/*
options.use_M_lines = 1;
options.use_cascade_auger = 1;
options.use_cascade_radiative = 1;
options.use_variance_reduction = 1;
options.use_sum_peaks = 0;
options.use_escape_peaks = 1;
options.use_poisson = 0;
options.verbose = 0;
options.use_opencl = 0;
options.extra_verbose = 0;
options.omp_num_threads = xmi_omp_get_max_threads();
options.use_advanced_compton = 0;
options.custom_detector_response = NULL;
*/
options = xmi_get_default_main_options();
#ifdef G_OS_WIN32
gchar *equalsignchar;
for (i = 0 ; i < argc ; i++) {
if (strncmp(argv[i], "--with-solid-angles-data=", strlen("--with-solid-angles-data=")) == 0) {
equalsignchar = strchr(argv[i], '=');
xmimsim_hdf5_solid_angles_utf8 = g_strdup(equalsignchar+1);
}
else if (strncmp(argv[i], "--with-escape-ratios-data=", strlen("--with-escape-ratios-data=")) == 0) {
equalsignchar = strchr(argv[i], '=');
xmimsim_hdf5_escape_ratios_utf8 = g_strdup(equalsignchar+1);
}
else if (strncmp(argv[i], "--with-hdf5-data=", strlen("--with-hdf5-data=")) == 0) {
equalsignchar = strchr(argv[i], '=');
hdf5_file_utf8 = g_strdup(equalsignchar+1);
int main(int argc, char **argv) {
Glib::set_application_name("app3");
#if defined(G_OS_WIN32)
setlocale(LC_ALL,"English_United States");
//g_setenv("LANG","en_US",TRUE);
#else
Glib::setenv("LANG","en_US",TRUE);
#endif
setbuf(stdout,NULL);
if (bam_xmlLoadCatalog() == 0) {
return 1;
}
if (xmi_xmlLoadCatalog() == 0) {
return 1;
}
static struct xmi_main_options options = xmi_get_default_main_options();
static std::string spe_file_noconv;
static std::string spe_file_conv;
static std::string csv_file_noconv;
static std::string csv_file_conv;
static std::string svg_file_noconv;
static std::string svg_file_conv;
static std::string htm_file_noconv;
static std::string htm_file_conv;
static std::string custom_detector_response;
static std::string hdf5_file;
static std::string xmimsim_hdf5_solid_angles;
static std::string xmimsim_hdf5_escape_ratios;
static double conv_threshold(BAM_QUANT_CONV_THRESHOLD_DEFAULT*100.0);
bool version = false;
std::vector<std::string> argv_files;
Glib::OptionContext option_context("inputfile XMSO-file");
option_context.set_help_enabled();
Glib::OptionGroup option_group("XMI-MSIM", "XMI-MSIM options", "Show all XMI-MSIM options");
//option_group.add_entry(App3OptionEntry( "enable-M-lines", 0, "Enable M lines (default)"), (bool&) options.use_M_lines);
option_group.add_entry(App3OptionEntry( "disable-M-lines", 0, "Disable M lines", "", Glib::OptionEntry::FLAG_REVERSE), (bool&) options.use_M_lines);
//option_group.add_entry(App3OptionEntry( "enable-auger-cascade", 0, "Enable Auger (non radiative) cascade effects (default)"), (bool&) options.use_cascade_auger);
option_group.add_entry(App3OptionEntry( "disable-auger-cascade", 0, "Disable Auger (non radiative) cascade effects", "", Glib::OptionEntry::FLAG_REVERSE), (bool&) options.use_cascade_auger);
//option_group.add_entry(App3OptionEntry( "enable-radiative-cascade", 0, "Enable radiative cascade effects (default)"), (bool&) options.use_cascade_radiative);
option_group.add_entry(App3OptionEntry( "disable-radiative-cascade", 0, "Disable radiative cascade effects", "", Glib::OptionEntry::FLAG_REVERSE), (bool&) options.use_cascade_radiative);
//option_group.add_entry(App3OptionEntry( "enable-variance-reduction", 0, "Enable variance reduction (default)"), (bool&) options.use_variance_reduction);
option_group.add_entry(App3OptionEntry( "disable-variance-reduction", 0, "Disable variance reduction", "", Glib::OptionEntry::FLAG_REVERSE), (bool&) options.use_variance_reduction);
option_group.add_entry_filename(App3OptionEntry( "with-hdf5-data", 0, "Select a HDF5 data file (advanced usage)", "file", Glib::OptionEntry::FLAG_HIDDEN), hdf5_file);
option_group.add_entry_filename(App3OptionEntry( "with-solid-angles-data", 0, "Select a HDF5 solid angles file (advanced usage)", "file", Glib::OptionEntry::FLAG_HIDDEN), xmimsim_hdf5_solid_angles);
option_group.add_entry_filename(App3OptionEntry( "with-escape-ratios-data", 0, "Select a HDF5 escape ratios file (advanced usage)", "file", Glib::OptionEntry::FLAG_HIDDEN), xmimsim_hdf5_escape_ratios);
option_group.add_entry_filename(App3OptionEntry( "spe-file", 0, "Write detector convoluted spectra to file", "file"), spe_file_conv);
option_group.add_entry_filename(App3OptionEntry( "spe-file-unconvoluted", 0, "Write detector unconvoluted spectra to file", "file"), spe_file_noconv);
option_group.add_entry_filename(App3OptionEntry( "csv-file", 0, "Write detector convoluted spectra to CSV file", "file"), csv_file_conv);
option_group.add_entry_filename(App3OptionEntry( "csv-file-unconvoluted", 0, "Write detector unconvoluted spectra to CSV file", "file"), csv_file_noconv);
option_group.add_entry_filename(App3OptionEntry( "svg-file", 0, "Write detector convoluted spectra to SVG file", "file"), svg_file_conv);
option_group.add_entry_filename(App3OptionEntry( "svg-file-unconvoluted", 0, "Write detector unconvoluted spectra to SVG file", "file"), svg_file_noconv);
option_group.add_entry_filename(App3OptionEntry( "htm-file", 0, "Write detector convoluted spectra to HTML file", "file"), htm_file_conv);
option_group.add_entry_filename(App3OptionEntry( "htm-file-unconvoluted", 0, "Write detector unconvoluted spectra to HTML file", "file"), htm_file_noconv);
option_group.add_entry(App3OptionEntry( "enable-pile-up", 0, "Enable pile-up"), (bool&) options.use_sum_peaks);
//option_group.add_entry(App3OptionEntry( "disable-pile-up", 0, "Disable pile-up (default)", "", Glib::OptionEntry::FLAG_REVERSE), (bool&) options.use_sum_peaks);
//option_group.add_entry(App3OptionEntry( "enable-escape-peaks", 0, "Enable escape peaks (default)"), (bool&) options.use_escape_peaks);
option_group.add_entry(App3OptionEntry( "disable-escape-peaks", 0, "Disable escape peaks", "", Glib::OptionEntry::FLAG_REVERSE), (bool&) options.use_escape_peaks);
option_group.add_entry(App3OptionEntry( "enable-poisson", 0, "Generate Poisson noise in the spectra"), (bool&) options.use_poisson);
//option_group.add_entry(App3OptionEntry( "disable-poisson", 0, "Disable the generating of spectral Poisson noise (default)", "", Glib::OptionEntry::FLAG_REVERSE), (bool&) options.use_poisson);
option_group.add_entry(App3OptionEntry( "enable-opencl", 0, "Enable OpenCL"), (bool&) options.use_opencl);
//option_group.add_entry(App3OptionEntry( "disable-opencl", 0, "Disable OpenCL (default)", "", Glib::OptionEntry::FLAG_REVERSE), (bool&) options.use_opencl);
option_group.add_entry(App3OptionEntry( "enable-advanced-compton", 0, "Enable advanced yet slower Compton simulation"), (bool&) options.use_advanced_compton);
//option_group.add_entry(App3OptionEntry( "disable-advanced-compton", 0, "Disable advanced yet slower Compton simulation (default)", "", Glib::OptionEntry::FLAG_REVERSE), (bool&) options.use_advanced_compton);
