#!/bin/sh

#   invwarp - wrapper script for invwarp_exe
#
#   All the script does (despite the many lines of code) is to
#    crop the warp and highres down tightly, run invwarp_exe on
#    the cropped images and then put the result back into the
#    larger FOV
#
#   Mark Jenkinson, FMRIB Image Analysis Group
#
#   Copyright (C) 2009 University of Oxford
#
#   Part of FSL - FMRIB's Software Library
#   http://www.fmrib.ox.ac.uk/fsl
#   fsl@fmrib.ox.ac.uk
#   
#   Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
#   Imaging of the Brain), Department of Clinical Neurology, Oxford
#   University, Oxford, UK
#   
#   
#   LICENCE
#   
#   FMRIB Software Library, Release 5.0 (c) 2012, The University of
#   Oxford (the "Software")
#   
#   The Software remains the property of the University of Oxford ("the
#   University").
#   
#   The Software is distributed "AS IS" under this Licence solely for
#   non-commercial use in the hope that it will be useful, but in order
#   that the University as a charitable foundation protects its assets for
#   the benefit of its educational and research purposes, the University
#   makes clear that no condition is made or to be implied, nor is any
#   warranty given or to be implied, as to the accuracy of the Software,
#   or that it will be suitable for any particular purpose or for use
#   under any specific conditions. Furthermore, the University disclaims
#   all responsibility for the use which is made of the Software. It
#   further disclaims any liability for the outcomes arising from using
#   the Software.
#   
#   The Licensee agrees to indemnify the University and hold the
#   University harmless from and against any and all claims, damages and
#   liabilities asserted by third parties (including claims for
#   negligence) which arise directly or indirectly from the use of the
#   Software or the sale of any products based on the Software.
#   
#   No part of the Software may be reproduced, modified, transmitted or
#   transferred in any form or by any means, electronic or mechanical,
#   without the express permission of the University. The permission of
#   the University is not required if the said reproduction, modification,
#   transmission or transference is done without financial return, the
#   conditions of this Licence are imposed upon the receiver of the
#   product, and all original and amended source code is included in any
#   transmitted product. You may be held legally responsible for any
#   copyright infringement that is caused or encouraged by your failure to
#   abide by these terms and conditions.
#   
#   You are not permitted under this Licence to use this Software
#   commercially. Use for which any financial return is received shall be
#   defined as commercial use, and includes (1) integration of all or part
#   of the source code or the Software into a product for sale or license
#   by or on behalf of Licensee to third parties or (2) use of the
#   Software or any derivative of it for research with the final aim of
#   developing software products for sale or license to a third party or
#   (3) use of the Software or any derivative of it for research with the
#   final aim of developing non-software products for sale or license to a
#   third party, or (4) use of the Software to provide any service to an
#   external organisation for which payment is received. If you are
#   interested in using the Software commercially, please contact Isis
#   Innovation Limited ("Isis"), the technology transfer company of the
#   University, to negotiate a licence. Contact details are:
#   innovation@isis.ox.ac.uk quoting reference DE/9564.

Usage () {
  $FSLDIR/bin/invwarp_exe -h > /tmp/invwarp_help_$PID 2>&1
  cat /tmp/invwarp_help_$PID | sed 's/-r,--ref.*/-r,--ref	filename for new brain-extracted reference image, i.e., what was originally the brain-extracted input image (used to determine FOV and pixdims for inverse warp)/' |  sed 's/--rel/--oldref	filename of old reference image (default="standard" or MNI152_T1_2mm)@	--rel/' |  sed 's/-v,/--force  	force process to run despite warnings@	-v,/' | tr '@' '\n'
## @	--nowarning	do not perform check for BET and large ROI size
  rm -f /tmp/invwarp_help_$PID
  exit 1;
}

#
# As part of testing the new invwarp (with the imaginative
# name new_invwarp) this script is retained but all its 
# functionality is bypassed and the parameters are fed
# straight into the executable. This makes it trivial to
# revert back to the old version by simply commenting out
# the call to new_invwarp and the exit below.
#
${FSLDIR}/bin/new_invwarp $*
exit $?

