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.brainflattenerview.MjCorticalAnalysis

All Implemented Interfaces:

com.sun.j3d.utils.behaviors.mouse.MouseBehaviorCallback, ViewImageUpdateInterface, java.awt.event.ActionListener, java.awt.event.MouseListener, java.awt.event.MouseMotionListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, java.util.EventListener, javax.accessibility.Accessible, javax.swing.event.ChangeListener
```
public class MjCorticalAnalysis
extends RenderViewBase
implements java.awt.event.MouseListener, java.awt.event.MouseMotionListener
```
Cortical analysis applet and viewer. This class contains the static 'main' method to launch the application. This class is an Applet which means that it can be embedded in a browser or it can be attached to a MainFrame when executed as an application.

See Also:

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
`private int[]`	`m_aiTriIndex`	DOCUMENT ME!
`private javax.vecmath.Color3f[]`	`m_akPickColors`	Colors for the picked points:.
`private javax.vecmath.Color4f[]`	`m_akTriColors`	DOCUMENT ME!
`private boolean`	`m_bCurvatureColors`	Flag set to indicate whether curvature colors are rendered on the mesh surface.
`private boolean`	`m_bInflationInitialized`	Flag set once inflation processing has been initialized.
`private boolean`	`m_bMousePressed`	Mouse events.
`private boolean`	`m_bMouseReleased`	DOCUMENT ME!
`private boolean`	`m_bPickCorrespondenceEnabled`	Turned on when picking with the mouse is enabled:.
`private boolean`	`m_bPickPunctureEnabled`	DOCUMENT ME!
`private int`	`m_iNumPicked`	number of picked points displayed.
`private int`	`m_iRunningNumPicked`	DOCUMENT ME!
`private MjCorticalMesh`	`m_kCortical`	Cortical mesh to be used in rendering scene.
`private javax.media.j3d.GeometryArray`	`m_kGeometryArrayPlane`	DOCUMENT ME!
`private javax.media.j3d.GeometryArray`	`m_kGeometryArraySphere`	DOCUMENT ME!
`private ModelLUT`	`m_kLUTConvexity`	DOCUMENT ME!
`private ModelLUT`	`m_kLUTCurvature`	local reference to ModelLUT.
`private javax.media.j3d.BranchGroup`	`m_kMeshBranchRoot`	BranchGroups for the Meshlines, for deleting and recreating the meshlines when the user changes the number of latitude and longitude lines:.
`private javax.media.j3d.BranchGroup`	`m_kMeshLinesBranchRoot`	DOCUMENT ME!
`private java.awt.event.MouseEvent`	`m_kMouseEvent`	DOCUMENT ME!
`private JPanelBrainSurfaceFlattener`	`m_kPanel`	DOCUMENT ME!
`private com.sun.j3d.utils.picking.PickCanvas`	`m_kPickCanvas`	DOCUMENT ME!
`private javax.media.j3d.Shape3D`	`m_kShapeMesh`	DOCUMENT ME!
`private javax.media.j3d.Shape3D`	`m_kShapePlane`	DOCUMENT ME!
`private javax.media.j3d.Shape3D`	`m_kShapeSphere`	DOCUMENT ME!
`private javax.media.j3d.Switch`	`m_kSwitchDisplay`	Switch between displaying the Sphere and the Plane:.
`private javax.media.j3d.Switch`	`m_kSwitchLinesMesh`	This node contains the latitude/longitude renderings for the mesh which can be enabled/disabled.
`private javax.media.j3d.Switch`	`m_kSwitchLinesPlane`	This node contains the latitude/longitude renderings for the plane which can be enabled/disabled.
`private javax.media.j3d.BranchGroup`	`m_kSwitchLinesPlaneBranch`	DOCUMENT ME!
`private javax.media.j3d.Switch`	`m_kSwitchLinesSphere`	This node contains the latitude/longitude renderings for the sphere which can be enabled/disabled.
`private javax.media.j3d.BranchGroup`	`m_kSwitchLinesSphereBranch`	DOCUMENT ME!
`private javax.media.j3d.TransformGroup`	`m_kTransformGroupActive`	Currently selected transform that gets modified by the handler for the keyboard behavior.
`private javax.media.j3d.TransformGroup`	`m_kTransformGroupMesh`	DOCUMENT ME!
`private javax.media.j3d.TransformGroup`	`m_kTransformGroupPlane`	DOCUMENT ME!
`private javax.media.j3d.TransformGroup`	`m_kTransformGroupPoseMesh`	This node contains all of the cortical mesh related nodes in the scene which can be manipulated as a group.
`private javax.media.j3d.TransformGroup`	`m_kTransformGroupPosePlane`	This node contains all of the plane related nodes in the scene which can be manipulated as a group.
`private javax.media.j3d.TransformGroup`	`m_kTransformGroupPoseSphere`	This node contains all of the sphere related nodes in the scene which can be manipulated as a group.
`private javax.media.j3d.TransformGroup`	`m_kTransformGroupSphere`	DOCUMENT ME!
`private ModelTriangleMesh`	`m_kTriangleMesh`	Geometry for the rendering of the cortical mesh is maintained here so that the scene can be updated when the mesh is inflated.
`private int`	`MAX_POINTS`	DOCUMENT ME!
`private int`	`MESH`	DOCUMENT ME!
`private int`	`PLANE`	DOCUMENT ME!
`private static long`	`serialVersionUID`	Use serialVersionUID for interoperability.
`private int`	`SPHERE`	DOCUMENT ME!

