diff options
| -rw-r--r-- | bin/2colorthresh | 168 | ||||
| -rw-r--r-- | bin/fuzzythresh | 407 | ||||
| -rw-r--r-- | bin/isodatathresh | 346 | ||||
| -rw-r--r-- | bin/kapurthresh | 329 | ||||
| -rw-r--r-- | bin/kmeansthresh | 428 | ||||
| -rw-r--r-- | bin/localthresh | 347 | ||||
| -rw-r--r-- | bin/otsuthresh | 368 | ||||
| -rw-r--r-- | bin/ptilethresh | 213 | ||||
| -rw-r--r-- | bin/sahoothresh | 385 | ||||
| -rw-r--r-- | bin/trianglethresh | 419 | ||||
| -rwxr-xr-x | photoblaster/modules/pbbreaker/__init__.py | 2 | ||||
| -rwxr-xr-x | share/frontend/imbreak/index.html | 2 |
12 files changed, 3412 insertions, 2 deletions
diff --git a/bin/2colorthresh b/bin/2colorthresh new file mode 100644 index 0000000..b05005c --- /dev/null +++ b/bin/2colorthresh @@ -0,0 +1,168 @@ +#!/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: 2colorthresh infile outfile +# USAGE: 2colorthresh [-help] +# +# OPTIONS: +# +# There are no options +# +### +# +# NAME: 2COLORTHRESH +# +# PURPOSE: To automatically thresholds an image to binary (b/w) format +# using an adaptive spatial subdivision color reduction technique. +# +# DESCRIPTION: 2COLORTHRESH automatically thresholds an image to binary +# (b/w) format using an adaptive spatial subdivision color reduction +# technique. This is the -colors IM operator as implemented with slight +# modification from Anthony's Examples at +# http://www.imagemagick.org/Usage/quantize/#two_color +# For algorithm details, see http://www.imagemagick.org/script/quantize.php +# +# OPTIONS: +# +# There are no options. +# +# 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. +# +# 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 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 2 ] + 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 + ;; + -) # 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 +[ "$outfile" = "" ] && errMsg "NO OUTPUT FILE SPECIFIED" + + +tmpA1="$dir/2colorsthresh_1_$$.mpc" +tmpA2="$dir/2colorsthresh_1_$$.cache" +trap "rm -f $tmpA1 $tmpA2; exit 0" 0 +trap "rm -f $tmpA1 $tmpA2; exit 1" 1 2 3 15 + +if convert -quiet "$infile" +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 + +# process image +convert $tmpA1 +dither -colors 2 -colorspace gray -contrast-stretch 0 "$outfile" + +exit 0 + + + diff --git a/bin/fuzzythresh b/bin/fuzzythresh new file mode 100644 index 0000000..51c269d --- /dev/null +++ b/bin/fuzzythresh @@ -0,0 +1,407 @@ +#!/bin/bash +# +# Developed by Fred Weinhaus 10/30/2008 .......... 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: fuzzythresh [-r radius] [-g graph] infile outfile +# USAGE: fuzzythresh [-help] +# +# OPTIONS: +# +# -r radius radius for spatial correlation; float; +# radius>=0; the default=0 signifies to +# ignore spatial correlation +# -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: FUZZYTHRESH +# +# PURPOSE: To automatically thresholds an image to binary (b/w) format +# using the fuzzy c-means technique. +# +# DESCRIPTION: FUZZYTHRESH 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 fuzzy c-means appoach iteratively thresholds the +# image, computes a weighted mean for 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. The weighting factors +# are the normalized inverse square difference between each pixel in the +# foreground or background data sets and the corresponding mean. However, +# to allow for spatial correlation of the graylevels among neighboring +# pixels, a Gaussian filtered version of the weighting factors may be used. +# This script is similar to the isodatathresh script, except uses a weighted +# mean calculation. +# +# OPTIONS: +# +# -r radius ... RADIUS is the radius of a Gaussian (blur) filter to apply +# to the weighting factors for the mean calculation. This permits spatial +# correlation of the graylevels among neighboring pixels and is useful +# to remove noise from the result. The radius value should be set to +# the size of the features in the image. Values are floats greater than +# zero. The default=0 signifies to ignore spatial correlation. +# +# -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.iiitmk.ac.in/wiki/images/d/d2/Fuzzy_CMeans.pdf +# http://www.quantlet.com/mdstat/scripts/xag/html/xaghtmlframe149.html +# http://home.dei.polimi.it/matteucc/Clustering/tutorial_html/cmeans.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 +radius=0 +graph="" #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 + ;; + -r) # get radius + shift # to get the next parameter + # test if parameter starts with minus sign + errorMsg="--- INVALID RADIUS SPECIFICATION ---" + checkMinus "$1" + radius=`expr "$1" : '\([.0-9]*\)'` + [ "$radius" = "" ] && errMsg "--- RADIUS=$radius MUST BE A NON-NEGATIVE 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_fuzzy.gif + +tmpA1="$dir/fuzzythresh_1_$$.mpc" +tmpA2="$dir/fuzzythresh_1_$$.cache" +tmpM1="$dir/fuzzythresh_M_$$.mpc" +tmpM2="$dir/fuzzythresh_M_$$.cache" +tmpL1="$dir/fuzzythresh_L_$$.mpc" +tmpL2="$dir/fuzzythresh_L_$$.cache" +tmpH1="$dir/fuzzythresh_H_$$.mpc" +tmpH2="$dir/fuzzythresh_H_$$.cache" +tmpD1="$dir/fuzzythresh_D_$$.mpc" +tmpD2="$dir/fuzzythresh_d_$$.cache" +trap "rm -f $tmpA1 $tmpA2 $tmpM1 $tmpM2 $tmpL1 $tmpL2 $tmpH1 $tmpH2 $tmpD1 $tmpD2; exit 0" 0 +trap "rm -f $tmpA1 $tmpA2 $tmpM1 $tmpM2 $tmpL1 $tmpL2 $tmpH1 $tmpH2 $tmpD1 $tmpD2 $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 fuzzythresh. +# 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 image width and heigh +ww=`convert $tmpA1 -format "%w" info:` +hh=`convert $tmpA1 -format "%h" info:` + +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 + } + + +# set gaussian filter +if [ "$radius" = "0" -o "$radius" = "0.0" ]; then + filter="" +else + filter="-blur 0x${radius}" +fi + + +# process image using isodata approach + +echo "" +echo "Compute Threshold" +# begin threshold at ave of min and max +getMinMax "$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 "$diff == 0" | bc` +k=1 +# iterate the following +# threshold image at newmean +# get weighted means above and below threshold +# where weights are the normalized inverse squared differences of each pixel from the class mean +# get average of hmean and lmean as new threshold +# repeat until difference between oldthresh and current thresh is zero +# +# Note: low and high (below threshold and above threshold) means +# are extracted by masking and not by histogram counting. +# Thus they need to be corrected for mixture of black pixels. +# So, mean from masks (Mmeasured) and actual low/high means, Mtrue, are related +# Mmeasured=(Sum(Cw*Gw)+Sum(Cb*0))/Ct = Sum(Cw*Gw)/Ct, summed over whole image +# where Cw=count of white mask pixels, Gw graylevel at those pixels, Ct=total image pixels +# Mtrue=Sum(Cw*Gw)/Ctw, where Ctw is total count of only white (non-black) mask pixels +# Ctw=Mean of the mask/100 +# All graylevels are in range 0-100 +# +while [ "$test" != "1" ]; do + echo "Iteration $k" + oldthresh=$thresh + + # get high mask and its mean + convert $tmpA1 -threshold ${thresh}% $tmpM1 + getMean "$tmpM1" + mmean=$mean + + # compute high membership as normalized inverse squared difference of each pixel from high mean + # in this case we just use -compose difference -evalute pow 2 and negate it (so inverse squared distance scaled to Q) + convert $tmpA1 \( -size ${ww}x${hh} xc:"gray($mmean%)" \) \ + -compose difference -evaluate pow 2 $filter -negate $tmpD1 + + # apply multiply membership image by image as weighting and mask to get the resulting mean + convert $tmpA1 $tmpD1 -compose multiply -composite \ + $tmpM1 -compose multiply -composite \ + $tmpH1 + getMean "$tmpH1" + hmean=$mean +# echo "mmean=$mmean; hmean=$hmean" + # correct hmean using mmean + hmean=`convert xc: -format "%[fx:(100*$hmean/$mmean)]" info:` + + # get low mean + # low mean = 100% - high mean + nmean=`convert xc: -format "%[fx:(100-$mmean)]" info:` + + # compute low membership as normalized inverse squared difference of each pixel from high mean + # in this case we just use -compose difference -evalute pow 2 and negate it (so inverse squared distance scaled to Q) + convert $tmpA1 \( -size ${ww}x${hh} xc:"gray($nmean%)" \) \ + -compose difference -evaluate pow 2 $filter -negate $tmpD1 + + # apply multiply membership image by image as weighting and mask to get the resulting mean + # note: low mask is just the complement of the high mask, i.e. $tmpM1 -negate + convert $tmpA1 $tmpD1 -compose multiply -composite \ + \( $tmpM1 -negate \) -compose multiply -composite \ + $tmpL1 + getMean "$tmpL1" + lmean=$mean +# echo "nmean=$nmean; lmean=$lmean" + # correct lmean using nmean + lmean=`convert xc: -format "%[fx:(100*$lmean/$nmean)]" info:` + + # get new threshold + thresh=`convert xc: -format "%[fx:($hmean+$lmean)/2]" info:` + diff=`convert xc: -format "%[fx:abs($thresh-$oldthresh)]" info:` +# test=`echo "$diff <= 0.000001" | bc` + test=`convert xc: -format "%[fx:($diff<=0.01)?1:0]" info:` + 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 + + + diff --git a/bin/isodatathresh b/bin/isodatathresh new file mode 100644 index 0000000..be10c4f --- /dev/null +++ b/bin/isodatathresh @@ -0,0 +1,346 @@ +#!/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 + + + diff --git a/bin/kapurthresh b/bin/kapurthresh new file mode 100644 index 0000000..c025ae9 --- /dev/null +++ b/bin/kapurthresh @@ -0,0 +1,329 @@ +#!