get rid of rotate_bvecs

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};
-