int psrfits_write_subint(struct psrfits *pf) {
int row, *status, nchan, nivals, mode, out_nbytes;
float ftmp;
struct hdrinfo *hdr;
struct subint *sub;
hdr = &(pf->hdr); // dereference the ptr to the header struct
sub = &(pf->sub); // dereference the ptr to the subint struct
status = &(pf->status); // dereference the ptr to the CFITSIO status
nchan = hdr->nchan / hdr->ds_freq_fact;
if (hdr->onlyI)
nivals = nchan;
else
nivals = nchan * hdr->npol;
mode = psrfits_obs_mode(hdr->obs_mode);
if (mode==fold)
out_nbytes = sub->bytes_per_subint / hdr->ds_freq_fact;
else {
out_nbytes = sub->bytes_per_subint / (hdr->ds_freq_fact * hdr->ds_time_fact);
if (hdr->onlyI)
out_nbytes /= hdr->npol;
}
// Create the initial file or change to a new one if needed.
// Stay with a single file for fold mode.
if (pf->filenum==0 ||
( (mode==search || pf->multifile==1)
&& pf->rownum > pf->rows_per_file)) {
if (pf->filenum) {
printf("Closing file '%s'\n", pf->filename);
fits_close_file(pf->fptr, status);
}
psrfits_create(pf);
}
row = pf->rownum;
fits_write_col(pf->fptr, TDOUBLE, 1, row, 1, 1, &(sub->tsubint), status);
fits_write_col(pf->fptr, TDOUBLE, 2, row, 1, 1, &(sub->offs), status);
fits_write_col(pf->fptr, TDOUBLE, 3, row, 1, 1, &(sub->lst), status);
fits_write_col(pf->fptr, TDOUBLE, 4, row, 1, 1, &(sub->ra), status);
fits_write_col(pf->fptr, TDOUBLE, 5, row, 1, 1, &(sub->dec), status);
fits_write_col(pf->fptr, TDOUBLE, 6, row, 1, 1, &(sub->glon), status);
fits_write_col(pf->fptr, TDOUBLE, 7, row, 1, 1, &(sub->glat), status);
ftmp = (float) sub->feed_ang;
fits_write_col(pf->fptr, TFLOAT, 8, row, 1, 1, &ftmp, status);
ftmp = (float) sub->pos_ang;
fits_write_col(pf->fptr, TFLOAT, 9, row, 1, 1, &ftmp, status);
ftmp = (float) sub->par_ang;
fits_write_col(pf->fptr, TFLOAT, 10, row, 1, 1, &ftmp, status);
ftmp = (float) sub->tel_az;
fits_write_col(pf->fptr, TFLOAT, 11, row, 1, 1, &ftmp, status);
ftmp = (float) sub->tel_zen;
fits_write_col(pf->fptr, TFLOAT, 12, row, 1, 1, &ftmp, status);
fits_write_col(pf->fptr, TDOUBLE, 13, row, 1, nchan, sub->dat_freqs, status);
fits_write_col(pf->fptr, TFLOAT, 14, row, 1, nchan, sub->dat_weights, status);
fits_write_col(pf->fptr, TFLOAT, 15, row, 1, nivals, sub->dat_offsets, status);
fits_write_col(pf->fptr, TFLOAT, 16, row, 1, nivals, sub->dat_scales, status);
if (mode==search) {
if (hdr->nbits==4) pf_8bit_to_4bit(pf);
fits_write_col(pf->fptr, TBYTE, 17, row, 1, out_nbytes,
sub->rawdata, status);
} else if (mode==fold) {
// Fold mode writes floats for now..
fits_write_col(pf->fptr, TFLOAT, 17, row, 1, out_nbytes/sizeof(float),
sub->data, status);
}
// Flush the buffers if not finished with the file
// Note: this use is not entirely in keeping with the CFITSIO
// documentation recommendations. However, manually
// correcting NAXIS2 and using fits_flush_buffer()
// caused occasional hangs (and extrememly large
// files due to some infinite loop).
