psrfits_singlepulse.c

/* psrfits_singlepulse.c
 *
 * "Fold" PSRFITS search mode data into single-pulse folded PSRFITS.
 */
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <string.h>
#include <fitsio.h>
#include <getopt.h>
#include <signal.h>
#include "polyco.h"
#include "fold.h"
#include "psrfits.h"

/* Signal handler */
int run=1;
void cc(int sig) { run=0; }

void usage() {
    printf(
            "Usage: psrfits_singlepulse [options] input_filename_base or filenames\n"
            "Options:\n"
            "  -h, --help               Print this\n"
            "  -o name, --output=name   Output base filename (auto-generate)\n"
            "  -n nn, --npulse=nn       Number of pulses per output file (64)\n"
            "  -b nn, --nbin=nn         Number of profile bins (256)\n"
            "  -i nn, --initial=nn      Starting input file number (1)\n"
            "  -f nn, --final=nn        Ending input file number (auto)\n"
            "  -T nn, --time=nn         Start nn seconds in (0)\n"
            "  -L nn, --length=nn       Process nn total seconds (all)\n"
            "  -s src, --src=src        Override source name from file\n"
            "  -p file, --polyco=file   Polyco file to use (polyco.dat)\n"
            "  -P file, --parfile=file  Use given .par file\n"
            "  -F nn, --foldfreq=nn     Fold at constant freq (Hz)\n"
            "  -C, --cal                Cal folding mode\n"
            "  -u, --unsigned           Raw data is unsigned\n"
            "  -U n, --nunsigned        Num of unsigned polns\n"
            "  -q, --quiet              No progress indicator\n"
          );
}

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

    /* Cmd line */
    static struct option long_opts[] = {
        {"output",  1, NULL, 'o'},
        {"npulse",  1, NULL, 'n'},
        {"nbin",    1, NULL, 'b'},
        {"nthread", 1, NULL, 'j'},
        {"initial", 1, NULL, 'i'},
        {"final",   1, NULL, 'f'},
        {"time",    1, NULL, 'T'},
        {"length",  1, NULL, 'L'},
        {"src",     1, NULL, 's'},
        {"polyco",  1, NULL, 'p'},
        {"parfile", 1, NULL, 'P'},
        {"foldfreq",1, NULL, 'F'},
        {"cal",     0, NULL, 'C'},
        {"unsigned",0, NULL, 'u'},
        {"nunsigned",1, NULL, 'U'},
        {"quiet",   0, NULL, 'q'},
        {"help",    0, NULL, 'h'},
        {0,0,0,0}
    };
    int opt, opti;
    int nbin=256, nthread=4, fnum_start=1, fnum_end=0;
    int quiet=0, raw_signed=1, use_polycos=1, cal=0;
    int npulse_per_file = 64;
    double start_time=0.0, process_time=0.0;
    double fold_frequency=0.0;
    char output_base[256] = "";
    char polyco_file[256] = "";
    char par_file[256] = "";
    char source[24];  source[0]='\0';
    while ((opt=getopt_long(argc,argv,"o:n:b:j:i:f:T:L:s:p:P:F:CuU:qh",long_opts,&opti))!=-1) {
        switch (opt) {
            case 'o':
                strncpy(output_base, optarg, 255);
                output_base[255]='\0';
                break;
            case 'n':
                npulse_per_file = atoi(optarg);
                break;
            case 'b':
                nbin = atoi(optarg);
                break;
            case 'j':
                nthread = atoi(optarg);
                break;
            case 'i':
                fnum_start = atoi(optarg);
                break;
            case 'f':
                fnum_end = atoi(optarg);
                break;
            case 'T':
                start_time = atof(optarg);
                break;
            case 'L':
                process_time = atof(optarg);
                break;
            case 's':
                strncpy(source, optarg, 24);
                source[23]='\0';
                break;
            case 'p':
                strncpy(polyco_file, optarg, 255);
                polyco_file[255]='\0';
                use_polycos = 1;
                break;
            case 'P':
                strncpy(par_file, optarg, 255);
                par_file[255] = '\0';
                break;
            case 'F':
                fold_frequency = atof(optarg);
                use_polycos = 0;
                break;
            case 'C':
                cal = 1;
                use_polycos = 0;
                break;
            case 'u':
                raw_signed=0;
                break;
            case 'U':
                raw_signed = 4 - atoi(optarg);
                break;
            case 'q':
                quiet=1;
                break;
            case 'h':
            default:
                usage();
                exit(0);
                break;
        }

