icy.vtk

Class VtkUtil

java.lang.Object

icy.vtk.VtkUtil

public class VtkUtil
extends java.lang.Object

Author:

Stephane

Field Summary

Fields

Modifier and Type	Field and Description
static int	VTK_BIT
static int	VTK_CHAR
static int	VTK_CUBIC_INTERPOLATION
static int	VTK_DOUBLE
static int	VTK_FLOAT
static int	VTK_FLY_CLOSEST_TRIAD
static int	VTK_FLY_FURTHEST_TRIAD
static int	VTK_FLY_OUTER_EDGES
static int	VTK_FLY_STATIC_EDGES
static int	VTK_FLY_STATIC_TRIAD
static int	VTK_GRID_LINES_ALL
static int	VTK_GRID_LINES_CLOSEST
static int	VTK_GRID_LINES_FURTHEST
static int	VTK_ID
static int	VTK_INT
static int	VTK_LINEAR_INTERPOLATION
static int	VTK_LONG
static int	VTK_NEAREST_INTERPOLATION
static int	VTK_SHORT
static int	VTK_SIGNED_CHAR
static int	VTK_TICKS_BOTH
static int	VTK_TICKS_INSIDE
static int	VTK_TICKS_OUTSIDE
static int	VTK_UNSIGNED_CHAR
static int	VTK_UNSIGNED_INT
static int	VTK_UNSIGNED_LONG
static int	VTK_UNSIGNED_SHORT
static int	VTK_VOID

Constructor Summary

Constructors

Constructor and Description
VtkUtil()

