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

Class SurfaceRender

java.lang.Object
java.awt.Component
java.awt.Canvas
javax.media.j3d.Canvas3D
gov.nih.mipav.view.renderer.J3D.VolumeCanvas3D
gov.nih.mipav.view.renderer.J3D.RenderViewBase
gov.nih.mipav.view.renderer.J3D.surfaceview.SurfaceRender
All Implemented Interfaces:
com.sun.j3d.utils.behaviors.mouse.MouseBehaviorCallback, ViewImageUpdateInterface, ActionListener, KeyListener, ImageObserver, MenuContainer, PropertyChangeListener, Serializable, EventListener, Accessible, ChangeListener
Direct Known Subclasses:
FlythruRender, SurfaceView
public class SurfaceRender extends RenderViewBase implements KeyListener, PropertyChangeListener
Frame that holds the surface renderer. This frame is only possible to activate if a three dimensional image is loaded. The image shows up in the frame as the three planes, with an axial view, a coronal view, and a sagittal view. The user can slide these planes up and down and can turn them on and off. The user can also load in surfaces created from the original image. These 3D surfaces will appear in the proper place within the three image planes. There are many options for viewing the surfaces. Additionally, the user can change the view mode, so that the mouse causes the view to "fly". The user can then record the different mouse actions and play them back.
See Also:
  • invalid reference 
    ViewJComponentSurfaceImage
  • invalid reference 
    JDialogSurface
  • invalid reference 
    JDialogView
  • invalid reference 
    JDialogMouseRecorder
  • Serialized Form

  • Field Details

    • serialVersionUID

      private static final long serialVersionUID
      Use serialVersionUID for interoperability.
      See Also:

    • ARTERIAL_SEG

      public static final int ARTERIAL_SEG
      Value which indicates a voxel that is part of the arterial vasculature tree.
      See Also:

    • VEINOUS_SEG

      public static final int VEINOUS_SEG
      Value which indicates a voxel in the segmenation image that is part of the veinous vasculature tree.
      See Also:

    • VASCULATURE_SEG

      public static final int VASCULATURE_SEG
      Value which indicates a voxel in the segmenation image that is part of the vasculature (arterial or veinous).
      See Also:

    • TUMOR_SEG

      public static final int TUMOR_SEG
      Value which indicates a voxel in the segmenation image that is part of the tumor.
      See Also:

    • BONE_SEG

      public static final int BONE_SEG
      Value which indicates a bone in the image.
      See Also:

    • ENTRY_POINT

      public static final int ENTRY_POINT
      Value which indicates the probe entry point color.
      See Also:

    • isViewTextureAligned

      protected boolean isViewTextureAligned
      Flag to indicate whether the view volume texture is aligned or not.

    • rayBasedRender

      protected VolumeRenderer rayBasedRender
      Raycast based renderer reference, raycast renderer or shear warp renderer.

    • isTriPlanarVolView

      boolean isTriPlanarVolView
      Mode is tri-planar volume view or not.

    • boxPanel

      private JPanelDisplay boxPanel
      Dialog to turn bounding box of surface renderer on and off, and to change the color of the frame.

    • boxSlices

      private final ViewJComponentBoxSlice[] boxSlices
      The frame around the AXIAL, CORONAL, SAGITTAL slices:

    • boxSliceVertices

      private javax.vecmath.Vector3f[][] boxSliceVertices
      The transformed boxSlices frames used to sample the volume data along diagonal slices:

    • clipPanel

      private JPanelClip clipPanel
      Dialog to turn the clipping palne box on and off.

    • triSliceImages

      private final ViewJComponentTriSliceImage[] triSliceImages
      ImageRenderers for the AXIAL, CORONAL, SAGITTAL slices:

    • triSliceGeometry

      private final javax.media.j3d.Shape3D[] triSliceGeometry

    • componentVolImage

      private ViewJComponentSurfaceVolume componentVolImage
      Volume image object.

    • cubicBehaviorBG

      private javax.media.j3d.BranchGroup cubicBehaviorBG
      The cubic roational behavior branch group.

    • cubicBG

      private javax.media.j3d.BranchGroup cubicBG
      Cubic branch group.

    • cubicRotate

      private com.sun.j3d.utils.behaviors.mouse.MouseRotate cubicRotate
      Cubic mouse rotation behavior.

    • cubicTG

      private javax.media.j3d.TransformGroup cubicTG
      Cubic transform group.

    • currentTransform

      private javax.media.j3d.Transform3D currentTransform
      Current transform matrix.

    • currentTransformType

      private int currentTransformType
      Current transform changes type.

    • first6ClipPlane

      private boolean first6ClipPlane
      flag indicate the first time 6 clipping plane branch switch.

    • firstClipArbi

      private boolean firstClipArbi
      flag indicate the first time arbitrary clipping plane branch switch.

    • geodesicPanel

      private JPanelGeodesic geodesicPanel
      Geodesic panel.

    • imageA

      private ModelImage imageA
      Current image A.

    • imageB

      private ModelImage imageB
      Current image B.

    • imageVolBufferA

      private float[] imageVolBufferA
      Buffer that holds image A volume data.

