EMAN::Refine3DAligner Class Reference

Refine alignment. More...

#include <aligner.h>

Inheritance diagram for EMAN::Refine3DAligner:

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Collaboration diagram for EMAN::Refine3DAligner:

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List of all members.

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.
virtual EMData *	align (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 Aligner *	NEW ()

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Detailed Description

Refine alignment.

Refines a preliminary 3D alignment using a simplex algorithm. Subpixel precision. Uses quaternions extensively, separates the in plane (phi) rotation and the 2 rotations that define a point on the sphere (POTS), manipulating them independently. The POTS is"jiggled" in a local circular sub manifold of the sphere (of radius stepdelta). Phi is allowed to vary as a normal variable. The result is combined into a single transform and then a similarity is computed, etc. Translation also varies.

Author:

David Woolford

Date:

June 23 2009

Definition at line 595 of file aligner.h.

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Member Function Documentation

EMData * Refine3DAligner::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 1229 of file aligner.cpp.

References EMAN::EMData::get_ndim(), EMAN::EMData::get_xsize(), EMAN::Dict::has_key(), ImageDimensionException, NullPointerException, EMAN::Aligner::params, phi, EMAN::EMData::process(), refalifn3d(), refalin3d_perturb(), EMAN::EMData::set_attr(), EMAN::Dict::set_default(), status, t, x, and y.

Referenced by align().

{

        if (!to || !this_img) throw NullPointerException("Input image is null"); // not sure if this is necessary, it was there before I started

        if (to->get_ndim() != 3 || this_img->get_ndim() != 3) throw ImageDimensionException("The Refine3D aligner only works for 3D images");

        float saz = 0.0;
        float sphi = 0.0;
        float salt = 0.0;
        float sdx = 0.0;
        float sdy = 0.0;
        float sdz = 0.0;
        bool mirror = false;
        Transform* t;
        if (params.has_key("xform.align3d") ) {
                // Unlike the 2d refine aligner, this class doesn't require the starting transform's
                // parameters to form the starting guess. Instead the Transform itself
                // is perturbed carefully (using quaternion rotation) to overcome problems that arise
                // when you use orthogonally-based Euler angles
                t = params["xform.align3d"];
        }else {
                t = new Transform(); // is the identity
        }

        int np = 6; // the number of dimensions
        Dict gsl_params;
        gsl_params["this"] = this_img;
        gsl_params["with"] = to;
        gsl_params["snr"]  = params["snr"];
        gsl_params["mirror"] = mirror;
        gsl_params["transform"] = t;

        const gsl_multimin_fminimizer_type *T = gsl_multimin_fminimizer_nmsimplex;
        gsl_vector *ss = gsl_vector_alloc(np);

        float stepx = params.set_default("stepx",1.0f);
        float stepy = params.set_default("stepy",1.0f);
        float stepz = params.set_default("stepz",1.0f);
        // Default step is 5 degree - note in EMAN1 it was 0.1 radians
        float half_circle_step = 180.0f; // This shouldn't be altered
        float stepphi = params.set_default("stephi",5.0f);
        float stepdelta = params.set_default("stepdelta",5.0f);

        gsl_vector_set(ss, 0, stepx);
        gsl_vector_set(ss, 1, stepy);
        gsl_vector_set(ss, 2, stepz);
        gsl_vector_set(ss, 3, half_circle_step);
        gsl_vector_set(ss, 4, stepdelta);
        gsl_vector_set(ss, 5, stepphi);

        gsl_vector *x = gsl_vector_alloc(np);
        gsl_vector_set(x, 0, sdx);
        gsl_vector_set(x, 1, sdy);
        gsl_vector_set(x, 2, sdz);
        gsl_vector_set(x, 3, saz);
        gsl_vector_set(x, 4, salt);
        gsl_vector_set(x, 5, sphi);

        gsl_multimin_function minex_func;
        Cmp *c = Factory < Cmp >::get(cmp_name, cmp_params);
        gsl_params["cmp"] = (void *) c;
        minex_func.f = &refalifn3d;

        minex_func.n = np;
        minex_func.params = (void *) &gsl_params;

        gsl_multimin_fminimizer *s = gsl_multimin_fminimizer_alloc(T, np);
        gsl_multimin_fminimizer_set(s, &minex_func, x, ss);

