AreaProcessor use pixel values and coordinates of a real-space square area. More...

#include <processor.h>

Inheritance diagram for EMAN::AreaProcessor:

[legend]

Collaboration diagram for EMAN::AreaProcessor:

Public Member Functions
	AreaProcessor ()

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

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

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

string	get_desc () const
	Get the descrition of this specific processor. 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 string	get_name () const =0
	Get the processor's name. More...

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

Protected Member Functions
virtual void	process_pixel (float pixel, float, float, float, float area_matrix) const

virtual void	create_kernel () const =0

Protected Attributes
int	areasize

int	matrix_size

float *	kernel

int	nx

int	ny

int	nz

Protected Attributes inherited from EMAN::Processor
Dict	params

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...

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...

Detailed Description

AreaProcessor use pixel values and coordinates of a real-space square area.

This is the base class. Specific AreaProcessor needs to implement function create_kernel().

Parameters

areasize The width of the area to process (not radius)

Definition at line 4356 of file processor.h.

Constructor & Destructor Documentation

◆ AreaProcessor()

EMAN::AreaProcessor::AreaProcessor ( )

inline

Definition at line 4359 of file processor.h.

                               :areasize(0), kernel(0), nx(0), ny(0), nz(0)
                {
                }

Member Function Documentation

◆ create_kernel()

virtual void EMAN::AreaProcessor::create_kernel ( ) const

protectedpure virtual

Implemented in EMAN::LaplacianProcessor, and EMAN::ZeroConstantProcessor.

Referenced by process_inplace().

◆ get_desc()

string EMAN::AreaProcessor::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.

Reimplemented in EMAN::LaplacianProcessor, and EMAN::ZeroConstantProcessor.

Definition at line 4378 of file processor.h.

                {
                        return "AreaProcessor use pixel values and coordinates of a real-space square area. This is the base class. Specific AreaProcessor needs to implement function create_kernel().";
                }

◆ get_param_types()

TypeDict EMAN::AreaProcessor::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 4371 of file processor.h.

                {
                        TypeDict d;
                        d.put("areasize", EMObject::INT, "The width of the area to process (not radius)");
                        return d;
                }

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

◆ process_inplace()

void AreaProcessor::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.

Reimplemented in EMAN::LaplacianProcessor.

Definition at line 2482 of file processor.cpp.

{
        if (!image) {
                LOGWARN("NULL Image");
                return;
        }
 
        float *data = image->get_data();
 
        nx = image->get_xsize();
        ny = image->get_ysize();
        nz = image->get_zsize();
 
        int n = (areasize - 1) / 2;
        matrix_size = areasize * areasize;
 
        if (nz > 1) {
                matrix_size *= areasize;
        }
 
        float *matrix = new float[matrix_size];
        kernel = new float[matrix_size];
 
        size_t cpysize = areasize * sizeof(float);
        size_t start = (nx * ny + nx + 1) * n;
 
        int xend = nx - n;
        int yend = ny - n;
 
        int zstart = n;
        int zend = nz - n;
 
        int zbox_start = 0;
        int zbox_end = areasize;
 
        if (nz == 1) {
                zstart = 0;
                zend = 1;
                zbox_end = 1;
        }
 
        size_t nsec = (size_t)nx * (size_t)ny;
        int box_nsec = areasize * areasize;
 
        create_kernel();
 
        size_t total_size = (size_t)nx * (size_t)ny * (size_t)nz;
        float *data2 = new float[total_size];
        memcpy(data2, data, total_size * sizeof(float));
 
        size_t k;
        for (int z = zstart; z < zend; z++) {
                for (int y = n; y < yend; y++) {
                        for (int x = n; x < xend; x++) {
 
                                k = (size_t)z * nsec + y * nx + x;
 
                                for (int bz = zbox_start; bz < zbox_end; bz++) {
                                        for (int by = 0; by < areasize; by++) {
                                                memcpy(&matrix[(size_t)bz * box_nsec + by * areasize],
                                                           &data2[k - start + bz * nsec + by * nx], cpysize);
                                        }
                                }
 
                                process_pixel(&data[k], (float) x, (float) y, (float) z, matrix);
                        }
                }
        }
 
        if( matrix )
        {
                delete[]matrix;
                matrix = 0;
        }
 
        if( kernel )
        {
                delete[]kernel;
                kernel = 0;
        }
        image->update();
}

References areasize, create_kernel(), kernel, LOGWARN, matrix_size, nx, ny, nz, process_pixel(), x, and y.

◆ process_pixel()

virtual void EMAN::AreaProcessor::process_pixel	(	float *	pixel,
		float	,
		float	,
		float	,
		float *	area_matrix
	)		const

inlineprotectedvirtual

Reimplemented in EMAN::ZeroConstantProcessor.

Definition at line 4384 of file processor.h.

                {
                        for (int i = 0; i < matrix_size; i++)
                        {
                                *pixel += area_matrix[i] * kernel[i];
                        }
                }

References kernel, and matrix_size.

Referenced by process_inplace().

◆ set_params()

void EMAN::AreaProcessor::set_params ( const Dict & new_params )

inlinevirtual

Set the processor parameters using a key/value dictionary.

Parameters

new_params A dictionary containing the new parameters.

Reimplemented from EMAN::Processor.

Definition at line 4365 of file processor.h.

                {
                        params = new_params;
                        areasize = params["areasize"];
                }

References areasize, and EMAN::Processor::params.

Member Data Documentation

◆ areasize

int EMAN::AreaProcessor::areasize

protected

Definition at line 4394 of file processor.h.

Referenced by EMAN::LaplacianProcessor::create_kernel(), process_inplace(), and set_params().

◆ kernel

float* EMAN::AreaProcessor::kernel

protected

Definition at line 4396 of file processor.h.

Referenced by EMAN::LaplacianProcessor::create_kernel(), process_inplace(), and process_pixel().

◆ matrix_size

int EMAN::AreaProcessor::matrix_size

protected

Definition at line 4395 of file processor.h.

Referenced by process_inplace(), and process_pixel().

◆ nx

int EMAN::AreaProcessor::nx

protected

Definition at line 4397 of file processor.h.

Referenced by process_inplace().

◆ ny

int EMAN::AreaProcessor::ny

protected

Definition at line 4398 of file processor.h.

Referenced by process_inplace().

◆ nz

int EMAN::AreaProcessor::nz

protected

Definition at line 4399 of file processor.h.

Referenced by EMAN::LaplacianProcessor::create_kernel(), and process_inplace().

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

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ AreaProcessor()

Member Function Documentation

◆ create_kernel()

◆ get_desc()

◆ get_param_types()

◆ process_inplace()

◆ process_pixel()

◆ set_params()

Member Data Documentation

◆ areasize

◆ kernel

◆ matrix_size

◆ nx

◆ ny

◆ nz