/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: kapurthresh [-g graph] infile outfile +# USAGE: kapurthresh [-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: KAPURTHRESH +# +# PURPOSE: To automatically thresholds an image to binary (b/w) format +# using Kapur's entropy technique. +# +# DESCRIPTION: KAPURTHRESH 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 Kapur 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: +# +# -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_kapur.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 +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_kapur.gif + +tmpA1="$dir/kapurthresh_1_$$.mpc" +tmpA2="$dir/kapurthresh_1_$$.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 kapurthresh. +# with IM 6.6.0.10, 6.7.2.10, 6.7.3.10, 6.7.4.10, 6.7.6.10, 6.7.7.6, 6.7.7.7, 6.7.8.10 +# Note: some images (esp. b/w) do not work for older versions. +# There seems to be a bug sometime between IM 6.7.2.10 and 6.7.3.10 through 6.7.7.7, which I cannot seem to fix +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` + + + # get value array from IM histogram + valueArr=(`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]; } } '`) +# echo ${valueArr[*]} +# echo ${#valueArr[*]} + numvals=${#valueArr[*]} + + # get count array from IM histogram + countArr=(`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 + { cbin[$2] += $1; } + END { for (i=0;i<256;i++) {print cbin[i]; } } '`) +# echo ${countArr[*]} +# echo ${#countArr[*]} + numcounts=${#countArr[*]} + + [ $numvals -ne $numcounts ] && errMsg "--- NUMBER OF COUNTS IS NOT THE SAME AS NUMBER OF VALUES ---" + + # compute normalized count array + ncountArr=( $(for ((i=0; i<$numcounts; i++)); do + echo "$i ${countArr[$i]}" + done |\ + awk -v totpix="$totpix" -v numcounts="$numcounts" ' + # AWK + { bin[$1] = $2; } + END { for (i=0;i<numcounts;i++) {print bin[i]/totpix; } } ') ) +# echo ${ncountArr[*]} +# echo ${#ncountArr[*]} + + # compute elowArr + elowArr=( $(for ((i=0; i<$numcounts; i++)); do + echo "$i ${ncountArr[$i]}" + done |\ + awk -v numcounts="$numcounts" ' + # AWK to generate a cumulative histogram 1D image... + { ncbin[$1] = $2; nlow += $2; nlowbin[$1] = nlow; qlow += $2*log($2); qlowbin[$1] = qlow;} + END { for (i=0;i<numcounts;i++) {if (ncbin[i]!=0) {elowbin[i]=log(nlowbin[i]) - qlowbin[i]/nlowbin[i]} else {elowbin[i]=0}; print elowbin[i] } } ') ) +# echo ${elowArr[*]} +# echo ${#elowArr[*]} + + # compute ehighArr + ehighArr=( $(for ((i=0; i<$numcounts; i++)); do + j=`expr $numcounts - 1 - $i` + echo "$j ${ncountArr[$j]}" + done |\ + awk -v numcounts="$numcounts" ' + # AWK to generate a cumulative histogram 1D image... + { ncbin[$1] = $2; nhigh += $2; nhighbin[$1] = nhigh; qhigh += $2*log($2); qhighbin[$1] = qhigh;} + END { for (i=0;i<numcounts;i++) {if (ncbin[i]!=0) {ehighbin[i]=log(nhighbin[i]) - qhighbin[i]/nhighbin[i]} else {ehighbin[i]=0}; print ehighbin[i] } } ') ) +# echo ${ehighArr[*]} +# echo ${#ehighArr[*]} + + # compute threshold + threshbin=$(for ((i=0; i<$numcounts; i++)); do + echo "$i ${elowArr[$i]} ${ehighArr[$i]}" + done |\ + awk -v numcounts="$numcounts" -v teold=0 -v threshbin=0 ' + # AWK to compute entropy threshold... + { tebin[$1] = ($2 + $3); } + END { for (i=0;i<numcounts;i++) { if (tebin[i]>teold) {teold=tebin[i]; threshbin=i}; } print threshbin } ') +# echo "threshbin=$threshbin" + thresh=${valueArr[$threshbin]} +# echo "thresh=$thresh" + threshpct=`convert xc: -format "%[fx:100*$thresh/255]" info:` + + + +# 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 + + + diff --git a/bin/kmeansthresh b/bin/kmeansthresh new file mode 100644 index 0000000..cde8cf8 --- /dev/null +++ b/bin/kmeansthresh @@ -0,0 +1,428 @@ +#!/bin/bash +# +# Developed by Fred Weinhaus 10/29/2008 .......... revised 3/19/2016 +# +# ------------------------------------------------------------------------------ +# +# 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: kmeansthresh [-g graph] infile outfile +# USAGE: kmeansthresh [-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: KMEANSTHRESH +# +# PURPOSE: To automatically thresholds an image to binary (b/w) format +# using the k-means technique. +# +# DESCRIPTION: KMEANSTHRESH 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 k-means 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 isodatathresh script, which is implemented using image +# masking rather than from the histogram of the image. The isodatathresh +# script is faster than the kmeansthresh script for smaller images. The +# timing transition occurs for images somewhere between 1000-2000 pixels +# on a side. The kmeansthresh script is moderatly insensitive to image +# size, but pays an initial timing penalty in order to compute the +# histogram related data and get the means for each class from the +# histogram using shell computations. +# +# 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_kmeans.