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.
354 lines
12 KiB
Java
354 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 array datatypes
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to an attribute. The program first writes integers arrays
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of dimension ADIM0xADIM1 to an attribute with a dataspace
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of DIM0, then closes the file. Next, it reopens the
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file, reads back the data, and 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_ArrayAttribute {
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private static String FILENAME = "H5Ex_T_ArrayAttribute.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 ADIM0 = 3;
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private static final int ADIM1 = 5;
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private static final int RANK = 1;
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private static final int NDIMS = 2;
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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 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[] dims = {DIM0};
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long[] adims = {ADIM0, ADIM1};
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int[][][] dset_data = new int[DIM0][ADIM0][ADIM1];
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// Initialize data. indx is the element in the dataspace, jndx and kndx the
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// elements within the array datatype.
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for (int indx = 0; indx < DIM0; indx++)
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for (int jndx = 0; jndx < ADIM0; jndx++)
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for (int kndx = 0; kndx < ADIM1; kndx++)
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dset_data[indx][jndx][kndx] = indx * jndx - jndx * kndx + indx * kndx;
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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 array datatypes for file.
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try {
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filetype_id =
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H5Tarray_create2(H5T_STD_I64LE_g(), NDIMS, arena.allocateFrom(ValueLayout.JAVA_LONG, adims));
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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 array datatypes for memory.
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try {
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memtype_id =
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H5Tarray_create2(H5T_NATIVE_INT_g(), NDIMS, arena.allocateFrom(ValueLayout.JAVA_LONG, adims));
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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 and write the array data to it.
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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 dataset.
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try {
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if ((attribute_id >= 0) && (memtype_id >= 0)) {
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// Flatten the 3D array to 1D for MemorySegment
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int totalSize = DIM0 * ADIM0 * ADIM1;
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int[] flatData = new int[totalSize];
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for (int i = 0; i < DIM0; i++) {
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for (int j = 0; j < ADIM0; j++) {
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for (int k = 0; k < ADIM1; k++) {
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flatData[i * ADIM0 * ADIM1 + j * ADIM1 + k] = dset_data[i][j][k];
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}
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}
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}
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MemorySegment dataSeg = arena.allocateFrom(ValueLayout.JAVA_INT, 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 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[] adims = {ADIM0, ADIM1};
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int[][][] dset_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.
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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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}
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catch (Exception e) {
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e.printStackTrace();
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}
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// Get the datatype's dimensions.
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try {
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if (filetype_id >= 0) {
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MemorySegment adimsSeg = arena.allocateFrom(ValueLayout.JAVA_LONG, adims);
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H5Tget_array_dims2(filetype_id, adimsSeg);
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// Read back the dimensions
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for (int i = 0; i < adims.length; i++) {
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adims[i] = adimsSeg.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 array of pointers to two-dimensional arrays (the
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// elements of the dataset.
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dset_data = new int[(int)dims[0]][(int)(adims[0])][(int)(adims[1])];
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// Create array datatypes for memory.
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try {
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memtype_id =
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H5Tarray_create2(H5T_NATIVE_INT_g(), 2, arena.allocateFrom(ValueLayout.JAVA_LONG, adims));
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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] * adims[0] * adims[1]);
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MemorySegment dataSeg = arena.allocate(ValueLayout.JAVA_INT, totalSize);
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H5Aread(attribute_id, memtype_id, dataSeg);
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// Unflatten the 1D MemorySegment to 3D array
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for (int i = 0; i < dims[0]; i++) {
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for (int j = 0; j < adims[0]; j++) {
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for (int k = 0; k < adims[1]; k++) {
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dset_data[i][j][k] = dataSeg.getAtIndex(
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ValueLayout.JAVA_INT, (int)(i * adims[0] * adims[1] + j * adims[1] + k));
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}
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}
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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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for (int indx = 0; indx < dims[0]; indx++) {
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System.out.println(ATTRIBUTENAME + " [" + indx + "]:");
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for (int jndx = 0; jndx < adims[0]; jndx++) {
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System.out.print(" [");
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for (int kndx = 0; kndx < adims[1]; kndx++)
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System.out.print(dset_data[indx][jndx][kndx] + " ");
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System.out.println("]");
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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 (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 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_ArrayAttribute.CreateDataset(arena);
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H5Ex_T_ArrayAttribute.ReadDataset(arena);
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}
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}
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}
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