: PowderPattern.cpp:1028

ObjCryst::PowderPatternDiffraction::CalcPowderReflProfile_FullDeriv
void CalcPowderReflProfile_FullDeriv(std::set< RefinablePar * > &vPar)
Definition: PowderPattern.cpp:1926

ObjCryst::PowderPatternDiffraction::mCorrTOF
TOFCorr mCorrTOF
Time-Of-Flight intensity correction.
Definition: PowderPattern.h:507

ObjCryst::PowderPatternDiffraction::SetMaxSinThetaOvLambda
virtual void SetMaxSinThetaOvLambda(const REAL max)
Set the maximum value for sin(theta)/lambda.
Definition: PowderPattern.cpp:2388

ObjCryst::PowderPatternDiffraction::HasPowderPatternCalcVariance
virtual bool HasPowderPatternCalcVariance() const
Does this component have a variance associated with each calculated point ? i.e., do we use maximum l...
Definition: PowderPattern.cpp:1023

ObjCryst::PowderPatternDiffraction::GetPowderPatternCalcVariance
virtual const CrystVector_REAL & GetPowderPatternCalcVariance() const
Get the variance associated to each point of the calculated powder pattern, for this component.
Definition: PowderPattern.cpp:1009

ObjCryst::PowderPatternDiffraction::GetGeneGroup
virtual void GetGeneGroup(const RefinableObj &obj, CrystVector_uint &groupIndex, unsigned int &firstGroup) const
Get the gene group assigned to each parameter.
Definition: PowderPattern.cpp:989

ObjCryst::PowderPatternDiffraction::CalcIntensityCorr
void CalcIntensityCorr() const
Definition: PowderPattern.cpp:2079

ObjCryst::PowderPatternDiffraction::SetReflectionProfilePar
void SetReflectionProfilePar(const ReflectionProfileType prof, const REAL fwhmCagliotiW, const REAL fwhmCagliotiU=0, const REAL fwhmCagliotiV=0, const REAL eta0=0.5, const REAL eta1=0.)
Set reflection profile parameters.
Definition: PowderPattern.cpp:882

ObjCryst::PowderPatternDiffraction::mCorrLorentz
LorentzCorr mCorrLorentz
Lorentz correction.
Definition: PowderPattern.h:497

ObjCryst::PowderPatternDiffraction::GetNbReflBelowMaxSinThetaOvLambda
virtual long GetNbReflBelowMaxSinThetaOvLambda() const
Recalc, and get the number of reflections which should be actually used, due to the maximuml sin(thet...
Definition: PowderPattern.cpp:1221

ObjCryst::PowderPatternDiffraction::CalcIhkl
virtual void CalcIhkl() const
Definition: PowderPattern.cpp:2169

ObjCryst::PowderPatternDiffraction::GetExtractionMode
bool GetExtractionMode() const
Return true if in extraction mode, i.e. using extracted intensities instead of computed structure fac...
Definition: PowderPattern.cpp:1123

ObjCryst::PowderPatternDiffraction::GetBraggLimits
virtual const CrystVector_long & GetBraggLimits() const
Get the pixel positions separating the integration intervals around reflections.
Definition: PowderPattern.cpp:2369

ObjCryst::PowderPatternDiffraction::mCorrTextureMarchDollase
TextureMarchDollase mCorrTextureMarchDollase
Preferred orientation (texture) correction following the March-Dollase model.
Definition: PowderPattern.h:503

ObjCryst::PowderPatternDiffraction::mIhklCalc
CrystVector_REAL mIhklCalc
Computed intensities for all reflections.
Definition: PowderPattern.h:512

ObjCryst::PowderPatternDiffraction::ExtractLeBail
void ExtractLeBail(unsigned int nbcycle=1)
Extract intensities using Le Bail method.
Definition: PowderPattern.cpp:1125

ObjCryst::PowderPatternDiffraction::GetClassName
virtual const string & GetClassName() const
Name for this class ("RefinableObj", "Crystal",...).
Definition: PowderPattern.cpp:846

ObjCryst::PowderPatternDiffraction::mvReflProfile
vector< ReflProfile > mvReflProfile
Reflection profiles for ALL reflections during the last powder pattern generation.
Definition: PowderPattern.h:529

ObjCryst::PowderPatternDiffraction::EndOptimization
virtual void EndOptimization()
This should be called by any optimization class at the end of an optimization.
Definition: PowderPattern.cpp:958

ObjCryst::PowderPatternDiffraction::mCorrSlitAperture
PowderSlitApertureCorr mCorrSlitAperture
Slit aperture correction.
Definition: PowderPattern.h:501

ObjCryst::PowderPatternDiffraction::mGenHKLBMatrix
CrystMatrix_REAL mGenHKLBMatrix
Bmatrix the last time the HKL parameters were generated.
Definition: PowderPattern.h:560

ObjCryst::PowderPatternDiffraction::SetParentPowderPattern
virtual void SetParentPowderPattern(PowderPattern &)
Set the PowderPattern object which uses this component.
Definition: PowderPattern.cpp:857

