Re: [Pytables-users] Can't open the group: '/'. 'File' object has no attribute 'root'
Hi Chao, On 6/2/12 11:55 AM, Chao YUE wrote: > if I use gdalinfo to check the file: > chaoyue@chaoyue-Aspire-4750:~/Downloads/LISOTD$ gdalinfo > LISOTD_HRMC_V2.3.2011.hdf > Driver: HDF4/Hierarchical Data Format Release 4 [clip] This says that the file has HDF4 format, not HDF5. Please note that PyTables only can deal with HDF5 files. For HDF4 I'd rather use pyhdf: http://pysclint.sourceforge.net/pyhdf/ -- Francesc Alted -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Pytables-users mailing list Pytables-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pytables-users
Re: [Pytables-users] Can't open the group: '/'. 'File' object has no attribute 'root'
if I use gdalinfo to check the file:
chaoyue@chaoyue-Aspire-4750:~/Downloads/LISOTD$ gdalinfo
LISOTD_HRMC_V2.3.2011.hdf
Driver: HDF4/Hierarchical Data Format Release 4
Files: LISOTD_HRMC_V2.3.2011.hdf
Size is 512, 512
Coordinate System is `'
Subdatasets:
SUBDATASET_1_NAME=HDF4_SDS:UNKNOWN:"LISOTD_HRMC_V2.3.2011.hdf":0
SUBDATASET_1_DESC=[360x720x12] HRMC_COM_FR (32-bit floating-point)
SUBDATASET_2_NAME=HDF4_SDS:UNKNOWN:"LISOTD_HRMC_V2.3.2011.hdf":4
SUBDATASET_2_DESC=[360x720x12] HRSC_COM_FR (32-bit floating-point)
Corner Coordinates:
Upper Left (0.0,0.0)
Lower Left (0.0, 512.0)
Upper Right ( 512.0,0.0)
Lower Right ( 512.0, 512.0)
Center ( 256.0, 256.0)
Chao
2012/6/2 Chao YUE
> 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/ in ()
> > 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
> ---
> AttributeErrorTraceback (most recent call last)
> /home/chaoyue/Downloads/LISOTD/ in ()
> > 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
>
> --
>
> ***
[Pytables-users] Can't open the group: '/'. 'File' object has no attribute 'root'
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/ in ()
> 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
---
AttributeErrorTraceback (most recent call last)
/home/chaoyue/Downloads/LISOTD/ in ()
> 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
--
***
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
--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___
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