BundleResults.h

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#ifndef BundleResults_h
#define BundleResults_h

// Qt Library
#include <QList>
#include <QObject>
#include <QPair>
#include <QString>
#include <QVector>

// hdf5 Library
#include <H5Cpp.h>
#include <hdf5_hl.h>
#include <hdf5.h>

// Isis Library
#include "BundleControlPoint.h"
#include "BundleObservationVector.h"
#include "BundleSettings.h"
#include "ControlNet.h"
#include "Distance.h"
#include "MaximumLikelihoodWFunctions.h"
#include "PvlObject.h"
#include "Statistics.h" // ???
#include "XmlStackedHandler.h"

// Qt Library
class QDataStream;
class QUuid;
class QXmlStreamWriter;

namespace Isis {
  // Isis Library
  class ControlNet;
  class CorrelationMatrix;
  class FileName;
  class Project;// ??? does xml stuff need project???
  class PvlObject;
  class SerialNumberList;
  class StatCumProbDistDynCalc;
  class XmlStackedHandlerReader;

  class BundleResults : public QObject {
    Q_OBJECT
    public:
      BundleResults(QObject *parent = 0);
      // TODO: does xml stuff need project???
      BundleResults(Project *project, XmlStackedHandlerReader *xmlReader, QObject *parent = 0);
      BundleResults(const BundleResults &src);
      ~BundleResults();
      BundleResults &operator=(const BundleResults &src);
      void initialize();

      // mutators and computation methods
      void resizeSigmaStatisticsVectors(int numberImages);
      void setRmsImageResidualLists(QList<Statistics> rmsImageLineResiduals,
                                    QList<Statistics> rmsImageSampleResiduals,
                                    QList<Statistics> rmsImageResiduals);
      void setRmsImageResidualLists(QVector<Statistics> rmsImageLineResiduals,
                                    QVector<Statistics> rmsImageSampleResiduals,
                                    QVector<Statistics> rmsImageResiduals);
      void setSigmaLatitudeRange(Distance minLatDist, Distance maxLatDist,
                                 QString minLatPointId, QString maxLatPointId);
      void setSigmaLongitudeRange(Distance minLonDist, Distance maxLonDist,
                                  QString minLonPointId, QString maxLonPointId);
      void setSigmaRadiusRange(Distance minRadDist, Distance maxRadDist,
                               QString minRadPointId, QString maxRadPointId);
      void setRmsFromSigmaStatistics(double rmsFromSigmaLatStats,
                                     double rmsFromSigmaLonStats,
                                     double rmsFromSigmaRadStats);
      void maximumLikelihoodSetUp(
          QList< QPair< MaximumLikelihoodWFunctions::Model, double > > modelsWithQuantiles);
      void printMaximumLikelihoodTierInformation();
      void initializeResidualsProbabilityDistribution(unsigned int nodes = 20);
      void initializeProbabilityDistribution(unsigned int nodes = 20);
      void addResidualsProbabilityDistributionObservation(double obsValue);
      void addProbabilityDistributionObservation(double obsValue);
      void addProbabilityDistributionObservation(double obsValue, bool residuals);
      void incrementMaximumLikelihoodModelIndex();

      void incrementFixedPoints();
      int numberFixedPoints() const;
      void incrementHeldImages();
      int numberHeldImages() const;
      void incrementIgnoredPoints();
      int numberIgnoredPoints() const; // currently unused ???
#if 0
      double computeRejectionLimit(ControlNet *p_Cnet,
                                   double outlierRejectionMultiplier,
                                   int numObservations);
#endif
      void setRejectionLimit(double rejectionLimit);
#if 0
      double computeResiduals(
               ControlNet *pCnet,
               std::vector< boost::numeric::ublas::bounded_vector< double, 3 > > pointWeights,
               std::vector< boost::numeric::ublas::bounded_vector< double, 3 > > pointCorrections,
               LinearAlgebra::Vector image_Corrections,
               std::vector< double > imageParameterWeights,
               int numImagePartials,
               int rank);
#endif
      void setRmsXYResiduals(double rx, double ry, double rxy);
#if 0
      bool flagOutliers(ControlNet *pCnet);
#endif
      void setNumberRejectedObservations(int numberObservations);
      void setNumberObservations(int numberObservations);
      void setNumberImageParameters(int numberParameters); // ??? this is the same value an m_nRank
      void resetNumberConstrainedPointParameters();
      void incrementNumberConstrainedPointParameters(int incrementAmount);
      void resetNumberConstrainedImageParameters();
      void incrementNumberConstrainedImageParameters(int incrementAmount);
      void resetNumberConstrainedTargetParameters();
      void incrementNumberConstrainedTargetParameters(int incrementAmount);
      void setNumberUnknownParameters(int numberParameters);
      void computeDegreesOfFreedom();
      void computeSigma0(double dvtpv, BundleSettings::ConvergenceCriteria criteria);
      void setDegreesOfFreedom(double degreesOfFreedom);
      void setSigma0(double sigma0);
      void setElapsedTime(double time);
      void setElapsedTimeErrorProp(double time);
      void setRadiansToMeters(double rtm);
      void setConverged(bool converged); // or initialze method
      void setBundleControlPoints(QVector<BundleControlPointQsp> controlPoints);
      void setOutputControlNet(ControlNetQsp outNet);
      void setIterations(int iterations);
      void setObservations(BundleObservationVector observations);
      
