diff options
Diffstat (limited to 'academic/ImageJ')
| -rw-r--r-- | academic/ImageJ/ImageJ.SlackBuild | 85 | ||||
| -rw-r--r-- | academic/ImageJ/ImageJ.info | 14 | ||||
| -rw-r--r-- | academic/ImageJ/README | 34 | ||||
| -rw-r--r-- | academic/ImageJ/doinst.sh | 3 | ||||
| -rw-r--r-- | academic/ImageJ/imagej | 483 | ||||
| -rw-r--r-- | academic/ImageJ/imagej.desktop | 8 | ||||
| -rw-r--r-- | academic/ImageJ/imagej.png | bin | 0 -> 234 bytes | |||
| -rw-r--r-- | academic/ImageJ/slack-desc | 19 |
8 files changed, 646 insertions, 0 deletions
diff --git a/academic/ImageJ/ImageJ.SlackBuild b/academic/ImageJ/ImageJ.SlackBuild new file mode 100644 index 0000000000..a10cf37730 --- /dev/null +++ b/academic/ImageJ/ImageJ.SlackBuild @@ -0,0 +1,85 @@ +#!/bin/sh + +# Slackware build script for ImageJ + +# Copyright 2012 Petar Petrov, ppetrov@paju.oulu.fi +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +PRGNAM=ImageJ +VERSION=${VERSION:-1.45} +ARCH=noarch +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +SRCNAM=ij +SRCVER=145 + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM +unzip $CWD/${SRCNAM}${SRCVER}.zip +cd $PRGNAM +unzip $CWD/ucsd-plugins.zip +chown -R root:root . +find . \ + \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \ + -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ + -exec chmod 644 {} \; + +mkdir -p $PKG/usr/share/$PRGNAM +cp -a luts macros plugins ij.jar $PKG/usr/share/$PRGNAM + +# Install bio-formats plugins +mkdir -p $PKG/usr/share/$PRGNAM/plugins/LOCI +cp -a $CWD/loci_tools.jar $PKG/usr/share/$PRGNAM/plugins/LOCI + +# Install UCSD confocal microscopy plugins +cp -a UCSD\ Plugins $PKG/usr/share/$PRGNAM/plugins/ + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a README.html $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +# Fix permissions +find $PKG -type d -exec chmod 755 {} \; -o \ + -type f -exec chmod 644 {} \; + +# Install wrapper of ij.jar +install -D -m755 $CWD/imagej $PKG/usr/bin/imagej + +mkdir -p $PKG/usr/share/{applications,pixmaps} +cp $CWD/imagej.desktop $PKG/usr/share/applications +cp $CWD/imagej.png $PKG/usr/share/pixmaps + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} diff --git a/academic/ImageJ/ImageJ.info b/academic/ImageJ/ImageJ.info new file mode 100644 index 0000000000..2d6110ba67 --- /dev/null +++ b/academic/ImageJ/ImageJ.info @@ -0,0 +1,14 @@ +PRGNAM="ImageJ" +VERSION="1.45" +HOMEPAGE="http://rsb.info.nih.gov/ij/" +DOWNLOAD="http://rsb.info.nih.gov/ij/download/zips/ij145.zip \ + http://www.loci.wisc.edu/files/software/loci_tools.jar \ + http://rsbweb.nih.gov/ij/plugins/download/ucsd-plugins.zip" +MD5SUM="c0e0202c4a358e886ce1582dd2c9b830 \ + 2914600d36ce0c077526a0380b59f099 \ + 277dec926cc27ade8ef01b8ae4bb69cb" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +MAINTAINER="Petar Petrov" +EMAIL="ppetrov@paju.oulu.fi" +APPROVED="dsomero" diff --git a/academic/ImageJ/README b/academic/ImageJ/README new file mode 100644 index 0000000000..3c15f5325e --- /dev/null +++ b/academic/ImageJ/README @@ -0,0 +1,34 @@ +ImageJ is a Java 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 is multi- +threaded, so time-consuming operations such as image file reading can +be performed in parallel with other operations. + +ImageJ 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. + +ImageJ does geometric transformations such as scaling, rotation and +flips. Image can be zoomed up to 32:1 and down to 1:32. All analysis +and processing functions are available at any magnification factor. +The program supports any number of windows (images) simultaneously, +limited only by available memory. + +Spatial calibration is available