Normalize such that the estimated histogram peak value is zero. More...

#include <processor.h>

Inheritance diagram for EMAN::NormalizeHistPeakProcessor:

Collaboration diagram for EMAN::NormalizeHistPeakProcessor:

[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...

Public Member Functions inherited from EMAN::NormalizeProcessor
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...

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

Static Public Member Functions
static Processor *	NEW ()

Static Public Member Functions inherited from EMAN::NormalizeProcessor
static string	get_group_desc ()

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.histpeak"

Protected Member Functions
float	calc_mean (EMData *image) const

Protected Member Functions inherited from EMAN::NormalizeProcessor
virtual float	calc_sigma (EMData *image) const

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 such that the estimated histogram peak value is zero.

Only works if the histogram peak is within +- 2*sigma of the mean.

Definition at line 5928 of file processor.h.

Member Function Documentation

◆ calc_mean()

float NormalizeHistPeakProcessor::calc_mean ( EMData * image ) const

protectedvirtual

Implements EMAN::NormalizeProcessor.

Definition at line 5018 of file processor.cpp.

{
        if (!image) {
                LOGWARN("NULL Image");
                return 0;
        }
        float mean = image->get_attr("mean");
        float sig = image->get_attr("sigma");
        size_t n=image->get_size();
        
        // We want at least 100 values per bin on average
        int hist_size = image->get_size()/100;
        if (hist_size>1000) hist_size=1000;
        if (hist_size<5) hist_size=5;
        vector<float> hist(hist_size,0.0f);
        
        float histmin=mean-2.0f*sig;
        float histmax=mean+2.0f*sig;
        float step=(histmax-histmin)/(hist_size-1);
        for (size_t i=0; i<n; i++) {
                int bin = (image->get_value_at_index(i)-histmin)/step;
                bin=bin<0?0:(bin>=hist_size?hist_size-1:bin);
                hist[bin]++;
        }
        
        // yes, probably could use fancy vector methods...
        int maxv=hist[1],maxn=1;
        for (int i=2; i<hist_size-1; i++) {
                if (hist[i]>maxv) { maxv=hist[i]; maxn=i; }
        }
        
        // weighted average position of the peak and nearest neighbors
        float v1=hist[maxn-1],v2=hist[maxn],v3=hist[maxn+1];
        float ret= (v1*(maxn-1)+v2*maxn+v3*(maxn+1))/(v1+v2+v3)*step+histmin;
        printf("%f %f %f %f %f %f\n",v1,v2,v3,mean,sig,ret);
        
        return ret;
}

References LOGWARN.

◆ get_desc()

string EMAN::NormalizeHistPeakProcessor::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 5941 of file processor.h.

                {
                        return "Normalize an image so the estimated histogram peak is zero and sigma=1. Only works if the histogram peak is within +-2*sigma of the mean";
                }

◆ get_name()

string EMAN::NormalizeHistPeakProcessor::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 5931 of file processor.h.

                {
                        return NAME;
                }

References NAME.

◆ NEW()

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

inlinestatic

Definition at line 5936 of file processor.h.

                {
                        return new NormalizeHistPeakProcessor();
                }

Member Data Documentation

◆ NAME

const string NormalizeHistPeakProcessor::NAME = "normalize.histpeak"

static

Definition at line 5946 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

Protected Member Functions

Additional Inherited Members