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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

static ProcessorNEW ()

Static Public Attributes

static const string NAME = "math.poly_radial_profile"

Detailed Description

Definition at line 6930 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 6945 of file processor.h.

06946                 {
06947                         return "Finds the CM of each z-axis slice and applies a polynomial radial profile about it.";
06948                 }

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 6935 of file processor.h.

References NAME.

06936                 {
06937                         return NAME;
06938                 }

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 6949 of file processor.h.

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

06950                 {
06951                         TypeDict d;
06952                         d.put("length", EMObject::FLOAT, "Helix length in angstroms.");
06953                         d.put("z0", EMObject::INT, "z coordinate in pixels for the midpoint of the cylinder's axis, defaults to center of map");
06954                         return d;
06955                 }

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

Definition at line 6940 of file processor.h.

06941                 {
06942                         return new ApplyPolynomialProfileToHelix();
06943                 }

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 10007 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::Util::round(), and EMAN::Dict::set_default().

10008 {
10009         EMData * cyl = in;
10010         int nx = cyl->get_xsize();
10011         int ny = cyl->get_ysize();
10012         int nz = cyl->get_zsize();
10013         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
10014         float apix_y = cyl->get_attr("apix_y");
10015         float apix_z = cyl->get_attr("apix_z");
10016         float lengthAngstroms = params["length"];
10017         int z0 = params.set_default("z0", -1); //in voxels
10018 
10019         if (z0 < 0 || z0 >= nz)
10020                 z0 = nz / 2;
10021 
10022         int z_start = Util::round( z0 - 0.5*lengthAngstroms/apix_z );
10023         int z_stop = Util::round( z0 + 0.5*lengthAngstroms/apix_z );
10024 
10025         float * dat = cyl->get_data();
10026         double rho_x_sum, rho_y_sum, rho_sum, x_cm, y_cm, radius;
10027 
10028         for (int k = 0; k < nz; k++) //taking slices along z axis
10029         {
10030                 rho_x_sum = rho_y_sum = rho_sum = 0; //Set to zero for a new slice
10031 
10032                 if (k >= z_start && k <= z_stop)
10033                 //Apply the radial profile only between z_start and z_stop on the z axis
10034                 {
10035                         //Calculating CM for the slice...
10036                         for (int j = 0; j < ny; j++)
10037                         {
10038                                 for (int i = 0; i < nx; i++, dat++)
10039                                 {
10040                                         rho_x_sum += (*dat)*i;
10041                                         rho_y_sum += (*dat)*j;
10042                                         rho_sum += *dat;
10043                                 }
10044                         }
10045                         if (rho_sum != 0)
10046                         {
10047                                 dat -= nx*ny;//going back to the beginning of the dat array
10048                                 x_cm = rho_x_sum/rho_sum;
10049                                 y_cm = rho_y_sum/rho_sum;
10050 
10051                                 //Applying radial profile...
10052                                 for (int j=0; j<ny;j++)
10053                                 {
10054                                         for (int i=0;i<nx;i++,dat++)
10055                                         {
10056                                                 radius = hypot( (i-x_cm)*apix_x, (j-y_cm)*apix_y );
10057                                                 *dat = radprofile((float)radius, 2);//Type 2 is the polynomial radial profile.
10058                                         }
10059                                 }
10060                         }
10061                 }
10062                 else
10063                 //Clear the map, setting the density to zero everywhere else.
10064                 {
10065                         for (int j=0; j<ny; j++)
10066                                 for(int i=0; i<nx; i++)
10067                                 {
10068                                         *dat = 0;
10069                                         dat++;
10070                                 }
10071                 }
10072 
10073         }
10074 }


Member Data Documentation

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

Definition at line 6957 of file processor.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Mon Jul 19 13:07:32 2010 for EMAN2 by  doxygen 1.4.4