fits_flush_file(pf->fptr, status);
// Print status if bad
if (*status) {
fprintf(stderr, "Error writing subint %d:\n", pf->rownum);
fits_report_error(stderr, *status);
fflush(stderr);
}
// Now update some key values if no CFITSIO errors
if (!(*status)) {
pf->rownum++;
pf->tot_rows++;
pf->N += hdr->nsblk / hdr->ds_time_fact;
pf->T += sub->tsubint;
// For fold mode, print info each subint written
if (mode==fold && pf->quiet!=1) {
printf("Wrote subint %d (total time %.1fs)\n", pf->rownum-1, pf->T);
fflush(stdout);
}
}
return *status;
}
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'},
{"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:Cuqh",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 '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;
strcpy(pf.basefilename, argv[optind]);
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) { fits_report_error(stderr, rv); }
exit(0);
}
int main(int argc, char *argv[])
{
int ii, ipol, nc = 0, ncnp = 0, gpubps = 0, status = 0, statsum = 0;
int fnum_start = 1, fnum_end = 0;
int numprocs, numbands, myid, baddata = 0, droppedrow = 0;
int *counts, *offsets;
unsigned char *tmpbuf = NULL;
struct psrfits pf;
struct {
double value;
int index;
} offs_in, offs_out;
char hostname[256];
char vegas_base_dir[256] = "\0";
char output_base[256] = "\0";
int starthpc = 0;
int reverse = 0;
MPI_Status mpistat;
/* Cmd line */
static struct option long_opts[] = {
{"output", 1, NULL, 'o'},
{"initial", 1, NULL, 'i'},
{"final", 1, NULL, 'f'},
{"vegas", 1, NULL, 'V'},
{"starthpc",1, NULL, 's'},
{"reverse" ,0, NULL, 'r'},
{0,0,0,0}
};
int opt, opti;
MPI_Init(&argc, &argv);
MPI_Comm_size(MPI_COMM_WORLD, &numprocs);
MPI_Comm_rank(MPI_COMM_WORLD, &myid);
numbands = numprocs - 1;
// Process the command line
while ((opt=getopt_long(argc,argv,"o:i:f:V:s:r",long_opts,&opti))!=-1) {
switch (opt) {
case 'o':
strncpy(output_base, optarg, 255);
output_base[255]='\0';
break;
case 'i':
fnum_start = atoi(optarg);
break;
case 'f':
fnum_end = atoi(optarg);
break;
case 'V':
strcpy(vegas_base_dir, optarg);
break;
case 's':
starthpc = atoi(optarg);
break;
case 'r':
reverse = 1;
break;
default:
if (myid==0) usage();
MPI_Finalize();
exit(0);
break;
}
}
if (optind==argc) {
if (myid==0) usage();
MPI_Finalize();
exit(1);
}
if (myid == 0) { // Master proc only
printf("\n\n");
printf(" MPI Search-mode PSRFITs Combiner\n");
printf(" by Scott M. Ransom\n\n");
}
// Determine the hostnames of the processes
{
if (gethostname(hostname, 255) < 0)
strcpy(hostname, "unknown");
MPI_Barrier(MPI_COMM_WORLD);
if (myid == 0) printf("\n");
fflush(NULL);
for (ii = 0 ; ii < numprocs ; ii++) {
MPI_Barrier(MPI_COMM_WORLD);
if (myid == ii)
printf("Process %3d is on machine %s\n", myid, hostname);
fflush(NULL);
MPI_Barrier(MPI_COMM_WORLD);
}
MPI_Barrier(MPI_COMM_WORLD);
fflush(NULL);
}
// Basefilenames for the GPU nodes
if (myid > 0) {
// Default to GUPPI mode
if (vegas_base_dir[0]=='\0')
sprintf(pf.basefilename, "/data/gpu/partial/%s/%s",
hostname, argv[optind]);
// VEGAS mode
else {
int hpcidx;
if (reverse)
hpcidx = starthpc - myid + 1;
else
hpcidx = myid + starthpc - 1;
sprintf(pf.basefilename, "%s/vegas-hpc%d-bdata1/%s",
vegas_base_dir, hpcidx, argv[optind]);
printf("**********: hostname = %s, myid = %d, datamnt = %d, basename=%s\n",
hostname, myid, hpcidx, pf.basefilename);
}
}
// Initialize some key parts of the PSRFITS structure
pf.tot_rows = pf.N = pf.T = pf.status = 0;
pf.filenum = fnum_start;
pf.filename[0] = '\0';
pf.filenames = NULL;
pf.numfiles = 0;
if (myid == 1) {
FILE *psrfitsfile;
char hdr[HDRLEN], filenm[200];
// Read the header info
sprintf(filenm, "%s_0001.fits", pf.basefilename);
psrfitsfile = fopen(filenm, "r");
fread(&hdr, 1, HDRLEN, psrfitsfile);
fclose(psrfitsfile);
// Send the header to the master proc
MPI_Send(hdr, HDRLEN, MPI_CHAR, 0, 0, MPI_COMM_WORLD);
} else if (myid == 0) {
FILE *psrfitsfile;
char hdr[HDRLEN], tmpfilenm[80];
// Receive the header info from proc 1
MPI_Recv(hdr, HDRLEN, MPI_CHAR, 1, 0, MPI_COMM_WORLD, &mpistat);
// Now write that header to a temp file
strcpy(tmpfilenm, "mpi_merge_psrfits.XXXXXX");
mkstemp(tmpfilenm);
