diff options
Diffstat (limited to 'process-video-beta')
| -rwxr-xr-x | process-video-beta | 229 |
1 files changed, 0 insertions, 229 deletions
diff --git a/process-video-beta b/process-video-beta deleted file mode 100755 index 97aeffa..0000000 --- a/process-video-beta +++ /dev/null @@ -1,229 +0,0 @@ -#!/bin/bash -usage() -{ -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[,...]] - -Copyright 2012 Calvin Morrison -EOF -} - -function log () { - if [[ $verbose -eq 1 ]]; then - echo "$@" - fi -} - -# Declaration of Variables -video_file= -crop_file= -set_type= -set_number= -output_dir= -start_dir=`pwd` -stage_1= -stage_2= -stage_3= -stage_4= - -server_list= - -while getopts "ht:n:l:d:v:S:V1234" OPTION -do - case $OPTION in - h) - usage - exit 1 - ;; - t) - set_type=$OPTARG - ;; - n) - set_number=$OPTARG - ;; - l) - crop_file=$OPTARG - ;; - d) - output_dir=$OPTARG - ;; - v) - video_file=$OPTARG - ;; - 1) - stage_1=1 - ;; - 2) - stage_2=1 - ;; - 3) - stage_3=1 - ;; - 4) - stage_4=1 - ;; - V) - verbose=1 - ;; - S) - server_list=$OPTARG - ;; - ?) - usage - exit - ;; - esac -done - - -# the bare minimum required for processing. -if [[ -z $video_file ]] || [[ -z $crop_file ]] || [[ -z $set_type ]] || [[ -z $set_number ]] || [[ -z $output_dir ]] -then - usage - exit 1 -fi - - -# if there are no stages set, execute them all -if [[ -z $stage_1 ]] && [[ -z $stage_2 ]] && [[ -z $stage_3 ]] && [[ -z $stage_4 ]] -then - log "no stages set - running all stages" - stage_1=1 - stage_2=1 - stage_3=1 - stage_4=1 -fi - - -# Check that the video exists, or else quit -if [ -f "$video_file" ]; then - log "$video_file exists." -else - echo "error: $video_file was not found" - exit 1 -fi - - -# Get absolute path of $output_dir OR create folder if it does not already exist -if [ -d "$output_dir" ]; then - cd $output_dir - output_dir=`pwd` -else - log "output directory $output_dir did not exist, creating now" - mkdir $output_dir -v - cd $output_dir - output_dir=`pwd` -fi - -cd $start_dir -log "full path of output_dir: $output_dir" - - -# set i; the set number to start at -i=$set_number - - -# check for the server list -if [[ -z $server_list ]]; then - log "no server specified, using localhost" - server_list=":" -fi - - -# Get the number of sets and the set range, as well as create directories -number_of_sets=`cat $crop_file | wc -l` -last_set=$(( $i + $number_of_sets - 1 )) -set_list= - -for num in $(seq $set_number $last_set); do - set_list=$set_list" $set_type$num" - mkdir $output_dir/Cropped/$set_type$num -pv - mkdir $output_dir/Masks/$set_type$num/Masks -pv - mkdir $output_dir/Final/$set_type$num/ -pv - mkdir $output_dir/Filtered/$set_type$num/final -pv -done - -while read crop; do - crop_list=$crop_list" $crop" -done < $crop_file -log "set_list $set_list" - - -# Stage 1: extract all of the pngs with Mplayer -if [[ $stage_1 -eq 1 ]]; then - - echo "Stage 1: Extracting Cropped PNGs" - - echo "$crop_list" - echo "$set_list" - - parallel -v --progress --xapply -S $server_list mplayer -quiet -vo png:prefix={1}"_":outdir=$output_dir/Cropped/{1} -nosound -vf crop={2} -speed 12 $video_file ::: $set_list ::: $crop_list - -fi - -# Stage 2: Deriving Backgrounds -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 - -fi - -if [[ $stage_3 -eq 1 ]]; then - -i=$set_number - -while read crop; do - - setname=$set_type$i - - 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 )) -done < $crop_file - -fi - - -if [[ $stage_4 -eq 1 ]]; then - -i=$set_number - -while read crop; do - - setname="$set_type$i" - - 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/ $setname & - - i=$(($i + 1)) -done < $crop_file - -wait -fi - |