Package com.xinapse.image

Class VolumeInterpolator

java.lang.Object

com.xinapse.image.VolumeInterpolator

public abstract class VolumeInterpolator
extends Object

An interpolator for a 3- (or fewer) dimensional array of pixels. Supported pixel data types are:

• PixelDataType.BINARY
• PixelDataType.BYTE
• PixelDataType.UBYTE
• PixelDataType.SHORT
• PixelDataType.USHORT
• PixelDataType.INT
• PixelDataType.UINT
• PixelDataType.LONG
• PixelDataType.FLOAT
• PixelDataType.DOUBLE
• PixelDataType.COMPLEX
• PixelDataType.DOUBLECOMPLEX

For Colour (R,G,B) images, use a ColourVolumeInterpolator.

The VolumeInterpolator always interpolates to produce a set of floating point interpolated values at an arbitrary set of locations, regardless of the PixelDataType of the pixel samples to be interpolated. For complex data types, the floating point values are in interleaved (real/imaginary) pairs and the length of the returned array of values is twice the number of locations to be interpolated.

Supported interpolation types are:

• InterpolationType.NEAREST_NEIGHBOUR. Nearest neighbour interpolation.
• InterpolationType.LINEAR. Tri-linear interpolation.
• InterpolationType.SINC. Blackman-Harris windowed sinc interpolation.

The origin (x=0, y=0, z=0) is assumed to be at the centre of the block of pixels, such that x values within the block go from x=-FoVx/2 to x=+FoVx/2 where FoVx is the field of view in the x-direction (with similar specification for y and z). The array of pixels to be interpolated is inset within the block such that there is half a pixel distance between the edges of the field of view and the first and last samples (i.e., FoVx = pixelXSize * number of columns, etc.).

Supplied coordinates outside the field of view will yield a value that depends on the BoundaryCondition. For BoundaryCondition.FIXED, the interpolated intensities are equal to the "fixedValue" outside the field of view. This fixed value defaults to zero, but can be set to any other (real) floating-point value. The result of any interpolation is the same as would result when iterpolating within an infinite array of pixel samples, where the central portion of samples is that supplied to form the VolumeInterpolator, and any pixel samples outside the central portion have an intensity equal to the "fixedValue".

Field Summary

Fields

Modifier and Type	Field	Description
protected PixelDataType	dataType	The PixelDataType of the pixel values to be interpolated.
protected static final int	MAX_INTERPOLATIONS_BEFORE_MULTITHREADING	The maximum number of interpolations that is performed in a singkle method call before the procedure is multi-threaded.
protected int	nCols	The number of columns in the block of pixels.
protected int	nRows	The number of rows in the block of pixels.
protected int	nSlices	The number of slices in the block of pixels.
protected final Object	pix	The array of pixel values to be interpolated.
protected float	pixelXSize	Horizontal pixel size in the block of pixels to be interpolated.
protected float	pixelYSize	Vertical pixel size in the block of pixels to be interpolated.
protected float	pixelZSize	Pixel depth in the block of pixels to be interpolated.
protected Boolean	stopMe	A Flag to indicate that this VolumeInterpolator should stop the current interpolation, (if an interpolation is in progress) and throw a CancellationException.

Method Summary

Modifier and Type	Method	Description
void	cancel()	Signal to this VolumeInterpolator to stop the current interpolation (if an interpolation is in progress) as soon as possible, and throw a CancellationException.
static InterpolationType[]	getImplementedInterpolationTypes()	Returns the types of interpolation that are implemented by the VolumeInterpolator class.
static VolumeInterpolator	getInstance(VolumeInterpolator interpolator, InterpolationType newType)	Returns a new VolumeInterpolator, constructed from an existing one.
static VolumeInterpolator	getInstance(Object pix, PixelDataType dataType, int nCols, int nRows, int nSlices, float pixelXSize, float pixelYSize, float pixelZSize, BoundaryCondition boundaryCondition, Float fixedValue, InterpolationType type)	Returns a new VolumeInterpolator for a block of pixel samples.
float[]	interpolate(float[] xyzArray, float[] intensityArray)	Interpolate the intensity samples at a set of supplied coordinates.
static void	main(String[] args)	Run the self-test for VolumeInterpolator.

Methods inherited from class java.lang.Object

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

Field Details

MAX_INTERPOLATIONS_BEFORE_MULTITHREADING

protected static final int MAX_INTERPOLATIONS_BEFORE_MULTITHREADING

The maximum number of interpolations that is performed in a singkle method call before the procedure is multi-threaded.

