EMAN2
Public Member Functions | Static Public Member Functions | Static Public Attributes
EMAN::RotateTranslateFlipAlignerIterative Class Reference

rotational, translational and flip alignment, iterative style More...

#include <aligner.h>

Inheritance diagram for EMAN::RotateTranslateFlipAlignerIterative:
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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_iterative"

Detailed Description

rotational, translational and flip alignment, iterative style

Parameters:
flip
r1inner ring
r2outer ring
maxitermaximum number of alignment iterations
maxshiftMaximum translation in pixels
Author:
John Flanagan
Date:
Oct 2010

Definition at line 925 of file aligner.h.


Member Function Documentation

EMData * RotateTranslateFlipAlignerIterative::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_imgThe image to be compared.
to_img'this_img" is aligned with 'to_img'.
cmp_nameThe comparison method to compare the two images.
cmp_paramsThe parameter dictionary for comparison method.
Returns:
The aligned image.

Implements EMAN::Aligner.

Definition at line 862 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().

{
        // Get the non flipped rotational, tranlsationally aligned image
        Dict rt_params("maxshift", params["maxshift"],"r1",params.set_default("r1",-1),"r2",params.set_default("r2",-1));
        EMData *rot_trans_align = this_img->align("rotate_translate_iterative",to,rt_params,cmp_name, cmp_params);

        // Do the same alignment, but using the flipped version of the image
        EMData *flipped = params.set_default("flip", (EMData *) 0);
        bool delete_flag = false;
        if (flipped == 0) {
                flipped = to->process("xform.flip", Dict("axis", "x"));
                delete_flag = true;
        }

        EMData * rot_trans_align_flip = this_img->align("rotate_translate_iterative", flipped, rt_params, cmp_name, cmp_params);
        Transform* t = rot_trans_align_flip->get_attr("xform.align2d");
        t->set_mirror(true);
        rot_trans_align_flip->set_attr("xform.align2d",t);
        delete t;

        // Now finally decide on what is the best answer
        float cmp1 = rot_trans_align->cmp(cmp_name, to, cmp_params);
        float cmp2 = rot_trans_align_flip->cmp(cmp_name, flipped, cmp_params);

        if (delete_flag){
                if(flipped) {
                        delete flipped;
                        flipped = 0;
                }
        }

        EMData *result = 0;
        if (cmp1 < cmp2 )  {

                if( rot_trans_align_flip ) {
                        delete rot_trans_align_flip;
                        rot_trans_align_flip = 0;
                }
                result = rot_trans_align;
        }
        else {
                if( rot_trans_align ) {
                        delete rot_trans_align;
                        rot_trans_align = 0;
                }
                result = rot_trans_align_flip;
                result->process_inplace("xform.flip",Dict("axis","x"));
        }

        return result;
}
virtual EMData* EMAN::RotateTranslateFlipAlignerIterative::align ( EMData this_img,
EMData to_img 
) const [inline, virtual]

Implements EMAN::Aligner.

Definition at line 930 of file aligner.h.

References align().

                {
                        return align(this_img, to_img, "sqeuclidean", Dict());
                }
virtual string EMAN::RotateTranslateFlipAlignerIterative::get_desc ( ) const [inline, virtual]

Implements EMAN::Aligner.

Definition at line 940 of file aligner.h.

                {
                        return " Does two 'rotate_translate.iterative' alignments, one to accommodate for possible handedness change. Decided which alignment is better using a comparitor and returns the aligned image as the solution";
                }
virtual string EMAN::RotateTranslateFlipAlignerIterative::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 935 of file aligner.h.

References NAME.

                {
                        return NAME;
                }
virtual TypeDict EMAN::RotateTranslateFlipAlignerIterative::get_param_types ( ) const [inline, virtual]

Implements EMAN::Aligner.

Definition at line 950 of file aligner.h.

References static_get_param_types().

                {
                        return static_get_param_types();
                }
static Aligner* EMAN::RotateTranslateFlipAlignerIterative::NEW ( ) [inline, static]

Definition at line 945 of file aligner.h.

                {
                        return new RotateTranslateFlipAlignerIterative();
                }
static TypeDict EMAN::RotateTranslateFlipAlignerIterative::static_get_param_types ( ) [inline, static]

Definition at line 955 of file aligner.h.

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

Referenced by get_param_types().

                                                         {
                        TypeDict d;
                        d.put("flip", EMObject::EMDATA);
                        d.put("r1", EMObject::INT, "Inner ring, pixels");
                        d.put("r2", EMObject::INT, "Outer ring, pixels");
                        d.put("maxiter", EMObject::INT, "Maximum number of iterations");
                        d.put("maxshift", EMObject::INT, "Maximum translation in pixels");
                        return d;
                }

Member Data Documentation

const string RotateTranslateFlipAlignerIterative::NAME = "rotate_translate_flip_iterative" [static]

Definition at line 965 of file aligner.h.

Referenced by get_name().


The documentation for this class was generated from the following files: