Image3DUniverse (3D Viewer 5.0.1 API)

java.lang.Object
- org.jogamp.java3d.VirtualUniverse
- - org.jogamp.java3d.utils.universe.SimpleUniverse
  - - ij3d.DefaultUniverse
    - - ij3d.DefaultAnimatableUniverse
      - ij3d.Image3DUniverse

All Implemented Interfaces:: BehaviorCallback

public class Image3DUniverse
extends DefaultAnimatableUniverse

Nested Class Summary
- Nested classes/interfaces inherited from class ij3d.DefaultUniverse
  DefaultUniverse.GlobalTransform

Field Summary

Fields
Modifier and Type Field and Description

static String NO_CONTENT_MESSAGE

static ArrayList<Image3DUniverse> universes
- Fields inherited from class ij3d.DefaultUniverse
  ANIMATE_TG, ATTRIBUTE_COORD_SYSTEM, ATTRIBUTE_SCALEBAR, attributesSwitch, bounds, CENTER_TG, contentTransformer, frameBehavior, globalCenter, globalCoord, globalMax, globalMin, light, mouseBehavior, picker, ROTATION_TG, scalebar, scene, TRANSLATE_TG, ui, useToFront, viewTransformer, win, ZOOM_TG
- Fields inherited from class org.jogamp.java3d.utils.universe.SimpleUniverse
  locale, viewer
- Fields inherited from interface ij3d.behaviors.BehaviorCallback
  ROTATE, TRANSLATE

Fields
Modifier and Type	Field and Description
`static String`	`NO_CONTENT_MESSAGE`
`static ArrayList<Image3DUniverse>`	`universes`

Constructor Summary

Constructors
Constructor and Description
`Image3DUniverse()` Default constructor.
`Image3DUniverse(int width, int height)` Constructs a new universe with the specified width and height.

