Package gov.nih.mipav.view.renderer.WildMagic.Render

Class VolumeImage

java.lang.Object
gov.nih.mipav.view.renderer.WildMagic.Render.VolumeImage
All Implemented Interfaces:
Serializable
public class VolumeImage extends Object implements Serializable
The VolumeImage class provides an interface between the MIPAV ModelImage and the 2D and 3D Textures used to render the ModelImage on the GPU. The VolumeImage creates the supporting Texture and GraphicImage objects that pass the ModelImage data to the GPU. It also creates Texture and GraphicsImage objects for the ModelImage Look-up Table (LUT) and the ModelImage opacity transfer function. Other textures that are used for advanced volume rendering, such as a normal map for surface rendering, and the gradient-magnitude and laplace images for the multi-histogram rendering are calculated and passed on-demand to the GPU when the user selects these options in the Volume-Renderer user-interface. The VolumeImage data structure handles all GPU content for rendering one ModelImage. All Textures and GraphicsImages are initialized and stored in the VolumeImage. When needed by the renderer they are loaded onto the GPU. Any images that are derived from the ModelImage: Normal map, Gradient Magnitude, Laplace, are either read from file or calculated and then written to file. The supporting files are stored in a directory on disk located next to the original ModelImage. The directory is named with the ModelImage name followed by "_RenderFiles".
See Also:

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    private WildMagic.LibFoundation.Mathematics.Vector2f[]
    m_akGradientMagMinMax
    3D sub-images (4D data)
    private WildMagic.LibFoundation.Mathematics.Vector2f[]
    m_akHistoTCoord
    Texture coordinates for displaying histogram in 2D
    private boolean
    m_bGMInit
    Set to true if the Gradient Magnitude texture map has been initialized.
    private boolean
    m_bHistoInit
    Set to true when the multi-histogram histogram texture has been initialized.
    private boolean
    m_bNormalsInit
    Set to true if the Normal Map has been initialized.
    private float
    m_fDRRNormalize
     
    private float
    m_fMax
    Image scale factors for display in 3D
    private float
    m_fX
    Image scale factors for display in 3D
    private float
    m_fY
    Image scale factors for display in 3D
    private float
    m_fZ
    Image scale factors for display in 3D
    private int
    m_iMaxExtent
     
    private int
    m_iTimeSlice
    Current position in time (4D data)
    private int
    m_iTimeSteps
    Total number of time-slices (4D data)
    private WildMagic.LibGraphics.Rendering.GraphicsImage
    m_kColorMap
    Data storage for color map:
    private WildMagic.LibGraphics.Rendering.Texture
    m_kColorMapTarget
    Texture object for color map:
    private String
    m_kDir
    Directory for calculated images
    private WildMagic.LibGraphics.Rendering.GraphicsImage[]
    m_kHisto
    Histogram data for multi-histogram interface
    private WildMagic.LibGraphics.Rendering.Texture
    m_kHistoTarget
    Texture object for data:
    private ModelImage
    m_kImage
    Reference to ModelImage image
    private ModelImage
    m_kImageGM
     
    private ModelLUT
    m_kLUT
    ModelLUT
    private WildMagic.LibGraphics.Rendering.GraphicsImage[]
    m_kNormal
    Data storage for normals:
    private WildMagic.LibGraphics.Rendering.Texture
    m_kNormalMapTarget
    Texture object for normal map:
    private WildMagic.LibGraphics.Rendering.GraphicsImage
    m_kOpacityMap_GM
    GraphicsImage contains GM opacity transfer function data:
    private WildMagic.LibGraphics.Rendering.Texture
    m_kOpacityMapTarget_GM
    Texture contains texture filter modes and GraphicsImage for opacity transfer function:
    private String
    m_kPostfix
    Image name post-fix typically either 'A' or 'B'
    private ModelRGB
    m_kRGBT
    ModelRGB
    private WildMagic.LibGraphics.Rendering.Texture
    m_kScratchTarget
    Texture object for GPU computations:
    private WildMagic.LibGraphics.Rendering.GraphicsImage
    m_kSurfaceImage
    Data storage for surfaces:
    private WildMagic.LibGraphics.Rendering.Texture
    m_kSurfaceTarget
    Texture object for surfaces:
    private WildMagic.LibGraphics.Rendering.GraphicsImage[]
    m_kVolume
    Data storage for volume:
    private WildMagic.LibGraphics.Rendering.GraphicsImage[]
    m_kVolumeGM
    Data storage for volume gradient magnitude:
    private WildMagic.LibGraphics.Rendering.Texture
    m_kVolumeGMTarget
    Texture object for volume gradient magnitude data:
    private WildMagic.LibGraphics.Rendering.Texture
    m_kVolumeTarget
    Texture object for data:
    private TransferFunction
    opacityTransferFn
     
    private static final long
    serialVersionUID
     
    protected Vector<WildMagic.LibFoundation.Mathematics.ColorRGB>
    surfaceColor
    A vector of BitSet masks, one for each surface loaded into the viewer.
    protected Vector<BitSet>
    surfaceMask
    A vector of BitSet masks, one for each surface loaded into the viewer.
    protected Vector<String>
    surfaceNames
    A vector of the mask names, so they can be accessed by name:

  • Constructor Summary

    Constructors
    Constructor
    Description
    VolumeImage()
     
    VolumeImage(boolean bClone, ModelImage kImage, String kPostfix, ViewJProgressBar kProgress, int iProgress)
    Create a Volume image with the input ModelImage.
    VolumeImage(boolean bClone, ModelImage kImage, String kPostfix, ViewJProgressBar kProgress, int iProgress, boolean initGradientMagnitude)
     

