3 ## Command line arguments
4 while [[ "$#" -gt 1 ]]; do
35 if [ -z "$input" ] || [ -z "$sx" ] || [ -z "$sy" ] || [ -z "$sz" ]; then
36 (>&2 echo "Usage: $0 -input input_raw_image -seed x y z [-mori mori_image_dfilename] [-labels labels_image_filename] [-output output_image_filename] [-mori_init_threshold value] [-mori_end_threshold value] [-mori_delta value] [-mori_minimum_threshold value] [-mori_inside_value value] [-mori_outside_value value] [-mori_signal_kernel_size value] [-mori_signal_threshold value] [-mori_signal_influence value] [-label_upper_threshold value] [-label_inside value] [-label_outside value] [-random_walker_beta value]")
39 if [ -z "$mori_init_threshold" ]; then mori_init_threshold="-1024"; fi
40 if [ -z "$mori_end_threshold" ]; then mori_end_threshold="0"; fi
41 if [ -z "$mori_delta" ]; then mori_delta="1"; fi
42 if [ -z "$mori_minimum_threshold" ]; then mori_minimum_threshold="-850"; fi
43 if [ -z "$mori_inside_value" ]; then mori_inside_value="255"; fi
44 if [ -z "$mori_outside_value" ]; then mori_outside_value="0"; fi
45 if [ -z "$mori_signal_kernel_size" ]; then mori_signal_kernel_size="20"; fi
46 if [ -z "$mori_signal_threshold" ]; then mori_signal_threshold="500"; fi
47 if [ -z "$mori_signal_influence" ]; then mori_signal_influence="0.5"; fi
48 if [ -z "$label_upper_threshold" ]; then label_upper_threshold="-600"; fi
49 if [ -z "$label_inside" ]; then label_inside="1"; fi
50 if [ -z "$label_outside" ]; then label_outside="2"; fi
51 if [ -z "$random_walker_beta" ]; then random_walker_beta="20"; fi
53 base_name=`dirname $input`/`basename $input .mhd`
54 if [ -z "$mori" ]; then
55 mori="$base_name"_mori.mhd
57 signal="$mori"_signal.txt
58 if [ -z "$labels" ]; then
59 labels="$base_name"_labels.mhd
61 if [ -z "$output" ]; then
62 output="$base_name"_rw.mhd
66 mori_seg=`dirname $0`/fpa_CTBronchi_MoriSegmentation
67 mori_lab=`dirname $0`/fpa_CTBronchi_MoriLabelling
68 random_walker=`dirname $0`/fpa_CTBronchi_RandomWalker
71 $input $mori $signal \
72 $mori_init_threshold \
75 $mori_minimum_threshold \
78 $mori_signal_kernel_size \
79 $mori_signal_threshold \
80 $mori_signal_influence \
84 $input $mori $labels \
85 $label_upper_threshold \
91 $input $labels $output \