Hi folks -
I'm just starting to get familiar with the HDF Object API, and I'm
interested in creating a nested compound Dataset. I've been
experimenting with H5File.createCompoundDS(), and am getting the
following stack trace:
Exception in thread "main" ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException
at ncsa.hdf.hdf5lib.H5._H5Tarray_create(Native Method)
at ncsa.hdf.hdf5lib.H5.H5Tarray_create(H5.java:4411)
at ncsa.hdf.object.h5.H5CompoundDS.create(H5CompoundDS.java:1167)
at ncsa.hdf.object.h5.H5File.createCompoundDS(H5File.java:1147)
at javaExample.H5CompoundDSCreate.main(H5CompoundDSCreate.java:126)
My naive implementation looks like this:
// retrieve an instance of H5File
FileFormat fileFormat =
FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5);
if (fileFormat == null) {
System.err.println("Cannot find HDF5 FileFormat.");
return;
}
// create a new file with a given file name.
H5File testFile = (H5File)fileFormat.create(fname);
if (testFile == null) {
System.err.println("Failed to create file:"+fname);
return;
}
// open the file and retrieve the root group
testFile.open();
Group root =
(Group)((javax.swing.tree.DefaultMutableTreeNode)testFile.getRootNode()).getUserObject();
// create groups at the root
Group topLevel = testFile.createGroup("top level", root);
Group secondLevel = testFile.createGroup("second level", topLevel);
String[] memberNames = {
"time",
"distance"
};
Datatype[] memberDatatypes = new Datatype[] {
new H5Datatype(Datatype.CLASS_FLOAT, 8, Datatype.NATIVE, -1),
new H5Datatype(Datatype.CLASS_FLOAT, 8, Datatype.NATIVE, -1)
};
int[] memberSizes = {1, 1};
int numEntries = 10;
double[] time = new double[numEntries];
double[] distance = new double[numEntries];
Random random = new Random();
for (int ii = 0; ii < numEntries; ii++) {
time[ii] = random.nextDouble();
distance[ii] = 100.0*random.nextDouble();
}
Vector<Object> data = new Vector<Object>();
data.add(time);
data.add(distance);
long[] dims = { numEntries };
Dataset compoundDS = testFile.createCompoundDS("time distance",
secondLevel,
dims,
null,
null,
0,
memberNames,
memberDatatypes,
memberSizes,
data);
memberNames = new String[] {
"height",
"width",
"time distance"
};
memberDatatypes = new Datatype[] {
new H5Datatype(Datatype.CLASS_FLOAT, 8, Datatype.NATIVE, -1),
new H5Datatype(Datatype.CLASS_FLOAT, 8, Datatype.NATIVE, -1),
compoundDS.getDatatype()
};
memberSizes = new int[]{1, 1, 1};
double[] height = new double[] { random.nextDouble() };
double[] width = new double[] { random.nextDouble() };
Vector<Object> topLevelData = new Vector<Object>();
topLevelData.add(height);
topLevelData.add(width);
topLevelData.add(compoundDS.getData());
dims = new long[] {1};
Dataset topLevelDS = testFile.createCompoundDS("compound ds",
topLevel,
dims,
null,
null,
0,
memberNames,
memberDatatypes,
memberSizes,
topLevelData);
// close file resource
testFile.close();
Is there a standard idiom that people use for this sort of thing?
Thanks in advance for any guidance.
-Josiah
--
Josiah Slack
MIT Lincoln Laboratory
Group 36
[email protected]
Ph: (781) 981-1754
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