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:

Collaboration diagram for EMAN::NormalizeByMassProcessor:

[legend]

Public Member Functions
string	get_name () const
	Get the processor's name. More...

string	get_desc () const
	Get the descrition of this specific processor. More...

TypeDict	get_param_types () const
	Get processor parameter information in a dictionary. More...

void	process_inplace (EMData *image)
	To process an image in-place. More...

Public Member Functions inherited from EMAN::Processor
virtual	~Processor ()

virtual EMData *	process (const EMData *const image)
	To proccess an image out-of-place. More...

virtual void	process_list_inplace (vector< EMData * > &images)
	To process multiple images using the same algorithm. More...

virtual Dict	get_params () const
	Get the processor parameters in a key/value dictionary. More...

virtual void	set_params (const Dict &new_params)
	Set the processor parameters using a key/value dictionary. More...

Static Public Member Functions
static Processor *	NEW ()

Static Public Member Functions inherited from EMAN::Processor
static string	get_group_desc ()
	Get the description of this group of processors. More...

static void	EMFourierFilterInPlace (EMData *fimage, Dict params)
	Compute a Fourier-filter processed image in place. More...

static EMData *	EMFourierFilter (EMData *fimage, Dict params)
	Compute a Fourier-processor processed image without altering the original image. More...

Static Public Attributes
static const string	NAME = "normalize.bymass"

Additional Inherited Members
Public Types inherited from EMAN::Processor
enum	fourier_filter_types { TOP_HAT_LOW_PASS , TOP_HAT_HIGH_PASS , TOP_HAT_BAND_PASS , TOP_HOMOMORPHIC , GAUSS_LOW_PASS , GAUSS_HIGH_PASS , GAUSS_BAND_PASS , GAUSS_INVERSE , GAUSS_HOMOMORPHIC , BUTTERWORTH_LOW_PASS , BUTTERWORTH_HIGH_PASS , BUTTERWORTH_HOMOMORPHIC , KAISER_I0 , KAISER_SINH , KAISER_I0_INVERSE , KAISER_SINH_INVERSE , SHIFT , TANH_LOW_PASS , TANH_HIGH_PASS , TANH_HOMOMORPHIC , TANH_BAND_PASS , RADIAL_TABLE , CTF_ }
	Fourier filter Processor type enum. More...

Protected Attributes inherited from EMAN::Processor
Dict	params

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 6027 of file processor.h.

Member Function Documentation

◆ get_desc()

string EMAN::NormalizeByMassProcessor::get_desc ( ) const

inlinevirtual

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 6040 of file processor.h.

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

◆ get_name()

string EMAN::NormalizeByMassProcessor::get_name ( ) const

inlinevirtual

Get the processor's name.

Each processor is identified by a unique name.

Returns: The processor's name.

Implements EMAN::Processor.

Definition at line 6030 of file processor.h.

                        {
                                return NAME;
                        }

References NAME.

◆ get_param_types()

TypeDict EMAN::NormalizeByMassProcessor::get_param_types ( ) const

inlinevirtual

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 6045 of file processor.h.

                        {
                                TypeDict d;
                                d.put("apix", EMObject::FLOAT,"Angstrom per pixel of the image. If not set will use the apix_x attribute of the image");
                                d.put("mass", EMObject::FLOAT,"The approximate mass of protein/structure in kilodaltons");
                                d.put("thr", EMObject::FLOAT,"The isosurface threshold which encapsulates the structure");
                                d.put("verbose", EMObject::INT,"If set will give details about the normalization");
                                return d;
                        }

References EMAN::EMObject::FLOAT, EMAN::EMObject::INT, and EMAN::TypeDict::put().

◆ NEW()

static Processor * EMAN::NormalizeByMassProcessor::NEW ( )

inlinestatic

Definition at line 6035 of file processor.h.

                        {
                                return new NormalizeByMassProcessor();
                        }

◆ process_inplace()

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 4756 of file processor.cpp.

{
        float mass = params.set_default("mass",-1.0f);
        int verbose = params.set_default("verbose",0);
 
        if (mass <= 0) throw InvalidParameterException("You must specify a positive non zero mass");
 
        float tthr = params.set_default("thr",(float)image->get_attr("mean")+(float)image->get_attr("sigma"));
 
        float apix = image->get_attr_default("apix_x",1.0f);
        apix = params.set_default("apix",apix);
 
        if (apix <= 0) throw InvalidParameterException("You must specify a positive non zero apix");
 
        float step = ((float)image->get_attr("sigma"))/5.0f;
 
        if (step==0) throw InvalidParameterException("This image has sigma=0, cannot give it mass");
 
 
        size_t n = image->get_size();
        float* d = image->get_data();
 
 
        float thr=(float)image->get_attr("mean")+(float)image->get_attr("sigma")/2.0;
        int count=0;
        for (size_t i=0; i<n; ++i) {
                if (d[i]>=thr) ++count;
        }
        if (verbose) printf("apix=%1.3f\tmass=%1.1f\tthr=%1.2f\tstep=%1.3g\n",apix,mass,thr,step);
 
        float max = image->get_attr("maximum");
        float min = image->get_attr("minimum");
        for (int j=0; j<4; j++) {
                int err=0;
                while (thr<max && count*apix*apix*apix*.81/1000.0>mass) {
                        thr+=step;
                        count=0;
                        for (size_t i=0; i<n; ++i) {
                                if (d[i]>=thr) ++count;
                        }
                        err+=1;
                        if (err>1000) throw InvalidParameterException("Specified mass could not be achieved");
                        if (verbose>1) printf("%d\t%d\t%1.3f\t%1.2f\n",err,count,thr,count*apix*apix*apix*.81/1000.0);
                }
 
                step/=4.0;
 
                while (thr>min && count*apix*apix*apix*.81/1000.0<mass) {
                        thr-=step;
                        count=0;
                        for (size_t i=0; i<n; ++i) {
                                if (d[i]>=thr) ++count;
                        }
                        err+=1;
                        if (err>1000) throw InvalidParameterException("Specified mass could not be achieved");
                        if (verbose>1) printf("%d\t%d\t%1.3f\t%1.2f\n",err,count,thr,count*apix*apix*apix*.81/1000.0);
 
                }
                step/=4.0;
        }
 
        // We don't adjust the map if we get a negative value
        if ((float)tthr/thr>0) image->mult((float)tthr/thr);
        else printf("WARNING: could not normalize map to specified mass.");
        image->update();
}

References InvalidParameterException, EMAN::Processor::params, and EMAN::Dict::set_default().

Member Data Documentation

◆ NAME

const string NormalizeByMassProcessor::NAME = "normalize.bymass"

static

Definition at line 6057 of file processor.h.

Referenced by get_name().

The documentation for this class was generated from the following files:

Public Member Functions

Static Public Member Functions

Static Public Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ get_desc()

◆ get_name()

◆ get_param_types()

◆ NEW()

◆ process_inplace()

Member Data Documentation

◆ NAME