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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

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 479 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 484 of file aligner.h.

References align().

00485                 {
00486                         return align(this_img, to_img, "sqeuclidean", Dict());
00487                 }

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 532 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(), EMAN::Transform::set_mirror(), EMAN::Transform::set_pre_trans(), t, and EMAN::EMData::unwrap().

Referenced by align().

00534 {
00535         EMData *flip = params.set_default("flip", (EMData *) 0);
00536         int maxshift = params.set_default("maxshift", this_img->get_xsize()/8);
00537         if (maxshift < 2) throw InvalidParameterException("maxshift must be greater than or equal to 2");
00538 
00539         int ny = this_img->get_ysize();
00540         int xst = (int) floor(2 * M_PI * ny);
00541         xst = Util::calc_best_fft_size(xst);
00542 
00543         Dict d("n",2);
00544         EMData *to_shrunk_unwrapped = to->process("math.medianshrink",d);
00545 
00546         int to_copy_r2 = to_shrunk_unwrapped->get_ysize() / 2 - 2 - maxshift / 2;
00547         EMData *tmp = to_shrunk_unwrapped->unwrap(4, to_copy_r2, xst / 2, 0, 0, true);
00548         if( to_shrunk_unwrapped )
00549         {
00550                 delete to_shrunk_unwrapped;
00551                 to_shrunk_unwrapped = 0;
00552         }
00553         to_shrunk_unwrapped = tmp;
00554 
00555         EMData *to_shrunk_unwrapped_copy = to_shrunk_unwrapped->copy();
00556         EMData* to_unwrapped = to->unwrap(4, to->get_ysize() / 2 - 2 - maxshift, xst, 0, 0, true);
00557         EMData *to_unwrapped_copy = to_unwrapped->copy();
00558 
00559         bool delete_flipped = true;
00560         EMData *flipped = 0;
00561         if (flip) {
00562                 delete_flipped = false;
00563                 flipped = flip;
00564         }
00565         else {
00566                 flipped = to->process("xform.flip", Dict("axis", "x"));
00567         }
00568         EMData *to_shrunk_flipped_unwrapped = flipped->process("math.medianshrink",d);
00569         tmp = to_shrunk_flipped_unwrapped->unwrap(4, to_copy_r2, xst / 2, 0, 0, true);
00570         if( to_shrunk_flipped_unwrapped )
00571         {
00572                 delete to_shrunk_flipped_unwrapped;
00573                 to_shrunk_flipped_unwrapped = 0;
00574         }
00575         to_shrunk_flipped_unwrapped = tmp;
00576         EMData *to_shrunk_flipped_unwrapped_copy = to_shrunk_flipped_unwrapped->copy();
00577         EMData* to_flip_unwrapped = flipped->unwrap(4, to->get_ysize() / 2 - 2 - maxshift, xst, 0, 0, true);
00578         EMData* to_flip_unwrapped_copy = to_flip_unwrapped->copy();
00579 
00580         if (delete_flipped && flipped != 0) {
00581                 delete flipped;
00582                 flipped = 0;
00583         }
00584 
00585         EMData *this_shrunk_2 = this_img->process("math.medianshrink",d);
00586 
00587         float bestval = FLT_MAX;
00588         float bestang = 0;
00589         int bestflip = 0;
00590         float bestdx = 0;
00591         float bestdy = 0;
00592 
00593         int half_maxshift = maxshift / 2;
00594 
00595         int ur2 = this_shrunk_2->get_ysize() / 2 - 2 - half_maxshift;
00596         for (int dy = -half_maxshift; dy <= half_maxshift; dy += 1) {
00597                 for (int dx = -half_maxshift; dx <= half_maxshift; dx += 1) {
00598 #ifdef  _WIN32
00599                         if (_hypot(dx, dy) <= half_maxshift) {
00600 #else
00601                         if (hypot(dx, dy) <= half_maxshift) {
00602 #endif
00603                                 EMData *uw = this_shrunk_2->unwrap(4, ur2, xst / 2, dx, dy, true);
00604                                 EMData *uwc = uw->copy();
00605                                 EMData *a = uw->calc_ccfx(to_shrunk_unwrapped);
00606 
00607                                 uwc->rotate_x(a->calc_max_index());
00608                                 float cm = uwc->cmp(cmp_name, to_shrunk_unwrapped_copy, cmp_params);
00609                                 if (cm < bestval) {
00610                                         bestval = cm;
00611                                         bestang = (float) (2.0 * M_PI * a->calc_max_index() / a->get_xsize());
00612                                         bestdx = (float)dx;
00613                                         bestdy = (float)dy;
00614                                         bestflip = 0;
00615                                 }
00616 
00617 
00618                                 if( a )
00619                                 {
00620                                         delete a;
