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 output_fundamentals(fourierprops * props, GSList * list,
accelobs * obs, infodata * idata)
{
double accel = 0.0, accelerr = 0.0, coherent_pow;
int ii, jj, numcols = 12, numcands, *width, *error;
int widths[12] = { 4, 5, 6, 8, 4, 16, 15, 15, 15, 11, 15, 20 };
int errors[12] = { 0, 0, 0, 0, 0, 1, 1, 2, 1, 2, 2, 0 };
char tmpstr[30], ctrstr[30], *notes;
accelcand *cand;
GSList *listptr;
rzwerrs errs;
static char **title;
static char *titles1[] = { "", "", "Summed", "Coherent", "Num", "Period",
"Frequency", "FFT 'r'", "Freq Deriv", "FFT 'z'",
"Accel", ""
};
static char *titles2[] = { "Cand", "Sigma", "Power", "Power", "Harm", "(ms)",
"(Hz)", "(bin)", "(Hz/s)", "(bins)",
"(m/s^2)", "Notes"
};
numcands = g_slist_length(list);
listptr = list;
/* Close the old work file and open the cand file */
if (!obs->dat_input)
fclose(obs->workfile); /* Why is this here? -A */
obs->workfile = chkfopen(obs->accelnm, "w");
/* Set our candidate notes to all spaces */
notes = (char *) malloc(numcands * widths[numcols - 1]);
memset(notes, ' ', numcands * widths[numcols - 1]);
/* Compare the candidates with the pulsar database */
if (dms2rad(idata->ra_h, idata->ra_m, idata->ra_s) != 0.0 &&
hms2rad(idata->dec_d, idata->dec_m, idata->dec_s) != 0.0) {
for (ii = 0; ii < numcands; ii++) {
comp_psr_to_cand(props + ii, idata, notes + ii * 20, 0);
}
}
/* Compare the candidates with themselves */
compare_rzw_cands(props, numcands, notes);
/* Print the header */
width = widths;
title = titles1;
for (ii = 0; ii < numcols - 1; ii++) {
center_string(ctrstr, *title++, *width++);
fprintf(obs->workfile, "%s ", ctrstr);
}
center_string(ctrstr, *title++, *width++);
fprintf(obs->workfile, "%s\n", ctrstr);
width = widths;
title = titles2;
for (ii = 0; ii < numcols - 1; ii++) {
center_string(ctrstr, *title++, *width++);
fprintf(obs->workfile, "%s ", ctrstr);
}
center_string(ctrstr, *title++, *width++);
fprintf(obs->workfile, "%s\n", ctrstr);
width = widths;
for (ii = 0; ii < numcols - 1; ii++) {
memset(tmpstr, '-', *width);
tmpstr[*width++] = '\0';
fprintf(obs->workfile, "%s--", tmpstr);
}
memset(tmpstr, '-', *width++);
tmpstr[widths[ii]] = '\0';
fprintf(obs->workfile, "%s\n", tmpstr);
/* Print the fundamentals */
for (ii = 0; ii < numcands; ii++) {
width = widths;
error = errors;
cand = (accelcand *) (listptr->data);
calc_rzwerrs(props + ii, obs->T, &errs);
{ /* Calculate the coherently summed power */
double coherent_r = 0.0, coherent_i = 0.0;
double phs0, phscorr, amp;
rderivs harm;
/* These phase calculations assume the fundamental is best */
/* Better to irfft them and check the amplitude */
phs0 = cand->derivs[0].phs;
for (jj = 0; jj < cand->numharm; jj++) {
harm = cand->derivs[jj];
if (obs->nph > 0.0)
amp = sqrt(harm.pow / obs->nph);
else
amp = sqrt(harm.pow / harm.locpow);
phscorr = phs0 - fmod((jj + 1.0) * phs0, TWOPI);
coherent_r += amp * cos(harm.phs + phscorr);
coherent_i += amp * sin(harm.phs + phscorr);
}
coherent_pow = coherent_r * coherent_r + coherent_i * coherent_i;
}
sprintf(tmpstr, "%-4d", ii + 1);
center_string(ctrstr, tmpstr, *width++);
error++;
fprintf(obs->workfile, "%s ", ctrstr);
sprintf(tmpstr, "%.2f", cand->sigma);
center_string(ctrstr, tmpstr, *width++);
error++;
fprintf(obs->workfile, "%s ", ctrstr);
sprintf(tmpstr, "%.2f", cand->power);
center_string(ctrstr, tmpstr, *width++);
error++;
fprintf(obs->workfile, "%s ", ctrstr);
sprintf(tmpstr, "%.2f", coherent_pow);
center_string(ctrstr, tmpstr, *width++);
error++;
fprintf(obs->workfile, "%s ", ctrstr);
sprintf(tmpstr, "%d", cand->numharm);
center_string(ctrstr, tmpstr, *width++);
error++;
fprintf(obs->workfile, "%s ", ctrstr);
write_val_with_err(obs->workfile, errs.p * 1000.0, errs.perr * 1000.0,
*error++, *width++);
write_val_with_err(obs->workfile, errs.f, errs.ferr, *error++, *width++);
write_val_with_err(obs->workfile, props[ii].r, props[ii].rerr,
*error++, *width++);
write_val_with_err(obs->workfile, errs.fd, errs.fderr, *error++, *width++);
write_val_with_err(obs->workfile, props[ii].z, props[ii].zerr,
*error++, *width++);
accel = props[ii].z * SOL / (obs->T * obs->T * errs.f);
accelerr = props[ii].zerr * SOL / (obs->T * obs->T * errs.f);
write_val_with_err(obs->workfile, accel, accelerr, *error++, *width++);
fprintf(obs->workfile, " %.20s\n", notes + ii * 20);
fflush(obs->workfile);
listptr = listptr->next;
}
fprintf(obs->workfile, "\n\n");
free(notes);
}
int main(int argc, char *argv[])
{
/* Any variable that begins with 't' means topocentric */
/* Any variable that begins with 'b' means barycentric */
FILE **outfiles = NULL;
float **outdata;
double dtmp, *dms, avgdm = 0.0, dsdt = 0, maxdm;
double *dispdt, tlotoa = 0.0, blotoa = 0.0, BW_ddelay = 0.0;
double max = -9.9E30, min = 9.9E30, var = 0.0, avg = 0.0;
double *btoa = NULL, *ttoa = NULL, avgvoverc = 0.0;
char obs[3], ephem[10], rastring[50], decstring[50];
long totnumtowrite, totwrote = 0, padwrote = 0, datawrote = 0;
int *idispdt, **offsets;
int ii, jj, numadded = 0, numremoved = 0, padding = 0, good_inputs = 1;
int numbarypts = 0, numread = 0, numtowrite = 0;
int padtowrite = 0, statnum = 0;
int numdiffbins = 0, *diffbins = NULL, *diffbinptr = NULL, good_padvals = 0;
double local_lodm;
char *datafilenm, *outpath, *outfilenm, *hostname;
struct spectra_info s;
infodata idata;
mask obsmask;
MPI_Init(&argc, &argv);
MPI_Comm_size(MPI_COMM_WORLD, &numprocs);
MPI_Comm_rank(MPI_COMM_WORLD, &myid);
#ifdef _OPENMP
omp_set_num_threads(1); // Explicitly turn off OpenMP
#endif
set_using_MPI();
{
FILE *hostfile;
char tmpname[100];
int retval;
hostfile = chkfopen("/etc/hostname", "r");
retval = fscanf(hostfile, "%s\n", tmpname);
if (retval==0) {
printf("Warning: error reading /etc/hostname on proc %d\n", myid);
}
hostname = (char *) calloc(strlen(tmpname) + 1, 1);
memcpy(hostname, tmpname, strlen(tmpname));
fclose(hostfile);
}
/* Call usage() if we have no command line arguments */
if (argc == 1) {
if (myid == 0) {
Program = argv[0];
usage();
}
MPI_Finalize();
exit(1);
}
make_maskbase_struct();
make_spectra_info_struct();
/* Parse the command line using the excellent program Clig */
cmd = parseCmdline(argc, argv);
spectra_info_set_defaults(&s);
// If we are zeroDMing, make sure that clipping is off.
