コード例 #1
0
ファイル: justBeadFind.cpp プロジェクト: bdiegel/TS
/*************************************************************************************************
 *************************************************************************************************
 *
 *  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);
}
コード例 #2
0
ファイル: justBeadFind.cpp プロジェクト: Brainiarc7/TS
/*************************************************************************************************
 *************************************************************************************************
 *
 *  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);
}