Field Detail

• GRADIENT_MAG

  public static final int GRADIENT_MAG

  chooses the gradient magnitude cost

  See Also:

  Constant Field Values

• MEDIALNESS

  public static final int MEDIALNESS

  chooses the medialness cost

  See Also:

  Constant Field Values

• INTENSITY

  public static final int INTENSITY

  chooses the intensity magnitude

  See Also:

  Constant Field Values

• GRADIENT_MAG_MED

  public static final int GRADIENT_MAG_MED

  chooses the gradient magnitude and medialness cost functions

  See Also:

  Constant Field Values

• GRADIENT_MAG_INT

  public static final int GRADIENT_MAG_INT

  chooses the gradient magnitude and intensity based cost functions

  See Also:

  Constant Field Values

• GRADIENT_ALL

  public static final int GRADIENT_ALL

  chooses all the gradient cost functions

  See Also:

  Constant Field Values

• m_bDrawVOI

  private boolean m_bDrawVOI

  Set to true when the user is actively drawing or modifying a VOI contour.

• m_bSelected

  protected boolean m_bSelected

  Set to true when the user has selected a VOI contour.

• DELETE_INTENSITY_LINE

  public static final java.lang.String DELETE_INTENSITY_LINE

  used in the popup menu when the user right-clicks over a voi intensity line.

  See Also:

  Constant Field Values

• SHOW_INTENSITY_GRAPH

  public static final java.lang.String SHOW_INTENSITY_GRAPH

  used in the popup menu when the user right-clicks over a voi intensity line.

  See Also:

  Constant Field Values

• SHOW_LINE_ENDPOINTS

  public static final java.lang.String SHOW_LINE_ENDPOINTS

  used in the popup menu when the user right-clicks over a voi intensity line.

  See Also:

  Constant Field Values

• PI_SEARCH

  private static final double[] PI_SEARCH

  Used for angle searches in line VOI creation

• PI_MULT

  private static final double[] PI_MULT

• NONE

  private static final int NONE

  See Also:

  Constant Field Values

• TEXT

  private static final int TEXT

  See Also:

  Constant Field Values

• POINT

  private static final int POINT

  See Also:

  Constant Field Values

• POLYPOINT

  private static final int POLYPOINT

  See Also:

  Constant Field Values

• LINE

  private static final int LINE

  See Also:

  Constant Field Values

• PROTRACTOR

  private static final int PROTRACTOR

  See Also:

  Constant Field Values

• RECTANGLE

  private static final int RECTANGLE

  See Also:

  Constant Field Values

• OVAL

  private static final int OVAL

  See Also:

  Constant Field Values

• POLYLINE

  private static final int POLYLINE

  See Also:

  Constant Field Values

• LEVELSET

  private static final int LEVELSET

  See Also:

  Constant Field Values

• LIVEWIRE

  private static final int LIVEWIRE

  See Also:

  Constant Field Values

• RECTANGLE3D

  private static final int RECTANGLE3D

  See Also:

  Constant Field Values

• SPLITLINE

  private static final int SPLITLINE

  See Also:

  Constant Field Values

• LUT

  private static final int LUT

  See Also:

  Constant Field Values

• RETRACE

  private static final int RETRACE

  See Also:

  Constant Field Values

• BSPLINE

  private static final int BSPLINE

  See Also:

  Constant Field Values

• m_iDrawType

  private int m_iDrawType

• m_kCurrentVOI

  protected VOIBase m_kCurrentVOI

  Current active voi contour.

• m_kCopyVOI

  private VOIBase m_kCopyVOI

  The contour to copy.

• m_kDrawingContext

  protected ScreenCoordinateListener m_kDrawingContext

  ScreenCoordinateListener translates between the current image dimensions, canvas size, and mouse coordinates for correct mouse interaction.

• levelSetStack

  private PointStack levelSetStack

  Used to calculate the levelset contour.

• map

  private java.util.BitSet map

  Used to calculate the levelset contour.

• stack

  private java.util.Stack<int[]> stack

  Used to calculate the levelset contour.

• m_bLeftMousePressed

  private boolean m_bLeftMousePressed

  Set to true when the left mouse is pressed.

• m_bFirstDrag

  protected boolean m_bFirstDrag

  Change the mouse cursor with the first mouseDrag event

• m_fMouseX

  protected float m_fMouseX

  Last/current mouse position.

• m_fMouseY

  protected float m_fMouseY

• m_aiAxisOrder

  private int[] m_aiAxisOrder

  Local orientation of the displayed image, used in the volume renderer and tri-planar views.

• m_abAxisFlip

  private boolean[] m_abAxisFlip

• m_akImages

  private ModelImage[] m_akImages

  ImageA and ImageB

• m_kImageActive

  protected ModelImage m_kImageActive

  Current active image.

• m_kLocalImage

  private ModelImage m_kLocalImage

  A re-oriented version of the active image, re-oriented so it matches the currently displayed image orientations in either the tri-planar or volume render views. This is used for level-set and livewire in the tri-planar view.

• m_aiLocalImageExtents

  private int[] m_aiLocalImageExtents

  The image extents in the local orientation.

