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.
281 lines
9.4 KiB
Java
281 lines
9.4 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 opaque datatypes
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to a dataset. The program first writes opaque data to a
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dataset with a dataspace of DIM0, then closes the file.
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Next, it reopens the file, reads back the data, and
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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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public class H5Ex_T_Opaque {
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private static String FILENAME = "H5Ex_T_Opaque.h5";
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private static String DATASETNAME = "DS1";
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private static final int DIM0 = 4;
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private static final int LEN = 7;
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private static final int RANK = 1;
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private static void CreateDataset(Arena arena)
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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 datatype_id = H5I_INVALID_HID();
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long dataset_id = H5I_INVALID_HID();
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long[] dims = {DIM0};
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byte[] dset_data = new byte[DIM0 * LEN];
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byte[] str_data = {'O', 'P', 'A', 'Q', 'U', 'E'};
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// Initialize data.
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for (int indx = 0; indx < DIM0; indx++) {
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for (int jndx = 0; jndx < LEN - 1; jndx++)
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dset_data[jndx + indx * LEN] = str_data[jndx];
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dset_data[LEN - 1 + indx * LEN] = (byte)(indx + '0');
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}
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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 opaque datatype and set the tag to something appropriate.
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// For this example we will write and view the data as a character
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// array.
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try {
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datatype_id = H5Tcreate(H5T_OPAQUE(), (long)LEN);
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if (datatype_id >= 0)
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H5Tset_tag(datatype_id, arena.allocateFrom("Character array"));
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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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dataspace_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 and write the integer data to it. In this
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// example we will save the data as 64 bit big endian integers,
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// regardless of the native integer type. The HDF5 library
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// automatically converts between different integer types.
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try {
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if ((file_id >= 0) && (datatype_id >= 0) && (dataspace_id >= 0))
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dataset_id = H5Dcreate2(file_id, arena.allocateFrom(DATASETNAME), datatype_id, 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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// Write the opaque data to the dataset.
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try {
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if ((dataset_id >= 0) && (datatype_id >= 0)) {
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MemorySegment dataSeg = arena.allocateFrom(ValueLayout.JAVA_BYTE, dset_data);
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H5Dwrite(dataset_id, datatype_id, 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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// 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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try {
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if (datatype_id >= 0)
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H5Tclose(datatype_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 ReadDataset(Arena arena)
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{
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long file_id = H5I_INVALID_HID();
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long datatype_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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long type_len = H5I_INVALID_HID();
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long[] dims = {DIM0};
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byte[] dset_data;
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String tag_name = null;
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// Open an existing file.
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try {
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file_id = H5Fopen(arena.allocateFrom(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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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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// Get datatype and properties for the datatype.
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try {
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if (dataset_id >= 0)
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datatype_id = H5Dget_type(dataset_id);
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if (datatype_id >= 0) {
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type_len = H5Tget_size(datatype_id);
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MemorySegment tagSeg = H5Tget_tag(datatype_id);
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tag_name = tagSeg.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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// Get dataspace and allocate memory for read buffer.
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try {
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if (dataset_id >= 0)
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dataspace_id = H5Dget_space(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 (dataspace_id >= 0) {
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MemorySegment dimsSeg = arena.allocateFrom(ValueLayout.JAVA_LONG, dims);
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H5Sget_simple_extent_dims(dataspace_id, dimsSeg, MemorySegment.NULL);
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// Read back the dimensions
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for (int i = 0; i < dims.length; i++) {
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dims[i] = dimsSeg.getAtIndex(ValueLayout.JAVA_LONG, i);
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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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// Allocate buffer.
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dset_data = new byte[(int)(dims[0] * type_len)];
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// Read data.
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try {
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if ((dataset_id >= 0) && (datatype_id >= 0)) {
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MemorySegment dataSeg = arena.allocate(ValueLayout.JAVA_BYTE, dset_data.length);
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H5Dread(dataset_id, datatype_id, H5S_ALL(), H5S_ALL(), H5P_DEFAULT(), dataSeg);
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// Copy from MemorySegment back to byte array
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for (int i = 0; i < dset_data.length; i++) {
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dset_data[i] = dataSeg.get(ValueLayout.JAVA_BYTE, i);
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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("Datatype tag for " + DATASETNAME + " is: \"" + tag_name + "\"");
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for (int indx = 0; indx < dims[0]; indx++) {
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System.out.print(DATASETNAME + "[" + indx + "]: ");
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for (int jndx = 0; jndx < type_len; jndx++) {
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char temp = (char)dset_data[jndx + indx * (int)type_len];
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System.out.print(temp);
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}
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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 (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 (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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try {
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if (datatype_id >= 0)
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H5Tclose(datatype_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_T_Opaque.CreateDataset(arena);
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H5Ex_T_Opaque.ReadDataset(arena);
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}
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}
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}
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