Method Summary

Methods

Modifier and Type	Method and Description
static void	addActor(vtk.vtkRenderer renderer, vtk.vtkActor actor) Deprecated. Use addProp(vtkRenderer, vtkProp) instead.
static void	addActor2D(vtk.vtkRenderer renderer, vtk.vtkActor2D actor) Deprecated. Use addProp(vtkRenderer, vtkProp) instead.
static void	addProp(vtk.vtkRenderer renderer, vtk.vtkProp prop) Add an actor (vtkProp) to the specified renderer.
static void	addProps(vtk.vtkRenderer renderer, vtk.vtkProp[] props) Add an array of actor (vtkProp) to the specified renderer.
static boolean	findActor(vtk.vtkRenderer renderer, vtk.vtkActor actor) Deprecated. Use hasProp(vtkRenderer, vtkProp) instead.
static boolean	findActor2D(vtk.vtkRenderer renderer, vtk.vtkActor2D actor) Deprecated. Use hasProp(vtkRenderer, vtkProp) instead.
static boolean	findProp(vtk.vtkRenderer renderer, vtk.vtkProp actor) Deprecated. Use hasProp(vtkRenderer, vtkProp) instead.
static vtk.vtkColorTransferFunction	getBinaryColorMap(java.awt.Color color) Creates and returns a binary color map in vtkColorTransferFunction format where 0 value is black and 1 is set to specified color.
static vtk.vtkImageData	getBinaryImageData(ROI roi, int sz, int t) Creates and returns a 3D binary (0/1 values) vtkImageData object corresponding to the ROI 3D boolean mask (C dimension is not considered) at specified T position.
static vtk.vtkImageData	getBinaryImageData(vtk.vtkPolyData polyData, double[] space) Transforms a vtkPolyData object to binary (0/1 values) vtkImageData
static vtk.vtkPiecewiseFunction	getBinaryOpacityMap(double opacity) Creates and returns a binary opacity map in vtkPiecewiseFunction format where 0 is 100% transparent and 1 to the specified opacity value.
static BooleanMask3D	getBooleanMaskFromBinaryImage(vtk.vtkImageData image, boolean optimizeBounds) Returns a BooleanMask3D from a binary (0/1 values) vtkImageData.
static vtk.vtkCellArray	getCells(int numCell, int[] cells) Get vtkCellArray from a 1D prepared cells array ( {n, i1, i2, ..., n, i1, i2,...} )
static vtk.vtkColorTransferFunction	getColorMap(LUT.LUTChannel lutChannel) Creates and returns the color map in vtkColorTransferFunction format from the specified LUT.LUTChannel.
static vtk.vtkDoubleArray	getDoubleArray(double[] array)
static vtk.vtkFloatArray	getFloatArray(float[] array)
static vtk.vtkIdTypeArray	getIdTypeArray(int[] array)
static vtk.vtkImageData	getImageData(java.lang.Object data, DataType dataType, int sizeX, int sizeY, int sizeZ, int sizeC) Creates and returns a vtkImageData object from the specified 1D array data.
static vtk.vtkImageData	getImageData(Sequence sequence, int posT, int posC) Build and return volume image data from given Sequence object.
static vtk.vtkIntArray	getIntArray(int[] array)
static java.lang.Object	getJavaArray(vtk.vtkDataArray dataArray) Returns a native java array from the specified vtkDataArray.
static int[]	getJavaArray(vtk.vtkIdTypeArray array)
static vtk.vtkProp[]	getLayerProps(Layer layer) Returns the vtkProp from the specified Layer object.
static vtk.vtkProp[]	getLayersProps(java.util.List<Layer> layers) Returns all vtkProp from the specified list of Layer object.
static vtk.vtkLongArray	getLongArray(long[] array)
static vtk.vtkPiecewiseFunction	getOpacityMap(LUT.LUTChannel lutChannel) Creates and returns the opacity map in vtkPiecewiseFunction format from the specified LUT.LUTChannel.
static vtk.vtkPolyData	getOutline(double xMin, double xMax, double yMin, double yMax, double zMin, double zMax) Returns a cube polydata object representing the specified bounding box coordinate
static vtk.vtkPoints	getPoints(double[] points) Get vtkPoints from double[]
static vtk.vtkPoints	getPoints(double[][] points) Get vtkPoints from double[][3]
static vtk.vtkPoints	getPoints(float[] points) Get vtkPoints from float[]
static vtk.vtkPoints	getPoints(float[][] points) Get vtkPoints from float[][3]
static vtk.vtkPoints	getPoints(int[] points) Get vtkPoints from int[]
static vtk.vtkPoints	getPoints(int[][] points) Get vtkPoints from int[][3]
static vtk.vtkPolyData	getPolyDataFromDataSet(vtk.vtkDataSet dataSet) Returns a vtkPolyData from vtkDataSet
static vtk.vtkPolyData	getPolyDataFromPoints(vtk.vtkPoints points) Returns a simple cell vtkPolyData from vtkPoints
static vtk.vtkProp[]	getProps(vtk.vtkRenderer renderer) Return all actor / view prop from the specified renderer
static ROI	getROIFromBinaryImage(vtk.vtkImageData image, boolean force3DROI) Deprecated. Uses #getBooleanMaskFromBinaryImage(vtkImageData) then ROI3DArea.ROI3DArea(BooleanMask3D) instead.
static vtk.vtkShortArray	getShortArray(short[] array)
static vtk.vtkPolyData	getSurfaceFromImage(vtk.vtkImageData imageData, double threshold) Create a 3D surface in VTK polygon format from the input VTK image data.
static vtk.vtkPolyData	getSurfaceFromOBJ(java.lang.String objPath) Read a OBJ 3D model file and returns it in VTK mesh format (vtkPolyData)
static vtk.vtkTransform	getTransform(double[] off, double[] scale, double[] rot) Get VTK transform object from specified transform infos
static vtk.vtkUnsignedCharArray	getUCharArray(byte[] array)
static vtk.vtkUnsignedIntArray	getUIntArray(int[] array)
static vtk.vtkUnsignedLongArray	getULongArray(long[] array)
static vtk.vtkUnsignedShortArray	getUShortArray(short[] array)
static vtk.vtkDataArray	getVtkArray(java.lang.Object array, boolean signed)
static int	getVtkType(DataType type) Returns the VTK type corresponding to the specified DataType
static boolean	hasProp(vtk.vtkRenderer renderer, vtk.vtkProp actor) Return true if the renderer contains the specified actor / view prop
static vtk.vtkImageData	polyDataToImageData(vtk.vtkPolyData polyData, double[] space) Deprecated. Use getBinaryImageData(vtkPolyData, double[]) instead.
static int[]	prepareCells(int[][] indexes) Return a 1D cells array from a 2D indexes array
static int[]	prepareCells(int numVertexPerCell, int[] indexes) Return a 1D cells array from a 1D indexes array and num vertex per cell (polygon)
static void	removeProp(vtk.vtkRenderer renderer, vtk.vtkProp actor) Remove an actor from the specified renderer.
static boolean	setOutlineBounds(vtk.vtkPolyData outline, double xMin, double xMax, double yMin, double yMax, double zMin, double zMax, VtkCanvas canvas) Set the bounds of specified outline polydata object (previously created with VtkUtil.getOutline(..)
static void	setPolyDataColor(vtk.vtkPolyData polyData, java.awt.Color color, VtkCanvas canvas) Set the Color of the specified vtkPolyData object.
static vtk.vtkPolyData	transformPolyData(vtk.vtkPolyData polyData, double[] off, double[] scale, double[] rot) Transform a polyData using specified rotation, scaling and offset informations (3D)
static vtk.vtkPolyData	transformPolyData(vtk.vtkPolyData polyData, vtk.vtkAbstractTransform transform) Transform a polyData using specified rotation, scaling and offset informations
static vtk.vtkObject[]	vtkCollectionToArray(vtk.vtkCollection collection) Transforms a vtkCollection to an array
static void	vtkGC() VTK forced garbage collection

