Astronomical Software

See also Required Astronomical Software.

Note: most of the headings on this page are links to more detailed information on that particular software package.

AIPS

AIPS, the NRAO Astronomical Image Processing System is used primarily for reducing data from synthesis radio telescopes. General information is given in the AIPS FAQ. We currently have version 31DEC07 installed.

Launching AIPS

To set up the environment for AIPS (on a Configured Workstation), enter:

aips-shell

And then to launch aips, enter:

aips tv=local tpok

Data Disks

The each CW has been set up with at least 12 data disks.

The location of your local aips data disks is:

/scratch/aips/data/'xxxx_x'

Please email the systems administrator regarding any issues in adding or activating your data disks.

ALADIN

Aladin is an interactive software sky atlas allowing the user to visualize digitized images of any part of the sky, to superimpose entries from astronomical catalogs or personal user data files, and to interactively access related data and information from the SIMBAD, NED, VizieR, or other archives for all known objects in the field (see available data). Aladin is particularly useful for multi-spectral cross-identifications of astronomical sources, observation preparation and quality control of new data sets. More information can be found here. We currently have version 3.7 installed.

Launching ALADIN

Typing 'aladin' at a terminal/shell will launch aladin.

CIAO

CIAO, is a data analysis system written for the needs of users of the Chandra X-ray Observatory. Because Chandra is the first mission with 4-dimensional data (2 spatial, time, energy) in which each dimension has many independent elements, CIAO was built to handle N-dimensional data without concern about which particular axes were being analyzed. Also, apart from a few Chandra instrument tools, CIAO is mission independent.

Launching CIAO

Typing 'ciao-shell' at a terminal/shell will launch CIAO version 3.4.

The contents of the shell script:

#!/bin/bash
. /opt/ciao/current/bin/ciao.bash
exec /bin/bash

To access CIAO version 4.0, you can add the following to your .bashrc file:

alias ciao=". /opt/ciao/ciao-4.0/bin/ciao.bash"

For csh or tcsh users, modify your .cshrc file with:

alias ciao "source /opt/ciao/ciao-4.0/bin/ciao.csh"

Typing 'ciao' at a terminal/shell will now launch CIAO version 4.0

FFTW

FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST). The FFTW package was developed at MIT by Matteo Frigo and Steven G. Johnson. Our workstation have version 3 installed.

GNU scientific library

The GNU Scientific Library (GSL) is a numerical C library. GSL Reference Manual

HEASOFT

HEASOFT is a unified release of the FTOOLS and XANADU Software Packages

XANADU High-level, multi-mission tasks for X-ray astronomical spectral, timing, and imaging data analysis FTOOLS General and mission-specific tools to manipulate FITS files FITSIO Core library responsible for reading and writing FITS files (distributed with FTOOLS) fv General FITS file browser/editor/plotter with a graphical user interface (distributed with FTOOLS) XSTAR Tool for calculating the physical conditions and emission spectra of photoionized gases. The current version of HEAsoft is 6.0.4 (November 28 2005)

Launching HEASOFT

Typing 'heasoft-shell' at a terminal will launch heasoft.

The contents of the shell script:

#!/bin/bash
HEADAS=/opt/heasoft/current/i686-pc-linux-gnu-libc2.2.4
export HEADAS
. /opt/heasoft/current/i686-pc-linux-gnu-libc2.2.4/headas-init.sh
exec /bin/bash

IDL

IDL, the Interactive Data Language, or IDL, is a product of Research Systems Inc (RSI). It is a package designed to reduce, analyse and display scientific data and images. IDL can be used for tasks such as: Line drawing and fitting, contour and surface plotting, animation. Matrix operations, solving nonlinear equations, ffts etc. Writing functions and procedures. and much more. More extensive information is given in the IDL FAQ. We currently have IDL 6.3 installed.

For more information about our local IDL set up, see the IDL page on this wiki.

Libraries/Utilities

Markwardt IDL Library

The IDL Astronomy User's Library

IDL + C Code - including idlutils, idlspec2d, and kcorrect.

  • Note: the IDL + C libraries are not in the default IDL search path. To use them on a Configured Workstation, run
    idl+c-shell
    
    before starting idl. For more details, see the IDL + C Code section of the IDL page on this wiki.

Maps

Dust Maps (installed under /opt/rsi/idl/resource/maps/dust)

TeXtoIDL

TeXtoIDL: The purpose of the TeXtoIDL routines is to make it simple to use Greek letters, subscripts and superscripts in making labels for plots in IDL. This is accomplished by allowing the user to use TeX control sequences for Greek letters and special symbols and for sub/superscripts. The TeX control sequences are simple and easy to remember, especially if you already use TeX for writing papers (for those unfamiliar with TeX, an explanation of that notation is below). The translation is done for either vector or PostScript? fonts.

