Package net.imglib2.util

Class Util

java.lang.Object

net.imglib2.util.Util

public class Util
extends java.lang.Object

A collection of general-purpose utility methods for working with ImgLib2 data structures.

Field Summary

Fields

Modifier and Type	Field	Description
private static int	MAX_ARRAY_SIZE	The possible java array size is JVM dependent an actually slightly below Integer.MAX_VALUE.

Constructor Summary

Constructors

Constructor	Description
Util()

Method Summary

Modifier and Type	Method	Description
static double[]	asDoubleArray(java.lang.Iterable<? extends RealType<?>> iterable)	Returns the content of Iterable<RealType> as array of doubles.
static double[]	asDoubleArray(RandomAccessibleInterval<? extends RealType<?>> rai)	Returns the pixels of an RandomAccessibleInterval of RealType as array of doubles.
static double	average(double[] values)
static float	average(float[] values)
static double	averageDouble(java.util.List<java.lang.Double> values)
static float	averageFloat(java.util.List<java.lang.Float> values)
static int	combineHash(int hash1, int hash2)
static double[]	createGaussianKernel1DDouble(double sigma, boolean normalize)	This method creates a gaussian kernel
static double	distance(long[] position1, long[] position2)
static double	distance(RealLocalizable position1, RealLocalizable position2)
static boolean	equalIterationOrder(IterableInterval<?>... intervals)	Checks whether n IterableInterval have the same iteration order.
static int[]	expandArray(int[] values, int newLength)	Expand or truncate the provided array of values to length newLength.
static long[]	expandArray(long[] values, int newLength)	Expand or truncate the provided array of values to length newLength.
static <T> T[]	genericArray(int length)	Deprecated.
static double[]	getArrayFromValue(double value, int numDimensions)
static float[]	getArrayFromValue(float value, int numDimensions)
static int[]	getArrayFromValue(int value, int numDimensions)
static long[]	getArrayFromValue(long value, int numDimensions)
static <T extends NativeType<T>> ImgFactory<T>	getArrayOrCellImgFactory(Dimensions targetSize, int targetCellSize, T type)	Create an ArrayImgFactory if an image of the requested targetSize could be held in an ArrayImg.
static <T extends NativeType<T>> ImgFactory<T>	getArrayOrCellImgFactory(Dimensions targetSize, T type)	Create an ArrayImgFactory if an image of the requested targetSize could be held in an ArrayImg.
static int	getSuggestedKernelDiameter(double sigma)
static <T> ImgFactory<T>	getSuitableImgFactory(Dimensions targetSize, T type)	Create an appropriate ImgFactory for the requested targetSize and type.
static <T,F extends Interval & RandomAccessible<T>> T	getTypeFromInterval(F rai)	Deprecated.
static <T,F extends RealInterval & RealRandomAccessible<T>> T	getTypeFromRealInterval(F rai)	Deprecated.
static double	gLog(double z, double c)
static float	gLog(float z, float c)
static double	gLogInv(double w, double c)
static double	gLogInv(float w, float c)
static <T extends ValueEquals<U>,U> boolean	imagesEqual(RandomAccessibleInterval<? extends T> a, RandomAccessibleInterval<? extends U> b)	Checks if both images have equal intervals and content.
static <T,U> boolean	imagesEqual(RandomAccessibleInterval<? extends T> a, RandomAccessibleInterval<? extends U> b, java.util.function.BiPredicate<T,U> pixelEquals)	Checks if both images have equal intervals and content.
static long[]	int2long(int[] i)
static boolean	isApproxEqual(double a, double b, double threshold)
static boolean	isApproxEqual(float a, float b, float threshold)
static int	ldu(int v)	(Hopefully) fast floor log2 of an unsigned(!) integer value.
static boolean	locationsEqual(Localizable l1, Localizable l2)	Determines whether the two Localizable objects have the same position, with long precision.
static boolean	locationsEqual(RealLocalizable l1, RealLocalizable l2)	Determines whether the two RealLocalizable objects have the same position, with double precision.
static double	log2(double value)
static int[]	long2int(long[] a)
static double	max(double[] values)
static void	max(double[] a, double[] b)	Writes max(a,b) into a
static float	max(java.util.List<java.lang.Float> values)
static <T extends Type<T> & java.lang.Comparable<T>> T	max(T value1, T value2)
static double	median(double[] values)
static float	median(float[] values)
static long	median(long[] values)
static double	min(double[] values)
static void	min(double[] a, double[] b)	Writes min(a,b) into a
static float	min(java.util.List<java.lang.Float> values)
static <T extends Type<T> & java.lang.Comparable<T>> T	min(T value1, T value2)
static double	percentile(double[] values, double percentile)	Computes the percentile of a collection of doubles (percentile 0.5 roughly corresponds to median)
static int	pow(int a, int b)
static java.lang.String	printCoordinates(boolean[] value)
static java.lang.String	printCoordinates(double[] value)
static java.lang.String	printCoordinates(float[] value)
static java.lang.String	printCoordinates(int[] value)
static java.lang.String	printCoordinates(long[] value)
static java.lang.String	printCoordinates(RealLocalizable localizable)
static java.lang.String	printInterval(Interval interval)
static void	quicksort(double[] data)
static void	quicksort(double[] data, int[] sortAlso, int left, int right)
static void	quicksort(double[] data, int left, int right)
static void	quicksort(float[] data)
static void	quicksort(float[] data, int left, int right)
static void	quicksort(long[] data)
static void	quicksort(long[] data, int left, int right)
static long	round(double value)
static int	round(float value)
static int	roundToInt(double value)
static int	roundToInt(float value)
static long	roundToLong(double value)
static long	roundToLong(float value)
static int	safeInt(long value)	Cast value to int, checking for overflow.
static <T extends ValueEquals<T>> boolean	valueEqualsObject(T a, java.lang.Object b)	This method should be used in implementations of ValueEquals, to override Object.equals(Object).

