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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"
namespace Melodic {
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class MelodicOptions {
public:
static MelodicOptions& getInstance();
~MelodicOptions() { delete gopt; }
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std::string version;
std::string binpath;
std::string logfname;
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Utilities::Option<std::string> logdir;
Utilities::Option< std::vector<std::string> > inputfname;
Utilities::Option<std::string> outputfname;
Utilities::Option<std::string> maskfname;
Utilities::Option<bool> use_mask;
Utilities::Option<bool> update_mask;
Utilities::Option<bool> perf_bet;
Utilities::Option<float> threshold;
Utilities::Option<int> pca_dim;
Utilities::Option<std::string> pca_est;
Utilities::Option<bool> joined_whiten;
Utilities::Option<bool> joined_vn;
Utilities::Option<bool> dr_pca;
Utilities::Option<bool> migp;
Utilities::Option<int> migpN;
Utilities::Option<bool> migp_shuffle;
Utilities::Option<int> migp_factor;
Utilities::Option<bool> dr;
Utilities::Option<bool> dr_out;
Utilities::Option<float> vn_level;
Utilities::Option<int> numICs;
Utilities::Option<std::string> approach;
Utilities::Option<bool> deflation;
Utilities::Option<std::string> nonlinearity;
Utilities::Option<bool> varnorm;
Utilities::Option<bool> varnorm2;
Utilities::Option<bool> pbsc;
Utilities::Option<bool> pspec;
Utilities::Option<std::string> segment;
Utilities::Option<bool> tsmooth;
Utilities::Option<float> epsilon;
Utilities::Option<float> epsilonS;
Utilities::Option<int> maxNumItt;
Utilities::Option<int> maxRestart;
Utilities::Option<int> rank1interval;
Utilities::Option<std::string> mmthresh;
Utilities::Option<bool> perf_mm;
Utilities::Option<std::string> ICsfname;
Utilities::Option<std::string> filtermix;
Utilities::Option<std::string> smodename;
Utilities::Option<std::string> filter;
Utilities::Option<bool> genreport;
Utilities::Option<std::string> guireport;
Utilities::Option<std::string> bgimage;
Utilities::Option<float> tr;
Utilities::Option<bool> logPower;
Utilities::Option<bool> addsigchng;
Utilities::Option<bool> allPPCA;
Utilities::Option<bool> varplots;
Utilities::Option<bool> varvals;
Utilities::Option<std::string> fn_Tdesign;
Utilities::Option<std::string> fn_Tcon;
Utilities::Option<std::string> fn_TconF;
Utilities::Option<std::string> fn_Sdesign;
Utilities::Option<std::string> fn_Scon;
Utilities::Option<std::string> fn_SconF;
Utilities::Option<bool> output_all;
Utilities::Option<bool> output_unmix;
Utilities::Option<bool> output_MMstats;
Utilities::Option<bool> output_pca;
Utilities::Option<bool> output_white;
Utilities::Option<bool> output_origIC;
Utilities::Option<bool> output_mean;
Utilities::Option<bool> verbose;
Utilities::Option<bool> vers;
Utilities::Option<bool> copyright;
Utilities::Option<bool> help;
Utilities::Option<bool> debug;
Utilities::Option<bool> readCIFTI;
Utilities::Option<std::string> guessfname;
Utilities::Option<std::string> paradigmfname;
Utilities::Option<std::string> axials_str;
Utilities::Option<int> dummy;
Utilities::Option<int> repeats;
Utilities::Option<int> seed;
Utilities::Option<float> nlconst1;
Utilities::Option<float> nlconst2;
Utilities::Option<float> smooth_probmap;
Utilities::Option<std::string> insta_fn;
Utilities::Option<bool> remove_meanvol;
Utilities::Option<bool> remove_meantc;
Utilities::Option<bool> remove_endslices;
Utilities::Option<bool> rescale_nht;
Utilities::Option<bool> guess_remderiv;
Utilities::Option<bool> temporal;
Utilities::Option<float> retryfactor;
Utilities::Option<int> econ;
void parse_command_line(int argc, char** argv, Utilities::Log& logger, const std::string &p_version);
private:
MelodicOptions();
const MelodicOptions& operator=(MelodicOptions&);
MelodicOptions(MelodicOptions&);
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Utilities::OptionParser options;
void print_usage(int argc, char *argv[]);
void print_version();
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};
inline MelodicOptions& MelodicOptions::getInstance(){
if(gopt == NULL)
gopt = new MelodicOptions();
return *gopt;
}
inline MelodicOptions::MelodicOptions() :
logdir(std::string("-o,--outdir"), std::string("log.txt"),
std::string("output directory name"),
false, Utilities::requires_argument),
inputfname(std::string("-i,--in"), std::vector<std::string>(),
