void fix_single::add_options ( CommandLine::Menu& menu)
{
CommandLine::Argument* arg;
menu.add("");
arg = menu.add (ext, 'e', "extension");
arg->set_help ("Write new files with this extension");
}
void Speed::parseOptions (int argc, char** argv)
{
CommandLine::Menu menu;
CommandLine::Argument* arg;
menu.set_help_header ("filterbank_speed - measure Filterbank speed");
menu.set_version ("filterbank_speed version 1.0");
arg = menu.add (real_to_complex, 'r');
arg->set_help ("real-to-complex FFT");
arg = menu.add (do_fwd_fft, 'b');
arg->set_help ("do (batched) backward FFTs only");
arg = menu.add (nfft, 'n', "nfft");
arg->set_help ("FFT length");
arg = menu.add (nchan, 'c', "nchan");
arg->set_help ("number of channels");
arg = menu.add (niter, 'N', "niter");
arg->set_help ("number of iterations");
menu.parse (argc, argv);
}
void psredit::add_options (CommandLine::Menu& menu)
{
CommandLine::Argument* arg;
// blank line in help
menu.add ("");
arg = menu.add (this, &psredit::add_commands, 'c', "command[s]");
arg->set_help ("one or more commands, separated by commas");
arg = menu.add (this, &psredit::detailed_help, 'H');
arg->set_help ("more detailed help");
arg = menu.add (prefix_name, 'Q');
arg->set_help ("do not prefix output with 'keyword='");
}
void psrflux::add_options (CommandLine::Menu& menu)
{
CommandLine::Argument* arg;
menu.add("\n" "Dynamic spectrum options:");
arg = menu.add (ext, 'e', "ext");
arg->set_help ("Append extention to output (default .ds)");
arg = menu.add (stdfile, 's', "std");
arg->set_help ("Standard profile file");
arg = menu.add (align, 'a', "align");
arg->set_help ("Align standard with each profile separately");
arg = menu.add (noalign, 'A', "noalign");
arg->set_help ("No fit for profile alignment at all");
}
void example::add_options (CommandLine::Menu& menu)
{
CommandLine::Argument* arg;
// add a blank line and a header to the output of -h
menu.add ("\n" "General options:");
arg = menu.add (subint_indeces, 'i', "subints");
arg->set_help ("select the sub-integration(s) to output");
arg = menu.add (chan_indeces, 'c', "chans");
arg->set_help ("select the frequency channel(s) to output");
arg = menu.add (bin_indeces, 'b', "bins");
arg->set_help ("select the phase bin(s) to output");
arg = menu.add (pol_indeces, 's', "pols");
arg->set_help ("select the polarization(s) to output");
}
void psrsh::add_options (CommandLine::Menu& menu)
{
CommandLine::Argument* arg;
arg = menu.add (this, &psrsh::interpreter_help, 'H');
arg->set_long_name ("cmd");
arg->set_help ("list available commands");
arg->set_has_arg (optional_argument);
arg = menu.add (load_files, 'n');
arg->set_long_name ("nofiles");
arg->set_help ("no filenames required");
menu.set_help_footer
("\n"
"If no files are specified, psrsh enters the interactive shell mode \n"
"\n"
"Otherwise, psrsh enters the shell script command processor mode: \n"
"the first file must be the script, and all subseqent archive files \n"
"will be processed using this script \n"
+ menu.get_help_footer ());
}
void psrpca::add_options ( CommandLine::Menu& menu )
{
CommandLine::Argument* arg;
arg = menu.add ( remove_arch_baseline, "ra" );
arg->set_help ( "Don't remove the baseline of input archives" );
arg = menu.add ( remove_std_baseline, "rs" );
arg->set_help ( "Don't remove the baseline of the template" );
menu.add ("");
menu.add ("Fitting options");
arg = menu.add (this, &psrpca::set_standard, 's', "stdfile");
arg->set_help ("Location of standard profile");
arg = menu.add ( apply_shift, "fp" );
arg->set_help ("Don't fit for phase shift");
arg = menu.add ( apply_offset, "fb" );
