Package gov.nih.mipav.model.algorithms.registration.vabra

Class VabraSubjectTargetPairs

java.lang.Object
gov.nih.mipav.model.algorithms.registration.vabra.VabraSubjectTargetPairs
All Implemented Interfaces:
de.jtem.numericalMethods.calculus.function.RealFunctionOfOneVariable
public class VabraSubjectTargetPairs extends Object implements de.jtem.numericalMethods.calculus.function.RealFunctionOfOneVariable

  • Field Details

    • maxDimensions

      private int maxDimensions

    • subject

      private VabraVolumeCollection subject

    • deformedSubject

      private VabraVolumeCollection deformedSubject

    • target

      private VabraVolumeCollection target

    • targetBinned

      private VabraVolumeCollection targetBinned

    • deformedSubjectBinned

      private VabraVolumeCollection deformedSubjectBinned

    • currentDownSampleFactor

      private double currentDownSampleFactor

    • boundingBox

      private int[] boundingBox

    • currentDeformField

      private float[] currentDeformField

    • totalDeformField

      private float[] totalDeformField

    • origSubjectList

      private ModelImage origSubjectList

    • origTargetList

      private ModelImage origTargetList

    • chInterpType

      private int chInterpType

    • numOfBins

      private int numOfBins

    • RobustMinThresh

      private float RobustMinThresh

    • RobustMaxThresh

      private float RobustMaxThresh

    • defFieldUpdateMode

      private int defFieldUpdateMode

    • curX

      private int curX

    • curY

      private int curY

    • curZ

      private int curZ

    • deformedSubjectCopy

      private VabraVolumeCollection deformedSubjectCopy

    • totalDeformFieldSplit

      private ModelImage[] totalDeformFieldSplit

    • levelCount

      private int levelCount

    • resCount

      private int resCount

    • rbf

      private VabraRBF rbf

    • lambda

      private static double lambda

    • localROI

      private int[] localROI

    • localCoarseGradient

      private double[] localCoarseGradient

    • coarseLocalRegionCenter

      private int[] coarseLocalRegionCenter

    • directionsOptmizationWeight

      private double[] directionsOptmizationWeight

    • domainMax

      private double domainMax

    • domainMin

      private double domainMin

    • tolerance

      private double tolerance

    • commitCount

      private int commitCount

    • origJointST

      private int[] origJointST

    • currentJointST

      private int[] currentJointST

    • defSTxPlus

      private int[] defSTxPlus

    • defSTxMinus

      private int[] defSTxMinus

    • defSTyPlus

      private int[] defSTyPlus

    • defSTyMinus

      private int[] defSTyMinus

    • defSTzPlus

      private int[] defSTzPlus

    • defSTzMinus

      private int[] defSTzMinus

    • defSxPlus

      private int[] defSxPlus

    • defSxMinus

      private int[] defSxMinus

    • defSyPlus

      private int[] defSyPlus

    • defSyMinus

      private int[] defSyMinus

    • defSzPlus

      private int[] defSzPlus

    • defSzMinus

      private int[] defSzMinus

    • origDeformedSubject

      private int[] origDeformedSubject

    • origTarget

      private int[] origTarget

    • currentDeformedSubject

      private int[] currentDeformedSubject

  • Constructor Details

    • VabraSubjectTargetPairs

      public VabraSubjectTargetPairs(ModelImage subjectVols, ModelImage targetVols, float robustMaxT, float robustMinT, int numBins, int interpType, boolean useMNMI, double[] directionsOptmizationWeight, int defFieldUpdateMode)

  • Method Details

    • robustMaximum

      private static final float robustMaximum(float[] image, float ratio, int scales, int nx, int ny, int nz)
      Robust maximum estimation
      Parameters:
      ratio - float fraction in [0,1]: the minimum number of points above or equal to the maximum over the total volume
      scales - int: the number of times the scale is refined for finding the robust maximum
      nx - ,ny,nz image dimensions
      Returns:
      the robust maximum value

    • robustMinimum

      private static final float robustMinimum(float[] image, float ratio, int scales, int nx, int ny, int nz)
      Robust maximum estimation
      Parameters:
      ratio - float fraction in [0,1]: the minimum number of points below or equal to the minimum over the total volume
      scales - int: the number of times the scale is refined for finding the robust minimum
      Returns:
      the robust minimum value

    • coarseGradientParameters

      public int coarseGradientParameters()

    • dispose

      public void dispose()

    • prepareForNextLevel

      public int[] prepareForNextLevel()

    • setResolution

      public void setResolution(float downSampleFactor)

    • threshAtRobustMaxAndMin

      private void threshAtRobustMaxAndMin(VabraVolumeCollection imgVec)

    • updateDefField

      private void updateDefField(int[] regionToUpdate)

    • calculateBoundingBox

      void calculateBoundingBox()

    • getDeformationField

      ModelImage getDeformationField()

    • getDeformedSubject

      ModelImage getDeformedSubject()

    • getDomainMax

      public double getDomainMax()

    • getDomainMin

      public double getDomainMin()

    • getDomainTolerance

      public double getDomainTolerance()

    • getValue

      public double getValue(double c)

    • coarseGradient

      public void coarseGradient(int[] regionCenter, double[] results)

    • updateFromCoarseOptimization

      void updateFromCoarseOptimization(double coeff)

    • coarseOptimize

      public double coarseOptimize(int[] regionCenter, double[] gradient)

    • coarseCostFunctionCommit

      private double coarseCostFunctionCommit(double coeff, boolean commitUpdate)

    • coarseCostFunction

      private double coarseCostFunction(double coeff)

    • getRBF

      public VabraRBF getRBF()

    • copyHist

      private int[] copyHist(int[] in)

    • copyHist

      private int[][] copyHist(int[][] in)

    • copyHist

      private int[][][] copyHist(int[][][] vol)

    • resetCurrentHistograms

      private void resetCurrentHistograms()

    • updateHistograms

      private void updateHistograms(VabraVolumeCollection normedTarget, VabraVolumeCollection normedDeformedSubject, int[] boundingBox)

    • getCurrentNMI

      private double getCurrentNMI()

    • adjustOrigBins

      private void adjustOrigBins(int subBin, int tarBin, int newBin)

    • getNMIGradients

      private void getNMIGradients(double[] results, double[] deltaC)

    • adjustGradientBins

      private void adjustGradientBins(VabraVolumeCollection subject, double x, double y, double z, int[] subjectHist, int[] jointHist, int targetBins, int subjectBins)

    • adjustBins

      private void adjustBins(int[] subjectHist, int[] jointHist, int subBin, int tarBin, int newBin)

    • eval

      public double eval(double arg0)
      Specified by:
      eval in interface de.jtem.numericalMethods.calculus.function.RealFunctionOfOneVariable