-
Christian Beckmann authoredChristian Beckmann authored
meloptions.h 10.67 KiB
/* MELODIC - Multivariate exploratory linear optimized decomposition into
independent components
meloptions.h - class for command line options
Christian F. Beckmann, FMRIB Image Analysis Group
Copyright (C) 1999-2002 University of Oxford */
/* CCOPYRIGHT */
#ifndef __MELODICOPTIONS_h
#define __MELODICOPTIONS_h
#include <string>
#include <strstream>
#include <iostream>
#include <fstream>
#include <stdlib.h>
#include <stdio.h>
#include "utils/options.h"
#include "utils/log.h"
#include "melodic.h"
using namespace Utilities;
namespace Melodic {
class MelodicOptions {
public:
static MelodicOptions& getInstance();
~MelodicOptions() { delete gopt; }
string version;
string binpath;
string logfname;
bool filtermode;
bool explicitnums;
Option<string> logdir;
Option<string> inputfname;
Option<string> outputfname;
Option<string> maskfname;
Option<bool> use_mask;
Option<bool> perf_bet;
Option<float> threshold;
Option<int> pca_dim;
Option<string> pca_est;
Option<int> numICs;
Option<string> approach;
Option<string> nonlinearity;
Option<bool> varnorm;
Option<string> segment;
Option<bool> tsmooth;
Option<float> epsilon;
Option<int> maxNumItt;
Option<int> maxRestart;
Option<string> mmthresh;
Option<bool> perf_mm;
Option<string> ICsfname;
Option<string> filtermix;
Option<string> filter;
Option<bool> genreport;
Option<float> tr;
Option<bool> logPower;
Option<bool> output_all;
Option<bool> output_unmix;
Option<bool> output_MMstats;
Option<bool> output_pca;
Option<bool> output_white;
Option<bool> output_origIC;
Option<bool> output_mean;
Option<bool> verbose;
Option<bool> vers;
Option<bool> copyright;
Option<bool> help;
Option<string> guessfname;
Option<string> paradigmfname;
Option<int> dummy;
Option<int> repeats;
Option<float> nlconst1;
Option<float> nlconst2;
Option<bool> remove_meanvol;
Option<bool> remove_endslices;
Option<bool> rescale_nht;
Option<bool> guess_remderiv;
Option<bool> temporal;
int retrystep;
void parse_command_line(int argc, char** argv, Log& logger, const string &p_version);
private:
MelodicOptions();
const MelodicOptions& operator=(MelodicOptions&);
MelodicOptions(MelodicOptions&);
OptionParser options;
static MelodicOptions* gopt;
void print_usage(int argc, char *argv[]);
void print_version();
void print_copyright();
void status();
};
inline MelodicOptions& MelodicOptions::getInstance(){
if(gopt == NULL)
gopt = new MelodicOptions();
return *gopt;
}
inline MelodicOptions::MelodicOptions() :
logdir(string("-o,--outdir"), string("melodic.log"),
string("output directory name\n"),
false, requires_argument),
inputfname(string("-i,--in"), string(""),
string("input file name"),
true, requires_argument),
outputfname(string("-O,--out"), string("melodic"),
string("output file name"),
false, requires_argument,false), maskfname(string("-m,--mask"), string(""),
string("file name of mask for thresholding"),
false, requires_argument),
use_mask(string("--nomask"), true,
string("switch off masking"),
false, no_argument),
perf_bet(string("--nobet"), true,
string("\tswitch off BET"),
false, no_argument),
threshold(string("--bgthreshold"), 0.00000001,
string("brain / non-brain threshold (only if --nobet selected)\n"),
false, requires_argument),
pca_dim(string("-d,--dim"), 0,
string("dimensionality reduction into #num dimensions (default: automatic estimation)"),
false, requires_argument),
pca_est(string("--dimest"), string("lap"),
string("use specific dim. estimation technique: lap, bic, mdl, aic, mean (default: lap)"),
false, requires_argument),
numICs(string("-n,--numICs"), -1,
string("numer of IC's to extract (for deflation approach)"),
false, requires_argument),
approach(string("-a,--approach"), string("symm"),
string("approach for ICA estimation: defl, symm"),
false, requires_argument),
nonlinearity(string("--nl"), string("pow3"),
string("\tnonlinearity: gauss, tanh, pow3, pow4"),
false, requires_argument),
varnorm(string("--vn,--varnorm"), true,
string("switch off variance normalisation"),
false, no_argument),
segment(string("--covarweight"), string(""),
string("voxel-wise weights for the covariance matrix (e.g. segmentation information)"),
false, requires_argument),
tsmooth(string("--spca"), false,
string("smooth the eigenvectors prior to IC decomposition"),
false, no_argument, false),
epsilon(string("--eps,--epsilon"), 0.00005,
string("minimum error change"),
false, requires_argument),
maxNumItt(string("--maxit"), 500,
string("\tmaximum number of iterations before restart"),
false, requires_argument),
maxRestart(string("--maxrestart"), 6,
string("maximum number of restarts\n"),
false, requires_argument),
mmthresh(string("--mmthresh"), string("0.5"),
string("threshold for Mixture Model based inference"),
false, requires_argument),
perf_mm(string("--no_mm"), true,
string("\tswitch off mixture modelling on IC maps\n "),
