diff options
| -rwxr-xr-x | scripts/process-video-beta | 68 |
1 files changed, 41 insertions, 27 deletions
diff --git a/scripts/process-video-beta b/scripts/process-video-beta index 3b80ec3..560b7aa 100755 --- a/scripts/process-video-beta +++ b/scripts/process-video-beta @@ -5,18 +5,19 @@ cat << EOF usage: $0 options OPTIONS: - -h Show this message - -v Video location - -l Crop list - -t Type of video being processed - -n Set number to start - -d output directory - -V verbose mode - -1 Execute Stage 1: Extraction and Cropping - -2 Execute Stage 2: Deriving Backgrounds - -3 Execute Stage 3: Mask Generation and Filtration - -4 Execute Stage 4: Generating Feature Vector - -S Server list - following the GNU Parallel convention [ncpu/]sshlogin[,[ncpu/]sshlogin[,...]] + -h Show this message + -v Video location + -l Crop list + -t Type of video being processed + -n Set number to start + -d output directory + -V verbose mode + -1 Execute Stage 1: Extraction and Cropping + -2 Execute Stage 2: Deriving Backgrounds + -3 Execute Stage 3: Mask Generation + -4 Execute Stage 4: Filteration + -5 Execute Stage 5: Generating Feature Vector + -S Server list - following the GNU Parallel convention [ncpu/]sshlogin[,[ncpu/]sshlogin[,...]] Copyright 2012 Calvin Morrison EOF @@ -39,10 +40,11 @@ stage_1= stage_2= stage_3= stage_4= +stage_5= server_list= -while getopts "ht:n:l:d:v:S:V1234" OPTION +while getopts "ht:n:l:d:v:S:V12354" OPTION do case $OPTION in h) @@ -64,6 +66,9 @@ do v) video_file=$OPTARG ;; + 5) + stage_5=5 + ;; 1) stage_1=1 ;; @@ -99,13 +104,14 @@ fi # if there are no stages set, execute them all -if [[ -z $stage_1 ]] && [[ -z $stage_2 ]] && [[ -z $stage_3 ]] && [[ -z $stage_4 ]] +if [[ -z $stage_1 ]] && [[ -z $stage_2 ]] && [[ -z $stage_3 ]] && [[ -z $stage_4 ]] && [[ -z $stage_5 ]] then log "no stages set - running all stages" stage_1=1 stage_2=1 stage_3=1 stage_4=1 + stage_5=1 fi @@ -178,7 +184,8 @@ fi if [[ $stage_2 -eq 1 ]]; then echo "Stage 2: Deriving Backgrounds" - parallel --xapply -v -j +0 -S $server_list -q "derivebackground.py <(find $output_dir"/Cropped/"{}"/"*) $output_dir/Masks/{}/Background.png" ::: $set_list + parallel -S $server_list find $output_dir/Cropped/{}/*.png \| head -n 3000 \> input_{}.txt ::: $set_list + parallel --xapply -v -j +0 -S $server_list derive-background -i input_{}.txt -o $output_dir/Masks/{}/Background.png ::: $set_list fi @@ -192,24 +199,31 @@ while read crop; do echo "Stage 3: Generating Masks" cd $output_dir/Cropped/$setname - - log $server_list - #parallel -i convert -composite -compose Difference {} $output_dir/Masks/$setname/Background.png -contrast-stretch 90%x%0% -threshold 30% $output_dir/Masks/$setname/Masks/{} -- *.png - find `pwd`/*.png | parallel -v -j +0 -S $server_list convert \\\( -composite -compose Difference $output_dir/Masks/$setname/Background.png {} \\\) \\\( -contrast-stretch 90%x0% \\\) \\\( -threshold 30% \\\) $output_dir/Masks/$setname/Masks/{/} - - # Filtering Stage - cd $output_dir - #parallel -i FlyTrackingIterativeFilter {} 15 $output_dir/Masks/$setname/Masks/ $output_dir/Filtered/$setname/ -- $( ls $output_dir/Masks/$setname/Masks/ ) - ls $output_dir/Masks/$setname/Masks/ | parallel -v -j +0 -S $server_list /site/kuiper/jcm357/FilterFlyMask {} 15 $output_dir/Masks/$setname/Masks/ $output_dir/Filtered/$setname/ - i=$(( $i + 1 )) + mask-generator -i <(find $output_dir/Cropped/$setname/*.png) -b $output_dir/Masks/$setname/Background.png -o $output_dir/Masks/$setname/Masks/ + #find `pwd`/*.png | parallel -v -j +0 -S $server_list convert \\\( -composite -compose Difference $output_dir/Masks/$setname/Background.png {} \\\) \\\( -contrast-stretch 90%x0% \\\) \\\( -threshold 30% \\\) $output_dir/Masks/$setname/Masks/{/} + done < $crop_file fi - if [[ $stage_4 -eq 1 ]]; then +i=$set_number + +while read crop; do + + setname=$set_type$i + + #Usage: FilterFlyMask -f <image filename> -r <ratio> -m <mask location> -o <outputFolderName> + + ls $output_dir/Masks/$setname/Masks/ | parallel -v -j +0 -S $server_list FilterFlyMask -f {} -r 15 -m $output_dir/Masks/$setname/Masks/ -o $output_dir/Filtered/$setname/ + i=$(( $i + 1 )) + +done < $crop_file + +fi +if [[ $stage_5 -eq 1 ]]; then i=$set_number while read crop; do @@ -218,7 +232,7 @@ while read crop; do echo "Stage 4: Generating the Feature Vector" # executablename <inputFile.txt> <originalImagePath> <finalOutputPath> <maskImagePath> <outputFilePrefix> - FlyTracking <(ls $output_dir/Filtered/$setname/final/) $output_dir/Cropped/$setname/ $output_dir/Final/$setname/ $output_dir/Filtered/$setname/final/ $setname & + FlyTracking <(ls $output_dir/Filtered/$setname/final/) $output_dir/Filtered/$setname/final/ $output_dir/Final/$setname/ $output_dir/Filtered/$setname/final/ $setname & i=$(($i + 1)) done < $crop_file |