java.lang.Object

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

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

public class VolumeSurface extends VolumeObject

Field Summary

Fields

Modifier and Type

Field

Description

private WildMagic.LibFoundation.Mathematics.ColorRGBA[]

m_akBackupColor

Backup of the per-vertex colors.

private WildMagic.LibGraphics.SceneGraph.Node[]

m_akGeodesicNodes

Contains geodesic display components.

private String[]

m_akUnitsLabel

private boolean

m_bFirstRender

private boolean

m_bPainted

Set to true when the surface has been painted.

private boolean

m_bTextureOn

Set to true when texture mapping is on.

private float

m_fBlend

private float

m_fSurfaceArea

Surface area.

private float

m_fVolume

Surface volume.

private int

m_iCurrentGeodesic

Current displayed geodesic component.

private WildMagic.LibGraphics.SceneGraph.BoxBV

m_kBoundingBox

private WildMagic.LibFoundation.Mathematics.Vector3f

m_kCenter

Center of surface.

private WildMagic.LibFoundation.Mathematics.Vector3f

m_kCenterScanner

private SurfaceLightingEffect

m_kLightShader

Surface shader effect.

private SurfaceLightingEffect

m_kLightShaderTransparent

private WildMagic.LibGraphics.Rendering.MaterialState

m_kMaterial

Surface material properties.

private WildMagic.LibFoundation.Mathematics.Vector3f

m_kMaxBB

private WildMagic.LibGraphics.SceneGraph.TriMesh

m_kMesh

TriMesh

private WildMagic.LibFoundation.Mathematics.Vector3f

m_kMinBB

private float

m_kOpacity

Surface opacity value.

private BitSet

m_kSurfaceMask

private SurfaceState

m_kSurfaceState

private BitSet

m_kVolumeMask

private VolumePreRenderEffect

m_kVolumePreShader

ShaderEffect for the plane bounding-boxes.

private VolumePreRenderEffect

m_kVolumePreShaderTransparent

Fields inherited from class gov.nih.mipav.view.renderer.WildMagic.Render.VolumeObject
m_bDisplay, m_bPickable, m_bTransparent, m_fVolumeDiv, m_fVolumeMult, m_fX, m_fY, m_fZ, m_kAlpha, m_kAlphaTransparency, m_kCull, m_kDeleteList, m_kLocalScale, m_kPolygonOffset, m_kResolutions, m_kScene, m_kTranslate, m_kVolumeImageA, m_kVolumeImageB, m_kVolumeScale, m_kVolumeTrans, m_kWireframe, m_kZBuffer, m_kZBufferTransparency
Constructor Summary

Constructors

Constructor

Description

VolumeSurface(VolumeImage[] images, WildMagic.LibGraphics.Rendering.Texture colormap, WildMagic.LibFoundation.Mathematics.Vector3f kTranslate, float fX, float fY, float fZ, SurfaceState kSurface, boolean bComputeSurfaceMask, boolean isFileCoords)

VolumeSurface(VolumeImage kImageA, VolumeImage kImageB, WildMagic.LibFoundation.Mathematics.Vector3f kTranslate, float fX, float fY, float fZ, SurfaceState kSurface)

Create a new VolumeSurface with the VolumeImage parameter.

VolumeSurface(VolumeImage kImageA, VolumeImage kImageB, WildMagic.LibFoundation.Mathematics.Vector3f kTranslate, float fX, float fY, float fZ, SurfaceState kSurface, boolean isFileCoords)

VolumeSurface(VolumeImage kImageA, VolumeImage kImageB, WildMagic.LibFoundation.Mathematics.Vector3f kTranslate, float fX, float fY, float fZ, SurfaceState kSurface, boolean bComputeSurfaceMask, boolean isFileCoords)
Method Summary

Modifier and Type

Method

Description

void

AddGeodesic(WildMagic.LibGraphics.SceneGraph.Geometry kMesh, int iGroup)

Add a new geodesic component to the surface.

void

Blend(float fValue)

Set object blend value.

private HashSet[]

buildConnections()

Builds a list of cross-references, so that connections[i] contains all the vertices that are connected to vertex at i.

private void

calcVolumeMask(BitSet mask, ModelImage kOutputImage, WildMagic.LibFoundation.Mathematics.Vector3f[] directions, int xMin, int xMax, int yMin, int yMax, int zMin, int zMax, int iDimX, int iDimY)

private void

ComputeCenter()

Compute the center of the surface.

private float

computeMeanEdgeLength(HashMap kEMap)

Compute the average length of all the edges in the triangle mesh.

float

ComputeSurfaceArea()

Calculate the surface mesh area.

static ModelImage

computeSurfaceImage(WildMagic.LibGraphics.SceneGraph.TriMesh mesh, ModelImage image)

private static ModelImage

computeSurfaceImage(WildMagic.LibGraphics.SceneGraph.TriMesh mesh, ModelImage image, float volume, WildMagic.LibFoundation.Mathematics.Vector3f trans, WildMagic.LibFoundation.Mathematics.Vector3f scale)

BitSet

computeSurfaceMask()

Computes a volume mask of the triangle mesh surface.

private static void

computeSurfaceMask(BitSet mask, WildMagic.LibGraphics.SceneGraph.TriMesh mesh, ModelImage image, float volume, WildMagic.LibFoundation.Mathematics.Vector3f trans, WildMagic.LibFoundation.Mathematics.Vector3f scale, int start, int stop)

static BitSet

computeSurfaceMask(WildMagic.LibGraphics.SceneGraph.TriMesh mesh, ModelImage image)

private static BitSet

computeSurfaceMask(WildMagic.LibGraphics.SceneGraph.TriMesh mesh, ModelImage image, float volume, WildMagic.LibFoundation.Mathematics.Vector3f trans, WildMagic.LibFoundation.Mathematics.Vector3f scale)

private void

computeVertexInformation(float[] afParams, float fMeanEdgeLength, WildMagic.LibFoundation.Mathematics.Vector3f[] akVNormal, WildMagic.LibFoundation.Mathematics.Vector3f[] akVMean, WildMagic.LibFoundation.System.UnorderedSetInt[] akAdjacent, WildMagic.LibFoundation.Mathematics.Vector3f[] akSTangent, WildMagic.LibFoundation.Mathematics.Vector3f[] akSNormal, float[] afCurvature)

Let V[i] be a vertex in the triangle mesh.

private void

computeVertexNormals(WildMagic.LibFoundation.Mathematics.Vector3f[] akVNormal)

Compute the vertex normals of the triangle mesh.

float

ComputeVolume()

Calculates volume of triangle mesh.

private void

CreateScene()

Creates the scene graph.