if (cmd->zerodmP) cmd->noclipP = 1;
s.clip_sigma = cmd->clip;
if (cmd->noclipP) {
cmd->clip = 0.0;
s.clip_sigma = 0.0;
}
if (cmd->ifsP) {
// 0 = default or summed, 1-4 are possible also
s.use_poln = cmd->ifs + 1;
}
if (!cmd->numoutP)
cmd->numout = LONG_MAX;
#ifdef DEBUG
showOptionValues();
#endif
if (myid == 0) { /* Master node only */
printf("\n\n");
printf(" Parallel Pulsar Subband De-dispersion Routine\n");
printf(" by Scott M. Ransom\n\n");
s.filenames = cmd->argv;
s.num_files = cmd->argc;
s.clip_sigma = cmd->clip;
// -1 causes the data to determine if we use weights, scales, &
// offsets for PSRFITS or flip the band for any data type where
// we can figure that out with the data
s.apply_flipband = (cmd->invertP) ? 1 : -1;
s.apply_weight = (cmd->noweightsP) ? 0 : -1;
s.apply_scale = (cmd->noscalesP) ? 0 : -1;
s.apply_offset = (cmd->nooffsetsP) ? 0 : -1;
s.remove_zerodm = (cmd->zerodmP) ? 1 : 0;
if (RAWDATA) {
if (cmd->filterbankP) s.datatype = SIGPROCFB;
else if (cmd->psrfitsP) s.datatype = PSRFITS;
else if (cmd->pkmbP) s.datatype = SCAMP;
else if (cmd->bcpmP) s.datatype = BPP;
else if (cmd->wappP) s.datatype = WAPP;
else if (cmd->spigotP) s.datatype = SPIGOT;
} else { // Attempt to auto-identify the data
identify_psrdatatype(&s, 1);
if (s.datatype==SIGPROCFB) cmd->filterbankP = 1;
else if (s.datatype==PSRFITS) cmd->psrfitsP = 1;
else if (s.datatype==SCAMP) cmd->pkmbP = 1;
else if (s.datatype==BPP) cmd->bcpmP = 1;
else if (s.datatype==WAPP) cmd->wappP = 1;
else if (s.datatype==SPIGOT) cmd->spigotP = 1;
else if (s.datatype==SUBBAND) insubs = 1;
else {
printf("\nError: Unable to identify input data files. Please specify type.\n\n");
good_inputs = 0;
}
}
// So far we can only handle PSRFITS, filterbank, and subbands
if (s.datatype!=PSRFITS &&
s.datatype!=SIGPROCFB &&
s.datatype!=SUBBAND) good_inputs = 0;
// For subbanded data
if (!RAWDATA) s.files = (FILE **)malloc(sizeof(FILE *) * s.num_files);
if (good_inputs && (RAWDATA || insubs)) {
char description[40];
psrdatatype_description(description, s.datatype);
if (s.num_files > 1)
printf("Reading %s data from %d files:\n", description, s.num_files);
else
printf("Reading %s data from 1 file:\n", description);
for (ii = 0; ii < s.num_files; ii++) {
printf(" '%s'\n", cmd->argv[ii]);
if (insubs) s.files[ii] = chkfopen(s.filenames[ii], "rb");
}
printf("\n");
if (RAWDATA) {
read_rawdata_files(&s);
print_spectra_info_summary(&s);
spectra_info_to_inf(&s, &idata);
} else { // insubs
char *root, *suffix;
cmd->nsub = s.num_files;
s.N = chkfilelen(s.files[0], sizeof(short));
s.start_subint = gen_ivect(1);
s.num_subint = gen_ivect(1);
s.start_MJD = (long double *)malloc(sizeof(long double));
s.start_spec = (long long *)malloc(sizeof(long long));
s.num_spec = (long long *)malloc(sizeof(long long));
s.num_pad = (long long *)malloc(sizeof(long long));
s.start_spec[0] = 0L;
s.start_subint[0] = 0;
s.num_spec[0] = s.N;
s.num_subint[0] = s.N / SUBSBLOCKLEN;
s.num_pad[0] = 0L;
s.padvals = gen_fvect(s.num_files);
for (ii = 0 ; ii < ii ; ii++)
s.padvals[ii] = 0.0;
if (split_root_suffix(s.filenames[0], &root, &suffix) == 0) {
printf("\nError: The input filename (%s) must have a suffix!\n\n", s.filenames[0]);
exit(1);
}
if (strncmp(suffix, "sub", 3) == 0) {
char *tmpname;
tmpname = calloc(strlen(root) + 10, 1);
sprintf(tmpname, "%s.sub", root);
readinf(&idata, tmpname);
free(tmpname);
strncpy(s.telescope, idata.telescope, 40);
strncpy(s.backend, idata.instrument, 40);
strncpy(s.observer, idata.observer, 40);
strncpy(s.source, idata.object, 40);
s.ra2000 = hms2rad(idata.ra_h, idata.ra_m,
idata.ra_s) * RADTODEG;
s.dec2000 = dms2rad(idata.dec_d, idata.dec_m,
idata.dec_s) * RADTODEG;
ra_dec_to_string(s.ra_str,
idata.ra_h, idata.ra_m, idata.ra_s);
ra_dec_to_string(s.dec_str,
idata.dec_d, idata.dec_m, idata.dec_s);
s.num_channels = idata.num_chan;
s.start_MJD[0] = idata.mjd_i + idata.mjd_f;
s.dt = idata.dt;
s.T = s.N * s.dt;
s.lo_freq = idata.freq;
s.df = idata.chan_wid;
s.hi_freq = s.lo_freq + (s.num_channels - 1.0) * s.df;
s.BW = s.num_channels * s.df;
s.fctr = s.lo_freq - 0.5 * s.df + 0.5 * s.BW;
s.beam_FWHM = idata.fov / 3600.0;
s.spectra_per_subint = SUBSBLOCKLEN;
print_spectra_info_summary(&s);
} else {
printf("\nThe input files (%s) must be subbands! (i.e. *.sub##)\n\n",
cmd->argv[0]);
MPI_Finalize();
exit(1);
}
free(root);
free(suffix);
}
}
}
// If we don't have good input data, exit
MPI_Bcast(&good_inputs, 1, MPI_INT, 0, MPI_COMM_WORLD);
if (!good_inputs) {
MPI_Finalize();
exit(1);
}
MPI_Bcast(&insubs, 1, MPI_INT, 0, MPI_COMM_WORLD);
if (insubs)
cmd->nsub = cmd->argc;
/* Determine the output file names and open them */
local_numdms = cmd->numdms / (numprocs - 1);
dms = gen_dvect(local_numdms);
if (cmd->numdms % (numprocs - 1)) {
if (myid == 0)
printf
("\nThe number of DMs must be divisible by (the number of processors - 1).\n\n");
MPI_Finalize();
exit(1);
}
local_lodm = cmd->lodm + (myid - 1) * local_numdms * cmd->dmstep;
