File: HDFArray.java

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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
 * Copyright by The HDF Group.                                               *
 * Copyright by the Board of Trustees of the University of Illinois.         *
 * All rights reserved.                                                      *
 *                                                                           *
 * This file is part of HDF5.  The full HDF5 copyright notice, including     *
 * terms governing use, modification, and redistribution, is contained in    *
 * the COPYING file, which can be found at the root of the source code       *
 * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
 * If you do not have access to either file, you may request a copy from     *
 * help@hdfgroup.org.                                                        *
 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */


package hdf.hdf5lib;

import hdf.hdf5lib.exceptions.HDF5Exception;
import hdf.hdf5lib.exceptions.HDF5JavaException;

/**
 * This is a class for handling multidimensional arrays for HDF.
 * <p>
 * The purpose is to allow the storage and retrieval of arbitrary array types
 * containing scientific data.
 * <p>
 * The methods support the conversion of an array to and from Java to a
 * one-dimensional array of bytes suitable for I/O by the C library.
 * <p>
 * This class heavily uses the <a
 * href="./hdf.hdf5lib.HDFNativeData.html">HDFNativeData</a> class to
 * convert between Java and C representations.
 */

public class HDFArray {

    private Object _theArray = null;
    private ArrayDescriptor _desc = null;
    private byte[] _barray = null;

    // public HDFArray() {}

    /**
     * The input must be a Java Array (possibly multidimensional) of primitive
     * numbers or sub-classes of Number.
     * <p>
     * The input is analysed to determine the number of dimensions and size of
     * each dimension, as well as the type of the elements.
     * <p>
     * The description is saved in private variables, and used to convert data.
     *
     * @param anArray
     *            The array object.
     *
     * @exception hdf.hdf5lib.exceptions.HDF5Exception
     *                object is not an array.
     */
    public HDFArray(Object anArray) throws HDF5Exception {

        if (anArray == null) {
            HDF5JavaException ex = new HDF5JavaException(
                    "HDFArray: array is null?: ");
        }
        Class tc = anArray.getClass();
        if (tc.isArray() == false) {
            /* exception: not an array */
            HDF5JavaException ex = new HDF5JavaException(
                    "HDFArray: not an array?: ");
            throw (ex);
        }
        _theArray = anArray;
        _desc = new ArrayDescriptor(_theArray);

        /* extra error checking -- probably not needed */
        if (_desc == null) {
            HDF5JavaException ex = new HDF5JavaException(
                    "HDFArray: internal error: array description failed?: ");
            throw (ex);
        }
    }

    /**
     * Allocate a one-dimensional array of bytes sufficient to store the array.
     *
     * @return A one-D array of bytes, filled with zeroes. The bytes are
     *         sufficient to hold the data of the Array passed to the
     *         constructor.
     * @exception hdf.hdf5lib.exceptions.HDF5JavaException
     *                Allocation failed.
     */

    public byte[] emptyBytes() throws HDF5JavaException {
        byte[] b = null;

        if ((ArrayDescriptor.dims == 1) && (ArrayDescriptor.NT == 'B')) {
            b = (byte[]) _theArray;
        }
        else {
            b = new byte[ArrayDescriptor.totalSize];
        }
        if (b == null) {
            HDF5JavaException ex = new HDF5JavaException(
                    "HDFArray: emptyBytes: allocation failed");
            throw (ex);
        }
        return (b);
    }

    /**
     * Given a Java array of numbers, convert it to a one-dimensional array of
     * bytes in correct native order.
     *
     * @return A one-D array of bytes, constructed from the Array passed to the
     *         constructor.
     * @exception hdf.hdf5lib.exceptions.HDF5JavaException
     *                the object not an array or other internal error.
     */
    public byte[] byteify() throws HDF5JavaException {

        if (_barray != null) {
            return _barray;
        }

        if (_theArray == null) {
            /* exception: not an array */
            HDF5JavaException ex = new HDF5JavaException(
                    "HDFArray: byteify not an array?: ");
            throw (ex);
        }

        if (ArrayDescriptor.dims == 1) {
            /* special case */
            if (ArrayDescriptor.NT == 'B') {
                /* really special case! */
                _barray = (byte[]) _theArray;
                return _barray;
            }
            else {
                try {
                    _barray = new byte[ArrayDescriptor.totalSize];

