[AstroPy] Practical Python for Astronomers web tutorial

Tom Aldcroft aldcroft at head.cfa.harvard.edu
Thu May 26 09:58:50 EDT 2011

Hi Juan,

In your example ATpy is looking at the table and inferring that it is
an IPAC table.  So by default it uses the internal ATpy IPAC table
reader. This does not have the fill_values keyword, but it
automatically deals with the missing values in an acceptable way.  So
either do:

data = atpy.Table('wise_matches.tbl')
  # OR
data = atpy.Table('wise_matches.tbl', type='ascii', fill_values=filler)

The latter specifically tells atpy to use the asciitable IPAC reader
instead of the atpy IPAC reader.  This is one case that is a little
confusing because there is overlapping functionality.  I would
recommend using the ATpy internal reader in most cases since it
automatically deals with common missing value cases.

- tom

On Thu, May 26, 2011 at 9:40 AM, Dr. Juan E Cabanela Ph.D.
<cabanela at mnstate.edu> wrote:
> On May 26, 2011, at 2:20 AM, Frederic Grollier wrote:
>> On Wed, May 25, 2011 at 02:29:09PM -0500, Dr. Juan E Cabanela Ph.D. wrote:
>>> t5 = atpy.Table(raw,type='ascii', fill_values=fill_values)
>>> fails for me.  In fact, there appears to be no way to get atpy.Table to fill
>>> values automatically as it triggers an error
>>> TypeError: read() got an unexpected keyword argument 'fill_values'
>>> I hope this can be fixed and if someone can tell me how to use fill_values
>>> within ATpy that would be appreciated.
>> This code snippet works for me here, using ATpy. and
>> asciitable.0.5.2. In the case of type='asciitable', the read() method
>> delegates most of its work to asciitable, and so 'fill_values' should
>> be a feature of this module. As far as I can tell, the 'fill_values'
>> parameter was introduced in version 0.4.0 of asciitable, can you check
>> your version info for this ?
> I am running ATpy and asciitable 0.5.2 as well, running on Python 2.7.1 -- EPD 7.0-2 (64-bit) on MacOS 10.6.7.
> In my script test.py I do the following:
> ===========================================================================
> import numpy
> import pylab
> import atpy
> filler = [('null',numpy.nan),('null',-999,'cntr_u','nb','na','ext_flg','w1nm','w1m','w2nm','w2m','w3nm','w3m','w4nm','w4m','tmass_key')]
> data = atpy.Table('wise_matches.tbl',fill_values=filler)
> ===========================================================================
> and that last line triggers the following error (with traceback):
> Traceback (most recent call last):
>  File "test.py", line 14, in <module>
>   data = atpy.Table('wise_matches.tbl',fill_values=filler)
>  File "/Users/juan/Library/Python/2.7/lib/python/site-packages/ATpy-", line 167, in __init__
>   self.read(*args, **kwargs)
>  File "/Users/juan/Library/Python/2.7/lib/python/site-packages/ATpy-", line 213, in read
>   atpy._readers[table_type](self, *args, **kwargs)
> TypeError: read() got an unexpected keyword argument 'fill_values'
> And so I have the same modules, but a different result.
> Juan
> --
> Dr. Juan Cabanela                    218-477-2453 (V)  218-477-2290 (F)
> Minnesota State University Moorhead     WWW: http://www.cabanela.com/
> Dept. of Physics and Astronomy      Twitter: Juan_Kinda_Guy
> 1104 Seventh Ave South, Hagen 307B       IM: AstroJuanCab (AIM)
> Moorhead, MN 56563                           cabanela at mnstate.edu (MSN)
>                                            juancab at gmail.com (GTalk)
>  Public PGP Key available at: http://www.cabanela.com/juan_public.asc
> _______________________________________________
> AstroPy mailing list
> AstroPy at scipy.org
> http://mail.scipy.org/mailman/listinfo/astropy

More information about the AstroPy mailing list