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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 string datatypes
to a dataset. The program first writes strings 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_String {
private static String FILENAME = "H5Ex_T_String.h5";
private static String DATASETNAME = "DS1";
private static final int DIM0 = 4;
private static final int SDIM = 8;
private static final int RANK = 1;
private static void CreateDataset()
{
long file_id = HDF5Constants.H5I_INVALID_HID;
long memtype_id = HDF5Constants.H5I_INVALID_HID;
long filetype_id = HDF5Constants.H5I_INVALID_HID;
long dataspace_id = HDF5Constants.H5I_INVALID_HID;
long dataset_id = HDF5Constants.H5I_INVALID_HID;
long[] dims = {DIM0};
byte[][] dset_data = new byte[DIM0][SDIM];
StringBuffer[] str_data = {new StringBuffer("Parting"), new StringBuffer("is such"),
new StringBuffer("sweet"), new StringBuffer("sorrow.")};
// 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 file and memory datatypes. For this example we will save
// the strings as FORTRAN strings, therefore they do not need space
// for the null terminator in the file.
try {
filetype_id = H5.H5Tcopy(HDF5Constants.H5T_FORTRAN_S1);
if (filetype_id >= 0)
H5.H5Tset_size(filetype_id, SDIM - 1);
}
catch (Exception e) {
e.printStackTrace();
}
try {
memtype_id = H5.H5Tcopy(HDF5Constants.H5T_C_S1);
if (memtype_id >= 0)
H5.H5Tset_size(memtype_id, SDIM);
}
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 string data to it.
try {
if ((file_id >= 0) && (filetype_id >= 0) && (dataspace_id >= 0))
dataset_id =
H5.H5Dcreate(file_id, DATASETNAME, filetype_id, dataspace_id, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
// Write the data to the dataset.
try {
for (int indx = 0; indx < DIM0; indx++) {
for (int jndx = 0; jndx < SDIM; jndx++) {
if (jndx < str_data[indx].length())
dset_data[indx][jndx] = (byte)str_data[indx].charAt(jndx);
else
dset_data[indx][jndx] = 0;
}
}
if ((dataset_id >= 0) && (memtype_id >= 0))
H5.H5Dwrite(dataset_id, memtype_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();
}
// Terminate access to the file type.
try {
if (filetype_id >= 0)
H5.H5Tclose(filetype_id);
}
catch (Exception e) {
e.printStackTrace();
}
// Terminate access to the mem type.
try {
if (memtype_id >= 0)
H5.H5Tclose(memtype_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 filetype_id = HDF5Constants.H5I_INVALID_HID;
long memtype_id = HDF5Constants.H5I_INVALID_HID;
long dataspace_id = HDF5Constants.H5I_INVALID_HID;
long dataset_id = HDF5Constants.H5I_INVALID_HID;
long sdim = 0;
long[] dims = {DIM0};
byte[][] dset_data;
StringBuffer[] str_data;
// 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 the datatype and its size.
try {
if (dataset_id >= 0)
filetype_id = H5.H5Dget_type(dataset_id);
if (filetype_id >= 0) {
sdim = H5.H5Tget_size(filetype_id);
sdim++; // Make room for null terminator
}
}
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 space for data.
dset_data = new byte[(int)dims[0]][(int)sdim];
str_data = new StringBuffer[(int)dims[0]];
// Create the memory datatype.
try {
memtype_id = H5.H5Tcopy(HDF5Constants.H5T_C_S1);
if (memtype_id >= 0)
H5.H5Tset_size(memtype_id, sdim);
}
catch (Exception e) {
e.printStackTrace();
}
// Read data.
try {
if ((dataset_id >= 0) && (memtype_id >= 0))
H5.H5Dread(dataset_id, memtype_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
HDF5Constants.H5P_DEFAULT, dset_data);
byte[] tempbuf = new byte[(int)sdim];
for (int indx = 0; indx < (int)dims[0]; indx++) {
for (int jndx = 0; jndx < sdim; jndx++) {
tempbuf[jndx] = dset_data[indx][jndx];
}
str_data[indx] = new StringBuffer(new String(tempbuf).trim());
}
}
catch (Exception e) {
e.printStackTrace();
}
// Output the data to the screen.
for (int indx = 0; indx < dims[0]; indx++) {
System.out.println(DATASETNAME + " [" + indx + "]: " + str_data[indx]);
}
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();
}
// Terminate access to the file type.
try {
if (filetype_id >= 0)
H5.H5Tclose(filetype_id);
}
catch (Exception e) {
e.printStackTrace();
}
// Terminate access to the mem type.
try {
if (memtype_id >= 0)
H5.H5Tclose(memtype_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_String.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_String.ReadDataset();
}
}
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