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

Class SurfaceView

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
gov.nih.mipav.view.renderer.J3D.surfaceview.SurfaceView
All Implemented Interfaces:
com.sun.j3d.utils.behaviors.mouse.MouseBehaviorCallback, ViewImageUpdateInterface, ActionListener, KeyListener, ImageObserver, MenuContainer, PropertyChangeListener, Serializable, EventListener, Accessible, ChangeListener
public class SurfaceView extends SurfaceRender
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:

    • 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:

    • bufferFactor

      private int bufferFactor
      Buffer factor, 1 usually, 4 for color images.

    • clipPanel

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

    • 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.

    • 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.

    • 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.

    • 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.

    • 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.

    • volRenderBG

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

    • 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

    • SurfaceView

      public SurfaceView(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

    • SurfaceView

      public SurfaceView(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
      Overrides:
      actionPerformed in class SurfaceRender
      Parameters:
      event - Event that triggered function.

    • addCubicControl

      public void addCubicControl()
      Attach cubic control branch group.
      Overrides:
      addCubicControl in class SurfaceRender

    • autoCapture

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

    • cleanMouseRecorder

      public void cleanMouseRecorder()
      Clean mouse recorder for any existing event items.
      Overrides:
      cleanMouseRecorder in class SurfaceRender

    • close

      public void close()
      Closes the image.
      Overrides:
      close in class SurfaceRender

    • 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.
      Overrides:
      configureVolumeFrame in class SurfaceRender

    • cropClipVolume

      public void cropClipVolume()
      Crop the region of the clipped volume.
      Overrides:
      cropClipVolume in class SurfaceRender

    • detachVolRender

      public void detachVolRender()
      Detach volume render branch group.
      Overrides:
      detachVolRender in class SurfaceRender

    • disableClipping

      public void disableClipping()
      Diable all the six clipping planes at a time.
      Overrides:
      disableClipping in class SurfaceRender

    • dispatchSavedEvent

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

    • disposeLocal

      public void disposeLocal(boolean flag)
      Sets all variables to null, disposes, and garbage collects.
      Overrides:
      disposeLocal in class SurfaceRender
      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.
      Overrides:
      drawRFAPoint in class SurfaceRender
      Parameters:
      kPoint - probe entry point in ModelStorageBase Coordinates

    • enableEntryPoint

      public void enableEntryPoint(boolean flag)
      Set entry point rotation flag.
      Overrides:
      enableEntryPoint in class SurfaceRender
      Parameters:
      flag - boolean

    • enableObjBehavior

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

    • getCameraControl

      public JPanelCamera getCameraControl()
      Get the rotation control dialog box.
      Overrides:
      getCameraControl in class SurfaceRender
      Returns:
      rotationControlDialog rotation control dialog

    • getClipDialog

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

    • getDisplayDialog

      public JPanelDisplay getDisplayDialog()
      Return the diaplay dialog.
      Overrides:
      getDisplayDialog in class SurfaceRender
      Returns:
      boxPanel Display dialog.

    • getDisplayMode3D

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

    • getGeodesicPanel

      public JPanelGeodesic getGeodesicPanel()
      Get the geodesic control panel.
      Overrides:
      getGeodesicPanel in class SurfaceRender
      Returns:
      JPanelGeodesic geodesic control panel.

    • getImageA

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

    • getImageB

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

    • getMouseDialog

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

    • getMouseMode

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

    • getObjPlane_BG

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

    • getOriginalScreenScale

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

    • getParentFrame

      public ViewJFrameVolumeView getParentFrame()
      Return the parent frame.
      Overrides:
      getParentFrame in class SurfaceRender
      Returns:
      ViewJFrameVolumeView parent frame

    • getProbeDialog

      public JPanelProbe getProbeDialog()
      Return probePanel from parent frame.
      Overrides:
      getProbeDialog in class SurfaceRender
      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.
      Overrides:
      getSceneState in class SurfaceRender
      Returns:
      A SceneState object with the variables set appropriately.

    • getSegmentationImage

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

    • getSlicePanel

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

    • getSurfaceDialog

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

    • getSurfaceTexture

      public JPanelSurfaceTexture getSurfaceTexture()
      Returns the surface texture panel interface.
      Overrides:
      getSurfaceTexture in class SurfaceRender
      Returns:
      surface texture panel.

    • getSurfaceTexturePanel

      public JPanel getSurfaceTexturePanel()
      Returns the surface texture panel mainPanel interface.
      Overrides:
      getSurfaceTexturePanel in class SurfaceRender
      Returns:
      surface texture mainPanel.