Fields inherited from class gov.nih.mipav.view.renderer.J3D.RenderViewBase
background, bounds, boxFrame, canvas, captureFrame, captureImage, config, displayMode, IMAGE_A, IMAGE_B, imageA, imageB, 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
`MjCorticalAnalysis(ModelImage _imageA, ModelImage _imageB, java.awt.GraphicsConfiguration _config, ViewJFrameVolumeView kParent)`	A simple universe is created that contains a viewing platform.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`actionPerformed(java.awt.event.ActionEvent e)`	actionPerformed.
`void`	`calculateConformal()`	Called on setup, when a new triangle mesh is loaded, or when the puncture triangle is selected and the "recalculate conformal" button is pressed by the user:
`private float`	`closestPlanePointIndex(javax.vecmath.Point3f kStart, int[] aiIndex)`	For the plane, all vertices have z-value set to zero.
`private static javax.vecmath.Point3f[]`	`combine(javax.vecmath.Point3f[] akPointA, javax.vecmath.Point3f[] akPointB)`	DOCUMENT ME!
`private static javax.media.j3d.GeometryArray`	`createGeometry(javax.vecmath.Point3f[] akPoint, javax.vecmath.Color4f[] akColor, int[] aiConnect)`	DOCUMENT ME!
`private static ModelTriangleMesh`	`createTriangleMesh(javax.vecmath.Point3f[] akPoint, javax.vecmath.Vector3f[] akNormal, javax.vecmath.Color4f[] akColor, int[] aiConnect)`	DOCUMENT ME!
`boolean`	`displayConvexityColors()`	toggle between display of mean curvature-based colors and average convexity-based colors.
`boolean`	`displayCurvatureColors()`	toggle between display of mean curvature-based colors and average convexity-based colors.
`void`	`displayPlane()`	Switch to displaying the plane:
`void`	`displaySphere()`	Switch to displaying the sphere:
`void`	`disposeLocal()`	DOCUMENT ME!
`void`	`drawPicked(javax.vecmath.Point3f kStart, int[] aiIndex, int iWhich)`	Draw the user-selected point, either as a sphere on the triangle mesh, or as a black triangle, depending on which picking is enabled:
`private void`	`drawPoint(javax.vecmath.Point3f kStart, int[] aiIndex, int iWhich)`	Draw the user-selected point as a sphere on the triangle mesh:
`private void`	`drawTriangle(javax.vecmath.Point3f kStart, int[] aiIndex, int iWhich)`	Draw the user-selected triangle as a black triangle, save the original color so it can be restored:
`protected void`	`finalize()`	DOCUMENT ME!
`javax.swing.JPanel`	`getMainPanel()`	DOCUMENT ME!
`float`	`getMaxAverageConvexity()`	DOCUMENT ME!
`float`	`getMaxCurvature()`	return the max mean curvature:
`javax.media.j3d.BranchGroup`	`getMesh()`	Display the mesh in the SurfaceRenderer:
`javax.media.j3d.BranchGroup`	`getMeshLines()`	Display the mesh lines in the SurfaceRenderer:
`float`	`getMinAverageConvexity()`	DOCUMENT ME!
`float`	`getMinCurvature()`	return the min mean curvature:
`java.lang.Object`	`getSceneState()`	Gets the scene state in terms of slices visible, which slice number, etc.
`ModelTriangleMesh`	`getTMesh()`	Display the mesh in the SurfaceRenderer:
`private static javax.vecmath.Vector3d`	`getTranslateToCenter(javax.media.j3d.Shape3D kShape)`	DOCUMENT ME!
`boolean`	`inflation()`	perform inflation step and then render shapes using the average convexity colors.
`boolean`	`isCorrespondencePickEnabled()`	Return whether or not picking correspondence points is enabled:
`boolean`	`isPickEnabled()`	Returns whether or not picking is enabled:
`boolean`	`isPuncturePickEnabled()`	Return whether or not picking the puncture triangle is enabled:
`void`	`mouseClicked(java.awt.event.MouseEvent kEvent)`	DOCUMENT ME!
`void`	`mouseDragged(java.awt.event.MouseEvent kEvent)`	DOCUMENT ME!
`void`	`mouseEntered(java.awt.event.MouseEvent kEvent)`	DOCUMENT ME!
`void`	`mouseExited(java.awt.event.MouseEvent kEvent)`	DOCUMENT ME!
`void`	`mouseMoved(java.awt.event.MouseEvent kEvent)`	DOCUMENT ME!
`void`	`mousePressed(java.awt.event.MouseEvent kMouseEvent)`	DOCUMENT ME!
`void`	`mouseReleased(java.awt.event.MouseEvent kEvent)`	DOCUMENT ME!
`void`	`removePoints()`	Remove all points drawn on the mesh, sphere, and plane:
`private void`	`restoreTriColor()`	Resets the previously picked triangle to it's orginal color:
`void`	`setAlphaBlend(int value)`	Sets the alpha blending of parameter for two image displaying.
`private static void`	`setColors(float fCMin, float fCMax, float[] afCArray, int iVQuantity, javax.vecmath.Color4f[] akColor)`	DOCUMENT ME!
`private void`	`setColorsLUT()`	Update the colormap based on the LUT:
`void`	`setGUI(java.lang.Object scene)`	Used by the JPanelMouse the redisplay the recorded actions.
`void`	`setLUTConvexity(ModelLUT kLUT)`	DOCUMENT ME!
`void`	`setLUTCurvature(ModelLUT kLUT)`	Update the colormap based on the LUT:
`void`	`setRGBTA(ModelRGB RGBT)`	setRGBTA.
`void`	`setRGBTB(ModelRGB RGBT)`	setRGBTB.
`void`	`setSlice(int slice)`	setSlice.
`void`	`setTimeSlice(int tSlice)`	setTimeSlice.
`void`	`setup(ModelTriangleMesh kTriangleMesh)`	Perform all initialization prior to executing.
`void`	`setupLatLon(int iNumLat, int iNumLon)`	Called when the mesh is created, or when the number of latitude or longitude lines is changed by the user.
`private void`	`setupLight()`	Sets up a direction lightsource for the scene.
`void`	`stateChanged(javax.swing.event.ChangeEvent e)`	stateChanged.
`void`	`toggleLatLonLines()`	Toggle between displaying the latitude and longitude lines:
`void`	`togglePickCorrespondence()`	Enables picking with the mouse and drawing the curve on the mesh.
`void`	`togglePickPuncture()`	Enables picking with the mouse and drawing the curve on the mesh.
`void`	`transformChanged(int type, javax.media.j3d.Transform3D transform)`	transformChanged.
`boolean`	`updateImageExtents()`	updateImageExtents.
`boolean`	`updateImages()`	updateImages.
`boolean`	`updateImages(boolean flag)`	updateImages.
`boolean`	`updateImages(ModelLUT LUTa, ModelLUT LUTb, boolean flag, int interpMode)`	updateImages.

