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[])
{
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);
}