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

VTK_VOID

public static final int VTK_VOID

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Constant Field Values

VTK_BIT

public static final int VTK_BIT

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VTK_CHAR

public static final int VTK_CHAR

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VTK_SIGNED_CHAR

public static final int VTK_SIGNED_CHAR

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VTK_UNSIGNED_CHAR

public static final int VTK_UNSIGNED_CHAR

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VTK_SHORT

public static final int VTK_SHORT

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VTK_UNSIGNED_SHORT

public static final int VTK_UNSIGNED_SHORT

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Constant Field Values

VTK_INT

public static final int VTK_INT

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Constant Field Values

VTK_UNSIGNED_INT

public static final int VTK_UNSIGNED_INT

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VTK_LONG

public static final int VTK_LONG

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VTK_UNSIGNED_LONG

public static final int VTK_UNSIGNED_LONG

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VTK_FLOAT

public static final int VTK_FLOAT

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VTK_DOUBLE

public static final int VTK_DOUBLE

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VTK_ID

public static final int VTK_ID

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VTK_NEAREST_INTERPOLATION

public static final int VTK_NEAREST_INTERPOLATION

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VTK_LINEAR_INTERPOLATION

public static final int VTK_LINEAR_INTERPOLATION

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VTK_CUBIC_INTERPOLATION

public static final int VTK_CUBIC_INTERPOLATION

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Constant Field Values

VTK_FLY_OUTER_EDGES

public static final int VTK_FLY_OUTER_EDGES

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VTK_FLY_CLOSEST_TRIAD

public static final int VTK_FLY_CLOSEST_TRIAD

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VTK_FLY_FURTHEST_TRIAD

public static final int VTK_FLY_FURTHEST_TRIAD

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VTK_FLY_STATIC_TRIAD

public static final int VTK_FLY_STATIC_TRIAD

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VTK_FLY_STATIC_EDGES

public static final int VTK_FLY_STATIC_EDGES

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VTK_TICKS_INSIDE

public static final int VTK_TICKS_INSIDE

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VTK_TICKS_OUTSIDE

public static final int VTK_TICKS_OUTSIDE

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VTK_TICKS_BOTH

public static final int VTK_TICKS_BOTH

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VTK_GRID_LINES_ALL

public static final int VTK_GRID_LINES_ALL

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VTK_GRID_LINES_CLOSEST

public static final int VTK_GRID_LINES_CLOSEST

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VTK_GRID_LINES_FURTHEST

public static final int VTK_GRID_LINES_FURTHEST

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Constant Field Values

Constructor Detail

VtkUtil

public VtkUtil()

