/*  FilmGlsOptions.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
    
    
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#if !defined(__FilmGlsOptions_h)
#define __FilmGlsOptions_h
#include <string>
#include <stdlib.h>
#include <stdio.h>
#include "utils/options.h"
#include "utils/log.h"

using namespace Utilities;

namespace FILM {

class FilmGlsOptions {
 public:
  static FilmGlsOptions& getInstance();
  ~FilmGlsOptions() { delete gopt; }
  
  Option<bool> ac_only;
  Option<float> thresh;  
  Option<bool> fitAutoRegressiveModel;
  Option<bool> help;
  Option<bool> noest;
  Option<bool> output_pwdata;
  Option<bool> pava;
  Option<bool> smoothACEst;
  Option<bool> verbose;
  Option<string> datadir;
  Option<string> analysisMode;
  Option<string> inputDataName;
  Option<string> inputDataName2;
  Option<string> meanInputFile;
  Option<string> minimumTimepointFile;
  Option<string> paradigmfname;
  Option<string> contrastFile;
  Option<string> fContrastFile;
  Option<int> epith;
  Option<int> ms;
  Option<int> tukeysize;
  Option<float> multitapersize;
  Option<vector<int> > voxelwise_ev_numbers;
  Option<vector<string> > voxelwiseEvFilenames;

  void parse_command_line(int argc, char** argv,Log& logger);
  
private:
  FilmGlsOptions();
  const FilmGlsOptions& operator=(FilmGlsOptions&);
  FilmGlsOptions(FilmGlsOptions&);
  OptionParser options; 
  static FilmGlsOptions* gopt;
};

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

 
inline FilmGlsOptions::FilmGlsOptions() :
  ac_only(string("--ac"), false,
        string("\tperform autocorrelation estimation only"),
        false, no_argument),
  thresh(string("--thr"),0,
	 string("~<num>\tinitial threshold to apply to input data"),
	 false, requires_argument),
  fitAutoRegressiveModel(string("--ar"), false,
	string("\tfits autoregressive model - default is to use tukey with M=sqrt(numvols)"),
        false, no_argument),
  help(string("--help"), false,
	string("\tprints this message"),
        false, no_argument),
  noest(string("--noest"), false,
	string("\tdo not estimate auto corrs"),
	false, no_argument),
  output_pwdata(string("--outputPWdata"), false,
	string("\toutput prewhitened data and average design matrix"),
	false, no_argument),
  pava(string("--pava"), false,
	string("\testimates autocorr using PAVA - default is to use tukey with M=sqrt(numvols)"),
	false, no_argument),
  smoothACEst(string("--sa"), false,
	string("\tsmooths auto corr estimates"),
	false, no_argument),
  verbose(string("-v"), false,
	string("\toutputs full data"),
	false, no_argument),
  datadir(string("--rn"), string("results"),
       string("~<file>\tdirectory name to store results in, default is results"),
       false, requires_argument),
  analysisMode(string("--mode"), string("volumetric"),
       string("~<mode>\tanalysis mode, options are volumetric ( default ) or surface. Caution: surface-based functionality is still BETA"), false, requires_argument),
  inputDataName(string("--in"), string(""),string("~<file>\tinput data file ( NIFTI for volumetric, GIFTI for surface )"),true, requires_argument),
  inputDataName2(string("--in2"), string(""),string("~<file>\tinput surface for autocorr smoothing in surface-based analyses"),false, requires_argument),
   meanInputFile(string("--mf"), string(""),
       string("~<file>\tre-estimate mean_func baseline - for use with perfusion subtraction"),
       false, requires_argument), 
   minimumTimepointFile(string("--mft"), string(""),
       string("~<file>\tminimum timepoint file"),
       false, requires_argument),
   paradigmfname(string("--pd"), string(""),
       string("~<file>\tparadigm file"),
        false, requires_argument),
   contrastFile(string("--con"), string(""),
       string("~<file>\tt-contrasts file"),
        false, requires_argument),
   fContrastFile(string("--fcon"), string(""),
       string("~<file>\tf-contrasts file"),
        false, requires_argument),

   epith(string("--epith"), 0,
        string("~<num>\tsusan brightness threshold for volumetric analysis/smoothing sigma for surface analysis"),
        false, requires_argument),
   ms(string("--ms"), 4,
        string("~<num>\tsusan mask size for volumetric analysis/smoothing extent for surface analysis"),
        false, requires_argument),
   tukeysize(string("--tukey"), 0,
        string("~<num>\tuses tukey window to estimate autocorr with window size num - default is to use tukey with M=sqrt(numvols)"),
        false, requires_argument),
   multitapersize(string("--mt"), -1,
        string("~<num>\tuses multitapering with slepian tapers and num is the time-bandwidth product - default is to use tukey with M=sqrt(numvols)"),
        false, requires_argument),
   voxelwise_ev_numbers(string("--ven"), vector<int>(), 
         string("\tlist of numbers indicating voxelwise EVs position in the design matrix (list order corresponds to files in vxf option). Caution BETA option, only use with volumetric analysis."), 
         false, requires_argument),
   voxelwiseEvFilenames(string("--vef"), vector<string>(), 
         string("\tlist of 4D images containing voxelwise EVs (list order corresponds to numbers in vxl option). Caution BETA option, only use with volumetric analysis."), 
			false, requires_argument),
  options("film_gls","film_gls")
   {
     try {
       options.add(ac_only);
       options.add(thresh);
       options.add(fitAutoRegressiveModel);
       options.add(help);
       options.add(noest);
       options.add(output_pwdata);
       options.add(pava);
       options.add(smoothACEst);
       options.add(verbose);
       options.add(datadir);      
       options.add(analysisMode);
       options.add(inputDataName);
       options.add(inputDataName2);
       options.add(meanInputFile);
       options.add(minimumTimepointFile);
       options.add(paradigmfname);
       options.add(contrastFile);
       options.add(fContrastFile); 
       options.add(epith);
       options.add(ms);
       options.add(tukeysize);
       options.add(multitapersize);
       options.add(voxelwise_ev_numbers);
       options.add(voxelwiseEvFilenames);
     }
     catch(X_OptionError& e) {
       options.usage();
       cerr << endl << e.what() << endl;
     } 
     catch(std::exception &e) {
       cerr << e.what() << endl;
     }    
     
   }

}
#endif