old_contents: import os, sys, glob
  
  from astropy.io import fits
  
  import imred
  from mosred import mosred
  import argparse
  
  bpmfile = os.path.dirname(imred.__file__)+'/data/bpm_rss_11.fits'
  
  
  parser = argparse.ArgumentParser(description='Reduce SALT Lens Data')
  parser.add_argument('ddir', help='Top level directory with SALT data')
  parser.add_argument('-s', dest='basic_red', default=True, action='store_false',
                      help='Skip basic reduction')
  parser.add_argument('--dy', dest='dy', default=-12, type=float, 
                      help='Mask offset')
  parser.add_argument('slitmask', help='Slitmask for observations')
  
  
  args = parser.parse_args()
  args.slitmask = os.path.abspath(args.slitmask)
  ddir = args.ddir
  
  
  os.chdir(ddir)
  if not os.path.isdir('sci'): os.mkdir('sci')
  os.chdir('sci')
  
  #basic image reuctions
  infile_list = glob.glob('../raw/P*fits')
  # remove alignment images
  spec_list = []
  for infile in infile_list:
      hdu = fits.open(infile)
      if hdu[0].header['OBSMODE'].strip() != 'IMAGING':
         spec_list.append(infile)
  infile_list = spec_list
  print spec_list
  
  if args.basic_red: imred.imred(infile_list, './', bpmfile, cleanup=True)
  
  #spectroscopic reductions
  propid=None
  infile_list = glob.glob('m*fits')
  mosred(infile_list, args.slitmask, dy=args.dy)
  
  #extract the data
  
  
  
  
new_contents: import os, sys, glob
  
  from astropy.io import fits
  
  import imred
  from mosred import mosred
  import argparse
  
  bpmfile = os.path.dirname(imred.__file__)+'/data/bpm_rss_11.fits'
  
  
  parser = argparse.ArgumentParser(description='Reduce SALT Lens Data')
  parser.add_argument('ddir', help='Top level directory with SALT data')
  parser.add_argument('slitmask', help='Slitmask for observations')
  parser.add_argument('-s', dest='basic_red', default=True, action='store_false',
                      help='Skip basic reduction')
  parser.add_argument('-p', dest='preprocess', default=False, action='store_true',
                      help='prepocess the line identification')
  parser.add_argument('-a', dest='auto', default=False, action='store_true',
                      help='Autoidentify the lines')
  parser.add_argument('--dy', dest='dy', default=None, type=float, 
                      help='Mask offset')
  
  
  args = parser.parse_args()
  args.slitmask = os.path.abspath(args.slitmask)
  ddir = args.ddir
  
  
  os.chdir(ddir)
  if not os.path.isdir('sci'): os.mkdir('sci')
  os.chdir('sci')
  
  #basic image reuctions
  infile_list = glob.glob('../raw/P*fits')
  # remove alignment images
  spec_list = []
  for infile in infile_list:
      hdu = fits.open(infile)
      if hdu[0].header['OBSMODE'].strip() != 'IMAGING':
         spec_list.append(infile)
  infile_list = spec_list
  print spec_list
  
  if args.basic_red: imred.imred(infile_list, './', bpmfile, cleanup=True)
  
  #spectroscopic reductions
  propid=None
  infile_list = glob.glob('m*fits')
  mosred(infile_list, args.slitmask, dy=args.dy, preprocess=args.preprocess)
  
  #extract the data
  
  
  
  
subject: update to reducemos.py