[Pytables-users] Can't open the group: '/'. 'File' object has no attribute 'root'

[Chao Y. <cha...@gm...>]

Dear all,

I tried to use pytalbes to read a hdf file, but I got error:
I searched a little bit online, there might be cases you have more than 2
file handlers for the same file and they are opened for both read and
write, you'll probably have this error.
But it's not my case that I open it only for the first time.  From the
error message, it seems that there is no root group.

In [1]: h5file=tables.openFile('LISOTD_HRMC_V2.3.2011.hdf','r')
---------------------------------------------------------------------------
HDF5ExtError                              Traceback (most recent call last)
/home/chaoyue/Downloads/LISOTD/<ipython-input-1-b53d861308cf> in <module>()
----> 1 h5file=tables.openFile('LISOTD_HRMC_V2.3.2011.hdf','r')

/usr/local/lib/python2.7/dist-packages/tables/file.pyc in
openFile(filename, mode, title, rootUEP, filters, **kwargs)
    256             return filehandle
    257     # Finally, create the File instance, and return it

--> 258     return File(filename, mode, title, rootUEP, filters, **kwargs)
    259
    260

/usr/local/lib/python2.7/dist-packages/tables/file.pyc in __init__(self,
filename, mode, title, rootUEP, filters, **kwargs)
    565
    566         # Get the root group from this file

--> 567         self.root = root = self.__getRootGroup(rootUEP, title,
filters)
    568         # Complete the creation of the root node

    569         # (see the explanation in ``RootGroup.__init__()``.


/usr/local/lib/python2.7/dist-packages/tables/file.pyc in
__getRootGroup(self, rootUEP, title, filters)
    614         # Create new attributes for the root Group instance and

    615         # create the object tree

--> 616         return RootGroup(self, rootUEP, title=title, new=new,
filters=filters)
    617
    618

/usr/local/lib/python2.7/dist-packages/tables/group.pyc in __init__(self,
ptFile, name, title, new, filters)
   1155         self._g_new(ptFile, name, init=True)
   1156         #   Open the node and get its object ID.

-> 1157         self._v_objectID = self._g_open()
   1158
   1159         # Set disk attributes and read children names.


/usr/local/lib/python2.7/dist-packages/tables/hdf5Extension.so in
tables.hdf5Extension.Group._g_open (tables/hdf5Extension.c:5521)()

HDF5ExtError: Can't open the group: '/'.

If I open the file with this command, it gave no error:

In [2]: h5file=tables.openFile('LISOTD_HRMC_V2.3.2011.hdf',mode='r')

But when I try to print the file information, I get:

In [3]: print h5file
Exception tables.exceptions.HDF5ExtError: HDF5ExtError('Problems closing
the Group /',) in  ignored
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
/home/chaoyue/Downloads/LISOTD/<ipython-input-3-64c76de88957> in <module>()
----> 1 print h5file

/usr/local/lib/python2.7/dist-packages/tables/file.pyc in __str__(self)
   2197         # Print all the nodes (Group and Leaf objects) on object
tree

   2198         date =
time.asctime(time.localtime(os.stat(self.filename)[8]))
-> 2199         astring =  self.filename + ' (File) ' + repr(self.title) +
'\n'
   2200 #         astring += 'rootUEP :=' + repr(self.rootUEP) + '; '

   2201 #         astring += 'format_version := ' + self.format_version +
'\n'


/usr/local/lib/python2.7/dist-packages/tables/file.pyc in _gettitle(self)
    474
    475     def _gettitle(self):
--> 476         return self.root._v_title
    477     def _settitle(self, title):
    478         self.root._v_title = title

AttributeError: 'File' object has no attribute 'root'

I have not too much experience handling HDF data but it's the second time I
have this problem.
In both cases the data are downloaded from official release of research
data so I think it's unlikely that the data itself are badly produced.
But if anyone has any interest trying to have a look of the issue, the data
is at:
ftp://ghrc.nsstc.nasa.gov/pub/lis/climatology/HRMC/data/

The ftp is anonymous and the data released by NASA.

thanks for any help in advance,

best regards,

Chao

-- 
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Chao YUE
Laboratoire des Sciences du Climat et de l'Environnement (LSCE-IPSL)
UMR 1572 CEA-CNRS-UVSQ
Batiment 712 - Pe 119
91191 GIF Sur YVETTE Cedex
Tel: (33) 01 69 08 29 02; Fax:01.69.08.77.16
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