#include <processor.h>

Inheritance diagram for EMAN::ModelEMCylinderProcessor:

Collaboration diagram for EMAN::ModelEMCylinderProcessor:

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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.model_em_cylinder"

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 9243 of file processor.h.

Member Function Documentation

◆ get_desc()

string EMAN::ModelEMCylinderProcessor::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 9258 of file processor.h.

                {
                        return "Adds a cylinder with a radial density profile similar to that of an alpha helix.";
                }

◆ get_name()

string EMAN::ModelEMCylinderProcessor::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 9248 of file processor.h.

                {
                        return NAME;
                }

References NAME.

◆ get_param_types()

virtual TypeDict EMAN::ModelEMCylinderProcessor::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 9263 of file processor.h.

                {
                        TypeDict d;
                        d.put("type", EMObject::INT, "Radial profile of density method, defaults to 2: 0 = pure Gaussian falloff; 1 = Gaussian falloff + dip, so mean is zero; 2 = polynomial fitting of real helix density");
                        d.put("length", EMObject::FLOAT, "cylinder length in angstroms, defaults to 3 turns (16.2 Angstroms)");
                        d.put("x0", EMObject::INT, "x coordinate in pixels for the midpoint of the cylinder's axis, defaults to center of map");
                        d.put("y0", EMObject::INT, "y coordinate in pixels for the midpoint of the cylinder's axis, defaults to center of map");
                        d.put("z0", EMObject::INT, "z coordinate in pixels for the midpoint of the cylinder's axis, defaults to center of map");
                        //TODO: Check with Matt Baker about description strings
                        return d;
                }

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

◆ NEW()

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

inlinestatic

Definition at line 9253 of file processor.h.

                {
                        return new ModelEMCylinderProcessor();
                }

◆ process_inplace()

void ModelEMCylinderProcessor::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 13171 of file processor.cpp.

{
        // synthesize model alpha helix, len is Angstrom, default to 2 turns
        //The helical axis is parallel to the z axis.
        EMData * cyl = in;
        int nx = cyl->get_xsize();
        int ny = cyl->get_ysize();
        int nz = cyl->get_zsize();
 
        int type = params.set_default("type", 2);
        float len = params.set_default("length", 16.2f); //in angstroms
        int x0 = params.set_default("x0", -1); //in voxels -- default value changed a few lines down
        int y0 = params.set_default("y0", -1); //in voxels
        int z0 = params.set_default("z0", -1); //in voxels
        //TODO: check with Matt about default values
 
        if (x0 < 0 || x0 >= nx)
                x0 = nx / 2;
        if (y0 < 0 || y0 >= ny)
                y0 = ny / 2;
        if (z0 < 0 || z0 >= nz)
                z0 = nz / 2;
 
        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 * dat = cyl->get_data();
        int cyl_voxel_len = (int) (len / apix_z);
        int cyl_k_min = z0 - cyl_voxel_len / 2;
        int cyl_k_max = z0 + cyl_voxel_len / 2;
 
        int x, y;
        for (int k = 0; k < nz; ++k) {
                for (int j = 0; j < ny; ++j) {
                        for (int i = 0; i < nx; ++i, ++dat) {
                                x = i - x0;//coordinate sys centered on cylinder
                                y = j - y0;//coordinate sys centered on cylinder
                                float radius = (float)hypot(x * apix_x, y * apix_y);
                                if ((k > cyl_k_min) && (k < cyl_k_max))
                                        *dat += radprofile(radius, type); //pointer arithmetic for array done in loop
                                //else
                                        //continue;
 
                        }
                }
        }
}

References EMAN::Processor::params, EMAN::ModelHelixProcessor::radprofile(), EMAN::Dict::set_default(), x, and y.

Member Data Documentation

◆ NAME

const string ModelEMCylinderProcessor::NAME = "math.model_em_cylinder"

static

Definition at line 9275 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