...

diff --git a/appli/CTBronchi/CTBronchi_process.sh b/appli/CTBronchi/CTBronchi_process.sh
index 26257bed106938519023c01fe7ddb6cedbc1829c..f22b699ce9c40efc1e692ed0120ac138bc65d958 100755 (executable)
--- a/appli/CTBronchi/CTBronchi_process.sh
+++ b/appli/CTBronchi/CTBronchi_process.sh
@@ -1,45 +1,74 @@
 #!/bin/bash
 
 ## Command line arguments
-if [ "$#" -lt 5 ]; then
-    echo "Usage: $0 input_image [index/point] seed_x seed_y seed_z"
+while [[ "$#" -gt 1 ]]; do
+    key="$1"
+    case $key in
+        -input)
+        input="$2"
+        shift
+        ;;
+        -seed)
+        sx="$2"
+        sy="$3"
+        sz="$4"
+        shift
+        ;;
+        -mori)
+        mori="$2"
+        shift
+        ;;
+        -labels)
+        labels="$2"
+        shift
+        ;;
+        -output)
+        output="$2"
+        shift
+        ;;
+        *)
+        # Do nothing
+        ;;
+    esac
+    shift
+done
+if [ -z "$input" ] || [ -z "$sx" ] || [ -z "$sy" ] || [ -z "$sz" ]; then
+    (>&2 echo "Usage: $0 -input input_raw_image -seed x y z [-mori mori_image_dfilename] [-labels labels_image_filename] [-output output_image_filename] [-mori_init_threshold value] [-mori_end_threshold value] [-mori_delta value] [-mori_minimum_threshold value] [-mori_inside_value value] [-mori_outside_value value] [-mori_signal_kernel_size value] [-mori_signal_threshold value] [-mori_signal_influence value] [-label_upper_threshold value] [-label_inside value] [-label_outside value] [-random_walker_beta value]")
     exit 1
 fi
+if [ -z "$mori_init_threshold" ]; then mori_init_threshold="-1024"; fi
+if [ -z "$mori_end_threshold" ]; then mori_end_threshold="0"; fi
+if [ -z "$mori_delta" ]; then mori_delta="1"; fi
+if [ -z "$mori_minimum_threshold" ]; then mori_minimum_threshold="-850"; fi
+if [ -z "$mori_inside_value" ]; then mori_inside_value="255"; fi
+if [ -z "$mori_outside_value" ]; then mori_outside_value="0"; fi
+if [ -z "$mori_signal_kernel_size" ]; then mori_signal_kernel_size="20"; fi
+if [ -z "$mori_signal_threshold" ]; then mori_signal_threshold="500"; fi
+if [ -z "$mori_signal_influence" ]; then mori_signal_influence="0.5"; fi
+if [ -z "$label_upper_threshold" ]; then label_upper_threshold="-600"; fi
+if [ -z "$label_inside" ]; then label_inside="1"; fi
+if [ -z "$label_outside" ]; then label_outside="2"; fi
+if [ -z "$random_walker_beta" ]; then random_walker_beta="20"; fi
+
+base_name=`dirname $input`/`basename $input .mhd`
+if [ -z "$mori" ]; then
+    mori="$base_name"_mori.mhd
+fi
+signal="$mori"_signal.txt
+if [ -z "$labels" ]; then
+    labels="$base_name"_labels.mhd
+fi
+if [ -z "$output" ]; then
+    output="$base_name"_rw.mhd
+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_beta=20
 
 $mori_seg \
-    $input_image $mori_output_image $mori_output_signal \
+    $input $mori $signal \
     $mori_init_threshold \
     $mori_end_threshold \
     $mori_delta \
@@ -49,18 +78,17 @@ $mori_seg \
     $mori_signal_kernel_size \
     $mori_signal_threshold \
     $mori_signal_influence \
-    $seed_type \
-    $seed_x $seed_y $seed_z
+    $sx $sy $sz
 
 $mori_lab \
-    $input_image $mori_output_image $labels_output_image \
+    $input $mori $labels \
     $label_upper_threshold \
     $mori_inside_value \
     $label_inside \
     $label_outside
 
 $random_walker \
-    $input_image $labels_output_image $random_walker_output_image \
+    $input $labels $output \
     $label_inside \
     $random_walker_beta
 

diff --git a/appli/CTBronchi/MoriSegmentation.cxx b/appli/CTBronchi/MoriSegmentation.cxx
index 0b266492488f3f84727696061f8a977e061f49a6..39b9e0dcb3bcec9978554fa19e2c6bdec5a8f35d 100644 (file)
--- a/appli/CTBronchi/MoriSegmentation.cxx
+++ b/appli/CTBronchi/MoriSegmentation.cxx
@@ -17,17 +17,17 @@ typedef fpa::Image::Mori< TInputImage, TLabelImage > TFilter;
 int main( int argc, char* argv[] )
 {
   // Get arguments
-  if( argc < 17 )
+  if( argc < 16 )
   {
     std::cerr
       << "Usage: " << argv[ 0 ] << std::endl
       << "   input_image output_image output_signal" << std::endl
-      << "   init_threshold(-1024) end_threshold(0) delta(1)" << std::endl
-      << "   minimum_threshold(-850)" << std::endl
-      << "   inside_value(255) outside_value(0)" << std::endl
-      << "   signal_kernel_size(20) signal_threshold(500) signal_influence(0.5)"
+      << "   init_threshold end_threshold delta" << std::endl
+      << "   minimum_threshold" << std::endl
+      << "   inside_value outside_value" << std::endl
+      << "   signal_kernel_size signal_threshold signal_influence"
       << std::endl
-      << "   [index/point] seed_x seed_y seed_z"
+      << "   seed_x seed_y seed_z"
       << std::endl;
     return( 1 );
 
