added threshold scripts

1 files changed, 419 insertions, 0 deletions

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+#!/bin/bash
+#
+# Developed by Fred Weinhaus 10/29/2008 .......... revised 11/3/2015
+#
+# ------------------------------------------------------------------------------
+# 
+# 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: trianglethresh [-g graph] infile outfile
+# USAGE: trianglethresh [-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: TRIANGLETHRESH
+# 
+# PURPOSE: To automatically thresholds an image to binary (b/w) format 
+# using the triangle technique.
+# 
+# DESCRIPTION: TRIANGLETHRESH automatically thresholds an image to binary
+# (b/w) format. It does not assume the histogram is bimodal. It finds the
+# bin with the highest value (the peak in the histogram) and also the end
+# of the histogram furthest from the peak. It then draws a line between
+# the two. It exhaustively searches along the line drawing a perpendicular
+# from the line to the top of each histogram bin and picks the threshold
+# value at that bin for which the perpendicular is the longest.
+# 
+# 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_triangle.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
+# 
+# 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_triangle.gif"
+
+tmpA1="$dir/trianglethresh_1_$$.mpc"
+tmpA2="$dir/trianglethresh_1_$$.cache"
+trap "rm -f $tmpA1 $tmpA2; exit 0" 0
+trap "rm -f $tmpA1 $tmpA2 $histfile; exit 1" 1 2 3 15
+
+# 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 trianglethresh.
+# 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 totpix in image
+width=`convert $tmpA1 -format "%w" info:`
+height=`convert $tmpA1 -format "%h" info:`
+totpix=`echo "scale=0; $width * $height / 1" | bc`
+
+
+# separate IM histogram into two arrays, value and count, and fill out for empty bins and normalize
+
+	# get filled value array from IM histogram
+	nvalueArr=(`convert $tmpA1 -depth 8 -format "%c" -define histogram:unique-colors=true histogram:info:- \
+	| tr -cs '0-9\012' ' ' | sed -n 's/[ ]*\([0-9]*\)[ ]*\([0-9]*\).*$/\1 \2/p' |\
+	awk '
+	# AWK 
+	{ vbin[$2] += $2;} 
+	END { for (i=0;i<256;i++) {print vbin[i]+0; } } '`)
+#	echo ${nvalueArr[*]}
+#	echo ${#nvalueArr[*]}
+	numvals=${#nvalueArr[*]}
+	
+	# get filled and normalized count array from IM histogram
+	ncountArr=(`convert $tmpA1 -depth 8 -format "%c" -define histogram:unique-colors=true histogram:info:- \
+	| tr -cs '0-9\012' ' ' | sed -n 's/[ ]*\([0-9]*\)[ ]*\([0-9]*\).*$/\1 \2/p' |\
+	awk -v totpix="$totpix" '
+	# AWK 
+	{ cbin[$2] += $1; } 
+	END { for (i=0;i<256;i++) {print (cbin[i]+0)/totpix; } } '`)
+#	echo ${ncountArr[*]}
+#	echo ${#ncountArr[*]}
+	numcounts=${#ncountArr[*]}
+	
+	[ $numvals -ne $numcounts ] && errMsg "--- NUMBER OF COUNTS IS NOT THE SAME AS NUMBER OF VALUES ---"
+	
+
+
+	# find start bin (first one not zero)
+	startbin=`for ((i=0; i<256; i++)); do
+	echo "$i ${ncountArr[$i]}"
+	done |\
+	awk '
+	# AWK to find startbin
+	{ cbin[$1] = $2; } 
+	END { for (i=0;i<256;i++) { if (cbin[i]!=0) { print i; break; } } } '`
+	eval startbincount=${ncountArr[$startbin]}
+#	echo "startbin=$startbin; startbincount=$startbincount;"
+
+
+	# find end bin (last one not zero)
+	endbin=`for ((i=0; i<256; i++)); do
+	echo "$i ${ncountArr[$i]}"
+	done |\
+	awk '
+	# AWK to find startbin
+	{ cbin[$1] = $2; } 
+	END { for (i=255;i>=0;i--) { if (cbin[i]!=0) { print i; break; } } } '`
+	endbincount=${ncountArr[$endbin]}
+#	echo "endbin=$endbin; endbincount=$endbincount;"
+
+
+	# find max bin (bin with largest count)
+	maxbin=`for ((i=0; i<256; i++)); do
+	echo "$i ${ncountArr[$i]}"
+	done |\
+	awk '
+	# AWK to find startbin
+	{ cbin[$1] = $2; maxbincount = 0; maxbin = 0; } 
+	END { for (i=0;i<256;i++) { if (cbin[i] > maxbincount) { maxbincount=cbin[i]; maxbin=i; } } print maxbin } '`
+	maxbincount=${ncountArr[$maxbin]}
+#	echo "maxbin=$maxbin; maxbincount=$maxbincount;"
+
+
+	# set x1,y1 for bin with max count
