Replace a source image as a Gaussian Blob. More...

#include <processor.h>

Inheritance diagram for EMAN::TestImageGaussian:

Collaboration diagram for EMAN::TestImageGaussian:

[legend]

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

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

virtual 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::TestImageProcessor
static string	get_group_desc ()

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 = "testimage.gaussian"

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 Member Functions inherited from EMAN::TestImageProcessor
void	preprocess (EMData *image)

Protected Attributes inherited from EMAN::TestImageProcessor
int	nx

int	ny

int	nz

Protected Attributes inherited from EMAN::Processor
Dict	params

Detailed Description

Replace a source image as a Gaussian Blob.

Parameters

sigma	sigma value for this Gaussian blob
axis	specify a major axis for asymmetric features
c	distance between focus and the center of an ellipse

Definition at line 8410 of file processor.h.

Member Function Documentation

◆ get_desc()

virtual string EMAN::TestImageGaussian::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 8420 of file processor.h.

                {
                        return "Replace a source image as a Gaussian Blob";
                }

◆ get_name()

virtual string EMAN::TestImageGaussian::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 8415 of file processor.h.

                {
                        return NAME;
                }

References NAME.

◆ get_param_types()

virtual TypeDict EMAN::TestImageGaussian::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 8430 of file processor.h.

                {
                        TypeDict d;
                        d.put("sigma", EMObject::FLOAT, "sigma value for this Gaussian blob");
                        d.put("axis", EMObject::STRING, "specify a major axis for asymmetric features");
                        d.put("c", EMObject::FLOAT, "distance between focus and the center of an ellipse");
                        return d;
                }

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

◆ NEW()

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

inlinestatic

Definition at line 8425 of file processor.h.

                {
                        return new TestImageGaussian();
                }

◆ process_inplace()

void TestImageGaussian::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 9303 of file processor.cpp.

{
        preprocess(image);
 
        float sigma = params["sigma"];
        string axis = (const char*)params["axis"];
        float c = params["c"];
 
        float *dat = image->get_data();
        float r; //this is the distance of pixel from the image center(nx/2, ny/2, nz/2)
        float x2, y2, z2; //this is the coordinates of this pixel from image center
        for (int k = 0; k < nz; ++k) {
                for (int j = 0; j < ny; ++j) {
                        for (int i = 0; i < nx; ++i, ++dat) {
                                x2 = (float)( i - nx/2 );
                                y2 = (float)( j - ny/2 );
                                z2 = (float)( k - nz/2 );
 
                                if(axis==""){
                                        r = (float)sqrt(x2*x2+y2*y2+z2*z2);
                                }
                                else if(axis == "x"){
                                        float lc = -c;
                                        float rc = c;
                                        r = ( (float)sqrt((x2-lc)*(x2-lc)+y2*y2+z2*z2) +
                                                  (float)sqrt((x2-rc)*(x2-rc)+y2*y2+z2*z2) ) /2.0f - c;
                                }
                                else if(axis == "y"){
                                        float lc = -c;
                                        float rc = c;
                                        r = ( (float)sqrt(x2*x2+(y2-lc)*(y2-lc)+z2*z2) +
                                                  (float)sqrt(x2*x2+(y2-rc)*(y2-rc)+z2*z2) ) /2.0f - c;
                                }
                                else if(axis == "z"){
                                        if( nz == 1 ){
                                                throw InvalidValueException(0, "This is a 2D image, no asymmetric feature for z axis");
                                        }
                                        float lc = -c;
                                        float rc = c;
                                        r = ( (float)sqrt(x2*x2+y2*y2+(z2-lc)*(z2-lc)) +
                                                  (float)sqrt(x2*x2+y2*y2+(z2-rc)*(z2-rc)) ) /2.0f - c;
                                }
                                else{
                                        throw InvalidValueException(0, "please specify a valid axis for asymmetric features");
                                }
                                //the amplitude of the pixel is proportional to the distance of this pixel from the center
                                *dat = (float)gsl_ran_gaussian_pdf((double)r,(double)sigma);
                        }
                }
        }
 
        image->update();
}

References InvalidValueException, EMAN::TestImageProcessor::nx, EMAN::TestImageProcessor::ny, EMAN::TestImageProcessor::nz, EMAN::Processor::params, EMAN::TestImageProcessor::preprocess(), and sqrt().

Member Data Documentation

◆ NAME

const string TestImageGaussian::NAME = "testimage.gaussian"

static

Definition at line 8439 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