JRenderer3D (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- jRenderer3D.JRenderer3D

```
public class JRenderer3D
extends Object
```
The framework JRenderer3D provides the possibility to implement easily a 3D display for ImageJ plugins.
The next section describes the basic scheme for rendering 3D scenes. After initializing a new 3D scene, objects are added, drawing parameters and global render parameters have to be set. At the end a rendering is performed that is written to an image, which can be displayed with ImageJ.

Example:
```
 // Setup 3D rendering
 JRenderer3D jRenderer3D;
 jRenderer3D = new JRenderer3D(xCenter, yCenter, zCenter); // size of the
                                                           // rendered image
 
 // Set or add one or more 3D objects like points or spheres:
 jRenderer3D.addPoint3D(250, 250, 20, 20, Color.WHITE);
 
 // Or lines, texts, cubes:
 jRenderer3D.add3DCube(0, 0, 0, xSize, ySize, zSize, 0xFF000000);
 
 // Set one image for a surface plot
 jRenderer3D.setSurfacePlot(imp);
 
 // Or set a volume (a 3D-stack)
 jRenderer3D.setVolume(imagePlus); // set the volume
 
 // Set the drawing modes
 jRenderer3D.setPoints3DDrawMode(JRenderer3D.POINTS_SPHERES);
 jRenderer3D.setSurfacePlotLut(JRenderer3D.LUT_ORANGE); // select a LUT
 jRenderer3D.setSurfacePlotLight(0.5); // set lighting
 jRenderer3D.setSurfacePlotMode(JRenderer3D.SURFACEPLOT_MESH); // set plot
                                                               // mode to mesh
 
 // Set global parameters
 jRenderer3D.setBackgroundColor(0xFF000050); // dark blue background
 jRenderer3D.setZAspect(4); // set the z-aspect ratio to 4
 jRenderer3D.setTransformScale(1.5); // scale factor
 jRenderer3D.setTransformRotationXYZ(80, 0, 160); // rotation angles (in
                                                  // degrees)
 
 // Render the image
 jRenderer3D.doRendering();
 
 // Get the rendered new image
 Image image = jRenderer3D.getImage();
 
 // And display it:
 ImagePlus impNew = new ImagePlus("Rendered Image", image);
 impNew.show();
 impNew.updateAndDraw();
 
```
Possible 3D elements to draw
Surface

Surface plots can be generate from all image types. Selections, which can be non-rectangular, are supported.

The luminance of an image is interpreted as height for the plot. Internally the image is scaled to a 256x256 image using nearest neighbor sampling. Other dimensions for this image can be set by the setSurfacePlotGridSize method.

The surface plot has several drawing modes which av be set by setSurfacePlotMode:
- Dots: All pixels are drawn as small dots.
- Lines: All pixels are connected in the x-direction.
- Mesh: All pixels are connected in the x- and y-direction.
- Filled: All pixels are connected without leaving holes
Display Colors can be chosen from the original color, grayscale, different LUTs and orange.

Noisy images can be smoothed using the applySurfaceSmoothingFilter method. Setting lighting with the setSurfacePlotLight methode gives the impression that the plot was illuminated and so improves the visibility of small differences.

Volume

Stacks can be shown as volumes or slices. 8, 16 and 32 bit stacks are supported. RGB-stacks are not supported for the moment.

The display mode of a volume may be set with the setVolumeDrawMode method by using these constants:
- VOLUME_SLICE_NEARESTNEIGHBOR: A slice through the volume. No interpolation is performed.
- VOLUME_SLICE_TRILINEAR: A slice through the volume using trilinear interpolation.
- VOLUME_DOTS: Voxels are shown according to their distance, no interpolation is performed.
- VOLUME_PROJECTION_TRILINEAR_BACK: A 3D volume is rendered. The opacity of the voxels is controlled by the setVolumeThreshold method. Values below the threshold are interpreted as transparent.
The setVolumeCutDistance method sets the distance of the slice. For volume rendering only voxels further away than this distance are displayed. The z-aspect ratio of a volume is read automatically, but it can also be set using the setTransformZAspectRatio.

Different LUTs can be used for display by using the setVolumeLut method.

