Grow a skeleton map toward a local direction. More...

#include <processor.h>

Inheritance diagram for EMAN::GrowSkeletonProcessor:

Collaboration diagram for EMAN::GrowSkeletonProcessor:

[legend]

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

virtual EMData *	process (const EMData *const image)
	To proccess an image out-of-place. More...

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

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 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 = "morph.grow"

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

Grow a skeleton map toward a local direction.

Image should be binarized.

Author: : Muyuan Chen

Date: : 06/2015

Definition at line 9657 of file processor.h.

Member Function Documentation

◆ get_desc()

string EMAN::GrowSkeletonProcessor::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 9671 of file processor.h.

                {
                        return "Grow a skeleton map toward a local direction.";
                }

◆ get_name()

virtual string EMAN::GrowSkeletonProcessor::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 9663 of file processor.h.

                {
                        return NAME;
                }

References NAME.

◆ get_param_types()

virtual TypeDict EMAN::GrowSkeletonProcessor::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 9675 of file processor.h.

                {
                        TypeDict d;
                        d.put("verbose", EMObject::INT, "Verbose");
                        d.put("radius", EMObject::INT, "Half of the box size to determine the local direction.");
                        return d;
                }

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

◆ NEW()

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

inlinestatic

Definition at line 9667 of file processor.h.

                {
                        return new GrowSkeletonProcessor();
                }

◆ process()

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

virtual

To proccess an image out-of-place.

For those processors which can only be processed out-of-place, override this function to give the right behavior.

Parameters

image The image will be copied, actual process happen on copy of image.

Returns: the image processing result, may or may not be the same size of the input image

Reimplemented from EMAN::Processor.

Definition at line 15013 of file processor.cpp.

{
        EMData* imageCp= image -> copy();
        process_inplace(imageCp);
        return imageCp;
}

References copy(), and process_inplace().

◆ process_inplace()

void GrowSkeletonProcessor::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 15020 of file processor.cpp.

                                                         {
        // This function is far from optimized, but it works...
 
        int nx = image->get_xsize();
        int ny = image->get_ysize();
        int nz = image->get_zsize();
 
        int verbose=params.set_default("verbose",0);
        int rad=params.set_default("radius",3);
 
 
        float *data = image->get_data();
        // the index of the boundary points of the box
        int *xlist=new int[2*rad*4];
        int *ylist=new int[2*rad*4];
        int count=0;
        for (int i=-rad; i<rad; i++){ xlist[count]=-rad; ylist[count]=i; count++;}
        for (int i=-rad; i<rad; i++){ xlist[count]=i; ylist[count]=rad; count++;}
        for (int i=-rad; i<rad; i++){ xlist[count]=rad; ylist[count]=-i; count++;}
        for (int i=-rad; i<rad; i++){ xlist[count]=-i; ylist[count]=-rad; count++;}
        size_t nxy = nx * ny;
        for (int k=0; k<nz; k++){
                if (verbose>0)
                        printf("Processing layer %d \n",k);
 
                size_t knxy = (size_t)k * nxy;
                // only grow on the endpoints
                for (int j=rad; j < ny-rad; j++) {
                        int jnx=j*nx;
                        for (int i=rad; i<nx-rad; i++) {
 
                                if (data[knxy+i+jnx]==0)
                                        continue;
                                int nb=-1;      // number of neighbors
                                for (int i2=i-1; i2<=i+1; i2++) {
                                        for (int j2=j-1; j2<=j+1; j2++) {
                                                nb+=(data[knxy+i2+j2*nx]>0 ? 1 : 0);
                                        }
                                }
                                if (nb==1){ // endpoint found
                                        int nv=0,cp=0;
                                        for (int ic=0; ic<count; ic++){
                                                int ix=i+xlist[ic], jy=j+ylist[ic];
                                                float v=data[knxy+ix+jy*nx];
                                                if (v>0){
                                                        nv++;
                                                        cp=ic;
                                                }
                                        }
                                        if (nv != 1)
                                                // more than one possible directions
                                                continue;
 
                                        // grow towards the oppisite direction
                                        for (int ig=1; ig<=rad; ig++){
                                                int ix=i-(float)xlist[cp]/rad*ig;
                                                int jy=j-(float)ylist[cp]/rad*ig;
                                                data[knxy+ix+jy*nx]=-1;
                                        }
                                }
                        }
                }
 
                for (int j=rad; j < ny-rad; j++) {
                        int jnx=j*nx;
                        for (int i=rad; i<nx-rad; i++) {
                                if (data[knxy+i+jnx]==-1)
                                        data[knxy+i+jnx]=1;
                        }
                }
        }
        image->update();
 
        delete[] xlist;
        delete[] ylist;
 
}

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

Referenced by process().

Member Data Documentation

◆ NAME

const string GrowSkeletonProcessor::NAME = "morph.grow"

static

Definition at line 9682 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()

◆ process_inplace()

Member Data Documentation

◆ NAME