split_path_file(cmd->outfile, &outpath, &outfilenm);
datafilenm = (char *) calloc(strlen(outfilenm) + 20, 1);
if (myid > 0) {
if (chdir(outpath) == -1) {
printf("\nProcess %d on %s cannot chdir() to '%s'. Exiting.\n\n",
myid, hostname, outpath);
MPI_Finalize();
exit(1);
}
outfiles = (FILE **) malloc(local_numdms * sizeof(FILE *));
for (ii = 0; ii < local_numdms; ii++) {
dms[ii] = local_lodm + ii * cmd->dmstep;
avgdm += dms[ii];
sprintf(datafilenm, "%s_DM%.2f.dat", outfilenm, dms[ii]);
outfiles[ii] = chkfopen(datafilenm, "wb");
}
avgdm /= local_numdms;
}
// Broadcast the raw data information
broadcast_spectra_info(&s, myid);
if (myid > 0) {
spectra_info_to_inf(&s, &idata);
if (s.datatype==SIGPROCFB) cmd->filterbankP = 1;
else if (s.datatype==PSRFITS) cmd->psrfitsP = 1;
else if (s.datatype==SCAMP) cmd->pkmbP = 1;
else if (s.datatype==BPP) cmd->bcpmP = 1;
else if (s.datatype==WAPP) cmd->wappP = 1;
else if (s.datatype==SPIGOT) cmd->spigotP = 1;
else if (s.datatype==SUBBAND) insubs = 1;
}
s.filenames = cmd->argv;
/* Read an input mask if wanted */
if (myid > 0) {
int numpad = s.num_channels;
if (insubs)
numpad = s.num_files;
s.padvals = gen_fvect(numpad);
for (ii = 0 ; ii < numpad ; ii++)
s.padvals[ii] = 0.0;
}
if (cmd->maskfileP) {
if (myid == 0) {
read_mask(cmd->maskfile, &obsmask);
printf("Read mask information from '%s'\n\n", cmd->maskfile);
good_padvals = determine_padvals(cmd->maskfile, &obsmask, s.padvals);
}
broadcast_mask(&obsmask, myid);
MPI_Bcast(&good_padvals, 1, MPI_INT, 0, MPI_COMM_WORLD);
MPI_Bcast(s.padvals, obsmask.numchan, MPI_FLOAT, 0, MPI_COMM_WORLD);
} else {
obsmask.numchan = obsmask.numint = 0;
MPI_Bcast(&good_padvals, 1, MPI_INT, 0, MPI_COMM_WORLD);
}
// The number of topo to bary time points to generate with TEMPO
numbarypts = (int) (s.T * 1.1 / TDT + 5.5) + 1;
// Identify the TEMPO observatory code
{
char *outscope = (char *) calloc(40, sizeof(char));
telescope_to_tempocode(idata.telescope, outscope, obs);
free(outscope);
}
// Broadcast or calculate a few extra important values
if (insubs) avgdm = idata.dm;
idata.dm = avgdm;
dsdt = cmd->downsamp * idata.dt;
maxdm = cmd->lodm + cmd->numdms * cmd->dmstep;
BW_ddelay = delay_from_dm(maxdm, idata.freq) -
delay_from_dm(maxdm, idata.freq + (idata.num_chan-1) * idata.chan_wid);
blocksperread = ((int) (BW_ddelay / idata.dt) / s.spectra_per_subint + 1);
worklen = s.spectra_per_subint * blocksperread;
if (cmd->nsub > s.num_channels) {
printf
("Warning: The number of requested subbands (%d) is larger than the number of channels (%d).\n",
cmd->nsub, s.num_channels);
printf(" Re-setting the number of subbands to %d.\n\n", s.num_channels);
cmd->nsub = s.num_channels;
}
if (s.spectra_per_subint % cmd->downsamp) {
if (myid == 0) {
printf
("\nError: The downsample factor (%d) must be a factor of the\n",
cmd->downsamp);
printf(" blocklength (%d). Exiting.\n\n", s.spectra_per_subint);
}
MPI_Finalize();
exit(1);
}
tlotoa = idata.mjd_i + idata.mjd_f; /* Topocentric epoch */
if (cmd->numoutP)
totnumtowrite = cmd->numout;
else
totnumtowrite = (long) idata.N / cmd->downsamp;
if (cmd->nobaryP) { /* Main loop if we are not barycentering... */
/* Dispersion delays (in bins). The high freq gets no delay */
/* All other delays are positive fractions of bin length (dt) */
dispdt = subband_search_delays(s.num_channels, cmd->nsub, avgdm,
idata.freq, idata.chan_wid, 0.0);
idispdt = gen_ivect(s.num_channels);
for (ii = 0; ii < s.num_channels; ii++)
idispdt[ii] = NEAREST_LONG(dispdt[ii] / idata.dt);
vect_free(dispdt);
/* The subband dispersion delays (see note above) */
offsets = gen_imatrix(local_numdms, cmd->nsub);
for (ii = 0; ii < local_numdms; ii++) {
double *subdispdt;
subdispdt = subband_delays(s.num_channels, cmd->nsub, dms[ii],
idata.freq, idata.chan_wid, 0.0);
dtmp = subdispdt[cmd->nsub - 1];
for (jj = 0; jj < cmd->nsub; jj++)
offsets[ii][jj] = NEAREST_LONG((subdispdt[jj] - dtmp) / dsdt);
vect_free(subdispdt);
}
/* Allocate our data array and start getting data */
if (myid == 0) {
printf("De-dispersing using %d subbands.\n", cmd->nsub);
if (cmd->downsamp > 1)
printf("Downsampling by a factor of %d (new dt = %.10g)\n",
cmd->downsamp, dsdt);
printf("\n");
}
/* Print the nodes and the DMs they are handling */
print_dms(hostname, myid, numprocs, local_numdms, dms);
outdata = gen_fmatrix(local_numdms, worklen / cmd->downsamp);
numread = get_data(outdata, blocksperread, &s,
&obsmask, idispdt, offsets, &padding);
while (numread == worklen) {
numread /= cmd->downsamp;
if (myid == 0)
print_percent_complete(totwrote, totnumtowrite);
/* Write the latest chunk of data, but don't */
/* write more than cmd->numout points. */
numtowrite = numread;
if (cmd->numoutP && (totwrote + numtowrite) > cmd->numout)
numtowrite = cmd->numout - totwrote;
if (myid > 0) {
write_data(outfiles, local_numdms, outdata, 0, numtowrite);
/* Update the statistics */
if (!padding) {
for (ii = 0; ii < numtowrite; ii++)
