There are several scripts used to create different Fledermaus scene files.

This project was done on hly0905 using a Windows PC with CYGWIN and X11.
After launching cygwin, X11 may be started from tehh cygwin window with
the command  startx


These scripts require programs  sioseis, display, convert, cvtgeo, and cmdop.
sioseis is available at http://sioseis.ucsd.edu
display & convert are part of ImageMagick and are on UNH machines
cvtgeo is availble from Brain Calder
cmdop is part of Fledermaus.
It is suggested that these programs be in either your bin directory or
/usr/local/bin and that the bin directory be in your search path.  e.g. in 
.bashrc in your home directory, add a line:
PATH=".:~/bin:/cygdrive/c/program files/ivs7/bin/:/cygdrive/c/program\ files/ivs
7/bin/:"$PATH:/cygdrive/x/Healy0905/Processing/bin

In this example the directory structure was:
/cygdrive/x/Healy0905/RawData/Knudsen320/
/home/usr/mkenv - script to convert correlates to envelopes
/home/usr/env - directory that holds all other scripts and output files

STEP 1:
     Convert a single Knudsen correlate file to an envelope file with 
         script mkenv.
     See example mkKnudsen for other chirp procesing scripts, 
         including one to convert all files in a directory.
     e.g.     mkenv 2009_250_1452_LF_067

STEP 2:
     Plot the data in depth and determine a start depth that eliminates
        as much of the water column as possible.  Also choose an end 
        depth that is below any data.  Use script mkdplt.
     e.g.   mkdplt 2009_250_1452_LF_067   (make sure you're in directory env)


STEP 3:
     Script mkdpltxy creates a Fledermaus scene file using the start and
        end depths picked above.
     e.g.   mkdpltxy 2009_250_1452_LF_067 3850 4000     
     
AGC vs GAINS
     AGC (automatic gain control) amplifies very low amplitudes such as
noise in the water column and below acoustic basement.  AGC also makes
every ping the same amplitude, thus distorting the amplitude relationship
spatially.
     agc.png vs. gains.png