void identify_psrdatatype(struct spectra_info *s, int output) { char *root, *suffix, ctmp[40]; /* Split the filename into a rootname and a suffix */ if (split_root_suffix(s->filenames[0], &root, &suffix) == 0) { fprintf(stderr, "Error!: The input filename (%s) must have a suffix!\n\n", s->filenames[0]); exit(1); } else { if (strcmp(suffix, "dat") == 0) s->datatype = DAT; else if (strcmp(suffix, "sdat") == 0) s->datatype = SDAT; else if (strncmp(suffix, "sub0", 4) == 0) s->datatype = SUBBAND; else if (strcmp(suffix, "events") == 0) s->datatype = EVENTS; else if (strcmp(suffix, "bcpm1") == 0 || strcmp(suffix, "bcpm2") == 0) s->datatype = BPP; else if (strcmp(suffix, "fil") == 0 || strcmp(suffix, "fb") == 0) s->datatype = SIGPROCFB; else if ((strcmp(suffix, "fits") == 0) || (strcmp(suffix, "sf") == 0)) { if (strstr(root, "spigot_5") != NULL) s->datatype = SPIGOT; // else if (is_PSRFITS(s->filenames[0])) s->datatype = PSRFITS; else s->datatype = PSRFITS; } else if (strcmp(suffix, "pkmb") == 0) s->datatype = SCAMP; else if (isdigit(suffix[0]) && isdigit(suffix[1]) && isdigit(suffix[2])) s->datatype = WAPP; else s->datatype = UNSET; } psrdatatype_description(ctmp, s->datatype); if (output) printf("Assuming the data are %s format...\n", ctmp); free(root); free(suffix); }
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 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 main(int argc, char *argv[]) { float minval = SMALLNUM, maxval = LARGENUM, inx = 0, iny = 0; int centern, offsetn; int zoomlevel, maxzoom = 0, minzoom, xid, psid; char *rootfilenm, inchar; datapart *lodp; dataview *dv; basicstats *statvals; if (argc == 1) { printf("\nusage: exploredat datafilename\n\n"); exit(0); } printf("\n\n"); printf(" Interactive Data Explorer\n"); printf(" by Scott M. Ransom\n"); printf(" November, 2001\n"); print_help(); { int hassuffix = 0; char *suffix; hassuffix = split_root_suffix(argv[1], &rootfilenm, &suffix); if (hassuffix) { if (strcmp(suffix, "dat") != 0) { printf ("\nInput file ('%s') must be a single PRESTO data file ('.dat')!\n\n", argv[1]); free(suffix); exit(0); } free(suffix); } else { printf("\nInput file ('%s') must be a PRESTO data file ('.dat')!\n\n", argv[1]); exit(0); } } /* Read the info file */ readinf(&idata, rootfilenm); if (idata.object) { printf("Examining %s data from '%s'.\n\n", remove_whitespace(idata.object), argv[1]); } else { printf("Examining data from '%s'.\n\n", argv[1]); } #ifdef USEMMAP mmap_file = open(argv[1], O_RDONLY); { int rt; struct stat buf; rt = fstat(mmap_file, &buf); if (rt == -1) { perror("\nError in fstat() in exploredat.c"); printf("\n"); exit(-1); } Ndat = buf.st_size / sizeof(float); } lodp = get_datapart(0, Ndat); #else { int numsamp; datfile = chkfopen(argv[1], "rb"); Ndat = chkfilelen(datfile, sizeof(float)); numsamp = (Ndat > MAXPTS) ? (int) MAXPTS : (int) Ndat; lodp = get_datapart(0, numsamp); } #endif /* Plot the initial data */ centern = 0.5 * INITIALNUMPTS; if (centern > lodp->nn) centern = lodp->nn / 2; zoomlevel = LOGMAXDISPNUM - LOGINITIALNUMPTS; minzoom = LOGMAXDISPNUM - LOGMAXPTS; maxzoom = LOGMAXDISPNUM - LOGMINDISPNUM; dv = get_dataview(centern, zoomlevel, lodp); /* Prep the XWIN device for PGPLOT */ xid = cpgopen("/XWIN"); if (xid <= 0) { free_datapart(lodp); #ifdef USEMMAP close(mmap_file); #else fclose(datfile); #endif free(dv); exit(EXIT_FAILURE); } cpgask(0); cpgpage(); offsetn = plot_dataview(dv, minval, maxval, 1.0); do { cpgcurs(&inx, &iny, &inchar); if (DEBUGOUT) printf("You pressed '%c'\n", inchar); switch (inchar) { case ' ': /* Toggle stats and sample plotting on/off */ /* 0 = both, 1 = stats only, 2 = data only */ plotstats++; plotstats = plotstats % 3; cpgpage(); offsetn = plot_dataview(dv, minval, maxval, 1.0); break; case 'M': /* Toggle between median and average */ case 'm': usemedian = (usemedian) ? 