EMAN::RotationalAligner Class Reference

rotational alignment using angular correlation More...

#include <aligner.h>

Inheritance diagram for EMAN::RotationalAligner:

Collaboration diagram for EMAN::RotationalAligner:

Public Member Functions
virtual EMData *	align (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. More...
virtual EMData *	align (EMData *this_img, EMData *to_img) const
virtual string	get_name () const
	Get the Aligner's name. More...
virtual string	get_desc () const
virtual TypeDict	get_param_types () const
Public Member Functions inherited from EMAN::Aligner
virtual	~Aligner ()
virtual Dict	get_params () const
	Get the Aligner parameters in a key/value dictionary. More...
virtual void	set_params (const Dict &new_params)
	Set the Aligner parameters using a key/value dictionary. More...
virtual vector< Dict >	xform_align_nbest (EMData *this_img, EMData *to_img, const unsigned int nsoln, const string &cmp_name, const Dict &cmp_params) const
	This function first added in the context of the 3D aligners used by e2tomohunter: which wants the n best solutions, as opposed to just the best. More...

Static Public Member Functions
static Aligner *	NEW ()
static EMData *	align_180_ambiguous (EMData *this_img, EMData *to_img, int rfp_mode=2, int zscore=0)

Static Public Attributes
static const string	NAME = "rotational"

Additional Inherited Members
Protected Attributes inherited from EMAN::Aligner
Dict	params

Detailed Description

rotational alignment using angular correlation

Parameters

rfp_mode

Either 0,1 or 2. A temporary flag for testing the rotational foot print. O is the original eman1 way. 1 is just using calc_ccf without padding. 2 is using calc_mutual_correlation without padding

Definition at line 281 of file aligner.h.

Member Function Documentation

align() [1/2]

virtual EMData * EMAN::RotationalAligner::align ( EMData *  this_img, EMData *  to_img  ) const

inlinevirtual

Implements EMAN::Aligner.

Definition at line 287 of file aligner.h.

                {
                        return align(this_img, to_img, "dot", Dict());
                }

References align().

align() [2/2]

virtual EMData * EMAN::RotationalAligner::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.

Referenced by align().

align_180_ambiguous()

EMData * RotationalAligner::align_180_ambiguous ( EMData *  this_img, EMData *  to_img, int  rfp_mode = 2, int  zscore = 0  )

static

Definition at line 446 of file aligner.cpp.

                                                                                                       {
 
        // Make translationally invariant rotational footprints
        EMData* this_img_rfp, * to_rfp;
        if (rfp_mode == 0) {
                this_img_rfp = this_img->make_rotational_footprint_e1();
                to_rfp = to->make_rotational_footprint_e1();
        } else if (rfp_mode == 1) {
                this_img_rfp = this_img->make_rotational_footprint();
                to_rfp = to->make_rotational_footprint();
        } else if (rfp_mode == 2) {
                this_img_rfp = this_img->make_rotational_footprint_cmc();
                to_rfp = to->make_rotational_footprint_cmc();
        } else {
                throw InvalidParameterException("rfp_mode must be 0,1 or 2");
        }
        int this_img_rfp_nx = this_img_rfp->get_xsize();
 
        // Do row-wise correlation, returning a sum.
        EMData *cf = this_img_rfp->calc_ccfx(to_rfp, 0, this_img->get_ysize(),false,false,zscore);
// cf->process_inplace("normalize");
// cf->write_image("ralisum.hdf",-1);
//
// EMData *cf2 = this_img_rfp->calc_ccfx(to_rfp, 0, this_img->get_ysize(),true);
// cf2->write_image("ralistack.hdf",-1);
// delete cf2;
 
        // Delete them, they're no longer needed
        delete this_img_rfp; this_img_rfp = 0;
        delete to_rfp; to_rfp = 0;
 
        // Now solve the rotational alignment by finding the max in the column sum
        float *data = cf->get_data();
 
        float peak = 0;
        int peak_index = 0;
        Util::find_max(data, this_img_rfp_nx, &peak, &peak_index);
 
        if( cf ) {
                delete cf;
                cf = 0;
        }
        float rot_angle = (float) (peak_index * 180.0f / this_img_rfp_nx);
 
        // Return the result
        Transform tmp(Dict("type","2d","alpha",rot_angle));
        cf=this_img->process("xform",Dict("transform",(Transform*)&tmp));
//      Transform* t = get_set_align_attr("xform.align2d",cf,this_img);
//      Dict d("type","2d","alpha",rot_angle);
//      t->set_rotation(d);
        cf->set_attr("xform.align2d",&tmp);
        return cf;
}

References EMAN::EMData::calc_ccfx(), EMAN::Util::find_max(), InvalidParameterException, EMAN::EMData::make_rotational_footprint(), EMAN::EMData::make_rotational_footprint_cmc(), and EMAN::EMData::make_rotational_footprint_e1().

get_desc()

virtual string EMAN::RotationalAligner::get_desc ( ) const

inlinevirtual

Implements EMAN::Aligner.

Definition at line 297 of file aligner.h.

                {
                        return "Performs rotational alignment, even on poorly centered images, but leaves a 180 degree ambiguity which requires a translational alignment to resolve. Usually called internally by rotate_translate aligner.";
                }

get_name()

virtual string EMAN::RotationalAligner::get_name ( ) const

inlinevirtual

Get the Aligner's name.

Each Aligner is identified by a unique name.

Returns

The Aligner's name.

Implements EMAN::Aligner.

Definition at line 292 of file aligner.h.

                {
                        return NAME;
                }

References NAME.

get_param_types()

virtual TypeDict EMAN::RotationalAligner::get_param_types ( ) const

inlinevirtual

Implements EMAN::Aligner.

Definition at line 309 of file aligner.h.

                {
                        TypeDict d;
                        d.put("rfp_mode", EMObject::INT,"Either 0,1 or 2. A temporary flag for testing the rotational foot print. O is the original eman1 way. 1 is just using calc_ccf without padding. 2 is using calc_mutual_correlation without padding.");
                        d.put("zscore", EMObject::INT,"Either 0 or 1. If set, will convert per-radius CCF curves into Z-score significnace curves before averaging. In theory this should produce better results by focusing on radii with more alignment information. (default=false)");
                        d.put("ambig180", EMObject::INT,"Either 0 or 1. If set, will not try and resolve the 180 degree ambiguity. If not set, it will assume the particle is well centered and resolve the ambiguity that way. default=false");
                        d.put("maxshift", EMObject::INT,"This is provided for compatibility with other aligners. It does absolutely nothing here, as there is an implicit maxshift=0.");
                        return d;
                }

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

NEW()

static Aligner * EMAN::RotationalAligner::NEW ( )

inlinestatic

Definition at line 302 of file aligner.h.

                {
                        return new RotationalAligner();
                }

Member Data Documentation

NAME

const string RotationalAligner::NAME = "rotational"

static

Definition at line 319 of file aligner.h.

Referenced by get_name().

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

• aligner.h
• aligner.cpp