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 5164 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 5179 of file processor.h.

05180                 {
05181                         return "ToMassCenterProcessor centers image at center of mass, with a threshold. Only values higher than the threshold are considered.";
05182                 }

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 5169 of file processor.h.

References NAME.

05170                 {
05171                         return NAME;
05172                 }

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 5184 of file processor.h.

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

05185                 {
05186                         TypeDict d;
05187                         d.put("int_shift_only", EMObject::INT, "set to 1 only shift by integer, no interpolation");
05188                         d.put("threshold", EMObject::FLOAT, "Only values larger than the threshold are included in the center of mass computation. Default is 0.");
05189 //                      d.put("positive", EMObject::INT, "uses only densities >0 for the calculatton");
05190                         return d;
05191                 }

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

Definition at line 5174 of file processor.h.

05175                 {
05176                         return new ToMassCenterProcessor();
05177                 }

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 5730 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().

05731 {
05732         if (!image) {
05733                 LOGWARN("NULL Image");
05734                 return;
05735         }
05736 
05737         int int_shift_only = params.set_default("int_shift_only",1);
05738         float threshold = params.set_default("threshold",0.0f);
05739 //      int positive = params.set_default("positive",0);
05740 
05741         if ((float)image->get_attr("sigma")==0.0f) return;              // Can't center a constant valued image
05742         if (threshold>(float)image->get_attr("maximum")) {
05743                 printf("Warning, centering threshold %1.2f, but image max %1.2f. Adjusting.",threshold,(float)image->get_attr("maximum"));
05744                 threshold=(float)image->get_attr("mean")+(float)image->get_attr("sigma");
05745         }
05746 
05747         FloatPoint com = image->calc_center_of_mass(threshold);
05748 
05749         int nx = image->get_xsize();
05750         int ny = image->get_ysize();
05751         int nz = image->get_zsize();
05752 
05753         if (int_shift_only) {
05754                 int dx = -(int)(floor(com[0] + 0.5f) - nx / 2);
05755                 int dy = -(int)(floor(com[1] + 0.5f) - ny / 2);
05756                 int dz = 0;
05757                 if (nz > 1) {
05758                         dz = -(int)(floor(com[2] + 0.5f) - nz / 2);
05759                 }
05760                 image->translate(dx, dy, dz);
05761 
05762                 Transform t;
05763                 t.set_trans((float)dx,(float)dy,(float)dz);
05764 
05765                 if (nz > 1) {
05766                         image->set_attr("xform.align3d",&t);
05767                 } else {
05768                         image->set_attr("xform.align2d",&t);
05769                 }
05770         }
05771         else {
05772                 float dx = -(com[0] - nx / 2);
05773                 float dy = -(com[1] - ny / 2);
05774                 float dz = 0;
05775                 if (nz > 1) {
05776                         dz = -(com[2] - nz / 2);
05777                 }
05778                 image->translate(dx, dy, dz);
05779 
05780                 Transform t;
05781                 t.set_trans(dx,dy,dz);
05782 
05783                 if (nz > 1) {
05784                         image->set_attr("xform.align3d",&t);
05785                 } else {
05786                         image->set_attr("xform.align2d",&t);
05787                 }
05788         }
05789 }


Member Data Documentation

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

Definition at line 5193 of file processor.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Thu May 3 10:10:37 2012 for EMAN2 by  doxygen 1.4.7