diff options
Diffstat (limited to 'scripts')
| -rwxr-xr-x | scripts/batch-process | 67 | ||||
| -rwxr-xr-x | scripts/process-video-beta | 229 |
2 files changed, 296 insertions, 0 deletions
diff --git a/scripts/batch-process b/scripts/batch-process new file mode 100755 index 0000000..bdd67a9 --- /dev/null +++ b/scripts/batch-process @@ -0,0 +1,67 @@ +#!/bin/sh +usage() +{ +cat << EOF +usage: $0 options + +OPTIONS: + -h Show this message + -i Input file + -V verbose mode + +Input file should contain the following format: + +VideoType:VideoLocation:StartNumber:CropList + +Ex First10MinSet:/path/to/video/First10MinGroup8:68:First10MinGroup8CropList.txt + +Copyright 2012 Calvin Morrison +EOF +} + +function log () { + if [[ $verbose -eq 1 ]]; then + echo "$@" + fi +} + +# Declaration of Variables +verbose= +input_file= + +while getopts "Vhi:" OPTION +do + case $OPTION in + h) + usage + exit 1 + ;; + V) + verbose=1 + ;; + i) + input_file=$OPTARG + ;; + ?) + usage + exit + ;; + esac +done + + +if [[ -z $input_file ]] +then + usage + exit 1 +fi + +if [ -f "$input_file" ]; then + log "$input_file exists." +else + echo "error: $input_file was not found" + exit 1 +fi + + + diff --git a/scripts/process-video-beta b/scripts/process-video-beta new file mode 100755 index 0000000..97aeffa --- /dev/null +++ b/scripts/process-video-beta @@ -0,0 +1,229 @@ +#!/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 + |