                    byte[] therow;
                    if (ArrayDescriptor.NT == 'I') {
                        therow = HDFNativeData.intToByte(0,
                                ArrayDescriptor.dimlen[1], (int[]) _theArray);
                    }
                    else if (ArrayDescriptor.NT == 'S') {
                        therow = HDFNativeData.shortToByte(0,
                                ArrayDescriptor.dimlen[1], (short[]) _theArray);
                    }
                    else if (ArrayDescriptor.NT == 'F') {
                        therow = HDFNativeData.floatToByte(0,
                                ArrayDescriptor.dimlen[1], (float[]) _theArray);
                    }
                    else if (ArrayDescriptor.NT == 'J') {
                        therow = HDFNativeData.longToByte(0,
                                ArrayDescriptor.dimlen[1], (long[]) _theArray);
                    }
                    else if (ArrayDescriptor.NT == 'D') {
                        therow = HDFNativeData
                                .doubleToByte(0, ArrayDescriptor.dimlen[1],
                                        (double[]) _theArray);
                    }
                    else if (ArrayDescriptor.NT == 'L') {
                        if (ArrayDescriptor.className.equals("java.lang.Byte")) {
                            therow = ByteObjToByte((Byte[]) _theArray);
                        }
                        else if (ArrayDescriptor.className
                                .equals("java.lang.Integer")) {
                            therow = IntegerToByte((Integer[]) _theArray);
                        }
                        else if (ArrayDescriptor.className
                                .equals("java.lang.Short")) {
                            therow = ShortToByte((Short[]) _theArray);
                        }
                        else if (ArrayDescriptor.className
                                .equals("java.lang.Float")) {
                            therow = FloatObjToByte((Float[]) _theArray);
                        }
                        else if (ArrayDescriptor.className
                                .equals("java.lang.Double")) {
                            therow = DoubleObjToByte((Double[]) _theArray);
                        }
                        else if (ArrayDescriptor.className
                                .equals("java.lang.Long")) {
                            therow = LongObjToByte((Long[]) _theArray);
                        }
                        else {
                            HDF5JavaException ex = new HDF5JavaException(
                                    "HDFArray: unknown type of Object?");
                            throw (ex);
                        }
                    }
                    else {
                        HDF5JavaException ex = new HDF5JavaException(
                                "HDFArray: unknown type of data?");
                        throw (ex);
                    }
                    System
                            .arraycopy(
                                    therow,
                                    0,
                                    _barray,
                                    0,
                                    (ArrayDescriptor.dimlen[1] * ArrayDescriptor.NTsize));
                    return _barray;
                }
                catch (OutOfMemoryError err) {
                    HDF5JavaException ex = new HDF5JavaException(
                            "HDFArray: byteify array too big?");
                    throw (ex);
                }
            }
        }

        try {
            _barray = new byte[ArrayDescriptor.totalSize];
        }
        catch (OutOfMemoryError err) {
            HDF5JavaException ex = new HDF5JavaException(
                    "HDFArray: byteify array too big?");
            throw (ex);
        }

        Object oo = _theArray;
        int n = 0; /* the current byte */
        int index = 0;
        int i;
        while (n < ArrayDescriptor.totalSize) {
            oo = ArrayDescriptor.objs[0];
            index = n / ArrayDescriptor.bytetoindex[0];
            index %= ArrayDescriptor.dimlen[0];
            for (i = 0; i < (ArrayDescriptor.dims); i++) {
                index = n / ArrayDescriptor.bytetoindex[i];
                index %= ArrayDescriptor.dimlen[i];

                if (index == ArrayDescriptor.currentindex[i]) {
                    /* then use cached copy */
                    oo = ArrayDescriptor.objs[i];
                }
                else {
                    /* check range of index */
                    if (index > (ArrayDescriptor.dimlen[i] - 1)) {
                        throw new java.lang.IndexOutOfBoundsException(
                                "HDFArray: byteify index OOB?");
                    }
                    oo = java.lang.reflect.Array.get(oo, index);
                    ArrayDescriptor.currentindex[i] = index;
                    ArrayDescriptor.objs[i] = oo;
                }
            }

