path: root/java/test/TestH5.java

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
 * Copyright by The HDF Group.                                               *
 * 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 test;

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

import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.io.Reader;
import java.io.StreamTokenizer;

import hdf.hdf5lib.H5;
import hdf.hdf5lib.HDF5Constants;
import hdf.hdf5lib.exceptions.HDF5Exception;
import hdf.hdf5lib.exceptions.HDF5LibraryException;

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

/**
 * @author xcao
 *
 */
public class TestH5 {
    @Rule public TestName testname = new TestName();
    private static final String H5_FILE = "testData.h5";
    private static final String EXPORT_FILE = "testExport.txt";
    private static final String H5_REGION_FILE = "trefer_reg.h5";
    private static final String EXPORT_REGION_FILE = "testExportReg.txt";
    private static final String H5_ATTR_FILE = "trefer_attr.h5";
    private static final String EXPORT_ATTR_FILE = "testExportAttr.txt";
    private static final String H5_DREG_FILE = "tdatareg.h5";
    private static final String EXPORT_DREG_FILE = "testExportDReg.txt";
    private static final String H5_AREG_FILE = "tattrreg.h5";
    private static final String EXPORT_AREG_FILE = "testExportAReg.txt";
    private static final int DIM_X = 4;
    private static final int DIM_Y = 6;
    private static final int DIM_BLKS = 36;
    private static final int DIM_PNTS = 10;
    private static final int DIM_ATTR = 12;
    private static final int RANK = 2;
    long H5fid = HDF5Constants.H5I_INVALID_HID;
    long H5dsid = HDF5Constants.H5I_INVALID_HID;
    long H5did = HDF5Constants.H5I_INVALID_HID;
    long[] H5dims = { DIM_X, DIM_Y };

    private final void _deleteFile(String filename) {
        File file = null;
        try {
            file = new File(filename);
        }
        catch (Throwable err) {}

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

    private final long _createDataset(long fid, long dsid, String name, long dapl) {
        long did = HDF5Constants.H5I_INVALID_HID;
        try {
            did = H5.H5Dcreate(fid, name, HDF5Constants.H5T_STD_I32LE, dsid,
                    HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, dapl);
        }
        catch (Throwable err) {
            err.printStackTrace();
            fail("H5.H5Dcreate: " + err);
        }
        assertTrue("TestH5._createDataset: ", did > 0);

        return did;
    }

    private final void _createH5File() {
        try {
            H5fid = H5.H5Fcreate(H5_FILE, HDF5Constants.H5F_ACC_TRUNC,
                    HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
            H5dsid = H5.H5Screate_simple(2, H5dims, null);
            H5did = _createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT);
        }
        catch (Throwable err) {
            err.printStackTrace();
            fail("TestH5Pfapl.createH5file: " + err);
        }
        assertTrue("TestH5.createH5file: H5.H5Fcreate: ", H5fid > 0);
        assertTrue("TestH5.createH5file: H5.H5Screate_simple: ", H5dsid > 0);
        assertTrue("TestH5.createH5file: _createDataset: ", H5did > 0);

        try {
            H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL);
        }
        catch (Throwable err) {
            err.printStackTrace();
        }
    }

    private final void _closeH5File() {
        if (H5did >= 0)
            try {H5.H5Dclose(H5did);} catch (Exception ex) {}
        if (H5dsid > 0)
            try {H5.H5Sclose(H5dsid);} catch (Exception ex) {}
        if (H5fid > 0)
            try {H5.H5Fclose(H5fid);} catch (Exception ex) {}
        H5fid = HDF5Constants.H5I_INVALID_HID;
        H5dsid = HDF5Constants.H5I_INVALID_HID;
        H5did = HDF5Constants.H5I_INVALID_HID;
    }

