#include <processor.h>

Inheritance diagram for EMAN::CTFSNRWeightProcessor:

Collaboration diagram for EMAN::CTFSNRWeightProcessor:

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

virtual string	get_name () const
	Get the processor's name. More...

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

virtual 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::TestImageProcessor
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 = "ctf.snr.weight"

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 Member Functions inherited from EMAN::TestImageProcessor
void	preprocess (EMData *image)

Protected Attributes inherited from EMAN::TestImageProcessor
int	nx

int	ny

int	nz

Protected Attributes inherited from EMAN::Processor
Dict	params

Detailed Description

Author: David Woolford

Date: June 15th 2009

Definition at line 8217 of file processor.h.

Member Function Documentation

◆ get_desc()

virtual string EMAN::CTFSNRWeightProcessor::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 8227 of file processor.h.

                        {
                                return "Weight the amplitudes of an image based on radial noise and snr curves ";
                        }

◆ get_name()

virtual string EMAN::CTFSNRWeightProcessor::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 8222 of file processor.h.

                        {
                                return NAME;
                        }

References NAME.

◆ get_param_types()

virtual TypeDict EMAN::CTFSNRWeightProcessor::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 8237 of file processor.h.

                        {
                                TypeDict d;
                                d.put("noise", EMObject::FLOATARRAY, "The noise profile, squared amplitude. As in, what is the EMAN2CTF.background attribute");
                                d.put("snr", EMObject::FLOATARRAY, "Squared amplitude divided by squared noise amplitude. As in, what is the EMAN2CTF.snr attribute");
                                d.put("boost", EMObject::FLOAT, "Multiplicative signal boost");
                                return d;
                        }

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

◆ NEW()

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

inlinestatic

Definition at line 8232 of file processor.h.

                        {
                                return new CTFSNRWeightProcessor();
                        }

◆ process_inplace()

void CTFSNRWeightProcessor::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 9089 of file processor.cpp.

                                                         {
        if (params.has_key("noise")==false) throw InvalidParameterException("You must supply the noise argument");
        if (params.has_key("snr")==false) throw InvalidParameterException("You must supply the snr argument");
 
        float boost = params.set_default("boost",1.0f);
 
        if (!image->is_complex()) {
                image->do_fft_inplace();
        }
        EMData* cpy = image->copy();
        cpy->ri2inten();
        vector<float> sf = cpy->calc_radial_dist(cpy->get_ysize()/2,0.0,1.0,1);
        transform(sf.begin(),sf.end(),sf.begin(),sqrtf);
        delete cpy;
 
        image->ri2ap();
 
        vector<float> noise = params["noise"];
        vector<float> snr = params["snr"];
 
//      copy(snr.begin(), snr.end(), ostream_iterator<float>(cout, "\n"));
//      copy(noise.begin(), noise.end(), ostream_iterator<float>(cout, "\n"));
 
        for(vector<float>::iterator it = noise.begin(); it != noise.end(); ++it){
                if ((*it) == 0) *it = 1;
        }
        for(vector<float>::iterator it = snr.begin(); it != snr.end(); ++it){
                if ((*it) < 0) *it = 0;
        }
        // Subtract the mean from the data and store it in data_mm
        transform(snr.begin(),snr.end(),noise.begin(),snr.begin(),std::multiplies<float>());
        transform(snr.begin(),snr.end(),snr.begin(),sqrtf);
//      copy(snr.begin(), snr.end(), ostream_iterator<float>(cout, "\n"));
//      copy(noise.begin(), noise.end(), ostream_iterator<float>(cout, "\n"));
 
        int i = static_cast<int>(snr.size());
 
        float * d = image->get_data();
        int nx = image->get_xsize();
//      int ny = image->get_ysize();
        int nxy = image->get_ysize()*nx;
        int nzon2 = image->get_zsize()/2;
        int nyon2 = image->get_ysize()/2;
        float rx, ry, rz, amp;
        int length;
        int twox;
        image->process_inplace("xform.fourierorigin.tocenter");
        for (int z = 0; z< image->get_zsize(); ++z) {
                for (int y = 0; y < image->get_ysize(); ++y) {
                        for (int x = 0; x < image->get_xsize()/2; ++x) {
                                rx = (float)x;
                                ry = (float)nyon2 - (float)y;
                                rz = (float)nzon2 - (float)z;
                                length = static_cast<int>(sqrt(rx*rx + ry*ry + rz*rz));
 
                                twox = 2*x;
                                size_t idx1 = twox + y*nx+(size_t)z*nxy;
                                if (length >= i || length >= (int)sf.size()) {
                                        d[idx1] = 0;
                                        continue;
                                } else {
                                        amp = boost*snr[length];
//                                      if (amp > 0) amp =sqrtf(amp);
//                                      else amp = 0;
                                }
 
                                if (sf[length] == 0) {
                                        d[idx1] = 0;
                                        continue;
                                }
 
//                              size_t idx2 = idx1 + 1;
//                              cout << d[idx1] << " " << sf[length] << endl;
                                d[idx1] /= sf[length];
                                if (d[idx1] < 0) {
                                        d[idx1] *= amp;
                                }else {
                                        d[idx1] *= -amp;
                                }
//                              d[idx2] = phase;
 
                        }
                }
        }
 
        image->ap2ri();
        if (image->get_ndim() != 1) image->process_inplace("xform.fourierorigin.tocorner");
        image->do_ift_inplace();
        image->depad();
}

References EMAN::EMData::calc_radial_dist(), EMAN::Dict::has_key(), InvalidParameterException, EMAN::length(), EMAN::TestImageProcessor::nx, EMAN::Processor::params, EMAN::Dict::set_default(), sqrt(), x, and y.

Member Data Documentation

◆ NAME

const string CTFSNRWeightProcessor::NAME = "ctf.snr.weight"

static

Definition at line 8246 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