int main (int argc, char *argv[]) { int ntimglobal=0; // number of time samples in original int ngulp_original=0; // number of time samples to look at at once int nskipstart=0; // number skipped at start int nrejects; //ZAPPER int zapswitch = 0; //ZAPPER double tsamp_orig=0; //gsearch setup & defaults float Gsigmacut=6.0; float delta, tstart; vector<Gpulse> * Giant = new vector<Gpulse>[MAXFILES]; bool Gsearched=false; int i,ntim,headersize[MAXFILES],noff=0,gulp; float *time_series[MAXFILES],sum=0.0,sumsq=0.0,mean,meansq,sigma; int MAXMARKERS = 1024; int nfiles = 0; FILE *inputfile[MAXFILES]; char filename[MAXFILES][256]; int spectra=0; int powerspectra=0; double dmoffirstfile; char *killfile; bool dokill=false; bool ssigned=true; bool fsigned=false; int topfold=-1; int topgiant=-1; int toppeak=-1; //?!? sarah added this bool askdevice=false; char devicename[200]; if (argc<2 || help_required(argv[1])) { helpmenu(); // fprintf(stderr,"Usage: giant filenames\n\t(e.g.>> giant *.tim)\n\n\t-s N\tskip N samples\n\t-n N\tread N samples\n\t-S read spectra instead of amplitudes\n-i interpret signed chars as unsigned\n\t-z make a zap list of bad time samples\n"); exit(0); } print_version(argv[0],argv[1]); i=1; while (i<argc) { if (file_exists(argv[i])) { inputfile[nfiles]=open_file(argv[i],"r"); strcpy(filename[nfiles],argv[i]); nfiles++; } if (strings_equal(argv[i],"-s")) sscanf(argv[++i],"%d",&nskipstart); if (strings_equal(argv[i],"-S")) spectra=1; if (strings_equal(argv[i],"-i")) ssigned=false; if (strings_equal(argv[i],"-f")) fsigned=true; if (strings_equal(argv[i],"-n")) sscanf(argv[++i],"%d",&ngulp_original); if (strings_equal(argv[i],"-c")) sscanf(argv[++i],"%f",&Gsigmacut); if (strings_equal(argv[i],"-z")) zapswitch=1; if (strings_equal(argv[i],"-g")) {askdevice=true;sscanf(argv[++i],"%s",&devicename);} if (strings_equal(argv[i],"-k")) {killfile=(char*)malloc(strlen(argv[++i])+1); strcpy(killfile,argv[i]);dokill=true;} if (nfiles>MAXFILES) error_message("too many open files"); i++; } int ntimglobal_smallest=0, nsamp; for (i=0; i<nfiles; i++) { if (spectra){ int npf; double rate; time_series[i]=Creadspec(filename[i],&npf,&rate); tsamp = 1.0/(rate); //normalise(npf,time_series[i]); nsamp = ntimglobal = ntimglobal_smallest = npf; } else { if ((headersize[i]=read_header(inputfile[i]))) { if (! fsigned){ if (isign > 0) { ssigned=false; fprintf(stderr,"using signed header variable to set UNSIGNED\n"); } if (isign < 0) { ssigned=true; fprintf(stderr,"using signed header variable to set SIGNED\n"); } } if (i==0) dmoffirstfile = refdm; if (nbits!=8 && nbits!