debian/0000755000000000000000000000000012253533736007177 5ustar debian/control0000644000000000000000000000314612253533070010575 0ustar Source: imagej Maintainer: Debian Med Packaging Team Uploaders: Paolo Ariano , Andreas Tille Section: science Priority: optional Build-Depends: default-jdk, debhelper (>= 9), ant, javahelper Standards-Version: 3.9.5 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/imagej/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/imagej/trunk/ Homepage: http://imagej.nih.gov/ij Package: imagej Architecture: all Depends: ${java:Depends}, ${misc:Depends}, default-jre | openjdk-7-jre Description: Image processing program inspired by NIH Image 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@codon.nih.gov), is at the Research Services Branch, National Institute of Mental Health, Bethesda, Maryland, USA. debian/install0000644000000000000000000000044512214301217010553 0ustar debian/extra/luts/* usr/share/imagej/luts debian/extra/microscope.xpm usr/share/pixmaps ij.jar usr/share/java plugins/*.class usr/share/imagej/plugins build/macros/* usr/share/imagej/macros debian/imagej.desktop usr/share/applications debian/rules0000755000000000000000000000042112214301217010234 0ustar #!/usr/bin/make -f # debian/rules for imagej %: dh $@ --with javahelper # install/imagej:: override_dh_auto_install: cp -a $(CURDIR)/debian/imagej.sh $(CURDIR)/debian/imagej/usr/bin/imagej override_dh_auto_build: ant build get-orig-source: . debian/get-orig-source debian/manpages0000644000000000000000000000002112214301217010666 0ustar debian/imagej.1 debian/watch0000644000000000000000000000031612232466465010231 0ustar # watch control file for imagej version=3 opts="uversionmangle=s/(\d)+(\d\d)/$1.$2/,dversionmangle=s/[~\+]dfsg//" \ http://imagej.nih.gov/ij/download/src/ij(\d+.)-src.zip \ debian debian/get-orig-source debian/menu0000644000000000000000000000023712214301217010050 0ustar ?package(imagej):\ needs="X11"\ section="Applications/Graphics"\ title="imagej"\ icon="/usr/share/pixmaps/microscope.xpm"\ command="/usr/bin/imagej" debian/imagej.desktop0000644000000000000000000000306212214301217012007 0ustar [Desktop Entry] Version=1.0 Type=Application Name=ImageJ GenericName=Image Editor GenericName[bg]=Редактор на изображения GenericName[ca]=Editor de imatge GenericName[cs]=Editor obrázků GenericName[da]=Billedredigering GenericName[de]=Bildeditor GenericName[en_CA]=Image Editor GenericName[en_GB]=Image Editor GenericName[es]=Editor de imagen GenericName[eu]=Irudi-editorea GenericName[fi]=Kuvaeditori GenericName[fr]=Éditeur d'images GenericName[hu]=Képszerkesztő GenericName[it]=Editor di immagini GenericName[ja]=画像エディタ GenericName[ko]=색상표 편집기 GenericName[mk]=Уредник за слики GenericName[nb]=Bildebehandler GenericName[nl]=Afbeelding-editor GenericName[no]=Bildebehandler GenericName[pa]=ਚਿੱਤਰ ਸੰਪਾਦਕ GenericName[pl]=Edytor obrazu GenericName[pt_BR]=Editor de Imagens GenericName[ru]=Редактор изображений GenericName[sk]=Editor obrázkov GenericName[sr]=Обрада слика GenericName[sr@Latn]=Obrada slika GenericName[sv]=Bildeditor GenericName[uk]=Редактор зображень GenericName[zh_CN]=图像编辑器 GenericName[zh_TW]=色盤編輯程序 Comment=Image processing and analysis Comment[en_GB]=Image processing and analysis Comment[fr]=Traitement et analyse de l'image Comment[it]=Trattamento ed analisi delle immagini Exec=imagej %f Icon=microscope Categories=Graphics;Science;Biology; MimeType=image/bmp;image/gif;image/jpeg;image/jpg;image/pjpeg;image/png;image/tiff;image/x-bmp;image/x-fits;image/x-png;image/x-psd;image/x-xbitmap;application/dicom; debian/upstream0000644000000000000000000000175012214301217010745 0ustar Reference: - Author: Norman Zerbe and Peter Hufnagl and Karsten Schlüns Title: Distributed computing in image analysis using open source frameworks and application to image sharpness assessment of histological whole slide images Journal: Diagn Pathology Year: 2011 Volume: 6 Number: Suppl 1 Pages: S16 DOI: 10.1186/1746-1596-6-S1-S16 PMID: 21489186 URL: http://www.diagnosticpathology.org/content/6/S1/S16 eprint: http://www.diagnosticpathology.org/content/pdf/1746-1596-6-S1-S16.pdf - Author: T. Vrekoussis and V. Chaniotis and I. Navrozoglou and V. Dousias and K. Pavlakis and E. N. Stathopoulos and O. Zoras Title: "Image analysis of breast cancer immunohistochemistry-stained sections using ImageJ: an RGB-based model" Journal: Anticancer Research Year: 2009 Volume: 29 Number: 12 Pages: 4995-8 PMID: 20044607 URL: http://ar.iiarjournals.org/content/29/12/4995.short eprint: http://ar.iiarjournals.org/content/29/12/4995.full.pdf+html debian/copyright0000644000000000000000000000222012214301217011106 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: ImageJ Upstream-Contact: Wayne Rasband , for the NIH Source: http://imagej.nih.gov/ij/download/src/ Files-Excluded: .FBC* .gdb_history .FBCLockFolder/ Files: * Copyright: © 1999-2011 Wayne Rasband License: PD http://imagej.nih.gov/ij/disclaimer.html says: . 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. Files: debian/* Copyright: © 2006-2008 Paolo Ariano © 2008-2011 Andreas Tille License: GPL On Debian systems, the complete text of the GNU General Public License can be found in `/usr/share/common-licenses/GPL'. debian/source/0000755000000000000000000000000012214301217010457 5ustar debian/source/format0000644000000000000000000000001412214301217011665 0ustar 3.0 (quilt) debian/get-orig-source0000755000000000000000000000306212232466240012131 0ustar #!/bin/sh -e # Remark: A new uscan that enables easier handling of removing files can be # obtained via # git clone git://tille@git.debian.org/git/users/tille/devscripts.git # and then copy scripts/uscan.pl as uscan at the beginning of your PATH if uscan --help | grep -q -- --repack-compression ; then echo "Use new enhanced uscan" uscan --verbose --force-download --repack-compression xz exit fi # Upstream provides source in ZIP file so we have to repack anyway and # thus it seems reasonable to remove some binary cruft NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'` ORIGNAME=ij if ! echo $@ | grep -q upstream-version ; then DVERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/\([0-9\.]\+\)-[0-9]\+$/\1/'` else DVERSION=`echo $@ | sed "s?^.*--upstream-version \([0-9.]\+[a-z]\) .*${ORIGNAME}.*-src\.zip?\1?"` if echo "$DVERSION" | grep -q "upstream-version" ; then echo "Unable to parse version number" exit fi fi UVERSION=${ORIGNAME}`echo ${DVERSION} | sed 's/\.//'` UPSTREAMZIP=${UVERSION}-src.zip UPSTREAMDIR=source cd .. mkdir -p tarballs if [ ! -f "$UPSTREAMZIP" ] ; then wget -q http://imagej.nih.gov/ij/download/src/"$UPSTREAMZIP" fi cd tarballs unzip -q ../"$UPSTREAMZIP" cd "$UPSTREAMDIR" # remove hidden binary files rm -rf .FBC* # remove gdb history rm -f .gdb_history cd .. mv "$UPSTREAMDIR" "$NAME"-"$DVERSION" GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX -caf "$NAME"_"$DVERSION".orig.tar.xz "$NAME"-"$DVERSION" rm -rf "$NAME"-"$DVERSION" debian/README.Debian0000644000000000000000000000071412214301217011222 0ustar 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 before copying them, maybe somthing like: perl -MMIME::Base64 -e 'print decode_base64(join("", <>))' < debian/extra/luts/*.enc > $(CURDIR)/debian/imagej/usr/share/imagej/luts/ need help :) -- Paolo Ariano , Thu, 03 Apr 2008 14:17:43 +0200 debian/imagej.sh0000644000000000000000000003345212253411455010767 0ustar #!/bin/bash # imagej.sh - a not so simple wrapper script used to run ImageJ # Copyright © 2008 Paolo Ariano, # © 2009 Andreas Tille # Authors: Paolo Ariano (paolo dot ariano at unito dot it) # Andreas Tille # Last modified date: 01 December 2009 # This is a not so simple wrapper script used to run ImageJ in Unix but # optimized for Debian GNU/Linux, this is a merge between my original script # and a more exhaustive one from Jon Jackson (jjackson at familyjackson dot net) # This program is free software; you can redistribute it and/or modify it # under the terms of the GNU Lesser General Public Licenseas published by # the Free Software Foundation, either version 3 of the License, or (at # your option) any later version. See the file Documentation/LGPL3 in the # original distribution for details. There is ABSOLUTELY NO