#!/bin/sh

#   slices - call slicer with default cuts and display
#
#   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.
#   
#   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.
export LC_NUMERIC=C


Usage() {
    echo ""
    echo "Usage: slices <input> [input2] [-s scale] [-i <intmin> <intmax>] [-o <output gif>]"
    echo ""
    exit 1
}

[ "$1" = "" ] && Usage

if [ _$FSLDIR = _ ] ; then
    FSLDIR=/usr/local/fsl
    export FSLDIR
fi

# NEED PARSING IN ORDER TO HAVE A -o OPTION
outputname=""
# if statement checks if -o option was given
if [ `echo "$@" | grep -- -o | wc -w` -gt 0 ] ; then
    # extract the <output gif> name if the -o option is present
    outputname=`echo "$@" | sed 's/.*-o *\([^ ]*\).*/\1/'`;
fi

if [ `$FSLDIR/bin/imtest $1` -eq 0 ] ; then
echo "cannot read file $1"
exit 1
fi

f=/tmp/`${FSLDIR}/bin/remove_ext $1 | sed "s/\//_/g"`
touch $f > /dev/null 2>&1
if [ ! -w $f ] ; then
    f=`${FSLDIR}/bin/tmpnam $f`
fi

# deal with complex images separately
if [ X`${FSLDIR}/bin/fslval $1 datatype` = X32 ] ; then
  nm1=${f}_abs
  nm2=${f}_ph
  nm0=`${FSLDIR}/bin/remove_ext $1`;
  if [ X$1 != X ] ; then
    shift ;
  fi
  ${FSLDIR}/bin/fslcomplex -realpolar $nm0 $nm1 $nm2
  ${FSLDIR}/bin/slices $nm1 $@
  ${FSLDIR}/bin/slices $nm2 $@
  ${FSLDIR}/bin/imrm $nm1 $nm2
  exit 0
fi  

# deal with 2D and 3D images separately

if [ X`${FSLDIR}/bin/fslval $1 dim3` = X1 ] ; then
  # 2D case
  slicenum=-0
  im1=`${FSLDIR}/bin/remove_ext $1`;
  if [ X$2 != X ] ; then
    shift ;
    im2=`${FSLDIR}/bin/remove_ext $1`;
  fi
  if [ X$1 != X ] ; then
    shift ;
  fi
  if [ X$im2 != X ] ; then
    if [ `$FSLDIR/bin/imtest $im2` -eq 1 ] ; then
      # make a stacked version for getting edges
      ${FSLDIR}/bin/fslmerge -z ${f}b $im1 $im1 $im1
      ${FSLDIR}/bin/fslmerge -z ${f}c $im2 $im2 $im2
      im1=${f}b
      im2=${f}c
      slicenum=-1
    fi
  fi

  # NEED PARSING IN ORDER TO HAVE A -o OPTION
  opts="$@"
  # remove the "-o <output gif>" from the command line list
  opts=`echo $opts | sed 's/-o *[^ ]*//'`;
  if ${FSLDIR}/bin/slicer $im1 $im2 $opts -z $slicenum ${f}a.png ; then 
    retval=0; # do nothing 
  else
    exit -1;
  fi
  ${FSLDIR}/bin/pngappend ${f}a.png ${f}.gif

else
  # 3D case

  # NEED PARSING IN ORDER TO HAVE A -o OPTION
  opts="$@"
  # remove the "-o <output gif>" from the command line list
  opts=`echo $opts | sed 's/-o *[^ ]*//'`;

  if ${FSLDIR}/bin/slicer $opts -x 0.4 ${f}a.png -x 0.5 ${f}b.png -x 0.6 ${f}c.png -y 0.4 ${f}d.png -y 0.5 ${f}e.png -y 0.6 ${f}f.png -z 0.4 ${f}g.png -z 0.5 ${f}h.png -z 0.6 ${f}i.png ; then
    retval=0; # do nothing 
  else
    exit -1;
  fi
  
  ${FSLDIR}/bin/pngappend ${f}a.png + ${f}b.png + ${f}c.png - ${f}d.png + ${f}e.png + ${f}f.png - ${f}g.png + ${f}h.png + ${f}i.png ${f}.gif

fi

# if using the -o option then just copy the file, otherwise display it
if [ X$outputname != X ] ; then
    cp ${f}.gif $outputname
else
    if [ X`uname | grep CYGWIN`X != XX ] ; then
	/cygdrive/c/Program\ Files/Internet\ Explorer/IEXPLORE.EXE C:/cygwin${f} &
    elif [ X`uname | grep -i darwin`X != XX ] ; then
	g=`${FSLDIR}/bin/tmpnam $f`.gif ;
	cp $f $g ;
	open ${f}.gif ;
    else
	$FSLWISH ${FSLDIR}/tcl/display.tcl $f.gif &
    fi
fi

\rm -f ${f}a.png ${f}b.png ${f}c.png ${f}d.png ${f}e.png ${f}f.png ${f}g.png ${f}h.png ${f}i.png 

( sleep 20 ; \rm -f ${f}.gif ) &