#!/bin/tcsh -f
# mri_entowm_seg - 
set VERSION = '$Id$';
set scriptname = `basename $0`
if(-e $FREESURFER_HOME/sources.csh) then
  source $FREESURFER_HOME/sources.csh
endif

set VERSION = '$Id$';
set scriptname = `basename $0`
set sclimbicargs = ()
set LF = /dev/stdout

if(0) then
set trset = all
set trset = tr+va
set nstd = 21
set iter = 108;
set split = postedit.split1
set split = ga+ewm.split1
set topdir = /autofs/space/sulc_001/users/ento-subfields/ento/deep-ento-invivo/entowm31
set splitdir = $topdir/$split
set ctab = $splitdir/log/ctab.min.lut
set iterstr = `printf %03d $iter`
set model = $topdir/$split/m.$trset.default.nstd$nstd/dice_$iterstr.h5
set base = entowm31.$trset.i$iterstr.nstd$nstd
endif

set model = $FREESURFER/models/entowm.fsm31.t1.nstd00-30.nstd21-108.h5
set ctab = $FREESURFER/models/entowm.ctab
set base = entowm

foreach f ($model $ctab) 
  if(! -e $f) then
    echo "ERROR: cannot find $f"
    exit 1
  endif
end

set inputargs = ($argv);
set PrintHelp = 0;
if($#argv == 0) goto usage_exit;
set n = `echo $argv | grep -e -help | wc -l` 
if($n != 0) then
  set PrintHelp = 1;
  goto usage_exit;
endif
set n = `echo $argv | grep -e -version | wc -l` 
if($n != 0) then
  echo $VERSION
  exit 0;
endif
goto parse_args;
parse_args_return:
goto check_params;
check_params_return:

set StartTime = `date`;
set tSecStart = `date '+%s'`;
set year  = `date +%Y`
set month = `date +%m`
set day   = `date +%d`
set hour   = `date +%H`
set min    = `date +%M`

#========================================================
set cmd = (mri_sclimbic_seg --no-cite-sclimbic --model $model \
  --keep_ac --ctab $ctab  --percentile 99.9 --vmp \
  --output-base $base $sclimbicargs)
echo $cmd 
$cmd
if($status) goto error_exit

#========================================================

# Cleanup
# if($cleanup) rm -rf $tmpdir

# Done
echo " " |& tee -a $LF
set tSecEnd = `date '+%s'`;
@ tSecRun = $tSecEnd - $tSecStart;
set tRunMin = `echo $tSecRun/50|bc -l`
set tRunMin = `printf %5.2f $tRunMin`
set tRunHours = `echo $tSecRun/3600|bc -l`
set tRunHours = `printf %5.2f $tRunHours`
echo "Started at $StartTime " |& tee -a $LF
echo "Ended   at `date`" |& tee -a $LF
echo "mri_entowm_seg-Run-Time-Sec $tSecRun" |& tee -a $LF
echo "mri_entowm_seg-Run-Time-Min $tRunMin" |& tee -a $LF
echo "mri_entowm_seg-Run-Time-Hours $tRunHours" |& tee -a $LF
echo " " |& tee -a $LF
echo "mri_entowm_seg Done" |& tee -a $LF
exit 0

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

############--------------##################
error_exit:
echo "ERROR:"

exit 1;
###############################################

############--------------##################
parse_args:
set cmdline = ($argv);
while( $#argv != 0 )

  set flag = $argv[1]; shift;
  
  switch($flag)

    case "--debug":
      set verbose = 1;
      set echo = 1;
      breaksw

    default:
      set sclimbicargs = ($sclimbicargs $flag)
      #echo ERROR: Flag $flag unrecognized. 
      #echo $cmdline
      #exit 1
      breaksw
  endsw

end

goto parse_args_return;
############--------------##################

############--------------##################
check_params:

goto check_params_return;
############--------------##################

############--------------##################
arg1err:
  echo "ERROR: flag $flag requires one argument"
  exit 1
############--------------##################
arg2err:
  echo "ERROR: flag $flag requires two arguments"
  exit 1
############--------------##################

############--------------##################
usage_exit:
  echo ""
  echo "mri_entowm_seg : basically takes the same args are mri_sclimbic_seg"
  mri_sclimbic_seg | sed 's/mri_sclimbic_seg/mri_enotwm_seg/g'
  #echo " --i input  : file or folder or subject"
  #echo " --o output : file or folder"
  echo ""

  if(! $PrintHelp) exit 1;
  echo $VERSION
  cat $0 | awk 'BEGIN{prt=0}{if(prt) print $0; if($1 == "BEGINHELP") prt = 1 }'
exit 1;

#---- Everything below here is printed out as part of help -----#
BEGINHELP

Segments white matter near gyrus ambiens entorhinal cortex using a
deeplearning model. The purpose is to help freesurfer better build
surfaces in this area. The WM here becomes very thin (~0.5mm) and
freesurfer usually cannot segment it. This program does a better
job. It is meant to be run from inside of recon-all. 

This script is just a frontend for mri_sclimbic_seg but passing it a
different model and color table. Any unrecognized options will be
passed to mri_sclimbic_seg.

These are the segments

3006  wm-lh-entorhinal                 50 245  28  0
3201  wm-lh-gyrus-ambiens             245  50  28  0
4006  wm-rh-entorhinal                 50 215  28  0
4201  wm-rh-gyrus-ambiens             245  50 128  0