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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 894 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.

00896 {
00897         EMData *flip = params.set_default("flip", (EMData *) 0);
00898         int maxshift = params.set_default("maxshift", this_img->get_xsize()/8);
00899         if (maxshift < 2) throw InvalidParameterException("maxshift must be greater than or equal to 2");
00900 
00901         int ny = this_img->get_ysize();
00902         int xst = (int) floor(2 * M_PI * ny);
00903         xst = Util::calc_best_fft_size(xst);
00904 
00905         Dict d("n",2);
00906         EMData *to_shrunk_unwrapped = to->process("math.medianshrink",d);
00907 
00908         int to_copy_r2 = to_shrunk_unwrapped->get_ysize() / 2 - 2 - maxshift / 2;
00909         EMData *tmp = to_shrunk_unwrapped->unwrap(4, to_copy_r2, xst / 2, 0, 0, true);
00910         if( to_shrunk_unwrapped )
00911         {
00912                 delete to_shrunk_unwrapped;
00913                 to_shrunk_unwrapped = 0;
00914         }
00915         to_shrunk_unwrapped = tmp;
00916 
00917         EMData *to_shrunk_unwrapped_copy = to_shrunk_unwrapped->copy();
00918         EMData* to_unwrapped = to->unwrap(4, to->get_ysize() / 2 - 2 - maxshift, xst, 0, 0, true);
00919         EMData *to_unwrapped_copy = to_unwrapped->copy();
00920 
00921         bool delete_flipped = true;
00922         EMData *flipped = 0;
00923         if (flip) {
00924                 delete_flipped = false;
00925                 flipped = flip;
00926         }
00927         else {
00928                 flipped = to->process("xform.flip", Dict("axis", "x"));
00929         }
00930         EMData *to_shrunk_flipped_unwrapped = flipped->process("math.medianshrink",d);
00931         tmp = to_shrunk_flipped_unwrapped->unwrap(4, to_copy_r2, xst / 2, 0, 0, true);
00932         if( to_shrunk_flipped_unwrapped )
00933         {
00934                 delete to_shrunk_flipped_unwrapped;
00935                 to_shrunk_flipped_unwrapped = 0;
00936         }
00937         to_shrunk_flipped_unwrapped = tmp;
00938         EMData *to_shrunk_flipped_unwrapped_copy = to_shrunk_flipped_unwrapped->copy();
00939         EMData* to_flip_unwrapped = flipped->unwrap(4, to->get_ysize() / 2 - 2 - maxshift, xst, 0, 0, true);
00940         EMData* to_flip_unwrapped_copy = to_flip_unwrapped->copy();
00941 
00942         if (delete_flipped && flipped != 0) {
00943                 delete flipped;
00944                 flipped = 0;
00945         }
00946 
00947         EMData *this_shrunk_2 = this_img->process("math.medianshrink",d);
00948 
00949         float bestval = FLT_MAX;
00950         float bestang = 0;
00951         int bestflip = 0;
00952         float bestdx = 0;
00953         float bestdy = 0;
00954 
00955         int half_maxshift = maxshift / 2;
00956 
00957         int ur2 = this_shrunk_2->get_ysize() / 2 - 2 - half_maxshift;
00958         for (int dy = -half_maxshift; dy <= half_maxshift; dy += 1) {
00959                 for (int dx = -half_maxshift; dx <= half_maxshift; dx += 1) {
00960 #ifdef  _WIN32
00961                         if (_hypot(dx, dy) <= half_maxshift) {
00962 #else
00963                         if (hypot(dx, dy) <= half_maxshift) {
00964 #endif
00965                                 EMData *uw = this_shrunk_2->unwrap(4, ur2, xst / 2, dx, dy, true);
00966                                 EMData *uwc = uw->copy();
00967                                 EMData *a = uw->calc_ccfx(to_shrunk_unwrapped);
00968 
00969                                 uwc->rotate_x(a->calc_max_index());
00970                                 float cm = uwc->cmp(cmp_name, to_shrunk_unwrapped_copy, cmp_params);
00971                                 if (cm < bestval) {
00972                                         bestval = cm;
00973                                         bestang = (float) (2.0 * M_PI * a->calc_max_index() / a->get_xsize());
00974                                         bestdx = (float)dx;
00975                                         bestdy = (float)dy;
00976                                         bestflip = 0;
00977                                 }
00978 
00979 
00980                                 if( a )
00981                                 {
00982                                         delete a;
00983                                         a = 0;
00984                                 }
00985                                 if( uw )
00986                                 {
00987                                         delete uw;
00988                                         uw = 0;
00989                                 }
00990                                 if( uwc )
00991                                 {
00992                                         delete uwc;
00993                                         uwc = 0;
00994                                 }
00995                                 uw = this_shrunk_2->unwrap(4, ur2, xst / 2, dx, dy, true);
00996                                 uwc = uw->copy();
00997                                 a = uw->calc_ccfx(to_shrunk_flipped_unwrapped);
00998 
00999                                 uwc->rotate_x(a->calc_max_index());
01000                                 cm = uwc->cmp(cmp_name, to_shrunk_flipped_unwrapped_copy, cmp_params);
01001                                 if (cm < bestval) {
01002                                         bestval = cm;
01003                                         bestang = (float) (2.0 * M_PI * a->calc_max_index() / a->get_xsize());
01004                                         bestdx = (float)dx;
01005                                         bestdy = (float)dy;
01006                                         bestflip = 1;
01007                                 }
01008 
01009                                 if( a )
01010                                 {
01011                                         delete a;
01012                                         a = 0;
01013                                 }
01014 
01015                                 if( uw )
01016                                 {
01017                                         delete uw;
01018                                         uw = 0;
01019                                 }
