Class SoOrthoSlice

  • All Implemented Interfaces:
    SafeDisposable

    public class SoOrthoSlice
    extends SoSlice
    Ortho slice shape node. This node defines an ortho (axis aligned) slice along the X, Y, or Z axis of the volume data defined by an SoVolumeData node. The slice orientation and position are defined by the axis and sliceNumber fields.

    For a non-RGBA (scalar valued) volume, each voxel's RGBA value is determined by the current SoDataRange and SoTransferFunction. The current diffuse color and transparency (set, for example, with an SoMaterial node) modifies the appearance of the slice. This means that, for example, the current transparency can be used as an global alpha value to modulate the overall opacity of the slice. For an RGBA volume each voxel's RGBA value comes directly from the volume data.

    The interpolation field controls how the texture is interpolated.

    The alphaUse field (SoSlice) controls how the voxel's alpha component is used when drawing the slice.

    Optionally a bump mapping effect may be applied. Normal vectors are automatically computed from the data value gradient. The enableBumpMapping and bumpScale fields (SoSlice) control whether bump mapping is active and the intensity of the effect.

    Notes:

    • Drawing position:
      The SoOrthoSlice geometry passes through the center of the voxels in the specified slice. So, for example, an ortho slice with sliceNumber = 0 will be drawn one-half voxel size (on the slice axis) in from the bounding box of the volume. This is slightly different from SoVolumeSkin. A volume skin is approximately the same as six ortho slices, but each face of the skin is drawn at the outer edge of the voxel.
    • Transformation matrices:
      The volume size and orientation (like geometry) can be modified by transformation nodes in the scene graph and this in turn modifies the appearance of volume visualization nodes. However, the same transformation must be applied to the volume data node and all volume visualization nodes associated with that volume. So effectively any transformation nodes that affect the volume must be placed before the volume data node.
    • Picking:
      The entire slice is pickable, even where it is transparent as a result of the current transfer function. The SoOrthoSliceDetail class allows you to get the voxel position and value after picking.
    • Dragging:
      It is possible to interactively translate and rotate slices using an Open Inventor dragger, e.g. SoTranslate1Dragger. However the dragger's position in XYZ space must be converted to a slice number. For a dragger that is specific to ortho slices, see the class SoOrthoSliceDragger.
    • Interpolation:
      Interpolation is specified using the interpolation field. The default (LINEAR) does bi-linear interpolation between voxel values. The NEAREST value can be used to display individual voxels. For best image quality we recommend using the MULTISAMPLE_12 value.
    • Data range:
      By default VolumeViz maps the entire range of the voxel's data type (e.g. 0..65535 for unsigned short) into the colormap. This is often correct for byte (8 bit) voxels, but seldom correct for 16 bit voxels and never correct for floating point voxels. Use an SoDataRange node to specify the actual (or desired) range of data values to be mapped. Also use an SoDataRange node to implement brightness/contrast control like the Window/Level setting commonly used with medical images.
    • Clipping:
      Volume primitives can be clipped using a region of interest (SoROI), geometry (SoVolumeClippingGroup) and/or height fields (SoUniformGridClipping). They are also clipped by OpenGL clipping planes (SoClipPlane), but we recommend using the VolumeViz clipping nodes instead.
      Optionally, this node also defines a clipping plane. Similar to SoClipPlane, this clipping plane affects all subsequent geometry, including SoVolumeRender, but does not of course affect the ortho slice itself. The clipping and clippingSide fields control whether clipping is active and which half-space is clipped. Clipping side FRONT means that the clip plane (removes) clips away geometry in the positive direction on the slice axis.
    • Border:
      Border can be enabled with the enableBorder field, which allows to draw a border around the slice following volume boundary. However, the border is invisible when an SoROI (or SoROIManip) is used in the scene.
    • Material:
      The color of each voxel is modulated by the current diffuse color in the traversal state. The default diffuse color is 0.8,0.8,0.8. This results in full intensity values in the color map being displayed as 80% intensity. Therefore we recommend adding an SoMaterial node before the slice and setting its diffuseColor field to full white (1,1,1).
    • Transparency:

      • Typically the color map (SoTransferFunction) used for volume rendering (SoVolumeRender) assigns transparency (alpha < 1) to some voxel values. You can use the same color map for slice rendering, but note that the default value of the alphaUse field (since Open Inventor 10.0) is ALPHA_OPAQUE, meaning that alpha values in the color map are ignored. However, it does not affect the transparency assigned by an SoMaterial node.

      • If you want to adjust the overall transparency of the slice, set the alphaUse field to ALPHA_AS_IS, add an SoMaterial node and set its transparency field. Effectively a scale factor 1-transparency is applied to each voxel's alpha value.

