[med-svn] [imagej] 09/10: d/extra/imagej: remove tabs, fix indentation, and remove trailing whitespace
Carnë Draug
carandraug+dev at gmail.com
Mon Aug 28 13:12:50 UTC 2017
This is an automated email from the git hooks/post-receive script.
carandraug-guest pushed a commit to branch master
in repository imagej.
commit b9020828dac208c1b631b03d3ab0ddde9ef916a5
Author: Carnë Draug <carandraug+dev at gmail.com>
Date: Sun Aug 27 16:43:17 2017 +0100
d/extra/imagej: remove tabs, fix indentation, and remove trailing whitespace
---
debian/extra/imagej | 309 ++++++++++++++++++++++++++--------------------------
1 file changed, 154 insertions(+), 155 deletions(-)
diff --git a/debian/extra/imagej b/debian/extra/imagej
index 0578498..02250c8 100755
--- a/debian/extra/imagej
+++ b/debian/extra/imagej
@@ -8,13 +8,13 @@
# Andreas Tille <tille at debian.org>
# 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
+# 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
+# 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
@@ -61,7 +61,7 @@ newwindow='true'
# macro argument conjoining character
separator=':'
# a ' ' may work provided no arguments would contain spaces
-# use macro functions: args=getArgument(); argArray=split(args, ':');
+# use macro functions: args=getArgument(); argArray=split(args, ':');
# to recover macro arguments
declare -i mem
@@ -70,7 +70,7 @@ declare -i min_mem=16
declare -i max_mem
declare -i free_mem
-# other variables
+# other variables
dir=`pwd`
user=`whoami`
host=`hostname`
@@ -80,7 +80,7 @@ if [[ -z "$DISPLAY" ]] ; then
echo '% setenv DISPLAY yourcomputer:0'
echo 'if you use the "csh" or for "bash" try'
echo '% export DISPLAY=yourcomputer:0'
- display='default'
+ display='default'
else
display="$DISPLAY"
fi
@@ -94,35 +94,35 @@ 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
+ 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
+ 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
+# create plugins,macro,tmp dirs
+mkdir -p $ij_user_path/plugins
mkdir -p $ij_user_path/macros
mkdir -p $ij_user_path/luts
-# create imagej socket-lock directory if non existant
+# create imagej socket-lock directory if non existant
if [[ ! -d "$ij_tmp" ]] ; then
mkdir -p "$ij_tmp"
#chmod 777 "$ij_user_path/tmp"
@@ -130,32 +130,33 @@ 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
+# 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
+# fi
# done
-# makes symbolik links from shared plugins, macros and luts
+# 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
+ 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/$p"
- fi
+ if [ ! -e "$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
+ ln -s /usr/share/imagej/luts/$p $ij_user_path/luts/$p
fi
done
@@ -164,153 +165,152 @@ done
##################### USAGE DESCRIPTION #####################
function usage {
- echo
+ echo
echo 'Image display and analysis program. Opens formats including:'
- echo 'UNC, Analyze, Dicom, NIFTI, Tiff, Jpeg, Gif, PNG ...'
+ 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
+ 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
echo 'Image display and analysis program. Opens formats including:'
- echo 'UNC, Analyze, Dicom, NIFTI, Tiff, Jpeg, Gif, PNG ...'
- echo
+ 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 ' -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 ' -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
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 ' -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 'all following arguments are passed to macro'
+ echo
echo "Documentation - $doc_url "
- echo "Report problems with this software to $ijadmin"
+ 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
+ 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
+# 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
+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 < $OPTIND )) ; do
- shift
- i=i+1
+ shift
+ i=i+1
done
#if (( "$#" == 0 )) ; then
-# usage
-#fi
+# usage
+#fi
# -b and -m options only:
-# remaining command line arguments are passed as macro arguments
+# remaining command line arguments are passed as macro arguments
# separated by $separator
if [[ -n "$macrocmd" && -z "$macroargs" ]] ; then
- while (( "$#" > 0 )) ; do
- if [[ -z "$macroargs" ]] ; then
+ while (( "$#" > 0 )) ; do
+ if [[ -z "$macroargs" ]] ; then
macroargs="${1}"
else
macroargs="${macroargs}${separator}${1}"
fi
- shift
- done
- macroargs="'$macroargs'"
+ shift
+ done
+ macroargs="'$macroargs'"
fi
-
+
# protect possible spaces in image filenames
if (( "$#" > 0 )) ; then
- while (( "$#" > 0 )) ; do
- images="${images}'${1}' "
- shift
- done
+ while (( "$#" > 0 )) ; do
+ images="${images}'${1}' "
+ shift
+ done
fi
##################### USING PORT #####################
@@ -330,7 +330,7 @@ if (( $port > 0 )) ; then
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
+ # 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
@@ -340,8 +340,8 @@ if (( $port > 0 )) ; then
if (( $verbosity > 0 )) ; then echo "Port lock: $lockname" ; fi
exit 1
fi
- done
- # specified port not in use
+ done
+ # specified port not in use
count=$port
# If existing window is requested, look for listening port
@@ -363,7 +363,7 @@ fi
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 (( "$port" == 0 )) ; then
if (( ${#locklist} == 0 )) ; then
# no active locks - use first port
count=1
@@ -387,20 +387,20 @@ if [[ "$portopen" == 'false' ]] ; then
# 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
+ if (( $verbosity > 0 )) ; then echo -n "creating lock $lockname ... " ; fi
+ touch $lockname
+ trap '\rm -f ${ij_tmp}/$lockname >/dev/null ; exit 1' EXIT TERM
+ # Quitting ImageJ sends EXIT, as does a kill/kill -9
+ # CTRL+C in terminal sends INT + EXIT
+ # System shutdown sends TERM (+EXIT??)
+
+ if (( $verbosity > 0 )) ; then echo 'done' ; fi
lockFileCreated='true'
- echo 'Open other images in this ImageJ panel as follows:'
- echo " imagej -p $count <image1> [<image2> ... <imageN>]"
+ echo 'Open other images in this ImageJ panel as follows:'
+ echo " imagej -p $count <image1> [<image2> ... <imageN>]"
if (( $verbosity > 0 )) ; then echo "Socket lock: $lockname" ; fi
- echo
+ echo
fi
# Report number of port locks - more than 50 may indicate error in this script
@@ -420,18 +420,17 @@ if [ -d /usr/share/imagej/jni/ ] ; then
fi
if [ "$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
+ 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
+ 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
-
--
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