java.lang.Object
- java.util.AbstractCollection<E>
- - java.util.AbstractList<E>
  - - java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f>
    - - gov.nih.mipav.model.structures.VOIBase
      - gov.nih.mipav.model.structures.VOIContour

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Iterable<WildMagic.LibFoundation.Mathematics.Vector3f>, java.util.Collection<WildMagic.LibFoundation.Mathematics.Vector3f>, java.util.List<WildMagic.LibFoundation.Mathematics.Vector3f>, java.util.RandomAccess
```
public class VOIContour
extends VOIBase
```
This class is fundamental to the VOI class in which points are stored that describe a curve of an VOI. The points are 3D and are floats (see Vector3f). It extends VOIBase and therefore it extends Vector. Vector makes it very easy to add points and remove points from the contour. An VOI is formed from one or many contours.
Routines that wish to sample all integer x,y values along a line must sample the line at 1/2 unit increments. As an example, suppose we have a line with the following (x,y) values: (0.2,0.7),(0.7,1.2),(1.2,1.7), (1.7,2.2). If we sample at unit increments with rounding we could either obtain the points (0,1),(1,2) or (1,1),(2,2). By sampling at 1/2 unit increments along the line we sample at (0,1),(1,1),(1,2),(2,2).

Version:

0.1 Oct 27, 1997

Author:

Matthew J. McAuliffe, Ph.D.

See Also:

VOIBase, VOILine, VOI, $Logfile: /mipav/src/gov/nih/mipav/model/structures/VOIContour.java $ $Revision: 114 $ $Date: 2/24/06 3:34p $, Serialized Form

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description
`private class`	`VOIContour.positionItem`
`private class`	`VOIContour.positionLowerComparator`
`private class`	`VOIContour.positionUpperComparator`

Field Summary

Fields
Modifier and Type Field Description

private static long serialVersionUID
Use serialVersionUID for interoperability.
- Fields inherited from class gov.nih.mipav.model.structures.VOIBase
  active, autoLabel, averagePt, cenMassPt, cenMassPtB, cenMassPtG, cenMassPtR, CIRCLE, closed, display, DOWN, fixed, gcPt, label, lastPoint, LEFT, LEFT_MIDDLE, LOWER_LEFT, LOWER_MIDDLE, LOWER_RIGHT, m_akImageMinMax, m_bQuickLUT, m_bReloadPoints, m_bSplit, m_bUpdateAverage, m_bUpdateBounds, m_bUpdateGeometricCenter, m_bUpdateMask, m_bUpdatePlane, m_iAnchorIndex, m_iPlane, m_iVOIType, m_kColor, m_kPositionSum, m_kVolumeVOI, nearBoundPoint, nearPoint, NOT_A_PLANE, NOT_A_POINT, numPixels, process, RIGHT, RIGHT_MIDDLE, SQUARE, UNKNOWN_SUBTYPE, UP, UPPER_LEFT, UPPER_MIDDLE, UPPER_RIGHT, voiGroup, volumeDisplayRange, XPLANE, YPLANE, ZPLANE
- Fields inherited from class java.util.Vector
  capacityIncrement, elementCount, elementData
- Fields inherited from class java.util.AbstractList
  modCount

