void get_PSRFITS_subint(float *fdata, unsigned char *cdata, struct spectra_info *s)
{
unsigned char *ctmp = cdata;
int ii, status = 0, anynull;
int numtoread = s->samples_per_subint;
// The following allows us to read byte-packed data
if (s->bits_per_sample < 8) {
numtoread = (s->samples_per_subint * s->bits_per_sample) / 8;
ctmp = gen_bvect(numtoread);
}
// or 16-bit data that is listed as being bytes
if (s->bits_per_sample == 16 && s->FITS_typecode == 11)
numtoread = s->samples_per_subint * 2;
// Read the weights, offsets, and scales if required
if (s->apply_weight)
fits_read_col(s->fitsfiles[cur_file], TFLOAT, s->dat_wts_col, cur_subint, 1L,
s->num_channels, 0, weights, &anynull, &status);
if (s->apply_offset)
fits_read_col(s->fitsfiles[cur_file], TFLOAT, s->dat_offs_col, cur_subint,
1L, s->num_channels * s->num_polns, 0, offsets, &anynull,
&status);
if (s->apply_scale)
fits_read_col(s->fitsfiles[cur_file], TFLOAT, s->dat_scl_col, cur_subint, 1L,
s->num_channels * s->num_polns, 0, scales, &anynull, &status);
// Now actually read the subint into the temporary buffer
fits_read_col(s->fitsfiles[cur_file], s->FITS_typecode,
s->data_col, cur_subint, 1L, numtoread,
0, ctmp, &anynull, &status);
if (status) {
fprintf(stderr, "Error!: Problem reading record from PSRFITS data file\n"
"\tfilename = '%s', subint = %d. FITS status = %d. Exiting.\n",
s->filenames[cur_file], cur_subint, status);
exit(1);
}
// The following converts that byte-packed data into bytes
if (s->bits_per_sample == 4) {
#ifdef _OPENMP
#pragma omp parallel for default(none) shared(numtoread,cdata,ctmp)
#endif
for (ii = 0; ii < numtoread; ii++) {
const unsigned char uctmp = ctmp[ii];
const int jj = 2 * ii;
cdata[jj] = uctmp >> 4;
cdata[jj + 1] = uctmp & 0x0F;
}
} else if (s->bits_per_sample == 2) {
void read_PSRFITS_files(struct spectra_info *s)
// Read and convert PSRFITS information from a group of files
// and place the resulting info into a spectra_info structure.
{
int IMJD, SMJD, itmp, ii, status = 0;
double OFFS, dtmp;
long double MJDf;
char ctmp[80], comment[120];
s->datatype = PSRFITS;
s->fitsfiles = (fitsfile **)malloc(sizeof(fitsfile *) * s->num_files);
s->start_subint = gen_ivect(s->num_files);
s->num_subint = gen_ivect(s->num_files);
s->start_spec = (long long *)malloc(sizeof(long long) * s->num_files);
s->num_spec = (long long *)malloc(sizeof(long long) * s->num_files);
s->num_pad = (long long *)malloc(sizeof(long long) * s->num_files);
s->start_MJD = (long double *)malloc(sizeof(long double) * s->num_files);
s->N = 0;
s->num_beams = 1;
s->get_rawblock = &get_PSRFITS_rawblock;
s->offset_to_spectra = &offset_to_PSRFITS_spectra;
// By default, don't flip the band. But don't change
// the input value if it is aleady set to flip the band always
if (s->apply_flipband==-1) s->apply_flipband = 0;
// Step through the other files
for (ii = 0 ; ii < s->num_files ; ii++) {
// Is the file a PSRFITS file?
if (!is_PSRFITS(s->filenames[ii])) {
fprintf(stderr,
"\nError! File '%s' does not appear to be PSRFITS!\n",
s->filenames[ii]);
exit(1);
}
// Open the PSRFITS file
fits_open_file(&(s->fitsfiles[ii]), s->filenames[ii], READONLY, &status);
// Is the data in search mode?
fits_read_key(s->fitsfiles[ii], TSTRING, "OBS_MODE", ctmp, comment, &status);
// Quick fix for Parkes DFB data (SRCH? why????)...
if (strcmp("SRCH", ctmp)==0) {
strncpy(ctmp, "SEARCH", 40);
}
if (strcmp(ctmp, "SEARCH")) {
fprintf(stderr,
"\nError! File '%s' does not contain SEARCH-mode data!\n",
s->filenames[ii]);
exit(1);
}
// Now get the stuff we need from the primary HDU header
fits_read_key(s->fitsfiles[ii], TSTRING, "TELESCOP", ctmp, comment, &status); \
// Quick fix for MockSpec data...
if (strcmp("ARECIBO 305m", ctmp)==0) {
strncpy(ctmp, "Arecibo", 40);
}
// Quick fix for Parkes DFB data...
{
char newctmp[80];
// Copy ctmp first since strlower() is in-place
strcpy(newctmp, ctmp);
if (strcmp("parkes", strlower(remove_whitespace(newctmp)))==0) {
strncpy(ctmp, "Parkes", 40);
}
}
if (status) {
printf("Error %d reading key %s\n", status, "TELESCOP");
if (ii==0) s->telescope[0]='\0';
if (status==KEY_NO_EXIST) status=0;
} else {
if (ii==0) strncpy(s->telescope, ctmp, 40);
else if (strcmp(s->telescope, ctmp)!=0)
printf("Warning!: %s values don't match for files 0 and %d!\n",
"TELESCOP", ii);
}
get_hdr_string("OBSERVER", s->observer);
get_hdr_string("SRC_NAME", s->source);
get_hdr_string("FRONTEND", s->frontend);
get_hdr_string("BACKEND", s->backend);
get_hdr_string("PROJID", s->project_id);
get_hdr_string("DATE-OBS", s->date_obs);
get_hdr_string("FD_POLN", s->poln_type);
get_hdr_string("RA", s->ra_str);
get_hdr_string("DEC", s->dec_str);
get_hdr_double("OBSFREQ", s->fctr);
get_hdr_int("OBSNCHAN", s->orig_num_chan);
get_hdr_double("OBSBW", s->orig_df);
//get_hdr_double("CHAN_DM", s->chan_dm);
get_hdr_double("BMIN", s->beam_FWHM);
/* This is likely not in earlier versions of PSRFITS so */
/* treat it a bit differently */
fits_read_key(s->fitsfiles[ii], TDOUBLE, "CHAN_DM",
&(s->chan_dm), comment, &status);
if (status==KEY_NO_EXIST) {
status = 0;
s->chan_dm = 0.0;
}
// Don't use the macros unless you are using the struct!
