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, java.awt.event.ActionListener, java.awt.event.KeyListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.beans.PropertyChangeListener, java.io.Serializable, java.util.EventListener, javax.accessibility.Accessible, javax.swing.event.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:

ViewJComponentSurfaceImage, JDialogSurface, JDialogView, JDialogMouseRecorder, Serialized Form

Nested Class Summary
- Nested classes/interfaces inherited from class gov.nih.mipav.view.renderer.J3D.RenderViewBase
  RenderViewBase.Matrix
- Nested classes/interfaces inherited from class java.awt.Canvas
  java.awt.Canvas.AccessibleAWTCanvas
- Nested classes/interfaces inherited from class java.awt.Component
  java.awt.Component.AccessibleAWTComponent, java.awt.Component.BaselineResizeBehavior, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy

Field Summary

Fields
Modifier and Type	Field	Description
`static int`	`ARTERIAL_SEG`	Value which indicates a voxel that is part of the arterial vasculature tree.
`static int`	`BONE_SEG`	Value which indicates a bone in the image.
`private JPanelDisplay`	`boxPanel`	Dialog to turn bounding box of surface renderer on and off, and to change the color of the frame.
`private ViewJComponentBoxSlice[]`	`boxSlices`	The frame around the AXIAL, CORONAL, SAGITTAL slices:
`private javax.vecmath.Vector3f[][]`	`boxSliceVertices`	The transformed boxSlices frames used to sample the volume data along diagonal slices:
`private int`	`bufferFactor`	Buffer factor, 1 usually, 4 for color images.
`private JPanelClip`	`clipPanel`	Dialog to turn the clipping palne box on and off.
`private javax.media.j3d.BranchGroup`	`cubicBehaviorBG`	The cubic roational behavior branch group.
`private javax.media.j3d.BranchGroup`	`cubicBG`	Cubic branch group.
`private com.sun.j3d.utils.behaviors.mouse.MouseRotate`	`cubicRotate`	Cubic mouse rotation behavior.
`private javax.media.j3d.TransformGroup`	`cubicTG`	Cubic transform group.
`private javax.media.j3d.Transform3D`	`currentTransform`	Current transform matrix.
`private int`	`currentTransformType`	Current transform changes type.
`static int`	`ENTRY_POINT`	Value which indicates the probe entry point color.
`private boolean`	`first6ClipPlane`	flag indicate the first time 6 clipping plane branch switch.
`private boolean`	`firstClipArbi`	flag indicate the first time arbitrary clipping plane branch switch.
`private JPanelGeodesic`	`geodesicPanel`	Geodesic panel.
`private ModelImage`	`imageA`	Current image A.
`private ModelImage`	`imageB`	Current image B.
`private boolean`	`isEntryPoint`	Flag indicates that probe rotate around the entry point or not.
`private boolean`	`m_bRenderModeLighting`	Flag set when texture volume is being rendered using lights.
`private double`	`m_dOriginalScreenScale`	Zoomfactor, zooming in screen scale space, and is relative to original position, this stores that original position:.
`private javax.media.j3d.TransformGroup[]`	`m_kObjBoxSliceProbe_TG`	TransformGroup[] used to rotate the AXIAL, CORONAL, SAGITTAL slice BOXES:
`private javax.media.j3d.TransformGroup[]`	`m_kObjPlaneProbe_TG`	TransformGroup[] used to rotate the AXIAL, CORONAL, SAGITTAL slice PLANES:
`private javax.media.j3d.Transform3D`	`m_kProbeTransform`	The Transform3D used to position the planes based on the Probe position and angle.
`(package private) javax.vecmath.Vector4f[][]`	`m_kRFACoordMaps`	Texture mapping for the RFA probe rotation:
`private SoftwareLightSet`	`m_kSoftwareLightSet`	Used to compute software lighting of composite texture volume.
`private SoftwareMaterial`	`m_kSoftwareMaterial`	DOCUMENT ME!
`private float`	`maxBox`	Numbers dicatating the sizes of the planes based on the extents and resolutions of the image.
