path: root/java/test/TestH5D.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://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 test;

import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;

import java.io.File;

import hdf.hdf5lib.H5;
import hdf.hdf5lib.HDF5Constants;
import hdf.hdf5lib.HDFNativeData;
import hdf.hdf5lib.callbacks.H5D_iterate_cb;
import hdf.hdf5lib.callbacks.H5D_iterate_t;
import hdf.hdf5lib.exceptions.HDF5Exception;
import hdf.hdf5lib.exceptions.HDF5LibraryException;

import org.junit.After;
import org.junit.Before;
import org.junit.Rule;
import org.junit.Test;
import org.junit.rules.TestName;

public class TestH5D {
    @Rule public TestName testname = new TestName();
    private static final String H5_FILE = "testD.h5";
    private static final int DIM_X = 4;
    private static final int DIM_Y = 6;
    private static final int RANK = 2;
    long H5fid = -1;
    long H5faplid = -1;
    long H5dsid = -1;
    long H5dtid = -1;
    long H5did = -1;
    long H5did0 = -1;
    long H5dcpl_id = -1;
    long[] H5dims = { DIM_X, DIM_Y };

    // Values for the status of space allocation
    enum H5D_space_status {
        H5D_SPACE_STATUS_ERROR(-1), H5D_SPACE_STATUS_NOT_ALLOCATED(0), H5D_SPACE_STATUS_PART_ALLOCATED(
                1), H5D_SPACE_STATUS_ALLOCATED(2);

        private int code;

        H5D_space_status(int space_status) {
            this.code = space_status;
        }

        public int getCode() {
            return this.code;
        }
    }

    private final void _deleteFile(String filename) {
        File file = new File(filename);

        if (file.exists()) {
            try {file.delete();}
            catch (SecurityException e) {}
        }
    }

    private final void _createPDataset(long fid, long dsid, String name, long dcpl_val) {

        try {
            H5dcpl_id = H5.H5Pcreate(dcpl_val);
        }
        catch (Exception err) {
            err.printStackTrace();
            fail("H5.H5Pcreate: " + err);
        }
        assertTrue("testH5D._createPDataset: H5.H5Pcreate: ", H5dcpl_id >= 0);

        // Set the allocation time to "early". This way we can be sure
        // that reading from the dataset immediately after creation will
        // return the fill value.
        try {
            H5.H5Pset_alloc_time(H5dcpl_id, HDF5Constants.H5D_ALLOC_TIME_EARLY);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        try {
            H5did0 = H5.H5Dcreate(fid, name,
                        HDF5Constants.H5T_STD_I32BE, dsid,
                        HDF5Constants.H5P_DEFAULT, H5dcpl_id, HDF5Constants.H5P_DEFAULT);
        }
        catch (Throwable err) {
            err.printStackTrace();
            fail("H5.H5Dcreate: " + err);
        }
        assertTrue("TestH5D._createPDataset.H5Dcreate: ", H5did0 >= 0);
    }

    private final void _createChunkDataset(long fid, long dsid, String name, long dapl) {

        try {
            H5dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE);
        }
        catch (Exception err) {
            err.printStackTrace();
            fail("H5.H5Pcreate: " + err);
        }
        assertTrue("testH5D._createChunkDataset: H5.H5Pcreate: ", H5dcpl_id >= 0);

        // Set the chunking.
        long[] chunk_dim = {4, 4};

        try {
            H5.H5Pset_chunk(H5dcpl_id, RANK, chunk_dim);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        try {
            H5did = H5.H5Dcreate(fid, name,
                        HDF5Constants.H5T_STD_I32BE, dsid,
                        HDF5Constants.H5P_DEFAULT, H5dcpl_id, dapl);
        }
        catch (Throwable err) {
            err.printStackTrace();
            fail("H5.H5Dcreate: " + err);
        }
        assertTrue("TestH5D._createChunkDataset.H5Dcreate: ", H5did >= 0);
    }

    private final void _createDataset(long fid, long dsid, String name, long dapl) {
        try {
            H5did = H5.H5Dcreate(fid, name,
                        HDF5Constants.H5T_STD_I32BE, dsid,
                        HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, dapl);
        }
        catch (Throwable err) {
            err.printStackTrace();
            fail("H5.H5Dcreate: " + err);
        }
        assertTrue("TestH5D._createDataset.H5Dcreate: ", H5did >= 0);
    }

