/*  MELODIC - Multivariate exploratory linear optimized decomposition into 
              independent components
    
    meloptions.cc - class for command line options

    Christian F. Beckmann, FMRIB Image Analysis Group
     
    Copyright (C) 1999-2008 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
    
    
    LICENCE
    
    FMRIB Software Library, Release 5.0 (c) 2012, The University of
    Oxford (the "Software")
    
    The Software remains the property of the University of Oxford ("the
    University").
    
    The Software is distributed "AS IS" under this Licence solely for
    non-commercial use in the hope that it will be useful, but in order
    that the University as a charitable foundation protects its assets for
    the benefit of its educational and research purposes, the University
    makes clear that no condition is made or to be implied, nor is any
    warranty given or to be implied, as to the accuracy of the Software,
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    You are not permitted under this Licence to use this Software
    commercially. Use for which any financial return is received shall be
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    by or on behalf of Licensee to third parties or (2) use of the
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    developing software products for sale or license to a third party or
    (3) use of the Software or any derivative of it for research with the
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#include <iostream>
#include <iomanip>
#include <fstream>
#include <stdlib.h>
#include <stdio.h>
#include "utils/log.h"
#include "meloptions.h"
#include "newimage/newimageall.h"

using namespace Utilities;
using namespace NEWIMAGE;

namespace Melodic {

MelodicOptions* MelodicOptions::gopt = NULL;

  void MelodicOptions::parse_command_line(int argc, char** argv, Log& logger, 
		const string &p_version){
  		//set version number and some other stuff
  		version = p_version;
  		filtermode = false;
  		explicitnums = false;
  		logfname = string("log.txt");

  		// work out the path to the $FSLDIR/bin directory
  		if(getenv("FSLDIR")!=0){
    		binpath = (string) getenv("FSLDIR") + "/bin/";
  		} else{
    		binpath = argv[0];
    		binpath = binpath.substr(0,binpath.length()-7);
  		}

  		// parse once to establish log directory name
  		for(int a = options.parse_command_line(argc, argv); a < argc; a++);

  		// act on simple command line arguments
  		if(help.value()){
      	print_usage(argc, argv);
      	exit(0);
    	} 
  		if(vers.value()){
      	print_version();
      	cout << endl;
      	exit(0);
    	} 
  		if(copyright.value()){
      	print_copyright();
      	exit(0);
    	} 
  		if(! options.check_compulsory_arguments()){
				print_usage(argc, argv);
      	exit(2);
    	}     

  		// check for invalid values
  		if (inputfname.value().size()<1) {
    		cerr << "ERROR:: Input volume not found\n\n";
    		print_usage(argc,argv);
    		exit(2);
  		}
  		if (approach.value() != "symm" && approach.value() != "defl"  && 
      	approach.value() != "jade" && approach.value() != "maxent" &&
      	approach.value() != "tica" && approach.value() != "concat"){
    			cerr << "ERROR:: unknown approach \n\n";
    			print_usage(argc,argv);
    			exit(2);
  			}
  		if (nonlinearity.value() != "pow3" && nonlinearity.value() != "pow4" && 
				nonlinearity.value() != "tanh"  && nonlinearity.value() != "gauss" ){
    			cerr << "ERROR:: unknown nonlinearity \n\n";
    			print_usage(argc,argv);
    			exit(2);
  			}
  		if (maxNumItt.value() < 1){
    		cerr << "ERROR:: maxItt too small \n\n";
    		print_usage(argc,argv);
    		exit(2);
  		}
  		if (epsilon.value() < 0.000000001){
    		cerr << "ERROR:: epsilon too small  \n\n";
    		print_usage(argc,argv);
    		exit(2);    
  		}
  		if (epsilon.value() >= 0.01){
    		cerr << "ERROR:: epsilon too large  \n\n";
    		print_usage(argc,argv);
    		exit(2);
  		}
  		if (nlconst1.value() <= 0){
    		cerr << "ERROR:: nlconst1 negative  \n\n";
    		print_usage(argc,argv);
    		exit(2);
  		}
  		if (!remove_meanvol.value()){
    		varnorm.set_T(false);
  		}
  		if (filter.value().length()>0){
    		if (filtermix.value().length()<0){
      		cerr << "ERROR:: no mixing matrix for filtering (use --mix='filename') \n\n"; 
      		print_usage(argc,argv);
      		exit(2);
    		} else {   
					temporal.set_T(false);
      		filtermode = true;
      		varnorm.set_T(false);
					pbsc.set_T(false);
					cerr << "WARNING: melodic denoising is deprecated, please use fsl_regfilt instead!" <<endl;
    		} 
  		}
  		if (output_all.value()){
    		output_unmix.set_T(true);
    		output_MMstats.set_T(true);
    		output_pca.set_T(true);
    		output_white.set_T(true);
    		output_origIC.set_T(true);
    		output_mean.set_T(true);
  		}
  		if (output_pca.value()){
    		output_white.set_T(true);
  		}
  		if(threshold.value()>=1){
    		threshold.set_T(threshold.value()/100);
    		if(threshold.value()>=1){
      		cerr << "ERROR:: threshold level not a percentage value  \n\n";
      		print_usage(argc,argv);
      		exit(2);
    		}
  		}
  		if (nlconst2.value() <= 0){
    		cerr << "ERROR:: nlconst2 negative  \n\n";
    		print_usage(argc,argv);
    		exit(2);
  		}
  		if (dummy.value() < 0){
    		cerr << "ERROR:: negative dummy value  \n\n";
    		print_usage(argc,argv);
    		exit(2);
  		}
  		if (repeats.value() < 1){
    		cerr << "ERROR:: repeats < 1 \n\n";
    		print_usage(argc,argv);
    		exit(2);
  		}
  		if (numICs.value() > 0){
    		explicitnums = true;
  		}
  
