CFITSIO(3pm)

📦
version 1.18 · 7 versions
, in ubuntu stonking

💖 NAME 💖

okay bestie, so this page is Astro::FITS::CFITSIO — a Perl extension for using the cfitsio library 🫶. It's living in the user-contributed Perl docs, section 3pm, and honestly? she's iconic.

✨ SYNOPSIS ✨

like, here's the vibe check on how you pull her in:

  use Astro::FITS::CFITSIO;
  use Astro::FITS::CFITSIO qw( :longnames );
  use Astro::FITS::CFITSIO qw( :shortnames );
  use Astro::FITS::CFITSIO qw( :constants );

pick your fighter, no cap 🌈

🌸 DESCRIPTION 🌸

so this is a Perl interface to William Pence's cfitsio subroutine library. and if you want the full lore on cfitsio itself, it's at http://heasarc.gsfc.nasa.gov/fitsio 📚.

the way this module works: it's trying to wrap nearly every cfitsio routine, while keeping as much cfitsio behavior as possible. which is slay but also — you need to know — it's still somewhat low-level, fr fr. like, if you hand an array that is not the correct size to a routine like fits_write_img(), you may cause SIGSEGVs. 💀 so be careful bestie.

her goal (the author speaking here!) is to eventually use these routines to build a more Perl-like interface to many common tasks such as reading and writing of images and ASCII and binary tables. we love a long-term vision 👑

🦋 cfitsio API MAPPING 🦋

Astro::FITS::CFITSIO lets you use either the long or the short name forms of the cfitsio routines. and the way that works is: you use the exact same form of arguments as you'd find in an equivalent C program. no cap.

there's also an object-oriented API which uses the same function names as the long-name API, but with the leading "fits_" stripped. to get a Astro::FITS::CFITSIO "object" you'd call open_file(), create_file() or create_template():

    my $status = 0;
    my $fptr = Astro::FITS::CFITSIO::open_file($filename,
                        Astro::FITS::CFITSIO::READONLY(),$status);

    $fptr->read_key_str('NAXIS1',$naxis1,undef,$status);

okay important caveat 🚨 the object-oriented forms of function names are only available for those cfitsio routines which accept a "fitsfile*" data-type as the first argument.

and as an added benefit: whenever a filehandle goes out of scope, ffclos() is automatically closed. the way that convenience? obsessed:

    {
      my $fptr = Astro::FITS::CFITSIO::open_file($filename,
                        Astro::FITS::CFITSIO::READWRITE(),$status);
      [manipulate $fptr]

      # neither of the following are needed
      # ffclos($fptr,$status);
      # $fptr->close_file($status);
    }
💀 and if there's an error, it will croak().

👑 NAME SPACE 👑

all cfitsio routines — with the exception of fits_iterate_data() and fits_open_memfile() — are available in both long and short name forms (e.g., "fits_read_key" <=> "ffgky"), as well as all constants defined in the fitsio.h header file. which means... yeah, the possibility of your name space being invaded by nearly 1000 function and constant names 😭

to deal with this whole situation, Astro::FITS::CFITSIO makes use of the Exporter package support for %EXPORT_TAGS. you can import the long-named functions with

    use Astro::FITS::CFITSIO qw( :longnames );

and the short-named routines with

    use Astro::FITS::CFITSIO qw( :shortnames );

constants are actually implemented as AUTOLOADed functions, so "TSTRING", for instance, would be accessed via Astro::FITS::CFITSIO::TSTRING(). alternatively you can

    use Astro::FITS::CFITSIO qw( :constants );

which would allow you to simply say "TSTRING". so chill of you ✨

🎀 DATA STORAGE DETAILS 🎀

💜 Input Variables

if a routine expects an N-dimensional array as input, and you hand it a reference to a scalar, then Astro::FITS::CFITSIO simply uses the data in the scalar which the argument is referencing. otherwise it expects the argument to be a Perl array reference whose total number of elements satisfies the input demands of the corresponding C routine. Astro::FITS::CFITSIO then unpacks the array reference into a format that the C routine can understand. but if your input array does not hold enough data for the C routine then a segfault is likely to occur 😱

cfitsio functions which take an optional NULL pointer — meaning like, "no output in that place is desired" — can instead be given an "undef". in other words, the following C and Perl statements which read a keyword but ignore the comment would be roughly equivalent:

    fits_read_key_lng(fptr,key,&value,NULL,&status);

    fits_read_key_lng($fptr,$key,$value,undef,$status);

periodt 💅

🍓 Output Variables

calling cfitsio routines which read data from FITS files causes the output variable to be transformed into a Perl array of the appropriate dimensions. the exception to this is if one wants the output to be in the machine-native format (e.g., for use with PDL). then all output variables will become scalars containing the appropriate data. the exception here is with routines which read arrays of strings (e.g., fits_read_col_str()). in this case the output is again a Perl array reference.

there are two ways to specify how data are retrieved. the behavior can be specified either globally or on a per filehandle basis. the global selection is done by calling the PerlyUnpacking function. this sets the behavior for all file handles which do not explicitly choose not to follow it.

