// SPDX-License-Identifier: LGPL-3.0-or-other
// Copyright (C) 2021 Contributors to the SLS Detector Package
// #include "sls/ansi.h"
#include <iostream>
#undef CORR

#define C_GHOST 0.0004

#define CM_ROWS 50

#define RAWDATA

#if !defined JFSTRX && !defined JFSTRXOLD && !defined JFSTRXCHIP1 &&           \
    !defined JFSTRXCHIP6
#ifndef MODULE
#include "jungfrauHighZSingleChipData.h"
#endif
#ifdef MODULE
#include "jungfrauModuleData.h"
#endif
#endif

#ifdef JFSTRX
#include "jungfrauLGADStrixelsData_new.h"
#endif
#if defined JFSTRXCHIP1 || defined JFSTRXCHIP6
#include "jungfrauLGADStrixelsDataSingleChip.h"
#endif
#ifdef JFSTRXOLD
#include "jungfrauStrixelsHalfModuleOldDesign.h"
#endif

#include "multiThreadedCountingDetector.h"
#include "singlePhotonDetector.h"

#include <fstream>
#include <map>
#include <stdio.h>
#include <sys/stat.h>

#include <ctime>
// using namespace std;

int main(int argc, char *argv[]) {

    if (argc < 5) {
        std::cout
            << "Usage is " << argv[0]
            << "indir outdir fname(with formatting, no extension) fextension "
               "[runmin] [runmax] [pedfile (raw or tiff)] [threshold] "
               "[nframes] [xmin xmax ymin ymax] [gainmap]"
            << std::endl;
        std::cout
            << "threshold <0 means analog; threshold=0 means cluster finder; "
               "threshold>0 means photon counting"
            << std::endl;
        std::cout
            << "nframes <0 means sum everything; nframes=0 means one file per "
               "run; nframes>0 means one file every nframes"
            << std::endl;
        return 1;
    }

    int fifosize = 1000;
    int nthreads = 10;
    int csize = 3; // 3
    int nsigma = 5;
    int nped = 10000;

    int cf = 0;

    double *gainmap = NULL;
    // float *gm;

    int ff, np;
    // cout << " data size is " << dsize;

    ifstream filebin;
    char *indir = argv[1];
    char *outdir = argv[2];
    char *fformat = argv[3];
    char *fext = argv[4];
    int runmin = 0;

    // cout << "argc is " << argc << endl;
    if (argc >= 6) {
        runmin = atoi(argv[5]);
    }

    int runmax = runmin;

    if (argc >= 7) {
        runmax = atoi(argv[6]);
    }

    char *pedfile = NULL;
    if (argc >= 8) {
        pedfile = argv[7];
    }
    double thr = 0;
    double thr1 = 1;

    if (argc >= 9) {
        thr = atof(argv[8]);
    }

    int nframes = 0;

    if (argc >= 10) {
        nframes = atoi(argv[9]);
    }

    char ffname[10000];
    char fname[10000];
    char imgfname[10000];
    char cfname[10000];

    // Define decoders...
#if !defined JFSTRX && !defined JFSTRXOLD && !defined JFSTRXCHIP1 &&           \
    !defined JFSTRXCHIP6
#ifndef MODULE
    jungfrauHighZSingleChipData *decoder = new jungfrauHighZSingleChipData();
    int nx = 256, ny = 256;
#endif
#ifdef MODULE
    jungfrauModuleData *decoder = new jungfrauModuleData();
    int nx = 1024, ny = 512;
#endif
#endif

#ifdef JFSTRX
    cout << "Jungfrau strixel full module readout" << endl;
    // ROI
    uint16_t xxmin = 0;
    uint16_t xxmax = 0;
    uint16_t yymin = 0;
    uint16_t yymax = 0;

