#include <processor.h>

Inheritance diagram for EMAN::ApplyPolynomialProfileToHelix:

Collaboration diagram for EMAN::ApplyPolynomialProfileToHelix:

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

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 = "math.poly_radial_profile"

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::ModelHelixProcessor
float	radprofile (float r, int type)

Protected Attributes inherited from EMAN::Processor
Dict	params

Detailed Description

Definition at line 9278 of file processor.h.

Member Function Documentation

◆ get_desc()

string EMAN::ApplyPolynomialProfileToHelix::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 9293 of file processor.h.

                {
                        return "Finds the CM of each z-axis slice and applies a polynomial radial profile about it.";
                }

◆ get_name()

string EMAN::ApplyPolynomialProfileToHelix::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 9283 of file processor.h.

                {
                        return NAME;
                }

References NAME.

◆ get_param_types()

virtual TypeDict EMAN::ApplyPolynomialProfileToHelix::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 9297 of file processor.h.

                {
                        TypeDict d;
                        d.put("length", EMObject::FLOAT, "Helix length in angstroms.");
                        d.put("z0", EMObject::INT, "z coordinate in pixels for the midpoint of the cylinder's axis, defaults to center of map");
                        return d;
                }

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

◆ NEW()

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

inlinestatic

Definition at line 9288 of file processor.h.

                {
                        return new ApplyPolynomialProfileToHelix();
                }

◆ process_inplace()

void ApplyPolynomialProfileToHelix::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 13221 of file processor.cpp.

{
        EMData * cyl = in;
        int nx = cyl->get_xsize();
        int ny = cyl->get_ysize();
        int nz = cyl->get_zsize();
        float apix_x = cyl->get_attr("apix_x"); //TODO: Ask Matt if I correctly handled cases where apix_x != apix_y or apix_x != apix_z are not equal
        float apix_y = cyl->get_attr("apix_y");
        float apix_z = cyl->get_attr("apix_z");
        float lengthAngstroms = params["length"];
        int z0 = params.set_default("z0", -1); //in voxels
 
        if (z0 < 0 || z0 >= nz)
                z0 = nz / 2;
 
        int z_start = Util::round( z0 - 0.5*lengthAngstroms/apix_z );
        int z_stop = Util::round( z0 + 0.5*lengthAngstroms/apix_z );
 
        float * dat = cyl->get_data();
        double rho_x_sum, rho_y_sum, rho_sum, x_cm, y_cm, radius;
 
        for (int k = 0; k < nz; ++k) //taking slices along z axis
        {
                rho_x_sum = rho_y_sum = rho_sum = 0; //Set to zero for a new slice
 
                if (k >= z_start && k <= z_stop)
                //Apply the radial profile only between z_start and z_stop on the z axis
                {
                        //Calculating CM for the slice...
                        for (int j = 0; j < ny; ++j)
                        {
                                for (int i = 0; i < nx; ++i, ++dat)
                                {
                                        rho_x_sum += (*dat)*i;
                                        rho_y_sum += (*dat)*j;
                                        rho_sum += *dat;
                                }
                        }
                        if (rho_sum != 0)
                        {
                                dat -= nx*ny;//going back to the beginning of the dat array
                                x_cm = rho_x_sum/rho_sum;
                                y_cm = rho_y_sum/rho_sum;
 
                                //Applying radial profile...
                                for (int j=0; j<ny;++j)
                                {
                                        for (int i=0;i<nx;++i,++dat)
                                        {
                                                radius = hypot( (i-x_cm)*apix_x, (j-y_cm)*apix_y );
                                                *dat = radprofile((float)radius, 2);//Type 2 is the polynomial radial profile.
                                        }
                                }
                        }
                }
                else
                //Clear the map, setting the density to zero everywhere else.
                {
                        for (int j=0; j<ny; j++)
                                for(int i=0; i<nx; i++)
                                {
                                        *dat = 0;
                                        dat++;
                                }
                }
 
        }
}

References EMAN::Processor::params, EMAN::ModelHelixProcessor::radprofile(), EMAN::Util::round(), and EMAN::Dict::set_default().

Member Data Documentation

◆ NAME

const string ApplyPolynomialProfileToHelix::NAME = "math.poly_radial_profile"

static

Definition at line 9305 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