    • imageVolBufferB

      private float[] imageVolBufferB
      Buffer that holds image B volume data.

    • isEntryPoint

      private boolean isEntryPoint
      Flag indicates that probe rotate around the entry point or not.

    • m_bRenderModeLighting

      private boolean m_bRenderModeLighting
      Flag set when texture volume is being rendered using lights.

    • m_dOriginalScreenScale

      private double m_dOriginalScreenScale
      Zoomfactor, zooming in screen scale space, and is relative to original position, this stores that original position:.

    • m_kObjBoxSliceProbe_TG

      private final javax.media.j3d.TransformGroup[] m_kObjBoxSliceProbe_TG
      TransformGroup[] used to rotate the AXIAL, CORONAL, SAGITTAL slice BOXES:

    • m_kObjPlaneProbe_TG

      private final javax.media.j3d.TransformGroup[] m_kObjPlaneProbe_TG
      TransformGroup[] used to rotate the AXIAL, CORONAL, SAGITTAL slice PLANES:

    • m_kProbeTransform

      private javax.media.j3d.Transform3D m_kProbeTransform
      The Transform3D used to position the planes based on the Probe position and angle. The planes are rotates about the intersection between the probe and the plane, which may or may not be in the center of the plane. This transform allows non-origin rotations by conactenating the translation to the origin, rotation, and translation matricies into one transform, which is used to set the Transforms for the TransformGroups above and also to sample the ModelImage data on the diagonal slice:

    • m_kSoftwareLightSet

      private SoftwareLightSet m_kSoftwareLightSet
      Used to compute software lighting of composite texture volume.

    • m_kSoftwareMaterial

      private SoftwareMaterial m_kSoftwareMaterial
      DOCUMENT ME!

    • mousePanel

      private JPanelMouse mousePanel
      Dialog for recording and playing back mouse events.

    • mouseRotateBehavior

      private MouseRotateExt mouseRotateBehavior
      Mouse Rotate behavior.

    • mouseTranslateBehavior

      private com.sun.j3d.utils.behaviors.mouse.MouseTranslate mouseTranslateBehavior
      Mouse Translate behavior.

    • mouseZoomBehavior

      private com.sun.j3d.utils.behaviors.mouse.MouseZoom mouseZoomBehavior
      Mouse Zoom behavior.

    • myEyePoint

      private final javax.vecmath.Point3d myEyePoint
      Initial center viewing point of the image.

    • objBoxSlices_BG

      private final javax.media.j3d.BranchGroup[] objBoxSlices_BG
      BranchGroup[] containing the slice BOXES:

    • objTransSlices_TG

      private final javax.media.j3d.TransformGroup[] objTransSlices_TG
      Group dictating how the XY plane is translated.

    • objPlane_BG

      private final javax.media.j3d.BranchGroup[] objPlane_BG
      BranchGroup[] containing the image planes.

    • parallelRotation

      private boolean parallelRotation
      Parallel rotation flag.

    • parallelScaleT3D

      private javax.media.j3d.Transform3D parallelScaleT3D
      Transformation matrix.

    • parent

      private ViewJFrameBase parent
      Controls for the image. ViewJFrameVolumeView

    • probePanel

      private JPanelProbe probePanel
      Dialog for loading and displaying probes.

    • resols

      private float[] resols
      Resolutions of image A.

    • rotationCount

      private int rotationCount
      fix one bug from threading.

    • sculptorPanel

      private JPanelSculptor sculptorPanel
      Sculptor panel.

    • segmentationImage

      private ModelImage segmentationImage
      Image with areas marked with values indicating that they are special tissue types (vessels, etc).

    • slicePanel

      private JPanelSlices slicePanel
      Dialog to turn the slices control box on and off.

    • surfacePanel

      private JPanelSurface surfacePanel
      Dialog for loading and displaying surfaces.

    • surfaceTexturePanel

      private JPanelSurfaceTexture surfaceTexturePanel
      Panel for displaying the SurfaceTexture interface:

    • switchGroup

      private javax.media.j3d.Switch switchGroup
      Tri planar view and the 3D texture volume view switch group.

    • rotationAlpha

      private javax.media.j3d.Alpha rotationAlpha

    • sliceTransparency

      private final javax.media.j3d.TransparencyAttributes[] sliceTransparency
      ViewJComponentTriSliceImages -> Texture2D transparency values:

    • texture

      private VolumeTexture texture
      Reference to 3D texture node for the volume.

    • sliceTextures

      private final javax.media.j3d.Texture2D[] sliceTextures
      ViewJComponentTriSliceImages -> Texture2D to display the image slices:

    • sliceImageComponent2D

      private final javax.media.j3d.ImageComponent2D[] sliceImageComponent2D
      Each Texture2D adds a ImageComponent2D:

    • m_kRFACoordMaps

      javax.vecmath.Vector4f[][] m_kRFACoordMaps
      Texture mapping for the RFA probe rotation:

    • transformCubic

      private javax.media.j3d.Transform3D transformCubic
      Cubic tansform3D.

