com.bitplane.xt.util

Class MapDimensions

java.lang.Object

com.bitplane.xt.util.MapDimensions

public final class MapDimensions
extends Object

Utilities for mapping between Imaris and ImgLib2 dimension arrays.

Author:

Tobias Pietzsch

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static interface	MapDimensions.SelectIntervalDimension Selects a particular element of the min and size vectors of an interval.

Method Summary

Modifier and Type	Method and Description
static int[]	createMapDimensions(int[] imarisDims, long[] imgDims) Tries to derive a mapDimensions array matching the specified Imaris and imglib2 dimension arrays.
static int[]	fromAxisOrder(AxisOrder axisOrder)
static int[]	invertMapDimensions(int[] mapDimensions) Return the reverse mapping for the given mapDimensions, such that mapDimensions[inv[i]] == i for all i.
static MapDimensions.SelectIntervalDimension	selectIntervalDimension(int d) Create a MapIntervalDimension that selects the d-th element of any min or size vectors.

Methods inherited from class java.lang.Object

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

Method Detail

createMapDimensions

public static int[] createMapDimensions(int[] imarisDims,
                                        long[] imgDims)

Tries to derive a mapDimensions array matching the specified Imaris and imglib2 dimension arrays.

mapDimensions maps Imaris dimension indices to imglib2 dimension indices. If i is dimension index from Imaris (0..4 means X,Y,Z,C,T) then mapDimensions[i] is the corresponding dimension in img. For img, dimensions with size=1 may be skipped.

For example, assume we have a XYC image, that is, a multi-channel 2D image, with imarisDims={800,600,1,3,1}. Let imgDims={800,600,3}, indicating that the imglib2 img should not have Z and T dimensions (instead of dimensions having size 1). Then the result is mapDimensions={0,1,-1,2,-1}.

Parameters:

imarisDims - dimensions of the Imaris dataset (int[5], with X,Y,Z,C,T)

imgDims - dimensions of the imglib2 image

Returns:

a int[5] array mapDimensions, that maps Imaris dimension indices to imglib2 dimension indices. If i is dimension index from Imaris (0..4 means X,Y,Z,C,T) then mapDimensions[i] is the corresponding dimension in the imglib2 Img. E.g., for a XYC image mapDimensions={0,1,-1,2,-1}.

fromAxisOrder

public static int[] fromAxisOrder(AxisOrder axisOrder)

invertMapDimensions

public static int[] invertMapDimensions(int[] mapDimensions)

Return the reverse mapping for the given mapDimensions, such that mapDimensions[inv[i]] == i for all i.

E.g., for mapDimensions={0,1,-1,2,-1} returns invMapDimensions={0,1,3}.

The length of the returned array is determined by the maximum dimension index occurring in mapDimensions.

selectIntervalDimension

public static MapDimensions.SelectIntervalDimension selectIntervalDimension(int d)

Create a MapIntervalDimension that selects the d-th element of any min or size vectors. If d < 0, then instead of selecting an element, min is always 0, and size is always 1.