update_stats(statnum + ii, outdata[0][ii], &min, &max, &avg, &var);
statnum += numtowrite;
}
}
totwrote += numtowrite;
/* Stop if we have written out all the data we need to */
if (cmd->numoutP && (totwrote == cmd->numout))
break;
numread = get_data(outdata, blocksperread, &s,
&obsmask, idispdt, offsets, &padding);
}
datawrote = totwrote;
} else { /* Main loop if we are barycentering... */
/* What ephemeris will we use? (Default is DE405) */
strcpy(ephem, "DE405");
/* Define the RA and DEC of the observation */
ra_dec_to_string(rastring, idata.ra_h, idata.ra_m, idata.ra_s);
ra_dec_to_string(decstring, idata.dec_d, idata.dec_m, idata.dec_s);
/* Allocate some arrays */
btoa = gen_dvect(numbarypts);
ttoa = gen_dvect(numbarypts);
for (ii = 0; ii < numbarypts; ii++)
ttoa[ii] = tlotoa + TDT * ii / SECPERDAY;
/* Call TEMPO for the barycentering */
if (myid == 0) {
double maxvoverc = -1.0, minvoverc = 1.0, *voverc = NULL;
printf("\nGenerating barycentric corrections...\n");
voverc = gen_dvect(numbarypts);
barycenter(ttoa, btoa, voverc, numbarypts, rastring, decstring, obs, ephem);
for (ii = 0; ii < numbarypts; ii++) {
if (voverc[ii] > maxvoverc)
maxvoverc = voverc[ii];
if (voverc[ii] < minvoverc)
minvoverc = voverc[ii];
avgvoverc += voverc[ii];
}
avgvoverc /= numbarypts;
vect_free(voverc);
printf(" Average topocentric velocity (c) = %.7g\n", avgvoverc);
printf(" Maximum topocentric velocity (c) = %.7g\n", maxvoverc);
printf(" Minimum topocentric velocity (c) = %.7g\n\n", minvoverc);
printf("De-dispersing using %d subbands.\n", cmd->nsub);
if (cmd->downsamp > 1) {
printf(" Downsample = %d\n", cmd->downsamp);
printf(" New sample dt = %.10g\n", dsdt);
}
printf("\n");
}
/* Print the nodes and the DMs they are handling */
print_dms(hostname, myid, numprocs, local_numdms, dms);
MPI_Bcast(btoa, numbarypts, MPI_DOUBLE, 0, MPI_COMM_WORLD);
MPI_Bcast(&avgvoverc, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD);
blotoa = btoa[0];
/* Dispersion delays (in bins). The high freq gets no delay */
/* All other delays are positive fractions of bin length (dt) */
dispdt = subband_search_delays(s.num_channels, cmd->nsub, avgdm,
idata.freq, idata.chan_wid, avgvoverc);
idispdt = gen_ivect(s.num_channels);
for (ii = 0; ii < s.num_channels; ii++)
idispdt[ii] = NEAREST_LONG(dispdt[ii] / idata.dt);
vect_free(dispdt);
/* The subband dispersion delays (see note above) */
offsets = gen_imatrix(local_numdms, cmd->nsub);
for (ii = 0; ii < local_numdms; ii++) {
double *subdispdt;
subdispdt = subband_delays(s.num_channels, cmd->nsub, dms[ii],
idata.freq, idata.chan_wid, avgvoverc);
dtmp = subdispdt[cmd->nsub - 1];
for (jj = 0; jj < cmd->nsub; jj++)
offsets[ii][jj] = NEAREST_LONG((subdispdt[jj] - dtmp) / dsdt);
vect_free(subdispdt);
}
/* Convert the bary TOAs to differences from the topo TOAs in */
/* units of bin length (dt) rounded to the nearest integer. */
dtmp = (btoa[0] - ttoa[0]);
for (ii = 0; ii < numbarypts; ii++)
btoa[ii] = ((btoa[ii] - ttoa[ii]) - dtmp) * SECPERDAY / dsdt;
/* Find the points where we need to add or remove bins */
{
int oldbin = 0, currentbin;
double lobin, hibin, calcpt;
numdiffbins = abs(NEAREST_LONG(btoa[numbarypts - 1])) + 1;
diffbins = gen_ivect(numdiffbins);
diffbinptr = diffbins;
for (ii = 1; ii < numbarypts; ii++) {
currentbin = NEAREST_LONG(btoa[ii]);
if (currentbin != oldbin) {
if (currentbin > 0) {
calcpt = oldbin + 0.5;
lobin = (ii - 1) * TDT / dsdt;
hibin = ii * TDT / dsdt;
} else {
calcpt = oldbin - 0.5;
lobin = -((ii - 1) * TDT / dsdt);
hibin = -(ii * TDT / dsdt);
}
while (fabs(calcpt) < fabs(btoa[ii])) {
/* Negative bin number means remove that bin */
/* Positive bin number means add a bin there */
*diffbinptr =
NEAREST_LONG(LININTERP
(calcpt, btoa[ii - 1], btoa[ii], lobin, hibin));
diffbinptr++;
calcpt = (currentbin > 0) ? calcpt + 1.0 : calcpt - 1.0;
}
oldbin = currentbin;
}
}
*diffbinptr = cmd->numout; /* Used as a marker */
}
diffbinptr = diffbins;
/* Now perform the barycentering */
outdata = gen_fmatrix(local_numdms, worklen / cmd->downsamp);
numread = get_data(outdata, blocksperread, &s,
&obsmask, idispdt, offsets, &padding);
while (numread == worklen) { /* Loop to read and write the data */
int numwritten = 0;
double block_avg, block_var;
numread /= cmd->downsamp;
/* Determine the approximate local average */
avg_var(outdata[0], numread, &block_avg, &block_var);
if (myid == 0)
print_percent_complete(totwrote, totnumtowrite);
/* Simply write the data if we don't have to add or */
/* remove any bins from this batch. */
/* OR write the amount of data up to cmd->numout or */
/* the next bin that will be added or removed. */
numtowrite = abs(*diffbinptr) - datawrote;
if (cmd->numoutP && (totwrote + numtowrite) > cmd->numout)
numtowrite = cmd->numout - totwrote;
if (numtowrite > numread)
numtowrite = numread;
if (myid > 0) {
write_data(outfiles, local_numdms, outdata, 0, numtowrite);
/* Update the statistics */
if (!padding) {
for (ii = 0; ii < numtowrite; ii++)
