######################### includes
-source `dirname $0`/create_midP_masks-2.0.sh using-as-lib 2 nn
+source `dirname $0`/create_midP_masks-2.0.sh using-as-lib
source `dirname $0`/registration.sh
source `dirname $0`/midp_common.sh
registration_elastix $reference_out $target_out $mask_ref_out $mask_targ_out $vf_out $result_out $params $log_out
fi
- motion_mask=$mask_dir/mm_$phase_nb.mhd
+ motion_mask=$mask_dir/${mask_type}_$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
+ # clitkCombineImage -i $result_in -j $result_out -m $motion_mask -o $out_result
+ combine_image $result_in $result_out $out_result $motion_mask
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
+ #clitkCombineImage -i $vf_in -j $vf_out -m $motion_mask -o $vf_result
+ combine_image $vf_in $vf_out $vf_result $motion_mask
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
+ #clitkCombineImage -i $vf_result -j vf_zero.mhd -m $patient_mask -o $vf_result
+ combine_image $vf_result vf_zero.mhd $vf_result $patient_mask
abort_on_error registration $? clean_up_registration
rm vf_zero.*
clitkZeroVF -i $vf_ref -o $vf_out
abort_on_error registration $? clean_up_registration
- motion_mask=$mask_dir/mm_${ref_phase_nb}.mhd
+ motion_mask=$mask_dir/${mask_type}_${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
+ #clitkCombineImage -i $reference_in -j $reference_out -m $motion_mask -o $out_result
+ combine_image $reference_in $reference_out $out_result $motion_mask
abort_on_error registration $? clean_up_registration
# create 4D vf
echo
}
+registration_no_motion_mask()
+{
+ echo
+ echo "----------- Registration Without Motion Masks ------------"
+ start=`date`
+ echo "start: $start"
+ echo
+
+ mkdir -p $vf_dir
+ mkdir -p $output_dir
+
+ # banded images may be created as separate files,
+ # with the specified preffix, which is interesting for debugging.
+ # if blank, it means that the original images (those without bands)
+ # will be used (see create_midP_masks-2.0.sh for details).
+ banded=""
+
+ # params read from conf file
+ use_coeffs=1
+ params="$nb_iter $nb_samples $sampling_algo $nb_hist_bins $nb_levels $bspline_spacing $metric $optimizer $interpolator"
+
+ # register all phases to the reference
+ for i in $( seq 0 $((${#phase_files[@]} - 1))); do
+ phase_file=${phase_files[$i]}
+ phase_nb=${phase_nbs[$i]}
+
+ if [ "$phase_nb" != "$ref_phase_nb" ]; then
+ # params
+ reference=$mask_dir/patient_$ref_phase_nb.mhd
+ target=$mask_dir/patient_$phase_nb.mhd
+ mask_ref=$mask_dir/patient_mask_$ref_phase_nb.mhd
+ mask_targ=$mask_dir/patient_mask_$phase_nb.mhd
+ vf=$vf_dir/vf_${ref_phase_nb}_$phase_nb.mhd
+ result=$output_dir/result_${ref_phase_nb}_$phase_nb.mhd
+ log=$log_dir/log_${ref_phase_nb}_$phase_nb.log
+ if [ $use_coeffs = 1 ]; then
+ init_coeff=$coeff_in # empty at first iteration
+ coeff=$vf_dir/coeff_${ref_phase_nb}_$phase_nb.mhd
+ fi
+
+ # registration
+ if [ "$method" == "blutdir" ]; then
+ registration_blutdir $reference $target $mask_ref $mask_targ $vf $result $params $log $coeff
+ elif [ "$method" == "elastix" ]; then
+ registration_elastix $reference $target $mask_ref $mask_targ $vf $result $params $log
+ fi
+
+ # save for later...
+ vf_ref=$vf
+ fi
+ done
+
+ clitkZeroVF -i $vf_ref -o $vf_dir/vf_${ref_phase_nb}_${ref_phase_nb}.mhd
+
+ # create 4D vf
+ create_mhd_4D_pattern.sh $vf_dir/vf_${ref_phase_nb}_
+
+ # create 4D coeffs
+ create_mhd_4D_pattern.sh $vf_dir/coeff_${ref_phase_nb}_ _0
+
+ # create 4D result image
+ create_mhd_4D_pattern.sh $output_dir/result_${ref_phase_nb}_
+
+ echo
+ echo "-------- Registration done ! --------"
+ end=`date`
+ echo "start: $start"
+ echo "end: $end"
+ echo
+}
+
midp()
{
echo
vf_midp=$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
+ #clitkAverageTemporalDimension -i $vf_dir/vf_${ref_phase_nb}_4D.mhd -o $vf_midp
+ average_temporal_dimension $vf_dir/vf_${ref_phase_nb}_4D.mhd $vf_midp
abort_on_error midp $? clean_up_midp
# invert the vf (why?)
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
+ #clitkAverageTemporalDimension -i $midp_dir/midp_4D.mhd -o $midp_dir/midp_avg.mhd
+ average_temporal_dimension $midp_dir/midp_4D.mhd $midp_dir/midp_avg.mhd
abort_on_error midp $? clean_up_midp
echo "Calculating midp_med.mhd..."