Before rendering a scene a geometrical transform is applied. Rotation angles for the x, y, and z-coordinate achses may be set by the setTransformRotation* methods. the global scale is set by the setTransformScale method. JRenderer3D assumes the following coordinate system:

The z-axis is pointing towards the viewer. The orientation of the z-axis may be changed with the method setTransformZOrientation. The entire scene is centered to the center coordinates that are passed with the constructor of JRenderer3D.

The 3D scene is rendered to an image buffer. The initial size of this buffer is 512x512 pixels: This size can be changed with the setBufferSize method.
Version:

1.0

Author:

Kai Uwe Barthel

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`LUT_BLACK` 3D representations of objects are drawn in black.
`static int`	`LUT_BLUE` 3D representations of objects are drawn in blue.
`static int`	`LUT_FIRE` 3D representations of objects are drawn with fire colors.
`static int`	`LUT_GRADIENT` 3D representations of objects are cored according to their gradient.
`static int`	`LUT_GRADIENT2`
`static int`	`LUT_GRAY` 3D representations of objects are drawn with grayscale colors.
`static int`	`LUT_ORANGE` 3D representations of objects are drawn in orange.
`static int`	`LUT_ORIGINAL` 3D represenations of objects are drawn with their original colors.
`static int`	`LUT_SPECTRUM` 3D representations of objects are drawn with spectrum colors.
`static int`	`LUT_THERMAL` 3D representations of objects are drawn with thermal colors.
`static int`	`POINT_CIRCLE` Draws a point as a (2D) circle.
`static int`	`POINT_DOT` Draws a point as a dot.
`static int`	`POINT_SPHERE` Draws a point as a sphere (slowest).
`static int`	`SURFACEPLOT_DOTS` Draws a surface plot using only dots, illumination is active.
`static int`	`SURFACEPLOT_DOTSNOLIGHT` Draws a surface plot using only dots, no illumination is used (fastest mode).
`static int`	`SURFACEPLOT_FILLED` Draws a filled surface plot .
`static int`	`SURFACEPLOT_ISOLINES` Draws a filled surface plot (Slowest mode).
`static int`	`SURFACEPLOT_LINES` Draws a surface plot using lines.
`static int`	`SURFACEPLOT_MESH` Draws a surface plot using a mesh.
`static int`	`VOLUME_DOTS` Draws a volume using only dots (fastest mode).
`static int`	`VOLUME_PROJECTION_TRILINEAR_FRONT` Draws a volume using trilinear interpolation projection from the front
`static int`	`VOLUME_SLICE_NEAREST_NEIGHBOR` Draws a volume using nearest neighbor interpolation.
`static int`	`VOLUME_SLICE_TRILINEAR` Draws a volume using trilinear interpolation.

