mirror of
https://github.com/HDFGroup/hdf5.git
synced 2026-09-25 04:09:44 +03:00
Allen Byrne
b754dcb8f2
FFM build requires Java 25, Jextract 25. Generates FFM bindings during configure. JNI is default when the requirements are not met or can be forced. Presets added for maven and FFM - JNI is default selection. Enhanced Maven options will work with either JNI or FFM New Workflows for testing and maven uploads. Extensive documentation changes for java.
284 lines
9.7 KiB
Java
284 lines
9.7 KiB
Java
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
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* Copyright by The HDF Group. *
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* Copyright by the Board of Trustees of the University of Illinois. *
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* All rights reserved. *
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* *
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* This file is part of HDF5. The full HDF5 copyright notice, including *
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* terms governing use, modification, and redistribution, is contained in *
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* the LICENSE file, which can be found at the root of the source code *
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* distribution tree, or in https://www.hdfgroup.org/licenses. *
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* If you do not have access to either file, you may request a copy from *
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* help@hdfgroup.org. *
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* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
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import static org.hdfgroup.javahdf5.hdf5_h.*;
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import java.lang.foreign.Arena;
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import java.lang.foreign.MemorySegment;
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import java.lang.foreign.ValueLayout;
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/**
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* <p>
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* Title: HDF Native Package (Java) Example
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* </p>
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* <p>
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* Description: this example shows how to select a subset using the
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* "HDF Native Package (Java)". The example creates an integer dataset, and read
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* subset of the dataset:
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*
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* <pre>
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* "/" (root)
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* 2D 32-bit integer 20x10
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* </pre>
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*
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* The whole 20x10 data set is
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*
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* <pre>
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* 1000, 1001, 1002, 1003, 1004, 1005, 1006, 1007, 1008, 1009
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* 1100, 1101, 1102, 1103, 1104, 1105, 1106, 1107, 1108, 1109
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* 1200, 1201, 1202, 1203, 1204, 1205, 1206, 1207, 1208, 1209
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* 1300, 1301, 1302, 1303, 1304, 1305, 1306, 1307, 1308, 1309
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* 1400, 1401, 1402, 1403, 1404, 1405, 1406, 1407, 1408, 1409
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* 1500, 1501, 1502, 1503, 1504, 1505, 1506, 1507, 1508, 1509
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* 1600, 1601, 1602, 1603, 1604, 1605, 1606, 1607, 1608, 1609
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* 1700, 1701, 1702, 1703, 1704, 1705, 1706, 1707, 1708, 1709
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* 1800, 1801, 1802, 1803, 1804, 1805, 1806, 1807, 1808, 1809
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* 1900, 1901, 1902, 1903, 1904, 1905, 1906, 1907, 1908, 1909
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* 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009
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* 2100, 2101, 2102, 2103, 2104, 2105, 2106, 2107, 2108, 2109
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* 2200, 2201, 2202, 2203, 2204, 2205, 2206, 2207, 2208, 2209
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* 2300, 2301, 2302, 2303, 2304, 2305, 2306, 2307, 2308, 2309
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* 2400, 2401, 2402, 2403, 2404, 2405, 2406, 2407, 2408, 2409
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* 2500, 2501, 2502, 2503, 2504, 2505, 2506, 2507, 2508, 2509
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* 2600, 2601, 2602, 2603, 2604, 2605, 2606, 2607, 2608, 2609
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* 2700, 2701, 2702, 2703, 2704, 2705, 2706, 2707, 2708, 2709
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* 2800, 2801, 2802, 2803, 2804, 2805, 2806, 2807, 2808, 2809
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* 2900, 2901, 2902, 2903, 2904, 2905, 2906, 2907, 2908, 2909
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* </pre>
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*
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* Subset: start=(4, 2), size=(5, 3) and stride=(3, 2). The subset values are:
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*
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* <pre>
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* 1402,1404,1406
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* 1702,1704,1706
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* 2002,2004,2006
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* 2302,2304,2306
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* 2602,2604,2606
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* </pre>
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*
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* </p>
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*
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* @author Peter X. Cao
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* @version 2.4
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*/
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public class HDF5SubsetSelect {
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private static String fname = "HDF5SubsetSelect.h5";
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private static String dsname = "2D 32-bit integer 20x10";
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private static long[] dims2D = {20, 10};
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private static void SubsetSelect(Arena arena)
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{
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long file_id = H5I_INVALID_HID();
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long dataset_id = H5I_INVALID_HID();
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long filespace_id = H5I_INVALID_HID();
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long memspace_id = H5I_INVALID_HID();
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// create the file and add groups and dataset into the file
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try {
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createFile(arena);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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// Open file using the default properties.
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try {
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file_id = H5Fopen(arena.allocateFrom(fname), H5F_ACC_RDWR(), H5P_DEFAULT());
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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// Open dataset using the default properties.
