Astro::FITS::CFITSIO(3) Perl extension for using the cfitsio library

SYNOPSIS


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

DESCRIPTION

Perl interface to William Pence's cfitsio subroutine library. For more information on cfitsio, see http://heasarc.gsfc.nasa.gov/fitsio.

This module attempts to provide a wrapper for nearly every cfitsio routine, while retaining as much cfitsio behavior as possible. As such, one should be aware that it is still somewhat low-level, in the sense that handing an array which is not the correct size to a routine like "fits_write_img()" may cause SIGSEGVs.

My goal 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.

cfitsio API MAPPING

Astro::FITS::CFITSIO allows one to use either the long or short name forms of the cfitsio routines. These work by using the exact same form of arguments as one would find in an equivalent C program.

There is 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'' one would 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);

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

As an added benefit, whenever a filehandle goes out of scope, ffclos() is automatically closed: 

    {
      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);
    }

It there is 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. This raises the possibility of your name space being invaded by nearly 1000 function and constant names.

To deal with this 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".

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. 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 - indicating 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);

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 is 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

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

AUTHOR

Pete Ratzlaff <[email protected]>, with a great deal of code taken from Karl Glazebrook's PGPLOT module.

Contributors include:

Diab Jerius, <[email protected]>
general improvements
Tim Jenness, <[email protected]>
convenience routines
Tim Conrow, <[email protected]>
function implementations, bug fixes

COPYRIGHT AND LICENSE

Copyright (C) 2002,2004,2006,2011 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/

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