01020                                 if( uwc )
01021                                 {
01022                                         delete uwc;
01023                                         uwc = 0;
01024                                 }
01025                         }
01026                 }
01027         }
01028         if( this_shrunk_2 )
01029         {
01030                 delete this_shrunk_2;
01031                 this_shrunk_2 = 0;
01032         }
01033         if( to_shrunk_unwrapped )
01034         {
01035                 delete to_shrunk_unwrapped;
01036                 to_shrunk_unwrapped = 0;
01037         }
01038         if( to_shrunk_unwrapped_copy )
01039         {
01040                 delete to_shrunk_unwrapped_copy;
01041                 to_shrunk_unwrapped_copy = 0;
01042         }
01043         if( to_shrunk_flipped_unwrapped )
01044         {
01045                 delete to_shrunk_flipped_unwrapped;
01046                 to_shrunk_flipped_unwrapped = 0;
01047         }
01048         if( to_shrunk_flipped_unwrapped_copy )
01049         {
01050                 delete to_shrunk_flipped_unwrapped_copy;
01051                 to_shrunk_flipped_unwrapped_copy = 0;
01052         }
01053         bestdx *= 2;
01054         bestdy *= 2;
01055         bestval = FLT_MAX;
01056 
01057         float bestdx2 = bestdx;
01058         float bestdy2 = bestdy;
01059         // Note I tried steps less than 1.0 (sub pixel precision) and it actually appeared detrimental
01060         // So my advice is to stick with dx += 1.0 etc unless you really are looking to fine tune this
01061         // algorithm
01062         for (float dy = bestdy2 - 3; dy <= bestdy2 + 3; dy += 1.0 ) {
01063                 for (float dx = bestdx2 - 3; dx <= bestdx2 + 3; dx += 1.0 ) {
01064 
01065 #ifdef  _WIN32
01066                         if (_hypot(dx, dy) <= maxshift) {
01067 #else
01068                         if (hypot(dx, dy) <= maxshift) {
01069 #endif
01070                                 EMData *uw = this_img->unwrap(4, this_img->get_ysize() / 2 - 2 - maxshift, xst, (int)dx, (int)dy, true);
01071                                 EMData *uwc = uw->copy();
01072                                 EMData *a = uw->calc_ccfx(to_unwrapped);
01073 
01074                                 uwc->rotate_x(a->calc_max_index());
01075                                 float cm = uwc->cmp(cmp_name, to_unwrapped_copy, cmp_params);
01076 
01077                                 if (cm < bestval) {
01078                                         bestval = cm;
01079                                         bestang = (float)(2.0 * M_PI * a->calc_max_index() / a->get_xsize());
01080                                         bestdx = dx;
01081                                         bestdy = dy;
01082                                         bestflip = 0;
01083                                 }
01084 
01085                                 if( a )
01086                                 {
01087                                         delete a;
01088                                         a = 0;
01089                                 }
01090                                 if( uw )
01091                                 {
01092                                         delete uw;
01093                                         uw = 0;
01094                                 }
01095                                 if( uwc )
01096                                 {
01097                                         delete uwc;
01098                                         uwc = 0;
01099                                 }
01100                                 uw = this_img->unwrap(4, this_img->get_ysize() / 2 - 2 - maxshift, xst, (int)dx, (int)dy, true);
01101                                 uwc = uw->copy();
01102                                 a = uw->calc_ccfx(to_flip_unwrapped);
01103 
01104                                 uwc->rotate_x(a->calc_max_index());
01105                                 cm = uwc->cmp(cmp_name, to_flip_unwrapped_copy, cmp_params);
01106 
01107                                 if (cm < bestval) {
01108                                         bestval = cm;
01109                                         bestang = (float)(2.0 * M_PI * a->calc_max_index() / a->get_xsize());
01110                                         bestdx = dx;
01111                                         bestdy = dy;
01112                                         bestflip = 1;
01113                                 }
01114 
01115                                 if( a )
01116                                 {
01117                                         delete a;
01118                                         a = 0;
01119                                 }
01120                                 if( uw )
01121                                 {
01122                                         delete uw;
01123                                         uw = 0;
01124                                 }
01125                                 if( uwc )
01126                                 {
01127                                         delete uwc;
01128                                         uwc = 0;
01129                                 }
01130                         }
01131                 }
01132         }
01133         if( to_unwrapped ) {delete to_unwrapped;to_unwrapped = 0;}
01134         if( to_shrunk_unwrapped ) {     delete to_shrunk_unwrapped;     to_shrunk_unwrapped = 0;}
01135         if (to_unwrapped_copy) { delete to_unwrapped_copy; to_unwrapped_copy = 0; }
01136         if (to_flip_unwrapped) { delete to_flip_unwrapped; to_flip_unwrapped = 0; }
01137         if (to_flip_unwrapped_copy) { delete to_flip_unwrapped_copy; to_flip_unwrapped_copy = 0;}
01138 
01139         bestang *= (float)EMConsts::rad2deg;
01140         Transform t(Dict("type","2d","alpha",(float)bestang));
01141         t.set_pre_trans(Vec2f(-bestdx,-bestdy));
01142         if (bestflip) {
01143                 t.set_mirror(true);
01144         }
01145 
01146         EMData* ret = this_img->process("xform",Dict("transform",&t));
01147         ret->set_attr("xform.align2d",&t);
01148 
01149         return ret;
01150 }

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 Thu Mar 10 22:59:49 2011 for EMAN2 by  doxygen 1.3.9.1