The limitation is stated at "About This Release", which is located at
the hdf-java top page.
We are going to have a separate page for known problems and limitations
so that users
can easily find the information.
Thanks
--pc
I seem to have an uncanny ability to find the unimplemented
features... Oh well, thanks for the info.
-Josiah
On 1/11/2011 4:59 PM, Peter Cao wrote:
The Java interface does not work on vlen except of vlen of strings.
In order to support vlen (other than strings) we need to map the
vlen_t data structure between C and Java, which is not implemented.
Thanks
--pc
On 1/11/2011 3:30 PM, Josiah Slack wrote:
Using h5ex_t_vlen.c as a rough model, I've taken a stab at a Java
version. Not surprisingly, it's failing.
Here's the code:
private static final String FNAME = "H5CreateVlen.h5";
private static double[] a = {1., 2., 3.};
private static double[] b = {1.};
private static double[][] allData = {
a, b
};
private static void createVlenCompound() throws Exception {
int DIM1 = 2;
long[] dims = {DIM1};
int fid = H5Fcreate(FNAME, HDF5Constants.H5F_ACC_TRUNC,
HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT);
int sid = H5Screate_simple(1, dims, null);
int tid = H5Tvlen_create(HDF5Constants.H5T_NATIVE_DOUBLE);
int did = H5Dcreate(fid, "ds1", tid, sid,
HDF5Constants.H5P_DEFAULT);
H5Dwrite(did, tid, HDF5Constants.H5S_ALL,
HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, allData);
H5Tclose(tid);
H5Sclose(sid);
H5Dclose(did);
H5Fclose(fid);
}
public static void main( String args[] ) throws Exception {
createVlenCompound();
}
Here's the stack trace:
Exception in thread "main" java.lang.IllegalArgumentException:
doubleToByte: start or len is out of bounds
at ncsa.hdf.hdf5lib.HDFNativeData.doubleToByte(Native Method)
at ncsa.hdf.hdf5lib.HDFArray.byteify(HDFArray.java:230)
at ncsa.hdf.hdf5lib.H5.H5Dwrite(H5.java:1172)
at ncsa.hdf.hdf5lib.H5.H5Dwrite(H5.java:1190)
at
javaExample.H5createVlen.createVlenCompound(H5createVlen.java:43)
at javaExample.H5createVlen.main(H5createVlen.java:51)
I didn't dig deep enough into the C++ to see how hvl_t (the datatype
being used in the sample) is defined, but it seems at the least to
have a pointer part and a size part. I was crossing my fingers that
the Java H5 class would use reflection or the like to derive the size
information needed.
Any further advice for me?
Thanks.
-Josiah
On 1/11/2011 11:06 AM, Josiah Slack wrote:
Thanks for the lead - I've grabbed the source and am about to look it
over.
-Josiah
On 1/11/2011 11:01 AM, Neil Fortner wrote:
Josiah,
There doesn't seem to be a Java example, but there is a C example:
http://www.hdfgroup.org/ftp/HDF5/examples/examples-by-api/hdf5-examples/1_8/C/H5T/h5ex_t_vlen.c
Also, is there a maximum size for the array of doubles? If so,
you may
be better off using a fixed length array and a separate field to
store
the actual length, then using compression to mostly eliminate the
wasted
space.
Thanks,
-Neil
On 01/11/2011 09:57 AM, Josiah Slack wrote:
I'll have a look, thanks.
-Josiah
On 1/11/2011 10:55 AM, Quincey Koziol wrote:
Hi Josiah,
On Jan 11, 2011, at 9:22 AM, Josiah Slack wrote:
Thanks. Can you point me to any examples using
H5Tvlen_create() in
context (preferably Java, but I'll take what I can get)?
Hmm, I don't see any code that uses H5Tvlen_create() in our
examples files, but you can look at test/tvltypes.c for examples of
how it's used in the context of our regression tests. Perhaps
Peter
has a pointer to a Java example...
Quincey
-Josiah
On 1/11/2011 7:44 AM, Quincey Koziol wrote:
Hi Josiah,
On Jan 10, 2011, at 3:00 PM, Josiah Slack wrote:
Hi folks -
I've got another naive question about building Datatypes.
I've got
a Datatype that I'm forming from arrays of doubles. Ultimately,
I'll be writing an array of this Datatype. The complicating
factor is that the arrays of doubles won't necessarily have the
same dimensions from one instance of the Datatype to the next.
Sounds like you might want a variable-length sequence of
doubles as your datatype. Look at the documentation for
H5Tvlen_create()...
Quincey
Here's a little pseudo-code to more concretely illustrate what I
mean:
Datatype {
double[] a;
double[][] b;
double[] c;
};
Datatype[] allData = {
{ a = {1., 2., 3.} } b = {{1.,2.},{3.,4.}}, c = {1.} },
{ a = {1.,} b = {{1.}}, c = {1., 2.} },
{ a = {}, b = {{1.}, {2.}}, c = {1., 2., 3.} }
};
I'm trying to use the Java H5 class to achieve this.
Thanks in advance for your time.
-Josiah
--
Josiah Slack
MIT Lincoln Laboratory
Group 36
[email protected]
Ph: (781) 981-1754
_______________________________________________
Hdf-forum is for HDF software users discussion.
[email protected]
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
_______________________________________________
Hdf-forum is for HDF software users discussion.
[email protected]
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
--
Josiah Slack
MIT Lincoln Laboratory
Group 36
[email protected]
Ph: (781) 981-1754
_______________________________________________
Hdf-forum is for HDF software users discussion.
[email protected]
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
_______________________________________________
Hdf-forum is for HDF software users discussion.
[email protected]
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
_______________________________________________
Hdf-forum is for HDF software users discussion.
[email protected]
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
_______________________________________________
Hdf-forum is for HDF software users discussion.
[email protected]
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
_______________________________________________
Hdf-forum is for HDF software users discussion.
[email protected]
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
