SubStructure Class Reference

#include <MStruct.h>

Collaboration diagram for SubStructure:

Public Types
enum	DistrType { EMD_PCA =0, EMD_GAUSS, EMD_RECT, EMD_RECTTF }
enum	Modes { MODE_NONE =0, MODE_NOSPAWN =2, MODE_SHOWSTATS =4 }

Public Member Functions
	SubStructure (const std::string &subStructName="", const std::string &supStructName="", const PropTF &transform=PropTF(0.f), int pivot=-1)
void	clear ()
void	analyseTF (const DMatrixf &tfmat)
EMDistribution *	generateEMDist (const PropVec &wprop, float ppmm, bool inverse=false, dword dtype=EMD_RECT) const
void	getLBUB (PropVec &lb, PropVec &ub, const PropVec &wprop, float ppmm, float radius=3) const
bool	read (ParseFile &is)

Public Attributes
std::string	m_SubStructName
std::string	m_SupStructName
PropTF	m_Transform
int	m_Pivot
bool	m_Polar
PropVec	m_Mean
PropVec	m_Stdev
DMatrixf	m_PC
DMatrixf	m_Sigma
DMatrixf	m_IPC
float	m_RateWeight
float	m_RateTH
dword	m_Mode

Friends
std::ostream &	operator<< (std::ostream &os, const SubStructure &ss)

Detailed Description

Definition at line 21 of file MStruct.h.

Member Enumeration Documentation

enum SubStructure::DistrType

Enumerator
EMD_PCA
EMD_GAUSS
EMD_RECT
EMD_RECTTF

Definition at line 24 of file MStruct.h.

{EMD_PCA=0, EMD_GAUSS, EMD_RECT, EMD_RECTTF};

enum SubStructure::Modes

Enumerator
MODE_NONE
MODE_NOSPAWN
MODE_SHOWSTATS

Definition at line 25 of file MStruct.h.

{MODE_NONE=0, MODE_NOSPAWN=2, MODE_SHOWSTATS=4 };

Constructor & Destructor Documentation

SubStructure::SubStructure	(	const std::string &	subStructName = "",
		const std::string &	supStructName = "",
		const PropTF &	transform = PropTF(0.f),
		int	pivot = -1
	)

Definition at line 636 of file MStruct.cpp.

    : m_SubStructName(subStructName),m_SupStructName(subStructName),
      m_Transform(transform), m_Pivot(pivot),
      m_Polar(false), m_RateWeight(SUBSTRUCT_RATEWEIGHT),
      m_RateTH(SUBSTRUCT_RATETH), m_Mode(MODE_NONE)
{
}

Member Function Documentation

void SubStructure::analyseTF

(

const DMatrixf &

tfmat

)

Definition at line 646 of file MStruct.cpp.

References StructTable::adjustByAvgDir(), DMatrix< T >::at(), dmutil::avg(), DUMP, DMatrix< T >::empty(), dmutil::expand(), DMatrix< T >::getDiag(), DMatrix< T >::getRange(), getSearchPara(), dmutil::inverse(), m_IPC, m_Mean, m_Mode, m_PC, SearcherParams::m_PCTH, m_Sigma, m_Stdev, MODE_SHOWSTATS, DMatrix< T >::mulRight(), PVEC_DIR, DMatrix< T >::resize(), DMatrix< T >::setRange(), VVector< T, D >::size(), DMatrix< T >::sizeX(), DMatrix< T >::sizeY(), dmutil::sqrt(), dmutil::stdev(), dmutil::SVD(), and DMatrix< T >::transpose().

Referenced by MStructure::buildAllStats().

