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Diffstat (limited to 'java/examples/datasets/H5Ex_D_UnlimitedGzip.java')
| -rw-r--r-- | java/examples/datasets/H5Ex_D_UnlimitedGzip.java | 505 |
1 files changed, 0 insertions, 505 deletions
diff --git a/java/examples/datasets/H5Ex_D_UnlimitedGzip.java b/java/examples/datasets/H5Ex_D_UnlimitedGzip.java deleted file mode 100644 index e084641..0000000 --- a/java/examples/datasets/H5Ex_D_UnlimitedGzip.java +++ /dev/null @@ -1,505 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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 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 = HDF5Constants.H5I_INVALID_HID; - long dcpl_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - 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 = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - 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 = HDF5Constants.H5I_INVALID_HID; - long dataspace_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}; - 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(); - } - } -} |