ObjFunc_nma_alignment Class Reference

#include <nma_alignment.h>

Inheritance diagram for ObjFunc_nma_alignment:

Collaboration diagram for ObjFunc_nma_alignment:

Public Member Functions
	ObjFunc_nma_alignment (int _t, int _n=0)
	~ObjFunc_nma_alignment ()
double	eval (Vector v, int *nerror=nullptr)
Public Member Functions inherited from UnconstrainedObjectiveFunction
	UnconstrainedObjectiveFunction ()
	~UnconstrainedObjectiveFunction ()
virtual double	evalNLConstraint (int j, Vector v, int *nerror=NULL)
virtual Vector	evalGradNLConstraint (int j, Vector v, int *nerror=NULL)
virtual void	evalGradNLConstraint (int j, Vector v, Vector result, int *nerror=NULL)
Public Member Functions inherited from ObjectiveFunction
	ObjectiveFunction ()
virtual	~ObjectiveFunction ()
int	dim ()
void	initData ()
virtual void	saveValue (Vector tmp, double valueOF, int nerror)
virtual void	printStats (char cc=1)
void	saveStats (char *filename, Vector vG, Matrix mH, Vector vLambda)
virtual void	finalize (Vector vG, Matrix mH, Vector vLambda)
void	setName (char *s)
void	setSaveFile (char *b=NULL)
void	updateCounter (double df, Vector vX, int nerror=0)
char	isFeasible (Vector vx, double *d=NULL)
void	initBounds ()
void	endInit ()
void	initTolLC (Vector vX)
void	initTolNLC (Vector c, double delta)
virtual int	getNFE ()
virtual int	getNFE2 ()

Additional Inherited Members
Public Attributes inherited from ObjectiveFunction
char	name [9]
char	startPointIsGiven
Vector	xStart
Vector	xBest
Vector	xOptimal
double	valueOptimal
double	valueBest
double	noiseAbsolute
double	noiseRelative
double	objectiveConst
Matrix	data
int	t
int	nNLConstraints
int	isConstrained
Vector	bl
Vector	bu
Matrix	A
Vector	b
double	tolRelFeasibilityForNLC
double	tolNLC
double	tolRelFeasibilityForLC
double	tolLC
Protected Attributes inherited from ObjectiveFunction
int	nfe
int	nfe2

Detailed Description

Definition at line 201 of file nma_alignment.h.

Constructor & Destructor Documentation

ObjFunc_nma_alignment()

ObjFunc_nma_alignment::ObjFunc_nma_alignment	(	int	_t,
		int	_n = 0
	)

Definition at line 377 of file nma_alignment.cpp.

                                                           {
}

~ObjFunc_nma_alignment()

ObjFunc_nma_alignment::~ObjFunc_nma_alignment ( )

inline

Definition at line 205 of file nma_alignment.h.

{};

Member Function Documentation

eval()

double ObjFunc_nma_alignment::eval ( Vector  v, int *  nerror = nullptr  )

virtual

Implements ObjectiveFunction.

Definition at line 325 of file nma_alignment.cpp.

                                                        {
    int dim = global_nma_prog->numberOfModes;

    for (int i = 0; i < dim; i++) {
        global_nma_prog->trial(i) = X[i];
    }

    int pyramidLevelDisc = 1;
    int pyramidLevelCont = (global_nma_prog->currentStage == 1) ? 1 : 0;

    FileName fnRandom = global_nma_prog->createDeformedPDB(pyramidLevelCont);
    const char * randStr = fnRandom.c_str();

    if (global_nma_prog->currentStage == 1) {
        global_nma_prog->performCompleteSearch(fnRandom, pyramidLevelDisc);
    } else {
        double rot, tilt, psi, xshift, yshift;
        MetaDataVec DF;

        rot = global_nma_prog->bestStage1(
                VEC_XSIZE(global_nma_prog->bestStage1) - 5);
        tilt = global_nma_prog->bestStage1(
                VEC_XSIZE(global_nma_prog->bestStage1) - 4);
        psi = global_nma_prog->bestStage1(
                VEC_XSIZE(global_nma_prog->bestStage1) - 3);
        xshift = global_nma_prog->bestStage1(
                VEC_XSIZE(global_nma_prog->bestStage1) - 2);
        yshift = global_nma_prog->bestStage1(
                VEC_XSIZE(global_nma_prog->bestStage1) - 1);

        size_t objId = DF.addObject();
        FileName fnDown = formatString("%s_downimg.xmp", randStr);
        DF.setValue(MDL_IMAGE, fnDown, objId);
        DF.setValue(MDL_ENABLED, 1, objId);
        DF.setValue(MDL_ANGLE_ROT, rot, objId);
        DF.setValue(MDL_ANGLE_TILT, tilt, objId);
        DF.setValue(MDL_ANGLE_PSI, psi, objId);
        DF.setValue(MDL_SHIFT_X, xshift, objId);
        DF.setValue(MDL_SHIFT_Y, yshift, objId);

        DF.write(formatString("%s_angledisc.xmd", randStr));
        copyImage(global_nma_prog->currentImgName.c_str(), fnDown.c_str());
    }
    double fitness = global_nma_prog->performContinuousAssignment(fnRandom,
            pyramidLevelCont);

    runSystem("rm", formatString("-rf %s* &", randStr));

    global_nma_prog->updateBestFit(fitness);
    return fitness;
}

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

• xmipp/libraries/reconstruction/nma_alignment.h
• xmipp/libraries/reconstruction/nma_alignment.cpp