warranty. # This program is free software, but comes with no warrenty or guarantee # send bug reports or feedback to me or to debian bug tracking system # setup environment set +u # don't give error for unset variables (matters for environment variables) shopt -s extglob # allow extended pattern matching ##################### DEFINE JAVA_HOME ##################### if [ -z "$JAVA_HOME" ] ; then # This does not work see #505315 JAVA_HOME=$(/usr/sbin/update-java-alternatives -l | sort | tail -1 | cut -d' ' -f 3) # Reverted to old version - see #558222 (Andreas Tille) # JAVA_HOME=$(dirname $(dirname $(dirname $(readlink /etc/alternatives/java)))) fi ##################### CREATE THE RIGHT ENVIRONMENT ##################### # ImageJ path ij_path=/usr/share/java #ImageJ user path ij_user_path=$HOME/.imagej # report errors to this user ijadmin='debian-med-packaging@lists.alioth.debian.org' # Documentation URL doc_url='http://imagej.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" max_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 open images in ImageJ panel number ' echo " -x 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 open images in existing ImageJ panel number ' echo " -x 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 [ ... ]" 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 # No, please don't do this - it bloats our mailing list! #if [[ $count -gt 50 && $port == 0 && "$ijadmin" != '' ]] ; then #mail -s "ImageJ ports on $host" $ijadmin << EOF #Port locks on $host reached $count #EOF #fi ##################### FINALLY RUN IMAGEJ ##################### popd > /dev/null if [ -d /usr/share/imagej/jni/ ] ; then jni=-Djava.library.path=$(cat /usr/share/imagej/jni/* | tr '\n' ':') fi if [ "$JAVA_HOME" ] ; then if (( $verbosity > 0 )) ; then echo ${modules} echo $JAVA_HOME/bin/java ${arch} -mx${mem}m ${jni} ${modules} ij.ImageJ -ijpath ${ij_user_path} -port${count} ${images} ${macrocmd} ${macroargs} else eval $JAVA_HOME/bin/java ${arch} -mx${mem}m ${jni} ${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 debian/changelog0000644000000000000000000002531312253533736011055 0ustar imagej (1.48k+dfsg-1) unstable; urgency=medium * New upstream version * debian/imagej.sh: Make sure we are using latest JVM version Closes: #732222 * Standards-Version: 3.9.5 (no changes needed) -- Andreas Tille Mon, 16 Dec 2013 09:12:23 +0100 imagej (1.48e+dfsg-1) unstable; urgency=low * New upstream version * debian/copyright: - DEP5 - Add Files-Excluded to document what was removed from original source * debian/imagej.sh: Do not bloat our mailing list with mails * debian/get-orig-source: Use enhanced uscan if available * debian/watch: mangle +dfsg in version number * debian/control: - cme fix dpkg-control - canonical Vcs URLs -- Andreas Tille Fri, 25 Oct 2013 15:02:25 +0200 imagej (1.47a-1) unstable; urgency=low * New upstream version * debian/get-orig-source: Better handling when called via watch file * debian/watch: call get-orig-source * debian/upstream: citations * debian/control: - Standards-Version: 3.9.3 (no changes needed) - Apply patch by James Page to ease Java transition (thanks to James) Closes: #683539 * debhelper 9 (control+compat) * debian/rules: prevent dh_auto_build from trying to run the program which would end up in a failure because of a lack of a valid display * debian/get-orig-source: Use xz compression -- Andreas Tille Thu, 02 Aug 2012 15:37:48 +0200 imagej (1.46a-1) unstable; urgency=low * New upstream version * Set may-mem variable (Thanks for the patch to Witold Baryluk ) Closes: #649119 * debian/copyright: DEP5 changes -- Andreas Tille Fri, 18 Nov 2011 09:38:02 +0100 imagej (1.45k-1) unstable; urgency=low * New upstream version debian/patches/600997.patch was applied - so remove this patch * Add sun-java6-jre as alternative Depends to openjdk6-jre. It is not a good idea to follow the suggestion of the bug reporter to enable java6-runtime because other packages which are providing this virtual package are known to fail running imagej Closes: #633965 * Debian/control: Fixed Vcs fields * debian/copyright: Format: http://dep.debian.net/deps/dep5 -- Andreas Tille Tue, 19 Jul 2011 14:43:06 +0200 imagej (1.45e-1) unstable; urgency=low * New upstream version * Standards-Version: 3.9.2 (no changes needed) * Debhelper 8 (control+compat) -- Andreas Tille Wed, 13 Apr 2011 15:22:04 +0200 imagej (1.44n-1) unstable; urgency=low * New upstream version * debian/get-orig-source: Fetch latest upstream version rather than currently packaged upstream tarball * debian/rules: dh $@ --with javahelper * debian/control: Build-Depends: javahelper -- Andreas Tille Tue, 25 Jan 2011 17:07:07 +0100 imagej (1.44i-1) unstable; urgency=low * Team upload. * New upstream release (Closes: #601020). - Solves a bug that prevented to quit (Closes: #600997, LP: 661545). * Stabilized gzipped tarball's MD5 sum in ‘debian/get-orig-source’. * New upstream URL (debian/control, debian/copyright, debian/get-orig-source, debian/imagej.1, debian/imagej.sh, debian/watch). * Removed build-dependancy on gif2png (debian/control). * debian/600997.patch and debian/exclude-quilt-from-ant.patch taken frome the testing branch (see below). -- Charles Plessy Sun, 31 Oct 2010 13:46:19 +0900 imagej (1.44c-3) testing; urgency=low * Team upload, see . * debian/600997.patch: patch to allow to close ImageJ after modifying an image (thanks to Frédéric Mothe). * debian/exclude-quilt-from-ant.patch: excludes the .pc directory, otherwise the package fails to build. Thanks to Miguel Landaeta. -- Charles Plessy Thu, 28 Oct 2010 23:35:59 +0900 imagej (1.44e-1) unstable; urgency=low * New upstream version * Standards-Version: 3.9.1 (no changes needed) -- Andreas Tille Tue, 10 Aug 2010 09:14:17 +0200 imagej (1.44c-2) unstable; urgency=low * Drop java2-runtime as alternative dependency Closes: #588445 * Standards-Version: 3.9.0 (no changes needed) -- Andreas Tille Thu, 08 Jul 2010 16:36:56 +0200 imagej (1.44c-1) unstable; urgency=low * New upstream version * Using dpkg source format version ‘3.0 (quilt)’ (debian/source/format) -- Andreas Tille Fri, 25 Jun 2010 13:46:07 +0200 imagej (1.43r-1) unstable; urgency=low * New upstream version * Standards-Version: 3.8.4 (no changes needed) -- Andreas Tille Thu, 11 Mar 2010 13:27:40 +0100 imagej (1.43l-1) unstable; urgency=low * New upstream version * Depend from OpenJdk instead of java-gcj-compat because the application crashes if OpenJdk is not installed Closes: #558222 Considering the fact that the workaround of #532498 seems to be solved as well in case openjdk-6-jre which contains the file /usr/lib/jvm/java-6-openjdk/jre/lib/ext/libjava-access-bridge-jni.so I think this also Closes: #532498 -- Andreas Tille Tue, 01 Dec 2009 19:24:37 +0100 imagej (1.43k-1) unstable; urgency=low * New upstream version * debian/control: - s/Debian-Med/Debian Med/ - dropped cdbs depencency * debian/rules: rewritten, drastically simplified using dh -- Andreas Tille Tue, 24 Nov 2009 11:21:32 +0100 imagej (1.43g-1) unstable; urgency=low * New upstream version * Fix regression of previos upload which again Closes: #505315 -- Andreas Tille Fri, 25 Sep 2009 08:15:46 +0200 imagej (1.43e-1) unstable; urgency=low * New upstream version * debian/control - Depends ${java:Depends} - Depends java-gcj-compat instead of gij - Suggests: java-virtual-machine * debian/imagej.sh: set jni=-Djava.library.path only if directory /usr/share/imagej/jni/ really exists * debhelper 7 * Standards-Version: 3.8.3 (no changes needed) -- Andreas Tille Wed, 19 Aug 2009 13:29:22 +0200 imagej (1.43b-1) unstable; urgency=low * New upstream version Closes: #532073 * Standards-Version: 3.8.2 (no changes needed) * Use dirname/readlink /usr/bin/java instead upf update-alternatives to obtain JVM (Thanks to "Onkar Shinde" ) Closes: #505315 * debian/imagej.sh: Improved imagej wrapper script by Johan Henriksson : It allows dependent packages to add JNI-paths. this is a critical update as an important package (micromanager-ij) depends on it. Closes: #507824 * debian/imagej.sh: set address to report bugs to to debian-med-packaging * debian/get-orig-source: less noisy * debian/patches/20_jpegwriter.patch: Fix Jpeg library issue to enable build with