#!/bin/sh

#   pnm_stage1
#
#   Mark Jenkinson, FMRIB Image Analysis Group
#
#   Copyright (C) 2011 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 "Usage: `basename $0` [popp options]"
  echo "   Runs popp (see options below) and then creates necessary scripts"
  echo "     to run manual webpage editing (and second stage if GUI was used)"
  echo " "
  $FSLDIR/bin/popp
}

if [ $# -eq 0 ] ; then
    usage
    exit 1;
fi

cpwd=`pwd`;
args="$@"

# extract output basename from the usage string
while [ $# -gt 0 ] ; do
    if [ $1 = "-o" ] ; then obase=$2; fi
    if [ X`echo $1 | grep -- --out=` != X ] ; then obase=`echo $1 | sed 's/--out=//'`; fi
    shift;
done
obase=`$FSLDIR/bin/fsl_abspath $obase`;

# run popp
echo $FSLDIR/bin/popp $args
$FSLDIR/bin/popp $args

jsdata=${obase}_pnm.js
odir=`dirname $obase`;
odir=`$FSLDIR/bin/fsl_abspath $odir`;

# make the next script - if GUI is run then this also includes the pnm_evs call
echo "#!/bin/sh" > ${obase}_pnm_stage2
echo "cd $cpwd" >> ${obase}_pnm_stage2
echo "obase=$obase" >> ${obase}_pnm_stage2
echo "export obase" >> ${obase}_pnm_stage2
echo "if [ \$# -gt 0 ] ; then $FSLDIR/bin/popp $args \$@ ; fi" >> ${obase}_pnm_stage2
if [ -f ${obase}_pnm_stage3 ] ; then 
    echo "${obase}_pnm_stage3" >> ${obase}_pnm_stage2 ; 
    chmod 755 ${obase}_pnm_stage3
fi
chmod 755 ${obase}_pnm_stage2

# copy webpage template and replace FSLDIR stubs and output basename data file
cat $FSLDIR/etc/js/pnm_main_frame.html | sed "s|pnm_lower_frame.html|${obase}_pnm3.html|" | sed "s|label-div.html|${obase}_pnm2.html|" > ${obase}_pnm1.html
cat $FSLDIR/etc/js/pnm_lower_frame.html | sed "s|./pnm_stage2|${obase}_pnm_stage2|" > ${obase}_pnm3.html
cat $FSLDIR/etc/js/label-div.html | sed "s|FSLDIR|$FSLDIR|g" | sed "s|PNMDATA.js|$jsdata|" | sed "s|PNMSTAGE2|${obase}_pnm_stage2|" > ${obase}_pnm2.html
## MJ TODO - do something about the lack of ./ in front of script name in previous line

# determine browser (javascript only works in Firefox - not Safari)
browser_comm=firefox
if [ X`echo $FSLMACHTYPE | grep apple` != X ] ; then
    browser_comm='open -a Firefox';
fi
cd $odir
# $browser_comm ${obase}_pnm1.html


