#!/bin/bash
#
# Developed by Fred Weinhaus 10/29/2008 .......... 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: isodatathresh [-g graph] infile outfile
# USAGE: isodatathresh [-help]
#
# OPTIONS:
#
# -g	  graph             graph specifies whether to generate a 
#                           histogram graph image displaying the 
#                           location and value of the threshold;
#                           choices are: view or save; 
#                           default is no graph
#
###
#
# NAME: ISODATATHRESH
# 
# PURPOSE: To automatically thresholds an image to binary (b/w) format 
# using the isodata technique.
# 
# DESCRIPTION: ISODATATHRESH automatically thresholds an image to binary
# (b/w) format. It assume the histogram is bimodal, i.e. is the composite
# of two bell-shaped distributions representing the foreground and
# background classes. The isodata appoach iteratively thresholds the
# image, computes the means of the foreground (above threshold data) and
# background (at and below threshold value), computes a new threshold
# equal to the average of these two means and repeats until there is no
# change in threshold between successive iterations. This script is 
# equivalent to the kmeansthresh script, but is implemented using image 
# masking rather than from the histogram of the image. It is faster 
# than the kmeansthresh script for smaller images. The timing transition 
# occurs for images somewhere between 1000-2000 pixels on a side.
# 
# OPTIONS: 
# 
# -g graph ... GRAPH specifies whether to generate a graph (image) of 
# the histogram, displaying the location and value of the threshold. 
# The choices are: view, save and none. If graph=view is selected, the 
# graph will be created and displayed automatically, but not saved. 
# If graph=save is selected, then the graph will be created and saved 
# to a file using the infile name, with "_histog_isodata.gif" appended,  
# but the graph will not be displayed automatically. If -g option is 
# not specified, then no graph will be created.
# 
# NOTE: It is highly recommended that the output not be specified 
# as a JPG image as that will cause compression and potentially a 
# non-binary (i.e. a graylevel) result. GIF is the recommended 
# output format.
# 
# REFERENCES: see the following:
# http://www.ph.tn.tudelft.nl/Courses/FIP/noframes/fip-Segmenta.html
# http://homepages.inf.ed.ac.uk/rbf/CVonline/LOCAL_COPIES/MORSE/threshold.pdf
# 
# CAVEAT: No guarantee that this script will work on all platforms, 
# nor that trapping of inconsistent parameters is complete and 
# foolproof. Use At Your Own Risk. 
# 
######
#

# set default values
graph=""		#none, save or view

# 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 4 ]
	then
	errMsg "--- TOO MANY ARGUMENTS WERE PROVIDED ---"
else
	while [ $# -gt 0 ]
		do
			# get parameter values
			case "$1" in
		  -h|-help)    # help information
					   echo ""
					   usage2
					   exit 0
					   ;;
				-g)    # get  graph
					   shift  # to get the next parameter
					   # test if parameter starts with minus sign 
					   errorMsg="--- INVALID GRAPH SPECIFICATION ---"
					   checkMinus "$1"
					   graph="$1"
					   [ "$graph" != "view" -a "$graph" != "save" ] && errMsg "--- GRAPH=$graph MUST BE EITHER VIEW OR SAVE ---"
					   ;;
				 -)    # 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"

# get outname from infile to use for graph
inname=`convert $infile -format "%t" info:`
histfile=${inname}_histog_isodata.gif

tmpA1="$dir/isodatathresh_1_$$.mpc"
tmpA2="$dir/isodatathresh_1_$$.cache"
tmpM1="$dir/isodatathresh_M_$$.mpc"
tmpM2="$dir/isodatathresh_M_$$.cache"
tmpL1="$dir/isodatathresh_L_$$.mpc"
tmpL2="$dir/isodatathresh_L_$$.cache"
tmpH1="$dir/isodatathresh_H_$$.mpc"
tmpH2="$dir/isodatathresh_H_$$.cache"
trap "rm -f $tmpA1 $tmpA2 $tmpM1 $tmpM2 $tmpL1 $tmpL2 $tmpH1 $tmpH2;" 0
trap "rm -f $tmpA1 $tmpA2 $tmpM1 $tmpM2 $tmpL1 $tmpL2 $tmpH1 $tmpH2 $histfile; exit 1" 1 2 3 15
trap "rm -f $tmpA1 $tmpA2 $tmpM1 $tmpM2 $tmpL1 $tmpL2 $tmpH1 $tmpH2 $histfile; exit 1" ERR

# get im_version
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`

# colorspace RGB and sRGB swapped between 6.7.5.5 and 6.7.6.7 
# though probably not resolved until the latter
# then -colorspace gray changed to linear between 6.7.6.7 and 6.7.8.2 
# then -separate converted to linear gray channels between 6.7.6.7 and 6.7.8.2,
# though probably not resolved until the latter
# so -colorspace HSL/HSB -separate and -colorspace gray became linear
# but we need to use -set colorspace RGB before using them at appropriate times
# so that results stay as in original script
# The following was determined from various version tests using isodatathresh.
# with IM 6.7.4.10, 6.7.6.10, 6.7.8.10
if [ "$im_version" -lt "06070607" -o "$im_version" -gt "06070707" ]; then
	setcspace="-set colorspace RGB"
else
	setcspace=""
fi
# no need for setcspace for grayscale or channels after 6.8.5.4
if [ "$im_version" -gt "06080504" ]; then
	setcspace=""
fi


if convert -quiet "$infile" $setcspace -colorspace Gray +repage "$tmpA1"
	then
	: ' do nothing '
else
	errMsg "--- FILE $infile DOES NOT EXIST OR IS NOT AN ORDINARY FILE, NOT READABLE OR HAG ZERO SIZE ---"
fi	

