org.janelia.saalfeldlab.n5.universe.metadata.axes

Class AxisUtils

java.lang.Object

org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

public class AxisUtils
extends Object

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	AxisUtils.DefaultAxisTypes

Field Summary

Fields

Modifier and Type	Field and Description
static String	channelType
static String	cLabel
static AxisUtils.DefaultAxisTypes	defaultAxisTypes
static String	SPACE_UNIT
static String	spaceType
static String	TIME_UNIT
static String	timeType
static String	tLabel
static String	unknownType
static String	xLabel
static String	yLabel
static String	zLabel

Constructor Summary

Constructors

Constructor and Description
AxisUtils()

Method Summary

Modifier and Type	Method and Description
static net.imglib2.realtransform.AffineGet	axisPermutationTransform(int[] p)
static Axis[]	buildAxes(String... labels)
static <T> boolean	contains(T t, T[] array) Returns true if any elements of array equal t
static <T> boolean	containsAny(Set<T> set, T[] array) Returns true if any elements of array are contained in the set
static Axis[]	defaultAxes(int N)
static Axis[]	defaultAxes(String... labels)
static Axis	defaultAxis(String label)
static String	defaultLabel(int i)
static DefaultAxisMetadata	defaultN5ViewerAxes(N5SpatialDatasetMetadata meta) The default axes for dialects that store only spatial data (n5viewer and cosem), when time dimension is allowed.
static void	fillPermutation(int[] p) Replaces "-1"s in the input permutation array with the largest value.
static <A extends AxisMetadata> int[]	findImagePlusPermutation(AxisMetadata axisMetadata) Finds and returns a permutation p such that source[p[i]] equals target[i]
static int[]	findImagePlusPermutation(String[] axisLabels) Finds and returns a permutation p such that source[p[i]] equals xyczt
static int[]	findImagePlusSpatialPermutation(int[] p)
static <T> int[]	findPermutation(T[] source, T[] target) Finds and returns a permutation p such that source[p[i]] equals target[i]
static String	getDefaultType(String label)
static String[]	getDefaultTypes(String[] labels)
static String	getDefaultUnit(String type)
static int[]	indexes(Axis[] axes, Predicate<Axis> predicate)
static int[]	invertPermutation(int[] p)
static boolean	isIdentityPermutation(int[] p)
static int[]	normalizeIndexes(int[] indexes) Converters an array of integers to a normalized array of integers such that the smallest integer is mapped to 0, the second smallest to 1 ... and the largest is mapped to N-1, where N is the number of unique integers in the array.
static double[]	permute(double[] in, int[] p)
static int[]	permute(int[] in, int[] p)
static <T> List<T>	permute(List<T> in, int[] p)
static long[]	permute(long[] in, int[] p)
static <T> net.imglib2.view.IntervalView<T>	permute(net.imglib2.RandomAccessibleInterval<T> source, int[] p) Permutes the dimensions of a RandomAccessibleInterval using the given permutation vector, where the ith value in p gives destination of the ith input dimension in the output.
static <T> void	permute(T[] in, T[] dest, int[] p) Permutes an input array into a destination array.
static <M extends AxisMetadata & N5Metadata> M	permuteForImagePlus(int[] spatialPermutation, M meta)
static <T,M extends AxisMetadata & N5Metadata> net.imglib2.RandomAccessibleInterval<T>	permuteForImagePlus(net.imglib2.RandomAccessibleInterval<T> img, M meta)
static <T,M extends N5Metadata,A extends AxisMetadata & N5Metadata> net.imglib2.util.Pair<net.imglib2.RandomAccessibleInterval<T>,M>	permuteImageAndMetadataForImagePlus(int[] p, net.imglib2.RandomAccessibleInterval<T> img, M meta)
static <T,M extends N5Metadata,A extends AxisMetadata & N5Metadata> net.imglib2.util.Pair<net.imglib2.RandomAccessibleInterval<T>,M>	permuteImageAndMetadataForImagePlus(net.imglib2.RandomAccessibleInterval<T> img, M meta)
static <T> net.imglib2.RandomAccessibleInterval<T>	reverseDimensions(net.imglib2.RandomAccessibleInterval<T> img)
static Axis	unknownAxis()

Methods inherited from class java.lang.Object

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

Field Detail

xLabel

public static final String xLabel

See Also:

Constant Field Values

yLabel

public static final String yLabel

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Constant Field Values

cLabel

public static final String cLabel

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Constant Field Values

zLabel

public static final String zLabel

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Constant Field Values

tLabel

public static final String tLabel

See Also:

Constant Field Values

spaceType

public static final String spaceType

See Also:

Constant Field Values

timeType

public static final String timeType

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Constant Field Values

channelType

public static final String channelType

See Also:

Constant Field Values

unknownType

public static final String unknownType

See Also:

Constant Field Values

defaultAxisTypes

public static final AxisUtils.DefaultAxisTypes defaultAxisTypes

SPACE_UNIT

public static String SPACE_UNIT

TIME_UNIT

public static String TIME_UNIT

Constructor Detail

AxisUtils

public AxisUtils()

Method Detail

findPermutation

public static <T> int[] findPermutation(T[] source,
                                        T[] target)

Finds and returns a permutation p such that source[p[i]] equals target[i]

Type Parameters:

T - the object type

Parameters:

source - the source objects

target - the target objects

Returns:

the permutation array

permute

public static <T> List<T> permute(List<T> in,
                                  int[] p)

permute

public static <T> void permute(T[] in,
                               T[] dest,
                               int[] p)

Permutes an input array into a destination array. The input and destination may be the same instance.

