cleanupFEAT

#!/bin/sh
#
#   Copyright (C) Eugene Duff 2004 University of Oxford
#
#   SHCOPYRIGHT

Usage() {
	function=`basename $0`
	echo $function [options] featdirs 
	echo 
	echo $function removes large files that are not typically necessary for subsequent second-level analyses or for the web-page report. 
	echo
	echo Files removed: 
	echo 
	echo 	var_filtered_func_data.\*
	echo 	rendered\*
	echo 	cluster_mask\*
	echo 	stats/res4d.\* 
	echo 	stats/tstat\* 
	echo 	reg_standard/ directory 
	echo 
	echo Options:
	echo
	echo -t remove tsplot files \(affects web-page report\)
	echo -r remove registration image directory reg/
	echo -z remove zstat images
    echo -thr remove thresh_ image files 
	echo -f remove filtered_func_data\* file
exit 1
}

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

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

nfflag=0
zflag=0

while [[ $firstchar == '-' ]]
do	
	if [[ $1 == -t ]]
	then 	tsplotflag=1
	shift 1
	fi

	if [[ $1 == -r ]]
	then 	regflag=1
	shift 1
	fi

	if [[ $1 == -f ]]
	then 	nfflag=1
	shift 1
	fi

	if [[ $1 == -thr ]]
	then 	thrflag=1
	shift 1
	fi

	if [[ $1 == -z ]]
	then 	zflag=1
	shift 1
	fi


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

origdir=`pwd`

for a in $@;do

	cd $a;
    dirs='.'
    currdir=`pwd`    

    if [[ ${currdir: -5} == 'gfeat' ]];
    then dirs=`ls -d cope*feat`
    fi

    for b in $dirs;
    do
        cd $b
        echo Cleaning up `pwd`

        rm -f rend*gz rend*nii
        rm -f cluster_mask*nii cluster_mask*gz
        rm -f stats/zflam*nii stats/zflam*gz
        rm -f stats/tsta*nii stats/tsta*gz
        rm -f var_filtered_func*
        rm -f stats/res4d*
        rm -f stats/correction*
        

        [[ $regflag == 1 && -d reg ]] &&  rm -fr reg_standard

        [[ $thrflag == 1 && -d reg ]] &&  rm -f thresh*nii thresh*gz

        [[ $nfflag == 1 ]] && rm -f filtered_func*[^a]

        [[ $zflag == 1 ]] && rm -f stats/zsta*nii stats/zsta*gz

        [[ "$tsplotflag" == 1 ]] && rm -rf tsplot

        [[ $regflag == 1 && -d reg ]] && rm -fr reg

        [[ $regflag == 1 && -d reg ]] && rm -fr reg_standard
        cd ../
    done

    echo $a	
    cd $origdir
	
done

cd $origdir