#!/bin/bash
#
# Developed by Fred Weinhaus 9/13/2007 .......... revised 4/25/2015
#
# ------------------------------------------------------------------------------
# 
# Licensing:
# 
# Copyright © Fred Weinhaus
# 
# My scripts are available free of charge for non-commercial use, ONLY.
# 
# For use of my scripts in commercial (for-profit) environments or 
# non-free applications, please contact me (Fred Weinhaus) for 
# licensing arrangements. My email address is fmw at alink dot net.
# 
# If you: 1) redistribute, 2) incorporate any of these scripts into other 
# free applications or 3) reprogram them in another scripting language, 
# then you must contact me for permission, especially if the result might 
# be used in a commercial or for-profit environment.
# 
# My scripts are also subject, in a subordinate manner, to the ImageMagick 
# license, which can be found at: http://www.imagemagick.org/script/license.php
# 
# ------------------------------------------------------------------------------
# 
####
#
# USAGE: isonoise [-r radius] [-t threshold] infile outfile
# USAGE: isonoise [-h or -help]
#
# OPTIONS:
#
# -r              radius         radius of filter; default=1
# -t              threshold      threshold percentage for separating noise from image; 
#                                (default=10)
# -h or -help                    get help
#
###
#
# NAME: ISONOISE 
# 
# PURPOSE: To reduce isolated noise in an image. 
# 
# DESCRIPTION: ISONOISE is a noise filter designed to try to 
# reduce impulse or isolated (sparce) noise in an image. It works by  
# using the median filtered image where it assesses that noise is  
# present and the original image where it assesses that no noise is 
# present.
# 
# Arguments: 
#
# -h or -help    ---  displays help information. 
# 
# -r     radius       radius is an integer >=1. It determines the neighborhood of pixels
# to use to compute the median at each pixel in the image. A radius=1 means use a 3x3 
# neighborhood about each pixel. A radius=2 means use a 5x5 neighborhood about each 
# pixel. The larger the radius, the longer the processing and the more blurring that 
# will occur. Noise filters generally trade some degree or blurring for noise reduction.
# 
#
# -t     threshold    threshold is in percent (without % symbol) and determines how much 
# of the image is assessed to be noise. A smaller threshold, will reduce noise more 
# effectively but cause more blurring. On the other hand, a larger threshold will 
# produce reduce noise less effectively, but cause less blurring.
# 
# 
######


# set default value for radius and threshold
radius=1
thresh=10

# set directory for temporary files
dir="."    # suggestions are dir="." or dir="/tmp"


# set up functions to report Usage and Usage with Description
PROGNAME=`type $0 | awk '{print $3}'`  # search for executable on path
PROGDIR=`dirname $PROGNAME`            # extract directory of program
PROGNAME=`basename $PROGNAME`          # base name of program
usage1() 
	{
	echo >&2 ""
	echo >&2 "$PROGNAME:" "$@"
	sed >&2 -e '1,/^####/d;  /^###/g;  /^#/!q;  s/^#//;  s/^ //;  4,$p' "$PROGDIR/$PROGNAME"
	}
usage2() 
	{
	echo >&2 ""
	echo >&2 "$PROGNAME:" "$@"
	sed >&2 -e '1,/^####/d;  /^######/g;  /^#/!q;  s/^#*//;  s/^ //;  4,$p' "$PROGDIR/$PROGNAME"
	}

# function to report error messages
errMsg()
	{
	echo ""
	echo $1
	echo ""
	usage1
	exit 1
	}

# function to test for minus at start of value of second part of option 1 or 2
checkMinus()
	{
	test=`echo "$1" | grep -c '^-.*$'`   # returns 1 if match; 0 otherwise
    [ $test -eq 1 ] && errMsg "$errorMsg"
	}