Method Summary

All Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`Content`	`addContent(Content c)` Add the specified Content to the universe.
`Content`	`addContent(ij.ImagePlus image, org.jogamp.vecmath.Color3f color, String name, int thresh, boolean[] channels, int resf, int type)` Add the specified image as a new Content to the universe.
`Content`	`addContent(ij.ImagePlus image, int type)` Add the specified image as a new Content to the universe.
`Content`	`addContent(ij.ImagePlus image, int type, int res)` Add the specified image as a new Content to the universe.
`Collection<Future<Content>>`	`addContentLater(Collection<Content> cc)` Add the specified collection of Content to the universe.
`Future<Content>`	`addContentLater(Content c)` Add the specified Content to the universe.
`Collection<Future<Content>>`	`addContentLater(String file)`
`Content`	`addCustomMesh(CustomMesh mesh, String name)` Add a custom mesh to the universe.
`Content`	`addCustomMesh(CustomMultiMesh mesh, String name)` Add a CustomMultiMesh to the universe.
`Content`	`addIcospheres(List<org.jogamp.vecmath.Point3f> points, org.jogamp.vecmath.Color3f color, int subdivisions, float radius, String name)` At every `Point3f` in @param points, place an icosphere created with @param subdivisions and @param radius.
`Content`	`addLineMesh(List<org.jogamp.vecmath.Point3f> mesh, org.jogamp.vecmath.Color3f color, String name, boolean strips)` Add a custom mesh, in particular a line mesh (a set of lines in 3D) to the universe.
`Content`	`addMesh(ij.ImagePlus img)` Add a new image as a content, displaying it as an isosurface.
`Content`	`addMesh(ij.ImagePlus image, org.jogamp.vecmath.Color3f color, String name, int threshold, boolean[] channels, int resamplingF)` Add a new image as a content, displaying it as an iso-surface.
`Content`	`addMesh(ij.ImagePlus img, int res)` Add a new image as a content, displaying it as an isosurface.
`Content`	`addMesh(List<org.jogamp.vecmath.Point3f> mesh, org.jogamp.vecmath.Color3f color, String name, int threshold)` Deprecated. This method will not be supported in the future. Use addTriangleMesh instead.
`Content`	`addMesh(List mesh, org.jogamp.vecmath.Color3f color, String name, float scale, int threshold)` Deprecated. This method will not be supported in the future. The specified 'scale' will be ignored, and the applied scale will be calculated automatically from the minimum and maximum coordinates of the specified mesh. Use addTriangleMesh instead.
`VolumeOctree`	`addOctree(String imageDir, String name)` Deprecated. The octree methods will be outsourced into a different plugin.
`Content`	`addOrthoslice(ij.ImagePlus image)` Add a new image as a content, displaying it as orthoslices.
`Content`	`addOrthoslice(ij.ImagePlus image, org.jogamp.vecmath.Color3f color, String name, int thresh, boolean[] channels, int resamplingF)` Add a new image as a content, displaying it as orthoslices.
`Content`	`addOrthoslice(ij.ImagePlus image, int res)` Add a new image as a content, displaying it as orthoslices.
`Content`	`addPointMesh(List<org.jogamp.vecmath.Point3f> mesh, org.jogamp.vecmath.Color3f color, float ptsize, String name)` Add a custom mesh, in particular a point mesh, to the universe.
`Content`	`addPointMesh(List<org.jogamp.vecmath.Point3f> mesh, org.jogamp.vecmath.Color3f color, String name)` Add a custom mesh, in particular a point mesh, to the universe.
`Content`	`addQuadMesh(List<org.jogamp.vecmath.Point3f> mesh, org.jogamp.vecmath.Color3f color, String name)` Add a custom mesh, in particular a mesh consisting of quads, to the universe.
`Content`	`addSurfacePlot(ij.ImagePlus image)` Add a new image as a content, displaying it as a 2D surface plot.
`Content`	`addSurfacePlot(ij.ImagePlus image, org.jogamp.vecmath.Color3f color, String name, int thresh, boolean[] channels, int resamplingF)` Add a new image as a content, displaying it as a 2D surface plot.
`Content`	`addSurfacePlot(ij.ImagePlus image, int res)` Add a new image as a content, displaying it as a 2D surface plot.
`void`	`addTimelapseListener(TimelapseListener l)`
`Content`	`addTriangleMesh(List<org.jogamp.vecmath.Point3f> mesh, org.jogamp.vecmath.Color3f color, String name)` Add a custom mesh, in particular a triangle mesh, to the universe.
`Content`	`addTriangleMesh(List<org.jogamp.vecmath.Point3f> mesh, List<org.jogamp.vecmath.Color3f> colors, String name)` Add a custom mesh, in particular a triangle mesh, to the universe.
`Content`	`addVoltex(ij.ImagePlus image)` Add a new image as a content, displaying it as a volume rendering.
`Content`	`addVoltex(ij.ImagePlus image, org.jogamp.vecmath.Color3f color, String name, int thresh, boolean[] channels, int resamplingF)` Add a new image as a content, displaying it as a volume rendering.
`Content`	`addVoltex(ij.ImagePlus image, int res)` Add a new image as a content, displaying it as a volume rendering.
`void`	`adjustView()` Fit all contents optimally into the canvas.
`void`	`adjustView(Content c)` Fit the specified content optimally into the canvas.
`void`	`adjustView(Content c, int dir)` Fit the specified content optimally into the canvas.
`void`	`adjustView(int dir)` Fit all contents optimally into the canvas.
`void`	`adjustView(Iterable<Content> contents)` Fit the specified contents optimally into the canvas.
`void`	`adjustView(Iterable<Content> contents, int dir)` Fit the specified contents optimally into the canvas.
`String`	`allContentsString()`
`void`	`cancelOctree()` Deprecated. The octree methods will be outsourced into a different plugin.
`void`	`centerAt(org.jogamp.vecmath.Point3d p)` Center the universe at the given point.
`void`	`centerSelected(Content c)` Select the view at the selected Content.
`void`	`cleanup()` Close this universe.
`void`	`clearSelection()` If any Content is selected, deselects it.
`boolean`	`contains(String name)` Returns true if a Content with the specified name is present in this universe.
`Iterator`	`contents()` Return an Iterator which iterates through all the contents of this universe.
`Content`	`createContent(CustomMesh mesh, String name)` Create a Content object from the mesh.
`Content`	`createContent(CustomMultiMesh node, String name)`
`boolean`	`getAutoAdjustView()` autoAdjustView indicates, whether the view is adjusted to fit the whole universe each time a Content is added.
`Content`	`getContent(String name)` Returns the Content with the specified name.
`Collection`	`getContents()` Returns a Collection containing the references to all the contents of this universe.
`int`	`getCurrentTimepoint()`
`int`	`getEndTime()`
`Executer`	`getExecuter()` Returns a reference to the Executer used by this universe.
`org.jogamp.vecmath.Point3d`	`getGlobalCenterPoint()` Get a reference to the global center point.
`void`	`getGlobalCenterPoint(org.jogamp.vecmath.Point3d p)` Copies the global center point into the specified Point3d.
`void`	`getGlobalMaxPoint(org.jogamp.vecmath.Point3d p)` Copies the global maximum point into the specified Point3d.
`void`	`getGlobalMinPoint(org.jogamp.vecmath.Point3d p)` Copies the global minimum point into the specified Point3d.
`JMenuBar`	`getMenuBar()` Returns a reference to the menu bar used by this universe.
`PointListDialog`	`getPointListDialog()` Returns a reference to the PointListDialog used by this universe
`RegistrationMenubar`	`getRegistrationMenuBar()` Returns a reference to the registration menu bar.
`String`	`getSafeContentName(String suggested)`
`Content`	`getSelected()` Returns the selected Content, or null if none is selected.
`ShortCuts`	`getShortcuts()` Returns a reference to the universe's shortcuts.
`boolean`	`getShowBoundingBoxUponSelection()` Returns true if the selection box is shown upon selecting a Content(Instant).
`int`	`getStartTime()`
`Timeline`	`getTimeline()`
`void`	`hideAllLandmarks()` Hide point list dialog and all landmark points.
`void`	`init(ImageWindow3D window)` Initializes a 3D window.
`boolean`	`isFullScreen()`
`void`	`loadSession(String file)`
`void`	`loadView(String file)` Load view transformations from file
`void`	`recalculateGlobalMinMax()` Calculates the global minimum, maximum and center point depending on all the available contents.
`void`	`recalculateGlobalMinMax(Content c)` If the specified Content is the only content in the universe, global minimum, maximum and center point are set accordingly to this Content.
`void`	`removeAllContents()` Remove all the contents of this universe.
`void`	`removeContent(String name)` Remove the Content with the specified name from the universe.
`void`	`removeOctree()` Deprecated. The octree methods will be outsourced into a different plugin.
`void`	`removeTimelapseListener(TimelapseListener l)`
`void`	`resetView()` Reset the transformations of the view side of the scene graph as if the Contents of this universe were just displayed.
`void`	`rotateToNegativeXY()` Rotate the univere so that the user looks in the negative direction of the z-axis.
`void`	`rotateToNegativeXZ()` Rotate the univere so that the user looks in the negative direction of the y-axis.
`void`	`rotateToNegativeYZ()` Rotate the univere so that the user looks in the negative direction of the x-axis.
`void`	`rotateToPositiveXY()` Rotate the univere so that the user looks in the positive direction of the z-axis.
`void`	`rotateToPositiveXZ()` Rotate the univere so that the user looks in the positive direction of the y-axis.
`void`	`rotateToPositiveYZ()` Rotate the univere so that the user looks in the positive direction of the x-axis.
`void`	`rotateUniverse(org.jogamp.vecmath.Vector3d axis, double angle)` Rotate the universe, using the given axis of rotation and angle; The center of rotation is the global center.
`void`	`saveSession(String file)`
`void`	`saveView(String file)` Save the current view transformations to a file
`void`	`select(Content c)` Select the specified Content.
`void`	`setAutoAdjustView(boolean b)` autoAdjustView indicates, whether the view is adjusted to fit the whole universe each time a Content is added.
`void`	`setFullScreen(boolean f)` Sets fullscreen mode on or of.
`void`	`setMenubar(JMenuBar mb)` Set a custom menu bar to the viewer
`void`	`setMenubar(MenuBar mb)` Deprecated. Use swing instead.
`void`	`setShowBoundingBoxUponSelection(boolean b)` Show/Hide the selection box upon selecting a Content(Instant).
`void`	`setStatus(String text)` Shows the specified status string at the bottom of the viewer window.
`void`	`show()` Display this universe in a window (an ImageWindow3D).
`void`	`showTimepoint(int tp)`
`void`	`sync(boolean b)` Syncs this window.
`void`	`updateOctree()` Deprecated. The octree methods will be outsourced into a different plugin.
`void`	`updateStartAndEndTime(int st, int e)`
`void`	`updateTimeline()`
`void`	`updateTimelineGUI()`

