[med-svn] r1867 - in trunk/packages: . imagej imagej/trunk imagej/trunk/debian
tille at alioth.debian.org
tille at alioth.debian.org
Thu May 15 17:15:01 UTC 2008
Author: tille
Date: 2008-05-15 17:15:01 +0000 (Thu, 15 May 2008)
New Revision: 1867
Added:
trunk/packages/imagej/
trunk/packages/imagej/tags/
trunk/packages/imagej/trunk/
trunk/packages/imagej/trunk/debian/
trunk/packages/imagej/trunk/debian/README.Debian
trunk/packages/imagej/trunk/debian/changelog
trunk/packages/imagej/trunk/debian/compat
trunk/packages/imagej/trunk/debian/control
trunk/packages/imagej/trunk/debian/copyright
trunk/packages/imagej/trunk/debian/dirs
trunk/packages/imagej/trunk/debian/docs
trunk/packages/imagej/trunk/debian/imagej.1
trunk/packages/imagej/trunk/debian/imagej.sh
trunk/packages/imagej/trunk/debian/menu
trunk/packages/imagej/trunk/debian/rules
trunk/packages/imagej/trunk/debian/watch
Log:
Injected imagej with some changes (group maintenance, watch file, homepage in control)
Added: trunk/packages/imagej/trunk/debian/README.Debian
===================================================================
--- trunk/packages/imagej/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/imagej/trunk/debian/README.Debian 2008-05-15 17:15:01 UTC (rev 1867)
@@ -0,0 +1,14 @@
+imagej for Debian
+-----------------
+
+Still have some problem with luts as files are binary so for the moment are
+base64 encoded but i've to write something in rules to base64 decode all luts file
+beforse copying them, matbe somthing like:
+perl -MMIME::Base64 -e 'print decode_base64(join("", <>))' < debian/extra/luts/*.enc > $(CURDIR)/debian/imagej/usr/share/imagej/luts/
+need help :)
+
+ -- Paolo Ariano <paolo.ariano at unito.it>, Thu, 03 Apr 2008 14:17:43 +0200
+
+The package was put into contrib because it is compiled with Sun Java 1.4.2_06.
+
+ -- Paolo Ariano <paolo.ariano at unito.it>, Fri, 28 Apr 2006 11:41:53 +0200
Added: trunk/packages/imagej/trunk/debian/changelog
===================================================================
--- trunk/packages/imagej/trunk/debian/changelog (rev 0)
+++ trunk/packages/imagej/trunk/debian/changelog 2008-05-15 17:15:01 UTC (rev 1867)
@@ -0,0 +1,106 @@
+imagej (1.40a-2) unstable; urgency=low
+
+ * Group maintenance according to Debian-Med group policy
+ * Added myself as Uploader
+ * VCS fields
+ * Added Homepage to debian/control
+ * Added watch file
+
+ -- Andreas Tille <tille at debian.org> Thu, 15 May 2008 17:20:37 +0200
+
+imagej (1.40a-1) unstable; urgency=high
+
+ * New Upstream Release.
+
+ * imagej.sh script doesn't symlink existent macros.
+
+ * imagej.sh script correctly symlink names with spaces.
+
+ * imagej.sh doesn't print redundant usage message.
+
+ * added again $HOME/.imagej/luts (closes: #470797).
+
+ * Thanks to Andre Lehovich (closes: #470810).
+
+ -- Paolo Ariano <paolo.ariano at unito.it> Fri, 28 Mar 2008 13:41:34 +0100
+
+imagej (1.39q-2) unstable; urgency=high
+
+ * New imagej.sh wrapper (closes: #468173).
+
+ * New man page.
+
+ -- Paolo Ariano <paolo.ariano at unito.it> Fri, 06 Mar 2008 15:29:56 +0100
+
+imagej (1.39q-1) unstable; urgency=low
+
+ * New Upstream Release.
+
+ * Symlinks in $HOME/.imagej/macro are ready, (closes: #447594).
+
+ -- Paolo Ariano <paolo.ariano at unito.it> Fri, 08 Feb 2008 11:29:56 +0100
+
+imagej (1.39b-5) unstable; urgency=high
+
+ * New sections graphics.
