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EMAN::ModelEMCylinderProcessor Class Reference

#include <processor.h>

Inheritance diagram for EMAN::ModelEMCylinderProcessor:

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Collaboration 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 6895 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 6910 of file processor.h.

06911                 {
06912                         return "Adds a cylinder with a radial density profile similar to that of an alpha helix.";
06913                 }

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 6900 of file processor.h.

References NAME.

06901                 {
06902                         return NAME;
06903                 }

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 6915 of file processor.h.

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

06916                 {
06917                         TypeDict d;
06918                         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");
06919                         d.put("length", EMObject::FLOAT, "cylinder length in angstroms, defaults to 3 turns (16.2 Angstroms)");
06920                         d.put("x0", EMObject::INT, "x coordinate in pixels for the midpoint of the cylinder's axis, defaults to center of map");
06921                         d.put("y0", EMObject::INT, "y coordinate in pixels for the midpoint of the cylinder's axis, defaults to center of map");
06922                         d.put("z0", EMObject::INT, "z coordinate in pixels for the midpoint of the cylinder's axis, defaults to center of map");
06923                         //TODO: Check with Matt Baker about description strings
06924                         return d;
06925                 }

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

Definition at line 6905 of file processor.h.

06906                 {
06907                         return new ModelEMCylinderProcessor();
06908                 }

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 9957 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(), EMAN::Processor::params, EMAN::ModelHelixProcessor::radprofile(), EMAN::Dict::set_default(), and x.

09958               : modified from EMAN1 Cylinder.C by Wen Jiang
09959 {
09960         // synthesize model alpha helix, len is Angstrom, default to 2 turns
09961         //The helical axis is parallel to the z axis.
09962         EMData * cyl = in;
09963         int nx = cyl->get_xsize();
09964         int ny = cyl->get_ysize();
09965         int nz = cyl->get_zsize();
09966 
09967         int type = params.set_default("type", 2);
09968         float len = params.set_default("length", 16.2f); //in angstroms
09969         int x0 = params.set_default("x0", -1); //in voxels -- default value changed a few lines down
09970         int y0 = params.set_default("y0", -1); //in voxels
09971         int z0 = params.set_default("z0", -1); //in voxels
09972         //TODO: check with Matt about default values
09973 
09974         if (x0 < 0 || x0 >= nx)
09975                 x0 = nx / 2;
09976         if (y0 < 0 || y0 >= ny)
09977                 y0 = ny / 2;
09978         if (z0 < 0 || z0 >= nz)
09979                 z0 = nz / 2;
09980 
09981         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
09982         float apix_y = cyl->get_attr("apix_y");
09983         float apix_z = cyl->get_attr("apix_z");
09984 
09985         float * dat = cyl->get_data();
09986         int cyl_voxel_len = (int) (len / apix_z);
09987         int cyl_k_min = z0 - cyl_voxel_len / 2;
09988         int cyl_k_max = z0 + cyl_voxel_len / 2;
09989 
09990         int x, y;
09991         for (int k = 0; k < nz; k++) {
09992                 for (int j = 0; j < ny; j++) {
09993                         for (int i = 0; i < nx; i++, dat++) {
09994                                 x = i - x0;//coordinate sys centered on cylinder
09995                                 y = j - y0;//coordinate sys centered on cylinder
09996                                 float radius = (float)hypot(x * apix_x, y * apix_y);
09997                                 if ((k > cyl_k_min) && (k < cyl_k_max))
09998                                         *dat += radprofile(radius, type); //pointer arithmetic for array done in loop
09999                                 //else
10000                                         //continue;
10001 
10002                         }
10003                 }
10004         }
10005 }


Member Data Documentation

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

Definition at line 6927 of file processor.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Mon Jul 19 13:07:31 2010 for EMAN2 by  doxygen 1.4.4