arg->set_help ("Don't fit for baseline offset");
arg = menu.add ( apply_scale, "fs" );
arg->set_help ("Don't fit for scale");
arg = menu.add ( prof_to_std, "ts" );
arg->set_help ( "Apply scaling, offset and shift to standard instead of profile");
menu.add ("");
menu.add ("Regression and Predictor Options");
arg = menu.add (residuals_file, 'r', "residuals");
arg->set_help ("File with residuals");
arg->set_long_help ("As output by tempo2 in the following format: {sat} {post} {err}\n"
"They need to be in the same order as the input archives \n"
"When used, corrected residuals are output in a file prefix_residuals \n"
"The format of the output is: {sat} {input residual} {output residual} {input error}\n"
"Note that the output units are us\n");
arg = menu.add (consecutive_points, 'c', "consecutive_points");
arg->set_help ("Choose the number of consecutive points above threshold used during determination of significant eigenvectors");
arg = menu.add (threshold_sigma,'t',"threshold_sigma");
arg->set_help ("Choose the threshold in the units of standard deviation");
menu.add ("");
menu.add ("Output options:");
arg = menu.add (save_diffs, "sd");
arg->set_help ("Don't save the difference profiles");
arg = menu.add (save_evecs, "se");
arg->set_help ("Don't save the eigenvectors");
arg = menu.add (save_evals, "sv");
arg->set_help ("Don't save the eigenvalues");
arg = menu.add (save_covariance_matrix, "sc");
arg->set_help ("Don't save the covariance matrix");
arg = menu.add (save_decomps, "sD");
arg->set_help ("Don't save the decompositions");
arg = menu.add (prefix, 'p', "prefix");
arg->set_help ("Set prefix for all the output files");
arg->set_long_help ("Default value: psrpca\n"
"The output files for differences profiles, eigenvectors, eigenvalues and covariance matrix\n"
"Are: prefix_diffs.ar, prefix_evecs.ar, prefix_evals.dat, prefix_covar.fits, respectively");
}
void psradd::add_options (CommandLine::Menu& menu)
{
CommandLine::Argument* arg;
arg = menu.add (unload_name, 'o', "fname");
arg->set_help ("output result to 'fname'");
// backward compatibility: -f == -o
menu.add( new CommandLine::Alias( arg, 'f' ) );
menu.add ("\n" "General options:");
arg = menu.add (parname, 'E', "f.eph");
arg->set_help ("Load and install new ephemeris from 'f.eph'");
// backward compatibility: -p == -E
menu.add( new CommandLine::Alias( arg, 'p' ) );
arg = menu.add (tscrunch_total, 'T');
arg->set_help ("Tscrunch result after each new file added");
// backward compatibility: -s == -T
menu.add( new CommandLine::Alias( arg, 's' ) );
arg = menu.add (time_direction, 'R');
arg->set_help ("Append data in the frequency direction");
arg = menu.add (patch_name, 'm', "domain");
arg->set_help ("Patch missing sub-integrations: domain = time or phase");
arg = menu.add (inplace_name, "inplace", "filename");
arg->set_help ("Append archives to the specified file");
arg = menu.add (phase_align, 'P');
arg->set_help ("Phase align archive with total before adding");
arg = menu.add (log_results, 'L');
arg->set_help ("Log results in <source>.log");
arg = menu.add (testing, 't');
arg->set_help ("Test mode: make no changes to file system");
menu.add ("\n" "Restrictions:");
arg = menu.add (this, &psradd::force, 'F');
arg->set_help ("Force append against all conventional wisdom");
arg = menu.add (centre_frequency, 'r', "freq");
arg->set_help ("Add archives only with this centre frequency");
arg = menu.add (check_has_data, 'z');
arg->set_help ("Only add archives that have integration length > 0");
arg = menu.add (required_archive_length, 'Z', "time");
arg->set_help ("Only add archives that are time (+/- 0.5) seconds long");