    public void _openH5File(String filename, String dsetname) {
       try {
           H5fid = H5.H5Fopen(filename,
                   HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT);
       }
       catch (Throwable err) {
           err.printStackTrace();
           fail("TestH5._openH5file: " + err);
       }
       assertTrue("TestH5._openH5file: H5.H5Fopen: ", H5fid >= 0);
       try {
           H5did = H5.H5Dopen(H5fid, dsetname, HDF5Constants.H5P_DEFAULT);
       }
       catch (Throwable err) {
           err.printStackTrace();
           fail("TestH5._openH5file: " + err);
       }
       assertTrue("TestH5._openH5file: H5.H5Dopen: ", H5did >= 0);
       try {
           H5dsid = H5.H5Dget_space(H5did);
       }
       catch (Throwable err) {
           err.printStackTrace();
           fail("TestH5._openH5file: " + err);
       }
       assertTrue("TestH5._openH5file: H5.H5Screate_simple: ",H5dsid > 0);
    }

    public final void _deleteH5file() {
        _closeH5File();
        _deleteFile(H5_FILE);
    }

    @After
    public void closeH5File() throws HDF5LibraryException {
        _closeH5File();
        assertTrue("H5 open ids is 0", H5.getOpenIDCount()==0);
        System.out.println();
    }

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

    /**
     * Test method for {@link hdf.hdf5lib.H5#J2C(int)}.
     * NOTE:
     * H5F_ACC_DEBUG no longer prints any special debug info. Even though the symbol is
     * being retained hdf java does not access the symbol.
     */
    @Test
    public void testJ2C() {
        int H5F_ACC_RDONLY = 0x0000;
        int H5F_ACC_RDWR = 0x0001;
        int H5F_ACC_TRUNC = 0x0002;
        int H5F_ACC_EXCL = 0x0004;
        int H5F_ACC_CREAT = 0x0010;
        int H5F_OBJ_FILE = 0x0001;
        int H5F_OBJ_DATASET = 0x0002;
        int H5F_OBJ_GROUP = 0x0004;
        int H5F_OBJ_DATATYPE = 0x0008;
        int H5F_OBJ_ATTR = 0x0010;
        int H5F_OBJ_ALL = H5F_OBJ_FILE | H5F_OBJ_DATASET | H5F_OBJ_GROUP
                | H5F_OBJ_DATATYPE | H5F_OBJ_ATTR;
        int H5F_OBJ_LOCAL = 0x0020;

        int definedValues[] = { H5F_ACC_RDONLY, H5F_ACC_RDWR, H5F_ACC_TRUNC,
                H5F_ACC_EXCL, H5F_ACC_CREAT, H5F_OBJ_FILE,
                H5F_OBJ_DATASET, H5F_OBJ_GROUP, H5F_OBJ_DATATYPE, H5F_OBJ_ATTR,
                H5F_OBJ_ALL, H5F_OBJ_LOCAL };

        int j2cValues[] = { HDF5Constants.H5F_ACC_RDONLY,
                HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5F_ACC_TRUNC,
                HDF5Constants.H5F_ACC_EXCL,
                HDF5Constants.H5F_ACC_CREAT, HDF5Constants.H5F_OBJ_FILE,
                HDF5Constants.H5F_OBJ_DATASET, HDF5Constants.H5F_OBJ_GROUP,
                HDF5Constants.H5F_OBJ_DATATYPE, HDF5Constants.H5F_OBJ_ATTR,
                HDF5Constants.H5F_OBJ_ALL, HDF5Constants.H5F_OBJ_LOCAL };

        for (int i = 0; i < definedValues.length; i++) {
            assertEquals(definedValues[i], j2cValues[i]);
        }

        assertFalse(H5F_ACC_RDONLY == HDF5Constants.H5F_ACC_RDWR);
        assertFalse(H5F_OBJ_FILE == HDF5Constants.H5F_OBJ_GROUP);
    }

    /**
     * Test method for {@link hdf.hdf5lib.H5#H5error_off()}.
     */
    @Test
    public void testH5error_off() {
        try {
            H5.H5error_off();
        }
        catch (Throwable err) {
            fail("H5.H5error_off failed: " + err);
        }
    }

    /**
     * Test method for {@link hdf.hdf5lib.H5#H5open()}.
     */
    @Test
    public void testH5open() {
        try {
            H5.H5open();
        }
        catch (Throwable err) {
            fail("H5.H5open failed: " + err);
        }
    }

