/*  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
*/
/*   LSQNumObj.h
*  header file for Least-Squares refinement witn Numerical derivatives Objects
*
*/
#ifndef _LSQOBJNUM_H
#define _LSQOBJNUM_H

#include "ObjCryst/CrystVector/CrystVector.h"
#include "ObjCryst/RefinableObj/RefinableObj.h"
#include <string>
#include <map>
#include <list>

namespace ObjCryst
{
/** \brief (Quick & dirty) Least-Squares Refinement Object with Numerical derivatives
*
* This is still highly experimental !
*/
class LSQNumObj
{
   public:
      LSQNumObj(std::string objName="Unnamed LSQ object");
      ~LSQNumObj();
      /// Fix one parameter.
      ///
      /// LSQNumObj::PrepareRefParList() must be called first!
      void SetParIsFixed(const std::string& parName,const bool fix);
      /// Fix one family of parameters
      ///
      /// LSQNumObj::PrepareRefParList() must be called first!
      void SetParIsFixed(const RefParType *type,const bool fix);
      /** Fix one parameter
      *
      * Note that this will fix the copied parameter, not the one
      * in the original object. The supplied RefinablePar
      * may be either the copied one or the original.
      *
      * LSQNumObj::PrepareRefParList() must be called first!
      **/
      void SetParIsFixed(RefinablePar &par,const bool fix);
      /** Fix all parameters within an object
      *
      * Note that this will fix the copied parameters, not the one
      * in the original objects.
      *
      * LSQNumObj::PrepareRefParList() must be called first!
      **/
      void SetParIsFixed(RefinableObj &obj,const bool fix);
      /// UnFix All parameters
      ///
      /// LSQNumObj::PrepareRefParList() must be called first!
      void UnFixAllPar();
      /// Set a parameter to be used
      ///
      /// LSQNumObj::PrepareRefParList() must be called first!
      void SetParIsUsed(const std::string& parName,const bool use);
      /// Set a family of parameters to be used
      ///
      /// LSQNumObj::PrepareRefParList() must be called first!
      void SetParIsUsed(const RefParType *type,const bool use);
      /** Do the refinement
      *
      * \param nbCycle: number of LSQ cycles - if negative, the algorithm will continue
      * until it reaches (-nbcycle) or until the relative variation in Chi2 is less
      * than minChi2var
      * \param useLevenbergMarquardt: enable Levenberg-Marquardt algorithm
      * to ensure that a decrease of Chi^2 will be obtained (actually a 1%
      * increase is allowed)
      * \param callBeginEndOptimization: if true, will call RefinableObj::BeginOptimization(true,...)
      * and RefinableObj::EndOptimization(). You may not want this if the LSQ is done during another
      * (e.g. monte-carlo) optimization - but then the calling function \b must ensure
      * that approximations are disabled (using RefinableObj::SetApproximationFlag)
      * for objects where that would render derivative calculations imprecise.
      * \param minChi2var: used for termination of the refinement if the relative variation
      * of Chi2 between two successive cyles is less than minChi2var
      */
      void Refine (int nbCycle=1,bool useLevenbergMarquardt=false,
                   const bool silent=false, const bool callBeginEndOptimization=true,
                   const float minChi2var=0.01);
      /** Run a refinement in a 'safe' way: if the Chi2 value increases by more that a given factor
      * the parameters are reverted to their initial values. Moreover, the listed 'new' parameters
      * or parameter types are then fixed.
      * \param vnewpar: list of parameters added for this optimization, which will be unfixed at the
      * beginning, and will be fixed at the end if Chi2 increases. This can be empty.
      * \param vnewpartype: list of parameter types, which will be unfixed at the
      * beginning, and will be fixed at the end if Chi2 increases. This can be empty.
