#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 5164 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 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.
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.
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.
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 }
const string ToMassCenterProcessor::NAME = "xform.centerofmass" [static] |