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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/************************************************************
This example shows how to read and write opaque datatypes
to a dataset. The program first writes opaque data to a
dataset with a dataspace of DIM0, then closes the file.
Next, it reopens the file, reads back the data, and
outputs it to the screen.
************************************************************/
import hdf.hdf5lib.H5;
import hdf.hdf5lib.HDF5Constants;
public class H5Ex_T_Opaque {
private static String FILENAME = "H5Ex_T_Opaque.h5";
private static String DATASETNAME = "DS1";
private static final int DIM0 = 4;
private static final int LEN = 7;
private static final int RANK = 1;
private static void CreateDataset()
{
long file_id = HDF5Constants.H5I_INVALID_HID;
long dataspace_id = HDF5Constants.H5I_INVALID_HID;
long datatype_id = HDF5Constants.H5I_INVALID_HID;
long dataset_id = HDF5Constants.H5I_INVALID_HID;
long[] dims = {DIM0};
byte[] dset_data = new byte[DIM0 * LEN];
byte[] str_data = {'O', 'P', 'A', 'Q', 'U', 'E'};
// Initialize data.
for (int indx = 0; indx < DIM0; indx++) {
for (int jndx = 0; jndx < LEN - 1; jndx++)
dset_data[jndx + indx * LEN] = str_data[jndx];
dset_data[LEN - 1 + indx * LEN] = (byte)(indx + '0');
}
// Create a new file using default properties.
try {
file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
// Create opaque datatype and set the tag to something appropriate.
// For this example we will write and view the data as a character
// array.
try {
datatype_id = H5.H5Tcreate(HDF5Constants.H5T_OPAQUE, (long)LEN);
if (datatype_id >= 0)
H5.H5Tset_tag(datatype_id, "Character array");
}
catch (Exception e) {
e.printStackTrace();
}
// Create dataspace. Setting maximum size to NULL sets the maximum
// size to be the current size.
try {
dataspace_id = H5.H5Screate_simple(RANK, dims, null);
}
catch (Exception e) {
e.printStackTrace();
}
// Create the dataset and write the integer data to it. In this
// example we will save the data as 64 bit big endian integers,
// regardless of the native integer type. The HDF5 library
// automatically converts between different integer types.
try {
if ((file_id >= 0) && (datatype_id >= 0) && (dataspace_id >= 0))
dataset_id =
H5.H5Dcreate(file_id, DATASETNAME, datatype_id, dataspace_id, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
// Write the opaque data to the dataset.
try {
if ((dataset_id >= 0) && (datatype_id >= 0))
H5.H5Dwrite(dataset_id, datatype_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
HDF5Constants.H5P_DEFAULT, dset_data);
}
catch (Exception e) {
e.printStackTrace();
}
// End access to the dataset and release resources used by it.
try {
if (dataset_id >= 0)
H5.H5Dclose(dataset_id);
}
catch (Exception e) {
e.printStackTrace();
}
// Terminate access to the data space.
try {
if (dataspace_id >= 0)
H5.H5Sclose(dataspace_id);
}
catch (Exception e) {
e.printStackTrace();
}
try {
if (datatype_id >= 0)
H5.H5Tclose(datatype_id);
}
catch (Exception e) {
e.printStackTrace();
}
// Close the file.
try {
if (file_id >= 0)
H5.H5Fclose(file_id);
}
catch (Exception e) {
e.printStackTrace();
}
}
private static void ReadDataset()
{
long file_id = HDF5Constants.H5I_INVALID_HID;
long datatype_id = HDF5Constants.H5I_INVALID_HID;
long dataspace_id = HDF5Constants.H5I_INVALID_HID;
long dataset_id = HDF5Constants.H5I_INVALID_HID;
long type_len = HDF5Constants.H5I_INVALID_HID;
long[] dims = {DIM0};
byte[] dset_data;
String tag_name = null;
// Open an existing file.
try {
file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
// Open an existing dataset.
try {
if (file_id >= 0)
dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
// Get datatype and properties for the datatype.
try {
if (dataset_id >= 0)
datatype_id = H5.H5Dget_type(dataset_id);
if (datatype_id >= 0) {
type_len = H5.H5Tget_size(datatype_id);
tag_name = H5.H5Tget_tag(datatype_id);
}
}
catch (Exception e) {
e.printStackTrace();
}
// Get dataspace and allocate memory for read buffer.
try {
if (dataset_id >= 0)
dataspace_id = H5.H5Dget_space(dataset_id);
}
catch (Exception e) {
e.printStackTrace();
}
try {
if (dataspace_id >= 0)
H5.H5Sget_simple_extent_dims(dataspace_id, dims, null);
}
catch (Exception e) {
e.printStackTrace();
}
// Allocate buffer.
dset_data = new byte[(int)(dims[0] * type_len)];
// Read data.
try {
if ((dataset_id >= 0) && (datatype_id >= 0))
H5.H5Dread(dataset_id, datatype_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
HDF5Constants.H5P_DEFAULT, dset_data);
}
catch (Exception e) {
e.printStackTrace();
}
// Output the data to the screen.
System.out.println("Datatype tag for " + DATASETNAME + " is: \"" + tag_name + "\"");
for (int indx = 0; indx < dims[0]; indx++) {
System.out.print(DATASETNAME + "[" + indx + "]: ");
for (int jndx = 0; jndx < type_len; jndx++) {
char temp = (char)dset_data[jndx + indx * (int)type_len];
System.out.print(temp);
}
System.out.println("");
}
System.out.println();
// End access to the dataset and release resources used by it.
try {
if (dataset_id >= 0)
H5.H5Dclose(dataset_id);
}
catch (Exception e) {
e.printStackTrace();
}
// Terminate access to the data space.
try {
if (dataspace_id >= 0)
H5.H5Sclose(dataspace_id);
}
catch (Exception e) {
e.printStackTrace();
}
try {
if (datatype_id >= 0)
H5.H5Tclose(datatype_id);
}
catch (Exception e) {
e.printStackTrace();
}
// Close the file.
try {
if (file_id >= 0)
H5.H5Fclose(file_id);
}
catch (Exception e) {
e.printStackTrace();
}
}
public static void main(String[] args)
{
H5Ex_T_Opaque.CreateDataset();
// Now we begin the read section of this example. Here we assume
// the dataset and array have the same name and rank, but can have
// any size. Therefore we must allocate a new array to read in
// data using malloc().
H5Ex_T_Opaque.ReadDataset();
}
}
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