BitSet

createVolumeMask()

Creates a BitSet mask that is the volume enclosed by the triangle mesh.

void

dispose(WildMagic.LibGraphics.Rendering.Renderer kRenderer)

Delete local memory.

void

Dropper(WildMagic.LibGraphics.Collision.PickRecord kRecord, WildMagic.LibFoundation.Mathematics.ColorRGBA rkDropperColor, WildMagic.LibFoundation.Mathematics.Vector3f rkPickPoint)

Paint can support.

void

Erase(WildMagic.LibGraphics.Rendering.Renderer kRenderer, WildMagic.LibGraphics.Collision.PickRecord kRecord, int iBrushSize)

Erase paint.

void

EraseAllPaint(WildMagic.LibGraphics.Rendering.Renderer kRenderer)

Erase all paint.

WildMagic.LibFoundation.Mathematics.Vector3f

GetCenter()

Return center of the surface.

WildMagic.LibFoundation.Mathematics.ColorRGB

GetColor()

private static float

getIntersectX(WildMagic.LibFoundation.Mathematics.Vector3f kV0, WildMagic.LibFoundation.Mathematics.Vector3f kV1, WildMagic.LibFoundation.Mathematics.Vector3f 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 static float

getIntersectY(WildMagic.LibFoundation.Mathematics.Vector3f kV0, WildMagic.LibFoundation.Mathematics.Vector3f kV1, WildMagic.LibFoundation.Mathematics.Vector3f 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 static float

getIntersectZ(WildMagic.LibFoundation.Mathematics.Vector3f kV0, WildMagic.LibFoundation.Mathematics.Vector3f kV1, WildMagic.LibFoundation.Mathematics.Vector3f 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.

WildMagic.LibGraphics.Rendering.MaterialState

GetMaterial()

Return the surface material properties.

WildMagic.LibGraphics.SceneGraph.TriMesh

GetMesh()

Return the TriMesh object (if, any) associated with this object.

WildMagic.LibFoundation.Mathematics.Vector3f[]

getMinMax()

Returns the min/max bounding box coordinates for the mesh in volume-index coordinates.

String

GetName()

Return the name of this object.

float

GetOpacity()

Return the surface opacity value.

float

GetSurfaceArea()

Return the surface area.

String

GetSurfaceAreaString()

Return the surface area.

float

GetVolume()

Return the volume of this surface.

String

GetVolumeString()

Return the volume of this surface.

private void

initBoundingBox()

Initializes the bounding box for the mesh.

void

Paint(WildMagic.LibGraphics.Rendering.Renderer kRenderer, WildMagic.LibGraphics.Collision.PickRecord kRecord, WildMagic.LibFoundation.Mathematics.ColorRGBA kPaintColor, int iBrushSize)

Painting support.

void

RemoveAllGeodesic()

Removes all geodesic components from the given surface.

void

RemoveGeodesic(int iNode, int iGroup)

Removes the specific geodesic component from the given surface.

void

Render(WildMagic.LibGraphics.Rendering.Renderer kRenderer, WildMagic.LibGraphics.SceneGraph.Culler kCuller, boolean bPreRender, boolean bSolid)

Render the object.

void

Render(WildMagic.LibGraphics.Rendering.Renderer kRenderer, WildMagic.LibGraphics.SceneGraph.Culler kCuller, SurfaceClipEffect[] kEffect, int index, float fClipM1, float fClipP1)

Render the object.

void

ReplaceGeodesic(WildMagic.LibGraphics.SceneGraph.TriMesh kMesh)

When the Geodesic object cuts the mesh along an open curve, the old mesh changes, but does not need to be deleted and no new mesh needs to be added.

private void

scaleMesh(float fValue, HashSet[] connections)

void

SetClip(int iWhich, float data, boolean bEnable)

Sets axis-aligned clipping for the VolumeShaderEffect.

void

SetClipArb(float[] afEquation, boolean bEnable)

Sets arbitrary clipping for the VolumeShaderEffect.

void

SetClipArbInv(float[] afEquation, boolean bEnable)

Sets arbitrary clipping for the VolumeShaderEffect.

void

SetClipEye(float[] afEquation, boolean bEnable)

Sets eye clipping for the VolumeShaderEffect.

void

SetClipEyeInv(float[] afEquation, boolean bEnable)

Sets inverse-eye clipping for the VolumeShaderEffect.

void

SetClipping(boolean bClip)

Enables/disables surface clipping for the per-pixel shader.

void

SetColor(WildMagic.LibFoundation.Mathematics.ColorRGB kColor, boolean bUpdate)

Set the object color.

void

SetImageNew(ModelImage kImage)

Sets the ModelImage to use as an alternative to the volume ModelImage for surface texturing.

void

SetLight(String kLightType, float[] afType)

Sets the light for the EllipsoidsShader.

void

SetLUTNew(ModelStorageBase kLUT)

Sets the LUT to use as an alternative to the volume lut for surface texturing.

void

SetMaterial(WildMagic.LibGraphics.Rendering.MaterialState kMaterial, boolean bUpdate)

Set the surface material properties

void

SetOpacity(float opacity)

Set the surface opacity properties

void

SetPerPixelLighting(WildMagic.LibGraphics.Rendering.Renderer kRenderer, boolean bOn)