    • getViewDialog

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

    • getVolOpacityPanel

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

    • getVolRenderBG

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

    • getVolRenderOG

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

    • getResolutions

      public float[] getResolutions()
      Returns the ModelImage resolutions.
      Overrides:
      getResolutions in class SurfaceRender
      Returns:
      ModelImage resolutions

    • hideBoxFrame

      public void hideBoxFrame()
      Makes the box frame invisible.
      Overrides:
      hideBoxFrame in class SurfaceRender

    • invokeClipping

      public void invokeClipping()
      Enable the six clipping planes at a time.
      Overrides:
      invokeClipping in class SurfaceRender

    • 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.
      Overrides:
      reConfigureVolumeFrame in class SurfaceRender

    • removeCubicControl

      public void removeCubicControl()
      Detach cubic control branch group.
      Overrides:
      removeCubicControl in class SurfaceRender

    • resetAxisX

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

    • resetAxisY

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

    • resetImage

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

    • rotateImage

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

    • saveCropVolume

      public void saveCropVolume()
      Save crop region with the clipped volume.
      Overrides:
      saveCropVolume in class SurfaceRender

    • setAlphaBlend

      public void setAlphaBlend(int value)
      Sets the alpha blending of parameter for two image displays.
      Overrides:
      setAlphaBlend in class SurfaceRender
      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.
      Overrides:
      setCompositeMode in class SurfaceRender

    • setDisplayMode3D

      public void setDisplayMode3D(boolean flag)
      Hack. Set the update 3D texture volume win-level flag.
      Overrides:
      setDisplayMode3D in class SurfaceRender
      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.
      Overrides:
      setGUI in class SurfaceRender
      Parameters:
      scene - The state of the scene.

    • setLightingMode

      public void setLightingMode()
      Set the texture render to render in lighting mode.
      Overrides:
      setLightingMode in class SurfaceRender

    • setLUTa

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

    • setLUTb

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

    • setMaterialShininess

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

    • setMouseMode

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

    • setMouseRotateEnable

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

    • setParallelRotation

      public void setParallelRotation(boolean flag)
      Set the parallel rotation flag from the viewJFrameVolumeView.
      Overrides:
      setParallelRotation in class SurfaceRender
      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:
      Overrides:
      setProbeTG in class SurfaceRender
      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.
      Overrides:
      setRayBasedRender in class SurfaceRender
      Parameters:
      _rayBasedRender - VolumeRenderer reference

    • setRenderPerspective

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

    • setRGBTA

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

    • setRGBTB

      public void setRGBTB(ModelRGB RGBT)
      Sets the RGB table for image B.
      Overrides:
      setRGBTB in class SurfaceRender
      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).
      Overrides:
      setSegmentationImage in class SurfaceRender
      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.
      Overrides:
      setCenter in class SurfaceRender
      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
      Overrides:
      setSlice in class SurfaceRender
      Parameters:
      slice - DOCUMENT ME!

    • setSliceColor

      public void setSliceColor(Color color, int orientation)
      Sets the color of the x slice frame.
      Overrides:
      setSliceColor in class SurfaceRender
      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
      Overrides:
      setTimeSlice in class SurfaceRender
      Parameters:
      slice - Indicates image time-slice (4th dimension) to be displayed.

    • 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.
      Overrides:
      setVolumeDisplayMode in class SurfaceRender
      Parameters:
      volDisplayMode - if true image is displayed as a volume ( 3D texture or 2D array Texture).

    • showBoxFrame

      public void showBoxFrame()
      Makes the box frame visible.
      Overrides:
      showBoxFrame in class SurfaceRender

    • 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
      Overrides:
      stateChanged in class SurfaceRender
      Parameters:
      e - Event that triggered this function.

    • switchToSliceView

      public void switchToSliceView(boolean firstTime)
      Perform some actions required when switching to the slice renderer.
      Overrides:
      switchToSliceView in class SurfaceRender
      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.
      Overrides:
      switchToVolView in class SurfaceRender
      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
      Overrides:
      transformChanged in class SurfaceRender
      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.
      Overrides:
      transformUpdate in class SurfaceRender
      Parameters:
      type - Type of transform.
      transform - Transform that was changed to.

    • undoCropVolume

      public void undoCropVolume()
      Undo crop region with the clipped volume.
      Overrides:
      undoCropVolume in class SurfaceRender

    • 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:
      Overrides:
      ModelToScreen in class SurfaceRender
      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.

    • updateCubicTransform

      public void updateCubicTransform(javax.media.j3d.Transform3D transform)
      Update the transform3D for the cubic.
      Overrides:
      updateCubicTransform in class SurfaceRender
      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.
      Overrides:
      updateData in class SurfaceRender

    • 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
      Overrides:
      updateImageExtents in class SurfaceRender
      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.
      Overrides:
      updateImageFromRotation in class SurfaceRender

    • 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
      Overrides:
      updateImages in class SurfaceRender
      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
      Overrides:
      updateImages in class SurfaceRender
      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
      Overrides:
      updateImages in class SurfaceRender
      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.
      Overrides:
      updateLighting in class SurfaceRender

    • 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.
      Overrides:
      updateProbe in class SurfaceRender
      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.
      Overrides:
      updateProbePos in class SurfaceRender

    • updateRaycastRender

      public void updateRaycastRender()
      Update the raycast based renderer. JPanelSurface mouse release event invokes this method call.
      Overrides:
      updateRaycastRender in class SurfaceRender

    • updateShininess

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

    • updateTransform

      public void updateTransform(javax.media.j3d.Transform3D transform)
      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.
      Overrides:
      updateVolume in class SurfaceRender
      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.

    • whichTissue

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

    • finalize

      protected void finalize() throws Throwable
      Calls disposeLocal.
      Overrides:
      finalize in class Object
      Throws:
      Throwable - DOCUMENT ME!

    • 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()
      Overrides:
      updateParent in class SurfaceRender