Methods inherited from class ij3d.DefaultAnimatableUniverse
getRotationAxis, getRotationInterval, pauseAnimation, record360, rotateX, rotateY, rotateZ, setRotationAxis, setRotationInterval, startAnimation, startFreehandRecording, stopFreehandRecording

Methods inherited from class org.jogamp.java3d.utils.universe.SimpleUniverse
addBranchGraph, getCanvas, getCanvas, getLocale, getPreferredConfiguration, getViewer, getViewingPlatform

Methods inherited from class org.jogamp.java3d.VirtualUniverse
addGraphStructureChangeListener, addRenderingErrorListener, addShaderErrorListener, getAllLocales, getJ3DThreadPriority, getProperties, numLocales, removeAllLocales, removeGraphStructureChangeListener, removeLocale, removeRenderingErrorListener, removeShaderErrorListener, setJ3DThreadPriority

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

- Field Detail
  - NO_CONTENT_MESSAGE
```
public static final String NO_CONTENT_MESSAGE
```
    See Also:
    
    Constant Field Values
  - universes
```
public static ArrayList<Image3DUniverse> universes
```
- Constructor Detail
  - Image3DUniverse
```
public Image3DUniverse()
```
    Default constructor. Creates a new universe using the Universe settings - either default settings or stored settings.
  - Image3DUniverse
```
public Image3DUniverse(int width,
                       int height)
```
    Constructs a new universe with the specified width and height.
    
    Parameters:
    
    width -
    
    height -
- Method Detail
  - show
```
public void show()
```
    Display this universe in a window (an ImageWindow3D).
    
    Overrides:
    
    show in class DefaultUniverse
  - init
```
public void init(ImageWindow3D window)
```
    Initializes a 3D window.
    
    Parameters:
    
    window - 3D window to initialize. It is assumed that the window already displays the Canvas3D as obtained from calling SimpleUniverse.getCanvas(). If the DefaultUniverse obtained from ImageWindow3D.getUniverse() is not exactly this universe, a RuntimeException is thrown. This method acts as an initialization of the ImageWindow3D, by adding the menubar to it as well as initializing the PointListDialog and adding a WindowAdapter to the window that does cleanup. The window is not shown; that is, Window.pack() and Window.setVisible(boolean) are not called.
  - setFullScreen
```
public void setFullScreen(boolean f)
```
    Sets fullscreen mode on or of.
  - isFullScreen
```
public boolean isFullScreen()
```
  - cleanup
```
public void cleanup()
```
    Close this universe. Remove all Contents and release all resources.
    
    Overrides:
    
    cleanup in class DefaultUniverse
  - setStatus
```
public void setStatus(String text)
```
    Shows the specified status string at the bottom of the viewer window.
    
    Parameters:
    
    text -
  - setMenubar
```
@Deprecated
public void setMenubar(MenuBar mb)
```
    Deprecated. Use swing instead.
    
    Set a custom menu bar to the viewer.
  - setMenubar
```
public void setMenubar(JMenuBar mb)
```
    Set a custom menu bar to the viewer
    
    Parameters:
    
    mb -
  - getMenuBar
```
public JMenuBar getMenuBar()
```
    Returns a reference to the menu bar used by this universe.
    
    Returns:
  - getRegistrationMenuBar
```
public RegistrationMenubar getRegistrationMenuBar()
```
    Returns a reference to the registration menu bar.
  - getExecuter
```
public Executer getExecuter()
```
    Returns a reference to the Executer used by this universe.
    