Methods inherited from class gov.nih.mipav.view.renderer.J3D.RenderViewBase
autoCapture, calcImageNormals, createBoxFrame, disableCamera, getBehaviorGroup, getBound, getBranchGroup, getCanvas, getImageA, getImageB, getNormals, getRGBTA, getRGBTB, getSceneRootTG, getSliderEvents, getTriPlanarViewBG, getUniverse, recordMouse, resetAxisX, resetAxisY, resetImage, rotateImage, 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
  - m_aiTriIndex
```
private int[] m_aiTriIndex
```
    DOCUMENT ME!
  - m_akPickColors
```
private javax.vecmath.Color3f[] m_akPickColors
```
    Colors for the picked points:.
  - m_akTriColors
```
private javax.vecmath.Color4f[] m_akTriColors
```
    DOCUMENT ME!
  - m_bCurvatureColors
```
private boolean m_bCurvatureColors
```
    Flag set to indicate whether curvature colors are rendered on the mesh surface. If not, then average convexity colors are rendered.
  - m_bInflationInitialized
```
private boolean m_bInflationInitialized
```
    Flag set once inflation processing has been initialized.
  - m_bMousePressed
```
private boolean m_bMousePressed
```
    Mouse events. Setting mousePressed and mouseReleased explicitly when the mouse events are received has deals with getting multiply mouse event notifications for the same mouse press.
  - m_bMouseReleased
```
private boolean m_bMouseReleased
```
    DOCUMENT ME!
  - m_bPickCorrespondenceEnabled
```
private boolean m_bPickCorrespondenceEnabled
```
    Turned on when picking with the mouse is enabled:.
  - m_bPickPunctureEnabled
```
private boolean m_bPickPunctureEnabled
```
    DOCUMENT ME!
  - m_iNumPicked
```
private int m_iNumPicked
```
    number of picked points displayed.
  - m_iRunningNumPicked
```
private int m_iRunningNumPicked
```
    DOCUMENT ME!
  - m_kCortical
```
private MjCorticalMesh m_kCortical
```
    Cortical mesh to be used in rendering scene.
  - m_kGeometryArrayPlane
```
private javax.media.j3d.GeometryArray m_kGeometryArrayPlane
```
    DOCUMENT ME!
  - m_kGeometryArraySphere
```
private javax.media.j3d.GeometryArray m_kGeometryArraySphere
```
    DOCUMENT ME!
  - m_kLUTConvexity
```
private ModelLUT m_kLUTConvexity
```
    DOCUMENT ME!
  - m_kLUTCurvature
```
private ModelLUT m_kLUTCurvature
```
    local reference to ModelLUT.
  - m_kMeshBranchRoot
```
private javax.media.j3d.BranchGroup m_kMeshBranchRoot
```
    BranchGroups for the Meshlines, for deleting and recreating the meshlines when the user changes the number of latitude and longitude lines:.
  - m_kMeshLinesBranchRoot
```
private javax.media.j3d.BranchGroup m_kMeshLinesBranchRoot
```
    DOCUMENT ME!
  - m_kMouseEvent
```
private java.awt.event.MouseEvent m_kMouseEvent
```
    DOCUMENT ME!
  - m_kPanel
```
private JPanelBrainSurfaceFlattener m_kPanel
```
    DOCUMENT ME!
  - m_kPickCanvas
```
private com.sun.j3d.utils.picking.PickCanvas m_kPickCanvas
```
    DOCUMENT ME!
  - m_kShapeMesh
```
private javax.media.j3d.Shape3D m_kShapeMesh
```
    DOCUMENT ME!
  - m_kShapePlane
```
private javax.media.j3d.Shape3D m_kShapePlane
```
    DOCUMENT ME!
  - m_kShapeSphere
```
private javax.media.j3d.Shape3D m_kShapeSphere