=32) error_message("giant currently only works for 8- or 32-bit data"); nsamp = nsamples(filename[i],headersize[i],nbits,nifs,nchans); if (i == 0) { ntimglobal_smallest=nsamp; } else { ntimglobal= nsamp; if (ntimglobal < ntimglobal_smallest) ntimglobal_smallest = ntimglobal; } // Space for data (time_series) time_series[i]=(float *) malloc((nsamp+2)*sizeof(float)); if (time_series[i]==NULL){ fprintf(stderr,"Error mallocing %d floats of %d size\n",nsamp, sizeof(float)); exit(-1); } tsamp_orig = tsamp; // Skip data fprintf(stderr,"Skipping %d bytes\n",nskipstart*nbits/8); fseek(inputfile[i],nskipstart*nbits/8,SEEK_CUR); } // each file } // spectra or not } // for (i...) puti(ntimglobal_smallest); if (ngulp_original==0) ngulp_original=ntimglobal_smallest; // ****** SAM'S ZAP SWITCH ****** // Sam Bates 2009 // Integrated into new giant by SBS // Switch to make a .killtchan file for time samples > 3.5 sigma // SARAHZAP tag means addition was added later by Sarah // ****************************** int ngulp=ngulp_original; // int nrejects_max=ngulp_original/100; int * mown = new int[ngulp_original]; int nstart=0; if (zapswitch){ float dummy; int NActuallyRead; char *buffer; buffer = new char[ngulp*nbits/8]; for (i=0; i<nfiles; i++){ NActuallyRead = fread(buffer,nbits/8,ngulp,inputfile[i]); if (nbits==32){ memcpy(time_series[i],buffer,sizeof(float)*ngulp); } else { for (int j=0;j<NActuallyRead;j++){ if (ssigned) time_series[i][j]=(float)buffer[j]; if (!ssigned) time_series[i][j]=(float)((unsigned char)buffer[j]); } } puti(ngulp); find_baseline(ngulp,time_series[i],10.0/tsamp,5.0); mowlawn(ngulp,time_series[i],5,256); } printf("%f\n",dummy); printf("Bad time samples found...\n"); exit(0); } int pgpID; if (askdevice){ pgpID = cpgbeg(0,devicename,1,1); } else { pgpID = cpgbeg(0,"/xs",1,1); } cpgsch(0.5); cpgtext(0.6,0.0,"Press 'h' over the main window for help and full options list."); cpgsch(1.0); /* create the dialog */ dialog * d = new dialog(); /* add the "action" buttons */ int QUIT = d->addbutton(0.02,0.95,"Quit"); int POWER = d->addbutton(0.07,0.85,"POWER"); int SMHRM = d->addbutton(0.075,0.80,"SMHRM"); int FFT = d->addbutton(0.02,0.85,"FFT"); int PLOT = d->addbutton(0.02,0.80,"Plot"); int NEXT = d->addbutton(0.02,0.75,"Next"); int ZAPPEAK = d->addbutton(0.075,0.75,"ZapPeak"); int RESET = d->addbutton(0.02,0.70,"Reset"); int GLOBALRESET = d->addbutton(0.02,0.65,"Global Reset"); int HALVEPLOT = d->addbutton(0.02,0.60,"Halve Plot"); int BASELINE = d->addbutton(0.02,0.50,"Baseline"); int ZAPCOMMON = d->addbutton(0.02,0.45,"Zap Common"); int SUBTRACTMEAN = d->addbutton(0.02,0.40,"ZAP Mean"); int BSCRUNCH = d->addbutton(0.02,0.35,"Bscrunch"); int NORMALISE = d->addbutton(0.02,0.30,"Normalise"); int HISTOGRAM = d->addbutton(0.02,0.25,"Histogram"); int GSEARCH = d->addbutton(0.02,0.20,"Find Giants"); int MOWLAWN = d->addbutton(0.08,0.70,"LAWN"); int SEEFIL = d->addbutton(0.02,0.15,"View Band"); int FWRITE = d->addbutton(0.02,0.05,"Write File"); /* add the plot regions */ d->addplotregion(0.2,0.99,0.98,0.99); float deltay = 0.9/(float)nfiles; for (i=0; i<nfiles; i++) d->addplotregion(0.2,0.99,0.95-deltay*(float)(i+1),0.95-deltay*(float)i); d->draw(); float x,y; char ans; int button=-1; int plotno=-1; int NPIXELS = 1024; float * xaxis = new float[NPIXELS]; float * ymaxes = new float[NPIXELS]; float * ymins = new float[NPIXELS]; int scrunch=1; int nmarkers=0; int * markers= new int[MAXMARKERS]; int nfileptr=nskipstart; int nplot=ngulp_original; nstart=0; //COMMENTED IN ZAPPER VERSION: MAY CAUSE CONFLICTS IN THIS VER. ngulp=ngulp_original; //COMMENTED IN ZAPPER VERSION: MAY CAUSE CONFLICTS IN THIS VER. double trialperiod; int doperiod=-1; double xperiod; bool zoneplot=false; int ngates=0; float xgate=0.0; button=NEXT; if (spectra) button = PLOT; while (button!