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

diff --git a/appli/CTBronchi/Process.sh b/appli/CTBronchi/Process.sh
index 618a3bc7cc8c4bfabb7d180435aa1cab02f34cf7..5f4220241880dff433df891707f02219dc832a80 100755 (executable)
--- a/appli/CTBronchi/Process.sh
+++ b/appli/CTBronchi/Process.sh
@@ -2,6 +2,7 @@
 
 ## -- Command line options
 curr_dir=`dirname $0`
+ext="mhd"
 vesselness_sigma="0.5"
 vesselness_alpha1="0.5"
 vesselness_alpha2="2"
@@ -13,7 +14,7 @@ mori_lower="-1024"
 mori_upper="0"
 mori_delta="1"
 slice_by_slice_vesselness_thr="5"
-labels_vesselness_thr="65"
+fast_vesselness_thr="65"
 labels_upper_thr="-400"
 beta="2.5"
 epsilon="1e-5"
@@ -111,14 +112,17 @@ if [ -z "$input" ] || [ -z "$seed" ] ; then
 fi
 
 base_dir=`dirname $input | xargs realpath`
-base_name=$base_dir/`basename $input .mha`
+base_name=$base_dir/`basename $input .$ext`
 
-vesselness=$base_name"_vesselness.mha"
-mori=$base_name"_mori.mha"
+vesselness=$base_name"_vesselness.$ext"
+mori=$base_name"_mori.$ext"
 mori_signal=$base_name"_mori_signal.txt"
-labels=$base_name"_labels.mha"
-fastrw=$base_name"_fastrw.mha"
-slicerw=$base_name"_slicerw.mha"
+labels=$base_name"_labels.$ext"
+fastrw=$base_name"_fastrw.$ext"
+slicerw=$base_name"_slicerw.$ext"
+skeleton_fastrw=$base_name"_fastrw_skeleton.txt"
+skeleton_slicerw=$base_name"_slicerw_skeleton.txt"
+points=$base_name"_points.txt"
 
 echo "************************************************"
 (>&2 echo "Processing $input... ")
@@ -173,6 +177,14 @@ if [ ! -f $slicerw ] || [ -n "$force" ] ; then
         -b $beta \
         -e $epsilon
 fi
+
+if [ ! -f $skeleton_slicerw ] || [ -n "$force" ] ; then
+    $curr_dir/fpa_CTBronchi_Skeleton \
+        -i $slicerw \
+        -o $skeleton_slicerw \
+        -e $points \
+        -p "$seed"
+fi
 (>&2 echo "done.")
 echo "done."
 echo "************************************************"