// Intialize options then parse the cmd line arguments
Options::Options( int argc, char **argv )
{
center = false;
pdbfile = NULL;
outputfile = NULL;
failure = false;
sameChain = false;
threshold = 7.0;
numLigands = 0;
gamessfolder = NULL;
outputGamessINP = false;
pdblist = NULL;
chain_list = NULL;
extension = ".pdb.gz";
resolution = 99999.0;
findCarbonRings = false;
parseCmdline( argc, argv );
}
int main(int argc, char* argv[]) {
std::string input, output;
OptionsMap options = create_map<OptionsMap::key_type, OptionsMap::mapped_type>
("d", Option())("s", Option());
try {
auto lefovers = parseCmdline(argc, argv, options);
if (lefovers.size() != 2)
throw std::runtime_error("Missing leftover args");
input = lefovers[0];
output = lefovers[1];
} catch (std::exception& e) {
std::cerr << "Error: " << e.what() << std::endl;
printUsage();
return 2;
}
std::ifstream ifile(input.c_str(), std::ios_base::binary);
if (!ifile) {
std::cerr << "Error: Unable to open input file: " << input << std::endl;
return 1;
}
std::ofstream ofile(output.c_str(), std::ios_base::binary);
if (!ofile) {
std::cerr << "Error: Unable to open output file: " << output << std::endl;
return 1;
}
try {
if (options["d"].isPresent) {
decompress(ifile, ofile);
} else {
if (options["s"].isPresent)
compressStaticly(ifile, ofile);
else
compressAdaptive(ifile, ofile);
}
} catch (std::exception& e) {
std::cerr << "Error: " << e.what() << std::endl;
return 1;
}
return 0;
}
int main(int argc, char *argv[])
{
struct Config_t config;
GDFS_MAPDATA *Source_MapHead_p, *Source_MapTail_p;
uint32 Noof_Source_Parameters = 0;
int result = 0;
memset(&config, 0x00, sizeof(struct Config_t));
/* Parse the input argument and if not correct print info and exit */
if (parseCmdline(argc, argv, &config) == -1)
{
result = -1;
goto exit;
}
/* First we open the CSPSA area */
if( InitCSPSA(&config) != 0)
{
result = -1;
goto exit;
}
if(!ReadMapFile( config.MAP_FileName, &Noof_Source_Parameters, &Source_MapHead_p, &Source_MapTail_p)){
fprintf(stderr, "CSPSA2MAP: Failed to open input map file.\n");
result = -1;
goto exit;
}
if(0 != write_parameters_to_cspsa(Source_MapHead_p, &config)){
fprintf(stderr, "CSPSA2MAP: Failed to write parameters to CSPSA.\n");
result = -1;
goto exit;
}
exit:
/* Clean up and close any open files etc.. */
if(config.CSPSA_Handle != 0x00){
UnInit(&config);
}
return result;
}
int main(int argc, char *argv[])
/* dftfold: Does complex plane vector addition of a DFT freq */
/* Written by Scott Ransom on 31 Aug 00 based on Ransom and */
/* Eikenberry paper I (to be completed sometime...). */
{
FILE *infile;
char infilenm[200], outfilenm[200];
int dataperread;
unsigned long N;
double T, rr = 0.0, norm = 1.0;
dftvector dftvec;
infodata idata;
Cmdline *cmd;
/* Call usage() if we have no command line arguments */
if (argc == 1) {
Program = argv[0];
usage();
exit(1);
}
/* Parse the command line using the excellent program Clig */
cmd = parseCmdline(argc, argv);
#ifdef DEBUG
showOptionValues();
#endif
printf("\n\n");
printf(" DFT Vector Folding Routine\n");
printf(" by Scott M. Ransom\n");
printf(" 31 August, 2000\n\n");
/* Open the datafile and read the info file */
sprintf(infilenm, "%s.dat", cmd->argv[0]);
infile = chkfopen(infilenm, "rb");
readinf(&idata, cmd->argv[0]);
/* The number of points in datafile */
N = chkfilelen(infile, sizeof(float));
dataperread = N / cmd->numvect;
/* N = cmd->numvect * dataperread; */
T = N * idata.dt;
/* Calculate the Fourier frequency */
if (!cmd->rrP) {
if (cmd->ffP)
rr = cmd->ff;
else if (cmd->ppP)
rr = T / cmd->pp;
else {
printf("\n You must specify a frequency to fold! Exiting.\n\n");
}
} else
rr = cmd->rr;
/* Calculate the amplitude normalization if required */
if (cmd->normP)
norm = 1.0 / sqrt(cmd->norm);
else if (cmd->fftnormP) {
FILE *fftfile;
int kern_half_width, fftdatalen, startbin;
double rrfrac, rrint;
char fftfilenm[200];
fcomplex *fftdata;
sprintf(fftfilenm, "%s.fft", cmd->argv[0]);
fftfile = chkfopen(fftfilenm, "rb");
kern_half_width = r_resp_halfwidth(HIGHACC);
fftdatalen = 2 * kern_half_width + 10;
rrfrac = modf(rr, &rrint);
startbin = (int) rrint - fftdatalen / 2;
fftdata = read_fcomplex_file(fftfile, startbin, fftdatalen);
norm = 1.0 / sqrt(get_localpower3d(fftdata, fftdatalen,
rrfrac + fftdatalen / 2, 0.0, 0.0));
vect_free(fftdata);
fclose(fftfile);
}
/* Initialize the dftvector */
init_dftvector(&dftvec, dataperread, cmd->numvect, idata.dt, rr, norm, T);
/* Show our folding values */
printf("\nFolding data from '%s':\n", infilenm);
printf(" Folding Fourier Freq = %.5f\n", rr);
printf(" Folding Freq (Hz) = %-.11f\n", rr / T);
printf(" Folding Period (s) = %-.14f\n", T / rr);
printf(" Points per sub-vector = %d\n", dftvec.n);
printf(" Number of sub-vectors = %d\n", dftvec.numvect);
printf(" Normalization constant = %g\n", norm * norm);
/* Perform the actual vector addition */
{
int ii, jj;
float *data;
double real, imag, sumreal = 0.0, sumimag = 0.0;
double theta, aa, bb, cc, ss, dtmp;
double powargr, powargi, phsargr, phsargi, phstmp;
data = gen_fvect(dftvec.n);
theta = -TWOPI * rr / (double) N;
dtmp = sin(0.5 * theta);
aa = -2.0 * dtmp * dtmp;
bb = sin(theta);
cc = 1.0;
ss = 0.0;
for (ii = 0; ii < dftvec.numvect; ii++) {
chkfread(data, sizeof(float), dftvec.n, infile);
real = 0.0;
imag = 0.0;
for (jj = 0; jj < dftvec.n; jj++) {
real += data[jj] * cc;
imag += data[jj] * ss;
cc = aa * (dtmp = cc) - bb * ss + cc;
ss = aa * ss + bb * dtmp + ss;
}
dftvec.vector[ii].r = norm * real;
dftvec.vector[ii].i = norm * imag;
sumreal += dftvec.vector[ii].r;
sumimag += dftvec.vector[ii].i;
}
vect_free(data);
printf("\nDone:\n");
printf(" Vector sum = %.3f + %.3fi\n", sumreal, sumimag);
printf(" Total phase (deg) = %.2f\n", PHASE(sumreal, sumimag));
printf(" Total power = %.2f\n", POWER(sumreal, sumimag));
printf("\n");
}
fclose(infile);
/* Write the output structure */
sprintf(outfilenm, "%s_%.3f.dftvec", cmd->argv[0], rr);
write_dftvector(&dftvec, outfilenm);
/* Free our vector and return */
free_dftvector(&dftvec);
return (0);
}
int
main (int argc, char **argv)
{
char *xmalloc ();
char *xrealloc ();
char *xstrdup ();
int infpop;
double nb;
/* Check parameters */
Cmdline *cmd = parseCmdline (argc, argv);
if ((cmd->show_helpP) | (argc == 1))
usage ();
if (cmd->show_versionP)
{
printf ("%s %s\n", argv[0], VERSION);
exit (0);
}
check_param (cmd);
infpop = (cmd->pop == 0) ? 1 : 0;
cmd->precision /= PC;
cmd->prevalence /= PC;
cmd->level /= PC;
cmd->alpha /= PC;
cmd->power /= PC;
cmd->exposed /= PC;
if (cmd->observedP)
{
nb = small_sampsi (cmd);
display_small (cmd, nb);
}
else if (cmd->odds_ratioP && !cmd->sampleP)
{
cmd->ratio = floor (cmd->ratio);
if (cmd->ratio < 1)
sperror ("option -c should be >= 1");
case_control (cmd);
}
/* Absolute precision then sample size equals population size */
else if (cmd->precision == 0 && cmd->pop > 0)
{
nb = cmd->pop;
display_surv (cmd, nb, infpop);
}
else if (cmd->precisionP)
{
nb = sampsi (cmd);
display_surv (cmd, nb, infpop);
}
else if (cmd->binomialP)
binom_ci (cmd);
else if (cmd->compP && !cmd->sampleP && !cmd->deltaP)
comp (cmd);
else if (cmd->meansP && !cmd->sampleP && !cmd->deltaP)
means (cmd);
else if (cmd->sampleP && cmd->exposedP && !cmd->odds_ratioP && cmd->powerP
&& !cmd->matchedP)
ccmin (cmd);
else if (cmd->sampleP && cmd->compP && !cmd->deltaP)
ppower (cmd);
else if (cmd->sampleP && cmd->meansP && !cmd->deltaP)
mpower (cmd);
else if (cmd->sampleP && cmd->odds_ratioP && cmd->exposedP
&& !cmd->matchedP)
ccpower (cmd);
else if (cmd->sampleP && cmd->matchedP && cmd->odds_ratioP && cmd->exposedP)
mccpower (cmd);
else if (cmd->deltaP && cmd->compP && !cmd->sampleP)
nequivp (cmd);
else if (cmd->deltaP && cmd->meansP && !cmd->sampleP)
nequivm (cmd);
else
sperror ("wrong combination of options, or missing options");
exit (0);
}
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 main(int argc, char **argv)
{
int i_file,i_scan,i_chan,i_bin,n_omit,status=0;
int NFirstTable, NumHDU, NDumps, TotDumps=0, hdutype;
// int OutChans;
int spk;
int got_bins=0, got_mjd1=0; //, zeroed_outprofs=0;
long NPtsProf=0, FirstNPtsProf=0;
float Weight=1.0, TotWeight=0.;
// int ProfSum=0;
double x, ptype;
double MJD_first=0., MJD_last=0., MJD_mid;
double IMJDMid, MJDSecsMid;
double SBase,Srms,Duty,SPeak,FinalMask[NBINMAX];
double OutFreq;
char ProgName[32];
char Outfile[128];
char Header[256];
struct ASPHdr *Hdr;
struct SubHdr Subhdr;
struct StdProfs *InProfile, OutProfile;
struct RunVars RunMode;
fitsfile **Fin;
FILE *Fout, *Fcheck;
Cmdline *Cmd;
/* Get command line variables */
Cmd = parseCmdline(argc, argv);
/* Normally use this somewhere, and not showOptionValues */
Cmd->tool = Cmd->tool;
strcpy(ProgName, argv[0]);
Fin = (fitsfile **)malloc(Cmd->InfileC*sizeof(fitsfile));
Hdr = (struct ASPHdr *)malloc(Cmd->InfileC*sizeof(struct ASPHdr));
/* Dynamically allocate RunMode variables */
if (AllocRunMode(&RunMode) < 0){
printf("Could not allocate RunMode structure. Exiting...\n");
exit(2);
}
strcpy(RunMode.Infile,Cmd->Infile);
// if(!zeroed_outprofs) {
/* if(Cmd->SortChansP){
OutChans=Hdr[0].obs.NChan;
}
else{ */
// OutChans=1;
// }
// OutProfile=(struct StdProfs *)malloc(OutChans*sizeof(struct StdProfs));
// TotWeight=(float *)malloc(OutChans*sizeof(float));
/* Zero out profiles */
// for(i_chan=0;i_chan<OutChans;i_chan++){
FZero(OutProfile.rstds,NBINMAX);
FZero(OutProfile.rstdq,NBINMAX);
FZero(OutProfile.rstdu,NBINMAX);
FZero(OutProfile.rstdv,NBINMAX);
// }
//zeroed_outprofs=1;
// }
/* Create an output file to check omissions if in vebose mode */
if (Cmd->VerboseP || Cmd->CheckOmitP){
if((Fcheck = fopen("check_omit.dat","w")) == 0)
{ printf("Cannot open %s. Exiting...\n",Outfile); exit(1); }
}
/* read in all input files and add each to the final profile */
/* read in all input file headers */
NPtsProf=0;
for (i_file=0;i_file<Cmd->InfileC;i_file++){
n_omit=0;
status=0;
if(fits_open_file(&Fin[i_file], Cmd->Infile[i_file], READONLY, &status)){
printf("Error opening FITS file %s !!!\n", Cmd->Infile[i_file]);
exit(1);
}
if(ReadASPHdr(&Hdr[i_file], Fin[i_file]) < 0){
printf("%s> Unable to read Header from file %s. Exiting...\n",
ProgName,Cmd->Infile[i_file]);
exit(1);
}
/* Write file name in verbose-mode omit check file */
if(Cmd->VerboseP || Cmd->CheckOmitP)
fprintf(Fcheck, "\n%s\n",Cmd->Infile[i_file]);
/* for now just check if all files have same number of channels */
/* if(Cmd->SortChansP)
if(i_file>0 && Hdr[i_file].obs.NChan!=Hdr[0].obs.NChan){
fprintf(stderr,"%s> Different numbers of channels in different files:\n\n",
ProgName);
fprintf(stderr,"%s: %d channels, %s: %d channels\n",
Cmd->Infile[0],Hdr[0].obs.NChan,
Cmd->Infile[i_file],Hdr[i_file].obs.NChan);
} */
/* now find the number of dumps in the file */
fits_get_num_hdus(Fin[i_file], &NumHDU, &status);
if(!strcmp(Hdr[i_file].gen.HdrVer,"Ver1.0")){
NDumps = NumHDU-3; /* the "3" is temporary, depending on how
many non-data tables we will be using */
}
else if(!strcmp(Hdr[i_file].gen.HdrVer,"Ver1.0.1")){
NDumps = (NumHDU-3)/2;
}
else{
fprintf(stderr,"%s> Do not recognize FITS file version in header.\n",
ProgName);
fprintf(stderr,"This header is %s. Exiting...\n",Hdr[i_file].gen.HdrVer);
exit(1);
}
printf("File %s:\n",Cmd->Infile[i_file]);
printf(" Number of channels: %d\n",Hdr[i_file].obs.NChan) ;
printf(" Number of dumps: %d\n",NDumps);
/* Move to the first data table HDU in the fits file */
if(!strcmp(Hdr[i_file].gen.HdrVer,"Ver1.0"))
fits_movnam_hdu(Fin[i_file], BINARY_TBL, "STOKES0", 0, &status);
else if (!strcmp(Hdr[i_file].gen.HdrVer,"Ver1.0.1"))
fits_movnam_hdu(Fin[i_file], ASCII_TBL, "DUMPREF0", 0, &status);
/* Get the current HDU number */
fits_get_hdu_num(Fin[i_file], &NFirstTable);
/* Set up Profile structure size */
for(i_scan=0;i_scan<NDumps;i_scan++){
InProfile=(struct StdProfs *)malloc(Hdr[i_file].obs.NChan*
sizeof(struct StdProfs));
/* move to next dump's data */
if(!strcmp(Hdr[i_file].gen.HdrVer,"Ver1.0")){
fits_movabs_hdu(Fin[i_file], NFirstTable+i_scan, &hdutype, &status);
}
else if(!strcmp(Hdr[i_file].gen.HdrVer,"Ver1.0.1")){
/* if we've reached the end of the FITS file then increase FileNo */
fits_movabs_hdu(Fin[i_file],NFirstTable+(i_scan%MAXDUMPS)*2+1,&hdutype,
&status);
fits_get_num_rows(Fin[i_file], &NPtsProf, &status);status=0;
fits_movrel_hdu(Fin[i_file], -1, NULL, &status);
}
/* IF not done so, use number of bins from first file to compare to
the rest of the files */
if(got_bins==0){
FirstNPtsProf=NPtsProf;
got_bins=1;
}
/********** FIX: SKIP THIS WITHOUT DOING THE OMIT THING ***********/
/********** AND DON'T ADD TO NUMBER COUNT ************/
if(NPtsProf != FirstNPtsProf) {
fprintf(stderr,"Warning: Skipping scan %d (%ld bins ",
i_scan,NPtsProf);
fprintf(stderr,"vs. %ld bins in others).\n",FirstNPtsProf);
n_omit += Hdr[i_file].obs.NChan;
}
else{
/* find NPtsProf */
ReadASPStokes(&Hdr[i_file], &Subhdr, Fin[i_file], NPtsProf,
InProfile, i_scan, Cmd->VerboseP);
/* Add this profile onto running output profile */
for(i_chan=0;i_chan<Hdr[i_file].obs.NChan;i_chan++){
/* Bad scans are zeroed so if summ of the profile is zero, it's
not to be used in summation */
// ProfSum = FSum(&InProfile[i_chan].rstds[0], NPtsProf);
// ProfSum = 0;
// ProfSum = ArrayZero(InProfile[i_chan].rstds, NPtsProf);
// if(ProfSum != 0.0) { // i.e. good data
/* Test that all bins in current profile are not zeroed */
if(!ArrayZero(InProfile[i_chan].rstds, NPtsProf)) { // i.e. good data
// if(InProfile[i_chan].rstds[0] > -99998.) { // i.e. good data
/* If first MJD has not been registered, then do so since this
would be the first non-omitted scan */
if (got_mjd1==0) {
MJD_first = (double)Hdr[i_file].obs.IMJDStart +
Subhdr.DumpMiddleSecs/86400.;
got_mjd1=1;
}
if (i_scan==NDumps-1) {
/* Just keep overwriting MJD_last every i_file -- that way we
ensure getting the last MJD of the FINAL non-omitted scan
used */
MJD_last = (double)Hdr[i_file].obs.IMJDStart +
Subhdr.DumpMiddleSecs/86400.;
}
/* Get SNR for each Profile if we want to use weighting;
otherwise weights will all be 1.0 */
if(Cmd->WeightP) {
Duty = DutyLookup(Hdr[i_file].target.PSRName);
BMask(InProfile[i_chan].rstds,&Hdr[i_file].redn.RNBinTimeDump,
&Duty,FinalMask);
Baseline(InProfile[i_chan].rstds,FinalMask,
&Hdr[i_file].redn.RNBinTimeDump,&SBase,&Srms);
SPeak = FindPeak(InProfile[i_chan].rstds,
&Hdr[i_file].redn.RNBinTimeDump,&spk);
InProfile[i_chan].SNR = SPeak*Srms;
// Weight = InProfile[i_chan].SNR;
Weight = Srms; // which is actually 1/RMS.
