From 28c1302520933032d26145985accfc1cdf1d8954 Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Mon, 24 Dec 2018 19:36:39 +0700 Subject: academic/fiji: Added (ImageJ Distribution). Signed-off-by: Willy Sudiarto Raharjo --- academic/fiji/ImageJ2.desktop | 8 +++ academic/fiji/README | 43 +++++++++++++ academic/fiji/References | 8 +++ academic/fiji/doinst.sh | 3 + academic/fiji/fiji | 3 + academic/fiji/fiji.SlackBuild | 140 ++++++++++++++++++++++++++++++++++++++++++ academic/fiji/fiji.info | 10 +++ academic/fiji/slack-desc | 19 ++++++ 8 files changed, 234 insertions(+) create mode 100644 academic/fiji/ImageJ2.desktop create mode 100644 academic/fiji/README create mode 100644 academic/fiji/References create mode 100644 academic/fiji/doinst.sh create mode 100644 academic/fiji/fiji create mode 100644 academic/fiji/fiji.SlackBuild create mode 100644 academic/fiji/fiji.info create mode 100644 academic/fiji/slack-desc (limited to 'academic') diff --git a/academic/fiji/ImageJ2.desktop b/academic/fiji/ImageJ2.desktop new file mode 100644 index 0000000000..87d25dddda --- /dev/null +++ b/academic/fiji/ImageJ2.desktop @@ -0,0 +1,8 @@ +[Desktop Entry] +Name=Fiji (ImageJ 2) +Comment=Fiji is just ImageJ +Type=Application +Categories=Education;Graphics; +Exec=fiji +Terminal=false +Icon=fiji diff --git a/academic/fiji/README b/academic/fiji/README new file mode 100644 index 0000000000..525d5bb3de --- /dev/null +++ b/academic/fiji/README @@ -0,0 +1,43 @@ +Fiji: Fiji is just ImageJ + +Fiji is an image processing package, a "batteries-included" +distribution of ImageJ, bundling a lot of plugins which facilitate +scientific image analysis. + +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. + +Fiji is Just ImageJ, with extras. It is a distribution of ImageJ with +many plugins useful for scientific image analysis in fields such as +life sciences. It is actively maintained, with updates released often. + +NOTE! +The download link points to an unversioned archive. This means that +he MD5SUM will change when the tarball is updated from upstream. When +this happens, please notify the maintainer. + +Citing +Schindelin, J.; Arganda-Carreras, I. & Frise, E. et al. (2012) +"Fiji: an open-source platform for biological-image analysis" +Nature methods 9(7): 676-682, PMID 22743772, doi:10.1038/nmeth.2019 diff --git a/academic/fiji/References b/academic/fiji/References new file mode 100644 index 0000000000..c4a2b3d40f --- /dev/null +++ b/academic/fiji/References @@ -0,0 +1,8 @@ +Citing Fiji + +Like most scientific software, funding for the Fiji project is driven by +citations. If you use Fiji, please cite it in your publications! + +Schindelin, J.; Arganda-Carreras, I. & Frise, E. et al. (2012), "Fiji: +an open-source platform for biological-image analysis", Nature methods +9(7): 676-682, PMID 22743772 (on Google Scholar). diff --git a/academic/fiji/doinst.sh b/academic/fiji/doinst.sh new file mode 100644 index 0000000000..5fb28930db --- /dev/null +++ b/academic/fiji/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/fiji/fiji b/academic/fiji/fiji new file mode 100644 index 0000000000..3cb2d286fe --- /dev/null +++ b/academic/fiji/fiji @@ -0,0 +1,3 @@ +#!/bin/sh +cd /opt/fiji +./fiji & diff --git a/academic/fiji/fiji.SlackBuild b/academic/fiji/fiji.SlackBuild new file mode 100644 index 0000000000..be3ff27eb1 --- /dev/null +++ b/academic/fiji/fiji.SlackBuild @@ -0,0 +1,140 @@ +#!