  • Method Summary

    Modifier and Type
    Method
    Description
    private void
    addNormals(ModelImage kImage, int iTimeSlice)
     
    static boolean
    checkImage(ModelImage kImage1, ModelImage kImage2)
    Checks that the two input images match extents, units of measure and resolutions.
    protected float
    computeIntegralNormalizationFactor()
    In order to map line integrals of image intensity to RGB colors where each color channel is 8 bits, it is necessary to make sure that the integrals are in [0,255].
    void
    CopyNormalFiles(int i, ModelImage kImage)
    When the ModelImage data is rendered as a solid surface, the Normal map is used in the rendering.
    private WildMagic.LibGraphics.Rendering.GraphicsImage
    createGM_Laplace(ModelImage kImageGM, ModelImage kImageL, WildMagic.LibGraphics.Rendering.GraphicsImage kVolumeImage, int iTimeSlice, boolean bSwap)
     
    static ModelImage
    CreateImageFromTexture(WildMagic.LibGraphics.Rendering.GraphicsImage kImage)
    Read the current Volume Texture from the GPU and return a new ModelImage of that data.
    static ModelImage
    CreateImageFromTexture(WildMagic.LibGraphics.Rendering.GraphicsImage kImage, boolean bSwap)
    Copy the data from the input GraphicsImage and return a new ModelImage of that data.
    void
    dispose()
    Memory cleanup.
    private void
    GenerateHistogram(WildMagic.LibGraphics.Rendering.GraphicsImage[] kImage, WildMagic.LibGraphics.Rendering.GraphicsImage[] kImageGM, String kPostFix, int start, int end)
    Generate 2D histogram from the input image and the gradient-magnitude
    void
    GenerateNormalFiles(VolumeTriPlanarInterface parentFrame)
    This function is called when the user selects the Surface or Composite Surface volume rendering option.
    WildMagic.LibGraphics.Rendering.Texture
    GetColorMapTarget()
    Return the Color Map Texture.
    float
    getDRRNorm()
    Return the normalization factor for DDR rendering mode.
    static ModelImage
    getGradientMagnitude(ModelImage kImage, int i)
    Calculates and stores the gradient magnitude images (3D or 4D) for the input image.
    ModelImage
    GetGradientMagnitudeImage()
     
    float
    GetGradientMagnitudeMax()
     
    float
    GetGradientMagnitudeMin()
     
    WildMagic.LibFoundation.Mathematics.Vector2f
    GetGradientMagnitudeMinMax()
     
    WildMagic.LibGraphics.Rendering.Texture
    GetGradientMapTarget()
    Return the Gradient Magnitude Texture.
    WildMagic.LibGraphics.Rendering.Texture
    GetHistoTarget()
    Returns the multi-histogram histogram Texture.
    WildMagic.LibFoundation.Mathematics.Vector2f[]
    GetHistoTCoords()
    Return the texture coordinates for the multi-histogram histogram texture.
    ModelImage
    GetImage()
    Return the ModelImage volume data.
    ModelStorageBase
    getLUT()
    Return the Volume RGBT.
    ModelLUT
    GetLUT()
    Return the ModelImage LUT.
    int
    GetMaxExtent()
     
    WildMagic.LibGraphics.Rendering.Texture
    GetNormalMapTarget()
    Return the Normal map Texture.
    TransferFunction
    getOpacityFn()
     
    WildMagic.LibGraphics.Rendering.Texture
    GetOpacityMapGMTarget()
    Return the gradient magnitude opacity transfer function Texture.
    String
    GetPostfix()
    Return the postfix for this VolumeImage.
    ModelRGB
    GetRGB()
    Return the Volume RGBT.
    float
    GetScaleMax()
    The ModelImage Volume max-scale factor.
    float
    GetScaleX()
    The ModelImage Volume x-scale factor.
    float
    GetScaleY()
    The ModelImage Volume y-scale factor.
    float
    GetScaleZ()
    The ModelImage Volume z-scale factor.
    WildMagic.LibGraphics.Rendering.Texture
    GetScratchTarget()
     
    WildMagic.LibGraphics.Rendering.Texture
    GetSurfaceTarget()
    Return the surface mask Texture.
    int
    GetTimeSlice()
    Returns the current rendered time-slice for 4D images.
    float
    GetTransferedValue(int x, int y, int z)
     
    WildMagic.LibGraphics.Rendering.Texture
    GetVolumeTarget()
    Return the Texture containing the volume data.
    Buffer
    GetVolumeTargetBuffer()
    Return the Buffer containing the volume data, which is stored in the Texture GrapicsImage.
    private void
    init(ViewJProgressBar kProgress, int iProgress, boolean initGradientMagnitude)
    Initialize the VolumeImage with the ModelImage data.
    private WildMagic.LibGraphics.Rendering.GraphicsImage
    initColorMap()
     
    static WildMagic.LibGraphics.Rendering.GraphicsImage
    InitColorMap(WildMagic.LibGraphics.Rendering.Texture kTexture, WildMagic.LibGraphics.Rendering.GraphicsImage kImage, ModelStorageBase kLUT, String kPostFix)
    Initialize the textures for the color lookup table.
    private void
    initImages()
    Intializes the Textures and GraphicsImages used to render the ModelImage this VolumeImage represents.
    private void
    initImagesColor()
     
    private void
    initLUT()
    Create a new LUT for the input image.
    WildMagic.LibGraphics.Rendering.GraphicsImage
    InitOpacityMap(ModelImage kImage, String kPostFix)
    Initialize the GraphicsImage for the opacity lookup table.
    private void
    InitScale()
    Initialize the scale factors.
    private WildMagic.LibGraphics.Rendering.GraphicsImage
    initVolumeData(ModelImage kImage, int iTimeSlice, WildMagic.LibGraphics.Rendering.Texture kVolumeTexture, String kImageName, boolean bSwap, boolean bRescale)
     