Sets the lighting shader to be per-pixel or per-vertex.

void

SetSurfaceTexture(boolean bOn, boolean bUseNewImage, boolean bUseNewLUT)

Sets the surface texture on/off.

void

SetTranslateVolumeCoords(WildMagic.LibFoundation.Mathematics.Vector3f position)

void

SetTranslateVolumeCoords(WildMagic.LibFoundation.Mathematics.Vector3f position, boolean compute)

void

smoothMesh(int iteration, float alpha, boolean volumeLimit, float volumePercent)

Smooth mesh.

void

smoothThree(int iteration, float lambda, float mu)

Smooth mesh.

void

smoothTwo(int iterations, float fStiffness, boolean volumeLimit, float volumePercent)

Derived from the first 2 of the 3 components of AlgorithmBrainExtraction Note that m_fStiffness does not increase and then decrease as in AlgorithmBrainExtraction but instead remains constant.

boolean

testIntersection(WildMagic.LibFoundation.Mathematics.Vector3f kP0, boolean bUseMask)

Test if the input point is inside the triangle mesh.

boolean

testIntersection(WildMagic.LibFoundation.Mathematics.Vector3f kP0, WildMagic.LibFoundation.Mathematics.Vector3f kP1, boolean bUseMask, boolean bPrint)

Tests if the line segment specified by the two input points intersects the mesh.

private boolean

testIntersectionMask(WildMagic.LibFoundation.Mathematics.Vector3f kPos)

private boolean

testIntersections(WildMagic.LibFoundation.Mathematics.Vector3f kP0, WildMagic.LibFoundation.Mathematics.Vector3f kP1)

Tests if the line segment determined by the two input end-points intersects the mesh.

static boolean

testIntersections(WildMagic.LibGraphics.SceneGraph.TriMesh mesh, WildMagic.LibFoundation.Mathematics.Vector3f origin, WildMagic.LibFoundation.Mathematics.Line3f[] akLines)

Test if the input point is inside the mesh.

void

ToggleGeodesicPathDisplay(int iWhich)

Switches between different ways of displaying the geodesic path (Euclidean, Geodesic, or Mesh).

private float

update2(int i, float[] afCurvature, float fStiffness, float[] afParam)

Compute the coefficient of the surface normal for the update of the mesh vertex V[i] in the SNormal[i] direction.

private void

updateMesh(HashMap kEMap, WildMagic.LibFoundation.Mathematics.Vector3f[] akVNormal, WildMagic.LibFoundation.Mathematics.Vector3f[] akVMean, WildMagic.LibFoundation.System.UnorderedSetInt[] akAdjacent, WildMagic.LibFoundation.Mathematics.Vector3f[] akSTangent, WildMagic.LibFoundation.Mathematics.Vector3f[] akSNormal, float[] afCurvature, float fStiffness)

The heart of the segmentation.

Methods inherited from class gov.nih.mipav.view.renderer.WildMagic.Render.VolumeObject
GetBackface, getDepth, GetDisplay, GetPickable, GetPolygonMode, GetScene, getTexCoord, GetTranslate, localToScannerCoords, localToVolumeCoords, PostRender, scale, SetBackface, SetDisplay, SetFrontface, setImageB, SetPickable, SetPolygonMode, SetTranslate, Translate, volumeToLocalCoords

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details
- m_kVolumePreShader
  
  private VolumePreRenderEffect m_kVolumePreShader
  
  ShaderEffect for the plane bounding-boxes.
- m_kVolumePreShaderTransparent
  
  private VolumePreRenderEffect m_kVolumePreShaderTransparent
- m_kMesh
  
  private WildMagic.LibGraphics.SceneGraph.TriMesh m_kMesh
  
  TriMesh
- m_kMaterial
  
  private WildMagic.LibGraphics.Rendering.MaterialState m_kMaterial
  
  Surface material properties.
- m_kOpacity
  
  private float m_kOpacity
  
  Surface opacity value.
- m_kLightShader
  
  private SurfaceLightingEffect m_kLightShader
  
  Surface shader effect.
- m_kLightShaderTransparent
  
  private SurfaceLightingEffect m_kLightShaderTransparent
- m_fVolume
  
  private float m_fVolume
  
  Surface volume.
- m_fSurfaceArea
  
  private float m_fSurfaceArea
  
  Surface area.
- m_kCenter
  
  private WildMagic.LibFoundation.Mathematics.Vector3f m_kCenter
  
  Center of surface.
- m_kCenterScanner
  
  private WildMagic.LibFoundation.Mathematics.Vector3f m_kCenterScanner
- m_akBackupColor
  
  private WildMagic.LibFoundation.Mathematics.ColorRGBA[] m_akBackupColor
  
  Backup of the per-vertex colors.
- m_bPainted
  
  private boolean m_bPainted
  
  Set to true when the surface has been painted.
- m_bTextureOn
  
  private boolean m_bTextureOn
  
  Set to true when texture mapping is on.
- m_akGeodesicNodes
  
  private WildMagic.LibGraphics.SceneGraph.Node[] m_akGeodesicNodes
  
  Contains geodesic display components.
- m_iCurrentGeodesic
  
  private int m_iCurrentGeodesic
  
  Current displayed geodesic component.
- m_fBlend
  
  private float m_fBlend
- m_kSurfaceState
  
  private SurfaceState m_kSurfaceState
- m_akUnitsLabel
  
  private String[] m_akUnitsLabel
- m_kBoundingBox
  
  private WildMagic.LibGraphics.SceneGraph.BoxBV m_kBoundingBox
- m_kMinBB
  
  private WildMagic.LibFoundation.Mathematics.Vector3f m_kMinBB
- m_kMaxBB
  
  private WildMagic.LibFoundation.Mathematics.Vector3f m_kMaxBB
- m_bFirstRender
  
  private boolean m_bFirstRender
- m_kVolumeMask
  
  private BitSet m_kVolumeMask
- m_kSurfaceMask
  
  private BitSet m_kSurfaceMask
Constructor Details
- VolumeSurface
  
  public VolumeSurface(VolumeImage kImageA, VolumeImage kImageB, WildMagic.LibFoundation.Mathematics.Vector3f kTranslate, float fX, float fY, float fZ, SurfaceState kSurface)
  
  Create a new VolumeSurface with the VolumeImage parameter.
  
