- actionPerformed(ActionEvent) - Method in class ij3d.contextmenu.ContextMenu
-
- actionPerformed(ActionEvent) - Method in class ij3d.gui.LUTDialog
-
- actionPerformed(ActionEvent) - Method in class ij3d.Image3DMenubar
-
- actionPerformed(ActionEvent) - Method in class ij3d.pointlist.PointListPanel
-
Handling the events coming from the popup menu.
- actionPerformed(ActionEvent) - Method in class ij3d.RegistrationMenubar
-
- actionPerformed(ActionEvent) - Method in class view4d.TimelineGUI
-
- add(CustomMesh) - Method in class customnode.CustomMultiMesh
-
- ADD - Static variable in class ij3d.Executer
-
- add(String, String, String, String, String, String, String, String, String) - Static method in class ij3d.ImageJ3DViewer
-
- add(Content) - Method in class ij3d.ViewAdjuster
-
Add another Content which should be completely visible in the canvas.
- add(Transform3D, Point3d) - Method in class ij3d.ViewAdjuster
-
Add another point which should be visible in the canvas; the point is
expected to be in local coordinates, with the given local-to-vworld
transformation.
- add(Point3d) - Method in class ij3d.ViewAdjuster
-
Add another point which should be visible in the canvas; the point is
expected to be in vworld coordinates.
- ADD_BOX - Static variable in class ij3d.Executer
-
- ADD_CONE - Static variable in class ij3d.Executer
-
- ADD_SPHERE - Static variable in class ij3d.Executer
-
- ADD_TUBE_POINT - Static variable in class ij3d.Executer
-
- addBox() - Method in class ij3d.Executer
-
- addBox(Image3DUniverse) - Static method in class ij3d.gui.PrimitiveDialogs
-
- addBox(String, String, String) - Static method in class ij3d.ImageJ3DViewer
-
Add a box into the current 3D universe
- addCenterOf(Iterable<Content>) - Method in class ij3d.ViewAdjuster
-
Make sure that the average center of all contents is visible in the canvas.
- addCone() - Method in class ij3d.Executer
-
- addCone(Image3DUniverse) - Static method in class ij3d.gui.PrimitiveDialogs
-
- addCone(String, String, String, String) - Static method in class ij3d.ImageJ3DViewer
-
Add a cone into the current 3D universe
- addContent(ImagePlus, File) - Method in class ij3d.Executer
-
- addContent(ImagePlus, Color3f, String, int, boolean[], int, int) - Method in class ij3d.Image3DUniverse
-
Add the specified image as a new Content to the universe.
- addContent(ImagePlus, int, int) - Method in class ij3d.Image3DUniverse
-
Add the specified image as a new Content to the universe.
- addContent(ImagePlus, int) - Method in class ij3d.Image3DUniverse
-
Add the specified image as a new Content to the universe.
- addContent(Content) - Method in class ij3d.Image3DUniverse
-
Add the specified Content to the universe.
- addContentFromFile() - Method in class ij3d.Executer
-
- addContentFromImage(ImagePlus) - Method in class ij3d.Executer
-
- addContentLater(Content) - Method in class ij3d.Image3DUniverse
-
Add the specified Content to the universe.
- addContentLater(String) - Method in class ij3d.Image3DUniverse
-
- addContentLater(Collection<Content>) - Method in class ij3d.Image3DUniverse
-
Add the specified collection of Content to the universe.
- addCtrlHint() - Method in class ij3d.gui.LUTDialog
-
- addCustomMesh(CustomMesh, String) - Method in class ij3d.Image3DUniverse
-
Add a custom mesh to the universe.
- addCustomMesh(CustomMultiMesh, String) - Method in class ij3d.Image3DUniverse
-
Add a CustomMultiMesh to the universe.
- added(BenesNamedPoint) - Method in class ij3d.pointlist.PointListPanel
-
- added(BenesNamedPoint) - Method in class ij3d.pointlist.PointListShape
-
- addFace(int, int, int) - Method in class customnode.FullInfoMesh
-
- addIcospheres(List<Point3f>, Color3f, int, float, String) - Method in class ij3d.Image3DUniverse
-
At every Point3f in @param points, place an icosphere created with @param
subdivisions and @param radius.
- addInstant(ContentInstant) - Method in class ij3d.Content
-
- addInteractiveBehavior(InteractiveBehavior) - Method in class ij3d.DefaultUniverse
-
- addLineMesh(List<Point3f>, Color3f, String, boolean) - Method in class ij3d.Image3DUniverse
-
Add a custom mesh, in particular a line mesh (a set of lines in 3D) to the
universe.
- addLines(Point3f[]) - Method in class customnode.CustomLineMesh
-
- addListener(LUTDialog.Listener) - Method in class ij3d.gui.LUTDialog
-
- addMesh(ImagePlus) - Method in class ij3d.Image3DUniverse
-
Add a new image as a content, displaying it as an isosurface.
- addMesh(ImagePlus, int) - Method in class ij3d.Image3DUniverse
-
Add a new image as a content, displaying it as an isosurface.
- addMesh(ImagePlus, Color3f, String, int, boolean[], int) - Method in class ij3d.Image3DUniverse
-
Add a new image as a content, displaying it as an iso-surface.
- addMesh(List, Color3f, String, float, int) - Method in class ij3d.Image3DUniverse
-
- addMesh(List<Point3f>, Color3f, String, int) - Method in class ij3d.Image3DUniverse
-
- addMeshes(Image3DUniverse, String) - Static method in class isosurface.AmiraSurface
-
- addOctree(String, String) - Method in class ij3d.Image3DUniverse
-
- addOrthoslice(ImagePlus) - Method in class ij3d.Image3DUniverse
-
Add a new image as a content, displaying it as orthoslices.
- addOrthoslice(ImagePlus, int) - Method in class ij3d.Image3DUniverse
-
Add a new image as a content, displaying it as orthoslices.
- addOrthoslice(ImagePlus, Color3f, String, int, boolean[], int) - Method in class ij3d.Image3DUniverse
-
Add a new image as a content, displaying it as orthoslices.
- addOrthoslice(String, String, String, String, String, String, String) - Static method in class ij3d.ImageJ3DViewer
-
- addPanel(Panel) - Method in class ij3d.pointlist.PointListDialog
-
Displays an optional panel at the bottom of the window.
- addPoint(Point3f) - Method in class customnode.CustomPointMesh
-
- addPoint(Content, int, int) - Method in class ij3d.behaviors.Picker
-
Adds a landmark point specfied by the canvas position
- addPoint(Content, MouseEvent) - Method in class ij3d.behaviors.Picker
-
Adds a landmark point specfied by the position of the MouseEvent.
- addPointList(String, PointListPanel) - Method in class ij3d.pointlist.PointListDialog
-
Adds the specified PointListPanel.
- addPointListPoint(Point3d) - Method in class ij3d.Content
-
Deprecated.
- addPointListPoint(Point3d) - Method in class ij3d.ContentInstant
-
Deprecated.
- addPointMesh(List<Point3f>, Color3f, String) - Method in class ij3d.Image3DUniverse
-
Add a custom mesh, in particular a point mesh, to the universe.
- addPointMesh(List<Point3f>, Color3f, float, String) - Method in class ij3d.Image3DUniverse
-
Add a custom mesh, in particular a point mesh, to the universe.
- addPoints(Point3f[]) - Method in class customnode.CustomPointMesh
-
- addQuad(Point3f, Point3f, Point3f, Point3f) - Method in class customnode.CustomQuadMesh
-
- addQuadMesh(List<Point3f>, Color3f, String) - Method in class ij3d.Image3DUniverse
-
Add a custom mesh, in particular a mesh consisting of quads, to the
universe.
- addQuads(Point3f[]) - Method in class customnode.CustomQuadMesh
-
- addSphere() - Method in class ij3d.Executer
-
- addSphere(Image3DUniverse) - Static method in class ij3d.gui.PrimitiveDialogs
-
- addSphere(String, String, String) - Static method in class ij3d.ImageJ3DViewer
-
Add a sphere into the current 3D universe
- addSurfacePlot(ImagePlus) - Method in class ij3d.Image3DUniverse
-
Add a new image as a content, displaying it as a 2D surface plot.
- addSurfacePlot(ImagePlus, int) - Method in class ij3d.Image3DUniverse
-
Add a new image as a content, displaying it as a 2D surface plot.
- addSurfacePlot(ImagePlus, Color3f, String, int, boolean[], int) - Method in class ij3d.Image3DUniverse
-
Add a new image as a content, displaying it as a 2D surface plot.
- AddSymbol(long, long) - Method in class customnode.u3d.ContextManager
-
- addText(String, Transform3D, Appearance) - Method in class ij3d.shapes.CoordinateSystem
-
- addTimelapseFromFile() - Method in class ij3d.Executer
-
- addTimelapseFromFolder() - Method in class ij3d.Executer
-
- addTimelapseFromHyperstack(ImagePlus) - Method in class ij3d.Executer
-
- addTimelapseListener(TimelapseListener) - Method in class ij3d.Image3DUniverse
-
- addTriangle(Point3f, Point3f, Point3f) - Method in class customnode.CustomTriangleMesh
-
- addTriangleMesh(List<Point3f>, Color3f, String) - Method in class ij3d.Image3DUniverse
-
Add a custom mesh, in particular a triangle mesh, to the universe.
- addTriangleMesh(List<Point3f>, List<Color3f>, String) - Method in class ij3d.Image3DUniverse
-
Add a custom mesh, in particular a triangle mesh, to the universe.
- addTriangles(Point3f[]) - Method in class customnode.CustomTriangleMesh
-
- addTube() - Method in class ij3d.Executer
-
- addTube(Image3DUniverse) - Static method in class ij3d.gui.PrimitiveDialogs
-
- addTubePoint(String) - Static method in class ij3d.ImageJ3DViewer
-
Add a point to the list that will conform a tube into the current
3D universe
- addUniverseListener(UniverseListener) - Method in class ij3d.DefaultUniverse
-
Register the specified UniverseListener
- addVertex(Point3f) - Method in class customnode.FullInfoMesh
-
- addVertices(Point3f[]) - Method in class customnode.CustomIndexedTriangleMesh
-
- addVertices(Point3f[]) - Method in class customnode.CustomMesh
-
- addVerticesToGeometryArray(Point3f[]) - Method in class customnode.CustomIndexedTriangleMesh
-
- addVerticesToGeometryArray(Point3f[]) - Method in class customnode.CustomMesh
-
- addVerticesToGeometryStripArray(Point3f[]) - Method in class customnode.CustomIndexedTriangleMesh
-
- addVerticesToGeometryStripArray(Point3f[]) - Method in class customnode.CustomMesh
-
- addVoltex(ImagePlus) - Method in class ij3d.Image3DUniverse
-
Add a new image as a content, displaying it as a volume rendering.
- addVoltex(ImagePlus, int) - Method in class ij3d.Image3DUniverse
-
Add a new image as a content, displaying it as a volume rendering.
- addVoltex(ImagePlus, Color3f, String, int, boolean[], int) - Method in class ij3d.Image3DUniverse
-
Add a new image as a content, displaying it as a volume rendering.
