EMAN::CtfSimProcessor Class Reference

CTF simulation processor. More...

#include <processor.h>

Inheritance diagram for EMAN::CtfSimProcessor:

Collaboration diagram for EMAN::CtfSimProcessor:

Public Member Functions
string	get_name () const
	Get the processor's name. More...
virtual EMData *	process (const EMData *const image)
	To proccess an image out-of-place. More...
void	process_inplace (EMData *image)
	To process an image in-place. 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.simulatectf"

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

CTF simulation processor.

Takes individual CTF parameters, suitable for use with programs like e2filtertool.py. Can use an internal noise profile or an external profile from a text file.

Parameters

defocus[in]	Defocus in microns (underfocus positive)
ampcont[in]	% amplitude contrast (0-100)
bfactor[in]	B-factor in A^2, uses MRC convention rather than EMAN1 convention
noiseamp[in]	Amplitude of the added empirical pink noise
noiseampwhite[in]	Amplitude of added white noise
voltage[in]	Microscope voltage in KV
cs[in]	Cs of microscope in mm
apix[in]	A/pix of data

Author

Steve Ludtke

Date

2011/11/03

Definition at line 1804 of file processor.h.

Member Function Documentation

get_desc()

string EMAN::CtfSimProcessor::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 1838 of file processor.h.

                {
                        return "Applies a simulated CTF with noise to an image. Astigmatism is always zero. The added noise is either white or based on an empirical curve generated from cryoEM data. ";
                }

get_name()

string EMAN::CtfSimProcessor::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 1807 of file processor.h.

                {
                        return NAME;
                }

References NAME.

get_param_types()

TypeDict EMAN::CtfSimProcessor::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 1816 of file processor.h.

                {
                        TypeDict d;
                        d.put("purectf", EMObject::BOOL, "If set, replaces image with simulated CTF instead of multiplying image by CTF");
                        d.put("defocus", EMObject::FLOAT, "Defocus in microns (underfocus positive)");
                        d.put("ampcont", EMObject::FLOAT, "% amplitude contrast (0-100)");
                        d.put("bfactor", EMObject::FLOAT, "B-factor in A^2, uses MRC convention rather than EMAN1 convention");
                        d.put("noiseamp", EMObject::FLOAT, "Amplitude of the added empirical pink noise");
//                      d.put("noiseampwhite", EMObject::FLOAT, "Amplitude of added white noise");
                        d.put("voltage", EMObject::FLOAT, "Microscope voltage in KV");
                        d.put("cs", EMObject::FLOAT, "Cs of microscope in mm");
                        d.put("apix", EMObject::FLOAT, "A/pix of data");
                        d.put("phaseflip", EMObject::INT, "If not true, applies fabs(CTF). default true");
                        d.put("bispectrumfp", EMObject::INT, "If set, the input must be the result of math.bispectrum.slice ffp= mode. Returns something comparable to fp=mode.");
                        return d;
                }

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

NEW()

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

inlinestatic

Definition at line 1833 of file processor.h.

                {
                        return new CtfSimProcessor();
                }

process()

EMData * CtfSimProcessor::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 6879 of file processor.cpp.

                                                           {
        if (!image) {
                LOGWARN("NULL Image");
                return NULL;
        }
 
        EMData *fft;
        if (!image->is_complex()) fft=image->do_fft();
        else fft=image->copy();
 
        bool purectf=(bool)params.set_default("purectf",0);
        EMAN2Ctf ctf;
        ctf.defocus=params["defocus"];
        ctf.bfactor=params["bfactor"];
        ctf.ampcont=params.set_default("ampcont",10.0f);
        ctf.voltage=params.set_default("voltage",200.0f);
        ctf.cs=params.set_default("cs",2.0);
        ctf.apix=params.set_default("apix",image->get_attr_default("apix_x",1.0));
        if (image->has_attr("dsbg")) ctf.dsbg=image->get_attr("dsbg");
        else ctf.dsbg=1.0/(ctf.apix*fft->get_ysize()*4.0);              //4x oversampling
        int doflip=(int)params.set_default("phaseflip",1);              // whether to use the CTF or abs(CTF)
        float noiseamp=params.set_default("noiseamp",0.0f);
        float noiseampwhite=params.set_default("noiseampwhite",0.0f);
        int bsfp=(int)params.set_default("bispectrumfp",0);             // special mode for bispectrum processing ... obsolete as of 8/16/18
 
        // compute the CTF
        vector <float> ctfc = ctf.compute_1d(fft->get_ysize()*12,ctf.dsbg,ctf.CTF_AMP,NULL); // *6 goes to corner, remember you provide 2x the number of points you need
        if (!doflip) {
                for (vector<float>::iterator it=ctfc.begin(); it!=ctfc.end(); ++it) *it=fabs(*it);
        }
 
//      for (int i=0; i<ctfc.size(); i++) printf("%d\t%f\n",i,ctfc[i]);
//      printf("apix %f\tdsbg %f\tdef %f\tbfac %f\tvol %f\tcs %f\n",ctf.apix,ctf.dsbg,ctf.defocus,ctf.bfactor,ctf.voltage,ctf.cs);
        