• m_kParent

  protected VOIManagerInterface m_kParent

  A reference to the VOIManagerInterface

• m_bFirstVOI

  private boolean m_bFirstVOI

  Calculations for the oval voi are calculated one time:

• m_iCirclePts

  private int m_iCirclePts

• m_adCos

  private double[] m_adCos

• m_adSin

  private double[] m_adSin

• NearNone

  protected static final int NearNone

  VOI contour near status:

  See Also:

  Constant Field Values

• NearPoint

  protected static final int NearPoint

  See Also:

  Constant Field Values

• NearLine

  protected static final int NearLine

  See Also:

  Constant Field Values

• NearBoundPoint

  protected static final int NearBoundPoint

  See Also:

  Constant Field Values

• m_iNearStatus

  protected int m_iNearStatus

  The near status of the mouse, used to set the mouse cursor.

• m_kComponent

  protected java.awt.Component m_kComponent

  The canvas

• m_iLiveWireSelection

  private int m_iLiveWireSelection

  Type of livewire cost function, gradient magnitude, laplace, intensity.

• activeTree

  private VOIManager.ActiveTree activeTree

  Livewire calculations:

• costGraph

  private byte[] costGraph

• grad_weight

  private float grad_weight

• localCosts

  private float[] localCosts

• processedIndicies

  private java.util.BitSet processedIndicies

• seededCosts

  private float[] seededCosts

• seedPoint

  private int seedPoint

• m_bLiveWireInit

  private boolean m_bLiveWireInit

• m_abInitLiveWire

  private boolean[] m_abInitLiveWire

• m_bLevelSetInit

  private boolean m_bLevelSetInit

• m_abInitLevelSet

  private boolean[] m_abInitLevelSet

• xDirections

  private float[] xDirections

• yDirections

  private float[] yDirections

• imageBufferActive

  private float[] imageBufferActive

• m_bQuickLUT

  private boolean m_bQuickLUT

  True if the user has selected the quick lut feature:

• m_kPopupVOI

  protected ViewJPopupVOI m_kPopupVOI

  Popup Menu for VOIs (non-point).

• m_kPopupPt

  protected ViewJPopupPt m_kPopupPt

  Popup Menu for VOIPoints.

• m_iPlane

  protected int m_iPlane

  Set to XPLANE, YPLANE, or ZPLANE, depending on the image orientation.

• m_kMouseOffset

  protected WildMagic.LibFoundation.Mathematics.Vector3f m_kMouseOffset

  m_kMouseOffset is used to determine movements. mousePressed() establishes the coordinates of m_kMouseOffset. mouseDragged() calculates distance from the m_kMouseOffset to the present location and uses this distance to move an object.

• m_bMouseDrag

  private boolean m_bMouseDrag

  Set to true if the left mouse is pressed during drag.

• m_bCtrlDown

  private boolean m_bCtrlDown

• indexRetrace

  private int indexRetrace

  Contour Retrace:

• oldContour

  private VOIContour oldContour

• lastX

  private int lastX

• lastY

  private int lastY

• lastZ

  private int lastZ

• knowDirection

  private boolean knowDirection

• isFirst

  private boolean isFirst

• resetStart

  private boolean resetStart

• m_bLiveWire

  private boolean m_bLiveWire

  Whether the livewire properties (e.g. gradient magnitude) should be recalculated

• m_bFirstScale

  private boolean m_bFirstScale

• m_kBackupVOI

  private VOIBase m_kBackupVOI

Constructor Detail

• VOIManager

  public VOIManager​(VOIManagerInterface kParent)

  Constructor. Passes in the VOIManagerInterface parent which communicates all user-interface commands to the VOIManager.

  Parameters:

  kParent - containing VOIManagerInterface.

Method Detail

• actionPerformed

  public void actionPerformed​(java.awt.event.ActionEvent event)

  Specified by:

  actionPerformed in interface java.awt.event.ActionListener

• add

  public void add​(VOIBase kVOI,
                  float fHue)

  Called from ViewJComponentTriImage to add the image-align protractor.

  Parameters:

  kVOI - the VOIProgractor

  fHue - default color for the protractor.

• deleteVOI

  public void deleteVOI​(VOIBase kVOI)

  Called from ViewJComponentTriImage to delete the VOIProtractor.

  Parameters:

  kVOI - VOIProtractor that will be deleted.

• dispose

  public void dispose()

  Cleans up local memory.

• doVOI

  public void doVOI​(java.lang.String kCommand,
                    boolean isDrawCommand)

  Called from VOIManagerInterface.

  Parameters:

  kCommand - VOI Command

  isDrawCommand - when true this command represents a drawing command.

• draw

  public void draw​(VOIBase kVOI,
                   float[] resolutions,
                   int[] unitsOfMeasure,
                   int slice,
                   java.awt.Graphics g,
                   boolean bShowAllPoints)

  Draws the input VOI in the ViewJComponentEditImage

  Parameters:

  kVOI - input VOI to draw.

  resolutions - image resolutions.

  unitsOfMeasure - image units of measure.

  slice - current image slice in the orientation displayed in the ViewJComponentEditImage.

  orientation - image orientation displayed in the ViewJComponentEditImage

  g - Graphics.

• editCircleDiameter

  public void editCircleDiameter​(VOIBase kVOI,
                                 float radius)

  Called from the JDialogEditCircleDiameter. Changes the diameter of a circly VOI.

  Parameters:

  kVOI - the selected VOI to change.

  radius - the new diameter.

• editSquareLength

  public void editSquareLength​(VOIBase kVOI,
                               float length)

  Called from JDialogEditSquareLenth, changes the length of the selected square VOI.

  Parameters:

  kVOI - the selected square VOI to change.

  length - the new length.

• getComponent

  public java.awt.Component getComponent()

  Called from VOIManagerInterface.

  Returns:

  returns the Component this VOIManager is attached to.

