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

static AlignerNEW ()

Static Public Attributes

static 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 910 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::Aligner::params, EMAN::EMData::process(), EMAN::EMConsts::rad2deg, EMAN::EMData::rotate_x(), EMAN::EMData::set_attr(), EMAN::Dict::set_default(), t, and EMAN::EMData::unwrap().

Referenced by align().

00912 {
00913         EMData *flip = params.set_default("flip", (EMData *) 0);
00914         int maxshift = params.set_default("maxshift", this_img->get_xsize()/8);
00915         if (maxshift < 2) throw InvalidParameterException("maxshift must be greater than or equal to 2");
00916 
00917         int ny = this_img->get_ysize();
00918         int xst = (int) floor(2 * M_PI * ny);
00919         xst = Util::calc_best_fft_size(xst);
00920 
00921         Dict d("n",2);
00922         EMData *to_shrunk_unwrapped = to->process("math.medianshrink",d);
00923 
00924         int to_copy_r2 = to_shrunk_unwrapped->get_ysize() / 2 - 2 - maxshift / 2;
00925         EMData *tmp = to_shrunk_unwrapped->unwrap(4, to_copy_r2, xst / 2, 0, 0, true);
00926         if( to_shrunk_unwrapped )
00927         {
00928                 delete to_shrunk_unwrapped;
00929                 to_shrunk_unwrapped = 0;
00930         }
00931         to_shrunk_unwrapped = tmp;
00932 
00933         EMData *to_shrunk_unwrapped_copy = to_shrunk_unwrapped->copy();
00934         EMData* to_unwrapped = to->unwrap(4, to->get_ysize() / 2 - 2 - maxshift, xst, 0, 0, true);
00935         EMData *to_unwrapped_copy = to_unwrapped->copy();
00936 
00937         bool delete_flipped = true;
00938         EMData *flipped = 0;
00939         if (flip) {
00940                 delete_flipped = false;
00941                 flipped = flip;
00942         }
00943         else {
00944                 flipped = to->process("xform.flip", Dict("axis", "x"));
00945         }
00946         EMData *to_shrunk_flipped_unwrapped = flipped->process("math.medianshrink",d);
00947         tmp = to_shrunk_flipped_unwrapped->unwrap(4, to_copy_r2, xst / 2, 0, 0, true);
00948         if( to_shrunk_flipped_unwrapped )
00949         {
00950                 delete to_shrunk_flipped_unwrapped;
00951                 to_shrunk_flipped_unwrapped = 0;
00952         }
00953         to_shrunk_flipped_unwrapped = tmp;
00954         EMData *to_shrunk_flipped_unwrapped_copy = to_shrunk_flipped_unwrapped->copy();
00955         EMData* to_flip_unwrapped = flipped->unwrap(4, to->get_ysize() / 2 - 2 - maxshift, xst, 0, 0, true);
00956         EMData* to_flip_unwrapped_copy = to_flip_unwrapped->copy();
00957 
00958         if (delete_flipped && flipped != 0) {
00959                 delete flipped;
00960                 flipped = 0;
00961         }
00962 
00963         EMData *this_shrunk_2 = this_img->process("math.medianshrink",d);
00964 
00965         float bestval = FLT_MAX;
00966         float bestang = 0;
00967         int bestflip = 0;
00968         float bestdx = 0;
00969         float bestdy = 0;
00970 
00971         int half_maxshift = maxshift / 2;
00972 
00973         int ur2 = this_shrunk_2->get_ysize() / 2 - 2 - half_maxshift;
00974         for (int dy = -half_maxshift; dy <= half_maxshift; dy += 1) {
00975                 for (int dx = -half_maxshift; dx <= half_maxshift; dx += 1) {
00976 #ifdef  _WIN32
00977                         if (_hypot(dx, dy) <= half_maxshift) {
00978 #else
00979                         if (hypot(dx, dy) <= half_maxshift) {
00980 #endif
00981                                 EMData *uw = this_shrunk_2->unwrap(4, ur2, xst / 2, dx, dy, true);
00982                                 EMData *uwc = uw->copy();
00983                                 EMData *a = uw->calc_ccfx(to_shrunk_unwrapped);
00984 
00985                                 uwc->rotate_x(a->calc_max_index());
00986                                 float cm = uwc->cmp(cmp_name, to_shrunk_unwrapped_copy, cmp_params);
00987                                 if (cm < bestval) {
00988                                         bestval = cm;
00989                                         bestang = (float) (2.0 * M_PI * a->calc_max_index() / a->get_xsize());
00990                                         bestdx = (float)dx;
00991                                         bestdy = (float)dy;
00992                                         bestflip = 0;
