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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 1082 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 1087 of file aligner.h.

References align().

01088                 {
01089                         return align(this_img, to_img, "sqeuclidean", Dict());
01090                 }

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 1113 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.

01115 {
01116         EMData *flip = params.set_default("flip", (EMData *) 0);
01117         int maxshift = params.set_default("maxshift", this_img->get_xsize()/8);
01118         if (maxshift < 2) throw InvalidParameterException("maxshift must be greater than or equal to 2");
01119 
01120         int ny = this_img->get_ysize();
01121         int xst = (int) floor(2 * M_PI * ny);
01122         xst = Util::calc_best_fft_size(xst);
01123 
01124         Dict d("n",2);
01125         EMData *to_shrunk_unwrapped = to->process("math.medianshrink",d);
01126 
01127         int to_copy_r2 = to_shrunk_unwrapped->get_ysize() / 2 - 2 - maxshift / 2;
01128         EMData *tmp = to_shrunk_unwrapped->unwrap(4, to_copy_r2, xst / 2, 0, 0, true);
01129         if( to_shrunk_unwrapped )
01130         {
01131                 delete to_shrunk_unwrapped;
01132                 to_shrunk_unwrapped = 0;
01133         }
01134         to_shrunk_unwrapped = tmp;
01135 
01136         EMData *to_shrunk_unwrapped_copy = to_shrunk_unwrapped->copy();
01137         EMData* to_unwrapped = to->unwrap(4, to->get_ysize() / 2 - 2 - maxshift, xst, 0, 0, true);
01138         EMData *to_unwrapped_copy = to_unwrapped->copy();
01139 
01140         bool delete_flipped = true;
01141         EMData *flipped = 0;
01142         if (flip) {
01143                 delete_flipped = false;
01144                 flipped = flip;
01145         }
01146         else {
01147                 flipped = to->process("xform.flip", Dict("axis", "x"));
01148         }
01149         EMData *to_shrunk_flipped_unwrapped = flipped->process("math.medianshrink",d);
01150         tmp = to_shrunk_flipped_unwrapped->unwrap(4, to_copy_r2, xst / 2, 0, 0, true);
01151         if( to_shrunk_flipped_unwrapped )
01152         {
01153                 delete to_shrunk_flipped_unwrapped;
01154                 to_shrunk_flipped_unwrapped = 0;
01155         }
01156         to_shrunk_flipped_unwrapped = tmp;
01157         EMData *to_shrunk_flipped_unwrapped_copy = to_shrunk_flipped_unwrapped->copy();
01158         EMData* to_flip_unwrapped = flipped->unwrap(4, to->get_ysize() / 2 - 2 - maxshift, xst, 0, 0, true);
01159         EMData* to_flip_unwrapped_copy = to_flip_unwrapped->copy();
01160 
01161         if (delete_flipped && flipped != 0) {
01162                 delete flipped;
01163                 flipped = 0;
01164         }
01165 
01166         EMData *this_shrunk_2 = this_img->process("math.medianshrink",d);
01167 
01168         float bestval = FLT_MAX;
01169         float bestang = 0;
01170         int bestflip = 0;
01171         float bestdx = 0;
01172         float bestdy = 0;
01173 
01174         int half_maxshift = maxshift / 2;
01175 
01176         int ur2 = this_shrunk_2->get_ysize() / 2 - 2 - half_maxshift;
01177         for (int dy = -half_maxshift; dy <= half_maxshift; dy += 1) {
01178                 for (int dx = -half_maxshift; dx <= half_maxshift; dx += 1) {
01179 #ifdef  _WIN32
01180                         if (_hypot(dx, dy) <= half_maxshift) {
01181 #else
01182                         if (hypot(dx, dy) <= half_maxshift) {
01183 #endif
01184                                 EMData *uw = this_shrunk_2->unwrap(4, ur2, xst / 2, dx, dy, true);
01185                                 EMData *uwc = uw->copy();
01186                                 EMData *a = uw->calc_ccfx(to_shrunk_unwrapped);
01187 
01188                                 uwc->rotate_x(a->calc_max_index());
01189                                 float cm = uwc->cmp(cmp_name, to_shrunk_unwrapped_copy, cmp_params);
01190                                 if (cm < bestval) {
01191                                         bestval = cm;
01192                                         bestang = (float) (2.0 * M_PI * a->calc_max_index() / a->get_xsize());
01193                                         bestdx = (float)dx;
01194                                         bestdy = (float)dy;
01195                                         bestflip = 0;
01196                                 }
01197 
01198 
01199                                 if( a )
01200                                 {
01201                                         delete a;
01202                                         a = 0;
01203                                 }
01204                                 if( uw )
01205                                 {
01206                                         delete uw;
01207                                         uw = 0;
01208                                 }
01209                                 if( uwc )
01210                                 {
01211                                         delete uwc;
01212                                         uwc = 0;
01213                                 }
01214                                 uw = this_shrunk_2->unwrap(4, ur2, xst / 2, dx, dy, true);
01215                                 uwc = uw->copy();
01216                                 a = uw->calc_ccfx(to_shrunk_flipped_unwrapped);
01217 
01218                                 uwc->rotate_x(a->calc_max_index());
01219                                 cm = uwc->cmp(cmp_name, to_shrunk_flipped_unwrapped_copy, cmp_params);
01220                                 if (cm < bestval) {
01221                                         bestval = cm;
01222                                         bestang = (float) (2.0 * M_PI * a->calc_max_index() / a->get_xsize());
01223                                         bestdx = (float)dx;
01224                                         bestdy = (float)dy;
01225                                         bestflip = 1;
01226                                 }
01227 
01228                                 if( a )
01229                                 {
01230                                         delete a;
01231                                         a = 0;
01232                                 }
01233 
01234                                 if( uw )
01235                                 {
01236                                         delete uw;
01237                                         uw = 0;
01238                                 }
01239                                 if( uwc )
01240                                 {
01241                                         delete uwc;
01242                                         uwc = 0;
01243                                 }
01244                         }
01245                 }
01246         }
01247         if( this_shrunk_2 )
01248         {
01249                 delete this_shrunk_2;
01250                 this_shrunk_2 = 0;
01251         }
01252         if( to_shrunk_unwrapped )
01253         {
01254                 delete to_shrunk_unwrapped;
01255                 to_shrunk_unwrapped = 0;
01256         }
01257         if( to_shrunk_unwrapped_copy )
01258         {
01259                 delete to_shrunk_unwrapped_copy;
01260                 to_shrunk_unwrapped_copy = 0;
01261         }
01262         if( to_shrunk_flipped_unwrapped )
01263         {
01264                 delete to_shrunk_flipped_unwrapped;
01265                 to_shrunk_flipped_unwrapped = 0;
01266         }
01267         if( to_shrunk_flipped_unwrapped_copy )
01268         {
01269                 delete to_shrunk_flipped_unwrapped_copy;
01270                 to_shrunk_flipped_unwrapped_copy = 0;
01271         }
01272         bestdx *= 2;
01273         bestdy *= 2;
01274         bestval = FLT_MAX;
01275 
01276         float bestdx2 = bestdx;
01277         float bestdy2 = bestdy;
01278         // Note I tried steps less than 1.0 (sub pixel precision) and it actually appeared detrimental
01279         // So my advice is to stick with dx += 1.0 etc unless you really are looking to fine tune this
01280         // algorithm
01281         for (float dy = bestdy2 - 3; dy <= bestdy2 + 3; dy += 1.0 ) {
01282                 for (float dx = bestdx2 - 3; dx <= bestdx2 + 3; dx += 1.0 ) {
01283 
01284 #ifdef  _WIN32
01285                         if (_hypot(dx, dy) <= maxshift) {
01286 #else
01287                         if (hypot(dx, dy) <= maxshift) {
01288 #endif
01289                                 EMData *uw = this_img->unwrap(4, this_img->get_ysize() / 2 - 2 - maxshift, xst, (int)dx, (int)dy, true);
01290                                 EMData *uwc = uw->copy();
01291                                 EMData *a = uw->calc_ccfx(to_unwrapped);
01292 
01293                                 uwc->rotate_x(a->calc_max_index());
01294                                 float cm = uwc->cmp(cmp_name, to_unwrapped_copy, cmp_params);
01295 
01296                                 if (cm < bestval) {
01297                                         bestval = cm;
01298                                         bestang = (float)(2.0 * M_PI * a->calc_max_index() / a->get_xsize());
01299                                         bestdx = dx;
01300                                         bestdy = dy;
01301                                         bestflip = 0;
01302                                 }
01303 
