/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 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 LICENSE 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 Scale-Offset filter. The program first checks if the Scale-Offset filter is available, then if it is it writes integers to a dataset using Scale-Offset, then closes the file Next, it reopens the file, reads back the data, and outputs the type of filter and the maximum value in the dataset to the screen. ************************************************************/ import static org.hdfgroup.javahdf5.hdf5_h.*; import java.lang.foreign.Arena; import java.lang.foreign.MemorySegment; import java.lang.foreign.ValueLayout; import java.util.EnumSet; import java.util.HashMap; import java.util.Map; public class H5Ex_D_Soint { private static String FILENAME = "H5Ex_D_Soint.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(H5Z_FILTER_ERROR()), H5Z_FILTER_NONE(H5Z_FILTER_NONE()), H5Z_FILTER_DEFLATE(H5Z_FILTER_DEFLATE()), H5Z_FILTER_SHUFFLE(H5Z_FILTER_SHUFFLE()), H5Z_FILTER_FLETCHER32(H5Z_FILTER_FLETCHER32()), H5Z_FILTER_SZIP(H5Z_FILTER_SZIP()), H5Z_FILTER_NBIT(H5Z_FILTER_NBIT()), H5Z_FILTER_SCALEOFFSET(H5Z_FILTER_SCALEOFFSET()), H5Z_FILTER_RESERVED(H5Z_FILTER_RESERVED()), H5Z_FILTER_MAX(H5Z_FILTER_MAX()); private static final Map lookup = new HashMap(); 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 checkScaleoffsetFilter() { try { int available = H5Zfilter_avail(H5Z_FILTER_SCALEOFFSET()); if (available == 0) { System.out.println("Scale-Offset filter not available."); return false; } } catch (Exception e) { e.printStackTrace(); } try { try (Arena arena = Arena.ofConfined()) { MemorySegment filterInfoSeg = arena.allocate(ValueLayout.JAVA_INT); H5Zget_filter_info(H5Z_FILTER_SCALEOFFSET(), filterInfoSeg); int filter_info = filterInfoSeg.get(ValueLayout.JAVA_INT, 0); if (((filter_info & H5Z_FILTER_CONFIG_ENCODE_ENABLED()) == 0) || ((filter_info & H5Z_FILTER_CONFIG_DECODE_ENABLED()) == 0)) { System.out.println("Scale-Offset filter not available for encoding and decoding."); return false; } } } catch (Exception e) { e.printStackTrace(); } return true; } private static void writeData(Arena arena) { long file_id = H5I_INVALID_HID(); long filespace_id = H5I_INVALID_HID(); long dataset_id = H5I_INVALID_HID(); long dcpl_id = 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 the default properties. try { file_id = H5Fcreate(arena.allocateFrom(FILENAME), H5F_ACC_TRUNC(), H5P_DEFAULT(), 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 = H5Screate_simple(RANK, arena.allocateFrom(ValueLayout.JAVA_LONG, dims), MemorySegment.NULL); } catch (Exception e) { e.printStackTrace(); } // Create the dataset creation property list, add the Scale-Offset // filter and set the chunk size. try { dcpl_id = H5Pcreate(H5P_CLS_DATASET_CREATE_ID_g()); if (dcpl_id >= 0) { H5Pset_scaleoffset(dcpl_id, H5Z_SO_INT(), H5Z_SO_INT_MINBITS_DEFAULT()); H5Pset_chunk(dcpl_id, NDIMS, arena.allocateFrom(ValueLayout.JAVA_LONG, chunk_dims)); } } catch (Exception e) { e.printStackTrace(); } // Create the dataset. try { if ((file_id >= 0) && (filespace_id >= 0) && (dcpl_id >= 0)) dataset_id = H5Dcreate2(file_id, arena.allocateFrom(DATASETNAME), H5T_STD_I32LE_g(), filespace_id, H5P_DEFAULT(), dcpl_id, H5P_DEFAULT()); } catch (Exception e) { e.printStackTrace(); } // Write