bionic (3) Astro::FITS::CFITSIO.3pm.gz
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/