java.lang.Object

gov.nih.mipav.view.renderer.J3D.surfaceview.rfaview.BurnBaseView

Direct Known Subclasses:: BurnCoolTipView, BurnHeatView, BurnRegularView

public class BurnBaseView extends Object

The default probe burning type view. The class define the default burning point's geometry shape, and burning path mark behavior.

Author:: Ruida Cheng

Nested Class Summary

Nested Classes

Modifier and Type

Class

Description

protected class

BurnBaseView.Edge

A representation of an edge for the vertex-edge-triangle table.

class

BurnBaseView.UnorderedSetInt

DOCUMENT ME!
Field Summary

Fields

Modifier and Type

Field

Description

(package private) javax.vecmath.Color3f

ambientColor

Define attenuation lighting colors.

(package private) javax.vecmath.Color3f

black

DOCUMENT ME!

(package private) javax.vecmath.Color3f

blue

DOCUMENT ME!

protected javax.vecmath.Color4f

burnColor

Burning point surface color.

protected int

burnIndex

Current burning point index.

protected javax.media.j3d.BranchGroup[]

burningBG

Burning point branch group array, used to switch between different buring point.

protected javax.media.j3d.BranchGroup

burnRootParentBG

The root branch group the default burning point.

protected int

burnType

Burning type.

(package private) javax.vecmath.Color3f

cyan

DOCUMENT ME!

(package private) javax.vecmath.Color3f

diffuseColor

DOCUMENT ME!

protected int

diffVoxels

Volume difference in voxels for the tumor surface and burning sphere, ellipsoid packings.

(package private) javax.vecmath.Color3f

emissiveColor

DOCUMENT ME!

(package private) javax.vecmath.Color3f

green

DOCUMENT ME!

(package private) Vector<Integer>

indexVector

vector stack to record the burning index.

protected float[]

m_afLength

DOCUMENT ME!

protected int[]

m_aiConnect

DOCUMENT ME!

protected int[]

m_aiImage

The 3D MRI image stored as a 1D array.

protected BitSet

m_aiMask

DOCUMENT ME!

protected BurnBaseView.UnorderedSetInt[]

m_akAdjacent

DOCUMENT ME!

private javax.media.j3d.Shape3D[]

m_akSurfaceShape

DOCUMENT ME!

protected javax.vecmath.Point3f[]

m_akVertex

DOCUMENT ME!

protected float

m_fXDelta

The size of a voxel, in voxel units.

protected float

m_fYDelta

The size of a voxel, in voxel units.

protected float

m_fZDelta

The size of a voxel, in voxel units.

protected int

m_iBackThreshold

DOCUMENT ME!

protected int

m_iBrightThreshold

DOCUMENT ME!

protected int

m_iDMax

DOCUMENT ME!

protected int

m_iEQuantity

DOCUMENT ME!

protected int

m_iMaxThreshold

DOCUMENT ME!

protected int

m_iMedianIntensity

DOCUMENT ME!

protected int

m_iMinThreshold

histogram parameters.

protected int

m_iQuantity

The MRI image bounds and quantity of voxels.

protected int

m_iTQuantity

DOCUMENT ME!

protected int

m_iVQuantity

mesh data.

protected int

m_iXBound

The MRI image bounds and quantity of voxels.

protected int

m_iYBound

The MRI image bounds and quantity of voxels.

protected int

m_iZBound

The MRI image bounds and quantity of voxels.

protected javax.vecmath.Point3f

m_kCenter

DOCUMENT ME!

protected HashMap<BurnBaseView.Edge,Integer>

m_kEMap

DOCUMENT ME!

protected javax.vecmath.Matrix3f

m_kRotate

DOCUMENT ME!

protected Vector<MaskBurnAttribute>

maskBurnVector

Reference to Mask burning attribute.

protected int

numBurn

Initialized the number of burning point.

private int

nVoxels

factor above median at which edge values are taken to zero.

