academic/ImageJ: Added (Image processing and analysis in Java)
Signed-off-by: dsomero <xgizzmo@slackbuilds.org>
This commit is contained in:
Petar Petrov
dsomero
parent
b06f8ace51
commit
64ae6500e3
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@ -0,0 +1,85 @@
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#!/bin/sh
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# Slackware build script for ImageJ
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# Copyright 2012 Petar Petrov, ppetrov@paju.oulu.fi
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# All rights reserved.
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#
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# Redistribution and use of this script, with or without modification, is
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# permitted provided that the following conditions are met:
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#
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# 1. Redistributions of this script must retain the above copyright
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# notice, this list of conditions and the following disclaimer.
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#
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# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
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# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
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# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
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# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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PRGNAM=ImageJ
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VERSION=${VERSION:-1.45}
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ARCH=noarch
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BUILD=${BUILD:-1}
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TAG=${TAG:-_SBo}
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SRCNAM=ij
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SRCVER=145
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CWD=$(pwd)
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TMP=${TMP:-/tmp/SBo}
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PKG=$TMP/package-$PRGNAM
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OUTPUT=${OUTPUT:-/tmp}
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set -e
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rm -rf $PKG
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mkdir -p $TMP $PKG $OUTPUT
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cd $TMP
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rm -rf $PRGNAM
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unzip $CWD/${SRCNAM}${SRCVER}.zip
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cd $PRGNAM
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unzip $CWD/ucsd-plugins.zip
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chown -R root:root .
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find . \
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\( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
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-exec chmod 755 {} \; -o \
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\( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
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-exec chmod 644 {} \;
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mkdir -p $PKG/usr/share/$PRGNAM
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cp -a luts macros plugins ij.jar $PKG/usr/share/$PRGNAM
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# Install bio-formats plugins
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mkdir -p $PKG/usr/share/$PRGNAM/plugins/LOCI
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cp -a $CWD/loci_tools.jar $PKG/usr/share/$PRGNAM/plugins/LOCI
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# Install UCSD confocal microscopy plugins
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cp -a UCSD\ Plugins $PKG/usr/share/$PRGNAM/plugins/
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mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
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cp -a README.html $PKG/usr/doc/$PRGNAM-$VERSION
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cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
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# Fix permissions
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find $PKG -type d -exec chmod 755 {} \; -o \
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-type f -exec chmod 644 {} \;
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# Install wrapper of ij.jar
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install -D -m755 $CWD/imagej $PKG/usr/bin/imagej
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mkdir -p $PKG/usr/share/{applications,pixmaps}
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cp $CWD/imagej.desktop $PKG/usr/share/applications
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cp $CWD/imagej.png $PKG/usr/share/pixmaps
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mkdir -p $PKG/install
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cat $CWD/slack-desc > $PKG/install/slack-desc
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cat $CWD/doinst.sh > $PKG/install/doinst.sh
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cd $PKG
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/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz}
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PRGNAM="ImageJ"
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VERSION="1.45"
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HOMEPAGE="http://rsb.info.nih.gov/ij/"
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DOWNLOAD="http://rsb.info.nih.gov/ij/download/zips/ij145.zip \
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http://www.loci.wisc.edu/files/software/loci_tools.jar \
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http://rsbweb.nih.gov/ij/plugins/download/ucsd-plugins.zip"
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MD5SUM="c0e0202c4a358e886ce1582dd2c9b830 \
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2914600d36ce0c077526a0380b59f099 \
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277dec926cc27ade8ef01b8ae4bb69cb"
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DOWNLOAD_x86_64=""
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MD5SUM_x86_64=""
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MAINTAINER="Petar Petrov"
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EMAIL="ppetrov@paju.oulu.fi"
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APPROVED="dsomero"
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ImageJ is a Java image processing program inspired by NIH Image for
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the Macintosh. It can display, edit, analyze, process, save and print
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8-bit, 16-bit and 32-bit images. It can read many image formats
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including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw". It supports
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"stacks", a series of images that share a single window. It is multi-
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threaded, so time-consuming operations such as image file reading can
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be performed in parallel with other operations.
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ImageJ can calculate area and pixel value statistics of user-defined
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selections. It can measure distances and angles. It can create density
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histograms and line profile plots. It supports standard image
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processing functions such as contrast manipulation, sharpening,
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smoothing, edge detection and median filtering.
