com.openinventor.volumeviz.nodes

Class SoOrthoSlice

java.lang.Object

com.openinventor.inventor.Inventor

com.openinventor.inventor.misc.SoBase

com.openinventor.inventor.fields.SoFieldContainer

com.openinventor.inventor.nodes.SoNode

com.openinventor.inventor.nodes.SoShape

com.openinventor.ldm.nodes.SoLdmShape

com.openinventor.volumeviz.nodes.SoVolumeShape

com.openinventor.volumeviz.nodes.SoSlice

com.openinventor.volumeviz.nodes.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 a 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 than 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.
• 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. If you want to use the same color map for slice rendering, but render the slice completely opaque, set the alphaUse field to ALPHA_OPAQUE. This overrides the alpha values in the color map (or an RGBA volume). However it does not affect transparency assigned using an SoMaterial node.
    
    
  • If you want to adjust the overall transparency of the slice, add an SoMaterial node and set its transparency field (keeping alphaUse set to ALPHA_AS_IS). 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_PIXELS_BLEND (or similar value) 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 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 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" );
 
 // Keep volume viz separate from geometry
 SoSeparator volSep = new SoSeparator();
   root.addChild(volSep);
 
 // Load volume data
 SoVolumeData volData = new SoVolumeData();
   volData.fileName.setValue( "$OIVJHOME/data/VolumeViz/3DHead.vol" );
   volSep.addChild( volData );
 
 // Set 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 );
 
 // Load opaque intensity ramp
 SoTransferFunction volTF = new SoTransferFunction();
   volTF.predefColorMap.setValue( SoTransferFunction.PredefColorMaps.INTENSITY );
   volSep.addChild( volTF );
 
 // Display slice at full intensity
 SoMaterial volMat = new SoMaterial();
   volMat.diffuseColor.setValue( 1, 1, 1 );
   volSep.addChild( volMat );
 
 // Remove tile boundary artifacts while moving.
 SoVolumeShader volShader = new SoVolumeShader();
   volShader.interpolateOnMove.setValue( true );
   volSep.addChild( volShader );
 
 // Display 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

}

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

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	SoOrthoSlice.AxisType Slice Axis (see discussion of medical data axes in the class description)
static class	SoOrthoSlice.ClippingSides Clipping Side mode.

Nested classes/interfaces inherited from class com.openinventor.volumeviz.nodes.SoSlice

SoSlice.AlphaUses

Nested classes/interfaces inherited from class com.openinventor.volumeviz.nodes.SoVolumeShape

SoVolumeShape.Compositions, SoVolumeShape.Interpolations

Nested classes/interfaces inherited from class com.openinventor.inventor.nodes.SoShape

SoShape.ShapeTypes

Nested classes/interfaces inherited from class com.openinventor.inventor.Inventor

Inventor.ConstructorCommand

Field Summary

Fields

Modifier and Type	Field and Description
SoSFEnum<SoOrthoSlice.AxisType>	axis Slice axis (X, Y, or Z).
static int	BACK Deprecated. Use SoOrthoSlice.ClippingSides.BACK instead.
SoSFBool	clipping Activate/deactivate a clipping plane on a per-slice basis.
SoSFEnum<SoOrthoSlice.ClippingSides>	clippingSide Specify the clipping side.
static int	FRONT Deprecated. Use SoOrthoSlice.ClippingSides.FRONT instead.
SoSFUInt32	sliceNumber Slice number.
static int	X Deprecated. Use SoOrthoSlice.AxisType.X instead.
static int	Y Deprecated. Use SoOrthoSlice.AxisType.Y instead.
static int	Z Deprecated. Use SoOrthoSlice.AxisType.Z instead.

Fields inherited from class com.openinventor.volumeviz.nodes.SoSlice

ALPHA_AS_IS, ALPHA_BINARY, ALPHA_OPAQUE, alphaUse, alternateRep, bumpScale, enableBumpMapping, largeSliceSupport, useRGBA

Fields inherited from class com.openinventor.volumeviz.nodes.SoVolumeShape

ALPHA_BLENDING, composition, COMPOSITION_LAST, CUBIC, interpolation, LINEAR, MAX_INTENSITY, MIN_INTENSITY, MULTISAMPLE_12, NEAREST, SUM_INTENSITY, TRILINEAR

Fields inherited from class com.openinventor.inventor.nodes.SoShape

boundingBoxIgnoring, LINES, POINTS, POLYGONS, TEXT

Fields inherited from class com.openinventor.inventor.Inventor

VERBOSE_LEVEL, ZeroHandle

Constructor Summary

Constructors

Constructor and Description
SoOrthoSlice() Constructor.

Method Summary

Methods inherited from class com.openinventor.ldm.nodes.SoLdmShape

intersect

Methods inherited from class com.openinventor.inventor.nodes.SoShape

getShapeType, isPrimitiveRestartAvailable, isPrimitiveRestartAvailable

Methods inherited from class com.openinventor.inventor.nodes.SoNode

affectsState, callback, copy, copy, distribute, doAction, getAlternateRep, getBoundingBox, getByName, getMatrix, getPrimitiveCount, getRenderUnitID, GLRender, GLRenderBelowPath, GLRenderInPath, GLRenderOffPath, grabEventsCleanup, grabEventsSetup, handleEvent, isBoundingBoxIgnoring, isOverride, pick, rayPick, search, setOverride, touch, write

Methods inherited from class com.openinventor.inventor.fields.SoFieldContainer

copyFieldValues, copyFieldValues, enableNotify, fieldsAreEqual, get, getAllFields, getEventIn, getEventOut, getField, getFieldName, hasDefaultValues, isNotifyEnabled, set, setToDefaults

Methods inherited from class com.openinventor.inventor.misc.SoBase

dispose, getEXTERNPROTO, getName, getPROTO, isDisposable, isSynchronizable, setName, setSynchronizable

Methods inherited from class com.openinventor.inventor.Inventor

getAddress, getNativeResourceHandle, startInternalThreads, stopInternalThreads

Methods inherited from class java.lang.Object

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

Field Detail

X

@Deprecated
public static final int X

Deprecated. Use SoOrthoSlice.AxisType.X instead.

Y

@Deprecated
public static final int Y

Deprecated. Use SoOrthoSlice.AxisType.Y instead.

Z

@Deprecated
public static final int Z

Deprecated. Use SoOrthoSlice.AxisType.Z instead.

FRONT

@Deprecated
public static final int FRONT

Deprecated. Use SoOrthoSlice.ClippingSides.FRONT instead.

BACK

@Deprecated
public static final int BACK

Deprecated. Use SoOrthoSlice.ClippingSides.BACK instead.

sliceNumber

public final SoSFUInt32 sliceNumber

Slice number.

axis

public final SoSFEnum<SoOrthoSlice.AxisType> axis

Slice axis (X, Y, or Z). . Default is Z.

clippingSide

public final SoSFEnum<SoOrthoSlice.ClippingSides> clippingSide

Specify 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.

These figures show an ortho slice clipping a data volume. Right: alphaUse = ALPHA_BINARY interpolation = LINEAR Bottom left: alphaUse = ALPHA_OPAQUE interpolation = LINEAR Bottom right: alphaUse = ALPHA_BINARY interpolation = NEAREST

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.

Constructor Detail

SoOrthoSlice

public SoOrthoSlice()

Constructor.