Installing the software

This tutorial uses the Gemini IRAF package, an IRAF implementation of L.A.Cosmic, and pyfu, an PyRAF package to combine GMOS IFU cubes. Finally, if you don’t have it already, the data package for this tutorial needs to be downloaded and unpacked. We will go through it all here.

Gemini AstroConda installation

Install Anaconda

The first step is to get anaconda. You can download it at:

It doesn’t matter whether you download the Python 3.6 or 2.7 version as we will force installation of 2.7 in the geminiconda environment later. Since the Python universe is moving to Python 3, it might be a good strategy, if you are planning to use Python for other purposes, to install the Python 3.6 version of anaconda.

If you have downloaded the graphical installer:

Follow the graphical installer instructions.  Install in your
home directory.  It should be the default.

If you have downloaded the command-line installer:

/bin/bash -l
chmod a+x Anaconda3-5.2.0-MacOSX-x86_64.sh
./Anaconda3-5.2.0-MacOSX-x86_64.sh

Install geminiconda

Anaconda requires the use of the bash shell. Tcsh or csh will not work. If you are using (t)csh, your first step is:

/bin/bash -l

Make sure that ~/anaconda/bin/activate is in your ``PATH, e.g. export PATH=~/anaconda/bin:$PATH in your .bash_profile. The Anaconda installer should have offered to add it for you.

Activate anaconda:

source ~/anaconda/bin/activate

Then let’s add the Astroconda channel and create our geminiconda environment with all the standard Gemini IRAF software and its necessary dependencies.

conda config --add channels http://ssb.stsci.edu/astroconda
conda create -n geminiconda python=2.7 iraf-all pyraf-all stsci gemini

Configure IRAF

source activate geminiconda
cd ~
mkdir iraf
cd iraf
mkiraf

At the mkiraf prompts choose xterm and re-initialize the uparm if asked.

Pyfu

Pyfu is software to align and combine GMOS IFU cubes. It is written and maintained by James Turner. Pyfu is a PyRAF package, ie. Python modules with an IRAF interface. James has shared his software on the Gemini Data Reduction Forum. It can be install with conda once the Gemini conda channel is configured. Version 0.10 is the minimum required version.

conda config --add channels http://astroconda.gemini.edu/public/
source activate geminiconda
conda install pyfu

That is it!

L.A.Cosmic

L.A.Cosmic is an algorithm written by P.G. van Dokkum to remove cosmic rays. The algorithm is described in P. G. van Dokkum, 2001, PASP, 113, 1420.

Because of licensing restrictions Gemini is not allowed to distribute it, therefore you will need to download it yourself. It is just one CL script.

Download lacos_spec.cl from this location:

Copy it to your home IRAF directory:

cp lacos_spec.cl /Users/youraccount/iraf/

(That’s a typical Mac OS X account path. For Linux, it probably looks like /home/youraccount/iraf/.)

Again, let’s tell IRAF where to find it. With your favorite editor, open the file /Users/youraccount/iraf/loginuser.cl. Then add these lines:

task lacos_spec = "/Users/youraccount/iraf/lacos_spec.cl"
keep

Data package

The data needed for this tutorial is packaged in this downloadable compressed archive file:

The document you are reading now is also contained in PDF and HTML in that download.

To set up, simply go to a directory on a disk with plenty of space ??? how much??? and unpack the archive:

cd /somewhere/
tar xvzf datapkg_GMOSIFU_Tutorial-v1.0.tar.gz

This will unpack in a directory called GMOSIFU_Tutorial and set up the directory we will be using throughout the tutorial. All input data are located in tutorial_data. The redux directory is where we will work. The calibrations directory is where we will store the processed calibration we will create.