Viewer3D (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- sc.fiji.snt.viewer.Viewer3D

```
public class Viewer3D
extends Object
```
Implements SNT's Reconstruction Viewer. Relies heavily on the org.jzy3d package.

Author:

Tiago Ferreira

Nested Class Summary

Nested Classes
Modifier and Type	Class and Description
`class`	`Viewer3D.ManagerPanel`
`protected static class`	`Viewer3D.Utils`
`static class`	`Viewer3D.ViewMode` Presets of a scene's view point.

Field Summary

Fields
Modifier and Type Field and Description

protected static float DEF_NODE_RADIUS

Fields
Modifier and Type	Field and Description
`protected static float`	`DEF_NODE_RADIUS`

Constructor Summary

Constructors
Modifier	Constructor and Description
	`Viewer3D()` Instantiates Viewer3D without the 'Controls' dialog ('kiosk mode').
	`Viewer3D(boolean interactive)` Script-friendly constructor.
	`Viewer3D(Context context)` Instantiates an interactive Viewer3D with GUI Controls to import, manage and customize the Viewer's scene.
`protected`	`Viewer3D(SNT snt)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`void`	`add(File[] files, String color)` Adds a collection of trees or meshes from input files.
`void`	`add(Object object)` Script friendly method to add a supported object (`Tree`, `OBJMesh`, `AbstractDrawable`, etc.) to this viewer.
`void`	`addColorBarLegend(ColorTable colorTable, double min, double max)` Adds a color bar legend (LUT ramp) using default settings.
`void`	`addColorBarLegend(ColorTable colorTable, double min, double max, Font font, int steps, int precision)` Adds a color bar legend (LUT ramp).
`<T extends ColorMapper> void`	`addColorBarLegend(T colorMapper)` Adds a color bar legend (LUT ramp) from a `ColorMapper`.
`void`	`addLabel(String label)` Adds an annotation label to the scene.
`boolean`	`addMesh(OBJMesh objMesh)` Loads a Wavefront .OBJ file.
`void`	`addTree(Tree tree)` Adds a tree to this viewer.
`void`	`addTrees(Collection<Tree> trees, boolean assignUniqueColors)` Deprecated. use `addTrees(Collection, String)` instead
`void`	`addTrees(Collection<Tree> trees, String color)` Adds a collection of trees.
`void`	`addTrees(Collection<Tree> trees, String color, double transparencyPercent)` Adds a collection of trees.
`void`	`addTrees(Collection<Tree> trees, String color, String... commonTags)` Adds a collection of trees.
`Annotation3D`	`annotateLine(Collection<? extends SNTPoint> points, String label)` Adds a line annotation to this viewer.
`Annotation3D`	`annotatePoint(SNTPoint point, String label)` Adds an highlighting point annotation to this viewer.
`Annotation3D`	`annotatePoint(SNTPoint node, String label, String color, float size)` Adds an highlighting point annotation to this viewer.
`Annotation3D`	`annotatePoints(Collection<? extends SNTPoint> points, String label)` Adds a scatter (point cloud) annotation to this viewer.
`Annotation3D`	`annotateSurface(Collection<? extends SNTPoint> points, String label)`
`Annotation3D`	`annotateSurface(Collection<? extends SNTPoint> points, String label, boolean computeVolume)` Computes a convex hull from a collection of points and adds it to the scene as an annotation.
`void`	`assignUniqueColors(Collection<String> treeLabels)`
`double[]`	`colorCode(Collection<String> treeLabels, String measurement, ColorTable colorTable)` Runs `MultiTreeColorMapper` on the specified collection of `Tree`s.
`double[]`	`colorCode(String treeLabel, String measurement, ColorTable colorTable)` Runs `TreeColorMapper` on the specified `Tree`.
`void`	`dispose()` Closes and releases all the resources used by this viewer.
`Viewer3D`	`duplicate()`
`boolean`	`equals(Object obj)`
`void`	`freeze()` Does not allow scene to be interactive.
`protected org.jzy3d.colors.Color`	`fromAWTColor(Color color)`
`Annotation3D`	`getAnnotation(String label)` Gets the annotation associated with the specified label.
`List<Annotation3D>`	`getAnnotations()` Returns all annotations added to this viewer.
`protected float`	`getDefaultThickness()` Returns the default line thickness.
`protected org.jzy3d.colors.Color`	`getDefColor()`
`int`	`getID()` Returns this Viewer's id.
`Viewer3D.ManagerPanel`	`getManagerPanel()` Returns a reference to 'RV Controls' panel.
`OBJMesh`	`getMesh(String label)` Gets the mesh associated with the specified label.
`List<OBJMesh>`	`getMeshes()` Returns all meshes added to this viewer.
`List<OBJMesh>`	`getMeshes(boolean visibleOnly)` Returns all meshes added to this viewer.
`Tree`	`getTree(String label)` Gets the tree associated with the specified label.
`List<Tree>`	`getTrees()` Returns all trees added to this viewer.
`List<Tree>`	`getTrees(boolean visibleOnly)` Returns all trees added to this viewer.
`int`	`hashCode()`
`boolean`	`isActive()` Checks whether this instance is currently active
`boolean`	`isDarkModeOn()` Checks if scene is being rendered under dark or light background.
