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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

AlignerNEW ()
TypeDict static_get_param_types ()

Static Public Attributes

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 811 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 816 of file aligner.h.

References align().

00817                 {
00818                         return align(this_img, to_img, "sqeuclidean", Dict());
00819                 }

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 793 of file aligner.cpp.

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

00795 {
00796         // Get the non flipped rotational, tranlsationally aligned image
00797         Dict rt_params("maxshift", params["maxshift"], "rfp_mode", params.set_default("rfp_mode",2),"useflcf",params.set_default("useflcf",0),"zscore",params.set_default("zscore",0));
00798         EMData *rot_trans_align = this_img->align("rotate_translate",to,rt_params,cmp_name, cmp_params);
00799         
00800         // Do the same alignment, but using the flipped version of the image
00801         EMData *flipped = params.set_default("flip", (EMData *) 0);
00802         bool delete_flag = false;
00803         if (flipped == 0) {
00804                 flipped = to->process("xform.flip", Dict("axis", "x"));
00805                 delete_flag = true;
00806         }
00807 
00808         EMData * rot_trans_align_flip = this_img->align("rotate_translate", flipped, rt_params, cmp_name, cmp_params);
00809         Transform * t = rot_trans_align_flip->get_attr("xform.align2d");
00810         t->set_mirror(true);
00811         rot_trans_align_flip->set_attr("xform.align2d",t);
00812         delete t;
00813 
00814         // Now finally decide on what is the best answer
00815         float cmp1 = rot_trans_align->cmp(cmp_name, to, cmp_params);
00816         float cmp2 = rot_trans_align_flip->cmp(cmp_name, flipped, cmp_params);
00817 
00818         if (delete_flag){
00819                 if(flipped) {
00820                         delete flipped;
00821                         flipped = 0;
00822                 }
00823         }
00824 
00825         EMData *result = 0;
00826         if (cmp1 < cmp2 )  {
00827 
00828                 if( rot_trans_align_flip ) {
00829                         delete rot_trans_align_flip;
00830                         rot_trans_align_flip = 0;
00831                 }
00832                 result = rot_trans_align;
00833         }
00834         else {
00835                 if( rot_trans_align ) {
00836                         delete rot_trans_align;
00837                         rot_trans_align = 0;
00838                 }
00839                 result = rot_trans_align_flip;
00840                 result->process_inplace("xform.flip",Dict("axis","x"));
00841         }
00842 
00843         return result;
00844 }

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

Implements EMAN::Aligner.

Definition at line 826 of file aligner.h.

00827                 {
00828                         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";
00829                 }

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 821 of file aligner.h.

00822                 {
00823                         return NAME;
00824                 }

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

Implements EMAN::Aligner.

Definition at line 836 of file aligner.h.

00837                 {
00838                         return static_get_param_types();
00839                 }

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

Definition at line 831 of file aligner.h.

00832                 {
00833                         return new RotateTranslateFlipAligner();
00834                 }

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

Definition at line 841 of file aligner.h.

References EMAN::TypeDict::put().

00841                                                          {
00842                         TypeDict d;
00843 
00844                         d.put("flip", EMObject::EMDATA);
00845                         d.put("usedot", EMObject::INT);
00846                         d.put("maxshift", EMObject::INT, "Maximum translation in pixels");
00847                         d.put("rfp_mode", EMObject::INT,"Either 0,1 or 2. A temporary flag for testing the rotational foot print");
00848                         d.put("useflcf", EMObject::INT,"Use Fast Local Correlation Function rather than CCF for translational alignment");
00849                         d.put("zscore", EMObject::INT,"Either 0 or 1. This option is passed directly to the rotational aligner (default=false)");
00850                         return d;
00851                 }


Member Data Documentation

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

Definition at line 71 of file aligner.cpp.


The documentation for this class was generated from the following files:
Generated on Tue Jun 11 13:47:45 2013 for EMAN2 by  doxygen 1.3.9.1