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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

ProcessorNEW ()

Static Public Attributes

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 5088 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 5103 of file processor.h.

05104                 {
05105                         return "ToMassCenterProcessor centers image at center of mass, with a threshold. Only values higher than the threshold are considered.";
05106                 }

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 5093 of file processor.h.

05094                 {
05095                         return NAME;
05096                 }

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 5108 of file processor.h.

References EMAN::TypeDict::put().

05109                 {
05110                         TypeDict d;
05111                         d.put("int_shift_only", EMObject::INT, "set to 1 only shift by integer, no interpolation");
05112                         d.put("threshold", EMObject::FLOAT, "Only values larger than the threshold are included in the center of mass computation. Default is 0.");
05113 //                      d.put("positive", EMObject::INT, "uses only densities >0 for the calculatton");
05114                         return d;
05115                 }

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

Definition at line 5098 of file processor.h.

05099                 {
05100                         return new ToMassCenterProcessor();
05101                 }

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 5572 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, nx, ny, EMAN::EMData::set_attr(), EMAN::Dict::set_default(), EMAN::Transform::set_trans(), t, and EMAN::EMData::translate().

05573 {
05574         if (!image) {
05575                 LOGWARN("NULL Image");
05576                 return;
05577         }
05578 
05579         int int_shift_only = params.set_default("int_shift_only",1);
05580         float threshold = params.set_default("threshold",0.0f);
05581 //      int positive = params.set_default("positive",0);
05582 
05583         if ((float)image->get_attr("sigma")==0.0f) return;              // Can't center a constant valued image
05584         if (threshold>(float)image->get_attr("maximum")) {
05585                 printf("Warning, centering threshold %1.2f, but image max %1.2f. Adjusting.",threshold,(float)image->get_attr("maximum"));
05586                 threshold=(float)image->get_attr("mean")+(float)image->get_attr("sigma");
05587         }
05588 
05589         FloatPoint com = image->calc_center_of_mass(threshold);
05590 
05591         int nx = image->get_xsize();
05592         int ny = image->get_ysize();
05593         int nz = image->get_zsize();
05594 
05595         if (int_shift_only) {
05596                 int dx = -(int)(floor(com[0] + 0.5f) - nx / 2);
05597                 int dy = -(int)(floor(com[1] + 0.5f) - ny / 2);
05598                 int dz = 0;
05599                 if (nz > 1) {
05600                         dz = -(int)(floor(com[2] + 0.5f) - nz / 2);
05601                 }
05602                 image->translate(dx, dy, dz);
05603 
05604                 Transform t;
05605                 t.set_trans((float)dx,(float)dy,(float)dz);
05606 
05607                 if (nz > 1) {
05608                         image->set_attr("xform.align3d",&t);
05609                 } else {
05610                         image->set_attr("xform.align2d",&t);
05611                 }
05612         }
05613         else {
05614                 float dx = -(com[0] - nx / 2);
05615                 float dy = -(com[1] - ny / 2);
05616                 float dz = 0;
05617                 if (nz > 1) {
05618                         dz = -(com[2] - nz / 2);
05619                 }
05620                 image->translate(dx, dy, dz);
05621 
05622                 Transform t;
05623                 t.set_trans(dx,dy,dz);
05624 
05625                 if (nz > 1) {
05626                         image->set_attr("xform.align3d",&t);
05627                 } else {
05628                         image->set_attr("xform.align2d",&t);
05629                 }
05630         }
05631 }


Member Data Documentation

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

Definition at line 177 of file processor.cpp.


The documentation for this class was generated from the following files:
Generated on Tue Jul 12 13:52:28 2011 for EMAN2 by  doxygen 1.3.9.1