int read_WAPP_lags(FILE * infiles[], int numfiles, int numwapps,
unsigned char *data, struct wappinfo *w)
// This routine reads a set of lags from the input files *infiles
// which contain 16 or 32 bit lag data from the WAPP correlator at
// Arecibo. A set of WAPP lags is bytes_per_sample * numchans * #bits
// * numwapps long. *data must be at least that long
{
int ii;
static int currentfile = 0, numread = 0;
// Make sure our current file number is valid
if (currentfile >= numfiles / numwapps)
return 0;
// First, attempt to read data from the current file
if (chkfread(data, w->bytes_per_sample, 1, infiles[currentfile * numwapps])) { // Got data
// Get data from other WAPPs
for (ii = 1; ii < numwapps; ii++)
chkfread(data + ii * w->bytes_per_sample, w->bytes_per_sample, 1,
infiles[currentfile * numwapps + ii]);
numread++;
return 1;
} else { // Didn't get data
if (feof(infiles[currentfile * numwapps])) { // End of file?
currentfile++;
return read_WAPP_lags(infiles, numfiles, numwapps, data, w);
} else {
printf("\nProblem reading record from WAPP data file:\n");
printf(" currentfile = %d. Exiting.\n", currentfile);
exit(1);
}
}
}
int read_database(void)
/* Reads the full pulsar database into the static array psrdata */
{
FILE *database;
char databasenm[200];
psrdata pdata;
binpsrdata bpdata;
/* Open the binary data file */
sprintf(databasenm, "%s/lib/pulsars.cat", getenv("PRESTO"));
database = chkfopen(databasenm, "rb");
while (chkfread(&pdata, sizeof(psrdata), 1, database)) {
if (np >= NP) {
printf("NP value set to small (%d) in $PRESTO/include/database.h\n", NP);
printf("Please increase it and recompile\n");
exit(-1);
}
strncpy(pulsardata[np].jname, pdata.jname, 13);
strncpy(pulsardata[np].bname, pdata.bname, 9);
strncpy(pulsardata[np].alias, pdata.alias, 10);
pulsardata[np].ra2000 = pdata.ra2000;
pulsardata[np].dec2000 = pdata.dec2000;
pulsardata[np].dm = pdata.dm;
pulsardata[np].timepoch = pdata.timepoch;
pulsardata[np].p = pdata.p;
pulsardata[np].pd = pdata.pd;
pulsardata[np].pdd = 0.0;
pulsardata[np].f = 1.0 / pdata.p;
pulsardata[np].fd = -pdata.pd / (pdata.p * pdata.p);
pulsardata[np].fdd = 0.0;
if (pdata.binary == 1.0) {
chkfread(&bpdata, sizeof(binpsrdata), 1, database);
pulsardata[np].orb.p = bpdata.pb;
pulsardata[np].orb.e = bpdata.e;
pulsardata[np].orb.x = bpdata.x;
pulsardata[np].orb.w = bpdata.w;
pulsardata[np].orb.t = bpdata.To;
} else {
pulsardata[np].orb.p = 0.0;
pulsardata[np].orb.e = 0.0;
pulsardata[np].orb.x = 0.0;
pulsardata[np].orb.w = 0.0;
pulsardata[np].orb.t = 0.0;
}
pulsardata[np].orb.pd = 0.0;
pulsardata[np].orb.wd = 0.0;
np++;
};
/* Close the database */
fclose(database);
have_database = 1;
return np;
}
void read_dftvector(dftvector * data, char *filename)
/* Read a dftvector data structure from a binary file */
{
FILE *infile;
int ii;
double dtmp;
infile = chkfopen(filename, "rb");
chkfread(&dtmp, sizeof(double), 1, infile);
data->n = (int) dtmp;
chkfread(&dtmp, sizeof(double), 1, infile);
data->numvect = (int) dtmp;
chkfread(&data->dt, sizeof(double), 1, infile);
chkfread(&data->r, sizeof(double), 1, infile);
chkfread(&data->norm, sizeof(double), 1, infile);
chkfread(&data->T, sizeof(double), 1, infile);
data->vector = gen_cvect(data->n);
for (ii = 0; ii < data->numvect; ii++) {
chkfread(&dtmp, sizeof(double), 1, infile);
data->vector[ii].r = (float) dtmp;
chkfread(&dtmp, sizeof(double), 1, infile);
data->vector[ii].i = (float) dtmp;
}
fclose(infile);
}
void read_offsets(float **loptr, float **optr, int numpts, int numchan)
{
static int firsttime = 1, useoffsets = 0;
static float *offsets1, *offsets2, *tempzz;
static FILE *offsetfile=NULL; //, *bandpassfile;
int ii;
if (firsttime) {
char *envval = getenv("OFFSETFILE");
if (envval != NULL) {
offsetfile = chkfopen(envval, "r");
if (offsetfile) {
printf("\nUsing offsets from the file '%s'.\n", envval);
useoffsets = 1;
}
}
/* Read the bandpass file */
//*bandpass = gen_fvect(numchan);
//printf("Reading 'bandpass.dat'\n");
//bandpassfile = chkfopen("bandpass.dat", "r");
//chkfread(*bandpass, sizeof(float), numchan, bandpassfile);
//fclose(bandpassfile);
offsets1 = gen_fvect(numpts);
offsets2 = gen_fvect(numpts);
*loptr = offsets2; // Start "backwards" since we'll switch them below
*optr = offsets1;
if (useoffsets) { // Read the data into offsets1
chkfread(*optr, sizeof(float), numpts, offsetfile);
for (ii = 0 ; ii < numpts ; ii++)
offsets1[ii] *= 1.0/(float)numchan;
} else { // Just fill the arrays with zeros
for (ii = 0 ; ii < numpts ; ii++) {
offsets1[ii] = 0.0;
offsets2[ii] = 0.0;
}
}
firsttime = 0;
return;
}
if (useoffsets) {
SWAP(*loptr, *optr); // Swap the buffer pointers
// Read the offsets and scale by the number of channels
chkfread(*optr, sizeof(float), numpts, offsetfile);
for (ii = 0 ; ii < numpts ; ii++)
(*optr)[ii] *= 1.0/(float)numchan;
}
}
int read_floats(FILE * file, float *data, int numpts, int numchan)
/* This routine reads a numpts records of numchan each from */
/* the input file *file which contains normal floating */
/* point data. */
/* It returns the number of points read. */
{
return chkfread(data, sizeof(float),
(unsigned long) (numpts * numchan), file) / numchan;
}
static int read_floats(FILE * file, float *data, int numpts, int numchan)
/* This routine reads a numpts records of numchan each from */
/* the input file *file which contains normal floating */
/* point data. */
/* It returns the number of points read. */
{
/* Read the raw data and return numbar read */