00993                                 }
00994 
00995 
00996                                 if( a )
00997                                 {
00998                                         delete a;
00999                                         a = 0;
01000                                 }
01001                                 if( uw )
01002                                 {
01003                                         delete uw;
01004                                         uw = 0;
01005                                 }
01006                                 if( uwc )
01007                                 {
01008                                         delete uwc;
01009                                         uwc = 0;
01010                                 }
01011                                 uw = this_shrunk_2->unwrap(4, ur2, xst / 2, dx, dy, true);
01012                                 uwc = uw->copy();
01013                                 a = uw->calc_ccfx(to_shrunk_flipped_unwrapped);
01014 
01015                                 uwc->rotate_x(a->calc_max_index());
01016                                 cm = uwc->cmp(cmp_name, to_shrunk_flipped_unwrapped_copy, cmp_params);
01017                                 if (cm < bestval) {
01018                                         bestval = cm;
01019                                         bestang = (float) (2.0 * M_PI * a->calc_max_index() / a->get_xsize());
01020                                         bestdx = (float)dx;
01021                                         bestdy = (float)dy;
01022                                         bestflip = 1;
01023                                 }
01024 
01025                                 if( a )
01026                                 {
01027                                         delete a;
01028                                         a = 0;
01029                                 }
01030 
01031                                 if( uw )
01032                                 {
01033                                         delete uw;
01034                                         uw = 0;
01035                                 }
01036                                 if( uwc )
01037                                 {
01038                                         delete uwc;
01039                                         uwc = 0;
01040                                 }
01041                         }
01042                 }
01043         }
01044         if( this_shrunk_2 )
01045         {
01046                 delete this_shrunk_2;
01047                 this_shrunk_2 = 0;
01048         }
01049         if( to_shrunk_unwrapped )
01050         {
01051                 delete to_shrunk_unwrapped;
01052                 to_shrunk_unwrapped = 0;
01053         }
01054         if( to_shrunk_unwrapped_copy )
01055         {
01056                 delete to_shrunk_unwrapped_copy;
01057                 to_shrunk_unwrapped_copy = 0;
01058         }
01059         if( to_shrunk_flipped_unwrapped )
01060         {
01061                 delete to_shrunk_flipped_unwrapped;
01062                 to_shrunk_flipped_unwrapped = 0;
01063         }
01064         if( to_shrunk_flipped_unwrapped_copy )
01065         {
01066                 delete to_shrunk_flipped_unwrapped_copy;
01067                 to_shrunk_flipped_unwrapped_copy = 0;
01068         }
01069         bestdx *= 2;
01070         bestdy *= 2;
01071         bestval = FLT_MAX;
01072 
01073         float bestdx2 = bestdx;
01074         float bestdy2 = bestdy;
01075         // Note I tried steps less than 1.0 (sub pixel precision) and it actually appeared detrimental
01076         // So my advice is to stick with dx += 1.0 etc unless you really are looking to fine tune this
01077         // algorithm
01078         for (float dy = bestdy2 - 3; dy <= bestdy2 + 3; dy += 1.0 ) {
01079                 for (float dx = bestdx2 - 3; dx <= bestdx2 + 3; dx += 1.0 ) {
01080 
01081 #ifdef  _WIN32
01082                         if (_hypot(dx, dy) <= maxshift) {
01083 #else
01084                         if (hypot(dx, dy) <= maxshift) {
01085 #endif
01086                                 EMData *uw = this_img->unwrap(4, this_img->get_ysize() / 2 - 2 - maxshift, xst, (int)dx, (int)dy, true);
01087                                 EMData *uwc = uw->copy();
01088                                 EMData *a = uw->calc_ccfx(to_unwrapped);
