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Using the Software

Setting up multislit observations
Setting up IFU observations
Spectral extractions
Important notes!

Setting up multislit observations

Before the start of observing:

For each mask:

• Take a direct image, 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 using defineobs
• Run mark-slits. Unless something is very wrong, the apertures should be close (±10 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.

If you wish to run the quick-look analysis at the telescope, you should also do the following:

• Take a comparison arc through each slitmask, with each disperser 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.
• Use defineobs to create an obsdef file for each mask/disperser combination
• Run align-mask on each sample arc. If align-mask does not produce a satisfactory solution, run mark-slits to check the alignment. This may show you that you need to (a) eliminate some of the comparison lines from your list or (b) you may need to run adjust-mask to tweak the initial dewar offset parameters.
• 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 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-spec to CR clean  and extract the spectra, then sumspec to combine the exposures..
• Use viewspectra to inspect them.
• Nod & shuffle data: see the notes in the COSMOS Cookbook for specifics of how COSMOS handles N&S data. See COSMOS Cookbook for helpful hints on reducing data.

 

Data reduction pipeline

After checking that processing of the first image is satisfactory, you can use process-dspec to pipeline the reduction of an entire set of exposrues.

 

Important Notes!

• At the present time, COSMOS programs cannot be executed from within IRAF. Run them from another window.
• Not all 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 cosmos[at]ociw.edu, so it can be added to the collection.
• Do not try installing the software on llama or burro on your home machine for data reduction. See Using COSMOS at home for information on installing COSMOS at your home institution.
• At the present time, badorders only works with 1x1 binned data.

Please report all bugs to cosmos[at]ociw.edu, but please first make sure that you have carefully read the documentation and are using the software correctly.

 

Next: Installing and running COSMOS

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