psrfitsfile = fopen(tmpfilenm, "w");
fwrite(&hdr, 1, HDRLEN, psrfitsfile);
fclose(psrfitsfile);
pf.filenames = (char **)malloc(sizeof(char *));
pf.filenames[0] = tmpfilenm;
pf.basefilename[0]='\0';
pf.filenum = 0;
pf.numfiles = 1;
// And read the key information into a PSRFITS struct
status = psrfits_open(&pf);
status = psrfits_close(&pf);
free(pf.filenames);
remove(tmpfilenm);
// Now create the output PSTFITS file
if (output_base[0]=='\0') {
/* Set up default output filename */
strcpy(output_base, argv[optind]);
}
strcpy(pf.basefilename, output_base);
pf.multifile = 1;
pf.filenum = 0;
pf.numfiles = 0;
pf.filename[0] = '\0';
pf.filenames = NULL;
nc = pf.hdr.nchan;
ncnp = pf.hdr.nchan * pf.hdr.npol;
gpubps = pf.sub.bytes_per_subint;
pf.hdr.orig_nchan *= numbands;
pf.hdr.nchan *= numbands;
pf.hdr.fctr = pf.hdr.fctr - 0.5 * pf.hdr.BW + numbands/2.0 * pf.hdr.BW;
pf.hdr.BW *= numbands;
pf.sub.bytes_per_subint *= numbands;
long long filelen = 40 * (1L<<30); // In GB
pf.rows_per_file = filelen / pf.sub.bytes_per_subint;
status = psrfits_create(&pf);
// For in-memory transpose of data
tmpbuf = (unsigned char *)malloc(pf.sub.bytes_per_subint);
}
// Open the input PSRFITs files for real
if (myid > 0) {
status = psrfits_open(&pf);
nc = pf.hdr.nchan;
ncnp = pf.hdr.nchan * pf.hdr.npol;
gpubps = pf.sub.bytes_per_subint;
}
// Alloc data buffers for the PSRFITS files
pf.sub.dat_freqs = (float *)malloc(sizeof(float) * pf.hdr.nchan);
pf.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.sub.dat_scales = (float *)malloc(sizeof(float) *
pf.hdr.nchan * pf.hdr.npol);
pf.sub.data = (unsigned char *)malloc(pf.sub.bytes_per_subint);
pf.sub.rawdata = pf.sub.data;
// Counts and offsets for MPI_Gatherv
counts = (int *)malloc(sizeof(int) * numprocs);
offsets = (int *)malloc(sizeof(int) * numprocs);
counts[0] = offsets[0] = 0; // master sends nothing
// Now loop over the rows (i.e. subints)...
do {
MPI_Barrier(MPI_COMM_WORLD);
// Read the current subint from each of the "slave" nodes
if ((myid > 0) && (!baddata)) {
status = psrfits_read_subint(&pf);
if (status) {
pf.sub.offs = FLAG; // High value so it won't be min
if (pf.rownum > pf.rows_per_file) {
// Shouldn't be here unless opening of new file failed...
printf("Proc %d: Can't open next file. Setting status=114.\n", myid);
status = 114;
}
}
} else { // Root process
pf.sub.offs = FLAG; // High value so it won't be min
}
// Find the minimum value of OFFS_SUB to see if we dropped a row
offs_in.value = pf.sub.offs;
offs_in.index = myid;
MPI_Allreduce(&offs_in, &offs_out, 1, MPI_DOUBLE_INT,
MPI_MINLOC, MPI_COMM_WORLD);
// If all procs are returning the FLAG value, break.
if (offs_out.value==FLAG) break;
// Identify dropped rows
if ((myid > 0) && (!status) && (!baddata) &&
(pf.sub.offs > (offs_out.value + 0.1 * pf.sub.tsubint))) {
printf("Proc %d, row %d: Dropped a row. Filling with zeros.\n",
myid, pf.rownum);
droppedrow = 1;
}
if (myid > 0) {
// Ignore errors for moving past EOF (107), read errors (108)
// and missing files (114)
if (droppedrow ||
status==108 ||
((myid > 0) && (status==114 || status==107) && (!baddata))) {
if (status) printf("Proc %d, row %d: Ignoring CFITSIO error %d. Filling with zeros.\n", myid, pf.rownum, status);
// Set the data and the weights to all zeros
for (ii = 0 ; ii < pf.hdr.nchan ; ii++)
pf.sub.dat_weights[ii] = 0.0;
for (ii = 0 ; ii < pf.sub.bytes_per_subint ; ii++)
pf.sub.data[ii] = 0;
// And the scales and offsets to nominal values
for (ii = 0 ; ii < pf.hdr.nchan * pf.hdr.npol ; ii++) {
pf.sub.dat_offsets[ii] = 0.0;
pf.sub.dat_scales[ii] = 1.0;
}
// reset the status to 0 and allow going to next row
if (status==114 || status==107) {
baddata = 1;
}
if (status==108) { // Try reading the next row...
pf.rownum++;
pf.tot_rows++;
pf.N += pf.hdr.nsblk;
pf.T = pf.N * pf.hdr.dt;
}
if (droppedrow) { // We want to read the current row again...
pf.rownum--;
pf.tot_rows--;
pf.N -= pf.hdr.nsblk;
pf.T = pf.N * pf.hdr.dt;
droppedrow = 0; // reset
}
status = 0;
}
}
// If we've passed final file, exit
if (fnum_end && pf.filenum > fnum_end) break;
// Combine statuses of all nodes by summing....