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_kmeans.gif + +tmpA1="$dir/kmeansthresh_1_$$.mpc" +tmpA2="$dir/kmeansthresh_1_$$.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 kmeansthresh. +# 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 * $height / 1" | bc` + +# get min and max in range 0 - 255 to correspond to 8-bit histogram and later set average to initial thresh +if [ "$im_version" -ge "06030901" ] + then + min=`convert $tmpA1 -format "%[min]" info:` + max=`convert $tmpA1 -format "%[max]" info:` + min=`convert xc: -format "%[fx:255*$min/quantumrange]" info:` + max=`convert xc: -format "%[fx:255*$max/quantumrange]" info:` +else + data=`convert $tmpA1 -verbose info:` + min=`echo "$data" | sed -n 's/^.*[Mm]in:.*[(]\([0-9.]*\).*$/\1/p ' | head -1` + max=`echo "$data" | sed -n 's/^.*[Mm]ax:.*[(]\([0-9.]*\).*$/\1/p ' | head -1` + min=`convert xc: -format "%[fx:255*$min)]" info:` + max=`convert xc: -format "%[fx:255*$max)]" info:` +fi +#echo "min=$min; max=$max;" + + +# 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++) {printf ("%f\n", (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 ---" + + numbins=256 + +# process image using k-means approach + +# Generate Cumulative Arrays +# p=c(i)/N (normalized count or probability, p, at bin i) +# v=v(i) (graylevel at bin i) +# note that as histogram has been filled that v=i +# t=threshold bin +# n=p0=sum(c(i)/N)=zeroth histogram moment => cumulative normalized count (from i=0 to t) = N(t) +# g=p1=sum(c(i)*v(i))=first histogram momement => cumulative normalized graylevel (from i=0 to t) = G(t) +# m=p1/p0=mean + + + # compute nlowArr + nlowArr=( $(for ((i=0; i<numbins; i++)); do + echo "$i ${ncountArr[$i]}" + done |\ + awk -v numbins="$numbins" ' + # AWK to generate a cumulative histogram 1D image... + { nlowbin[$1] = $2; } + END { for (i=0;i<numbins;i++) { nlow += nlowbin[i]; print nlow } } ') ) +# echo ${nlowArr[*]} +# echo ${#nlowArr[*]} + + + # compute glowArr + glowArr=( $( for ((i=0; i<numbins; i++)); do + echo "$i ${nvalueArr[$i]} ${ncountArr[$i]}" + done |\ + awk -v numbins="$numbins" ' + # AWK to generate a cumulative histogram 1D image... + { vlowbin[$1] = $2; nclowbin[$1] = $3; } + END { for (i=0;i<numbins;i++) { glow += vlowbin[i]*nclowbin[i]; print glow } } ') ) +# echo ${glowArr[*]} +# echo ${#glowArr[*]} + + + # compute mlowArr + [ `echo "${ncountArr[0]} == 0" | bc` -eq 1 ] && mlowold=0 + mlowArr=( $( for ((i=0; i<numbins; i++)); do + echo "$i ${nlowArr[$i]} ${glowArr[$i]}" + done |\ + awk -v numbins="$numbins" -v mlowold="$mlowold" ' + # AWK to generate a cumulative histogram 1D image... + { nlowbin[$1] = $2; glowbin[$1] = $3; } + END { for (i=0;i<numbins;i++) + { if ( nlowbin[i] != 0 ) { mlow = glowbin[i]/nlowbin[i]; mlowold = mlow; } else { mlow = mlowold; } print mlow } }') ) +# echo ${mlowArr[*]} +# echo ${mlowArr[*]} + + + # compute nhighArr + nhighArr=( $(for ((i=0; i<numbins; i++)); do + echo "$i ${ncountArr[$i]}" + done |\ + awk -v numbins="$numbins" ' + # AWK to generate a cumulative histogram 1D image... + { nhighbin[$1] = $2; } + END { for (i=0;i<numbins;i++) { j = (numbins - 1 - i); nhigh += nhighbin[j]; print nhigh } } ') ) +# echo ${nhighArr[*]} +# echo ${#nhighArr[*]} + + + # compute ghighArr + ghighArr=( $( for ((i=0; i<numbins; i++)); do + echo "$i ${nvalueArr[$i]} ${ncountArr[$i]}" + done |\ + awk -v numbins="$numbins" ' + # AWK to generate a cumulative histogram 1D image... + { vhighbin[$1] = $2; nchighbin[$1] = $3; } + END { for (i=0;i<numbins;i++) { j = (numbins - 1 - i); ghigh += vhighbin[j]*nchighbin[j]; print ghigh } } ') ) +# echo ${glowArr[*]} +# echo ${#glowArr[*]} + + + # compute mhighArr + [ `echo "${ncountArr[0]} == 0" | bc` -eq 1 ] && mhighold=0 + mhighArr=( $( for ((i=0; i<numbins; i++)); do + echo "$i ${nhighArr[$i]} ${ghighArr[$i]}" + done |\ + awk -v numbins="$numbins" -v mhighold="$mhighold" ' + # AWK to generate a cumulative histogram 1D image... + { nhighbin[$1] = $2; ghighbin[$1] = $3; } + END { for (i=0;i<numbins;i++) + { if ( nhighbin[i] != 0 ) { mhigh = ghighbin[i]/nhighbin[i]; mhighold = mhigh; } else { mhigh = mhighold; } print mhigh } }') ) +# echo ${mlowArr[*]} +# echo ${mlowArr[*]} + + +#for ((i=0;i<numbins;i++)); do +#echo "i=$i; j=$j; ncount=${ncountArr[$i]}; nlow=${nlowArr[$i]}; nhigh=${nhighArr[$i]}; mlow=${mlowArr[$i]}; mhigh=${mhighArr[$i]}" +#done + +# Compute Threshold +# iterate the following +# start with