  Parameters:
  
  kImageA - the VolumeImage containing shared data and textures for rendering.
  
  kTranslate - translation in the scene-graph for this object.
  
  fX - the size of the volume in the x-dimension (extent * resolutions)
  
  fY - the size of the volume in the y-dimension (extent * resolutions)
  
  fZ - the size of the volume in the z-dimension (extent * resolutions)
  
  kVolumeImageB - second VolumeImage.
- VolumeSurface
  
  public VolumeSurface(VolumeImage kImageA, VolumeImage kImageB, WildMagic.LibFoundation.Mathematics.Vector3f kTranslate, float fX, float fY, float fZ, SurfaceState kSurface, boolean bComputeSurfaceMask, boolean isFileCoords)
- VolumeSurface
  
  public VolumeSurface(VolumeImage[] images, WildMagic.LibGraphics.Rendering.Texture colormap, WildMagic.LibFoundation.Mathematics.Vector3f kTranslate, float fX, float fY, float fZ, SurfaceState kSurface, boolean bComputeSurfaceMask, boolean isFileCoords)
- VolumeSurface
  
  public VolumeSurface(VolumeImage kImageA, VolumeImage kImageB, WildMagic.LibFoundation.Mathematics.Vector3f kTranslate, float fX, float fY, float fZ, SurfaceState kSurface, boolean isFileCoords)
Method Details
- AddGeodesic
  
  public void AddGeodesic(WildMagic.LibGraphics.SceneGraph.Geometry kMesh, int iGroup)
  
  Add a new geodesic component to the surface.
  
  Parameters:
  
  iGroup - the display group to add to.
  
  kNew - the new geodesic component.
- Blend
  
  public void Blend(float fValue)
  
  Description copied from class: VolumeObject
  
  Set object blend value.
  
  Overrides:
  
  Blend in class VolumeObject
  
  Parameters:
  
  fValue - blend value.
- ComputeSurfaceArea
  
  public float ComputeSurfaceArea()
  
  Calculate the surface mesh area. Each surface mesh is composed of triangles. Calculate the surface area from the summation of the each triangle area. Based on the Area by Stokes' Theorem. Area(S) = 1/2 * Normal dot ( Sum from i = 0 to n-1 of ( V1 cross V2) ) ==> Area(S) = 1/2 * ( Sum from i = 0 to n-1 of ( Normal dot ( V1 cross V2) ) )
  
  Returns:
  
  float
- ComputeVolume
  
  public float ComputeVolume()
  Calculates volume of triangle mesh. The mesh consists of triangle faces and encloses a bounded region. Face j, 0 invalid input: '<'= j invalid input: '<'= n-1 has verticies P0, P1, and P2. The order of the verticies is counterclockwise as you view the face from outside the bounded region. The mesh is closed and manifold in the sense that each edge is shared by exactly two triangles. The volume of the bounded region is:
  
  V = 1/6 (Sum from j=0 to n-1 of {P0 dot P1 cross P2})
  The terms of the summation can be positive, negative, or zero. The term is positive if the face is counterclockwise when viewed from the zero vector, or zero if the face appears to be a line segment when viewed from the zero vector. NOTICE THAT THERE ARE 2 DIFFERENT DEFINITIONS OF COUNTERCLOCKWISE, COUNTERCLOCKWISE AS VIEWED FROM OUTSIDE THE BOUNDED REGION AND COUNTERCLOCKWISE AS VIEWED FROM THE ZERO VECTOR.
  A 3D image on a rectangular lattice contains points (i0, i1, i2) where 0 invalid input: '<'= ik invalid input: '<' Bk for specified dimension bounds Bk. These are just indicies. The actual physical measurements are provided by scaling factors Dk > 0. For example, a 256x256x256 MRI has B0 = B1 = B2 = 256. If each voxel is 1 mm in x, 1 mm in y, and 5 mm in z, then D0 = D1 = 1 and D2 = 5. The 3D image encloses a rectangular region [0,C0] x [0,C1] x [0,C2] in physical space where Ck = Dk*Bk. In the example, C0 = D0*B0 = 256 mm in x, C1 = D1*B1 = 256 mm in y, and C2 = D2*B2 = 1280 mm in z. Volume calculations are required to use physical measurements. In the example, volume will be in cubic millimeters.
  
  The surface extraction is performed by mapping [0,C0] x [0,C1] x [0,C2] into [-1,1] x [-1,1] x [-1,1] using uniform scaling. This is done to keep the floating point values within order 1 to avoid the floating point errors that occur if you were to use the index values themselves. The topology of a level surface is invariant under any scaling (not just uniform), but the continuous level of detail algorithm for triangle decimation does edge collapses based on various geometric measurements of the mesh representing the level surface. The geometric measurements are not invariant under nonuniform scaling. Map the image into a cube using uniform scaling so that the triangle collapse order is invariant. The uniform scaling is done so that the largest image dimension [0,M] is mapped to [-1,1]. The other ranges are mapped to intervals of the form [-L,L) where L invalid input: '<' 1. If (i0,i1,i2) is in [0,B0) x [0,B1) x [0,B2), the corresponding (x0,x1,x2) in [-1,1) is:
  
  2*Dk*ik - Ck xk = ------------ max{C0,C1,C2}
  
  However, we want to map from [0,Bk) to an inclusive interval [-Rk,Rk], where 0 invalid input: '<' Rk invalid input: '<' 1 and Rk = 1 - Dk/max{C0,C1,C2}. This ensures that surfaces begin in the center of a voxel rather than at the (0,0,0) corner of the voxel. The problem is easiest to see in the Z direction: a surface that should cover the full Z range will end before the last slice. Therefore, the formula should be:
  
  2*Dk*ik - Ck + Dk xk = ----------------- max{C0,C1,C2}
  
  Once a closed manifold triangle mesh is extracted, the problem is now to compute its volume in physical space. Note that ik are indicies in the original image, but the true physical length that is measured (relative to other index locations) is yk = Dk*ik. Any triangle mesh (x0,x1,x2) must be mapped to (y0,y1,y2) before the volume calculation. The mapping is:
  
  max{C0,C1,C2}*xk + Ck - Dk yk = -------------------------- 2
  
  The volume calculations use the previously mentioned formula where the P points are the (y0,y1,y2) values.
  Returns:
  
  The volume of the surface.
- dispose
  
  public void dispose(WildMagic.LibGraphics.Rendering.Renderer kRenderer)
  
  Delete local memory.
  