• getImage

  public ModelImage getImage()

  Returns:

• getLocalImage

  public ModelImage getLocalImage()

  Returns a ModelImage in the local image space, if a local ModelImage has already been created it is returned.

  Returns:

  a ModelImage in the local image space.

• getParent

  public VOIManagerInterface getParent()

  Called from ViewJComponentEditImage. Each ViewJComponentEditImage has a VOIManager attached.

  Returns:

  the VOIManagerInterface parent of this VOIManager.

• getPlane

  public int getPlane()

  Returns the plane this VOIManager is drawing into. From VOIBase: XPLANE, YPLANE, ZPLANE.

  Returns:

  XPLANE, YPLANE, or ZPLANE.

• init

  public void init​(javax.swing.JFrame kFrame,
                   ModelImage kImageA,
                   ModelImage kImageB,
                   java.awt.Component kComponent,
                   ScreenCoordinateListener kContext,
                   int iOrientation)

  Initialize the VOIManager.

  Parameters:

  kImageA - imageA.

  kImageB - imageB.

  kComponent - ViewJComponentEditImage this VOIManager is attached to.

  kContext - ScreenCoordinateListener for converting between screen coordinates and image file coordinates.

  iOrientation - orientation of the ViewJComponentEditImage.

• isActive

  public boolean isActive()

  Returns true if the VOIManager is currently drawing a VOI, or if the defaultPointer button in the VOIManagerInterface is selected.

  Returns:

• keyPressed

  public void keyPressed​(java.awt.event.KeyEvent e)

  Specified by:

  keyPressed in interface java.awt.event.KeyListener

• keyReleased

  public void keyReleased​(java.awt.event.KeyEvent e)

  Specified by:

  keyReleased in interface java.awt.event.KeyListener

• keyTyped

  public void keyTyped​(java.awt.event.KeyEvent e)

  Specified by:

  keyTyped in interface java.awt.event.KeyListener

• liveWire

  public void liveWire​(int iSelection)

  Called from VOIManagerInterface. Initializes the livewire.

  Parameters:

  iSelection - livewire cost function.

• mouseClicked

  public void mouseClicked​(java.awt.event.MouseEvent kEvent)

  Specified by:

  mouseClicked in interface java.awt.event.MouseListener

• mouseDragged

  public void mouseDragged​(java.awt.event.MouseEvent kEvent)

  Specified by:

  mouseDragged in interface java.awt.event.MouseMotionListener

• mouseEntered

  public void mouseEntered​(java.awt.event.MouseEvent arg0)

  Specified by:

  mouseEntered in interface java.awt.event.MouseListener

• mouseExited

  public void mouseExited​(java.awt.event.MouseEvent arg0)

  Specified by:

  mouseExited in interface java.awt.event.MouseListener

• mouseMoved

  public void mouseMoved​(java.awt.event.MouseEvent kEvent)

  Specified by:

  mouseMoved in interface java.awt.event.MouseMotionListener

• mousePressed

  public void mousePressed​(java.awt.event.MouseEvent kEvent)

  Specified by:

  mousePressed in interface java.awt.event.MouseListener

• mouseReleased

  public void mouseReleased​(java.awt.event.MouseEvent kEvent)

  Specified by:

  mouseReleased in interface java.awt.event.MouseListener

• move

  public void move​(VOIBase kVOI,
                   WildMagic.LibFoundation.Mathematics.Vector3f kDiff)

  Moves the input VOI by the input Vector amount.

  Parameters:

  kVOI - input VOIBase to move.

  kDiff - vector amount to move the input VOI, vales are in image file-coordinates.

• pasteAllVOI

  public void pasteAllVOI​(VOIBase kVOI)

  Called from VOIManagerInterface. Pastes the input VOI onto all slices.

  Parameters:

  kVOI - input VOI.

• pasteVOI

  public void pasteVOI​(VOIBase kVOI)

  Called from VOIManagerInterface. Pastes the input VOI onto the current slice.

  Parameters:

  kVOI - input VOI.

• propagateVOI

  public void propagateVOI​(VOIBase kVOI,
                           int dir)

  Called from VOIManagerInterface. Propagates the input VOI in the input direction.

  Parameters:

  kVOI - input VOI.

  dir - +1 or -1

• scaleCircleVOI

  public void scaleCircleVOI​(VOIBase kVOI,
                             float scale)

  Parameters:

  kVOI -

  scale -

• scaleSquareVOI

  public void scaleSquareVOI​(VOIBase kVOI,
                             float scale)

  Parameters:

  kVOI -

  scale -

• setActive

  public boolean setActive​(boolean active)

  Programmatically sets whether the GUI should be in a state to draw VOIs. Components that are managed by this manager can use this method to indicate that VOI drawing should be stopped.

  Parameters:

  active - Whether VOI drawing should be successful.

  Returns:

  Whether this action is successful.

• setActiveImage

  public void setActiveImage​(int iActive)

  Sets the current active image.

  Parameters:

  iActive -

• setImage

  public void setImage​(ModelImage image,
                       int iOrientation)

• setImageB

  public void setImageB​(ModelImage imageB)

  Sets a new imageB.

  Parameters:

  imageB - new ModelImage imageB.

• setPopupPt

  public void setPopupPt​(ViewJPopupPt kPopupPt)

  Called from VOIManagerInterface. Sets the ViewJPopupPt.

  Parameters:

  kPopupPt -

• setPopupVOI

  public void setPopupVOI​(ViewJPopupVOI kPopupVOI)

  Called from VOIManagerInterface. Sets the ViewJPopupVOI.

