#include <processor.h>
Inheritance diagram for EMAN::NormalizeByMassProcessor:


Public Member Functions | |
| string | get_name () const |
| Get the processor's name. | |
| string | get_desc () const |
| Get the descrition of this specific processor. | |
| TypeDict | get_param_types () const |
| Get processor parameter information in a dictionary. | |
| void | process_inplace (EMData *image) |
| To process an image in-place. | |
Static Public Member Functions | |
| Processor * | NEW () |
Static Public Attributes | |
| const string | NAME = "normalize.bymass" |
Only works for 3D images. Essentially a replica of Volume.C in EMAN1.
| apix | Angstrom per pixel of the image. If not set will use the apix_x attribute of the image | |
| mass | The approximate mass of protein/structure in kilodaltons | |
| thr | The isosurface threshold which encapsulates the structure |
Definition at line 4203 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 4216 of file processor.h. 04217 {
04218 return "Normalize the mass of the image assuming a density of 1.35 g/ml (0.81 Da/A^3) (3D only)";
04219 }
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Get the processor's name. Each processor is identified by a unique name.
Implements EMAN::Processor. Definition at line 4206 of file processor.h. 04207 {
04208 return NAME;
04209 }
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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 4221 of file processor.h. References EMAN::TypeDict::put(). 04222 {
04223 TypeDict d;
04224 d.put("apix", EMObject::FLOAT,"Angstrom per pixel of the image. If not set will use the apix_x attribute of the image");
04225 d.put("mass", EMObject::FLOAT,"The approximate mass of protein/structure in kilodaltons");
04226 d.put("thr", EMObject::FLOAT,"The isosurface threshold which encapsulates the structure");
04227 return d;
04228 }
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Definition at line 4211 of file processor.h. 04212 {
04213 return new NormalizeByMassProcessor();
04214 }
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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 3606 of file processor.cpp. References EMAN::EMObject::f, EMAN::EMData::get_attr(), EMAN::EMData::get_data(), EMAN::EMData::get_size(), EMAN::EMData::has_attr(), InvalidParameterException, max, min, EMAN::EMData::mult(), EMAN::Dict::set_default(), and EMAN::EMData::update(). 03607 {
03608 float mass = params.set_default("mass",-1.0f);
03609
03610 if (mass <= 0) throw InvalidParameterException("You must specify a positive non zero mass");
03611
03612 float thr = params.set_default("thr",(float)image->get_attr("mean")+(float)image->get_attr("sigma"));
03613
03614 float apix = params.set_default("apix",-1.123456789f);
03615 if (apix == -1.123456789 ) {
03616 if (image->has_attr("apix_x")) {
03617 apix = image->get_attr("apix_x");
03618 }
03619 }
03620
03621 if (apix <= 0) throw InvalidParameterException("You must specify a positive non zero apix");
03622
03623 float step = ((float)image->get_attr("sigma"))/2.0f;
03624
03625 int count=0;
03626 size_t n = image->get_size();
03627 float* d = image->get_data();
03628
03629 for (size_t i=0; i<n; ++i) {
03630 if (d[i]>=thr) ++count;
03631 }
03632
03633 float max = image->get_attr("maximum");
03634 float min = image->get_attr("minimum");
03635 for (int j=0; j<4; j++) {
03636 while (thr<max && count*apix*apix*apix*.81/1000.0>mass) {
03637 thr+=step;
03638 count=0;
03639 for (size_t i=0; i<n; ++i) {
03640 if (d[i]>=thr) ++count;
03641 }
03642 }
03643
03644 step/=4.0;
03645
03646 while (thr>min && count*apix*apix*apix*.81/1000.0<mass) {
03647 thr-=step;
03648 count=0;
03649 for (size_t i=0; i<n; ++i) {
03650 if (d[i]>=thr) ++count;
03651 }
03652 }
03653
03654 step/=4.0;
03655 }
03656
03657 image->mult((float)1.0/thr);
03658 image->update();
03659 }
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Definition at line 153 of file processor.cpp. |
1.3.9.1