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

rotational, translational and flip alignment More...

#include <aligner.h>

Inheritance diagram for EMAN::RotateTranslateFlipAligner:

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Collaboration diagram for EMAN::RotateTranslateFlipAligner:

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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 TypeDict static_get_param_types ()

Static Public Attributes

static const string NAME = "rotate_translate_flip"

Detailed Description

rotational, translational and flip alignment

Parameters:
flip 
usedot 
maxshift Maximum translation in pixels
rfp_mode Either 0,1 or 2. A temporary flag for testing the rotational foot print

Definition at line 431 of file aligner.h.


Member Function Documentation

virtual EMData* EMAN::RotateTranslateFlipAligner::align EMData this_img,
EMData to_img
const [inline, virtual]
 

Implements EMAN::Aligner.

Definition at line 436 of file aligner.h.

References align().

00437                 {
00438                         return align(this_img, to_img, "sqeuclidean", Dict());
00439                 }

EMData * RotateTranslateFlipAligner::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 419 of file aligner.cpp.

References EMAN::EMData::align(), EMAN::EMData::cmp(), cmp1(), cmp2(), EMAN::EMData::get_attr(), EMAN::Aligner::params, EMAN::EMData::process(), EMAN::EMData::process_inplace(), EMAN::EMData::set_attr(), EMAN::Dict::set_default(), EMAN::Transform::set_mirror(), and t.

Referenced by align().

00421 {
00422         // Get the non flipped rotational, tranlsationally aligned image
00423         Dict rt_params("maxshift", params["maxshift"], "rfp_mode", params.set_default("rfp_mode",0),"useflcf",params.set_default("useflcf",0));
00424         EMData *rot_trans_align = this_img->align("rotate_translate",to,rt_params,cmp_name, cmp_params);
00425 
00426         // Do the same alignment, but using the flipped version of the image
00427         EMData *flipped = params.set_default("flip", (EMData *) 0);
00428         bool delete_flag = false;
00429         if (flipped == 0) {
00430                 flipped = to->process("xform.flip", Dict("axis", "x"));
00431                 delete_flag = true;
00432         }
00433 
00434         EMData * rot_trans_align_flip = this_img->align("rotate_translate", flipped, rt_params, cmp_name, cmp_params);
00435         Transform* t = rot_trans_align_flip->get_attr("xform.align2d");
00436         t->set_mirror(true);
00437         rot_trans_align_flip->set_attr("xform.align2d",t);
00438         delete t;
00439 
00440         // Now finally decide on what is the best answer
00441         float cmp1 = rot_trans_align->cmp(cmp_name, to, cmp_params);
00442         float cmp2 = rot_trans_align_flip->cmp(cmp_name, flipped, cmp_params);
00443 
00444         if (delete_flag){
00445                 if(flipped) {
00446                         delete flipped;
00447                         flipped = 0;
00448                 }
00449         }
00450 
00451         EMData *result = 0;
00452         if (cmp1 < cmp2 )  {
00453 
00454                 if( rot_trans_align_flip ) {
00455                         delete rot_trans_align_flip;
00456                         rot_trans_align_flip = 0;
00457                 }
00458                 result = rot_trans_align;
00459         }
00460         else {
00461                 if( rot_trans_align ) {
00462                         delete rot_trans_align;
00463                         rot_trans_align = 0;
00464                 }
00465                 result = rot_trans_align_flip;
00466                 result->process_inplace("xform.flip",Dict("axis","x"));
00467         }
00468 
00469         return result;
00470 }

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

Implements EMAN::Aligner.

Definition at line 446 of file aligner.h.

00447                 {
00448                         return " Does two 'rotate_translate' alignments, one to accommodate for possible handedness change. Decided which alignment is better using a comparitor and returns the aligned image as the solution";
00449                 }

virtual string EMAN::RotateTranslateFlipAligner::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 441 of file aligner.h.

References NAME.

00442                 {
00443                         return NAME;
00444                 }

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

Implements EMAN::Aligner.

Definition at line 456 of file aligner.h.

References static_get_param_types().

00457                 {
00458                         return static_get_param_types();
00459                 }

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

Definition at line 451 of file aligner.h.

00452                 {
00453                         return new RotateTranslateFlipAligner();
00454                 }

static TypeDict EMAN::RotateTranslateFlipAligner::static_get_param_types  )  [inline, static]
 

Definition at line 461 of file aligner.h.

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

Referenced by get_param_types().

00461                                                          {
00462                         TypeDict d;
00463 
00464                         d.put("flip", EMObject::EMDATA);
00465                         d.put("usedot", EMObject::INT);
00466                         d.put("maxshift", EMObject::INT, "Maximum translation in pixels");
00467                         d.put("rfp_mode", EMObject::INT,"Either 0,1 or 2. A temporary flag for testing the rotational foot print");
00468                         d.put("useflcf", EMObject::INT,"Use Fast Local Correlation Function rather than CCF for translational alignment");
00469                         return d;
00470                 }


Member Data Documentation

const string RotateTranslateFlipAligner::NAME = "rotate_translate_flip" [static]
 

Definition at line 472 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