+
+ -- Paolo Ariano <paolo.ariano at unito.it> Wed, 26 Sep 2007 13:02:02 +0200
+
+imagej (1.39b-4) unstable; urgency=high
+
+ * New man page.
+
+ -- Paolo Ariano <paolo.ariano at unito.it> Wed, 26 Sep 2007 12:02:02 +0200
+
+imagej (1.39b-3) unstable; urgency=high
+
+ * You can pass extra arguments to java, such as amount of memory.
+
+ -- Paolo Ariano <paolo.ariano at unito.it> Tue, 25 Sep 2007 16:24:02 +0200
+
+imagej (1.39b-2) unstable; urgency=high
+
+ * New startup script (Closes: #439247).
+
+ * Deleted Disclaimer from Copyright (Closes: #439627).
+
+ * Filled a man page (Closes: #439252).
+
+ -- Paolo Ariano <paolo.ariano at unito.it> Tue, 25 Sep 2007 15:24:02 +0200
+
+imagej (1.39b-1) unstable; urgency=low
+
+ * New Upstream Release.
+
+ -- Paolo Ariano <paolo.ariano at unito.it> Thu, 02 Aug 2007 16:09:06 +0200
+
+imagej (1.37m-5) unstable; urgency=low
+
+ * Changhed path for /usr/sbin/update-java-alternatives in imagej.sh (thanks fog).
+
+ -- Paolo Ariano <paolo.ariano at unito.it> Wed, 13 Jun 2007 23:50:06 +0200
+
+imagej (1.37m-4) unstable; urgency=low
+
+ * Added possibility to pass extra arguments to java (thanks to Mike Miller).
+
+ -- Paolo Ariano <paolo.ariano at unito.it> Wed, 10 May 2006 23:48:28 +0200
+
+imagej (1.37m-3) unstable; urgency=low
+
+ * Added lut.
+
+ -- Paolo Ariano <paolo.ariano at unito.it> Mon, 07 Aug 2006 22:41:53 +0200
+
+imagej (1.37m-2) unstable; urgency=low
+
+ * Added the amount of memory as command line parameter.
+
+ -- Paolo Ariano <paolo.ariano at unito.it> Mon, 07 Aug 2006 22:41:53 +0200
+
+imagej (1.37m-1) unstable; urgency=low
+
+ * Initial release (Closes: #4526773, #6353442).
+
+ -- Paolo Ariano <paolo.ariano at unito.it> Fri, 28 Apr 2006 11:41:53 +0200
+
Added: trunk/packages/imagej/trunk/debian/compat
===================================================================
--- trunk/packages/imagej/trunk/debian/compat (rev 0)
+++ trunk/packages/imagej/trunk/debian/compat 2008-05-15 17:15:01 UTC (rev 1867)
@@ -0,0 +1 @@
+4
Added: trunk/packages/imagej/trunk/debian/control
===================================================================
--- trunk/packages/imagej/trunk/debian/control (rev 0)
+++ trunk/packages/imagej/trunk/debian/control 2008-05-15 17:15:01 UTC (rev 1867)
@@ -0,0 +1,36 @@
+Source: imagej
+Section: contrib/science
+Priority: optional
+Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Paolo Ariano <paolo.ariano at unito.it>,
+ Andreas Tille <tille at debian.org>
+Build-Depends: ecj | java2-compiler, cdbs, debhelper, ant, gif2png
+Standards-Version: 3.7.3
+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/
+
+Package: imagej
+Architecture: all
+Depends: gij | java2-runtime
+Suggests: java2-compiler
+Description: Image processing program inspired by NIH Image for the Macintosh
+ It can display, edit, analyze, process, save and print 8-bit, 16-bit and
+ 32-bit images. It can read many image formats including TIFF, GIF, JPEG,
+ BMP, DICOM, FITS and "raw". It supports "stacks", a series of images that
+ share a single window.
+ .
+ It can calculate area and pixel value statistics of user-defined
+ selections. It can measure distances and angles. It can create density
+ histograms and line profile plots. It supports standard image processing
+ functions such as contrast manipulation, sharpening, smoothing, edge
+ detection and median filtering.