      * \param maxChi2factor: if Chi2_end> maxChi2factor * Chi2_begin, parameters are reverted to their
      * initial value, and new parameters are fixed.
      * All the other parameters are the same as in LSQNumObj::Refine.
      * \return: true if the minimization was succesful, false otherwise.
      */
      bool SafeRefine(std::list<RefinablePar*> vnewpar, std::list<const RefParType*> vnewpartype,
                      REAL maxChi2factor=1.01,
                      int nbCycle=1, bool useLevenbergMarquardt=false,
                      const bool silent=false, const bool callBeginEndOptimization=true,
                      const float minChi2var=0.01);
      CrystVector_REAL Sigma()const;
      CrystMatrix_REAL CorrelMatrix()const;
      void CalcRfactor()const;
      REAL Rfactor()const;
      void CalcRwFactor()const;
      REAL RwFactor()const;
      void CalcChiSquare() const;
      REAL ChiSquare()const;   //uses the weight if specified
      /** Choose the object to refine. The minimization will be done
      * against its LSQ function and its parameters, as well as the LSQ functions
      * and parameters of its sub-objects (if recursive==true)
      *
      * \param LSQFuncIndex: one object can have a choice of several LSQ
      * functions to minimize- this allows to choose which one to minimize.
      *
      * \param init: if true, the list of refined objects is first cleared. otherwise
      * the new object (and its sub-objects) is just added to the list.
      *
      * \param recursive: if false, only the supplied object is added, and not its sub-objects
      */
      void SetRefinedObj(RefinableObj &obj, const unsigned int LSQFuncIndex=0, const bool init=true, const bool recursive=false);
      // Access to the full list of refined objects. The list is initially built
      // recursively from one object. This function allows to modify the list
      // of sub-objects before refinement (such as for removing certain types
      // of objects).
      //ObjRegistry<RefinableObj> &GetRefinedObjList();
      /** Get the map of refined objects - this is a recursive list of all the objects
      * that are taken into account for the refinement. The key is a pointer to the
      * object and the value is the LSQ function index for that object.
      */
      const std::map<RefinableObj*,unsigned int>& GetRefinedObjMap() const;
      /** Get the map of refined objects - this is a recursive list of all the objects
      * that are taken into account for the refinement. The key is a pointer to the
      * object and the value is the LSQ function index for that object.
      */
      std::map<RefinableObj*,unsigned int>& GetRefinedObjMap();
      /** Access to the RefinableObj which is the compilation of all parameters
      * from the object supplied for optimization and its sub-objects.
      *
      * Since this compilation is only updated from the suplied refinableobj and
      * its sub-objects when SetRefinedObj() and PrepareRefParList() are called,
      * it is possible to alter the fixed/limited status of parameters
      * here without affecting the parameters in the refined objects.
      */
      RefinableObj& GetCompiledRefinedObj();
      /** Access to the RefinableObj which is the compilation of all parameters
      * from the object supplied for optimization and its sub-objects.
      *
      * Since this compilation is only updated from the suplied refinableobj and
      * its sub-objects when SetRefinedObj() and PrepareRefParList() are called,
      * it is possible to alter the fixed/limited status of parameters
      * here without affecting the parameters in the refined objects.
      */
      const RefinableObj& GetCompiledRefinedObj()const;
      void SetUseSaveFileOnEachCycle(bool yesOrNo=true);
      void SetSaveFile(std::string fileName="refine.save");
      void PrintRefResults()const;
      void SetDampingFactor(const REAL newDampFact);
      void PurgeSaveFile();
      void WriteReportToFile()const;