Constructor Summary

Constructors
Constructor	Description
`VOIContour(boolean flag)`	Construct a new closed or open VOI.
`VOIContour(boolean bFixed, boolean bClosed)`	Construct a new VOIContour.
`VOIContour(boolean bFixed, boolean bClosed, java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> kPositions)`	Construct a new VOIContour.
`VOIContour(VOIContour kVOI)`	Copy Constructor.
`VOIContour(VOIContour kVOI, int iPropDir)`	Copies the input contour and changes it's slice +/-
`VOIContour(VOIContour kVOI, TransMatrix tMatrix)`	Copies the input VOIBase, transformed by the input TransMatrix.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`double`	`boxCountBoundary2D(int xDim, int yDim)`
`double`	`calcAsymmetryIndex(int xDim, int yDim)`
`double`	`calcLargestSliceDistance(int[] extents, float[] res, WildMagic.LibFoundation.Mathematics.Vector3f kPos1, WildMagic.LibFoundation.Mathematics.Vector3f kPos2)`	Calculate the distance of the largest line segment contained entirely within the slice of the VOI
`private boolean`	`ccw(double[][] P, int i, int j, int k)`
`VOIBase`	`clone()`
`boolean`	`contains3D(WildMagic.LibFoundation.Mathematics.Vector3f pt)`
`void`	`convexHull()`
`private double`	`det(double x1, double x2, double x3, double y1, double y2, double y3)`
`double`	`euclideanDistance2D(int xDim, int yDim)`
`java.awt.Polygon`	`exportPolygon()`	Exports the points of the contour as a polygon (z data can not be encoded in the polygon).
`int`	`getPositionAndIntensity(WildMagic.LibFoundation.Mathematics.Vector3f[] position, float[] intensity, float[] imageBuffer, int xDim)`	Gets position/intensity along the boundary of this contour VOI.
`int`	`getPositionAndIntensityIndex(int[] position, float[] intensity, float[] imageBuffer, int xDim)`	Gets the position/intensity along the boundary of this contour VOI.
`void`	`importPolygon(java.awt.Polygon gon, int slice)`	Saves the polygon in the contour.
`double[]`	`invariantMoments(int xDim, int yDim)`
`boolean`	`isCounterClockwise()`	Determines if the points are ordered in a counterClockwise manner.
`private int`	`make_chain(double[][] V, int offset, int n, boolean lower)`
`void`	`makeClockwise()`	Make contour clockwise.
`void`	`makeCounterClockwise()`	Checks to see if Contour is counter-clockwise.
`void`	`makeCounterClockwise(int start)`	Checks to see if Contour is counter-clockwise.
`double`	`pinpol(double xpoint, double ypoint, boolean[] snear, int[] index1, int[] index2)`
`double`	`principalAxis(int xDim, int yDim)`	From statics it is known that any planar shape or closed curve possesses two principal axes 90 degrees apart intersecting at the centroid of the area.
`void`	`reloadPoints(float[] xPts, float[] yPts)`	Reloads points in this array for speed purposes.
`void`	`removeActivePt()`	Forget about the last clicked (active) point in the contour.
`void`	`residuals_ellipse(double[] residualSumOfSquares, double[][] xyproj, java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> xy, double centerX, double centerY, double majorAxis, double minorAxis, double angle)`	This is a port of the MATLAB file Reisduals_ellipse written by Hui Ma on May 24, 2010.
`void`	`secondOrderAttributes(ModelImage kImage, float[] pAxis, float[] eccentricity, float[] majorAxis, float[] minorAxis)`	Find the least squares fit of the points in the contour to an ellipsoid.
`void`	`secondOrderAttributeslsq(float xRes, float yRes, int xUnits, int yUnits, double[] angleAxis, double[] eccentricity, double[] majorAxis, double[] minorAxis, double[] xCenter, double[] yCenter)`	Finds the second order attributes.
`void`	`transformContour(TransMatrix tMatrix, boolean doRound)`	Transforms self.
`void`	`translate(float xT, float yT, float zT)`	Translates a VOI by some amount in x and y.

Methods inherited from class gov.nih.mipav.model.structures.VOIBase
addElement, addElement, area, areaTwice, calcIntensity, calcIntensity, calcIntensityThreshold, calcRGBIntensity, calcRGBIntensity, calcRGBIntensityThreshold, contain, contains, contains, contains, createVolumeVOI, cycleActivePt, delete, deleteVolumeVOI, display, dispose, distanceToVOI, equals, exportArrays, exportArrays, fillVolume, findPositionAndCurvature, findPositionAndIntensity, findPositionAndIntensity, findVOIIndentations2D, getActivePt, getAllContourPoints, getAnchor, getAverage, getBounds, getBounds, getCenterOfMass, getCenterOfMass, getCenterOfMassB, getCenterOfMassG, getCenterOfMassR, getContourID, getDoGeometricCenterLabel, getGeometricCenter, getGeometricCenterA, getGroup, getImageBoundingBox, getLabel, getLastNumPixels, getLengthPtToPt, getLengthPtToPt, getLengthString, getMaskPositions, getName, getNearBoundPoint, getNearPoint, getNumVoxels, getPlane, getProcess, getSelectedPoint, getSubtype, getTotalLengthString, getType, getVolumeDisplayRange, getVolumeVOI, importArrays, importArrays, importPoints, isActive, isClosed, isFixed, isM_bUpdateBounds, isM_bUpdateGeometricCenter, isQuickLUT, isSplit, nearLine, nearLine, planeFit, reloadPoints, setActive, setAnchor, setClosed, setDoGeometricCenterLabel, setFixed, setGroup, setLabel, setMask, setMaskSlice, setNearBoundPoint, setNearPoint, setPlane, setProcess, setQuickLUT, setSelectedPoint, setSplit, setSubtype, setVolumeDisplayRange, slice, slice, transform, trimPoints, update, update, update

