/*  ranopts.h

    Matthew Webster, Tim Behrens & Steve Smith (FMRIB) & Tom Nichols (UMich)

    Copyright (C) 2008-2010 University of Oxford  */

/*  Part of FSL - FMRIB's Software Library
    http://www.fmrib.ox.ac.uk/fsl
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    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(ranopts_h)
#define ranopts_h

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

using namespace Utilities;

namespace RANDOMISE {

class ranopts {
 public:
  static ranopts& getInstance();
  ~ranopts() { delete gopt; }
  
  Option<bool> demean_data;
  Option<bool> one_samp;
  Option<string> in_fileroot;
  Option<string> maskname;
  Option<string> out_fileroot;
  Option<string> dm_file;
  Option<string> tc_file;
  Option<string> fc_file;
  Option<string> gp_file;
  Option<string> effectiveDesignFile;
  Option<bool> how_many_perms;
  Option<bool> parallelData;
  Option<int> n_perm;
  Option<bool> voxelwiseOutput;
  Option<bool> doFOnly;
  Option<bool> tfce;
  Option<bool> tfce2D;
  Option<float> cluster_thresh;
  Option<float> clustermass_thresh;
  Option<float> f_thresh;
  Option<float> fmass_thresh;
  Option<float> tfce_height;
  Option<float> tfce_delta;
  Option<float> tfce_size;
  Option<int> tfce_connectivity;
  Option<float> var_sm_sig;
  Option<bool> help;
  Option<bool> verbose;
  Option<bool> cluster_norm;
  Option<bool> outputRaw;
  Option<bool> outputTextPerm;
  Option<bool> outputTextNull;
  Option<bool> output_permstat;
  Option<bool> disableNonConstantMask;
  Option<int> randomSeed;
  Option<vector<int> > voxelwise_ev_numbers;
  Option<vector<string> > voxelwise_ev_filenames;
  Option<int> nMultiVariate;
  Option<bool> isDebugging;
  Option<int> confoundMethod;
  Option<bool> detectNullSubjects;
  Option<bool> permuteBlocks;
  Option<bool> verbose_old;
  Option<int>  skipTo;
  Option<bool> outputGlm;

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

  OptionParser options; 
      
  static ranopts* gopt;
  
};

