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/* MELODIC - Multivariate exploratory linear optimized decomposition into
independent components
meloptions.h - class for command line options
Christian F. Beckmann, FMRIB Analysis Group
Copyright (C) 1999-2013 University of Oxford */
/* CCOPYRIGHT */
#ifndef __MELODICOPTIONS_h
#define __MELODICOPTIONS_h
#include <string>
#include <strstream>
#include <iostream>
#include <iomanip>
#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< std::vector<string> > inputfname;
Option<string> outputfname;
Option<string> maskfname;
Option<bool> use_mask;
Option<bool> update_mask;
Option<bool> perf_bet;
Option<float> threshold;
Option<int> pca_dim;
Option<string> pca_est;
Option<bool> joined_whiten;
Option<bool> joined_vn;
Option<bool> dr_pca;
Option<bool> migp;
Option<int> migpN;
Option<bool> migp_shuffle;
Option<int> migp_factor;
Option<bool> dr;
Option<bool> dr_out;
Option<float> vn_level;
Option<int> numICs;
Option<string> approach;
Option<string> nonlinearity;
Option<bool> varnorm;
Option<bool> varnorm2;
Option<bool> pbsc;
Option<bool> pspec;
Option<string> segment;
Option<bool> tsmooth;
Option<float> epsilon;
Option<float> epsilonS;
Option<int> maxNumItt;
Option<int> maxRestart;
Option<int> rank1interval;
Option<string> mmthresh;
Option<bool> perf_mm;
Option<string> ICsfname;
Option<string> filtermix;
Option<string> smodename;
Option<string> filter;
Option<bool> genreport;
Option<string> guireport;
Option<string> bgimage;
Option<float> tr;
Option<bool> logPower;
Option<bool> addsigchng;
Option<bool> allPPCA;
Option<bool> varplots;
Option<bool> varvals;
Option<string> fn_Tdesign;
Option<string> fn_Tcon;
Option<string> fn_TconF;
Option<string> fn_Sdesign;
Option<string> fn_Scon;
Option<string> fn_SconF;
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<bool> debug;
Option<string> guessfname;
Option<string> paradigmfname;
Option<string> axials_str;
Option<int> dummy;
Option<int> repeats;
Option<int> seed;
Option<float> nlconst1;
Option<float> nlconst2;
Option<float> smooth_probmap;
Option<string> insta_fn;
Option<bool> remove_meanvol;
Option<bool> remove_meantc;
Option<bool> remove_endslices;
Option<bool> rescale_nht;
Option<bool> guess_remderiv;
Option<bool> temporal;
Option<float> retryfactor;
Option<int> econ;
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("log.txt"),
string("output directory name\n"),
false, requires_argument),
inputfname(string("-i,--in"), std::vector<string>(),
string("input file names (either single file name or comma-separated list or text file)"),
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),
update_mask(string("--update_mask"), true,
string("switch off mask updating"),
false, no_argument),
perf_bet(string("--nobet"), true,
string("\tswitch off BET"),
false, no_argument),
threshold(string("--bgthreshold"), 0.01,
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),
joined_whiten(string("--sep_whiten"), false,
string("switch on separate whitening"),
false, no_argument, false),
joined_vn(string("--sep_vn"), true,
string("switch on separate variance nomalisation (as opposed to separate VN)"),
false, no_argument),
dr_pca(string("--mod_pca"), true,
string("switch off modified PCA for concat ICA"),
false, no_argument, false),
migp(string("--disableMigp"), true,
string("switch off MIGP data reduction"),
false, no_argument),
migpN(string("--migpN"), 0,
string("Number of internal Eigenmaps"),
false, requires_argument),
migp_shuffle(string("--migp_shuffle"), true,
string("Randomise MIGP file order (default: TRUE)"),
false, no_argument),
migp_factor(string("--migp_factor"), 2,
string("Internal Factor of mem-threshold relative to number of Eigenmaps (default: 2)"),
false, requires_argument),
dr(string("--dr"), false,
string("Dual Regression (default: false)"),
false, no_argument, false),
dr_out(string("--dr_out"), false,
string("Dual Regression output for MIGP/concat ICA"),
false, no_argument, false),
vn_level(string("--vn_level"), float(2.3),
string("variance nomalisation threshold level (Z> value is ignored)"),
false, requires_argument, false),
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 decomposition, 2D: defl, symm (default), 3D: tica, concat (default)"),
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),
varnorm2(string("--vn2"), true,
string("switch off 2nd level variance normalisation"),
false, no_argument, false),
pbsc(string("--pbsc"), false,
string(" switch on conversion to percent BOLD signal change"),
false, no_argument, false),
pspec(string("--pspec"), false,
string(" switch on conversion to powerspectra"),
false, no_argument, false),
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"), 0.00005,
string("minimum error change"),
false, requires_argument),
epsilonS(string("--epsS"), 0.03,
string("minimum error change for rank-1 approximation in TICA"),
false, requires_argument),
maxNumItt(string("--maxit"), 500,
string("\tmaximum number of iterations before restart"),
false, requires_argument),
maxRestart(string("--maxrestart"), -1,
string("maximum number of restarts\n"),
false, requires_argument),
rank1interval(string("--rank1interval"), 10,
string("number of iterations between rank-1 approximation (TICA)\n"),
false, requires_argument,false),
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("\tinput filename of the IC components file for mixture modelling"),
false, requires_argument),
filtermix(string("--mix"), string(""),
string("\tinput filename of mixing matrix for mixture modelling / filtering"),
