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.
364 lines
14 KiB
Java
364 lines
14 KiB
Java
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
|
* Copyright by The HDF Group. *
|
|
* All rights reserved. *
|
|
* *
|
|
* This file is part of HDF5. The full HDF5 copyright notice, including *
|
|
* terms governing use, modification, and redistribution, is contained in *
|
|
* the LICENSE file, which can be found at the root of the source code *
|
|
* distribution tree, or in https://www.hdfgroup.org/licenses. *
|
|
* If you do not have access to either file, you may request a copy from *
|
|
* help@hdfgroup.org. *
|
|
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
|
|
|
|
/************************************************************
|
|
This example shows how to read and write object references
|
|
to a dataset. The program first creates objects in the
|
|
file and writes references to those objects to a dataset
|
|
with a dataspace of DIM0, then closes the file. Next, it
|
|
reopens the file, dereferences the references, and outputs
|
|
the names of their targets to the screen.
|
|
************************************************************/
|
|
|
|
import static org.hdfgroup.javahdf5.hdf5_h.*;
|
|
|
|
import java.lang.foreign.Arena;
|
|
import java.lang.foreign.MemorySegment;
|
|
import java.lang.foreign.ValueLayout;
|
|
import java.util.EnumSet;
|
|
import java.util.HashMap;
|
|
import java.util.Map;
|
|
|
|
public class H5Ex_T_ObjectReference {
|
|
private static String FILENAME = "H5Ex_T_ObjectReference.h5";
|
|
private static String DATASETNAME = "DS1";
|
|
private static String DATASETNAME2 = "DS2";
|
|
private static String GROUPNAME = "G1";
|
|
private static final int DIM0 = 2;
|
|
private static final int RANK = 1;
|
|
|
|
// Values for the status of space allocation
|
|
enum H5G_obj {
|
|
H5G_UNKNOWN(H5O_TYPE_UNKNOWN()), /* Unknown object type */
|
|
H5G_GROUP(H5O_TYPE_GROUP()), /* Object is a group */
|
|
H5G_DATASET(H5O_TYPE_DATASET()), /* Object is a dataset */
|
|
H5G_TYPE(H5O_TYPE_NAMED_DATATYPE()); /* Object is a named data type */
|
|
private static final Map<Integer, H5G_obj> lookup = new HashMap<Integer, H5G_obj>();
|
|
|
|
static
|
|
{
|
|
for (H5G_obj s : EnumSet.allOf(H5G_obj.class))
|
|
lookup.put(s.getCode(), s);
|
|
}
|
|
|
|
private int code;
|
|
|
|
H5G_obj(int layout_type) { this.code = layout_type; }
|
|
|
|
public int getCode() { return this.code; }
|
|
|
|
public static H5G_obj get(int code) { return lookup.get(code); }
|
|
}
|
|
|
|
private static void writeObjRef(Arena arena)
|
|
{
|
|
long file_id = H5I_INVALID_HID();
|
|
long dataspace_id = H5I_INVALID_HID();
|
|
long filespace_id = H5I_INVALID_HID();
|
|
long group_id = H5I_INVALID_HID();
|
|
long dataset_id = H5I_INVALID_HID();
|
|
long[] dims = {DIM0};
|
|
|
|
// Allocate MemorySegments for references
|
|
MemorySegment[] refs = new MemorySegment[DIM0];
|
|
for (int i = 0; i < DIM0; i++) {
|
|
refs[i] = arena.allocate(H5R_REF_BUF_SIZE());
|
|
}
|
|
|
|
// Create a new file using default properties.
|
|
try {
|
|
file_id = H5Fcreate(arena.allocateFrom(FILENAME), H5F_ACC_TRUNC(), H5P_DEFAULT(), H5P_DEFAULT());
|
|
}
|
|
catch (Exception e) {
|
|
e.printStackTrace();
|
|
}
|
|
|
|
// Create dataset with a scalar dataspace.
|
|
try {
|
|
dataspace_id = H5Screate(H5S_SCALAR());
|
|
if ((file_id >= 0) && (dataspace_id >= 0)) {
|
|
dataset_id = H5Dcreate2(file_id, arena.allocateFrom(DATASETNAME2), H5T_STD_I32LE_g(),
|
|
dataspace_id, H5P_DEFAULT(), H5P_DEFAULT(), H5P_DEFAULT());
|
|
if (dataset_id >= 0)
|
|
H5Dclose(dataset_id);
|
|
dataset_id = H5I_INVALID_HID();
|
|
H5Sclose(dataspace_id);
|
|
dataspace_id = H5I_INVALID_HID();
|
|
}
|
|
}
|
|
catch (Exception e) {
|
|
e.printStackTrace();
|
|
}
|
|
|
|
// Create a group in the file.