update_stats(statnum + ii, outdata[0][ii], &min, &max, &avg, &var);
statnum += numtowrite;
}
}
datawrote += numtowrite;
totwrote += numtowrite;
numwritten += numtowrite;
if ((datawrote == abs(*diffbinptr)) &&
(numwritten != numread) &&
(totwrote < cmd->numout)) { /* Add/remove a bin */
int skip, nextdiffbin;
skip = numtowrite;
/* Write the rest of the data after adding/removing a bin */
do {
if (*diffbinptr > 0) {
/* Add a bin */
if (myid > 0)
write_padding(outfiles, local_numdms, block_avg, 1);
numadded++;
totwrote++;
} else {
/* Remove a bin */
numremoved++;
datawrote++;
numwritten++;
skip++;
}
diffbinptr++;
/* Write the part after the diffbin */
numtowrite = numread - numwritten;
if (cmd->numoutP && (totwrote + numtowrite) > cmd->numout)
numtowrite = cmd->numout - totwrote;
nextdiffbin = abs(*diffbinptr) - datawrote;
if (numtowrite > nextdiffbin)
numtowrite = nextdiffbin;
if (myid > 0) {
write_data(outfiles, local_numdms, outdata, skip, numtowrite);
/* Update the statistics and counters */
if (!padding) {
for (ii = 0; ii < numtowrite; ii++)
update_stats(statnum + ii,
outdata[0][skip + ii], &min, &max, &avg, &var);
statnum += numtowrite;
}
}
numwritten += numtowrite;
datawrote += numtowrite;
totwrote += numtowrite;
skip += numtowrite;
/* Stop if we have written out all the data we need to */
if (cmd->numoutP && (totwrote == cmd->numout))
break;
} while (numwritten < numread);
}
/* Stop if we have written out all the data we need to */
if (cmd->numoutP && (totwrote == cmd->numout))
break;
numread = get_data(outdata, blocksperread, &s,
&obsmask, idispdt, offsets, &padding);
}
}
if (myid > 0) {
/* Calculate the amount of padding we need */
if (cmd->numoutP && (cmd->numout > totwrote))
padwrote = padtowrite = cmd->numout - totwrote;
/* Write the new info file for the output data */
idata.dt = dsdt;
update_infodata(&idata, totwrote, padtowrite, diffbins,
numdiffbins, cmd->downsamp);
for (ii = 0; ii < local_numdms; ii++) {
idata.dm = dms[ii];
if (!cmd->nobaryP) {
double baryepoch, barydispdt, baryhifreq;
baryhifreq = idata.freq + (s.num_channels - 1) * idata.chan_wid;
barydispdt = delay_from_dm(dms[ii], doppler(baryhifreq, avgvoverc));
baryepoch = blotoa - (barydispdt / SECPERDAY);
idata.bary = 1;
idata.mjd_i = (int) floor(baryepoch);
idata.mjd_f = baryepoch - idata.mjd_i;
}
sprintf(idata.name, "%s_DM%.2f", outfilenm, dms[ii]);
writeinf(&idata);
}
/* Set the padded points equal to the average data point */
if (idata.numonoff >= 1) {
int index, startpad, endpad;
for (ii = 0; ii < local_numdms; ii++) {
fclose(outfiles[ii]);
sprintf(datafilenm, "%s_DM%.2f.dat", outfilenm, dms[ii]);
outfiles[ii] = chkfopen(datafilenm, "rb+");
}
for (ii = 0; ii < idata.numonoff; ii++) {
index = 2 * ii;
startpad = idata.onoff[index + 1];
if (ii == idata.numonoff - 1)
endpad = idata.N - 1;
else
endpad = idata.onoff[index + 2];
for (jj = 0; jj < local_numdms; jj++)
chkfseek(outfiles[jj], (startpad + 1) * sizeof(float), SEEK_SET);
padtowrite = endpad - startpad;
write_padding(outfiles, local_numdms, avg, padtowrite);
}
}
}
/* Print simple stats and results */
var /= (datawrote - 1);
if (myid == 0)
print_percent_complete(1, 1);
if (myid == 1) {
printf("\n\nDone.\n\nSimple statistics of the output data:\n");
printf(" Data points written: %ld\n", totwrote);
if (padwrote)
printf(" Padding points written: %ld\n", padwrote);
if (!cmd->nobaryP) {
if (numadded)
printf(" Bins added for barycentering: %d\n", numadded);
if (numremoved)
printf(" Bins removed for barycentering: %d\n", numremoved);
}
printf(" Maximum value of data: %.2f\n", max);
printf(" Minimum value of data: %.2f\n", min);
printf(" Data average value: %.2f\n", avg);
printf(" Data standard deviation: %.2f\n", sqrt(var));
printf("\n");
}
/* Close the files and cleanup */
if (cmd->maskfileP)
free_mask(obsmask);
if (myid > 0) {
for (ii = 0; ii < local_numdms; ii++)
fclose(outfiles[ii]);
free(outfiles);
}
vect_free(outdata[0]);
vect_free(outdata);
vect_free(dms);
free(hostname);
vect_free(idispdt);
vect_free(offsets[0]);
vect_free(offsets);
free(datafilenm);
free(outfilenm);
free(outpath);
if (!cmd->nobaryP) {
vect_free(btoa);
vect_free(ttoa);
vect_free(diffbins);
}
MPI_Finalize();
return (0);
}
int comp_rawbin_to_cand(rawbincand * cand, infodata * idata, char *output, int full)
/* Compares a binary PSR candidate defined by its props found in */
/* *cand, and *idata with all of the pulsars in the pulsar */
/* database. It returns a string (verbose if full==1) describing */
/* the results of the search in *output. */
{
int ii, jj, kk;
static int np;
double theop, ra, dec, beam2, difft = 0.0, epoch;
double bmod, pmod, orbperr, psrperr;
char tmp1[80], tmp2[80], tmp3[80];
/* Read the database if needed */
if (!have_database)
np = read_database();
/* Convert the beam width to radians */
beam2 = 2.0 * ARCSEC2RAD * idata->fov;
/* Convert RA and DEC to radians (Use J2000) */
ra = hms2rad(idata->ra_h, idata->ra_m, idata->ra_s);