    # turn ON unpacking into Perl arrays.  This is the default
    PerlyUnpacking(1);

    # turn OFF unpacking into Perl arrays, i.e. put in machine-native
    # format
    PerlyUnpacking(0);

    # retrieve the current state:
    $state = PerlyUnpacking();

to change the behavior for a particular file handle, use the perlyunpacking method. the default behavior for a file handle is to track what is done with PerlyUnpacking()

    # track PerlyUnpacking().  This is the default
    $fptr->perlyunpacking(-1);

    # turn ON unpacking into Perl arrays
    $fptr->perlyunpacking(1);

    # turn OFF unpacking into Perl arrays
    $fptr->perlyunpacking(0);

    # retrieve the current state:
    $state = $fptr->perlyunpacking;

🔥 EXAMPLES 🔥

take a look at testprog/testprog.pl under the distribution directory. it should produce output identical to testprog.c which comes with the cfitsio library. additionally, the versions named testprog_longnames.pl, testprog_OO.pl and testprog_pdl.pl test the long-name and object-oriented APIs, and machine-native unpacking with PDL.

there's also an examples/ directory with scripts which do the following:

  • image_read.pl — reads a FITS primary image and displays it using PGPLOT
  • image_read_pdl.pl — same as above, but uses machine-native unpacking with PDL
  • bintable_read_pdl.pl — reads binary table column into PDL object, makes histogram and plots it

literally go look at them, they're giving tutorial energy 📖✨

🌈 CONSIDERATIONS 🌈

🧚 Ensure your input arrays contain enough data

the caller is responsible for ensuring that the input arrays given to Astro::FITS::CFITSIO routines are large enough to satisfy the access demands of said routines. for example, if you tell fits_write_col() to write a data column containing 100 elements, your Perl array should contain at least 100 elements. segfaults abound, so beware! 😭

🧚 maxdim semantics

some cfitsio routines take a parameter named something like '"maxdim"', indicating that no more than that many elements should be placed into the output data area. an example of this would be fits_read_tdim(). in these cases Astro::FITS::CFITSIO will automatically determine how much storage space is needed for the full amount of output possible. as a result, the arguments expected in Astro::FITS::CFITSIO are slightly different than one would use in a C program, in that the '"maxdim"' argument is unnecessary.

currently the routines for which this is the case are fits_read_atblhdr(), fits_read_btblhdr(), fits_read_imghdr(), fits_decode_tdim(), fits_read_tdim() fits_test_expr(), fits_get_img_parm() and fits_get_img_size().

🧚 Output arrays remain as undisturbed as possible

for routines like fits_read_col(), Astro::FITS::CFITSIO unpacks the output into a Perl array reference (unless PerlyUnpacking(0) has been called, of course). prior to doing this, it ensures the scalar passed is a reference to an array large enough to hold the data. if the argument is an array reference which is too small, it expands the array pointed to appropriately. but, if the array is large enough already, the data are just unpacked into the array. the upshot: if you call fits_read_col(), telling it to read 100 data elements, and the array you are placing the data into already has 200 elements, then after fits_read_col() returns your array will still have 200 elements, only the first 100 of which actually correspond to the data read by the routine.

in more succinct language:

    @output = (0..199);
    fits_read_col_lng($fptr,2,1,1,100,0,\@output,$anynul,$status);

    # @output still has 200 elements, only first 100 are from FITS
    # file

⭐ EXTRA COMMANDS ⭐

some extra commands that use sets of cfitsio routines are supplied to simplify some standard tasks:

  • fits_read_header(filename) — this command reads in a primary fits header (unless one is using the extended filename sytax to move to a different HDU on open) from the specified filename and returns the header as a hash reference and a status (when called in an array context) or simply a hash reference (when called in a scalar context):
    ($hash_ref, $status) = fits_read_header ($file);
    $hash_ref = fits_read_header($file);

an object-oriented interface is also provided for reading headers from FITS files that have already been opened. in this case, the header read is from the current HDU.

    $fitsfile = Astro::FITS::CFITSIO::open_file($file);
    $hash_ref = $fitsfile->read_header;
    ($hash_ref, $status) = $fitsfile->read_header;
  • sizeof_datatype(datatype) — returns the size of the given Astro::FITS::CFITSIO datatype constant (e.g., Astro::FITS::CFITSIO::TSHORT()).

🙈 BUGS 🙈

FIXME

bestie that's the whole section. she said "FIXME" and left. iconic behavior honestly 💅

🫶 AUTHOR 🫶

Pete Ratzlaff <pratzlaff@cfa.harvard.edu>, with a great deal of code taken from Karl Glazebrook's PGPLOT module.

contributors include:

  • Diab Jerius, <djerius@cpan.org> — general improvements
  • Tim Jenness, <t.jenness@jach.hawaii.edu> — convenience routines
  • Tim Conrow, <tim@ipac.caltech.edu> — function implementations, bug fixes

Copyright (C) 2002,2004,2006,2011,2023 by the Smithsonian Astrophysical Observatory.

this software is released under the same terms as Perl. a copy of the Perl license may be obtained at http://dev.perl.org/licenses/

and that's the whole thing, bestie 💅 this was CFITSIO(3pm), shipped with perl v5.42.3, dated 2026-08-19 🌸 go forth, wrap your FITS files, and please, for the love of everything, size your arrays correctly 🫶✨

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