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.
374 lines
12 KiB
Java
374 lines
12 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 string datatypes
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to an attribute. The program first writes strings to an
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attribute 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_StringAttribute {
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private static String FILENAME = "H5Ex_T_StringAttribute.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 final int DIM0 = 4;
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private static final int SDIM = 8;
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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 memtype_id = H5I_INVALID_HID();
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long filetype_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 attribute_id = H5I_INVALID_HID();
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long[] dims = {DIM0};
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byte[][] dset_data = new byte[DIM0][SDIM];
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StringBuffer[] str_data = {new StringBuffer("Parting"), new StringBuffer("is such"),
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new StringBuffer("sweet"), new StringBuffer("sorrow.")};
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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 file and memory datatypes. For this example we will save
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// the strings as FORTRAN strings, therefore they do not need space
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// for the null terminator in the file.
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try {
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filetype_id = H5Tcopy(H5T_FORTRAN_S1_g());
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if (filetype_id >= 0)
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H5Tset_size(filetype_id, SDIM - 1);
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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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memtype_id = H5Tcopy(H5T_C_S1_g());
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if (memtype_id >= 0)
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H5Tset_size(memtype_id, SDIM);
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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 a scalar dataspace.
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try {
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dataspace_id = H5Screate(H5S_SCALAR());
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if (dataspace_id >= 0) {
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dataset_id = H5Dcreate2(file_id, arena.allocateFrom(DATASETNAME), H5T_STD_I32LE_g(),
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dataspace_id, H5P_DEFAULT(), H5P_DEFAULT(), H5P_DEFAULT());
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H5Sclose(dataspace_id);
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dataspace_id = H5I_INVALID_HID();
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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 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 attribute.
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try {
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if ((dataset_id >= 0) && (dataspace_id >= 0) && (filetype_id >= 0))
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attribute_id = H5Acreate2(dataset_id, arena.allocateFrom(ATTRIBUTENAME), filetype_id,
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dataspace_id, 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 data to the dataset.
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try {
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for (int indx = 0; indx < DIM0; indx++) {
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for (int jndx = 0; jndx < SDIM; jndx++) {
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if (jndx < str_data[indx].length())
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dset_data[indx][jndx] = (byte)str_data[indx].charAt(jndx);
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else
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dset_data[indx][jndx] = 0;
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}
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}
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if ((attribute_id >= 0) && (memtype_id >= 0)) {
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// Flatten 2D byte array to 1D for MemorySegment
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byte[] flatData = new byte[DIM0 * SDIM];
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for (int i = 0; i < DIM0; i++) {
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for (int j = 0; j < SDIM; j++) {
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flatData[i * SDIM + j] = dset_data[i][j];
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}
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}
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MemorySegment dataSeg = arena.allocateFrom(ValueLayout.JAVA_BYTE, flatData);
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H5Awrite(attribute_id, memtype_id, 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 (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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// 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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// Terminate access to the file type.
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try {
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if (filetype_id >= 0)
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H5Tclose(filetype_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 mem type.
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try {
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if (memtype_id >= 0)
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H5Tclose(memtype_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 filetype_id = H5I_INVALID_HID();
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long memtype_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 attribute_id = H5I_INVALID_HID();
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long sdim = 0;
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long[] dims = {DIM0};
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byte[][] dset_data;
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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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}
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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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try {
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if (dataset_id >= 0)
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attribute_id =
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H5Aopen_by_name(dataset_id, arena.allocateFrom("."), arena.allocateFrom(ATTRIBUTENAME),
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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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// Get the datatype and its size.
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try {
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if (attribute_id >= 0)
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filetype_id = H5Aget_type(attribute_id);
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if (filetype_id >= 0) {
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sdim = H5Tget_size(filetype_id);
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sdim++; // Make room for null terminator
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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 (attribute_id >= 0)
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dataspace_id = H5Aget_space(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 (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 space for data.
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dset_data = new byte[(int)dims[0]][(int)sdim];
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str_data = new StringBuffer[(int)dims[0]];
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// Create the memory datatype.
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try {
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memtype_id = H5Tcopy(H5T_C_S1_g());
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if (memtype_id >= 0)
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H5Tset_size(memtype_id, sdim);
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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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// Read data.
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try {
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if ((attribute_id >= 0) && (memtype_id >= 0)) {
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int totalSize = (int)dims[0] * (int)sdim;
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MemorySegment dataSeg = arena.allocate(ValueLayout.JAVA_BYTE, totalSize);
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H5Aread(attribute_id, memtype_id, dataSeg);
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// Unflatten 1D MemorySegment to 2D byte array
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for (int i = 0; i < (int)dims[0]; i++) {
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for (int j = 0; j < sdim; j++) {
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dset_data[i][j] = dataSeg.get(ValueLayout.JAVA_BYTE, i * sdim + j);
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}
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}
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}
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byte[] tempbuf = new byte[(int)sdim];
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for (int indx = 0; indx < (int)dims[0]; indx++) {
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for (int jndx = 0; jndx < sdim; jndx++) {
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tempbuf[jndx] = dset_data[indx][jndx];
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}
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str_data[indx] = new StringBuffer(new String(tempbuf).trim());
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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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for (int indx = 0; indx < dims[0]; indx++) {
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System.out.println(DATASETNAME + " [" + indx + "]: " + str_data[indx]);
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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 (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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// 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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// Terminate access to the file type.
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try {
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if (filetype_id >= 0)
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H5Tclose(filetype_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 mem type.
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try {
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if (memtype_id >= 0)
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H5Tclose(memtype_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_StringAttribute.CreateDataset(arena);
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H5Ex_T_StringAttribute.ReadDataset(arena);
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}
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}
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}
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