This is an ABS for use in constructing, rt_scale, rt_flip, etc scale aligners. More...

#include <aligner.h>

Inheritance diagram for EMAN::ScaleAlignerABS:

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Collaboration diagram for EMAN::ScaleAlignerABS:

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Public Member Functions
	ScaleAlignerABS (const string &ba)
	Constructor to initialize the basealigner string. More...

EMData *	align_using_base (EMData this_img, EMData to_img, const string &cmp_name="dot", const Dict &cmp_params=Dict()) const
	implmentation of the scale alignment using the base aligner set in set_base_aligner More...

Public Member Functions inherited from EMAN::Aligner
virtual	~Aligner ()

virtual EMData *	align (EMData this_img, EMData to_img) const =0

virtual EMData *	align (EMData this_img, EMData to_img, const string &cmp_name, const Dict &cmp_params) const =0
	To align 'this_img' with another image passed in through its parameters. More...

virtual string	get_name () const =0
	Get the Aligner's name. More...

virtual string	get_desc () const =0

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 TypeDict	get_param_types () const =0

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...

Protected Attributes
const string	basealigner

Dict	basealigner_params

Protected Attributes inherited from EMAN::Aligner
Dict	params

Detailed Description

This is an ABS for use in constructing, rt_scale, rt_flip, etc scale aligners.

Hence this class is not be be initialized To use, inherit this class and set the base aligner name This stragtegy uses the Template design pattern

Definition at line 166 of file aligner.h.

Constructor & Destructor Documentation

◆ ScaleAlignerABS()

EMAN::ScaleAlignerABS::ScaleAlignerABS ( const string & ba )

inline

Constructor to initialize the basealigner string.

Definition at line 170 of file aligner.h.

                                                   : basealigner(ba)
                 {
                 }

Member Function Documentation

◆ align_using_base()

EMData * ScaleAlignerABS::align_using_base	(	EMData *	this_img,
		EMData *	to_img,
		const string &	cmp_name = `"dot"`,
		const Dict &	cmp_params = `Dict()`
	)		const

implmentation of the scale alignment using the base aligner set in set_base_aligner

Definition at line 141 of file aligner.cpp.

{
        //get the scale range
        float min =  params.set_default("min",0.95f);
        float max = params.set_default("max",1.05f);
        float step = params.set_default("step",0.01f);
 
        // crate the starting transform
        Transform t = Transform();
        t.set_scale(max);
 
        //save orignal data
        float* oridata = this_img->get_data();
 
        //get the transform processor and cast to correct factory product
        Processor* proc = Factory <Processor>::get("xform", Dict());
        TransformProcessor* xform = dynamic_cast<TransformProcessor*>(proc);
 
        // Using the following method we only create one EMdata object. If I just used the processor, then I would create many EMdata objects
        EMData* result = 0;
//      float bestscore = numeric_limits<float>::infinity();
        float bestscore = 1.0e37;
 
        for(float i = max; i > min; i-=step){
 
                //scale the image
                float* des_data = xform->transform(this_img,t);
                this_img->set_data(des_data);
                this_img->update();
 
                //check compairsion
                EMData* aligned = this_img->align(basealigner, to, basealigner_params, cmp_name, cmp_params);
                float score = aligned->cmp(cmp_name, to, cmp_params);
                if(score < bestscore){
                        bestscore = score;
                        //If we just reassign w/o cleaing up we will get memory leaks!
                        if(result != 0) delete result;
                        result = aligned;
                        Transform *tt=(Transform*)(result->get_attr("xform.align2d"));
                        tt->set_scale(i);
                        result->set_attr("xform.align2d",tt);
//                      result->set_attr("scalefactor",i);      // I don't know why this was done instead of updating the transform, but it breaks a bunch of things
                }else{
                        delete aligned;
                }
                //clean up scaled image data
                delete des_data;
 
                t.set_scale(i);
 
                //reset original data
                this_img->set_data(oridata);
        }
 
        if (!result) throw UnexpectedBehaviorException("Alignment score is infinity! Something is seriously wrong with the data!");
        if (proc != 0) delete proc;
 
        return result;
 
};

References basealigner, basealigner_params, EMAN::Aligner::params, EMAN::Dict::set_default(), EMAN::Transform::set_scale(), and UnexpectedBehaviorException.

Member Data Documentation

◆ basealigner

const string EMAN::ScaleAlignerABS::basealigner

protected

Definition at line 179 of file aligner.h.

Referenced by align_using_base().

◆ basealigner_params

Dict EMAN::ScaleAlignerABS::basealigner_params