#ifndef ALDO
    using header = sls::defs::sls_receiver_header;
    // check if there is a roi in the header
    typedef struct {
        uint16_t xmin;
        uint16_t xmax;
        uint16_t ymin;
        uint16_t ymax;
    } receiverRoi_compact;
    receiverRoi_compact croi;
    sprintf(ffname, "%s/%s.%s", indir, fformat, fext);
    sprintf(fname, (const char *)ffname, runmin);
    std::cout << "Reading header of file " << fname << " to check for ROI "
              << std::endl;
    filebin.open((const char *)(fname), ios::in | ios::binary);
    if (filebin.is_open()) {
        header hbuffer;
        std::cout << "sizeof(header) = " << sizeof(header) << std::endl;
        if (filebin.read((char *)&hbuffer, sizeof(header))) {
            memcpy(&croi, &hbuffer.detHeader.detSpec1, 8);
            std::cout << "Read ROI [" << croi.xmin << ", " << croi.xmax << ", "
                      << croi.ymin << ", " << croi.ymax << "]" << std::endl;
            xxmin = croi.xmin;
            xxmax = croi.xmax;
            yymin = croi.ymin;
            yymax = croi.ymax;
        } else
            std::cout << "reading error" << std::endl;
        filebin.close();
    } else
        std::cout << "Could not open " << fname << " for reading " << std::endl;
#endif

    jungfrauLGADStrixelsData *decoder =
        new jungfrauLGADStrixelsData(xxmin, xxmax, yymin, yymax);
    int nx = 1024 / 3, ny = 512 * 5;
#endif
#ifdef JFSTRXCHIP1
    std::cout << "Jungfrau strixel LGAD single chip 1" << std::endl;
    jungfrauLGADStrixelsDataSingleChip *decoder =
        new jungfrauLGADStrixelsDataSingleChip(1);
    int nx = 256 / 3, ny = 256 * 5;
#endif
#ifdef JFSTRXCHIP6
    std::cout << "Jungfrau strixel LGAD single chip 6" << std::endl;
    jungfrauLGADStrixelsDataSingleChip *decoder =
        new jungfrauLGADStrixelsDataSingleChip(6);
    int nx = 256 / 3, ny = 256 * 5;
#endif
#ifdef JFSTRXOLD
    std::cout << "Jungfrau strixels old design" << std::endl;
    jungfrauStrixelsHalfModuleOldDesign *decoder =
        new jungfrauStrixelsHalfModuleOldDesign();
    int nx = 1024 * 3, ny = 512 / 3;
#endif

    decoder->getDetectorSize(nx, ny);
    std::cout << "Detector size is " << nx << " " << ny << std::endl;

    int xmin = 0, xmax = nx, ymin = 0, ymax = ny;
    if (argc >= 14) {
        xmin = atoi(argv[10]);
        xmax = atoi(argv[11]);
        ymin = atoi(argv[12]);
        ymax = atoi(argv[13]);
    }
    std::cout << xmin << " " << xmax << " " << ymin << " " << ymax << " "
              << std::endl;

    char *gainfname = NULL;
    if (argc > 14) {
        gainfname = argv[14];
        std::cout << "Gain map file name is: " << gainfname << std::endl;
    }

    std::time_t end_time;

    FILE *of = NULL;
    std::cout << "input directory is " << indir << std::endl;
    std::cout << "output directory is " << outdir << std::endl;
    std::cout << "input file is " << fformat << std::endl;
    std::cout << "runmin is " << runmin << std::endl;
    std::cout << "runmax is " << runmax << std::endl;
    if (pedfile)
        std::cout << "pedestal file is " << pedfile << std::endl;
    if (thr > 0)
        std::cout << "threshold is " << thr << std::endl;
    std::cout << "Nframes is " << nframes << std::endl;

    // std::cout << "HHHEEEEEEEEEEEEEEEEEEEEEEERE!!!!!" << std::endl;
    uint32_t nnx, nny;

    singlePhotonDetector *filter = new singlePhotonDetector(
        decoder, 3, nsigma, 1, NULL, nped, 200, -1, -1, gainmap, NULL);

    if (gainfname) {

        if (filter->readGainMap(gainfname))
            std::cout << "using gain map " << gainfname << std::endl;
        else
            std::cout << "Could not open gain map " << gainfname << std::endl;
    } else
        thr = 0.15 * thr;
    filter->newDataSet();
    // int dsize = decoder->getDataSize();

    if (thr > 0) {
        std::cout << "threshold is " << thr << std::endl;
        filter->setThreshold(thr);
        cf = 0;

