ProgDimRed Class Reference

#include <matrix_dimred.h>

Inheritance diagram for ProgDimRed:

Collaboration diagram for ProgDimRed:

Public Member Functions
	ProgDimRed ()
	Empty constructor. More...
virtual void	readParams ()
	Read argument from command line. More...
virtual void	show ()
	Show. More...
virtual void	defineParams ()
	Define parameters. More...
virtual void	produceSideInfo ()
	Produce side info. 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	run ()
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	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

Program Dimred.

Definition at line 47 of file matrix_dimred.h.

Constructor & Destructor Documentation

ProgDimRed()

ProgDimRed::ProgDimRed

(

)

Empty constructor.

Definition at line 29 of file matrix_dimred.cpp.

{
    algorithm=NULL;
}

Member Function Documentation

defineParams()

void ProgDimRed::defineParams ( )

virtual

Define parameters.

Reimplemented from XmippProgram.

Reimplemented in ProgMatrixDimRed, and ProgTransformDimRed.

Definition at line 83 of file matrix_dimred.cpp.

{
    processDefaultComment("-i","-i <input>");
    processDefaultComment("-o","[-o <output=\"\">]");
    addParamsLine("  [-m <dimRefMethod=PCA>]: Dimensionality Reduction method selected");
    addParamsLine("      where <dimRefMethod>");
    addParamsLine("             PCA            : Principal Component Analysis");
    addParamsLine("             LTSA <k=12>    : Local Tangent Space Alignment, k=number of nearest neighbours");
    addParamsLine("             DM <s=1> <t=1> : Diffusion map, t=Markov random walk, s=kernel sigma");
    addParamsLine("             LLTSA <k=12>   : Linear Local Tangent Space Alignment, k=number of nearest neighbours");
    addParamsLine("             LPP <k=12> <s=1> : Linearity Preserving Projection, k=number of nearest neighbours, s=kernel sigma");
    addParamsLine("             kPCA <s=1>     : Kernel PCA, s=kernel sigma");
    addParamsLine("             pPCA <n=200>   : Probabilistic PCA, n=number of iterations");
    addParamsLine("             LE <k=7> <s=1> : Laplacian Eigenmap, k=number of nearest neighbours, s=kernel sigma");
    addParamsLine("             HLLE <k=12>    : Hessian Locally Linear Embedding, k=number of nearest neighbours");
    addParamsLine("             SPE <k=12> <global=1> : Stochastic Proximity Embedding, k=number of nearest neighbours, global embedding or not");
    addParamsLine("             NPE <k=12>     : Neighborhood Preserving Embedding, k=number of nearest neighbours");
    addParamsLine("  [--dout <d=2> <method=CorrDim>] : Output dimension. Set to -1 for automatic estimation with a specific method");
    addParamsLine("       where <method>");
    addParamsLine("                  CorrDim: Correlation dimension");
    addParamsLine("                  MLE: Maximum Likelihood Estimate");
    addParamsLine("  [--saveMapping <fn=\"\">] : Save mapping if available (PCA, LLTSA, LPP, pPCA, NPE) so that it can be reused later (Y=X*M) (use the flag --more for details)");
    addParamsLine("                            :+Y is the output matrix with individuals as rows, M is the mapping matrix");
    addParamsLine("                            :+X is the input matrix with individuals as rows, with the mean subtracted from the columns");
    addParamsLine("                            :+Python code to generate X:");
    addParamsLine("                            :+    from numpy import loadtxt, mean, outer, ones");
    addParamsLine("                            :+    X_original = loadtxt('data.txt')");
    addParamsLine("                            :+    X = X_original - outer(ones(X_original.shape[0]),mean(X_original, axis=0))");
}

estimateDimension()

void ProgDimRed::estimateDimension

(

)

Estimate dimensionality.

Definition at line 166 of file matrix_dimred.cpp.

