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EMAN::CTFSNRWeightProcessor Class Reference

#include <processor.h>

Inheritance diagram for EMAN::CTFSNRWeightProcessor:

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Collaboration diagram for EMAN::CTFSNRWeightProcessor:

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List of all members.

Public Member Functions

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

Static Public Member Functions

static ProcessorNEW ()

Static Public Attributes

static const string NAME = "ctf.snr.weight"

Detailed Description

Author:
David Woolford
Date:
June 15th 2009

Definition at line 5892 of file processor.h.


Member Function Documentation

virtual string EMAN::CTFSNRWeightProcessor::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 5902 of file processor.h.

05903                         {
05904                                 return "Weight the amplitudes of an image based on radial noise and snr curves ";
05905                         }

virtual string EMAN::CTFSNRWeightProcessor::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 5897 of file processor.h.

References NAME.

05898                         {
05899                                 return NAME;
05900                         }

virtual TypeDict EMAN::CTFSNRWeightProcessor::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 5912 of file processor.h.

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

05913                         {
05914                                 TypeDict d;
05915                                 d.put("noise", EMObject::FLOATARRAY, "The noise profile, squared amplitude. As in, what is the EMAN2CTF.background attribute");
05916                                 d.put("snr", EMObject::FLOATARRAY, "Squared amplitude divided by squared noise amplitude. As in, what is the EMAN2CTF.snr attribute");
05917                                 d.put("boost", EMObject::FLOAT, "Multiplicative signal boost");
05918                                 return d;
05919                         }

static Processor* EMAN::CTFSNRWeightProcessor::NEW  )  [inline, static]
 

Definition at line 5907 of file processor.h.

05908                         {
05909                                 return new CTFSNRWeightProcessor();
05910                         }

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 6709 of file processor.cpp.

References EMAN::EMData::ap2ri(), EMAN::EMData::calc_radial_dist(), EMAN::EMData::copy(), EMAN::EMData::depad(), EMAN::EMData::do_fft_inplace(), EMAN::EMData::do_ift_inplace(), EMAN::EMData::get_data(), EMAN::EMData::get_ndim(), get_xsize(), EMAN::EMData::get_xsize(), get_ysize(), EMAN::EMData::get_ysize(), get_zsize(), EMAN::EMData::get_zsize(), EMAN::Dict::has_key(), InvalidParameterException, EMAN::EMData::is_complex(), EMAN::length(), EMAN::Processor::params, EMAN::EMData::process_inplace(), EMAN::EMData::ri2ap(), EMAN::EMData::ri2inten(), EMAN::Dict::set_default(), sqrt(), and x.

06709                                                          {
06710         if (params.has_key("noise")==false) throw InvalidParameterException("You must supply the noise argument");
06711         if (params.has_key("snr")==false) throw InvalidParameterException("You must supply the snr argument");
06712 
06713         float boost = params.set_default("boost",1.0f);
06714 
06715         if (!image->is_complex()) {
06716                 image->do_fft_inplace();
06717         }
06718         EMData* cpy = image->copy();
06719         cpy->ri2inten();
06720         vector<float> sf = cpy->calc_radial_dist(cpy->get_ysize()/2,0.0,1.0,1);
06721         transform(sf.begin(),sf.end(),sf.begin(),sqrtf);
06722         delete cpy;
06723 
06724         image->ri2ap();
06725 
06726         vector<float> noise = params["noise"];
06727         vector<float> snr = params["snr"];
06728 
06729 //      copy(snr.begin(), snr.end(), ostream_iterator<float>(cout, "\n"));
06730 //      copy(noise.begin(), noise.end(), ostream_iterator<float>(cout, "\n"));
06731 
06732         for(vector<float>::iterator it = noise.begin(); it != noise.end(); ++it){
06733                 if ((*it) == 0) *it = 1;
06734         }
06735         for(vector<float>::iterator it = snr.begin(); it != snr.end(); ++it){
06736                 if ((*it) < 0) *it = 0;
06737         }
06738         // Subtract the mean from the data and store it in data_mm
06739         transform(snr.begin(),snr.end(),noise.begin(),snr.begin(),std::multiplies<float>());
06740         transform(snr.begin(),snr.end(),snr.begin(),sqrtf);
06741 //      copy(snr.begin(), snr.end(), ostream_iterator<float>(cout, "\n"));
06742 //      copy(noise.begin(), noise.end(), ostream_iterator<float>(cout, "\n"));
06743 
06744         int i = static_cast<int>(snr.size());
06745 
06746         float * d = image->get_data();
06747         int nx = image->get_xsize();
06748 //      int ny = image->get_ysize();
06749         int nxy = image->get_ysize()*nx;
06750         int nzon2 = image->get_zsize()/2;
06751         int nyon2 = image->get_ysize()/2;
06752         float rx, ry, rz, amp;
06753         int length;
06754         int twox;
06755         image->process_inplace("xform.fourierorigin.tocenter");
06756         for (int z = 0; z< image->get_zsize(); ++z) {
06757                 for (int y = 0; y < image->get_ysize(); ++y) {
06758                         for (int x = 0; x < image->get_xsize()/2; ++x) {
06759                                 rx = (float)x;
06760                                 ry = (float)nyon2 - (float)y;
06761                                 rz = (float)nzon2 - (float)z;
06762                                 length = static_cast<int>(sqrt(rx*rx + ry*ry + rz*rz));
06763 
06764                                 twox = 2*x;
06765                                 size_t idx1 = twox + y*nx+z*nxy;
06766                                 if (length >= i || length >= (int)sf.size()) {
06767                                         d[idx1] = 0;
06768                                         continue;
06769                                 } else {
06770                                         amp = boost*snr[length];
06771 //                                      if (amp > 0) amp =sqrtf(amp);
06772 //                                      else amp = 0;
06773                                 }
06774 
06775                                 if (sf[length] == 0) {
06776                                         d[idx1] = 0;
06777                                         continue;
06778                                 }
06779 
06780 //                              size_t idx2 = idx1 + 1;
06781 //                              cout << d[idx1] << " " << sf[length] << endl;
06782                                 d[idx1] /= sf[length];
06783                                 if (d[idx1] < 0) {
06784                                         d[idx1] *= amp;
06785                                 }else {
06786                                         d[idx1] *= -amp;
06787                                 }
06788 //                              d[idx2] = phase;
06789 
06790                         }
06791                 }
06792         }
06793 
06794         image->ap2ri();
06795         if (image->get_ndim() != 1) image->process_inplace("xform.fourierorigin.tocorner");
06796         image->do_ift_inplace();
06797         image->depad();
06798 }


Member Data Documentation

const string CTFSNRWeightProcessor::NAME = "ctf.snr.weight" [static]
 

Definition at line 5921 of file processor.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Tue May 25 17:37:45 2010 for EMAN2 by  doxygen 1.4.4