#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 726 of file aligner.h.
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Implements EMAN::Aligner. Definition at line 732 of file aligner.h. References align(). 00733 {
00734 return align(this_img, to_img, "sqeuclidean", Dict());
00735 }
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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 724 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. 00726 {
00727 if (cmp_name != "dot" && cmp_name != "ccc") throw InvalidParameterException("Resample aligner only works for dot and ccc");
00728
00729 int maxtx = params.set_default("tx", 0);
00730 int maxty = params.set_default("ty", 0);
00731 int r1 = params.set_default("r1",-1);
00732 int r2 = params.set_default("r2",-1);
00733
00734 if(this_img->get_xsize()/2 - 1 - r2 - maxtx <= 0 || (r2 == -1 && maxtx > 0)){
00735 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++
00736 throw InvalidParameterException("nx/2 - 1 - r2 - tx must be greater than or = 0");
00737 }
00738 if(this_img->get_ysize()/2 - 1 - r2 - maxty <= 0 || (r2 == -1 && maxty > 0)){
00739 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++
00740 throw InvalidParameterException("ny/2 - 1 - r2 - ty must be greater than or = 0");
00741 }
00742
00743 float best_peak = -numeric_limits<float>::infinity();
00744 int best_peak_index = 0;
00745 int best_tx = 0;
00746 int best_ty = 0;
00747 int polarxsize = 0;
00748 bool flip = false;
00749
00750 for(int x = -maxtx; x <= maxtx; x++){
00751 for(int y = -maxty; y <= maxty; y++){
00752
00753 EMData * to_polar = to->unwrap(r1,r2,-1,0,0,true);
00754 EMData * this_img_polar = this_img->unwrap(r1,r2,-1,x,y,true);
00755 EMData * cfflip = this_img_polar->calc_ccfx(to_polar, 0, this_img_polar->get_ysize(), false, true);
00756 EMData * cf = this_img_polar->calc_ccfx(to_polar, 0, this_img_polar->get_ysize());
00757
00758 polarxsize = this_img_polar->get_xsize();
00759
00760 //take out the garbage
00761 delete to_polar; to_polar = 0;
00762 delete this_img_polar; this_img_polar = 0;
00763
00764 float *data = cf->get_data();
00765 float peak = 0;
00766 int peak_index = 0;
00767 Util::find_max(data, polarxsize, &peak, &peak_index);
00768 delete cf; cf = 0;
00769
00770 if(peak > best_peak) {
00771 best_peak = peak;
00772 best_peak_index = peak_index;
00773 best_tx = x;
00774 best_ty = y;
00775 flip = false;
00776 }
00777
00778 data = cfflip->get_data();
00779 Util::find_max(data, polarxsize, &peak, &peak_index);
00780 delete cfflip; cfflip = 0;
00781
00782 if(peak > best_peak) {
00783 best_peak = peak;
00784 best_peak_index = peak_index;
00785 best_tx = x;
00786 best_ty = y;
00787 flip = true;
00788 }
00789 }
00790 }
00791
00792 float rot_angle = (float) (best_peak_index * 360.0f / polarxsize);
00793
00794 //return the result
00795 Transform tmptt(Dict("type","2d","alpha",0,"tx",-best_tx,"ty",-best_ty));
00796 Transform tmprot(Dict("type","2d","alpha",rot_angle,"tx",0,"ty",0));
00797 Transform total = tmprot*tmptt;
00798 EMData* rotimg=this_img->process("xform",Dict("transform",(Transform*)&total));
00799 rotimg->set_attr("xform.align2d",&total);
00800 if(flip == true) {
00801 rotimg->process_inplace("xform.flip",Dict("axis", "x"));
00802 }
00803
00804 return rotimg;
00805
00806 }
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Implements EMAN::Aligner. Definition at line 742 of file aligner.h. 00743 {
00744 return "Performs rotational alignment, translation align, and flip by resampling to polar coordinates in real space.";
00745 }
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Get the Aligner's name. Each Aligner is identified by a unique name.
Implements EMAN::Aligner. Definition at line 737 of file aligner.h. 00738 {
00739 return NAME;
00740 }
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Implements EMAN::Aligner. Definition at line 752 of file aligner.h. References EMAN::TypeDict::put(). 00753 {
00754 TypeDict d;
00755 //d.put("usedot", EMObject::INT);
00756 d.put("tx", EMObject::INT, "Maximum x translation in pixels, Default = 0");
00757 d.put("ty", EMObject::INT, "Maximum y translation in pixels, Default = 0");
00758 d.put("r1", EMObject::INT, "Inner ring, pixels");
00759 d.put("r2", EMObject::INT, "Outer ring, pixels");
00760 return d;
00761 }
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Definition at line 747 of file aligner.h. 00748 {
00749 return new RotateTranslateFlipAlignerPawel();
00750 }
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Definition at line 70 of file aligner.cpp. |
1.3.9.1