    Returns:
  - getShortcuts
```
public ShortCuts getShortcuts()
```
    Returns a reference to the universe's shortcuts.
  - getPointListDialog
```
public PointListDialog getPointListDialog()
```
    Returns a reference to the PointListDialog used by this universe
  - hideAllLandmarks
```
public void hideAllLandmarks()
```
    Hide point list dialog and all landmark points.
  - saveSession
```
public void saveSession(String file)
                 throws IOException
```
    Throws:
    
    IOException
  - loadSession
```
public void loadSession(String file)
                 throws IOException
```
    Throws:
    
    IOException
  - addTimelapseListener
```
public void addTimelapseListener(TimelapseListener l)
```
  - removeTimelapseListener
```
public void removeTimelapseListener(TimelapseListener l)
```
  - getTimeline
```
public Timeline getTimeline()
```
  - showTimepoint
```
public void showTimepoint(int tp)
```
  - getCurrentTimepoint
```
public int getCurrentTimepoint()
```
  - getStartTime
```
public int getStartTime()
```
  - getEndTime
```
public int getEndTime()
```
  - updateStartAndEndTime
```
public void updateStartAndEndTime(int st,
                                  int e)
```
  - updateTimeline
```
public void updateTimeline()
```
  - updateTimelineGUI
```
public void updateTimelineGUI()
```
  - select
```
public void select(Content c)
```
    Select the specified Content. If another Content is already selected, it will be deselected. fireContentSelected() is thrown.
    
    Parameters:
    
    c -
  - getSelected
```
public Content getSelected()
```
    Returns the selected Content, or null if none is selected.
    
    Specified by:
    
    getSelected in class DefaultUniverse
  - clearSelection
```
public void clearSelection()
```
    If any Content is selected, deselects it.
  - setShowBoundingBoxUponSelection
```
public void setShowBoundingBoxUponSelection(boolean b)
```
    Show/Hide the selection box upon selecting a Content(Instant).
  - getShowBoundingBoxUponSelection
```
public boolean getShowBoundingBoxUponSelection()
```
    Returns true if the selection box is shown upon selecting a Content(Instant).
  - setAutoAdjustView
```
public void setAutoAdjustView(boolean b)
```
    autoAdjustView indicates, whether the view is adjusted to fit the whole universe each time a Content is added.
  - getAutoAdjustView
```
public boolean getAutoAdjustView()
```
    autoAdjustView indicates, whether the view is adjusted to fit the whole universe each time a Content is added.
  - recalculateGlobalMinMax
```
public void recalculateGlobalMinMax()
```
    Calculates the global minimum, maximum and center point depending on all the available contents.
  - recalculateGlobalMinMax
```
public void recalculateGlobalMinMax(Content c)
```
    If the specified Content is the only content in the universe, global minimum, maximum and center point are set accordingly to this Content. If not, the extrema of the specified Content are compared with the current global extrema, and these are set accordingly.
    
    Parameters:
    
    c -
  - getGlobalCenterPoint
```
public org.jogamp.vecmath.Point3d getGlobalCenterPoint()
```
    Get a reference to the global center point. Attention: Changing the returned point results in unspecified behavior.
  - getGlobalCenterPoint
```
public void getGlobalCenterPoint(org.jogamp.vecmath.Point3d p)
```
    Copies the global center point into the specified Point3d.
    
    Parameters:
    
    p -
  - getGlobalMinPoint
```
public void getGlobalMinPoint(org.jogamp.vecmath.Point3d p)
```
    Copies the global minimum point into the specified Point3d.
    
    Parameters:
    
    p -
  - getGlobalMaxPoint
```
public void getGlobalMaxPoint(org.jogamp.vecmath.Point3d p)
```
    Copies the global maximum point into the specified Point3d.
    
    Parameters:
    
    p -
  - updateOctree
```
@Deprecated
public void updateOctree()
```
    Deprecated. The octree methods will be outsourced into a different plugin.
  - cancelOctree
```
@Deprecated
public void cancelOctree()
```
    Deprecated. The octree methods will be outsourced into a different plugin.
  - removeOctree
```
@Deprecated
public void removeOctree()
```
    Deprecated. The octree methods will be outsourced into a different plugin.
  - addOctree
```
@Deprecated
public VolumeOctree addOctree(String imageDir,
                                          String name)
```
    Deprecated. The octree methods will be outsourced into a different plugin.
  - addContent
```
public Content addContent(ij.ImagePlus image,
                          org.jogamp.vecmath.Color3f color,
                          String name,
                          int thresh,
                          boolean[] channels,
                          int resf,
                          int type)
```
    Add the specified image as a new Content to the universe. The specified type is one of the constants defined in Content, e.g. VOLUME, SURFACE etc. For meaning about color, threshold, channels, ... see the documentation for Content.
    
    Parameters:
    
    image - the image to display
    
    color - the color in which the Content is displayed
    
    name - a name for the Content to be added
    
    thresh - a threshold
    
    channels - the color channels to display.
    
    resf - a resampling factor.
    
    type - the type which determines how the image is displayed.
    
