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.
264 lines
8.9 KiB
Java
264 lines
8.9 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 an
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external dataset. The program first writes integers to an
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external dataset with dataspace dimensions of DIM_XxDIM_Y,
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then closes the file. Next, it reopens the file, reads
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back the data, and outputs the name of the external data
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file and the data 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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public class H5Ex_D_External {
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private static String FILENAME = "H5Ex_D_External.h5";
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private static String EXTERNALNAME = "H5Ex_D_External.data";
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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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private static final int NAME_BUF_SIZE = 32;
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private static void writeExternal(Arena arena)
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{
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long file_id = H5I_INVALID_HID();
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long dcpl_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[] dims = {DIM_X, DIM_Y};
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int[][] dset_data = new int[DIM_X][DIM_Y];
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// Initialize the dataset.
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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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file_id = H5Fcreate(arena.allocateFrom(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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filespace_id =
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H5Screate_simple(RANK, arena.allocateFrom(ValueLayout.JAVA_LONG, dims), 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 external file.
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try {
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if (dcpl_id >= 0)
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H5Pset_external(dcpl_id, arena.allocateFrom(EXTERNALNAME), 0, H5F_UNLIMITED());
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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 HDF5Constants.dataset.
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try {
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if ((file_id >= 0) && (filespace_id >= 0) && (dcpl_id >= 0))
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dataset_id = H5Dcreate2(file_id, arena.allocateFrom(DATASETNAME), H5T_STD_I32LE_g(),
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filespace_id, H5P_DEFAULT(), dcpl_id, 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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// Write the dataset.
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try {
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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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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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// Terminate access to the data space.
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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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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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// 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 readExternal(Arena arena)
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{
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long file_id = H5I_INVALID_HID();
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long dcpl_id = H5I_INVALID_HID();
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long dataset_id = H5I_INVALID_HID();
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int[][] dset_data = new int[DIM_X][DIM_Y];
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String[] Xname = new String[1];
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// Open file using the default properties.
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try {
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file_id = H5Fopen(arena.allocateFrom(FILENAME), 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(DATASETNAME), 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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// 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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// Retrieve and print the name of the external file.
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String externalFileName = "";
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try {
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if (dcpl_id >= 0) {
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MemorySegment namelenSeg = arena.allocate(ValueLayout.JAVA_LONG);
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MemorySegment nameSeg = arena.allocate(256);
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MemorySegment offsetSeg = arena.allocate(ValueLayout.JAVA_LONG);
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MemorySegment sizeSeg = arena.allocate(ValueLayout.JAVA_LONG);
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H5Pget_external(dcpl_id, 0, 256, nameSeg, offsetSeg, sizeSeg);
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externalFileName = nameSeg.getString(0);
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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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System.out.println(DATASETNAME + " is stored in file: " + externalFileName);
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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(DATASETNAME + ":");
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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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// 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 (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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// 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_External.writeExternal(arena);
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H5Ex_D_External.readExternal(arena);
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}
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}
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}
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