[med-svn] r2519 - trunk/packages/imagej/trunk/debian
tille at alioth.debian.org
tille at alioth.debian.org
Tue Sep 23 12:12:52 UTC 2008
Author: tille
Date: 2008-09-23 12:12:51 +0000 (Tue, 23 Sep 2008)
New Revision: 2519
Added:
trunk/packages/imagej/trunk/debian/dirs
trunk/packages/imagej/trunk/debian/imagej.sh
Removed:
trunk/packages/imagej/trunk/debian/imagej
Modified:
trunk/packages/imagej/trunk/debian/changelog
trunk/packages/imagej/trunk/debian/control
trunk/packages/imagej/trunk/debian/install
trunk/packages/imagej/trunk/debian/rules
Log:
Fixed debhelper issues to build the package
Modified: trunk/packages/imagej/trunk/debian/changelog
===================================================================
--- trunk/packages/imagej/trunk/debian/changelog 2008-09-23 11:36:21 UTC (rev 2518)
+++ trunk/packages/imagej/trunk/debian/changelog 2008-09-23 12:12:51 UTC (rev 2519)
@@ -18,6 +18,8 @@
* debian/compat: 5
* debian/rules: Excluded sun java from JAVA_HOME to make sure imagej
can go to main
+ * Standards-Version: 3.8.0 (no changes needed)
+ * Added versioned Build-Depends debhelper (>= 5)
[ Charles Plessy ]
* Added a FreeDesktopt menu entry.
@@ -26,8 +28,11 @@
* A lot of correction to the run script, thanks to Jonathan (closes: #496798).
* The socket-lock directory is now /tmp/imagej
- -- Paolo Ariano <paolo.ariano at unito.it> Fri, 19 Sep 2008 13:04:23 +0100
+ [ Andreas Tille ]
+ *
+ -- Andreas Tille <tille at debian.org> Tue, 23 Sep 2008 12:04:34 +0200
+
imagej (1.40a-1) unstable; urgency=high
* New Upstream Release.
Modified: trunk/packages/imagej/trunk/debian/control
===================================================================
--- trunk/packages/imagej/trunk/debian/control 2008-09-23 11:36:21 UTC (rev 2518)
+++ trunk/packages/imagej/trunk/debian/control 2008-09-23 12:12:51 UTC (rev 2519)
@@ -5,8 +5,8 @@
DM-Upload-Allowed: yes
Uploaders: Paolo Ariano <paolo.ariano at unito.it>,
Andreas Tille <tille at debian.org>
-Build-Depends: gcj | java2-compiler, cdbs, debhelper, ant, gif2png
-Standards-Version: 3.7.3
+Build-Depends: sun-java5-jdk, cdbs, debhelper, ant, gif2png, debhelper (>= 5)
+Standards-Version: 3.8.0
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/imagej/trunk/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/imagej/trunk/
Homepage: http://rsb.info.nih.gov/ij/
Added: trunk/packages/imagej/trunk/debian/dirs
===================================================================
--- trunk/packages/imagej/trunk/debian/dirs (rev 0)
+++ trunk/packages/imagej/trunk/debian/dirs 2008-09-23 12:12:51 UTC (rev 2519)
@@ -0,0 +1 @@
+usr/bin
Deleted: trunk/packages/imagej/trunk/debian/imagej
===================================================================
--- trunk/packages/imagej/trunk/debian/imagej 2008-09-23 11:36:21 UTC (rev 2518)
+++ trunk/packages/imagej/trunk/debian/imagej 2008-09-23 12:12:51 UTC (rev 2519)
@@ -1,506 +0,0 @@
-#!/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)
-
-# 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 .DEB #####################
-
-if [ -z "$JAVA_HOME" ] ; then
- JAVA_HOME=$(/usr/sbin/update-java-alternatives -l | head -1 | cut -d' ' -f 3)
-fi
-
-##################### CREATE THE RIGHT ENVIRONMENT .DEB #####################
-
-# ImageJ path
-ij_path=/usr/share/java
-
-#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 $ij_user_path/luts
-
-# makes symbolik links from shared plugins, macros and luts
-
-ls /usr/share/imagej/plugins | while read p ; do
- if [ ! -e "$ij_user_path/plugins/$p" ] ; then
- ln -s /usr/share/imagej/plugins/$p $ij_user_path/plugins/$p
- fi
-done
-
-ls /usr/share/imagej/macros | while read p; do
- if [ ! -e "$ij_user_path/macros/$p" ] ; then
- ln -s "/usr/share/imagej/macros/$p" "$ij_user_path/macros/$p"
- fi
-done
-
-ls /usr/share/imagej/luts | while read p ; do
- if [ ! -e "$ij_user_path/luts/$p" ] ; then
- ln -s /usr/share/imagej/luts/$p $ij_user_path/luts/$p
- fi
-done
-
-
-# report errors to this user
-# ijadmin='paolo.ariano at 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
-
-# Warning on syntax change
-for var in "$@" ; do
- if [[ "$var" == @(-batch|-eval|-macro|-mem|-new|-port|-run|-verbose) ]] ; then
- echo "ImageJ command line options have changed!" 1>&2
- echo "$var is no longer a valid option." 1>&2
- echo "Type 'imagej -h' for full usage" 1>&2
- exit 1
- fi
-done
-
-
-##################### USAGE DESCRIPTION #####################
-
-function usage {
- echo
- echo 'Image display and analysis program. Opens formats including:'
- echo 'UNC, Analyze, Dicom, NIFTI, Tiff, Jpeg, Gif, PNG ...'
