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EMAN::RTFExhaustiveAligner Class Reference

rotational, translational and flip alignment using real-space methods. More...

#include <aligner.h>

Inheritance diagram for EMAN::RTFExhaustiveAligner:

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List of all members.

Public Member Functions

virtual EMDataalign (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 EMDataalign (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

AlignerNEW ()

Static Public Attributes

const string NAME = "rtf_exhaustive"

Detailed Description

rotational, translational and flip alignment using real-space methods.

slow

Parameters:
flip 
maxshift Maximum translation in pixels

Definition at line 770 of file aligner.h.


Member Function Documentation

virtual EMData* EMAN::RTFExhaustiveAligner::align EMData this_img,
EMData to_img
const [inline, virtual]
 

Implements EMAN::Aligner.

Definition at line 775 of file aligner.h.

References align().

00776                 {
00777                         return align(this_img, to_img, "sqeuclidean", Dict());
00778                 }

EMData * RTFExhaustiveAligner::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.

Parameters:
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.
Returns:
The aligned image.

Implements EMAN::Aligner.

Definition at line 892 of file aligner.cpp.

References EMAN::Util::calc_best_fft_size(), EMAN::EMData::calc_ccfx(), EMAN::EMData::calc_max_index(), EMAN::EMData::cmp(), EMAN::EMData::copy(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), InvalidParameterException, ny, EMAN::EMData::process(), EMAN::EMData::rotate_x(), EMAN::EMData::set_attr(), EMAN::Dict::set_default(), EMAN::Transform::set_mirror(), EMAN::Transform::set_pre_trans(), t, EMAN::EMData::unwrap(), and EMAN::Vec2f.