    private final void _createVLDataset(long fid, long dsid, String name, long dapl) {
        try {
            H5dtid = H5.H5Tcopy(HDF5Constants.H5T_C_S1);
        }
        catch (Throwable err) {
            err.printStackTrace();
            fail("H5.H5Tcopy: " + err);
        }
        assertTrue("TestH5D._createVLDataset.H5Tcopy: ", H5dtid >= 0);
        try {
            H5.H5Tset_size(H5dtid, HDF5Constants.H5T_VARIABLE);
            assertTrue("TestH5D._createVLDataset.H5Tis_variable_str", H5.H5Tis_variable_str(H5dtid));
        }
        catch (Throwable err) {
            err.printStackTrace();
            fail("H5.H5Tset_size: " + err);
        }
        try {
            H5did = H5.H5Dcreate(fid, name, H5dtid, dsid,
                        HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, dapl);
        }
        catch (Throwable err) {
            err.printStackTrace();
            fail("H5.H5Dcreate: " + err);
        }
        assertTrue("TestH5D._createVLDataset.H5Dcreate: ", H5did >= 0);
    }

    private final void _closeH5file() throws HDF5LibraryException {
        if (H5dcpl_id >= 0)
            try {H5.H5Pclose(H5dcpl_id);} catch (Exception ex) {}
        if (H5did0 >= 0)
            try {H5.H5Dclose(H5did0);} catch (Exception ex) {}
        if (H5did >= 0)
            try {H5.H5Dclose(H5did);} catch (Exception ex) {}
        if (H5dtid > 0)
            try {H5.H5Tclose(H5dtid);} catch (Exception ex) {}
        if (H5dsid > 0)
            try {H5.H5Sclose(H5dsid);} catch (Exception ex) {}
        if (H5fid > 0)
            try {H5.H5Fclose(H5fid);} catch (Exception ex) {}
    }

    private final void _openH5file(String name, long dapl) {
       try {
           H5fid = H5.H5Fopen(H5_FILE,
                   HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT);
       }
       catch (Throwable err) {
           err.printStackTrace();
           fail("TestH5D._openH5file: " + err);
       }
       assertTrue("TestH5D._openH5file: H5.H5Fopen: ",H5fid >= 0);
       try {
           H5did = H5.H5Dopen(H5fid, name, dapl);
       }
       catch (Throwable err) {
           err.printStackTrace();
           fail("TestH5D._openH5file: " + err);
       }
       assertTrue("TestH5D._openH5file: H5.H5Dopen: ",H5did >= 0);
       try {
           H5dsid = H5.H5Dget_space(H5did);
       }
       catch (Throwable err) {
           err.printStackTrace();
           fail("TestH5D._openH5file: " + err);
       }
       assertTrue("TestH5D._openH5file: H5.H5Screate_simple: ",H5dsid > 0);
    }

    @Before
    public void createH5file()
            throws NullPointerException, HDF5Exception {
       assertTrue("H5 open ids is 0",H5.getOpenIDCount()==0);
       System.out.print(testname.getMethodName());

        try {
            H5faplid = H5.H5Pcreate(HDF5Constants.H5P_FILE_ACCESS);
            H5fid = H5.H5Fcreate(H5_FILE, HDF5Constants.H5F_ACC_TRUNC,
                    HDF5Constants.H5P_DEFAULT, H5faplid);
            H5dsid = H5.H5Screate_simple(RANK, H5dims, null);
        }
        catch (Throwable err) {
            err.printStackTrace();
            fail("TestH5D.createH5file: " + err);
        }
        assertTrue("TestH5D.createH5file: H5.H5Fcreate: ",H5fid >= 0);
        assertTrue("TestH5D.createH5file: H5.H5Screate_simple: ",H5dsid >= 0);