arg = menu.add (this, &psradd::ignore_phase, "ip");
arg->set_help ("Do not apply model, ignore phase alignment");
menu.add ("\n" "AUTO ADD: tscrunch and unload when ...");
arg = menu.add (cal_phase_diff, 'C', "turns");
arg->set_help ("... CAL phase changes by >= turns");
arg->set_notification (auto_add);
arg = menu.add (division_seconds, 'D', "sec");
arg->set_help ("... next archive is from different 'sec' division of MJD");
arg->set_notification (auto_add);
arg = menu.add (max_interval_between, 'G', "sec");
arg->set_help ("... time to next archive > 'sec' seconds");
arg->set_notification (auto_add);
arg = menu.add (max_interval_within, 'g', "sec");
arg->set_help ("... time spanned exceeds 'sec' seconds");
arg->set_notification (auto_add);
arg = menu.add (max_integration_length, 'I', "sec");
arg->set_help ("... integration length exceeds 'sec' seconds");
arg->set_notification (auto_add);
arg = menu.add (max_signal_to_noise, 'S', "s/n");
arg->set_help ("... signal-to-noise ratio exceeds 's/n'");
arg->set_notification (auto_add);
arg = menu.add (auto_add_tscrunch, "autoT");
arg->set_help ("Disable tscrunch before unloading");
menu.add ("\n" "Note: AUTO ADD options are incompatible with -o and -T");
}
//! Add command line options
void dsp::SingleThread::Config::add_options (CommandLine::Menu& menu)
{
CommandLine::Argument* arg;
arg = menu.add (this, &Config::set_quiet, 'q');
arg->set_long_name ("Q");
arg->set_help ("quiet mode");
arg = menu.add (this, &Config::set_verbose, 'v');
arg->set_help ("verbose mode");
arg = menu.add (this, &Config::set_very_verbose, 'V');
arg->set_help ("very verbose mode");
menu.add ("\n" "Input handling options:");
arg = menu.add (input_buffering, "overlap");
arg->set_help ("disable input buffering");
arg = menu.add (force_contiguity, "cont");
arg->set_help ("input files are contiguous (disable check)");
arg = menu.add (run_repeatedly, "repeat");
arg->set_help ("repeatedly read from input until an empty is encountered");
arg = menu.add (seek_seconds, 'S', "seek");
arg->set_help ("start processing at t=seek seconds");
arg = menu.add (total_seconds, 'T', "total");
arg->set_help ("process only t=total seconds");
arg = menu.add (&editor, &TextEditor<Observation>::add_commands,
"set", "key=value");
arg->set_help ("set observation attributes");
arg = menu.add (list_attributes, "list");
arg->set_help ("list observation attributes");
if (weighted_time_series)
{
arg = menu.add (weighted_time_series, 'W');
arg->set_help ("disable weights (allow bad data)");
}
menu.add ("\n" "Processor options:");
if (can_thread)
{
arg = menu.add (this, &Config::set_nthread, 't', "threads");
arg->set_help ("number of processor threads");
}
#if HAVE_SCHED_SETAFFINITY
arg = menu.add (this, &Config::set_affinity, "cpu", "cores");
arg->set_help ("comma-separated list of CPU cores");
#endif
#if HAVE_CUFFT
if (can_cuda)
{
arg = menu.add (this, &Config::set_cuda_device, "cuda", "devices");
arg->set_help ("comma-separated list of CUDA devices");
}
#endif
arg = menu.add (this, &Config::set_fft_library, 'Z', "lib");
arg->set_help ("choose the FFT library ('-Z help' for availability)");
dsp::Operation::report_time = false;
arg = menu.add (dsp::Operation::record_time, 'r');
arg->set_help ("report time spent performing each operation");
arg = menu.add (dump_before, "dump", "op");
arg->set_help ("dump time series before performing operation");
}
//! Parse the command line options
void Pulsar::Application::parse (int argc, char** argv)
{
CommandLine::Menu menu;
CommandLine::Argument* arg;
menu.set_help_header
("\n" + name + " - " + description + "\n"
"\n"