dec = dms2rad(idata->dec_d, idata->dec_m, idata->dec_s);
/* Calculate the time related variables */
epoch = (double) idata->mjd_i + idata->mjd_f;
/* Calculate the approximate error in our value of orbital period */
orbperr = 0.5 * cand->full_T / cand->mini_N;
/* Calculate the approximate error in our value of spin period */
if (cand->full_lo_r == 0.0)
psrperr = cand->psr_p;
else
psrperr = fabs(cand->full_T /
(cand->full_lo_r + 0.5 * cand->mini_N) -
cand->full_T / cand->full_lo_r);
/* Run through RAs in database looking for things close */
/* If find one, check the DEC as well (the angle between */
/* the sources < 2*beam diam). If find one, check its */
/* period. If this matches within 2*perr, return the */
/* number of the pulsar. If no matches, return 0. */
for (ii = 0; ii < np; ii++) {
/* See if we're close in RA */
if (fabs(pulsardata[ii].ra2000 - ra) < 5.0 * beam2) {
/* See if we're close in RA and DEC */
if (sphere_ang_diff(pulsardata[ii].ra2000, pulsardata[ii].dec2000,
ra, dec) < 5.0 * beam2) {
/* Check that the psr in the database is in a binary */
if (pulsardata[ii].orb.p != 0.0) {
/* Predict the period of the pulsar at the observation MJD */
difft = SECPERDAY * (epoch - pulsardata[ii].timepoch);
theop = pulsardata[ii].p + pulsardata[ii].pd * difft;
/* Check the predicted period and its harmonics against the */
/* measured period. Use both pulsar and binary periods. */
for (jj = 1; jj < 41; jj++) {
pmod = 1.0 / (double) jj;
if (fabs(theop * pmod - cand->psr_p) < psrperr) {
for (kk = 1; kk < 10; kk++) {
bmod = (double) kk;
if (fabs
(pulsardata[ii].orb.p * bmod - cand->orb_p / SECPERDAY) <
orbperr) {
if (strlen(pulsardata[ii].bname) == 0) {
if (jj > 1) {
if (full) {
sprintf(tmp1,
"Possibly the %s phasemod harmonic ",
num[kk]);
sprintf(tmp2, "of the %s harmonic of PSR ",
num[jj]);
sprintf(tmp3,
"J%s (p = %11.7f s, pbin = %9.4f d).\n",
pulsardata[ii].jname, theop,
pulsardata[ii].orb.p);
sprintf(output, "%s%s%s", tmp1, tmp2, tmp3);
} else {
sprintf(output, "%s H J%.12s", num[kk],
pulsardata[ii].jname);
}
} else {
if (full) {
sprintf(tmp1,
"Possibly the %s phasemod harmonic ",
num[kk]);
sprintf(tmp2,
"of PSR J%s (p = %11.7f s, pbin = %9.4f d).\n",
pulsardata[ii].jname, theop,
pulsardata[ii].orb.p);
sprintf(output, "%s%s", tmp1, tmp2);
} else {
sprintf(output, "PSR J%.12s",
pulsardata[ii].jname);
}
}
} else {
if (jj > 1) {
if (full) {
sprintf(tmp1,
"Possibly the %s modulation harmonic ",
num[kk]);
sprintf(tmp2, "of the %s harmonic of PSR ",
num[jj]);
sprintf(tmp3,
"B%s (p = %11.7f s, pbin = %9.4f d).\n",
pulsardata[ii].bname, theop,
pulsardata[ii].orb.p);
sprintf(output, "%s%s%s", tmp1, tmp2, tmp3);
} else {
sprintf(output, "%s H B%s", num[kk],
pulsardata[ii].bname);
}
} else {
if (full) {
sprintf(tmp1,
"Possibly the %s phasemod harmonic ",
num[kk]);
sprintf(tmp2,
"of PSR B%s (p = %11.7f s, pbin = %9.4f d).\n",
pulsardata[ii].bname, theop,
pulsardata[ii].orb.p);
sprintf(output, "%s%s", tmp1, tmp2);
} else {
sprintf(output, "PSR B%s", pulsardata[ii].bname);
}
}
}
}
return ii + 1;
}
}
}
}
}
}
}
/* Didn't find a match */
if (full) {
sprintf(output, "I don't recognize this candidate in the pulsar database.\n");
} else {
sprintf(output, " ");
}
return 0;
}
int comp_psr_to_cand(fourierprops * cand, infodata * idata, char *output, int full)
/* Compares a pulsar candidate defined by its properties found in */
/* *cand, and *idata with all of the pulsars in the pulsar */
/* database. It returns a string (verbose if full==1) describing */
/* the results of the search in *output. */
{
int ii, jj;
static infodata *old_idata;
double theor, theoz, sidedr = 20.0;
double r_criteria, z_criteria, rdiff, zdiff, difft = 0;
static double T, beam2, ra, dec, epoch;
char tmp1[80], tmp2[80], tmp3[80], shortout[30], psrname[20];
rzwerrs rzws;
/* Read the database if needed */
if (!have_database)
np = read_database();
/* If calling for the first time for a certain data set, */
/* initialize some values. */
if (idata != old_idata) {
/* Convert the beam width to radians */
beam2 = 2.0 * ARCSEC2RAD * idata->fov;
/* Convert RA and DEC to radians (Use J2000) */
ra = hms2rad(idata->ra_h, idata->ra_m, idata->ra_s);
dec = dms2rad(idata->dec_d, idata->dec_m, idata->dec_s);
T = idata->N * idata->dt;
epoch = (double) idata->mjd_i + idata->mjd_f + T / (2.0 * SECPERDAY);
/* Set up old_idata for next time */
old_idata = idata;
}
/* Calculate the measured r, z, w's and their derivatives */
calc_rzwerrs(cand, T, &rzws);
/* Run through RAs in database looking for things close */
/* If find one, check the DEC as well (the angle between */
/* the sources < 2*beam diam). If find one, check its */
/* period. If this matches within 2*perr, return the */
/* number of the pulsar. If no matches, return 0. */
for (ii = 0; ii < np; ii++) {
/* See if we're close in RA */
if (fabs(pulsardata[ii].ra2000 - ra) < 5 * beam2) {
/* See if we're close in RA and DEC */
