/*!
 * \file Registration.cpp
 * \date 2019/07/03
 *
 * \author Lou.Lixuan
 * Contact: Lou.Lixuan@hzleaper.com
 *
 *
 * \note
*/
#ifndef ImageRegistrator_h_
#define ImageRegistrator_h_

#include "StdUtils.h"
#include "CVUtils.h"
#include "CyclopsModules.h"
using namespace cv;

struct nifti_image;
struct mat44;

class ImageRegistrator : public ICyclopsModuleInstance
{
	/*! \fn setAffineAcce
	* Define whether to accelerate rigid affine calculation, default to false
	* \fn getAffineAcce
	* Get value of whether to accelerate rigid affine calculation
	*/
	DECLARE_PARAMETER(bool, AffineAcce)
	/*! \fn setAccelerate
	* Define whether to accelerate nonrigid calculation, default to false
	* \fn getAccelerate
	* Get value of whether to accelerate nonrigid calculation
	*/
	DECLARE_PARAMETER(bool, NonRigidAcce)
	/*! \fn setNonRigPrecision
	* Define precision of nonrigid calculation, 0 to 0.2, default to 0, which influence operation speed significantly
	* \fn getNonRigPrecision
	* Get value of NonRigPrecision
	*/
	DECLARE_PARAMETER2(float, NonRigPrecision, 0, 0.201)

public:
	ImageRegistrator() : mAffineAcce(false), mNonRigidAcce(false), mNonRigPrecision(0.0) {}
	virtual ~ImageRegistrator() {}

	//! Smart pointer to hold an instance of CircleDetector
	typedef std::shared_ptr<ImageRegistrator> Ptr;
	DECL_GET_INSTANCE(ImageRegistrator::Ptr)

	/*! registration are performed using affine and non-linear algorithm
	* @param refImg input the reference image, data will be changed
	* @param floImg input float image, which will Mapping to warped image, data will be changed
	* @param affineWarpedImg output image using affine transformation
	* @param nonRigidWarpedImg output image using  non-rigid transformation
	* @param score output score of non_rigid transformation
	* @return whether algorithm work properly
	*/
	virtual bool runRegistration(Mat& refImg, Mat& floImg, Mat* pAffineWarpedImg,
		Mat* pNonRigidWarpedImg = nullptr, float* score = nullptr);

protected:
	// convert a nifti_image to opencv::mat
	void NiftiImage2Mat(nifti_image* niiImage, Mat& dst);
	// convert affineMatrix to warpMatrix
	void getWarpMat(const mat44& src, Mat& dst, float rescale);
	// run nonRigid
	float runNonRigid(nifti_image* refNii, nifti_image* floNii, mat44& affineMat, Mat& warpedImg);
};


#endif // ImageRegistrator_h_