#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 | |
| Processor * | NEW () |
Static Public Attributes | |
| const string | NAME = "ctf.snr.weight" |
Definition at line 5898 of file processor.h.
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Get the descrition of this specific processor. This function must be overwritten by a subclass.
Implements EMAN::Processor. Definition at line 5908 of file processor.h. 05909 {
05910 return "Weight the amplitudes of an image based on radial noise and snr curves ";
05911 }
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Get the processor's name. Each processor is identified by a unique name.
Implements EMAN::Processor. Definition at line 5903 of file processor.h. 05904 {
05905 return NAME;
05906 }
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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 5918 of file processor.h. References EMAN::TypeDict::put(). 05919 {
05920 TypeDict d;
05921 d.put("noise", EMObject::FLOATARRAY, "The noise profile, squared amplitude. As in, what is the EMAN2CTF.background attribute");
05922 d.put("snr", EMObject::FLOATARRAY, "Squared amplitude divided by squared noise amplitude. As in, what is the EMAN2CTF.snr attribute");
05923 d.put("boost", EMObject::FLOAT, "Multiplicative signal boost");
05924 return d;
05925 }
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Definition at line 5913 of file processor.h. 05914 {
05915 return new CTFSNRWeightProcessor();
05916 }
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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.
Implements EMAN::Processor. Definition at line 6808 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. 06808 {
06809 if (params.has_key("noise")==false) throw InvalidParameterException("You must supply the noise argument");
06810 if (params.has_key("snr")==false) throw InvalidParameterException("You must supply the snr argument");
06811
06812 float boost = params.set_default("boost",1.0f);
06813
06814 if (!image->is_complex()) {
06815 image->do_fft_inplace();
06816 }
06817 EMData* cpy = image->copy();
06818 cpy->ri2inten();
06819 vector<float> sf = cpy->calc_radial_dist(cpy->get_ysize()/2,0.0,1.0,1);
06820 transform(sf.begin(),sf.end(),sf.begin(),sqrtf);
06821 delete cpy;
06822
06823 image->ri2ap();
06824
06825 vector<float> noise = params["noise"];
06826 vector<float> snr = params["snr"];
06827
06828 // copy(snr.begin(), snr.end(), ostream_iterator<float>(cout, "\n"));
06829 // copy(noise.begin(), noise.end(), ostream_iterator<float>(cout, "\n"));
06830
06831 for(vector<float>::iterator it = noise.begin(); it != noise.end(); ++it){
06832 if ((*it) == 0) *it = 1;
06833 }
06834 for(vector<float>::iterator it = snr.begin(); it != snr.end(); ++it){
06835 if ((*it) < 0) *it = 0;
06836 }
06837 // Subtract the mean from the data and store it in data_mm
06838 transform(snr.begin(),snr.end(),noise.begin(),snr.begin(),std::multiplies<float>());
06839 transform(snr.begin(),snr.end(),snr.begin(),sqrtf);
06840 // copy(snr.begin(), snr.end(), ostream_iterator<float>(cout, "\n"));
06841 // copy(noise.begin(), noise.end(), ostream_iterator<float>(cout, "\n"));
06842
06843 int i = static_cast<int>(snr.size());
06844
06845 float * d = image->get_data();
06846 int nx = image->get_xsize();
06847 // int ny = image->get_ysize();
06848 int nxy = image->get_ysize()*nx;
06849 int nzon2 = image->get_zsize()/2;
06850 int nyon2 = image->get_ysize()/2;
06851 float rx, ry, rz, amp;
06852 int length;
06853 int twox;
06854 image->process_inplace("xform.fourierorigin.tocenter");
06855 for (int z = 0; z< image->get_zsize(); ++z) {
06856 for (int y = 0; y < image->get_ysize(); ++y) {
06857 for (int x = 0; x < image->get_xsize()/2; ++x) {
06858 rx = (float)x;
06859 ry = (float)nyon2 - (float)y;
06860 rz = (float)nzon2 - (float)z;
06861 length = static_cast<int>(sqrt(rx*rx + ry*ry + rz*rz));
06862
06863 twox = 2*x;
06864 size_t idx1 = twox + y*nx+(size_t)z*nxy;
06865 if (length >= i || length >= (int)sf.size()) {
06866 d[idx1] = 0;
06867 continue;
06868 } else {
06869 amp = boost*snr[length];
06870 // if (amp > 0) amp =sqrtf(amp);
06871 // else amp = 0;
06872 }
06873
06874 if (sf[length] == 0) {
06875 d[idx1] = 0;
06876 continue;
06877 }
06878
06879 // size_t idx2 = idx1 + 1;
06880 // cout << d[idx1] << " " << sf[length] << endl;
06881 d[idx1] /= sf[length];
06882 if (d[idx1] < 0) {
06883 d[idx1] *= amp;
06884 }else {
06885 d[idx1] *= -amp;
06886 }
06887 // d[idx2] = phase;
06888
06889 }
06890 }
06891 }
06892
06893 image->ap2ri();
06894 if (image->get_ndim() != 1) image->process_inplace("xform.fourierorigin.tocorner");
06895 image->do_ift_inplace();
06896 image->depad();
06897 }
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Definition at line 198 of file processor.cpp. |
1.3.9.1