Methods inherited from class java.lang.Object

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

Field Detail

MAX_ARRAY_SIZE

private static final int MAX_ARRAY_SIZE

The possible java array size is JVM dependent an actually slightly below Integer.MAX_VALUE. This is the same MAX_ARRAY_SIZE as used for example in ArrayList in OpenJDK8.

See Also:

Constant Field Values

Constructor Detail

Util

public Util()

Method Detail

genericArray

@Deprecated
public static <T> T[] genericArray(int length)

Deprecated.

This does only work when T is erased to Object at call site.

See https://github.com/imglib/imglib2/issues/253

log2

public static double log2(double value)

getArrayFromValue

public static double[] getArrayFromValue(double value,
                                         int numDimensions)

getArrayFromValue

public static float[] getArrayFromValue(float value,
                                        int numDimensions)

getArrayFromValue

public static int[] getArrayFromValue(int value,
                                      int numDimensions)

getArrayFromValue

public static long[] getArrayFromValue(long value,
                                       int numDimensions)

expandArray

public static long[] expandArray(long[] values,
                                 int newLength)

Expand or truncate the provided array of values to length newLength.

If values.length < newLength then the last value is repeated. That is, the remaining elements are filled with values[values.length - 1].

If values.length == newLength then values is returned, otherwise a new array is created.

Parameters:

values - values to copy

newLength - length of expanded array

Returns:

an array where array.length == newLength and array[i] == values[Math.max(i, values.length)]

expandArray

public static int[] expandArray(int[] values,
                                int newLength)

Expand or truncate the provided array of values to length newLength.

If values.length < newLength then the last value is repeated. That is, the remaining elements are filled with values[values.length - 1].

If values.length == newLength then values is returned, otherwise a new array is created.

Parameters:

values - values to copy

newLength - length of expanded array

Returns:

an array where array.length == newLength and array[i] == values[Math.max(i, values.length)]

distance

public static double distance(RealLocalizable position1,
                              RealLocalizable position2)

distance

public static double distance(long[] position1,
                              long[] position2)

percentile

public static double percentile(double[] values,
                                double percentile)

Computes the percentile of a collection of doubles (percentile 0.5 roughly corresponds to median)

Parameters:

values - - the values

percentile - - the percentile [0...1]