`private JPanelMouse`	`mousePanel`	Dialog for recording and playing back mouse events.
`private MouseRotateExt`	`mouseRotateBehavior`	Mouse Rotate behavior.
`private com.sun.j3d.utils.behaviors.mouse.MouseTranslate`	`mouseTranslateBehavior`	Mouse Translate behavior.
`private com.sun.j3d.utils.behaviors.mouse.MouseZoom`	`mouseZoomBehavior`	Mouse Zoom behavior.
`private javax.vecmath.Point3d`	`myEyePoint`	Initial center viewing point of the image.
`private javax.media.j3d.BranchGroup[]`	`objPlane_BG`	BranchGroup[] containing the image planes.
`private javax.media.j3d.TransformGroup[]`	`objTransSlices_TG`	Group dictating how the XY plane is translated.
`private boolean`	`parallelRotation`	Parallel rotation flag.
`private javax.media.j3d.Transform3D`	`parallelScaleT3D`	Transformation matrix.
`private ViewJFrameBase`	`parent`	Controls for the image.
`private JPanelProbe`	`probePanel`	Dialog for loading and displaying probes.
`private float[]`	`resols`	Resolutions of image A.
`private int`	`rotationCount`	fix one bug from threading.
`private ModelImage`	`segmentationImage`	Image with areas marked with values indicating that they are special tissue types (vessels, etc).
`private static long`	`serialVersionUID`	Use serialVersionUID for interoperability.
`private JPanelSlices`	`slicePanel`	Dialog to turn the slices control box on and off.
`private JPanelSurface`	`surfacePanel`	Dialog for loading and displaying surfaces.
`private JPanelSurfaceTexture`	`surfaceTexturePanel`	Panel for displaying the SurfaceTexture interface:
`private javax.media.j3d.Switch`	`switchGroup`	Tri planar view and the 3D texture volume view switch group.
`private int`	`tDim`	Dimensions of image A.
`private javax.media.j3d.Transform3D`	`transformCubic`	Cubic tansform3D.
`private javax.media.j3d.Transform3D`	`transformNode3d`	Setup the initial position of the image, added to ScenerootTG transform group.
`static int`	`TUMOR_SEG`	Value which indicates a voxel in the segmenation image that is part of the tumor.
`static int`	`VASCULATURE_SEG`	Value which indicates a voxel in the segmenation image that is part of the vasculature (arterial or veinous).
`static int`	`VEINOUS_SEG`	Value which indicates a voxel in the segmenation image that is part of the veinous vasculature tree.
`private javax.media.j3d.View`	`view`	View object in rendering a three dimensional scene from one viewpoint.
`private javax.media.j3d.BranchGroup`	`volBG`	Volume branch group.
`private javax.media.j3d.BranchGroup`	`volRenderBG`	Volume render branch group.
`private javax.media.j3d.OrderedGroup`	`volRenderOG`	Volume render order group, specify the rendering order.
`private boolean`	`volumeDisplayMode3D`	If true display 3D volume as a 3D texture map or 2D array of texture maps.
`private float`	`xBox`	Numbers dicatating the sizes of the planes based on the extents and resolutions of the image.
`private int`	`xDim`	Dimensions of image A.
`private float`	`yBox`	Numbers dicatating the sizes of the planes based on the extents and resolutions of the image.
`private int`	`yDim`	Dimensions of image A.
`private float`	`zBox`	Numbers dicatating the sizes of the planes based on the extents and resolutions of the image.
`private int`	`zDim`	Dimensions of image A.

Fields inherited from class gov.nih.mipav.view.renderer.J3D.surfaceview.SurfaceRender
isTriPlanarVolView, isViewTextureAligned, rayBasedRender

Fields inherited from class gov.nih.mipav.view.renderer.J3D.RenderViewBase
background, bounds, boxFrame, canvas, captureFrame, captureImage, config, displayMode, IMAGE_A, IMAGE_B, LUTa, LUTb, objBehaviorBG, objBoxFrameBG, objRootBG, rotationAngle, rotationAxis, rotationControlPanel, rotationTimes, rotationTotal, sceneRootTG, sliderEvents, transRotation, transRotationMatrix, triPlanarViewBG, universe, viewPanel

