In the next three chapters, more detailed information as well as examples will be explained for manipulating the header, the image data, and the table data respectively.
Every HDU normally has two components: header and data. In PyFITS these two components are accessed through the two attributes of the HDU, .header and .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:
>>> hdu = pyfits.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. PyFITS will strip the required keywords from the input header first and then add back the required keywords compatible to the new HDU. 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.
As shown in the Quick Tutorial, keyword values can be accessed via keyword name or index of an HDU’s header attribute. Here is a quick summary:
>>> hdulist = pyfits.open('input.fits') # open a FITS file
>>> prihdr = hdulist[0].header # the primary HDU header
>>> print prihdr[3] # get the 4th keyword's value
10
>>> prihdr[3] = 20 # change its value
>>> prihdr['darkcorr'] # get the value of the keyword 'darkcorr'
'OMIT'
>>> prihdr['darkcorr'] = 'PERFORM' # change darkcorr's value
Keyword names are case-insenstive except in a few special cases (see the sections on HIERARCH card and record-valued cards). Thus, prihdr['abc'], prihdr['ABC'], or prihdr['aBc'] are all equivalent.
A keyword (and its corresponding card) can be deleted using the same index/name syntax:
>>> del prihdr[3] # delete the 2nd keyword
>>> del prihdr['abc'] # get the value of the keyword 'abc'
Note that, like a regular Python list, the indexing updates after each delete, so if del prihdr[3] is done two times in a row, the 2nd and 3rd keywords are removed from the original header.
It is also possible to delete an entire range of cards using the slice syntax:
>>> del prihdr[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:
>>> prihdr.set('target', 'NGC1234', 'target name')
>>> # place the next new keyword before the 'target' keyword
>>> prihdr.set('newkey', 666, before='target') # comment is optional
>>> # place the next new keyword after the 21st keyword
>>> prihdr.set('newkey2', 42.0, 'another new key', after=20)
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:
>>> prihdr['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 diplay just the last HISTORY entry, use prihdr['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
COMMENT comment 1
COMMENT comment 2
blank 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.
A FITS header consists of card images.
A card images 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 PyFITS, 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 that header that provide the logic for parsing and formatting individual cards in a header. But there’s 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 = pyfits.Card('temp', 80.0, 'temperature, floating value')
>>> c2 = pyfits.Card('detector', 1) # comment is optional
>>> c3 = pyfits.Card('mir_revr', True, 'mirror reversed? Boolean value)>>>
c4 = pyfits.Card('abc', 2+3j, 'complex value')
>>> c5 = pyfits.Card('observer', 'Hubble', 'string value')
>>> print c1; print c2; print c3; print c4; print c5 # show the card images
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 .key, .value, and .comment. Both .value and .comment can be changed but not the .key attribute.
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 PyFITS will be discussed in a later chapter.
>>> c1 = pyfits.Card.fromstring('ABC = 3.456D023')
>>> c2 = pyfits.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.
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. PyFITS 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.
>>> header = pyfits.Header()
>>> header['abc'] = 'abcdefg' * 20
>>> header
ABC = 'abcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcd&'
CONTINUE 'efgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefga&'
CONTINUE 'bcdefg&'
>>> header['abc']
'abcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefg'
>>> # both value and comments are long
>>> header['abc'] = ('abcdefg' * 10, 'abcdefg' * 10)
>>> header
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 PyFITS 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 PyFITS 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.
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. PyFITS supports this convention as well.
If a keyword contains more than 8 characters PyFITS 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). However, they can be accessed without prefixing the keyword with ‘HIERARCH ‘ (and in fact doing so is in error). HIEARARCH keywords also differ from normal FITS keywords in that they are case-sensitive.
Examples follow:
>>> c = pyfits.Card('abcdefghi', 10)
Keyword name 'abcdefghi' is greater than 8 characters; a HIERARCH card will
be created.
>>> print c
HIERARCH abcdefghi = 10
>>> c = pyfits.Card('hierarch abcdefghi', 10)
>>> print c
HIERARCH abcdefghi = 10
>>> h = pyfits.PrimaryHDU()
>>> h.header['hierarch abcdefghi'] = 99
>>> h.header['abcdefghi']
99
>>> h.header['abcdefghi'] = 10
>>> h.header['abcdefghi']
10
>>> h.header['ABCDEFGHI']
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "pyfits/header.py", line 121, in __getitem__
return self._cards[self._cardindex(key)].value
File "pyfits/header.py", line 1106, in _cardindex
raise KeyError("Keyword %r not found." % keyword)
KeyError: "Keyword 'ABCDEFGI.' not found."
>>> h.header
SIMPLE = T / conforms to FITS standard
BITPIX = 8 / array data type
NAXIS = 0 / number of array dimensions
EXTEND = T
HIERARCH abcdefghi = 1000