ProgTransformDimRed Class Reference

#include <transform_dimred.h>

Inheritance diagram for ProgTransformDimRed:

Collaboration diagram for ProgTransformDimRed:

Public Member Functions
void	readParams ()
	Read argument from command line. More...
void	show ()
	Show. More...
void	defineParams ()
	Define parameters. More...
void	produceSideInfo ()
	Produce side info. More...
void	run ()
	Main routine. More...
void	insertImageInDataMatrix (size_t index, const MultidimArray< double > &mImg)
	From image to data matrix. More...
void	extractImageFromDataMatrix (size_t index, MultidimArray< double > &mImg)
	From image to data matrix. More...
double	progCorrelationDistance (size_t i1, size_t i2)
	Correlation distance between two images. More...
void	extractRandomProjections ()
Public Member Functions inherited from ProgDimRed
	ProgDimRed ()
	Empty constructor. More...
void	estimateDimension ()
	Estimate dimensionality. More...
Public Member Functions inherited from XmippProgram
const char *	getParam (const char *param, int arg=0)
const char *	getParam (const char *param, const char *subparam, int arg=0)
int	getIntParam (const char *param, int arg=0)
int	getIntParam (const char *param, const char *subparam, int arg=0)
double	getDoubleParam (const char *param, int arg=0)
double	getDoubleParam (const char *param, const char *subparam, int arg=0)
float	getFloatParam (const char *param, int arg=0)
float	getFloatParam (const char *param, const char *subparam, int arg=0)
void	getListParam (const char *param, StringVector &list)
int	getCountParam (const char *param)
bool	checkParam (const char *param)
bool	existsParam (const char *param)
void	addParamsLine (const String &line)
void	addParamsLine (const char *line)
ParamDef *	getParamDef (const char *param) const
virtual void	quit (int exit_code=0) const
virtual int	tryRun ()
void	initProgress (size_t total, size_t stepBin=60)
void	setProgress (size_t value=0)
void	endProgress ()
void	processDefaultComment (const char *param, const char *left)
void	setDefaultComment (const char *param, const char *comment)
virtual void	initComments ()
void	setProgramName (const char *name)
void	addUsageLine (const char *line, bool verbatim=false)
void	clearUsage ()
void	addExampleLine (const char *example, bool verbatim=true)
void	addSeeAlsoLine (const char *seeAlso)
void	addKeywords (const char *keywords)
const char *	name () const
virtual void	usage (int verb=0) const
virtual void	usage (const String &param, int verb=2)
int	version () const
virtual void	show () const
virtual void	read (int argc, const char **argv, bool reportErrors=true)
virtual void	read (int argc, char **argv, bool reportErrors=true)
void	read (const String &argumentsLine)
	XmippProgram ()
	XmippProgram (int argc, const char **argv)
virtual	~XmippProgram ()

Public Attributes
FileName	fnRandomSampling
int	numGrids
String	distance
MetaDataVec	SFin
Mask	mask
MultidimArray< double >	I1
MultidimArray< double >	I2
Matrix2D< double >	M
AlignmentAux	aux
CorrelationAux	aux2
RotationalCorrelationAux	aux3
Public Attributes inherited from ProgDimRed
FileName	fnIn
FileName	fnOut
FileName	fnMapping
int	outputDim
String	dimRefMethod
String	dimEstMethod
int	kNN
int	Niter
double	t
double	sigma
bool	global
Matrix2D< double >	X
DimRedAlgorithm *	algorithm
PCA	algorithmPCA
LTSA	algorithmLTSA
DiffusionMaps	algorithmDiffusionMaps
LLTSA	algorithmLLTSA
LPP	algorithmLPP
KernelPCA	algorithmKernelPCA
ProbabilisticPCA	algorithmProbabilisticPCA
LaplacianEigenmap	algorithmLaplacianEigenmap
HessianLLE	algorithmHessianLLE
NPE	algorithmNPE
SPE	algorithmSPE
Public Attributes inherited from XmippProgram
bool	doRun
bool	runWithoutArgs
int	verbose
	Verbosity level. More...
int	debug

Additional Inherited Members
Protected Member Functions inherited from XmippProgram
void	defineCommons ()
Protected Attributes inherited from XmippProgram
int	errorCode
ProgramDef *	progDef
	Program definition and arguments parser. More...
std::map< String, CommentList >	defaultComments
int	argc
	Original command line arguments. More...
const char **	argv

Detailed Description

Analyze cluster parameters.

Definition at line 38 of file transform_dimred.h.

Member Function Documentation

defineParams()

void ProgTransformDimRed::defineParams ( )

virtual

Define parameters.

Reimplemented from ProgDimRed.

Definition at line 55 of file transform_dimred.cpp.

{
    addUsageLine("This program takes an input metadata and projects each image onto a lower dimensional space using the selected method");
    setDefaultComment("-i","Input metadata");
    setDefaultComment("-o","Output metadata");
    ProgDimRed::defineParams();
    addParamsLine("  [--distance <d=Correlation>]    : Distance between images");
    addParamsLine("    where <d>");
    addParamsLine("         Euclidean:    Euclidean distance between images, no alignment");
    addParamsLine("         Correlation:  Correlation between images after alignment");
    addParamsLine("  [--randomSample <file> <num=3>] : Generates a random sample of the reduced map with num grids in each direction");
    addExampleLine("xmipp_transform_dimred -i images.xmd --randomSample randomSample.xmd");
}

extractImageFromDataMatrix()

void ProgTransformDimRed::extractImageFromDataMatrix	(	size_t	index,
		MultidimArray< double > &	mImg
	)

From image to data matrix.

Definition at line 146 of file transform_dimred.cpp.

{
    size_t index2 = 0;
    const MultidimArray<int> &mMask=mask.get_binary_mask();
    mImg.initZeros(mMask);
    FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(mImg)
    if (DIRECT_MULTIDIM_ELEM(mMask,n))
    {
        DIRECT_MULTIDIM_ELEM(mImg,n)=MAT_ELEM(X,index,index2);
        index2++;
    }
}

extractRandomProjections()

void ProgTransformDimRed::extractRandomProjections

(

)

Definition at line 159 of file transform_dimred.cpp.

{
    //number of grids in each axis
    int num = numGrids;

    size_t numParticles = SFin.size();
    std::vector<double> dimredProj;
    std::vector< Matrix1D< double > > coor;
    Matrix1D<double> dummy;
    dummy.resizeNoCopy(numParticles);
    for (int n = 0; n < outputDim; ++n)
        coor.push_back(dummy);

    // Keep the reduced coefficients
    size_t i = 0;
    for (size_t objId : SFin.ids())
    {
        SFin.getValue(MDL_DIMRED, dimredProj, objId);
        for (int n = 0; n < outputDim; ++n)
            VEC_ELEM(coor[n],i) = dimredProj[n];
        i++;
    }

    // We obtain the max and min coordinate values
    std::vector<double> minCoor, maxCoor;
    for (int n=0; n<outputDim; ++n)
    {
        double minval, maxval;
        coor[n].computeMinMax(minval, maxval);
        minCoor.push_back(minval);
        maxCoor.push_back(maxval);

    }

    Matrix2D <int> squares;
    squares.resizeNoCopy(numParticles, (int)pow(num+1,outputDim));

    Matrix1D <int> numElems;
    numElems.resizeNoCopy(MAT_XSIZE(squares));

    for (size_t i=0; i<numParticles; i++)
    {
        int index=0;
        for (int n=(outputDim-1); n>=0; --n)
        {
            index*=num;
            //std::cout << "minCoor : " << minCoor[n] << std::endl;
            //std::cout << "maxCoor : " << maxCoor[n] << std::endl;
            //std::cout << "VEC_ELEM(coor[n],i) : " << VEC_ELEM(coor[n],i) << std::endl;

            index+=(int)floor(( ( VEC_ELEM(coor[n],i) - minCoor[n]) / (maxCoor[n] - minCoor[n]))*num);
        }


