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EMAN::ApplyPolynomialProfileToHelix Class Reference

#include <processor.h>

Inheritance diagram for EMAN::ApplyPolynomialProfileToHelix:

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Collaboration diagram for EMAN::ApplyPolynomialProfileToHelix:
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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

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 6904 of file processor.h.

06905                 {
06906                         return "Finds the CM of each z-axis slice and applies a polynomial radial profile about it.";
06907                 }

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 6894 of file processor.h.

06895                 {
06896                         return NAME;
06897                 }

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 6908 of file processor.h.

References EMAN::TypeDict::put().

06909                 {
06910                         TypeDict d;
06911                         d.put("length", EMObject::FLOAT, "Helix length in angstroms.");
06912                         d.put("z0", EMObject::INT, "z coordinate in pixels for the midpoint of the cylinder's axis, defaults to center of map");
06913                         return d;
06914                 }

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

Definition at line 6899 of file processor.h.

06900                 {
06901                         return new ApplyPolynomialProfileToHelix();
06902                 }

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 9869 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().

09870 {
09871         EMData * cyl = in;
09872         int nx = cyl->get_xsize();
09873         int ny = cyl->get_ysize();
09874         int nz = cyl->get_zsize();
09875         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
09876         float apix_y = cyl->get_attr("apix_y");
09877         float apix_z = cyl->get_attr("apix_z");
09878         float lengthAngstroms = params["length"];
09879         int z0 = params.set_default("z0", -1); //in voxels
09880 
09881         if (z0 < 0 || z0 >= nz)
09882                 z0 = nz / 2;
09883 
09884         int z_start = Util::round( z0 - 0.5*lengthAngstroms/apix_z );
09885         int z_stop = Util::round( z0 + 0.5*lengthAngstroms/apix_z );
09886 
09887         float * dat = cyl->get_data();
09888         double rho_x_sum, rho_y_sum, rho_sum, x_cm, y_cm, radius;
09889 
09890         for (int k = 0; k < nz; k++) //taking slices along z axis
09891         {
09892                 rho_x_sum = rho_y_sum = rho_sum = 0; //Set to zero for a new slice
09893 
09894                 if (k >= z_start && k <= z_stop)
09895                 //Apply the radial profile only between z_start and z_stop on the z axis
09896                 {
09897                         //Calculating CM for the slice...
09898                         for (int j = 0; j < ny; j++)
09899                         {
09900                                 for (int i = 0; i < nx; i++, dat++)
09901                                 {
09902                                         rho_x_sum += (*dat)*i;
09903                                         rho_y_sum += (*dat)*j;
09904                                         rho_sum += *dat;
09905                                 }
09906                         }
09907                         if (rho_sum != 0)
09908                         {
09909                                 dat -= nx*ny;//going back to the beginning of the dat array
09910                                 x_cm = rho_x_sum/rho_sum;
09911                                 y_cm = rho_y_sum/rho_sum;
09912 
09913                                 //Applying radial profile...
09914                                 for (int j=0; j<ny;j++)
09915                                 {
09916                                         for (int i=0;i<nx;i++,dat++)
09917                                         {
09918                                                 radius = hypot( (i-x_cm)*apix_x, (j-y_cm)*apix_y );
09919                                                 *dat = radprofile((float)radius, 2);//Type 2 is the polynomial radial profile.
09920                                         }
09921                                 }
09922                         }
09923                 }
09924                 else
09925                 //Clear the map, setting the density to zero everywhere else.
09926                 {
09927                         for (int j=0; j<ny; j++)
09928                                 for(int i=0; i<nx; i++)
09929                                 {
09930                                         *dat = 0;
09931                                         dat++;
09932                                 }
09933                 }
09934 
09935         }
09936 }


Member Data Documentation

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

Definition at line 218 of file processor.cpp.


The documentation for this class was generated from the following files:
Generated on Fri Apr 30 15:39:30 2010 for EMAN2 by  doxygen 1.3.9.1