ObjCryst::PowderPatternDiffraction::CalcPowderReflProfile
void CalcPowderReflProfile() const
Definition: PowderPattern.cpp:1751

ObjCryst::PowderPatternDiffraction::SetProfile
void SetProfile(ReflectionProfile *prof)
Assign a new profile.
Definition: PowderPattern.cpp:892

ObjCryst::PowderPatternDiffraction::CreateCopy
virtual PowderPatternDiffraction * CreateCopy() const
So-called virtual copy constructor.
Definition: PowderPattern.cpp:852

ObjCryst::PowderPatternDiffraction::HasFhklObsSq
bool HasFhklObsSq() const
Return true if there are extracted (le Bail) squared structure factors, false otherwise.
Definition: PowderPattern.cpp:1304

ObjCryst::PowderPatternDiffraction::GetBMatrix
virtual const CrystMatrix_REAL & GetBMatrix() const
This can use either locally stored lattice parameters from mLocalLatticePar, or the Crystal's,...
Definition: PowderPattern.cpp:2391

ObjCryst::PowderPatternDiffraction::CalcFrozenBMatrix
void CalcFrozenBMatrix() const
Calculate the local BMatrix, used if mFreezeLatticePar is true.
Definition: PowderPattern.cpp:2397

ObjCryst::PowderPatternDiffraction::mIhklCalcVariance
CrystVector_REAL mIhklCalcVariance
Variance on computed intensities for all reflections.
Definition: PowderPattern.h:515

ObjCryst::PowderPatternDiffraction::mpReflectionProfile
ReflectionProfile * mpReflectionProfile
Profile.
Definition: PowderPattern.h:473

ObjCryst::PowderPatternDiffraction::mFrozenLatticePar
CrystVector_REAL mFrozenLatticePar
a,b and c in Angstroems, angles (stored) in radians This is used to override lattice parameter from t...
Definition: PowderPattern.h:554

ObjCryst::PowderPatternDiffraction::mClockIntensityCorr
RefinableObjClock mClockIntensityCorr
Last time the Lorentz-Polar-Slit correction was computed.
Definition: PowderPattern.h:467

ObjCryst::PowderPatternDiffraction::mIntensityCorr
CrystVector_REAL mIntensityCorr
Calculated corrections for all reflections.
Definition: PowderPattern.h:495

ObjCryst::PowderPatternDiffraction::mpLeBailData
DiffractionDataSingleCrystal * mpLeBailData
Single crystal data extracted from the powder pattern.
Definition: PowderPattern.h:549

ObjCryst::PowderPatternDiffraction::SetApproximationFlag
virtual void SetApproximationFlag(const bool allow)
Enable or disable numerical approximations.
Definition: PowderPattern.cpp:975

ObjCryst::PowderPatternDiffraction::FreezeLatticePar
bool FreezeLatticePar() const
Do we use local cell parameters ? (see mFrozenLatticePar)
Definition: PowderPattern.cpp:1274

ObjCryst::PowderPatternDiffraction::GetRadiation
virtual const Radiation & GetRadiation() const
Get the radiation object for this data.
Definition: PowderPattern.cpp:1044

ObjCryst::PowderPatternDiffraction::mFrozenBMatrix
CrystMatrix_REAL mFrozenBMatrix
Local B Matrix, used if mFreezeLatticePar is true.
Definition: PowderPattern.h:558

ObjCryst::PowderPatternDiffraction::BeginOptimization
virtual void BeginOptimization(const bool allowApproximations=false, const bool enableRestraints=false)
This should be called by any optimization class at the begining of an optimization.
Definition: PowderPattern.cpp:944

ObjCryst::PowderPatternDiffraction::XMLOutput
virtual void XMLOutput(ostream &os, int indent=0) const
Output to stream in well-formed XML.
Definition: ObjCryst/IO.cpp:1794

ObjCryst::PowderPatternDiffraction::mCorrTextureEllipsoid
TextureEllipsoid mCorrTextureEllipsoid
Preferred orientation (texture) correction following the Ellipsoidal function.
Definition: PowderPattern.h:505

ObjCryst::PowderPatternDiffraction::ReflProfile
Profile of a single reflection.
Definition: PowderPattern.h:520

ObjCryst::PowderPatternDiffraction::ReflProfile::first
long first
First point of the pattern for which the profile is calculated.
Definition: PowderPattern.h:522

ObjCryst::PowderPatternDiffraction::ReflProfile::last
long last
Last point of the pattern for which the profile is calculated.
Definition: PowderPattern.h:524

ObjCryst::PowderPatternDiffraction::ReflProfile::profile
CrystVector_REAL profile
The profile.
Definition: PowderPattern.h:526

ObjCryst::PowderPattern
Powder pattern class, with an observed pattern and several calculated components to modelize the patt...
Definition: PowderPattern.h:581

ObjCryst::PowderPattern::X2Pixel
REAL X2Pixel(const REAL x) const
Get the pixel number on the experimental pattern, corresponding to a given (experimental) x coordinat...
Definition: PowderPattern.cpp:2926

