Gradient removed by least square plane fit. More...

#include <processor.h>

Inheritance diagram for EMAN::GradientPlaneRemoverProcessor:

Collaboration diagram for EMAN::GradientPlaneRemoverProcessor:

[legend]

Public Member Functions
void	process_inplace (EMData *image)
	To process an image in-place. More...

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

string	get_desc () const
	Get the descrition of this specific processor. More...

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

Public Member Functions inherited from EMAN::Processor
virtual	~Processor ()

virtual EMData *	process (const EMData *const image)
	To proccess an image out-of-place. More...

virtual void	process_list_inplace (vector< EMData * > &images)
	To process multiple images using the same algorithm. More...

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

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

Static Public Member Functions
static Processor *	NEW ()

Static Public Member Functions inherited from EMAN::Processor
static string	get_group_desc ()
	Get the description of this group of processors. More...

static void	EMFourierFilterInPlace (EMData *fimage, Dict params)
	Compute a Fourier-filter processed image in place. More...

static EMData *	EMFourierFilter (EMData *fimage, Dict params)
	Compute a Fourier-processor processed image without altering the original image. More...

Static Public Attributes
static const string	NAME = "filter.gradientPlaneRemover"

Additional Inherited Members
Public Types inherited from EMAN::Processor
enum	fourier_filter_types { TOP_HAT_LOW_PASS , TOP_HAT_HIGH_PASS , TOP_HAT_BAND_PASS , TOP_HOMOMORPHIC , GAUSS_LOW_PASS , GAUSS_HIGH_PASS , GAUSS_BAND_PASS , GAUSS_INVERSE , GAUSS_HOMOMORPHIC , BUTTERWORTH_LOW_PASS , BUTTERWORTH_HIGH_PASS , BUTTERWORTH_HOMOMORPHIC , KAISER_I0 , KAISER_SINH , KAISER_I0_INVERSE , KAISER_SINH_INVERSE , SHIFT , TANH_LOW_PASS , TANH_HIGH_PASS , TANH_HOMOMORPHIC , TANH_BAND_PASS , RADIAL_TABLE , CTF_ }
	Fourier filter Processor type enum. More...

Protected Attributes inherited from EMAN::Processor
Dict	params

Detailed Description

Gradient removed by least square plane fit.

Parameters

mask[in]	optional EMData object to mask the pixels used to fit the plane
changeZero[in]	optional bool to specify if the zero value pixels are modified
planeParam[out]	optional return parameters [nx, ny, nz, cx, cy, cz] for the fitted plane defined as (x-cx)nx+(y-cy)ny+(z-cz)*nz=0

Author: Wen Jiang

Date: 2006/7/18

Definition at line 5203 of file processor.h.

Member Function Documentation

◆ get_desc()

string EMAN::GradientPlaneRemoverProcessor::get_desc ( ) const

inlinevirtual

Get the descrition of this specific processor.

This function must be overwritten by a subclass.

Returns: The description of this processor.

Implements EMAN::Processor.

Definition at line 5217 of file processor.h.

                {
                        return "Remove gradient by least square plane fit";
                }

◆ get_name()

string EMAN::GradientPlaneRemoverProcessor::get_name ( ) const

inlinevirtual

Get the processor's name.

Each processor is identified by a unique name.

Returns: The processor's name.

Implements EMAN::Processor.

Definition at line 5208 of file processor.h.

                {
                        return NAME;
                }

References NAME.

Referenced by process_inplace().

◆ get_param_types()

TypeDict EMAN::GradientPlaneRemoverProcessor::get_param_types ( ) const

inlinevirtual

Get processor 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.

Reimplemented from EMAN::Processor.

Definition at line 5222 of file processor.h.

                {
                        TypeDict d;
                        d.put("mask", EMObject::EMDATA, "mask object: nonzero pixel positions will be used to fit plane. default = 0");
                        d.put("changeZero", EMObject::INT, "if zero pixels are modified when removing gradient. default = 0");
                        d.put("planeParam", EMObject::FLOATARRAY, "fitted plane parameters output");
                        return d;
                }

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

◆ NEW()

static Processor * EMAN::GradientPlaneRemoverProcessor::NEW ( )

inlinestatic

Definition at line 5212 of file processor.h.

                {
                        return new GradientPlaneRemoverProcessor();
                }

◆ process_inplace()

void GradientPlaneRemoverProcessor::process_inplace ( EMData * image )

virtual

To process an image in-place.

For those processors which can only be processed out-of-place, override this function to just print out some error message to remind user call the out-of-place version.

Parameters

image The image to be processed.

Implements EMAN::Processor.

Definition at line 3809 of file processor.cpp.

{
        if (!image) {
                LOGWARN("NULL Image");
                return;
        }
 
        int nz = image->get_zsize();
        if (nz > 1) {
                LOGERR("%s Processor doesn't support 3D model", get_name().c_str());
                throw ImageDimensionException("3D map not supported");
        }
 
        int nx = image->get_xsize();
        int ny = image->get_ysize();
        float *d = image->get_data();
        EMData *mask = 0;
        float *dm = 0;
        if (params.has_key("mask")) {
                mask = params["mask"];
                if (nx!=mask->get_xsize() || ny!=mask->get_ysize()) {
                        LOGERR("%s Processor requires same size mask image", get_name().c_str());
                        throw ImageDimensionException("wrong size mask image");
                }
                dm = mask->get_data();
        }
        int count = 0;
        if (dm) {
                for(int i=0; i<nx*ny; i++) {
                        if(dm[i]) count++;
                }
        }
        else {
                count = nx * ny;
        }
        if(count<3) {
                LOGERR("%s Processor requires at least 3 pixels to fit a plane", get_name().c_str());
                throw ImageDimensionException("too few usable pixels to fit a plane");
        }
        // Allocate the working space
        gsl_vector *S=gsl_vector_calloc(3);
        gsl_matrix *A=gsl_matrix_calloc(count,3);
        gsl_matrix *V=gsl_matrix_calloc(3,3);
 