        H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL);
    }

    @After
    public void deleteH5file() throws HDF5LibraryException {
        if (H5dcpl_id >= 0)
            try {H5.H5Pclose(H5dcpl_id);} catch (Exception ex) {}
        if (H5did0 >= 0)
            try {H5.H5Dclose(H5did0);} catch (Exception ex) {}
        if (H5did >= 0)
            try {H5.H5Dclose(H5did);} catch (Exception ex) {}
        if (H5dtid > 0)
            try {H5.H5Tclose(H5dtid);} catch (Exception ex) {}
        if (H5dsid > 0)
            try {H5.H5Sclose(H5dsid);} catch (Exception ex) {}
        if (H5faplid >= 0)
            try {H5.H5Pclose(H5faplid);} catch (Exception ex) {}
        if (H5fid > 0)
            try {H5.H5Fclose(H5fid);} catch (Exception ex) {}

        _deleteFile(H5_FILE);
        System.out.println();
    }

    @Test
    public void testH5Dcreate() {
        long dataset_id = -1;
        try {
            dataset_id = H5.H5Dcreate(H5fid, "dset",
                HDF5Constants.H5T_STD_I32BE, H5dsid,
                HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
        }
        catch (Exception err) {
            err.printStackTrace();
            fail("testH5Dcreate: " + err);
        }
        assertTrue(dataset_id >= 0);

        // End access to the dataset and release resources used by it.
        try {
            if (dataset_id >= 0)
                H5.H5Dclose(dataset_id);
        }
        catch (Exception err) {
            err.printStackTrace();
        }
    }

    @Test
    public void testH5Dcreate_anon() {
        long dataset_id = -1;
        try {
            dataset_id = H5.H5Dcreate_anon(H5fid, HDF5Constants.H5T_STD_I32BE,
                    H5dsid, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
        }
        catch (Exception err) {
            err.printStackTrace();
            fail("testH5Dcreate_anon: " + err);
        }
        assertTrue(dataset_id >= 0);

        // End access to the dataset and release resources used by it.
        try {
            if (dataset_id >= 0)
                H5.H5Dclose(dataset_id);
        }
        catch (Exception err) {
            err.printStackTrace();
        }
    }

    @Test
    public void testH5Dopen() {
        long dataset_id = -1;
        _createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT);

        try {
            H5.H5Dclose(H5did);
            H5did = -1;
            dataset_id = H5.H5Dopen(H5fid, "dset", HDF5Constants.H5P_DEFAULT);
        }
        catch (Exception err) {
            err.printStackTrace();
            fail("testH5Dopen: " + err);
        }
        assertTrue("testH5Dopen: ", dataset_id >= 0);

        // End access to the dataset and release resources used by it.
        try {
            if (dataset_id >= 0)
                H5.H5Dclose(dataset_id);
        }
        catch (Exception err) {
            err.printStackTrace();
        }
    }

    @Test
    public void testH5Dget_storage_size_empty() {
        long storage_size = 0;
        _createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT);

        try {
            storage_size = H5.H5Dget_storage_size(H5did);
        }
        catch (Exception err) {
            err.printStackTrace();
            fail("testH5Dget_storage_size: " + err);
        }
        assertTrue("testH5Dget_storage_size: ", storage_size == 0);
    }

    @Test
    public void testH5Dget_storage_size() {
        long storage_size = 0;
        int[][] dset_data = new int[DIM_X][DIM_Y];
        int FILLVAL = 99;
        _createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT);

        // Initialize the dataset.
        for (int indx = 0; indx < DIM_X; indx++)
            for (int jndx = 0; jndx < DIM_Y; jndx++)
                dset_data[indx][jndx] = FILLVAL;

        try {
            if (H5did >= 0)
                H5.H5Dwrite(H5did, HDF5Constants.H5T_NATIVE_INT,
                        HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
                        HDF5Constants.H5P_DEFAULT, dset_data[0]);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        try {
            storage_size = H5.H5Dget_storage_size(H5did);
        }
        catch (Exception err) {
            err.printStackTrace();
            fail("testH5Dget_storage_size: " + err);
        }
        assertTrue("testH5Dget_storage_size: "+storage_size, storage_size == DIM_X*DIM_Y*4);
    }

