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#!/bin/bash
# A wrapper script to launch imagej from the UNIX command line
# Images given as arguments will be opened, macros may also be given as arguments
# Looks for macros in the imagej macro directory
#
# This program is free software, but comes with no warrenty or guarantee
# send bug reports or feedback to jjackson at familyjackson dot net
# Author: Jon Jackson
# Last modified date: $Date: 2008-09-17 10:31:27 +0100 (Wed, 17 Sep 2008) $
# $Revision: 51 $
#
# INSTALLATION INSTRUCTIONS
#
### WARNING ###########################################################
# This file must be edited with a program that supports unix new line characters
# - it won't run if edited in 'Notepad' !
#######################################################################
# Source location: http://rsb.info.nih.gov/ij/download/linux/unix-script.txt
# 1) Save this script in the ImageJ directory as 'imagej'
# 2) Modify path variables according to your system
# 3) Give the new file execute permission
# 4) Be sure the 'imagej' wrapper is in the 'PATH'
### MODIFICATION ###
# With minor modifications to use with Slackware, by Petar Petrov 2012
# ppetrov at paju dot oulu dot fi
####################
# setup environment
set +u # don't give error for unset variables (matters for environment variables)
shopt -s extglob # allow extended pattern matching
############ SITE SPECIFIC VARIABLES #########################
# Trailing / is not required for path variables
# IMAGEJ PATH - production installation
ij_path='/usr/share/ImageJ'
# Path to ImageJ development installation
#ij_path_dev='/home/jjackson/ImageJ'
# JAVA PATH
# assumes executable is ${java_home}/bin/java
# set java_home variables ='' to use JAVA_HOME environment variable
#if [[ -d /usr/java/jdk1.5 ]] ; then
# java_home='/usr/java/jdk1.5'
#else
# # Optionally specify java path for all available OS / architecture combinations
# java_home_Linux="${ij_path}/jre"
# java_home_Linux_x86_64="${ij_path}/jre64"
# java_home_SunOS="${ij_path}/jre64"
# #
#fi
ijadmin=''
# DOCUMENTATION URL
doc_url='http://rsb.info.nih.gov/ij/'
# TEMP FOLDER
ij_tmp='/tmp/imagej'
# LOG FILE
#ij_log="${ij_tmp}/log.txt"
# default behaviour when an ImageJ window is already open
newwindow='true'
#newwindow='false'
# macro argument delimiter character
separator=':'
# a ' ' may work provided no arguments would contain spaces
# use macro functions: args=getArgument(); argArray=split(args, ':');
# to recover macro arguments
############ 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
############ SITE SPECIFIC MODULES #########################
# JAR libraries for additional modules may be placed in ${ij_path}/lib
# jmf.jar jai_codec.jar jai_core.jar mlibwrapper_jai.jar
# Native libraries may be placed in ${ij_path}/lib/$OS
# where OS matches the output of the 'uname' command
############ END SITE SPECIFIC VARIABLES #########################
OS=$(uname)
processor=$(uname -m) # -p doesn't work on 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
# if tools.jar is not in ${ij_path}/jre/lib/ext/ edit the 'tools=' line
# to point to tools.jar. The -compile switch will load tools.jar into the
# classpath and enable plugins to be compiled in imagej
if [[ -f "${ij_path}/tools.jar" ]] ; then
tools="${ij_path}/tools.jar"
else
tools=''
fi
# End Site specific variables ---------------------------------------------------------
# other variables
dir=`pwd`
user=`whoami`
host=`hostname`
if [[ -z "$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="$DISPLAY"
fi
declare -i port=0
declare -i verbosity=0
images=''
macrocmd=''
macroargs=''
function usage {
echo
echo 'Image display and analysis program. Opens formats including:'
echo 'UNC, Analyze, Dicom, NIFTI, Tiff, Jpeg, Gif, PNG ...'
echo
echo 'imagej [options] image [ image2 ... image3 ]'
echo ' -h print help and more options'
echo ' -o open images in an open ImageJ panel'
echo ' -p <N> open images in ImageJ panel number <N>'
echo " -x <MB> set available memory (default=${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
}
# parse input arguments
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
#for ((i=1; i < $OPTIND; i++))
#do
# shift
#done
## above syntax not supported in bash < 2.05
declare -i i=1
while (( i < $OPTIND )) ; do
shift
i=i+1
done
if [[ "$#" == 0 && -z "$macrocmd" ]] ; then
usage
fi
# 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
# -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}'$filearg' "
shift
done
fi
# CREATE IMAGEJ SOCKET-LOCK DIRECTORY IF NON EXISTANT
if [[ ! -d "$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 "$$\t$(date)\tCreating lock\t$lockname" >> "$ij_log" 2> /dev/null
if (( $verbosity > 0 )) ; then echo -n "creating lock $lockname ... " ; fi
touch $lockname
trap '\rm -f ${ij_tmp}/$lockname >/dev/null ; [[ -n "$ij_log" ]] && echo -e "$$\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
if (( $verbosity > 0 )) ; then
echo ${JAVA_HOME}/bin/java ${java_arch} -mx${mem}m ${modules} ij.ImageJ -ijpath ${ij_path} -port${count} ${images} ${macrocmd} ${macroargs}
fi
cd "$dir"
eval "${JAVA_HOME}/bin/java ${java_arch} -mx${mem}m ${modules} ij.ImageJ -ijpath ${ij_path} -port${count} ${images} ${macrocmd} ${macroargs} "
exit 0
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