3 ###############################################################################
5 # FILE: create_midP-2.0.sh
6 # AUTHOR: RĂ´mulo Pinho 05/08/2011
8 # Version 2.0 of the create_midP.sh script. The most relevant changes are:
9 # * receives a .conf file as input, with variables related to the registration
10 # parameters and to paramters of the script itself (see accompanying midp_template.conf)
12 # * separates execution steps: it's now possible to choose which operation to execute
13 # (mask, registration, midp, or all).
14 # * some steps are now in different modules, to facilitate re-use (see "includes" section).
15 # * minor modifications on output file names.
16 # * attempt to simplify the code a bit.
18 ###############################################################################
20 ######################### includes
22 source `dirname $0`/create_midP_masks-2.0.sh using-as-lib 2 nn
23 source `dirname $0`/registration.sh
24 source `dirname $0`/midp_common.sh
29 echo "----------- Registration ------------"
37 # banded images may be created as separate files,
38 # with the specified preffix, which is interesting for debugging.
39 # if blank, it means that the original images (those without bands)
40 # will be used (see create_midP_masks-2.0.sh for details).
43 # params read from conf file
44 params="$nb_iter $nb_samples $sampling_algo $nb_hist_bins $nb_levels $bspline_spacing $metric $optimizer $interpolator"
46 # register all phases to the reference
47 for i in $( seq 0 $((${#phase_files[@]} - 1))); do
48 phase_file=${phase_files[$i]}
49 phase_nb=${phase_nbs[$i]}
51 if [ "$phase_nb" != "$ref_phase_nb" ]; then
53 reference_in=$mask_dir/${banded}inside_$ref_phase_nb.mhd
54 target_in=$mask_dir/${banded}inside_$phase_nb.mhd
55 mask_ref_in=$mask_dir/mask_inside_$ref_phase_nb.mhd
56 mask_targ_in=$mask_dir/mask_inside_$phase_nb.mhd
57 vf_in=$vf_dir/vf_inside_${ref_phase_nb}_$phase_nb.mhd
58 result_in=$output_dir/result_inside_${ref_phase_nb}_$phase_nb.mhd
59 log_in=$log_dir/log_inside_${ref_phase_nb}_$phase_nb.log
62 reference_out=$mask_dir/${banded}outside_$ref_phase_nb.mhd
63 target_out=$mask_dir/${banded}outside_$phase_nb.mhd
64 mask_ref_out=$mask_dir/mask_outside_$ref_phase_nb.mhd
65 mask_targ_out=$mask_dir/mask_outside_$phase_nb.mhd
66 vf_out=$vf_dir/vf_outside_$ref_phase_nb\_$phase_nb.mhd
67 result_out=$output_dir/result_outside_$ref_phase_nb\_$phase_nb.mhd
68 log_out=$log_dir/log_outside_${ref_phase_nb}_$phase_nb.log
71 if [ "$method" == "blutdir" ]; then
72 registration_blutdir $reference_in $target_in $mask_ref_in $mask_targ_in $vf_in $result_in $params $log_in
73 registration_blutdir $reference_out $target_out $mask_ref_out $mask_targ_out $vf_out $result_out $params $log_out
74 elif [ "$method" == "elastix" ]; then
75 registration_elastix $reference_in $target_in $mask_ref_in $mask_targ_in $vf_in $result_in $params $log_in
76 registration_elastix $reference_out $target_out $mask_ref_out $mask_targ_out $vf_out $result_out $params $log_out
79 motion_mask=$mask_dir/mm_$phase_nb.mhd
81 # combine in and out results
82 out_result=$output_dir/result_${ref_phase_nb}_$phase_nb.mhd
83 clitkCombineImage -i $result_in -j $result_out -m $motion_mask -o $out_result
84 abort_on_error registration $? clean_up_registration
86 # combine in and out vf
87 vf_result=$vf_dir/vf_${ref_phase_nb}_$phase_nb.mhd
88 clitkCombineImage -i $vf_in -j $vf_out -m $motion_mask -o $vf_result
89 abort_on_error registration $? clean_up_registration
91 clitkZeroVF -i $vf_in -o vf_zero.mhd
92 abort_on_error registration $? clean_up_registration
94 patient_mask=$mask_dir/patient_mask_$phase_nb.mhd
95 clitkCombineImage -i $vf_result -j vf_zero.mhd -m $patient_mask -o $vf_result
96 abort_on_error registration $? clean_up_registration
105 # create (zero) vf from reference to reference and associated images
106 vf_in=$vf_dir/vf_inside_${ref_phase_nb}_${ref_phase_nb}.mhd
107 vf_out=$vf_dir/vf_outside_${ref_phase_nb}_${ref_phase_nb}.mhd
108 clitkZeroVF -i $vf_ref -o $vf_dir/vf_${ref_phase_nb}_${ref_phase_nb}.mhd
109 clitkZeroVF -i $vf_ref -o $vf_in
110 clitkZeroVF -i $vf_ref -o $vf_out
111 abort_on_error registration $? clean_up_registration
113 motion_mask=$mask_dir/mm_${ref_phase_nb}.mhd
114 reference_in=$mask_dir/${banded}inside_${ref_phase_nb}.mhd
115 reference_out=$mask_dir/${banded}outside_$ref_phase_nb.mhd
116 out_result=$output_dir/result_${ref_phase_nb}_${ref_phase_nb}.mhd
117 clitkCombineImage -i $reference_in -j $reference_out -m $motion_mask -o $out_result
118 abort_on_error registration $? clean_up_registration
121 create_mhd_4D_pattern.sh $vf_dir/vf_${ref_phase_nb}_
122 create_mhd_4D_pattern.sh $vf_dir/vf_inside_${ref_phase_nb}_
123 create_mhd_4D_pattern.sh $vf_dir/vf_outside_${ref_phase_nb}_
125 # create 4D result image
126 create_mhd_4D_pattern.sh $output_dir/result_inside_${ref_phase_nb}_
127 create_mhd_4D_pattern.sh $output_dir/result_outside_${ref_phase_nb}_
128 create_mhd_4D_pattern.sh $output_dir/result_${ref_phase_nb}_
131 echo "-------- Registration done ! --------"
141 echo "----------- Mid-position ------------"
148 ########### calculate the midp wrt the reference phase
149 phase_nb=$ref_phase_nb
150 echo "Calculating midp_$phase_nb.mhd..."