    @Test
    public void testH5Dget_access_plist() {
        long dapl_id = -1;
        long test_dapl_id = -1;
        int[] mdc_nelmts1 = {0};
        int[] mdc_nelmts2 = {0};
        long[] rdcc_nelmts1 = {0};
        long[] rdcc_nelmts2 = {0};
        long[] rdcc_nbytes1 = {0};
        long[] rdcc_nbytes2 = {0};
        double[] rdcc_w01 = {0};
        double[] rdcc_w02 = {0};

        try {
            test_dapl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_ACCESS);
        }
        catch (Exception err) {
            err.printStackTrace();
            fail("testH5Dget_access_plist: H5.H5Pcreate: " + err);
        }
        assertTrue("testH5Dget_access_plist: test_dapl_id: ", test_dapl_id >= 0);

        try {
            H5.H5Pget_cache(H5faplid, mdc_nelmts1, rdcc_nelmts1, rdcc_nbytes1, rdcc_w01);
        }
        catch (Exception err) {
            err.printStackTrace();
            fail("testH5Dget_access_plist: H5.H5Pget_cache: " + err);
        }

        _createChunkDataset(H5fid, H5dsid, "dset", test_dapl_id);

        try {
            dapl_id = H5.H5Dget_access_plist(H5did);
            assertTrue("testH5Dget_access_plist: dapl_id: ", dapl_id >= 0);
            H5.H5Pget_chunk_cache(dapl_id, rdcc_nelmts2, rdcc_nbytes2, rdcc_w02);
        }
        catch (Exception err) {
            err.printStackTrace();
            fail("testH5Dget_access_plist: H5.H5Dget_access_plist: " + err);
        }

        // End access to the dataset and release resources used by it.
        try {
            if (dapl_id >= 0)
                H5.H5Pclose(dapl_id);
        }
        catch (Exception err) {
            err.printStackTrace();
        }
        try {
            if (test_dapl_id >= 0)
                H5.H5Pclose(test_dapl_id);
        }
        catch (Exception err) {
            err.printStackTrace();
        }
        assertTrue("testH5Dget_access_plist: ", rdcc_nelmts2==rdcc_nelmts2 && rdcc_nbytes2==rdcc_nbytes2);
    }

    @Test
    public void testH5Dget_space_status() {
        int[][] write_dset_data = new int[DIM_X][DIM_Y];
        int space_status = -1;
        int space_status0 = -1;

        // Initialize the dataset.
        for (int indx = 0; indx < DIM_X; indx++)
            for (int jndx = 0; jndx < DIM_Y; jndx++)
                write_dset_data[indx][jndx] = indx * jndx - jndx;

        _createPDataset(H5fid, H5dsid, "dset0", HDF5Constants.H5P_DATASET_CREATE);
        _createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT);

        // Retrieve and print space status and storage size for dset0.
        try {
            space_status0 = H5.H5Dget_space_status(H5did0);
        }
        catch (Exception e) {
            e.printStackTrace();
        }
        assertTrue("testH5Dget_space_status0 - H5.H5Dget_space_status: ", space_status0 == H5D_space_status.H5D_SPACE_STATUS_ALLOCATED.getCode());

        // Retrieve and print space status and storage size for dset.
        try {
            space_status = H5.H5Dget_space_status(H5did);
        }
        catch (Exception e) {
            e.printStackTrace();
        }
        assertFalse("testH5Dget_space_status - H5.H5Dget_space_status: ", space_status == H5D_space_status.H5D_SPACE_STATUS_ALLOCATED.getCode());

        // Write the data to the dataset.
        try {
            H5.H5Dwrite(H5did, HDF5Constants.H5T_NATIVE_INT,
                        HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
                        HDF5Constants.H5P_DEFAULT, write_dset_data);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Retrieve and print space status and storage size for dset.
        try {
            space_status = H5.H5Dget_space_status(H5did);
        }
        catch (Exception e) {
            e.printStackTrace();
        }
        assertTrue("testH5Dget_space_status - H5.H5Dget_space_status: ", space_status == H5D_space_status.H5D_SPACE_STATUS_ALLOCATED.getCode());
    }

    @Test(expected = HDF5LibraryException.class)
    public void testH5Dget_space_closed() throws Throwable {
        long dataset_id = -1;
        try {
            dataset_id = H5.H5Dcreate(H5fid, "dset",
                        HDF5Constants.H5T_STD_I32BE, H5dsid,
                        HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
        }
        catch (Throwable err) {
            err.printStackTrace();
            fail("H5.H5Dcreate: " + err);
        }
        assertTrue("TestH5D.testH5Dget_space_closed: ", dataset_id >= 0);
        H5.H5Dclose(dataset_id);

