meloptions.cc

/*  MELODIC - Multivariate exploratory linear optimized decomposition into
              independent components

    meloptions.cc - class for command line options

    Christian F. Beckmann, FMRIB Analysis Group

    Copyright (C) 1999-2013 University of Oxford */

/*  CCOPYRIGHT  */

#include <iostream>
#include <iomanip>
#include <fstream>
#include <stdlib.h>
#include <stdio.h>
#include "utils/log.h"
#include "newimage/newimageall.h"
#include "meloptions.h"

using namespace std;
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()){
			std::cout << "--keep_meanvol set, adding --varnorm advised, but not enforced" << std::endl;
  		}
  		if (filter.set()){
    		if (filtermix.set()){
      		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;
  		}
		if (insta_fn.value() > ""){
			varnorm.set_T(false);
		}

  		//in the case of indirect inputs, create the vector of input names here
  		if(!FslFileExists(inputfname.value().at(0))){
    		std::vector< string > tmpfnames;
    		ifstream fs(inputfname.value().at(0).c_str() );
		if (!fs.good()) {
		  cerr << "Error reading input file: " << inputfname.value().at(0).c_str() << endl;
		  exit(1);
		}
    		string cline;
    		while (fs.good()) {
		  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;
}

}