    • transformNode3d

      private javax.media.j3d.Transform3D transformNode3d
      Setup the initial position of the image, added to ScenerootTG transform group.

    • view

      private javax.media.j3d.View view
      View object in rendering a three dimensional scene from one viewpoint.

    • volBG

      private javax.media.j3d.BranchGroup volBG
      Volume branch group.

    • volOpacityPanel

      private JPanelVolumeOpacity volOpacityPanel
      Volume opacity control dialog.

    • volRenderBG

      private javax.media.j3d.BranchGroup volRenderBG
      Volume render branch group.

    • volRenderNode

      private NodeVolumeTextureRender volRenderNode
      Add here.

    • volRenderOG

      private javax.media.j3d.OrderedGroup volRenderOG
      Volume render order group, specify the rendering order.

    • volumeDisplayMode3D

      private boolean volumeDisplayMode3D
      If true display 3D volume as a 3D texture map or 2D array of texture maps. If false display 3 orthogonal image planes.

    • xBox

      private float xBox
      Numbers dicatating the sizes of the planes based on the extents and resolutions of the image.

    • yBox

      private float yBox
      Numbers dicatating the sizes of the planes based on the extents and resolutions of the image.

    • zBox

      private float zBox
      Numbers dicatating the sizes of the planes based on the extents and resolutions of the image.

    • maxBox

      private float maxBox
      Numbers dicatating the sizes of the planes based on the extents and resolutions of the image.

    • xDim

      private int xDim
      Dimensions of image A.

    • yDim

      private int yDim
      Dimensions of image A.

    • zDim

      private int zDim
      Dimensions of image A.

    • tDim

      private int tDim
      Dimensions of image A.

  • Constructor Details

    • SurfaceRender

      public SurfaceRender(ModelImage _imageA, ModelImage _imageB, GraphicsConfiguration _config)
      Constructor called by the VirtualEndoscopyView. Used for instantiation.
      Parameters:
      _imageA - ModelImage imageA
      _imageB - ModelImage imageB always null
      _config - GraphicsConfiguration graphics configuration

    • SurfaceRender

      public SurfaceRender(ModelImage _imageA, ModelLUT _LUTa, ModelImage _imageB, ModelLUT _LUTb, ViewJFrameBase _parent, GraphicsConfiguration _config, ViewJProgressBar _pBar)
      Makes a frame and puts the three image planes into it. Creates the scene graph which dictates the behavior of the image planes and surfaces. Initializes the surface dialog and the mouse recorder dialog, so that this original view is saved. When the user opens these dialogs, they have already been created; they are just set to visible.
      Parameters:
      _imageA - First image to display, cannot be null.
      _LUTa - LUT of the imageA (if null grayscale LUT is constructed).
      _imageB - Second loaded image, may be null.
      _LUTb - LUT of the imageB, may be null.
      _parent - Frame base reference.
      _config - configuration reference.
      _pBar - progress bar

  • Method Details

    • actionPerformed

      public void actionPerformed(ActionEvent event)
      Calls various methods depending on the action.
      • Surface - opens the surface dialog
      • View - opens the view control dialog
      • Mouse - opens the mouse recorder dialog
      • About - displays a message about this renderer
      • Exit - sets variables to null and disposes of this frame
      • X, Y, Z checkboxes - toggles the appropriate image planes on or off
      Specified by:
      actionPerformed in interface ActionListener
      Parameters:
      event - Event that triggered function.

    • addBoxSlice

      private void addBoxSlice(int orientation)
      Adds the slice frame for slice of the given orientation to the scene graph. It is necessary to make a new branch group and transform group because otherwise there is a RestrictedAccessException.
      Parameters:
      orientation - the slice to add: AXIAL, CORONAL, or SAGITTAL

    • addCubicControl

      public void addCubicControl()
      Attach cubic control branch group.

    • autoCapture

      public void autoCapture()
      Overrides the parent autoCapture method. Camera use this method to take snapshot automatically.
      Overrides:
      autoCapture in class RenderViewBase

    • cleanMouseRecorder

      public void cleanMouseRecorder()
      Clean mouse recorder for any existing event items.

    • close

      public void close()
      Closes the image.

    • configureVolumeFrame

      public void configureVolumeFrame()
      Constructs main frame structures for 3 image planes. Makes the LUT if necessary, then sets up the buffer arrays appropriately and calls the constructors for the three image planes.

    • cropClipVolume

      public void cropClipVolume()
      Crop the region of the clipped volume.

    • detachVolRender

      public void detachVolRender()
      Detach volume render branch group.

    • disableClipping

      public void disableClipping()
      Diable all the six clipping planes at a time.

    • dispatchSavedEvent

      public void dispatchSavedEvent(EventObject event)
      Dispatches event to appropriate object.
      Parameters:
      event - Event to dispatch.

    • disposeLocal

      public void disposeLocal(boolean flag)
      Sets all variables to null, disposes, and garbage collects.
      Parameters:
      flag - DOCUMENT ME!

