#!/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
    -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
}

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=
stage_5=

server_list=

while getopts "ht:n:l:d:v:S:V12354" 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
      ;;
		5) 
			stage_5=1
			;;
		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 ]] && [[ -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


# 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"
	log "creating directory structure"
	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

	# 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
	echo "Stage 1: Extracting Cropped PNGs"

	echo "$crop_list"
	echo "$set_list"

	parallel -v --progress --xapply -S $server_list mplayer -quiet -vo png:outdir=$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 -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

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 

  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/{/}
  i=$(($i + 1 )) 
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

	setname="$set_type$i"
	
	echo "Stage 4: Generating the Feature Vector" 

  #Usage: FlyTracking -i <inputFile.txt> -o <originalImagePath> -f <finalOutputPath> -m <maskImagePath> -p <outputFilePrefix>
  
  FlyTracking -i <(ls $output_dir/Filtered/$setname/final/) -o $output_dir/Filtered/$setname/final/ -f $output_dir/Final/$setname/ -m $output_dir/Filtered/$setname/final/ -p $setname -x -v &
  
	i=$(($i + 1)) 	
done < $crop_file

wait
fi