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| Original file line number | Diff line number | Diff line change |
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| Copyright Notice and License Terms for | ||
| HDF5 (Hierarchical Data Format 5) Software Library and Utilities | ||
| ----------------------------------------------------------------------------- | ||
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| HDF5 (Hierarchical Data Format 5) Software Library and Utilities | ||
| Copyright 2006-2016 by The HDF Group. | ||
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| NCSA HDF5 (Hierarchical Data Format 5) Software Library and Utilities | ||
| Copyright 1998-2006 by the Board of Trustees of the University of Illinois. | ||
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| All rights reserved. | ||
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| Redistribution and use in source and binary forms, with or without | ||
| modification, are permitted for any purpose (including commercial purposes) | ||
| provided that the following conditions are met: | ||
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| 1. Redistributions of source code must retain the above copyright notice, | ||
| this list of conditions, and the following disclaimer. | ||
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| 2. Redistributions in binary form must reproduce the above copyright notice, | ||
| this list of conditions, and the following disclaimer in the documentation | ||
| and/or materials provided with the distribution. | ||
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| 3. In addition, redistributions of modified forms of the source or binary | ||
| code must carry prominent notices stating that the original code was | ||
| changed and the date of the change. | ||
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| 4. All publications or advertising materials mentioning features or use of | ||
| this software are asked, but not required, to acknowledge that it was | ||
| developed by The HDF Group and by the National Center for Supercomputing | ||
| Applications at the University of Illinois at Urbana-Champaign and | ||
| credit the contributors. | ||
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| 5. Neither the name of The HDF Group, the name of the University, nor the | ||
| name of any Contributor may be used to endorse or promote products derived | ||
| from this software without specific prior written permission from | ||
| The HDF Group, the University, or the Contributor, respectively. | ||
|
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| DISCLAIMER: | ||
| THIS SOFTWARE IS PROVIDED BY THE HDF GROUP AND THE CONTRIBUTORS | ||
| "AS IS" WITH NO WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED. In no | ||
| event shall The HDF Group or the Contributors be liable for any damages | ||
| suffered by the users arising out of the use of this software, even if | ||
| advised of the possibility of such damage. | ||
|
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| ----------------------------------------------------------------------------- | ||
| ----------------------------------------------------------------------------- | ||
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| Contributors: National Center for Supercomputing Applications (NCSA) at | ||
| the University of Illinois, Fortner Software, Unidata Program Center (netCDF), | ||
| The Independent JPEG Group (JPEG), Jean-loup Gailly and Mark Adler (gzip), | ||
| and Digital Equipment Corporation (DEC). | ||
|
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| ----------------------------------------------------------------------------- | ||
|
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| Portions of HDF5 were developed with support from the Lawrence Berkeley | ||
| National Laboratory (LBNL) and the United States Department of Energy | ||
| under Prime Contract No. DE-AC02-05CH11231. | ||
|
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| ----------------------------------------------------------------------------- | ||
|
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| Portions of HDF5 were developed with support from the University of | ||
| California, Lawrence Livermore National Laboratory (UC LLNL). | ||
| The following statement applies to those portions of the product and must | ||
| be retained in any redistribution of source code, binaries, documentation, | ||
| and/or accompanying materials: | ||
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| This work was partially produced at the University of California, | ||
| Lawrence Livermore National Laboratory (UC LLNL) under contract | ||