ObjCryst::PowderPattern::AddPowderPatternComponent
void AddPowderPatternComponent(PowderPatternComponent &)
Add a component (phase, backround) to this pattern.
Definition: PowderPattern.cpp:2580

ObjCryst::PowderPattern::X2STOL
REAL X2STOL(const REAL x) const
Convert X (either 2theta or TOF) to sin(theta)/lambda, depending on the type of radiation.
Definition: PowderPattern.cpp:5488

ObjCryst::PowderPattern::mPowderPatternCalc
CrystVector_REAL mPowderPatternCalc
The calculated powder pattern.
Definition: PowderPattern.h:1008

ObjCryst::PowderPattern::mRadiation
Radiation mRadiation
The Radiation corresponding to this experiment.
Definition: PowderPattern.h:1055

ObjCryst::PowderPattern::STOL2X
REAL STOL2X(const REAL stol) const
Convert sin(theta)/lambda to X (i.e.
Definition: PowderPattern.cpp:5471

ObjCryst::PowderPattern::SetEnergy
void SetEnergy(const REAL energy)
Set the energy of the experiment [in keV, lambda(A)=12398/E(keV)].

ObjCryst::PowderPattern::GetLSQObs
virtual const CrystVector_REAL & GetLSQObs(const unsigned int) const
Get the observed values for the LSQ function.
Definition: PowderPattern.cpp:5332

ObjCryst::PowderPattern::GetClockNbPointUsed
const RefinableObjClock & GetClockNbPointUsed() const
Clock corresponding to the last time the number of points used was changed.
Definition: PowderPattern.cpp:2734

ObjCryst::PowderPattern::mChi2Cumul
CrystVector_REAL mChi2Cumul
The cumulative Chi^2 (integrated or not, depending on the option)
Definition: PowderPattern.h:1032

ObjCryst::PowderPattern::PrepareIntegratedRfactor
void PrepareIntegratedRfactor() const
Prepare the calculation of the integrated R-factors.
Definition: PowderPattern.cpp:6624

ObjCryst::PowderPattern::GetIntegratedChi2
REAL GetIntegratedChi2() const
Return integrated Chi^2.
Definition: PowderPattern.cpp:4390

ObjCryst::PowderPattern::GetWavelength
REAL GetWavelength() const
wavelength of the experiment (in Angstroems)
Definition: PowderPattern.cpp:2763

ObjCryst::PowderPattern::mPowderPatternBackgroundIntegratedCalc
CrystVector_REAL mPowderPatternBackgroundIntegratedCalc
The calculated powder pattern part which corresponds to 'background' (eg non-scalable components),...
Definition: PowderPattern.h:1018

ObjCryst::PowderPattern::mNbPoint
unsigned long mNbPoint
Number of points in the pattern.
Definition: PowderPattern.h:1052

ObjCryst::PowderPattern::GetPowderPatternXMax
REAL GetPowderPatternXMax() const
Get the maximum 2theta.
Definition: PowderPattern.cpp:2810

ObjCryst::PowderPattern::ImportPowderPattern2ThetaObs
void ImportPowderPattern2ThetaObs(const string &fileName, const int nbSkip=0)
Import file with 2 columns 2Theta Iobs.
Definition: PowderPattern.cpp:3300

ObjCryst::PowderPattern::ImportPowderPatternPSI_DMC
void ImportPowderPatternPSI_DMC(const string &filename)
Import powder pattern, format DMC from PSI.
Definition: PowderPattern.cpp:3056

ObjCryst::PowderPattern::GetIntegratedProfileMin
const CrystVector_long & GetIntegratedProfileMin() const
Get the list of first pixels for the integration intervals.
Definition: PowderPattern.cpp:5454

ObjCryst::PowderPattern::SetSigmaToSqrtIobs
void SetSigmaToSqrtIobs()
Set sigma=sqrt(Iobs)
Definition: PowderPattern.cpp:5201

ObjCryst::PowderPattern::CalcPowderPatternIntegrated
void CalcPowderPatternIntegrated() const
Calc the integrated powder pattern.
Definition: PowderPattern.cpp:6266

ObjCryst::PowderPattern::ImportPowderPatternFullprof4
void ImportPowderPatternFullprof4(const string &fileName)
Import diffraction data from a file, with the first line has 2ThetaMin, step, 2thetaMax,...
Definition: PowderPattern.cpp:3440

ObjCryst::PowderPattern::GetR
REAL GetR() const
Unweighted R-factor.
Definition: PowderPattern.cpp:3915

ObjCryst::PowderPattern::GetLSQWeight
virtual const CrystVector_REAL & GetLSQWeight(const unsigned int) const
Get the weight values for the LSQ function.
Definition: PowderPattern.cpp:5354

ObjCryst::PowderPattern::GetClockPowderPatternPar
const RefinableObjClock & GetClockPowderPatternPar() const
When were the pattern parameters (2theta range, step) changed ?
Definition: PowderPattern.cpp:2881