coeff_midp_in=$midp_dir/coeff_inside_midp_$phase_nb.mhd
coeff_midp_out=$midp_dir/coeff_outside_midp_$phase_nb.mhd
# average the vf's from reference phase to phase
- # clitkAverageTemporalDimension -i $vf_dir/vf_inside_${ref_phase_nb}_4D.mhd -o $vf_midp_in
- clitkAverageTemporalDimension -i $vf_dir/coeff_inside_${ref_phase_nb}_4D_0.mhd -o $coeff_midp_in
+ average_temporal_dimension $vf_dir/coeff_inside_${ref_phase_nb}_4D_0.mhd $coeff_midp_in
abort_on_error midp $? clean_up_midp
- # clitkAverageTemporalDimension -i $vf_dir/vf_outside_${ref_phase_nb}_4D.mhd -o $vf_midp_out
- clitkAverageTemporalDimension -i $vf_dir/coeff_outside_${ref_phase_nb}_4D_0.mhd -o $coeff_midp_out
+ average_temporal_dimension $vf_dir/coeff_outside_${ref_phase_nb}_4D_0.mhd $coeff_midp_out
abort_on_error midp $? clean_up_midp
# invert the vf
- # clitkInvertVF -i $vf_midp_in -o $vf_midp_in
clitkInvertVF -i $coeff_midp_in -o $vf_midp_in --type 1 --like $ref_phase_file
abort_on_error midp $? clean_up_midp
- # clitkInvertVF -i $vf_midp_out -o $vf_midp_out
clitkInvertVF -i $coeff_midp_out -o $vf_midp_out --type 1 --like $ref_phase_file
abort_on_error midp $? clean_up_midp
ref_vf_midp_in=$vf_midp_in
ref_vf_midp_out=$vf_midp_out
vf_midp=$midp_dir/vf_midp_$phase_nb.mhd
- clitkCombineImage -i $vf_midp_in -j $vf_midp_out -o $vf_midp -m $mask_dir/mm_$phase_nb.mhd
+ combine_image $vf_midp_in $vf_midp_out $vf_midp $mask_dir/${mask_type}_$phase_nb.mhd
clitkZeroVF -i $vf_midp -o vf_zero.mhd
- clitkCombineImage -i $vf_midp -j vf_zero.mhd -o $vf_midp -m $mask_dir/patient_mask_$phase_nb.mhd
+ combine_image $vf_midp vf_zero.mhd $vf_midp $mask_dir/patient_mask_$phase_nb.mhd
# create the midp by warping the reference phase with the reference vf
midp=$midp_dir/midp_$phase_nb.mhd
# combine in and out VF's
vf_midp=$midp_dir/vf_midp_$phase_nb.mhd
- clitkCombineImage -i $vf_midp_in -j $vf_midp_out -o $vf_midp -m $mask_dir/mm_$phase_nb.mhd
+ combine_image $vf_midp_in $vf_midp_out $vf_midp $mask_dir/${mask_type}_$phase_nb.mhd
clitkZeroVF -i $vf_midp -o vf_zero.mhd
- clitkCombineImage -i $vf_midp -j vf_zero.mhd -o $vf_midp -m $mask_dir/patient_mask_$phase_nb.mhd
+ combine_image $vf_midp vf_zero.mhd $vf_midp $mask_dir/patient_mask_$phase_nb.mhd
midp=$midp_dir/midp_$phase_nb.mhd
clitkWarpImage -i $phase_file -o $midp --vf=$vf_midp -s 1
create_mhd_4D_pattern.sh $midp_dir/vf_outside_midp_
echo "Calculating midp_avg.mhd..."
- clitkAverageTemporalDimension -i $midp_dir/midp_4D.mhd -o $midp_dir/midp_avg.mhd
+ average_temporal_dimension $midp_dir/midp_4D.mhd $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_*
-
echo
echo "-------- Mid-position done ! --------"
end=`date`
extract_4d_phases_ref $mhd4d $ref_phase
if [ "$step" == "mask" -o "$step" == "all" ]; then
- motion_mask $mhd4d $mask_interpolation_spacing $mask_interpolation_algorithm
+ motion_mask $mhd4d $mask_type $mask_interpolation_spacing $mask_interpolation_algorithm
fi
if [ "$step" == "registration" -o "$step" == "all" ]; then
- registration
+ if [ "$mask_type" == "mm" ]; then
+ registration
+ elif [ "$mask_type" == "lungs" ]; then
+ registration
+ elif [ "$mask_type" == "patient" ]; then
+ registration_no_motion_mask
+ midp_combined_vf=1
+ fi
fi
-midp_combined_vf=0
if [ "$step" == "midp" -o "$step" == "all" ]; then
if [ $midp_combined_vf = 0 ]; then
midp_in_out
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff