MeanShrinkProcessor shrinks an image by in an integer amount taking the median of the pixel neighbourhood. More...

#include <processor.h>

Inheritance diagram for EMAN::MedianShrinkProcessor:

Collaboration diagram for EMAN::MedianShrinkProcessor:

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Public Member Functions
virtual EMData *	process (const EMData *const image)
	The medianshrink processor has its own process function to minise memory usage - if this function was not over written the base Processor class would create copy of the input image and hand it to the process_inplace function. More...

virtual void	process_inplace (EMData *image)
	Median shrink the image. More...

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

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

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

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

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 = "math.medianshrink"

Private Member Functions
void	accrue_median (EMData to, const EMData const from, const int shrink_factor)
	Accrue the local median in the image 'from' to the image 'to' using the given shrinkfactor An internal function that encapsulates a routine common to both process and process inplace. More...

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

MeanShrinkProcessor shrinks an image by in an integer amount taking the median of the pixel neighbourhood.

Author: David Woolford (But is basically a copy of the old EMData::median_shrink, probably written by Steven Ludtke )

Date: May 2008

Parameters

n	The shrink factor

Definition at line 5065 of file processor.h.

Member Function Documentation

◆ accrue_median()

void MedianShrinkProcessor::accrue_median	(	EMData *	to,
		const EMData *const	from,
		const int	shrink_factor
	)

private

Accrue the local median in the image 'from' to the image 'to' using the given shrinkfactor An internal function that encapsulates a routine common to both process and process inplace.

Parameters

to	the smaller image that will store the calculated median values
from	the larger image that will be used to calculate the median values
shrink_factor	the shrink amount

Definition at line 2911 of file processor.cpp.

{
 
        int nx_old = from->get_xsize();
        int ny_old = from->get_ysize();
 
        int threed_shrink_factor = shrink_factor * shrink_factor;
        int z_shrink_factor = 1;
        if (from->get_zsize() > 1) {
                threed_shrink_factor *= shrink_factor;
                z_shrink_factor = shrink_factor;
        }
 
        float *mbuf = new float[threed_shrink_factor];
 
 
        int nxy_old = nx_old * ny_old;
 
        int nx = to->get_xsize();
        int ny = to->get_ysize();
        int nz = to->get_zsize();
        int nxy_new = nx * ny;
 
        float * rdata = to->get_data();
        const float *const data_copy = from->get_const_data();
 
        for (int l = 0; l < nz; l++) {
                int l_min = l * shrink_factor;
                int l_max = l * shrink_factor + z_shrink_factor;
                size_t cur_l = (size_t)l * nxy_new;
 
                for (int j = 0; j < ny; j++) {
                        int j_min = j * shrink_factor;
                        int j_max = (j + 1) * shrink_factor;
                        size_t cur_j = j * nx + cur_l;
 
                        for (int i = 0; i < nx; i++) {
                                int i_min = i * shrink_factor;
                                int i_max = (i + 1) * shrink_factor;
 
                                size_t k = 0;
                                for (int l2 = l_min; l2 < l_max; l2++) {
                                        size_t cur_l2 = l2 * nxy_old;
 
                                        for (int j2 = j_min; j2 < j_max; j2++) {
                                                size_t cur_j2 = j2 * nx_old + cur_l2;
 
                                                for (int i2 = i_min; i2 < i_max; i2++) {
                                                        mbuf[k] = data_copy[i2 + cur_j2];
                                                        ++k;
                                                }
                                        }
                                }
 
                                for (k = 0; k < size_t(threed_shrink_factor / 2 + 1); k++) {
                                        for (int i2 = k + 1; i2 < threed_shrink_factor; i2++) {
                                                if (mbuf[i2] < mbuf[k]) {
                                                        float f = mbuf[i2];
                                                        mbuf[i2] = mbuf[k];
                                                        mbuf[k] = f;
                                                }
                                        }
                                }
 
                                rdata[i + cur_j] = mbuf[threed_shrink_factor / 2];
                        }
                }
        }
 
        if( mbuf )
        {
                delete[]mbuf;
                mbuf = 0;
        }
 
        to->scale_pixel((float)shrink_factor);
}

References rdata.

Referenced by process(), and process_inplace().

◆ get_desc()

string EMAN::MedianShrinkProcessor::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 5088 of file processor.h.

                {
                        return "Shrink an image by a given amount , using the median value found in the pixel neighborhood.";
                }

◆ get_name()

virtual string EMAN::MedianShrinkProcessor::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 5093 of file processor.h.