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ImageJ does geometric transformations such as scaling, rotation and
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flips. Image can be zoomed up to 32:1 and down to 1:32. All analysis
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and processing functions are available at any magnification factor.
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The program supports any number of windows (images) simultaneously,
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limited only by available memory.
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Spatial calibration is available to provide real world dimensional
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measurements in units such as millimeters. Density or gray scale
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calibration is also available.
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ImageJ was designed with an open architecture that provides
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extensibility via Java plugins. User-written plugins make it possible
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to solve almost any image processing or analysis problem.
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This includes the following additional plugins:
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1) Bio-Formats.
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2) UCSD confocal microscopy plugins.
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For a complete list of available plugins, check the corresponding
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section at the program website.
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if [ -x /usr/bin/update-desktop-database ]; then
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/usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1
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fi
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@ -0,0 +1,483 @@
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#!/bin/bash
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# A wrapper script to launch imagej from the UNIX command line
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# Images given as arguments will be opened, macros may also be given as arguments
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# Looks for macros in the imagej macro directory
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#
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# This program is free software, but comes with no warrenty or guarantee
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# send bug reports or feedback to jjackson at familyjackson dot net
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# Author: Jon Jackson
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# Last modified date: $Date: 2008-09-17 10:31:27 +0100 (Wed, 17 Sep 2008) $
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# $Revision: 51 $
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#
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# INSTALLATION INSTRUCTIONS
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#
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### WARNING ###########################################################
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# This file must be edited with a program that supports unix new line characters
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# - it won't run if edited in 'Notepad' !
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#######################################################################
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# Source location: http://rsb.info.nih.gov/ij/download/linux/unix-script.txt
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# 1) Save this script in the ImageJ directory as 'imagej'
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# 2) Modify path variables according to your system
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# 3) Give the new file execute permission
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# 4) Be sure the 'imagej' wrapper is in the 'PATH'
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### MODIFICATION ###
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# With minor modifications to use with Slackware, by Petar Petrov 2012
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# ppetrov at paju dot oulu dot fi
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####################
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# setup environment
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set +u # don't give error for unset variables (matters for environment variables)
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shopt -s extglob # allow extended pattern matching
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############ SITE SPECIFIC VARIABLES #########################
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# Trailing / is not required for path variables
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# IMAGEJ PATH - production installation
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ij_path='/usr/share/ImageJ'
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# Path to ImageJ development installation
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#ij_path_dev='/home/jjackson/ImageJ'
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# JAVA PATH
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# assumes executable is ${java_home}/bin/java
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# set java_home variables ='' to use JAVA_HOME environment variable
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#if [[ -d /usr/java/jdk1.5 ]] ; then
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# java_home='/usr/java/jdk1.5'
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#else
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# # Optionally specify java path for all available OS / architecture combinations
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# java_home_Linux="${ij_path}/jre"
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# java_home_Linux_x86_64="${ij_path}/jre64"
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# java_home_SunOS="${ij_path}/jre64"
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# #
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#fi
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ijadmin=''
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# DOCUMENTATION URL
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doc_url='http://rsb.info.nih.gov/ij/'
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# TEMP FOLDER
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ij_tmp='/tmp/imagej'
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# LOG FILE
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#ij_log="${ij_tmp}/log.txt"
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# default behaviour when an ImageJ window is already open
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newwindow='true'
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#newwindow='false'
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# macro argument delimiter character
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separator=':'
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# a ' ' may work provided no arguments would contain spaces
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# use macro functions: args=getArgument(); argArray=split(args, ':');
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# to recover macro arguments