(package private) javax.vecmath.Color3f

orange

DOCUMENT ME!

(package private) javax.vecmath.Color4f

orangeColor

DOCUMENT ME!

protected com.sun.j3d.utils.picking.PickCanvas

pickCanvas

Agent to set the burning point sphere pickable.

(package private) javax.vecmath.Color3f

pink

DOCUMENT ME!

protected JPanelProbe

probePanel

JPanelProbe reference.

(package private) javax.vecmath.Color3f

purple

DOCUMENT ME!

(package private) javax.vecmath.Color4f

purpleColor

DOCUMENT ME!

private float

radius

image space burning point radius.

protected javax.vecmath.Point3f

radiusPt

Burning sphere radius, semiX, Y, Z in point format.

(package private) javax.vecmath.Color3f

red

Define colors.

(package private) javax.vecmath.Color3f

sepcualarColor

DOCUMENT ME!

protected boolean

showLabels

Flag to show the burning point label.

(package private) javax.vecmath.Color3f

silver

DOCUMENT ME!

protected javax.media.j3d.BranchGroup[]

sphereBG

Default burning point array.

protected com.sun.j3d.utils.geometry.Sphere

spheres

Burning point sphere.

protected SurfaceRender

surfaceRender

Surface Render reference.

protected javax.media.j3d.BranchGroup[]

textLabelBG

Burning point label array.

protected javax.vecmath.Vector3f

translate

Burning point center.

protected BitSet

volumeMask

Reference to burning point voluem mask.

protected float

volumeSpaceRadius

Default volume space burning point radius.

(package private) javax.vecmath.Color3f

yellow

DOCUMENT ME!
Constructor Summary

Constructors

Constructor

Description

BurnBaseView(SurfaceRender _surfaceRender, JPanelProbe _probePanel, javax.media.j3d.BranchGroup _burnRootParentBG)

Constructor.
Method Summary

Modifier and Type

Method

Description

void

buildBurnSceneGraph(float radius, float time)

Build the image scene graph structure.

void

buildBurnSceneGraph(float radius, float time, javax.vecmath.Color3f color, int index)

Only used by the default burning point type to reset the image sence graph when the burning sphere radius and time changes.

protected javax.media.j3d.BranchGroup

buildEntryPoint()

Build the entry point image scene graph structure.

protected void

buildText(int index, String str, javax.vecmath.Vector3f pos)

Attach some 3D text to a BranchGroup or TransformGroup.

void

calcTotalVolume(SurfaceAttributes surface, TreatmentInformation treatment)

Calculate the burning points total volume.

protected void

calcVoxels()

Identify all voxels that are inside or on the mesh that represents the brain surface.

protected javax.media.j3d.BranchGroup

createSurface(ModelTriangleMesh[] meshes, javax.vecmath.Color4f color, int mode)

Creates a surface in the scene graph from an array of triangle meshes.

void

dispose()

Dispose memory.

void

enableBurnLabels(boolean flag)

Attach or detach burn labels.

protected void

estimateEllipsoid()

Approximate the brain surface by an ellipsoid.

int

findBurnPoint(javax.media.j3d.Shape3D pickedShape)

Check whether the burning sphere is picked or not.

protected void

floodFill(int iX, int iY, int iZ)

Identify voxels enclosed by the brain surface by using a flood fill.

protected void

generateEllipsoidMesh(int burnType, float tipLen, int iSubdivisions, boolean isImageSpace)

Tessellate a unit sphere centered at the origin.

protected void

generateSphereMesh(int iSubdivisions, boolean isImageSpace)

Tessellate a unit sphere centered at the origin.