01304                                 if( a )
01305                                 {
01306                                         delete a;
01307                                         a = 0;
01308                                 }
01309                                 if( uw )
01310                                 {
01311                                         delete uw;
01312                                         uw = 0;
01313                                 }
01314                                 if( uwc )
01315                                 {
01316                                         delete uwc;
01317                                         uwc = 0;
01318                                 }
01319                                 uw = this_img->unwrap(4, this_img->get_ysize() / 2 - 2 - maxshift, xst, (int)dx, (int)dy, true);
01320                                 uwc = uw->copy();
01321                                 a = uw->calc_ccfx(to_flip_unwrapped);
01322 
01323                                 uwc->rotate_x(a->calc_max_index());
01324                                 cm = uwc->cmp(cmp_name, to_flip_unwrapped_copy, cmp_params);
01325 
01326                                 if (cm < bestval) {
01327                                         bestval = cm;
01328                                         bestang = (float)(2.0 * M_PI * a->calc_max_index() / a->get_xsize());
01329                                         bestdx = dx;
01330                                         bestdy = dy;
01331                                         bestflip = 1;
01332                                 }
01333 
01334                                 if( a )
01335                                 {
01336                                         delete a;
01337                                         a = 0;
01338                                 }
01339                                 if( uw )
01340                                 {
01341                                         delete uw;
01342                                         uw = 0;
01343                                 }
01344                                 if( uwc )
01345                                 {
01346                                         delete uwc;
01347                                         uwc = 0;
01348                                 }
01349                         }
01350                 }
01351         }
01352         if( to_unwrapped ) {delete to_unwrapped;to_unwrapped = 0;}
01353         if( to_shrunk_unwrapped ) {     delete to_shrunk_unwrapped;     to_shrunk_unwrapped = 0;}
01354         if (to_unwrapped_copy) { delete to_unwrapped_copy; to_unwrapped_copy = 0; }
01355         if (to_flip_unwrapped) { delete to_flip_unwrapped; to_flip_unwrapped = 0; }
01356         if (to_flip_unwrapped_copy) { delete to_flip_unwrapped_copy; to_flip_unwrapped_copy = 0;}
01357 
01358         bestang *= (float)EMConsts::rad2deg;
01359         Transform t(Dict("type","2d","alpha",(float)bestang));
01360         t.set_pre_trans(Vec2f(-bestdx,-bestdy));
01361         if (bestflip) {
01362                 t.set_mirror(true);
01363         }
01364 
01365         EMData* ret = this_img->process("xform",Dict("transform",&t));
01366         ret->set_attr("xform.align2d",&t);
01367 
01368         return ret;
01369 }

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

Implements EMAN::Aligner.

Definition at line 1097 of file aligner.h.

01098                 {
01099                         return "Experimental full 2D alignment with handedness check using semi-exhaustive search (not necessarily better than RTFBest)";
01100                 }

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 1092 of file aligner.h.

01093                 {
01094                         return NAME;
01095                 }

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

Implements EMAN::Aligner.

Definition at line 1107 of file aligner.h.

References EMAN::TypeDict::put().

01108                 {
01109                         TypeDict d;
01110 
01111                         d.put("flip", EMObject::EMDATA);
01112                         d.put("maxshift", EMObject::INT, "Maximum translation in pixels");
01113                         return d;
01114                 }

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

Definition at line 1102 of file aligner.h.

01103                 {
01104                         return new RTFExhaustiveAligner();
01105                 }


Member Data Documentation

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

Definition at line 76 of file aligner.cpp.


The documentation for this class was generated from the following files:
Generated on Tue Jun 11 13:47:47 2013 for EMAN2 by  doxygen 1.3.9.1