OpenJDK (Thanks to Johan Henriksson ) * Patches applied upstream, removed quilt dependency -- Andreas Tille Tue, 09 Jun 2009 08:17:14 +0200 imagej (1.41n-1) unstable; urgency=low [ Andreas Tille ] * New upstream release Closes: #496802 * Group maintenance according to Debian-Med group policy * Added myself as Uploader * VCS fields * Added Homepage to debian/control * Added watch file * Added get-orig-source * Moved extra image files into debian directory to keep all additions there and install them via debian/install file instead of copying in debian/rules * Machine readable copyright file * Do the copying work in debian/install instead of debian/rules * debian/manpages * Build-Depends: s/ecj/openjdk-6-jdk/ which finally makes imagej fit for Debian main because no non-free components are needed any more * 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. [ Paolo Ariano ] * A lot of correction to the run script, thanks to Jonathan (closes: #496798). * The socket-lock directory is now /tmp/imagej [ Andreas Tille ] * -- Andreas Tille Tue, 23 Sep 2008 12:04:34 +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 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 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 Fri, 08 Feb 2008 11:29:56 +0100 imagej (1.39b-5) unstable; urgency=high * New sections graphics. -- Paolo Ariano Wed, 26 Sep 2007 13:02:02 +0200 imagej (1.39b-4) unstable; urgency=high * New man page. -- Paolo Ariano 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 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 Tue, 25 Sep 2007 15:24:02 +0200 imagej (1.39b-1) unstable; urgency=low * New Upstream Release. -- Paolo Ariano 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 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 Wed, 10 May 2006 23:48:28 +0200 imagej (1.37m-3) unstable; urgency=low * Added lut. -- Paolo Ariano 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 Mon, 07 Aug 2006 22:41:53 +0200 imagej (1.37m-1) unstable; urgency=low * Initial release (Closes: #4526773, #6353442). -- Paolo Ariano Fri, 28 Apr 2006 11:41:53 +0200 debian/patches/0000755000000000000000000000000012214301217010606 5ustar debian/patches/series0000644000000000000000000000003512214301217012021 0ustar exclude-quilt-from-ant.patch debian/patches/exclude-quilt-from-ant.patch0000644000000000000000000000114012214301217016131 0ustar Description: Excludes the quilt management directory from the build system. See http://bugs.debian.org/600997 Author: Miguel Landaeta Forwarded: no --- imagej-1.47a.orig/build.xml +++ imagej-1.47a/build.xml @@ -10,6 +10,9 @@ + + debian/imagej.10000644000000000000000000000625312214301217010503 0ustar .\" 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 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 . .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 $HOME/.imagej. The system wide equivalent is in /usr/share/imagej/ .TP .B \ HOME/.imagej/plugins/, you can find and put new plugins here .TP .B \ HOME/.imagej/macros/, you can find and put new macros here .TP .B \ HOME/.imagej/luts/, you can find and put new look up tables here .SH "EXAMPLES" .LP For compiling plugins: .LP imagej \-c .SH "SEE ALSO" .\"/.BR bar (1), .\"/.BR baz (1). .br The program is fully documented at http://imagej.nih.gov/ij/download/src/docs/ .SH "AUTHOR" .LP ImageJ was written by Wayne Rasband .PP This manual page, the wrapper and packaging was done by Paolo Ariano , for the Debian project. debian/compat0000644000000000000000000000000212214301217010355 0ustar 9 debian/dirs0000644000000000000000000000001012214301217010032 0ustar usr/bin debian/docs0000644000000000000000000000005412214301217010031 0ustar aREADME.txt IJ_Props.txt release-notes.html debian/extra/0000755000000000000000000000000012214301217010302 5ustar debian/extra/microscope.xpm0000644000000000000000000000120112214301217013165 0ustar /* XPM */ static char * microscope_xpm[] = { "20 20 7 1", " c None", ". c #C3D100", "+ c #D1C700", "@ c #D1B500", "# c #D1A900", "$ c #CB8E00", "% c #C57700", " %% ", " %. 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