}
// printf("SNR %d = %lf\n",i_chan,InProfile[i_chan].SNR);
/* Need to figure out how to organize input channels to match
* output channels */
/* if(Cmd->SortChansP){
for(i_bin=0;i_bin<NPtsProf;i_bin++) {
OutProfile[i_chan].rstds[i_bin] +=
Weight*InProfile[i_chan].rstds[i_bin];
OutProfile[i_chan].rstdq[i_bin] +=
Weight*InProfile[i_chan].rstdq[i_bin];
OutProfile[i_chan].rstdu[i_bin] +=
Weight*InProfile[i_chan].rstdu[i_bin];
OutProfile[i_chan].rstdv[i_bin] +=
Weight*InProfile[i_chan].rstdv[i_bin];
}
}
else{ */
for(i_bin=0;i_bin<NPtsProf;i_bin++) {
OutProfile.rstds[i_bin] +=
Weight*InProfile[i_chan].rstds[i_bin];
OutProfile.rstdq[i_bin] +=
Weight*InProfile[i_chan].rstdq[i_bin];
OutProfile.rstdu[i_bin] +=
Weight*InProfile[i_chan].rstdu[i_bin];
OutProfile.rstdv[i_bin] +=
Weight*InProfile[i_chan].rstdv[i_bin];
// printf("%f\n",OutProfile[0].rstds[i_bin]);fflush(stdout);
}
// }
TotWeight += Weight; // for now keep at zero index
/* Print profile weights for each scan, for each channel */
if(RunMode.Verbose) {
if(i_chan==0) printf("Profile weights -- scan %d: \n ",i_scan);
printf("%6.2f ",Weight);
if(i_chan==Hdr[i_file].obs.NChan-1) printf("\n");fflush(stdout);
}
}
else {
n_omit++;
if(Cmd->VerboseP || Cmd->CheckOmitP){
fprintf(Fcheck, "%6d %.1lf\n",
i_scan,Hdr[i_file].obs.ChanFreq[i_chan]);
/* printf("File %d, Dump %d, Channel %d (%lf MHz) were found to be\n",
i_file,i_scan,i_chan,Hdr[i_file].obs.ChanFreq[i_chan]);
printf(" zeroed and so are not included.\n");fflush(stdout); */
}
}
// if(i_chan==0) {for(i=0;i<50;i++) printf("%lf ",OutProfile[0].rstds[i]);printf("\n\n");fflush(stdout);};
}
/*****************/
/* } */
} /* else from positive check on NPtsProf */
free(InProfile);
}
/****** maybe bring this inside the ELSE where entire scans aren't being omitted ******/
/* if (Cmd->SortChansP)
TotDumps += (NDumps - n_omit);
else */
TotDumps += (NDumps*Hdr[i_file].obs.NChan - n_omit);
//free(InProfile);
printf("Reading of file %s complete and successful.\n",
Cmd->Infile[i_file]);
printf("%d scans omitted.\n\n",n_omit);fflush(stdout);
}
if(Cmd->VerboseP || Cmd->CheckOmitP) fclose(Fcheck);
/* Appease the format of the MakePol routine by making up these RunMode
structure members */
strcpy(RunMode.Source,Hdr[0].target.PSRName);
RunMode.Verbose = Cmd->VerboseP;
RunMode.FlipPA = 0;
RunMode.NoBase = Cmd->NoBaseP;
/* divide out total number of dumps to get the average */
// for(i_chan=0;i_chan<OutChans;i_chan++){
printf("Totdumps = %d\n",TotDumps);
fflush(stdout);
for(i_bin=0;i_bin<NPtsProf;i_bin++) {
OutProfile.rstds[i_bin] /= TotWeight;
OutProfile.rstdq[i_bin] /= TotWeight;
OutProfile.rstdu[i_bin] /= TotWeight;
OutProfile.rstdv[i_bin] /= TotWeight;
}
MakePol(&RunMode, (int)NPtsProf, &OutProfile);
/* Open file for writing */
sprintf(Outfile,"AddProf.out");
/* now write the output ascii added profile */
if ((Fout = fopen(Outfile,"w")) == 0)
{ printf("Cannot open %s. Exiting...\n",Outfile); exit(1); }
/* take average MJD of first to last scan */
MJD_mid = (MJD_first + MJD_last)/2.;
IMJDMid = floor(MJD_mid);
MJDSecsMid = (MJD_mid - IMJDMid)*86400.;
printf("MJD_mid = %lf, IMJDMid = %lf, MJDSecsMid = %lf\n",MJD_mid,IMJDMid,MJDSecsMid);fflush(stdout);
/* to choose a channel to put in the header for now, ust use the average
of the first datafile's channels */
OutFreq=0.;
for(i_chan=0; i_chan<Hdr[0].obs.NChan; i_chan++){
OutFreq += Hdr[0].obs.ChanFreq[i_chan];
}
OutFreq /= Hdr[0].obs.NChan;
/* Create and print header line for output file(s) */
sprintf(Header,"# %.1f %.7f %.10f %ld %.3f %.3f %d %s %d %9s %.10f",
IMJDMid,
MJDSecsMid,
// Subhdr.DumpRefPeriod[i_chan],
0.,
(long)1, OutFreq,
// Hdr[0].obs.DM, Hdr[i_file].redn.RNBinTimeDump,
Hdr[0].obs.DM, (int)NPtsProf,
Hdr[0].obs.ObsvtyCode, 1, Hdr[0].target.PSRName,
0.);
// Subhdr.DumpRefPhase[i_chan]);
fprintf(Fout,"%s\n",Header);
for(i_bin=0;i_bin<NPtsProf;i_bin++) {
/* see how strong the linear polarization is */
x = OutProfile.stdlin[i_bin]*OutProfile.Srms;
ptype = 43.1;
if (x > 1.) ptype=43.2;
if (x > 2.) ptype=43.3;
if (x > 3.) ptype=43.4;
if (x > 4.) ptype=43.5;
if (x > 5.) ptype=43.6;
fprintf(Fout,"%5d%15.7f%15.7f%15.7f%15.7f%15.7f%15.7f%15.7f%6.1f\n",i_bin,
OutProfile.rstds[i_bin],OutProfile.rstdq[i_bin],
OutProfile.rstdu[i_bin],
OutProfile.rstdv[i_bin],
/* phi in degrees */
OutProfile.stdlin[i_bin],
OutProfile.stdphi[i_bin]*180.0/TWOPI,
OutProfile.stdphierr[i_bin]*180.0/TWOPI,ptype);
}
printf("Created output file %s\n",Outfile);
fclose(Fout);
// }
/* Write all this to file */
printf("\nCompleted successfully.\n\n");fflush(stdout);
exit(0);
}
int main(int argc, char **argv)
{
void *retval;
int engine, evaltype, record, errorcode, usevaluefile = 1;
Board *state;
threadParameter *threadparameter;
char *errorstring;
char *tempcheck;
FILE *logfile, *gamefile;
pthread_t inputThread, outputThread; /* thread that takes care of input/output to user/front end */
prodcons *input, *output; /* communication buffers for iothread */
Cmdline *cmd;
logfile = gamefile = NULL;
#ifdef WIN32
/* copied from Dann Corbit to use under windows environment */
/* No buffering, please... */
setbuf(stdout, NULL);
setbuf(stdin, NULL);
/* and I *really* mean it, too! */
setvbuf(stdout, NULL, _IONBF, 0);
setvbuf(stdin, NULL, _IONBF, 0);
fflush(NULL);
#endif
srandom((unsigned int) time(NULL));
state = (Board *) xmalloc(sizeof(Board));
threadparameter = (threadParameter *) xmalloc(sizeof(threadParameter));
cmd = parseCmdline(argc, argv);
if (cmd->show_helpP)
usage();
if (cmd->show_versionP) {
printf("%s %s\n", argv[0], VERSION);
exit(0);
}
if (cmd->configfileP) {
processConfigFile(cmd->configfile);
} else {
processConfigFile(NULL);
}
if ((cmd->verboseP) && (cmd->verbose > 0)){
configvalues.verbose = cmd->verbose;
}
if (configvalues.verbose > 0) {
if (cmd->logfileP) {
logfile = fopen(cmd->logfile, "w");
} else if (configvalues.logfilename) {
logfile = fopen(configvalues.logfilename, "w");
} else {
logfile = NULL;
configvalues.verbose = 0;
}
if (logfile) {
/* Make log file line buffered*/
setlinebuf(logfile);
}
state->logfile = logfile;
} else {
state->logfile = NULL;
}
state->verbosity = configvalues.verbose;
record = 0;
gamefile = NULL;
if ((cmd->recordP) || (configvalues.record)) {
if (!cmd->norecordP) {
record = 1;
if (cmd->gamefileP) {
gamefile = fopen(cmd->gamefile, "a");
} else if (configvalues.gamefilename) {
gamefile = fopen(configvalues.gamefilename, "a");
} else {
gamefile = NULL;
record = 0;
}
}
}
state->record = record;
state->gamefile = gamefile;
if (cmd->randomvarianceP) {
state->random = cmd->randomvariance;
} else {
state->random = configvalues.random;
}
engine = configvalues.engine;
if (cmd->randomP) {
engine = RANDOM_ENGINE;
}
if (cmd->onestepP) {
engine = ONESTEP_ENGINE;
}
if (cmd->completeP) {
engine = COMPLETENEGAMAX_ENGINE;
}
if (cmd->multistepP) {
engine = MULTISTEP_ENGINE;
}
if (cmd->negascoutP) {
engine = NEGASCOUT_ENGINE;
}
evaltype = configvalues.evaltype;
usevaluefile = configvalues.usevaluefile;
if (cmd->fixedevalP) {
usevaluefile = 0;
}
if (cmd->relativeevalP) {
evaltype = RELATIVEPOSITIONPIECE_EVAL;
} else if (cmd->positionevalP) {
evaltype = POSITIONPIECE_EVAL;
}
switch (engine) {
case RANDOM_ENGINE:
state->engine = randomPlay;
break;
case ONESTEP_ENGINE:
state->engine = oneStep;
break;
case COMPLETENEGAMAX_ENGINE:
state->engine = multiNegamax;
break;
case MULTISTEP_ENGINE:
state->engine = multiStep;
break;
case NEGASCOUT_ENGINE:
state->engine = timedIterative;
state->searcher = negaScoutDriver;
break;
default:
state->engine = NULL;
}
if (cmd->resignP) {
configvalues.resign = - ((int) (cmd->resign * 100));
}
switch (evaltype) {
case POSITIONPIECE_EVAL:
if (cmd->noresignP) {
state->resign = MINVALUE - 1;
} else {
state->resign = configvalues.resign;
}
state->evalboard = positionheuri;
break;
case RELATIVEPOSITIONPIECE_EVAL:
state->evalboard = relativepositionheuri;
state->resign = MINVALUE - 1;
break;
default:
state->evalboard = NULL;
}
if (!cmd->nobookP) {
if (cmd->bookfileP) {
errorcode = initialiseOpeningBook(cmd->bookfile);
if (errorcode) {
errorstring = bookErrorToString(errorcode);
fprintf(stderr,"%s\n",errorstring);
free(errorstring);
}
} else if ((configvalues.usebook) && (configvalues.bookfilename)) {
errorcode = initialiseOpeningBook(configvalues.bookfilename);
if (errorcode) {
errorstring = bookErrorToString(errorcode);
fprintf(stderr,"%s\n",errorstring);
free(errorstring);
}
}
}
if (usevaluefile) {
if (cmd->valuefileP) {
initialisePieceValues(cmd->valuefile);
configvalues.valuefilename = cmd->valuefile;
} else if (configvalues.valuefilename) {
initialisePieceValues(configvalues.valuefilename);
} else {
initialisePieceValues(NULL);
}
} else {
initialisePieceValues(NULL);
}
if (cmd->computernameP) {
state->name = xstrdup(cmd->computername);
} else if (configvalues.computername) {
state->name = xstrdup(configvalues.computername);
} else {
if (configvalues.valuefilename) {
state->name =
(char *) xmalloc(strlen(PACKAGE_STRING) +
strlen(configvalues.valuefilename) + 2);
tempcheck = state->name;
state->name = strcpy(state->name, PACKAGE_STRING);
state->name = strcat(state->name, " ");
state->name = strcat(state->name, configvalues.valuefilename);
if (tempcheck != state->name) {
printf("f****d\n");
}
} else {
state->name = (char *) xstrdup (PACKAGE_STRING);
}
}
if (cmd->dP) {
configvalues.maxdepth = cmd->d;
}
state->depth = configvalues.maxdepth;
if (cmd->epdmindepthP) {
configvalues.epdmindepth = cmd->epdmindepth;
}
state->epdmindepth = configvalues.epdmindepth;
if (cmd->drawvalueP) {
configvalues.drawvalue = cmd->drawvalue;
}
state->drawvalue = configvalues.drawvalue;
state->timeaggression = configvalues.timeaggression;
if (cmd->hashsizeP) {
state->hashtable = initialiseHashTable(cmd->hashsize);
} else if (cmd->hashkilobytesP) {
state->hashtable = initialiseHashTableBySize(cmd->hashkilobytes);
} else if (configvalues.hashentries) {
state->hashtable = initialiseHashTable(configvalues.hashentries);
} else if (configvalues.hashkilobytes) {
state->hashtable = initialiseHashTableBySize(configvalues.hashkilobytes);
} else {
state->hashtable = initialiseHashTable(0);
}
initialiseMoveLists();
initialiseGenerateFunctions();
input = (prodcons *) xmalloc(sizeof(prodcons));
output = (prodcons *) xmalloc(sizeof(prodcons));
initComms(input);
initComms(output);
state->input = input;
state->output = output;
threadparameter->input = input;
threadparameter->output = output;
threadparameter->name = state->name;
pthread_create(&inputThread, NULL, doInput, (void *) threadparameter);
pthread_create(&outputThread, NULL, doOutput, (void *) threadparameter);
play(state);
pthread_cancel(inputThread);
pthread_join(outputThread, &retval);
finaliseComms(input);
finaliseComms(output);
closeOpeningBook();
free(state);
free(input);
free(output);
if (configvalues.verbose) {
fflush(logfile);
fclose(logfile);
}
if (record) {
fflush(gamefile);
fclose(gamefile);
}
exit(0);
}
int main(int argc, char **argv)
{
int index = -1, need_type = 0;
int objs_read, objs_to_read, has_suffix;
long i, j, ct;
char *cptr, *data, *short_filenm, *extension, key = '\n';
FILE *infile;
Cmdline *cmd;
infodata inf;
/* Call usage() if we have no command line arguments */
if (argc == 1) {
Program = argv[0];
usage();
exit(0);
}
/* Parse the command line using the excellent program Clig */
cmd = parseCmdline(argc, argv);
#ifdef DEBUG
showOptionValues();
#endif
//fprintf(stdout, "\n\n PRESTO Binary File Reader\n");
//fprintf(stdout, " by Scott M. Ransom\n\n");
/* Set our index value */
if (cmd->bytP || cmd->sbytP)
index = BYTE;
else if (cmd->fltP || cmd->sfltP)
index = FLOAT;
else if (cmd->dblP || cmd->sdblP)
index = DOUBLE;
else if (cmd->fcxP || cmd->sfcxP)
index = FCPLEX;
else if (cmd->dcxP || cmd->sdcxP)
index = DCPLEX;
else if (cmd->shtP || cmd->sshtP)
index = SHORT;
else if (cmd->igrP || cmd->sigrP)
index = INT;
else if (cmd->lngP || cmd->slngP)
index = LONG;
else if (cmd->rzwP || cmd->srzwP)
index = RZWCAND;
else if (cmd->binP || cmd->sbinP)
index = BINCAND;
else if (cmd->posP || cmd->sposP)
index = POSITION;
else if (cmd->pkmbP)
index = PKMBHDR;
else if (cmd->bcpmP)
index = BCPMHDR;
else if (cmd->wappP)
index = WAPPHDR;
else if (cmd->spigotP)
index = SPIGOTHDR;
else if (cmd->filterbankP)
index = SPECTRAINFO;
#ifdef USELOFAR
else if (cmd->lofarhdf5P)
index = SPECTRAINFO;
#endif
else if (cmd->psrfitsP)
index = SPECTRAINFO;
/* Try to determine the data type from the file name */
if (index == -1) {
has_suffix = split_root_suffix(cmd->argv[0], &short_filenm, &extension);
if (!has_suffix) {
need_type = 1;
} else {
if (strlen(extension) < 2) {
need_type = 1;
} else {
if (0 == strcmp(extension, "dat")) {
index = FLOAT;
fprintf(stdout, "Assuming the data is floating point.\n\n");
} else if (0 == strcmp(extension, "sdat")) {
index = SHORT;
fprintf(stdout, "Assuming the data is short integers.\n\n");
} else if (0 == strcmp(extension, "fft")) {
index = FCPLEX;
fprintf(stdout, "Assuming the data is single precision complex.\n\n");
} else if ((0 == strcmp(extension, "fits")) ||
(0 == strcmp(extension, "sf"))) {
if (strstr(short_filenm, "spigot_5") != NULL) {
cmd->spigotP = 1;
index = SPIGOTHDR;
fprintf(stdout,
"Assuming the data is from the Caltech/NRAO Spigot.\n\n");
} else if (is_PSRFITS(cmd->argv[0])) {
cmd->psrfitsP = 1;
index = SPECTRAINFO;
fprintf(stdout,
"Assuming the data is in PSRFITS format.\n\n");
}
} else if (0 == strcmp(extension, "bcpm1") ||
0 == strcmp(extension, "bcpm2")) {
cmd->bcpmP = 1;
index = BCPMHDR;
fprintf(stdout, "Assuming the data is from a BCPM machine.\n\n");
} else if (0 == strcmp(extension, "pkmb")) {
cmd->pkmbP = 1;
index = PKMBHDR;
fprintf(stdout,
"Assuming the data is from the Parkes Multibeam machine.\n\n");
} else if (0 == strcmp(extension, "fil") || 0 == strcmp(extension, "fb")) {
cmd->filterbankP = 1;
index = SPECTRAINFO;
fprintf(stdout,
"Assuming the data is a SIGPROC filterbank file.\n\n");
} else if (0 == strcmp(extension, "h5")) {
cmd->lofarhdf5P = 1;
index = SPECTRAINFO;
fprintf(stdout,
"Assuming the data is a LOFAR HDF5 file.\n\n");
} else if (isdigit(extension[0]) &&
isdigit(extension[1]) && isdigit(extension[2])) {
cmd->wappP = 1;
index = WAPPHDR;
fprintf(stdout, "Assuming the data is from a WAPP machine.\n\n");
} else if (0 == strcmp(extension, "pos")) {
index = POSITION;
fprintf(stdout,
"Assuming the data contains 'position' structures.\n\n");
} else if (0 == strcmp(extension, "cand")) {
/* A binary or RZW search file? */
if (NULL != (cptr = strstr(cmd->argv[0], "_bin"))) {
index = BINCAND;
fprintf(stdout,
"Assuming the file contains binary candidates.\n\n");
} else if (NULL != (cptr = strstr(cmd->argv[0], "_rzw"))) {
index = RZWCAND;
ct = (long) (cptr - cmd->argv[0]);
fprintf(stdout, "Assuming the file contains 'RZW' candidates.\n");
free(short_filenm);
short_filenm = (char *) malloc(ct + 1);
short_filenm[ct] = '\0';
strncpy(short_filenm, cmd->argv[0], ct);
fprintf(stdout, "\nAttempting to read '%s.inf'. ", short_filenm);
readinf(&inf, short_filenm);
fprintf(stdout, "Successful.\n");
N = (long) (inf.N + DBLCORRECT);
dt = inf.dt;
if (cmd->nphP)
nph = cmd->nph;
else
nph = 1.0;
fprintf(stdout,
"\nUsing N = %ld, dt = %g, and DC Power = %f\n\n",
N, dt, nph);
} else if (NULL != (cptr = strstr(cmd->argv[0], "_ACCEL"))) {
index = RZWCAND;
ct = (long) (cptr - cmd->argv[0]);
fprintf(stdout, "Assuming the file contains 'RZW' candidates.\n");
free(short_filenm);
short_filenm = (char *) malloc(ct + 1);
short_filenm[ct] = '\0';
strncpy(short_filenm, cmd->argv[0], ct);
fprintf(stdout, "\nAttempting to read '%s.inf'. ", short_filenm);
readinf(&inf, short_filenm);
fprintf(stdout, "Successful.\n");
N = (long) (inf.N + DBLCORRECT);
dt = inf.dt;
if (cmd->nphP)
nph = cmd->nph;
else
nph = 1.0;
fprintf(stdout,
"\nUsing N = %ld, dt = %g, and DC Power = %f\n\n",
N, dt, nph);
} else
need_type = 1;
} else
need_type = 1;
}
}
/* If no file extension or if we don't understand the extension, exit */
if (need_type) {
fprintf(stdout, "You must specify a data type for this file.\n\n");
free(short_filenm);
exit(-1);
}
free(short_filenm);
if (has_suffix)
free(extension);
}
if (cmd->index[1] == -1 || cmd->index[1] == 0)
cmd->index[1] = INT_MAX;
if (cmd->index[1] < cmd->index[0]) {
fprintf(stdout, "\nThe high index must be >= the low index.");
fprintf(stdout, " Exiting.\n\n");
exit(-1);
}
// Use new-style backend reading stuff
if (cmd->psrfitsP || cmd->filterbankP || cmd->lofarhdf5P) {
struct spectra_info s;
// Eventually we should use this...
