Sorry for the pun. More...

#include <processor.h>

Inheritance diagram for EMAN::SubtractOptProcessor:

Collaboration diagram for EMAN::SubtractOptProcessor:

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

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

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

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

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

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

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 = "math.sub.optimal"

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

Sorry for the pun.

This processor will take a second image and try to filter/scale it to optimally subtract it from the original image. The idea here is that if you have an image with noise plus a linear-filter modified projection, that a good measure of the similarity of the image to the projection would be to try and remove the projection from the image as optimally as possible, then compute the standard deviation of what's left.

Now you might say that if the total energy in the noisy image is normalized then this should be equivalent to just integrating the FSC, which is what we use to do the optimal subtraction in the first place. This would be true, but this "optimal subtraction" has other purposes as well, such as the e2extractsubparticles program.

Parameters

ref	Reference image to subtract
return_radial	Will return the radial filter function applied to ref as filter_curve

Definition at line 6217 of file processor.h.

Member Function Documentation

◆ get_desc()

string EMAN::SubtractOptProcessor::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 6248 of file processor.h.

                {
                        return "This will filter/scale 'ref' optimally and subtract it from image using ring dot products in Fourier space for normalization. Cutoff frequencies apply a bandpass tophat filter to the output.";
                }

◆ get_name()

string EMAN::SubtractOptProcessor::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 6223 of file processor.h.

                {
                        return NAME;
                }

References NAME.

◆ get_param_types()

TypeDict EMAN::SubtractOptProcessor::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 6233 of file processor.h.

                {
                        TypeDict d;
                        d.put("ref", EMObject::EMDATA, "Reference image to subtract");
                        d.put("actual", EMObject::EMDATA, "If specified, ref is used for normalization, but actual is subtracted.");
                        d.put("low_cutoff_frequency", EMObject::FLOAT, "Absolute [0,0.5] low cut-off frequency.");
                        d.put("high_cutoff_frequency", EMObject::FLOAT, "Absolute [0,0.5] high cut-off frequency.");
                        d.put("ctfweight",EMObject::BOOL, "Filter the image by CTF before subtraction");
                        d.put("return_fft",EMObject::BOOL, "Skips the final IFT, and returns the FFT of the subtracted image");
                        d.put("return_subim", EMObject::BOOL, "Instead of returning the image after subtraction, returns the filtered image which would have been subtracted from the image.");
                        d.put("return_radial", EMObject::BOOL, "Return the radial filter function as an attribute (filter_curve)");
                        d.put("return_presigma", EMObject::BOOL, "Return the sigma of the pre-subtracted image in real-space with the specified filter applied as sigma_presub. This is an expensive option.");
                        return d;
                }

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

◆ NEW()

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

inlinestatic

Definition at line 6228 of file processor.h.

                {
                        return new SubtractOptProcessor();
                }

◆ process()

EMData * SubtractOptProcessor::process ( const EMData *const image )

virtual

To proccess an image out-of-place.

For those processors which can only be processed out-of-place, override this function to give the right behavior.

Parameters

image The image will be copied, actual process happen on copy of image.

Returns: the image processing result, may or may not be the same size of the input image

Reimplemented from EMAN::Processor.

Definition at line 5059 of file processor.cpp.

{
        if (!image) {
                LOGWARN("NULL Image");
                return NULL;
        }
 
        EMData *refr = params["ref"];
        EMData *actual = params.set_default("actual",(EMData*)NULL);
        EMData *ref;
        bool return_radial = params.set_default("return_radial",false);
        bool return_fft = params.set_default("return_fft",false);
        bool ctfweight = params.set_default("ctfweight",false);
        bool return_presigma = params.set_default("return_presigma",false);
        bool return_subim = params.set_default("return_subim",false);
        int si0=(int)floor(params.set_default("low_cutoff_frequency",0.0f)*image->get_ysize());
        int si1=(int)ceil(params.set_default("high_cutoff_frequency",0.7071f)*image->get_ysize());              // include the corners unless explicitly excluded
 
        // We will be modifying imf, so it needs to be a copy
        EMData *imf;
        if (image->is_complex()) imf=image->copy();
        else imf=image->do_fft();
 
        if (ctfweight) {
                EMData *ctfi=imf->copy_head();
                Ctf *ctf;
//              if (image->has_attr("ctf"))
                        ctf=(Ctf *)(image->get_attr("ctf"));
//              else ctf=(Ctf *)(ref->get_attr("ctf"));
                ctf->compute_2d_complex(ctfi,Ctf::CTF_INTEN);
                imf->mult(*ctfi);
                delete ctfi;
        }
 
        // Make sure ref is complex
        if (refr->is_complex()) ref=refr;
        else ref=refr->do_fft();
 
