Using the Software

Setting up multislit observations

• Take direct images of each slitmask, using either the internal continuum lamp, or the flat-field screen at the secondary.. For alignment purposes, 2x2 binning gives adequate resolution, and ccd readout is much quicker than 1x1 binning. 
• Prepare a direct image obsdef file for each mask. Template files for each camera/dewar orientation may be found in $COSMOS_HOME/examples/obsdef. For alignment purposes, the template dewar offset files found in $COSMOS_HOME/examples/dewoff are sufficient.
• Run apertures,  display the images with display8 (or make mosaic images of the masks with mosaic and display), then overlay the aperture positions, using the iraf routine tvmark to check approximate alignment. Unless something is very wrong, the apertures should be close (+- ten pixels or so) to the predicted positions. If they are not close, a first guess is that the masks have been mounted incorrectly in their holders. See the
IMACS Users Manual for instructions.

• Take a comparison arc through each slitmask, with each grating/grism you intend to use.
• Prepare a suitable list of comparison lines. The lines should be clean and isolated, to ensure correct convergence of the alignment routines. Some example linelists can be found in $COSMOSHOME/examples/linelists.
• Starting with the default dewar offset files found in $COSMOSHOME/examples/dewoff, run align-mask on each arc image, to produce a dewar offset file for each observing setup. If align-mask does not produce a satisfactory solution, run spectral-lines and overlay the predicted line positions on the arc image. This may show you that you need to (a) eliminate some of the comparison lines from your list or (b) adjust the size of the search region you are using: too small may miss lines, too large may find the wrong line.
• Run map-spectra to produce a spectral map for each mask/disperser/disperser-angle combination.
• Now, run adjust-map to correct any residual errors in the map.
• If the number of slits on  your masks is large (in the hundreds) you may want to use quick-list to prepare an abbreviated SMF file for the quick-look reductions.
• Setting up on your field:

• CDisplay a direct ccd image of the target field with display8, or create a mosaic with mosaic and display. 
• Run apertures to create an xy file, containing the positions of all apertures on the slitmask, including slits and alignment holes.
• Overlay the slitmask apertures, using the IRAF routine tvmark.
• Comparison of this overlay with a finding chart of your field should find the correct offset.

Setting up IFU observations

Checking the IFU alignment.

Because the images of each IFU fiber are very small, and adjacent fiber images are quite close together (only a few pixels with the short camera), very precise alignment is necessary for reliable image and spectral extraction. To check the IFU alignment, do the following:

• Take a direct image of the IFU, using either the internal continuum lamp, or the flat-field screen at the secondary, using 1x1 binning (in fact, always use 1x1 binning for IFU exposures.)
• Make a mosaic of this image using mosaic
• Copy the appropriate IFU dewar offset file from $COSMOS_HOME/examples/dewoff, and the appropriate IFU obsdef file from $COSMOS_HOME/examples/obsdef into your working directory.
• Copy the IFU.SMF file from $COSMOS_HOME/sdata into your working directory
• Run apertures to produce an xy file for the IFU fiber images.
• Use the IRAF routine tvmark to overlay the positions on the ifu mosaic (set mark type to "point"). The agreement will not be prefect: the individual fiber positions have not yet been totally calibrated, but there should be no systematic offset of greater than 1 pixel.
• If there is a significant offset, you will need to adjust the IFU.dewoff file. At the present time, ifu-offset is not yet available, so you must make the adjustments manually, using adjust-offset.

Spectral extractions

• If you have already performed the steps listed above to set-up for quick look reductions, then spectral extraction requires only the following steps:
• Flat-field and bias subtract your spectra. First prepare a spectroscopic flat field using Sflats, then use biasflat.
• Prepare an adjusted map for each object exposure, using adjacent arc exposure
• Use subsky to do sky subtraction.
• Use extract to CR clean, combine, and extract the spectra, or use extract-2dspec followed by sumspec to do the same more robustl
• Use viewspec to inspect them
• Nod & shuffle data: see the notes in the COSMOS Cookbook for specifics of how COSMOS handles N&S data.

Data reduction pipeline

Important Notes:

• At the present time, COSMOS programs cannot be executed from within IRAF. Run them from another window. (ialign, display8, and imcombine8 are  iraf programs, and should be run under cl.)
• Only a fraction of the disperser elements currently have default dewoff files. They will be added as each disperser is characterized. If you create a satisfactory dewoff file for a disperser element for which none exists, please send it to oemler@ociw.edu, so it can be added to the collection.
• Optical distortions in the camera, collimator, gratings, and grisms have not been completetly characterised. Images may, even after careful alignment, have systematic position errors of up to several pixels. As a consequence, the initial spectral mapping produced by map-spectra may have significant errors. Pay careful attention to the suggested procedure for testing spectral mapping described in the documentation on adjust-map.
• The ccd6 chip was replaced within IMACS on August 01, 2005. Be sure and correctly identify the dewar in the observation definition file, "SITE" for data taken prior to that date, "SITE2" for data taken later. If you use defineobs to construct the file, as you should, then secify the instruments as "IMACS" or "IMACS2".
• Do not try installing the software on llama on your home machine for data reduction. See Using COSMOS at home for information on installing COSMOS at your home institution. 
• Please report all bugs to oemler@ociw.edu, but please first make sure that you have carefully read the documentation and are using the software correctly.