std::string("input file names (either single file name or comma-separated list or text file)"),
true, Utilities::requires_argument),
outputfname(std::string("-O,--out"), std::string("melodic"),
std::string("output file name"),
false, Utilities::requires_argument,false),
maskfname(std::string("-m,--mask"), std::string(""),
std::string("file name of mask for thresholding"),
false, Utilities::requires_argument),
use_mask(std::string("--nomask"), true,
std::string("switch off masking"),
false, Utilities::no_argument),
update_mask(std::string("--update_mask"), true,
std::string("switch off mask updating"),
false, Utilities::no_argument),
perf_bet(std::string("--nobet"), true,
std::string("\tswitch off BET"),
false, Utilities::no_argument),
threshold(std::string("--bgthreshold"), 0.01,
std::string("brain / non-brain threshold (only if --nobet selected)\n"),
false, Utilities::requires_argument),
pca_dim(std::string("-d,--dim"), 0,
std::string("dimensionality reduction into #num dimensions (default: automatic estimation)"),
false, Utilities::requires_argument),
pca_est(std::string("--dimest"), std::string("lap"),
std::string("use specific dim. estimation technique: lap, bic, mdl, aic, mean (default: lap)"),
false, Utilities::requires_argument),
joined_whiten(std::string("--sep_whiten"), false,
std::string("switch on separate whitening"),
false, Utilities::no_argument, false),
joined_vn(std::string("--sep_vn"), true,
std::string("switch on separate variance nomalisation for each input dataset (off by default)"),
false, Utilities::no_argument),
dr_pca(std::string("--mod_pca"), true,
std::string("switch off modified PCA for concat ICA"),
false, Utilities::no_argument, false),
migp(std::string("--disableMigp"), true,
std::string("switch off MIGP data reduction when using -a concat (full temporal concatenation will be used)"),
false, Utilities::no_argument),
migpN(std::string("--migpN"), 0,
std::string("Number of internal Eigenmaps"),
false, Utilities::requires_argument),
migp_shuffle(std::string("--migp_shuffle"), true,
std::string("Randomise MIGP file order (default: TRUE)"),
false, Utilities::no_argument),
migp_factor(std::string("--migp_factor"), 2,
std::string("Internal Factor of mem-threshold relative to number of Eigenmaps (default: 2)"),
false, Utilities::requires_argument),
dr(std::string("--dr"), false,
std::string("Dual Regression (default: false)"),
false, Utilities::no_argument, false),
dr_out(std::string("--dr_out"), false,
std::string("Dual Regression output for MIGP/concat ICA"),
false, Utilities::no_argument, false),
vn_level(std::string("--vn_level"), float(2.3),
std::string("variance nomalisation threshold level (Z> value is ignored)"),
false, Utilities::requires_argument, false),
numICs(std::string("-n,--numICs"), -1,
std::string("numer of IC's to extract (for deflation approach)"),
false, Utilities::requires_argument),
approach(std::string("-a,--approach"), std::string("concat"),
std::string("approach for multi-session/subject data:\n"
"\t concat\ttemporally-concatenated group-ICA using MIGP ( default )\n"
"\t tica \ttensor-ICA"),
false, Utilities::requires_argument),
deflation(std::string("--defl"),false,
std::string("switch single-subject ICA method from symmetric to deflation"),
false, Utilities::no_argument,false),
nonlinearity(std::string("--nl"), std::string("pow3"),
std::string("\tnonlinearity: gauss, tanh, pow3 (default), pow4"),
false, Utilities::requires_argument),
varnorm(std::string("--vn,--varnorm"), true,
std::string("switch off variance normalisation"),
false, Utilities::no_argument),
varnorm2(std::string("--vn2"), true,
std::string("switch off 2nd level variance normalisation"),
false, Utilities::no_argument, false),
pbsc(std::string("--pbsc"), false,
std::string(" switch on conversion to percent BOLD signal change"),
false, Utilities::no_argument, false),
pspec(std::string("--pspec"), false,
std::string(" switch on conversion to powerspectra"),
false, Utilities::no_argument, false),
segment(std::string("--covarweight"), std::string(""),
std::string("voxel-wise weights for the covariance matrix (e.g. segmentation information)"),
false, Utilities::requires_argument),
tsmooth(std::string("--spca"), false,
std::string("smooth the eigenvectors prior to IC decomposition"),
false, Utilities::no_argument, false),
epsilon(std::string("--eps"), 0.00005,
std::string("minimum error change"),
false, Utilities::requires_argument),
epsilonS(std::string("--epsS"), 0.03,