ObjCryst::PowderPattern::GetIntegratedProfileLimitsClock
const RefinableObjClock & GetIntegratedProfileLimitsClock() const
When were the integration intervals last changed ?
Definition: PowderPattern.cpp:5466

ObjCryst::PowderPattern::SetWeightPolynomial
void SetWeightPolynomial(const REAL a, const REAL b, const REAL c, const REAL minRelatIobs=1e-3)
Set w = 1/(a+ Iobs + b*Iobs^2+c*Iobs^3)
Definition: PowderPattern.cpp:5227

ObjCryst::PowderPattern::GetPowderPatternComponent
const PowderPatternComponent & GetPowderPatternComponent(const string &name) const
Access to a component of the powder pattern.
Definition: PowderPattern.cpp:2650

ObjCryst::PowderPattern::GetPowderPatternWeight
const CrystVector_REAL & GetPowderPatternWeight() const
Get the weight for each point of the powder pattern.
Definition: PowderPattern.cpp:2792

ObjCryst::PowderPattern::CalcNbPointUsed
void CalcNbPointUsed() const
Calculate the number of points of the pattern actually used, from the maximum value of sin(theta)/lam...
Definition: PowderPattern.cpp:6814

ObjCryst::PowderPattern::ImportPowderPatternFullprof
void ImportPowderPatternFullprof(const string &fullprofFileName)
Import fullprof-style diffraction data.
Definition: PowderPattern.cpp:3011

ObjCryst::PowderPattern::GetLSQ_FullDeriv
virtual std::map< RefinablePar *, CrystVector_REAL > & GetLSQ_FullDeriv(const unsigned int, std::set< RefinablePar * > &vPar)
Get the first derivative for the LSQ function for each parameter supplied in a list.
Definition: PowderPattern.cpp:5379

ObjCryst::PowderPattern::SetMaxSinThetaOvLambda
virtual void SetMaxSinThetaOvLambda(const REAL max)
Set the maximum value for sin(theta)/lambda.
Definition: PowderPattern.cpp:5443

ObjCryst::PowderPattern::mPowderPatternUsedCalc
CrystVector_REAL mPowderPatternUsedCalc
The calculated powder pattern. Cropped to the maximum sin(theta)/lambda for LSQ.
Definition: PowderPattern.h:1036

ObjCryst::PowderPattern::ImportPowderPatternXdd
void ImportPowderPatternXdd(const string &fileName)
Import *.xdd diffraction data (Topas,...).
Definition: PowderPattern.cpp:3149

ObjCryst::PowderPattern::GetNbLSQFunction
virtual unsigned int GetNbLSQFunction() const
Number of LSQ functions.
Definition: PowderPattern.cpp:5307

ObjCryst::PowderPattern::GetPowderPatternVariance
const CrystVector_REAL & GetPowderPatternVariance() const
Get the variance (obs+model) for each point of the powder pattern.
Definition: PowderPattern.cpp:2787

ObjCryst::PowderPattern::ImportPowderPatternCIF
void ImportPowderPatternCIF(const CIF &cif)
Import CIF powder pattern data.
Definition: PowderPattern.cpp:3810

ObjCryst::PowderPattern::mPowderPatternUsedObs
CrystVector_REAL mPowderPatternUsedObs
The calculated powder pattern. Cropped to the maximum sin(theta)/lambda for LSQ.
Definition: PowderPattern.h:1039

ObjCryst::PowderPattern::GetMuR
REAL GetMuR() const
Get the $\mu R$ value.
Definition: PowderPattern.cpp:6006

ObjCryst::PowderPattern::SetWeightToUnit
void SetWeightToUnit()
Set w = 1.
Definition: PowderPattern.cpp:5221

ObjCryst::PowderPattern::mMaxSinThetaOvLambda
REAL mMaxSinThetaOvLambda
Displacement correction :  REAL m2ThetaDisplacement; Transparency correction :  REAL m2ThetaTranspare...
Definition: PowderPattern.h:1144

ObjCryst::PowderPattern::SetXZero
void SetXZero(const REAL newZero)
Change Zero in x (2theta,tof)
Definition: PowderPattern.cpp:2893

ObjCryst::PowderPattern::ExportFullprof
void ExportFullprof(const std::string &prefix) const
Export powder pattern & crystal structure in Fullprof format.
Definition: PowderPattern.cpp:5732

ObjCryst::PowderPattern::SetScaleFactor
void SetScaleFactor(const int i, REAL s)
Access to the scale factor of components (will be 1 for background components)
Definition: PowderPattern.cpp:2686

ObjCryst::PowderPattern::XMLOutput
virtual void XMLOutput(ostream &os, int indent=0) const
Output to stream in well-formed XML.
Definition: ObjCryst/IO.cpp:2154

ObjCryst::PowderPattern::SetPowderPatternX
void SetPowderPatternX(const CrystVector_REAL &x)
Set the x coordinate of the powder pattern : either the 2theta or time-of-flight values for each reco...
Definition: PowderPattern.cpp:2713