{
    using namespace dmutil;
    if(tfmat.empty() ||tfmat.sizeX()!=PropVec::size()) {
        m_PC = m_IPC = makeIdentity<float>(PropVec::size()+1);
        m_Sigma.resize(1,4); m_Sigma = 0.f;
        m_Mean = m_Stdev = 0.f;
        return;
    }
    bool show = false && (m_Mode&MODE_SHOWSTATS);
    if(show) DUMP(tfmat);
    DMatrixf ntfmat(tfmat);
    DMatrixf angles(1,ntfmat.sizeY());
    ntfmat.getRange(PVEC_DIR, 0, angles);
    StructTable::adjustByAvgDir(angles);
    ntfmat.setRange(PVEC_DIR, 0, angles);
    //todo: switch to polar position (translation)
//         ofstream f1("tfmat.dat");
//         f1 << tfmat;
//         ofstream f2("ids.dat");
//         copy(comod.begin(), comod.end(), ostream_iterator<dword>(f2, "\n"));
    //build a (0,1) standardized matrix of the distribution
    DMatrixf avghg(avg(ntfmat));
    DMatrixf stdevhg(stdev(ntfmat));
    DMatrixf mavg(expand(avghg, 1,ntfmat.sizeY()));
    DMatrixf mstdev(expand(stdevhg, 1,ntfmat.sizeY()));
    ntfmat -= mavg; ntfmat /= mstdev;
    //build a normalized covariance matrix
    DMatrixf tfcov(ntfmat);
    tfcov.transpose();
    tfcov = tfcov.mulRight(ntfmat);
    tfcov *= (1.f/(ntfmat.sizeY())); //normalize by number of samples
    if(show) DUMP(tfcov);
    DMatrixf mU, mS, mV;
    dmutil::SVD(tfcov, mU, mS, mV); // TODO
    m_Sigma = mS.getDiag();
    float relvar = 1.f/4; //1.f/dmutil::sum(m_Sigma).at(0,0); // has to be 1/4
    for(dword i=0;i<m_Sigma.sizeY(); i++)
        if(m_Sigma.at(0,i)*relvar < getSearchPara().m_PCTH)
            m_Sigma.at(0,i) = 0.f;
    dmutil::sqrt(m_Sigma);
    m_Mean = &avghg.at(0,0);
    m_Stdev = &stdevhg.at(0,0);
    if(show) DUMP(mU << mS << mV);
//make a homogeneous matrix to integrate de-standardization
    //m_Sigma.resize(1,m_Sigma.sizeY()+1,1.f);
    //mS = makeDiag(m_Sigma);
//     avghg.transpose();
//     avghg.resize(1,avghg.sizeY()+1,1.f);
//     stdevhg.transpose();
//     stdevhg.resize(1,stdevhg.sizeY()+1,1.f);
//     DMatrixf mVhg(makeIdentity<float>(mV.sizeX()+1));
//     mVhg.setRange(0,0,mV);
//     //mVhg.transpose(); //no transposed, or not?
//     //m_PC = makeDiag(stdevhg).mulRight(mVhg.mulRight(mS));
//     m_PC = makeDiag(stdevhg).mulRight(mVhg);
//     m_PC.setRange(m_PC.sizeX()-1,0,avghg);
    m_PC = mV;
    m_IPC = inverse(m_PC);
    //cout << m_Sigma << m_Mean << endl << m_Stdev << endl;
//     DUMP(m_SubStructName);
//     DUMP(m_Mean);
//     DUMP(m_Stdev);
}

void SubStructure::clear

(

)

Definition at line 822 of file MStruct.cpp.

References m_Mode, m_Pivot, m_Polar, m_RateTH, m_RateWeight, m_SubStructName, m_SupStructName, m_Transform, MODE_NONE, SUBSTRUCT_RATETH, and SUBSTRUCT_RATEWEIGHT.

Referenced by read().

{
    m_SubStructName.clear();
    m_SupStructName.clear();
    m_Transform = 0.f;
    m_Pivot = -1;
    m_Polar = false;
    m_Mode = MODE_NONE;
    m_RateWeight = SUBSTRUCT_RATEWEIGHT;
    m_RateTH = SUBSTRUCT_RATETH;
}

EMDistribution * SubStructure::generateEMDist	(	const PropVec &	wprop,
		float	ppmm,
		bool	inverse = false,
		dword	dtype = EMD_RECT
	)		const

Definition at line 711 of file MStruct.cpp.

References DMatrix< T >::at(), ExpectationMap::correctLBUB(), EMD_GAUSS, EMD_PCA, EMD_RECT, EMD_RECTTF, DMatrix< T >::empty(), fwdPropTF(), getIdentityPropTF(), getPropPos(), getSearchPara(), invPropTF(), m_IPC, m_Mean, m_PC, SearcherParams::m_ScaleStd, m_Sigma, m_Stdev, DMatrix< T >::mulLeft(), NULL, PVEC_POSX, PVEC_POSY, EMDXformer::setMean(), setPropPos(), DMatrix< T >::sizeX(), and dmutil::sqrt().

Referenced by MStructure::addExpectation(), and MStructure::showStats().

