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 5168 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 5183 of file processor.h.

05184                 {
05185                         return "ToMassCenterProcessor centers image at center of mass, with a threshold. Only values higher than the threshold are considered.";
05186                 }

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 5173 of file processor.h.

References NAME.

05174                 {
05175                         return NAME;
05176                 }

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 5188 of file processor.h.

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

05189                 {
05190                         TypeDict d;
05191                         d.put("int_shift_only", EMObject::INT, "set to 1 only shift by integer, no interpolation");
05192                         d.put("threshold", EMObject::FLOAT, "Only values larger than the threshold are included in the center of mass computation. Default is 0.");
05193 //                      d.put("positive", EMObject::INT, "uses only densities >0 for the calculatton");
05194                         return d;
05195                 }

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

Definition at line 5178 of file processor.h.

05179                 {
05180                         return new ToMassCenterProcessor();
05181                 }

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 5736 of file processor.cpp.

References abs, 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().

05737 {
05738         if (!image) {
05739                 LOGWARN("NULL Image");
05740                 return;
05741         }
05742 
05743         int int_shift_only = params.set_default("int_shift_only",1);
05744         float threshold = params.set_default("threshold",0.0f);
05745 //      int positive = params.set_default("positive",0);
05746 
05747         if ((float)image->get_attr("sigma")==0.0f) return;              // Can't center a constant valued image
05748         if (threshold>(float)image->get_attr("maximum")) {
05749                 printf("Warning, centering threshold %1.2f, but image max %1.2f. Adjusting.",threshold,(float)image->get_attr("maximum"));
05750                 threshold=(float)image->get_attr("mean")+(float)image->get_attr("sigma");
05751         }
05752 
05753         FloatPoint com = image->calc_center_of_mass(threshold);
05754 
05755         int nx = image->get_xsize();
05756         int ny = image->get_ysize();
05757         int nz = image->get_zsize();
05758 
05759         if (int_shift_only) {
05760                 int dx = -(int)(floor(com[0] + 0.5f) - nx / 2);
05761                 int dy = -(int)(floor(com[1] + 0.5f) - ny / 2);
05762                 int dz = 0;
05763                 if (nz > 1) {
05764                         dz = -(int)(floor(com[2] + 0.5f) - nz / 2);
05765                 }
05766                 if (abs(dx)>=nx-1 || abs(dy)>=ny-1 || abs(dz)>=nz) {
05767                         printf("ERROR, center of mass outside image\n");
05768                 }
05769                 else {
05770                         image->translate(dx, dy, dz);
05771 
05772                         Transform t;
05773                         t.set_trans((float)dx,(float)dy,(float)dz);
05774 
05775                         if (nz > 1) {
05776                                 image->set_attr("xform.align3d",&t);
05777                         } else {
05778                                 image->set_attr("xform.align2d",&t);
05779                         }
05780                 }
05781         }
05782         else {
05783                 float dx = -(com[0] - nx / 2);
05784                 float dy = -(com[1] - ny / 2);
05785                 float dz = 0;
05786                 if (nz > 1) {
05787                         dz = -(com[2] - nz / 2);
05788                 }
05789                 if (fabs(dx)>=nx-1 || fabs(dy)>=ny-2 || fabs(dz)>=nz) {
05790                         printf("ERROR, center of mass outside image\n");
05791                 }
05792                 else {
05793                         image->translate(dx, dy, dz);
05794 
05795                         Transform t;
05796                         t.set_trans(dx,dy,dz);
05797 
05798                         if (nz > 1) {
05799                                 image->set_attr("xform.align3d",&t);
05800                         } else {
05801                                 image->set_attr("xform.align2d",&t);
05802                         }
05803                 }
05804         }
05805 }


Member Data Documentation

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

Definition at line 5197 of file processor.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Tue Jun 11 12:44:26 2013 for EMAN2 by  doxygen 1.4.7