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/* MELODIC - Multivariate exploratory linear optimized decomposition into
independent components
meldata.cc - data handler / container class
Christian F. Beckmann, FMRIB Image Analysis Group
#include "meloptions.h"
#include "meldata.h"
#include "melodic.h"
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using namespace Utilities;
using namespace NEWIMAGE;
namespace Melodic{
void MelodicData::setup()
{
{
volume4D<float> RawData;
message("Reading data file " << opts.inputfname.value() << " ... ");
read_volume4D(RawData,opts.inputfname.value(),tempInfo);
message(" done" << endl);
for(int ctr=1; ctr<=opts.dummy.value(); ctr++){
RawData.deletevolume(ctr);
}
// calculate a Mean image and save it
Mean = meanvol(RawData);
tmpnam(Mean_fname); // generate a tmp name
save_volume(Mean,Mean_fname);
create_mask(RawData, Mask);
if(Mask.xsize()==RawData.xsize() &&
Mask.ysize()==RawData.ysize() &&
Mask.zsize()==RawData.zsize())
Data = RawData.matrix(Mask);
else{
cerr << "ERROR:: mask and data have different dimensions \n\n";
exit(2);
}
// clean /tmp
char callRMstr[1000];
ostrstream osc(callRMstr,1000);
osc << "rm " << string(Mean_fname) <<"* " << '\0';
system(callRMstr);
//mask out constant voxels
message("Excluding voxels with constant value " << endl);
Matrix DStDev=stdev(Data);
volume4D<float> tmpMask;
tmpMask.setmatrix(DStDev,Mask);
float tMmax;
volume<float> tmpMask2;
tmpMask2 = tmpMask[0];
tMmax = tmpMask2.max();
double st_mean = DStDev.Sum()/DStDev.Ncols();
double st_std = stdev(DStDev.t()).AsScalar();
Mask = binarise(tmpMask2,(float) max((float) st_mean-3*st_std,
(float) 0.01*st_mean),tMmax);
Data = RawData.matrix(Mask);
}
message("Data size : " << Data.Nrows() << " x " << Data.Ncols() <<endl);
{// remove mean volume
// if((opts.remove_meanvol.value()||opts.varnorm.value())){
message(string("Removing mean image ... "));
meanR=mean(Data);
Data=remmean(Data);
message("done" << endl);
//}else{
// meanR=zeros(1,Data.Ncols());
//}
}
{// remove mean time course
meanC=mean(Data,2);
Data=remmean(Data,2);
}
{//switch dimension in case temporal ICA is required
if(opts.temporal.value()){
message(string("Switching dimensions for temporal ICA") << endl);
Data = Data.t();
Matrix tmp;
tmp = meanC;
meanC = meanR.t();
meanR = tmp.t();
message("Data size : " << Data.Nrows() << " x " << Data.Ncols() <<endl);
}
}
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{// variance-normalize the data
DiagonalMatrix tmpD;Matrix tmpE;
message(string("Estimating data covariance ... "));
SymmetricMatrix Corr;
Corr = cov(Data.t());
EigenValues(Corr,tmpD,tmpE);
Matrix RE; DiagonalMatrix RD;
//RE = tmpE.Columns(2,Corr.Ncols());
RE = tmpE;
//RD << abs(tmpD.SymSubMatrix(2,Corr.Ncols()));
RD << abs(tmpD);
Matrix tmpWhite;Matrix tmpDeWhite;
tmpWhite = sqrt(abs(RD.i()))*RE.t();
tmpDeWhite = RE*sqrt(RD);
message("done"<<endl);
if(opts.varnorm.value())
message(string("Perform variance-normalisation ... "));