| no. W-7405-ENG-48 (Contract 48) between the U.S. Department of Energy | ||
| (DOE) and The Regents of the University of California (University) | ||
| for the operation of UC LLNL. | ||
|
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| DISCLAIMER: | ||
| This work was prepared as an account of work sponsored by an agency of | ||
| the United States Government. Neither the United States Government nor | ||
| the University of California nor any of their employees, makes any | ||
| warranty, express or implied, or assumes any liability or responsibility | ||
| for the accuracy, completeness, or usefulness of any information, | ||
| apparatus, product, or process disclosed, or represents that its use | ||
| would not infringe privately- owned rights. Reference herein to any | ||
| specific commercial products, process, or service by trade name, | ||
| trademark, manufacturer, or otherwise, does not necessarily constitute | ||
| or imply its endorsement, recommendation, or favoring by the United | ||
| States Government or the University of California. The views and | ||
| opinions of authors expressed herein do not necessarily state or reflect | ||
| those of the United States Government or the University of California, | ||
| and shall not be used for advertising or product endorsement purposes. | ||
|
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| ----------------------------------------------------------------------------- | ||
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| HDF5 is available with the SZIP compression library but SZIP is not part | ||
| of HDF5 and has separate copyright and license terms. See “Szip Compression | ||
| in HDF Products” (www.hdfgroup.org/doc_resource/SZIP/) for further details. | ||
|
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| ----------------------------------------------------------------------------- | ||
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| JavaCPP Presets for HDF5 | ||
| ======================== | ||
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| Introduction | ||
| ------------ | ||
| This directory contains the JavaCPP Presets module for: | ||
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| * HDF5 1.10.0-patch1 https://support.hdfgroup.org/HDF5/ | ||
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| Please refer to the parent README.md file for more detailed information about the JavaCPP Presets. | ||
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| Documentation | ||
| ------------- | ||
| Java API documentation is available here: | ||
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| * http://bytedeco.org/javacpp-presets/hdf5/apidocs/ | ||
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| Sample Usage | ||
| ------------ | ||
| Here is a simple example of HDF5 ported to Java from this C++ source file: | ||
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| * https://support.hdfgroup.org/ftp/HDF5/current/src/unpacked/c++/examples/h5tutr_cmprss.cpp | ||
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| We can use [Maven 3](http://maven.apache.org/) to download and install automatically all the class files as well as the native binaries. To run this sample code, after creating the `pom.xml` and `src/main/java/H5tutrCmprss.java` source files below, simply execute on the command line: | ||
| ```bash | ||
| $ mvn compile exec:java | ||
| ``` | ||
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| ### The `pom.xml` build file | ||
| ```xml | ||
| <project> | ||
| <modelVersion>4.0.0</modelVersion> | ||
| <groupId>org.bytedeco.javacpp-presets.hdf5</groupId> | ||
| <artifactId>H5tutrCmprss</artifactId> | ||
| <version>1.2.5-SNAPSHOT</version> | ||
| <properties> | ||
| <exec.mainClass>H5tutrCmprss</exec.mainClass> | ||
| </properties> | ||
| <dependencies> | ||
| <dependency> | ||
| <groupId>org.bytedeco.javacpp-presets</groupId> | ||
| <artifactId>hdf5</artifactId> | ||
| <version>1.10.0-patch1-1.2.5-SNAPSHOT</version> | ||
| </dependency> | ||
| </dependencies> | ||
| </project> | ||
| ``` | ||
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| ### The `src/main/java/H5tutrCmprss.java` source file | ||
| ```java | ||
| /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * | ||
| * 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 * | ||
| * https://support.hdfgroup.org/HDF5/doc/Copyright.html. If you do not have * | ||
| * access to either file, you may request a copy from help@hdfgroup.org. * | ||
| * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ | ||
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| /* | ||
| * This example illustrates how to create a compressed dataset. | ||
| * It is used in the HDF5 Tutorial. | ||
| */ | ||
