astanin/imagej.sh

## imagej.sh
#!/bin/bash

# imagej.sh - a not so simple wrapper script used to run ImageJ

#	Copyright © 2008 Paolo Ariano
#	Authors: Paolo Ariano (paolo dot ariano at unito dot it)
#	Last modified date: 19 Sept 2008

# This is a not so simple wrapper script used to run ImageJ in Unix but
# optimized for Debian GNU/Linux, this is a merge between my original script
# and a more exhaustive one from Jon Jackson (jjackson at familyjackson dot net)

#	Edited 2009 Giulio Guzzinati
#	Authors: Giulio Guzzinati (skarn86junk () gmail DOT it)
#	Last modified date: 24 May 2009

#This script has been edited for usage with Arch Linux by Giulio Guzzinati

# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU Lesser General Public Licenseas published by
# the Free Software Foundation, either version 3 of the License, or (at
# your option) any later version. See the file Documentation/LGPL3 in the
# original distribution for details. There is ABSOLUTELY NO warranty.
# This program is free software, but comes with no warrenty or guarantee
# send bug reports or feedback to me or to debian bug tracking system


# setup environment
set +u # don't give error for unset variables (matters for environment variables)
shopt -s extglob # allow extended pattern matching

##################### DEFINE JAVA_HOME #####################

# Not necessary in Archlinux.
# See https://wiki.archlinux.org/index.php/Java_Package_Guidelines

##################### CREATE THE RIGHT ENVIRONMENT #####################

# ImageJ path
ij_path=/usr/share/imagej

#ImageJ user path
ij_user_path=$HOME/.imagej

# Documentation URL
doc_url='http://rsb.info.nih.gov/ij/'

# temp folder
ij_tmp='/tmp/imagej'

# default behaviour when an ImageJ window is already open
newwindow='true'
#newwindow='false'

# macro argument conjoining character
separator=':'
# a ' ' may work provided no arguments would contain spaces
# use macro functions:  args=getArgument(); argArray=split(args, ':');
# to recover macro arguments

# create plugins,macro,tmp dirs
mkdir -p ${ij_user_path}/plugins
mkdir -p ${ij_user_path}/macros
mkdir -p ${ij_user_path}/luts

# makes symbolik links from shared plugins, macros and luts

ls ${ij_path}/plugins | while read p ; do
  if [ ! -e "${ij_user_path}/plugins/$p" ] ; then
    ln -s "${ij_path}/plugins/$p" "${ij_user_path}/plugins/$p"
  fi
done

ls ${ij_path}/macros | while read p; do
  if [ ! -e "${ij_user_path}/macros/$p" ] ; then
      ln -s "${ij_path}/macros/$p" "${ij_user_path}/macros/$p"
  fi
done

ls ${ij_path}/luts | while read p ; do
    if [ ! -e "${ij_user_path}/luts/$p" ] ; then
	ln -s "${ij_path}/luts/$p" "${ij_user_path}/luts/$p"
    fi
done


# report errors to this user
# ijadmin='paolo.ariano@unito.it'

# other variables
dir=`pwd`
user=`whoami`
host=`hostname`
if [[ -z "$DISPLAY" ]] ; then
    echo 'Display variable not set'
    echo 'If ImageJ fails to load, try '
    echo '% setenv DISPLAY yourcomputer:0'
    echo 'if you use the "csh" or for "bash" try'
    echo '% export DISPLAY=yourcomputer:0'
    display='default'
else
    display="$DISPLAY"
fi

declare -i port=0
declare -i verbosity=0
images=''
macrocmd=''
macroargs=''

############ DEFAULT MEMORY SETTINGS  #########################

declare -i default_mem=768
declare -i min_mem=32
declare -i max_32bit=1800 # empirical
declare -i max_64bit=17000000000 # conservative

############ MEMORY ALLOCATION #########################

OS=$(uname)
processor=$(uname -m) # -p doesn't work on debian/ubuntu
declare -i mem
declare -i max_mem
declare -i free_mem

java_home="${java_home:-$JAVA_HOME}"