return chkfread(data, sizeof(float), (numpts * numchan), file) / numchan;
}
void get_rzw_cand(char *filenm, int candnum, fourierprops * cand)
/* Read the rzw candidate file 'filenm' and return a */
/* pointer to the fourierprops that describes it. */
{
FILE *candfile;
candfile = chkfopen(filenm, "rb");
chkfileseek(candfile, candnum - 1, sizeof(fourierprops), SEEK_SET);
chkfread(cand, sizeof(fourierprops), 1, candfile);
fclose(candfile);
}
void get_rawbin_cand(char *filenm, int candnum, rawbincand * cand)
/* Read the rawbin candidate file 'filenm' and return a */
/* pointer to the rawbincand that describe it. */
{
FILE *candfile;
candfile = chkfopen(filenm, "rb");
chkfileseek(candfile, candnum - 1, sizeof(rawbincand), SEEK_SET);
chkfread(cand, sizeof(rawbincand), 1, candfile);
fclose(candfile);
}
static int simple_read_subbands(FILE * infiles[], int numfiles, short *subbanddata)
/* Read short int subband data written by prepsubband */
{
int ii, numread = 0;
/* Read the data */
for (ii = 0; ii < numfiles; ii++) {
numread = chkfread(subbanddata + ii * SUBSBLOCKLEN,
sizeof(short), SUBSBLOCKLEN, infiles[ii]);
}
return numread;
}
int determine_padvals(char *maskfilenm, mask * obsmask, float *padvals[])
/* Determine reasonable padding values from the rfifind produced */
/* *.stats file if it is available. Return the allocated vector */
/* (of length numchan) in padvals. Return a '1' if the routine */
/* used the stats file, return 0 if the padding was set to aeros. */
{
FILE *statsfile;
int ii, numchan, numint, ptsperint, lobin, numbetween;
float **dataavg, tmp1, tmp2;
char *statsfilenm, *root, *suffix;
if (split_root_suffix(maskfilenm, &root, &suffix) == 0) {
printf("\nThe mask filename (%s) must have a suffix!\n\n", maskfilenm);
exit(1);
} else {
/* Determine the stats file name */
statsfilenm = calloc(strlen(maskfilenm) + 2, sizeof(char));
sprintf(statsfilenm, "%s.stats", root);
free(root);
free(suffix);
*padvals = gen_fvect(obsmask->numchan);
/* Check to see if the file exists */
printf("Attempting to read the data statistics from '%s'...\n", statsfilenm);
statsfile = chkfopen(statsfilenm, "rb");
free(statsfilenm);
if (statsfile) { /* Read the stats */
chkfread(&numchan, sizeof(int), 1, statsfile);
chkfread(&numint, sizeof(int), 1, statsfile);
chkfread(&ptsperint, sizeof(int), 1, statsfile);
chkfread(&lobin, sizeof(int), 1, statsfile);
chkfread(&numbetween, sizeof(int), 1, statsfile);
dataavg = gen_fmatrix(numint, numchan);
/* These are the powers */
chkfread(dataavg[0], sizeof(float), numchan * numint, statsfile);
/* These are the averages */
chkfread(dataavg[0], sizeof(float), numchan * numint, statsfile);
/* Set the padding values equal to the mid-80% channel averages */
for (ii = 0; ii < numchan; ii++)
calc_avgmedstd(dataavg[0] + ii, numint, 0.8, numchan,
*padvals + ii, &tmp1, &tmp2);
printf
("...succeded. Set the padding values equal to the mid-80%% channel averages.\n");
vect_free(dataavg[0]);
vect_free(dataavg);
fclose(statsfile);
return 1;
} else {
/* This is a temporary solution */
for (ii = 0; ii < obsmask->numchan; ii++)
(*padvals)[ii] = 0.0;
printf("...failed.\n Set the padding values to 0.\n");
return 0;
}
}
}
int fread_multifile(void *data, size_t type, size_t number, multifile * mfile)
/* Read binary data from a multifile. */
/* 'data' is an array of the proper type to store the data */
/* 'type' is the size of each nugget of data to read */
/* 'number' is the number of nuggets to read */
/* 'mfile' is a pointer to a valid multifile structure */
{
int findex;
size_t readbytes, bytesread, tmpbytesread;
findex = mfile->currentfile;
readbytes = number * type;
bytesread = chkfread((char *) data, 1, readbytes, mfile->fileptrs[findex]);
mfile->currentpos += bytesread;
mfile->position += bytesread;
readbytes -= bytesread;
while (readbytes) {
if (feof(mfile->fileptrs[findex])) {
if (findex == mfile->numfiles - 1) {
return bytesread / type;
} else {
findex++;
mfile->currentfile++;
mfile->currentpos = 0;
tmpbytesread = chkfread((char *) data + bytesread, 1,
readbytes, mfile->fileptrs[findex]);
bytesread += tmpbytesread;
mfile->currentpos += tmpbytesread;
mfile->position += tmpbytesread;
readbytes -= tmpbytesread;
}
} else {
printf("\nRead error in read_multifile():\n");
printf("\tTried to read %zd bytes, only read %zd!\n\n",
number * type, bytesread);
return bytesread / type;
}
}
return bytesread / type;
}
int main(int argc, char *argv[])
{
FILE *infile, *outfile;
int ii, numread;
long long N = 0;
float offset = 0.0, fbuffer[sizeof(float) * BUFFLEN];
short sbuffer[sizeof(short) * BUFFLEN];
char *outname;
if (argc != 2 && argc != 3) {
printf("\nUsage: sdat2dat sdatfilename [offset to add]\n\n");
exit(1);
}
printf("\n Shorts to Floats Data Conversion Program\n\n");
/* Get the root of the input filename and */
/* generate the output filenames from it. */
{
char *rootnm, *suffix;
split_root_suffix(argv[1], &rootnm, &suffix);
outname = (char *) calloc(strlen(rootnm) + 5, sizeof(char));
sprintf(outname, "%s.dat", rootnm);
free(rootnm);
free(suffix);
}
if (argc == 3) {
offset = strtod(argv[2], NULL);
printf(" Converting, adding %g, and writing to '%s'...", offset, outname);
} else {
printf(" Converting the data and writing to '%s'...", outname);
}
fflush(NULL);
infile = chkfopen(argv[1], "rb");
outfile = chkfopen(outname, "wb");
while ((numread = chkfread(sbuffer, sizeof(short), BUFFLEN, infile))) {
N += numread;
for (ii = 0; ii < numread; ii++)
fbuffer[ii] = (float) (sbuffer[ii]) + offset;
fwrite(fbuffer, sizeof(float), numread, outfile);
