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 1092 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().

01094 {
01095         EMData *flip = params.set_default("flip", (EMData *) 0);
01096         int maxshift = params.set_default("maxshift", this_img->get_xsize()/8);
01097         if (maxshift < 2) throw InvalidParameterException("maxshift must be greater than or equal to 2");
01098 
01099         int ny = this_img->get_ysize();
01100         int xst = (int) floor(2 * M_PI * ny);
01101         xst = Util::calc_best_fft_size(xst);
01102 
01103         Dict d("n",2);
01104         EMData *to_shrunk_unwrapped = to->process("math.medianshrink",d);
01105 
01106         int to_copy_r2 = to_shrunk_unwrapped->get_ysize() / 2 - 2 - maxshift / 2;
01107         EMData *tmp = to_shrunk_unwrapped->unwrap(4, to_copy_r2, xst / 2, 0, 0, true);
01108         if( to_shrunk_unwrapped )
01109         {
01110                 delete to_shrunk_unwrapped;
01111                 to_shrunk_unwrapped = 0;
01112         }
01113         to_shrunk_unwrapped = tmp;
01114 
01115         EMData *to_shrunk_unwrapped_copy = to_shrunk_unwrapped->copy();
01116         EMData* to_unwrapped = to->unwrap(4, to->get_ysize() / 2 - 2 - maxshift, xst, 0, 0, true);
01117         EMData *to_unwrapped_copy = to_unwrapped->copy();
01118 
01119         bool delete_flipped = true;
01120         EMData *flipped = 0;
01121         if (flip) {
01122                 delete_flipped = false;
01123                 flipped = flip;
01124         }
01125         else {
01126                 flipped = to->process("xform.flip", Dict("axis", "x"));
01127         }
01128         EMData *to_shrunk_flipped_unwrapped = flipped->process("math.medianshrink",d);
01129         tmp = to_shrunk_flipped_unwrapped->unwrap(4, to_copy_r2, xst / 2, 0, 0, true);
01130         if( to_shrunk_flipped_unwrapped )
01131         {
01132                 delete to_shrunk_flipped_unwrapped;
01133                 to_shrunk_flipped_unwrapped = 0;
01134         }
01135         to_shrunk_flipped_unwrapped = tmp;
01136         EMData *to_shrunk_flipped_unwrapped_copy = to_shrunk_flipped_unwrapped->copy();
01137         EMData* to_flip_unwrapped = flipped->unwrap(4, to->get_ysize() / 2 - 2 - maxshift, xst, 0, 0, true);
01138         EMData* to_flip_unwrapped_copy = to_flip_unwrapped->copy();
01139 
01140         if (delete_flipped && flipped != 0) {
01141                 delete flipped;
01142                 flipped = 0;
01143         }
01144 
01145         EMData *this_shrunk_2 = this_img->process("math.medianshrink",d);
01146 
01147         float bestval = FLT_MAX;
01148         float bestang = 0;
01149         int bestflip = 0;
01150         float bestdx = 0;
01151         float bestdy = 0;
01152 
01153         int half_maxshift = maxshift / 2;
01154 
01155         int ur2 = this_shrunk_2->get_ysize() / 2 - 2 - half_maxshift;
01156         for (int dy = -half_maxshift; dy <= half_maxshift; dy += 1) {
01157                 for (int dx = -half_maxshift; dx <= half_maxshift; dx += 1) {
01158 #ifdef  _WIN32
01159                         if (_hypot(dx, dy) <= half_maxshift) {
01160 #else
01161                         if (hypot(dx, dy) <= half_maxshift) {
01162 #endif
01163                                 EMData *uw = this_shrunk_2->unwrap(4, ur2, xst / 2, dx, dy, true);
01164                                 EMData *uwc = uw->copy();
01165                                 EMData *a = uw->calc_ccfx(to_shrunk_unwrapped);
01166 
01167                                 uwc->rotate_x(a->calc_max_index());
01168                                 float cm = uwc->cmp(cmp_name, to_shrunk_unwrapped_copy, cmp_params);
01169                                 if (cm < bestval) {
01170                                         bestval = cm;
01171                                         bestang = (float) (2.0 * M_PI * a->calc_max_index() / a->get_xsize());
01172                                         bestdx = (float)dx;
01173                                         bestdy = (float)dy;
01174                                         bestflip = 0;
01175                                 }
01176 
01177 
01178                                 if( a )
01179                                 {
01180                                         delete a;
01181                                         a = 0;
01182                                 }
01183                                 if( uw )
01184                                 {
01185                                         delete uw;
01186                                         uw = 0;
01187                                 }
01188                                 if( uwc )
01189                                 {
01190                                         delete uwc;
01191                                         uwc = 0;
01192                                 }
01193                                 uw = this_shrunk_2->unwrap(4, ur2, xst / 2, dx, dy, true);
01194                                 uwc = uw->copy();
01195                                 a = uw->calc_ccfx(to_shrunk_flipped_unwrapped);
01196 
01197                                 uwc->rotate_x(a->calc_max_index());
01198                                 cm = uwc->cmp(cmp_name, to_shrunk_flipped_unwrapped_copy, cmp_params);
01199                                 if (cm < bestval) {
01200                                         bestval = cm;
01201                                         bestang = (float) (2.0 * M_PI * a->calc_max_index() / a->get_xsize());
01202                                         bestdx = (float)dx;
01203                                         bestdy = (float)dy;
01204                                         bestflip = 1;
01205                                 }
01206 
01207                                 if( a )
01208                                 {
01209                                         delete a;
01210                                         a = 0;
01211                                 }
01212 
01213                                 if( uw )
01214                                 {
01215                                         delete uw;
01216                                         uw = 0;
01217                                 }
01218                                 if( uwc )
