renameToOffByLst.sh

#!/bin/bash

# call: "renameOffFilesByLst.sh norm/157"

runnum=${1##*/}
class=${1%/*}
destdir="${class}_off_named/$runnum"
listfile="0000${runnum}_c2.lst"
echo $listfile
liststring=$(cat $listfile |tr "\n" " ")
list=($liststring)
listLen=${#list[@]}
filesnum=$(ls $1 | wc -l)
# check if number of files in directory matches number of lines in .lst file
if [ "$listLen" -eq "$filesnum" ]; then
	mkdir $destdir
	shapesubdir="/ShapeTranslator_1.ShapeOutputDirectory-"
	count=1
	for nucleolus in "${list[@]}"; do
		nucleolusname=${nucleolus%.nii*}
		leadingzeros="$(ls $1 | wc -l)"
		leadingzeros="$(echo $leadingzeros)"
		leadingzerosnum="${#leadingzeros}"
		idxformat="%0${leadingzerosnum}d"
		printf -v idx $idxformat $count
		currdir=$1$shapesubdir$idx
		filename="/182_QEM_SubDiv.off"
		target=$currdir$filename
		dest="$destdir/$nucleolusname.off"
		cp $target $dest

		((count++))
	done;
fi < $1