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author | Allen Byrne <byrn@hdfgroup.org> | 2016-02-29 02:43:00 (GMT) |
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committer | Allen Byrne <byrn@hdfgroup.org> | 2016-02-29 02:43:00 (GMT) |
commit | 63249be0e10a8726acb5a7cf64491319eaa46227 (patch) | |
tree | ebb2b75ece8852e8a58804631c0004f06a9bba9f /java/examples/datasets | |
parent | a1617b7cdbe14173fcf690b4627059fa4528c19b (diff) | |
download | hdf5-63249be0e10a8726acb5a7cf64491319eaa46227.zip hdf5-63249be0e10a8726acb5a7cf64491319eaa46227.tar.gz hdf5-63249be0e10a8726acb5a7cf64491319eaa46227.tar.bz2 |
[svn-r29226] HDFFV-9552: merge in java code.
Diffstat (limited to 'java/examples/datasets')
21 files changed, 6415 insertions, 0 deletions
diff --git a/java/examples/datasets/CMakeLists.txt b/java/examples/datasets/CMakeLists.txt new file mode 100644 index 0000000..2338325 --- /dev/null +++ b/java/examples/datasets/CMakeLists.txt @@ -0,0 +1,121 @@ +cmake_minimum_required (VERSION 3.1.0) +PROJECT (HDFJAVA_EXAMPLES_DATASETS Java) + +set (CMAKE_VERBOSE_MAKEFILE 1) + +INCLUDE_DIRECTORIES ( + ${HDF5_JAVA_JNI_BINARY_DIR} + ${HDF5_JAVA_HDF5_LIB_DIR} +) + +set (HDF_JAVA_EXAMPLES + H5Ex_D_Alloc + H5Ex_D_Checksum + H5Ex_D_Chunk + H5Ex_D_Compact + H5Ex_D_External + H5Ex_D_FillValue + H5Ex_D_Gzip + H5Ex_D_Hyperslab + H5Ex_D_ReadWrite + H5Ex_D_Shuffle + H5Ex_D_Szip + H5Ex_D_UnlimitedAdd + H5Ex_D_UnlimitedGzip + H5Ex_D_UnlimitedMod + H5Ex_D_Nbit + H5Ex_D_Transform + H5Ex_D_Sofloat + H5Ex_D_Soint +) + +if (WIN32) + set (CMAKE_JAVA_INCLUDE_FLAG_SEP ";") +else (WIN32) + set (CMAKE_JAVA_INCLUDE_FLAG_SEP ":") +endif (WIN32) + +set (CMAKE_JAVA_INCLUDE_PATH "${HDF5_JAVA_JARS}") + +set (CMAKE_JAVA_CLASSPATH ".") +foreach (CMAKE_INCLUDE_PATH ${CMAKE_JAVA_INCLUDE_PATH}) + set (CMAKE_JAVA_CLASSPATH "${CMAKE_JAVA_CLASSPATH}${CMAKE_JAVA_INCLUDE_FLAG_SEP}${CMAKE_INCLUDE_PATH}") +endforeach (CMAKE_INCLUDE_PATH) + +foreach (example ${HDF_JAVA_EXAMPLES}) + file (WRITE ${PROJECT_BINARY_DIR}/${example}_Manifest.txt + "Main-Class: examples.datasets.${example} +" + ) + add_jar (${example} MANIFEST ${PROJECT_BINARY_DIR}/${example}_Manifest.txt ${example}.java) + get_target_property (${example}_JAR_FILE ${example} JAR_FILE) +# install_jar (${example} ${HJAVA_INSTALL_DATA_DIR}/examples examples) + get_target_property (${example}_CLASSPATH ${example} CLASSDIR) + add_dependencies (${example} ${HDF5_JAVA_HDF5_LIB_TARGET}) +endforeach (example ${HDF_JAVA_EXAMPLES}) + +set (CMAKE_JAVA_INCLUDE_PATH "${HDF5_JAVA_JARS};${HDF5_JAVA_LOGGING_JAR};${HDF5_JAVA_LOGGING_NOP_JAR}") + +set (CMAKE_JAVA_CLASSPATH ".") +foreach (HDFJAVA_JAR ${CMAKE_JAVA_INCLUDE_PATH}) + set (CMAKE_JAVA_CLASSPATH "${CMAKE_JAVA_CLASSPATH}${CMAKE_JAVA_INCLUDE_FLAG_SEP}${HDFJAVA_JAR}") +endforeach (HDFJAVA_JAR) + +MACRO (ADD_H5_TEST resultfile resultcode) + add_test ( + NAME JAVA_datasets-${resultfile} + COMMAND "${CMAKE_COMMAND}" + -D "TEST_TESTER=${CMAKE_Java_RUNTIME};${CMAKE_Java_RUNTIME_FLAGS}" + -D "TEST_CLASSPATH:STRING=${CMAKE_JAVA_CLASSPATH}${CMAKE_JAVA_INCLUDE_FLAG_SEP}${${resultfile}_JAR_FILE}" + -D "TEST_ARGS:STRING=${ARGN}" + -D "TEST_PROGRAM=examples.datasets.${resultfile}" + -D "TEST_LIBRARY_DIRECTORY=${CMAKE_TEST_OUTPUT_DIRECTORY}" + -D "TEST_FOLDER=${HDFJAVA_EXAMPLES_BINARY_DIR}" + -D "TEST_OUTPUT=datasets/${resultfile}.out" + -D "TEST_EXPECT=${resultcode}" + -D "TEST_REFERENCE=datasets/${resultfile}.txt" + -P "${HDF_RESOURCES_DIR}/jrunTest.cmake" + ) + if (NOT "${last_test}" STREQUAL "") + set_tests_properties (JAVA_datasets-${resultfile} PROPERTIES DEPENDS ${last_test}) + endif (NOT "${last_test}" STREQUAL "") + set (last_test "JAVA_datasets-${resultfile}") +ENDMACRO (ADD_H5_TEST file) + +if (BUILD_TESTING) + foreach (example ${HDF_JAVA_EXAMPLES}) + if (${example} STREQUAL "H5Ex_D_External") + add_test ( + NAME JAVA_datasets-${example}-clearall-objects + COMMAND ${CMAKE_COMMAND} + -E remove + ${HDFJAVA_EXAMPLES_BINARY_DIR}/${example}.h5 + ${HDFJAVA_EXAMPLES_BINARY_DIR}/${example}.data + ${example}.out + ${example}.out.err + ) + else (${example} STREQUAL "H5Ex_D_External") + add_test ( + NAME JAVA_datasets-${example}-clearall-objects + COMMAND ${CMAKE_COMMAND} + -E remove + ${HDFJAVA_EXAMPLES_BINARY_DIR}/${example}.h5 + ${example}.out + ${example}.out.err + ) + endif (${example} STREQUAL "H5Ex_D_External") + if (NOT "${last_test}" STREQUAL "") + set_tests_properties (JAVA_datasets-${example}-clearall-objects PROPERTIES DEPENDS ${last_test}) + endif (NOT "${last_test}" STREQUAL "") + add_test ( + NAME JAVA_datasets-${example}-copy-objects + COMMAND ${CMAKE_COMMAND} + -E copy_if_different + ${HDFJAVA_EXAMPLES_SOURCE_DIR}/testfiles/examples.datasets.${example}.txt + ${HDFJAVA_EXAMPLES_DATASETS_BINARY_DIR}/${example}.txt + ) + set_tests_properties (JAVA_datasets-${example}-copy-objects PROPERTIES DEPENDS JAVA_datasets-${example}-clearall-objects) + set (last_test "JAVA_datasets-${example}-copy-objects") + ADD_H5_TEST (${example} 0) + endforeach (example ${HDF_JAVA_EXAMPLES}) +endif (BUILD_TESTING) diff --git a/java/examples/datasets/H5Ex_D_Alloc.java b/java/examples/datasets/H5Ex_D_Alloc.java new file mode 100644 index 0000000..69fee38 --- /dev/null +++ b/java/examples/datasets/H5Ex_D_Alloc.java @@ -0,0 +1,301 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * 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 set the space allocation time + for a dataset. The program first creates two datasets, + one with the default allocation time (late) and one with + early allocation time, and displays whether each has been + allocated and their allocation size. Next, it writes data + to the datasets, and again displays whether each has been + allocated and their allocation size. + ************************************************************/ +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_Alloc { + private static String FILENAME = "H5Ex_D_Alloc.h5"; + private static String DATASETNAME1 = "DS1"; + private static String DATASETNAME2 = "DS2"; + private static final int DIM_X = 4; + private static final int DIM_Y = 7; + private static final int FILLVAL = 99; + private static final int RANK = 2; + + // Values for the status of space allocation + enum H5D_space_status { + H5D_SPACE_STATUS_ERROR(-1), H5D_SPACE_STATUS_NOT_ALLOCATED(0), H5D_SPACE_STATUS_PART_ALLOCATED(1), H5D_SPACE_STATUS_ALLOCATED( + 2); + private static final Map<Integer, H5D_space_status> lookup = new HashMap<Integer, H5D_space_status>(); + + static { + for (H5D_space_status s : EnumSet.allOf(H5D_space_status.class)) + lookup.put(s.getCode(), s); + } + + private int code; + + H5D_space_status(int space_status) { + this.code = space_status; + } + + public int getCode() { + return this.code; + } + + public static H5D_space_status get(int code) { + return lookup.get(code); + } + } + + private static void allocation() { + long file_id = -1; + long filespace_id = -1; + long dataset_id1 = -1; + long dataset_id2 = -1; + long dcpl_id = -1; + long[] dims = { DIM_X, DIM_Y }; + int[][] dset_data = new int[DIM_X][DIM_Y]; + int space_status = 0; + long storage_size = 0; + + // Initialize the dataset. + for (int indx = 0; indx < DIM_X; indx++) + for (int jndx = 0; jndx < DIM_Y; jndx++) + dset_data[indx][jndx] = FILLVAL; + + // Create a 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, and set the chunk size. + try { + dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE); + } + catch (Exception e) { + e.printStackTrace(); + } + + // Set the allocation time to "early". This way we can be sure + // that reading from the dataset immediately after creation will + // return the fill value. + try { + if (dcpl_id >= 0) + H5.H5Pset_alloc_time(dcpl_id, HDF5Constants.H5D_ALLOC_TIME_EARLY); + } + catch (Exception e) { + e.printStackTrace(); + } + + System.out.println("Creating datasets..."); + System.out.println(DATASETNAME1 + " has allocation time H5D_ALLOC_TIME_LATE"); + System.out.println(DATASETNAME2 + " has allocation time H5D_ALLOC_TIME_EARLY"); + System.out.println(); + + // Create the dataset using the dataset default creation property list. + try { + if ((file_id >= 0) && (filespace_id >= 0)) + dataset_id1 = H5.H5Dcreate(file_id, DATASETNAME1, HDF5Constants.H5T_NATIVE_INT, filespace_id, + HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); + } + catch (Exception e) { + e.printStackTrace(); + } + + // Create the dataset using the dataset creation property list. + try { + if ((file_id >= 0) && (filespace_id >= 0) && (dcpl_id >= 0)) + dataset_id2 = H5.H5Dcreate(file_id, DATASETNAME2, HDF5Constants.H5T_NATIVE_INT, filespace_id, + HDF5Constants.H5P_DEFAULT, dcpl_id, HDF5Constants.H5P_DEFAULT); + } + catch (Exception e) { + e.printStackTrace(); + } + + // Retrieve and print space status and storage size for dset1. + try { + if (dataset_id1 >= 0) + space_status = H5.H5Dget_space_status(dataset_id1); + } + catch (Exception e) { + e.printStackTrace(); + } + try { + if (dataset_id1 >= 0) + storage_size = H5.H5Dget_storage_size(dataset_id1); + } + catch (Exception e) { + e.printStackTrace(); + } + String the_space = " "; + if (H5D_space_status.get(space_status) != H5D_space_status.H5D_SPACE_STATUS_ALLOCATED) + the_space += "not "; + System.out.println("Space for " + DATASETNAME1 + " has" + the_space + "been allocated."); + System.out.println("Storage size for " + DATASETNAME1 + " is: " + storage_size + " bytes."); + + // Retrieve and print space status and storage size for dset2. + try { + if (dataset_id2 >= 0) + space_status = H5.H5Dget_space_status(dataset_id2); + } + catch (Exception e) { + e.printStackTrace(); + } + try { + if (dataset_id2 >= 0) + storage_size = H5.H5Dget_storage_size(dataset_id2); + } + catch (Exception e) { + e.printStackTrace(); + } + the_space = " "; + if (H5D_space_status.get(space_status) != H5D_space_status.H5D_SPACE_STATUS_ALLOCATED) + the_space += "not "; + System.out.println("Space for " + DATASETNAME2 + " has" + the_space + "been allocated."); + System.out.println("Storage size for " + DATASETNAME2 + " is: " + storage_size + " bytes."); + System.out.println(); + + System.out.println("Writing data..."); + System.out.println(); + + // Write the data to the datasets. + try { + if (dataset_id1 >= 0) + H5.H5Dwrite(dataset_id1, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + HDF5Constants.H5P_DEFAULT, dset_data[0]); + } + catch (Exception e) { + e.printStackTrace(); + } + try { + if (dataset_id2 >= 0) + H5.H5Dwrite(dataset_id2, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + HDF5Constants.H5P_DEFAULT, dset_data[0]); + } + catch (Exception e) { + e.printStackTrace(); + } + + // Retrieve and print space status and storage size for dset1. + try { + if (dataset_id1 >= 0) + space_status = H5.H5Dget_space_status(dataset_id1); + } + catch (Exception e) { + e.printStackTrace(); + } + try { + if (dataset_id1 >= 0) + storage_size = H5.H5Dget_storage_size(dataset_id1); + } + catch (Exception e) { + e.printStackTrace(); + } + the_space = " "; + if (H5D_space_status.get(space_status) != H5D_space_status.H5D_SPACE_STATUS_ALLOCATED) + the_space += "not "; + System.out.println("Space for " + DATASETNAME1 + " has" + the_space + "been allocated."); + System.out.println("Storage size for " + DATASETNAME1 + " is: " + storage_size + " bytes."); + + // Retrieve and print space status and storage size for dset2. + try { + if (dataset_id2 >= 0) + space_status = H5.H5Dget_space_status(dataset_id2); + } + catch (Exception e) { + e.printStackTrace(); + } + try { + if (dataset_id2 >= 0) + storage_size = H5.H5Dget_storage_size(dataset_id2); + } + catch (Exception e) { + e.printStackTrace(); + } + the_space = " "; + if (H5D_space_status.get(space_status) != H5D_space_status.H5D_SPACE_STATUS_ALLOCATED) + the_space += "not "; + System.out.println("Space for " + DATASETNAME2 + " has" + the_space + "been allocated."); + System.out.println("Storage size for " + DATASETNAME2 + " is: " + storage_size + " bytes."); + 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_id1 >= 0) + H5.H5Dclose(dataset_id1); + } + catch (Exception e) { + e.printStackTrace(); + } + + try { + if (dataset_id2 >= 0) + H5.H5Dclose(dataset_id2); + } + 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_Alloc.allocation(); + } + +} diff --git a/java/examples/datasets/H5Ex_D_Checksum.java b/java/examples/datasets/H5Ex_D_Checksum.java new file mode 100644 index 0000000..3a2f98f --- /dev/null +++ b/java/examples/datasets/H5Ex_D_Checksum.java @@ -0,0 +1,347 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * 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 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. + ************************************************************/ +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_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 = -1; + long filespace_id = -1; + long dataset_id = -1; + long dcpl_id = -1; + 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 = -1; + long dataset_id = -1; + long dcpl_id = -1; + 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(); + } + } + +} diff --git a/java/examples/datasets/H5Ex_D_Chunk.java b/java/examples/datasets/H5Ex_D_Chunk.java new file mode 100644 index 0000000..7f02e5a --- /dev/null +++ b/java/examples/datasets/H5Ex_D_Chunk.java @@ -0,0 +1,366 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * 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 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. + ************************************************************/ +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_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_NLAYOUTS(3); + 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 = -1; + long filespace_id = -1; + long dataset_id = -1; + long dcpl_id = -1; + 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 = -1; + long filespace_id = -1; + long dataset_id = -1; + long dcpl_id = -1; + 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_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(); + } + +} diff --git a/java/examples/datasets/H5Ex_D_Compact.java b/java/examples/datasets/H5Ex_D_Compact.java new file mode 100644 index 0000000..4f1e2f0 --- /dev/null +++ b/java/examples/datasets/H5Ex_D_Compact.java @@ -0,0 +1,289 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * 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 read and write data to a compact + dataset. The program first writes integers to a compact + dataset with dataspace dimensions of DIM_XxDIM_Y, then + closes the file. Next, it reopens the file, 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_Compact { + private static String FILENAME = "H5Ex_D_Compact.h5"; + private static String DATASETNAME = "DS1"; + private static final int DIM_X = 4; + private static final int DIM_Y = 7; + private static final int RANK = 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_NLAYOUTS(3); + 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 writeCompact() { + long file_id = -1; + long filespace_id = -1; + long dataset_id = -1; + long dcpl_id = -1; + long[] dims = { DIM_X, DIM_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. + try { + dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE); + } + catch (Exception e) { + e.printStackTrace(); + } + + // Set the layout to compact. + try { + if (dcpl_id >= 0) + H5.H5Pset_layout(dcpl_id, H5D_layout.H5D_COMPACT.getCode()); + } + catch (Exception e) { + e.printStackTrace(); + } + + // Create the dataset. We will use all default properties for this example. + 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 readCompact() { + long file_id = -1; + long filespace_id = -1; + long dataset_id = -1; + long dcpl_id = -1; + int[][] dset_data = new int[DIM_X][DIM_Y]; + + // Open file and dataset using the default properties. + 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_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 for " + DATASETNAME + " is: "); + 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_Compact.writeCompact(); + H5Ex_D_Compact.readCompact(); + } + +} diff --git a/java/examples/datasets/H5Ex_D_External.java b/java/examples/datasets/H5Ex_D_External.java new file mode 100644 index 0000000..5fdc696 --- /dev/null +++ b/java/examples/datasets/H5Ex_D_External.java @@ -0,0 +1,238 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * 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 read and write data to an + external dataset. The program first writes integers to an + external dataset with dataspace dimensions of DIM_XxDIM_Y, + then closes the file. Next, it reopens the file, reads + back the data, and outputs the name of the external data + file and the data to the screen. + ************************************************************/ +package examples.datasets; + +import hdf.hdf5lib.H5; +import hdf.hdf5lib.HDF5Constants; + +public class H5Ex_D_External { + private static String FILENAME = "H5Ex_D_External.h5"; + private static String EXTERNALNAME = "H5Ex_D_External.data"; + private static String DATASETNAME = "DS1"; + private static final int DIM_X = 4; + private static final int DIM_Y = 7; + private static final int RANK = 2; + private static final int NAME_BUF_SIZE = 32; + + private static void writeExternal() { + long file_id = -1; + long dcpl_id = -1; + long filespace_id = -1; + long dataset_id = -1; + long[] dims = { DIM_X, DIM_Y }; + 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. 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 external file. + try { + if (dcpl_id >= 0) + H5.H5Pset_external(dcpl_id, EXTERNALNAME, 0, HDF5Constants.H5F_UNLIMITED); + } + catch (Exception e) { + e.printStackTrace(); + } + + // Create the HDF5Constants.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 dataset. + try { + 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(); + } + + // Terminate access to the data space. + try { + if (filespace_id >= 0) + H5.H5Sclose(filespace_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 readExternal() { + long file_id = -1; + long dcpl_id = -1; + long dataset_id = -1; + int[][] dset_data = new int[DIM_X][DIM_Y]; + String[] Xname = new String[1]; + + // Open file using the default properties. + try { + file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT); + } + catch (Exception e) { + e.printStackTrace(); + } + + // Open dataset using the default properties. + 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 name of the external file. + long[] Xsize = new long[NAME_BUF_SIZE]; + try { + if (dcpl_id >= 0) + H5.H5Pget_external(dcpl_id, 0, Xsize.length, Xname, Xsize); + } + catch (Exception e) { + e.printStackTrace(); + } + System.out.println(DATASETNAME + " is stored in file: " + Xname[0]); + + // 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(DATASETNAME + ":"); + 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(); + + // Close the dataset. + try { + if (dataset_id >= 0) + H5.H5Dclose(dataset_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(); + } + } + + public static void main(String[] args) { + H5Ex_D_External.writeExternal(); + H5Ex_D_External.readExternal(); + } + +} diff --git a/java/examples/datasets/H5Ex_D_FillValue.java b/java/examples/datasets/H5Ex_D_FillValue.java new file mode 100644 index 0000000..982d2cb --- /dev/null +++ b/java/examples/datasets/H5Ex_D_FillValue.java @@ -0,0 +1,246 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * 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 set the fill value for a + dataset. The program first sets the fill value to + FILLVAL, creates a dataset with dimensions of DIM_XxDIM_Y, + reads from the uninitialized dataset, and outputs the + contents to the screen. Next, it writes integers to the + dataset, reads the data back, and outputs it to the + screen. Finally it extends the dataset, reads from it, + and outputs the result to the screen. + ************************************************************/ +package examples.datasets; + +import hdf.hdf5lib.H5; +import hdf.hdf5lib.HDF5Constants; + +public class H5Ex_D_FillValue { + private static String FILENAME = "H5Ex_D_FillValue.h5"; + private static String DATASETNAME = "ExtendibleArray"; + 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; + private static final int FILLVAL = 99; + + private static void fillValue() { + long file_id = -1; + long dcpl_id = -1; + long dataspace_id = -1; + long dataset_id = -1; + long[] dims = { DIM_X, DIM_Y }; + long[] extdims = { EDIM_X, EDIM_Y }; + long[] chunk_dims = { CHUNK_X, CHUNK_Y }; + long[] maxdims = { HDF5Constants.H5S_UNLIMITED, HDF5Constants.H5S_UNLIMITED }; + int[][] write_dset_data = new int[DIM_X][DIM_Y]; + int[][] read_dset_data = new int[DIM_X][DIM_Y]; + int[][] extend_dset_data = new int[EDIM_X][EDIM_Y]; + + // Initialize the dataset. + for (int indx = 0; indx < DIM_X; indx++) + for (int jndx = 0; jndx < DIM_Y; jndx++) + write_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. + 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(); + } + + // Set the fill value for the dataset + try { + int[] fill_value = { FILLVAL }; + if (dcpl_id >= 0) + H5.H5Pset_fill_value(dcpl_id, HDF5Constants.H5T_NATIVE_INT, fill_value); + } + catch (Exception e) { + e.printStackTrace(); + } + + // Set the allocation time to "early". This way we can be sure + // that reading from the dataset immediately after creation will + // return the fill value. + try { + if (dcpl_id >= 0) + H5.H5Pset_alloc_time(dcpl_id, HDF5Constants.H5D_ALLOC_TIME_EARLY); + } + catch (Exception e) { + e.printStackTrace(); + } + + // Create the dataset using the dataset creation property list. + 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(); + } + + // Read values from the dataset, which has not been written to yet. + try { + if (dataset_id >= 0) + H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + HDF5Constants.H5P_DEFAULT, read_dset_data); + } + catch (Exception e) { + e.printStackTrace(); + } + + // Output the data to the screen. + System.out.println("Dataset before being written to:"); + for (int indx = 0; indx < DIM_X; indx++) { + System.out.print(" [ "); + for (int jndx = 0; jndx < DIM_Y; jndx++) + System.out.print(read_dset_data[indx][jndx] + " "); + System.out.println("]"); + } + System.out.println(); + + // 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, write_dset_data); + } + catch (Exception e) { + e.printStackTrace(); + } + + // Read the data back. + try { + if (dataset_id >= 0) + H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + HDF5Constants.H5P_DEFAULT, read_dset_data); + } + catch (Exception e) { + e.printStackTrace(); + } + + // Output the data to the screen. + System.out.println("Dataset after being written to:"); + for (int indx = 0; indx < DIM_X; indx++) { + System.out.print(" [ "); + for (int jndx = 0; jndx < DIM_Y; jndx++) + System.out.print(read_dset_data[indx][jndx] + " "); + System.out.println("]"); + } + System.out.println(); + + // Extend the dataset. + try { + if (dataset_id >= 0) + H5.H5Dset_extent(dataset_id, extdims); + } + catch (Exception e) { + e.printStackTrace(); + } + + // Read from the extended dataset. + try { + if (dataset_id >= 0) + H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + HDF5Constants.H5P_DEFAULT, extend_dset_data); + } + catch (Exception e) { + e.printStackTrace(); + } + + // Output the data to the screen. + System.out.println("Dataset after extension:"); + for (int indx = 0; indx < EDIM_X; indx++) { + System.out.print(" [ "); + for (int jndx = 0; jndx < EDIM_Y; jndx++) + System.out.print(extend_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(); + } + + 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(); + } + + } + + public static void main(String[] args) { + H5Ex_D_FillValue.fillValue(); + } + +} diff --git a/java/examples/datasets/H5Ex_D_Gzip.java b/java/examples/datasets/H5Ex_D_Gzip.java new file mode 100644 index 0000000..b813367 --- /dev/null +++ b/java/examples/datasets/H5Ex_D_Gzip.java @@ -0,0 +1,336 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * 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 read and write data to a dataset + using gzip compression (also called zlib or deflate). The + program first checks if gzip compression is available, + then if it is it writes integers to a dataset using gzip, + then closes the file. Next, it reopens the file, reads + back the data, and outputs the type of compression and the + maximum value in the dataset 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_Gzip { + private static String FILENAME = "H5Ex_D_Gzip.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(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 writeGzip() { + long file_id = -1; + long filespace_id = -1; + long dataset_id = -1; + long dcpl_id = -1; + 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 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 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 readGzip() { + long file_id = -1; + long dataset_id = -1; + long dcpl_id = -1; + 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; + 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) { + H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + HDF5Constants.H5P_DEFAULT, dset_data); + } + } + 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 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_Gzip.checkGzipFilter()) { + H5Ex_D_Gzip.writeGzip(); + H5Ex_D_Gzip.readGzip(); + } + } + +} diff --git a/java/examples/datasets/H5Ex_D_Hyperslab.java b/java/examples/datasets/H5Ex_D_Hyperslab.java new file mode 100644 index 0000000..482e2c0 --- /dev/null +++ b/java/examples/datasets/H5Ex_D_Hyperslab.java @@ -0,0 +1,269 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * 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 read and write data to a + dataset by hyberslabs. The program first writes integers + in a hyperslab selection to a dataset with dataspace + dimensions of DIM_XxDIM_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. + ************************************************************/ +package examples.datasets; + +import hdf.hdf5lib.H5; +import hdf.hdf5lib.HDF5Constants; + +public class H5Ex_D_Hyperslab { + private static String FILENAME = "H5Ex_D_Hyperslab.h5"; + private static String DATASETNAME = "DS1"; + private static final int DIM_X = 6; + private static final int DIM_Y = 8; + private static final int RANK = 2; + + private static void