  Parameters:

  kPopupPt -

• testMove

  public boolean testMove​(WildMagic.LibFoundation.Mathematics.Vector3f kDiff,
                          WildMagic.LibFoundation.Mathematics.Vector3f[] akMinMax,
                          boolean bUseMouse)

  Called from VOIManagerInterface when several VOIs are selected and moved as a group. This function first tests that the move does not move any of the VOIs in the group out of bounds. If the move keeps all VOIs in-bounds, then the move is executed.

  Parameters:

  kDiff - the amount to move the VOIs.

  akMinMax - the VOI group bounding-box.

  Returns:

  true if the move remains in-bounds, false otherwise.

• add

  private boolean add​(VOIBase kVOI,
                      int iPos,
                      WildMagic.LibFoundation.Mathematics.Vector3f kNewPoint,
                      boolean bIsFile)

  Add a point to the voi contour

  Parameters:

  kVOI - the voi to add to

  iPos - the position the new point will be added after

  kNewPoint - new point

  bIsFile - when true the point is already in file coordinates, when false translate the point to file coordinates.

  Returns:

• add

  private boolean add​(VOIBase kVOI,
                      WildMagic.LibFoundation.Mathematics.Vector3f kNewPoint,
                      boolean bIsFile)

  Add a new point to the end of the current contour.

  Parameters:

  kVOI - current contour

  kNewPoint - new point to add

  bIsFile - if true the point is in file coordinates.

  Returns:

  true if the point was added.

• addPopup

  private void addPopup​(VOIBase kVOI)

  Link the popup menu to the input voi so the popup menu will operate on the input voi.

  Parameters:

  kVOI - input voi for the popup menu.

• addVOIPoint

  private void addVOIPoint​(int iX,
                           int iY)

  Adds a point to the current voi.

  Parameters:

  iX - x in screen coordinates.

  iY - y in screen coordinates.

• anchor

  private void anchor​(int iX,
                      int iY,
                      boolean bSeed)

  Add an anchor point to the livewire contour.

  Parameters:

  iX - x value of the anchor point in file coordinates.

  iY - y value of the anchor point in file coordinates.

  bSeed - when true calculate a new seed from the anchor to the current mouse point, when false the anchor is the last point to add.

• anchorPolyline

  private void anchorPolyline​(int iX,
                              int iY,
                              boolean bFinished)

  Add an anchor point to the poly line contour.

  Parameters:

  iX - x value of the anchor point in file coordinates.

  iY - y value of the anchor point in file coordinates.

  bFinished - when true the current voi is set to active.

• anchorBSpline

  private void anchorBSpline​(int iX,
                             int iY,
                             boolean bFinished)

  Add an anchor point to the BSpline line contour.

  Parameters:

  iX - x value of the anchor point in file coordinates.

  iY - y value of the anchor point in file coordinates.

  bFinished - when true the current voi is set to active.

• SplineSmooth

  private void SplineSmooth​(VOIBase voiLine)

  Bspline smoothing

  Parameters:

  voiLine - VOI contour

• BsplineCurve

  private void BsplineCurve​(WildMagic.LibFoundation.Mathematics.Vector3f[] BsplinePts,
                            int numPts,
                            int pointReduced,
                            int degree,
                            java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> result)

  Compute Bspline segment

  Parameters:

  BsplinePts - BSpline init line points

  numPts - number points

  pointReduced - reduced number to create control points

  degree - Bspline degree

  result - resulting smoothed Bspline curve

• computeNormalLine

  private void computeNormalLine​(WildMagic.LibFoundation.Mathematics.Vector3f startPt,
                                 WildMagic.LibFoundation.Mathematics.Vector3f endPt,
                                 WildMagic.LibFoundation.Mathematics.Vector3f midPt,
                                 WildMagic.LibFoundation.Mathematics.Vector3f outNormPt,
                                 WildMagic.LibFoundation.Mathematics.Vector3f inNormPt,
                                 float stepPct,
                                 WildMagic.LibFoundation.Mathematics.Vector3f normStep,
                                 WildMagic.LibFoundation.Mathematics.Vector3f interpPt)

  When the line segment is drawn, take the mid point, create the normal line across the mid point. The drawn normal line will be the search range of the best gradient changes.

  Parameters:

  startPt - start point

  endPt - end point

  midPt - mid point

  outNormPt - normal line outward point

  inNormPt - normal line inward point

  stepPct - normal line step percentile

  normStep - number of steps to trace the normal line

  interpPt - the interpolated point, actually just the middle point

• computeGradient

  private void computeGradient​(float xCoord,
                               float yCoord,
                               float zCoord,
                               double[] result,
                               double[] grad,
                               double[] gradDir)

  With given x, y, z point coordinate, compute the gradient magnitude and gradient direction

  Parameters:

  xCoord - x coordinate

  yCoord - y coordinate

  zCoord - z coordinate

  result - result x, y direction gradient sum.

  grad - gradient magnitude

  gradDir - gradient direction.

• findBestGradientChange

  private void findBestGradientChange​(WildMagic.LibFoundation.Mathematics.Vector3f interpPt,
                                      WildMagic.LibFoundation.Mathematics.Vector3f normStep,
                                      float sliceZ,
                                      float[] x,
                                      float[] y)

  From the mid point of normal line, tracing both inward and outward diection along the normal line

  Parameters:

  interpPt - mid point

  normStep - normline step, which needed to compute the tracing steps

  sliceZ - z slice number

  x - best gradient change point x coordinate

  y - best gradient change point y coordinate

• avgPix

  private float avgPix​(int index)

  This method calculates the average pixel value based on the four neighbors (N, S, E, W).