Returns:

the corresponding value

averageDouble

public static double averageDouble(java.util.List<java.lang.Double> values)

averageFloat

public static float averageFloat(java.util.List<java.lang.Float> values)

min

public static float min(java.util.List<java.lang.Float> values)

max

public static float max(java.util.List<java.lang.Float> values)

average

public static float average(float[] values)

average

public static double average(double[] values)

min

public static double min(double[] values)

max

public static double max(double[] values)

median

public static long median(long[] values)

median

public static double median(double[] values)

median

public static float median(float[] values)

quicksort

public static void quicksort(long[] data)

quicksort

public static void quicksort(long[] data,
                             int left,
                             int right)

quicksort

public static void quicksort(double[] data)

quicksort

public static void quicksort(double[] data,
                             int left,
                             int right)

quicksort

public static void quicksort(float[] data)

quicksort

public static void quicksort(float[] data,
                             int left,
                             int right)

quicksort

public static void quicksort(double[] data,
                             int[] sortAlso,
                             int left,
                             int right)

gLog

public static double gLog(double z,
                          double c)

gLog

public static float gLog(float z,
                         float c)

gLogInv

public static double gLogInv(double w,
                             double c)

gLogInv

public static double gLogInv(float w,
                             float c)

isApproxEqual

public static boolean isApproxEqual(float a,
                                    float b,
                                    float threshold)

isApproxEqual

public static boolean isApproxEqual(double a,
                                    double b,
                                    double threshold)

round

public static int round(float value)

round

public static long round(double value)

roundToInt

public static int roundToInt(float value)

roundToInt

public static int roundToInt(double value)

roundToLong

public static long roundToLong(float value)

roundToLong

public static long roundToLong(double value)

createGaussianKernel1DDouble

public static double[] createGaussianKernel1DDouble(double sigma,
                                                    boolean normalize)

This method creates a gaussian kernel

Parameters:

sigma - Standard Derivation of the gaussian function

normalize - Normalize integral of gaussian function to 1 or not...

Returns:

double[] The gaussian kernel

getSuggestedKernelDiameter

public static int getSuggestedKernelDiameter(double sigma)

printCoordinates

public static java.lang.String printCoordinates(float[] value)

printCoordinates

public static java.lang.String printCoordinates(double[] value)

printCoordinates

public static java.lang.String printCoordinates(RealLocalizable localizable)

printInterval

public static java.lang.String printInterval(Interval interval)

printCoordinates

public static java.lang.String printCoordinates(int[] value)

printCoordinates

public static java.lang.String printCoordinates(long[] value)

printCoordinates

public static java.lang.String printCoordinates(boolean[] value)

pow

public static int pow(int a,
                      int b)

max

public static <T extends Type<T> & java.lang.Comparable<T>> T max(T value1,
                                                                  T value2)

min

public static <T extends Type<T> & java.lang.Comparable<T>> T min(T value1,
                                                                  T value2)

long2int

public static final int[] long2int(long[] a)

int2long

public static final long[] int2long(int[] i)

safeInt

public static int safeInt(long value)

Cast value to int, checking for overflow.

Parameters:

value - value to cast to int

Returns:

value cast to int

Throws:

java.lang.IllegalArgumentException - if value > Integer.MAX_VALUE

getTypeFromInterval

@Deprecated
public static <T,F extends Interval & RandomAccessible<T>> T getTypeFromInterval(F rai)

Deprecated.

This method has been deprecated. Use Typed.getType() instead. TODO: Cannot deprecate because rai parameter is not actually a RandomAccessibleInterval Gets an instance of T from the RandomAccessibleInterval by querying the value at the min coordinate

Type Parameters:

T - - the T

Parameters:

rai - - the RandomAccessibleInterval

Returns:

- an instance of T

getTypeFromRealInterval

@Deprecated
public static <T,F extends RealInterval & RealRandomAccessible<T>> T getTypeFromRealInterval(F rai)

Deprecated.

Gets an instance of T from the RandomAccessibleInterval by querying the value at the min coordinate

Type Parameters:

T - - the T

Parameters:

rai - - the RandomAccessibleInterval

Returns:

- an instance of T

getArrayOrCellImgFactory

public static <T extends NativeType<T>> ImgFactory<T> getArrayOrCellImgFactory(Dimensions targetSize,
                                                                               T type)

Create an ArrayImgFactory if an image of the requested targetSize could be held in an ArrayImg. Otherwise return a CellImgFactory with as large as possible cell size.