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try {
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if (file_id >= 0)
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dataset_id = H5Dopen2(file_id, arena.allocateFrom(dsname), H5P_DEFAULT());
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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// Allocate array of pointers to two-dimensional arrays (the
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// elements of the dataset.
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int[][] dataRead = new int[5][3];
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// Define and select the hyperslab to use for reading.
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try {
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if (dataset_id >= 0) {
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filespace_id = H5Dget_space(dataset_id);
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long[] start = {4, 2};
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long[] stride = {3, 2};
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long[] count = {5, 3};
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long[] block = null;
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if (filespace_id >= 0) {
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// Convert arrays to MemorySegments for hyperslab selection
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MemorySegment startSeg = arena.allocateFrom(ValueLayout.JAVA_LONG, start);
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MemorySegment strideSeg = arena.allocateFrom(ValueLayout.JAVA_LONG, stride);
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MemorySegment countSeg = arena.allocateFrom(ValueLayout.JAVA_LONG, count);
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H5Sselect_hyperslab(filespace_id, H5S_SELECT_SET(), startSeg, strideSeg, countSeg,
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MemorySegment.NULL);
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memspace_id = H5Screate_simple(2, arena.allocateFrom(ValueLayout.JAVA_LONG, count),
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MemorySegment.NULL);
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// Read the data using the previously defined hyperslab.
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if ((dataset_id >= 0) && (filespace_id >= 0) && (memspace_id >= 0)) {
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// Allocate MemorySegment for reading
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int totalSize = 5 * 3;
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MemorySegment readSeg = arena.allocate(ValueLayout.JAVA_INT, totalSize);
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H5Dread(dataset_id, H5T_NATIVE_INT_g(), memspace_id, filespace_id, H5P_DEFAULT(),
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readSeg);
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// Unflatten 1D MemorySegment to 2D array
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for (int i = 0; i < 5; i++)
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for (int j = 0; j < 3; j++)
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dataRead[i][j] = readSeg.getAtIndex(ValueLayout.JAVA_INT, i * 3 + j);
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}
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}
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}
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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// print out the data values
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System.out.println("\n\nSubset Data Values");
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for (int i = 0; i < 5; i++) {
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System.out.print("\n" + dataRead[i][0]);
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for (int j = 1; j < 3; j++) {
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System.out.print("," + dataRead[i][j]);
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}
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}
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// Close the dataset.
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try {
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if (dataset_id >= 0)
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H5Dclose(dataset_id);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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try {
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if (filespace_id >= 0)
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H5Sclose(filespace_id);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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// Close the file.
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try {
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if (file_id >= 0)
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H5Fclose(file_id);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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}
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/**
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* create the file and add groups ans dataset into the file, which is the
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* same as javaExample.H5DatasetCreate
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*
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* @see javaExample.HDF5DatasetCreate
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* @throws Exception
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*/
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private static void createFile(Arena arena) throws Exception
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{
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long file_id = H5I_INVALID_HID();
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long dataspace_id = H5I_INVALID_HID();
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long dataset_id = H5I_INVALID_HID();
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// Create a new file using default properties.
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try {
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file_id = H5Fcreate(arena.allocateFrom(fname), H5F_ACC_TRUNC(), H5P_DEFAULT(), H5P_DEFAULT());
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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// Create the data space for the dataset.
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try {
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dataspace_id =
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H5Screate_simple(2, arena.allocateFrom(ValueLayout.JAVA_LONG, dims2D), MemorySegment.NULL);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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// Create the dataset.
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try {
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if ((file_id >= 0) && (dataspace_id >= 0))
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dataset_id = H5Dcreate2(file_id, arena.allocateFrom(dsname), H5T_STD_I32LE_g(), dataspace_id,
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H5P_DEFAULT(), H5P_DEFAULT(), H5P_DEFAULT());
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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// Terminate access to the data space.
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try {
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if (dataspace_id >= 0)
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H5Sclose(dataspace_id);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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// set the data values
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int[] dataIn = new int[20 * 10];
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for (int i = 0; i < 20; i++) {
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for (int j = 0; j < 10; j++) {
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dataIn[i * 10 + j] = 1000 + i * 100 + j;
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}
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}
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// Write the data to the dataset.
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try {
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if (dataset_id >= 0) {
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MemorySegment dataSeg = arena.allocateFrom(ValueLayout.JAVA_INT, dataIn);
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H5Dwrite(dataset_id, H5T_NATIVE_INT_g(), H5S_ALL(), H5S_ALL(), H5P_DEFAULT(), dataSeg);
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}
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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// End access to the dataset and release resources used by it.
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try {
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if (dataset_id >= 0)
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H5Dclose(dataset_id);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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// Close the file.
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try {
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if (file_id >= 0)
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H5Fclose(file_id);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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}
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public static void main(String[] args)
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{
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try (Arena arena = Arena.ofConfined()) {
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HDF5SubsetSelect.SubsetSelect(arena);
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}
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}
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}
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