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############ DEFAULT MEMORY SETTINGS #########################
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declare -i default_mem=768
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declare -i min_mem=32
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declare -i max_32bit=1800 # empirical
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declare -i max_64bit=17000000000 # conservative
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############ SITE SPECIFIC MODULES #########################
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# JAR libraries for additional modules may be placed in ${ij_path}/lib
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# jmf.jar jai_codec.jar jai_core.jar mlibwrapper_jai.jar
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# Native libraries may be placed in ${ij_path}/lib/$OS
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# where OS matches the output of the 'uname' command
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############ END SITE SPECIFIC VARIABLES #########################
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OS=$(uname)
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processor=$(uname -m) # -p doesn't work on ubuntu
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declare -i mem
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declare -i max_mem
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declare -i free_mem
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java_home="${java_home:-$JAVA_HOME}"
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if [[ "$OS" == 'SunOS' ]] ; then
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java_arch='-d64'
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JAVA_HOME="${java_home_SunOS:-$java_home}"
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max_mem=`vmstat | awk 'BEGIN{maxMem='$max_64bit'} NR == 3 {fmem=int($5 / 1024); if (fmem < maxMem) {print fmem} else {print maxMem}}'`
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free_mem="max_mem"
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mem=${free_mem}/2
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if (( $mem > $default_mem || $mem < $min_mem )) ; then mem=$default_mem ; fi
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elif [[ "$OS" == 'Linux' ]] ; then
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if [[ "$processor" == 'x86_64' ]] ; then
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java_arch='-d64'
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JAVA_HOME="${java_home_Linux_x86_64:-$java_home}"
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max_mem=`free | awk -v maxMem=$max_64bit 'NR == 2 {fmem=int($2 / 1024); if (fmem < maxMem) {print fmem} else {print maxMem}}'`
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free_mem=`free | awk -v maxMem=$max_64bit 'NR == 3 {fmem=int($4 / 1024); if (fmem < maxMem) {print fmem} else {print maxMem}}'`
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mem=${free_mem}/3*2
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if (( $mem > $default_mem || $mem < $min_mem )) ; then mem=$default_mem ; fi
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else
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java_arch='-d32'
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JAVA_HOME="${java_home_Linux:-$java_home}"
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max_mem=`free | awk -v maxMem=$max_32bit 'NR == 2 {fmem=int($2 / 1024); if (fmem < maxMem) {print fmem} else {print maxMem}}'`
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free_mem=`free | awk -v maxMem=$max_32bit 'NR == 3 {fmem=int($4 / 1024); if (fmem < maxMem) {print fmem} else {print maxMem}}'`
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mem=${free_mem}/3*2
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if (( $mem > $default_mem || $mem < $min_mem )) ; then mem=$default_mem ; fi
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fi
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fi
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# if tools.jar is not in ${ij_path}/jre/lib/ext/ edit the 'tools=' line
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# to point to tools.jar. The -compile switch will load tools.jar into the
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# classpath and enable plugins to be compiled in imagej
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if [[ -f "${ij_path}/tools.jar" ]] ; then
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tools="${ij_path}/tools.jar"
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else
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tools=''
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fi
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# End Site specific variables ---------------------------------------------------------
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# other variables
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dir=`pwd`
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user=`whoami`
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host=`hostname`
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if [[ -z "$DISPLAY" ]] ; then
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echo 'Display variable not set'
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echo 'If ImageJ fails to load, try '
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echo '% setenv DISPLAY yourcomputer:0'
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echo 'if you use the "csh" or for "bash" try'
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echo '% export DISPLAY=yourcomputer:0'
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display='default'
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else
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display="$DISPLAY"
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fi
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declare -i port=0
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declare -i verbosity=0
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images=''
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macrocmd=''
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macroargs=''
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function usage {
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echo
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echo 'Image display and analysis program. Opens formats including:'
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echo 'UNC, Analyze, Dicom, NIFTI, Tiff, Jpeg, Gif, PNG ...'
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echo
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echo 'imagej [options] image [ image2 ... image3 ]'
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echo ' -h print help and more options'
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echo ' -o open images in an open ImageJ panel'
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echo ' -p <N> open images in ImageJ panel number <N>'
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echo " -x <MB> set available memory (default=${mem} max=${max_mem})"
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echo
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}
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function fullusage {
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echo
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echo 'Image display and analysis program. Opens formats including:'
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echo 'UNC, Analyze, Dicom, NIFTI, Tiff, Jpeg, Gif, PNG ...'
