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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the COPYING file, which can be found at the root of the source code *
* distribution tree, or in https://www.hdfgroup.org/licenses. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/************************************************************
This example shows how to read and write compound
datatypes to an attribute. The program first writes
compound structures to an attribute with a dataspace of
DIM0, then closes the file. Next, it reopens the file,
reads back the data, and outputs it to the screen.
************************************************************/
package examples.datatypes;
import hdf.hdf5lib.H5;
import hdf.hdf5lib.HDF5Constants;
import java.nio.ByteBuffer;
import java.nio.ByteOrder;
import java.nio.charset.Charset;
public class H5Ex_T_CompoundAttribute {
private static String FILENAME = "H5Ex_T_CompoundAttribute.h5";
private static String DATASETNAME = "DS1";
private static String ATTRIBUTENAME = "A1";
private static final int DIM0 = 4;
private static final int RANK = 1;
protected static final int INTEGERSIZE = 4;
protected static final int DOUBLESIZE = 8;
protected final static int MAXSTRINGSIZE = 80;
// Using Java Externalization will add a two-byte object header in
// the stream, which needs to be called out in the datatypes.
static class Sensor_Datatype {
static int numberMembers = 4;
static int[] memberDims = { 1, 1, 1, 1 };
static String[] memberNames = { "Serial number", "Location", "Temperature (F)", "Pressure (inHg)" };
static long[] memberMemTypes = { HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5T_C_S1,
HDF5Constants.H5T_NATIVE_DOUBLE, HDF5Constants.H5T_NATIVE_DOUBLE };
static long[] memberFileTypes = { HDF5Constants.H5T_STD_I32BE, HDF5Constants.H5T_C_S1,
HDF5Constants.H5T_IEEE_F64BE, HDF5Constants.H5T_IEEE_F64BE };
static int[] memberStorage = { INTEGERSIZE, MAXSTRINGSIZE, DOUBLESIZE, DOUBLESIZE };
// Data size is the storage size for the members not the object.
static long getTotalDataSize() {
long data_size = 0;
for (int indx = 0; indx < numberMembers; indx++)
data_size += memberStorage[indx] * memberDims[indx];
return DIM0 * data_size;
}
static long getDataSize() {
long data_size = 0;
for (int indx = 0; indx < numberMembers; indx++)
data_size += memberStorage[indx] * memberDims[indx];
return data_size;
}
static int getOffset(int memberItem) {
int data_offset = 0;
for (int indx = 0; indx < memberItem; indx++)
data_offset += memberStorage[indx];
return data_offset;
}
}
static class Sensor {
public int serial_no;
public String location;
public double temperature;
public double pressure;
Sensor(int serial_no, String location, double temperature, double pressure) {
this.serial_no = serial_no;
this.location = location;
this.temperature = temperature;
this.pressure = pressure;
}
Sensor(ByteBuffer databuf, int dbposition) {
readBuffer(databuf, dbposition);
}
void writeBuffer(ByteBuffer databuf, int dbposition) {
databuf.putInt(dbposition + Sensor_Datatype.getOffset(0), serial_no);
byte[] temp_str = location.getBytes(Charset.forName("UTF-8"));
int arraylen = (temp_str.length > MAXSTRINGSIZE) ? MAXSTRINGSIZE : temp_str.length;
for (int ndx = 0; ndx < arraylen; ndx++)
databuf.put(dbposition + Sensor_Datatype.getOffset(1) + ndx, temp_str[ndx]);
for (int ndx = arraylen; ndx < MAXSTRINGSIZE; ndx++)
databuf.put(dbposition + Sensor_Datatype.getOffset(1) + arraylen, (byte) 0);
databuf.putDouble(dbposition + Sensor_Datatype.getOffset(2), temperature);
databuf.putDouble(dbposition + Sensor_Datatype.getOffset(3), pressure);
}
void readBuffer(ByteBuffer databuf, int dbposition) {
this.serial_no = databuf.getInt(dbposition + Sensor_Datatype.getOffset(0));
ByteBuffer stringbuf = databuf.duplicate();
stringbuf.position(dbposition + Sensor_Datatype.getOffset(1));
stringbuf.limit(dbposition + Sensor_Datatype.getOffset(1) + MAXSTRINGSIZE);
byte[] bytearr = new byte[stringbuf.remaining()];
stringbuf.get(bytearr);
this.location = new String(bytearr, Charset.forName("UTF-8")).trim();
this.temperature = databuf.getDouble(dbposition + Sensor_Datatype.getOffset(2));
this.pressure = databuf.getDouble(dbposition + Sensor_Datatype.getOffset(3));
}
@Override
public String toString() {
return String.format("Serial number : " + serial_no + "%n" +
"Location : " + location + "%n" +
"Temperature (F) : " + temperature + "%n" +
"Pressure (inHg) : " + pressure + "%n");
}
}
private static void CreateDataset() {
long file_id = -1;
long strtype_id = -1;
long memtype_id = -1;
long filetype_id = -1;
long dataspace_id = -1;
long dataset_id = -1;
long attribute_id = -1;
long[] dims = { DIM0 };
Sensor[] object_data = new Sensor[DIM0];
byte[] dset_data = null;
// Initialize data.