    • drawRFAPoint

      public void drawRFAPoint(javax.vecmath.Point3f kPoint)
      Called from the parent class when the Probe Entry Point is selected in the PlaneRender object.
      Parameters:
      kPoint - probe entry point in ModelStorageBase Coordinates

    • enableEntryPoint

      public void enableEntryPoint(boolean flag)
      Set entry point rotation flag.
      Parameters:
      flag - boolean

    • enableObjBehavior

      public void enableObjBehavior(boolean flag)
      Enable objBehavior branch group.
      Parameters:
      flag - true means turn on, false means turn off.

    • getCameraControl

      public JPanelCamera getCameraControl()
      Get the rotation control dialog box.
      Returns:
      rotationControlDialog rotation control dialog

    • getClipDialog

      public JPanelClip getClipDialog()
      Return clipPanel from parent frame.
      Returns:
      clipPanel Clip Dialog box.

    • getDisplayDialog

      public JPanelDisplay getDisplayDialog()
      Return the diaplay dialog.
      Returns:
      boxPanel Display dialog.

    • getDisplayMode3D

      public boolean getDisplayMode3D()
      Return the current volume display mode.
      Returns:
      volumeDisplayMode3D volume 3D diaplay mode.

    • getGeodesicPanel

      public JPanelGeodesic getGeodesicPanel()
      Get the geodesic control panel.
      Returns:
      JPanelGeodesic geodesic control panel.

    • getImageA

      public ModelImage getImageA()
      Accessor that returns the reference to image A.
      Overrides:
      getImageA in class RenderViewBase
      Returns:
      Image A.

    • getImageB

      public ModelImage getImageB()
      Accessor that returns the reference to image B.
      Overrides:
      getImageB in class RenderViewBase
      Returns:
      Image B.

    • getMouseDialog

      public JPanelMouse getMouseDialog()
      Return mousePanel from parent frame.
      Returns:
      mousePanel Mouse Dialog box.

    • getMouseMode

      public int getMouseMode()
      Gets the mouse pointer mode - standard or fly - from the view dialog.
      Returns:
      The mouse pointer mode.

    • getObjBoxSlice_BG

      public javax.media.j3d.BranchGroup getObjBoxSlice_BG(int orientation)
      Return the X box color frame.
      Returns:
      objBoxSliceX_BG Called be the JDialogSliceBox

    • getObjPlane_BG

      public javax.media.j3d.BranchGroup getObjPlane_BG(int orientation)
      Gets the objXYPlaneBG branch group.
      Returns:
      objXYPlaneBG called by JDialogSliceBox

    • getOriginalScreenScale

      public double getOriginalScreenScale()
      Return the original ScreenScale for orthographic projection:
      Returns:
      DOCUMENT ME!

    • getParentFrame

      public ViewJFrameVolumeView getParentFrame()
      Return the parent frame.
      Returns:
      ViewJFrameVolumeView parent frame

    • getProbeDialog

      public JPanelProbe getProbeDialog()
      Return probePanel from parent frame.
      Returns:
      probePanel Probe Dialog box.

    • getSceneState

      public Object getSceneState()
      Gets the current scene state, in terms of what numbers the slices are on and whether or not they are visible.
      Specified by:
      getSceneState in class RenderViewBase
      Returns:
      A SceneState object with the variables set appropriately.

    • getSculptorPanel

      public JPanelSculptor getSculptorPanel()
      Return the sculptor panel.
      Returns:
      JPanelSculptor sculptor control panel.

    • getSegmentationImage

      public ModelImage getSegmentationImage()
      Return the segmentation region map image which contains info on where the vascualture, etc are located.
      Returns:
      (vessel, etc) segmentation image

    • getSlicePanel

      public JPanelSlices getSlicePanel()
      return the current active slicePanel interface.
      Returns:
      slicePanel called by JDialogMouseRecorder

    • getSliceSpacingCoarse

      public float getSliceSpacingCoarse()
      Retrieve the current "coarse" spacing between slices.
      Returns:
      float Current "coarse" spacing between slices.

    • getSliceSpacingFine

      public float getSliceSpacingFine()
      Retrieve the current "fine" spacing between slices.
      Returns:
      float Current "fine" spacing between slices.

    • getSurfaceDialog

      public JPanelSurface getSurfaceDialog()
      Return surfacePanel from parent frame.
      Returns:
      surfacePanel Surface Dialog box.

    • getSurfaceTexture

      public JPanelSurfaceTexture getSurfaceTexture()
      Returns the surface texture panel interface.
      Returns:
      surface texture panel.

    • getSurfaceTexturePanel

      public JPanel getSurfaceTexturePanel()
      Returns the surface texture panel mainPanel interface.
      Returns:
      surface texture mainPanel.

    • getViewDialog

      public JPanelView getViewDialog()
      Return the viewPanel from parent frame.
      Returns:
      viewPanel View Dialog box.

    • getVolOpacityPanel

      public JPanelVolumeOpacity getVolOpacityPanel()
      Return volume opacity control Dialog from parent frame.
      Returns:
      volOpacityPanel volume opacity dialog box.

    • getVolRenderBG

      public javax.media.j3d.BranchGroup getVolRenderBG()
      Return volume render Branch Group.
      Returns:
      volRenderBG volume render branch group.

