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Diffstat (limited to 'HDF5Examples/JAVA/H5D/H5Ex_D_Checksum.java')
| -rw-r--r-- | HDF5Examples/JAVA/H5D/H5Ex_D_Checksum.java | 349 |
1 files changed, 349 insertions, 0 deletions
diff --git a/HDF5Examples/JAVA/H5D/H5Ex_D_Checksum.java b/HDF5Examples/JAVA/H5D/H5Ex_D_Checksum.java new file mode 100644 index 0000000..f4716ad --- /dev/null +++ b/HDF5Examples/JAVA/H5D/H5Ex_D_Checksum.java @@ -0,0 +1,349 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * 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 data to a dataset + using the Fletcher32 checksum filter. The program first + checks if the Fletcher32 filter is available, then if it + is it writes integers to a dataset using Fletcher32, then + closes the file. Next, it reopens the file, reads back + the data, checks if the filter detected an error and + outputs the type of filter and the maximum value in the + dataset to the screen. + ************************************************************/ + +import java.util.EnumSet; +import java.util.HashMap; +import java.util.Map; + +import hdf.hdf5lib.H5; +import hdf.hdf5lib.HDF5Constants; + +public class H5Ex_D_Checksum { + private static String FILENAME = "H5Ex_D_Checksum.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(-1), + H5Z_FILTER_NONE(0), + H5Z_FILTER_DEFLATE(1), + H5Z_FILTER_SHUFFLE(2), + H5Z_FILTER_FLETCHER32(3), + H5Z_FILTER_SZIP(4), + H5Z_FILTER_NBIT(5), + H5Z_FILTER_SCALEOFFSET(6), + H5Z_FILTER_RESERVED(256), + H5Z_FILTER_MAX(65535); + 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 checkFletcher32Filter() + { + try { + int available = H5.H5Zfilter_avail(H5Z_filter.H5Z_FILTER_FLETCHER32.getCode()); + if (available == 0) { + System.out.println("N-Bit filter not available."); + return false; + } + } + catch (Exception e) { + e.printStackTrace(); + } + + try { + int filter_info = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_FLETCHER32); + if (((filter_info & HDF5Constants.H5Z_FILTER_CONFIG_ENCODE_ENABLED) == 0) || + ((filter_info & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) == 0)) { + System.out.println("N-Bit filter not available for encoding and decoding."); + return false; + } + } + catch (Exception e) { + e.printStackTrace(); + } + return true; + } + + private static void writeChecksum() + { + 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 N-Bit filter. + try { + dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE); + if (dcpl_id >= 0) { + H5.H5Pset_fletcher32(dcpl_id); + // 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 readChecksum() + { + 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 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(); + } + + // Read the data using the default properties. + try { + if (dataset_id >= 0) { + int status = H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, + HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); + // Check if the read was successful. 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 is how the + // fletcher32 checksum filter reports data errors. + if (status < 0) { + System.out.print("Dataset read failed!"); + try { + if (dcpl_id >= 0) + H5.H5Pclose(dcpl_id); + if (dataset_id >= 0) + H5.H5Dclose(dataset_id); + if (file_id >= 0) + H5.H5Fclose(file_id); + } + catch (Exception e) { + e.printStackTrace(); + } + return; + } + } + } + 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 the Fletcher32 filter is available and can be used for + // both encoding and decoding. 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. + // size to be the current size. + if (H5Ex_D_Checksum.checkFletcher32Filter()) { + H5Ex_D_Checksum.writeChecksum(); + H5Ex_D_Checksum.readChecksum(); + } + } +} |