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

 inline ranopts::ranopts() :
   demean_data(string("-D"), false,
	string("\tdemean data temporally before model fitting"),
	false, no_argument),
   one_samp(string("-1"), false,
	    string("\tperform 1-sample group-mean test instead of generic permutation test"),
	    false, no_argument),
   in_fileroot(string("-i"), "",
       string("~<input>\t4D input image"),
       true, requires_argument),
   maskname(string("-m"), "",
       string("~<mask>\tmask image"),
       false, requires_argument),
   out_fileroot(string("-o"), string(""),
	    string("~<out_root>\toutput file-rootname"),
	    true, requires_argument),  
   dm_file(string("-d"), string(""),
	    string("~<design.mat>\tdesign matrix file"),
	    false, requires_argument),  
   tc_file(string("-t"), string(""),
	    string("~<design.con>\tt contrasts file"),
	    false, requires_argument),  
   fc_file(string("-f"), string(""),
            string("~<design.fts>\tf contrasts file"),
	   false, requires_argument),  
   gp_file(string("-e"), string(""),
            string("~<design.grp>\texchangeability block labels file"),
	   false, requires_argument),  
   effectiveDesignFile(string("--effective_design"), string(""),
            string("~<design2.mat>\talternative design for determining valid permutations"),
	   false, requires_argument),
   how_many_perms(string("-q"), false,
	    string("\tprint out how many unique permutations would be generated and exit"),
	    false, no_argument), 
   parallelData(string("-Q"), false,
	    string("\tprint out information required for parallel mode and exit"),
	    false, no_argument),
   n_perm(string("-n"), 5000,
	    string("~<n_perm>\tnumber of permutations (default 5000, set to 0 for exhaustive)"),
	    false, requires_argument),  
   voxelwiseOutput(string("-x"),false,
	    string("\toutput voxelwise (corrected and uncorrected) p-value images"),
		 false, no_argument),  
   doFOnly(string("--fonly"), false, 
	   string("\tcalculate f-statistics only"), 
	   false, no_argument),
   tfce(string("-T"), false, 
	   string("\tcarry out Threshold-Free Cluster Enhancement"), 
	   false, no_argument),
   tfce2D(string("--T2"), false, 
	   string("\tcarry out Threshold-Free Cluster Enhancement with 2D optimisation (e.g. for TBSS data); H=2, E=1, C=26"), 
	   false, no_argument),
   cluster_thresh(string("-c"), -1,
	  string("~<thresh>\tcarry out cluster-based thresholding"),
	  false, requires_argument),
   clustermass_thresh(string("-C"), -1,
	  string("~<thresh>\tcarry out cluster-mass-based thresholding"),
	  false, requires_argument),
   f_thresh(string("-F"), -1,
	  string("~<thresh>\tcarry out f cluster thresholding"),
	  false, requires_argument),
   fmass_thresh(string("-S"), -1,
	  string("~<thresh>\tcarry out f cluster-mass thresholding"),
	  false, requires_argument),
   tfce_height(string("--tfce_H"), 2, string("~<H>\tTFCE height parameter (default=2)"), false, requires_argument),
   tfce_delta(string("--tfce_D"), 1, string("~<H>\tTFCE delta parameter overide"), false, requires_argument),
   tfce_size(string("--tfce_E"), 0.5, string("~<E>\tTFCE extent parameter (default=0.5)"), false, requires_argument),
   tfce_connectivity(string("--tfce_C"), 6, string("~<C>\tTFCE connectivity (6 or 26; default=6)"), false, requires_argument),
   var_sm_sig(string("-v"), 0,
	    string("~<std>\tuse variance smoothing for t-stats (std is in mm)"),
	     false, requires_argument),
   help(string("-h,--help"), false,
	string("display this message"),
	false, no_argument),
   verbose(string("--quiet"), true, 
	   string("\tswitch off diagnostic messages"),
	   false, no_argument),
   cluster_norm(string("--twopass"), false, 
	   string("carry out cluster normalisation thresholding"), 
		false, no_argument),
   outputRaw(string("-R"), false, 
	   string("\toutput raw ( unpermuted ) statistic images"), 
		false, no_argument),
   outputTextPerm(string("-P"), false, 
	   string("\toutput permutation vector text file"), 
		false, no_argument),
   outputTextNull(string("-N"), false, 
	   string("\toutput null distribution text files"), 
		false, no_argument),
   output_permstat(string("--permout"), false, 
	   string("\toutput permuted tstat"), 
		false, no_argument,false),
   disableNonConstantMask(string("--norcmask"), false, 
	   string("don't remove constant voxels from mask"), 
		false, no_argument),
   randomSeed(string("--seed"),0,
	    string("~<seed>\tspecific integer seed for random number generator"),
		 false, requires_argument),
   voxelwise_ev_numbers(string("--vxl"), 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."), 
         false, requires_argument),
   voxelwise_ev_filenames(string("--vxf"), vector<string>(), 
         string("\tlist of 4D images containing voxelwise EVs (list order corresponds to numbers in vxl option). caution BETA option."), 
         false, requires_argument),
   nMultiVariate(string("--multi"),1,
	    string("~<dim>\tmultivariate dimension (default 1). caution BETA option."),
		 false, requires_argument, false),
   isDebugging(string("--debug"), false, 
	   string("\tOutput debug information"),
	       false, no_argument,false),
   confoundMethod(string("-U"),1,
	    string("~<mode>\tconfound mode. 0: Kennedy Y_a on X_a (old) 1: Freedman-Lane Y_a on X|Z (default) 2: Y on X|Z. 3: ter Braak Y_aFull on X|Z Caution BETA option."),
		  false, requires_argument, false),
   detectNullSubjects(string("--detectNull"), false, 
	   string("attempt to detect uninformative rows in the effective regressor and not permute them"), 
		      false, no_argument, false),
   permuteBlocks(string("--permuteBlocks"), false, 
	   string("permute exchangeability blocks. Caution BETA option"), 
		 false, no_argument),
   verbose_old(string("-V"), false, 
	   string("\tswitch on diagnostic messages (deprecated: now always on unless quiet)"),
	       false, no_argument, false),
   skipTo(string("--skipTo"),0,
	    string("~<number>\tdo only contrast<number>. A setting of 0 will do all contrasts, numbering starts with f- and then t-contrasts"),
		false, requires_argument, false),
   outputGlm(string("--glm_output"), false, 
	   string("output glm information for t-statistics ( unpermuted case only )"), 
		false, no_argument),

   options("randomise v2.9", "randomise -i <input> -o <output> -d <design.mat> -t <design.con> [options]")
     {
    
     try {
       options.add(demean_data);
       options.add(one_samp);
       options.add(in_fileroot);
       options.add(maskname);
       options.add(out_fileroot);
       options.add(dm_file);
       options.add(tc_file);
       options.add(fc_file);
       options.add(gp_file);
       options.add(effectiveDesignFile);
       options.add(how_many_perms);
       options.add(parallelData);
       options.add(n_perm);    
       options.add(voxelwiseOutput);   
       options.add(doFOnly);
       options.add(tfce);
       options.add(tfce2D);
       options.add(cluster_thresh);
       options.add(clustermass_thresh);
       options.add(f_thresh);     
       options.add(fmass_thresh);
       options.add(var_sm_sig);
       options.add(help);
       options.add(verbose);
       options.add(cluster_norm);
       options.add(outputRaw);
       options.add(outputTextPerm);
       options.add(outputTextNull);
       options.add(output_permstat);
       options.add(disableNonConstantMask);
       options.add(randomSeed);
       options.add(tfce_height);   
       options.add(tfce_delta);  
       options.add(tfce_size);     
       options.add(tfce_connectivity); 
       options.add(voxelwise_ev_numbers);
       options.add(voxelwise_ev_filenames); 
       options.add(nMultiVariate); 
       options.add(isDebugging);
       options.add(confoundMethod);
       options.add(detectNullSubjects);
       options.add(permuteBlocks);
       options.add(verbose_old);
       options.add(skipTo);
       options.add(outputGlm);
     }
     catch(X_OptionError& e) {
       options.usage();
       cerr << endl << e.what() << endl;
     } 
     catch(std::exception &e) {
       cerr << e.what() << endl;
     }    
     
   }
}

#endif