    /**
     * Test method for {@link hdf.hdf5lib.H5#H5garbage_collect()}.
     */
    @Test
    public void testH5garbage_collect() {
        try {
            H5.H5garbage_collect();
        }
        catch (Throwable err) {
            fail("H5.H5garbage_collect failed: " + err);
        }
    }

    /**
     * Test method for
     * {@link hdf.hdf5lib.H5#H5set_free_list_limits(int, int, int, int, int, int)}
     * .
     */
    @Test
    public void testH5set_free_list_limits() {
        int reg_global_lim = 1;
        int reg_list_lim = 1;
        int arr_global_lim = 1;
        int arr_list_lim = 1;
        int blk_global_lim = 1;
        int blk_list_lim = 1;

        try {
            H5.H5set_free_list_limits(reg_global_lim, reg_list_lim,
                    arr_global_lim, arr_list_lim, blk_global_lim, blk_list_lim);
        }
        catch (Throwable err) {
            fail("H5.H5set_free_list_limits failed: " + err);
        }
    }

    /**
     * Test method for {@link hdf.hdf5lib.H5#H5get_libversion(int[])}.
     */
    @Test
    public void testH5get_libversion() {
        int libversion[] = { 1, 13, 2 };

        try {
            H5.H5get_libversion(libversion);
        }
        catch (Throwable err) {
            fail("H5.H5get_libversion: " + err);
        }

        for (int i = 0; i < 2; i++)
            assertEquals(H5.LIB_VERSION[i], libversion[i]);

        for (int i = 0; i < 2; i++)
            assertFalse(libversion[i] == 0);
    }

    /**
     * Test method for {@link hdf.hdf5lib.H5#H5get_libversion(int[])}
     * to ensure a null libversion parameter causes the function to
     * fail.
     */
    @Test
    public void testH5get_libversion_null_param() {
        try {
            H5.H5get_libversion(null);
        }
        catch (Throwable err) {
            return;
        }

        fail("H5.H5get_libversion: succeeded with a null libversion parameter!");
    }

    /**
     * Test method for
     * {@link hdf.hdf5lib.H5#H5check_version(int, int, int)}.
     */
    @Test
    public void testH5check_version() {
        int majnum = 1, minnum = 13, relnum = 2;

        try {
            H5.H5check_version(majnum, minnum, relnum);
        }
        catch (Throwable err) {
            fail("H5.H5check_version failed: " + err);
        }

        try {
            H5.H5check_version(-1, 0, 0);
        }
        catch (Throwable err) {
            fail("H5.H5check_version failed: " + err);
        }
    }

    @Test
    public void testIsSerializable() {
        H5 test = new H5();
        ByteArrayOutputStream out = new ByteArrayOutputStream();
        ObjectOutputStream oos;
        try {
            oos = new ObjectOutputStream(out);
            oos.writeObject(test);
            oos.close();
        }
        catch (IOException err) {
            err.printStackTrace();
            fail("ObjectOutputStream failed: " + err);
        }
        assertTrue(out.toByteArray().length > 0);

    }

    @SuppressWarnings("static-access")
    @Test
    public void serializeToDisk()
    {
        try {
            H5 test = new H5();

            FileOutputStream fos = new FileOutputStream("temph5.ser");
            ObjectOutputStream oos = new ObjectOutputStream(fos);
            oos.writeObject(test);
            oos.close();
        }
        catch (Exception ex) {
            fail("Exception thrown during test: " + ex.toString());
        }

        try {
            FileInputStream fis = new FileInputStream("temph5.ser");
            ObjectInputStream ois = new ObjectInputStream(fis);
            H5 test = (hdf.hdf5lib.H5) ois.readObject();
            ois.close();

            assertTrue("H5.LIB_VERSION[0]", test.LIB_VERSION[0]==H5.LIB_VERSION[0]);
            assertTrue("H5.LIB_VERSION[1]", test.LIB_VERSION[1]==H5.LIB_VERSION[1]);
//            assertTrue("H5.LIB_VERSION[2]", test.LIB_VERSION[2]==H5.LIB_VERSION[2]);

            // Clean up the file
            new File("temph5.ser").delete();
        }
        catch (Exception ex) {
            fail("Exception thrown during test: " + ex.toString());
        }
    }