std::string("minimum error change for rank-1 approximation in TICA"),
false, Utilities::requires_argument),
maxNumItt(std::string("--maxit"), 500,
std::string("\tmaximum number of iterations before restart"),
false, Utilities::requires_argument),
maxRestart(std::string("--maxrestart"), -1,
std::string("maximum number of restarts\n"),
false, Utilities::requires_argument),
rank1interval(std::string("--rank1interval"), 10,
std::string("number of iterations between rank-1 approximation (TICA)\n"),
false, Utilities::requires_argument,false),
mmthresh(std::string("--mmthresh"), std::string("0.5"),
std::string("threshold for Mixture Model based inference"),
false, Utilities::requires_argument),
perf_mm(std::string("--no_mm"), true,
std::string("\tswitch off mixture modelling on IC maps\n "),
false, Utilities::no_argument),
ICsfname(std::string("--ICs"), std::string(""),
std::string("\tinput filename of the IC components file for mixture modelling"),
false, Utilities::requires_argument),
filtermix(std::string("--mix"), std::string(""),
std::string("\tinput filename of mixing matrix for mixture modelling / filtering"),
false, Utilities::requires_argument),
smodename(std::string("--smode"), std::string(""),
std::string("\tinput filename of matrix of session modes for report generation"),
false, Utilities::requires_argument),
filter(std::string("-f,--filter"), std::string(""),
std::string("list of component numbers to remove\n "),
false, Utilities::requires_argument),
genreport(std::string("--report"), false,
std::string("generate Melodic web report"),
false, Utilities::no_argument),
guireport(std::string("--guireport"), std::string(""),
std::string("modify report for GUI use"),
false, Utilities::requires_argument, false),
bgimage(std::string("--bgimage"), std::string(""),
std::string("specify background image for report (default: mean image)\n "),
false, Utilities::requires_argument),
tr(std::string("--tr"), 0.0,
std::string("\tTR in seconds"),
false, Utilities::requires_argument),
logPower(std::string("--logPower"), false,
std::string("calculate log of power for frequency spectrum\n"),
false, Utilities::no_argument),
addsigchng(std::string("--sigchng"), false,
std::string("add signal change estimates to report pages\n"),
false, Utilities::no_argument, false),
allPPCA(std::string("--allPPCA"), false,
std::string("add all PPCA plots\n"),
false, Utilities::no_argument, false),
varplots(std::string("--varplots"), false,
std::string("add std error envelopes to time course plots\n"),
false, Utilities::no_argument, false),
varvals(std::string("--varvals"), false,
std::string("add rank1 values after plots\n"),
false, Utilities::no_argument, false),
fn_Tdesign(std::string("--Tdes"), std::string(""),
std::string(" design matrix across time-domain"),
false, Utilities::requires_argument),
fn_Tcon(std::string("--Tcon"), std::string(""),
std::string(" t-contrast matrix across time-domain"),
false, Utilities::requires_argument),
fn_TconF(std::string("--Tconf"), std::string(""),
std::string(" F-contrast matrix across time-domain"),
false, Utilities::requires_argument, false),
fn_Sdesign(std::string("--Sdes"), std::string(""),
std::string(" design matrix across subject-domain"),
false, Utilities::requires_argument),
fn_Scon(std::string("--Scon"), std::string(""),
std::string(" t-contrast matrix across subject-domain"),
false, Utilities::requires_argument),
fn_SconF(std::string("--Sconf"), std::string(""),
std::string(" F-contrast matrix across subject-domain"),
false, Utilities::requires_argument,false),
output_all(std::string("--Oall"), false,
std::string(" output everything"),
false, Utilities::no_argument),
output_unmix(std::string("--Ounmix"), false,
std::string("output unmixing matrix"),
false, Utilities::no_argument),
output_MMstats(std::string("--Ostats"), false,
std::string("output thresholded maps and probability maps"),
false, Utilities::no_argument),
output_pca(std::string("--Opca"), false,
std::string("\toutput PCA results"),
false, Utilities::no_argument),
output_white(std::string("--Owhite"), false,
std::string("output whitening/dewhitening matrices"),
false, Utilities::no_argument),
output_origIC(std::string("--Oorig"), false,
std::string("\toutput the original ICs"),
false, Utilities::no_argument),
output_mean(std::string("--Omean"), false,
std::string("\toutput mean volume\n"),
false, Utilities::no_argument),
verbose(std::string("-v,--verbose"), false,
