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[FrontAlgorithms.git] / appli / CTBronchi / Process.sh

diff --git a/appli/CTBronchi/Process.sh b/appli/CTBronchi/Process.sh
index bebf539f5a067b7ea35a3035cec1b52eb77908e6..47954b752fac95797956d3c0e1313a180255f1a1 100755 (executable)
--- a/appli/CTBronchi/Process.sh
+++ b/appli/CTBronchi/Process.sh
@@ -1,6 +1,7 @@
 #!/bin/bash
 
 ## -- Command line options
+exec_dir=`dirname $0`
 vesselness_sigma="0.5"
 vesselness_alpha1="0.5"
 vesselness_alpha2="2"
@@ -11,7 +12,8 @@ mori_signal_influence="0.5"
 mori_lower="-1024"
 mori_upper="0"
 mori_delta="1"
-labels_vesselness_thr="5"
+slicebyslice_vesselness_thr="5"
+fast_vesselness_thr="95"
 labels_upper_thr="-400"
 beta="2.5"
 epsilon="1e-5"
@@ -65,8 +67,12 @@ while [[ "$#" -gt 0 ]]; do
         mori_delta="$2"
         shift
         ;;
-        -labels_vesselness_thr)
-        labels_vesselness_thr="$2"
+        -slicebyslice_vesselness_thr)
+        slicebyslice_vesselness_thr="$2"
+        shift
+        ;;
+        -fast_vesselness_thr)
+        fast_vesselness_thr="$2"
         shift
         ;;
         -labels_upper_thr)
@@ -114,13 +120,13 @@ echo "************************************************"
 (>&2 echo "Processing $input... ")
 echo "Processing $input..."
 if [ ! -f $vesselness ] || [ -n "$force" ] ; then
-    ./fpa_CTBronchi_Vesselness \
+    $exec_dir/fpa_CTBronchi_Vesselness \
         -i $input -o $vesselness \
         -s $vesselness_sigma -a $vesselness_alpha1 -b $vesselness_alpha2
 fi
 
 if [ ! -f $mori ] || [ -n "$force" ] ; then
-    ./fpa_CTBronchi_MoriSegmentation \
+    $exec_dir/fpa_CTBronchi_MoriSegmentation \
         -i $input \
         -o $mori \
         -s $mori_signal \
@@ -135,17 +141,17 @@ if [ ! -f $mori ] || [ -n "$force" ] ; then
 fi
 
 if [ ! -f $labels ] || [ -n "$force" ] ; then
-    ./fpa_CTBronchi_MoriLabelling \
+    $exec_dir/fpa_CTBronchi_MoriLabelling \
         -i $input \
         -l $mori \
         -v $vesselness \
         -o $labels \
-        -a $labels_vesselness_thr \
+        -a $fast_vesselness_thr \
         -u $labels_upper_thr
 fi
 
 if [ ! -f $fastrw ] || [ -n "$force" ] ; then
-    ./fpa_CTBronchi_FastRandomWalker \
+    $exec_dir/fpa_CTBronchi_FastRandomWalker \
         -i $input \
         -l $labels \
         -o $fastrw \
@@ -154,12 +160,12 @@ if [ ! -f $fastrw ] || [ -n "$force" ] ; then
 fi
 
 if [ ! -f $slicerw ] || [ -n "$force" ] ; then
-    ./fpa_CTBronchi_SliceBySliceRandomWalker \
+    $exec_dir/fpa_CTBronchi_SliceBySliceRandomWalker \
         -i $input \
         -l $mori \
         -v $vesselness \
         -o $slicerw \
-        -t $labels_vesselness_thr \
+        -t $slicebyslice_vesselness_thr \
         -b $beta \
         -e $epsilon
 fi