Replace the value of each pixel with the sum of density of the object it belongs to. More...

#include <processor.h>

Inheritance diagram for EMAN::ObjDensityProcessor:

Collaboration diagram for EMAN::ObjDensityProcessor:

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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.object.density"

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

Replace the value of each pixel with the sum of density of the object it belongs to.

Objects are defined by continius density above the given threshold.

Author: : Muyuan Chen

Date: : 03/2015

Definition at line 9476 of file processor.h.

Member Function Documentation

◆ get_desc()

string EMAN::ObjDensityProcessor::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 9490 of file processor.h.

                {
                        return "Sum of density of each object above threshold. Treats a 3D volume as 2D slices.";
                }

◆ get_name()

virtual string EMAN::ObjDensityProcessor::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 9482 of file processor.h.

                {
                        return NAME;
                }

References NAME.

◆ get_param_types()

virtual TypeDict EMAN::ObjDensityProcessor::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 9494 of file processor.h.

                {
                        TypeDict d;
                        d.put("thresh", EMObject::FLOAT, "The threshold to seperate objects.");
                        return d;
                }

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

◆ NEW()

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

inlinestatic

Definition at line 9486 of file processor.h.

                {
                        return new ObjDensityProcessor();
                }

◆ process()

EMData * ObjDensityProcessor::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 14508 of file processor.cpp.

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

References copy(), and process_inplace().

◆ process_inplace()

void ObjDensityProcessor::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 14517 of file processor.cpp.

{
        int nx = image->get_xsize();
        int ny = image->get_ysize();
        int nz = image->get_zsize();
 
        float threshold=params.set_default("thresh",0);
 
        // label each object first
        EMData *label=image->process("threshold.belowtozero",Dict("minval",threshold));
        label->process_inplace("threshold.notzero");
        label->process_inplace("morph.object.label");
        int nobj=int(label->get_attr("maximum"))+1;
        vector<float> sden(nobj);       // sum density of each object
        for (int i=0; i<nobj; i++) sden[i]=0;
 
        for (int x=0; x<nx; x++){
                for (int y=0; y<ny; y++){
                        for (int z=0; z<nz; z++){
                                float v=image->get_value_at(x,y,z);
                                if (v<threshold)
                                        continue;
 
                                int li=label->get_value_at(x,y,z);
                                sden[li]+=v;
                        }
                }
        }
        for (int x=0; x<nx; x++){
                for (int y=0; y<ny; y++){
                        for (int z=0; z<nz; z++){
                                int li=label->get_value_at(x,y,z);
                                if (li==0)
                                        continue;
                                image->set_value_at_fast(x,y,z,sden[li]);
                        }
                }
        }
        delete label;
}

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

Referenced by process().

Member Data Documentation

◆ NAME

const string ObjDensityProcessor::NAME = "morph.object.density"

static

Definition at line 9500 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