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.
319 lines
10 KiB
Java
319 lines
10 KiB
Java
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
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* Copyright by The HDF Group. *
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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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/************************************************************
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This example shows how to read and write data to a compact
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dataset. The program first writes integers to a compact
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dataset with dataspace dimensions of DIM_XxDIM_Y, then
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closes the file. Next, it reopens the file, reads back
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the data, and outputs it to the screen.
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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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import java.util.EnumSet;
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import java.util.HashMap;
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import java.util.Map;
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public class H5Ex_D_Compact {
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private static String FILENAME = "H5Ex_D_Compact.h5";
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private static String DATASETNAME = "DS1";
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private static final int DIM_X = 4;
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private static final int DIM_Y = 7;
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private static final int RANK = 2;
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// Values for the status of space allocation
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enum H5D_layout {
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H5D_LAYOUT_ERROR(-1),
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H5D_COMPACT(0),
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H5D_CONTIGUOUS(1),
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H5D_CHUNKED(2),
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H5D_VIRTUAL(3),
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H5D_NLAYOUTS(4);
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private static final Map<Integer, H5D_layout> lookup = new HashMap<Integer, H5D_layout>();
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static
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{
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for (H5D_layout s : EnumSet.allOf(H5D_layout.class))
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lookup.put(s.getCode(), s);
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}
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private int code;
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H5D_layout(int layout_type) { this.code = layout_type; }
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public int getCode() { return this.code; }
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public static H5D_layout get(int code) { return lookup.get(code); }
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}
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private static void writeCompact(Arena arena)
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{
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long file_id = H5I_INVALID_HID();
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long filespace_id = H5I_INVALID_HID();
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long dataset_id = H5I_INVALID_HID();
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long dcpl_id = H5I_INVALID_HID();
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long[] dims = {DIM_X, DIM_Y};
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int[][] dset_data = new int[DIM_X][DIM_Y];
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// Initialize data.
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for (int indx = 0; indx < DIM_X; indx++)
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for (int jndx = 0; jndx < DIM_Y; jndx++)
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dset_data[indx][jndx] = indx * jndx - jndx;
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// Create a new file using default properties.
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try {
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MemorySegment filename = arena.allocateFrom(FILENAME);
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file_id = H5Fcreate(filename, 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 dataspace. Setting maximum size to NULL sets the maximum
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// size to be the current size.
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try {
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MemorySegment dimsSeg = arena.allocateFrom(ValueLayout.JAVA_LONG, dims);
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filespace_id = H5Screate_simple(RANK, dimsSeg, 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 creation property list.
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try {
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dcpl_id = H5Pcreate(H5P_CLS_DATASET_CREATE_ID_g());
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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 layout to compact.
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try {
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if (dcpl_id >= 0)
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H5Pset_layout(dcpl_id, H5D_layout.H5D_COMPACT.getCode());
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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. We will use all default properties for this example.
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try {
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if ((file_id >= 0) && (filespace_id >= 0) && (dcpl_id >= 0)) {
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MemorySegment datasetname = arena.allocateFrom(DATASETNAME);
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dataset_id = H5Dcreate2(file_id, datasetname, H5T_STD_I32LE_g(), filespace_id, H5P_DEFAULT(),
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dcpl_id, H5P_DEFAULT());
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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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// Write the data to the dataset.
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try {
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if (dataset_id >= 0) {
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// Flatten 2D array for FFM
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int[] flatData = new int[DIM_X * DIM_Y];
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for (int i = 0; i < DIM_X; i++) {
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for (int j = 0; j < DIM_Y; j++) {
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flatData[i * DIM_Y + j] = dset_data[i][j];
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}
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}
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MemorySegment dataSeg = arena.allocate(ValueLayout.JAVA_INT, flatData.length);
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for (int i = 0; i < flatData.length; i++) {
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dataSeg.setAtIndex(ValueLayout.JAVA_INT, i, flatData[i]);
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}
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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 (dcpl_id >= 0)
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H5Pclose(dcpl_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 (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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private static void readCompact(Arena arena)
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{
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long file_id = H5I_INVALID_HID();
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long filespace_id = H5I_INVALID_HID();
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long dataset_id = H5I_INVALID_HID();
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long dcpl_id = H5I_INVALID_HID();
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int[][] dset_data = new int[DIM_X][DIM_Y];
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// Open file and dataset using the default properties.
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try {
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MemorySegment filename = arena.allocateFrom(FILENAME);
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file_id = H5Fopen(filename, H5F_ACC_RDONLY(), 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 an existing dataset.
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try {
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if (file_id >= 0) {
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MemorySegment datasetname = arena.allocateFrom(DATASETNAME);
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dataset_id = H5Dopen2(file_id, datasetname, H5P_DEFAULT());
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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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// Retrieve the dataset creation property list.
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try {
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if (dataset_id >= 0)
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dcpl_id = H5Dget_create_plist(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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// Print the storage layout.
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try {
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if (dcpl_id >= 0) {
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int layout_type = H5Pget_layout(dcpl_id);
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System.out.print("Storage layout for " + DATASETNAME + " is: ");
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switch (H5D_layout.get(layout_type)) {
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case H5D_COMPACT:
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System.out.println("H5D_COMPACT");
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break;
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case H5D_CONTIGUOUS:
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System.out.println("H5D_CONTIGUOUS");
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break;
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case H5D_CHUNKED:
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System.out.println("H5D_CHUNKED");
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break;
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case H5D_VIRTUAL:
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System.out.println("H5D_VIRTUAL");
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break;
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case H5D_LAYOUT_ERROR:
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break;
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case H5D_NLAYOUTS:
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break;
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default:
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break;
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}
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System.out.println();
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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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// Read the data using the default properties.
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try {
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if (dataset_id >= 0) {
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MemorySegment dataSeg = arena.allocate(ValueLayout.JAVA_INT, DIM_X * DIM_Y);
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H5Dread(dataset_id, H5T_NATIVE_INT_g(), H5S_ALL(), H5S_ALL(), H5P_DEFAULT(), dataSeg);
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// Unflatten to 2D array
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for (int i = 0; i < DIM_X; i++) {
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for (int j = 0; j < DIM_Y; j++) {
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dset_data[i][j] = dataSeg.getAtIndex(ValueLayout.JAVA_INT, i * DIM_Y + 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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// Output the data to the screen.
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System.out.println("Data for " + DATASETNAME + " is: ");
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for (int indx = 0; indx < DIM_X; indx++) {
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System.out.print(" [ ");
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for (int jndx = 0; jndx < DIM_Y; jndx++)
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System.out.print(dset_data[indx][jndx] + " ");
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System.out.println("]");
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}
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System.out.println();
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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 (dcpl_id >= 0)
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H5Pclose(dcpl_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 (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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public static void main(String[] args)
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{
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try (Arena arena = Arena.ofConfined()) {
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H5Ex_D_Compact.writeCompact(arena);
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H5Ex_D_Compact.readCompact(arena);
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}
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}
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}
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