  Overrides:
  
  dispose in class VolumeObject
- Dropper
  
  public void Dropper(WildMagic.LibGraphics.Collision.PickRecord kRecord, WildMagic.LibFoundation.Mathematics.ColorRGBA rkDropperColor, WildMagic.LibFoundation.Mathematics.Vector3f rkPickPoint)
  
  Description copied from class: VolumeObject
  
  Paint can support.
  
  Overrides:
  
  Dropper in class VolumeObject
  
  Parameters:
  
  kRecord - pick record.
  
  rkPickPoint - , picked point.
- Erase
  
  public void Erase(WildMagic.LibGraphics.Rendering.Renderer kRenderer, WildMagic.LibGraphics.Collision.PickRecord kRecord, int iBrushSize)
  
  Description copied from class: VolumeObject
  
  Erase paint.
  
  Overrides:
  
  Erase in class VolumeObject
  
  Parameters:
  
  kRenderer - Renderer.
  
  kRecord - pick record.
  
  iBrushSize - brush size.
- EraseAllPaint
  
  public void EraseAllPaint(WildMagic.LibGraphics.Rendering.Renderer kRenderer)
  
  Erase all paint.
  
  Parameters:
  
  kRenderer - renderer.
- GetCenter
  
  public WildMagic.LibFoundation.Mathematics.Vector3f GetCenter()
  
  Return center of the surface.
  
  Returns:
  
  center of the surface.
- GetMaterial
  
  public WildMagic.LibGraphics.Rendering.MaterialState GetMaterial()
  
  Return the surface material properties.
  
  Returns:
  
  surface material properties.
- GetMesh
  
  public WildMagic.LibGraphics.SceneGraph.TriMesh GetMesh()
  
  Description copied from class: VolumeObject
  
  Return the TriMesh object (if, any) associated with this object.
  
  Overrides:
  
  GetMesh in class VolumeObject
  
  Returns:
  
  the TriMesh object (if, any) associated with this object.
- GetName
  
  public String GetName()
  
  Description copied from class: VolumeObject
  
  Return the name of this object.
  
  Overrides:
  
  GetName in class VolumeObject
  
  Returns:
  
  name of this object.
- GetOpacity
  
  public float GetOpacity()
  
  Return the surface opacity value.
  
  Returns:
  
  surface opacity value.
- GetSurfaceArea
  
  public float GetSurfaceArea()
  
  Return the surface area.
  
  Returns:
  
  surface area.
- GetSurfaceAreaString
  
  public String GetSurfaceAreaString()
  
  Return the surface area.
  
  Returns:
  
  surface area.
- GetVolume
  
  public float GetVolume()
  
  Return the volume of this surface.
  
  Returns:
  
  volume of this surface.
- GetVolumeString
  
  public String GetVolumeString()
  
  Return the volume of this surface.
  
  Returns:
  
  volume of this surface.
- Paint
  
  public void Paint(WildMagic.LibGraphics.Rendering.Renderer kRenderer, WildMagic.LibGraphics.Collision.PickRecord kRecord, WildMagic.LibFoundation.Mathematics.ColorRGBA kPaintColor, int iBrushSize)
  
  Description copied from class: VolumeObject
  
  Painting support.
  
  Overrides:
  
  Paint in class VolumeObject
  
  Parameters:
  
  kRenderer - Renderer.
  
  kRecord - pick record.
  
  kPaintColor - paint color.
  
  iBrushSize - brush size.
- RemoveAllGeodesic
  
  public void RemoveAllGeodesic()
  
  Removes all geodesic components from the given surface.
- RemoveGeodesic
  
  public void RemoveGeodesic(int iNode, int iGroup)
  
  Removes the specific geodesic component from the given surface.
  
  Parameters:
  
  iNode -
  
  iGroup -
- Render
  
  public void Render(WildMagic.LibGraphics.Rendering.Renderer kRenderer, WildMagic.LibGraphics.SceneGraph.Culler kCuller, boolean bPreRender, boolean bSolid)
  
  Description copied from class: VolumeObject
  
  Render the object.
  
  Specified by:
  
  Render in class VolumeObject
  
  Parameters:
  
  kRenderer - the OpenGLRenderer object.
  
  kCuller - the Culler object.
- Render
  
  public void Render(WildMagic.LibGraphics.Rendering.Renderer kRenderer, WildMagic.LibGraphics.SceneGraph.Culler kCuller, SurfaceClipEffect[] kEffect, int index, float fClipM1, float fClipP1)
  
  Render the object.
  
  Parameters:
  
  kRenderer - the OpenGLRenderer object.
  
  kCuller - the Culler object.
- ReplaceGeodesic
  
  public void ReplaceGeodesic(WildMagic.LibGraphics.SceneGraph.TriMesh kMesh)
  
  When the Geodesic object cuts the mesh along an open curve, the old mesh changes, but does not need to be deleted and no new mesh needs to be added. This function allows the Geodesic object to replace the original mesh with the sliced mesh in the surface renderer. ReplaceMesh is also used to undo cutting operations.
  
  Parameters:
  
  kNew - TriMesh new surface mesh
- SetClip
  
  public void SetClip(int iWhich, float data, boolean bEnable)
  
  Sets axis-aligned clipping for the VolumeShaderEffect.
  
