/*  qbootOptions.h

    Stamatios Sotiropoulos - FMRIB Image Analysis Group

    Copyright (C) 2010 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(qbootOptions_h)
#define qbootOptions_h

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

using namespace Utilities;

namespace ODFs {

class qbootOptions {
 public:
  static qbootOptions& getInstance();
  ~qbootOptions() { delete gopt; }
  
  Option<string> logdir;
  Option<bool> forcedir;
  Option<string> datafile;
  Option<string> maskfile;
  Option<string> bvecsfile;
  Option<string> bvalsfile;
  Option<string> qshellsfile;
  Option<int> modelnum;
  Option<int> lmax;
  Option<int> npeaks;
  Option<float> peak_threshold;
  FmribOption<int> peak_finder;
  Option<int> nsamples;
  Option<float> lambda;
  Option<float> delta;
  Option<float> alpha;
  Option<int> seed;
  Option<bool> gfa;
  Option<bool> savecoeff;
  Option<bool> savemeancoeff;
  Option<bool> verbose;
  Option<bool> help;
  
  //Explanation of possible Output files
  //a) If --savecoeff, then only the samples of the coefficients will be saved and no peaks. This is very fast, but the output files can be huge.
  //b) If --savecoeff --savemeancoeff, then only the mean ODF coefficients (across the samples) will be saved for each voxel and again no peaks. This is very fast and also requires less memory/storage.
  //c) If --savemeancoeff, then the mean ODF coefficients (across the samples) will be saved for each voxel, along with the ODF peaks.
  //d) If none of the above is set, only the ODF peaks are saved.


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

  OptionParser options; 
      
  static qbootOptions* gopt;
};

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

 inline qbootOptions::qbootOptions() :
   logdir(string("--ld,--logdir"), string("logdir"),
	 string("Output directory (default is logdir)"),
	 false, requires_argument),
   forcedir(string("--forcedir"),false,string("Use the actual directory name given - i.e. don't add + to make a new directory"),false,no_argument),
   datafile(string("-k,--data"), string("data"),
	      string("Data file"),
	      true, requires_argument),  
   maskfile(string("-m,--mask"), string("nodif_brain_mask"),
	    string("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), 
   qshellsfile(string("--q"), string(""),
   	     string("\tFile provided with multi-shell data. Indicates the number of directions for each shell"),
   	     false, requires_argument), 
   modelnum(string("--model"),2, 
   	    string("\tWhich model to use. 1=Tuch's ODFs, 2=CSA ODFs (default), 3=multi-shell CSA ODFs"), 
   	    false,requires_argument),
   lmax(string("--lmax"),4, 
   	    string("\tMaximum spherical harmonic oder employed (must be even, default=4)"), 
   	    false,requires_argument),
   npeaks(string("--npeaks"),2, 
   	    string("Maximum number of ODF peaks to be detected (default 2)"), 
   	    false,requires_argument),
   peak_threshold(string("--thr"),0.4, 
   	    string("\tMinimum threshold for a local maxima to be considered an ODF peak. Expressed as a fraction of the maximum ODF value (default 0.4)"), 
   	    false,requires_argument),
   peak_finder(string("--pf"),1, 
   	    string("\tWhich peak finder to use. 1=Discrete, 2=Semi-continuous (can be only used with lmax=4) (default=1)"), 
   	    false,requires_argument),
   nsamples(string("--ns,--nsamples"),50, 
	   string("Number of bootstrap samples (default is 50)"), 
	   false,requires_argument),
   lambda(string("--lambda"),0,  //use 0.006 for model1
	   string("Laplace-Beltrami regularization parameter (default is 0)"), 
	   false,requires_argument),
   delta(string("--delta"),0.01, 
	   string("\tSignal attenuation regularization parameter for models=2,3 (default is 0.01)"), 
	   false,requires_argument),
   alpha(string("--alpha"),0, 
	   string("\tLaplacian sharpening parameter for model=1 (default is 0, should be smaller than 1)"), 
	   false,requires_argument),
   seed(string("--seed"),8665904,
	   string("\tSeed for pseudo-random number generator"),
           false,requires_argument),
   gfa(string("--gfa"),false,
	   string("\tCompute a generalised FA, using the mean ODF in each voxel"),
           false,no_argument),
   savecoeff(string("--savecoeff"),false,
	   string("Save the ODF coefficients instead of the peaks. WARNING: These can be huge files, please use a few bootstrap samples and a low lmax!"),
           false,no_argument),
   savemeancoeff(string("--savemeancoeff"),false,
	   string("Save the mean ODF coefficients across all samples"),
           false,no_argument),
   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),
  
   options("qboot", "qboot --help (for list of options)\n")
   {
    
     try {
       options.add(logdir);
       options.add(forcedir);
       options.add(datafile);
       options.add(maskfile);
       options.add(bvecsfile);
       options.add(bvalsfile);
       options.add(qshellsfile);
       options.add(modelnum);
       options.add(lmax);
       options.add(npeaks);
       options.add(peak_threshold);
       options.add(peak_finder);
       options.add(nsamples);
       options.add(lambda);
       options.add(delta);
       options.add(alpha);
       options.add(seed);
       options.add(gfa);
       options.add(savecoeff);
       options.add(savemeancoeff);
       options.add(verbose);
       options.add(help);
     }
     catch(X_OptionError& e) {
       options.usage();
       cerr << endl << e.what() << endl;
     } 
     catch(std::exception &e) {
       cerr << e.what() << endl;
     }    
   }
}
#endif