This expands a multilevel mask volume so inter-mask boundaries are preserved. More...

#include <processor.h>

Inheritance diagram for EMAN::IterMultiMaskProcessor:

Collaboration diagram for EMAN::IterMultiMaskProcessor:

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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.multilevel"

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

This expands a multilevel mask volume so inter-mask boundaries are preserved.

Parameters

nshells number of shells to add

Definition at line 6990 of file processor.h.

Member Function Documentation

◆ get_desc()

virtual string EMAN::IterMultiMaskProcessor::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 7000 of file processor.h.

                {
                        return "A multilevel mask has an integer value at each pixel location. -1 indicates unmasked regions. 0-n-1 are individual masks. Expands the masked regions into unmasked areas by nshells.";
                }

◆ get_name()

virtual string EMAN::IterMultiMaskProcessor::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 6995 of file processor.h.

                {
                        return NAME;
                }

References NAME.

◆ get_param_types()

virtual TypeDict EMAN::IterMultiMaskProcessor::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 7010 of file processor.h.

                {
                        TypeDict d;
                        d.put("nshells", EMObject::INT, "number of shells to add");
                        return d;
                }

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

◆ NEW()

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

inlinestatic

Definition at line 7005 of file processor.h.

                {
                        return new IterMultiMaskProcessor();
                }

◆ process_inplace()

void IterMultiMaskProcessor::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 7096 of file processor.cpp.

{
        if (!image) {
                LOGWARN("NULL Image");
                return;
        }
 
        int nx = image->get_xsize();
        int ny = image->get_ysize();
        int nz = image->get_zsize();
 
        if (ny == 1) {
                LOGERR("Error: mask.addshells.multilevel works only in 2/3-D");
                return;
        }
 
        int num_shells = params.set_default("nshells",1);
 
        // there are other strategies which might allow us to avoid the extra copy, but this will have to do for now
        EMData *image1=image;
        EMData *image2=image->copy();
        if (nz == 1) {
                for (int i = 0; i < num_shells; i++) {
                        for (int y = 1; y < ny - 1; y++) {
                                for (int x = 1; x < nx - 1; x++) {
                                        if (image1->get_value_at(x,y)>0) continue;              // already part of a masked region
 
                                        // Note that this produces a directional bias in the case of ambiguous pixels
                                        // While this could be improved upon slightly, there can be truly ambiguous cases
                                        // and at least this method is deterministic
                                        if              (image1->get_value_at(x-1,y)>0) image2->set_value_at_fast(x,y,image1->get_value_at(x-1,y));
                                        else if (image1->get_value_at(x+1,y)>0) image2->set_value_at_fast(x,y,image1->get_value_at(x+1,y));
                                        else if (image1->get_value_at(x,y-1)>0) image2->set_value_at_fast(x,y,image1->get_value_at(x,y-1));
                                        else if (image1->get_value_at(x,y+1)>0) image2->set_value_at_fast(x,y,image1->get_value_at(x,y+1));
 
                                }
                        }
                        memcpy(image1->get_data(),image2->get_data(),image1->get_size()*sizeof(float));
                }
        }
        else {
                for (int i = 0; i < num_shells; i++) {
                        for (int z = 1; z < nz - 1; z++) {
                                for (int y = 1; y < ny - 1; y++) {
                                        for (int x = 1; x < nx - 1; x++) {
                                                if (image1->get_value_at(x,y,z)>0) continue;            // already part of a masked region
 
                                                // Note that this produces a directional bias in the case of ambiguous pixels
                                                // While this could be improved upon slightly, there can be truly ambiguous cases
                                                // and at least this method is deterministic
                                                if              (image1->get_value_at(x-1,y,z)>0) image2->set_value_at_fast(x,y,z,image1->get_value_at(x-1,y,z));
                                                else if (image1->get_value_at(x+1,y,z)>0) image2->set_value_at_fast(x,y,z,image1->get_value_at(x+1,y,z));
                                                else if (image1->get_value_at(x,y-1,z)>0) image2->set_value_at_fast(x,y,z,image1->get_value_at(x,y-1,z));
                                                else if (image1->get_value_at(x,y+1,z)>0) image2->set_value_at_fast(x,y,z,image1->get_value_at(x,y+1,z));
                                                else if (image1->get_value_at(x,y,z-1)>0) image2->set_value_at_fast(x,y,z,image1->get_value_at(x,y,z-1));
                                                else if (image1->get_value_at(x,y,z+1)>0) image2->set_value_at_fast(x,y,z,image1->get_value_at(x,y,z+1));
 
                                        }
                                }
                        }
                        memcpy(image1->get_data(),image2->get_data(),image1->get_size()*sizeof(float));
                }
        }
 
        delete image2;
        image->update();
}

References LOGERR, LOGWARN, EMAN::Processor::params, EMAN::Dict::set_default(), x, and y.

Member Data Documentation

◆ NAME

const string IterMultiMaskProcessor::NAME = "mask.addshells.multilevel"

static

Definition at line 7017 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