void setup (Integration* subint, unsigned ichan) { Pulsar::MoreProfiles* more = NULL; unsigned npol = subint->get_npol(); if (auxiliary) { more = subint->get_Profile (0,ichan)->get<Pulsar::MoreProfiles>(); npol = more->get_size(); } try { vector<unsigned> pols = ::indeces (npol, indeces); profiles.resize (pols.size()); for (unsigned ipol=0; ipol < pols.size(); ipol++) { if (more) profiles[ipol] = more->get_Profile( pols[ipol] ); else profiles[ipol] = subint->get_Profile ( pols[ipol],ichan); } } catch (...) { // if parsing indeces fails, then assume that letter codes are used Reference::To<const PolnProfile> profile = new_Stokes (subint, ichan); profiles.resize (indeces.length()); for (unsigned ipol=0; ipol < indeces.length(); ipol++) profiles[ipol] = new_Profile (profile, indeces[ipol]); } }
int main(int argc, char *argv[]) { /* Process any args */ int opt=0; int verb=0; string expression; while ((opt=getopt(argc,argv,"hve:E:"))!=-1) { switch (opt) { case 'v': verb++; Archive::set_verbosity(verb); break; case 'e': output_ext.assign(optarg); break; case 'E': expression = optarg; break; case 'h': default: usage(); usage_interactive(); exit(0); break; } } if (optind==argc) { usage(); cerr << PROG ": No filename given" << endl; exit(-1); } /* Load file */ string filename = argv[optind]; Reference::To<Archive> orig_arch = Archive::load(filename); Reference::To<Archive> arch = orig_arch->clone(); arch->dedisperse(); arch->remove_baseline(); double bw = arch->get_bandwidth(); string output_filename = replace_extension(filename, output_ext); string psrsh_filename = replace_extension(filename,"psh"); // Create profile plots Reference::To<Archive> tot_arch=NULL,pf_arch=NULL,pt_arch=NULL; ProfilePlot *totplot=NULL; PhaseVsFrequency *pfplot=NULL; PhaseVsTime *ptplot=NULL; int totplot_id; totplot = new ProfilePlot; pfplot = new PhaseVsFrequency; ptplot= new PhaseVsTime; // Create window and subdivide totplot_id = cpgopen("/xs"); cpgpap(0.0,1.5); cpgsubp(1,3); // Create Dynamic Spectrum Plot DynamicBaselineSpectrumPlot *dsplot = new DynamicBaselineSpectrumPlot; if (!expression.empty()) dsplot->configure("exp="+expression); else dsplot->configure("var=1"); dsplot->set_reuse_baseline(); int dsplot_id = cpgopen("/xs"); if (dsplot_id<=0) { cerr << PROG ": PGPLOT xwindows device open failed, exiting." << endl; exit(1); } cpgask(0); /* Input loop */ char ch='\0'; enum cursor_type curs=both_cursor; float x0=0.0, y0=0.0, x1, y1; int click=0, mode=0; int pol=0,izap=0; bool redraw=true, var=true, log=false, resum=true,remove_baseline=false,method=false; struct zap_range zap; vector<struct zap_range> zap_list; do { /* Redraw the plot if necessary */ if (redraw) { char conf[256]; sprintf(conf, "above:c=$file\\n%s %s, %s scale, %s baseline, pol %d.", method ? "total" : "off-pulse" , var ? "variance" : "mean", log ? "log" : "linear", remove_baseline ? "variable" : "constant", pol); dsplot->configure(conf); cpgslct(dsplot_id); //cpgeras(); cpgpage(); dsplot->plot(arch); if (resum) { // Total tot_arch = arch->total(); cpgslct(totplot_id); cpgpanl(1,1); cpgeras(); totplot->plot(tot_arch); // pulse vs frequency pf_arch = arch->clone(); pf_arch->pscrunch(); pt_arch = pf_arch->clone(); pf_arch->tscrunch(); // pf_arch->remove_baseline(); cpgpanl(1,2); cpgeras(); pfplot->plot(pf_arch); // pulse vs time pt_arch->fscrunch(); // pt_arch->remove_baseline(); cpgpanl(1,3); cpgeras(); ptplot->plot(pt_arch); cpgslct(dsplot_id); resum = false; } redraw = false; cpgslct(dsplot_id); } // Mark zapped profiles for (unsigned i=izap; i<zap_list.size(); i++) { float df=zap_list[i].freq0-zap_list[i].freq1; float dt=zap_list[i].sub0-zap_list[i].sub1; cpgsfs(2); cpgsci(2); if (fabs(df)<0.001 && fabs(dt)<0.001) cpgpt1(zap_list[i].sub0+0.5,zap_list[i].freq0,2); else cpgrect(zap_list[i].sub0+0.5,zap_list[i].sub1+0.5,zap_list[i].freq0,zap_list[i].freq1); cpgsci(1); } /* On click 0 get start of a range */ if (click==0) { if (curs==freq_cursor) mode=5; else if (curs==time_cursor) mode=6; else if (curs==both_cursor) mode=7; cpgband(mode,0,0,0,&x0,&y0,&ch); } /* On click 1 get the end of a range */ else if (click==1) { if (curs==freq_cursor) mode=3; else if (curs==time_cursor) mode=4; else if (curs==both_cursor) mode=2; cpgband(mode,0,x0,y0,&x1,&y1,&ch); } #if 0 /* Debug */ printf("x0=%.3f y0=%.3f x1=%.3f y1=%.3f ch='%c' click=%d\n", x0, y0, x1, y1, ch, click); #endif /* Left mouse click = zoom*/ if (ch=='A') { if (click==0) { click=1; continue; } if (click==1) { /* Do zoom here */ char conf[256]; float tmp,t0,t1; if (curs==freq_cursor || curs==both_cursor) { if (bw>0 && y0>y1) { tmp=y0; y0=y1; y1=tmp; } if (bw<0 && y0<y1) { tmp=y0; y0=y1; y1=tmp; } sprintf(conf,"y:win=(%.3f,%.3f)",y0,y1); dsplot->configure(string(conf)); pfplot->configure(string(conf)); } if (curs==time_cursor || curs==both_cursor) { if (x0>x1) { tmp=x0; x0=x1; x1=tmp; } sprintf(conf,"srange=(%d,%d)",(int)x0,(int)x1); dsplot->configure(string(conf)); t0=sub2time(pt_arch,(int) x0); t1=sub2time(pt_arch,(int) x1); sprintf(conf,"y:win=(%.3f,%.3f)",t0,t1); ptplot->configure(string(conf)); } redraw = true; click = 0; continue; } } /* Middle mouse click = redraw diagnostics */ if (ch=='D' || ch==CMD_UPDATE) { redraw = true; resum = true; izap=zap_list.size(); continue; } /* Right mouse click = zap */ if (ch=='X') { /* Zap a single row or pixel */ if (click==0) { zap.freq0 = zap.freq1 = y0; zap.sub0 = zap.sub1 = (int)x0; } /* Zap a range */ if (click==1) { zap.freq0 = y0; zap.freq1 = y1; zap.sub0 = (int)x0; zap.sub1 = (int)x1; } /* Apply it */ zap.type = curs; apply_zap(arch, &zap); zap_list.push_back(zap); redraw = false; resum = false; click=0; continue; } /* Undo last zap */ if (ch==CMD_UNDO) { if (!zap_list.empty()) { zap = zap_list.back(); apply_zap_range(arch, &zap, true, orig_arch); zap_list.pop_back(); /* Reapply whole list in case of overlapping zaps */ for (unsigned i=0; i<zap_list.size(); i++) { zap = zap_list[i]; apply_zap_range(arch, &zap); } redraw = true; resum = false; } click = 0; continue; } /* Show help */ if (ch==CMD_HELP) { usage_interactive(); click = 0; continue; } /* Esc = cancel */ if (ch==27) { click=0; continue; } /* Switch to freq mode */ if (ch==CMD_FREQMODE) { curs = freq_cursor; click = 0; continue; } /* Switch to time mode */ if (ch==CMD_TIMEMODE) { curs = time_cursor; click = 0; continue; } /* Switch to time/freq mode */ if (ch==CMD_BOTHMODE) { curs = both_cursor; click = 0; continue; } /* Toggle variance plot */ if (ch==CMD_VAR) { var = !var; redraw = true; if (var) dsplot->configure("var=1"); else dsplot->configure("var=0"); click = 0; continue; } // Toggle dynamic spectrum if (ch==CMD_METHOD) { method = !method; redraw = true; if (method) dsplot->configure("method=1"); else dsplot->configure("method=0"); click = 0; continue; } /* toggle log scale */ if (ch==CMD_LOG) { log = !log; redraw = true; if (log) dsplot->configure("cmap:log=1"); else dsplot->configure("cmap:log=0"); click = 0; continue; } /* Flip through polarizations */ if (ch==CMD_POL) { pol = (pol + 1) % arch->get_npol(); char conf[256]; sprintf(conf, "pol=%d", pol); dsplot->configure(conf); redraw = true; click = 0; continue; } /* Unset zoom */ if (ch==CMD_UNZOOM) { dsplot->configure("srange=(-1,-1)"); dsplot->configure("y:win=(0,0)"); pfplot->configure("y:win=(0,0)"); ptplot->configure("y:win=(0,0)"); redraw = true; click = 0; izap=zap_list.size(); continue; } /* Save file */ if (ch==CMD_SAVE || ch==CMD_SAVE_QUIT) { /* Apply zaps to original file */ for (unsigned i=0; i<zap_list.size(); i++) { zap = zap_list[i]; apply_zap_range(orig_arch, &zap); } cout << "Unloading '" << output_filename << "'..." << endl; orig_arch->unload(output_filename); click = 0; if (ch==CMD_SAVE_QUIT) { ch=CMD_QUIT; } continue; } /* Print paz command */ if (ch==CMD_PRINT) { char *cstr; cstr=new char [output_ext.size()+1]; strcpy(cstr,output_ext.c_str()); if (zap_list.size()>0) printf("paz -e %s",cstr); /* Full time/freq zaps */ for (unsigned i=0; i<zap_list.size(); i++) { if (zap_list[i].type == freq_cursor) { int chan0 = freq2chan(arch, zap_list[i].freq0); int chan1 = freq2chan(arch, zap_list[i].freq1); if (chan1<chan0) { int tmp=chan0; chan0=chan1; chan1=tmp; } if (chan0==chan1) printf(" -z %d", chan0); else printf(" -Z \"%d %d\"", chan0, chan1); } else if (zap_list[i].type == time_cursor) { if (zap_list[i].sub0==zap_list[i].sub1) printf(" -w %d", zap_list[i].sub0); else printf(" -W \"%d %d\"", zap_list[i].sub0, zap_list[i].sub1); } } if (zap_list.size()>0) printf(" %s\n", filename.c_str()); /* Small ranges */ for (unsigned i=0; i<zap_list.size(); i++) { if (zap_list[i].type == both_cursor) { printf("paz -m -I"); int chan0 = freq2chan(arch, zap_list[i].freq0); int chan1 = freq2chan(arch, zap_list[i].freq1); if (chan1<chan0) { int tmp=chan0; chan0=chan1; chan1=tmp; } if (chan0==chan1) printf(" -z %d", chan0); else printf(" -Z \"%d %d\"", chan0, chan1); if (zap_list[i].sub0==zap_list[i].sub1) printf(" -w %d", zap_list[i].sub0); else printf(" -W \"%d %d\"", zap_list[i].sub0, zap_list[i].sub1); cstr=new char [output_filename.size()+1]; strcpy(cstr,output_filename.c_str()); printf(" %s\n", (char *) cstr); } } } // Toggle variable baseline if (ch==CMD_BASELINE) { // Set baselining strategy if (remove_baseline) { fprintf(stderr, "Unsetting remove_baseline_strategy.\n"); Pulsar::Archive::remove_baseline_strategy.set (new Pulsar::RemoveBaseline::Total, &Pulsar::RemoveBaseline::Total::transform); remove_baseline=false; arch=orig_arch->clone(); arch->dedisperse(); arch->remove_baseline(); for (unsigned i=0; i<zap_list.size(); i++) { zap = zap_list[i]; apply_zap_range(arch, &zap); } } else { fprintf(stderr, "Set remove_baseline_strategy.\n"); Pulsar::Archive::remove_baseline_strategy.set (new Pulsar::RemoveVariableBaseline, &Pulsar::RemoveVariableBaseline::transform); remove_baseline=true; arch=orig_arch->clone(); arch->dedisperse(); arch->remove_baseline(); for (unsigned i=0; i<zap_list.size(); i++) { zap = zap_list[i]; apply_zap_range(arch, &zap); } } redraw=true; resum=true; } // Generate PSRSH script if (ch==CMD_PSRSH) { FILE *file; file=fopen(psrsh_filename.c_str(),"w"); fprintf(file,"#!/usr/bin/env psrsh\n\n# Run with psrsh -e <ext> <script>.psh <archive>.ar\n\n"); // Full sub/chan zap for (unsigned i=0; i<zap_list.size(); i++) { if (zap_list[i].type == freq_cursor) { int chan0 = freq2chan(arch, zap_list[i].freq0); int chan1 = freq2chan(arch, zap_list[i].freq1); if (chan1<chan0) { int tmp=chan0; chan0=chan1; chan1=tmp; } if (chan0==chan1) fprintf(file,"zap chan %d\n",chan0); else fprintf(file,"zap chan %d-%d\n", chan0, chan1); } else if (zap_list[i].type == time_cursor) { if (zap_list[i].sub0==zap_list[i].sub1) fprintf(file,"zap subint %d\n", zap_list[i].sub0); else fprintf(file,"zap subint %d-%d\n", zap_list[i].sub0, zap_list[i].sub1); } } // Subint/channel intersections for (unsigned i=0; i<zap_list.size(); i++) { if (zap_list[i].type == both_cursor) { int chan0 = freq2chan(arch, zap_list[i].freq0); int chan1 = freq2chan(arch, zap_list[i].freq1); int sub0 = zap_list[i].sub0; int sub1 = zap_list[i].sub1; if (chan1<chan0) { int tmp=chan0; chan0=chan1; chan1=tmp; } if (chan0==chan1 && sub0==sub1) { fprintf(file,"zap such %d,%d\n",sub0,chan0); } else { fprintf(file,"zap such"); for (int sub=sub0;sub<=sub1;sub++) { for (int chan=chan0;chan<=chan1;chan++) { fprintf(file," %d,%d",sub,chan); } } fprintf(file,"\n"); } } } fclose(file); printf("PSRSH script written\n"); } } while (ch!=CMD_QUIT); }
int main (int argc, char *argv[]) try { bool verbose = false; char* metafile = 0; string ulpath; bool save = false; string ext; bool tscr = false; int tscr_fac = 0; bool fscr = false; int fscr_fac = 0; bool bscr = false; int bscr_fac = 0; bool newdm = false; double dm = 0.0; bool scattered_power_correction = false; bool defaraday = false; bool newrm = false; double rm = 0.0; bool reset_weights = false; float new_weight = 1.0; float smear_dc = 0.0; bool rotate = false; double rphase = 0.0; bool dedisperse = false; bool dededisperse = false; bool pscr = false; bool invint = false; bool stokesify = false; bool unstokesify = false; bool flipsb = false; bool flip_freq = false; double flip_freq_mhz = 0.0; Pulsar::Parameters* new_eph = 0; string command = "pam"; char* archive_class = 0; int new_nchn = 0; int new_nsub = 0; int new_nbin = 0; float tsub = 0.0; bool circ = false; bool lin = false; unsigned ronsub = 0; bool cbppo = false; bool cbpao = false; bool cblpo = false; bool cblao = false; int subint_extract_start = -1; int subint_extract_end = -1; bool new_cfreq = false; double new_fr = 0.0; Signal::Source new_type = Signal::Unknown; string instrument; bool reverse_freqs = false; string site; string name; float mult = -1.0; double new_folding_period = -1.0; bool update_dm_from_eph = false; double aux_rm = 0.0; Reference::To<Pulsar::IntegrationOrder> myio; Reference::To<Pulsar::Receiver> install_receiver; Pulsar::ReflectStokes reflections; int c = 0; const int TYPE = 1208; const int INST = 1209; const int REVERSE_FREQS = 1210; const int SITE = 1211; const int NAME = 1212; const int DD = 1213; const int RR = 1214; const int SPC = 1215; const int RM = 1216; const int MULT = 1218; const int PERIOD=1219; const int SS = 1220; const int FLIP = 1221; const int UPDATE_DM = 1222; const int AUX_RM = 1223; while (1) { int options_index = 0; static struct option long_options[] = { {"setnchn", 1, 0, 200}, {"setnsub", 1, 0, 201}, {"setnbin", 1, 0, 202}, {"binphsperi", 1, 0, 203}, {"binphsasc", 1, 0, 204}, {"binlngperi", 1, 0, 205}, {"binlngasc", 1, 0, 206}, {"receiver", 1, 0, 207}, {"settsub", 1, 0, 208}, {"type", 1, 0, TYPE}, {"inst", 1, 0, INST}, {"reverse_freqs",no_argument,0,REVERSE_FREQS}, {"flip", 1 ,0, FLIP}, {"site", 1, 0, SITE}, {"name", 1, 0, NAME}, {"DD", no_argument, 0,DD}, {"RR", no_argument, 0,RR}, {"RM", required_argument,0,RM}, {"spc", no_argument, 0,SPC}, {"mult", required_argument,0,MULT}, {"period", required_argument,0,PERIOD}, {"SS", no_argument, 0,SS}, {"update_dm", no_argument, 0,UPDATE_DM}, {"aux_rm", required_argument,0,AUX_RM}, {0, 0, 0, 0} }; c = getopt_long(argc, argv, "hqvViM:mn:a:e:E:TFpIt:f:b:d:o:s:r:u:w:DSBLCx:R:", long_options, &options_index); if (c == -1) break; switch (c) { case 'h': usage(); return (0); break; case 'q': Pulsar::Archive::set_verbosity(0); break; case 'v': verbose = true; Pulsar::Archive::set_verbosity(2); break; case 'V': verbose = true; Pulsar::Archive::set_verbosity(3); break; case 'i': cout << "$Id: pam.C,v 1.101 2010/10/05 23:59:50 jonathan_khoo Exp $" << endl; return 0; case 'm': save = true; break; case 'M': metafile = optarg; break; case 'L': lin = true; break; case 'C': circ = true; break; case 'a': archive_class = optarg; break; case 'e': ext = optarg; if( !ext.empty() ) save = true; break; case 'E': try { new_eph = factory<Pulsar::Parameters> (optarg); } catch (Error& error) { cerr << "Could not load new ephemeris from " << optarg << endl; return -1; } command += " -E"; break; case 'T': tscr = true; command += " -T"; break; case 'F': fscr = true; command += " -F"; break; case 'p': pscr = true; command += " -p"; break; case 