BitSet

getBurnMask()

Get the burnning point ( sphere packing or ellipsoid packing ) mask.

javax.vecmath.Color4f

getColor()

Get the buring point surface color.

final float

getDiffVolume()

Get the volume difference btw tumor surface and burning sphere packings.

protected final int

getIndex(int iX, int iY, int iZ)

A convenience function for mapping the 3D voxel position (iX,iY,iZ) to a 1D array index.

protected void

getInsideVoxels()

Identify all voxels that are inside or on the mesh that represents the brain surface.

protected int

getIntersectX(javax.vecmath.Point3f kV0, javax.vecmath.Point3f kV1, javax.vecmath.Point3f kV2, int iY, int iZ)

Compute the point of intersection between a line (0,iY,iZ)+t(1,0,0) and the triangle defined by the three input points.

protected int

getIntersectY(javax.vecmath.Point3f kV0, javax.vecmath.Point3f kV1, javax.vecmath.Point3f kV2, int iX, int iZ)

Compute the point of intersection between a line (iX,0,iZ)+t(0,1,0) and the triangle defined by the three input points.

protected int

getIntersectZ(javax.vecmath.Point3f kV0, javax.vecmath.Point3f kV1, javax.vecmath.Point3f kV2, int iX, int iY)

Compute the point of intersection between a line (iX,iY,0)+t(0,0,1) and the triangle defined by the three input points.

javax.vecmath.Point3f

getRadius()

Get the radius( semiX, semiY, semiZ).

static javax.vecmath.Vector3f

getRotAngle(javax.media.j3d.Transform3D t3D)

DOCUMENT ME!

protected javax.media.j3d.Shape3D

getShape(javax.media.j3d.BranchGroup root)

Get the shape burning point surface.

javax.media.j3d.BranchGroup

getSphereBG()

Get the current burning point brach group.

javax.vecmath.Vector3f

getTranslate()

Get the burning point center coordinates.

final float

getVolume()

Get the total tumor voxels of the current treatment in mm^3.

void

histogramAnalysis()

Analyze the histogram of the 10-bit binned 3D MRI.

protected javax.media.j3d.BranchGroup

markProbe()

Mark the probing guide line.

protected void

reGenerateEllipsoidMesh(int iSubdivisions, float tipLen, boolean isImageSpace, javax.vecmath.Point3f center, javax.media.j3d.Transform3D centerTransform)

Tessellate a unit sphere centered at the origin.

protected void

reGenerateSphereMesh(int iSubdivisions, javax.vecmath.Point3f center, javax.media.j3d.Transform3D centerTransform)

Tessellate a unit sphere centered at the origin.

protected void

setMaskBurnVector(Vector<MaskBurnAttribute> _vector)

Initialize the mask burning vector.

protected void

setVolumeMask(BitSet _volumeMask)

Initial the volume mask from burnBase.

void

startBurn(float tipLen, float time, int _index)

Start burning.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details
- burnColor
  
  protected javax.vecmath.Color4f burnColor
  
  Burning point surface color.
- burnIndex
  
  protected int burnIndex
  
  Current burning point index.
- burningBG
  
  protected javax.media.j3d.BranchGroup[] burningBG
  
  Burning point branch group array, used to switch between different buring point.
- burnRootParentBG
  
  protected javax.media.j3d.BranchGroup burnRootParentBG
  
  The root branch group the default burning point.
- burnType
  
  protected int burnType
  
  Burning type.
- diffVoxels
  
  protected int diffVoxels
  
  Volume difference in voxels for the tumor surface and burning sphere, ellipsoid packings.
- m_afLength
  
  protected float[] m_afLength
  
  DOCUMENT ME!
- m_aiConnect
  
  protected int[] m_aiConnect
  
  DOCUMENT ME!
- m_aiImage
  
  protected int[] m_aiImage
  
  The 3D MRI image stored as a 1D array. The mapping from (x,y,z) to 1D is: index = x + xbound*(y + ybound*z).
- m_aiMask
  
  protected BitSet m_aiMask
  
  DOCUMENT ME!
- m_akAdjacent
  
  protected BurnBaseView.UnorderedSetInt[] m_akAdjacent
  
  DOCUMENT ME!
- m_akVertex
  
  protected javax.vecmath.Point3f[] m_akVertex
  
  DOCUMENT ME!
- m_fXDelta
  
  protected float m_fXDelta
  
  The size of a voxel, in voxel units.
- m_fYDelta
  
  protected float m_fYDelta
  
  The size of a voxel, in voxel units.
- m_fZDelta
  
  protected float m_fZDelta
  
  The size of a voxel, in voxel units.
- m_iBackThreshold
  
  protected int m_iBackThreshold
  
  DOCUMENT ME!
- m_iBrightThreshold
  
  protected int m_iBrightThreshold
  
  DOCUMENT ME!
- m_iDMax
  
  protected int m_iDMax
  
  DOCUMENT ME!
- m_iEQuantity
  
  protected int m_iEQuantity
  
  DOCUMENT ME!
- m_iMaxThreshold
  
  protected int m_iMaxThreshold
  
  DOCUMENT ME!
- m_iMedianIntensity
  
  protected int m_iMedianIntensity
  
  DOCUMENT ME!
- m_iMinThreshold
  
  protected int m_iMinThreshold
  
  histogram parameters.
- m_iTQuantity
  
  protected int m_iTQuantity
  
  DOCUMENT ME!
- m_iVQuantity
  
  protected int m_iVQuantity
  
  mesh data.
- m_iXBound
  
  protected int m_iXBound
  
  The MRI image bounds and quantity of voxels.
- m_iYBound
  
  protected int m_iYBound
  
  The MRI image bounds and quantity of voxels.
- m_iZBound
  
  protected int m_iZBound
  
  The MRI image bounds and quantity of voxels.
- m_iQuantity
  
  protected int m_iQuantity
  
  The MRI image bounds and quantity of voxels.
- m_kCenter
  
  protected javax.vecmath.Point3f m_kCenter
  
  DOCUMENT ME!
- m_kEMap
  
  protected HashMap<BurnBaseView.Edge,Integer> m_kEMap
  
  DOCUMENT ME!
- m_kRotate
  
  protected javax.vecmath.Matrix3f m_kRotate
  
  DOCUMENT ME!
- maskBurnVector
  
  protected Vector<MaskBurnAttribute> maskBurnVector
  
  Reference to Mask burning attribute.
- numBurn
  
  protected int numBurn
  
  Initialized the number of burning point.
- pickCanvas
  
  protected com.sun.j3d.utils.picking.PickCanvas pickCanvas
  
  Agent to set the burning point sphere pickable.
- probePanel
  
  protected JPanelProbe probePanel
  
  JPanelProbe reference.
- radiusPt
  
  protected javax.vecmath.Point3f radiusPt
  
  Burning sphere radius, semiX, Y, Z in point format.
- showLabels
  
  protected boolean showLabels
  
  Flag to show the burning point label.
- sphereBG
  
  protected javax.media.j3d.BranchGroup[] sphereBG
  
  Default burning point array.
- spheres
  
  protected com.sun.j3d.utils.geometry.Sphere spheres
  
  Burning point sphere.
- surfaceRender
  
  protected SurfaceRender surfaceRender
  
  Surface Render reference.
- textLabelBG
  
  protected javax.media.j3d.BranchGroup[] textLabelBG
  
  Burning point label array.
- translate
  
  protected javax.vecmath.Vector3f translate
  
  Burning point center.
- volumeMask
  
  protected BitSet volumeMask
  
  Reference to burning point voluem mask.
- volumeSpaceRadius
  
  protected float volumeSpaceRadius
  
  Default volume space burning point radius.
- ambientColor
  
  javax.vecmath.Color3f ambientColor
  
  Define attenuation lighting colors.
- black
  
  javax.vecmath.Color3f black
  
  DOCUMENT ME!
- blue
  
  javax.vecmath.Color3f blue
  
  DOCUMENT ME!
- cyan
  
  javax.vecmath.Color3f cyan
  
  DOCUMENT ME!
