edit  "refsm.py"  for your cruise (it is currently set up for 
                     this lta demo) and run it as a script.



This is what refsm.py does:



Makes as.cnt, ref.cnt, and sm.cnt for pairs of 
reference layers, runs adcpsect, refabs and smoothr
on each of the reference layers to make the .sm files


details:

adcpsect:
         runs "adcpsect as.cnt"       (output 20_40)
         Gets a conservative estimate (80pg)  of when to use the 
         reference layer from bin 35-40. (i.e. output 35_40_80
          - decide when the deep layer is OK)

refabs:
         runs "refabs ref.cnt"   
         (reads lta.gps2; fix and output 20_40)

smoothr: 
         runs "smoothr sm.cnt"     (output: 20_40)


runs blend_sm.m   (in matlab)
       use nav_mask_file  from adcpsect.cnt (35_40_80.nav)
       deepreffile (20_40.sm)
       shallowreffile (05_10.sm)
       create blendreffile (blend.sm)

runs putnav