#include <aligner.h>
Inheritance diagram for EMAN::RotateTranslateFlipAlignerPawel:
Public Member Functions | |
virtual EMData * | align (EMData *this_img, EMData *to_img, const string &cmp_name="dot", const Dict &cmp_params=Dict()) const |
To align 'this_img' with another image passed in through its parameters. | |
virtual EMData * | align (EMData *this_img, EMData *to_img) const |
virtual string | get_name () const |
Get the Aligner's name. | |
virtual string | get_desc () const |
virtual TypeDict | get_param_types () const |
Static Public Member Functions | |
Aligner * | NEW () |
Static Public Attributes | |
const string | NAME = "rotate_translate_flip_resample" |
translation if found by varing to origin using for polar coordinate resampling in real space
tx | maximum transltion in x direction, must by less than (n/2 - 1 - r2) | |
tu | maximum transltion in y direction, must by less than (n/2 - 1 - r2) | |
r1 | inner ring | |
r2 | outer ring |
Definition at line 1038 of file aligner.h.
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Implements EMAN::Aligner. Definition at line 1044 of file aligner.h. References align(). 01045 { 01046 return align(this_img, to_img, "sqeuclidean", Dict()); 01047 }
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To align 'this_img' with another image passed in through its parameters. The alignment uses a user-given comparison method to compare the two images. If none is given, a default one is used.
Implements EMAN::Aligner. Definition at line 931 of file aligner.cpp. References EMAN::EMData::calc_ccfx(), data, EMAN::Util::find_max(), EMAN::EMData::get_data(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), InvalidParameterException, EMAN::EMData::process(), EMAN::EMData::process_inplace(), EMAN::EMData::set_attr(), EMAN::Dict::set_default(), EMAN::EMData::unwrap(), x, and y. 00933 { 00934 if (cmp_name != "dot" && cmp_name != "ccc") throw InvalidParameterException("Resample aligner only works for dot and ccc"); 00935 00936 int maxtx = params.set_default("tx", 0); 00937 int maxty = params.set_default("ty", 0); 00938 int r1 = params.set_default("r1",-1); 00939 int r2 = params.set_default("r2",-1); 00940 00941 if(this_img->get_xsize()/2 - 1 - r2 - maxtx <= 0 || (r2 == -1 && maxtx > 0)){ 00942 cout << "\nRunTimeError: nx/2 - 1 - r2 - tx must be greater than or = 0\n" << endl; // For some reason the expection message is not being print, stupid C++ 00943 throw InvalidParameterException("nx/2 - 1 - r2 - tx must be greater than or = 0"); 00944 } 00945 if(this_img->get_ysize()/2 - 1 - r2 - maxty <= 0 || (r2 == -1 && maxty > 0)){ 00946 cout << "\nRunTimeError:ny/2 - 1 - r2 - ty must be greater than or = 0\n" << endl; // For some reason the expection message is not being print, stupid C++ 00947 throw InvalidParameterException("ny/2 - 1 - r2 - ty must be greater than or = 0"); 00948 } 00949 00950 // float best_peak = -numeric_limits<float>::infinity(); 00951 float best_peak = -1.0e37; 00952 int best_peak_index = 0; 00953 int best_tx = 0; 00954 int best_ty = 0; 00955 int polarxsize = 0; 00956 bool flip = false; 00957 00958 for(int x = -maxtx; x <= maxtx; x++){ 00959 for(int y = -maxty; y <= maxty; y++){ 00960 00961 EMData * to_polar = to->unwrap(r1,r2,-1,0,0,true); 00962 EMData * this_img_polar = this_img->unwrap(r1,r2,-1,x,y,true); 00963 EMData * cfflip = this_img_polar->calc_ccfx(to_polar, 0, this_img_polar->get_ysize(), false, true); 00964 EMData * cf = this_img_polar->calc_ccfx(to_polar, 0, this_img_polar->get_ysize()); 00965 00966 polarxsize = this_img_polar->get_xsize(); 00967 00968 //take out the garbage 00969 delete to_polar; to_polar = 0; 00970 delete this_img_polar; this_img_polar = 0; 00971 00972 float *data = cf->get_data(); 00973 float peak = 0; 00974 int peak_index = 0; 00975 Util::find_max(data, polarxsize, &peak, &peak_index); 00976 delete cf; cf = 0; 00977 00978 if(peak > best_peak) { 00979 best_peak = peak; 00980 best_peak_index = peak_index; 00981 best_tx = x; 00982 best_ty = y; 00983 flip = false; 00984 } 00985 00986 data = cfflip->get_data(); 00987 Util::find_max(data, polarxsize, &peak, &peak_index); 00988 delete cfflip; cfflip = 0; 00989 00990 if(peak > best_peak) { 00991 best_peak = peak; 00992 best_peak_index = peak_index; 00993 best_tx = x; 00994 best_ty = y; 00995 flip = true; 00996 } 00997 } 00998 } 00999 01000 float rot_angle = (float) (best_peak_index * 360.0f / polarxsize); 01001 01002 //return the result 01003 Transform tmptt(Dict("type","2d","alpha",0,"tx",-best_tx,"ty",-best_ty)); 01004 Transform tmprot(Dict("type","2d","alpha",rot_angle,"tx",0,"ty",0)); 01005 Transform total = tmprot*tmptt; 01006 EMData * rotimg=this_img->process("xform",Dict("transform",(Transform*)&total)); 01007 rotimg->set_attr("xform.align2d",&total); 01008 if(flip == true) { 01009 rotimg->process_inplace("xform.flip",Dict("axis", "x")); 01010 } 01011 01012 return rotimg; 01013 01014 }
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Implements EMAN::Aligner. Definition at line 1054 of file aligner.h. 01055 { 01056 return "Performs rotational alignment, translation align, and flip by resampling to polar coordinates in real space."; 01057 }
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Get the Aligner's name. Each Aligner is identified by a unique name.
Implements EMAN::Aligner. Definition at line 1049 of file aligner.h. 01050 {
01051 return NAME;
01052 }
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Implements EMAN::Aligner. Definition at line 1064 of file aligner.h. References EMAN::TypeDict::put(). 01065 { 01066 TypeDict d; 01067 //d.put("usedot", EMObject::INT); 01068 d.put("tx", EMObject::INT, "Maximum x translation in pixels, Default = 0"); 01069 d.put("ty", EMObject::INT, "Maximum y translation in pixels, Default = 0"); 01070 d.put("r1", EMObject::INT, "Inner ring, pixels"); 01071 d.put("r2", EMObject::INT, "Outer ring, pixels"); 01072 return d; 01073 }
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Definition at line 1059 of file aligner.h. 01060 { 01061 return new RotateTranslateFlipAlignerPawel(); 01062 }
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Definition at line 75 of file aligner.cpp. |