#include "startTransmissionReconstruction.h"
#include "./detection/getTransmissionData.h"
#include "Matrix.h"
#include "CudaMatrix.h"
#include "log/log.h"
#include "common/dataBlockCreation/removeDataFromArrays.h"
#include "log/notify.h"
#include "src/transmissionReconstruction/dataFilter/dataFilter.h"
#include "src/transmissionReconstruction/dataPreperation.h"
#include "src/common/getMeasurementMetaData.h"
#include "src/common/qualityReview.h"
#include "src/transmissionReconstruction/reconstruction/reconstruction.h"
#include "src/config/config.h"

#include "Function2D.h"

#include "MatlabWriter.h"

using namespace Aurora;
using namespace Recon;

TransmissionReconstructionResult Recon::startTransmissionReconstruction(const Aurora::Matrix& aMotorPos, const Aurora::Matrix& aMotoPosRef, const Aurora::Matrix& aSlList,
                                     const Aurora::Matrix& aSnList, const Aurora::Matrix& aRlList, const Aurora::Matrix& aRnList,
                                     const TempInfo& aTemp, const TempInfo& aTempRef, Recon::GeometryInfo& aGeom,
                                     GeometryInfo& aGeomRef, const MeasurementInfo& aExpInfo, const MeasurementInfo& aExpInfoRef,
                                     const PreComputes& aPreComputes, Parser* aParser, Parser* aParserRef)
{
    RECON_INFO("Start getTransmissionData.");
    auto transmissionData = getTransmissionData(aMotorPos, aMotoPosRef, aSlList, aSnList, aRlList, aRnList, aTemp, aTempRef, 
                                                aGeom, aGeomRef, aExpInfo, aExpInfoRef, aPreComputes, aParser, aParserRef);    
    Matrix dists = Recon::distanceBetweenTwoPoints(transmissionData.senderList, transmissionData.receiverList);
    Matrix sosRef = Recon::temperatureToSoundSpeed(transmissionData.waterTempList, "marczak");   
    //Recon::notifyProgress(17);      

    Matrix valid = Recon::checkTofDetections(transmissionData.tofDataTotal, dists, sosRef, 
                                             Recon::transParams::minSpeedOfSound,Recon::transParams::maxSpeedOfSound).valid;
    //Recon::notifyProgress(18);      
    if(transParams::qualityCheck)
    {
        qualityReview(sum(valid,Aurora::All)[0], transmissionData.dataInfo.numPossibleScans);
    }
    //Recon::notifyProgress(19);      
    DiscretizePositionValues positionValues  = Recon::discretizePositions(transmissionData.senderList, transmissionData.receiverList, Recon::transParams::numPixelXY);                                       
    Matrix tofData = removeDataFromArrays(transmissionData.tofDataTotal, valid);
    Matrix attData = removeDataFromArrays(transmissionData.attDataTotal, valid);
    Matrix senderList = removeDataFromArrays(positionValues.senderCoordList, valid);
    Matrix reveiverList = removeDataFromArrays(positionValues.receiverCoordList, valid);
    //Recon::notifyProgress(20);
    RECON_INFO("Start reconstructArt.");
    auto transmissionReon = reconstructArt(tofData, attData, positionValues.dims, senderList, reveiverList, positionValues.res, aTemp.expectedSOSWater[0]);

    TransmissionReconstructionResult result;
    result.recoATT = transmissionReon.outATT;
    result.recoSOS = transmissionReon.outSOS;
    result.ddmis = positionValues.ddims;
    return result;
}