java.lang.Object
- gov.nih.mipav.view.renderer.J3D.surfaceview.rfaview.BurnBaseView

Direct Known Subclasses:

BurnCoolTipView, BurnHeatView, BurnRegularView
```
public class BurnBaseView
extends java.lang.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) java.util.Vector<java.lang.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 java.util.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 java.util.HashMap<BurnBaseView.Edge,java.lang.Integer>`	`m_kEMap`	DOCUMENT ME!
`protected javax.vecmath.Matrix3f`	`m_kRotate`	DOCUMENT ME!
`protected java.util.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 java.util.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

All Methods Static Methods Instance Methods Concrete Methods
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, java.lang.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.
`java.util.BitSet`	`getBurnMask()`	Get the burnning point ( sphere packing or ellipsoid packing ) mask.
`javax.vecmath.Color4f`	`getColor()`	Get the buring point surface color.
`float`	`getDiffVolume()`	Get the volume difference btw tumor surface and burning sphere packings.
`protected 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.
`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(java.util.Vector<MaskBurnAttribute> _vector)`	Initialize the mask burning vector.
`protected void`	`setVolumeMask(java.util.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 Detail
  - 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 java.util.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 java.util.HashMap<BurnBaseView.Edge,java.lang.Integer> m_kEMap
```
    DOCUMENT ME!
  - m_kRotate
```
protected javax.vecmath.Matrix3f m_kRotate
```
    DOCUMENT ME!
  - maskBurnVector
```
protected java.util.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 java.util.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
```
java.util.Vector<java.lang.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 Detail
  - 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 Detail
  - 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 java.util.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,
                         java.lang.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(java.util.Vector<MaskBurnAttribute> _vector)
```
    Initialize the mask burning vector.
    
    Parameters:
    
    _vector - MaskBurnVector reference.
  - setVolumeMask
```
protected void setVolumeMask(java.util.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 Detail

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 Detail

BurnBaseView

Method Detail

getRotAngle

buildBurnSceneGraph

buildBurnSceneGraph

calcTotalVolume

dispose

enableBurnLabels