initial threshold at average of image min and max values +# get low and high means corresponding to below and above threshold +# compute new threshold=(Ml+Mh)/2 +# repeat until difference between old and new thresholds is zero + +lastbin=`expr $numbins - 1` +thresh=`echo "scale=0; ($min + $max)/2" | bc` +oldthresh=0 +diff=`echo "scale=10; ($thresh - $oldthresh)" | bc` +diff=`echo "scale=10; sqrt($diff * $diff)" | bc` +test=`echo "$diff == 0" | bc` +while [ $test != 1 ]; do + i=$thresh + j=`expr $lastbin - $i - 1` + oldthresh=$thresh + mlow=${mlowArr[$i]} + mhigh=${mhighArr[$j]} + thresh=`echo "scale=0; ($mlow+$mhigh)/2" | bc` + diff=`echo "scale=10; ($thresh - $oldthresh)" | bc` + diff=`echo "scale=10; sqrt($diff * $diff)" | bc` + test=`echo "$diff == 0" | bc` +#echo "i=$i; j=$j; mlow=$mlow; mhigh=$mhigh; oldthresh=$oldthresh; thresh=$thresh; diff=$diff; test=$test" +done + + +# 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 + + + diff --git a/bin/localthresh b/bin/localthresh new file mode 100644 index 0000000..03d6f06 --- /dev/null +++ b/bin/localthresh @@ -0,0 +1,347 @@ +#!/bin/bash +# +# Developed by Fred Weinhaus 10/30/2008 .......... 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: localthresh [-m method] [-s size] [-b bias] [-n negate] infile outfile +# USAGE: localthresh [-help] +# +# OPTIONS: +# +# -m method method for computing threshold statistics; +# method=1 uses only the local mean; +# method=2 uses the local mean and standard deviation; +# method=3 used the local mean and mean absolute deviation; +# default=1 +# -r radius radius of window to use; float; radius>=3; default=15 +# -b bias bias parameter (in percent) for thresholding; +# float; bias>=0; default=20 +# -n negate negate indicates whether to negate the image +# before and after processing; negate=yes or no; +# default=no +# +### +# +# NAME: LOCALTHRESH +# +# PURPOSE: To threshold an image to binary (b/w) format using a moving +# window adaptive thresholding approach. +# +# DESCRIPTION: LOCALTHRESH thresholds an image to binary (b/w) format +# using a moving window adaptive thresholding approach. For each window +# placement the center pixel is compared to some measure of either mean or +# combination of mean and either standard deviation or mean absolute +# deviation within the window. If the center pixel is larger than this +# measure by some bias value, then the center pixel is made white; +# otherwise it is made black. The moving window is a circle with Gaussian +# profile. NOTE: the image MUST have the "objects" or foreground as white +# and the "non-objects" or background as black. Thus the image must either +# be preprocessed using the IM function -negate or have the script do that +# using its negate parameter. IMPORTANT: For acceptable results, the +# window size generally should be larger than the dimension of the +# "objects" to be detected in the image by the thresholding. Consequently, +# this method is best applied to images of text, small objects or edges. +# +# OPTIONS: +# +# -m method ... METHOD specifies what statistical measure to use to +# compute the threshold for each window placement. Method 1 compares +# the center pixel to the window mean, and if larger than the bias, +# the center is made white; otherwise black. Method 2 compares the +# center pixel to the window mean plus the bias times the window +# standard deviation, and if the center pixels is larger, it is made +# white; otherwise black. Method 3 compares the center pixel to the +# window mean plus the bias times the square root of window mean +# absolute deviation and if the center pixel is larger, it is made white; +# otherwise black. The default is method=1. Note that method=1 is similar +# to the IM function -lat (but uses a circular gaussian weighted window +# rather than a square uniform weighted window and more importantly +# does not suffer from the image shift resulting with the IM -lat +# function). +# +# -r radius ... RADIUS specifies the radius for the gaussian profile +# window. The value may be a float, but must be greater than or equal +# to 3. The default=15. For acceptable results, the radius generally +# must be larger than the feature dimension that is to be detected by +# the thresholding. +# +# -b bias ... BIAS is the bias parameter used in each of the two +# methods to determine the threshold. Larger bias values will have +# the effect of removing more "noise" from the result, but too large +# a value may remove parts of the foreground objects that are detected. +# Values for bias are expressed as (percent) floats where bias>=0. +# The default=20. +# +# -n negate ... NEGATE indicates whether to negate the image before +# and after processing, since this technique only works when the "object" +# or foreground is white and the "non-object" or background is black. +# Values may be either yes or no. The default=yes. +# +# REFERENCES: see the following: +# http://www.dfki.uni-kl.de/~shafait/papers/Shafait-efficient-binarization-SPIE08.pdf +# http://www.busim.ee.boun.edu.tr/~sankur/SankurFolder/Threshold_survey.