  Parameters:
  
  afClip - the clipping parameters for axis-aligned clipping.
- SetClipArb
  
  public void SetClipArb(float[] afEquation, boolean bEnable)
  
  Sets arbitrary clipping for the VolumeShaderEffect.
  
  Parameters:
  
  afEquation - the arbitrary-clip plane equation.
- SetClipArbInv
  
  public void SetClipArbInv(float[] afEquation, boolean bEnable)
  
  Sets arbitrary clipping for the VolumeShaderEffect.
  
  Parameters:
  
  afEquation - the arbitrary-clip plane equation.
- SetClipEye
  
  public void SetClipEye(float[] afEquation, boolean bEnable)
  
  Sets eye clipping for the VolumeShaderEffect.
  
  Parameters:
  
  afEquation - the eye clipping equation.
- SetClipEyeInv
  
  public void SetClipEyeInv(float[] afEquation, boolean bEnable)
  
  Sets inverse-eye clipping for the VolumeShaderEffect.
  
  Parameters:
  
  afEquation - the inverse-eye clipping equation.
- SetClipping
  
  public void SetClipping(boolean bClip)
  
  Enables/disables surface clipping for the per-pixel shader.
  
  Parameters:
  
  bClip - surface clipping on/off.
- SetColor
  
  public void SetColor(WildMagic.LibFoundation.Mathematics.ColorRGB kColor, boolean bUpdate)
  
  Description copied from class: VolumeObject
  
  Set the object color.
  
  Overrides:
  
  SetColor in class VolumeObject
  
  Parameters:
  
  kColor - new color.
- GetColor
  
  public WildMagic.LibFoundation.Mathematics.ColorRGB GetColor()
- SetImageNew
  
  public void SetImageNew(ModelImage kImage)
  
  Sets the ModelImage to use as an alternative to the volume ModelImage for surface texturing.
  
  Parameters:
  
  kImage - the alternate ModelImage to use for the surface texture.
- SetLight
  
  public void SetLight(String kLightType, float[] afType)
  
  Description copied from class: VolumeObject
  
  Sets the light for the EllipsoidsShader.
  
  Overrides:
  
  SetLight in class VolumeObject
  
  Parameters:
  
  kLightType - the name of the light to set (Light0, Light1, etc.)
  
  afType - the type of light (Ambient = 0, Directional = 1, Point = 2, Spot = 3).
- SetLUTNew
  
  public void SetLUTNew(ModelStorageBase kLUT)
  
  Sets the LUT to use as an alternative to the volume lut for surface texturing.
  
  Parameters:
  
  kLUT - the new LUT.
  
  kRGBT - the new ModelRGB (for color images).
- SetMaterial
  
  public void SetMaterial(WildMagic.LibGraphics.Rendering.MaterialState kMaterial, boolean bUpdate)
  
  Set the surface material properties
  
  Parameters:
  
  kMaterial - surface material properties.
- SetOpacity
  
  public void SetOpacity(float opacity)
  
  Set the surface opacity properties
  
  Parameters:
  
  kMaterial - surface opacity value.
- SetPerPixelLighting
  
  public void SetPerPixelLighting(WildMagic.LibGraphics.Rendering.Renderer kRenderer, boolean bOn)
  
  Sets the lighting shader to be per-pixel or per-vertex.
  
  Parameters:
  
  kRenderer - OpenGL renderer.
  
  bOn - turns per-pixel lighting on/off.
- SetSurfaceTexture
  
  public void SetSurfaceTexture(boolean bOn, boolean bUseNewImage, boolean bUseNewLUT)
  
  Sets the surface texture on/off.
  
  Parameters:
  
  bUseNewImage - indicates which volume to use as the texture.
  
  bUseNewLUT - indicates which LUT to use.
  
  bTextureOn - texture on/off
- SetTranslateVolumeCoords
  
  public void SetTranslateVolumeCoords(WildMagic.LibFoundation.Mathematics.Vector3f position)
- SetTranslateVolumeCoords
  
  public void SetTranslateVolumeCoords(WildMagic.LibFoundation.Mathematics.Vector3f position, boolean compute)
- smoothMesh
  
  public void smoothMesh(int iteration, float alpha, boolean volumeLimit, float volumePercent)
  Smooth mesh. The formula can be found in "The Visualization Toolkit" by Will Schoeder, Ken Martin, and Bill Lorensen, p. 389. Mesh smoothing moves the verticies of the mesh closer to an average of the points. Each point is moved so that it is the average of the points around it. The formula is:
  xi+1 = xi + (alpha * (Sum from j=0 to n of {xj - xi}))
  where xi+1 is the new point, xi is the orginal point, and the xjs are points that are connected to xi. Alpha is some smoothing factor between .01 and .10. This formula is run for a number of iterations to obtain a smooth mesh. Usually the iterations will be between 50 and 100.
  Parameters:
  
  iteration - Number of times to run smoothing formula on data set.
  
  alpha - Smoothing factor.
  
  volumeLimit - if true stop iterations when the present volume is volumePercent or more different from the initial
  
  volumePercent - percentage from initial volume for stopping iterations
- smoothThree
  
  public void smoothThree(int iteration, float lambda, float mu)
  
  Smooth mesh. This method smoothes without shrinking by 2 Gaussian smoothing steps. First, a Gaussian smoothing is performed with a positive scale factor lambda. Second, a Gaussian smoothing is performed with a negative scale factor mu, which is greater in magnitude than lambda. To produce a significant smoothing, these steps must be repeated a number of times. 3 references for this smoothing: 1.) Curve and Surface Smoothing Without Shrinkage by Gabriel Taubin, Technical Report RC-19536, IBM Research, April, 1994. (also in Proceedings, Fifth International Conference on Computer Vision, pages 852-857, June, 1995). 2.) A Signal Processing Approach to Fair Surface Design by Gabriel Taubin, Computer Graphics, pages 351-358, August, 1995 (Proceedings SIGGRAPH '95). 3.) Optimal Surface Smoothing as Filter Design by Gabriel Taubin, Tong Zhang, and Gene Golub, IBM Research Report RC-20404 (#90237). Usually the iterations will be between 30 and 100.
  
