path: root/java/src/hdf/hdf5lib/HDFArray.java

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
 * 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://www.hdfgroup.org/licenses.               *
 * 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;
import java.util.Arrays;

/**
 * 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.HDF5JavaException
     *                object is not an array.
     */
    public HDFArray(Object anArray) throws HDF5JavaException
    {
        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]);
                }
                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 m = 0; /* the current array index */
        int index = 0;
        int i;
        Object flattenedArray = null;

        switch (ArrayDescriptor.NT) {
        case 'J':
            flattenedArray = (Object) HDFNativeData.byteToLong(_barray);
            break;
        case 'S':
            flattenedArray = (Object) HDFNativeData.byteToShort(_barray);
            break;
        case 'I':
            flattenedArray = (Object) HDFNativeData.byteToInt(_barray);
            break;
        case 'F':
            flattenedArray = (Object) HDFNativeData.byteToFloat(_barray);
            break;
        case 'D':
            flattenedArray = (Object) HDFNativeData.byteToDouble(_barray);
            break;
        case 'B':
            flattenedArray = (Object) _barray;
            break;
        case 'L':
            {
                if (ArrayDescriptor.className.equals("java.lang.Byte"))
                    flattenedArray = (Object) ByteToByteObj(_barray);
                else if (ArrayDescriptor.className.equals("java.lang.Short"))
                    flattenedArray = (Object) ByteToShort(_barray);
                else if (ArrayDescriptor.className.equals("java.lang.Integer"))
                    flattenedArray = (Object) ByteToInteger(_barray);
                else if (ArrayDescriptor.className.equals("java.lang.Long"))
                    flattenedArray = (Object) ByteToLongObj(_barray);
                else if (ArrayDescriptor.className.equals("java.lang.Float"))
                    flattenedArray = (Object) ByteToFloatObj(_barray);
                else if (ArrayDescriptor.className.equals("java.lang.Double"))
                    flattenedArray = (Object) ByteToDoubleObj(_barray);
                else {
                    HDF5JavaException ex = new HDF5JavaException("HDFArray: unsupported Object type: " + ArrayDescriptor.NT);
                    throw (ex);
                }
            } // end of statement for arrays of boxed objects
        default:
            HDF5JavaException ex = new HDF5JavaException("HDFArray: unknown or unsupported type: " + ArrayDescriptor.NT);
            throw (ex);
        } // end of switch statement for arrays of primitives

        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 {
                Object arow = null;
                int mm = m + ArrayDescriptor.dimlen[ArrayDescriptor.dims];
                switch (ArrayDescriptor.NT) {
                case 'B':
                    arow = (Object) Arrays.copyOfRange((byte[]) flattenedArray, m, mm);
                    break;
                case 'S':
                    arow = (Object) Arrays.copyOfRange((short[]) flattenedArray, m, mm);
                    break;
                case 'I':
                    arow = (Object) Arrays.copyOfRange((int[]) flattenedArray, m, mm);
                    break;
                case 'J':
                    arow = (Object) Arrays.copyOfRange((long[]) flattenedArray, m, mm);
                    break;
                case 'F':
                    arow = (Object) Arrays.copyOfRange((float[]) flattenedArray, m, mm);
                    break;
                case 'D':
                    arow = (Object) Arrays.copyOfRange((double[]) flattenedArray, m, mm);
                    break;
                case 'L':
                    {
                        if (ArrayDescriptor.className.equals("java.lang.Byte"))
                            arow = (Object) Arrays.copyOfRange((Byte[]) flattenedArray, m, mm);
                        else if (ArrayDescriptor.className.equals("java.lang.Short"))
                            arow = (Object) Arrays.copyOfRange((Short[]) flattenedArray, m, mm);
                        else if (ArrayDescriptor.className.equals("java.lang.Integer"))
                            arow = (Object) Arrays.copyOfRange((Integer[]) flattenedArray, m, mm);
                        else if (ArrayDescriptor.className.equals("java.lang.Long"))
                            arow = (Object) Arrays.copyOfRange((Long[]) flattenedArray, m, mm);
                        else if (ArrayDescriptor.className.equals("java.lang.Float"))
                            arow = (Object) Arrays.copyOfRange((Float[]) flattenedArray, m, mm);
                        else if (ArrayDescriptor.className.equals("java.lang.Double"))
                            arow = (Object) Arrays.copyOfRange((Double[]) flattenedArray, m, mm);
                        else {
                            HDF5JavaException ex = new HDF5JavaException("HDFArray: unsupported Object type: " + ArrayDescriptor.NT);
                            throw (ex);
                        }
                    } // end of statement for arrays of boxed numerics
                } // end of switch statement for arrays of primitives

                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]++;
                m = mm;
            }
            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.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]) + "?"));
        }

        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] = Integer.valueOf(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] = Integer.valueOf(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] = Short.valueOf(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] = Short.valueOf(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] = Byte.valueOf(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] = Byte.valueOf(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] = Float.valueOf(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] = Float.valueOf(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] = Double.valueOf(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] = Double.valueOf(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] = Long.valueOf(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] = Long.valueOf(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 int totalElements = 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 HDF5JavaException
    {
        Class tc = anArray.getClass();
        if (tc.isArray() == false) {
            /* exception: not an array */
            HDF5JavaException 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 elements = 1;
        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;
            elements *= dimlen[i];
        }
        totalElements = elements;

        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, " + totalElements + " elements)");
        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);
        }
    }
}