It looks like I reduced by "minimal example" too far - the exception gets thrown if a dataset's name contains a symbol and you look at its properties in HDFView (new test file attached) - tested with HDFView 2.9 and 2.10 on Win7, 64-bit.
<image.png>
h5dump gives expected results:
HDF5 "test-symb.h5" {
GROUP "/" {
DATASET "data (°C)" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 3, 4 ) / ( 3, 4 ) }
DATA {
(0,0): 1, 2, 3, 4,
(1,0): 9, 8, 7, 6,
(2,0): 100, 200, 300, 400
}
ATTRIBUTE "name" {
DATATYPE H5T_STRING {
STRSIZE H5T_VARIABLE;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
DATA {
(0): "this is a test"
}
}
}
}
}
Potentially this is because reading the name incorrectly leads to a failure of probing the dataset's type (even though the program thinks it should exist!). Interestingly, if you create a group whose name is entirely symbols, it's interpreted as blank and turns into a link to the root node in HDFView!
Finally, if a compound type is created with a name containing a symbol (the original problem I had), that column is read out with default values (test-symb2.h5). Again, I assume this is because the read compound is not constructed correctly because of incorrect strings.
Cheers,
Martijn
On 27 December 2013 12:18, Elena Pourmal <epourmal@hdfgroup.org> wrote:
Hi Martijn,
I can reproduce "truncated" name with HDFView - ")" is missing, but I am not getting an exception with 2.10 on OS X 10.8.5. Which system are you using?
h5dump produces correct result:
HDF5 "test-symb.h5" {
GROUP "/" {
GROUP "T (°C)" {
}
}
}
HDFView output is attached.
I will enter a bug report to fix the name in HDFView, but we will need to reproduce the exception you are getting.
Thank you!
Elena
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Elena Pourmal The HDF Group http://hdfgroup.org
1800 So. Oak St., Suite 203, Champaign IL 61820
217.531.6112
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<HDFView-window.png>
On Dec 23, 2013, at 6:47 PM, Martijn Jasperse <m.jasperse@gmail.com> wrote:
Hi all,
I'm having some difficulty with HDFview when names (e.g. dataset names/compound member names) contain standard symbols (e.g. degrees °). HDF5 itself works fine, but unexpected behaviour is observed in HDFview (seen in both 2.9 and 2.10) - such objects cannot be opened or queried.
In the simplest example, I've created a dataset that cannot be opened in HDFview (double clicking the name has no effect), and choosing "Show Properties" on the dataset results in a java.lang.reflect.InvocationTargetException. Interestingly the last character of the dataset name is culled; which is potentially why there is an error.
The same dataset can be opened and queried in C as follows:
#include <hdf5.h>
#include <stdio.h>
int main()
{
char S[32];
hid_t f = H5Fopen( "test-symb.h5", H5P_DEFAULT,H5P_DEFAULT );
H5Lget_name_by_idx( f, ".", H5_INDEX_NAME, H5_ITER_DEC, 0, S, 32, H5P_DEFAULT );
H5Fclose( f );
puts( S );
}
Although some terminals have trouble with symbols, piping the output to a file shows the expected result "T (°C)"
Any ideas on why HDFview seems to have problems with it?
Merry Christmas all!
Cheers,
Martijn
<test-symb.h5>_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
<test-symb.h5><test-symb2.h5>_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