}
printf("done.\n Wrote %lld points.\n\n", N);
fclose(infile);
fclose(outfile);
free(outname);
exit(0);
}
int read_subband_rawblocks(FILE * infiles[], int numfiles, short *subbanddata,
int numsamples, int *padding)
{
int ii, jj, index, numread = 0;
for (ii = 0; ii < numfiles; ii++) {
index = ii * numsamples;
numread =
chkfread(subbanddata + index, sizeof(short), numsamples, infiles[ii]);
for (jj = numread; jj < numsamples; jj++)
subbanddata[index + jj] = 0.0;
}
/* Subband data cannot currently be padded */
*padding = 0;
return numread;
}
float get_numphotons(FILE * file)
/* Return the total number of photons in the FFT file */
/* i.e. it returns the value of the 0th frequency bin. */
/* Arguments: */
/* 'file' is a pointer to the file you want to access. */
{
float nph;
chkfileseek(file, 0, sizeof(fcomplex), SEEK_SET);
chkfread(&nph, sizeof(float), 1, file);
/* The following protects against pre-normalized time-series */
if (nph <= 0)
nph = 1.0;
return nph;
}
static void read_rfifile(char *rfifilenm, rfi ** rfivect, int *numrfi,
int *numchan, int *numint, int *ptsperint,
int *lobin, int *numbetween, int *harmsum,
float *fracterror, float *freqsigma)
{
FILE *outfile;
int ii;
outfile = chkfopen(rfifilenm, "rb");
chkfread(numchan, sizeof(int), 1, outfile);
chkfread(numint, sizeof(int), 1, outfile);
chkfread(ptsperint, sizeof(int), 1, outfile);
chkfread(lobin, sizeof(int), 1, outfile);
chkfread(numbetween, sizeof(int), 1, outfile);
chkfread(harmsum, sizeof(int), 1, outfile);
chkfread(numrfi, sizeof(int), 1, outfile);
chkfread(fracterror, sizeof(float), 1, outfile);
chkfread(freqsigma, sizeof(float), 1, outfile);
*rfivect = rfi_vector(*rfivect, *numchan, *numint, 0, *numrfi);
for (ii = 0; ii < *numrfi; ii++)
read_rfi(outfile, *rfivect + ii, *numchan, *numint);
fclose(outfile);
}
int read_PRESTO_subbands(FILE * infiles[], int numfiles, float *subbanddata,
double timeperblk, int *maskchans,
int *nummasked, mask * obsmask, float *padvals)
/* Read short int subband data written by prepsubband */
/* Note: This version returns a transpose of the version */
/* listed in prepsubband.c */
{
int ii, jj, index, numread = 0;
short subsdata[SUBSBLOCKLEN];
static int currentblock = 0;
/* Read the data */
for (ii = 0; ii < numfiles; ii++) {
index = ii * SUBSBLOCKLEN;
numread = chkfread(subsdata, sizeof(short), SUBSBLOCKLEN, infiles[ii]);
for (jj = 0; jj < numread; jj++, index++)
subbanddata[index] = (float) subsdata[jj];
for (jj = numread; jj < SUBSBLOCKLEN; jj++, index++)
subbanddata[index] = 0.0;
}
/* Mask it if required */
if (obsmask->numchan && numread) {
double starttime;
starttime = currentblock * timeperblk;
*nummasked = check_mask(starttime, timeperblk, obsmask, maskchans);
if (*nummasked == -1) { /* If all channels are masked */
for (ii = 0; ii < numfiles; ii++) {
index = ii * SUBSBLOCKLEN;
for (jj = 0; jj < SUBSBLOCKLEN; jj++, index++)
subbanddata[index] = padvals[ii];
}
} else if (*nummasked > 0) { /* Only some of the channels are masked */
int channum;
for (ii = 0; ii < *nummasked; ii++) {
channum = maskchans[ii];
index = channum * SUBSBLOCKLEN;
for (jj = 0; jj < SUBSBLOCKLEN; jj++, index++)
subbanddata[index] = padvals[channum];
}
}
}
currentblock += 1;
return numread;
}
static void read_statsfile(char *statsfilenm, float ***datapow,
float ***dataavg, float ***datastd,
int *numchan, int *numint, int *ptsperint,
int *lobin, int *numbetween)
{
FILE *outfile;
outfile = chkfopen(statsfilenm, "rb");
chkfread(numchan, sizeof(int), 1, outfile);
chkfread(numint, sizeof(int), 1, outfile);
chkfread(ptsperint, sizeof(int), 1, outfile);
chkfread(lobin, sizeof(int), 1, outfile);
chkfread(numbetween, sizeof(int), 1, outfile);
*dataavg = gen_fmatrix(*numint, *numchan);
*datastd = gen_fmatrix(*numint, *numchan);
*datapow = gen_fmatrix(*numint, *numchan);
chkfread(*(datapow[0]), sizeof(float), *numchan * *numint, outfile);
chkfread(*(dataavg[0]), sizeof(float), *numchan * *numint, outfile);
chkfread(*(datastd[0]), sizeof(float), *numchan * *numint, outfile);
fclose(outfile);
}
int read_shorts(FILE * file, float *data, int numpts, int numchan)
/* This routine reads a numpts records of numchan each from */
/* the input file *file which contains short integer data. */
/* The equivalent floats are placed in *data. */
/* It returns the number of points read. */
{
short *sdata;
int ii, numread;
sdata = (short *) malloc((size_t) (sizeof(short) * (numpts * numchan)));
if (!sdata) {
perror("\nError allocating short array in read_shorts()");
printf("\n");
exit(-1);
}
numread = chkfread(sdata, sizeof(short),
(unsigned long) (numpts * numchan), file) / numchan;
for (ii = 0; ii < numread; ii++)
data[ii] = (float) sdata[ii];
free(sdata);
return numread;
}
int read_rawbin_cand(FILE * file, rawbincand * cands)
/* Read the next rawbin candidate from the file */
/* If successful, return 1, else 0 */
{
return chkfread(cands, sizeof(rawbincand), 1, file);
}
int read_bin_cand(FILE * file, binaryprops * cands)
/* Read the next binary candidate from the file */
/* If successful, return 1, else 0 */
{
return chkfread(cands, sizeof(binaryprops), 1, file);
}
int read_resid_rec(FILE * file, double *toa, double *obsf)
/* This routine reads a single record (i.e. 1 TOA) from */
/* the file resid2.tmp which is written by TEMPO. */
/* It returns 1 if successful, 0 if unsuccessful. */
{
static int firsttime = 1, use_ints = 0;
static double d[9];
// The default Fortran binary block marker has changed
// several times in recent versions of g77 and gfortran.