Method Detail

getVtkType

public static int getVtkType(DataType type)

Returns the VTK type corresponding to the specified DataType

getVtkArray

public static vtk.vtkDataArray getVtkArray(java.lang.Object array,
                           boolean signed)

getUCharArray

public static vtk.vtkUnsignedCharArray getUCharArray(byte[] array)

getUShortArray

public static vtk.vtkUnsignedShortArray getUShortArray(short[] array)

getUIntArray

public static vtk.vtkUnsignedIntArray getUIntArray(int[] array)

getULongArray

public static vtk.vtkUnsignedLongArray getULongArray(long[] array)

getShortArray

public static vtk.vtkShortArray getShortArray(short[] array)

getIntArray

public static vtk.vtkIntArray getIntArray(int[] array)

getLongArray

public static vtk.vtkLongArray getLongArray(long[] array)

getFloatArray

public static vtk.vtkFloatArray getFloatArray(float[] array)

getDoubleArray

public static vtk.vtkDoubleArray getDoubleArray(double[] array)

getIdTypeArray

public static vtk.vtkIdTypeArray getIdTypeArray(int[] array)

getJavaArray

public static java.lang.Object getJavaArray(vtk.vtkDataArray dataArray)

Returns a native java array from the specified vtkDataArray.

getJavaArray

public static int[] getJavaArray(vtk.vtkIdTypeArray array)

vtkCollectionToArray

public static vtk.vtkObject[] vtkCollectionToArray(vtk.vtkCollection collection)

Transforms a vtkCollection to an array

getPoints

public static vtk.vtkPoints getPoints(double[] points)

Get vtkPoints from double[]

getPoints

public static vtk.vtkPoints getPoints(double[][] points)

Get vtkPoints from double[][3]

getPoints

public static vtk.vtkPoints getPoints(float[] points)

Get vtkPoints from float[]

getPoints

public static vtk.vtkPoints getPoints(float[][] points)

Get vtkPoints from float[][3]

getPoints

public static vtk.vtkPoints getPoints(int[] points)

Get vtkPoints from int[]

getPoints

public static vtk.vtkPoints getPoints(int[][] points)

Get vtkPoints from int[][3]

getCells

public static vtk.vtkCellArray getCells(int numCell,
                        int[] cells)

Get vtkCellArray from a 1D prepared cells array ( {n, i1, i2, ..., n, i1, i2,...} )

getPolyDataFromPoints

public static vtk.vtkPolyData getPolyDataFromPoints(vtk.vtkPoints points)

Returns a simple cell vtkPolyData from vtkPoints

getPolyDataFromDataSet

public static vtk.vtkPolyData getPolyDataFromDataSet(vtk.vtkDataSet dataSet)

Returns a vtkPolyData from vtkDataSet

getLayerProps

public static vtk.vtkProp[] getLayerProps(Layer layer)

Returns the vtkProp from the specified Layer object.
Returns a 0 sized array if the specified layer is null or does not contains any vtkProp.

getLayersProps

public static vtk.vtkProp[] getLayersProps(java.util.List<Layer> layers)

Returns all vtkProp from the specified list of Layer object.
Returns a 0 sized array if specified layers does not contains any vtkProp.

getProps

public static vtk.vtkProp[] getProps(vtk.vtkRenderer renderer)

Return all actor / view prop from the specified renderer

hasProp

public static boolean hasProp(vtk.vtkRenderer renderer,
              vtk.vtkProp actor)