        MAT_ELEM(squares,VEC_ELEM(numElems,index),index)=i;
        VEC_ELEM(numElems,index)++;
    }

    int numElemFirstRow = 0;
    for (size_t k=0; k < MAT_XSIZE(squares); k++)
        if (VEC_ELEM(numElems,k)!=0)
            numElemFirstRow++;

    std::vector<Matrix1D<double> > selectedCoor;
    dummy.resizeNoCopy(numElemFirstRow);
    for (int n=0; n<outputDim; ++n)
        selectedCoor.push_back(dummy);

    //Metadata with the well sampled projection and random projections assigned
    MetaDataVec SFout;
    int indx = 0;
    randomize_random_generator();
    std::vector<String> fnImg;
    SFin.getColumnValues(MDL_IMAGE,fnImg);
    for (size_t k=0; k <MAT_XSIZE(squares); k++)
    {
        if (MAT_ELEM(squares,0,k)!=0)
        {
            int randomN = round((rnd_unif(0,1))*VEC_ELEM(numElems,k));
            for (int n=0; n<outputDim; ++n)
                VEC_ELEM(selectedCoor[n],indx)=VEC_ELEM(coor[n],MAT_ELEM(squares,randomN,k));
            size_t id=SFout.addObject();
            SFout.setValue(MDL_IMAGE,fnImg[MAT_ELEM(squares,randomN,k)],id);
            SFout.setValue(MDL_ANGLE_ROT,(rnd_unif(0,360)-180),id);
            SFout.setValue(MDL_ANGLE_TILT,(rnd_unif(0,180)),id);
            SFout.setValue(MDL_ANGLE_TILT,(rnd_unif(0,180)),id);
            SFout.setValue(MDL_ANGLE_PSI,(rnd_unif(0,360)),id);
            indx++;
        }
    }

    SFout.write(fnRandomSampling);
}

insertImageInDataMatrix()

void ProgTransformDimRed::insertImageInDataMatrix	(	size_t	index,
		const MultidimArray< double > &	mImg
	)

From image to data matrix.

Definition at line 134 of file transform_dimred.cpp.

{
    size_t index2 = 0;
    const MultidimArray<int> &mMask=mask.get_binary_mask();
    FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(mImg)
    if (DIRECT_MULTIDIM_ELEM(mMask,n))
    {
        MAT_ELEM(X,index,index2)=DIRECT_MULTIDIM_ELEM(mImg,n);
        index2++;
    }
}

produceSideInfo()

void ProgTransformDimRed::produceSideInfo ( )

virtual

Produce side info.

Reimplemented from ProgDimRed.

Definition at line 85 of file transform_dimred.cpp.

{
    ProgDimRed::produceSideInfo();

    // Read input selfile
    SFin.read(fnIn);
    if (SFin.size()==0)
        return;
    SFin.removeDisabled();

    // Adjust number of grid points
    //JV I do not know why is this line below here and who has written!
    //numGrids=floor(sqrt((double)(SFin.size())));

    MetaDataVec SFaux;
    SFaux.removeDuplicates(SFin,MDL_IMAGE);
    SFin=SFaux;

    // Design Mask
    size_t Xdim, Ydim, Zdim, Ndim;
    getImageSize(SFin,Xdim,Ydim,Zdim,Ndim);

    mask.type = BINARY_CIRCULAR_MASK;
    mask.mode = INNER_MASK;
    mask.R1 = std::sqrt(0.25*Xdim*Xdim+0.25*Ydim*Ydim);
    mask.resize(Ydim,Xdim);
    mask.generate_mask();

    const MultidimArray<int> &mMask=mask.get_binary_mask();
    X.resizeNoCopy(SFin.size(),mMask.sum());

    // Copy images
    Image<double> img;
    size_t index = 0;
    for (size_t objId : SFin.ids())
    {
        img.readApplyGeo(SFin, objId);
        insertImageInDataMatrix(index++, img());
    }
    algorithm->setInputData(X);

    // Set distance
    prog=this;
    if (distance=="Correlation")
        algorithm->distance=&correlationDistance;
    else
        algorithm->distance=NULL;
}

progCorrelationDistance()

double ProgTransformDimRed::progCorrelationDistance	(	size_t	i1,
		size_t	i2
	)

Correlation distance between two images.

