Adrian Price-Whelan, Adam Ginsburg, Stephanie T. Douglas, Kelle Cruz
FITS, file input/output
This tutorial describes how to read in and edit a FITS header, and then write
it back out to disk. For this example we're going to change the OBJECT
keyword.
In [ ]:
from astropy.io import fits
astropy.io.fits provides a lot of flexibility for reading FITS
files and headers, but most of the time the convenience functions are
the easiest way to access the data. fits.getdata() reads only the
data from a FITS file, but with the header=True keyword argument will
also read the header.
In [ ]:
data, header = fits.getdata("input_file.fits", header=True)
There is also a dedicated function for reading only the header:
In [ ]:
hdu_number = 0 # HDU means header data unit
fits.getheader('input_file.fits', hdu_number)
But getdata() can get both the data and the header, so it's a useful
command to remember. Since the primary HDU of a FITS file must contain image data,
the data is now stored in a numpy array. The header is stored in an
object that acts like a standard Python dictionary.
In [ ]:
# But hdu_number = 0 is the PRIMARY HDU.How many HDUs are in this file?
fits_inf = fits.open("input_file.fits")
fits_inf.info()
fits_inf[0].header
Using fits.open allows us to look more generally at our data. fits_inf[0].header gives us the same output as fits.getheader. What will you learn if you type fits_inf[1].header? Based on fits_inf.info() can you guess what will happen if you type fits_inf[2].header?
Now let's change the header to give it the correct object:
In [ ]:
header['OBJECT'] = "M31"
Finally, we have to write out the FITS file. Again, the convenience function for this is the most useful command to remember:
In [ ]:
fits.writeto('output_file.fits', data, header, overwrite=True)
That's it; you're done!
Two common and more complicated cases are worth mentioning (but if your needs are much more complex, you should consult the full documentation http://docs.astropy.org/en/stable/io/fits/).
The first complication is that the FITS file you're examining and editing might have multiple HDU's (extensions), in which case you can specify the extension like this:
In [ ]:
data1, header1 = fits.getdata("input_file.fits", ext=1, header=True)
This will get you the data and header associated with the index=1 extension
in the FITS file. Without specifying a number, getdata() will get the
0th extension (equivalent to saying ext=0).
Another useful tip is if you want to overwrite an existing FITS
file. By default, writeto() won't let you do this, so you need to
explicitly give it permission using the clobber keyword argument:
In [ ]:
fits.writeto('output_file.fits', data, header, overwrite=True)
A final example is if you want to make a small change to a FITS file, like updating a header keyword, but you don't want to read in and write out the whole file, which can take a while. Instead you can use the mode='update' read mode to do this:
In [ ]:
with fits.open('input_file.fits', mode='update') as filehandle:
filehandle[0].header['MYHDRKW'] = "My Header Keyword"
Read in the file you just wrote and add three header keywords:
Then write the updated header back out to a new file:
In [ ]: