appli/CTBronchi/Process.sh

   1 #!/bin/bash
   2
   3 ## -- Command line options
   4 curr_dir=`dirname $0`
   5 vesselness_sigma="0.5"
   6 vesselness_alpha1="0.5"
   7 vesselness_alpha2="2"
   8 mori_min_thr="-850"
   9 mori_kernel="20"
  10 mori_signal_thr="100"
  11 mori_signal_influence="0.5"
  12 mori_lower="-1024"
  13 mori_upper="0"
  14 mori_delta="1"
  15 slice_by_slice_vesselness_thr="5"
  16 labels_vesselness_thr="65"
  17 labels_upper_thr="-400"
  18 beta="2.5"
  19 epsilon="1e-5"
  20 while [[ "$#" -gt 0 ]]; do
  21     key="$1"
  22     case $key in
  23         -input)
  24         input=`realpath $2`
  25         shift
  26         ;;
  27         -force)
  28         force="1"
  29         ;;
  30         -vesselness_sigma)
  31         vesselness_sigma="$2"
  32         shift
  33         ;;
  34         -vesselness_alpha1)
  35         vesselness_alpha1="$2"
  36         shift
  37         ;;
  38         -vesselness_alpha2)
  39         vesselness_alpha2="$2"
  40         shift
  41         ;;
  42         -mori_min_thr)
  43         mori_min_thr="$2"
  44         shift
  45         ;;
  46         -mori_kernel)
  47         mori_kernel="$2"
  48         shift
  49         ;;
  50         -mori_signal_thr)
  51         mori_signal_thr="$2"
  52         shift
  53         ;;
  54         -mori_signal_influence)
  55         mori_signal_influence="$2"
  56         shift
  57         ;;
  58         -mori_lower)
  59         mori_lower="$2"
  60         shift
  61         ;;
  62         -mori_upper)
  63         mori_upper="$2"
  64         shift
  65         ;;
  66         -mori_delta)
  67         mori_delta="$2"
  68         shift
  69         ;;
  70         -slicebyslice_vesselness_thr)
  71         slicebyslice_vesselness_thr="$2"
  72         shift
  73         ;;
  74         -fast_vesselness_thr)
  75         fast_vesselness_thr="$2"
  76         shift
  77         ;;
  78         -slice_by_slice_vesselness_thr)
  79         slice_by_slice_vesselness_thr="$2"
  80         shift
  81         ;;
  82         -labels_upper_thr)
  83         labels_upper_thr="$2"
  84         shift
  85         ;;
  86         -beta)
  87         beta="$2"
  88         shift
  89         ;;
  90         -epsilon)
  91         epsilon="$2"
  92         shift
  93         ;;
  94         -seed)
  95         seed="$2 $3 $4"
  96         shift
  97         shift
  98         shift
  99         ;;
 100         *)
 101         # Do nothing
 102         ;;
 103     esac
 104     shift
 105 done
 106
 107 ## -- Check command line options
 108 if [ -z "$input" ] || [ -z "$seed" ] ; then
 109     (>&2 echo "Usage: $0 -input <file> -seed <x y z> [-force]")
 110     exit 1
 111 fi
 112
 113 base_dir=`dirname $input | xargs realpath`
 114 base_name=$base_dir/`basename $input .mha`
 115
 116 vesselness=$base_name"_vesselness.mha"
 117 mori=$base_name"_mori.mha"
 118 mori_signal=$base_name"_mori_signal.txt"
 119 labels=$base_name"_labels.mha"
 120 fastrw=$base_name"_fastrw.mha"
 121 slicerw=$base_name"_slicerw.mha"
 122
 123 echo "************************************************"
 124 (>&2 echo "Processing $input... ")
 125 echo "Processing $input..."
 126 if [ ! -f $vesselness ] || [ -n "$force" ] ; then
 127     $curr_dir/fpa_CTBronchi_Vesselness \
 128         -i $input -o $vesselness \
 129         -s $vesselness_sigma -a $vesselness_alpha1 -b $vesselness_alpha2
 130 fi
 131
 132 if [ ! -f $mori ] || [ -n "$force" ] ; then
 133     $curr_dir/fpa_CTBronchi_MoriSegmentation \
 134         -i $input \
 135         -o $mori \
 136         -s $mori_signal \
 137         -p "$seed" \
 138         -t $mori_min_thr \
 139         -k $mori_kernel \
 140         -r $mori_signal_thr \
 141         -f $mori_signal_influence \
 142         -l $mori_lower \
 143         -u $mori_upper \
 144         -d $mori_delta
 145 fi
 146
 147 if [ ! -f $labels ] || [ -n "$force" ] ; then
 148     $curr_dir/fpa_CTBronchi_MoriLabelling \
 149         -i $input \
 150         -l $mori \
 151         -v $vesselness \
 152         -o $labels \
 153         -a $fast_vesselness_thr \
 154         -u $labels_upper_thr
 155 fi
 156
 157 if [ ! -f $fastrw ] || [ -n "$force" ] ; then
 158     $curr_dir/fpa_CTBronchi_FastRandomWalker \
 159         -i $input \
 160         -l $labels \
 161         -o $fastrw \
 162         -b $beta \
 163         -e $epsilon
 164 fi
 165
 166 if [ ! -f $slicerw ] || [ -n "$force" ] ; then
 167     $curr_dir/fpa_CTBronchi_SliceBySliceRandomWalker \
 168         -i $input \
 169         -l $mori \
 170         -v $vesselness \
 171         -o $slicerw \
 172         -t $slice_by_slice_vesselness_thr \
 173         -b $beta \
 174         -e $epsilon
 175 fi
 176 (>&2 echo "done.")
 177 echo "done."
 178 echo "************************************************"
 179
 180 ## eof - $RCSfile$