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 $0`/midp_common.sh
29 echo "----------- Registration ------------"
37 # banded images may be created as separate files,
38 # with the specified preffix, which is interesting for debugging.
39 # if blank, it means that the original images (those without bands)
40 # will be used (see create_midP_masks-2.0.sh for details).
43 # params read from conf file
45 params="$nb_iter $nb_samples $sampling_algo $nb_hist_bins $nb_levels $bspline_spacing $metric $optimizer $interpolator"
47 # register all phases to the reference
48 for i in $( seq 0 $((${#phase_files[@]} - 1))); do
49 phase_file=${phase_files[$i]}
50 phase_nb=${phase_nbs[$i]}
52 if [ "$phase_nb" != "$ref_phase_nb" ]; then
54 reference_in=$mask_dir/${banded}inside_$ref_phase_nb.mhd
55 target_in=$mask_dir/${banded}inside_$phase_nb.mhd
56 mask_ref_in=$mask_dir/mask_inside_$ref_phase_nb.mhd
57 mask_targ_in=$mask_dir/mask_inside_$phase_nb.mhd
58 vf_in=$vf_dir/vf_inside_${ref_phase_nb}_$phase_nb.mhd
59 result_in=$output_dir/result_inside_${ref_phase_nb}_$phase_nb.mhd
60 log_in=$log_dir/log_inside_${ref_phase_nb}_$phase_nb.log
61 if [ $use_coeffs = 1 ]; then
62 init_coeff_in=$coeff_in # empty at first iteration
63 coeff_in=$vf_dir/coeff_inside_${ref_phase_nb}_$phase_nb.mhd
67 reference_out=$mask_dir/${banded}outside_$ref_phase_nb.mhd
68 target_out=$mask_dir/${banded}outside_$phase_nb.mhd
69 mask_ref_out=$mask_dir/mask_outside_$ref_phase_nb.mhd
70 mask_targ_out=$mask_dir/mask_outside_$phase_nb.mhd
71 vf_out=$vf_dir/vf_outside_$ref_phase_nb\_$phase_nb.mhd
72 result_out=$output_dir/result_outside_$ref_phase_nb\_$phase_nb.mhd
73 log_out=$log_dir/log_outside_${ref_phase_nb}_$phase_nb.log
74 if [ $use_coeffs = 1 ]; then
75 init_coeff_out=$coeff_out # empty at first iteration
76 coeff_out=$vf_dir/coeff_outside_${ref_phase_nb}_$phase_nb.mhd
80 if [ "$method" == "blutdir" ]; then
81 registration_blutdir $reference_in $target_in $mask_ref_in $mask_targ_in $vf_in $result_in $params $log_in $coeff_in $init_coeff_in
82 registration_blutdir $reference_out $target_out $mask_ref_out $mask_targ_out $vf_out $result_out $params $log_out $coeff_out $init_coeff_out
83 elif [ "$method" == "elastix" ]; then
84 registration_elastix $reference_in $target_in $mask_ref_in $mask_targ_in $vf_in $result_in $params $log_in
85 registration_elastix $reference_out $target_out $mask_ref_out $mask_targ_out $vf_out $result_out $params $log_out
88 motion_mask=$mask_dir/mm_$phase_nb.mhd
90 # combine in and out results
91 out_result=$output_dir/result_${ref_phase_nb}_$phase_nb.mhd
92 clitkCombineImage -i $result_in -j $result_out -m $motion_mask -o $out_result
93 abort_on_error registration $? clean_up_registration
95 # combine in and out vf
96 vf_result=$vf_dir/vf_${ref_phase_nb}_$phase_nb.mhd
97 clitkCombineImage -i $vf_in -j $vf_out -m $motion_mask -o $vf_result
98 abort_on_error registration $? clean_up_registration
100 clitkZeroVF -i $vf_in -o vf_zero.mhd
101 abort_on_error registration $? clean_up_registration
103 patient_mask=$mask_dir/patient_mask_$phase_nb.mhd
104 clitkCombineImage -i $vf_result -j vf_zero.mhd -m $patient_mask -o $vf_result
105 abort_on_error registration $? clean_up_registration
114 # create (zero) vf from reference to reference and associated images
115 vf_in=$vf_dir/vf_inside_${ref_phase_nb}_${ref_phase_nb}.mhd
116 vf_out=$vf_dir/vf_outside_${ref_phase_nb}_${ref_phase_nb}.mhd
117 clitkZeroVF -i $vf_ref -o $vf_dir/vf_${ref_phase_nb}_${ref_phase_nb}.mhd
118 clitkZeroVF -i $vf_ref -o $vf_in
119 clitkZeroVF -i $vf_ref -o $vf_out
120 abort_on_error registration $? clean_up_registration
122 motion_mask=$mask_dir/mm_${ref_phase_nb}.mhd
123 reference_in=$mask_dir/${banded}inside_${ref_phase_nb}.mhd
124 reference_out=$mask_dir/${banded}outside_$ref_phase_nb.mhd
125 out_result=$output_dir/result_${ref_phase_nb}_${ref_phase_nb}.mhd
126 clitkCombineImage -i $reference_in -j $reference_out -m $motion_mask -o $out_result
127 abort_on_error registration $? clean_up_registration
130 create_mhd_4D_pattern.sh $vf_dir/vf_${ref_phase_nb}_
131 create_mhd_4D_pattern.sh $vf_dir/vf_inside_${ref_phase_nb}_
132 create_mhd_4D_pattern.sh $vf_dir/vf_outside_${ref_phase_nb}_
134 # create 4D result image
135 create_mhd_4D_pattern.sh $output_dir/result_inside_${ref_phase_nb}_
136 create_mhd_4D_pattern.sh $output_dir/result_outside_${ref_phase_nb}_
137 create_mhd_4D_pattern.sh $output_dir/result_${ref_phase_nb}_
140 echo "-------- Registration done ! --------"
150 echo "----------- Mid-position ------------"
157 ########### calculate the midp wrt the reference phase
158 phase_nb=$ref_phase_nb
159 echo "Calculating midp_$phase_nb.mhd..."