        EMData *actf;
        if (actual==NULL) actf=ref;
        else {
                if (ctfweight) throw InvalidCallException("math.sub.optimal: Sorry, cannot use ctfweight in combination with actual");
                if (actual->is_complex()) actf=actual;
                else actf=actual->do_fft();
        }
 
        int ny2=(int)(image->get_ysize()*sqrt(2.0)/2);
        vector <double>rad(ny2+1);
        vector <double>norm(ny2+1);
 
        // We are essentially computing an FSC here, but while the reference (the image
        // we plan to subtract) is normalized, the other image is not. This gives us a filter
        // to apply to the reference to optimally eliminate its contents from 'image'.
        for (int y=-ny2; y<ny2; y++) {
                for (int x=0; x<ny2; x++) {
                        int r=int(Util::hypot_fast(x,y));
                        if (r>ny2) continue;
                        std::complex<float> v1=imf->get_complex_at(x,y);
                        std::complex<float> v2=ref->get_complex_at(x,y);
                        rad[r]+=(double)(v1.real()*v2.real()+v1.imag()*v2.imag());
//                      norm[r]+=v2.real()*v2.real()+v2.imag()*v2.imag()+v1.real()*v1.real()+v1.imag()*v1.imag();
                        norm[r]+=(double)(v2.real()*v2.real()+v2.imag()*v2.imag());
                }
        }
        for (int i=1; i<ny2; i++) rad[i]/=norm[i];
        rad[0]=0;
//      FILE *out=fopen("dbug.txt","w");
//      for (int i=0; i<ny2; i++) fprintf(out,"%lf\t%lf\t%lf\n",(float)i,rad[i],norm[i]);
//      fclose(out);
 
        float oldsig=-1.0;
        // This option computes the real-space sigma on the input-image after the specified filter
        // This is an expensive option, but more efficient than computing the same using other means
        if (return_presigma) {
                for (int y=-ny2; y<ny2; y++) {
                        for (int x=0; x<imf->get_xsize()/2; x++) {
                                int r=int(Util::hypot_fast(x,y));
                                if (r>=ny2 || r>=si1 || r<si0) {
                                        imf->set_complex_at(x,y,0);
                                        continue;
                                }
                                std::complex<float> v1=imf->get_complex_at(x,y);
                                imf->set_complex_at(x,y,v1);
                        }
                }
                EMData *tmp=imf->do_ift();
                oldsig=(float)tmp->get_attr("sigma");
                delete tmp;
        }
 
        for (int y=-ny2; y<ny2; y++) {
                for (int x=0; x<imf->get_xsize()/2; x++) {
                        int r=int(Util::hypot_fast(x,y));
                        if (r>=ny2 || r>=si1 || r<si0) {
                                imf->set_complex_at(x,y,0);
                                continue;
                        }
                        std::complex<float> v1=imf->get_complex_at(x,y);
                        std::complex<float> v2=actf->get_complex_at(x,y);
                        v2*=(float)rad[r];
                        if (return_subim) imf->set_complex_at(x,y,v2);
                        else imf->set_complex_at(x,y,v1-v2);
                }
        }
 
        if (!refr->is_complex()) delete ref;
        if (actual!=NULL && !actual->is_complex()) delete actf;
 
        vector <float>radf;
        if (return_radial) {
                radf.resize(ny2);
                for (int i=0; i<ny2; i++) radf[i]=(float)rad[i];
        }
 
        if (!return_fft) {
                EMData *ret=imf->do_ift();
                delete imf;
                if (return_radial) ret->set_attr("filter_curve",radf);
                if (return_presigma) {
                        ret->set_attr("sigma_presub",oldsig);
//                      printf("Set %f\n",(float)image->get_attr("sigma_presub"));
                }
                return ret;
        }
        if (return_radial) imf->set_attr("filter_curve",radf);
        if (return_presigma) imf->set_attr("sigma_presub",oldsig);
        return imf;
}

References EMAN::Ctf::compute_2d_complex(), EMAN::Ctf::CTF_INTEN, EMAN::Util::hypot_fast(), InvalidCallException, LOGWARN, EMAN::Processor::params, EMAN::Dict::set_default(), sqrt(), x, and y.

Referenced by process_inplace().

◆ process_inplace()

void SubtractOptProcessor::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 5188 of file processor.cpp.

{
        if (!image) {
                LOGWARN("NULL image");
                return;
        }
 
        EMData *tmp=process(image);
        memcpy(image->get_data(),tmp->get_data(),(size_t)image->get_xsize()*image->get_ysize()*image->get_zsize()*sizeof(float));
        delete tmp;
        image->update();
        return;
}

References LOGWARN, and process().

Member Data Documentation

◆ NAME

const string SubtractOptProcessor::NAME = "math.sub.optimal"

static

Definition at line 6253 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()

◆ process_inplace()

Member Data Documentation

◆ NAME