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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 5976 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 5986 of file processor.h.

05987                         {
05988                                 return "Weight the amplitudes of an image based on radial noise and snr curves ";
05989                         }

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 5981 of file processor.h.

05982                         {
05983                                 return NAME;
05984                         }

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 5996 of file processor.h.

References EMAN::TypeDict::put().

05997                         {
05998                                 TypeDict d;
05999                                 d.put("noise", EMObject::FLOATARRAY, "The noise profile, squared amplitude. As in, what is the EMAN2CTF.background attribute");
06000                                 d.put("snr", EMObject::FLOATARRAY, "Squared amplitude divided by squared noise amplitude. As in, what is the EMAN2CTF.snr attribute");
06001                                 d.put("boost", EMObject::FLOAT, "Multiplicative signal boost");
06002                                 return d;
06003                         }

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

Definition at line 5991 of file processor.h.

05992                         {
05993                                 return new CTFSNRWeightProcessor();
05994                         }

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 6981 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.

06981                                                          {
06982         if (params.has_key("noise")==false) throw InvalidParameterException("You must supply the noise argument");
06983         if (params.has_key("snr")==false) throw InvalidParameterException("You must supply the snr argument");
06984 
06985         float boost = params.set_default("boost",1.0f);
06986 
06987         if (!image->is_complex()) {
06988                 image->do_fft_inplace();
06989         }
06990         EMData* cpy = image->copy();
06991         cpy->ri2inten();
06992         vector<float> sf = cpy->calc_radial_dist(cpy->get_ysize()/2,0.0,1.0,1);
06993         transform(sf.begin(),sf.end(),sf.begin(),sqrtf);
06994         delete cpy;
06995 
06996         image->ri2ap();
06997 
06998         vector<float> noise = params["noise"];
06999         vector<float> snr = params["snr"];
07000 
07001 //      copy(snr.begin(), snr.end(), ostream_iterator<float>(cout, "\n"));
07002 //      copy(noise.begin(), noise.end(), ostream_iterator<float>(cout, "\n"));
07003 
07004         for(vector<float>::iterator it = noise.begin(); it != noise.end(); ++it){
07005                 if ((*it) == 0) *it = 1;
07006         }
07007         for(vector<float>::iterator it = snr.begin(); it != snr.end(); ++it){
07008                 if ((*it) < 0) *it = 0;
07009         }
07010         // Subtract the mean from the data and store it in data_mm
07011         transform(snr.begin(),snr.end(),noise.begin(),snr.begin(),std::multiplies<float>());
07012         transform(snr.begin(),snr.end(),snr.begin(),sqrtf);
07013 //      copy(snr.begin(), snr.end(), ostream_iterator<float>(cout, "\n"));
07014 //      copy(noise.begin(), noise.end(), ostream_iterator<float>(cout, "\n"));
07015 
07016         int i = static_cast<int>(snr.size());
07017 
07018         float * d = image->get_data();
07019         int nx = image->get_xsize();
07020 //      int ny = image->get_ysize();
07021         int nxy = image->get_ysize()*nx;
07022         int nzon2 = image->get_zsize()/2;
07023         int nyon2 = image->get_ysize()/2;
07024         float rx, ry, rz, amp;
07025         int length;
07026         int twox;
07027         image->process_inplace("xform.fourierorigin.tocenter");
07028         for (int z = 0; z< image->get_zsize(); ++z) {
07029                 for (int y = 0; y < image->get_ysize(); ++y) {
07030                         for (int x = 0; x < image->get_xsize()/2; ++x) {
07031                                 rx = (float)x;
07032                                 ry = (float)nyon2 - (float)y;
07033                                 rz = (float)nzon2 - (float)z;
07034                                 length = static_cast<int>(sqrt(rx*rx + ry*ry + rz*rz));
07035 
07036                                 twox = 2*x;
07037                                 size_t idx1 = twox + y*nx+(size_t)z*nxy;
07038                                 if (length >= i || length >= (int)sf.size()) {
07039                                         d[idx1] = 0;
07040                                         continue;
07041                                 } else {
07042                                         amp = boost*snr[length];
07043 //                                      if (amp > 0) amp =sqrtf(amp);
07044 //                                      else amp = 0;
07045                                 }
07046 
07047                                 if (sf[length] == 0) {
07048                                         d[idx1] = 0;
07049                                         continue;
07050                                 }
07051 
07052 //                              size_t idx2 = idx1 + 1;
07053 //                              cout << d[idx1] << " " << sf[length] << endl;
07054                                 d[idx1] /= sf[length];
07055                                 if (d[idx1] < 0) {
07056                                         d[idx1] *= amp;
07057                                 }else {
07058                                         d[idx1] *= -amp;
07059                                 }
07060 //                              d[idx2] = phase;
07061 
07062                         }
07063                 }
07064         }
07065 
07066         image->ap2ri();
07067         if (image->get_ndim() != 1) image->process_inplace("xform.fourierorigin.tocorner");
07068         image->do_ift_inplace();
07069         image->depad();
07070 }


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 Fri Aug 10 16:38:09 2012 for EMAN2 by  doxygen 1.3.9.1