- diffuseColor
  
  javax.vecmath.Color3f diffuseColor
  
  DOCUMENT ME!
- emissiveColor
  
  javax.vecmath.Color3f emissiveColor
  
  DOCUMENT ME!
- green
  
  javax.vecmath.Color3f green
  
  DOCUMENT ME!
- indexVector
  
  Vector<Integer> indexVector
  
  vector stack to record the burning index.
- orange
  
  javax.vecmath.Color3f orange
  
  DOCUMENT ME!
- orangeColor
  
  javax.vecmath.Color4f orangeColor
  
  DOCUMENT ME!
- pink
  
  javax.vecmath.Color3f pink
  
  DOCUMENT ME!
- purple
  
  javax.vecmath.Color3f purple
  
  DOCUMENT ME!
- purpleColor
  
  javax.vecmath.Color4f purpleColor
  
  DOCUMENT ME!
- red
  
  javax.vecmath.Color3f red
  
  Define colors.
- sepcualarColor
  
  javax.vecmath.Color3f sepcualarColor
  
  DOCUMENT ME!
- silver
  
  javax.vecmath.Color3f silver
  
  DOCUMENT ME!
- yellow
  
  javax.vecmath.Color3f yellow
  
  DOCUMENT ME!
- m_akSurfaceShape
  
  private javax.media.j3d.Shape3D[] m_akSurfaceShape
  
  DOCUMENT ME!
- nVoxels
  
  private int nVoxels
  
  factor above median at which edge values are taken to zero.
- radius
  
  private float radius
  
  image space burning point radius.
Constructor Details
- BurnBaseView
  
  public BurnBaseView(SurfaceRender _surfaceRender, JPanelProbe _probePanel, javax.media.j3d.BranchGroup _burnRootParentBG)
  
  Constructor. Setup the burning point related branch groups.
  
  Parameters:
  
  _surfaceRender - SurfaceRender refernece.
  
  _probePanel - JPanelProbe probe control panel reference.
  
  _burnRootParentBG - BranchGroup root of the burning point.
Method Details
- getRotAngle
  
  public static javax.vecmath.Vector3f getRotAngle(javax.media.j3d.Transform3D t3D)
  
  DOCUMENT ME!
  
  Parameters:
  
  t3D - DOCUMENT ME!
  
  Returns:
  
  DOCUMENT ME!
- buildBurnSceneGraph
  
  public void buildBurnSceneGraph(float radius, float time)
  
  Build the image scene graph structure.
  
  Parameters:
  
  radius - burning point sphere radius
  
  time - burning point burning time duration.
- buildBurnSceneGraph
  
  public void buildBurnSceneGraph(float radius, float time, javax.vecmath.Color3f color, int index)
  
  Only used by the default burning point type to reset the image sence graph when the burning sphere radius and time changes.
  
  Parameters:
  
  radius - burning sphere radius
  
  time - burning sphere duration time
  
  color - burning sphere color
  
  index - selected burning sphere index
- calcTotalVolume
  
  public void calcTotalVolume(SurfaceAttributes surface, TreatmentInformation treatment)
  
  Calculate the burning points total volume.
  
  Parameters:
  
  surface - SurfaceAttributes reference
  
  treatment - TreatmentInformation reference
- dispose
  
  public void dispose()
  
  Dispose memory.
- enableBurnLabels
  
  public void enableBurnLabels(boolean flag)
  
  Attach or detach burn labels.
  
  Parameters:
  
  flag - whether to show the labels
- findBurnPoint
  
  public int findBurnPoint(javax.media.j3d.Shape3D pickedShape)
  
  Check whether the burning sphere is picked or not.
  
  Parameters:
  
  pickedShape - sphere burning shape.
  
  Returns:
  
  int burning point index
- getBurnMask
  
  public BitSet getBurnMask()
  
  Get the burnning point ( sphere packing or ellipsoid packing ) mask.
  
