From d9b7653700040bf25cb5681b5dc7021bc505d975 Mon Sep 17 00:00:00 2001 From: yo mama Date: Sat, 1 Oct 2016 13:14:48 -0700 Subject: added threshold scripts --- bin/sahoothresh | 385 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 385 insertions(+) create mode 100644 bin/sahoothresh (limited to 'bin/sahoothresh') diff --git a/bin/sahoothresh b/bin/sahoothresh new file mode 100644 index 0000000..3f89ab6 --- /dev/null +++ b/bin/sahoothresh @@ -0,0 +1,385 @@ +#!/bin/bash +# +# Developed by Fred Weinhaus 10/29/2008 .......... revised11/3/2015 +# +# ------------------------------------------------------------------------------ +# +# 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: sahoothresh [-p power] [-g graph] infile outfile +# USAGE: sahoothresh [-help] +# +# OPTIONS: +# +# -p power power or exponent to use with method=4 +# float; power>0; default=2 +# -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: SAHOOTHRESH +# +# PURPOSE: To automatically thresholds an image to binary (b/w) format +# using Sahoo's technique. +# +# DESCRIPTION: SAHOOTHRESH 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 Sahoo appoach computes computes one measure of +# Entropy for each of the foreground (above threshold data) and background +# (at and below threshold value) classes. The optimal threshold is the one +# that maximizes the Sum of the Foreground and Background Entropies. +# +# OPTIONS: +# +# -p power ... POWER is the exponent used in method 4. The value for +# power may be a float greater than zero. The default is 2. +# +# -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_sahoo.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://climate.gsfc.nasa.gov/publications/fulltext/RSEpaper.pdf +# http://www.istanbul.edu.tr/eng/ee/jeee/main/pages/issues/is62/62008.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 +pow=2 #pow>0 and cannot equal 1 exactly +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 6 ] + 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 + ;; + -p) # get power + shift # to get the next parameter + # test if parameter starts with minus sign + errorMsg="--- INVALID POWER SPECIFICATION ---" + checkMinus "$1" + pow=`expr "$1" : '\([.0-9]*\)'` + [ "$pow" = "" ] && errMsg "--- POWER=$pow MUST BE A NON-NEGATIVE FLOAT ---" + powtest=`echo "$pow <= 0" | bc` + [ $powtest -eq 1 ] && errMsg "--- POWER=$pow MUST BE A POSITIVE FLOAT ---" + ;; + -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_sahoo.gif + +tmpA1="$dir/sahoothresh_1_$$.mpc" +tmpA2="$dir/sahoothresh_1_$$.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 sahoo thresh. +# with IM 6.6.0.10, 6.7.4.10, 6.7.6.10, 6.7.5.5, 6.7.5.6, 6.7.5.7, 6.7.8.10 +# Note: some images (esp. flower) do not work the same as the examples for versions greater than 6.7.5.6. +# There seems to be a bug 6.7.5.6, which I cannot seem to fix. But it appears very slightly different. +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` + +# function to convert IM histogram into two arrays, value and count +getHistog() + { + echo "Generate Histogram" + img="$1" + # get lists of values and counts from histogram + # note that IM histograms are not well sorted (and have multiple bins with counts for the same values) + value=`convert $img -format %c -depth 8 -define histogram:unique-colors=true histogram:info: | sort -k 2 -b | sed -n 's/^ *[0-9]*: [(]\([0-9 ]*\).*$/\1/ p'` + count=`convert $img -format %c -depth 8 -define histogram:unique-colors=true histogram:info: | sort -k 2 -b | sed -n 's/^ *\([0-9]*\): [(].