MeanShrinkProcessor shrinks an image by in an integer amount (and optionally by 1.5) taking the mean of the pixel neighbourhood. More...

#include <processor.h>

Inheritance diagram for EMAN::MeanShrinkProcessor:

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Collaboration diagram for EMAN::MeanShrinkProcessor:

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Public Member Functions
virtual EMData *	process (const EMData *const image)
	The meanshrink 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)
	Mean shrink inplace. 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.meanshrink"

Private Member Functions
void	accrue_mean (EMData to, const EMData const from, const int shrinkfactor)
	Accrue the local mean 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...

void	accrue_mean_one_p_five (EMData to, const EMData const from)
	Accrue the local mean in the image 'from' to the image 'to' using the the special case shrink factor of 1.5 This is 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 (and optionally by 1.5) taking the mean of the pixel neighbourhood.

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

Date: May 2008

Parameters

n	The shrink factor

Definition at line 4993 of file processor.h.

Member Function Documentation

◆ accrue_mean()

void MeanShrinkProcessor::accrue_mean	(	EMData *	to,
		const EMData *const	from,
		const int	shrinkfactor
	)

private

Accrue the local mean 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 mean values
from	the larger image that will be used to calculate the mean values
shrinkfactor	the shrink amount

Definition at line 3229 of file processor.cpp.

{
        const float * const data = from->get_const_data();
        float* rdata = to->get_data();
 
        size_t nx = from->get_xsize();
        size_t ny = from->get_ysize();
        size_t nz = from->get_zsize();
        size_t nxy = nx*ny;
 
 
        size_t shrunken_nx = nx / shrink_factor;
        size_t shrunken_ny = ny / shrink_factor;
        size_t shrunken_nz = 1;
        size_t shrunken_nxy = shrunken_nx * shrunken_ny;
 
        int normalize_shrink_factor = shrink_factor * shrink_factor;
        int z_shrink_factor = 1;
 
        if (nz > 1) {
                shrunken_nz = nz / shrink_factor;
                normalize_shrink_factor *= shrink_factor;
                z_shrink_factor = shrink_factor;
        }
 
        float invnormfactor = 1.0f/(float)normalize_shrink_factor;
 
        for (size_t k = 0; k < shrunken_nz; k++) {
                size_t k_min = k * shrink_factor;
                size_t k_max = k * shrink_factor + z_shrink_factor;
                size_t cur_k = k * shrunken_nxy;
 
                for (size_t j = 0; j < shrunken_ny; j++) {
                        size_t j_min = j * shrink_factor;
                        size_t j_max = j * shrink_factor + shrink_factor;
                        size_t cur_j = j * shrunken_nx + cur_k;
 
                        for (size_t i = 0; i < shrunken_nx; i++) {
                                size_t i_min = i * shrink_factor;
                                size_t i_max = i * shrink_factor + shrink_factor;
 
                                float sum = 0;
                                for (size_t kk = k_min; kk < k_max; kk++) {
                                        size_t cur_kk = kk * nxy;
 
                                        for (size_t jj = j_min; jj < j_max; jj++) {
                                                size_t cur_jj = jj * nx + cur_kk;
                                                for (size_t ii = i_min; ii < i_max; ii++) {
                                                        sum += data[ii + cur_jj];
                                                }
                                        }
                                }
                                rdata[i + cur_j] = sum * invnormfactor;
                        }
                }
        }
        to->scale_pixel((float)shrink_factor);
}

References rdata.

Referenced by process(), and process_inplace().

◆ accrue_mean_one_p_five()

void MeanShrinkProcessor::accrue_mean_one_p_five	(	EMData *	to,
		const EMData *const	from
	)

private

Accrue the local mean in the image 'from' to the image 'to' using the the special case shrink factor of 1.5 This is an internal function that encapsulates a routine common to both process and process inplace.

Parameters

to	the smaller image that will store the mean values
from	the larger image that will be used to calculate the mean values

Definition at line 3289 of file processor.cpp.

{
        int nx0 = from->get_xsize(), ny0 = from->get_ysize();   // the original size
 
        int nx = to->get_xsize(), ny = to->get_ysize();
 
        float *data = to->get_data();
        const float * const data0 = from->get_const_data();
 
        for (int j = 0; j < ny; j++) {
                int jj = int(j * 1.5);
                float jw0 = 1.0F, jw1 = 0.5F;   // 3x3 -> 2x2, so each new pixel should have 2.25 of the old pixels
                if ( j%2 ) {
                        jw0 = 0.5F;
                        jw1 = 1.0F;
                }
                for (int i = 0; i < nx; i++) {
                        int ii = int(i * 1.5);
                        float iw0 = 1.0F, iw1 = 0.5F;
                        float w = 0.0F;
 
                        if ( i%2 ) {
                                iw0 = 0.5F;
                                iw1 = 1.0F;
                        }
                        if ( jj < ny0 ) {
                                if ( ii < nx0 ) {
                                        data[j * nx + i] = data0[ jj * nx0 + ii ] * jw0 * iw0 ;
                                        w += jw0 * iw0 ;
                                        if ( ii+1 < nx0 ) {
                                                data[j * nx + i] += data0[ jj * nx0 + ii + 1] * jw0 * iw1;
                                                w += jw0 * iw1;
                                        }
                                }
                                if ( jj +1 < ny0 ) {
                                        if ( ii < nx0 ) {
                                                data[j * nx + i] += data0[ (jj+1) * nx0 + ii ] * jw1 * iw0;
                                                w += jw1 * iw0;
                                                if ( ii+1 < nx0 ) {
                                                        data[j * nx + i] += data0[ (jj+1) * nx0 + ii + 1] * jw1 * iw1;
                                                        w += jw1 * iw1;
                                                }
                                        }
                                }
                        }
                        if ( w>0 ) data[j * nx + i] /= w;
                }
        }
 
        to->update();
        to->scale_pixel((float)1.5);
}

Referenced by process(), and process_inplace().

