EMAN::BinarySkeletonizerProcessor Class Reference

#include <processor.h>

Inheritance diagram for EMAN::BinarySkeletonizerProcessor:

Collaboration diagram for EMAN::BinarySkeletonizerProcessor:

Public Member Functions
virtual EMData *	process (EMData *image)
virtual void	process_inplace (EMData *image)
	To process an image in-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 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 ="gorgon.binary_skel"

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

Definition at line 9308 of file processor.h.

Member Function Documentation

get_desc()

string EMAN::BinarySkeletonizerProcessor::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 9323 of file processor.h.

                {
                        return "Creates a skeleton of the 3D image by considering whether density is above or below a threshold value.";
                }

get_name()

virtual string EMAN::BinarySkeletonizerProcessor::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 9314 of file processor.h.

                {
                        return NAME;
//                      return "gorgon.binary_skel";
                }

References NAME.

get_param_types()

virtual TypeDict EMAN::BinarySkeletonizerProcessor::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 9327 of file processor.h.

                {
                        TypeDict d;
                        d.put("threshold", EMObject::FLOAT, "Threshold value.");
                        d.put("min_curve_width", EMObject::INT, "Minimum curve width.");
                        d.put("min_surface_width", EMObject::INT, "Minimum surface width.");
                        d.put("mark_surfaces", EMObject::BOOL, "Mark surfaces with a value of 2.0f, whereas curves are 1.0f.");
                        return d;
                }

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

NEW()

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

inlinestatic

Definition at line 9319 of file processor.h.

                {
                        return new BinarySkeletonizerProcessor();
                }

process()

EMData * BinarySkeletonizerProcessor::process ( EMData *  image )

virtual

Definition at line 13291 of file processor.cpp.

{
        using namespace wustl_mm::GraySkeletonCPP;
        using namespace wustl_mm::SkeletonMaker;
 
        Volume * vimage = new Volume(image);
        float threshold = params["threshold"];
        int min_curvew = params.set_default("min_curve_width", 4);
        int min_srfcw = params.set_default("min_surface_width", 4);
        bool mark_surfaces = params.set_default("mark_surfaces", true);
        Volume* vskel = VolumeSkeletonizer::PerformPureJuSkeletonization(vimage, "unused", static_cast<double>(threshold), min_curvew, min_srfcw);
        //VolumeSkeletonizer::CleanUpSkeleton(vskel, 4, 0.01f);
        if (mark_surfaces) {
                VolumeSkeletonizer::MarkSurfaces(vskel);
        }
 
        vskel->getVolumeData()->owns_emdata = false; //ensure the EMData object will remain when the Volume and its VolumeData object are freed
        EMData* skel = vskel->get_emdata();
        skel->update();
        return skel;
}

References wustl_mm::SkeletonMaker::Volume::get_emdata(), wustl_mm::SkeletonMaker::Volume::getVolumeData(), wustl_mm::SkeletonMaker::VolumeData::owns_emdata, EMAN::Processor::params, and EMAN::Dict::set_default().

Referenced by process_inplace().

process_inplace()

void BinarySkeletonizerProcessor::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 13313 of file processor.cpp.

{
        EMData* em_skel = this->process(image);
        //TODO: use memcpy and copy metadata explicitly
        *image = *em_skel; //Deep copy performed by EMData::operator=
        image->update();
        delete em_skel;
        em_skel = NULL;
        return;
}

References process().

Member Data Documentation

NAME

const string BinarySkeletonizerProcessor::NAME ="gorgon.binary_skel"

static

Definition at line 9336 of file processor.h.

Referenced by get_name().

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The documentation for this class was generated from the following files:

• processor.h
• processor.cpp