`boolean`	`isSNTInstance()` Checks whether this instance is SNT's Reconstruction Viewer.
`boolean`	`isSplitDendritesFromAxons()` Checks whether axons and dendrites of imported Trees are set to be imported as separated objects.
`OBJMesh`	`loadMesh(String filePath, ColorRGB color, double transparencyPercent)` Loads a Wavefront .OBJ file.
`OBJMesh`	`loadRefBrain(String template)` Loads the surface mesh of a supported reference brain/neuropil.
`void`	`logSceneControls()` Logs API calls controlling the scene (view point, bounds, etc.) to Console.
`static void`	`main(String[] args)`
`Annotation3D`	`mergeAnnotations(Collection<Annotation3D> annotations, String label)` Merges a collection of annotations into a single object.
`void`	`recordRotation(float angle, int frames, File destinationDirectory)` Records an animated rotation of the scene as a sequence of images.
`void`	`remove(Object object)` Script friendly method to remove an object (`Tree`, `OBJMesh`, `AbstractDrawable`, `String` (object label), etc.) from this viewer's scene.
`protected void`	`removeAllAnnotations()` Removes all the Annotations from current viewer
`void`	`removeAllMeshes()` Removes all loaded OBJ meshes from current viewer
`void`	`removeAllTrees()` Removes all the Trees from current viewer
`boolean`	`removeMesh(OBJMesh mesh)` Removes the specified OBJ mesh.
`boolean`	`removeMesh(String meshLabel)` Removes the specified OBJ mesh.
`boolean`	`removeTree(String treeLabel)` Removes the specified Tree.
`boolean`	`removeTree(Tree tree)` Removes the specified Tree.
`void`	`rotate(float degrees)` Rotates the scene.
`boolean`	`saveSnapshot()` Saves a snapshot of current scene as a PNG image.
`protected boolean`	`saveSnapshot(File file)`
`boolean`	`saveSnapshot(String filePath)` Saves a snapshot of current scene as a PNG image to the specified path.
`void`	`setAnimationEnabled(boolean enabled)` Toggles the Viewer's animation.
`void`	`setBounds(float xMin, float xMax, float yMin, float yMax, float zMin, float zMax)` Sets a manual bounding box for the scene.
`void`	`setDefaultColor(ColorRGB color)` Sets the default color for rendering `Tree`s.
`void`	`setDefaultThickness(float thickness)` Sets the line thickness for rendering `Tree`s that have no specified radius.
`void`	`setEnableDarkMode(boolean enable)` Enables/disables "Dark Mode" mode
`void`	`setEnableDebugMode(boolean enable)` Enables/disables debug mode
`void`	`setFont(Font font, float angle, ColorRGB color)` Sets the font for label annotations
`void`	`setFrameSize(int width, int height)` Resizes the viewer to the specified dimensions.
`void`	`setLabelLocation(float x, float y)` Sets the location for annotation labels
`void`	`setLookAndFeel(String lookAndFeelName)`
`void`	`setSceneUpdatesEnabled(boolean enabled)` Sets whether the scene should update (refresh) every time a new reconstruction (or mesh) is added/removed from the scene.
`void`	`setSnapshotDir(String path)` Sets the directory for storing snapshots.
`void`	`setSomasDisplayed(boolean displayed)` Toggles the visibility of somas for all trees in the scene.
`void`	`setSomasDisplayed(Collection<String> labels, boolean displayed)` Toggles the visibility of somas for subset of trees.
`void`	`setSplitDendritesFromAxons(boolean split)` Sets whether axons and dendrites should be imported as separated objects.
`void`	`setTreeColor(Collection<String> labels, ColorRGB color, String compartment)` Recolors a subset of rendered trees.
`void`	`setTreeColor(Collection<String> labels, String color, String compartment)` Recolors a subset of rendered trees.
`void`	`setTreeThickness(Collection<String> labels, float thickness, String compartment)` Applies a constant thickness (line width) to a subset of rendered trees.
`void`	`setTreeThickness(float thickness)` Applies a constant thickness to all rendered trees.
`void`	`setTreeThickness(float thickness, String compartment)` Applies a constant thickness (line width) to all rendered trees.Note that by default, trees are rendered using their nodes' diameter.
`void`	`setViewMode(String viewMode)` Renders the scene from a specified camera angle (script-friendly).
`void`	`setViewMode(Viewer3D.ViewMode viewMode)` Renders the scene from a specified camera angle.
`void`	`setViewPoint(double r, double t)` Renders the scene from a specified camera angle using polar coordinates relative to the the center of the scene.
`void`	`setViewPointCC(double x, double y)` Calls `setViewPoint(double, double)` using Cartesian coordinates.
`void`	`setVisible(String label, boolean visible)` Toggles the visibility of a rendered Tree, a loaded OBJ mesh, or an annotation.
`Frame`	`show()` Displays the Viewer and returns a reference to its frame.
`Frame`	`show(int width, int height)` Displays the viewer under specified dimensions.
`boolean`	`syncPathManagerList()` (Re)loads the current list of Paths in the Path Manager list.
`void`	`translate(Collection<String> treeLabels, SNTPoint offset)` Translates the specified collection of `Tree`s.
`void`	`translate(Tree tree, SNTPoint offset)` Translates the specified Tree.
