Iterative expansion of a binary mask, val1 is number of pixels to expand, if val2!=0 will make a soft Gaussian edge starting after val2 pixels. More...

#include <processor.h>

Inheritance diagram for EMAN::IterBinMaskProcessor:

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Collaboration diagram for EMAN::IterBinMaskProcessor:

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

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

virtual string	get_desc () const
	Get the descrition of this specific processor. 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 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 = "mask.addshells.gauss"

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

Iterative expansion of a binary mask, val1 is number of pixels to expand, if val2!=0 will make a soft Gaussian edge starting after val2 pixels.

Parameters

val1	number of pixels to expand
val2	number of Gaussian pixels to expand, following the first expansion

Definition at line 8020 of file processor.h.

Member Function Documentation

◆ get_desc()

virtual string EMAN::IterBinMaskProcessor::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 8030 of file processor.h.

                {
                        return "Iterative expansion of a binary mask, val1 is number of pixels to expand, if val2!=0 will make a soft Gaussian edge starting after val2 pixels.";
                }

◆ get_name()

virtual string EMAN::IterBinMaskProcessor::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 8025 of file processor.h.

                {
                        return NAME;
                }

References NAME.

◆ get_param_types()

virtual TypeDict EMAN::IterBinMaskProcessor::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 8040 of file processor.h.

                {
                        TypeDict d;
                        d.put("val1", EMObject::FLOAT, "number of pixels to expand");
                        d.put("val2", EMObject::FLOAT, "number of Gaussian pixels to expand, following the first expansion");
                        return d;
                }

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

◆ NEW()

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

inlinestatic

Definition at line 8035 of file processor.h.

                {
                        return new IterBinMaskProcessor();
                }

◆ process_inplace()

void IterBinMaskProcessor::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 8745 of file processor.cpp.

{
        if (!image) {
                LOGWARN("NULL Image");
                return;
        }
 
        float val1 = params["val1"];
        float val2 = params["val2"];
 
        int nx = image->get_xsize();
        int ny = image->get_ysize();
        int nz = image->get_zsize();
        EMData *image2 = new EMData(nx,ny,nz);
 
        // Got a compile warning complaining that these things were never used. Hope I didn't break anything - apologies if so (d.woolford)
//      float *dat = image->get_data();
//      float *dat2 = image2->get_data();
 
 
        float *d = image->get_data();
        float *d2 = image2->get_data();
 
        const int nxy = nx * ny;
        size_t size = (size_t)nx * ny * nz;
 
        // TODO: THIS IS EXTREMELY INEFFICIENT
        if (nz != 1) {
                for (int l = 1; l <= (int) val1+val2; ++l) {
                        for (size_t i=0; i<size; i++) d2[i]=d[i];
                        for (int k = 1; k < nz - 1; ++k) {
                                for (int j = 1; j < ny - 1; ++j) {
                                        for (int i = 1; i < nx - 1; ++i) {
                                                size_t t = i + j*nx+(size_t)k*nx*ny;
                                                if (d[t]) continue;
                                                if (d2[t - 1] || d2[t + 1] || d2[t + nx] || d2[t - nx] || d2[t + nxy] || d2[t - nxy]) d[t] = (float) l + 1;
                                        }
                                }
                        }
                }
        }
        else {
                for (int l = 1; l <= (int) val1+val2; ++l) {
                        for (size_t i=0; i<size; i++) d2[i]=d[i];
                        for (int j = 1; j < ny - 1; ++j) {
                                for (int i = 1; i < nx - 1; ++i) {
                                        size_t t = i + j * nx;
                                        if (d[t]) continue;
                                        if (d2[t - 1] || d2[t + 1] || d2[t + nx] || d2[t - nx]) d[t] = (float) l + 1;
                                }
                        }
                }
        }
 
        vector<float> vec;
        for (int i=0; i<val1+2; i++) vec.push_back(1.0);
        for (int i=0; i<val2; i++) {
                vec.push_back(exp(-pow(2.0f*i/(val2),2.0f)));
//              printf("%f\n",exp(-pow(2.0*i/(val1-val2),2.0)));
        }
        for (size_t i = 0; i < size; ++i) if (d[i]) d[i]=vec[(int)d[i]];
 
        image->update();
        delete image2;
}

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

Member Data Documentation

◆ NAME

const string IterBinMaskProcessor::NAME = "mask.addshells.gauss"

static

Definition at line 8048 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