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.
335 lines
11 KiB
Java
335 lines
11 KiB
Java
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
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* Copyright by The HDF Group. *
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* Copyright by the Board of Trustees of the University of Illinois. *
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* All rights reserved. *
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* *
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* This file is part of HDF5. The full HDF5 copyright notice, including *
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* terms governing use, modification, and redistribution, is contained in *
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* the LICENSE file, which can be found at the root of the source code *
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* distribution tree, or in https://www.hdfgroup.org/licenses. *
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* If you do not have access to either file, you may request a copy from *
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* help@hdfgroup.org. *
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* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
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import static org.hdfgroup.javahdf5.hdf5_h.*;
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import java.lang.foreign.Arena;
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import java.lang.foreign.MemorySegment;
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import java.lang.foreign.ValueLayout;
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import hdf.hdf5lib.H5;
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import hdf.hdf5lib.structs.H5G_info_t;
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import hdf.hdf5lib.structs.H5O_token_t;
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/**
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* <p>
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* Title: HDF Native Package (Java) Example
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* </p>
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* <p>
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* Description: this example shows how to retrieve HDF file structure using the
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* "HDF Native Package (Java)". The example created the group structure and
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* datasets, and print out the file structure:
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*
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* <pre>
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* "/" (root)
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* integer arrays
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* 2D 32-bit integer 20x10
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* 3D unsigned 8-bit integer 20x10x5
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* float arrays
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* 2D 64-bit double 20x10
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* 3D 32-bit float 20x10x5
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* </pre>
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*
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* </p>
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*/
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public class HDF5FileStructure {
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private static String fname = "HDF5FileStructure.h5";
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private static void FileStructure(Arena arena)
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{
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long file_id = H5I_INVALID_HID();
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long group_id = H5I_INVALID_HID();
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// create the file and add groups and dataset into the file
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try {
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createFile(arena);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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// Open file using the default properties.
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try {
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file_id = H5Fopen(arena.allocateFrom(fname), H5F_ACC_RDWR(), H5P_DEFAULT());
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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// Open the group, obtaining a new handle.
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try {
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if (file_id >= 0)
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group_id = H5Gopen2(file_id, arena.allocateFrom("/"), 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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printGroup(arena, group_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 group.
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try {
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if (group_id >= 0)
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H5Gclose(group_id);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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// Close the file.
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try {
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if (file_id >= 0)
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H5Fclose(file_id);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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}
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/**
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* Recursively print a group and its members.
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*
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* @throws Exception
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*/
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private static void printGroup(Arena arena, long g_id, String gname, String indent) throws Exception
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{
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if (g_id < 0)
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return;
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MemorySegment ginfo = arena.allocate(org.hdfgroup.javahdf5.H5G_info_t.sizeof());
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H5Gget_info(g_id, ginfo);
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long nlinks = org.hdfgroup.javahdf5.H5G_info_t.nlinks(ginfo);
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String objNames[] = new String[(int)nlinks];
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int objTypes[] = new int[(int)nlinks];
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int lnkTypes[] = new int[(int)nlinks];
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H5O_token_t objTokens[] = new H5O_token_t[(int)nlinks];
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int names_found = 0;
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try {
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names_found =
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H5.H5Gget_obj_info_all(g_id, null, objNames, objTypes, lnkTypes, objTokens, H5_INDEX_NAME());
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}
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catch (Throwable err) {
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err.printStackTrace();
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}
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indent += " ";
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for (int i = 0; i < names_found; i++) {
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System.out.println(indent + objNames[i]);
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long group_id = H5I_INVALID_HID();
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if (objTypes[i] == H5O_TYPE_GROUP()) {
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// Open the group, obtaining a new handle.
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try {
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if (g_id >= 0)
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group_id = H5Gopen2(g_id, arena.allocateFrom(objNames[i]), 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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if (group_id >= 0)
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printGroup(arena, group_id, objNames[i], indent);
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// Close the group.
