#!/bin/bash
#

Usage() {
cat << EOF

    Usage: make_confounds -out <confound_mat> [-ts "fl1 fl2 ..."]  [-pos "fl1 fl2 ..."]

            Given a list of ascii files this function produces a single ascii-matrix.
            Input files could contain values for each volume <-ts> or specify volumes
            that set to 1 while all the others are 0.

    OPTIONS:
            -out    name of output file - supresses output to screen.
            -ts     list of ascii files with 1 value per volume.
            -pos    list of ascii files that specify confound volumes.
            -vol    Number of volumes - required if <-ts> is not used.

            ###########################################################
            ##   (c) wolf zinke (2008) - part of the MaFIA toolbox   ##
            ##       for comments and questions: <a href="/cgi-bin/wa-jisc.exe?LOGON=A3%3Dind0903%26L%3DFSL%26E%3D7bit%26P%3D403399%26B%3D--------------080802040607000903050008%26T%3Dtext%252Fplain%3B%2520name%3D%2522make_confounds%2522%26N%3Dmake_confounds" target="_parent" >[log in to unmask]</a>   ##
            ###########################################################

EOF
    exit 1
}

#----------------------------------------------------------------------#
comp_vol=0
get_pos=0
get_ts=0
ts_vol=-1
num_vol=-1
wrt_fl=0
wrt_usg=1
while [ $# -gt 0 ] ;
do
    case $1 in
        -out)   outfl=$2
                wrt_fl=1
                shift 2
                ;;
        -ts)    ts_lst=$2
                shift 2
                get_ts=1
                wrt_usg=0
                ;;
        -pos)   pos_lst=$2
                get_pos=1
                wrt_usg=0
                shift 2
                ;;
        -vol)   num_vol=$2
                comp_vol=1
                shift 2
                ;;
          -*)   echo "Wrong option: <$1>"
                echo ""
                Usage
                ;;
           *)   break
                ;;
    esac
done

if [ $wrt_usg -eq 1 ]
then
    Usage
fi

#----------------------------------------------------------------------#
ts_vol=-1
if [ $get_ts -eq 1 ]
then
    for curr_ts in $ts_lst
    do
        if [ ! -e $curr_ts ]
        then
            echo ""
            echo "ERROR: File does not exist!"
            echo "       file: $curr_ts"
            echo ""
            exit
        fi
        cvol=$(wc -l "$curr_ts" | awk '{print $1}')

        if [ $ts_vol -gt 0 ]
        then
            if [ ! $cvol -eq  $ts_vol ]
            then
                echo ""
                echo "ERROR: Different number ov volumes ($cvol instead of $ts_vol)!"
                echo "       file: $curr_ts"
                echo ""
                exit
            fi
        else
            ts_vol=$cvol
        fi
    done

    if [ $num_vol -lt 0 ]
    then
        num_vol=$ts_vol
    else
        if [ ! $num_vol -eq $ts_vol ]
        then
            echo ""
            echo "ERROR: Mismatch between number of volumes ($num_vol) and time points ($ts_vol)!"
            echo ""
            exit
        fi
    fi
fi

#----------------------------------------------------------------------#
if [ $get_pos -eq 1 ]
then
    if [ $num_vol -lt 0 ]
    then
        echo ""
        echo "ERROR: Number of volumes not specified!"
        Usage
    fi

    pos_arr=""
    for curr_pos in $pos_lst
    do
        cpos=`cat $curr_pos`

        for givpos in $cpos
        do
            if [ $givpos -gt $num_vol ]
            then
                echo ""
                echo "ERROR: Position number ($givpos) greater than number of volumes ($ts_vol) specified!"
                echo ""
                exit
            fi
            pos_arr="$pos_arr $givpos"
        done
    done

    all_pos=`echo "$pos_arr" | sort -u `
fi

#----------------------------------------------------------------------#
if [ $wrt_fl -eq 1 ]
then
    echo -n "" > $outfl
fi

cnt=0
while [ $cnt -lt $num_vol ]
do
    curr_line=""

#----------------------------------------------------------------------#
    if [ $get_ts -eq 1 ]
    then
        for curr_ts in $ts_lst
        do
            declare -a vals=(`cat $curr_ts`)
            curr_line="$curr_line ${vals[$cnt]}"
        done
    fi

#----------------------------------------------------------------------#
    cnt=$(($cnt+1))
    if [ $get_pos -eq 1 ]
    then
        for cpos in $all_pos
        do
            if [ $cpos -eq $cnt ]
            then
                curr_line="$curr_line 1"
            else
                curr_line="$curr_line 0"
            fi
        done
    fi

#----------------------------------------------------------------------#
    if [ $wrt_fl -eq 1 ]
    then
        echo "$curr_line" >> $outfl
    else
        echo "$curr_line"
    fi
done