// g77 used 4 bytes, gfortran 4.0 and 4.1 used 8 bytes
// and gfortrans 4.2 and higher use 4 bytes again.
// So here we try to auto-detect what is going on.
// The current version should be OK on 32- and 64-bit systems
if (firsttime) {
int ii;
long long ll;
double dd;
chkfread(&ll, sizeof(long long), 1, file);
chkfread(&dd, sizeof(double), 1, file);
if (0) printf("(long long) index = %lld (MJD = %17.10f)\n", ll, dd);
if (ll != 72 || dd < 40000.0 || dd > 70000.0) { // 9 * doubles
rewind(file);
chkfread(&ii, sizeof(int), 1, file);
chkfread(&dd, sizeof(double), 1, file);
if (0) printf("(int) index = %d (MJD = %17.10f)\n", ii, dd);
if (ii == 72 && (dd > 40000.0 && dd < 70000.0)) {
use_ints = 1;
} else {
fprintf(stderr, "\nError: Can't read the TEMPO residuals correctly!\n");
exit(1);
}
}
rewind(file);
firsttime = 0;
}
if (use_ints) {
int ii;
chkfread(&ii, sizeof(int), 1, file);
} else {
long long ll;
chkfread(&ll, sizeof(long long), 1, file);
}
// Now read the rest of the binary record
chkfread(&d, sizeof(double), 9, file);
if (0) { // For debugging
printf("Barycentric TOA = %17.10f\n", d[0]);
printf("Postfit residual (pulse phase) = %g\n", d[1]);
printf("Postfit residual (seconds) = %g\n", d[2]);
printf("Orbital phase = %g\n", d[3]);
printf("Barycentric Observing freq = %g\n", d[4]);
printf("Weight of point in the fit = %g\n", d[5]);
printf("Timing uncertainty = %g\n", d[6]);
printf("Prefit residual (seconds) = %g\n", d[7]);
printf("??? = %g\n\n", d[8]);
}
*toa = d[0];
*obsf = d[4];
if (use_ints) {
int ii;
return chkfread(&ii, sizeof(int), 1, file);
} else {
long ll;
return chkfread(&ll, sizeof(long), 1, file);
}
}
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[])
{
float *data;
int status, isign;
unsigned long numdata;
/* unsigned long next2ton; */
FILE *datafile, *scratchfile;
char datafilenm[100], scratchfilenm[100], resultfilenm[100];
char command[80];
struct tms runtimes;
double ttim, stim, utim, tott;
tott = times(&runtimes) / (double) CLK_TCK;
printf("\n\n");
printf(" Real-Valued Data FFT Program v2.0\n");
printf(" by Scott M. Ransom\n");
printf(" 8 June, 1997\n\n");
if ((argc > 1) && (argc < 7)) {
/* Open and check data file. */
if (argc == 3) {
sprintf(datafilenm, "%s.", argv[2]);
sprintf(scratchfilenm, "%s.tmp", argv[2]);
sprintf(resultfilenm, "%s.", argv[2]);
}
if (argc == 4) {
sprintf(datafilenm, "%s/%s.", argv[3], argv[2]);
sprintf(scratchfilenm, "%s/%s.tmp", argv[3], argv[2]);
sprintf(resultfilenm, "%s/%s.", argv[3], argv[2]);
}
if (argc == 5) {
sprintf(datafilenm, "%s/%s.", argv[3], argv[2]);
sprintf(scratchfilenm, "%s/%s.tmp", argv[4], argv[2]);
sprintf(resultfilenm, "%s/%s.", argv[3], argv[2]);
}
isign = atoi(argv[1]);
/* Add the appropriate suffix to the filenames. */
if (isign == 1) {
strcat(datafilenm, "fft");
strcat(resultfilenm, "dat");
} else {
strcat(datafilenm, "dat");
strcat(resultfilenm, "fft");
}
/* Check the input data set... */
printf("Checking data in \"%s\".\n", datafilenm);
datafile = chkfopen(datafilenm, "rb");
/* # of real data points */
numdata = chkfilelen(datafile, sizeof(float));
/* next2ton = next2_to_n(numdata); */
/* if (numdata != next2ton) { */
/* printf("\nNumber of data pts must be an integer power of two,\n"); */
/* printf(" or data must be single precision floats.\n"); */
/* printf("Exiting.\n\n"); */
/* fclose(datafile); */
/* exit(1); */
/* } */
printf("Data OK. There are %ld points.\n\n", numdata);
fclose(datafile);
} else {
printf("\nUsage: realfft sign datafilename [ data path] ");
printf("[scratch path]\n\n");
printf(" This program calculates the FFT of a file containing\n");
printf(" a power-of-two number of floats representing\n");
printf(" real numbers. (i.e. a normal time series)\n\n");
printf(" THE INPUT FILE WILL BE OVERWRITTEN.\n\n");
printf(" \"sign\" is the sign of the exponential during the FFT. \n");
printf(" (i.e. -1 is the standard forward transform, 1 is the\n");
printf(" inverse transform times N (the number of floats))\n");
printf(" If both paths are omitted, the data is assumed to be\n");
printf(" located in the working directory, and the scratch space\n");
printf(" if needed will be located there. If only one path is\n");
printf(" given, both input and scratch files will reside there.\n\n");
printf(" Notes:\n");
printf(" - datafilename must not include \".dat\" or \".fft\"\n");
printf(" suffix. It will be added by the program.\n");
printf(" - Do not end paths in \"/\".\n");
printf(" - The scratch file is the same size as the input file.\n");
printf(" - If \"sign\"=1, the file to be transformed should end\n");
printf(" with \".fft\". Otherwise, it should end with\n");
printf(" \".dat\".\n\n");
