A Friday 10 December 2010 21:24:35 Dominik Szczerba escrigué:
> Hi,
>
> When calling:
>
> f = tables.openFile(fname)
> points = array(f.getNode("/points").read())
> tets = array(f.getNode("/tetrahedrons").read())
> domain = array(f.getNode("/domain").read())
> f.clos
Hi Francesc,
Thanks for confirming my guess.
I would vote for a different solution than removing this warning in the
'expert' mode.
How about explicitly declaring ordering somewhere in pytables?
Or is this warning the only place where the ordering matters?
Thanks,
Dominik
On Mon, Dec 13, 2010 at
A Monday 13 December 2010 09:34:25 Dominik Szczerba escrigué:
> Hi Francesc,
>
> Thanks for confirming my guess.
> I would vote for a different solution than removing this warning in
> the 'expert' mode.
> How about explicitly declaring ordering somewhere in pytables?
> Or is this warning the only
Hi Francesc,
Hearing that row-major order is hardcoded behind the scene is rather a bad
news for me. You are right, there is no way to store ordering metadata in
HDF5, but I do not see any need for any. I have been using HDF5 with
fortran/matlab data for a very long time. One just needs to know th
Hi Francesc,
The challenge I face is getting it off my machine - I've ordered an encrypted
USB stick that I'll post to you in due course.
Currently, it appears that memory is consumed in the numpy loadtxt code (whilst
loading the csv) and not released until I do a file close() PyTables statemen
A Monday 13 December 2010 10:44:59 Dominik Szczerba escrigué:
> Hi Francesc,
>
> Hearing that row-major order is hardcoded behind the scene is rather
> a bad news for me.
Mind that the data ordering affects mainly the iterators and the out-of-
core computing machinery (the `tables.Expr` module).
A Monday 13 December 2010 10:56:04 david.bri...@ubs.com escrigué:
> Hi Francesc,
>
> The challenge I face is getting it off my machine - I've ordered an
> encrypted USB stick that I'll post to you in due course.
Okay.
> Currently, it appears that memory is consumed in the numpy loadtxt
> code (w
One thing that I need is to access columns of my matrix with the same
efficiency as I would access them using rows, e.g.
for col in tetrahedrons:
# get indices of one element
For the moment I implement the above like:
for i in range(NCELL):
col = tetrahedrons[:,i] # get the element vertices
A Monday 13 December 2010 12:51:39 Dominik Szczerba escrigué:
> One thing that I need is to access columns of my matrix with the same
> efficiency as I would access them using rows, e.g.
>
> for col in tetrahedrons:
> # get indices of one element
>
> For the moment I implement the above like:
>
On Mon, Dec 13, 2010 at 1:48 PM, Francesc Alted wrote:
> As we know, HDF5 is ignorant on how the data in file is ordered. So, if
> you have created the dataset using a Fortran program, then clearly the
> data is ordered column-wise on disk. But, as you are reading the file
> by using a C-based
A Monday 13 December 2010 14:05:28 Dominik Szczerba escrigué:
> On Mon, Dec 13, 2010 at 1:48 PM, Francesc Alted
wrote:
> > As we know, HDF5 is ignorant on how the data in file is ordered.
> > So, if you have created the dataset using a Fortran program, then
> > clearly the data is ordered column
On Mon, Dec 13, 2010 at 2:20 PM, Francesc Alted wrote:
> A Monday 13 December 2010 14:05:28 Dominik Szczerba escrigué:
> > On Mon, Dec 13, 2010 at 1:48 PM, Francesc Alted
> wrote:
> > > As we know, HDF5 is ignorant on how the data in file is ordered.
> > > So, if you have created the dataset usi
A Monday 13 December 2010 14:56:26 Dominik Szczerba escrigué:
> > But, for knowing if accessing columns this is efficient for your
> > case, I'd need more info on your datasets. Are they contiguous or
> > chunked? If chunked, which is the chunkshape you have chosen?
>
> Both. Files saved from mat
David, your screen captures were too large and your message bounced.
I'm copying your message here. Your scripts are also attached. See my
comments interspersed in your message.
A Monday 13 December 2010 10:56:04 david.bri...@ubs.com escrigué:
> ;o) here's the screen captures
>
> The file I
A Monday 13 December 2010 15:08:03 Francesc Alted escrigué:
> A Monday 13 December 2010 14:56:26 Dominik Szczerba escrigué:
> > > But, for knowing if accessing columns this is efficient for your
> > > case, I'd need more info on your datasets. Are they contiguous
> > > or chunked? If chunked, whic
Thanks a lot for your insight.
Regards,
Dominik
On Mon, Dec 13, 2010 at 8:09 PM, Francesc Alted wrote:
> A Monday 13 December 2010 15:08:03 Francesc Alted escrigué:
> > A Monday 13 December 2010 14:56:26 Dominik Szczerba escrigué:
> > > > But, for knowing if accessing columns this is efficient
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