// identify_psrdatatype(struct spectra_info *s, int output);
spectra_info_set_defaults(&s);
if (cmd->psrfitsP) s.datatype=PSRFITS;
if (cmd->filterbankP) s.datatype=SIGPROCFB;
if (cmd->lofarhdf5P) s.datatype=LOFARHDF5;
s.filenames = cmd->argv;
s.num_files = cmd->argc;
s.clip_sigma = 0.0;
s.apply_flipband = s.apply_weight = s.apply_scale = s.apply_offset = -1;
s.remove_zerodm = 0;
read_rawdata_files(&s);
SPECTRAINFO_print(0, (char *)(&s));
printf("\n");
exit(0);
}
if (cmd->spigotP) {
SPIGOT_INFO spigot;
if (read_SPIGOT_header(cmd->argv[0], &spigot)) {
print_SPIGOT_header(&spigot);
printf("\n");
} else {
printf("\n Error reading spigot file!\n\n");
}
exit(0);
}
if (cmd->wappP) {
struct HEADERP *hdr = NULL;
infile = chkfopen(cmd->argv[0], "rb");
hdr = head_parse(infile);
set_WAPP_HEADER_version(hdr);
if (hdr) {
print_WAPP_hdr(hdr);
printf("\n");
} else {
printf("\n Error reading WAPP file!\n\n");
}
exit(0);
}
/* Open the file */
infile = chkfopen(cmd->argv[0], "rb");
if (cmd->fortranP) {
chkfileseek(infile, 1, sizeof(long), SEEK_SET);
}
/* Skip to the correct first object */
if (cmd->index[0] > 0) {
chkfileseek(infile, (long) (cmd->index[0]), type_sizes[index], SEEK_CUR);
}
/* Read the file */
objs_to_read = objs_at_a_time[index];
data = (char *) malloc(type_sizes[index] * objs_at_a_time[index]);
i = cmd->index[0];
do {
if (objs_to_read > cmd->index[1] - i)
objs_to_read = cmd->index[1] - i;
objs_read = chkfread(data, type_sizes[index], objs_to_read, infile);
for (j = 0; j < objs_read; j++)
print_funct_ptrs[index] (i + j, data + j * type_sizes[index]);
/* Just print 1 header for BCPM and WAPP files */
if (index == BCPMHDR || index == WAPPHDR || index == SPIGOTHDR)
break;
i += objs_read;
if (cmd->pageP) {
fflush(NULL);
fprintf(stdout, "\nPress ENTER for next page, or any other key and ");
fprintf(stdout, "then ENTER to exit.\n\n");
key = getchar();
}
} while (!feof(infile) && i < cmd->index[1] && key == '\n');
fflush(NULL);
if (feof(infile)) {
fprintf(stdout, "\nEnd of file.\n\n");
}
free(data);
fclose(infile);
exit(0);
}
int main(int argc, char *argv[])
{
/* Any variable that begins with 't' means topocentric */
/* Any variable that begins with 'b' means barycentric */
FILE *outfile;
float *outdata = NULL;
double tdf = 0.0, dtmp = 0.0, barydispdt = 0.0, dsdt = 0.0;
double *dispdt, *tobsf = NULL, tlotoa = 0.0, blotoa = 0.0;
double max = -9.9E30, min = 9.9E30, var = 0.0, avg = 0.0;
char obs[3], ephem[10], *datafilenm, *outinfonm;
char rastring[50], decstring[50];
int numchan = 1, newper = 0, oldper = 0, nummasked = 0, useshorts = 0;
int numadded = 0, numremoved = 0, padding = 0, *maskchans = NULL, offset = 0;
long slen, ii, numbarypts = 0, worklen = 65536;
long numread = 0, numtowrite = 0, totwrote = 0, datawrote = 0;
long padwrote = 0, padtowrite = 0, statnum = 0;
int numdiffbins = 0, *diffbins = NULL, *diffbinptr = NULL, good_padvals = 0;
int *idispdt;
struct spectra_info s;
infodata idata;
Cmdline *cmd;
mask obsmask;
/* Call usage() if we have no command line arguments */
if (argc == 1) {
Program = argv[0];
printf("\n");
usage();
exit(0);
}
/* Parse the command line using the excellent program Clig */
cmd = parseCmdline(argc, argv);
spectra_info_set_defaults(&s);
s.filenames = cmd->argv;
s.num_files = cmd->argc;
// If we are zeroDMing, make sure that clipping is off.
if (cmd->zerodmP)
cmd->noclipP = 1;
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 (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->ncpus > 1) {
#ifdef _OPENMP
int maxcpus = omp_get_num_procs();
int openmp_numthreads = (cmd->ncpus <= maxcpus) ? cmd->ncpus : maxcpus;
// Make sure we are not dynamically setting the number of threads
omp_set_dynamic(0);
omp_set_num_threads(openmp_numthreads);
printf("Using %d threads with OpenMP\n\n", openmp_numthreads);
#endif
} else {
#ifdef _OPENMP
omp_set_num_threads(1); // Explicitly turn off OpenMP
#endif
}
#ifdef DEBUG
showOptionValues();
#endif
printf("\n\n");
printf(" Pulsar Data Preparation Routine\n");
printf(" Type conversion, de-dispersion, barycentering.\n");
printf(" by Scott M. Ransom\n\n");
if (RAWDATA) {
if (cmd->filterbankP)
s.datatype = SIGPROCFB;
else if (cmd->psrfitsP)
s.datatype = PSRFITS;
} 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 == SDAT)
useshorts = 1;
else if (s.datatype != DAT) {
printf
("Error: Unable to identify input data files. Please specify type.\n\n");
exit(1);
}
}
if (!RAWDATA) {
char *root, *suffix;
/* Split the filename into a rootname and a suffix */
if (split_root_suffix(s.filenames[0], &root, &suffix) == 0) {
printf("\nThe input filename (%s) must have a suffix!\n\n",
s.filenames[0]);
exit(1);
}
printf("Reading input data from '%s'.\n", s.filenames[0]);
printf("Reading information from '%s.inf'.\n\n", root);
/* Read the info file if available */
readinf(&idata, root);
free(root);
free(suffix);
s.files = (FILE **) malloc(sizeof(FILE *));
s.files[0] = chkfopen(s.filenames[0], "rb");
} else {
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]);
}
printf("\n");
}
/* Determine the other file names and open the output data file */
slen = strlen(cmd->outfile) + 8;
datafilenm = (char *) calloc(slen, 1);
sprintf(datafilenm, "%s.dat", cmd->outfile);
outfile = chkfopen(datafilenm, "wb");
sprintf(idata.name, "%s", cmd->outfile);
outinfonm = (char *) calloc(slen, 1);
sprintf(outinfonm, "%s.inf", cmd->outfile);
if (RAWDATA) {
read_rawdata_files(&s);
if (cmd->ignorechanstrP) {
s.ignorechans = get_ignorechans(cmd->ignorechanstr, 0, s.num_channels-1,
&s.num_ignorechans, &s.ignorechans_str);
if (s.ignorechans_str==NULL) {
s.ignorechans_str = (char *)malloc(strlen(cmd->ignorechanstr)+1);
strcpy(s.ignorechans_str, cmd->ignorechanstr);
}
}
print_spectra_info_summary(&s);
spectra_info_to_inf(&s, &idata);
/* Finish setting up stuff common to all raw formats */
idata.dm = cmd->dm;
worklen = s.spectra_per_subint;
/* If we are offsetting into the file, change inf file start time */
if (cmd->start > 0.0 || cmd->offset > 0) {
if (cmd->start > 0.0) /* Offset in units of worklen */
cmd->offset = (long) (cmd->start *
idata.N / worklen) * worklen;
add_to_inf_epoch(&idata, cmd->offset * idata.dt);
offset_to_spectra(cmd->offset, &s);
printf("Offsetting into the input files by %ld spectra (%.6g sec)\n",
cmd->offset, cmd->offset * idata.dt);
}
if (cmd->maskfileP)
maskchans = gen_ivect(idata.num_chan);
/* Compare the size of the data to the size of output we request */
if (cmd->numoutP) {
dtmp = idata.N;
idata.N = cmd->numout;
writeinf(&idata);
idata.N = dtmp;
} else {
/* Set the output length to a good number if it wasn't requested */
cmd->numoutP = 1;
cmd->numout = choose_good_N((long long)(idata.N/cmd->downsamp));
writeinf(&idata);
printf("Setting a 'good' output length of %ld samples\n", cmd->numout);
}
/* The number of topo to bary time points to generate with TEMPO */
numbarypts = (long) (idata.dt * idata.N * 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);
}
}
/* Read an input mask if wanted */
if (cmd->maskfileP) {
read_mask(cmd->maskfile, &obsmask);
printf("Read mask information from '%s'\n\n", cmd->maskfile);
good_padvals = determine_padvals(cmd->maskfile, &obsmask, s.padvals);
} else {
obsmask.numchan = obsmask.numint = 0;
}
/* Determine our initialization data if we do _not_ have Parkes, */
/* Green Bank BCPM, or Arecibo WAPP data sets. */
if (!RAWDATA) {
/* If we will be barycentering... */
if (!cmd->nobaryP) {
/* The number of topo to bary time points to generate with TEMPO */
numbarypts = (long) (idata.dt * idata.N * 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);
}
}
/* The number of data points to work with at a time */
if (worklen > idata.N)
worklen = idata.N;
worklen = (long) (worklen / 1024) * 1024;
/* If we are offsetting into the file, change inf file start time */
if (cmd->start > 0.0 || cmd->offset > 0) {
if (cmd->start > 0.0) /* Offset in units of worklen */
cmd->offset = (long) (cmd->start *
idata.N / worklen) * worklen;
add_to_inf_epoch(&idata, cmd->offset * idata.dt);
printf("Offsetting into the input files by %ld samples (%.6g sec)\n",
cmd->offset, cmd->offset * idata.dt);
if (useshorts) {
chkfileseek(s.files[0], cmd->offset, sizeof(short), SEEK_SET);
} else {
chkfileseek(s.files[0], cmd->offset, sizeof(float), SEEK_SET);
}
}
/* Set the output length to a good number if it wasn't requested */
if (!cmd->numoutP) {
cmd->numoutP = 1;
cmd->numout = choose_good_N((long long)(idata.N/cmd->downsamp));
printf("Setting a 'good' output length of %ld samples\n", cmd->numout);
}
}
/* Check if we are downsampling */
dsdt = idata.dt * cmd->downsamp;
if (cmd->downsamp > 1) {
printf("Downsampling by a factor of %d\n", cmd->downsamp);
printf("New sample dt = %.10g\n\n", dsdt);
if (worklen % cmd->downsamp) {
printf("Error: The downsample factor (%d) must be a factor of the\n",
cmd->downsamp);
printf(" worklength (%ld). Exiting.\n\n", worklen);
exit(1);
}
}
printf("Writing output data to '%s'.\n", datafilenm);
printf("Writing information to '%s'.\n\n", outinfonm);
/* The topocentric epoch of the start of the data */
tlotoa = (double) idata.mjd_i + idata.mjd_f;
if (!strcmp(idata.band, "Radio") && RAWDATA) {
/* The topocentric spacing between channels */
tdf = idata.chan_wid;
numchan = idata.num_chan;
/* The topocentric observation frequencies */
tobsf = gen_dvect(numchan);
tobsf[0] = idata.freq;
for (ii = 0; ii < numchan; ii++)
tobsf[ii] = tobsf[0] + ii * tdf;
/* The dispersion delays (in time bins) */
dispdt = gen_dvect(numchan); // full float bins
idispdt = gen_ivect(numchan); // nearest integer bins
if (cmd->nobaryP) {
/* Determine our dispersion time delays for each channel */
for (ii = 0; ii < numchan; ii++)
dispdt[ii] = delay_from_dm(cmd->dm, tobsf[ii]);
/* The highest frequency channel gets no delay */
/* All other delays are positive fractions of bin length (dt) */
dtmp = dispdt[numchan - 1];
for (ii = 0; ii < numchan; ii++) {
dispdt[ii] = (dispdt[ii] - dtmp) / idata.dt;
idispdt[ii] = (int) (dispdt[ii] + 0.5);
}
worklen *= ((int) (fabs(dispdt[0])) / worklen) + 1;
}
} else { /* For unknown radio raw data (Why is this here?) */
tobsf = gen_dvect(numchan);
dispdt = gen_dvect(numchan);
idispdt = gen_ivect(numchan);
dispdt[0] = 0.0;
idispdt[0] = 0;
if (!strcmp(idata.band, "Radio")) {
tobsf[0] = idata.freq + (idata.num_chan - 1) * idata.chan_wid;
cmd->dm = idata.dm;
} else {
tobsf[0] = 0.0;
cmd->dm = 0.0;
}
}
if (cmd->nobaryP) { /* Main loop if we are not barycentering... */
/* Allocate our data array */
outdata = gen_fvect(worklen);
printf("Massaging the data ...\n\n");
printf("Amount Complete = 0%%");
do {
if (RAWDATA)
numread = read_psrdata(outdata, worklen, &s, idispdt, &padding,
maskchans, &nummasked, &obsmask);
else if (useshorts)
numread = read_shorts(s.files[0], outdata, worklen, numchan);
else
numread = read_floats(s.files[0], outdata, worklen, numchan);
if (numread == 0)
break;
/* Downsample if requested */
if (cmd->downsamp > 1)
numread = downsample(outdata, numread, cmd->downsamp);
/* Print percent complete */
newper = (int) ((float) totwrote / cmd->numout * 100.0) + 1;
if (newper > oldper) {
printf("\rAmount Complete = %3d%%", newper);
fflush(stdout);
oldper = newper;
}
/* Write the latest chunk of data, but don't */
/* write more than cmd->numout points. */
numtowrite = numread;
if ((totwrote + numtowrite) > cmd->numout)
numtowrite = cmd->numout - totwrote;
chkfwrite(outdata, sizeof(float), numtowrite, outfile);
totwrote += numtowrite;
/* Update the statistics */
if (!padding) {
for (ii = 0; ii < numtowrite; ii++)
update_stats(statnum + ii, outdata[ii], &min, &max, &avg, &var);
statnum += numtowrite;
}
/* Stop if we have written out all the data we need to */
if (totwrote == cmd->numout)
break;
} while (numread);
datawrote = totwrote;
} else { /* Main loop if we are barycentering... */
double avgvoverc = 0.0, maxvoverc = -1.0, minvoverc = 1.0, *voverc = NULL;
double *bobsf = NULL, *btoa = NULL, *ttoa = NULL;
/* 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 */
bobsf = gen_dvect(numchan);
btoa = gen_dvect(numbarypts);
ttoa = gen_dvect(numbarypts);
voverc = gen_dvect(numbarypts);
for (ii = 0; ii < numbarypts; ii++)
ttoa[ii] = tlotoa + TDT * ii / SECPERDAY;
/* Call TEMPO for the barycentering */
printf("Generating barycentric corrections...\n");
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);
blotoa = btoa[0];
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("Collecting and barycentering %s...\n\n", cmd->argv[0]);
/* Determine the initial dispersion time delays for each channel */
for (ii = 0; ii < numchan; ii++) {
bobsf[ii] = doppler(tobsf[ii], avgvoverc);
dispdt[ii] = delay_from_dm(cmd->dm, bobsf[ii]);
}
/* The highest frequency channel gets no delay */
/* All other delays are positive fractions of bin length (dt) */
barydispdt = dispdt[numchan - 1];
for (ii = 0; ii < numchan; ii++) {
dispdt[ii] = (dispdt[ii] - barydispdt) / idata.dt;
idispdt[ii] = (int) (dispdt[ii] + 0.5);
}
if (RAWDATA)
worklen *= ((int) (dispdt[0]) / worklen) + 1;
/* If the data is de-dispersed radio data... */
if (!strcmp(idata.band, "Radio")) {
printf("The DM of %.2f at the barycentric observing freq of %.3f MHz\n",
idata.dm, bobsf[numchan - 1]);
printf(" causes a delay of %f seconds compared to infinite freq.\n",
barydispdt);
printf(" This delay is removed from the barycented times.\n\n");
}
printf("Topocentric epoch (at data start) is:\n");
printf(" %17.11f\n\n", tlotoa);
printf("Barycentric epoch (infinite obs freq at data start) is:\n");
printf(" %17.11f\n\n", blotoa - (barydispdt / SECPERDAY));
/* Convert the bary TOAs to differences from the topo TOAs in */
/* units of bin length (dsdt) 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 */
printf("Massaging the data...\n\n");
printf("Amount Complete = 0%%");
/* Allocate our data array */
outdata = gen_fvect(worklen);
do { /* Loop to read and write the data */
int numwritten = 0;
double block_avg, block_var;
if (RAWDATA)
numread = read_psrdata(outdata, worklen, &s, idispdt, &padding,
maskchans, &nummasked, &obsmask);
else if (useshorts)
numread = read_shorts(s.files[0], outdata, worklen, numchan);
else
numread = read_floats(s.files[0], outdata, worklen, numchan);
if (numread == 0)
break;
/* Downsample if requested */
if (cmd->downsamp > 1)
numread = downsample(outdata, numread, cmd->downsamp);
/* Determine the approximate local average */
avg_var(outdata, numread, &block_avg, &block_var);
/* Print percent complete */
newper = (int) ((float) totwrote / cmd->numout * 100.0) + 1;
if (newper > oldper) {
printf("\rAmount Complete = %3d%%", newper);
fflush(stdout);
oldper = newper;
}
/* 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;
/* FIXME: numtowrite+totwrote can wrap! */
if ((totwrote + numtowrite) > cmd->numout)
numtowrite = cmd->numout - totwrote;
if (numtowrite > numread)
numtowrite = numread;
chkfwrite(outdata, sizeof(float), numtowrite, outfile);
datawrote += numtowrite;
totwrote += numtowrite;
numwritten += numtowrite;
/* Update the statistics */
if (!padding) {
for (ii = 0; ii < numtowrite; ii++)
update_stats(statnum + ii, outdata[ii], &min, &max, &avg, &var);
statnum += numtowrite;
}
if ((datawrote == abs(*diffbinptr)) && (numwritten != numread) && (totwrote < cmd->numout)) { /* Add/remove a bin */
float favg;
int skip, nextdiffbin;
skip = numtowrite;
do { /* Write the rest of the data after adding/removing a bin */
if (*diffbinptr > 0) {
/* Add a bin */
favg = (float) block_avg;
chkfwrite(&favg, sizeof(float), 1, outfile);
numadded++;
totwrote++;
} else {
/* Remove a bin */
numremoved++;
datawrote++;
numwritten++;
skip++;
}
diffbinptr++;
/* Write the part after the diffbin */
numtowrite = numread - numwritten;
if ((totwrote + numtowrite) > cmd->numout)
numtowrite = cmd->numout - totwrote;
nextdiffbin = abs(*diffbinptr) - datawrote;
if (numtowrite > nextdiffbin)
numtowrite = nextdiffbin;
chkfwrite(outdata + skip, sizeof(float), numtowrite, outfile);
numwritten += numtowrite;
datawrote += numtowrite;
totwrote += numtowrite;
/* Update the statistics and counters */
if (!padding) {
for (ii = 0; ii < numtowrite; ii++)
update_stats(statnum + ii, outdata[skip + ii],
&min, &max, &avg, &var);
statnum += numtowrite;
}
skip += numtowrite;
/* Stop if we have written out all the data we need to */
if (totwrote == cmd->numout)
break;
} while (numwritten < numread);
}
/* Stop if we have written out all the data we need to */
if (totwrote == cmd->numout)
break;
} while (numread);
/* Free the arrays used in barycentering */
vect_free(bobsf);
vect_free(btoa);
vect_free(ttoa);
