Reading object references from Java

Hdf-forum archives
1

Hi everyone,

when I read an array of datatype "object reference" using the high-level Java interface, I get an array of long integers. How can I get the corresponding objects?

Thanks in advance,
   Konrad.

···

--
---------------------------------------------------------------------
Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: research AT khinsen DOT fastmail DOT net
---------------------------------------------------------------------

2

Try this:

···

===============
         // open the file and the dataset with refs
         file.open();
         ds = (H5ScalarDS)file.get(dname);
          long[] refs = (long[])ds.getData();

          // use low level API function, H5.H5Rget_name
            String[] name = {""};;
          for (int i=0; i<refs.length; i++) {
              H5.H5Rget_name(file.getFID(), HDF5Constants.H5R_OBJECT, HDFNativeData.longToByte(refs[i]), name, 32);
             System.out.println(name[0]);
         }

          // if file.open() was called, search objects in memory by high level function, findObject()
         long[] oid = new long[1];
         for (int i=0; i<refs.length; i++) {
             oid[0] = refs[i];
              HObject obj = FileFormat.findObject(file, oid);
             System.out.println(obj.getFullName());
         }

On 3/28/2011 6:07 AM, Konrad Hinsen wrote:

Hi everyone,

when I read an array of datatype "object reference" using the high-level Java interface, I get an array of long integers. How can I get the corresponding objects?

Thanks in advance,
    Konrad.
--
---------------------------------------------------------------------
Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: research AT khinsen DOT fastmail DOT net
---------------------------------------------------------------------

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

3

Thanks, that works fine!

Konrad.

···

On 28 Mar, 2011, at 19:11 , Peter Cao wrote:

Try this:

--
---------------------------------------------------------------------
Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: research AT khinsen DOT fastmail DOT net
---------------------------------------------------------------------

4

I am now at the point where I would like to write reference attributes as well. But what do I supply as the attribute value? I first tried to provide the objects themselves, but that results in invalid references. A look at the source code (H5File.java) shows that there is a special case for a single reference which can be supplied as a string (path to the object). So I tried an array of strings, but that also leads to invalid references. Do I have to use the low-level routines again for some conversion?

Konrad.

···

On 28 Mar, 2011, at 19:11 , Peter Cao wrote:

Try this:

===============
       // open the file and the dataset with refs
       file.open();
       ds = (H5ScalarDS)file.get(dname);
        long[] refs = (long[])ds.getData();

        // use low level API function, H5.H5Rget_name
          String[] name = {""};;
        for (int i=0; i<refs.length; i++) {
            H5.H5Rget_name(file.getFID(), HDF5Constants.H5R_OBJECT, HDFNativeData.longToByte(refs[i]), name, 32);
           System.out.println(name[0]);
       }

        // if file.open() was called, search objects in memory by high level function, findObject()
       long[] oid = new long[1];
       for (int i=0; i<refs.length; i++) {
           oid[0] = refs[i];
            HObject obj = FileFormat.findObject(file, oid);
           System.out.println(obj.getFullName());
       }

--
---------------------------------------------------------------------
Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: research AT khinsen DOT fastmail DOT net
---------------------------------------------------------------------

5

The best way to write ref attributes is to use a byte buffer.
However, if an attribute is a single value of reference, using
the object path will also work. Here is an example of using
both ways.

···

=======================================
         H5File file = new H5File(fname, H5File.CREATE);
         file.open();

         // create a ref dataset
         Group grp = file.createGroup("grp", null);
         Dataset ds = file.createScalarDS("dset", grp, new H5Datatype(Datatype.CLASS_FLOAT, -1, -1, -1), dims, maxdims, null, 0, data);
         ref_buf[0] = H5.H5Rcreate(file.getFID(), grp.getFullName(), HDF5Constants.H5R_OBJECT, -1);
         ref_buf[1] = H5.H5Rcreate(file.getFID(), ds.getFullName(), HDF5Constants.H5R_OBJECT, -1);
         ds = file.createScalarDS(dname, null, new H5Datatype(Datatype.CLASS_REFERENCE, -1, -1, -1), new long[] {2}, null, null, 0, ref_buf);

         // create ref attributes
         Datatype attr_dtype = file.createDatatype( Datatype.CLASS_REFERENCE, Datatype.NATIVE, Datatype.NATIVE, Datatype.NATIVE);
         Attribute attr = new Attribute("ref", attr_dtype, new long[] {1});
         attr.setValue(ds.getFullName());
         file.writeAttribute(ds, attr, false);
         attr = new Attribute("refs", attr_dtype, new long[] {2});
         attr.setValue(ref_buf);
         ds.writeMetadata(attr);

         file.close();

On 3/30/2011 9:11 AM, Konrad Hinsen wrote:

On 28 Mar, 2011, at 19:11 , Peter Cao wrote:

Try this:

===============
        // open the file and the dataset with refs
        file.open();
        ds = (H5ScalarDS)file.get(dname);
         long[] refs = (long[])ds.getData();

         // use low level API function, H5.H5Rget_name
           String[] name = {""};;
         for (int i=0; i<refs.length; i++) {
             H5.H5Rget_name(file.getFID(), HDF5Constants.H5R_OBJECT, HDFNativeData.longToByte(refs[i]), name, 32);
            System.out.println(name[0]);
        }

         // if file.open() was called, search objects in memory by high level function, findObject()
        long[] oid = new long[1];
        for (int i=0; i<refs.length; i++) {
            oid[0] = refs[i];
             HObject obj = FileFormat.findObject(file, oid);
            System.out.println(obj.getFullName());
        }

I am now at the point where I would like to write reference attributes as well. But what do I supply as the attribute value? I first tried to provide the objects themselves, but that results in invalid references. A look at the source code (H5File.java) shows that there is a special case for a single reference which can be supplied as a string (path to the object). So I tried an array of strings, but that also leads to invalid references. Do I have to use the low-level routines again for some conversion?

Konrad.
--
---------------------------------------------------------------------
Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: research AT khinsen DOT fastmail DOT net
---------------------------------------------------------------------

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org