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echo
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echo 'imagej [options] image [ image2 ... image3 ] -> open images'
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echo
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echo 'basic options:'
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echo ' -h print help and more options'
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echo ' -o open images in existing ImageJ panel if one exists'
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echo ' -p <N> open images in existing ImageJ panel number <N>'
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echo " -x <MB> set available memory (default=${mem} max=${max_mem})"
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echo
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echo 'advanced options:'
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echo ' -c enable plugin compilation within imagej'
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echo ' -d use development version'
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echo ' -v be verbose (vv or vvv increases verbosity)'
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echo
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echo 'options for batch processing:'
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echo " -e 'Macro Code' execute macro code"
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echo " -r 'Menu Command' run menu command"
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echo "Quotation marks '' are required around commands including spaces"
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echo 'Commands can be sent to open ImageJ panels with the -p option'
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echo
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echo 'options for macros:'
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echo 'imagej [-i image] [-b|-m] [arg1 ... argN] '
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echo ' -b macro run macro without graphics window'
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echo ' -m macro run macro'
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echo '"image" will be opened before macro is run'
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echo 'all following arguments are passed to macro'
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echo
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echo "Documentation - $doc_url "
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echo "Report problems with this software to $ijadmin"
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echo
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}
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function macroCmdError {
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fullusage
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echo 'Only one command option (-b -e -m OR -r) may be specified' 1>&2
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exit 1
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}
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function getFullPath {
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# Return full path to file
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# treats multiple arguments as a single file with spaces
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if (( $# == 0 )) ; then
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echo "error getting full path for '${*}'" 1>&2
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fi
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pwd_getFullPath="$PWD"
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\cd $(dirname "${*}") > /dev/null
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dir_getFullPath="$PWD"
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\cd "$pwd_getFullPath" > /dev/null
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echo "$dir_getFullPath"/$(basename "${*}")
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}
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function derefln {
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# Returns the full path of file to which link points
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# following multiple levels of symbolic links.
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# NOTE: if you use this function in a script, don't use any
|
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# of the variable names used here
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if (( $# == 0 )) ; then
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return
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fi
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local the_link="$1"
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local link_dir
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local current_dir="$PWD"
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while file "$the_link" | grep symbolic > /dev/null ; do # resolve links until target is regular file
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if [[ "$the_link" == */* ]] ; then # path contains /
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\cd $(dirname "${the_link}") > /dev/null
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the_link=$(basename "$the_link")
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fi
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link_dir="$PWD"
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# some versions of 'file' surround the path in `' quotes, hence the tr to remove them
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the_link=$(file "${the_link}" | awk '/symbolic link/ {print $NF}' | tr -d "\140\047" )
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if [[ "$the_link" != /* ]] ; then # path is not absolute path - make it one
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the_link="$link_dir/$the_link"
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fi
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\cd "$current_dir" > /dev/null
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done
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echo $the_link
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}
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||||
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# parse input arguments
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while getopts b:cde:hi:m:nop:r:vx: options
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do
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case $options in
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b) if [[ -n "$macrocmd" ]] ; then macroCmdError ; fi
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||||
macrocmd="-batch ${OPTARG}"
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;;
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c) modules="${modules:-}${modules+:}${tools}"
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;;
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d) ij_path="$ij_path_dev"
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;;
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e) if [[ -n "$macrocmd" ]] ; then macroCmdError ; fi
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macrocmd='-eval'
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macroargs="'${OPTARG}'"
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;;
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h) fullusage
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||||
exit 0
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||||
;;
|
||||
i) images="${images}'${OPTARG}' "
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;;
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||||
m) if [[ -n "$macrocmd" ]] ; then macroCmdError ; fi
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macrocmd="-macro ${OPTARG}"
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;;
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||||
n) newwindow='true'
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||||
;;
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||||
o) newwindow='false'
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;;
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p) newwindow='false'
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port="${OPTARG}"
|
||||
if (( "$port" < 1 || "$port" > 99 )) ; then
|
||||
echo "${OPTARG} is not a permissible value for port number (-p)" 1>&2
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exit 1
|
||||
fi
|
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;;
|
||||
r) if [[ -n "$macrocmd" ]] ; then macroCmdError ; fi
|
||||
macrocmd='-run'
|
||||
macroargs="'${OPTARG}'"
|
||||
;;
|
||||
v) verbosity=verbosity+1
|
||||
if (( $verbosity == 2 )) ; then set -x ; fi
|
||||
if (( $verbosity == 3 )) ; then set -v ; fi
|
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;;
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x) mem="${OPTARG}"
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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
|
||||
|
|
@ -0,0 +1,8 @@
|
|||
[Desktop Entry]
|
||||
Categories=Education;
|
||||
Comment=Scientific image manipulation software
|
||||
Exec=imagej
|
||||
Icon=imagej
|
||||
Name=ImageJ
|
||||
StartupNotify=false
|
||||
Type=Application
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 234 B |
|
|
@ -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:
|
||||
Loading…
Reference in New Issue