std::string("switch on diagnostic messages\n\n\n"),
false, Utilities::no_argument),
vers(std::string("-V,--version"), false,
std::string("prints version information"),
false, Utilities::no_argument),
copyright(std::string("--copyright"), false,
std::string("prints copyright information"),
false, Utilities::no_argument),
help(std::string("-h,--help"), false,
std::string("prints this help message"),
false, Utilities::no_argument),
debug(std::string("--debug"), false,
std::string(" switch on debug messages"),
false, Utilities::no_argument),
readCIFTI(std::string("--CIFTI"), false,
std::string(" input/output as CIFTI (warning: auto-dimensionality estimation for CIFTI data is currently inaccurate)"),
false, Utilities::no_argument),
guessfname(std::string("--init_ica"), std::string(""),
std::string("file name of FEAT paradigm file (design.mat) for ICA initialisation"),
false, Utilities::requires_argument, false),
paradigmfname(std::string("--init_pca"), std::string(""),
std::string("file name of FEAT paradigm file (design.mat) for PCA initialisation"),
false, Utilities::requires_argument, false),
axials_str(std::string("--report_maps"), std::string(" -s 2 -A 950 "),
std::string("control string for spatial map images (see slicer)"),
false, Utilities::requires_argument),
dummy(std::string("--dummy"), 0,
std::string("number of dummy volumes"),
false, Utilities::requires_argument,false),
repeats(std::string("--repeats"), 1,
std::string("number of repeats (multistart)"),
false, Utilities::requires_argument, false),
seed(std::string("--seed"), -1,
std::string("integer seed for random number generator within melodic"),
false, Utilities::requires_argument, false),
nlconst1(std::string("--nl1,--nlconst1"), 1.0,
std::string("nonlinear constant 1"),
false, Utilities::requires_argument, false),
nlconst2(std::string("--nl2,--nlconst2"), 1.0,
std::string("nonlinear constant 2"),
false, Utilities::requires_argument, false),
smooth_probmap(std::string("--smooth_pm"), 0.0,
std::string("width of smoothing kernel for probability maps"),
false, Utilities::requires_argument, false),
insta_fn(std::string("--insta_fn"), std::string(""),
std::string(" mask file name for instacorr calculation"),
false, Utilities::requires_argument, false),
remove_meanvol(std::string("--keep_meanvol"), true,
std::string("do not subtract mean volume"),
false, Utilities::no_argument, true),
remove_meantc(std::string("--remove_meantc"), false,
std::string("remove mean time course"),
false, Utilities::no_argument, false),
remove_endslices(std::string("--remEndslices"), false,
std::string("delete end slices (motion correction artefacts)"),
false, Utilities::no_argument,false),
rescale_nht(std::string("--rescale_nht"), true,
std::string("switch off map rescaling after mixture-modelling"),
false, Utilities::no_argument,false),
guess_remderiv(std::string("--remove_deriv"), false,
std::string("removes every second entry in paradigm file (EV derivatives)"),
false, Utilities::no_argument, false),
temporal(std::string("--temporal"), false,
std::string("perform temporal ICA"),
false, Utilities::no_argument, false),
retryfactor(std::string("--retryfactor"), float(0.95),
std::string("multiplicative factor for determining new dim if estimated dim fails to converge"),
false, Utilities::requires_argument, false),
econ(std::string("--econ"), 20000,
std::string("set ctrl parameter for helperfns econ mode"),
false, Utilities::requires_argument, false),
options(title, usageexmpl)
{
try {
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options.add(inputfname);
options.add(outputfname);
options.add(output_all);
options.add(maskfname);
options.add(pca_dim);
options.add(approach);
options.add(genreport);
options.add(readCIFTI);
options.add(varnorm);
options.add(verbose);
options.add(guessfname);
options.add(use_mask);
options.add(update_mask);
options.add(perf_bet);
options.add(threshold);
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(nonlinearity);
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(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_unmix);
options.add(output_MMstats);
options.add(output_pca);
options.add(output_white);
options.add(output_origIC);
options.add(output_mean);
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(Utilities::X_OptionError& e) {
options.usage();
std::cerr << std::endl << e.what() << std::endl;
}
catch(std::exception &e) {
std::cerr << e.what() << std::endl;
}
}