Constructor Summary

Constructors
Constructor and Description
`JRenderer3D()` Creates a new JRenderer3D object.
`JRenderer3D(double xCenter, double yCenter, double zCenter)` Creates a new JRenderer3D object.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`add3DCube(int xMin, int yMin, int zMin, int xMax, int yMax, int zMax, Color color)` Adds a cube (drawn with 12 lines) to the 3D scene.
`void`	`add3DCube(int xMin, int yMin, int zMin, int xMax, int yMax, int zMax, int rgb)` Adds a cube (drawn with 12 lines) to the 3D scene.
`void`	`addLine3D(int xStart, int yStart, int zStart, int xEnd, int yEnd, int zEnd, Color color)` Adds a single 3D line to the 3D scene.
`void`	`addLine3D(Line3D line3D)` Adds a single 3D line to the 3D scene.
`void`	`addLines3D(Line3D[] lines3D)` Adds an array of lines to the 3D scene.
`void`	`addPoint3D(int x, int y, int z, int size, Color color, int drawMode)` Adds a point to the 3D scene.
`void`	`addPoint3D(int x, int y, int z, int size, int rgb, int drawMode)` Adds a point to the 3D scene.
`void`	`addPoint3D(Point3D point3D)` Adds a single `Point3D` to the 3D scene.
`void`	`addPoints3D(Point3D[] points3D)` Adds an array with `Point3D` to the 3D scene.
`void`	`addText3D(String text, int x, int y, int z, Color color, int size)` Adds a text to the 3D scene.
`void`	`addText3D(String text, int x, int y, int z, int rgb, int size)` Adds a text to the 3D scene.
`void`	`addText3D(Text3D text3D)` Adds a single 3D text to the 3D scene.
`void`	`addText3D(Text3D[] text3D)` Adds an array of text to the 3D scene.
`void`	`addTextPair3D(Text3D text1_3D, Text3D text2_3D)`
`void`	`applyTransformRotationXYZ(double changeX, double changeY, double changeZ)` Changes the rotation of x-, y-, and z-axis by the values of changeX and changeY.
`void`	`changeTransformRotationXYZ(double changeX, double changeY, double changeZ)` Changes the rotation of x-, y-, and z-axis by the values of changeX and changeY.
`void`	`changeTransformRotationXZ(double changeX, double changeZ)` Changes the rotation of x- and z-axis by the values of changeX and changeY.
`void`	`clearCubes()`
`void`	`clearLines()`
`void`	`clearText()`
`void`	`doRendering()` This methods does the rendering and creates the 3D output.
`int`	`getHeight()` Returns the buffer height of the image.
`Image`	`getImage()` Returns actual rendered image.
`Color`	`getLegendTextColor()`
`int`	`getNumPoints3D()`
`int`	`getSurfacePlotMode()`
`double`	`getTransformRotationX()`
`double`	`getTransformRotationY()`
`double`	`getTransformRotationZ()`
`double`	`getTransformScale()`
`double`	`getTransformZAspectRatio()` Gets the z-aspect ratio (the relative z-height of a voxel).
`int`	`getWidth()` Returns the buffer width of the image.
`void`	`removeLastLine3D()`
`void`	`removeLastPoint3D()`
`void`	`setAxes(boolean axes)`
`void`	`setBackgroundColor(Color color)` Sets the background color of the rendered 3D presentation
`void`	`setBackgroundColor(int rgb)` Sets the background color of the rendered 3D presenation
`void`	`setBufferSize(int width, int height)` Sets the buffer size.
`void`	`setLegend(boolean legend)`
`void`	`setLegendTextColor(Color legendTextColor)`
`void`	`setLines(boolean lines)`
`void`	`setMaxZValue(double maxZ)`
`void`	`setMinZValue(double minZ)`
`void`	`setSurfacePlot(ij.ImagePlus imp)` Creates the surface plot.
`void`	`setSurfacePlotGridSize(int width, int height)` Sets the surface grid size (sampling rate).
`void`	`setSurfacePlotLight(double surfacePlot_light)` Sets the lightning for the surface plot illumination .
`void`	`setSurfacePlotLut(int surfacePlot_lutNr)` Sets the color lut for the surface plot.
`void`	`setSurfacePlotMask(ij.ImagePlus impMask)`
`void`	`setSurfacePlotMinMax(int surfacePlot_min, int surfacePlot_max)`
`void`	`setSurfacePlotMode(int surfacePlot_plotMode)` Sets the surface plot mode.
`void`	`setSurfacePlotTexture(ij.ImagePlus impTexture)`
`void`	`setSurfacePlotWithTexture(ij.ImagePlus imp, ij.ImagePlus impTexture)` Creates the surface plot with texture.
`void`	`setSurfaceSmoothingFactor(double smoothRadius)` Aplies a smoothing to the surface plot data
`void`	`setText(boolean text)`
`void`	`setTransformMaxDistance(double maxDistance)`
`void`	`setTransformPerspective(double perspective)`
`void`	`setTransformRotationX(double ax)` Sets the rotation on the x-axis.
`void`	`setTransformRotationXYZ(double ax, double ay, double az)` Sets the rotation on x-, y- and z-axis.
`void`	`setTransformRotationXZ(double ax, double az)` Sets the rotation on both x- and z-axis.
`void`	`setTransformRotationY(double ay)` Sets the rotation on the y-axis.
`void`	`setTransformRotationZ(double az)` Sets the rotation on the z-axis.
`void`	`setTransformScale(double scale)` Sets scale of the redered 3D scene.
`void`	`setTransformZAspectRatio(double zAspectRatio)` Sets the z-aspect ratio (the relative z-height of a voxel).
`void`	`setTransformZOrientation(int zOrientation)` Chooses the coordinate system.
`void`	`setVolume(ij.ImagePlus imagePlus)` Sets a volume stack.
`void`	`setVolumeCutDistance(int volume_cutDist)` Sets the view distance.
`void`	`setVolumeDotsSubsampling(int volume_dotsDeltaX, int volume_dotsDeltaY, int volume_dotsDeltaZ)` Set subsampling factors (used by the drawing mode volume dots).
`void`	`setVolumeDrawMode(int volume_drawMode)` Sets the mode for drawing volumes.
`void`	`setVolumeLut(int volume_lutNr)`
`void`	`setVolumeThreshold(int threshold)` Sets the threshold.
`void`	`showRotation()`
`void`	`surfacePlotSetInverse(boolean b)`

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

- Field Detail
  - POINT_SPHERE
```
public static final int POINT_SPHERE
```
    Draws a point as a sphere (slowest).
    
