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+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group. *
+ * Copyright by the Board of Trustees of the University of Illinois. *
+ * 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 files COPYING and Copyright.html. COPYING can be found at the root *
+ * of the source code distribution tree; Copyright.html can be found at the *
+ * root level of an installed copy of the electronic HDF5 document set and *
+ * is linked from the top-level documents page. It can also be found at *
+ * http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
+ * access to either file, you may request a copy from help@hdfgroup.org. *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+/************************************************************
+ This example shows how to create and extend an unlimited
+ dataset with gzip compression. The program first writes
+ integers to a gzip compressed dataset with dataspace
+ dimensions of DIM_XxDIM_Y, then closes the file. Next, it
+ reopens the file, reads back the data, outputs it to the
+ screen, extends the dataset, and writes new data to the
+ extended portions of the dataset. Finally it reopens the
+ file again, reads back the data, and outputs it 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_UnlimitedGzip {
+ private static String FILENAME = "H5Ex_D_UnlimitedGzip.h5";
+ private static String DATASETNAME = "DS1";
+ private static final int DIM_X = 4;
+ private static final int DIM_Y = 7;
+ private static final int EDIM_X = 6;
+ private static final int EDIM_Y = 10;
+ private static final int CHUNK_X = 4;
+ private static final int CHUNK_Y = 4;
+ 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 void writeUnlimited() {
+ long file_id = -1;
+ long dcpl_id = -1;
+ long dataspace_id = -1;
+ long dataset_id = -1;
+ long[] dims = { DIM_X, DIM_Y };
+ long[] chunk_dims = { CHUNK_X, CHUNK_Y };
+ long[] maxdims = { HDF5Constants.H5S_UNLIMITED, HDF5Constants.H5S_UNLIMITED };
+ int[][] dset_data = new int[DIM_X][DIM_Y];
+
+ // Initialize the dataset.
+ 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 with unlimited dimensions.
+ try {
+ dataspace_id = H5.H5Screate_simple(RANK, dims, maxdims);
+ }
+ catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ // Create the dataset creation property list, add the gzip compression
+ // filter.
+ try {
+ dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE);
+ if (dcpl_id >= 0) {
+ 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 unlimited dataset.
+ try {
+ if ((file_id >= 0) && (dataspace_id >= 0) && (dcpl_id >= 0))
+ dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_I32LE, dataspace_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 (dataset_id >= 0)
+ H5.H5Dclose(dataset_id);
+ }
+ catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ try {
+ if (dataspace_id >= 0)
+ H5.H5Sclose(dataspace_id);
+ }
+ catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ try {
+ if (dcpl_id >= 0)
+ H5.H5Pclose(dcpl_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 extendUnlimited() {
+ long file_id = -1;
+ long dataspace_id = -1;
+ long dataset_id = -1;
+ long[] dims = { DIM_X, DIM_Y };
+ long[] extdims = { EDIM_X, EDIM_Y };
+ long[] start = { 0, 0 };
+ long[] count = new long[2];
+ int[][] dset_data;
+ int[][] extend_dset_data = new int[EDIM_X][EDIM_Y];
+
+ // Open an existing file.
+ try {
+ file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDWR, 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();
+ }
+
+ // Get dataspace and allocate memory for read buffer. This is a
+ // two dimensional dataset so the dynamic allocation must be done
+ // in steps.
+ try {
+ if (dataset_id >= 0)
+ dataspace_id = H5.H5Dget_space(dataset_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();
+ }
+
+ // Allocate array of pointers to rows.
+ dset_data = new int[(int) dims[0]][(int) dims[1]];
+
+ // 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();
+ }
+
+ // Output the data to the screen.
+ System.out.println("Dataset before extension:");
+ for (int indx = 0; indx < DIM_X; indx++) {
+ System.out.print(" [ ");
+ for (int jndx = 0; jndx < DIM_Y; jndx++)
+ System.out.print(dset_data[indx][jndx] + " ");
+ System.out.println("]");
+ }
+ System.out.println();
+
+ try {
+ if (dataspace_id >= 0)
+ H5.H5Sclose(dataspace_id);
+ }
+ catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ // Extend the dataset.
+ try {
+ if (dataset_id >= 0)
+ H5.H5Dset_extent(dataset_id, extdims);
+ }
+ catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ // Retrieve the dataspace for the newly extended dataset.
+ try {
+ if (dataset_id >= 0)
+ dataspace_id = H5.H5Dget_space(dataset_id);
+ }
+ catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ // Initialize data for writing to the extended dataset.
+ for (int indx = 0; indx < EDIM_X; indx++)
+ for (int jndx = 0; jndx < EDIM_Y; jndx++)
+ extend_dset_data[indx][jndx] = jndx;
+
+ // Select the entire dataspace.
+ try {
+ if (dataspace_id >= 0) {
+ H5.H5Sselect_all(dataspace_id);
+
+ // Subtract a hyperslab reflecting the original dimensions from the
+ // selection. The selection now contains only the newly extended
+ // portions of the dataset.
+ count[0] = dims[0];
+ count[1] = dims[1];
+ H5.H5Sselect_hyperslab(dataspace_id, HDF5Constants.H5S_SELECT_NOTB, start, null, count, null);
+
+ // Write the data to the selected portion of the dataset.
+ if (dataset_id >= 0)
+ H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, dataspace_id,
+ HDF5Constants.H5P_DEFAULT, extend_dset_data);
+ }
+ }
+ catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ // End access to the dataset and release resources used by it.
+ try {
+ if (dataset_id >= 0)
+ H5.H5Dclose(dataset_id);
+ }
+ catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ try {
+ if (dataspace_id >= 0)
+ H5.H5Sclose(dataspace_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 readUnlimited() {
+ long file_id = -1;
+ long dataspace_id = -1;
+ long dataset_id = -1;
+ long dcpl_id = -1;
+ long[] dims = { DIM_X, DIM_Y };
+ int[][] 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();
+ }
+
+ // 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 and print the filter type. Here we only retrieve the
+ // first filter because we know that we only added one filter.
+ try {
+ if (dcpl_id >= 0) {
+ // 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, 0, flags, cd_nelmts, cd_values, 120, filter_name, filter_config);
+ System.out.print("Filter 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;
+ default:
+ System.out.println("H5Z_FILTER_ERROR");
+ }
+ System.out.println();
+ }
+ }
+ catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ // Get dataspace and allocate memory for the read buffer as before.
+ try {
+ if (dataset_id >= 0)
+ dataspace_id = H5.H5Dget_space(dataset_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();
+ }
+ // Allocate array of pointers to rows.
+ dset_data = new int[(int) dims[0]][(int) dims[1]];
+
+ // 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();
+ }
+
+ // Output the data to the screen.
+ System.out.println("Dataset after extension:");
+ for (int indx = 0; indx < dims[0]; indx++) {
+ System.out.print(" [ ");
+ for (int jndx = 0; jndx < dims[1]; jndx++)
+ System.out.print(dset_data[indx][jndx] + " ");
+ System.out.println("]");
+ }
+ System.out.println();
+
+ // End access to the dataset and release resources used by it.
+ try {
+ if (dataset_id >= 0)
+ H5.H5Dclose(dataset_id);
+ }
+ catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ try {
+ if (dataspace_id >= 0)
+ H5.H5Sclose(dataspace_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.
+ if (H5Ex_D_UnlimitedGzip.checkGzipFilter()) {
+ H5Ex_D_UnlimitedGzip.writeUnlimited();
+ H5Ex_D_UnlimitedGzip.extendUnlimited();
+ H5Ex_D_UnlimitedGzip.readUnlimited();
+ }
+ }
+
+}