+ .
+ Spatial calibration is available to provide real world dimensional
+ measurements in units such as millimeters. Density or gray scale
+ calibration is also available.
+ .
+ ImageJ is developed by Wayne Rasband (wayne at codon.nih.gov), is at the
+ Research Services Branch, National Institute of Mental Health, Bethesda,
+ Maryland, USA.
Added: trunk/packages/imagej/trunk/debian/copyright
===================================================================
--- trunk/packages/imagej/trunk/debian/copyright (rev 0)
+++ trunk/packages/imagej/trunk/debian/copyright 2008-05-15 17:15:01 UTC (rev 1867)
@@ -0,0 +1,16 @@
+This package was debianized by Paolo Ariano <paolo.ariano at unito.it> on
+Fri, 28 Apr 2006 11:41:53 +0200.
+
+It was downloaded from <http://rsb.info.nih.gov/ij/download/src/>
+
+Author : Wayne Rasband, rwsr at nih.gov, for the NIH
+
+License:
+
+ ImageJ is being developed at the National Institutes of Health by an employee
+ of the Federal Government in the course of his official duties. Pursuant to
+Title 17, Section 105 of the United States Code, this software is not subject
+to copyright protection and is in the public domain. ImageJ is an experimental
+system. NIH assumes no responsibility whatsoever for its use by other parties,
+and makes no guarantees, expressed or implied, about its quality, reliability,
+or any other characteristic.
Added: trunk/packages/imagej/trunk/debian/dirs
===================================================================
--- trunk/packages/imagej/trunk/debian/dirs (rev 0)
+++ trunk/packages/imagej/trunk/debian/dirs 2008-05-15 17:15:01 UTC (rev 1867)
@@ -0,0 +1,7 @@
+usr/bin
+usr/share/java
+usr/share/pixmaps
+usr/share/imagej
+usr/share/imagej/plugins
+usr/share/imagej/macros
+usr/share/imagej/luts
Added: trunk/packages/imagej/trunk/debian/docs
===================================================================
--- trunk/packages/imagej/trunk/debian/docs (rev 0)
+++ trunk/packages/imagej/trunk/debian/docs 2008-05-15 17:15:01 UTC (rev 1867)
@@ -0,0 +1,3 @@
+aREADME.txt
+IJ_Props.txt
+release-notes.html
Added: trunk/packages/imagej/trunk/debian/imagej.1
===================================================================
--- trunk/packages/imagej/trunk/debian/imagej.1 (rev 0)
+++ trunk/packages/imagej/trunk/debian/imagej.1 2008-05-15 17:15:01 UTC (rev 1867)
@@ -0,0 +1,102 @@
+.\" Hey, EMACS: -*- nroff -*-
+.\" First parameter, NAME, should be all caps
+.\" Second parameter, SECTION, should be 1-8, maybe w/ subsection
+.\" other parameters are allowed: see man(7), man(1)
+.\" Please adjust this date whenever revising the manpage.
+.\"
+.\" Some roff macros, for reference:
+.\" .nh disable hyphenation
+.\" .hy enable hyphenation
+.\" .ad l left justify
+.\" .ad b justify to both left and right margins
+.\" .nf disable filling
+.\" .fi enable filling
+.\" .br insert line break
+.\" .sp <n> insert n+1 empty lines
+.\" for manpage-specific macros, see man(7)
+.TH "IMAGEJ" "1" "March 14, 2008" "Paolo Ariano" ""
+.SH "NAME"
+.LP
+imagej \- A Java image processing program inspired by NIH Image.
+.SH "SYNTAX"
+.LP
+imagej [\fIoption\fP] <\fIfilename\fP>
+.br
+imagej [\-i image] [\-b|\-m] [arg1 ... argN]
+.SH "DESCRIPTION"
+.LP
+\fBImagej\fP is a Java\-based image processing program developed at the National Institutes of Health. ImageJ was designed with an open architecture that provides extensibility via Java plugins and recordable macros.
+Custom acquisition, analysis and processing plugins can be developed using ImageJ's built\-in editor and a Java compiler.
+User\-written plugins make it possible to solve many image processing and
+analysis problems, from 3\-dimensional live\-cell imaging,
+ to radiological image processing, multiple imaging system data comparisons
+to automated hematology systems.
+ImageJ's plugin architecture and built in development environment has made
+it a popular platform for teaching image processing.
+
+ImageJ can be run as an online applet, a downloadable application, or on
+any computer with a Java 1.1 or later virtual machine.
+.SH "OPTIONS"
+.LP
+.TP
+\fB\-h\fR
+Output help information and exit.
+.TP
+\fB\-o\fR
+Open images in existing ImageJ panel if one exists.
+.TP
+\fB\-p\fR <\fIN\fP>
+Open images in existing ImageJ panel number <N>.
+.TP
+\fB\-x\fR <\fIMB\fP>
+Set available memory.
+.TP
+\fB\-c\fR
+Enable plugin compilation within imagej.
+.TP
+\fB\-v\fR
+Be verbose (vv or vvv increases verbosity).
+.TP
+\fB\-e\fR \fIMacro Code\fP
+Execute macro code.
+.TP
+\fB\-r\fR \fIMenu Command\fP
+Run menu command.
+Quotation marks are required around commands including spaces
+Commands can be sent to open ImageJ panels with the \-p option.
+.TP
+\fB\-b\fR \fImacro\fP
+Run macro without graphics window.
+.TP
+\fB\-m\fR \fImacro\fP
+Run macro, image will be opened before macro is run all following arguments are passed to macro.
+.SH "FILES"
+.LP
+Most IMAGEJ add\-on are taken from $HOME/.imagej. The system wide
+ equivalent is in /usr/share/imagej/
+.TP
+.B \ HOME/.imagej/plugins/,
+you can find and put new plugins here
+.TP
+.B \ HOME/.imagej/macros/,
+you can find and put new macros here
+.TP
+.B \ HOME/.imagej/luts/,
+you can find and put new look up tables here
+
+.SH "EXAMPLES"
+.LP
+For compiling plugins:
+.LP
+imagej \-c
+.SH "SEE ALSO"
+.\"/.BR bar (1),
+.\"/.BR baz (1).
+.br
+The program is fully documented at
+http://rsb.info.nih.gov/ij/docs/
+.SH "AUTHOR"
+.LP
+ImageJ was written by Wayne Rasband <wsr at nih.gov>
+.PP
+This manual page, the wrapper and packaging was done by Paolo Ariano <paolo.ariano at unito.it>, for the Debian project.
Added: trunk/packages/imagej/trunk/debian/imagej.sh
===================================================================
--- trunk/packages/imagej/trunk/debian/imagej.sh (rev 0)
+++ trunk/packages/imagej/trunk/debian/imagej.sh 2008-05-15 17:15:01 UTC (rev 1867)
@@ -0,0 +1,424 @@
+#!/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: 04 March 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 #####################
+
+if [ -z "$JAVA_HOME" ] ; then
+ JAVA_HOME=$(/usr/sbin/update-java-alternatives -l | head -1 | cut -d' ' -f 3)
+fi
+
+##################### CREATE THE RIGHT ENVIRONMENT #####################
+
+# ImageJ path
+ij_path=/usr/share/java
+
+#ImageJ user path
+ij_user_path=$HOME/.imagej
+
+# report errors to this user
+ijadmin='paolo.ariano at unito.it'
+
+# Documentation URL
+doc_url='http://rsb.info.nih.gov/ij/'
+
+# temp folder
+ij_tmp=$HOME/.imagej/tmp
+
+# default behaviour when an ImageJ window is already open
+newwindow='true'
+#newwindow='false'
+
+# macro argument conjoining character
+separator=':'
+# a ' ' may work provided no arguments would contain spaces
+# use macro functions: args=getArgument(); argArray=split(args, ':');
+# to recover macro arguments
+
+declare -i mem
+declare -i default_mem=500
+declare -i min_mem=16
+declare -i max_mem
+declare -i free_mem
+
+# other variables
+dir=`pwd`