if [[ "$OS" == 'SunOS' ]] ; then
    java_arch='-d64'
	JAVA_HOME="${java_home_SunOS:-$java_home}"
	max_mem=`vmstat | awk 'BEGIN{maxMem='$max_64bit'} NR == 3 {fmem=int($5 / 1024); if (fmem < maxMem) {print fmem} else {print maxMem}}'`
	free_mem="max_mem"
	mem=${free_mem}/2
	if (( $mem > $default_mem || $mem < $min_mem )) ; then mem=$default_mem ; fi
elif [[ "$OS" == 'Linux' ]] ; then
	if [[ "$processor" == 'x86_64' ]] ; then
    	java_arch='-d64'
        JAVA_HOME="${java_home_Linux_x86_64:-$java_home}"
    	max_mem=`free | awk -v maxMem=$max_64bit 'NR == 2 {fmem=int($2 / 1024); if (fmem < maxMem) {print fmem} else {print maxMem}}'`
		free_mem=`free | awk -v maxMem=$max_64bit 'NR == 3 {fmem=int($4 / 1024); if (fmem < maxMem) {print fmem} else {print maxMem}}'`
		mem=${free_mem}/3*2
		if (( $mem > $default_mem || $mem < $min_mem )) ; then mem=$default_mem ; fi
	else
		java_arch='-d32'
    	JAVA_HOME="${java_home_Linux:-$java_home}"
    	max_mem=`free | awk -v maxMem=$max_32bit 'NR == 2 {fmem=int($2 / 1024); if (fmem < maxMem) {print fmem} else {print maxMem}}'`
		free_mem=`free | awk -v maxMem=$max_32bit 'NR == 3 {fmem=int($4 / 1024); if (fmem < maxMem) {print fmem} else {print maxMem}}'`
		mem=${free_mem}/3*2
		if (( $mem > $default_mem || $mem < $min_mem )) ; then mem=$default_mem ; fi
	fi
fi


##################### USAGE DESCRIPTION #####################

function usage {
    echo
    echo 'Image display and analysis program. Opens formats including:'
    echo 'UNC, Analyze, Dicom, NIFTI, Tiff, Jpeg, Gif, PNG ...'
    echo
    echo 'imagej [options] image [ image2 ... image3 ]'
    echo '    -h        print help and more options'
    echo '    -o        open images in an open ImageJ panel'
    echo '    -p <N>    open images in ImageJ panel number <N>'
    echo "    -x <MB>   set available memory (default=${mem} max=${max_mem})"
    echo
}

function fullusage {
    echo
    echo 'Image display and analysis program. Opens formats including:'
    echo 'UNC, Analyze, Dicom, NIFTI, Tiff, Jpeg, Gif, PNG ...'
    echo
    echo 'imagej [options] image [ image2 ... image3 ] -> open images'
    echo
    echo 'basic options:'
    echo '  -h        print help and more options'
    echo '  -o        open images in existing ImageJ panel if one exists'
    echo '  -p <N>    open images in existing ImageJ panel number <N>'
    echo "  -x <MB>   set available memory (default=${mem} max=${max_mem})"
    echo
    echo 'advanced options:'
    echo '  -c        enable plugin compilation within imagej'
    echo '  -d        use development version'
    echo '  -v        be verbose (vv or vvv increases verbosity)'
    echo
    echo 'options for batch processing:'
    echo "  -e 'Macro Code'            execute macro code"
    echo "  -r 'Menu Command'          run menu command"
    echo "Quotation marks '' are required around commands including spaces"
    echo 'Commands can be sent to open ImageJ panels with the -p option'
    echo
    echo 'options for macros:'
    echo 'imagej [-i image] [-b|-m] [arg1 ... argN] '
    echo '  -b macro    run macro without graphics window'
    echo '  -m macro    run macro'
    echo '"image" will be opened before macro is run'
    echo 'all following arguments are passed to macro'
    echo
    echo "Documentation - $doc_url "
	echo "Report problems with this software to $ijadmin"
    echo
}

function macroCmdError {
	fullusage
	echo 'Only one command option (-b -e -m OR -r) may be specified' 1>&2
	exit 1
}

function getFullPath {
    # Return full path to file
    # treats multiple arguments as a single file with spaces
    if (( $# == 0 )) ; then
        echo "error getting full path for '${*}'" 1>&2
    fi
    pwd_getFullPath="$PWD"
    \cd $(dirname "${*}") > /dev/null
    dir_getFullPath="$PWD"
    \cd "$pwd_getFullPath" > /dev/null
    echo "$dir_getFullPath"/$(basename "${*}")
}
function derefln {
    # Returns the full path of file to which link points
    # following multiple levels of symbolic links.
    # NOTE: if you use this function in a script, don't use any
    # of the variable names used here
    if (( $# == 0 )) ; then
        return
    fi
    local the_link="$1"
    local link_dir
    local current_dir="$PWD"
    while file "$the_link" | grep symbolic > /dev/null ; do # resolve links until target is regular file
        if [[ "$the_link" == */* ]] ; then # path contains  /
            \cd $(dirname "${the_link}") > /dev/null
            the_link=$(basename "$the_link")
        fi
        link_dir="$PWD"
	    # some versions of 'file' surround the path in `' quotes, hence the tr to remove them
        the_link=$(file "${the_link}" | awk '/symbolic link/ {print $NF}' | tr -d "\140\047" )
        if [[ "$the_link" != /* ]] ; then # path is not absolute path  - make it one
            the_link="$link_dir/$the_link"
        fi
        \cd "$current_dir" > /dev/null
    done
    echo $the_link
}


# The best way to install .jar libraries required by plugins is to copy them
# to the imagej plugins/jars directory
# Alternatively, either copy them to ${ij_path}/jre/lib/ext/ or add the .jar
# filepath to the modules line below. Paths are separated by a colon
# Classpath must follow command line arguments, as ij_path is dependent on the -d option