'I': invint = true; pscr = false; command += " -I"; break; case 'f': fscr = true; if (sscanf(optarg, "%d", &fscr_fac) != 1) { cout << "That is not a valid fscrunch factor" << endl; return -1; } command += " -f "; command += optarg; break; case 'n': reflections.add_reflection( optarg[0] ); command += " -n "; command += optarg; break; case 'o': new_cfreq = true; if (sscanf(optarg, "%lf", &new_fr) != 1) { cout << "That is not a valid centre frequency" << endl; return -1; } command += " -o "; command += optarg; break; case 't': tscr = true; if (sscanf(optarg, "%d", &tscr_fac) != 1) { cout << "That is not a valid tscrunch factor" << endl; return -1; } command += " -t "; command += optarg; break; case 'b': bscr = true; if (sscanf(optarg, "%d", &bscr_fac) != 1) { cout << "That is not a valid bscrunch factor" << endl; return -1; } if (bscr_fac <= 0) { cout << "That is not a valid bscrunch factor" << endl; return -1; } command += " -b "; command += optarg; break; case 'd': newdm = true; if (sscanf(optarg, "%lf", &dm) != 1) { cout << "That is not a valid dispersion measure" << endl; return -1; } command += " -d "; command += optarg; break; case 'D': dedisperse = true; command += " -D "; break; case 'R': if (sscanf(optarg, "%lf", &rm) != 1) { cout << "That is not a valid rotation measure" << endl; return -1; } newrm = true; defaraday = true; command += " -R "; command += optarg; break; case 's': if (sscanf(optarg, "%f", &smear_dc) != 1) { cout << "That is not a valid smearing duty cycle" << endl; return -1; } command += " -s "; command += optarg; break; case 'r': rotate = true; if (sscanf(optarg, "%lf", &rphase) != 1) { cout << "That is not a valid rotation phase" << endl; return -1; } if (rphase <= -1.0 || rphase >= 1.0) { cout << "That is not a valid rotation phase" << endl; return -1; } command += " -r "; command += optarg; break; case 'u': ulpath = optarg; if( !ulpath.empty() ) { save = true; if (ulpath.substr(ulpath.length()-1,1) != "/") ulpath += "/"; } break; case 'w': reset_weights = true; if (sscanf(optarg, "%f", &new_weight) != 1) { cout << "That is not a valid weight" << endl; return -1; } command += " -w "; command += optarg; break; case 'S': stokesify = true; break; case SS: unstokesify = true; break; case 'B': flipsb = true; break; case 'x' : if (sscanf(optarg, "%d %d", &subint_extract_start, &subint_extract_end) !=2 ) { cout << "That is not a valid subint range" << endl; return -1; } subint_extract_end++; break; case 200: fscr = true; if (sscanf(optarg, "%d", &new_nchn) != 1) { cout << "That is not a valid number of channels" << endl; return -1; } if (new_nchn <= 0) { cout << "That is not a valid number of channels" << endl; return -1; } command += " --setnchn "; command += optarg; break; case 201: tscr = true; if (sscanf(optarg, "%d", &new_nsub) != 1) { cout << "That is not a valid number of subints" << endl; return -1; } if (new_nsub <= 0) { cout << "That is not a valid number of subints" << endl; return -1; } command += " --setnsub "; command += optarg; break; case 202: bscr = true; if (sscanf(optarg, "%d", &new_nbin) != 1) { cout << "That is not a valid number of bins" << endl; return -1; } if (new_nbin <= 0) { cout << "That is not a valid number of bins" << endl; return -1; } command += " --setnbin "; command += optarg; break; case 203: { if (cbpao || cblpo || cblao) { cerr << "You can only specify one re-ordering scheme!" << endl; return -1; } if (sscanf(optarg, "%ud", &ronsub) != 1) { cerr << "Invalid nsub given" << endl; return -1; } cbppo = true; break; } case 204: { if (cbppo || cblpo || cblao) { cerr << "You can only specify one re-ordering scheme!" << endl; return -1; } if (sscanf(optarg, "%ud", &ronsub) != 1) { cerr << "Invalid nsub given" << endl; return -1; } cbpao = true; break; } case 205: { if (cblao || cbppo || cbpao) { cerr << "You can only specify one re-ordering scheme!" << endl; return -1; } if (sscanf(optarg, "%ud", &ronsub) != 1) { cerr << "Invalid nsub given" << endl; return -1; } cblpo = true; break; } case 206: { if (cblpo || cbppo || cbpao) { cerr << "You can only specify one re-ordering scheme!" << endl; return -1; } if (sscanf(optarg, "%ud", &ronsub) != 1) { cerr << "Invalid nsub given" << endl; return -1; } cblao = true; break; } case 207: try { install_receiver = Pulsar::Receiver::load (optarg); break; } catch (Error& error) { cerr << "pam: Error loading Receiver from " << optarg << endl << error.get_message() << endl; return -1; } case 208: { if (sscanf(optarg, "%f", &tsub) != 1) { cerr << "Invalid tsub given" << endl; return -1; } tscr = true; break; } case TYPE: { string s = optarg; if(s=="Pulsar") new_type = Signal::Pulsar; else if(s=="PolnCal") new_type = Signal::PolnCal; else if(s=="FluxCalOn") new_type = Signal::FluxCalOn; else if(s=="FluxCalOff") new_type = Signal::FluxCalOff; else if(s=="Calibrator") new_type = Signal::Calibrator; else{ fprintf(stderr,"Unrecognised argument to --type: '%s'\n",optarg); exit(-1); } command += " --type " + s; } break; case INST: instrument = optarg; break; case REVERSE_FREQS: reverse_freqs = true; break; case SITE: site = optarg; break; case NAME: name = optarg; break; case DD: dededisperse = true; break; case RM: aux_rm = fromstring<double>(optarg); newrm = true; command += " --RM "; command += optarg; break; case SPC: scattered_power_correction = true; break; case MULT: mult = atof(optarg); break; case PERIOD: new_folding_period = fromstring<double>(optarg); break; case FLIP: flip_freq = true; flip_freq_mhz = atof(optarg); break; case UPDATE_DM: update_dm_from_eph = true; break; case AUX_RM: aux_rm = fromstring<double>(optarg); command += " --aux_rm "; command += optarg; break; default: cout << "Unrecognised option" << endl; } } if (verbose) cerr << "pam: parsing filenames" << endl; vector <string> filenames; if (metafile) stringfload (&filenames, metafile); else for (int ai=optind; ai<argc; ai++) dirglob (&filenames, argv[ai]); if (filenames.empty()) { cerr << "pam: no filenames were specified" << endl; exit(-1); } Reference::To<Pulsar::Archive> arch; if (!save) { cout << "Changes will not be saved. Use -m, -u or -e to write results to disk" << endl; } if (stokesify && unstokesify) { cerr << "pam: Both -S and --SS options were given. Poln state will not be changed!" << endl; stokesify = false; unstokesify = false; } int flip_option_count=0; if (flipsb) flip_option_count++; if (flip_freq) flip_option_count++; if (reverse_freqs) flip_option_count++; if (flip_option_count > 1) { cerr << "pam: More than one band-flip option was given, exiting." << endl; exit(-1); } for (unsigned i = 0; i < filenames.size(); i++) try { if (verbose) cerr << "Loading " << filenames[i] << endl; arch = Pulsar::Archive::load(filenames[i]); if( mult > 0.0 ){ for( unsigned isub=0; isub<arch->get_nsubint();isub++) for( unsigned ichan=0; ichan<arch->get_nchan();ichan++) for( unsigned ipol=0; ipol<arch->get_npol();ipol++) arch->get_Profile(isub,ipol,ichan)->scale( mult ); } if( new_folding_period > 0.0 ){ Pulsar::counter_drift( arch, new_folding_period, 0.0); for( unsigned isub=0; isub<arch->get_nsubint();isub++) arch->get_Integration(isub)->set_folding_period( new_folding_period ); } if (install_receiver) { if (verbose) cerr << "pam: Installing receiver: " << install_receiver->get_name() << " in archive" << endl; arch->add_extension (install_receiver); } if (lin || circ) { Pulsar::Receiver* receiver = arch->get<Pulsar::Receiver>(); if (!receiver) cerr << "No Receiver Extension in " << filenames[i] << endl; else { if (lin) { receiver->set_basis (Signal::Linear); cout << "Feed basis set to Linear" << endl; } if (circ) { receiver->set_basis (Signal::Circular); cout << "Feed basis set to Circular" << endl; } } } reflections.transform( arch ); if (new_cfreq) { double nc = arch->get_nchan(); double bw = arch->get_bandwidth(); double cw = bw / nc; double fr = new_fr - (bw / 2.0) + (cw / 2.0); for (unsigned i = 0; i < arch->get_nsubint(); i++) { for (unsigned j = 0; j < arch->get_nchan(); j++) { arch->get_Integration(i)->set_centre_frequency(j,(fr + (j*cw))); } } arch->set_centre_frequency(new_fr); } if( new_type != Signal::Unknown ) arch->set_type( new_type ); if( instrument != string() ){ Pulsar::Backend* b = arch->get<Pulsar::Backend>(); if( !b ) fprintf(stderr,"Could not change instrument name- archive does not have Backend extension\n"); else b->set_name(instrument); } if( site != string() ) arch->set_telescope( site ); if( name != string() ) arch->set_source( name ); if (new_eph) try { arch->set_ephemeris(new_eph); if (update_dm_from_eph) { update_dm(arch); } } catch (Error& error) { cerr << "Error while installing new ephemeris: " << error.get_message() << endl; continue; } if (flipsb) { for (unsigned i = 0; i < arch->get_nsubint(); i++) { vector<double> labels; labels.resize(arch->get_nchan()); for (unsigned j = 0; j < arch->get_nchan(); j++) { labels[j] = arch->get_Integration(i)->get_centre_frequency(j); } for (unsigned j = 0; j < arch->get_nchan(); j++) { double new_frequency = labels[labels.size()-1-j]; arch->get_Integration(i)->set_centre_frequency(j,new_frequency); } } arch->set_bandwidth(-1.0 * arch->get_bandwidth()); } if (flip_freq) { for (unsigned isub = 0; isub < arch->get_nsubint(); isub++) { Reference::To<Pulsar::Integration> subint = arch->get_Integration(isub); for (unsigned ichan = 0; ichan < arch->get_nchan(); ichan++) { double new_freq = flip_freq_mhz - (subint->get_centre_frequency(ichan) - flip_freq_mhz); subint->set_centre_frequency(ichan, new_freq); } } arch->set_bandwidth(-1.0 * arch->get_bandwidth()); } if( reverse_freqs ) { // Of course it would be nice to do this with pointers.... but oh well I guess copying will have to do HSK 27/8/04 unsigned nchan = arch->get_nchan(); for( unsigned isub=0; isub<arch->get_nsubint(); isub++){ for( unsigned ipol =0; ipol<arch->get_npol(); ipol++){ for( unsigned ichan=0; ichan<nchan/2; ichan++){ Reference::To<Pulsar::Profile> lo = arch->get_Profile(isub,ipol,ichan); Reference::To<Pulsar::Profile> tmp = lo->clone(); Reference::To<Pulsar::Profile> hi = arch->get_Profile(isub,ipol,nchan-1-ichan); lo->operator=(*hi); hi->operator=(*tmp); } } } arch->set_bandwidth( -1.0 * arch->get_bandwidth() ); } if (reset_weights) { arch->uniform_weight(new_weight); if (verbose) cout << "All profile weights set to " << new_weight << endl; } if (rotate) arch->rotate_phase (rphase); if (scattered_power_correction) { Pulsar::ScatteredPowerCorrection spc; if (arch->get_state() == Signal::Stokes) arch->convert_state(Signal::Coherence); spc.correct (arch); } if (newdm) { arch->set_dispersion_measure(dm); if (verbose) cout << "Archive dispersion measure set to " << dm << endl; if (arch->get_dedispersed()) { arch->dedisperse(); if (verbose) cout << "Archive re-dedipsersed" << endl; } } if (dedisperse) { arch->dedisperse(); if (verbose) cout << "Archive dedipsersed" << endl; } if (dededisperse) { Pulsar::Dispersion correction; correction.revert (arch); } if (stokesify) { if (arch->get_npol() != 4) throw Error(InvalidState, "Convert to Stokes", "Not enough polarisation information"); arch->convert_state(Signal::Stokes); if (verbose) cout << "Archive converted to Stokes parameters" << endl; } if (unstokesify) { if (arch->get_npol() != 4) throw Error(InvalidState, "Convert to coherence", "Not enough polarisation information"); arch->convert_state(Signal::Coherence); if (verbose) cout << "Archive converted to coherence parameters" << endl; } if (cbppo) { myio = new Pulsar::PeriastronOrder(); arch->add_extension(myio); myio->organise(arch, ronsub); } if (cbpao) { myio = new Pulsar::BinaryPhaseOrder(); arch->add_extension(myio); myio->organise(arch, ronsub); } if (cblpo) { myio = new Pulsar::BinLngPeriOrder(); arch->add_extension(myio); myio->organise(arch, ronsub); } if (cblao) { myio = new Pulsar::BinLngAscOrder(); arch->add_extension(myio); myio->organise(arch, ronsub); } if( subint_extract_start >= 0 && subint_extract_end >= 0 ) { vector<unsigned> subints; unsigned isub = subint_extract_start; while ( isub<arch->get_nsubint() && isub<unsigned(subint_extract_end) ) { subints.push_back( isub ); isub++; } Reference::To<Pulsar::Archive> extracted( arch->extract(subints) ); extracted->set_filename( arch->get_filename() ); arch = extracted; } if (tscr) { if (tsub > 0.0) { unsigned factor = unsigned (tsub / arch->get_Integration(0)->get_duration()); if (factor == 0) { cerr << "Warning: subints already too long" << endl; } else { arch->tscrunch(factor); } if (verbose) cout << arch->get_filename() << " tscrunched by a factor of " << factor << endl; } else if (new_nsub > 0) { arch->tscrunch_to_nsub(new_nsub); if (verbose) cout << arch->get_filename() << " tscrunched to " << new_nsub << " subints" << endl; } else if (tscr_fac > 0) { arch->tscrunch(tscr_fac); if (verbose) cout << arch->get_filename() << " tscrunched by a factor of " << tscr_fac << endl; } else { arch->tscrunch(); if (verbose) cout << arch->get_filename() << " tscrunched" << endl; } } if (pscr) { arch->pscrunch(); if (verbose) cout << arch->get_filename() << " pscrunched" << endl; } if (invint) { arch->invint(); if (verbose) cout << arch->get_filename() << " invinted" << endl; } if (newrm) { arch->set_rotation_measure (rm); if (verbose) cout << arch->get_filename() << " RM set to " << rm << endl; } if (defaraday) { arch->defaraday(); if (verbose) cout << arch->get_filename() << " defaradayed" <<endl; } if (aux_rm) { if (verbose) cout << "pam: correct auxiliary Faraday rotation; iono RM=" << aux_rm << endl; correct_auxiliary_rm (arch, aux_rm); } if (fscr) { if (new_nchn > 0) { arch->fscrunch_to_nchan(new_nchn); if (verbose) cout << arch->get_filename() << " fscrunched to " << new_nchn << " channels" << endl; } else if (fscr_fac > 0) { arch->fscrunch(fscr_fac); if (verbose) cout << arch->get_filename() << " fscrunched by a factor of " << fscr_fac << endl; } else { arch->fscrunch(); if (verbose) cout << arch->get_filename() << " fscrunched" << endl; } } if (bscr) { if (new_nbin > 0) { arch->bscrunch_to_nbin(new_nbin); if (verbose) cout << arch->get_filename() << " bscrunched to " << new_nbin << " bins" << endl; } else { arch->bscrunch(bscr_fac); if (verbose) cout << arch->get_filename() << " bscrunched by a factor of " << bscr_fac << endl; } } if (smear_dc) { for (unsigned i = 0; i < arch->get_nsubint(); i++) { for (unsigned j = 0; j < arch->get_npol(); j++) { for (unsigned k = 0; k < arch->get_nchan(); k++) { smear (arch->get_Profile(i,j,k), smear_dc); } } } } if (save) { if (archive_class) { // unload an archive of the specified class Reference::To<Pulsar::Archive> output; output = Pulsar::Archive::new_Archive (archive_class); output -> copy (*arch); output -> set_filename ( arch->get_filename() ); arch = output; } // See if the archive contains a history that should be updated: Pulsar::ProcHistory* fitsext = arch->get<Pulsar::ProcHistory>(); if (fitsext) { if (command.length() > 80) { cout << "WARNING: ProcHistory command string truncated to 80 chars" << endl; fitsext->set_command_str(command.substr(0, 80)); } else { fitsext->set_command_str(command); } } string out_filename = arch->get_filename(); if( !ext.empty() ) out_filename = replace_extension( out_filename, ext ); if( !ulpath.empty() ) out_filename = ulpath + basename(out_filename); arch->unload( out_filename ); cout << out_filename << " written to disk" << endl; } } catch (Error& error) { cerr << error << endl; } return 0; } catch(Error& er) { cerr << er << endl; return -1; } catch (string& error) { cerr << "exception thrown: " << error << endl; return -1; } catch (bad_alloc& ba) { cerr << "Caught a bad_alloc: '" << ba.what() << "'" << endl ; return -1; } catch (exception& e) { cerr << "caught an exception of type '" << typeid(e).name() << "'" << endl; return -1; } catch(...) { fprintf(stderr,"Unknown exception caught\n"); return -1; }