}
/* Calculate what the amount of padding we need */
if (cmd->numout > totwrote)
padwrote = padtowrite = cmd->numout - totwrote;
/* Write the new info file for the output data */
if (!cmd->nobaryP) {
idata.bary = 1;
idata.mjd_i = (int) floor(blotoa - (barydispdt / SECPERDAY));
idata.mjd_f = blotoa - (barydispdt / SECPERDAY) - idata.mjd_i;
}
if (cmd->downsamp > 1)
idata.dt = dsdt;
update_infodata(&idata, totwrote, padtowrite, diffbins, numdiffbins);
writeinf(&idata);
/* Set the padded points equal to the average data point */
if (idata.numonoff >= 1) {
int jj, index, startpad, endpad;
for (ii = 0; ii < worklen; ii++)
outdata[ii] = avg;
fclose(outfile);
outfile = 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];
chkfseek(outfile, (startpad + 1) * sizeof(float), SEEK_SET);
padtowrite = endpad - startpad;
for (jj = 0; jj < padtowrite / worklen; jj++)
chkfwrite(outdata, sizeof(float), worklen, outfile);
chkfwrite(outdata, sizeof(float), padtowrite % worklen, outfile);
}
}
vect_free(outdata);
// Close all the raw files and free their vectors
close_rawfiles(&s);
/* Print simple stats and results */
var /= (datawrote - 1);
/* Conver the '.dat' file to '.sdat' if requested */
if (cmd->shortsP) {
FILE *infile;
int safe_convert = 1, bufflen = 65536;
char *sdatafilenm;
float *fbuffer;
short *sbuffer;
offset = (int) (floor(avg));
if ((max - min) > (SHRT_MAX - SHRT_MIN)) {
if ((max - min) < 1.5 * (SHRT_MAX - SHRT_MIN)) {
printf("Warning: There is more dynamic range in the data\n"
" than can be handled perfectly:\n"
" max - min = %.2f - %.2f = %.2f\n"
" Clipping the low values...\n\n", max, min,
max - min);
offset = max - SHRT_MAX;
} else {
printf("Error: There is way too much dynamic range in the data:\n"
" max - min = %.2f - %.2f = %.2f\n"
" Not converting to shorts.\n\n", max, min, max - min);
safe_convert = 0;
}
}
if (safe_convert) {
fbuffer = gen_fvect(bufflen);
sbuffer = gen_svect(bufflen);
sdatafilenm = (char *) calloc(slen, 1);
sprintf(sdatafilenm, "%s.sdat", cmd->outfile);
printf("\n\nConverting floats in '%s' to shorts in '%s'.",
datafilenm, sdatafilenm);
fflush(NULL);
infile = chkfopen(datafilenm, "rb");
outfile = chkfopen(sdatafilenm, "wb");
while ((numread = chkfread(fbuffer, sizeof(float), bufflen, infile))) {
for (ii = 0; ii < numread; ii++)
sbuffer[ii] = (short) (fbuffer[ii] + 1e-20 - offset);
chkfwrite(sbuffer, sizeof(short), numread, outfile);
}
fclose(infile);
fclose(outfile);
remove(datafilenm);
vect_free(fbuffer);
vect_free(sbuffer);
}
}
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));
if (cmd->shortsP && offset != 0)
printf(" Offset applied to data: %d\n", -offset);
printf("\n");
/* Cleanup */
if (cmd->maskfileP) {
free_mask(obsmask);
vect_free(maskchans);
}
vect_free(tobsf);
vect_free(dispdt);
vect_free(idispdt);
free(outinfonm);
free(datafilenm);
if (!cmd->nobaryP)
vect_free(diffbins);
return (0);
}
int main(int argc, char *argv[])
{
prepfoldinfo search;
Cmdline *cmd;
plotflags flags;
/* Call usage() if we have no command line arguments */
if (argc == 1) {
Program = argv[0];
usage();
exit(0);
}
/* Parse the command line using the excellent program Clig */
cmd = parseCmdline(argc, argv);
flags.events = cmd->eventsP;
flags.scaleparts = cmd->scalepartsP;
flags.justprofs = cmd->justprofsP;
flags.allgrey = cmd->allgreyP;
flags.nosearch = 1;
/*
* Read the raw prepfoldinfo structure
*/
read_prepfoldinfo(&search, argv[1]);
/*
* Print the main prepfoldinfo structure values
*/
print_prepfoldinfo(&search);
if(cmd->infoonlyP)
return 0;
/*
* Zap requested subbands or intervals
*/
{
int *killparts, *killsubs, ii, jj, kk, index;
int numkillparts = 0, numkillsubs = 0;
if (cmd->killpartsstrP) {
killparts = ranges_to_ivect(cmd->killpartsstr, 0,
search.npart - 1, &numkillparts);
for (ii = 0; ii < numkillparts; ii++) {
if ((killparts[ii] >= 0) && (killparts[ii] < search.npart)) {
index = killparts[ii] * search.proflen * search.nsub;
for (jj = 0; jj < search.nsub; jj++) {
search.stats[killparts[ii] * search.nsub + jj].prof_var = 0.0;
search.stats[killparts[ii] * search.nsub + jj].prof_avg = 0.0;
for (kk = 0; kk < search.proflen ; kk++)
search.rawfolds[index + kk] = 0.0;
index += search.proflen;
}
}
}
free(killparts);
}
if (cmd->killsubsstrP) {
killsubs = ranges_to_ivect(cmd->killsubsstr, 0,
search.nsub - 1, &numkillsubs);
for (ii = 0; ii < numkillsubs; ii++) {
if ((killsubs[ii] >= 0) && (killsubs[ii] < search.nsub)) {
for (jj = 0; jj < search.npart; jj++) {
index = search.proflen * (jj * search.nsub + killsubs[ii]);
search.stats[jj * search.nsub + killsubs[ii]].prof_var = 0.0;
search.stats[jj * search.nsub + killsubs[ii]].prof_avg = 0.0;
for (kk = 0; kk < search.proflen ; kk++)
search.rawfolds[index + kk] = 0.0;
}
}
}
free(killsubs);
}
}
/* Switch to portrait mode */
if (cmd->portraitP) {
int goodlen;
char *substr, *tmpdev;
substr = strstr(search.pgdev, "/CPS");
goodlen = substr - search.pgdev;
*substr = '\0';
tmpdev = calloc(goodlen + 6, sizeof(char));
sprintf(tmpdev, "%s/VCPS", search.pgdev);
free(search.pgdev);
search.pgdev = calloc(goodlen + 6, sizeof(char));
strncpy(search.pgdev, tmpdev, strlen(tmpdev));
free(tmpdev);
printf("New device is '%s'\n", search.pgdev);
}
if (0) {
int goodlen;
char *substr, *tmpdev;
substr = strstr(search.pgdev, "ps/CPS");
goodlen = substr - search.pgdev;
*substr = '\0';
tmpdev = calloc(goodlen + 9, sizeof(char));
strncpy(tmpdev, search.pgdev, goodlen);
strcpy(tmpdev + goodlen, "png/TPNG");
free(search.pgdev);
search.pgdev = calloc(goodlen + 9, sizeof(char));
strncpy(search.pgdev, tmpdev, strlen(tmpdev));
free(tmpdev);
printf("New device is '%s'\n", search.pgdev);
}
/*
* Plot our results
*/
prepfold_plot(&search, &flags, !cmd->noxwinP, NULL);
/* Free our memory */
delete_prepfoldinfo(&search);
return (0);
}
int main(int argc, char *argv[])
{
Cmdline *cmd;
struct psrfits pfupper, pflower, pfo;
fitsfile *infits, *outfits;
char *pc1, *pc2;
char outfilename[200]; //Name of outfile if not specified on command line
int stat = 0, padding = 0, userN = 0, status;
// Call usage() if we have no command line arguments
if (argc == 1) {
Program = argv[0];
usage();
exit(0);
}
// Parse the command line using the excellent program Clig
cmd = parseCmdline(argc, argv);
pfupper.tot_rows = pfupper.N = pfupper.T = pfupper.status = 0; //Initialize upper band
pflower.tot_rows = pflower.N = pflower.T = pflower.status = 0; //Initialize lower band
pfupper.filenum = pflower.filenum = 1;
pfo.tot_rows = pfo.N = pfo.T = pfo.status = pfo.multifile = 0; //Initialize output
sprintf(pfupper.filename, cmd->argv[0]); //Copy filename specified on command line to
sprintf(pflower.filename, cmd->argv[0]); //upper and lower bands, will correct filenames shortly
if ((pc2 = strstr(pfupper.filename, "s1")) != NULL) //Upper contains s1, change to s0
strncpy(pc2, "s0", 2);
else if ((pc2 = strstr(pflower.filename, "s0")) != NULL) //Lower contains s0, change to s1
strncpy(pc2, "s1", 2);
else {
printf("Unable to determine which sideband is which\n");
exit(EXIT_FAILURE);
}
//Setting the name of the output file, setting as same name as input file, but removing s0/s1.
pc1 = strstr(pflower.filename, "s1");
pc2 = strrchr(pflower.filename, '.'); //At '.fits'
pc2--;
while ((pc2 >= pflower.filename) && isdigit(*pc2)) //Move through the digits to the separation char.
pc2--;
strncpy(outfilename, pflower.filename, pc1 - pflower.filename); //Copy everything up to s1 into outfilename
strncpy(outfilename + (pc1 - pflower.filename), pc1 + 2, pc2 - pc1 - 2); //Concatenate from after s1 to char before the separation char.
pc1 = outfilename + (pc2 - pflower.filename - 2);
*pc1 = 0;
int rv = psrfits_open(&pfupper); //Open upper band
if (rv) {
fits_report_error(stderr, rv);
exit(1);
}
rv = psrfits_open(&pflower); //Open lower band
if (rv) {
fits_report_error(stderr, rv);
exit(1);
}
pfo = pflower; //Copy all lower band variables into the output struct
if (!cmd->outputbasenameP)
sprintf(pfo.basefilename, basename(outfilename));
else
sprintf(pfo.basefilename, cmd->outputbasename);
pfo.filenum = 0;
sprintf(pfo.filename, "\0"); //Set filename to null so psrfits_open will create the filename for me
pfo.rownum = 1;
pfo.tot_rows = 0;
pfo.N = 0;
printf("lower rows_per_file=%d\n",pflower.rows_per_file);
printf("upper rows_per_file=%d\n",pfupper.rows_per_file);
if (pfupper.rows_per_file != pflower.rows_per_file) { //Sanity check for the two input frequency bands
fprintf(stderr, "rows_per_file in input files do not match!\n");
exit(1);
}
double upperfreqoflower, nextfromlower, lowerfreqofupper, numchandiff; //Used to find which frequencies to take from each band
double offsetfactor, scalefactor; //Factors which will be applied to offsets and scales
int upchanskip, lowchanskip; //Number of channels to skip in each banda
//Variables used to make code cleaner
int extrachanoffset, outoffset, upperoffset, numtocopyupper, loweroffset_skip,
loweroffset, numtocopylower, newuppernchan, newlowernchan;
double df = pflower.hdr.df;
int nchan = pflower.hdr.nchan;
int outnchan;
int npol = pflower.hdr.npol;
int nbits = pflower.hdr.nbits;
int nsblk = pflower.hdr.nsblk;
//Allocate memory for all upper and lower data
pflower.sub.dat_freqs = (double *) malloc(sizeof(double) * nchan);
pflower.sub.dat_weights = (float *) malloc(sizeof(float) * nchan);
pflower.sub.dat_offsets = (float *) malloc(sizeof(float) * nchan * npol);
pflower.sub.dat_scales = (float *) malloc(sizeof(float) * nchan * npol);
pflower.sub.rawdata = (unsigned char *) malloc(pflower.sub.bytes_per_subint);
pflower.sub.data = (unsigned char *) malloc(pflower.sub.bytes_per_subint*2);
pfupper.sub.dat_freqs = (double *) malloc(sizeof(double) * nchan);
pfupper.sub.dat_weights = (float *) malloc(sizeof(float) * nchan);
pfupper.sub.dat_offsets = (float *) malloc(sizeof(float) * nchan * npol);
pfupper.sub.dat_scales = (float *) malloc(sizeof(float) * nchan * npol);
pfupper.sub.rawdata = (unsigned char *) malloc(pfupper.sub.bytes_per_subint);
pfupper.sub.data = (unsigned char *) malloc(pfupper.sub.bytes_per_subint*2);
int firsttime = 1; //First time through do while loop
do {
print_percent_complete(pflower.rownum, pflower.rows_per_file,
pflower.rownum == 1 ? 1 : 0);
psrfits_read_subint(&pflower);
psrfits_read_subint(&pfupper);
if (firsttime) { //First time through loop, calculate factors for scales and offsets and number of channels to skip
firsttime = 0;
//Find the number of channels in the upper band which will be skipped
if (df < 0) { //Find channel order, low to high or high to low
upperfreqoflower = pflower.sub.dat_freqs[0]; //Highest frequency channel in lower band
lowerfreqofupper = pfupper.sub.dat_freqs[nchan - 1]; //Lowest frequency channel in upper band
} else {
upperfreqoflower = pflower.sub.dat_freqs[nchan - 1]; //Highest frequency channel in lower band
lowerfreqofupper = pfupper.sub.dat_freqs[0]; //Lowest frequency channel in upper band
}
nextfromlower = upperfreqoflower + fabs(df); //Second highest channel in lower band
numchandiff = (nextfromlower - lowerfreqofupper) / fabs(df); //Number of channels to skip in float form
int chanskip;
if (numchandiff > 0) { //Make sure there are channels which need to be skipped
if (numchandiff - (double) ((int) numchandiff) > .5) // See whether we need to round up integer channels to skip
chanskip = (int) numchandiff + 1;
else
chanskip = (int) numchandiff;
} else
chanskip = 0; //No need to skip any channels
if (chanskip % 2 == 1) { //Odd number of channels, give lower band the extra channel
upchanskip = chanskip / 2;
lowchanskip = chanskip / 2 + 1;
} else //Even number of channels to skip
upchanskip = lowchanskip = chanskip / 2;
if (upchanskip % 2 == 1) { //We want an even number of channels in upper band for 4-bit data to get copied correctly
++lowchanskip;
--upchanskip;
}
//Find new values given the number of channels skipped
pfo.hdr.nchan = outnchan = nchan + nchan - chanskip + 2; //New number of channels, plus 2 to make nchan=960 (many factors of 2)
pfo.hdr.BW = (double) outnchan *fabs(df); //New bandwidth
pfo.hdr.fctr = //New center frequency
(pflower.hdr.fctr - (double) (nchan / 2) * fabs(df)) + pfo.hdr.BW / 2.0;
pfo.sub.bytes_per_subint = //Calculate new number of bytes in each subint
outnchan * nsblk * nbits / 8 * npol;
//Allocate space for output data now that we know the new number of channels
pfo.sub.dat_freqs = (double *) malloc(sizeof(double) * outnchan);
pfo.sub.dat_weights = (float *) malloc(sizeof(float) * outnchan);
pfo.sub.dat_offsets = (float *) malloc(sizeof(float) * outnchan * npol);
pfo.sub.dat_scales = (float *) malloc(sizeof(float) * outnchan * npol);
pfo.sub.rawdata = (unsigned char *) malloc(pfo.sub.bytes_per_subint);
pfo.sub.data = (unsigned char *) malloc(pfo.sub.bytes_per_subint*2);
newuppernchan = nchan - upchanskip; //The number of channels to copy from the upper sideband.
newlowernchan = nchan - lowchanskip; //The number of channels to copy from the lower sideband.
extrachanoffset = 2; //Offset for 2 extra freq channels making nchan 960 in bytes
outoffset = (outnchan * npol); //Offset in each loop due to previously written data
upperoffset = (nchan * npol); //Offset in loop for upper band
numtocopyupper = (newuppernchan * npol); //Number of bytes to copy from upper band
loweroffset_skip = (lowchanskip * npol); //Number of bytes to skip when copying lower band due to
//having written upper band
loweroffset = //Number of bytes to skip due to having written previous lower band data
(nchan * npol);
numtocopylower = (newlowernchan * npol); //Number of bytes to copy from lower band
float upmean, upvar, lowmean, lowvar;
avg_var(pfupper.sub.dat_offsets + (nchan - upchanskip), //Find the mean and variance of the upper band's offsets
upchanskip, &upmean, &upvar);
printf("Upper offset stats: mean=%f variance=%f\n", upmean, upvar);
avg_var(pflower.sub.dat_offsets, lowchanskip, &lowmean, &lowvar); //Find the mean and variance of the lower band's offsets
printf("Lower offset stats: mean=%f variance=%f\n", lowmean, lowvar);
printf("Applying factor of %f to upper offsets\n", (lowmean / upmean));
offsetfactor = lowmean / upmean; //Set offset factor used to correct variance differences in the two bands
avg_var(pfupper.sub.dat_scales + (nchan - upchanskip), //Find the mean and var. of the upper band's scales
upchanskip, &upmean, &upvar);
printf("Upper scales stats: mean=%f variance=%f\n", upmean, upvar);
avg_var(pflower.sub.dat_scales, lowchanskip, &lowmean, &lowvar); //Find the mean and var. of the lower band's scales
printf("Lower scales stats: mean=%f variance=%f\n", lowmean, lowvar);
printf("Applying factor of %f to upper scales\n", (lowmean / upmean));
scalefactor = lowmean / upmean; //Set scale factor used to correct variance differences in the two bands
}
if (pflower.status == 0 && pfupper.status == 0) {
//Copy info from the lower band subint struct to the output file's subint struct
pfo.sub.tsubint = pflower.sub.tsubint;
pfo.sub.offs = pflower.sub.offs;
pfo.sub.lst = pflower.sub.lst;
pfo.sub.ra = pflower.sub.ra;
pfo.sub.dec = pflower.sub.dec;
pfo.sub.glon = pflower.sub.glon;
pfo.sub.glat = pflower.sub.glat;
pfo.sub.feed_ang = pflower.sub.feed_ang;
pfo.sub.pos_ang = pflower.sub.pos_ang;
pfo.sub.par_ang = pflower.sub.par_ang;
pfo.sub.tel_az = pflower.sub.tel_az;
pfo.sub.tel_zen = pflower.sub.tel_zen;
pfo.sub.FITS_typecode = pflower.sub.FITS_typecode;
//Create variables to reduce column width of lines below
double *dat_freqs = pfo.sub.dat_freqs;
double *udat_freqs = pfupper.sub.dat_freqs;
double *ldat_freqs = pflower.sub.dat_freqs;
float *dat_weights = pfo.sub.dat_weights;
float *udat_weights = pfupper.sub.dat_weights;
float *ldat_weights = pflower.sub.dat_weights;
float *dat_offsets = pfo.sub.dat_offsets;
float *udat_offsets = pfupper.sub.dat_offsets;
float *ldat_offsets = pflower.sub.dat_offsets;
float *dat_scales = pfo.sub.dat_scales;
float *udat_scales = pfupper.sub.dat_scales;
float *ldat_scales = pflower.sub.dat_scales;
unsigned char *data = pfo.sub.data;
unsigned char *udata = pfupper.sub.data;
unsigned char *ldata = pflower.sub.data;
if (df < 0) {
//Copy frequency labels
dat_freqs[1] = udat_freqs[0] + fabs(df); //Calculate the frequency labels
dat_freqs[0] = dat_freqs[1] + fabs(df); //for our two empty frequency channels
int newuppernchan = nchan - upchanskip; //The number of channels to copy from the upper band
int newlowernchan = nchan - lowchanskip; //The number of channels to copy from the lower band
memcpy(dat_freqs + 2, udat_freqs, sizeof(double) * newuppernchan); //Copy from the upper band, skipping first two chans.
