FITS Headers

In the next three chapters, more detailed information as well as examples will be explained for manipulating FITS headers, image/array data, and table data respectively.

Header of an HDU

Every HDU normally has two components: header and data. In Astropy these two components are accessed through the two attributes of the HDU, hdu.header and hdu.data.

While an HDU may have empty data, i.e. the .data attribute is None, any HDU will always have a header. When an HDU is created with a constructor, e.g. hdu = PrimaryHDU(data, header), the user may supply the header value from an existing HDU’s header and the data value from a numpy array. If the defaults (None) are used, the new HDU will have the minimal required keywords for an HDU of that type:

>>> from astropy.io import fits
>>> hdu = fits.PrimaryHDU()
>>> hdu.header  # show the all of the header cards
SIMPLE  =                    T / conforms to FITS standard
BITPIX  =                    8 / array data type
NAXIS   =                    0 / number of array dimensions
EXTEND  =                    T

A user can use any header and any data to construct a new HDU. Astropy will strip any keywords that describe the data structure leaving only your informational keywords. Later it will add back in the required structural keywords for compatibility with the new HDU and any data added to it. So, a user can use a table HDU’s header to construct an image HDU and vice versa. The constructor will also ensure the data type and dimension information in the header agree with the data.

The Header Attribute

Value Access, Updating, and Creating

As shown in the Getting Started tutorial, keyword values can be accessed via keyword name or index of an HDU’s header attribute. You can also use the wildcard character * to get the keyword value pairs that match your search string. Here is a quick summary:

>>> fits_image_filename = fits.util.get_testdata_filepath('test0.fits')
>>> hdul = fits.open(fits_image_filename)  # open a FITS file
>>> hdr = hdul[0].header  # the primary HDU header
>>> print(hdr[34])  # get the 2nd keyword's value
96
>>> hdr[34] = 20  # change its value
>>> hdr['DARKCORR']  # get the value of the keyword 'darkcorr'
'OMIT'
>>> hdr['DARKCOR*']  # get keyword values using wildcard matching
DARKCORR= 'OMIT              ' / Do dark correction: PERFORM, OMIT, COMPLETE
>>> hdr['darkcorr'] = 'PERFORM'  # change darkcorr's value

Keyword names are case-insensitive except in a few special cases (see the sections on HIERARCH card and record-valued cards). Thus, hdr['abc'], hdr['ABC'], or hdr['aBc'] are all equivalent.

Like with Python’s dict type, new keywords can also be added to the header using assignment syntax:

>>> hdr = hdul[1].header
>>> 'DARKCORR' in hdr  # Check for existence
False
>>> hdr['DARKCORR'] = 'OMIT'  # Add a new DARKCORR keyword

You can also add a new value and comment by assigning them as a tuple:

>>> hdr['DARKCORR'] = ('OMIT', 'Dark Image Subtraction')

Note

An important point to note when adding new keywords to a header is that by default they are not appended immediately to the end of the file. Rather, they are appended to the last non-commentary keyword. This is in order to support the common use case of always having all HISTORY keywords grouped together at the end of a header. A new non-commentary keyword will be added at the end of the existing keywords, but before any HISTORY/COMMENT keywords at the end of the header.

There are a couple of ways to override this functionality:

  • Use the Header.append() method with the end=True argument:

    >>> hdr.append(('DARKCORR', 'OMIT', 'Dark Image Subtraction'), end=True)
    

    This forces the new keyword to be added at the actual end of the header.

  • The Header.insert() method will always insert a new keyword exactly where you ask for it:

    >>> hdr.insert(20, ('DARKCORR', 'OMIT', 'Dark Image Subtraction'))
    

    This inserts the DARKCORR keyword before the 20th keyword in the header no matter what it is.

A keyword (and its corresponding card) can be deleted using the same index/name syntax:

>>> del hdr[3]  # delete the 2nd keyword
>>> del hdr['DARKCORR']  # delete the value of the keyword 'DARKCORR'

Note that, like a regular Python list, the indexing updates after each delete, so if del hdr[3] is done two times in a row, the 4th and 5th keywords are removed from the original header. Likewise, del hdr[-1] will delete the last card in the header.