    }
    if (optind==argc) { 
        usage();
        exit(1);
    }

    /* If no polyco/par file given, default to polyco.dat */
    if (use_polycos && (par_file[0]=='\0' && polyco_file[0]=='\0'))
        sprintf(polyco_file, "polyco.dat");

    /* Open first file */
    struct psrfits pf;
    psrfits_set_files(&pf, argc - optind, argv + optind);
    // Use the dynamic filename allocation
    if (pf.numfiles==0) pf.filenum = fnum_start;
    pf.tot_rows = pf.N = pf.T = pf.status = 0;
    pf.hdr.chan_dm = 0.0; // What if folding data that has been partially de-dispersed?
    pf.filename[0]='\0';
    int rv = psrfits_open(&pf);
    if (rv) { fits_report_error(stderr, rv); exit(1); }

    /* Check any constraints */
    if (pf.hdr.nbits!=8) { 
        fprintf(stderr, "Only implemented for 8-bit data (read nbits=%d).\n",
                pf.hdr.nbits);
        exit(1);
    }

    /* Check for calfreq */
    if (cal) {
        if (pf.hdr.cal_freq==0.0) {
            if (fold_frequency==0.0) {
                fprintf(stderr, "Error: Cal mode selected, but CAL_FREQ=0.  "
                        "Set cal frequency with -F\n");
                exit(1);
            } else {
                pf.hdr.cal_freq = fold_frequency;
            }
        } else {
            fold_frequency = pf.hdr.cal_freq;
        }
    }

    /* Set up output file */
    struct psrfits pf_out;
    memcpy(&pf_out, &pf, sizeof(struct psrfits));
    if (source[0]!='\0') { strncpy(pf_out.hdr.source, source, 24); }
    else { strncpy(source, pf.hdr.source, 24); source[23]='\0'; }
    if (output_base[0]=='\0') {
        /* Set up default output filename */
        if (start_time>0.0) 
            sprintf(output_base, "%s_SP_%s_%5.5d_%5.5d_%4.4d_%3.3d%s", 
                    pf_out.hdr.backend, 
                    pf_out.hdr.source, pf_out.hdr.start_day, 
                    (int)pf_out.hdr.start_sec, fnum_start,
                    (int)start_time,
                    cal ? "_cal" : "");
        else
            sprintf(output_base, "%s_SP_%s_%5.5d_%5.5d%s", pf_out.hdr.backend, 
                    pf_out.hdr.source, pf_out.hdr.start_day, 
                    (int)pf_out.hdr.start_sec, cal ? "_cal" : "");
    }
    strcpy(pf_out.basefilename, output_base);
    if (cal) {
        sprintf(pf_out.hdr.obs_mode, "CAL");
        sprintf(pf_out.hdr.cal_mode, "SYNC");
    } else
        sprintf(pf_out.hdr.obs_mode, "PSR");
    strncpy(pf_out.fold.parfile,par_file,255); pf_out.fold.parfile[255]='\0';
    pf_out.fptr = NULL;
    pf_out.filenum=0;
    pf_out.status=0;
    pf_out.hdr.nbin=nbin;
    pf_out.sub.FITS_typecode = TFLOAT;
    pf_out.sub.bytes_per_subint = sizeof(float) * 
        pf_out.hdr.nchan * pf_out.hdr.npol * pf_out.hdr.nbin;
    pf_out.multifile = 1;
    pf_out.quiet = 1;
    pf_out.rows_per_file = npulse_per_file;
    rv = psrfits_create(&pf_out);
    if (rv) { fits_report_error(stderr, rv); exit(1); }

    /* Alloc data buffers */
    pf.sub.dat_freqs = (float *)malloc(sizeof(float) * pf.hdr.nchan);
    pf_out.sub.dat_freqs = pf.sub.dat_freqs;
    pf.sub.dat_weights = (float *)malloc(sizeof(float) * pf.hdr.nchan);
    pf_out.sub.dat_weights = (float *)malloc(sizeof(float) * pf.hdr.nchan);
    pf.sub.dat_offsets = (float *)malloc(sizeof(float) 
            * pf.hdr.nchan * pf.hdr.npol);
    pf_out.sub.dat_offsets = (float *)malloc(sizeof(float) 
            * pf.hdr.nchan * pf.hdr.npol);
    pf.sub.dat_scales  = (float *)malloc(sizeof(float) 
            * pf.hdr.nchan * pf.hdr.npol);
    pf_out.sub.dat_scales  = (float *)malloc(sizeof(float) 
            * pf.hdr.nchan * pf.hdr.npol);
    pf_out.sub.data  = (unsigned char *)malloc(pf_out.sub.bytes_per_subint);