fits_read_key(s->fitsfiles[ii], TINT, "STT_IMJD", &IMJD, comment, &status);
s->start_MJD[ii] = (long double) IMJD;
fits_read_key(s->fitsfiles[ii], TINT, "STT_SMJD", &SMJD, comment, &status);
fits_read_key(s->fitsfiles[ii], TDOUBLE, "STT_OFFS", &OFFS, comment, &status);
s->start_MJD[ii] += ((long double) SMJD + (long double) OFFS) / SECPERDAY;
// Are we tracking?
fits_read_key(s->fitsfiles[ii], TSTRING, "TRK_MODE", ctmp, comment, &status);
itmp = (strcmp("TRACK", ctmp)==0) ? 1 : 0;
if (ii==0) s->tracking = itmp;
else if (s->tracking != itmp)
printf("Warning!: TRK_MODE values don't match for files 0 and %d!\n", ii);
// Now switch to the SUBINT HDU header
fits_movnam_hdu(s->fitsfiles[ii], BINARY_TBL, "SUBINT", 0, &status);
get_hdr_double("TBIN", s->dt);
get_hdr_int("NCHAN", s->num_channels);
get_hdr_int("NPOL", s->num_polns);
get_hdr_string("POL_TYPE", s->poln_order);
fits_read_key(s->fitsfiles[ii], TINT, "NCHNOFFS", &itmp, comment, &status);
if (itmp > 0)
printf("Warning!: First freq channel is not 0 in file %d!\n", ii);
get_hdr_int("NSBLK", s->spectra_per_subint);
get_hdr_int("NBITS", s->bits_per_sample);
fits_read_key(s->fitsfiles[ii], TINT, "NAXIS2",
&(s->num_subint[ii]), comment, &status);
fits_read_key(s->fitsfiles[ii], TINT, "NSUBOFFS",
&(s->start_subint[ii]), comment, &status);
s->time_per_subint = s->dt * s->spectra_per_subint;
/* This is likely not in earlier versions of PSRFITS so */
/* treat it a bit differently */
fits_read_key(s->fitsfiles[ii], TFLOAT, "ZERO_OFF",
&(s->zero_offset), comment, &status);
if (status==KEY_NO_EXIST) {
status = 0;
s->zero_offset = 0.0;
}
s->zero_offset = fabs(s->zero_offset);
// Get the time offset column info and the offset for the 1st row
{
double offs_sub;
int colnum, anynull, numrows;
// Identify the OFFS_SUB column number
fits_get_colnum(s->fitsfiles[ii], 0, "OFFS_SUB", &colnum, &status);
if (status==COL_NOT_FOUND) {
printf("Warning!: Can't find the OFFS_SUB column!\n");
status = 0; // Reset status
} else {
if (ii==0) {
s->offs_sub_col = colnum;
} else if (colnum != s->offs_sub_col) {
printf("Warning!: OFFS_SUB column changes between files!\n");
}
}
// Read the OFFS_SUB column value for the 1st row
fits_read_col(s->fitsfiles[ii], TDOUBLE,
s->offs_sub_col, 1L, 1L, 1L,
0, &offs_sub, &anynull, &status);
numrows = (int)((offs_sub - 0.5 * s->time_per_subint) /
s->time_per_subint + 1e-7);
// Check to see if any rows have been deleted or are missing
if (numrows > s->start_subint[ii]) {
printf("Warning: NSUBOFFS reports %d previous rows\n"
" but OFFS_SUB implies %d. Using OFFS_SUB.\n"
" Will likely be able to correct for this.\n",
s->start_subint[ii], numrows);
}
s->start_subint[ii] = numrows;
}
// This is the MJD offset based on the starting subint number
MJDf = (s->time_per_subint * s->start_subint[ii]) / SECPERDAY;
// The start_MJD values should always be correct
s->start_MJD[ii] += MJDf;
// Compute the starting spectra from the times
MJDf = s->start_MJD[ii] - s->start_MJD[0];
if (MJDf < 0.0) {
fprintf(stderr, "Error!: File %d seems to be from before file 0!\n", ii);
exit(1);
}
s->start_spec[ii] = (long long)(MJDf * SECPERDAY / s->dt + 0.5);
// Now pull stuff from the other columns
{
float ftmp;
long repeat, width;
int colnum, anynull;
// Identify the data column and the data type
fits_get_colnum(s->fitsfiles[ii], 0, "DATA", &colnum, &status);
if (status==COL_NOT_FOUND) {
printf("Warning!: Can't find the DATA column!\n");
status = 0; // Reset status
} else {
if (ii==0) {
s->data_col = colnum;
fits_get_coltype(s->fitsfiles[ii], colnum, &(s->FITS_typecode),
&repeat, &width, &status);
} else if (colnum != s->data_col) {
printf("Warning!: DATA column changes between files!\n");
}
}
// Telescope azimuth
fits_get_colnum(s->fitsfiles[ii], 0, "TEL_AZ", &colnum, &status);
if (status==COL_NOT_FOUND) {
s->azimuth = 0.0;
status = 0; // Reset status
} else {
fits_read_col(s->fitsfiles[ii], TFLOAT, colnum,
1L, 1L, 1L, 0, &ftmp, &anynull, &status);
if (ii==0) s->azimuth = (double) ftmp;
}
// Telescope zenith angle
fits_get_colnum(s->fitsfiles[ii], 0, "TEL_ZEN", &colnum, &status);
if (status==COL_NOT_FOUND) {
s->zenith_ang = 0.0;
status = 0; // Reset status
} else {
fits_read_col(s->fitsfiles[ii], TFLOAT, colnum,
1L, 1L, 1L, 0, &ftmp, &anynull, &status);
if (ii==0) s->zenith_ang = (double) ftmp;
}
// Observing frequencies
fits_get_colnum(s->fitsfiles[ii], 0, "DAT_FREQ", &colnum, &status);
if (status==COL_NOT_FOUND) {