    • getVolRenderOG

      public javax.media.j3d.OrderedGroup getVolRenderOG()
      Return volume render Order Group.
      Returns:
      volRenderOG volume render order group.

    • getVolumeTexture

      public VolumeTexture getVolumeTexture()
      Return texture, the VolumeTexture member variable.
      Returns:
      DOCUMENT ME!

    • getVolumeTextureCopy

      public javax.media.j3d.Group getVolumeTextureCopy(int iView)
      Returns the left of right eye copy of the NodeVolumeTextureRender:
      Parameters:
      iView - determines which view to return, 0 for left and 1 for right:
      Returns:
      the NodeVolumeTextureRender for displaying the volume texture in the stereo window.

    • getResolutions

      public float[] getResolutions()
      Returns the ModelImage resolutions.
      Returns:
      ModelImage resolutions

    • hideBoxFrame

      public void hideBoxFrame()
      Makes the box frame invisible.

    • invokeClipping

      public void invokeClipping()
      Enable the six clipping planes at a time.

    • isVolViewMode

      public boolean isVolViewMode()
      Check is volume view frame or not.
      Returns:
      boolean true means mode on, false means mode off.

    • reConfigureVolumeFrame

      public void reConfigureVolumeFrame()
      Constructs main frame structures for 3 image planes. Makes the LUT if necessary, then sets up the buffer arrays appropriately and calls the constructors for the three image planes. Used by the switch between aligned volume texture rendering and the volume texture rendering. Changed to public to allow updating after the volume is sculpted.

    • removeBoxSlice

      public void removeBoxSlice(int orientation)
      Detaches the slice frame on the slice for the given orientation.
      Parameters:
      orientation - the slice to add: AXIAL, CORONAL, or SAGITTAL

    • removeCubicControl

      public void removeCubicControl()
      Detach cubic control branch group.

    • resetAxisX

      public void resetAxisX()
      Overrides the parent resetImage method. This method reset the surface volume to the original position.
      Overrides:
      resetAxisX in class RenderViewBase

    • resetAxisY

      public void resetAxisY()
      Overrides the parent resetImage method. This method reset the surface volume to the original position.
      Overrides:
      resetAxisY in class RenderViewBase

    • resetImage

      public void resetImage()
      Overrides the parent resetImage method. This method reset the surface volume to the original position.
      Overrides:
      resetImage in class RenderViewBase

    • rotateImage

      public void rotateImage()
      Overrides the rotateImage to rotate the surface volume.
      Overrides:
      rotateImage in class RenderViewBase

    • saveCropVolume

      public void saveCropVolume()
      Save crop region with the clipped volume.

    • setAlphaBlend

      public void setAlphaBlend(int value)
      Sets the alpha blending of parameter for two image displays.
      Specified by:
      setAlphaBlend in class RenderViewBase
      Parameters:
      value - Amount [0,100] that is the percentage of Image A to be displayed.

    • setCompositeMode

      public void setCompositeMode()
      Set the texture renderer to render in composite mode.

    • setDisplayMode3D

      public void setDisplayMode3D(boolean flag)
      Hack. Set the update 3D texture volume win-level flag.
      Parameters:
      flag - true update 3D texture volume with win-level, false not update.

    • setGUI

      public void setGUI(Object scene)
      Sets the GUI components to their proper state before the action is dispatched from the player.
      Specified by:
      setGUI in class RenderViewBase
      Parameters:
      scene - The state of the scene.

    • setLightingMode

      public void setLightingMode()
      Set the texture render to render in lighting mode.

    • setLUTa

      public void setLUTa(ModelLUT LUT)
      Accessor that sets the LUT for image A.
      Parameters:
      LUT - The LUT.

    • setLUTb

      public void setLUTb(ModelLUT LUT)
      Accessor that sets the LUT for image B.
      Parameters:
      LUT - The LUT

    • setMaterialShininess

      public void setMaterialShininess(float value)
      Set the texture material shininess value.
      Parameters:
      value - shininess value.

    • setMouseMode

      public void setMouseMode(int mode)
      Sets the mouse pointer mode - standard or fly - in the view dialog.
      Parameters:
      mode - Mode to set to.

    • setMouseRotateEnable

      public void setMouseRotateEnable(boolean bEnable)
      Allow disabling or enabling mouse rotation:
      Parameters:
      bEnable - DOCUMENT ME!

    • setParallelRotation

      public void setParallelRotation(boolean flag)
      Set the parallel rotation flag from the viewJFrameVolumeView.
      Parameters:
      flag - true set all the renderer to parallel rotation, false parallel rotation mode off.