# get im version
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`

getMinMax()
	{
	img="$1"
	if [ "$im_version" -ge "06030901" ]
		then 
		min=`convert $img -format "%[min]" info:`
		max=`convert $img -format "%[max]" info:`
		min=`convert xc: -format "%[fx:100*$min/quantumrange]" info:`
		max=`convert xc: -format "%[fx:100*$max/quantumrange]" info:`
	else
		data=`convert $img -verbose info:`
		min=`echo "$data" | sed -n 's/^.*[Mm]in:.*[(]\([0-9.]*\).*$/\1/p ' | head -1`
		max=`echo "$data" | sed -n 's/^.*[Mm]ax:.*[(]\([0-9.]*\).*$/\1/p ' | head -1`
		min=`convert xc: -format "%[fx:100*$min)]" info:`
		max=`convert xc: -format "%[fx:100*$max)]" info:`
	fi
	}


getMean()
	{
	img="$1"
	if [ "$im_version" -ge "06030901" ]
		then 
		mean=`convert $img -format "%[mean]" info:`
		mean=`convert xc: -format "%[fx:100*$mean/quantumrange]" info:`
	else
		data=`convert $img -verbose info:`
		mean=`echo "$data" | sed -n 's/^.*[Mm]ean:.*[(]\([0-9.]*\).*$/\1/p ' | head -1`
		mean=`convert xc: -format "%[fx:100*$mean]" info:`
	fi
	}


# process image using isodata approach

echo ""
echo "Compute Threshold"
# begin threshold at ave of min and max
getMinMax "$tmpA1"
min=$min
max=$max
thresh=`convert xc: -format "%[fx:($min+$max)/2]" info:`
oldthresh=0
diff=`convert xc: -format "%[fx:abs($thresh-$oldthresh)]" info:`
test=`echo "$diff == 0" | bc`
k=1
# iterate the following
# threshold image at newmean
# get means above and below threshold
# get average of hmean and lmean as newmean
# repeat until difference between oldmean and newmean is <= diffstop
#
# Note: low and high (below threshold and above threshold) means 
# are extracted by masking and not by histogram counting.
# Thus they need to be corrected for mixture of black pixels.
# So, mean from masks (Mmeasured) and actual low/high means, Mtrue, are related
# Mmeasured=(Sum(Cw*Gw)+Sum(Cb*0))/Ct = Sum(Cw*Gw)/Ct, summed over whole image
# where Cw=count of white mask pixels, Gw graylevel at those pixels, Ct=total image pixels
# Mtrue=Sum(Cw*Gw)/Ctw, where Ctw is total count of only white (non-black) mask pixels
# Ctw=Mean of the mask/100
# All graylevels are in range 0-100
#
while [ $test != 1 ]; do
	echo "Iteration $k"
	oldthresh=$thresh
	convert $tmpA1 -threshold ${thresh}% $tmpM1
	getMean "$tmpM1"
	mmean=$mean
	convert $tmpA1 $tmpM1 -compose multiply -composite $tmpH1
	getMean "$tmpH1"
	hmean=$mean
#	echo "mmean=$mmean; hmean=$hmean"
	hmean=`convert xc: -format "%[fx:(100*$hmean/$mmean)]" info:`
	nmean=`convert xc: -format "%[fx:(100-$mmean)]" info:`
	convert $tmpA1 \( $tmpM1 -negate \) -compose multiply -composite $tmpL1
	getMean "$tmpL1"
	lmean=$mean
#	echo "nmean=$nmean; lmean=$lmean"
	lmean=`convert xc: -format "%[fx:(100*$lmean/$nmean)]" info:`
	thresh=`convert xc: -format "%[fx:($hmean+$lmean)/2]" info:`
	diff=`convert xc: -format "%[fx:abs($thresh-$oldthresh)]" info:`
	test=`echo "$diff ==0" | bc`
	k=`expr $k + 1`
#echo "hmean=$hmean; lmean=$lmean; oldthresh=$oldthresh; thresh=$thresh; diff=$diff"
done
convert $tmpM1 "$outfile"

echo "Image Thresholded At $thresh%"
echo ""


if [ "$graph" != "" ]; then
	xx=`convert xc: -format "%[fx:floor(255*$thresh/100)]" info:`
	convert $tmpA1 -define histogram:unique-colors=false histogram:- | \
		convert - -negate \
		-stroke red -strokewidth 1 -draw "line $xx,0 $xx,200" \
		-background gray -splice 0x30 \
		-fill white -stroke white -strokewidth 1 \
		-font ArialB -pointsize 24 \
		-draw "text 4,22 'threshold=$thresh%'" -resize 50% \
		-bordercolor gray50 -border 5 \
		"$histfile"
fi

if [ "$graph" = "view" ]; then
	convert $histfile x:
	rm -f "$histfile"
fi

exit 0