      • Intersecting transparent slices cannot be rendered correctly by the basic blending transparency algorithms. To render this case correctly, set the transparency algorithm to SORTED_PIXEL using the viewer class or SoGLRenderAction.
    • Voxel edges:
      The edges of the voxels can also be rendered. See options in the SoVolumeRenderingQuality node.
    • Custom shaders:
      The current SoVolumeShader node, if any, allows custom shaders to be defined for special computation or rendering effects, including blending multiple volumes.
    • Large Slice mode:
      When the "large slice" mode is enabled (see SoSlice.largeSliceSupport), if all the required full resolution tiles have already been loaded, then the slice data is taken from LDM system memory cache as usual. But if some required tiles are not currently in memory, the required slice data will be loaded directly from the volume reader without loading the complete tiles. This reduces disk I/O and reduces the amount of system memory required to display the slice at full resolution, so larger (or more) slices can be displayed. The required tiles are then scheduled to be loaded asynchronously in case adjacent slices are displayed later. For example, loading a 1024x1024 SoOrthoSlice from an 8-bit dataset with 128x128x128 tiles would normally require loading 1024x1024x128 bytes of data (as complete tiles). With largeSliceSupport enabled, only 1024x1024 bytes (maximum) of data need to be loaded (in the worst case where no high resolution data is currently in memory).
    • Performance:
      • Tile size:
        For backward compatibility, the default tile size is still only 64. This is quite small for modern CPU/GPU hardware. The smaller the tile size, the larger the total number of tiles that must be managed by VolumeViz. This overhead can be significant, especially for operations that require reloading the data textures on the GPU, for example, changing the data range (SoDataRange). For smaller volumes, like 512^3, it can be efficient to set the tile size large enough to contain the entire volume. For very large volumes, larger tile sizes are efficient for SoVolumeRender but somewhat inefficient for slice rendering because complete tiles must be loaded even though the slice only uses a part of the data. Applications should experiment.
        For volumes stored in LDM file format, the tile size must be specified when the volume is converted to LDM (see SoConverter and the "-t" option). For other data formats the tile size can be specified using the SoVolumeData node's ldmResourceParameters field, but only after setting the filename field or calling the setReader() method.

      • LDM_USE_IN_MEM_COMPRESSION
        VolumeViz always manages data as "tiles", regardless of the data format. In many cases VolumeViz must create (or uncompress) the tiles at run time. These cases include in-memory volumes, any volume reader that does not implement the readTile() method (this includes all built-in formats except LDM, e.g. DICOM, SEGY, ...) and compressed LDM format files. If this variable is true (the default), VolumeViz only keeps a small cache of created/uncompressed tiles in CPU memory. If a tile's data is needed and that tile is not in the cache, the tile must be recreated. This overhead can be significant, especially for operations that require recreating all the data textures on the GPU, for example changing the data range (SoDataRange). We recommend setting this variable to false (see SoPreferences) unless saving CPU memory is critical.

      • Compressed textures
        For performance reasons, SoOrthoSlice accumulates small textures into a bigger one. When using compressed RGBA textures (via SoDataSet's field useCompressedTexture), this optimization cannot be done. If you want to favor performance rather than memory usage, you should disable compression (enabled by default if supported by the graphic card)
    • Medical data axes:
      The three standard axes (or viewing planes) are Axial, Coronal and Sagittal. How these axes correspond to the IJK axes in voxel space and the XYZ axes in 3D space depends on the data set. However DICOM volumes typically have LPS (Left, Posterior, Superior) orientation and in this case:
      • Axial is the Z axis
        i.e., toward the head (Superior) is the K / +Z / Axial axis.

      • Coronal is the Y axis
        i.e., toward the back of the body (Posterior) is the J / +Y / Coronal axis.

      • Sagittal is the X axis
        i.e., toward the left side of the body (Left) is the I / +X / Sagittal axis.

    EXAMPLE

    For simple data sets, a basic VolumeViz rendering could be achieved with only a few nodes: minimally an SoVolumeData node to identify the data set and one rendering node. However most data sets need at least some of the additional nodes shown here in order to get a correct and useful rendering. Most applications will need additional nodes to take advantage of region of interest, interaction, clipping and other VolumeViz features. Please consider the code shown here as simply a guideline and a starting point for exploring the many powerful features available in Open Inventor.

    Note that some of the property nodes (data, material, color map, etc) will typically be shared by multiple rendering nodes. In other words the volume usually only needs to be loaded once, using a single SoVolumeData node, then multiple slices and/or regions can be rendered using that data node.

    Also note that this example is for a data volume, where each voxel can be considered a discrete sample from a continuous data field and interpolation should be used to compute values between voxel centers. If you are rendering a label volume, then each voxel is an "id" assigning that voxel to a specific material, object, etc. In this case, set the interpolation field to NEAREST to disable interpolation.

