#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 5892 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 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.
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.
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.
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(), 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.
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 }
const string CTFSNRWeightProcessor::NAME = "ctf.snr.weight" [static] |