if [ $# -lt 3 ] ; then
    Usage
fi

# Process the options
#   old syntax: invwarp <warpvol=$inwarp> <refvol=$refvol> <out=$outvol> $args
args="";
verbose=no;
warning=yes;
force=no;
while [ $# -gt 0 ] ; do
    aa=$1;
    bb=`echo $aa | sed 's/=.*//'`;
    cc=`echo $aa | sed 's/.*=//'`;
    if [ $aa = "-w" ]  ; then
	inwarp=$2;
	shift; shift;
    elif [ $bb = "--warp" ] ; then
	inwarp=$cc;
	shift;
    elif [ $aa = "-o" ] ; then
	outvol=$2;
	shift; shift;
    elif [ $bb = "--out" ] ; then
	outvol=$cc;
	shift;
    elif [ $aa = "-r" ] ; then
	refvol=$2;
	shift; shift;
    elif [ $bb = "--ref" ] ; then
	refvol=$cc;
	shift;
    elif [ $bb = "--oldref" ] ; then
	stdvol=$cc;
	shift;
    elif [ $bb = "--nowarning" ] ; then
	warning=no;
	shift;
    elif [ $bb = "--force" ] ; then
	force=yes;
	shift;
    elif [ $aa = "-v" ] ; then
	args="$args -v";
	verbose=yes;
	shift;
    elif [ $bb = "--verbose" ] ; then
	args="$args --verbose";
	verbose=yes;
	shift;
    else
	args="$args $aa";
	shift;
    fi
done

# Do a quick sanity check on the options
if [ $verbose = yes ] ; then
    echo warp=$inwarp out=$outvol ref=$refvol stdvol=$stdvol args="$args"
fi
if [ `$FSLDIR/bin/imtest $refvol` = 0 ] ; then  Usage ; fi
if [ `$FSLDIR/bin/imtest $inwarp` = 0 ] ; then  Usage ; fi
if [ X$outvol = X ] ; then Usage ; fi

# Now start doing some work!
if [ $verbose = yes ] ; then  echo "Extracting ROI" ; fi
roivals=`$FSLDIR/bin/fslstats $refvol -w`;

xmin=`echo $roivals | awk '{ print $1 }'`;
ymin=`echo $roivals | awk '{ print $3 }'`;
zmin=`echo $roivals | awk '{ print $5 }'`;
xsize=`echo $roivals | awk '{ print $2 }'`;
ysize=`echo $roivals | awk '{ print $4 }'`;
zsize=`echo $roivals | awk '{ print $6 }'`;

if [ $warning = yes ] ; then
 # test if it looks like BET has been run or not (see if ROI is
 #  actually any smaller and ROI is not more than 20% bigger than MNI brain)
 # MNI brain size is 140 180 150 -> 170 220 180  (with 20% increase)
  badroi=no;
  if [ $xsize -gt 170 ] ; then badroi=yes; fi
  if [ $ysize -gt 220 ] ; then badroi=yes; fi
  if [ $zsize -gt 180 ] ; then badroi=yes; fi
  if [ `$FSLDIR/bin/fslval $refvol dim1` -le `echo "$xsize + 2" | bc` ] ; then
      if [ `$FSLDIR/bin/fslval $refvol dim2` -le `echo "$ysize + 2" | bc` ] ; then 
	  if [ `$FSLDIR/bin/fslval $refvol dim3` -le `echo "$zsize + 2" | bc` ] ; then 
	      badroi=yes; 
	  fi
      fi
  fi
  if [ $badroi = yes ] ; then
      echo " "
      echo "WARNING!! Reference image has large non-zero ROI. Check that BET has run successfully on this."
      echo " "
      if [ $force = no ] ; then exit 1; fi
  fi
fi

if [ $verbose = yes ] ; then  echo "Enlarging initial ROI: $roivals"; fi
# take an extra couple of voxels around the ROI if possible
if [ $xmin -ge 2 ] ; then 
   xmin=`echo $xmin - 2 | bc`; 
   xsize=`echo $xsize + 2 | bc`; 
fi
if [ $ymin -ge 2 ] ; then 
   ymin=`echo $ymin - 2 | bc`; 
   ysize=`echo $ysize + 2 | bc`; 
fi
if [ $zmin -ge 2 ] ; then 
   zmin=`echo $zmin - 2 | bc`; 
   zsize=`echo $zsize + 2 | bc`; 
fi
if [ `$FSLDIR/bin/fslval $refvol dim1` -ge `echo "$xmin + $xsize + 2" | bc` ] ; then
  xsize=`echo $xsize + 2 | bc`;
fi
if [ `$FSLDIR/bin/fslval $refvol dim2` -ge `echo "$ymin + $ysize + 2" | bc` ] ; then
  ysize=`echo $ysize + 2 | bc`;
fi
if [ `$FSLDIR/bin/fslval $refvol dim3` -ge `echo "$zmin + $zsize + 2" | bc` ] ; then
  zsize=`echo $zsize + 2 | bc`;
fi