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 +method=1 #1=mean, 2=mean and std, 3=mean and sqrt(mad) +radius=15 #radius>=3 +bias=20 #percent bias>=0 +negate="no" #yes or no + +# 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 10 ] + 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 + ;; + -m) # get method + shift # to get the next parameter + # test if parameter starts with minus sign + errorMsg="--- INVALID METHOD SPECIFICATION ---" + checkMinus "$1" + method=`expr "$1" : '\([0-9]*\)'` + [ "$method" = "" ] && errMsg "--- METHOD=$method MUST BE A NON-NEGATIVE INTEGER ---" + [ $method -lt 1 -o $method -gt 3 ] && errMsg "--- METHOD=$method MUST BE EITHER 1 OR 2 ---" + ;; + -r) # get radius + shift # to get the next parameter + # test if parameter starts with minus sign + errorMsg="--- INVALID RADIUS SPECIFICATION ---" + checkMinus "$1" + radius=`expr "$1" : '\([.0-9]*\)'` + [ "$radius" = "" ] && errMsg "--- RADIUS=$radius MUST BE A NON-NEGATIVE FLOAT ---" + radiustest=`echo "$radius < 3" | bc` + [ $radiustest -eq 1 ] && errMsg "--- RADIUS=$radius MUST BE A FLOAT GREATER THAN OR EQUAL TO 3 ---" + ;; + -b) # get bias + shift # to get the next parameter + # test if parameter starts with minus sign + errorMsg="--- INVALID BIAS SPECIFICATION ---" + checkMinus "$1" + bias=`expr "$1" : '\([.0-9]*\)'` + [ "$bias" = "" ] && errMsg "--- BIAS=$bias MUST BE A NON-NEGATIVE FLOAT ---" + ;; + -n) # get negate + shift # to get the next parameter + # test if parameter starts with minus sign + errorMsg="--- INVALID NEGATE SPECIFICATION ---" + checkMinus "$1" + negate="$1" + negate=`echo "$negate" | tr '[A-Z]' '[a-z]'` + case "$negate" in + yes|y) negate="yes";; + no|n) negate="no";; + *) errMsg "--- NEGATE=$negate MUST BE EITHER YES OR NO ---";; + esac + ;; + -) # 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 +[ "$outfile" = "" ] && errMsg "NO OUTPUT FILE SPECIFIED" + +tmpA1="$dir/autothresh1_A_$$.mpc" +tmpA2="$dir/autothresh1_A_$$.cache" +tmpT1="$dir/autothresh1_T_$$.mpc" +tmpT2="$dir/autothresh1_T_$$.cache" +tmpM1="$dir/autothresh1_M_$$.mpc" +tmpM2="$dir/autothresh1_M_$$.cache" +tmpS1="$dir/autothresh1_S_$$.mpc" +tmpS2="$dir/autothresh1_S_$$.cache" +trap "rm -f $tmpA1 $tmpA2 $tmpT1 $tmpT2 $tmpM1 $tmpM2 $tmpS1 $tmpS2; exit 0" 0 +trap "rm -f $tmpA1 $tmpA2 $tmpT1 $tmpT2 $tmpM1 $tmpM2 $tmpS1 $tmpS2; 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 localthresh. +# 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" $setcspace -colorspace gray -alpha off +repage "$tmpA1" + then + : ' do nothing ' +else + errMsg "--- FILE $infile DOES NOT EXIST OR IS NOT AN ORDINARY FILE, NOT READABLE OR HAG ZERO SIZE ---" +fi + +# setup window filters + radius=`convert xc: -format "%[fx:$radius/3]" info:` + size="0x${radius}" + + +# process image +[ "$negate" = "yes" ] && convert $tmpA1 -negate $tmpA1 + +# get mean image +convert $tmpA1 -blur "$size" $tmpM1 + +# NOTE: to form (image1-image2), +# use convert image2 image1 -compose minus -composite +# or convert image1 image2 +swap -compose minus -composite + +# get sos=second order statistic = either std or sqrt(mad) +if [ $method -eq 2 ]; then + # get standard deviation=std image; std = sqrt( ave(x^2) - ave(x)^2 ); + # ave=mean; -gamma 2 is equivalent to sqrt + convert \( $tmpA1 $tmpA1 -compose multiply -composite -blur "$size" \) \ + \( $tmpM1 $tmpM1 -compose multiply -composite \) +swap \ + -compose minus -composite -gamma 2 $tmpS1 + +elif [ $method -eq 3 ]; then + # get sqrt(mean absolute deviation)=sqrt(mad) image; + # mad=absolute difference of (image - mean) + convert $tmpA1 $tmpM1 -compose difference -composite -gamma 2 $tmpS1 +fi + + +if [ $method -eq 1 ]; then + # threshold to white if image > (mean + K) or + # image - (mean + K) > 0 or + # (image - mean) - K > 0 or + # (image - mean) > K + # where K is percent + #convert $tmpA1 \( $tmpM1 -evaluate add ${bias}% \) +swap -compose minus -composite -threshold 1 $tmpT1 + #convert $tmpA1 $tmpM1 +swap -compose minus -composite -evaluate subtract ${bias}% -threshold 1 $tmpT1 + + convert $tmpA1 $tmpM1 +swap -compose minus -composite -threshold ${bias}% $tmpT1 + +else + # threshold to white if image > (mean +k*sos) or + # image - (mean +k*sos) > 0 or + # (image - mean) - k*sos > 0 + # where k is fraction, k=K/100 and K is percent + + bias=`convert xc: -format "%[fx:$bias/100]" info:` + convert $tmpA1 $tmpM1 +swap -compose minus -composite \ + \( $tmpS1 -evaluate multiply ${bias} \) \ + +swap -compose minus -composite \ + -threshold 1 \ + $tmpT1 +fi + +if [ "$negate" = "yes" ]; then + convert $tmpT1 -negate "$outfile" +else + convert $tmpT1 "$outfile" +fi + +exit 0 diff --git a/bin/otsuthresh b/bin/otsuthresh new file mode 100644 index 0000000..2889230 --- /dev/null +++ b/bin/otsuthresh @@ -0,0 +1,368 @@ +#!