- addVolume(String, String, String, String, String, String, String) - Static method in class ij3d.ImageJ3DViewer
-
- ADJUST_BOTH - Static variable in class ij3d.ViewAdjuster
-
Fit the points both horizontally and vertically
- ADJUST_HORIZONTAL - Static variable in class ij3d.ViewAdjuster
-
Fit the points horizontally
- ADJUST_VERTICAL - Static variable in class ij3d.ViewAdjuster
-
Fit the points vertically
- adjustChannels(ImagePlus, boolean[]) - Static method in class ij3d.ColorTable
-
- adjustLight() - Method in class ij3d.Executer
-
- adjustLUTs(Content) - Method in class ij3d.Executer
-
- adjustmentValueChanged(AdjustmentEvent) - Method in class surfaceplot.SurfacePlotGroup
-
Implements AdjustmentListener interface to automatically update the surface
plot when the slice slider in the stack window is dragged.
- adjustView() - Method in class ij3d.Image3DUniverse
-
Fit all contents optimally into the canvas.
- adjustView(int) - Method in class ij3d.Image3DUniverse
-
Fit all contents optimally into the canvas.
- adjustView(Iterable<Content>) - Method in class ij3d.Image3DUniverse
-
Fit the specified contents optimally into the canvas.
- adjustView(Iterable<Content>, int) - Method in class ij3d.Image3DUniverse
-
Fit the specified contents optimally into the canvas.
- adjustView(Content, int) - Method in class ij3d.Image3DUniverse
-
Fit the specified content optimally into the canvas.
- adjustView(Content) - Method in class ij3d.Image3DUniverse
-
Fit the specified content optimally into the canvas.
- AlignTo4Byte() - Method in class customnode.u3d.BitStreamWrite
-
- AlignToByte() - Method in class customnode.u3d.BitStreamWrite
-
- allContentsString() - Method in class ij3d.Image3DUniverse
-
- aLUT - Variable in class ij3d.ContentInstant
-
- ambigous - Static variable in class marchingcubes.MCCube
-
- AmiraSurface - Class in isosurface
-
- AmiraSurface() - Constructor for class isosurface.AmiraSurface
-
- ANIMATE_TG - Static variable in class ij3d.DefaultUniverse
-
The index of the transform group in the viewing platform's
MultiTransformGroup which is responsible for animation
- appCreator - Variable in class voltex.VolumeRenderer
-
The AppearanceCreator, which creates the textures.
- AppearanceCreator - Class in octree
-
- AppearanceCreator - Class in voltex
-
This class is a helper class whose main task is to create Appearance objects
for a specified axis and direction.
- AppearanceCreator(VoltexVolume) - Constructor for class voltex.AppearanceCreator
-
Constructor.
- AppearanceCreator(VoltexVolume, Color3f, float) - Constructor for class voltex.AppearanceCreator
-
Initializes this AppearanceCreator with the given image data, color and
transparency values.
- applied() - Method in interface ij3d.gui.LUTDialog.Listener
-
- apply(HashMap<String, String>, Image3DUniverse) - Method in class ij3d.SaveSession
-
- apply(Image3DUniverse) - Static method in class ij3d.UniverseSettings
-
- apply() - Method in class ij3d.ViewAdjuster
-
After all points/contents were added, apply() finally adjusts center and
zoom transformations of the view.
- APPLY_TRANSFORM - Static variable in class ij3d.Executer
-
- applyRotation(int, double) - Method in class ij3d.Content
-
- applySurfaceColors(ImagePlus) - Method in class ij3d.Content
-
- applySurfaceColors(ImagePlus) - Method in class ij3d.ContentInstant
-
- applySurfaceColors(Content) - Method in class ij3d.Executer
-
- applyTransform(double[]) - Method in class ij3d.Content
-
- applyTransform(Transform3D) - Method in class ij3d.Content
-
- applyTransform(double[]) - Method in class ij3d.ContentInstant
-
- applyTransform(Transform3D) - Method in class ij3d.ContentInstant
-
- applyTransform(Content) - Method in class ij3d.Executer
-
- applyTransform(String) - Static method in class ij3d.ImageJ3DViewer
-
- applyTranslation(float, float, float) - Method in class ij3d.Content
-
- AreaListVolume - Class in ij3d
-
Wraps a list of
Areas to be triangulated.
- AreaListVolume(List<List<Area>>, double, double, double, double) - Constructor for class ij3d.AreaListVolume
-
- ASCII - Static variable in class isosurface.MeshExporter
-
- ATTRIBUTE_COORD_SYSTEM - Static variable in class ij3d.DefaultUniverse
-
Constant used in showAttribute() specifying whether a global coordinate
system should be displayed or not.
- ATTRIBUTE_SCALEBAR - Static variable in class ij3d.DefaultUniverse
-
Constant used in showAttribute() specifying whether a scalebar should be
displayed or not.
- attributesSwitch - Variable in class ij3d.DefaultUniverse
-
Switch which holds the optionally displayable scalebar and coordinate
system.
- average - Variable in class ij3d.Volume
-
Flag indicating that the channels should be averaged
- AverageByteLoader(Volume.InputImage) - Constructor for class ij3d.Volume.AverageByteLoader
-
- AxisConstants - Interface in ij3d
-
This interface stores some common constants.
- axisIndex - Variable in class voltex.VolumeRenderer
-
The index in the switch, given the direction
- axisSwitch - Variable in class voltex.VolumeRenderer
-
A Switch, which holds 6 OrderedGroups, one for each direction
- generateGlobe(int, int) - Static method in class customnode.MeshMaker
-
Generate a globe of radius 1.0 that can be used for any Ball.
- generateTriangles(double[][][], double) - Static method in class ij3d.Pipe
-
- generateTriangles(double[][][], double, List<Color3f>, List<Color3f>) - Static method in class ij3d.Pipe
-
Accepts an arrays as that returned from methods generateJoints and
makeTube: first dimension is the list of points, second dimension is the
number of vertices defining the circular cross section of the tube, and
third dimension is the x,y,z of each vertex. pointColorList is input,
telling this method what the colour of each point along the path is, while
vertexColorList should be an empty list used for output - the color of each
vertex in the triangulation will be returned in there.
- geomCreator - Variable in class voltex.VolumeRenderer
-
The GeometryCreator, which creates the corresponding geomentries.
- GeometryCreator - Class in octree
-
- GeometryCreator - Class in voltex
-
This class is a helper class whose main task is to create Geometry objects
for a specified axis and direction.
- GeometryCreator(VoltexVolume) - Constructor for class voltex.GeometryCreator
-
Initializes this GeometryCreator with the given volume
- get(int, int, int) - Method in class ij3d.Volume.ByteImage
-
- get(int, int, int, int[]) - Method in class ij3d.Volume.ByteImage
-
- get(int, int, int) - Method in interface ij3d.Volume.InputImage
-
- get(int, int, int, int[]) - Method in interface ij3d.Volume.InputImage
-
- get(int, int, int) - Method in class ij3d.Volume.IntImage
-
- get(int, int, int, int[]) - Method in class ij3d.Volume.IntImage
-
- getAlphaLUT(int[]) - Method in class ij3d.Content
-
- getAlphaLUT(int[]) - Method in class ij3d.ContentInstant
-
- getAlphaLUT(int[]) - Method in class ij3d.Volume
-
Copies the current color table into the given array.
- getAlphaMethod() - Method in class voltex.Mask
-
- getAlphaSource(int) - Method in class voltex.Mask
-
- getAnimationTG() - Method in class ij3d.DefaultUniverse
-
Returns the TransformGroup of the viewing platform's MultiTransformGroup
which is responsible for animation.
- getAppearance(CubeData, int) - Method in class octree.AppearanceCreator
-
- getAppearance(int, int) - Method in class voltex.AppearanceCreator
-
Returns the Appearance object for the specified direction and index.
- getAppearance(int, int) - Method in class voltex.VolumeRenderer
-
Get the Appearance object for the Shape3D of the specified axis; Note that
both front and back shapes share the same Appearance.
- getAreas() - Method in class ij3d.AreaListVolume
-
- getAutoAdjustView() - Method in class ij3d.Image3DUniverse
-
autoAdjustView indicates, whether the view is adjusted to fit the whole
universe each time a Content is added.
- getAverage(int, int, int) - Method in class ij3d.Volume.ByteImage
-
- getAverage(int, int, int) - Method in class ij3d.Volume
-
Load the average value at the specified position
- getAverage(int, int, int) - Method in interface ij3d.Volume.InputImage
-
- getAverage(int, int, int) - Method in class ij3d.Volume.IntImage
-
- getAverageGrayColorModel(ImagePlus, boolean[]) - Static method in class ij3d.ColorTable
-
- getAxisVworld(Vector3d, Vector3d) - Method in class ij3d.behaviors.ViewPlatformTransformer
-
Calculates from the specified axis in image plate coordinate system the
corresponding vector in the vworld coordinate system.
- getBG() - Method in class ij3d.ImageCanvas3D
-
- getBlockType() - Method in class customnode.u3d.DataBlock
-
- getBlueLUT(int[]) - Method in class ij3d.Content
-
- getBlueLUT(int[]) - Method in class ij3d.ContentInstant
-
- getBlueLUT(int[]) - Method in class ij3d.Volume
-
Copies the current color table into the given array.
- getBounceBack() - Method in class view4d.Timeline
-
- getCanvas() - Method in class ij3d.ImageWindow3D
-
- getCenter(Tuple3d) - Method in class customnode.CustomMeshNode
-
- getCenter(Tuple3d) - Method in class customnode.CustomMultiMesh
-
- getCenter(Tuple3d) - Method in class ij3d.ContentNode
-
Stores the center coordinate of this ContentNode in the specified Tuple3d
- getCenter(Tuple3d) - Method in class isosurface.MeshGroup
-
- getCenter(Tuple3d) - Method in class surfaceplot.SurfacePlotGroup
-
- getCenter(Tuple3d) - Method in class voltex.VoltexGroup
-
- getCenterTG() - Method in class ij3d.DefaultUniverse
-
Returns the TransformGroup of the viewing platform's MultiTransformGroup
which is responsible for centering the universe.
- getCenterTranslation(Vector3d) - Method in class ij3d.behaviors.ViewPlatformTransformer
-
Retrieves the translation vector which is responsible for centering the
view.
- getChannels() - Method in class ij3d.Content
-
- getChannels() - Method in class ij3d.ContentInstant
-
- getChannels() - Method in class ij3d.gui.ContentCreatorDialog
-
- getChildren() - Method in class octree.Cube
-
- getColor() - Method in class customnode.CustomIndexedTriangleMesh
-
- getColor() - Method in class customnode.CustomMesh
-
- getColor(String) - Static method in class ij3d.ColorTable
-
- getColor() - Method in class ij3d.Content
-
- getColor() - Method in class ij3d.ContentInstant
-
- getColor() - Method in class ij3d.gui.ContentCreatorDialog
-
- getColor() - Method in class ij3d.pointlist.PointListShape
-
- getColor() - Method in class ij3d.shapes.Scalebar
-
- getColorMethod() - Method in class voltex.Mask
-
- getColorName(Color3f) - Static method in class ij3d.ColorTable
-
- getColorSource(int) - Method in class voltex.Mask
-
- getCommand(int) - Method in class ij3d.shortcuts.ShortCuts
-
- getCommands() - Method in class ij3d.shortcuts.ShortCuts
-
- getContent() - Method in class ij3d.Content
-
- getContent() - Method in class ij3d.ContentInstant
-
- getContent(String) - Method in class ij3d.Image3DUniverse
-
Returns the Content with the specified name.
- getContents() - Method in class ij3d.Image3DUniverse
-
Returns a Collection containing the references to all the contents of this
universe.
- getContentTransformer() - Method in class ij3d.DefaultUniverse
-
Returns a reference to the ContentTransformer which is used by this
universe to handle mouse and keyboard input which aims to transform
individual Contents.