# Resolving ij.jar path.  If ij.jar is a symbolic link to ij_<version>.jar
# this allows updating ij.jar without crashing running sessions
ij_jar_path=$(derefln ${ij_path}/ij.jar)

for mod_jar in ${ij_path}/lib/*jar  ; do
    modules="${modules:-}${modules+:}$mod_jar"
done
modules="-cp ${ij_jar_path}:${modules+:}${modules:-}"
#${ij_path}/plugins/jars/dcmie.jar

export LD_LIBRARY_PATH="${ij_path}/lib/${OS}_$processor"
if (( $verbosity > 0 )) ; then
    echo "LD_LIBRARY_PATH=$LD_LIBRARY_PATH"
fi

# enable plugins to be compiled in imagej
tools="$JAVA_HOME/lib/tools.jar"


#####################  ARGUMENTS PARSING #####################

while getopts b:cde:hi:m:nop:r:vx: options
do
	case $options in
		b)	if [[ -n "$macrocmd" ]] ; then macroCmdError ; fi
			macrocmd="-batch ${OPTARG}"
			;;
		c)	modules="${modules:-}${modules+:}${tools}"
			;;
		d)	ij_path="$ij_path_dev"
			;;
		e)  if [[ -n "$macrocmd" ]] ; then macroCmdError ; fi
			macrocmd='-eval'
			macroargs="'${OPTARG}'"
			;;
		h)  fullusage
			exit 0
			;;
		i)  images="${images}'${OPTARG}' "
			;;
		m)	if [[ -n "$macrocmd" ]] ; then macroCmdError ; fi
			macrocmd="-macro ${OPTARG}"
			;;
        n)  newwindow='true'
            ;;
		o)  newwindow='false'
			;;
		p)	newwindow='false'
			port="${OPTARG}"
        	if (( "$port" < 1 || "$port" > 99 )) ; then
            	echo "${OPTARG} is not a permissible value for port number (-p)" 1>&2
            	exit 1
        	fi
			;;
		r)	if [[ -n "$macrocmd" ]] ; then macroCmdError ; fi
			macrocmd='-run'
			macroargs="'${OPTARG}'"
			;;
		v)	verbosity=verbosity+1
			if (( $verbosity == 2 )) ; then set -x ; fi
			if (( $verbosity == 3 )) ; then set -v ; fi
			;;
		x)	mem="${OPTARG}"
            newwindow='true'
			if (( $mem < $min_mem || $mem > $max_mem )) ; then
            	echo "${OPTARG} is not a permissible value for memory (-x)" 1>&2
            	echo "min=${min_mem}, max=${max_mem}" 1>&2
            	exit 1
			fi
			;;
		\?) usage
			exit 1
			;;
	esac
done


declare -i i=1
while (( i < $OPTIND )) ; do
	shift
	i=i+1
done

#if (( "$#" == 0 )) ; then
#	usage
#fi

# -b and -m options only:
# remaining command line arguments are passed as macro arguments
# separated by $separator
if [[ -n "$macrocmd" && -z "$macroargs" ]] ; then
	while (( "$#" > 0 )) ; do
        if [[ -z "$macroargs" ]] ; then
            macroargs="${1}"
        else
            macroargs="${macroargs}${separator}${1}"
        fi
        shift
	done
	macroargs="'$macroargs'"
fi

# PROTECT POSSIBLE SPACES IN IMAGE FILENAMES
if (( "$#" > 0 )) ; then
	while (( "$#" > 0 )) ; do
        filearg="${1}"
        # full file path required when sending images to running ImageJ panel
        if [[ "${newwindow}" == 'false' && -f "${filearg}" ]]  && ! expr "${filearg}" : '/.*' > /dev/null; then
            filearg="$(getFullPath ${filearg})"
        fi
		images="${images}'$filearg' "
		shift
	done
fi

##################### USING PORT #####################

# CREATE IMAGEJ SOCKET-LOCK DIRECTORY IF NON EXISTANT
if [[ ! -d "$ij_tmp" ]] ; then
    mkdir "$ij_tmp"
    chmod 777 "$ij_tmp"
fi

# CREATE IMAGEJ LOG FILE IF NON EXISTANT
if [[ -n "$ij_log" && ! -f "$ij_log" ]] ; then
    touch "$ij_log"
    chmod 666 "$ij_log"
fi

# CREATES A TEMP FILE INDICATING A PORT IS IN USE BY IMAGEJ
cd "$ij_tmp"
declare -i count=1
portopen='false'
lockFileCreated='false'
declare -a locklist=(`ls | grep '[0-9][0-9]-.*'`)

[[ -n "$ij_log" ]] && echo -e "$$\t$(date)\tNew Window = $newwindow" >> "$ij_log" 2> /dev/null
[[ -n "$ij_log" ]] && echo -e "$$\t$(date)\tPort = $port" >> "$ij_log" 2> /dev/null
[[ -n "$ij_log" ]] && echo -e "$$\t$(date)\tlocklist: \n ${locklist[*]}" >> "$ij_log" 2> /dev/null
if (( $verbosity > 0 )) ; then echo -e "locklist: \n ${locklist[*]}" ; fi