int main(int argc, char* argv[]) try { if (argc < 2) { usage(); return EXIT_SUCCESS; } int gotc = 0; while ((gotc = getopt(argc, argv, "hvV")) != -1) { switch (gotc) { case 'h': usage(); return EXIT_SUCCESS; case 'V': Pulsar::Archive::set_verbosity(3); break; case 'v': Pulsar::Archive::set_verbosity(2); break; } } if (optind >= argc) { cerr << "pazi: please specify filename" << endl; return -1; } string filename = argv[optind]; string extension = filename.substr(filename.length() - 2, 2); if (extension == "rf") extension = "rz"; else if (extension == "cf") extension = "cz"; else extension = "pazi"; string write_filename = filename + "."; write_filename += extension; cerr << "pazi: loading data" << endl; base_archive = Archive::load(filename); if (base_archive->get_npol() == 4) { original_state = base_archive->get_state(); base_archive->convert_state( Signal::Stokes ); } backup_archive = base_archive->clone(); cerr << "pazi: making fscrunched clone" << endl; mod_archive = base_archive->clone(); mod_archive->pscrunch(); mod_archive->remove_baseline(); mod_archive->dedisperse(); mod_archive->fscrunch(); scrunched_archive = mod_archive->clone(); scrunched_archive->tscrunch(); ranges.second = get_max_value(base_archive, plot_type); positive_direction = base_archive->get_bandwidth() < 0.0; time_orig_plot = factory.construct("time"); time_mod_plot = factory.construct("time"); time_fui = time_mod_plot->get_frame_interface(); freq_orig_plot = factory.construct("freq"); freq_mod_plot = factory.construct("freq"); freq_fui = freq_mod_plot->get_frame_interface(); total_plot = factory.construct("flux"); total_plot->configure("info=1"); subint_orig_plot = new ProfilePlot; subint_mod_plot = new ProfilePlot; subint_fui = subint_mod_plot->get_frame_interface(); subint_orig_plot->configure("info=1"); subint_mod_plot->configure("info=1"); unsigned window = 0; char device [8]; for (unsigned i=0; i<2; i++) do { window ++; snprintf (device, 8, "%u/XS", window); } while ( cpgopen (device) < 0 ); cpgask(0); cerr << endl << "Total S/N = " << scrunched_archive->get_Profile(0,0,0)->snr() << endl << endl; total_plot->plot(scrunched_archive); cpgslct(1); time_orig_plot->plot(mod_archive); do { cpgswin(0, 1, 0, 1); // plot: // frequency = horizontal mouse band // time = horizontal mouse band // profile = vertical mouse band int band = 0; if (prune_start != UNDEF_MOUSE) { band = BOX_ANCHOR; mouse_ref = prune_start; } else if (mouse_ref != UNDEF_MOUSE) { if (plot_type == FscrunchedSubint) band = VERTICAL_ANCHOR; else band = HORIZONTAL_ANCHOR; } else { if (plot_type == FscrunchedSubint) band = VERTICAL_LINE; else band = HORIZONTAL_LINE; } cpgband(band, 0, mouse_ref.first, mouse_ref.second, &(mouse.first), &(mouse.second), &ch); switch (ch) { case 'A': // zoom { constrain_range(mouse.first); constrain_range(mouse.second); if (mouse_ref == UNDEF_MOUSE) { mouse_ref = mouse; continue; } // store the current range so it can be restored if the user selects // a zoom region too small const RangeType old_ranges = ranges; bool horizontal = plot_type == FscrunchedSubint ? false : true; ranges = get_range(mouse_ref, mouse, ranges, horizontal); // ignore mouse clicks if the index values are too close (< 1) if (ranges.first == ranges.second) { ranges = old_ranges; break; } zoomed = true; const unsigned max_value = get_max_value(base_archive, plot_type); const string zoom_option = get_zoom_option(ranges, max_value); switch (plot_type) { case PhaseVsTime: time_fui->set_value("y:range", zoom_option); redraw(mod_archive, time_orig_plot, time_mod_plot, zoomed); break; case PhaseVsFrequency: freq_fui->set_value("y:range", zoom_option); freq_redraw(mod_archive, base_archive, freq_orig_plot, freq_mod_plot, zoomed); break; case FscrunchedSubint: subint_fui->set_value("x:range", zoom_option); redraw(mod_archive, subint_orig_plot, subint_mod_plot, zoomed); break; } } break; // case 'A' case 'h': usage(); break; case 'b': // plot specific subint if (plot_type == PhaseVsTime) { plot_type = FscrunchedSubint; zoomed = false; *mod_archive = *base_archive; mod_archive->set_dispersion_measure(0); mod_archive->fscrunch(); mod_archive->pscrunch(); mod_archive->remove_baseline(); subint = get_indexed_value(mouse); ranges.first = 0; ranges.second = get_max_value(base_archive, plot_type); char add[3]; sprintf(add, "%d", subint); string