- GetCumulativeSymbolFrequency(long, long) - Method in class customnode.u3d.ContextManager
-
- getCurrent() - Method in class ij3d.Content
-
- getCurrentTimepoint() - Method in class ij3d.Image3DUniverse
-
- getData() - Method in class customnode.u3d.DataBlock
-
- GetDataBlock() - Method in class customnode.u3d.BitStreamWrite
-
- getDataSize() - Method in class customnode.u3d.DataBlock
-
- getDataType() - Method in class ij3d.AreaListVolume
-
- getDataType() - Method in class ij3d.Volume
-
Get the current set data type.
- getDefaultResamplingFactor(ImagePlus, int) - Static method in class ij3d.Content
-
- getDefaultResamplingFactor(ImagePlus, int) - Static method in class ij3d.ContentInstant
-
- getDefaultThreshold(ImagePlus, int) - Static method in class ij3d.Content
-
- getDefaultThreshold(ImagePlus, int) - Static method in class ij3d.ContentInstant
-
- getEdges() - Method in class customnode.FullInfoMesh.Vertex
-
- getEndTime() - Method in class ij3d.Content
-
- getEndTime() - Method in class ij3d.Image3DUniverse
-
- getExecuter() - Method in class ij3d.Image3DUniverse
-
Returns a reference to the Executer used by this universe.
- getExternalBehaviors() - Method in class ij3d.behaviors.InteractiveBehavior
-
- getFace(int) - Method in class customnode.FullInfoMesh
-
- getFaceCount() - Method in class customnode.FullInfoMesh
-
- getFaceNormal(int, Vector3f) - Method in class customnode.FullInfoMesh
-
- getFile() - Method in class customnode.CustomIndexedTriangleMesh
-
- getFile() - Method in class customnode.CustomMesh
-
- getFile() - Method in class ij3d.gui.ContentCreatorDialog
-
- getGlobalCenterPoint() - Method in class ij3d.Image3DUniverse
-
Get a reference to the global center point.
- getGlobalCenterPoint(Point3d) - Method in class ij3d.Image3DUniverse
-
Copies the global center point into the specified Point3d.
- getGlobalMaxPoint(Point3d) - Method in class ij3d.Image3DUniverse
-
Copies the global maximum point into the specified Point3d.
- getGlobalMinPoint(Point3d) - Method in class ij3d.Image3DUniverse
-
Copies the global minimum point into the specified Point3d.
- getGlobalTransform(DefaultUniverse.GlobalTransform) - Method in class ij3d.DefaultUniverse
-
Obtain a copy of all the Transform3D that describe the view such as zoom,
pan, and rotation.
- getGreenLUT(int[]) - Method in class ij3d.Content
-
- getGreenLUT(int[]) - Method in class ij3d.ContentInstant
-
- getGreenLUT(int[]) - Method in class ij3d.Volume
-
Copies the current color table into the given array.
- getHistogramMax(ImagePlus) - Static method in class ij3d.ColorTable
-
- getImage() - Method in class ij3d.Content
-
- getImage() - Method in class ij3d.ContentInstant
-
- getImage() - Method in class ij3d.gui.ContentCreatorDialog
-
- getImageComponentX(int) - Method in class voltex.VoltexVolume
-
- getImageComponentY(int) - Method in class voltex.VoltexVolume
-
- getImageComponentZ(int) - Method in class voltex.VoltexVolume
-
- getImageDir() - Method in class octree.OctreeDialog
-
- getImagePath() - Method in class octree.OctreeDialog
-
- getImagePlus() - Method in class ij3d.ImageWindow3D
-
- getImagePlus() - Method in class ij3d.Volume
-
- getImages(ImagePlus) - Static method in class ij3d.ContentCreator
-
Get an array of images of the specified image; if the image is a
hyperstack, it is splitted into several individual images, otherwise, it
the returned array contains the given image only.
- getImages(File) - Static method in class ij3d.ContentCreator
-
If file is a regular file, it is opened using IJ.openImage(),
and then given to getImages(ImagePlus); If file however is a
directory, all the files in it are sorted alphabetically and then loaded,
failing silently if an image can not be opened by IJ.openImage().
- getIndex(Point3f) - Method in class customnode.FullInfoMesh
-
- getIndexedColorModel(ImagePlus, boolean[]) - Static method in class ij3d.ColorTable
-
- getInstant(int) - Method in class ij3d.Content
-
- getInstants() - Method in class ij3d.Content
-
- getJava3DVersion() - Static method in class ij3d.ImageJ_3D_Viewer
-
- getLandmarkColor() - Method in class ij3d.Content
-
- getLandmarkColor() - Method in class ij3d.ContentInstant
-
- getLandmarkPointSize() - Method in class ij3d.Content
-
- getLandmarkPointSize() - Method in class ij3d.ContentInstant
-
- getLength() - Method in class ij3d.shapes.Scalebar
-
- getLight() - Method in class ij3d.DefaultUniverse
-
Returns the point light source of this universe.
- getLightNodeBlock(String, String) - Static method in class customnode.u3d.U3DExporter
-
- getLightResourceBlock(String) - Static method in class customnode.u3d.U3DExporter
-
- getLineWidth() - Method in class customnode.CustomLineMesh
-
- getLitTextureShaderBlock(String, String) - Static method in class customnode.u3d.U3DExporter
-
- getLocalRotate() - Method in class ij3d.Content
-
- getLocalRotate(Transform3D) - Method in class ij3d.Content
-
- getLocalRotate() - Method in class ij3d.ContentInstant
-
- getLocalRotate(Transform3D) - Method in class ij3d.ContentInstant
-
- getLocalTranslate() - Method in class ij3d.Content
-
- getLocalTranslate(Transform3D) - Method in class ij3d.Content
-
- getLocalTranslate() - Method in class ij3d.ContentInstant
-
- getLocalTranslate(Transform3D) - Method in class ij3d.ContentInstant
-
- getMask() - Method in class voltex.Mask
-
- getMaskAttributes() - Method in class voltex.Mask
-
- getMaterialResourceBlock(String, float, float, float, float) - Static method in class customnode.u3d.U3DExporter
-
- getMax(Tuple3d) - Method in class customnode.CustomMeshNode
-
- getMax(Tuple3d) - Method in class customnode.CustomMultiMesh
-
- getMax(Point3d) - Method in class ij3d.Content
-
- getMax(Tuple3d) - Method in class ij3d.ContentNode
-
Stores the maximum coordinate of this ContentNode in the specified Tuple3d
- getMax(Tuple3d) - Method in class isosurface.MeshGroup
-
- getMax(Tuple3d) - Method in class surfaceplot.SurfacePlotGroup
-
- getMax(Tuple3d) - Method in class voltex.VoltexGroup
-
- getMenuBar() - Method in class ij3d.Image3DUniverse
-
Returns a reference to the menu bar used by this universe.
- getMesh() - Method in class customnode.CustomIndexedTriangleMesh
-
- getMesh() - Method in class customnode.CustomMesh
-
- getMesh() - Method in class customnode.CustomMeshNode
-
- getMesh(int) - Method in class customnode.CustomMultiMesh
-
- getMesh() - Method in class customnode.FullInfoMesh
-
- getMesh() - Method in class isosurface.MeshGroup
-
- getMeshes() - Method in class customnode.EdgeContraction
-
- getMetaData() - Method in class customnode.u3d.DataBlock
-
- getMetaDataSize() - Method in class customnode.u3d.DataBlock
-
- getMin(Tuple3d) - Method in class customnode.CustomMeshNode
-
- getMin(Tuple3d) - Method in class customnode.CustomMultiMesh
-
- getMin(Point3d) - Method in class ij3d.Content
-
- getMin(Tuple3d) - Method in class ij3d.ContentNode
-
Stores the minimum coordinate of this ContentNode in the specified Tuple3d
- getMin(Tuple3d) - Method in class isosurface.MeshGroup
-
- getMin(Tuple3d) - Method in class surfaceplot.SurfacePlotGroup
-
- getMin(Tuple3d) - Method in class voltex.VoltexGroup
-
- getMinMax(Point3f, Point3f) - Method in class customnode.u3d.U3DExporter.Mesh
-
- getMode() - Method in class customnode.CustomLineMesh
-
- getName() - Method in class customnode.CustomIndexedTriangleMesh
-
- getName() - Method in class customnode.CustomMesh
-
- getName() - Method in class ij3d.Content
-
- getName() - Method in class ij3d.ContentInstant
-
- getName() - Method in class ij3d.gui.ContentCreatorDialog
-
- getName() - Method in class octree.OctreeDialog
-
- getNormals() - Method in class customnode.CustomIndexedTriangleMesh
-
- getNumberOfCommands() - Method in class ij3d.shortcuts.ShortCuts
-
- getNumberOfInstants() - Method in class ij3d.Content
-
- getOpaqueAverageGrayColorModel(ImagePlus, boolean[]) - Static method in class ij3d.ColorTable
-
- getOpaqueIndexedColorModel(ImagePlus, boolean[]) - Static method in class ij3d.ColorTable
-
- getOpaqueTextures() - Method in class voltex.AppearanceCreator
-
Returns whether the created textures are supposed to be opaque.
- getPanel() - Method in class view4d.TimelineGUI
-
- getPickedContent(int, int) - Method in class ij3d.behaviors.Picker
-
Get the Content at the specified canvas position
- getPickedVertexIndices(BranchGroup, int, int) - Method in class ij3d.behaviors.Picker
-
- getPicker() - Method in class ij3d.DefaultUniverse
-
Returns a reference to the Picker which is used by this universe to handle
mouse input which aims to pick Contents and change landmark sets.
- getPickPointColumn(Content, int, int) - Method in class ij3d.behaviors.Picker
-
- getPickPointGeometry(Content, Point3d, Vector3d) - Method in class ij3d.behaviors.Picker
-
Get the picked point using geometry picking.
- getPickPointGeometry(Content, MouseEvent) - Method in class ij3d.behaviors.Picker
-
Get the picked point, using geometry picking, for the specified canvas
position.
- getPickPointGeometry(Content, int, int) - Method in class ij3d.behaviors.Picker
-
Get the picked point, using geometry picking, for the specified canvas
position.
- getPointColors(double[], double[], double[], Color3f, ImagePlus) - Static method in class ij3d.Pipe
-
- getPointList() - Method in class ij3d.Content
-
- getPointList() - Method in class ij3d.ContentInstant
-
- getPointListDialog() - Method in class ij3d.Image3DUniverse
-
Returns a reference to the PointListDialog used by this universe
- getPointSize() - Method in class customnode.CustomPointMesh
-
- getPrefsDir() - Static method in class ij3d.UniverseSettings
-
- getPriority() - Method in class customnode.u3d.DataBlock
-
- getQuad(CubeData, int) - Method in class octree.GeometryCreator
-
- getQuad(int, int) - Method in class voltex.GeometryCreator
-
Returns the QuadArray for the specified axis and slice index.
- getQuadCoordinates(CubeData, int) - Method in class octree.GeometryCreator
-
- getQuadCoords(int, int) - Method in class voltex.GeometryCreator
-
Returns the coordinates of the rectangle of the specified axis and slice
index as a double array.
- getRadius() - Method in class ij3d.pointlist.PointListShape
-
Returns the radius of the points.
- getRedLUT(int[]) - Method in class ij3d.Content
-
- getRedLUT(int[]) - Method in class ij3d.ContentInstant
-
- getRedLUT(int[]) - Method in class ij3d.Volume
-
Copies the current color table into the given array.