                {
                        return NAME;
                }

References NAME.

◆ get_param_types()

virtual TypeDict EMAN::MedianShrinkProcessor::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 5102 of file processor.h.

                {
                        TypeDict d;
                        d.put("n", EMObject::INT, "The shrink factor");
                        return d;
                }

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

◆ NEW()

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

inlinestatic

Definition at line 5097 of file processor.h.

                {
                        return new MedianShrinkProcessor();
                }

◆ process()

EMData * MedianShrinkProcessor::process ( const EMData *const image )

virtual

The medianshrink processor has its own process function to minise memory usage - if this function was not over written the base Processor class would create copy of the input image and hand it to the process_inplace function.

This latter approach mallocs and copies more memory than necessary

Parameters

image the image that will be used to generate a 'median shrunken' image

Exceptions

ImageFormatException	if the image is complex
InvalidValueException	if the shrink amount is not a non zero, positive integer
InvalidValueException	if any of the image dimensions are not divisible by the the shrink amount

Reimplemented from EMAN::Processor.

Definition at line 2878 of file processor.cpp.

{
        if (image->is_complex()) throw ImageFormatException("Error, the median shrink processor does not work on complex images");
 
        int shrink_factor =      params.set_default("n",0);
        if (shrink_factor <= 1) {
                throw InvalidValueException(shrink_factor,
                                                                        "median shrink: shrink factor must > 1");
        }
        int nx = image->get_xsize();
        int ny = image->get_ysize();
        int nz = image->get_zsize();
 
 
//      if ((nx % shrink_factor != 0) || (ny % shrink_factor != 0) || (nz > 1 && (nz % shrink_factor != 0))) {
//              throw InvalidValueException(shrink_factor, "Image size not divisible by shrink factor");
//      }
 
 
        int shrunken_nx = nx / shrink_factor;
        int shrunken_ny = ny / shrink_factor;
        int shrunken_nz = 1;
        if (nz > 1) shrunken_nz = nz / shrink_factor;
 
//      EMData* ret = new EMData(shrunken_nx, shrunken_ny, shrunken_nz);
        EMData *ret = image->copy_head();
        ret->set_size(shrunken_nx, shrunken_ny, shrunken_nz);
 
        accrue_median(ret,image,shrink_factor);
        ret->update();
        return ret;
}

References accrue_median(), ImageFormatException, InvalidValueException, EMAN::Processor::params, and EMAN::Dict::set_default().

◆ process_inplace()

void MedianShrinkProcessor::process_inplace ( EMData * image )

virtual

Median shrink the image.

Parameters

image the image the image that will be 'median shrunken' inplace

Exceptions

ImageFormatException	if the image is complex
InvalidValueException	if the shrink amount is not a non zero, positive integer
InvalidValueException	if any of the image dimensions are not divisible by the the shrink amount

Implements EMAN::Processor.

Definition at line 2842 of file processor.cpp.

{
        if (image->is_complex()) throw ImageFormatException("Error, the median shrink processor does not work on complex images");
 
        int shrink_factor =      params.set_default("n",0);
        if (shrink_factor <= 1) {
                throw InvalidValueException(shrink_factor,
                                                                        "median shrink: shrink factor must > 1");
        }
 
        int nx = image->get_xsize();
        int ny = image->get_ysize();
        int nz = image->get_zsize();
 
//      if ((nx % shrink_factor != 0) || (ny % shrink_factor != 0) || (nz > 1 && (nz % shrink_factor != 0))) {
//              throw InvalidValueException(shrink_factor, "Image size not divisible by shrink factor");
//      }
 
 
        int shrunken_nx = nx / shrink_factor;
        int shrunken_ny = ny / shrink_factor;
        int shrunken_nz = 1;
        if (nz > 1) shrunken_nz = nz / shrink_factor;
 
        EMData* copy = image->copy();
        image->set_size(shrunken_nx, shrunken_ny, shrunken_nz);
        accrue_median(image,copy,shrink_factor);
        image->update();
        if( copy )
        {
                delete copy;
                copy = 0;
        }
}

References accrue_median(), copy(), ImageFormatException, InvalidValueException, EMAN::Processor::params, and EMAN::Dict::set_default().

Member Data Documentation

◆ NAME

const string MedianShrinkProcessor::NAME = "math.medianshrink"

static

Definition at line 5109 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

Private Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ accrue_median()

◆ get_desc()

◆ get_name()

◆ get_param_types()

◆ NEW()

◆ process()

◆ process_inplace()

Member Data Documentation

◆ NAME