Package gov.nih.mipav.model.algorithms

Class AlgorithmConstPowellOptBase

  • All Implemented Interfaces:
    de.jtem.numericalMethods.calculus.function.RealFunctionOfSeveralVariables, java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
    Direct Known Subclasses:
    AlgorithmConstPowellOpt3D
    public abstract class AlgorithmConstPowellOptBase
extends AlgorithmBase
implements de.jtem.numericalMethods.calculus.function.RealFunctionOfSeveralVariables
    Powell's Method

    Runs Powell's method. Powell's method is a way to find minimums without finding derivatives. Basically, it starts at some point P in N-dimensional space, proceeds in a direction, and minimizes along that line using a 1-dimensional minimization method. It continues like this until the point has moved by less than the tolerance. It starts with the initial point defined in the constructor and initial directions of (1 0 ... 0) (0 1 0 ... ) ..., the basis vectors. At the end, "point" is the best point found and functionAtBest is the value at "point".

    This is an abstract class which contains many of the basic functions needed to run Powell's method. 2D and 3D versions extend this version.

    This optimization technique is based on FLIRT. FLIRT stands for FMRIB's Linear Image Registration Tool. For more information on FLIRT, visit their homepage at http://www.fmrib.ox.ac.uk/fsl/flirt/. Their main paper is:

    Jenkinson, M. and Smith, S. (2001a).
    A global optimisation method for robust affine registration of brain images.
    Medical Image Analysis, 5(2):143-156.

    Version:
    0.1 Oct 1, 2001
    Author:
    Neva Cherniavsky

    • Field Detail

      • bracketBound

        protected int bracketBound
        The initial bracket size for first iteration of Powell.

      • finalPoint

        protected double[] finalPoint
        Final point when optimization is complete.

      • fromOrigin

        protected TransMatrixd fromOrigin
        The transformation matrix from the origin of the input image.

      • functionAtBest

        protected double functionAtBest
        The cost of the function at the best minimum.

      • maxIterations

        protected int maxIterations
        The maximum number of iterations the optimization allows.

      • myProgressBar

        protected ViewJProgressBar myProgressBar
        Progress bar that may be set for long optimization runs.

      • nDims

        protected int nDims
        Degress of freedom.

      • parent

        protected AlgorithmBase parent
        Parent algorithm that called this optimization.

      • point

        protected double[] point
        Point that is currently being optimized.

      • progressBegin

        protected int progressBegin
        Where progress is when sent in.

      • progressMax

        protected int progressMax
        The max the progress can go to.

      • start

        protected double[] start
        Point that was initially passed into function.

      • success

        protected boolean success
        Indicates whether the Powell algorithm succeeded in finding a minimum.

      • tolerance

        protected double[] tolerance
        Array of tolerances for each dimension.

      • toOrigin

        protected TransMatrixd toOrigin
        The transformation matrix to the origin of the input image.

      • trLimits

        protected float[][] trLimits
        Array of translation and rotation limits for each dimension.

    • Constructor Detail

      • AlgorithmConstPowellOptBase

        public AlgorithmConstPowellOptBase​(AlgorithmBase parentAlgo,
                                   int degreeOfFreedom,
                                   AlgorithmOptimizeFunctionBase costFunc,
                                   double[] initial,
                                   double[] tols,
                                   int maxIter,
                                   int coords,
                                   int bracket)
        Constructs a new algorithm with the given centers of mass (needed for setting the transformations), the given cost function (which was constructed with the proper images), the initial point we're looking at, and some tolerance within that point to look for the minimum. The initial point contains rotations, translations, scales, and skews.
        Parameters:
        parentAlgo - DOCUMENT ME!
        degreeOfFreedom - Degree of freedom for transformation (must be 3, 4, 6, 7, 9, or 12).
        costFunc - Cost function to use.
        initial - Initial point to start from, length of 12.
        tols - Tolerance for each dimension (tols.length == degreeOfFreedom).
        maxIter - The maximum iterations.
        coords - 2 or 3 for 2D or 3D
        bracket - the bracket bound for the first iteration of powell

    • Method Detail

      • convertToMatrix

        public abstract TransMatrixd convertToMatrix​(double[] vector)
        Helper method that converts a vector with certain values set to a matrix. For values not set, uses those in start variable.
        Parameters:
        vector - Point with possible rotations, translations, etc. set.
        Returns:
        Matrix representation of that point.

      • getFinal

        public abstract double[] getFinal()
        Returns the final point with translations, rotations, scales, and skews representing the best Transformation.
        Returns:
        A vector representing the best transformation in terms of translations, rotations, scales, and skews.

      • getFinal

        public abstract double[] getFinal​(double[] point)
        Returns the final point with translations, rotations, scales, and skews representing the best Transformation.
        Returns:
        A vector representing the best transformation in terms of translations, rotations, scales, and skews.

      • getMatrix

        public abstract TransMatrixd getMatrix()
        Returns the matrix representing the best transformation.
        Returns:
        A matrix representing the best transformation.

      • getMatrix

        public abstract TransMatrixd getMatrix​(double sample)
        Returns the matrix representing the best transformation. The passed in parameter represents the resolution (same in all directions and for both input and reference images, since resampled isotropically). Since the optimization was done in pixel space, not millimeter space, the translation parameters need to be scaled by the sample value.
        Parameters:
        sample - Sample size.
        Returns:
        A matrix representing the best transformation.

      • measureCost

        public abstract void measureCost()
        Calls cost function with inputed point and saves result in functionAtBest.

      • setInitialPoint

        public abstract void setInitialPoint​(double[] initial)
        Sets the initial point to the value passed in.
        Parameters:
        initial - Initial point.

      • setLimits

        public abstract void setLimits​(float[][] limits)
        Sets the limits on rotation and translation.
        Parameters:
        limits - limits

      • didSucceed

        public boolean didSucceed()
        Returns whether or not a minimum was found.
        Returns:
        whether or not a minimum was found.

      • disposeLocal

        public void disposeLocal()
        Sets everything to null and prepares this class for destruction.

      • getCost

        public double getCost()
        Returns the cost of the best transformation.
        Returns:
        The cost of the best transformation.

      • getPoint

        public double[] getPoint()
        Returns the optimized point, with length == degrees of freedom.
        Returns:
        The optimized point.

      • setMaxIterations

        public void setMaxIterations​(int max)
        Sets the maximum number of iterations.
        Parameters:
        max - The max number of iterations.

      • debugPoint

        protected void debugPoint​(double[] point,
                          java.lang.String message)
        Method to display current point values.
        Parameters:
        point - DOCUMENT ME!
        message - DOCUMENT ME!

      • eval

        public double eval​(double[] x)
        Specified by:
        eval in interface de.jtem.numericalMethods.calculus.function.RealFunctionOfSeveralVariables

      • getNumberOfVariables

        public int getNumberOfVariables()
        Specified by:
        getNumberOfVariables in interface de.jtem.numericalMethods.calculus.function.RealFunctionOfSeveralVariables