object_data[0] = new Sensor(1153, new String("Exterior (static)"), 53.23, 24.57);
object_data[1] = new Sensor(1184, new String("Intake"), 55.12, 22.95);
object_data[2] = new Sensor(1027, new String("Intake manifold"), 103.55, 31.23);
object_data[3] = new Sensor(1313, new String("Exhaust manifold"), 1252.89, 84.11);
// Create a new file using default properties.
try {
file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
// Create string datatype.
try {
strtype_id = H5.H5Tcopy(HDF5Constants.H5T_C_S1);
if (strtype_id >= 0)
H5.H5Tset_size(strtype_id, MAXSTRINGSIZE);
}
catch (Exception e) {
e.printStackTrace();
}
// Create the compound datatype for memory.
try {
memtype_id = H5.H5Tcreate(HDF5Constants.H5T_COMPOUND, Sensor_Datatype.getDataSize());
if (memtype_id >= 0) {
for (int indx = 0; indx < Sensor_Datatype.numberMembers; indx++) {
long type_id = Sensor_Datatype.memberMemTypes[indx];
if (type_id == HDF5Constants.H5T_C_S1)
type_id = strtype_id;
H5.H5Tinsert(memtype_id, Sensor_Datatype.memberNames[indx], Sensor_Datatype.getOffset(indx),
type_id);
}
}
}
catch (Exception e) {
e.printStackTrace();
}
// Create the compound datatype for the file. Because the standard
// types we are using for the file may have different sizes than
// the corresponding native types, we must manually calculate the
// offset of each member.
try {
filetype_id = H5.H5Tcreate(HDF5Constants.H5T_COMPOUND, Sensor_Datatype.getDataSize());
if (filetype_id >= 0) {
for (int indx = 0; indx < Sensor_Datatype.numberMembers; indx++) {
long type_id = Sensor_Datatype.memberFileTypes[indx];
if (type_id == HDF5Constants.H5T_C_S1)
type_id = strtype_id;
H5.H5Tinsert(filetype_id, Sensor_Datatype.memberNames[indx], Sensor_Datatype.getOffset(indx),
type_id);
}
}
}
catch (Exception e) {
e.printStackTrace();
}
// Create dataset with a scalar dataspace.
try {
dataspace_id = H5.H5Screate(HDF5Constants.H5S_SCALAR);
if (dataspace_id >= 0) {
dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_I32LE, dataspace_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
H5.H5Sclose(dataspace_id);
dataspace_id = -1;
}
}
catch (Exception e) {
e.printStackTrace();
}
// Create dataspace. Setting maximum size to NULL sets the maximum
// size to be the current size.
try {
dataspace_id = H5.H5Screate_simple(RANK, dims, null);
}
catch (Exception e) {
e.printStackTrace();
}
// Create the attribute.
try {
if ((dataset_id >= 0) && (dataspace_id >= 0) && (filetype_id >= 0))
attribute_id = H5.H5Acreate(dataset_id, ATTRIBUTENAME, filetype_id, dataspace_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
// Write the compound data.
dset_data = new byte[(int) dims[0] * (int)Sensor_Datatype.getDataSize()];
ByteBuffer outBuf = ByteBuffer.wrap(dset_data);
outBuf.order(ByteOrder.nativeOrder());
for (int indx = 0; indx < (int) dims[0]; indx++) {
object_data[indx].writeBuffer(outBuf, indx * (int)Sensor_Datatype.getDataSize());
}
try {
if ((attribute_id >= 0) && (memtype_id >= 0))
H5.H5Awrite(attribute_id, memtype_id, dset_data);
}
catch (Exception e) {
e.printStackTrace();
}
// End access to the dataset and release resources used by it.
try {
if (attribute_id >= 0)
H5.H5Aclose(attribute_id);
}
catch (Exception e) {
e.printStackTrace();
}
try {
if (dataset_id >= 0)
H5.H5Dclose(dataset_id);
}
catch (Exception e) {
e.printStackTrace();
}
// Terminate access to the data space.
