NOTE: To browse what Gemini Users have exchanged about tricks, issues and solutions regarding reduction of NIFS data, please go to the DR forum (tag=NIFS).
The basic format of all Gemini data is explained in the data section of the Gemini website. The Example NIFS processing scripts for baseline calibration data, telluric data, and science data are very good starting points for reducing your data. See the notes at the top of each to learn how to update the scripts and run a nearly non-interactive data reduction for publicly available SV data. These scripts can also be accessed in your IRAF session by typing at the cl prompt:
ni> nifsexamples calibration
ni> nifsexamples telluric
ni> nifsexamples science
Pyraf-compatible adaptations of these scripts are available here: NIFS_Basecalib.py, NIFS_Telluric.py, NIFS_Science.py, which can be used with the following tutorial data set. This data set and an associated presentation (ppt|pdf) were used at a Gemini Data Reduction Workshop held in Tucson, July 2010.
Detailed information on NIFS data and reduction is displayed below. This information is the output of nifs.nifsinfo in the NIFS IRAF package and can be accessed from within your IRAF session by typing at the cl prompt:
nifsinfo -- Generic information on NIFS data and reduction
The NIFS package contains tasks for processing NIFS integral-field (IFU) spectroscopy data. The specifics of the individual tasks can be found in their help files. This document describes the common features of the generic tasks and gives a description of the NIFS data format. NIFSEXAMPLES provides sample "recipes" (processing scripts).
Because some of the routines for proper reduction of infrared spectral data already exist within the Gemini IRAF package, reduction of NIFS data uses some tasks that are inherent in the Gemini IRAF package for GNIRS data reduction. These GNIRS scripts have the prefix "ns". Tasks that are NIFS-specific and will work only with NIFS IFU data have the prefix "nf".
All of the tasks used for NIFS reduction produce logfiles of the performed processing steps. The name of the logfile may be set in each individual task, or at the package level by setting logfile.
The tasks add header keywords to the output images. These header keywords contain information about the performed processing steps and the values of the critical parameters that were used.
All NIFS images are written as multi-extension FITS (MEF) files. Raw data have two unnamed extensions. Most of the header information is written to the primary header unit (PHU) which is extension . The data read from the array is in extension .
DATA FORMAT AND PREPARATION
Processing with NFPREPARE (this task is used only for NIFS data - see below - but other instruments have their own preparation tasks with similar actions) will rename the data extension and add variance and data quality extensions. By default (see NSHEADERS) the extension names are SCI for science data, VAR for variance, and DQ for data quality (0 = good). Generation of the data quality plane (DQ) is important in order to fix hot and dark pixels on the NIFS detector in subsequent steps in the data reduction process. Various header keywords (used later) are also added in NFPREPARE.
NFPREPARE will also add an MDF file (extension MDF) describing the NIFS image slicer pattern and how the IFU maps to the sky field.
MEF STRUCTURE OF REDUCED DATA
NIFS data reduction will cut the image slices and extract the regions of interest from the raw data. In the case of NIFS IFU frames, data that has been run through the first few reduction steps will have many extensions - one extension for the SCI, VAR and DQ planes for each of the 29 different slices in the IFU. The second extension containing science data, for example, is denoted by [SCI,2]. So, NIFS data reduced with variance and data quality planes will have 87 different extensions after being NSCUT - 29 SCI, 29 VAR and 29 DQ.
The task GEMEXTN, when used with default parameters and no arguments, will display all the extensions in a file:
> unlearn gemextn
> gemextn snN20060202S0015
This includes both the index (inside the first ) and the extension name and version (second ). It is only necessary to use one of these, since either uniquely identifies an extension. Name and version are recommended because they specify the type of data contained. There is no guarantee about the ordering of indices apart from extension , the PHU, which always contains only header information.
Additional information and ways to handle MEF files can be found in http://www.gemini.edu/sciops/data/dataFormat.html
HEADER PARAMETERS AND INSTRUMENT SPECIFIC OPTIONS
The task NSHEADERS lists the header parameters used by the various tasks in the NIFS package (some header values which have values fixed by IRAF or FITS conventions are not included since they cannot be changed).
Before reducing data from NIFS, the user should always run
> nsheaders nifs
Note that not all header parameters named in NSHEADERS need appear
in the raw data. Some are used internally by the NIFS package. Others are used by NFPREPARE alone.
SUMMARY OF THE NIFS DATA REDUCTION TASKS
NSHEADERS - Prepare the session for NIFS data reduction (task resides in the GNIRS package)
This task is describedin more detail above. It should be called before all other scripts to configure the package for processing data from NIFS.
NFACQUIRE - Construct quick-look NIFS images Derive quick-look images of the NIFS IFU field from flip-mirror acquisition data. This task is primarily used for acquisition of faint targets at the telescope. The option exists to derive offsets to center a target within the IFU field.