printf("Warning!: Can't find the channel freq column!\n");
status = 0; // Reset status
} else {
int jj;
float *freqs = (float *)malloc(sizeof(float) * s->num_channels);
fits_read_col(s->fitsfiles[ii], TFLOAT, colnum, 1L, 1L,
s->num_channels, 0, freqs, &anynull, &status);
if (ii==0) {
s->df = freqs[1]-freqs[0];
s->lo_freq = freqs[0];
s->hi_freq = freqs[s->num_channels-1];
// Now check that the channel spacing is the same throughout
for (jj = 0 ; jj < s->num_channels - 1 ; jj++) {
ftmp = freqs[jj+1] - freqs[jj];
if (fabs(ftmp - s->df) > 1e-7)
printf("Warning!: Channel spacing changes in file %d!\n", ii);
}
} else {
ftmp = fabs(s->df-(freqs[1]-freqs[0]));
if (ftmp > 1e-7)
printf("Warning!: Channel spacing changes between files!\n");
ftmp = fabs(s->lo_freq-freqs[0]);
if (ftmp > 1e-7)
printf("Warning!: Low channel changes between files!\n");
ftmp = fabs(s->hi_freq-freqs[s->num_channels-1]);
if (ftmp > 1e-7)
printf("Warning!: High channel changes between files!\n");
}
free(freqs);
}
// Data weights
fits_get_colnum(s->fitsfiles[ii], 0, "DAT_WTS", &colnum, &status);
if (status==COL_NOT_FOUND) {
printf("Warning!: Can't find the channel weights!\n");
status = 0; // Reset status
} else {
if (s->apply_weight < 0) { // Use the data to decide
int jj;
if (ii==0) {
s->dat_wts_col = colnum;
} else if (colnum != s->dat_wts_col) {
printf("Warning!: DAT_WTS column changes between files!\n");
}
float *fvec = (float *)malloc(sizeof(float) * s->num_channels);
fits_read_col(s->fitsfiles[ii], TFLOAT, s->dat_wts_col, 1L, 1L,
s->num_channels, 0, fvec, &anynull, &status);
for (jj = 0 ; jj < s->num_channels ; jj++) {
// If the weights are not 1, apply them
if (fvec[jj] != 1.0) {
s->apply_weight = 1;
break;
}
}
free(fvec);
}
if (s->apply_weight < 0) s->apply_weight = 0; // not needed
}
// Data offsets
fits_get_colnum(s->fitsfiles[ii], 0, "DAT_OFFS", &colnum, &status);
if (status==COL_NOT_FOUND) {
printf("Warning!: Can't find the channel offsets!\n");
status = 0; // Reset status
} else {
if (s->apply_offset < 0) { // Use the data to decide
int jj;
if (ii==0) {
s->dat_offs_col = colnum;
} else if (colnum != s->dat_offs_col) {
printf("Warning!: DAT_OFFS column changes between files!\n");
}
float *fvec = (float *)malloc(sizeof(float) *
s->num_channels * s->num_polns);
fits_read_col(s->fitsfiles[ii], TFLOAT, s->dat_offs_col, 1L, 1L,
s->num_channels * s->num_polns,
0, fvec, &anynull, &status);
for (jj = 0 ; jj < s->num_channels * s->num_polns ; jj++) {
// If the offsets are not 0, apply them
if (fvec[jj] != 0.0) {
s->apply_offset = 1;
break;
}
}
free(fvec);
}
if (s->apply_offset < 0) s->apply_offset = 0; // not needed
}
// Data scalings
fits_get_colnum(s->fitsfiles[ii], 0, "DAT_SCL", &colnum, &status);
if (status==COL_NOT_FOUND) {
printf("Warning!: Can't find the channel scalings!\n");
status = 0; // Reset status
} else {
if (s->apply_scale < 0) { // Use the data to decide
int jj;
if (ii==0) {
s->dat_scl_col = colnum;
} else if (colnum != s->dat_scl_col) {
printf("Warning!: DAT_SCL column changes between files!\n");
}
float *fvec = (float *)malloc(sizeof(float) *
s->num_channels * s->num_polns);
fits_read_col(s->fitsfiles[ii], TFLOAT, colnum, 1L, 1L,
s->num_channels * s->num_polns,
0, fvec, &anynull, &status);
for (jj = 0 ; jj < s->num_channels * s->num_polns ; jj++) {
// If the scales are not 1, apply them
if (fvec[jj] != 1.0) {
s->apply_scale = 1;
break;
}
}
free(fvec);
}
if (s->apply_scale < 0) s->apply_scale = 0; // not needed
}
}
// Compute the samples per file and the amount of padding
// that the _previous_ file has
s->num_pad[ii] = 0;
s->num_spec[ii] = s->spectra_per_subint * s->num_subint[ii];
if (ii > 0) {
if (s->start_spec[ii] > s->N) { // Need padding
s->num_pad[ii-1] = s->start_spec[ii] - s->N;
s->N += s->num_pad[ii-1];
}
}
s->N += s->num_spec[ii];
}
// Convert the position strings into degrees
{
int d, h, m;
double sec;
ra_dec_from_string(s->ra_str, &h, &m, &sec);
s->ra2000 = hms2rad(h, m, sec) * RADTODEG;
ra_dec_from_string(s->dec_str, &d, &m, &sec);
s->dec2000 = dms2rad(d, m, sec) * RADTODEG;
}
// Are the polarizations summed?
if ((strncmp("AA+BB", s->poln_order, 5)==0) ||
(strncmp("INTEN", s->poln_order, 5)==0))
s->summed_polns = 1;
else
s->summed_polns = 0;
// Calculate some others
s->T = s->N * s->dt;
s->orig_df /= (double) s->orig_num_chan;
s->samples_per_spectra = s->num_polns * s->num_channels;
// Note: the following is the number of bytes that will be in
// the returned array from CFITSIO.