    boolean
    IsColorImage()
    Return true if the Volume image is a color image.
    boolean
    isHistoInit()
    Returns true if the multi-histogram histogram texture has been initialized, false otherwise.
    private static ModelImage
    ReadFromDisk(String kImageName, String kDir)
    Reads an image from disk.
    private void
    readObject(ObjectInputStream in)
     
    void
    ReleaseVolume()
    Release the Textures containing the volume data.
    void
    removeSurfaceMask(String name)
    Delete the surface mask, using the name of the mask as reference.
    private WildMagic.LibGraphics.Rendering.GraphicsImage
    resetVolumeData(ModelImage kImage, int iTimeSlice, WildMagic.LibGraphics.Rendering.GraphicsImage kGraphicsImage, WildMagic.LibGraphics.Rendering.Texture kVolumeTexture, String kImageName, boolean bSwap, boolean bRescale)
     
    void
    SetGradientMagnitude(ModelImage kGradientMagnitude, boolean bComputeLaplace, String kPostfix)
    Called when the user selects the Gradient Magnitude option or the Multi-Histogram option in the Volume Renderer.
    void
    SetRGBT(ModelRGB kRGBT)
    Sets the ModelRGB for the iImage.
    void
    setSurfaceMask(String name, WildMagic.LibFoundation.Mathematics.ColorRGB color, BitSet mask)
    Add a new surface mask.
    void
    setSurfaceMaskColor(String name, WildMagic.LibFoundation.Mathematics.ColorRGB color)
    Delete the surface mask, using the name of the mask as reference.
    void
    SetTimeSlice(int iSlice)
    Sets the time slices for 4D data.
    private float
    TransferValue(float value)
     
    private void
    update4D()
    Go to the next 3D volume sub-image for the 4D animation.
    void
    update4D(boolean bForward)
    Updates the current time slice.
    void
    UpdateData(ModelImage kImage, boolean reload)
    Update the image data.
    static WildMagic.LibGraphics.Rendering.GraphicsImage
    UpdateData(ModelImage kImage, int iTimeSlice, ModelImage kNewImage, WildMagic.LibGraphics.Rendering.GraphicsImage kVolumeImage, WildMagic.LibGraphics.Rendering.Texture kVolumeTexture, String kImageName, boolean bSwap, boolean bRescale)
    When a ModelImage changes on the CPU, this function is used to update the ModelImage data on the CPU.
    void
    UpdateData(ModelImage kImage, ModelLUT kLUT, boolean reload)
    Changes the underlying image data and LUT.
    static WildMagic.LibGraphics.Rendering.GraphicsImage
    UpdateData(ModelSimpleImage kImage, String kImageName)
    Creates a new GraphicsImage for the input ModelSimpleImage.
    private boolean
    UpdateImages(ModelImage kImage, WildMagic.LibGraphics.Rendering.Texture kOpacityTexture, WildMagic.LibGraphics.Rendering.GraphicsImage kOpacityMap, TransferFunction kTransfer)
    Called when the opacity transfer function changes.
    void
    UpdateImages(ModelLUT kLUT)
    Update the LUT for the ModelImage.
    void
    UpdateImages(ModelStorageBase kLUT)
    Update the LUT for the ModelImage.
    boolean
    UpdateImages(TransferFunction kTransfer, int iImage, ModelImage kImage)
    Update the transfer function for the image iImage.
    static void
    UpdateImages(WildMagic.LibGraphics.Rendering.Texture kColorTexture, WildMagic.LibGraphics.Rendering.GraphicsImage kColorMap, ModelLUT kLUT)
    When the LUT changes, this function updates the LUT data on the GPU.
    private boolean
    UpdateImages2(ModelImage kImage, WildMagic.LibGraphics.Rendering.Texture kOpacityTexture, WildMagic.LibGraphics.Rendering.GraphicsImage kOpacityMap, TransferFunction kTransfer)
    Update the opacity transfer function.
    private void
    updateMask()
     
    private void
    writeObject(ObjectOutputStream out)
     

    Methods inherited from class java.lang.Object

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

  • Field Details

    • serialVersionUID

      private static final long serialVersionUID
      See Also:

    • m_kImage

      private ModelImage m_kImage
      Reference to ModelImage image

    • m_kImageGM

      private ModelImage m_kImageGM

    • m_kOpacityMap_GM

      private WildMagic.LibGraphics.Rendering.GraphicsImage m_kOpacityMap_GM
      GraphicsImage contains GM opacity transfer function data:

    • m_kOpacityMapTarget_GM

      private WildMagic.LibGraphics.Rendering.Texture m_kOpacityMapTarget_GM
      Texture contains texture filter modes and GraphicsImage for opacity transfer function:

    • m_kVolume

      private WildMagic.LibGraphics.Rendering.GraphicsImage[] m_kVolume
      Data storage for volume:

    • m_kVolumeTarget

      private WildMagic.LibGraphics.Rendering.Texture m_kVolumeTarget
      Texture object for data:

    • m_kNormal

      private WildMagic.LibGraphics.Rendering.GraphicsImage[] m_kNormal
      Data storage for normals:

    • m_bNormalsInit

      private boolean m_bNormalsInit
      Set to true if the Normal Map has been initialized.