MPI_Allreduce(&status, &statsum, 1,
MPI_INT, MPI_SUM, MPI_COMM_WORLD);
if (statsum) break;
if (myid == offs_out.index) { // Send all of the non-band-specific parts to master
MPI_Send(&pf.sub.tsubint, 1, MPI_DOUBLE, 0, 0, MPI_COMM_WORLD);
MPI_Send(&pf.sub.offs, 1, MPI_DOUBLE, 0, 0, MPI_COMM_WORLD);
MPI_Send(&pf.sub.lst, 1, MPI_DOUBLE, 0, 0, MPI_COMM_WORLD);
MPI_Send(&pf.sub.ra, 1, MPI_DOUBLE, 0, 0, MPI_COMM_WORLD);
MPI_Send(&pf.sub.dec, 1, MPI_DOUBLE, 0, 0, MPI_COMM_WORLD);
MPI_Send(&pf.sub.glon, 1, MPI_DOUBLE, 0, 0, MPI_COMM_WORLD);
MPI_Send(&pf.sub.glat, 1, MPI_DOUBLE, 0, 0, MPI_COMM_WORLD);
MPI_Send(&pf.sub.feed_ang, 1, MPI_DOUBLE, 0, 0, MPI_COMM_WORLD);
MPI_Send(&pf.sub.pos_ang, 1, MPI_DOUBLE, 0, 0, MPI_COMM_WORLD);
MPI_Send(&pf.sub.par_ang, 1, MPI_DOUBLE, 0, 0, MPI_COMM_WORLD);
MPI_Send(&pf.sub.tel_az, 1, MPI_DOUBLE, 0, 0, MPI_COMM_WORLD);
MPI_Send(&pf.sub.tel_zen, 1, MPI_DOUBLE, 0, 0, MPI_COMM_WORLD);
} else if (myid == 0) { // Receive all of the non-data parts
MPI_Recv(&pf.sub.tsubint, 1, MPI_DOUBLE, offs_out.index, 0, MPI_COMM_WORLD, &mpistat);
MPI_Recv(&pf.sub.offs, 1, MPI_DOUBLE, offs_out.index, 0, MPI_COMM_WORLD, &mpistat);
MPI_Recv(&pf.sub.lst, 1, MPI_DOUBLE, offs_out.index, 0, MPI_COMM_WORLD, &mpistat);
MPI_Recv(&pf.sub.ra, 1, MPI_DOUBLE, offs_out.index, 0, MPI_COMM_WORLD, &mpistat);
MPI_Recv(&pf.sub.dec, 1, MPI_DOUBLE, offs_out.index, 0, MPI_COMM_WORLD, &mpistat);
MPI_Recv(&pf.sub.glon, 1, MPI_DOUBLE, offs_out.index, 0, MPI_COMM_WORLD, &mpistat);
MPI_Recv(&pf.sub.glat, 1, MPI_DOUBLE, offs_out.index, 0, MPI_COMM_WORLD, &mpistat);
MPI_Recv(&pf.sub.feed_ang, 1, MPI_DOUBLE, offs_out.index, 0, MPI_COMM_WORLD, &mpistat);
MPI_Recv(&pf.sub.pos_ang, 1, MPI_DOUBLE, offs_out.index, 0, MPI_COMM_WORLD, &mpistat);
MPI_Recv(&pf.sub.par_ang, 1, MPI_DOUBLE, offs_out.index, 0, MPI_COMM_WORLD, &mpistat);
MPI_Recv(&pf.sub.tel_az, 1, MPI_DOUBLE, offs_out.index, 0, MPI_COMM_WORLD, &mpistat);
MPI_Recv(&pf.sub.tel_zen, 1, MPI_DOUBLE, offs_out.index, 0, MPI_COMM_WORLD, &mpistat);
}
// Now gather the vector quantities...
// Vectors of length nchan
for (ii = 1 ; ii < numprocs ; ii++) {
counts[ii] = nc;
offsets[ii] = (ii - 1) * nc;
}
status = MPI_Gatherv(pf.sub.dat_freqs, nc, MPI_FLOAT,
pf.sub.dat_freqs, counts, offsets, MPI_FLOAT,
0, MPI_COMM_WORLD);
status = MPI_Gatherv(pf.sub.dat_weights, nc, MPI_FLOAT,
pf.sub.dat_weights, counts, offsets, MPI_FLOAT,
0, MPI_COMM_WORLD);
// Vectors of length nchan * npol
for (ipol=0; ipol < pf.hdr.npol; ipol++) {
for (ii = 1 ; ii < numprocs ; ii++) {
counts[ii] = nc;
offsets[ii] = ipol*nc*numbands + (ii - 1) * nc;
}
status = MPI_Gatherv(pf.sub.dat_offsets+(ipol*nc), nc, MPI_FLOAT,
pf.sub.dat_offsets, counts, offsets,
MPI_FLOAT, 0, MPI_COMM_WORLD);
status = MPI_Gatherv(pf.sub.dat_scales+(ipol*nc), nc, MPI_FLOAT,
pf.sub.dat_scales, counts, offsets,
MPI_FLOAT, 0, MPI_COMM_WORLD);
}
// Vectors of length pf.sub.bytes_per_subint for the raw data
for (ii = 1 ; ii < numprocs ; ii++) {
counts[ii] = gpubps;
offsets[ii] = (ii - 1) * gpubps;
}
status = MPI_Gatherv(pf.sub.data, gpubps, MPI_UNSIGNED_CHAR,
tmpbuf, counts, offsets, MPI_UNSIGNED_CHAR,
0, MPI_COMM_WORLD);
// Reorder and write the new row to the output file
if (myid == 0) {
reorder_data(pf.sub.data, tmpbuf, numbands,
pf.hdr.nsblk, pf.hdr.npol, nc);
status = psrfits_write_subint(&pf);
}
} while (statsum == 0);
// Free the arrays
free(pf.sub.dat_freqs);
free(pf.sub.dat_weights);
free(pf.sub.dat_offsets);
free(pf.sub.dat_scales);
free(pf.sub.data);
if (myid == 0) free(tmpbuf);
free(counts);
free(offsets);
// Close the files and finalize things
status = psrfits_close(&pf);
MPI_Finalize();
exit(0);
}
int main(int argc, char *argv[]) {
