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 1076 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 1081 of file aligner.h.

References align().

01082                 {
01083                         return align(this_img, to_img, "sqeuclidean", Dict());
01084                 }

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 1097 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().

01099 {
01100         EMData *flip = params.set_default("flip", (EMData *) 0);
01101         int maxshift = params.set_default("maxshift", this_img->get_xsize()/8);
01102         if (maxshift < 2) throw InvalidParameterException("maxshift must be greater than or equal to 2");
01103 
01104         int ny = this_img->get_ysize();
01105         int xst = (int) floor(2 * M_PI * ny);
01106         xst = Util::calc_best_fft_size(xst);
01107 
01108         Dict d("n",2);
01109         EMData *to_shrunk_unwrapped = to->process("math.medianshrink",d);
01110 
01111         int to_copy_r2 = to_shrunk_unwrapped->get_ysize() / 2 - 2 - maxshift / 2;
01112         EMData *tmp = to_shrunk_unwrapped->unwrap(4, to_copy_r2, xst / 2, 0, 0, true);
01113         if( to_shrunk_unwrapped )
01114         {
01115                 delete to_shrunk_unwrapped;
01116                 to_shrunk_unwrapped = 0;
01117         }
01118         to_shrunk_unwrapped = tmp;
01119 
01120         EMData *to_shrunk_unwrapped_copy = to_shrunk_unwrapped->copy();
01121         EMData* to_unwrapped = to->unwrap(4, to->get_ysize() / 2 - 2 - maxshift, xst, 0, 0, true);
01122         EMData *to_unwrapped_copy = to_unwrapped->copy();
01123 
01124         bool delete_flipped = true;
01125         EMData *flipped = 0;
01126         if (flip) {
01127                 delete_flipped = false;
01128                 flipped = flip;
01129         }
01130         else {
01131                 flipped = to->process("xform.flip", Dict("axis", "x"));
01132         }
01133         EMData *to_shrunk_flipped_unwrapped = flipped->process("math.medianshrink",d);
01134         tmp = to_shrunk_flipped_unwrapped->unwrap(4, to_copy_r2, xst / 2, 0, 0, true);
01135         if( to_shrunk_flipped_unwrapped )
01136         {
01137                 delete to_shrunk_flipped_unwrapped;
01138                 to_shrunk_flipped_unwrapped = 0;
01139         }
01140         to_shrunk_flipped_unwrapped = tmp;
01141         EMData *to_shrunk_flipped_unwrapped_copy = to_shrunk_flipped_unwrapped->copy();
01142         EMData* to_flip_unwrapped = flipped->unwrap(4, to->get_ysize() / 2 - 2 - maxshift, xst, 0, 0, true);
01143         EMData* to_flip_unwrapped_copy = to_flip_unwrapped->copy();
01144 
01145         if (delete_flipped && flipped != 0) {
01146                 delete flipped;
01147                 flipped = 0;
01148         }
01149 
01150         EMData *this_shrunk_2 = this_img->process("math.medianshrink",d);
01151 
01152         float bestval = FLT_MAX;
01153         float bestang = 0;
01154         int bestflip = 0;
01155         float bestdx = 0;
01156         float bestdy = 0;
01157 
01158         int half_maxshift = maxshift / 2;
01159 
01160         int ur2 = this_shrunk_2->get_ysize() / 2 - 2 - half_maxshift;
01161         for (int dy = -half_maxshift; dy <= half_maxshift; dy += 1) {
01162                 for (int dx = -half_maxshift; dx <= half_maxshift; dx += 1) {
01163 #ifdef  _WIN32
01164                         if (_hypot(dx, dy) <= half_maxshift) {
01165 #else
01166                         if (hypot(dx, dy) <= half_maxshift) {
01167 #endif
01168                                 EMData *uw = this_shrunk_2->unwrap(4, ur2, xst / 2, dx, dy, true);
01169                                 EMData *uwc = uw->copy();
01170                                 EMData *a = uw->calc_ccfx(to_shrunk_unwrapped);
01171 
01172                                 uwc->rotate_x(a->calc_max_index());
01173                                 float cm = uwc->cmp(cmp_name, to_shrunk_unwrapped_copy, cmp_params);
01174                                 if (cm < bestval) {
01175                                         bestval = cm;
01176                                         bestang = (float) (2.0 * M_PI * a->calc_max_index() / a->get_xsize());
01177                                         bestdx = (float)dx;
01178                                         bestdy = (float)dy;
01179                                         bestflip = 0;
01180                                 }
01181 
01182 
01183                                 if( a )
01184                                 {
01185                                         delete a;
01186                                         a = 0;
01187                                 }
01188                                 if( uw )
