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Christian Beckmann authoredChristian Beckmann authored
melgmix.h 8.05 KiB
/* MELODIC - Multivariate exploratory linear optimized decomposition into
independent components
melgmix.h - class for Gaussian/Gamma Mixture Model
Christian F. Beckmann, FMRIB Image Analysis Group
Copyright (C) 1999-2008 University of Oxford */
/* Part of FSL - FMRIB's Software Library
http://www.fmrib.ox.ac.uk/fsl
fsl@fmrib.ox.ac.uk
Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
Imaging of the Brain), Department of Clinical Neurology, Oxford
University, Oxford, UK
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#ifndef __MELGMIX_h
#define __MELGMIX_h
#include "newimage/newimageall.h"
#include "utils/log.h"
#include "melodic.h"
#include "utils/options.h"
#include "meloptions.h"
//#include "melreport.h"
using namespace Utilities;
using namespace NEWIMAGE;
namespace Melodic{
class MelGMix{
public:
MelGMix(MelodicOptions &popts, Log &plogger):
opts(popts),
logger(plogger){}
~MelGMix() {
//mainhtml << endl << "<hr></CENTER></BODY></HTML>" << endl;
}
void save();
void setup(const RowVector& dat, const string dirname,
int here, volume<float> themask,
volume<float> themean, int num_mix = 3,
float eps = 0.0, bool fixdim = false);
void gmmfit();
void ggmfit();
inline void fit(string mtype = string("GGM")){
mmtype = mtype;
if(mmtype==string("GGM"))
this->ggmfit();
else
this->gmmfit();
//re-insert mean and stdev
data = data*datastdev + datamean;
//threshmaps = threshmaps*datastdev + datamean;
means = means*datastdev + datamean;
vars = vars*datastdev*datastdev;
}
inline Matrix threshold(string levels){
return this->threshold(data, levels);
}
inline Matrix threshold(RowVector& levels){
return this->threshold(data, levels);
}
Matrix threshold(const RowVector& dat, Matrix& levels);
Matrix threshold(const RowVector& dat, string levels);
void status(const string &txt);
inline RowVector& get_means() {return means;}
inline void set_means(RowVector& Arg) {means = Arg;}
inline RowVector& get_vars() {return vars;}
inline void set_vars(RowVector& Arg) {vars = Arg;}
inline RowVector& get_pi() {return props;}
inline void set_pi(RowVector& Arg) {props = Arg;}
inline RowVector& get_data() {return data;}
inline void set_data(RowVector& Arg) {data = Arg;}
inline RowVector& get_prob() {return probmap;}
inline float get_eps() {return epsilon;}
inline void set_eps(float Arg) {epsilon = Arg;}
inline Matrix& get_threshmaps() {return threshmaps;}
inline void set_threshmaps(Matrix& Arg) {threshmaps = Arg;}
inline bool isfitted(){return fitted;}
inline int mixtures(){return nummix;}
inline string get_type() { return mmtype;}
inline void set_type(string Arg) { mmtype = Arg;}
inline string get_prefix() { return prefix;}
inline void set_prefix(string Arg) { prefix = Arg;}
inline RowVector get_probmap() {return probmap;}
inline float get_offset() {return offset;}
inline void set_offset(float Arg) {offset = Arg;}
inline void flipres(int num){
means = -means;
data = -data;
threshmaps = -threshmaps;
if(mmtype=="GGM"){
float tmp;
tmp= means(2);means(2)=means(3);means(3)=tmp;
tmp=vars(2);vars(2)=vars(3);vars(3)=tmp;
tmp=props(2);props(2)=props(3);props(3)=tmp;
}
}
void create_rep();
inline void add_infstr(string what){
threshinfo.push_back(what);
}
inline string get_infstr(int num){
if((threshinfo.size()<(unsigned int)(num-1))||(num<1))
return string("");
else
return threshinfo[num-1];
}
inline int size_infstr(){
return threshinfo.size();
}
inline void clear_infstr(){
threshinfo.clear();
}
inline void smooth_probs(float howmuch){
volume4D<float> tempVol;
tempVol.setmatrix(probmap,Mask);
tempVol[0]= smooth(tempVol[0],howmuch);
probmap = tempVol.matrix(Mask);
}
double datamean;
double datastdev;
private:
MelodicOptions &opts;
Log &logger; //global log file
//Log mainhtml;
void gmmupdate();
float gmmevidence();
void gmmreducemm();
void add_params(Matrix& mu, Matrix& sig, Matrix& pi,
float logLH, float MDL, float Evi, bool advance = false);
void get_params(int index, Matrix& mu, Matrix& sig, Matrix& pi,
float logLH, float MDL, float Evi);
Matrix Params;
Matrix threshmaps;
RowVector means;
RowVector vars;
RowVector props;
RowVector data;
RowVector probmap;
volume<float> Mean;
volume<float> Mask;
float epsilon;
float logprobY;
float MDL;
float Evi;
float offset;
int nummix;
int numdata;
int cnumber;
bool fitted;
bool fixdim;
string prefix;
string mmtype;
string dirname;
vector<string> threshinfo;
};
}
#endif