Type Parameters:

T - the type

Parameters:

in - the input array

dest - the destination array

p - the permutation

permute

public static long[] permute(long[] in,
                             int[] p)

permute

public static int[] permute(int[] in,
                            int[] p)

permute

public static double[] permute(double[] in,
                               int[] p)

buildAxes

public static Axis[] buildAxes(String... labels)

findImagePlusPermutation

public static <A extends AxisMetadata> int[] findImagePlusPermutation(AxisMetadata axisMetadata)

Finds and returns a permutation p such that source[p[i]] equals target[i]

Type Parameters:

A - the axis type

Parameters:

axisMetadata - the axis metadata

Returns:

the permutation

findImagePlusPermutation

public static int[] findImagePlusPermutation(String[] axisLabels)

Finds and returns a permutation p such that source[p[i]] equals xyczt

Parameters:

axisLabels - the axis labels

Returns:

the permutation array

findImagePlusSpatialPermutation

public static int[] findImagePlusSpatialPermutation(int[] p)

normalizeIndexes

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

Converters an array of integers to a normalized array of integers such that the smallest integer is mapped to 0, the second smallest to 1 ... and the largest is mapped to N-1, where N is the number of unique integers in the array.

Parameters:

indexes - the indexes

Returns:

normalized indexes

fillPermutation

public static void fillPermutation(int[] p)

Replaces "-1"s in the input permutation array with the largest value.

Parameters:

p - the permutation

axisPermutationTransform

public static net.imglib2.realtransform.AffineGet axisPermutationTransform(int[] p)

isIdentityPermutation

public static boolean isIdentityPermutation(int[] p)

permuteForImagePlus

public static <T,M extends AxisMetadata & N5Metadata> net.imglib2.RandomAccessibleInterval<T> permuteForImagePlus(net.imglib2.RandomAccessibleInterval<T> img,
                                                                                                                  M meta)

permuteForImagePlus

public static <M extends AxisMetadata & N5Metadata> M permuteForImagePlus(int[] spatialPermutation,
                                                                          M meta)

permuteImageAndMetadataForImagePlus

public static <T,M extends N5Metadata,A extends AxisMetadata & N5Metadata> net.imglib2.util.Pair<net.imglib2.RandomAccessibleInterval<T>,M> permuteImageAndMetadataForImagePlus(net.imglib2.RandomAccessibleInterval<T> img,
                                                                                                                                                                                M meta)

permuteImageAndMetadataForImagePlus

public static <T,M extends N5Metadata,A extends AxisMetadata & N5Metadata> net.imglib2.util.Pair<net.imglib2.RandomAccessibleInterval<T>,M> permuteImageAndMetadataForImagePlus(int[] p,
                                                                                                                                                                                net.imglib2.RandomAccessibleInterval<T> img,
                                                                                                                                                                                M meta)

reverseDimensions

public static <T> net.imglib2.RandomAccessibleInterval<T> reverseDimensions(net.imglib2.RandomAccessibleInterval<T> img)

permute

public static final <T> net.imglib2.view.IntervalView<T> permute(net.imglib2.RandomAccessibleInterval<T> source,
                                                                 int[] p)

Permutes the dimensions of a RandomAccessibleInterval using the given permutation vector, where the ith value in p gives destination of the ith input dimension in the output.

Type Parameters:

T - the image type

Parameters:

source - the source data

p - the permutation

Returns:

the permuted source

invertPermutation

public static int[] invertPermutation(int[] p)

indexes

public static int[] indexes(Axis[] axes,
                            Predicate<Axis> predicate)

defaultAxes

public static Axis[] defaultAxes(int N)

defaultAxes

public static Axis[] defaultAxes(String... labels)

defaultAxis

public static Axis defaultAxis(String label)

unknownAxis

public static Axis unknownAxis()

defaultN5ViewerAxes

public static DefaultAxisMetadata defaultN5ViewerAxes(N5SpatialDatasetMetadata meta)

The default axes for dialects that store only spatial data (n5viewer and cosem), when time dimension is allowed.

Parameters:

meta - the metadata

Returns:

axes default axis metadata

getDefaultTypes

public static String[] getDefaultTypes(String[] labels)

getDefaultType

public static String getDefaultType(String label)

getDefaultUnit

public static String getDefaultUnit(String type)

defaultLabel

public static String defaultLabel(int i)

containsAny

public static <T> boolean containsAny(Set<T> set,
                                      T[] array)

Returns true if any elements of array are contained in the set

Type Parameters:

T - the type

Parameters:

set - the set

array - the array

Returns:

true if any elements of the array are contained in the set.

contains

public static <T> boolean contains(T t,
                                   T[] array)

Returns true if any elements of array equal t

Type Parameters:

T - the type

Parameters:

t - some element

array - the array

Returns:

true if array contains t