The following comments refer to HIRES data reductions. I have not yet (November 2000) made serious attempts to flux calibrate ESI data, although I am hopeful the ESI spectra may flux calibrate more successfully than has been my experience so far with HIRES data.
The Flux-###.fits 2D spectrum files produced by makee are not flux calibrated. The values are in counts divided by the flat field spectrum. It is possible to do an approximate flux calibration using a standard star , however since the response function across echelle orders varies as a function of telescope position in a (as of now) unpredictable manner, the response function derived from the standard star will often not correctly flux calibrate the object. Furthermore, with respect to the shape of the spectrum and alignment between orders, flux calibration can sometimes make things worse.
Nevertheless, the following programs can be used to (approximately) flux calibrate your object spectrum. This process has been divided into four steps so you can inspect the spectra at each stage.
Look in ./makee/StanStarDataBase/ to find the FITS file of your standard star. If your star is not in this directory you cannot use these programs to flux calibrate. Look for the ".bwr" (bad wavelength regions) file which gives the sections to be masked in the response function. This file is used by starzero to mask bad regions. You can edit this file if too many bad features appear in your response spectrum. You can give these filenames in the program arguments, or the program will be search for these files using the OBJECT name in the FITS header. (See fix note .)
EXAMPLE: starzero Flux-###.fits Flux-###-zero.fits
EXAMPLE: star2resp Flux-###-zero.fits Resp-###.fits
EXAMPLE: smthresp Resp-###.fits Resp-###-smooth.fits
EXAMPLE: opim mul Resp-###-smooth.fits Flux-###.fits F-###.fits
Your flux calibrated spectrum will be in F-###.fits.
(Note: opim is a general image operation tool for multiplying,
dividing, adding, etc. any FITS image(s).)