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 807 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 812 of file aligner.h.

References align().

00813                 {
00814                         return align(this_img, to_img, "sqeuclidean", Dict());
00815                 }

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 774 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().

00776 {
00777         // Get the non flipped rotational, tranlsationally aligned image
00778         Dict rt_params("maxshift", params["maxshift"], "rfp_mode", params.set_default("rfp_mode",0),"useflcf",params.set_default("useflcf",0));
00779         EMData *rot_trans_align = this_img->align("rotate_translate",to,rt_params,cmp_name, cmp_params);
00780         
00781         // Do the same alignment, but using the flipped version of the image
00782         EMData *flipped = params.set_default("flip", (EMData *) 0);
00783         bool delete_flag = false;
00784         if (flipped == 0) {
00785                 flipped = to->process("xform.flip", Dict("axis", "x"));
00786                 delete_flag = true;
00787         }
00788 
00789         EMData * rot_trans_align_flip = this_img->align("rotate_translate", flipped, rt_params, cmp_name, cmp_params);
00790         Transform * t = rot_trans_align_flip->get_attr("xform.align2d");
00791         t->set_mirror(true);
00792         rot_trans_align_flip->set_attr("xform.align2d",t);
00793         delete t;
00794 
00795         // Now finally decide on what is the best answer
00796         float cmp1 = rot_trans_align->cmp(cmp_name, to, cmp_params);
00797         float cmp2 = rot_trans_align_flip->cmp(cmp_name, flipped, cmp_params);
00798 
00799         if (delete_flag){
00800                 if(flipped) {
00801                         delete flipped;
00802                         flipped = 0;
00803                 }
00804         }
00805 
00806         EMData *result = 0;
00807         if (cmp1 < cmp2 )  {
00808 
00809                 if( rot_trans_align_flip ) {
00810                         delete rot_trans_align_flip;
00811                         rot_trans_align_flip = 0;
00812                 }
00813                 result = rot_trans_align;
00814         }
00815         else {
00816                 if( rot_trans_align ) {
00817                         delete rot_trans_align;
00818                         rot_trans_align = 0;
00819                 }
00820                 result = rot_trans_align_flip;
00821                 result->process_inplace("xform.flip",Dict("axis","x"));
00822         }
00823 
00824         return result;
00825 }

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

Implements EMAN::Aligner.

Definition at line 822 of file aligner.h.

00823                 {
00824                         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";
00825                 }

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 817 of file aligner.h.

References NAME.

00818                 {
00819                         return NAME;
00820                 }

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

Implements EMAN::Aligner.

Definition at line 832 of file aligner.h.

References static_get_param_types().

00833                 {
00834                         return static_get_param_types();
00835                 }

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

Definition at line 827 of file aligner.h.

00828                 {
00829                         return new RotateTranslateFlipAligner();
00830                 }

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

Definition at line 837 of file aligner.h.

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

Referenced by get_param_types().

00837                                                          {
00838                         TypeDict d;
00839 
00840                         d.put("flip", EMObject::EMDATA);
00841                         d.put("usedot", EMObject::INT);
00842                         d.put("maxshift", EMObject::INT, "Maximum translation in pixels");
00843                         d.put("rfp_mode", EMObject::INT,"Either 0,1 or 2. A temporary flag for testing the rotational foot print");
00844                         d.put("useflcf", EMObject::INT,"Use Fast Local Correlation Function rather than CCF for translational alignment");
00845                         return d;
00846                 }


Member Data Documentation

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

Definition at line 848 of file aligner.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Thu May 3 10:08:44 2012 for EMAN2 by  doxygen 1.4.7