medcorrect.c: This program corrects x-ray image files taken by the
    medoptics detector, but can be easily adapted for other
    detectors. 

    FEATURES: 

    1) The images may be dezingered, background subtracted, distortion
       and/or intensity corrected.  Corrections are chosen by command
       line options.

    2) The background images may also be dezingered. This is always
       done if more than one background image (eventually more than
       two will be allowed, but not now)

    3) Command line substitution can be used to specificy multiple
       image files. See example (4)

    NOTE: Although the program allows complete flexibility, the proper
    correction order is determined when correction files are made (see
    TV6 command 'cath'). For the medoptics detector intensity
    correction file medi12b1.tif, this order is raw->dezing -> back
    sub -> intensity correct -> distortion correct. If using the
    intensity correction file moi12b1.tif, the order of intensity and
    distortion correction are swapped.

    

Usage: medcorrect [i|id|d|di]  
       -s[z] image_file(s) 
       [-o output_filename]
       [-t int_correct_file] 
       [-x x_distortion_file]
       [-b back_file(s)]
       [--help]

At least two arguments are required: '-s[z]' and an image filename.

If present, [i|id|d|di] must come first. Other arguments in any order.

OPTIONS:

   i: intensity correction. uses default intensity correction unless
      -t is also present
   d: distortion correction. uses default files unless -x is also present

   NOTE 1: Correction is done in the order specificied. Make sure that
           the this order (id vs. di) matches the type of intensity
           correction file being used. (For the Medoptics decector,
           see C:\\perm\\README on the Medoptics computer).

   -t: explicitly name intensity correction file (see NOTE 2)

   -x: explicitly name only the x-distortion correction file. (see
       NOTE 2) The y-distortion file must have the same name but with
       'y' in place of the final appearance of 'x' in the filename ,
       e.g. medxbin1.tif & medybin1.tif

   -s[z] image_file(s): if more than one is specified, images are
        either combined and dezingered (if z is present) or processed
        sequentially. Current limit of 2 images for dezingering

   -b background file(s). If more than one is specified, images are combined and 
        dezingered.

   -o output_file_name. If present, this takes precedence. If not
        present, then the output filename depends on the action. If
        multiple images are being corrected but NOT dezingered, then
        the name is generated from the input file by the insertion of
        \"_c\" before the extension (e.g. fish.tif -> fish_c.tif, fish
        -> fish_c). This is useful for correcting a whole sequence of
        images that do not need to be dezingered in a single command
        (see example below). If two images are being dezingered, the
        default name medcorr.out is used unless an explicit filename
        is specified. NOTE that medcorrect NEVER overwrites files. If
        the output filename it wants to already exists, medcorrect
        aborts with a message to that effect.

    --help: Print this help message and exit

    NOTE 2: If distortion or intensity correction files are not explicitly named:
       1) Look for environment variable CCDCORR_FILES to determine directory in which
          to look for the correction files named in (default to /usr/local/lib).
       2) Filenames found in the CCDCORR_FILES directory are
          SUPERCEDED by the contents of medcorrect.cfg, if found inthe
          local directory. This file is written whenever intensity and
          distortion correction are both performed

       Successfully opened correction filenames are saved to
       medcorrect.cfg which, if found in the working directory,
       supercedes the default files in /usr/local/lib.

    EXAMPLES:

       1) Dezinger a pair of images:
          >medcorrect -sz image1.tif image2.tif -o image1z2.tif
               ** or using tcsh command line substitution **
          >medcorrect -sz image[12].tif -o image1z2.tif

       2) Dezinger two images and backgrounds and subtract the
          dezingered background from the dezingered image:
          >medcorrect -sz image1.tif image2.tif -o image1z2.tif -b b1.tif b2.tif
               ** or using tcsh command line substitution **
          >medcorrect -sz image[12].tif -b b[12].tif -o image1z2.tif

       3) The whole shabang (dezinger image & backs, then subtract
          background, then intensity and distortion correct).

          >medcorrect id -sz image[12].tif -b b[12].tif 
               ** output stored in medcorr.out ** 

       4) Correct but don't dezinger many files at once.

          >medcorrect id -s images*.tif -b backround.tif


Originally written by Sandor L. Barna Princeton University Physics
   Department Biophysics Group December 1993

Marian Szebenyi (CHESS) made many modifications, including pedestal,
   through 2003.

Converted from text-menu/prompt to UNIX command-line-option style 
   by Arthur Woll, March 2003

NOTE: The UNIX shell expands wildcard characters like *, ?, and []
  before sending the command line to the program. See your sh or csh
  manual for details.  Turbo C++ and Borland C++ expand wildcard
  characters if the file WILDARG.OBJ is linked with your program. See
  the manual for details.  Almost all UNIX commands use a standard
  command-line format. This standard has carried over into other
  environments. A standard UNIX command has the form:

  command options file1 file1 file3

Please refer to TV6 (Gruner, Eikenberry and Tate) for more information
on the correction procedures.