Matrix WS;
WS = tmpWhite * Data;
for(int ctr1 =1; ctr1<=WS.Nrows(); ctr1++){
for(int ctr2 =1; ctr2<=WS.Ncols(); ctr2++){
if(abs(WS(ctr1,ctr2))<3.1)
WS(ctr1,ctr2)=0.0;
}
}
stdDevi = pow(stdev(Data - tmpDeWhite*WS),-1);
Data = Data + meanC*ones(1,Data.Ncols());
}
DataVN = SP(Data,ones(Data.Nrows(),1)*stdDevi);
if(opts.output_all.value()){
volume4D<float> tempVol;
tempVol.setmatrix(stdDevi,Mask);
save_volume4D(tempVol,logger.appendDir(opts.outputfname.value()
+ "_vn_stdev"),tempInfo);
tempVol.setmatrix(DataVN,Mask);
save_volume4D(tempVol,logger.appendDir(opts.outputfname.value()
+ "_vn"),tempInfo);
}
if(opts.varnorm.value()){
Data = DataVN;
message("done"<<endl);
}
{//remove row mean
if(opts.temporal.value()){
message(string("Removing mean image ... "));
}else{
message(string("Removing mean time course ... "));
}
meanC=mean(Data,2);
Data=remmean(Data,2);
message("done"<<endl);
}
if(opts.segment.value().length()>0){
create_RXweight();
}
//save the mask
save_volume(Mask,logger.appendDir("mask"));
//seed the random number generator
double tmptime = time(NULL);
srand((unsigned int) tmptime/Data.Ncols()*Data.Nrows());
} // void setup()
void MelodicData::save()
{
//check for temporal ICA
if(opts.temporal.value()){
message(string("temporal ICA: transform back the data ... "));
Matrix tmpIC = mixMatrix.t();
mixMatrix=IC.t();
IC=tmpIC;
unmixMatrix=pinv(mixMatrix);
Data = Data.t();
tmpIC = meanC;
meanC = meanR.t();
meanR = tmpIC.t();
// whiteMatrix = whiteMatrix.t;
// dewhiteMatrix = dewhiteMatrix.t();
message(string("done") << endl);
opts.temporal.set_T(false); // Do not switch again!
}
message("Writing results to : " << endl);
//Output IC
if((IC.Storage()>0)&&(opts.output_origIC.value())&&(after_mm==false)){
volume4D<float> tempVol;
tempVol.setmatrix(IC,Mask);
//strncpy(tempInfo.header.hist.aux_file,"render3",24);
save_volume4D(tempVol,logger.appendDir(opts.outputfname.value()
message(" " << logger.appendDir(opts.outputfname.value() + "_oIC") <<endl);
}
//Output IC -- adjusted for noise
if(IC.Storage()>0){
volume4D<float> tempVol;
// volumeinfo tempInfo;
// read_volume4D(tempVol,opts.inputfname.value(),tempInfo);
//Matrix ICadjust = IC;
if(after_mm)
ICadjust = IC;
else{
stdNoisei = pow(stdev(Data - mixMatrix * IC)*std::sqrt((float)(Data.Nrows()-1))/
std::sqrt((float)(Data.Nrows()-IC.Nrows())),-1);
ColumnVector diagvals;
diagvals=pow(diag(unmixMatrix*unmixMatrix.t()),-0.5);
ICadjust = SP(IC,diagvals*stdNoisei);
}
tempVol.setmatrix(ICadjust,Mask);
//strncpy(tempInfo.header.hist.aux_file,"render3",24);
save_volume4D(tempVol,logger.appendDir(opts.outputfname.value()
+ "_IC"),tempInfo);
message(" " << logger.appendDir(opts.outputfname.value() + "_IC") <<endl);
if(opts.output_origIC.value()){
tempVol.setmatrix(stdNoisei,Mask);
save_volume4D(tempVol,logger.appendDir(string("Noise_stddev_inv")),tempInfo);
message(" " << logger.appendDir(string("Noise_stddev_inv")) <<endl);
}
}
//Output mixMatrix
if(mixMatrix.Storage()>0){
