Package gov.nih.mipav.view.renderer.WildMagic

Class VolumeTriPlanarRenderBase

  • All Implemented Interfaces:
    com.jogamp.opengl.GLEventListener, SpaceNavigatorListener, java.awt.event.KeyListener, java.awt.event.MouseListener, java.awt.event.MouseMotionListener, java.awt.event.MouseWheelListener, java.io.Serializable, java.util.EventListener, javax.swing.event.ChangeListener
    Direct Known Subclasses:
    VolumeTriPlanarRender
    public class VolumeTriPlanarRenderBase
extends GPURenderBase
implements com.jogamp.opengl.GLEventListener, java.awt.event.KeyListener, java.awt.event.MouseMotionListener, java.awt.event.MouseListener, javax.swing.event.ChangeListener
    See Also:
    Serialized Form

    • Field Detail

      • glp

        protected static com.jogamp.opengl.GLProfile glp

      • caps

        protected static com.jogamp.opengl.GLCapabilities caps

      • gl_width

        protected static int gl_width

      • gl_height

        protected static int gl_height

      • sharedDrawable

        protected com.jogamp.opengl.GLOffscreenAutoDrawable sharedDrawable

      • init

        protected static boolean init

      • m_kSculptor

        protected Sculptor_WM m_kSculptor
        New sculpting object for WM-based sculpting.

      • m_afArbEquation

        protected float[] m_afArbEquation
        Arbitrary clip plane equation:

      • m_afArbEquationInv

        protected float[] m_afArbEquationInv

      • m_kArbitraryClip

        protected WildMagic.LibFoundation.Mathematics.Vector4f m_kArbitraryClip

      • m_kArbitraryClipInv

        protected WildMagic.LibFoundation.Mathematics.Vector4f m_kArbitraryClipInv

      • m_bArbClipOn

        protected boolean m_bArbClipOn
        Enable Arbitrary clip plane:

      • m_bDisplaySecond

        protected boolean m_bDisplaySecond
        Enables/Disables rendering the second pass. When disabled, the back-facing polygons of the proxy-geometry are shown instead of the volume:

      • m_kSlices

        protected VolumeSlices m_kSlices
        3D Slice renderer.

      • m_akSlicesColor

        protected WildMagic.LibFoundation.Mathematics.ColorRGB[] m_akSlicesColor

      • m_kVolumeRayCast

        protected VolumeRayCast m_kVolumeRayCast
        GPU-based ray cast renderer.

      • m_kVolumeClip

        protected VolumeClip m_kVolumeClip
        Clipping planes renderer

      • m_kDTIDisplay

        protected VolumeDTI m_kDTIDisplay
        DTI renderer.

      • m_kVolumeBox

        protected VolumeBoundingBox m_kVolumeBox
        Volume bounding box renderer.

      • m_bFirstRender

        protected boolean m_bFirstRender
        The first time the frame is rendererd use the shader to calculate the normals for the volume data.

      • m_bFirstDisplay

        protected boolean m_bFirstDisplay

      • m_bResetImages

        protected boolean m_bResetImages

      • m_bPaintEnabled

        protected boolean m_bPaintEnabled
        Painting parameters:

      • m_bPaint

        protected boolean m_bPaint

      • m_bErase

        protected boolean m_bErase

      • m_bDropper

        protected boolean m_bDropper

      • m_bPaintCan

        protected boolean m_bPaintCan

      • m_kPaintColor

        protected WildMagic.LibFoundation.Mathematics.ColorRGBA m_kPaintColor

      • m_iBrushSize

        protected int m_iBrushSize

      • m_bGeodesicEnabled

        protected boolean m_bGeodesicEnabled
        Geodesic enabled on/off.

      • m_iStereo

        protected int m_iStereo
        Stereo on/off.

      • m_bPickCorrespondence

        protected boolean m_bPickCorrespondence
        BrainSurfaceFlattener pick correspondence enabled on/off.

      • m_bCrop

        protected boolean m_bCrop
        Set to true when cropping the volume in the shader.

      • m_iExtractLevel

        protected int m_iExtractLevel
        Intensity level for GPU-surface extraction.

      • fSample_mouseReleased

        protected float fSample_mouseReleased
        sample rate when mouse is released.

      • fSample_mouseDragged

        protected float fSample_mouseDragged
        sample rate when mouse is dragged.

      • m_bPlay4D

        protected boolean m_bPlay4D

      • m_bPlay4DVOIs

        protected boolean m_bPlay4DVOIs

      • m_fAnimateRate

        protected float m_fAnimateRate

      • m_iAnimateCount

        protected int m_iAnimateCount

      • m_kFBO

        protected WildMagic.LibRenderers.OpenGLRenderer.OpenGLFrameBuffer m_kFBO

      • m_spkPlaneEffect

        protected WildMagic.LibGraphics.Effects.ShaderEffect m_spkPlaneEffect

      • m_pkPlane

        protected WildMagic.LibGraphics.SceneGraph.TriMesh m_pkPlane

      • m_pkScreenCamera

        protected WildMagic.LibGraphics.Rendering.Camera m_pkScreenCamera

      • m_bUpdateCenterOnDisplay

        protected boolean m_bUpdateCenterOnDisplay

      • m_kNewCenter

        protected WildMagic.LibFoundation.Mathematics.Vector3f m_kNewCenter

      • m_bDisplay

        protected boolean m_bDisplay

      • m_akSceneTarget

        protected WildMagic.LibGraphics.Rendering.Texture[] m_akSceneTarget

      • m_bWriteImage

        protected boolean m_bWriteImage

      • ms_NumHistogramLUTs

        protected static int ms_NumHistogramLUTs

      • ms_akLUTTexture

        protected static WildMagic.LibGraphics.Rendering.Texture[] ms_akLUTTexture

      • isNavigationEnabled

        protected boolean isNavigationEnabled
        is nagivation mode enabled or not.

      • navigationBehavior

        protected NavigationBehavior navigationBehavior
        navigation behavior.

      • annotatePtsCounter

        protected int annotatePtsCounter
        number of annotate points along the specified path.