# PORT SPECIFIED BY USER
if (( $port > 0 )) ; then
    # look for a lock on the port specified
    for lockname in ${locklist[*]} ; do
        prefix=`printf '%02u' $port`
        if [[ "$lockname" == ${prefix}-${user}-${host}* ]] ; then
        	# found lock on the requested port, owned by user on current display
            portopen='true'
            if (( $verbosity > 0 )) ; then echo "Using socket lock: $lockname" ; fi
            count=$port
            break
        elif [[ "$lockname" == ${prefix}-* ]] ; then
            echo "Port $port is in use by some other user or a different host" 1>&2
            if (( $verbosity > 0 )) ; then echo "Port lock: $lockname" ; fi
            exit 1
        fi
    done
    # specified port not in use
    count=$port

# IF EXISTING WINDOW IS REQUESTED, LOOK FOR LISTENING PORT
elif [[ "$newwindow" == 'false' && ${#locklist} != 0 ]] ; then
    # look for a lock on the current display for this user
    for lockname in ${locklist[*]} ; do
        if [[ "$lockname" == [0-9][0-9]-${user}-${host}-${display} ]] ; then
            portopen='true'
            if (( $verbosity > 0 )) ; then echo "Found socket lock: $lockname" ; fi
            # if a matching user/display is found, use this one
            count="${lockname%-*-*-*}"
            #count=`echo $lockname | sed  -e 's/^\([0-9][0-9]\).*/\1/' -e 's/^0//'` # csh?
            break
        fi
    done
fi

# IF A NEW PORT IS TO BE USED
if [[ "$portopen" == 'false' ]] ; then
    # new window requested or no matching port found
    # if port is not specified, look for first free port
    if (( "$port" == 0 )) ; then
        if (( ${#locklist} == 0 )) ; then
            # no active locks - use first port
            count=1
        else
            # active locks - check each port number so see if it is in use
            # this is not synchronised!!
            count=0
            inuse='true'
            while [[ "$inuse" == 'true' ]] ; do
                count=count+1
                prefix=`printf '%02u' $count`
                inuse='false'
                for lockname in ${locklist[*]} ; do
                    if [[ "$lockname" == ${prefix}-* ]] ; then
                        inuse='true'
                    fi
                done
            done
        fi
    fi
    # CREATING A NEW PORT LOCK
    prefix=`printf '%02u' $count`
    lockname=${prefix}-${user}-${host}-${display}

    [[ -n "$ij_log" ]] && echo -e "$$\t$(date)\tCreating lock\t$lockname" >> "$ij_log" 2> /dev/null
	if (( $verbosity > 0 )) ; then echo -n "creating lock $lockname ... " ; fi
	touch $lockname
	trap '\rm -f ${ij_tmp}/$lockname >/dev/null ; echo -e "$$\t$(date)\tReleasing lock\t$lockname" >> "$ij_log" 2> /dev/null' EXIT TERM KILL
	# Quitting ImageJ sends EXIT, as does a kill/kill -9
	# CTRL+C in terminal sends INT + EXIT
	# System shutdown sends TERM (+EXIT??)

	if (( $verbosity > 0 )) ; then  echo 'done' ; fi

    lockFileCreated='true'
    if [[ -z "$macrocmd" ]] ; then
	    echo 'Open other images in this ImageJ panel as follows:'
	    echo "  imagej -p $count <image1> [<image2> ... <imageN>]"
    fi
    [[ -n "$ij_log" ]] && echo -e "$$\t$(date)\tSocket lock:\t$lockname" >> "$ij_log" 2> /dev/null
    if (( $verbosity > 0 )) ; then echo "Socket lock: $lockname" ; fi
	echo
fi

##################### FINALLY RUN IMAGEJ #####################

#popd > /dev/null

#if [ "$JAVA_HOME" ] ; then
#	if (( $verbosity > 0 )) ; then
#		echo ${modules}
#   		echo $JAVA_HOME/bin/java ${java_arch} -mx${mem}m ${modules} ij.ImageJ -ijpath ${ij_user_path} -port${count} ${images} ${macrocmd} ${macroargs}
#	else
#	eval $JAVA_HOME/bin/java ${java_arch} -mx${mem}m ${modules} ij.ImageJ -ijpath ${ij_user_path} -port${count} ${images} ${macrocmd} ${macroargs}
#	fi
#else
#  echo "No JVM found to run ImageJ"
#  echo "Please pacman -S java-runtime a JVM to run ImageJ or "
#  echo "check JAVA_HOME."
#  exit 1
#fi

exec java ${java_arch} -mx${mem}m ${modules} ij.ImageJ -ijpath ${ij_user_path} -port${count} ${images} ${macrocmd} ${macroargs}
	#!/bin/bash

	# imagej.sh - a not so simple wrapper script used to run ImageJ

	# Copyright © 2008 Paolo Ariano
	# Authors: Paolo Ariano (paolo dot ariano at unito dot it)
	# Last modified date: 19 Sept 2008

