/*  FilmGlsOptions.cc

    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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    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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#define WANT_STREAM
#define WANT_MATH

#include <iostream>
#include <cstring>
#include <fstream>
#include <stdlib.h>
#include <stdio.h>
#include "FilmGlsOptions.h"
#include "utils/log.h"

using namespace Utilities;

namespace FILM {

FilmGlsOptions* FilmGlsOptions::gopt = NULL;

void FilmGlsOptions::parse_command_line(int argc, char** argv, Log& logger)
{
  if(argc<2){
    print_usage(argc,argv);
    exit(1);
  }
  
  int inp = 1;
  int n=1;
  string arg;
  char first;
  
  while (n<argc) {
    arg=argv[n];
  
    if (arg.size()<1) { n++; continue; }
    first = arg[0];
    if (first!='-' || inp==3) {
      if(inp == 1)
	gopt->inputfname = arg;
      else if(inp == 2)
	{
	  if(ac_only)
	    gopt->thresh = atof(argv[n]);
	  else
	    gopt->paradigmfname = arg;
	}
      else if(inp == 3 && !ac_only)
	gopt->thresh = atof(argv[n]);
      else throw Exception(("Mismatched argument "+arg).c_str());
      n++;
      inp++;
      continue;
    }
    
    // put options without arguments here
    if ( arg == "-help" ) {
      print_usage(argc,argv);
      exit(0);
    } else if ( arg == "-v" ) {
      gopt->verbose = true;
      n++;
      continue;
    } else if ( arg == "-ar" ) {
      gopt->fitAutoRegressiveModel = true;
      gopt->tukey = false;
      n++;
      continue;
    } else if ( arg == "-ac" ) {
      gopt->ac_only = true;
      n++;
      continue;
    } else if ( arg == "-pava" ) {
      gopt->pava = true;
      gopt->tukey = false;
      n++;
      continue;
    } else if ( arg == "-sa" ) {
      gopt->smoothACEst = true;
      n++;
      continue;    
    } else if ( arg == "-noest" ) {
      gopt->noest = true;
      n++;
      continue;
    } else if ( arg == "-output_pwdata" ) {
      gopt->output_pwdata = true;
      n++;
      continue;
    } 

    if (n+1>=argc) 
      throw Exception(("Lacking argument to option "+arg).c_str());

    // put options with 1 argument here
    if ( arg == "-ms") {
      gopt->ms = atoi(argv[n+1]);
      n+=2;
    } else if ( arg == "-mf") {
      gopt->meanInputFile = string(argv[n+1]);
      n+=2;
    } else if ( arg == "-mft") {
      gopt->minimumTimepointFile = string(argv[n+1]);
      n+=2;
    } else if ( arg == "-ven" ) {
      n++;
      int size=1;
	while(strspn(argv[n],"0123456789")==strlen(argv[n])) {
	 voxelwise_ev_numbers.resize(size++,atoi(argv[n++]));      
	 if (n>=argc) 
	   throw Exception("Not enough arguments for -ven option");
      }
    } else if ( arg == "-vef" ) {
      n++;
      if (n+(signed)voxelwise_ev_numbers.size()>=argc)
	throw Exception("Not enough arguments for -ven option");
      voxelwiseEvFilenames.resize(voxelwise_ev_numbers.size()); 
      for (int i=0;i<(int)voxelwise_ev_numbers.size();i++)
	voxelwiseEvFilenames[i]=argv[n++];
    } else if ( arg == "-rn" ) {
      gopt->datadir = argv[n+1];      
      n+=2;
    } else if ( arg == "-tukey" ) {
      gopt->tukeysize = atoi(argv[n+1]);
      gopt->tukey = true;
      n+=2;
    } else if ( arg == "-mt" ) {
      gopt->multitapersize = atoi(argv[n+1]);
      gopt->tukey = false;
      gopt->multitaper = true;
      n+=2;
    }
    else if ( arg == "-epith" ) {
      gopt->epith = atoi(argv[n+1]);      
      n+=2;
    } else throw Exception(("Unrecognised option "+arg).c_str());
  }  // while (n<argc)

  logger.makeDir(gopt->datadir);
  cout << "Log directory is: " << logger.getDir() << endl;
  for(int a = 0; a < argc; a++)
    logger.str() << argv[a] << " ";
  logger.str() << endl << "---------------------------------------------" << endl << endl;

  if (gopt->inputfname.size()<1) {
    print_usage(argc,argv);
    throw Exception("Input filename not found");
  }
  if (gopt->paradigmfname.size()<1 && !ac_only) {
    print_usage(argc,argv);
    throw Exception("Paradigm filename needs to be specified");
  }

}

void FilmGlsOptions::print_usage(int argc, char *argv[])
{
  cout << "Usage: " << argv[0] << " [options] <groupfile> [optional:<paradigmfile>] <thresh>\n\n"
       << "  Available options are:\n"
       << "        -sa                                (smooths auto corr estimates)\n"
       << "        -ms <num>                          (susan mask size)\n"
       << "        -epith <num>                       (set susan brightness threshold - otherwise it is estimated)\n"
       << "        -v                                 (outputs full data)\n"
       << "        -ven                               ( List of numbers indicating voxelwise EVs position in the design matrix, list corresponds in order to files in -vef. caution BETA option)\n" 
       << "        -vef                               ( List of 4D niftii files containing voxelwise EVs, list corresponds in order to numbers in -ven. caution BETA option)\n" 
       << "        -ac                                (perform autocorrelation estimation only)" 
       << "        -ar                                (fits autoregressive model - default " 
       << "is to use tukey with M=sqrt(numvols))\n"
       << "        -tukey <num>                       (uses tukey window to estimate autocorr with window size num - default "
       << "is to use tukey with M=sqrt(numvols))\n"
       << "        -mt <num>                          (uses multitapering with slepian tapers and num is the time-bandwidth product - default " 
       << "is to use tukey with M=sqrt(numvols))\n"
       << "        -pava                              (estimates autocorr using PAVA - default " 
       << "is to use tukey with M=sqrt(numvols))\n"
       << "        -noest                             (do not estimate auto corrs)\n"
       << "        -mf <file>                         (re-estimate mean_func baseline - for use with perfusion subtraction)\n"
       << "        -mft <file>                        (minimum timepoint file)\n"
       << "        -output_pwdata                     (output prewhitened data and average design matrix)\n" 
       << "        -rn <dir>                          (directory name to store results in, default is "
       << gopt->datadir << ")\n"
       << "        -help\n\n";
}

#ifndef NO_NAMESPACE
}
#endif