subint_option = "subint="; subint_option += add; subint_orig_plot->configure(subint_option); subint_mod_plot->configure(subint_option); cpgeras(); subint_orig_plot->plot(mod_archive); update_total(scrunched_archive, base_archive, total_plot); } break; /*case 'c': // center pulse set_centre(mod_archive, base_archive, centered, plot_type, dedispersed); if (plot_type == "freq") redraw(mod_archive, freq_orig_plot, freq_mod_plot, zoomed); else if (plot_type == "time") redraw(mod_archive, time_orig_plot, time_mod_plot, zoomed); update_total(scrunched_archive, base_archive, total_plot); break;*/ case 'd': // toggle dedispersion on/off set_dedispersion(mod_archive, base_archive, dedispersed); if (plot_type == PhaseVsFrequency) { mod_archive->tscrunch(); redraw(mod_archive, freq_orig_plot, freq_mod_plot, zoomed); } else if (plot_type == PhaseVsTime) { mod_archive->fscrunch(); redraw(mod_archive, time_orig_plot, time_mod_plot, zoomed); } update_total(scrunched_archive, base_archive, total_plot); break; case 'f': // frequency plot plot_type = PhaseVsFrequency; ranges.first = 0; ranges.second = get_max_value(base_archive, plot_type); zoomed = false; freq_redraw(mod_archive, base_archive, freq_orig_plot, freq_mod_plot, zoomed); break; case 'm': if (plot_type != FscrunchedSubint) { cerr << "pazi: can only mow lawn in binzap-subint mode" << endl; continue; } cerr << "pazi: mowing lawn" << endl; mowlawn (mod_archive, base_archive, subint); cerr << "pazi: replotting" << endl; redraw(mod_archive, subint_orig_plot, subint_mod_plot, zoomed); cerr << "pazi: updating total" << endl; update_total(scrunched_archive, base_archive, total_plot); break; case 'x': // prune if (plot_type != FscrunchedSubint) { cerr << "pazi: can only prune hedge in binzap-subint mode" << endl; continue; } constrain_range(mouse.first); constrain_range(mouse.second); if (prune_start == UNDEF_MOUSE) { prune_start = mouse; continue; } prune_end = mouse; cerr << "pazi: pruning hedge" << endl; prune_hedge (mod_archive, base_archive, subint); cerr << "pazi: replotting" << endl; redraw(mod_archive, subint_orig_plot, subint_mod_plot, zoomed); cerr << "pazi: updating total" << endl; update_total(scrunched_archive, base_archive, total_plot); break; case 'o': // toggle frequency scrunching on/off if (plot_type == PhaseVsTime) { if (fscrunched) { fscrunched = false; *mod_archive = *base_archive; } else { fscrunched = true; mod_archive->fscrunch(); } redraw(mod_archive, time_orig_plot, time_mod_plot, zoomed); } break; case 'q': // quit cpgclos(); return EXIT_SUCCESS; case 'p': print_command(channels_to_zap, subints_to_zap, extension, filename); break; case 'r': // reset zoom zoomed = false; ranges.first = 0; ranges.second = get_max_value(base_archive, plot_type); switch (plot_type) { case PhaseVsTime: redraw(mod_archive, time_orig_plot, time_mod_plot, zoomed); break; case PhaseVsFrequency: freq_redraw(mod_archive, base_archive, freq_orig_plot, freq_mod_plot, zoomed); break; case FscrunchedSubint: redraw(mod_archive, subint_orig_plot, subint_mod_plot, zoomed); break; } break; case 's': // save current archive changes: { Pulsar::ProcHistory* ext = base_archive->get<Pulsar::ProcHistory>(); if (ext) { ext->set_command_str("pazi"); } if ( base_archive->get_npol() == 4 ) base_archive->convert_state( original_state ); base_archive->unload(write_filename); if ( base_archive->get_npol() == 4 ) base_archive->convert_state( Signal::Stokes ); break; } case 't': // time plot plot_type = PhaseVsTime; ranges.first = 0; ranges.second = get_max_value(base_archive, plot_type); zoomed = false; time_redraw(mod_archive, base_archive, time_orig_plot, time_mod_plot, zoomed); break; case 'u': // undo last change if (mouse_ref != UNDEF_MOUSE) { mouse_ref = UNDEF_MOUSE; continue; } switch (plot_type) { case PhaseVsTime: { const unsigned value = get_indexed_value(mouse); remove_channel(value, subints_to_zap); time_unzap_subint(base_archive, backup_archive, value); time_redraw(mod_archive, base_archive, time_orig_plot, time_mod_plot, zoomed); } break; case PhaseVsFrequency: { const unsigned value = get_indexed_value(mouse); remove_channel(value, channels_to_zap); freq_unzap_chan(base_archive, backup_archive, value); freq_redraw(mod_archive, base_archive, freq_orig_plot, freq_mod_plot, zoomed); } break; case FscrunchedSubint: if (bins_to_zap.size()) { bins_to_zap.erase(bins_to_zap.end() - 5, bins_to_zap.end()); *base_archive = *backup_archive; *mod_archive = *backup_archive; mod_archive->set_dispersion_measure(0); mod_archive->pscrunch(); mod_archive->fscrunch(); mod_archive->remove_baseline(); redraw(mod_archive, subint_orig_plot, subint_mod_plot, zoomed); } break; } update_total(scrunched_archive, base_archive, total_plot); break; case 'z': case 'X': // zap single channel if (mouse_ref == UNDEF_MOUSE) zap_single (); else zap_multiple (); break; } prune_start = UNDEF_MOUSE; mouse_ref = UNDEF_MOUSE; } while (ch != 'q'); return 0; } // end main catch (Error& error) { cerr << "pazi: " << error << endl; return -1; }