      • annotatePtsList

        protected java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> annotatePtsList
        annotate path planning points list

      • m_kNormalColorPathUnvisited

        protected WildMagic.LibFoundation.Mathematics.ColorRGB m_kNormalColorPathUnvisited
        Color for the parts of the path that have not yet been visited (Dark Green)

      • m_kFlyPathGraphCurve

        protected FlyPathGraphCurve m_kFlyPathGraphCurve
        Fly path curve.

      • isPathPlanningEnabled

        protected boolean isPathPlanningEnabled
        is path planning mode enabled or not.

      • isMouseControlEnabled

        protected boolean isMouseControlEnabled
        is mouse control enabled or not.

      • isAnnotateEnabled

        protected boolean isAnnotateEnabled
        is annotation mode is enabled or not.

      • kPolyNode

        protected WildMagic.LibGraphics.SceneGraph.Node kPolyNode

      • kPoly

        protected WildMagic.LibGraphics.SceneGraph.Polyline kPoly

      • kGeometryBranchPath

        protected WildMagic.LibGraphics.SceneGraph.Polyline kGeometryBranchPath

      • cameraPosition

        private WildMagic.LibFoundation.Mathematics.Vector3f cameraPosition

      • profile

        boolean profile

      • opacitySlider

        private javax.swing.JSlider opacitySlider
        Opacity sliders for when this renderer is displayed as a stand-alone app.

      • opacityLabel

        private javax.swing.JLabel opacityLabel

      • sphereClip

        protected WildMagic.LibFoundation.Mathematics.Vector3f sphereClip

      • sphereRadius

        protected float sphereRadius

      • latticeClip

        protected boolean latticeClip

      • latticeClipPos

        protected WildMagic.LibFoundation.Mathematics.Vector3f latticeClipPos

      • latticeClipAxes

        protected WildMagic.LibFoundation.Mathematics.Vector3f[] latticeClipAxes

      • latticeClipExtents

        protected float[] latticeClipExtents

      • latticeClipBox

        protected WildMagic.LibFoundation.Mathematics.Box3f latticeClipBox

      • animateLattices

        private boolean animateLattices

      • animateStop

        private boolean animateStop

      • takeScreenShot

        private boolean takeScreenShot

      • screenShotRotateCount

        private int screenShotRotateCount

      • animateCurve

        private boolean animateCurve

      • animateSlice

        protected boolean animateSlice

      • sliceDir

        protected int sliceDir

      • animateLatticeModel

        private LatticeModel animateLatticeModel

      • planeVOI

        private VOI planeVOI

      • segmentIndex

        private int segmentIndex

      • plane

        private WildMagic.LibGraphics.SceneGraph.TriMesh plane

      • planeName

        private java.lang.String planeName

      • screenShots

        private java.util.Vector<java.awt.image.BufferedImage> screenShots

    • Constructor Detail

      • VolumeTriPlanarRenderBase

        public VolumeTriPlanarRenderBase()
        Default Constructor.

      • VolumeTriPlanarRenderBase

        public VolumeTriPlanarRenderBase​(com.jogamp.opengl.util.Animator kAnimator,
                                 VolumeImage kVolumeImageA,
                                 VolumeImage kVolumeImageB)
        Construct the Volume/Surface/Tri-Planar renderer.
        Parameters:
        kParent - parent user-interface and frame.
        kAnimator - animator used to display the canvas.
        kVolumeImageA - volume data and textures for ModelImage A.
        kVolumeImageB - volume data and textures for ModelImage B.

      • VolumeTriPlanarRenderBase

        public VolumeTriPlanarRenderBase​(VolumeTriPlanarRenderBase kShared,
                                 com.jogamp.opengl.awt.GLCanvas kCanvas,
                                 VolumeImage kVolumeImageA,
                                 VolumeImage kVolumeImageB)
        Construct the Volume/Surface/Tri-Planar renderer.
        Parameters:
        kParent - parent user-interface and frame.
        kAnimator - animator used to display the canvas.
        kVolumeImageA - volume data and textures for ModelImage A.
        kVolumeImageB - volume data and textures for ModelImage B.

    • Method Detail

      • initClass

        public static boolean initClass()

      • newSharedCanvas

        public com.jogamp.opengl.awt.GLCanvas newSharedCanvas()

      • addGeodesic

        public void addGeodesic​(WildMagic.LibGraphics.SceneGraph.TriMesh kSurface,
                        WildMagic.LibGraphics.SceneGraph.Geometry kNew,
                        int iGroup)
        Add a new geodesic component to the surface.
        Parameters:
        kSurface - the surface the geodesic component is added to.
        kNew - the new geodesic component.
        iGroup - the display group to add to.

      • addSurface

        public void addSurface​(SurfaceState kSurface)
        Add surfaces to the display list.
        Parameters:
        akSurfaces -

      • addSurface

        public void addSurface​(SurfaceState kSurface,
                       boolean isFileCoords)
        Add surfaces to the display list.
        Parameters:
        akSurfaces -

      • addSurface

        public void addSurface​(SurfaceState kSurface,
                       boolean computeSurfaceMask,
                       boolean isFileCoords)

      • addTract

        public void addTract​(VOIContour kContour,
                     WildMagic.LibGraphics.SceneGraph.Polyline kLine,
                     int iGroup)
        Add tract into the DTI display
        Parameters:
        kLine - polyline
        iGroup - counter number
        centerIndex - center index color

      • addVolumeVOI

        public void addVolumeVOI​(VolumeVOI kVOI)

      • applySculpt

        public boolean applySculpt​(boolean bAll)
        Apply the sculpt region to the volume.

      • blend

        public void blend​(java.lang.String kSurfaceName,
                  float fValue)
        Sets blending between imageA and imageB.
        Parameters:
        fValue - the blend value (0-1)

      • clearSculpt

        public void clearSculpt()
        Clear the sculpt region.

      • CMPMode

        public void CMPMode()
        Display the volume in Composite mode.

      • cropClipVolume

        public void cropClipVolume()
        Crop the clipped volume.