// CFITSIO turns bits into bytes when FITS_typecode=1
// and we turn 2-bits or 4-bits into bytes if bits_per_sample < 8
if (s->bits_per_sample < 8)
s->bytes_per_spectra = s->samples_per_spectra;
else
s->bytes_per_spectra = (s->bits_per_sample * s->samples_per_spectra) / 8;
s->samples_per_subint = s->samples_per_spectra * s->spectra_per_subint;
s->bytes_per_subint = s->bytes_per_spectra * s->spectra_per_subint;
// Flip the band?
if (s->hi_freq < s->lo_freq) {
float ftmp = s->hi_freq;
s->hi_freq = s->lo_freq;
s->lo_freq = ftmp;
s->df *= -1.0;
s->apply_flipband = 1;
}
// Compute the bandwidth
s->BW = s->num_channels * s->df;
// Flip the bytes for Parkes FB_1BIT data
if (s->bits_per_sample==1 &&
strcmp(s->telescope, "Parkes")==0 &&
strcmp(s->backend, "FB_1BIT")==0) {
printf("Flipping bit ordering since Parkes FB_1BIT data.\n");
s->flip_bytes = 1;
} else {
s->flip_bytes = 0;
}
// Allocate the buffers
cdatabuffer = gen_bvect(s->bytes_per_subint);
// Following is twice as big because we use it as a ringbuffer too
fdatabuffer = gen_fvect(2 * s->spectra_per_subint * s->num_channels);
s->padvals = gen_fvect(s->num_channels);
for (ii = 0 ; ii < s->num_channels ; ii++)
s->padvals[ii] = 0.0;
offsets = gen_fvect(s->num_channels * s->num_polns);
scales = gen_fvect(s->num_channels * s->num_polns);
weights = gen_fvect(s->num_channels);
// Initialize these if we won't be reading them from the file
if (s->apply_offset==0)
for (ii = 0 ; ii < s->num_channels * s->num_polns ; ii++)
offsets[ii] = 0.0;
if (s->apply_scale==0)
for (ii = 0 ; ii < s->num_channels * s->num_polns ; ii++)
scales[ii] = 1.0;
if (s->apply_weight==0)
for (ii = 0 ; ii < s->num_channels ; ii++)
weights[ii] = 1.0;
}
void fill_psrfits_struct(int numwapps, int numbits, struct HEADERP *h,
struct wappinfo *w, struct psrfits *pf)
{
int slen, ii;
char *cptr;
pf->filenum = 0; // Crucial for initialization
pf->hdr.nsblk = (int) (1.0 / w->dt); // _might_ be a problem...
// Now set values for our hdrinfo structure
strcpy(pf->hdr.telescope, "Arecibo");
cptr = get_hdr_string(h, "obs_type", &slen);
if (strncmp("PULSAR_SEARCH", cptr, slen) == 0) {
strcpy(pf->hdr.obs_mode, "SEARCH");
} else {
printf("Error: Wapp data is not in search format!\n\n");
exit(1);
}
strcpy(pf->hdr.backend, "WAPP");
cptr = get_hdr_string(h, "frontend", &slen);
if(cptr != NULL)
strncpy(pf->hdr.frontend, cptr, slen);
else
strncpy(pf->hdr.frontend, "alfa", 4);
cptr = get_hdr_string(h, "observers", &slen);
strncpy(pf->hdr.observer, cptr, slen);
cptr = get_hdr_string(h, "project_id", &slen);
strncpy(pf->hdr.project_id, cptr, slen);
cptr = get_hdr_string(h, "src_name", &slen);
strncpy(pf->hdr.source, cptr, slen);
strcpy(pf->hdr.date_obs, w->date_obs);
pf->hdr.scanlen = get_hdr_double(h, "obs_time");
strcpy(pf->hdr.poln_type, "LIN"); // set based on known receivers
if (get_hdr_int(h, "sum")) {
strcpy(pf->hdr.poln_order, "AA+BB");
pf->hdr.summed_polns = 1;
} else if (w->numifs == 1) {
strcpy(pf->hdr.poln_order, "AA");
pf->hdr.summed_polns = 0;
}
strcpy(pf->hdr.track_mode, "TRACK"); // Potentially not-true?
strcpy(pf->hdr.cal_mode, "OFF"); // Potentially not-true?
strcpy(pf->hdr.feed_mode, "FA"); // check this...
