#include <processor.h>
Inheritance diagram for EMAN::ToMassCenterProcessor:
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 Processor * | NEW () |
Static Public Attributes | |
static const string | NAME = "xform.centerofmass" |
int_shift_only | set to 1 only shift by integer, no interpolation |
Definition at line 4994 of file processor.h.
virtual string EMAN::ToMassCenterProcessor::get_desc | ( | ) | const [inline, virtual] |
Get the descrition of this specific processor.
This function must be overwritten by a subclass.
Implements EMAN::Processor.
Definition at line 5009 of file processor.h.
05010 { 05011 return "ToMassCenterProcessor centers image at center of mass, with a threshold. Only values higher than the threshold are considered."; 05012 }
virtual string EMAN::ToMassCenterProcessor::get_name | ( | ) | const [inline, virtual] |
Get the processor's name.
Each processor is identified by a unique name.
Implements EMAN::Processor.
Definition at line 4999 of file processor.h.
References NAME.
05000 { 05001 return NAME; 05002 }
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.
Reimplemented from EMAN::Processor.
Definition at line 5014 of file processor.h.
References EMAN::EMObject::FLOAT, EMAN::EMObject::INT, and EMAN::TypeDict::put().
05015 { 05016 TypeDict d; 05017 d.put("int_shift_only", EMObject::INT, "set to 1 only shift by integer, no interpolation"); 05018 d.put("threshold", EMObject::FLOAT, "Only values larger than the threshold are included in the center of mass computation. Default is 0."); 05019 // d.put("positive", EMObject::INT, "uses only densities >0 for the calculatton"); 05020 return d; 05021 }
static Processor* EMAN::ToMassCenterProcessor::NEW | ( | ) | [inline, static] |
Definition at line 5004 of file processor.h.
05005 { 05006 return new ToMassCenterProcessor(); 05007 }
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.
image | The image to be processed. |
Implements EMAN::Processor.
Definition at line 5546 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().
05547 { 05548 if (!image) { 05549 LOGWARN("NULL Image"); 05550 return; 05551 } 05552 05553 int int_shift_only = params.set_default("int_shift_only",1); 05554 float threshold = params.set_default("threshold",0.0f); 05555 // int positive = params.set_default("positive",0); 05556 05557 if ((float)image->get_attr("sigma")==0.0f) return; // Can't center a constant valued image 05558 05559 FloatPoint com = image->calc_center_of_mass(threshold); 05560 05561 int nx = image->get_xsize(); 05562 int ny = image->get_ysize(); 05563 int nz = image->get_zsize(); 05564 05565 if (int_shift_only) { 05566 int dx = -(int)(floor(com[0] + 0.5f) - nx / 2); 05567 int dy = -(int)(floor(com[1] + 0.5f) - ny / 2); 05568 int dz = 0; 05569 if (nz > 1) { 05570 dz = -(int)(floor(com[2] + 0.5f) - nz / 2); 05571 } 05572 image->translate(dx, dy, dz); 05573 05574 Transform t; 05575 t.set_trans((float)dx,(float)dy,(float)dz); 05576 05577 if (nz > 1) { 05578 image->set_attr("xform.align3d",&t); 05579 } else { 05580 image->set_attr("xform.align2d",&t); 05581 } 05582 } 05583 else { 05584 float dx = -(com[0] - nx / 2); 05585 float dy = -(com[1] - ny / 2); 05586 float dz = 0; 05587 if (nz > 1) { 05588 dz = -(com[2] - nz / 2); 05589 } 05590 image->translate(dx, dy, dz); 05591 05592 Transform t; 05593 t.set_trans(dx,dy,dz); 05594 05595 if (nz > 1) { 05596 image->set_attr("xform.align3d",&t); 05597 } else { 05598 image->set_attr("xform.align2d",&t); 05599 } 05600 } 05601 }
const string ToMassCenterProcessor::NAME = "xform.centerofmass" [static] |