/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: otsuthresh [-g graph] infile outfile +# USAGE: otsuthresh [-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: OTSUTHRESH +# +# PURPOSE: To automatically thresholds an image to binary (b/w) format +# using Otsu's between class variance technique. +# +# DESCRIPTION: OTSUTHRESH 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 Otsu appoach computes the Between Class Variance +# from the foreground (above threshold data) and background (at and below +# threshold value) for every possible threshold value. The optimal threshold +# is the one that maximizes the Between Class Variance. This is equivalent +# to finding the threshold that minimizes the overlap between the two +# bell-shaped class curves. +# +# 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_otsu.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 +# http://www.cse.unr.edu/~bebis/CS791E/Notes/Thresholding.pdf +# http://www.ifi.uio.no/in384/info/threshold.ps +# http://www.supelec.fr/ecole/radio/JPPS01.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_otsu.gif + +tmpA1="$dir/otsuthresh_1_$$.mpc" +tmpA2="$dir/otsuthresh_1_$$.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 otsuthresh. +# 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` + + # get value array from IM histogram + valueArr=(`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]; } } '`) +# echo ${valueArr[*]} +# echo ${#valueArr[*]} + numvals=${#valueArr[*]} + + # get count array from IM histogram + countArr=(`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 + { cbin[$2] += $1; } + END { for (i=0;i<256;i++) {print cbin[i]; } } '`) +# echo ${countArr[*]} +# echo ${#countArr[*]} + numcounts=${#countArr[*]} + + [ $numvals -ne $numcounts ] && errMsg "--- NUMBER OF COUNTS IS NOT THE SAME AS NUMBER OF VALUES ---" + + # compute normalized count array + ncountArr=( $(for ((i=0; i<$numcounts; i++)); do + echo "$i ${countArr[$i]}" + done |\ + awk -v totpix="$totpix" -v numcounts="$numcounts" ' + # AWK + { bin[$1] = $2; } + END { for (i=0;i<numcounts;i++) {print bin[i]/totpix; } } ') ) +# echo ${ncountArr[*]} +# echo ${#ncountArr[*]} + + # get global mean from values and normalized counts + mean=$( for ((i=0; i<$numcounts; i++)); do + echo "$i ${valueArr[$i]} ${ncountArr[$i]}" + done |\ + awk -v numcounts="$numcounts" ' + # AWK + { vbin[$1] = $2; ncbin[$1] = $3; } + END { for (i=0;i<numcounts;i++) { mean += vbin[i]*ncbin[i]; } print mean } ' ) +# echo "mean=$mean" + + +#Generate Cumulative Arrays +# p=c(i)/N (normalized count or probability, p, at bin i) +# v=v(i) (graylevel 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) +# g=p1=sum(c(i)*v(i))=first histogram momement => cumulative normalized graylevel (from i=0 to t) = G(t) + + + # compute nlowArr + nlowArr=( $(for ((i=0; i<$numcounts; i++)); do + echo "$i ${ncountArr[$i]}" + done |\ + awk -v numcounts="$numcounts" ' + # AWK to generate a cumulative histogram 1D image... + { nlowbin[$1] = $2; } + END { for (i=0;i<numcounts;i++) { nlow += nlowbin[i]; print nlow } } ') ) +# echo ${nlowArr[*]} +# echo ${#nlowArr[*]} + + # compute glowArr + glowArr=( $( for ((i=0; i<$numcounts; i++)); do + echo "$i ${valueArr[$i]} ${ncountArr[$i]}" + done |\ + awk -v numcounts="$numcounts" ' + # AWK to generate a cumulative histogram 1D image... + { vlowbin[$1] = $2; nclowbin[$1] = $3; } + END { for (i=0;i<numcounts;i++) { glow += vlowbin[i]*nclowbin[i]; print glow } } ') ) +# echo ${glowArr[*]} +# echo ${#glowArr[*]} + + +# Compute Threshold +# loop through histogram using normalized counts and values +# compute threshold by maximizing between class variance +# bcv=Nl*(Ml-M)^2 + Nh*(Mh-M)^2 = (M*Nl-Gl)^2/(Nl*(1-Nl)) + +# m=p1/p0=mean => M(t)=G(t)/N(t) +# where Nh and Nl are normalized counts above and below threshold (zeroth moments, p0) +# Mh and Ml are means of pixels above and below threshold +# Gh and Gl are normalized cumulative graylevels (first moments, p1) +# ML=Gl/Nl +# above derived using +# Nh=(1-Nl) for normalized histogram +# Mh=(M-Ml*Nl)/(1-Nl) where M is overall mean of image + + + # compute threshold + #note: must