    /* Output scale/offset */
    int i, j, ipol, ichan;
    float offset_uv=0.0;  
    // Extra cross-term offset for GUPPI
    if (strcmp("GUPPI",pf.hdr.backend)==0) { 
        offset_uv=0.5;
        fprintf(stderr, "Found backend=GUPPI, setting offset_uv=%f\n",
                offset_uv);
    }
    // TODO: copy these from the input file
    for (ipol=0; ipol<pf.hdr.npol; ipol++) {
        for (ichan=0; ichan<pf.hdr.nchan; ichan++) {
            float offs = 0.0;
            if (ipol>1) offs = offset_uv;
            pf_out.sub.dat_scales[ipol*pf.hdr.nchan + ichan] = 1.0;
            pf_out.sub.dat_offsets[ipol*pf.hdr.nchan + ichan] = offs;
        }
    }
    for (i=0; i<pf.hdr.nchan; i++) { pf_out.sub.dat_weights[i]=1.0; }

    /* Read or make polycos */
    int npc=0, ipc=0;
    struct polyco *pc = NULL;
    if (use_polycos) {
        if (polyco_file[0]=='\0') {
            /* Generate from par file */
            npc = make_polycos(par_file, &pf.hdr, source, &pc);
            if (npc<=0) {
                fprintf(stderr, "Error generating polycos.\n");
                exit(1);
            }
            printf("Auto-generated %d polycos, src=%s\n", npc, source);
        } else {
            /* Read from polyco file */
            FILE *pcfile = fopen(polyco_file, "r");
            if (pcfile==NULL) { 
                fprintf(stderr, "Couldn't open polyco file.\n");
                exit(1);
            }
            npc = read_all_pc(pcfile, &pc);
            if (npc==0) {
                fprintf(stderr, "Error parsing polyco file.\n");
                exit(1);
            }
            fclose(pcfile);
        }
    } else {
        // Const fold period mode, generate a fake polyco?
        pc = (struct polyco *)malloc(sizeof(struct polyco));
        sprintf(pc[0].psr, "CONST");
        pc[0].mjd = (int)pf.hdr.MJD_epoch;
        pc[0].fmjd = fmod(pf.hdr.MJD_epoch,1.0);
        pc[0].rphase = 0.0;
        pc[0].f0 = fold_frequency;
        pc[0].nsite = 0; // Does this matter?
        pc[0].nmin = 24 * 60;
        pc[0].nc = 1;
        pc[0].rf = pf.hdr.fctr;
        pc[0].c[0] = 0.0;
        pc[0].used = 0;
        npc = 1;
    }
    int *pc_written = (int *)malloc(sizeof(int) * npc);
    for (i=0; i<npc; i++) pc_written[i]=0;

    /* Set up fold buf */
    struct foldbuf fb;
    fb.nchan = pf.hdr.nchan;
    fb.npol = pf.hdr.npol;
    fb.nbin = pf_out.hdr.nbin;
    malloc_foldbuf(&fb);
    clear_foldbuf(&fb);
    struct fold_args fargs;
    fargs.data = (char *)malloc(sizeof(char)*pf.sub.bytes_per_subint);
    fargs.fb = &fb;
    fargs.nsamp = 1;
    fargs.tsamp = pf.hdr.dt;
    fargs.raw_signed = raw_signed;

    /* Main loop */
    rv=0;
    int imjd;
    double fmjd, fmjd0=0, fmjd_samp, fmjd_epoch;
    long long cur_pulse=0, last_pulse=0;
    double psr_freq=0.0;
    int first_loop=1, first_data=1, sampcount=0, last_filenum=0;
    int bytes_per_sample = pf.hdr.nchan * pf.hdr.npol;
    signal(SIGINT, cc);
    while (run) { 

        /* Read data block */
        pf.sub.data = (unsigned char *)fargs.data;
        rv = psrfits_read_subint(&pf);
        if (rv) { 
            if (rv==FILE_NOT_OPENED) rv=0; // Don't complain on file not found
            run=0; 
            break; 
        }

        /* If we've passed final file, exit */
        if (fnum_end && pf.filenum>fnum_end) { run=0; break; }

        /* Get start date, etc */
        imjd = (int)pf.hdr.MJD_epoch;
        fmjd = (double)(pf.hdr.MJD_epoch - (long double)imjd);
        fmjd += (pf.sub.offs-0.5*pf.sub.tsubint)/86400.0;

