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.
503 lines
18 KiB
Java
503 lines
18 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 compound
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datatypes to an attribute. The program first writes
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compound structures to an attribute with a dataspace of
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DIM0, then closes the file. Next, it reopens the file,
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reads back the data, and outputs it to the screen.
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************************************************************/
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import java.nio.ByteBuffer;
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import java.nio.ByteOrder;
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import java.nio.charset.Charset;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.List;
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import hdf.hdf5lib.H5;
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import hdf.hdf5lib.HDF5Constants;
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public class H5Ex_T_CompoundAttribute {
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private static String FILENAME = "H5Ex_T_CompoundAttribute.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 RANK = 1;
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protected static final int INTEGERSIZE = 4;
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protected static final int DOUBLESIZE = 8;
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protected final static int MAXSTRINGSIZE = 80;
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static class Sensor_Datatype {
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static int numberMembers = 4;
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static int[] memberDims = {1, 1, 1, 1};
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static String[] memberNames = {"Serial number", "Location", "Temperature (F)", "Pressure (inHg)"};
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static long[] memberMemTypes = {HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5T_C_S1,
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HDF5Constants.H5T_NATIVE_DOUBLE, HDF5Constants.H5T_NATIVE_DOUBLE};
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static long[] memberFileTypes = {HDF5Constants.H5T_STD_I32BE, HDF5Constants.H5T_C_S1,
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HDF5Constants.H5T_IEEE_F64BE, HDF5Constants.H5T_IEEE_F64BE};
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static int[] memberStorage = {INTEGERSIZE, MAXSTRINGSIZE, DOUBLESIZE, DOUBLESIZE};
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// Data size is the storage size for the members not the object.
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static long getTotalDataSize()
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{
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long data_size = 0;
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for (int indx = 0; indx < numberMembers; indx++)
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data_size += memberStorage[indx] * memberDims[indx];
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return DIM0 * data_size;
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}
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static long getDataSize()
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{
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long data_size = 0;
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for (int indx = 0; indx < numberMembers; indx++)
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data_size += memberStorage[indx] * memberDims[indx];
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return data_size;
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}
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static int getOffset(int memberItem)
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{
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int data_offset = 0;
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for (int indx = 0; indx < memberItem; indx++)
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data_offset += memberStorage[indx];
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return data_offset;
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}
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}
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static class Sensor {
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public int serial_no;
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public String location;
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public double temperature;
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public double pressure;
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Sensor(int serial_no, String location, double temperature, double pressure)
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{
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this.serial_no = serial_no;
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this.location = location;
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this.temperature = temperature;
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this.pressure = pressure;
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}
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Sensor(List data)
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{
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this.serial_no = (int)data.get(0);
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this.location = (String)data.get(1);
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this.temperature = (double)data.get(2);
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this.pressure = (double)data.get(3);
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}
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Sensor(ByteBuffer databuf, int dbposition) { readBuffer(databuf, dbposition); }
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void writeBuffer(ByteBuffer databuf, int dbposition)
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{
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databuf.putInt(dbposition + Sensor_Datatype.getOffset(0), serial_no);
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byte[] temp_str = location.getBytes(Charset.forName("UTF-8"));
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int arraylen = (temp_str.length > MAXSTRINGSIZE) ? MAXSTRINGSIZE : temp_str.length;
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for (int ndx = 0; ndx < arraylen; ndx++)
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databuf.put(dbposition + Sensor_Datatype.getOffset(1) + ndx, temp_str[ndx]);
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for (int ndx = arraylen; ndx < MAXSTRINGSIZE; ndx++)
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databuf.put(dbposition + Sensor_Datatype.getOffset(1) + arraylen, (byte)0);
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databuf.putDouble(dbposition + Sensor_Datatype.getOffset(2), temperature);
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databuf.putDouble(dbposition + Sensor_Datatype.getOffset(3), pressure);
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}
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void readBuffer(ByteBuffer databuf, int dbposition)
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{
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this.serial_no = databuf.getInt(dbposition + Sensor_Datatype.getOffset(0));
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ByteBuffer stringbuf = databuf.duplicate();