```
    DOCUMENT ME!
  - m_kSwitchDisplay
```
private javax.media.j3d.Switch m_kSwitchDisplay
```
    Switch between displaying the Sphere and the Plane:.
  - m_kSwitchLinesMesh
```
private javax.media.j3d.Switch m_kSwitchLinesMesh
```
    This node contains the latitude/longitude renderings for the mesh which can be enabled/disabled.
  - m_kSwitchLinesPlane
```
private javax.media.j3d.Switch m_kSwitchLinesPlane
```
    This node contains the latitude/longitude renderings for the plane which can be enabled/disabled.
  - m_kSwitchLinesPlaneBranch
```
private javax.media.j3d.BranchGroup m_kSwitchLinesPlaneBranch
```
    DOCUMENT ME!
  - m_kSwitchLinesSphere
```
private javax.media.j3d.Switch m_kSwitchLinesSphere
```
    This node contains the latitude/longitude renderings for the sphere which can be enabled/disabled.
  - m_kSwitchLinesSphereBranch
```
private javax.media.j3d.BranchGroup m_kSwitchLinesSphereBranch
```
    DOCUMENT ME!
  - m_kTransformGroupActive
```
private javax.media.j3d.TransformGroup m_kTransformGroupActive
```
    Currently selected transform that gets modified by the handler for the keyboard behavior.
  - m_kTransformGroupMesh
```
private javax.media.j3d.TransformGroup m_kTransformGroupMesh
```
    DOCUMENT ME!
  - m_kTransformGroupPlane
```
private javax.media.j3d.TransformGroup m_kTransformGroupPlane
```
    DOCUMENT ME!
  - m_kTransformGroupPoseMesh
```
private javax.media.j3d.TransformGroup m_kTransformGroupPoseMesh
```
    This node contains all of the cortical mesh related nodes in the scene which can be manipulated as a group.
  - m_kTransformGroupPosePlane
```
private javax.media.j3d.TransformGroup m_kTransformGroupPosePlane
```
    This node contains all of the plane related nodes in the scene which can be manipulated as a group.
  - m_kTransformGroupPoseSphere
```
private javax.media.j3d.TransformGroup m_kTransformGroupPoseSphere
```
    This node contains all of the sphere related nodes in the scene which can be manipulated as a group.
  - m_kTransformGroupSphere
```
private javax.media.j3d.TransformGroup m_kTransformGroupSphere
```
    DOCUMENT ME!
  - m_kTriangleMesh
```
private ModelTriangleMesh m_kTriangleMesh
```
    Geometry for the rendering of the cortical mesh is maintained here so that the scene can be updated when the mesh is inflated.
  - MAX_POINTS
```
private int MAX_POINTS
```
    DOCUMENT ME!
  - MESH
```
private int MESH
```
    DOCUMENT ME!
  - PLANE
```
private int PLANE
```
    DOCUMENT ME!
  - SPHERE
```
private int SPHERE
```
    DOCUMENT ME!
- Constructor Detail
  - MjCorticalAnalysis
```
public MjCorticalAnalysis(ModelImage _imageA,
                          ModelImage _imageB,
                          java.awt.GraphicsConfiguration _config,
                          ViewJFrameVolumeView kParent)
```
    A simple universe is created that contains a viewing platform. A canvas is created and attached to the simple universe and is added to this instance The canvas is used for the 3D rendering. An initially empty scene graph for the application is created and assigned to the universe.
    
    Parameters:
    
    _imageA - DOCUMENT ME!
    
    _imageB - DOCUMENT ME!
    
    _config - DOCUMENT ME!
    
    kParent - DOCUMENT ME!
- Method Detail
  - actionPerformed
```
public void actionPerformed(java.awt.event.ActionEvent e)
```
    actionPerformed.
    
    Specified by:
    
    actionPerformed in interface java.awt.event.ActionListener
    
    Parameters:
    
    e - ActionEvent
  - calculateConformal
```
public void calculateConformal()
```
    Called on setup, when a new triangle mesh is loaded, or when the puncture triangle is selected and the "recalculate conformal" button is pressed by the user:
  - displayConvexityColors
```
public boolean displayConvexityColors()
```
    toggle between display of mean curvature-based colors and average convexity-based colors.
    
    Returns:
    
    DOCUMENT ME!
  - displayCurvatureColors
```
public boolean displayCurvatureColors()
```
    toggle between display of mean curvature-based colors and average convexity-based colors.
    
    Returns:
    
    DOCUMENT ME!
  - displayPlane
```
public void displayPlane()
```
    Switch to displaying the plane:
  - displaySphere
```
public void displaySphere()
```
    Switch to displaying the sphere:
  - disposeLocal
```
public void disposeLocal()
```
    DOCUMENT ME!
    
    Overrides:
    
    disposeLocal in class RenderViewBase
  - drawPicked
```
public void drawPicked(javax.vecmath.Point3f kStart,
                       int[] aiIndex,
                       int iWhich)
```
    Draw the user-selected point, either as a sphere on the triangle mesh, or as a black triangle, depending on which picking is enabled:
    
    Parameters:
    
    kStart - DOCUMENT ME!
    
    aiIndex - DOCUMENT ME!
    
    iWhich - DOCUMENT ME!
  - getMainPanel
```
public javax.swing.JPanel getMainPanel()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getMaxAverageConvexity
```
public float getMaxAverageConvexity()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getMaxCurvature
```
public float getMaxCurvature()
```
    return the max mean curvature:
    
    Returns:
    
    DOCUMENT ME!
  - getMesh
```
public javax.media.j3d.BranchGroup getMesh()
```
    Display the mesh in the SurfaceRenderer:
    
    Returns:
    
    a Branchgroup containing a copy of the ModelTriangleMesh
  - getMeshLines
```
public javax.media.j3d.BranchGroup getMeshLines()
```
    Display the mesh lines in the SurfaceRenderer:
    
    Returns:
    
    a BranchGroup containing a copy of the TriangleMesh Lat/Lon Lines
  - getMinAverageConvexity
```
public float getMinAverageConvexity()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getMinCurvature
```
public float getMinCurvature()
```
    return the min mean curvature:
    
    Returns:
    
    DOCUMENT ME!
  - getSceneState
```
public java.lang.Object getSceneState()
```
    Gets the scene state in terms of slices visible, which slice number, etc.
    
    Specified by:
    
    getSceneState in class RenderViewBase
    
    Returns:
    
    A private object extension specific to the class that extends this one.
  - getTMesh
```
public ModelTriangleMesh getTMesh()
```
    Display the mesh in the SurfaceRenderer:
    
    Returns:
    
    DOCUMENT ME!
  - inflation
```
public boolean inflation()
```
    perform inflation step and then render shapes using the average convexity colors.
    
    Returns:
    
    DOCUMENT ME!
  - isCorrespondencePickEnabled
```
public boolean isCorrespondencePickEnabled()
```
    Return whether or not picking correspondence points is enabled:
    
    Returns:
    
    DOCUMENT ME!
  - isPickEnabled
```
public boolean isPickEnabled()
```
    Returns whether or not picking is enabled:
    
    Returns:
    
    DOCUMENT ME!
  - isPuncturePickEnabled
```
public boolean isPuncturePickEnabled()
```
    Return whether or not picking the puncture triangle is enabled:
    
    Returns:
    
    DOCUMENT ME!
  - mouseClicked
```
public void mouseClicked(java.awt.event.MouseEvent kEvent)
```
    DOCUMENT ME!
    
    Specified by:
    
    mouseClicked in interface java.awt.event.MouseListener
    
    Parameters:
    
    kEvent - the mouse event generated by a mouse clicked
  - mouseDragged
```
public void mouseDragged(java.awt.event.MouseEvent kEvent)
```
    DOCUMENT ME!
    
    Specified by:
    
    mouseDragged in interface java.awt.event.MouseMotionListener
    
    Parameters:
    
    kEvent - the mouse event generated by a mouse drag
  - mouseEntered
```
public void mouseEntered(java.awt.event.MouseEvent kEvent)
```
    DOCUMENT ME!
    
    Specified by:
    
    mouseEntered in interface java.awt.event.MouseListener
    
    Parameters:
    
    kEvent - the mouse event generated by a mouse entered
  - mouseExited
```
public void mouseExited(java.awt.event.MouseEvent kEvent)
```
    DOCUMENT ME!
    
    Specified by:
    
    mouseExited in interface java.awt.event.MouseListener
    
    Parameters:
    
    kEvent - the mouse event generated by a mouse exit
  - mouseMoved
```
public void mouseMoved(java.awt.event.MouseEvent kEvent)
```
    DOCUMENT ME!
    
    Specified by:
    
    mouseMoved in interface java.awt.event.MouseMotionListener
    
    Parameters:
    
    kEvent - the event generated by a mouse movement
  - mousePressed
```
public void mousePressed(java.awt.event.MouseEvent kMouseEvent)
```
    DOCUMENT ME!
    
    Specified by:
    
    mousePressed in interface java.awt.event.MouseListener
    
    Parameters:
    
    kMouseEvent - the mouse event generated by a mouse press
  - mouseReleased
```
public void mouseReleased(java.awt.event.MouseEvent kEvent)
```
    DOCUMENT ME!
    
    Specified by:
    
    mouseReleased in interface java.awt.event.MouseListener
    
    Parameters:
    
    kEvent - the mouse event generated by a mouse release
  - removePoints
```
public void removePoints()
```
    Remove all points drawn on the mesh, sphere, and plane:
  - setAlphaBlend
```
public void setAlphaBlend(int value)
```
    Sets the alpha blending of parameter for two image displaying.
    
    Specified by:
    
    setAlphaBlend in class RenderViewBase
    
    Parameters:
    
    value - amount [0,100] that is the percentage of Image A to be displayed and (1-percentage) of Image B to be displayed
  - setGUI
```
public void setGUI(java.lang.Object scene)
```
    Used by the JPanelMouse the redisplay the recorded actions.
    
    Specified by:
    
    setGUI in class RenderViewBase
    
    Parameters:
    
    scene - Object
  - setLUTConvexity
```
public void setLUTConvexity(ModelLUT kLUT)
```
    DOCUMENT ME!
    
    Parameters:
    
    kLUT - DOCUMENT ME!
  - setLUTCurvature
```
public void setLUTCurvature(ModelLUT kLUT)
```
    Update the colormap based on the LUT:
    
    Parameters:
    
    kLUT - DOCUMENT ME!
