EMAN::CtfSimProcessor Class Reference

CTF simulation processor. More...

#include <processor.h>

Inheritance diagram for EMAN::CtfSimProcessor:

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Collaboration diagram for EMAN::CtfSimProcessor:

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List of all members.

Public Member Functions

string get_name () const
 Get the processor's name.
virtual EMDataprocess (const EMData *const image)
 To proccess an image out-of-place.
void process_inplace (EMData *image)
 To process an image in-place.
TypeDict get_param_types () const
 Get processor parameter information in a dictionary.
string get_desc () const
 Get the descrition of this specific processor.

Static Public Member Functions

static ProcessorNEW ()

Static Public Attributes

static const string NAME = "math.simulatectf"

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 772 of file processor.h.


Member Function Documentation

string EMAN::CtfSimProcessor::get_desc (  )  const [inline, virtual]

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 803 of file processor.h.

00804                 {
00805                         return "Applies a simulated CTF with noise to an image. The added noise is either white or based on an empirical curve generated from cryoEM data. ";
00806                 }

string EMAN::CtfSimProcessor::get_name (  )  const [inline, virtual]

Get the processor's name.

Each processor is identified by a unique name.

Returns:
The processor's name.

Implements EMAN::Processor.

Definition at line 775 of file processor.h.

References NAME.

00776                 {
00777                         return NAME;
00778                 }

TypeDict EMAN::CtfSimProcessor::get_param_types (  )  const [inline, virtual]

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 784 of file processor.h.

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

00785                 {
00786                         TypeDict d;
00787                         d.put("defocus", EMObject::FLOAT, "Defocus in microns (underfocus positive)");
00788                         d.put("ampcont", EMObject::FLOAT, "% amplitude contrast (0-100)");
00789                         d.put("bfactor", EMObject::FLOAT, "B-factor in A^2, uses MRC convention rather than EMAN1 convention");
00790                         d.put("noiseamp", EMObject::FLOAT, "Amplitude of the added empirical pink noise");
00791                         d.put("noiseampwhite", EMObject::FLOAT, "Amplitude of added white noise");
00792                         d.put("voltage", EMObject::FLOAT, "Microscope voltage in KV");
00793                         d.put("cs", EMObject::FLOAT, "Cs of microscope in mm");
00794                         d.put("apix", EMObject::FLOAT, "A/pix of data");
00795                         return d;
00796                 }

static Processor* EMAN::CtfSimProcessor::NEW (  )  [inline, static]

Definition at line 798 of file processor.h.

00799                 {
00800                         return new CtfSimProcessor();
00801                 }

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 5435 of file processor.cpp.

References EMAN::EMData::add(), EMAN::EMAN2Ctf::ampcont, EMAN::Ctf::apix, EMAN::EMData::apply_radial_func(), EMAN::Ctf::bfactor, EMAN::EMAN2Ctf::compute_1d(), EMAN::EMData::copy(), EMAN::Ctf::cs, EMAN::Ctf::CTF_AMP, EMAN::Ctf::defocus, EMAN::EMData::do_fft(), EMAN::EMData::do_fft_inplace(), EMAN::EMData::do_ift(), EMAN::EMAN2Ctf::dsbg, EMAN::EMData::get_attr_default(), EMAN::EMData::get_ysize(), EMAN::EMData::is_complex(), LOGWARN, EMAN::EMData::mult(), EMAN::Processor::params, EMAN::EMData::process_inplace(), EMAN::Dict::set_default(), and EMAN::Ctf::voltage.

Referenced by process_inplace().

05435                                                            {
05436         if (!image) {
05437                 LOGWARN("NULL Image");
05438                 return NULL;
05439         }
05440 
05441         EMData *fft;
05442         if (!image->is_complex()) fft=image->do_fft();
05443         else fft=image->copy();
05444 
05445         EMAN2Ctf ctf;
05446         ctf.defocus=params["defocus"];
05447         ctf.bfactor=params["bfactor"];
05448         ctf.ampcont=params.set_default("ampcont",10.0);
05449         ctf.voltage=params.set_default("voltage",200.0);
05450         ctf.cs=params.set_default("cs",2.0);
05451         ctf.apix=params.set_default("apix",image->get_attr_default("apix_x",1.0));
05452         ctf.dsbg=1.0/(ctf.apix*fft->get_ysize()*4.0);           //4x oversampling
05453         
05454         float noiseamp=params.set_default("noiseamp",0.0);
05455         float noiseampwhite=params.set_default("noiseampwhite",0.0);
05456         
05457         // compute and apply the CTF
05458         vector <float> ctfc = ctf.compute_1d(fft->get_ysize()*6,ctf.dsbg,ctf.CTF_AMP,NULL); // *6 goes to corner, remember you provide 2x the number of points you need
05459 
05460 //      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());
05461 //      FILE *out=fopen("x.txt","w");
05462 //      for (int i=0; i<ctfc.size(); i++) fprintf(out,"%f\t%1.3g\n",0.25*i/(float)fft->get_ysize(),ctfc[i]);
05463 //      fclose(out);
05464         
05465         fft->apply_radial_func(0,0.25/fft->get_ysize(),ctfc,1);
05466         
05467         // Add noise
05468         if (noiseamp!=0 or noiseampwhite!=0) {
05469                 EMData *noise = new EMData(image->get_ysize(),image->get_ysize(),1);
05470                 noise->process_inplace("testimage.noise.gauss");
05471                 noise->do_fft_inplace();
05472         
05473                 // White noise
05474                 if (noiseampwhite!=0) {
05475                         noise->mult((float)noiseampwhite*15.0f);                // The 15.0 is to roughly compensate for the stronger pink noise curve
05476                         fft->add(*noise);
05477                         noise->mult((float)1.0/(noiseampwhite*15.0f));
05478                 }
05479                 
05480                 // Pink noise
05481                 if (noiseamp!=0) {
05482                         vector <float> pinkbg;
05483                         pinkbg.resize(500);
05484                         float nyimg=0.5/ctf.apix;       // image nyquist
05485                         // This pink curve came from a typical image in the GroEL 4A data set
05486                         for (int i=0; i<500; i++) pinkbg[i]=noiseamp*(44.0*exp(-5.0*nyimg*i/250.0)+10.0*exp(-90.0*nyimg*i/250.0));              // compute curve to image Nyquist*2
05487                         noise->apply_radial_func(0,.002,pinkbg,1);              // Image nyquist is at 250 -> 0.5
05488                         fft->add(*noise);
05489                 }
05490                 
05491         }
05492         
05493         EMData *ret=fft->do_ift();
05494         delete fft;
05495         
05496         return ret;
05497 }

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 5427 of file processor.cpp.

References EMAN::EMData::get_data(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), process(), and EMAN::EMData::update().

05427                                                    {
05428         EMData *tmp=process(image);
05429         memcpy(image->get_data(),tmp->get_data(),image->get_xsize()*image->get_ysize()*image->get_zsize()*sizeof(float));
05430         delete tmp;
05431         image->update();
05432         return;
05433 }


Member Data Documentation

const string CtfSimProcessor::NAME = "math.simulatectf" [static]

Definition at line 808 of file processor.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Thu Nov 17 12:45:53 2011 for EMAN2 by  doxygen 1.4.7