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#!/bin/sh
#
#
# This file is part of MIA - a toolbox for medical image analysis
# Copyright (c) Leipzig, Madrid 1999-2015 Gert Wollny
#
# MIA is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, see <http://www.gnu.org/licenses/>.
#
#
# extract the boundary between masks
# params: tissue_1_files tissue_2_files outfile
# example:
# extract_boundary.sh enamel/e000.png dentine/d000.png de-boundary
#
TMPDIR="/tmp/segment-$$"
mkdir -p $TMPDIR
mkdir -p $TMPDIR/a
mkdir -p $TMPDIR/b
mia-2dstackfilter -i $1 -o $TMPDIR/a/ -t png dilate:shape=6n -V message
mia-2dstackfilter -i $2 -o $TMPDIR/b/ -t png dilate:shape=6n -V message
pushd $TMPDIR/a
files=`ls *`
popd
for f in $files; do
echo $f
mia-2dbinarycombine -1 $TMPDIR/a/$f -2 $TMPDIR/b/$f -o $3$f -p and
done
rm -fr $TMPDIR
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