        /* Select polyco set.
         * We'll assume same one is valid for whole data block.
         */
        if (use_polycos) {
            ipc = select_pc(pc, npc, source, imjd, fmjd);
            //ipc = select_pc(pc, npc, NULL, imjd, fmjd);
            if (ipc<0) { 
                fprintf(stderr, 
                        "No matching polycos (src=%s, imjd=%d, fmjd=%f)\n",
                        source, imjd, fmjd);
                break;
            }
        } else {
            ipc = 0;
        }
        pc[ipc].used = 1; // Mark this polyco set as used for folding

        /* First time stuff */
        if (first_loop) {
            fmjd0 = fmjd;
            psr_phase(&pc[ipc], imjd, fmjd, NULL, &last_pulse);
            pf_out.sub.offs=0.0;
            first_loop=0;
            for (i=0; i<pf.hdr.nchan; i++) { 
                pf_out.sub.dat_weights[i]=pf.sub.dat_weights[i];
            }
            last_filenum = pf_out.filenum;
        }

        /* Check to see if its time to process data */
        if (start_time>0.0) {
            double cur_time = (fmjd - fmjd0) * 86400.0;
            if (cur_time<start_time) 
                continue; 
        }

        if (first_data) {
           psr_phase(&pc[ipc], imjd, fmjd, NULL, &last_pulse);
           first_data=0;
        }

        /* Check to see if we're done */
        if (process_time>0.0) {
            double cur_time = (fmjd - fmjd0) * 86400.0;
            if (cur_time > start_time + process_time) {
                run=0;
                break;
            }
        }

        /* for singlepulse: loop over samples, output a new subint
         * whenever pulse number increases.
         */
        for (i=0; i<pf.hdr.nsblk; i++) {
        
            /* Keep track of timestamp */
            // TODO also pointing stuff?
            fmjd_samp = fmjd + i*pf.hdr.dt/86400.0;
            pf_out.sub.offs += pf.sub.offs - 0.5*pf.sub.tsubint + i*pf.hdr.dt;
            sampcount++;

            /* Calc current pulse number */
            psr_phase(&pc[ipc], imjd, fmjd_samp, &psr_freq, &cur_pulse);

            /* TODO: deal with scale/offset? */

            /* Fold this sample */
            fargs.pc = &pc[ipc];
            fargs.imjd = imjd;
            fargs.fmjd = fmjd_samp;
            rv = fold_8bit_power(fargs.pc, 
                    fargs.imjd, fargs.fmjd, 
                    fargs.data + i*bytes_per_sample,
                    fargs.nsamp, fargs.tsamp, fargs.raw_signed, fargs.fb);
            if (rv!=0) {
                fprintf(stderr, "Fold error.\n");
                exit(1);
            }

            /* See if integration needs to be written, etc */
            if (cur_pulse > last_pulse) {

                /* Figure out timestamp */
                pf_out.sub.offs /= (double)sampcount;
                pf_out.sub.tsubint = 1.0/psr_freq;
                fmjd_epoch = fmjd0 + pf_out.sub.offs/86400.0;

                /* Transpose, output subint */
                normalize_transpose_folds((float *)pf_out.sub.data, &fb);
                psrfits_write_subint(&pf_out);

                /* If file incremented, clear polyco flags */
                if (pf_out.filenum > last_filenum) 
                    for (j=0; j<npc; j++) 
                        pc_written[j]=0;

                /* Write this polyco if needed */
                if (pc_written[ipc]==0) {
                    psrfits_write_polycos(&pf_out, pc, npc);
                    pc_written[ipc] = 1;
                }

                /* Check for write errors */
                if (pf_out.status) {
                    fprintf(stderr, "Error writing subint.\n");
                    fits_report_error(stderr, pf_out.status);
                    exit(1);
                }

                /* Clear counters, avgs */
                clear_foldbuf(&fb);
                pf_out.sub.offs = 0.0;
                sampcount=0;
                last_pulse = cur_pulse;
                last_filenum = pf_out.filenum;

            }
        }


        /* Progress report */
        if (!quiet) {
            printf("\rFile %d %5.1f%%", pf.filenum, 
                    100.0 * (float)(pf.rownum-1)/(float)pf.rows_per_file);
            fflush(stdout);
        }
    }

    psrfits_close(&pf_out);
    psrfits_close(&pf);

    if (rv>100) { fits_report_error(stderr, rv); }
    exit(0);
}