memcpy(dat_freqs + newuppernchan + 2, //Copy from the lower band
ldat_freqs + lowchanskip, sizeof(double) * newlowernchan);
//Copy weights
dat_weights[0] = dat_weights[1] = 0; //Set the weights of first two channels to 0, so they shouldn't be used in calculations
memcpy(dat_weights + 2, udat_weights, //Copy weights from the upper band
sizeof(float) * newuppernchan);
memcpy(dat_weights + 2 + newuppernchan, //Copy weights from the lower band
ldat_weights + lowchanskip, sizeof(float) * newlowernchan);
//Copy offsets
dat_offsets[0] = dat_offsets[1] = //Set offsets of first two channels to the same as upper's first channel
udat_offsets[0]; //(shouldn't matter since they should be ignored)
int ii;
for (ii = 0; ii < newuppernchan; ++ii) //Apply offset factor to upper band
udat_offsets[ii] = udat_offsets[ii] * (offsetfactor);
memcpy(dat_offsets + 2 * npol, udat_offsets, //Copy upper offsets
sizeof(float) * newuppernchan * npol);
memcpy(dat_offsets + (newuppernchan + 2) * npol, //Copy lower offsets
ldat_offsets + lowchanskip, sizeof(float) * newlowernchan * npol);
//Copy scales
for (ii = 0; ii < newuppernchan; ++ii) //Apply scale factor to upper band
udat_scales[ii] = udat_scales[ii] * (scalefactor);
dat_scales[0] = dat_scales[1] = udat_scales[0];
memcpy(dat_scales + 2 * npol, udat_scales, //Copy upper scales
sizeof(float) * newuppernchan * npol);
memcpy(dat_scales + (newuppernchan + 2) * npol, //Copy lower scales
ldat_scales + lowchanskip, sizeof(float) * newlowernchan * npol);
//Copy the data
for (ii = 0; ii < nsblk; ++ii) { //Loop through data copying into place
memcpy(data + ii * outoffset + extrachanoffset,
udata + ii * upperoffset, numtocopyupper);
memcpy(data + ii * outoffset + extrachanoffset +
numtocopyupper,
ldata + ii * loweroffset + loweroffset_skip, numtocopylower);
}
psrfits_write_subint(&pfo);
} else {
}
}
} while (pfo.rownum <= pfo.rows_per_file && pfupper.status==0 && pflower.status==0);
printf("Closing file '%s'\n", pflower.filename);
fits_close_file(pfupper.fptr, &status);
printf("Closing file '%s'\n", pfupper.filename);
fits_close_file(pflower.fptr, &status);
if(pflower.status!=0||pfupper.status!=0)
{
fprintf(stderr,"An error occurred when combining the two Mock files!\n");
if(pflower.status==108||pfupper.status==108)
fprintf(stderr,"One or both of the files is incomplete.\n");
exit(1);
}
exit(0);
}
int main(int argc, char *argv[])
{
int ii, jj, numbirds;
double lofreq, hifreq;
char *rootfilenm;
birdie *newbird;
GSList *zapped = NULL;
infodata idata;
Cmdline *cmd;
/* Call usage() if we have no command line arguments */
if (argc == 1) {
Program = argv[0];
printf("\n");
usage();
exit(1);
}
/* Parse the command line using the excellent program Clig */
cmd = parseCmdline(argc, argv);
#ifdef DEBUG
showOptionValues();
#endif
printf("\n\n");
printf(" Interactive/Automatic Birdie Zapping Program\n");
printf(" by Scott M. Ransom\n");
printf(" January, 2001\n\n");
if (!cmd->zapP && !cmd->inzapfileP && !cmd->outzapfileP) {
printf("You must specify '-in' and '-out' if you are not\n");
printf("automatically zapping a file (with '-zap').\n\n");
exit(0);
}
{
int hassuffix = 0;
char *suffix;
hassuffix = split_root_suffix(cmd->argv[0], &rootfilenm, &suffix);
if (hassuffix) {
if (strcmp(suffix, "fft") != 0) {
printf("\nInput file ('%s') must be a FFT file ('.fft')!\n\n",
cmd->argv[0]);
free(suffix);
exit(0);
}
free(suffix);
} else {
printf("\nInput file ('%s') must be a FFT file ('.fft')!\n\n",
cmd->argv[0]);
exit(0);
}
}
/* Read the info file */
readinf(&idata, rootfilenm);
if (idata.object) {
printf("Examining %s data from '%s'.\n\n",
remove_whitespace(idata.object), cmd->argv[0]);
} else {
printf("Examining data from '%s'.\n\n", cmd->argv[0]);
}
T = idata.dt * idata.N;
dr = 1.0 / NUMBETWEEN;
if (cmd->zapP) { /* Automatic */
double *bird_lobins, *bird_hibins, hibin;
if (!cmd->zapfileP) {
printf("You must specify a 'zapfile' containing freqs\n");
printf("and widths if you want to write to the FFT file.\n\n");
free(rootfilenm);
exit(0);
}
hibin = idata.N / 2;
/* Read the Standard bird list */
numbirds = get_birdies(cmd->zapfile, T, cmd->baryv,
&bird_lobins, &bird_hibins);
/* Zap the birdies */
fftfile = chkfopen(cmd->argv[0], "rb+");
for (ii = 0; ii < numbirds; ii++) {
if (bird_lobins[ii] >= hibin)
break;
if (bird_hibins[ii] >= hibin)
bird_hibins[ii] = hibin - 1;
zapbirds(bird_lobins[ii], bird_hibins[ii], fftfile, NULL);
}
vect_free(bird_lobins);
vect_free(bird_hibins);
} else { /* Interactive */
int *bird_numharms;
double *bird_basebins;
/* Read the Standard bird list */
numbirds = get_std_birds(cmd->inzapfile, T, cmd->baryv,
&bird_basebins, &bird_numharms);
/* Create our correlation kernel */
{
int numkern;
fcomplex *resp;
khw = r_resp_halfwidth(LOWACC);
numkern = 2 * NUMBETWEEN * khw;
resp = gen_r_response(0.0, NUMBETWEEN, numkern);
kernel = gen_cvect(FFTLEN);
place_complex_kernel(resp, numkern, kernel, FFTLEN);
COMPLEXFFT(kernel, FFTLEN, -1);
vect_free(resp);
}
/* Loop over the birdies */
fftfile = chkfopen(cmd->argv[0], "rb");
cpgstart_x("landscape");
cpgask(0);
for (ii = 0; ii < numbirds; ii++) {
for (jj = 0; jj < bird_numharms[ii]; jj++) {
process_bird(bird_basebins[ii], jj + 1, &lofreq, &hifreq);
if (lofreq && hifreq) {
newbird = birdie_create(lofreq, hifreq, cmd->baryv);
zapped = g_slist_insert_sorted(zapped, newbird, birdie_compare);
}
}
}
cpgclos();
/* Output the birdies */
{
FILE *outfile;
outfile = chkfopen(cmd->outzapfile, "w");
fprintf(outfile, "#\n");
fprintf(outfile,
"# Topocentric birdies found using 'zapbirds' for '%s'\n",
cmd->argv[0]);
fprintf(outfile, "#\n");
fprintf(outfile, "# Frequency (Hz) Width (Hz)\n");
fprintf(outfile, "#\n");
g_slist_foreach(zapped, birdie_print, outfile);
fclose(outfile);
}
printf("\nOutput birdie file is '%s'.\n\n", cmd->outzapfile);
/* Free the memory */
g_slist_foreach(zapped, birdie_free, NULL);
g_slist_free(zapped);
vect_free(kernel);
vect_free(bird_numharms);
vect_free(bird_basebins);
}
fclose(fftfile);
free(rootfilenm);
printf("Done\n\n");
return 0;
}
int main(int argc, char *argv[])
{
FILE *fftfile, *candfile;
float powargr, powargi, *powers = NULL, *minifft;
float norm, numchunks, *powers_pos;
int nbins, newncand, nfftsizes, fftlen, halffftlen, binsleft;
int numtoread, filepos = 0, loopct = 0, powers_offset, ncand2;
int ii, ct, newper = 0, oldper = 0, numsumpow = 1;
double T, totnumsearched = 0.0, minsig = 0.0, min_orb_p, max_orb_p;
char *rootfilenm, *notes;
fcomplex *data = NULL;
rawbincand tmplist[MININCANDS], *list;
infodata idata;
struct tms runtimes;
double ttim, utim, stim, tott;
Cmdline *cmd;
fftwf_plan fftplan;
/* Prep the timer */
tott = times(&runtimes) / (double) CLK_TCK;
/* Call usage() if we have no command line arguments */
if (argc == 1) {
Program = argv[0];
printf("\n");
usage();
exit(1);
}
/* Parse the command line using the excellent program Clig */
cmd = parseCmdline(argc, argv);
#ifdef DEBUG
showOptionValues();
#endif
printf("\n\n");
printf(" Phase Modulation Pulsar Search Routine\n");
printf(" by Scott M. Ransom\n\n");
{
int hassuffix = 0;
char *suffix;
hassuffix = split_root_suffix(cmd->argv[0], &rootfilenm, &suffix);
if (hassuffix) {
if (strcmp(suffix, "fft") != 0) {
printf("\nInput file ('%s') must be a FFT file ('.fft')!\n\n",
cmd->argv[0]);
free(suffix);
exit(0);
}
free(suffix);
} else {
printf("\nInput file ('%s') must be a FFT file ('.fft')!\n\n",
cmd->argv[0]);
exit(0);
}
}
/* Read the info file */
readinf(&idata, rootfilenm);
T = idata.N * idata.dt;
if (strlen(remove_whitespace(idata.object)) > 0) {
printf("Analyzing '%s' data from '%s'.\n\n",
remove_whitespace(idata.object), cmd->argv[0]);
} else {
printf("Analyzing data from '%s'.\n\n", cmd->argv[0]);
}
min_orb_p = MINORBP;
if (cmd->noaliasP)
max_orb_p = T / 2.0;
else
max_orb_p = T / 1.2;
/* open the FFT file and get its length */
fftfile = chkfopen(cmd->argv[0], "rb");
nbins = chkfilelen(fftfile, sizeof(fcomplex));
/* Check that cmd->maxfft is an acceptable power of 2 */
ct = 4;
ii = 1;
while (ct < MAXREALFFT || ii) {
if (ct == cmd->maxfft)
ii = 0;
ct <<= 1;
}
if (ii) {
printf("\n'maxfft' is out of range or not a power-of-2.\n\n");
exit(1);
}
/* Check that cmd->minfft is an acceptable power of 2 */
ct = 4;
ii = 1;
while (ct < MAXREALFFT || ii) {
if (ct == cmd->minfft)
ii = 0;
ct <<= 1;
}
if (ii) {
printf("\n'minfft' is out of range or not a power-of-2.\n\n");
exit(1);
}
/* Low and high Fourier freqs to check */
if (cmd->floP) {
cmd->rlo = floor(cmd->flo * T);
if (cmd->rlo < cmd->lobin)
cmd->rlo = cmd->lobin;
if (cmd->rlo > cmd->lobin + nbins - 1) {
printf("\nLow frequency to search 'flo' is greater than\n");
printf(" the highest available frequency. Exiting.\n\n");
exit(1);
}
} else {
cmd->rlo = 1.0;
if (cmd->rlo < cmd->lobin)
cmd->rlo = cmd->lobin;
if (cmd->rlo > cmd->lobin + nbins - 1) {
printf("\nLow frequency to search 'rlo' is greater than\n");
printf(" the available number of points. Exiting.\n\n");
exit(1);
}
}
if (cmd->fhiP) {
cmd->rhi = ceil(cmd->fhi * T);
if (cmd->rhi > cmd->lobin + nbins - 1)
cmd->rhi = cmd->lobin + nbins - 1;
if (cmd->rhi < cmd->rlo) {
printf("\nHigh frequency to search 'fhi' is less than\n");
printf(" the lowest frequency to search 'flo'. Exiting.\n\n");
exit(1);
}
} else if (cmd->rhiP) {
if (cmd->rhi > cmd->lobin + nbins - 1)
cmd->rhi = cmd->lobin + nbins - 1;
if (cmd->rhi < cmd->rlo) {
printf("\nHigh frequency to search 'rhi' is less than\n");
printf(" the lowest frequency to search 'rlo'. Exiting.\n\n");
exit(1);
}
}
/* Determine how many different mini-fft sizes we will use */
nfftsizes = 1;
ii = cmd->maxfft;
while (ii > cmd->minfft) {
ii >>= 1;
nfftsizes++;
}
/* Allocate some memory and prep some variables. */
/* For numtoread, the 6 just lets us read extra data at once */
numtoread = 6 * cmd->maxfft;
if (cmd->stack == 0)
powers = gen_fvect(numtoread);
minifft = (float *) fftwf_malloc(sizeof(float) *
(cmd->maxfft * cmd->numbetween + 2));
ncand2 = 2 * cmd->ncand;
list = (rawbincand *) malloc(sizeof(rawbincand) * ncand2);
for (ii = 0; ii < ncand2; ii++)
list[ii].mini_sigma = 0.0;
for (ii = 0; ii < MININCANDS; ii++)
tmplist[ii].mini_sigma = 0.0;
filepos = cmd->rlo - cmd->lobin;
numchunks = (float) (cmd->rhi - cmd->rlo) / numtoread;
printf("Searching...\n");
printf(" Amount complete = %3d%%", 0);
fflush(stdout);
/* Prep FFTW */
read_wisdom();
/* Loop through fftfile */
while ((filepos + cmd->lobin) < cmd->rhi) {
/* Calculate percentage complete */
newper = (int) (loopct / numchunks * 100.0);
if (newper > oldper) {
newper = (newper > 99) ? 100 : newper;
printf("\r Amount complete = %3d%%", newper);
oldper = newper;
fflush(stdout);
}
/* Adjust our search parameters if close to end of zone to search */
binsleft = cmd->rhi - (filepos + cmd->lobin);
if (binsleft < cmd->minfft)
break;
if (binsleft < numtoread) { /* Change numtoread */
numtoread = cmd->maxfft;
while (binsleft < numtoread) {
cmd->maxfft /= 2;
numtoread = cmd->maxfft;
}
}
fftlen = cmd->maxfft;
/* Read from fftfile */
if (cmd->stack == 0) {
data = read_fcomplex_file(fftfile, filepos, numtoread);
for (ii = 0; ii < numtoread; ii++)
powers[ii] = POWER(data[ii].r, data[ii].i);
numsumpow = 1;
} else {
powers = read_float_file(fftfile, filepos, numtoread);
numsumpow = cmd->stack;
}
if (filepos == 0)
powers[0] = 1.0;
/* Chop the powers that are way above the median level */
prune_powers(powers, numtoread, numsumpow);
/* Loop through the different small FFT sizes */
while (fftlen >= cmd->minfft) {
halffftlen = fftlen / 2;
powers_pos = powers;
powers_offset = 0;
/* Create the appropriate FFT plan */
fftplan = fftwf_plan_dft_r2c_1d(cmd->interbinP ? fftlen : 2 * fftlen,
minifft, (fftwf_complex *) minifft,
FFTW_PATIENT);
/* Perform miniffts at each section of the powers array */
while ((numtoread - powers_offset) >
(int) ((1.0 - cmd->overlap) * cmd->maxfft + DBLCORRECT)) {
/* Copy the proper amount and portion of powers into minifft */
memcpy(minifft, powers_pos, fftlen * sizeof(float));
/* For Fourier interpolation use a zeropadded FFT */
if (cmd->numbetween > 1 && !cmd->interbinP) {
for (ii = fftlen; ii < cmd->numbetween * fftlen; ii++)
minifft[ii] = 0.0;
}
/* Perform the minifft */
fftwf_execute(fftplan);
/* Normalize and search the miniFFT */
norm = sqrt(fftlen * numsumpow) / minifft[0];
for (ii = 0; ii < (cmd->interbinP ? fftlen + 1 : 2 * fftlen + 1); ii++)
minifft[ii] *= norm;
search_minifft((fcomplex *) minifft, halffftlen, min_orb_p,
max_orb_p, tmplist, MININCANDS, cmd->harmsum,
cmd->numbetween, idata.N, T,
(double) (powers_offset + filepos + cmd->lobin),
cmd->interbinP ? INTERBIN : INTERPOLATE,
cmd->noaliasP ? NO_CHECK_ALIASED : CHECK_ALIASED);
/* Check if the new cands should go into the master cand list */
for (ii = 0; ii < MININCANDS; ii++) {
if (tmplist[ii].mini_sigma > minsig) {
/* Check to see if another candidate with these properties */
/* is already in the list. */
if (not_already_there_rawbin(tmplist[ii], list, ncand2)) {
list[ncand2 - 1] = tmplist[ii];
minsig = percolate_rawbincands(list, ncand2);
}
} else {
break;
}
/* Mini-fft search for loop */
}
totnumsearched += fftlen;
powers_pos += (int) (cmd->overlap * fftlen);
powers_offset = powers_pos - powers;
/* Position of mini-fft in data set while loop */
}
fftwf_destroy_plan(fftplan);
fftlen >>= 1;
/* Size of mini-fft while loop */
}
if (cmd->stack == 0)
vect_free(data);
else
vect_free(powers);
filepos += (numtoread - (int) ((1.0 - cmd->overlap) * cmd->maxfft));
loopct++;
/* File position while loop */
}
/* Print the final percentage update */
printf("\r Amount complete = %3d%%\n\n", 100);
/* Print the number of frequencies searched */
printf("Searched %.0f pts (including interbins).\n\n", totnumsearched);
printf("Timing summary:\n");
tott = times(&runtimes) / (double) CLK_TCK - tott;
utim = runtimes.tms_utime / (double) CLK_TCK;
stim = runtimes.tms_stime / (double) CLK_TCK;
ttim = utim + stim;
printf(" CPU time: %.3f sec (User: %.3f sec, System: %.3f sec)\n",
ttim, utim, stim);
printf(" Total time: %.3f sec\n\n", tott);
printf("Writing result files and cleaning up.\n");
/* Count how many candidates we actually have */
ii = 0;
while (ii < ncand2 && list[ii].mini_sigma != 0)
ii++;
newncand = (ii > cmd->ncand) ? cmd->ncand : ii;
/* Set our candidate notes to all spaces */
notes = malloc(sizeof(char) * newncand * 18 + 1);
for (ii = 0; ii < newncand; ii++)
strncpy(notes + ii * 18, " ", 18);
/* Check the database for possible known PSR detections */
if (idata.ra_h && idata.dec_d) {
for (ii = 0; ii < newncand; ii++) {
comp_rawbin_to_cand(&list[ii], &idata, notes + ii * 18, 0);
}
}
/* Compare the candidates with each other */
compare_rawbin_cands(list, newncand, notes);
/* Send the candidates to the text file */
file_rawbin_candidates(list, notes, newncand, cmd->harmsum, rootfilenm);
/* Write the binary candidate file */
{
char *candnm;
candnm = (char *) calloc(strlen(rootfilenm) + 15, sizeof(char));
sprintf(candnm, "%s_bin%d.cand", rootfilenm, cmd->harmsum);
candfile = chkfopen(candnm, "wb");
chkfwrite(list, sizeof(rawbincand), (unsigned long) newncand, candfile);
fclose(candfile);
free(candnm);
}
/* Free our arrays and close our files */
if (cmd->stack == 0)
vect_free(powers);
free(list);
fftwf_free(minifft);
free(notes);
free(rootfilenm);
fclose(fftfile);
printf("Done.\n\n");
return (0);
}
int main(int argc, char *argv[])
{
FILE **infiles, *outfile = NULL, *scalingfile, *zerolagfile = NULL;
int filenum, ptsperblock, numlags, numfiles, outnumlags;
int bytes_per_read, scaling = 0, numscalings, firstfile, firstspec;
int write_data = 1, update_posn = 0;
long long N, numconverted = 0, numwritten = 0;
char *path, *filenm, rawlags[4096];
