#!/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.

if [ $# -lt 1 ]; then
echo "Usage: facalc <basename> [-mode]"
echo "e.g. facalc dti "
echo "This will use dti_L1 dti_L2 and dti_L3 to compute dti_FA"
echo "If -mode is set, the mode is calculated as well"
echo "Usage: facalc basename outbase"
echo "e.g. facalc dti test"
echo "will write test_FA instead of dti_FA"
exit
fi

bn=$1
if [ $# -lt 2 ];then 
ob=$bn
else
if [ "$2" != -mode ];then
ob=$2
else
ob=$bn
fi
fi


if [ `${FSLDIR}/bin/imtest ${bn}_L1` -eq 0 -o  `${FSLDIR}/bin/imtest ${bn}_L2` -eq 0 -o `${FSLDIR}/bin/imtest ${bn}_L3` -eq 0 ];
then echo "Not all eigenvalue images exist"
echo "stopping"
exit
fi


${FSLDIR}/bin/fslmaths ${bn}_L1 -add ${bn}_L2 -add ${bn}_L3 -div 3 tmpMD
${FSLDIR}/bin/fslmaths ${bn}_L1 -sqr tmpL1sq
${FSLDIR}/bin/fslmaths ${bn}_L2 -sqr tmpL2sq
${FSLDIR}/bin/fslmaths ${bn}_L3 -sqr tmpL3sq
${FSLDIR}/bin/fslmaths ${bn}_L1 -sub tmpMD -sqr tmpl1subsq
${FSLDIR}/bin/fslmaths ${bn}_L2 -sub tmpMD -sqr tmpl2subsq
${FSLDIR}/bin/fslmaths ${bn}_L3 -sub tmpMD -sqr tmpl3subsq
${FSLDIR}/bin/fslmaths tmpL1sq -add tmpL2sq -add tmpL3sq denom
${FSLDIR}/bin/fslmaths tmpl1subsq -add tmpl2subsq -add tmpl3subsq -mul 1.5 numer
${FSLDIR}/bin/fslmaths numer -div denom -sqrt ${ob}_FA

if [ "$2" == -mode -o "$3" == -mode ];then
    ${FSLDIR}/bin/fslmaths ${bn}_L1 -sub tmpMD tmpE1
    ${FSLDIR}/bin/fslmaths ${bn}_L2 -sub tmpMD tmpE2
    ${FSLDIR}/bin/fslmaths ${bn}_L3 -sub tmpMD tmpE3
    ${FSLDIR}/bin/fslmaths tmpE3 -mul -2 -add tmpE1 -add tmpE2 tmpN1 
    ${FSLDIR}/bin/fslmaths tmpE1 -mul -2 -add tmpE2 -add tmpE3 tmpN2 
    ${FSLDIR}/bin/fslmaths tmpE2 -mul -2 -add tmpE1 -add tmpE3 tmpN3 
    ${FSLDIR}/bin/fslmaths tmpN1 -mul tmpN2 -mul tmpN3 -mul -1 tmpN

    ${FSLDIR}/bin/fslmaths tmpE1 -sub tmpE2 -sub tmpE3 -mul tmpE1 tmpD
    ${FSLDIR}/bin/fslmaths tmpE2 -sub tmpE3 -mul tmpE2 -add tmpD tmpD
    ${FSLDIR}/bin/fslmaths tmpE3 -mul tmpE3 -add tmpD
    ${FSLDIR}/bin/fslmaths tmpD -thr 0 -sqrt tmpD
    ${FSLDIR}/bin/fslmaths tmpD -mul tmpD -mul tmpD -mul 2 tmpD

    ${FSLDIR}/bin/fslmaths tmpN -div tmpD -max -1 -min 1 ${ob}_MO
fi

${FSLDIR}/bin/imrm tmpMD tmpL1sq tmpL2sq tmpL3sq tmpl1subsq tmpl2subsq tmpl3subsq numer denom tmpE1 tmpE2 tmpE3 tmpD tmpN1 tmpN2 tmpN3