# test for correct number of arguments and get values
if [ $# -eq 0 ]
	then
	# help information
	echo ""
	usage2
	exit 0
elif [ $# -gt 6 ]
	then
	errMsg "--- TOO MANY ARGUMENTS WERE PROVIDED ---"
else
	while [ $# -gt 0 ]
		do
		# get parameters
		case "$1" in
	  -h|-help)    # help information
				   echo ""
				   usage2
				   ;;
			-r)    # radius
				   shift  # to get the next parameter - radius
				   # test if parameter starts with minus sign 
				   errorMsg="--- INVALID RADIUS SPECIFICATION ---"
				   checkMinus "$1"
				   radius=`expr "$1" : '\([0-9]*\)'`
				   [ "$radius" = "" ] && errMsg "--- RADIUS=$radius MUST BE AN INTEGER ---"
				   radiustest=`echo "$radius < 1" | bc`
				   [ $radiustest -eq 1 ] && errMsg "--- RADIUS=$radius MUST BE AN INTEGER GREATER THAN 0 ---"
				   ;;
			-t)    # threshold
				   shift  # to get the next parameter - threshold
				   # test if parameter starts with minus sign 
				   errorMsg="--- INVALID THRESHOLD SPECIFICATION ---"
				   checkMinus "$1"
				   thresh=`expr "$1" : '\([.0-9]*\)'`
				   [ "$thresh" = "" ] && errMsg "--- THRESH=$thresh MUST BE A POSITIVE FLOATING POINT VALUE (with no sign) ---"
				   threshtestA=`echo "$thresh < 0" | bc`
				   threshtestB=`echo "$thresh > 100" | bc`
				   [ $threshtestA -eq 1 -o $threshtestB -eq 1 ] && errMsg "--- THRESH=$thresh MUST BE A POSITIVE FLOATING POINT VALUE BETWEEN 0 AND 100 ---"
				   ;;
			 -)    # STDIN and end of arguments
				   break
				   ;;
			-*)    # any other - argument
				   errMsg "--- UNKNOWN OPTION ---"
				   ;;
			*)     # end of arguments
				   break
				   ;;
		esac
		shift   # next option
	done
	#
	# get infile and outfile
	infile="$1"
	outfile="$2"
fi

# test that infile provided
[ "$infile" = "" ] && errMsg "NO INPUT FILE SPECIFIED"
# test that outfile provided
[ "$outfile" = "" ] && errMsg "NO OUTPUT FILE SPECIFIED"

# setup temporary images and auto delete upon exit
# use mpc/cache to hold input image temporarily in memory
tmpA="$dir/isonoise_$$.mpc"
tmpB="$dir/isonoise_$$.cache"
tmp0="$dir/isonoise_0_$$.png"
tmp1="$dir/isonoise_1_$$.png"
trap "rm -f $tmpA $tmpB $tmp0 $tmp1;" 0
trap "rm -f $tmpA $tmpB $tmp0 $tmp1; exit 1" 1 2 3 15
trap "rm -f $tmpA $tmpB $tmp0 $tmp1; exit 1" ERR


#correct for change in median at IM 6.6.8-6 from radius to widthxheight
#and to go from -median to -statistic median
im_version=`convert -list configure | \
	sed '/^LIB_VERSION_NUMBER */!d;  s//,/;  s/,/,0/g;  s/,0*\([0-9][0-9]\)/\1/g' | head -n 1`
if [ "$im_version" -ge "06060806" ]; then
	radius=$((2*$radius+1))
	proc="-statistic median"
else
	proc="-median"
fi


# process data
# create median filtered version
# get absolute difference image between input and median
# threshold the difference image to locate the noise areas
# multiply median by threshold, original by complement of threshold, and then add results together
#
if convert -quiet "$infile" +repage "$tmpA"
	then
	convert $tmpA $proc $radius $tmp0
	convert $tmpA $tmp0 -compose Difference -composite -threshold $thresh% $tmp1
	convert $tmpA $tmp0 $tmp1 -compose src -composite "$outfile"
else
	errMsg "--- FILE $infile DOES NOT EXIST OR IS NOT AN ORDINARY FILE, NOT READABLE OR HAS ZERO SIZE ---"
fi
exit 0