#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 720 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. 00722 {
00723 if (cmp_name != "dot" && cmp_name != "ccc") throw InvalidParameterException("Resample aligner only works for dot and ccc");
00724
00725 int maxtx = params.set_default("tx", 0);
00726 int maxty = params.set_default("ty", 0);
00727 int r1 = params.set_default("r1",-1);
00728 int r2 = params.set_default("r2",-1);
00729
00730 if(this_img->get_xsize()/2 - 1 - r2 - maxtx <= 0 || (r2 == -1 && maxtx > 0)) throw InvalidParameterException("nx/2 - 1 - r2 - tx must be greater than or = 0");
00731 if(this_img->get_ysize()/2 - 1 - r2 - maxty <= 0 || (r2 == -1 && maxty > 0)) throw InvalidParameterException("ny/2 - 1 - r2 - ty must be greater than or = 0");
00732
00733 float best_peak = -numeric_limits<float>::infinity();
00734 int best_peak_index = 0;
00735 int best_tx = 0;
00736 int best_ty = 0;
00737 int polarxsize = 0;
00738 bool flip = false;
00739
00740 for(int x = -maxtx; x <= maxtx; x++){
00741 for(int y = -maxty; y <= maxty; y++){
00742
00743 EMData * to_polar = to->unwrap(r1,r2,-1,0,0,true);
00744 EMData * this_img_polar = this_img->unwrap(r1,r2,-1,x,y,true);
00745 EMData * cfflip = this_img_polar->calc_ccfx(to_polar, 0, this_img_polar->get_ysize(), false, true);
00746 EMData * cf = this_img_polar->calc_ccfx(to_polar, 0, this_img_polar->get_ysize());
00747
00748 polarxsize = this_img_polar->get_xsize();
00749
00750 //take out the garbage
00751 delete to_polar; to_polar = 0;
00752 delete this_img_polar; this_img_polar = 0;
00753
00754 float *data = cf->get_data();
00755 float peak = 0;
00756 int peak_index = 0;
00757 Util::find_max(data, polarxsize, &peak, &peak_index);
00758 delete cf; cf = 0;
00759
00760 if(peak > best_peak) {
00761 best_peak = peak;
00762 best_peak_index = peak_index;
00763 best_tx = x;
00764 best_ty = y;
00765 flip = false;
00766 }
00767
00768 data = cfflip->get_data();
00769 Util::find_max(data, polarxsize, &peak, &peak_index);
00770 delete cfflip; cfflip = 0;
00771
00772 if(peak > best_peak) {
00773 best_peak = peak;
00774 best_peak_index = peak_index;
00775 best_tx = x;
00776 best_ty = y;
00777 flip = true;
00778 }
00779 }
00780 }
00781
00782 float rot_angle = (float) (best_peak_index * 360.0f / polarxsize);
00783
00784 //return the result
00785 Transform tmp(Dict("type","2d","alpha",rot_angle,"tx",best_tx,"ty",best_ty));
00786 EMData* rotimg=this_img->process("xform",Dict("transform",(Transform*)&tmp));
00787 rotimg->set_attr("xform.align2d",&tmp);
00788 if(flip == true) {
00789 rotimg->process_inplace("xform.flip",Dict("axis", "x"));
00790 }
00791
00792 return rotimg;
00793
00794 }
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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 x 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