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HDFArray.java

/****************************************************************************
 * NCSA HDF                                                                 *
 * National Comptational Science Alliance                                   *
 * University of Illinois at Urbana-Champaign                               *
 * 605 E. Springfield, Champaign IL 61820                                   *
 *                                                                          *
 * For conditions of distribution and use, see the accompanying             *
 * hdf-java/COPYING file.                                                   *
 *                                                                          *
 ****************************************************************************/

package ncsa.hdf.hdf5lib;

import ncsa.hdf.hdf5lib.exceptions.*;
/**
 *  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="./ncsa.hdf.hdf5lib.HDFNativeData.html">HDFNativeData</a>
 *  class to convert between Java and C representations.
 */

00030 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.
 *
 *  @exception  ncsa.hdf.hdf5lib.exceptions.HDF5Exception  object is not an array.
 */
00050 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 ncsa.hdf.hdf5lib.exception.HDF5JavaException  Allocation failed.
 */

00084 public byte[] emptyBytes()
throws HDF5Exception
{
    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 ncsa.hdf.hdf5lib.exception.HDF5Exception  thrown for errors in HDF5
 *  @exception ncsa.hdf.hdf5lib.exception.HDF5JavaException  the object not an array or other internal error.
 */
00111 public byte[] byteify() throws HDF5Exception
{

    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 ncsa.hdf.hdf5lib.exception.HDF5Exception  thrown for errors in HDF5
 *  @exception ncsa.hdf.hdf5lib.exception.HDF5JavaException  the object not an array or other internal error.
 */
00290 public Object arrayify(byte[] bytes) throws HDF5Exception {

    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((Object)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((Object)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[] = (short [])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.
  */
00735 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")) {
            throw new HDF5JavaException(new String("ArrayDesciptor: Error:  String array not 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
          */
00858     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);
        }
    }
}

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