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stringbuf.position(dbposition + Sensor_Datatype.getOffset(1));
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stringbuf.limit(dbposition + Sensor_Datatype.getOffset(1) + MAXSTRINGSIZE);
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byte[] bytearr = new byte[stringbuf.remaining()];
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stringbuf.get(bytearr);
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this.location = new String(bytearr, Charset.forName("UTF-8")).trim();
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this.temperature = databuf.getDouble(dbposition + Sensor_Datatype.getOffset(2));
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this.pressure = databuf.getDouble(dbposition + Sensor_Datatype.getOffset(3));
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}
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List get()
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{
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List data = new ArrayList<>();
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data.add(this.serial_no);
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data.add(this.location);
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data.add(this.temperature);
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data.add(this.pressure);
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return data;
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}
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void put(List data)
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{
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this.serial_no = (int)data.get(0);
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this.location = (String)data.get(1);
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this.temperature = (double)data.get(2);
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this.pressure = (double)data.get(3);
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}
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@Override
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public String toString()
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{
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return String.format("Serial number : " + serial_no + "%n"
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+ "Location : " + location + "%n"
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+ "Temperature (F) : " + temperature + "%n"
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+ "Pressure (inHg) : " + pressure + "%n");
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}
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}
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private static void CreateDataset()
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{
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long file_id = HDF5Constants.H5I_INVALID_HID;
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long strtype_id = HDF5Constants.H5I_INVALID_HID;
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long memtype_id = HDF5Constants.H5I_INVALID_HID;
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long filetype_id = HDF5Constants.H5I_INVALID_HID;
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long dataspace_id = HDF5Constants.H5I_INVALID_HID;
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long dataset_id = HDF5Constants.H5I_INVALID_HID;
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long attribute_id = HDF5Constants.H5I_INVALID_HID;
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long[] dims = {DIM0};
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ArrayList[] object_data = new ArrayList[DIM0];
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byte[] dset_data = null;
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// Initialize data.
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object_data[0] = (ArrayList) new Sensor(1153, new String("Exterior (static)"), 53.23, 24.57).get();
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object_data[1] = (ArrayList) new Sensor(1184, new String("Intake"), 55.12, 22.95).get();
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object_data[2] = (ArrayList) new Sensor(1027, new String("Intake manifold"), 103.55, 31.23).get();
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object_data[3] = (ArrayList) new Sensor(1313, new String("Exhaust manifold"), 1252.89, 84.11).get();
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// Create a new file using default properties.
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try {
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file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT,
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HDF5Constants.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 string datatype.
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try {
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strtype_id = H5.H5Tcopy(HDF5Constants.H5T_C_S1);
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if (strtype_id >= 0)
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H5.H5Tset_size(strtype_id, MAXSTRINGSIZE);
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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 compound datatype for memory.
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try {
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memtype_id = H5.H5Tcreate(HDF5Constants.H5T_COMPOUND, Sensor_Datatype.getDataSize());
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if (memtype_id >= 0) {
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for (int indx = 0; indx < Sensor_Datatype.numberMembers; indx++) {
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long type_id = Sensor_Datatype.memberMemTypes[indx];
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if (type_id == HDF5Constants.H5T_C_S1)
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type_id = strtype_id;
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H5.H5Tinsert(memtype_id, Sensor_Datatype.memberNames[indx],
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Sensor_Datatype.getOffset(indx), type_id);
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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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// Create the compound datatype for the file. Because the standard
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// types we are using for the file may have different sizes than
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// the corresponding native types, we must manually calculate the
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// offset of each member.
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try {
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filetype_id = H5.H5Tcreate(HDF5Constants.H5T_COMPOUND, Sensor_Datatype.getDataSize());
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if (filetype_id >= 0) {
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for (int indx = 0; indx < Sensor_Datatype.numberMembers; indx++) {
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long type_id = Sensor_Datatype.memberFileTypes[indx];
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if (type_id == HDF5Constants.H5T_C_S1)
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type_id = strtype_id;
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H5.H5Tinsert(filetype_id, Sensor_Datatype.memberNames[indx],
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Sensor_Datatype.getOffset(indx), type_id);
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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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// Create dataset with a scalar dataspace.