*$/\1/ p'` + + # put value and count into arrays + valueArr=($value) + countArr=($count) + + # check if both arrays are the same size + if [ ${#valueArr[*]} -ne ${#countArr[*]} ] + then + errMsg "--- ARRAY SIZES DO NOT MATCH ---" + exit 1 + else + numbins=${#valueArr[*]} +#echo "numbins=$numbins" + fi +} + +# function to normalize histog +getNormlizedHistog() + { + echo "Normalize Histogram" + j=0 + while [ $j -lt $numbins ]; do + countArr[$j]=`echo "scale=10; ${countArr[$j]}/$totpix" | bc` + j=`expr $j + 1` + done + } + + +# process image using Kapur's approach + +echo "" +getHistog "$tmpA1" +getNormlizedHistog +[ "$pow" = "1" ] && pow=0.999999 + +echo "Generate Cumulative Arrays" +# p=c(i)/N (normalized count or probability, p, at bin i) +# t=threshold bin +# n=p0=sum(c(i)/N)zeroth histogram moment => cumulative normalized count (from i=0 to t) = N(t) +# entropy=ln(sum((p/n)^pow))=ln(sum(p^pow)/n^pow)=ln(r/n^pow)=ln(r)-ln(n^pow) +# b^x=e^(x*ln(b)); law of base change in raising number to power + +i=0 +nlow=0 +nhigh=0 +rlow=0 +rhigh=0 +# test if integer; returns 1 if integer and 0 if not integer +test=`convert xc: -format "%[fx:($pow-floor($pow))==0?1:0]" info:` +while [ $i -lt $numbins ]; do + if [ $test -eq 0 ]; then + nlow=`echo "scale=10; $nlow + ${countArr[$i]}" | bc` + nlowArr[$i]=`echo "scale=10; e($pow*l($nlow))" | bc -l` + rlow=`echo "scale=10; $rlow + e($pow*l(${countArr[$i]}))" | bc -l` + rlowArr[$i]=$rlow + j=`expr $numbins - $i - 1` + nhigh=`echo "scale=6; $nhigh + ${countArr[$j]}" | bc` + nhighArr[$i]=`echo "scale=10; e($pow*l($nhigh))" | bc -l` + rhigh=`echo "scale=10; $rhigh + e($pow*l(${countArr[$j]}))" | bc -l` + rhighArr[$i]=$rhigh + else + nlow=`echo "scale=10; $nlow + ${countArr[$i]}" | bc` + nlowArr[$i]=`echo "scale=10; $nlow^$pow" | bc` + rlow=`echo "scale=10; $rlow + (${countArr[$i]})^$pow" | bc` + rlowArr[$i]=$rlow + j=`expr $numbins - $i - 1` + nhigh=`echo "scale=6; $nhigh + ${countArr[$j]}" | bc` + nhighArr[$i]=`echo "scale=10; $nhigh^$pow" | bc` + rhigh=`echo "scale=10; $rhigh + (${countArr[$j]})^$pow" | bc` + rhighArr[$i]=$rhigh + fi +#echo "i=$i; j=$j; nlow=${nlowArr[$i]}; nhigh=${nhighArr[$i]}; rlow=${rlowArr[$i]}; rhigh=${rhighArr[$i]}" + i=`expr $i + 1` +done + + +echo "Compute Threshold" +# loop through histogram +# compute threshold by maximizing total low and high class entropies +# te=El+Eh + +i=0 +teold=0 +threshbin=0 +lastbin=`expr $numbins - 1` +frac=`echo "scale=10; 1/(1 - $pow)" | bc` +#echo "frac=$frac" +while [ $i -lt $lastbin ]; do + j=`expr $lastbin - $i - 1` + nlow=${nlowArr[$i]} + nhigh=${nhighArr[$j]} + rlow=${rlowArr[$i]} + rhigh=${rhighArr[$j]} + te=`echo "scale=10; $frac*(l($rlow) -l($nlow) + l($rhigh) -l($nhigh)) / 1" | bc -l` + test=`echo "$te > $teold" | bc` + if [ $test -eq 1 ]; then + teold=$te + threshbin=$i + fi +#echo "i=$i; rlow=$rlow; rhigh=$rhigh; te=$te; teold=$teold; test=$test; threshbin=$threshbin" + i=`expr $i + 1` +done +thresh=${valueArr[$threshbin]} + + +# compute threshold graph x coord and threshold in percent +xx=$thresh +threshpct=`convert xc: -format "%[fx:100*$thresh/255]" info:` +#echo "xx=$xx; threshpct=$threshpct" + + +echo "Thresholding Image At $threshpct%" +convert $tmpA1 -threshold $threshpct% "$outfile" +echo "" + + +if [ "$graph" != "" ]; then + convert $tmpA1 -define histogram:unique-colors=false histogram:- | \ + convert - -negate \ + -stroke red -strokewidth 1 -draw "line $xx,0 $xx,200" \ + -background gray -splice 0x30 \ + -fill white -stroke white -strokewidth 1 \ + -font ArialB -pointsize 24 \ + -draw "text 4,22 'threshold=$threshpct%'" -resize 50% \ + -bordercolor gray50 -border 5 \ + $histfile +fi + +if [ "$graph" = "view" ]; then + convert $histfile x: + rm -f $histfile +fi + +exit 0 + + + -- cgit v1.2.3-70-g09d2