char outfilenm[200], filenmbase[200], zerolagnm[200], scalingnm[200];
unsigned char output_samples[2048];
float *scalings = NULL, lags[2048], tmp_floats[2048];
double dt, T, time_offset;
SPIGOT_INFO *spigots;
sigprocfb fb;
infodata idata;
Cmdline *cmd;
/* Call usage() if we have no command line arguments */
if (argc == 1) {
Program = argv[0];
usage();
exit(0);
}
/* Parse the command line using the excellent program Clig */
cmd = parseCmdline(argc, argv);
// showOptionValues();
numfiles = cmd->argc;
/* If requesting that we skip values or only write */
/* a specific number of values, require an output file name */
if ((cmd->skip > 0) || cmd->numoutP){
if (!cmd->outfileP && !cmd->stdoutP) {
fprintf(stderr,
"\nspigot2filterbank ERROR: You need to specify an output\n"
" filename (or -stdout) when using the -skip and/or \n"
" -numout options!\n\n");
exit(1);
}
}
/* Give an error if specifying stdout and an output file */
if (cmd->stdoutP && cmd->outfileP){
fprintf(stderr,
"\nspigot2filterbank ERROR: You cannot specify both an output\n"
" file and that the data should go to STDOUT!\n\n");
exit(1);
}
if (!cmd->stdoutP)
printf("\nConverting SPIGOT FITs lags into SIGPROC filterbank format...\n\n");
/* Determine the filename base from the first spigot file */
split_path_file(cmd->argv[0], &path, &filenm);
strncpy(filenmbase, filenm, strlen(filenm) - 5);
filenmbase[strlen(filenm) - 5] = '\0';
free(path);
free(filenm);
/* Open a file to store the zerolags */
if (cmd->zerolagsP) {
if (cmd->outfileP) {
sprintf(zerolagnm, "%s.zerolags", cmd->outfile);
} else {
sprintf(zerolagnm, "%s.zerolags", filenmbase);
}
zerolagfile = chkfopen(zerolagnm, "wb");
}
/* Attempt to read a file with lag scalings in it */
sprintf(scalingnm, "%s.scaling", filenmbase);
if ((scalingfile = fopen(scalingnm, "rb"))) {
/* Determine the length of the file */
numscalings = (int) chkfilelen(scalingfile, sizeof(float));
/* Create the array and read 'em */
scalings = gen_fvect(numscalings);
chkfread(scalings, sizeof(float), numscalings, scalingfile);
scaling = 1;
/* close the scaling file */
fclose(scalingfile);
if (!cmd->stdoutP)
printf("Scaling the lags with the %d values found in '%s'\n\n",
numscalings, scalingnm);
}
/* Read and convert the basic SPIGOT file information */
if (!cmd->stdoutP)
printf("Spigot card input file information:\n");
spigots = (SPIGOT_INFO *) malloc(sizeof(SPIGOT_INFO) * numfiles);
infiles = (FILE **) malloc(sizeof(FILE *) * numfiles);
for (filenum = 0; filenum < numfiles; filenum++) {
if (!cmd->stdoutP)
printf(" '%s'\n", cmd->argv[filenum]);
infiles[filenum] = chkfopen(cmd->argv[filenum], "rb");
read_SPIGOT_header(cmd->argv[filenum], spigots + filenum);
rewind(infiles[filenum]);
}
if (!cmd->stdoutP)
printf("\n");
/* The following is necessary in order to initialize all the */
/* static variables in spigot.c */
get_SPIGOT_file_info(infiles, spigots, numfiles, 0, 0, &N,
&ptsperblock, &numlags, &dt, &T, &idata,
!cmd->stdoutP);
/* Compute the first file required */
firstfile = cmd->skip / spigots[0].samples_per_file;
firstspec = cmd->skip % spigots[0].samples_per_file;
if (!cmd->numoutP) {
cmd->numout = (N - cmd->skip) / cmd->downsamp;
}
bytes_per_read = numlags * spigots[0].bits_per_lag / 8;
outnumlags = numlags - cmd->lokill - cmd->hikill;
/* Step through the SPIGOT files */
filenum = firstfile;
while (numwritten < cmd->numout){
split_path_file(cmd->argv[filenum], &path, &filenm);
strncpy(filenmbase, filenm, strlen(filenm) - 5);
filenmbase[strlen(filenm) - 5] = '\0';
if (cmd->outfileP) {
if (filenum==firstfile) {
sprintf(outfilenm, "%s", cmd->outfile);
outfile = chkfopen(outfilenm, "wb");
}
} else {
sprintf(outfilenm, "%s.fil", filenmbase);
if (cmd->stdoutP) {
outfile = stdout;
} else {
outfile = chkfopen(outfilenm, "wb");
}
}
if (!cmd->stdoutP) {
if (filenum==firstfile)
printf("Reading Spigot lags from '%s' (starting at sample %d)\n",
cmd->argv[filenum], firstspec);
else
printf("Reading Spigot lags from '%s'\n",
cmd->argv[filenum]);
printf("Writing filterbank spectra to '%s'\n\n", outfilenm);
}
/* Update the filterbank header information for each file */
if (!spigots[filenum].tracking) {
if (cmd->outfileP || cmd->stdoutP) {
time_offset = 0.5 * cmd->numout * \
spigots[filenum].dt_us * 1e-6 * cmd->downsamp;
} else { // Just normal files
time_offset = 0.5 * spigots[filenum].file_duration;
}
update_posn = 1;
} else {
update_posn = 0;
time_offset = 0.0;
}
/* Adjust the Spigot start time for the skip */
spigots[filenum].elapsed_time += cmd->skip * spigots[filenum].dt_us * 1e-6;
/* Determine the SIGPROC header */
spigot2sigprocfb(&(spigots[filenum]), &fb, filenmbase,
cmd->lokill, cmd->hikill, cmd->downsamp,
update_posn, time_offset);
/* Correct the structure if we are using floats */
if (cmd->floatsP) fb.nbits = 32;
/* Write a filterbank header if we have not been told not to. */
/* Don't write it, though, if using stdio or a specified output */
/* file and the input file is not the first. */
if (!cmd->nohdrP) {
if ((!cmd->stdoutP && !cmd->outfileP) ||
((cmd->stdoutP || cmd->outfileP) && filenum==firstfile)) {
write_filterbank_header(&fb, outfile);
}
}
/* Go to the correct autocorrelation in the correct first FITs file */
chkfseek(infiles[filenum],
spigots[filenum].header_len + bytes_per_read*firstspec,
SEEK_SET);
/* Loop over the samples in the file */
while ((numwritten < cmd->numout) &&
(chkfread(rawlags, bytes_per_read, 1, infiles[filenum]))) {
if (cmd->zerolagsP) {
/* Correct the lags so we can write the zerolag */
get_calibrated_lags(rawlags, lags);
chkfwrite(lags, sizeof(float), 1, zerolagfile);
}
if (scaling) {
convert_SPIGOT_point(rawlags, output_samples, SUMIFS,
scalings[cmd->skip+numconverted]);
} else {
convert_SPIGOT_point(rawlags, output_samples, SUMIFS, 1.0);
}
/* If downsampling, average the current spectra */
if (cmd->downsamp > 1) {
int ii;
if (numconverted % cmd->downsamp == 0) {
write_data = 0;
/* Zero the array used for averaging */
for (ii = 0; ii < outnumlags; ii++)
tmp_floats[ii] = 0.0;
} else {
/* Add the current data to the array used for averaging */
for (ii = 0; ii < outnumlags; ii++)
tmp_floats[ii] += (float) output_samples[ii+cmd->lokill];
/* If that was the last sample to be added, average them */
/* and put them back into output_samples */
if (numconverted % cmd->downsamp == (cmd->downsamp-1)) {
write_data = 1;
for (ii = 0; ii < outnumlags; ii++) {
tmp_floats[ii] /= (float) cmd->downsamp;
output_samples[ii+cmd->lokill] = \
(unsigned char)(tmp_floats[ii]+0.5);
}
}
}
}
numconverted++;
if (write_data) {
int ii;
/* Invert the band so that the high freqs are first */
/* This is how SIGPROC stores its data. */
if (cmd->floatsP) {
float tempzz = 0.0, *loptr, *hiptr;
loptr = tmp_floats; // killed channels are already gone
hiptr = tmp_floats + outnumlags - 1;
for (ii = 0; ii < outnumlags / 2; ii++, loptr++, hiptr--) {
SWAP(*loptr, *hiptr);
}
} else {
unsigned char tempzz = 0.0, *loptr, *hiptr;
loptr = output_samples + cmd->lokill;
hiptr = output_samples + cmd->lokill + outnumlags - 1;
for (ii = 0; ii < outnumlags / 2; ii++, loptr++, hiptr--) {
SWAP(*loptr, *hiptr);
}
}
/* Now actually write the data */
if (cmd->floatsP) {
/* Copy the bytes to floats */
for (ii = 0; ii < outnumlags; ii++)
tmp_floats[ii] = (float) output_samples[ii+cmd->lokill];
chkfwrite(tmp_floats, sizeof(float), fb.nchans, outfile);
} else {
chkfwrite(output_samples+cmd->lokill,
sizeof(unsigned char), fb.nchans, outfile);
}
numwritten++;
}
}
if ((!cmd->stdoutP) && (!cmd->outfileP))
fclose(outfile);
fclose(infiles[filenum]);
firstspec = 0;
filenum++;
free(path);
free(filenm);
}
if ((!cmd->stdoutP) && (cmd->outfileP))
fclose(outfile);
if (cmd->zerolagsP)
fclose(zerolagfile);
if (!cmd->stdoutP)
fprintf(stderr, "Converted %lld samples and wrote %lld.\n\n",
numconverted, numwritten);
if (scaling)
free(scalings);
free(spigots);
free(infiles);
return 0;
}
int main(int argc, char *argv[])
{
int ii;
double ttim, utim, stim, tott;
struct tms runtimes;
subharminfo **subharminfs;
accelobs obs;
infodata idata;
GSList *cands = NULL;
Cmdline *cmd;
/* Prep the timer */
tott = times(&runtimes) / (double) CLK_TCK;
/* Call usage() if we have no command line arguments */
if (argc == 1) {
Program = argv[0];
printf("\n");
usage();
exit(1);
}
/* Parse the command line using the excellent program Clig */
cmd = parseCmdline(argc, argv);
#ifdef DEBUG
showOptionValues();
#endif
printf("\n\n");
printf(" Fourier-Domain Acceleration Search Routine\n");
printf(" by Scott M. Ransom\n\n");
/* Create the accelobs structure */
create_accelobs(&obs, &idata, cmd, 1);
/* Zap birdies if requested and if in memory */
if (cmd->zaplistP && !obs.mmap_file && obs.fft) {
int numbirds;
double *bird_lobins, *bird_hibins, hibin;
/* Read the Standard bird list */
numbirds = get_birdies(cmd->zaplist, obs.T, cmd->baryv,
&bird_lobins, &bird_hibins);
/* Zap the birdies */
printf("Zapping them using a barycentric velocity of %.5gc.\n\n", cmd->baryv);
hibin = obs.N / 2;
for (ii = 0; ii < numbirds; ii++) {
if (bird_lobins[ii] >= hibin)
break;
if (bird_hibins[ii] >= hibin)
bird_hibins[ii] = hibin - 1;
zapbirds(bird_lobins[ii], bird_hibins[ii], NULL, obs.fft);
}
free(bird_lobins);
free(bird_hibins);
}
printf("Searching with up to %d harmonics summed:\n",
1 << (obs.numharmstages - 1));
printf(" f = %.1f to %.1f Hz\n", obs.rlo / obs.T, obs.rhi / obs.T);
printf(" r = %.1f to %.1f Fourier bins\n", obs.rlo, obs.rhi);
printf(" z = %.1f to %.1f Fourier bins drifted\n\n", obs.zlo, obs.zhi);
/* Generate the correlation kernels */
printf("Generating correlation kernels:\n");
subharminfs = create_subharminfos(obs.numharmstages, (int) obs.zhi);
printf("Done generating kernels.\n\n");
printf("Starting the search.\n");
/* Don't use the *.txtcand files on short in-memory searches */
if (!obs.dat_input) {
printf(" Working candidates in a test format are in '%s'.\n\n",
obs.workfilenm);
}
/* Start the main search loop */
{
double startr = obs.rlo, lastr = 0, nextr = 0;
ffdotpows *fundamental;
while (startr + ACCEL_USELEN * ACCEL_DR < obs.highestbin) {
/* Search the fundamental */
print_percent_complete(startr - obs.rlo,
obs.highestbin - obs.rlo, "search", 0);
nextr = startr + ACCEL_USELEN * ACCEL_DR;
lastr = nextr - ACCEL_DR;
fundamental = subharm_ffdot_plane(1, 1, startr, lastr,
&subharminfs[0][0], &obs);
cands = search_ffdotpows(fundamental, 1, &obs, cands);
if (obs.numharmstages > 1) { /* Search the subharmonics */
int stage, harmtosum, harm;
ffdotpows *subharmonic;
for (stage = 1; stage < obs.numharmstages; stage++) {
harmtosum = 1 << stage;
for (harm = 1; harm < harmtosum; harm += 2) {
subharmonic = subharm_ffdot_plane(harmtosum, harm, startr, lastr,
&subharminfs[stage][harm - 1],
&obs);
add_ffdotpows(fundamental, subharmonic, harmtosum, harm);
free_ffdotpows(subharmonic);
}
cands = search_ffdotpows(fundamental, harmtosum, &obs, cands);
}
}
free_ffdotpows(fundamental);
startr = nextr;
}
print_percent_complete(obs.highestbin - obs.rlo,
obs.highestbin - obs.rlo, "search", 0);
}
printf("\n\nDone searching. Now optimizing each candidate.\n\n");
free_subharminfos(obs.numharmstages, subharminfs);
{ /* Candidate list trimming and optimization */
int numcands;
GSList *listptr;
accelcand *cand;
fourierprops *props;
numcands = g_slist_length(cands);
if (numcands) {
/* Sort the candidates according to the optimized sigmas */
cands = sort_accelcands(cands);
/* Eliminate (most of) the harmonically related candidates */
if ((cmd->numharm > 1) && !(cmd->noharmremoveP))
eliminate_harmonics(cands, &numcands);
/* Now optimize each candidate and its harmonics */
print_percent_complete(0, 0, NULL, 1);
listptr = cands;
for (ii = 0; ii < numcands; ii++) {
print_percent_complete(ii, numcands, "optimization", 0);
cand = (accelcand *) (listptr->data);
optimize_accelcand(cand, &obs);
listptr = listptr->next;
}
print_percent_complete(ii, numcands, "optimization", 0);
/* Calculate the properties of the fundamentals */
props = (fourierprops *) malloc(sizeof(fourierprops) * numcands);
listptr = cands;
for (ii = 0; ii < numcands; ii++) {
cand = (accelcand *) (listptr->data);
/* In case the fundamental harmonic is not significant, */
/* send the originally determined r and z from the */
/* harmonic sum in the search. Note that the derivs are */
/* not used for the computations with the fundamental. */
calc_props(cand->derivs[0], cand->r, cand->z, 0.0, props + ii);
/* Override the error estimates based on power */
props[ii].rerr = (float) (ACCEL_DR) / cand->numharm;
props[ii].zerr = (float) (ACCEL_DZ) / cand->numharm;
listptr = listptr->next;
}
/* Write the fundamentals to the output text file */
output_fundamentals(props, cands, &obs, &idata);
/* Write the harmonics to the output text file */
output_harmonics(cands, &obs, &idata);
/* Write the fundamental fourierprops to the cand file */
obs.workfile = chkfopen(obs.candnm, "wb");
chkfwrite(props, sizeof(fourierprops), numcands, obs.workfile);
fclose(obs.workfile);
free(props);
printf("\n\n");
} else {
printf("No candidates above sigma = %.2f were found.\n\n", obs.sigma);
}
}
/* Finish up */
printf("Searched the following approx numbers of independent points:\n");
printf(" %d harmonic: %9lld\n", 1, obs.numindep[0]);
for (ii = 1; ii < obs.numharmstages; ii++)
printf(" %d harmonics: %9lld\n", 1 << ii, obs.numindep[ii]);
printf("\nTiming summary:\n");
tott = times(&runtimes) / (double) CLK_TCK - tott;
utim = runtimes.tms_utime / (double) CLK_TCK;
stim = runtimes.tms_stime / (double) CLK_TCK;
ttim = utim + stim;
printf(" CPU time: %.3f sec (User: %.3f sec, System: %.3f sec)\n",
ttim, utim, stim);
printf(" Total time: %.3f sec\n\n", tott);
printf("Final candidates in binary format are in '%s'.\n", obs.candnm);
printf("Final Candidates in a text format are in '%s'.\n\n", obs.accelnm);
free_accelobs(&obs);
g_slist_foreach(cands, free_accelcand, NULL);
g_slist_free(cands);
return (0);
}
int main(int argc, char *argv[])
{
FILE *infile, *outfile;
int ii, jj, bufflen = 10000, numread;
long long N = 0;
float *inbuffer = NULL, *outbuffer = NULL;
short useshorts = 0, *sinbuffer = NULL, *soutbuffer = NULL;
char *rootfilenm, *outname;
infodata idata;
Cmdline *cmd;
/* Call usage() if we have no command line arguments */
if (argc == 1) {
Program = argv[0];
printf("\n");
usage();
exit(1);
}
/* Parse the command line using the excellent program Clig */
cmd = parseCmdline(argc, argv);
#ifdef DEBUG
showOptionValues();
#endif
printf("\n\n");
printf(" Time Series Downsampling Routine\n");
printf(" Sept, 2002\n\n");
{
int hassuffix = 0;
char *suffix;
hassuffix = split_root_suffix(cmd->argv[0], &rootfilenm, &suffix);
if (hassuffix) {
if (strcmp(suffix, "sdat") == 0)
useshorts = 1;
if (strcmp(suffix, "dat") != 0 && strcmp(suffix, "sdat") != 0) {
printf
("\nInput file ('%s') must be a time series ('.dat' or '.sdat')!\n\n",
cmd->argv[0]);
free(suffix);
exit(0);
}
free(suffix);
} else {
printf("\nInput file ('%s') must be a time series ('.dat' or '.sdat')!\n\n",
cmd->argv[0]);
exit(0);
}
if (cmd->outfileP) {
outname = cmd->outfile;
} else {
outname = (char *) calloc(strlen(rootfilenm) + 11, sizeof(char));
if (useshorts)
sprintf(outname, "%s_D%d.sdat", rootfilenm, cmd->factor);
else
sprintf(outname, "%s_D%d.dat", rootfilenm, cmd->factor);
}
}
/* Read the info file */
readinf(&idata, rootfilenm);
if (idata.object) {
printf("Downsampling %s data from '%s'.\n\n",
remove_whitespace(idata.object), cmd->argv[0]);
} else {
printf("Downsampling data from '%s'.\n\n", cmd->argv[0]);
}
/* Open files and create arrays */
infile = chkfopen(argv[1], "rb");
outfile = chkfopen(outname, "wb");
/* Read and downsample */
if (useshorts) {
sinbuffer = gen_svect(bufflen * cmd->factor);
soutbuffer = gen_svect(bufflen);