`void`	`unfreeze()` Allows scene to be interactive.
`void`	`updateColorBarLegend(double min, double max)` Updates the existing color bar legend to new properties.
`void`	`updateView()` Updates the scene bounds to ensure all visible objects are displayed.
`void`	`validate()` Checks if all drawables in the 3D scene are being rendered properly, rebuilding the entire scene if not.
`protected static void`	`workaroundIntelGraphicsBug()`
`void`	`zoomTo(Object... objects)` Zooms the scene into the bounding box enclosing the specified objects.

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

- Field Detail
  - DEF_NODE_RADIUS
```
protected static final float DEF_NODE_RADIUS
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - Viewer3D
```
public Viewer3D()
```
    Instantiates Viewer3D without the 'Controls' dialog ('kiosk mode'). Such a viewer is more suitable for large datasets and allows for Trees to be added concurrently.
  - Viewer3D
```
public Viewer3D(Context context)
```
    Instantiates an interactive Viewer3D with GUI Controls to import, manage and customize the Viewer's scene.
    
    Parameters:
    
    context - the SciJava application context providing the services required by the class
  - Viewer3D
```
public Viewer3D(boolean interactive)
```
    Script-friendly constructor.
    
    Parameters:
    
    interactive - if true, the viewer is displayed with GUI Controls to import, manage and customize the Viewer's scene.
  - Viewer3D
```
protected Viewer3D(SNT snt)
```
- Method Detail
  - workaroundIntelGraphicsBug
```
protected static void workaroundIntelGraphicsBug()
```
  - getID
```
public int getID()
```
    Returns this Viewer's id.
    
    Returns:
    
    this this Viewer's unique numeric ID.
  - setSceneUpdatesEnabled
```
public void setSceneUpdatesEnabled(boolean enabled)
```
    Sets whether the scene should update (refresh) every time a new reconstruction (or mesh) is added/removed from the scene.
    
    Parameters:
    
    enabled - Whether scene updates should be enabled. Should be set to false when performing bulk operations. Scene will update if set to true
  - duplicate
```
public Viewer3D duplicate()
```
  - validate
```
public void validate()
```
    Checks if all drawables in the 3D scene are being rendered properly, rebuilding the entire scene if not. Useful to "hard-reset" the viewer, e.g., to ensure all meshes are redrawn.
    
    See Also:
    
    updateView()
  - setEnableDebugMode
```
public void setEnableDebugMode(boolean enable)
```
    Enables/disables debug mode
    
    Parameters:
    
    enable - true to enable debug mode, otherwise false
  - setEnableDarkMode
```
public void setEnableDarkMode(boolean enable)
```
    Enables/disables "Dark Mode" mode
    
    Parameters:
    
    enable - true to enable "Dark Mode", "Light Mode" otherwise
  - setSplitDendritesFromAxons
```
public void setSplitDendritesFromAxons(boolean split)
```
    Sets whether axons and dendrites should be imported as separated objects.
    
    Parameters:
    
    split - true to segregate imported Trees into axonal and dendritic subtrees. This is likely only relevant to allow for subtree customizations using the GUI commands provided by the "RV Controls" dialog. This parameter is ignored if Trees have no annotations.
  - rotate
```
public void rotate(float degrees)
            throws IllegalArgumentException
```
    Rotates the scene.
    
    Parameters:
    
    degrees - the angle, in degrees
    
    Throws:
    
    IllegalArgumentException - if current view mode does not allow rotations
  - recordRotation
```
public void recordRotation(float angle,
                           int frames,
                           File destinationDirectory)
                    throws IllegalArgumentException,
                           SecurityException
```
    Records an animated rotation of the scene as a sequence of images.
    
    Parameters:
    
    angle - the rotation angle (e.g., 360 for a full rotation)
    
    frames - the number of frames in the animated sequence
    
    destinationDirectory - the directory where the image sequence will be stored.
    
    Throws:
    
    IllegalArgumentException - if no view exists, or current view is constrained and does not allow 360 degrees rotation
    
    SecurityException - if it was not possible to save files to destinationDirectory
  - isDarkModeOn
```
public boolean isDarkModeOn()
```
    Checks if scene is being rendered under dark or light background.
    
    Returns:
    
    true, if "Dark Mode" is active
  - isSplitDendritesFromAxons
```
public boolean isSplitDendritesFromAxons()
```
    Checks whether axons and dendrites of imported Trees are set to be imported as separated objects.
    
    Returns:
    
    if imported trees are set to be split into axonal and dendritic subtrees.
  - freeze
```
public void freeze()
```
    Does not allow scene to be interactive. Only static orthogonal views allowed.
    
    See Also:
    
    unfreeze()
  - unfreeze
```
public void unfreeze()
```
    Allows scene to be interactive.
    
    See Also:
    
    freeze()
  - fromAWTColor
```
protected org.jzy3d.colors.Color fromAWTColor(Color color)
```
  - addTree
```
public void addTree(Tree tree)
```
    Adds a tree to this viewer. Note that calling updateView() may be required to ensure that the current View's bounding box includes the added Tree.
    
    Parameters:
    
    tree - the Tree to be added. The Tree's label will be used as identifier. It is expected to be unique when rendering multiple Trees, if not (or no label exists) a unique label will be generated.
