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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 5119 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 5134 of file processor.h.

05135                 {
05136                         return "ToMassCenterProcessor centers image at center of mass, with a threshold. Only values higher than the threshold are considered.";
05137                 }

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 5124 of file processor.h.

05125                 {
05126                         return NAME;
05127                 }

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 5139 of file processor.h.

References EMAN::TypeDict::put().

05140                 {
05141                         TypeDict d;
05142                         d.put("int_shift_only", EMObject::INT, "set to 1 only shift by integer, no interpolation");
05143                         d.put("threshold", EMObject::FLOAT, "Only values larger than the threshold are included in the center of mass computation. Default is 0.");
05144 //                      d.put("positive", EMObject::INT, "uses only densities >0 for the calculatton");
05145                         return d;
05146                 }

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

Definition at line 5129 of file processor.h.

05130                 {
05131                         return new ToMassCenterProcessor();
05132                 }

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 5658 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().

05659 {
05660         if (!image) {
05661                 LOGWARN("NULL Image");
05662                 return;
05663         }
05664 
05665         int int_shift_only = params.set_default("int_shift_only",1);
05666         float threshold = params.set_default("threshold",0.0f);
05667 //      int positive = params.set_default("positive",0);
05668 
05669         if ((float)image->get_attr("sigma")==0.0f) return;              // Can't center a constant valued image
05670         if (threshold>(float)image->get_attr("maximum")) {
05671                 printf("Warning, centering threshold %1.2f, but image max %1.2f. Adjusting.",threshold,(float)image->get_attr("maximum"));
05672                 threshold=(float)image->get_attr("mean")+(float)image->get_attr("sigma");
05673         }
05674 
05675         FloatPoint com = image->calc_center_of_mass(threshold);
05676 
05677         int nx = image->get_xsize();
05678         int ny = image->get_ysize();
05679         int nz = image->get_zsize();
05680 
05681         if (int_shift_only) {
05682                 int dx = -(int)(floor(com[0] + 0.5f) - nx / 2);
05683                 int dy = -(int)(floor(com[1] + 0.5f) - ny / 2);
05684                 int dz = 0;
05685                 if (nz > 1) {
05686                         dz = -(int)(floor(com[2] + 0.5f) - nz / 2);
05687                 }
05688                 image->translate(dx, dy, dz);
05689 
05690                 Transform t;
05691                 t.set_trans((float)dx,(float)dy,(float)dz);
05692 
05693                 if (nz > 1) {
05694                         image->set_attr("xform.align3d",&t);
05695                 } else {
05696                         image->set_attr("xform.align2d",&t);
05697                 }
05698         }
05699         else {
05700                 float dx = -(com[0] - nx / 2);
05701                 float dy = -(com[1] - ny / 2);
05702                 float dz = 0;
05703                 if (nz > 1) {
05704                         dz = -(com[2] - nz / 2);
05705                 }
05706                 image->translate(dx, dy, dz);
05707 
05708                 Transform t;
05709                 t.set_trans(dx,dy,dz);
05710 
05711                 if (nz > 1) {
05712                         image->set_attr("xform.align3d",&t);
05713                 } else {
05714                         image->set_attr("xform.align2d",&t);
05715                 }
05716         }
05717 }


Member Data Documentation

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

Definition at line 172 of file processor.cpp.


The documentation for this class was generated from the following files:
Generated on Thu Nov 17 12:46:28 2011 for EMAN2 by  doxygen 1.3.9.1