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| import java.io.*; | ||
| import org.bytedeco.javacpp.*; | ||
| import static org.bytedeco.javacpp.hdf5.*; | ||
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| public class H5tutrCmprss { | ||
| static final String FILE_NAME = "h5tutr_cmprss.h5"; | ||
| static final String DATASET_NAME = "Compressed_Data"; | ||
| static final int DIM0 = 100; | ||
| static final int DIM1 = 20; | ||
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| public static void main(String[] args) { | ||
| long[] dims = { DIM0, DIM1 }; // dataset dimensions | ||
| long[] chunk_dims = { 20, 20 }; // chunk dimensions | ||
| int[] buf = new int[DIM0 * DIM1]; | ||
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| // Try block to detect exceptions raised by any of the calls inside it | ||
| try { | ||
| // Turn off the auto-printing when failure occurs so that we can | ||
| // handle the errors appropriately | ||
| org.bytedeco.javacpp.hdf5.Exception.dontPrint(); | ||
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| // Create a new file using the default property lists. | ||
| H5File file = new H5File(FILE_NAME, H5F_ACC_TRUNC); | ||
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| // Create the data space for the dataset. | ||
| DataSpace dataspace = new DataSpace(2, dims); | ||
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| // Modify dataset creation property to enable chunking | ||
| DSetCreatPropList plist = new DSetCreatPropList(); | ||
| plist.setChunk(2, chunk_dims); | ||
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| // Set ZLIB (DEFLATE) Compression using level 6. | ||
| // To use SZIP compression comment out this line. | ||
| plist.setDeflate(6); | ||
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| // Uncomment these lines to set SZIP Compression | ||
| // unsigned szip_options_mask = H5_SZIP_NN_OPTION_MASK; | ||
| // unsigned szip_pixels_per_block = 16; | ||
| // plist->setSzip(szip_options_mask, szip_pixels_per_block); | ||
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| // Create the dataset. | ||
| DataSet dataset = new DataSet(file.asCommonFG().createDataSet(DATASET_NAME, | ||
| new DataType(PredType.STD_I32BE()), dataspace, plist)); | ||
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| for (int i = 0; i < DIM0; i++) | ||
| for (int j = 0; j < DIM1; j++) | ||
| buf[i * DIM1 + j] = i + j; | ||
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| // Write data to dataset. | ||
| dataset.write(new IntPointer(buf), new DataType(PredType.NATIVE_INT())); | ||
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| // Close objects and file. Either approach will close the HDF5 item. | ||
| dataspace.close(); | ||
| dataset.close(); | ||
| plist.close(); | ||
| file.close(); | ||
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| // ----------------------------------------------- | ||
| // Re-open the file and dataset, retrieve filter | ||
| // information for dataset and read the data back. | ||
| // ----------------------------------------------- | ||
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| int[] rbuf = new int[DIM0 * DIM1]; | ||
| int numfilt; | ||
| long nelmts = 1, namelen = 1; | ||
| int[] flags = new int[1], filter_info = new int[1], cd_values = new int[1]; | ||
| byte[] name = new byte[1]; | ||
| int filter_type; | ||
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| // Open the file and the dataset in the file. | ||
| file = new H5File(); | ||
| file.openFile(FILE_NAME, H5F_ACC_RDONLY); | ||
| dataset = new DataSet(file.asCommonFG().openDataSet(DATASET_NAME)); | ||
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| // Get the create property list of the dataset. | ||
| plist = new DSetCreatPropList(dataset.getCreatePlist()); | ||
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| // Get the number of filters associated with the dataset. | ||
| numfilt = plist.getNfilters(); | ||
| System.out.println("Number of filters associated with dataset: " + numfilt); | ||
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| for (int idx = 0; idx < numfilt; idx++) { | ||
| nelmts = 0; | ||
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| filter_type = plist.getFilter(idx, flags, new SizeTPointer(1).put(nelmts), cd_values, namelen, name, filter_info); | ||
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| System.out.print("Filter Type: "); | ||
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| switch (filter_type) { | ||
| case H5Z_FILTER_DEFLATE: | ||
| System.out.println("H5Z_FILTER_DEFLATE"); | ||
| break; | ||
| case H5Z_FILTER_SZIP: | ||
| System.out.println("H5Z_FILTER_SZIP"); | ||
| break; | ||
| default: | ||
| System.out.println("Other filter type included."); | ||
| } | ||