pf->hdr.beamnum = 0;
if (get_hdr_int(h, "isalfa"))
pf->hdr.beamnum = w->beamnum;
pf->hdr.dt = w->dt;
pf->hdr.fctr = w->fctr + 0.5 * (numwapps - 1.0) * w->BW;
pf->hdr.BW = w->BW * numwapps;
pf->hdr.beam_FWHM = beam_FWHM(pf->hdr.fctr, 300.0);
pf->hdr.nchan = w->numchans * numwapps;
pf->hdr.orig_nchan = w->numchans * numwapps;
pf->hdr.orig_df = pf->hdr.df = pf->hdr.BW / pf->hdr.nchan;
pf->hdr.nbits = numbits;
pf->hdr.npol = w->numifs;
pf->hdr.MJD_epoch = w->MJD_epoch;
pf->hdr.start_day = (int) (w->MJD_epoch);
pf->hdr.start_sec = (w->MJD_epoch - pf->hdr.start_day) * 86400.0;
pf->hdr.scan_number = get_hdr_int(h, "scan_number");
pf->hdr.ra2000 = w->ra;
dec2hms(pf->hdr.ra_str, pf->hdr.ra2000 / 15.0, 0);
pf->hdr.dec2000 = w->dec;
dec2hms(pf->hdr.dec_str, pf->hdr.dec2000, 1);
pf->hdr.azimuth = get_hdr_double(h, "start_az");
pf->hdr.zenith_ang = get_hdr_double(h, "start_za");
pf->hdr.rcvr_polns = 2;
pf->hdr.offset_subint = 0;
pf->hdr.onlyI = 0;
pf->hdr.ds_time_fact = 1;
pf->hdr.ds_freq_fact = 1;
pf->hdr.chan_dm = 0.0;
pf->hdr.fd_hand = pf->hdr.be_phase = 0; // This is almost certainly not correct
pf->hdr.fd_sang = pf->hdr.fd_xyph = 0.0; // This is almost certainly not correct
pf->hdr.feed_angle = 0.0; // This is almost certainly not correct
pf->hdr.cal_freq = pf->hdr.cal_dcyc = pf->hdr.cal_phs = 0.0; // ditto
// Now set values for our subint structure
pf->sub.tel_az = get_hdr_double(h, "start_az");
pf->sub.tel_zen = get_hdr_double(h, "start_za");
pf->sub.lst = get_hdr_double(h, "start_lst");
pf->hdr.start_lst = pf->sub.lst;
pf->sub.tsubint = pf->hdr.nsblk * pf->hdr.dt;
pf->sub.ra = pf->hdr.ra2000;
pf->sub.dec = pf->hdr.dec2000;
pf->sub.offs = 0.5 * pf->sub.tsubint;
slaEqgal(pf->hdr.ra2000 * DEGTORAD, pf->hdr.dec2000 * DEGTORAD,
&pf->sub.glon, &pf->sub.glat);
pf->sub.glon *= RADTODEG;
pf->sub.glat *= RADTODEG;
// The following three are unknown or hard to get, I think (SMR)
pf->sub.feed_ang = 0.0;
pf->sub.pos_ang = 0.0;
pf->sub.par_ang = 0.0;
pf->sub.bytes_per_subint = (pf->hdr.nbits * pf->hdr.nchan *
pf->hdr.npol * pf->hdr.nsblk) / 8;
pf->sub.FITS_typecode = TBYTE; // 11 = byte
// Create and initialize the subint arrays
pf->sub.dat_freqs = gen_fvect(pf->hdr.nchan);
pf->sub.dat_weights = gen_fvect(pf->hdr.nchan);
for (ii = 0; ii < pf->hdr.nchan; ii++) {
pf->sub.dat_freqs[ii] = w->lofreq + ii * pf->hdr.df;
pf->sub.dat_weights[ii] = 1.0;
}
// The following are re-set to try to preserve the band shape later
pf->sub.dat_offsets = gen_fvect(pf->hdr.nchan * pf->hdr.npol);
pf->sub.dat_scales = gen_fvect(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 the raw data block that will be updated
// for each row of the PSRFITS file
pf->sub.data = gen_bvect(pf->sub.bytes_per_subint);
}
int prep_subbands(float *fdata, float *rawdata, int *delays, int numsubbands,
struct spectra_info *s, int transpose,
int *maskchans, int *nummasked, mask * obsmask)
// This routine preps a block of raw spectra for subbanding. It uses
// dispersion delays in 'delays' to de-disperse the data into
// 'numsubbands' subbands. It stores the resulting data in vector
// 'fdata' of length 'numsubbands' * 's->spectra_per_subint'. The low
// freq subband is stored first, then the next highest subband etc,
// with 's->spectra_per_subint' floating points per subband. It
// returns the # of points read if succesful, 0 otherwise.
// 'maskchans' is an array of length numchans which contains a list of
// the number of channels that were masked. The # of channels masked
// is returned in 'nummasked'. 'obsmask' is the mask structure to use
// for masking. If 'transpose'==0, the data will be kept in time
// order instead of arranged by subband as above.
{
int ii, jj, trtn, offset;
double starttime = 0.0;
static float *tmpswap, *rawdata1, *rawdata2;
static float *currentdata, *lastdata;
static unsigned char *move;
static int firsttime = 1, move_size = 0, mask = 0;
*nummasked = 0;
if (firsttime) {
if (obsmask->numchan)
mask = 1;
move_size = (s->spectra_per_subint + numsubbands) / 2;
move = gen_bvect(move_size);
rawdata1 = gen_fvect(s->spectra_per_subint * s->num_channels);
rawdata2 = gen_fvect(s->spectra_per_subint * s->num_channels);
currentdata = rawdata1;
lastdata = rawdata2;
}
/* Read and de-disperse */
memcpy(currentdata, rawdata, s->spectra_per_subint * s->num_channels * sizeof(float));
starttime = currentspectra * s->dt; // or -1 subint?
if (mask)
*nummasked = check_mask(starttime, s->time_per_subint, obsmask, maskchans);
/* Clip nasty RFI if requested and we're not masking all the channels*/
if ((s->clip_sigma > 0.0) && !(mask && (*nummasked == -1)))
clip_times(currentdata, s->spectra_per_subint, s->num_channels, s->clip_sigma, s->padvals);
if (mask) {
if (*nummasked == -1) { /* If all channels are masked */
for (ii = 0; ii < s->spectra_per_subint; ii++)
memcpy(currentdata + ii * s->num_channels,
s->padvals, s->num_channels * sizeof(float));
} else if (*nummasked > 0) { /* Only some of the channels are masked */
int channum;
for (ii = 0; ii < s->spectra_per_subint; ii++) {
offset = ii * s->num_channels;
for (jj = 0; jj < *nummasked; jj++) {
channum = maskchans[jj];
currentdata[offset + channum] = s->padvals[channum];
}
}
}
}
// In mpiprepsubband, the nodes do not call read_subbands() where
// currentspectra gets incremented.
