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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 select a subset using the
* "HDF Native Package (Java)". The example creates an integer dataset, and read
* subset of the dataset:
*
* <pre>
* "/" (root)
* 2D 32-bit integer 20x10
* </pre>
*
* The whole 20x10 data set is
*
* <pre>
* 1000, 1001, 1002, 1003, 1004, 1005, 1006, 1007, 1008, 1009
* 1100, 1101, 1102, 1103, 1104, 1105, 1106, 1107, 1108, 1109
* 1200, 1201, 1202, 1203, 1204, 1205, 1206, 1207, 1208, 1209
* 1300, 1301, 1302, 1303, 1304, 1305, 1306, 1307, 1308, 1309
* 1400, 1401, 1402, 1403, 1404, 1405, 1406, 1407, 1408, 1409
* 1500, 1501, 1502, 1503, 1504, 1505, 1506, 1507, 1508, 1509
* 1600, 1601, 1602, 1603, 1604, 1605, 1606, 1607, 1608, 1609
* 1700, 1701, 1702, 1703, 1704, 1705, 1706, 1707, 1708, 1709
* 1800, 1801, 1802, 1803, 1804, 1805, 1806, 1807, 1808, 1809
* 1900, 1901, 1902, 1903, 1904, 1905, 1906, 1907, 1908, 1909
* 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009
* 2100, 2101, 2102, 2103, 2104, 2105, 2106, 2107, 2108, 2109
* 2200, 2201, 2202, 2203, 2204, 2205, 2206, 2207, 2208, 2209
* 2300, 2301, 2302, 2303, 2304, 2305, 2306, 2307, 2308, 2309
* 2400, 2401, 2402, 2403, 2404, 2405, 2406, 2407, 2408, 2409
* 2500, 2501, 2502, 2503, 2504, 2505, 2506, 2507, 2508, 2509
* 2600, 2601, 2602, 2603, 2604, 2605, 2606, 2607, 2608, 2609
* 2700, 2701, 2702, 2703, 2704, 2705, 2706, 2707, 2708, 2709
* 2800, 2801, 2802, 2803, 2804, 2805, 2806, 2807, 2808, 2809
* 2900, 2901, 2902, 2903, 2904, 2905, 2906, 2907, 2908, 2909
* </pre>
*
* Subset: start=(4, 2), size=(5, 3) and stride=(3, 2). The subset values are:
*
* <pre>
* 1402,1404,1406
* 1702,1704,1706
* 2002,2004,2006
* 2302,2304,2306
* 2602,2604,2606
* </pre>
*
* </p>
*
* @author Peter X. Cao
* @version 2.4
*/
public class HDF5SubsetSelect {
private static String fname = "HDF5SubsetSelect.h5";
private static String dsname = "2D 32-bit integer 20x10";
private static long[] dims2D = {20, 10};
private static void SubsetSelect()
{
long file_id = HDF5Constants.H5I_INVALID_HID;
long dataset_id = HDF5Constants.H5I_INVALID_HID;
long filespace_id = HDF5Constants.H5I_INVALID_HID;
long memspace_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[5][3];
// Define and select the hyperslab to use for reading.
try {
if (dataset_id >= 0) {
filespace_id = H5.H5Dget_space(dataset_id);
long[] start = {4, 2};
long[] stride = {3, 2};
long[] count = {5, 3};
long[] block = null;
if (filespace_id >= 0) {
H5.H5Sselect_hyperslab(filespace_id, HDF5Constants.H5S_SELECT_SET, start, stride, count,
block);
memspace_id = H5.H5Screate_simple(2, count, null);
// Read the data using the previously defined hyperslab.
if ((dataset_id >= 0) && (filespace_id >= 0) && (memspace_id >= 0))
H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, memspace_id, filespace_id,
HDF5Constants.H5P_DEFAULT, dataRead);
}
}
}
catch (Exception e) {
e.printStackTrace();
}
// print out the data values
System.out.println("\n\nSubset Data Values");
for (int i = 0; i < 5; i++) {
System.out.print("\n" + dataRead[i][0]);
for (int j = 1; j < 3; j++) {
System.out.print("," + dataRead[i][j]);
}
}
// Close the dataset.
try {
if (dataset_id >= 0)
H5.H5Dclose(dataset_id);
}
catch (Exception e) {
e.printStackTrace();
}
try {
if (filespace_id >= 0)
H5.H5Sclose(filespace_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 javaExample.HDF5DatasetCreate
* @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] = 1000 + 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) { HDF5SubsetSelect.SubsetSelect(); }
}
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