exit(0);
}
/* Start the transform sequence */
if (numdata > MAXREALFFT) {
/* Perform Two-Pass, Out-of-Core, FFT */
printf("Performing Out-of-Core Two-Pass FFT on data.\n\n");
printf("Result will be stored in the file \"%s\".\n", resultfilenm);
/* Initialize files. */
datafile = chkfopen(datafilenm, "rb+");
scratchfile = chkfopen(scratchfilenm, "wb+");
printf("\nTransforming...\n");
/* Call Two-Pass routine */
if (isign == 1) {
realfft_scratch_inv(datafile, scratchfile, numdata);
} else {
realfft_scratch_fwd(datafile, scratchfile, numdata);
}
fclose(scratchfile);
sprintf(command, "rm -f %s\n", scratchfilenm);
if ((status = (system(command))) == -1 || status == 127) {
perror("\nSystem call (rm) failed");
printf("\n");
exit(1);
}
printf("Finished.\n\n");
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 usage: %.3f sec total (%.3f sec user, %.3f sec system)\n",
ttim, utim, stim);
printf("Total time elapsed: %.3f sec.\n\n", tott);
} else {
/* Perform standard FFT for real functions */
printf("Performing in-core FFT for real functions on data.\n\n");
printf("FFT will be stored in the file \"%s\".\n\n", resultfilenm);
/* Open the data and fft results files. */
datafile = chkfopen(datafilenm, "rb+");
/* Read data from file to data array */
printf("Reading data.\n\n");
data = gen_fvect(numdata);
chkfread(data, sizeof(float), (unsigned long) numdata, datafile);
chkfileseek(datafile, 0L, sizeof(char), SEEK_SET);
/* Start and time the transform */
printf("Transforming...\n");
realfft(data, numdata, isign);
printf("Finished.\n\n");
/* Write data from FFT array to file */
printf("Writing FFT data.\n\n");
chkfwrite(data, sizeof(float), (unsigned long) numdata, datafile);
vect_free(data);
/* Output the timing information */
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 usage: %.3f sec total (%.3f sec user, %.3f sec system)\n",
ttim, utim, stim);
printf("Total time elapsed: %.3f sec.\n\n", tott);
}
sprintf(command, "mv %s %s\n", datafilenm, resultfilenm);
if ((status = (system(command))) == -1 || status == 127) {
perror("\nSystem call (mv) failed");
printf("\n");
exit(1);
}
fclose(datafile);
/*
fftw_print_max_memory_usage();
fftw_check_memory_leaks();
*/
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[])
{
FILE *fftfile, *candfile = NULL, *psfile = NULL;
char filenm[100], candnm[100], psfilenm[120];
float locpow, norm, powargr, powargi;
float *powr, *spreadpow, *minizoompow, *freqs;
fcomplex *data, *minifft, *minizoom, *spread;
fcomplex *resp, *kernel;
double T, dr, ftobinp;
int ii, nbins, ncands, candnum, lofreq = 0, nzoom, numsumpow = 1;
int numbetween, numkern, kern_half_width;
binaryprops binprops;
infodata idata;
if (argc < 3 || argc > 6) {
usage();
exit(1);
}
printf("\n\n");
printf(" Binary Candidate Display Routine\n");
printf(" by Scott M. Ransom\n\n");
/* Initialize the filenames: */
sprintf(filenm, "%s.fft", argv[1]);
sprintf(candnm, "%s_bin.cand", argv[1]);
/* Read the info file */
readinf(&idata, argv[1]);
if (idata.object) {
printf("Plotting a %s candidate from '%s'.\n", idata.object, filenm);
} else {
printf("Plotting a candidate from '%s'.\n", filenm);
}
T = idata.N * idata.dt;
/* Open the FFT file and get its length */
fftfile = chkfopen(filenm, "rb");
nbins = chkfilelen(fftfile, sizeof(fcomplex));
/* Open the candidate file and get its length */
candfile = chkfopen(candnm, "rb");
ncands = chkfilelen(candfile, sizeof(binaryprops));
/* The candidate number to examine */
candnum = atoi(argv[2]);
/* Check that candnum is in range */
if ((candnum < 1) || (candnum > ncands)) {
printf("\nThe candidate number is out of range.\n\n");
exit(1);
}
/* The lowest freq present in the FFT file */
if (argc >= 4) {
lofreq = atoi(argv[3]);
if ((lofreq < 0) || (lofreq > nbins - 1)) {
printf("\n'lofreq' is out of range.\n\n");
exit(1);
}
}
/* Is the original FFT a sum of other FFTs with the amplitudes added */
/* in quadrature? (i.e. an incoherent sum) */
if (argc >= 5) {
numsumpow = atoi(argv[4]);
if (numsumpow < 1) {
printf("\nNumber of summed powers must be at least one.\n\n");
exit(1);
}
}
/* Initialize PGPLOT using Postscript if requested */
if ((argc == 6) && (!strcmp(argv[5], "ps"))) {
sprintf(psfilenm, "%s_bin_cand_%d.ps", argv[1], candnum);
cpgstart_ps(psfilenm, "landscape");
} else {
cpgstart_x("landscape");
}
/* Read the binary candidate */
chkfileseek(candfile, (long) (candnum - 1), sizeof(binaryprops), SEEK_SET);
chkfread(&binprops, sizeof(binaryprops), 1, candfile);
fclose(candfile);
/* Output the binary candidate */
print_bin_candidate(&binprops, 2);
/* Allocate some memory */
powr = gen_fvect(binprops.nfftbins);
minifft = gen_cvect(binprops.nfftbins / 2);