if (sphere_ang_diff(pulsardata[ii].ra2000, pulsardata[ii].dec2000,
ra, dec) < 5 * beam2) {
/* Predict the period of the pulsar at the observation MJD */
difft = SECPERDAY * (epoch - pulsardata[ii].timepoch);
theor = T / (pulsardata[ii].p + pulsardata[ii].pd * difft);
theoz = -pulsardata[ii].pd * theor * theor;
/* Check the predicted period and its harmonics against the */
/* measured period. */
for (jj = 1; jj < 41; jj++) {
/* If the psr from the database is in a */
/* binary orbit, loosen the match criteria. */
/* This accounts for Doppler variations in period. */
if (pulsardata[ii].orb.p != 0.0) {
r_criteria = 0.001 * theor * jj; /* 0.1% fractional error */
z_criteria = 9999999999.0; /* Always match for binary */
strcpy(tmp1, "?");
if (full) {
strcpy(tmp3, "Possibly (large error) ");
}
} else {
r_criteria = 5.0; /* 5 bin error matching... */
z_criteria = 9999999999.0; /* Always match for binary */
/* z_criteria = 2.5 * cand->zerr; */
strcpy(tmp1, "");
if (full) {
strcpy(tmp3, "Looks like ");
}
}
if (theor * jj > 1.5 * cand->r)
break;
rdiff = fabs(theor * jj - cand->r);
zdiff = fabs(theoz * jj - cand->z);
if (rdiff < r_criteria && zdiff < z_criteria) {
if (strlen(pulsardata[ii].bname) == 0)
sprintf(psrname, "J%s", pulsardata[ii].jname);
else
sprintf(psrname, "B%s", pulsardata[ii].bname);
if (jj == 1) {
if (full) {
sprintf(tmp1, "the fundamental of ");
sprintf(tmp2, "PSR %s. (predicted p = %11.7f s).\n",
psrname, T / theor);
sprintf(output, "%s%s\n %s", tmp3, tmp1, tmp2);
} else {
sprintf(shortout, "PSR %s%s", psrname, tmp1);
strncpy(output, shortout, 20);
}
} else {
if (full) {
sprintf(tmp1, "the %s harmonic of ", num[jj]);
sprintf(tmp2, "PSR %s. (predicted p = %11.7f s).\n",
psrname, T / theor);
sprintf(output, "%s%s\n %s", tmp3, tmp1, tmp2);
} else {
sprintf(shortout, "%s H %s%s", num[jj], psrname, tmp1);
strncpy(output, shortout, 20);
}
}
return ii + 1;
} else if (rdiff < sidedr) {
if (strlen(pulsardata[ii].bname) == 0)
sprintf(psrname, "J%s", pulsardata[ii].jname);
else
sprintf(psrname, "B%s", pulsardata[ii].bname);
if (full) {
sprintf(tmp1, "a sidelobe of the %s harmonic of ", num[jj]);
sprintf(tmp2, "PSR %s. (predicted p = %11.7f s).\n",
psrname, T / theor);
sprintf(output, "%s%s\n %s", tmp3, tmp1, tmp2);
} else {
sprintf(shortout, "SL H%d %s", jj, psrname);
strncpy(output, shortout, 20);
}
return ii + 1;
}
}
}
}
}
/* Didn't find a match */
if (full) {
sprintf(output, "I don't recognize this candidate in the pulsar database.\n");
} else {
strncpy(output, " ", 20);
}
return 0;
}
int get_psr_from_parfile(char *parfilenm, double epoch, psrparams * psr)
/* Converts info from a "par" file to the "current" epoch. */
/* Returned values go in *psr. The name of the parfile is */
/* in *parfilenm. epoch is the time in question in MJD. */
/* The int returned is 1 if successful, 0 otherwise. */
{
FILE *parfile;
int binary = 0;
double orbdifft = 0.0, difft = 0.0, f = 0.0, fd = 0.0;
double eps1 = 0.0, eps2 = 0.0, eps1d = 0.0, eps2d = 0.0, ed = 0.0, xd = 0.0;
char line[80], *keyword, *value;
psr->f = psr->fd = psr->fdd = psr->p = psr->pd = psr->pdd = psr->dm = 0.0;
psr->orb.p = psr->orb.pd = psr->orb.x = psr->orb.e = 0.0;
psr->orb.w = psr->orb.wd = psr->orb.t = 0.0;
parfile = chkfopen(parfilenm, "r");
while (fgets(line, 80, parfile)) {
keyword = strtok(line, " \t\n");
if (keyword != NULL) {
if (strncmp("PSR", keyword, 80) == 0 || strncmp("PSRJ", keyword, 80) == 0) {
strncpy(psr->jname, strtok(NULL, " \t\n"), 20);
if (psr->jname[0] == 'J' || psr->jname[0] == 'B') {
int ii = 0;
do {
ii++;
psr->jname[ii - 1] = psr->jname[ii];
} while (psr->jname[ii] != '\0');
}
if (DEBUGOUT)
printf("The pulsar is '%s'\n", psr->jname);
} else if (strncmp("RAJ", keyword, 80) == 0 ||
strncmp("RA", keyword, 80) == 0) {
int h, m;
double s;
ra_dec_from_string(strtok(NULL, " \t\n"), &h, &m, &s);
psr->ra2000 = hms2rad(h, m, s);
if (DEBUGOUT)
printf("The RA is %d %d %f (%f)\n", h, m, s, psr->ra2000);
} else if (strncmp("DECJ", keyword, 80) == 0 ||
strncmp("DEC", keyword, 80) == 0) {
int d, m;
double s;
ra_dec_from_string(strtok(NULL, " \t\n"), &d, &m, &s);
psr->dec2000 = dms2rad(d, m, s);
if (DEBUGOUT)
printf("The DEC is %d %d %f (%f)\n", d, m, s, psr->dec2000);
} else if (strncmp("F0", keyword, 80) == 0 ||
strncmp("F", keyword, 80) == 0) {
value = strtok(NULL, " \t\n");
f = strtod(fortran_double_convert(value), &value);
if (DEBUGOUT)
printf("The freq is %.15g\n", f);
} else if (strncmp("P0", keyword, 80) == 0 ||
strncmp("P", keyword, 80) == 0) {
value = strtok(NULL, " \t\n");
f = 1.0 / strtod(fortran_double_convert(value), &value);
if (DEBUGOUT)
printf("The period is %.15g\n", 1.0 / f);
} else if (strncmp("F1", keyword, 80) == 0) {
value = strtok(NULL, " \t\n");
fd = strtod(fortran_double_convert(value), &value);
if (DEBUGOUT)
printf("The f-dot is %.15g\n", fd);
} else if (strncmp("P1", keyword, 80) == 0) {
value = strtok(NULL, " \t\n");
fd = -strtod(fortran_double_convert(value), &value) * f * f;