  Parameters:

  index - the center pixel where the average pixel value is to be calculated.

  Returns:

  the average pixel value as a float.

• contains

  protected boolean contains​(VOIBase kVOI,
                             int iX,
                             int iY,
                             int iZ)

  Used to determine which contour is selected. Called by selectVOI and showSelectedVOI. For a closed or open contour, the point must be entirely within the contour. If the input voi is a line or point, returns true if the input point is near the line or point.

  Parameters:

  kVOI - input contour to test.

  iX - x value in screen coordinates.

  iY - y value in screen coordinates.

  iZ - z value in screen coordinates.

  Returns:

  true if inside the contour, or true if near the VOILine or near the VOIPoint.

• convertGraphToInt

  private int convertGraphToInt​(int next,
                                int xDim)

  Takes a byte and gets appropriate addition from current position.

  Parameters:

  next - Byte to check (0-8).

  Returns:

  Value to add to current location.

• createTextVOI

  private void createTextVOI​(int iX,
                             int iY)

  Creates a new VOIText at the local point. Causes the JDialogAnnotation to open so the user can specify the parameters and content of the text.

  Parameters:

  iX - x position in screen coordinates.

  iY - y position in screen coordinates.

• createVOI

  private VOIBase createVOI​(int iType,
                            boolean bClosed,
                            boolean bFixed,
                            java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> kPositions)

  Creates a new VOI Contour based on the input type.

  Parameters:

  iType - the type of contour to create.

  bClosed - when true the contour is closed.

  bFixed - when true the contour is fixed (cannot be changed).

  kPositions - the positions of the contour in screen coordinates.

  Returns:

  the new VOI Contour.

• createPointVOI

  public void createPointVOI​(int[] x,
                             int[] y,
                             int n,
                             int slice)

• createPolygonVOI

  public void createPolygonVOI​(int[] x,
                               int[] y,
                               int n,
                               int slice)

• createOvalVOI

  public void createOvalVOI​(int left,
                            int top,
                            int width,
                            int height,
                            int slice)

• createVOI

  private void createVOI​(java.awt.event.MouseEvent mouseEvent)

  Creates a new VOI Contour or adds a new point to the existing VOI Contour.

  Parameters:

  iX - new x position in screen coordinates.

  iY - new y position in screen coordinates.

• defaultOrientation

  private boolean defaultOrientation()

  Checks the axisOrder and axisFlip data members. If they do not change the volume orientation then the default orientation is true, otherwise the default orientation is false.

  Returns:

  true if this orientation matches the default image orientation, false if it changes the image orientation.

• drawArrow

  private void drawArrow​(VOIText kVOI,
                         java.awt.Graphics2D g2d,
                         int xCenter,
                         int yCenter,
                         int x,
                         int y,
                         float stroke)

  Draw the VOIText arror on screen.

  Parameters:

  kVOI -

  g2d -

  xCenter -

  yCenter -

  x -

  y -

  stroke -

• drawGeometricCenter

  private void drawGeometricCenter​(VOIBase kVOI,
                                   java.awt.Graphics g)

  Draws the geometric center on screen.

  Parameters:

  kVOI -

  g -

• drawLength

  private void drawLength​(java.awt.Graphics g,
                          VOIBase kVOI,
                          float[] resols,
                          int[] unitsOfMeasure)

  Draws length of the open contour.

  Parameters:

  g -

  kVOI -

  resols -

  unitsOfMeasure -

• drawNext

  private void drawNext​(int iX,
                        int iY)

  Draws the livewire from the last anchor point to the current mouse position.

  Parameters:

  iX - current mouse x-position in screen coordinates.

  iY - current mouse y-position in screen coordinates.

• drawNextPolyline

  private void drawNextPolyline​(int iX,
                                int iY)

  Draws the open contour from the last anchor point to the current mouse point.

  Parameters:

  iX - current mouse x-position in screen coordinates.

  iY - current mouse y-position in screen coordinates.

• drawTickMarks

  private void drawTickMarks​(VOIBase kVOI,
                             java.awt.Graphics g,
                             java.awt.Color color,
                             int[] unitsOfMeasure,
                             int xD,
                             int yD,
                             float[] res)

  Draws the tick marks on the VOILine.

  Parameters:

  kVOI -

  g -

  color -

  unitsOfMeasure -

  xD -

  yD -

  res -

• drawTickMarks

  private void drawTickMarks​(VOIBase kVOI,
                             java.awt.Graphics g,
                             int[] unitsOfMeasure,
                             int xD,
                             int yD,
                             float[] res)

  Draw the tick marks for the VOIProtractor

  Parameters:

  kVOI -

  g -

  unitsOfMeasure -

  xD -

  yD -

  res -

• drawVOI

  private void drawVOI​(VOIBase kVOI,
                       float[] resols,
                       int[] unitsOfMeasure,
                       java.awt.Graphics g)

  Draw the VOI Contour (open or closed).

  Parameters:

  kVOI -

  resols -

  unitsOfMeasure -

  g -

• drawVOILine

  private void drawVOILine​(VOIBase kVOI,
                           float[] resols,
                           int[] unitsOfMeasure,
                           java.awt.Graphics g,
                           int thickness)

  Draw the VOILine.

  Parameters:

  kVOI - input VOILine to draw.

  resols - image resolutions.

  unitsOfMeasure - image units.

  g - Graphics for drawing.

  thickness - line thickness.

