#ifndef ITKREG23_H
#define ITKREG23_h

#include "itkCommand.h"

#include "itkExhaustiveOptimizer.h"
#include "itkMutualInformationTwoImageToOneImageMetric.h"
#include "itkNormalizedCorrelationTwoImageToOneImageMetric.h"
#include "itkPowellOptimizer.h"
#include "itkTwoProjectionImageRegistrationMethod.h"
#include "itkAmoebaOptimizer.h"

#include "itkCommand.h"
#include "itkObject.h"
#include "itkObjectFactory.h"
#include "itkSmartPointer.h"

#include "itkImageProcessorHelpers.h"
#include "itkQtIterationUpdate.h"

#include "itkReg23MetaInformation.h"


namespace itk{

class ITK_EXPORT itkReg23 : public itk::Object
{

public:

    /** Standard "Self" typedef. */
    typedef itkReg23  Self;
    /** Standard "Superclass" typedef. */
    typedef Object Superclass;
    /** Smart pointer typedef support */
    typedef itk::SmartPointer<Self>  Pointer;
    typedef itk::SmartPointer<const Self>  ConstPointer;
    /** Method of creation through the object factory. */
    itkNewMacro(Self);
    /** Run-time type information (and related methods). */
    itkTypeMacro(itkReg23, Object);

    using ChangeInformationFilterType = itk::ChangeInformationImageFilter<InternalImageType>;
    using RoiForRegistration = itk::ImageRegion<Dimension>;
    using InterpolatorType = itk::gSiddonJacobsRayCastInterpolateImageFunction<InternalImageType, double>;

    /* ---- User provided */

    itkSetMacro(OptimizerObserver, CommandIterationUpdate::Pointer);
    itkGetMacro(OptimizerObserver, CommandIterationUpdate::Pointer);

    itkSetMacro(r23Meta, R23MetaInformation::Pointer);
    itkGetMacro(r23Meta, R23MetaInformation::Pointer);

    itkSetMacro(PowellMeta, PowellOptimizerMetaInformation::Pointer);
    itkGetMacro(PowellMeta, PowellOptimizerMetaInformation::Pointer);

    itkSetMacro(AmoebaMeta, AmoebaOptimizerMetaInformation::Pointer);
    itkGetMacro(AmoebaMeta, AmoebaOptimizerMetaInformation::Pointer);

    itkSetMacro(MIMeta, MIMetricMetaInformation::Pointer);
    itkGetMacro(MIMeta, MIMetricMetaInformation::Pointer);

    itkSetMacro(NCCMeta, NCCMetricMetaInformation::Pointer);
    itkGetMacro(NCCMeta, NCCMetricMetaInformation::Pointer);


    itkSetMacro(Volume, InternalImageType::Pointer);
    itkGetMacro(Volume, InternalImageType::Pointer);

    itkSetMacro(PA, InternalImageType::Pointer);
    itkGetMacro(PA, InternalImageType::Pointer);

    itkSetMacro(LAT, InternalImageType::Pointer);
    itkGetMacro(LAT, InternalImageType::Pointer);

    itkSetMacro(InternalTransf1, InternalTransformMetaInformation::Pointer);
    itkGetMacro(InternalTransf1, InternalTransformMetaInformation::Pointer);

    itkSetMacro(InternalTransf2, InternalTransformMetaInformation::Pointer);
    itkGetMacro(InternalTransf2, InternalTransformMetaInformation::Pointer);

    itkSetMacro(filter1, ChangeInformationFilterType::Pointer);
    itkGetMacro(filter1, ChangeInformationFilterType::Pointer);

    itkSetMacro(filter2, ChangeInformationFilterType::Pointer);
    itkGetMacro(filter2, ChangeInformationFilterType::Pointer);

    itkSetMacro(interpolator1, InterpolatorType::Pointer);
    itkGetMacro(interpolator1, InterpolatorType::Pointer);

    itkSetMacro(interpolator2, InterpolatorType::Pointer);
    itkGetMacro(interpolator2, InterpolatorType::Pointer);

    itkSetMacro(TransformMetaInfo, TransformMetaInformation::Pointer);
    itkGetMacro(TransformMetaInfo, TransformMetaInformation::Pointer);