ObjCryst::PowderPattern::mExcludedRegionMinX
CrystVector_REAL mExcludedRegionMinX
Min coordinate for for all excluded regions.
Definition: PowderPattern.h:1075

ObjCryst::PowderPattern::mPowderPatternWeight
CrystVector_REAL mPowderPatternWeight
The weight for each point of the pattern.
Definition: PowderPattern.h:1024

ObjCryst::PowderPattern::GetNbPoint
unsigned long GetNbPoint() const
Number of points ?
Definition: PowderPattern.cpp:2726

ObjCryst::PowderPattern::GetPowderPatternXStep
REAL GetPowderPatternXStep() const
Get the average step in 2theta.
Definition: PowderPattern.cpp:2804

ObjCryst::PowderPattern::GetRw
REAL GetRw() const
Get the weighted R-factor.
Definition: PowderPattern.cpp:4108

ObjCryst::PowderPattern::Set2ThetaTransparency
void Set2ThetaTransparency(const REAL transparency)
Change transparency correction .
Definition: PowderPattern.cpp:2905

ObjCryst::PowderPattern::GetLSQCalc
virtual const CrystVector_REAL & GetLSQCalc(const unsigned int) const
Get the current calculated value for the LSQ function.
Definition: PowderPattern.cpp:5310

ObjCryst::PowderPattern::mExcludedRegionMaxX
CrystVector_REAL mExcludedRegionMaxX
Max coordinate for 2theta for all excluded regions.
Definition: PowderPattern.h:1077

ObjCryst::PowderPattern::ImportPowderPatternGSAS
void ImportPowderPatternGSAS(const string &fileName)
Import GSAS standard powder pattern data (see GSAS manual).
Definition: PowderPattern.cpp:3580

ObjCryst::PowderPattern::SetRadiation
void SetRadiation(const Radiation &radiation)
Set the radiation.
Definition: PowderPattern.cpp:2736

ObjCryst::PowderPattern::mPowderPatternVarianceIntegrated
CrystVector_REAL mPowderPatternVarianceIntegrated
The complete variance associated to each point of the powder pattern, taking into account observation...
Definition: PowderPattern.h:1030

ObjCryst::PowderPattern::GetRadiationType
RadiationType GetRadiationType() const
Neutron or x-ray experiment ?
Definition: PowderPattern.cpp:2750

ObjCryst::PowderPattern::RemovePowderPatternComponent
void RemovePowderPatternComponent(PowderPatternComponent &)
Remove a powder pattern component.
Definition: PowderPattern.cpp:2607

ObjCryst::PowderPattern::SetPowderPatternObs
void SetPowderPatternObs(const CrystVector_REAL &obs)
Set observed powder pattern from vector array.
Definition: PowderPattern.cpp:3841

ObjCryst::PowderPattern::X2PixelCorr
REAL X2PixelCorr(const REAL x) const
Get the pixel number on the experimental pattern, from the theoretical (uncorrected) x coordinate,...
Definition: PowderPattern.cpp:2921

ObjCryst::PowderPattern::GetRadiation
const Radiation & GetRadiation() const
Neutron or x-ray experiment ?
Definition: PowderPattern.cpp:2741

ObjCryst::PowderPattern::mClockPowderPatternIntegratedCalc
RefinableObjClock mClockPowderPatternIntegratedCalc
When was the powder pattern (integrated) last computed ?
Definition: PowderPattern.h:1065

ObjCryst::PowderPattern::ImportPowderPatternILL_D1A5
void ImportPowderPatternILL_D1A5(const string &filename)
Import powder pattern, format from ILL D1A/D2B (format without counter info)
Definition: PowderPattern.cpp:3101

ObjCryst::PowderPattern::GetClockPowderPatternAbsCorr
const RefinableObjClock & GetClockPowderPatternAbsCorr() const
When were the absorption correction parameters (muR) last changed ?
Definition: PowderPattern.cpp:2890

ObjCryst::PowderPattern::CalcPowderPattern
void CalcPowderPattern() const
Calc the powder pattern.
Definition: PowderPattern.cpp:6008

ObjCryst::PowderPattern::GetPowderPatternX
const CrystVector_REAL & GetPowderPatternX() const
Get the vector of X (2theta or time-of-flight) coordinates.
Definition: PowderPattern.cpp:2816

ObjCryst::PowderPattern::GetNbPointUsed
unsigned long GetNbPointUsed() const
Number of points actually calculated (below the chosen max(sin(theta)/lambda)) ?
Definition: PowderPattern.cpp:2728

ObjCryst::PowderPattern::AddExcludedRegion
void AddExcludedRegion(const REAL min2Theta, const REAL max2theta)
Add an Exclusion region, in 2theta, which will be ignored when computing R's XMLInput values must be,...
Definition: PowderPattern.cpp:5267

ObjCryst::PowderPattern::GlobalOptRandomMove
virtual void GlobalOptRandomMove(const REAL mutationAmplitude, const RefParType *type=gpRefParTypeObjCryst)
Make a random move of the current configuration.
Definition: PowderPattern.cpp:5260

