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 6974 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 6989 of file processor.h.

06990                 {
06991                         return "Finds the CM of each z-axis slice and applies a polynomial radial profile about it.";
06992                 }

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 6979 of file processor.h.

References NAME.

06980                 {
06981                         return NAME;
06982                 }

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 6993 of file processor.h.

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

06994                 {
06995                         TypeDict d;
06996                         d.put("length", EMObject::FLOAT, "Helix length in angstroms.");
06997                         d.put("z0", EMObject::INT, "z coordinate in pixels for the midpoint of the cylinder's axis, defaults to center of map");
06998                         return d;
06999                 }

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

Definition at line 6984 of file processor.h.

06985                 {
06986                         return new ApplyPolynomialProfileToHelix();
06987                 }

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 9833 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().

09834 {
09835         EMData * cyl = in;
09836         int nx = cyl->get_xsize();
09837         int ny = cyl->get_ysize();
09838         int nz = cyl->get_zsize();
09839         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
09840         float apix_y = cyl->get_attr("apix_y");
09841         float apix_z = cyl->get_attr("apix_z");
09842         float lengthAngstroms = params["length"];
09843         int z0 = params.set_default("z0", -1); //in voxels
09844 
09845         if (z0 < 0 || z0 >= nz)
09846                 z0 = nz / 2;
09847 
09848         int z_start = Util::round( z0 - 0.5*lengthAngstroms/apix_z );
09849         int z_stop = Util::round( z0 + 0.5*lengthAngstroms/apix_z );
09850 
09851         float * dat = cyl->get_data();
09852         double rho_x_sum, rho_y_sum, rho_sum, x_cm, y_cm, radius;
09853 
09854         for (int k = 0; k < nz; ++k) //taking slices along z axis
09855         {
09856                 rho_x_sum = rho_y_sum = rho_sum = 0; //Set to zero for a new slice
09857 
09858                 if (k >= z_start && k <= z_stop)
09859                 //Apply the radial profile only between z_start and z_stop on the z axis
09860                 {
09861                         //Calculating CM for the slice...
09862                         for (int j = 0; j < ny; ++j)
09863                         {
09864                                 for (int i = 0; i < nx; ++i, ++dat)
09865                                 {
09866                                         rho_x_sum += (*dat)*i;
09867                                         rho_y_sum += (*dat)*j;
09868                                         rho_sum += *dat;
09869                                 }
09870                         }
09871                         if (rho_sum != 0)
09872                         {
09873                                 dat -= nx*ny;//going back to the beginning of the dat array
09874                                 x_cm = rho_x_sum/rho_sum;
09875                                 y_cm = rho_y_sum/rho_sum;
09876 
09877                                 //Applying radial profile...
09878                                 for (int j=0; j<ny;++j)
09879                                 {
09880                                         for (int i=0;i<nx;++i,++dat)
09881                                         {
09882                                                 radius = hypot( (i-x_cm)*apix_x, (j-y_cm)*apix_y );
09883                                                 *dat = radprofile((float)radius, 2);//Type 2 is the polynomial radial profile.
09884                                         }
09885                                 }
09886                         }
09887                 }
09888                 else
09889                 //Clear the map, setting the density to zero everywhere else.
09890                 {
09891                         for (int j=0; j<ny; j++)
09892                                 for(int i=0; i<nx; i++)
09893                                 {
09894                                         *dat = 0;
09895                                         dat++;
09896                                 }
09897                 }
09898 
09899         }
09900 }


Member Data Documentation

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

Definition at line 7001 of file processor.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Fri Aug 10 16:36:55 2012 for EMAN2 by  doxygen 1.4.7