ProgMatrixDimRed Class Reference

#include <matrix_dimred.h>

Inheritance diagram for ProgMatrixDimRed:

Collaboration diagram for ProgMatrixDimRed:

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...
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
int	inputDim
int	Nsamples
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

Dimensionality reduction for matrices

Definition at line 101 of file matrix_dimred.h.

Member Function Documentation

defineParams()

void ProgMatrixDimRed::defineParams ( )

virtual

Define parameters.

Reimplemented from ProgDimRed.

Definition at line 198 of file matrix_dimred.cpp.

{
    addUsageLine("This program takes an input matrix, whose rows are individual observations and ");
    addUsageLine("projects each sample onto a lower dimensional space using the selected method. Note: ");
    addUsageLine("that each observation component in a row should be separated by white spaces.");
    setDefaultComment("-i","Input matrix with data. Each observation is a row.");
    setDefaultComment("-o","Output matrix with projected data");
    ProgDimRed::defineParams();
    addParamsLine("   --din <d>             : Input dimension");
    addParamsLine("   --samples <N>         : Number of observations in the input matrix");
    addExampleLine("xmipp_matrix_dimred -i matrixIn.txt -o matrixOut.txt --din 30 --dout 2 --samples 1000");
}

produceSideInfo()

void ProgMatrixDimRed::produceSideInfo ( )

virtual

Produce side info.

Reimplemented from ProgDimRed.

Definition at line 212 of file matrix_dimred.cpp.

{
    ProgDimRed::produceSideInfo();
    X.resizeNoCopy(Nsamples,inputDim);
    X.read(fnIn);
    algorithm->setInputData(X);
}

readParams()

void ProgMatrixDimRed::readParams ( )

virtual

Read argument from command line.

Reimplemented from ProgDimRed.

Definition at line 175 of file matrix_dimred.cpp.

{
    ProgDimRed::readParams();
    inputDim  = getIntParam("--din");
    Nsamples  = getIntParam("--samples");

    if (outputDim != -1 && outputDim > inputDim)
        throw std::invalid_argument("Error, output dimension should be smaller or equal to input dimension");

}

run()

void ProgMatrixDimRed::run ( )

virtual

Main routine.

Reimplemented from XmippProgram.

Definition at line 221 of file matrix_dimred.cpp.

{
    show();
    produceSideInfo();
    if (outputDim<0)
        estimateDimension();
    algorithm->reduceDimensionality();
    algorithm->getReducedData().write(fnOut);
}

show()

void ProgMatrixDimRed::show ( )

virtual

Show.

Reimplemented from ProgDimRed.

Definition at line 186 of file matrix_dimred.cpp.

{
    if (verbose>0)
    {
        ProgDimRed::show();
        std::cerr
        << "Dimension in:           " << inputDim      << std::endl
        << "Number of samples:      " << Nsamples      << std::endl
        ;
    }
}

Member Data Documentation

inputDim

int ProgMatrixDimRed::inputDim

Definition at line 104 of file matrix_dimred.h.

Nsamples

int ProgMatrixDimRed::Nsamples

Definition at line 104 of file matrix_dimred.h.

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

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