Hi Francesc
Thanks for your reply. However, the reason I was using Tables is
because Arrays didn't seem to support compression algorithms, that is,
when I write all my data its larger in the hdf5 files than they are in
an ascii text file. I forget, but does EArray support compression?
thanks,
Grace
On Tue, Oct 12, 2010 at 2:22 PM, Francesc Alted <fal...@pytables.org> wrote:
> A Tuesday 12 October 2010 01:25:20 Grace Li escrigué:
>> Hi all,
>>
>> I read in the pytables user manual that description field of the
>> method tables.createTable can be a numpy array object and that if the
>> numpy array has data, the data will be directly appended into the
>> table created.
>> I was trying to do this for my data which is written in a txt file,
>> but encountered problems.
>>
>> First I used numpy.genfromtxt to create a numpy ndarray holding all
>> the data (the data is basically a homogeneous array with integer
>> types for the columns).
>> Then I passed this array object by doing
>>
>> data = genfromtxt('a.txt', dtype=None) # setting dype=None lets
>> genfromtxt automatically determine data types
>> #assume that h5file object exists
>> h5file.createTable('my_group', 'my_data', description=data)
>>
>> I get this exception:
>>
>> table = h5file.createTable(my_group', 'my_data',
>> description=data) File
>> "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/sit
>> e-packages/tables-2.2.1.dev-py2.6-macosx-10.6-fat.egg/tables/file.py"
>> , line 761, in createTable
>> chunkshape=chunkshape, byteorder=byteorder)
>> File
>> "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/sit
>> e-packages/tables-2.2.1.dev-py2.6-macosx-10.6-fat.egg/tables/table.py
>> ", line 547, in __init__
>> descr_from_dtype(description)
>> File
>> "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/sit
>> e-packages/tables-2.2.1.dev-py2.6-macosx-10.6-fat.egg/tables/descript
>> ion.py", line 725, in descr_from_dtype
>> for (name, (dtype, pos)) in dtype_.fields.items():
>> AttributeError: 'NoneType' object has no attribute 'items'
>> Closing remaining open files: test.h5... done
>>
>>
>> I think the reason is that for a homogenous array the dtype is simply
>> a scalar value so far example for my data array:
>> its dtype('int32'). Can someone tell me what I'm doing wrong or is
>> this maybe a bug in pytables?
>> I would think that such a numpy data type should be supported well in
>> pytables.
>
> The problem here is that you are trying to feed an homogeneous array
> into a Table object, which is rather meant for heterogeneous data (i.e.
> the equivalent of numpy structured arrays). For saving homogeneous
> data, using an Array/CArray/EArray is the way to go.
>
> But I recognize that the error message for your example should be
> clearer. Could you open a ticket on this so that I can get track of it?
>
> Thanks,
>
> --
> Francesc Alted
>
> ------------------------------------------------------------------------------
> Beautiful is writing same markup. Internet Explorer 9 supports
> standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3.
> Spend less time writing and rewriting code and more time creating great
> experiences on the web. Be a part of the beta today.
> http://p.sf.net/sfu/beautyoftheweb
> _______________________________________________
> Pytables-users mailing list
> Pytables-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pytables-users
>
------------------------------------------------------------------------------
Beautiful is writing same markup. Internet Explorer 9 supports
standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3.
Spend less time writing and rewriting code and more time creating great
experiences on the web. Be a part of the beta today.
http://p.sf.net/sfu/beautyoftheweb
_______________________________________________
Pytables-users mailing list
Pytables-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pytables-users
