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

Class 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

      All Methods Instance Methods Concrete Methods 
      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