{
    //ATTENTION: backward transform isn't working the way I'm doing it here
    // so, only use forward transform
    EMDistribution* emdist = NULL;
    switch(DistrType(dtype)) {
    case EMD_PCA:
    {
        if(m_Sigma.empty()) break;
        //generate a transformed gaussian distribution (using PCA xform)
        DMatrixf stddm(m_Sigma);
        stddm *= getSearchPara().m_ScaleStd;
        PropVec stdtf(&stddm.at(0,0));
        EMDGauss* eminput = new EMDGauss(PropVec(0.f), stdtf);
        //EMDRect* eminput = new EMDRect(stdtf*-1.f, stdtf);
        DMatrixf tfmat = backwards ? m_IPC : m_PC;
#ifndef _PROPTF_NORMALIZE_SCALE_
        DMatrixf mmmat = dmutil::makeIdentity<float>(tfmat.sizeX());
        mmmat.at(PVEC_POSX,PVEC_POSX) = ppmm;
        mmmat.at(PVEC_POSY,PVEC_POSY) = ppmm;
        tfmat = tfmat.mulLeft(mmmat);
#endif
        emdist = (EMDistribution*) new EMDXformer(eminput, wprop, tfmat);
        ((EMDXformer*)emdist)->setMean(m_Mean);
        ((EMDXformer*)emdist)->setStdev(m_Stdev);
    }
    break;
    case EMD_RECT:
    {
        //generate a rectangular uniform distribution
        PropVec propsd(m_Stdev);
        //propsd*=sqrt(3.f);
        PropVec lb(m_Mean-propsd);
        PropVec ub(m_Mean+propsd);
#ifndef _PROPTF_NORMALIZE_SCALE_
        setPropPos(lb, getPropPos(lb)*ppmm);
        setPropPos(ub, getPropPos(ub)*ppmm);
#endif
        PropVec olb(wprop), oub(wprop);
        if(backwards) { invPropTF(olb, ub); invPropTF(oub, lb); }
        else { fwdPropTF(olb, lb); fwdPropTF(oub, ub); }
        PropVec mean(m_Mean);
        setPropPos(mean, getPropPos(mean)*ppmm);
        PropVec a(wprop);
        ExpectationMap::correctLBUB(olb, oub);
        emdist = (EMDistribution*) new EMDRect(olb,oub);
    }
    break;
    case EMD_RECTTF:
    {
        //generate a rectangular uniform distribution
        PropVec propsd(m_Stdev);
        propsd*=sqrt(3.f);
        PropVec lb(m_Mean-propsd);
        PropVec ub(m_Mean+propsd);
#ifndef _PROPTF_NORMALIZE_SCALE_
        setPropPos(lb, getPropPos(lb)*ppmm);
        setPropPos(ub, getPropPos(ub)*ppmm);
#endif
        PropVec olb(getIdentityPropTF()), oub(getIdentityPropTF());
        if(backwards) { invPropTF(olb, lb); invPropTF(oub, ub); }
        else { fwdPropTF(olb, lb); fwdPropTF(oub, ub); }
        ExpectationMap::correctLBUB(olb, oub);
        EMDistribution* inpdist = (EMDistribution*) new EMDRect(olb,oub);
        emdist = (EMDistribution*) new EMDXformer(inpdist, wprop);
    }
    break;
    case EMD_GAUSS:
    {
        //generate a multidimensional axis-aligned gaussian distribution
        PropVec sdevpv(m_Stdev);
        sdevpv *= getSearchPara().m_ScaleStd;
        PropVec meanpv(m_Mean);
#ifndef _PROPTF_NORMALIZE_SCALE_
        setPropPos(sdevpv, getPropPos(sdevpv)*ppmm);
        setPropPos(meanpv, getPropPos(meanpv)*ppmm);
#endif
        PropVec cprop(getIdentityPropTF());
        if(backwards) invPropTF(cprop, meanpv);
        else fwdPropTF(cprop, meanpv); //cool form of: cprop = meanpv
        EMDistribution* inpdist =
            (EMDistribution*) new EMDGauss(PropVec(0.f), sdevpv);
        emdist = (EMDistribution*) new EMDXformer(inpdist, wprop);
        ((EMDXformer*)emdist)->setMean(cprop);
    }
    break;
    }
    return emdist;
}

void SubStructure::getLBUB	(	PropVec &	lb,
		PropVec &	ub,
		const PropVec &	wprop,
		float	ppmm,
		float	radius = 3
	)		const

Definition at line 803 of file MStruct.cpp.

References fwdPropTF(), getPropPos(), getPropScale(), m_Mean, M_PI, m_Stdev, setPropDir(), setPropPos(), and setPropScale().

Referenced by MStructure::addExpectation().

{
    lb = ub = wprop;
    PropVec tflb(m_Mean);
    tflb -= (m_Stdev*radius);
    PropVec tfub(m_Mean);
    tfub += (m_Stdev*radius);
#ifndef _PROPTF_NORMALIZE_SCALE_
    setPropPos(tflb, getPropPos(tflb)*ppmm);
    setPropPos(tfub, getPropPos(tfub)*ppmm);
#endif
    fwdPropTF(lb, tflb);
    fwdPropTF(ub, tfub);
    if(getPropScale(lb)<0.001) setPropScale(lb, 0.001);
    setPropDir(lb, 0);
    setPropDir(ub, 2*M_PI);
}

bool SubStructure::read

(

ParseFile &

is

)

Definition at line 834 of file MStruct.cpp.