    See Also:
    
    Constant Field Values
  - POINT_CIRCLE
```
public static final int POINT_CIRCLE
```
    Draws a point as a (2D) circle.
    
    See Also:
    
    Constant Field Values
  - POINT_DOT
```
public static final int POINT_DOT
```
    Draws a point as a dot. Size information has no effect.
    
    See Also:
    
    Constant Field Values
  - SURFACEPLOT_DOTSNOLIGHT
```
public static final int SURFACEPLOT_DOTSNOLIGHT
```
    Draws a surface plot using only dots, no illumination is used (fastest mode).
    
    See Also:
    
    Constant Field Values
  - SURFACEPLOT_DOTS
```
public static final int SURFACEPLOT_DOTS
```
    Draws a surface plot using only dots, illumination is active.
    
    See Also:
    
    Constant Field Values
  - SURFACEPLOT_LINES
```
public static final int SURFACEPLOT_LINES
```
    Draws a surface plot using lines. Number of lines can be adjusted.
    
    See Also:
    
    Constant Field Values
  - SURFACEPLOT_MESH
```
public static final int SURFACEPLOT_MESH
```
    Draws a surface plot using a mesh. Mesh size can be adapted.
    
    See Also:
    
    Constant Field Values
  - SURFACEPLOT_FILLED
```
public static final int SURFACEPLOT_FILLED
```
    Draws a filled surface plot .
    
    See Also:
    
    Constant Field Values
  - SURFACEPLOT_ISOLINES
```
public static final int SURFACEPLOT_ISOLINES
```
    Draws a filled surface plot (Slowest mode).
    
    See Also:
    
    Constant Field Values
  - VOLUME_DOTS
```
public static final int VOLUME_DOTS
```
    Draws a volume using only dots (fastest mode).
    
    See Also:
    
    Constant Field Values
  - VOLUME_SLICE_NEAREST_NEIGHBOR
```
public static final int VOLUME_SLICE_NEAREST_NEIGHBOR
```
    Draws a volume using nearest neighbor interpolation.
    
    See Also:
    
    Constant Field Values
  - VOLUME_SLICE_TRILINEAR
```
public static final int VOLUME_SLICE_TRILINEAR
```
    Draws a volume using trilinear interpolation.
    
    See Also:
    
    Constant Field Values
  - VOLUME_PROJECTION_TRILINEAR_FRONT
```
public static final int VOLUME_PROJECTION_TRILINEAR_FRONT
```
    Draws a volume using trilinear interpolation projection from the front
    
    See Also:
    
    Constant Field Values
  - LUT_ORIGINAL
```
public static final int LUT_ORIGINAL
```
    3D represenations of objects are drawn with their original colors.
    
    See Also:
    
    Constant Field Values
  - LUT_GRAY
```
public static final int LUT_GRAY
```
    3D representations of objects are drawn with grayscale colors.
    
    See Also:
    
    Constant Field Values
  - LUT_SPECTRUM
```
public static final int LUT_SPECTRUM
```
    3D representations of objects are drawn with spectrum colors.
    
    See Also:
    
    Constant Field Values
  - LUT_FIRE
```
public static final int LUT_FIRE
```
    3D representations of objects are drawn with fire colors.
    
    See Also:
    
    Constant Field Values
  - LUT_THERMAL
```
public static final int LUT_THERMAL
```
    3D representations of objects are drawn with thermal colors.
    
    See Also:
    
    Constant Field Values
  - LUT_ORANGE
```
public static final int LUT_ORANGE
```
    3D representations of objects are drawn in orange.
    
    See Also:
    
    Constant Field Values
  - LUT_BLUE
```
public static final int LUT_BLUE
```
    3D representations of objects are drawn in blue.
    
