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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 5125 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 5140 of file processor.h.

05141                 {
05142                         return "ToMassCenterProcessor centers image at center of mass. Note: includes only values > mean+0.75*sigma";
05143                 }

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 5130 of file processor.h.

References NAME.

05131                 {
05132                         return NAME;
05133                 }

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 5145 of file processor.h.

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

05146                 {
05147                         TypeDict d;
05148                         d.put("int_shift_only", EMObject::INT, "set to 1 only shift by integer, no interpolation");
05149 //                      d.put("positive", EMObject::INT, "uses only densities >0 for the calculatton");
05150                         return d;
05151                 }

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

Definition at line 5135 of file processor.h.

05136                 {
05137                         return new ToMassCenterProcessor();
05138                 }

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 5621 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(), EMAN::Transform::set_trans(), t, and EMAN::EMData::translate().

05622 {
05623         if (!image) {
05624                 LOGWARN("NULL Image");
05625                 return;
05626         }
05627 
05628         int int_shift_only = params.set_default("int_shift_only",1);
05629 //      int positive = params.set_default("positive",0);
05630 
05631         if ((float)image->get_attr("sigma")==0.0f) return;              // Can't center a constant valued image
05632 
05633         FloatPoint com = image->calc_center_of_mass();
05634 
05635         int nx = image->get_xsize();
05636         int ny = image->get_ysize();
05637         int nz = image->get_zsize();
05638 
05639         if (int_shift_only) {
05640                 int dx = -(int)(floor(com[0] + 0.5f) - nx / 2);
05641                 int dy = -(int)(floor(com[1] + 0.5f) - ny / 2);
05642                 int dz = 0;
05643                 if (nz > 1) {
05644                         dz = -(int)(floor(com[2] + 0.5f) - nz / 2);
05645                 }
05646                 image->translate(dx, dy, dz);
05647 
05648                 Transform t;
05649                 t.set_trans((float)dx,(float)dy,(float)dz);
05650 
05651                 if (nz > 1) {
05652                         image->set_attr("xform.align3d",&t);
05653                 } else {
05654                         image->set_attr("xform.align2d",&t);
05655                 }
05656         }
05657         else {
05658                 float dx = -(com[0] - nx / 2);
05659                 float dy = -(com[1] - ny / 2);
05660                 float dz = 0;
05661                 if (nz > 1) {
05662                         dz = -(com[2] - nz / 2);
05663                 }
05664                 image->translate(dx, dy, dz);
05665 
05666                 Transform t;
05667                 t.set_trans(dx,dy,dz);
05668 
05669                 if (nz > 1) {
05670                         image->set_attr("xform.align3d",&t);
05671                 } else {
05672                         image->set_attr("xform.align2d",&t);
05673                 }
05674         }
05675 }


Member Data Documentation

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

Definition at line 5153 of file processor.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Mon Jul 19 13:07:12 2010 for EMAN2 by  doxygen 1.4.4