=QUIT){ // Plot the zone // Entire file is white if (button!=NEXT)button=d->manage(&x,&y,&ans,&plotno); if (ans=='h'){ buttonexplain(); continue; } // printf("manage x %f y %f plotno %d\n",x,y,plotno); if (button==BASELINE) { for (i=0; i<nfiles; i++){ find_baseline(ngulp,time_series[i],10.0/tsamp,5.0); } button = PLOT; zoneplot=false; plotno = -1; } if (button==FWRITE) { // reread first header and close it. Sets globals. fclose(inputfile[0]); inputfile[0]=open_file(argv[1],"r"); headersize[0]=read_header(inputfile[0]); output = open_file("giant.tim","w"); nobits=32; nbands=1; dedisperse_header(); fprintf(stderr,"Opened file, writing data\n"); fwrite(time_series[0],sizeof(float),ngulp,output); fclose(output); button = -1; zoneplot=false; plotno =-1; } if (button==BSCRUNCH) { for (i=0; i<nfiles; i++){ bscrunch(ngulp,time_series[i]); } tsamp*=2; scrunch*=2; ngulp/=2; nplot/=2; button = PLOT; zoneplot=false; Gsearched=false; plotno = -1; } if (button==FFT) { for (i=0; i<nfiles; i++){ ngulp = ngulp_original; find_fft(&ngulp,time_series[i]); // Zap DC spike time_series[i][0]=0.0; time_series[i][1]=0.0; } spectra = 1; nplot = ngulp; button = PLOT; Gsearched=false; plotno = -1; } if (button==POWER) { for (i=0; i<nfiles; i++){ find_formspec(ngulp,time_series[i]); } ngulp/=2; powerspectra = 1; nplot = ngulp; button = PLOT; plotno = -1; } if (button==SMHRM) { nfiles = 6; for (i=1; i<nfiles; i++){ time_series[i]=(float *) malloc((ngulp+2)*sizeof(float)); if (time_series[i]==NULL){ fprintf(stderr,"Error allocating memory\n"); exit(-1); } } for (i=1;i<nfiles;i++) memcpy(time_series[i],time_series[0], (ngulp+2)*sizeof(float)); d->nplotregion=1; float deltay = 0.9/(float)nfiles; for (i=0; i<nfiles; i++) d->addplotregion(0.2,0.99,0.95-deltay*(float)(i+1), 0.95-deltay*(float)i); cpgeras(); d->draw(); float * workspace = new float[ngulp]; // Set up space for data, now actually sumhrm int one=1; newoldsumhrm_(&time_series[0][1],workspace,&ngulp,&one, // newoldsumhrm_(&time_series[0][0],workspace,&ngulp,&one, time_series[1],time_series[2],time_series[3], time_series[4],time_series[5]); /* newnewsumhrm_(time_series[0],&ngulp,&one, time_series[1],time_series[2],time_series[3], time_series[4],time_series[5]);*/ for (int iff=2;iff<6;iff++){ for (int i=0;i<ngulp;i++){ time_series[iff][i]/=sqrt(pow(2.0,(float)(iff-1))); } } delete [] workspace; button = PLOT; plotno = -1; } if (button==NORMALISE) { for (i=0; i<nfiles; i++){ normalise(ngulp,time_series[i],5.0); } button = PLOT; Gsearched=false; plotno = -1; } if (button==HISTOGRAM) { float pdfs[nfiles][MAXSIGMA]; // create pdfs for each beam