/*  FilmbabeOptions.h

    Mark Woolrich, FMRIB Image Analysis Group

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

/*  Part of FSL - FMRIB's Software Library
    http://www.fmrib.ox.ac.uk/fsl
    fsl@fmrib.ox.ac.uk
    
    Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
    Imaging of the Brain), Department of Clinical Neurology, Oxford
    University, Oxford, UK
    
    
    LICENCE
    
    FMRIB Software Library, Release 5.0 (c) 2012, The University of
    Oxford (the "Software")
    
    The Software remains the property of the University of Oxford ("the
    University").
    
    The Software is distributed "AS IS" under this Licence solely for
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    makes clear that no condition is made or to be implied, nor is any
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#if !defined(FilmbabeOptions_h)
#define FilmbabeOptions_h

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

using namespace Utilities;

namespace Filmbabe {

class FilmbabeOptions {
 public:
  static FilmbabeOptions& getInstance();
  ~FilmbabeOptions() { delete gopt; }
  
  Option<bool> verbose;
  Option<int> debuglevel;
  Option<bool> timingon;
  Option<bool> help;
  Option<bool> flobsprioroff;
  Option<string> datafile;
  Option<string> maskfile;
  Option<string> designfile;
  Option<string> flobsregressorsfile;
  Option<string> flobsdir;
  Option<string> priorcovarfile;
  Option<string> priormeanfile;
  Option<string> logdir;
  Option<int> niters;
  Option<float> tarmrfprec;
  Option<bool> tarard;
  Option<int> ntracesamps;
  Option<int> ntar;

  void parse_command_line(int argc, char** argv, Log& logger);
  
 private:
  FilmbabeOptions();  
  const FilmbabeOptions& operator=(FilmbabeOptions&);
  FilmbabeOptions(FilmbabeOptions&);

  OptionParser options; 
      
  static FilmbabeOptions* gopt;
  
};

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

 inline FilmbabeOptions::FilmbabeOptions() :
   verbose(string("-V,--verbose"), false, 
	   string("switch on diagnostic messages"), 
	   false, no_argument),
   debuglevel(string("--db,--debug,--debuglevel"), 0,
		       string("set debug level"), 
		       false, requires_argument),
   timingon(string("--to,--timingon"), false, 
		       string("turn timing on"), 
		       false, no_argument),
   help(string("-h,--help"), false,
		    string("display this message"),
		    false, no_argument),   
   flobsprioroff(string("--fpo,--flobsprioroff"), false,
		    string("Turn FLOBS prior off"),
		    false, no_argument),
   datafile(string("--df,--datafile"), string(""),
			  string("data file"),
		     true, requires_argument),  
   maskfile(string("-m,--mask"), string(""),
	    string("mask file"),
	    true, requires_argument),
   designfile(string("-d,--dm,--designfile"), string(""),
	      string("design matrix file"),
	      true, requires_argument),
   flobsregressorsfile(string("--frf"), string(""),
	      string("file indicating which regressors belong to which original ev design matrix file (a -1 label indicates a non-flobs regerssor)"),
	      true, requires_argument),
   flobsdir(string("--fd"), string(""),
	      string("flobs directory, when using flobs constraints need this or to explicitly specify --pcf and--pmf"),
	    false, requires_argument),
   priorcovarfile(string("--pcf,--priorcovarfile"), string(""),
	      string("priorcovar matrix file"),
	      false, requires_argument),
   priormeanfile(string("--pmf,--priormeanfile"), string(""),
	      string("priormean matrix file"),
	      false, requires_argument),
   logdir(string("-l,--ld,--logdir"), string("logdir"),
	  string("log directory"),
	  false, requires_argument),  
   niters(string("--ni"), 5,
	  string("Num pf VB iterations (default is 5)"),
	  false, requires_argument),
   tarmrfprec(string("--tmp,--tarmrfprec"), -1, 
	      string("MRF precision to impose on temporal AR maps, default is -1 for a proper full Bayes approach"),
	      false, requires_argument),
   tarard(string("--tarard"), false, 
	  string("Impose ARD/MRF on temporal AR"),	       
	  false, no_argument),
   ntracesamps(string("--nts,--ntracesamps"), 0,
	       string("No of samples to take to estimate trace (default is 0, which uses only diagonal elements of the precision matrix to estimate trace)"),
	       false, requires_argument),
   ntar(string("--ntar"), 3,
	string("Order of temporal AR (default is 3)"),
	false, requires_argument),
   options("filmbabe", "filmbabe -df <filename>\n filmbabe --verbose\n")
 {
     try {
       options.add(verbose);
       options.add(debuglevel);
       options.add(timingon);
       options.add(help);
       options.add(flobsprioroff);
       options.add(datafile);
       options.add(maskfile);
       options.add(designfile);
       options.add(flobsregressorsfile);
       options.add(flobsdir);
       options.add(priorcovarfile);
       options.add(priormeanfile);
       options.add(logdir);
       options.add(niters);
       options.add(tarmrfprec);
       options.add(tarard);
       options.add(ntracesamps);
       options.add(ntar);

     }
     catch(X_OptionError& e) {
       options.usage();
       cerr << endl << e.what() << endl;
     } 
     catch(std::exception &e) {
       cerr << e.what() << endl;
     }    
     
   }
}

#endif