"usage: " + name + " [options] filename[s] \n"
"\n"
"where options are:");
if (has_manual) menu.set_help_footer
("\n" "See "PSRCHIVE_HTTP"/manuals/" + name + " for more details \n");
menu.set_version (version);
arg = menu.add (this, &Application::set_quiet, 'q');
arg->set_help ("quiet mode");
arg = menu.add (this, &Application::set_verbose, 'v');
arg->set_help ("verbose mode");
arg = menu.add (this, &Application::set_very_verbose, 'V');
arg->set_help ("very verbose mode");
arg = menu.add (metafile, 'M', "metafile");
arg->set_help ("metafile contains list of archive filenames");
arg = menu.add (Config::get_configuration(), &Config::set_filename,
"config", "file");
arg->set_help ("configuration file");
for (unsigned i=0; i<options.size(); i++)
options[i]->add_options (menu);
add_options (menu);
menu.parse (argc, argv);
dirglob_program = name;
if ( stow_script && optind < argc )
{
script = argv[optind];
optind ++;
}
if (!metafile.empty())
stringfload (&filenames, metafile);
else
{
for (int i=optind; i<argc; i++)
dirglob (&filenames, argv[i]);
if (sort_filenames)
sort (filenames.begin(), filenames.end());
}
if (update_history)
{
string separator = " ";
command += name + separator;
for (int i=1; i<optind; i++)
command += argv[i] + separator;
if (command.length () > 80)
{
cerr << "WARNING: ProcHistory command string truncated to 80 characters"
<< endl;
command = command.substr (0, 80);
}
}
}
void parse_options (int argc, char** argv) try
{
CommandLine::Menu menu;
CommandLine::Argument* arg;
menu.set_help_header ("digifits - convert dspsr input to PSRFITS search mode output");
menu.set_version ("digifits " + tostring(dsp::version) +
" <" + FTransform::get_library() + ">");
config->add_options (menu);
// Need to rename default threading option due to conflict
// with original digifil -t (time average) setting.
arg = menu.find("t");
arg->set_short_name('\0');
arg->set_long_name("threads");
arg->set_type("nthread");
menu.add ("\n" "Source options:");
arg = menu.add (config->dispersion_measure, 'D', "dm");
arg->set_help (" set the dispersion measure");
menu.add ("\n" "Processing options:");
arg = menu.add (config->block_size, 'B', "MB");
arg->set_help ("block size in megabytes");
string ram_limit;
arg = menu.add (ram_limit, 'U', "MB");
arg->set_help ("upper limit on RAM usage");
arg->set_long_help ("specify the floating point number of megabytes; e.g. -U 256 \n");
arg = menu.add (&config->filterbank,
&dsp::Filterbank::Config::set_freq_res,
'x', "nfft");
arg->set_help ("set backward FFT length in voltage filterbank");
arg = menu.add (config->coherent_dedisp, "do_dedisp", "bool");
arg->set_help ("enable coherent dedispersion (default: false)");
arg = menu.add (config->rescale_constant, 'c');
arg->set_help ("keep offset and scale constant");
arg = menu.add (config->rescale_seconds, 'I', "secs");
arg->set_help ("rescale interval in seconds");
menu.add ("\n" "Output options:");
arg = menu.add (config->tsamp, 't', "tsamp");
arg->set_help ("integration time (s) per output sample (default=64mus)");
arg = menu.add (config->npol, 'p', "npol");
arg->set_help ("output 1 (Intensity), 2 (AABB), or 4 (Coherence) products");
arg = menu.add (config->nbits, 'b', "bits");
arg->set_help ("number of bits per sample output to file [1,2,4,8]");
arg = menu.add (config->filterbank, 'F', "nchan[:D]");
arg->set_help ("create a filterbank (voltages only)");
arg->set_long_help
("Specify number of filterbank channels; e.g. -F 256\n"
"Select coherently dedispersing filterbank with -F 256:D\n"
"Set leakage reduction factor with -F 256:<N>\n");
arg = menu.add (config->nsblk, "nsblk", "N");