            /* byte-ify */
            byte arow[];
            try {
                if (ArrayDescriptor.NT == 'J') {
                    arow = HDFNativeData
                            .longToByte(
                                    0,
                                    ArrayDescriptor.dimlen[ArrayDescriptor.dims],
                                    (long[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]);
                    arow = HDFNativeData
                            .longToByte(
                                    0,
                                    ArrayDescriptor.dimlen[ArrayDescriptor.dims],
                                    (long[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]);
                }
                else if (ArrayDescriptor.NT == 'I') {
                    arow = HDFNativeData
                            .intToByte(
                                    0,
                                    ArrayDescriptor.dimlen[ArrayDescriptor.dims],
                                    (int[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]);
                }
                else if (ArrayDescriptor.NT == 'S') {
                    arow = HDFNativeData
                            .shortToByte(
                                    0,
                                    ArrayDescriptor.dimlen[ArrayDescriptor.dims],
                                    (short[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]);
                }
                else if (ArrayDescriptor.NT == 'B') {
                    arow = (byte[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1];
                }
                else if (ArrayDescriptor.NT == 'F') {
                    /* 32 bit float */
                    arow = HDFNativeData
                            .floatToByte(
                                    0,
                                    ArrayDescriptor.dimlen[ArrayDescriptor.dims],
                                    (float[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]);
                }
                else if (ArrayDescriptor.NT == 'D') {
                    /* 64 bit float */
                    arow = HDFNativeData
                            .doubleToByte(
                                    0,
                                    ArrayDescriptor.dimlen[ArrayDescriptor.dims],
                                    (double[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]);
                }
                else if (ArrayDescriptor.NT == 'L') {
                    if (ArrayDescriptor.className.equals("java.lang.Byte")) {
                        arow = ByteObjToByte((Byte[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]);
                    }
                    else if (ArrayDescriptor.className
                            .equals("java.lang.Integer")) {
                        arow = IntegerToByte((Integer[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]);
                    }
                    else if (ArrayDescriptor.className
                            .equals("java.lang.Short")) {
                        arow = ShortToByte((Short[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]);
                    }
                    else if (ArrayDescriptor.className
                            .equals("java.lang.Float")) {
                        arow = FloatObjToByte((Float[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]);
                    }
                    else if (ArrayDescriptor.className
                            .equals("java.lang.Double")) {
                        arow = DoubleObjToByte((Double[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]);
                    }
                    else if (ArrayDescriptor.className.equals("java.lang.Long")) {
                        arow = LongObjToByte((Long[]) ArrayDescriptor.objs[ArrayDescriptor.dims - 1]);
                    }
                    else {
                        HDF5JavaException ex = new HDF5JavaException(
                                "HDFArray: byteify Object type not implemented?");
                        throw (ex);
                    }
                }
                else {
                    HDF5JavaException ex = new HDF5JavaException(
                            "HDFArray: byteify unknown type not implemented?");
                    throw (ex);
                }
                System
                        .arraycopy(
                                arow,
                                0,
                                _barray,
                                n,
                                (ArrayDescriptor.dimlen[ArrayDescriptor.dims] * ArrayDescriptor.NTsize));
                n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1];
            }
            catch (OutOfMemoryError err) {
                HDF5JavaException ex = new HDF5JavaException(
                        "HDFArray: byteify array too big?");
                throw (ex);
            }
        }
        /* assert: the whole array is completed--currentindex should == len - 1 */

        /* error checks */

        if (n < ArrayDescriptor.totalSize) {
            throw new java.lang.InternalError(new String(
                    "HDFArray::byteify: Panic didn't complete all input data: n=  "
                            + n + " size = " + ArrayDescriptor.totalSize));
        }
        for (i = 0; i < ArrayDescriptor.dims; i++) {
            if (ArrayDescriptor.currentindex[i] != ArrayDescriptor.dimlen[i] - 1) {
                throw new java.lang.InternalError(new String(
                        "Panic didn't complete all data: currentindex[" + i
                                + "] = " + ArrayDescriptor.currentindex[i]
                                + " (should be "
                                + (ArrayDescriptor.dimlen[i] - 1) + " ?)"));
            }
        }
        return _barray;
    }

    /**
     * Given a one-dimensional array of bytes representing numbers, convert it
     * to a java array of the shape and size passed to the constructor.
     *
     * @param bytes
     *            The bytes to construct the Array.
     * @return An Array (possibly multidimensional) of primitive or number
     *         objects.
     * @exception hdf.hdf5lib.exceptions.HDF5JavaException
     *                the object not an array or other internal error.
     */
    public Object arrayify(byte[] bytes) throws HDF5JavaException {

        if (_theArray == null) {
            /* exception: not an array */
            HDF5JavaException ex = new HDF5JavaException(
                    "arrayify: not an array?: ");
            throw (ex);
        }

        if (java.lang.reflect.Array.getLength(bytes) != ArrayDescriptor.totalSize) {
            /* exception: array not right size */
            HDF5JavaException ex = new HDF5JavaException(
                    "arrayify: array is wrong size?: ");
            throw (ex);
        }
        _barray = bytes; /* hope that the bytes are correct.... */
        if (ArrayDescriptor.dims == 1) {
            /* special case */
            /* 2 data copies here! */
            try {
                if (ArrayDescriptor.NT == 'I') {
                    int[] x = HDFNativeData.byteToInt(_barray);
                    System.arraycopy(x, 0, _theArray, 0,
                            ArrayDescriptor.dimlen[1]);
                    return _theArray;
                }
                else if (ArrayDescriptor.NT == 'S') {
                    short[] x = HDFNativeData.byteToShort(_barray);
                    System.arraycopy(x, 0, _theArray, 0,
                            ArrayDescriptor.dimlen[1]);
                    return _theArray;
                }
                else if (ArrayDescriptor.NT == 'F') {
                    float x[] = HDFNativeData.byteToFloat(_barray);
                    System.arraycopy(x, 0, _theArray, 0,
                            ArrayDescriptor.dimlen[1]);
                    return _theArray;
                }
                else if (ArrayDescriptor.NT == 'J') {
                    long x[] = HDFNativeData.byteToLong(_barray);
                    System.arraycopy(x, 0, _theArray, 0,
                            ArrayDescriptor.dimlen[1]);
                    return _theArray;
                }
                else if (ArrayDescriptor.NT == 'D') {
                    double x[] = HDFNativeData.byteToDouble(_barray);
                    System.arraycopy(x, 0, _theArray, 0,
                            ArrayDescriptor.dimlen[1]);
                    return _theArray;
                }
                else if (ArrayDescriptor.NT == 'B') {
                    System.arraycopy(_barray, 0, _theArray, 0,
                            ArrayDescriptor.dimlen[1]);
                    return _theArray;
                }
                else if (ArrayDescriptor.NT == 'L') {
                    if (ArrayDescriptor.className.equals("java.lang.Byte")) {
                        Byte I[] = ByteToByteObj(_barray);
                        System.arraycopy(I, 0, _theArray, 0,
                                ArrayDescriptor.dimlen[1]);
                        return _theArray;
                    }
                    else if (ArrayDescriptor.className
                            .equals("java.lang.Integer")) {
                        Integer I[] = ByteToInteger(_barray);
                        System.arraycopy(I, 0, _theArray, 0,
                                ArrayDescriptor.dimlen[1]);
                        return _theArray;
                    }
                    else if (ArrayDescriptor.className
                            .equals("java.lang.Short")) {
                        Short I[] = ByteToShort(_barray);
                        System.arraycopy(I, 0, _theArray, 0,
                                ArrayDescriptor.dimlen[1]);
                        return _theArray;
                    }
                    else if (ArrayDescriptor.className
                            .equals("java.lang.Float")) {
                        Float I[] = ByteToFloatObj(_barray);
                        System.arraycopy(I, 0, _theArray, 0,
                                ArrayDescriptor.dimlen[1]);
                        return _theArray;
                    }
                    else if (ArrayDescriptor.className
                            .equals("java.lang.Double")) {
                        Double I[] = ByteToDoubleObj(_barray);
                        System.arraycopy(I, 0, _theArray, 0,
                                ArrayDescriptor.dimlen[1]);
                        return _theArray;
                    }
                    else if (ArrayDescriptor.className.equals("java.lang.Long")) {
                        Long I[] = ByteToLongObj(_barray);
                        System.arraycopy(I, 0, _theArray, 0,
                                ArrayDescriptor.dimlen[1]);
                        return _theArray;
                    }
                    else {
                        HDF5JavaException ex = new HDF5JavaException(
                                "arrayify:  Object type not implemented yet...");
                        throw (ex);
                    }
                }
                else {
                    HDF5JavaException ex = new HDF5JavaException(
                            "arrayify:  unknown type not implemented yet...");
                    throw (ex);
                }
            }
            catch (OutOfMemoryError err) {
                HDF5JavaException ex = new HDF5JavaException(
                        "HDFArray: arrayify array too big?");
                throw (ex);
            }
        }
        /* Assert dims >= 2 */

        Object oo = _theArray;
        int n = 0; /* the current byte */
        int index = 0;
        int i;
        while (n < ArrayDescriptor.totalSize) {
            oo = ArrayDescriptor.objs[0];
            index = n / ArrayDescriptor.bytetoindex[0];
            index %= ArrayDescriptor.dimlen[0];
            for (i = 0; i < (ArrayDescriptor.dims); i++) {
                index = n / ArrayDescriptor.bytetoindex[i];
                index %= ArrayDescriptor.dimlen[i];

                if (index == ArrayDescriptor.currentindex[i]) {
                    /* then use cached copy */
                    oo = ArrayDescriptor.objs[i];
                }
                else {
                    /* check range of index */
                    if (index > (ArrayDescriptor.dimlen[i] - 1)) {
                        System.out.println("out of bounds?");
                        return null;
                    }
                    oo = java.lang.reflect.Array.get(oo, index);
                    ArrayDescriptor.currentindex[i] = index;
                    ArrayDescriptor.objs[i] = oo;
                }
            }