    • m_kNormalMapTarget

      private WildMagic.LibGraphics.Rendering.Texture m_kNormalMapTarget
      Texture object for normal map:

    • m_kScratchTarget

      private WildMagic.LibGraphics.Rendering.Texture m_kScratchTarget
      Texture object for GPU computations:

    • m_kColorMap

      private WildMagic.LibGraphics.Rendering.GraphicsImage m_kColorMap
      Data storage for color map:

    • m_kColorMapTarget

      private WildMagic.LibGraphics.Rendering.Texture m_kColorMapTarget
      Texture object for color map:

    • m_kVolumeGM

      private WildMagic.LibGraphics.Rendering.GraphicsImage[] m_kVolumeGM
      Data storage for volume gradient magnitude:

    • m_bGMInit

      private boolean m_bGMInit
      Set to true if the Gradient Magnitude texture map has been initialized.

    • m_kVolumeGMTarget

      private WildMagic.LibGraphics.Rendering.Texture m_kVolumeGMTarget
      Texture object for volume gradient magnitude data:

    • m_kSurfaceImage

      private WildMagic.LibGraphics.Rendering.GraphicsImage m_kSurfaceImage
      Data storage for surfaces:

    • m_kSurfaceTarget

      private WildMagic.LibGraphics.Rendering.Texture m_kSurfaceTarget
      Texture object for surfaces:

    • m_kLUT

      private ModelLUT m_kLUT
      ModelLUT

    • m_kRGBT

      private ModelRGB m_kRGBT
      ModelRGB

    • m_fX

      private float m_fX
      Image scale factors for display in 3D

    • m_fY

      private float m_fY
      Image scale factors for display in 3D

    • m_fZ

      private float m_fZ
      Image scale factors for display in 3D

    • m_fMax

      private float m_fMax
      Image scale factors for display in 3D

    • m_iMaxExtent

      private int m_iMaxExtent

    • m_kPostfix

      private String m_kPostfix
      Image name post-fix typically either 'A' or 'B'

    • m_kDir

      private String m_kDir
      Directory for calculated images

    • m_kHisto

      private WildMagic.LibGraphics.Rendering.GraphicsImage[] m_kHisto
      Histogram data for multi-histogram interface

    • m_bHistoInit

      private boolean m_bHistoInit
      Set to true when the multi-histogram histogram texture has been initialized.

    • m_kHistoTarget

      private WildMagic.LibGraphics.Rendering.Texture m_kHistoTarget
      Texture object for data:

    • m_akHistoTCoord

      private WildMagic.LibFoundation.Mathematics.Vector2f[] m_akHistoTCoord
      Texture coordinates for displaying histogram in 2D

    • m_fDRRNormalize

      private float m_fDRRNormalize

    • m_iTimeSlice

      private int m_iTimeSlice
      Current position in time (4D data)

    • m_iTimeSteps

      private int m_iTimeSteps
      Total number of time-slices (4D data)

    • m_akGradientMagMinMax

      private WildMagic.LibFoundation.Mathematics.Vector2f[] m_akGradientMagMinMax
      3D sub-images (4D data)

    • opacityTransferFn

      private TransferFunction opacityTransferFn

    • surfaceMask

      protected Vector<BitSet> surfaceMask
      A vector of BitSet masks, one for each surface loaded into the viewer.

    • surfaceNames

      protected Vector<String> surfaceNames
      A vector of the mask names, so they can be accessed by name:

    • surfaceColor

      protected Vector<WildMagic.LibFoundation.Mathematics.ColorRGB> surfaceColor
      A vector of BitSet masks, one for each surface loaded into the viewer.

  • Constructor Details

    • VolumeImage

      public VolumeImage()

    • VolumeImage

      public VolumeImage(boolean bClone, ModelImage kImage, String kPostfix, ViewJProgressBar kProgress, int iProgress)
      Create a Volume image with the input ModelImage. The supporting images for advanced volume rendering, such as the normal map, gradient magnitude and laplace images are generated on-demand and stored in a directory for later use. The directory is created if it does not already exist, with the ModelImage name + "_RenderFiles" as the directory name.
      Parameters:
      bClone - , when true clone the input ModelImage, when false reference the ModelImage
      kImage - input ModelImage
      kPostfix - Postfix for images 'A' or 'B'
      kProgress - progress bar
      iProgress - progress bar increment

    • VolumeImage

      public VolumeImage(boolean bClone, ModelImage kImage, String kPostfix, ViewJProgressBar kProgress, int iProgress, boolean initGradientMagnitude)

  • Method Details

    • CreateImageFromTexture

      public static ModelImage CreateImageFromTexture(WildMagic.LibGraphics.Rendering.GraphicsImage kImage, boolean bSwap)
      Copy the data from the input GraphicsImage and return a new ModelImage of that data. Any changes to the GraphicsImage that occur only on the GPU can first be written from the GPU back into the GraphicsImage CPU data storage. This enables calculations that are performed on the GPU to be written back into a ModelImage data structure.
      Parameters:
      kImage - Graphics Image to copy
      bSwap - when true convert from RGBA (graphics format) to ARGB (ModelImage format)
      Returns:
      new ModelImage from Volume Texture on GPU.

    • InitColorMap

      public static WildMagic.LibGraphics.Rendering.GraphicsImage InitColorMap(WildMagic.LibGraphics.Rendering.Texture kTexture, WildMagic.LibGraphics.Rendering.GraphicsImage kImage, ModelStorageBase kLUT, String kPostFix)
      Initialize the textures for the color lookup table.
      Parameters:
      kLUT - the new LUT.
      kRGBT - the new RGB table.
      kPostfix - the string postfix to concatenate to the "ColorMap" image name.
      Returns:
      GraphicsImage, the new GraphicsImage storing the colormap lookup table.

