#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 5119 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 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 }
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Get the processor's name. Each processor is identified by a unique name.
Implements EMAN::Processor. Definition at line 5124 of file processor.h. 05125 {
05126 return NAME;
05127 }
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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 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 }
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Definition at line 5129 of file processor.h. 05130 { 05131 return new ToMassCenterProcessor(); 05132 }
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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 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 }
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Definition at line 172 of file processor.cpp. |