for (int i=0;i<nfiles;i++) formpdf(pdfs[i],MAXSIGMA,ngulp,time_series[i]); for (int i=0;i<nfiles;i++){ for (int j=0;j<MAXSIGMA; j++){ fprintf(stderr, "pdfs[%d][%2d]=%8.0f %f \%\n", i, j+1, pdfs[i][j], 100*pdfs[i][j]/ngulp); } } button = PLOT; plotno = -1; } if (button==HALVEPLOT) { nplot/=2; button = PLOT; zoneplot=true; Gsearched=false; plotno = -1; } if (button==GLOBALRESET) { plotno = -1; nstart = 0; scrunch=1; tsamp = tsamp_orig; nplot=ngulp_original; ngulp=ngulp_original; button=PLOT; // Skip to end of skipped data for (i=0; i<nfiles; i++){ fseek(inputfile[i],-(nfileptr-nskipstart)*nbits/8,SEEK_CUR); Giant[i].clear(); } nfileptr=nskipstart; zoneplot=false; Gsearched=false; doperiod=-1; button=NEXT; } if (button==SUBTRACTMEAN && nfiles>1) { plotno = -1; nstart = 0; nplot=ngulp_original; ngulp=ngulp_original; button=PLOT; // Skip to end of skipped data for (int jj=0;jj<ngulp;jj++){ float sum; sum=0.0; for (i=1;i<nfiles;i++){ sum+=time_series[i][jj]; } time_series[0][jj]-=sum/(float(nfiles-1)); } Gsearched=false; } if (button==ZAPCOMMON && nfiles>1) { plotno = -1; nstart = 0; nplot=ngulp_original; ngulp=ngulp_original; button=PLOT; float pdfs[nfiles][MAXSIGMA]; // create pdfs for each beam for (int i=0;i<nfiles;i++) formpdf(pdfs[i],MAXSIGMA,ngulp,time_series[i]); // for each point in each beam, mask if improbable float thresh = 3.0; int nbeammax = 5; zap_improbables(pdfs,time_series,nfiles,ngulp,MAXSIGMA,thresh,nbeammax); // Skip to end of skipped data //for (int jj=0;jj<ngulp;jj++){ // float sum; // sum=0.0; // for (i=1;i<nfiles;i++){ // sum+=time_series[i][jj]; // } // time_series[0][jj]-=sum/(float(nfiles-1)); //} //Gsearched=false; } if (button==NEXT) { ngulp=ngulp_original; nstart=0; nplot=ngulp_original; // Read the data int NActuallyRead; // unsigned char *buffer; char *buffer; buffer = new char[ngulp*nbits/8]; //buffer = new char[ngulp*nbits/8]; for (i=0; i<nfiles; i++) { // NActuallyRead = fread(time_series[i],sizeof(float),ngulp,inputfile[i]); NActuallyRead = fread(buffer,nbits/8,ngulp,inputfile[i]); if (nbits==32){ memcpy(time_series[i],buffer,sizeof(float)*ngulp); } else { for (int j=0;j<NActuallyRead;j++){ if (ssigned) time_series[i][j]=(float)buffer[j]; if (!ssigned) time_series[i][j]=(float)((unsigned char)buffer[j]); } } puti(ngulp); if (NActuallyRead!=ngulp){ fprintf(stderr,"Could not read %d floats from file\n",ngulp); ngulp = NActuallyRead; } if(nfiles==1){ // Add fake pulsar here.... // for (int ii=0;ii<ngulp;ii++) time_series[i][ii]+= 10.0*pow(sin(float(ii*2.0*M_PI/60.0)),250.0); } //normalise(ngulp,time_series[i]); } nfileptr+=ngulp; button = PLOT; plotno= -1; zoneplot=true; } if (button==RESET) { button = plotno = -1; nstart=0; nplot=ngulp; button=PLOT; zoneplot=true; Gsearched=false; if (ans=='p'){ doperiod=-1; } } if (plotno>0){ /* if (ans=='p'){ // hit p on a plot to type in a period d->plotregions[plotno].reset(); //plot the thing; fprintf(stderr,"Please enter a period in seconds: "); cin>>trialperiod; xperiod = x; doperiod=plotno; button=PLOT; }*/ if (ans=='p'){ // hit p on a plot to type in a period d->plotregions[plotno].reset(); //plot the thing; fprintf(stderr,"Please enter a period in seconds: "); cin>>trialperiod; xperiod = (double)x; doperiod=plotno; button=PLOT; } if (ans=='m'){ // subtract 0.0000005 seconds from period d->plotregions[plotno].reset(); trialperiod-=0.0000005; fprintf(stderr,"Trial period is now %lf\n",trialperiod); doperiod=plotno; button=PLOT; } if (ans=='/'){ // add 0.0000005 seconds to period d->plotregions[plotno].reset(); trialperiod+=0.0000005; fprintf(stderr,"Trial period is now %lf\n",trialperiod); doperiod=plotno; button=PLOT; } if (ans==','){ // subtract 0.000005 seconds from period d->plotregions[plotno].reset(); trialperiod-=0.000005; fprintf(stderr,"Trial period is now %lf\n",trialperiod); doperiod=plotno; button=PLOT; } if (ans=='.'){ // add 0.000005 seconds to period d->plotregions[plotno].reset(); trialperiod+=0.000005; fprintf(stderr,"Trial period is now %lf\n",trialperiod); doperiod=plotno; button=PLOT; } if (ans=='<'){ // subtract 0.001 seconds from period d->plotregions[plotno].reset(); trialperiod-=0.001; fprintf(stderr,"Trial period is now %lf\n",trialperiod); doperiod=plotno; button=PLOT; } if (ans=='>'){ // add 0.001 seconds to period d->plotregions[plotno].reset(); trialperiod+=0.001; fprintf(stderr,"Trial period is now %lf\n",trialperiod); doperiod=plotno; button=PLOT; } if (ans=='X'){ // right click two points on a plot to calculate and plot a period d->plotregions[plotno].reset(); cpgsci(3); cpgmove(x,-1000); cpgdraw(x,1000); if (ngates==0){ xgate=x; ngates++; } else { min_means_min(&x,&xgate); printf("Period from %f to %f is %f\n",x,xgate,xgate-x); doperiod=plotno; xperiod = (double)x; trialperiod=(double)(xgate-x); ngates=0; button=PLOT; } } if (ans=='D'){ markers[nmarkers]=(int)(x/NPIXELS)*nplot+nstart+nfileptr-ngulp; nmarkers++; zoneplot=true; } if (ans=='A'){ d->plotregions[plotno].reset(); cpgsci(2); cpgmove(x,-1000); cpgdraw(x,1000); if (ngates==0){ xgate=x; ngates++; } else { min_means_min(&x,&xgate); // printf("x %f xgate %f tstart %f\n",x,xgate,tstart); nstart=(int)((x-tstart)/delta)+nstart; nplot=(int)((xgate-x)/delta); //if (nplot<NPIXELS) nplot=NPIXELS; ngates=0; button=PLOT; zoneplot=true; // printf("nplot %d nstart %d\n",nplot,nstart); } } if (ans=='z'){ if (NPIXELS>nplot) { nstart+=(int)x; }else nstart=(int)(x/(float)NPIXELS*nplot)+nstart; printf("nstart %d\n",nstart); nplot/=4; printf("nplot %d\n",nplot); nstart-=nplot/2; printf("nstart %d\n",nstart); //if (nplot<NPIXELS){nplot=NPIXELS;} button=PLOT; zoneplot=true; } }
/** * baseline method using exponential smoothing, smoothing factor set at 0.02 default. * ndat is the size of the timeseries * dat is the timeseries * overloaded method takes threshold which will cut out spikes above specified * threshold in sigma's. **/ void find_baseline( int ndat, float * dat,float smooth_nsamp) { find_baseline(ndat,dat,smooth_nsamp,std::numeric_limits<float>::max()); }