[Pytables-users] Problems with chunked datasets

[Antonio V. <val...@co...>]

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

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

this is the test program

# BEGIN file test-uchar.py
import tables
h5file = tables.openFile('data.h5')
print h5file
# END file test-uchar.py

an this is the data

# chunk (128x128x2)

[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 ) }
   }
}
}

When i run the test program i get a segfault

[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


If I try it with a *non* chunked dataset ...

[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 += str(leaf) + '\n'
  File "/usr/lib/python2.3/site-packages/tables/Leaf.py", line 472, in
__str__
    title = self.attrs.TITLE
  File "/usr/lib/python2.3/site-packages/tables/AttributeSet.py", line
166, in __getattr__
    raise AttributeError, \

[SNIP]

  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 = 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


in this case the file seems to be correctly opened but some problem is
met in the print statement.

antonio


-- 
Antonio Valentino
Consorzio Innova S.r.l.
via della Scienza - Zona Paip I
75100 Matera (MT) Italy
Tel.:      +39 0835 309180
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Home Page: www.consorzio-innova.it
Email:     val...@co...