Return true if the renderer contains the specified actor / view prop

findProp

@Deprecated
public static boolean findProp(vtk.vtkRenderer renderer,
                          vtk.vtkProp actor)

Deprecated. Use hasProp(vtkRenderer, vtkProp) instead.

findActor

@Deprecated
public static boolean findActor(vtk.vtkRenderer renderer,
                           vtk.vtkActor actor)

Deprecated. Use hasProp(vtkRenderer, vtkProp) instead.

findActor2D

@Deprecated
public static boolean findActor2D(vtk.vtkRenderer renderer,
                             vtk.vtkActor2D actor)

Deprecated. Use hasProp(vtkRenderer, vtkProp) instead.

addProp

public static void addProp(vtk.vtkRenderer renderer,
           vtk.vtkProp prop)

Add an actor (vtkProp) to the specified renderer.
If the actor is already existing in the renderer then no operation is done.

addActor

@Deprecated
public static void addActor(vtk.vtkRenderer renderer,
                       vtk.vtkActor actor)

Deprecated. Use addProp(vtkRenderer, vtkProp) instead.

addActor2D

@Deprecated
public static void addActor2D(vtk.vtkRenderer renderer,
                         vtk.vtkActor2D actor)

Deprecated. Use addProp(vtkRenderer, vtkProp) instead.

addProps

public static void addProps(vtk.vtkRenderer renderer,
            vtk.vtkProp[] props)

Add an array of actor (vtkProp) to the specified renderer.
If an actor is already existing in the renderer then nothing is done for this actor.

removeProp

public static void removeProp(vtk.vtkRenderer renderer,
              vtk.vtkProp actor)

Remove an actor from the specified renderer.

prepareCells

public static int[] prepareCells(int[][] indexes)

Return a 1D cells array from a 2D indexes array

prepareCells

public static int[] prepareCells(int numVertexPerCell,
                 int[] indexes)

Return a 1D cells array from a 1D indexes array and num vertex per cell (polygon)

getBooleanMaskFromBinaryImage

public static BooleanMask3D getBooleanMaskFromBinaryImage(vtk.vtkImageData image,
                                          boolean optimizeBounds)

Returns a BooleanMask3D from a binary (0/1 values) vtkImageData.

getROIFromBinaryImage

public static ROI getROIFromBinaryImage(vtk.vtkImageData image,
                        boolean force3DROI)

Deprecated. Uses #getBooleanMaskFromBinaryImage(vtkImageData) then ROI3DArea.ROI3DArea(BooleanMask3D) instead.

getImageData

public static vtk.vtkImageData getImageData(Sequence sequence,
                            int posT,
                            int posC)
                                     throws TooLargeArrayException,
                                            java.lang.OutOfMemoryError

Build and return volume image data from given Sequence object.

Parameters:

sequence - the sequence object we want to get volume image data

posT - frame index

posC - channel index (-1 for all channel)

Throws:

TooLargeArrayException

java.lang.OutOfMemoryError

getImageData

public static vtk.vtkImageData getImageData(java.lang.Object data,
                            DataType dataType,
                            int sizeX,
                            int sizeY,
                            int sizeZ,
                            int sizeC)

Creates and returns a vtkImageData object from the specified 1D array data.

getSurfaceFromImage

public static vtk.vtkPolyData getSurfaceFromImage(vtk.vtkImageData imageData,
                                  double threshold)

Create a 3D surface in VTK polygon format from the input VTK image data.

Parameters:

imageData - the input image to construct surface from

threshold - the threshold intensity value used to build the surface

getBinaryImageData

public static vtk.vtkImageData getBinaryImageData(ROI roi,
                                  int sz,
                                  int t)
                                           throws java.lang.IllegalArgumentException

Creates and returns a 3D binary (0/1 values) vtkImageData object corresponding to the ROI 3D boolean mask (C dimension is not considered) at specified T position.