    See Also:
    
    Constant Field Values
  - LUT_BLACK
```
public static final int LUT_BLACK
```
    3D representations of objects are drawn in black.
    
    See Also:
    
    Constant Field Values
  - LUT_GRADIENT
```
public static final int LUT_GRADIENT
```
    3D representations of objects are cored according to their gradient.
    
    See Also:
    
    Constant Field Values
  - LUT_GRADIENT2
```
public static final int LUT_GRADIENT2
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - JRenderer3D
```
public JRenderer3D()
```
    Creates a new JRenderer3D object. This has always to be the first step to generate a 3D scene. The center is assumed at (0,0,0)
  - JRenderer3D
```
public JRenderer3D(double xCenter,
                   double yCenter,
                   double zCenter)
```
    Creates a new JRenderer3D object.
    This has always to be the first step to generate a 3D scene.
    
    Parameters:
    
    xCenter - The x-coordinate of the rotation / plot center.
    
    yCenter - The y-coordinate of the rotation / plot center.
    
    zCenter - The z-coordinate of the rotation / plot center.
- Method Detail
  - showRotation
```
public void showRotation()
```
  - getLegendTextColor
```
public Color getLegendTextColor()
```
  - setLegendTextColor
```
public void setLegendTextColor(Color legendTextColor)
```
  - doRendering
```
public void doRendering()
```
    This methods does the rendering and creates the 3D output. It has to be redone after all setting changes (scale, angle, surface modes, lightning modes, color modes etc.) Draws all given input data (lines, text, points, cubes, surfaces).
  - addPoints3D
```
public void addPoints3D(Point3D[] points3D)
```
    Adds an array with Point3D to the 3D scene.
    
    Parameters:
    
    points3D - array with points in a threedimensional coordinate system
  - addPoint3D
```
public void addPoint3D(Point3D point3D)
```
    Adds a single Point3D to the 3D scene.
    
    Parameters:
    
    point3D - the 3D point to add
  - addPoint3D
```
public void addPoint3D(int x,
                       int y,
                       int z,
                       int size,
                       Color color,
                       int drawMode)
```
    Adds a point to the 3D scene.
    
    Parameters:
    
    x -
    
    y -
    
    z -
    
    size -
    
    color -
    
    drawMode -
  - addPoint3D
```
public void addPoint3D(int x,
                       int y,
                       int z,
                       int size,
                       int rgb,
                       int drawMode)
```
    Adds a point to the 3D scene.
    
    Parameters:
    
    x -
    
    y -
    
    z -
    
    size -
    
    rgb -
    
    drawMode -
  - setSurfacePlotMask
```
public void setSurfacePlotMask(ij.ImagePlus impMask)
```
  - setSurfacePlot
```
public void setSurfacePlot(ij.ImagePlus imp)
```
    Creates the surface plot.
    
    Parameters:
    
    imp - The images to be drawn in 3D.
  - setSurfacePlotTexture
```
public void setSurfacePlotTexture(ij.ImagePlus impTexture)
```
  - setSurfacePlotWithTexture
```
public void setSurfacePlotWithTexture(ij.ImagePlus imp,
                                      ij.ImagePlus impTexture)
```
    Creates the surface plot with texture.
    
    Parameters:
    
    imp - The images to be drawn in 3D.
    
    impTexture - The image which shall be used as texture
  - setSurfacePlotMode
```
public void setSurfacePlotMode(int surfacePlot_plotMode)
```
    Sets the surface plot mode.
    Available options:
    - PLOT_DOTSNOLIGHT: if used, no lightning options are applied (fastest)
    - PLOT_DOTS: draws dots
    - PLOT_LINES: draws lines
    - PLOT_MESH: draws a mesh
    - PLOT_FILLED: fills the 3d object completely (slowest)
    Parameters:
    
    surfacePlot_plotMode - the surface plot mode
  - getSurfacePlotMode
```
public int getSurfacePlotMode()
```
  - setVolumeDrawMode
```
public void setVolumeDrawMode(int volume_drawMode)
```
    Sets the mode for drawing volumes.
    - VOLUME_DOTS: draws volumes with dots(fastest)
    Parameters:
    
    volume_drawMode -
  - setVolumeLut
```
public void setVolumeLut(int volume_lutNr)
```
  - setVolumeDotsSubsampling
```
