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

diff --git a/appli/CTBronchi/CTBronchi_process.sh b/appli/CTBronchi/CTBronchi_process.sh
new file mode 100755 (executable)
index 0000000..15bd591
--- /dev/null
+++ b/appli/CTBronchi/CTBronchi_process.sh
@@ -0,0 +1,69 @@
+#!/bin/bash
+
+## Command line arguments
+if [ "$#" -lt 5 ]; then
+    echo "Usage: $0 input_image [index/point] seed_x seed_y seed_z"
+    exit 1
+fi
+
+exec_dir=`dirname $0`
+mori_seg=`dirname $0`/fpa_CTBronchi_MoriSegmentation
+mori_lab=`dirname $0`/fpa_CTBronchi_MoriLabelling
+random_walker=`dirname $0`/fpa_CTBronchi_RandomWalker
+input_image=$1
+seed_type=$2
+seed_x=$3
+seed_y=$4
+seed_z=$5
+
+base_name=`dirname $input_image`/`basename $input_image .mhd`
+
+mori_output_image="$base_name"_mori.mhd
+mori_output_signal="$base_name"_mori_signal.txt
+mori_init_threshold=-1024
+mori_end_threshold=0
+mori_delta=1
+mori_minimum_threshold=-850
+mori_inside_value=255
+mori_outside_value=0
+mori_signal_kernel_size=20
+mori_signal_threshold=500
+mori_signal_influence=500
+
+labels_output_image="$base_name"_labels.mhd
+label_upper_threshold=-600
+label_inside=1
+label_outside=2
+
+random_walker_output_image="$base_name"_rw.mhd
+random_walker_alpha=0
+random_walker_beta=20
+
+$mori_seg \
+    $input_image $mori_output_image $mori_output_signal \
+    $mori_init_threshold \
+    $mori_end_threshold \
+    $mori_delta \
+    $mori_minimum_threshold \
+    $mori_inside_value \
+    $mori_outside_value \
+    $mori_signal_kernel_size \
+    $mori_signal_threshold \
+    $mori_signal_influence \
+    $seed_type \
+    $seed_x $seed_y $seed_z
+
+$mori_lab \
+    $input_image $mori_output_image $labels_output_image \
+    $label_upper_threshold \
+    $mori_inside_value \
+    $label_inside \
+    $label_outside
+
+$random_walker \
+    $input_image $labels_output_image $random_walker_output_image \
+    $label_inside \
+    $random_walker_alpha \
+    $random_walker_beta
+
+## eof - $RCSfile$