#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 | |
static Processor * | NEW () |
Static Public Attributes | |
static 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 4240 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 4253 of file processor.h. 04254 { 04255 return "Normalize the mass of the image assuming a density of 1.35 g/ml (0.81 Da/A^3) (3D only)"; 04256 }
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Get the processor's name. Each processor is identified by a unique name.
Implements EMAN::Processor. Definition at line 4243 of file processor.h. References NAME. 04244 { 04245 return NAME; 04246 }
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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 4258 of file processor.h. References EMAN::EMObject::FLOAT, and EMAN::TypeDict::put(). 04259 { 04260 TypeDict d; 04261 d.put("apix", EMObject::FLOAT,"Angstrom per pixel of the image. If not set will use the apix_x attribute of the image"); 04262 d.put("mass", EMObject::FLOAT,"The approximate mass of protein/structure in kilodaltons"); 04263 d.put("thr", EMObject::FLOAT,"The isosurface threshold which encapsulates the structure"); 04264 return d; 04265 }
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Definition at line 4248 of file processor.h. 04249 { 04250 return new NormalizeByMassProcessor(); 04251 }
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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 3639 of file processor.cpp. References EMAN::EMData::get_attr(), EMAN::EMData::get_data(), EMAN::EMData::get_size(), EMAN::EMData::has_attr(), InvalidParameterException, max, min, EMAN::EMData::mult(), EMAN::Processor::params, EMAN::Dict::set_default(), and EMAN::EMData::update(). 03640 { 03641 float mass = params.set_default("mass",-1.0f); 03642 03643 if (mass <= 0) throw InvalidParameterException("You must specify a positive non zero mass"); 03644 03645 float thr = params.set_default("thr",(float)image->get_attr("mean")+(float)image->get_attr("sigma")); 03646 03647 float apix = params.set_default("apix",-1.123456789f); 03648 if (apix == -1.123456789 ) { 03649 if (image->has_attr("apix_x")) { 03650 apix = image->get_attr("apix_x"); 03651 } 03652 } 03653 03654 if (apix <= 0) throw InvalidParameterException("You must specify a positive non zero apix"); 03655 03656 float step = ((float)image->get_attr("sigma"))/2.0f; 03657 03658 int count=0; 03659 size_t n = image->get_size(); 03660 float* d = image->get_data(); 03661 03662 for (size_t i=0; i<n; ++i) { 03663 if (d[i]>=thr) ++count; 03664 } 03665 03666 float max = image->get_attr("maximum"); 03667 float min = image->get_attr("minimum"); 03668 for (int j=0; j<4; j++) { 03669 while (thr<max && count*apix*apix*apix*.81/1000.0>mass) { 03670 thr+=step; 03671 count=0; 03672 for (size_t i=0; i<n; ++i) { 03673 if (d[i]>=thr) ++count; 03674 } 03675 } 03676 03677 step/=4.0; 03678 03679 while (thr>min && count*apix*apix*apix*.81/1000.0<mass) { 03680 thr-=step; 03681 count=0; 03682 for (size_t i=0; i<n; ++i) { 03683 if (d[i]>=thr) ++count; 03684 } 03685 } 03686 03687 step/=4.0; 03688 } 03689 03690 image->mult((float)1.0/thr); 03691 image->update(); 03692 }
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Definition at line 4269 of file processor.h. Referenced by get_name(). |