|
|
try {
|
|
if (file_id >= 0)
|
|
group_id = H5Gcreate2(file_id, arena.allocateFrom(GROUPNAME), H5P_DEFAULT(), H5P_DEFAULT(),
|
|
H5P_DEFAULT());
|
|
if (group_id >= 0)
|
|
H5Gclose(group_id);
|
|
group_id = H5I_INVALID_HID();
|
|
}
|
|
catch (Exception e) {
|
|
e.printStackTrace();
|
|
}
|
|
|
|
try {
|
|
if (file_id >= 0) {
|
|
// Create object reference to group
|
|
try {
|
|
H5Rcreate_object(file_id, arena.allocateFrom(GROUPNAME), H5P_DEFAULT(), refs[0]);
|
|
}
|
|
catch (Throwable err) {
|
|
err.printStackTrace();
|
|
}
|
|
|
|
// Create object reference to dataset
|
|
try {
|
|
H5Rcreate_object(file_id, arena.allocateFrom(DATASETNAME2), H5P_DEFAULT(), refs[1]);
|
|
}
|
|
catch (Throwable err) {
|
|
err.printStackTrace();
|
|
}
|
|
}
|
|
|
|
// Create dataspace. Setting maximum size to NULL sets the maximum
|
|
// size to be the current size.
|
|
try {
|
|
filespace_id = H5Screate_simple(RANK, arena.allocateFrom(ValueLayout.JAVA_LONG, dims),
|
|
MemorySegment.NULL);
|
|
}
|
|
catch (Exception e) {
|
|
e.printStackTrace();
|
|
}
|
|
|
|
// Create the dataset.
|
|
try {
|
|
if ((file_id >= 0) && (filespace_id >= 0))
|
|
dataset_id = H5Dcreate2(file_id, arena.allocateFrom(DATASETNAME), H5T_STD_REF_g(),
|
|
filespace_id, H5P_DEFAULT(), H5P_DEFAULT(), H5P_DEFAULT());
|
|
}
|
|
catch (Exception e) {
|
|
e.printStackTrace();
|
|
}
|
|
|
|
// Write the object references to it.
|
|
try {
|
|
if (dataset_id >= 0) {
|
|
// Pack references into contiguous MemorySegment
|
|
int refSize = H5R_REF_BUF_SIZE();
|
|
MemorySegment refData = arena.allocate(refSize * DIM0);
|
|
for (int i = 0; i < DIM0; i++) {
|
|
MemorySegment.copy(refs[i], 0, refData, i * refSize, refSize);
|
|
}
|
|
H5Dwrite(dataset_id, H5T_STD_REF_g(), H5S_ALL(), H5S_ALL(), H5P_DEFAULT(), refData);
|
|
}
|
|
}
|
|
catch (Exception e) {
|
|
e.printStackTrace();
|
|
}
|
|
}
|
|
catch (Exception ex) {
|
|
ex.printStackTrace();
|
|
}
|
|
finally {
|
|
try {
|
|
H5Rdestroy(refs[1]);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
try {
|
|
H5Rdestroy(refs[0]);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
}
|
|
|
|
// End access to the dataset and release resources used by it.
|
|
|
|
try {
|
|
if (dataset_id >= 0)
|
|
H5Dclose(dataset_id);
|
|
}
|
|
catch (Exception e) {
|
|
e.printStackTrace();
|
|
}
|
|
|
|
try {
|
|
if (filespace_id >= 0)
|
|
H5Sclose(filespace_id);
|
|
}
|
|
catch (Exception e) {
|
|
e.printStackTrace();
|
|
}
|
|
|
|
// Close the file.
|
|
try {
|
|
if (file_id >= 0)
|
|
H5Fclose(file_id);
|
|
}
|
|
catch (Exception e) {
|
|
e.printStackTrace();
|
|
}
|
|
}
|
|
|
|
private static void readObjRef(Arena arena)
|
|
{
|
|
long file_id = H5I_INVALID_HID();
|
|
long dataset_id = H5I_INVALID_HID();
|
|
long dataspace_id = H5I_INVALID_HID();
|
|
int object_type = -1;
|
|
long object_id = H5I_INVALID_HID();
|
|
long[] dims = {DIM0};
|
|
|
|
// Allocate MemorySegments for references
|
|
MemorySegment[] refs = new MemorySegment[DIM0];
|
|
for (int i = 0; i < DIM0; i++) {
|
|
refs[i] = arena.allocate(H5R_REF_BUF_SIZE());
|
|
}
|
|
|
|
// Open an existing file.
|
|
try {
|
|
file_id = H5Fopen(arena.allocateFrom(FILENAME), H5F_ACC_RDONLY(), H5P_DEFAULT());
|
|
|
|
// Open an existing dataset.
|
|
try {
|
|
dataset_id = H5Dopen2(file_id, arena.allocateFrom(DATASETNAME), H5P_DEFAULT());
|
|
|
|
try {
|
|
// Get dataspace and allocate memory for read buffer.