Methods inherited from class java.util.Vector
add, add, addAll, addAll, addElement, capacity, clear, contains, containsAll, copyInto, elementAt, elements, ensureCapacity, firstElement, forEach, get, hashCode, indexOf, indexOf, insertElementAt, isEmpty, iterator, lastElement, lastIndexOf, lastIndexOf, listIterator, listIterator, remove, remove, removeAll, removeAllElements, removeElement, removeElementAt, removeIf, removeRange, replaceAll, retainAll, set, setElementAt, setSize, size, sort, spliterator, subList, toArray, toArray, toString, trimToSize

Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.Collection
parallelStream, stream, toArray

- Field Detail
  - serialVersionUID
```
private static final long serialVersionUID
```
    Use serialVersionUID for interoperability.
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - VOIContour
```
public VOIContour(boolean flag)
```
    Construct a new closed or open VOI.
    
    Parameters:
    
    flag - whether the voi contour is closed
  - VOIContour
```
public VOIContour(boolean bFixed,
                  boolean bClosed)
```
    Construct a new VOIContour.
    
    Parameters:
    
    bFixed - , true if this VOIContour is fixed (cannot be changed).
    
    bClosed - , true if this VOIContour is closed.
  - VOIContour
```
public VOIContour(boolean bFixed,
                  boolean bClosed,
                  java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> kPositions)
```
    Construct a new VOIContour.
    
    Parameters:
    
    bFixed - , true if this VOIContour is fixed (cannot be changed).
    
    bClosed - , true if this VOIContour is closed.
    
    kLocal -
  - VOIContour
```
public VOIContour(VOIContour kVOI)
```
    Copy Constructor.
    
    Parameters:
    
    kVOI -
  - VOIContour
```
public VOIContour(VOIContour kVOI,
                  int iPropDir)
```
    Copies the input contour and changes it's slice +/-
    
    Parameters:
    
    kBase -
    
    iPropDir -
  - VOIContour
```
public VOIContour(VOIContour kVOI,
                  TransMatrix tMatrix)
```
    Copies the input VOIBase, transformed by the input TransMatrix.
    
    Parameters:
    
    kBase - VOI to copy.
    
    tMatrix - transformation
- Method Detail
  - calcLargestSliceDistance
```
public double calcLargestSliceDistance(int[] extents,
                                       float[] res,
                                       WildMagic.LibFoundation.Mathematics.Vector3f kPos1,
                                       WildMagic.LibFoundation.Mathematics.Vector3f kPos2)
```
    Calculate the distance of the largest line segment contained entirely within the slice of the VOI
    
    Parameters:
    
    xRes -
    
    yRes -
    
    Returns:
    
    largestDistance
  - clone
```
public VOIBase clone()
```
    Specified by:
    
    clone in class VOIBase
  - pinpol
```
public double pinpol(double xpoint,
                     double ypoint,
                     boolean[] snear,
                     int[] index1,
                     int[] index2)
```
  - det
```
private double det(double x1,
                   double x2,
                   double x3,
                   double y1,
                   double y2,
                   double y3)
```
  - euclideanDistance2D
```
public double euclideanDistance2D(int xDim,
                                  int yDim)
```
  - boxCountBoundary2D
```
public double boxCountBoundary2D(int xDim,
                                 int yDim)
```
  - invariantMoments
```
public double[] invariantMoments(int xDim,
                                 int yDim)
```
  - principalAxis
```
public double principalAxis(int xDim,
                            int yDim)
```
    From statics it is known that any planar shape or closed curve possesses two principal axes 90 degrees apart intersecting at the centroid of the area. (For certain areas such as a circle, there may be more than two principal axes about the centroid, but there are always at least two.) The moment of inertia is maximum about one principal axis and minimum about the other principal axis. Here the angle in degrees with the principal axis having the minimum moment of inertia is reported. For an ellipse with semimajor axis = a and semiminor axis = b, the moment of inertia has its smallest value of PI*a*b^3/8 about the major axis and its largest value of PI*a^3*b/8 about the minor axis. Reference: On the Computation of the Moments of a Polygon, with Some Applications by Soerjadi
    