false, requires_argument),
smodename(string("--smode"), string(""),
string("\tinput filename of matrix of session modes for report generation"),
false, requires_argument),
filter(string("-f,--filter"), string(""),
string("list of component numbers to remove\n "),
false, requires_argument),
genreport(string("--report"), false,
string("generate Melodic web report"),
false, no_argument),
guireport(string("--guireport"), string(""),
string("modify report for GUI use"),
false, requires_argument, false),
bgimage(string("--bgimage"), string(""),
string("specify background image for report (default: mean image)\n "),
false, requires_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),
addsigchng(string("--sigchng"), false,
string("add signal change estimates to report pages\n"),
false, no_argument, false),
allPPCA(string("--allPPCA"), false,
string("add all PPCA plots\n"),
false, no_argument, false),
varplots(string("--varplots"), false,
string("add std error envelopes to time course plots\n"),
false, no_argument, false),
varvals(string("--varvals"), false,
string("add rank1 values after plots\n"),
false, no_argument, false),
fn_Tdesign(string("--Tdes"), string(""),
string(" design matrix across time-domain"),
false, requires_argument),
fn_Tcon(string("--Tcon"), string(""),
string(" t-contrast matrix across time-domain"),
false, requires_argument),
fn_TconF(string("--Tconf"), string(""),
string(" F-contrast matrix across time-domain"),
false, requires_argument, false),
fn_Sdesign(string("--Sdes"), string(""),
string(" design matrix across subject-domain"),
false, requires_argument),
fn_Scon(string("--Scon"), string(""),
string(" t-contrast matrix across subject-domain"),
false, requires_argument),
fn_SconF(string("--Sconf"), string(""),
string(" F-contrast matrix across subject-domain"),
false, requires_argument,false),
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),
debug(string("--debug"), false,
string(" switch on debug messages"),
false, no_argument),
guessfname(string("--init_ica"), string(""),
string("file name of FEAT paradigm file (design.mat) for ICA initialisation"),
false, requires_argument, false),
paradigmfname(string("--init_pca"), string(""),
string("file name of FEAT paradigm file (design.mat) for PCA initialisation"),
false, requires_argument, false),
axials_str(string("--report_maps"), string(" -s 2 -A 950 "),
string("control string for spatial map images (see slicer)"),
false, requires_argument),
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),
seed(string("--seed"), -1,
string("integer seed for random number generator within melodic"),
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),
smooth_probmap(string("--smooth_pm"), 0.0,
string("width of smoothing kernel for probability maps"),
false, requires_argument, false),
insta_fn(string("--insta_fn"), string(""),
string(" mask file name for instacorr calculation"),
false, requires_argument, false),
remove_meanvol(string("--keep_meanvol"), true,
string("do not subtract mean volume"),
false, no_argument, false),
remove_meantc(string("--remove_meantc"), false,
string("remove mean time course"),
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("--remove_deriv"), 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),
retryfactor(string("--retryfactor"), float(0.95),
string("multiplicative factor for determining new dim if estimated dim fails to converge"),
false, requires_argument, false),
econ(string("--econ"), 20000,
string("set ctrl parameter for helperfns econ mode"),
false, requires_argument, false),
options(title, usageexmpl)
{
try {
options.add(logdir);
options.add(inputfname);
options.add(outputfname);
options.add(guessfname);
options.add(maskfname);
options.add(use_mask);
options.add(update_mask);
options.add(perf_bet);
options.add(threshold);
options.add(pca_dim);
options.add(pca_est);
options.add(joined_whiten);
options.add(joined_vn);
options.add(dr_pca);
options.add(migp);
options.add(migpN);
options.add(migp_shuffle);
options.add(migp_factor);
options.add(dr);
options.add(dr_out);
options.add(vn_level);
options.add(numICs);
options.add(approach);
options.add(nonlinearity);
options.add(varnorm);
options.add(varnorm2);
options.add(pbsc);
options.add(pspec);
options.add(segment);
options.add(tsmooth);
options.add(epsilon);
options.add(epsilonS);
options.add(maxNumItt);
options.add(maxRestart);
options.add(rank1interval);
options.add(mmthresh);
options.add(perf_mm);
options.add(ICsfname);
options.add(filtermix);
options.add(smodename);
options.add(filter);
options.add(genreport);
options.add(guireport);
options.add(bgimage);
options.add(tr);
options.add(logPower);
options.add(addsigchng);
options.add(allPPCA);
options.add(varplots);
options.add(varvals);
options.add(fn_Tdesign);
options.add(fn_Tcon);
options.add(fn_TconF);
options.add(fn_Sdesign);
options.add(fn_Scon);
options.add(fn_SconF);
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(debug);
options.add(guessfname);
options.add(paradigmfname);
options.add(axials_str);
options.add(dummy);
options.add(repeats);
options.add(seed);
options.add(nlconst1);
options.add(nlconst2);
options.add(smooth_probmap);
options.add(insta_fn);
options.add(remove_meanvol);
options.add(remove_meantc);
options.add(remove_endslices);
options.add(rescale_nht);
options.add(guess_remderiv);
options.add(temporal);
options.add(retryfactor);
options.add(econ);
}
catch(X_OptionError& e) {
options.usage();
cerr << endl << e.what() << endl;
}
catch(std::exception &e) {
cerr << e.what() << endl;
}
}
}
#endif