◆ get_desc()

string EMAN::MeanShrinkProcessor::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 5016 of file processor.h.

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

◆ get_name()

virtual string EMAN::MeanShrinkProcessor::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 5021 of file processor.h.

                        {
                                return NAME;
                        }

References NAME.

◆ get_param_types()

virtual TypeDict EMAN::MeanShrinkProcessor::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 5030 of file processor.h.

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

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

◆ NEW()

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

inlinestatic

Definition at line 5025 of file processor.h.

                        {
                                return new MeanShrinkProcessor();
                        }

◆ process()

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

virtual

The meanshrink 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 'mean shrunken' image

Exceptions

ImageFormatException	if the image is complex
ImageDimensionException	if the image is 1D
InvalidValueException	if the shrink amount is a nonzero integer, unless it is 1.5, which is an exceptional circumstance

Reimplemented from EMAN::Processor.

Definition at line 3124 of file processor.cpp.

{
        if (image->is_complex()) throw ImageFormatException("Error, the mean shrink processor does not work on complex images");
 
        if (image->get_ndim() == 1) { throw ImageDimensionException("Error, mean shrink works only for 2D & 3D images"); }
 
        float shrink_factor0 = params.set_default("n",0.0f);
        int shrink_factor = int(shrink_factor0);
        if (shrink_factor0 <= 1.0F || ((shrink_factor0 != shrink_factor) && (shrink_factor0 != 1.5F) ) ) {
                throw InvalidValueException(shrink_factor0,
                                                                        "mean shrink: shrink factor must be >1 integer or 1.5");
        }
 
        int nx = image->get_xsize();
        int ny = image->get_ysize();
        int nz = image->get_zsize();
 
 
        // here handle the special averaging by 1.5 for 2D case
        if (shrink_factor0==1.5 ) {
                if (nz > 1 ) throw InvalidValueException(shrink_factor0, "mean shrink: only support 2D images for shrink factor = 1.5");
 
                int shrunken_nx = (int(nx / 1.5)+1)/2*2;        // make sure the output size is even
                int shrunken_ny = (int(ny / 1.5)+1)/2*2;
                EMData* result = new EMData(shrunken_nx,shrunken_ny,1);
 
                accrue_mean_one_p_five(result,image);
                result->update();
 
                return result;
        }
 
        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* result = new EMData(shrunken_nx,shrunken_ny,shrunken_nz);
        EMData* result = image->copy_head();
        result->set_size(shrunken_nx,shrunken_ny,shrunken_nz);
        accrue_mean(result,image,shrink_factor);
 
        result->update();
 
        return result;
}

References accrue_mean(), accrue_mean_one_p_five(), ImageDimensionException, ImageFormatException, InvalidValueException, EMAN::Processor::params, and EMAN::Dict::set_default().

◆ process_inplace()

void MeanShrinkProcessor::process_inplace ( EMData * image )

virtual

Mean shrink inplace.

Parameters

image the image that will be 'mean shrunken' inplace

Exceptions

ImageFormatException	if the image is complex
ImageDimensionException	if the image is 1D
InvalidValueException	if the shrink amount is a nonzero integer, unless it is 1.5, which is an exceptional circumstance

Implements EMAN::Processor.

Definition at line 3174 of file processor.cpp.

{
        if (image->is_complex()) throw ImageFormatException("Error, the mean shrink processor does not work on complex images");
 
        if (image->get_ndim() == 1) { throw ImageDimensionException("Error, mean shrink works only for 2D & 3D images"); }
 
        float shrink_factor0 = params.set_default("n",0.0f);
        int shrink_factor = int(shrink_factor0);
        if (shrink_factor0 <= 1.0F || ((shrink_factor0 != shrink_factor) && (shrink_factor0 != 1.5F) ) ) {
                throw InvalidValueException(shrink_factor0,
                                                                        "mean shrink: shrink factor must be >1 integer or 1.5");
        }
 
/*      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 nx = image->get_xsize();
        int ny = image->get_ysize();
        int nz = image->get_zsize();
        // here handle the special averaging by 1.5 for 2D case
        if (shrink_factor0==1.5 ) {
                if (nz > 1 ) throw InvalidValueException(shrink_factor0, "mean shrink: only support 2D images for shrink factor = 1.5");
 
                int shrunken_nx = (int(nx / 1.5)+1)/2*2;        // make sure the output size is even
                int shrunken_ny = (int(ny / 1.5)+1)/2*2;
 
                EMData* orig = image->copy();
                image->set_size(shrunken_nx, shrunken_ny, 1);   // now nx = shrunken_nx, ny = shrunken_ny
                image->to_zero();
 
                accrue_mean_one_p_five(image,orig);
 
                if( orig ) {
                        delete orig;
                        orig = 0;
                }
                image->update();
 
                return;
        }
 
        accrue_mean(image,image,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;
 
        image->update();
        image->set_size(shrunken_nx, shrunken_ny, shrunken_nz);
}

References accrue_mean(), accrue_mean_one_p_five(), ImageDimensionException, ImageFormatException, InvalidValueException, EMAN::Processor::params, and EMAN::Dict::set_default().

Member Data Documentation

◆ NAME

const string MeanShrinkProcessor::NAME = "math.meanshrink"

static

Definition at line 5037 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_mean()

◆ accrue_mean_one_p_five()

◆ get_desc()

◆ get_name()

◆ get_param_types()

◆ NEW()

◆ process()

◆ process_inplace()

Member Data Documentation

◆ NAME