      void OptimizeDerivativeSteps();
      const std::map<pair<const RefinablePar*,const RefinablePar*>,REAL > &GetVarianceCovarianceMap()const;
      /** Prepare the full parameter list for the refinement
      * \param copy_param: if false (the default), then the lsq algorithm will work directly
      * on the parameters of the refined object and sub-object. So that any modification
      * to the fixed/used/limited status applies permanently to the parameters.
      * if true, then the parameters are copied and therefore only the value of the
      * parameter is changed (and the clocks are ticked).
      *
      * \note: if copy_param==true, then any modification to the parameters (fixed, limited, used
      * status) only affects the copy and not the original. Also, calling again PrepareRefParList
      * cancels any such modification.
      *
      * \note This will be called automatically before starting the refinement only if
      * the parameter list is empty. Otherwise it should be called before refinement.
      */
      void PrepareRefParList(const bool copy_param=false);

      /// Get the LSQ calc vector (using either only the top or the hierarchy of object)
      const CrystVector_REAL& GetLSQCalc() const;
      /// Get the LSQ obs vector (using either only the top or the hierarchy of object)
      const CrystVector_REAL& GetLSQObs() const;
      /// Get the LSQ weight vector (using either only the top or the hierarchy of object)
      const CrystVector_REAL& GetLSQWeight() const;
      /// Get the LSQ deriv vector (using either only the top or the hierarchy of object)
      const CrystVector_REAL& GetLSQDeriv(RefinablePar&par);
      const std::map<RefinablePar*,CrystVector_REAL>& GetLSQ_FullDeriv();
      /** Tell all refined object that the refinement is beginning
      */
      void BeginOptimization(const bool allowApproximations=false, const bool enableRestraints=false);
      /** Tell all refined object that the refinement is finished
      */
      void EndOptimization();
   protected:
   private:
      // Refined object
         /// The recursive list of all refined sub-objects
         ObjRegistry<RefinableObj> mRecursiveRefinedObjList;
      /** The refinable par list used during refinement. It is only a compilation
      * of the parameters in RefinableObj and its sub-objects
      *
      * This list is only updated from the suplied refinableobj and
      * its sub-objects when SetRefinedObj() and PrepareRefParList() are called,
      * so it is possible to alter the fixed/limited status of parameters
      * here without affecting the parameters in the refined objects.
      */
      mutable RefinableObj mRefParList;
      /// Damping factor for the refinement (unused yet...)
      REAL mDampingFactor;
      ///Save result to file after each cycle ?
      bool mSaveReportOnEachCycle;
      /// Name of the refined object
      std::string mName;
      /// File name where refinement info is saved
      std::string mSaveFileName;
      mutable REAL mR,mRw,mChiSq;
      /// Correlation matrix between all refined parameters.
      CrystMatrix_REAL mCorrelMatrix;
      ///Variance-Covariance matrix, as a std::map
      std::map<pair<const RefinablePar*,const RefinablePar*>,REAL > mvVarCovar;
      /// Observed values.
      CrystVector_REAL mObs;
      /// Weight corresponding to all observed values.
      CrystVector_REAL mWeight;
      /// Index of the set of saved values for all refinable parameters, before refinement
      /// and before the last cycle.
      int mIndexValuesSetInitial, mIndexValuesSetLast;
      /// If true, then stop at the end of the cycle. Used in multi-threading environment
      bool mStopAfterCycle;
      // The optimized object
      //RefinableObj *mpRefinedObj;
      // The index of the LSQ function in the refined object (if there are several...)
      //unsigned int mLSQFuncIndex;

      /** Map of the recursive list of the objects to be refined. The key is the pointer
      * to the object and the value the LSQ function index
      *
      * Individual LSQ functions can be changed using GetRefinedObjMap().
      */
      std::map<RefinableObj*,unsigned int> mvRefinedObjMap;
      /// Size of each object LSQ data. This is initialized in LSQNumObj::GetLSQObs()
      mutable std::map<RefinableObj*,unsigned int> mvRefinedObjLSQSize;

      /// If true, then parameters to be refined will be copied instead of referenced.
      /// Therefore only their values and the parameter's clocks are affected when
      /// working on the copy.
      bool mCopyRefPar;
      /// Temporary arrays for LSQ functions evaluation - used when
      /// using recursive LSQ function
      mutable CrystVector_REAL mLSQObs,mLSQCalc,mLSQWeight,mLSQDeriv;
      mutable std::map<RefinablePar*,CrystVector_REAL> mLSQ_FullDeriv;
#ifdef __WX__CRYST__
   public:
      virtual WXCrystObjBasic* WXCreate(wxWindow* parent);
      WXCrystObjBasic* WXGet();
      void WXDelete();
      void WXNotifyDelete();
   protected:
      WXCrystObjBasic *mpWXCrystObj;
#endif
};

}//namespace
#endif //_LSQOBJNUM_H