arg->set_help ("output block size in samples (default=2048)");
arg = menu.add (config->integration_length, 'L', "seconds");
arg->set_help ("set maximum file length");
arg = menu.add (config->dedisperse, 'K');
arg->set_help ("remove inter-channel dispersion delays");
//arg = menu.add (config->fscrunch_factor, 'f', "nchan");
//arg->set_help ("decimate in frequency");
arg = menu.add (config->output_filename, 'o', "file");
arg->set_help ("output filename");
//bool revert = false;
//arg = menu.add (revert, 'p');
//arg->set_help ("revert to FPT order");
menu.parse (argc, argv);
if (!ram_limit.empty())
{
double MB = fromstring<double> (ram_limit);
config->set_maximum_RAM (uint64_t( MB * 1024.0 * 1024.0 ));
}
//if (revert)
// config->order = dsp::TimeSeries::OrderFPT;
}
catch (Error& error)
{
cerr << error << endl;
exit (-1);
}
catch (std::exception& error)
{
cerr << error.what() << endl;
exit (-1);
}
void paz::add_options (CommandLine::Menu& menu)
{
CommandLine::Argument* arg = 0;
// backward compatibility: -u == -O
menu.add( new CommandLine::Alias( menu.find("O"), 'u' ) );
menu.add ("\n" "Manual zapping options:");
arg = menu.add (zero_intersection, 'I');
arg->set_help ("Zero weight the intersection of -[wW] and -[zZk]");
arg = menu.add (killfile, 'k', "filename");
arg->set_help ("Zero weight chans listed in this kill file");
arg = menu.add (this, &paz::range_bins_to_zap, 'B', "\"a b\"");
arg->set_help ("Zap pulse phase bins between a and b inclusive");
arg = menu.add (this, &paz::add_chans_to_zero, 'z', "\"a b c ...\"");
arg->set_help ("Zero weight these particular channels");
arg = menu.add (this, &paz::range_chans_to_zero, 'Z', "\"a b\"");
arg->set_help ("Zero weight chans between a & b inclusive");
arg = menu.add (this, &paz::add_freqs_to_zero, 'f', "\"a b c ...\"");
arg->set_help ("Zero weight channels with these frequencies (MHz)");
arg = menu.add (this, &paz::range_freqs_to_zero, 'F', "\"a b\"");
arg->set_help ("Zero weight this frequency range, inclusive (MHz)");
arg = menu.add (this, &paz::add_subs_no_delete, 'x', "\"a b c ...\"");
arg->set_help ("Delete all sub-integrations except these");
arg = menu.add (this, &paz::range_subs_no_delete, 'X', "\"a b\"");
arg->set_help ("Delete all sub-ints except a to b inclusive");
arg = menu.add (edge_zap_percent, 'E', "percent");
arg->set_help ("Zero weight this much of each band edge");
arg = menu.add (this, &paz::add_subs_to_delete, 's', "\"a b c ...\"");
arg->set_help ("Delete these sub-integrations");
arg = menu.add (this, &paz::range_subs_to_delete, 'S', "\"a b\"");
arg->set_help ("Delete sub-ints between a & b inclusive");
arg = menu.add (this, &paz::add_subs_to_zero, 'w', "\"a b c ...\"");
arg->set_help ("Zero weight these sub-integrations");
arg = menu.add (this, &paz::range_subs_to_zero, 'W', "\"a b\"");
arg->set_help ("Zero weight sub-ints between a & b inclusive");
arg = menu.add (this, &paz::parse_periodic_zap, 'p', "\"p i\"");
arg->set_help ("Interpolate over every p-th phase bin, start at i");
arg = menu.add (pol_to_delete, "poln", "0/1");
arg->set_help ("Delete the specified polarization");
menu.add ("\n" "Automatic zapping algorithms:");
arg = menu.add (median_zap, 'r');
arg->set_help ("Zap channels using median smoothed difference");
arg = menu.add (median_zap_window, 'R', "size");
arg->set_help ("Set the size of the median smoothing window");
arg = menu.add (this, &paz::add_subints_to_mow, 'l', "subint");
arg->set_help ("Mow the lawn of the specified subint");
arg = menu.add (mow_all_subints, 'L');
arg->set_help ("Mow the lawn of all subints");
arg = menu.add (simple, 'd');
