EMAN::ModelEMCylinderProcessor Class Reference

#include <processor.h>

Inheritance diagram for EMAN::ModelEMCylinderProcessor:

Inheritance graph
[legend]
Collaboration diagram for EMAN::ModelEMCylinderProcessor:

Collaboration graph
[legend]
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 6939 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 6954 of file processor.h.

06955                 {
06956                         return "Adds a cylinder with a radial density profile similar to that of an alpha helix.";
06957                 }

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 6944 of file processor.h.

References NAME.

06945                 {
06946                         return NAME;
06947                 }

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 6959 of file processor.h.

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

06960                 {
06961                         TypeDict d;
06962                         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");
06963                         d.put("length", EMObject::FLOAT, "cylinder length in angstroms, defaults to 3 turns (16.2 Angstroms)");
06964                         d.put("x0", EMObject::INT, "x coordinate in pixels for the midpoint of the cylinder's axis, defaults to center of map");
06965                         d.put("y0", EMObject::INT, "y coordinate in pixels for the midpoint of the cylinder's axis, defaults to center of map");
06966                         d.put("z0", EMObject::INT, "z coordinate in pixels for the midpoint of the cylinder's axis, defaults to center of map");
06967                         //TODO: Check with Matt Baker about description strings
06968                         return d;
06969                 }

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

Definition at line 6949 of file processor.h.

06950                 {
06951                         return new ModelEMCylinderProcessor();
06952                 }

void ModelEMCylinderProcessor::process_inplace ( EMData in  )  [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 9783 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, EMAN::Processor::params, EMAN::ModelHelixProcessor::radprofile(), EMAN::Dict::set_default(), and x.

09784               : modified from EMAN1 Cylinder.C by Wen Jiang
09785 {
09786         // synthesize model alpha helix, len is Angstrom, default to 2 turns
09787         //The helical axis is parallel to the z axis.
09788         EMData * cyl = in;
09789         int nx = cyl->get_xsize();
09790         int ny = cyl->get_ysize();
09791         int nz = cyl->get_zsize();
09792 
09793         int type = params.set_default("type", 2);
09794         float len = params.set_default("length", 16.2f); //in angstroms
09795         int x0 = params.set_default("x0", -1); //in voxels -- default value changed a few lines down
09796         int y0 = params.set_default("y0", -1); //in voxels
09797         int z0 = params.set_default("z0", -1); //in voxels
09798         //TODO: check with Matt about default values
09799 
09800         if (x0 < 0 || x0 >= nx)
09801                 x0 = nx / 2;
09802         if (y0 < 0 || y0 >= ny)
09803                 y0 = ny / 2;
09804         if (z0 < 0 || z0 >= nz)
09805                 z0 = nz / 2;
09806 
09807         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
09808         float apix_y = cyl->get_attr("apix_y");
09809         float apix_z = cyl->get_attr("apix_z");
09810 
09811         float * dat = cyl->get_data();
09812         int cyl_voxel_len = (int) (len / apix_z);
09813         int cyl_k_min = z0 - cyl_voxel_len / 2;
09814         int cyl_k_max = z0 + cyl_voxel_len / 2;
09815 
09816         int x, y;
09817         for (int k = 0; k < nz; ++k) {
09818                 for (int j = 0; j < ny; ++j) {
09819                         for (int i = 0; i < nx; ++i, ++dat) {
09820                                 x = i - x0;//coordinate sys centered on cylinder
09821                                 y = j - y0;//coordinate sys centered on cylinder
09822                                 float radius = (float)hypot(x * apix_x, y * apix_y);
09823                                 if ((k > cyl_k_min) && (k < cyl_k_max))
09824                                         *dat += radprofile(radius, type); //pointer arithmetic for array done in loop
09825                                 //else
09826                                         //continue;
09827 
09828                         }
09829                 }
09830         }
09831 }


Member Data Documentation

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

Definition at line 6971 of file processor.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Fri Aug 10 16:36:54 2012 for EMAN2 by  doxygen 1.4.7