Package gov.nih.mipav.view.renderer.J3D.surfaceview

Class SurfaceMask

java.lang.Object

gov.nih.mipav.view.renderer.J3D.surfaceview.SurfaceMask

public class SurfaceMask
extends java.lang.Object

SurfaceMask. Calculates the surface volume mask (BitSet) for a triangle mesh surface displayed in the SurfaceRender class. Both boundary masks and filled-volume masks are calculated by the maskInsideVoxels() function.

The boundary-mask is stored in the ModelStorageBase class and is used to display the triangle mesh intersection with the 2D plane in the PlaneRender class. The volume-mask is stored in the SurfaceAttributes class and is accessed through the SurfaceAttributes.getMask() member function. The volume mask is used in the BurnBaseView.calcTotalVolume() function.

See Also:

JPanelSurface.java, SurfaceRender.java, SurfaceAttributes.java, ModelStorageBase.java, BurnBaseView.java

Field Summary

Fields

Modifier and Type	Field	Description
private float	m_fX0	The plane coordinate x,y dimensions:
private float	m_fX1	The plane coordinate x,y dimensions:
private float	m_fY0	The plane coordinate x,y dimensions:
private float	m_fY1	The plane coordinate x,y dimensions:
private float	m_fZ0	The plane coordinate x,y dimensions:
private float	m_fZ1	The plane coordinate x,y dimensions:
private int	m_iQuantity	Product of the image dimensions.
private int	m_iXBound	Dimensions of imageA.
private int	m_iYBound	Dimensions of imageA.
private int	m_iZBound	Dimensions of imageA.
private ModelLUT	m_kLUT	ModelLUT for getModelImageColor w/LUT changes:
private ModelRGB	m_kRGBT	ModelRGB for getModelImageColor w/RGB LUT changes:
private java.util.BitSet	mVolumeMask	Volume-Filled TriangleMesh mask.
private int	xDim	ModelImage image array dimensions:
private int	yDim	ModelImage image array dimensions:
private int	zDim	ModelImage image array dimensions:

Constructor Summary

Constructors

Constructor	Description
SurfaceMask()	Default Constructor:

Method Summary

Modifier and Type	Method	Description
private float	calcMaxNormColors(ModelImage kImage, javax.vecmath.Color3f kOffset)	calculates the color normalization factors
private void	floodFill(int iX, int iY, int iZ)	Identify voxels enclosed by the brain surface by using a flood fill.
private void	getColorMapped(int[] RGBIndexBuffer, javax.vecmath.Color3f kOffset, float fNorm, javax.vecmath.Color4f currentColor)	Get the color from the RGB lookup table:
private 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.
private float	getIntersectX(javax.vecmath.Point3f kV0, javax.vecmath.Point3f kV1, javax.vecmath.Point3f kV2, float iY, float 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.
private float	getIntersectY(javax.vecmath.Point3f kV0, javax.vecmath.Point3f kV1, javax.vecmath.Point3f kV2, float iX, float 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.
private float	getIntersectZ(javax.vecmath.Point3f kV0, javax.vecmath.Point3f kV1, javax.vecmath.Point3f kV2, float iX, float 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.Color4f	getModelImageColor(ModelImage imageA, float fTransparency, javax.vecmath.Point3f kModelPoint)	Given a triangle vertex point from a ModelTriangleMesh, determines the corresponding ModelImage index point, and recreates the color that would have originally been assigned to the vertex.
javax.vecmath.Point3f	getModelImagePoint(javax.vecmath.Point3f kTrianglePoint)	Given a triangle vertex point from a ModelTriangleMesh, determines the corresponding ModelImage index point.
java.util.BitSet	getVolumeMask()	Get the current added surface bit mask.
void	maskInsideVoxels(int index, ModelImage imageA, ModelTriangleMesh[] kMesh, boolean bHasVertexColor, boolean bCreateVertexColors, boolean bUseImageMask, float fOpacity, WildMagic.LibFoundation.Mathematics.ColorRGBA surColor)	Mask the mesh surface volume in voxels.
void	setLUT(ModelLUT kLUT)
void	setRGBT(ModelRGB kRGBT)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

mVolumeMask

private java.util.BitSet mVolumeMask

Volume-Filled TriangleMesh mask.

m_iXBound

private int m_iXBound

Dimensions of imageA.

m_iYBound

private int m_iYBound

Dimensions of imageA.

