Singular Value Decomposition from GSL. More...

#include <analyzer.h>

Inheritance diagram for EMAN::SVDAnalyzer:

Collaboration diagram for EMAN::SVDAnalyzer:

[legend]

Public Member Functions
	SVDAnalyzer ()

virtual int	insert_image (EMData *image)
	insert a image to the list of input images More...

virtual int	insert_images_list (vector< EMData * > image_list)
	insert a list of images to the list of input images More...

virtual vector< EMData * >	analyze ()
	main function for Analyzer, analyze input images and create output images More...

string	get_name () const
	Get the Analyzer's name. More...

string	get_desc () const
	Get the Analyzer's description. More...

void	set_params (const Dict &new_params)
	Set the Analyzer parameters using a key/value dictionary. More...

TypeDict	get_param_types () const
	Get Analyzer parameter information in a dictionary. More...

Public Member Functions inherited from EMAN::Analyzer
	Analyzer ()

virtual	~Analyzer ()

virtual Dict	get_params () const
	Get the Reconstructor's parameters in a key/value dictionary. More...

Static Public Member Functions
static Analyzer *	NEW ()

Static Public Attributes
static const string	NAME = "svd_gsl"

Protected Attributes
EMData *	mask

int	nvec

int	pixels

int	nimg

Protected Attributes inherited from EMAN::Analyzer
Dict	params

vector< EMData * >	images

Private Attributes
int	nsofar

gsl_matrix *	A

Detailed Description

Singular Value Decomposition from GSL.

Comparable to pca

Parameters

mask	mask image
nvec	number of desired basis vectors
nimg	total number of input images, required even with insert_image()

Definition at line 307 of file analyzer.h.

Constructor & Destructor Documentation

◆ SVDAnalyzer()

EMAN::SVDAnalyzer::SVDAnalyzer ( )

inline

Definition at line 310 of file analyzer.h.

310: mask(0), nvec(0), nimg(0), A(NULL) {}

EMAN::SVDAnalyzer::nvec

int nvec

Definition: analyzer.h:354

EMAN::SVDAnalyzer::A

gsl_matrix * A

Definition: analyzer.h:360

EMAN::SVDAnalyzer::nimg

int nimg

Definition: analyzer.h:356

EMAN::SVDAnalyzer::mask

EMData * mask

Definition: analyzer.h:353

Referenced by NEW().

Member Function Documentation

◆ analyze()

vector< EMData * > SVDAnalyzer::analyze ( )

virtual

main function for Analyzer, analyze input images and create output images

Returns: vector<EMData *> result os images analysis

Implements EMAN::Analyzer.

Definition at line 959 of file analyzer.cpp.

{
// Allocate the working space
gsl_vector *work=gsl_vector_alloc(nimg);
gsl_vector *S=gsl_vector_alloc(nimg);
gsl_matrix *V=gsl_matrix_alloc(nimg,nimg);
gsl_matrix *X=gsl_matrix_alloc(nimg,nimg);
 
 
// Do the decomposition. All the real work is here
gsl_linalg_SV_decomp_mod (A,X, V, S, work);
//else gsl_linalg_SV_decomp_jacobi(A,V,S);
 
vector<EMData*> ret;
//unpack the results and write the output file
float *md=mask->get_data();
size_t totpix=mask->get_xsize()*mask->get_ysize()*mask->get_zsize();
for (int k=0; k<nvec; k++) {
        EMData *img = new EMData;
        img->set_size(mask->get_xsize(),mask->get_ysize(),mask->get_zsize());
 
        float  *d=img->get_data();
        for (size_t i=0,j=0; i<totpix; ++i) {
                if (md[i]) {
                        d[i]=(float)gsl_matrix_get(A,j,k);
                        j++;
                }
        }
        img->set_attr( "eigval", gsl_vector_get(S,k));
        ret.push_back(img);
}
 
gsl_vector_free(work);
gsl_vector_free(S);
gsl_matrix_free(V);
gsl_matrix_free(X);
 
gsl_matrix_free(A);
A=NULL;
mask=NULL;
 
return ret;
}

References A, mask, nimg, nvec, and V.

◆ get_desc()

string EMAN::SVDAnalyzer::get_desc ( ) const

inlinevirtual

Get the Analyzer's description.

Returns: The Analyzer's description.

Implements EMAN::Analyzer.

Definition at line 329 of file analyzer.h.

                {
                        return "Singular Value Decomposition from GSL. Comparable to pca";
                }

◆ get_name()

string EMAN::SVDAnalyzer::get_name ( ) const

inlinevirtual

Get the Analyzer's name.

Each Analyzer is identified by a unique name.

Returns: The Analyzer's name.

Implements EMAN::Analyzer.

Definition at line 324 of file analyzer.h.

                {
                        return NAME;
                }

References NAME.