/* Cmd line */
static struct option long_opts[] = {
{"frontend", 1, NULL, 'F'},
{"offset", 0, NULL, 'o'},
{"srcname", 1, NULL, 's'},
};
int ii;
double dtmp;
char filename[256], *adr;
struct psrfits pf;
int c1,c2;
double c3;
int opt, opti;
int scan_id, beam_id;
bool have_Stokes = false;
bool have_chan_offset = false;
bool have_frontend = false; char frontend[3];
bool have_srcname = false; char srcname[24];
while ((opt=getopt_long(argc,argv,"ob:t:j:i:F:s:p:P:F:CuU:SAqh",long_opts,&opti))!=-1) {
switch (opt) {
case 'F':
have_frontend = true;
strncpy(frontend, optarg, 3);
break;
case 'o':
have_chan_offset = true;
break;
case 's':
have_srcname = true;
strncpy(srcname, optarg, 24);
break;
case 'S':
have_Stokes = true;
break;
case 'h':
default:
usage();
exit(0);
break;
}
}
// Only set the basefilename and not "filename"
// Also, fptr will be set by psrfits_create_searchmode()
FILE *pfi;
strcpy(filename, argv[optind]);
printf("Filename = %s\n", filename);
// Read filterbank
if((pfi=fopen(filename,"r"))==NULL) {
printf("Cannot open file %s\n", filename);
exit(-2);
} else {
printf("Opening file %s\n", filename);
}
/* try to read the header */
long long header_size, numsamps;
header iheader;
if (!(header_size=read_header(pfi,&iheader))) {
printf("Error reading header\n");
exit(-2);
}
//printf("header_size = %lld\n", header_size);
// Get the number of samples
numsamps=nsamples(filename, header_size, &iheader);
//printf("numsamps = %lld ra=%lf dec=%lf\n", numsamps, iheader.src_raj, iheader.src_dej);
//fflush(stdout);
pf.filenum = 0; // This is the crucial one to set to initialize things
pf.rows_per_file = 4000; // Need to set this based on PSRFITS_MAXFILELEN
// Now set values for our hdrinfo structure
pf.hdr.scanlen = 3600; // in sec
strcpy(pf.hdr.observer, "Observer");
strcpy(pf.hdr.telescope, "Effelsberg");
strcpy(pf.hdr.obs_mode, "SEARCH");
strcpy(pf.hdr.backend, "PFFTS");
strncpy(pf.hdr.source, iheader.source_name, 24);
strcpy(pf.hdr.frontend, "LBand");
strcpy(pf.hdr.project_id, "HTRUN");
strcpy(pf.hdr.date_obs, "2010-01-01T05:15:30.000");
strcpy(pf.hdr.poln_type, "LIN");
strcpy(pf.hdr.poln_order, "IQUV");
strcpy(pf.hdr.track_mode, "TRACK");
strcpy(pf.hdr.cal_mode, "OFF");
strcpy(pf.hdr.feed_mode, "FA");
//printf("filename = %s\n", filename); fflush(stdout);
if(strstr(filename,"/") != NULL) { adr=(char *)strrchr(filename,'/')+1; sprintf(pf.filename,"%s",adr); }
else strncpy(pf.filename, filename, 80);
//printf("filename = %s\n", pf.filename); fflush(stdout);
sscanf(pf.filename, "%d_%d_%d_%dbit.fil", &scan_id, &c1, &beam_id, &c2);
pf.hdr.dt = iheader.tsamp;
pf.hdr.fctr = iheader.fch1+iheader.foff*iheader.nchans/2. - iheader.foff/2.;
if (have_chan_offset)
pf.hdr.fctr += iheader.foff/2.;
pf.hdr.BW = iheader.nchans * iheader.foff;
angle_split(iheader.src_raj, &c1, &c2, &c3);
sprintf(pf.hdr.ra_str, "%2.2d:%2.2d:%07.4lf", c1, c2, c3);
angle_split(iheader.src_dej, &c1, &c2, &c3);
sprintf(pf.hdr.dec_str, "%2.2d:%2.2d:%07.4lf", c1, c2, c3);
pf.hdr.azimuth = iheader.az_start;
pf.hdr.zenith_ang = iheader.za_start;
pf.hdr.beam_FWHM = 0.25;
pf.hdr.start_lst = 0.0;
pf.hdr.start_sec = 0.0;
pf.hdr.start_day = 55000;
pf.hdr.scan_number = scan_id;
pf.hdr.rcvr_polns = 2;
pf.hdr.summed_polns = 0;
pf.hdr.offset_subint = 0;
pf.hdr.nchan = iheader.nchans;
pf.hdr.orig_nchan = pf.hdr.nchan;
pf.hdr.orig_df = pf.hdr.df = pf.hdr.BW / pf.hdr.nchan;
pf.hdr.nbits = iheader.nbits;
pf.hdr.npol = iheader.nifs;
pf.hdr.onlyI = 0;
if (pf.hdr.npol==1) pf.hdr.onlyI = 1;
pf.hdr.chan_dm = 0.0;
pf.hdr.fd_hand = 1;
pf.hdr.fd_sang = 0;
pf.hdr.fd_xyph = 0;
pf.hdr.be_phase = 1;
pf.hdr.ibeam = beam_id;
pf.hdr.nsblk = 2048;
pf.hdr.MJD_epoch = iheader.tstart; // Note the "L" for long double
