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336 lines
12 KiB
336 lines
12 KiB
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
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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 COPYING 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 data to a dataset
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using the Scale-Offset filter. The program first checks
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if the Scale-Offset filter is available, then if it is it
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writes integers to a dataset using Scale-Offset, then
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closes the file Next, it reopens the file, reads back the
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data, and outputs the type of filter and the maximum value
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in the dataset to the screen.
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************************************************************/
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package examples.datasets;
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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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import hdf.hdf5lib.H5;
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import hdf.hdf5lib.HDF5Constants;
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public class H5Ex_D_Soint {
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private static String FILENAME = "H5Ex_D_Soint.h5";
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private static String DATASETNAME = "DS1";
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private static final int DIM_X = 32;
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private static final int DIM_Y = 64;
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private static final int CHUNK_X = 4;
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private static final int CHUNK_Y = 8;
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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 H5Z_filter {
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H5Z_FILTER_ERROR(HDF5Constants.H5Z_FILTER_ERROR),
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H5Z_FILTER_NONE(HDF5Constants.H5Z_FILTER_NONE),
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H5Z_FILTER_DEFLATE(HDF5Constants.H5Z_FILTER_DEFLATE),
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H5Z_FILTER_SHUFFLE(HDF5Constants.H5Z_FILTER_SHUFFLE),
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H5Z_FILTER_FLETCHER32(HDF5Constants.H5Z_FILTER_FLETCHER32),
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H5Z_FILTER_SZIP(HDF5Constants.H5Z_FILTER_SZIP),
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H5Z_FILTER_NBIT(HDF5Constants.H5Z_FILTER_NBIT),
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H5Z_FILTER_SCALEOFFSET(HDF5Constants.H5Z_FILTER_SCALEOFFSET),
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H5Z_FILTER_RESERVED(HDF5Constants.H5Z_FILTER_RESERVED),
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H5Z_FILTER_MAX(HDF5Constants.H5Z_FILTER_MAX);
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private static final Map<Integer, H5Z_filter> lookup = new HashMap<Integer, H5Z_filter>();
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static
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{
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for (H5Z_filter s : EnumSet.allOf(H5Z_filter.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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H5Z_filter(int layout_type) { this.code = layout_type; }
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public int getCode() { return this.code; }
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public static H5Z_filter get(int code) { return lookup.get(code); }
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}
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private static boolean checkScaleoffsetFilter()
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{
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try {
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int available = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_SCALEOFFSET);
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if (available == 0) {
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System.out.println("Scale-Offset filter not available.");
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return false;
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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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try {
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int filter_info = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_SCALEOFFSET);
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if (((filter_info & HDF5Constants.H5Z_FILTER_CONFIG_ENCODE_ENABLED) == 0) ||
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((filter_info & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) == 0)) {
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System.out.println("Scale-Offset filter not available for encoding and decoding.");
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return false;
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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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return true;
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}
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private static void writeData()
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{
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long file_id = HDF5Constants.H5I_INVALID_HID;
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long filespace_id = HDF5Constants.H5I_INVALID_HID;
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long dataset_id = HDF5Constants.H5I_INVALID_HID;
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long dcpl_id = HDF5Constants.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.
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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] = indx * jndx - jndx;
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// Create a new file using the 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 dataspace. Setting maximum size to NULL sets the maximum size to be the current size.
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try {
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filespace_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 dataset creation property list, add the Scale-Offset
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// filter and set the chunk size.
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try {
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dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE);
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if (dcpl_id >= 0) {
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H5.H5Pset_scaleoffset(dcpl_id, HDF5Constants.H5Z_SO_INT,
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HDF5Constants.H5Z_SO_INT_MINBITS_DEFAULT);
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H5.H5Pset_chunk(dcpl_id, NDIMS, chunk_dims);
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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 dataset.
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try {
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if ((file_id >= 0) && (filespace_id >= 0) && (dcpl_id >= 0))
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dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_I32LE, filespace_id,
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HDF5Constants.H5P_DEFAULT, dcpl_id, 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 data to the dataset.
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try {
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if (dataset_id >= 0)
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H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL,
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HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_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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// Close and release resources.
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try {
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if (dcpl_id >= 0)
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H5.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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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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try {
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if (filespace_id >= 0)
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H5.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 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 readData()
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{
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long file_id = HDF5Constants.H5I_INVALID_HID;
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long dataset_id = HDF5Constants.H5I_INVALID_HID;
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long dcpl_id = HDF5Constants.H5I_INVALID_HID;
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int[][] dset_data = new int[DIM_X][DIM_Y];
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// Open file using the default properties.
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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 dataset using the default properties.
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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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// Retrieve dataset creation property list.
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try {
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if (dataset_id >= 0)
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dcpl_id = H5.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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// Retrieve and print the filter type. Here we only retrieve the
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// first filter because we know that we only added one filter.
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try {
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if (dcpl_id >= 0) {
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// Java lib requires a valid filter_name object and cd_values
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int[] flags = {0};
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long[] cd_nelmts = {1};
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int[] cd_values = {0};
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String[] filter_name = {""};
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int[] filter_config = {0};
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int filter_type = -1;
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filter_type = H5.H5Pget_filter(dcpl_id, 0, flags, cd_nelmts, cd_values, 120, filter_name,
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filter_config);
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System.out.print("Filter type is: ");
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switch (H5Z_filter.get(filter_type)) {
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case H5Z_FILTER_DEFLATE:
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System.out.println("H5Z_FILTER_DEFLATE");
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break;
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case H5Z_FILTER_SHUFFLE:
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System.out.println("H5Z_FILTER_SHUFFLE");
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break;
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case H5Z_FILTER_FLETCHER32:
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System.out.println("H5Z_FILTER_FLETCHER32");
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break;
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case H5Z_FILTER_SZIP:
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System.out.println("H5Z_FILTER_SZIP");
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break;
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case H5Z_FILTER_NBIT:
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System.out.println("H5Z_FILTER_NBIT");
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break;
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case H5Z_FILTER_SCALEOFFSET:
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System.out.println("H5Z_FILTER_SCALEOFFSET");
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break;
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default:
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System.out.println("H5Z_FILTER_ERROR");
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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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H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL,
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HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_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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// Find the maximum value in the dataset, to verify that it was read correctly.
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int max = dset_data[0][0];
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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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if (max < dset_data[indx][jndx])
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max = dset_data[indx][jndx];
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}
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// Print the maximum value.
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System.out.println("Maximum value in " + DATASETNAME + " is: " + max);
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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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H5.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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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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// 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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public static void main(String[] args)
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{
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// Check if Scale-Offset compression is available and can be used
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// for both compression and decompression. Normally we do not
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// perform error checking in these examples for the sake of
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// clarity, but in this case we will make an exception because this
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// filter is an optional part of the hdf5 library.
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if (H5Ex_D_Soint.checkScaleoffsetFilter()) {
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H5Ex_D_Soint.writeData();
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H5Ex_D_Soint.readData();
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}
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}
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}
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