    Parameters:
    
    xDim -
    
    yDim -
    
    Returns:
  - calcAsymmetryIndex
```
public double calcAsymmetryIndex(int xDim,
                                 int yDim)
```
    Parameters:
    
    xDim -
    
    yDim -
    
    Returns:
  - convexHull
```
public void convexHull()
```
  - make_chain
```
private int make_chain(double[][] V,
                       int offset,
                       int n,
                       boolean lower)
```
  - ccw
```
private boolean ccw(double[][] P,
                    int i,
                    int j,
                    int k)
```
  - exportPolygon
```
public java.awt.Polygon exportPolygon()
```
    Exports the points of the contour as a polygon (z data can not be encoded in the polygon).
    
    Returns:
    
    returns polygon
  - getPositionAndIntensity
```
public int getPositionAndIntensity(WildMagic.LibFoundation.Mathematics.Vector3f[] position,
                                   float[] intensity,
                                   float[] imageBuffer,
                                   int xDim)
```
    Gets position/intensity along the boundary of this contour VOI.
    
    Parameters:
    
    position - array that is filled with all x,y coordinates
    
    intensity - the corresponding intensities along the line
    
    imageBuffer - image array in which VOIs and lines are found
    
    xDim - x-Dimension of image
    
    Returns:
    
    the number of points in the position and intensity array that have valid data.
  - getPositionAndIntensityIndex
```
public int getPositionAndIntensityIndex(int[] position,
                                        float[] intensity,
                                        float[] imageBuffer,
                                        int xDim)
```
    Gets the position/intensity along the boundary of this contour VOI.
    
    Parameters:
    
    position - array that is filled with all the indices in the form of indexY*xDim + indexX
    
    intensity - the corresponding intensities along the line
    
    imageBuffer - image array in which the VOis and lines are found
    
    xDim - x-Dimension of image
    
    Returns:
    
    the number of points in the position and intensity array that hava valid data.
  - importPolygon
```
public void importPolygon(java.awt.Polygon gon,
                          int slice)
```
    Saves the polygon in the contour.
    
    Parameters:
    
    gon - polygon to be saved
    
    slice - index to save the polygon at
  - isCounterClockwise
```
public boolean isCounterClockwise()
```
    Determines if the points are ordered in a counterClockwise manner.
    
    Returns:
    
    true if points are counter clockwise and false if clockwise.
  - makeClockwise
```
public void makeClockwise()
```
    Make contour clockwise.
  - makeCounterClockwise
```
public void makeCounterClockwise()
```
    Checks to see if Contour is counter-clockwise. If not it makes the contour counter-clockwise.
  - makeCounterClockwise
```
public void makeCounterClockwise(int start)
```
    Checks to see if Contour is counter-clockwise. If not it makes the contour counter-clockwise.
    
    Parameters:
    
    start - , the index of the first point.
  - reloadPoints
```
public void reloadPoints(float[] xPts,
                         float[] yPts)
```
    Reloads points in this array for speed purposes.
    
    Parameters:
    
    xPts - loads the x-values into the xPts array.
    
    yPts - loads the y-values into the yPts array.
  - removeActivePt
```
public void removeActivePt()
```
    Forget about the last clicked (active) point in the contour.
  - secondOrderAttributes
```
public void secondOrderAttributes(ModelImage kImage,
                                  float[] pAxis,
                                  float[] eccentricity,
                                  float[] majorAxis,
                                  float[] minorAxis)
```
    Find the least squares fit of the points in the contour to an ellipsoid. Uses a variant of Powell's algorithm to find the minimum of the 9D function: center x,y,z, rotation x,y,z, and axis x,y,z.
    