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try {
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if (group_id >= 0)
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H5Gclose(group_id);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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}
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}
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}
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/**
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* create the file and add groups ans dataset into the file, which is the
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* same as javaExample.H5DatasetCreate
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*
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* @see javaExample.HDF5DatasetCreate
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* @throws Exception
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*/
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private static void createFile(Arena arena) throws Exception
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{
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long[] dims2D = {20, 10};
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long[] dims3D = {20, 10, 5};
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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_id1 = H5I_INVALID_HID();
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long dataspace_id2 = H5I_INVALID_HID();
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long group_id1 = H5I_INVALID_HID();
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long group_id2 = H5I_INVALID_HID();
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// Create a new file using default properties.
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try {
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file_id = H5Fcreate(arena.allocateFrom(fname), H5F_ACC_TRUNC(), H5P_DEFAULT(), H5P_DEFAULT());
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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// Create groups in the file.
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try {
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if (file_id >= 0) {
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group_id1 = H5Gcreate2(file_id, arena.allocateFrom("/integer arrays"), H5P_DEFAULT(),
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H5P_DEFAULT(), H5P_DEFAULT());
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group_id1 = H5Gcreate2(file_id, arena.allocateFrom("/float arrays"), H5P_DEFAULT(),
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H5P_DEFAULT(), 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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// Create the data space for the datasets.
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try {
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dataspace_id1 =
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H5Screate_simple(2, arena.allocateFrom(ValueLayout.JAVA_LONG, dims2D), MemorySegment.NULL);
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dataspace_id2 =
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H5Screate_simple(3, arena.allocateFrom(ValueLayout.JAVA_LONG, dims3D), 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 2D 32-bit (4 bytes) integer dataset of 20 by 10
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try {
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if ((file_id >= 0) && (dataspace_id1 >= 0))
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dataset_id =
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H5Dcreate2(file_id, arena.allocateFrom("/integer arrays/2D 32-bit integer 20x10"),
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H5T_STD_I32LE_g(), dataspace_id1, 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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// 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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dataset_id = H5I_INVALID_HID();
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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 3D 8-bit (1 byte) unsigned integer dataset of 20 by 10 by 5
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try {
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if ((file_id >= 0) && (dataspace_id2 >= 0))
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dataset_id = H5Dcreate2(
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file_id, arena.allocateFrom("/integer arrays/3D 8-bit unsigned integer 20x10x5"),
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H5T_STD_I64LE_g(), dataspace_id2, 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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// 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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dataset_id = H5I_INVALID_HID();
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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 2D 64-bit (8 bytes) double dataset of 20 by 10
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try {
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if ((file_id >= 0) && (dataspace_id1 >= 0))
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dataset_id = H5Dcreate2(file_id, arena.allocateFrom("/float arrays/2D 64-bit double 20x10"),
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H5T_NATIVE_DOUBLE_g(), dataspace_id1, H5P_DEFAULT(), H5P_DEFAULT(),
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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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// 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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dataset_id = H5I_INVALID_HID();
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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 3D 32-bit (4 bytes) float dataset of 20 by 10 by 5
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try {
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if ((file_id >= 0) && (dataspace_id2 >= 0))
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dataset_id = H5Dcreate2(file_id, arena.allocateFrom("/float arrays/3D 32-bit float 20x10x5"),
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H5T_NATIVE_FLOAT_g(), dataspace_id2, H5P_DEFAULT(), H5P_DEFAULT(),
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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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// 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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dataset_id = H5I_INVALID_HID();
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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 data space.
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try {
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if (dataspace_id1 >= 0)
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H5Sclose(dataspace_id1);
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dataspace_id1 = H5I_INVALID_HID();
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if (dataspace_id2 >= 0)
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H5Sclose(dataspace_id2);
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dataspace_id2 = H5I_INVALID_HID();
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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 groups.
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try {
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if (group_id1 >= 0)
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H5Gclose(group_id1);
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if (group_id2 >= 0)
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H5Gclose(group_id2);
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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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HDF5FileStructure.FileStructure(arena);
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}
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}
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}
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