01189                                 {
01190                                         delete uw;
01191                                         uw = 0;
01192                                 }
01193                                 if( uwc )
01194                                 {
01195                                         delete uwc;
01196                                         uwc = 0;
01197                                 }
01198                                 uw = this_shrunk_2->unwrap(4, ur2, xst / 2, dx, dy, true);
01199                                 uwc = uw->copy();
01200                                 a = uw->calc_ccfx(to_shrunk_flipped_unwrapped);
01201 
01202                                 uwc->rotate_x(a->calc_max_index());
01203                                 cm = uwc->cmp(cmp_name, to_shrunk_flipped_unwrapped_copy, cmp_params);
01204                                 if (cm < bestval) {
01205                                         bestval = cm;
01206                                         bestang = (float) (2.0 * M_PI * a->calc_max_index() / a->get_xsize());
01207                                         bestdx = (float)dx;
01208                                         bestdy = (float)dy;
01209                                         bestflip = 1;
01210                                 }
01211 
01212                                 if( a )
01213                                 {
01214                                         delete a;
01215                                         a = 0;
01216                                 }
01217 
01218                                 if( uw )
01219                                 {
01220                                         delete uw;
01221                                         uw = 0;
01222                                 }
01223                                 if( uwc )
01224                                 {
01225                                         delete uwc;
01226                                         uwc = 0;
01227                                 }
01228                         }
01229                 }
01230         }
01231         if( this_shrunk_2 )
01232         {
01233                 delete this_shrunk_2;
01234                 this_shrunk_2 = 0;
01235         }
01236         if( to_shrunk_unwrapped )
01237         {
01238                 delete to_shrunk_unwrapped;
01239                 to_shrunk_unwrapped = 0;
01240         }
01241         if( to_shrunk_unwrapped_copy )
01242         {
01243                 delete to_shrunk_unwrapped_copy;
01244                 to_shrunk_unwrapped_copy = 0;
01245         }
01246         if( to_shrunk_flipped_unwrapped )
01247         {
01248                 delete to_shrunk_flipped_unwrapped;
01249                 to_shrunk_flipped_unwrapped = 0;
01250         }
01251         if( to_shrunk_flipped_unwrapped_copy )
01252         {
01253                 delete to_shrunk_flipped_unwrapped_copy;
01254                 to_shrunk_flipped_unwrapped_copy = 0;
01255         }
01256         bestdx *= 2;
01257         bestdy *= 2;
01258         bestval = FLT_MAX;
01259 
01260         float bestdx2 = bestdx;
01261         float bestdy2 = bestdy;
01262         // Note I tried steps less than 1.0 (sub pixel precision) and it actually appeared detrimental
01263         // So my advice is to stick with dx += 1.0 etc unless you really are looking to fine tune this
01264         // algorithm
01265         for (float dy = bestdy2 - 3; dy <= bestdy2 + 3; dy += 1.0 ) {
01266                 for (float dx = bestdx2 - 3; dx <= bestdx2 + 3; dx += 1.0 ) {
01267 
01268 #ifdef  _WIN32
01269                         if (_hypot(dx, dy) <= maxshift) {
01270 #else
01271                         if (hypot(dx, dy) <= maxshift) {
01272 #endif
01273                                 EMData *uw = this_img->unwrap(4, this_img->get_ysize() / 2 - 2 - maxshift, xst, (int)dx, (int)dy, true);
01274                                 EMData *uwc = uw->copy();
01275                                 EMData *a = uw->calc_ccfx(to_unwrapped);
01276 
01277                                 uwc->rotate_x(a->calc_max_index());
01278                                 float cm = uwc->cmp(cmp_name, to_unwrapped_copy, cmp_params);
01279 
01280                                 if (cm < bestval) {
01281                                         bestval = cm;
01282                                         bestang = (float)(2.0 * M_PI * a->calc_max_index() / a->get_xsize());
01283                                         bestdx = dx;
01284                                         bestdy = dy;
01285                                         bestflip = 0;
01286                                 }
01287 
01288                                 if( a )