- getRegistrationMenuBar() - Method in class ij3d.Image3DUniverse
-
Returns a reference to the registration menu bar.
- getRemainingVertexCount() - Method in class customnode.EdgeContraction
-
- getRenderer() - Method in class voltex.VoltexGroup
-
Get a reference VolumeRenderer which is used by this class
- getResamplingFactor() - Method in class ij3d.Content
-
- getResamplingFactor() - Method in class ij3d.ContentInstant
-
- getResamplingFactor() - Method in class ij3d.gui.ContentCreatorDialog
-
- getRoi() - Method in class ij3d.ImageCanvas3D
-
- getRoiCanvas() - Method in class ij3d.ImageCanvas3D
-
- getRootBranchGroup() - Method in class octree.VolumeOctree
-
- getRootCube() - Method in class octree.VolumeOctree
-
- getRotationAxis(Vector3f) - Method in class ij3d.DefaultAnimatableUniverse
-
Copy the current rotation axis into the given Vector3f.
- getRotationCenter(Tuple3d) - Method in class ij3d.behaviors.ViewPlatformTransformer
-
Copies the rotation center into the given Tuple3d.
- getRotationInterval() - Method in class ij3d.DefaultAnimatableUniverse
-
Returns the rotation interval (in degree)
- getRotationTG() - Method in class ij3d.DefaultUniverse
-
Returns the TransformGroup of the viewing platform's MultiTransformGroup
which is responsible for rotation.
- getSafeContentName(String) - Method in class ij3d.Image3DUniverse
-
- getScalebar() - Method in class ij3d.DefaultUniverse
-
Returns a reference to the optionally displayable scale bar.
- getScene() - Method in class ij3d.DefaultUniverse
-
Returns a reference to the root BranchGroup of this universe.
- getSelected() - Method in class ij3d.DefaultUniverse
-
- getSelected() - Method in class ij3d.Image3DUniverse
-
Returns the selected Content, or null if none is selected.
- getShortCut(String) - Method in class ij3d.shortcuts.ShortCuts
-
- getShortcuts() - Method in class ij3d.Image3DUniverse
-
Returns a reference to the universe's shortcuts.
- getShowAllTimepoints() - Method in class ij3d.Content
-
- getShowBoundingBoxUponSelection() - Method in class ij3d.Image3DUniverse
-
Returns true if the selection box is shown upon selecting a
Content(Instant).
- getSize() - Method in class ij3d.DefaultUniverse
-
Returns the dimensions of this universe.
- getSlice(int) - Method in class orthoslice.OrthoGroup
-
Get the slice index of the specified axis
- getSlice(int) - Method in class orthoslice.Orthoslice
-
Returns the current index of the specified plane
- getSlice() - Method in class surfaceplot.SurfacePlot
-
Returns the currently displayed slice.
- getSlice() - Method in class surfaceplot.SurfacePlotGroup
-
Returns the currently displayed slice.
- getSliceCount(int) - Method in class orthoslice.MultiOrthoGroup
-
- getSliceCount(int) - Method in class orthoslice.MultiOrthoslice
-
- getStartTime() - Method in class ij3d.Content
-
- getStartTime() - Method in class ij3d.Image3DUniverse
-
- getStatusLabel() - Method in class ij3d.ImageWindow3D
-
- getSubmeshes() - Method in class customnode.FullInfoMesh
-
- GetSymbolFrequency(long, long) - Method in class customnode.u3d.ContextManager
-
- GetSymbolFromFrequency(long, long) - Method in class customnode.u3d.ContextManager
-
- getTexStub(Image3DUniverse, String) - Static method in class customnode.u3d.U3DExporter
-
- getTexture(int, int) - Method in class voltex.AppearanceCreator
-
Returns the texture for the specified axis and slice
- getTexture(int, int, VoltexVolume) - Method in class voltex.AppearanceCreator
-
Returns the texture for the specified axis and slice
- getTexturesOpaque() - Method in class orthoslice.MultiOrthoGroup
-
Returns whether the textures are transparent or not.
- getTexturesOpaque() - Method in class orthoslice.MultiOrthoslice
-
Returns whether the textures are transparent or not.
- getTg(int) - Method in class voltex.AppearanceCreator
-
Get the TextureGeneration of the specified direction.
- getThreshold() - Method in class ij3d.Content
-
- getThreshold() - Method in class ij3d.ContentInstant
-
- getThreshold() - Method in class ij3d.gui.ContentCreatorDialog
-
- getTimeline() - Method in class ij3d.Image3DUniverse
-
- getTimepoint() - Method in class ij3d.ContentInstant
-
- getTimepoint() - Method in class ij3d.gui.ContentCreatorDialog
-
- getToolId() - Method in class ij3d.IJAdapter
-
- getToolId() - Method in class ij3d.NoopAdapter
-
- getToolId() - Method in interface ij3d.UIAdapter
-
- GetTotalSymbolFrequency(long) - Method in class customnode.u3d.ContextManager
-
- getTransform(Transform3D) - Method in class ij3d.shapes.BoundingSphere
-
- getTransformInverse(Transform3D) - Method in class ij3d.shapes.BoundingSphere
-
- getTranslateTG() - Method in class ij3d.DefaultUniverse
-
Returns the TransformGroup of the viewing platform's MultiTransformGroup
which is responsible for translation.
- getTranslateTranslation(Vector3d) - Method in class ij3d.behaviors.ViewPlatformTransformer
-
Retrieves the manual translation vector of the view.
- getTransparency() - Method in class customnode.CustomIndexedTriangleMesh
-
- getTransparency() - Method in class customnode.CustomMesh
-
- getTransparency() - Method in class ij3d.Content
-
- getTransparency() - Method in class ij3d.ContentInstant
-
- getTriangles() - Method in class customnode.FullInfoMesh.Vertex
-
- getTriangles(ImagePlus, int, boolean[], int) - Method in interface isosurface.Triangulator
-
This method must return a list of elements of class Point3f.
- getTriangles(Volume, int) - Static method in class marchingcubes.MCCube
-
Create a list of triangles from the specified image data and the given
isovalue.
- getTriangles(ImagePlus, int, boolean[], int) - Method in class marchingcubes.MCTriangulator
-
- getTriangles(AreaListVolume) - Method in class marchingcubes.MCTriangulator
-
Triangulates the specifified volume.
- getType() - Method in class ij3d.Content
-
- getType() - Method in class ij3d.ContentInstant
-
- getType() - Method in class ij3d.gui.ContentCreatorDialog
-
- getUniqueContentLabel(Image3DUniverse, String) - Method in class ij3d.gui.ContentCreatorDialog
-
- getUnit() - Method in class ij3d.shapes.Scalebar
-
- getUniverse() - Method in class ij3d.ImageWindow3D
-
- getUniverse() - Method in class view4d.Timeline
-
- getUseToFront() - Method in class ij3d.DefaultUniverse
-
Returns the value of the useToFront flag.
- getVertex(int) - Method in class customnode.FullInfoMesh
-
- getVertexCount() - Method in class customnode.EdgeContraction
-
- getVertexCount() - Method in class customnode.FullInfoMesh
-
- getVertexNormal(FullInfoMesh.Vertex, Vector3f) - Method in class customnode.FullInfoMesh
-
- getVertexNormal(int, Vector3f) - Method in class customnode.FullInfoMesh
-
- getVertices() - Method in class customnode.FullInfoMesh
-
- getViewPlatformTransformer() - Method in class ij3d.DefaultUniverse
-
Returns a reference to the InteractiveViewPlatformTransformer which is used
by this universe to handle mouse and keyboard input which aims to transform
the viewing platform.
- getVolume() - Method in class customnode.CustomIndexedTriangleMesh
-
- getVolume() - Method in class customnode.CustomLineMesh
-
- getVolume() - Method in class customnode.CustomMesh
-
- getVolume() - Method in class customnode.CustomMeshNode
-
- getVolume() - Method in class customnode.CustomMultiMesh
-
- getVolume() - Method in class customnode.CustomPointMesh
-
- getVolume() - Method in class customnode.CustomTransparentTriangleMesh
-
- getVolume() - Method in class customnode.CustomTriangleMesh
-
- getVolume() - Method in class ij3d.ContentNode
-
Returns the volume of this ContentNode.
- getVolume() - Method in class isosurface.MeshGroup
-
- getVolume() - Method in class surfaceplot.SurfacePlotGroup
-
- getVolume() - Method in class voltex.VoltexGroup
-
- getVolume() - Method in class voltex.VolumeRenderer
-
Returns the image data of this rendering.
- getVolumeNode() - Method in class voltex.VolumeRenderer
-
Returns the root BranchGroup below which the whole volume rendering is
organized.
- getVworldToCamera(Transform3D) - Method in class ij3d.DefaultUniverse
-
Copy the whole transformation, which transforms any point from the vworld
coordinate system to the observer coordinate system.
- getVworldToCameraInverse(Transform3D) - Method in class ij3d.DefaultUniverse
-
Copy the inverse vworld to camera transformation, which transforms any
point from the observer coordinate system to vworld coordinate system to
the
- getWindow() - Method in class ij3d.DefaultUniverse
-
Returns a reference to the window in which this universe is displayed.
- getX() - Method in class ij3d.shapes.Scalebar
-
- getXDir(Vector3d) - Method in class ij3d.behaviors.ViewPlatformTransformer
-
Transforms the x-direction of the image plate to a normalized vector
representing this direction in the vworld space.
- getXDir(Vector3d, Transform3D) - Method in class ij3d.behaviors.ViewPlatformTransformer
-
Transforms the x-direction of the image plate to a normalized vector
representing this direction in the vworld space.
- getY() - Method in class ij3d.shapes.Scalebar
-
- getYDir(Vector3d) - Method in class ij3d.behaviors.ViewPlatformTransformer
-
Stores the y-direction in the image plate coordinate system, i.e. the
direction towards the user, in the given Vector3d.
- getYDir(Vector3d, Transform3D) - Method in class ij3d.behaviors.ViewPlatformTransformer
-
Transforms the y-direction of the image plate to a normalized vector
representing this direction in the vworld space.
- getZDir(Vector3d) - Method in class ij3d.behaviors.ViewPlatformTransformer
-
Transforms the z-direction of the image plate to a normalized vector
representing this direction in the vworld space.
- getZDir(Vector3d, Transform3D) - Method in class ij3d.behaviors.ViewPlatformTransformer
-
Transforms the z-direction of the image plate to a normalized vector
representing this direction in the vworld space.
- getZoomTG() - Method in class ij3d.DefaultUniverse
-
Returns the TransformGroup of the viewing platform's MultiTransformGroup
which is responsible for zooming.
- getZoomTranslation(Vector3d) - Method in class ij3d.behaviors.ViewPlatformTransformer
-
Retrieves the translation vector which is responsible for the current
zooming and stores it in the given Vector3d.
- globalCenter - Variable in class ij3d.DefaultUniverse
-
The global center point
- globalCoord - Variable in class ij3d.DefaultUniverse
-
Reference to the global coordinate system, which is optionally displayable.
