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/* 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 */
#include <fstream>
#include <stdlib.h>
#include <stdio.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;
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// 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 {
pbsc.set_T(false);
cerr << "WARNING: melodic denoising is deprecated, please use fsl_regfilt instead!" <<endl;
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}
}
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(!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
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[]){
cout << endl <<"MELODIC Version " << version << endl;
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;
}
}