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/site-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/site-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/site-packages/tables-2.2.1.dev-py2.6-macosx-10.6-fat.egg/tables/description.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.
thanks,
Grace
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