to provide real world dimensional +measurements in units such as millimeters. Density or gray scale +calibration is also available. + +ImageJ was designed with an open architecture that provides +extensibility via Java plugins. User-written plugins make it possible +to solve almost any image processing or analysis problem. + +This includes the following additional plugins: +1) Bio-Formats. +2) UCSD confocal microscopy plugins. + +For a complete list of available plugins, check the corresponding +section at the program website. diff --git a/academic/ImageJ/doinst.sh b/academic/ImageJ/doinst.sh new file mode 100644 index 0000000000..5fb28930db --- /dev/null +++ b/academic/ImageJ/doinst.sh @@ -0,0 +1,3 @@ +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi diff --git a/academic/ImageJ/imagej b/academic/ImageJ/imagej new file mode 100644 index 0000000000..44922f4fd7 --- /dev/null +++ b/academic/ImageJ/imagej @@ -0,0 +1,483 @@ +#!/bin/bash +# A wrapper script to launch imagej from the UNIX command line +# Images given as arguments will be opened, macros may also be given as arguments +# Looks for macros in the imagej macro directory +# +# This program is free software, but comes with no warrenty or guarantee +# send bug reports or feedback to jjackson at familyjackson dot net +# Author: Jon Jackson +# Last modified date: $Date: 2008-09-17 10:31:27 +0100 (Wed, 17 Sep 2008) $ +# $Revision: 51 $ +# +# INSTALLATION INSTRUCTIONS +# +### WARNING ########################################################### +# This file must be edited with a program that supports unix new line characters +# - it won't run if edited in 'Notepad' ! +####################################################################### + +# Source location: http://rsb.info.nih.gov/ij/download/linux/unix-script.txt +# 1) Save this script in the ImageJ directory as 'imagej' +# 2) Modify path variables according to your system +# 3) Give the new file execute permission +# 4) Be sure the 'imagej' wrapper is in the 'PATH' + +### MODIFICATION ### +# With minor modifications to use with Slackware, by Petar Petrov 2012 +# ppetrov at paju dot oulu dot fi +#################### + +# setup environment +set +u # don't give error for unset variables (matters for environment variables) +shopt -s extglob # allow extended pattern matching + +############ SITE SPECIFIC VARIABLES ######################### +# Trailing / is not required for path variables +# IMAGEJ PATH - production installation +ij_path='/usr/share/ImageJ' +# Path to ImageJ development installation +#ij_path_dev='/home/jjackson/ImageJ' +# JAVA PATH +# assumes executable is ${java_home}/bin/java +# set java_home variables ='' to use JAVA_HOME environment variable +#if [[ -d /usr/java/jdk1.5 ]] ; then +# java_home='/usr/java/jdk1.5' +#else +# # Optionally specify java path for all available OS / architecture combinations +# java_home_Linux="${ij_path}/jre" +# java_home_Linux_x86_64="${ij_path}/jre64" +# java_home_SunOS="${ij_path}/jre64" +# # +#fi +ijadmin='' +# DOCUMENTATION URL +doc_url='http://rsb.info.nih.gov/ij/' + +# TEMP FOLDER +ij_tmp='/tmp/imagej' +# LOG FILE +#ij_log="${ij_tmp}/log.txt" +# default behaviour when an ImageJ window is already open +newwindow='true' +#newwindow='false' +# macro argument delimiter character +separator=':' +# a ' ' may work provided no arguments would contain spaces +# use macro functions: args=getArgument(); argArray=split(args, ':'); +# to recover macro arguments + +############ DEFAULT MEMORY SETTINGS ######################### + +declare -i default_mem=768 +declare -i min_mem=32 +declare -i max_32bit=1800 # empirical +declare -i max_64bit=17000000000 # conservative + +############ SITE SPECIFIC MODULES ######################### + +# JAR libraries for additional modules may be placed in ${ij_path}/lib +# jmf.jar jai_codec.jar jai_core.jar mlibwrapper_jai.jar + +# Native libraries may be placed in ${ij_path}/lib/$OS +# where OS matches the output of the 'uname' command + +############ END SITE SPECIFIC VARIABLES ######################### + +OS=$(uname) +processor=$(uname -m) # -p doesn't work on ubuntu +declare -i mem +declare -i max_mem +declare -i free_mem + +java_home="${java_home:-$JAVA_HOME}" + +if [[ "$OS" == 'SunOS' ]] ; then + java_arch='-d64' + JAVA_HOME="${java_home_SunOS:-$java_home}" + max_mem=`vmstat | awk 'BEGIN{maxMem='$max_64bit'} NR == 3 {fmem=int($5 / 1024); if (fmem < maxMem) {print fmem} else {print maxMem}}'` + free_mem="max_mem" + mem=${free_mem}/2 + if (( $mem > $default_mem || $mem < $min_mem )) ; then mem=$default_mem ; fi +elif [[ "$OS" == 'Linux' ]] ; then + if [[ "$processor" == 'x86_64' ]] ; then + java_arch='-d64' + JAVA_HOME="${java_home_Linux_x86_64:-$java_home}" + max_mem=`free | awk -v maxMem=$max_64bit 'NR == 2 {fmem=int($2 / 1024); if (fmem < maxMem) {print fmem} else {print maxMem}}'` + free_mem=`free | awk -v maxMem=$max_64bit 'NR == 3 {fmem=int($4 / 1024); if (fmem < maxMem) {print fmem} else {print maxMem}}'` + mem=${free_mem}/3*2 + if (( $mem > $default_mem || $mem < $min_mem )) ; then mem=$default_mem ; fi + else + java_arch='-d32' + JAVA_HOME="${java_home_Linux:-$java_home}" + max_mem=`free | awk -v maxMem=$max_32bit 'NR == 2 {fmem=int($2 / 1024); if (fmem < maxMem) {print fmem} else {print maxMem}}'` + free_mem=`free | awk -v maxMem=$max_32bit 'NR == 3 {fmem=int($4 / 1024); if (fmem < maxMem) {print fmem} else {print maxMem}}'` + mem=${free_mem}/3*2 + if (( $mem > $default_mem || $mem < $min_mem )) ; then mem=$default_mem ; fi + fi +fi + + +# if tools.jar is not in ${ij_path}/jre/lib/ext/ edit the 'tools=' line +# to point to tools.jar. The -compile switch will load tools.jar into the +# classpath and enable plugins to be compiled in imagej + +if [[ -f "${ij_path}/tools.jar" ]] ; then + tools="${ij_path}/tools.jar" +else + tools='' +fi + +# End Site specific variables --------------------------------------------------------- + +# other variables +dir=`pwd` +user=`whoami` +host=`hostname` +if [[ -z "$DISPLAY" ]] ; then + echo 'Display variable not set' + echo 'If ImageJ fails to load, try ' + echo '% setenv DISPLAY yourcomputer:0' + echo 'if you use the "csh" or for "bash" try' + echo '% export DISPLAY=yourcomputer:0' + display='default' +else + display="$DISPLAY" +fi + +declare -i port=0 +declare -i verbosity=0 +images='' +macrocmd='' +macroargs='' + + +function usage { + echo + echo 'Image display and analysis program. Opens formats including:' + echo 'UNC, Analyze, Dicom, NIFTI, Tiff, Jpeg, Gif, PNG ...' + echo + echo 'imagej [options] image [ image2 ... image3 ]' + echo ' -h print help and more options' + echo ' -o open images in an open ImageJ panel' + echo ' -p <N> open images in ImageJ panel number <N>' + echo " -x <MB> set available memory (default=${mem} max=${max_mem})" + echo +} + +function fullusage { + echo + echo 'Image display and analysis program. Opens formats including:' + echo 'UNC, Analyze, Dicom, NIFTI, Tiff, Jpeg, Gif, PNG ...' + echo + echo 'imagej [options] image [ image2 ... image3 ] -> open images' + echo + echo 'basic options:' + echo ' -h print help and more options' + echo ' -o open images in existing ImageJ panel if one exists' + echo ' -p <N> open images in existing ImageJ panel number <N>' + echo " -x <MB> set available memory (default=${mem} max=${max_mem})" + echo + echo 'advanced options:' + echo ' -c enable plugin compilation within imagej' + echo ' -d use development version' + echo ' -v be verbose (vv or vvv increases verbosity)' + echo + echo 'options for batch processing:' + echo " -e 'Macro Code' execute macro code" + echo " -r 'Menu Command' run menu command" + echo "Quotation marks '' are required around commands including spaces" + echo 'Commands can be sent to open ImageJ panels with the -p option' + echo + echo 'options for macros:' + echo 'imagej [-i image] [-b|-m] [arg1 ... argN] ' + echo ' -b macro run macro without graphics window' + echo ' -m macro run macro' + echo '"image" will be opened before macro is run' + echo 'all following arguments are passed to macro' + echo + echo "Documentation - $doc_url " + echo "Report problems with this software to $ijadmin" + echo +} + +function macroCmdError { + fullusage + echo 'Only one command option (-b -e -m OR -r) may be specified' 1>&2 + exit 1 +} + +function getFullPath { + # Return full path to file + # treats multiple arguments as a single file with spaces + if (( $# == 0 )) ; then + echo "error getting full path for '${*}'" 1>&2 + fi + pwd_getFullPath="$PWD" + \cd $(dirname "${*}") > /dev/null + dir_getFullPath="$PWD" + \cd "$pwd_getFullPath" > /dev/null + echo "$dir_getFullPath"/$(basename "${*}") +} +function derefln { + # Returns the full path of file to which link points + # following multiple levels of symbolic links. + # NOTE: if you use this function in a script, don't use any + # of the variable names used here + if (( $# == 0 )) ; then + return + fi + local the_link="$1" + local link_dir + local current_dir="$PWD" + while file "$the_link" | grep symbolic > /dev/null ; do # resolve links until target is regular file + if [[ "$the_link" == */* ]] ; then # path contains / + \cd $(dirname "${the_link}") > /dev/null + the_link=$(basename "$the_link") + fi + link_dir="$PWD" + # some versions of 'file' surround the path in `' quotes, hence the tr to remove them + the_link=$(file "${the_link}" | awk '/symbolic link/ {print $NF}' | tr -d "\140\047" ) + if [[ "$the_link" != /* ]] ; then # path is not absolute path - make it one + the_link="$link_dir/$the_link" + fi + \cd "$current_dir" > /dev/null + done + echo $the_link +} + + +# parse input arguments +while getopts b:cde:hi:m:nop:r:vx: options +do + case $options in + b) if [[ -n "$macrocmd" ]] ; then macroCmdError ; fi + macrocmd="-batch ${OPTARG}" + ;; + c) modules="${modules:-}${modules+:}${tools}" + ;; + d) ij_path="$ij_path_dev" + ;; + e) if [[ -n "$macrocmd" ]] ; then macroCmdError ; fi + macrocmd='-eval' + macroargs="'${OPTARG}'" + ;; + h) fullusage + exit 0 + ;; + i) images="${images}'${OPTARG}' " + ;; + m) if [[ -n "$macrocmd" ]] ; then macroCmdError ; fi + macrocmd="-macro ${OPTARG}" + ;; + n) newwindow='true' + ;; + o) newwindow='false' + ;; + p) newwindow='false' + port="${OPTARG}" + if (( "$port" < 1 || "$port" > 99 )) ; then + echo "${OPTARG} is not a permissible value for port number (-p)" 1>&2 + exit 1 + fi + ;; + r) if [[ -n "$macrocmd" ]] ; then macroCmdError ; fi + macrocmd='-run' + macroargs="'${OPTARG}'" + ;; + v) verbosity=verbosity+1 + if (( $verbosity == 2 )) ; then set -x ; fi + if (( $verbosity == 3 )) ; then set -v ; fi + ;; + x) mem="${OPTARG}" + newwindow='true' + if (( $mem < $min_mem || $mem > $max_mem )) ; then + echo "${OPTARG} is not a permissible value for memory (-x)" 1>&2 + echo "min=${min_mem}, max=${max_mem}" 1>&2 + exit 1 + fi + ;; + \?) usage + exit 1 + ;; + esac +done + +#for ((i=1; i < $OPTIND; i++)) +#do +# shift +#done +## above syntax not supported in bash < 2.05 +declare -i i=1 +while (( i < $OPTIND )) ; do + shift + i=i+1 +done + +if [[ "$#" == 0 && -z "$macrocmd" ]] ; then + usage +fi + +# The best way to install .jar libraries required by plugins is to copy them +# to the imagej plugins/jars directory +# Alternatively, either copy them to ${ij_path}/jre/lib/ext/ or add the .jar +# filepath to the modules line below. Paths are separated by a colon +# Classpath must follow command line arguments, as ij_path is dependent on the -d option + +# Resolving ij.jar path. If ij.jar is a symbolic link to ij_<version>.jar +# this allows updating ij.jar without crashing running sessions +ij_jar_path=$(derefln ${ij_path}/ij.jar) + +for mod_jar in ${ij_path}/lib/*jar ; do + modules="${modules:-}${modules+:}$mod_jar" +done +modules="-cp ${ij_jar_path}:${modules+:}${modules:-}" +#${ij_path}/plugins/jars/dcmie.jar + +export LD_LIBRARY_PATH="${ij_path}/lib/${OS}_$processor" +if (( $verbosity > 0 )) ; then + echo "LD_LIBRARY_PATH=$LD_LIBRARY_PATH" +fi + +# -b and -m options only: +# remaining command line arguments are passed as macro arguments +# separated by $separator +if [[ -n "$macrocmd" && -z "$macroargs" ]] ; then + while (( "$#" > 0 )) ; do + if [[ -z "$macroargs" ]] ; then + macroargs="${1}" + else + macroargs="${macroargs}${separator}${1}" + fi + shift + done + macroargs="'$macroargs'" +fi + +# PROTECT POSSIBLE SPACES IN IMAGE FILENAMES +if (( "$#" > 0 )) ; then + while (( "$#" > 0 )) ; do + filearg="${1}" + # full file path required when sending images to running ImageJ panel + if [[ "${newwindow}" == 'false' && -f "${filearg}" ]] && ! expr "${filearg}" : '/.*' > /dev/null; then + filearg="$(getFullPath ${filearg})" + fi + images="${images}'$filearg' " + shift + done +fi + +# CREATE IMAGEJ SOCKET-LOCK DIRECTORY IF NON EXISTANT +if [[ ! -d "$ij_tmp" ]] ; then + mkdir "$ij_tmp" + chmod 777 "$ij_tmp" +fi + +# CREATE IMAGEJ LOG FILE IF NON EXISTANT +if [[ -n "$ij_log" && ! -f "$ij_log" ]] ; then + touch "$ij_log" + chmod 666 "$ij_log" +fi + +# CREATES A TEMP FILE INDICATING A PORT IS IN USE BY IMAGEJ +cd "$ij_tmp" +declare -i count=1 +portopen='false' +lockFileCreated='false' +declare -a locklist=(`ls | grep '[0-9][0-9]-.*'`) + +[[ -n "$ij_log" ]] && echo -e "$$\t$(date)\tNew Window = $newwindow" >> "$ij_log" 2> /dev/null +[[ -n "$ij_log" ]] && echo -e "$$\t$(date)\tPort = $port" >> "$ij_log" 2> /dev/null +[[ -n "$ij_log" ]] && echo -e "$$\t$(date)\tlocklist: \n ${locklist[*]}" >> "$ij_log" 2> /dev/null +if (( $verbosity > 0 )) ; then echo -e "locklist: \n ${locklist[*]}" ; fi + +# PORT SPECIFIED BY USER +if (( $port > 0 )) ; then + # look for a lock on the port specified + for lockname in ${locklist[*]} ; do + prefix=`printf '%02u' $port` + if [[ "$lockname" == ${prefix}-${user}-${host}* ]] ; then + # found lock on the requested port, owned by user on current display + portopen='true' + if (( $verbosity > 0 )) ; then echo "Using socket lock: $lockname" ; fi + count=$port + break + elif [[ "$lockname" == ${prefix}-* ]] ; then + echo "Port $port is in use by some other user or a different host" 1>&2 + if (( $verbosity > 0 )) ; then echo "Port lock: $lockname" ; fi + exit 1 + fi + done + # specified port not in use + count=$port + +# IF EXISTING WINDOW IS REQUESTED, LOOK FOR LISTENING PORT +elif [[ "$newwindow" == 'false' && ${#locklist} != 0 ]] ; then + # look for a lock on the current display for this user + for lockname in ${locklist[*]} ; do + if [[ "$lockname" == [0-9][0-9]-${user}-${host}-${display} ]] ; then + portopen='true' + if (( $verbosity > 0 )) ; then echo "Found socket lock: $lockname" ; fi + # if a matching user/display is found, use this one + count="${lockname%-*-*-*}" + #count=`echo $lockname | sed -e 's/^\([0-9][0-9]\).