    
    See Also:
    
    Tree.getLabel(), removeTree(String), updateView(), setSplitDendritesFromAxons(boolean)
  - addTrees
```
public void addTrees(Collection<Tree> trees,
                     String color,
                     String... commonTags)
```
    Adds a collection of trees.
    
    Parameters:
    
    trees - the trees to be added
    
    color - Set it to null, none or "" to ignore this option altogether. Set it to unique to assign unique colors to each tree in the collection.
    
    commonTags - common tag(s) to be assigned to the group (to be displayed in 'RV Controls' list.
  - addTrees
```
public void addTrees(Collection<Tree> trees,
                     String color)
```
    Adds a collection of trees.
    
    Parameters:
    
    trees - the trees to be added.
    
    color - the rendering color. Set it to null, none or "" to ignore this option altogether. Set it to unique to assign unique colors to each tree in the collection.
  - addTrees
```
public void addTrees(Collection<Tree> trees,
                     String color,
                     double transparencyPercent)
```
    Adds a collection of trees.
    
    Parameters:
    
    trees - the trees to be added.
    
    color - the color to be applied, either a HTML color codes starting with hash (#), a color preset ("red", "blue", etc.), or integer triples of the form r,g,b and range [0, 255]
    
    transparencyPercent - the color transparency (in percentage)
  - addTrees
```
@Deprecated
public void addTrees(Collection<Tree> trees,
                                 boolean assignUniqueColors)
```
    Deprecated. use addTrees(Collection, String) instead
  - add
```
public void add(File[] files,
                String color)
```
    Adds a collection of trees or meshes from input files.
    
    Parameters:
    
    files - the files to be imported
    
    color - the color to be assigned to imported reconstructions/meshes. If empty, null or unique, objects will be assigned a unique color.
    
    See Also:
    
    setSplitDendritesFromAxons(boolean)
  - getTree
```
public Tree getTree(String label)
```
    Gets the tree associated with the specified label.
    
    Parameters:
    
    label - the (unique) label as displayed in Viewer's list
    
    Returns:
    
    the Tree or null if no Tree is associated with the specified label
  - getAnnotation
```
public Annotation3D getAnnotation(String label)
```
    Gets the annotation associated with the specified label.
    
    Parameters:
    
    label - the (unique) label as displayed in Viewer's list
    
    Returns:
    
    the annotation or null if no annotation is associated with the specified label
  - getMesh
```
public OBJMesh getMesh(String label)
```
    Gets the mesh associated with the specified label.
    
    Parameters:
    
    label - the (unique) label as displayed in Viewer's list
    
    Returns:
    
    the mesh or null if no mesh is associated with the specified label
  - getTrees
```
public List<Tree> getTrees()
```
    Returns all trees added to this viewer.
    
    Returns:
    
    the Tree list
  - getTrees
```
public List<Tree> getTrees(boolean visibleOnly)
```
    Returns all trees added to this viewer.
    
    Parameters:
    
    visibleOnly - If true, only visible Trees are retrieved.
    
    Returns:
    
    the Tree list
  - getMeshes
```
public List<OBJMesh> getMeshes()
```
    Returns all meshes added to this viewer.
    
    Returns:
    
    the mesh list
  - getMeshes
```
public List<OBJMesh> getMeshes(boolean visibleOnly)
```
    Returns all meshes added to this viewer.
    
    Parameters:
    
    visibleOnly - If true, only visible meshes are retrieved.
    
    Returns:
    
    the mesh list
  - getAnnotations
```
public List<Annotation3D> getAnnotations()
```
    Returns all annotations added to this viewer.
    
    Returns:
    
    the annotation list
  - annotateSurface
```
public Annotation3D annotateSurface(Collection<? extends SNTPoint> points,
                                    String label)
```
  - annotateSurface
```
public Annotation3D annotateSurface(Collection<? extends SNTPoint> points,
                                    String label,
                                    boolean computeVolume)
```
    Computes a convex hull from a collection of points and adds it to the scene as an annotation.
    
    Parameters:
    
    points - the collection of points defining the convex set.
    
    label - the (optional) annotation identifier. If null or empty, a unique label will be generated.
    
    computeVolume - whether or not to compute the volume of the convex hull. If true, the volume is stored in the "volume" field of the returned Annotation3D object.
    
    Returns:
    
    the Annotation3D
  - annotatePoint
```
public Annotation3D annotatePoint(SNTPoint point,
                                  String label)
```
    Adds an highlighting point annotation to this viewer.
    
    Parameters:
    
    point - the point to be highlighted
    
    label - the (optional) annotation identifier. If null or empty, a unique label will be generated.
    
    Returns:
    
    the Annotation3D
  - annotatePoint
```
public Annotation3D annotatePoint(SNTPoint node,
                                  String label,
                                  String color,
                                  float size)
```
    Adds an highlighting point annotation to this viewer.
    
    Parameters:
    
    node - the node to be highlighted
    
    label - the (optional) annotation identifier. If null or empty, a unique label will be generated.
    
    color - the annotation color
    
    size - the annotation size
    
    Returns:
    
    the Annotation3D
  - annotatePoints
```
public Annotation3D annotatePoints(Collection<? extends SNTPoint> points,
                                   String label)
```
    Adds a scatter (point cloud) annotation to this viewer.