160 vf_midp=$midp_dir/vf_midp_$phase_nb.mhd
161 midp=$midp_dir/midp_$phase_nb.mhd
162 # average the vf's from reference phase to phase
163 clitkAverageTemporalDimension -i $vf_dir/vf_${ref_phase_nb}_4D.mhd -o $vf_midp
164 abort_on_error midp $? clean_up_midp
166 # invert the vf (why?)
167 clitkInvertVF -i $vf_midp -o $vf_midp
168 abort_on_error midp $? clean_up_midp
170 # create the midp by warping the reference phase with the reference vf
171 clitkWarpImage -i $ref_phase_file -o $midp --vf=$vf_midp -s 1
172 abort_on_error midp $? clean_up_midp
176 clitkImageConvert -i $ref_midp -o $ref_midp -t float
177 abort_on_error midp $? clean_up_midp
179 ########### calculate the midp wrt the other phases
180 for i in $( seq 0 $((${#phase_files[@]} - 1))); do
181 phase_file=${phase_files[$i]}
182 phase_nb=${phase_nbs[$i]}
183 vf_midp=$midp_dir/vf_midp_$phase_nb.mhd
184 midp=$midp_dir/midp_$phase_nb.mhd
186 if [ "$phase_nb" != "$ref_phase_nb" ]; then
187 echo "Calculating midp_$phase_nb.mhd..."
188 # calculate vf from phase to midp, using the vf from reference phase to midp (-i)
189 # and the vf from reference phase to phase (-j)
190 clitkComposeVF -i $ref_vf_midp -j $vf_dir/vf_$ref_phase_nb\_$phase_nb.mhd -o $vf_midp
191 abort_on_error midp $? clean_up_midp
193 clitkWarpImage -i $phase_file -o $midp --vf=$vf_midp -s 1
194 abort_on_error midp $? clean_up_midp
196 clitkImageConvert -i $midp -o $midp -t float
197 abort_on_error midp $? clean_up_midp
202 create_mhd_4D_pattern.sh $midp_dir/midp_
203 create_mhd_4D_pattern.sh $midp_dir/vf_midp_
205 echo "Calculating midp_avg.mhd..."
206 clitkAverageTemporalDimension -i $midp_dir/midp_4D.mhd -o $midp_dir/midp_avg.mhd
207 abort_on_error midp $? clean_up_midp
209 echo "Calculating midp_med.mhd..."
210 clitkMedianTemporalDimension -i $midp_dir/midp_4D.mhd -o $midp_dir/midp_med.mhd
211 abort_on_error midp $? clean_up_midp
217 echo "-------- Mid-position done ! --------"
227 echo "----------- Mid-position ------------"
234 ########### calculate the midp wrt the reference phase
235 phase_nb=$ref_phase_nb
236 phase_file=$ref_phase_file
237 echo "Calculating midp_$phase_nb.mhd..."
238 vf_midp_in=$midp_dir/vf_inside_midp_$phase_nb.mhd
239 vf_midp_out=$midp_dir/vf_outside_midp_$phase_nb.mhd
240 # average the vf's from reference phase to phase
241 clitkAverageTemporalDimension -i $vf_dir/vf_inside_${ref_phase_nb}_4D.mhd -o $vf_midp_in
242 abort_on_error midp $? clean_up_midp
243 clitkAverageTemporalDimension -i $vf_dir/vf_outside_${ref_phase_nb}_4D.mhd -o $vf_midp_out
244 abort_on_error midp $? clean_up_midp
246 # invert the vf (why?)
247 clitkInvertVF -i $vf_midp_in -o $vf_midp_in
248 abort_on_error midp $? clean_up_midp
249 clitkInvertVF -i $vf_midp_out -o $vf_midp_out
250 abort_on_error midp $? clean_up_midp
252 # combine in and out VF's
253 ref_vf_midp_in=$vf_midp_in
254 ref_vf_midp_out=$vf_midp_out
255 vf_midp=$midp_dir/vf_midp_$phase_nb.mhd
256 clitkCombineImage -i $vf_midp_in -j $vf_midp_out -o $vf_midp -m $mask_dir/mm_$phase_nb.mhd
257 clitkZeroVF -i $vf_midp -o vf_zero.mhd
258 clitkCombineImage -i $vf_midp -j vf_zero.mhd -o $vf_midp -m $mask_dir/patient_mask_$phase_nb.mhd
260 # create the midp by warping the reference phase with the reference vf
261 midp=$midp_dir/midp_$phase_nb.mhd
262 clitkWarpImage -i $phase_file -o $midp --vf=$vf_midp -s 1
263 abort_on_error midp $? clean_up_midp
265 clitkImageConvert -i $midp -o $midp -t float
266 abort_on_error midp $? clean_up_midp
268 ########### calculate the midp wrt the other phases
269 for i in $( seq 0 $((${#phase_files[@]} - 1))); do
270 phase_file=${phase_files[$i]}
271 phase_nb=${phase_nbs[$i]}
272 vf_midp_in=$midp_dir/vf_inside_midp_$phase_nb.mhd
273 vf_midp_out=$midp_dir/vf_outside_midp_$phase_nb.mhd
275 if [ "$phase_nb" != "$ref_phase_nb" ]; then
276 echo "Calculating midp_$phase_nb.mhd..."
277 # calculate vf from phase to midp, using the vf from reference phase to midp (-i)
278 # and the vf from reference phase to phase (-j)
279 clitkComposeVF -i $ref_vf_midp_in -j $vf_dir/vf_inside_$ref_phase_nb\_$phase_nb.mhd -o $vf_midp_in
280 abort_on_error midp $? clean_up_midp
281 clitkComposeVF -i $ref_vf_midp_out -j $vf_dir/vf_outside_$ref_phase_nb\_$phase_nb.mhd -o $vf_midp_out
282 abort_on_error midp $? clean_up_midp
284 # combine in and out VF's
285 vf_midp=$midp_dir/vf_midp_$phase_nb.mhd
286 clitkCombineImage -i $vf_midp_in -j $vf_midp_out -o $vf_midp -m $mask_dir/mm_$phase_nb.mhd
287 clitkZeroVF -i $vf_midp -o vf_zero.mhd
288 clitkCombineImage -i $vf_midp -j vf_zero.mhd -o $vf_midp -m $mask_dir/patient_mask_$phase_nb.mhd
290 midp=$midp_dir/midp_$phase_nb.mhd
291 clitkWarpImage -i $phase_file -o $midp --vf=$vf_midp -s 1
292 abort_on_error midp $? clean_up_midp
294 clitkImageConvert -i $midp -o $midp -t float
295 abort_on_error midp $? clean_up_midp
302 create_mhd_4D_pattern.sh $midp_dir/midp_
303 create_mhd_4D_pattern.sh $midp_dir/vf_midp_
304 create_mhd_4D_pattern.sh $midp_dir/vf_inside_midp_
305 create_mhd_4D_pattern.sh $midp_dir/vf_outside_midp_
307 echo "Calculating midp_avg.mhd..."
308 clitkAverageTemporalDimension -i $midp_dir/midp_4D.mhd -o $midp_dir/midp_avg.mhd
309 abort_on_error midp $? clean_up_midp
311 echo "Calculating midp_med.mhd..."
312 clitkMedianTemporalDimension -i $midp_dir/midp_4D.mhd -o $midp_dir/midp_med.mhd
313 abort_on_error midp $? clean_up_midp
319 echo "-------- Mid-position done ! --------"
327 ######################### main
330 echo "Usage: create_midP-2.0.sh CT_4D REF_PHASE CONF_FILE"
335 echo "--------------- START ---------------"
336 begining=`date --rfc-3339=seconds`
337 # echo "beginning: $begining"
340 # variable declarations
349 mask_dir="MASK-${mask_interpolation_spacing}mm-$mask_interpolation_algorithm"
351 extract_4d_phases_ref $mhd4d $ref_phase
353 if [ "$step" == "mask" -o "$step" == "all" ]; then
354 motion_mask $mhd4d $mask_interpolation_spacing $mask_interpolation_algorithm
357 if [ "$step" == "registration" -o "$step" == "all" ]; then
362 if [ "$step" == "midp" -o "$step" == "all" ]; then
363 if [ $midp_combined_vf = 0 ]; then
371 echo "---------------- END ----------------"
372 terminating=`date --rfc-3339=seconds`
373 echo "beginning: $begining"
374 echo "terminating: $terminating"