#!/bin/sh

#   sliceanimate - make animated gif of a volume, slice at a time
#
#   Stephen Smith, Mark Jenkinson and Matthew Webster FMRIB Image Analysis Group
#
#   Copyright (C) 1999-2007 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.
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#   No part of the Software may be reproduced, modified, transmitted or
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#   
#   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
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#   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.
export LC_NUMERIC=C

if [ $# -lt 1 ] ; then
  echo "Usage: $0 <volume> [slicer args]"
  exit -1
fi

volname=`${FSLDIR}/bin/remove_ext $1`;
bnm=`basename $volname`;
shift

nn=`$FSLDIR/bin/fslval $volname dim3`;
n=0;

tmpnam=`basename ${volname}`_TMP
tmpdir=/tmp

while [ $n -lt $nn ] ; do
  # echo $FSLDIR/bin/slicer $volname $@ -z -$n $tmpdir/${tmpnam}
  $FSLDIR/bin/slicer $volname $@ -z -$n $tmpdir/${tmpnam}.png
  snum=`echo "0000${n}" | sed 's/^.*\(....\)$/\1/'`;
  echo slice $snum
  ${FSLDIR}/bin/pngappend $tmpdir/${tmpnam}.png $tmpdir/${bnm}_slice${snum}.gif
  n=`echo $n + 1 | bc`;
done

rm -f $tmpdir/${tmpnam}.png

$FSLDIR/bin/whirlgif -o ${volname}_sliceanim.gif -time 35 -loop 0  $tmpdir/${bnm}_slice*.gif

rm -f $tmpdir/${bnm}_slice*.gif

