3 ###############################################################################
5 # FILE: create_midP-2.0.sh
6 # AUTHOR: RĂ´mulo Pinho 05/08/2011
8 # Version 2.0 of the create_midP_masks.sh script. The most relevant changes are:
9 # * creation of bands around input and output image regions to try to improve
10 # the registration along lung boundaries (naturally, it depends on the quality
11 # of motion mask generation).
12 # * some steps are now in different modules, to facilitate re-use (see "includes" section).
13 # * minor modifications on output file names.
14 # * attempt to simplify the code a bit.
16 ###############################################################################
18 source `dirname $0`/midp_common.sh
22 echo "$phase_file -> Extracting patient..."
23 clitkExtractPatient -i $phase_file -o $mask_dir_tmp/patient_mask_$phase_nb.mhd --noAutoCrop -a $afdb_file $ExtractPatientExtra
24 # abort_on_error clitkExtractPatient $?
26 clitkSetBackground -i $phase_file -o $mask_dir_tmp/patient_$phase_nb.mhd --mask $mask_dir_tmp/patient_mask_$phase_nb.mhd --outsideValue -1000
27 # abort_on_error clitkSetBackground $?
32 if [ x = x$ExtractBonesLower1 ]; then
33 ExtractBonesLower1=120
35 if [ x = x$ExtractBonesLower2 ]; then
38 echo "$phase_file -> Extracting bones..."
39 clitkImageConvert -i $phase_file -o $mask_dir_tmp/float_$phase_nb.mhd -t float
40 clitkExtractBones -i $mask_dir_tmp/float_$phase_nb.mhd -o $mask_dir_tmp/bones_$phase_nb.mhd -a $afdb_file --lower1 $ExtractBonesLower1 --upper1 2000 --lower2 $ExtractBonesLower2 --upper2 2000 --smooth --time 0.0625 --noAutoCrop
45 echo "$phase_file -> Extracting lungs..."
46 clitkExtractLung -i $phase_file -o $mask_dir_tmp/lungs_$phase_nb.mhd -a $afdb_file --noAutoCrop --doNotSeparateLungs --type 1
53 echo "$phase_file -> Resampling..."
54 clitkResampleImage -i $mask_dir_tmp/patient_$phase_nb.mhd -o $mask_dir_tmp/patient_$phase_nb.mhd --spacing $resample_spacing --interp $resample_algo
55 clitkResampleImage -i $mask_dir_tmp/patient_mask_$phase_nb.mhd -o $mask_dir_tmp/patient_mask_$phase_nb.mhd --spacing $resample_spacing --interp $resample_algo
56 if [ "$mask_type" != "patient" ]; then
57 clitkResampleImage -i $mask_dir_tmp/lungs_$phase_nb.mhd -o $mask_dir_tmp/lungs_$phase_nb.mhd --like $mask_dir_tmp/patient_$phase_nb.mhd
59 if [ "$mask_type" == "mm" ]; then
60 clitkResampleImage -i $mask_dir_tmp/bones_$phase_nb.mhd -o $mask_dir_tmp/bones_$phase_nb.mhd --like $mask_dir_tmp/patient_$phase_nb.mhd
66 if [ x = x$MotionMaskOffsetDetect ]; then
67 MotionMaskOffsetDetect="0,-5,0"
69 if [ x = x$FillingLevel ]; then
73 clitkMotionMask -i $mask_dir_tmp/patient_$phase_nb.mhd -o $mask_dir_tmp/mm_$phase_nb.mhd --featureLungs $mask_dir_tmp/lungs_$phase_nb.mhd --upperThresholdLungs -400 --featureBones $mask_dir_tmp/bones_$phase_nb.mhd --fillingLevel $FillingLevel --offsetDetect $MotionMaskOffsetDetect --pad --writeFeature $mask_dir_tmp/feature_$phase_nb.mhd $MotionMaskExtra
74 #--monitor=$mask_dir_tmp/monitor_$phase_nb.mhd
85 input_dir=`dirname $input`
86 input_base=`basename $input`
89 clitkMorphoMath -i $input_mask -o $input_dir/extra1_$input_base --type 1 --radius $radius
90 clitkImageArithm -i $input_dir/extra1_$input_base -j $input_mask -o $input_dir/band1_$input_base -t 7
91 clitkBinarizeImage -i $input_dir/band1_$input_base -o $input_dir/band1_$input_base -l 1 -u 1 --fg 100 --mode both
92 clitkImageConvert -i $input_dir/band1_$input_base -o $input_dir/short_band1_$input_base -t short
95 clitkMorphoMath -i $input_dir/extra1_$input_base -o $input_dir/extra2_$input_base --type 1 --radius $radius
96 clitkImageArithm -i $input_dir/extra2_$input_base -j $input_dir/extra1_$input_base -o $input_dir/band2_$input_base -t 7
97 clitkBinarizeImage -i $input_dir/band2_$input_base -o $input_dir/band2_$input_base -l 1 -u 1 --fg 200 --mode both
98 clitkImageConvert -i $input_dir/band2_$input_base -o $input_dir/short_band2_$input_base -t short
100 # combine bands with masks
101 clitkImageArithm -i $input_mask -j $input_dir/band1_$input_base -o $output_mask -t 0
102 clitkImageArithm -i $output_mask -j $input_dir/band2_$input_base -o $output_mask -t 0
103 # combine bands with image
104 combine_image $input_dir/short_band1_$input_base $input $output $input_dir/band1_$input_base
105 combine_image $input_dir/short_band2_$input_base $output $output $input_dir/band2_$input_base
108 rm `echo $input_dir/extra?_$input_base | sed 's:.mhd:.*:g'`
109 rm `echo $input_dir/band?_$input_base | sed 's:.mhd:.*:g'`
110 rm `echo $input_dir/short_band?_$input_base | sed 's:.mhd:.*:g'`
113 create_registration_masks()
115 # extract inside and outside regions from the patient image,
116 # using the motion mask computed previously
117 echo "$phase_file -> Setting Background..."