     // Default setting can be a performance bottleneck
     SoPreferences.setValue( "LDM_USE_IN_MEM_COMPRESSION", "0" );
     
     // Keeps volume viz separate from geometry
     SoSeparator volSep = new SoSeparator();
       root.addChild(volSep);
     
     // Loads volume data
     SoVolumeData volData = new SoVolumeData();
       volData.fileName.setValue( "$OIVJHOME/data/VolumeViz/3DHead.vol" );
       volSep.addChild( volData );
     
     // Sets range of data values to visualize.
     // Not required for 8-bit voxels, critical for larger data types.
     // The getMinMax() call may be expensive for non-LDM file formats.
     SoDataRange volRange = new SoDataRange();
       if (volData.getDatumSize() > 1) {
         double[] minmax;
         minmax = volData.getDoubleMinMax();
         volRange.min.setValue( minmax[0] );
         volRange.max.setValue( minmax[1] );
       }
       volSep.addChild( volRange );
     
     // Loads opaque intensity ramp
     SoTransferFunction volTF = new SoTransferFunction();
       volTF.predefColorMap.setValue( SoTransferFunction.PredefColorMaps.INTENSITY );
       volSep.addChild( volTF );
     
     // Displays slice at full intensity
     SoMaterial volMat = new SoMaterial();
       volMat.diffuseColor.setValue( 1, 1, 1 );
       volSep.addChild( volMat );
     
     // Removes tile boundary artifacts while moving.
     SoVolumeShader volShader = new SoVolumeShader();
       volShader.interpolateOnMove.setValue( true );
       volSep.addChild( volShader );
     
     // Displays a Z axis slice at center of volume
     SoOrthoSlice slice = new SoOrthoSlice();
       SbVec3i32 voldim = volData.data.getSize();
       slice.axis.setValue( SoOrthoSlice.AxisType.Z );
       slice.sliceNumber.setValue( voldim.getZ() / 2 );
       slice.interpolation.setValue( SoVolumeShape.Interpolations.MULTISAMPLE_12 );
       volSep.addChild( slice );

    File format/default:

    OrthoSlice {

      sliceNumber 0
      axis Z
      interpolation LINEAR
      alphaUse ALPHA_BINARY
      useRGBA false
      clipping false
      clippingSide BACK
      alternateRep NULL
      enableBumpMapping false
      bumpScale 1.0
      enableBorder false
      borderColor 0.84 0.43 0.02
      borderWidth 2.0
      enableImage true
    }

    Action behavior:

    SoGLRenderAction
    Draws a textured rectangle based on current SoVolumeData, SoTransferFunction, and SoROI nodes. Sets: SoClipPlaneElement

    SoGetBoundingBoxAction
    Computes the bounding box that encloses the slice.

    See Also:
    SoDataRange, SoObliqueSlice, SoOrthoSliceDragger, SoROI, SoSlice, SoTransferFunction, SoVolumeData
    • Field Detail

      • sliceNumber

        public final SoSFUInt32 sliceNumber
        Slice number.
      • clippingSide

        public final SoSFEnum<SoOrthoSlice.ClippingSides> clippingSide
        Specifies the clipping side. . Default is BACK. Clipping side FRONT means that the clip plane (removes) clips away geometry in the positive direction on the slice axis. BACK means that the clip plane clips away geometry in the negative direction on the slice axis.
        <TABLE border=0 cellspacing=0 cellpadding=5>
           <TR><TD valign=_top> These figures show an ortho slice clipping a data volume.
        
              Right:
                - #alphaUse = ALPHA_BINARY <BR>
                - #interpolation = LINEAR
        
              Bottom left:
                - #alphaUse = ALPHA_OPAQUE <BR>
                - #interpolation = LINEAR
        
              Bottom right:
                - #alphaUse = ALPHA_BINARY <BR>
                - #interpolation = NEAREST
        
           <TD valign=_top> @image html binarylinear.jpg
           <TR><TD valign=_top> @image html opaquelinear.jpg
           <TD valign=_top> @image html binarynearest.jpg
        </TABLE>
      • clipping

        public final SoSFBool clipping
        Activate/deactivate a clipping plane on a per-slice basis. Optionally, this node also defines a clipping plane. Similar to SoClipPlane, this clipping plane affects all subsequent geometry, including SoVolumeRender, but does not of course affect the ortho slice itself. The clippingSide field controls which half-space is clipped.
      • enableBorder

        public final SoSFBool enableBorder
        Enables drawing the border. Default is false.

        Since:
        Open Inventor 10.10

      • borderColor

        public final SoSFColor borderColor
        Border color. Default is [0.84, 0.43, 0.02] (orange luminance 55%).

        Since:
        Open Inventor 10.10

      • borderWidth

        public final SoSFFloat borderWidth
        Border width in pixels. Default is 2. For more information about borderWidth units: see SoDrawStyle.lineWidth

        Since:
        Open Inventor 10.10

      • enableImage

        public final SoSFBool enableImage
        Enables drawing the slice image. Default is true. Note that setting this field to false makes the slice image invisible, but the slice is still detectable by picking if the border is enabled.

        Example of a typical use case : The folling code shows how to use a boolean engine to disable the image rendering while dragging.

         SoBoolOperation engine = new SoBoolOperation();
         engine.a.connectFrom(dragger.isActive);
         orthoslice.enableImage.connectFrom(engine.inverse);

        Another typical usecase is if you want to display the slice image in a 2D view and also show only the slice position in a 3D view (without the slice image).

        Since:
        Open Inventor 10.10

    • Constructor Detail

      • SoOrthoSlice

        public SoOrthoSlice()
        Constructor.