Parameters:

roi - the roi we want to retrieve the vtkImageData mask

sz - the Z size to use for ROI with infinite Z dimension (if ROI has a finite Z dimension then ROI Z size is used).

t - the T position we want to retrieve the 3D mask data

Throws:

java.lang.IllegalArgumentException

getBinaryImageData

public static vtk.vtkImageData getBinaryImageData(vtk.vtkPolyData polyData,
                                  double[] space)

Transforms a vtkPolyData object to binary (0/1 values) vtkImageData

Parameters:

space - spacing between each image point

polyDataToImageData

@Deprecated
public static vtk.vtkImageData polyDataToImageData(vtk.vtkPolyData polyData,
                                              double[] space)

Deprecated. Use getBinaryImageData(vtkPolyData, double[]) instead.

getTransform

public static vtk.vtkTransform getTransform(double[] off,
                            double[] scale,
                            double[] rot)

Get VTK transform object from specified transform infos

transformPolyData

public static vtk.vtkPolyData transformPolyData(vtk.vtkPolyData polyData,
                                vtk.vtkAbstractTransform transform)

Transform a polyData using specified rotation, scaling and offset informations

transformPolyData

public static vtk.vtkPolyData transformPolyData(vtk.vtkPolyData polyData,
                                double[] off,
                                double[] scale,
                                double[] rot)

Transform a polyData using specified rotation, scaling and offset informations (3D)

getSurfaceFromOBJ

public static vtk.vtkPolyData getSurfaceFromOBJ(java.lang.String objPath)

Read a OBJ 3D model file and returns it in VTK mesh format (vtkPolyData)

getColorMap

public static vtk.vtkColorTransferFunction getColorMap(LUT.LUTChannel lutChannel)

Creates and returns the color map in vtkColorTransferFunction format from the specified LUT.LUTChannel.

getOpacityMap

public static vtk.vtkPiecewiseFunction getOpacityMap(LUT.LUTChannel lutChannel)

Creates and returns the opacity map in vtkPiecewiseFunction format from the specified LUT.LUTChannel.

getBinaryColorMap

public static vtk.vtkColorTransferFunction getBinaryColorMap(java.awt.Color color)

Creates and returns a binary color map in vtkColorTransferFunction format where 0 value is black and 1 is set to specified color.

getBinaryOpacityMap

public static vtk.vtkPiecewiseFunction getBinaryOpacityMap(double opacity)

Creates and returns a binary opacity map in vtkPiecewiseFunction format where 0 is 100% transparent and 1 to the specified opacity value.

setPolyDataColor

public static void setPolyDataColor(vtk.vtkPolyData polyData,
                    java.awt.Color color,
                    VtkCanvas canvas)

Set the Color of the specified vtkPolyData object.

Parameters:

polyData - the vtkPolyData we want to change color

color - the color to set

canvas - the VtkCanvas object to lock during the color change operation for safety (can be null if we don't need to lock the VtkCanvas here)

getOutline

public static vtk.vtkPolyData getOutline(double xMin,
                         double xMax,
                         double yMin,
                         double yMax,
                         double zMin,
                         double zMax)

Returns a cube polydata object representing the specified bounding box coordinate

See Also:

setOutlineBounds(vtkPolyData, double, double, double, double, double, double, VtkCanvas)

setOutlineBounds

public static boolean setOutlineBounds(vtk.vtkPolyData outline,
                       double xMin,
                       double xMax,
                       double yMin,
                       double yMax,
                       double zMin,
                       double zMax,
                       VtkCanvas canvas)

Set the bounds of specified outline polydata object (previously created with VtkUtil.getOutline(..))

Parameters:

canvas - the VtkCanvas object to lock during the color change operation for safety (can be null if we don't need to lock the VtkCanvas here)

Returns:

false if the specified polydata object is not a valid outline object

See Also:

getOutline(double, double, double, double, double, double)

vtkGC

public static void vtkGC()

VTK forced garbage collection