• showLineEndPoints

  private void showLineEndPoints​(VOIBase kVOI,
                                 java.awt.Graphics g)

• drawVOIPoint

  private void drawVOIPoint​(VOIPoint kVOI,
                            java.awt.Graphics g)

  Draw the input VOIPoint.

  Parameters:

  kVOI - VOIPoint to draw.

  g - Graphics object.

• drawVOIPoint

  private void drawVOIPoint​(VOIPoint kVOI,
                            java.awt.Graphics g,
                            java.lang.String label)

  Draw the input VOIPoint with the input label.

  Parameters:

  kVOI - input VOIPoint.

  g - Graphics.

  label - point label.

• drawVOIPolyLineSlice

  private void drawVOIPolyLineSlice​(VOIPolyLineSlice kVOI,
                                    float[] resols,
                                    int[] unitsOfMeasure,
                                    java.awt.Graphics g)

  Draws the input VOIPolyLineSlice. A PolyLineSlice voi is a set of linked points. This function calls drawVOIPoint for each VOIPoint in the PolyLine, which may be defined over multiple slices. When two contiguous points are on the same slice, the are drawn connected by a line with the line lenght displayed in the image resolutions and units.

  Parameters:

  kVOI - input VOIPolyLineSlice

  resols - image resolutions

  unitsOfMeasure - image units

  g - Graphics.

• drawVOIProtractor

  private void drawVOIProtractor​(VOIBase kVOI,
                                 float[] resols,
                                 int[] unitsOfMeasure,
                                 java.awt.Graphics g)

  Draws the input VOIProtractor. Displays the angle and lengths of the protractor arms.

  Parameters:

  kVOI - input VOIProtractor.

  resols - image resolutions.

  unitsOfMeasure - image units.

  g - Graphics.

• drawVOIText

  private void drawVOIText​(VOIText kVOI,
                           java.awt.Graphics g)

  Draws the input VOIText.

  Parameters:

  kVOI - input VOIText.

  g - Graphics.

• fileCoordinatesToPatient

  private WildMagic.LibFoundation.Mathematics.Vector3f fileCoordinatesToPatient​(WildMagic.LibFoundation.Mathematics.Vector3f volumePt)

  Converts the input position from file coordinates to the local patient coordinates.

  Parameters:

  volumePt -

  Returns:

• getBoundingBoxLeftMiddle

  private WildMagic.LibFoundation.Mathematics.Vector3f getBoundingBoxLeftMiddle​(VOIBase kVOI)

  Calculates and returns the bounding box middle left-edge point for the input VOI.

  Parameters:

  kVOI - input VOI.

  Returns:

  the bounding box middle left-edge pointsfor the input VOI.

• getBoundingBoxLowerLeft

  private WildMagic.LibFoundation.Mathematics.Vector3f getBoundingBoxLowerLeft​(VOIBase kVOI)

  Calculates and returns the bounding box lower edge left corner for the input VOI.

  Parameters:

  kVOI - input VOI.

  Returns:

  the bounding box lower edge left corner for the input VOI.

• getBoundingBoxLowerMiddle

  private WildMagic.LibFoundation.Mathematics.Vector3f getBoundingBoxLowerMiddle​(VOIBase kVOI)

  Calculates and returns the bounding box lower edge middle point for the input VOI.

  Parameters:

  kVOI - input VOI.

  Returns:

  the bounding box lower edge middle point for the input VOI.

• getBoundingBoxLowerRight

  private WildMagic.LibFoundation.Mathematics.Vector3f getBoundingBoxLowerRight​(VOIBase kVOI)

  Calculates and returns the bounding box lower edge right corner for the input VOI.

  Parameters:

  kVOI - input VOI.

  Returns:

  the bounding box lower edge right corner for the input VOI.

• getBoundingBoxRightMiddle

  private WildMagic.LibFoundation.Mathematics.Vector3f getBoundingBoxRightMiddle​(VOIBase kVOI)

  Calculates and returns the bounding box middle right-edge point for the input VOI.

  Parameters:

  kVOI - input VOI.

  Returns:

  the bounding box middle right-edge pointsfor the input VOI.

• getBoundingBoxUpperLeft

  private WildMagic.LibFoundation.Mathematics.Vector3f getBoundingBoxUpperLeft​(VOIBase kVOI)

  Calculates and returns the bounding box upper edge left corner for the input VOI.

  Parameters:

  kVOI - input VOI.

  Returns:

  the bounding box upper edge left corner for the input VOI.

• getBoundingBoxUpperMiddle

  private WildMagic.LibFoundation.Mathematics.Vector3f getBoundingBoxUpperMiddle​(VOIBase kVOI)

  Calculates and returns the bounding box upper edge middle point for the input VOI.

  Parameters:

  kVOI - input VOI.

  Returns:

  the bounding box upper edge middle point for the input VOI.

• getBoundingBoxUpperRight

  private WildMagic.LibFoundation.Mathematics.Vector3f getBoundingBoxUpperRight​(VOIBase kVOI)

  Calculates and returns the bounding box upper edge right corner for the input VOI.

  Parameters:

  kVOI - input VOI.

  Returns:

  the bounding box upper edge right corner for the input VOI.

• getCoordsLine

  private void getCoordsLine​(float[] linePtsX,
                             float[] linePtsY,
                             double fraction,
                             float[] coords)

  Calculates the screen coordinates for the VOILine tickmarks. The inputs are the endpoints of the VOILine and a fraction distance along that line where the perpendicular tick-mark lines will intersect the VOILine. This function returns the screen coordinates for the tickmark line at that location along the VOILine.