NFIMAGE - Construct quick-look NIFS images from dispersed data. Derive quick-look images of the NIFS IFU field from dispersed science exposures. This task can be used for acquisition of bright targets at the telescope, but has also proved to be very useful for viewing the IFU field sky region from any dispersed data. The option exists to derive offsets to center a target within the IFU field.
NFPREPARE - Prepare NIFS data for reduction
This task is described in more detail above. It must be called before the other tasks listed below.
NSFLAT - Produce a normalized spectral flatfield (task resides in the GNIRS package)
NSFLAT is used to produce a normalized spectralflatfield image. For IFU data it is usually used after calling NSREDUCE or NSCUT. To preserve a consistent normalization between slices, IFU flats must also be processed subsequently with
NSREDUCE - Process NearIR Spectral data (task resides in the GNIRS package)
NSREDUCE is used for basic reduction of raw data - it provides a single, unified interface to several tasks and also allows for the subtraction of dark frames and dividing by the flat. For NIFS reduction, NSREDUCE is used to call the NSCUT and NSAPPWAVE routines.
Note that NSREDUCE will not call NFPREPARE.
NSSLITFUNCTION - Correct the flat field for inter-slice variations (task resides in the GNIRS package)
NSSLITFUNCTION extends the flatfield produced by correcting the NSFLAT normalization for inter-slice variations. The output from this task is used as the flatfield image forfurther reduction.
NSAPPWAVE - Determines a simple wavelength calibration (task resides in the GNIRS package)
NSAPPWAVE provides a quick, approximate wavelength solution for NIFS spectroscopic data. The wavelength solution is based on the header information and (by default) information in the table gnirs$data/nsappwave.fits (use the TTOOLS package to examine this - TPRINT will display the contents - but if it is necessary to add/delete entries or create a new table, this can be done with the dedicated NSWEDIT task).
The task is for quick reduction purposes and to provide a starting point for the wavelength calibration derived by NSWAVELENGTH.
NSWAVELENGTH - Establish an accurate wavelength calibration (task resides in the GNIRS package)
NSWAVELENGTH (automatically, if possible) determines the wavelength solution for NIFS calibration lamp images, starting with the initial value supplied by NSAPPWAVE (this is done using the underlying IRAF tasks autoidentify and reidentify).
This task does not calibrate the data directly, but provides a database entry that can be used by NSTRANSFORM (described below).
NFSDIST - Establish a spatial calibration
NFSDIST uses the information in the "Ronchi" Calibration images to calibrate the spatial dimension of the NIFS IFU field. The Ronchi frame is a dispersed flat field image with a slit-mask in the field so that the illumination on the IFU is in a
pattern of ~10 different slitlets that are stackedin the y-dimension on the field. Proper alignment of the slits across the image slicer pattern can be used for spatial rectification of the on-sky science data. The spatial solution determined by NFSDIST is linked to the science data in NFFITCOORDS.
NFFIXBAD - Fix Hot/Cold pixels on the NIFS detector
This routine uses the information in the Data Quality extensions to fix hot and cold pixels in the NIFS science fields. NFFIXBAD is a wrapper script which callsthe task FIXPIX, using the DQ plane to define the pixels to be corrected.
NFFITCOORDS - Compute 2D dispersion and distortion maps
This routine uses as inputs the output from the NSWAVELENGTH and NFSDIST routines. NFFITCOORDS takes the spatial and spectral rectification information from NSWAVELENGTH and NFSDIST and converts this into a calculation of where the data information should map to in a final IFU dataset.
NSTRANSFORM - Spatially rectify and wavelength calibrate data
NFTRANSFORM applies the wavelength solution found by NSWAVELENGTH and the spatial correction found by NFSDIST, aligning all the IFU extensions consistently onto a common coordinate system. The output of this routine is still in 2D format, with each of the IFU slices represented by its own data extension.
NIFCUBE - Construct 3D NIFS datacubes
NIFCUBE takes input from data output by either NFFITCOORDS or NFTRANSFORM and converts the2D data images into data cubes that have coordinates of x, y, lambda.
NFEXTRACT - Extract NIFS spectra
This could be used to extract a 1D spectra from IFU data and is particularly useful for extracting the bright spectra of telluric calibrator stars. Note that this routine only works on data that has been run through NFTRANSFORM.
NFTELLURIC uses input science and a 1D spectrum of a telluric calibrator to correct atmospheric absorption features.
For typical reductions the user will need appropriate flat fields, arc calibration images, darks, Ronchi calibration frames and science images.
NOTE - USE the NIFSEXAMPLES option at the IRAF prompt to obtain example scripts for calibration, telluric and science reductions.