See Also:

• Constant Field Values

pix

protected final Object pix

The array of pixel values to be interpolated.

dataType

protected PixelDataType dataType

The PixelDataType of the pixel values to be interpolated.

nCols

protected int nCols

The number of columns in the block of pixels.

nRows

protected int nRows

The number of rows in the block of pixels.

nSlices

protected int nSlices

The number of slices in the block of pixels.

pixelXSize

protected float pixelXSize

Horizontal pixel size in the block of pixels to be interpolated.

pixelYSize

protected float pixelYSize

Vertical pixel size in the block of pixels to be interpolated.

pixelZSize

protected float pixelZSize

Pixel depth in the block of pixels to be interpolated.

stopMe

protected Boolean stopMe

A Flag to indicate that this VolumeInterpolator should stop the current interpolation, (if an interpolation is in progress) and throw a CancellationException.

Method Details

cancel

public void cancel()

Signal to this VolumeInterpolator to stop the current interpolation (if an interpolation is in progress) as soon as possible, and throw a CancellationException.

interpolate

public float[] interpolate(float[] xyzArray,
 float[] intensityArray)
                    throws CancellationException

Interpolate the intensity samples at a set of supplied coordinates.

Parameters:

xyzArray - the x,y,z coordinates of each of the new sample locations. The x, y and z coordinates are supplied in interlaced order: x0, y0, z0, x1, y1, z1, .... xN-1, yN-1, zN-1.

intensityArray - the array into which the interpolated pixel intensities will be placed. If intensityArray is null, a new array will be allocated.

Returns:

the array of pixel intensities - either the newly-allocated one, or the one supplied. Pixel intensities are always returned as an array of float values, regardless of the data type of pixels to be interpolated.

Throws:

IndexOutOfBoundsException - if the intensityArray is of the wrong length for the number of pixel (x,y,z) coordinates supplied.

CancellationException - if the interpolation halts prematurely because it has been cancelled.

getInstance

public static VolumeInterpolator getInstance(Object pix,
 PixelDataType dataType,
 int nCols,
 int nRows,
 int nSlices,
 float pixelXSize,
 float pixelYSize,
 float pixelZSize,
 BoundaryCondition boundaryCondition,
 Float fixedValue,
 InterpolationType type)
                                      throws InstantiationException

Returns a new VolumeInterpolator for a block of pixel samples.

Parameters:

pix - the set of intensities to be interpolated.

dataType - the PixelDataType of the block of pixels.

nCols - the number of columns in the block of pixels.

nRows - the number of rows in the block of pixels.

nSlices - the number of slices in the block of pixels.

pixelXSize - the pixel width.

pixelYSize - the pixel height.

pixelZSize - the pixel depth.

boundaryCondition - the BoundaryCondition to apply for interpolated points that are outside the block of pixels.

fixedValue - if non-null, the fixed value interpolated values outside the pixel array if the boundary condition is BoundaryCondition.FIXED.

type - the InterpolationType to be used for interpolation. One of:

• InterpolationType.NEAREST_NEIGHBOUR.
• InterpolationType.LINEAR.
• InterpolationType.SINC.

Returns:

a VolumeInterpolator.

Throws:

InstantiationException - if a VolumeInterpolator cannot be created.

getInstance

public static VolumeInterpolator getInstance(VolumeInterpolator interpolator,
 InterpolationType newType)
                                      throws InstantiationException

Returns a new VolumeInterpolator, constructed from an existing one. This method can be used to change the InterpolationType of an existing VolumeInterpolator.

Parameters:

interpolator - the existing VolumeInterpolator.

newType - the new InterpolationType to be used for interpolation. One of:

• InterpolationType.NEAREST_NEIGHBOUR.
• InterpolationType.LINEAR.
• InterpolationType.SINC.

Returns:

a VolumeInterpolator using the new type of interpolation.

Throws:

InstantiationException - if a VolumeInterpolator cannot be created.

main

public static void main(String[] args)

Run the self-test for VolumeInterpolator.

Parameters:

args - ignored.

getImplementedInterpolationTypes

public static InterpolationType[] getImplementedInterpolationTypes()

Returns the types of interpolation that are implemented by the VolumeInterpolator class.

Returns:

an array of InterpolationTypes that can be used for volume interpolation.