    Parameters:
    
    kImage - input image
    
    pAxis - output principal axis
    
    eccentricity - output eccentricity
    
    majorAxis - output major axis length
    
    minorAxis - output minor axis length
  - secondOrderAttributeslsq
```
public void secondOrderAttributeslsq(float xRes,
                                     float yRes,
                                     int xUnits,
                                     int yUnits,
                                     double[] angleAxis,
                                     double[] eccentricity,
                                     double[] majorAxis,
                                     double[] minorAxis,
                                     double[] xCenter,
                                     double[] yCenter)
```
    Finds the second order attributes.
    Reference: Fitzgibbon, Pilu, Fisher: Direct Least Squares Fitting of Ellipses at http://www.robots.ox.ac.uk/~awf/ellipse/fitellipse.html
    
    Parameters:
    
    xRes - DOCUMENT ME!
    
    yRes - DOCUMENT ME!
    
    xUnits - DOCUMENT ME!
    
    yUnits - DOCUMENT ME!
    
    angleAxis - angle in radians with major axis
    
    eccentricity - shape (circle = 0; line = 1)
    
    majorAxis - diameter of major axis
    
    minorAxis - diameter of minor axis
    
    xCenter -
    
    yCenter -
  - residuals_ellipse
```
public void residuals_ellipse(double[] residualSumOfSquares,
                              double[][] xyproj,
                              java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> xy,
                              double centerX,
                              double centerY,
                              double majorAxis,
                              double minorAxis,
                              double angle)
```
    This is a port of the MATLAB file Reisduals_ellipse written by Hui Ma on May 24, 2010. This code is covered by a BSD license. On the MATLAB exchange it was listed under distance from points to an ellipse. file ID #27708. The text at the front of the file is as follows: % Projecting a given set of points onto an ellipse % and computing the distances from the points to the ellipse % % This is a modified version of an iterative algorithm published by D. Eberly % Internet publication: "Distance from a point to an ellipse in 2D" (2004) % Geometric Tools, LLC, www.geometrictools.com % Book publication: "3D Game Engine Design", 2nd edition. % Morgan Kaufmann Publishers, San Francisco, CA, 2007. % (see Section 14.13.1) % % Input: XY(n,2) is the array of coordinates of n points x(i)=XY(i,1), y(i)=XY(i,2) % ParG is a vector 5x1 of the ellipse parameters % ParG = [Center(1:2), Axes(1:2), Angle]' % Center - the coordinates of the ellipse's center % Axes - the axes (major, minor) % Angle - the angle of tilt of the ellipse % % Output: RSS is the Residual Sum of Squares (the sum of squares of the distances) % XYproj is the array of coordinates of projections % % The algorithm is proven to converge and reaches an accuracy of 7-8 significant digit % It takes 4-5 iterations per point, on average. input axes are diameters input angle is in radians Calling routine should supply xyproj as a double[][] = new double[xy.size()][2]
  - transformContour
```
public void transformContour(TransMatrix tMatrix,
                             boolean doRound)
```
    Transforms self.
    
    Parameters:
    
    tMatrix - transformation matrix
    
    doRound - if true round point coordinates to integers
  - translate
```
public void translate(float xT,
                      float yT,
                      float zT)
```
    Translates a VOI by some amount in x and y.
    
    Parameters:
    
    xT - translate this amount in the x direction
    
    yT - translate this amount in the y direction
  - contains3D
```
public boolean contains3D(WildMagic.LibFoundation.Mathematics.Vector3f pt)
```

Class VOIContour

Nested Class Summary

Field Summary

Fields inherited from class gov.nih.mipav.model.structures.VOIBase

Fields inherited from class java.util.Vector

Fields inherited from class java.util.AbstractList

Constructor Summary

Method Summary

Methods inherited from class gov.nih.mipav.model.structures.VOIBase

Methods inherited from class java.util.Vector

Methods inherited from class java.lang.Object

Methods inherited from interface java.util.Collection

Field Detail

serialVersionUID

Constructor Detail

VOIContour

VOIContour

VOIContour

VOIContour

VOIContour

VOIContour

Method Detail

calcLargestSliceDistance

clone

pinpol

det

euclideanDistance2D

boxCountBoundary2D

invariantMoments

principalAxis

calcAsymmetryIndex

convexHull

make_chain

ccw

exportPolygon

getPositionAndIntensity

getPositionAndIntensityIndex

importPolygon

isCounterClockwise

makeClockwise

makeCounterClockwise

makeCounterClockwise

reloadPoints

removeActivePt

secondOrderAttributes

secondOrderAttributeslsq

residuals_ellipse

transformContour

translate

contains3D