# 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
+ use_coeffs=1
params="$nb_iter $nb_samples $sampling_algo $nb_hist_bins $nb_levels $bspline_spacing $metric $optimizer $interpolator"
# register all phases to the reference
vf_in=$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
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 $log_out
fi
done
- # create (zero) vf from reference to reference
+ # create (zero) vf from reference to reference and associated images
+ vf_in=$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
########### 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
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
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
# clean-up
- rm $midp_dir/vf_*
+ #rm $midp_dir/vf_*
echo
echo "-------- Mid-position done ! --------"