mapsproj

#!/bin/sh
set -e

if [ ! -e $TOOLBOX_PATH/bart ] ; then
	echo "\$TOOLBOX_PATH is not set correctly!" >&2
	exit 1
fi
export PATH=$TOOLBOX_PATH:$PATH
export BART_COMPAT_VERSION="v0.4.04"


RVC=0

while getopts "c" opt; do
	case $opt in
	c)
		RVC=1
	;;
	\?)
		echo "Invalid option: -$OPTARG" >&2
	;;
	esac
done

shift $((OPTIND-1))


if [ $# -lt 3 ] ; then

	echo "Usage: $0 <kspace> <maps> <output>"
	exit 1
fi

kspace=$(readlink -f "$1")
maps=$(readlink -f "$2")
output=$(readlink -f "$3")



#WORKDIR=$(mktemp -d)
# Mac: http://unix.stackexchange.com/questions/30091/fix-or-alternative-for-mktemp-in-os-x
WORKDIR=`mktemp -d 2>/dev/null || mktemp -d -t 'mytmpdir'`
trap 'rm -rf "$WORKDIR"' EXIT
cd $WORKDIR

# Alternative implementation using pocsense
#pocsense 1. 1 $kspace $maps proj.coo
#sub $kspace proj.coo diff.coo
#fft -i -u 7 diff.coo idiff.coo
#rss 8 idiff.coo $output

bart fft -i -u 7 $kspace cimg.coo
bart fmac -C -s8 cimg.coo $maps img.coo

if [ $RVC = 1 ]; then

	bart creal img.coo imgR.coo
	bart fmac -s16 imgR.coo $maps proj.coo

else

	bart fmac -s16 img.coo $maps proj.coo

fi

bart saxpy -- -1. cimg.coo proj.coo idiff.coo
bart rss 8 idiff.coo $output