ObjCryst::PowderPattern::ImportPowderPatternTOF_ISIS_XYSigma
void ImportPowderPatternTOF_ISIS_XYSigma(const string &fileName)
Import TOF file (ISIS type, 3 columns t, Iobs, sigma(Iobs))
Definition: PowderPattern.cpp:3503

ObjCryst::PowderPattern::GetChi2Cumul
const CrystVector_REAL & GetChi2Cumul(const int mode=-1) const
Get the powder pattern cumulative Chi^2.
Definition: PowderPattern.cpp:2821

ObjCryst::PowderPattern::mPowderPatternBackgroundCalc
CrystVector_REAL mPowderPatternBackgroundCalc
The calculated powder pattern part which corresponds to 'background' (eg non-scalable components).
Definition: PowderPattern.h:1015

ObjCryst::PowderPattern::XMLInput
virtual void XMLInput(istream &is, const XMLCrystTag &tag)
Input From stream.
Definition: ObjCryst/IO.cpp:2266

ObjCryst::PowderPattern::mPowderPatternObs
CrystVector_REAL mPowderPatternObs
The observed powder pattern.
Definition: PowderPattern.h:1020

ObjCryst::PowderPattern::GetGeneGroup
virtual void GetGeneGroup(const RefinableObj &obj, CrystVector_uint &groupIndex, unsigned int &firstGroup) const
Get the gene group assigned to each parameter.
Definition: PowderPattern.cpp:5418

ObjCryst::PowderPattern::mClockPowderPatternCalc
RefinableObjClock mClockPowderPatternCalc
When was the powder pattern last computed ?
Definition: PowderPattern.h:1063

ObjCryst::PowderPattern::mPowderPatternObsSigma
CrystVector_REAL mPowderPatternObsSigma
The sigma of the observed pattern.
Definition: PowderPattern.h:1022

ObjCryst::PowderPattern::GetLogLikelihood
virtual REAL GetLogLikelihood() const
Get -log(likelihood) of the current configuration for the object.
Definition: PowderPattern.cpp:5299

ObjCryst::PowderPattern::mPowderPatternUsedWeight
CrystVector_REAL mPowderPatternUsedWeight
The weight for each point of the pattern. Cropped to the maximum sin(theta)/lambda for LSQ.
Definition: PowderPattern.h:1041

ObjCryst::PowderPattern::STOL2Pixel
REAL STOL2Pixel(const REAL stol) const
Convert sin(theta)/lambda to pixel, depending on the type of radiation.
Definition: PowderPattern.cpp:5507

ObjCryst::PowderPattern::GetPowderPatternXMin
REAL GetPowderPatternXMin() const
Get the Minimum 2theta.
Definition: PowderPattern.cpp:2797

ObjCryst::PowderPattern::InitOptions
virtual void InitOptions()
Initialize options.
Definition: PowderPattern.cpp:6838

ObjCryst::PowderPattern::Init
virtual void Init()
Init parameters and options.
Definition: PowderPattern.cpp:6578

ObjCryst::PowderPattern::FitScaleFactorForRw
void FitScaleFactorForRw() const
Fit the scale(s) factor of each component to minimize Rw.
Definition: PowderPattern.cpp:4766

ObjCryst::PowderPattern::GetChi2
REAL GetChi2() const
Return conventionnal Chi^2.
Definition: PowderPattern.cpp:4311

ObjCryst::PowderPattern::GetMaxSinThetaOvLambda
REAL GetMaxSinThetaOvLambda() const
Get the maximum value for sin(theta)/lambda.
Definition: PowderPattern.cpp:5452

ObjCryst::PowderPattern::mClockScaleFactor
RefinableObjClock mClockScaleFactor
Last modification of the scale factor.
Definition: PowderPattern.h:1069

ObjCryst::PowderPattern::mPowderPatternIntegratedCalc
CrystVector_REAL mPowderPatternIntegratedCalc
The calculated powder pattern, integrated.
Definition: PowderPattern.h:1011

ObjCryst::PowderPattern::ImportPowderPatternMultiDetectorLLBG42
void ImportPowderPatternMultiDetectorLLBG42(const string &fileName)
diffraction data in a multi-detector format (fullprof format #6).
Definition: PowderPattern.cpp:3358

ObjCryst::PowderPattern::PrintObsCalcData
void PrintObsCalcData(ostream &os=cout) const
Print to thee screen/console the observed and calculated pattern (long, mostly useful for debugging)
Definition: PowderPattern.cpp:3902

ObjCryst::PowderPattern::GetPowderPatternObs
const CrystVector_REAL & GetPowderPatternObs() const
Get the observed powder pattern.
Definition: PowderPattern.cpp:2777

ObjCryst::PowderPattern::mX
CrystVector_REAL mX
Vector of x coordinates (either 2theta or time-of-flight) for the pattern.
Definition: PowderPattern.h:1048

ObjCryst::PowderPattern::GetNbPowderPatternComponent
unsigned int GetNbPowderPatternComponent() const
Number of components.
Definition: PowderPattern.cpp:2644

