install

#!/bin/bash

# This script is shamelessly adapted from https://github.com/saalfeldlab/n5-utils, thanks @axtimwalde & co!

VERSION="2.3.5-SNAPSHOT"
INSTALL_DIR=${1:-$(pwd)}

echo ""
echo "Installing into $INSTALL_DIR"

# check for operating system
if [[ "$OSTYPE" == "linux-gnu" ]]; then
  echo "Assuming on Linux operating system"
  MEM=$(cat /proc/meminfo | grep MemTotal | sed s/^MemTotal:\\\s*\\\|\\\s\\+[^\\\s]*$//g)
  MEMGB=$(($MEM/1024/1024))
  MEM=$((($MEMGB/5)*4))
elif [[ "$OSTYPE" == "darwin"* ]]; then
  echo "Assuming on MacOS X operating system"
  # sysctl returns total hardware memory size in bytes
  MEM=$(sysctl hw.memsize | grep hw.memsize | sed s/hw.memsize://g)
  MEMGB=$(($MEM/1024/1024/1024))
  MEM=$((($MEMGB/5)*4))
else
  echo "ERROR - Operating system (arg2) must be either linux or osx - EXITING (on windows please run as a normal Java class from e.g. Eclipse)"
  exit
fi

echo "Available memory:" $MEMGB "GB, setting Java memory limit to" $MEM "GB"

mvn clean install
mvn -Dmdep.outputFile=cp.txt -Dmdep.includeScope=runtime dependency:build-classpath

echo ""
echo "Installing 'rs-fish' command into" $INSTALL_DIR
echo ""

echo '#!/bin/bash' > rs-fish
echo '' >> rs-fish
echo "JAR=\$HOME/.m2/repository/net/preibisch/Radial_SymmetryLocalization/${VERSION}/Radial_SymmetryLocalization-${VERSION}.jar" >> rs-fish
echo 'java \' >> rs-fish
echo "  -Xmx${MEM}g \\" >> rs-fish
echo '  -XX:+UseConcMarkSweepGC \' >> rs-fish
echo -n '  -cp $JAR:' >> rs-fish
echo -n $(cat cp.txt) >> rs-fish
echo ' \' >> rs-fish
echo '  cmd.RadialSymmetry "$@"' >> rs-fish


echo ""
echo "Installing 'rs-fish-anisotropy' command into" $INSTALL_DIR
echo ""

echo '#!/bin/bash' > rs-fish-anisotropy
echo '' >> rs-fish-anisotropy
echo "JAR=\$HOME/.m2/repository/net/preibisch/Radial_SymmetryLocalization/${VERSION}/Radial_SymmetryLocalization-${VERSION}.jar" >> rs-fish-anisotropy
echo 'java \' >> rs-fish-anisotropy
echo "  -Xmx${MEM}g \\" >> rs-fish-anisotropy
echo '  -XX:+UseConcMarkSweepGC \' >> rs-fish-anisotropy
echo -n '  -cp $JAR:' >> rs-fish-anisotropy
echo -n $(cat cp.txt) >> rs-fish-anisotropy
echo ' \' >> rs-fish-anisotropy
echo '  cmd.Anisotropy "$@"' >> rs-fish-anisotropy

echo ""
echo "Installing 'csv-overlay-imagej' command into" $INSTALL_DIR
echo ""

echo '#!/bin/bash' > csv-overlay-imagej
echo '' >> csv-overlay-imagej
echo "JAR=\$HOME/.m2/repository/net/preibisch/Radial_SymmetryLocalization/${VERSION}/Radial_SymmetryLocalization-${VERSION}.jar" >> csv-overlay-imagej
echo 'java \' >> csv-overlay-imagej
echo "  -Xmx${MEM}g \\" >> csv-overlay-imagej
echo '  -XX:+UseConcMarkSweepGC \' >> csv-overlay-imagej
echo -n '  -cp $JAR:' >> csv-overlay-imagej
echo -n $(cat cp.txt) >> csv-overlay-imagej
echo ' \' >> csv-overlay-imagej
echo '  cmd.OverlayCSV "$@"' >> csv-overlay-imagej

echo ""
echo "Installing 'csv-overlay-bdv' command into" $INSTALL_DIR
echo ""

echo '#!/bin/bash' > csv-overlay-bdv
echo '' >> csv-overlay-bdv
echo "JAR=\$HOME/.m2/repository/net/preibisch/Radial_SymmetryLocalization/${VERSION}/Radial_SymmetryLocalization-${VERSION}.jar" >> csv-overlay-bdv
echo 'java \' >> csv-overlay-bdv
echo "  -Xmx${MEM}g \\" >> csv-overlay-bdv
echo '  -XX:+UseConcMarkSweepGC \' >> csv-overlay-bdv
echo -n '  -cp $JAR:' >> csv-overlay-bdv
echo -n $(cat cp.txt) >> csv-overlay-bdv
echo ' \' >> csv-overlay-bdv
echo '  cmd.VisualizePointsBDV "$@"' >> csv-overlay-bdv

echo ""
echo "Installing 'embryo-correction' command into" $INSTALL_DIR
echo ""

echo '#!/bin/bash' > embryo-correction
echo '' >> embryo-correction
echo "JAR=\$HOME/.m2/repository/net/preibisch/Radial_SymmetryLocalization/${VERSION}/Radial_SymmetryLocalization-${VERSION}.jar" >> embryo-correction
echo 'java \' >> embryo-correction
echo "  -Xmx${MEM}g \\" >> embryo-correction
echo '  -XX:+UseConcMarkSweepGC \' >>embryo-correction
echo -n '  -cp $JAR:' >> embryo-correction
echo -n $(cat cp.txt) >> embryo-correction
echo ' \' >> embryo-correction
echo '  corrections.ZCorrection "$@"' >> embryo-correction

chmod a+x rs-fish
chmod a+x rs-fish-anisotropy
chmod a+x csv-overlay-imagej
chmod a+x csv-overlay-bdv
chmod a+x embryo-correction

if [ $(pwd) == "$INSTALL_DIR" ]; then
    echo "Installation directory equals current directory, we are done."
else
	echo "Creating directory $INSTALL_DIR and moving files..."
    mkdir -p $INSTALL_DIR
    mv st-view $INSTALL_DIR/
fi

rm cp.txt

echo "Installation finished."