#!/bin/bash

ARGS=( "$@" )

#parse options
DCMTAG=""
DCMVALUE=""
LINKBASE=""
for ((n=0; n<${#ARGS[@]}; n++)) ; do
	case "${ARGS[$n]}" in
	--tag)
		let n=n+1
		DCMTAG="${ARGS[$n]}"
		;;
 	--value)
		let n=n+1
		DCMVALUE="${ARGS[$n]}"
		;;
	--link)
		let n=n+1
		LINKBASE="${ARGS[$n]}"
		;;
	--version)
		echo "RegisterPETwithMRImatch: matchPETwithMRI.sh"
		echo "v20201208"
		exit 0
		;;
	--help)
		echo "--help    show help"
		echo "--tag     DICOM tag in JSON"
		echo "--value   value of DICOM tag"
		echo "--link    base name of the linked file (for NII and JSON)"
		echo "--version script version"
		exit 0
		;;
	esac
done

if [ -z "$DCMTAG" ] || [ -z "$DCMVALUE" ] || [ -z "$LINKBASE" ] ; then
	echo "Error: not enough parameters; use --help" >&2
	exit 1
fi

find . -name '*.nii*' | while read fn ; do
	fnj="$(echo "$fn" | sed 's/\.nii.*$/\.json/')"
	if grep "\"$DCMTAG\"" "$fnj" | grep -q ":.*$DCMVALUE" ; then
		rm -f "$LINKBASE".$EXT "$LInKBASE".json
		
		EXT=$(echo "$fn" | sed 's/^.*\.\(nii.*\)$/\1/')
		ln -s "$fn"  "$LINKBASE.$EXT"
		ln -s "$fnj" "$LINKBASE.json"
		
	fi
done

if ! [ -e "$LINKBASE.json" ] ; then
	exit -1
fi