/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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 *
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* help@hdfgroup.org. *
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/************************************************************
This example shows how to read and write data to a dataset
using the shuffle filter with gzip compression. The
program first checks if the shuffle and gzip filters are
available, then if they are it writes integers to a
dataset using shuffle+gzip, then closes the file. Next,
it reopens the file, reads back the data, and outputs the
types of filters and the maximum value in the dataset to
the screen.
************************************************************/
package examples.datasets;
import java.util.EnumSet;
import java.util.HashMap;
import java.util.Map;
import hdf.hdf5lib.H5;
import hdf.hdf5lib.HDF5Constants;
public class H5Ex_D_Shuffle {
private static String FILENAME = "H5Ex_D_Shuffle.h5";
private static String DATASETNAME = "DS1";
private static final int DIM_X = 32;
private static final int DIM_Y = 64;
private static final int CHUNK_X = 4;
private static final int CHUNK_Y = 8;
private static final int RANK = 2;
private static final int NDIMS = 2;
// Values for the status of space allocation
enum H5Z_filter {
H5Z_FILTER_ERROR(HDF5Constants.H5Z_FILTER_ERROR),
H5Z_FILTER_NONE(HDF5Constants.H5Z_FILTER_NONE),
H5Z_FILTER_DEFLATE(HDF5Constants.H5Z_FILTER_DEFLATE),
H5Z_FILTER_SHUFFLE(HDF5Constants.H5Z_FILTER_SHUFFLE),
H5Z_FILTER_FLETCHER32(HDF5Constants.H5Z_FILTER_FLETCHER32),
H5Z_FILTER_SZIP(HDF5Constants.H5Z_FILTER_SZIP),
H5Z_FILTER_NBIT(HDF5Constants.H5Z_FILTER_NBIT),
H5Z_FILTER_SCALEOFFSET(HDF5Constants.H5Z_FILTER_SCALEOFFSET),
H5Z_FILTER_RESERVED(HDF5Constants.H5Z_FILTER_RESERVED),
H5Z_FILTER_MAX(HDF5Constants.H5Z_FILTER_MAX);
private static final Map<Integer, H5Z_filter> lookup = new HashMap<Integer, H5Z_filter>();
static
{
for (H5Z_filter s : EnumSet.allOf(H5Z_filter.class))
lookup.put(s.getCode(), s);
}
private int code;
H5Z_filter(int layout_type) { this.code = layout_type; }
public int getCode() { return this.code; }
public static H5Z_filter get(int code) { return lookup.get(code); }
}
private static boolean checkGzipFilter()
{
try {
int available = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_DEFLATE);
if (available == 0) {
System.out.println("gzip filter not available.");
return false;
}
}
catch (Exception e) {
e.printStackTrace();
}
try {
int filter_info = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_DEFLATE);
if (((filter_info & HDF5Constants.H5Z_FILTER_CONFIG_ENCODE_ENABLED) == 0) ||
((filter_info & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) == 0)) {
System.out.println("gzip filter not available for encoding and decoding.");
return false;
}
}
catch (Exception e) {
e.printStackTrace();
}
return true;
}
private static boolean checkShuffleFilter()
{
try {
int available = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_SHUFFLE);
if (available == 0) {
System.out.println("Shuffle filter not available.");
return false;
}
}
catch (Exception e) {
e.printStackTrace();
}
try {
int filter_info = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_SHUFFLE);
if (((filter_info & HDF5Constants.H5Z_FILTER_CONFIG_ENCODE_ENABLED) == 0) ||
((filter_info & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) == 0)) {
System.out.println("Shuffle filter not available for encoding and decoding.");
return false;
}
}
catch (Exception e) {
e.printStackTrace();
}
return true;
}
private static void writeShuffle()
{
long file_id = HDF5Constants.H5I_INVALID_HID;
long filespace_id = HDF5Constants.H5I_INVALID_HID;
long dataset_id = HDF5Constants.H5I_INVALID_HID;
long dcpl_id = HDF5Constants.H5I_INVALID_HID;
long[] dims = {DIM_X, DIM_Y};
long[] chunk_dims = {CHUNK_X, CHUNK_Y};
int[][] dset_data = new int[DIM_X][DIM_Y];
// Initialize data.
for (int indx = 0; indx < DIM_X; indx++)
for (int jndx = 0; jndx < DIM_Y; jndx++)
dset_data[indx][jndx] = indx * jndx - jndx;
// 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 dataspace. Setting maximum size to NULL sets the maximum
// size to be the current size.
try {
filespace_id = H5.H5Screate_simple(RANK, dims, null);
}
catch (Exception e) {
e.printStackTrace();
}
// Create the dataset creation property list, add the shuffle
// filter and the gzip compression filter.
