EMAN::RotateTranslateAligner Class Reference
[a function or class that is CUDA enabled]

rotational, translational alignment More...

#include <aligner.h>

Inheritance diagram for EMAN::RotateTranslateAligner:

Inheritance graph
[legend]
Collaboration diagram for EMAN::RotateTranslateAligner:

Collaboration graph
[legend]
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 = "rotate_translate"

Detailed Description

rotational, translational alignment

Parameters:
maxshift Maximum translation in pixels
nozero Zero translation not permitted (useful for CCD images)
rfp_mode Either 0,1 or 2. A temporary flag for testing the rotational foot print

Definition at line 343 of file aligner.h.


Member Function Documentation

virtual EMData* EMAN::RotateTranslateAligner::align ( EMData this_img,
EMData to_img 
) const [inline, virtual]

Implements EMAN::Aligner.

Definition at line 349 of file aligner.h.

References align().

00350                 {
00351                         return align(this_img, to_img, "sqeuclidean", Dict());
00352                 }

EMData * RotateTranslateAligner::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 544 of file aligner.cpp.

References EMAN::EMData::align(), EMAN::RotationalAligner::align_180_ambiguous(), EMAN::EMData::cmp(), cmp1(), cmp2(), EMAN::EMData::copy(), EMAN::EMData::get_attr(), EMAN::Transform::get_rotation(), EMAN::Aligner::params, EMAN::EMData::process_inplace(), EMAN::EMData::set_attr(), EMAN::Dict::set_default(), and t.

Referenced by align().

00546 {
00547 
00548 #ifdef EMAN2_USING_CUDA
00549         if(EMData::usecuda == 1) {
00550                 //if(!this_img->getcudarwdata()) this_img->copy_to_cuda();
00551                 //if(!to->getcudarwdata()) to->copy_to_cuda();
00552         }
00553 #endif
00554 
00555         // Get the 180 degree ambiguously rotationally aligned and its 180 degree rotation counterpart
00556         int rfp_mode = params.set_default("rfp_mode",0);
00557         EMData *rot_align  =  RotationalAligner::align_180_ambiguous(this_img,to,rfp_mode);
00558         Transform * tmp = rot_align->get_attr("xform.align2d");
00559         Dict rot = tmp->get_rotation("2d");
00560         float rotate_angle_solution = rot["alpha"];
00561         delete tmp;
00562 
00563         EMData *rot_align_180 = rot_align->copy();
00564         rot_align_180->process_inplace("math.rotate.180");
00565 
00566         Dict trans_params;
00567         trans_params["intonly"]  = 0;
00568         trans_params["maxshift"] = params.set_default("maxshift", -1);
00569         trans_params["useflcf"]=params.set_default("useflcf",0);
00570 
00571         // Do the first case translational alignment
00572         trans_params["nozero"]   = params.set_default("nozero",false);
00573         EMData* rot_trans = rot_align->align("translational", to, trans_params, cmp_name, cmp_params);
00574         if( rot_align ) { // Clean up
00575                 delete rot_align;
00576                 rot_align = 0;
00577         }
00578 
00579         // Do the second case translational alignment
00580         EMData*  rot_180_trans = rot_align_180->align("translational", to, trans_params, cmp_name, cmp_params);
00581         if( rot_align_180 )     { // Clean up
00582                 delete rot_align_180;
00583                 rot_align_180 = 0;
00584         }
00585 
00586         // Finally decide on the result
00587         float cmp1 = rot_trans->cmp(cmp_name, to, cmp_params);
00588         float cmp2 = rot_180_trans->cmp(cmp_name, to, cmp_params);
00589 
00590         EMData *result = 0;
00591         if (cmp1 < cmp2) { // Assumes smaller is better - thus all comparitors should support "smaller is better"
00592                 if( rot_180_trans )     {
00593                         delete rot_180_trans;
00594                         rot_180_trans = 0;
00595                 }
00596                 result = rot_trans;
00597         }
00598         else {
00599                 if( rot_trans ) {
00600                         delete rot_trans;
00601                         rot_trans = 0;
00602                 }
00603                 result = rot_180_trans;
00604                 rotate_angle_solution -= 180.f;
00605         }
00606 
00607         Transform* t = result->get_attr("xform.align2d");
00608         t->set_rotation(Dict("type","2d","alpha",rotate_angle_solution));
00609         result->set_attr("xform.align2d",t);
00610         delete t;
00611 
00612         return result;
00613 }

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

Implements EMAN::Aligner.

Definition at line 359 of file aligner.h.

00360                 {
00361                         return "Performs rotational alignment and follows this with translational alignment.";
00362                 }

virtual string EMAN::RotateTranslateAligner::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 354 of file aligner.h.

References NAME.

00355                 {
00356                         return NAME;
00357                 }

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

Implements EMAN::Aligner.

Definition at line 369 of file aligner.h.

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

00370                 {
00371                         TypeDict d;
00372                         //d.put("usedot", EMObject::INT);
00373                         d.put("maxshift", EMObject::INT, "Maximum translation in pixels");
00374                         d.put("nozero", EMObject::INT,"Zero translation not permitted (useful for CCD images)");
00375                         d.put("rfp_mode", EMObject::INT,"Either 0,1 or 2. A temporary flag for testing the rotational foot print");
00376                         d.put("useflcf", EMObject::INT,"Use Fast Local Correlation Function rather than CCF for translational alignment");
00377                         return d;
00378                 }

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

Definition at line 364 of file aligner.h.

00365                 {
00366                         return new RotateTranslateAligner();
00367                 }


Member Data Documentation

const string RotateTranslateAligner::NAME = "rotate_translate" [static]

Definition at line 380 of file aligner.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Tue Jul 12 13:47:52 2011 for EMAN2 by  doxygen 1.4.7