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EMAN::NormalizeByMassProcessor Class Reference

Normalize the mass of the image assuming a density of 1.35 g/ml (0.81 Da/A^3). More...

#include <processor.h>

Inheritance diagram for EMAN::NormalizeByMassProcessor:

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List of all members.

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

ProcessorNEW ()

Static Public Attributes

const string NAME = "normalize.bymass"

Detailed Description

Normalize the mass of the image assuming a density of 1.35 g/ml (0.81 Da/A^3).

Only works for 3D images. Essentially a replica of Volume.C in EMAN1.

Author:
David Woolford (a direct port of Steve Ludtke's code)
Date:
01/17/09
Parameters:
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 4024 of file processor.h.


Member Function Documentation

string EMAN::NormalizeByMassProcessor::get_desc  )  const [inline, virtual]
 

Get the descrition of this specific processor.

This function must be overwritten by a subclass.

Returns:
The description of this processor.

Implements EMAN::Processor.

Definition at line 4037 of file processor.h.

04038                         {
04039                                 return "Normalize the mass of the image assuming a density of 1.35 g/ml (0.81 Da/A^3) (3D only)";
04040                         }

string EMAN::NormalizeByMassProcessor::get_name  )  const [inline, virtual]
 

Get the processor's name.

Each processor is identified by a unique name.

Returns:
The processor's name.

Implements EMAN::Processor.

Definition at line 4027 of file processor.h.

04028                         {
04029                                 return NAME;
04030                         }

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.

Returns:
A dictionary containing the parameter info.

Reimplemented from EMAN::Processor.

Definition at line 4042 of file processor.h.

References EMAN::TypeDict::put().

04043                         {
04044                                 TypeDict d;
04045                                 d.put("apix", EMObject::FLOAT,"Angstrom per pixel of the image. If not set will use the apix_x attribute of the image");
04046                                 d.put("mass", EMObject::FLOAT,"The approximate mass of protein/structure in kilodaltons");
04047                                 d.put("thr", EMObject::FLOAT,"The isosurface threshold which encapsulates the structure");
04048                                 return d;
04049                         }

Processor* EMAN::NormalizeByMassProcessor::NEW  )  [inline, static]
 

Definition at line 4032 of file processor.h.

04033                         {
04034                                 return new NormalizeByMassProcessor();
04035                         }

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.

Parameters:
image The image to be processed.

Implements EMAN::Processor.

Definition at line 3487 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().

03488 {
03489         float mass = params.set_default("mass",-1.0f);
03490 
03491         if (mass <= 0) throw InvalidParameterException("You must specify a positive non zero mass");
03492 
03493         float thr = params.set_default("thr",(float)image->get_attr("mean")+(float)image->get_attr("sigma"));
03494 
03495         float apix = params.set_default("apix",-1.123456789f);
03496         if (apix == -1.123456789 ) {
03497                 if (image->has_attr("apix_x")) {
03498                         apix = image->get_attr("apix_x");
03499                 }
03500         }
03501 
03502         if (apix <= 0) throw InvalidParameterException("You must specify a positive non zero apix");
03503 
03504         float step = ((float)image->get_attr("sigma"))/2.0f;
03505 
03506         int count=0;
03507         size_t n = image->get_size();
03508         float* d = image->get_data();
03509 
03510         for (size_t i=0; i<n; ++i) {
03511                 if (d[i]>=thr) ++count;
03512         }
03513 
03514         float max = image->get_attr("maximum");
03515         float min = image->get_attr("minimum");
03516         for (int j=0; j<4; j++) {
03517                 while (thr<max && count*apix*apix*apix*.81/1000.0>mass) {
03518                         thr+=step;
03519                         count=0;
03520                         for (size_t i=0; i<n; ++i) {
03521                                 if (d[i]>=thr) ++count;
03522                         }
03523                 }
03524 
03525                 step/=4.0;
03526 
03527                 while (thr>min && count*apix*apix*apix*.81/1000.0<mass) {
03528                         thr-=step;
03529                         count=0;
03530                         for (size_t i=0; i<n; ++i) {
03531                                 if (d[i]>=thr) ++count;
03532                         }
03533                 }
03534 
03535                 step/=4.0;
03536         }
03537 
03538         image->mult((float)1.0/thr);
03539         image->update();
03540 }


Member Data Documentation

const string NormalizeByMassProcessor::NAME = "normalize.bymass" [static]
 

Definition at line 142 of file processor.cpp.


The documentation for this class was generated from the following files:
Generated on Thu Dec 9 13:48:05 2010 for EMAN2 by  doxygen 1.3.9.1