writeHyperslab() { + long file_id = -1; + long filespace_id = -1; + long dataset_id = -1; + long[] dims = { DIM_X, DIM_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. We will use all default properties for this example. + try { + if ((file_id >= 0) && (filespace_id >= 0)) + dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_I32LE, filespace_id, + HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, 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 (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 readHyperslab() { + long file_id = -1; + long filespace_id = -1; + long dataset_id = -1; + long dcpl_id = -1; + 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(); + } + + // 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_Hyperslab.writeHyperslab(); + H5Ex_D_Hyperslab.readHyperslab(); + } + +} diff --git a/java/examples/datasets/H5Ex_D_Nbit.java b/java/examples/datasets/H5Ex_D_Nbit.java new file mode 100644 index 0000000..f74b675 --- /dev/null +++ b/java/examples/datasets/H5Ex_D_Nbit.java @@ -0,0 +1,305 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * 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 read and write data to a dataset + using the N-Bit filter. The program first checks if the + N-Bit filter is available, then if it is it writes integers + to a dataset using N-Bit, 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. + ************************************************************/ + +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_Nbit { + private static String FILENAME = "H5Ex_D_Nbit.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(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 checkNbitFilter() { + try { + // Check if N-Bit compression is available and can be used for both compression and decompression. + int available = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_NBIT); + 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_NBIT); + 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 writeData() throws Exception { + long file_id = -1; + long filespace_id = -1; + long dataset_id = -1; + long dtype_id = -1; + long dcpl_id = -1; + 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; + + try { + // Create a new file using the default properties. + file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, + HDF5Constants.H5P_DEFAULT); + + // Create dataspace. Setting maximum size to NULL sets the maximum + // size to be the current size. + filespace_id = H5.H5Screate_simple(RANK, dims, null); + + // Create the datatype to use with the N-Bit filter. It has an uncompressed size of 32 bits, + // but will have a size of 16 bits after being packed by the N-Bit filter. + dtype_id = H5.H5Tcopy(HDF5Constants.H5T_STD_I32LE); + H5.H5Tset_precision(dtype_id, 16); + H5.H5Tset_offset(dtype_id, 5); + + // Create the dataset creation property list, add the N-Bit filter and set the chunk size. + dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE); + H5.H5Pset_nbit(dcpl_id); + H5.H5Pset_chunk(dcpl_id, NDIMS, chunk_dims); + + // Create the dataset. + dataset_id = H5.H5Dcreate(file_id, DATASETNAME, dtype_id, filespace_id, HDF5Constants.H5P_DEFAULT, dcpl_id, + HDF5Constants.H5P_DEFAULT); + + // Write the data to the dataset. + H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + HDF5Constants.H5P_DEFAULT, dset_data); + } + catch (Exception e) { + e.printStackTrace(); + } + finally { + // Close and release resources. + if (dcpl_id >= 0) + H5.H5Pclose(dcpl_id); + if (dtype_id >= 0) + H5.H5Tclose(dtype_id); + if (dataset_id >= 0) + H5.H5Dclose(dataset_id); + if (filespace_id >= 0) + H5.H5Sclose(filespace_id); + if (file_id >= 0) + H5.H5Fclose(file_id); + } + } + + private static void readData() throws Exception { + long file_id = -1; + long dataset_id = -1; + long dcpl_id = -1; + 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; + 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) { + 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. + if (status < 0) + System.out.print("Dataset read failed!"); + } + } + 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 N-Bit 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. + */ + try { + if (H5Ex_D_Nbit.checkNbitFilter()) { + H5Ex_D_Nbit.writeData(); + H5Ex_D_Nbit.readData(); + } + } + catch (Exception ex) { + ex.printStackTrace(); + } + } +} diff --git a/java/examples/datasets/H5Ex_D_ReadWrite.java b/java/examples/datasets/H5Ex_D_ReadWrite.java new file mode 100644 index 0000000..de94ccb --- /dev/null +++ b/java/examples/datasets/H5Ex_D_ReadWrite.java @@ -0,0 +1,179 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * 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 read and write data to a + dataset. The program first writes integers to a dataset + with dataspace dimensions of DIM_XxDIM_Y, then closes the + file. Next, it reopens the file, reads back the data, and + outputs it to the screen. + ************************************************************/ +package examples.datasets; + +import hdf.hdf5lib.H5; +import hdf.hdf5lib.HDF5Constants; + +public class H5Ex_D_ReadWrite { + private static String FILENAME = "H5Ex_D_ReadWrite.h5"; + private static String DATASETNAME = "DS1"; + private static final int DIM_X = 4; + private static final int DIM_Y = 7; + private static final int RANK = 2; + + private static void WriteDataset() { + long file_id = -1; + long filespace_id = -1; + long dataset_id = -1; + long[] dims = { DIM_X, DIM_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. We will use all default properties for this example. + try { + if ((file_id >= 0) && (filespace_id >= 0)) + dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_I32LE, filespace_id, + HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, 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 (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 ReadDataset() { + long file_id = -1; + long dataset_id = -1; + int[][] dset_data = new int[DIM_X][DIM_Y]; + + // Open file using the default properties. + try { + file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT); + } + catch (Exception e) { + e.printStackTrace(); + } + + // Open dataset using the default properties. + try { + if (file_id >= 0) + dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); + } + 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(DATASETNAME + ":"); + 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(); + + // Close the dataset. + 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) { + H5Ex_D_ReadWrite.WriteDataset(); + H5Ex_D_ReadWrite.ReadDataset(); + } + +} diff --git a/java/examples/datasets/H5Ex_D_Shuffle.java b/java/examples/datasets/H5Ex_D_Shuffle.java new file mode 100644 index 0000000..ac3c1b4 --- /dev/null +++ b/java/examples/datasets/H5Ex_D_Shuffle.java @@ -0,0 +1,373 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * 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 read and write data to a dataset + using the shuffle filter with gzip compression. The + program first checks if the shuffle and gzip filters are + available, then if they are it writes integers to a + dataset using shuffle+gzip, then closes the file. Next, + it reopens the file, reads back the data, and outputs the + types of filters and the maximum value in the dataset 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_Shuffle { + private static String FILENAME = "H5Ex_D_Shuffle.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(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 boolean checkShuffleFilter() { + try { + int available = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_SHUFFLE); + if (available == 0) { + System.out.println("Shuffle filter not available."); + return false; + } + } + catch (Exception e) { + e.printStackTrace(); + } + + try { + int filter_info = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_SHUFFLE); + if (((filter_info & HDF5Constants.H5Z_FILTER_CONFIG_ENCODE_ENABLED) == 0) + || ((filter_info & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) == 0)) { + System.out.println("Shuffle filter not available for encoding and decoding."); + return false; + } + } + catch (Exception e) { + e.printStackTrace(); + } + return true; + } + + private static void writeShuffle() { + long file_id = -1; + long filespace_id = -1; + long dataset_id = -1; + long dcpl_id = -1; + 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 shuffle + // filter and the gzip compression filter. + // The order in which the filters are added here is significant - + // we will see much greater results when the shuffle is applied + // first. The order in which the filters are added to the property + // list is the order in which they will be invoked when writing + // data. + try { + dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE); + if (dcpl_id >= 0) { + H5.H5Pset_shuffle(dcpl_id); + 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 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 readShuffle() { + long file_id = -1; + long dataset_id = -1; + long dcpl_id = -1; + 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 the number of filters, and retrieve and print the + // type of each. + try { + if (dcpl_id >= 0) { + int nfilters = H5.H5Pget_nfilters(dcpl_id); + for (int indx = 0; indx < nfilters; indx++) { + // 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, indx, flags, cd_nelmts, cd_values, 120, filter_name, + filter_config); + System.out.print("Filter " + indx + ": 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) { + H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + HDF5Constants.H5P_DEFAULT, dset_data); + } + } + 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 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. + // Similarly, check for availability of the shuffle filter. + if (H5Ex_D_Shuffle.checkGzipFilter() && H5Ex_D_Shuffle.checkShuffleFilter()) { + H5Ex_D_Shuffle.writeShuffle(); + H5Ex_D_Shuffle.readShuffle(); + } + } + +} diff --git a/java/examples/datasets/H5Ex_D_Sofloat.java b/java/examples/datasets/H5Ex_D_Sofloat.java new file mode 100644 index 0000000..26c8d49 --- /dev/null +++ b/java/examples/datasets/H5Ex_D_Sofloat.java @@ -0,0 +1,356 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * 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 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 floating point numbers 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. + ************************************************************/ +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_Sofloat { + + private static String FILENAME = "H5Ex_D_Sofloat.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(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 checkScaleoffsetFilter() { + try { + int available = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_SCALEOFFSET); + if (available == 0) { + System.out.println("Scale-Offset filter not available."); + return false; + } + } + catch (Exception e) { + e.printStackTrace(); + } + + try { + int filter_info = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_SCALEOFFSET); + if (((filter_info & HDF5Constants.H5Z_FILTER_CONFIG_ENCODE_ENABLED) == 0) + || ((filter_info & HDF5Constants.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() { + long file_id = -1; + long filespace_id = -1; + long dataset_id = -1; + long dcpl_id = -1; + long[] dims = { DIM_X, DIM_Y }; + long[] chunk_dims = { CHUNK_X, CHUNK_Y }; + double[][] dset_data = new double[DIM_X][DIM_Y]; + + // Initialize data. + for (int indx = 0; indx < DIM_X; indx++) + for (int jndx = 0; jndx < DIM_Y; jndx++) { + double x = indx; + double y = jndx; + dset_data[indx][jndx] = (x + 1) / (y + 0.3) + y; + } + + // Find the maximum value in the dataset, to verify that it was read correctly. + double max = dset_data[0][0]; + double min = 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]; + if (min > dset_data[indx][jndx]) + min = dset_data[indx][jndx]; + } + + // Print the maximum value. + System.out.println("Maximum value in write buffer is: " + max); + System.out.println("Minimum value in write buffer is: " + min); + + // Create a new file using the 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 Scale-Offset + // filter and set the chunk size. + try { + dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE); + if (dcpl_id >= 0) { + H5.H5Pset_scaleoffset(dcpl_id, HDF5Constants.H5Z_SO_FLOAT_DSCALE, 2); + 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_IEEE_F64LE, 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_DOUBLE, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + HDF5Constants.H5P_DEFAULT, dset_data); + } + catch (Exception e) { + e.printStackTrace(); + } + + // Close and release resources. + 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 file + try { + if (file_id >= 0) + H5.H5Fclose(file_id); + } + catch (Exception e) { + e.printStackTrace(); + } + } + + private static void readData() { + long file_id = -1; + long dataset_id = -1; + long dcpl_id = -1; + double[][] dset_data = new double[DIM_X][DIM_Y]; + + // Open file using the default properties. + try { + file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); + } + catch (Exception e) { + e.printStackTrace(); + } + // Open dataset using the default properties. + try { + if (file_id >= 0) + dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); + } + catch (Exception e) { + e.printStackTrace(); + } + + // Retrieve 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; + 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) + H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_DOUBLE, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + HDF5Constants.H5P_DEFAULT, dset_data); + } + catch (Exception e) { + e.printStackTrace(); + } + + // Find the maximum value in the dataset, to verify that it was read correctly. + double max = dset_data[0][0]; + double min = 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]; + if (min > dset_data[indx][jndx]) + min = dset_data[indx][jndx]; + } + + // Print the maximum value. + System.out.println("Maximum value in " + DATASETNAME + " is: " + max); + System.out.println("Minimum value in " + DATASETNAME + " is: " + min); + + // 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 Scale-Offset 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_Sofloat.checkScaleoffsetFilter()) { + H5Ex_D_Sofloat.writeData(); + H5Ex_D_Sofloat.readData(); + } + } +} diff --git a/java/examples/datasets/H5Ex_D_Soint.java b/java/examples/datasets/H5Ex_D_Soint.java new file mode 100644 index 0000000..7939883 --- /dev/null +++ b/java/examples/datasets/H5Ex_D_Soint.java @@ -0,0 +1,335 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * 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 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. + ************************************************************/ +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_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(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 checkScaleoffsetFilter() { + try { + int available = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_SCALEOFFSET); + if (available == 0) { + System.out.println("Scale-Offset filter not available."); + return false; + } + } + catch (Exception e) { + e.printStackTrace(); + } + + try { + int filter_info = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_SCALEOFFSET); + if (((filter_info & HDF5Constants.H5Z_FILTER_CONFIG_ENCODE_ENABLED) == 0) + || ((filter_info & HDF5Constants.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() { + long file_id = -1; + long filespace_id = -1; + long dataset_id = -1; + long dcpl_id = -1; + 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 = 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 Scale-Offset + // filter and set the chunk size. + try { + dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE); + if (dcpl_id >= 0) { + H5.H5Pset_scaleoffset(dcpl_id, HDF5Constants.H5Z_SO_INT, HDF5Constants.H5Z_SO_INT_MINBITS_DEFAULT); + 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(); + } + + // Close and release resources. + 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 file + try { + if (file_id >= 0) + H5.H5Fclose(file_id); + } + catch (Exception e) { + e.printStackTrace(); + } + } + + private static void readData() { + long file_id = -1; + long dataset_id = -1; + long dcpl_id = -1; + int[][] dset_data = new int[DIM_X][DIM_Y]; + + // Open file using the default properties. + try { + file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); + } + catch (Exception e) { + e.printStackTrace(); + } + // Open dataset using the default properties. + try { + if (file_id >= 0) + dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); + } + catch (Exception e) { + e.printStackTrace(); + } + + // Retrieve 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; + 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) + H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + HDF5Constants.H5P_DEFAULT, dset_data); + } + 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 Scale-Offset 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_Soint.checkScaleoffsetFilter()) { + H5Ex_D_Soint.writeData(); + H5Ex_D_Soint.readData(); + } + } + +} diff --git a/java/examples/datasets/H5Ex_D_Szip.java b/java/examples/datasets/H5Ex_D_Szip.java new file mode 100644 index 0000000..5258234 --- /dev/null +++ b/java/examples/datasets/H5Ex_D_Szip.java @@ -0,0 +1,337 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * 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 read and write data to a dataset + using szip compression. The program first checks if + szip compression is available, then if it is it writes + integers to a dataset using szip, then closes the file. + Next, it reopens the file, reads back the data, and + outputs the type of compression and the maximum value in + the dataset 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_Szip { + private static String FILENAME = "H5Ex_D_Szip.