  Parameters:
  
  iteration - Number of times to run smoothing formula on data set.
  
  lambda - positive scale factor
  
  mu - negative scale factor
  
  pVisible - if true display progress bar Require: 0 invalid input: '<' lambda invalid input: '<' -mu (1/lambda) + (1/mu) invalid input: '<' 2
- smoothTwo
  
  public void smoothTwo(int iterations, float fStiffness, boolean volumeLimit, float volumePercent)
  
  Derived from the first 2 of the 3 components of AlgorithmBrainExtraction Note that m_fStiffness does not increase and then decrease as in AlgorithmBrainExtraction but instead remains constant. This is because the change in m_fStiffness only applies to the third component of AlgorithmBrainExtraction which uses image intensities.
  
  Parameters:
  
  iterations - DOCUMENT ME!
  
  volumeLimit - if true stop iterations when the present volume is volumePercent or more different from the initial
  
  volumePercent - percentage from initial volume for stopping iterations
  
  m_fStiffness - DOCUMENT ME!
- ToggleGeodesicPathDisplay
  
  public void ToggleGeodesicPathDisplay(int iWhich)
  
  Switches between different ways of displaying the geodesic path (Euclidean, Geodesic, or Mesh).
  
  Parameters:
  
  iWhich - the type of display.
- createVolumeMask
  
  public BitSet createVolumeMask()
  
  Creates a BitSet mask that is the volume enclosed by the triangle mesh. This function is not accurate if the mesh is not closed, however it will still return a mask.
  
  Returns:
- calcVolumeMask
  
  private void calcVolumeMask(BitSet mask, ModelImage kOutputImage, WildMagic.LibFoundation.Mathematics.Vector3f[] directions, int xMin, int xMax, int yMin, int yMax, int zMin, int zMax, int iDimX, int iDimY)
- initBoundingBox
  
  private void initBoundingBox()
  
  Initializes the bounding box for the mesh. The volume bounding box is in volume-index coordinats.
- getMinMax
  
  public WildMagic.LibFoundation.Mathematics.Vector3f[] getMinMax()
  
  Returns the min/max bounding box coordinates for the mesh in volume-index coordinates.
  
  Returns:
  
  the min/max bounding box coordinates for the mesh in volume-index coordinates.
- testIntersection
  
  public boolean testIntersection(WildMagic.LibFoundation.Mathematics.Vector3f kP0, boolean bUseMask)
  
  Test if the input point is inside the triangle mesh.
  
  Parameters:
  
  kP0 - input point.
  
  Returns:
  
  true if the point is inside the mesh, false otherwise.
- testIntersection
  
  public boolean testIntersection(WildMagic.LibFoundation.Mathematics.Vector3f kP0, WildMagic.LibFoundation.Mathematics.Vector3f kP1, boolean bUseMask, boolean bPrint)
  
  Tests if the line segment specified by the two input points intersects the mesh.
  
  Parameters:
  
  kP0 - first end-point of the line sement in volume-index coordinates.
  
  kP1 - second end-point of the line sement in volume-index coordinates.
  
  bPrint - flag to print debugging printouts.
  
  Returns:
  
  true if the line segment intersects the mesh, false otherwise.
- testIntersectionMask
  
  private boolean testIntersectionMask(WildMagic.LibFoundation.Mathematics.Vector3f kPos)
- buildConnections
  
  private HashSet[] buildConnections()
  
  Builds a list of cross-references, so that connections[i] contains all the vertices that are connected to vertex at i.
- ComputeCenter
  
  private void ComputeCenter()
  
  Compute the center of the surface.
- computeMeanEdgeLength
  
  private float computeMeanEdgeLength(HashMap kEMap)
  
  Compute the average length of all the edges in the triangle mesh.
- computeVertexInformation
  
  private void computeVertexInformation(float[] afParams, float fMeanEdgeLength, WildMagic.LibFoundation.Mathematics.Vector3f[] akVNormal, WildMagic.LibFoundation.Mathematics.Vector3f[] akVMean, WildMagic.LibFoundation.System.UnorderedSetInt[] akAdjacent, WildMagic.LibFoundation.Mathematics.Vector3f[] akSTangent, WildMagic.LibFoundation.Mathematics.Vector3f[] akSNormal, float[] afCurvature)
  
  Let V[i] be a vertex in the triangle mesh. This function computes VMean[i], the average of the immediate neighbors of V[i]. Define S[i] = VMean[i] - V[i]. The function also computes a surface normal SNormal[i], the component of S[i] in the vertex normal direction. STangent[i] = S[i] - SNormal[i] is computed as an approximation to a tangent to the surface. Finally, Curvature[i] is an approximation of the surface curvature at V[i].
- computeVertexNormals
  
  private void computeVertexNormals(WildMagic.LibFoundation.Mathematics.Vector3f[] akVNormal)
  
  Compute the vertex normals of the triangle mesh. Each vertex normal is the unitized average of the non-unit triangle normals for those triangles sharing the vertex.
- CreateScene
  
  private void CreateScene()
  
  Creates the scene graph.
- scaleMesh
  
  private void scaleMesh(float fValue, HashSet[] connections)
- update2
  
  private float update2(int i, float[] afCurvature, float fStiffness, float[] afParam)
  
  Compute the coefficient of the surface normal for the update of the mesh vertex V[i] in the SNormal[i] direction. See BrainExtraction.pdf for a description of the update.
  