    • setProbeTG

      public void setProbeTG(javax.media.j3d.Transform3D kTransform, boolean bTwist)
      Sets the Transform3D for the slices based on the Probe Transform. To allow rotation about the probe position, and not just the center of the slices, the probe translation and rotation protions of the matrix are separated. First the center of the slice is translated from the probe position to the origin, then rotated, then translated back to the probe position. The three transformations are concatenated into one Transform3D, which is used to display the slices, boxes, and to sample the ModelImage on the diagonal:
      Parameters:
      kTransform - current probe transform
      bTwist - true if there is twist about the probe axis

    • setRayBasedRender

      public void setRayBasedRender(VolumeRenderer _rayBasedRender)
      Set the reference to ray based renderer, raycast renderer or shear warp renderer. This method set the clipping dialog to control the both the 3D texture renderer and raycast based renderer.
      Parameters:
      _rayBasedRender - VolumeRenderer reference

    • setRenderPerspective

      public void setRenderPerspective(boolean bEnable)
      Enable perspective projection rendering; otherwise use orthographic projection.
      Parameters:
      bEnable - true to enable perspective projection

    • setRGBTA

      public void setRGBTA(ModelRGB RGBT)
      Sets the RGB table for image A.
      Specified by:
      setRGBTA in class RenderViewBase
      Parameters:
      RGBT - New RGB table for image A.

    • setRGBTB

      public void setRGBTB(ModelRGB RGBT)
      Sets the RGB table for image B.
      Specified by:
      setRGBTB in class RenderViewBase
      Parameters:
      RGBT - New RGB table for image B.

    • setSegmentationImage

      public void setSegmentationImage(ModelImage img)
      Set the image which we can check to see if the probe is hitting anything important (such as vessels, etc).
      Parameters:
      img - segmentation image

    • setCenter

      public void setCenter(javax.vecmath.Vector3f center)
      Sets the values for JPanelSlices, based on the positions in the PlaneRender class for the AXIAL, CORONAL, and SAGITTAL views.
      Parameters:
      center - the three slider values in File Coordinates

    • setSlice

      public void setSlice(int slice)
      Does nothing but must instantiate for this to implements ViewImageUpdateInterface.
      Specified by:
      setSlice in interface ViewImageUpdateInterface
      Parameters:
      slice - DOCUMENT ME!

    • setSliceSpacingCoarse

      public void setSliceSpacingCoarse(float fSpacing)
      Set the desired "coarse" spacing between slices.
      Parameters:
      fSpacing - float Desired "coarse" spacing between slices.

    • setSliceSpacingFine

      public void setSliceSpacingFine(float fSpacing)
      Set the desired "fine" spacing between slices.
      Parameters:
      fSpacing - float Desired "fine" spacing between slices.

    • setSliceColor

      public void setSliceColor(Color color, int orientation)
      Sets the color of the x slice frame.
      Parameters:
      color - Color to set to.

    • setTimeSlice

      public void setTimeSlice(int slice)
      Sets the time slice to be displayed and changes the image planes displayed.
      Specified by:
      setTimeSlice in interface ViewImageUpdateInterface
      Parameters:
      slice - Indicates image time-slice (4th dimension) to be displayed.

    • setViewTextureAligned

      public void setViewTextureAligned(boolean flag)
      Switch between the volume texture mode and the regular volume texture mode.
      Parameters:
      flag - texture aligned view enabled or not

    • setVolumeDisplayMode

      public void setVolumeDisplayMode(boolean volDisplayMode)
      Accessor that sets the volumeDisplayMode flag. If true image is displayed as a volume. If false image is displayed as three orthogonal planes.
      Parameters:
      volDisplayMode - if true image is displayed as a volume ( 3D texture or 2D array Texture).

    • setVolView

      public void setVolView(boolean flag)
      Set the volume view mode to true from the ViewJFrameVolumeView During mouse recorder displaying, the flag control the updating of the opacity histogram.
      Parameters:
      flag - true means mode on, false means mode off.

    • showBoxFrame

      public void showBoxFrame()
      Makes the box frame visible.

    • showBoxSlice

      public void showBoxSlice(int orientation)
      Makes the box slice for the given orientation visible.
      Parameters:
      orientation - : AXIAL, CORONAL, or SAGITTAL

    • stateChanged

      public void stateChanged(ChangeEvent e)
      Sets how the image plane should be displayed depending on value of slider.
      Specified by:
      stateChanged in interface ChangeListener
      Parameters:
      e - Event that triggered this function.

    • switchToSliceView

      public void switchToSliceView(boolean firstTime)
      Perform some actions required when switching to the slice renderer.
      Parameters:
      firstTime - perform special actions required when switching for the first time

    • switchToVolView

      public void switchToVolView(boolean firstTime)
      Perform some actions required when switching to the volume renderer.
      Parameters:
      firstTime - perform special actions required when switching for the first time

    • transformChanged

      public void transformChanged(int type, javax.media.j3d.Transform3D transform)
      Tells the mouse dialog that the transform has changed. Does not use the type parameter.
      Specified by:
      transformChanged in interface com.sun.j3d.utils.behaviors.mouse.MouseBehaviorCallback
      Parameters:
      type - Type of transform.
      transform - Transform that was changed to.

    • transformUpdate

      public void transformUpdate(int type, javax.media.j3d.Transform3D transform)
      The raybased renderer invokes this method when a mouse release event occurs.
      Parameters:
      type - Type of transform.
      transform - Transform that was changed to.

    • undoCropVolume

      public void undoCropVolume()
      Undo crop region with the clipped volume.

