Uses a 1/0 mask defining a region to use for the zero-normalization.if no_sigma is 1, standard deviation not modified. More...

#include <processor.h>

Inheritance diagram for EMAN::NormalizeMaskProcessor:

[legend]

Collaboration diagram for EMAN::NormalizeMaskProcessor:

[legend]

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

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...

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.mask"

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

Uses a 1/0 mask defining a region to use for the zero-normalization.if no_sigma is 1, standard deviation not modified.

Parameters

mask	The 0-1 mask defining the region for the normalization. Any non-zero values will be considered
no_sigma	If set, the mean will be set to zero, but sigma will not be modified
apply_mask	If set, the mask will also be applied (multiplied) to the volume

Definition at line 5958 of file processor.h.

Member Function Documentation

◆ get_desc()

string EMAN::NormalizeMaskProcessor::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 5968 of file processor.h.

                {
                        return "Uses a 1/0 mask defining a region to use for the zero-normalization.if no_sigma is 1, standard deviation not modified.";
                }

◆ get_name()

string EMAN::NormalizeMaskProcessor::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 5963 of file processor.h.

                {
                        return NAME;
                }

References NAME.

◆ get_param_types()

TypeDict EMAN::NormalizeMaskProcessor::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 5978 of file processor.h.

                {
                        TypeDict d;
                        d.put("mask", EMObject::EMDATA, "The 0-1 mask defining the region for the normalization. Any non-zero values will be considered");
                        d.put("no_sigma", EMObject::INT, "If set, the mean will be set to zero, but sigma will not be modified");
                        d.put("apply_mask", EMObject::INT, "If set, the mask will also be applied (multiplied) to the volume");
                        return d;
                }

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

◆ NEW()

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

inlinestatic

Definition at line 5973 of file processor.h.

                {
                        return new NormalizeMaskProcessor();
                }

◆ process_inplace()

void NormalizeMaskProcessor::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 4685 of file processor.cpp.

{
        if (!image) {
                LOGWARN("NULL Image");
                return;
        }
        EMData *mask = params["mask"];
        int no_sigma = params.set_default("no_sigma",0);
        int apply_mask = params.set_default("apply_mask",0);
 
        int nx=image->get_xsize();
        int ny=image->get_ysize();
        int nz=image->get_zsize();
        
        double sum=0;
        double sumsq=0;
        double nnz=0;
        
        for (int z=0; z<nz; z++) {
                for (int y=0; y<ny; y++) {
                        for (int x=0; x<nx; x++) {
                                double m=mask->get_value_at(x,y,z);
                                if (m==0) continue;
                                if (!apply_mask) m=1.0;         // If not applying the mask (which may have values between 0 and 1) we don't want to alter the values
                                double v=(double)image->get_value_at(x,y,z)*m;
                                sum+=v;
                                sumsq+=v*v;
                                nnz+=1.0;
                        }
                }
        }
        
        float mean=(float)(sum/nnz);
        float sigma=sqrt((float)(sumsq-sum*sum/nnz)/nnz);
        if (no_sigma) sigma=1.0f;
        
        for (int z=0; z<nz; z++) {
                for (int y=0; y<ny; y++) {
                        for (int x=0; x<nx; x++) {
                                float m=mask->get_value_at(x,y,z);
                                if (!apply_mask) m=1.0;         // If not applying the mask (which may have values between 0 and 1) we don't want to alter the values
                                if (m==0) image->set_value_at(x,y,z,0);
                                else image->set_value_at(x,y,z,(image->get_value_at(x,y,z)*m-mean)/sigma);
                        }
                }
        }
}

References LOGWARN, EMAN::Processor::params, EMAN::Dict::set_default(), sqrt(), x, and y.

Member Data Documentation

◆ NAME

const string NormalizeMaskProcessor::NAME = "normalize.mask"

static

Definition at line 5987 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