Perl as a tool in Astronomy

Making easy jobs easy

Ulrike Heiter

UAO

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Outline

• Introduction
• Basic concepts
• Examples
• Module archive
• Perl Data Language
• Resources for further reading

Introduction

• PERL = Practical Extraction and Report Language
• History of Perl
• 1987: Larry Wall takes features of several Unix tools and merges them into new scripting language: Perl 1.000
• Four more major releases over the next few years, introducing many new features
• Since 1993: current standard Perl 5 - both simple and rich programming language
• Several minor releases of Perl 5 by team of programmers
• Purpose
• "Perl is designed to make the easy jobs easy, without making the hard jobs impossible."

Introduction

• Perl can be used to perform tasks for which
• Shell scripts are not powerful enough
• Shell scripts are not portable enough
• Higher level languages (C, etc.) are not worth the trouble
• Properties
• Readily available (included in most Unix distributions)
• Portable
• Concise
• Programs are easy to read and to maintain, when sticking to some simple guidelines

Basic concepts

• Programs are parsed and compiled before execution
• Free format - amount and kind of whitespace between elements is arbitrary
• Statements listed after one another, separated by ";"
• Comments start with "#" and end at new line
• Variables can be "scalars", "lists" (arrays), or "hashes"

  $number = 10; $number = 1.234; $string = 'Uppsala';
  @somelist = ('Sirius', 'HD 10000', 'Vega');
       $somelist[0] = 'Sirius';
  %somehash = ('Sirius', 10, 'HD 10000', 20, 'Vega', 30);
       $somehash{'Sirius'} = 10;
  

Basic concepts

• Calculations are always done in double precision
• Type conversions are done automatically, when necessary
• $_ contains default input and pattern-searching space
• @_ contains parameters passed to subroutine
• Control statements similar to those of C
• Regular expressions (pattern to be matched against string) similar to those in grep, sed, awk, vi, emacs
• Input/Output is done via FILEHANDLES

Example

# Read a list of star names and altitudes from a file,
# print names of selected stars

# Inititalize

@starlist = ();
%altitude = ();

# Read file

read_file(); # subroutine call

# Print selected stars

foreach $star (@starlist) {
   if ( select_star($star,$altitude{$star}) ) {
      print $star;
   }
} # -----  end foreach  -----

Example

sub read_file {
   open FILE, "< starfile";
   while (<FILE>) {
      push @starlist, $_;
      $altitude{$_} = <FILE>;
   }
   close FILE;
} 

Sirius
20
HD 10000
30
HD 20000
5
Vega
-5
HD 30000
50

Example

sub select_star {
   my ($name, $altitude) = @_;
   if ( ($name =~ /^HD/) and ($altitude > 10) ) {
      return 1; # anything else but "0" or "" is TRUE
   }
   else {
      return 0; # "0" is FALSE
   }
}

Link to starfile

More examples

• Writing into a command's standard input:
  

  open PRINTER, "| lpr");
  print PRINTER "some stuff to print\n";
  close PRINTER;
  

• Reading a command's standard output:
  

  open DIR, "ls some_directory |");
  while (<DIR>) { } # do something with file
  close DIR;
  

More examples

• Collection of various subroutines: libUH.pm
  e.g. sub common compares two sets of numbers and returns the set of numbers common to both sets within a certain tolerance
• Collection of Perl scripts: libUH.html
  Ulrike's Homepage → Toolbox → Various Perl scripts
  
  • histogram.pl calculates frequency distribution for a dataset
  • print_csvlist.pl prints selected fields from comma separated list

Stellar Model Grid Tool (SMGT)

• Object-oriented set of Perl packages, which calculates grids of iterative stellar models
• Written by W. Schmidt at Univ. Vienna in 1999
• Currently only ATLAS9 atmosphere models (R. Kurucz) implemented
• Manages input/output of ATLAS9 processes
• Generates initialization models and estimates number of iterations required to satisfy given convergence criteria
• Used for study of convection treatment in ATLAS9 models (Heiter et al. 2002, A&A 392, 619)

Perl Modules

• Packages of user contributed subroutines, extending basic features
• Collected at CPAN (Comprehensive Perl Archive Network)
• Included in scripts with

  use Modulename;

• Examples:
• Statistics::Descriptive - basic functions used in descriptive statistics
• Astro::FITS::CFITSIO - Perl interface to William Pence's cfitsio subroutine library
• Astro::STSDAS::Table - Access STSDAS format table files
• Astro::Cosmology - Set of routines to calculate a number of cosmological quantities based on distance and time

Perl Data Language (PDL)s

• Perl extension for efficient storage and manipulation of large N-dimensional data sets
• Example: variable $a holding a 1024x1024 floating point image
  → stored in 4MB of memory
  → expressions like $a=sqrt($a)+2 manipulate whole image in a few milliseconds
  
• Includes matrix multiplication, slicing and sectioning operators
• Input/Output functions for various data formats
• Visualisation using existing graphics libraries, e.g. PGPLOT
• Maintainers are astronomers and software engineers

Resources for further reading

• Perl manpages ("man perl")
• The Perl Directory at http://www.perl.org/
• Modules Archive: http://cpan.perl.org/
• PDL: http://pdl.perl.org/
• Books
• "Learning Perl" by Randal Schwartz, Tom Phoenix and Brian Foy
• "Programming Perl" by Jon Orwant, Larry Wall and Tom Christiansen
• List at http://books.perl.org/