use of coefficient images in mid-P creation

diff --git a/scripts/create_midP-2.0.sh b/scripts/create_midP-2.0.sh
index 1f18830311102decf806136bd23f1c7ef4ca9a97..3cd023ccc726a1e3f797349de3f0462c666bd48e 100755 (executable)
--- a/scripts/create_midP-2.0.sh
+++ b/scripts/create_midP-2.0.sh
@@ -41,6 +41,7 @@ registration()
   banded=""
 
   # params read from conf file
+  use_coeffs=1
   params="$nb_iter $nb_samples $sampling_algo $nb_hist_bins $nb_levels $bspline_spacing $metric $optimizer $interpolator"
 
   # register all phases to the reference
@@ -57,6 +58,10 @@ registration()
       vf_in=$vf_dir/vf_inside_${ref_phase_nb}_$phase_nb.mhd
       result_in=$output_dir/result_inside_${ref_phase_nb}_$phase_nb.mhd
       log_in=$log_dir/log_inside_${ref_phase_nb}_$phase_nb.log
+      if [ $use_coeffs = 1 ]; then
+        init_coeff_in=$coeff_in # empty at first iteration
+        coeff_in=$vf_dir/coeff_inside_${ref_phase_nb}_$phase_nb.mhd
+      fi
 
       # outside params
       reference_out=$mask_dir/${banded}outside_$ref_phase_nb.mhd
@@ -66,11 +71,15 @@ registration()
       vf_out=$vf_dir/vf_outside_$ref_phase_nb\_$phase_nb.mhd
       result_out=$output_dir/result_outside_$ref_phase_nb\_$phase_nb.mhd
       log_out=$log_dir/log_outside_${ref_phase_nb}_$phase_nb.log
+      if [ $use_coeffs = 1 ]; then
+        init_coeff_out=$coeff_out # empty at first iteration
+        coeff_out=$vf_dir/coeff_outside_${ref_phase_nb}_$phase_nb.mhd
+      fi
 
       # registration
       if [ "$method" == "blutdir" ]; then
-        registration_blutdir $reference_in $target_in $mask_ref_in $mask_targ_in $vf_in $result_in $params $log_in
-        registration_blutdir $reference_out $target_out $mask_ref_out $mask_targ_out $vf_out $result_out $params $log_out
+        registration_blutdir $reference_in $target_in $mask_ref_in $mask_targ_in $vf_in $result_in $params $log_in $coeff_in $init_coeff_in
+        registration_blutdir $reference_out $target_out $mask_ref_out $mask_targ_out $vf_out $result_out $params $log_out $coeff_out $init_coeff_out
       elif [ "$method" == "elastix" ]; then
         registration_elastix $reference_in $target_in $mask_ref_in $mask_targ_in $vf_in $result_in $params $log_in
         registration_elastix $reference_out $target_out $mask_ref_out $mask_targ_out $vf_out $result_out $params $log_out

diff --git a/scripts/registration.sh b/scripts/registration.sh
index 724e3ac392f804e842e408bc67e92733fd52c6fa..5431342394d4c70346169dbabbe985e71527e89e 100755 (executable)
--- a/scripts/registration.sh
+++ b/scripts/registration.sh
@@ -37,26 +37,37 @@ 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