  - setRGBTA
```
public void setRGBTA(ModelRGB RGBT)
```
    setRGBTA.
    
    Specified by:
    
    setRGBTA in class RenderViewBase
    
    Parameters:
    
    RGBT - ModelRGB
  - setRGBTB
```
public void setRGBTB(ModelRGB RGBT)
```
    setRGBTB.
    
    Specified by:
    
    setRGBTB in class RenderViewBase
    
    Parameters:
    
    RGBT - ModelRGB
  - setSlice
```
public void setSlice(int slice)
```
    setSlice.
    
    Specified by:
    
    setSlice in interface ViewImageUpdateInterface
    
    Parameters:
    
    slice - int
  - setTimeSlice
```
public void setTimeSlice(int tSlice)
```
    setTimeSlice.
    
    Specified by:
    
    setTimeSlice in interface ViewImageUpdateInterface
    
    Parameters:
    
    tSlice - int
  - setup
```
public void setup(ModelTriangleMesh kTriangleMesh)
```
    Perform all initialization prior to executing. Loads the sample mesh surface and sets up the rendering of the scene.
    
    Parameters:
    
    kTriangleMesh - DOCUMENT ME!
  - setupLatLon
```
public void setupLatLon(int iNumLat,
                        int iNumLon)
```
    Called when the mesh is created, or when the number of latitude or longitude lines is changed by the user. When the user changes the number of latitude or longitude lines, the meshes are removed from the scene and recreated.
    
    Parameters:
    
    iNumLat - DOCUMENT ME!
    
    iNumLon - DOCUMENT ME!
  - stateChanged
```
public void stateChanged(javax.swing.event.ChangeEvent e)
```
    stateChanged.
    
    Specified by:
    
    stateChanged in interface javax.swing.event.ChangeListener
    
    Parameters:
    
    e - ChangeEvent
  - toggleLatLonLines
```
public void toggleLatLonLines()
```
    Toggle between displaying the latitude and longitude lines:
  - togglePickCorrespondence
```
public void togglePickCorrespondence()
```
    Enables picking with the mouse and drawing the curve on the mesh.
  - togglePickPuncture
```
public void togglePickPuncture()
```
    Enables picking with the mouse and drawing the curve on the mesh.
  - transformChanged
```
public void transformChanged(int type,
                             javax.media.j3d.Transform3D transform)
```
    transformChanged.
    
    Specified by:
    
    transformChanged in interface com.sun.j3d.utils.behaviors.mouse.MouseBehaviorCallback
    
    Parameters:
    
    type - int
    
    transform - Transform3D
  - updateImageExtents
```
public boolean updateImageExtents()
```
    updateImageExtents.
    
    Specified by:
    
    updateImageExtents in interface ViewImageUpdateInterface
    
    Returns:
    
    boolean
  - updateImages
```
public boolean updateImages()
```
    updateImages.
    
    Specified by:
    
    updateImages in interface ViewImageUpdateInterface
    
    Returns:
    
    boolean
  - updateImages
```
public boolean updateImages(boolean flag)
```
    updateImages.
    
    Specified by:
    
    updateImages in interface ViewImageUpdateInterface
    
    Parameters:
    
    flag - boolean
    
    Returns:
    
    boolean
  - updateImages
```
public boolean updateImages(ModelLUT LUTa,
                            ModelLUT LUTb,
                            boolean flag,
                            int interpMode)
```
    updateImages.
    
    Specified by:
    
    updateImages in interface ViewImageUpdateInterface
    
    Parameters:
    
    LUTa - ModelLUT
    
    LUTb - ModelLUT
    
    flag - boolean
    
    interpMode - int
    
    Returns:
    
    boolean
  - finalize
```
protected void finalize()
                 throws java.lang.Throwable
```
    DOCUMENT ME!
    
    Overrides:
    
    finalize in class java.lang.Object
    
    Throws:
    
    java.lang.Throwable - DOCUMENT ME!
  - combine
```
private static javax.vecmath.Point3f[] combine(javax.vecmath.Point3f[] akPointA,
                                               javax.vecmath.Point3f[] akPointB)
```
    DOCUMENT ME!
    
    Parameters:
    
    akPointA - DOCUMENT ME!
    
    akPointB - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - createGeometry
```
private static javax.media.j3d.GeometryArray createGeometry(javax.vecmath.Point3f[] akPoint,
                                                            javax.vecmath.Color4f[] akColor,
                                                            int[] aiConnect)
```
