/*************************************************************************************************
*************************************************************************************************
*
* Start of Main Function
*
*************************************************************************************************
************************************************************************************************/
int main (int argc, char *argv[])
{
init_salute();
#ifdef _DEBUG
atexit (memstatus);
dbgmemInit();
#endif /* _DEBUG */
ofstream null_ostream("/dev/null"); // must stay live for entire scope, or crash when writing
TheSilenceOfTheArmadillos(null_ostream);
TrackProgress my_progress;
DumpStartingStateOfProgram (argc,argv,my_progress);
CommandLineOpts inception_state (argc, argv);
SeqListClass my_keys;
ImageSpecClass my_image_spec;
SlicedPrequel my_prequel_setup;
SetUpOrLoadInitialState(inception_state, my_keys, my_progress, my_image_spec, my_prequel_setup);
// Start logging process parameters & timing now that we have somewhere to log
my_progress.InitFPLog(inception_state);
// Write processParameters.parse file now that processing is about to begin
my_progress.WriteProcessParameters(inception_state);
// Do separator
Region wholeChip(0, 0, my_image_spec.cols, my_image_spec.rows);
IsolatedBeadFind( my_prequel_setup, my_image_spec, wholeChip, inception_state,
inception_state.sys_context.GetResultsFolder(), inception_state.sys_context.analysisLocation, my_keys, my_progress);
exit (EXIT_SUCCESS);
}
/*************************************************************************************************
*************************************************************************************************
*
* Start of Main Function
*
*************************************************************************************************
************************************************************************************************/
int main (int argc, char *argv[])
{
init_salute();
ofstream null_ostream("/dev/null"); // must stay live for entire scope, or crash when writing
TheSilenceOfTheArmadillos(null_ostream);
TrackProgress my_progress;
DumpStartingStateOfProgram (argc,argv,my_progress);
if(argc < 2)
{
PrintHelp();
}
for(int i = 1; i < argc; ++i)
{
string s = argv[i];
if(s == "-" || s == "--")
{
cerr << "ERROR: command line input \"-\" must be followed by a short option name (a letter) and \"--\" must be followed by a long option name." << endl;
exit ( EXIT_FAILURE );
}
else if(s == "-?" || s == "-h" || s == "--help")
{
PrintHelp();
}
}
ValidateOpts validater;
validater.Validate(argc, argv);
char** argv2 = new char*[argc];
int datind = TrapAndDeprecateOldArgs(argc, argv, argv2);
OptArgs opts;
opts.ParseCmdLine(argc, (const char**)argv2);
for(int k = 0; k < argc ; ++k)
{
delete [] argv2[k];
}
delete [] argv2;
Json::Value json_params;
CommandLineOpts inception_state;
inception_state.SetOpts(opts, json_params);
if(datind < 0) // there is no "--dat-source-directory"
{
inception_state.sys_context.dat_source_directory = argv[argc - 1];
cout << "dat_source_directory = " << inception_state.sys_context.dat_source_directory << endl;
}
inception_state.PostProcessArgs(opts);
SeqListClass my_keys;
ImageSpecClass my_image_spec;
SlicedPrequel my_prequel_setup;
SetUpOrLoadInitialState(inception_state, my_keys, my_progress, my_image_spec, my_prequel_setup);
// Start logging process parameters & timing now that we have somewhere to log
my_progress.InitFPLog(inception_state);
// Write processParameters.parse file now that processing is about to begin
my_progress.WriteProcessParameters(inception_state);
// Do separator
Region wholeChip(0, 0, my_image_spec.cols, my_image_spec.rows);
IsolatedBeadFind( my_prequel_setup, my_image_spec, wholeChip, inception_state,
inception_state.sys_context.GetResultsFolder(), inception_state.sys_context.analysisLocation, my_keys, my_progress);
exit (EXIT_SUCCESS);
}
