EMAN::RotateTranslateFlipAligner Class Reference

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 621 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 626 of file aligner.h.

References align().

00627                 {
00628                         return align(this_img, to_img, "sqeuclidean", Dict());
00629                 }

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 623 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(), and t.

Referenced by align().

00625 {
00626         // Get the non flipped rotational, tranlsationally aligned image
00627         Dict rt_params("maxshift", params["maxshift"], "rfp_mode", params.set_default("rfp_mode",0),"useflcf",params.set_default("useflcf",0));
00628         EMData *rot_trans_align = this_img->align("rotate_translate",to,rt_params,cmp_name, cmp_params);
00629         
00630         // Do the same alignment, but using the flipped version of the image
00631         EMData *flipped = params.set_default("flip", (EMData *) 0);
00632         bool delete_flag = false;
00633         if (flipped == 0) {
00634                 flipped = to->process("xform.flip", Dict("axis", "x"));
00635                 delete_flag = true;
00636         }
00637 
00638         EMData * rot_trans_align_flip = this_img->align("rotate_translate", flipped, rt_params, cmp_name, cmp_params);
00639         Transform* t = rot_trans_align_flip->get_attr("xform.align2d");
00640         t->set_mirror(true);
00641         rot_trans_align_flip->set_attr("xform.align2d",t);
00642         delete t;
00643 
00644         // Now finally decide on what is the best answer
00645         float cmp1 = rot_trans_align->cmp(cmp_name, to, cmp_params);
00646         float cmp2 = rot_trans_align_flip->cmp(cmp_name, flipped, cmp_params);
00647 
00648         if (delete_flag){
00649                 if(flipped) {
00650                         delete flipped;
00651                         flipped = 0;
00652                 }
00653         }
00654 
00655         EMData *result = 0;
00656         if (cmp1 < cmp2 )  {
00657 
00658                 if( rot_trans_align_flip ) {
00659                         delete rot_trans_align_flip;
00660                         rot_trans_align_flip = 0;
00661                 }
00662                 result = rot_trans_align;
00663         }
00664         else {
00665                 if( rot_trans_align ) {
00666                         delete rot_trans_align;
00667                         rot_trans_align = 0;
00668                 }
00669                 result = rot_trans_align_flip;
00670                 result->process_inplace("xform.flip",Dict("axis","x"));
00671         }
00672 
00673         return result;
00674 }

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

Implements EMAN::Aligner.

Definition at line 636 of file aligner.h.

00637                 {
00638                         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";
00639                 }

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 631 of file aligner.h.

References NAME.

00632                 {
00633                         return NAME;
00634                 }

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

Implements EMAN::Aligner.

Definition at line 646 of file aligner.h.

References static_get_param_types().

00647                 {
00648                         return static_get_param_types();
00649                 }

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

Definition at line 641 of file aligner.h.

00642                 {
00643                         return new RotateTranslateFlipAligner();
00644                 }

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

Definition at line 651 of file aligner.h.

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

Referenced by get_param_types().

00651                                                          {
00652                         TypeDict d;
00653 
00654                         d.put("flip", EMObject::EMDATA);
00655                         d.put("usedot", EMObject::INT);
00656                         d.put("maxshift", EMObject::INT, "Maximum translation in pixels");
00657                         d.put("rfp_mode", EMObject::INT,"Either 0,1 or 2. A temporary flag for testing the rotational foot print");
00658                         d.put("useflcf", EMObject::INT,"Use Fast Local Correlation Function rather than CCF for translational alignment");
00659                         return d;
00660                 }


Member Data Documentation

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

Definition at line 662 of file aligner.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Thu Nov 17 12:45:08 2011 for EMAN2 by  doxygen 1.4.7