#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 | |
Processor * | NEW () |
Static Public Attributes | |
const string | NAME = "xform.centerofmass" |
int_shift_only | set to 1 only shift by integer, no interpolation |
Definition at line 5088 of file processor.h.
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Get the descrition of this specific processor. This function must be overwritten by a subclass.
Implements EMAN::Processor. Definition at line 5103 of file processor.h. 05104 { 05105 return "ToMassCenterProcessor centers image at center of mass, with a threshold. Only values higher than the threshold are considered."; 05106 }
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Get the processor's name. Each processor is identified by a unique name.
Implements EMAN::Processor. Definition at line 5093 of file processor.h. 05094 {
05095 return NAME;
05096 }
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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 5108 of file processor.h. References EMAN::TypeDict::put(). 05109 { 05110 TypeDict d; 05111 d.put("int_shift_only", EMObject::INT, "set to 1 only shift by integer, no interpolation"); 05112 d.put("threshold", EMObject::FLOAT, "Only values larger than the threshold are included in the center of mass computation. Default is 0."); 05113 // d.put("positive", EMObject::INT, "uses only densities >0 for the calculatton"); 05114 return d; 05115 }
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Definition at line 5098 of file processor.h. 05099 { 05100 return new ToMassCenterProcessor(); 05101 }
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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.
Implements EMAN::Processor. Definition at line 5572 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(). 05573 { 05574 if (!image) { 05575 LOGWARN("NULL Image"); 05576 return; 05577 } 05578 05579 int int_shift_only = params.set_default("int_shift_only",1); 05580 float threshold = params.set_default("threshold",0.0f); 05581 // int positive = params.set_default("positive",0); 05582 05583 if ((float)image->get_attr("sigma")==0.0f) return; // Can't center a constant valued image 05584 if (threshold>(float)image->get_attr("maximum")) { 05585 printf("Warning, centering threshold %1.2f, but image max %1.2f. Adjusting.",threshold,(float)image->get_attr("maximum")); 05586 threshold=(float)image->get_attr("mean")+(float)image->get_attr("sigma"); 05587 } 05588 05589 FloatPoint com = image->calc_center_of_mass(threshold); 05590 05591 int nx = image->get_xsize(); 05592 int ny = image->get_ysize(); 05593 int nz = image->get_zsize(); 05594 05595 if (int_shift_only) { 05596 int dx = -(int)(floor(com[0] + 0.5f) - nx / 2); 05597 int dy = -(int)(floor(com[1] + 0.5f) - ny / 2); 05598 int dz = 0; 05599 if (nz > 1) { 05600 dz = -(int)(floor(com[2] + 0.5f) - nz / 2); 05601 } 05602 image->translate(dx, dy, dz); 05603 05604 Transform t; 05605 t.set_trans((float)dx,(float)dy,(float)dz); 05606 05607 if (nz > 1) { 05608 image->set_attr("xform.align3d",&t); 05609 } else { 05610 image->set_attr("xform.align2d",&t); 05611 } 05612 } 05613 else { 05614 float dx = -(com[0] - nx / 2); 05615 float dy = -(com[1] - ny / 2); 05616 float dz = 0; 05617 if (nz > 1) { 05618 dz = -(com[2] - nz / 2); 05619 } 05620 image->translate(dx, dy, dz); 05621 05622 Transform t; 05623 t.set_trans(dx,dy,dz); 05624 05625 if (nz > 1) { 05626 image->set_attr("xform.align3d",&t); 05627 } else { 05628 image->set_attr("xform.align2d",&t); 05629 } 05630 } 05631 }
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Definition at line 177 of file processor.cpp. |