            /* array-ify */
            try {
                if (ArrayDescriptor.NT == 'J') {
                    long[] arow = HDFNativeData.byteToLong(n,
                            ArrayDescriptor.dimlen[ArrayDescriptor.dims],
                            _barray);
                    java.lang.reflect.Array
                            .set(
                                    ArrayDescriptor.objs[ArrayDescriptor.dims - 2],
                                    (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]),
                                    arow);
                    n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1];
                    ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++;
                }
                else if (ArrayDescriptor.NT == 'I') {
                    int[] arow = HDFNativeData.byteToInt(n,
                            ArrayDescriptor.dimlen[ArrayDescriptor.dims],
                            _barray);
                    java.lang.reflect.Array
                            .set(
                                    ArrayDescriptor.objs[ArrayDescriptor.dims - 2],
                                    (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]),
                                    arow);

                    n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1];
                    ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++;
                }
                else if (ArrayDescriptor.NT == 'S') {
                    short[] arow = HDFNativeData.byteToShort(n,
                            ArrayDescriptor.dimlen[ArrayDescriptor.dims],
                            _barray);
                    java.lang.reflect.Array
                            .set(
                                    ArrayDescriptor.objs[ArrayDescriptor.dims - 2],
                                    (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]),
                                    arow);

                    n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1];
                    ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++;
                }
                else if (ArrayDescriptor.NT == 'B') {
                    System.arraycopy(_barray, n,
                            ArrayDescriptor.objs[ArrayDescriptor.dims - 1], 0,
                            ArrayDescriptor.dimlen[ArrayDescriptor.dims]);
                    n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1];
                }
                else if (ArrayDescriptor.NT == 'F') {
                    float arow[] = HDFNativeData.byteToFloat(n,
                            ArrayDescriptor.dimlen[ArrayDescriptor.dims],
                            _barray);
                    java.lang.reflect.Array
                            .set(
                                    ArrayDescriptor.objs[ArrayDescriptor.dims - 2],
                                    (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]),
                                    arow);

                    n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1];
                    ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++;
                }
                else if (ArrayDescriptor.NT == 'D') {
                    double[] arow = HDFNativeData.byteToDouble(n,
                            ArrayDescriptor.dimlen[ArrayDescriptor.dims],
                            _barray);
                    java.lang.reflect.Array
                            .set(
                                    ArrayDescriptor.objs[ArrayDescriptor.dims - 2],
                                    (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]),
                                    arow);

                    n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1];
                    ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++;
                }
                else if (ArrayDescriptor.NT == 'L') {
                    if (ArrayDescriptor.className.equals("java.lang.Byte")) {
                        Byte I[] = ByteToByteObj(n,
                                ArrayDescriptor.dimlen[ArrayDescriptor.dims],
                                _barray);
                        java.lang.reflect.Array
                                .set(
                                        ArrayDescriptor.objs[ArrayDescriptor.dims - 2],
                                        (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]),
                                        I);

                        n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1];
                        ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++;
                    }
                    else if (ArrayDescriptor.className
                            .equals("java.lang.Integer")) {
                        Integer I[] = ByteToInteger(n,
                                ArrayDescriptor.dimlen[ArrayDescriptor.dims],
                                _barray);
                        java.lang.reflect.Array
                                .set(
                                        ArrayDescriptor.objs[ArrayDescriptor.dims - 2],
                                        (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]),
                                        I);

                        n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1];
                        ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++;
                    }
                    else if (ArrayDescriptor.className
                            .equals("java.lang.Short")) {
                        Short I[] = ByteToShort(n,
                                ArrayDescriptor.dimlen[ArrayDescriptor.dims],
                                _barray);
                        java.lang.reflect.Array
                                .set(
                                        ArrayDescriptor.objs[ArrayDescriptor.dims - 2],
                                        (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]),
                                        I);

                        n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1];
                        ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++;
                    }
                    else if (ArrayDescriptor.className
                            .equals("java.lang.Float")) {
                        Float I[] = ByteToFloatObj(n,
                                ArrayDescriptor.dimlen[ArrayDescriptor.dims],
                                _barray);
                        java.lang.reflect.Array
                                .set(
                                        ArrayDescriptor.objs[ArrayDescriptor.dims - 2],
                                        (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]),
                                        I);

                        n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1];
                        ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++;
                    }
                    else if (ArrayDescriptor.className
                            .equals("java.lang.Double")) {
                        Double I[] = ByteToDoubleObj(n,
                                ArrayDescriptor.dimlen[ArrayDescriptor.dims],
                                _barray);
                        java.lang.reflect.Array
                                .set(
                                        ArrayDescriptor.objs[ArrayDescriptor.dims - 2],
                                        (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]),
                                        I);