01089 
01090                                 uwc->rotate_x(a->calc_max_index());
01091                                 float cm = uwc->cmp(cmp_name, to_unwrapped_copy, cmp_params);
01092 
01093                                 if (cm < bestval) {
01094                                         bestval = cm;
01095                                         bestang = (float)(2.0 * M_PI * a->calc_max_index() / a->get_xsize());
01096                                         bestdx = dx;
01097                                         bestdy = dy;
01098                                         bestflip = 0;
01099                                 }
01100 
01101                                 if( a )
01102                                 {
01103                                         delete a;
01104                                         a = 0;
01105                                 }
01106                                 if( uw )
01107                                 {
01108                                         delete uw;
01109                                         uw = 0;
01110                                 }
01111                                 if( uwc )
01112                                 {
01113                                         delete uwc;
01114                                         uwc = 0;
01115                                 }
01116                                 uw = this_img->unwrap(4, this_img->get_ysize() / 2 - 2 - maxshift, xst, (int)dx, (int)dy, true);
01117                                 uwc = uw->copy();
01118                                 a = uw->calc_ccfx(to_flip_unwrapped);
01119 
01120                                 uwc->rotate_x(a->calc_max_index());
01121                                 cm = uwc->cmp(cmp_name, to_flip_unwrapped_copy, cmp_params);
01122 
01123                                 if (cm < bestval) {
01124                                         bestval = cm;
01125                                         bestang = (float)(2.0 * M_PI * a->calc_max_index() / a->get_xsize());
01126                                         bestdx = dx;
01127                                         bestdy = dy;
01128                                         bestflip = 1;
01129                                 }
01130 
01131                                 if( a )
01132                                 {
01133                                         delete a;
01134                                         a = 0;
01135                                 }
01136                                 if( uw )
01137                                 {
01138                                         delete uw;
01139                                         uw = 0;
01140                                 }
01141                                 if( uwc )
01142                                 {
01143                                         delete uwc;
01144                                         uwc = 0;
01145                                 }
01146                         }
01147                 }
01148         }
01149         if( to_unwrapped ) {delete to_unwrapped;to_unwrapped = 0;}
01150         if( to_shrunk_unwrapped ) {     delete to_shrunk_unwrapped;     to_shrunk_unwrapped = 0;}
01151         if (to_unwrapped_copy) { delete to_unwrapped_copy; to_unwrapped_copy = 0; }
01152         if (to_flip_unwrapped) { delete to_flip_unwrapped; to_flip_unwrapped = 0; }
01153         if (to_flip_unwrapped_copy) { delete to_flip_unwrapped_copy; to_flip_unwrapped_copy = 0;}
01154 
01155         bestang *= (float)EMConsts::rad2deg;
01156         Transform t(Dict("type","2d","alpha",(float)bestang));
01157         t.set_pre_trans(Vec2f(-bestdx,-bestdy));
01158         if (bestflip) {
01159                 t.set_mirror(true);
01160         }
01161 
01162         EMData* ret = this_img->process("xform",Dict("transform",&t));
01163         ret->set_attr("xform.align2d",&t);
01164 
01165         return ret;
01166 }

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.

References NAME.

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::EMObject::EMDATA, EMAN::EMObject::INT, and 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                 }

static 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 804 of file aligner.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Thu Nov 17 12:45:09 2011 for EMAN2 by  doxygen 1.4.7