  Returns:
  
  BitSet Burning point volume mask.
- getColor
  
  public javax.vecmath.Color4f getColor()
  
  Get the buring point surface color.
  
  Returns:
  
  Color4f burning color.
- getDiffVolume
  
  public final float getDiffVolume()
  
  Get the volume difference btw tumor surface and burning sphere packings.
  
  Returns:
  
  float differenct volume in mm space.
- getRadius
  
  public javax.vecmath.Point3f getRadius()
  
  Get the radius( semiX, semiY, semiZ).
  
  Returns:
  
  Point3f radius
- getSphereBG
  
  public javax.media.j3d.BranchGroup getSphereBG()
  
  Get the current burning point brach group.
  
  Returns:
  
  BranchGroup burning point branch group reference.
- getTranslate
  
  public javax.vecmath.Vector3f getTranslate()
  
  Get the burning point center coordinates. Called by the probe control panel to show the current burning point center.
  
  Returns:
  
  Vector3f burning point center coordinate.
- getVolume
  
  public final float getVolume()
  
  Get the total tumor voxels of the current treatment in mm^3.
  
  Returns:
  
  float tumor volume in mm space.
- histogramAnalysis
  
  public void histogramAnalysis()
  
  Analyze the histogram of the 10-bit binned 3D MRI. The function computes a minimum threshold, a maximum threshold, and a background threshold that are used in the image term of the surface evolution. A brightness threshold is also computed that is used for determining the initial ellipsoid that approximates the brain surface.
- startBurn
  
  public void startBurn(float tipLen, float time, int _index)
  
  Start burning. Show the burning sphere and probing path.
  
  Parameters:
  
  tipLen - the length of the probe tip (cm)
  
  time - the time spent burning
  
  _index - index of the new burn
- buildEntryPoint
  
  protected javax.media.j3d.BranchGroup buildEntryPoint()
  
  Build the entry point image scene graph structure.
  
  Returns:
  
  BranchGroup the entry point root branch group.
- buildText
  
  protected void buildText(int index, String str, javax.vecmath.Vector3f pos)
  
  Attach some 3D text to a BranchGroup or TransformGroup.
  
  Parameters:
  
  index - the group to attach the text to
  
  str - the text to show
  
  pos - where to place the text
- calcVoxels
  
  protected void calcVoxels()
  
  Identify all voxels that are inside or on the mesh that represents the brain surface. The surface voxels are constructed by rasterizing the triangles of the mesh in 3D. The centroid of these voxels is used as a seed point for a flood fill of the region enclosed by the surface.
- createSurface
  
  protected javax.media.j3d.BranchGroup createSurface(ModelTriangleMesh[] meshes, javax.vecmath.Color4f color, int mode)
  
  Creates a surface in the scene graph from an array of triangle meshes.
  
  Parameters:
  
  meshes - Triangle meshes that make up surface
  
  color - Color of surface
  
  mode - DOCUMENT ME!
  
  Returns:
  
  Parent node of surface.
- estimateEllipsoid
  
  protected void estimateEllipsoid()
  
  Approximate the brain surface by an ellipsoid. The approximation is based on locating all voxels of intensity larger than a brightness threshold and that are part of the upper-half of the head. The idea is that the scalp voxels in the upper-half form lie approximately on an ellipsoidal surface.
  
  NOTE. The assumption is that the traversal from bottom to top of head is in the y-direction of the 3D image. It does not matter if the top of the head has y-values smaller/larger than those for the bottom of the head. If this assumption is not met, the image should be permuted OR this code must be modified to attempt to recognize the orientation of the head
- floodFill
  
  protected void floodFill(int iX, int iY, int iZ)
  
  Identify voxels enclosed by the brain surface by using a flood fill. The flood fill is nonrecursive to avoid overflowing the program stack.
  
  Parameters:
  
  iX - the x-value of the seed point for the fill
  
  iY - the y-value of the seed point for the fill
  
  iZ - the z-value of the seed point for the fill
- generateEllipsoidMesh
  
  protected void generateEllipsoidMesh(int burnType, float tipLen, int iSubdivisions, boolean isImageSpace)
  
  Tessellate a unit sphere centered at the origin. Start with an octahedron and subdivide. The final mesh is then affinely mapped to the initial ellipsoid produced by estimateEllipsoid(). The subdivision scheme is described in BrainExtraction.pdf.
  
  Parameters:
  
  burnType - the type of the burn
  
  tipLen - the length of the probe tip, in cm
  
  iSubdivisions - the number of levels to subdivide the ellipsoid
  
  isImageSpace - whether to get the mesh in image space
- generateSphereMesh
  
  protected void generateSphereMesh(int iSubdivisions, boolean isImageSpace)
  
  Tessellate a unit sphere centered at the origin. Start with an octahedron and subdivide. The final mesh is then affinely mapped to the initial ellipsoid produced by estimateEllipsoid(). The subdivision scheme is described in BrainExtraction.pdf.
  
  Parameters:
  
  iSubdivisions - the number of levels to subdivide the ellipsoid
  
  isImageSpace - DOCUMENT ME!
- getIndex
  
  protected final int getIndex(int iX, int iY, int iZ)
  
  A convenience function for mapping the 3D voxel position (iX,iY,iZ) to a 1D array index. The images are stored as 1D arrays, so this function is used frequently.
  
  Parameters:
  
  iX - the x-value of the voxel position
  
  iY - the y-value of the voxel position
  
  iZ - the z-value of the voxel position
  
  Returns:
  
  the 1D array index corresponding to (iX,iY,iZ)
- getInsideVoxels
  
  protected void getInsideVoxels()
  
  Identify all voxels that are inside or on the mesh that represents the brain surface. The surface voxels are constructed by rasterizing the triangles of the mesh in 3D. The centroid of these voxels is used as a seed point for a flood fill of the region enclosed by the surface.
- getIntersectX
  
  protected int getIntersectX(javax.vecmath.Point3f kV0, javax.vecmath.Point3f kV1, javax.vecmath.Point3f kV2, int iY, int iZ)
  
  Compute the point of intersection between a line (0,iY,iZ)+t(1,0,0) and the triangle defined by the three input points. All calculations are in voxel coordinates and the x-value of the intersection point is truncated to an integer.
  
  Parameters:
  
  kV0 - a 3D vertex of the triangle
  
  kV1 - a 3D vertex of the triangle
  
  kV2 - a 3D vertex of the triangle
  
  iY - the y-value of the origin of the line
  
  iZ - the z-value of the origin of the line
  
  Returns:
  
  the x-value of the intersection
- getIntersectY
  
  protected int getIntersectY(javax.vecmath.Point3f kV0, javax.vecmath.Point3f kV1, javax.vecmath.Point3f kV2, int iX, int iZ)
  
  Compute the point of intersection between a line (iX,0,iZ)+t(0,1,0) and the triangle defined by the three input points. All calculations are in voxel coordinates and the y-value of the intersection point is truncated to an integer.
  
  Parameters:
  
  kV0 - a 3D vertex of the triangle
  
  kV1 - a 3D vertex of the triangle
  
  kV2 - a 3D vertex of the triangle
  
  iX - the x-value of the origin of the line
  
  iZ - the z-value of the origin of the line
  
  Returns:
  
  the y-value of the intersection
- getIntersectZ
  
  protected int getIntersectZ(javax.vecmath.Point3f kV0, javax.vecmath.Point3f kV1, javax.vecmath.Point3f kV2, int iX, int iY)
  
  Compute the point of intersection between a line (iX,iY,0)+t(0,0,1) and the triangle defined by the three input points. All calculations are in voxel coordinates and the z-value of the intersection point is truncated to an integer.
  