Use GEMTOOLS.GEMLIST to make separate lists of the files associated with different exposure types. Tasks can then be invoked on all the data of one type using iraf's "@" syntax. For example, NFPREPARE might be called with inimages=@flatlist and then NSREDUCE with inimages=n@flatlist (which prepends the letter "n" - nsprepare.outprefix - to each filename).
MDF SHIFT DETERMINATION:
Step 0. Run NFPREPARE on a single "lamps on" flat to determine the shift between your IFU data and the definition of the Image Slicer position in the MDF file. The output from this step will be used in all subsequence calls to NFPREPARE as the "shiftimage".
FLAT FIELD REDUCTION:
Step 1. Use NFPREPARE on the lamps on/lamps off flats to update the raw data headers and attach the mask definition file (MDF) as a binary table on all files. Note that dark frames will not have an MDF attached by default. Instead, the appropriate MDF is added in NSREDUCE or NSFLAT to match the data being reduced.
Step 2. Use NSREDUCE to cut the calibration (flat/arc) spectra to the size specified by the MDF, placing different IFU slices in separate image extensions.
Step 3. Use NSFLAT to generate a normalized flat field (for each IFU slice or cross-dispersed order) from lamp flats. A mask (BPM) will also be generated by thresholding - this can be used to flag bad pixels in other data.
Step 4. Use NSSLITFUNCTION to produce the final flat.
Step 5. Repeat steps 1 & 2 for the arcs and arc darks (use the appropriate flat field and arc darks in the call to NSREDUCE).
Step 6. Use NSWAVELENGTH to calibrate arc data (after cutting and optionally applying a flatfield with NSREDUCE).
Step 7. Repeat steps 1 & 2 for the Ronchi calibration frames. Use the dark frame generated by the flat fielding steps in NSREDUCE.
STEP 8. Measure spatial mapping for the image slices with NFSDIST, using the output from step 7 after cutting with NSCUT in NSREDUCE (this step is required for accurate alignment of the slices).
SCIENCE DATA REDUCTION:
Step 9. If necessary, Repeat Steps 1 & 2 for the Dark frames observed at the science exposure time.
Step 10. Repeat Step 1 for the science data. Make sure to use NSREDUCE not only to process the object data to cut the frames from NSCUT, but also to apply the approximate wavelength calibration from NSAPPWAVE. Use the darks generated in Step 9 as input into NSREDUCE.
Step 11. Run the science data through NFFIXBAD to clean bad pixels - note that this step can be time consuming.
Step 12. Use the output from the calibration Step 6 (NSWAVELENGTH) and Step 8 (NFSDIST) as input into the NFFITCOORDS routine to generate the mapping for the IFU datacube.
Step 13. Use NFTRANSFORM to resample the combined object data to a uniform wavelength scale, with consistent spatial alignment between different slices and wavelengths.
Step 14. TELLURIC CALIBRATOR: Repeat Steps 10 through 13 on the data for the telluric calibration star.
Step 15. TELLURIC CALIBRATOR: Extract 1-D spectra from the telluric calibrator using the NFEXTRACT routine. If necessary, merge several extracted 1-D spectra using the GEMCOMBINE routine in the Gemini IRAF package (with statsec="[*]" for 1D data).
Step 16. Use the NIFS NFTRANSFORMED data and the 1D telluric calibrator Spectra in the NFTELLURIC routine to correct out telluric absorption features.
Step 17. Use NIFCUBE to construct a datacube from the final science data.
FINAL PRODUCT = Telluric corrected 3D science data cubes with proper wavelength and spatial calibration.
CURRENT LIMITATIONS OF THE REDUCTION:
In the NIFS data reduction package, there is currently no way to:
-Flux calibrate the NIFS datacubes.
-Correct for instrument flexure in multiple exposures.
-Correct out photospheric absorption features in telluric standards.
-Correct for heliocentric radial velocity variations.
-Combine dithered datasets into a single, larger cube.
-Rectify data for atmospheric refraction effects.
Example reduction scripts are available, see NIFSEXAMPLES.
ABBREVIATIONS USED IN THE NIFS HELPFILES
NIFS Near-IR Integral Field Spectrograph
IFU Integral field unit
MDF Mask defintion file (a binary FITS table)
MEF Multi-extension FITS
PHU Primary header unit (extension  of a MEF file)
BUGS AND LIMITATIONS
The tasks in the NIFS package are designed to operate on MEF FITS images that have been processed using NFPREPARE (for NIFS data)
nifsexamples, nsflat, nfprepare, nsreduce, nsappwave, nswavelength, nffitcoords, nftransform, nfextract, nffixbad nfsdist, nifcube, gemlist, gemcombine, gemarith.