public void setVolumeDotsSubsampling(int volume_dotsDeltaX,
                                     int volume_dotsDeltaY,
                                     int volume_dotsDeltaZ)
```
    Set subsampling factors (used by the drawing mode volume dots). This allows faster drawing in the VOLUME_DOTS mode. (default values are 1)
    
    Parameters:
    
    volume_dotsDeltaX - subsampling factor in x direction
    
    volume_dotsDeltaY - subsampling factor in y direction
    
    volume_dotsDeltaZ - subsampling factor in z direction
  - setVolumeCutDistance
```
public void setVolumeCutDistance(int volume_cutDist)
```
    Sets the view distance. Just the voxels behind the distance are drawn.
    
    Parameters:
    
    volume_cutDist - the cut distance
  - setSurfacePlotGridSize
```
public void setSurfacePlotGridSize(int width,
                                   int height)
```
    Sets the surface grid size (sampling rate). Should be set to an integer fraction of the image of which the surface plot has to be generated.
    
    Parameters:
    
    width - the width of surface grid
    
    height - the height of surface grid
  - setTransformZOrientation
```
public void setTransformZOrientation(int zOrientation)
```
    Chooses the coordinate system.
    
    Parameters:
    
    zOrientation -
    -1: left hand coordinate system
    1: right hand coordinate system
  - setTransformScale
```
public void setTransformScale(double scale)
```
    Sets scale of the redered 3D scene.
    
    Parameters:
    
    scale - scales the scene
  - setTransformRotationX
```
public void setTransformRotationX(double ax)
```
    Sets the rotation on the x-axis.
    
    Parameters:
    
    ax - angle in degree
  - setTransformRotationY
```
public void setTransformRotationY(double ay)
```
    Sets the rotation on the y-axis.
    
    Parameters:
    
    ay - angle in degree
  - setTransformRotationZ
```
public void setTransformRotationZ(double az)
```
    Sets the rotation on the z-axis.
    
    Parameters:
    
    az - angle in degree
  - setTransformRotationXZ
```
public void setTransformRotationXZ(double ax,
                                   double az)
```
    Sets the rotation on both x- and z-axis.
    
    Parameters:
    
    ax - angle of x-axis in degree
    
    az - angle of z-axis in degree
  - setTransformRotationXYZ
```
public void setTransformRotationXYZ(double ax,
                                    double ay,
                                    double az)
```
    Sets the rotation on x-, y- and z-axis.
    
    Parameters:
    
    ax - rotation angle of x-axis in degree
    
    ay - rotation angle of y-axis in degree
    
    az - rotation angle of z-axis in degree
  - changeTransformRotationXZ
```
public void changeTransformRotationXZ(double changeX,
                                      double changeZ)
```
    Changes the rotation of x- and z-axis by the values of changeX and changeY.
    
    Parameters:
    
    changeX - change of rotation angle of x-axis in degree
    
    changeZ - change of rotation angle of z-axis in degree
  - applyTransformRotationXYZ
```
public void applyTransformRotationXYZ(double changeX,
                                      double changeY,
                                      double changeZ)
```
    Changes the rotation of x-, y-, and z-axis by the values of changeX and changeY.
    
    Parameters:
    
    changeX - change of rotation angle of x-axis in degree
    
    changeY - change of rotation angle of y-axis in degree
    
    changeZ - change of rotation angle of z-axis in degree
  - changeTransformRotationXYZ
```
public void changeTransformRotationXYZ(double changeX,
                                       double changeY,
                                       double changeZ)
```
    Changes the rotation of x-, y-, and z-axis by the values of changeX and changeY.
    
    Parameters:
    
    changeX - change of rotation angle of x-axis in degree
    
    changeY - change of rotation angle of y-axis in degree
    
    changeZ - change of rotation angle of z-axis in degree
  - setBackgroundColor
```
public void setBackgroundColor(int rgb)
```
    Sets the background color of the rendered 3D presenation
    
    Parameters:
    
    rgb - the background color (argb int)