                        n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1];
                        ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++;
                    }
                    else if (ArrayDescriptor.className.equals("java.lang.Long")) {
                        Long I[] = ByteToLongObj(n,
                                ArrayDescriptor.dimlen[ArrayDescriptor.dims],
                                _barray);
                        java.lang.reflect.Array
                                .set(
                                        ArrayDescriptor.objs[ArrayDescriptor.dims - 2],
                                        (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]),
                                        I);

                        n += ArrayDescriptor.bytetoindex[ArrayDescriptor.dims - 1];
                        ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1]++;
                    }
                    else {
                        HDF5JavaException ex = new HDF5JavaException(
                                "HDFArray: unsupported Object type: "
                                        + ArrayDescriptor.NT);
                        throw (ex);
                    }
                }
                else {
                    HDF5JavaException ex = new HDF5JavaException(
                            "HDFArray: unknown or unsupported type: "
                                    + ArrayDescriptor.NT);
                    throw (ex);
                }
            }
            catch (OutOfMemoryError err) {
                HDF5JavaException ex = new HDF5JavaException(
                        "HDFArray: arrayify array too big?");
                throw (ex);
            }

        }

        /* assert: the whole array is completed--currentindex should == len - 1 */

        /* error checks */

        if (n < ArrayDescriptor.totalSize) {
            throw new java.lang.InternalError(new String(
                    "HDFArray::arrayify Panic didn't complete all input data: n=  "
                            + n + " size = " + ArrayDescriptor.totalSize));
        }
        for (i = 0; i <= ArrayDescriptor.dims - 2; i++) {
            if (ArrayDescriptor.currentindex[i] != ArrayDescriptor.dimlen[i] - 1) {
                throw new java.lang.InternalError(new String(
                        "HDFArray::arrayify Panic didn't complete all data: currentindex["
                                + i + "] = " + ArrayDescriptor.currentindex[i]
                                + " (should be "
                                + (ArrayDescriptor.dimlen[i] - 1) + "?"));
            }
        }
        if (ArrayDescriptor.NT != 'B') {
            if (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1] != ArrayDescriptor.dimlen[ArrayDescriptor.dims - 1]) {
                throw new java.lang.InternalError(new String(
                        "HDFArray::arrayify Panic didn't complete all data: currentindex["
                                + i + "] = " + ArrayDescriptor.currentindex[i]
                                + " (should be " + (ArrayDescriptor.dimlen[i])
                                + "?"));
            }
        }
        else {
            if (ArrayDescriptor.currentindex[ArrayDescriptor.dims - 1] != (ArrayDescriptor.dimlen[ArrayDescriptor.dims - 1] - 1)) {
                throw new java.lang.InternalError(new String(
                        "HDFArray::arrayify Panic didn't complete all data: currentindex["
                                + i + "] = " + ArrayDescriptor.currentindex[i]
                                + " (should be "
                                + (ArrayDescriptor.dimlen[i] - 1) + "?"));
            }
        }

        return _theArray;
    }

    private byte[] IntegerToByte(Integer in[]) {
        int nelems = java.lang.reflect.Array.getLength(in);
        int[] out = new int[nelems];

        for (int i = 0; i < nelems; i++) {
            out[i] = in[i].intValue();
        }
        return HDFNativeData.intToByte(0, nelems, out);
    }

    private Integer[] ByteToInteger(byte[] bin) {
        int in[] = HDFNativeData.byteToInt(bin);
        int nelems = java.lang.reflect.Array.getLength(in);
        Integer[] out = new Integer[nelems];

        for (int i = 0; i < nelems; i++) {
            out[i] = new Integer(in[i]);
        }
        return out;
    }

    private Integer[] ByteToInteger(int start, int len, byte[] bin) {
        int in[] = HDFNativeData.byteToInt(start, len, bin);
        int nelems = java.lang.reflect.Array.getLength(in);
        Integer[] out = new Integer[nelems];

        for (int i = 0; i < nelems; i++) {
            out[i] = new Integer(in[i]);
        }
        return out;
    }

    private byte[] ShortToByte(Short in[]) {
        int nelems = java.lang.reflect.Array.getLength(in);
        short[] out = new short[nelems];

        for (int i = 0; i < nelems; i++) {
            out[i] = in[i].shortValue();
        }
        return HDFNativeData.shortToByte(0, nelems, out);
    }

    private Short[] ByteToShort(byte[] bin) {
        short in[] = HDFNativeData.byteToShort(bin);
        int nelems = java.lang.reflect.Array.getLength((Object) in);
        Short[] out = new Short[nelems];

        for (int i = 0; i < nelems; i++) {
            out[i] = new Short(in[i]);
        }
        return out;
    }