    
    Parameters:
    
    points - the collection of points in the annotation
    
    label - the (optional) annotation identifier. If null or empty, a unique label will be generated.
    
    Returns:
    
    the Annotation3D
  - annotateLine
```
public Annotation3D annotateLine(Collection<? extends SNTPoint> points,
                                 String label)
```
    Adds a line annotation to this viewer.
    
    Parameters:
    
    points - the collection of points in the line annotation (at least 2 elements required). Start and end of line are highlighted if 2 points are specified.
    
    label - the (optional) annotation identifier. If null or empty, a unique label will be generated.
    
    Returns:
    
    the Annotation3D or null if collection contains less than 2 elements
  - mergeAnnotations
```
public Annotation3D mergeAnnotations(Collection<Annotation3D> annotations,
                                     String label)
```
    Merges a collection of annotations into a single object.
    
    Parameters:
    
    annotations - the collection of annotations.
    
    label - the (optional) identifier for the merged annotation. If null or empty, a unique label will be generated.
    
    Returns:
    
    the merged Annotation3D
  - updateView
```
public void updateView()
```
    Updates the scene bounds to ensure all visible objects are displayed.
    
    See Also:
    
    rebuild()
  - zoomTo
```
public void zoomTo(Object... objects)
```
    Zooms the scene into the bounding box enclosing the specified objects.
    
    Parameters:
    
    objects - the objects to be zoomed into. These can be OBJMesh, Tree, Annotation3D, etc., or string(s) defining objects listed in the "RV Controls" dialog. Collections of supported objects are also supported.
  - addColorBarLegend
```
public <T extends ColorMapper> void addColorBarLegend(T colorMapper)
```
    Adds a color bar legend (LUT ramp) from a ColorMapper.
    
    Parameters:
    
    colorMapper - the class extending ColorMapper (TreeColorMapper, etc.)
  - addColorBarLegend
```
public void addColorBarLegend(ColorTable colorTable,
                              double min,
                              double max)
```
    Adds a color bar legend (LUT ramp) using default settings.
    
    Parameters:
    
    colorTable - the color table
    
    min - the minimum value in the color table
    
    max - the maximum value in the color table
  - updateColorBarLegend
```
public void updateColorBarLegend(double min,
                                 double max)
```
    Updates the existing color bar legend to new properties. Does nothing if no legend exists.
    
    Parameters:
    
    min - the minimum value in the color table
    
    max - the maximum value in the color table
  - addColorBarLegend
```
public void addColorBarLegend(ColorTable colorTable,
                              double min,
                              double max,
                              Font font,
                              int steps,
                              int precision)
```
    Adds a color bar legend (LUT ramp).
    
    Parameters:
    
    colorTable - the color table
    
    min - the minimum value in the color table
    
    max - the maximum value in the color table
    
    font - the font the legend font.
    
    steps - the number of ticks in the legend. Tick placement is computed automatically if negative.
    
    precision - the number of decimal places of tick labels. scientific notation is used if negative.
  - show
```
public Frame show()
```
    Displays the Viewer and returns a reference to its frame. If the frame has been made displayable, this will simply make the frame visible. Typically, it should only be called once all objects have been added to the scene. If this is an interactive viewer, the 'Controls' dialog is also displayed.
    
    Returns:
    
    the frame containing the viewer.
  - show
```
public Frame show(int width,
                  int height)
```
    Displays the viewer under specified dimensions. Useful when generating scene animations programmatically.
    
    Parameters:
    
    width - the width of the frame. -1 will set width to its maximum.
    
    height - the height of the frame. -1 will set height to its maximum.
    
    Returns:
    
    the frame containing the viewer.
    
    See Also:
    
    show()
  - setFrameSize
```
public void setFrameSize(int width,
                         int height)
```
    Resizes the viewer to the specified dimensions. Useful when generating scene animations programmatically. Does nothing if viewer's frame does not exist.
    
    Parameters:
    
    width - the width of the frame. -1 will set width to its maximum.
    
    height - the height of the frame. -1 will set height to its maximum.
    
    See Also:
    
    show(int, int)
  - setLookAndFeel
```
public void setLookAndFeel(String lookAndFeelName)
```
  - removeTree
```
public boolean removeTree(Tree tree)
```
    Removes the specified Tree.
    
    Parameters:
    
    tree - the tree to be removed.
    
    Returns:
    
    true, if tree was successfully removed.
    
    See Also:
    
    addTree(Tree)
  - removeTree
```
public boolean removeTree(String treeLabel)
```
    Removes the specified Tree.
    
    Parameters:
    
    treeLabel - the key defining the tree to be removed.
    
    Returns:
    
    true, if tree was successfully removed.
    
    See Also:
    
    addTree(Tree)
  - removeMesh
```
public boolean removeMesh(OBJMesh mesh)
```
    Removes the specified OBJ mesh.
    
    Parameters:
    
    mesh - the OBJ mesh to be removed.
    
    Returns:
    
    true, if mesh was successfully removed.
    
    See Also:
    
    loadMesh(String, ColorRGB, double)
  - removeMesh
```
public boolean removeMesh(String meshLabel)
```
    Removes the specified OBJ mesh.
    
    Parameters:
    
    meshLabel - the key defining the OBJ mesh to be removed.
