#### As of tetracorder 6, in the mapping directory after tetracorder runs,
#    simply do:

./cmd.get.average.spectra.of.mapped.materials  dirs all   # gets spectra for all tetracorder results

./cmd.get.average.spectra.of.mapped.materials  box a b c d  dirs all  # gets spectra for all
								# tetracorder results within bounding pixel box
								# a= upper left x,  b=upper left y, 
								# c= lower right x, d= lower right y
								# range: 1 to size of cube in pixels

./cmd.get.average.spectra.of.mapped.materials  dirs  list_of_directories  # only do these directories,
								# exmaple: group.1um group.2um case.veg.type

./cmd.get.average.spectra.of.mapped.materials  box a b c d  dirs  list_of_directoriesa # bounding box,
								# selected directories



#############################################################################
# below is the OLD manual way:

Post tetracorder process, which created many files of results,
to get average spectra, do the following.

The examples will use EMIT data

Create a specpr file for collecting the average spectra in the
    directory where a mappign runs has completed

    cubepath=`cat AAA.info/cubefilename.txt`
    cube=`basename $cubepath | cut -c 1-40`

    cp /sl1/usgs/library06.conv/startfiles/s06emitc.start spreslt1
    sp_stamp spreslt1
    spsettitle  spreslt1 1 '*************  spreslt1  ****************' -force
    spsettitle  spreslt1 2 '**** extracted spectra from cube:   *****' -force
    spsettitle  spreslt1 3 "$cube                                   " -force
    # cube isze:
    xpx=`cat AAA.info/image-xpixels.txt`
    ypx=`cat AAA.info/image-ypixels.txt`
    # get average spectra for all mapped materials:
    avspec='cmds.all.support/cmd.get.mapped.material.spectral.averages-v4'
    shortid=`cat AAA.info/shortcubeid.txt`   # short cube ID  up to 10 characters
    cscale=`cat AAA.info/cube-scale-factor`
    $avspec  $shortid  $cubepath  $cscale  spreslt1 box 1 1 $xpx $ypx

The command creates specpr file spreslt1:

cmds.all.support/make.spreslt1.file.for.spectral.extractions

then run:
cmds.all.support/cmd.get.mapped.material.spectral.averages-v4

cmds.all.support/cmd.get.mapped.material.spectral.averages-v4  shortcubeID  cube scale_factor specproutputfile box upperleftx upperlefty lowerrightx lowerrighty

Note: the cube size and the short cube ID after a tetracorder run are stored in
the AAA.info directory:

cube-bands.txt	cubefilename.txt  image-xpixels.txt  image-ypixels.txt	shortcubeid.txt

example (cube size = 1000 x 1000):
cmds.all.support/cmd.get.mapped.material.spectral.averages-v4  FRT03BFB  ../cubes2/FRT00003BFB_07_IF166J_MTR3.v  0.00005  spreslt1  box 1 1 1000 1000

Note: the box size can be a small area, not just the full cube size.

NOTE on cube: if the cube is an envi file with no vicar header give the envi  hdr file, e.g.
       ../cube/f180625t01p00r07_rfl.hdr

     If the cube has a vicar header, use the cube file.  Example:
       ../cube/f180625t01p00r07_rfl.v.hdr   # envi header
       ../cube/f180625t01p00r07_rfl.v       # image cube with vicar header
  then use:
        ../cube/f180625t01p00r07_rfl.v

When complete, run specpr and assign the spreslt1 file to view the results.