Fields inherited from class gov.nih.mipav.view.renderer.J3D.VolumeCanvas3D
m_dAccumulatedTime, m_dFrameRate, m_dLastTime, m_iAccumulatedFrameCount, m_iFrameCount, m_iMaxTimer, m_iTimer

Fields inherited from class javax.media.j3d.Canvas3D
FIELD_ALL, FIELD_LEFT, FIELD_RIGHT

Fields inherited from class java.awt.Component
accessibleContext, BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface java.awt.image.ImageObserver
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Fields inherited from interface com.sun.j3d.utils.behaviors.mouse.MouseBehaviorCallback
ROTATE, TRANSLATE, ZOOM

Constructor Summary

Constructors
Constructor	Description
`SurfaceView(ModelImage _imageA, ModelImage _imageB, java.awt.GraphicsConfiguration _config)`	Constructor called by the VirtualEndoscopyView.
`SurfaceView(ModelImage _imageA, ModelLUT _LUTa, ModelImage _imageB, ModelLUT _LUTb, ViewJFrameBase _parent, java.awt.GraphicsConfiguration _config, ViewJProgressBar _pBar)`	Makes a frame and puts the three image planes into it.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`actionPerformed(java.awt.event.ActionEvent event)`	Calls various methods depending on the action.
`void`	`addCubicControl()`	Attach cubic control branch group.
`void`	`autoCapture()`	Overrides the parent autoCapture method.
`private com.sun.j3d.utils.geometry.Box`	`buildCubicBox()`	Create the rotation control cubic box.
`private void`	`buildCubicBranch()`	Build the cubic branch under the objRootBG.
`void`	`cleanMouseRecorder()`	Clean mouse recorder for any existing event items.
`void`	`close()`	Closes the image.
`private void`	`configureSliceFrame()`	Constructs main frame structures for 3 image planes.
`void`	`configureVolumeFrame()`	Constructs main frame structures for 3 image planes.
`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.
`void`	`cropClipVolume()`	Crop the region of the clipped volume.
`void`	`detachVolRender()`	Detach volume render branch group.
`void`	`disableClipping()`	Diable all the six clipping planes at a time.
`void`	`dispatchSavedEvent(java.util.EventObject event)`	Dispatches event to appropriate object.
`void`	`disposeLocal(boolean flag)`	Sets all variables to null, disposes, and garbage collects.
`void`	`drawRFAPoint(javax.vecmath.Point3f kPoint)`	Called from the parent class when the Probe Entry Point is selected in the PlaneRender object.
`void`	`enableEntryPoint(boolean flag)`	Set entry point rotation flag.
`void`	`enableObjBehavior(boolean flag)`	Enable objBehavior branch group.
`protected void`	`finalize()`	Calls disposeLocal.
`private void`	`generateRFACoordMaps()`	Generates the texture coord map vectors for the three orthogonal slices.
`private javax.vecmath.Vector4f`	`generateRFACoordMaps(int orientation, int texCoord)`	create texture coordmaps for the texture-mapped planes displaying the triSliceImages.
`private void`	`getBoxSliceInScreen(javax.vecmath.Vector3f[] screenBoxPoints, int[] boxSliceConstants)`	sets up the values for the ViewJComponentBoxSlice array.
`JPanelCamera`	`getCameraControl()`	Get the rotation control dialog box.
`JPanelClip`	`getClipDialog()`	Return clipPanel from parent frame.
`JPanelDisplay`	`getDisplayDialog()`	Return the diaplay dialog.
`boolean`	`getDisplayMode3D()`	Return the current volume display mode.
`JPanelGeodesic`	`getGeodesicPanel()`	Get the geodesic control panel.
`ModelImage`	`getImageA()`	Accessor that returns the reference to image A.
`ModelImage`	`getImageB()`	Accessor that returns the reference to image B.
`JPanelMouse`	`getMouseDialog()`	Return mousePanel from parent frame.
`int`	`getMouseMode()`	Gets the mouse pointer mode - standard or fly - from the view dialog.