if (DEBUGOUT)
printf("The p-dot is %.15g\n", -fd / (f * f));
} else if (strncmp("F2", keyword, 80) == 0) {
value = strtok(NULL, " \t\n");
psr->fdd = strtod(fortran_double_convert(value), &value);
psr->pdd = (2.0 * (fd * fd) / f - psr->fdd) / (f * f);
if (DEBUGOUT)
printf("The f-dotdot is %.15g\n", psr->fdd);
} else if (strncmp("PEPOCH", keyword, 80) == 0) {
value = strtok(NULL, " \t\n");
psr->timepoch = strtod(fortran_double_convert(value), &value);
difft = (epoch - psr->timepoch) * SECPERDAY;
if (DEBUGOUT)
printf("The PEPOCH is %.15g\n", psr->timepoch);
} else if (strncmp("DM", keyword, 80) == 0) {
value = strtok(NULL, " \t\n");
psr->dm = strtod(fortran_double_convert(value), &value);
if (DEBUGOUT)
printf("The DM is %.15g\n", psr->dm);
} else if (strncmp("BINARY", keyword, 80) == 0) {
binary = 1;
value = strtok(NULL, " \t\n");
if (DEBUGOUT)
printf("This is a binary PSR ('%s')...\n", value);
} else if (strncmp("PB", keyword, 80) == 0) {
value = strtok(NULL, " \t\n");
psr->orb.p = strtod(fortran_double_convert(value), &value) * SECPERDAY;
if (DEBUGOUT)
printf(" P_orb = %.15g\n", psr->orb.p);
} else if (strncmp("PBDOT", keyword, 80) == 0) {
value = strtok(NULL, " \t\n");
psr->orb.pd = strtod(fortran_double_convert(value), &value) * 1.0E-12;
if (DEBUGOUT)
printf(" P_orb-dot = %.15g\n", psr->orb.pd);
} else if (strncmp("OM", keyword, 80) == 0) {
value = strtok(NULL, " \t\n");
psr->orb.w = strtod(fortran_double_convert(value), &value);
if (DEBUGOUT)
printf(" w_orb = %.15g\n", psr->orb.w);
} else if (strncmp("OMDOT", keyword, 80) == 0) {
value = strtok(NULL, " \t\n");
psr->orb.wd =
strtod(fortran_double_convert(value), &value) / SECPERJULYR;
if (DEBUGOUT)
printf(" w_orb-dot = %.15g\n", psr->orb.wd);
} else if (strncmp("A1", keyword, 80) == 0) {
value = strtok(NULL, " \t\n");
psr->orb.x = strtod(fortran_double_convert(value), &value);
if (DEBUGOUT)
printf(" x_orb = %.15g\n", psr->orb.x);
} else if (strncmp("XDOT", keyword, 80) == 0) {
value = strtok(NULL, " \t\n");
xd = strtod(fortran_double_convert(value), &value) * 1.0E-12;
if (DEBUGOUT)
printf(" x_orb-dot = %.15g\n", xd);
} else if (strncmp("E", keyword, 80) == 0 ||
strncmp("ECC", keyword, 80) == 0) {
value = strtok(NULL, " \t\n");
psr->orb.e = strtod(fortran_double_convert(value), &value);
if (DEBUGOUT)
printf(" e_orb = %.15g\n", psr->orb.e);
} else if (strncmp("EDOT", keyword, 80) == 0) {
value = strtok(NULL, " \t\n");
ed = strtod(fortran_double_convert(value), &value) * 1.0E-12;
if (DEBUGOUT)
printf(" e_orb-dot = %.15g\n", ed);
} else if (strncmp("T0", keyword, 80) == 0 ||
strncmp("TASC", keyword, 80) == 0) {
value = strtok(NULL, " \t\n");
psr->orb.t = strtod(fortran_double_convert(value), &value);
/* TEMPO bases the orbital params on T0, not PEPOCH */
orbdifft = (epoch - psr->orb.t) * SECPERDAY;
if (DEBUGOUT)
printf(" T_orb = %.15g\n", psr->orb.t);
} else if (strncmp("EPS1", keyword, 80) == 0) {
value = strtok(NULL, " \t\n");
eps1 = strtod(fortran_double_convert(value), &value);
if (DEBUGOUT)
printf(" EPS1 = %.15g\n", eps1);
} else if (strncmp("EPS2", keyword, 80) == 0) {
value = strtok(NULL, " \t\n");
eps2 = strtod(fortran_double_convert(value), &value);
if (DEBUGOUT)
printf(" EPS2 = %.15g\n", eps2);
} else if (strncmp("EPS1DOT", keyword, 80) == 0) {
value = strtok(NULL, " \t\n");
eps1d = strtod(fortran_double_convert(value), &value);
if (DEBUGOUT)
printf(" EPS1DOT = %.15g\n", eps1d);
} else if (strncmp("EPS2DOT", keyword, 80) == 0) {
value = strtok(NULL, " \t\n");
eps2d = strtod(fortran_double_convert(value), &value);
if (DEBUGOUT)
printf(" EPS2DOT = %.15g\n", eps2d);
} else if (strncmp("OM2DOT", keyword, 80) == 0 ||
strncmp("X2DOT", keyword, 80) == 0 ||
strncmp("F3", keyword, 80) == 0 ||
strncmp("F4", keyword, 80) == 0 ||
strncmp("F5", keyword, 80) == 0) {
printf(" readpar: Warning! '%s' is currently unused!\n", keyword);
}
}
}
/* Update the spin parameters */
psr->f = f + fd * difft + 0.5 * psr->fdd * difft * difft;
psr->fd = fd + psr->fdd * difft;
psr->p = 1.0 / psr->f;
psr->pd = -psr->fd * psr->p * psr->p;
psr->pdd = (2.0 * (fd * fd) / f - psr->fdd) / (f * f);
if (binary) {
psr->orb.p += psr->orb.pd * orbdifft;
psr->orb.w += psr->orb.wd * orbdifft;
psr->orb.x += xd * orbdifft;
psr->orb.e += ed * orbdifft;
eps1 += eps1d * orbdifft;
eps2 += eps1d * orbdifft;
if (eps1 != 0.0 || eps2 != 0.0) {
/* Convert Laplace-Lagrange params to e and w */
/* Warning! This is presently untested! */
psr->orb.e = sqrt(eps1 * eps1 + eps2 * eps2);
psr->orb.w = atan2(eps1, eps2);
psr->orb.t += psr->orb.p / SECPERDAY * (psr->orb.w / TWOPI);
psr->orb.w *= RADTODEG;
}
/* psr->orb.t is in seconds, _not_ MJD. It represents the */
/* time in sec _since_ the last periastron passage, _not_ */
/* when the next periastron will occur.... */
psr->orb.t = fmod((epoch - psr->orb.t) * SECPERDAY, psr->orb.p);
if (psr->orb.t < 0.0)
psr->orb.t += psr->orb.p;
psr->orb.w = fmod(psr->orb.w, 360.0);
}
fclose(parfile);
return 1;
}