      // Accessors...
      QList<Statistics> rmsImageSampleResiduals() const;
      QList<Statistics> rmsImageLineResiduals() const;
      QList<Statistics> rmsImageResiduals() const;
      QVector<Statistics> rmsImageXSigmas() const;       // currently unused ???
      QVector<Statistics> rmsImageYSigmas() const;       // currently unused ???
      QVector<Statistics> rmsImageZSigmas() const;       // currently unused ???
      QVector<Statistics> rmsImageRASigmas() const;      // currently unused ???
      QVector<Statistics> rmsImageDECSigmas() const;     // currently unused ???
      QVector<Statistics> rmsImageTWISTSigmas() const;   // currently unused ???
      Distance minSigmaLatitudeDistance() const;
      Distance maxSigmaLatitudeDistance() const;
      Distance minSigmaLongitudeDistance() const;
      Distance maxSigmaLongitudeDistance() const;
      Distance minSigmaRadiusDistance() const;
      Distance maxSigmaRadiusDistance() const;
      QString maxSigmaLatitudePointId() const;
      QString minSigmaLatitudePointId() const;
      QString minSigmaLongitudePointId() const;
      QString maxSigmaLongitudePointId() const;
      QString minSigmaRadiusPointId() const;
      QString maxSigmaRadiusPointId() const;
      double sigmaLatitudeStatisticsRms() const;
      double sigmaLongitudeStatisticsRms() const;
      double sigmaRadiusStatisticsRms() const;
      double rmsRx() const;  // currently unused ???
      double rmsRy() const;  // currently unused ???
      double rmsRxy() const; // currently unused ???
      double rejectionLimit() const;
      double radiansToMeters() const;
      int numberRejectedObservations() const;
      int numberObservations() const;

      int numberImageParameters() const; // ??? this is the same value an m_nRank
      int numberConstrainedPointParameters() const;
      int numberConstrainedImageParameters() const;
      int numberConstrainedTargetParameters() const;
      int numberUnknownParameters() const;
      int degreesOfFreedom() const;
      double sigma0() const;
      double elapsedTime() const;
      double elapsedTimeErrorProp() const;
      bool converged() const; // or initialze method
      QVector<BundleControlPointQsp> &bundleControlPoints();
      ControlNetQsp outputControlNet() const;
      int iterations() const;
      const BundleObservationVector &observations() const;
      
      int numberMaximumLikelihoodModels() const;
      int maximumLikelihoodModelIndex() const;
      StatCumProbDistDynCalc cumulativeProbabilityDistribution() const;
      StatCumProbDistDynCalc residualsCumulativeProbabilityDistribution() const;
      double maximumLikelihoodMedianR2Residuals() const;
      MaximumLikelihoodWFunctions maximumLikelihoodModelWFunc(int modelIndex) const;
      double maximumLikelihoodModelQuantile(int modelIndex) const;

      QList< QPair< MaximumLikelihoodWFunctions, double > > maximumLikelihoodModels() const;

      bool setNumberHeldImages(SerialNumberList pHeldSnList,
                               SerialNumberList *pSnList);

      PvlObject pvlObject(QString name = "BundleResults") const;

      // Correlation Matrix accessors for cnetsuite and mutators for bundle adjust.
      CorrelationMatrix correlationMatrix() const;
      void setCorrMatCovFileName(FileName name);
      void setCorrMatImgsAndParams(QMap<QString, QStringList> imgsAndParams);

      // TODO: does xml stuff need project???
      void save(QXmlStreamWriter &stream, const Project *project) const;
      
      QDataStream &write(QDataStream &stream) const;
      QDataStream &read(QDataStream &stream);

      void createH5Group(hid_t locationId, QString locationName) const;// delete these
      void parseH5Group(hid_t locationId, QString locationName);       // delete these

      void createH5Group(H5::CommonFG &locationObject, QString locationName) const;
      void openH5Group(H5::CommonFG &locationObject, QString locationName);
      BundleResults(H5::CommonFG &locationObject, QString locationName);

    private:
      class XmlHandler : public XmlStackedHandler {
        public:
          // TODO: does xml stuff need project???
          XmlHandler(BundleResults *statistics, Project *project);
          ~XmlHandler();
   
          virtual bool startElement(const QString &namespaceURI, const QString &localName,
                                    const QString &qName, const QXmlAttributes &atts);
          virtual bool characters(const QString &ch);
          virtual bool endElement(const QString &namespaceURI, const QString &localName,
                                  const QString &qName);
   
        private:
          Q_DISABLE_COPY(XmlHandler);
   
