ModelML2D Class Reference

#include <ml2d.h>

Public Member Functions
	ModelML2D ()
	ModelML2D (int n_ref)
void	initData ()
void	setNRef (int n_ref)
void	combineModel (const ModelML2D &model, int sign)
void	addModel (const ModelML2D &model)
void	substractModel (const ModelML2D &model)
void	update ()
void	print (int tabs=0) const
	Just for debugging now. More...

Public Attributes
int	n_ref
std::vector< Image< double > >	Iref
std::vector< Image< double > >	WsumMref
double	sigma_noise
double	wsum_sigma_noise
double	sigma_offset
double	wsum_sigma_offset
std::vector< double >	sumwsc
std::vector< double >	sumw_mirror
std::vector< double >	alpha_k
std::vector< double >	mirror_fraction
std::vector< double >	scale
double	sumw_allrefs
double	sumw_allrefs2
double	avePmax
double	sumfracweight
double	LL
int	dim
bool	do_student
bool	do_student_sigma_trick
bool	do_norm

Detailed Description

Definition at line 79 of file ml2d.h.

Constructor & Destructor Documentation

ModelML2D() [1/2]

ModelML2D::ModelML2D

(

)

Definition at line 317 of file ml2d.cpp.

{
    initData();
}//close default constructor

ModelML2D() [2/2]

ModelML2D::ModelML2D

(

int

n_ref

)

Definition at line 322 of file ml2d.cpp.

{
    initData();
    setNRef(n_ref);
}//close constructor

Member Function Documentation

addModel()

void ModelML2D::addModel

(

const ModelML2D &

model

)

Definition at line 404 of file ml2d.cpp.

{
    combineModel(model, 1);
}//close function addModel

combineModel()

void ModelML2D::combineModel	(	const ModelML2D &	model,
		int	sign
	)

Definition at line 360 of file ml2d.cpp.

{
    if (n_ref != model.n_ref)
        REPORT_ERROR(ERR_VALUE_INCORRECT, "Can not add models with different 'n_ref'");

#define COMBINE(var) var += sign * model.var
    COMBINE(wsum_sigma_offset);
    COMBINE(wsum_sigma_noise);
    COMBINE(sumw_allrefs);
    COMBINE(sumw_allrefs2);
    COMBINE(sumfracweight);
    COMBINE(LL);

    MultidimArray<double> tmp;
    double sumweight = 0., w1 = 0., w2 = 0.;

    for (int refno = 0; refno < n_ref; refno++)
    {
        w1 = WsumMref[refno].weight();
        w2 = sign * model.WsumMref[refno].weight();
        tmp = model.WsumMref[refno]();
        tmp *= sign;
        WsumMref[refno]() += tmp;
        sumweight = w1 + w2;

        if (sumweight > 0.)
        {
            Iref[refno].setWeight(sumweight);
            WsumMref[refno].setWeight(sumweight);
            COMBINE(sumw_mirror[refno]);
            COMBINE(sumwsc[refno]);
        }
        else
        {
            Iref[refno]().initZeros();
            WsumMref[refno]().initZeros();
            Iref[refno].setWeight(0);
            WsumMref[refno].setWeight(0.);
            sumw_mirror[refno] = 0.;
            sumwsc[refno] = 0.;
        }
    }
}//close function combineModel

initData()

void ModelML2D::initData

(

)

Definition at line 328 of file ml2d.cpp.

{
    n_ref = -1;
    sumw_allrefs2 = sumw_allrefs = 0.;
    do_student = do_norm = false;
    do_student_sigma_trick = true;
    sigma_noise = sigma_offset = LL = avePmax = 0.;
    wsum_sigma_noise = wsum_sigma_offset = 0.;
    sumfracweight = 0.;
    dim = 0;
}//close function initData

print()

void ModelML2D::print

(

int

tabs = 0

)

const

Just for debugging now.

Definition at line 475 of file ml2d.cpp.

{
    String stabs = "";
    for (int t = 0; t < tabs; ++t)
        stabs += " ";

    std::cerr << "======================= Block ==================== " << std::endl;

    std::cerr << "sumw_allrefs: " << sumw_allrefs << std::endl;
    std::cerr << "wsum_sigma_offset: " << wsum_sigma_offset << std::endl;
    std::cerr << "wsum_sigma_noise: " << wsum_sigma_noise << std::endl;
    std::cerr << "sigma_offset: " << sigma_offset << std::endl;
    std::cerr << "sigma_noise: " << sigma_noise << std::endl;
    std::cerr << "LL: " << LL << std::endl;

    std::stringstream ss1, ss2, ss3, ss4, ss5, ss6, ss7;
    pp(ss1, "refno:");
    pp(ss3, "sumw_mirror:");
    pp(ss4, "alpha_k:");
    pp(ss5, "mirror_fraction");
    pp(ss6, "WsumMref.weight");
    pp(ss7, "Iref.weight");

    for (int refno = 0; refno < n_ref; refno++)
    {
        pp(ss1, refno);
        pp(ss3, sumw_mirror[refno]);
        pp(ss4, alpha_k[refno]);
        pp(ss5, mirror_fraction[refno]);
        pp(ss6, WsumMref[refno].weight());
        pp(ss7, Iref[refno].weight());
    }
    std::cerr << ss1.str() << std::endl<< ss3.str() << std::endl
    << ss4.str() << std::endl<< ss5.str() << std::endl << ss6.str() << std::endl << ss7.str()<< std::endl;

}//close function print

setNRef()

void ModelML2D::setNRef

(

int

n_ref

)

Before call this function model.n_ref should be properly setted.

Definition at line 342 of file ml2d.cpp.

{
    Image<double> Iempty;
    Iempty().initZeros(dim,dim);
    Iempty().setXmippOrigin();
    this->n_ref = n_ref;
    Iref.resize(n_ref, Iempty);
    WsumMref.resize(n_ref, Iempty);
    alpha_k.resize(n_ref, 0.);
    mirror_fraction.resize(n_ref, 0.);
    scale.resize(n_ref, 1.);
    sumw_mirror.resize(n_ref, 0.);
    sumwsc.resize(n_ref, 0.);

}//close function setNRef

substractModel()

void ModelML2D::substractModel

(

const ModelML2D &

model

)

Definition at line 409 of file ml2d.cpp.

{
    combineModel(model, -1);
}//close function substractModel

update()

void ModelML2D::update

(

)

Definition at line 414 of file ml2d.cpp.

{
    if (sumw_allrefs < 0)
        REPORT_ERROR(ERR_VALUE_INCORRECT, "updateFractions: sumw_allrefs should be greater than 0 ");

    //update sigma_noise
    double sum = (do_student && do_student_sigma_trick) ? sumw_allrefs2
                 : sumw_allrefs;
    double sigma_noise2 = wsum_sigma_noise / (sum * dim * dim);

    if (sigma_noise2 < 0.)
        REPORT_ERROR(ERR_VALUE_INCORRECT, "sqrt of negative 'sigma_noise2'");
    sigma_noise = sqrt(sigma_noise2);

    //update sigma_offset
    if (wsum_sigma_offset < 0.)
        REPORT_ERROR(ERR_VALUE_INCORRECT, "sqrt of negative 'wsum_sigma_offset'");
    sigma_offset = sqrt(wsum_sigma_offset / (2. * sumw_allrefs));

    //update avePmax
    avePmax = sumfracweight / sumw_allrefs;

    double weight, inv_weight;

//    std::cerr << "DEBUG_JM: sumw_allrefs: " << sumw_allrefs << std::endl;

    for (int refno = 0; refno < n_ref; ++refno)
    {
        weight = WsumMref[refno].weight();

//        std::cerr << "    DEBUG_JM: refno: " << refno << std::endl;

        if (weight > 0.)
        {
            //update weights
            Iref[refno].setWeight(weight);
            inv_weight = 1 / weight; //just to speed-up
            Iref[refno]() = WsumMref[refno]();
            Iref[refno]() *= inv_weight;
            //update fractions
            alpha_k[refno] = weight / sumw_allrefs;
            mirror_fraction[refno] = sumw_mirror[refno] * inv_weight;
            scale[refno] = sumwsc[refno] * inv_weight;
//            std::cerr << "    DEBUG_JM: weight:     " << weight << std::endl;
//            std::cerr << "    DEBUG_JM: sumw_mirror[refno]: " << sumw_mirror[refno] << std::endl;
        }
        else
        {
//          std::cerr << "    DEBUG_JM: all zeros... " << std::endl;
            //zero weights
            Iref[refno].setWeight(0.);
            Iref[refno]().initZeros(WsumMref[refno]());
            alpha_k[refno] = 0.;
            mirror_fraction[refno] = 0.;
            scale[refno] = 0.;
        }
    }
}

Member Data Documentation

alpha_k

std::vector<double> ModelML2D::alpha_k

this is redundant information, since it can be obtained from the sums

Definition at line 93 of file ml2d.h.

avePmax

double ModelML2D::avePmax

Average height of the probability distribution at its maximum

Definition at line 97 of file ml2d.h.

dim

int ModelML2D::dim

Dimension of images

Definition at line 102 of file ml2d.h.

do_norm

bool ModelML2D::do_norm

Definition at line 104 of file ml2d.h.

do_student

bool ModelML2D::do_student

Algorithmic variants

Definition at line 104 of file ml2d.h.

do_student_sigma_trick

bool ModelML2D::do_student_sigma_trick

Definition at line 104 of file ml2d.h.

Iref

std::vector< Image<double> > ModelML2D::Iref

References images

Definition at line 85 of file ml2d.h.

LL

double ModelML2D::LL

the Log Likelihood

Definition at line 99 of file ml2d.h.

mirror_fraction

std::vector<double> ModelML2D::mirror_fraction

Definition at line 93 of file ml2d.h.

n_ref

int ModelML2D::n_ref

Number of reference images

Definition at line 83 of file ml2d.h.

scale

std::vector<double> ModelML2D::scale

Definition at line 93 of file ml2d.h.

sigma_noise

double ModelML2D::sigma_noise

Sigma value for expected pixel noise

Definition at line 87 of file ml2d.h.

sigma_offset

double ModelML2D::sigma_offset

sigma-value for origin offsets and its sum

Definition at line 89 of file ml2d.h.

sumfracweight

double ModelML2D::sumfracweight

Definition at line 97 of file ml2d.h.

sumw_allrefs

double ModelML2D::sumw_allrefs

Sums of weights

Definition at line 95 of file ml2d.h.

sumw_allrefs2

double ModelML2D::sumw_allrefs2

Definition at line 95 of file ml2d.h.

sumw_mirror

std::vector<double> ModelML2D::sumw_mirror

Definition at line 91 of file ml2d.h.

sumwsc

std::vector<double> ModelML2D::sumwsc

Vector containing sum of the weights of each reference and the mirrored ones

Definition at line 91 of file ml2d.h.

wsum_sigma_noise

double ModelML2D::wsum_sigma_noise

Definition at line 87 of file ml2d.h.

wsum_sigma_offset

double ModelML2D::wsum_sigma_offset

Definition at line 89 of file ml2d.h.

WsumMref

std::vector< Image<double> > ModelML2D::WsumMref

Definition at line 85 of file ml2d.h.

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The documentation for this class was generated from the following files:

• xmipp/libraries/reconstruction/ml2d.h
• xmipp/libraries/reconstruction/ml2d.cpp