Multiplies image by a 'linear pyramid' 1-(|x-xsize/2|*|y-ysize/2|*4/(xsize*ysize)) This is useful in averaging together boxed out regions with 50% overlap. More...

#include <processor.h>

Inheritance diagram for EMAN::GridKernelFixProcessor:

[legend]

Collaboration diagram for EMAN::GridKernelFixProcessor:

[legend]

Public Member Functions
string	get_name () const
	Get the processor's name. More...

void	process_inplace (EMData *image)
	To process an image in-place. More...

virtual TypeDict	get_param_types () const
	Get processor parameter information in a dictionary. More...

string	get_desc () const
	Get the descrition of this specific processor. 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 = "math.gridkernelfix"

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

Multiplies image by a 'linear pyramid' 1-(|x-xsize/2|*|y-ysize/2|*4/(xsize*ysize)) This is useful in averaging together boxed out regions with 50% overlap.

Definition at line 4182 of file processor.h.

Member Function Documentation

◆ get_desc()

string EMAN::GridKernelFixProcessor::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 4204 of file processor.h.

                {
                        return "This corrects the real-space effects of using one of the gridding insertion functions on the Fourier reconstructor. Valid options for mode are 'gridding_5' and 'gridding7'.";
                }

◆ get_name()

string EMAN::GridKernelFixProcessor::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 4185 of file processor.h.

                {
                        return NAME;
                }

References NAME.

◆ get_param_types()

virtual TypeDict EMAN::GridKernelFixProcessor::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 4197 of file processor.h.

                {
                        TypeDict d;
                        d.put("mode", EMObject::STRING);
                        return d;
                }

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

◆ NEW()

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

inlinestatic

Definition at line 4192 of file processor.h.

                {
                        return new GridKernelFixProcessor();
                }

◆ process_inplace()

void GridKernelFixProcessor::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 818 of file processor.cpp.

{
        if (!image) {
                LOGWARN("NULL Image");
                return;
        }
 
        string mode=(string)params["mode"];
 
        int nx = image->get_xsize();
        int ny = image->get_ysize();
        int nz = image->get_zsize();
 
        // make an empty FFT object. 
        EMData *fft=new EMData((nx&0xfffffffe)+2,ny,nz);
        fft->set_complex(1);
        fft->set_ri(1);
        if (nx&1) fft->set_fftpad(1);
        fft->to_zero();
        
        // Copy the kernel. Note that the kernel is 3x oversampled, so we are just computing an approximate kernel locally
        if (mode=="gridding_5") {
                for (int z=-2; z<3; z++) {
                        for (int y=-2; y<3; y++) {
                                for (int x=0; x<3; x++) {
                                        fft->set_complex_at(x,y,z,FourierInserter3DMode7::kernel[x*3][abs(y)*3][abs(z)*3]);
                                }
                        }
                }
        }
        else if (mode=="gridding_7") {
                for (int z=-3; z<4; z++) {
                        for (int y=-3; y<4; y++) {
                                for (int x=0; x<4; x++) {
                                        fft->set_complex_at(x,y,z,FourierInserter3DMode11::kernel[x*3][abs(y)*3][abs(z)*3]);
                                }
                        }
                }
        }
        else throw InvalidParameterException("Gridding kernel correction of unknown mode, only gridding_5 or gridding_7 allowed");
        
        EMData *real=fft->do_ift();                                     // this is the kernel ift
        real->process_inplace("xform.phaseorigin.tocenter");
        real->mult(2.0f/(float)real->get_attr("maximum"));
        real->process_inplace("math.reciprocal");       // reciprocal to make a correction volume
        real->process_inplace("threshold.clampminmax",Dict("minval",-4.0f,"maxval",4.0f));      // block overcorrection of noise near the edges
//      real->write_image("invkernel.hdf");
        
        image->mult(*real);             // apply the correction
        delete real;
        delete fft;
}

References InvalidParameterException, EMAN::FourierInserter3DMode11::kernel, EMAN::FourierInserter3DMode7::kernel, LOGWARN, EMAN::Processor::params, real(), x, and y.

Member Data Documentation

◆ NAME

const string GridKernelFixProcessor::NAME = "math.gridkernelfix"

static

Definition at line 4209 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