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
82 registration_blutdir $reference_out $target_out $mask_ref_out $mask_targ_out $vf_out $result_out $params $log_out $coeff_out
83 elif [ "$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}_
135 create_mhd_4D_pattern.sh $vf_dir/coeff_inside_${ref_phase_nb}_ _0
136 create_mhd_4D_pattern.sh $vf_dir/coeff_outside_${ref_phase_nb}_ _0
138 # create 4D result image
139 create_mhd_4D_pattern.sh $output_dir/result_inside_${ref_phase_nb}_
140 create_mhd_4D_pattern.sh $output_dir/result_outside_${ref_phase_nb}_
141 create_mhd_4D_pattern.sh $output_dir/result_${ref_phase_nb}_
144 echo "-------- Registration done ! --------"
154 echo "----------- Mid-position ------------"
161 ########### calculate the midp wrt the reference phase
162 phase_nb=$ref_phase_nb
163 echo "Calculating midp_$phase_nb.mhd..."
164 vf_midp=$midp_dir/vf_midp_$phase_nb.mhd
165 midp=$midp_dir/midp_$phase_nb.mhd
166 # average the vf's from reference phase to phase
167 clitkAverageTemporalDimension -i $vf_dir/vf_${ref_phase_nb}_4D.mhd -o $vf_midp
168 abort_on_error midp $? clean_up_midp
170 # invert the vf (why?)
171 clitkInvertVF -i $vf_midp -o $vf_midp
172 abort_on_error midp $? clean_up_midp
174 # create the midp by warping the reference phase with the reference vf
175 clitkWarpImage -i $ref_phase_file -o $midp --vf=$vf_midp -s 1
176 abort_on_error midp $? clean_up_midp
180 clitkImageConvert -i $ref_midp -o $ref_midp -t float
181 abort_on_error midp $? clean_up_midp
183 ########### calculate the midp wrt the other phases
184 for i in $( seq 0 $((${#phase_files[@]} - 1))); do
185 phase_file=${phase_files[$i]}
186 phase_nb=${phase_nbs[$i]}
187 vf_midp=$midp_dir/vf_midp_$phase_nb.mhd
188 midp=$midp_dir/midp_$phase_nb.mhd
190 if [ "$phase_nb" != "$ref_phase_nb" ]; then
191 echo "Calculating midp_$phase_nb.mhd..."
192 # calculate vf from phase to midp, using the vf from reference phase to midp (-i)
193 # and the vf from reference phase to phase (-j)
194 clitkComposeVF -i $ref_vf_midp -j $vf_dir/vf_$ref_phase_nb\_$phase_nb.mhd -o $vf_midp
195 abort_on_error midp $? clean_up_midp
197 clitkWarpImage -i $phase_file -o $midp --vf=$vf_midp -s 1
198 abort_on_error midp $? clean_up_midp
200 clitkImageConvert -i $midp -o $midp -t float
201 abort_on_error midp $? clean_up_midp
206 create_mhd_4D_pattern.sh $midp_dir/midp_
207 create_mhd_4D_pattern.sh $midp_dir/vf_midp_
209 echo "Calculating midp_avg.mhd..."
210 clitkAverageTemporalDimension -i $midp_dir/midp_4D.mhd -o $midp_dir/midp_avg.mhd
211 abort_on_error midp $? clean_up_midp
213 echo "Calculating midp_med.mhd..."
214 clitkMedianTemporalDimension -i $midp_dir/midp_4D.mhd -o $midp_dir/midp_med.mhd
215 abort_on_error midp $? clean_up_midp
221 echo "-------- Mid-position done ! --------"
231 echo "----------- Mid-position ------------"
238 ########### calculate the midp wrt the reference phase
239 phase_nb=$ref_phase_nb
240 phase_file=$ref_phase_file
241 echo "Calculating midp_$phase_nb.mhd..."
