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/************************************************************
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.
This file is intended for use with HDF5 Library verion 1.6
************************************************************/
package examples.datatypes;
import ncsa.hdf.hdf5lib.H5;
import ncsa.hdf.hdf5lib.HDF5Constants;
import ncsa.hdf.object.FileFormat;
import ncsa.hdf.object.Group;
import ncsa.hdf.object.h5.H5File;
import ncsa.hdf.object.h5.H5ScalarDS;
public class H5ObjectEx_T_String {
private static String FILENAME = "H5ObjectEx_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() {
H5File file = null;
H5ScalarDS dset = null;
int file_id = -1;
int memtype_id = -1;
int filetype_id = -1;
int dataspace_id = -1;
int dataset_id = -1;
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 = new H5File(FILENAME, FileFormat.CREATE);
file_id = file.open();
}
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);
dset = new H5ScalarDS(file, DATASETNAME, "/");
Group pgroup = (Group) file.get("/");
pgroup.addToMemberList(dset);
}
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)
dset.close(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 {
file.close();
}
catch (Exception e) {
e.printStackTrace();
}
}
private static void ReadDataset() {
H5File file = null;
H5ScalarDS dset = null;
int filetype_id = -1;
int memtype_id = -1;
int dataspace_id = -1;
int dataset_id = -1;
int sdim = 0;
long[] dims = { DIM0 };
byte[][] dset_data;
StringBuffer[] str_data;
// Open an existing file.
try {
file = new H5File(FILENAME, FileFormat.READ);
file.open();
}
catch (Exception e) {
e.printStackTrace();
}
// Open an existing dataset.
try {
dset = (H5ScalarDS) file.get(DATASETNAME);
dataset_id = dset.open();
}
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]][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[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)
dset.close(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 {
file.close();
}
catch (Exception e) {
e.printStackTrace();
}
}
public static void main(String[] args) {
H5ObjectEx_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().
H5ObjectEx_T_String.ReadDataset();
}
}
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