Build status for all platforms: 
Commercial support:
This directory contains the JavaCPP Presets module for:
- HDF5 1.12.2 https://support.hdfgroup.org/HDF5/
Please refer to the parent README.md file for more detailed information about the JavaCPP Presets.
Java API documentation is available here:
Here is a simple example of HDF5 ported to Java from this C++ source file:
We can use Maven 3 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 H5tutrCmprss.java source files below, simply execute on the command line:
$ mvn compile exec:java<project>
<modelVersion>4.0.0</modelVersion>
<groupId>org.bytedeco.hdf5</groupId>
<artifactId>H5tutrCmprss</artifactId>
<version>1.5.8-SNAPSHOT</version>
<properties>
<exec.mainClass>H5tutrCmprss</exec.mainClass>
</properties>
<dependencies>
<dependency>
<groupId>org.bytedeco</groupId>
<artifactId>hdf5-platform</artifactId>
<version>1.12.2-1.5.8-SNAPSHOT</version>
</dependency>
</dependencies>
<build>
<sourceDirectory>.</sourceDirectory>
</build>
</project>/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*
* This example illustrates how to create a compressed dataset.
* It is used in the HDF5 Tutorial.
*/
import java.io.*;
import org.bytedeco.javacpp.*;
import org.bytedeco.hdf5.*;
import static org.bytedeco.hdf5.global.hdf5.*;
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;
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];
// 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.hdf5.Exception.dontPrint();
// Create a new file using the default property lists.
H5File file = new H5File(FILE_NAME, H5F_ACC_TRUNC);
// Create the data space for the dataset.
DataSpace dataspace = new DataSpace(2, dims);
// Modify dataset creation property to enable chunking
DSetCreatPropList plist = new DSetCreatPropList();
plist.setChunk(2, chunk_dims);
// Set ZLIB (DEFLATE) Compression using level 6.
// To use SZIP compression comment out this line.
plist.setDeflate(6);
// 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);
// Create the dataset.
DataSet dataset = new DataSet(file.createDataSet(DATASET_NAME,
new DataType(PredType.STD_I32BE()), dataspace, plist, null, null));
for (int i = 0; i < DIM0; i++)
for (int j = 0; j < DIM1; j++)
buf[i * DIM1 + j] = i + j;
// Write data to dataset.
dataset.write(new IntPointer(buf), new DataType(PredType.NATIVE_INT()));
// Close objects and file. Either approach will close the HDF5 item.
dataspace.close();
dataset.close();
plist.close();
file.close();
// -----------------------------------------------
// Re-open the file and dataset, retrieve filter
// information for dataset and read the data back.
// -----------------------------------------------
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;
// Open the file and the dataset in the file.
file = new H5File();
file.openFile(FILE_NAME, H5F_ACC_RDONLY);
dataset = new DataSet(file.openDataSet(DATASET_NAME));
// Get the create property list of the dataset.
plist = new DSetCreatPropList(dataset.getCreatePlist());
// Get the number of filters associated with the dataset.
numfilt = plist.getNfilters();
System.out.println("Number of filters associated with dataset: " + numfilt);
for (int idx = 0; idx < numfilt; idx++) {
nelmts = 0;
filter_type = plist.getFilter(idx, flags, new SizeTPointer(1).put(nelmts), cd_values, namelen, name, filter_info);
System.out.print("Filter Type: ");
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.");
}
}
// Read data.
IntPointer p = new IntPointer(rbuf);
dataset.read(p, PredType.NATIVE_INT());
p.get(rbuf);
plist.close();
dataset.close();
file.close(); // can be skipped
} // end of try block
// catch failure caused by the H5File, DataSet, and DataSpace operations
catch (RuntimeException error) {
System.err.println(error);
error.printStackTrace();
System.exit(-1);
}
System.exit(0); // successfully terminated
}
}