#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 4200 of file processor.h.
string EMAN::NormalizeByMassProcessor::get_desc | ( | ) | const [inline, virtual] |
Get the descrition of this specific processor.
This function must be overwritten by a subclass.
Implements EMAN::Processor.
Definition at line 4213 of file processor.h.
04214 { 04215 return "Normalize the mass of the image assuming a density of 1.35 g/ml (0.81 Da/A^3) (3D only)"; 04216 }
string EMAN::NormalizeByMassProcessor::get_name | ( | ) | const [inline, virtual] |
Get the processor's name.
Each processor is identified by a unique name.
Implements EMAN::Processor.
Definition at line 4203 of file processor.h.
References NAME.
04204 { 04205 return NAME; 04206 }
TypeDict EMAN::NormalizeByMassProcessor::get_param_types | ( | ) | const [inline, virtual] |
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 4218 of file processor.h.
References EMAN::EMObject::FLOAT, and EMAN::TypeDict::put().
04219 { 04220 TypeDict d; 04221 d.put("apix", EMObject::FLOAT,"Angstrom per pixel of the image. If not set will use the apix_x attribute of the image"); 04222 d.put("mass", EMObject::FLOAT,"The approximate mass of protein/structure in kilodaltons"); 04223 d.put("thr", EMObject::FLOAT,"The isosurface threshold which encapsulates the structure"); 04224 return d; 04225 }
static Processor* EMAN::NormalizeByMassProcessor::NEW | ( | ) | [inline, static] |
Definition at line 4208 of file processor.h.
04209 { 04210 return new NormalizeByMassProcessor(); 04211 }
void NormalizeByMassProcessor::process_inplace | ( | EMData * | image | ) | [virtual] |
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.
image | The image to be processed. |
Implements EMAN::Processor.
Definition at line 3532 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().
03533 { 03534 float mass = params.set_default("mass",-1.0f); 03535 03536 if (mass <= 0) throw InvalidParameterException("You must specify a positive non zero mass"); 03537 03538 float thr = params.set_default("thr",(float)image->get_attr("mean")+(float)image->get_attr("sigma")); 03539 03540 float apix = params.set_default("apix",-1.123456789f); 03541 if (apix == -1.123456789 ) { 03542 if (image->has_attr("apix_x")) { 03543 apix = image->get_attr("apix_x"); 03544 } 03545 } 03546 03547 if (apix <= 0) throw InvalidParameterException("You must specify a positive non zero apix"); 03548 03549 float step = ((float)image->get_attr("sigma"))/2.0f; 03550 03551 int count=0; 03552 size_t n = image->get_size(); 03553 float* d = image->get_data(); 03554 03555 for (size_t i=0; i<n; ++i) { 03556 if (d[i]>=thr) ++count; 03557 } 03558 03559 float max = image->get_attr("maximum"); 03560 float min = image->get_attr("minimum"); 03561 for (int j=0; j<4; j++) { 03562 while (thr<max && count*apix*apix*apix*.81/1000.0>mass) { 03563 thr+=step; 03564 count=0; 03565 for (size_t i=0; i<n; ++i) { 03566 if (d[i]>=thr) ++count; 03567 } 03568 } 03569 03570 step/=4.0; 03571 03572 while (thr>min && count*apix*apix*apix*.81/1000.0<mass) { 03573 thr-=step; 03574 count=0; 03575 for (size_t i=0; i<n; ++i) { 03576 if (d[i]>=thr) ++count; 03577 } 03578 } 03579 03580 step/=4.0; 03581 } 03582 03583 image->mult((float)1.0/thr); 03584 image->update(); 03585 }
const string NormalizeByMassProcessor::NAME = "normalize.bymass" [static] |