    • initColorMap

      private WildMagic.LibGraphics.Rendering.GraphicsImage initColorMap()

    • UpdateData

      public static WildMagic.LibGraphics.Rendering.GraphicsImage UpdateData(ModelImage kImage, int iTimeSlice, ModelImage kNewImage, WildMagic.LibGraphics.Rendering.GraphicsImage kVolumeImage, WildMagic.LibGraphics.Rendering.Texture kVolumeTexture, String kImageName, boolean bSwap, boolean bRescale)
      When a ModelImage changes on the CPU, this function is used to update the ModelImage data on the CPU.
      Parameters:
      kImage - Modified ModelImage to copy into the GPU Texture and GraphicsImage
      iTimeSlice - time value for 4D image, 0 otherwise
      kNewImage - a new ModelImage (always 3D) that the data or data subset for 4D image can be copied into (when non-null).
      kVolumeImage - GraphicsImage that will hold the ModelImage data
      kVolumeTexture - Texture object containing the GraphicsImage
      kImageName - new image name for the new ModelImage.
      bSwap - when true swap the ARGB (ModelImage) color data representation to a RGBA (GPU) color representation.
      Returns:

    • initVolumeData

      private WildMagic.LibGraphics.Rendering.GraphicsImage initVolumeData(ModelImage kImage, int iTimeSlice, WildMagic.LibGraphics.Rendering.Texture kVolumeTexture, String kImageName, boolean bSwap, boolean bRescale)

    • resetVolumeData

      private WildMagic.LibGraphics.Rendering.GraphicsImage resetVolumeData(ModelImage kImage, int iTimeSlice, WildMagic.LibGraphics.Rendering.GraphicsImage kGraphicsImage, WildMagic.LibGraphics.Rendering.Texture kVolumeTexture, String kImageName, boolean bSwap, boolean bRescale)

    • addNormals

      private void addNormals(ModelImage kImage, int iTimeSlice)

    • createGM_Laplace

      private WildMagic.LibGraphics.Rendering.GraphicsImage createGM_Laplace(ModelImage kImageGM, ModelImage kImageL, WildMagic.LibGraphics.Rendering.GraphicsImage kVolumeImage, int iTimeSlice, boolean bSwap)

    • UpdateData

      public static WildMagic.LibGraphics.Rendering.GraphicsImage UpdateData(ModelSimpleImage kImage, String kImageName)
      Creates a new GraphicsImage for the input ModelSimpleImage. The ModelSimpleImage data is referenced by the new GraphicsImage and will be passed to the GPU as a texture.
      Parameters:
      kImage - input ModelSimpleImage.
      kImageName - name for the GraphicsImage.
      Returns:
      a new GraphcisImage.

    • UpdateImages

      public static void UpdateImages(WildMagic.LibGraphics.Rendering.Texture kColorTexture, WildMagic.LibGraphics.Rendering.GraphicsImage kColorMap, ModelLUT kLUT)
      When the LUT changes, this function updates the LUT data on the GPU.
      Parameters:
      kColorTexture - the color-map Texture object.
      kColorMap - the color-map GraphicsImage object (stores data).
      kLUT - the updated or new LUT.

    • CopyNormalFiles

      public void CopyNormalFiles(int i, ModelImage kImage)
      When the ModelImage data is rendered as a solid surface, the Normal map is used in the rendering. The Normal map is calculated on the GPU by one of the GLSL shader programs. This function is called after the GPU calculation has finished and the GPU data has been copied into a new ModelImage on the CPU the new ModelImage then contains the Normal map information, which is written into a file and copied into the Normal map GraphicsImage used to render the original ModelImage.
      Parameters:
      i - current 3D sub-image for 4D data. If the data is 3D this value should be 0.
      kImage - a new ModelImage containing the calculated Normals.

    • CreateImageFromTexture

      public static ModelImage CreateImageFromTexture(WildMagic.LibGraphics.Rendering.GraphicsImage kImage)
      Read the current Volume Texture from the GPU and return a new ModelImage of that data.
      Returns:
      new ModelImage from Volume Texture on GPU.

    • dispose

      public void dispose()
      Memory cleanup.

    • GenerateNormalFiles

      public void GenerateNormalFiles(VolumeTriPlanarInterface parentFrame)
      This function is called when the user selects the Surface or Composite Surface volume rendering option. If the normals have already been initialized the function returns. Otherwise the function checks if the normals are available in a file on disk, and if so if they match the parameters (size, units, resolutions) of the original ModelImage. If the files match they are used and the Normal map is read from file. Otherwise this function launches the GPU-based Normal calculation. That calculation when finished calls the CopyNormalFiles which writes the calculated normals to disk and updates the Normal map on the GPU for rendering.

    • GetColorMapTarget

      public WildMagic.LibGraphics.Rendering.Texture GetColorMapTarget()
      Return the Color Map Texture.
      Returns:
      Volume color map Texture.

    • getDRRNorm

      public float getDRRNorm()
      Return the normalization factor for DDR rendering mode.
      Returns:
      normalization factor for DDR rendering mode.

    • GetGradientMapTarget

      public WildMagic.LibGraphics.Rendering.Texture GetGradientMapTarget()
      Return the Gradient Magnitude Texture.
      Returns:
      Gradient Magnitude Texture.

    • isHistoInit

      public boolean isHistoInit()
      Returns true if the multi-histogram histogram texture has been initialized, false otherwise.
      Returns:
      true if the multi-histogram histogram texture has been initialized, false otherwise.

    • GetHistoTarget

      public WildMagic.LibGraphics.Rendering.Texture GetHistoTarget()
      Returns the multi-histogram histogram Texture.
      Returns:
      the multi-histogram histogram Texture.

