Re: [Pytables-users] Problems with chunked datasets

[Francesc A. <fa...@ca...>]

Hi Antonio,

Can you send me privately both files so as to see what's going on with them?

Cheers,

A Diumenge 16 Gener 2005 16:19, Antonio Valentino va escriure:
> hi,
> I'm not an expert user and I'm having some problems trying to open an
> hdf5 file containing a chunked dataset.
> Here it is some infos
>=20
> Python 2.3.4
> [GCC 3.4.2 20041017 (Red Hat 3.4.2-6.fc3)] on linux2
> numarray v. 1.1.1
> tables v. 0.9.1
> hdf5   v. 1.6.3-patch
>=20
> this is the test program
>=20
> # BEGIN file test-uchar.py
> import tables
> h5file =3D tables.openFile('data.h5')
> print h5file
> # END file test-uchar.py
>=20
> an this is the data
>=20
> # chunk (128x128x2)
>=20
> [antonio@m6n h5]$ h5dump -A data.h5
> HDF5 "data.h5" {
> GROUP "/" {
>    DATASET "ComplexUCharArray" {
>       DATATYPE  H5T_STD_U8LE
>       DATASPACE  SIMPLE { ( 200, 150, 2 ) / ( 200, 150, 2 ) }
>    }
> }
> }
>=20
> When i run the test program i get a segfault
>=20
> [antonio@m6n h5]$ python test-uchar.py
> /usr/lib/python2.3/site-packages/tables/File.py:192: UserWarning:
> 'data.h5' does exist, is an HDF5 file, but has not a PyTables format.
> Trying toguess what's there using HDF5 metadata. I can't promise you
> getting the correctobjects, but I will do my best!.
>   path, UserWarning)
> Segmentation fault
>=20
>=20
> If I try it with a *non* chunked dataset ...
>=20
> [antonio@m6n h5]$ python test-uchar.py
> /usr/lib/python2.3/site-packages/tables/File.py:192: UserWarning:
> 'data.h5' does exist, is an HDF5 file, but has not a PyTables format.
> Trying to guess what's there using HDF5 metadata. I can't promise you
> getting the correct objects, but I will do my best!.
>   path, UserWarning)
> Traceback (most recent call last):
>   File "test-uchar.py", line 6, in ?
>     print h5file
>   File "/usr/lib/python2.3/site-packages/tables/File.py", line 1000, in
> __str__
>     astring +=3D str(leaf) + '\n'
>   File "/usr/lib/python2.3/site-packages/tables/Leaf.py", line 472, in
> __str__
>     title =3D self.attrs.TITLE
>   File "/usr/lib/python2.3/site-packages/tables/AttributeSet.py", line
> 166, in __getattr__
>     raise AttributeError, \
>=20
> [SNIP]
>=20
>   File "/usr/lib/python2.3/site-packages/tables/AttributeSet.py", line
> 166, in __getattr__
>     raise AttributeError, \
>   File "/usr/lib/python2.3/site-packages/tables/Leaf.py", line 472, in
> __str__
>     title =3D self.attrs.TITLE
>   File "/usr/lib/python2.3/site-packages/tables/Leaf.py", line 189, in
> _get_attrs
>     return AttributeSet(self)
> RuntimeError: maximum recursion depth exceeded
>=20
>=20
> in this case the file seems to be correctly opened but some problem is
> met in the print statement.
>=20
> antonio
>=20
>=20

=2D-=20
>OO< =A0 Francesc Altet    ||  http://www.carabos.com/
V =A0V =A0 Carabos Coop. V.  ||  Who is your data daddy? PyTables
 ""