    private Short[] ByteToShort(int start, int len, byte[] bin) {
        short in[] = (short[]) HDFNativeData.byteToShort(start, len, bin);
        int nelems = java.lang.reflect.Array.getLength((Object) in);
        Short[] out = new Short[nelems];

        for (int i = 0; i < nelems; i++) {
            out[i] = new Short(in[i]);
        }
        return out;
    }

    private byte[] ByteObjToByte(Byte in[]) {
        int nelems = java.lang.reflect.Array.getLength((Object) in);
        byte[] out = new byte[nelems];

        for (int i = 0; i < nelems; i++) {
            out[i] = in[i].byteValue();
        }
        return out;
    }

    private Byte[] ByteToByteObj(byte[] bin) {
        int nelems = java.lang.reflect.Array.getLength((Object) bin);
        Byte[] out = new Byte[nelems];

        for (int i = 0; i < nelems; i++) {
            out[i] = new Byte(bin[i]);
        }
        return out;
    }

    private Byte[] ByteToByteObj(int start, int len, byte[] bin) {
        Byte[] out = new Byte[len];

        for (int i = 0; i < len; i++) {
            out[i] = new Byte(bin[i]);
        }
        return out;
    }

    private byte[] FloatObjToByte(Float in[]) {
        int nelems = java.lang.reflect.Array.getLength((Object) in);
        float[] out = new float[nelems];

        for (int i = 0; i < nelems; i++) {
            out[i] = in[i].floatValue();
        }
        return HDFNativeData.floatToByte(0, nelems, out);
    }

    private Float[] ByteToFloatObj(byte[] bin) {
        float in[] = (float[]) HDFNativeData.byteToFloat(bin);
        int nelems = java.lang.reflect.Array.getLength((Object) in);
        Float[] out = new Float[nelems];

        for (int i = 0; i < nelems; i++) {
            out[i] = new Float(in[i]);
        }
        return out;
    }

    private Float[] ByteToFloatObj(int start, int len, byte[] bin) {
        float in[] = (float[]) HDFNativeData.byteToFloat(start, len, bin);
        int nelems = java.lang.reflect.Array.getLength((Object) in);
        Float[] out = new Float[nelems];

        for (int i = 0; i < nelems; i++) {
            out[i] = new Float(in[i]);
        }
        return out;
    }

    private byte[] DoubleObjToByte(Double in[]) {
        int nelems = java.lang.reflect.Array.getLength((Object) in);
        double[] out = new double[nelems];

        for (int i = 0; i < nelems; i++) {
            out[i] = in[i].doubleValue();
        }
        return HDFNativeData.doubleToByte(0, nelems, out);
    }

    private Double[] ByteToDoubleObj(byte[] bin) {
        double in[] = (double[]) HDFNativeData.byteToDouble(bin);
        int nelems = java.lang.reflect.Array.getLength((Object) in);
        Double[] out = new Double[nelems];

        for (int i = 0; i < nelems; i++) {
            out[i] = new Double(in[i]);
        }
        return out;
    }

    private Double[] ByteToDoubleObj(int start, int len, byte[] bin) {
        double in[] = (double[]) HDFNativeData.byteToDouble(start, len, bin);
        int nelems = java.lang.reflect.Array.getLength((Object) in);
        Double[] out = new Double[nelems];

        for (int i = 0; i < nelems; i++) {
            out[i] = new Double(in[i]);
        }
        return out;
    }

    private byte[] LongObjToByte(Long in[]) {
        int nelems = java.lang.reflect.Array.getLength((Object) in);
        long[] out = new long[nelems];

        for (int i = 0; i < nelems; i++) {
            out[i] = in[i].longValue();
        }
        return HDFNativeData.longToByte(0, nelems, out);
    }

    private Long[] ByteToLongObj(byte[] bin) {
        long in[] = (long[]) HDFNativeData.byteToLong(bin);
        int nelems = java.lang.reflect.Array.getLength((Object) in);
        Long[] out = new Long[nelems];

        for (int i = 0; i < nelems; i++) {
            out[i] = new Long(in[i]);
        }
        return out;
    }

    private Long[] ByteToLongObj(int start, int len, byte[] bin) {
        long in[] = (long[]) HDFNativeData.byteToLong(start, len, bin);
        int nelems = java.lang.reflect.Array.getLength((Object) in);
        Long[] out = new Long[nelems];

        for (int i = 0; i < nelems; i++) {
            out[i] = new Long(in[i]);
        }
        return out;
    }
}