Parameters:

targetSize - size of image that the factory should be able to create.

type - type of the factory.

Returns:

an ArrayImgFactory or a CellImgFactory.

getArrayOrCellImgFactory

public static <T extends NativeType<T>> ImgFactory<T> getArrayOrCellImgFactory(Dimensions targetSize,
                                                                               int targetCellSize,
                                                                               T type)

Create an ArrayImgFactory if an image of the requested targetSize could be held in an ArrayImg. Otherwise return a CellImgFactory with cell size targetCellSize (or as large as possible if targetCellSize is too large).

Parameters:

targetSize - size of image that the factory should be able to create.

targetCellSize - if a CellImgFactory is created, what should be the cell size.

type - type of the factory.

Returns:

an ArrayImgFactory or a CellImgFactory.

getSuitableImgFactory

public static <T> ImgFactory<T> getSuitableImgFactory(Dimensions targetSize,
                                                      T type)

Create an appropriate ImgFactory for the requested targetSize and type. If the target size is a Img, return its ImgFactory. If the type is a NativeType, then getArrayOrCellImgFactory(Dimensions, NativeType) is used; if not, a ListImgFactory is returned.

Parameters:

targetSize - size of image that the factory should be able to create.

type - type of the factory.

Returns:

an ArrayImgFactory, CellImgFactory or ListImgFactory as appropriate.

ldu

public static final int ldu(int v)

(Hopefully) fast floor log₂ of an unsigned(!) integer value.

Parameters:

v - unsigned integer

Returns:

floor log₂

equalIterationOrder

public static boolean equalIterationOrder(IterableInterval<?>... intervals)

Checks whether n IterableInterval have the same iteration order.

locationsEqual

public static boolean locationsEqual(Localizable l1,
                                     Localizable l2)

Determines whether the two Localizable objects have the same position, with long precision.

At first glance, this method may appear to be unnecessary, since there is also locationsEqual(RealLocalizable, RealLocalizable), which is more general. The difference is that this method compares the positions using Localizable.getLongPosition(int), which has higher precision in integer space than RealLocalizable.getDoublePosition(int) does, which is what the locationsEqual(RealLocalizable, RealLocalizable) method uses.

Parameters:

l1 - The first Localizable.

l2 - The second Localizable.

Returns:

True iff the positions are the same, including dimensionality.

See Also:

Localizable.getLongPosition(int)

locationsEqual

public static boolean locationsEqual(RealLocalizable l1,
                                     RealLocalizable l2)

Determines whether the two RealLocalizable objects have the same position, with double precision.

Parameters:

l1 - The first RealLocalizable.

l2 - The second RealLocalizable.

Returns:

True iff the positions are the same, including dimensionality.

See Also:

RealLocalizable.getDoublePosition(int)

imagesEqual

public static <T extends ValueEquals<U>,U> boolean imagesEqual(RandomAccessibleInterval<? extends T> a,
                                                                     RandomAccessibleInterval<? extends U> b)

Checks if both images have equal intervals and content.

imagesEqual

public static <T,U> boolean imagesEqual(RandomAccessibleInterval<? extends T> a,
                                              RandomAccessibleInterval<? extends U> b,
                                              java.util.function.BiPredicate<T,U> pixelEquals)

Checks if both images have equal intervals and content. A predicate must be given to check if two pixels are equal.

min

public static final void min(double[] a,
                             double[] b)

Writes min(a,b) into a

Parameters:

a -

b -

max

public static final void max(double[] a,
                             double[] b)

Writes max(a,b) into a

Parameters:

a -

b -

asDoubleArray

public static double[] asDoubleArray(java.lang.Iterable<? extends RealType<?>> iterable)

Returns the content of Iterable<RealType> as array of doubles.

asDoubleArray

public static double[] asDoubleArray(RandomAccessibleInterval<? extends RealType<?>> rai)

Returns the pixels of an RandomAccessibleInterval of RealType as array of doubles. The pixels are sorted in flat iteration order.

valueEqualsObject

public static <T extends ValueEquals<T>> boolean valueEqualsObject(T a,
                                                                   java.lang.Object b)

This method should be used in implementations of ValueEquals, to override Object.equals(Object).

See Also:

Object.equals(Object)

combineHash

public static int combineHash(int hash1,
                              int hash2)