    DOCUMENT ME!
    
    Parameters:
    
    akPoint - DOCUMENT ME!
    
    akColor - DOCUMENT ME!
    
    aiConnect - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - createTriangleMesh
```
private static ModelTriangleMesh createTriangleMesh(javax.vecmath.Point3f[] akPoint,
                                                    javax.vecmath.Vector3f[] akNormal,
                                                    javax.vecmath.Color4f[] akColor,
                                                    int[] aiConnect)
```
    DOCUMENT ME!
    
    Parameters:
    
    akPoint - DOCUMENT ME!
    
    akNormal - DOCUMENT ME!
    
    akColor - DOCUMENT ME!
    
    aiConnect - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getTranslateToCenter
```
private static javax.vecmath.Vector3d getTranslateToCenter(javax.media.j3d.Shape3D kShape)
```
    DOCUMENT ME!
    
    Parameters:
    
    kShape - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - setColors
```
private static void setColors(float fCMin,
                              float fCMax,
                              float[] afCArray,
                              int iVQuantity,
                              javax.vecmath.Color4f[] akColor)
```
    DOCUMENT ME!
    
    Parameters:
    
    fCMin - DOCUMENT ME!
    
    fCMax - DOCUMENT ME!
    
    afCArray - DOCUMENT ME!
    
    iVQuantity - DOCUMENT ME!
    
    akColor - DOCUMENT ME!
  - closestPlanePointIndex
```
private float closestPlanePointIndex(javax.vecmath.Point3f kStart,
                                     int[] aiIndex)
```
    For the plane, all vertices have z-value set to zero. Because the mesh is closed, even for the plane, the edge triangles wrap around the back of the mesh, and are co-planar with the forward-facing triangles (the ones that display the data) -- when picking is done, the pickClosest sometimes returns the back-facing triangle. This function returns the correct, visible triangle for the plane:
    
    Parameters:
    
    kStart - DOCUMENT ME!
    
    aiIndex - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - drawPoint
```
private void drawPoint(javax.vecmath.Point3f kStart,
                       int[] aiIndex,
                       int iWhich)
```
    Draw the user-selected point as a sphere on the triangle mesh:
    
    Parameters:
    
    kStart - DOCUMENT ME!
    
    aiIndex - DOCUMENT ME!
    
    iWhich - DOCUMENT ME!
  - drawTriangle
```
private void drawTriangle(javax.vecmath.Point3f kStart,
                          int[] aiIndex,
                          int iWhich)
```
    Draw the user-selected triangle as a black triangle, save the original color so it can be restored:
    
    Parameters:
    
    kStart - DOCUMENT ME!
    
    aiIndex - DOCUMENT ME!
    
    iWhich - DOCUMENT ME!
  - restoreTriColor
```
private void restoreTriColor()
```
    Resets the previously picked triangle to it's orginal color:
  - setColorsLUT
```
private void setColorsLUT()
```
    Update the colormap based on the LUT:
  - setupLight
```
private void setupLight()
```
    Sets up a direction lightsource for the scene.

Class MjCorticalAnalysis

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.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.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

m_aiTriIndex

m_akPickColors

m_akTriColors

m_bCurvatureColors

m_bInflationInitialized

m_bMousePressed

m_bMouseReleased

m_bPickCorrespondenceEnabled

m_bPickPunctureEnabled

m_iNumPicked

m_iRunningNumPicked

m_kCortical

m_kGeometryArrayPlane

m_kGeometryArraySphere

m_kLUTConvexity

m_kLUTCurvature

m_kMeshBranchRoot

m_kMeshLinesBranchRoot

m_kMouseEvent

m_kPanel

m_kPickCanvas

m_kShapeMesh

m_kShapePlane

m_kShapeSphere

m_kSwitchDisplay

m_kSwitchLinesMesh

m_kSwitchLinesPlane

m_kSwitchLinesPlaneBranch

m_kSwitchLinesSphere

m_kSwitchLinesSphereBranch

m_kTransformGroupActive

m_kTransformGroupMesh

m_kTransformGroupPlane

m_kTransformGroupPoseMesh

m_kTransformGroupPosePlane

m_kTransformGroupPoseSphere

m_kTransformGroupSphere

m_kTriangleMesh

MAX_POINTS

MESH

PLANE

SPHERE

Constructor Detail

MjCorticalAnalysis

Method Detail

actionPerformed

calculateConformal

displayConvexityColors

displayCurvatureColors

displayPlane

displaySphere

disposeLocal

drawPicked

getMainPanel

getMaxAverageConvexity

getMaxCurvature

getMesh

getMeshLines