    • update3DTriplanar

      public boolean update3DTriplanar(ModelLUT LUTa, ModelLUT LUTb, boolean forceShow)
      This methods calls the componentImage's update method to redraw the screen.
      Parameters:
      LUTa - LUT used to update imageA.
      LUTb - LUT used to update imageB.
      forceShow - Forces show to reimport image and calculate java image.
      Returns:
      Confirms successful update.

    • transformBoxSlices

      private void transformBoxSlices(javax.media.j3d.Transform3D kTransform)
      transform the points used to render the triSliceImages textures.
      Parameters:
      kTransform - the Transform3D used to rotate the boxes.

    • ScreenToModel

      private void ScreenToModel(javax.vecmath.Vector3f screen, javax.vecmath.Vector3f model)
      Translate from normalized plane coordinates to Model coordinates:
      Parameters:
      screen - the input point to be transformed from normalized plane coordinates
      model - the output point in Model coordinates

    • ModelToScreen

      public void ModelToScreen(javax.vecmath.Vector3f model, javax.vecmath.Vector3f screen)
      Translate from Model coordinates to normalized plane coordinates:
      Parameters:
      model - the input point in Model coordinates
      screen - the output point in normalized plane coordinates

    • getBoxSliceInScreen

      private void getBoxSliceInScreen(javax.vecmath.Vector3f[] screenBoxPoints, int[] boxSliceConstants)
      sets up the values for the ViewJComponentBoxSlice array. Reorders the three boxSlice (x,y,z) coordinates and mode value into local ModelCoordinates.
      Parameters:
      boxSliceConstants - the reordered mode value (X_SLICE, Y_SLICE, Z_SLICE) remapped into ModelCoordinates
      Vector3f - [] the reordered (x,y,z) coordinates for each boxSlice remapped into ModelCoordinates.

    • updateBoxSlicePos

      public void updateBoxSlicePos(boolean bParentUpdate)
      Update the X, Y, Z box frame positions.
      Parameters:
      bParentUpdate - if true, update the positions in the ParentFrame.

    • updateBoxSlices

      public void updateBoxSlices()
      Sets new frame around slice x based on the new position.

    • updateCubicTransform

      public void updateCubicTransform(double[] mat)
      Update the transform3D for the cubic.
      Parameters:
      transform - Transform3D

    • updateCubicTransform

      public void updateCubicTransform(javax.media.j3d.Transform3D transform)
      Update the transform3D for the cubic.
      Parameters:
      transform - Transform3D

    • updateData

      public void updateData()
      Called when the underlying data has changed, due to sculpting. Calls the ViewJFrameVolumeView updateSliceData function to update the data in the slices.

    • updateImageExtents

      public boolean updateImageExtents()
      This methods calls the componentImage's REPAINT method to redraw the screen. The extents on this image have changed, so the extents need to be read in again and menus, panes and slide bars adjusted accordingly.
      Specified by:
      updateImageExtents in interface ViewImageUpdateInterface
      Returns:
      DOCUMENT ME!

    • updateImageFromRotation

      public void updateImageFromRotation()
      Build a image with the current rotational transformation matrix. Step.1 convert the java3D transform matrix into a quaternion component. Step.2 convert the quaternion into image( our world ) coordinate system. Step.3 convert the quaternion into a rotatin matrix. Quaternion q ( w, x, y, z ): rotation of w around the vector ( x, y, z ); Convert the quaternion into a rotation matrix. / \ | 1-2*y^2-2*z^2 2*x*y-2*w*z 2*x*z+2*w*y | | 2*xy+2*w*z 1-2*x^2-2*z^2 2*y*z-2*w*x | | 2*x*z-2*w*y 2*y*z+2*w*x 1-2*x^2-2*y^2 | \ / Step.4 Calling the transform algorithm to extract the image.

    • updateImages

      public boolean updateImages()
      This methods calls the componentImage's update method to redraw the screen - fastest of the three update methods.
      Specified by:
      updateImages in interface ViewImageUpdateInterface
      Returns:
      Confirms successful update.

    • updateImages

      public boolean updateImages(boolean flag)
      This methods calls the componentImage's update method to redraw the screen. Without LUT changes.
      Specified by:
      updateImages in interface ViewImageUpdateInterface
      Parameters:
      flag - forces show to re import image and calc. java image
      Returns:
      boolean confirming successful update

    • updateImages

      public boolean updateImages(ModelLUT LUTa, ModelLUT LUTb, boolean forceShow, int interpMode)
      This methods calls the componentImage's update method to redraw the screen. Without LUT changes.
      Specified by:
      updateImages in interface ViewImageUpdateInterface
      Parameters:
      LUTa - DOCUMENT ME!
      LUTb - DOCUMENT ME!
      forceShow - Forces show to reimport image and calculate java image.
      interpMode - DOCUMENT ME!
      Returns:
      Confirms successful update.

    • updateLighting

      public void updateLighting()
      This method is normally called by JPanelLights when a light bulb property changes. It is up to this instance to decide how to update the rendering.