  Parameters:
  
  i - the index of the vertex to update
  
  Returns:
  
  the coefficient of SNormal[i] for the update
- updateMesh
  
  private void updateMesh(HashMap kEMap, WildMagic.LibFoundation.Mathematics.Vector3f[] akVNormal, WildMagic.LibFoundation.Mathematics.Vector3f[] akVMean, WildMagic.LibFoundation.System.UnorderedSetInt[] akAdjacent, WildMagic.LibFoundation.Mathematics.Vector3f[] akSTangent, WildMagic.LibFoundation.Mathematics.Vector3f[] akSNormal, float[] afCurvature, float fStiffness)
  
  The heart of the segmentation. This function is responsible for the evolution of the triangle mesh that approximates the brain surface. The update has a tangential component, a surface normal component, and a vertex normal component for each vertex in the mesh. The first two components control the geometry of the mesh. The last component is based on the MRI data itself. See BrainExtraction.pdf for a detailed description of the update terms.
- testIntersections
  
  public static boolean testIntersections(WildMagic.LibGraphics.SceneGraph.TriMesh mesh, WildMagic.LibFoundation.Mathematics.Vector3f origin, WildMagic.LibFoundation.Mathematics.Line3f[] akLines)
  
  Test if the input point is inside the mesh.
  
  Parameters:
  
  origin - point to test for inside/outside mesh.
  
  directions - set of randomised directions for counting mesh-intersections (odd = inside, even = outside).
  
  Returns:
  
  true when the point is inside the mesh, false otherwise.
- testIntersections
  
  private boolean testIntersections(WildMagic.LibFoundation.Mathematics.Vector3f kP0, WildMagic.LibFoundation.Mathematics.Vector3f kP1)
  
  Tests if the line segment determined by the two input end-points intersects the mesh.
  
  Parameters:
  
  kP0 - end-point of the line segment.
  
  kP1 - end-point of the line segment.
  
  Returns:
  
  true if the line segment intersects the mesh.
- computeSurfaceMask
  
  public BitSet computeSurfaceMask()
  
  Computes a volume mask of the triangle mesh surface. The BitSet mask volume has the same volume dimensions as the current image. The mask is used to show the surface-plane intersections in the slice views.
  
  Parameters:
  
  mesh - triangle mesh to convert to a volume mask representation.
  
  Returns:
  
  BitSet mask, which is set to true wherever the triangle mesh intersects the volume voxel.
- computeSurfaceMask
  
  public static BitSet computeSurfaceMask(WildMagic.LibGraphics.SceneGraph.TriMesh mesh, ModelImage image)
- computeSurfaceMask
  
  private static BitSet computeSurfaceMask(WildMagic.LibGraphics.SceneGraph.TriMesh mesh, ModelImage image, float volume, WildMagic.LibFoundation.Mathematics.Vector3f trans, WildMagic.LibFoundation.Mathematics.Vector3f scale)
- computeSurfaceMask
  
  private static void computeSurfaceMask(BitSet mask, WildMagic.LibGraphics.SceneGraph.TriMesh mesh, ModelImage image, float volume, WildMagic.LibFoundation.Mathematics.Vector3f trans, WildMagic.LibFoundation.Mathematics.Vector3f scale, int start, int stop)
- computeSurfaceImage
  
  public static ModelImage computeSurfaceImage(WildMagic.LibGraphics.SceneGraph.TriMesh mesh, ModelImage image)
- computeSurfaceImage
  
  private static ModelImage computeSurfaceImage(WildMagic.LibGraphics.SceneGraph.TriMesh mesh, ModelImage image, float volume, WildMagic.LibFoundation.Mathematics.Vector3f trans, WildMagic.LibFoundation.Mathematics.Vector3f scale)
- getIntersectX
  
  private static float getIntersectX(WildMagic.LibFoundation.Mathematics.Vector3f kV0, WildMagic.LibFoundation.Mathematics.Vector3f kV1, WildMagic.LibFoundation.Mathematics.Vector3f 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 static float getIntersectY(WildMagic.LibFoundation.Mathematics.Vector3f kV0, WildMagic.LibFoundation.Mathematics.Vector3f kV1, WildMagic.LibFoundation.Mathematics.Vector3f 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 static float getIntersectZ(WildMagic.LibFoundation.Mathematics.Vector3f kV0, WildMagic.LibFoundation.Mathematics.Vector3f kV1, WildMagic.LibFoundation.Mathematics.Vector3f 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

Class VolumeSurface

Field Summary

Fields inherited from class gov.nih.mipav.view.renderer.WildMagic.Render.VolumeObject

Constructor Summary

Method Summary

Methods inherited from class gov.nih.mipav.view.renderer.WildMagic.Render.VolumeObject

Methods inherited from class java.lang.Object

Field Details

m_kVolumePreShader

m_kVolumePreShaderTransparent

m_kMesh

m_kMaterial

m_kOpacity

m_kLightShader

m_kLightShaderTransparent

m_fVolume

m_fSurfaceArea

m_kCenter

m_kCenterScanner

m_akBackupColor

m_bPainted

m_bTextureOn

m_akGeodesicNodes

m_iCurrentGeodesic

m_fBlend

m_kSurfaceState

m_akUnitsLabel

m_kBoundingBox

m_kMinBB

m_kMaxBB

m_bFirstRender

m_kVolumeMask

m_kSurfaceMask

Constructor Details

VolumeSurface

VolumeSurface

VolumeSurface

VolumeSurface

Method Details

AddGeodesic

Blend

ComputeSurfaceArea

ComputeVolume

dispose

Dropper

Erase

EraseAllPaint

GetCenter

GetMaterial

GetMesh

GetName

GetOpacity

GetSurfaceArea

GetSurfaceAreaString

GetVolume

GetVolumeString

Paint

RemoveAllGeodesic

RemoveGeodesic

Render

Render

ReplaceGeodesic

SetClip

SetClipArb

SetClipArbInv

SetClipEye

SetClipEyeInv

SetClipping

SetColor

GetColor

SetImageNew

SetLight

SetLUTNew

SetMaterial

SetOpacity

SetPerPixelLighting

SetSurfaceTexture

SetTranslateVolumeCoords

SetTranslateVolumeCoords

smoothMesh