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

static ProcessorNEW ()

Static Public Attributes

static const string NAME = "math.poly_radial_profile"

Detailed Description

Definition at line 6972 of file processor.h.


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 6987 of file processor.h.

06988                 {
06989                         return "Finds the CM of each z-axis slice and applies a polynomial radial profile about it.";
06990                 }

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 6977 of file processor.h.

References NAME.

06978                 {
06979                         return NAME;
06980                 }

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 6991 of file processor.h.

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

06992                 {
06993                         TypeDict d;
06994                         d.put("length", EMObject::FLOAT, "Helix length in angstroms.");
06995                         d.put("z0", EMObject::INT, "z coordinate in pixels for the midpoint of the cylinder's axis, defaults to center of map");
06996                         return d;
06997                 }

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

Definition at line 6982 of file processor.h.

06983                 {
06984                         return new ApplyPolynomialProfileToHelix();
06985                 }

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 9818 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::Util::round(), and EMAN::Dict::set_default().

09819 {
09820         EMData * cyl = in;
09821         int nx = cyl->get_xsize();
09822         int ny = cyl->get_ysize();
09823         int nz = cyl->get_zsize();
09824         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
09825         float apix_y = cyl->get_attr("apix_y");
09826         float apix_z = cyl->get_attr("apix_z");
09827         float lengthAngstroms = params["length"];
09828         int z0 = params.set_default("z0", -1); //in voxels
09829 
09830         if (z0 < 0 || z0 >= nz)
09831                 z0 = nz / 2;
09832 
09833         int z_start = Util::round( z0 - 0.5*lengthAngstroms/apix_z );
09834         int z_stop = Util::round( z0 + 0.5*lengthAngstroms/apix_z );
09835 
09836         float * dat = cyl->get_data();
09837         double rho_x_sum, rho_y_sum, rho_sum, x_cm, y_cm, radius;
09838 
09839         for (int k = 0; k < nz; ++k) //taking slices along z axis
09840         {
09841                 rho_x_sum = rho_y_sum = rho_sum = 0; //Set to zero for a new slice
09842 
09843                 if (k >= z_start && k <= z_stop)
09844                 //Apply the radial profile only between z_start and z_stop on the z axis
09845                 {
09846                         //Calculating CM for the slice...
09847                         for (int j = 0; j < ny; ++j)
09848                         {
09849                                 for (int i = 0; i < nx; ++i, ++dat)
09850                                 {
09851                                         rho_x_sum += (*dat)*i;
09852                                         rho_y_sum += (*dat)*j;
09853                                         rho_sum += *dat;
09854                                 }
09855                         }
09856                         if (rho_sum != 0)
09857                         {
09858                                 dat -= nx*ny;//going back to the beginning of the dat array
09859                                 x_cm = rho_x_sum/rho_sum;
09860                                 y_cm = rho_y_sum/rho_sum;
09861 
09862                                 //Applying radial profile...
09863                                 for (int j=0; j<ny;++j)
09864                                 {
09865                                         for (int i=0;i<nx;++i,++dat)
09866                                         {
09867                                                 radius = hypot( (i-x_cm)*apix_x, (j-y_cm)*apix_y );
09868                                                 *dat = radprofile((float)radius, 2);//Type 2 is the polynomial radial profile.
09869                                         }
09870                                 }
09871                         }
09872                 }
09873                 else
09874                 //Clear the map, setting the density to zero everywhere else.
09875                 {
09876                         for (int j=0; j<ny; j++)
09877                                 for(int i=0; i<nx; i++)
09878                                 {
09879                                         *dat = 0;
09880                                         dat++;
09881                                 }
09882                 }
09883 
09884         }
09885 }


Member Data Documentation

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

Definition at line 6999 of file processor.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Thu May 3 10:11:03 2012 for EMAN2 by  doxygen 1.4.7