    /* ---- User provided  END */
    itkSetMacro(roiAutoReg1, RoiForRegistration);
    itkGetMacro(roiAutoReg1, RoiForRegistration);

    itkSetMacro(roiAutoReg2, RoiForRegistration);
    itkGetMacro(roiAutoReg2, RoiForRegistration);



    /** Auto Reg23 methods */

    /** Initialize the registration pipeline*/
    void InitializeRegistration();
    /** Start the registration process*/
    int StartRegistration(std::string extraInfo);
    /** Get the current cost function value from the optimizer*/
    double GetOptimizerValue();

    /** Get the cost function value for the current transform*/
    double GetCurrentMetricValue();

    /** Get the cost function value for the current transform*/
    Optimizer::ParametersType GetCurrentPosition();

    /** Auto Reg23 methods END */

    void setROISizeToZero();

protected:
    itkReg23();
    virtual ~itkReg23();
    void PrintSelf(std::ostream& os, itk::Indent indent) const;


private:
    itkReg23(const Self&); //purposely not implemented
    void operator=(const Self&); //purposely not implemented

    /** Optimizer which tries to find the minimun (Powell Optimizer)*/
    using PowellOptimizerType = itk::PowellOptimizer;
    /** Optimizer which tries to find the minimn (Powell Optimizer)*/
    using AmoebaOptimizerType = itk::AmoebaOptimizer;
    /** Optimizer which samples the whol space */
    using ExhaustiveOptimizerType = itk::ExhaustiveOptimizer;
    /** Metric to calculate similarites between images*/
    using MetricType = itk::NormalizedCorrelationTwoImageToOneImageMetric<InternalImageType, InternalImageType>;
    using MIMetricType = itk::MutualInformationTwoImageToOneImageMetric<InternalImageType, InternalImageType>;
    /** The thing which actuall does the image registration*/
    using RegistrationType = itk::TwoProjectionImageRegistrationMethod<InternalImageType, InternalImageType>;



    RegistrationType::Pointer
    registration;
    MetricType::Pointer
    NCCmetric;
    MIMetricType::Pointer
    MImetric;
    PowellOptimizerType::Pointer
    PowellOptimizer;
    AmoebaOptimizerType::Pointer
    AmoebaOptimizer;
    ExhaustiveOptimizerType::Pointer
    ExhaustiveOptimizer;

    /* ---- User provided */
    
    R23MetaInformation::Pointer
    m_r23Meta;

    PowellOptimizerMetaInformation::Pointer
    m_PowellMeta;

    AmoebaOptimizerMetaInformation::Pointer
    m_AmoebaMeta;

    MIMetricMetaInformation::Pointer
    m_MIMeta;

    NCCMetricMetaInformation::Pointer
    m_NCCMeta;

    InternalImageType::Pointer
    m_Volume,
    m_PA,
    m_LAT;

    InternalTransformMetaInformation::Pointer
    m_InternalTransf1,
    m_InternalTransf2;

    ChangeInformationFilterType::Pointer
    m_filter1,
    m_filter2;

    InterpolatorType::Pointer
    m_interpolator1,
    m_interpolator2;

    TransformMetaInformation::Pointer
    m_TransformMetaInfo;

    CommandIterationUpdate::Pointer
    m_OptimizerObserver;

    /* ----  User provided  END */

    TransformType::Pointer
    IsocTransform,
    Transform1,
    Transform2;

    RoiForRegistration
    m_roiAutoReg1,
    m_roiAutoReg2;

    bool m_UseDumptoFile;


    double m_OptmizerValue;


};

}

#endif