dicom structure in cmd line

[clitk.git] / scripts / create_midP-2.0.sh

diff --git a/scripts/create_midP-2.0.sh b/scripts/create_midP-2.0.sh
index 93290c860baca2be7924e711ede155c768857be8..1f18830311102decf806136bd23f1c7ef4ca9a97 100755 (executable)
--- a/scripts/create_midP-2.0.sh
+++ b/scripts/create_midP-2.0.sh
@@ -38,7 +38,7 @@ registration()
   # with the specified preffix, which is interesting for debugging. 
   # if blank, it means that the original images (those without bands) 
   # will be used (see create_midP_masks-2.0.sh for details).
-  banded="banded_"
+  banded=""
 
   # params read from conf file
   params="$nb_iter $nb_samples $sampling_algo $nb_hist_bins $nb_levels $bspline_spacing $metric $optimizer $interpolator"
@@ -76,12 +76,25 @@ registration()
         registration_elastix $reference_out $target_out $mask_ref_out $mask_targ_out $vf_out $result_out $params $log_out
       fi
 
-      # combine in and out vf
       motion_mask=$mask_dir/mm_$phase_nb.mhd
+
+      # combine in and out results
+      out_result=$output_dir/result_${ref_phase_nb}_$phase_nb.mhd
+      clitkCombineImage -i $result_in -j $result_out -m $motion_mask -o $out_result
+      abort_on_error registration $? clean_up_registration
+
+      # combine in and out vf
       vf_result=$vf_dir/vf_${ref_phase_nb}_$phase_nb.mhd
       clitkCombineImage -i $vf_in -j $vf_out -m $motion_mask -o $vf_result
+      abort_on_error registration $? clean_up_registration
+
       clitkZeroVF -i $vf_in -o vf_zero.mhd
+      abort_on_error registration $? clean_up_registration
+
+      patient_mask=$mask_dir/patient_mask_$phase_nb.mhd
       clitkCombineImage -i $vf_result -j vf_zero.mhd -m $patient_mask -o $vf_result
+      abort_on_error registration $? clean_up_registration
+
       rm vf_zero.*
 
       # save for later...
@@ -89,11 +102,30 @@ registration()
     fi
   done
 
-  # create (zero) vf from reference to reference
+  # create (zero) vf from reference to reference and associated images
+  vf_in=$vf_dir/vf_inside_${ref_phase_nb}_${ref_phase_nb}.mhd
+  vf_out=$vf_dir/vf_outside_${ref_phase_nb}_${ref_phase_nb}.mhd
   clitkZeroVF -i $vf_ref -o $vf_dir/vf_${ref_phase_nb}_${ref_phase_nb}.mhd
+  clitkZeroVF -i $vf_ref -o $vf_in
+  clitkZeroVF -i $vf_ref -o $vf_out
+  abort_on_error registration $? clean_up_registration
+
+  motion_mask=$mask_dir/mm_${ref_phase_nb}.mhd
+  reference_in=$mask_dir/${banded}inside_${ref_phase_nb}.mhd
+  reference_out=$mask_dir/${banded}outside_$ref_phase_nb.mhd
+  out_result=$output_dir/result_${ref_phase_nb}_${ref_phase_nb}.mhd
+  clitkCombineImage -i $reference_in -j $reference_out -m $motion_mask -o $out_result
+  abort_on_error registration $? clean_up_registration
 
   # create 4D vf
   create_mhd_4D_pattern.sh $vf_dir/vf_${ref_phase_nb}_
+  create_mhd_4D_pattern.sh $vf_dir/vf_inside_${ref_phase_nb}_
+  create_mhd_4D_pattern.sh $vf_dir/vf_outside_${ref_phase_nb}_
+
+  # create 4D result image
+  create_mhd_4D_pattern.sh $output_dir/result_inside_${ref_phase_nb}_
+  create_mhd_4D_pattern.sh $output_dir/result_outside_${ref_phase_nb}_
+  create_mhd_4D_pattern.sh $output_dir/result_${ref_phase_nb}_
 
   echo
   echo "-------- Registration done ! --------"
@@ -116,24 +148,30 @@ midp()
   ########### calculate the midp wrt the reference phase
   phase_nb=$ref_phase_nb
   echo "Calculating midp_$phase_nb.mhd..."
-  vf_midp=$midp_dir/vf_$phase_nb\_midp.mhd
+  vf_midp=$midp_dir/vf_midp_$phase_nb.mhd
   midp=$midp_dir/midp_$phase_nb.mhd
   # average the vf's from reference phase to phase
   clitkAverageTemporalDimension -i $vf_dir/vf_${ref_phase_nb}_4D.mhd -o $vf_midp
+  abort_on_error midp $? clean_up_midp
+
   # invert the vf (why?)
   clitkInvertVF -i $vf_midp -o $vf_midp
+  abort_on_error midp $? clean_up_midp
+
   # create the midp by warping the reference phase with the reference vf
   clitkWarpImage -i $ref_phase_file -o $midp --vf=$vf_midp -s 1
+  abort_on_error midp $? clean_up_midp
 
   ref_vf_midp=$vf_midp
   ref_midp=$midp
   clitkImageConvert -i $ref_midp -o $ref_midp -t float
+  abort_on_error midp $? clean_up_midp
 
   ########### calculate the midp wrt the other phases
   for i in $( seq 0 $((${#phase_files[@]} - 1))); do
     phase_file=${phase_files[$i]}
     phase_nb=${phase_nbs[$i]}
-    vf_midp=$midp_dir/vf_$phase_nb\_midp.mhd
+    vf_midp=$midp_dir/vf_midp_$phase_nb.mhd
     midp=$midp_dir/midp_$phase_nb.mhd
 
     if [ "$phase_nb" != "$ref_phase_nb" ]; then
@@ -141,19 +179,30 @@ midp()
       # calculate vf from phase to midp, using the vf from reference phase to midp (-i)
       # and the vf from reference phase to phase (-j)
       clitkComposeVF -i $ref_vf_midp -j $vf_dir/vf_$ref_phase_nb\_$phase_nb.mhd -o $vf_midp
+      abort_on_error midp $? clean_up_midp
+      
       clitkWarpImage -i $phase_file -o $midp --vf=$vf_midp -s 1
+      abort_on_error midp $? clean_up_midp
+      
       clitkImageConvert -i $midp -o $midp -t float
+      abort_on_error midp $? clean_up_midp
     fi
   done
 
+  # create 4D midp
   create_mhd_4D_pattern.sh $midp_dir/midp_
+  create_mhd_4D_pattern.sh $midp_dir/vf_midp_
+
   echo "Calculating midp_avg.mhd..."
   clitkAverageTemporalDimension -i $midp_dir/midp_4D.mhd -o $midp_dir/midp_avg.mhd
+  abort_on_error midp $? clean_up_midp
+
   echo "Calculating midp_med.mhd..."
   clitkMedianTemporalDimension -i $midp_dir/midp_4D.mhd -o $midp_dir/midp_med.mhd
+  abort_on_error midp $? clean_up_midp
 
   # clean-up
-  rm $midp_dir/vf_*
+  #rm $midp_dir/vf_*
       
   echo
   echo "-------- Mid-position done ! --------"
@@ -184,6 +233,8 @@ ref_phase=$2
 conf=$3
 source $conf
 
+cd `dirname $mhd4d`
+
 mkdir -p $log_dir
 mask_dir="MASK-${mask_interpolation_spacing}mm-$mask_interpolation_algorithm"