        H5.H5Dget_space(dataset_id);
    }

    @Test
    public void testH5Dget_space() {
        long dataspace_id = -1;
        _createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT);

        try {
            dataspace_id = H5.H5Dget_space(H5did);
        }
        catch (Exception err) {
            err.printStackTrace();
            fail("H5.H5Dget_space: " + err);
        }
        assertTrue("TestH5D.testH5Dget_space: ", dataspace_id >= 0);

        // End access to the dataspace and release resources used by it.
        try {
            if (dataspace_id >= 0)
                H5.H5Sclose(dataspace_id);
        }
        catch (Exception err) {
            err.printStackTrace();
        }
    }

    @Test(expected = HDF5LibraryException.class)
    public void testH5Dget_type_closed() throws Throwable {
        long dataset_id = -1;
        try {
            dataset_id = H5.H5Dcreate(H5fid, "dset",
                        HDF5Constants.H5T_STD_I32BE, H5dsid,
                        HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
        }
        catch (Throwable err) {
            err.printStackTrace();
            fail("H5.H5Dcreate: " + err);
        }
        assertTrue("TestH5D.testH5Dget_type_closed: ", dataset_id >= 0);
        H5.H5Dclose(dataset_id);

        H5.H5Dget_type(dataset_id);
    }

    @Test
    public void testH5Dget_type() {
        long datatype_id = -1;
        _createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT);

        try {
            datatype_id = H5.H5Dget_type(H5did);
        }
        catch (Exception err) {
            err.printStackTrace();
            fail("H5.H5Dget_type: " + err);
        }
        assertTrue("TestH5D.testH5Dget_type: ", datatype_id >= 0);

        // End access to the datatype and release resources used by it.
        try {
            if (datatype_id >= 0)
                H5.H5Tclose(datatype_id);
        }
        catch (Exception err) {
            err.printStackTrace();
        }
    }

    @Test
    public void testH5Dget_offset() {
        int[][] write_dset_data = new int[DIM_X][DIM_Y];
        long dset_address = 0;
        _createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT);

        try {
            // Test dataset address.  Should be undefined.
            dset_address = H5.H5Dget_offset(H5did);
        }
        catch (HDF5LibraryException hdfex) {
            ;
        }
        catch (Exception err) {
            err.printStackTrace();
            fail("H5.H5Dget_offset: " + err);
        }
        // Write the data to the dataset.
        try {
            H5.H5Dwrite(H5did, HDF5Constants.H5T_NATIVE_INT,
                        HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
                        HDF5Constants.H5P_DEFAULT, write_dset_data);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        try {
            // Test dataset address.
            dset_address = H5.H5Dget_offset(H5did);
        }
        catch (Exception err) {
            err.printStackTrace();
            fail("H5.H5Dget_offset: " + err);
        }

        assertTrue("TestH5D.testH5Dget_offset: ", dset_address >= 0);
    }

    @Test
    public void testH5Dfill_null() {
        int[] buf_data = new int[DIM_X*DIM_Y];

        // Initialize memory buffer
        for (int indx = 0; indx < DIM_X; indx++)
            for (int jndx = 0; jndx < DIM_Y; jndx++) {
                buf_data[(indx * DIM_Y) + jndx] = indx * jndx - jndx;
            }
        byte[] buf_array = HDFNativeData.intToByte(0, DIM_X*DIM_Y, buf_data);

        // Fill selection in memory
        try {
            H5.H5Dfill(null, HDF5Constants.H5T_NATIVE_UINT, buf_array, HDF5Constants.H5T_NATIVE_UINT, H5dsid);
        }
        catch (Exception err) {
            err.printStackTrace();
            fail("H5.H5Dfill: " + err);
        }
        buf_data = HDFNativeData.byteToInt(buf_array);

        // Verify memory buffer the hard way
        for (int indx = 0; indx < DIM_X; indx++)
            for (int jndx = 0; jndx < DIM_Y; jndx++)
                assertTrue("H5.H5Dfill: [" + indx+","+jndx + "] ", buf_data[(indx * DIM_Y) + jndx] == 0);
    }