00894 {
00895         EMData *flip = params.set_default("flip", (EMData *) 0);
00896         int maxshift = params.set_default("maxshift", this_img->get_xsize()/8);
00897         if (maxshift < 2) throw InvalidParameterException("maxshift must be greater than or equal to 2");
00898 
00899         int ny = this_img->get_ysize();
00900         int xst = (int) floor(2 * M_PI * ny);
00901         xst = Util::calc_best_fft_size(xst);
00902 
00903         Dict d("n",2);
00904         EMData *to_shrunk_unwrapped = to->process("math.medianshrink",d);
00905 
00906         int to_copy_r2 = to_shrunk_unwrapped->get_ysize() / 2 - 2 - maxshift / 2;
00907         EMData *tmp = to_shrunk_unwrapped->unwrap(4, to_copy_r2, xst / 2, 0, 0, true);
00908         if( to_shrunk_unwrapped )
00909         {
00910                 delete to_shrunk_unwrapped;
00911                 to_shrunk_unwrapped = 0;
00912         }
00913         to_shrunk_unwrapped = tmp;
00914 
00915         EMData *to_shrunk_unwrapped_copy = to_shrunk_unwrapped->copy();
00916         EMData* to_unwrapped = to->unwrap(4, to->get_ysize() / 2 - 2 - maxshift, xst, 0, 0, true);
00917         EMData *to_unwrapped_copy = to_unwrapped->copy();
00918 
00919         bool delete_flipped = true;
00920         EMData *flipped = 0;
00921         if (flip) {
00922                 delete_flipped = false;
00923                 flipped = flip;
00924         }
00925         else {
00926                 flipped = to->process("xform.flip", Dict("axis", "x"));
00927         }
00928         EMData *to_shrunk_flipped_unwrapped = flipped->process("math.medianshrink",d);
00929         tmp = to_shrunk_flipped_unwrapped->unwrap(4, to_copy_r2, xst / 2, 0, 0, true);
00930         if( to_shrunk_flipped_unwrapped )
00931         {
00932                 delete to_shrunk_flipped_unwrapped;
00933                 to_shrunk_flipped_unwrapped = 0;
00934         }
00935         to_shrunk_flipped_unwrapped = tmp;
00936         EMData *to_shrunk_flipped_unwrapped_copy = to_shrunk_flipped_unwrapped->copy();
00937         EMData* to_flip_unwrapped = flipped->unwrap(4, to->get_ysize() / 2 - 2 - maxshift, xst, 0, 0, true);
00938         EMData* to_flip_unwrapped_copy = to_flip_unwrapped->copy();
00939 
00940         if (delete_flipped && flipped != 0) {
00941                 delete flipped;
00942                 flipped = 0;
00943         }
00944 
00945         EMData *this_shrunk_2 = this_img->process("math.medianshrink",d);
00946 
00947         float bestval = FLT_MAX;
00948         float bestang = 0;
00949         int bestflip = 0;
00950         float bestdx = 0;
00951         float bestdy = 0;
00952 
00953         int half_maxshift = maxshift / 2;
00954 
00955         int ur2 = this_shrunk_2->get_ysize() / 2 - 2 - half_maxshift;
00956         for (int dy = -half_maxshift; dy <= half_maxshift; dy += 1) {
00957                 for (int dx = -half_maxshift; dx <= half_maxshift; dx += 1) {
00958 #ifdef  _WIN32
00959                         if (_hypot(dx, dy) <= half_maxshift) {
00960 #else
00961                         if (hypot(dx, dy) <= half_maxshift) {
00962 #endif
00963                                 EMData *uw = this_shrunk_2->unwrap(4, ur2, xst / 2, dx, dy, true);
00964                                 EMData *uwc = uw->copy();
00965                                 EMData *a = uw->calc_ccfx(to_shrunk_unwrapped);
00966 
00967                                 uwc->rotate_x(a->calc_max_index());
00968                                 float cm = uwc->cmp(cmp_name, to_shrunk_unwrapped_copy, cmp_params);
00969                                 if (cm < bestval) {
00970                                         bestval = cm;
00971                                         bestang = (float) (2.0 * M_PI * a->calc_max_index() / a->get_xsize());
00972                                         bestdx = (float)dx;
00973                                         bestdy = (float)dy;
00974                                         bestflip = 0;
00975                                 }
00976 
00977 
00978                                 if( a )
00979                                 {
00980                                         delete a;
00981                                         a = 0;
00982                                 }
00983                                 if( uw )
00984                                 {
00985                                         delete uw;
00986                                         uw = 0;
00987                                 }
00988                                 if( uwc )
00989                                 {
00990                                         delete uwc;
00991                                         uwc = 0;
00992                                 }
00993                                 uw = this_shrunk_2->unwrap(4, ur2, xst / 2, dx, dy, true);
00994                                 uwc = uw->copy();
00995                                 a = uw->calc_ccfx(to_shrunk_flipped_unwrapped);
00996 
00997                                 uwc->rotate_x(a->calc_max_index());
00998                                 cm = uwc->cmp(cmp_name, to_shrunk_flipped_unwrapped_copy, cmp_params);
00999                                 if (cm < bestval) {
01000                                         bestval = cm;
01001                                         bestang = (float) (2.0 * M_PI * a->calc_max_index() / a->get_xsize());
01002                                         bestdx = (float)dx;
01003                                         bestdy = (float)dy;
01004                                         bestflip = 1;
01005                                 }
01006 
01007                                 if( a )
01008                                 {
01009                                         delete a;
01010                                         a = 0;
01011                                 }
01012 
01013                                 if( uw )
01014                                 {
01015                                         delete uw;
01016                                         uw = 0;
01017                                 }
01018                                 if( uwc )
01019                                 {
01020                                         delete uwc;
01021                                         uwc = 0;
01022                                 }
01023                         }
01024                 }
01025         }
01026         if( this_shrunk_2 )
01027         {
01028                 delete this_shrunk_2;
01029                 this_shrunk_2 = 0;
01030         }
01031         if( to_shrunk_unwrapped )
01032         {
01033                 delete to_shrunk_unwrapped;
01034                 to_shrunk_unwrapped = 0;
01035         }
01036         if( to_shrunk_unwrapped_copy )
01037         {
01038                 delete to_shrunk_unwrapped_copy;
01039                 to_shrunk_unwrapped_copy = 0;
01040         }
01041         if( to_shrunk_flipped_unwrapped )
01042         {
01043                 delete to_shrunk_flipped_unwrapped;
01044                 to_shrunk_flipped_unwrapped = 0;
01045         }
01046         if( to_shrunk_flipped_unwrapped_copy )
01047         {
01048                 delete to_shrunk_flipped_unwrapped_copy;
01049                 to_shrunk_flipped_unwrapped_copy = 0;
01050         }
01051         bestdx *= 2;
01052         bestdy *= 2;
01053         bestval = FLT_MAX;
01054 
01055         float bestdx2 = bestdx;
01056         float bestdy2 = bestdy;
01057         // Note I tried steps less than 1.0 (sub pixel precision) and it actually appeared detrimental
01058         // So my advice is to stick with dx += 1.0 etc unless you really are looking to fine tune this
01059         // algorithm
01060         for (float dy = bestdy2 - 3; dy <= bestdy2 + 3; dy += 1.0 ) {
01061                 for (float dx = bestdx2 - 3; dx <= bestdx2 + 3; dx += 1.0 ) {
01062 
01063 #ifdef  _WIN32
01064                         if (_hypot(dx, dy) <= maxshift) {
01065 #else
01066                         if (hypot(dx, dy) <= maxshift) {
01067 #endif
01068                                 EMData *uw = this_img->unwrap(4, this_img->get_ysize() / 2 - 2 - maxshift, xst, (int)dx, (int)dy, true);
01069                                 EMData *uwc = uw->copy();
01070                                 EMData *a = uw->calc_ccfx(to_unwrapped);
01071 
01072                                 uwc->rotate_x(a->calc_max_index());
01073                                 float cm = uwc->cmp(cmp_name, to_unwrapped_copy, cmp_params);
01074 
01075                                 if (cm < bestval) {
01076                                         bestval = cm;
01077                                         bestang = (float)(2.0 * M_PI * a->calc_max_index() / a->get_xsize());
01078                                         bestdx = dx;
01079                                         bestdy = dy;
01080                                         bestflip = 0;
01081                                 }
01082 
01083                                 if( a )
01084                                 {
01085                                         delete a;
01086                                         a = 0;
01087                                 }
01088                                 if( uw )
01089                                 {
01090                                         delete uw;
01091                                         uw = 0;
01092                                 }
01093                                 if( uwc )
01094                                 {
01095                                         delete uwc;
01096                                         uwc = 0;
01097                                 }
01098                                 uw = this_img->unwrap(4, this_img->get_ysize() / 2 - 2 - maxshift, xst, (int)dx, (int)dy, true);
01099                                 uwc = uw->copy();
01100                                 a = uw->calc_ccfx(to_flip_unwrapped);
01101 
01102                                 uwc->rotate_x(a->calc_max_index());
01103                                 cm = uwc->cmp(cmp_name, to_flip_unwrapped_copy, cmp_params);
01104 
01105                                 if (cm < bestval) {
01106                                         bestval = cm;
01107                                         bestang = (float)(2.0 * M_PI * a->calc_max_index() / a->get_xsize());
01108                                         bestdx = dx;
01109                                         bestdy = dy;
01110                                         bestflip = 1;
01111                                 }
01112 
01113                                 if( a )
01114                                 {
01115                                         delete a;
01116                                         a = 0;
01117                                 }
01118                                 if( uw )
01119                                 {
01120                                         delete uw;
01121                                         uw = 0;
01122                                 }
01123                                 if( uwc )
01124                                 {
01125                                         delete uwc;
01126                                         uwc = 0;
01127                                 }
01128                         }
01129                 }
01130         }
01131         if( to_unwrapped ) {delete to_unwrapped;to_unwrapped = 0;}
01132         if( to_shrunk_unwrapped ) {     delete to_shrunk_unwrapped;     to_shrunk_unwrapped = 0;}
01133         if (to_unwrapped_copy) { delete to_unwrapped_copy; to_unwrapped_copy = 0; }
01134         if (to_flip_unwrapped) { delete to_flip_unwrapped; to_flip_unwrapped = 0; }
01135         if (to_flip_unwrapped_copy) { delete to_flip_unwrapped_copy; to_flip_unwrapped_copy = 0;}
01136 
01137         bestang *= (float)EMConsts::rad2deg;
01138         Transform t(Dict("type","2d","alpha",(float)bestang));
01139         t.set_pre_trans(Vec2f(-bestdx,-bestdy));
01140         if (bestflip) {
01141                 t.set_mirror(true);
01142         }
01143 
01144         EMData* ret = this_img->process("xform",Dict("transform",&t));
01145         ret->set_attr("xform.align2d",&t);
01146 
01147         return ret;
01148 }

