EMAN::AreaProcessor Class Reference

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

#include <processor.h>

Inheritance diagram for EMAN::AreaProcessor:

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Collaboration diagram for EMAN::AreaProcessor:

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List of all members.

Public Member Functions
	AreaProcessor ()
void	process_inplace (EMData *image)
	To process an image in-place.
void	set_params (const Dict &new_params)
	Set the processor parameters using a key/value dictionary.
TypeDict	get_param_types () const
	Get processor parameter information in a dictionary.
string	get_desc () const
	Get the descrition of this specific processor.
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

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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 2761 of file processor.h.

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Constructor & Destructor Documentation

EMAN::AreaProcessor::AreaProcessor

(

)

[inline]

Definition at line 2764 of file processor.h.

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

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Member Function Documentation

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.

Definition at line 1485 of file processor.cpp.

References areasize, create_kernel(), data, EMAN::EMData::get_data(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), kernel, LOGWARN, matrix(), matrix_size, nx, ny, nz, process_pixel(), EMAN::EMData::update(), x, and y.

{
        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];

        int cpysize = areasize * (int) sizeof(float);
        int 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 = z * nsec + y * nx + x;

                                for (int bz = zbox_start; bz < zbox_end; bz++) {
                                        for (int by = 0; by < areasize; by++) {
                                                memcpy(&matrix[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();
}

void EMAN::AreaProcessor::set_params

(

const Dict &

new_params

)

[inline, virtual]

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 2770 of file processor.h.

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

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

TypeDict EMAN::AreaProcessor::get_param_types

(

)

const [inline, virtual]

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 2776 of file processor.h.

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

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

string EMAN::AreaProcessor::get_desc

(

)

const [inline, virtual]

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 2783 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().";
                }

virtual void EMAN::AreaProcessor::process_pixel	(	float *	pixel,
		float	,
		float	,
		float	,
		float *	area_matrix
	)			const [inline, protected, virtual]

Reimplemented in EMAN::ZeroConstantProcessor.

Definition at line 2789 of file processor.h.

References kernel, and matrix_size.

Referenced by process_inplace().

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

virtual void EMAN::AreaProcessor::create_kernel

(

)

const [protected, pure virtual]

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

Referenced by process_inplace().

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Member Data Documentation

int EMAN::AreaProcessor::areasize [protected]

Definition at line 2799 of file processor.h.

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

int EMAN::AreaProcessor::matrix_size [protected]

Definition at line 2800 of file processor.h.

Referenced by process_inplace(), and process_pixel().

float* EMAN::AreaProcessor::kernel [protected]

Definition at line 2801 of file processor.h.

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

int EMAN::AreaProcessor::nx [protected]

Definition at line 2802 of file processor.h.

Referenced by process_inplace().

int EMAN::AreaProcessor::ny [protected]

Definition at line 2803 of file processor.h.

Referenced by process_inplace().

int EMAN::AreaProcessor::nz [protected]

Definition at line 2804 of file processor.h.

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

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

• processor.h
• processor.cpp