#!/bin/bash
set -e
#   Copyright (C) 2012 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 "`basename $0` <input matrix> <input contrast> <output basename> <mask1> <mask2> ..."
  echo " "
  echo "The list of mask images (<mask1> <mask2> ...) must be from subjects in the same order as used in the design matrix"
  exit 1
}

CleanUp() {
    out=$1
    rm -f ${out}.mat.txt ${out}.con.txt ${out}.mat.ext ${out}.con.ext ${out}.mat2 ${out}.con2
}

if [ $# -lt 4 ] ; then Usage; fi
numsubj=`echo $# - 3 | bc`

dmat=$1
dcon=$2
out=$3
shift
shift
shift
imlist="$@"

CleanUp ${out}

# convert matrices to text format
$FSLDIR/bin/Vest2Text ${dmat} ${out}.mat.txt
$FSLDIR/bin/Vest2Text ${dcon} ${out}.con.txt
# sanity check on size of matrix
maxrow=`cat ${out}.mat.txt | wc -l`;
if [ $maxrow != $numsubj ] ; then 
  echo "ERROR:: design matrix of different size to number of masks specified"
  exit 2
fi
maxcol=`cat ${out}.mat.txt | wc -w`;
maxcol=`echo $maxcol / $maxrow | bc`;
echo "MATRIX SIZE IS $maxrow $maxcol"

# MAKE 4D VOXELWISE EVS
# make base 4D file
echo $FSLDIR/bin/fslmerge -t $out $imlist
$FSLDIR/bin/fslmerge -t $out $imlist

subjnum=0;
vxlopts="";
vxfopts="";
while [ $subjnum -lt $numsubj ] ; do
    znum=`echo $subjnum + $maxcol + 1 | bc`
    vxlopts="${vxlopts},${znum}";
    znum=`$FSLDIR/bin/zeropad $znum 4`;
    $FSLDIR/bin/fslmaths $out -roi 0 -1 0 -1 0 -1 $subjnum 1 ${out}_${znum}
    vxfopts="${vxfopts},${out}_${znum}";
    subjnum=`echo $subjnum + 1 | bc`;
done
# remove leading comma
vxlopts=${vxlopts/,/}
vxfopts=${vxfopts/,/}
$FSLDIR/bin/imrm $out

# MAKE NEW DESIGN MATRIX
# build up an identity matrix and zero contrast vector of appropriate sizes
row=1; 
while [ $row -le $maxrow ] ; do 
  col=1; 
  cs="" ; 
  zerocon="";
  while [ $col -le $maxrow ] ; do 
    if [ $row = $col ] ; then cs="${cs}1 " ; 
    else cs="${cs}0 " ; fi ; 
    zerocon="${zerocon} 0"
    col=`echo $col + 1 | bc`;
  done ; 
  echo "$cs" >> ${out}.mat.ext ; 
  row=`echo $row + 1 | bc` ;
done
# form zero contrast vector into a matrix
ncon=1;
totcon=`cat ${out}.con.txt | wc -l`;
while [ $ncon -le $totcon ] ; do
  echo $zerocon >> ${out}.con.ext
  ncon=`echo $ncon + 1 | bc`;
done
# tack on the matrices made above
paste ${out}.mat.txt ${out}.mat.ext > ${out}.mat2
paste ${out}.con.txt ${out}.con.ext > ${out}.con2
# convert back to vest format
$FSLDIR/bin/Text2Vest ${out}.mat2 ${out}.mat
$FSLDIR/bin/Text2Vest ${out}.con2 ${out}.con

# clean up
CleanUp ${out}


echo "Example randomise call:"
echo "  randomise -i <input> -o <output> -d ${out}.mat -t ${out}.con --vxl=${vxlopts} --vxf=${vxfopts} [other options]"

