#include <processor.h>
Inheritance diagram for EMAN::CTFSNRWeightProcessor:
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 Processor * | NEW () |
Static Public Attributes | |
static const string | NAME = "ctf.snr.weight" |
Definition at line 5976 of file processor.h.
virtual string EMAN::CTFSNRWeightProcessor::get_desc | ( | ) | const [inline, virtual] |
Get the descrition of this specific processor.
This function must be overwritten by a subclass.
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.
Implements EMAN::Processor.
Definition at line 5981 of file processor.h.
References NAME.
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.
Reimplemented from EMAN::Processor.
Definition at line 5996 of file processor.h.
References EMAN::EMObject::FLOAT, EMAN::EMObject::FLOATARRAY, and 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 }
static 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.
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::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.
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 }
const string CTFSNRWeightProcessor::NAME = "ctf.snr.weight" [static] |