	# This is a not so simple wrapper script used to run ImageJ in Unix but
	# optimized for Debian GNU/Linux, this is a merge between my original script
	# and a more exhaustive one from Jon Jackson (jjackson at familyjackson dot net)

	# Edited 2009 Giulio Guzzinati
	# Authors: Giulio Guzzinati (skarn86junk () gmail DOT it)
	# Last modified date: 24 May 2009

	#This script has been edited for usage with Arch Linux by Giulio Guzzinati

	# This program is free software; you can redistribute it and/or modify it
	# under the terms of the GNU Lesser General Public Licenseas published by
	# the Free Software Foundation, either version 3 of the License, or (at
	# your option) any later version. See the file Documentation/LGPL3 in the
	# original distribution for details. There is ABSOLUTELY NO warranty.
	# This program is free software, but comes with no warrenty or guarantee
	# send bug reports or feedback to me or to debian bug tracking system


	# setup environment
	set +u # don't give error for unset variables (matters for environment variables)
	shopt -s extglob # allow extended pattern matching

	##################### DEFINE JAVA_HOME #####################

	# Not necessary in Archlinux.
	# See https://wiki.archlinux.org/index.php/Java_Package_Guidelines

	##################### CREATE THE RIGHT ENVIRONMENT #####################

	# ImageJ path
	ij_path=/usr/share/imagej

	#ImageJ user path
	ij_user_path=$HOME/.imagej

	# Documentation URL
	doc_url='http://rsb.info.nih.gov/ij/'

	# temp folder
	ij_tmp='/tmp/imagej'

	# default behaviour when an ImageJ window is already open
	newwindow='true'
	#newwindow='false'

	# macro argument conjoining character
	separator=':'
	# a ' ' may work provided no arguments would contain spaces
	# use macro functions: args=getArgument(); argArray=split(args, ':');
	# to recover macro arguments

	# create plugins,macro,tmp dirs
	mkdir -p ${ij_user_path}/plugins
	mkdir -p ${ij_user_path}/macros
	mkdir -p ${ij_user_path}/luts

	# makes symbolik links from shared plugins, macros and luts

	ls ${ij_path}/plugins \| while read p ; do
	if [ ! -e "${ij_user_path}/plugins/$p" ] ; then
	ln -s "${ij_path}/plugins/$p" "${ij_user_path}/plugins/$p"
	fi
	done

	ls ${ij_path}/macros \| while read p; do
	if [ ! -e "${ij_user_path}/macros/$p" ] ; then
	ln -s "${ij_path}/macros/$p" "${ij_user_path}/macros/$p"
	fi
	done

	ls ${ij_path}/luts \| while read p ; do
	if [ ! -e "${ij_user_path}/luts/$p" ] ; then
	ln -s "${ij_path}/luts/$p" "${ij_user_path}/luts/$p"
	fi
	done


	# report errors to this user
	# ijadmin='paolo.ariano@unito.it'

	# other variables
	dir=`pwd`
	user=`whoami`
	host=`hostname`
	if [[ -z "$DISPLAY" ]] ; then
	echo 'Display variable not set'
	echo 'If ImageJ fails to load, try '
	echo '% setenv DISPLAY yourcomputer:0'
	echo 'if you use the "csh" or for "bash" try'
	echo '% export DISPLAY=yourcomputer:0'
	display='default'
	else
	display="$DISPLAY"
	fi

	declare -i port=0
	declare -i verbosity=0
	images=''
	macrocmd=''
	macroargs=''

	############ DEFAULT MEMORY SETTINGS #########################

	declare -i default_mem=768
	declare -i min_mem=32
	declare -i max_32bit=1800 # empirical
	declare -i max_64bit=17000000000 # conservative

	############ MEMORY ALLOCATION #########################

	OS=$(uname)
	processor=$(uname -m) # -p doesn't work on debian/ubuntu
	declare -i mem
	declare -i max_mem
	declare -i free_mem

	java_home="${java_home:-$JAVA_HOME}"

