Getting Started

Processing and calibrating your GMOS data requires some preparation. In this section, you will find details on how to set up your software environment and retrieve/organize the data of interest. There is also a comprehensive list of reference materials that may be of interest to the user.

Warning

The GMOS tutorial scripts were written using v1.14 of the Gemini IRAF package, which is the version provided by the instructions in this page. Use of prior versions is unlikely to be compatible. Please follow the installation steps in the Software Environment section below. For computers running Mac OSX 10.15 and above, users should skip the Software Environment section and install the Gemini Virtual Machine. For computers using the new Apple M1 chip, an alternative environment is under development by the Gemini staff (see announcement). Further details can be found in the Gemini Data Processing website.

Contents

• Getting Started

  • Software Environment

  • Data Downloads

  • Reference Materials

  • Getting Organized

Software Environment

The IRAF Gemini package is presently the most comprehensive set of utilities for reducing data from GMOS. There is more than one way to install and configure the software needed to reduce your GMOS data. However, most users prefer a relatively simple installation process that is robust, easy to upgrade, and that does not interfere with other software that is installed on their hardware. This section will describe the recommended path (which, happily, requires the least time and trouble) to install the software you will need.

IRAF, PyRAF, the Gemini data reduction package, and all required dependency packages are, as of 2016 May, distributed through the AstroConda software repository. The instructions below describe the essentials of setting up the software environment, but for full details see the full AstroConda Installation Instructions.

First-Time Setup

The first step is to install python and various supporting packages on your system; this is a prerequisite for the PyRAF environment. That may seem odd if you only want to use IRAF for your data reductions. But the platform supported by Gemini Observatory is PyRAF, and there are known problems and incompatibilities with the Gemini package using the standard IRAF distribution. It is also critical to select a python version and a consistent set of dependency packages, which may or may not be fully compatible with what you currently have on your personal machine.

The solution is to install the Anaconda distribution of python from Continuum Analytics, and then install PyRAF and related packages from the AstroConda distribution at Space Telescope Science Institute.

Note

Anaconda and AstroConda do not interfere with your current defaults for IRAF, python and related packages if they are already installed on your computer. It merely provides a way to install and use one or more consistent and compatible sets of software environments for Gemini/IRAF. AstroConda provides shell commands that allow you to switch between environments.

Anaconda

Anaconda Update

If you already have the Anaconda distribution installed on your system, ensure that the packages are up to date:

conda update --all

First-Time Install

If this is a first-time setup, install and configure python and related packages from Anaconda.

1. Use bash. Be sure you are using the bash shell (the response to typing echo $SHELL should be something like /bin/bash). If this is not your default shell, start one (e.g., by typing bash -l in your current terminal window).

2. Download Anaconda. Fetch the command-line installer appropriate to your system for python version 2.7, and place it in a suitable directory.

3. Invoke the installer. From the directory where you placed the downloaded install script, invoke it:

# Mac OSX users:
bash AnacondaX-X.X-MacOSX-x86_64.sh

# Linux users:
bash AnacondaX-X.X-Linux-x86_64.sh

The exact name of the file will depend upon the version number and the name of your platform. The installation process may take awhile, as it downloads, unpacks, and installs a lot of software including IRAF, python, and supporting packages.

4. Start a new terminal window for the changes to your login file to take effect. Then type which conda; the response should be the path to the Anaconda installation. If instead the response is a blank line, update your bash shell configuration file to include the path to the anaconda installation.

AstroConda

You should review the detailed documentation for AstroConda, particularly the installation instructions. The instructions to get pyraf running are summarized below.

First-Time Install

The first step is to configure Anaconda to install software packages directly from the STScI AstroConda repository. The following will add AstroConda to the Conda search path (defined in the ~/.condarc file):

conda config --add channels http://ssb.stsci.edu/astroconda

Now software can be installed from the AstroConda repository:

conda create -n iraf27 python=2.7 iraf pyraf stsci

Subsequent Uses

Once all the software has been installed, activate the data analysis environment of your choice each time you start a shell:

# Python with IRAF and PyRAF:
source activate iraf27

Now start your preferred data reduction environment as usual. To return to your default (non-AstroConda) installation of IRAF and python, type source deactivate iraf27 at the Unix prompt, or close the terminal window.

IRAF, PyRAF, and Python

Configure your IRAF setup if you have not already done so, preferably in a directory that is by default compatible with PyRAF:

cd ~
mkdir iraf
cd iraf
mkiraf
...
# Respond to the prompt to select an IRAF terminal type, e.g.:
Enter terminal type [default: xterm]: xgterm

Finally, start the analysis environment of your choice from the command-line prompt:

• cl for IRAF

• pyraf for PyRAF

• python

For an interactive python session, import the relevant portion of the pyraf package.

import sys
from pyraf import iraf

See the PyRAF Programmer’s Guide by Phil Hodge, specifically the chapter Writing Python Scripts that Use IRAF/PyRAF Tasks.

Add-on Task for CR Rejection

Rejecting cosmic rays (CRs) from individual spectral images is challenging, particularly from a narrow emission-line source or from closely packed IFU fibers. An add-on task, the L.A.Cosmic program developed by Pieter van Dokkum (see [VD]), rejects CRs very well under these circumstances. This program is invoked by the gemtools.gemcrspec task, which is an MEF-aware wrapper for lacos_spec.cl.

To install this task for use in the gmos package:

• Download the script: lacos_spec.cl

• Place the script in your IRAF login directory

• Install the task in an IRAF session as:

task lacos_spec= /path/to/iraf_home/lacos_spec.cl

Place this definition in your IRAF login.cl or loginuser.cl file (after the gemini and gemtools packages are loaded) to ensure that it is available for all subsequent IRAF sessions.

Getting Help

Problems with installing or invoking the software should be directed to: help@stsci.edu. Problems with using the software should be directed to Gemini staff: see GMOS Help.

Data Downloads

Search and retrieve the science and calibration data from the Gemini Observatory Archive for each program, source, or calendar night of interest. See the GOA overview for details.

First-Time Access

If you are a general archive user, no login is necessary to search for any data, or to retrieve non-proprietary data including calibration frames. Only if you are a PI or Co-I of an observing program and you wish to retrieve your proprietary data, you must do the following before you can access these files:

1. Request an account if you don’t already have one. You will receive an e-mail telling you how to establish a password (or data access key in their vernacular).

2. Navigate to the Gemini Observatory Archive in your browser.

3. Click the Not logged in link at the upper right of the page and login using your account credentials. You will need your program ID and password to retrieve your proprietary data.

PIs of Gemini observing programs should have received in their award notification email the instructions for how to establish an account.

Caution

Note that applicable ancillary data (arc lamp, flat-field, or standard star exposures) may have been obtained on a night other than that of the science observation(s) of interest. You may need these exposures to calibrate the science data, particularly if they were obtained in Queue mode. These calibration data are normally accessible by clicking the Associated Calibrations tab following a successful search.

Archive Searches

Science Data

GOA searches for GMOS data begin with selecting GMOS (or one of the variants) from the Instrument pull-down menu, as shown below.

Interface for GOA search for GMOS-N or GMOS-S data, also showing the available metadata that may be displayed in columns of the results table. The tabs at the bottom allow access to the calibration data for the specified program.

Information about specific targets that were observed in a spectroscopic mode are not recorded in Archive metadata. This makes searching for spectra of scientific targets of interest more challenging, and in general requires that you download data and/or mask definition files in order to figure out if spectra exist of specific targets.

Calibration Data

Calibration exposures are routinely obtained by Gemini staff to support queue observations, and to monitor the health and performance of the instruments. Some calibrations are obtained at night to support queue mode. The exposures of most potential interest for data reduction include:

• Bias

• Nod-and-Shuffle Darks

• Arcs

• Flat-fields (GCAL and Twilight)

• Standard stars

Very often observers include additional arc, flat-field, and standard star exposures in their programs, depending upon the science goals. It is important, after a successful search for science exposures, to click the Associated Calibrations tab and retrieve all calibration exposures that are applicable to your program.

