EMAN2
Public Member Functions | Static Public Member Functions | Static Public Attributes
EMAN::ModelEMCylinderProcessor Class Reference

#include <processor.h>

Inheritance diagram for EMAN::ModelEMCylinderProcessor:
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List of all members.

Public Member Functions

void process_inplace (EMData *in)
 To process an image in-place.
string get_name () const
 Get the processor's name.
string get_desc () const
 Get the descrition of this specific processor.
virtual TypeDict get_param_types () const
 Get processor parameter information in a dictionary.

Static Public Member Functions

static ProcessorNEW ()

Static Public Attributes

static const string NAME = "math.model_em_cylinder"

Detailed Description

Definition at line 7350 of file processor.h.


Member Function Documentation

string EMAN::ModelEMCylinderProcessor::get_desc ( ) const [inline, virtual]

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 7365 of file processor.h.

                {
                        return "Adds a cylinder with a radial density profile similar to that of an alpha helix.";
                }
string EMAN::ModelEMCylinderProcessor::get_name ( ) const [inline, virtual]

Get the processor's name.

Each processor is identified by a unique name.

Returns:
The processor's name.

Implements EMAN::Processor.

Definition at line 7355 of file processor.h.

References NAME.

                {
                        return NAME;
                }
virtual TypeDict EMAN::ModelEMCylinderProcessor::get_param_types ( ) const [inline, virtual]

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 7370 of file processor.h.

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

                {
                        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;
                }
static Processor* EMAN::ModelEMCylinderProcessor::NEW ( ) [inline, static]

Definition at line 7360 of file processor.h.

                {
                        return new ModelEMCylinderProcessor();
                }
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:
imageThe image to be processed.

Implements EMAN::Processor.

Definition at line 10482 of file processor.cpp.

References EMAN::EMData::get_attr(), EMAN::EMData::get_data(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), in, nx, ny, EMAN::Processor::params, EMAN::Dict::set_default(), x, and y.

{
        // 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;

                        }
                }
        }
}

Member Data Documentation

const string ModelEMCylinderProcessor::NAME = "math.model_em_cylinder" [static]

Definition at line 7382 of file processor.h.

Referenced by get_name().


The documentation for this class was generated from the following files: