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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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Collaboration 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 893 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.

00895 {
00896         EMData *flip = params.set_default("flip", (EMData *) 0);
00897         int maxshift = params.set_default("maxshift", this_img->get_xsize()/8);
00898         if (maxshift < 2) throw InvalidParameterException("maxshift must be greater than or equal to 2");
00899 
00900         int ny = this_img->get_ysize();
00901         int xst = (int) floor(2 * M_PI * ny);
00902         xst = Util::calc_best_fft_size(xst);
00903 
00904         Dict d("n",2);
00905         EMData *to_shrunk_unwrapped = to->process("math.medianshrink",d);
00906 
00907         int to_copy_r2 = to_shrunk_unwrapped->get_ysize() / 2 - 2 - maxshift / 2;
00908         EMData *tmp = to_shrunk_unwrapped->unwrap(4, to_copy_r2, xst / 2, 0, 0, true);
00909         if( to_shrunk_unwrapped )
00910         {
00911                 delete to_shrunk_unwrapped;
00912                 to_shrunk_unwrapped = 0;
00913         }
00914         to_shrunk_unwrapped = tmp;
00915 
00916         EMData *to_shrunk_unwrapped_copy = to_shrunk_unwrapped->copy();
00917         EMData* to_unwrapped = to->unwrap(4, to->get_ysize() / 2 - 2 - maxshift, xst, 0, 0, true);
00918         EMData *to_unwrapped_copy = to_unwrapped->copy();
00919 
00920         bool delete_flipped = true;
00921         EMData *flipped = 0;
00922         if (flip) {
00923                 delete_flipped = false;
00924                 flipped = flip;
00925         }
00926         else {
00927                 flipped = to->process("xform.flip", Dict("axis", "x"));
00928         }
00929         EMData *to_shrunk_flipped_unwrapped = flipped->process("math.medianshrink",d);
00930         tmp = to_shrunk_flipped_unwrapped->unwrap(4, to_copy_r2, xst / 2, 0, 0, true);
00931         if( to_shrunk_flipped_unwrapped )
00932         {
00933                 delete to_shrunk_flipped_unwrapped;
00934                 to_shrunk_flipped_unwrapped = 0;
00935         }
00936         to_shrunk_flipped_unwrapped = tmp;
00937         EMData *to_shrunk_flipped_unwrapped_copy = to_shrunk_flipped_unwrapped->copy();
00938         EMData* to_flip_unwrapped = flipped->unwrap(4, to->get_ysize() / 2 - 2 - maxshift, xst, 0, 0, true);
00939         EMData* to_flip_unwrapped_copy = to_flip_unwrapped->copy();
00940 
00941         if (delete_flipped && flipped != 0) {
00942                 delete flipped;
00943                 flipped = 0;
00944         }
00945 
00946         EMData *this_shrunk_2 = this_img->process("math.medianshrink",d);
00947 
00948         float bestval = FLT_MAX;
00949         float bestang = 0;
00950         int bestflip = 0;
00951         float bestdx = 0;
00952         float bestdy = 0;
00953 
00954         int half_maxshift = maxshift / 2;
00955 
00956         int ur2 = this_shrunk_2->get_ysize() / 2 - 2 - half_maxshift;
00957         for (int dy = -half_maxshift; dy <= half_maxshift; dy += 1) {
00958                 for (int dx = -half_maxshift; dx <= half_maxshift; dx += 1) {
00959 #ifdef  _WIN32
00960                         if (_hypot(dx, dy) <= half_maxshift) {
00961 #else
00962                         if (hypot(dx, dy) <= half_maxshift) {
00963 #endif
00964                                 EMData *uw = this_shrunk_2->unwrap(4, ur2, xst / 2, dx, dy, true);
00965                                 EMData *uwc = uw->copy();
00966                                 EMData *a = uw->calc_ccfx(to_shrunk_unwrapped);
00967 
00968                                 uwc->rotate_x(a->calc_max_index());
00969                                 float cm = uwc->cmp(cmp_name, to_shrunk_unwrapped_copy, cmp_params);
00970                                 if (cm < bestval) {
00971                                         bestval = cm;
00972                                         bestang = (float) (2.0 * M_PI * a->calc_max_index() / a->get_xsize());
00973                                         bestdx = (float)dx;
00974                                         bestdy = (float)dy;
00975                                         bestflip = 0;
00976                                 }
00977 
00978 
00979                                 if( a )
00980                                 {
00981                                         delete a;
00982                                         a = 0;
00983                                 }
00984                                 if( uw )
00985                                 {
00986                                         delete uw;
00987                                         uw = 0;
00988                                 }
00989                                 if( uwc )
00990                                 {
00991                                         delete uwc;
00992                                         uwc = 0;
00993                                 }
00994                                 uw = this_shrunk_2->unwrap(4, ur2, xst / 2, dx, dy, true);
00995                                 uwc = uw->copy();
00996                                 a = uw->calc_ccfx(to_shrunk_flipped_unwrapped);
00997 
00998                                 uwc->rotate_x(a->calc_max_index());
00999                                 cm = uwc->cmp(cmp_name, to_shrunk_flipped_unwrapped_copy, cmp_params);
01000                                 if (cm < bestval) {
01001                                         bestval = cm;
01002                                         bestang = (float) (2.0 * M_PI * a->calc_max_index() / a->get_xsize());
01003                                         bestdx = (float)dx;
01004                                         bestdy = (float)dy;
01005                                         bestflip = 1;
01006                                 }
01007 
01008                                 if( a )
01009                                 {
01010                                         delete a;
01011                                         a = 0;
01012                                 }
01013 
01014                                 if( uw )
01015                                 {
01016                                         delete uw;
01017                                         uw = 0;
01018                                 }
01019                                 if( uwc )
01020                                 {
01021                                         delete uwc;
01022                                         uwc = 0;
01023                                 }
01024                         }
01025                 }
01026         }
01027         if( this_shrunk_2 )
01028         {
01029                 delete this_shrunk_2;
01030                 this_shrunk_2 = 0;
01031         }
01032         if( to_shrunk_unwrapped )
01033         {
01034                 delete to_shrunk_unwrapped;
01035                 to_shrunk_unwrapped = 0;
01036         }
01037         if( to_shrunk_unwrapped_copy )
01038         {
01039                 delete to_shrunk_unwrapped_copy;
01040                 to_shrunk_unwrapped_copy = 0;
01041         }
01042         if( to_shrunk_flipped_unwrapped )
01043         {
01044                 delete to_shrunk_flipped_unwrapped;
01045                 to_shrunk_flipped_unwrapped = 0;
01046         }
01047         if( to_shrunk_flipped_unwrapped_copy )
01048         {
01049                 delete to_shrunk_flipped_unwrapped_copy;
01050                 to_shrunk_flipped_unwrapped_copy = 0;
01051         }
01052         bestdx *= 2;
01053         bestdy *= 2;
01054         bestval = FLT_MAX;
01055 
01056         float bestdx2 = bestdx;
01057         float bestdy2 = bestdy;
01058         // Note I tried steps less than 1.0 (sub pixel precision) and it actually appeared detrimental
01059         // So my advice is to stick with dx += 1.0 etc unless you really are looking to fine tune this
01060         // algorithm
01061         for (float dy = bestdy2 - 3; dy <= bestdy2 + 3; dy += 1.0 ) {
01062                 for (float dx = bestdx2 - 3; dx <= bestdx2 + 3; dx += 1.0 ) {
01063 
01064 #ifdef  _WIN32
01065                         if (_hypot(dx, dy) <= maxshift) {
01066 #else
01067                         if (hypot(dx, dy) <= maxshift) {
01068 #endif
01069                                 EMData *uw = this_img->unwrap(4, this_img->get_ysize() / 2 - 2 - maxshift, xst, (int)dx, (int)dy, true);
01070                                 EMData *uwc = uw->copy();
01071                                 EMData *a = uw->calc_ccfx(to_unwrapped);
01072 
01073                                 uwc->rotate_x(a->calc_max_index());
01074                                 float cm = uwc->cmp(cmp_name, to_unwrapped_copy, cmp_params);
01075 
01076                                 if (cm < bestval) {
01077                                         bestval = cm;
01078                                         bestang = (float)(2.0 * M_PI * a->calc_max_index() / a->get_xsize());
01079                                         bestdx = dx;
01080                                         bestdy = dy;
01081                                         bestflip = 0;
01082                                 }
01083 
01084                                 if( a )
01085                                 {
01086                                         delete a;
01087                                         a = 0;
01088                                 }
01089                                 if( uw )
01090                                 {
01091                                         delete uw;
01092                                         uw = 0;
01093                                 }
01094                                 if( uwc )
01095                                 {
01096                                         delete uwc;
01097                                         uwc = 0;
01098                                 }
01099                                 uw = this_img->unwrap(4, this_img->get_ysize() / 2 - 2 - maxshift, xst, (int)dx, (int)dy, true);
01100                                 uwc = uw->copy();
01101                                 a = uw->calc_ccfx(to_flip_unwrapped);
01102 
01103                                 uwc->rotate_x(a->calc_max_index());
01104                                 cm = uwc->cmp(cmp_name, to_flip_unwrapped_copy, cmp_params);
01105 
01106                                 if (cm < bestval) {
01107                                         bestval = cm;
01108                                         bestang = (float)(2.0 * M_PI * a->calc_max_index() / a->get_xsize());
01109                                         bestdx = dx;
01110                                         bestdy = dy;
01111                                         bestflip = 1;
01112                                 }
01113 
01114                                 if( a )
01115                                 {
01116                                         delete a;
01117                                         a = 0;
01118                                 }
01119                                 if( uw )
01120                                 {
01121                                         delete uw;
01122                                         uw = 0;
01123                                 }
01124                                 if( uwc )
01125                                 {
01126                                         delete uwc;
01127                                         uwc = 0;
01128                                 }
01129                         }
01130                 }
01131         }
01132         if( to_unwrapped ) {delete to_unwrapped;to_unwrapped = 0;}
01133         if( to_shrunk_unwrapped ) {     delete to_shrunk_unwrapped;     to_shrunk_unwrapped = 0;}
01134         if (to_unwrapped_copy) { delete to_unwrapped_copy; to_unwrapped_copy = 0; }
01135         if (to_flip_unwrapped) { delete to_flip_unwrapped; to_flip_unwrapped = 0; }
01136         if (to_flip_unwrapped_copy) { delete to_flip_unwrapped_copy; to_flip_unwrapped_copy = 0;}
01137 
01138         bestang *= (float)EMConsts::rad2deg;
01139         Transform t(Dict("type","2d","alpha",(float)bestang));
01140         t.set_pre_trans(Vec2f(-bestdx,-bestdy));
01141         if (bestflip) {
01142                 t.set_mirror(true);
01143         }
01144 
01145         EMData* ret = this_img->process("xform",Dict("transform",&t));
01146         ret->set_attr("xform.align2d",&t);
01147 
01148         return ret;
01149 }

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 May 2 13:29:18 2011 for EMAN2 by  doxygen 1.3.9.1