  Parameters:

  linePtsX - input position x-coordinates

  linePtsY - input position y-coordinates

  fraction - fraction along the VOILine for the current tick mark.

  coords - calculated tickmark xy-coordinates

• getCoordsProtractor

  private void getCoordsProtractor​(float[] x,
                                   float[] y,
                                   double fraction,
                                   float[] coords)

  Calculates and returns the screen location for the angle and length display for the VOIProtractor. The function is called with the end points along one of the protractors 'arms' and a fraction of a distance along that arm. It returns the on-screen pixel location for where to draw the annotation, which will be either the lenght of the arm or the angle the two arms make.

  Parameters:

  x - input protractor x-coordinates.

  y - input protractor x-coordinates.

  fraction -

  coords - returned screen coordinates for drawing the protractor annotation.

• getEndLinesLine

  private void getEndLinesLine​(float[] linePtsX,
                               float[] linePtsY,
                               int line,
                               float[] coords)

  Calculates and returns the inverted-arrow coordinates for the VOILine tickmark display. The inputs are the coordinates of the VOILine and the component of the inverted-arrow to calculate. This function returns the coordinates of the inverted-arrow component for drawing on screen.

  Parameters:

  linePtsX -

  linePtsY -

  line -

  coords -

• getEndLinesProtractor

  private void getEndLinesProtractor​(float[] x,
                                     float[] y,
                                     int line,
                                     float[] coords)

  Calculates and returns the arrow-head coordinates for the VOIProtractor tickmark display. The inputs are the coordinates of one of the 'arms' of the VOIProtractor and the component of the arrow-head to calculate. This function returns the coordinates of the arrow-head component for drawing on screen.

  Parameters:

  linePtsX -

  linePtsY -

  line -

  coords -

• getSlice

  protected int getSlice​(VOIBase kVOI)

  Returns the slice of the input VOI in the patient coordinates displayed locally. This function is used to determine if a particular VOI should be drawn in the currently-displayed image slice. If the VOI is a VOIProtractor from the image-align toolbar, the protractor is displayed on all slices so the current slice is returned.

  Parameters:

  kVOI - input VOI.

  Returns:

  the slice that the VOI is on in local patient coordinates.

• handleIntensityLineBtn3

  private void handleIntensityLineBtn3​(java.awt.event.MouseEvent mouseEvent)

  Opens the VOIIntensity line drawing popup menu.

  Parameters:

  mouseEvent - the MouseEvent that triggered the popup.

• initLevelSet

  private void initLevelSet​(int iSlice)

  Initializes the Levelset VOI calculation. LevelSet VOI calculations is based on image data, and uses the data from the currently-displayed image slice. This function determines if the levelset data has been initialized for the current slice. If it has, no re-initialization occurs. If the levelset has not yet been calculated for the given slice, or if the levelset has been calculated most recently for a different slice, the levelset data is initialized.

  Parameters:

  iSlice - currently displayed image slice.

• initLiveWire

  private void initLiveWire​(int iSlice,
                            boolean bLiveWire)

  Initializes the Livewire VOI calculation. Livewire VOI calculations is based on image data, and uses the data from the currently-displayed image slice. This function determines if the Livewire data has been initialized for the current slice. If it has, no re-initialization occurs. If the Livewire has not yet been calculated for the given slice, or if the Livewire has been calculated most recently for a different slice, the Livewire data is initialized.

  Parameters:

  iSlice - currently displayed image slice.

  bLiveWire - when true this was triggered by the first livewire for the slice, so the cost calculation is calculated.

• moveVOIPoint

  private void moveVOIPoint​(java.awt.event.MouseEvent kEvent)

  Called when the left-mouse is used to drag a point on the VOI.

  Parameters:

  kEvent - current MouseEvent.

• nearBoundPoint

  protected boolean nearBoundPoint​(VOIBase kVOI,
                                   int iX,
                                   int iY,
                                   int iZ)

  Calculates the bounding box of the voi contour and returns true if the input point is near the bounding box.

  Parameters:

  kVOI -

  iX -

  iY -

  iZ -

  Returns:

• nearLine

  protected boolean nearLine​(VOIBase kVOI,
                             int iX,
                             int iY,
                             int iZ)

  Called when the user is selecting a VOI or during MouseDrag to show if a VOI can be selected, or for selected VOIs, to show if the Mouse is close enough to the contour for the user to add a point to the contour line.

  Parameters:

  kVOI - input VOI to test.

  iX - input Mouse x-position.

  iY - input MOuse y-position.

  iZ - current slice.

  Returns:

  true if the mouse is near enough to the input VOI contour for adding a point to the line or showing that the voi can be selected.

• nearPoint

  protected boolean nearPoint​(VOIBase kVOI,
                              int iX,
                              int iY,
                              int iZ)

  Called when the user is selecting a VOI or during MouseDrag to show if a VOI can be selected, or for selected VOIs, to show if the Mouse is close enough to one of the points on the contour for the user to move that contour point

  Parameters:

  kVOI - input VOI to test.

  iX - input Mouse x-position.

  iY - input MOuse y-position.

  iZ - current slice.

  Returns:

  true if the mouse is near a point on the contour of the input VOI.

• pasteVOI

  private void pasteVOI​(int iSlice)

• paths

  private void paths​(int index,
                     int i,
                     float level)

  Generates the possible paths of the level set and pushes them onto a stack. Looks in the 8 neighborhood directions for the possible paths.

