bundleFEAT

#!/bin/sh
#
#   Copyright (C) Eugene Duff 2013 University of Oxford
#
#   SHCOPYRIGHT

Usage() {
	function=`basename $0`
	echo $function [options] featdir outputdir
    echo Takes a FEAT directory and bundles all essential data of all levels of analysis into a single directory.
    echo 
    echo -tar  featdir outputdir  - tar final directory into single file
    echo -untar ouputdir newbasedir - untars directory and updates directory locations 
    echo
    echo Requires setFEAT,cleanupFEAT,queryFEAT
	exit 1
}

[ "$1" = "" ] && Usage

firstchar=`echo $1 | head -c 1`

while [[ $firstchar == '-' ]]
do
        if [[ $1 == -tar ]]
        then tar=1
        else 
            tar=''
        fi

        if [[ $1 == -untar ]]
        then untar=1
        else 
            untar=''
        fi

        shift 1
        firstchar=`echo $1 | head -c 1`
done


echo $1  $untar


if [[ $untar == 1 ]];
then 
    echo Extracting..
    echo tar -xcf  $1
    tar -xvf  $1

    echo Refreshing output directories

    oldoutput=`grep "feat_files(1)" design.fsf | grep -o \".*\" | sed 's/\"//g;s/[^\/]*feat//g'`
    newoutput=`pwd`

    for a in `find . -name design.fsf`;
    do  setFEAT $a $a -replace $oldoutput $newoutput
    done
    exit
fi

featdir=$1
outputdir=$2

if [ ! -e $featdir ];
then echo $outputdir does not exist!
     exit
fi

if [[ $# == 2 ]];
then
    echo Making copy of directory
    if [ -e $outputdir ];
    then echo $outputdir is already a directory!
         exit
    fi

    cp -rL $featdir $outputdir
else    outputdir=$featdir
fi
# backup old design file
designfile=$outputdir/design.fsf
cp $designfile $outputdir/design_orig.fsf
level=`queryFEAT $designfile -level`
fsfile=`cat $outputdir/design.fsf`

case $outputdir in
    /*) outputfulldir=$outputdir ;;
    ~*) outputfulldir=$outputdir ;;
    *) outputfulldir=`pwd`/$outputdir
esac

setFEAT $designfile $designfile -outputfulldir $outputdir 

cnt=1

infiles=`grep feat_files $designfile | grep -o \".*\" | sed 's/\"//g'`

if [[ $level == 2 ]];
then
    echo Copying input dirs
    for b in $infiles;
    do  
        newdir=$outputfulldir/input_$cnt.feat
        echo Copying $b to $newdir
        echo Bundling lower level directory $b as $newdir
        bundleFEAT $b $newdir
        setFEAT -i $designfile -replace $b $newdir
        cleanupFEAT -r -thr $newdir

        let cnt=$cnt+1
    done

    for c in threshmask; do
        
        fsf_settings=`grep $c $designfile | grep -o \".*\" | sed 's/\"//g'`
        if [[ ! $fsf_settings == '' ]];then
            echo Copying and updating $c
        fi


        cnt=1
        for d in $fsf_settings;do
            
            newfile=$outputfulldir/${c}_${cnt}
            if [ `imtest $d` == 1 ];
            then  imcp $d $newfile
            else
                  imcp $d $newfile
            fi

            setFEAT -i $designfile -replace $d $newfile
            let cnt=cnt+1

        done
    done

    # copy design.fsf to cope.feat dirs
    for copedir in $outputfulldir/cope*feat;do
        cp $designfile $copedir;
    done

else

    for c in custom highres_files initial_highres init_highres unwarp_files unwarp_files_mag feat_files st_file motionevsbeta scriptevsbeta threshmask regstandard alternative_example_func alternative_mask init_initial_highres init_highres init_standard; do

        fsf_settings=`grep $c $designfile | grep -o \".*\" | sed 's/\"//g'`
        if [[ ! $fsf_settings == '' ]];then
            echo Copying and updating $c
        fi

        cnt=1
        for d in $fsf_settings;do
            
            newfile=$outputfulldir/${c}_${cnt}

            # copy file, testing if image and "_brain" image
            echo $d
            if [ `imtest $d` == 1 ] && [ ${d/_brain/} == ${d} ];
            then  imcp $d $newfile
            elif  [ `imtest $d` == 1 ];
            then  
                imcp ${d/_brain/} $newfile
                newfile=${newfile}_brain
                imcp $d $newfile 
            else
                  cp $d $newfile
            fi

            setFEAT -i $designfile -replace $d $newfile

            let cnt=cnt+1

        done

    done
fi

cleanupFEAT -r -thr $outputdir

if [[ ! $tar == '' ]]; then 
    echo Creating tar file
    tar -cvf ${outputdir}.tar $outputdir
fi

# create rerun script