ObjCryst::PowderPattern::mPowderPatternVariance
CrystVector_REAL mPowderPatternVariance
The complete variance associated to each point of the powder pattern, taking into account observation...
Definition: PowderPattern.h:1027

ObjCryst::PowderPattern::mClockCorrAbs
RefinableObjClock mClockCorrAbs
Last modification of absorption correction parameters.
Definition: PowderPattern.h:1071

ObjCryst::PowderPattern::GetClockPowderPatternCalc
const RefinableObjClock & GetClockPowderPatternCalc() const
Last time the pattern was calculated.
Definition: PowderPattern.cpp:2878

ObjCryst::PowderPattern::X2XCorr
REAL X2XCorr(const REAL x) const
Get the experimental x (2theta, tof) from the theoretical value, taking into account all corrections ...
Definition: PowderPattern.cpp:2911

ObjCryst::PowderPattern::SetRadiationType
void SetRadiationType(const RadiationType radiation)
Set the radiation type.
Definition: PowderPattern.cpp:2745

ObjCryst::PowderPattern::FindPeaks
PeakList FindPeaks(const float dmin=2.0, const float maxratio=0.01, const unsigned int maxpeak=100)
Find peaks in the pattern.
Definition: PowderPattern.cpp:5512

ObjCryst::PowderPattern::ImportPowderPatternSietronicsCPI
void ImportPowderPatternSietronicsCPI(const string &fileName)
Import *.cpi Sietronics diffraction data.
Definition: PowderPattern.cpp:3192

ObjCryst::PowderPattern::SetPowderPatternPar
void SetPowderPatternPar(const REAL min, const REAL step, unsigned long nbPoint)
\briefSet the powder pattern angular range & resolution parameter.
Definition: PowderPattern.cpp:2700

ObjCryst::PowderPattern::GetIntegratedProfileMax
const CrystVector_long & GetIntegratedProfileMax() const
Get the list of last pixels for the integration intervals.
Definition: PowderPattern.cpp:5460

ObjCryst::PowderPattern::SetWeightToInvSigmaSq
void SetWeightToInvSigmaSq(const REAL minRelatSigma=1e-3)
Set w = 1/sigma^2.
Definition: PowderPattern.cpp:5207

ObjCryst::PowderPattern::FitScaleFactorForR
void FitScaleFactorForR() const
Fit the scale(s) factor of each component to minimize R.
Definition: PowderPattern.cpp:4450

ObjCryst::PowderPattern::Prepare
void Prepare()
Definition: PowderPattern.cpp:5409

ObjCryst::PowderPattern::GetPowderPatternCalc
const CrystVector_REAL & GetPowderPatternCalc() const
Get the calculated powder pattern.
Definition: PowderPattern.cpp:2765

ObjCryst::PowderPattern::BeginOptimization
virtual void BeginOptimization(const bool allowApproximations=false, const bool enableRestraints=false)
This should be called by any optimization class at the begining of an optimization.
Definition: PowderPattern.cpp:5243

ObjCryst::PowderPattern::mClockPowderPatternXCorr
RefinableObjClock mClockPowderPatternXCorr
Corrections to 2Theta.
Definition: PowderPattern.h:1067

ObjCryst::PowderPattern::mIsXAscending
bool mIsXAscending
Is the mX vector sorted in ascending order ? (true for 2theta, false for TOF)
Definition: PowderPattern.h:1050

ObjCryst::PowderPattern::mClockPowderPatternPar
RefinableObjClock mClockPowderPatternPar
When were the pattern parameters (2theta or time-of-flight range) changed ?
Definition: PowderPattern.h:1059

ObjCryst::PowderPattern::mXZero
REAL mXZero
Zero correction :  Thus mPowderPattern2ThetaMin=(mPowderPattern2ThetaMin-m2ThetaZero)
Definition: PowderPattern.h:1083

ObjCryst::PowderPattern::GetClockPowderPatternRadiation
const RefinableObjClock & GetClockPowderPatternRadiation() const
When were the radiation parameter (radiation type, wavelength) changed ?
Definition: PowderPattern.cpp:2884

ObjCryst::PowderPattern::SetMuR
void SetMuR(const REAL muR)
Set the $\mu R$ value for cylinder absorption correction.
Definition: PowderPattern.cpp:6004

ObjCryst::PowderPattern::GetChi2_Option
REAL GetChi2_Option() const
Return the conventionnal or integrated Chi^2, depending on the option.
Definition: PowderPattern.cpp:4444

ObjCryst::PowderPattern::SavePowderPattern
void SavePowderPattern(const string &filename="powderPattern.out") const
Save powder pattern to one file, text format, 3 columns theta Iobs Icalc.
Definition: PowderPattern.cpp:3880

ObjCryst::PowderPattern::SetWavelength
void SetWavelength(const REAL lambda)
Set the wavelength of the experiment (in Angstroems).
Definition: PowderPattern.cpp:2751