    Returns:
    
    The Content which is added, null if any error occurred.
  - addContent
```
public Content addContent(ij.ImagePlus image,
                          int type,
                          int res)
```
    Add the specified image as a new Content to the universe. The specified type is one of the constants defined in Content, e.g. VOLUME, SURFACE etc. For meaning about color, threshold, channels, ... see the documentation for Content. Default parameters are used for its attributes:
    - color: null
    - name: title of the image
    - threshold: the default threshold, as returned by Content.getDefaultTreshold()
    - channels: all color channels r, g, b
    Parameters:
    
    image - the image to display
    
    type - the type which determines how the image is displayed.
    
    Returns:
    
    The Content which is added, null if any error occurred.
  - addContent
```
public Content addContent(ij.ImagePlus image,
                          int type)
```
    Add the specified image as a new Content to the universe. The specified type is one of the constants defined in Content, e.g. VOLUME, SURFACE etc. For meaning about color, threshold, channels, ... see the documentation for Content. Default parameters are used for its attributes:
    - color: null
    - name: title of the image
    - threshold: the default threshold, as returned by Content.getDefaultTreshold()
    - channels: all color channels r, g, b
    - resampling factor: the default resampling factor, as returned by Content.getDefaultResamplingFactor()
    Parameters:
    
    image - the image to display
    
    type - the type which determines how the image is displayed.
    
    Returns:
    
    The Content which is added, null if any error occurred.
  - addVoltex
```
public Content addVoltex(ij.ImagePlus image)
```
    Add a new image as a content, displaying it as a volume rendering. Default parameters are used for its attributes:
    - color: null
    - name: title of the image
    - threshold: the default threshold, as returned by Content.getDefaultTreshold()
    - channels: all color channels r, g, b
    - resampling factor: the default resampling factor, as returned by Content.getDefaultResamplingFactor()
    Parameters:
    
    image - the image to display
    
    Returns:
    
    the Content which was added, null if any error occurred.
  - addVoltex
```
public Content addVoltex(ij.ImagePlus image,
                         int res)
```
    Add a new image as a content, displaying it as a volume rendering. Default parameters are used for its attributes:
    - color: null
    - name: title of the image
    - threshold: the default threshold, as returned by Content.getDefaultTreshold()
    - channels: all color channels r, g, b
    Parameters:
    
    image - the image to display
    
    Returns:
    
    the Content which was added, null if any error occurred.
  - addVoltex
```
public Content addVoltex(ij.ImagePlus image,
                         org.jogamp.vecmath.Color3f color,
                         String name,
                         int thresh,
                         boolean[] channels,
                         int resamplingF)
```
    Add a new image as a content, displaying it as a volume rendering. For the meaning of color, threshold, channels, resampling factor etc see the documentation of Content.
    
    Parameters:
    
    image - the image to display
    
    color - the color in which this volume rendering is displayed.
    
    name - the name of the displayed Content.
    
    thresh - the threshold used for the displayed volume rendering
    
    channels - the displayed color channels, must be a boolean array of length 3
    
    resamplingF - a resampling factor.
    
    Returns:
    
    the added Content, null if any error occurred
  - addOrthoslice
```
public Content addOrthoslice(ij.ImagePlus image)
```
    Add a new image as a content, displaying it as orthoslices. Default parameters are used for its attributes:
    - color: null
    - name: title of the image
    - threshold: the default threshold, as returned by Content.getDefaultTreshold()
    - channels: all color channels r, g, b
    - resampling factor: the default resampling factor, as returned by Content.getDefaultResamplingFactor()
    Parameters:
    
    image - the image to display
    
    Returns:
    
    the Content which was added, null if any error occurred.
  - addOrthoslice
```
public Content addOrthoslice(ij.ImagePlus image,
                             int res)
```
    Add a new image as a content, displaying it as orthoslices. Default parameters are used for its attributes:
    - color: null
    - name: title of the image
    - threshold: the default threshold, as returned by Content.getDefaultTreshold()
    - channels: all color channels r, g, b
    Parameters:
    
    image - the image to display
    
    Returns:
    
    the Content which was added, null if any error occurred.
  - addOrthoslice
```
public Content addOrthoslice(ij.ImagePlus image,
                             org.jogamp.vecmath.Color3f color,
                             String name,
                             int thresh,
                             boolean[] channels,
                             int resamplingF)
```
    Add a new image as a content, displaying it as orthoslices. For the meaning of color, threshold, channels, resampling factor etc see the documentation of Content.
    
    Parameters:
    
    image - the image to display
    
    color - the color in which these orthoslices are displayed.
    
    name - the name of the displayed Content.
    
    thresh - the threshold used for the displayed orthoslices
    
    channels - the displayed color channels, must be a boolean array of length 3
    
    resamplingF - a resampling factor.
    
    Returns:
    
    the added Content, null if any error occurred
  - addSurfacePlot
```
public Content addSurfacePlot(ij.ImagePlus image)
```
    Add a new image as a content, displaying it as a 2D surface plot. Default parameters are used for its attributes:
    - color: null
    - name: title of the image
    - threshold: the default threshold, as returned by Content.getDefaultTreshold()
    - channels: all color channels r, g, b
    - resampling factor: the default resampling factor, as returned by Content.getDefaultResamplingFactor()
    Parameters:
    
    image - the image to display
    
    Returns:
    
    the Content which was added, null if any error occurred.
  - addSurfacePlot
```
public Content addSurfacePlot(ij.ImagePlus image,
                              int res)
```
    Add a new image as a content, displaying it as a 2D surface plot. Default parameters are used for its attributes:
    - color: null
    - name: title of the image
    - threshold: the default threshold, as returned by Content.getDefaultTreshold()
    - channels: all color channels r, g, b
    Parameters:
    
    image - the image to display
    
    Returns:
    
    the Content which was added, null if any error occurred.
  - addSurfacePlot
```
public Content addSurfacePlot(ij.ImagePlus image,
                              org.jogamp.vecmath.Color3f color,
                              String name,
                              int thresh,
                              boolean[] channels,
                              int resamplingF)
```
    Add a new image as a content, displaying it as a 2D surface plot. For the meaning of color, threshold, channels, resampling factor etc see the documentation of Content.
    