|
|
dataspace_id = H5Dget_space(dataset_id);
|
|
MemorySegment dimsSeg = arena.allocateFrom(ValueLayout.JAVA_LONG, dims);
|
|
H5Sget_simple_extent_dims(dataspace_id, dimsSeg, MemorySegment.NULL);
|
|
// Read back the dimensions
|
|
for (int i = 0; i < dims.length; i++) {
|
|
dims[i] = dimsSeg.getAtIndex(ValueLayout.JAVA_LONG, i);
|
|
}
|
|
|
|
// Read data into contiguous MemorySegment
|
|
int refSize = H5R_REF_BUF_SIZE();
|
|
MemorySegment refData = arena.allocate(refSize * dims[0]);
|
|
H5Dread(dataset_id, H5T_STD_REF_g(), H5S_ALL(), H5S_ALL(), H5P_DEFAULT(), refData);
|
|
|
|
// Unpack references from contiguous MemorySegment
|
|
for (int i = 0; i < dims[0]; i++) {
|
|
MemorySegment.copy(refData, i * refSize, refs[i], 0, refSize);
|
|
}
|
|
|
|
// Output the data to the screen.
|
|
for (int indx = 0; indx < dims[0]; indx++) {
|
|
System.out.println(DATASETNAME + "[" + indx + "]:");
|
|
System.out.print(" ->");
|
|
// Open the referenced object, get its name and type.
|
|
try {
|
|
object_id = H5Ropen_object(refs[indx], H5P_DEFAULT(), H5P_DEFAULT());
|
|
try {
|
|
// Get object type
|
|
MemorySegment objTypeSeg = arena.allocate(ValueLayout.JAVA_INT);
|
|
H5Rget_obj_type3(refs[indx], H5P_DEFAULT(), objTypeSeg);
|
|
object_type = objTypeSeg.get(ValueLayout.JAVA_INT, 0);
|
|
|
|
String obj_name = null;
|
|
if (object_type >= 0) {
|
|
// Get the name - first query size
|
|
long name_size = H5Iget_name(object_id, MemorySegment.NULL, 0);
|
|
if (name_size > 0) {
|
|
MemorySegment nameBuffer = arena.allocate(name_size + 1);
|
|
H5Iget_name(object_id, nameBuffer, name_size + 1);
|
|
obj_name = nameBuffer.getString(0);
|
|
}
|
|
}
|
|
if ((object_id >= 0) && (object_type >= -1)) {
|
|
switch (H5G_obj.get(object_type)) {
|
|
case H5G_GROUP:
|
|
System.out.print("H5G_GROUP");
|
|
break;
|
|
case H5G_DATASET:
|
|
System.out.print("H5G_DATASET");
|
|
break;
|
|
case H5G_TYPE:
|
|
System.out.print("H5G_TYPE");
|
|
break;
|
|
default:
|
|
System.out.print("UNHANDLED");
|
|
}
|
|
}
|
|
// Print the name.
|
|
System.out.println(": " + obj_name);
|
|
}
|
|
catch (Exception e) {
|
|
e.printStackTrace();
|
|
}
|
|
finally {
|
|
try {
|
|
H5Oclose(object_id);
|
|
}
|
|
catch (Exception e) {
|
|
}
|
|
}
|
|
}
|
|
catch (Exception e4) {
|
|
e4.printStackTrace();
|
|
}
|
|
finally {
|
|
try {
|
|
H5Rdestroy(refs[indx]);
|
|
}
|
|
catch (Exception e4) {
|
|
}
|
|
}
|
|
} // end for
|
|
}
|
|
catch (Exception e3) {
|
|
e3.printStackTrace();
|
|
}
|
|
finally {
|
|
try {
|
|
H5Sclose(dataspace_id);
|
|
}
|
|
catch (Exception e3) {
|
|
}
|
|
}
|
|
}
|
|
catch (Exception e2) {
|
|
e2.printStackTrace();
|
|
}
|
|
finally {
|
|
try {
|
|
H5Dclose(dataset_id);
|
|
}
|
|
catch (Exception e2) {
|
|
}
|
|
}
|
|
}
|
|
catch (Exception e1) {
|
|
e1.printStackTrace();
|
|
}
|
|
finally {
|
|
try {
|
|
H5Fclose(file_id);
|
|
}
|
|
catch (Exception e1) {
|
|
}
|
|
}
|
|
}
|
|
|
|
public static void main(String[] args)
|
|
{
|
|
|
|
try (Arena arena = Arena.ofConfined()) {
|
|
H5Ex_T_ObjectReference.writeObjRef(arena);
|
|
H5Ex_T_ObjectReference.readObjRef(arena);
|
|
}
|
|
}
|
|
}
|