    
    Returns:
    
    true, if mesh was successfully removed.
    
    See Also:
    
    loadMesh(String, ColorRGB, double)
  - removeAllMeshes
```
public void removeAllMeshes()
```
    Removes all loaded OBJ meshes from current viewer
  - removeAllTrees
```
public void removeAllTrees()
```
    Removes all the Trees from current viewer
  - removeAllAnnotations
```
protected void removeAllAnnotations()
```
    Removes all the Annotations from current viewer
  - add
```
public void add(Object object)
```
    Script friendly method to add a supported object (Tree, OBJMesh, AbstractDrawable, etc.) to this viewer. Note that collections of supported objects are also supported, which is an effective way of adding multiple items since the scene is only rebuilt once all items have been added.
    
    Parameters:
    
    object - the object to be added. No exception is triggered if null
    
    Throws:
    
    IllegalArgumentException - if object is not supported
  - remove
```
public void remove(Object object)
```
    Script friendly method to remove an object (Tree, OBJMesh, AbstractDrawable, String (object label), etc.) from this viewer's scene.
    
    Parameters:
    
    object - the object to be removed, or the unique String identifying it. Collections supported.
    
    Throws:
    
    IllegalArgumentException - if object is not supported
  - syncPathManagerList
```
public boolean syncPathManagerList()
                            throws UnsupportedOperationException
```
    (Re)loads the current list of Paths in the Path Manager list.
    
    Returns:
    
    true, if synchronization was apparently successful, false otherwise
    
    Throws:
    
    UnsupportedOperationException - if SNT is not running
  - setVisible
```
public void setVisible(String label,
                       boolean visible)
```
    Toggles the visibility of a rendered Tree, a loaded OBJ mesh, or an annotation.
    
    Parameters:
    
    label - the unique identifier of the Tree (as per addTree(Tree)), the filename/identifier of the loaded OBJ loadMesh(String, ColorRGB, double), or annotation label.
    
    visible - whether the Object should be displayed
  - colorCode
```
public double[] colorCode(Collection<String> treeLabels,
                          String measurement,
                          ColorTable colorTable)
```
    Runs MultiTreeColorMapper on the specified collection of Trees.
    
    Parameters:
    
    treeLabels - the collection of Tree identifiers (as per addTree(Tree)) specifying the Trees to be color mapped
    
    measurement - the mapping measurement e.g., MultiTreeColorMapper.LENGTH MultiTreeColorMapper.N_TIPS, etc.
    
    colorTable - the mapping color table (LUT), e.g., ColorTables.ICE), or any other known to LutService
    
    Returns:
    
    the double[] the limits (min and max) of the mapped values
  - setAnimationEnabled
```
public void setAnimationEnabled(boolean enabled)
```
    Toggles the Viewer's animation.
    
    Parameters:
    
    enabled - if true animation starts. Stops if false
  - setBounds
```
public void setBounds(float xMin,
                      float xMax,
                      float yMin,
                      float yMax,
                      float zMin,
                      float zMax)
```
    Sets a manual bounding box for the scene. The bounding box determines the zoom and framing of the scene. Current view point is logged to the Console when interacting with the Reconstruction Viewer in debug mode.
    
    Parameters:
    
    xMin - the X coordinate of the box origin
    
    xMax - the X coordinate of the box origin opposite
    
    yMin - the Y coordinate of the box origin
    
    yMax - the Y coordinate of the box origin opposite
    
    zMin - the Z coordinate of the box origin
    
    zMax - the X coordinate of the box origin opposite
  - colorCode
```
public double[] colorCode(String treeLabel,
                          String measurement,
                          ColorTable colorTable)
```
    Runs TreeColorMapper on the specified Tree.
    
    Parameters:
    
    treeLabel - the identifier of the Tree (as per addTree(Tree))to be color mapped
    
    measurement - the mapping measurement e.g., TreeColorMapper.PATH_ORDER TreeColorMapper.PATH_DISTANCE, etc.
    
    colorTable - the mapping color table (LUT), e.g., ColorTables.ICE), or any other known to LutService
    
    Returns:
    
    the double[] the limits (min and max) of the mapped values
  - assignUniqueColors
```
public void assignUniqueColors(Collection<String> treeLabels)
```
  - setViewMode
```
public void setViewMode(Viewer3D.ViewMode viewMode)
```
    Renders the scene from a specified camera angle.
    
    Parameters:
    
    viewMode - the view mode, e.g., Viewer3D.ViewMode.DEFAULT, Viewer3D.ViewMode.SIDE , etc.
  - setViewMode
```
public void setViewMode(String viewMode)
```
    Renders the scene from a specified camera angle (script-friendly).
    
    Parameters:
    
    viewMode - the view mode (case insensitive): "side" or "sagittal"; "top" or "coronal"; "perspective" or "overview"; "default" or "".
  - setViewPoint
```
public void setViewPoint(double r,
                         double t)
```
    Renders the scene from a specified camera angle using polar coordinates relative to the the center of the scene. Only X and Y dimensions are required, as the distance to center is automatically computed. Current view point is logged to the Console by calling logSceneControls().
    
    Parameters:
    
    r - the radial coordinate
    
    t - the angle coordinate (in radians)
  - setViewPointCC
```
public void setViewPointCC(double x,
                           double y)
```
    Calls setViewPoint(double, double) using Cartesian coordinates.
