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/* MELODIC - Multivariate exploratory linear optimized decomposition into
Christian F. Beckmann, FMRIB Analysis Group
Copyright (C) 1999-2013 University of Oxford */
#ifndef __MELODICREPORT_h
#define __MELODICREPORT_h
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#include <time.h>
#include <strstream>
#include "armawrap/newmat.h"
#include "libvis/miscplot.h"
#include "libvis/miscpic.h"
#include "utils/options.h"
#include "newimage/newimageall.h"
#include "utils/log.h"
#include "melpca.h"
#include "meloptions.h"
#include "meldata.h"
#include "melgmix.h"
#include "melodic.h"
namespace Melodic{
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public:
MelodicReport(MelodicData &pmelodat, MelodicOptions &popts, Utilities::Log &plogger):
melodat(pmelodat),
opts(popts),
logger(plogger){
if( bool(opts.genreport.value()) ){
const time_t tmptime = time(NULL);
system(("mkdir "+ logger.appendDir("report") + " 2>/dev/null").c_str());
report.setDir(logger.appendDir("report"),"00index.html",true,false,std::ios::out);
report << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
(std::string) getenv("FSLDIR") +"/doc/fsl.css>"
<< "<TITLE>MELODIC report</TITLE></HEAD><BODY>"
<< std::endl <<std::endl;
loghtml.setDir(report.getDir(),"log.html");
loghtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
(std::string) getenv("FSLDIR") +"/doc/fsl.css>"
<< "<TITLE>MELODIC report</TITLE></HEAD><BODY>"
<< std::endl <<std::endl;
navigator.setDir(report.getDir(),"nav.html");
head.setDir(report.getDir(),"head.html");
navigator << "<link REL=stylesheet TYPE=text/css href=file:"+
(std::string) getenv("FSLDIR") +"/doc/fsl.css>" << std::endl;
head << "<link REL=stylesheet TYPE=text/css href=file:"+
(std::string) getenv("FSLDIR") +"/doc/fsl.css>" << std::endl;
head <<"<TABLE BORDER=0><TR>" << std::endl
<<" <TD ALIGN=CENTER WIDTH=100%>"<< std::endl
<<"<TABLE BORDER=0>"<< std::endl
<<"<tr><td align=center><font size=+3><b>MELODIC Report</b>"<< std::endl
<<"</font><tr><td valign=center align=center> <p>"<< std::endl
<< report.getDir() << "/" << report.getLogFileName() << "<br>"
<< ctime(&tmptime) << "</tr>"<< std::endl
<<"<tr valign=bottom><td align=center>"<< std::endl
<< "</tr></table>" << std::endl
<< "<TD ALIGN=RIGHT>" << std::endl
<< "<a href=http://www.fmrib.ox.ac.uk/fsl target=_top>" << std::endl
<< "<IMG BORDER=0 SRC=file:"<< getenv("FSLDIR")
<< "/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << std::endl
<< "</TD>"<<std::endl<<"</TR></TABLE> <hr>"<<std::endl;
if(opts.guireport.value()==""){
report <<"<OBJECT data=head.html></OBJECT>" << std::endl;
loghtml <<"<OBJECT data=head.html></OBJECT>" << std::endl;
}else{
report <<"<OBJECT data="<<opts.guireport.value()<< "></OBJECT>"<< std::endl;
loghtml <<"<OBJECT data="<<opts.guireport.value()<< "></OBJECT>"<< std::endl;
}
report << "<IFRAME height=80px width=100% src=nav.html frameborder=0></IFRAME><p>"<< std::endl;
loghtml << "<IFRAME height=100px width=100% src=nav.html frameborder=0></IFRAME><p>"
<<"<IFRAME width=100% height=100% src=\"../log.txt\"></IFRAME>" <<std::endl;
navigator <<"<CENTER><TABLE BORDER=0><TR>" << std::endl
<<"<TD ALIGN=CENTER WIDTH=100%><FONT SIZE=-1>"<<std::endl
<<"<A HREF=\"00index.html\" target=\"_top\">Main</A> - ";
if(opts.guireport.value()=="")
navigator << "<A HREF=\"log.html\" target=\"_top\">Log</A> - ";
navigator <<"Components: ";
navigator.flush();
axials_instr = opts.axials_str.value();
}
}
~MelodicReport(){
if( bool(opts.genreport.value()) ){
report << "<HR><CENTER><FONT SIZE=1>This page produced automatically by "
<< "<A HREF=\"http://www.fmrib.ox.ac.uk/fsl/melodic/index.html\"> MELODIC</A> Version "
<< version << " - a part of <A HREF=\"http://www.fmrib.ox.ac.uk/fsl\">FSL - "
<< "FMRIB Software Library</A>.</FONT></CENTER>" << std::endl
<< "</BODY></HTML>" <<std::endl;