spread = gen_cvect(binprops.nfftbins);
spreadpow = gen_fvect(binprops.nfftbins);
nzoom = 2 * ZOOMFACT * ZOOMNEIGHBORS;
minizoom = gen_cvect(nzoom);
minizoompow = gen_fvect(nzoom);
/* Allocate and initialize our interpolation kernel */
numbetween = 2;
kern_half_width = r_resp_halfwidth(LOWACC);
numkern = 2 * numbetween * kern_half_width;
resp = gen_r_response(0.0, numbetween, numkern);
kernel = gen_cvect(binprops.nfftbins);
place_complex_kernel(resp, numkern, kernel, binprops.nfftbins);
COMPLEXFFT(kernel, binprops.nfftbins, -1);
/* Read the data from the FFT file */
data = read_fcomplex_file(fftfile, binprops.lowbin - lofreq, binprops.nfftbins);
/* Turn the Fourier amplitudes into powers */
for (ii = 0; ii < binprops.nfftbins; ii++)
powr[ii] = POWER(data[ii].r, data[ii].i);
/* Chop the powers that are way above the median level */
prune_powers(powr, binprops.nfftbins, numsumpow);
/* Perform the minifft */
memcpy((float *) minifft, powr, sizeof(float) * binprops.nfftbins);
realfft((float *) minifft, binprops.nfftbins, -1);
/* Calculate the normalization constant */
norm = sqrt((double) binprops.nfftbins * (double) numsumpow) / minifft[0].r;
locpow = minifft[0].r / binprops.nfftbins;
/* Divide the original power spectrum by the local power level */
for (ii = 0; ii < binprops.nfftbins; ii++)
powr[ii] /= locpow;
/* Now normalize the miniFFT */
minifft[0].r = 1.0;
minifft[0].i = 1.0;
for (ii = 1; ii < binprops.nfftbins / 2; ii++) {
minifft[ii].r *= norm;
minifft[ii].i *= norm;
}
/* Interpolate the minifft and convert to power spectrum */
corr_complex(minifft, binprops.nfftbins / 2, RAW,
kernel, binprops.nfftbins, FFT,
spread, binprops.nfftbins, kern_half_width,
numbetween, kern_half_width, CORR);
for (ii = 0; ii < binprops.nfftbins; ii++)
spreadpow[ii] = POWER(spread[ii].r, spread[ii].i);
/* Plot the initial data set */
freqs = gen_freqs(binprops.nfftbins, binprops.lowbin / T, 1.0 / T);
xyline(binprops.nfftbins, freqs, powr, "Pulsar Frequency (hz)",
"Power / Local Power", 1);
vect_free(freqs);
printf("The initial data set (with high power outliers removed):\n\n");
/* Plot the miniFFT */
freqs = gen_freqs(binprops.nfftbins, 0.0, T / (2 * binprops.nfftbins));
xyline(binprops.nfftbins, freqs, spreadpow, "Binary Period (sec)",
"Normalized Power", 1);
vect_free(freqs);
printf("The miniFFT:\n\n");
/* Interpolate and plot the actual candidate peak */
ftobinp = T / binprops.nfftbins;
freqs = gen_freqs(nzoom, (binprops.rdetect - ZOOMNEIGHBORS) *
ftobinp, ftobinp / (double) ZOOMFACT);
for (ii = 0; ii < nzoom; ii++) {
dr = -ZOOMNEIGHBORS + (double) ii / ZOOMFACT;
rz_interp(minifft, binprops.nfftbins / 2, binprops.rdetect + dr,
0.0, kern_half_width, &minizoom[ii]);
minizoompow[ii] = POWER(minizoom[ii].r, minizoom[ii].i);
}
xyline(nzoom, freqs, minizoompow, "Binary Period (sec)", "Normalized Power", 1);
vect_free(freqs);
printf("The candidate itself:\n\n");
printf("Done.\n\n");
/* Cleanup */
cpgend();
vect_free(data);
vect_free(powr);
vect_free(resp);
vect_free(kernel);
vect_free(minifft);
vect_free(spread);
vect_free(spreadpow);
vect_free(minizoom);
vect_free(minizoompow);
fclose(fftfile);
if ((argc == 6) && (!strcmp(argv[5], "ps"))) {
fclose(psfile);
}
return (0);
}
int main(int argc, char *argv[])
{
FILE **infiles, *outfile = NULL, *scalingfile;
int filenum, argnum = 1, ii = 0, ptsperblock, numlags, numfiles;
int bytes_per_read, scaling = 0, numscalings, output = 1;
long long N;
char *path, *filenm;
char outfilenm[200], filenmbase[200], scalingnm[200], rawlags[4096];
unsigned char output_samples[2048];
float *scalings = NULL;
double dt, T;
SPIGOT_INFO *spigots;
sigprocfb fb;
infodata idata;
if (argc == 1) {
fprintf(stderr, "Usage: spigotSband2filterbank [-stdout] SPIGOT_files\n");
exit(0);
}
if (!strcmp(argv[argnum], "-stdout")) { /* Use STDOUT */
argnum++;
output = 0;
outfile = stdout;
} else {
printf
("\nConverting raw SPIGOT S-band FITs data into SIGPROC\n"
"filterbank format and throwing out the bottom 200MHz...\n\n");
}
/* 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 (outfile != stdout)
printf("Scaling the lags with the %d values found in '%s'\n\n",
numscalings, scalingnm);
}
/* Read and convert the basic SPIGOT file information */
numfiles = argc - 1;
if (outfile == stdout)
numfiles--;
else
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++, argnum++) {
if (outfile != stdout)
printf(" '%s'\n", argv[argnum]);
infiles[filenum] = chkfopen(argv[argnum], "rb");
read_SPIGOT_header(argv[argnum], spigots + filenum);
rewind(infiles[filenum]);
}
if (outfile != stdout)
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, output);
/* Step through the SPIGOT files */