    Parameters:
    
    image - the image to display
    
    color - the color in which this surface plot is displayed.
    
    name - the name of the displayed Content.
    
    thresh - the threshold used for the displayed surface plot
    
    channels - the displayed color channels, must be a boolean array of length 3
    
    resamplingF - a resampling factor.
    
    Returns:
    
    the added Content, null if any error occurred
  - addMesh
```
public Content addMesh(ij.ImagePlus img)
```
    Add a new image as a content, displaying it as an isosurface. Default parameters are used for its attributes:
    - color: null
    - name: title of the image
    - threshold: the default threshold, as returned by Content.getDefaultTreshold()
    - channels: all color channels r, g, b
    - resampling factor: the default resampling factor, as returned by Content.getDefaultResamplingFactor()
    Parameters:
    
    img - the image to display
    
    Returns:
    
    the Content which was added, null if any error occurred.
  - addMesh
```
public Content addMesh(ij.ImagePlus img,
                       int res)
```
    Add a new image as a content, displaying it as an isosurface. Default parameters are used for its attributes:
    - color: null
    - name: title of the image
    - threshold: the default threshold, as returned by Content.getDefaultTreshold()
    - channels: all color channels r, g, b
    Parameters:
    
    img - the image to display
    
    res -
    
    Returns:
    
    the Content which was added, null if any error occurred.
  - addMesh
```
public Content addMesh(ij.ImagePlus image,
                       org.jogamp.vecmath.Color3f color,
                       String name,
                       int threshold,
                       boolean[] channels,
                       int resamplingF)
```
    Add a new image as a content, displaying it as an iso-surface. For the meaning of color, threshold, channels, resampling factor etc see the documentation of Content.
    
    Parameters:
    
    image - the image to display
    
    color - the color in which this surface is displayed.
    
    name - the name of the displayed Content.
    
    threshold - the threshold used for generating the surface
    
    channels - the displayed color channels, must be a boolean array of length 3
    
    resamplingF - a resampling factor.
    
    Returns:
    
    the added Content, null if any error occurred
  - addCustomMesh
```
public Content addCustomMesh(CustomMesh mesh,
                             String name)
```
    Add a custom mesh to the universe. For more details on custom meshes, read the package API docs of the package customnode.
    
    Parameters:
    
    mesh - the CustomMesh to display
    
    name - the name for the added Content
    
    Returns:
    
    the added Content
  - addCustomMesh
```
public Content addCustomMesh(CustomMultiMesh mesh,
                             String name)
```
    Add a CustomMultiMesh to the universe. For more details on custom meshes, read the package API docs of the package customnode.
    
    Parameters:
    
    mesh - the CustomMultiMesh to display
    
    name - the name for the added Content
    
    Returns:
    
    the added Content
  - createContent
```
public Content createContent(CustomMesh mesh,
                             String name)
```
    Create a Content object from the mesh. Does not add the Content to the view; it merely creates it with all the appropriate default parameters. Does not check if the view already contains a Content object with the same name, which is not allowed.
    
    Parameters:
    
    mesh - the CustomMesh to display
    
    name - the name for the added Content
    
    Returns:
    
    the created Content
  - createContent
```
public Content createContent(CustomMultiMesh node,
                             String name)
```
  - addLineMesh
```
public Content addLineMesh(List<org.jogamp.vecmath.Point3f> mesh,
                           org.jogamp.vecmath.Color3f color,
                           String name,
                           boolean strips)
```
    Add a custom mesh, in particular a line mesh (a set of lines in 3D) to the universe. For the line parameters, default values are used: The width of the line is 1.0 and the pattern is solid. There exist two styles of line meshes:
    - a normal line mesh. In this case, the specified strips flag should be false. mesh is a list of points which are connected pairwise, i.e. the 1st point is connected to the 2nd, the 3rd to the 4th, and so on.
    - a strip line. In this case, the specified strip flag should be true. mesh is a list of points which are connected continuously, i.e.the 1st point is connected to the 2nd, the 2nd to the 2rd, the 3rd to the 4th, and so on.
    For more details on custom meshes, read the package API docs of the package customnode.
    Parameters:
    
    mesh - a list of points which make up the mesh
    
    color - the color in which the line is displayed
    
    name - a name for the added Content
    
    strips - flag specifying wheter the line is continuously or pairwise connected
    
    Returns:
    
    the connected Content.
  - addPointMesh
```
public Content addPointMesh(List<org.jogamp.vecmath.Point3f> mesh,
                            org.jogamp.vecmath.Color3f color,
                            String name)
```
    Add a custom mesh, in particular a point mesh, to the universe. For the size of the points, a default value is used which is 1.0. For more details on custom meshes, read the package API docs of the package customnode.
    