pf.hdr.ds_time_fact = 1;
pf.hdr.ds_freq_fact = 1;
//sprintf(pf.basefilename, "%s_%04d_%02d", pf.hdr.backend, pf.hdr.scan_number, pf.hdr.ibeam);
//psrfits_create(&pf);
// Now set values for our subint structure
pf.sub.tsubint = pf.hdr.nsblk * pf.hdr.dt;
pf.tot_rows = 0.0;
pf.sub.offs = (pf.tot_rows + 0.5) * pf.sub.tsubint;
pf.sub.lst = pf.hdr.start_lst;
pf.sub.ra = pf.hdr.ra2000;
pf.sub.dec = pf.hdr.dec2000;
// GD slaEqgal(pf.hdr.ra2000*DEGTORAD, pf.hdr.dec2000*DEGTORAD,
//&pf.sub.glon, &pf.sub.glat);
//pf.sub.glon *= RADTODEG;
//pf.sub.glat *= RADTODEG;
pf.sub.feed_ang = 0.0;
pf.sub.pos_ang = 0.0;
pf.sub.par_ang = 0.0;
pf.sub.tel_az = pf.hdr.azimuth;
pf.sub.tel_zen = pf.hdr.zenith_ang;
pf.sub.bytes_per_subint = (pf.hdr.nbits * pf.hdr.nchan *
pf.hdr.npol * pf.hdr.nsblk) / 8;
if (pf.hdr.nbits==32) pf.sub.FITS_typecode = TFLOAT;
else pf.sub.FITS_typecode = TBYTE; // 11 = byte
//
if (have_frontend) {
if (strncmp(frontend,"S36",3)==0) {
strcpy(pf.hdr.backend, "PSRIX");
strcpy(pf.hdr.frontend, "S36");
strcpy(pf.hdr.poln_type, "CIRC");
strcpy(pf.hdr.poln_order, "AABBCRCI");
pf.hdr.fd_hand = -1; // To conform PA and Stokes V to PSR/IEEE
}
else if (strncmp(frontend,"S60",3)==0) {
strcpy(pf.hdr.backend, "PSRIX");
strcpy(pf.hdr.frontend, "S60");
strcpy(pf.hdr.poln_type, "CIRC");
strcpy(pf.hdr.poln_order, "AABBCRCI");
}
else if (strncmp(frontend,"S110",3)==0) {
strcpy(pf.hdr.backend, "PSRIX");
strcpy(pf.hdr.frontend, "S110");
strcpy(pf.hdr.poln_type, "CIRC");
strcpy(pf.hdr.poln_order, "AABBCRCI");
pf.hdr.be_phase = -1; // To conform Stokes V to PSR/IEEE
}
else if (strncmp(frontend,"S45",3)==0) {
strcpy(pf.hdr.backend, "PSRIX");
strcpy(pf.hdr.frontend, "S45");
strcpy(pf.hdr.poln_type, "LIN");
strcpy(pf.hdr.poln_order, "AABBCRCI");
pf.hdr.be_phase = -1; // To conform Stokes V to PSR/IEEE
}
else {printf("Frontend %s not recognised\n", frontend);}
}
if (have_srcname) strncpy(pf.hdr.source, srcname, 24);
if (have_Stokes) strcpy(pf.hdr.poln_order, "IQUV");
if (strncmp(pf.hdr.backend, "PFFTS",5)==0)
sprintf(pf.basefilename, "%s_%04d_%02d", pf.hdr.backend, pf.hdr.scan_number, pf.hdr.ibeam);
else
sprintf(pf.basefilename, "%s_%s_%5d_%d", pf.hdr.backend, pf.hdr.source, (int) pf.hdr.MJD_epoch, (int) pf.hdr.fctr);
psrfits_create(&pf);
// Create and initialize the subint arrays
pf.sub.dat_freqs = (float *)malloc(sizeof(float) * pf.hdr.nchan);
pf.sub.dat_weights = (float *)malloc(sizeof(float) * pf.hdr.nchan);
dtmp = pf.hdr.fctr - 0.5 * pf.hdr.BW + 0.5 * pf.hdr.df;
for (ii = 0 ; ii < pf.hdr.nchan ; ii++) {
pf.sub.dat_freqs[ii] = dtmp + ii * pf.hdr.df;
pf.sub.dat_weights[ii] = 1.0;
}
pf.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);
for (ii = 0 ; ii < pf.hdr.nchan * pf.hdr.npol ; ii++) {
pf.sub.dat_offsets[ii] = 0.0;
pf.sub.dat_scales[ii] = 1.0;
}
// This is what you would update for each time sample (likely just
// adjusting the pointer to point to your data)
pf.sub.rawdata = (unsigned char *)malloc(pf.sub.bytes_per_subint);
// Here is the real data-writing loop
do {
// Update the pf.sub entries here for each subint
// as well as the pf.sub.data pointer
fread(pf.sub.rawdata, pf.sub.bytes_per_subint, 1, pfi);
pf.sub.offs = (pf.tot_rows + 0.5) * pf.sub.tsubint;
psrfits_write_subint(&pf);
} while (pf.T < pf.hdr.scanlen && !feof (pfi) && !pf.status);
// Close the last file and cleanup
fits_close_file(pf.fptr, &(pf.status));
free(pf.sub.dat_freqs);
free(pf.sub.dat_weights);
free(pf.sub.dat_offsets);
free(pf.sub.dat_scales);
free(pf.sub.rawdata);
printf("Done. Wrote %d subints (%f sec) in %d files. status = %d\n",
pf.tot_rows, pf.T, pf.filenum, pf.status);
exit(0);
}
int main(int argc, char *argv[]) {