- globalMax - Variable in class ij3d.DefaultUniverse
-
The global maximum point
- globalMin - Variable in class ij3d.DefaultUniverse
-
The global minimum point
- GlobalTransform() - Constructor for class ij3d.DefaultUniverse.GlobalTransform
-
- gLUT - Variable in class ij3d.ContentInstant
-
- greyCM - Static variable in class voltex.VoltexVolume
-
The ColorModel used for 8-bit textures
- readCalibration(String, float[]) - Static method in class octree.CubeData
-
- ReadCompressedU16(long) - Method in class customnode.u3d.BitStreamRead
-
- ReadCompressedU32(long) - Method in class customnode.u3d.BitStreamRead
-
- ReadCompressedU8(long) - Method in class customnode.u3d.BitStreamRead
-
- readContent(BufferedReader) - Method in class ij3d.SaveSession
-
- readContentInstant(BufferedReader) - Method in class ij3d.SaveSession
-
- ReadF32() - Method in class customnode.u3d.BitStreamRead
-
- ReadI32() - Method in class customnode.u3d.BitStreamRead
-
- ReadU16() - Method in class customnode.u3d.BitStreamRead
-
- ReadU32() - Method in class customnode.u3d.BitStreamRead
-
- ReadU8() - Method in class customnode.u3d.BitStreamRead
-
- realWorldXDim() - Method in class octree.VolumeOctree
-
- realWorldYDim() - Method in class octree.VolumeOctree
-
- realWorldZDim() - Method in class octree.VolumeOctree
-
- recalculateGlobalMinMax() - Method in class ij3d.Image3DUniverse
-
Calculates the global minimum, maximum and center point depending on all
the available contents.
- recalculateGlobalMinMax(Content) - Method in class ij3d.Image3DUniverse
-
If the specified Content is the only content in the universe, global
minimum, maximum and center point are set accordingly to this Content.
- recalculateNormals(GeometryArray) - Method in class customnode.CustomIndexedTriangleMesh
-
- recalculateNormals(GeometryArray) - Method in class customnode.CustomMesh
-
- record(String, String...) - Static method in class ij3d.Executer
-
- record() - Method in class view4d.Timeline
-
- record360() - Method in class ij3d.DefaultAnimatableUniverse
-
Records a full 360 degree rotation and returns an ImagePlus containing the
frames of the animation.
- record360() - Method in class ij3d.Executer
-
- record360() - Static method in class ij3d.ImageJ3DViewer
-
- RECORD_360 - Static variable in class ij3d.Executer
-
- register() - Method in class ij3d.Executer
-
- register() - Method in class ij3d.RegistrationMenubar
-
- RegistrationMenubar - Class in ij3d
-
- RegistrationMenubar(Image3DUniverse) - Constructor for class ij3d.RegistrationMenubar
-
- release() - Method in class voltex.AppearanceCreator
-
Release all stored data.
- releaseKey(int) - Method in class ij3d.ImageCanvas3D
-
- reload() - Method in class ij3d.shortcuts.ShortCuts
-
- remove(int) - Method in class customnode.CustomMultiMesh
-
- remove(CustomMesh) - Method in class customnode.CustomMultiMesh
-
- removeAllContents() - Method in class ij3d.Image3DUniverse
-
Remove all the contents of this universe.
- removeContent(String) - Method in class ij3d.Image3DUniverse
-
Remove the Content with the specified name from the universe.
- removed(BenesNamedPoint) - Method in class ij3d.pointlist.PointListPanel
-
- removed(BenesNamedPoint) - Method in class ij3d.pointlist.PointListShape
-
- removeExtraPanel() - Method in class ij3d.pointlist.PointListDialog
-
Remove the optional panel at the bottom of the window (if there is one).
- removeFace(int) - Method in class customnode.FullInfoMesh
-
- removeInstant(int) - Method in class ij3d.Content
-
- removeListener(LUTDialog.Listener) - Method in class ij3d.gui.LUTDialog
-
- removeNext(int) - Method in class customnode.EdgeContraction
-
- removeOctree() - Method in class ij3d.Image3DUniverse
-
- removePointList(PointListPanel) - Method in class ij3d.pointlist.PointListDialog
-
Removes the specified PointListPanel and hides the window, if it was the
last one.
- removeTimelapseListener(TimelapseListener) - Method in class ij3d.Image3DUniverse
-
- removeTriangle(int) - Method in class customnode.CustomTriangleMesh
-
- removeTriangles(int[]) - Method in class customnode.CustomTriangleMesh
-
- removeUniverseListener(UniverseListener) - Method in class ij3d.DefaultUniverse
-
Remove the specified UniverseListener
- removeUntil(float) - Method in class customnode.EdgeContraction
-
- removeVertex(Point3f) - Method in class customnode.FullInfoMesh
-
- removeVertex(int) - Method in class customnode.FullInfoMesh
-
- removeVertices(int[]) - Method in class customnode.CustomIndexedTriangleMesh
-
- removeVertices(int[]) - Method in class customnode.CustomMesh
-
- renamed(BenesNamedPoint) - Method in class ij3d.pointlist.PointListPanel
-
- renamed(BenesNamedPoint) - Method in class ij3d.pointlist.PointListShape
-
- renamePoint(BenesNamedPoint) - Method in class ij3d.pointlist.PointListPanel
-
Opens an input dialog to ask the user for a new name for the specified
point
- render() - Method in class ij3d.ImageCanvas3D
-
- renderer - Variable in class voltex.VoltexGroup
-
The VolumeRenderer behind this VoltexGroup
- reordered() - Method in class ij3d.pointlist.PointListPanel
-
- reordered() - Method in class ij3d.pointlist.PointListShape
-
- RES_THRESHOLD - Static variable in class octree.Cube
-
- resamplingF - Variable in class ij3d.ContentInstant
-
- reset() - Method in class ij3d.gui.LUTDialog
-
- RESET_TRANSFORM - Static variable in class ij3d.Executer
-
- RESET_VIEW - Static variable in class ij3d.Executer
-
- resetTransform(Content) - Method in class ij3d.Executer
-
- resetTransform() - Static method in class ij3d.ImageJ3DViewer
-
- resetView() - Method in class ij3d.Executer
-
- resetView() - Method in class ij3d.Image3DUniverse
-
Reset the transformations of the view side of the scene graph as if the
Contents of this universe were just displayed.
- resetView() - Static method in class ij3d.ImageJ3DViewer
-
- RESOLUTION_SUFFICIENT - Static variable in class octree.Cube
-
- RESOLUTION_UNSUFFICIENT - Static variable in class octree.Cube
-
- restore(String) - Method in class ij3d.Volume
-
- restore(String) - Method in class voltex.VoltexVolume
-
- restoreDisplayedData(String, String) - Method in class customnode.CustomIndexedTriangleMesh
-
- restoreDisplayedData(String, String) - Method in class customnode.CustomMesh
-
- restoreDisplayedData(String, String) - Method in class customnode.CustomMeshNode
-
- restoreDisplayedData(String, String) - Method in class customnode.CustomMultiMesh
-
- restoreDisplayedData() - Method in class ij3d.ContentInstant
-
- restoreDisplayedData(String, String) - Method in class ij3d.ContentNode
-
- restoreDisplayedData(String, String) - Method in class isosurface.MeshGroup
-
- restoreDisplayedData(String, String) - Method in class surfaceplot.SurfacePlotGroup
-
- restoreDisplayedData(String, String) - Method in class voltex.VoltexGroup
-
- retain(Canvas3D, Polygon) - Method in class customnode.CustomTriangleMesh
-
- rgbCM - Static variable in class voltex.VoltexVolume
-
The ColorModel used for RGB textures
- rLUT - Variable in class ij3d.ContentInstant
-
- root - Variable in class voltex.VolumeRenderer
-
The root BranchGroup whose subtree contains the volume rendering
- ROTATE - Static variable in interface ij3d.behaviors.BehaviorCallback
-
- rotate(MouseEvent) - Method in class ij3d.behaviors.ContentTransformer
-
Rotate the selected Content suitably to the specified MouseEvent.
- rotate(MouseEvent) - Method in class ij3d.behaviors.InteractiveViewPlatformTransformer
-
This method should be called during the mouse is dragged, if the mouse
event should result in a rotation.
- rotate(Vector3d, double) - Method in class ij3d.behaviors.ViewPlatformTransformer
-
Rotates the view around the center of view by the specified angle around
the given axis (of the image plate).
- rotateToNegativeXY() - Method in class ij3d.Image3DUniverse
-
Rotate the univere so that the user looks in the negative direction of the
z-axis.
- rotateToNegativeXZ() - Method in class ij3d.Image3DUniverse
-
Rotate the univere so that the user looks in the negative direction of the
y-axis.
- rotateToNegativeYZ() - Method in class ij3d.Image3DUniverse
-
Rotate the univere so that the user looks in the negative direction of the
x-axis.
- rotateToPositiveXY() - Method in class ij3d.Image3DUniverse
-
Rotate the univere so that the user looks in the positive direction of the
z-axis.
- rotateToPositiveXZ() - Method in class ij3d.Image3DUniverse
-
Rotate the univere so that the user looks in the positive direction of the
y-axis.
- rotateToPositiveYZ() - Method in class ij3d.Image3DUniverse
-
Rotate the univere so that the user looks in the positive direction of the
x-axis.
- rotateUniverse(Vector3d, double) - Method in class ij3d.Image3DUniverse
-
Rotate the universe, using the given axis of rotation and angle; The center
of rotation is the global center.
- rotateX(double) - Method in class ij3d.behaviors.ViewPlatformTransformer
-
Rotates the view around the global rotation center by the specified angle
around the x axis (of the image plate).
- rotateX(double) - Method in class ij3d.DefaultAnimatableUniverse
-
Convenience method which rotates the universe around the x-axis (regarding
the view, not the vworld) the specified amount of degrees (in rad).
- rotateXY(double, double) - Method in class ij3d.behaviors.ViewPlatformTransformer
-
Rotates the view around the center of view by the specified angles around
the x and y axis (of the image plate).
- rotateY(double) - Method in class ij3d.behaviors.ViewPlatformTransformer
-
Rotates the view around the global rotation center by the specified angle
around the y axis (of the image plate).
- rotateY(double) - Method in class ij3d.DefaultAnimatableUniverse
-
Convenience method which rotates the universe around the y-axis (regarding
the view, not the vworld) the specified amount of degrees (in rad).
- rotateZ(double) - Method in class ij3d.behaviors.ViewPlatformTransformer
-
Rotates the view around the global rotation center by the specified angle
around the z axis (of the image plate).
- rotateZ(double) - Method in class ij3d.DefaultAnimatableUniverse
-
Convenience method which rotates the universe around the z-axis (regarding
the view, not the vworld) the specified amount of degrees (in rad).
- ROTATION_TG - Static variable in class ij3d.DefaultUniverse
-
The index of the transform group in the viewing platform's
MultiTransformGroup which is responsible for rotation
- rotCenter - Variable in class ij3d.behaviors.ViewPlatformTransformer
-
- run(String) - Method in class customnode.Mesh_Maker
-
- run(CustomTriangleMesh) - Method in class ij3d.gui.InteractiveMeshDecimation
-
- run(String) - Method in class ij3d.ImageJ3DViewer
-
- run(String) - Method in class ij3d.ImageJ_3D_Viewer
-
- run(String) - Method in class ij3d.Test_Single_Voxel
-
- run(String) - Method in class isosurface.AmiraSurface
-
- run(String) - Method in class isosurface.Show_Colour_Surfaces
-
- run(ImageProcessor) - Method in class process3d.Smooth_
-
- SaturatedIntLoader(Volume.InputImage) - Constructor for class ij3d.Volume.SaturatedIntLoader
-
- saturatedVolumeRendering - Variable in class ij3d.Volume
-
Flag indicating that channels should be saturated
- save(Map<String, CustomMesh>, String) - Static method in class customnode.WavefrontExporter
-
- save(Map<String, CustomMesh>, String, Writer, Writer) - Static method in class customnode.WavefrontExporter
-
Write the given collection of CustomMeshes;
- save() - Method in class ij3d.shortcuts.ShortCuts
-
- save() - Static method in class ij3d.UniverseSettings
-
- SAVE_TRANSFORM - Static variable in class ij3d.Executer
-
- saveAsAsciiSTL() - Method in class ij3d.Executer
-
- saveAsBinarySTL() - Method in class ij3d.Executer
-
- saveAsDXF() - Method in class ij3d.Executer
-
- saveAsDXF(Collection) - Static method in class isosurface.MeshExporter
-
Deprecated.
