Installing NIRES Spectral Extraction program 
---------------------------------------------------

1) Un-tar the nsx.tar file.

2) Run 'make'.   ( Make changes to Makefile if needed. )

3) Set two environment variables:
      NSXDIR (location of nsx.tar directory)
      NSXOUT (location of program output, default will be
              in the current directory)

4) The executable 'nsx' should exist.



Running NIRES Spectral Extraction program 
---------------------------------------------------

You can create a listing of your raw NIRES FITS data files like this:
    ls *.fits > file.ls
    nsx file.ls list=nsx.tbl

The current version allows for both manual and automatic spectral extraction.
The profiles for each echelle order are calibrated on a single arcsecond scale.
It is assumed the arcseconds per pixel is 0.123 (may change later with better
calibration.)

If you run nsx on a single exposure:

  nsx s170215_0040.fits

it will produce a profile table 's170215_0040-pro.tbl' and then stop.
You will also get individual profile tables for each order.  The files will
be numbered from red to blue (3, 4, 5, 6, and 7) = (K, H, J, z/J, and z).

You can examine the profile and choose arcsecond ranges for the object
window and the background window(s).

  nsx s170215_0040.fits sp=3,6 bk=1,2 bk=8,12

You can also allow the program to automatically choose the object and
background windows:

  nsx s170215_0040.fits -autox

In either case, you will get 5 spectral tables for each order.

You will also get a log file ( s170215_0040.log ) and a table of the
night skyline residuals ( s170215_0040-skyres.tbl ).

There is also a corrected image ( s170215_0040-corrected.fits ) where
the echelle curvature has been made horizontal and the slant across the
slit window has been made vertical.

There is also a background fit image ( s170215_0040-bck.fits ).

You can also use a 'B image' which will be subtracted off the primary
'A image' exposure.  This usually produces better skyline subtraction
in the final spectrum, but increases the error and usually decreases
the available background window.

  nsx s170215_0040.fits s170215_0041.fits  sp=3,6 bk=1,2 bk=8,12

Note that the resulting spectral files will have the root
's170215_0040-0041'.  (You will need to reverse the order of the
FITS filenames to get the spectrum for the other exposure.)



Description of Output Files
---------------------------

-pro#.tbl : profile data.

Columns: 
         arcsec : arcsecond scale from lower edge of echelle order
         median : median flux value
         average: average flux value
         obj    : object window mask (1 = object region)
         bck    : background window mask (1 = background region)
         row    : relative row pixel value from lower edge


-sp#.tbl  : spectral data.

Columns: 
         wave        : wavelength of pixel in microns
         object      : summation of counts in object window (with background subtraction)
         error       : 1 sigma error of 'object'
         backgnd     : background averaged over pixels in background window(s)
         sky         : background averaged over pixels in object window
         col         : column number on CCD
         row         : row position on CCD of center of object window
         angstrom    : wavelength of pixel in Angstroms
         disp        : dispersion in Angstroms per pixel



Future Changes
--------------

  Flat field correction.
  
  Hot pixel correction.
  
  Atmospheric absorption correction.
  
  Flux calibration.
  
  More documentation.
  
  
Last modified: 2018 February 27