00621                                         a = 0;
00622                                 }
00623                                 if( uw )
00624                                 {
00625                                         delete uw;
00626                                         uw = 0;
00627                                 }
00628                                 if( uwc )
00629                                 {
00630                                         delete uwc;
00631                                         uwc = 0;
00632                                 }
00633                                 uw = this_shrunk_2->unwrap(4, ur2, xst / 2, dx, dy, true);
00634                                 uwc = uw->copy();
00635                                 a = uw->calc_ccfx(to_shrunk_flipped_unwrapped);
00636 
00637                                 uwc->rotate_x(a->calc_max_index());
00638                                 cm = uwc->cmp(cmp_name, to_shrunk_flipped_unwrapped_copy, cmp_params);
00639                                 if (cm < bestval) {
00640                                         bestval = cm;
00641                                         bestang = (float) (2.0 * M_PI * a->calc_max_index() / a->get_xsize());
00642                                         bestdx = (float)dx;
00643                                         bestdy = (float)dy;
00644                                         bestflip = 1;
00645                                 }
00646 
00647                                 if( a )
00648                                 {
00649                                         delete a;
00650                                         a = 0;
00651                                 }
00652 
00653                                 if( uw )
00654                                 {
00655                                         delete uw;
00656                                         uw = 0;
00657                                 }
00658                                 if( uwc )
00659                                 {
00660                                         delete uwc;
00661                                         uwc = 0;
00662                                 }
00663                         }
00664                 }
00665         }
00666         if( this_shrunk_2 )
00667         {
00668                 delete this_shrunk_2;
00669                 this_shrunk_2 = 0;
00670         }
00671         if( to_shrunk_unwrapped )
00672         {
00673                 delete to_shrunk_unwrapped;
00674                 to_shrunk_unwrapped = 0;
00675         }
00676         if( to_shrunk_unwrapped_copy )
00677         {
00678                 delete to_shrunk_unwrapped_copy;
00679                 to_shrunk_unwrapped_copy = 0;
00680         }
00681         if( to_shrunk_flipped_unwrapped )
00682         {
00683                 delete to_shrunk_flipped_unwrapped;
00684                 to_shrunk_flipped_unwrapped = 0;
00685         }
00686         if( to_shrunk_flipped_unwrapped_copy )
00687         {
00688                 delete to_shrunk_flipped_unwrapped_copy;
00689                 to_shrunk_flipped_unwrapped_copy = 0;
00690         }
00691         bestdx *= 2;
00692         bestdy *= 2;
00693         bestval = FLT_MAX;
00694 
00695         float bestdx2 = bestdx;
00696         float bestdy2 = bestdy;
00697         // Note I tried steps less than 1.0 (sub pixel precision) and it actually appeared detrimental
00698         // So my advice is to stick with dx += 1.0 etc unless you really are looking to fine tune this
00699         // algorithm
00700         for (float dy = bestdy2 - 3; dy <= bestdy2 + 3; dy += 1.0 ) {
00701                 for (float dx = bestdx2 - 3; dx <= bestdx2 + 3; dx += 1.0 ) {
00702 
00703 #ifdef  _WIN32
00704                         if (_hypot(dx, dy) <= maxshift) {
00705 #else
00706                         if (hypot(dx, dy) <= maxshift) {
00707 #endif
00708                                 EMData *uw = this_img->unwrap(4, this_img->get_ysize() / 2 - 2 - maxshift, xst, (int)dx, (int)dy, true);
00709                                 EMData *uwc = uw->copy();
00710                                 EMData *a = uw->calc_ccfx(to_unwrapped);
00711 
00712                                 uwc->rotate_x(a->calc_max_index());
00713                                 float cm = uwc->cmp(cmp_name, to_unwrapped_copy, cmp_params);
00714 
00715                                 if (cm < bestval) {
00716                                         bestval = cm;
00717                                         bestang = (float)(2.0 * M_PI * a->calc_max_index() / a->get_xsize());
00718                                         bestdx = dx;
00719                                         bestdy = dy;
00720                                         bestflip = 0;