01219                                 {
01220                                         delete uwc;
01221                                         uwc = 0;
01222                                 }
01223                         }
01224                 }
01225         }
01226         if( this_shrunk_2 )
01227         {
01228                 delete this_shrunk_2;
01229                 this_shrunk_2 = 0;
01230         }
01231         if( to_shrunk_unwrapped )
01232         {
01233                 delete to_shrunk_unwrapped;
01234                 to_shrunk_unwrapped = 0;
01235         }
01236         if( to_shrunk_unwrapped_copy )
01237         {
01238                 delete to_shrunk_unwrapped_copy;
01239                 to_shrunk_unwrapped_copy = 0;
01240         }
01241         if( to_shrunk_flipped_unwrapped )
01242         {
01243                 delete to_shrunk_flipped_unwrapped;
01244                 to_shrunk_flipped_unwrapped = 0;
01245         }
01246         if( to_shrunk_flipped_unwrapped_copy )
01247         {
01248                 delete to_shrunk_flipped_unwrapped_copy;
01249                 to_shrunk_flipped_unwrapped_copy = 0;
01250         }
01251         bestdx *= 2;
01252         bestdy *= 2;
01253         bestval = FLT_MAX;
01254 
01255         float bestdx2 = bestdx;
01256         float bestdy2 = bestdy;
01257         // Note I tried steps less than 1.0 (sub pixel precision) and it actually appeared detrimental
01258         // So my advice is to stick with dx += 1.0 etc unless you really are looking to fine tune this
01259         // algorithm
01260         for (float dy = bestdy2 - 3; dy <= bestdy2 + 3; dy += 1.0 ) {
01261                 for (float dx = bestdx2 - 3; dx <= bestdx2 + 3; dx += 1.0 ) {
01262 
01263 #ifdef  _WIN32
01264                         if (_hypot(dx, dy) <= maxshift) {
01265 #else
01266                         if (hypot(dx, dy) <= maxshift) {
01267 #endif
01268                                 EMData *uw = this_img->unwrap(4, this_img->get_ysize() / 2 - 2 - maxshift, xst, (int)dx, (int)dy, true);
01269                                 EMData *uwc = uw->copy();
01270                                 EMData *a = uw->calc_ccfx(to_unwrapped);
01271 
01272                                 uwc->rotate_x(a->calc_max_index());
01273                                 float cm = uwc->cmp(cmp_name, to_unwrapped_copy, cmp_params);
01274 
01275                                 if (cm < bestval) {
01276                                         bestval = cm;
01277                                         bestang = (float)(2.0 * M_PI * a->calc_max_index() / a->get_xsize());
01278                                         bestdx = dx;
01279                                         bestdy = dy;
01280                                         bestflip = 0;
01281                                 }
01282 
01283                                 if( a )
01284                                 {
01285                                         delete a;
01286                                         a = 0;
01287                                 }
01288                                 if( uw )
01289                                 {
01290                                         delete uw;
01291                                         uw = 0;
01292                                 }
01293                                 if( uwc )
01294                                 {
01295                                         delete uwc;
01296                                         uwc = 0;
01297                                 }
01298                                 uw = this_img->unwrap(4, this_img->get_ysize() / 2 - 2 - maxshift, xst, (int)dx, (int)dy, true);
01299                                 uwc = uw->copy();
01300                                 a = uw->calc_ccfx(to_flip_unwrapped);
01301 
01302                                 uwc->rotate_x(a->calc_max_index());
01303                                 cm = uwc->cmp(cmp_name, to_flip_unwrapped_copy, cmp_params);
01304 
01305                                 if (cm < bestval) {
01306                                         bestval = cm;
01307                                         bestang = (float)(2.0 * M_PI * a->calc_max_index() / a->get_xsize());
01308                                         bestdx = dx;
01309                                         bestdy = dy;
01310                                         bestflip = 1;
01311                                 }
01312 
01313                                 if( a )
01314                                 {
01315                                         delete a;
01316                                         a = 0;
01317                                 }
01318                                 if( uw )
01319                                 {
01320                                         delete uw;
01321                                         uw = 0;
01322                                 }
01323                                 if( uwc )
01324                                 {
01325                                         delete uwc;
01326                                         uwc = 0;
01327                                 }
01328                         }
01329                 }
01330         }
01331         if( to_unwrapped ) {delete to_unwrapped;to_unwrapped = 0;}
01332         if( to_shrunk_unwrapped ) {     delete to_shrunk_unwrapped;     to_shrunk_unwrapped = 0;}
01333         if (to_unwrapped_copy) { delete to_unwrapped_copy; to_unwrapped_copy = 0; }
01334         if (to_flip_unwrapped) { delete to_flip_unwrapped; to_flip_unwrapped = 0; }
01335         if (to_flip_unwrapped_copy) { delete to_flip_unwrapped_copy; to_flip_unwrapped_copy = 0;}
01336 
01337         bestang *= (float)EMConsts::rad2deg;
01338         Transform t(Dict("type","2d","alpha",(float)bestang));
01339         t.set_pre_trans(Vec2f(-bestdx,-bestdy));
01340         if (bestflip) {
01341                 t.set_mirror(true);
01342         }
01343 
01344         EMData* ret = this_img->process("xform",Dict("transform",&t));
01345         ret->set_attr("xform.align2d",&t);
01346 
01347         return ret;
01348 }

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 Thu May 3 10:08:47 2012 for EMAN2 by  doxygen 1.4.7