      • Move

        protected void Move()
        Description copied from class: GPURenderBase
        Updates the camera and displayed objects for rendering.
        Overrides:
        Move in class GPURenderBase

      • display

        public void display​(com.jogamp.opengl.GLAutoDrawable arg0)
        Specified by:
        display in interface com.jogamp.opengl.GLEventListener

      • displayArbitraryClipPlane

        public void displayArbitraryClipPlane​(boolean bDisplay)
        Displays the arbitrary clip plane position.
        Parameters:
        bDisplay - on/off.

      • displayBoundingBox

        public void displayBoundingBox​(boolean bDisplay)
        Called from JPanelDisplay. Sets the bounding box display on/off.
        Parameters:
        bDisplay - on/off.

      • displayClipPlane

        public void displayClipPlane​(int iWhich,
                             boolean bDisplay)
        Called from JPanelClip. Sets the axis-aligned clip plane display on/off.
        Parameters:
        iWhich - the clip plane to set.
        bDisplay - on/off.

      • displayClipPlane

        public void displayClipPlane​(int iWhich,
                             boolean bDisplay,
                             WildMagic.LibFoundation.Mathematics.ColorRGB kColor)
        Called from JPanelClip. Sets the axis-aligned clip plane display on/off and color.
        Parameters:
        iWhich - the clip plane to set.
        bDisplay - on/off.
        kColor - the clipping plane color.

      • displayNode

        public void displayNode​(WildMagic.LibGraphics.SceneGraph.Node kNode,
                        boolean bDisplay)
        Toggle display of the scene-graphe node on/off.
        Parameters:
        kNode - the node to toggle.
        bDisplay - on/off.

      • displayOrientationCube

        public void displayOrientationCube​(boolean bDisplay)
        Called from JPanelDisplay. Sets the orientation cube display on/off.
        Parameters:
        bDisplay - on/off.

      • displaySurface

        public void displaySurface​(boolean bDisplay)
        Toggle surface display on/off.
        Parameters:
        bDisplay -

      • displayVOIs

        public void displayVOIs​(boolean bDisplay)
        Toggle surface display on/off.
        Parameters:
        bDisplay -

      • displayVolumeRaycast

        public void displayVolumeRaycast​(boolean bDisplay)
        Toggle volume display on/off.
        Parameters:
        bDisplay -

      • displayVolumeSlices

        public void displayVolumeSlices​(boolean bDisplay)
        Toggle 3D Slice display on/off.
        Parameters:
        bDisplay -

      • toggleDisplayVolumeSlices

        public void toggleDisplayVolumeSlices()
        Toggle 3D Slice display on/off.

      • toggleDisplaySurface

        public void toggleDisplaySurface()
        Toggle Surface display on/off.

      • toggleDisplayVOI

        public void toggleDisplayVOI()
        Toggle 3D VOI display on/off.

      • toggleDisplayVolume

        public void toggleDisplayVolume()
        Toggle 3D Volume display on/off.

      • dispose

        public void dispose​(com.jogamp.opengl.GLAutoDrawable kDrawable)
        Description copied from class: GPURenderBase
        memory cleanup.
        Specified by:
        dispose in interface com.jogamp.opengl.GLEventListener
        Overrides:
        dispose in class GPURenderBase

      • releaseShared

        protected void releaseShared()

      • DRRMode

        public void DRRMode()
        Display the volume in DDR mode.

      • enableArbitraryClipPlane

        public void enableArbitraryClipPlane​(boolean bEnable,
                                     boolean bDisplay,
                                     WildMagic.LibFoundation.Mathematics.ColorRGB kColor)
        Enables the arbitrary clip plane position.
        Parameters:
        bEnable - clipping enabled
        bDisplay - on/off.
        kColor - the arbitrary clip plane color.

      • enableClipPlane

        public void enableClipPlane​(int iWhich,
                            boolean bEnable,
                            boolean bDisplay)
        Enables the axis-aligned clipping planes.
        Parameters:
        iWhich - the clip plane to enable.
        bEnable - clipping enabled
        bDisplay - on/off.

      • enableEyeClipPlane

        public void enableEyeClipPlane​(boolean bEnable,
                               boolean bDisplay,
                               WildMagic.LibFoundation.Mathematics.ColorRGB kColor)
        Enables the eye clip plane.
        Parameters:
        bEnable - clipping enabled
        bDisplay - on/off.
        kColor - the eye clip plane color.

      • enableEyeInvClipPlane

        public void enableEyeInvClipPlane​(boolean bEnable,
                                  boolean bDisplay,
                                  WildMagic.LibFoundation.Mathematics.ColorRGB kColor)
        Enables the inverse-eye clip plane.
        Parameters:
        bEnable - clipping enabled
        bDisplay - on/off.
        kColor - the inverse-eye clip plane color.

      • enableGeodesic

        public void enableGeodesic​(boolean bEnable)
        Enable geodesic curve calculations/display.
        Parameters:
        bEnable -

      • enablePaint

        public void enablePaint​(WildMagic.LibFoundation.Mathematics.ColorRGBA kPaintColor,
                        int iBrushSize,
                        boolean bEnabled,
                        boolean bPaint,
                        boolean bDropper,
                        boolean bPaintCan,
                        boolean bErase)
        Enable painting on TriMesh surfaces.
        Parameters:
        kPaintColor - paint color.
        iBrushSize - brush size.
        bEnabled - painting on/off.
        bPaint - when true apply paint.
        bDropper - when true do dropper mode.
        bPaintCan - when true do paint can mode.
        bErase - when true erase.

      • enableSculpt

        public void enableSculpt​(boolean bSculpt)
        Enables and disables sculpting.
        Parameters:
        bSculpt - true to enable sculpting, false to disable.

      • eraseAllPaint

        public void eraseAllPaint()
        Erase all surface paint.

      • extractMeshFromVolume

        public void extractMeshFromVolume()
        Extract a TriMesh surface from the Volume Rendering.