◆ get_param_types()

TypeDict EMAN::SVDAnalyzer::get_param_types ( ) const

inlinevirtual

Get Analyzer parameter information in a dictionary.

Each parameter has one record in the dictionary. Each record contains its name, data-type, and description.

Returns: A dictionary containing the parameter info.

Implements EMAN::Analyzer.

Definition at line 341 of file analyzer.h.

                {
                        TypeDict d;
                        d.put("mask", EMObject::EMDATA, "mask image");
                        d.put("nvec", EMObject::INT, "number of desired basis vectors");
                        d.put("nimg", EMObject::INT, "total number of input images, required even with insert_image()");
                        return d;
                }

References EMAN::EMObject::EMDATA, EMAN::EMObject::INT, and EMAN::TypeDict::put().

◆ insert_image()

int SVDAnalyzer::insert_image ( EMData * image )

virtual

insert a image to the list of input images

Parameters

image

Returns: int 0 for success, <0 for fail

Implements EMAN::Analyzer.

Definition at line 937 of file analyzer.cpp.

{
        if (mask==0)
                throw NullPointerException("Null mask image pointer, set_params() first");
 
        // count pixels under mask
        size_t totpix=mask->get_xsize()*mask->get_ysize()*mask->get_zsize();
        float  *d=image->get_data();
        float *md=mask ->get_data();
        for (size_t i=0,j=0; i<totpix; ++i) {
                if (md[i]) {
                        gsl_matrix_set(A,j,nsofar,d[i]);
                        j++;
                }
        }
        nsofar++;
 
   return 0;
}

References A, mask, nsofar, and NullPointerException.

◆ insert_images_list()

virtual int EMAN::SVDAnalyzer::insert_images_list ( vector< EMData * > image_list )

inlinevirtual

insert a list of images to the list of input images

Parameters

image_list

Returns: int 0 for success, <0 for fail

Reimplemented from EMAN::Analyzer.

Definition at line 314 of file analyzer.h.

                                                                            {
                        vector<EMData*>::const_iterator iter;
                        for(iter=image_list.begin(); iter!=image_list.end(); ++iter) {
                                images.push_back(*iter);
                        }
                        return 0;
                }

References EMAN::Analyzer::images.

◆ NEW()

static Analyzer * EMAN::SVDAnalyzer::NEW ( )

inlinestatic

Definition at line 334 of file analyzer.h.

                {
                        return new SVDAnalyzer();
                }

References SVDAnalyzer().

◆ set_params()

void SVDAnalyzer::set_params ( const Dict & new_params )

virtual

Set the Analyzer parameters using a key/value dictionary.

Parameters

new_params A dictionary containing the new parameters.

Reimplemented from EMAN::Analyzer.

Definition at line 1003 of file analyzer.cpp.

{
        params = new_params;
        mask = params["mask"];
        nvec = params["nvec"];
        nimg = params["nimg"];
 
        // count pixels under mask
        pixels=0;
        size_t totpix=mask->get_xsize()*mask->get_ysize()*mask->get_zsize();
        float *d=mask->get_data();
        for (size_t i=0; i<totpix; ++i) if (d[i]) ++pixels;
 
        printf("%d,%d\n",pixels,nimg);
        A=gsl_matrix_alloc(pixels,nimg);
        nsofar=0;
}

References A, mask, nimg, nsofar, nvec, EMAN::Analyzer::params, and pixels.

Member Data Documentation

◆ A

gsl_matrix* EMAN::SVDAnalyzer::A

private

Definition at line 360 of file analyzer.h.

Referenced by analyze(), insert_image(), and set_params().

◆ mask

EMData* EMAN::SVDAnalyzer::mask

protected

Definition at line 353 of file analyzer.h.

Referenced by analyze(), insert_image(), and set_params().

◆ NAME

const string EMAN::SVDAnalyzer::NAME = "svd_gsl"

static

Definition at line 350 of file analyzer.h.

Referenced by get_name().

◆ nimg

int EMAN::SVDAnalyzer::nimg

protected

Definition at line 356 of file analyzer.h.

Referenced by analyze(), and set_params().

◆ nsofar

int EMAN::SVDAnalyzer::nsofar

private

Definition at line 359 of file analyzer.h.

Referenced by insert_image(), and set_params().

◆ nvec

int EMAN::SVDAnalyzer::nvec

protected

Definition at line 354 of file analyzer.h.

Referenced by analyze(), and set_params().

◆ pixels

int EMAN::SVDAnalyzer::pixels

protected

Definition at line 355 of file analyzer.h.

Referenced by set_params().

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

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ SVDAnalyzer()

Member Function Documentation

◆ analyze()

◆ get_desc()

◆ get_name()

◆ get_param_types()

◆ insert_image()

◆ insert_images_list()

◆ NEW()

◆ set_params()

Member Data Documentation

◆ A

◆ mask

◆ NAME

◆ nimg

◆ nsofar

◆ nvec

◆ pixels