    • GetHistoTCoords

      public WildMagic.LibFoundation.Mathematics.Vector2f[] GetHistoTCoords()
      Return the texture coordinates for the multi-histogram histogram texture.
      Returns:
      the texture coordinates for the multi-histogram histogram texture.

    • GetGradientMagnitudeImage

      public ModelImage GetGradientMagnitudeImage()

    • GetGradientMagnitudeMinMax

      public WildMagic.LibFoundation.Mathematics.Vector2f GetGradientMagnitudeMinMax()

    • GetGradientMagnitudeMin

      public float GetGradientMagnitudeMin()

    • GetGradientMagnitudeMax

      public float GetGradientMagnitudeMax()

    • GetImage

      public ModelImage GetImage()
      Return the ModelImage volume data.
      Returns:
      ModelImage volume data.

    • GetLUT

      public ModelLUT GetLUT()
      Return the ModelImage LUT.
      Returns:
      Volume LUT.

    • GetNormalMapTarget

      public WildMagic.LibGraphics.Rendering.Texture GetNormalMapTarget()
      Return the Normal map Texture.
      Returns:
      Normal map Texture.

    • GetScratchTarget

      public WildMagic.LibGraphics.Rendering.Texture GetScratchTarget()

    • GetOpacityMapGMTarget

      public WildMagic.LibGraphics.Rendering.Texture GetOpacityMapGMTarget()
      Return the gradient magnitude opacity transfer function Texture.
      Returns:
      gradient magnitude opacity transfer function Texture.

    • GetPostfix

      public String GetPostfix()
      Return the postfix for this VolumeImage.
      Returns:
      postfix for this VolumeImage.

    • getLUT

      public ModelStorageBase getLUT()
      Return the Volume RGBT.
      Returns:
      Volume RGBT.

    • GetRGB

      public ModelRGB GetRGB()
      Return the Volume RGBT.
      Returns:
      Volume RGBT.

    • GetTransferedValue

      public float GetTransferedValue(int x, int y, int z)

    • TransferValue

      private float TransferValue(float value)

    • GetScaleMax

      public float GetScaleMax()
      The ModelImage Volume max-scale factor.
      Returns:
      Volume max-scale factor.

    • GetMaxExtent

      public int GetMaxExtent()

    • GetScaleX

      public float GetScaleX()
      The ModelImage Volume x-scale factor.
      Returns:
      Volume x-scale factor.

    • GetScaleY

      public float GetScaleY()
      The ModelImage Volume y-scale factor.
      Returns:
      Volume y-scale factor.

    • GetScaleZ

      public float GetScaleZ()
      The ModelImage Volume z-scale factor.
      Returns:
      Volume z-scale factor.

    • GetSurfaceTarget

      public WildMagic.LibGraphics.Rendering.Texture GetSurfaceTarget()
      Return the surface mask Texture.
      Returns:
      surface mask Texture.

    • setSurfaceMask

      public void setSurfaceMask(String name, WildMagic.LibFoundation.Mathematics.ColorRGB color, BitSet mask)
      Add a new surface mask.
      Parameters:
      name - surface name.
      mask - surface mask volume.

    • updateMask

      private void updateMask()

    • removeSurfaceMask

      public void removeSurfaceMask(String name)
      Delete the surface mask, using the name of the mask as reference.
      Parameters:
      name - the surface name.

    • setSurfaceMaskColor

      public void setSurfaceMaskColor(String name, WildMagic.LibFoundation.Mathematics.ColorRGB color)
      Delete the surface mask, using the name of the mask as reference.
      Parameters:
      name - the surface name.

    • GetTimeSlice

      public int GetTimeSlice()
      Returns the current rendered time-slice for 4D images. Otherwise returns 0.
      Returns:
      the current rendered time-slice for 4D images. Otherwise returns 0.

    • GetVolumeTarget

      public WildMagic.LibGraphics.Rendering.Texture GetVolumeTarget()
      Return the Texture containing the volume data.
      Returns:
      Texture containing the volume data.

    • GetVolumeTargetBuffer

      public Buffer GetVolumeTargetBuffer()
      Return the Buffer containing the volume data, which is stored in the Texture GrapicsImage.
      Returns:
      Buffer containing the volume data.

    • InitOpacityMap

      public WildMagic.LibGraphics.Rendering.GraphicsImage InitOpacityMap(ModelImage kImage, String kPostFix)
      Initialize the GraphicsImage for the opacity lookup table.
      Parameters:
      kImage - the ModelImage the opacity transfer function applies to.
      kPostfix - the string postfix to concatenate to the "OpacityMap" image name.
      Returns:
      GraphicsImage, the new GraphicsImage storing opacity lookup table.

    • IsColorImage

      public boolean IsColorImage()
      Return true if the Volume image is a color image.
      Returns:
      true if the Volume image is a color image.

    • ReleaseVolume

      public void ReleaseVolume()
      Release the Textures containing the volume data. Once Textures are released, they will be re-loaded onto the GPU during the next frame.

    • SetGradientMagnitude

      public void SetGradientMagnitude(ModelImage kGradientMagnitude, boolean bComputeLaplace, String kPostfix)
      Called when the user selects the Gradient Magnitude option or the Multi-Histogram option in the Volume Renderer.
      Parameters:
      kGradientMagnitude - pre-computed GradientMagnitude image or null
      bComputeLaplace - when true the Laplace image and multi-histogram histogram Textures are computed.
      kPostfix - GraphicsImage postfix string.