  		//in the case of indirect inputs, create the vector of input names here
  		if(!fsl_imageexists(inputfname.value().at(0))){
    		std::vector< string > tmpfnames;
    		ifstream fs(inputfname.value().at(0).c_str());
    		string cline;
    		while (!fs.eof()) {
		  getline(fs,cline);
		  if(cline.length()>0) {
		    while ( cline.find(' ') != cline.npos )
		      cline.erase( cline.find(' '),1);
		    tmpfnames.push_back(cline);
		  }
    		}	
    		fs.close();
    		inputfname.set_T(tmpfnames);
  		}

  		//transform inputfnames to their basenames
  		std::vector< string > tmpfnames;
  		for(int ctr=0; ctr < (int)inputfname.value().size() ; ctr++){
    		string basename;
    		basename = inputfname.value().at(ctr);
    		make_basename(basename);
    		tmpfnames.push_back(basename);
  		}
  		inputfname.set_T(tmpfnames);

  		//create melodic directory name
  		if(logdir.value()==string("log.txt")){
    		logdir.set_T(string(inputfname.value().at(0)+".ica"));
    		logger.makeDir(logdir.value(),logfname);
 			} else{
    		// setup logger directory
    		system(("mkdir "+ logdir.value() + " 2>/dev/null").c_str());
    		logger.setDir(logdir.value(),logfname);
  		}
  		message(endl << "Melodic Version " << version << endl << endl);

  		// parse again so that options are logged
  		for(int a = 0; a < argc; a++)
    		logger.str() << argv[a] << " ";
  			logger.str() << endl << "---------------------------------------------" 
					<< endl << endl;
  			message("Melodic results will be in " << logger.getDir() << endl << endl);
    }

void MelodicOptions::print_usage(int argc, char *argv[]){
 // print_copyright();
  options.usage();
  /* cout << "Usage: " << argv[0] << " ";
    Have own usage output here
  */
}

void MelodicOptions::print_version(){
	cout << endl <<"MELODIC Version " << version << endl;
  cout.flush();
}

void MelodicOptions::print_copyright(){
  cout << endl << title << endl;
  cout.flush();
}

void MelodicOptions::status(){
  cout << " version = " << version << endl;
 
  cout << " logdir = "  << logdir.value() << endl;
  cout << " inputfname = "  << inputfname.value().at(0) << inputfname.value().at(inputfname.value().size()-1) << endl;
  cout << " outputfname = "  << outputfname.value() << endl;
  cout << " guessfname = "  << guessfname.value() << endl;
  cout << " maskfname = "  << maskfname.value() << endl;
  cout << " paradigmfname = "  <<  paradigmfname.value() << endl;
  cout << " nonlinearity = "  << nonlinearity.value() << endl;
  cout << " approach = "  << approach.value() << endl;
  
  cout << " pca_dim = "  << pca_dim.value() << endl;
  cout << " segment = "  << segment.value() << endl;
  cout << " numICs = "  << numICs.value() << endl;
  cout << " maxNumItt = "  << maxNumItt.value() << endl;
  cout << " maxRestart = "  << maxRestart.value() << endl;
  cout << " dummy = "  << dummy.value() << endl;
  cout << " repeats = "  << repeats.value() << endl;
  cout << " nlconst1 = "  << nlconst1.value() << endl;
  cout << " nlconst2 = "  << nlconst2.value() << endl;
  cout << " smooth_probmap = "  << smooth_probmap.value() << endl;
  cout << " epsilon = "  << epsilon.value() << endl;
  cout << " threshold = "  << threshold.value() << endl;
  
  cout << " help = "  << help.value() << endl;
  cout << " verbose = "  << verbose.value() << endl;
  cout << " vers = "  << vers.value() << endl;
  cout << " copyright = "  << copyright.value() << endl;
  cout << " perf_bet = "  << perf_bet.value() << endl;
  cout << " remove_meanvol = "  << remove_meanvol.value() << endl;
  cout << " remove_endslices  = " << remove_endslices.value() << endl;
  cout << " output_pca = "  << output_pca.value() << endl;
  cout << " output_white = "  << output_white.value() << endl;
  cout << " output_mean = "  << output_mean.value() << endl;
  cout << " use_mask = "  << use_mask.value() << endl;
  cout << " output_unmix = "  << output_unmix.value() << endl;
  cout << " guess_remderiv = "  << guess_remderiv.value() << endl;
  cout << " filter  = " << filter.value() << endl;
  cout << " logPower  = " << logPower.value() << endl;
}

}