drive_afni_xyz

#!/bin/bash
set -e

#MH April 2015
#This is a script to send coordinates to AFNI for navigating through a file in which rows contains ROIs/coordinates of interest.
#For example the output of a 3dclust command can be used to navigate to each of the clusters on the command line.
#This depends on AFNI plugouts being turned on/available.

if [ $# -eq 0 ]; then
    echo "Usage: drive_afni_xyz -coord_file <file with xyz coords> -lr <left/right column> -pa <posterior/anterior column> -is <inferior/superior column>"
    exit 0
fi

#cleanup tmpfile on quit/exist
trap "rm -f .tmpfile" EXIT SIGHUP SIGINT SIGTERM

coord_file=
lrcol=1 #defaults
pacol=2
iscol=3
lpi=1 #only support LPI coords at the moment...
comment_char="#" #default to # as comment
image_file=
delim="\t" #default

while [ _$1 != _ ] ; do
    if [ $1 = -coord_file ]; then
	coord_file="$2"
	shift 2
    elif [ $1 = -image_file ]; then
	image_file="$2"
	shift 2
    elif [ $1 = -lr ]; then
	lrcol=$2
	shift 2
    elif [ $1 = -pa ]; then
	pacol=$2
	shift 2
    elif [ $1 = -is ]; then
	iscol=$2
	shift 2
    elif [[ $1 = -lpi || $1 = -spm ]]; then
	lpi=1
	shift 1
    elif [ $1 = -delim ]; then
	delim="$2"
	shift 2
    elif [ $1 = -comment_char ]; then
	comment_char="$2"
	shift 2
    else
	echo "Don't know what this means: $1"
	exit 1
    fi
done

if [ -n "$image_file" ]; then
    if [ -r "$image_file" ]; then
	plugout_drive -com "SET_FUNCTION $image_file" -quit 2>&1 >/dev/null
    else
	echo "Cannot locate -image_file $image_file"
	exit 1
    fi
fi

echo "Assuming coordinates are in LPI order."

#remove any comment lines
sed "/^${comment_char}/ d" < "${coord_file}" > .tmpfile

#tail -n +2 "$extremaFile" > .tmpfile

#3dclust does not write a trailing newline at the end of the file.
#Consequently, read chokes on the file (error = 1), but this is a trivial error.
#thus, trap and ignore
OLDIFS=$IFS
IFS=$'\n' read -d '' -r -a lines < .tmpfile || eof=true
IFS=$OLDIFS

echo "length of lines is ${#lines[@]}"
echo "first line is ${lines[0]}"

nlines=${#lines[@]}
curline=0

while [ $curline -lt $nlines ]
do
    repline=$( echo "${lines[$curline]}" | perl -pe "s/${delim}/ /g")
    echo "$((curline+1)): ${repline}"
    echo ""
    xyz=$( echo "${lines[$curline]}" | awk -F"${delim}" "{print \$${lrcol},\$${pacol},\$${iscol}}" )
    plugout_drive -com "SET_SPM_XYZ ${xyz}" -quit 2>&1 >/dev/null
    read -sn1 -p "Press # to enter rownum, n for next, p for previous, r for reload, q for quit" key
    echo ""
    if [ $key = p ]; then
	[ "$curline" -gt 0 ] && curline=$((curline - 1))
    elif [ $key = q ]; then
	echo "Quitting"
	exit 0
    elif [ $key = r ]; then
	plugout_drive -com "SET_SPM_XYZ ${xyz}" -quit 2>&1 >/dev/null
    elif [ $key = "#" ]; then
	    read -p "Enter goto row: " row
	    curline=$((row - 1)) #account for 0-based index
    elif [ $key = n ]; then
	[ $curline -lt $(( nlines - 1 )) ] && curline=$((curline + 1))
    else
	curline=$((curline + 1)) #default to next
    fi
done


#need to read in file through different i/o stream 9
#otherwise, read command for prompts will collide with file lines
# while read -u 9 line
# do
#     echo -e "\n\n$line"
#     xyz=$( echo "$line" | awk '{print $5,$6,$7}' )
#     plugout_drive -com "SET_SPM_XYZ ${xyz}" -quit 2>&1 >/dev/null
#     read -sn1 -p "Press enter to go to the next activation"
# done 9< .tmpfile