	if [[ "$OS" == 'SunOS' ]] ; then
	java_arch='-d64'
	JAVA_HOME="${java_home_SunOS:-$java_home}"
	max_mem=`vmstat \| awk 'BEGIN{maxMem='$max_64bit'} NR == 3 {fmem=int($5 / 1024); if (fmem < maxMem) {print fmem} else {print maxMem}}'`
	free_mem="max_mem"
	mem=${free_mem}/2
	if (( $mem > $default_mem \|\| $mem < $min_mem )) ; then mem=$default_mem ; fi
	elif [[ "$OS" == 'Linux' ]] ; then
	if [[ "$processor" == 'x86_64' ]] ; then
	java_arch='-d64'
	JAVA_HOME="${java_home_Linux_x86_64:-$java_home}"
	max_mem=`free \| awk -v maxMem=$max_64bit 'NR == 2 {fmem=int($2 / 1024); if (fmem < maxMem) {print fmem} else {print maxMem}}'`
	free_mem=`free \| awk -v maxMem=$max_64bit 'NR == 3 {fmem=int($4 / 1024); if (fmem < maxMem) {print fmem} else {print maxMem}}'`
	mem=${free_mem}/3*2
	if (( $mem > $default_mem \|\| $mem < $min_mem )) ; then mem=$default_mem ; fi
	else
	java_arch='-d32'
	JAVA_HOME="${java_home_Linux:-$java_home}"
	max_mem=`free \| awk -v maxMem=$max_32bit 'NR == 2 {fmem=int($2 / 1024); if (fmem < maxMem) {print fmem} else {print maxMem}}'`
	free_mem=`free \| awk -v maxMem=$max_32bit 'NR == 3 {fmem=int($4 / 1024); if (fmem < maxMem) {print fmem} else {print maxMem}}'`
	mem=${free_mem}/3*2
	if (( $mem > $default_mem \|\| $mem < $min_mem )) ; then mem=$default_mem ; fi
	fi
	fi


	##################### USAGE DESCRIPTION #####################

	function usage {
	echo
	echo 'Image display and analysis program. Opens formats including:'
	echo 'UNC, Analyze, Dicom, NIFTI, Tiff, Jpeg, Gif, PNG ...'
	echo
	echo 'imagej [options] image [ image2 ... image3 ]'
	echo ' -h print help and more options'
	echo ' -o open images in an open ImageJ panel'
	echo ' -p <N> open images in ImageJ panel number <N>'
	echo " -x <MB> set available memory (default=${mem} max=${max_mem})"
	echo
	}

	function fullusage {
	echo
	echo 'Image display and analysis program. Opens formats including:'
	echo 'UNC, Analyze, Dicom, NIFTI, Tiff, Jpeg, Gif, PNG ...'
	echo
	echo 'imagej [options] image [ image2 ... image3 ] -> open images'
	echo
	echo 'basic options:'
	echo ' -h print help and more options'
	echo ' -o open images in existing ImageJ panel if one exists'
	echo ' -p <N> open images in existing ImageJ panel number <N>'
	echo " -x <MB> set available memory (default=${mem} max=${max_mem})"
	echo
	echo 'advanced options:'
	echo ' -c enable plugin compilation within imagej'
	echo ' -d use development version'
	echo ' -v be verbose (vv or vvv increases verbosity)'
	echo
	echo 'options for batch processing:'
	echo " -e 'Macro Code' execute macro code"
	echo " -r 'Menu Command' run menu command"
	echo "Quotation marks '' are required around commands including spaces"
	echo 'Commands can be sent to open ImageJ panels with the -p option'
	echo
	echo 'options for macros:'
	echo 'imagej [-i image] [-b\|-m] [arg1 ... argN] '
	echo ' -b macro run macro without graphics window'
	echo ' -m macro run macro'
	echo '"image" will be opened before macro is run'
	echo 'all following arguments are passed to macro'
	echo
	echo "Documentation - $doc_url "
	echo "Report problems with this software to $ijadmin"
	echo
	}

	function macroCmdError {
	fullusage
	echo 'Only one command option (-b -e -m OR -r) may be specified' 1>&2
	exit 1
	}

	function getFullPath {
	# Return full path to file
	# treats multiple arguments as a single file with spaces
	if (( $# == 0 )) ; then
	echo "error getting full path for '${*}'" 1>&2
	fi
	pwd_getFullPath="$PWD"
	\cd $(dirname "${*}") > /dev/null
	dir_getFullPath="$PWD"
	\cd "$pwd_getFullPath" > /dev/null
	echo "$dir_getFullPath"/$(basename "${*}")
	}
	function derefln {
	# Returns the full path of file to which link points
	# following multiple levels of symbolic links.
	# NOTE: if you use this function in a script, don't use any
	# of the variable names used here
	if (( $# == 0 )) ; then
	return
	fi
	local the_link="$1"
	local link_dir
	local current_dir="$PWD"
	while file "$the_link" \| grep symbolic > /dev/null ; do # resolve links until target is regular file
	if [[ "$the_link" == / ]] ; then # path contains /
	\cd $(dirname "${the_link}") > /dev/null
	the_link=$(basename "$the_link")
	fi
	link_dir="$PWD"
	# some versions of 'file' surround the path in `' quotes, hence the tr to remove them
	the_link=$(file "${the_link}" \| awk '/symbolic link/ {print $NF}' \| tr -d "\140\047" )
	if [[ "$the_link" != /* ]] ; then # path is not absolute path - make it one
	the_link="$link_dir/$the_link"
	fi
	\cd "$current_dir" > /dev/null
	done
	echo $the_link
	}


	# The best way to install .jar libraries required by plugins is to copy them
	# to the imagej plugins/jars directory
	# Alternatively, either copy them to ${ij_path}/jre/lib/ext/ or add the .jar
	# filepath to the modules line below. Paths are separated by a colon
	# Classpath must follow command line arguments, as ij_path is dependent on the -d option