`javax.media.j3d.BranchGroup`	`getObjPlane_BG(int orientation)`	Gets the objXYPlaneBG branch group.
`double`	`getOriginalScreenScale()`	Return the original ScreenScale for orthographic projection:
`ViewJFrameVolumeView`	`getParentFrame()`	Return the parent frame.
`JPanelProbe`	`getProbeDialog()`	Return probePanel from parent frame.
`float[]`	`getResolutions()`	Returns the ModelImage resolutions.
`java.lang.Object`	`getSceneState()`	Gets the current scene state, in terms of what numbers the slices are on and whether or not they are visible.
`ModelImage`	`getSegmentationImage()`	Return the segmentation region map image which contains info on where the vascualture, etc are located.
`JPanelSlices`	`getSlicePanel()`	return the current active slicePanel interface.
`JPanelSurface`	`getSurfaceDialog()`	Return surfacePanel from parent frame.
`JPanelSurfaceTexture`	`getSurfaceTexture()`	Returns the surface texture panel interface.
`javax.swing.JPanel`	`getSurfaceTexturePanel()`	Returns the surface texture panel mainPanel interface.
`JPanelView`	`getViewDialog()`	Return the viewPanel from parent frame.
`JPanelVolumeOpacity`	`getVolOpacityPanel()`	Return volume opacity control Dialog from parent frame.
`javax.media.j3d.BranchGroup`	`getVolRenderBG()`	Return volume render Branch Group.
`javax.media.j3d.OrderedGroup`	`getVolRenderOG()`	Return volume render Order Group.
`void`	`hideBoxFrame()`	Makes the box frame invisible.
`void`	`invokeClipping()`	Enable the six clipping planes at a time.
`void`	`ModelToScreen(javax.vecmath.Vector3f model, javax.vecmath.Vector3f screen)`	Translate from Model coordinates to normalized plane coordinates:
`void`	`reConfigureVolumeFrame()`	Constructs main frame structures for 3 image planes.
`void`	`removeCubicControl()`	Detach cubic control branch group.
`void`	`resetAxisX()`	Overrides the parent resetImage method.
`void`	`resetAxisY()`	Overrides the parent resetImage method.
`void`	`resetImage()`	Overrides the parent resetImage method.
`void`	`rotateImage()`	Overrides the rotateImage to rotate the surface volume.
`void`	`saveCropVolume()`	Save crop region with the clipped volume.
`private void`	`ScreenToModel(javax.vecmath.Vector3f screen, javax.vecmath.Vector3f model)`	Translate from normalized plane coordinates to Model coordinates:
`void`	`setAlphaBlend(int value)`	Sets the alpha blending of parameter for two image displays.
`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.
`void`	`setCompositeMode()`	Set the texture renderer to render in composite mode.
`void`	`setDisplayMode3D(boolean flag)`	Hack.
`void`	`setGUI(java.lang.Object scene)`	Sets the GUI components to their proper state before the action is dispatched from the player.
`void`	`setLightingMode()`	Set the texture render to render in lighting mode.
`void`	`setLUTa(ModelLUT LUT)`	Accessor that sets the LUT for image A.
`void`	`setLUTb(ModelLUT LUT)`	Accessor that sets the LUT for image B.
`void`	`setMaterialShininess(float value)`	Set the texture material shininess value.
`void`	`setMouseMode(int mode)`	Sets the mouse pointer mode - standard or fly - in the view dialog.
`void`	`setMouseRotateEnable(boolean bEnable)`	Allow disabling or enabling mouse rotation:
`void`	`setParallelRotation(boolean flag)`	Set the parallel rotation flag from the viewJFrameVolumeView.
`void`	`setProbeTG(javax.media.j3d.Transform3D kTransform, boolean bTwist)`	Sets the Transform3D for the slices based on the Probe Transform.
`void`	`setRayBasedRender(VolumeRenderer _rayBasedRender)`	Set the reference to ray based renderer, raycast renderer or shear warp renderer.
`void`	`setRenderPerspective(boolean bEnable)`	Enable perspective projection rendering; otherwise use orthographic projection.
