3 ## -- Command line options
6 vesselness_alpha1="0.5"
11 mori_signal_influence="0.5"
15 slice_by_slice_vesselness_thr="5"
16 labels_vesselness_thr="65"
17 labels_upper_thr="-400"
20 while [[ "$#" -gt 0 ]]; do
35 vesselness_alpha1="$2"
39 vesselness_alpha2="$2"
54 -mori_signal_influence)
55 mori_signal_influence="$2"
70 -labels_vesselness_thr)
71 labels_vesselness_thr="$2"
74 -slice_by_slice_vesselness_thr)
75 slice_by_slice_vesselness_thr="$2"
103 ## -- Check command line options
104 if [ -z "$input" ] || [ -z "$seed" ] ; then
105 (>&2 echo "Usage: $0 -input <file> -seed <x y z> [-force]")
109 base_dir=`dirname $input | xargs realpath`
110 base_name=$base_dir/`basename $input .mha`
112 vesselness=$base_name"_vesselness.mha"
113 mori=$base_name"_mori.mha"
114 mori_signal=$base_name"_mori_signal.txt"
115 labels=$base_name"_labels.mha"
116 fastrw=$base_name"_fastrw.mha"
117 slicerw=$base_name"_slicerw.mha"
119 echo "************************************************"
120 (>&2 echo "Processing $input... ")
121 echo "Processing $input..."
122 if [ ! -f $vesselness ] || [ -n "$force" ] ; then
123 $curr_dir/fpa_CTBronchi_Vesselness \
124 -i $input -o $vesselness \
125 -s $vesselness_sigma -a $vesselness_alpha1 -b $vesselness_alpha2
128 if [ ! -f $mori ] || [ -n "$force" ] ; then
129 $curr_dir/fpa_CTBronchi_MoriSegmentation \
136 -r $mori_signal_thr \
137 -f $mori_signal_influence \
143 if [ ! -f $labels ] || [ -n "$force" ] ; then
144 $curr_dir/fpa_CTBronchi_MoriLabelling \
149 -a $labels_vesselness_thr \
153 if [ ! -f $fastrw ] || [ -n "$force" ] ; then
154 $curr_dir/fpa_CTBronchi_FastRandomWalker \
162 if [ ! -f $slicerw ] || [ -n "$force" ] ; then
163 $curr_dir/fpa_CTBronchi_SliceBySliceRandomWalker \
168 -t $slice_by_slice_vesselness_thr \
174 echo "************************************************"