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EMAN::AutoMaskAsymUnit Class Reference

Tries to mask out only interesting density. More...

#include <processor.h>

Inheritance diagram for EMAN::AutoMaskAsymUnit:

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Collaboration diagram for EMAN::AutoMaskAsymUnit:

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List of all members.

Public Member Functions

virtual void process_inplace (EMData *image)
 To process an image in-place.
virtual string get_name () const
 Get the processor's name.
virtual TypeDict get_param_types () const
 Get processor parameter information in a dictionary.
virtual string get_desc () const
 Get the descrition of this specific processor.

Static Public Member Functions

ProcessorNEW ()

Static Public Attributes

const string NAME = "mask.asymunit"

Detailed Description

Tries to mask out only interesting density.

Parameters:
au The asymmetric unit to mask, if -1 masks all asymmetric units but assigns each a unique value
sym The symmetry type, for example, "tet"
Author:
David Woolford
Date:
February 2009

Definition at line 4904 of file processor.h.


Member Function Documentation

virtual string EMAN::AutoMaskAsymUnit::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 4927 of file processor.h.

04928                         {
04929                                 return "Masks out a specific asymmetric unit of the given symmetry. If the au parameter is -1 will mask all asymmetric units, assigning the asymetric unit number to the masked area.";
04930                         }

virtual string EMAN::AutoMaskAsymUnit::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 4909 of file processor.h.

04910                         {
04911                                 return NAME;
04912                         }

virtual TypeDict EMAN::AutoMaskAsymUnit::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 4919 of file processor.h.

References EMAN::TypeDict::put().

04920                         {
04921                                 TypeDict d;
04922                                 d.put("au", EMObject::INT, "The asymmetric unit to mask out. If this is -1 will mask all asymmetric units, giving each a unique number.");
04923                                 d.put("sym", EMObject::STRING, "The symmetry, for example, d7");
04924                                 return d;
04925                         }

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

Definition at line 4914 of file processor.h.

04915                         {
04916                                 return new AutoMaskAsymUnit();
04917                         }

void AutoMaskAsymUnit::process_inplace EMData image  )  [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 5256 of file processor.cpp.

References EMAN::Factory< T >::get(), EMAN::EMData::get_data(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), LOGWARN, nx, ny, EMAN::Symmetry3D::point_in_which_asym_unit(), v, and EMAN::Vec3f.

05256                                                     {
05257         if (!image) {
05258                 LOGWARN("NULL Image");
05259                 return;
05260         }
05261 
05262         int nx = image->get_xsize();
05263         int ny = image->get_ysize();
05264         int nz = image->get_zsize();
05265 
05266         int ox = nx/2;
05267         int oy = ny/2;
05268         int oz = nz/2;
05269 
05270         Symmetry3D* sym = Factory<Symmetry3D>::get((string)params["sym"]);
05271         int au = params.set_default("au",0);
05272 
05273         float *d = image->get_data();
05274         for(int k = 0; k < nz; ++k ) {
05275                 for(int j = 0; j < ny; ++j ) {
05276                         for (int i = 0; i< nx; ++i, ++d) {
05277                                 //cout << i << " " << j << " " << k << endl;
05278                                 Vec3f v(i-ox,j-oy,k-oz);
05279 //                              v.normalize();
05280                                 int a = sym->point_in_which_asym_unit(v);
05281                                 if (au == -1) {
05282                                         *d = (float)a;
05283                                 } else {
05284                                         if ( a == au ) *d = 1;
05285                                         else *d = 0;
05286                                 }
05287                         }
05288                 }
05289         }
05290 
05291         delete sym;
05292 
05293 }


Member Data Documentation

const string AutoMaskAsymUnit::NAME = "mask.asymunit" [static]
 

Definition at line 172 of file processor.cpp.


The documentation for this class was generated from the following files:
Generated on Tue Jul 12 13:51:20 2011 for EMAN2 by  doxygen 1.3.9.1