while ((numread =
chkfread(sinbuffer, sizeof(short), bufflen * cmd->factor, infile))) {
for (ii = 0; ii < numread / cmd->factor; ii++) {
soutbuffer[ii] = 0;
for (jj = 0; jj < cmd->factor; jj++)
soutbuffer[ii] += sinbuffer[cmd->factor * ii + jj];
}
chkfwrite(soutbuffer, sizeof(short), numread / cmd->factor, outfile);
N += numread / cmd->factor;
}
vect_free(sinbuffer);
vect_free(soutbuffer);
} else {
inbuffer = gen_fvect(bufflen * cmd->factor);
outbuffer = gen_fvect(bufflen);
while ((numread =
chkfread(inbuffer, sizeof(float), bufflen * cmd->factor, infile))) {
for (ii = 0; ii < numread / cmd->factor; ii++) {
outbuffer[ii] = 0;
for (jj = 0; jj < cmd->factor; jj++)
outbuffer[ii] += inbuffer[cmd->factor * ii + jj];
}
chkfwrite(outbuffer, sizeof(float), numread / cmd->factor, outfile);
N += numread / cmd->factor;
}
vect_free(inbuffer);
vect_free(outbuffer);
}
printf("Done. Wrote %lld points.\n\n", N);
/* Write the new info file */
idata.dt = idata.dt * cmd->factor;
idata.numonoff = 0;
idata.N = (double) N;
strncpy(idata.name, outname, strlen(outname) - 4);
if (useshorts)
idata.name[strlen(outname) - 5] = '\0';
else
idata.name[strlen(outname) - 4] = '\0';
writeinf(&idata);
fclose(infile);
fclose(outfile);
free(rootfilenm);
if (!cmd->outfileP)
free(outname);
exit(0);
}
int main(int argc, char **argv)
{
int i, j, indx, n_file, special_key, knul=0, anynull, hdutype, status=0;
int LastSlashIndex;
int NDump, NChan, NumHDU;
long nrows=0;
double ChanFreq, BW, CentFreq, DM;
double TDump, StartTime, DumpMiddleSecs, ScanLen;
char KeyValue[32], err_text[256];
char cur_file[256], cur_file_short[64];
char HdrVer[16];
char aspoutstr[11], dumprefstr[11];
fitsfile *Fin;
Cmdline *Cmd;
/* Get command line variables */
Cmd = parseCmdline(argc, argv);
/* Normally use this somewhere, and not showOptionValues */
Cmd->tool = Cmd->tool;
/* InfileP = (argc > 1); printf("InfileP = %d\n", InfileP);
InfileC = (argc - 1); printf("InfileC = %d\n", InfileC);
Infile = (char **)malloc(InfileC);
for (i=0; i<InfileC; i++) {
Infile[i] = (char *)malloc(256);
if (strlen(argv[i+1]) > 255) {
fprintf(stderr, "Error: argument %d is too long.\n", i+1);
exit(1);
}
else{
strcpy(Infile[i], argv[i+1]);
}
printf("Argument %d: %s = %s\n", i+1, Infile[i], argv[i+1]);
} */
/************* Keyword list output **************/
if (Cmd->ListP) {
if (argc > 2) {
fprintf(stderr,"\n-list option must be used alone. Exiting...\n");
exit(1);
}
else{
printf("\nSome available keywords/info options useable with the ");
printf("-key flag:\n");
printf("\nObserving frequency-related options:\n");
printf("\nNCHAN: No. of channels\n");
printf("CFRQ: Centre frequecy\n");
printf("BW: Bandwidth\n");
printf("STARTCHAN: First (0th) frequency channel\n");
printf("ENDCHAN: Last (NCHAN-th) frequency channel\n");
printf("ALLCHAN: List all channels (ALLCHAN keyword output does\n");
printf(" not follow convention of -col flag)\n");
printf("\nIntegration-related options:\n");
printf("\nNDUMP: No. of integrations\n");
printf("TDUMP: Individual integration time (s)\n");
printf("SCANLEN: Full scan length of input file (s)\n");
printf("NPTSPROF: No. of bins in integrated profiles\n");
printf("\nOther options:\n");
printf("\nSRC_NAME: Source Name\n");
printf("DM: Dispersion measure\n");
printf("OBS_MODE: PSR/CAL -- normal or calibration scan\n");
printf("OBSVTY: Observatory code\n");
printf("FD_POLN: Polarisation basis (e.g. L or C for linear or\n");
printf(" circular, respectively)\n");
printf("RA: Right ascension of source\n");
printf("DEC: Declination of source\n");
printf("\nNote that all -key arguments are NOT case-sensitive.\n");
}
}
else if(Cmd->TDiffP) {
if (Cmd->KeywordP) {
fprintf(stderr,"\n-tdiff option must be used alone. Exiting...\n");
exit(1);
}
}
else{
if(!Cmd->KeywordP){
printf("Must use -key option with appropriate arguments if not\n");
printf("using -list or -tdiff flag\n");
exit(1);
}
if(!Cmd->InfileP){
printf("Must use -infile option with input file arguments if not\n");
printf("using -list or -tdiff flag\n");
exit(1);
}
}
/*************************************************/
/* Print header line */
if(Cmd->KeywordP && Cmd->ColumnP) {
printf("%s ","File");
for(i=0;i<Cmd->KeywordC;i++)
printf("%s ",Cmd->Keyword[i]);
printf("\n");
}
else if(Cmd->TDiffP){ // for Tdiff
printf("File Source MJD TDIFF [ns]\n");
}
for(n_file=0;n_file<Cmd->InfileC;n_file++){
strcpy(cur_file,Cmd->Infile[n_file]);
/* Open fits file */
if(fits_open_file(&Fin, cur_file, READONLY, &status)){
printf("\nError opening FITS file %s\n",
cur_file);
fits_get_errstatus(status, err_text);
printf("FITS Error status %d: %s\n",status,err_text);
exit(1);
}
status=0;
/* get rid of everthing before and including last forward slash
in the filename for printing to screen: */
LastSlashIndex = -1;
for(i=strlen(cur_file)-1;i>0;i--){
if(!strncasecmp(&cur_file[i],"/",1)){
LastSlashIndex = i;
break;
}
}
strncpy(cur_file_short,&cur_file[LastSlashIndex+1],strlen(cur_file)-LastSlashIndex);
if(Cmd->TDiffP){
/******************** TDIFF ***********************/
int i_dump;
int IMJDStart, SMJDStart;
double StartMJD, MJD, TDiff;
char ObsCode[4], psr[12];
/* Check this is Nancay data */
fits_read_key(Fin, TSTRING, "OBSVTY", ObsCode, NULL, &status);
if(strncmp(ObsCode,"f",1)) {
printf("\nError: File %s does not contain Nancay data (obs code = %s).",
cur_file_short,ObsCode);
printf(" Cannot extract TDIFF from this file. Exiting.\n");
exit(2);
}
/* Get pulsar name */
fits_read_key(Fin, TSTRING, "SRC_NAME", psr, NULL, &status);
/* Calculate start MJD */
fits_read_key(Fin, TINT, "STT_IMJD",
&(IMJDStart),NULL, &status); status = 0;
fits_read_key(Fin, TINT, "STT_SMJD",
&(SMJDStart),NULL, &status); status = 0;
StartMJD = (double)IMJDStart + (double)SMJDStart/86400.;
/* Find nuber of dumps in this file */
fits_get_num_hdus(Fin, &NumHDU, &status);
NDump = NumHDU-3; // Nancay data is always Ver1.0
/* Loop through each dump and pick out time stamp and phase */
fits_movnam_hdu(Fin, BINARY_TBL, "ASPOUT0", 0, &status);
for (i_dump=0;i_dump<NDump;i_dump++){
fits_movrel_hdu(Fin, 1, NULL, &status);
fits_read_key(Fin, TDOUBLE, "DUMPMIDSECS",
&(DumpMiddleSecs),NULL, &status); status = 0;
fits_read_key(Fin, TDOUBLE, "DUMPTDIFF",
&(TDiff),NULL, &status); status = 0;
MJD = StartMJD + DumpMiddleSecs/86400.;
printf("%s ",cur_file_short);
printf("%s ",psr);
printf("%14.8lf ",MJD);
printf("%7.3lf \n",TDiff);
}
}
// else
if(Cmd->ColumnP) printf("%s ",cur_file_short);
else printf("\nKeywords in %s:\n\n", cur_file_short);
/* For each keyword requested... */
for(i=0;i<Cmd->KeywordC;i++){
special_key=0;
/* Clear Keyword */
strcpy(KeyValue,"\0");
/**************** Channel-based keywords: *****************/
if(!strcasecmp(Cmd->Keyword[i],"NChan") || // # of channels
!strncasecmp(Cmd->Keyword[i],"CFRQ",4) || // centre frequency
!strncasecmp(Cmd->Keyword[i],"BW",2) || // bandwidth in MHz
!strcasecmp(Cmd->Keyword[i],"StartChan") || // first channel (MHz)
!strcasecmp(Cmd->Keyword[i],"EndChan") || // last channel (MHz)
!strcasecmp(Cmd->Keyword[i],"AllChan")){ // all channels (MHz)
/* move to channel table */
fits_movnam_hdu(Fin, ASCII_TBL, "BECONFIG", 0, &status);
ffgnrw(Fin, &nrows, &status);
indx = 1;
fits_read_col(Fin, TINT, indx++, 1, 1, 1, &knul,
&NChan, &anynull, &status);
/* Write heading for AllChans keyword if requested */
if (!strcasecmp(Cmd->Keyword[i],"AllChan"))
printf("\nAll Channels:\n");
/* Read NChans number, copy to keyword */
if (!strcasecmp(Cmd->Keyword[i],"NChan"))
sprintf(KeyValue,"%d",NChan);
/* Initialize BW and CentFreq variables */
BW=CentFreq=0.;
for (j=0; j<NChan; j++) {
/* read each channel in succession */
fits_read_col(Fin, TDOUBLE, indx++, 1, 1, 1, NULL,
&ChanFreq, &anynull, &status);
/* Take not of first channel if StartChan keyword is requested */
if (!strcasecmp(Cmd->Keyword[i],"StartChan") && j==0)
sprintf(KeyValue,"%6.1lf",ChanFreq);
/* Calculate bandwidth or centre frequency using first and last
channels */
if((!strncasecmp(Cmd->Keyword[i],"BW",2) ||
!strncasecmp(Cmd->Keyword[i],"CFRQ",4))){
if (j==0)
BW = CentFreq = ChanFreq;
if (j==NChan-1) {
/* +4 because we are subtracting centres of channels,
so this includes the edges... */
BW = fabs(ChanFreq-BW)+4.;
CentFreq = 0.5*(CentFreq + ChanFreq);
}
}
/* Print each channel separately if AllChans keyword is requestes */
if (!strcasecmp(Cmd->Keyword[i],"AllChan"))
printf("%6.1lf ",ChanFreq);
}
/* Take note of last channel if requested */
if (!strcasecmp(Cmd->Keyword[i],"EndChan"))
sprintf(KeyValue,"%6.1lf",ChanFreq);
/* Copy centre frequency and bandwidth keywords to keyword variable
if requested */
if (!strncasecmp(Cmd->Keyword[i],"CFRQ",4))
sprintf(KeyValue,"%6.1lf",CentFreq);
if(!strncasecmp(Cmd->Keyword[i],"BW",2))
sprintf(KeyValue,"%6.1lf",BW);
/* If AllChans is requested, print newline */
if (!strcasecmp(Cmd->Keyword[i],"AllChan")) {
special_key=1;
printf("\n");
}
/* Move file pointer back to beginning of file */
fits_movrel_hdu(Fin, -1, NULL, &status);
/**************** End channel-based keywords: *****************/
}
/**************** DM keyword: *****************/
else if(!strcasecmp(Cmd->Keyword[i],"DM")) {
// special_key=1;
fits_movnam_hdu(Fin, ASCII_TBL, "COHDDISP", 0, &status);
ffgnrw(Fin, &nrows, &status);
indx = 1;
fits_read_col(Fin, TDOUBLE, indx, 1, 1, 1, NULL,
&DM, &anynull, &status);
sprintf(KeyValue,"%8.5lf",DM);
fits_movrel_hdu(Fin, -2, NULL, &status);
/**************** End DM keyword: *****************/
}
/**************** NDUMPS or SCANLEN keyword: *****************/
else if(!strcasecmp(Cmd->Keyword[i],"NDUMP") || // # of dumps
!strcasecmp(Cmd->Keyword[i],"NDUMPS") ||
!strcasecmp(Cmd->Keyword[i],"TDUMP") || // dump length in secs
!strcasecmp(Cmd->Keyword[i],"SCANLEN")){ // length of scans in secs
/* Get the number of dumps. this depensd on version of asp file code */
fits_get_num_hdus(Fin, &NumHDU, &status);
fits_read_key(Fin, TSTRING, "HDRVER", HdrVer, NULL, &status);
status=0;
if(!strcasecmp(HdrVer,"Ver1.0")){
/* divided by 2 since half the tables are phase/period vs. freq
before each data table */
NDump = NumHDU-3;
}
else if(!strcasecmp(HdrVer,"Ver1.0.1")){
/* the "3" is temporary, depending on how many non-data tables we
will be using */
NDump = (NumHDU-3)/2;
}
else{
printf("Do not recognize FITS file version number in header.\n");
printf("This header %s. Exiting...\n",HdrVer);
exit(3);
}
if (!strncasecmp(Cmd->Keyword[i],"NDUMP",4)) { // covers NDUMPS also...
sprintf(KeyValue,"%d",NDump);
}
// if need TDUMP or Total Scan Length (SCANLEN):
if (!strcasecmp(Cmd->Keyword[i],"TDUMP") || // dump length in secs
!strcasecmp(Cmd->Keyword[i],"SCANLEN")) {
/* Get time between successive scans */
/* Get start time */
fits_read_key(Fin, TDOUBLE, "STT_SMJD", &StartTime, NULL, &status);
if (NDump > 1) {
sprintf(aspoutstr,"ASPOUT%d",NDump-2);
sprintf(dumprefstr,"DUMPREF%d",NDump-2);
// printf ("\n%s %s\n",aspoutstr,dumprefstr);
/* Move to first data table , get central time stamp */
if(!strcasecmp(HdrVer,"Ver1.0")) {
fits_movnam_hdu(Fin, BINARY_TBL, "ASPOUT0", 0, &status);
fits_read_key(Fin, TDOUBLE, "DUMPMIDSECS",
&(DumpMiddleSecs),NULL, &status); status = 0;
}
else if (!strcasecmp(HdrVer,"Ver1.0.1")) {
fits_movnam_hdu(Fin, ASCII_TBL, "DUMPREF0", 0, &status);
fits_read_key(Fin, TDOUBLE, "MIDSECS", &(DumpMiddleSecs),
NULL, &status); status = 0;
}
TDump = DumpMiddleSecs;
/* Move to second data table , get central time stamp */
sprintf(aspoutstr,"ASPOUT%d",234);
sprintf(dumprefstr,"DUMPREF%d",234);
// printf ("\n%s %s\n",aspoutstr,dumprefstr);
if(!strcasecmp(HdrVer,"Ver1.0")) {
fits_movnam_hdu(Fin, BINARY_TBL, "ASPOUT1", 0, &status);
fits_read_key(Fin, TDOUBLE, "DUMPMIDSECS",
&(DumpMiddleSecs),NULL, &status); status = 0;
}
else if (!strcasecmp(HdrVer,"Ver1.0.1")) {
fits_movnam_hdu(Fin, ASCII_TBL, "DUMPREF1", 0, &status);
fits_read_key(Fin, TDOUBLE, "MIDSECS", &(DumpMiddleSecs),
NULL, &status); status = 0;
}
if(DumpMiddleSecs < TDump) DumpMiddleSecs += 86400.;
// printf("First = %lf, Second = %lf\n", TDump, DumpMiddleSecs);
TDump = DumpMiddleSecs - TDump;
}
else {
/* We may have switched over to the next MJD, so take care of
this if it's the case */
if (DumpMiddleSecs < StartTime) DumpMiddleSecs += 86400.;
/* TDump is twice the difference between the middle time stamp
and the start time */
TDump = 2.* ((double)floor(DumpMiddleSecs) - StartTime);
}
if (!strncasecmp(Cmd->Keyword[i],"TDUMP",4)) {
sprintf(KeyValue,"%9.3lf",TDump);
}
if (!strcasecmp(Cmd->Keyword[i],"SCANLEN")) {
ScanLen = NDump*TDump;
sprintf(KeyValue,"%7.1lf",ScanLen);
}
/* Move back to first HDU again */
fits_movabs_hdu(Fin,1,&hdutype,&status);status = 0;
}
}
/**************** Other keywords: *****************/
else{
fits_read_key(Fin, TSTRING, Cmd->Keyword[i], KeyValue, NULL, &status);
if(status == VALUE_UNDEFINED || !strcasecmp(KeyValue,"")) {
sprintf(KeyValue,"<not_found>");
}
/**************** End other keywords: *****************/
}
/* The only special keyword is AllChans. If it's not, do the following */
if(!special_key){
/* Column format */
if(Cmd->ColumnP) {
printf("%s ",KeyValue);
if(i==Cmd->KeywordC-1 && n_file<Cmd->InfileC-1) printf("\n");
}
/* Non-column format */
else {
printf("%15s: %s\n",Cmd->Keyword[i],KeyValue);
}
}
}
status=0;
fits_close_file(Fin, &status);
}
printf("\n");
fflush(stdout);
exit(0);
}
int main(int argc, char *argv[]) {
Cmdline *cmd;
struct psrfits pfi, pfo; // input and output
struct subband_info si;
int stat=0, padding=0, userN=0;
// Call usage() if we have no command line arguments
if (argc == 1) {
Program = argv[0];
usage();
exit(0);
}
// Parse the command line using the excellent program Clig
cmd = parseCmdline(argc, argv);
// Open the input PSRFITs files
psrfits_set_files(&pfi, cmd->argc, cmd->argv);
// Use the dynamic filename allocation
if (pfi.numfiles==0) pfi.filenum = cmd->startfile;
pfi.tot_rows = pfi.N = pfi.T = pfi.status = 0;
int rv = psrfits_open(&pfi);
if (rv) { fits_report_error(stderr, rv); exit(1); }
// Read the user weights if requested
si.userwgts = NULL;
if (cmd->wgtsfileP) {
read_weights(cmd->wgtsfile, &userN, &si.userwgts);
if (userN != pfi.hdr.nchan) {
printf("Error!: Input data has %d channels, but '%s' contains only %d weights!\n",
pfi.hdr.nchan, cmd->wgtsfile, userN);
exit(0);
}
printf("Overriding input channel weights with those in '%s'\n",
cmd->wgtsfile);
}
// Initialize the subbanding
// (including reading the first row of data and
// putting it in si->fbuffer)
init_subbanding(&pfi, &pfo, &si, cmd);
if (cmd->outputbasenameP)
strcpy(pfo.basefilename, cmd->outputbasename);
// Loop through the data
do {
// Put the overlapping parts from the next block into si->buffer
float *ptr = pfi.sub.fdata + si.buflen * si.bufwid;
if (padding==0)
stat = psrfits_read_part_DATA(&pfi, si.max_overlap, si.numunsigned, ptr);
if (stat || padding) { // Need to use padding since we ran out of data
printf("Adding a missing row (#%d) of padding to the subbands.\n",
pfi.tot_rows);
// Now fill the last part of si->fbuffer with the chan_avgs so that
// it acts like a correctly read block (or row)
fill_chans_with_avgs(si.max_overlap, si.bufwid,
ptr, si.chan_avgs);
}
//print_raw_chan_stats(pfi.sub.data, pfi.hdr.nsblk,
// pfi.hdr.nchan, pfi.hdr.npol);
// if the input data isn't 8 bit, unpack:
if (pfi.hdr.nbits == 2)
pf_unpack_2bit_to_8bit(&pfi, si.numunsigned);
else if (pfi.hdr.nbits == 4)
pf_unpack_4bit_to_8bit(&pfi, si.numunsigned);
if ((pfo.hdr.ds_time_fact == 1) &&
(pfo.hdr.ds_freq_fact == 1)) {
// No subbanding is needed, so just copy the float buffer
// This is useful if we are just changing the number of bits
// Could do it without a copy by simply exchanging pointers
// to the fdata buffers in pfo and pfi...
