On 11/16/10 8:44 AM, Gerrit Holl wrote:
> [Gerrit Holl]
>>> I am moving from NetCDF to HDF5. In NetCDF, I can assign attributes to
>>> each variable/column. That is very useful for self-documenting the
>>> file like this:
>>>
>>> double AVHRR_LONG(Collocations) ;
>>> AVHRR_LONG:long_name = "AVHRR Longitude" ;
>>> AVHRR_LONG:units = "degrees_east" ;
>>> AVHRR_LONG:valid_range = -180., 180. ;
>>>
>>> I know that in HDF5, I can assign attributes to each node. But I think
>>> the columns of a table are not nodes. Is there an equivalent in HDF5
>>> to NetCDF's variable attributes? How would I use this in pytables?
> [Jeff Whitaker]
>> Gerrit: Are you aware that if you use netcdf 4, then your data is
>> actually saved in an HDF5 file (readable by hdf5 and netcdf clients)?
> A bit, but I don't understand the details of it. I should specify that
> I was using NetCDF 3 before.
>
> But then how would I use all of pytables' nice HDF5 features (blosc
> compression, fast searching, possibly indexing if I buy the
> professional version) in a NetCDF4 file? Some combination of your
> netcdf4-python with pytables?
Gerrit: You can use zlib compression (with the shuffle filter) with
netcdf, but not those other features you mention. It's possible that a
netcdf 4 compatible HDF file can be opened with pytables, but I've
never tried that. The main benefit of sticking to the netcdf api for
creating HDF5 is interoperability - netcdf is pretty much the de-facto
standard in the geophysical sciences.
-Jeff
> [David E. Sallis]
>> You can store arbitrary key/value pairs on a node by using the node's
>> _f_setAttr() method. I use this frequently and in much the same way as in
>> your
>> example. The key is the column name, and the value is a Python dictionary
>> containing the long name, units, etc.
>>
>> Example: n._f_setAttr('AVHRR_LONG':{'long_name':'AVHRR_Longitude',
>> 'units':'degrees_east', 'valid_range':(-180.0,180.0)})
> What is 'n' in this case? The table containing those columns? So then
> I actually set the properties to the table, with property names equal
> to the column, rather than setting properties to the variable, or am I
> misunderstanding things?
>
> Gerrit.
>
--
Jeffrey S. Whitaker Phone : (303)497-6313
Meteorologist FAX : (303)497-6449
NOAA/OAR/PSD R/PSD1 Email : [email protected]
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