/* Cmd line */
static struct option long_opts[] = {
{"output", 1, NULL, 'o'},
{"nbin", 1, NULL, 'b'},
{"tsub", 1, NULL, 't'},
{"nthread", 1, NULL, 'j'},
{"initial", 1, NULL, 'i'},
{"final", 1, NULL, 'f'},
{"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'},
{"split", 1, NULL, 'S'},
{"apply", 0, NULL, 'A'},
{"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, apply_scale=0;
double split_size_gb = 1.0;
double tfold = 60.0;
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:b:t:j:i:f:s:p:P:F:CuU:S:Aqh",long_opts,&opti))!=-1) {
switch (opt) {
case 'o':
strncpy(output_base, optarg, 255);
output_base[255]='\0';
break;
case 'b':
nbin = atoi(optarg);
break;
case 't':
tfold = atof(optarg);
break;
case 'j':
nthread = atoi(optarg);
break;
case 'i':
fnum_start = atoi(optarg);
break;
case 'f':
fnum_end = atoi(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 'S':
split_size_gb = atof(optarg);
break;
case 'A':
apply_scale = 1;
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;
sprintf(pf.basefilename, argv[optind]);
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 */
sprintf(output_base, "%s_%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" : "");
}
sprintf(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.quiet=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;
if (split_size_gb > 0.0) {
pf_out.multifile = 1;
pf_out.rows_per_file = (int) (split_size_gb * (1024.0*1024.0*1024.0)
/ (double)pf_out.sub.bytes_per_subint);
printf("Writing a maximum of %d subintegrations (~%.1f GB) per output file.\n",
pf_out.rows_per_file, split_size_gb);
} else {
pf_out.multifile = 0;
printf("Writing a single output file.\n");
}
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, ipol, ichan;
float offset_uv=0.0;
// Extra cross-term offset for GUPPI
if (strcmp("GUPPI",pf.hdr.backend)==0 && apply_scale==0) {
offset_uv=0.5;
fprintf(stderr, "Found backend=GUPPI, setting offset_uv=%f\n",
offset_uv);
}
// Initialize scale/output and weights.
// These get copied from the input file later during the main loop.
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;
/* Alloc total 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);
/* Set up thread management */
pthread_t *thread_id;
struct fold_args *fargs;
thread_id = (pthread_t *)malloc(sizeof(pthread_t) * nthread);
fargs = (struct fold_args *)malloc(sizeof(struct fold_args) * nthread);
for (i=0; i<nthread; i++) {
thread_id[i] = 0;
fargs[i].data = (char *)malloc(sizeof(char)*pf.sub.bytes_per_subint);
fargs[i].fb = (struct foldbuf *)malloc(sizeof(struct foldbuf));
fargs[i].fb->nbin = pf_out.hdr.nbin;
fargs[i].fb->nchan = pf.hdr.nchan;
fargs[i].fb->npol = pf.hdr.npol;
fargs[i].nsamp = pf.hdr.nsblk;
fargs[i].tsamp = pf.hdr.dt;
fargs[i].raw_signed=raw_signed;
malloc_foldbuf(fargs[i].fb);
clear_foldbuf(fargs[i].fb);
fargs[i].scale = (float *)malloc(sizeof(float)
* pf.hdr.nchan * pf.hdr.npol);
fargs[i].offset = (float *)malloc(sizeof(float)
* pf.hdr.nchan * pf.hdr.npol);
}
/* Main loop */
rv=0;
int imjd;
double fmjd, fmjd0=0, fmjd_next=0, fmjd_epoch;
double offs0=0, offs1=0;
//double phase=0.0, freq=1.0;
int first=1, subcount=0;
int cur_thread = 0;
signal(SIGINT, cc);
while (run) {
/* Read data block */
pf.sub.data = (unsigned char *)fargs[cur_thread].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;
/* First time stuff */
if (first) {
fmjd0 = fmjd;
fmjd_next = fmjd + tfold/86400.0;
pf_out.sub.offs=0.0;
offs0 = pf.sub.offs - 0.5*pf.sub.tsubint;
offs1 = pf.sub.offs + 0.5*pf.sub.tsubint;
first=0;
for (i=0; i<pf.hdr.nchan; i++) {
pf_out.sub.dat_weights[i]=pf.sub.dat_weights[i];
}
}
/* Keep track of timestamp */
// TODO also pointing stuff.
