#include "Parser.h"
#include "Parser.h"
#include "config/config.h"
#include "log/notify.h"
#include "log/notify.h"
#include <cstdio>
#include <vector>
#include "MatlabReader.h"
#define EIGEN_USE_MKL_ALL

#include "src/common/fileHelper.h"
#include "startReconstructions.h"

#include "transmissionReconstruction/detection/detection.h"
#include "transmissionReconstruction/detection/detection.cuh"
#include "startReconstructions.h"
#include "log/log.h"
/* 0 is data path.
    1 is dataRef path.
    2 is output path.
    3 is config file path.
*/

int main(int argc, char *argv[])
{
    int argNum = 5; 
    std::vector<std::string> args(argNum);
    args[0] = "/home/AScans_Data/CAS0.1Phantom/20230823T165617/";
    args[1] = "/home/AScans_Data/CAS0.1Phantom/20230823T171851/";
    args[2] = "/home/krad/Storage/DICOM/00e04b741e9f_20240619T145752/";
    args[3] = Recon::DEFAULT_CONFIG_PATH;
    argc = argc <= argNum? argc-1 : argNum;
    for (int i = 0; i < argc; i++)
    {
        args[i] = argv[i+1];
    }
    std::string outPutPath = args[2];
    std::string directoryPath = outPutPath;
    auto defaultLogger = getLogger("Main",outPutPath.data());
    spdlog::set_default_logger(defaultLogger);
    RECON_INFO("Read UR Args =====================");
    if(args[0].empty())
    {
        RECON_INFO("No reconstruction data.");
        return -2;
    }
    std::string configPath = Recon::fixPathSlash(args[3]);
    Recon::initalizeConfig(configPath);
    if( args[1].empty() && Recon::transParams::runTransmissionReco)
    {
        RECON_INFO("Running transmission reconstruction, but no refrence data.");
        return -3;
    }
    RECON_INFO("configPath:{0}",configPath);

    
    outPutPath = Recon::fixPathSlash(outPutPath);

    if(!Recon::isDirectory(directoryPath))
    {
        RECON_INFO("Output directory is not valid.");
        return -4;
    }
    RECON_INFO("outPutPath:{0}",outPutPath);
    std::string dataPath = Recon::fixPathSlash(args[0]);
    RECON_INFO("dataPath:{0}",dataPath);
    std::string dataRefPath = Recon::fixPathSlash(args[1]);
    RECON_INFO("dataRefPath:{0}",dataRefPath);
    RECON_INFO("UR Args End=======================");
    RECON_INFO("UR Start");
    int exitcode = Recon::startReconstructions(dataPath, dataRefPath, outPutPath);
    if (exitcode == 0)
    {
        RECON_INFO("UR Finish");
        return exitcode;
    }
    else{
    return exitcode;
    }
}