rotate_bvecs

#!/bin/sh

if [ "$2" == "" ];then
    echo ""
    echo "Usage: rotate_bvecs <ecclogfile> <bvecs>"
    echo "will save bvecs file into <bvecs>_unrotated and create new bvecs file called <bvecs>"
    echo ""
    exit 1
fi

ecclog=$1
bvecs=$2

if [ -f ${bvecs}_unrotated ];then
    echo ""
    echo "Error: Found that ${bvecs}_unrotated already exists"
    echo "This probably means that you have run this script before. Be aware that this also means ${bvecs} have already been rotated!"
    echo "If you want to force this program to run, please remove the file ${bvecs}_unrotated"
    echo ""
    exit 1
fi
/bin/cp ${bvecs} ${bvecs}_unrotated
#/bin/rm -f ${bvecs}


# this only works if the bvecs are in lines...
Xs=$(cat ${bvecs}_unrotated | head -1 | tail -1)
Ys=$(cat ${bvecs}_unrotated | head -2 | tail -1)
Zs=$(cat ${bvecs}_unrotated | head -3 | tail -1)

rnd=${$}
cat ${ecclog} | while read line; do
    #create a file name from processed volumes
    matfile=$(remove_ext $(echo ${line} | grep processing | awk '{print $2}'));

    if [ "${matfile}" != "" ] ; then
	   matfile=/tmp/grot${rnd}_${matfile}.mat;

       # following two reads will deal with unimportant lines
       read line;
       read line;
       # read matrix and store it in the current matfile
       read line;
       echo ${line} > ${matfile};
       read line;
       echo ${line} >> ${matfile};
       read line;
       echo ${line} >> ${matfile};
       read line;
       echo ${line} >> ${matfile};

    fi
 done

# now use these files
i=1
for matfile in /tmp/grot${rnd}_*.mat;do

    # read that file from disk and extract params
    output=`avscale --allparams ${matfile} | head -2 | tail -1`
    m11=`echo $output | awk '{print $1}' | sed 's/E/\\*10\\^/' | sed 's/e/\\*10\\^/' | sed 's/+//'` 
    m12=`echo $output | awk '{print $2}' | sed 's/E/\\*10\\^/' | sed 's/e/\\*10\\^/' | sed 's/+//'` 
    m13=`echo $output | awk '{print $3}' | sed 's/E/\\*10\\^/' | sed 's/e/\\*10\\^/' | sed 's/+//'` 
    
    output=`avscale --allparams ${matfile} | head -3 | tail -1`
    m21=`echo $output | awk '{print $1}' | sed 's/E/\\*10\\^/' | sed 's/e/\\*10\\^/' | sed 's/+//'` 
    m22=`echo $output | awk '{print $2}' | sed 's/E/\\*10\\^/' | sed 's/e/\\*10\\^/' | sed 's/+//'` 
    m23=`echo $output | awk '{print $3}' | sed 's/E/\\*10\\^/' | sed 's/e/\\*10\\^/' | sed 's/+//'` 
    
    output=`avscale --allparams ${matfile} | head -4 | tail -1`
    m31=`echo $output | awk '{print $1}' | sed 's/E/\\*10\\^/' | sed 's/e/\\*10\\^/' | sed 's/+//'` 
    m32=`echo $output | awk '{print $2}' | sed 's/E/\\*10\\^/' | sed 's/e/\\*10\\^/' | sed 's/+//'` 
    m33=`echo $output | awk '{print $3}' | sed 's/E/\\*10\\^/' | sed 's/e/\\*10\\^/' | sed 's/+//'` 
    
    X=`echo $Xs | cut -d " " -f "$i"  | sed 's/E/\\*10\\^/' | sed 's/e/\\*10\\^/' | sed 's/+//'`
    Y=`echo $Ys | cut -d " " -f "$i"  | sed 's/E/\\*10\\^/' | sed 's/e/\\*10\\^/' | sed 's/+//'`
    Z=`echo $Zs | cut -d " " -f "$i"  | sed 's/E/\\*10\\^/' | sed 's/e/\\*10\\^/' | sed 's/+//'`
    
    # apply rotation
    rX=$(echo "scale=7;  ($m11 * $X) + ($m12 * $Y) + ($m13 * $Z)" | bc -l);
    rY=$(echo "scale=7;  ($m21 * $X) + ($m22 * $Y) + ($m23 * $Z)" | bc -l);
    rZ=$(echo "scale=7;  ($m31 * $X) + ($m32 * $Y) + ($m33 * $Z)" | bc -l);

    
    # reformat
    rX=$(printf "%1.7g" $rX)
    rY=$(printf "%1.7g" $rY)
    rZ=$(printf "%1.7g" $rZ)
    
    
    # concatenate
    rXs=${rXs}${rX}" ";
    rYs=${rYs}${rY}" ";
    rZs=${rZs}${rZ}" ";
    
    i=$(echo "$i + 1" | bc) ;
done

echo "$rXs" > ${bvecs};
echo "$rYs" >> ${bvecs};
echo "$rZs" >> ${bvecs};