ii = 0;
if (outfile == stdout)
argnum = 2;
else
argnum = 1;
for (filenum = 0; filenum < numfiles; filenum++, argnum++) {
split_path_file(argv[argnum], &path, &filenm);
strncpy(filenmbase, filenm, strlen(filenm) - 5);
filenmbase[strlen(filenm) - 5] = '\0';
sprintf(outfilenm, "%s.fil", filenmbase);
if (outfile != stdout){
printf("Reading S-band Spigot lags from '%s'\n", argv[argnum]);
printf("Writing filterbank spectra to '%s'\n\n", outfilenm);
outfile = chkfopen(outfilenm, "wb");
}
// Update the filterbank header information for each file
spigot2sigprocfb(&(spigots[filenum]), &fb, filenmbase);
write_filterbank_header(&fb, outfile);
chkfseek(infiles[filenum], spigots[filenum].header_len, SEEK_SET);
bytes_per_read = numlags * spigots[filenum].bits_per_lag / 8;
/* Loop over the samples in the file */
while (chkfread(rawlags, bytes_per_read, 1, infiles[filenum])) {
if (scaling)
convert_SPIGOT_point(rawlags, output_samples, SUMIFS, scalings[ii]);
else
convert_SPIGOT_point(rawlags, output_samples, SUMIFS, 1.0);
ii++;
/* Invert the band so that the high freqs are first */
/* This is how SIGPROC stores its data. */
{
int jj;
unsigned char tempzz = 0.0, *loptr, *hiptr;
loptr = output_samples + 0;
hiptr = output_samples + numlags - 1;
for (jj = 0; jj < numlags / 2; jj++, loptr++, hiptr--) {
SWAP(*loptr, *hiptr);
}
}
chkfwrite(output_samples, sizeof(unsigned char), fb.nchans, outfile);
}
fclose(infiles[filenum]);
if (outfile != stdout)
fclose(outfile);
}
if (outfile != stdout)
fprintf(stderr, "Converted and wrote %d samples.\n\n", ii);
if (scaling)
vect_free(scalings);
free(spigots);
free(path);
free(filenm);
free(infiles);
return 0;
}
int read_rzw_cand(FILE * file, fourierprops * cands)
/* Read the next rzw candidate from the file */
/* If successful, return 1, else 0 */
{
return chkfread(cands, sizeof(fourierprops), 1, file);
}
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);
}
void create_accelobs(accelobs * obs, infodata * idata, Cmdline * cmd, int usemmap)
{
int ii, rootlen, input_shorts = 0;
{
int hassuffix = 0;
char *suffix;
hassuffix = split_root_suffix(cmd->argv[0], &(obs->rootfilenm), &suffix);
if (hassuffix) {
if (strcmp(suffix, "fft") != 0 &&
strcmp(suffix, "dat") != 0 && strcmp(suffix, "sdat") != 0) {
printf("\nInput file ('%s') must be an '.fft' or '.[s]dat' file!\n\n",
cmd->argv[0]);
free(suffix);
exit(0);
}
/* If the input file is a time series */
if (strcmp(suffix, "dat") == 0 || strcmp(suffix, "sdat") == 0) {
obs->dat_input = 1;
obs->mmap_file = 0;
if (strcmp(suffix, "sdat") == 0)
input_shorts = 1;
} else {
obs->dat_input = 0;
}
free(suffix);
} else {
printf("\nInput file ('%s') must be an '.fft' or '.[s]dat' file!\n\n",
cmd->argv[0]);
exit(0);
}
}
if (cmd->noharmpolishP)
obs->use_harmonic_polishing = 0;
else
obs->use_harmonic_polishing = 1; // now default
/* Read the info file */
readinf(idata, obs->rootfilenm);
if (idata->object) {
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]);
}
/* Prepare the input time series if required */
if (obs->dat_input) {
FILE *datfile;
long long filelen;
float *ftmp;
printf("Reading and FFTing the time series...");
fflush(NULL);
datfile = chkfopen(cmd->argv[0], "rb");
/* Check the length of the file to see if we can handle it */
filelen = chkfilelen(datfile, sizeof(float));
if (input_shorts)
filelen *= 2;
if (filelen > 67108864) { /* Small since we need memory for the templates */
printf("\nThe input time series is too large. Use 'realfft' first.\n\n");
exit(0);
}
/* Read the time series into a temporary buffer */
/* Note: The padding allows us to search very short time series */
/* using correlations without having to worry about */
/* accessing data before or after the valid FFT freqs. */
if (input_shorts) {
short *stmp = gen_svect(filelen);
ftmp = gen_fvect(filelen+2*ACCEL_PADDING);
for (ii = 0; ii < ACCEL_PADDING; ii++) {
ftmp[ii] = 0.0;
ftmp[ii+filelen+ACCEL_PADDING] = 0.0;
}
chkfread(stmp, sizeof(short), filelen, datfile);
for (ii = 0; ii < filelen; ii++)
ftmp[ii+ACCEL_PADDING] = (float) stmp[ii];
free(stmp);
} else {
ftmp = read_float_file(datfile, -ACCEL_PADDING, filelen+2*ACCEL_PADDING);
}
/* Now, offset the pointer so that we are pointing at the first */
/* bits of valid data. */
ftmp += ACCEL_PADDING;
fclose(datfile);
/* FFT it */
realfft(ftmp, filelen, -1);
obs->fftfile = NULL;
obs->fft = (fcomplex *) ftmp;
obs->numbins = filelen / 2;
printf("done.\n");
/* De-redden it */
printf("Removing red-noise...");
deredden(obs->fft, obs->numbins);
printf("done.\n\n");
}
/* Determine the output filenames */
rootlen = strlen(obs->rootfilenm) + 25;
obs->candnm = (char *) calloc(rootlen, 1);
