dtifitOptions.h

/*  BpmOptions.h

    Mark Woolrich, FMRIB Image Analysis Group

    Copyright (C) 1999-2000 University of Oxford  */

/*  CCOPYRIGHT  */

#if !defined(dtifitOptions_h)
#define dtifitOptions_h

#include <string>
#include <iostream>
#include <fstream>
#include <stdlib.h>
#include <stdio.h>
#include "utils/options.h"
#include "commonopts.h"
//#include "newmatall.h"

using namespace Utilities;

namespace DTIFIT {

class dtifitOptions {
 public:
  static dtifitOptions& getInstance();
  ~dtifitOptions() { delete gopt; }
  
  Option<bool> verbose;
  Option<bool> help;
  Option<string> dtidatafile;
  Option<string> ofile;
  Option<string> maskfile;
  Option<string> bvecsfile;
  Option<string> bvalsfile;
  Option<string> cni; //confounds of no interest. 
  Option<bool> littlebit;
  Option<bool> savetensor;
  Option<int> z_min;
  Option<int> z_max;
  Option<int> y_min;
  Option<int> y_max;
  Option<int> x_min;
  Option<int> x_max;
  bool parse_command_line(int argc, char** argv);
  
 private:
  dtifitOptions();  
  const dtifitOptions& operator=(dtifitOptions&);
  dtifitOptions(dtifitOptions&);

  OptionParser options; 
      
  static dtifitOptions* gopt;
  
};

 inline dtifitOptions& dtifitOptions::getInstance(){
   if(gopt == NULL)
     gopt = new dtifitOptions();
   
   return *gopt;
 }

 inline dtifitOptions::dtifitOptions() :
  verbose(string("-V,--verbose"), false, 
	  string("switch on diagnostic messages"), 
	  false, no_argument),
   help(string("-h,--help"), false,
	string("display this message"),
	false, no_argument),
   dtidatafile(string("-k,--data"), string("dtidata"),
	       string("dti data file"),
	       true, requires_argument),  
   ofile(string("-o,--out"), string("dti"),
	       string("Output basename"),
	       true, requires_argument),
   maskfile(string("-m,--mask"), string("mask"),
	    string("Bet binary mask file"),
	    true, requires_argument),
   bvecsfile(string("-r,--bvecs"), string("bvecs"),
	     string("b vectors file"),
	     true, requires_argument),  
   bvalsfile(string("-b,--bvals"), string("bvals"),
	     string("b values file"),
	     true, requires_argument), 
   cni(string("--cni"), string(""),
	     string("counfound regressors"),
	     false, requires_argument), 
   littlebit(string("--littlebit"), false, 
	     string("Only process small area of brain"), 
	     false, no_argument),
   savetensor(string("--save_tensor"), false, 
	     string("Save the elements of the tensor"), 
	     false, no_argument),
   z_min(string("-z,--zmin"), 0, 
	 string("min z"), 
	 false, requires_argument),
   z_max(string("-Z,--zmax"), 42, 
	 string("max z"), 
	 false, requires_argument),
   y_min(string("-y,--ymin"), 0, 
	 string("min y"), 
	 false, requires_argument),
   y_max(string("-Y,--ymax"), 128, 
	 string("max y"), 
	 false, requires_argument),
   x_min(string("-x,--xmin"), 0, 
	 string("min x"), 
	 false, requires_argument),
   x_max(string("-X,--xmax"), 128, 
	 string("max x"), 
	 false, requires_argument),
   options("dtifit", "dtifit -k <filename>\n dtifit --verbose\n")
   {
     
    
     try {
       options.add(verbose);
       options.add(help);
       options.add(dtidatafile);
       options.add(ofile);
       options.add(maskfile);
       options.add(bvecsfile);
       options.add(bvalsfile);
       options.add(cni);
       options.add(littlebit);
       options.add(savetensor);
       options.add(z_min);
       options.add(z_max);
       options.add(y_min);
       options.add(y_max);
       options.add(x_min);
       options.add(x_max);
       
     }
     catch(X_OptionError& e) {
       options.usage();
       cerr << endl << e.what() << endl;
     } 
     catch(std::exception &e) {
       cerr << e.what() << endl;
     }    
     
   }
}

#endif