#!/bin/sh
#   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 ""
    echo "Usage: design_ttest2 <design_files_rootname> <NgroupA> <NgroupB> [-m]"
    echo "-m : include individual group mean contrasts"
    echo ""
    exit 1
}

[ "$3" = "" ] && Usage

OUT=$1
NA=$2
NB=$3
NAandB=`echo "$NA $NB + p" | dc -`

echo "/NumWaves 2" > ${OUT}.mat
echo "/NumPoints $NAandB" >> ${OUT}.mat
echo "/PPheights 1 1" >> ${OUT}.mat
echo "/Matrix" >> ${OUT}.mat
while [ ! $NA -eq 0 ] ; do
    echo "1 0" >> ${OUT}.mat
    NA=`echo "$NA 1 - p" | dc -`
done
while [ ! $NB -eq 0 ] ; do
    echo "0 1" >> ${OUT}.mat
    NB=`echo "$NB 1 - p" | dc -`
done

NCON=2
if [ "$4" != "" ] ; then
  NCON=4
fi

echo "/NumWaves 2" > ${OUT}.con
echo "/NumContrasts $NCON" >> ${OUT}.con
echo "/PPheights 1 1" >> ${OUT}.con
echo "/Matrix" >> ${OUT}.con
if [ $NCON = 4 ] ; then
    echo "1 0" >> ${OUT}.con
    echo "0 1" >> ${OUT}.con
fi
echo "1 -1" >> ${OUT}.con
echo "-1 1" >> ${OUT}.con