        int rval = GSL_CONTINUE;
        int status = GSL_SUCCESS;
        int iter = 1;

        float precision = params.set_default("precision",0.04f);
        int maxiter = params.set_default("maxiter",60);
        while (rval == GSL_CONTINUE && iter < maxiter) {
                iter++;
                status = gsl_multimin_fminimizer_iterate(s);
                if (status) {
                        break;
                }
                rval = gsl_multimin_test_size(gsl_multimin_fminimizer_size(s), precision);
        }

        int maxshift = params.set_default("maxshift",-1);

        if (maxshift <= 0) {
                maxshift = this_img->get_xsize() / 4;
        }
        float fmaxshift = static_cast<float>(maxshift);
        EMData *result;
        if ( fmaxshift >= (float)gsl_vector_get(s->x, 0) && fmaxshift >= (float)gsl_vector_get(s->x, 1)  && fmaxshift >= (float)gsl_vector_get(s->x, 2))
        {
                float x = (float)gsl_vector_get(s->x, 0);
                float y = (float)gsl_vector_get(s->x, 1);
                float z = (float)gsl_vector_get(s->x, 2);

                float arc = (float)gsl_vector_get(s->x, 3);
                float delta = (float)gsl_vector_get(s->x, 4);
                float phi = (float)gsl_vector_get(s->x, 5);

                Transform tsoln = refalin3d_perturb(t,delta,arc,phi,x,y,z);

                result = this_img->process("math.transform",Dict("transform",&tsoln));
                result->set_attr("xform.align3d",&tsoln);

        } else { // The refine aligner failed - this shift went beyond the max shift
                result = this_img->process("math.transform",Dict("transform",t));
                result->set_attr("xform.align3d",t);
        }

        delete t;
        t = 0;

        gsl_vector_free(x);
        gsl_vector_free(ss);
        gsl_multimin_fminimizer_free(s);

        if ( c != 0 ) delete c;
        return result;
}

virtual EMData* EMAN::Refine3DAligner::align	(	EMData *	this_img,
		EMData *	to_img
	)			const [inline, virtual]

Implements EMAN::Aligner.

Definition at line 601 of file aligner.h.

References align().

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

virtual string EMAN::Refine3DAligner::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 606 of file aligner.h.

                        {
                                return "refine.3d";
                        }

virtual string EMAN::Refine3DAligner::get_desc

(

)

const [inline, virtual]

Implements EMAN::Aligner.

Definition at line 611 of file aligner.h.

                        {
                                return "Refines a preliminary 3D alignment using a simplex algorithm. Subpixel precision.";
                        }

static Aligner* EMAN::Refine3DAligner::NEW

(

)

[inline, static]

Definition at line 616 of file aligner.h.

                        {
                                return new Refine3DAligner();
                        }

virtual TypeDict EMAN::Refine3DAligner::get_param_types

(

)

const [inline, virtual]

Implements EMAN::Aligner.

Definition at line 621 of file aligner.h.

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

                        {
                                TypeDict d;
                                d.put("xform.align3d", EMObject::TRANSFORM,"The Transform storing the starting guess. If unspecified the identity matrix is used");
                                d.put("stepx", EMObject::FLOAT, "The x increment used to create the starting simplex. Default is 1");
                                d.put("stepy", EMObject::FLOAT,"The y increment used to create the starting simplex. Default is 1");
                                d.put("stepz", EMObject::FLOAT, "The z increment used to create the starting simplex. Default is 1." );
                                d.put("stepphi", EMObject::FLOAT, "The phi incremenent used to creat the starting simplex. This is the increment applied to the inplane rotation. Default is 5." );
                                d.put("stepdelta", EMObject::FLOAT,"The angular increment which represents a good initial step along the sphere, thinking in terms of quaternions. Default is 5.");
                                d.put("precision", EMObject::FLOAT, "The precision which, if achieved, can stop the iterative refinement before reaching the maximum iterations. Default is 0.04." );
                                d.put("maxiter", EMObject::INT, "The maximum number of iterations that can be performed by the Simplex minimizer. Default is 60.");
                                d.put("maxshift", EMObject::INT,"Maximum translation in pixels in any direction. If the solution yields a shift beyond this value in any direction, then the refinement is judged a failure and the original alignment is used as the solution.");
                                return d;
                        }

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

• aligner.h
• aligner.cpp