- saveAsDXF(Collection, File) - Static method in class isosurface.MeshExporter
-
- saveAsSTL(Collection, int) - Static method in class isosurface.MeshExporter
-
Deprecated.
- saveAsSTL(Collection, File, int) - Static method in class isosurface.MeshExporter
-
- saveAsU3D() - Method in class ij3d.Executer
-
- saveAsWaveFront() - Method in class ij3d.Executer
-
- saveAsWaveFront(Collection) - Static method in class isosurface.MeshExporter
-
Deprecated.
- saveAsWaveFront(Collection, File) - Static method in class isosurface.MeshExporter
-
Accepts a collection of MeshGroup objects.
- savePointList() - Method in class ij3d.Content
-
- savePointList() - Method in class ij3d.ContentInstant
-
- savePointList(PrintStream) - Method in class ij3d.ContentInstant
-
- savePointList(Content) - Method in class ij3d.Executer
-
- saveScene(Image3DUniverse, String) - Static method in class ij3d.SaveSession
-
- saveSession() - Method in class ij3d.Executer
-
- saveSession(String) - Method in class ij3d.Image3DUniverse
-
- SaveSession - Class in ij3d
-
- SaveSession() - Constructor for class ij3d.SaveSession
-
- saveToFile(File, String) - Static method in class customnode.WavefrontExporter
-
Utility method to encode text data in 8859_1.
- saveToFile(File, String) - Static method in class isosurface.MeshExporter
-
Utility method to encode text data in 8859_1.
- saveTransform(Content) - Method in class ij3d.Executer
-
- saveTransform(String, String) - Static method in class ij3d.ImageJ3DViewer
-
- saveView() - Method in class ij3d.Executer
-
- saveView(String) - Method in class ij3d.Image3DUniverse
-
Save the current view transformations to a file
- saveView(Image3DUniverse, String) - Static method in class ij3d.SaveSession
-
- scalebar - Variable in class ij3d.DefaultUniverse
-
Reference to the optionally displayable scale bar.
- SCALEBAR - Static variable in class ij3d.Executer
-
- Scalebar - Class in ij3d.shapes
-
- Scalebar() - Constructor for class ij3d.shapes.Scalebar
-
- Scalebar(float) - Constructor for class ij3d.shapes.Scalebar
-
- scene - Variable in class ij3d.DefaultUniverse
-
Reference to root BranchGroup.
- ScenegraphDebugger - Class in ij3d
-
- ScenegraphDebugger() - Constructor for class ij3d.ScenegraphDebugger
-
- select(String) - Method in class ij3d.Executer
-
- select(Content) - Method in class ij3d.Image3DUniverse
-
Select the specified Content.
- select(String) - Static method in class ij3d.ImageJ3DViewer
-
- selected - Variable in class ij3d.ContentInstant
-
- set(int, int, int, int) - Method in class ij3d.AreaListVolume
-
- set(int, int, int, int) - Method in class ij3d.Volume.AverageByteLoader
-
- set(int, int, int, int) - Method in class ij3d.Volume.ByteImage
-
- set(int, int, int, int) - Method in class ij3d.Volume.ByteLoader
-
- set(int, int, int, int) - Method in interface ij3d.Volume.InputImage
-
- set(int, int, int, int) - Method in class ij3d.Volume.IntImage
-
- set(int, int, int, int) - Method in class ij3d.Volume.IntLoader
-
- set(int, int, int, int) - Method in interface ij3d.Volume.Loader
-
- set(int, int, int, int) - Method in class ij3d.Volume
-
- SET_CHANNELS - Static variable in class ij3d.Executer
-
- SET_COLOR - Static variable in class ij3d.Executer
-
- SET_CS - Static variable in class ij3d.Executer
-
- SET_SLICES - Static variable in class ij3d.Executer
-
- SET_THRESHOLD - Static variable in class ij3d.Executer
-
- SET_TRANSFORM - Static variable in class ij3d.Executer
-
- SET_TRANSPARENCY - Static variable in class ij3d.Executer
-
- setAlphaLUTFullyOpaque() - Method in class ij3d.Volume
-
Set the alpha channel to fully opaque.
- setAlphaLUTFullyOpaque() - Method in class voltex.VoltexVolume
-
Set the alpha channel to fully opaque.
- setAlphaMethod(Mask.BlendMethod) - Method in class voltex.Mask
-
- setAlphaSource(int, Mask.BlendSource) - Method in class voltex.Mask
-
- setAntiAliasing(boolean) - Method in class customnode.CustomLineMesh
-
- setAntiAliasing(boolean) - Method in class customnode.CustomPointMesh
-
- setAutoAdjustView(boolean) - Method in class ij3d.Image3DUniverse
-
autoAdjustView indicates, whether the view is adjusted to fit the whole
universe each time a Content is added.
- setAverage(boolean) - Method in class ij3d.AreaListVolume
-
- setAverage(boolean) - Method in class ij3d.Volume
-
If true, build an average byte from the specified channels (for each
pixel).
- setAverage(boolean) - Method in class voltex.VoltexVolume
-
- setBlendColor(Color4f) - Method in class voltex.Mask
-
- setBlockType(long) - Method in class customnode.u3d.DataBlock
-
- setBounceBack(boolean) - Method in class view4d.Timeline
-
- setCenter(Point3f) - Method in class ij3d.shapes.BoundingSphere
-
- setChannels(boolean[]) - Method in class ij3d.Content
-
- setChannels(boolean[]) - Method in class ij3d.ContentInstant
-
- setChannels(String, String, String) - Static method in class ij3d.ImageJ3DViewer
-
- setChannels(boolean[]) - Method in class ij3d.Volume
-
Specify the channels which should be read from the image.
- setChannels(boolean[]) - Method in class surfaceplot.SurfacePlot
-
Change the displayed channels of this surface plot.
- setChannels(boolean[]) - Method in class voltex.VoltexVolume
-
Sets the channels which are to be used in this volume rendering.
- setChannels(boolean[]) - Method in class voltex.VolumeRenderer
-
Set the displayed color channels for this volume rendering.
- setColor(Color3f) - Method in class customnode.CustomIndexedTriangleMesh
-
- setColor(List<Color3f>) - Method in class customnode.CustomIndexedTriangleMesh
-
- setColor(int, Color3f) - Method in class customnode.CustomIndexedTriangleMesh
-
- setColor(Color3f) - Method in class customnode.CustomMesh
-
- setColor(List<Color3f>) - Method in class customnode.CustomMesh
-
- setColor(int, Color3f) - Method in class customnode.CustomMesh
-
- setColor(Color3f) - Method in class customnode.CustomTransparentTriangleMesh
-
- setColor(Color3f) - Method in class ij3d.Content
-
- setColor(Color3f) - Method in class ij3d.ContentInstant
-
- setColor(String, String, String) - Static method in class ij3d.ImageJ3DViewer
-
- setColor(Color3f) - Method in class ij3d.pointlist.PointListShape
-
Set the color of the points.
- setColor(Color3f) - Method in class ij3d.shapes.Scalebar
-
- setColor(Color3f) - Method in class octree.AppearanceCreator
-
- setColor(Color3f) - Method in class surfaceplot.SurfacePlot
-
Changes the color of this surface plot.
- setColor(Color3f) - Method in class voltex.AppearanceCreator
-
Set the color for all the textures that were loaded by this
AppearanceCreator.
- setColor(Color3f) - Method in class voltex.VolumeRenderer
-
Set the color for this volume rendering
- setColorMethod(Mask.BlendMethod) - Method in class voltex.Mask
-
- setColorSource(int, Mask.BlendSource) - Method in class voltex.Mask
-
- setCoordinate(int, Point3f) - Method in class customnode.CustomIndexedTriangleMesh
-
- setCoordinate(int, Point3f) - Method in class customnode.CustomMesh
-
- setCoordinates(int[], Point3f) - Method in class customnode.CustomIndexedTriangleMesh
-
- setCoordinates(int[], Point3f) - Method in class customnode.CustomMesh
-
- setCoordinateSystem(String) - Static method in class ij3d.ImageJ3DViewer
-
- setData(long[]) - Method in class customnode.u3d.DataBlock
-
- SetDataBlock(DataBlock) - Method in class customnode.u3d.BitStreamRead
-
- setDataSize(long) - Method in class customnode.u3d.DataBlock
-
- setExternalBehaviours(List<InteractiveBehavior>) - Method in class ij3d.behaviors.InteractiveBehavior
-
- setFullScreen(boolean) - Method in class ij3d.Executer
-
- setFullScreen(boolean) - Method in class ij3d.Image3DUniverse
-
Sets fullscreen mode on or of.
- setGlobalTransform(DefaultUniverse.GlobalTransform) - Method in class ij3d.DefaultUniverse
-
Set the transforms for zoom, pan, and rotation.
- setHandTool() - Method in class ij3d.IJAdapter
-
- setHandTool() - Method in class ij3d.NoopAdapter
-
- setHandTool() - Method in interface ij3d.UIAdapter
-
- setImage(ImagePlus, boolean[]) - Method in class ij3d.Volume
-
- setImage(ImagePlus, boolean[]) - Method in class voltex.VoltexVolume
-
- setInteractiveBehavior(InteractiveBehavior) - Method in class ij3d.DefaultUniverse
-
- setLandmarkColor(Color3f) - Method in class ij3d.Content
-
- setLandmarkColor(Color3f) - Method in class ij3d.ContentInstant
-
- setLandmarkPointSize(float) - Method in class ij3d.Content
-
- setLandmarkPointSize(float) - Method in class ij3d.ContentInstant
-
- setLength(float) - Method in class ij3d.shapes.Scalebar
-
- setLineWidth(float) - Method in class customnode.CustomLineMesh
-
- setListPointPos(int, Point3d) - Method in class ij3d.Content
-
Deprecated.
- setListPointPos(int, Point3d) - Method in class ij3d.ContentInstant
-
Deprecated.
- setLocked(boolean) - Method in class ij3d.Content
-
- setLocked(boolean) - Method in class ij3d.ContentInstant
-
- setLocked(Content, boolean) - Method in class ij3d.Executer
-
- setLUT(int[], int[], int[], int[]) - Method in class ij3d.Content
-
- setLUT(int[], int[], int[], int[]) - Method in class ij3d.ContentInstant
-
- setLUTs(int[], int[], int[], int[]) - Method in class ij3d.Volume
-
Set the lookup tables for this volume.
- setLUTs(int[], int[], int[], int[]) - Method in class voltex.VoltexVolume
-
Set the lookup tables for this volume rendering.
- setLUTs(int[], int[], int[], int[]) - Method in class voltex.VolumeRenderer
-
Update the lookup tables for this volume rendering.