//      printf("%1.3f\t%1.3f\t%1.3f\t%1.3f\t%1.3f\t%d\n",ctf.defocus,ctf.bfactor,ctf.ampcont,ctf.dsbg,ctf.apix,fft->get_ysize());
//      FILE *out=fopen("x.txt","w");
//      for (int i=0; i<ctfc.size(); i++) fprintf(out,"%f\t%1.3g\n",0.25*i/(float)fft->get_ysize(),ctfc[i]);
//      fclose(out);
 
        if (bsfp) {
                int fp=fft->get_zsize();
                int nx=fft->get_xsize();
                int ny=fft->get_ysize();
                EMData *ret=new EMData((nx-2)/2,ny*fp,1);
//              for (int j=ny*2-4; j<ctfc.size(); j++) ctfc[j]*=exp(-pow(j-ny*2+4,2.0)/8.0);    // soft Gaussian falloff to CTF modification to avoid corner/edge effects
                for (int k=0; k<fp; k++) {
                        EMData *plnf=fft->get_clip(Region(0,0,k,nx,ny,1));
                        plnf->set_complex(1);
                        plnf->set_ri(1);
                        plnf->set_fftpad(1);
//                      plnf->apply_radial_func(0,0.25f/fft->get_ysize(),ctfc,1);
                        for (int jy=-ny/2; jy<ny/2; jy++) {
                                for (int jx=0; jx<nx/2; jx++) {
                                        if (jx==0 && jy<0) continue;
                                        int r1=Util::hypot_fast_int(jx*4,jy*4);
                                        int r2=(k+2)*4;
                                        int r3=Util::hypot_fast_int((jx+k+2)*4,jy*4);
                                        float ctfmod=ctfc[r1]*ctfc[r2]*ctfc[r3];
//                                      if (jx==0|| jx==1) printf("%d %d\t%d %d %d\t%g %g %g\t%g\n",jx,jy,r1,r2,r3,ctfc[r1],ctfc[r2],ctfc[r3],ctfmod);
                                        
                                        // Turns out that it shouldn't BE rotationally symmetric
//                                      // To make this rotationally symmetric we have to integrate over the j+k vector
//                                      float avgr=0.0f;
//                                      float norm=0.0f;
//                                      for (float ang=0.0f; ang<2.0*M_PI; ang+=2.0*M_PI/float(k*8)) {
//                                              float jkx=jx*4+k*4.0*cos(ang);
//                                              float jky=jy*4+k*4.0*sin(ang);
// 
//                                              int r3=int(hypot(jkx,jky)+0.5);
//                                              avgr+=ctfc[r3];
//                                              norm+=1.0;
//                                      }
//                                      ctfmod*=(avgr/norm);
 
                                        if (purectf) plnf->set_complex_at(jx,jy,ctfmod);
                                        else plnf->set_complex_at(jx,jy,plnf->get_complex_at(jx,jy)*ctfmod);
//                                      plnf->set_complex_at(jx,jy,plnf->get_complex_at(jx,jy);
//                                      plnf->set_complex_at(jx,jy,ctfmod);
                                }
                        }
//                      plnf->write_image("tst.hdf",-1);
                        
                        EMData *pln=plnf->do_ift();
                        pln->process_inplace("xform.phaseorigin.tocenter");
                        pln->process_inplace("normalize");
                        ret->insert_clip(pln,IntPoint(-nx/2,k*ny,0));
                        delete plnf;
                        delete pln;
                }
                delete fft;
                return ret;
        }
        else {
                if (purectf) {
                        for (size_t i=0; i<fft->get_size(); i++) fft->set_value_at_fast(i,i%2==0?1.0f:0.0f);
                }
                fft->apply_radial_func(0,0.25f/fft->get_ysize(),ctfc,1);
        }
 
        // Add noise
        if (noiseamp!=0 || noiseampwhite!=0) {
                EMData *noise = new EMData(image->get_ysize(),image->get_ysize(),1);
                noise->process_inplace("testimage.noise.gauss");
                noise->do_fft_inplace();
 
                // White noise
                if (noiseampwhite!=0) {
                        noise->mult((float)noiseampwhite*15.0f);                // The 15.0 is to roughly compensate for the stronger pink noise curve
                        fft->add(*noise);
                        noise->mult((float)1.0/(noiseampwhite*15.0f));
                }
 
                // Pink noise
                if (noiseamp!=0) {
                        vector <float> pinkbg;
                        pinkbg.resize(500);
                        float nyimg=0.5f/ctf.apix;      // image nyquist
                        // This pink curve came from a typical image in the GroEL 4A data set
                        for (int i=0; i<500; i++) pinkbg[i]=noiseamp*(44.0f*exp(-5.0f*nyimg*i/250.0f)+10.0f*exp(-90.0f*nyimg*i/250.0f));                // compute curve to image Nyquist*2
                        noise->apply_radial_func(0,.002f,pinkbg,1);             // Image nyquist is at 250 -> 0.5
                        fft->add(*noise);
                }
 
        }
 
        EMData *ret=fft->do_ift();
        delete fft;
 
        return ret;
}

References EMAN::EMAN2Ctf::ampcont, EMAN::Ctf::apix, EMAN::EMData::apply_radial_func(), EMAN::Ctf::bfactor, EMAN::EMAN2Ctf::compute_1d(), EMAN::Ctf::cs, EMAN::Ctf::CTF_AMP, EMAN::Ctf::defocus, EMAN::EMAN2Ctf::dsbg, EMAN::EMData::get_clip(), EMAN::Util::hypot_fast_int(), LOGWARN, EMAN::Processor::params, EMAN::Dict::set_default(), and EMAN::Ctf::voltage.

Referenced by process_inplace().

process_inplace()

void CtfSimProcessor::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 6871 of file processor.cpp.

                                                   {
        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 process().

Member Data Documentation

NAME

const string CtfSimProcessor::NAME = "math.simulatectf"

static

Definition at line 1843 of file processor.h.

Referenced by get_name().

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The documentation for this class was generated from the following files:

• processor.h
• processor.cpp