    
    Parameters:
    
    x - the X coordinate
    
    y - the Y coordinate
  - addLabel
```
public void addLabel(String label)
```
    Adds an annotation label to the scene.
    
    Parameters:
    
    label - the annotation text
    
    See Also:
    
    setFont(Font, float, ColorRGB), setLabelLocation(float, float)
  - setLabelLocation
```
public void setLabelLocation(float x,
                             float y)
```
    Sets the location for annotation labels
    
    Parameters:
    
    x - the x position of the label
    
    y - the y position of the label
  - setFont
```
public void setFont(Font font,
                    float angle,
                    ColorRGB color)
```
    Sets the font for label annotations
    
    Parameters:
    
    font - the font label, e.g., new Font(Font.SANS_SERIF, Font.ITALIC, 20)
    
    angle - the angle in degrees for rotated labels
    
    color - the font color, e.g., org.scijava.util.Colors.ORANGE
  - saveSnapshot
```
public boolean saveSnapshot()
```
    Saves a snapshot of current scene as a PNG image. Image is saved using an unique time stamp as a file name in the directory specified in the preferences dialog or through setSnapshotDir(String)
    
    Returns:
    
    true, if successful
  - saveSnapshot
```
public boolean saveSnapshot(String filePath)
```
    Saves a snapshot of current scene as a PNG image to the specified path.
    
    Parameters:
    
    filePath - the absolute path of the destination file
    
    Returns:
    
    true, if file was successfully saved
  - saveSnapshot
```
protected boolean saveSnapshot(File file)
                        throws IllegalArgumentException,
                               IOException
```
    Throws:
    
    IllegalArgumentException
    
    IOException
  - setSnapshotDir
```
public void setSnapshotDir(String path)
```
    Sets the directory for storing snapshots.
    
    Parameters:
    
    path - the absolute path to the new snapshot directory.
  - loadMesh
```
public OBJMesh loadMesh(String filePath,
                        ColorRGB color,
                        double transparencyPercent)
                 throws IllegalArgumentException
```
    Loads a Wavefront .OBJ file. Files should be loaded _before_ displaying the scene, otherwise, if the scene is already visible, validate() should be called to ensure all meshes are visible.
    
    Parameters:
    
    filePath - the absolute file path (or URL) of the file to be imported. The filename is used as unique identifier of the object (see setVisible(String, boolean))
    
    color - the color to render the imported file
    
    transparencyPercent - the color transparency (in percentage)
    
    Returns:
    
    the loaded OBJ mesh
    
    Throws:
    
    IllegalArgumentException - if filePath is invalid or file does not contain a compilable mesh
  - addMesh
```
public boolean addMesh(OBJMesh objMesh)
                throws IllegalArgumentException
```
    Loads a Wavefront .OBJ file. Should be called before_ displaying the scene, otherwise, if the scene is already visible, validate() should be called to ensure all meshes are visible.
    
    Parameters:
    
    objMesh - the mesh to be loaded
    
    Returns:
    
    true, if successful
    
    Throws:
    
    IllegalArgumentException - if mesh could not be compiled
  - loadRefBrain
```
public OBJMesh loadRefBrain(String template)
                     throws IllegalArgumentException
```
    Loads the surface mesh of a supported reference brain/neuropil. Internet connection may be required.
    
    Parameters:
    
    template - the reference brain to be loaded (case-insensitive). E.g., "zebrafish" (MP ZBA); "mouse" (Allen CCF); "JFRC2", "JFRC3" "JFRC2018", "FCWB"(adult), "L1", "L3", "VNC" (Drosophila)
    
    Returns:
    
    a reference to the loaded mesh
    
    Throws:
    
    IllegalArgumentException - if template is not recognized
    
    See Also:
    
    AllenUtils, VFBUtils, ZBAtlasUtils
  - getDefColor
```
protected org.jzy3d.colors.Color getDefColor()
```
  - logSceneControls
```
public void logSceneControls()
```
    Logs API calls controlling the scene (view point, bounds, etc.) to Console. Useful for programmatic control of animations.
  - getManagerPanel
```
public Viewer3D.ManagerPanel getManagerPanel()
```
    Returns a reference to 'RV Controls' panel.
    
    Returns:
    
    the ManagerPanel associated with this Viewer, or null if the 'RV Controls' dialog is not being displayed.
  - dispose
```
public void dispose()
```
    Closes and releases all the resources used by this viewer.
  - setDefaultThickness
```
public void setDefaultThickness(float thickness)
```
    Sets the line thickness for rendering Trees that have no specified radius.
    
    Parameters:
    
    thickness - the new line thickness. Note that this value only applies to Paths that have no specified radius
  - setDefaultColor
```
public void setDefaultColor(ColorRGB color)
```
    Sets the default color for rendering Trees.
    
    Parameters:
    
    color - the new color. Note that this value only applies to Paths that have no specified color and no colors assigned to its nodes
  - getDefaultThickness
```
protected float getDefaultThickness()
```
    Returns the default line thickness.
    
    Returns:
    
    the default line thickness used to render Paths without radius
  - setTreeThickness
```
public void setTreeThickness(Collection<String> labels,
                             float thickness,
                             String compartment)
```
    Applies a constant thickness (line width) to a subset of rendered trees.
