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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

ProcessorNEW ()

Static Public Attributes

const string NAME = "ctf.snr.weight"

Detailed Description

Author:
David Woolford
Date:
June 15th 2009

Definition at line 5929 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 5939 of file processor.h.

05940                         {
05941                                 return "Weight the amplitudes of an image based on radial noise and snr curves ";
05942                         }

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 5934 of file processor.h.

05935                         {
05936                                 return NAME;
05937                         }

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 5949 of file processor.h.

References EMAN::TypeDict::put().

05950                         {
05951                                 TypeDict d;
05952                                 d.put("noise", EMObject::FLOATARRAY, "The noise profile, squared amplitude. As in, what is the EMAN2CTF.background attribute");
05953                                 d.put("snr", EMObject::FLOATARRAY, "Squared amplitude divided by squared noise amplitude. As in, what is the EMAN2CTF.snr attribute");
05954                                 d.put("boost", EMObject::FLOAT, "Multiplicative signal boost");
05955                                 return d;
05956                         }

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

Definition at line 5944 of file processor.h.

05945                         {
05946                                 return new CTFSNRWeightProcessor();
05947                         }

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 6894 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::Dict::end(), EMAN::EMData::get_data(), EMAN::EMData::get_ndim(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), EMAN::Dict::has_key(), InvalidParameterException, EMAN::EMData::is_complex(), EMAN::length(), nx, EMAN::EMData::process_inplace(), EMAN::EMData::ri2ap(), EMAN::EMData::ri2inten(), EMAN::Dict::set_default(), sqrt(), x, and y.

06894                                                          {
06895         if (params.has_key("noise")==false) throw InvalidParameterException("You must supply the noise argument");
06896         if (params.has_key("snr")==false) throw InvalidParameterException("You must supply the snr argument");
06897 
06898         float boost = params.set_default("boost",1.0f);
06899 
06900         if (!image->is_complex()) {
06901                 image->do_fft_inplace();
06902         }
06903         EMData* cpy = image->copy();
06904         cpy->ri2inten();
06905         vector<float> sf = cpy->calc_radial_dist(cpy->get_ysize()/2,0.0,1.0,1);
06906         transform(sf.begin(),sf.end(),sf.begin(),sqrtf);
06907         delete cpy;
06908 
06909         image->ri2ap();
06910 
06911         vector<float> noise = params["noise"];
06912         vector<float> snr = params["snr"];
06913 
06914 //      copy(snr.begin(), snr.end(), ostream_iterator<float>(cout, "\n"));
06915 //      copy(noise.begin(), noise.end(), ostream_iterator<float>(cout, "\n"));
06916 
06917         for(vector<float>::iterator it = noise.begin(); it != noise.end(); ++it){
06918                 if ((*it) == 0) *it = 1;
06919         }
06920         for(vector<float>::iterator it = snr.begin(); it != snr.end(); ++it){
06921                 if ((*it) < 0) *it = 0;
06922         }
06923         // Subtract the mean from the data and store it in data_mm
06924         transform(snr.begin(),snr.end(),noise.begin(),snr.begin(),std::multiplies<float>());
06925         transform(snr.begin(),snr.end(),snr.begin(),sqrtf);
06926 //      copy(snr.begin(), snr.end(), ostream_iterator<float>(cout, "\n"));
06927 //      copy(noise.begin(), noise.end(), ostream_iterator<float>(cout, "\n"));
06928 
06929         int i = static_cast<int>(snr.size());
06930 
06931         float * d = image->get_data();
06932         int nx = image->get_xsize();
06933 //      int ny = image->get_ysize();
06934         int nxy = image->get_ysize()*nx;
06935         int nzon2 = image->get_zsize()/2;
06936         int nyon2 = image->get_ysize()/2;
06937         float rx, ry, rz, amp;
06938         int length;
06939         int twox;
06940         image->process_inplace("xform.fourierorigin.tocenter");
06941         for (int z = 0; z< image->get_zsize(); ++z) {
06942                 for (int y = 0; y < image->get_ysize(); ++y) {
06943                         for (int x = 0; x < image->get_xsize()/2; ++x) {
06944                                 rx = (float)x;
06945                                 ry = (float)nyon2 - (float)y;
06946                                 rz = (float)nzon2 - (float)z;
06947                                 length = static_cast<int>(sqrt(rx*rx + ry*ry + rz*rz));
06948 
06949                                 twox = 2*x;
06950                                 size_t idx1 = twox + y*nx+(size_t)z*nxy;
06951                                 if (length >= i || length >= (int)sf.size()) {
06952                                         d[idx1] = 0;
06953                                         continue;
06954                                 } else {
06955                                         amp = boost*snr[length];
06956 //                                      if (amp > 0) amp =sqrtf(amp);
06957 //                                      else amp = 0;
06958                                 }
06959 
06960                                 if (sf[length] == 0) {
06961                                         d[idx1] = 0;
06962                                         continue;
06963                                 }
06964 
06965 //                              size_t idx2 = idx1 + 1;
06966 //                              cout << d[idx1] << " " << sf[length] << endl;
06967                                 d[idx1] /= sf[length];
06968                                 if (d[idx1] < 0) {
06969                                         d[idx1] *= amp;
06970                                 }else {
06971                                         d[idx1] *= -amp;
06972                                 }
06973 //                              d[idx2] = phase;
06974 
06975                         }
06976                 }
06977         }
06978 
06979         image->ap2ri();
06980         if (image->get_ndim() != 1) image->process_inplace("xform.fourierorigin.tocorner");
06981         image->do_ift_inplace();
06982         image->depad();
06983 }


Member Data Documentation

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

Definition at line 193 of file processor.cpp.


The documentation for this class was generated from the following files:
Generated on Thu Nov 17 12:46:35 2011 for EMAN2 by  doxygen 1.3.9.1