if [ $verbose = yes ] ; then  
  echo "Enlarged ROI: $xmin $xsize $ymin $ysize $zmin $zsize" ; 
fi
# make xminmm version (in mm not voxels)
xvox=`$FSLDIR/bin/fslval $refvol pixdim1`;
yvox=`$FSLDIR/bin/fslval $refvol pixdim2`;
zvox=`$FSLDIR/bin/fslval $refvol pixdim3`;
xminmm=`echo "$xmin * $xvox" | bc -l`;
yminmm=`echo "$ymin * $yvox" | bc -l`;
zminmm=`echo "$zmin * $zvox" | bc -l`;
xsizemm=`echo "$xsize * $xvox" | bc -l`;
ysizemm=`echo "$ysize * $yvox" | bc -l`;
zsizemm=`echo "$zsize * $zvox" | bc -l`;

if [ $verbose = yes ] ; then  echo "Making tmp directory" ; fi
tmpdir=`$FSLDIR/bin/tmpnam`;
origdir=$tmpdir;
tmpdir="${tmpdir}A"
if [ -d $tmpdir ] ; then
  echo "Temporary directory $tmpdir already exists!  Exiting.";
  exit 1;
else
  mkdir $tmpdir
fi

if [ $verbose = yes ] ; then  echo "Generating field"; fi
# pick a standard (either set via options or use "standard" in pwd 
#    or MNI152_T1_2mm  - in that order)
if [ X$stdvol = X ] ; then
    stdvol=$FSLDIR/data/standard/MNI152_T1_2mm
    if [ `$FSLDIR/bin/imtest standard` = 1 ] ; then stdvol=standard; fi
fi
# Note: on line below need "standard" in pwd!  - What to do about this?!?
$FSLDIR/bin/fnirtfileutils -i $inwarp -f field -o $tmpdir/hr2std_field -a

if [ $verbose = yes ] ; then  echo "Extracting ROI and offsetting field" ; fi
$FSLDIR/bin/fslroi $refvol $tmpdir/refvol_roi $xmin $xsize $ymin $ysize $zmin $zsize 0 1

# need to adjust field for different starting position in roi images
$FSLDIR/bin/fslroi $tmpdir/hr2std_field $tmpdir/fieldx 0 1
$FSLDIR/bin/fslroi $tmpdir/hr2std_field $tmpdir/fieldy 1 1
$FSLDIR/bin/fslroi $tmpdir/hr2std_field $tmpdir/fieldz 2 1

# NEUROLOGICAL FIX
if [ `$FSLDIR/bin/fslorient $refvol ` = NEUROLOGICAL ] ; then
    dim1=`$FSLDIR/bin/fslval $refvol dim1`;
    transx=`echo " ( $dim1 - 1 - ( $xmin + $xsize - 1 ) )  * $xvox " | bc -l`;
else
    transx=$xminmm;
fi

$FSLDIR/bin/fslmaths $tmpdir/fieldx -sub $transx $tmpdir/fieldx
$FSLDIR/bin/fslmaths $tmpdir/fieldy -sub $yminmm $tmpdir/fieldy
$FSLDIR/bin/fslmaths $tmpdir/fieldz -sub $zminmm $tmpdir/fieldz
$FSLDIR/bin/fslmerge -t $tmpdir/roi2std_field $tmpdir/fieldx $tmpdir/fieldy $tmpdir/fieldz

if [ $verbose = yes ] ; then  echo "Running real INVWARP"; fi
$FSLDIR/bin/invwarp_exe -w $tmpdir/roi2std_field -o $tmpdir/standard2highres_warp -r $tmpdir/refvol_roi $args

if [ $verbose = yes ] ; then  echo "Undoing offset" ; fi
$FSLDIR/bin/fslroi $tmpdir/standard2highres_warp $tmpdir/fieldx 0 1
$FSLDIR/bin/fslroi $tmpdir/standard2highres_warp $tmpdir/fieldy 1 1
$FSLDIR/bin/fslroi $tmpdir/standard2highres_warp $tmpdir/fieldz 2 1
$FSLDIR/bin/fslmaths $tmpdir/fieldx -sub $transx $tmpdir/fieldx
$FSLDIR/bin/fslmaths $tmpdir/fieldy -sub $yminmm $tmpdir/fieldy
$FSLDIR/bin/fslmaths $tmpdir/fieldz -sub $zminmm $tmpdir/fieldz
$FSLDIR/bin/fslmerge -t $tmpdir/standard2highres_full_warp $tmpdir/fieldx $tmpdir/fieldy $tmpdir/fieldz

