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#!/bin/sh
##
## Copyright 2012, 2014 SRI International
##
## Copyright 2012 Torsten Rohlfing
##
## This file is part of the Computational Morphometry Toolkit.
##
## http://www.nitrc.org/projects/cmtk/
##
## The Computational Morphometry Toolkit 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.
##
## The Computational Morphometry Toolkit 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 the Computational Morphometry Toolkit. If not, see
## <http://www.gnu.org/licenses/>.
##
## $Revision: 5378 $
##
## $LastChangedDate: 2015-01-17 11:31:55 -0800 (Sat, 17 Jan 2015) $
##
## $LastChangedBy: torstenrohlfing $
##
export CMTK_BINARY_DIR=${CMTK_BINARY_DIR:-@CMTK_BINARY_DIR_CONFIG@}
# Get the cmtk_functions.sh script from the scripts/ directory in the CMTK source tree
. ${CMTK_BINARY_DIR}/cmtk_functions.sh
# Check for command line arguments, print help if none given
if test $# -lt 3; then
echo "Reformat all floating images previously aligned by one of CMTK's groupwise registration tools."
echo
echo "USAGE: $0 [OPTIONS] groupwiseXform templateGrid outputPathPattern [XFORMS ...]"
exit 2
fi
# put all arguments starting with "-" into reformat options
reformatOptions=""
while expr "$1" : ^- >/dev/null; do
reformatOptions="${reformatOptions}$1 "
shift
done
# first non-option argument is groupwise xform
groupwiseXform=$1
if [ ! -f ${groupwiseXform} ]; then
groupwiseXform=${groupwiseXform}.gz
if [ ! -f ${groupwiseXform} ]; then
echo "ERROR: could not find groupwise transformation $1"
exit 1
fi
fi
# second argument is template grid path
templateGrid=$2
if ! ${CMTK_BINARY_DIR}/describe ${templateGrid} > /dev/null; then
echo "ERROR: template grid ${templateGrid} is not a valid image."
exit 1
fi
# third argument is output pattern
outPattern=$3
# everything else is optional xforms to be added before the groupwise alignment
shift 3
reformatXforms="$*"
make_output_path()
{
local target=$1
local pattern=$2
local base=`basename $target | sed 's/\..*//g'`
local dir=`dirname $target`
local idx=1
while [ "${base}" != "" ]; do
pattern=`eval "echo $pattern | sed 's/%${idx}/${base}/g'"`
base=`basename $dir | sed 's/\.,*//g'`
dir=`dirname $dir`
$((idx=idx+1))
done
echo ${pattern}
}
process_target()
{
local target=$1
local tmp=`mktemp`
echo "! TYPEDSTREAM 1.1" > ${tmp}
while IFS="" read line; do
if expr "${line}" : ^\} >/dev/null; then
break;
fi
echo "${line}" >> ${tmp}
done
echo "}" >> ${tmp}
outputPath=`make_output_path ${target} ${outPattern}`
if [ "${outputPath}" != "" ]; then
${CMTK_BINARY_DIR}/reformatx ${reformatOptions} --floating ${target} --outfile ${outputPath} ${templateGrid} ${tmp} ${reformatXforms}
fi
rm -rf ${tmp}
}
parse_xform_file()
{
while read line; do
if expr "${line}" : "target" >/dev/null; then
target=`echo ${line} | sed 's/target \"//g; s/\".*//g'`
process_target ${target}
fi
done
}
gzip -cdf ${groupwiseXform} | parse_xform_file
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