      • getABBlend

        public float getABBlend()

      • getArbitratyClip

        public WildMagic.LibFoundation.Mathematics.Matrix3f getArbitratyClip()

      • getArbitratyClipOn

        public boolean getArbitratyClipOn()

      • getContainingPanel

        public javax.swing.JPanel getContainingPanel()
        Returns the container for this object. The container has a scroll pane and slider for the depth.
        Returns:

      • getDPIScale

        public double getDPIScale()

      • getGroupColor

        public WildMagic.LibFoundation.Mathematics.ColorRGB getGroupColor​(int groupID)
        Get the group color with given group ID.
        Parameters:
        groupID - given group id
        Returns:
        ColorRGB group color

      • getIPD

        public float getIPD()
        Sets the inter-pupillary distance for stereo rendering.
        Parameters:
        fIPD - the IPD value.

      • getMaterial

        public WildMagic.LibGraphics.Rendering.MaterialState getMaterial​(java.lang.String kSurfaceName)
        Return the material properties of the given surface.
        Parameters:
        kSurfaceName - the surface to query.
        Returns:
        the material properties of the surface.

      • getOpacity

        public float getOpacity​(java.lang.String kSurfaceName)
        Return the opacity properties of the given surface.
        Parameters:
        kSurfaceName - the surface to query.
        Returns:
        the opacity value of the surface.

      • getSculptEnabled

        public boolean getSculptEnabled()
        Returns true when sculpting is enabled.
        Returns:
        true when sculpting is enabled, false otherwise.

      • getSurface

        public WildMagic.LibGraphics.SceneGraph.TriMesh getSurface​(java.lang.String kSurfaceName)
        Return the TriMesh surface with the given name.
        Parameters:
        kSurfaceName - the name of the surface.
        Returns:
        TriMesh.

      • getVolumeSurface

        public VolumeSurface getVolumeSurface​(java.lang.String kSurfaceName)
        Return the TriMesh surface with the given name.
        Parameters:
        kSurfaceName - the name of the surface.
        Returns:
        TriMesh.

      • getSurfaceArea

        public float getSurfaceArea​(java.lang.String kSurfaceName)
        Return the surface area for the given TriMesh surface.
        Parameters:
        kSurfaceName - the surface name.
        Returns:
        the surface-area of the mesh.

      • getSurfaceAreaString

        public java.lang.String getSurfaceAreaString​(java.lang.String kSurfaceName)
        Return the surface area for the given TriMesh surface.
        Parameters:
        kSurfaceName - the surface name.
        Returns:
        the surface-area of the mesh.

      • getSurfaceCenter

        public WildMagic.LibFoundation.Mathematics.Vector3f getSurfaceCenter​(java.lang.String kSurfaceName)
        Return the center of the TriMesh surface.
        Parameters:
        kSurfaceName - the surface name.
        Returns:
        the calculated center.

      • getSurfaceVolume

        public float getSurfaceVolume​(java.lang.String kSurfaceName)
        Return the volume of the TriMesh surface.
        Parameters:
        kSurfaceName - the surface name.
        Returns:
        the calculated volume.

      • getSurfaceVolumeString

        public java.lang.String getSurfaceVolumeString​(java.lang.String kSurfaceName)
        Return the volume of the TriMesh surface.
        Parameters:
        kSurfaceName - the surface name.
        Returns:
        the calculated volume.

      • getTranslateSurface

        public WildMagic.LibFoundation.Mathematics.Vector3f getTranslateSurface​(java.lang.String kSurfaceName)
        Return the translation vector for the surface with the given name.
        Parameters:
        kSurfaceName - the surface to move.
        Returns:
        the translation vector

      • init

        public void init​(com.jogamp.opengl.GLAutoDrawable arg0)
        Part of the GLEventListener interface. Init is called once when the GLCanvas is first displayed. Called again if the GLCanvas is removed from the frame and added to another window or panel. Initializes the display.
        Specified by:
        init in interface com.jogamp.opengl.GLEventListener
        Parameters:
        arg0 - GLCanvas

      • setView

        public void setView​(WildMagic.LibFoundation.Mathematics.Vector3f[] basisVectors)

      • resetView

        public void resetView()

      • init

        public void init()

      • invertSculpt

        public void invertSculpt()
        Invert the sculpt region.

      • rollbackToCenter

        public void rollbackToCenter()
        Roll back the image back to center, reset the camera view close to original view.

      • keyPressed

        public void keyPressed​(java.awt.event.KeyEvent e)
        Part of the KeyListener interface. Pressing 'b' toggles displaying the proxy-geometry versus the ray-traced volume.
        Specified by:
        keyPressed in interface java.awt.event.KeyListener
        Overrides:
        keyPressed in class GPURenderBase
        Parameters:
        e - the key event.

      • MIPMode

        public void MIPMode()
        Display the volume in MIP mode.

      • mouseClicked

        public void mouseClicked​(java.awt.event.MouseEvent arg0)
        Specified by:
        mouseClicked in interface java.awt.event.MouseListener
        Overrides:
        mouseClicked in class WildMagic.LibApplications.OpenGLApplication.JavaApplication3D

      • mouseDragged

        public void mouseDragged​(java.awt.event.MouseEvent e)
        Rotates the object with a virtual trackball:
        Specified by:
        mouseDragged in interface java.awt.event.MouseMotionListener
        Overrides:
        mouseDragged in class WildMagic.LibApplications.OpenGLApplication.JavaApplication3D
        Parameters:
        e - the MouseEvent

      • mousePressed

        public void mousePressed​(java.awt.event.MouseEvent e)
        Rotates the object with a virtual trackball:
        Specified by:
        mousePressed in interface java.awt.event.MouseListener
        Overrides:
        mousePressed in class GPURenderBase
        Parameters:
        e - the MouseEvent

      • mouseReleased

        public void mouseReleased​(java.awt.event.MouseEvent e)
        Rotates the object with a virtual trackball:
        Specified by:
        mouseReleased in interface java.awt.event.MouseListener
        Overrides:
        mouseReleased in class WildMagic.LibApplications.OpenGLApplication.JavaApplication3D
        Parameters:
        e - the MouseEvent

      • MULTIHISTOMode

        public void MULTIHISTOMode​(boolean bOn)
        Display the volume in Mullti-histo mode.

      • pickCorrespondence

        public void pickCorrespondence​(boolean bOn)
        Enables/disables picking correspondence points between the mesh and BrainSurfaceFlattener render.
        Parameters:
        bOn -

      • play4D

        public void play4D​(boolean bOn)

      • addAnimationVOIs

        public void addAnimationVOIs​(VOIVector vois)

      • play4DVOIs

        public void play4DVOIs​(boolean bOn)

      • play4DVOIs

        public boolean play4DVOIs()

      • startStopVOIAnimation

        public void startStopVOIAnimation()

      • startRecording

        public void startRecording()

      • setAnnotationVOIColor

        public void setAnnotationVOIColor​(java.lang.String name,
                                  WildMagic.LibFoundation.Mathematics.ColorRGB color)

      • redrawSurfaceTexture

        public void redrawSurfaceTexture()
        Causes the texture representation of all the surface meshes to be recalculated.

      • reloadShaders

        public void reloadShaders()
        Called by the ApplicationGUI. Causes the current shader to be reloaded from file, compiled and applied to the proxy-geometry.
        Overrides:
        reloadShaders in class WildMagic.LibApplications.OpenGLApplication.Application

      • removeAllGeodesic

        public void removeAllGeodesic​(WildMagic.LibGraphics.SceneGraph.TriMesh kSurface)
        Removes all geodesic components from the given surface.
        Parameters:
        kSurface -

      • removeGeodesic

        public void removeGeodesic​(WildMagic.LibGraphics.SceneGraph.TriMesh kSurface,
                           int iNode,
                           int iGroup)
        Removes the specific geodesic component from the given surface.
        Parameters:
        kSurface -
        iNode -
        iGroup -

      • getPolylines

        public java.util.Vector<VOIContour> getPolylines​(int iGroup)

      • removePolyline

        public void removePolyline​(int iGroup)
        Removes the specified polyline tract group.
        Parameters:
        iGroup - the group of polylines to remove.

      • removeSurface

        public void removeSurface​(java.lang.String kSurfaceName)
        Sets blending between imageA and imageB.
        Parameters:
        fValue - the blend value (0-1)

      • removeAll

        public void removeAll​(java.lang.String kSurfaceName)

      • removeAllSurfaces

        public void removeAllSurfaces()

      • replaceGeodesic

        public void replaceGeodesic​(WildMagic.LibGraphics.SceneGraph.TriMesh kOld,
                            WildMagic.LibGraphics.SceneGraph.TriMesh kNew)
        When the Geodesic object cuts the mesh along an open curve, the old mesh changes, but does not need to be deleted and no new mesh needs to be added. This function allows the Geodesic object to replace the original mesh with the sliced mesh in the surface renderer. ReplaceMesh is also used to undo cutting operations.
        Parameters:
        kOld - TriMesh old surface mesh
        kNew - TriMesh new surface mesh

      • reshape

        public void reshape​(com.jogamp.opengl.GLAutoDrawable arg0,
                    int iX,
                    int iY,
                    int iWidth,
                    int iHeight)
        Description copied from class: GPURenderBase
        Part of the GLEventListener interface. Called when the GLCanvas is resized.
        Specified by:
        reshape in interface com.jogamp.opengl.GLEventListener
        Overrides:
        reshape in class GPURenderBase
        Parameters:
        arg0 - the GLCanvas
        iX - the new x-position in screen coordinates.
        iY - the new y-position in screen coordinates.
        iWidth - the new width
        iHeight - the new height

      • save

        public boolean save​(FileWriteOptions options,
                    int filterType)
        Save the sculpted volume.
        Parameters:
        options - file writing options
        filtertype -
        Returns:
        boolean, true on sucess.

      • saveCroppedImage

        public void saveCroppedImage()
        Copies the volume data from the texture representation into the ModelImage and writes it to disk.

      • selfShadow

        public void selfShadow​(boolean bShadow)
        Enables/Disables self-shadowing in the Surface mode.
        Parameters:
        bShadow - shadow on/off.

      • setABBlend

        public void setABBlend​(float fValue)
        Sets blending between imageA and imageB.
        Parameters:
        fValue - the blend value (0-1)

      • setAnimationSpeed

        public void setAnimationSpeed​(float fValue)

      • setAnimationSpeed

        public void setAnimationSpeed​(int value)

      • setArbColor

        public void setArbColor​(WildMagic.LibFoundation.Mathematics.ColorRGB kColor)
        Sets the arbitrary clip plane color.
        Parameters:
        kColor - the new color.

      • setArbitraryClipPlane

        public void setArbitraryClipPlane​(float f4,
                                  boolean bEnable,
                                  float thickness)
        Enables the arbitrary clip plane position.
        Parameters:
        f4 - clip position (same value as aSlice in JPanelClip)

      • setArbitratyClip

        public void setArbitratyClip​(WildMagic.LibFoundation.Mathematics.Matrix3f kRotate)

      • setArbitratyClip

        public void setArbitratyClip​(WildMagic.LibFoundation.Mathematics.Matrix3f kRotate,
                             boolean on)

      • setBackface

        public void setBackface​(java.lang.String kSurfaceName,
                        boolean bOn)
        Turn backface culling on/off for the given surface.
        Parameters:
        kSurfaceName - surface name.
        bOn -

      • setBackgroundColor

        public void setBackgroundColor​(WildMagic.LibFoundation.Mathematics.ColorRGBA kColor)
        Sets the background color.
        Parameters:
        kColor - new background color.

      • setBoundingBoxColor

        public void setBoundingBoxColor​(WildMagic.LibFoundation.Mathematics.ColorRGB kColor)
        Called from JPanelDisplay. Sets the bounding box color.
        Parameters:
        kColor - bounding box color.

      • setBoundingBoxColor

        public void setBoundingBoxColor​(int i,
                                WildMagic.LibFoundation.Mathematics.ColorRGB kColor)
        Sets the color for the input slice frame.
        Parameters:
        i - , the slice bounding frame.
        color - the new color.

      • setCenter

        public void setCenter​(WildMagic.LibFoundation.Mathematics.Vector3f kCenter)
        Sets the position of the 3D slices.
        Parameters:
        kCenter - the intersection point of the three slices.