Retrieving Data

After a successful search for your data of interest, do the following:

• Scroll to the bottom of the search results and click the Download all [NNN] files button. This will create a tar of the selected files and download it to your machine. Naturally you can download only selected files from the search table, if you have the patience.

• Click the Load Associated Calibrations tab on the search results page, and click the Download all [NNN] files button. It is common for these files to include some exposures you do not need, but but it is easier to ignore them during data reduction than to attempt to filter them out with tighter archive search criteria.

• Move the tar files to your desired working directory and un-tar. Move all the raw files to a subdirectory called /raw, then use bunzip2 to uncompress the files.

Data Packaging

GMOS raw data, and processed data as produced by tasks in the gmos package, are stored in FITS files and structured internally in Multi-Extension FITS (MEF)—i.e., FITS files with one or more standard extensions. MEF files are used to group logically connected data objects, as explained below and on the GMOS website. The structure of an MEF file is shown at right: a Primary Header-data unit (PHDU), followed by one or more standard FITS extensions. The extensions are numbered sequentially, and normally will contain a header keyword record called EXTVER with a value equal to the extension number.

GMOS MEF files follow the convention that the PHDU never contains image pixel data; the extensions are either of type IMAGE or BINTABLE, and no other type. The number and type of extensions in GMOS files depends upon the level of processing and the content, and the extensions can appear in any order. The table below summarizes the structure of the contents for common data products. Optional extensions in grey are added if the fl_vardq+ flags are specified during processing.

Reference Materials

In addition to the material in the Useful Resources chapter, it may be handy to have the following documents available when reducing your data:

• GMOS Instrument pages

• Data reduction recipes, see Processing Tutorials

• Supplemental calibration files, see Calibration Material

Getting Organized

Many GMOS observing programs (on clear nights, at least) generate hundreds of exposures. Some of them (such as acq exposures) may have been obtained to configure the instrument for observing and are not relevant for data reduction.

Types of Observations

The following types of GMOS observations are routinely obtained, depending upon the observing program. Types in italics are rarely useful for data reduction.

Types of Observations

Type	Frequency	Description
Focus	a few to several per night	Part of a sequence of exposures of a bright star or a flat-field lamp used to obtain the best focus of the telescope or the spectrograph. Not used for calibration.
Bias (zero)	10 or more per day and per read-out RoI	Sequence of zero-second exposures used to characterize the bias structure. Routinely obtained as a regular part of dayCal exposures. They are combined and used to apply a correction for residual bias.
Dark	10 or more per night and per read-out region	Sequence of finite-duration exposures with the shutter closed that are used to correct hot pixels and general dark current level. Not usually used except with Nod-and-Shuffle observations.
Flat-field	several nightly per filter	Sequence of exposures of the twilight sky (typically for imaging) or with the GCAL flat-field lamp (for spectroscopy). They are combined and normalized to apply the pixel-level sensitivity correction.
Comparison Arc	one or more per night per slit/grating combination	Exposures of the CuAr comparison arc used to derive geometric rectification and wavelength calibration.
Image	one or more per filter per target field	Science image obtained with ObsMode = imaging. May also be obtained for target field acquisition.
Acquisition image	one or more per target field	Short-duration image obtained through a custom Slit-mask (ObsMode = acq). Used to determine offsets from targets to slits; not used for data reductions.
Long-slit spectrum	one or more per target position	Science spectrum obtained with a facility longslit (MASKNAME = <X.X>arcsec).
MOS spectrum	one or more per target position	Science spectra obtained with a custom Slit-mask (MASKNAME = <mask>); one spectrum per slit including field stars. Mask names include the observing program ID.
IFU spectrum	one or more per target position	Science spectra obtained with MASKNAME = IFU; one spectrum per fiber in the field(s)

Proceed to data reduction with Processing Science Data.