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Diffstat (limited to 'HDF5Examples/JAVA/H5D/H5Ex_D_Chunk.java')
| -rw-r--r-- | HDF5Examples/JAVA/H5D/H5Ex_D_Chunk.java | 370 |
1 files changed, 370 insertions, 0 deletions
diff --git a/HDF5Examples/JAVA/H5D/H5Ex_D_Chunk.java b/HDF5Examples/JAVA/H5D/H5Ex_D_Chunk.java new file mode 100644 index 0000000..6ca2608 --- /dev/null +++ b/HDF5Examples/JAVA/H5D/H5Ex_D_Chunk.java @@ -0,0 +1,370 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * 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 a chunked dataset. The + program first writes integers in a hyperslab selection to + a chunked dataset with dataspace dimensions of DIM_XxDIM_Y + and chunk size of CHUNK_XxCHUNK_Y, then closes the file. + Next, it reopens the file, reads back the data, and + outputs it to the screen. Finally it reads the data again + using a different hyperslab selection, and outputs + the result 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_Chunk { + private static String FILENAME = "H5Ex_D_Chunk.h5"; + private static String DATASETNAME = "DS1"; + private static final int DIM_X = 6; + private static final int DIM_Y = 8; + 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 H5D_layout { + H5D_LAYOUT_ERROR(-1), + H5D_COMPACT(0), + H5D_CONTIGUOUS(1), + H5D_CHUNKED(2), + H5D_VIRTUAL(3), + H5D_NLAYOUTS(4); + private static final Map<Integer, H5D_layout> lookup = new HashMap<Integer, H5D_layout>(); + + static + { + for (H5D_layout s : EnumSet.allOf(H5D_layout.class)) + lookup.put(s.getCode(), s); + } + + private int code; + + H5D_layout(int layout_type) { this.code = layout_type; } + + public int getCode() { return this.code; } + + public static H5D_layout get(int code) { return lookup.get(code); } + } + + private static void writeChunk() + { + 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 to "1", to make it easier to see the selections. + for (int indx = 0; indx < DIM_X; indx++) + for (int jndx = 0; jndx < DIM_Y; jndx++) + dset_data[indx][jndx] = 1; + + // Print the data to the screen. + System.out.println("Original Data:"); + 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(); + + // 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. + try { + dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE); + } + catch (Exception e) { + e.printStackTrace(); + } + + // Set the chunk size. + try { + if (dcpl_id >= 0) + H5.H5Pset_chunk(dcpl_id, NDIMS, chunk_dims); + } + catch (Exception e) { + e.printStackTrace(); + } + + // Create the chunked 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(); + } + + // Define and select the first part of the hyperslab selection. + long[] start = {0, 0}; + long[] stride = {3, 3}; + long[] count = {2, 3}; + long[] block = {2, 2}; + try { + if ((filespace_id >= 0)) + H5.H5Sselect_hyperslab(filespace_id, HDF5Constants.H5S_SELECT_SET, start, stride, count, + block); + } + catch (Exception e) { + e.printStackTrace(); + } + // Define and select the second part of the hyperslab selection, + // which is subtracted from the first selection by the use of + // H5S_SELECT_NOTB + block[0] = 1; + block[1] = 1; + try { + if ((filespace_id >= 0)) { + H5.H5Sselect_hyperslab(filespace_id, HDF5Constants.H5S_SELECT_NOTB, start, stride, count, + block); + + // Write the data to the dataset. + if (dataset_id >= 0) + H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, filespace_id, + 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 readChunk() + { + 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; + 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(); + } + + // Print the storage layout. + try { + if (dcpl_id >= 0) { + int layout_type = H5.H5Pget_layout(dcpl_id); + System.out.print("Storage layout for " + DATASETNAME + " is: "); + switch (H5D_layout.get(layout_type)) { + case H5D_COMPACT: + System.out.println("H5D_COMPACT"); + break; + case H5D_CONTIGUOUS: + System.out.println("H5D_CONTIGUOUS"); + break; + case H5D_CHUNKED: + System.out.println("H5D_CHUNKED"); + break; + case H5D_VIRTUAL: + System.out.println("H5D_VIRTUAL"); + break; + case H5D_LAYOUT_ERROR: + break; + case H5D_NLAYOUTS: + break; + default: + break; + } + 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(); + } + + // Output the data to the screen. + System.out.println("Data as written to disk by hyberslabs:"); + 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(); + + // Initialize the read array. + for (int indx = 0; indx < DIM_X; indx++) + for (int jndx = 0; jndx < DIM_Y; jndx++) + dset_data[indx][jndx] = 0; + + // Define and select the hyperslab to use for reading. + try { + if (dataset_id >= 0) { + filespace_id = H5.H5Dget_space(dataset_id); + + long[] start = {0, 1}; + long[] stride = {4, 4}; + long[] count = {2, 2}; + long[] block = {2, 3}; + + if (filespace_id >= 0) { + H5.H5Sselect_hyperslab(filespace_id, HDF5Constants.H5S_SELECT_SET, start, stride, count, + block); + + // Read the data using the previously defined hyperslab. + if ((dataset_id >= 0) && (filespace_id >= 0)) + H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, + filespace_id, HDF5Constants.H5P_DEFAULT, dset_data); + } + } + } + catch (Exception e) { + e.printStackTrace(); + } + + // Output the data to the screen. + System.out.println("Data as read from disk by hyberslab:"); + 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(); + + // 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(); + } + } + + public static void main(String[] args) + { + H5Ex_D_Chunk.writeChunk(); + H5Ex_D_Chunk.readChunk(); + } +} |