// The order in which the filters are added here is significant -
// we will see much greater results when the shuffle is applied
// first. The order in which the filters are added to the property
// list is the order in which they will be invoked when writing
// data.
try {
dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE);
if (dcpl_id >= 0) {
H5.H5Pset_shuffle(dcpl_id);
H5.H5Pset_deflate(dcpl_id, 9);
// Set the chunk size.
H5.H5Pset_chunk(dcpl_id, NDIMS, chunk_dims);
}
}
catch (Exception e) {
e.printStackTrace();
}
// Create the dataset.
try {
if ((file_id >= 0) && (filespace_id >= 0) && (dcpl_id >= 0))
dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_I32LE, filespace_id,
HDF5Constants.H5P_DEFAULT, dcpl_id, HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
// Write the data to the dataset.
try {
if (dataset_id >= 0)
H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL,
HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data);
}
catch (Exception e) {
e.printStackTrace();
}
// End access to the dataset and release resources used by it.
try {
if (dcpl_id >= 0)
H5.H5Pclose(dcpl_id);
}
catch (Exception e) {
e.printStackTrace();
}
try {
if (dataset_id >= 0)
H5.H5Dclose(dataset_id);
}
catch (Exception e) {
e.printStackTrace();
}
try {
if (filespace_id >= 0)
H5.H5Sclose(filespace_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 readShuffle()
{
long file_id = HDF5Constants.H5I_INVALID_HID;
long dataset_id = HDF5Constants.H5I_INVALID_HID;
long dcpl_id = HDF5Constants.H5I_INVALID_HID;
int[][] dset_data = new int[DIM_X][DIM_Y];
// 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();
}
// Retrieve the dataset creation property list.
try {
if (dataset_id >= 0)
dcpl_id = H5.H5Dget_create_plist(dataset_id);
}
catch (Exception e) {
e.printStackTrace();
}
// Retrieve the number of filters, and retrieve and print the
// type of each.
try {
if (dcpl_id >= 0) {
int nfilters = H5.H5Pget_nfilters(dcpl_id);
for (int indx = 0; indx < nfilters; indx++) {
// Java lib requires a valid filter_name object and cd_values
int[] flags = {0};
long[] cd_nelmts = {1};
int[] cd_values = {0};
String[] filter_name = {""};
int[] filter_config = {0};
int filter_type = -1;
filter_type = H5.H5Pget_filter(dcpl_id, indx, flags, cd_nelmts, cd_values, 120,
filter_name, filter_config);
System.out.print("Filter " + indx + ": Type is: ");
switch (H5Z_filter.get(filter_type)) {
case H5Z_FILTER_DEFLATE:
System.out.println("H5Z_FILTER_DEFLATE");
break;
case H5Z_FILTER_SHUFFLE:
System.out.println("H5Z_FILTER_SHUFFLE");
break;
case H5Z_FILTER_FLETCHER32:
System.out.println("H5Z_FILTER_FLETCHER32");
break;
case H5Z_FILTER_SZIP:
System.out.println("H5Z_FILTER_SZIP");
break;
case H5Z_FILTER_NBIT:
System.out.println("H5Z_FILTER_NBIT");
break;
case H5Z_FILTER_SCALEOFFSET:
System.out.println("H5Z_FILTER_SCALEOFFSET");
break;
default:
System.out.println("H5Z_FILTER_ERROR");
}
System.out.println();
}
}
}
catch (Exception e) {
e.printStackTrace();
}
// Read the data using the default properties.
try {
if (dataset_id >= 0) {
H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL,
HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data);
}
}
catch (Exception e) {
e.printStackTrace();
}
// Find the maximum value in the dataset, to verify that it was read
// correctly.
int max = dset_data[0][0];
for (int indx = 0; indx < DIM_X; indx++) {
for (int jndx = 0; jndx < DIM_Y; jndx++)
if (max < dset_data[indx][jndx])
max = dset_data[indx][jndx];
}
// Print the maximum value.
System.out.println("Maximum value in " + DATASETNAME + " is: " + max);
// End access to the dataset and release resources used by it.
try {
if (dcpl_id >= 0)
H5.H5Pclose(dcpl_id);
}
catch (Exception e) {
e.printStackTrace();
}
try {
if (dataset_id >= 0)
H5.H5Dclose(dataset_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)
{
// Check if gzip compression is available and can be used for both
// compression and decompression. Normally we do not perform error
// checking in these examples for the sake of clarity, but in this
// case we will make an exception because this filter is an
// optional part of the hdf5 library.
// Similarly, check for availability of the shuffle filter.
if (H5Ex_D_Shuffle.checkGzipFilter() && H5Ex_D_Shuffle.checkShuffleFilter()) {
H5Ex_D_Shuffle.writeShuffle();
H5Ex_D_Shuffle.readShuffle();
}
}
}