write_ascii_matrix(logger.appendDir(opts.outputfname.value() + "_mix"),
mixMatrix);
mixFFT=calc_FFT(mixMatrix);
write_ascii_matrix(logger.appendDir(opts.outputfname.value() + "_FTmix"),
mixFFT);
message(" "<<
logger.appendDir(opts.outputfname.value() + "_mix") <<endl);
message(" "<<
logger.appendDir(opts.outputfname.value() + "_FTmix") <<endl);
}
//Output unmixMatrix
if(opts.output_unmix.value() && unmixMatrix.Storage()>0){
write_ascii_matrix(logger.appendDir(opts.outputfname.value() + "_unmix"),unmixMatrix);
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message(" "<<
logger.appendDir(opts.outputfname.value() + "_unmix") <<endl);
}
//Output Mask
message(" "<< logger.appendDir("mask") <<endl);
//Output mean
if(opts.output_mean.value() && meanC.Storage()>0 && meanR.Storage()>0){
write_ascii_matrix(logger.appendDir(opts.outputfname.value() + "_meanR"),
meanR);
write_ascii_matrix(logger.appendDir(opts.outputfname.value() + "_meanC"),
meanC);
message(" "<<
logger.appendDir(opts.outputfname.value() + "_meanR") <<endl);
message(" "<<
logger.appendDir(opts.outputfname.value() + "_meanC") <<endl);
}
//Output white
if(opts.output_white.value() && whiteMatrix.Storage()>0&&
dewhiteMatrix.Storage()>0){
write_ascii_matrix(logger.appendDir(opts.outputfname.value() + "_white"),
whiteMatrix);
write_ascii_matrix(logger.appendDir(opts.outputfname.value() + "_dewhite"),dewhiteMatrix);
Matrix tmp;
tmp=calc_FFT(dewhiteMatrix);
write_ascii_matrix(logger.appendDir(opts.outputfname.value() + "_FTdewhite"),tmp);
message(" "<<
logger.appendDir(opts.outputfname.value() + "_white") <<endl);
message(" "<<
logger.appendDir(opts.outputfname.value() + "_dewhite") <<endl);
}
//Output PCA
if(opts.output_pca.value() && pcaD.Storage()>0&&pcaE.Storage()>0){
write_ascii_matrix(logger.appendDir(opts.outputfname.value() + "_pcaE"),
pcaE);
message(" "<<
logger.appendDir(opts.outputfname.value() + "_pcaE") <<endl);
write_ascii_matrix(logger.appendDir(opts.outputfname.value() + "_pcaD"),
(Matrix) diag(pcaD));
message(" "<<
logger.appendDir(opts.outputfname.value() + "_pcaD") <<endl);
if(whiteMatrix.Ncols()==Data.Ncols()){
PCAmaps = dewhiteMatrix.t();
}else
PCAmaps = whiteMatrix * Data;
tempVol.setmatrix(PCAmaps,Mask);
//strncpy(tempInfo.header.hist.aux_file,"render3",24);
save_volume4D(tempVol,logger.appendDir(opts.outputfname.value()
+ "_pca"),tempInfo);
message(" " <<
logger.appendDir(opts.outputfname.value() + "_pca") <<endl);
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} //void save()
int MelodicData::remove_components()
{
message("Reading " << opts.filtermix.value() << endl)
mixMatrix = read_ascii_matrix(opts.filtermix.value());
if (mixMatrix.Storage()<=0) {
cerr <<" Please specify the mixing matrix correctly" << endl;
exit(2);
}
unmixMatrix = pinv(mixMatrix);
IC = unmixMatrix * Data;
string tmpstr;
tmpstr = opts.filter.value();
Matrix noiseMix;
Matrix noiseIC;
int ctr=0;
char *p;
char t[1024];
const char *discard = ", [];{(})abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ~!@#$%^&*_-=+|\':><./?";