  Parameters:
  
  kV0 - a 3D vertex of the triangle
  
  kV1 - a 3D vertex of the triangle
  
  kV2 - a 3D vertex of the triangle
  
  iX - the x-value of the origin of the line
  
  iY - the y-value of the origin of the line
  
  Returns:
  
  the z-value of the intersection
- getShape
  
  protected javax.media.j3d.Shape3D getShape(javax.media.j3d.BranchGroup root)
  
  Get the shape burning point surface.
  
  Parameters:
  
  root - Burning point branchGroup
  
  Returns:
  
  Shape3D Shape object
- markProbe
  
  protected javax.media.j3d.BranchGroup markProbe()
  
  Mark the probing guide line.
  
  Returns:
  
  BranchGroup return the guide line root reference.
- reGenerateEllipsoidMesh
  
  protected void reGenerateEllipsoidMesh(int iSubdivisions, float tipLen, boolean isImageSpace, javax.vecmath.Point3f center, javax.media.j3d.Transform3D centerTransform)
  
  Tessellate a unit sphere centered at the origin. Start with an octahedron and subdivide. The final mesh is then affinely mapped to the initial ellipsoid produced by estimateEllipsoid(). The subdivision scheme is described in BrainExtraction.pdf.
  
  Parameters:
  
  iSubdivisions - the number of levels to subdivide the ellipsoid
  
  tipLen - float the tip length
  
  isImageSpace - is image space, always true
  
  center - Point3f burning center point coordinate
  
  centerTransform - burning center transform
- reGenerateSphereMesh
  
  protected void reGenerateSphereMesh(int iSubdivisions, javax.vecmath.Point3f center, javax.media.j3d.Transform3D centerTransform)
  
  Tessellate a unit sphere centered at the origin. Start with an octahedron and subdivide. The final mesh is then affinely mapped to the initial ellipsoid produced by estimateEllipsoid(). The subdivision scheme is described in BrainExtraction.pdf.
  
  Parameters:
  
  iSubdivisions - the number of levels to subdivide the ellipsoid
  
  center - Point3f burning center point coordinate
  
  centerTransform - burning center transform
- setMaskBurnVector
  
  protected void setMaskBurnVector(Vector<MaskBurnAttribute> _vector)
  
  Initialize the mask burning vector.
  
  Parameters:
  
  _vector - MaskBurnVector reference.
- setVolumeMask
  
  protected void setVolumeMask(BitSet _volumeMask)
  
  Initial the volume mask from burnBase.
  
  Parameters:
  
  _volumeMask - byte[] array volume mask array.

Class BurnBaseView

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Details

burnColor

burnIndex

burningBG

burnRootParentBG

burnType

diffVoxels

m_afLength

m_aiConnect

m_aiImage

m_aiMask

m_akAdjacent

m_akVertex

m_fXDelta

m_fYDelta

m_fZDelta

m_iBackThreshold

m_iBrightThreshold

m_iDMax

m_iEQuantity

m_iMaxThreshold

m_iMedianIntensity

m_iMinThreshold

m_iTQuantity

m_iVQuantity

m_iXBound

m_iYBound

m_iZBound

m_iQuantity

m_kCenter

m_kEMap

m_kRotate

maskBurnVector

numBurn

pickCanvas

probePanel

radiusPt

showLabels

sphereBG

spheres

surfaceRender

textLabelBG

translate

volumeMask

volumeSpaceRadius

ambientColor

black

blue

cyan

diffuseColor

emissiveColor

green

indexVector

orange

orangeColor

pink

purple

purpleColor

red

sepcualarColor

silver

yellow

m_akSurfaceShape

nVoxels

radius

Constructor Details

BurnBaseView

Method Details

getRotAngle

buildBurnSceneGraph

buildBurnSceneGraph

calcTotalVolume

dispose

enableBurnLabels