242 vf_midp_in=$midp_dir/vf_inside_midp_$phase_nb.mhd
243 vf_midp_out=$midp_dir/vf_outside_midp_$phase_nb.mhd
244 coeff_midp_in=$midp_dir/coeff_inside_midp_$phase_nb.mhd
245 coeff_midp_out=$midp_dir/coeff_outside_midp_$phase_nb.mhd
246 # average the vf's from reference phase to phase
247 # clitkAverageTemporalDimension -i $vf_dir/vf_inside_${ref_phase_nb}_4D.mhd -o $vf_midp_in
248 clitkAverageTemporalDimension -i $vf_dir/coeff_inside_${ref_phase_nb}_4D_0.mhd -o $coeff_midp_in
249 abort_on_error midp $? clean_up_midp
250 # clitkAverageTemporalDimension -i $vf_dir/vf_outside_${ref_phase_nb}_4D.mhd -o $vf_midp_out
251 clitkAverageTemporalDimension -i $vf_dir/coeff_outside_${ref_phase_nb}_4D_0.mhd -o $coeff_midp_out
252 abort_on_error midp $? clean_up_midp
255 # clitkInvertVF -i $vf_midp_in -o $vf_midp_in
256 clitkInvertVF -i $coeff_midp_in -o $vf_midp_in --type 1 --like $ref_phase_file
257 abort_on_error midp $? clean_up_midp
258 # clitkInvertVF -i $vf_midp_out -o $vf_midp_out
259 clitkInvertVF -i $coeff_midp_out -o $vf_midp_out --type 1 --like $ref_phase_file
260 abort_on_error midp $? clean_up_midp
262 # combine in and out VF's
263 ref_vf_midp_in=$vf_midp_in
264 ref_vf_midp_out=$vf_midp_out
265 vf_midp=$midp_dir/vf_midp_$phase_nb.mhd
266 clitkCombineImage -i $vf_midp_in -j $vf_midp_out -o $vf_midp -m $mask_dir/mm_$phase_nb.mhd
267 clitkZeroVF -i $vf_midp -o vf_zero.mhd
268 clitkCombineImage -i $vf_midp -j vf_zero.mhd -o $vf_midp -m $mask_dir/patient_mask_$phase_nb.mhd
270 # create the midp by warping the reference phase with the reference vf
271 midp=$midp_dir/midp_$phase_nb.mhd
272 clitkWarpImage -i $phase_file -o $midp --vf=$vf_midp -s 1
273 abort_on_error midp $? clean_up_midp
275 clitkImageConvert -i $midp -o $midp -t float
276 abort_on_error midp $? clean_up_midp
278 ########### calculate the midp wrt the other phases
279 for i in $( seq 0 $((${#phase_files[@]} - 1))); do
280 phase_file=${phase_files[$i]}
281 phase_nb=${phase_nbs[$i]}
282 vf_midp_in=$midp_dir/vf_inside_midp_$phase_nb.mhd
283 vf_midp_out=$midp_dir/vf_outside_midp_$phase_nb.mhd
285 if [ "$phase_nb" != "$ref_phase_nb" ]; then
286 echo "Calculating midp_$phase_nb.mhd..."
287 # calculate vf from phase to midp, using the vf from reference phase to midp (-i)
288 # and the vf from reference phase to phase (-j)
289 clitkComposeVF -i $ref_vf_midp_in -j $vf_dir/vf_inside_$ref_phase_nb\_$phase_nb.mhd -o $vf_midp_in
290 abort_on_error midp $? clean_up_midp
291 clitkComposeVF -i $ref_vf_midp_out -j $vf_dir/vf_outside_$ref_phase_nb\_$phase_nb.mhd -o $vf_midp_out
292 abort_on_error midp $? clean_up_midp
294 # combine in and out VF's
295 vf_midp=$midp_dir/vf_midp_$phase_nb.mhd
296 clitkCombineImage -i $vf_midp_in -j $vf_midp_out -o $vf_midp -m $mask_dir/mm_$phase_nb.mhd
297 clitkZeroVF -i $vf_midp -o vf_zero.mhd
298 clitkCombineImage -i $vf_midp -j vf_zero.mhd -o $vf_midp -m $mask_dir/patient_mask_$phase_nb.mhd
300 midp=$midp_dir/midp_$phase_nb.mhd
301 clitkWarpImage -i $phase_file -o $midp --vf=$vf_midp -s 1
302 abort_on_error midp $? clean_up_midp
304 clitkImageConvert -i $midp -o $midp -t float
305 abort_on_error midp $? clean_up_midp
312 create_mhd_4D_pattern.sh $midp_dir/midp_
313 create_mhd_4D_pattern.sh $midp_dir/vf_midp_
314 create_mhd_4D_pattern.sh $midp_dir/vf_inside_midp_
315 create_mhd_4D_pattern.sh $midp_dir/vf_outside_midp_
317 echo "Calculating midp_avg.mhd..."
318 clitkAverageTemporalDimension -i $midp_dir/midp_4D.mhd -o $midp_dir/midp_avg.mhd
319 abort_on_error midp $? clean_up_midp
321 echo "Calculating midp_med.mhd..."
322 clitkMedianTemporalDimension -i $midp_dir/midp_4D.mhd -o $midp_dir/midp_med.mhd
323 abort_on_error midp $? clean_up_midp
329 echo "-------- Mid-position done ! --------"
337 ######################### main
340 echo "Usage: create_midP-2.0.sh CT_4D REF_PHASE CONF_FILE"
345 echo "--------------- START ---------------"
346 begining=`date --rfc-3339=seconds`
347 # echo "beginning: $begining"
350 # variable declarations
359 mask_dir="MASK-${mask_interpolation_spacing}mm-$mask_interpolation_algorithm"
361 extract_4d_phases_ref $mhd4d $ref_phase
363 if [ "$step" == "mask" -o "$step" == "all" ]; then
364 motion_mask $mhd4d $mask_interpolation_spacing $mask_interpolation_algorithm
367 if [ "$step" == "registration" -o "$step" == "all" ]; then
372 if [ "$step" == "midp" -o "$step" == "all" ]; then
373 if [ $midp_combined_vf = 0 ]; then
381 echo "---------------- END ----------------"
382 terminating=`date --rfc-3339=seconds`
383 echo "beginning: $begining"
384 echo "terminating: $terminating"