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 5974 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 5984 of file processor.h.

05985                         {
05986                                 return "Weight the amplitudes of an image based on radial noise and snr curves ";
05987                         }

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 5979 of file processor.h.

References NAME.

05980                         {
05981                                 return NAME;
05982                         }

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 5994 of file processor.h.

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

05995                         {
05996                                 TypeDict d;
05997                                 d.put("noise", EMObject::FLOATARRAY, "The noise profile, squared amplitude. As in, what is the EMAN2CTF.background attribute");
05998                                 d.put("snr", EMObject::FLOATARRAY, "Squared amplitude divided by squared noise amplitude. As in, what is the EMAN2CTF.snr attribute");
05999                                 d.put("boost", EMObject::FLOAT, "Multiplicative signal boost");
06000                                 return d;
06001                         }

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

Definition at line 5989 of file processor.h.

05990                         {
05991                                 return new CTFSNRWeightProcessor();
05992                         }

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 6966 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(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), 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.

06966                                                          {
06967         if (params.has_key("noise")==false) throw InvalidParameterException("You must supply the noise argument");
06968         if (params.has_key("snr")==false) throw InvalidParameterException("You must supply the snr argument");
06969 
06970         float boost = params.set_default("boost",1.0f);
06971 
06972         if (!image->is_complex()) {
06973                 image->do_fft_inplace();
06974         }
06975         EMData* cpy = image->copy();
06976         cpy->ri2inten();
06977         vector<float> sf = cpy->calc_radial_dist(cpy->get_ysize()/2,0.0,1.0,1);
06978         transform(sf.begin(),sf.end(),sf.begin(),sqrtf);
06979         delete cpy;
06980 
06981         image->ri2ap();
06982 
06983         vector<float> noise = params["noise"];
06984         vector<float> snr = params["snr"];
06985 
06986 //      copy(snr.begin(), snr.end(), ostream_iterator<float>(cout, "\n"));
06987 //      copy(noise.begin(), noise.end(), ostream_iterator<float>(cout, "\n"));
06988 
06989         for(vector<float>::iterator it = noise.begin(); it != noise.end(); ++it){
06990                 if ((*it) == 0) *it = 1;
06991         }
06992         for(vector<float>::iterator it = snr.begin(); it != snr.end(); ++it){
06993                 if ((*it) < 0) *it = 0;
06994         }
06995         // Subtract the mean from the data and store it in data_mm
06996         transform(snr.begin(),snr.end(),noise.begin(),snr.begin(),std::multiplies<float>());
06997         transform(snr.begin(),snr.end(),snr.begin(),sqrtf);
06998 //      copy(snr.begin(), snr.end(), ostream_iterator<float>(cout, "\n"));
06999 //      copy(noise.begin(), noise.end(), ostream_iterator<float>(cout, "\n"));
07000 
07001         int i = static_cast<int>(snr.size());
07002 
07003         float * d = image->get_data();
07004         int nx = image->get_xsize();
07005 //      int ny = image->get_ysize();
07006         int nxy = image->get_ysize()*nx;
07007         int nzon2 = image->get_zsize()/2;
07008         int nyon2 = image->get_ysize()/2;
07009         float rx, ry, rz, amp;
07010         int length;
07011         int twox;
07012         image->process_inplace("xform.fourierorigin.tocenter");
07013         for (int z = 0; z< image->get_zsize(); ++z) {
07014                 for (int y = 0; y < image->get_ysize(); ++y) {
07015                         for (int x = 0; x < image->get_xsize()/2; ++x) {
07016                                 rx = (float)x;
07017                                 ry = (float)nyon2 - (float)y;
07018                                 rz = (float)nzon2 - (float)z;
07019                                 length = static_cast<int>(sqrt(rx*rx + ry*ry + rz*rz));
07020 
07021                                 twox = 2*x;
07022                                 size_t idx1 = twox + y*nx+(size_t)z*nxy;
07023                                 if (length >= i || length >= (int)sf.size()) {
07024                                         d[idx1] = 0;
07025                                         continue;
07026                                 } else {
07027                                         amp = boost*snr[length];
07028 //                                      if (amp > 0) amp =sqrtf(amp);
07029 //                                      else amp = 0;
07030                                 }
07031 
07032                                 if (sf[length] == 0) {
07033                                         d[idx1] = 0;
07034                                         continue;
07035                                 }
07036 
07037 //                              size_t idx2 = idx1 + 1;
07038 //                              cout << d[idx1] << " " << sf[length] << endl;
07039                                 d[idx1] /= sf[length];
07040                                 if (d[idx1] < 0) {
07041                                         d[idx1] *= amp;
07042                                 }else {
07043                                         d[idx1] *= -amp;
07044                                 }
07045 //                              d[idx2] = phase;
07046 
07047                         }
07048                 }
07049         }
07050 
07051         image->ap2ri();
07052         if (image->get_ndim() != 1) image->process_inplace("xform.fourierorigin.tocorner");
07053         image->do_ift_inplace();
07054         image->depad();
07055 }


Member Data Documentation

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

Definition at line 6003 of file processor.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Thu May 3 10:10:49 2012 for EMAN2 by  doxygen 1.4.7