ObjCryst::PowderPattern::Set2ThetaDisplacement
void Set2ThetaDisplacement(const REAL displacement)
Change displacement correction .
Definition: PowderPattern.cpp:2899

ObjCryst::PowderPattern::ImportPowderPattern2ThetaObsSigma
void ImportPowderPattern2ThetaObsSigma(const string &fileName, const int nbSkip=0)
Import file with 3 columns 2Theta Iobs Sigma.
Definition: PowderPattern.cpp:3240

ObjCryst::PowderPattern::SetPowderPatternObsSigma
void SetPowderPatternObsSigma(const CrystVector_REAL &sigma)
Set sigma for each point of the observed powder pattern.
Definition: PowderPattern.cpp:3866

ObjCryst::PowderPattern::GetClassName
virtual const string & GetClassName() const
Name for this class ("RefinableObj", "Crystal",...).
Definition: PowderPattern.cpp:2574

ObjCryst::PowderPattern::GetScaleFactor
const CrystVector_REAL & GetScaleFactor() const
Access the scale factors (see PowderPattern::mScaleFactor)
Definition: PowderPattern.cpp:5700

ObjCryst::PowderPattern::GetClockPowderPatternXCorr
const RefinableObjClock & GetClockPowderPatternXCorr() const
When were the parameters for 2theta/TOF correction (zero, transparency, displacement) last changed ?
Definition: PowderPattern.cpp:2887

ObjCryst::PowderPattern::mClockPowderPatternRadiation
RefinableObjClock mClockPowderPatternRadiation
When were the radiation parameter (radiation type, wavelength) changed ?
Definition: PowderPattern.h:1061

ObjCryst::PowderPattern::GetPowderPatternObsSigma
const CrystVector_REAL & GetPowderPatternObsSigma() const
Get the sigma for each point of the observed powder pattern.
Definition: PowderPattern.cpp:2782

ObjCryst::SPGScore
Structure to hold the score corresponding to a given spacegroup.
Definition: PowderPattern.h:1189

ObjCryst::SPGScore::SPGScore
SPGScore(const string &s, const REAL r, const REAL g, const unsigned int nbextinct, const REAL ngof=0, const unsigned int nbrefl=0)
Structure to hold the score corresponding to a given spacegroup.
Definition: PowderPattern.cpp:6875

ObjCryst::ReflectionProfile
Abstract base class for reflection profiles.
Definition: ReflectionProfile.h:65

ObjCryst::ScatteringCorr
Base class to compute all kind of corrections to intensities: Lorentz, Polar, absorption,...
Definition: ScatteringCorr.h:36

ObjCryst::LorentzCorr
Lorentz Correction.
Definition: ScatteringCorr.h:69

ObjCryst::PolarizationCorr
Polarization Correction.
Definition: ScatteringCorr.h:95

ObjCryst::PowderSlitApertureCorr
Slit aperture correction (for powder)
Definition: ScatteringCorr.h:114

ObjCryst::TextureMarchDollase
Texture correction using the March-Dollase model.
Definition: ScatteringCorr.h:162

ObjCryst::TextureEllipsoid
Texture correction using the Ellipsoidal preferred orientation function.
Definition: ScatteringCorr.h:209

ObjCryst::TOFCorr
Time-Of-Flight Correction.
Definition: ScatteringCorr.h:253

ObjCryst::Radiation
Class to define the radiation (type, monochromaticity, wavelength(s)) of an experiment.
Definition: ScatteringData.h:175

ObjCryst::ScatteringData
Class to compute structure factors for a set of reflections and a Crystal.
Definition: ScatteringData.h:320

CubicSpline
Cubic spline interpolation.
Definition: CrystVector.h:565

ObjCryst::XMLCrystTag
class to input or output a well-formatted xml beginning or ending tag.
Definition: RefinableObj/IO.h:73

ObjCryst::RefParType
class of refinable parameter types.
Definition: RefinableObj.h:80

ObjCryst::RefinableObjClock
We need to record exactly when refinable objects have been modified for the last time (to avoid re-co...
Definition: RefinableObj.h:140

ObjCryst::RefObjOpt
Base class for options.
Definition: RefinableObj.h:552

ObjCryst::ObjRegistry
Object Registry.
Definition: RefinableObj.h:645

ObjCryst::RefinableObj
Generic Refinable Object.
Definition: RefinableObj.h:784

ObjCryst::WXCrystObjBasic
Abstract base class for all objects in wxCryst.
Definition: wxCryst.h:128

ObjCryst::WXPowderPattern
WX Class for PowderPattern objects.
Definition: wxPowderPattern.h:35

ObjCryst::WXPowderPatternGraph
Class to display a Powder Pattern (calc,obs) in a graphic window.
Definition: wxPowderPattern.h:79

ObjCryst::WXPowderPatternBackground
Class to display a Powder Pattern Background.
Definition: wxPowderPattern.h:184

ObjCryst::WXPowderPatternDiffraction
Class to display a Powder Pattern for a crystalline phase.
Definition: wxPowderPattern.h:257