Provided by: libastro-fits-cfitsio-perl_1.16-1build2_amd64 
NAME
Astro::FITS::CFITSIO - 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 <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 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/