m_iZBound

private int m_iZBound

Dimensions of imageA.

m_iQuantity

private int m_iQuantity

Product of the image dimensions.

m_fX0

private float m_fX0

The plane coordinate x,y dimensions:

m_fY0

private float m_fY0

The plane coordinate x,y dimensions:

m_fZ0

private float m_fZ0

The plane coordinate x,y dimensions:

m_fX1

private float m_fX1

The plane coordinate x,y dimensions:

m_fY1

private float m_fY1

The plane coordinate x,y dimensions:

m_fZ1

private float m_fZ1

The plane coordinate x,y dimensions:

xDim

private int xDim

ModelImage image array dimensions:

yDim

private int yDim

ModelImage image array dimensions:

zDim

private int zDim

ModelImage image array dimensions:

m_kLUT

private ModelLUT m_kLUT

ModelLUT for getModelImageColor w/LUT changes:

m_kRGBT

private ModelRGB m_kRGBT

ModelRGB for getModelImageColor w/RGB LUT changes:

Constructor Detail

SurfaceMask

SurfaceMask()

Default Constructor:

Method Detail

maskInsideVoxels

public void maskInsideVoxels(int index,
                             ModelImage imageA,
                             ModelTriangleMesh[] kMesh,
                             boolean bHasVertexColor,
                             boolean bCreateVertexColors,
                             boolean bUseImageMask,
                             float fOpacity,
                             WildMagic.LibFoundation.Mathematics.ColorRGBA surColor)

Mask the mesh surface volume in voxels.

Parameters:

index - Mask index in the ModelImage imageA

imageA - ModelImage for storing the surface-mask

kMesh - ModelTriangleMesh[] surfaces

bHasVertexColor - use per-vertex color from the ModelTriangleMesh, otherwise use the surColor parameter

bCreateVertexColor - create the per-vertex color from the imageA ModleImage,

bUseImageMask - create the per-vertex color from the imageA ModleImage, with the ModelImage mask

fOpacity - Mask opacity

surColor - default Mask color

getModelImagePoint

public javax.vecmath.Point3f getModelImagePoint(javax.vecmath.Point3f kTrianglePoint)

Given a triangle vertex point from a ModelTriangleMesh, determines the corresponding ModelImage index point.

Parameters:

kTrianglePoint - ModelTriangleMesh point in mesh coordinates

Returns:

ModelImage index point.

setRGBT

public void setRGBT(ModelRGB kRGBT)

setLUT

public void setLUT(ModelLUT kLUT)

getColorMapped

private void getColorMapped(int[] RGBIndexBuffer,
                            javax.vecmath.Color3f kOffset,
                            float fNorm,
                            javax.vecmath.Color4f currentColor)

Get the color from the RGB lookup table:

Parameters:

RGBIndexBuffer - the color lookup table index buffer

kOffset - the color offset

fNorm - the color normalization

currentColor - the current color (changed)

calcMaxNormColors

private float calcMaxNormColors(ModelImage kImage,
                                javax.vecmath.Color3f kOffset)

calculates the color normalization factors

Parameters:

kImage - the model image from which the normalization factors are calculated

kOffset - the calculated color offset

Returns:

the color normalization factor.

getModelImageColor

public javax.vecmath.Color4f getModelImageColor(ModelImage imageA,
                                                float fTransparency,
                                                javax.vecmath.Point3f kModelPoint)

Given a triangle vertex point from a ModelTriangleMesh, determines the corresponding ModelImage index point, and recreates the color that would have originally been assigned to the vertex.

Parameters:

kTrianglePoint - ModelTriangleMesh point in ModelImage coordinates

Returns:

original color of the triangle point.

getVolumeMask

public java.util.BitSet getVolumeMask()

Get the current added surface bit mask.

Returns:

BitSet surface volume bit set mask.

floodFill

private 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

getIndex

private 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)

getIntersectX

private float getIntersectX(javax.vecmath.Point3f kV0,
                            javax.vecmath.Point3f kV1,
                            javax.vecmath.Point3f kV2,
                            float iY,
                            float 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

private float getIntersectY(javax.vecmath.Point3f kV0,
                            javax.vecmath.Point3f kV1,
                            javax.vecmath.Point3f kV2,
                            float iX,
                            float 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

private float getIntersectZ(javax.vecmath.Point3f kV0,
                            javax.vecmath.Point3f kV1,
                            javax.vecmath.Point3f kV2,
                            float iX,
                            float 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