References clear(), ParseFile::error(), fromString(), ParseFile::getKey(), ParseFile::getNextLine(), ParseFile::getValue(), m_Mode, m_Pivot, m_RateTH, m_RateWeight, m_SubStructName, m_Transform, MODE_NOSPAWN, MODE_SHOWSTATS, and ParseFile::setParseError().

Referenced by MStructure::hasSupStruct(), and MStructure::read().

{
    if(is.getKey() != "substruct") return false;
    clear();
    m_SubStructName = is.getValue();
    bool readon = true;
    while(readon && is.getNextLine()) {
        const string& key = is.getKey();
        const string& value = is.getValue();
        if(key == "transform") {
            fromString(value, m_Transform);
        } else if(key == "pivot") {
            fromString(value, m_Pivot);
            m_Pivot--;
        } else if(key == "rateweight") {
            fromString(value, m_RateWeight);
        } else if(key == "rateth") {
            fromString(value, m_RateTH);
        } else if(key == "mode") {
            if(value.find("nospawn") != value.npos)
                m_Mode |= MODE_NOSPAWN;
            if(value.find("showstats") != value.npos)
                m_Mode |= MODE_SHOWSTATS;
        } else if (key == "end") readon = false;
        else { is.setParseError("error parsing substructure"); return false; }
    }
    if(is.error()) return false;
    return true;
}

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  os, const SubStructure &  ss  )

friend

Definition at line 864 of file MStruct.cpp.

{
    os << "  substruct " << ss.m_SubStructName << endl;
    os << "    transform " << ss.m_Transform << endl;
    if(ss.m_Pivot>=0)
        os << "    pivot " << ss.m_Pivot+1 << endl;
    if(ss.m_Polar) os << "    polar" << endl;
    if(ss.m_RateWeight != SUBSTRUCT_RATEWEIGHT)
        os << "    rateweight " << ss.m_RateWeight << endl;
    if(ss.m_Mode != SubStructure::MODE_NONE) {
        os << "    mode"
           << (ss.m_Mode&SubStructure::MODE_NOSPAWN ? " nospawn" : "")
           << (ss.m_Mode&SubStructure::MODE_SHOWSTATS ? " showstats" : "")
           << endl;
    }
    os << "  end    # of substruct" << endl;
    return os;
}

Member Data Documentation

DMatrixf SubStructure::m_IPC

Definition at line 46 of file MStruct.h.

Referenced by analyseTF(), and generateEMDist().

PropVec SubStructure::m_Mean

Definition at line 45 of file MStruct.h.

Referenced by analyseTF(), generateEMDist(), getLBUB(), and MStructure::showStats().

dword SubStructure::m_Mode

Definition at line 48 of file MStruct.h.

Referenced by MStructure::addExpectation(), analyseTF(), MStructure::buildAllStats(), clear(), operator<<(), and read().

DMatrixf SubStructure::m_PC

Definition at line 46 of file MStruct.h.

Referenced by analyseTF(), and generateEMDist().

int SubStructure::m_Pivot

Definition at line 43 of file MStruct.h.

Referenced by MStructure::addExpectation(), MStructure::buildAllStats(), clear(), operator<<(), read(), and MStructure::showStats().

bool SubStructure::m_Polar

Definition at line 44 of file MStruct.h.

Referenced by clear(), and operator<<().

float SubStructure::m_RateTH

Definition at line 47 of file MStruct.h.

Referenced by clear(), StructTable::findBestConnection(), and read().

float SubStructure::m_RateWeight

Definition at line 47 of file MStruct.h.

Referenced by MStructure::addExpectation(), clear(), StructTable::findBestConnection(), operator<<(), StructPath::print(), and read().

DMatrixf SubStructure::m_Sigma

Definition at line 46 of file MStruct.h.

Referenced by analyseTF(), generateEMDist(), and MStructure::showStats().

PropVec SubStructure::m_Stdev

Definition at line 45 of file MStruct.h.

Referenced by analyseTF(), generateEMDist(), getLBUB(), and MStructure::showStats().

std::string SubStructure::m_SubStructName

Definition at line 41 of file MStruct.h.

Referenced by MStructure::addSubStruct(), MStructure::buildAllStats(), clear(), operator<<(), read(), and MStructure::showStats().

std::string SubStructure::m_SupStructName

Definition at line 41 of file MStruct.h.

Referenced by clear(), and MStructure::showStats().

PropTF SubStructure::m_Transform

Definition at line 42 of file MStruct.h.

Referenced by clear(), operator<<(), and read().

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

• src/MStruct.h
• src/MStruct.cpp