      • setClipping

        public void setClipping​(java.lang.String kSurfaceName,
                        boolean bClip)
        Enable clipping for the given surface.
        Parameters:
        kSurfaceName - the surface to modify.
        bClip - true enables clipping, false disables clipping.

      • getClip

        public WildMagic.LibFoundation.Mathematics.Vector3f getClip()

      • getClipEnable

        public boolean[] getClipEnable()

      • getClipAEEnable

        public boolean[] getClipAEEnable()

      • getClipDisplay

        public boolean[] getClipDisplay()

      • getClipInv

        public WildMagic.LibFoundation.Mathematics.Vector3f getClipInv()

      • getClipInvEnable

        public boolean[] getClipInvEnable()

      • getClipInvDisplay

        public boolean[] getClipInvDisplay()

      • getClipColor

        public java.awt.Color[] getClipColor()

      • setClipPlane

        public void setClipPlane​(int iWhich,
                         float fValue,
                         boolean bEnable)
        Called from JPanelClip. Sets the axis-aligned clip plane.
        Parameters:
        iWhich - the clip plane to set.
        fValue - the new position of the clip plane (the same value as the slider in JPanelClip).

      • setClipPlaneColor

        public void setClipPlaneColor​(int iWhich,
                              WildMagic.LibFoundation.Mathematics.ColorRGB kColor)
        Sets the axis-aligned clip plane color.
        Parameters:
        iWhich - one of the 6 clip planes
        kColor - the new color.

      • setColor

        public void setColor​(java.lang.String kSurfaceName,
                     WildMagic.LibFoundation.Mathematics.ColorRGB kColor,
                     boolean bUpdate)
        Parameters:
        kSurfaceName -
        kColor -
        bUpdate -

      • SetCustomBlend

        public void SetCustomBlend​(int iBlendEquation,
                           int iLogicOp,
                           int iSrcBlend,
                           int iDstBlend,
                           WildMagic.LibFoundation.Mathematics.ColorRGBA kColor)

      • setDisplayAllGlyphs

        public void setDisplayAllGlyphs​(boolean bDisplay)
        Turns on/off displaying all the glyphs.
        Parameters:
        bDisplay - when true display all the glyphs in the volume.

      • setDisplayArrows

        public void setDisplayArrows​(boolean bDisplay)
        Turns on/off displaying the fiber bundle tracts with 3D arrows.
        Parameters:
        bDisplay - when true display the tracts with 3D arrows.

      • setDisplayCylinders

        public void setDisplayCylinders​(boolean bDisplay)
        Turns on/off displaying the fiber bundle tracts with ellipsoids.
        Parameters:
        bDisplay - when true display the tracts with Cylinders.

      • setDisplayEllipsoids

        public void setDisplayEllipsoids​(boolean bDisplay)
        Turns on/off displaying the fiber bundle tracts with ellipsoids.
        Parameters:
        bDisplay - when true display the tracts with ellipsods.

      • setDisplayTubes

        public void setDisplayTubes​(boolean bDisplay)
        Turns on/off displaying the fiber bundle tracts with tubes.
        Parameters:
        bDisplay - when true display the tracts with tubes.

      • setDrawingShape

        public void setDrawingShape​(int shape)
        Sets the sculpt drawing shape.
        Parameters:
        shape - (0 = free-hand, 1 = rectangular)

      • setDTIImage

        public void setDTIImage​(ModelImage kDTIImage,
                        ModelImage kEigenVectorImage,
                        ModelImage kEigenValueImage)
        Sets the DTI Image for displaying the tensors as ellipsoids.
        Parameters:
        kDTIImage - .

      • setEllipseMod

        public void setEllipseMod​(int iMod)
        Set the m_iEllipsoidMod value.
        Parameters:
        iMod - new m_iEllipsoidMod value.

      • setEyeClipPlane

        public void setEyeClipPlane​(float f4,
                            boolean bDisplay,
                            boolean bEnable)
        Sets the eye clip plane position.
        Parameters:
        f4 - clip position (same value as sSlice in JPanelClip)
        bDisplay - on/off.

      • setEyeColor

        public void setEyeColor​(WildMagic.LibFoundation.Mathematics.ColorRGB kColor)
        Sets the eye clip plane color.
        Parameters:
        kColor - the new color.

      • setEyeInvClipPlane

        public void setEyeInvClipPlane​(float f4,
                               boolean bDisplay,
                               boolean bEnable)
        Sets the inverse-eye clip plane position.
        Parameters:
        f4 - clip position (same value as sSliceInv in JPanelClip)
        bDisplay - on/off.

      • setEyeInvColor

        public void setEyeInvColor​(WildMagic.LibFoundation.Mathematics.ColorRGB kColor)
        Sets the inverse-eye clip plane color.
        Parameters:
        kColor - the new color.

      • getGradientMagnitude

        public boolean getGradientMagnitude()

      • setGradientMagnitude

        public void setGradientMagnitude​(boolean bShow)
        Enables/Disables Gradient Magnitude filter.
        Parameters:
        bShow - gradient magnitude filter on/off

      • setImages

        public void setImages​(VolumeImage imageA)

      • setImageB

        public void setImageB​(VolumeImage imageB)

      • setHyperStack

        public void setHyperStack​(VolumeImage[] images,
                          WildMagic.LibGraphics.Rendering.Texture colormap)

      • setImageOn

        public void setImageOn​(int which,
                       boolean on)

      • setImageNew

        public void setImageNew​(java.lang.String kSurfaceName,
                        ModelImage kImage)
        Sets the ModelImage to use as an alternative to the volume ModelImage for surface texturing.
        Parameters:
        kSurfaceName - the surface to modify.
        kImage - the alternate ModelImage to use for the surface texture.

      • setIntenstityLevel

        public void setIntenstityLevel​(int iLevel)
        Set intensity level for GPU-based surface extraction.
        Parameters:
        iLevel -

      • setIPD

        public void setIPD​(float fIPD)
        Sets the inter-pupillary distance for stereo rendering.
        Parameters:
        fIPD - the IPD value.

      • setLUTNew

        public void setLUTNew​(java.lang.String kSurfaceName,
                      ModelStorageBase kLUT)
        Sets the LUT to use as an alternative to the volume lut for surface texturing.
        Parameters:
        kSurfaceName - the surface to modify.
        kLUT - the new LUT.
        kRGBT - the new ModelRGB (for color images).

      • setMaterial

        public void setMaterial​(java.lang.String kSurfaceName,
                        WildMagic.LibGraphics.Rendering.MaterialState kMaterial,
                        boolean bUpdate)
        Sets the material for the given surface.
        Parameters:
        kSurfaceName - the surface to update.
        kMaterial - the new material.

      • setPickable

        public void setPickable​(java.lang.String kSurfaceName,
                        boolean bOn)
        Enable surface picking for the given surface.
        Parameters:
        kSurfaceName - surface name.
        bOn - picking on/off.

      • setPolygonMode

        public void setPolygonMode​(java.lang.String kSurfaceName,
                           WildMagic.LibGraphics.Rendering.WireframeState.FillMode eMode)
        Set the polygon mode (FILL, LINE, POINT) for the given surface.
        Parameters:
        kSurfaceName - the surface to modify.
        eMode - FILL, LINE, or POINT.

      • setPolylineColor

        public void setPolylineColor​(int iGroup,
                             WildMagic.LibFoundation.Mathematics.ColorRGB kColor)
        Sets the polyline color for the specified fiber bundle tract group.
        Parameters:
        iGroup - the fiber bundle group to set.
        kColor - the new polyline color for the specified fiber bundle tract group.

      • setRGBTA

        public void setRGBTA​(ModelRGB RGBT)

      • setRGBTB

        public void setRGBTB​(ModelRGB RGBT)

      • setSliceOpacity

        public void setSliceOpacity​(int i,
                            float fAlpha)
        Set the transparency value for the slice.
        Parameters:
        i - the slice to modify.
        fAlpha - the new transparency value.

      • setStereo

        public void setStereo​(int iWhich)
        Enable/disable stereo rendering.
        Parameters:
        bEnable -

      • setSurfaceTexture

        public void setSurfaceTexture​(java.lang.String kSurfaceName,
                              boolean bOn,
                              boolean bUseNewImage,
                              boolean bUseNewLUT)
        Turns on surface texture display for the given surface. The user can use a separate ModelImage and LUT than the one displayed in the volume renderer.
        Parameters:
        kSurfaceName - the name of the surface to texture.
        bOn - texture on/off.
        bUseNewImage - when false use the current ModelImage, when true the user specifies the model image.
        bUseNewLUT - when false use the current LUT, when true the user specifies the LUT.

      • setVolumeBlend

        public void setVolumeBlend​(float fBlend)
        Sets the blend factor for displaying the ray-cast volume with other objects in the scene.
        Parameters:
        fBlend - the blend factor for the ray-cast volume.

      • setVolumeColor

        public void setVolumeColor​(boolean flag)

      • setVolumeSamplesMouseDragged

        public int setVolumeSamplesMouseDragged​(float fSample)
        Set the sampling rate when the mouse is Dragged.

      • setVolumeSamplesMouseReleased

        public int setVolumeSamplesMouseReleased​(float fSample)
        Set the sampling rate when the mouse is released.

      • setMouseTranslationSpeed

        public void setMouseTranslationSpeed​(float translationSpeed)
        Set the mouse translation speed from the translation control slider
        Parameters:
        translationSpeed - mouse translation speed
        rotationSpeed - mouse rotation speed

      • setMouseRotationSpeed

        public void setMouseRotationSpeed​(float rotationSpeed)
        Set the mouse rotation speed from the rotation control slider
        Parameters:
        rotationSpeed - mouse rotation speed

      • setMouseZoomSpeed

        public void setMouseZoomSpeed​(float zoomSpeed)
        Set the mouse zoom speed from the zoom control slider
        Parameters:
        zoomSpeed - mouse zoom speed

      • showBoundingBox

        public void showBoundingBox​(int i,
                            boolean bShow)
        Turns on/off displaying the bounding box for the given plane.
        Parameters:
        i - the plane index (0-3) in file coordinates.
        bShow - when true, the bounding box is displayed.

      • showSlice

        public void showSlice​(int i,
                      boolean bShow)
        Turns on/off displaying the given plane.
        Parameters:
        i - the plane index (0-3) in file coordinates.
        bShow - when true, the plane is displayed.

      • smoothMesh

        public void smoothMesh​(java.lang.String kSurfaceName,
                       int iteration,
                       float alpha,
                       boolean volumeLimit,
                       float volumePercent)
        Smooth the given surface.
        Parameters:
        kSurfaceName - the name of the surface to smooth.
        iteration - smooth iterations.
        alpha - smooth factor.
        volumeLimit - whether to use a volume % change limit.
        volumePercent - the % volume change limiting factor

      • smoothThree

        public void smoothThree​(java.lang.String kSurfaceName,
                        int iteration,
                        float lambda,
                        float mu)
        Smooth the given surface.
        Parameters:
        kSurfaceName - the name of the surface to smooth.
        iteration - smooth iterations.
        lambda - smooth factor.
        mu - smooth factor.

      • smoothTwo

        public void smoothTwo​(java.lang.String kSurfaceName,
                      int iteration,
                      float fStiffness,
                      boolean volumeLimit,
                      float volumePercent)
        Smooth the given surface.
        Parameters:
        kSurfaceName - the name of the surface to smooth.
        iteration - smooth iterations.
        fStiffness - stiffness factor.
        volumeLimit - whether to use a volume % change limit.
        volumePercent - the % volume change limiting factor.

      • SURFASTMode

        public void SURFASTMode()
        Display the volume in Surface mode.

      • SURMode

        public void SURMode()
        Display the volume in Composite Surface mode.

      • toggleGeodesicPathDisplay

        public void toggleGeodesicPathDisplay​(java.lang.String kSurfaceName,
                                      int iWhich)
        Switches between different ways of displaying the geodesic path (Euclidean, Geodesic, or Mesh).
        Parameters:
        kSurfaceName - the surface the path is on.
        iWhich - the type of display.

