#include <processor.h>

Inheritance diagram for EMAN::TestImageFourierNoiseProfile:

Collaboration diagram for EMAN::TestImageFourierNoiseProfile:

[legend]

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 = "testimage.noise.fourier.profile"

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 8182 of file processor.h.

Member Function Documentation

◆ get_desc()

virtual string EMAN::TestImageFourierNoiseProfile::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 8192 of file processor.h.

                {
                        return "Replace a source image with Fourier noise using amplitude information that is stored in a profile.";
                }

◆ get_name()

virtual string EMAN::TestImageFourierNoiseProfile::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 8187 of file processor.h.

                {
                        return NAME;
                }

References NAME.

◆ get_param_types()

virtual TypeDict EMAN::TestImageFourierNoiseProfile::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 8202 of file processor.h.

                {
                        TypeDict d;
                        d.put("profile", EMObject::FLOATARRAY, "The noise profile, squared amplitude. As in, what is the EMAN2CTF.background attribute");
                        return d;
                }

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

◆ NEW()

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

inlinestatic

Definition at line 8197 of file processor.h.

                {
                        return new TestImageFourierNoiseProfile();
                }

◆ process_inplace()

void TestImageFourierNoiseProfile::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 9180 of file processor.cpp.

                                                                 {
 
        if (params.has_key("profile")==false) throw InvalidParameterException("You must supply the profile argument");
 
        if (!image->is_complex()) {
                int nx = image->get_xsize();
                int offset = 2 - nx%2;
 
                image->set_size(nx+offset,image->get_ysize(),image->get_zsize());
                image->set_complex(true);
                if (1 == offset) image->set_fftodd(true);
                else image->set_fftodd(false);
                image->set_fftpad(true);
        }
        image->to_zero();
        image->ri2ap();
 
        vector<float> profile = params["profile"];
        transform(profile.begin(),profile.end(),profile.begin(),sqrtf);
 
        int i = static_cast<int>(profile.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, phase;
        int length;
        int twox;
        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;
                                size_t idx2 = idx1 + 1;
 
 
                                if (length >= i) {
                                        d[idx1] = 0;
                                        d[idx2] = 0;
                                        continue;
                                }
                                amp = profile[length];
                                phase = Util::get_frand(0,1)*2*M_PI;
 
 
                                d[idx1] = amp;
                                d[idx2] = phase;
 
                        }
                }
        }
 
        image->ap2ri();
        if (image->get_ndim() == 2) {
                bool yodd = image->get_ysize() % 2 == 1;
 
                int yit = image->get_ysize()/2-1;
                int offset = 1;
                if (yodd) {
                        offset = 0;
                }
                for (int y = 0; y < yit; ++y) {
                        int bot_idx = (y+offset)*nx;
                        int top_idx = (ny-1-y)*nx;
                        float r1 = d[bot_idx];
                        float i1 = d[bot_idx+1];
                        float r2 = d[top_idx];
                        float i2 = d[top_idx+1];
                        float r = (r1 + r2)/2.0f;
                        float i = (i1 + i2)/2.0f;
                        d[bot_idx] = r;
                        d[top_idx] = r;
                        d[bot_idx+1] = i;
                        d[top_idx+1] = -i;
 
                        bot_idx = (y+offset)*nx+nx-2;
                        top_idx = (ny-1-y)*nx+nx-2;
                        r1 = d[bot_idx];
                        i1 = d[bot_idx+1];
                        r2 = d[top_idx];
                        i2 = d[top_idx+1];
                        r = (r1 + r2)/2.0f;
                        i = (i1 + i2)/2.0f;
                        d[bot_idx] = r;
                        d[top_idx] = r;
                        d[bot_idx+1] = i;
                        d[top_idx+1] = -i;
                }
 
                d[1] = 0; // 0 phase for this componenet
                d[nx-1] = 0; // 0 phase for this component
                d[ny/2*nx+nx-1] = 0;// 0 phase for this component
                d[ny/2*nx+1] = 0;// 0 phase for this component
        }
 
        if (image->get_ndim() != 1) image->process_inplace("xform.fourierorigin.tocorner");
        image->do_ift_inplace();
        image->depad();
}

References EMAN::Util::get_frand(), EMAN::Dict::has_key(), InvalidParameterException, EMAN::length(), EMAN::TestImageProcessor::nx, EMAN::TestImageProcessor::ny, EMAN::Processor::params, phase(), sqrt(), x, and y.

Member Data Documentation

◆ NAME

const string TestImageFourierNoiseProfile::NAME = "testimage.noise.fourier.profile"

static

Definition at line 8209 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