IDLWAVE

IDLWAVE: This package has been installed as part of Emacs to enable it to understand IDL syntax, which is very useful when writing IDL scripts. IDLWAVE also enables running an IDL shell within emacs - type:

M-X idlwave-shell

which runs your settup defined by the environment variable IDL_STARTUP.

IRAF

IRAF is a heterogeneous collection of routines and packages for all sorts of tasks, but it is first of all a data reduction environment, for which there is extensive on-line documentation.

Launching IRAF

To begin using the IRAF system, at a terminal and from the directory you wish to use as your iraf login directory type:

           mkiraf  # creates a login.cl file

By default, the login.cl file will try to use the shared 'imdirs' directory---which is not accessible as it is on a read only NFS counted partition. Instead, create a directory 'imdirs' on your local x and modify the specified location in the login.cl file.

           cl      # launches IRAF

Note that it is possible for the default imtype in IRAF to be set to .imh upon the initial build. Normally, you'll be dealing with fits files, so you will want to change this if this happens. You can check which imtype you are using with the command:

           show imtype    #returns the current imtype

To reset the imtype to fits use the command

           set imtype=fits

If it's not already there, putting this command in your login.cl file is recommended.

pyRAF

PyRAF is a new command language for IRAF based on the Python scripting language. It is useful both for interactive data analysis and for writing analysis scripts. PyRAF coexists with the current IRAF CL. We currently have version v1.2.1 installed, which includes a number new PyRAF packages for the HST instruments e.g. Pydrizzle and Multidrizzle.

Launching PYRAF

Typing 'pyraf' at a terminal will launch pyraf.

JObserve: Java Based Observe

JObserve is a rewrite of the older observe program for generating observing schedules for the VLA. More information can be found here Version 1.7.4 is currently installed.

Launching JObserve

To launch the application, type 'jobserve' at a terminal/shell.

KARMA

KARMA is a toolkit for interprocess communications, authentication, encryption, graphics display, user interface and manipulating the Karma network data structure. It contains KarmaLib? (the structured libraries and API) and a large number of modules (applications) to perform many standard tasks. A suite of visualisation tools are distributed with the library.

Launching KARMA

Typing 'karma-shell' at a terminal will launch karma.

The contents of the shell script:

#!/bin/csh
source /opt/karma/.login
exec /bin/csh

LAPACK

LAPACK is written in Fortran77 and provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems. The associated matrix factorizations (LU, Cholesky, QR, SVD, Schur, generalized Schur) are also provided, as are related computations such as reordering of the Schur factorizations and estimating condition numbers. Dense and banded matrices are handled, but not general sparse matrices. In all areas, similar functionality is provided for real and complex matrices, in both single and double precision.

Mathematica

Mathematica is NOT currently installed on the CAL system. We are investigating licensing options. In the meantime, if you have a Columbia 'uni', you can use mathematica installed on the cunix system.

Running Mathematica on cunix

To run mathematica on Ubuntu a number of tricks need to be employed.

First, you will need to download the mathematica fonts from this page and install them in your home directory at CAL (not cunix). Make the directory tree structure look like this:

~/.fonts/Mathematica/BDF

~/.fonts/Mathematica/Type1

Note that other packages come along for the ride, but they aren't needed for Mathematica 5.1.

To use the fonts, do:

 xset fp+ ~/.fonts/Mathematica/BDF

 xset fp+ ~/.fonts/Mathematica/Type1

 xset fp rehash

Now you can ssh into cunix and run mathematica with the following commands:

 ssh -Y username@cunix.columbia.edu

Enter your password. Then:

 Mathematica

Right now there is an issue with the Mathematica fonts being rendered transparent on Ubuntu and if a white screen is in the background of your notebook, your inputs and outputs will disappear. CUIT has been made aware of this problem, but it's anybody's guess whether they'll fix it.

Note that if either numlock and/or scroll lock is engaged, the mathematica interface won't work properly. So disengage them already! If you absolutely must have numlock engaged, there is a workaround discussed here.

For a more detailed description of how to install mathematica fonts and how to print mathematica notebooks from cal, please consult the attachment at the bottom of the screen entitled "mathematicafonts.txt".

Matlab

Matlab is NOT currently installed on the CAL system. If you have a Columbia 'uni', you can use matlab installed on the cunix system.

Running Matlab on cunix

ssh -X username@cunix.columbia.edu

matlab

MIRIAD

MIRIAD is radio interferometry data reduction package. It has particular emphasis on aspects of interest to users of the Australia Telescope Compact Array (ATCA). Miriad can be used for the reduction of continuum and spectral line experiments. Miriad, in particular, supports a number of niche areas. These include calibration and analysis of polarimetric data from the ATCA, multi-frequency synthesis imaging, mosaicing, ATCA pulsar bin mode, and some spectral line observing applications (e.g. Zeeman experiments).