{
    outputDim=intrinsicDimensionality(X, dimEstMethod, false, algorithm->distance);
    algorithm->setOutputDimensionality(outputDim);
    std::cout << "Estimated dimensionality: " << outputDim << std::endl;
    if (outputDim<=0)
        REPORT_ERROR(ERR_NUMERICAL,"Cannot proceed without an output dimension");
}

produceSideInfo()

void ProgDimRed::produceSideInfo ( )

virtual

Produce side info.

Reimplemented in ProgMatrixDimRed, and ProgTransformDimRed.

Definition at line 114 of file matrix_dimred.cpp.

{
    if (dimRefMethod=="PCA")
    {
        algorithm=&algorithmPCA;
    } else if (dimRefMethod=="LTSA")
    {
        algorithm=&algorithmLTSA;
        algorithmLTSA.setSpecificParameters(kNN);
    } else if (dimRefMethod=="DM")
    {
        algorithm=&algorithmDiffusionMaps;
        algorithmDiffusionMaps.setSpecificParameters(t,sigma);
    } else if (dimRefMethod=="LLTSA")
    {
        algorithm=&algorithmLLTSA;
        algorithmLLTSA.setSpecificParameters(kNN);
    } else if (dimRefMethod=="LPP")
    {
        algorithm=&algorithmLPP;
        algorithmLPP.setSpecificParameters(kNN,sigma);
    } else if (dimRefMethod=="kPCA")
    {
        algorithm=&algorithmKernelPCA;
        algorithmKernelPCA.setSpecificParameters(sigma);
    } else if (dimRefMethod=="pPCA")
    {
        algorithm=&algorithmProbabilisticPCA;
        algorithmProbabilisticPCA.setSpecificParameters(Niter);
    } else if (dimRefMethod=="LE")
    {
        algorithm=&algorithmLaplacianEigenmap;
        algorithmLaplacianEigenmap.setSpecificParameters(sigma,kNN);
    } else if (dimRefMethod=="HLLE")
    {
        algorithm=&algorithmHessianLLE;
        algorithmHessianLLE.setSpecificParameters(kNN);
    } else if (dimRefMethod=="NPE")
    {
        algorithm=&algorithmNPE;
        algorithmNPE.setSpecificParameters(kNN);
    } else if (dimRefMethod=="SPE")
    {
        algorithm=&algorithmSPE;
        algorithmSPE.setSpecificParameters(kNN,global);
    }

    algorithm->setOutputDimensionality(outputDim);
    algorithm->fnMapping=fnMapping;
}

readParams()

void ProgDimRed::readParams ( )

virtual

Read argument from command line.

Reimplemented from XmippProgram.

Reimplemented in ProgMatrixDimRed, and ProgTransformDimRed.

Definition at line 34 of file matrix_dimred.cpp.

{
    fnIn = getParam("-i");
    fnOut = getParam("-o");
    fnMapping = getParam("--saveMapping");
    dimRefMethod = getParam("-m");
    outputDim  = getIntParam("--dout");
    dimEstMethod = getParam("--dout",1);

    if (dimRefMethod=="LTSA" || dimRefMethod=="LLTSA" || dimRefMethod=="LPP" || dimRefMethod=="LE" || dimRefMethod=="HLLE" ||
        dimRefMethod=="NPE" || dimRefMethod=="SPE")
        kNN=getIntParam("-m",1);
    if (dimRefMethod=="DM" || dimRefMethod=="kPCA")
        sigma=getDoubleParam("-m",1);
    if (dimRefMethod=="LPP" || dimRefMethod=="LE")
        sigma=getDoubleParam("-m",2);
    if (dimRefMethod=="DM")
        t=getDoubleParam("-m",2);
    if (dimRefMethod=="pPCA")
        Niter=getIntParam("-m",1);
    if (dimRefMethod=="SPE")
        global=getIntParam("-m",2)==1;
}

show()

void ProgDimRed::show ( )

virtual

Show.

Reimplemented in ProgMatrixDimRed, and ProgTransformDimRed.

Definition at line 59 of file matrix_dimred.cpp.