message("Filtering the data...");
strcpy(t, tmpstr.c_str());
p=strtok(t,discard);
ctr = atoi(p);
if(ctr>0 && ctr<=mixMatrix.Ncols()){
message(" "<< ctr );
noiseMix = mixMatrix.Column(ctr);
noiseIC = IC.Row(ctr).t();
}else{
cerr << endl<< "component number "<<ctr<<" does not exist" << endl;
}
do{
p=strtok(NULL,discard);
if(p){
ctr = atoi(p);
if(ctr>0 && ctr<=mixMatrix.Ncols()){
message(" "<<ctr);
noiseMix |= mixMatrix.Column(ctr);
noiseIC |= IC.Row(ctr).t();
}
else{
cerr << endl<< "component number "<<ctr<<" does not exist" << endl;
}
}
}while(p);
message(endl);
Matrix newData;
newData = Data - noiseMix * noiseIC.t();
//cerr << newData.Nrows() << " x " << newData.Ncols() << endl;
//cerr << meanC.Nrows() << " x " << meanC.Ncols() << endl;
//cerr << meanR.Nrows() << " x " << meanR.Ncols() << endl;
newData = newData + meanC*ones(1,newData.Ncols());
newData = newData + ones(newData.Nrows(),1)*meanR;
volume4D<float> tmp;
read_volume4D(tmp,opts.inputfname.value());
tmp.setmatrix(newData,Mask);
save_volume4D(tmp,logger.appendDir(opts.outputfname.value() + "_ICAfiltered"));
return 0;
} // int remove_components()
void MelodicData::create_RXweight()
{
message("Reading the weights for the covariance R_X from file "<< opts.segment.value() << endl);
volume4D<float> tmpRX;
read_volume4D(tmpRX,opts.segment.value());
RXweight = tmpRX.matrix(Mask);
}
void MelodicData::create_mask(volume4D<float> &theData,
volume<float> &theMask)
{
if(opts.use_mask.value() && opts.maskfname.value().size()>0){ // mask provided
read_volume(theMask,opts.maskfname.value());
message("Mask provided : " << opts.maskfname.value()<<endl);
}
else{
if(opts.perf_bet.value() && opts.use_mask.value()){ //use BET
message("Create mask ... ");
// set up all strings
string BET_outputfname = string(Mean_fname)+"_brain";
string BET_path = opts.binpath + "bet";
string BET_optarg = "-m -f 0.4"; // see man bet
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// Setup external call to BET:
char callBETstr[1000];
ostrstream osc(callBETstr,1000);
osc << BET_path << " " << Mean_fname << " "
<< BET_outputfname << " " << BET_optarg << " > /dev/null " << '\0';
message(" Calling BET: " << callBETstr << endl);
system(callBETstr);
// read back the Mask file
read_volume(theMask,Mask_fname);
message("done" << endl);
}
else{
if(opts.use_mask.value()){ //just threshold the Mean
message("Create mask ... ");
float Mmin, Mmax, Mtmp;
Mmin = Mean.min(); Mmax = Mean.max();
theMask = binarise(Mean,Mmin + opts.threshold.value()* (Mmax-Mmin),Mmax);
Mtmp = Mmin + opts.threshold.value()* (Mmax-Mmin);
message("done" << endl);
}
else{ //well, don't threshold then
theMask = Mean;
theMask = 1.0;
}
}
}
if(opts.remove_endslices.value()){
// just in case mc introduced something nasty
message(" Deleting end slices" << endl);
for(int ctr1=theMask.miny(); ctr1<=theMask.maxy(); ctr1++){
for(int ctr2=theMask.minx(); ctr2<=theMask.maxx(); ctr2++){
theMask(ctr2,ctr1,Mask.minz()) = 0.0;