- setMenubar(MenuBar) - Method in class ij3d.Image3DUniverse
-
- setMenubar(JMenuBar) - Method in class ij3d.Image3DUniverse
-
Set a custom menu bar to the viewer
- setMesh(List<Point3f>) - Method in class customnode.CustomTriangleMesh
-
- setMetaData(long[]) - Method in class customnode.u3d.DataBlock
-
- setMetaDataSize(long) - Method in class customnode.u3d.DataBlock
-
- setNoCheck(int, int, int, int) - Method in class ij3d.AreaListVolume
-
- setNoCheck(int, int, int, int) - Method in class ij3d.Volume.AverageByteLoader
-
- setNoCheck(int, int, int, int) - Method in class ij3d.Volume.ByteLoader
-
- setNoCheck(int, int, int, int) - Method in class ij3d.Volume.IntLoader
-
- setNoCheck(int, int, int, int) - Method in interface ij3d.Volume.Loader
-
- setNoCheck(int, int, int, int) - Method in class ij3d.Volume
-
- setNoCheckNoUpdate(int, int, int, int) - Method in class voltex.VoltexVolume
-
- setNoCheckNoUpdate(int, int, int, int) - Method in interface voltex.VoltexVolume.VoltexLoader
-
Only set the values, without updating the ImageComponent2Ds.
- setOpaqueTextures(boolean) - Method in class voltex.AppearanceCreator
-
This flag indicates whether textures are opaque or not.
- setPattern(int) - Method in class customnode.CustomLineMesh
-
- setPointList(PointList) - Method in class ij3d.ContentInstant
-
- setPointList(PointList) - Method in class ij3d.pointlist.PointListPanel
-
Set the PointList which should be displayed by this PointListPanel
- setPointList(PointList) - Method in class ij3d.pointlist.PointListShape
-
Set the PointList which is represented by this PointListShape.
- setPointListDialog(PointListDialog) - Method in class ij3d.Content
-
- setPointListDialog(PointListDialog) - Method in class ij3d.ContentInstant
-
- setPointSize(float) - Method in class customnode.CustomPointMesh
-
- setPointTool() - Method in class ij3d.IJAdapter
-
- setPointTool() - Method in class ij3d.NoopAdapter
-
- setPointTool() - Method in interface ij3d.UIAdapter
-
- setPosition(float, float) - Method in class ij3d.shapes.Scalebar
-
- setPriority(long) - Method in class customnode.u3d.DataBlock
-
- setRadius(float) - Method in class ij3d.pointlist.PointListShape
-
Set the radius of the points.
- setRadius(float) - Method in class ij3d.shapes.BoundingSphere
-
- setRotation(int, double) - Method in class ij3d.Content
-
- setRotationAxis(Vector3f) - Method in class ij3d.DefaultAnimatableUniverse
-
Set the rotation axis to the specified Vector3f.
- setRotationInterval(float) - Method in class ij3d.DefaultAnimatableUniverse
-
Set the rotation interval (in degree)
- setSaturatedVolumeRendering(boolean) - Method in class ij3d.Content
-
- setSaturatedVolumeRendering(boolean) - Method in class ij3d.ContentInstant
-
- setSaturatedVolumeRendering(Content, boolean) - Method in class ij3d.Executer
-
- setSaturatedVolumeRendering(boolean) - Method in class ij3d.Volume
-
If true, saturate the channels of RGB images; the RGB values of each pixels
are scaled so that at least one of the values is 255, the alpha value is
the average of the original RGB values.
- setSaturatedVolumeRendering(boolean) - Method in class voltex.VoltexVolume
-
- setSelected(boolean) - Method in class ij3d.Content
-
- setSelected(boolean) - Method in class ij3d.ContentInstant
-
- setShaded(boolean) - Method in class customnode.CustomIndexedTriangleMesh
-
- setShaded(boolean) - Method in class customnode.CustomMesh
-
- setShaded(boolean) - Method in class ij3d.Content
-
- setShaded(boolean) - Method in class ij3d.ContentInstant
-
- setShaded(Content, boolean) - Method in class ij3d.Executer
-
- setShaded(boolean) - Method in class surfaceplot.SurfacePlot
-
Shade the surface or not.
- setShortCut(String, String) - Method in class ij3d.shortcuts.ShortCuts
-
- setShowAllTimepoints(boolean) - Method in class ij3d.Content
-
- setShowBoundingBoxUponSelection(boolean) - Method in class ij3d.Image3DUniverse
-
Show/Hide the selection box upon selecting a Content(Instant).
- setSize(int, int) - Method in class ij3d.DefaultUniverse
-
Set the dimensions of this universe.
- setSlice(int, int) - Method in class orthoslice.OrthoGroup
-
Alter the slice index of the given direction.
- setSlice(int, int) - Method in class orthoslice.Orthoslice
-
Sets the slice index of the specified plane to the given value.
- setSlice(int) - Method in class surfaceplot.SurfacePlot
-
Sets the currently displayed slice.
- setSlice(int) - Method in class surfaceplot.SurfacePlotGroup
-
Set the slice to display.
- setSlices(String, String, String) - Static method in class ij3d.ImageJ3DViewer
-
- setStatus(String) - Method in class ij3d.Image3DUniverse
-
Shows the specified status string at the bottom of the viewer window.
- setTexturesOpaque(boolean) - Method in class orthoslice.MultiOrthoGroup
-
Makes the textures transparent or not.
- setTexturesOpaque(boolean) - Method in class orthoslice.MultiOrthoslice
-
Makes the textures transparent or not.
- setThreshold(int) - Method in class ij3d.Content
-
- setThreshold(int) - Method in class ij3d.ContentInstant
-
- setThreshold(String) - Static method in class ij3d.ImageJ3DViewer
-
- setThreshold(float) - Method in class octree.AppearanceCreator
-
- setThreshold(float) - Method in class voltex.AppearanceCreator
-
Set the threshold for all the textures that were loaded by this
AppearanceCreator.
- setThreshold(int) - Method in class voltex.VolumeRenderer
-
Set the threshold.
- setTool(int) - Method in class ij3d.IJAdapter
-
- setTool(int) - Method in class ij3d.NoopAdapter
-
- setTool(int) - Method in interface ij3d.UIAdapter
-
- setTransform(double[]) - Method in class ij3d.Content
-
- setTransform(Transform3D) - Method in class ij3d.Content
-
- setTransform(double[]) - Method in class ij3d.ContentInstant
-
- setTransform(Transform3D) - Method in class ij3d.ContentInstant
-
- setTransform(Content) - Method in class ij3d.Executer
-
- setTransform(String) - Static method in class ij3d.ImageJ3DViewer
-
- setTranslation(float, float, float) - Method in class ij3d.Content
-
- setTransparency(float) - Method in class customnode.CustomIndexedTriangleMesh
-
- setTransparency(float) - Method in class customnode.CustomMesh
-
- setTransparency(float) - Method in class customnode.CustomTransparentTriangleMesh
-
- setTransparency(float) - Method in class ij3d.Content
-
- setTransparency(float) - Method in class ij3d.ContentInstant
-
- setTransparency(String) - Static method in class ij3d.ImageJ3DViewer
-
- setTransparency(float) - Method in class octree.AppearanceCreator
-
- setTransparency(float) - Method in class surfaceplot.SurfacePlot
-
Change the transparency of this surface plot.
- setTransparency(float) - Method in class voltex.AppearanceCreator
-
Set the transparency for all the textures that were loaded by this
AppearanceCreator.
- setTransparency(float) - Method in class voltex.VolumeRenderer
-
Set the transparency for this rendering
- setTransparentColor(List<Color4f>) - Method in class customnode.CustomTransparentTriangleMesh
-
- setUnit(String) - Method in class ij3d.shapes.Scalebar
-
- setup(String, ImagePlus) - Method in class process3d.Smooth_
-
- setUseToFront(boolean) - Method in class ij3d.DefaultUniverse
-
For some interactive applications, the use of toFront() in ImageWindow3D
creates usability problems, so these methods allow one to supress this
behaviour by calling setUseToFront(false).
- setVisible(boolean) - Method in class ij3d.Content
-
- setVisible(boolean) - Method in class ij3d.ContentInstant
-
- setVisible(int, boolean) - Method in class orthoslice.MultiOrthoGroup
-
Show/hide all slices in the given axis.
- setVisible(int, int, int, int) - Method in class orthoslice.MultiOrthoGroup
-
Show a slice every
- setVisible(int, boolean[]) - Method in class orthoslice.MultiOrthoGroup
-
Set the visibility of each slice in the given axis.
- setVisible(int, boolean[]) - Method in class orthoslice.MultiOrthoslice
-
- setVisible(int, boolean) - Method in class orthoslice.MultiOrthoslice
-
Hide/show the whole set of slices in the given axis.
- setVisible(int, int, int, int) - Method in class orthoslice.MultiOrthoslice
-
Show a slice every
- setVisible(int, boolean) - Method in class orthoslice.OrthoGroup
-
Set the specified slice visible
- setVisible(int, boolean) - Method in class orthoslice.Orthoslice
-
Sets the specified plane visible.
- setVolume(VoltexVolume) - Method in class voltex.AppearanceCreator
-
Change the image data of this AppearanceCreator
- setVolume(VoltexVolume) - Method in class voltex.GeometryCreator
-
Change the image data for this GeometryCreator
- shaded - Variable in class customnode.CustomMesh
-
- shaded - Variable in class ij3d.ContentInstant
-
- shadeUpdated(boolean) - Method in class customnode.CustomMeshNode
-
- shadeUpdated(boolean) - Method in class customnode.CustomMultiMesh
-
- shadeUpdated(boolean) - Method in class ij3d.ContentNode
-
This method is called when the 'shade' attribute of the Content has
changed.
- shadeUpdated(boolean) - Method in class isosurface.MeshGroup
-
- shadeUpdated(boolean) - Method in class surfaceplot.SurfacePlotGroup
-
- shadeUpdated(boolean) - Method in class voltex.VoltexGroup
-
- ShapeGroup - Class in octree
-
- ShapeGroup() - Constructor for class octree.ShapeGroup
-
- ShortCutDialog - Class in ij3d.shortcuts
-
- ShortCutDialog(ShortCuts) - Constructor for class ij3d.shortcuts.ShortCutDialog
-
- ShortCuts - Class in ij3d.shortcuts
-
- ShortCuts(JMenuBar) - Constructor for class ij3d.shortcuts.ShortCuts
-
- shortcuts - Static variable in class ij3d.UniverseSettings
-
- ShortCutTable - Class in ij3d.shortcuts
-
- ShortCutTable(ShortCuts) - Constructor for class ij3d.shortcuts.ShortCutTable
-
- shouldCreateData() - Method in class octree.OctreeDialog
-
- show() - Method in class ij3d.DefaultUniverse
-
Show this universe in a new window.
- show() - Method in class ij3d.Image3DUniverse
-
Display this universe in a window (an ImageWindow3D).
- show() - Method in class octree.CubeData
-
- show(CubeData, int) - Method in class octree.ShapeGroup
-
- Show_Colour_Surfaces - Class in isosurface
-
- Show_Colour_Surfaces() - Constructor for class isosurface.Show_Colour_Surfaces
-
- SHOW_CONTENT - Static variable in class ij3d.Executer
-
- showAllCoordinateSystems(boolean) - Method in class ij3d.Executer
-
- showAttribute(int, boolean) - Method in class ij3d.DefaultUniverse
-
Show or hide the specified attribute.