+user=`whoami`
+host=`hostname`
+if [[ -z "$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="$DISPLAY"
+fi
+
+declare -i port=0
+declare -i verbosity=0
+images=''
+macrocmd=''
+macroargs=''
+
+# max memory allocation is 1800MB on 32bit java and 4000 on 64bit java
+if [[ `uname` == 'SunOS' ]] ; then
+ arch='-d64'
+ java_path="${ij_path}/jre64/bin/java"
+ max_mem=`vmstat | awk 'NR == 3 {fmem=int($5 / 1024); if (fmem < 4000) {print fmem} else {print 4000}}'`
+ free_mem="max_mem"
+ mem=${free_mem}/2*3
+ if (( $mem > $default_mem || $mem < $min_mem )) ; then mem=$default_mem ; fi
+elif [[ `uname` == 'Linux' ]] ; then
+ if [[ `uname -m` == 'x86_64' ]] ; then
+ arch='-d64'
+ java_path="${ij_path}/jre64/bin/java"
+ max_mem=`free | awk 'NR == 2 {fmem=int($2 / 1024); if (fmem < 4000) {print fmem} else {print 4000}}'`
+ free_mem=`free | awk 'NR == 3 {fmem=int($4 / 1024); if (fmem < 4000) {print fmem} else {print 4000}}'`
+ mem=${free_mem}/3*2
+ if (( $mem > $default_mem || $mem < $min_mem )) ; then mem=$default_mem ; fi
+ else
+ arch='-d32'
+ java_path="${ij_path}/jre/bin/java"
+ free_mem=`free | awk 'NR == 2 {fmem=int($2 / 1024); if (fmem < 1800) {print fmem} else {print 1800}}'`
+ free_mem=`free | awk 'NR == 3 {fmem=int($4 / 1024); if (fmem < 1800) {print fmem} else {print 1800}}'`
+ mem=${free_mem}/3*2
+ if (( $mem > $default_mem || $mem < $min_mem )) ; then mem=$default_mem ; fi
+ fi
+fi
+
+# create plugins,macro,tmp dirs
+mkdir -p $ij_user_path/plugins
+mkdir -p $ij_user_path/macros
+mkdir -p $ij_user_path/luts
+
+# create imagej socket-lock directory if non existant
+if [[ ! -d "$ij_tmp" ]] ; then
+ mkdir -p "$ij_tmp"
+ #chmod 777 "$ij_user_path/tmp"
+fi
+
+# Warning on syntax change
+# for var in "$@" ; do
+ #if [[ "$var" == @(-batch|-eval|-macro|-mem|-new|-port|-run|-verbose) ]] ; then
+# 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, type 'imagej -h'" 1>&2
+# echo "for full usage" 1>&2
+# exit 1
+# fi
+# done
+
+# 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
+
+
+
+##################### 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
+}
+
+# The best way to install .jar libraries required by plugins is to copy them
+# to the imagej ij_path=/usr/share/java alternatively or add the .jar
+# filepath to the modules line below. Paths are separated by a colon
+# modules="-cp ${ij_path}/ij.jar:${ij_path}/plugins/jars/dcmie.jar"
+modules="-cp ${ij_path}/ij.jar"
+
+# enable plugins to be compiled in imagej
+tools="$JAVA_HOME/lib/tools.jar"
+
+
+##################### ARGUMENTS PARSING #####################
+
+while getopts b:ce:hi:m:op:r:vx: options
+do
+ case $options in
+ b) if [[ -n "$macrocmd" ]] ; then macroCmdError ; fi
+ macrocmd="-batch ${OPTARG}"
+ ;;
+ c) modules="${modules}:${tools}"
+ ;;
+ e) if [[ -n "$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 ${OPTARG}"
+ ;;
+ o) newwindow='false'
+ ;;
+ p) newwindow='false'
+ port="${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}"
+ 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
+ images="${images}'${1}' "
+ shift
+ done
+fi
+
+##################### USING PORT #####################
+
+# Creates a temp file indicating a port is in use by imagej
+pushd "$ij_tmp" > /dev/null
+declare -i count=1
+portopen='false'
+lockFileCreated='false'
+declare -a locklist=(`ls | grep '[0-9][0-9]-.*'`)
+
+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}
+ if (( $verbosity > 0 )) ; then echo -n "creating lock $lockname ... " ; fi
+ touch $lockname
+ trap '\rm -f ${ij_tmp}/$lockname >/dev/null ; exit 1' EXIT TERM
+ # 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'
+ echo 'Open other images in this ImageJ panel as follows:'
+ echo " imagej -p $count <image1> [<image2> ... <imageN>]"
+ if (( $verbosity > 0 )) ; then echo "Socket lock: $lockname" ; fi
+ echo
+fi
+
+# Report number of port locks - more than 50 may indicate error in this script
+if [[ $count -gt 50 && $port == 0 && "$ijadmin" != '' ]] ; then
+mail -s "ImageJ ports on $host" $ijadmin << EOF
+Port locks on $host reached $count
+EOF
+fi
+
+##################### FINALLY RUN IMAGEJ #####################
+
+popd > /dev/null
+
+if [ "$JAVA_HOME" ] ; then
+ if (( $verbosity > 0 )) ; then
+ echo ${modules}
+ echo $JAVA_HOME/bin/java ${arch} -mx${mem}m ${modules} ij.ImageJ -ijpath ${ij_user_path} -port${count} ${images} ${macrocmd} ${macroargs}
+ else
+ eval $JAVA_HOME/bin/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
+
Added: trunk/packages/imagej/trunk/debian/menu
===================================================================
--- trunk/packages/imagej/trunk/debian/menu (rev 0)
+++ trunk/packages/imagej/trunk/debian/menu 2008-05-15 17:15:01 UTC (rev 1867)
@@ -0,0 +1,6 @@
+?package(imagej):\
+ needs="X11"\
+ section="Applications/Graphics"\
+ title="imagej"\
+ icon="/usr/share/pixmaps/microscope.xpm"\
+ command="/usr/bin/imagej"
Added: trunk/packages/imagej/trunk/debian/rules
===================================================================
--- trunk/packages/imagej/trunk/debian/rules (rev 0)
+++ trunk/packages/imagej/trunk/debian/rules 2008-05-15 17:15:01 UTC (rev 1867)
@@ -0,0 +1,28 @@
+#!/usr/bin/make -f
+# debian/rules for imagej (uses CDBS)
+
+# Uncomment this to turn on verbose mode.
+export DH_VERBOSE=1
+
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/ant.mk
+include /usr/share/cdbs/1/rules/simple-patchsys.mk
+
+JAVA_HOME := $(shell /usr/sbin/update-java-alternatives -l | head -1 | cut -d' ' -f 3)
+JAVACMD := $(JAVA_HOME)/bin/java
+DEB_BUILDDIR := $(CURDIR)
+DEB_ANT_BUILD_TARGET := build
+ANT_HOME := /usr/share/ant
+DEB_CLASSPATH := $(ANT_HOME)/lib/ant.jar:$(ANT_HOME)/lib/ant-launcher.jar:$(JAVA_HOME)/lib/tools.jar
+VERSION := $(shell dpkg-parsechangelog | egrep '^Version:' | cut -f 2 -d ' ' | cut -f 1 -d '-')
+
+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 -r $(CURDIR)/plugins/*.class $(CURDIR)/debian/imagej/usr/share/imagej/plugins/
+ cp -r $(CURDIR)/build/macros/* $(CURDIR)/debian/imagej/usr/share/imagej/macros/
+ #base64 -d < debian/extra/luts
+ cp -r $(CURDIR)/extra/luts/* $(CURDIR)/debian/imagej/usr/share/imagej/luts/
+ install -m 644 $(CURDIR)/extra/microscope.xpm $(CURDIR)/debian/imagej/usr/share/pixmaps/
+ dh_installman -i debian/imagej.1
+
Property changes on: trunk/packages/imagej/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/imagej/trunk/debian/watch
===================================================================
--- trunk/packages/imagej/trunk/debian/watch (rev 0)
+++ trunk/packages/imagej/trunk/debian/watch 2008-05-15 17:15:01 UTC (rev 1867)
@@ -0,0 +1,5 @@
+# watch control file for imagej
+version=3
+
+opts="uversionmangle=s/(\d)+(\d\d)/$1.$2/" \
+http://rsb.info.nih.gov/ij/download/src/ij(141b)-src.zip
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