00721                                 }
00722 
00723                                 if( a )
00724                                 {
00725                                         delete a;
00726                                         a = 0;
00727                                 }
00728                                 if( uw )
00729                                 {
00730                                         delete uw;
00731                                         uw = 0;
00732                                 }
00733                                 if( uwc )
00734                                 {
00735                                         delete uwc;
00736                                         uwc = 0;
00737                                 }
00738                                 uw = this_img->unwrap(4, this_img->get_ysize() / 2 - 2 - maxshift, xst, (int)dx, (int)dy, true);
00739                                 uwc = uw->copy();
00740                                 a = uw->calc_ccfx(to_flip_unwrapped);
00741 
00742                                 uwc->rotate_x(a->calc_max_index());
00743                                 cm = uwc->cmp(cmp_name, to_flip_unwrapped_copy, cmp_params);
00744 
00745                                 if (cm < bestval) {
00746                                         bestval = cm;
00747                                         bestang = (float)(2.0 * M_PI * a->calc_max_index() / a->get_xsize());
00748                                         bestdx = dx;
00749                                         bestdy = dy;
00750                                         bestflip = 1;
00751                                 }
00752 
00753                                 if( a )
00754                                 {
00755                                         delete a;
00756                                         a = 0;
00757                                 }
00758                                 if( uw )
00759                                 {
00760                                         delete uw;
00761                                         uw = 0;
00762                                 }
00763                                 if( uwc )
00764                                 {
00765                                         delete uwc;
00766                                         uwc = 0;
00767                                 }
00768                         }
00769                 }
00770         }
00771         if( to_unwrapped ) {delete to_unwrapped;to_unwrapped = 0;}
00772         if( to_shrunk_unwrapped ) {     delete to_shrunk_unwrapped;     to_shrunk_unwrapped = 0;}
00773         if (to_unwrapped_copy) { delete to_unwrapped_copy; to_unwrapped_copy = 0; }
00774         if (to_flip_unwrapped) { delete to_flip_unwrapped; to_flip_unwrapped = 0; }
00775         if (to_flip_unwrapped_copy) { delete to_flip_unwrapped_copy; to_flip_unwrapped_copy = 0;}
00776 
00777         bestang *= (float)EMConsts::rad2deg;
00778         Transform t(Dict("type","2d","alpha",(float)bestang));
00779         t.set_pre_trans(Vec2f(-bestdx,-bestdy));
00780         if (bestflip) {
00781                 t.set_mirror(true);
00782         }
00783 
00784         EMData* ret = this_img->process("xform",Dict("transform",&t));
00785         ret->set_attr("xform.align2d",&t);
00786 
00787         return ret;
00788 }

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

Implements EMAN::Aligner.

Definition at line 494 of file aligner.h.

00495                 {
00496                         return "Experimental full 2D alignment with handedness check using semi-exhaustive search (not necessarily better than RTFBest)";
00497                 }

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 489 of file aligner.h.

References NAME.

00490                 {
00491                         return NAME;
00492                 }

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

Implements EMAN::Aligner.

Definition at line 504 of file aligner.h.

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

00505                 {
00506                         TypeDict d;
00507 
00508                         d.put("flip", EMObject::EMDATA);
00509                         d.put("maxshift", EMObject::INT, "Maximum translation in pixels");
00510                         return d;
00511                 }

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

Definition at line 499 of file aligner.h.

00500                 {
00501                         return new RTFExhaustiveAligner();
00502                 }


Member Data Documentation

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

Definition at line 513 of file aligner.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Mon Jul 19 13:05:47 2010 for EMAN2 by  doxygen 1.4.4