/bin/sh + +# Slackware build script for fiji + +# Copyright 2018 Petar Petrov slackalaxy@gmail.com +# 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=fiji +DIRNAM=Fiji.app +VERSION=${VERSION:-20181207} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i386 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +UPDATER=imagej-updater-0.9.3.jar + +set -e + +# Stop if arch is not supported +if [ "$ARCH" != "i386" ] && [ "$ARCH" != "x86_64" ]; then + printf "\n\n$ARCH is not supported... \n" + exit 1 +fi + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $DIRNAM +tar xvf $CWD/${PRGNAM}-nojre.tar.gz +cd $DIRNAM +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +# Rename the binary we need +if [ "$ARCH" = "x86_64" ]; then + mv ImageJ-linux64 $PRGNAM +else + mv ImageJ-linux32 $PRGNAM +fi + +# We will put here two tools, so they are not run at startup. +mkdir -p unused +cd unused + +# Remove the check for required updates. If you want it, comment out +# the next lines. You can "enable" it any time by just placing it in the +# plugins/Scripts/Plugins/AutoRun/ folder. +mv ../plugins/Scripts/Plugins/AutoRun/Check_Required_Update_Sites.js . + +# We do not want updates when the program is installed. As above, it +# is your system, so if you want this functionality, then comment out +# the line below. You can always "enable it, by placing it in the jars +# folder. +mv ../jars/$UPDATER . + +cd .. + +# Update plugins, so that the latest are included in the package. This +# will download stuff during the package creation, something that is +# against the policy of SlackBuilds.org. However, it is your system, +# so if you _really_ want this, uncomment the line below. +# ./$PRGNAM --update list-local-only + +# Copy the folders, db.xml and the renamed binary to /opt +mkdir -p $PKG/opt/$PRGNAM +cp -a \ + images \ + jars \ + luts \ + macros \ + plugins \ + retro \ + scripts \ + db.xml.gz \ + $PRGNAM \ +$PKG/opt/$PRGNAM + +# If a file called "ImageJ2.desktop" is not present in the directory +# of fiji, it will create (and re-create it if you delete it) the file +# "~/.local/share/applications/ImageJ2.desktop" upon start. So, let it +# have its desktop file. This is a very stupid workaround, but it is +# really the best I could think of. At first I thought that deleting +# "plugins/Scripts/Plugins/Utilities/Create_Desktop_Icon.bsh" will do +# the trick, but no... +cp $CWD/ImageJ2.desktop $PKG/opt/$PRGNAM + +# Install the simple wrapper +install -D -m755 $CWD/$PRGNAM $PKG/usr/bin/$PRGNAM + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/share/{applications,pixmaps} +cp $CWD/ImageJ2.desktop $PKG/usr/share/applications +cp images/icon.png $PKG/usr/share/pixmaps/$PRGNAM.png + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a README.md WELCOME.md $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References + +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/fiji/fiji.info b/academic/fiji/fiji.info new file mode 100644 index 0000000000..81d6d231b8 --- /dev/null +++ b/academic/fiji/fiji.info @@ -0,0 +1,10 @@ +PRGNAM="fiji" +VERSION="20181207" +HOMEPAGE="https://fiji.sc/" +DOWNLOAD="https://downloads.imagej.net/fiji/latest/fiji-nojre.tar.gz" +MD5SUM="53d7ebea5cc9e0310b32ef42e5894590" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="jdk" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/fiji/slack-desc b/academic/fiji/slack-desc new file mode 100644 index 0000000000..997a5af7f0 --- /dev/null +++ b/academic/fiji/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 ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +fiji: fiji (Fiji is just ImageJ) +fiji: +fiji: Fiji is Just ImageJ, with extras. It is a distribution of ImageJ +fiji: with many plugins useful for scientific image analysis in fields +fiji: such as life sciences. +fiji: +fiji: Home: https://fiji.sc/ +fiji: +fiji: +fiji: +fiji: -- cgit v1.2.3