+	y1=$maxbincount
+	x1=$maxbin
+	
+	# set x2,y2 for furthest end bin from bin with max count
+	lowdiff=`expr $maxbin - $startbin`
+	highdiff=`expr $endbin - $maxbin`
+	if [ $lowdiff -ge $highdiff ]; then
+		x2=$startbin
+		y2=0
+	else
+		x2=$endbin
+		y2=0
+	fi
+#echo "lowdiff=$lowdiff; highdiff=$highdiff; x1=$x1; y1=$y1; x2=$x2; y2=$y2"
+
+
+# compute threshold
+
+# equation of line between x1,y1 and x2,y2 is Ax+By+C=0
+# where A=(y1-y2), B=(x2-x1), C=-(A*x1+B*y1)
+# Dist=abs(A*x1+B*y1+C)/sqrt(A^2+B^2+C^2)
+aa=`echo "scale=10; ($y1 - $y2)/1" | bc`
+bb=`echo "scale=10; ($x2 - $x1)/1" | bc`
+cc=`echo "scale=10; -($aa*$x1 + $bb*$y1)/1" | bc`
+ir=`echo "scale=10; 1/sqrt($aa*$aa + $bb*$bb + $cc*$cc)" | bc`
+#echo "aa=$aa; bb=$bb; cc=$cc; ir=$ir"
+
+
+# increment from appropriate end to bin with max count
+# and compute dist and save bin where dist is max
+
+if [ $x2 -eq $startbin ]; then
+
+	distbin=`for ((i=0; i<256; i++)); do
+	echo "$i ${ncountArr[$i]}"
+	done |\
+	awk -v startbin="$startbin" -v maxbin="$maxbin" -v aa="$aa" -v bb="$bb" -v cc="$cc" -v ir="$ir" '
+	# AWK to find threshold
+	{ x[$1] = $1; y[$1] = $2; dist=0; }
+	END { for (i=startbin;i<maxbin;i++) { dd = ir*(aa*x[i]+bb*y[i]+cc); ddabs = sqrt(dd*dd); 
+		if (ddabs>dist && dd>0) { distbin=i; dist=ddabs; } } print distbin } '`
+#	echo "$distbin"
+	
+else
+
+	distbin=`for ((i=0; i<256; i++)); do
+	echo "$i ${ncountArr[$i]}"
+	done |\
+	awk -v endbin="$endbin" -v maxbin="$maxbin" -v aa="$aa" -v bb="$bb" -v cc="$cc" -v ir="$ir" '
+	# AWK to find threshold
+	{ x[$1] = $1; y[$1] = $2; dist=0; }
+	END { for (i=endbin;i>maxbin;i--) { dd = ir*(aa*x[i]+bb*y[i]+cc); ddabs = sqrt(dd*dd); 
+		if (ddabs>dist && dd<0) { distbin=i; dist=ddabs; } } print distbin } '`
+#	echo "$distbin"
+fi
+
+
+# set threshold to value (0 to 255) of bin where dist is max
+x0=$distbin
+y0=${ncountArr[$distbin]}
+#echo "x0=$x0; y0=$y0"
+
+# convert threshold value to range 0 to 100
+threshpct=`convert xc: -format "%[fx:100*$x0/255]" info:`
+
+
+echo "Thresholding Image At $threshpct%"
+# threshold image
+convert $tmpA1 -threshold $threshpct% "$outfile"
+echo ""
+
+
+
+if [ "$graph" != "" ]; then
+
+# compute triangle lines for graphing
+
+	# histogram image scales maxbincount to 200 pixels
+	# counts need to be complemented with 200 
+	# as 0 is at image top and 200 at image bottom
+	
+	# convert y1 and y2 to points on histogram image
+	xx1=$x1
+	yy1=0
+	xx2=$x2
+	yy2=200
+#	echo "xx1=$xx1; yy1=$yy1; xx2=$xx2; yy2=$yy2"
+
+	# convert x0,y0 to point on histogram image
+	xx0=$x0
+	yy0=`echo "scale=10; 200*(1 - $y0/$y1)/1" | bc`
+#echo "y0=$y0; y1=$y1; yy0=$yy0"
+	
+	# find intersection of perpendicular through xx0,yy0 and line between xx1,yy1 and x2,y2
+	# get slope and intercept of line between xx1,yy1 and xx2,yy2
+	sl=`echo "scale=10; ($yy2 - $yy1)/($xx2 - $xx1)" | bc`
+	il=`echo "scale=10; ($yy1 - $sl*$xx1)/1" | bc`
+	
+	# get slope and intercept of perpendicular
+	# slope is negative inverse of that of line between xx1,yy1 and xx2,yy2
+	sp=`echo "scale=10; -1/$sl" | bc`
+	ip=`echo "scale=10; ($yy0 - $sp*$xx0)/1" | bc`
+	
+	# compute intersection point xx3,yy3
+	xx3=`echo "scale=10; ($ip - $il)/($sl - $sp)" | bc`
+	yy3=`echo "scale=10; ($sl*$xx3 + $il)/1" | bc`
+
+#	echo "sl=$sl; il=$il; sp=$sp; ip=$ip; xx3=$xx3; yy3=$yy3"
+#	echo "xx0=$xx0; yy0=$yy0; xx3=$xx3; yy3=$yy3"
+
+	convert $tmpA1 -define histogram:unique-colors=false histogram:- | \
+		convert - -negate \
+		-stroke blue -strokewidth 1 -draw "line $xx1,$yy1 $xx2,$yy2" \
+		-stroke green1 -strokewidth 1 -draw "line $xx0,$yy0 $xx3,$yy3" \
+		-stroke red -strokewidth 1 -draw "line $xx0,0 $xx0,200" \
+		-background gray -splice 0x30 \
+		-fill white -stroke white -strokewidth 1 \
+		-font ArialB -pointsize 24 \
+		-draw "text 4,22 'threshold=$threshpct%'" -resize 50% \
+		-bordercolor gray50 -border 5 \
+		"$histfile"
+fi
+
+
+if [ "$graph" = "view" ]; then
+	convert $histfile x:
+	rm -f "$histfile"
+fi
+
+exit 0
+
+
+