Launching MIRIAD

Typing 'miriad-shell' at a terminal will launch miriad.

The contents of the shell script:

#!/bin/bash
. /opt/miriad/miriad_start.sh
exec /bin/bash

PHYSICA

PHYSICA is a high level, interactive programming environment with user friendly graphics and sophisticated mathematical analysis capabilities. Version 2.77

Launching PHYSICA

Typing 'physica-shell' at a terminal will launch physica.

The contents of the shell script:

#!/bin/bash
. /opt/physica/current/bin/physica.bash
exec /opt/physica/current/physica

PIMMS

PIMMS (Portable, Interactive, Multi-Mission Simulator) is intended as a versatile simulation tool for X-ray astronomers. It is primarily intended as a planning tool for future observations.

We currently have version 3.9b installed.

Launching PIMMS

Typing 'pimms' at a terminal will launch pimms.

SAS

SAS is the XMM-Newton Science Analysis System. We currently have version 7.0.0 installed.

Launching SAS

Typing 'sas-shell' at a terminal will launch sas.

The contents of the shell script:

#!/bin/bash
. /opt/sas/current/setsas.sh
exec /bin/bash

SCILAB

Scilab is a scientific software package for numerical computations providing a powerful open computing environment for engineering and scientific applications. Scilab includes hundreds of mathematical functions with the possibility to add interactively programs from various languages (C, Fortran...). It has sophisticated data structures (including lists, polynomials, rational functions, linear systems...), an interpreter and a high level programming language.

Launching SCILAB

Typing 'scilab' at a terminal will launch scilab.

Spitzer tools

Spitzer telescope observation preparation tool (SPOT). SPOT is the observation preparation tool for the Spitzer telescope. Leopard is the software package used to download data. A SPOT User Guide and Leopard User Guide are available. We currently have version spot v15.1 and leopard v6.1 installed.

Launching SPITZER (LEOPARD/SPOT)

Typing 'leopard' at a terminal will launch leopard. Typing 'spot' at a terminal will launch spot.

SExtractor

SExtractor is a program that builds a catalogue of objects from an astronomical image. Although it is particularly oriented towards reduction of large scale galaxy-survey data, it performs rather well on moderately crowded star fields. Documentation can be found on the website and in /usr/share/doc/sextractor/.

Launching SExtractor

For a minimal sextractor run, without customizing any of the parameters, use

sextractor file.fits -c /usr/share/sextractor/default.sex -PARAMETERS_NAME /usr/share/sextractor/default.param -FILTER N

The Starlink Software Collection is a collection of programs maintained by the Joint Astronomy Centre. There doesn't seem to be any centralized place for documentation for this collection, so to find out about it, you can either look through the website or look around in the directory /opt/star.

To set up the right environment for Starlink, enter:

star-shell

All the Starlink programs will then be available to you.

Then, for example, to run 'dipso', you would run

dipsosetup

and then

dipso

Stellarium

Stellarium is a free open source planetarium for your computer. It shows a realistic sky in 3D, just like what you see with the naked eye, binoculars or a telescope. It is being used in planetarium projectors. Just set your coordinates and go. version 0.7.1

Launching Stellarium

Typing 'stellarium' at a terminal will launch stellarium. Hit ctrl-q to exit.

STSDAS

STSDAS is the software for reducing and analyzing data from the Hubble Space Telescope. It is layered on top of IRAF and provides general purpose tools for astronomical data analysis as well as routines specifically designed for HST analysis. We currently have version 3.4 installed.

TEMPO

Tempo is a program for the analysis of pulsar timing data. Pulsar rotation, astrometric, and binary parameters are deduced by fitting models to pulse times of arrival measured at one or more terrestrial observatories. Tempo is maintained and distributed by Princeton University and the Australia Telescope National Facility. The code is freely available, and others are encouraged to extend, modify, and improve it as they see fit.

Launching TEMPO

Typing 'tempo' at a terminal will launch tempo.

The contents of the shell script:

#!/bin/bash
TEMPO=/opt/tempo/current exec /opt/tempo/current/tempo

Image Display Programs

ds9

SAOImage DS9 is an astronomical imaging and data visualization application. DS9 supports FITS images and binary tables, multiple frame buffers, region manipulation, and many scale algorithms and colormaps. It provides for easy communication with external analysis tasks and is highly configurable and extensible. The currently installed version is 4.0b8.

Launching DS9

Typing 'ds9' at a terminal will launch ds9.

PGPLOT

PGPLOT is a large subroutine library for plotting scientific data. The PGPLOT Graphics Subroutine Library is a Fortran- or C-callable, device-independent graphics package for making simple scientific graphs. It is intended for making graphical images of publication quality with minimum effort on the part of the user. For most applications, the program can be device-independent, and the output can be directed to the appropriate device at run time.

Attachments