attached is an example of writing a pdf file to an HDF5 dataset of opaque.
On 3/6/2012 2:54 AM, kuki wrote:
Hi people..
i am very new to hdf5
i have an object (message is the name of the object in the given code)which
carries a serialized text.
i want to write it to hdf5 file using opaque data type specifically.
how do i go about doing it?
private static int count = 0;
public static void record(Message message)
{
try
{
BufferedOutputStream buf=new BufferedOutputStream(new
FileOutputStream("E:/proj/"+count+".bin"));
byte[] b =serializer.serialize(message);
buf.write(b);
buf.flush();
count++;
}
catch(Exception e){}
}
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Thank you!
--pc
import java.io.BufferedInputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.util.StringTokenizer;
import ncsa.hdf.hdf5lib.H5;
import ncsa.hdf.hdf5lib.HDF5Constants;
import ncsa.hdf.hdf5lib.exceptions.HDF5Exception;
public class PDF2H5 {
private String gName = "/";
private int pdfToH5(String fname, String h5Name, String dname) throws IOException {
int fid = -1;
// create HDF5 file
try {
fid = H5.H5Fcreate(h5Name, HDF5Constants.H5F_ACC_TRUNC,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
} catch (HDF5Exception ex) {
ex.printStackTrace();
System.exit(0);
}
int idx = dname.lastIndexOf('/');
if (idx > 0) {
gName = dname.substring(0, idx);
try {
createH5Group(fid, gName);
} catch (Exception ex) {
}
}
try {
createH5Dataset(fid, dname, fname);
} catch (Exception ex) {
ex.printStackTrace();
return fid;
}
return fid;
}
private void createH5Group(int fid, String gname) throws Exception {
int gid = -1;
if (fid < 0 || gname == null || gname.length() <= 0)
return;
StringTokenizer st = new StringTokenizer(gname, "/");
gname = "";
while (st.hasMoreTokens()) {
gname += "/" + st.nextToken();
gid = -1;
try {
gid = H5.H5Gopen(fid, gname);
} catch (Exception ex) {
}
if (gid < 0) // group does not exist
gid = H5.H5Gcreate(fid, gname, 0);
try {
H5.H5Gclose(gid);
} catch (Exception ex) {
}
}
}
private boolean createH5Dataset(int fid, String dsetName, String fname)
throws Exception {
int did = -1, tid = -1, sid = -1;
long size = (new File(fname)).length();
long dims[] = {size};
if (size <=0)
return false; // nothing to write
tid = H5.H5Tcreate (HDF5Constants.H5T_OPAQUE, 1);
H5.H5Tset_tag (tid, "Content-Type: application/pdf");
sid = H5.H5Screate_simple (1, dims, null);
did = H5.H5Dcreate (fid, dsetName, tid, sid, HDF5Constants.H5P_DEFAULT);
BufferedInputStream bufferedInput = null;
byte[] buffer = new byte[(int)size];
bufferedInput = new BufferedInputStream(new FileInputStream(fname));
bufferedInput.read(buffer);
H5.H5Dwrite (did, tid, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, buffer);
try {
H5.H5Tclose(tid);
} catch (HDF5Exception ex) {
}
try {
H5.H5Sclose(sid);
} catch (HDF5Exception ex) {
}
try {
H5.H5Dclose(did);
} catch (HDF5Exception ex) {
}
return (did > 0);
}
/**
* Closes file associated with this H5File instance.
*
* @see ncsa.hdf.object.FileFormat#close()
* @throws HDF5Exception
*/
private void closeH5File(int fid) throws HDF5Exception {
// Close all open objects associated with this file.
int n = 0, type = -1, oids[];
if (fid < 0)
return;
n = H5.H5Fget_obj_count(fid, HDF5Constants.H5F_OBJ_ALL);
if (n > 0) {
oids = new int[n];
H5.H5Fget_obj_ids(fid, HDF5Constants.H5F_OBJ_ALL, n, oids);
for (int i = 0; i < n; i++) {
type = H5.H5Iget_type(oids[i]);
if (HDF5Constants.H5I_DATASET == type) {
try {
H5.H5Dclose(oids[i]);
} catch (Exception ex2) {
}
} else if (HDF5Constants.H5I_GROUP == type) {
try {
H5.H5Gclose(oids[i]);
} catch (Exception ex2) {
}
} else if (HDF5Constants.H5I_DATATYPE == type) {
try {
H5.H5Tclose(oids[i]);
} catch (Exception ex2) {
}
} else if (HDF5Constants.H5I_ATTR == type) {
try {
H5.H5Aclose(oids[i]);
} catch (Exception ex2) {
}
}
} // for (int i=0; i<n; i++)
} // if ( n>0)
try {
H5.H5Fflush(fid, HDF5Constants.H5F_SCOPE_GLOBAL);
} catch (Exception ex) {
}
try {
H5.H5Fclose(fid);
} catch (Exception ex) {
}
}
/**
* @param args
*/
public static void main(String[] args) {
String dsetName = null, fname = null, h5Name = null;
// Validate input.
if (args.length < 1) {
System.out.println("Usage: java PDF2H5 [OPTIONS] pdf_filename.");
System.out.println(" OPTIONS:");
System.out
.println(" \t--dset_name name\tName of the HDF5 dataset, e.g. \"dset\" or \"/g1/dset\".");
System.out
.println(" \t--output h5_filename\tName of the output HDF5 file.");
System.exit(-1);
}
int idx = 0;
for (int i = 0; i < args.length; i++) {
if ("--dset_name".equalsIgnoreCase(args[i])) {
dsetName = args[i + 1];
idx = i + 2;
} else if ("--output".equalsIgnoreCase(args[i])) {
h5Name = args[i + 1];
idx = i + 2;
}
}
fname = args[idx];
PDF2H5 t2h5 = new PDF2H5();
try {
int fid = t2h5.pdfToH5(fname, h5Name, dsetName);
t2h5.closeH5File(fid);
} catch (Exception ex) {
ex.printStackTrace();
}
}
}
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