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.
420 lines
15 KiB
Java
420 lines
15 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 create a chunked dataset. The
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program first writes integers in a hyperslab selection to
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a chunked dataset with dataspace dimensions of DIM_XxDIM_Y
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and chunk size of CHUNK_XxCHUNK_Y, 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. Finally it reads the data again
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using a different hyperslab selection, and outputs
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the result 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_D_Chunk {
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private static String FILENAME = "H5Ex_D_Chunk.h5";
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private static String DATASETNAME = "DS1";
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private static final int DIM_X = 6;
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private static final int DIM_Y = 8;
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private static final int CHUNK_X = 4;
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private static final int CHUNK_Y = 4;
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private static final int RANK = 2;
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private static final int NDIMS = 2;
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// Values for the status of space allocation
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enum H5D_layout {
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H5D_LAYOUT_ERROR(-1),
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H5D_COMPACT(0),
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H5D_CONTIGUOUS(1),
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H5D_CHUNKED(2),
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H5D_VIRTUAL(3),
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H5D_NLAYOUTS(4);
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private static final Map<Integer, H5D_layout> lookup = new HashMap<Integer, H5D_layout>();
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static
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{
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for (H5D_layout s : EnumSet.allOf(H5D_layout.class))
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lookup.put(s.getCode(), s);
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}
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private int code;
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H5D_layout(int layout_type) { this.code = layout_type; }
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public int getCode() { return this.code; }
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public static H5D_layout get(int code) { return lookup.get(code); }
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}
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private static void writeChunk(Arena arena)
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{
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long file_id = H5I_INVALID_HID();
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long filespace_id = H5I_INVALID_HID();
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long dataset_id = H5I_INVALID_HID();
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long dcpl_id = H5I_INVALID_HID();
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long[] dims = {DIM_X, DIM_Y};
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long[] chunk_dims = {CHUNK_X, CHUNK_Y};
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int[][] dset_data = new int[DIM_X][DIM_Y];
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// Initialize data to "1", to make it easier to see the selections.
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for (int indx = 0; indx < DIM_X; indx++)
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for (int jndx = 0; jndx < DIM_Y; jndx++)
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dset_data[indx][jndx] = 1;
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// Print the data to the screen.
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System.out.println("Original Data:");
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for (int indx = 0; indx < DIM_X; indx++) {
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System.out.print(" [ ");
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for (int jndx = 0; jndx < DIM_Y; jndx++)
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System.out.print(dset_data[indx][jndx] + " ");
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System.out.println("]");
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}
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System.out.println();
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// Create a new file using default properties.
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try {
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MemorySegment filename = arena.allocateFrom(FILENAME);
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file_id = H5Fcreate(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 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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MemorySegment dimsSeg = arena.allocateFrom(ValueLayout.JAVA_LONG, dims);
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filespace_id = H5Screate_simple(RANK, dimsSeg, 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 dataset creation property list.
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try {
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dcpl_id = H5Pcreate(H5P_CLS_DATASET_CREATE_ID_g());
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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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// Set the chunk size.
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try {
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if (dcpl_id >= 0) {
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MemorySegment chunkDimsSeg = arena.allocateFrom(ValueLayout.JAVA_LONG, chunk_dims);
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H5Pset_chunk(dcpl_id, NDIMS, chunkDimsSeg);
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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 chunked dataset.
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try {
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if ((file_id >= 0) && (filespace_id >= 0) && (dcpl_id >= 0)) {
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MemorySegment datasetname = arena.allocateFrom(DATASETNAME);
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dataset_id = H5Dcreate2(file_id, datasetname, H5T_STD_I32LE_g(), filespace_id, H5P_DEFAULT(),
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dcpl_id, 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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// Define and select the first part of the hyperslab selection.
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long[] start = {0, 0};
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long[] stride = {3, 3};
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long[] count = {2, 3};
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long[] block = {2, 2};
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try {
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if ((filespace_id >= 0)) {
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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(filespace_id, H5S_SELECT_SET(), startSeg, strideSeg, countSeg, blockSeg);
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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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// Define and select the second part of the hyperslab selection,
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// which is subtracted from the first selection by the use of
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// H5S_SELECT_NOTB
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block[0] = 1;
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block[1] = 1;
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try {
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if ((filespace_id >= 0)) {
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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(filespace_id, H5S_SELECT_NOTB(), startSeg, strideSeg, countSeg, blockSeg);
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// Write the data to the dataset.
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if (dataset_id >= 0) {
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// Flatten 2D array for FFM
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int[] flatData = new int[DIM_X * DIM_Y];
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for (int i = 0; i < DIM_X; i++) {
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for (int j = 0; j < DIM_Y; j++) {
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flatData[i * DIM_Y + j] = dset_data[i][j];
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}
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}
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MemorySegment dataSeg = arena.allocate(ValueLayout.JAVA_INT, flatData.length);
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for (int i = 0; i < flatData.length; i++) {
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dataSeg.setAtIndex(ValueLayout.JAVA_INT, i, flatData[i]);
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}
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H5Dwrite(dataset_id, H5T_NATIVE_INT_g(), H5S_ALL(), filespace_id, H5P_DEFAULT(), dataSeg);
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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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// End access to the dataset and release resources used by it.
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try {
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if (dcpl_id >= 0)
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H5Pclose(dcpl_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 readChunk(Arena arena)
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{
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long file_id = H5I_INVALID_HID();
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long filespace_id = H5I_INVALID_HID();
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long dataset_id = H5I_INVALID_HID();
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long dcpl_id = H5I_INVALID_HID();
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int[][] dset_data = new int[DIM_X][DIM_Y];
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// Open an existing file.
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try {
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MemorySegment filename = arena.allocateFrom(FILENAME);
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file_id = H5Fopen(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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MemorySegment datasetname = arena.allocateFrom(DATASETNAME);
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dataset_id = H5Dopen2(file_id, datasetname, 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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// Retrieve the dataset creation property list.
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try {
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if (dataset_id >= 0)
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dcpl_id = H5Dget_create_plist(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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// Print the storage layout.
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try {
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if (dcpl_id >= 0) {
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int layout_type = H5Pget_layout(dcpl_id);
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System.out.print("Storage layout for " + DATASETNAME + " is: ");
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switch (H5D_layout.get(layout_type)) {
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case H5D_COMPACT:
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System.out.println("H5D_COMPACT");
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break;
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case H5D_CONTIGUOUS:
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System.out.println("H5D_CONTIGUOUS");
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break;
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case H5D_CHUNKED:
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System.out.println("H5D_CHUNKED");
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break;
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case H5D_VIRTUAL:
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System.out.println("H5D_VIRTUAL");
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break;
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case H5D_LAYOUT_ERROR:
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break;
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case H5D_NLAYOUTS:
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break;
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default:
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break;
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}
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System.out.println();
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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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// Read the data using the default properties.
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try {
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if (dataset_id >= 0) {
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MemorySegment dataSeg = arena.allocate(ValueLayout.JAVA_INT, DIM_X * DIM_Y);
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H5Dread(dataset_id, H5T_NATIVE_INT_g(), H5S_ALL(), H5S_ALL(), H5P_DEFAULT(), dataSeg);
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// Unflatten to 2D array
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for (int i = 0; i < DIM_X; i++) {
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for (int j = 0; j < DIM_Y; j++) {
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dset_data[i][j] = dataSeg.getAtIndex(ValueLayout.JAVA_INT, i * DIM_Y + j);
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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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System.out.println("Data as written to disk by hyberslabs:");
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for (int indx = 0; indx < DIM_X; indx++) {
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System.out.print(" [ ");
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for (int jndx = 0; jndx < DIM_Y; jndx++)
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System.out.print(dset_data[indx][jndx] + " ");
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System.out.println("]");
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}
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System.out.println();
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// Initialize the read array.
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for (int indx = 0; indx < DIM_X; indx++)
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for (int jndx = 0; jndx < DIM_Y; jndx++)
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dset_data[indx][jndx] = 0;
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// Define and select the hyperslab to use for reading.
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try {
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if (dataset_id >= 0) {
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filespace_id = H5Dget_space(dataset_id);
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long[] start = {0, 1};
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long[] stride = {4, 4};
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long[] count = {2, 2};
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long[] block = {2, 3};
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if (filespace_id >= 0) {
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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(filespace_id, H5S_SELECT_SET(), startSeg, strideSeg, countSeg,
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blockSeg);
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// Read the data using the previously defined hyperslab.
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if ((dataset_id >= 0) && (filespace_id >= 0)) {
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MemorySegment dataSeg = arena.allocate(ValueLayout.JAVA_INT, DIM_X * DIM_Y);
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H5Dread(dataset_id, H5T_NATIVE_INT_g(), H5S_ALL(), filespace_id, H5P_DEFAULT(),
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dataSeg);
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// Unflatten to 2D array
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for (int i = 0; i < DIM_X; i++) {
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for (int j = 0; j < DIM_Y; j++) {
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dset_data[i][j] = dataSeg.getAtIndex(ValueLayout.JAVA_INT, i * DIM_Y + j);
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}
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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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System.out.println("Data as read from disk by hyberslab:");
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for (int indx = 0; indx < DIM_X; indx++) {
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System.out.print(" [ ");
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for (int jndx = 0; jndx < DIM_Y; jndx++)
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System.out.print(dset_data[indx][jndx] + " ");
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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 (dcpl_id >= 0)
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H5Pclose(dcpl_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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public static void main(String[] args)
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{
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try (Arena arena = Arena.ofConfined()) {
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H5Ex_D_Chunk.writeChunk(arena);
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H5Ex_D_Chunk.readChunk(arena);
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}
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}
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}
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