    @Test
    public void testH5Dfill() {
        int[] buf_data = new int[DIM_X*DIM_Y];
        byte[] fill_value = HDFNativeData.intToByte(254);

        // Initialize memory buffer
        for (int indx = 0; indx < DIM_X; indx++)
            for (int jndx = 0; jndx < DIM_Y; jndx++) {
                buf_data[(indx * DIM_Y) + jndx] = indx * jndx - jndx;
            }
        byte[] buf_array = HDFNativeData.intToByte(0, DIM_X*DIM_Y, buf_data);

        // Fill selection in memory
        try {
            H5.H5Dfill(fill_value, HDF5Constants.H5T_NATIVE_UINT, buf_array, HDF5Constants.H5T_NATIVE_UINT, H5dsid);
        }
        catch (Exception err) {
            err.printStackTrace();
            fail("H5.H5Dfill: " + err);
        }
        buf_data = HDFNativeData.byteToInt(buf_array);

        // Verify memory buffer the hard way
        for (int indx = 0; indx < DIM_X; indx++)
            for (int jndx = 0; jndx < DIM_Y; jndx++)
                assertTrue("H5.H5Dfill: [" + indx+","+jndx + "] ", buf_data[(indx * DIM_Y) + jndx] == 254);
    }

    @Test
    public void testH5Diterate() {
        final int SPACE_RANK = 2;
        final int SPACE_FILL = 254;

        class H5D_iter_data implements H5D_iterate_t {
            public int fill_value;             /* The fill value to check */
            public long fill_curr_coord;          /* Current coordinate to examine */
            public long[] fill_coords;            /* Pointer to selection's coordinates */
        }

        H5D_iterate_t iter_data = new H5D_iter_data();

        class H5D_iter_callback implements H5D_iterate_cb {
            public int callback(byte[] elem_buf, long elem_id, int ndim, long[] point, H5D_iterate_t op_data) {
                //Check value in current buffer location
                int element = HDFNativeData.byteToInt(elem_buf, 0);
                if(element != ((H5D_iter_data)op_data).fill_value)
                    return -1;
                //Check number of dimensions
                if(ndim != SPACE_RANK)
                    return(-1);
                //Check Coordinates
                long[] fill_coords = new long[2];
                fill_coords[0] = ((H5D_iter_data)op_data).fill_coords[(int) (2 * ((H5D_iter_data)op_data).fill_curr_coord)];
                fill_coords[1] = ((H5D_iter_data)op_data).fill_coords[(int) (2 * ((H5D_iter_data)op_data).fill_curr_coord) + 1];
                ((H5D_iter_data)op_data).fill_curr_coord++;
                if(fill_coords[0] != point[0])
                    return(-1);
                if(fill_coords[1] != point[1])
                    return(-1);

                return(0);
            }
        }

        int[] buf_data = new int[DIM_X*DIM_Y];
        byte[] fill_value = HDFNativeData.intToByte(SPACE_FILL);

        // Initialize memory buffer
        for (int indx = 0; indx < DIM_X; indx++)
            for (int jndx = 0; jndx < DIM_Y; jndx++) {
                buf_data[(indx * DIM_Y) + jndx] = indx * jndx - jndx;
            }
        byte[] buf_array = HDFNativeData.intToByte(0, DIM_X*DIM_Y, buf_data);

        // Fill selection in memory
        try {
            H5.H5Dfill(fill_value, HDF5Constants.H5T_NATIVE_UINT, buf_array, HDF5Constants.H5T_NATIVE_UINT, H5dsid);
        }
        catch (Exception err) {
            err.printStackTrace();
            fail("H5.H5Diterate: " + err);
        }

        // Initialize the iterator structure
        ((H5D_iter_data)iter_data).fill_value = SPACE_FILL;
        ((H5D_iter_data)iter_data).fill_curr_coord = 0;
        // Set the coordinates of the selection
        ((H5D_iter_data)iter_data).fill_coords = new long[DIM_X*DIM_Y*SPACE_RANK];   /* Coordinates of selection */
        for (int indx = 0; indx < DIM_X; indx++)
            for (int jndx = 0; jndx < DIM_Y; jndx++) {
                ((H5D_iter_data)iter_data).fill_coords[2*(indx * DIM_Y + jndx)] = indx;
                ((H5D_iter_data)iter_data).fill_coords[2*(indx * DIM_Y + jndx) + 1] = jndx;
            } /* end for */

