(writing both to the forum & helpdesk, since the mailing list seems to
be down or in flux)
I have a set of C++ classes that creates an HDF5 file, and I am trying
to replace them (for maintainability & other reasons) with Java. I can't
figure out the right way in Java to read a file and store the results in
the HDF5 file as a compressed string, though. Here's what "h5ls -v -r"
shows for this dataset that I have created in C++:
/foo/bar/baz/ESPDF Dataset {1/1}
Location: 1:10744
Links: 1
Chunks: {1} 2656 bytes
Storage: 2656 logical bytes, 626 allocated bytes, 424.28%
utilization
Filter-0: deflate-1 OPT {9}
Type: 2656-byte null-terminated ASCII string
and here's my attempt at doing something like this in Java:
Group g;
FileChannel fileChannel;
ByteBuffer bbuf;
int x;
/* ... successfully-running (but not-very-relevant) code
removed
which sets up g, fileChannel and bbuf,
and counts the size of the input file with the result in
x...
The value of "x" could be large so I want to be able to
write the HDF5
dataset in smaller pieces rather than one big monolithic
chunk. */
long dims[] = {x};
long maxdims[] = dims;
long chunks[] = {1};
int gzip = 9;
// these following two lines are essentially verbatim
int tid = H5.H5Tcopy( HDF5Constants.H5T_C_S1);
H5.H5Tset_size(tid, x);
Datatype dtype = new H5Datatype(tid);
FileFormat ff = g.getFileFormat();
ncsa.hdf.object.Dataset ds = ff.createScalarDS(
"ESPDF", g, dtype, dims, maxdims,
chunks, gzip, null);
while (fileChannel.read(buffer) >= 0)
{
buffer.flip();
/* do something here to write the dataset to the
HDF5 file.
What? ds.write seems to expect
an array of Java strings, which makes no
sense. */
buffer.rewind();
}
--Jason
···
from my C++ program
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