Definition at line 71 of file transform_dimred.cpp.

{
    extractImageFromDataMatrix(i1,I1);
    extractImageFromDataMatrix(i2,I2);
    double corr=alignImages(I1,I2,M,true,aux,aux2,aux3);
    return 1.-corr;
}

readParams()

void ProgTransformDimRed::readParams ( )

virtual

Read argument from command line.

Reimplemented from ProgDimRed.

Definition at line 30 of file transform_dimred.cpp.

{
    ProgDimRed::readParams();
    if (checkParam("--randomSample"))
    {
        fnRandomSampling  = getParam("--randomSample",0);
        numGrids  =  getIntParam("--randomSample",1);
    }
    distance=getParam("--distance");
}

run()

void ProgTransformDimRed::run ( )

virtual

Main routine.

Reimplemented from XmippProgram.

Definition at line 254 of file transform_dimred.cpp.

{
    show();

    produceSideInfo();
    if (outputDim<0)
        estimateDimension();

    if (!SFin.containsLabel(MDL_DIMRED))
    {

        algorithm->reduceDimensionality();

        std::vector<double> dimredProj;
        dimredProj.resize(outputDim);
        int i=0;
        const Matrix2D<double> &Y=algorithm->getReducedData();
        for (size_t objId : SFin.ids())
        {
            memcpy(&dimredProj[0],&MAT_ELEM(Y,i,0),outputDim*sizeof(double));
            SFin.setValue(MDL_DIMRED, dimredProj, objId);
            i++;
        }

        SFin.write(fnIn,MD_APPEND);
    }

    if (fnRandomSampling!="")
        extractRandomProjections();
}

show()

void ProgTransformDimRed::show ( )

virtual

Show.

Reimplemented from ProgDimRed.

Definition at line 42 of file transform_dimred.cpp.

{
    if (verbose>0)
    {
        ProgDimRed::show();
        std::cout << "Distance:      " << distance << std::endl;
        if (fnRandomSampling!="")
            std::cout << "Random sample output:     " << fnRandomSampling << std::endl
                      << "Number of sampling grids: " << numGrids         << std::endl;
    }
}

Member Data Documentation

aux

AlignmentAux ProgTransformDimRed::aux

Definition at line 54 of file transform_dimred.h.

aux2

CorrelationAux ProgTransformDimRed::aux2

Definition at line 55 of file transform_dimred.h.

aux3

RotationalCorrelationAux ProgTransformDimRed::aux3

Definition at line 56 of file transform_dimred.h.

distance

String ProgTransformDimRed::distance

Distance between images

Definition at line 46 of file transform_dimred.h.

fnRandomSampling

FileName ProgTransformDimRed::fnRandomSampling

Filename selection file containing the images

Definition at line 42 of file transform_dimred.h.

I1

MultidimArray<double> ProgTransformDimRed::I1

Definition at line 52 of file transform_dimred.h.

I2

MultidimArray<double> ProgTransformDimRed::I2

Definition at line 52 of file transform_dimred.h.

M

Matrix2D<double> ProgTransformDimRed::M

Definition at line 53 of file transform_dimred.h.

mask

Mask ProgTransformDimRed::mask

Definition at line 49 of file transform_dimred.h.

numGrids

int ProgTransformDimRed::numGrids

Number of grids for the random sampling

Definition at line 44 of file transform_dimred.h.

SFin

MetaDataVec ProgTransformDimRed::SFin

Definition at line 48 of file transform_dimred.h.

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

• xmipp/libraries/dimred/transform_dimred.h
• xmipp/libraries/dimred/transform_dimred.cpp