        // Iterate through selection, verifying correct data
        H5D_iterate_cb iter_cb = new H5D_iter_callback();
        int op_status = -1;
        try {
            op_status = H5.H5Diterate(buf_array, HDF5Constants.H5T_NATIVE_UINT, H5dsid, iter_cb, iter_data);
        }
        catch (Throwable err) {
            err.printStackTrace();
            fail("H5.H5Diterate: " + err);
        }
        assertTrue("H5Diterate ", op_status == 0);
    }

    @Test
    public void testH5Diterate_write() {
        final int SPACE_RANK = 2;
        final int SPACE_FILL = 254;

        class H5D_iter_data implements H5D_iterate_t {
            public int fill_value;             /* The fill value to check */
            public long fill_curr_coord;          /* Current coordinate to examine */
            public long[] fill_coords;            /* Pointer to selection's coordinates */
        }

        H5D_iterate_t iter_data = new H5D_iter_data();

        class H5D_iter_callback implements H5D_iterate_cb {
            public int callback(byte[] elem_buf, long elem_id, int ndim, long[] point, H5D_iterate_t op_data) {
                //Check value in current buffer location
                int element = HDFNativeData.byteToInt(elem_buf, 0);
                if(element != ((H5D_iter_data)op_data).fill_value)
                    return -1;
                //Check number of dimensions
                if(ndim != SPACE_RANK)
                    return(-1);
                //Check Coordinates
                long[] fill_coords = new long[2];
                fill_coords[0] = ((H5D_iter_data)op_data).fill_coords[(int) (2 * ((H5D_iter_data)op_data).fill_curr_coord)];
                fill_coords[1] = ((H5D_iter_data)op_data).fill_coords[(int) (2 * ((H5D_iter_data)op_data).fill_curr_coord) + 1];
                ((H5D_iter_data)op_data).fill_curr_coord++;
                if(fill_coords[0] != point[0])
                    return(-1);
                if(fill_coords[1] != point[1])
                    return(-1);
                element -= 128;
                byte[] new_elembuf = HDFNativeData.intToByte(element);
                elem_buf[0] = new_elembuf[0];
                elem_buf[1] = new_elembuf[1];
                elem_buf[2] = new_elembuf[2];
                elem_buf[3] = new_elembuf[3];
                return(0);
            }
        }

        int[] buf_data = new int[DIM_X*DIM_Y];
        byte[] fill_value = HDFNativeData.intToByte(SPACE_FILL);

        // Initialize memory buffer
        for (int indx = 0; indx < DIM_X; indx++)
            for (int jndx = 0; jndx < DIM_Y; jndx++) {
                buf_data[(indx * DIM_Y) + jndx] = indx * jndx - jndx;
            }
        byte[] buf_array = HDFNativeData.intToByte(0, DIM_X*DIM_Y, buf_data);

        // Fill selection in memory
        try {
            H5.H5Dfill(fill_value, HDF5Constants.H5T_NATIVE_UINT, buf_array, HDF5Constants.H5T_NATIVE_UINT, H5dsid);
        }
        catch (Exception err) {
            err.printStackTrace();
            fail("H5.H5Diterate: " + err);
        }

        // Initialize the iterator structure
        ((H5D_iter_data)iter_data).fill_value = SPACE_FILL;
        ((H5D_iter_data)iter_data).fill_curr_coord = 0;
        // Set the coordinates of the selection
        ((H5D_iter_data)iter_data).fill_coords = new long[DIM_X*DIM_Y*SPACE_RANK];   /* Coordinates of selection */
        for (int indx = 0; indx < DIM_X; indx++)
            for (int jndx = 0; jndx < DIM_Y; jndx++) {
                ((H5D_iter_data)iter_data).fill_coords[2*(indx * DIM_Y + jndx)] = indx;
                ((H5D_iter_data)iter_data).fill_coords[2*(indx * DIM_Y + jndx) + 1] = jndx;
            } /* end for */