    Parameters:
    
    mesh - a list of points which make up the mesh.
    
    color - the color in which the points is displayed
    
    name - a name for the added Content
    
    Returns:
    
    the connected Content.
  - addPointMesh
```
public Content addPointMesh(List<org.jogamp.vecmath.Point3f> mesh,
                            org.jogamp.vecmath.Color3f color,
                            float ptsize,
                            String name)
```
    Add a custom mesh, in particular a point mesh, to the universe. For more details on custom meshes, read the package API docs of the package customnode.
    
    Parameters:
    
    mesh - a list of points which make up the mesh.
    
    color - the color in which the points is displayed
    
    name - a name for the added Content
    
    ptsize - the size of the points.
    
    Returns:
    
    the connected Content.
  - addIcospheres
```
public Content addIcospheres(List<org.jogamp.vecmath.Point3f> points,
                             org.jogamp.vecmath.Color3f color,
                             int subdivisions,
                             float radius,
                             String name)
```
    At every Point3f in @param points, place an icosphere created with @param subdivisions and @param radius. A reasonable @param subdivision value is 2. Higher values will result in excessively detailed and very large meshes.
  - addQuadMesh
```
public Content addQuadMesh(List<org.jogamp.vecmath.Point3f> mesh,
                           org.jogamp.vecmath.Color3f color,
                           String name)
```
    Add a custom mesh, in particular a mesh consisting of quads, to the universe. The number of points in the specified list must be devidable by 4. 4 consecutive points represent one quad. For more details on custom meshes, read the package API docs of the package customnode.
    
    Parameters:
    
    mesh - a list of points which make up the mesh.
    
    color - the color in which the points is displayed
    
    name - a name for the added Content
    
    Returns:
    
    the connected Content.
  - addTriangleMesh
```
public Content addTriangleMesh(List<org.jogamp.vecmath.Point3f> mesh,
                               org.jogamp.vecmath.Color3f color,
                               String name)
```
    Add a custom mesh, in particular a triangle mesh, to the universe. For more details on custom meshes, read the package API docs of the package customnode.
    
    Parameters:
    
    mesh - a list of points which make up the mesh. The number of points must be devidable by 3. 3 successive points make up one triangle.
    
    color - the color in which the line is displayed
    
    name - a name for the added Content
    
    Returns:
    
    the connected Content.
  - addTriangleMesh
```
public Content addTriangleMesh(List<org.jogamp.vecmath.Point3f> mesh,
                               List<org.jogamp.vecmath.Color3f> colors,
                               String name)
```
    Add a custom mesh, in particular a triangle mesh, to the universe. With this method, the color of each vertex may be set to produce multi-colored meshes. For more details on custom meshes, read the package API docs of the package customnode.
    
    Parameters:
    
    mesh - a list of points which make up the mesh. The number of points must be devidable by 3. 3 successive points make up one triangle.
    
    colors - a List of the colors at each vertex in the mesh
    
    name - a name for the added Content
    
    Returns:
    
    the connected Content.
  - addMesh
```
@Deprecated
public Content addMesh(List mesh,
                                   org.jogamp.vecmath.Color3f color,
                                   String name,
                                   float scale,
                                   int threshold)
```
    Deprecated. This method will not be supported in the future. The specified 'scale' will be ignored, and the applied scale will be calculated automatically from the minimum and maximum coordinates of the specified mesh. Use addTriangleMesh instead.
  - addMesh
```
@Deprecated
public Content addMesh(List<org.jogamp.vecmath.Point3f> mesh,
                                   org.jogamp.vecmath.Color3f color,
                                   String name,
                                   int threshold)
```
    Deprecated. This method will not be supported in the future. Use addTriangleMesh instead.
  - removeAllContents
```
public void removeAllContents()
```
    Remove all the contents of this universe.
  - removeContent
```
public void removeContent(String name)
```
    Remove the Content with the specified name from the universe.
    
    Parameters:
    
    name -
  - contents
```
public Iterator contents()
```
    Return an Iterator which iterates through all the contents of this universe.
    
    Specified by:
    
    contents in class DefaultUniverse
  - getContents
```
public Collection getContents()
```
    Returns a Collection containing the references to all the contents of this universe.
    
    Returns:
  - contains
```
public boolean contains(String name)
```
    Returns true if a Content with the specified name is present in this universe.
    
    Parameters:
    
    name -
    
    Returns:
  - getContent
```
public Content getContent(String name)
```
    Returns the Content with the specified name. Null if no Content with the specified name is present.
    
    Parameters:
    
    name -
    
    Returns:
  - sync
```
public void sync(boolean b)
```
    Syncs this window.
  - saveView
```
public void saveView(String file)
              throws IOException
```
    Save the current view transformations to a file
    
    Throws:
    
    IOException
  - loadView
```
public void loadView(String file)
              throws IOException
```
    Load view transformations from file
    
    Throws:
    
    IOException
  - resetView
```
public void resetView()
```
    Reset the transformations of the view side of the scene graph as if the Contents of this universe were just displayed.
  - rotateUniverse
```
public void rotateUniverse(org.jogamp.vecmath.Vector3d axis,
                           double angle)
```
    Rotate the universe, using the given axis of rotation and angle; The center of rotation is the global center.
    