- showBoundingBox(boolean) - Method in class ij3d.Content
-
- showBoundingBox(boolean) - Method in class ij3d.ContentInstant
-
- showBoundingBox(Content, boolean) - Method in class ij3d.Executer
-
- showColorDialog(String, Color3f, Executer.ColorListener, boolean, boolean) - Method in class ij3d.Executer
-
- showContent(Content, boolean) - Method in class ij3d.Executer
-
- showContent(String, String) - Static method in class ij3d.ImageJ3DViewer
-
- showCoordinateSystem(boolean) - Method in class ij3d.Content
-
- showCoordinateSystem(boolean) - Method in class ij3d.ContentInstant
-
- showCoordinateSystem(Content, boolean) - Method in class ij3d.Executer
-
- showDialog(Image3DUniverse, ImagePlus, File) - Method in class ij3d.gui.ContentCreatorDialog
-
- showDialog() - Method in class octree.OctreeDialog
-
- showGlobalCoordinateSystem - Static variable in class ij3d.UniverseSettings
-
- showLocalCoordinateSystemsByDefault - Static variable in class ij3d.UniverseSettings
-
- showPointList(boolean) - Method in class ij3d.Content
-
- showPointList(boolean) - Method in class ij3d.ContentInstant
-
- showPointList(Content, boolean) - Method in class ij3d.Executer
-
- showPopup(MouseEvent) - Method in class ij3d.contextmenu.ContextMenu
-
- showProgress(int, int) - Method in class ij3d.IJAdapter
-
- showProgress(int, int) - Method in class ij3d.NoopAdapter
-
- showProgress(int, int) - Method in interface ij3d.UIAdapter
-
- showScalebar - Static variable in class ij3d.UniverseSettings
-
- showSelectionBox - Static variable in class ij3d.UniverseSettings
-
- showStatus(String) - Method in class ij3d.IJAdapter
-
- showStatus(String) - Method in class ij3d.NoopAdapter
-
- showStatus(String) - Method in interface ij3d.UIAdapter
-
- showTimepoint(int) - Method in class ij3d.Content
-
- showTimepoint(int, boolean) - Method in class ij3d.Content
-
- showTimepoint(int) - Method in class ij3d.Image3DUniverse
-
- showTree(Node) - Static method in class ij3d.ScenegraphDebugger
-
- size() - Method in class customnode.CustomMultiMesh
-
- SIZE - Static variable in class octree.VolumeOctree
-
- size() - Method in class view4d.Timeline
-
Returns the number of time points.
- SizeBuff - Static variable in class customnode.u3d.Constants
-
- slower() - Method in class view4d.Timeline
-
Slows the animation down.
- SMOOTH - Static variable in class ij3d.Executer
-
- smooth(CustomTriangleMesh, float) - Static method in class isosurface.MeshEditor
-
If the Content instance wraps a mesh, smooth it by the fraction K (0, 1).
- smooth2(CustomTriangleMesh, int) - Static method in class isosurface.MeshEditor
-
Implemented Blender-style vertex smoothing.
- smooth2(List<Point3f>, int) - Static method in class isosurface.MeshEditor
-
- Smooth_ - Class in process3d
-
Smooth_es an ImagePlus, either uniformly or by Gaussian blur.
- Smooth_() - Constructor for class process3d.Smooth_
-
- smoothAllMeshes() - Method in class ij3d.Executer
-
- smoothControl() - Method in class ij3d.Executer
-
Interactively smooth meshes, with undo.
- SmoothControl - Class in isosurface
-
- SmoothControl(Image3DUniverse) - Constructor for class isosurface.SmoothControl
-
- smoothMesh(Content) - Method in class ij3d.Executer
-
- SNAPSHOT - Static variable in class ij3d.Executer
-
- snapshot() - Method in class ij3d.Executer
-
- snapshot(String, String) - Static method in class ij3d.ImageJ3DViewer
-
- SOLID - Static variable in class customnode.CustomLineMesh
-
- Sphere - Class in customnode
-
- Sphere(Point3f, float) - Constructor for class customnode.Sphere
-
- Sphere(Point3f, float, int, int) - Constructor for class customnode.Sphere
-
- START_ANIMATE - Static variable in class ij3d.Executer
-
- START_FREEHAND_RECORDING - Static variable in class ij3d.Executer
-
- startAnimate() - Static method in class ij3d.ImageJ3DViewer
-
- startAnimation() - Method in class ij3d.DefaultAnimatableUniverse
-
Starts animating the universe.
- startAnimation() - Method in class ij3d.Executer
-
- startFramePattern - Static variable in class ij3d.Content
-
- startFreehandRecording() - Method in class ij3d.DefaultAnimatableUniverse
-
Start freehand recording.
- startFreehandRecording() - Method in class ij3d.Executer
-
- startFreehandRecording() - Static method in class ij3d.ImageJ3DViewer
-
- startupHeight - Static variable in class ij3d.UniverseSettings
-
- startupWidth - Static variable in class ij3d.UniverseSettings
-
- StaticFull - Static variable in class customnode.u3d.Constants
-
- STLLoader - Class in customnode
-
- STOP_ANIMATE - Static variable in class ij3d.Executer
-
- STOP_FREEHAND_RECORDING - Static variable in class ij3d.Executer
-
- stopAnimate() - Static method in class ij3d.ImageJ3DViewer
-
- stopAnimation() - Method in class ij3d.Executer
-
- stopFreehandRecording() - Method in class ij3d.DefaultAnimatableUniverse
-
Stop freehand recording.
- stopFreehandRecording() - Method in class ij3d.Executer
-
- stopFreehandRecording() - Static method in class ij3d.ImageJ3DViewer
-
- stopMoving() - Method in class ij3d.behaviors.Picker
-
Stop moving.
- subtract(Canvas3D, Roi) - Method in class voltex.Mask
-
- subtractInverse(Canvas3D, Roi) - Method in class voltex.Mask
-
- SURFACE - Static variable in interface ij3d.ContentConstants
-
- SURFACE_PLOT2D - Static variable in interface ij3d.ContentConstants
-
- surfaceplot - package surfaceplot
-
- SurfacePlot - Class in surfaceplot
-
This class displays an image stack as a surface plot.
- SurfacePlot(Volume, Color3f, float, int) - Constructor for class surfaceplot.SurfacePlot
-
Constructs a SurfacePlot from the given image data, color and transparency
of the specified slice.
- SurfacePlotGroup - Class in surfaceplot
-
This class extends ContentNode to render a Content as a surface plot.
- SurfacePlotGroup(Content) - Constructor for class surfaceplot.SurfacePlotGroup
-
Constructs a surface plot for the given ContentInstant.
- SurfacePlotGroup(ContentInstant) - Constructor for class surfaceplot.SurfacePlotGroup
-
Constructs a surface plot for the given Content.
- swap(String) - Method in class ij3d.Volume
-
- swap(String) - Method in class voltex.VoltexVolume
-
- Swap8 - Static variable in class customnode.u3d.Constants
-
- swapDisplayedData(String, String) - Method in class customnode.CustomIndexedTriangleMesh
-
- swapDisplayedData(String, String) - Method in class customnode.CustomMesh
-
- swapDisplayedData(String, String) - Method in class customnode.CustomMeshNode
-
- swapDisplayedData(String, String) - Method in class customnode.CustomMultiMesh
-
- swapDisplayedData() - Method in class ij3d.ContentInstant
-
- swapDisplayedData(String, String) - Method in class ij3d.ContentNode
-
- swapDisplayedData(String, String) - Method in class isosurface.MeshGroup
-
- swapDisplayedData(String, String) - Method in class surfaceplot.SurfacePlotGroup
-
- swapDisplayedData(String, String) - Method in class voltex.VoltexGroup
-
- sync(boolean) - Method in class ij3d.Executer
-
- sync(boolean) - Method in class ij3d.Image3DUniverse
-
Syncs this window.
- valueOf(String) - Static method in enum voltex.Mask.BlendMethod
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum voltex.Mask.BlendSource
-
Returns the enum constant of this type with the specified name.
- values() - Static method in enum voltex.Mask.BlendMethod
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum voltex.Mask.BlendSource
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- vertexIndexOfPoint(Point3f) - Method in class customnode.CustomIndexedTriangleMesh
-
- vertexIndicesOfPoint(Point3f) - Method in class customnode.CustomIndexedTriangleMesh
-
- vertexIndicesOfPoint(Point3f) - Method in class customnode.CustomMesh
-
- vertices - Variable in class customnode.CustomIndexedTriangleMesh
-
- view4d - package view4d
-
- ViewAdjuster - Class in ij3d
-
- ViewAdjuster(Image3DUniverse, int) - Constructor for class ij3d.ViewAdjuster
-
Create a new ViewAdjuster.
- ViewPlatformTransformer - Class in ij3d.behaviors
-
This class is a helper class which implements some functions for transforming
the view part of the scene graph.
- ViewPlatformTransformer(DefaultUniverse, BehaviorCallback) - Constructor for class ij3d.behaviors.ViewPlatformTransformer
-
Initialize this ViewPlatformTransformer.
- viewPreferences() - Method in class ij3d.Executer
-
- viewTransformer - Variable in class ij3d.DefaultUniverse
-
Reference to the InteractiveViewPlatformTransformer.
- voltex - package voltex
-
- VoltexGroup - Class in voltex
-
This class extends ContentNode to display a Content as a Volume Rendering.
- VoltexGroup() - Constructor for class voltex.VoltexGroup
-
This constructor only exists to allow subclasses to access the super
constructor of BranchGroup.
- VoltexGroup(Content) - Constructor for class voltex.VoltexGroup
-
Initialize this VoltexGroup with the specified Content.
- VoltexGroup(ContentInstant) - Constructor for class voltex.VoltexGroup
-
Initialize this VoltexGroup with the specified ContentInstant.
- VoltexVolume - Class in voltex
-
This class encapsulates an image stack and provides various methods for
retrieving data.
- VoltexVolume(ImagePlus) - Constructor for class voltex.VoltexVolume
-
Initializes this Volume with the specified image.
- VoltexVolume(ImagePlus, boolean[]) - Constructor for class voltex.VoltexVolume
-
Initializes this Volume with the specified image and channels.
- VoltexVolume.VoltexLoader - Interface in voltex
-
Abstract interface for the loader classes.
- VOLUME - Static variable in interface ij3d.ContentConstants
-
- Volume - Class in ij3d
-
This class encapsulates an image stack and provides various methods for
retrieving data.
- Volume() - Constructor for class ij3d.Volume
-
Create instance with a null imp.
- Volume(ImagePlus) - Constructor for class ij3d.Volume
-
Initializes this Volume with the specified image.
- Volume(ImagePlus, boolean[]) - Constructor for class ij3d.Volume
-
Initializes this Volume with the specified image and channels.
- volume - Variable in class voltex.VolumeRenderer
-
The image data which is rendered by this VolumeRenderer
- Volume.AverageByteLoader - Class in ij3d
-
- Volume.ByteImage - Class in ij3d
-
- Volume.ByteLoader - Class in ij3d
-
- Volume.InputImage - Interface in ij3d
-
Abstract interface for the input image.
- Volume.IntImage - Class in ij3d
-
- Volume.IntLoader - Class in ij3d
-
- Volume.Loader - Interface in ij3d
-
Abstract interface for the loader classes.
- Volume.SaturatedIntLoader - Class in ij3d
-
- VolumeOctree - Class in octree
-
- VolumeOctree(String, Canvas3D) - Constructor for class octree.VolumeOctree
-
- VolumeRenderer - Class in voltex
-
This class is the main class for creating a volume rendering.
- VolumeRenderer(ImagePlus, Color3f, float, boolean[]) - Constructor for class voltex.VolumeRenderer
-
Constructor.
- volumeToImagePlate(Transform3D) - Method in class voltex.VoltexGroup
-
Stores the matrix which transforms this VoltexGroup to the image plate in
the specified Transform3D.