Information for installing:

Cornean: Cornea Topography Analysis System, ver. 1.1
(c) J. S. Marron and N. Locantore, 1998
Department of Statistics, University of North Carolina

This is intended for MATLAB 5, Windows 95 (or NT)

1.  Copy the Cornean Folder (and subfolders) from this disk
  into the Matlab folder.

2.  Copy the file startup.m into the \matlab\toolbox\local
  folder.  It may be good to first take the existing file
  "startup.m", and rename it something like "startup.old".

3.  Start matlab (Cornean should automatically start).

4.  This installation should automatically copy some test 
  data sets (especially in the ".mat" Matlab form of Zernike
  feature vectors).  In particular all of the default
  examples should be there, e.g.:

  a.  Feature vectors are present for each member of the 
    list file "prkpreop.lst" (allowing easy demo of the
    population analyses).

  b.  Feature vectors are present for easy demo of the
    "morphing memo" in the Difference Analysis Menu.

5.  To work with a single new image:

  a.  Copy the .xla, .zla, .tla (or the .xlb, .zlb,.tlb) 
    files to the folder:
              \matlab\cornean\indata

  b.  Type the file prefix into the window in the individual
    analysis menu.

6.  To work with a collection of new images:

  a.  Copy the data files as in 5a above.

  b.  With a file editor, create a "list file" (a file where
    each line is the file prefix for one image), in the 
    directory:
                 \matlab\cornean\zfm
    (note: this MUST have the suffix ".lst").

7.  The only feature of Cornean which is known not to work 
  is the contruction of MPEG files, to save movies.  The
  mpeg converter for Matlab 5 is not working yet.




Anticipated Possible Problems and Solutions:

I.  Problem:  things might take longer than you want to 
  wait in a demo.  Solution:  Use ctrl-C to kill anything
  that is currently running.  Here are some possible 
  guidelines about times (although this varies A LOT
  depending on hardware, and also Matlab version):

  a.  Decomposition of plot of single image:   a few seconds
  b.  Difference movie:  5-10 minutes.
  c.  A PCA type analysis:  5-10 minutes
  d.  Listwise decomposition:   quite a few minutes
  e.  Plot of images in a list:   quite a few minutes
  f.  PCA Movie:  40-90 minutes.



II.  Error messages about file reads:

  a.  Most common problem is a file is not in the expected
    directory.  This can be quickly checked by using the 
    "dir" buttons.  Info about where Cornean is looking for
    files is available using the "help" buttons.

  b.  A rare problem that can come up when BOTH Matlab 4 and 
    Matlab 5 have been used is that Matlab 4 cannot read
    files (.mat files) that have been created by Matlab 5
    (and this gives the cryptic message "Cannot read file").
    This is fixed by redoing needed Zernike decompositions.


III.  The Matlab window shows an "OUT OF MEMORY" message.
  Problem: this machine doesn't have enough memory.  Quick
  and dirty solutions: reset the value of NMAX, by issuing 
  the MATLAB command(at the prompt line >>):
           >> NMAX = 6     
  (maybe 8 could work too).


IV.  There are a number of other problems that might occur.
  Most of these can be fixed by editing the file CORNEAN.M.
  The first place to look when there are problems, is at the
  setting of the variable:
                   ienviron
  A large number of other variables are set in blocks, 
  depending on the value of this.