      • translateSurface

        public void translateSurface​(java.lang.String kSurfaceName,
                             WildMagic.LibFoundation.Mathematics.Vector3f kTranslate)
        Changes the translation vector for the surface with the given name.
        Parameters:
        kSurfaceName - the surface to move.
        kTranslate - the new translation vector

      • undoSculpt

        public void undoSculpt​(boolean bAll)
        Undo applying the sculpt region to the volume.

      • updateData

        public void updateData()
        Causes the VolumeShader to update the copy of the ModelImage on the GPU.
        Parameters:
        kImage - the new image.

      • updateLevWidgetState

        public void updateLevWidgetState​(java.util.Vector<ClassificationWidget> kLWS)

      • CreateRenderTarget

        protected void CreateRenderTarget​(com.jogamp.opengl.GLAutoDrawable kDrawable,
                                  int iWidth,
                                  int iHeight,
                                  boolean forceReload)
        Creates the three render-to-texture targets for rendering semi-transparent surfaces. Creates the screen-space polygon and OrderIndTransparencyEffect that display the final result. The first render target is for the solid objects. Second render target is for translucent objects. Third render target is for accumulating the count of translucent objects per-pixel.
        Parameters:
        arg0 -
        iWidth -
        iHeight -

      • CreateScene

        protected void CreateScene()
        Called by the init() function. Creates and initialized the scene-graph.

      • reCreateScene

        public void reCreateScene​(VolumeImage image)
        Called by the init() function. Creates and initialized the scene-graph.

      • doClip

        protected void doClip​(boolean bEnable)
        Calculates the rotation for the arbitrary clip plane.
        Parameters:
        bEnable - arbitrary clip plane on/off.

      • getHistogramLUTTextureIndex

        public static int getHistogramLUTTextureIndex​(java.lang.String kCommand)

      • getHistogramLUTTexture

        public static WildMagic.LibGraphics.Rendering.Texture getHistogramLUTTexture​(int index,
                                                                             boolean bReverse)

      • initLUT

        private void initLUT​(WildMagic.LibGraphics.Rendering.Texture[] m_akLUTTexture,
                     ModelLUT kLUT,
                     int index)

      • loadShared

        private void loadShared()

      • Render

        protected void Render​(com.jogamp.opengl.GLAutoDrawable kDraw)
        Render the display list objects without the raycast volume.

      • RenderSculpt

        private void RenderSculpt()
        Render the sculpt image.

      • RenderWithTransparency

        private void RenderWithTransparency​(boolean bPreRender,
                                    WildMagic.LibFoundation.Mathematics.Vector2d[] sortedList)
        Rendering multiple translucent surfaces is accomplished with the following steps: 1. A FrameBuffer Object (FBO) is created with three render-to-texture targets, and a depth buffer. 2. The first render target is activated. Solid objects are rendered: writing color and depth information to the FBO target1. The color information displays the solid objects, the depth information enables the solid objects to properly occlude the translucent objects. 3. The second and third render targets are activated. Translucent objects are rendered: writing accumulated color and alpha to the second target and the number of overlapping surfaces per pixel to the third target. In this pass the depth buffer is read-only. 4. Rendering to the three texture targets is disabled. 5. A screen-space polygon is rendered, it reads the three textures generated in the previous pass. The first texture contains the color from the solid objects, the next two textures contain the color information and weighted-average for rendering the translucent textures.
        Parameters:
        bPreRender - when true rendering into the VolumeRayCast back-image texture for compositing with the VolumeRayCast rendering.

      • update4D

        protected void update4D​(boolean bForward)

      • update4DVOIs

        protected void update4DVOIs​(boolean bForward)

      • updateCenterOnDisplay

        protected void updateCenterOnDisplay()

      • updateVOIs

        protected void updateVOIs​(VOIVector kVOIs)

      • deleteVOIs

        public void deleteVOIs​(VOIVector kVOIs)

      • Pick

        protected void Pick()
        Picking. If a display list object has picking enabled, find the picked polygon based on the mouse position.

      • UpdateSceneRotation

        protected void UpdateSceneRotation()
        Description copied from class: GPURenderBase
        Updates the displayed objects based on any user mouse rotation.
        Overrides:
        UpdateSceneRotation in class GPURenderBase

      • NormalKernel

        void NormalKernel​(float[] a,
                  float[] b,
                  int width,
                  int height,
                  int depth,
                  int color,
                  int numElements)

      • createContainer

        private void createContainer​(com.jogamp.opengl.awt.GLCanvas canvas)
        Creates the containing JPanel that will display this object. The JPanel contains a scroll pane with both horizontal and vertical scroll bars and a horizontal slider for changing where the slice plane intersects the volume in depth.
        Parameters:
        imageComponent -

      • stateChanged

        public void stateChanged​(javax.swing.event.ChangeEvent arg0)
        Specified by:
        stateChanged in interface javax.swing.event.ChangeListener

      • toggleNavigation

        public void toggleNavigation​(boolean _isNavigationEnabled)
        Toggle navigation fly-thru tracking mode
        Parameters:
        _isNavigationEnabled - is Navigation checkbox selected or not.

      • setPlaneConstant

        public void setPlaneConstant​(float constant)
        Set the VolumeRayCast front clipping plane constant
        Parameters:
        constant - front clipping plane constant

      • updateSphere

        protected static void updateSphere​(WildMagic.LibGraphics.SceneGraph.TriMesh sphere,
                                   float x,
                                   float y,
                                   float z,
                                   WildMagic.LibFoundation.Mathematics.ColorRGBA c)

      • applyClipFilter

        protected void applyClipFilter​(boolean clip)

      • setLatticeClip

        public void setLatticeClip​(boolean clip,
                           WildMagic.LibFoundation.Mathematics.Vector3f pos,
                           WildMagic.LibFoundation.Mathematics.Vector3f[] axes,
                           float[] extents)

      • addAnimationLattice

        public void addAnimationLattice​(VOIVector latticeAnim)

      • createSamplePlane

        private void createSamplePlane​(VOIBase box)

      • addSphereVOIs

        public void addSphereVOIs​(VOI annotations)

      • writeData

        private void writeData​(java.lang.String fileName)