          BundleResults *m_xmlHandlerBundleResults;
          Project *m_xmlHandlerProject;   // TODO: does xml stuff need project???
          QString m_xmlHandlerCharacters;
          int m_xmlHandlerResidualsListSize;
          int m_xmlHandlerSampleResidualsListSize;
          int m_xmlHandlerLineResidualsListSize;
          int m_xmlHandlerXSigmasListSize;
          int m_xmlHandlerYSigmasListSize;
          int m_xmlHandlerZSigmasListSize;
          int m_xmlHandlerRASigmasListSize;
          int m_xmlHandlerDECSigmasListSize;
          int m_xmlHandlerTWISTSigmasListSize;
          QList<Statistics *> m_xmlHandlerStatisticsList;
          StatCumProbDistDynCalc *m_xmlHandlerCumProCalc;

          QString m_xmlHandlerCorrelationImageId;
          QStringList m_xmlHandlerCorrelationParameterList;
          QMap<QString, QStringList> m_xmlHandlerCorrelationMap;
      };

      QUuid *m_id;
//???      QString m_instrumentId;               //!< The spacecraft instrument id for this observation.
      CorrelationMatrix *m_correlationMatrix; 

// ???       Statistics m_statsx;                       //!<  x errors
// ???       Statistics m_statsy;                       //!<  y errors
// ???       Statistics m_statsrx;                      //!<  x residuals
// ???       Statistics m_statsry;                      //!<  y residuals
// ???       Statistics m_statsrxy;                     //!< xy residuals

      int m_numberFixedPoints;                
      // Currently set but unused
      int m_numberIgnoredPoints;              
      int m_numberHeldImages;                 

      // The following three members are set but unused.
      double m_rmsXResiduals;                 
      double m_rmsYResiduals;                 
      double m_rmsXYResiduals;                
      
      double m_rejectionLimit;                
      // TODO:??? reorder read/write data stream, init, copy constructor, operator= 
      int m_numberObservations;                
      int m_numberRejectedObservations;        
      int m_numberUnknownParameters;           
      int m_numberImageParameters;             
      int m_numberConstrainedImageParameters;  
      int m_numberConstrainedPointParameters;  
      int m_numberConstrainedTargetParameters; 
      int m_degreesOfFreedom;                  
      double m_sigma0;                         
      double m_elapsedTime;                    
      double m_elapsedTimeErrorProp;           
      double m_radiansToMeters;                
      bool m_converged;

      // Variables for output methods in BundleSolutionInfo
      
      QVector<BundleControlPointQsp> m_bundleControlPoints; 
      ControlNetQsp m_outNet;                               
      int m_iterations;                                     
      BundleObservationVector m_observations;               
      //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      // variables set in computeBundleResults()
      //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 
      // QList??? jigsaw apptest gives - ASSERT failure in QList<T>::operator[]: "index out of range", 
      QList<Statistics> m_rmsImageSampleResiduals;
      QList<Statistics> m_rmsImageLineResiduals;  
      QList<Statistics> m_rmsImageResiduals;      
      QVector<Statistics> m_rmsImageXSigmas;     // unset and unused ???
      QVector<Statistics> m_rmsImageYSigmas;     // unset and unused ???
      QVector<Statistics> m_rmsImageZSigmas;     // unset and unused ???
      QVector<Statistics> m_rmsImageRASigmas;    // unset and unused ???
      QVector<Statistics> m_rmsImageDECSigmas;   // unset and unused ???
      QVector<Statistics> m_rmsImageTWISTSigmas; // unset and unused ???

      Distance m_minSigmaLatitudeDistance;  
      Distance m_maxSigmaLatitudeDistance;  
      Distance m_minSigmaLongitudeDistance; 
      Distance m_maxSigmaLongitudeDistance; 
      Distance m_minSigmaRadiusDistance;    
      Distance m_maxSigmaRadiusDistance;    

      QString m_minSigmaLatitudePointId;    
      QString m_maxSigmaLatitudePointId;    
      QString m_minSigmaLongitudePointId;   
      QString m_maxSigmaLongitudePointId;   
      QString m_minSigmaRadiusPointId;      
      QString m_maxSigmaRadiusPointId;      

      double m_rmsSigmaLatitudeStats;       
      double m_rmsSigmaLongitudeStats;      
      double m_rmsSigmaRadiusStats;         

      //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      // variables for maximum likelihood estimation
      //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      
      QList< QPair< MaximumLikelihoodWFunctions, double > > m_maximumLikelihoodFunctions;

      int m_maximumLikelihoodIndex;            
      StatCumProbDistDynCalc *m_cumPro;        
      StatCumProbDistDynCalc *m_cumProRes;     
      double m_maximumLikelihoodMedianR2Residuals; 
  };
  // operators to read/write BundleResults to/from binary disk file
  QDataStream &operator<<(QDataStream &stream, const BundleResults &bundleResults);
  QDataStream &operator>>(QDataStream &stream, BundleResults &bundleResults);
};

Q_DECLARE_METATYPE(Isis::BundleResults);

#endif // BundleResults_h