151 vf_midp=$midp_dir/vf_midp_$phase_nb.mhd
152 midp=$midp_dir/midp_$phase_nb.mhd
153 # average the vf's from reference phase to phase
154 clitkAverageTemporalDimension -i $vf_dir/vf_${ref_phase_nb}_4D.mhd -o $vf_midp
155 abort_on_error midp $? clean_up_midp
157 # invert the vf (why?)
158 clitkInvertVF -i $vf_midp -o $vf_midp
159 abort_on_error midp $? clean_up_midp
161 # create the midp by warping the reference phase with the reference vf
162 clitkWarpImage -i $ref_phase_file -o $midp --vf=$vf_midp -s 1
163 abort_on_error midp $? clean_up_midp
167 clitkImageConvert -i $ref_midp -o $ref_midp -t float
168 abort_on_error midp $? clean_up_midp
170 ########### calculate the midp wrt the other phases
171 for i in $( seq 0 $((${#phase_files[@]} - 1))); do
172 phase_file=${phase_files[$i]}
173 phase_nb=${phase_nbs[$i]}
174 vf_midp=$midp_dir/vf_midp_$phase_nb.mhd
175 midp=$midp_dir/midp_$phase_nb.mhd
177 if [ "$phase_nb" != "$ref_phase_nb" ]; then
178 echo "Calculating midp_$phase_nb.mhd..."
179 # calculate vf from phase to midp, using the vf from reference phase to midp (-i)
180 # and the vf from reference phase to phase (-j)
181 clitkComposeVF -i $ref_vf_midp -j $vf_dir/vf_$ref_phase_nb\_$phase_nb.mhd -o $vf_midp
182 abort_on_error midp $? clean_up_midp
184 clitkWarpImage -i $phase_file -o $midp --vf=$vf_midp -s 1
185 abort_on_error midp $? clean_up_midp
187 clitkImageConvert -i $midp -o $midp -t float
188 abort_on_error midp $? clean_up_midp
193 create_mhd_4D_pattern.sh $midp_dir/midp_
194 create_mhd_4D_pattern.sh $midp_dir/vf_midp_
196 echo "Calculating midp_avg.mhd..."
197 clitkAverageTemporalDimension -i $midp_dir/midp_4D.mhd -o $midp_dir/midp_avg.mhd
198 abort_on_error midp $? clean_up_midp
200 echo "Calculating midp_med.mhd..."
201 clitkMedianTemporalDimension -i $midp_dir/midp_4D.mhd -o $midp_dir/midp_med.mhd
202 abort_on_error midp $? clean_up_midp
208 echo "-------- Mid-position done ! --------"
217 ######################### main
220 echo "Usage: create_midP-2.0.sh CT_4D REF_PHASE CONF_FILE"
225 echo "--------------- START ---------------"
226 begining=`date --rfc-3339=seconds`
227 # echo "beginning: $begining"
230 # variable declarations
239 mask_dir="MASK-${mask_interpolation_spacing}mm-$mask_interpolation_algorithm"
241 extract_4d_phases_ref $mhd4d $ref_phase
243 if [ "$step" == "mask" -o "$step" == "all" ]; then
244 motion_mask $mhd4d $mask_interpolation_spacing $mask_interpolation_algorithm
247 if [ "$step" == "registration" -o "$step" == "all" ]; then
251 if [ "$step" == "midp" -o "$step" == "all" ]; then
256 echo "---------------- END ----------------"
257 terminating=`date --rfc-3339=seconds`
258 echo "beginning: $begining"
259 echo "terminating: $terminating"