#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. |
1.3.9.1