This directory contains the JavaCPP Presets module for:
- HDF5 1.10.0-patch1 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 src/main/java/H5tutrCmprss.java source files below, simply execute on the command line:
$ mvn compile exec:java<project>
<modelVersion>4.0.0</modelVersion>
<groupId>org.bytedeco.javacpp-presets.hdf5</groupId>
<artifactId>H5tutrCmprss</artifactId>
<version>1.3</version>
<properties>
<exec.mainClass>H5tutrCmprss</exec.mainClass>
</properties>
<dependencies>
<dependency>
<groupId>org.bytedeco.javacpp-presets</groupId>
<artifactId>hdf5-platform</artifactId>
<version>1.10.0-patch1-1.3</version>
</dependency>
</dependencies>
</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 [email protected]. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*
* This example illustrates how to create a compressed dataset.
* It is used in the HDF5 Tutorial.
*/
import java.io.*;
import org.bytedeco.javacpp.*;
import static org.bytedeco.javacpp.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.javacpp.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.asCommonFG().createDataSet(DATASET_NAME,
new DataType(PredType.STD_I32BE()), dataspace, plist));
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.asCommonFG().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
}
}