01289                                 {
01290                                         delete a;
01291                                         a = 0;
01292                                 }
01293                                 if( uw )
01294                                 {
01295                                         delete uw;
01296                                         uw = 0;
01297                                 }
01298                                 if( uwc )
01299                                 {
01300                                         delete uwc;
01301                                         uwc = 0;
01302                                 }
01303                                 uw = this_img->unwrap(4, this_img->get_ysize() / 2 - 2 - maxshift, xst, (int)dx, (int)dy, true);
01304                                 uwc = uw->copy();
01305                                 a = uw->calc_ccfx(to_flip_unwrapped);
01306 
01307                                 uwc->rotate_x(a->calc_max_index());
01308                                 cm = uwc->cmp(cmp_name, to_flip_unwrapped_copy, cmp_params);
01309 
01310                                 if (cm < bestval) {
01311                                         bestval = cm;
01312                                         bestang = (float)(2.0 * M_PI * a->calc_max_index() / a->get_xsize());
01313                                         bestdx = dx;
01314                                         bestdy = dy;
01315                                         bestflip = 1;
01316                                 }
01317 
01318                                 if( a )
01319                                 {
01320                                         delete a;
01321                                         a = 0;
01322                                 }
01323                                 if( uw )
01324                                 {
01325                                         delete uw;
01326                                         uw = 0;
01327                                 }
01328                                 if( uwc )
01329                                 {
01330                                         delete uwc;
01331                                         uwc = 0;
01332                                 }
01333                         }
01334                 }
01335         }
01336         if( to_unwrapped ) {delete to_unwrapped;to_unwrapped = 0;}
01337         if( to_shrunk_unwrapped ) {     delete to_shrunk_unwrapped;     to_shrunk_unwrapped = 0;}
01338         if (to_unwrapped_copy) { delete to_unwrapped_copy; to_unwrapped_copy = 0; }
01339         if (to_flip_unwrapped) { delete to_flip_unwrapped; to_flip_unwrapped = 0; }
01340         if (to_flip_unwrapped_copy) { delete to_flip_unwrapped_copy; to_flip_unwrapped_copy = 0;}
01341 
01342         bestang *= (float)EMConsts::rad2deg;
01343         Transform t(Dict("type","2d","alpha",(float)bestang));
01344         t.set_pre_trans(Vec2f(-bestdx,-bestdy));
01345         if (bestflip) {
01346                 t.set_mirror(true);
01347         }
01348 
01349         EMData* ret = this_img->process("xform",Dict("transform",&t));
01350         ret->set_attr("xform.align2d",&t);
01351 
01352         return ret;
01353 }

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

Implements EMAN::Aligner.

Definition at line 1091 of file aligner.h.

01092                 {
01093                         return "Experimental full 2D alignment with handedness check using semi-exhaustive search (not necessarily better than RTFBest)";
01094                 }

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 1086 of file aligner.h.

References NAME.

01087                 {
01088                         return NAME;
01089                 }

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

Implements EMAN::Aligner.

Definition at line 1101 of file aligner.h.

References EMAN::EMObject::EMDATA, EMAN::EMObject::INT, and EMAN::TypeDict::put().

01102                 {
01103                         TypeDict d;
01104 
01105                         d.put("flip", EMObject::EMDATA);
01106                         d.put("maxshift", EMObject::INT, "Maximum translation in pixels");
01107                         return d;
01108                 }

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

Definition at line 1096 of file aligner.h.

01097                 {
01098                         return new RTFExhaustiveAligner();
01099                 }


Member Data Documentation

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

Definition at line 1110 of file aligner.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Fri Aug 10 16:34:45 2012 for EMAN2 by  doxygen 1.4.7