Re: [Pytables-users] My use of PyTables and a question

[Francesc A. <fa...@py...>]

Hi Chuck,

A Dimecres 28 Abril 2004 19:15, chuck clark va escriure:
> So far everything is working out well but I can't say that I've used
> PyTables enough yet to make any suggestions.  As I get deeper into it I'll
> be sure to post.  Also I'd like to express my thanks for the great
> documentation that goes along with this project.  It is responsible for me
> getting this far without having to post to the list.

Documentation is an area that I very much want to care about. I'm happy that
you like it :).

> However, I do have a few questions:
> Is there a way to get a Column of a table returned as a numarray so I can
> computed means and standard deviations with NumPy?  Or do I just read the
> column as a Python list and then create a numarray out of it?

There are several ways to do that. I consider the one introduced in the
latest release (0.8) to be the most convenient in this case. Say that your
column is named "energy" and you want to compute the mean and standard
deviation. Look at that:

>>> fileh = tables.openFile("test.h5", "r")
>>> fileh.root.tuple0.cols.energy
/tuple0.cols.energy (Column(1,), Float64)  # elements of column are scalars
>>> fileh.root.tuple0.cols.energy[:].nelements()
20000  # 20,000 elements in the columns
>>> fileh.root.tuple0.cols.energy[:].mean()
19999.0  # self-explanatory
>>> fileh.root.tuple0.cols.energy[:].stddev()
11547.294055318762  # self-explanatory

This is explained in documentation too (with some examples) in:
http://pytables.sourceforge.net/html-doc/usersguide4.html#subsection4.5.5
and 
http://pytables.sourceforge.net/html-doc/usersguide4.html#subsection4.5.6

> 
> One of my fields is a timestamp.  I don't see such a datatype in Appendix
> A.  However, upon digging further it appears that timestamps are supported
> by the HDF5 spec but have not yet been implemented.  Is this correct?

Yeah, it is. I've have not (free) time to implement that yet.

> If so, how are other people getting around this?  I use the excellent
> mx.DateTime library and am heading down the path of calling .ticks() on
> any timestamp fields and storing that as a Float32Col.

That could be a nice workaround, of course.

Regards,

-- 
Francesc Alted