0 : 1; free(dv); dv = get_dataview(centern, zoomlevel, lodp); cpgpage(); offsetn = plot_dataview(dv, minval, maxval, 1.0); break; case 'A': /* Zoom in */ case 'a': centern = inx + offsetn; case 'I': case 'i': if (DEBUGOUT) printf(" Zooming in (zoomlevel = %d)...\n", zoomlevel); if (zoomlevel < maxzoom) { zoomlevel++; free(dv); dv = get_dataview(centern, zoomlevel, lodp); cpgpage(); offsetn = plot_dataview(dv, minval, maxval, 1.0); } else printf(" Already at maximum zoom level (%d).\n", zoomlevel); break; case 'X': /* Zoom out */ case 'x': case 'O': case 'o': if (DEBUGOUT) printf(" Zooming out (zoomlevel = %d)...\n", zoomlevel); if (zoomlevel > minzoom) { zoomlevel--; free(dv); dv = get_dataview(centern, zoomlevel, lodp); cpgpage(); offsetn = plot_dataview(dv, minval, maxval, 1.0); } else printf(" Already at minimum zoom level (%d).\n", zoomlevel); break; case '<': /* Shift left 1 full screen */ centern -= dv->numsamps + dv->numsamps / 8; case ',': /* Shift left 1/8 screen */ if (DEBUGOUT) printf(" Shifting left...\n"); centern -= dv->numsamps / 8; { /* Should probably get the previous chunk from the datfile... */ double lowestr; lowestr = 0.5 * dv->numsamps; if (centern < lowestr) centern = lowestr; } free(dv); dv = get_dataview(centern, zoomlevel, lodp); cpgpage(); offsetn = plot_dataview(dv, minval, maxval, 1.0); break; case '>': /* Shift right 1 full screen */ centern += dv->numsamps - dv->numsamps / 8; case '.': /* Shift right 1/8 screen */ centern += dv->numsamps / 8; if (DEBUGOUT) printf(" Shifting right...\n"); { /* Should probably get the next chunk from the datfile... */ double highestr; highestr = lodp->nlo + lodp->nn - 0.5 * dv->numsamps; if (centern > highestr) centern = highestr; } free(dv); dv = get_dataview(centern, zoomlevel, lodp); cpgpage(); offsetn = plot_dataview(dv, minval, maxval, 1.0); break; case '+': /* Increase height of top edge */ { float dy; if (maxval > 0.5 * LARGENUM) { printf(" Auto-scaling of top edge is off.\n"); if (minval < 0.5 * SMALLNUM) dy = dv->maxval - dv->minval; else dy = dv->maxval - minval; maxval = dv->maxval + 0.1 * dy; } else { if (minval < 0.5 * SMALLNUM) dy = maxval - dv->minval; else dy = maxval - minval; maxval += 0.1 * dy; } cpgpage(); offsetn = plot_dataview(dv, minval, maxval, 1.0); break; } case '_': /* Decrease height of top edge */ { float dy; if (maxval > 0.5 * LARGENUM) { printf(" Auto-scaling of top edge is off.\n"); if (minval < 0.5 * SMALLNUM) dy = dv->maxval - dv->minval; else dy = dv->maxval - minval; maxval = dv->maxval - 0.1 * dy; } else { if (minval < 0.5 * SMALLNUM) dy = maxval - dv->minval; else dy = maxval - minval; maxval -= 0.1 * dy; } cpgpage(); offsetn = plot_dataview(dv, minval, maxval, 1.0); break; } case '=': /* Increase height of bottom edge */ { float dy; if (minval < 0.5 * SMALLNUM) { printf(" Auto-scaling of bottom edge is off.\n"); if (maxval > 0.5 * LARGENUM) dy = dv->maxval - dv->minval; else dy = maxval - dv->minval; minval = dv->minval + 0.1 * dy; } else { if (maxval > 0.5 * LARGENUM) dy = dv->maxval - minval; else dy = maxval - minval; minval += 0.1 * dy; } cpgpage(); offsetn = plot_dataview(dv, minval, maxval, 1.0); break; } case '-': /* Decrease height of bottom edge */ { float dy; if (minval < 0.5 * SMALLNUM) { printf(" Auto-scaling of bottom edge is off.\n"); if (maxval > 0.5 * LARGENUM) dy = dv->maxval - dv->minval; else dy = maxval - dv->minval; minval = dv->minval - 0.1 * dy; } else { if (maxval > 0.5 * LARGENUM) dy = dv->maxval - minval; else dy = maxval - minval; minval -= 0.1 * dy; } cpgpage(); offsetn = plot_dataview(dv, minval, maxval, 1.0); break; } case 'S': /* Auto-scale */ case 's': printf(" Auto-scaling is on.\n"); minval = SMALLNUM; maxval = LARGENUM; cpgpage(); offsetn = plot_dataview(dv, minval, maxval, 1.0); break; case 'G': /* Goto a time */ case 'g': { char timestr[50]; double time = -1.0; while (time < 0.0) { printf (" Enter the time (s) from the beginning of the file to go to:\n"); fgets(timestr, 50, stdin); timestr[strlen(timestr) - 1] = '\0'; time = atof(timestr); } offsetn = 0.0; centern = (int) (time / idata.dt + 0.5); printf(" Moving to time %.15g (data point %d).\n", time, centern); free(dv); dv = get_dataview(centern, zoomlevel, lodp); cpgpage(); offsetn = plot_dataview(dv, minval, maxval, 1.0); } break; case '?': /* Print help screen */ print_help(); break; case 'P': /* Print the current plot */ case 'p': { int len; char filename[200]; printf(" Enter the filename to save the plot as:\n"); fgets(filename, 195, stdin); len = strlen(filename) - 1; filename[len + 0] = '/'; filename[len + 1] = 'C'; filename[len + 2] = 'P'; filename[len + 3] = 'S'; filename[len + 4] = '\0'; psid = cpgopen(filename); cpgslct(psid); cpgpap(10.25, 8.5 / 11.0); cpgiden(); offsetn = plot_dataview(dv, minval, maxval, 1.0); cpgclos(); cpgslct(xid); filename[len] = '\0'; printf(" Wrote the plot to the file '%s'.\n", filename); } break; case 'V': /* Show the basic statistics for the current dataview */ case 'v': statvals = calc_stats(dv, lodp); printf("\n Statistics:\n" " Low sample %d\n" " Number of samples %d\n" " Low time (s) %.7g\n" " Duration of samples (s) %.7g\n" " Maximum value %.7g\n" " Minimum value %.7g\n" " Average value %.7g\n" " Median value %.7g\n" " Standard Deviation %.7g\n" " Skewness %.7g\n" " Kurtosis %.7g\n\n", dv->lon, dv->numsamps, dv->lon * idata.dt, dv->numsamps * idata.dt, statvals->max, statvals->min, statvals->average, statvals->median, statvals->stdev, statvals->skewness, statvals->kurtosis); free(statvals); break; case 'Q': /* Quit */ case 'q': printf(" Quitting...\n"); free(dv); cpgclos(); break; default: printf(" Unrecognized option '%c'.\n", inchar); break; } } while (inchar != 'Q' && inchar != 'q'); free_datapart(lodp); #ifdef USEMMAP close(mmap_file); #else fclose(datfile); #endif printf("Done\n\n"); 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 *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[]) { 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[]) { /* 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 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[]) { 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[]) { float maxpow = 0.0, inx = 0.0, iny = 0.0; double centerr, offsetf; int zoomlevel, maxzoom, minzoom, xid, psid; char *rootfilenm, inchar; fftpart *lofp; fftview *fv; if (argc == 1) { printf("\nusage: explorefft fftfilename\n\n"); exit(0); } printf("\n\n"); printf(" Interactive FFT Explorer\n"); printf(" by Scott M. Ransom\n"); printf(" October, 2001\n"); print_help(); { int hassuffix = 0; char *suffix; hassuffix = split_root_suffix(argv[1], &rootfilenm, &suffix); if (hassuffix) { if (strcmp(suffix, "fft") != 0) { printf("\nInput file ('%s') must be a FFT file ('.fft')!\n\n", argv[1]); free(suffix); exit(0); } free(suffix); } else { printf("\nInput file ('%s') must be a FFT file ('.fft')!\n\n", argv[1]); exit(0); } } /* Read the info file */ readinf(&idata, rootfilenm); if (strlen(remove_whitespace(idata.object)) > 0) { printf("Examining %s data from '%s'.\n\n", remove_whitespace(idata.object), argv[1]); } else { printf("Examining data from '%s'.\n\n", argv[1]); } N = idata.N; T = idata.dt * idata.N; #ifdef USEMMAP printf("Memory mapping the input FFT. This may take a while...\n"); mmap_file = open(argv[1], O_RDONLY); { int rt; struct stat buf; rt = fstat(mmap_file, &buf); if (rt == -1) { perror("\nError in fstat() in explorefft.c"); printf("\n"); exit(-1); } Nfft = buf.st_size / sizeof(fcomplex); } lofp = get_fftpart(0, Nfft); #else { int numamps; fftfile = chkfopen(argv[1], "rb"); Nfft = chkfilelen(fftfile, sizeof(fcomplex)); numamps = (Nfft > MAXBINS) ? (int) MAXBINS : (int) Nfft; lofp = get_fftpart(0, numamps); } #endif /* Plot the initial data */ { int initnumbins = INITIALNUMBINS; if (initnumbins > Nfft) { initnumbins = next2_to_n(Nfft) / 2; zoomlevel = LOGDISPLAYNUM - (int) (log(initnumbins) / log(2.0)); minzoom = zoomlevel; } else { zoomlevel = LOGDISPLAYNUM - LOGINITIALNUMBINS; minzoom = LOGDISPLAYNUM - LOGMAXBINS; } maxzoom = LOGDISPLAYNUM - LOGMINBINS; centerr = initnumbins / 2; } fv = get_fftview(centerr, zoomlevel, lofp); /* Prep the XWIN device for PGPLOT */ xid = cpgopen("/XWIN"); if (xid <= 0) { free(fv); #ifdef USEMMAP close(mmap_file); #else fclose(fftfile); #endif free_fftpart(lofp); exit(EXIT_FAILURE); } cpgscr(15, 0.4, 0.4, 0.4); cpgask(0); cpgpage(); offsetf = plot_fftview(fv, maxpow, 1.0, 0.0, 0); do { cpgcurs(&inx, &iny, &inchar); if (DEBUGOUT) printf("You pressed '%c'\n", inchar); switch (inchar) { case 'A': /* Zoom in */ case 'a': centerr = (inx + offsetf) * T; case 'I': case 'i': if (DEBUGOUT) printf(" Zooming in (zoomlevel = %d)...\n", zoomlevel); if (zoomlevel < maxzoom) { zoomlevel++; free(fv); fv = get_fftview(centerr, zoomlevel, lofp); cpgpage(); offsetf = plot_fftview(fv, maxpow, 1.0, 0.0, 0); } else printf(" Already at maximum zoom level (%d).\n", zoomlevel); break; case 'X': /* Zoom out */ case 'x': case 'O': case 'o': if (DEBUGOUT) printf(" Zooming out (zoomlevel = %d)...\n", zoomlevel); if (zoomlevel > minzoom) { zoomlevel--; free(fv); fv = get_fftview(centerr, zoomlevel, lofp); cpgpage(); offsetf = plot_fftview(fv, maxpow, 1.0, 0.0, 0); } else printf(" Already at minimum zoom level (%d).\n", zoomlevel); break; case '<': /* Shift left 1 full screen */ centerr -= fv->numbins + fv->numbins / 8; case ',': /* Shift left 1/8 screen */ if (DEBUGOUT) printf(" Shifting left...\n"); centerr -= fv->numbins / 8; { /* Should probably get the previous chunk from the fftfile... */ double lowestr; lowestr = 0.5 * fv->numbins; if (centerr < lowestr) centerr = lowestr; } free(fv); fv = get_fftview(centerr, zoomlevel, lofp); cpgpage(); offsetf = plot_fftview(fv, maxpow, 1.0, 0.0, 0); break; case '>': /* Shift right 1 full screen */ centerr += fv->numbins - fv->numbins / 8; case '.': /* Shift right 1/8 screen */ if (DEBUGOUT) printf(" Shifting right...