/**
 * This private class is used by HDFArray to discover the shape and type of an
 * arbitrary array.
 * <p>
 * We use java.lang.reflection here.
 */
class ArrayDescriptor {

    static String theType = "";
    static Class theClass = null;
    static int[] dimlen = null;
    static int[] dimstart = null;
    static int[] currentindex = null;
    static int[] bytetoindex = null;
    static int totalSize = 0;
    static Object[] objs = null;
    static char NT = ' '; /* must be B,S,I,L,F,D, else error */
    static int NTsize = 0;
    static int dims = 0;
    static String className;

    public ArrayDescriptor(Object anArray) throws HDF5Exception {

        Class tc = anArray.getClass();
        if (tc.isArray() == false) {
            /* exception: not an array */
            HDF5Exception ex = new HDF5JavaException(
                    "ArrayDescriptor: not an array?: ");
            throw (ex);
        }

        theClass = tc;

        /*
         * parse the type descriptor to discover the shape of the array
         */
        String ss = tc.toString();
        theType = ss;
        int n = 6;
        dims = 0;
        char c = ' ';
        while (n < ss.length()) {
            c = ss.charAt(n);
            n++;
            if (c == '[') {
                dims++;
            }
        }

        String css = ss.substring(ss.lastIndexOf('[') + 1);
        Class compC = tc.getComponentType();
        String cs = compC.toString();
        NT = c; /* must be B,S,I,L,F,D, else error */
        if (NT == 'B') {
            NTsize = 1;
        }
        else if (NT == 'S') {
            NTsize = 2;
        }
        else if ((NT == 'I') || (NT == 'F')) {
            NTsize = 4;
        }
        else if ((NT == 'J') || (NT == 'D')) {
            NTsize = 8;
        }
        else if (css.startsWith("Ljava.lang.Byte")) {
            NT = 'L';
            className = "java.lang.Byte";
            NTsize = 1;
        }
        else if (css.startsWith("Ljava.lang.Short")) {
            NT = 'L';
            className = "java.lang.Short";
            NTsize = 2;
        }
        else if (css.startsWith("Ljava.lang.Integer")) {
            NT = 'L';
            className = "java.lang.Integer";
            NTsize = 4;
        }
        else if (css.startsWith("Ljava.lang.Float")) {
            NT = 'L';
            className = "java.lang.Float";
            NTsize = 4;
        }
        else if (css.startsWith("Ljava.lang.Double")) {
            NT = 'L';
            className = "java.lang.Double";
            NTsize = 8;
        }
        else if (css.startsWith("Ljava.lang.Long")) {
            NT = 'L';
            className = "java.lang.Long";
            NTsize = 8;
        }
        else if (css.startsWith("Ljava.lang.String")) {
            NT = 'L';
            className = "java.lang.String";
            NTsize = 1;
            throw new HDF5JavaException(new String(
                    "ArrayDesciptor: Warning:  String array not fully supported yet"));
        }
        else {
            /*
             * exception: not a numeric type
             */
            throw new HDF5JavaException(new String(
                    "ArrayDesciptor: Error:  array is not numeric (type is "
                            + css + ") ?"));
        }

        /* fill in the table */
        dimlen = new int[dims + 1];
        dimstart = new int[dims + 1];
        currentindex = new int[dims + 1];
        bytetoindex = new int[dims + 1];
        objs = new Object[dims + 1];

        Object o = anArray;
        objs[0] = o;
        dimlen[0] = 1;
        dimstart[0] = 0;
        currentindex[0] = 0;
        int i;
        for (i = 1; i <= dims; i++) {
            dimlen[i] = java.lang.reflect.Array.getLength((Object) o);
            o = java.lang.reflect.Array.get((Object) o, 0);
            objs[i] = o;
            dimstart[i] = 0;
            currentindex[i] = 0;
        }

        int j;
        int dd;
        bytetoindex[dims] = NTsize;
        for (i = dims; i >= 0; i--) {
            dd = NTsize;
            for (j = i; j < dims; j++) {
                dd *= dimlen[j + 1];
            }
            bytetoindex[i] = dd;
        }

        totalSize = bytetoindex[0];
    }

    /**
     * Debug dump
     */
    public void dumpInfo() {
        System.out.println("Type: " + theType);
        System.out.println("Class: " + theClass);
        System.out.println("NT: " + NT + " NTsize: " + NTsize);
        System.out.println("Array has " + dims + " dimensions (" + totalSize
                + " bytes)");
        int i;
        for (i = 0; i <= dims; i++) {
            Class tc = objs[i].getClass();
            String ss = tc.toString();
            System.out.println(i + ":  start " + dimstart[i] + ": len "
                    + dimlen[i] + " current " + currentindex[i]
                    + " bytetoindex " + bytetoindex[i] + " object " + objs[i]
                    + " otype " + ss);
        }
    }
}