`void`	`setRGBTA(ModelRGB RGBT)`	Sets the RGB table for image A.
`void`	`setRGBTB(ModelRGB RGBT)`	Sets the RGB table for image B.
`void`	`setSegmentationImage(ModelImage img)`	Set the image which we can check to see if the probe is hitting anything important (such as vessels, etc).
`void`	`setSlice(int slice)`	Does nothing but must instantiate for this to implements ViewImageUpdateInterface.
`void`	`setSliceColor(java.awt.Color color, int orientation)`	Sets the color of the x slice frame.
`void`	`setTimeSlice(int slice)`	Sets the time slice to be displayed and changes the image planes displayed.
`private void`	`setupEye()`	Set up the center point of the red line boxframe.
`void`	`setVolumeDisplayMode(boolean volDisplayMode)`	Accessor that sets the volumeDisplayMode flag.
`void`	`showBoxFrame()`	Makes the box frame visible.
`void`	`stateChanged(javax.swing.event.ChangeEvent e)`	Sets how the image plane should be displayed depending on value of slider.
`void`	`switchToSliceView(boolean firstTime)`	Perform some actions required when switching to the slice renderer.
`void`	`switchToVolView(boolean firstTime)`	Perform some actions required when switching to the volume renderer.
`private void`	`transformBoxSlices(javax.media.j3d.Transform3D kTransform)`	transform the points used to render the triSliceImages textures.
`void`	`transformChanged(int type, javax.media.j3d.Transform3D transform)`	Tells the mouse dialog that the transform has changed.
`void`	`transformUpdate(int type, javax.media.j3d.Transform3D transform)`	The raybased renderer invokes this method when a mouse release event occurs.
`void`	`undoCropVolume()`	Undo crop region with the clipped volume.
`void`	`updateCubicTransform(javax.media.j3d.Transform3D transform)`	Update the transform3D for the cubic.
`void`	`updateData()`	Called when the underlying data has changed, due to sculpting.
`boolean`	`updateImageExtents()`	This methods calls the componentImage's REPAINT method to redraw the screen.
`void`	`updateImageFromRotation()`	Build a image with the current rotational transformation matrix.
`boolean`	`updateImages()`	This methods calls the componentImage's update method to redraw the screen - fastest of the three update methods.
`boolean`	`updateImages(boolean flag)`	This methods calls the componentImage's update method to redraw the screen.
`boolean`	`updateImages(ModelLUT LUTa, ModelLUT LUTb, boolean forceShow, int interpMode)`	This methods calls the componentImage's update method to redraw the screen.
`void`	`updateLighting()`	This method is normally called by JPanelLights when a light bulb property changes.
`void`	`updateParent()`
`void`	`updateProbe(boolean forceShow, boolean bInterpolate, boolean bReset)`	Updates the slice textures based on the Probe position and rotation angle.
`void`	`updateProbePos()`	Not used now.
`void`	`updateRaycastRender()`	Update the raycast based renderer.
`void`	`updateShininess(float value)`	Update the shininess from the JPanelLights.
`private void`	`updateTextureVolumeRender()`	Determine the current viewing transformation and pass it to the texture volume renderer so that it can update itself.
`void`	`updateTransform(javax.media.j3d.Transform3D transform)`	Tells the mouse dialog that the transform has changed.
`private void`	`updateViewScreenScale(javax.media.j3d.Transform3D kTransform)`	This function calculates the scale factor for zooming in parallel projection.
`boolean`	`updateVolume(ModelLUT LUTa, ModelLUT LUTb, boolean forceShow)`	This methods calls the componentImage's update method to redraw the screen.
`int`	`whichTissue(float x, float y, float z)`	Check the given voxel belong to which segmentation.

