#!/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: $0 data_dir"
    exit 1;
fi

DIR=$1;
for img in ${DIR}/data ${DIR}/nodif_brain_mask ;do
    if [ `${FSLDIR}/bin/imtest $img` -eq 1 ] ; then
	echo $img
	${FSLDIR}/bin/fslinfo $img;
	echo ""
    else
	echo $img does not exist;
    fi
done

for bv in ${DIR}/bvals ${DIR}/bvecs;do
    echo " num lines in $bv "
    cat $bv |grep -v "^[ 	]*$"|wc -l
    echo " num words in $bv "
    cat $bv|wc -w
done

if [ `${FSLDIR}/bin/imtest ${DIR}/data` -eq 1 ] && [ `${FSLDIR}/bin/imtest ${DIR}/nodif_brain_mask` -eq 1 ];then

    dx=`${FSLDIR}/bin/fslval ${DIR}/data dim1`
    dy=`${FSLDIR}/bin/fslval ${DIR}/data dim2`
    dz=`${FSLDIR}/bin/fslval ${DIR}/data dim3`
    dt=`${FSLDIR}/bin/fslval ${DIR}/data dim4`
    
    nbmx=`${FSLDIR}/bin/fslval ${DIR}/nodif_brain_mask dim1`
    nbmy=`${FSLDIR}/bin/fslval ${DIR}/nodif_brain_mask dim2`
    nbmz=`${FSLDIR}/bin/fslval ${DIR}/nodif_brain_mask dim3`
    
    
    if [ $dx -ne $nbmx ] || [ $dy -ne $nbmy ] || [ $dz -ne $nbmz ];then 
	echo "data dimensions do not match mask dimensions"
    fi
    
    bvallenw=`cat ${DIR}/bvals|wc -w`
    bvallenl=`cat ${DIR}/bvals|grep -v "^[ 	]*$"|wc -l`
    bvallen=`echo "$bvallenw / $bvallenl"|bc`

    bveclenw=`cat ${DIR}/bvecs|wc -w`
    bveclenl=`cat ${DIR}/bvecs|grep -v "^[ 	]*$"|wc -l`
    bveclen=`echo "$bveclenw / $bveclenl"|bc`

    if [ $bveclenl -ne 3 -a $bveclen -ne 3 ];then
	echo "bvecs is not 3xN or Nx3 format"
    fi

    if [ $bvallenl -ge 2 -a $bvallen -ge 2 ];then
	echo "bvals is not 1xN or Nx1 format"
    fi
 
    if [ $bveclen -ne $bvallenw -a $bveclenl -ne $bvallenw ];then
	echo "bvecs and bvals are incompatible"
    fi

    if [ $bvallenw -ne $dt ];then 
	echo "number of elements in bvals is not equal to number of vols in data"
    fi

    if [ $bveclen -ne $dt -a $bveclenl -ne $dt ];then 
	echo "number of vectors in bvecs is not equal to number of vols in data"
    fi
	
fi