added threshold scripts

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+#!/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
+
+
+