  - setBackgroundColor
```
public void setBackgroundColor(Color color)
```
    Sets the background color of the rendered 3D presentation
    
    Parameters:
    
    color - Color
  - addLines3D
```
public void addLines3D(Line3D[] lines3D)
```
    Adds an array of lines to the 3D scene.
    
    Parameters:
    
    lines3D - array of 3d lines
  - addLine3D
```
public void addLine3D(Line3D line3D)
```
    Adds a single 3D line to the 3D scene.
    
    Parameters:
    
    line3D - the 3D line to add
  - addLine3D
```
public void addLine3D(int xStart,
                      int yStart,
                      int zStart,
                      int xEnd,
                      int yEnd,
                      int zEnd,
                      Color color)
```
    Adds a single 3D line to the 3D scene.
    
    Parameters:
    
    xStart -
    
    yStart -
    
    zStart -
    
    xEnd -
    
    yEnd -
    
    zEnd -
    
    color -
  - clearLines
```
public void clearLines()
```
  - addText3D
```
public void addText3D(Text3D[] text3D)
```
    Adds an array of text to the 3D scene.
    
    Parameters:
    
    text3D -
  - addText3D
```
public void addText3D(String text,
                      int x,
                      int y,
                      int z,
                      Color color,
                      int size)
```
    Adds a text to the 3D scene.
    
    Parameters:
    
    text -
    
    x - the x position of the text
    
    y - the y position
    
    z - the z position
    
    color - the text color
    
    size - the font size
  - addText3D
```
public void addText3D(String text,
                      int x,
                      int y,
                      int z,
                      int rgb,
                      int size)
```
    Adds a text to the 3D scene.
    
    Parameters:
    
    text -
    
    x - the x position of the text
    
    y - the y position
    
    z - the z position
    
    rgb - the text color
    
    size - the font size
  - addText3D
```
public void addText3D(Text3D text3D)
```
    Adds a single 3D text to the 3D scene.
    
    Parameters:
    
    text3D - the 3D text to add
  - addTextPair3D
```
public void addTextPair3D(Text3D text1_3D,
                          Text3D text2_3D)
```
  - clearText
```
public void clearText()
```
  - setBufferSize
```
public void setBufferSize(int width,
                          int height)
```
    Sets the buffer size. (The size of the rendered 2D image)
    
    Parameters:
    
    width - The width to be set.
    
    height - The height to be set.
  - add3DCube
```
public void add3DCube(int xMin,
                      int yMin,
                      int zMin,
                      int xMax,
                      int yMax,
                      int zMax,
                      Color color)
```
    Adds a cube (drawn with 12 lines) to the 3D scene.
    
    Parameters:
    
    xMin - minimum value x
    
    yMin - minimum value y
    
    zMin - minimum value z
    
    xMax - maximum value x
    
    yMax - maximum value y
    
    zMax - maximum value z
    
    color - Color of cube lines (argb)
  - add3DCube
```
public void add3DCube(int xMin,
                      int yMin,
                      int zMin,
                      int xMax,
                      int yMax,
                      int zMax,
                      int rgb)
```
    Adds a cube (drawn with 12 lines) to the 3D scene.
    
    Parameters:
    
    xMin - minimum value x
    
    yMin - minimum value y
    
    zMin - minimum value z
    
    xMax - maximum value x
    
    yMax - maximum value y
    
    zMax - maximum value z
    
    rgb - Color of cube lines (argb)
  - clearCubes
```
public void clearCubes()
```
  - setVolume
```
public void setVolume(ij.ImagePlus imagePlus)
```
    Sets a volume stack.
    
    Parameters:
    
    imagePlus - the volume stack to be set
  - setSurfacePlotLut
```
public void setSurfacePlotLut(int surfacePlot_lutNr)
```
    Sets the color lut for the surface plot.
    - ORIGINAL
    - GRAY
    - SPECTRUM
    - FIRE
    - THERMAL
    - ORANGE
    - BLUE
    - BLACK
    Parameters:
    
    surfacePlot_lutNr - color of look-up-table
  - setSurfacePlotLight
```
