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.
391 lines
16 KiB
Java
391 lines
16 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 object references
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to a dataset. The program first creates objects in the
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file and writes references to those objects to a dataset
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with a dataspace of DIM0, then closes the file. Next, it
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reopens the file, dereferences the references, and outputs
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the names of their targets 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_T_RegionReferenceAttribute {
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private static String FILENAME = "H5Ex_T_RegionReferenceAttribute.h5";
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private static String DATASETNAME = "DS1";
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private static String ATTRIBUTENAME = "A1";
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private static String DATASETNAME2 = "DS2";
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private static String GROUPNAME = "G1";
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private static final int DIM0 = 2;
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private static final int DS2DIM0 = 3;
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private static final int DS2DIM1 = 16;
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private static final int RANK = 1;
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private static void writeRegRef(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 filespace_id = H5I_INVALID_HID();
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long group_id = H5I_INVALID_HID();
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long dataset_id = H5I_INVALID_HID();
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long attribute_id = H5I_INVALID_HID();
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long[] dims = {DIM0};
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long[] dims2 = {DS2DIM0, DS2DIM1};
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// data buffer for writing region reference
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// Allocate MemorySegments for references
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MemorySegment[] refs = new MemorySegment[DIM0];
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for (int i = 0; i < DIM0; i++) {
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refs[i] = arena.allocate(H5R_REF_BUF_SIZE());
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}
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// data buffer for writing dataset
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byte[][] write_data = new byte[DS2DIM0][DS2DIM1];
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StringBuffer[] str_data = {new StringBuffer("The quick brown"), new StringBuffer("fox jumps over "),
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new StringBuffer("the 5 lazy dogs")};
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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 dataset with character data.
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try {
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dataspace_id =
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H5Screate_simple(2, arena.allocateFrom(ValueLayout.JAVA_LONG, dims2), MemorySegment.NULL);
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if ((file_id >= 0) && (dataspace_id >= 0)) {
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dataset_id = H5Dcreate2(file_id, arena.allocateFrom(DATASETNAME2), H5T_STD_I8LE_g(),
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dataspace_id, H5P_DEFAULT(), H5P_DEFAULT(), H5P_DEFAULT());
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for (int indx = 0; indx < DS2DIM0; indx++) {
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for (int jndx = 0; jndx < DS2DIM1; jndx++) {
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if (jndx < str_data[indx].length())
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write_data[indx][jndx] = (byte)str_data[indx].charAt(jndx);
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else
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write_data[indx][jndx] = 0;
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}
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}
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// Flatten 2D byte array to 1D for MemorySegment
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byte[] flatData = new byte[DS2DIM0 * DS2DIM1];
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for (int i = 0; i < DS2DIM0; i++) {
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for (int j = 0; j < DS2DIM1; j++) {
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flatData[i * DS2DIM1 + j] = write_data[i][j];
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}
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}
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MemorySegment writeSeg = arena.allocateFrom(ValueLayout.JAVA_BYTE, flatData);
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H5Dwrite(dataset_id, H5T_STD_I8LE_g(), H5S_ALL(), H5S_ALL(), H5P_DEFAULT(), writeSeg);
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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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// Create reference to a list of elements in dset2.
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try {
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long[][] coords = {{0, 1}, {2, 11}, {1, 0}, {2, 4}};
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// Flatten coords for MemorySegment
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long[] flatCoords = new long[4 * 2];
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for (int i = 0; i < 4; i++) {
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flatCoords[i * 2] = coords[i][0];
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flatCoords[i * 2 + 1] = coords[i][1];
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}
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MemorySegment coordsSeg = arena.allocateFrom(ValueLayout.JAVA_LONG, flatCoords);
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H5Sselect_elements(dataspace_id, H5S_SELECT_SET(), 4, coordsSeg);
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if (file_id >= 0)
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H5Rcreate_region(file_id, arena.allocateFrom(DATASETNAME2), dataspace_id, H5P_DEFAULT(),
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refs[0]);
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}
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catch (Exception ex) {
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ex.printStackTrace();
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}
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// Create reference to a hyperslab in dset2.
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try {
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long[] start = {0, 0}; // Starting location of hyperslab
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long[] stride = {2, 11}; // Stride of hyperslab
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long[] count = {2, 2}; // Element count of hyperslab
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long[] block = {1, 3}; // Block size of hyperslab
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// Convert arrays to MemorySegments
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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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MemorySegment blockSeg = arena.allocateFrom(ValueLayout.JAVA_LONG, block);
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H5Sselect_hyperslab(dataspace_id, H5S_SELECT_SET(), startSeg, strideSeg, countSeg, blockSeg);
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if (file_id >= 0)
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H5Rcreate_region(file_id, arena.allocateFrom(DATASETNAME2), dataspace_id, H5P_DEFAULT(),
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refs[1]);
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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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try {
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H5Sclose(dataspace_id);
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}
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catch (Exception e) {
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}
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// Create dataset with a null dataspace to serve as the parent for the attribute.
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try {
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dataspace_id = H5Screate(H5S_NULL());
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dataset_id = H5Dcreate2(file_id, arena.allocateFrom(DATASETNAME), 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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try {
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H5Sclose(dataspace_id);
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}
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catch (Exception e) {
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}
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// Create the attribute and write the region references to it.
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try {
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dataspace_id =
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H5Screate_simple(1, arena.allocateFrom(ValueLayout.JAVA_LONG, dims), MemorySegment.NULL);
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if ((file_id >= 0) && (attribute_id >= 0)) {
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attribute_id = H5Acreate2(file_id, arena.allocateFrom(ATTRIBUTENAME), H5T_STD_REF_g(),
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dataspace_id, H5P_DEFAULT(), H5P_DEFAULT());
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// Pack references into contiguous MemorySegment
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int refSize = H5R_REF_BUF_SIZE();
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MemorySegment refData = arena.allocate(refSize * DIM0);
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for (int i = 0; i < DIM0; i++) {
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MemorySegment.copy(refs[i], 0, refData, i * refSize, refSize);
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}
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H5Awrite(attribute_id, H5T_STD_REF_g(), refData);
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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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try {
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H5Rdestroy(refs[0]);
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}
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catch (Exception ex) {
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}
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try {
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H5Rdestroy(refs[1]);
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}
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catch (Exception ex) {
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}
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// End access to theattribute, dataset and release resources used by it.
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try {
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H5Sclose(dataspace_id);
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}
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catch (Exception e) {
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}
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try {
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if (attribute_id >= 0)
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H5Aclose(attribute_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 readRegRef(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 dataspace_id = H5I_INVALID_HID();
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long attribute_id = H5I_INVALID_HID();
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int object_type = -1;
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long object_id = H5I_INVALID_HID();
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long region_id = H5I_INVALID_HID();
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long[] dims = {DIM0};
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// Allocate MemorySegments for references
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MemorySegment[] refs = new MemorySegment[DIM0];
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for (int i = 0; i < DIM0; i++) {
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refs[i] = arena.allocate(H5R_REF_BUF_SIZE());
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}
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StringBuffer str_data;
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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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// Open an existing attribute.
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try {
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attribute_id = H5Aopen(file_id, arena.allocateFrom(ATTRIBUTENAME), H5P_DEFAULT());
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try {
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// Get dataspace and allocate memory for read buffer.
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dataspace_id = H5Aget_space(attribute_id);
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MemorySegment dimsSeg = arena.allocateFrom(ValueLayout.JAVA_LONG, dims);
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H5Sget_simple_extent_dims(attribute_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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// Read data.
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// Read data into contiguous MemorySegment
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int refSize = H5R_REF_BUF_SIZE();
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MemorySegment refData = arena.allocate(refSize * dims[0]);
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H5Aread(attribute_id, H5T_STD_REF_g(), refData);
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// Unpack references from contiguous MemorySegment
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for (int i = 0; i < dims[0]; i++) {
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MemorySegment.copy(refData, i * refSize, refs[i], 0, refSize);
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}
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// Output the data to the screen.
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for (int indx = 0; indx < dims[0]; indx++) {
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System.out.println(DATASETNAME + "[" + indx + "]:");
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System.out.print(" ->");
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// Open the referenced object.
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try {
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object_id = H5Ropen_object(refs[indx], H5P_DEFAULT(), H5P_DEFAULT());
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try {
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// Get the name - first query size
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long name_size = H5Iget_name(object_id, MemorySegment.NULL, 0);
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String obj_name = null;
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if (name_size > 0) {
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MemorySegment nameBuffer = arena.allocate(name_size + 1);
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H5Iget_name(object_id, nameBuffer, name_size + 1);
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obj_name = nameBuffer.getString(0);
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}
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region_id = H5Ropen_region(refs[indx], H5P_DEFAULT(), H5P_DEFAULT());
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if ((object_id >= 0) && (region_id >= 0)) {
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try {
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long reg_npoints = H5Sget_select_npoints(region_id);
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long[] dims2 = new long[1];
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dims2[0] = (int)reg_npoints;
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dataspace_id = H5Screate_simple(
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1, arena.allocateFrom(ValueLayout.JAVA_LONG, dims2),
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MemorySegment.NULL);
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// Read data.
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MemorySegment refbuf = arena.allocate((int)reg_npoints + 1);
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H5Dread(object_id, H5T_STD_I8LE_g(), dataspace_id, region_id,
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H5P_DEFAULT(), refbuf);
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refbuf.set(ValueLayout.JAVA_BYTE, (int)reg_npoints, (byte)0);
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str_data = new StringBuffer(refbuf.getString(0).trim());
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System.out.println(" " + obj_name + ": " + str_data);
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}
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catch (Throwable err2) {
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err2.printStackTrace();
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}
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}
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}
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catch (Throwable err1) {
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err1.printStackTrace();
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}
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finally {
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try {
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H5Sclose(region_id);
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}
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catch (Exception ex) {
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}
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}
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}
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catch (Throwable err0) {
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err0.printStackTrace();
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}
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finally {
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try {
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H5Dclose(object_id);
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}
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catch (Exception ex) {
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}
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}
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} // end for
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}
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catch (Exception e4) {
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e4.printStackTrace();
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}
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finally {
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try {
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H5Sclose(dataspace_id);
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for (int indx = 0; indx < dims[0]; indx++)
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H5Rdestroy(refs[indx]);
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}
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catch (Exception e4) {
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}
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}
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}
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catch (Exception e3) {
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e3.printStackTrace();
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}
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finally {
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try {
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H5Aclose(attribute_id);
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}
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catch (Exception e3) {
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}
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}
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}
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catch (Exception e2) {
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e2.printStackTrace();
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}
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finally {
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try {
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H5Fclose(file_id);
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}
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catch (Exception e2) {
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}
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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_RegionReferenceAttribute.writeRegRef(arena);
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H5Ex_T_RegionReferenceAttribute.readRegRef(arena);
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}
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}
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}
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