	# Resolving ij.jar path. If ij.jar is a symbolic link to ij_<version>.jar
	# this allows updating ij.jar without crashing running sessions
	ij_jar_path=$(derefln ${ij_path}/ij.jar)

	for mod_jar in ${ij_path}/lib/*jar ; do
	modules="${modules:-}${modules+:}$mod_jar"
	done
	modules="-cp ${ij_jar_path}:${modules+:}${modules:-}"
	#${ij_path}/plugins/jars/dcmie.jar

	export LD_LIBRARY_PATH="${ij_path}/lib/${OS}_$processor"
	if (( $verbosity > 0 )) ; then
	echo "LD_LIBRARY_PATH=$LD_LIBRARY_PATH"
	fi

	# enable plugins to be compiled in imagej
	tools="$JAVA_HOME/lib/tools.jar"


	##################### ARGUMENTS PARSING #####################

	while getopts b:cde:hi:m:nop:r:vx: options
	do
	case $options in
	b) if [[ -n "$macrocmd" ]] ; then macroCmdError ; fi
	macrocmd="-batch ${OPTARG}"
	;;
	c) modules="${modules:-}${modules+:}${tools}"
	;;
	d) ij_path="$ij_path_dev"
	;;
	e) if [[ -n "$macrocmd" ]] ; then macroCmdError ; fi
	macrocmd='-eval'
	macroargs="'${OPTARG}'"
	;;
	h) fullusage
	exit 0
	;;
	i) images="${images}'${OPTARG}' "
	;;
	m) if [[ -n "$macrocmd" ]] ; then macroCmdError ; fi
	macrocmd="-macro ${OPTARG}"
	;;
	n) newwindow='true'
	;;
	o) newwindow='false'
	;;
	p) newwindow='false'
	port="${OPTARG}"
	if (( "$port" < 1 \|\| "$port" > 99 )) ; then
	echo "${OPTARG} is not a permissible value for port number (-p)" 1>&2
	exit 1
	fi
	;;
	r) if [[ -n "$macrocmd" ]] ; then macroCmdError ; fi
	macrocmd='-run'
	macroargs="'${OPTARG}'"
	;;
	v) verbosity=verbosity+1
	if (( $verbosity == 2 )) ; then set -x ; fi
	if (( $verbosity == 3 )) ; then set -v ; fi
	;;
	x) mem="${OPTARG}"
	newwindow='true'
	if (( $mem < $min_mem \|\| $mem > $max_mem )) ; then
	echo "${OPTARG} is not a permissible value for memory (-x)" 1>&2
	echo "min=${min_mem}, max=${max_mem}" 1>&2
	exit 1
	fi
	;;
	\?) usage
	exit 1
	;;
	esac
	done


	declare -i i=1
	while (( i < $OPTIND )) ; do
	shift
	i=i+1
	done

	#if (( "$#" == 0 )) ; then
	# usage
	#fi

	# -b and -m options only:
	# remaining command line arguments are passed as macro arguments
	# separated by $separator
	if [[ -n "$macrocmd" && -z "$macroargs" ]] ; then
	while (( "$#" > 0 )) ; do
	if [[ -z "$macroargs" ]] ; then
	macroargs="${1}"
	else
	macroargs="${macroargs}${separator}${1}"
	fi
	shift
	done
	macroargs="'$macroargs'"
	fi

	# PROTECT POSSIBLE SPACES IN IMAGE FILENAMES
	if (( "$#" > 0 )) ; then
	while (( "$#" > 0 )) ; do
	filearg="${1}"
	# full file path required when sending images to running ImageJ panel
	if [[ "${newwindow}" == 'false' && -f "${filearg}" ]] && ! expr "${filearg}" : '/.*' > /dev/null; then
	filearg="$(getFullPath ${filearg})"
	fi
	images="${images}'$filearg' "
	shift
	done
	fi

	##################### USING PORT #####################

	# CREATE IMAGEJ SOCKET-LOCK DIRECTORY IF NON EXISTANT
	if [[ ! -d "$ij_tmp" ]] ; then
	mkdir "$ij_tmp"
	chmod 777 "$ij_tmp"
	fi

	# CREATE IMAGEJ LOG FILE IF NON EXISTANT
	if [[ -n "$ij_log" && ! -f "$ij_log" ]] ; then
	touch "$ij_log"
	chmod 666 "$ij_log"
	fi

	# CREATES A TEMP FILE INDICATING A PORT IS IN USE BY IMAGEJ
	cd "$ij_tmp"
	declare -i count=1
	portopen='false'
	lockFileCreated='false'
	declare -a locklist=(`ls \| grep '[0-9][0-9]-.*'`)