public void setSurfacePlotLight(double surfacePlot_light)
```
    Sets the lightning for the surface plot illumination .
    - 0: no light
    - 1: strong light
    Parameters:
    
    surfacePlot_light - intensity value between 0 and 1 (default is 0)
  - setSurfacePlotMinMax
```
public void setSurfacePlotMinMax(int surfacePlot_min,
                                 int surfacePlot_max)
```
  - setSurfaceSmoothingFactor
```
public void setSurfaceSmoothingFactor(double smoothRadius)
```
    Aplies a smoothing to the surface plot data
    
    Parameters:
    
    smoothRadius - the radius of the smoothing kernel
  - setVolumeThreshold
```
public void setVolumeThreshold(int threshold)
```
    Sets the threshold. All voxels below this threshold are displayed transparent.
    
    Parameters:
    
    threshold - Threshold to be set (0 .. 255).
  - setTransformZAspectRatio
```
public void setTransformZAspectRatio(double zAspectRatio)
```
    Sets the z-aspect ratio (the relative z-height of a voxel). When setting a volume, the z-aspect ratio is reset to ratio read from the stack. If the z-aspect ratio needs to set this has to be done after calling the setVolume method.
    
    Parameters:
    
    zAspectRatio - z-aspect ratio (the relative z-ratio of a voxel) to be set.
  - getWidth
```
public int getWidth()
```
    Returns the buffer width of the image.
    
    Returns:
    
    buffer width
  - getHeight
```
public int getHeight()
```
    Returns the buffer height of the image.
    
    Returns:
    
    buffer height
  - getImage
```
public Image getImage()
```
    Returns actual rendered image.
    
    Returns:
    
    image
  - getTransformZAspectRatio
```
public double getTransformZAspectRatio()
```
    Gets the z-aspect ratio (the relative z-height of a voxel).
    
    Returns:
    
    the z-aspect ratio
  - removeLastPoint3D
```
public void removeLastPoint3D()
```
  - removeLastLine3D
```
public void removeLastLine3D()
```
  - getNumPoints3D
```
public int getNumPoints3D()
```
  - setTransformPerspective
```
public void setTransformPerspective(double perspective)
```
  - setTransformMaxDistance
```
public void setTransformMaxDistance(double maxDistance)
```
  - setAxes
```
public void setAxes(boolean axes)
```
  - setLines
```
public void setLines(boolean lines)
```
  - setText
```
public void setText(boolean text)
```
  - setLegend
```
public void setLegend(boolean legend)
```
  - surfacePlotSetInverse
```
public void surfacePlotSetInverse(boolean b)
```
  - getTransformScale
```
public double getTransformScale()
```
  - setMinZValue
```
public void setMinZValue(double minZ)
```
  - setMaxZValue
```
public void setMaxZValue(double maxZ)
```
  - getTransformRotationX
```
public double getTransformRotationX()
```
  - getTransformRotationY
```
public double getTransformRotationY()
```
  - getTransformRotationZ
```
public double getTransformRotationZ()
```

Class JRenderer3D

Example:

Possible 3D elements to draw

Surface

Volume

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

POINT_SPHERE

POINT_CIRCLE

POINT_DOT

SURFACEPLOT_DOTSNOLIGHT

SURFACEPLOT_DOTS

SURFACEPLOT_LINES

SURFACEPLOT_MESH

SURFACEPLOT_FILLED

SURFACEPLOT_ISOLINES

VOLUME_DOTS

VOLUME_SLICE_NEAREST_NEIGHBOR

VOLUME_SLICE_TRILINEAR

VOLUME_PROJECTION_TRILINEAR_FRONT

LUT_ORIGINAL

LUT_GRAY

LUT_SPECTRUM

LUT_FIRE

LUT_THERMAL

LUT_ORANGE

LUT_BLUE

LUT_BLACK

LUT_GRADIENT

LUT_GRADIENT2

Constructor Detail

JRenderer3D

JRenderer3D

Method Detail

showRotation

getLegendTextColor

setLegendTextColor

doRendering

addPoints3D

addPoint3D

addPoint3D

addPoint3D

setSurfacePlotMask

setSurfacePlot

setSurfacePlotTexture

setSurfacePlotWithTexture

setSurfacePlotMode

getSurfacePlotMode

setVolumeDrawMode

setVolumeLut

setVolumeDotsSubsampling

setVolumeCutDistance

setSurfacePlotGridSize

setTransformZOrientation

setTransformScale

setTransformRotationX

setTransformRotationY

setTransformRotationZ

setTransformRotationXZ

setTransformRotationXYZ

changeTransformRotationXZ

applyTransformRotationXYZ

changeTransformRotationXYZ

setBackgroundColor

setBackgroundColor

addLines3D

addLine3D

addLine3D

clearLines

addText3D

addText3D

addText3D

addText3D

addTextPair3D

clearText

setBufferSize

add3DCube