Methods inherited from class gov.nih.mipav.view.renderer.J3D.surfaceview.SurfaceRender
getObjBoxSlice_BG, getSculptorPanel, getSliceSpacingCoarse, getSliceSpacingFine, getVolumeTexture, getVolumeTextureCopy, isVolViewMode, keyPressed, keyReleased, keyTyped, propertyChange, removeBoxSlice, setSliceSpacingCoarse, setSliceSpacingFine, setViewTextureAligned, setVolView, showBoxSlice, update3DTriplanar, updateBoxSlicePos, updateBoxSlices, updateCubicTransform, updateOpacityOfOthrogPlanes, updateTransform, useSliceSpacingCoarse, useSliceSpacingFine

Methods inherited from class gov.nih.mipav.view.renderer.J3D.RenderViewBase
calcImageNormals, createBoxFrame, disableCamera, disposeLocal, getBehaviorGroup, getBound, getBranchGroup, getCanvas, getNormals, getRGBTA, getRGBTB, getSceneRootTG, getSliderEvents, getTriPlanarViewBG, getUniverse, recordMouse, setBackgroundColor, setBoxColor, setRotationAngle, setRotationAxis, writeImage, writeImageAuto

Methods inherited from class gov.nih.mipav.view.renderer.J3D.VolumeCanvas3D
GetTestFrameRate, MeasureTime, paint, postSwap, ResetTime, SetTestFrameRate, supportsTexture3D, update, UpdateFrameCount

Methods inherited from class javax.media.j3d.Canvas3D
addNotify, getBounds, getBounds, getCenterEyeInImagePlate, getDoubleBufferAvailable, getDoubleBufferEnable, getGraphics2D, getGraphicsContext3D, getHeight, getImagePlateToVworld, getInverseVworldProjection, getLeftEyeInImagePlate, getLeftManualEyeInImagePlate, getLocation, getLocation, getLocationOnScreen, getMonoscopicViewPolicy, getOffScreenBuffer, getOffScreenLocation, getOffScreenLocation, getPhysicalHeight, getPhysicalWidth, getPixelLocationFromImagePlate, getPixelLocationInImagePlate, getPixelLocationInImagePlate, getRightEyeInImagePlate, getRightManualEyeInImagePlate, getSceneAntialiasingAvailable, getScreen3D, getSize, getSize, getStereoAvailable, getStereoEnable, getView, getVworldProjection, getVworldToImagePlate, getWidth, getX, getY, isOffScreen, isRendererRunning, isShadingLanguageSupported, postRender, preRender, queryProperties, removeNotify, renderField, renderOffScreenBuffer, setDoubleBufferEnable, setLeftManualEyeInImagePlate, setMonoscopicViewPolicy, setOffScreenBuffer, setOffScreenLocation, setOffScreenLocation, setRightManualEyeInImagePlate, setStereoEnable, startRenderer, stopRenderer, swap, waitForOffScreenRendering

Methods inherited from class java.awt.Canvas
createBufferStrategy, createBufferStrategy, getAccessibleContext, getBufferStrategy

Methods inherited from class java.awt.Component
action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, bounds, checkImage, checkImage, coalesceEvents, contains, contains, createImage, createImage, createVolatileImage, createVolatileImage, deliverEvent, disable, disableEvents, dispatchEvent, doLayout, enable, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getAlignmentX, getAlignmentY, getBackground, getBaseline, getBaselineResizeBehavior, getColorModel, getComponentAt, getComponentAt, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeys, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphics, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getListeners, getLocale, getMaximumSize, getMinimumSize, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPreferredSize, getPropertyChangeListeners, getPropertyChangeListeners, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, hide, imageUpdate, inside, invalidate, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusCycleRoot, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isOpaque, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, layout, list, list, list, list, list, locate, location, lostFocus, minimumSize, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, paramString, postEvent, preferredSize, prepareImage, prepareImage, print, printAll, processComponentEvent, processEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, repaint, requestFocus, requestFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, requestFocusInWindow, reshape, resize, resize, revalidate, setBackground, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeys, setFocusTraversalKeysEnabled, setFont, setForeground, setIgnoreRepaint, setLocale, setLocation, setLocation, setMaximumSize, setMinimumSize, setMixingCutoutShape, setName, setPreferredSize, setSize, setSize, setVisible, show, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCycle, validate

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

- Field Detail
  - serialVersionUID
```
private static final long serialVersionUID
```
    Use serialVersionUID for interoperability.
    
    See Also:
    
    Constant Field Values
  - ARTERIAL_SEG
```
public static final int ARTERIAL_SEG
```
    Value which indicates a voxel that is part of the arterial vasculature tree.
    