loghtml << "<HR><CENTER><FONT SIZE=1>This page produced automatically by "
<< "<A HREF=\"http://www.fmrib.ox.ac.uk/fsl/melodic/index.html\"> MELODIC</A> Version "
<< version << " - a part of <A HREF=\"http://www.fmrib.ox.ac.uk/fsl\">FSL - "
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<< "FMRIB Software Library</A>.</FONT></CENTER>" << std::endl
<< "</BODY></HTML>" <<std::endl;
navigator << "</FONT></TD>"<<std::endl<<"</TR></TABLE></CENTER><hr>" <<std::endl;
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}
inline void analysistxt(){
if( bool(opts.genreport.value()) ){
report << "<b>Analysis methods</b> <br>"<<std::endl;
report << "Analysis was carried out using ";
if(opts.approach.value() != std::string("tica"))
report << "Probabilistic Independent Component Analysis"
<<" [Beckmann 2004] as implemented in "<<std::endl;
else
report << "Tensorial Independent Component Analysis "
<<"[Beckmann 2005] as implemented in "<< std::endl;
report << " MELODIC (Multivariate"
<<" Exploratory Linear Decomposition into Independent Components)"
<<" Version "<< version <<", part of FSL (FMRIB's Software"
<<" Library, <A HREF=\"http://www.fmrib.ox.ac.uk/fsl/\">"
<<"www.fmrib.ox.ac.uk/fsl</A>).<br>";
report << "The following data pre-processing was applied to"
<<" the input data: "<< std::endl;
if(opts.use_mask.value())
report << " masking of non-brain voxels;";
report << " voxel-wise de-meaning of the data;" << std::endl;
if(opts.varnorm.value())
report << " normalisation of the voxel-wise variance; ";
if(opts.pbsc.value())
report << " conversion to %BOLD signal change; ";
report << "<br>"<<std::endl;
report << " Pre-processed data were whitened and projected into a "
<< melodat.get_mix().Ncols()<< "-dimensional subspace using ";
if(melodat.get_PPCA().Storage()>0){
report << "probabilistic Principal Component Analysis where the"
<<" number of dimensions was estimated using ";
if(opts.pca_est.value() == std::string("lap"))
report << "the Laplace approximation to the Bayesian"
<<" evidence of the model order [Minka 2000, Beckmann 2004]. " << std::endl;
else
if(opts.pca_est.value() == std::string("bic"))
report << "the <em> Bayesian Information Criterion</em>"
<<" (BIC) [Kass 1993]. " << std::endl;
else
if(opts.pca_est.value() == std::string("mdl"))
report << "<em> Minimum Description Length</em> (MDL)"
<<" [Rissanen 1978]. " << std::endl;
else
if(opts.pca_est.value() == std::string("aic"))
report << "the <em> Akaike Information Criterion</em>"
<<" (AIC) [Akaike 1969]. " << std::endl;
else
report << " approximations to Bayesian the"
<<" model order [Beckmann 2004]. " << std::endl;
}
else
report << "Principal Component Analysis. ";
report << " <BR>The whitened observations were decomposed into "
<<" sets of vectors which describe signal variation across"
<<" the temporal domain (time-courses)";
if(opts.approach.value() == std::string("tica") ||
opts.approach.value() == std::string("concat"))
report << ", the session/subject domain ";
report <<" and across the spatial domain (maps) by optimising for"
<<" non-Gaussian spatial source distributions using a"
<<" fixed-point iteration technique [Hyvärinen 1999]. " << std::endl;
report << "Estimated Component maps were divided by the standard"
<<" deviation of the residual noise";
if(opts.perf_mm.value())
report << " and thresholded by fitting a mixture model "
<<"to the histogram of intensity values [Beckmann 2004]. <p>" << std::endl;
else
report <<".<p>" << std::endl;
refstxt();
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}
inline void refstxt(){
if( bool(opts.genreport.value()) ){
report << "<b>References</b> <br>"<<std::endl;
report << "[Hyvärinen 1999] A. Hyvärinen. Fast and"
<<" Robust Fixed-Point Algorithms for Independent Component"
<<" Analysis. IEEE Transactions on Neural Networks 10(3):"
<<"626-634, 1999.<br> " << std::endl;
report << "[Beckmann 2004] C.F. Beckmann and S.M. Smith."