stop at second to last bin so that nlow != 1 exactly or get divide by zero + threshbin=$(for ((i=0; i<$numcounts; i++)); do + echo "$i ${nlowArr[$i]} ${glowArr[$i]}" + done |\ + awk -v numcounts="$numcounts" -v mean="$mean" -v bcvold=0 -v threshbin=0 ' + # AWK to compute entropy threshold... + { nlowbin[$1] = $2; glowbin[$1] = $3; } + END { for (i=0;i<(numcounts-1);i++) + { dmean = (mean*nlowbin[i] - glowbin[i]); bcv = dmean*dmean/(nlowbin[i]*(1-nlowbin[i])); + if (bcv>bcvold) { bcvold=bcv; threshbin=i; } } print threshbin } ') +# echo "threshbin=$threshbin" + thresh=${valueArr[$threshbin]} +# echo "thresh=$thresh" + threshpct=`convert xc: -format "%[fx:100*$thresh/255]" info:` + + + +# 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 + + + diff --git a/bin/ptilethresh b/bin/ptilethresh new file mode 100644 index 0000000..9838b95 --- /dev/null +++ b/bin/ptilethresh @@ -0,0 +1,213 @@ +#!/bin/bash +# +# Developed by Fred Weinhaus 8/30/2012 .......... 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: ptilethresh [-p percentile] infile outfile +# USAGE: ptilethresh [-h or -help] +# +# OPTIONS: +# +# -p percentile percentile on cumulative histogram for desired threshold; +# 0<=float<=100; default=50 +# +### +# +# NAME: PTILETHRESH +# +# PURPOSE: To automatically thresholds an image to binary (b/w) format +# at a specified percentile on the cumulative histogram. +# +# DESCRIPTION: PTILETHRESH automatically thresholds an image to binary +# (b/w) format at a specified percentile on the cumulative histogram. When +# the percentile is 50%, this technique is also known as balanced thresholding. +# +# OPTIONS: +# +# -p percentile ... PERCENTILE is the desired threshold point on the cumulative +# histogram. Values are floats between 0 and 100. The default=50. +# +# 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: +# http://en.wikipedia.org/wiki/Balanced_histogram_thresholding +# http://www.pvv.org/~perchrh/papers/datasyn/paper2/report.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 +percentile=50 + + +# 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 + ;; + -p) # get percentile + shift # to get the next parameter + # test if parameter starts with minus sign + errorMsg="--- INVALID PERCENTILE SPECIFICATION ---" + checkMinus "$1" + percentile=`expr "$1" : '\([.0-9]*\)'` + [ "$percentile" = "" ] && errMsg "--- PERCENTILE=$percentile MUST BE A NON-NEGATIVE FLOAT ---" + testA=`echo "$percentile < 0" | bc` + testB=`echo "$percentile > 100" | bc` + [ $testA -eq 1 -o $testB -eq 1 ] && errMsg "--- PERCENTILE=$percentile MUST BE A FLOAT 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 +[ "$outfile" = "" ] && errMsg "NO OUTPUT FILE SPECIFIED" + + +tmpA1="$dir/ptilethresh_1_$$.mpc" +tmpA2="$dir/ptilethresh_1_$$.cache" +trap "rm -f $tmpA1 $tmpA2 exit 0;" 0 +trap "rm -f $tmpA1 $tmpA2; 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 ptilethresh. +# with IM 6.7.4.10, 6.7.6.10, 6.7.9.10 +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" +repage "$tmpA1" + then + : ' do nothing ' +else + errMsg "--- FILE $infile DOES NOT EXIST OR IS NOT AN ORDINARY FILE, NOT READABLE OR HAG ZERO SIZE ---" +fi + +bpt=$percentile +wpt=`convert xc: -format "%[fx:100-$bpt]" info:` +# process image +convert $tmpA1 $setcspace -colorspace gray -linear-stretch $bpt%,$wpt% "$outfile" + +exit 0 + + + 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 + + + diff --git a/bin/trianglethresh b/bin/trianglethresh new file mode 100644 index 0000000..7c8119a --- /dev/null +++ b/bin/trianglethresh @@ -0,0 +1,419 @@ +#!/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 + + + diff --git a/photoblaster/modules/pbbreaker/__init__.py b/photoblaster/modules/pbbreaker/__init__.py index fb3f26a..93c7568 100755 --- a/photoblaster/modules/pbbreaker/__init__.py +++ b/photoblaster/modules/pbbreaker/__init__.py @@ -24,7 +24,7 @@ _BREAKTYPE_TRANSLATE = { 'RGB_WASH_2': 'psb', 'NOISY_BREAK': 'palm', 'NOISY_BREAK_2': 'fig', - 'BROKEN_VIGNETTE': 'pbm', + 'BROKEN_THRESH': 'pbm', 'FAX_MACHINE': 'cals', 'STRIPES': 'exr', 'PHOTOCOPY': 'art', diff --git a/share/frontend/imbreak/index.html b/share/frontend/imbreak/index.html index 7bab966..db1e272 100755 --- a/share/frontend/imbreak/index.html +++ b/share/frontend/imbreak/index.html @@ -202,7 +202,7 @@ BREAK TYPE: <select id="breaktype"> <option value="RGB_WASH">RGB WASH</option> <option value="RGB_WASH_2">CHOP AND BLUR</option> <option value="NOISY_BREAK">NOISY BREAK</option> - <option value="BROKEN_VIGNETTE">BROKEN VIGNETTE</option> + <option value="BROKEN_THRESH">BROKEN THRESH</option> <option value="FAX_MACHINE">FAX MACHINE</option> <option value="STRIPES">STRIPES</option> |