if [ $verbose = yes ] ; then  echo "Restoring full FOV" ; fi
# extend ROI by copying the extreme slices
warp=$tmpdir/standard2highres_full_warp
refdim1=`$FSLDIR/bin/fslval $refvol dim1`;
refdim2=`$FSLDIR/bin/fslval $refvol dim2`;
refdim3=`$FSLDIR/bin/fslval $refvol dim3`;
dim1=`$FSLDIR/bin/fslval $warp dim1`;
dim2=`$FSLDIR/bin/fslval $warp dim2`;
dim3=`$FSLDIR/bin/fslval $warp dim3`;
# extend in z first
bottom_slice=$tmpdir/bottom_slice
top_slice=$tmpdir/top_slice
$FSLDIR/bin/fslroi $warp $bottom_slice 0 $dim1 0 $dim2 0 1 0 3
$FSLDIR/bin/fslroi $warp $top_slice 0 $dim1 0 $dim2 `echo $dim3 - 1 | bc` 1 0 3
com="$FSLDIR/bin/fslmerge -z $warp ";
sl=0;
while [ $sl -lt $zmin ] ; do com="$com $bottom_slice "; sl=`echo $sl + 1 | bc`; done
com="$com $warp ";
sl=`echo $zmin + $zsize | bc`;
if [ $verbose = yes ] ; then  echo Starting slice=$sl and finish=$refdim3 ; fi
if [ $verbose = yes ] ; then  echo zmin=$zmin and zsize=$zsize ; fi
while [ $sl -lt $refdim3 ] ; do com="$com $top_slice "; sl=`echo $sl + 1 | bc`; done
#echo $com 
$com
dim3=`$FSLDIR/bin/fslval $warp dim3`;
# extend in y next
back_slice=$tmpdir/back_slice
front_slice=$tmpdir/front_slice
$FSLDIR/bin/fslroi $warp $back_slice 0 $dim1 0 1 0 $dim3 0 3
$FSLDIR/bin/fslroi $warp $front_slice 0 $dim1 `echo $dim2 - 1 | bc` 1 0 $dim3 0 3
com="$FSLDIR/bin/fslmerge -y $warp ";
sl=0;
while [ $sl -lt $ymin ] ; do com="$com $back_slice "; sl=`echo $sl + 1 | bc`; done
com="$com $warp ";
sl=`echo $ymin + $ysize | bc`;
while [ $sl -lt $refdim2 ] ; do com="$com $front_slice "; sl=`echo $sl + 1 | bc`; done
#echo $com
$com
dim2=`$FSLDIR/bin/fslval $warp dim2`;
# extend in x next
left_slice=$tmpdir/left_slice
right_slice=$tmpdir/right_slice
$FSLDIR/bin/fslroi $warp $left_slice 0 1 0 $dim2 0 $dim3 0 3
$FSLDIR/bin/fslroi $warp $right_slice `echo $dim1 - 1 | bc` 1 0 $dim2 0 $dim3 0 3
lcom=""; rcom=""; com="";
sl=0;
while [ $sl -lt $xmin ] ; do lcom="$lcom $left_slice "; sl=`echo $sl + 1 | bc`; done
sl=`echo $xmin + $xsize | bc`;
while [ $sl -lt $refdim1 ] ; do rcom="$rcom $right_slice "; sl=`echo $sl + 1 | bc`; done
if [ `$FSLDIR/bin/fslorient $refvol ` = NEUROLOGICAL ] ; then
    # neurological case
    com="$FSLDIR/bin/fslmerge -x $warp $rcom $warp $lcom";
else
    # radiological case
    com="$FSLDIR/bin/fslmerge -x $warp $lcom $warp $rcom";
fi
#echo $com
$com
dim1=`$FSLDIR/bin/fslval $warp dim1`;

$FSLDIR/bin/imcp $warp $outvol

if [ $verbose = yes ] ; then  echo "Cleanup temporary files"; fi
rm -f ${tmpdir}/*.nii*
rm -f ${tmpdir}/*.hdr*
rm -f ${tmpdir}/*.img*
rm -f ${tmpdir}/*.mat
rmdir ${tmpdir}
if [ X$origdir != X ] ; then rm ${origdir} ; fi