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(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 checkSzipFilter() { + try { + int available = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_SZIP); + if (available == 0) { + System.out.println("szip filter not available."); + return false; + } + } + catch (Exception e) { + e.printStackTrace(); + } + + try { + int filter_info = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_SZIP); + if (((filter_info & HDF5Constants.H5Z_FILTER_CONFIG_ENCODE_ENABLED) == 0) + || ((filter_info & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) == 0)) { + System.out.println("szip filter not available for encoding and decoding."); + return false; + } + } + catch (Exception e) { + e.printStackTrace(); + } + return true; + } + + private static void writeSzip() { + long file_id = -1; + long filespace_id = -1; + long dataset_id = -1; + long dcpl_id = -1; + 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 szip compression + // filter. + try { + dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE); + if (dcpl_id >= 0) { + H5.H5Pset_szip(dcpl_id, HDF5Constants.H5_SZIP_NN_OPTION_MASK, 8); + // 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 readSzip() { + long file_id = -1; + long dataset_id = -1; + long dcpl_id = -1; + 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; + 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) { + H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + HDF5Constants.H5P_DEFAULT, dset_data); + } + } + 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 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_Szip.checkSzipFilter()) { + H5Ex_D_Szip.writeSzip(); + H5Ex_D_Szip.readSzip(); + } + } + +} diff --git a/java/examples/datasets/H5Ex_D_Transform.java b/java/examples/datasets/H5Ex_D_Transform.java new file mode 100644 index 0000000..1f289f3 --- /dev/null +++ b/java/examples/datasets/H5Ex_D_Transform.java @@ -0,0 +1,250 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * 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 read and write data to a dataset + using a data transform expression. The program first + writes integers to a dataset using the transform + expression TRANSFORM, then closes the file. Next, it + reopens the file, reads back the data without a transform, + and outputs the data to the screen. Finally it reads the + data using the transform expression RTRANSFORM and outputs + the results to the screen. + ************************************************************/ +package examples.datasets; + +import hdf.hdf5lib.H5; +import hdf.hdf5lib.HDF5Constants; + +public class H5Ex_D_Transform { + + private static String FILE = "H5Ex_D_Transform.h5"; + private static String DATASET = "DS1"; + private static final int DIM_X = 4; + private static final int DIM_Y = 7; + private static String TRANSFORM = "x+1"; + private static String RTRANSFORM = "x-1"; + + private static void writeData() { + long file_id = -1; + long filespace_id = -1; + long dataset_id = -1; + long dxpl_id = -1; + + long[] dims = { DIM_X, DIM_Y }; + int[][] dset_data = new int[DIM_X][DIM_Y]; + + // Initialize data. + for (int i = 0; i < DIM_X; i++) + for (int j = 0; j < DIM_Y; j++) + dset_data[i][j] = i * j - j; + + // Output the data to the screen. + System.out.println("Original Data:"); + for (int i = 0; i < DIM_X; i++) { + System.out.print(" ["); + for (int j = 0; j < DIM_Y; j++) + System.out.print(" " + dset_data[i][j] + " "); + System.out.println("]"); + } + + // Create a new file using the default properties. + try { + file_id = H5.H5Fcreate(FILE, 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(2, dims, null); + } + catch (Exception e) { + e.printStackTrace(); + } + + // Create the dataset transfer property list and define the transform expression. + try { + dxpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_XFER); + if (dxpl_id >= 0) + H5.H5Pset_data_transform(dxpl_id, TRANSFORM); + } + catch (Exception e) { + e.printStackTrace(); + } + + // Create the dataset using the default properties. Unfortunately we must save as + // a native type or the transform operation will fail. + try { + if ((file_id >= 0) && (filespace_id >= 0)) + dataset_id = H5.H5Dcreate(file_id, DATASET, HDF5Constants.H5T_NATIVE_INT, filespace_id, + HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); + } + catch (Exception e) { + e.printStackTrace(); + } + + // Write the data to the dataset using the dataset transfer property list. + try { + if ((dataset_id >= 0) && (dxpl_id >= 0)) + H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + dxpl_id, dset_data); + } + catch (Exception e) { + e.printStackTrace(); + } + + // End access to the dataset and release resources used by it. + try { + if (dxpl_id >= 0) + H5.H5Pclose(dxpl_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 readData() { + + long file_id = -1; + long dataset_id = -1; + long dxpl_id = -1; + int[][] dset_data = new int[DIM_X][DIM_Y]; + + // Open an existing file using the default properties. + try { + file_id = H5.H5Fopen(FILE, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); + } + catch (Exception e) { + e.printStackTrace(); + } + + // Open an existing dataset using the default properties. + try { + if (file_id >= 0) + dataset_id = H5.H5Dopen(file_id, DATASET, HDF5Constants.H5P_DEFAULT); + } + 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 with transform '" + TRANSFORM + "'"); + for (int i = 0; i < DIM_X; i++) { + System.out.print(" ["); + for (int j = 0; j < DIM_Y; j++) + System.out.print(" " + dset_data[i][j] + " "); + System.out.println("]"); + } + + // Create the dataset transfer property list and define the transform expression. + try { + dxpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_XFER); + if (dxpl_id >= 0) + H5.H5Pset_data_transform(dxpl_id, RTRANSFORM); + } + catch (Exception e) { + e.printStackTrace(); + } + + // Read the data using the dataset transfer property list. + try { + if ((dataset_id >= 0) && (dxpl_id >= 0)) + H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + dxpl_id, dset_data); + } + catch (Exception e) { + e.printStackTrace(); + } + + // Output the data to the screen. + + System.out.println("Data as written with transform '" + TRANSFORM + "' and read with transform '" + + RTRANSFORM + "'"); + for (int i = 0; i < DIM_X; i++) { + System.out.print(" ["); + for (int j = 0; j < DIM_Y; j++) + System.out.print(" " + dset_data[i][j] + " "); + System.out.println("]"); + } + + // Close and release resources. + try { + if (dxpl_id >= 0) + H5.H5Pclose(dxpl_id); + } + catch (Exception e) { + e.printStackTrace(); + } + try { + if (dataset_id >= 0) + H5.H5Dclose(dataset_id); + } + catch (Exception e) { + e.printStackTrace(); + } + try { + if (file_id >= 0) + H5.H5Fclose(file_id); + } + catch (Exception e) { + e.printStackTrace(); + } + } + + public static void main(String[] args) { + H5Ex_D_Transform.writeData(); + H5Ex_D_Transform.readData(); + } + +} diff --git a/java/examples/datasets/H5Ex_D_UnlimitedAdd.java b/java/examples/datasets/H5Ex_D_UnlimitedAdd.java new file mode 100644 index 0000000..ada8df0 --- /dev/null +++ b/java/examples/datasets/H5Ex_D_UnlimitedAdd.java @@ -0,0 +1,393 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * 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. The program first writes integers to a 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 hdf.hdf5lib.H5; +import hdf.hdf5lib.HDF5Constants; + +public class H5Ex_D_UnlimitedAdd { + private static String FILENAME = "H5Ex_D_UnlimitedAdd.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; + + 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. + 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 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[] 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(); + } + + // 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) { + H5Ex_D_UnlimitedAdd.writeUnlimited(); + H5Ex_D_UnlimitedAdd.extendUnlimited(); + H5Ex_D_UnlimitedAdd.readUnlimited(); + } + +} diff --git a/java/examples/datasets/H5Ex_D_UnlimitedGzip.java b/java/examples/datasets/H5Ex_D_UnlimitedGzip.java new file mode 100644 index 0000000..c08ceef --- /dev/null +++ b/java/examples/datasets/H5Ex_D_UnlimitedGzip.java @@ -0,0 +1,504 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * 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(); + } + } + +} diff --git a/java/examples/datasets/H5Ex_D_UnlimitedMod.java b/java/examples/datasets/H5Ex_D_UnlimitedMod.java new file mode 100644 index 0000000..884cad3 --- /dev/null +++ b/java/examples/datasets/H5Ex_D_UnlimitedMod.java @@ -0,0 +1,379 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * 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. The program first writes integers to a 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 entire extended dataset. Finally it + reopens the file again, reads back the data, and utputs it + to the screen. + ************************************************************/ +package examples.datasets; + +import hdf.hdf5lib.H5; +import hdf.hdf5lib.HDF5Constants; + +public class H5Ex_D_UnlimitedMod { + private static String FILENAME = "H5Ex_D_UnlimitedMod.