appli/CTBronchi/CTBronchi_process.sh

   1 #!/bin/bash
   2
   3 ## Command line arguments
   4 while [[ "$#" -gt 1 ]]; do
   5     key="$1"
   6     case $key in
   7         -input)
   8         input="$2"
   9         shift
  10         ;;
  11         -seed)
  12         sx="$2"
  13         sy="$3"
  14         sz="$4"
  15         shift
  16         ;;
  17         -mori)
  18         mori="$2"
  19         shift
  20         ;;
  21         -labels)
  22         labels="$2"
  23         shift
  24         ;;
  25         -output)
  26         output="$2"
  27         shift
  28         ;;
  29         *)
  30         # Do nothing
  31         ;;
  32     esac
  33     shift
  34 done
  35 if [ -z "$input" ] || [ -z "$sx" ] || [ -z "$sy" ] || [ -z "$sz" ]; then
  36     (>&2 echo "Usage: $0 -input input_raw_image -seed x y z [-mori mori_image_dfilename] [-labels labels_image_filename] [-output output_image_filename] [-mori_init_threshold value] [-mori_end_threshold value] [-mori_delta value] [-mori_minimum_threshold value] [-mori_inside_value value] [-mori_outside_value value] [-mori_signal_kernel_size value] [-mori_signal_threshold value] [-mori_signal_influence value] [-label_upper_threshold value] [-label_inside value] [-label_outside value] [-random_walker_beta value]")
  37     exit 1
  38 fi
  39 if [ -z "$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
  52
  53 base_name=`dirname $input`/`basename $input .mhd`
  54 if [ -z "$mori" ]; then
  55     mori="$base_name"_mori.mhd
  56 fi
  57 signal="$mori"_signal.txt
  58 if [ -z "$labels" ]; then
  59     labels="$base_name"_labels.mhd
  60 fi
  61 if [ -z "$output" ]; then
  62     output="$base_name"_rw.mhd
  63 fi
  64
  65 exec_dir=`dirname $0`
  66 mori_seg=`dirname $0`/fpa_CTBronchi_MoriSegmentation
  67 mori_lab=`dirname $0`/fpa_CTBronchi_MoriLabelling
  68 random_walker=`dirname $0`/fpa_CTBronchi_RandomWalker
  69
  70 $mori_seg \
  71     $input $mori $signal \
  72     $mori_init_threshold \
  73     $mori_end_threshold \
  74     $mori_delta \
  75     $mori_minimum_threshold \
  76     $mori_inside_value \
  77     $mori_outside_value \
  78     $mori_signal_kernel_size \
  79     $mori_signal_threshold \
  80     $mori_signal_influence \
  81     $sx $sy $sz
  82
  83 $mori_lab \
  84     $input $mori $labels \
  85     $label_upper_threshold \
  86     $mori_inside_value \
  87     $label_inside \
  88     $label_outside
  89
  90 $random_walker \
  91     $input $labels $output \
  92     $label_inside \
  93     $random_walker_beta
  94
  95 ## eof - $RCSfile$