#!/usr/bin/env tcsh
@global_parse `basename $0` "$*" ; if ($status) exit 0

# [PT: Apr 19, 2019] Updated some INIT_VARS and then names of some
# places where they are used, because the demoarch no longer existed
# (!) online, and we now mostly use *.gii files, anyways.  Appears to
# work...

INIT_VARS:
set stat = 0
set demo_name = suma_TT_N27
set demo_tgz  = ${demo_name}.tgz
set demoarch = https://afni.nimh.nih.gov/pub/dist/tgz/${demo_tgz} 
set surf1 = lh.pial.gii   
set sph1 = lh.sphere.gii  
set surf2 = lh.smoothwm.gii 
set spec = TT_N27_lh.spec 
set ld = 35
set spec_std = ld${ld}.$spec
set order = 15
set sphnpb = 777
set s = 0.001

PARSE:
   set cnt = 1
   set Narg = $#argv
   while ($cnt <= $Narg)
      set donext = 1;
      if ($donext && "$argv[$cnt]" == '-h' || "$argv[$cnt]" == '-help') then
         goto HELP
      endif

      if ($donext && "$argv[$cnt]" == "-echo") then
         set echo      
         set donext = 0      
      endif
      
      if ($donext == 1) then
         echo "Error: Option or parameter '$argv[$cnt]' not understood"
         apsearch -popt `basename $0` -word $argv[$cnt]
         goto BEND
      endif
      
      @ cnt ++
   end
      
CHECKS:
if ( ! -f $spec || ! -f $surf2 ) then
   echo ""
   echo "Missing $spec or other related files. Perhaps you are not running"
   echo "the script from a directory containing the sample surfaces."
   echo ""
   echo "Do you want to download and install the demo surfaces from:"
   echo "   $demoarch"
   printf "[Y|n]: "
   set an = $<
   if ($an == 'Y' || $an == '' || $an == 'y') then
      curl -O $demoarch
      if ($status) then
         echo "Failed to download"
         goto BEND
      endif
      tar xvzf ${demo_tgz}
      if ($status) then
         echo "Failed to untar"
         goto BEND
      endif
      mkdir SpharmDemo
      cp -p ${demo_name}/*lh* SpharmDemo/
      echo ""
      echo "Have needed data in directory SpharmDemo/"
      echo "Now cd into that directory and rerun the script"
      echo ""
      echo "cd SpharmDemo/"
      echo "`basename $0`"
      echo ""
      goto END
   else 
      goto BEND
   endif
endif

   prompt_user -pause "\
Hit enter to start suma in 'listening mode' and begin recording."


@Quiet_Talkers -npb_val $sphnpb 
suma -npb $sphnpb -niml &
sleep 3
#start recorder
DriveSuma -npb $sphnpb -com viewer_cont -key 'R' 

DOMAIN:
   prompt_user -pause "\
Creating a standard-mesh version of all surfaces involved\n\
All surfaces used in a SPHARM analysis should be isotopic\
and all datasets must be defined on the same domain (mesh).\n\
Typically, creating standard meshes should be done after\
surface-based registration (-morph sphere.reg), but for this \
example it does not matter."

#Change the density of the mesh 
#(this is not necessary when all surfaces involved are isotopic)
if ( ! -f $spec_std) then
   MapIcosahedron -echo_edu -spec $spec -ld $ld -morph sphere -prefix ld${ld}.
   CreateIcosahedron -echo_edu -rad 1.0 -ld $ld -prefix ld${ld}.unitsph 
else
   echo ""
   echo "Reusing existing standard-mesh surfaces."
   echo "" 
endif
   set surf1 = ld${ld}.$surf1
   set surf2 = ld${ld}.$surf2
   set sph1 = ld35.unitsph.asc
   set spec = $spec_std

DATA: #create some toy data
   prompt_user -pause "Creating sample data"

   SurfMeasures   -echo_edu -overwrite \
                  -spec ${spec} -surf_A smoothwm -surf_B pial \
                  -func thick -out_1D ld${ld}.lh_std.thick.1D.dset