false, no_argument),
ICsfname(string("--ICs"), string(""),
string("\tfilename of the IC components file for mixture modelling"),
false, requires_argument),
filtermix(string("--mix"), string(""),
string("\tmixing matrix for mixture modelling / filtering"),
false, requires_argument),
filter(string("-f,--filter"), string(""),
string("component numbers to remove\n "),
false, requires_argument),
genreport(string("--report"), false,
string("generate Melodic web report"),
false, no_argument),
tr(string("--tr"), 0.0,
string("\tTR in seconds"),
false, requires_argument),
logPower(string("--logPower"), false,
string("calculate log of power for frequency spectrum\n"),
false, no_argument),
output_all(string("--Oall"), false, string("output everything"),
false, no_argument),
output_unmix(string("--Ounmix"), false,
string("output unmixing matrix"),
false, no_argument),
output_MMstats(string("--Ostats"), false,
string("output thresholded maps and probability maps"),
false, no_argument),
output_pca(string("--Opca"), false,
string("\toutput PCA results"),
false, no_argument),
output_white(string("--Owhite"), false,
string("output whitening/dewhitening matrices"),
false, no_argument),
output_origIC(string("--Oorig"), false,
string("\toutput the original ICs"),
false, no_argument),
output_mean(string("--Omean"), false,
string("\toutput mean volume\n"),
false, no_argument),
verbose(string("-v,--verbose"), false,
string("switch on diagnostic messages"),
false, no_argument),
vers(string("-V,--version"), false,
string("prints version information"),
false, no_argument),
copyright(string("--copyright"), false,
string("prints copyright information"),
false, no_argument),
help(string("-h,--help"), false,
string("prints this help message"),
false, no_argument),
guessfname(string("-g,--guess"), string(""),
string("file name of guess of mixing matrix"),
false, requires_argument, false),
paradigmfname(string("-p,--paradigm"), string(""),
string("file name of FEAT paradigm file"),
false, requires_argument, false),
dummy(string("--dummy"), 0,
string("number of dummy volumes"),
false, requires_argument,false),
repeats(string("--repeats"), 1,
string("number of repeats (multistart)"),
false, requires_argument, false),
nlconst1(string("--nl1,--nlconst1"), 1.0,
string("nonlinear constant 1"),
false, requires_argument, false),
nlconst2(string("--nl2,--nlconst2"), 1.0,
string("nonlinear constant 2"),
false, requires_argument, false),
remove_meanvol(string("--keepmeanvol"), true,
string("do not subtract mean volume"),
false, no_argument, false),
remove_endslices(string("--remEndslices"), false,
string("delete end slices (motion correction artefacts)"),
false, no_argument,false),
rescale_nht(string("--rescale_nht"), true,
string("switch off map rescaling after mixture-modelling"),
false, no_argument,false),
guess_remderiv(string("--remderiv"), false,
string("removes every second entry in paradigm file (EV derivatives)"),
false, no_argument, false),
temporal(string("--temporal"), false,
string("perform temporal ICA"),
false, no_argument, false),
retrystep(3),
options(string(""),
string(" melodic -i <filename> <options>")+
string("\n \t \t to run melodic")+
string("\n melodic -i <filename> --mix=melodic_mix")+ string(" --filter=\"string of component numbers\"")+
string("\n \t \t to remove estimated ICs from input")+
string("\n melodic -i <filename> --ICs=melodic_IC")+
string(" --mix=melodic_mix <options>")+
string("\n \t \t to run Mixture Model based inference on estimated ICs")+
string("\n melodic --help "))
{
try {
options.add(logdir);
options.add(inputfname);
options.add(outputfname);
options.add(guessfname);
options.add(maskfname);
options.add(use_mask);
options.add(perf_bet);
options.add(threshold);
options.add(pca_dim);
options.add(pca_est);
options.add(numICs);
options.add(approach);
options.add(nonlinearity);
options.add(varnorm);
options.add(segment);
options.add(tsmooth);
options.add(epsilon);
options.add(maxNumItt);
options.add(maxRestart);
options.add(mmthresh);
options.add(perf_mm);
options.add(ICsfname);
options.add(filtermix);
options.add(filter);
options.add(genreport);
options.add(tr);
options.add(logPower);
options.add(output_all);
options.add(output_unmix);
options.add(output_MMstats);
options.add(output_pca);
options.add(output_white);
options.add(output_origIC);
options.add(output_mean);
options.add(verbose);
options.add(vers);
options.add(copyright);
options.add(help);
options.add(guessfname);
options.add(paradigmfname);
options.add(dummy);
options.add(repeats);
options.add(nlconst1);
options.add(nlconst2);
options.add(remove_meanvol);
options.add(remove_endslices);
options.add(rescale_nht);
options.add(guess_remderiv);
options.add(temporal);
}
catch(X_OptionError& e) {
options.usage();
cerr << endl << e.what() << endl;
}
catch(std::exception &e) {
cerr << e.what() << endl;
}
}
}
#endif