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|
#!/bin/bash
# Copyright 2018. Martin Uecker.
# All rights reserved. Use of this source code is governed by
# a BSD-style license which can be found in the LICENSE file.
#
# Authors:
# 2018 Martin Uecker <martin.uecker@med.uni-goettingen.de>
#
# Memory-saving ESPIRiT
#
set -e
LOGFILE=/dev/stdout
title=$(cat <<- EOF
ESPIRiT-ECON
EOF
)
helpstr=$(cat <<- EOF
-l logfile
-h help
EOF
)
usage="Usage: $0 [-h] <kspace> <output>"
echo "$title"
echo
while getopts "hl:" opt; do
case $opt in
h)
echo "$usage"
echo
echo "$helpstr"
exit 0
;;
l)
LOGFILE=$(readlink -f "$OPTARG")
;;
\?)
echo "$usage" >&2
exit 1
;;
esac
done
shift $((OPTIND - 1))
if [ $# -lt 2 ] ; then
echo "$usage" >&2
exit 1
fi
if [ ! -e "$BART_TOOLBOX_PATH"/bart ] ; then
if [ -e "$TOOLBOX_PATH"/bart ] ; then
BART_TOOLBOX_PATH="$TOOLBOX_PATH"
else
echo "\$BART_TOOLBOX_PATH is not set correctly!" >&2
exit 1
fi
fi
export PATH="$BART_TOOLBOX_PATH:$PATH"
input=$(readlink -f "$1")
output=$(readlink -f "$2")
if [ ! -e $input.cfl ] ; then
echo "Input file does not exist." >&2
echo "$usage" >&2
exit 1
fi
if [ ! -e $TOOLBOX_PATH/bart ] ; then
echo "\$TOOLBOX_PATH is not set correctly!" >&2
exit 1
fi
#WORKDIR=$(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 $WORKDIR
# start group for redirection of output to the logfile
{
XX=$(bart show -d0 $input)
YY=$(bart show -d1 $input)
ZZ=$(bart show -d2 $input)
DIM=2
# To decouple along another dimension:
# 1. change DIM
# 2. replace ZZ below
# 3. change the ecaltwo command
bart ecalib -1 $input eon
# zero-pad
bart fft $(bart bitmask ${DIM}) eon eon_fft
bart resize -c ${DIM} ${ZZ} eon_fft eon_fft2
bart fft -i $(bart bitmask ${DIM}) eon_fft2 eon
for i in `seq -w 0 $(($ZZ - 1))` ; do
bart slice ${DIM} $i eon sl
bart ecaltwo ${XX} ${YY} 1 sl sens-$i.coo
done
# # join slices back together
bart join ${DIM} sens-*.coo $output
} > $LOGFILE
exit 0
|
