[AstroPy] Error when opening Vizier FITS table with astropy Table.read

[Phil Hodge]

The keyword (and ones like it) should be TNULL3, not TBNUL3.  You can 
fix this by downloading the FITS file and then opening the file as follows:

import astropy.io.fits as fits
fd = fits.open("J_ApJS_186_111_table4.dat.fits")

Then modify the table header:

hdr = fd[1].header
hdr.rename_keyword("tbnul3", "tnull3")
hdr.rename_keyword("tbnul4", "tnull4")
hdr.rename_keyword("tbnul5", "tnull5")
hdr.rename_keyword("tbnul7", "tnull7")
hdr.rename_keyword("tbnul8", "tnull8")
hdr.rename_keyword("tbnul10", "tnull10")
hdr.rename_keyword("tbnul13", "tnull13")
hdr.rename_keyword("tbnul14", "tnull14")

And save it to a new file:

fd.writeto("J_ApJS_186_111_table4_mod.fits")  # or some other name

Phil



On 05/31/2016 03:25 PM, Eric Jensen wrote:
>
> On May 31, 2016, at 2:56 PM, Paul Kuin <npkuin at gmail.com 
> <mailto:npkuin at gmail.com>> wrote:
>
>> Have you tried to read the fits file with astropy.io.fits ? What do 
>> you get then for the table?
>
> It opens the file without error, and I can examine the header.  But as 
> soon as I try to access any part of the data structure, I get the same 
> ValueError about TNULL3 shown below.
>
>
>
>>
>> On Tue, May 31, 2016 at 7:07 PM, Eric Jensen <ejensen1 at swarthmore.edu 
>> <mailto:ejensen1 at swarthmore.edu>> wrote:
>>
>>     Hi all,
>>
>>     I’m trying to read a FITS table associated with an ApJ paper, and
>>     getting an error I don’t understand.  The table in question
>>     doesn’t have a standard ASCII/CDS version with the full header
>>     that astropy handles very well (in my experience) with
>>     format=‘ascii.cds’, so I was trying to use the FITS version
>>     linked here:
>>
>>     http://cdsarc.u-strasbg.fr/viz-bin/nph-Cat/fits?J%2FApJS%2F186%2F111/table4.dat
>>
>>     Looking at that URL, it would appear that Vizier may be doing an
>>     on-the-fly conversion to FITS?  But my hope was that using that
>>     would take into account the information in the Vizier README, and
>>     thus generate a nice table structure in Python without my having
>>     to identify columns by hand.  The plain-text version
>>     (http://cdsarc.u-strasbg.fr/vizier/ftp/cats/J/ApJS/186/111/table4.dat)
>>     doesn’t have header info, though such info is present in the
>>     separate README file.
>>
>>     However, when I read the FITS file like this:
>>
>>     from astropy.table import Table
>>     datafile = 'J_ApJS_186_111_table4.dat.fits'
>>     t2 = Table.read(datafile, format='fits')
>>
>>     I get this error:
>>
>>     ValueError: invalid literal for int() with base 10: ' '; the
>>     header may be missing the necessary TNULL3 keyword or the table
>>     contains invalid data
>>
>>     Looking at the FITS header, there is indeed no TNULL3 keyword,
>>     but there is a TBNUL3 keyword:
>>
>>     TBNUL3 = '        '           / NULL (undefined) value
>>
>>     So presumably that keyword has the needed info, but not in the
>>     field astropy is expecting.  Is there any way to work around this?
>>
>>     Possibly related - reading in that file in its text version,
>>     specifying format=‘cds’ and readme=‘ReadMe’ doesn’t work
>>     correctly either, because the ReadMe has a combined entry for
>>     Tables 4 and 5, and says in a note that the third field only
>>     applies to Table 5.  So this could just be a pathological case
>>     for this particular file, but I’m curious to know if anyone has
>>     encountered anything like this or has any recommendations.
>>
>>     Thanks in advance for your help with this,
>>
>>     Eric
>>
>
>
>
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