Migrate DataTools methods from SCIFIO/Bio-Formats

The io.scif.common.DataTools class (originally from Bio-Formats at
loci.common.DataTools) contains many useful methods for working with
primitive numerical types, and arrays of those types. In particular,
it includes methods for converting between types, endianness, and
signedness. These utility methods will continue to be extremely
useful for the various DataHandle implementations, especially for
proper support for both big- and little-endian byte ordering.

The class was split as follows:
* org.scijava.util.Bytes - primitive numeric methods
* org.scijava.util.StringUtils - utility methods for strings
* org.scijava.util.ArrayUtils - utility methods for arrays

Regarding provenance of the code: I originally wrote much of it for
the Bio-Formats library; Melissa Linkert wrote a lot as well, with
additional contributions by Chris Allan and probably others on the
OME team. The relevant code is all BSD-2 licensed; I have added an
appropriate extra legal notice at the top of each affected file.

Author: ctrueden

src/main/java/org/scijava/util/ArrayUtils.java

@@ -29,6 +29,35 @@
  * #L%
  */
 
+// Portions of this class were derived from the loci.common.DataTools class of
+// the Bio-Formats library, licensed according to Simplified BSD, as follows:
+//
+// Copyright (C) 2005 - 2015 Open Microscopy Environment:
+//   - Board of Regents of the University of Wisconsin-Madison
+//   - Glencoe Software, Inc.
+//   - University of Dundee
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+// 1. Redistributions of source code must retain the above copyright notice,
+//    this list of conditions and the following disclaimer.
+// 2. Redistributions in binary form must reproduce the above copyright notice,
+//    this list of conditions and the following disclaimer in the documentation
+//    and/or other materials provided with the distribution.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+// LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+// CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+// SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+// INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+// CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+// ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+// POSSIBILITY OF SUCH DAMAGE.
+
 package org.scijava.util;
 
 import java.util.Collection;
@@ -38,6 +67,9 @@
  * Utility class for creating and manipulating {@link PrimitiveArray} instances.
  * 
  * @author Mark Hiner
+ * @author Curtis Rueden
+ * @author Melissa Linkert
+ * @author Chris Allan
  */
 public final class ArrayUtils {
 
@@ -91,4 +123,246 @@ public static Collection<?> toCollection(final Object value) {
 		return list;
 	}
 
