Calculate the z thickness of each pixel in a binarized 3d image. More...

#include <processor.h>

Inheritance diagram for EMAN::ZThicknessProcessor:

Collaboration diagram for EMAN::ZThicknessProcessor:

[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 = "misc.zthick"

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

Calculate the z thickness of each pixel in a binarized 3d image.

Author: : Muyuan Chen

Date: : 02/2016

Definition at line 9689 of file processor.h.

Member Function Documentation

◆ get_desc()

string EMAN::ZThicknessProcessor::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 9703 of file processor.h.

                {
                        return "Calculate the z thickness of each pixel in a binarized 3d image. For each white voxel, use the number of continus white voxels above and below this voxel in z direction as the thickness.";
                }

◆ get_name()

virtual string EMAN::ZThicknessProcessor::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 9695 of file processor.h.

                {
                        return NAME;
                }

References NAME.

◆ get_param_types()

virtual TypeDict EMAN::ZThicknessProcessor::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 9707 of file processor.h.

                {
                        TypeDict d;
                        d.put("thresh", EMObject::FLOAT, "Threshold for binarization");
                        return d;
                }

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

◆ NEW()

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

inlinestatic

Definition at line 9699 of file processor.h.

                {
                        return new ZThicknessProcessor();
                }

◆ process()

EMData * ZThicknessProcessor::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 15384 of file processor.cpp.

{
        EMData* proc = image->copy();
        proc->process_inplace("misc.zthick",params);
        return proc;
}

References EMAN::Processor::params.

◆ process_inplace()

void ZThicknessProcessor::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 15391 of file processor.cpp.

{
        float thresh=params.set_default("thresh",0);
        int nx = image->get_xsize();
        int ny = image->get_ysize();
        int nz = image->get_zsize();
 
        for (int i=0; i<nx; i++) {
                for (int j=0; j<ny; j++) {
                        // depth
                        int dep=0, starti=0;
                        bool counting=false;
                        for (int k=0; k<nz; k++) {
                                if (image->get_value_at(i,j,k)>thresh){
                                        if (!counting){
                                                // start counting
                                                starti=k;
                                                dep=0;
                                                counting=true;
                                        }
                                        dep++;
                                }
                                else{
                                        if (counting){
                                                counting=false;
                                                // go back and set the voxels to the depth value
                                                for (int u=starti; u<k; u++){
                                                        image->set_value_at_fast(i,j,u,dep);
//                                                      printf("%d,%d,%d,%d\n", i,j,u,dep);
 
                                                }
                                        }
                                }
                        }
                }
        }
 
 
}

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

Member Data Documentation

◆ NAME

const string ZThicknessProcessor::NAME = "misc.zthick"

static

Definition at line 9713 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