*/\1/' -e 's/^0//'` # csh? + break + fi + done +fi + +# IF A NEW PORT IS TO BE USED +if [[ "$portopen" == 'false' ]] ; then + # new window requested or no matching port found + # if port is not specified, look for first free port + if (( "$port" == 0 )) ; then + if (( ${#locklist} == 0 )) ; then + # no active locks - use first port + count=1 + else + # active locks - check each port number so see if it is in use + # this is not synchronised!! + count=0 + inuse='true' + while [[ "$inuse" == 'true' ]] ; do + count=count+1 + prefix=`printf '%02u' $count` + inuse='false' + for lockname in ${locklist[*]} ; do + if [[ "$lockname" == ${prefix}-* ]] ; then + inuse='true' + fi + done + done + fi + fi + # CREATING A NEW PORT LOCK + prefix=`printf '%02u' $count` + lockname=${prefix}-${user}-${host}-${display} + + [[ -n "$ij_log" ]] && echo -e "$$\t$(date)\tCreating lock\t$lockname" >> "$ij_log" 2> /dev/null + if (( $verbosity > 0 )) ; then echo -n "creating lock $lockname ... " ; fi + touch $lockname + trap '\rm -f ${ij_tmp}/$lockname >/dev/null ; [[ -n "$ij_log" ]] && echo -e "$$\t$(date)\tReleasing lock\t$lockname" >> "$ij_log" 2> /dev/null' EXIT TERM KILL + # Quitting ImageJ sends EXIT, as does a kill/kill -9 + # CTRL+C in terminal sends INT + EXIT + # System shutdown sends TERM (+EXIT??) + + if (( $verbosity > 0 )) ; then echo 'done' ; fi + + lockFileCreated='true' + if [[ -z "$macrocmd" ]] ; then + echo 'Open other images in this ImageJ panel as follows:' + echo " imagej -p $count <image1> [<image2> ... <imageN>]" + fi + [[ -n "$ij_log" ]] && echo -e "$$\t$(date)\tSocket lock:\t$lockname" >> "$ij_log" 2> /dev/null + if (( $verbosity > 0 )) ; then echo "Socket lock: $lockname" ; fi + echo +fi + +if (( $verbosity > 0 )) ; then + echo ${JAVA_HOME}/bin/java ${java_arch} -mx${mem}m ${modules} ij.ImageJ -ijpath ${ij_path} -port${count} ${images} ${macrocmd} ${macroargs} +fi + +cd "$dir" +eval "${JAVA_HOME}/bin/java ${java_arch} -mx${mem}m ${modules} ij.ImageJ -ijpath ${ij_path} -port${count} ${images} ${macrocmd} ${macroargs} " +exit 0 diff --git a/academic/ImageJ/imagej.desktop b/academic/ImageJ/imagej.desktop new file mode 100644 index 0000000000..bd6bde5fa7 --- /dev/null +++ b/academic/ImageJ/imagej.desktop @@ -0,0 +1,8 @@ +[Desktop Entry] +Categories=Education; +Comment=Scientific image manipulation software +Exec=imagej +Icon=imagej +Name=ImageJ +StartupNotify=false +Type=Application diff --git a/academic/ImageJ/imagej.png b/academic/ImageJ/imagej.png Binary files differnew file mode 100644 index 0000000000..8041fc114a --- /dev/null +++ b/academic/ImageJ/imagej.png diff --git a/academic/ImageJ/slack-desc b/academic/ImageJ/slack-desc new file mode 100644 index 0000000000..637ac00056 --- /dev/null +++ b/academic/ImageJ/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. Line +# up the first '|' above the ':' following the base package name, and the '|' +# on the right side marks the last column you can put a character in. You must +# make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':'. + + |-----handy-ruler------------------------------------------------------| +ImageJ: ImageJ (Image processing and analysis in Java) +ImageJ: +ImageJ: ImageJ is a Java image processing program inspired by NIH Image +ImageJ: for the Macintosh. It was designed with an open architecture that +ImageJ: provides extensibility via Java plugins. User-written plugins make +ImageJ: it possible to solve almost any image processing or analysis problem. +ImageJ: +ImageJ: Home: http://rsb.info.nih.gov/ij/ +ImageJ: +ImageJ: +ImageJ: |