virtual string EMAN::RTFExhaustiveAligner::get_desc  )  const [inline, virtual]
 

Implements EMAN::Aligner.

Definition at line 785 of file aligner.h.

00786                 {
00787                         return "Experimental full 2D alignment with handedness check using semi-exhaustive search (not necessarily better than RTFBest)";
00788                 }

virtual string EMAN::RTFExhaustiveAligner::get_name  )  const [inline, virtual]
 

Get the Aligner's name.

Each Aligner is identified by a unique name.

Returns:
The Aligner's name.

Implements EMAN::Aligner.

Definition at line 780 of file aligner.h.

00781                 {
00782                         return NAME;
00783                 }

virtual TypeDict EMAN::RTFExhaustiveAligner::get_param_types  )  const [inline, virtual]
 

Implements EMAN::Aligner.

Definition at line 795 of file aligner.h.

References EMAN::TypeDict::put().

00796                 {
00797                         TypeDict d;
00798 
00799                         d.put("flip", EMObject::EMDATA);
00800                         d.put("maxshift", EMObject::INT, "Maximum translation in pixels");
00801                         return d;
00802                 }

Aligner* EMAN::RTFExhaustiveAligner::NEW  )  [inline, static]
 

Definition at line 790 of file aligner.h.

00791                 {
00792                         return new RTFExhaustiveAligner();
00793                 }


Member Data Documentation

const string RTFExhaustiveAligner::NAME = "rtf_exhaustive" [static]
 

Definition at line 71 of file aligner.cpp.


The documentation for this class was generated from the following files:
Generated on Mon Mar 7 18:20:01 2011 for EMAN2 by  doxygen 1.3.9.1