if (using_MPI) currentspectra += s->spectra_per_subint;
if (firsttime) {
SWAP(currentdata, lastdata);
firsttime = 0;
return 0;
} else {
dedisp_subbands(currentdata, lastdata, s->spectra_per_subint, s->num_channels,
delays, numsubbands, fdata);
SWAP(currentdata, lastdata);
/* Transpose the data into vectors in the result array */
if (transpose) {
if ((trtn = transpose_float(fdata, s->spectra_per_subint, numsubbands,
move, move_size)) < 0)
printf("Error %d in transpose_float().\n", trtn);
}
return s->spectra_per_subint;
}
}
void fill_psrfits_struct(int numbits, struct psrfits *pf, float dt, char* source, int nchantot, float df, int imjd, int smjd, float offs, char* ra, char* dec, float lofreq, char *basename)
{
int ii;
pf->filenum = 0; // Crucial for initialization
strcpy(pf->basefilename, basename);
pf->hdr.nsblk = (int) (roundf(1.0 / dt));
// Now set values for our hdrinfo structure
strcpy(pf->hdr.telescope, "VLA");
strcpy(pf->hdr.obs_mode, "SEARCH");
strcpy(pf->hdr.backend, "YUPPI");
strcpy(pf->hdr.frontend, "HFF");
strcpy(pf->hdr.observer, " ");
strcpy(pf->hdr.project_id, " ");
strcpy(pf->hdr.source, source);
strcpy(pf->hdr.date_obs, " ");
//pf->hdr.scanlen = get_hdr_double(h, "obs_time");
strcpy(pf->hdr.poln_type, "LIN"); // set based on known receivers
strcpy(pf->hdr.poln_order, "AA");
pf->hdr.summed_polns = 0;
strcpy(pf->hdr.track_mode, "TRACK"); // Potentially not-true?
strcpy(pf->hdr.cal_mode, "OFF"); // Potentially not-true?
strcpy(pf->hdr.feed_mode, "FA"); // check this...
pf->hdr.dt = dt;
pf->hdr.fctr = lofreq + (nchantot/2.0 - 0.5)*df;
pf->hdr.BW = nchantot*df;
pf->hdr.beam_FWHM = beam_FWHM(pf->hdr.fctr, 34.0);
pf->hdr.nchan = nchantot;
pf->hdr.orig_nchan = nchantot;
pf->hdr.df = df;
pf->hdr.orig_df = df;
pf->hdr.nbits = numbits;
pf->hdr.npol = 1;
pf->hdr.start_day = imjd;
pf->hdr.start_sec = smjd;
pf->hdr.MJD_epoch = (long double)imjd + ((long double)smjd + (long double)offs)/((long double)(24*3600));
pf->hdr.scan_number = 0;
strcpy(pf->hdr.ra_str, ra);
strcpy(pf->hdr.dec_str, dec);
pf->hdr.ra2000 = 0.0;
pf->hdr.dec2000 = 0.0;
pf->hdr.azimuth = 0.0;
pf->hdr.zenith_ang = 0.0;
pf->hdr.rcvr_polns = 1;
pf->hdr.offset_subint = 0;
pf->hdr.onlyI = 0;
pf->hdr.ds_time_fact = 1;
pf->hdr.ds_freq_fact = 1;
pf->hdr.chan_dm = 0.0;
pf->hdr.fd_hand = 1.0;
pf->hdr.be_phase = 0; // This is almost certainly not correct
pf->hdr.fd_sang = pf->hdr.fd_xyph = 0.0; // This is almost certainly not correct
pf->hdr.feed_angle = 0.0; // This is almost certainly not correct
pf->hdr.cal_freq = pf->hdr.cal_dcyc = pf->hdr.cal_phs = 0.0; // ditto
// Now set values for our subint structure
pf->sub.tel_az = 0.0;
pf->sub.tel_zen = 0.0;
pf->sub.lst = 0.0;
pf->sub.tsubint = pf->hdr.nsblk * pf->hdr.dt;
pf->sub.ra = pf->hdr.ra2000;
pf->sub.dec = pf->hdr.dec2000;
pf->sub.offs = 0.5 * pf->sub.tsubint;
//slaEqgal(pf->hdr.ra2000 * DEGTORAD, pf->hdr.dec2000 * DEGTORAD,
// &pf->sub.glon, &pf->sub.glat);
//pf->sub.glon *= RADTODEG;
//pf->sub.glat *= RADTODEG;
// The following three are unknown or hard to get, I think (SMR)
pf->sub.feed_ang = 0.0;
pf->sub.pos_ang = 0.0;
pf->sub.par_ang = 0.0;
pf->sub.bytes_per_subint = (pf->hdr.nbits/8) * pf->hdr.nchan * pf->hdr.npol * pf->hdr.nsblk;
pf->sub.FITS_typecode = TBYTE; // newer, back to bytes
//pf->sub.FITS_typecode = TFLOAT; // new
//pf->sub.FITS_typecode = TBYTE; // 11 = byte
// Create and initialize the subint arrays
pf->sub.dat_freqs = gen_fvect(pf->hdr.nchan);
pf->sub.dat_weights = gen_fvect(pf->hdr.nchan);
for (ii = 0; ii < pf->hdr.nchan; ii++) {
pf->sub.dat_freqs[ii] = lofreq + ii * pf->hdr.df;
pf->sub.dat_weights[ii] = 1.0;
}
// The following are re-set to try to preserve the band shape later
pf->sub.dat_offsets = gen_fvect(pf->hdr.nchan * pf->hdr.npol);
pf->sub.dat_scales = gen_fvect(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 the raw data block that will be updated
// for each row of the PSRFITS file
pf->sub.data = gen_bvect( pf->sub.bytes_per_subint ); // newest
//pf->sub.data = gen_bvect( (pf->sub.bytes_per_subint)/4 ); // newer
//pf->sub.data = gen_fvect( (pf->sub.bytes_per_subint)/4 ); // new
//pf->sub.data = gen_bvect(pf->sub.bytes_per_subint);
}
int main(int argc, char *argv[])
{
int numfiles, ii, numrows, rownum, ichan, itsamp, datidx;
int spec_per_row, status, maxrows;
unsigned long int maxfilesize;
float offset, scale, datum, packdatum, maxval, fulltsubint;
float *datachunk;
FILE **infiles;
struct psrfits pfin, pfout;
Cmdline *cmd;
fitsfile *infits, *outfits;
char outfilename[128], templatename[128], tform[8];
char *pc1, *pc2;
int first = 1, dummy = 0, nclipped;
short int *inrowdata;
unsigned char *outrowdata;
if (argc == 1) {
Program = argv[0];
usage();
exit(1);
}
// Parse the command line using the excellent program Clig
cmd = parseCmdline(argc, argv);
numfiles = cmd->argc;
infiles = (FILE **) malloc(numfiles * sizeof(FILE *));
//Set the max. total size (in bytes) of all rows in an output file,
//leaving some room for PSRFITS header
maxfilesize = (unsigned long int)(cmd->numgb * GB);
maxfilesize = maxfilesize - 1000*KB;
//fprintf(stderr,"cmd->numgb: %f maxfilesize: %ld\n",cmd->numgb,maxfilesize);
#ifdef DEBUG
showOptionValues();
#endif
printf("\n PSRFITS 16-bit to 4-bit Conversion Code\n");
printf(" by J. Deneva, S. Ransom, & S. Chatterjee\n\n");
// Open the input files
status = 0; //fits_close segfaults if this is not initialized
printf("Reading input data from:\n");
for (ii = 0; ii < numfiles; ii++) {
printf(" '%s'\n", cmd->argv[ii]);
//Get the file basename and number from command-line argument
//(code taken from psrfits2fil)
pc2 = strrchr(cmd->argv[ii], '.'); // at .fits
*pc2 = 0; // terminate string
pc1 = pc2 - 1;
while ((pc1 >= cmd->argv[ii]) && isdigit(*pc1))
pc1--;
if (pc1 <= cmd->argv[ii]) { // need at least 1 char before filenum
puts("Illegal input filename. must have chars before the filenumber");
exit(1);
}
pc1++; // we were sitting on "." move to first digit
pfin.filenum = atoi(pc1);
pfin.fnamedigits = pc2 - pc1; // how many digits in filenumbering scheme.