    See Also:
    
    Constant Field Values
  - 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:
    
    Constant Field Values
  - 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:
    
    Constant Field Values
  - 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:
    
    Constant Field Values
  - BONE_SEG
```
public static final int BONE_SEG
```
    Value which indicates a bone in the image.
    
    See Also:
    
    Constant Field Values
  - ENTRY_POINT
```
public static final int ENTRY_POINT
```
    Value which indicates the probe entry point color.
    
    See Also:
    
    Constant Field Values
  - 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 Detail
  - SurfaceView
```
public SurfaceView(ModelImage _imageA,
                   ModelImage _imageB,
                   java.awt.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,
                   java.awt.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 Detail
  - actionPerformed
```
public void actionPerformed(java.awt.event.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 java.awt.event.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(java.util.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 java.lang.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 javax.swing.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(java.lang.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(java.awt.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(javax.swing.event.ChangeEvent e)
```
    Sets how the image plane should be displayed depending on value of slider.
    
    Specified by:
    
    stateChanged in interface javax.swing.event.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:
    
    Vector3f - [] the reordered (x,y,z) coordinates for each boxSlice remapped into ModelCoordinates.
    
    boxSliceConstants - the reordered mode value (X_SLICE, Y_SLICE, Z_SLICE) 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 java.lang.Throwable
```
    Calls disposeLocal.
    
    Overrides:
    
    finalize in class java.lang.Object
    
    Throws:
    
    java.lang.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

Class SurfaceView

Nested Class Summary

Nested classes/interfaces inherited from class gov.nih.mipav.view.renderer.J3D.RenderViewBase

Nested classes/interfaces inherited from class java.awt.Canvas

Nested classes/interfaces inherited from class java.awt.Component

Field Summary

Fields inherited from class gov.nih.mipav.view.renderer.J3D.surfaceview.SurfaceRender

Fields inherited from class gov.nih.mipav.view.renderer.J3D.RenderViewBase

Fields inherited from class gov.nih.mipav.view.renderer.J3D.VolumeCanvas3D

Fields inherited from class javax.media.j3d.Canvas3D

Fields inherited from class java.awt.Component

Fields inherited from interface java.awt.image.ImageObserver

Fields inherited from interface com.sun.j3d.utils.behaviors.mouse.MouseBehaviorCallback

Constructor Summary

Method Summary

Methods inherited from class gov.nih.mipav.view.renderer.J3D.surfaceview.SurfaceRender

Methods inherited from class gov.nih.mipav.view.renderer.J3D.RenderViewBase

Methods inherited from class gov.nih.mipav.view.renderer.J3D.VolumeCanvas3D

Methods inherited from class javax.media.j3d.Canvas3D

Methods inherited from class java.awt.Canvas

Methods inherited from class java.awt.Component

Methods inherited from class java.lang.Object

Field Detail

serialVersionUID

ARTERIAL_SEG

VEINOUS_SEG

VASCULATURE_SEG

TUMOR_SEG

BONE_SEG

ENTRY_POINT

boxPanel

boxSlices

boxSliceVertices

bufferFactor

clipPanel

cubicBehaviorBG

cubicBG

cubicRotate

cubicTG

currentTransform

currentTransformType

first6ClipPlane

firstClipArbi

geodesicPanel

imageA

imageB

isEntryPoint

m_bRenderModeLighting

m_dOriginalScreenScale

m_kObjBoxSliceProbe_TG

m_kObjPlaneProbe_TG

m_kProbeTransform

m_kSoftwareLightSet

m_kSoftwareMaterial

mousePanel

mouseRotateBehavior

mouseTranslateBehavior

mouseZoomBehavior

myEyePoint

objTransSlices_TG

objPlane_BG

parallelRotation

parallelScaleT3D

parent

probePanel

resols

rotationCount

segmentationImage

slicePanel

surfacePanel

surfaceTexturePanel

switchGroup

m_kRFACoordMaps

transformCubic

transformNode3d

view

volBG

volRenderBG

volRenderOG

volumeDisplayMode3D