+	/**
+	 * Allocates a 1-dimensional byte array matching the product of the given
+	 * sizes.
+	 *
+	 * @param sizes list of sizes from which to allocate the array
+	 * @return a byte array of the appropriate size
+	 * @throws IllegalArgumentException if the total size exceeds 2GB, which is
+	 *           the maximum size of an array in Java; or if any size argument is
+	 *           zero or negative
+	 */
+	public static byte[] allocate(final long... sizes)
+		throws IllegalArgumentException
+	{
+		if (sizes == null) return null;
+		if (sizes.length == 0) return new byte[0];
+		final int total = safeMultiply32(sizes);
+		return new byte[total];
+	}
+
+	/**
+	 * Checks that the product of the given sizes does not exceed the 32-bit
+	 * integer limit (i.e., {@link Integer#MAX_VALUE}).
+	 *
+	 * @param sizes list of sizes from which to compute the product
+	 * @return the product of the given sizes
+	 * @throws IllegalArgumentException if the total size exceeds 2GiB, which is
+	 *           the maximum size of an int in Java; or if any size argument is
+	 *           zero or negative
+	 */
+	public static int safeMultiply32(final long... sizes)
+		throws IllegalArgumentException
+	{
+		if (sizes.length == 0) return 0;
+		long total = 1;
+		for (final long size : sizes) {
+			if (size < 1) {
+				throw new IllegalArgumentException("Invalid array size: " +
+					sizeAsProduct(sizes));
+			}
+			total *= size;
+			if (total > Integer.MAX_VALUE) {
+				throw new IllegalArgumentException("Array size too large: " +
+					sizeAsProduct(sizes));
+			}
+		}
+		// NB: The downcast to int is safe here, due to the checks above.
+		return (int) total;
+	}
+
+	/**
+	 * Checks that the product of the given sizes does not exceed the 64-bit
+	 * integer limit (i.e., {@link Long#MAX_VALUE}).
+	 *
+	 * @param sizes list of sizes from which to compute the product
+	 * @return the product of the given sizes
+	 * @throws IllegalArgumentException if the total size exceeds 8EiB, which is
+	 *           the maximum size of a long in Java; or if any size argument is
+	 *           zero or negative
+	 */
+	public static long safeMultiply64(final long... sizes)
+		throws IllegalArgumentException
+	{
+		if (sizes.length == 0) return 0;
+		long total = 1;
+		for (final long size : sizes) {
+			if (size < 1) {
+				throw new IllegalArgumentException("Invalid array size: " +
+					sizeAsProduct(sizes));
+			}
+			if (willOverflow(total, size)) {
+				throw new IllegalArgumentException("Array size too large: " +
+					sizeAsProduct(sizes));
+			}
+			total *= size;
+		}
+		return total;
+	}
+
+	/** Returns true if the given value is contained in the specified array. */
+	public static boolean contains(final byte[] array, final byte value) {
+		return indexOf(array, value) != -1;
+	}
+
+	/** Returns true if the given value is contained in the specified array. */
+	public static boolean contains(final boolean[] array, final boolean value) {
+		return indexOf(array, value) != -1;
+	}
+
+	/** Returns true if the given value is contained in the specified array. */
+	public static boolean contains(final char[] array, final char value) {
+		return indexOf(array, value) != -1;
+	}
+
+	/** Returns true if the given value is contained in the specified array. */
+	public static boolean contains(final double[] array, final double value) {
+		return indexOf(array, value) != -1;
+	}
+
+	/** Returns true if the given value is contained in the specified array. */
+	public static boolean contains(final float[] array, final float value) {
+		return indexOf(array, value) != -1;
+	}
+
+	/** Returns true if the given value is contained in the specified array. */
+	public static boolean contains(final int[] array, final int value) {
+		return indexOf(array, value) != -1;
+	}
+
+	/** Returns true if the given value is contained in the specified array. */
+	public static boolean contains(final long[] array, final long value) {
+		return indexOf(array, value) != -1;
+	}
+
+	/** Returns true if the given value is contained in the specified array. */
+	public static boolean contains(final short[] array, final short value) {
+		return indexOf(array, value) != -1;
+	}
+
+	/** Returns true if the given value is contained in the specified array. */
+	public static boolean contains(final Object[] array, final Object value) {
+		return indexOf(array, value) != -1;
+	}
+
+	/**
+	 * Returns the index of the first occurrence of the given value in the given
+	 * array. If the value is not in the array, returns -1.
+	 */
+	public static int indexOf(final boolean[] array, final boolean value) {
+		for (int i = 0; i < array.length; i++) {
+			if (array[i] == value) return i;
+		}
+		return -1;
+	}
+
+	/**
+	 * Returns the index of the first occurrence of the given value in the given
+	 * array. If the value is not in the array, returns -1.
+	 */
+	public static int indexOf(final byte[] array, final byte value) {
+		for (int i = 0; i < array.length; i++) {
+			if (array[i] == value) return i;
+		}
+		return -1;
+	}
+
+	/**
+	 * Returns the index of the first occurrence of the given value in the given
+	 * array. If the value is not in the array, returns -1.
+	 */
+	public static int indexOf(final char[] array, final char value) {
+		for (int i = 0; i < array.length; i++) {
+			if (array[i] == value) return i;
+		}
+		return -1;
+	}
+
+	/**
+	 * Returns the index of the first occurrence of the given value in the given
+	 * array. If the value is not in the array, returns -1.
+	 */
+	public static int indexOf(final double[] array, final double value) {
+		for (int i = 0; i < array.length; i++) {
+			if (array[i] == value) return i;
+		}
+		return -1;
+	}
+
+	/**
+	 * Returns the index of the first occurrence of the given value in the given
+	 * array. If the value is not in the array, returns -1.
+	 */
+	public static int indexOf(final float[] array, final float value) {
+		for (int i = 0; i < array.length; i++) {
+			if (array[i] == value) return i;
+		}
+		return -1;
+	}
+
+	/**
+	 * Returns the index of the first occurrence of the given value in the given
+	 * array. If the value is not in the array, returns -1.
+	 */
+	public static int indexOf(final int[] array, final int value) {
+		for (int i = 0; i < array.length; i++) {
+			if (array[i] == value) return i;
+		}
+		return -1;
+	}
+
+	/**
+	 * Returns the index of the first occurrence of the given value in the given
+	 * array. If the value is not in the array, returns -1.
+	 */
+	public static int indexOf(final long[] array, final long value) {
+		for (int i = 0; i < array.length; i++) {
+			if (array[i] == value) return i;
+		}
+		return -1;
+	}
+
+	/**
+	 * Returns the index of the first occurrence of the given value in the given
+	 * array. If the value is not in the array, returns -1.
+	 */
+	public static int indexOf(final short[] array, final short value) {
+		for (int i = 0; i < array.length; i++) {
+			if (array[i] == value) return i;
+		}
+		return -1;
+	}
+
+	/**
+	 * Returns the index of the first occurrence of the given value in the given
+	 * Object array. If the value is not in the array, returns -1.
+	 */
+	public static int indexOf(final Object[] array, final Object value) {
+		for (int i = 0; i < array.length; i++) {
+			if (value == null) {
+				if (array[i] == null) return i;
+			}
+			else if (value.equals(array[i])) return i;
+		}
+		return -1;
+	}
+
+	// -- Helper methods --
+
+	private static String sizeAsProduct(final long... sizes) {
+		final StringBuilder sb = new StringBuilder();
+		boolean first = true;
+		for (final long size : sizes) {
+			if (first) first = false;
+			else sb.append(" x ");
+			sb.append(size);
+		}
+		return sb.toString();
+	}
+
+	private static boolean willOverflow(final long v1, final long v2) {
+		return Long.MAX_VALUE / v1 < v2;
+	}
+
 }