    @Test
    public void testH5export_dataset() {
        int[][] dset_data = new int[DIM_X][DIM_Y];
        int[][] dset_indata = new int[DIM_X][DIM_Y];
        int FILLVAL = 99;

        _createH5File();

        // 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_STD_I32LE,
                        HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
                        HDF5Constants.H5P_DEFAULT, dset_data);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        _closeH5File();

        _openH5File(H5_FILE, "/dset");

        try {
            H5.H5export_dataset(EXPORT_FILE, H5fid, "/dset", 99);
        }
        catch (HDF5LibraryException err) {
            err.printStackTrace();
            fail("H5export_dataset failed: " + err);
        }

        File file = new File(EXPORT_FILE);

        try {
            Reader reader = new FileReader(EXPORT_FILE);
            StreamTokenizer streamTokenizer = new StreamTokenizer(reader);
            int indx = 0;
            int jndx = 0;
            while(streamTokenizer.nextToken() != StreamTokenizer.TT_EOF){
                if(streamTokenizer.ttype == StreamTokenizer.TT_NUMBER) {
                    dset_indata[indx][jndx] = (int)streamTokenizer.nval;
                    jndx++;
                    if (jndx >= DIM_Y) {
                        jndx = 0;
                        indx++;
                    }
                }
            }
            reader.close();
        }
        catch (IOException err) {
            err.printStackTrace();
            fail("read file failed: " + err);
        }
        for(int row = 0; row < DIM_X; row++)
            for(int col = 0; col < DIM_Y; col++) {
                assertTrue("H5export_dataset: <"+row+","+col+">"+dset_indata[row][col]+"=99", dset_indata[row][col]==99);
            }
        _deleteH5file();
    }

    @Test
    public void testH5export_region() {
        int[] dset_data_expect = {66, 69, 72, 75, 78, 81, 96, 99, 102, 105, 108,
                111, 126, 129, 132, 135, 138, 141, 156, 159, 162, 165, 168, 171,
                186, 189, 192, 195, 198, 201, 216, 219, 222, 225, 228, 231,
                207, 66, 252, 48, 84, 96, 12, 14, 213, 99};
        int[] dset_indata = new int[DIM_BLKS+DIM_PNTS];
        String objName = "/Dataset1";

        _openH5File(H5_REGION_FILE, objName);

        try {
            H5.H5export_dataset(EXPORT_REGION_FILE, H5fid, objName, 99);
        }
        catch (HDF5LibraryException err) {
            err.printStackTrace();
            fail("H5export_dataset failed: " + err);
        }

        File file = new File(EXPORT_REGION_FILE);

        try {
            Reader reader = new FileReader(EXPORT_REGION_FILE);
            StreamTokenizer streamTokenizer = new StreamTokenizer(reader);
            int indx = 0;
            while(streamTokenizer.nextToken() != StreamTokenizer.TT_EOF){
                if(streamTokenizer.ttype == StreamTokenizer.TT_NUMBER) {
                    dset_indata[indx] = (int)streamTokenizer.nval;
                    indx++;
                }
            }
            reader.close();
        }
        catch (IOException err) {
            err.printStackTrace();
            fail("read file failed: " + err);
        }
        for(int row = 0; row < DIM_X; row++)
            assertTrue("testH5export_region: <"+row+">"+dset_indata[row], dset_indata[row]==dset_data_expect[row]);
    }

    @Test
    public void testH5export_attribute() {
        int[] dset_data_expect = {0, 3, 6, 9, 1, 4, 7, 10, 2, 5, 8, 11};
        int[] dset_indata = new int[DIM_ATTR];
        String objName = "/Dataset3";

        _openH5File(H5_ATTR_FILE, objName);

        try {
            H5.H5export_dataset(EXPORT_ATTR_FILE, H5did, objName, 99);
        }
        catch (HDF5LibraryException err) {
            err.printStackTrace();
            fail("H5export_dataset failed: " + err);
        }

