Hi,
Sorry for the late response.
First of all, I have managed to achieve what I wanted to do differently.
Then the code Francesc send works well (I had to adapt it because I use
version 2.3.1 under Ubuntu 12.04).
I was able to reproduce something similar with a class like this (copied
& pasted from the tutorial):
import tables as tb
import numpy as np
class Subject(tb.IsDescription):
# Subject information
Id = tb.UInt16Col()
Image = tb.Float32Col(shape=(121, 145, 121))
h5file = tb.openFile("tutorial1.h5", mode = "w", title = "Test file")
group = h5file.createGroup("/", 'subject', 'Suject information')
table = h5file.createTable(group, 'readout', Subject, "Readout example")
subject = table.row
for i in xrange(10):
subject['Id'] = i
subject['Image'] = np.ones((121, 145, 121))
subject.append()
This code works well too.
So I don't really know why nothing was working yesterday: this was the
same class and a very close program. I will try to investigate later on
this.
Thanks for everything,
Mahtieu
Le 05/07/2013 16:54, Anthony Scopatz a écrit :
On Fri, Jul 5, 2013 at 8:40 AM, Francesc Alted <fal...@gmail.com
<mailto:fal...@gmail.com>> wrote:
On 7/5/13 1:33 AM, Mathieu Dubois wrote:
> tables.tableExtension.Table._createTable
(tables/tableExtension.c:2181)
>>
>> tables.exceptions.HDF5ExtError: Problems creating the table
>>
>> I think that the size of the column is too large (if I
remove the
>> Image
>> field, everything works perfectly).
>>
>>
>> Hi Mathieu,
>>
>> This shouldn't be the case. What is the value of IMAGE_SIZE?
>
> IMAGE_SIZE is a tuple containing (121, 145, 121).
This is a bit large for a row in the Table object. My recommendation
for these cases is to use an associated EArray with shape (0, 121,
145,
121) and then append the images there. You can always refer to the
image by issuing a __getitem__() operation on the EArray object
with the
index of the row in the table. Easy as a pie and you will allow the
compression library (in case you are using compression) to work much
more efficiently for the table.
Hi Francesc,
I disagree that this shape is too large for a table. Here is a
minimal example that works for me:
import tables as tb
import numpy as np
images = np.ones(100, dtype=[('id', np.uint16),
('image', np.float32, (121, 145, 121))
])
with tb.open_file('temp.h5', 'w') as f:
f.create_table('/', 'images', images)
I think that there is something else going on with the initialization
but Mathieu hasn't given us enough information to figure it out =/. A
minimal failing script would be super helpful here!
(BTW Mathieu, Tables can also take advantage of compression. Though
Francesc's solution is nicer for a lot of reason too.)
Be Well
Anthony
HTH,
-- Francesc Alted
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