memcpy(pfo.sub.fdata, pfi.sub.fdata,
pfi.hdr.nsblk * pfi.hdr.npol * pfi.hdr.nchan * sizeof(float));
} else {
// Now create the subbanded row in the output buffer
make_subbands(&pfi, &si);
}
// Output only Stokes I (in place via floats)
if (pfo.hdr.onlyI && pfo.hdr.npol==4)
get_stokes_I(&pfo);
// Downsample in time (in place via floats)
if (pfo.hdr.ds_time_fact > 1)
downsample_time(&pfo);
// Compute new scales and offsets so that we can pack
// into 8-bits reliably
if (pfo.rownum == 1)
new_scales_and_offsets(&pfo, si.numunsigned, cmd);
// Convert the floats back to bytes in the output array
un_scale_and_offset_data(&pfo, si.numunsigned);
//print_raw_chan_stats(pfo.sub.data, pfo.hdr.nsblk / pfo.hdr.ds_time_fact,
// pfo.hdr.nchan / pfo.hdr.ds_freq_fact, pfo.hdr.npol);
// pack into 2 or 4 bits if needed
if (pfo.hdr.nbits == 2)
pf_pack_8bit_to_2bit(&pfo, si.numunsigned);
else if (pfo.hdr.nbits == 4)
pf_pack_8bit_to_4bit(&pfo, si.numunsigned);
// Write the new row to the output file
pfo.sub.offs = (pfo.tot_rows+0.5) * pfo.sub.tsubint;
psrfits_write_subint(&pfo);
// Break out of the loop here if stat is set
if (stat) break;
// shift the last part of the current row into the "last-row"
// part of the data buffer
memcpy(si.fbuffer, si.fbuffer + si.buflen * si.bufwid,
si.max_overlap * si.bufwid * sizeof(float));
// Read the next row (or padding)
padding = get_current_row(&pfi, &si);
// Set the new weights properly
new_weights(&pfi, &pfo);
} while (pfi.status == 0);
print_clips(&pfo);
rv = psrfits_close(&pfi);
if (rv>100) { fits_report_error(stderr, rv); }
rv = psrfits_close(&pfo);
if (rv>100) { fits_report_error(stderr, rv); }
exit(0);
}
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;
}
int main(int argc, char *argv[])
{
FILE *bytemaskfile;
float **dataavg = NULL, **datastd = NULL, **datapow = NULL;
float *chandata = NULL, powavg, powstd, powmax;
float inttime, norm, fracterror = RFI_FRACTERROR;
float *rawdata = NULL;
unsigned char **bytemask = NULL;
short *srawdata = NULL;
char *outfilenm, *statsfilenm, *maskfilenm;
char *bytemaskfilenm, *rfifilenm;
int numchan = 0, numint = 0, newper = 0, oldper = 0, good_padvals = 0;
int blocksperint, ptsperint = 0, ptsperblock = 0, padding = 0;
int numcands, candnum, numrfi = 0, numrfivect = NUM_RFI_VECT;
int ii, jj, kk, slen, numread = 0, insubs = 0;
int harmsum = RFI_NUMHARMSUM, lobin = RFI_LOBIN, numbetween = RFI_NUMBETWEEN;
double davg, dvar, freq;
struct spectra_info s;
presto_interptype interptype;
rfi *rfivect = NULL;
mask oldmask, newmask;
fftcand *cands;
infodata idata;
Cmdline *cmd;
/* Call usage() if we have no command line arguments */
if (argc == 1) {
Program = argv[0];
printf("\n");
usage();
exit(0);
}
/* Parse the command line using the excellent program Clig */
cmd = parseCmdline(argc, argv);
spectra_info_set_defaults(&s);
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 (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;
}
slen = strlen(cmd->outfile) + 20;
#ifdef DEBUG
showOptionValues();
#endif
printf("\n\n");
printf(" Pulsar Data RFI Finder\n");
printf(" by Scott M. Ransom\n\n");
/* The following is the root of all the output files */
outfilenm = (char *) calloc(slen, sizeof(char));
sprintf(outfilenm, "%s_rfifind", cmd->outfile);
/* And here are the output file names */
maskfilenm = (char *) calloc(slen, sizeof(char));
sprintf(maskfilenm, "%s.mask", outfilenm);
bytemaskfilenm = (char *) calloc(slen, sizeof(char));
sprintf(bytemaskfilenm, "%s.bytemask", outfilenm);
rfifilenm = (char *) calloc(slen, sizeof(char));
sprintf(rfifilenm, "%s.rfi", outfilenm);
statsfilenm = (char *) calloc(slen, sizeof(char));
sprintf(statsfilenm, "%s.stats", outfilenm);
sprintf(idata.name, "%s", outfilenm);
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("Error: Unable to identify input data files. Please specify type.\n\n");
exit(1);
}
}
if (!cmd->nocomputeP) {
if (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);
if (insubs) s.files = (FILE **)malloc(sizeof(FILE *) * s.num_files);
for (ii = 0; ii < s.num_files; ii++) {
printf(" '%s'\n", cmd->argv[ii]);
if (insubs) s.files[ii] = chkfopen(cmd->argv[ii], "rb");
}
printf("\n");
}
if (RAWDATA) {
read_rawdata_files(&s);
print_spectra_info_summary(&s);
spectra_info_to_inf(&s, &idata);
ptsperblock = s.spectra_per_subint;
numchan = s.num_channels;
idata.dm = 0.0;
}
if (insubs) {
/* Set-up values if we are using subbands */
char *tmpname, *root, *suffix;
if (split_root_suffix(s.filenames[0], &root, &suffix) == 0) {
printf("Error: The input filename (%s) must have a suffix!\n\n", s.filenames[0]);
exit(1);
}
if (strncmp(suffix, "sub", 3) == 0) {
tmpname = calloc(strlen(root) + 6, 1);
sprintf(tmpname, "%s.sub", root);
readinf(&idata, tmpname);
free(tmpname);
} else {
printf("\nThe input files (%s) must be subbands! (i.e. *.sub##)\n\n",
s.filenames[0]);
exit(1);
}
free(root);
free(suffix);
ptsperblock = 1;
/* Compensate for the fact that we have subbands and not channels */
idata.freq = idata.freq - 0.5 * idata.chan_wid +
0.5 * idata.chan_wid * (idata.num_chan / s.num_files);
idata.chan_wid = idata.num_chan / s.num_files * idata.chan_wid;
idata.num_chan = numchan = s.num_files;
idata.dm = 0.0;
sprintf(idata.name, "%s", outfilenm);
writeinf(&idata);
s.padvals = gen_fvect(s.num_files);
for (ii = 0 ; ii < s.num_files ; ii++)
s.padvals[ii] = 0.0;
}
/* Read an input mask if wanted */
if (cmd->maskfileP) {
read_mask(cmd->maskfile, &oldmask);
printf("Read old mask information from '%s'\n\n", cmd->maskfile);
good_padvals = determine_padvals(cmd->maskfile, &oldmask, s.padvals);
} else {
oldmask.numchan = oldmask.numint = 0;
}
/* The number of data points and blocks to work with at a time */
if (cmd->blocksP) {
blocksperint = cmd->blocks;
cmd->time = blocksperint * ptsperblock * idata.dt;
} else {
blocksperint = (int) (cmd->time / (ptsperblock * idata.dt) + 0.5);
}
ptsperint = blocksperint * ptsperblock;
numint = (long long) idata.N / ptsperint;
if ((long long) idata.N % ptsperint)
numint++;
inttime = ptsperint * idata.dt;
printf("Analyzing data sections of length %d points (%.6g sec).\n",
ptsperint, inttime);
{
int *factors, numfactors;
factors = get_prime_factors(ptsperint, &numfactors);
printf(" Prime factors are: ");
for (ii = 0; ii < numfactors; ii++)
printf("%d ", factors[ii]);
printf("\n");
if (factors[numfactors - 1] > 13) {
printf(" WARNING: The largest prime factor is pretty big! This will\n"
" cause the FFTs to take a long time to compute. I\n"
" recommend choosing a different -time value.\n");
}
printf("\n");
free(factors);
}
/* Allocate our workarrays */
if (RAWDATA)
rawdata = gen_fvect(idata.num_chan * ptsperblock * blocksperint);
else if (insubs)
srawdata = gen_svect(idata.num_chan * ptsperblock * blocksperint);
dataavg = gen_fmatrix(numint, numchan);
datastd = gen_fmatrix(numint, numchan);
datapow = gen_fmatrix(numint, numchan);
chandata = gen_fvect(ptsperint);
bytemask = gen_bmatrix(numint, numchan);
for (ii = 0; ii < numint; ii++)
for (jj = 0; jj < numchan; jj++)
bytemask[ii][jj] = GOODDATA;
rfivect = rfi_vector(rfivect, numchan, numint, 0, numrfivect);
if (numbetween == 2)
interptype = INTERBIN;
else
interptype = INTERPOLATE;
/* Main loop */
printf("Writing mask data to '%s'.\n", maskfilenm);
printf("Writing RFI data to '%s'.\n", rfifilenm);
printf("Writing statistics to '%s'.\n\n", statsfilenm);
printf("Massaging the data ...\n\n");
printf("Amount Complete = %3d%%", oldper);
fflush(stdout);
for (ii = 0; ii < numint; ii++) { /* Loop over the intervals */
newper = (int) ((float) ii / numint * 100.0 + 0.5);
if (newper > oldper) {
printf("\rAmount Complete = %3d%%", newper);
fflush(stdout);
oldper = newper;
}
/* Read a chunk of data */
if (RAWDATA)
numread = read_rawblocks(rawdata, blocksperint, &s, &padding);
else if (insubs)
numread = read_subband_rawblocks(s.files, s.num_files,
srawdata, blocksperint, &padding);
if (padding)
for (jj = 0; jj < numchan; jj++)
bytemask[ii][jj] |= PADDING;
for (jj = 0; jj < numchan; jj++) { /* Loop over the channels */
if (RAWDATA)
get_channel(chandata, jj, blocksperint, rawdata, &s);
else if (insubs)
get_subband(jj, chandata, srawdata, blocksperint);
/* Calculate the averages and standard deviations */
/* for each point in time. */
if (padding) {
dataavg[ii][jj] = 0.0;
datastd[ii][jj] = 0.0;
datapow[ii][jj] = 1.0;
} else {
avg_var(chandata, ptsperint, &davg, &dvar);
dataavg[ii][jj] = davg;
datastd[ii][jj] = sqrt(dvar);
realfft(chandata, ptsperint, -1);
numcands = 0;
norm = datastd[ii][jj] * datastd[ii][jj] * ptsperint;
if (norm == 0.0)
norm = (chandata[0] == 0.0) ? 1.0 : chandata[0];
cands = search_fft((fcomplex *) chandata, ptsperint / 2,
lobin, ptsperint / 2, harmsum,
numbetween, interptype, norm, cmd->freqsigma,
&numcands, &powavg, &powstd, &powmax);
datapow[ii][jj] = powmax;
/* Record the birdies */
if (numcands) {
for (kk = 0; kk < numcands; kk++) {
freq = cands[kk].r / inttime;
candnum = find_rfi(rfivect, numrfi, freq, RFI_FRACTERROR);
if (candnum >= 0) {
update_rfi(rfivect + candnum, freq, cands[kk].sig, jj, ii);
} else {
update_rfi(rfivect + numrfi, freq, cands[kk].sig, jj, ii);
numrfi++;
if (numrfi == numrfivect) {
numrfivect *= 2;
rfivect = rfi_vector(rfivect, numchan, numint,
numrfivect / 2, numrfivect);
}
}
}
free(cands);
}
}
}
}
printf("\rAmount Complete = 100%%\n");
/* Write the data to the output files */
write_rfifile(rfifilenm, rfivect, numrfi, numchan, numint,
ptsperint, lobin, numbetween, harmsum,
fracterror, cmd->freqsigma);
write_statsfile(statsfilenm, datapow[0], dataavg[0], datastd[0],
numchan, numint, ptsperint, lobin, numbetween);
} else { /* If "-nocompute" */
float freqsigma;
/* Read the data from the output files */
printf("Reading RFI data from '%s'.\n", rfifilenm);
printf("Reading statistics from '%s'.\n", statsfilenm);
readinf(&idata, outfilenm);
read_rfifile(rfifilenm, &rfivect, &numrfi, &numchan, &numint,
&ptsperint, &lobin, &numbetween, &harmsum,
&fracterror, &freqsigma);
numrfivect = numrfi;
read_statsfile(statsfilenm, &datapow, &dataavg, &datastd,
&numchan, &numint, &ptsperint, &lobin, &numbetween);
bytemask = gen_bmatrix(numint, numchan);
printf("Reading bytemask from '%s'.\n\n", bytemaskfilenm);
bytemaskfile = chkfopen(bytemaskfilenm, "rb");
chkfread(bytemask[0], numint * numchan, 1, bytemaskfile);
fclose(bytemaskfile);
for (ii = 0; ii < numint; ii++)
for (jj = 0; jj < numchan; jj++)
bytemask[ii][jj] &= PADDING; /* Clear all but the PADDING bits */
inttime = ptsperint * idata.dt;
}
/* Make the plots and set the mask */
{
int *zapints, *zapchan;
int numzapints = 0, numzapchan = 0;
if (cmd->zapintsstrP) {
zapints = ranges_to_ivect(cmd->zapintsstr, 0, numint - 1, &numzapints);
zapints = (int *) realloc(zapints, (size_t) (sizeof(int) * numint));
} else {
zapints = gen_ivect(numint);
}
if (cmd->zapchanstrP) {
zapchan = ranges_to_ivect(cmd->zapchanstr, 0, numchan - 1, &numzapchan);
zapchan = (int *) realloc(zapchan, (size_t) (sizeof(int) * numchan));
} else {
zapchan = gen_ivect(numchan);
}
rfifind_plot(numchan, numint, ptsperint, cmd->timesigma, cmd->freqsigma,
cmd->inttrigfrac, cmd->chantrigfrac,
dataavg, datastd, datapow, zapchan, numzapchan,
zapints, numzapints, &idata, bytemask,
&oldmask, &newmask, rfivect, numrfi,
cmd->rfixwinP, cmd->rfipsP, cmd->xwinP);
vect_free(zapints);
vect_free(zapchan);
}
/* Write the new mask and bytemask to the file */
write_mask(maskfilenm, &newmask);
bytemaskfile = chkfopen(bytemaskfilenm, "wb");
chkfwrite(bytemask[0], numint * numchan, 1, bytemaskfile);
fclose(bytemaskfile);
/* Determine the percent of good and bad data */
{
int numpad = 0, numbad = 0, numgood = 0;
for (ii = 0; ii < numint; ii++) {
for (jj = 0; jj < numchan; jj++) {
if (bytemask[ii][jj] == GOODDATA) {
numgood++;
} else {
if (bytemask[ii][jj] & PADDING)
numpad++;
else
numbad++;
}
}
}
printf("\nTotal number of intervals in the data: %d\n\n", numint * numchan);
printf(" Number of padded intervals: %7d (%6.3f%%)\n",
numpad, (float) numpad / (float) (numint * numchan) * 100.0);
printf(" Number of good intervals: %7d (%6.3f%%)\n",
numgood, (float) numgood / (float) (numint * numchan) * 100.0);
printf(" Number of bad intervals: %7d (%6.3f%%)\n\n",
numbad, (float) numbad / (float) (numint * numchan) * 100.0);
qsort(rfivect, numrfi, sizeof(rfi), compare_rfi_sigma);
printf(" Ten most significant birdies:\n");
printf("# Sigma Period(ms) Freq(Hz) Number \n");
printf("----------------------------------------------------\n");
for (ii = 0; ii < 10; ii++) {
double pperr;
char temp1[40], temp2[40];
if (rfivect[ii].freq_var == 0.0) {
pperr = 0.0;
sprintf(temp1, " %-14g", rfivect[ii].freq_avg);
sprintf(temp2, " %-14g", 1000.0 / rfivect[ii].freq_avg);
} else {
pperr = 1000.0 * sqrt(rfivect[ii].freq_var) /
(rfivect[ii].freq_avg * rfivect[ii].freq_avg);
nice_output_2(temp1, rfivect[ii].freq_avg, sqrt(rfivect[ii].freq_var),
-15);
nice_output_2(temp2, 1000.0 / rfivect[ii].freq_avg, pperr, -15);
}
printf("%-2d %-8.2f %13s %13s %-8d\n", ii + 1, rfivect[ii].sigma_avg,
temp2, temp1, rfivect[ii].numobs);
}
qsort(rfivect, numrfi, sizeof(rfi), compare_rfi_numobs);
printf("\n Ten most numerous birdies:\n");
printf("# Number Period(ms) Freq(Hz) Sigma \n");
printf("----------------------------------------------------\n");
for (ii = 0; ii < 10; ii++) {
double pperr;
char temp1[40], temp2[40];
if (rfivect[ii].freq_var == 0.0) {
pperr = 0.0;
sprintf(temp1, " %-14g", rfivect[ii].freq_avg);
sprintf(temp2, " %-14g", 1000.0 / rfivect[ii].freq_avg);
} else {
pperr = 1000.0 * sqrt(rfivect[ii].freq_var) /
(rfivect[ii].freq_avg * rfivect[ii].freq_avg);
nice_output_2(temp1, rfivect[ii].freq_avg, sqrt(rfivect[ii].freq_var),
-15);
nice_output_2(temp2, 1000.0 / rfivect[ii].freq_avg, pperr, -15);
}
printf("%-2d %-8d %13s %13s %-8.2f\n", ii + 1, rfivect[ii].numobs,
temp2, temp1, rfivect[ii].sigma_avg);
}
printf("\nDone.\n\n");
}
/* Close the files and cleanup */
free_rfi_vector(rfivect, numrfivect);
free_mask(newmask);
if (cmd->maskfileP)
free_mask(oldmask);
free(outfilenm);
free(statsfilenm);
free(bytemaskfilenm);
free(maskfilenm);
free(rfifilenm);
vect_free(dataavg[0]);
vect_free(dataavg);
vect_free(datastd[0]);
vect_free(datastd);
vect_free(datapow[0]);
vect_free(datapow);
vect_free(bytemask[0]);
vect_free(bytemask);
if (!cmd->nocomputeP) {
// Close all the raw files and free their vectors
close_rawfiles(&s);
vect_free(chandata);
if (insubs)
vect_free(srawdata);
else
vect_free(rawdata);
}
return (0);
}
int main(int argc, char **argv)
{
int n_poly=0, poly_set_used;
double mjd, HoursElapsed, RefPhase, RefFreq, RefPeriod;
char tempo_cmd[256];
struct Polyco Polyco[MAX_PC_SETS];
Cmdline *Cmd;
/* Get command line variables */
Cmd = parseCmdline(argc, argv);
/* showOptionValues(); */
/* Normally use this somewhere, and not showOptionValues */
Cmd->tool = Cmd->tool;
/* Store program name */
//strcpy(ProgName,argv[0]);
/* Make sure parfile exists */
if(FileExists(Cmd->ParFile)){
if (Cmd->VerboseP)
printf("Creating polycos for PSR %s from input parameter file %s.\n",
Cmd->PSRName, Cmd->ParFile);
}
else{
fprintf(stderr,"Could not open file %s.\n", Cmd->ParFile);
return -1;
}
/* If we made it this far, we have a par file we can now use to create
a polyco file. */
/* Open final output file and close right away to create it -- sort of
like a "touch" command, in effect */
/* if((Fpoly=fopen("poly_final.dat", "w"))==NULL){
fprintf(stderr,"Could not open file poly_final.dat. \n");
return -1;
}
fclose(Fpoly); */
/* Now create polycos for the observing times, timespan of validity, and
observing frequency specified by user */
sprintf(tempo_cmd,
"tempo -f %s -Zpsr=%s -Zfreq=%.3lf -Zstart=%.3lf -Ztobsh=%.2lf -Zspan=%d -Zsite=%s",
Cmd->ParFile, Cmd->PSRName, Cmd->ObsFreq,
/* Start polyco set to be 1 hour early, (and so end 1 hour later) */
Cmd->MJDStart-0.04 /* start one hour early */,
/* allow an extra 2 hours of polycos */
Cmd->TObsHours + 2., /* End two hour later */
/* default at 30 minutes valid span */
Cmd->NSpan, Cmd->Site);
if (Cmd->VerboseP) printf("tempo command:\n%s\n\n\n", tempo_cmd);
system(tempo_cmd);
/* Polyco file is now made. Now read it in and save into Polyco array*/
char testchar[16], testfile[32];
double testfreq, testmjd;
strcpy(testfile, "polyco.dat");
strcpy(testchar, Cmd->PSRName);
testfreq = Cmd->ObsFreq;
testmjd = Cmd->MJDStart;
if (Cmd->VerboseP) {
printf("Time step = %.2lf minutes = %.4lf hours = %.5lf days\n",
Cmd->TimeStep, Cmd->TimeStep/60.0, Cmd->TimeStep/1440.);fflush(stdout);
printf("MJDStart = %.4lf, TObsHours = %.3lf\n",
Cmd->MJDStart, Cmd->TObsHours);fflush(stdout);
}
if((n_poly=GetPoly("polyco.dat",
Cmd->PSRName,
&Polyco[0],
Cmd->ObsFreq,
Cmd->MJDStart)) < 1) {
printf("Could not find polycos for all input parameters from \n");
printf("par file %s. Exiting...\n", Cmd->ParFile);
exit(1);
}
printf("# MJD Hours RefPhase RefFreq RefPeriod\n");
/* Run loop over dates and get out PhaseCalc info */
for (mjd=Cmd->MJDStart;
mjd<(Cmd->MJDStart + Cmd->TObsHours/24.0);
mjd+=Cmd->TimeStep/1440.) {
HoursElapsed = (mjd - Cmd->MJDStart)*24.0;
/* Run PhaseCalc */
if((poly_set_used = PhaseCalc(Polyco, n_poly, floor(mjd),
(mjd-floor(mjd)), &RefPhase, &RefFreq)) < 0){
printf("Could not find any polyco sets to match MJD. Exiting...\n");
exit(2);
}
if(Cmd->MilliSecsP)
RefPeriod = 1000./RefFreq;
else
RefPeriod = 1.0/RefFreq;
/* Display PhaseCalc output info */
printf("%.6lf %.4lf %lf %lf %.8lf\n",
mjd, HoursElapsed, RefPhase, RefFreq, RefPeriod);
}
exit(0);
}