DECO:
   prompt_user -pause "\
Decompose the coordinates of two surfaces and write out the\n\
reconstructed surfaces and the coefficients"

SpharmDeco  -i $sph1 -unit_sph ${sph1} \
            -i ${surf1} -i ${surf2} \
            -l ${order} \
            -bases_prefix ld${ld}.harmo \
            -o_fs {$surf1:r}_reco${order} \
            -prefix {$surf1:r}_reco${order} \
            -sigma $s  -overwrite   \
            -talk_suma -npb $sphnpb -echo_edu 

   prompt_user -pause "\
Redo the reconstruction of one surface but reuse bases computed above"

SpharmDeco  -i ${surf1} -l ${order} \
            -bases_prefix ld${ld}.harmo \
            -o_fs {$surf1:r}_recob${order} \
            -sigma $s  -overwrite \
            -talk_suma -npb $sphnpb -echo_edu 

   prompt_user -pause "Decompose data defined over the surface's nodes"

SpharmDeco  -i ${surf1} -l ${order} \
            -bases_prefix ld${ld}.harmo \
            -data ld${ld}.lh_std.thick.1D.dset'[1]'   \
            -prefix ld${ld}.lh_std.thick_reco${order} \
            -sigma $s -overwrite \
            -talk_suma -npb $sphnpb -echo_edu 

RECO:
set order2 = `ccalc -i $order - 5`
if ($order2 < 2) then
   set order2 = $order
endif
   prompt_user -pause "\
Given spherical harmonics and corresponding coefficients,\
reconstruct surfaces at order $order2\n\
Note that two surfaces will be written to disk and the coordinates of these\
reconstructed surfaces are also in {$surf1:r}_RECO${order2}.1D.dset"

SpharmReco               \
            -i ${surf1}            \
            -l $order2                         \
            -bases_prefix  ld${ld}.harmo   \
            -coef          ld${ld}.lh.pial.tlrc_reco{$order}.beta.col000.1D   \
            -coef          ld${ld}.lh.pial.tlrc_reco{$order}.beta.col001.1D   \
            -coef          ld${ld}.lh.pial.tlrc_reco{$order}.beta.col002.1D   \
            -coef          ld${ld}.lh.pial.tlrc_reco{$order}.beta.col003.1D   \
            -coef          ld${ld}.lh.pial.tlrc_reco{$order}.beta.col004.1D   \
            -coef          ld${ld}.lh.pial.tlrc_reco{$order}.beta.col005.1D   \
            -o_ply {$surf1:r}_RECO${order2} -overwrite \
            -prefix {$surf1:r}_RECO${order2} -talk_suma -npb $sphnpb -echo_edu


   prompt_user -pause "\
Now reconstruct data only,  not XYZ of surfaces"

SpharmReco               \
            -i ${surf1}            \
            -l $order2                         \
            -bases_prefix  ld${ld}.harmo   \
            -coef          ld${ld}.lh_std.thick_reco${order}.beta.col000.1D \
            -prefix {$surf1:r}.thick_RECO${order2} -overwrite \
            -talk_suma  -npb $sphnpb -echo_edu
    
goto END

HELP:
   echo ""
   echo "Usage: `basename $0`"
   echo "A script to demonstrate the usage of spherical harmonics decomposition "
   echo "with SUMA"
   echo ""
   echo "To run it you will need some of SUMA's N27 tlrc surfaces, which can be "
   echo "downloaded from: $demoarch"
   echo "The surfaces needed are $surf1, $surf2, $sph1, and $spec"
   echo ""
   echo "To change the parameter settings, make a copy of this script"
   echo "and modify the section at the top called 'INIT_VARS'"
   echo "If you do not make a copy of this script, future AFNI updates will"
   echo "overwrite your changes."
   echo ""
   @global_parse -gopts_help
   echo ""
   echo "         Ziad S. Saad               SSCC/NIMH/NIH"
   echo ""
   goto END

BEND:
   set stat = 1
   goto END

END:
   exit $stat