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|
#!/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 -j 1 -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
|