    • SetRGBT

      public void SetRGBT(ModelRGB kRGBT)
      Sets the ModelRGB for the iImage.
      Parameters:
      kRGBT - new ModelRGB

    • SetTimeSlice

      public void SetTimeSlice(int iSlice)
      Sets the time slices for 4D data.
      Parameters:
      iSlice - new time slice value.

    • update4D

      public void update4D(boolean bForward)
      Updates the current time slice.
      Parameters:
      bForward - when true the time advances on step forward or wraps to the beginning. When false the time moves backward.

    • UpdateData

      public void UpdateData(ModelImage kImage, boolean reload)
      Update the image data.
      Parameters:
      kImage - the modified ModelImage
      bCopytoCPU - when true the data is copied from the GPU GraphicsImage into the ModelImage

    • UpdateData

      public void UpdateData(ModelImage kImage, ModelLUT kLUT, boolean reload)
      Changes the underlying image data and LUT. If the new image data is a different size than then previous one, recreate the volume image on the GPU, otherwise just overwrite it with the new data.
      Parameters:
      kImage -
      kLUT -
      reload -

    • UpdateImages

      public void UpdateImages(ModelLUT kLUT)
      Update the LUT for the ModelImage.
      Parameters:
      kLUT - new LUT for ModelImage.

    • UpdateImages

      public void UpdateImages(ModelStorageBase kLUT)
      Update the LUT for the ModelImage.
      Parameters:
      kLUT - new LUT for ModelImage.

    • UpdateImages

      public boolean UpdateImages(TransferFunction kTransfer, int iImage, ModelImage kImage)
      Update the transfer function for the image iImage.
      Parameters:
      kTransfer - the new opacity transfer function
      iImage - the image to modify (0 = volume image, 2 = gradient mag)
      kImage - GradientMagitude image.
      Returns:
      boolean true when updated, false otherwise.

    • computeIntegralNormalizationFactor

      protected float computeIntegralNormalizationFactor()
      In order to map line integrals of image intensity to RGB colors where each color channel is 8 bits, it is necessary to make sure that the integrals are in [0,255]. Producing a theoretical maximum value of a line integral is not tractable in an application. This method constructs an approximate maximum by integrating along each line of voxels in the image with line directions parallel to the coordinate axes. The 'processRay' call adjusts the line integrals using the estimate, but still clamps the integrals to 255 since the estimate might not be the true maximum.
      Returns:
      float Integral normalization factor.

    • checkImage

      public static boolean checkImage(ModelImage kImage1, ModelImage kImage2)
      Checks that the two input images match extents, units of measure and resolutions. The images may had different sizes (3D or 4D) the first 3-dimensions must match.
      Parameters:
      kImage1 -
      kImage2 -
      Returns:
      true if the images match extends, units and resolutions.

    • GenerateHistogram

      private void GenerateHistogram(WildMagic.LibGraphics.Rendering.GraphicsImage[] kImage, WildMagic.LibGraphics.Rendering.GraphicsImage[] kImageGM, String kPostFix, int start, int end)
      Generate 2D histogram from the input image and the gradient-magnitude
      Parameters:
      kImage - input GraphicsImage containing the ModelImage data
      kImageGM - input GraphcisImage containing the Gradient Magnitude data.
      kPostFix - post-fix for the image name.