  Parameters:

  index - image location

  i - DOCUMENT ME!

• patientCoordinatesToFile

  private WildMagic.LibFoundation.Mathematics.Vector3f patientCoordinatesToFile​(WildMagic.LibFoundation.Mathematics.Vector3f patientPt)

  Converts the local patient point into file coordinates.

  Parameters:

  patientPt -

  Returns:

• processLeftMouseDrag

  protected void processLeftMouseDrag​(java.awt.event.MouseEvent kEvent)

  Parameters:

  kEvent - the mouse event generated by a mouse drag

• resetIndex

  private void resetIndex()

• resetStart

  private void resetStart()

  Resets all retrace variables and allows it to start anewA

• retraceContour

  private void retraceContour​(VOIBase kVOIIn,
                              int x1,
                              int y1)

• scalePolygon

  private java.awt.Polygon scalePolygon​(VOIBase kVOI)

• scaleVOI

  private void scaleVOI​(VOIBase kVOI,
                        java.awt.event.MouseEvent mouseEvent)

• seed

  private void seed​(int iX,
                    int iY)

  Sets up directed graph from the seed point. A point (x,y) is mapped to its absolute value in the image, y*xDim + x. This along with its cost is stored in Node. The structure costGraph holds the "edges" of the graph. Each location has an integer associated with it which represents where that node is pointing to. Thus costGraph[7] = 8 would mean the node at 7 (really (0,7)) is pointing to position 8 (really (0,8)). The only possibilities for a location in costGraph are the 8 neighbors surrounding that node. For this reason we might use a byte array instead of an integer array. The seed point points nowhere, to indicate that it's the seed; costGraph[seed.location] = -1. We also need to know if a point has been processed, that is, expanded with the cost set. For this we use a BitSet whose size is the same as the number of pixels in the image. Once a point is processed, its location in the BitSet is set to true.

  The array seededCosts holds the costs so far for a location. If a cost has not been assigned yet, the cost is -2. ActiveList is simply a linked list of Integers; the Integer refers to the location in the seededCosts array. ActiveList is sorted by cost, so that the minimum cost in the ActiveList is the first element of the linked list. Thus finding the minimum is O(1). Finding out if an element is in the ActiveList is also O(1), because for an element to be in the list, it must have already been assigned a cost. Therefore, if seededCosts[location] != -2, it is in the ActiveList. And finding the cost of an item in the ActiveList is O(1), because it's just seededCosts[location], where location is the Integer in the ActiveList. Obviously we're winning speed at the expense of memory, but it's not too much memory in the overall scheme of things.

  The gradient direction component of the cost is added in on the fly. This is because to precalculate would mean an array of 8n, where n is the size of the image. The link from p to q is not the same as the link from q to p. Furthermore, it may never be necessary to calculate some of the links, because the graph would never look at that pair. For more information on how the gradient direction cost is calculated, look at the comments directly above the code.

  Parameters:

  pt - Point to seed with.

• selectVOI

  protected VOIBase selectVOI​(java.awt.event.MouseEvent kEvent)

• setCanvas

  private void setCanvas​(java.awt.Component kComponent)

• setDrawingContext

  private void setDrawingContext​(ScreenCoordinateListener kContext)

• getDrawingContext

  public ScreenCoordinateListener getDrawingContext()

• setOrientation

  private void setOrientation​(int iOrientation)

• setPosition

  private void setPosition​(VOIBase kVOI,
                           int iPos,
                           float fX,
                           float fY,
                           float fZ)

• setPosition

  private void setPosition​(VOIBase kVOI,
                           int iPos,
                           float fX,
                           float fY,
                           float fZ,
                           boolean isCtrlDown)

• setPosition

  private void setPosition​(VOIBase kVOI,
                           int iPos,
                           WildMagic.LibFoundation.Mathematics.Vector3f kPos)

• setPosition

  private void setPosition​(VOIBase kVOI,
                           int iPos,
                           WildMagic.LibFoundation.Mathematics.Vector3f kPos,
                           boolean isCtrlDown)

• showSelectedVOI

  protected void showSelectedVOI​(java.awt.event.MouseEvent kEvent)

• doLevelset

  public void doLevelset​(WildMagic.LibFoundation.Mathematics.Vector3f point)

• singleLevelSet2

  private VOIBase singleLevelSet2​(float startPtX,
                                  float startPtY)

  Creates a single level set. Takes a starting point and finds a closed path along the levelset back to the starting point.

  Parameters:

  startPtX - the start point

  startPtY - the start point

  level - the level of the level set

• split

  private VOIBase split​(VOIBase kVOI,
                        WildMagic.LibFoundation.Mathematics.Vector3f kStartPt,
                        WildMagic.LibFoundation.Mathematics.Vector3f kEndPt)

• splitVOIs

  private void splitVOIs​(boolean bAllSlices,
                         boolean bOnlyActive,
                         VOIBase kSplitVOI)

• straightenLineVOI

  private WildMagic.LibFoundation.Mathematics.Vector3f straightenLineVOI​(WildMagic.LibFoundation.Mathematics.Vector3f kPos,
                                                                         VOIBase kOld)

  Modifies kPos to form an angle with its origin point that is a multiple of 15 degrees.

• updateRectangle

  private void updateRectangle​(int iX,
                               int iMouseX,
                               int iY,
                               int iYStart)

• getDrawVOIflag

  public boolean getDrawVOIflag()