- echo
- echo 'imagej [options] image [ image2 ... image3 ]'
- echo ' -h print help and more options'
- echo ' -o open images in an open ImageJ panel'
- echo ' -p <N> open images in ImageJ panel number <N>'
- echo " -x <MB> set available memory (default=${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 apt-get install a JVM to run ImageJ or "
- echo "set JAVA_HOME if it's not a JVM from a Debian Package."
- exit 1
-fi
-
-exit 0
-
Copied: trunk/packages/imagej/trunk/debian/imagej.sh (from rev 2517, trunk/packages/imagej/trunk/debian/imagej)
===================================================================
--- trunk/packages/imagej/trunk/debian/imagej.sh (rev 0)
+++ trunk/packages/imagej/trunk/debian/imagej.sh 2008-09-23 12:12:51 UTC (rev 2519)
@@ -0,0 +1,506 @@
+#!/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)
+
+# 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 .DEB #####################
+
+if [ -z "$JAVA_HOME" ] ; then
+ JAVA_HOME=$(/usr/sbin/update-java-alternatives -l | head -1 | cut -d' ' -f 3)
+fi
+
+##################### CREATE THE RIGHT ENVIRONMENT .DEB #####################
+
+# ImageJ path
+ij_path=/usr/share/java
+
+#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 /usr/share/imagej/plugins | while read p ; do
+ if [ ! -e "$ij_user_path/plugins/$p" ] ; then
+ ln -s /usr/share/imagej/plugins/$p $ij_user_path/plugins/$p
+ fi
+done
+
+ls /usr/share/imagej/macros | while read p; do
+ if [ ! -e "$ij_user_path/macros/$p" ] ; then
+ ln -s "/usr/share/imagej/macros/$p" "$ij_user_path/macros/$p"
+ fi
+done
+
+ls /usr/share/imagej/luts | while read p ; do
+ if [ ! -e "$ij_user_path/luts/$p" ] ; then
+ ln -s /usr/share/imagej/luts/$p $ij_user_path/luts/$p
+ fi
+done
+
+
+# report errors to this user
+# ijadmin='paolo.ariano at 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
+
+# Warning on syntax change
+for var in "$@" ; do
+ if [[ "$var" == @(-batch|-eval|-macro|-mem|-new|-port|-run|-verbose) ]] ; then
+ echo "ImageJ command line options have changed!" 1>&2
+ echo "$var is no longer a valid option." 1>&2
+ echo "Type 'imagej -h' for full usage" 1>&2
+ exit 1
+ fi
+done
+
+
+##################### 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 apt-get install a JVM to run ImageJ or "
+ echo "set JAVA_HOME if it's not a JVM from a Debian Package."
+ exit 1
+fi
+
+exit 0
+
Property changes on: trunk/packages/imagej/trunk/debian/imagej.sh
___________________________________________________________________
Name: svn:mergeinfo
+
Modified: trunk/packages/imagej/trunk/debian/install
===================================================================
--- trunk/packages/imagej/trunk/debian/install 2008-09-23 11:36:21 UTC (rev 2518)
+++ trunk/packages/imagej/trunk/debian/install 2008-09-23 12:12:51 UTC (rev 2519)
@@ -1,7 +1,6 @@
debian/extra/luts/* usr/share/imagej/luts
debian/extra/microscope.xpm usr/share/pixmaps
ij.jar usr/share/java
-debian/imagej usr/bin/imagej
plugins/*.class usr/share/imagej/plugins
build/macros/* usr/share/imagej/macros
debian/imagej.desktop usr/share/applications
Modified: trunk/packages/imagej/trunk/debian/rules
===================================================================
--- trunk/packages/imagej/trunk/debian/rules 2008-09-23 11:36:21 UTC (rev 2518)
+++ trunk/packages/imagej/trunk/debian/rules 2008-09-23 12:12:51 UTC (rev 2519)
@@ -27,6 +27,7 @@
install/imagej::
# install -m 644 $(DEB_BUILDDIR)/ij.jar $(CURDIR)/debian/imagej/usr/share/java/
# install -m 755 $(CURDIR)/debian/imagej.sh $(CURDIR)/debian/imagej/usr/bin/imagej
+ cp -a $(CURDIR)/debian/imagej.sh $(CURDIR)/debian/imagej/usr/bin/imagej
# cp -r $(CURDIR)/plugins/*.class $(CURDIR)/debian/imagej/usr/share/imagej/plugins/
# cp -r $(CURDIR)/build/macros/* $(CURDIR)/debian/imagej/usr/share/imagej/macros/
# dh_installman -i debian/imagej.1
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