{
    if (verbose>0)
        std::cout
        << "Input metadata file:    " << fnIn          << std::endl
        << "Output metadata:        " << fnOut         << std::endl
        << "Output mapping:         " << fnMapping     << std::endl
        << "Dim Red Method:         " << dimRefMethod  << std::endl
        << "Dimension out:          " << outputDim     << std::endl
        ;
    if (dimRefMethod=="LTSA" || dimRefMethod=="LLTSA" || dimRefMethod=="LPP" || dimRefMethod=="LE" || dimRefMethod=="HLLE" ||
        dimRefMethod=="SPE" || dimRefMethod=="NPE")
        std::cout << "k=" << kNN << std::endl;
    if (dimRefMethod=="DM" || dimRefMethod=="kPCA" || dimRefMethod=="LPP" || dimRefMethod=="LE")
        std::cout << "sigma=" << sigma << std::endl;
    if (dimRefMethod=="DM")
        std::cout << "t=" << t << std::endl;
    if (dimRefMethod=="pPCA")
        std::cout << "Niter=" << Niter << std::endl;
    if (dimRefMethod=="SPE")
        std::cout << "Global=" << global << std::endl;
}

Member Data Documentation

algorithm

DimRedAlgorithm* ProgDimRed::algorithm

Definition at line 68 of file matrix_dimred.h.

algorithmDiffusionMaps

DiffusionMaps ProgDimRed::algorithmDiffusionMaps

Definition at line 71 of file matrix_dimred.h.

algorithmHessianLLE

HessianLLE ProgDimRed::algorithmHessianLLE

Definition at line 77 of file matrix_dimred.h.

algorithmKernelPCA

KernelPCA ProgDimRed::algorithmKernelPCA

Definition at line 74 of file matrix_dimred.h.

algorithmLaplacianEigenmap

LaplacianEigenmap ProgDimRed::algorithmLaplacianEigenmap

Definition at line 76 of file matrix_dimred.h.

algorithmLLTSA

LLTSA ProgDimRed::algorithmLLTSA

Definition at line 72 of file matrix_dimred.h.

algorithmLPP

LPP ProgDimRed::algorithmLPP

Definition at line 73 of file matrix_dimred.h.

algorithmLTSA

LTSA ProgDimRed::algorithmLTSA

Definition at line 70 of file matrix_dimred.h.

algorithmNPE

NPE ProgDimRed::algorithmNPE

Definition at line 78 of file matrix_dimred.h.

algorithmPCA

PCA ProgDimRed::algorithmPCA

Definition at line 69 of file matrix_dimred.h.

algorithmProbabilisticPCA

ProbabilisticPCA ProgDimRed::algorithmProbabilisticPCA

Definition at line 75 of file matrix_dimred.h.

algorithmSPE

SPE ProgDimRed::algorithmSPE

Definition at line 79 of file matrix_dimred.h.

dimEstMethod

String ProgDimRed::dimEstMethod

Definition at line 59 of file matrix_dimred.h.

dimRefMethod

String ProgDimRed::dimRefMethod

Method

Definition at line 59 of file matrix_dimred.h.

fnIn

FileName ProgDimRed::fnIn

Input metadata

Definition at line 51 of file matrix_dimred.h.

fnMapping

FileName ProgDimRed::fnMapping

Output mapping

Definition at line 55 of file matrix_dimred.h.

fnOut

FileName ProgDimRed::fnOut

Output metadata

Definition at line 53 of file matrix_dimred.h.

global

bool ProgDimRed::global

Definition at line 65 of file matrix_dimred.h.

kNN

int ProgDimRed::kNN

Method parameters

Definition at line 61 of file matrix_dimred.h.

Niter

int ProgDimRed::Niter

Definition at line 62 of file matrix_dimred.h.

outputDim

int ProgDimRed::outputDim

Output dimension

Definition at line 57 of file matrix_dimred.h.

sigma

double ProgDimRed::sigma

Definition at line 64 of file matrix_dimred.h.

t

double ProgDimRed::t

Definition at line 63 of file matrix_dimred.h.

X

Matrix2D<double> ProgDimRed::X

Definition at line 67 of file matrix_dimred.h.

---

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

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