    • updateOpacityOfOthrogPlanes

      public void updateOpacityOfOthrogPlanes(int opX, int opY, int opZ)
      Updates the 3 orthogonal 2D texture maps' opacities.
      Parameters:
      opX - the opacity of the x plane, range [0,100] and -1 if no updating is required
      opY - the opacity of the y plane, range [0,100] and -1 if no updating is required
      opZ - the opacity of the z plane, range [0,100] and -1 if no updating is required

    • updateProbe

      public void updateProbe(boolean forceShow, boolean bInterpolate, boolean bReset)
      Updates the slice textures based on the Probe position and rotation angle. The ModelImage data is sampled along the diagonal, not axis-aligned. bInterpolate indicates whether to use nearest-neighbors or to interpolate the data.
      Parameters:
      forceShow - Forces triSliceImages[i].show to re-calculate the image texture.
      bInterpolate - uses nearest-neighbors when false, interpolates data when true
      bReset - when true indicates that the probe navigation has been reset and the slice bounding boxes should be displayed, when false the probe is no axis-aligned and the slice bounding boxes are not displayed

    • updateProbePos

      public void updateProbePos()
      Not used now. Might be used later on.

    • updateRaycastRender

      public void updateRaycastRender()
      Update the raycast based renderer. JPanelSurface mouse release event invokes this method call.

    • updateShininess

      public void updateShininess(float value)
      Update the shininess from the JPanelLights.
      Parameters:
      value - shininess value.

    • updateTransform

      public void updateTransform()
      Tells the mouse dialog that the transform has changed. Does not use the type parameter.
      Parameters:
      transform - Transform that was changed to.

    • updateVolume

      public boolean updateVolume(ModelLUT LUTa, ModelLUT LUTb, boolean forceShow)
      This methods calls the componentImage's update method to redraw the screen.
      Parameters:
      LUTa - LUT used to update imageA.
      LUTb - LUT used to update imageB.
      forceShow - Forces show to reimport image and calculate java image.
      Returns:
      Confirms successful update.

    • useSliceSpacingCoarse

      public void useSliceSpacingCoarse()
      Select the "coarse" slice sampling for rendering.

    • useSliceSpacingFine

      public void useSliceSpacingFine()
      Retrieves whether the "fine" slice sampling is currently selected.

    • whichTissue

      public int whichTissue(float x, float y, float z)
      Check the given voxel belong to which segmentation.
      Parameters:
      x - float given voxel x coordinate
      y - float given voxel y coordinate
      z - float given voxel z coordinate
      Returns:
      int segmentation component type

    • buildCubicBox

      private com.sun.j3d.utils.geometry.Box buildCubicBox()
      Create the rotation control cubic box.
      Returns:
      A cube representing the image orientation, with labels painted on the cube faces showing which axis corresponds to which axis in patient coordinates.

    • buildCubicBranch

      private void buildCubicBranch()
      Build the cubic branch under the objRootBG.

    • configureSliceFrame

      private void configureSliceFrame()
      Constructs main frame structures for 3 image planes. Makes the LUT if necessary, then sets up the buffer arrays appropriately and calls the constructors for the three image planes.

    • generateRFACoordMaps

      private void generateRFACoordMaps()
      Generates the texture coord map vectors for the three orthogonal slices.

    • generateRFACoordMaps

      private javax.vecmath.Vector4f generateRFACoordMaps(int orientation, int texCoord)
      create texture coordmaps for the texture-mapped planes displaying the triSliceImages.
      Parameters:
      orientation - the orientation of the plane for which the texture coordinates are generated (AXIAL, CORONAL, or SAGITTAL)
      texCoord - the dimension along which the texture coordinate varies

    • createImageSceneGraph

      private void createImageSceneGraph()
      Creates the scene graph, made up of a branch group parent, a transform group under that which applies mouse behavior and lights to the scene, and three branch groups under the transform group for each of the three image planes. The surfaces that can be added would be children of the transform group. Each image plane has a transform group associated with it and beneath that, a box shape where the texture maps are applied. The shape is what is actually displayed.

    • setupEye

      private void setupEye()
      Set up the center point of the red line boxframe.

    • updateTextureVolumeRender

      private void updateTextureVolumeRender()
      Determine the current viewing transformation and pass it to the texture volume renderer so that it can update itself.

    • updateViewScreenScale

      private void updateViewScreenScale(javax.media.j3d.Transform3D kTransform)
      This function calculates the scale factor for zooming in parallel projection. The scenario is to calculate the distance between the origin boxframe center and tranformed boxframe center. This distance is used to compute the screen scale factor.
      Parameters:
      kTransform - The tranformation matrix from tranformChanged().

    • updateParent

      public void updateParent()

    • keyPressed

      public void keyPressed(KeyEvent arg0)
      Specified by:
      keyPressed in interface KeyListener

    • keyReleased

      public void keyReleased(KeyEvent arg0)
      Specified by:
      keyReleased in interface KeyListener

    • keyTyped

      public void keyTyped(KeyEvent arg0)
      Specified by:
      keyTyped in interface KeyListener

    • propertyChange

      public void propertyChange(PropertyChangeEvent arg0)
      Specified by:
      propertyChange in interface PropertyChangeListener