Moved from repository clitk to clitk.private/tests_dav

[clitk.git] / scripts / registration.sh

diff --git a/scripts/registration.sh b/scripts/registration.sh
index 397965460a11b4b3da76802c4ef41d57265549de..5431342394d4c70346169dbabbe985e71527e89e 100755 (executable)
--- a/scripts/registration.sh
+++ b/scripts/registration.sh
@@ -31,31 +31,46 @@
 #
 ###############################################################################
 
+source `dirname $0`/midp_common.sh
+
 
 ################# BLUTDIR #####################
 registration_blutdir()
 {
-  reference=$1
-  target=$2
-  mask_ref=$3
-  mask_targ=$4
-  vf=$5
-  result=$6
-  nb_iter=$7
-  nb_samples=$8
-  sampling_algo=$9
-  hist_bins=${10}
-  nb_levels=${11}
-  spacing=${12}
-  metric=${13}
-  optimizer=${14}
-  interpolator=${15}
-  log=${16}
+  local reference=$1
+  local target=$2
+  local mask_ref=$3
+  local mask_targ=$4
+  local vf=$5
+  local result=$6
+  local nb_iter=$7
+  local nb_samples=$8
+  local sampling_algo=$9
+  local hist_bins=${10}
+  local nb_levels=${11}
+  local spacing=${12}
+  local metric=${13}
+  local optimizer=${14}
+  local interpolator=${15}
+  local log=${16}
+  local coeff=${17}
+  local init_coeff=${18}
 
   echo "Computing BLUTDIR $reference -> $target ..."
   blutdir_params="--levels $nb_levels  --metric $metric --optimizer $optimizer --samples $nb_samples --spacing $spacing,$spacing,$spacing --bins $hist_bins --maxIt $nb_iter --interp $interpolator --verbose"
-  cmd="clitkBLUTDIR -r $reference -t $target -m $mask_ref --targetMask $mask_targ --vf $vf -o $result $blutdir_params"
+
+  if [ -n "$coeff" ]; then
+    coeff="--coeff $coeff"
+  fi
+  
+  if [ -n "$init_coeff" ]; then
+    init_coeff="--initCoeff $init_coeff"
+  fi
+  
+  cmd="clitkBLUTDIR -r $reference -t $target -m $mask_ref --targetMask $mask_targ --vf $vf $coeff $init_coeff -o $result $blutdir_params"
   $cmd > $log
+
+  abort_on_error registration_blutdir $? clean_up_registration
 }
 
 ################# ELASTIX #####################
@@ -88,13 +103,14 @@ registration_elastix()
   echo "Computing ELASTIX $reference -> $target ..."
   exec_dir=`which elastix`
   exec_dir=`dirname $exec_dir`
+  suffix=${nb_samples}_${nb_iter}_${nb_levels}
   cat $exec_dir/params_BSpline.txt | sed -e "s+<NbIterations>+$nb_iter+" \
                               -e "s+<LabelsFile>++" \
                               -e "s+<HistBins>+$hist_bins+" \
                               -e "s+<Levels>+$nb_levels+" \
                               -e "s+<NbSamples>+$nb_samples+" \
                               -e "s+<SamplerType>+$sampling_algo+" \
-                              -e "s+<Spacing>+$spacing+" > params_BSpline.txt 
+                              -e "s+<Spacing>+$spacing+" > params_BSpline_${suffix}.txt 
 
   vf_dir=`dirname $vf`
   vf_base=`basename $vf .mhd`
@@ -102,12 +118,14 @@ registration_elastix()
   result_base=`basename $result .mhd`
 
   # image registration
-  cmd="elastix -f $reference -m $target -fMask $mask_ref -mMask $mask_targ -out $result_dir -p params_BSpline.txt"
+  cmd="elastix -f $reference -m $target -fMask $mask_ref -mMask $mask_targ -out $result_dir -p params_BSpline_${suffix}.txt"
   $cmd  > /dev/null
+  abort_on_error registration_elastix $? clean_up_registration
 
   # generate vector field
   cmd="transformix -tp $result_dir/TransformParameters.0.txt -out $vf_dir -def all"
   $cmd  > /dev/null
+  abort_on_error registration_elastix $? clean_up_registration
 
   # post-processing
   mv $vf_dir/deformationField.mhd $vf