arg->set_help ("Zero weight chans using mean offset rejection");
arg = menu.add (ston_cutoff, 'C', "cutoff");
arg->set_help ("Zero weight chans based on S/N (std optional)");
arg = menu.add (std_filename, 'P', "stdfile");
arg->set_help ("Use this standard profile");
arg = menu.add (dropout_sigma, 'o', "cutoff");
arg->set_help ("Zero weight subints with negative dropouts");
arg = menu.add (eightBinZap, '8');
arg->set_help ("Fix ATNF WBCORR 8 bin problem (see also -p)");
menu.add
("\n"
"The format of the kill file used with the -k option is simply\n"
"a list of channel numbers, separated by white space\n"
"\n"
"The cutoff S/N value used with -C is largely arbitrary. You will\n"
"need to experiment to find the best value for your archives");
}
void psrspa::add_options ( CommandLine::Menu& menu )
{
CommandLine::Argument* arg;
menu.add ( "" );
menu.add ( "Common options" );
arg = menu.add ( log, 'l' );
arg->set_help ( "Use a logarithmic flux scale" );
arg = menu.add ( bins, 'b', "bins" );
arg->set_help ( "Set the number of all bins" );
arg = menu.add ( dynamic_histogram, 'd' );
arg->set_help ( "Allow dynamic setting of range of histograms" );
menu.add ( "" );
menu.add ( "Scan pulses and find giants - options:" );
arg = menu.add ( this, &psrspa::set_finder, 'a',"algorithm");
arg->set_help ( "Set the algorithm used to find pulses" );
arg->set_long_help ( "\t\tThis is a different implementation of the pulse searching\n"
"\t\tAvailable algorithms (name):\n"
"\t\t - OnPulseThreshold (above)\n"
"\t\t - PeakConsecutive (consecutive)\n"
"\t\t - PeakCumulative (cumulative)\n"
"\t\t - ProfileWeightStatic (set)\n"
"\t\t - ExponentialBaseline (exponential)\n"
"\t\t - GaussianBaseline (normal)\n"
"\t\t - BaselineWindow (minimum)\n" );
menu.add ( "" );
menu.add ( "Phased resolved histograms" );
arg = menu.add ( this, &psrspa::choose_range, "pr","min,max(,min,max...)" );
arg->set_help ( "Specify phase range (in turns) for the phase resolved algorithms and max amplitude algorithm" );
arg->set_long_help ( "Multiple ranges can be provided, e.g., '0.0,0.1,0.3,0.35' will create two ranges 0.0-0.1 and 0.3-0.35" );
arg = menu.add ( create_flux, "hf");
arg->set_help ( "Create phase resolved histogram of flux" );
arg = menu.add ( create_polar_degree, "hd");
arg->set_help ( "Create phase resolved histogram of polarisation degree" );
arg = menu.add ( create_polar_angle, "ha");
arg->set_help ( "Create phase resolved histogram of polarisation angle" );
arg = menu.add ( find_max_amp_in_range, "fm");
arg->set_help ( "Find maximum amplitude in the given phase range as provided by -pr" );
arg = menu.add ( flux_pr_bins, "hfb", "bins" );
arg->set_help ( "Set the number of phase resolved flux bins" );
arg = menu.add ( polar_degree_bins, "hdb", "bins" );
arg->set_help ( "Set the number of polarisation degree bins" );
arg = menu.add ( polar_angle_bins, "hab", "bins" );
arg->set_help ( "Set the number of polarisation angle bins" );
arg = menu.add ( this, &psrspa::choose_bscrunch, "bl", "max_bscrunch" );
arg->set_help ( "When searching for maximum amplitude in the given phase range, perform calculations\n"
"also for bscrunched profiles, with the given maximum bscrunch factor" );
menu.add ( "" );
menu.add ( "Output of the histograms" );
arg = menu.add ( prefix, "pfix","prefix" );
arg->set_help ( "Write files with this prefix" );
arg = menu.add ( ext, 'e', "extension" );
arg->set_help ( "Write files with this extension" );
arg = menu.add ( path, 'O', "path" );
arg->set_help ( "Write files in this location" );
arg = menu.add ( binary_output, "bo" );
arg->set_help ( "write the phase resolved histograms in binary format" );
}