theMask(ctr2,ctr1,Mask.maxz()) = 0.0;
}
}
}
} //void create_mask()
void MelodicData::status(const string &txt)
{
cout << "MelodicData Object " << txt << endl;
if(Data.Storage()>0){cout << "Data: " << Data.Nrows() <<"x" << Data.Ncols() << endl;}else{cout << "Data empty " <<endl;}
if(pcaE.Storage()>0){cout << "pcaE: " << pcaE.Nrows() <<"x" << pcaE.Ncols() << endl;}else{cout << "pcaE empty " <<endl;}
if(pcaD.Storage()>0){cout << "pcaD: " << pcaD.Nrows() <<"x" << pcaD.Ncols() << endl;}else{cout << "pcaD empty " <<endl;}
if(whiteMatrix.Storage()>0){cout << "white: " << whiteMatrix.Nrows() <<"x" << whiteMatrix.Ncols() << endl;}else{cout << "white empty " <<endl;}
if(dewhiteMatrix.Storage()>0){cout << "dewhite: " << dewhiteMatrix.Nrows() <<"x" << dewhiteMatrix.Ncols() << endl;}else{cout << "dewhite empty " <<endl;}
if(mixMatrix.Storage()>0){cout << "mix: " << mixMatrix.Nrows() <<"x" << mixMatrix.Ncols() << endl;}else{cout << "mix empty " <<endl;}
if(unmixMatrix.Storage()>0){cout << "unmix: " << unmixMatrix.Nrows() <<"x" << unmixMatrix.Ncols() << endl;}else{cout << "unmix empty " <<endl;}
if(IC.Storage()>0){cout << "IC: " << IC.Nrows() <<"x" << IC.Ncols() << endl;}else{cout << "IC empty " <<endl;}
} //void status()
Matrix MelodicData::calc_FFT(const Matrix& Mat)
{
Matrix res;
for(int ctr=1; ctr <= Mat.Ncols(); ctr++)
{
ColumnVector tmpCol;
tmpCol=Mat.Column(ctr);
ColumnVector FtmpCol_real;
ColumnVector FtmpCol_imag;
ColumnVector tmpPow;
if(tmpCol.Nrows()%2 != 0){
Matrix empty(1,1); empty=0;
tmpCol &= empty;}
RealFFT(tmpCol,FtmpCol_real,FtmpCol_imag);
tmpPow = pow(FtmpCol_real,2)+pow(FtmpCol_imag,2);
tmpPow = tmpPow.Rows(2,tmpPow.Nrows());
if(opts.logPower.value()) tmpPow = log(tmpPow);
if(res.Storage()==0){res= tmpPow;}else{res|=tmpPow;}
}
return res;
} //Matrix calc_FFT()
Matrix MelodicData::smoothColumns(const Matrix &inp)
{
Matrix temp(inp);
int ctr1 = temp.Nrows();
Matrix temp2(temp);
temp2=0;
temp = temp.Row(4) & temp.Row(3) & temp.Row(2) & temp & temp.Row(ctr1-1)
& temp.Row(ctr1-2) &temp.Row(ctr1-3);
double kern[] ={0.0045 , 0.055, 0.25, 0.4, 0.25, 0.055, 0.0045};
double fac = 0.9090909;
// Matrix FFTinp;
//FFTinp = calc_FFT(inp);
//write_ascii_matrix(logger.appendDir(opts.outputfname.value() + "_FT"),
// FFTinp); FFTinp = calc_FFT(inp);
//write_ascii_matrix(logger.appendDir(opts.outputfname.value() + "_Sinp"),
// inp);
for(int cc=1;cc<=temp2.Ncols();cc++){
// double all = FFTinp.Column(cc).Rows(1,30).SumAbsoluteValue() / FFTinp.Column(cc).SumAbsoluteValue();
// if( all > 0.5){
for(int cr=1;cr<=temp2.Nrows();cr++){
temp2(cr,cc) = fac*( kern[0] * temp(cr,cc) + kern[1] * temp(cr+1,cc) +
kern[2] * temp(cr+2,cc) + kern[3] * temp(cr+3,cc) +
kern[4] * temp(cr+4,cc) + kern[5] * temp(cr+5,cc) +
kern[6] * temp(cr+6,cc));
}//}
//else{
// for(int cr=1;cr<=temp2.Nrows();cr++){
// temp2(cr,cc) = temp(cr+3,cc);
// }
//}
}
//write_ascii_matrix(logger.appendDir(opts.outputfname.value() + "_Sout"),
// temp2);
return temp2;
}
}