EMAN::RT3DSymmetryAligner Class Reference

3D rotational symmetry aligner. More...

#include <aligner.h>

Inheritance diagram for EMAN::RT3DSymmetryAligner:

Collaboration diagram for EMAN::RT3DSymmetryAligner:

Public Member Functions
virtual EMData *	align (EMData *this_img, EMData *to_img, const string &cmp_name="ccc.tomo", const Dict &cmp_params=Dict()) const
	See Aligner comments for more details. More...
virtual EMData *	align (EMData *this_img, EMData *to_img) const
	See Aligner comments for more details. 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
	See Aligner comments for more details. More...
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...

Static Public Member Functions
static Aligner *	NEW ()

Static Public Attributes
static const string	NAME = "rotate_symmetry_3d"

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

Detailed Description

3D rotational symmetry aligner.

This aligner takes a map, which must be first aligned to the symmetry axis, and rotates it to it symmetric positions. This is used to check for pseudo symmetry (such as finding the tail of an icosahedral virus). A list of best matches (moving to a reference is produced. Alternativly, a rotated verison of the moving map is returned.

Parameters

sym	The symmtery to use
verbose	Turn this on to have useful information printed to standard out

Author

John Flanagan

Date

Mar 2011

Definition at line 2030 of file aligner.h.

Member Function Documentation

align() [1/2]

virtual EMData * EMAN::RT3DSymmetryAligner::align ( EMData *  this_img, EMData *  to_img  ) const

inlinevirtual

See Aligner comments for more details.

Implements EMAN::Aligner.

Definition at line 2039 of file aligner.h.

                        {
                                return align(this_img, to_img, "ccc.tomo", Dict());
                        }

References align().

align() [2/2]

virtual EMData * EMAN::RT3DSymmetryAligner::align ( EMData *  this_img, EMData *  to_img, const string &  cmp_name = "ccc.tomo", const Dict &  cmp_params = Dict()  ) const

virtual

See Aligner comments for more details.

Implements EMAN::Aligner.

Referenced by align().

get_desc()

virtual string EMAN::RT3DSymmetryAligner::get_desc ( ) const

inlinevirtual

Implements EMAN::Aligner.

Definition at line 2054 of file aligner.h.

                        {
                                return "3D symmetry aligner";
                        }

get_name()

virtual string EMAN::RT3DSymmetryAligner::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 2049 of file aligner.h.

                        {
                                return NAME;
                        }

References NAME.

get_param_types()

virtual TypeDict EMAN::RT3DSymmetryAligner::get_param_types ( ) const

inlinevirtual

Implements EMAN::Aligner.

Definition at line 2064 of file aligner.h.

                        {
                                TypeDict d;
                                d.put("sym", EMObject::FLOAT,"The symmetry. Default is icos");
                                d.put("transform", EMObject::TRANSFORM,"The transform to move to symmetry axis");
                                d.put("verbose", EMObject::BOOL,"Turn this on to have useful information printed to standard out.");
                                return d;
                        }

References EMAN::EMObject::BOOL, EMAN::EMObject::FLOAT, EMAN::TypeDict::put(), and EMAN::EMObject::TRANSFORM.

NEW()

static Aligner * EMAN::RT3DSymmetryAligner::NEW ( )

inlinestatic

Definition at line 2059 of file aligner.h.

                        {
                                return new RT3DSymmetryAligner();
                        }

xform_align_nbest()

vector< Dict > RT3DSymmetryAligner::xform_align_nbest ( EMData *  this_img, EMData *  to_img, const unsigned int  nsoln, const string &  cmp_name, const Dict &  cmp_params  ) const

virtual

See Aligner comments for more details.

Reimplemented from EMAN::Aligner.

Definition at line 4592 of file aligner.cpp.

{
 
        bool verbose = params.set_default("verbose",false);
        Transform* ixform;
        if (params.has_key("transform") ) {
                ixform = params["transform"];
        }else{
                ixform = new Transform(); // is the identity
        }
 
        //Initialize a soln dict
        vector<Dict> solns;
        if (nsoln == 0) return solns; // What was the user thinking?
        for (unsigned int i = 0; i < nsoln; ++i ) {
                Dict d;
                d["score"] = 1.e24;
                Transform t; // identity by default
                d["xform.align3d"] = &t; // deep copy is going on here
                solns.push_back(d);
        }
 
        #ifdef EMAN2_USING_CUDA
        if(EMData::usecuda == 1) {
                cout << "Using CUDA for 3D sym alignment" << endl;
                if(!this_img->getcudarwdata()) this_img->copy_to_cudaro();
                if(!to->getcudarwdata()) to->copy_to_cuda();
        }
        #endif
 
        //Generate symmetry related orientations
        vector<Transform> syms = Symmetry3D::get_symmetries((string)params.set_default("sym","icos"));
        Cmp* c = Factory <Cmp>::get(cmp_name, cmp_params);
 
        float score = 0.0f;
        for ( vector<Transform>::const_iterator symit = syms.begin(); symit != syms.end(); ++symit ) {
                //Here move to sym position and compute the score
                Transform sympos = (*symit)*(*ixform);
                EMData* transformed = this_img->process("xform",Dict("transform", &sympos));
                score = c->cmp(transformed,to);
                delete transformed; transformed = 0;
 
                if (verbose) {
                        Dict rots = sympos.get_rotation("eman");
                        cout <<"Score is: " << score << " az " << float(rots["az"]) << " alt " << float(rots["alt"]) << " phi " << float(rots["phi"]) << endl;
                }
 
                unsigned int j = 0;
                for ( vector<Dict>::iterator it = solns.begin(); it != solns.end(); ++it, ++j ) {
                        if ( (float)(*it)["score"] > score ) { // Note greater than - EMAN2 preferes minimums as a matter of policy
                                vector<Dict>::reverse_iterator rit = solns.rbegin();
                                copy(rit+1,solns.rend()-j,rit);
                                Dict& d = (*it);
                                d["score"] = score;
                                d["xform.align3d"] = &sympos; // deep copy is going on here
                                break;
                        }
                }
        }
 
        if (c != 0) delete c;
 
        return solns;
}

References EMAN::Cmp::cmp(), copy(), EMAN::Transform::get_rotation(), EMAN::Symmetry3D::get_symmetries(), EMAN::Dict::has_key(), EMAN::Aligner::params, and EMAN::Dict::set_default().

Member Data Documentation

NAME

const string RT3DSymmetryAligner::NAME = "rotate_symmetry_3d"

static

Definition at line 2073 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