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; + + 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. + 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 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 }; + 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; + + // Write the data tto the extended dataset. + try { + if ((dataspace_id >= 0) && (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[] 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(); + } + + // 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) { + H5Ex_D_UnlimitedMod.writeUnlimited(); + H5Ex_D_UnlimitedMod.extendUnlimited(); + H5Ex_D_UnlimitedMod.readUnlimited(); + } + +} diff --git a/java/examples/datasets/Makefile.am b/java/examples/datasets/Makefile.am new file mode 100644 index 0000000..49888a0 --- /dev/null +++ b/java/examples/datasets/Makefile.am @@ -0,0 +1,78 @@ +# +# 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. +## +## Makefile.am +## Run automake to generate a Makefile.in from this file. +## +# +# HDF5 Java Library Examples Makefile(.in) + +include $(top_srcdir)/config/commence.am + +# Mark this directory as part of the JNI API +JAVA_API=yes + +JAVAROOT = .classes + +classes: + $(MKDIR_P) $(@D)/$(JAVAROOT) + +pkgpath = examples/datasets +hdfjarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar +CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-1.7.5.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.5.jar:$$CLASSPATH + +jarfile = jar$(PACKAGE_TARNAME)datasets.jar + +AM_JAVACFLAGS = $(H5_JAVACFLAGS) -deprecation + +TESTPACKAGE = + +noinst_JAVA = \ + H5Ex_D_Alloc.java \ + H5Ex_D_Checksum.java \ + H5Ex_D_Chunk.java \ + H5Ex_D_Compact.java \ + H5Ex_D_External.java \ + H5Ex_D_FillValue.java \ + H5Ex_D_Gzip.java \ + H5Ex_D_Hyperslab.java \ + H5Ex_D_ReadWrite.java \ + H5Ex_D_Shuffle.java \ + H5Ex_D_Szip.java \ + H5Ex_D_UnlimitedAdd.java \ + H5Ex_D_UnlimitedGzip.java \ + H5Ex_D_UnlimitedMod.java \ + H5Ex_D_Nbit.java \ + H5Ex_D_Transform.java \ + H5Ex_D_Sofloat.java \ + H5Ex_D_Soint.java + +$(jarfile): classnoinst.stamp classes + $(JAR) cvf $@ -C $(JAVAROOT)/ $(pkgpath) + +noinst_DATA = $(jarfile) + +.PHONY: classes + +check_SCRIPTS = runExample.sh +TEST_SCRIPT = $(check_SCRIPTS) + +CLEANFILES = classnoinst.stamp $(jarfile) $(JAVAROOT)/$(pkgpath)/*.class runExample.sh + +clean: + rm -rf $(JAVAROOT) + rm -f $(jarfile) + rm -f classnoinst.stamp + +include $(top_srcdir)/config/conclude.am diff --git a/java/examples/datasets/runExample.sh.in b/java/examples/datasets/runExample.sh.in new file mode 100644 index 0000000..8ac28a7 --- /dev/null +++ b/java/examples/datasets/runExample.sh.in @@ -0,0 +1,413 @@ +#! /bin/sh +# +# Copyright by The HDF Group. +# Copyright by the Board of Trustees of the University of Illinois. +# All rights reserved. +# +# This file is part of HDF5. The full HDF5 copyright notice, including +# terms governing use, modification, and redistribution, is contained in +# the files COPYING and Copyright.html. COPYING can be found at the root +# of the source code distribution tree; Copyright.html can be found at the +# root level of an installed copy of the electronic HDF5 document set and +# is linked from the top-level documents page. It can also be found at +# http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have +# access to either file, you may request a copy from help@hdfgroup.org. +# + +top_builddir=@top_builddir@ +top_srcdir=@top_srcdir@ +srcdir=@srcdir@ + +USE_FILTER_SZIP="@USE_FILTER_SZIP@" +USE_FILTER_DEFLATE="@USE_FILTER_DEFLATE@" + +TESTNAME=EX_Datasets +EXIT_SUCCESS=0 +EXIT_FAILURE=1 + +# Set up default variable values if not supplied by the user. +RM='rm -rf' +CMP='cmp' +DIFF='diff -c' +CP='cp' +DIRNAME='dirname' +LS='ls' +AWK='awk' + +nerrors=0 + +# where the libs exist +HDFLIB_HOME="$top_srcdir/java/lib" +BLDLIBDIR="./lib" +BLDDIR="." +HDFTEST_HOME="$top_srcdir/java/examples/datasets" +JARFILE=jar@PACKAGE_TARNAME@-@PACKAGE_VERSION@.jar +TESTJARFILE=jar@PACKAGE_TARNAME@datasets.jar +test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR + +###################################################################### +# library files +# -------------------------------------------------------------------- +# All the library files copy from source directory to test directory +# NOTE: Keep this framework to add/remove test files. +# This list are also used for checking exist. +# Comment '#' without space can be used. +# -------------------------------------------------------------------- +LIST_LIBRARY_FILES=" +$HDFLIB_HOME/slf4j-api-1.7.5.jar +$HDFLIB_HOME/ext/slf4j-simple-1.7.5.jar +$top_builddir/src/.libs/libhdf5.* +$top_builddir/java/src/jni/.libs/libhdf5_java.* +$top_builddir/java/src/$JARFILE +" +LIST_DATA_FILES=" +$HDFTEST_HOME/../testfiles/examples.datasets.H5Ex_D_Alloc.txt +$HDFTEST_HOME/../testfiles/examples.datasets.H5Ex_D_Checksum.txt +$HDFTEST_HOME/../testfiles/examples.datasets.H5Ex_D_Chunk.txt +$HDFTEST_HOME/../testfiles/examples.datasets.H5Ex_D_Compact.txt +$HDFTEST_HOME/../testfiles/examples.datasets.H5Ex_D_External.txt +$HDFTEST_HOME/../testfiles/examples.datasets.H5Ex_D_FillValue.txt +$HDFTEST_HOME/../testfiles/examples.datasets.H5Ex_D_Gzip.txt +$HDFTEST_HOME/../testfiles/examples.datasets.H5Ex_D_Hyperslab.txt +$HDFTEST_HOME/../testfiles/examples.datasets.H5Ex_D_ReadWrite.txt +$HDFTEST_HOME/../testfiles/examples.datasets.H5Ex_D_Shuffle.txt +$HDFTEST_HOME/../testfiles/examples.datasets.H5Ex_D_Szip.txt +$HDFTEST_HOME/../testfiles/examples.datasets.H5Ex_D_UnlimitedAdd.txt +$HDFTEST_HOME/../testfiles/examples.datasets.H5Ex_D_UnlimitedGzip.txt +$HDFTEST_HOME/../testfiles/examples.datasets.H5Ex_D_UnlimitedMod.txt +$HDFTEST_HOME/../testfiles/examples.datasets.H5Ex_D_Nbit.txt +$HDFTEST_HOME/../testfiles/examples.datasets.H5Ex_D_Transform.txt +$HDFTEST_HOME/../testfiles/examples.datasets.H5Ex_D_Sofloat.txt +$HDFTEST_HOME/../testfiles/examples.datasets.H5Ex_D_Soint.txt +" + +# +# copy files from source dirs to test dir +# +COPY_LIBFILES="$LIST_LIBRARY_FILES" + +COPY_LIBFILES_TO_BLDLIBDIR() +{ + # copy test files. Used -f to make sure get a new copy + for tstfile in $COPY_LIBFILES + do + # ignore '#' comment + echo $tstfile | tr -d ' ' | grep '^#' > /dev/null + RET=$? + if [ $RET -eq 1 ]; then + # skip cp if srcdir is same as destdir + # this occurs when build/test performed in source dir and + # make cp fail + SDIR=`$DIRNAME $tstfile` + INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'` + INODE_DDIR=`$LS -i -d $TESTDIR | $AWK -F' ' '{print $1}'` + if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then + $CP -f $tstfile $BLDLIBDIR + if [ $? -ne 0 ]; then + echo "Error: FAILED to copy $tstfile ." + + # Comment out this to CREATE expected file + exit $EXIT_FAILURE + fi + fi + fi + done +} + +CLEAN_LIBFILES_AND_BLDLIBDIR() +{ + # skip rm if srcdir is same as destdir + # this occurs when build/test performed in source dir and + # make cp fail + SDIR=`$DIRNAME $tstfile` + INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'` + INODE_DDIR=`$LS -i -d $TESTDIR | $AWK -F' ' '{print $1}'` + if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then + $RM $BLDLIBDIR + fi +} + +COPY_DATAFILES="$LIST_DATA_FILES" + +COPY_DATAFILES_TO_BLDDIR() +{ + # copy test files. Used -f to make sure get a new copy + for tstfile in $COPY_DATAFILES + do + # ignore '#' comment + echo $tstfile | tr -d ' ' | grep '^#' > /dev/null + RET=$? + if [ $RET -eq 1 ]; then + # skip cp if srcdir is same as destdir + # this occurs when build/test performed in source dir and + # make cp fail + SDIR=`$DIRNAME $tstfile` + INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'` + INODE_DDIR=`$LS -i -d $TESTDIR | $AWK -F' ' '{print $1}'` + if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then + $CP -f $tstfile $BLDDIR + if [ $? -ne 0 ]; then + echo "Error: FAILED to copy $tstfile ." + + # Comment out this to CREATE expected file + exit $EXIT_FAILURE + fi + fi + fi + done +} + +CLEAN_DATAFILES_AND_BLDDIR() +{ + # skip rm if srcdir is same as destdir + # this occurs when build/test performed in source dir and + # make cp fail + SDIR=`$DIRNAME $tstfile` + INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'` + INODE_DDIR=`$LS -i -d $TESTDIR | $AWK -F' ' '{print $1}'` + if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then + $RM $BLDDIR/*.txt + $RM $BLDDIR/*.out + fi +} + +# Print a line-line message left justified in a field of 70 characters +# beginning with the word "Testing". +# +TESTING() { + SPACES=" " + echo "Testing $* $SPACES" | cut -c1-70 | tr -d '\012' +} + +# where Java is installed (requires jdk1.7.x) +JAVAEXE=@JAVA@ +JAVAEXEFLAGS=@H5_JAVAFLAGS@ + +############################################################################### +# DO NOT MODIFY BELOW THIS LINE +############################################################################### + +# prepare for test +COPY_LIBFILES_TO_BLDLIBDIR +COPY_DATAFILES_TO_BLDDIR + +CPATH=".:"$BLDLIBDIR"/"$JARFILE":"$BLDLIBDIR"/slf4j-api-1.7.5.jar:"$BLDLIBDIR"/slf4j-simple-1.7.5.jar:"$TESTJARFILE"" + +TEST=/usr/bin/test +if [ ! -x /usr/bin/test ] +then +TEST=`which test` +fi + +if $TEST -z "$CLASSPATH"; then + CLASSPATH="" +fi +CLASSPATH=$CPATH":"$CLASSPATH +export CLASSPATH + +if $TEST -n "$JAVAPATH" ; then + PATH=$JAVAPATH":"$PATH + export PATH +fi + +if $TEST -e /bin/uname; then + os_name=`/bin/uname -s` +elif $TEST -e /usr/bin/uname; then + os_name=`/usr/bin/uname -s` +else + os_name=unknown +fi + +if $TEST -z "$LD_LIBRARY_PATH" ; then + LD_LIBRARY_PATH="" +fi + +case $os_name in + Darwin) + DYLD_LIBRARY_PATH=$BLDLIBDIR:$DYLD_LIBRARY_PATH + export DYLD_LIBRARY_PATH + LD_LIBRARY_PATH=$DYLD_LIBRARY_PATH + ;; + *) + LD_LIBRARY_PATH=$BLDLIBDIR:$LD_LIBRARY_PATH + ;; +esac + +export LD_LIBRARY_PATH + +echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Alloc" +($JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Alloc > H5Ex_D_Alloc.out) +if diff H5Ex_D_Alloc.out examples.datasets.H5Ex_D_Alloc.txt > /dev/null; then + echo " PASSED datasets.H5Ex_D_Alloc" +else + echo "**FAILED** datasets.H5Ex_D_Alloc" + nerrors="`expr $nerrors + 1`" +fi + +echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Checksum" +($JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Checksum > H5Ex_D_Checksum.out) +if diff H5Ex_D_Checksum.out examples.datasets.H5Ex_D_Checksum.txt > /dev/null; then + echo " PASSED datasets.H5Ex_D_Checksum" +else + echo "**FAILED** datasets.H5Ex_D_Checksum" + nerrors="`expr $nerrors + 1`" +fi + +echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Chunk" +($JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Chunk > H5Ex_D_Chunk.out) +if diff H5Ex_D_Chunk.out examples.datasets.H5Ex_D_Chunk.txt > /dev/null; then + echo " PASSED datasets.H5Ex_D_Chunk" +else + echo "**FAILED** datasets.H5Ex_D_Chunk" + nerrors="`expr $nerrors + 1`" +fi + +echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Compact" +($JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Compact > H5Ex_D_Compact.out) +if diff H5Ex_D_Compact.out examples.datasets.H5Ex_D_Compact.txt > /dev/null; then + echo " PASSED datasets.H5Ex_D_Compact" +else + echo "**FAILED** datasets.H5Ex_D_Compact" + nerrors="`expr $nerrors + 1`" +fi + +echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_External" +($JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_External > H5Ex_D_External.out) +if diff H5Ex_D_External.out examples.datasets.H5Ex_D_External.txt > /dev/null; then + echo " PASSED datasets.H5Ex_D_External" +else + echo "**FAILED** datasets.H5Ex_D_External" + nerrors="`expr $nerrors + 1`" +fi + +echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_FillValue" +($JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_FillValue > H5Ex_D_FillValue.out) +if diff H5Ex_D_FillValue.out examples.datasets.H5Ex_D_FillValue.txt > /dev/null; then + echo " PASSED datasets.H5Ex_D_FillValue" +else + echo "**FAILED** datasets.H5Ex_D_FillValue" + nerrors="`expr $nerrors + 1`" +fi + +echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Gzip" +($JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Gzip > H5Ex_D_Gzip.out) +if diff H5Ex_D_Gzip.out examples.datasets.H5Ex_D_Gzip.txt > /dev/null; then + echo " PASSED datasets.H5Ex_D_Gzip" +else + echo "**FAILED** datasets.H5Ex_D_Gzip" + nerrors="`expr $nerrors + 1`" +fi + +echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Hyperslab" +($JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Hyperslab > H5Ex_D_Hyperslab.out) +if diff H5Ex_D_Hyperslab.out examples.datasets.H5Ex_D_Hyperslab.txt > /dev/null; then + echo " PASSED datasets.H5Ex_D_Hyperslab" +else + echo "**FAILED** datasets.H5Ex_D_Hyperslab" + nerrors="`expr $nerrors + 1`" +fi + +echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_ReadWrite" +($JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_ReadWrite > H5Ex_D_ReadWrite.out) +if diff H5Ex_D_ReadWrite.out examples.datasets.H5Ex_D_ReadWrite.txt > /dev/null; then + echo " PASSED datasets.H5Ex_D_ReadWrite" +else + echo "**FAILED** datasets.H5Ex_D_ReadWrite" + nerrors="`expr $nerrors + 1`" +fi + +echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Shuffle" +($JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Shuffle > H5Ex_D_Shuffle.out) +if diff H5Ex_D_Shuffle.out examples.datasets.H5Ex_D_Shuffle.txt > /dev/null; then + echo " PASSED datasets.H5Ex_D_Shuffle" +else + echo "**FAILED** datasets.H5Ex_D_Shuffle" + nerrors="`expr $nerrors + 1`" +fi + +if test $USE_FILTER_SZIP = "yes"; then + echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Szip" + ($JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Szip > H5Ex_D_Szip.out) + if diff H5Ex_D_Szip.out examples.datasets.H5Ex_D_Szip.txt > /dev/null; then + echo " PASSED datasets.H5Ex_D_Szip" + else + echo "**FAILED** datasets.H5Ex_D_Szip" + nerrors="`expr $nerrors + 1`" + fi +fi + +echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_UnlimitedAdd" +($JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_UnlimitedAdd > H5Ex_D_UnlimitedAdd.out) +if diff H5Ex_D_UnlimitedAdd.out examples.datasets.H5Ex_D_UnlimitedAdd.txt > /dev/null; then + echo " PASSED datasets.H5Ex_D_UnlimitedAdd" +else + echo "**FAILED** datasets.H5Ex_D_UnlimitedAdd" + nerrors="`expr $nerrors + 1`" +fi + +echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_UnlimitedGzip" +($JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_UnlimitedGzip > H5Ex_D_UnlimitedGzip.out) +if diff H5Ex_D_External.out examples.datasets.H5Ex_D_External.txt > /dev/null; then + echo " PASSED datasets.H5Ex_D_UnlimitedGzip" +else + echo "**FAILED** datasets.H5Ex_D_UnlimitedGzip" + nerrors="`expr $nerrors + 1`" +fi + +echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_UnlimitedMod" +($JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_UnlimitedMod > H5Ex_D_UnlimitedMod.out) +if diff H5Ex_D_UnlimitedMod.out examples.datasets.H5Ex_D_UnlimitedMod.txt > /dev/null; then + echo " PASSED datasets.H5Ex_D_UnlimitedMod" +else + echo "**FAILED** datasets.H5Ex_D_UnlimitedMod" + nerrors="`expr $nerrors + 1`" +fi + +echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Nbit" +($JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Nbit > H5Ex_D_Nbit.out) +if diff H5Ex_D_Nbit.out examples.datasets.H5Ex_D_Nbit.txt > /dev/null; then + echo " PASSED datasets.H5Ex_D_Nbit" +else + echo "**FAILED** datasets.H5Ex_D_Nbit" + nerrors="`expr $nerrors + 1`" +fi + +echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Transform" +($JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Transform > H5Ex_D_Transform.out) +if diff H5Ex_D_Transform.out examples.datasets.H5Ex_D_Transform.txt > /dev/null; then + echo " PASSED datasets.H5Ex_D_Transform" +else + echo "**FAILED** datasets.H5Ex_D_Transform" + nerrors="`expr $nerrors + 1`" +fi + +echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Sofloat" +($JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Sofloat > H5Ex_D_Sofloat.out) +if diff H5Ex_D_Sofloat.out examples.datasets.H5Ex_D_Sofloat.txt > /dev/null; then + echo " PASSED datasets.H5Ex_D_Sofloat" +else + echo "**FAILED** datasets.H5Ex_D_Sofloat" + nerrors="`expr $nerrors + 1`" +fi + +echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Soint" +($JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Soint > H5Ex_D_Soint.out) +if diff H5Ex_D_Soint.out examples.datasets.H5Ex_D_Soint.txt > /dev/null; then + echo " PASSED datasets.H5Ex_D_Soint" +else + echo "**FAILED** datasets.H5Ex_D_Soint" + nerrors="`expr $nerrors + 1`" +fi + +# Clean up temporary files/directories +CLEAN_LIBFILES_AND_BLDLIBDIR +CLEAN_DATAFILES_AND_BLDDIR + +# Report test results and exit +if test $nerrors -eq 0 ; then + echo "All $TESTNAME tests passed." + exit $EXIT_SUCCESS +else + echo "$TESTNAME tests failed with $nerrors errors." + exit $EXIT_FAILURE +fi |