118 clitkSetBackground -i $mask_dir_tmp/patient_$phase_nb.mhd -o $mask_dir_tmp/inside_$phase_nb.mhd --mask $mask_dir_tmp/${mask_type}_$phase_nb.mhd --outsideValue -1200
119 clitkSetBackground -i $mask_dir_tmp/patient_$phase_nb.mhd -o $mask_dir_tmp/outside_$phase_nb.mhd --mask $mask_dir_tmp/${mask_type}_$phase_nb.mhd --outsideValue -1200 --fg
121 # the registration masks for inside (and outside) region correspond
122 # to the motion mask (and its complement) plus extra grey value bands,
123 # obtained with morphological dilations.
125 echo "$phase_file -> Creating registration masks..."
127 clitkMorphoMath -i $mask_dir_tmp/${mask_type}_$phase_nb.mhd -o $mask_dir_tmp/mask_inside_$phase_nb.mhd --type 1 --radius 8
128 create_banded_mask $mask_dir_tmp/inside_$phase_nb.mhd $mask_dir_tmp/${mask_type}_$phase_nb.mhd $mask_dir_tmp/banded_inside_$phase_nb.mhd $mask_dir_tmp/banded_mask_inside_$phase_nb.mhd 4
130 clitkBinarizeImage -i $mask_dir_tmp/outside_$phase_nb.mhd -o $mask_dir_tmp/${mask_type}_outside_$phase_nb.mhd -l -999 -u 4000 --mode both
131 #clitkExtractPatient -i $mask_dir_tmp/outside_$phase_nb.mhd -o $mask_dir_tmp/${mask_type}_outside_$phase_nb.mhd --noAutoCrop
132 clitkMorphoMath -i $mask_dir_tmp/${mask_type}_outside_$phase_nb.mhd -o $mask_dir_tmp/mask_outside_$phase_nb.mhd --type 1 --radius 8
133 create_banded_mask $mask_dir_tmp/outside_$phase_nb.mhd $mask_dir_tmp/${mask_type}_outside_$phase_nb.mhd $mask_dir_tmp/banded_outside_$phase_nb.mhd $mask_dir_tmp/banded_mask_outside_$phase_nb.mhd 4
140 if [ "$mask_type" != "patient" ]; then
144 if [ "$mask_type" == "mm" ]; then
149 if [ $resample_spacing -ne 0 ] ; then
159 create_registration_masks
160 # if [ "$mask_type" == "mm" ]; then
161 # create_registration_motion_masks
162 # elif [ "$mask_type" == "lungs" ]; then
163 # create_registration_lung_masks
169 # the motion masks are first created in a tmp directory. this directory is
170 # later going to be renamed to the final motion mask directory. concurrent
171 # executions trying to create the same set of masks will be blocked until
172 # the first execution finishes. naturally, these other executions will not
173 # recreate the masks. so first we try to create the tmp directory.
174 # if the creation fails, it means that another execution is
175 # already creating the masks, so this execution will be blocked. the
176 # execution is unblocked only when the creation of masks is finished and
177 # the mask directory is renamed.
180 if [ -e $mask_dir ]; then
181 # check that the final mask dir exists and that it contains all files it needs.
182 # the check assumes that the inside and outside masks are the key files to exist.
184 nb_phases=${#phase_nbs[@]}
185 if [ "$mask_type" == "patient" ]; then
186 nb_masks=`ls $mask_dir/lungs_*.mhd | wc -l`
187 if [ $nb_masks != $nb_phases ]; then
188 # if the mask dir is invalid, remove it and recreate all masks, just in case.