pf_out.sub.offs += pf.sub.offs;
subcount++;
/* Update output block end time */
offs1 = pf.sub.offs + 0.5*pf.sub.tsubint;
/* Select polyco set */
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
/* Copy scale/offset from input to output if we're not applying it */
if (apply_scale==0) {
for (i=0; i<pf.hdr.nchan*pf.hdr.npol; i++) {
pf_out.sub.dat_scales[i] = pf.sub.dat_scales[i];
pf_out.sub.dat_offsets[i] = pf.sub.dat_offsets[i];
}
}
/* Fold this subint */
fargs[cur_thread].pc = &pc[ipc];
fargs[cur_thread].imjd = imjd;
fargs[cur_thread].fmjd = fmjd;
rv = pthread_create(&thread_id[cur_thread], NULL,
fold_8bit_power_thread, &fargs[cur_thread]);
if (rv) {
fprintf(stderr, "Thread creation error.\n");
exit(1);
}
if (apply_scale) {
for (i=0; i<pf.hdr.nchan*pf.hdr.npol; i++) {
fargs[cur_thread].scale[i] = pf.sub.dat_scales[i];
fargs[cur_thread].offset[i] = pf.sub.dat_offsets[i];
}
}
cur_thread++;
/* Combine thread results if needed */
if (cur_thread==nthread || fmjd>fmjd_next) {
/* Loop over active threads */
for (i=0; i<cur_thread; i++) {
/* Wait for thread to finish */
rv = pthread_join(thread_id[i], NULL);
if (rv) {
fprintf(stderr, "Thread join error.\n");
exit(1);
}
/* Apply scale and offset here */
if (apply_scale)
scale_offset_folds(fargs[i].fb, fargs[i].scale,
fargs[i].offset);
/* Combine its result into total fold */
accumulate_folds(&fb, fargs[i].fb);
/* Reset thread info */
clear_foldbuf(fargs[i].fb);
thread_id[i] = 0;
}
/* Reset active thread count */
cur_thread = 0;
}
/* See if integration needs to be written, etc */
if (fmjd > fmjd_next) {
/* Figure out timestamp */
pf_out.sub.offs /= (double)subcount;
pf_out.sub.tsubint = offs1 - offs0;
fmjd_epoch = fmjd0 + pf_out.sub.offs/86400.0;
/*
// Don't need this stuff if we set EPOCHS=MIDTIME
ipc = select_pc(pc, npc, pf.hdr.source, imjd, fmjd_epoch);
if (ipc<0) {
fprintf(stderr, "Polyco error, exiting.\n");
exit(1);
}
phase = psr_phase(&pc[ipc], imjd, fmjd_epoch, &freq);
phase = fmod(phase, 1.0);
pf_out.sub.offs -= phase/freq; // ref epoch needs 0 phase
*/
/* Transpose, output subint */
normalize_transpose_folds((float *)pf_out.sub.data, &fb);
int last_filenum = pf_out.filenum;
psrfits_write_subint(&pf_out);
/* Check for write errors */
if (pf_out.status) {
fprintf(stderr, "Error writing subint.\n");
fits_report_error(stderr, pf_out.status);
exit(1);
}
/* Check if we started a new file */
if (pf_out.filenum!=last_filenum) {
/* No polycos yet written to this file */
for (i=0; i<npc; i++) pc_written[i]=0;
}
/* Write the current polyco if needed */
if (pc_written[ipc]==0) {
psrfits_write_polycos(&pf_out, &pc[ipc], 1);
if (pf_out.status) {
fprintf(stderr, "Error writing polycos.\n");
fits_report_error(stderr, pf_out.status);
exit(1);
}
pc_written[ipc] = 1;
}
/* Clear counters, avgs */
clear_foldbuf(&fb);
pf_out.sub.offs = 0.0;
offs0 = pf.sub.offs - 0.5*pf.sub.tsubint;
subcount=0;
/* Set next output time */
fmjd_next = fmjd + tfold/86400.0;
}
/* Progress report */
if (!quiet) {
printf("\rFile %d %5.1f%%", pf.filenum,
100.0 * (float)(pf.rownum-1)/(float)pf.rows_per_file);
fflush(stdout);
}
}
/* Join any running threads */
for (i=0; i<cur_thread; i++)
if (thread_id[i]) pthread_join(thread_id[i], NULL);
/* Remove polyco table in cal mode */
if (cal) {
rv = psrfits_remove_polycos(&pf_out);
if (rv) { fits_report_error(stderr, rv); }
}
psrfits_close(&pf_out);
psrfits_close(&pf);
if (rv) { fits_report_error(stderr, rv); }
exit(0);
}