    } else
        cf = 1;

    filter->setROI(xmin, xmax, ymin, ymax);
    std::time(&end_time);
    std::cout << std::ctime(&end_time) << std::endl;

    char *buff;

    // multiThreadedAnalogDetector *mt=new
    // multiThreadedAnalogDetector(filter,nthreads,fifosize);
    multiThreadedCountingDetector *mt =
        new multiThreadedCountingDetector(filter, nthreads, fifosize);
    mt->setClusterSize(csize, csize);

#ifndef ANALOG
    mt->setDetectorMode(ePhotonCounting);
    std::cout << "Counting!" << std::endl;
    if (thr > 0) {
        cf = 0;
    }
#endif
//{
#ifdef ANALOG
    mt->setDetectorMode(eAnalog);
    std::cout << "Analog!" << std::endl;
    cf = 0;
    // thr1=thr;
#endif
    //  }

    mt->StartThreads();
    mt->popFree(buff);

    //  cout << "mt " << endl;

    int ifr = 0;

    char froot[1000];
    double *ped = new double[nx * ny]; //, *ped1;

    int pos, pos1;

    if (pedfile) {

        if (string(pedfile).find(".dat") != std::string::npos) {
            pos1 = string(pedfile).rfind("/");
            strcpy(froot, pedfile + pos1);
            pos = string(froot).find(".dat");
            froot[pos] = '\0';
        }

        std::cout << "PEDESTAL " << std::endl;
        // sprintf(imgfname, "%s/pedestals.tiff", outdir);

        if (string(pedfile).find(".tif") == std::string::npos) {
            sprintf(fname, "%s", pedfile);
            std::cout << fname << std::endl;
            std::time(&end_time);
            std::cout << "aaa" << std::ctime(&end_time) << std::endl;

            mt->setFrameMode(ePedestal);
            // sprintf(fn,fformat,irun);
            filebin.open((const char *)(fname), ios::in | ios::binary);
            //      //open file
            if (filebin.is_open()) {
                std::cout << "bbbb" << std::ctime(&end_time) << std::endl;

                ff = -1;
                while (decoder->readNextFrame(filebin, ff, np, buff)) {
                    // if (np == 40) {
                    if ((ifr + 1) % 100 == 0) {
                        std::cout
                            << " ****"
                            << decoder->getValue(buff, 20, 20); // << endl;
                    }
                    mt->pushData(buff);
                    mt->nextThread();
                    mt->popFree(buff);
                    ifr++;
                    if (ifr % 100 == 0) {
                        std::cout << " ****" << ifr << " " << ff << " " << np
                                  << std::endl;
                    } // else
                    // cout << ifr << " " << ff << " " << np << endl;
                    if (ifr >= 1000)
                        break;
                    ff = -1;
                }
                filebin.close();
                while (mt->isBusy()) {
                    ;
                }

                sprintf(imgfname, "%s/%s_ped.tiff", outdir, froot);
                mt->writePedestal(imgfname);
                sprintf(imgfname, "%s/%s_rms.tiff", outdir, froot);
                mt->writePedestalRMS(imgfname);

