#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 | |
static Aligner * | NEW () |
Static Public Attributes | |
static 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.
virtual EMData* EMAN::RotateTranslateFlipAlignerPawel::align | ( | EMData * | this_img, | |
EMData * | to_img | |||
) | const [inline, virtual] |
Implements EMAN::Aligner.
Definition at line 732 of file aligner.h.
References align().
00733 { 00734 return align(this_img, to_img, "sqeuclidean", Dict()); 00735 }
EMData * RotateTranslateFlipAlignerPawel::align | ( | EMData * | this_img, | |
EMData * | to_img, | |||
const string & | cmp_name = "dot" , |
|||
const Dict & | cmp_params = Dict() | |||
) | const [virtual] |
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.
this_img | The image to be compared. | |
to_img | 'this_img" is aligned with 'to_img'. | |
cmp_name | The comparison method to compare the two images. | |
cmp_params | The parameter dictionary for comparison method. |
Implements EMAN::Aligner.
Definition at line 721 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::Aligner::params, EMAN::EMData::process(), EMAN::EMData::process_inplace(), EMAN::EMData::set_attr(), EMAN::Dict::set_default(), EMAN::EMData::unwrap(), x, and y.
Referenced by align().
00723 { 00724 if (cmp_name != "dot" && cmp_name != "ccc") throw InvalidParameterException("Resample aligner only works for dot and ccc"); 00725 00726 int maxtx = params.set_default("tx", 0); 00727 int maxty = params.set_default("ty", 0); 00728 int r1 = params.set_default("r1",-1); 00729 int r2 = params.set_default("r2",-1); 00730 00731 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"); 00732 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"); 00733 00734 float best_peak = -numeric_limits<float>::infinity(); 00735 int best_peak_index = 0; 00736 int best_tx = 0; 00737 int best_ty = 0; 00738 int polarxsize = 0; 00739 bool flip = false; 00740 00741 for(int x = -maxtx; x <= maxtx; x++){ 00742 for(int y = -maxty; y <= maxty; y++){ 00743 00744 EMData * to_polar = to->unwrap(r1,r2,-1,0,0,true); 00745 EMData * this_img_polar = this_img->unwrap(r1,r2,-1,x,y,true); 00746 EMData * cfflip = this_img_polar->calc_ccfx(to_polar, 0, this_img_polar->get_ysize(), false, true); 00747 EMData * cf = this_img_polar->calc_ccfx(to_polar, 0, this_img_polar->get_ysize()); 00748 00749 polarxsize = this_img_polar->get_xsize(); 00750 00751 //take out the garbage 00752 delete to_polar; to_polar = 0; 00753 delete this_img_polar; this_img_polar = 0; 00754 00755 float *data = cf->get_data(); 00756 float peak = 0; 00757 int peak_index = 0; 00758 Util::find_max(data, polarxsize, &peak, &peak_index); 00759 delete cf; cf = 0; 00760 00761 if(peak > best_peak) { 00762 best_peak = peak; 00763 best_peak_index = peak_index; 00764 best_tx = x; 00765 best_ty = y; 00766 flip = false; 00767 } 00768 00769 data = cfflip->get_data(); 00770 Util::find_max(data, polarxsize, &peak, &peak_index); 00771 delete cfflip; cfflip = 0; 00772 00773 if(peak > best_peak) { 00774 best_peak = peak; 00775 best_peak_index = peak_index; 00776 best_tx = x; 00777 best_ty = y; 00778 flip = true; 00779 } 00780 } 00781 } 00782 00783 float rot_angle = (float) (best_peak_index * 360.0f / polarxsize); 00784 00785 //return the result 00786 Transform tmp(Dict("type","2d","alpha",rot_angle,"tx",best_tx,"ty",best_ty)); 00787 EMData* rotimg=this_img->process("xform",Dict("transform",(Transform*)&tmp)); 00788 rotimg->set_attr("xform.align2d",&tmp); 00789 if(flip == true) { 00790 rotimg->process_inplace("xform.flip",Dict("axis", "x")); 00791 } 00792 00793 return rotimg; 00794 00795 }
virtual string EMAN::RotateTranslateFlipAlignerPawel::get_desc | ( | ) | const [inline, virtual] |
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 }
virtual string EMAN::RotateTranslateFlipAlignerPawel::get_name | ( | ) | const [inline, virtual] |
virtual TypeDict EMAN::RotateTranslateFlipAlignerPawel::get_param_types | ( | ) | const [inline, virtual] |
Implements EMAN::Aligner.
Definition at line 752 of file aligner.h.
References EMAN::EMObject::INT, and 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 }
static Aligner* EMAN::RotateTranslateFlipAlignerPawel::NEW | ( | ) | [inline, static] |
const string RotateTranslateFlipAlignerPawel::NAME = "rotate_translate_flip_resample" [static] |