option_group.add_entry_filename(App3OptionEntry( "custom-detector-response", 0, "Use the supplied library for the detector response routine", "file"), custom_detector_response);
option_group.add_entry(App3OptionEntry( "set-threads", 0, "Set the number of threads (default=max)", "N"), options.omp_num_threads);
option_group.add_entry(App3OptionEntry( "verbose", 'v', "Verbose mode"), (bool&) options.verbose);
option_group.add_entry(App3OptionEntry( "very-verbose", 'V', "Even more verbose mode"), (bool&) options.extra_verbose);
option_group.add_entry(App3OptionEntry( "version", 0, "Display version information"), version);
Glib::OptionGroup option_group2("BAM-quant options", "BAM-quant options");
option_group2.add_entry(App3OptionEntry( "convergence-threshold", 0, "Convergence threshold for each of the relative X-ray intensities (default = 1%)", "VAL"), conv_threshold);
option_group2.add_entry_filename(App3OptionEntry( G_OPTION_REMAINING), argv_files);
option_context.set_main_group(option_group2);
option_context.add_group(option_group);
option_context.set_ignore_unknown_options();
try {
if (option_context.parse(argc, argv) == false) {
std::cerr << option_context.get_help(true) << std::endl;
return 1;
}
}
catch (Glib::OptionError &e) {
std::cerr << "Exception caught: " << e.what() << std::endl;
std::cerr << option_context.get_help(true) << std::endl;
return 1;
}
if (conv_threshold < 0) {
std::cerr << "convergence-threshold must be greater than 0!" << std::endl;
return 1;
}
//convert to fraction
conv_threshold /= 100.0;
if (version) {
std::cout << xmi_version_string() << std::endl;
return 0;
}
if (argv_files.size() != 2) {
std::cerr << option_context.get_help(true) << std::endl;
return 1;
}
if (options.extra_verbose) {
options.verbose = 1;
std::cout << "Option M-lines: " << options.use_M_lines << std::endl;
std::cout << "Option non-radiative cascade: " << options.use_cascade_auger << std::endl;
std::cout << "Option radiative cascade: " << options.use_cascade_radiative << std::endl;
std::cout << "Option variance reduction: " << options.use_variance_reduction << std::endl;
std::cout << "Option pile-up: " << options.use_sum_peaks << std::endl;
std::cout << "Option Poisson noise: " << options.use_poisson << std::endl;
std::cout << "Option escape peaks: " << options.use_escape_peaks << std::endl;
std::cout << "Option OpenCL: " << options.use_opencl << std::endl;
std::cout << "Option number of threads: " << options.omp_num_threads << std::endl;
std::cout << "Option advanced Compton: " << options.use_advanced_compton << std::endl;
}
try {
BAM::Job::XMSI::RandomNumberAcquisitionStart();
//disable xraylib's error messages
SetErrorMessages(0);
//start by reading in the inputfile
BAM::File::RXI::Common *common = BAM::File::RXI::Parse(argv_files[0]);
BAM::Job::Quant job(common, argv_files[1], options, conv_threshold);
BAM::Job::XMSI::RandomNumberAcquisitionStop();
}
catch (BAM::Exception &e) {
std::cerr << "Fatal BAM exception: " << e.what() << std::endl;
return 1;
}
catch (std::exception &e) {
std::cerr << "Fatal non-BAM exception: " << e.what() << std::endl;
return 1;
}
catch (Glib::Exception &e) {
std::cerr << "Fatal Glib exception: " << e.what() << std::endl;
return 1;
}
catch (...) {
std::cerr << "Unknown exception occurred" << std::endl;
return 1;
}
return 0;
}
