/
reconstruct.sh
executable file
·138 lines (124 loc) · 7.22 KB
/
reconstruct.sh
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#!/bin/bash
############################################################################
# Script: reconstruct.sh #
# Task: This script searches for files ending in _segm.vti and #
# passes the batch of them through a meshing and centerline #
# analysis. Other methods will be implemented in future #
# This can be run as a stand-alone program. #
# Author: Dave Welch #
# Contact: david.m.welch@gmail.com #
# Date: 10 Feb, 2010 #
# Licence: Copyright (C) 2010 David M. Welch #
# #
# This program 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/>. # # #
############################################################################
############################################################################
# #
# global variables #
# #
############################################################################
SCRIPTNAME=$(basename ${0} .sh)
# Number of parameters needed (Edit line 55 logic)
NUMOFPARAMS=0
EXIT_SUCCESS=0
EXIT_FAILURE=1
EXIT_ERROR=2
EXIT_BUG=10
# variables for option switches with default values
VERBOSE="n"
OPTFILE=""
LICENSE="COPYING"
############################################################################
# #
# functions #
# #
############################################################################
function usage {
echo "Usage: ${SCRIPTNAME} [-h] [-v] [-c] [-o arg] file ..." >&2
[[ ${#} -eq 1 ]] && exit ${1} || exit ${EXIT_FAILURE}
}
function copyright {
DIR=`find / -type d -name "name" 2>/dev/null`
exec < "${DIR}/${LICENSE}"
while read LINE ; do
echo ${LINE}
done
}
############################################################################
# #
# main program #
# #
############################################################################
# the options -h for help should always be present. Options -v and
# -o are examples. -o needs a parameter, indicated by the colon ":"
# following in the getopts call
while getopts ':o:vhc' OPTION ; do
case ${OPTION} in
c) copyright
;;
v) VERBOSE=y
;;
o) OPTFILE="${OPTARG}"
;;
h) usage ${EXIT_SUCCESS}
;;
\?) echo "unknown option \"-${OPTARG}\"." >&2
usage ${EXIT_ERROR}
;;
:) echo "option \"-${OPTARG}\" requires an argument." >&2
usage ${EXIT_ERROR}
;;
*) echo "Impossible error. parameter: ${OPTION}" >&2
usage ${EXIT_BUG}
;;
esac
done
# skip parsed options
shift $(( OPTIND - 1 ))
# if you want to check for a minimum or maximum number of arguments,
# do it here
if [[ $# -ne $NUMOFPARAMS ]] ; then
echo "Wrong number of parameters" >&2
usage ${EXIT_ERROR}
fi
# loop through all arguments
for ARG ; do
if [[ ${VERBOSE} = y ]] ; then
echo -n "argument: "
fi
echo ${ARG}
done
if [[ -z ${PATIENTPATH} ]] ; then
. get_patient_path.sh
# Needed on BIOMOST000
#export PYTHONPATH=/usr/css/opt/vmtk-0.8/lib:/usr/css/opt/vmtk-0.8/lib/vmtk:/usr/css/opt/vtk-5.4.2/lib64/python2.6/site-packages
#export LD_LIBRARY_PATH=/usr/css/opt/vtk-5.4.2/lib/vtk-5.4:/usr/css/opt/InsightToolkit-3.16.0/lib/InsightToolkit:/usr/css/opt/vmtk-0.8/lib:/usr/css/opt/vmtk-0.8/lib/vmtk
fi
INPUT=`zenity --file-selection --filename=$PATIENTPATH/ --title="Select segm file to mesh"`
# Manasi wants Tecplot ASAP here!
###vmtkmarchingcubes -ifile ${INPUT} --pipe vmtksurfacesubdivision -method loop -ofile ${INPUT%%segm.vti}mesh.vtp --pipe vmtksurfacetomesh --pipe vmtkmeshscaling -scale 0.1 --pipe vmtkmeshwriter -f tecplot -ofile ${INPUT%%segm.vti}mesh.dat # Write tecplot file in cgs units, not in mm, that is C^2continuous
vmtkmarchingcubes -ifile ${INPUT} --pipe vmtksurfacetriangle -pipe vmtksurfacewriter -f tecplot -ofile ${INPUT%%.vti}.dat # Tecplot files need .dat extention, but no interior manipulations
# # #Automatically cut ends by identifying endpoints to centerlines
# # # vmtksurfacereader -ifile ${INPUT%%segm.vti}mesh.vtp --pipe vmtkcenterlines -ofile ${INPUT%%segm.vti}ctrlines.vtp --pipe vmtkendpointextractor --pipe vmtkbranchclipper --pipe vmtksurfaceconnectivity -cleanoutput 1 --pipe vmtkrenderer --pipe vmtksurfaceviewer -opacity 0.25 --pipe vmtksurfaceviewer -i @vmtkcenterlines.voronoidiagram -array MaximumInscribedSphereRadius --pipe vmtksurfaceviewer -i @vmtkcenterlines.o --pipe vmtksurfacewriter -ofile ${INPUT%%segm.vti}clip.vtp # Did we get them all?
# # # `zenity --question --width=150 --title="Automated Clipping" --text="Did this clip the surface accurately?" --ok-label="_Yes" --cancel-label="_No"`
# # # case $? in
# # # 0) ;;
# # # -1 | 1)
# # # vmtksurfacereader -ifile ${INPUT%%segm.vti}clip.vtp --pipe vmtkbranchclipper -ofile ${INPUT%%segm.vti}clip.vtp --pipe vmtksurfacereader --pipe vmtkcenterlines -seedselector openprofiles -ofile ${INPUT%%segm.vti}ctrlines.vtp --pipe vmtkrenderer --pipe vmtksurfaceviewer -opacity 0.25 --pipe vmtksurfaceviewer -i @vmtkcenterlines.voronoidiagram -array MaximumInscribedSphereRadius --pipe vmtksurfaceviewer -i @vmtkcenterlines.o ;;
# # # esac
# # #
# # # # Add flow extensions
# # # vmtksurfacereader -ifile ${INPUT%%segm.vti}clip.vtp --pipe vmtkcenterlines -seedselector openprofiles --pipe vmtkflowextensions -adaptivelength 1 -extensionratio 20 -normalestimationratio 1 -interactive 0 --pipe vmtksurfacewriter -ofile ${INPUT%%segm.vti}flow.vtp --pipe vmtksurfacetomesh --pipe vmtkmeshscaling -scale 0.1 --pipe vmtkmeshwriter -f tecplot -ofile ${INPUT%%segm.vti}flow_mesh.dat
tecplot ${INPUT%%segm.vti}mesh.dat
exit ${EXIT_SUCCESS}