    • getGradientMagnitude

      public static ModelImage getGradientMagnitude(ModelImage kImage, int i)
      Calculates and stores the gradient magnitude images (3D or 4D) for the input image. Or reads from disk. The data is stored in the GraphicsImage data structures and will be passed to the GPU to use in rendering.
      Parameters:
      kImage - input image
      kGradientMagnitude - input Gradient Magnitude image, or null.
      bComputeLaplace - when true the Laplace image is also calculated or read from dis. private void GradientMagnitudeImage(final ModelImage kImage, ModelImage kGradientMagnitude, boolean bComputeLaplace) { if ( !m_bGMInit ) { ModelImage[] kImageGM = new ModelImage[m_iTimeSteps]; String[] kImageName = new String[m_iTimeSteps]; for (int i = 0; i invalid input: '<' m_iTimeSteps; i++) { kImageName[i] = ModelImage.makeImageName(kImage.getFileInfo(0).getFileName(), new String("_GM_" + i)); if ( kGradientMagnitude != null invalid input: '&'invalid input: '&' checkImage(kImage, kGradientMagnitude )) { m_kVolumeGM[i] = VolumeImage.UpdateData(kGradientMagnitude, i, null, m_kVolumeGM[i], m_kVolumeGMTarget, m_kVolumeGM[i].GetName(), true, false); ModelImage.saveImage( kGradientMagnitude, kImageName[i] + ".xml", m_kDir ); } else { kImageGM[i] = ReadFromDisk(kImageName[i] + ".xml", m_kDir); if ( kImageGM[i] != null invalid input: '&'invalid input: '&' !checkImage(kImage, kImageGM[i] ) ) { kImageGM[i].disposeLocal(); kImageGM[i] = null; } if (kImageGM[i] == null) { JDialogGradientMagnitude kCalcMagnitude = new JDialogGradientMagnitude(null, m_akImages[i]); kCalcMagnitude.setVisible(false); kCalcMagnitude.setOutputNewImage(true); kCalcMagnitude.setDisplayProgressBar(true); kCalcMagnitude.setSeparateThread(false); kCalcMagnitude.setSeparable(true); kCalcMagnitude.setUseOCL(true); kCalcMagnitude.actionPerformed(new ActionEvent(this, 0, "OK")); kImageGM[i] = kCalcMagnitude.getResultImage(); kCalcMagnitude = null; } if (kImageGM[i] == null) { System.err.println("Gradient magnitude calculation returned null"); m_kVolumeGM[i] = VolumeImage.UpdateData(kImage, i, null, m_kVolumeGM[i], m_kVolumeGMTarget, kImageName[i], true, false); } else { kImageGM[i].calcMinMax(); m_akGradientMagMinMax[i] = new Vector2f( (float)kImageGM[i].getMin(), (float)kImageGM[i].getMax() ); if ( !( bComputeLaplace invalid input: '&'invalid input: '&' !m_kImage.isColorImage() ) ) { m_kVolumeGM[i] = VolumeImage.UpdateData(kImageGM[i], 0, null, m_kVolumeGM[i], m_kVolumeGMTarget, kImageName[i], true, false); } } } } if ( bComputeLaplace invalid input: '&'invalid input: '&' !m_kImage.isColorImage() ) { for (int i = 0; i invalid input: '<' m_iTimeSteps; i++) { final String kImageNameL = ModelImage.makeImageName(kImage.getFileInfo(0).getFileName(), new String( "_Laplacian_" + i)); ModelImage kImageGMGM = null; kImageGMGM = ReadFromDisk(kImageNameL + ".xml", m_kDir); if ( kImageGMGM != null invalid input: '&'invalid input: '&' !checkImage(kImage, kImageGMGM ) ) { kImageGMGM.disposeLocal(); kImageGMGM = null; } if (kImageGMGM == null) { final JDialogLaplacian kCalcLaplacian = new JDialogLaplacian(null, m_akImages[i]); kCalcLaplacian.setVisible(false); kCalcLaplacian.setOutputNewImage(true); kCalcLaplacian.setDisplayProgressBar(true); kCalcLaplacian.setSeparateThread(false); kCalcLaplacian.setUseOCL(true); kCalcLaplacian.setSeparable(true); kCalcLaplacian.actionPerformed(new ActionEvent(this, 0, "OK")); kImageGMGM = kCalcLaplacian.getResultImage(); } if (kImageGMGM != null) { m_kVolumeGM[i] = createGM_Laplace(kImageGM[i], kImageGMGM, m_kVolumeGM[i], i, true); } else { m_kVolumeGM[i] = VolumeImage.UpdateData(kImageGM[i], 0, null, m_kVolumeGM[i], m_kVolumeGMTarget, kImageName[i], true, false); } final ViewJFrameImage kImageFrame = ViewUserInterface.getReference().getFrameContainingImage(kImageGMGM); if (kImageFrame != null) { kImageFrame.close(); } else if (kImageGMGM != null) { kImageGMGM.disposeLocal(); kImageGMGM = null; } } } m_bGMInit = true; m_kVolumeGMTarget.SetImage(m_kVolumeGM[0]); m_kVolumeGMTarget.Reload(true); for ( int i = 0; i invalid input: '<' kImageGM.length; i++ ) { if (kImageGM[i] != null) { kImageGM[i].setImageDirectory( m_kDir ); kImageGM[i].setImageName( kImageName[i] + ".xml" ); ModelImage.saveImage(kImageGM[i], kImageName[i] + ".xml", m_kDir ); final ViewJFrameImage kImageFrame = ViewUserInterface.getReference().getFrameContainingImage(kImageGM[i]); if (kImageFrame != null) { kImageFrame.close(); } kImageGM[i].disposeLocal(); kImageGM[i] = null; } } } }

    • init

      private void init(ViewJProgressBar kProgress, int iProgress, boolean initGradientMagnitude)
      Initialize the VolumeImage with the ModelImage data.
      Parameters:
      kProgress - progress bar
      iProgress - progress bar increment

    • initImages

      private void initImages()
      Intializes the Textures and GraphicsImages used to render the ModelImage this VolumeImage represents.

    • initImagesColor

      private void initImagesColor()

    • initLUT

      private void initLUT()
      Create a new LUT for the input image.
      Parameters:
      kImage - ModelImage.

    • InitScale

      private void InitScale()
      Initialize the scale factors. Based on the ModelImage Volume.

    • ReadFromDisk

      private static ModelImage ReadFromDisk(String kImageName, String kDir)
      Reads an image from disk.
      Parameters:
      kImageName - image name
      kDir - directory
      Returns:
      ModelImage

    • readObject

      private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
      Throws:
      IOException
      ClassNotFoundException

    • update4D

      private void update4D()
      Go to the next 3D volume sub-image for the 4D animation. Updates the Textures and causes them to be reloaded onto the GPU.

    • UpdateImages

      private boolean UpdateImages(ModelImage kImage, WildMagic.LibGraphics.Rendering.Texture kOpacityTexture, WildMagic.LibGraphics.Rendering.GraphicsImage kOpacityMap, TransferFunction kTransfer)
      Called when the opacity transfer function changes. This function updates the Texture and causes the data to be reloaded onto the GPU.
      Parameters:
      kImage - the ModelImage the transfer function applies to.
      kOpacityTexture - the opacity Texture passed to the GPU
      kOpacityMap - the opacity data stored in the GraphicsImage
      kTransfer - the new transfer function.

    • getOpacityFn

      public TransferFunction getOpacityFn()

    • UpdateImages2

      private boolean UpdateImages2(ModelImage kImage, WildMagic.LibGraphics.Rendering.Texture kOpacityTexture, WildMagic.LibGraphics.Rendering.GraphicsImage kOpacityMap, TransferFunction kTransfer)
      Update the opacity transfer function.
      Parameters:
      kImage - the ModelImage the transfer function applies to.
      kOpacityTexture - the opacity Texture passed to the GPU
      kOpacityMap - the opacity data stored in the GraphicsImage
      kTransfer - the new transfer function.

    • writeObject

      private void writeObject(ObjectOutputStream out) throws IOException
      Throws:
      IOException