\n"); centerr += fv->numbins / 8; { /* Should probably get the next chunk from the fftfile... */ double highestr; highestr = lofp->rlo + lofp->numamps - 0.5 * fv->numbins; if (centerr > highestr) centerr = highestr; } free(fv); fv = get_fftview(centerr, zoomlevel, lofp); cpgpage(); offsetf = plot_fftview(fv, maxpow, 1.0, 0.0, 0); break; case '+': /* Increase height of powers */ case '=': if (maxpow == 0.0) { printf(" Auto-scaling is off.\n"); maxpow = 1.1 * fv->maxpow; } maxpow = 3.0 / 4.0 * maxpow; cpgpage(); offsetf = plot_fftview(fv, maxpow, 1.0, 0.0, 0); break; case '-': /* Decrease height of powers */ case '_': if (maxpow == 0.0) { printf(" Auto-scaling is off.\n"); maxpow = 1.1 * fv->maxpow; } maxpow = 4.0 / 3.0 * maxpow; cpgpage(); offsetf = plot_fftview(fv, maxpow, 1.0, 0.0, 0); break; case 'S': /* Auto-scale */ case 's': if (maxpow == 0.0) break; else { printf(" Auto-scaling is on.\n"); maxpow = 0.0; cpgpage(); offsetf = plot_fftview(fv, maxpow, 1.0, 0.0, 0); break; } case 'G': /* Goto a frequency */ case 'g': { char freqstr[50]; double freq = -1.0; while (freq < 0.0) { printf(" Enter the frequency (Hz) to go to:\n"); fgets(freqstr, 50, stdin); freqstr[strlen(freqstr) - 1] = '\0'; freq = atof(freqstr); } offsetf = 0.0; centerr = freq * T; printf(" Moving to frequency %.15g.\n", freq); free(fv); fv = get_fftview(centerr, zoomlevel, lofp); cpgpage(); offsetf = plot_fftview(fv, maxpow, 1.0, centerr, 2); } break; case 'H': /* Show harmonics */ case 'h': { double retval; retval = harmonic_loop(xid, centerr, zoomlevel, lofp); if (retval > 0.0) { offsetf = 0.0; centerr = retval; free(fv); fv = get_fftview(centerr, zoomlevel, lofp); cpgpage(); offsetf = plot_fftview(fv, maxpow, 1.0, centerr, 2); } } break; case '?': /* Print help screen */ print_help(); break; case 'D': /* Show details about a selected point */ case 'd': { double newr; printf(" Searching for peak near freq = %.7g Hz...\n", (inx + offsetf)); newr = find_peak(inx + offsetf, fv, lofp); centerr = newr; free(fv); fv = get_fftview(centerr, zoomlevel, lofp); cpgpage(); offsetf = plot_fftview(fv, maxpow, 1.0, centerr, 2); } break; case 'L': /* Load a zaplist */ case 'l': { int ii, len; char filename[200]; double *lobins, *hibins; printf(" Enter the filename containing the zaplist to load:\n"); fgets(filename, 199, stdin); len = strlen(filename) - 1; filename[len] = '\0'; numzaplist = get_birdies(filename, T, 0.0, &lobins, &hibins); lenzaplist = numzaplist + 20; /* Allow some room to add more */ if (lenzaplist) free(zaplist); zaplist = (bird *) malloc(sizeof(bird) * lenzaplist); for (ii = 0; ii < numzaplist; ii++) { zaplist[ii].lobin = lobins[ii]; zaplist[ii].hibin = hibins[ii]; } vect_free(lobins); vect_free(hibins); printf("\n"); cpgpage(); offsetf = plot_fftview(fv, maxpow, 1.0, 0.0, 0); } break; case 'Z': /* Add a birdie to a zaplist */ case 'z': { int badchoice = 2; float lox, hix, loy, hiy; double rs[2]; char choice; if (numzaplist + 1 > lenzaplist) { lenzaplist += 10; zaplist = (bird *) realloc(zaplist, sizeof(bird) * lenzaplist); } cpgqwin(&lox, &hix, &loy, &hiy); printf(" Click the left mouse button on the first frequency limit.\n"); while (badchoice) { cpgcurs(&inx, &iny, &choice); if (choice == 'A' || choice == 'a') { rs[2 - badchoice] = ((double) inx + offsetf) * T; cpgsave(); cpgsci(7); cpgmove(inx, 0.0); cpgdraw(inx, hiy); cpgunsa(); badchoice--; if (badchoice == 1) printf (" Click the left mouse button on the second frequency limit.\n"); } else { printf(" Option not recognized.