Main Page | Modules | Namespace List | Class Hierarchy | Alphabetical List | Class List | Directories | File List | Namespace Members | Class Members | File Members

EMAN::ApplyPolynomialProfileToHelix Class Reference

#include <processor.h>

Inheritance diagram for EMAN::ApplyPolynomialProfileToHelix:

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

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

ProcessorNEW ()

Static Public Attributes

const string NAME = "math.poly_radial_profile"

Member Function Documentation

string EMAN::ApplyPolynomialProfileToHelix::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 7028 of file processor.h.

07029                 {
07030                         return "Finds the CM of each z-axis slice and applies a polynomial radial profile about it.";
07031                 }

string EMAN::ApplyPolynomialProfileToHelix::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 7018 of file processor.h.

07019                 {
07020                         return NAME;
07021                 }

virtual TypeDict EMAN::ApplyPolynomialProfileToHelix::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 7032 of file processor.h.

References EMAN::TypeDict::put().

07033                 {
07034                         TypeDict d;
07035                         d.put("length", EMObject::FLOAT, "Helix length in angstroms.");
07036                         d.put("z0", EMObject::INT, "z coordinate in pixels for the midpoint of the cylinder's axis, defaults to center of map");
07037                         return d;
07038                 }

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

Definition at line 7023 of file processor.h.

07024                 {
07025                         return new ApplyPolynomialProfileToHelix();
07026                 }

void ApplyPolynomialProfileToHelix::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 9896 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(), nx, ny, EMAN::ModelHelixProcessor::radprofile(), EMAN::Util::round(), and EMAN::Dict::set_default().

09897 {
09898         EMData * cyl = in;
09899         int nx = cyl->get_xsize();
09900         int ny = cyl->get_ysize();
09901         int nz = cyl->get_zsize();
09902         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
09903         float apix_y = cyl->get_attr("apix_y");
09904         float apix_z = cyl->get_attr("apix_z");
09905         float lengthAngstroms = params["length"];
09906         int z0 = params.set_default("z0", -1); //in voxels
09907 
09908         if (z0 < 0 || z0 >= nz)
09909                 z0 = nz / 2;
09910 
09911         int z_start = Util::round( z0 - 0.5*lengthAngstroms/apix_z );
09912         int z_stop = Util::round( z0 + 0.5*lengthAngstroms/apix_z );
09913 
09914         float * dat = cyl->get_data();
09915         double rho_x_sum, rho_y_sum, rho_sum, x_cm, y_cm, radius;
09916 
09917         for (int k = 0; k < nz; ++k) //taking slices along z axis
09918         {
09919                 rho_x_sum = rho_y_sum = rho_sum = 0; //Set to zero for a new slice
09920 
09921                 if (k >= z_start && k <= z_stop)
09922                 //Apply the radial profile only between z_start and z_stop on the z axis
09923                 {
09924                         //Calculating CM for the slice...
09925                         for (int j = 0; j < ny; ++j)
09926                         {
09927                                 for (int i = 0; i < nx; ++i, ++dat)
09928                                 {
09929                                         rho_x_sum += (*dat)*i;
09930                                         rho_y_sum += (*dat)*j;
09931                                         rho_sum += *dat;
09932                                 }
09933                         }
09934                         if (rho_sum != 0)
09935                         {
09936                                 dat -= nx*ny;//going back to the beginning of the dat array
09937                                 x_cm = rho_x_sum/rho_sum;
09938                                 y_cm = rho_y_sum/rho_sum;
09939 
09940                                 //Applying radial profile...
09941                                 for (int j=0; j<ny;++j)
09942                                 {
09943                                         for (int i=0;i<nx;++i,++dat)
09944                                         {
09945                                                 radius = hypot( (i-x_cm)*apix_x, (j-y_cm)*apix_y );
09946                                                 *dat = radprofile((float)radius, 2);//Type 2 is the polynomial radial profile.
09947                                         }
09948                                 }
09949                         }
09950                 }
09951                 else
09952                 //Clear the map, setting the density to zero everywhere else.
09953                 {
09954                         for (int j=0; j<ny; j++)
09955                                 for(int i=0; i<nx; i++)
09956                                 {
09957                                         *dat = 0;
09958                                         dat++;
09959                                 }
09960                 }
09961 
09962         }
09963 }


Member Data Documentation

const string ApplyPolynomialProfileToHelix::NAME = "math.poly_radial_profile" [static]
 

Definition at line 219 of file processor.cpp.


The documentation for this class was generated from the following files:
Generated on Tue Jun 11 13:49:18 2013 for EMAN2 by  doxygen 1.3.9.1