1. Introduction

1.1. About This Cookbook

This cookbook provides python programs for reducing imaging and long-slit spectroscopic data taken with the FLAMINGOS-2 instrument on the Gemini South telescope, and descriptions of how to use and modify them. While these programs do group together reduction steps and can be run from start to finish to fully reduce scientific data with a minimal amount of preparation, they are not intended to be autonomous pipelines. You should always visually inspect your data for obvious defects and understand the processes involved in reducing your data so you can pinpoint where any problems arise.

No prior knowledge of python is assumed or required, although a basic understanding will be helpful: due to the rather awkward way in which PyRAF acts as an interface between python and IRAF, the tutorial scripts are not the best learning material.

Citations to this Cookbook should read:

Shaw, R. A., Simpson, C. 2020, FLAMINGOS-2 Data Reduction Cookbook (Version 1.1.1; Hilo, HI: Gemini Observatory)

1.2. Software Environment

The IRAF gemini package is presently the most comprehensive set of utilities for reducing data from F2. The only fully-supported way of obtaining the up-to-date version of this software is through the AstroConda distribution channel of Anaconda.

Full details of how to obtain and install Gemini IRAF and its dependencies can be found on the Gemini website and will not be addressed here.

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

conda update --all

1.2.1. Getting Help

Help is available if you run into problems. Contact:

1.3. 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.

1.3.1. 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 Load Associated Calibrations tab following a successful search.

1.3.2. Archive Searches

1.3.2.1. Science Data

There will always be multiple ways to select the science data you want from the GOA search page, including via Program ID, Target Name, or celestial coordinates. Note that, although proprietary data will appear in a search, only non-proprietary archival data (or your own proprietary data) will be available for download (the proprietary period for Gemini data is currently 12 months).

_images/GOA_search.jpg

Interface for GOA search for FLAMINGOS-2 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. This search was for spectroscopic data from program GS-2014B-Q-17 with a restricted date range.

After a successful search for your data of interest, you should 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 local disk. If you are only interested in a few files, you can manually check those files and click the Download Marked Files button.

1.3.2.2. Calibration Data

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

  • Darks
  • Flat-fields
  • Arcs
  • Telluric standard stars

Very often observers include additional standard star exposures in their programs, depending upon the science goals.

To find the appropriate calibrations for your chosen science exposures, click the Load Associated Calibrations tab on the search results page. Note that this will find the calibrations appropriate for all the science exposures, and not just those that have been checked. It is therefore worth being as precise as possible in your science data search to ensure that only relevant calibrations are found.

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.

After downloading all files, you should create a working directory for the raw data, and extract the files from the tarballs there, using tar xvf /path/to/gemini_data.tar. Then use bunzip2 to uncompress the files. If an unnecessarily large number of calibration files have been downloaded, this is a sensible time to delete any extraneous ones.

1.3.3. Types of Observations

The following types of FLAMINGOS-2 observations are routinely obtained, depending upon the observing program. Types in italics are rarely useful for data reduction.

Types of Observations
Type Frequency Description
Dark several per week Sequence of finite-duration exposures with the shutter closed. Duration of darks must match the duration of science exposures and be taken with the same readout mode.
Flat-field several monthly per filter Sequence of exposures of the GCAL flat-field lamp. 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 Argon 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. Usually these are dithered to allow background subtraction.
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>pix-slit). Usually these are dithered along the slit to allow subtraction of bright sky lines.
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.

1.4. Data Packaging

1.4.1. File Nomenclature

It is usually simplest during data reduction to retain the filenames of raw exposures as provided by the Gemini Observatory Archive, and to allow processing tasks to take care of naming output files. The raw filename template is the following:

<site><yyyy><mm><dd> S <nnnn> .fits

where S and .fits are literals, and:

  • <site> is either N or S, indicating which telescope took the data
  • <yyyy><mm><dd> is the year, numerical month, and UT date of observation
  • <nnnn> is a 4-digit (prefixed with zeroes if necessary) running sequence number within a UT day

1.4.2. Multi-Extension FITS

_images/MEF.png

FLAMINGOS-2 raw data, and processed data as produced by tasks in the f2 and related packages, 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 FLAMINGOS-2 website. Each MEF file contains a Primary Header-data unit (PHU), followed by one or more standard FITS extensions. The extensions are numbered sequentially, and will contain header keywords EXTNAME describing the type of data they contain and EXTVER with a value equal to the extension number.

F2 MEF files follow the FITS Standard recommendation that the PHU 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 F2 data files depends upon the level of processing and the content, and the extensions can appear in any order. Raw exposures contain a \(2048\times2048\times1\) pixel array in the first extension. The table below summarizes the structure of the contents for reduced data products. Optional extensions in grey are added if the fl_vardq+ flags are specified during processing.

_images/Extn_Table.png