EMAN::ToMassCenterProcessor Class Reference
[unit test in Python]

ToMassCenterProcessor centers image at center of mass, ignores old dx, dy. More...

#include <processor.h>

Inheritance diagram for EMAN::ToMassCenterProcessor:

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Collaboration diagram for EMAN::ToMassCenterProcessor:

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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 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 = "xform.centerofmass"

Detailed Description

ToMassCenterProcessor centers image at center of mass, ignores old dx, dy.

Parameters:
int_shift_only set to 1 only shift by integer, no interpolation

Definition at line 5085 of file processor.h.


Member Function Documentation

virtual string EMAN::ToMassCenterProcessor::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 5100 of file processor.h.

05101                 {
05102                         return "ToMassCenterProcessor centers image at center of mass. Note: includes only values > mean+0.75*sigma";
05103                 }

virtual string EMAN::ToMassCenterProcessor::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 5090 of file processor.h.

References NAME.

05091                 {
05092                         return NAME;
05093                 }

virtual TypeDict EMAN::ToMassCenterProcessor::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 5105 of file processor.h.

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

05106                 {
05107                         TypeDict d;
05108                         d.put("int_shift_only", EMObject::INT, "set to 1 only shift by integer, no interpolation");
05109 //                      d.put("positive", EMObject::INT, "uses only densities >0 for the calculatton");
05110                         return d;
05111                 }

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

Definition at line 5095 of file processor.h.

05096                 {
05097                         return new ToMassCenterProcessor();
05098                 }

void ToMassCenterProcessor::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 5514 of file processor.cpp.

References EMAN::EMData::calc_center_of_mass(), EMAN::EMObject::f, EMAN::EMData::get_attr(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), LOGWARN, EMAN::Processor::params, EMAN::EMData::set_attr(), EMAN::Dict::set_default(), t, and EMAN::EMData::translate().

05515 {
05516         if (!image) {
05517                 LOGWARN("NULL Image");
05518                 return;
05519         }
05520 
05521         int int_shift_only = params.set_default("int_shift_only",1);
05522 //      int positive = params.set_default("positive",0);
05523 
05524         if ((float)image->get_attr("sigma")==0.0f) return;              // Can't center a constant valued image
05525 
05526         FloatPoint com = image->calc_center_of_mass();
05527 
05528         int nx = image->get_xsize();
05529         int ny = image->get_ysize();
05530         int nz = image->get_zsize();
05531 
05532         if (int_shift_only) {
05533                 int dx = -(int)(floor(com[0] + 0.5f) - nx / 2);
05534                 int dy = -(int)(floor(com[1] + 0.5f) - ny / 2);
05535                 int dz = 0;
05536                 if (nz > 1) {
05537                         dz = -(int)(floor(com[2] + 0.5f) - nz / 2);
05538                 }
05539                 image->translate(dx, dy, dz);
05540 
05541                 Transform t;
05542                 t.set_trans((float)dx,(float)dy,(float)dz);
05543 
05544                 if (nz > 1) {
05545                         image->set_attr("xform.align3d",&t);
05546                 } else {
05547                         image->set_attr("xform.align2d",&t);
05548                 }
05549         }
05550         else {
05551                 float dx = -(com[0] - nx / 2);
05552                 float dy = -(com[1] - ny / 2);
05553                 float dz = 0;
05554                 if (nz > 1) {
05555                         dz = -(com[2] - nz / 2);
05556                 }
05557                 image->translate(dx, dy, dz);
05558 
05559                 Transform t;
05560                 t.set_trans(dx,dy,dz);
05561 
05562                 if (nz > 1) {
05563                         image->set_attr("xform.align3d",&t);
05564                 } else {
05565                         image->set_attr("xform.align2d",&t);
05566                 }
05567         }
05568 }


Member Data Documentation

const string ToMassCenterProcessor::NAME = "xform.centerofmass" [static]

Definition at line 5113 of file processor.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Tue May 25 17:17:21 2010 for EMAN2 by  doxygen 1.4.7