3 ## -- Command line options
5 vesselness_alpha1="0.5"
10 mori_signal_influence="0.5"
14 labels_vesselness_thr="5"
15 labels_upper_thr="-400"
18 while [[ "$#" -gt 0 ]]; do
33 vesselness_alpha1="$2"
37 vesselness_alpha2="$2"
52 -mori_signal_influence)
53 mori_signal_influence="$2"
68 -labels_vesselness_thr)
69 labels_vesselness_thr="$2"
97 ## -- Check command line options
98 if [ -z "$input" ] || [ -z "$seed" ] ; then
99 (>&2 echo "Usage: $0 -input <file> -seed <x y z> [-force]")
103 base_dir=`dirname $input | xargs realpath`
104 base_name=$base_dir/`basename $input .mhd`
106 vesselness=$base_name"_vesselness.mhd"
107 mori=$base_name"_mori.mhd"
108 mori_signal=$base_name"_mori_signal.txt"
109 labels=$base_name"_labels.mhd"
110 fastrw=$base_name"_fastrw.mhd"
111 slicerw=$base_name"_slicerw.mhd"
113 (>&2 echo "Processing $input... ")
114 echo "************************************************"
115 if [ ! -f $vesselness ] || [ -n "$force" ] ; then
116 ./fpa_CTBronchi_Vesselness \
117 -i $input -o $vesselness \
118 -s $vesselness_sigma -a $vesselness_alpha1 -b $vesselness_alpha2
121 if [ ! -f $mori ] || [ -n "$force" ] ; then
122 ./fpa_CTBronchi_MoriSegmentation \
129 -r $mori_signal_thr \
130 -f $mori_signal_influence \
136 if [ ! -f $labels ] || [ -n "$force" ] ; then
137 ./fpa_CTBronchi_MoriLabelling \
142 -a $labels_vesselness_thr \
146 if [ ! -f $fastrw ] || [ -n "$force" ] ; then
147 ./fpa_CTBronchi_FastRandomWalker \
155 if [ ! -f $slicerw ] || [ -n "$force" ] ; then
156 ./fpa_CTBronchi_SliceBySliceRandomWalker \
161 -t $labels_vesselness_thr \
165 echo "************************************************"