This directory contains the Tetracorder expert system and support programs.

Watch the training videos at:

      https://www.youtube.com/user/PSITucson/featured

   Go to: Spectroscopy and Tetracorder Training

      The youtube left-right scroll shows only the first 12 videos.  To see all videos,
      click on the PLAY ALL button and the full list of videos is on the right.


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First complete the configuration for your system:

There are 3 directories:
        cmds.color.support
        cmds.color.support-env-s
        cmds.color.support-pre-env8.30

The commands in cmds.color.support are what are used and the shipped version
will work for most linux systems.  The versions in cmds.color.support-env-s
have the first line:

#!/usr/bin/env -S davinci -f  

and requires env version 8.30 or higher.  You only need these versions if
you have an unusual situation, like a Beowulf cluster.
Linux mint verion 20+ has env 8.30

Check you system with: env --version

If you have a newer env version and need the #!/usr/bin/env -S davinci -f
first line, do:

cp -a cmds.color.support-env-s/* cmds.color.support



Similarly, for the scrips in directories:

         davinci-cmds.for.usr.local.bin
    and  davinci-cmds.for.usr.local.bin-pre-env8.30

for env --version = 8.30 or later, do:

cp -a davinci-cmds.for.usr.local.bin/*   /usr/local/bin

and if an older env version, do:

cp -a davinci-cmds.for.usr.local.bin-pre-env8.30/*  /usr/local/bin




##########################################

Tetracorder commands: what to edit for version changes
For example, from tetracorder5.2 to tetracorder5.26, change 5.2 to 5.26 in:

cmd-setup-tetrun
cmd.tetracorder.rover.ASD.setup.and.autostart
cmd.runtet

e.g.:

vi cmd-setup-tetrun  cmd.tetracorder.rover.ASD.setup.and.autostart  cmd.runtet


##########################################

To add a new instrument:

1) convolve the spectral libraries.

2) cd DATASETS
   copy an existing entry to the new name.
   edit the new file
   example:  cp aviris_2018 emit-a
             vi emit_a     # result:
             data=    EMIT-2022  
             restart= r1-emita
   
3) add an entry for the new instrument in DELETED.channels
   cd DELETED.channels
   add new file or edit DELETED.channels.txt.
   Example new file:
   delete_emit_a
    c   # emit_a   (no deleted points at this time)

4) copy a restart file to the new instrument name and edit the spectral library names.
     example, for  restart_files/r1-emita, change the lines:
                   (get the number of channels from the target spectrometer)
        cp restart_files/r1-av18a  restart_files/r1_emita
        edit  restart_files/r1_emita   and change the follor to:
        iwfl=/sl1/usgs/rlib06/r06emita                                                       
        iyfl=/sl1/usgs/library06.conv/s06emita                                             
        irfl=r1-r06emita
        #
        iwdgt=      r06emita  # file device letter w
        inmy=       s06emita  # file device letter y
        nchans=          288  # num wave chans



##########################################

Example runs

to set up a tetracorder run, cd to the directory where you want to create
a tetracorder directory for a run.  For example, if you want to do a 
tetracorder run in /data1/project3/mapping/arches-np
first cd to:
    /data1/project3/mapping/

The run the command:
/t1/tetracorder.cmds/tetracorder5.26e.cmds/cmd-setup-tetrun

With no arguments, cmd-setup-tetrun will tell you all the options.
The first option is the sub-directory where all results would be placed.

Example:

/t1/tetracorder.cmds/tetracorder5.26e.cmds/cmd-setup-tetrun   arches-np    aviris_1995 \
              cube ../cube/cuprite.95.cal.rtgc.v  0.0005 -T 0 80 C     -P 0.9 1.1 bar  \
              shortcubeid archs95a

/t1/tetracorder.cmds/tetracorder5.26e.cmds/cmd-setup-tetrun   map-schrod1   MMM_09c \
              cube ../cubes/Schrodinger_UARFLRC  1.0  -T -100 140 C -P 0.00000001 0.0001 bar \
              shortcubeid m3schrod1


Note the full path + filename to the cube must be less than 73 characters.
(Set up symbolic links to shorten path+filename.)


#################  Auto-Extracting Spectra of Pixel Averages  #################

See:
     AAA.cmds.to.get.average.spectra.of.mapped.materials


###############  Red Edge Shift  ################################################

The veg anomaly run set a max of band depth 0.5 = 255.  Max response
would be about a 7 nm shift in the red edge (dn=255).  A dn of ~107
would be ~3nm shift

shift     peak height    DN    Possible image stretch
-----------------------------------------------------
  0  nm       0           0
  0.5         0.035      18     purple 0.5 to 1 nm
  1           0.07       36     blue     1 to 2 nm
  2           0.14       71     green    2 to 3 nm
  3           0.21      107     red      3 to 4 nm
  4           0.28      143     white    > 4 nm 



##############   KNOWN ISSUES   ################################################

Read: AAAAA.KNOWN-ISSUES.txt