        File file = new File(EXPORT_ATTR_FILE);

        try {
            Reader reader = new FileReader(EXPORT_ATTR_FILE);
            StreamTokenizer streamTokenizer = new StreamTokenizer(reader);
            int indx = 0;
            int jndx = 0;
            while(streamTokenizer.nextToken() != StreamTokenizer.TT_EOF){
                if(streamTokenizer.ttype == StreamTokenizer.TT_NUMBER) {
                    dset_indata[indx] = (int)streamTokenizer.nval;
                    indx++;
                }
            }
            reader.close();
        }
        catch (IOException err) {
            err.printStackTrace();
            fail("read file failed: " + err);
        }
        for(int row = 0; row < DIM_X; row++)
            assertTrue("testH5export_attribute: <"+row+">"+dset_indata[row], dset_indata[row]==dset_data_expect[row]);
    }

    @Test
    public void testH5export_regdataset() {
        int[] dset_data_expect = {66, 69, 72, 75, 78, 81, 96, 99, 102, 105, 108,
                111, 126, 129, 132, 135, 138, 141, 156, 159, 162, 165, 168, 171,
                186, 189, 192, 195, 198, 201, 216, 219, 222, 225, 228, 231,
                207, 66, 252, 48, 84, 96, 12, 14, 213, 99};
        int[] dset_indata = new int[DIM_BLKS+DIM_PNTS];
        String objName = "/Dataset1";

        _openH5File(H5_DREG_FILE, objName);

        try {
            H5.H5export_dataset(EXPORT_DREG_FILE, H5fid, objName, 99);
        }
        catch (HDF5LibraryException err) {
            err.printStackTrace();
            fail("H5export_dataset failed: " + err);
        }

        File file = new File(EXPORT_DREG_FILE);

        try {
            Reader reader = new FileReader(EXPORT_DREG_FILE);
            StreamTokenizer streamTokenizer = new StreamTokenizer(reader);
            int indx = 0;
            while(streamTokenizer.nextToken() != StreamTokenizer.TT_EOF){
                if(streamTokenizer.ttype == StreamTokenizer.TT_NUMBER) {
                    dset_indata[indx] = (int)streamTokenizer.nval;
                    indx++;
                }
            }
            reader.close();
        }
        catch (IOException err) {
            err.printStackTrace();
            fail("read file failed: " + err);
        }
        for(int row = 0; row < DIM_X; row++)
            assertTrue("testH5export_regdataset: <"+row+">"+dset_indata[row], dset_indata[row]==dset_data_expect[row]);
    }

    @Test
    public void testH5export_attrdataset() {
        int[] dset_data_expect = {66, 69, 72, 75, 78, 81, 96, 99, 102, 105, 108,
                111, 126, 129, 132, 135, 138, 141, 156, 159, 162, 165, 168, 171,
                186, 189, 192, 195, 198, 201, 216, 219, 222, 225, 228, 231,
                207, 66, 252, 48, 84, 96, 12, 14, 213, 99};
        int[] dset_indata = new int[DIM_BLKS+DIM_PNTS];
        String dsetName = "/Dataset1";
        String objName = "Attribute1";

        _openH5File(H5_AREG_FILE, dsetName);

        try {
            H5.H5export_attribute(EXPORT_AREG_FILE, H5did, objName, 99);
        }
        catch (HDF5LibraryException err) {
            err.printStackTrace();
            fail("H5export_attribute failed: " + err);
        }

        File file = new File(EXPORT_AREG_FILE);

        try {
            Reader reader = new FileReader(EXPORT_AREG_FILE);
            StreamTokenizer streamTokenizer = new StreamTokenizer(reader);
            int indx = 0;
            int jndx = 0;
            while(streamTokenizer.nextToken() != StreamTokenizer.TT_EOF){
                if(streamTokenizer.ttype == StreamTokenizer.TT_NUMBER) {
                    dset_indata[indx] = (int)streamTokenizer.nval;
                    indx++;
                }
            }
            reader.close();
        }
        catch (IOException err) {
            err.printStackTrace();
            fail("read file failed: " + err);
        }
        for(int row = 0; row < DIM_X; row++)
            assertTrue("testH5export_attrdataset: <"+row+">"+dset_indata[row], dset_indata[row]==dset_data_expect[row]);
    }
}