dcm2niiXL

#! /bin/bash
# Run multiple instances of dcm2niix in parallel
#Example
# ./dcm2niiXL -f %p_%s -i y -z y -o ~/tst/out ~/dcm_qa/In/

#SETTINGS
# set numCores to 0 for autodetect, otherwise number of threads desired
numCores=0
# set number of depth of subdirectories to search
searchDepth=10

#CHECK INPUT
if [ $# -lt 1 ]; then
	echo "Please call this script with input arguments"
	echo " $0 -f %p_%s -i y -z y -o "~/tst/out" "~/dcm_qa/In/""
	exit 1
fi
#get last input argument https://stackoverflow.com/questions/1853946/getting-the-last-argument-passed-to-a-shell-script
for lastArg; do true; done
if [ "$lastArg" == "" ];then
   echo "Error: no input folder provided"
   exit 1
fi
#CHECK NUMBER OF THREADS
if [ $numCores -lt 1 ] ; then
	numCores=$(getconf _NPROCESSORS_ONLN)
	if [ $numCores -lt 1 ] ; then
		echo "unable to detect cores"
		exit 1
	fi
fi
echo "dcm2niix running $numCores threads"
#FIND EXECUTABLE
scriptdir=$(dirname $0)
if [ "$scriptdir" = "." ]; then
	scriptdir=$(pwd)
fi
unameOut="$(uname -s)"
case "${unameOut}" in
    Linux*)     exe=$scriptdir/dcm2niixLinux;;
    Darwin*)    exe=$scriptdir/dcm2niixMacOS;;
esac
if [ ! -e $exe ]
then
    echo "Error: Unable to find $exe"
    exit 1
fi
#REMOVE LAST ARGUMENT
set -- "${@:1:$(($#-1))}"
#PROCESS FOLDERS
# n.b. limit number of active jobs
# https://stackoverflow.com/questions/1537956/bash-limit-the-number-of-concurrent-jobs?utm_medium=organic&utm_source=google_rich_qa&utm_campaign=google_rich_qa
# https://stackoverflow.com/questions/1131484/wait-for-bash-background-jobs-in-script-to-be-finished?utm_medium=organic&utm_source=google_rich_qa&utm_campaign=google_rich_qa
n=1
for d in $(find $lastArg -maxdepth $searchDepth -type d)
do
	echo $exe -d 0 "$@" "$d"
	$exe -d 0 "$@" "$d" &
	nPID=`jobs -pr | wc  -l`
	while [ $nPID -ge $numCores ]; do
		sleep 0.4
		nPID=`jobs -pr | wc  -l`
	done
	n=`expr $n + 1`
done
%pause until everything is done
nPID=`jobs -pr | wc  -l`
while [ $nPID -ge 1 ]; do
	sleep 0.4
	nPID=`jobs -pr | wc  -l`
done

exit 0