189 rm -fr $mask_dir 2> /dev/null
193 nb_mm_masks=`ls $mask_dir/${mask_type}_outside*.mhd | wc -l`
194 nb_in_masks=`ls $mask_dir/mask_in*.mhd | wc -l`
195 nb_out_masks=`ls $mask_dir/mask_out*.mhd | wc -l`
196 if [ $nb_mm_masks != $nb_phases -o $nb_in_masks != $nb_phases -o $nb_out_masks != $nb_phases ]; then
197 # if the mask dir is invalid, remove it and recreate all masks, just in case.
198 rm -fr $mask_dir 2> /dev/null
204 if [ $do_mm = 1 ]; then
205 if ! mkdir $mask_dir_tmp 2> /dev/null; then
206 if [ ! -e $mask_dir_tmp ]; then
207 # if the temp dir couldn't be created, but it doesn't exist, abort
208 abort_on_error wait_mm_creation $? clean_up_masks
210 # assumes another process is creating the maks in the temp dir.
211 # now we need to wait until the masks are complete or until the
212 # time limit is reached.
215 max_wait=3600 # one hour
216 nb_files0=`ls $mask_dir_tmp/* | wc -l`
217 while [ ! -e $mask_dir -a $sleeping -le $max_wait ]; do
218 echo "waiting creation of motion masks..."
220 sleeping=$(( $sleeping + $interval ))
221 nb_files1=`ls $mask_dir_tmp/* | wc -l`
222 if [ $nb_files1 != $nb_files0 ]; then
228 if [ $sleeping -gt $max_wait ]; then
229 abort_on_error wait_mm_creation -1 clean_up_masks
231 echo "finished waiting"
241 #set cmd line variables
242 local mhd4d=`basename $1`
244 if [ $# -eq 4 ] ; then
255 # import variables specific to each patient
256 if test -e ./variables; then
260 #set other global variables
261 if [ $resample_spacing -ne 0 ] ; then
262 mask_dir="MASK-${resample_spacing}mm-$resample_algo"
266 mask_dir_tmp="tmp.$mask_dir"
267 extract_4d_phases $mhd4d
270 echo "------------ Motion mask from create_midP_masks.sh ------------"
278 # mask_dir_tmp=$mask_dir
279 if [ $do_mm == 1 ]; then
280 mask_log_dir=$mask_dir_tmp/LOG
281 mkdir -p $mask_log_dir
283 # multi-threaded pre-processing for motion mask calcs
285 for i in $( seq 0 $((${#phase_nbs[@]} - 1))); do
286 phase_nb=${phase_nbs[$i]}
287 phase_file=${phase_files[$i]}
288 afdb_file=`echo $phase_file | sed 's/mhd/afdb/'`
290 check_threads $MAX_THREADS
292 pids=( "${pids[@]}" "$!" )
296 for ret in $ret_codes; do
297 abort_on_error mm_preprocessing $ret clean_up_masks
300 if [ "$mask_type" == "mm" ]; then
301 # single-threaded motion mask calc
302 for i in $( seq 0 $((${#phase_nbs[@]} - 1))); do
303 phase_nb=${phase_nbs[$i]}
304 phase_file=${phase_files[$i]}
307 echo "$phase_file -> Computing motion mask..."
308 compute_motion_mask > $mask_log_dir/motion_mask_$phase_file.log
309 abort_on_error compute_motion_mask $? clean_up_masks
313 # multi-threaded post-processing of motion mask calcs
314 if [ "$mask_type" != "patient" ]; then
316 for i in $( seq 0 $((${#phase_nbs[@]} - 1))); do
317 phase_nb=${phase_nbs[$i]}
318 phase_file=${phase_files[$i]}
320 check_threads $MAX_THREADS
322 pids=( "${pids[@]}" "$!" )
326 for ret in $ret_codes; do
327 abort_on_error mm_postprocessing $ret clean_up_masks
331 # rename tmp mask directory after mask creation
333 mv -f $mask_dir_tmp $mask_dir
337 echo "-------- Motion mask done ! ---------"
349 if [ $# -ne 4 -a $# -ne 2 -a $# -ne 1 ]; then
350 echo "Usage: $0 CT_4D TYPE [RESAMPLE_SPACING RESAMPLE_ALGORITHM]"
351 echo " TYPE: \"mm\" (traditional motion masks); \"lungs\" (lung masks); \"patient\" (patient mask only)"
356 # variables exported in this scope
358 # mask_dir: directory where all masks are kept
361 if [ $1 != "using-as-lib" ]; then
362 if [ $# -eq 4 ] ; then
363 motion_mask $1 $2 $3 $4
364 elif [ $# -eq 2 ] ; then