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try {
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dataspace_id = H5.H5Screate(HDF5Constants.H5S_SCALAR);
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if (dataspace_id >= 0) {
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dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_I32LE, dataspace_id,
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HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT,
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HDF5Constants.H5P_DEFAULT);
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H5.H5Sclose(dataspace_id);
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dataspace_id = HDF5Constants.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 = H5.H5Screate_simple(RANK, dims, 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 = H5.H5Acreate(dataset_id, ATTRIBUTENAME, filetype_id, dataspace_id,
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HDF5Constants.H5P_DEFAULT, HDF5Constants.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 compound data.
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try {
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if ((attribute_id >= 0) && (memtype_id >= 0))
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H5.H5AwriteVL(attribute_id, memtype_id, (Object[])object_data);
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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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H5.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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H5.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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H5.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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H5.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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H5.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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try {
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if (strtype_id >= 0)
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H5.H5Tclose(strtype_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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H5.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()
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{
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long file_id = HDF5Constants.H5I_INVALID_HID;
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long strtype_id = HDF5Constants.H5I_INVALID_HID;
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long memtype_id = HDF5Constants.H5I_INVALID_HID;
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long dataspace_id = HDF5Constants.H5I_INVALID_HID;
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long dataset_id = HDF5Constants.H5I_INVALID_HID;
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long attribute_id = HDF5Constants.H5I_INVALID_HID;
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long[] dims = {DIM0};
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Sensor[] object_data2 = new Sensor[(int)dims[0]];
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// Open an existing file.
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try {
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file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.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 = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.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 = H5.H5Aopen_by_name(dataset_id, ".", ATTRIBUTENAME, HDF5Constants.H5P_DEFAULT,
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HDF5Constants.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 dataspace and allocate memory for read buffer. This is a
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// three dimensional dataset when the array datatype is included so
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// the dynamic allocation must be done in steps.
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try {
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if (attribute_id >= 0)
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dataspace_id = H5.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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H5.H5Sget_simple_extent_dims(dataspace_id, dims, 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 string datatype.
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try {
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strtype_id = H5.H5Tcopy(HDF5Constants.H5T_C_S1);
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if (strtype_id >= 0)
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H5.H5Tset_size(strtype_id, MAXSTRINGSIZE);
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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 compound datatype for memory.
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try {
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memtype_id = H5.H5Tcreate(HDF5Constants.H5T_COMPOUND, Sensor_Datatype.getDataSize());
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if (memtype_id >= 0) {
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for (int indx = 0; indx < Sensor_Datatype.numberMembers; indx++) {
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long type_id = Sensor_Datatype.memberMemTypes[indx];
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if (type_id == HDF5Constants.H5T_C_S1)
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type_id = strtype_id;
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H5.H5Tinsert(memtype_id, Sensor_Datatype.memberNames[indx],
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Sensor_Datatype.getOffset(indx), type_id);
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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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ArrayList[] object_data = new ArrayList[(int)dims[0]];
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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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H5.H5AreadVL(attribute_id, memtype_id, (Object[])object_data);
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for (int indx = 0; indx < (int)dims[0]; indx++) {
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object_data2[indx] = new Sensor(object_data[indx]);
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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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System.out.println(object_data2[indx].toString());
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}
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System.out.println();
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try {
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if (attribute_id >= 0)
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H5.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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H5.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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H5.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 mem type.
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try {
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if (memtype_id >= 0)
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H5.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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try {
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if (strtype_id >= 0)
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H5.H5Tclose(strtype_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)
|
|
H5.H5Fclose(file_id);
|
|
}
|
|
catch (Exception e) {
|
|
e.printStackTrace();
|
|
}
|
|
}
|
|
|
|
public static void main(String[] args)
|
|
{
|
|
H5Ex_T_CompoundAttribute.CreateDataset();
|
|
// Now we begin the read section of this example. Here we assume
|
|
// the dataset and array have the same name and rank, but can have
|
|
// any size. Therefore we must allocate a new array to read in
|
|
// data using malloc().
|
|
H5Ex_T_CompoundAttribute.ReadDataset();
|
|
}
|
|
}
|