#! /bin/tcsh -f

#
# unpackimadir
#
# Purpose: converts data in an IMA directory to MINC and
# then calls unpackmincdir to convert to Sessions format
# (deletes the original MINC). Any arguments that unpackimadir
# does not recognize are passed to unpackmincdir.  The
# temporary minc files can be kept by specifying -keepminc.
# The temporary minc directory can be specified with -mincdir,
# otherwise it will be put in the output directory.
#
#
# Copyright © 2021 The General Hospital Corporation (Boston, MA) "MGH"
#
# Terms and conditions for use, reproduction, distribution and contribution
# are found in the 'FreeSurfer Software License Agreement' contained
# in the file 'LICENSE' found in the FreeSurfer distribution, and here:
#
# https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense
#
# Reporting: freesurfer@nmr.mgh.harvard.edu
#
#


set VERSION = 'unpackimadir dev';
set unpackmincdiropts = ();
set srcdir   = ();
set targdir  = ();
set mincdir  = ();
set removeminc = 1;

set n = `echo $argv | egrep -e -version | wc -l`
if($n != 0) then
  echo $VERSION
  exit 0;
endif

if($#argv == 0) then
  goto usage_exit;
  exit 1;
endif

echo $VERSION
set  StartDate = `date`;
echo $StartDate

set cmdargs = ($argv);

source $FREESURFER_HOME/sources.csh

goto parse_args;
parse_args_return:

goto check_params;
check_params_return:

# use pawd (if it exists) instead of pwd #
which pawd;
if(! $status) alias pwd pawd;

## Check if the target directory exists ##
if(-d $targdir) then
  echo "WARNING: destination directory $targdir already exists, overwriting."
endif

## Create the Target Directory ##
mkdir -p $targdir;
if(! -e $targdir) then
  echo "ERROR: could not create target directory"
  exit 1;
endif

## get full path name for target directory ##
pushd $targdir > /dev/null;
set targdir = `pwd`;
popd > /dev/null;

## Set up a log file ##
set LF = $targdir/unpackima.log
rm -f $LF
touch $LF
echo "Log file for unpackimadir" >> $LF
echo "$VERSION"         >> $LF
pwd                     >> $LF
echo "$0"               >> $LF
echo "$cmdargs"         >> $LF
uname -a                >> $LF
id                      >> $LF
date                    >> $LF
echo "Source: $srcdir"  >> $LF
echo "Target: $targdir" >> $LF
echo " " >> $LF
echo "ima2mnc: `which ima2mnc` " >> $LF
echo " " >> $LF

# Set up the minc directory. ima2mnc will put the output in a
# subdirectory of mincdir. We don't know what the name of that
# subdirectory will be, so we restrict mincdir to be empty so
# that we know that anything new will have been created by
# ima2mnc.
if($#mincdir == 0) set mincdir = $targdir/mincfiles_$$
mkdir -p $mincdir
pushd $mincdir > /dev/null
set mincdir = `pwd`;
set n = `ls | wc -w`;
if($n != 0) then
  echo "ERROR: mincdir $mincdir is not empty"
  exit 1;
endif
popd > /dev/null
echo "mincdir is $mincdir"

# Convert ima to minc #
set cmd = (ima2mnc $srcdir $mincdir)
echo "---------------------------------------------------"
pwd
echo $cmd
echo "---------------------------------------------------"
$cmd |& tee -a $LF
if($status) then
  echo "ERROR: ima2mnc failed" | tee -a $LF
  exit 1;
endif

# Go into mincdir to get the name of the directory where
# the mincfiles are stored. This will be called mincsrcdir.
pushd $mincdir > /dev/null
set mincdir = `pwd`;
set n = `ls | wc -w`;
if($n == 0) then
  echo "ERROR: no minc files created in $mincdir"
  exit 1;
endif
if($n > 1) then
  echo "ERROR: too many minc subdirectories in $mincdir"
  exit 1;
endif
set tmp = `ls`;
set mincsrcdir = $mincdir/$tmp
popd > /dev/null
echo "mincsrcdir is $mincsrcdir"

# Convert minc into sessions format #
set cmd = (unpackmincdir -src $mincsrcdir -targ $targdir)
echo "---------------------------------------------------"
pwd
echo $cmd
echo "---------------------------------------------------"
$cmd |& tee -a $LF
if($status) then
  echo "ERROR: unpackmincdir failed" | tee -a $LF
  exit 1;
endif

# Clean up #
if($removeminc) then
  echo "INFO: removing temporary minc files"
  rm -r $mincdir
endif

set EndDate = `date`;
echo "Started on $StartDate"  | tee -a $LF
echo "Ended   on $EndDate"    | tee -a $LF
echo " "  | tee -a $LF
echo "unpackimadir COMPLETED SUCCESSFULLY"  | tee -a $LF
echo " "  | tee -a $LF

exit 0;
###########################################################################
###########################################################################
###########################################################################

############--------------##################
parse_args:

set cmdline = "$argv";
while( $#argv != 0 )

  set flag = $argv[1]; shift;

  switch($flag)

    case "-src":
      if ( $#argv == 0) goto arg1err;
      set srcdir = $argv[1]; shift;
      breaksw

    case "-targ":
      if ( $#argv == 0) goto arg1err;
      set targdir = $argv[1]; shift;
      breaksw

    case "-mincdir":
      if ( $#argv == 0) goto arg1err;
      set mincdir = $argv[1]; shift;
      breaksw

    case "-umask":
      if ( $#argv == 0) goto arg1err;
      setenv MRI_UMASK $1; shift;
      breaksw

    case "-removeminc":
      set removeminc = 1;
      breaksw

    case "-noremoveminc":
    case "-keepminc":
      set removeminc = 0;
      breaksw

    case "-verbose":
      set unpackmincdiropts = ($unpackmincdiropts $flag);
      set verbose = 1;
      breaksw

    case "-echo":
      set unpackmincdiropts = ($unpackmincdiropts $flag);
      set echo = 1;
      breaksw

    case "-debug":
      set unpackmincdiropts = ($unpackmincdiropts $flag);
      set verbose = 1;
      set echo = 1;
      breaksw

    default:
      set unpackmincdiropts = ($unpackmincdiropts $flag);
      breaksw
  endsw

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

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

  if ($#srcdir == 0) then
     echo "ERROR: must specify a source directory";
     exit 1
  endif

  if(! -d $srcdir ) then
    echo "ERROR: $srcdir does not exist"
    exit 1;
  endif

  if ($#targdir == 0) then
     echo "ERROR: must specify a target directory";
     exit 1
  endif

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

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

############--------------##################
usage_exit:
  echo "USAGE: unpackimadir -src sourcedir -targ targdir"
exit 1;