try {
if (dataspace_id >= 0)
H5.H5Sclose(dataspace_id);
}
catch (Exception e) {
e.printStackTrace();
}
// Terminate access to the file type.
try {
if (filetype_id >= 0)
H5.H5Tclose(filetype_id);
}
catch (Exception e) {
e.printStackTrace();
}
// Terminate access to the mem type.
try {
if (memtype_id >= 0)
H5.H5Tclose(memtype_id);
}
catch (Exception e) {
e.printStackTrace();
}
try {
if (strtype_id >= 0)
H5.H5Tclose(strtype_id);
}
catch (Exception e) {
e.printStackTrace();
}
// Close the file.
try {
if (file_id >= 0)
H5.H5Fclose(file_id);
}
catch (Exception e) {
e.printStackTrace();
}
}
private static void ReadDataset() {
long file_id = -1;
long strtype_id = -1;
long memtype_id = -1;
long dataspace_id = -1;
long dataset_id = -1;
long attribute_id = -1;
long[] dims = { DIM0 };
Sensor[] object_data2;
byte[] dset_data;
// Open an existing file.
try {
file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
// Open an existing dataset.
try {
if (file_id >= 0)
dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
try {
if (dataset_id >= 0)
attribute_id = H5.H5Aopen_by_name(dataset_id, ".", ATTRIBUTENAME, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
// Get dataspace and allocate memory for read buffer. This is a
// three dimensional dataset when the array datatype is included so
// the dynamic allocation must be done in steps.
try {
if (attribute_id >= 0)
dataspace_id = H5.H5Aget_space(attribute_id);
}
catch (Exception e) {
e.printStackTrace();
}
try {
if (dataspace_id >= 0)
H5.H5Sget_simple_extent_dims(dataspace_id, dims, null);
}
catch (Exception e) {
e.printStackTrace();
}
// Create string datatype.
try {
strtype_id = H5.H5Tcopy(HDF5Constants.H5T_C_S1);
if (strtype_id >= 0)
H5.H5Tset_size(strtype_id, MAXSTRINGSIZE);
}
catch (Exception e) {
e.printStackTrace();
}
// Create the compound datatype for memory.
try {
memtype_id = H5.H5Tcreate(HDF5Constants.H5T_COMPOUND, Sensor_Datatype.getDataSize());
if (memtype_id >= 0) {
for (int indx = 0; indx < Sensor_Datatype.numberMembers; indx++) {
long type_id = Sensor_Datatype.memberMemTypes[indx];
if (type_id == HDF5Constants.H5T_C_S1)
type_id = strtype_id;
H5.H5Tinsert(memtype_id, Sensor_Datatype.memberNames[indx], Sensor_Datatype.getOffset(indx),
type_id);
}
}
}
catch (Exception e) {
e.printStackTrace();
}
// allocate memory for read buffer.
dset_data = new byte[(int) dims[0] * (int)Sensor_Datatype.getDataSize()];
object_data2 = new Sensor[(int) dims[0]];
// Read data.
try {
if ((attribute_id >= 0) && (memtype_id >= 0))
H5.H5Aread(attribute_id, memtype_id, dset_data);
ByteBuffer inBuf = ByteBuffer.wrap(dset_data);
inBuf.order(ByteOrder.nativeOrder());
for (int indx = 0; indx < (int) dims[0]; indx++) {
object_data2[indx] = new Sensor(inBuf, indx * (int)Sensor_Datatype.getDataSize());
}
}
catch (Exception e) {
e.printStackTrace();
}
// Output the data to the screen.
for (int indx = 0; indx < dims[0]; indx++) {
System.out.println(ATTRIBUTENAME + " [" + indx + "]:");
System.out.println(object_data2[indx].toString());
}
System.out.println();
try {
if (attribute_id >= 0)
H5.H5Aclose(attribute_id);
}
catch (Exception e) {
e.printStackTrace();
}
try {
if (dataset_id >= 0)
H5.H5Dclose(dataset_id);
}
catch (Exception e) {
e.printStackTrace();
}
// Terminate access to the data space.
try {
if (dataspace_id >= 0)
H5.H5Sclose(dataspace_id);
}
catch (Exception e) {
e.printStackTrace();
}
// Terminate access to the mem type.
try {
if (memtype_id >= 0)
H5.H5Tclose(memtype_id);
}
catch (Exception e) {
e.printStackTrace();
}
try {
if (strtype_id >= 0)
H5.H5Tclose(strtype_id);
}
catch (Exception e) {
e.printStackTrace();
}
// Close the file.
try {
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();
}
}
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