\n"); } }; if (rs[1] > rs[0]) { zaplist[numzaplist].lobin = rs[0]; zaplist[numzaplist].hibin = rs[1]; } else { zaplist[numzaplist].lobin = rs[1]; zaplist[numzaplist].hibin = rs[0]; } printf(" The new birdie has: f_avg = %.15g f_width = %.15g\n\n", 0.5 * (zaplist[numzaplist].hibin + zaplist[numzaplist].lobin) / T, (zaplist[numzaplist].hibin - zaplist[numzaplist].lobin) / T); numzaplist++; qsort(zaplist, numzaplist, sizeof(bird), compare_birds); cpgpage(); offsetf = plot_fftview(fv, maxpow, 1.0, 0.0, 0); } break; case 'P': /* Print the current plot */ case 'p': { int len; char filename[200]; printf(" Enter the filename to save the plot as:\n"); fgets(filename, 196, stdin); len = strlen(filename) - 1; filename[len + 0] = '/'; filename[len + 1] = 'P'; filename[len + 2] = 'S'; filename[len + 3] = '\0'; psid = cpgopen(filename); cpgslct(psid); cpgpap(10.25, 8.5 / 11.0); cpgiden(); cpgscr(15, 0.8, 0.8, 0.8); offsetf = plot_fftview(fv, maxpow, 1.0, 0.0, 0); cpgclos(); cpgslct(xid); cpgscr(15, 0.4, 0.4, 0.4); filename[len] = '\0'; printf(" Wrote the plot to the file '%s'.\n", filename); } break; case 'N': /* Changing power normalization */ case 'n': { float inx2 = 0.0, iny2 = 0.0; char choice; unsigned char badchoice = 1; printf(" Specify the type of power normalization:\n" " m,M : Median values determined locally\n" " d,D : DC frequency amplitude\n" " r,R : Raw powers (i.e. no normalization)\n" " u,U : User specified interval (the average powers)\n"); while (badchoice) { cpgcurs(&inx2, &iny2, &choice); switch (choice) { case 'M': case 'm': norm_const = 0.0; maxpow = 0.0; badchoice = 0; printf (" Using local median normalization. Autoscaling is on.\n"); break; case 'D': case 'd': norm_const = 1.0 / r0; maxpow = 0.0; badchoice = 0; printf (" Using DC frequency (%f) normalization. Autoscaling is on.\n", r0); break; case 'R': case 'r': norm_const = 1.0; maxpow = 0.0; badchoice = 0; printf (" Using raw powers (i.e. no normalization). Autoscaling is on.\n"); break; case 'U': case 'u': { char choice2; float xx = inx, yy = iny; int lor, hir, numr; double avg, var; printf (" Use the left mouse button to select a left and right boundary\n" " of a region to calculate the average power.\n"); do { cpgcurs(&xx, &yy, &choice2); } while (choice2 != 'A' && choice2 != 'a'); lor = (int) ((xx + offsetf) * T); cpgsci(7); cpgmove(xx, 0.0); cpgdraw(xx, 10.0 * fv->maxpow); do { cpgcurs(&xx, &yy, &choice2); } while (choice2 != 'A' && choice2 != 'a'); hir = (int) ((xx + offsetf) * T); cpgmove(xx, 0.0); cpgdraw(xx, 10.0 * fv->maxpow); cpgsci(1); if (lor > hir) { int tempr; tempr = hir; hir = lor; lor = tempr; } numr = hir - lor + 1; avg_var(lofp->rawpowers + lor - lofp->rlo, numr, &avg, &var); printf(" Selection has: average = %.5g\n" " std dev = %.5g\n", avg, sqrt(var)); norm_const = 1.0 / avg; maxpow = 0.0; badchoice = 0; printf (" Using %.5g as the normalization constant. Autoscaling is on.\n", avg); break; } default: printf(" Unrecognized choice '%c'.\n", choice); break; } } free(fv); fv = get_fftview(centerr, zoomlevel, lofp); cpgpage(); offsetf = plot_fftview(fv, maxpow, 1.0, 0.0, 0); } break; case 'Q': /* Quit */ case 'q': printf(" Quitting...\n"); free(fv); cpgclos(); break; default: printf(" Unrecognized option '%c'.\n", inchar); break; } } while (inchar != 'Q' && inchar != 'q'); free_fftpart(lofp); #ifdef USEMMAP close(mmap_file); #else fclose(fftfile); #endif if (lenzaplist) free(zaplist); 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[]) { /* 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); }