        double m[3] = {0, 0, 0};
        int index=0;
        if (dm) {
                for(int j=0; j<ny; j++){
                        for(int i=0; i<nx; i++){
                                int ij=j*nx+i;
                                if(dm[ij]) {
                                        m[0]+=i;        // x
                                        m[1]+=j;        // y
                                        m[2]+=d[ij];    // z
                                        /*printf("index=%d/%d\ti,j=%d,%d\tval=%g\txm,ym,zm=%g,%g,%g\n", \
                                                        index,count,i,j,d[ij],m[0]/(index+1),m[1]/(index+1),m[2]/(index+1));*/
                                        index++;
                                }
                        }
                }
        }
        else {
                for(int j=0; j<ny; j++){
                        for(int i=0; i<nx; i++){
                                int ij=j*nx+i;
                                        m[0]+=i;        // x
                                        m[1]+=j;        // y
                                        m[2]+=d[ij];    // z
                                        /*printf("index=%d/%d\ti,j=%d,%d\tval=%g\txm,ym,zm=%g,%g,%g\n", \
                                                        index,count,i,j,d[ij],m[0]/(index+1),m[1]/(index+1),m[2]/(index+1));*/
                                        index++;
                        }
                }
        }
 
        for(int i=0; i<3; i++) m[i]/=count; // compute center of the plane
 
        index=0;
        if (dm) {
                for(int j=0; j<ny; j++){
                        for(int i=0; i<nx; i++){
                                int ij=j*nx+i;
                                if(dm[ij]) {
                                        //printf("index=%d/%d\ti,j=%d,%d\tval=%g\n",index,count,i,j,d[index]);
                                        gsl_matrix_set(A,index,0,i-m[0]);
                                        gsl_matrix_set(A,index,1,j-m[1]);
                                        gsl_matrix_set(A,index,2,d[ij]-m[2]);
                                        index++;
                                }
                        }
                }
                mask->update();
        }
        else {
                for(int j=0; j<ny; j++){
                        for(int i=0; i<nx; i++){
                                int ij=j*nx+i;
                                        //printf("index=%d/%d\ti,j=%d,%d\tval=%g\n",index,count,i,j,d[index]);
                                        gsl_matrix_set(A,index,0,i-m[0]);
                                        gsl_matrix_set(A,index,1,j-m[1]);
                                        gsl_matrix_set(A,index,2,d[ij]-m[2]);
                                        index++;
                        }
                }
        }
 
        // SVD decomposition and use the V vector associated with smallest singular value as the plan normal
        gsl_linalg_SV_decomp_jacobi(A, V, S);
 
        double n[3];
        for(int i=0; i<3; i++) n[i] = gsl_matrix_get(V, i, 2);
 
        #ifdef DEBUG
        printf("S=%g,%g,%g\n",gsl_vector_get(S,0), gsl_vector_get(S,1), gsl_vector_get(S,2));
        printf("V[0,:]=%g,%g,%g\n",gsl_matrix_get(V,0,0), gsl_matrix_get(V,0,1),gsl_matrix_get(V,0,2));
        printf("V[1,:]=%g,%g,%g\n",gsl_matrix_get(V,1,0), gsl_matrix_get(V,1,1),gsl_matrix_get(V,1,2));
        printf("V[2,:]=%g,%g,%g\n",gsl_matrix_get(V,2,0), gsl_matrix_get(V,2,1),gsl_matrix_get(V,2,2));
        printf("Fitted plane: p0=%g,%g,%g\tn=%g,%g,%g\n",m[0],m[1],m[2],n[0],n[1],n[2]);
        #endif
 
        int changeZero = 0;
        if (params.has_key("changeZero")) changeZero = params["changeZero"];
        if (changeZero) {
                for(int j=0; j<nx; j++){
                        for(int i=0; i<ny; i++){
                                int ij = j*nx+i;
                                d[ij]-=static_cast<float>(-((i-m[0])*n[0]+(j-m[1])*n[1])/n[2]+m[2]);
                        }
                }
        }
        else {
                for(int j=0; j<nx; j++){
                        for(int i=0; i<ny; i++){
                                int ij = j*nx+i;
                                if(d[ij]) d[ij]-=static_cast<float>(-((i-m[0])*n[0]+(j-m[1])*n[1])/n[2]+m[2]);
                        }
                }
        }
        image->update();
        // set return plane parameters
        vector< float > planeParam;
        planeParam.resize(6);
        for(int i=0; i<3; i++) planeParam[i] = static_cast<float>(n[i]);
        for(int i=0; i<3; i++) planeParam[i+3] = static_cast<float>(m[i]);
        params["planeParam"]=EMObject(planeParam);
}

References dm, get_name(), EMAN::Dict::has_key(), ImageDimensionException, LOGERR, LOGWARN, EMAN::Processor::params, and V.

Member Data Documentation

◆ NAME

const string GradientPlaneRemoverProcessor::NAME = "filter.gradientPlaneRemover"

static

Definition at line 5231 of file processor.h.

Referenced by get_name().

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

Public Member Functions

Static Public Member Functions

Static Public Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ get_desc()

◆ get_name()

◆ get_param_types()

◆ NEW()

◆ process_inplace()

Member Data Documentation

◆ NAME