        // Iterate through selection, verifying correct data
        H5D_iterate_cb iter_cb = new H5D_iter_callback();
        int op_status = -1;
        try {
            op_status = H5.H5Diterate(buf_array, HDF5Constants.H5T_NATIVE_UINT, H5dsid, iter_cb, iter_data);
        }
        catch (Throwable err) {
            err.printStackTrace();
            fail("H5.H5Diterate: " + err);
        }
        assertTrue("H5Diterate ", op_status == 0);

        buf_data = HDFNativeData.byteToInt(buf_array);

        // Verify memory buffer the hard way
        for (int indx = 0; indx < DIM_X; indx++)
            for (int jndx = 0; jndx < DIM_Y; jndx++)
                assertTrue("H5.H5Diterate: [" + indx+","+jndx + "] "+buf_data[(indx * DIM_Y) + jndx], buf_data[(indx * DIM_Y) + jndx] == 126);
    }

    @Test
    public void testH5Dvlen_get_buf_size() {
        String[] str_data = { "Parting", "is such", "sweet", "sorrow.",
                "Testing", "one", "two", "three.",
                "Dog,", "man's", "best", "friend.",
                "Diamonds", "are", "a", "girls!",
                "S A", "T U R", "D A Y", "night",
                "That's", "all", "folks", "!!!" };
        long vl_size = -1;  /* Number of bytes used */
        long str_data_bytes = 0;
        for (int idx = 0; idx < str_data.length; idx++)
            str_data_bytes += str_data[idx].length() + 1;  //Account for terminating null

        _createVLDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT);

        try {
            if ((H5did >= 0) && (H5dtid >= 0))
                H5.H5Dwrite_VLStrings(H5did, H5dtid,
                        HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
                        HDF5Constants.H5P_DEFAULT, str_data);
        }
        catch (Exception e) {
            e.printStackTrace();
        }
        try {
            vl_size = H5.H5Dvlen_get_buf_size(H5did, H5dtid, H5dsid);
        }
        catch (Exception e) {
            e.printStackTrace();
        }
        assertTrue("H5Dvlen_get_buf_size " + vl_size + " == " + str_data_bytes, vl_size == str_data_bytes);
    }

    @Test(expected = IllegalArgumentException.class)
    public void testH5Dvlen_read_invalid_buffer() throws Throwable {
        String[] str_data = { "Parting", "is such", "sweet", "sorrow.",
                "Testing", "one", "two", "three.",
                "Dog,", "man's", "best", "friend.",
                "Diamonds", "are", "a", "girls!",
                "S A", "T U R", "D A Y", "night",
                "That's", "all", "folks", "!!!" };
        byte[] read_data = new byte[512];

        _createVLDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT);

        try {
            H5.H5Dwrite_VLStrings(H5did, H5dtid,
                    HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
                    HDF5Constants.H5P_DEFAULT, str_data);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        H5.H5Dread(H5did, H5dtid,
                     HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
                     HDF5Constants.H5P_DEFAULT, read_data);
    }

    @Test
    public void testH5Dvlen_write_read() {
        String[] str_wdata = { "Parting", "is such", "sweet", "sorrow.",
                "Testing", "one", "two", "three.",
                "Dog,", "man's", "best", "friend.",
                "Diamonds", "are", "a", "girls!",
                "S A", "T U R", "D A Y", "night",
                "That's", "all", "folks", "!!!" };
        String[] str_rdata = new String[DIM_X * DIM_Y];

        _createVLDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT);

        try {
            if ((H5did >= 0) && (H5dtid >= 0))
                H5.H5Dwrite_VLStrings(H5did, H5dtid,
                        HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
                        HDF5Constants.H5P_DEFAULT, str_wdata);
        }
        catch (Exception e) {
            e.printStackTrace();
        }
        try {
            if ((H5did >= 0) && (H5dtid >= 0))
                H5.H5Dread_VLStrings(H5did, H5dtid,
                        HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
                        HDF5Constants.H5P_DEFAULT, str_rdata);
        }
        catch (Exception e) {
            e.printStackTrace();
        }
        for (int v = 0; v < DIM_X * DIM_Y; v++)
            assertTrue("testH5Dvlen_write_read " + str_wdata[v] + " == " + str_rdata[v], str_wdata[v] == str_wdata[v]);
    }

}