	[[ -n "$ij_log" ]] && echo -e "$$\t$(date)\tNew Window = $newwindow" >> "$ij_log" 2> /dev/null
	[[ -n "$ij_log" ]] && echo -e "$$\t$(date)\tPort = $port" >> "$ij_log" 2> /dev/null
	[[ -n "$ij_log" ]] && echo -e "$$\t$(date)\tlocklist: \n ${locklist[*]}" >> "$ij_log" 2> /dev/null
	if (( $verbosity > 0 )) ; then echo -e "locklist: \n ${locklist[*]}" ; fi

	# PORT SPECIFIED BY USER
	if (( $port > 0 )) ; then
	# look for a lock on the port specified
	for lockname in ${locklist[*]} ; do
	prefix=`printf '%02u' $port`
	if [[ "$lockname" == ${prefix}-${user}-${host}* ]] ; then
	# found lock on the requested port, owned by user on current display
	portopen='true'
	if (( $verbosity > 0 )) ; then echo "Using socket lock: $lockname" ; fi
	count=$port
	break
	elif [[ "$lockname" == ${prefix}-* ]] ; then
	echo "Port $port is in use by some other user or a different host" 1>&2
	if (( $verbosity > 0 )) ; then echo "Port lock: $lockname" ; fi
	exit 1
	fi
	done
	# specified port not in use
	count=$port

	# IF EXISTING WINDOW IS REQUESTED, LOOK FOR LISTENING PORT
	elif [[ "$newwindow" == 'false' && ${#locklist} != 0 ]] ; then
	# look for a lock on the current display for this user
	for lockname in ${locklist[*]} ; do
	if [[ "$lockname" == [0-9][0-9]-${user}-${host}-${display} ]] ; then
	portopen='true'
	if (( $verbosity > 0 )) ; then echo "Found socket lock: $lockname" ; fi
	# if a matching user/display is found, use this one
	count="${lockname%---*}"
	#count=`echo $lockname \| sed -e 's/^\([0-9][0-9]\).*/\1/' -e 's/^0//'` # csh?
	break
	fi
	done
	fi

	# IF A NEW PORT IS TO BE USED
	if [[ "$portopen" == 'false' ]] ; then
	# new window requested or no matching port found
	# if port is not specified, look for first free port
	if (( "$port" == 0 )) ; then
	if (( ${#locklist} == 0 )) ; then
	# no active locks - use first port
	count=1
	else
	# active locks - check each port number so see if it is in use
	# this is not synchronised!!
	count=0
	inuse='true'
	while [[ "$inuse" == 'true' ]] ; do
	count=count+1
	prefix=`printf '%02u' $count`
	inuse='false'
	for lockname in ${locklist[*]} ; do
	if [[ "$lockname" == ${prefix}-* ]] ; then
	inuse='true'
	fi
	done
	done
	fi
	fi
	# CREATING A NEW PORT LOCK
	prefix=`printf '%02u' $count`
	lockname=${prefix}-${user}-${host}-${display}

	[[ -n "$ij_log" ]] && echo -e "$$\t$(date)\tCreating lock\t$lockname" >> "$ij_log" 2> /dev/null
	if (( $verbosity > 0 )) ; then echo -n "creating lock $lockname ... " ; fi
	touch $lockname
	trap '\rm -f ${ij_tmp}/$lockname >/dev/null ; echo -e "$$\t$(date)\tReleasing lock\t$lockname" >> "$ij_log" 2> /dev/null' EXIT TERM KILL
	# Quitting ImageJ sends EXIT, as does a kill/kill -9
	# CTRL+C in terminal sends INT + EXIT
	# System shutdown sends TERM (+EXIT??)

	if (( $verbosity > 0 )) ; then echo 'done' ; fi

	lockFileCreated='true'
	if [[ -z "$macrocmd" ]] ; then
	echo 'Open other images in this ImageJ panel as follows:'
	echo " imagej -p $count <image1> [<image2> ... <imageN>]"
	fi
	[[ -n "$ij_log" ]] && echo -e "$$\t$(date)\tSocket lock:\t$lockname" >> "$ij_log" 2> /dev/null
	if (( $verbosity > 0 )) ; then echo "Socket lock: $lockname" ; fi
	echo
	fi

	##################### FINALLY RUN IMAGEJ #####################

	#popd > /dev/null

	#if [ "$JAVA_HOME" ] ; then
	# if (( $verbosity > 0 )) ; then
	# echo ${modules}
	# echo $JAVA_HOME/bin/java ${java_arch} -mx${mem}m ${modules} ij.ImageJ -ijpath ${ij_user_path} -port${count} ${images} ${macrocmd} ${macroargs}
	# else
	# eval $JAVA_HOME/bin/java ${java_arch} -mx${mem}m ${modules} ij.ImageJ -ijpath ${ij_user_path} -port${count} ${images} ${macrocmd} ${macroargs}
	# fi
	#else
	# echo "No JVM found to run ImageJ"
	# echo "Please pacman -S java-runtime a JVM to run ImageJ or "
	# echo "check JAVA_HOME."
	# exit 1
	#fi

	exec java ${java_arch} -mx${mem}m ${modules} ij.ImageJ -ijpath ${ij_user_path} -port${count} ${images} ${macrocmd} ${macroargs}