/*  gsoptions.h

    Mark Woolrich, Tim Behrens - FMRIB Image Analysis Group

    Copyright (C) 2002 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(GsOptions_h)
#define GsOptions_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 Gs {

  class GsOptions {
  public:
    static GsOptions& getInstance();
    ~GsOptions() { delete gopt; }
  
    Option<bool> verbose;
    Option<int> debuglevel;
    Option<bool> timingon;
    Option<bool> help;
    Option<string> copefile;
    Option<string> varcopefile;
    Option<string> dofvarcopefile;
    Option<string> maskfile;
    Option<string> designfile;
    Option<string> covsplitfile;
    Option<string> tcontrastsfile;
    Option<string> fcontrastsfile;
    Option<string> logdir;
    Option<int> njumps;
    Option<int> burnin;
    Option<int> sampleevery;
    Option<float> zlowerthreshold;
    Option<float> zupperthreshold;
    Option<bool> fixmeanfortfit;
    Option<bool> infer_outliers;
    Option<bool> no_pe_output;
    Option<string> runmode;
    Option<int> seed;
    Option<vector<int> > voxelwise_ev_numbers;
    Option<vector<string> > voxelwise_ev_filenames;
    Option<float> sigma_smooth_flame2_dofs;
    Option<float> sigma_smooth_globalproboutlier;
    Option<int> io_niters;
    Option<bool> outputDof;
  
    void parse_command_line(int argc, char** argv, Log& logger);
  
  private:
    GsOptions();  
    const GsOptions& operator=(GsOptions&);
    GsOptions(GsOptions&);

    OptionParser options; 
      
    static GsOptions* gopt;
  
  };

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

  inline GsOptions::GsOptions() :
    verbose(string("-v,-V,--verbose"), false, 
	    string("switch on diagnostic messages"), 
	    false, no_argument),
    debuglevel(string("--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),
    copefile(string("--cope,--copefile"), string("cope"),
	     string("cope regressor data file"),
	     true, requires_argument),  
    varcopefile(string("--vc,--vcope,--varcope,--varcopefile"), string(""),
		string("varcope weightings data file"),
		false, requires_argument),
    dofvarcopefile(string("--dvc,--dvcope,--dofvarcope,--dofvarcopefile"), string(""),
		   string("DOF data file for the varcope data"),
		   false, requires_argument),
    maskfile(string("--mask,--maskfile"), string(""),
	     string("mask file"),
	     true, requires_argument),
    designfile(string("--dm,--designfile"), string("design.mat"),
	       string("design matrix file"),
	       true, requires_argument), 
    covsplitfile(string("--cs,--csf,--covsplitfile"), string("design.gs"),
		 string("file containing an ASCII matrix specifying the groups the covariance is split into"),
		 true, requires_argument),
    tcontrastsfile(string("--tc,--tcf,--tcontrastsfile"), string("design.con"),
		   string("file containing an ASCII matrix specifying the t contrasts"),
		   true, requires_argument),  
    fcontrastsfile(string("--fc,--fcf,--fcontrastsfile"), string(""),
		   string("file containing an ASCII matrix specifying the f contrasts"),
		   false, requires_argument),  
    logdir(string("--ld,--logdir"), string("logdir"),
	   string("log directory"),
	   false, requires_argument),  
    njumps(string("--nj,--njumps"), 5000,
	   string("Num of jumps to be made by MCMC"),
	   false, requires_argument),
    burnin(string("--bi,--burnin"), 500,
	   string("Num of jumps at start of MCMC to be discarded"),
	   false, requires_argument),
    sampleevery(string("--se,--sampleevery"), 1,
		string("Num of jumps for each sample"),
		false, requires_argument),
    zlowerthreshold(string("--zlt"), 0,
		    string("Absolute value of lower threshold on FLAME stage 1 z-stats, used to see which voxels are passed to FLAME stage 2"),
		    false, requires_argument),
    zupperthreshold(string("--zut"), 0,
		    string("Absolute value of upper threshold on FLAME stage 1 z-stats, used to see which voxels are passed to FLAME stage 2"),
		    false, requires_argument),
    fixmeanfortfit(string("--fm,--fixmean"), false, 
		   string("Fix mean for tfit"), 
		   false, no_argument),
    infer_outliers(string("--io,--inferoutliers"), false, 
		   string("Infer outliers -- note that does not apply to fixed effects"), 
		   false, no_argument),
    no_pe_output(string("--npo,--nopeoutput"), false, 
		   string("Do not output PE files"), 
		   false, no_argument),
    runmode(string("--runmode"), string(""), 
	    string("Inference to perform: runmode=fe (fixed effects), runmode=ols (mixed effects - OLS), runmode=flame1 (mixed effects - FLAME stage 1), runmode=flame12 (mixed effects - FLAME stage 1+2)"), 
	    true, requires_argument),
    seed(string("--seed"), 10, 
	 string("seed for pseudo random number generator"), 
	 false, requires_argument),
    voxelwise_ev_numbers(string("--voxelwise_ev_numbers,--ven"), vector<int>(), 
	 string("List of numbers indicating voxelwise EVs position in the design matrix (list corresponds in order to files in voxelwise_ev_filenames)"), 
	 false, requires_argument),
    voxelwise_ev_filenames(string("--voxelwise_ev_filenames,--vef"), vector<string>(), 
	 string("List of 4D niftii files containing voxelwise EVs (list corresponds in order to numbers in voxelwise_ev_numbers)"), 
	 false, requires_argument),
    sigma_smooth_flame2_dofs(string("--sdof,--sigma_dofs"), 1,
				   string("sigma (in mm) to use for Gaussian smoothing the DOFs in FLAME 2. Default is 1mm, -1 indicates no smoothing"),
	 false, requires_argument),
    sigma_smooth_globalproboutlier(string("--so"), -1,
				   string(""),
	 false, requires_argument),
    io_niters(string("--ioni"), 12,
				   string("Number of max iterations to use when inferring outliers. Default is 12."),
	 false, requires_argument),
    outputDof(string("--outputdof"), false, 
	    string("output dof for lower-level compatibility usage"), 
	    false, no_argument),
    options("flameo"," flameo --cope=filtered_func_data --mask=mask --dm=design.mat --tc=design.con --cs=design.grp --runmode=ols\n flameo --cope=filtered_func_data --varcope=var_filtered_func_data --mask=mask --dm=design.mat --tc=design.con --cs=design.grp --runmode=flame1")
  {
    try {
      options.add(verbose);
      options.add(debuglevel);
      options.add(timingon);
      options.add(help);
      options.add(copefile);
      options.add(varcopefile);
      options.add(dofvarcopefile);
      options.add(maskfile);
      options.add(designfile);
      options.add(tcontrastsfile);
      options.add(fcontrastsfile);
      options.add(covsplitfile);
      options.add(logdir);
      options.add(njumps);
      options.add(burnin);
      options.add(sampleevery);
      options.add(zlowerthreshold);
      options.add(zupperthreshold);
      options.add(fixmeanfortfit);
      options.add(infer_outliers);
      options.add(no_pe_output);
      options.add(runmode);
      options.add(seed);
      options.add(voxelwise_ev_numbers);
      options.add(voxelwise_ev_filenames);
      options.add(sigma_smooth_flame2_dofs);
      options.add(sigma_smooth_globalproboutlier);
      options.add(io_niters);
      options.add(outputDof);
    }
    catch(X_OptionError& e) {
      options.usage();
      cerr << endl << e.what() << endl;
    } 
    catch(std::exception &e) {
      cerr << e.what() << endl;
    }    
     
  }
}

#endif