<<" Probabilistic Independent Component Analysis for Functional"
<<" Magnetic Resonance Imaging. IEEE Transactions on Medical"
<<" Imaging 23(2):137-152 2004. <br>" << std::endl;
if(opts.approach.value() == std::string("tica") ||
opts.approach.value() == std::string("concat") )
report << "[Beckmann 2005] C.F. Beckmann and S.M. Smith."
<<" Tensorial extensions of independent component analysis"
<< " for multisubject FMRI analysis. Neuroimage "
<< " 25(1):294-311 2005. <br>";
if(melodat.get_PPCA().Storage()>0){
report << "[Everson 2000] R. Everson and S. Roberts."
<<" Inferring the eigenvalues of covariance matrices from"
<<" limited, noisy data. IEEE Trans Signal Processing,"
<<" 48(7):2083-2091, 2000<br>"<<std::endl;
report << "[Tipping 1999] M.E. Tipping and C.M.Bishop."
<<" Probabilistic Principal component analysis. J Royal"
<<" Statistical Society B, 61(3), 1999. <br>" << std::endl;
report << "[Beckmann 2001] C.F. Beckmann, J.A. Noble and"
<<" S.M. Smith. Investigating the intrinsic dimensionality"
<<" of FMRI data for ICA. In Seventh Int. Conf. on Functional"
<<" Mapping of the Human Brain, 2001. <br>" << std::endl;
if(opts.pca_est.value() == std::string("lap"))
report << "[Minka 2000] T. Minka. Automatic choice of"
<<" dimensionality for PCA. Technical Report 514, MIT"
<<" Media Lab Vision and Modeling Group, 2000. <BR>"<< std::endl;
else
if(opts.pca_est.value() == std::string("bic"))
report << "[Kass 1995] R.E. Kass and A. E. Raftery. Bayes"
<<" factors. Journal of the American Statistical"
<<" Association, 90:733-795, 1995 <br>" << std::endl;
else
if(opts.pca_est.value() == std::string("mdl"))
report << "[Rissanen 1978]. J. Rissanen. Modelling by"
<<" shortest data description. Automatica,"
<<" 14:465-471, 1978. <br>" << std::endl;
else
if(opts.pca_est.value() == std::string("aic"))
report << "[Akaike 1974]. H. Akaike. A new look at"
<<" statistical model identification. IEEE Transactions"
<<" on Automatic Control, 19:716-723, 1974. <br>" << std::endl;
else
report << "[Minka 2000]. T. Minka. Automatic choice of"
<<" dimensionality for PCA. Technical Report 514, MIT"
<<" Media Lab Vision and Modeling Group, 2000. <BR>" << std::endl;
}
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}
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inline void addtxt(std::string what){
if( bool(opts.genreport.value()) ){
report << what << std::endl;
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}
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inline void addpar(std::string what){
if( bool(opts.genreport.value()) ){
report << "<p>" << what << std::endl;
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}
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inline void addlink(std::string where, std::string what){
if( bool(opts.genreport.value()) ){
navigator << "<A HREF=\"" << where << " \"target=\"_top\"> " << what << "</A> ";
navigator.flush();
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}
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inline void addpic(std::string what, std::string link = ""){
if( bool(opts.genreport.value()) ){
if( link.length() > 0)
report << "<A HREF=\"" << link << "\"> ";
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report << "<img BORDER=0 SRC=\"" << what<< ".png\"><p>";
if( link.length() > 0)
report << "</A> ";
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}
inline std::string getDir(){
return report.getDir();
}
void IC_rep(MelGMix &mmodel, int cnum, int dim, NEWMAT::Matrix ICstats);
void IC_simplerep(std::string prefix, int cnum, int dim);
void PPCA_rep();
void Smode_rep();
private:
MelodicData &melodat;
MelodicOptions &opts;
Utilities::Log &logger;
Utilities::Log report;
Utilities::Log navigator;
Utilities::Log head;
Utilities::Log loghtml;
Utilities::Log IChtml;
Utilities::Log IChtml2;
std::string axials_instr;
void IC_rep_det(MelGMix &mmodel, int cnum, int dim);
std::string int2str(int n){
std::ostrstream os;
// os.fill(' ');
// os.width(width);
os.setf(std::ios::internal, std::ios::adjustfield);
os << n << '\0';
return os.str();
}
std::string float2str(float f, int width, int prec, int scientif){
std::ostrstream os;
int redw = int(std::abs(std::log10(std::abs(f))))+1;
if(width>0)
os.width(width);
if(scientif>0)
os.setf(std::ios::scientific);
os.precision(redw+std::abs(prec));
os.setf(std::ios::internal, std::ios::adjustfield);
os << f << '\0';
return os.str();
}