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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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://www.hdfgroup.org/licenses. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
import hdf.hdf5lib.H5;
import hdf.hdf5lib.HDF5Constants;
/**
* <p>
* Title: HDF Native Package (Java) Example
* </p>
* <p>
* Description: this example shows how to read/write HDF datasets using the
* "HDF Native Package (Java)". The example creates an integer dataset, and read
* and write data values:
*
* <pre>
* "/" (root)
* 2D 32-bit integer 20x10
* </pre>
*
* </p>
*/
public class HDF5DatasetRead {
private static String fname = "HDF5DatasetRead.h5";
private static String dsname = "2D 32-bit integer 20x10";
private static long[] dims2D = {20, 10};
private static void ReadWriteDataset()
{
long file_id = HDF5Constants.H5I_INVALID_HID;
long dataset_id = HDF5Constants.H5I_INVALID_HID;
// create the file and add groups and dataset into the file
try {
createFile();
}
catch (Exception e) {
e.printStackTrace();
}
// Open file using the default properties.
try {
file_id = H5.H5Fopen(fname, HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
// Open dataset using the default properties.
try {
if (file_id >= 0)
dataset_id = H5.H5Dopen(file_id, dsname, HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
// Allocate array of pointers to two-dimensional arrays (the
// elements of the dataset.
int[][] dataRead = new int[(int)dims2D[0]][(int)(dims2D[1])];
try {
if (dataset_id >= 0)
H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL,
HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dataRead);
}
catch (Exception e) {
e.printStackTrace();
}
// print out the data values
System.out.println("\n\nOriginal Data Values");
for (int i = 0; i < 20; i++) {
System.out.print("\n" + dataRead[i][0]);
for (int j = 1; j < 10; j++) {
System.out.print(", " + dataRead[i][j]);
}
}
// change data value and write it to file.
for (int i = 0; i < 20; i++) {
for (int j = 0; j < 10; j++) {
dataRead[i][j]++;
}
}
// Write the data to the dataset.
try {
if (dataset_id >= 0)
H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL,
HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dataRead);
}
catch (Exception e) {
e.printStackTrace();
}
// reload the data value
int[][] dataModified = new int[(int)dims2D[0]][(int)(dims2D[1])];
try {
if (dataset_id >= 0)
H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL,
HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dataModified);
}
catch (Exception e) {
e.printStackTrace();
}
// print out the modified data values
System.out.println("\n\nModified Data Values");
for (int i = 0; i < 20; i++) {
System.out.print("\n" + dataModified[i][0]);
for (int j = 1; j < 10; j++) {
System.out.print(", " + dataModified[i][j]);
}
}
// Close the dataset.
try {
if (dataset_id >= 0)
H5.H5Dclose(dataset_id);
}
catch (Exception e) {
e.printStackTrace();
}
// Close the file.
try {
if (file_id >= 0)
H5.H5Fclose(file_id);
}
catch (Exception e) {
e.printStackTrace();
}
}
/**
* create the file and add groups ans dataset into the file, which is the
* same as javaExample.H5DatasetCreate
*
* @see HDF5DatasetCreate.H5DatasetCreate
* @throws Exception
*/
private static void createFile() throws Exception
{
long file_id = HDF5Constants.H5I_INVALID_HID;
long dataspace_id = HDF5Constants.H5I_INVALID_HID;
long dataset_id = HDF5Constants.H5I_INVALID_HID;
// Create a new file using default properties.
try {
file_id = H5.H5Fcreate(fname, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
// Create the data space for the dataset.
try {
dataspace_id = H5.H5Screate_simple(2, dims2D, null);
}
catch (Exception e) {
e.printStackTrace();
}
// Create the dataset.
try {
if ((file_id >= 0) && (dataspace_id >= 0))
dataset_id = H5.H5Dcreate(file_id, dsname, HDF5Constants.H5T_STD_I32LE, dataspace_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT);
}
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();
}
// set the data values
int[] dataIn = new int[20 * 10];
for (int i = 0; i < 20; i++) {
for (int j = 0; j < 10; j++) {
dataIn[i * 10 + j] = i * 100 + j;
}
}
// Write the data to the dataset.
try {
if (dataset_id >= 0)
H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL,
HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dataIn);
}
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();
}
// Close the file.
try {
if (file_id >= 0)
H5.H5Fclose(file_id);
}
catch (Exception e) {
e.printStackTrace();
}
}
public static void main(String[] args) { HDF5DatasetRead.ReadWriteDataset(); }
}
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