It is also possible to delete an entire range of cards using the slice syntax:

>>> del hdr[3:5]

The method Header.set() is another way to update they value or comment associated with an existing keyword, or to create a new keyword. Most of its functionality can be duplicated with the dict-like syntax shown above. But in some cases it might be more clear. It also has the advantage of allowing one to either move cards within the header, or specify the location of a new card relative to existing cards:

>>> hdr.set('target', 'NGC1234', 'target name')
>>> # place the next new keyword before the 'TARGET' keyword
>>> hdr.set('newkey', 666, before='TARGET')  # comment is optional
>>> # place the next new keyword after the 21st keyword
>>> hdr.set('newkey2', 42.0, 'another new key', after=20)

In FITS headers, each keyword may also have a comment associated with it explaining its purpose. The comments associated with each keyword are accessed through the comments attribute:

>>> hdr['NAXIS']
2
>>> hdr.comments['NAXIS']
'number of data axes'
>>> hdr.comments['NAXIS'] = 'The number of image axes'  # Update
>>> hdul.close()  # close the HDUList again

Comments can be accessed in all the same ways that values are accessed, whether by keyword name or card index. Slices are also possible. The only difference is that you go through hdr.comments instead of just hdr by itself.

COMMENT, HISTORY, and Blank Keywords

Most keywords in a FITS header have unique names. If there are more than two cards sharing the same name, it is the first one accessed when referred by name. The duplicates can only be accessed by numeric indexing.

There are three special keywords (their associated cards are sometimes referred to as commentary cards), which commonly appear in FITS headers more than once. They are (1) blank keyword, (2) HISTORY, and (3) COMMENT. Unlike other keywords, when accessing these keywords they are returned as a list:

>>> filename = fits.util.get_testdata_filepath('history_header.fits')
>>> with fits.open(filename) as hdul:  # open a FITS file
...     hdr = hdul[0].header

>>> hdr['HISTORY']
I updated this file on 02/03/2011
I updated this file on 02/04/2011

These lists can be sliced like any other list. For example, to display just the last HISTORY entry, use hdr['history'][-1]. Existing commentary cards can also be updated by using the appropriate index number for that card.

New commentary cards can be added like any other card by using the dict-like keyword assignment syntax, or by using the Header.set() method. However, unlike with other keywords, a new commentary card is always added and appended to the last commentary card with the same keyword, rather than to the end of the header. Here is an example:

>>> hdu.header['HISTORY'] = 'history 1'
>>> hdu.header[''] = 'blank 1'
>>> hdu.header['COMMENT'] = 'comment 1'
>>> hdu.header['HISTORY'] = 'history 2'
>>> hdu.header[''] = 'blank 2'
>>> hdu.header['COMMENT'] = 'comment 2'

and the part in the modified header becomes:

HISTORY history 1
HISTORY history 2
        blank 1
        blank 2
COMMENT comment 1
COMMENT comment 2

Users can also directly control exactly where in the header to add a new commentary card by using the Header.insert() method.

Note

Ironically, there is no comment in a commentary card, only a string value.

Card Images

A FITS header consists of card images.

A card image in a FITS header consists of a keyword name, a value, and optionally a comment. Physically, it takes 80 columns (bytes)–without carriage return–in a FITS file’s storage format. In Astropy, each card image is manifested by a Card object. There are also special kinds of cards: commentary cards (see above) and card images taking more than one 80-column card image. The latter will be discussed later.

Most of the time the details of dealing with cards are handled by the Header object, and it is not necessary to directly manipulate cards. In fact, most Header methods that accept a (keyword, value) or (keyword, value, comment) tuple as an argument can also take a Card object as an argument. Card objects are just wrappers around such tuples that provide the logic for parsing and formatting individual cards in a header. But there’s usually nothing gained by manually using a Card object, except to examine how a card might appear in a header before actually adding it to the header.

A new Card object is created with the Card constructor: Card(key, value, comment). For example:

>>> c1 = fits.Card('TEMP', 80.0, 'temperature, floating value')
>>> c2 = fits.Card('DETECTOR', 1)  # comment is optional
>>> c3 = fits.Card('MIR_REVR', True,
...                'mirror reversed? Boolean value')
>>> c4 = fits.Card('ABC', 2+3j, 'complex value')
>>> c5 = fits.Card('OBSERVER', 'Hubble', 'string value')

>>> print(c1); print(c2); print(c3); print(c4); print(c5)  # show the cards
TEMP    =                 80.0 / temperature, floating value
DETECTOR=                    1
MIR_REVR=                    T / mirror reversed? Boolean value
ABC     =           (2.0, 3.0) / complex value
OBSERVER= 'Hubble  '           / string value

Cards have the attributes .keyword, .value, and .comment. Both .value and .comment can be changed but not the .keyword attribute. In other words, once a card is created, it is created for a specific, immutable keyword.

The Card() constructor will check if the arguments given are conforming to the FITS standard and has a fixed card image format. If the user wants to create a card with a customized format or even a card which is not conforming to the FITS standard (e.g. for testing purposes), the Card.fromstring() class method can be used.

Cards can be verified with Card.verify(). The non-standard card c2 in the example below is flagged by such verification. More about verification in Astropy will be discussed in a later chapter.

>>> c1 = fits.Card.fromstring('ABC = 3.456D023')
>>> c2 = fits.Card.fromstring("P.I. ='Hubble'")
>>> print(c1); print(c2)
ABC     =            3.456D023
P.I. ='Hubble'
>>> c2.verify()  
Output verification result:
Unfixable error: Illegal keyword name 'P.I.'

A list of the Card objects underlying a Header object can be accessed with the Header.cards attribute. This list is only meant for observing, and should not be directly manipulated. In fact, it is only a copy–modifications to it will not affect the header it came from. Use the methods provided by the Header class instead.

CONTINUE Cards

The fact that the FITS standard only allows up to 8 characters for the keyword name and 80 characters to contain the keyword, the value, and the comment is restrictive for certain applications. To allow long string values for keywords, a proposal was made in:

by using the CONTINUE keyword after the regular 80-column containing the keyword. Astropy does support this convention, even though it is not a FITS standard. The examples below show the use of CONTINUE is automatic for long string values:

>>> hdr = fits.Header()
>>> hdr['abc'] = 'abcdefg' * 20
>>> hdr
ABC     = 'abcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcd&'
CONTINUE  'efgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefga&'
CONTINUE  'bcdefg'
>>> hdr['abc']
'abcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefg'
>>> # both value and comments are long
>>> hdr['abc'] = ('abcdefg' * 10, 'abcdefg' * 10)
>>> hdr
ABC     = 'abcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcd&'
CONTINUE  'efg&'
CONTINUE  '&' / abcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefga
CONTINUE  '' / bcdefg

Note that when a CONTINUE card is used, at the end of each 80-characters card image, an ampersand is present. The ampersand is not part of the string value. Also, there is no “=” at the 9th column after CONTINUE. In the first example, the entire 240 characters is treated by Astropy as a single card. So, if it is the nth card in a header, the (n+1)th card refers to the next keyword, not the next CONTINUE card. As such, CONTINUE cards are transparently handled by Astropy as a single logical card, and it’s generally not necessary to worry about the details of the format. Keywords that resolve to a set of CONTINUE cards can be accessed and updated just like regular keywords.

HIERARCH Cards

For keywords longer than 8 characters, there is a convention originated at ESO to facilitate such use. It uses a special keyword HIERARCH with the actual long keyword following. Astropy supports this convention as well.

If a keyword contains more than 8 characters Astropy will automatically use a HIERARCH card, but will also issue a warning in case this is in error. However, one may explicitly request a HIERARCH card by prepending the keyword with ‘HIERARCH ‘ (just as it would appear in the header). For example, hdr['HIERARCH abcdefghi'] will create the keyword abcdefghi without displaying a warning. Once created, HIERARCH keywords can be accessed like any other: hdr['abcdefghi'], without prepending ‘HIERARCH’ to the keyword.

Examples follow:

>>> # this will print a Warning because a HIERARCH card is implicitly created
>>> c = fits.Card('abcdefghi', 10)
>>> print(c)
HIERARCH abcdefghi = 10
>>> c = fits.Card('hierarch abcdefghi', 10)
>>> print(c)
HIERARCH abcdefghi = 10
>>> hdu = fits.PrimaryHDU()
>>> hdu.header['hierarch abcdefghi'] =  99
>>> hdu.header['abcdefghi']
99
>>> hdu.header['abcdefghi'] = 10
>>> hdu.header['abcdefghi']
10
>>> hdu.header
SIMPLE  =                    T / conforms to FITS standard
BITPIX  =                    8 / array data type
NAXIS   =                    0 / number of array dimensions
EXTEND  =                    T
HIERARCH abcdefghi = 10

Note

A final point to keep in mind about the Header class is that much of its design is intended to abstract away quirks about the FITS format. This is why, for example, it will automatically created CONTINUE and HIERARCH cards. The Header is just a data structure, and as user you shouldn’t have to worry about how it ultimately gets serialized to a header in a FITS file.

Though there are some areas where it’s almost impossible to hide away the quirks of the FITS format, Astropy tries to make it so that you have to think about it as little as possible. If there are any areas where you have concern yourself unnecessarily about how the header is constructed, then let help@stsci.edu know, as there are probably areas where this can be improved on even more.