EMAN::RotateTranslateAligner Class Reference
[a function or class that is CUDA enabled]

rotational, translational alignment More...

#include <aligner.h>

Inheritance diagram for EMAN::RotateTranslateAligner:

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Collaboration diagram for EMAN::RotateTranslateAligner:

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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

rotational, translational alignment

Parameters:

	maxshift	Maximum translation in pixels
	nozero	Zero translation not permitted (useful for CCD images)
	rfp_mode	Either 0,1 or 2. A temporary flag for testing the rotational foot print

Definition at line 291 of file aligner.h.

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Member Function Documentation

EMData * RotateTranslateAligner::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 328 of file aligner.cpp.

References EMAN::EMData::align(), EMAN::RotationalAligner::align_180_ambiguous(), EMAN::EMData::cmp(), cmp1(), cmp2(), EMAN::EMData::copy(), EMAN::EMData::get_attr(), EMAN::Transform::get_rotation(), EMAN::Aligner::params, EMAN::EMData::process_inplace(), EMAN::EMData::set_attr(), EMAN::Dict::set_default(), EMAN::Transform::set_rotation(), and t.

Referenced by align().

{
        // Get the 180 degree ambiguously rotationally aligned and its 180 degree rotation counterpart
        int rfp_mode = params.set_default("rfp_mode",0);
        EMData *rot_align  =  RotationalAligner::align_180_ambiguous(this_img,to,rfp_mode);
        Transform * tmp = rot_align->get_attr("xform.align2d");
        Dict rot = tmp->get_rotation("2d");
        float rotate_angle_solution = rot["alpha"];
        delete tmp;

        EMData *rot_align_180 = rot_align->copy();
        rot_align_180->process_inplace("math.rotate.180");

        Dict trans_params;
        trans_params["intonly"]  = 0;
        trans_params["maxshift"] = params.set_default("maxshift", -1);

        // Do the first case translational alignment
        trans_params["nozero"]   = params.set_default("nozero",false);
        EMData* rot_trans = rot_align->align("translational", to, trans_params, cmp_name, cmp_params);
        if( rot_align ) { // Clean up
                delete rot_align;
                rot_align = 0;
        }

        // Do the second case translational alignment
        EMData*  rot_180_trans = rot_align_180->align("translational", to, trans_params, cmp_name, cmp_params);
        if( rot_align_180 )     { // Clean up
                delete rot_align_180;
                rot_align_180 = 0;
        }

        // Finally decide on the result
        float cmp1 = rot_trans->cmp(cmp_name, to, cmp_params);
        float cmp2 = rot_180_trans->cmp(cmp_name, to, cmp_params);

        EMData *result = 0;
        if (cmp1 < cmp2) { // Assumes smaller is better - thus all comparitors should support "smaller is better"
                if( rot_180_trans )     {
                        delete rot_180_trans;
                        rot_180_trans = 0;
                }
                result = rot_trans;
        }
        else {
                if( rot_trans ) {
                        delete rot_trans;
                        rot_trans = 0;
                }
                result = rot_180_trans;
                rotate_angle_solution -= 180.f;
        }

        Transform* t = result->get_attr("xform.align2d");
        t->set_rotation(Dict("type","2d","alpha",rotate_angle_solution));
        result->set_attr("xform.align2d",t);
        delete t;

        return result;
}

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

Implements EMAN::Aligner.

Definition at line 297 of file aligner.h.

References align().

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

virtual string EMAN::RotateTranslateAligner::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 302 of file aligner.h.

                {
                        return "rotate_translate";
                }

virtual string EMAN::RotateTranslateAligner::get_desc

(

)

const [inline, virtual]

Implements EMAN::Aligner.

Definition at line 307 of file aligner.h.

                {
                        return "Performs rotational alignment and follows this with translational alignment.";
                }

static Aligner* EMAN::RotateTranslateAligner::NEW

(

)

[inline, static]

Definition at line 312 of file aligner.h.

                {
                        return new RotateTranslateAligner();
                }

virtual TypeDict EMAN::RotateTranslateAligner::get_param_types

(

)

const [inline, virtual]

Implements EMAN::Aligner.

Definition at line 317 of file aligner.h.

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

                {
                        TypeDict d;
                        //d.put("usedot", EMObject::INT);
                        d.put("maxshift", EMObject::INT, "Maximum translation in pixels");
                        d.put("nozero", EMObject::INT,"Zero translation not permitted (useful for CCD images)");
                        d.put("rfp_mode", EMObject::INT,"Either 0,1 or 2. A temporary flag for testing the rotational foot print");
                        return d;
                }

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

• aligner.h
• aligner.cpp