@@ -44,17 +44,9 @@ int main( int argc, char* argv[] )
   unsigned long signal_kernel_size = std::atoi( argv[ 10 ] );
   double signal_threshold = std::atof( argv[ 11 ] );
   double signal_influence = std::atof( argv[ 12 ] );
-  std::string seed_type = argv[ 13 ];
-  TInputImage::IndexType iseed;
   TInputImage::PointType pseed;
-  for( unsigned int i = 0; i < Dim; ++i )
-  {
-    if( seed_type == "index" )
-      iseed[ i ] = std::atoi( argv[ 14 + i ] );
-    else
-      pseed[ i ] = std::atof( argv[ 14 + i ] );
-
-  } // rof
+  for( int i = 0; i < Dim; ++i )
+    pseed[ i ] = std::atof( argv[ 13 + i ] );
 
   // Read image
   itk::ImageFileReader< TInputImage >::Pointer input_image_reader =
@@ -64,10 +56,7 @@ int main( int argc, char* argv[] )
   // Prepare filter
   TFilter::Pointer filter = TFilter::New( );
   filter->SetInput( input_image_reader->GetOutput( ) );
-  if( seed_type == "index" )
-    filter->SetSeed( iseed );
-  else
-    filter->SetSeed( pseed );
+  filter->SetSeed( pseed );
   filter->SetThresholds( init_threshold, end_threshold, delta );
   filter->SetMinimumThreshold( minimum_threshold );
   filter->SetInsideValue( inside_value );

diff --git a/appli/CTBronchi/Process.cxx b/appli/CTBronchi/Process.cxx
new file mode 100644 (file)
index 0000000..8fb3e17
--- /dev/null
+++ b/appli/CTBronchi/Process.cxx
@@ -0,0 +1,28 @@
+int main( int argc, char* argv[] )
+{
+  /* TODO
+     -input input_raw_image
+     -seed x y z
+     [-mori mori_image_dfilename]
+     [-labels labels_image_filename]
+     [-output output_image_filename]
+  */
+
+    /* TODO
+       if [ -z "$mori_init_threshold" ]; then mori_init_threshold="-1024"; fi
+       if [ -z "$mori_end_threshold" ]; then mori_end_threshold="0"; fi
+       if [ -z "$mori_delta" ]; then mori_delta="1"; fi
+       if [ -z "$mori_minimum_threshold" ]; then mori_minimum_threshold="-850"; fi
+       if [ -z "$mori_inside_value" ]; then mori_inside_value="255"; fi
+       if [ -z "$mori_outside_value" ]; then mori_outside_value="0"; fi
+       if [ -z "$mori_signal_kernel_size" ]; then mori_signal_kernel_size="20"; fi
+       if [ -z "$mori_signal_threshold" ]; then mori_signal_threshold="500"; fi
+       if [ -z "$mori_signal_influence" ]; then mori_signal_influence="0.5"; fi
+       if [ -z "$label_upper_threshold" ]; then label_upper_threshold="-600"; fi
+       if [ -z "$label_inside" ]; then label_inside="1"; fi
+       if [ -z "$label_outside" ]; then label_outside="2"; fi
+       if [ -z "$random_walker_beta" ]; then random_walker_beta="20"; fi
+    */
+
+    return( 0 );
+}

diff --git a/lib/fpa/Base/Mori.h b/lib/fpa/Base/Mori.h
index e7ea726eab3c61809d5c7f2b8f9e1cc878ee5b61..0cc7a248410458bfe45573458e4cbb3b0e7ec270 100644 (file)
--- a/lib/fpa/Base/Mori.h
+++ b/lib/fpa/Base/Mori.h
@@ -33,15 +33,6 @@ namespace fpa
       typedef typename _TAlgorithm::TTraits TTraits;
       fpa_Base_TraitTypes( typename TTraits );
 
-      /* TODO
-         typedef typename _TAlgorithm::TNode        TNode;
-         typedef typename _TAlgorithm::TNodes       TNodes;
-         typedef typename _TAlgorithm::TInputValue  TInputValue;
-         typedef typename _TAlgorithm::TOutputValue TOutputValue;
-         typedef typename _TAlgorithm::TFrontId     TFrontId;
-         typedef typename _TAlgorithm::TVertex      TVertex;
-      */
-
       typedef std::deque< TNode >     TQueue;
       typedef std::set< TInputValue > TThresholds;