the data to the dataset. try { if (dataset_id >= 0) { // Flatten 2D array for FFM int[] flatData = new int[DIM_X * DIM_Y]; for (int i = 0; i < DIM_X; i++) { for (int j = 0; j < DIM_Y; j++) { flatData[i * DIM_Y + j] = dset_data[i][j]; } } MemorySegment dataSeg = arena.allocate(ValueLayout.JAVA_INT, flatData.length); for (int i = 0; i < flatData.length; i++) { dataSeg.setAtIndex(ValueLayout.JAVA_INT, i, flatData[i]); } H5Dwrite(dataset_id, H5T_NATIVE_INT_g(), H5S_ALL(), H5S_ALL(), H5P_DEFAULT(), dataSeg); } } catch (Exception e) { e.printStackTrace(); } // Close and release resources. try { if (dcpl_id >= 0) H5Pclose(dcpl_id); } catch (Exception e) { e.printStackTrace(); } try { if (dataset_id >= 0) H5Dclose(dataset_id); } catch (Exception e) { e.printStackTrace(); } try { if (filespace_id >= 0) H5Sclose(filespace_id); } catch (Exception e) { e.printStackTrace(); } // Close file try { if (file_id >= 0) H5Fclose(file_id); } catch (Exception e) { e.printStackTrace(); } } private static void readData(Arena arena) { long file_id = H5I_INVALID_HID(); long dataset_id = H5I_INVALID_HID(); long dcpl_id = H5I_INVALID_HID(); int[][] dset_data = new int[DIM_X][DIM_Y]; // Open file using the default properties. try { file_id = H5Fopen(arena.allocateFrom(FILENAME), H5F_ACC_RDONLY(), H5P_DEFAULT()); } catch (Exception e) { e.printStackTrace(); } // Open dataset using the default properties. try { if (file_id >= 0) dataset_id = H5Dopen2(file_id, arena.allocateFrom(DATASETNAME), H5P_DEFAULT()); } catch (Exception e) { e.printStackTrace(); } // Retrieve dataset creation property list. try { if (dataset_id >= 0) dcpl_id = 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) { // FFM requires MemorySegment parameters MemorySegment flagsSeg = arena.allocate(ValueLayout.JAVA_INT); MemorySegment cdNeltsSeg = arena.allocate(ValueLayout.JAVA_LONG); cdNeltsSeg.set(ValueLayout.JAVA_LONG, 0, 10L); MemorySegment cdValuesSeg = arena.allocate(ValueLayout.JAVA_INT, 10); MemorySegment nameSegment = arena.allocate(256); MemorySegment filterConfigSeg = arena.allocate(ValueLayout.JAVA_INT); int filter_type = H5Pget_filter2(dcpl_id, 0, flagsSeg, cdNeltsSeg, cdValuesSeg, 256, nameSegment, filterConfigSeg); 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; case H5Z_FILTER_NBIT: System.out.println("H5Z_FILTER_NBIT"); break; case H5Z_FILTER_SCALEOFFSET: System.out.println("H5Z_FILTER_SCALEOFFSET"); 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) { MemorySegment dataSeg = arena.allocate(ValueLayout.JAVA_INT, DIM_X * DIM_Y); H5Dread(dataset_id, H5T_NATIVE_INT_g(), H5S_ALL(), H5S_ALL(), H5P_DEFAULT(), dataSeg); // Unflatten to 2D array for (int i = 0; i < DIM_X; i++) { for (int j = 0; j < DIM_Y; j++) { dset_data[i][j] = dataSeg.getAtIndex(ValueLayout.JAVA_INT, i * DIM_Y + j); } } } } 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) H5Pclose(dcpl_id); } catch (Exception e) { e.printStackTrace(); } try { if (dataset_id >= 0) H5Dclose(dataset_id); } catch (Exception e) { e.printStackTrace(); } // Close the file. try { if (file_id >= 0) H5Fclose(file_id); } catch (Exception e) { e.printStackTrace(); } } public static void main(String[] args) { try (Arena arena = Arena.ofConfined()) { if (H5Ex_D_Soint.checkScaleoffsetFilter()) { H5Ex_D_Soint.writeData(arena); H5Ex_D_Soint.readData(arena); } } } }