| } | ||
|
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| // Read data. | ||
| IntPointer p = new IntPointer(rbuf); | ||
| dataset.read(p, PredType.NATIVE_INT()); | ||
| p.get(rbuf); | ||
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| plist.close(); | ||
| dataset.close(); | ||
| file.close(); // can be skipped | ||
|
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| } // end of try block | ||
|
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| // catch failure caused by the H5File, DataSet, and DataSpace operations | ||
| catch (RuntimeException error) { | ||
| System.err.println(error); | ||
| error.printStackTrace(); | ||
| System.exit(-1); | ||
| } | ||
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| System.exit(0); // successfully terminated | ||
| } | ||
| } | ||
| ``` |
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| #!/bin/bash | ||
| # This file is meant to be included by the parent cppbuild.sh script | ||
| if [[ -z "$PLATFORM" ]]; then | ||
| pushd .. | ||
| bash cppbuild.sh "$@" hdf5 | ||
| popd | ||
| exit | ||
| fi | ||
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| HDF5_VERSION=1.10.0-patch1 | ||
| download https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-$HDF5_VERSION/src/hdf5-$HDF5_VERSION.tar.bz2 hdf5-$HDF5_VERSION.tar.bz2 | ||
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| mkdir -p $PLATFORM | ||
| cd $PLATFORM | ||
| INSTALL_PATH=`pwd` | ||
| tar -xvf ../hdf5-$HDF5_VERSION.tar.bz2 | ||
| cd hdf5-$HDF5_VERSION | ||
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| case $PLATFORM in | ||
| android-arm) | ||
| patch -Np1 < ../../../hdf5-$HDF5_VERSION-android.patch | ||
| ./configure --prefix=$INSTALL_PATH --host="arm-linux-androideabi" --with-sysroot="$ANDROID_ROOT" AR="$ANDROID_BIN-ar" RANLIB="$ANDROID_BIN-ranlib" CPP="$ANDROID_BIN-cpp" CC="$ANDROID_BIN-gcc" CXX="$ANDROID_BIN-g++" STRIP="$ANDROID_BIN-strip" CPPFLAGS="--sysroot=$ANDROID_ROOT -DANDROID -I$ANDROID_CPP/include/ -I$ANDROID_CPP/include/backward/ -I$ANDROID_CPP/libs/armeabi/include/ -fPIC -ffunction-sections -funwind-tables -fstack-protector -march=armv7-a -mfloat-abi=softfp -mfpu=vfpv3-d16 -fomit-frame-pointer -fstrict-aliasing -funswitch-loops -finline-limit=300" LDFLAGS="-L$ANDROID_ROOT/usr/lib/ -L$ANDROID_CPP/libs/armeabi/ -nostdlib -Wl,--fix-cortex-a8 -z text -L./" LIBS="-lgnustl_static -lgcc -ldl -lz -lm -lc" --without-getpwuid --enable-cxx | ||
| make -j $MAKEJ | ||
| make install-strip | ||
| ;; | ||
| android-x86) | ||
| patch -Np1 < ../../../hdf5-$HDF5_VERSION-android.patch | ||
| ./configure --prefix=$INSTALL_PATH --host="i686-linux-android" --with-sysroot="$ANDROID_ROOT" AR="$ANDROID_BIN-ar" RANLIB="$ANDROID_BIN-ranlib" CPP="$ANDROID_BIN-cpp" CC="$ANDROID_BIN-gcc" CXX="$ANDROID_BIN-g++" STRIP="$ANDROID_BIN-strip" CPPFLAGS="--sysroot=$ANDROID_ROOT -DANDROID -I$ANDROID_CPP/include/ -I$ANDROID_CPP/include/backward/ -I$ANDROID_CPP/libs/x86/include/ -fPIC -ffunction-sections -funwind-tables -mssse3 -mfpmath=sse -fomit-frame-pointer -fstrict-aliasing -funswitch-loops -finline-limit=300" LDFLAGS="-L$ANDROID_ROOT/usr/lib/ -L$ANDROID_CPP/libs/x86/ -nostdlib -z text -L." LIBS="-lgnustl_static -lgcc -ldl -lz -lm -lc" --without-getpwuid --enable-cxx | ||
| make -j $MAKEJ | ||
| make install-strip | ||
| ;; | ||
| linux-x86) | ||
| ./configure --prefix=$INSTALL_PATH CC="$OLDCC -m32" CXX="$OLDCXX -m32" --enable-cxx | ||
| make -j $MAKEJ | ||
| make install-strip | ||
| ;; | ||
| linux-armhf) | ||
| ./configure --prefix=$INSTALL_PATH --host="arm-linux-gnueabihf" CC="arm-linux-gnueabihf-gcc" CXX="arm-linux-gnueabihf-g++" --enable-cxx | ||
| make -j $MAKEJ | ||
| make install-strip | ||
| ;; | ||
| linux-x86_64) | ||
| ./configure --prefix=$INSTALL_PATH CC="$OLDCC -m64" CXX="$OLDCXX -m64" --enable-cxx | ||
| make -j $MAKEJ | ||
| make install-strip | ||
| ;; | ||
| linux-ppc64le) | ||
| ./configure --prefix=$INSTALL_PATH CC="$OLDCC -m64" CXX="$OLDCXX -m64" --enable-cxx | ||
| make -j $MAKEJ | ||
| make install-strip | ||
| ;; | ||
| macosx-*) | ||
| ./configure --prefix=$INSTALL_PATH --enable-cxx | ||
| make -j $MAKEJ | ||
| make install-strip | ||
| ;; | ||
| windows-x86) | ||
| ./configure --prefix=$INSTALL_PATH --host="i686-w64-mingw32" CC="gcc -m32" CXX="g++ -m32" --enable-cxx | ||
| make -j $MAKEJ | ||
| make install-strip | ||
| ;; | ||
| windows-x86_64) | ||
| ./configure --prefix=$INSTALL_PATH --host="x86_64-w64-mingw32" CC="gcc -m64" CXX="g++ -m64" --enable-cxx | ||
| make -j $MAKEJ | ||
| make install-strip | ||
| ;; | ||
| *) | ||
| echo "Error: Platform \"$PLATFORM\" is not supported" | ||
| ;; | ||
| esac | ||
|
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| cd ../.. |
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