            } else
                std::cout << "Could not open pedestal file " << fname
                          << " for reading " << std::endl;
        } else {
            float *pp = ReadFromTiff(pedfile, nny, nnx);
            if (pp && (int)nnx == nx && (int)nny == ny) {
                for (int i = 0; i < nx * ny; i++) {
                    ped[i] = pp[i];
                }
                delete[] pp;
                mt->setPedestal(ped);
                std::cout << "Pedestal set from tiff file " << pedfile
                          << std::endl;
            } else {
                std::cout << "Could not open pedestal tiff file " << pedfile
                          << " for reading " << std::endl;
            }
        }
        std::time(&end_time);
        std::cout << std::ctime(&end_time) << std::endl;
    }

    ifr = 0;
    int ifile = 0;

    mt->setFrameMode(eFrame);

    for (int irun = runmin; irun <= runmax; irun++) {
        std::cout << "DATA ";
        // sprintf(fn,fformat,irun);
        sprintf(ffname, "%s/%s.%s", indir, fformat, fext);
        sprintf(fname, (const char *)ffname, irun);
        sprintf(ffname, "%s/%s.tiff", outdir, fformat);
        sprintf(imgfname, (const char *)ffname, irun);
        sprintf(ffname, "%s/%s.clust", outdir, fformat);
        sprintf(cfname, (const char *)ffname, irun);
        std::cout << fname << " ";
        std::cout << imgfname << std::endl;
        std::time(&end_time);
        std::cout << std::ctime(&end_time) << std::endl;
        //  cout <<  fname << " " << outfname << " " << imgfname <<  endl;
        filebin.open((const char *)(fname), ios::in | ios::binary);
        //      //open file
        ifile = 0;
        if (filebin.is_open()) {
            if (thr <= 0 && cf != 0) { // cluster finder
                if (of == NULL) {
                    of = fopen(cfname, "w");
                    if (of) {
                        mt->setFilePointer(of);
                        std::cout << "file pointer set " << std::endl;
                    } else {
                        std::cout << "Could not open " << cfname
                                  << " for writing " << std::endl;
                        mt->setFilePointer(NULL);
                        return 1;
                    }
                }
            }
            //     //while read frame
            ff = -1;
            ifr = 0;
            while (decoder->readNextFrame(filebin, ff, np, buff)) {
                //  if (np == 40) {
                //         //push

                if ((ifr + 1) % 100 == 0) {
                    std::cout << " ****"
                              << decoder->getValue(buff, 20, 20); // << endl;
                }
                mt->pushData(buff);
                // 	//         //pop
                mt->nextThread();
                mt->popFree(buff);

                ifr++;
                if (ifr % 100 == 0)
                    std::cout << " " << ifr << " " << ff << std::endl;
                if (nframes > 0) {
                    if (ifr % nframes == 0) {
                        sprintf(ffname, "%s/%s_f%05d.tiff", outdir, fformat,
                                ifile);
                        sprintf(imgfname, (const char *)ffname, irun);
                        mt->writeImage(imgfname, thr1);
                        mt->clearImage();
                        ifile++;
                    }
                }
                // } else
                //     cout << ifr << " " << ff << " " << np << endl;
                ff = -1;
            }
            std::cout << "--" << std::endl;
            filebin.close();
            while (mt->isBusy()) {
                ;
            }
            if (nframes >= 0) {
                if (nframes > 0) {
                    sprintf(ffname, "%s/%s_f%05d.tiff", outdir, fformat, ifile);
                    sprintf(imgfname, (const char *)ffname, irun);
                } else {
                    sprintf(ffname, "%s/%s.tiff", outdir, fformat);
                    sprintf(imgfname, (const char *)ffname, irun);
                }
                std::cout << "Writing tiff to " << imgfname << " " << thr1
                          << std::endl;
                mt->writeImage(imgfname, thr1);
                mt->clearImage();
                if (of) {
                    fclose(of);
                    of = NULL;
                    mt->setFilePointer(NULL);
                }
            }
            std::time(&end_time);
            std::cout << std::ctime(&end_time) << std::endl;
        } else
            std::cout << "Could not open " << fname << " for reading "
                      << std::endl;
    }
    if (nframes < 0) {
        sprintf(ffname, "%s/%s.tiff", outdir, fformat);
        strcpy(imgfname, ffname);
        std::cout << "Writing tiff to " << imgfname << " " << thr1 << std::endl;
        mt->writeImage(imgfname, thr1);
    }

    return 0;
}