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Data Reduction Utilities in IDL and IRAF
Additional Michelle Data Reduction Tools/Utility Scripts
This page provides links to a number of IRAF or IDL tasks that are useful utilities for either Michelle data reduction, or examining a set of data. Some of the IRAF tasks are likely to be released with the next revision of the Gemini IRAF package, whereas others are private routines that are never going to be part of the Gemini/IRAF package.
The IDL utilities cannot be officially supported because they use IDL, which is not freely available software, but are provided here for use by Michelle PIs if they so wish.
Questions about these routines should be directed to Scott Fisher (IDL) or Kevin Volk (IRAF). Note, however, that we do not guarantee that we will be allowed to support these routines. You may be on your own with them.
The IRAF scripts were written by Kevin Volk, usually initially for
his own use, and so do not necessarily comply with the coding standards
that are enforced for the Gemini IRAF package. Some of the IRAF scripts
have a help page in the usual IRAF format, which can be displayed within
IRAF via the help command by specifying the path to the help file
and specifying the file_template flag. For example
cl> help /some/file/path/miclean.hlp file_template+
will show the help page for miclean.cl provided that the path
("/some/file/path/" above) is replaced by the proper path to where the file
is stored. Not all the scripts have help files at the moment.
The IRAF tasks can be defined at the IRAF prompt as in the following
cl> task miclean = /some/file/path/miclearn.cl
where again one has to provide the proper path to the script file.
The IDL Defringing Widget
The IDL procedure mdefringe.pro is a widget for defringing Michelle spectra working with the stacked data file. This procedure works in IDL versions 6 and 7. It will probably not work in earlier versions of IDL. The procedure can read in a Michelle stacked image and display a two-dimensional fourier transform of the image. If one then masks out regions of the fourier image with the cursor, these are blanked off. Once regions are blanked off one can transform the fourier image back to the original domain and see what effect the masking has had. Especially for Michelle medN2 spectroscopy this is able to get rid of a large part of the spectral fringes in the data. It works better than the IRAF routine for defringing the one-dimensional extracted spectra in the test cases we have been working with.
For low-resolution N-band spectra the defringing in IRAF is usually
quite sufficient and this tool is not needed for such data. For the medN1
Michelle spectral mode the results of using the IDL procedure appear to be
less satisfactory than is the case for the medN2 mode, but its still better
than what the IRAF defringing produces.
This IDL procedure requires the installation of the IDL Astronomy User's Library for it to work.
An example of the use of the procedure is given here.
Noise Masking procedures
Once a stacked Michelle or T-ReCS image has been read into IDL, the following two procedures can be used to remove vertical or horizontal pattern noise. These are stand-alone IDL procedures, originally written by Jim deBuizer (here is a link to his professional web page where there is a link to his IDL tools for T-ReCS image reduction for anyone who may be interested).
Additional IRAF Utility Scripts
Links are provided below to the scripts and the associated help files where these exist. A short description of each routine is provided.
This is a script to remove certain types of noise from stacked Michelle (or T-ReCS) images. It can in princple be used on raw data as well but this is not recommended. The task generally is able to remove the channel to channel offsets, vertical band noise, and horizontal band noise in Michelle images.
This script produces rough polarimetry maps (Stokes parameters and the polarization vector quantities) from a stacked polarimetry image produced by the mipstack routine. While it is not a substitute for reduction using a polarimetry package, it does produce a good first look at Michelle polarimetry data.
In some cases one may wish to stack the "A" and "B" nods separately. This script carries out this operation. Note that telescope radiative offset and sky residuals will be present in the stacked images. Nonetheless in some instances it is useful to examine the two nod positions separately if there is something unusual seen in the straight stack of the nod images.
There is no help file for this script. It is fairly self-explanatory.
The minods.cl script splits off the individual nod images from a regular T-ReCS or Michelle raw data file or prepared data file and writes these out to disk as individual simple FITS files. For polarimtery files it is better to use mipsplit.cl for this type of purpose.
Again there is no help file for this script as it is reasonably simple in concept.
For those who like to work with the individual images of a polarimetry file, the script mipsplit.cl writes each polarimetry wave-plate image to a separate simple FITS file.
The purpose of this task is to sequentially display a series of Michelle stacked images, with the option of using imexam on each one. It is useful if one downloads a large set of files from a Michelle program and wishes to look at the various files to see what is what. Note that if one has a set of raw data files these would have to be run through the mireduce script as a group first before using this script.
Here is another data examination script. This one is intended to look through the individual nods in a Michelle or T-ReCS raw data file (or a "prepared" file) by displaying the nods in groups in the DS9 or XIMTOOL window, with the option of going into imexam to look at each set of NOD images. As with some of the other utilities here, this is most useful if something unusual appears to be present in a stacked Michelle or T-ReCS image. In normal IRAF one may be limited to 4 images displayed at once, but in PyRAF I think one can go up to 16 images at once.
There is no help file for this script.