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

#include "src/common/fileHelper.h"
#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 = 4; 
    std::vector<std::string> args(argNum);
    args[0] = "/home/sun/20230418T141000/";
    args[1] = "/home/sun/20230418T145123/";
    args[2] = Recon::DEFAULT_OUTPUT_PATH;
    args[3] = Recon::DEFAULT_CONFIG_PATH;
    argc = argc <= argNum? argc-1 : argNum;
    for (int i = 0; i < argc; i++)
    {
        args[i] = argv[i+1];
    }

    if(args[0].empty())
    {
        RECON_INFO("No reconstruction data.");
        return 0;
    }
    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 0;
    }

    std::string outPutPath = args[2];
    std::string directoryPath = outPutPath;
    if(Recon::endsWithMat(outPutPath))
    {
       directoryPath =  Recon::getPath(outPutPath);
    }
    else
    {
        outPutPath = Recon::fixPathSlash(outPutPath) + Recon::DEFAULT_OUTPUT_FILENAME;
    }
    if(!Recon::isDirectory(directoryPath))
    {
        RECON_INFO("Output directory is not valid.");
        return 0;
    }
    
    std::string dataPath = Recon::fixPathSlash(args[0]);
    std::string dataRefPath = Recon::fixPathSlash(args[1]);
    RECON_INFO("start");
    Recon::startReconstructions(dataPath, dataRefPath, outPutPath);
    SPDLOG_INFO("finish");
    return 0;
}