obs->accelnm = (char *) calloc(rootlen, 1);
obs->workfilenm = (char *) calloc(rootlen, 1);
sprintf(obs->candnm, "%s_ACCEL_%d.cand", obs->rootfilenm, cmd->zmax);
sprintf(obs->accelnm, "%s_ACCEL_%d", obs->rootfilenm, cmd->zmax);
sprintf(obs->workfilenm, "%s_ACCEL_%d.txtcand", obs->rootfilenm, cmd->zmax);
/* Open the FFT file if it exists appropriately */
if (!obs->dat_input) {
obs->fftfile = chkfopen(cmd->argv[0], "rb");
obs->numbins = chkfilelen(obs->fftfile, sizeof(fcomplex));
if (usemmap) {
fclose(obs->fftfile);
obs->fftfile = NULL;
printf("Memory mapping the input FFT. This may take a while...\n");
obs->mmap_file = open(cmd->argv[0], O_RDONLY);
if (obs->mmap_file == -1) {
perror("\nError in open() in accel_utils.c");
printf("\n");
exit(-1);
}
obs->fft = (fcomplex *) mmap(0, sizeof(fcomplex) * obs->numbins, PROT_READ,
MAP_SHARED, obs->mmap_file, 0);
if (obs->fft == MAP_FAILED) {
perror("\nError in mmap() in accel_utils.c");
printf("Falling back to a non-mmaped approach\n");
obs->fftfile = chkfopen(cmd->argv[0], "rb");
obs->mmap_file = 0;
}
} else {
obs->mmap_file = 0;
}
}
/* Determine the other parameters */
if (cmd->zmax % ACCEL_DZ)
cmd->zmax = (cmd->zmax / ACCEL_DZ + 1) * ACCEL_DZ;
if (!obs->dat_input)
obs->workfile = chkfopen(obs->workfilenm, "w");
obs->N = (long long) idata->N;
if (cmd->photonP) {
if (obs->mmap_file || obs->dat_input) {
obs->nph = obs->fft[0].r;
} else {
obs->nph = get_numphotons(obs->fftfile);
}
printf("Normalizing powers using %.0f photons.\n\n", obs->nph);
} else {
obs->nph = 0.0;
/* For short FFTs insure that we don't pick up the DC */
/* or Nyquist component as part of the interpolation */
/* for higher frequencies. */
if (cmd->locpowP) {
obs->norm_type = 1;
printf("Normalizing powers using local-power determination.\n\n");
} else if (cmd->medianP) {
obs->norm_type = 0;
printf("Normalizing powers using median-blocks.\n\n");
} else {
obs->norm_type = 0;
printf("Normalizing powers using median-blocks (default).\n\n");
}
if (obs->dat_input) {
obs->fft[0].r = 1.0;
obs->fft[0].i = 1.0;
}
}
obs->lobin = cmd->lobin;
if (obs->lobin > 0) {
obs->nph = 0.0;
if (cmd->lobin > obs->numbins - 1) {
printf("\n'lobin' is greater than the total number of\n");
printf(" frequencies in the data set. Exiting.\n\n");
exit(1);
}
}
if (cmd->numharm != 1 &&
cmd->numharm != 2 &&
cmd->numharm != 4 && cmd->numharm != 8 && cmd->numharm != 16) {
printf("\n'numharm' = %d must be a power-of-two! Exiting\n\n", cmd->numharm);
exit(1);
}
obs->numharmstages = twon_to_index(cmd->numharm) + 1;
obs->dz = ACCEL_DZ;
obs->numz = cmd->zmax * 2 + 1;
obs->numbetween = ACCEL_NUMBETWEEN;
obs->dt = idata->dt;
obs->T = idata->dt * idata->N;
if (cmd->floP) {
obs->rlo = floor(cmd->flo * obs->T);
if (obs->rlo < obs->lobin)
obs->rlo = obs->lobin;
if (obs->rlo > obs->numbins - 1) {
printf("\nLow frequency to search 'flo' is greater than\n");
printf(" the highest available frequency. Exiting.\n\n");
exit(1);
}
} else {
if (cmd->rloP)
obs->rlo = cmd->rlo;
else
obs->rlo = 1.0;
if (obs->rlo < obs->lobin)
obs->rlo = obs->lobin;
if (obs->rlo > obs->numbins - 1) {
printf("\nLow frequency to search 'rlo' is greater than\n");
printf(" the available number of points. Exiting.\n\n");
exit(1);
}
}
obs->highestbin = obs->numbins - 1;
if (cmd->fhiP) {
obs->highestbin = ceil(cmd->fhi * obs->T);
if (obs->highestbin > obs->numbins - 1)
obs->highestbin = obs->numbins - 1;
obs->rhi = obs->highestbin;
if (obs->highestbin < obs->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) {
obs->highestbin = cmd->rhi;
if (obs->highestbin > obs->numbins - 1)
obs->highestbin = obs->numbins - 1;
obs->rhi = obs->highestbin;
if (obs->highestbin < obs->rlo) {
printf("\nHigh frequency to search 'rhi' is less than\n");
printf(" the lowest frequency to search 'rlo'. Exiting.\n\n");
exit(1);
}
}
obs->dr = ACCEL_DR;
obs->zhi = cmd->zmax;
obs->zlo = -cmd->zmax;
obs->sigma = cmd->sigma;
obs->powcut = (float *) malloc(obs->numharmstages * sizeof(float));
obs->numindep = (long long *) malloc(obs->numharmstages * sizeof(long long));
for (ii = 0; ii < obs->numharmstages; ii++) {
if (obs->numz == 1)
obs->numindep[ii] = (obs->rhi - obs->rlo) / index_to_twon(ii);
else
/* The numz+1 takes care of the small amount of */
/* search we get above zmax and below zmin. */
obs->numindep[ii] = (obs->rhi - obs->rlo) * (obs->numz + 1) *
(obs->dz / 6.95) / index_to_twon(ii);
obs->powcut[ii] = power_for_sigma(obs->sigma,
index_to_twon(ii), obs->numindep[ii]);
}
obs->numzap = 0;
/*
if (zapfile!=NULL)
obs->numzap = get_birdies(cmd->zapfile, obs->T, obs->baryv,
&(obs->lobins), &(obs->hibins));
else
obs->numzap = 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);
}