    Parameters:
    
    axis - The axis of rotation (in the image plate coordinate system)
    
    angle - The angle in radians.
  - rotateToNegativeXY
```
public void rotateToNegativeXY()
```
    Rotate the univere so that the user looks in the negative direction of the z-axis.
  - rotateToPositiveXY
```
public void rotateToPositiveXY()
```
    Rotate the univere so that the user looks in the positive direction of the z-axis.
  - rotateToNegativeXZ
```
public void rotateToNegativeXZ()
```
    Rotate the univere so that the user looks in the negative direction of the y-axis.
  - rotateToPositiveXZ
```
public void rotateToPositiveXZ()
```
    Rotate the univere so that the user looks in the positive direction of the y-axis.
  - rotateToNegativeYZ
```
public void rotateToNegativeYZ()
```
    Rotate the univere so that the user looks in the negative direction of the x-axis.
  - rotateToPositiveYZ
```
public void rotateToPositiveYZ()
```
    Rotate the univere so that the user looks in the positive direction of the x-axis.
  - centerSelected
```
public void centerSelected(Content c)
```
    Select the view at the selected Content.
  - centerAt
```
public void centerAt(org.jogamp.vecmath.Point3d p)
```
    Center the universe at the given point.
  - adjustView
```
public void adjustView()
```
    Fit all contents optimally into the canvas.
  - adjustView
```
public void adjustView(int dir)
```
    Fit all contents optimally into the canvas.
    
    Parameters:
    
    dir - One of ViewAdjuster.ADJUST_HORIZONTAL, ViewAdjuster.ADJUST_VERTICAL or ViewAdjuster.ADJUST_BOTH
  - adjustView
```
public void adjustView(Iterable<Content> contents)
```
    Fit the specified contents optimally into the canvas.
  - adjustView
```
public void adjustView(Iterable<Content> contents,
                       int dir)
```
    Fit the specified contents optimally into the canvas.
    
    Parameters:
    
    dir - One of ViewAdjuster.ADJUST_HORIZONTAL, ViewAdjuster.ADJUST_VERTICAL or ViewAdjuster.ADJUST_BOTH
  - adjustView
```
public void adjustView(Content c,
                       int dir)
```
    Fit the specified content optimally into the canvas.
    
    Parameters:
    
    dir - One of ViewAdjuster.ADJUST_HORIZONTAL, ViewAdjuster.ADJUST_VERTICAL or ViewAdjuster.ADJUST_BOTH
  - adjustView
```
public void adjustView(Content c)
```
    Fit the specified content optimally into the canvas.
  - allContentsString
```
public String allContentsString()
```
  - getSafeContentName
```
public String getSafeContentName(String suggested)
```
  - addContent
```
public Content addContent(Content c)
```
    Add the specified Content to the universe. It is assumed that the specified Content is constructed correctly. Will wait until the Content is fully added; for asynchronous additions of Content, use the @addContentLater method.
    
    Parameters:
    
    c -
    
    Returns:
    
    the added Content, or null if an error occurred.
  - addContentLater
```
public Future<Content> addContentLater(Content c)
```
    Add the specified Content to the universe. It is assumed that the specified Content is constructed correctly. The Content is added asynchronously, and this method returns immediately.
    
    Parameters:
    
    c - The Content to add
    
    Returns:
    
    a Future holding the added Content, or null if an error occurred.
  - addContentLater
```
public Collection<Future<Content>> addContentLater(String file)
```
  - addContentLater
```
public Collection<Future<Content>> addContentLater(Collection<Content> cc)
```
    Add the specified collection of Content to the universe. It is assumed that the specified Content is constructed correctly. The Content is added asynchronously, and this method returns immediately.
    
    Parameters:
    
    cc - The Collection of Content to add
    
    Returns:
    
    a Collection of Future objects, each holding an added Content. The returned Collection is never null, but its Future objects may return null on calling get() on them if an error ocurred when adding a specific Content object.

Class Image3DUniverse

Nested Class Summary

Nested classes/interfaces inherited from class ij3d.DefaultUniverse

Field Summary

Fields inherited from class ij3d.DefaultUniverse

Fields inherited from class org.jogamp.java3d.utils.universe.SimpleUniverse

Fields inherited from interface ij3d.behaviors.BehaviorCallback

Constructor Summary

Method Summary

Methods inherited from class ij3d.DefaultAnimatableUniverse

Methods inherited from class ij3d.DefaultUniverse

Methods inherited from class org.jogamp.java3d.utils.universe.SimpleUniverse

Methods inherited from class org.jogamp.java3d.VirtualUniverse

Methods inherited from class java.lang.Object

Field Detail

NO_CONTENT_MESSAGE

universes

Constructor Detail

Image3DUniverse

Image3DUniverse

Method Detail

show

init

setFullScreen

isFullScreen

cleanup

setStatus

setMenubar

setMenubar

getMenuBar

getRegistrationMenuBar

getExecuter

getShortcuts

getPointListDialog

hideAllLandmarks

saveSession

loadSession

addTimelapseListener

removeTimelapseListener

getTimeline

showTimepoint

getCurrentTimepoint

getStartTime

getEndTime

updateStartAndEndTime

updateTimeline

updateTimelineGUI

select

getSelected

clearSelection

setShowBoundingBoxUponSelection

getShowBoundingBoxUponSelection

setAutoAdjustView

getAutoAdjustView

recalculateGlobalMinMax

recalculateGlobalMinMax

getGlobalCenterPoint

getGlobalCenterPoint

getGlobalMinPoint

getGlobalMaxPoint

updateOctree

cancelOctree

removeOctree

addOctree

addContent

addContent

addContent

addVoltex

addVoltex

addVoltex

addOrthoslice

addOrthoslice

addOrthoslice

addSurfacePlot

addSurfacePlot

addSurfacePlot

addMesh

addMesh

addMesh

addCustomMesh