#!/bin/sh
set -e

#   Extended syntax for fslswapdim
#
#   Mark Jenkinson
#   FMRIB Image Analysis Group
#
#   Copyright (C) 2007-2008 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
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#   
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get_axis(){
    # search for either $1 or its reverse in $2 $3 $4
    # e.g. get_axis RL AP SI LR would return -z (as $1 = $4 but backwards)
    # whereas get_axis RL AP SI RL would return z (as $1 = $4)
    ax="";
    pre="";
    k2=`echo $1 | tr RLAPSI LRPAIS`;
    for fn in "$2:x" "$3:y" "$4:z" ; do
	ff=`echo $fn | sed 's/:.*//'`;
	aa=`echo $fn | sed 's/.*://'`;
	if [ $ff = $1 ] ; then ax=$aa ; fi
	if [ $ff = $k2 ] ; then ax=$aa ; pre="-" ; fi
    done
    ax="${pre}${ax}";
    echo $ax;
}

if [ $# -lt 4 ] ; then
  echo "Usage: fslswapdim <input> <a> <b> <c> [output]

  where a,b,c represent the new x,y,z axes in terms of the
  old axes.  They can take values of -x,x,y,-y,z,-z
  or RL,LR,AP,PA,SI,IS (in the case of nifti inputs)
  e.g.  fslswapdim invol y x -z outvol
  or    fslswapdim invol RL PA IS outvol
  where the latter will convert to axial slicing 
  (to match the avg152 images)"
  exit 1;
fi


filetype=`$FSLDIR/bin/fslval $1 file_type`;
if [ $filetype = "ANALYZE-7.5" ] ; then
    nifti=no;
else 
    nifti=yes;
fi

orient=yes;
if [ $nifti = yes ] ; then
    if [ `$FSLDIR/bin/fslval $1 sform_code` -gt 0 ] ; then
	labs=`$FSLDIR/bin/fslhd $1 | grep sform_.orient | sed 's/[^A-Z]//g'`;
    elif [ `$FSLDIR/bin/fslval $1 qform_code` -gt 0 ] ; then
	labs=`$FSLDIR/bin/fslhd $1 | grep qform_.orient | sed 's/[^A-Z]//g'`;
    else
	labs="RL PA IS";  # default - but not safe
	orient=no;
    fi
fi

uselabels=no

comm1="$FSLDIR/bin/fslswapdim_exe $1"
comm2=""
swaplabs=""
for fn in $2 $3 $4 ; do
    cc=`echo Q$fn | sed 's/[RLAPIS]//g'`;
    if [ $cc = "Q" ] ; then
	uselabels=yes;
	if [ $nifti = no ] ; then
	    echo "Cannot use RLAPSI notation for non-nifti files"
	    exit 2
	fi
	if [ $orient = no ] ; then
	    echo "Cannot use RLAPSI notation for nifti files without either sform or qform set"
	    exit 2
	fi
	cc=`get_axis $fn $labs`;
    else 
	cc=$fn;
    fi
    comm2="$comm2 $cc";
    swaplabs="$swaplabs $cc"
done

# check if just a simple copy is good enough (only if an output filename is specified)
if [ "$swaplabs" = " x y z" ] ; then
    if [ X$5 != X ] ; then
	if [ `$FSLDIR/bin/remove_ext $1` != `$FSLDIR/bin/remove_ext $5` ] ; then
	    comm="$FSLDIR/bin/imcp $1 $5"
	    $comm
	    exit 0
	fi
    else
	cat $FSLDIR/etc/flirtsch/ident.mat
	exit 0
    fi
fi


# Check if the labels are used *and* it is doing a left-right inversion
if [ $uselabels = yes ] ; then
    # the line below just checks the swapping syntax - it does not require the true image, as any will do since the arguments are now reduced to x/y/z format
    check="`$FSLDIR/bin/fslswapdim_exe $FSLDIR/data/standard/MNI152_T1_2mm_brain $comm2 --checkLR`"
    wl=`echo $check | grep -i changed | wc -l`;
    if [ $wl -gt 0 ] ; then
	echo "Cannot perform requested swap (NEUROLOGICAL/RADIOLOGICAL storage inverted)"
	echo "Try the following command instead:"
	arg234=`echo "$2 $3 $4" | sed 's/RL/LRXX/g' | sed 's/LR/RL/g' | sed 's/RLXX/LR/g' | sed 's/-x/XX-x/g' | sed 's/ x / -x /g' | sed 's/XX-x/x/g'`;
	echo "fslswapdim $1 $arg234 $5"
	exit 1
    fi
fi

comm="$comm1 $comm2 $5"

# verbose?
#echo $comm

$comm