*pc1 = 0; // null terminate the basefilename
strcpy(pfin.basefilename, cmd->argv[ii]);
pfin.initialized = 0; // set to 1 in psrfits_open()
pfin.status = 0;
//(end of code taken from psrfits2fil)
//Open the existing psrfits file
if (psrfits_open(&pfin, READONLY) != 0) {
fprintf(stderr, "error opening file\n");
fits_report_error(stderr, pfin.status);
exit(1);
}
// Create the subint arrays
if (first) {
pfin.sub.dat_freqs = (float *) malloc(sizeof(float) * pfin.hdr.nchan);
pfin.sub.dat_weights = (float *) malloc(sizeof(float) * pfin.hdr.nchan);
pfin.sub.dat_offsets =
(float *) malloc(sizeof(float) * pfin.hdr.nchan * pfin.hdr.npol);
pfin.sub.dat_scales =
(float *) malloc(sizeof(float) * pfin.hdr.nchan * pfin.hdr.npol);
//first is set to 0 after data buffer allocation further below
}
infits = pfin.fptr;
spec_per_row = pfin.hdr.nsblk;
fits_read_key(infits, TINT, "NAXIS2", &dummy, NULL, &status);
pfin.tot_rows = dummy;
numrows = dummy;
//If dealing with 1st input file, create output template
if (ii == 0) {
sprintf(templatename, "%s.template.fits",cmd->outfile);
fits_create_file(&outfits, templatename, &status);
//fprintf(stderr,"pfin.basefilename: %s\n", pfin.basefilename);
//fprintf(stderr,"status: %d\n", status);
//Instead of copying HDUs one by one, can move to the SUBINT
//HDU, and copy all the HDUs preceding it
fits_movnam_hdu(infits, BINARY_TBL, "SUBINT", 0, &status);
fits_copy_file(infits, outfits, 1, 0, 0, &status);
//Copy the SUBINT table header
fits_copy_header(infits, outfits, &status);
fits_flush_buffer(outfits, 0, &status);
//Set NAXIS2 in the output SUBINT table to 0 b/c we haven't
//written any rows yet
dummy = 0;
fits_update_key(outfits, TINT, "NAXIS2", &dummy, NULL, &status);
//Edit the NBITS key
if (DEBUG) {
dummy = 8;
fits_update_key(outfits, TINT, "NBITS", &dummy, NULL, &status);
} else {
fits_update_key(outfits, TINT, "NBITS", &(cmd->numbits), NULL,
&status);
}
//Edit the TFORM17 column: # of data bytes per row
//fits_get_colnum(outfits,1,"DATA",&dummy,&status);
if (DEBUG)
sprintf(tform, "%dB",
pfin.hdr.nsblk * pfin.hdr.nchan * pfin.hdr.npol);
else
sprintf(tform, "%dB", pfin.hdr.nsblk * pfin.hdr.nchan *
pfin.hdr.npol * cmd->numbits / 8);
fits_update_key(outfits, TSTRING, "TTYPE17", "DATA", NULL, &status);
fits_update_key(outfits, TSTRING, "TFORM17", tform, NULL, &status);
//Edit NAXIS1: row width in bytes
fits_read_key(outfits, TINT, "NAXIS1", &dummy, NULL, &status);
if (DEBUG) {
dummy = dummy - pfin.hdr.nsblk * pfin.hdr.nchan *
pfin.hdr.npol * (pfin.hdr.nbits - 8) / 8;
} else {
dummy = dummy - pfin.hdr.nsblk * pfin.hdr.nchan *
pfin.hdr.npol * (pfin.hdr.nbits - cmd->numbits) / 8;
}
fits_update_key(outfits, TINT, "NAXIS1", &dummy, NULL, &status);
//Set the max # of rows per file, based on the requested
//output file size
maxrows = maxfilesize / dummy;
//fprintf(stderr,"maxrows: %d\n",maxrows);
fits_close_file(outfits, &status);
rownum = 0;
}
while (psrfits_read_subint(&pfin, first) == 0) {
fprintf(stderr, "Working on row %d\n", ++rownum);
//If this is the first row, store the length of a full subint
if (ii == 0 && rownum == 1)
fulltsubint = pfin.sub.tsubint;
//If this is the last row and it's partial, drop it.