    
    Parameters:
    
    labels - the Collection of keys specifying the subset of trees
    
    thickness - the thickness (line width)
    
    compartment - a string with at least 2 characters describing the Tree compartment (e.g., 'axon', 'axn', 'dendrite', 'dend', etc.)
    
    See Also:
    
    setTreeThickness(float, String)
  - setTreeThickness
```
public void setTreeThickness(float thickness)
```
    Applies a constant thickness to all rendered trees. Note that by default, trees are rendered using their nodes' diameter.
    
    Parameters:
    
    thickness - the thickness (line width)
    
    See Also:
    
    setTreeThickness(float, String)
  - setTreeThickness
```
public void setTreeThickness(float thickness,
                             String compartment)
```
    Applies a constant thickness (line width) to all rendered trees.Note that by default, trees are rendered using their nodes' diameter.
    
    Parameters:
    
    thickness - the thickness (line width)
    
    compartment - a string with at least 2 characters describing the Tree compartment (e.g., 'axon', 'axn', 'dendrite', 'dend', etc.)
    
    See Also:
    
    setTreeThickness(float)
  - setTreeColor
```
public void setTreeColor(Collection<String> labels,
                         String color,
                         String compartment)
```
    Recolors a subset of rendered trees.
    
    Parameters:
    
    labels - the Collection of keys specifying the subset of trees
    
    color - the color to be applied, either a 1) HTML color codes starting with hash (#), a color preset ("red", "blue", etc.), or integer triples of the form r,g,b and range [0, 255]
    
    compartment - a string with at least 2 characters describing the Tree compartment (e.g., 'axon', 'axn', 'dendrite', 'dend', etc.)
  - setTreeColor
```
public void setTreeColor(Collection<String> labels,
                         ColorRGB color,
                         String compartment)
```
    Recolors a subset of rendered trees.
    
    Parameters:
    
    labels - the Collection of keys specifying the subset of trees
    
    color - the color to be applied.
    
    compartment - a string with at least 2 characters describing the Tree compartment (e.g., 'axon', 'axn', 'dendrite', 'dend', etc.)
  - translate
```
public void translate(Tree tree,
                      SNTPoint offset)
```
    Translates the specified Tree. Does nothing if tree is not present in scene.
    
    Parameters:
    
    tree - the Tree to be translated
    
    offset - the translation offset. If null, tree position will be reset to their original location.
  - translate
```
public void translate(Collection<String> treeLabels,
                      SNTPoint offset)
```
    Translates the specified collection of Trees.
    
    Parameters:
    
    treeLabels - the collection of Tree identifiers (as per addTree(Tree)) specifying the Trees to be translated
    
    offset - the translation offset. If null, trees position will be reset to their original location.
  - setSomasDisplayed
```
public void setSomasDisplayed(Collection<String> labels,
                              boolean displayed)
```
    Toggles the visibility of somas for subset of trees.
    
    Parameters:
    
    labels - the Collection of keys specifying the subset of trees to be affected
    
    displayed - whether soma should be displayed
  - setSomasDisplayed
```
public void setSomasDisplayed(boolean displayed)
```
    Toggles the visibility of somas for all trees in the scene.
    
    Parameters:
    
    displayed - whether soma should be displayed
  - isSNTInstance
```
public boolean isSNTInstance()
```
    Checks whether this instance is SNT's Reconstruction Viewer.
    
    Returns:
    
    true, if SNT instance, false otherwise
  - isActive
```
public boolean isActive()
```
    Checks whether this instance is currently active
    
    Returns:
    
    true, if active, false otherwise
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class Object
  - equals
```
public boolean equals(Object obj)
```
    Overrides:
    
    equals in class Object
  - main
```
public static void main(String[] args)
                 throws InterruptedException
```
    Throws:
    
    InterruptedException

Class Viewer3D

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

DEF_NODE_RADIUS

Constructor Detail

Viewer3D

Viewer3D

Viewer3D

Viewer3D

Method Detail

workaroundIntelGraphicsBug

getID

setSceneUpdatesEnabled

duplicate

validate

setEnableDebugMode

setEnableDarkMode

setSplitDendritesFromAxons

rotate

recordRotation

isDarkModeOn

isSplitDendritesFromAxons

freeze

unfreeze

fromAWTColor

addTree

addTrees

addTrees

addTrees

addTrees

add

getTree

getAnnotation

getMesh

getTrees

getTrees

getMeshes

getMeshes

getAnnotations

annotateSurface

annotateSurface

annotatePoint

annotatePoint

annotatePoints

annotateLine

mergeAnnotations

updateView

zoomTo

addColorBarLegend

addColorBarLegend

updateColorBarLegend

addColorBarLegend

show

show

setFrameSize

setLookAndFeel

removeTree

removeTree

removeMesh

removeMesh

removeAllMeshes

removeAllTrees

removeAllAnnotations

add

remove

syncPathManagerList

setVisible

colorCode

setAnimationEnabled

setBounds

colorCode

assignUniqueColors

setViewMode

setViewMode

setViewPoint

setViewPointCC