//(It's pfin.rownum-1 below because the rownum member of the psrfits struct seems to be intended to indicate at the *start* of what row we are, i.e. a row that has not yet been read. In contrast, pfout.rownum indicates how many rows have been written, i.e. at the *end* of what row we are in the output.)
if (pfin.rownum-1 == numrows && fabs(pfin.sub.tsubint - fulltsubint) > pfin.hdr.dt) {
fprintf(stderr,
"Dropping partial row of length %f s (full row is %f s)\n",
pfin.sub.tsubint, fulltsubint);
break;
}
//If we just read in the 1st row, or if we already wrote the last row in the current output file, create a new output file
if ((ii == 0 && rownum == 1) || pfout.rownum == maxrows) {
//Create new output file from the template
pfout.fnamedigits = pfin.fnamedigits;
if(ii == 0)
pfout.filenum = pfin.filenum;
else
pfout.filenum++;
sprintf(outfilename, "%s.%0*d.fits", cmd->outfile, pfout.fnamedigits, pfout.filenum);
fits_create_template(&outfits, outfilename, templatename, &status);
//fprintf(stderr,"After fits_create_template, status: %d\n",status);
fits_close_file(outfits, &status);
//Now reopen the file so that the pfout structure is initialized
pfout.status = 0;
pfout.initialized = 0;
sprintf(pfout.basefilename, "%s.", cmd->outfile);
if (psrfits_open(&pfout, READWRITE) != 0) {
fprintf(stderr, "error opening file\n");
fits_report_error(stderr, pfout.status);
exit(1);
}
outfits = pfout.fptr;
maxval = pow(2, cmd->numbits) - 1;
pfout.rows_per_file = maxrows;
//fprintf(stderr, "maxval: %f\n", maxval);
//fprintf(stderr, "pfout.rows_per_file: %d\n",pfout.rows_per_file);
//These are not initialized in psrfits_open but are needed
//in psrfits_write_subint (not obvious what are the corresponding
//fields in any of the psrfits table headers)
pfout.hdr.ds_freq_fact = 1;
pfout.hdr.ds_time_fact = 1;
}
//Copy the subint struct from pfin to pfout, but correct
//elements that are not the same
pfout.sub = pfin.sub; //this copies array pointers too
pfout.sub.bytes_per_subint =
pfin.sub.bytes_per_subint * pfout.hdr.nbits / pfin.hdr.nbits;
pfout.sub.dataBytesAlloced = pfout.sub.bytes_per_subint;
pfout.sub.FITS_typecode = TBYTE;
if (first) {
//Allocate scaling buffer and output buffer
datachunk = gen_fvect(spec_per_row);
outrowdata = gen_bvect(pfout.sub.bytes_per_subint);
first = 0;
}
pfout.sub.data = outrowdata;
inrowdata = (short int *) pfin.sub.data;
nclipped = 0;
// Loop over all the channels:
for (ichan = 0; ichan < pfout.hdr.nchan * pfout.hdr.npol; ichan++) {
// Populate datachunk[] by picking out all time samples for ichan
for (itsamp = 0; itsamp < spec_per_row; itsamp++)
datachunk[itsamp] = (float) (inrowdata[ichan + itsamp *
pfout.hdr.nchan *
pfout.hdr.npol]);
// Compute the statistics here, and put the offsets and scales in
// pf.sub.dat_offsets[] and pf.sub.dat_scales[]
if (rescale(datachunk, spec_per_row, cmd->numbits, &offset, &scale)
!= 0) {
printf("Rescale routine failed!\n");
return (-1);
}
pfout.sub.dat_offsets[ichan] = offset;
pfout.sub.dat_scales[ichan] = scale;
// Since we have the offset and scale ready, rescale the data:
for (itsamp = 0; itsamp < spec_per_row; itsamp++) {
datum = (scale == 0.0) ? 0.0 :
roundf((datachunk[itsamp] - offset) / scale);
if (datum < 0.0) {
datum = 0;
nclipped++;
} else if (datum > maxval) {
datum = maxval;
nclipped++;
}
inrowdata[ichan + itsamp * pfout.hdr.nchan * pfout.hdr.npol] =
(short int) datum;
}
// Now inrowdata[ichan] contains rescaled ints.
}
// Then do the conversion and store the
// results in pf.sub.data[]
if (cmd->numbits == 8 || DEBUG) {
for (itsamp = 0; itsamp < spec_per_row; itsamp++) {
datidx = itsamp * pfout.hdr.nchan * pfout.hdr.npol;
for (ichan = 0; ichan < pfout.hdr.nchan * pfout.hdr.npol;
ichan++, datidx++) {
pfout.sub.data[datidx] = (unsigned char) inrowdata[datidx];
}
}
} else if (cmd->numbits == 4) {
for (itsamp = 0; itsamp < spec_per_row; itsamp++) {
datidx = itsamp * pfout.hdr.nchan * pfout.hdr.npol;
for (ichan = 0; ichan < pfout.hdr.nchan * pfout.hdr.npol;
ichan += 2, datidx += 2) {
packdatum = inrowdata[datidx] * 16 + inrowdata[datidx + 1];
pfout.sub.data[datidx / 2] = (unsigned char) packdatum;
}
}
} else {
fprintf(stderr, "Only 4 or 8-bit output formats supported.\n");
fprintf(stderr, "Bits per sample requested: %d\n", cmd->numbits);
exit(1);
}
//pfout.sub.offs = (pfout.tot_rows+0.5) * pfout.sub.tsubint;
fprintf(stderr, "nclipped: %d fraction clipped: %f\n", nclipped,
(float) nclipped / (pfout.hdr.nchan * pfout.hdr.npol *
pfout.hdr.nsblk));
// Now write the row.
status = psrfits_write_subint(&pfout);
if (status) {
printf("\nError (%d) writing PSRFITS...\n\n", status);
break;
}
//If current output file has reached the max # of rows, close it
if (pfout.rownum == maxrows)
fits_close_file(outfits, &status);
}
//Close the files
fits_close_file(infits, &status);
}
fits_close_file(outfits, &status);
// Free the structure arrays too...
free(datachunk);
free(infiles);
free(pfin.sub.dat_freqs);
free(pfin.sub.dat_weights);
free(pfin.sub.dat_offsets);
free(pfin.sub.dat_scales);
free(pfin.sub.data);
free(pfout.sub.data);
free(pfin.sub.stat);
return 0;
}