add install

install.sh

@@ -0,0 +1,60 @@
+#!/bin/bash
+
+# This script is shamelessly adapted from https://github.com/saalfeldlab/n5-utils, thanks @axtimwalde & co!
+
+VERSION="10.3.2-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 'bdv' command into" $INSTALL_DIR
+
+echo '#!/bin/bash' > bdv
+echo '' >> bdv
+echo "JAR=\$HOME/.m2/repository/sc/fiji/bigdataviewer-core/${VERSION}/bigdataviewer-core-${VERSION}.jar" >> bdv
+echo 'java \' >> bdv
+echo "  -Xmx${MEM}g \\" >> bdv
+echo '  -XX:+UseConcMarkSweepGC \' >> bdv
+echo -n '  -cp $JAR:' >> bdv
+echo -n $(cat cp.txt) >> bdv
+echo ' \' >> bdv
+echo '  bdv.BigDataViewer "$@"' >> bdv
+
+
+chmod a+x bdv
+
+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 bdv $INSTALL_DIR/
+fi
+
+rm cp.txt
+
+echo "Installation finished."

pom.xml

@@ -11,7 +11,7 @@
 
 	<groupId>sc.fiji</groupId>
 	<artifactId>bigdataviewer-core</artifactId>
-	<version>10.3.1-SNAPSHOT</version>
+	<version>10.3.2-SNAPSHOT</version>
 
 	<name>BigDataViewer Core</name>
 	<description>BigDataViewer core classes with minimal dependencies.</description>

src/main/java/bdv/BigDataViewer.java

@@ -749,9 +749,11 @@ public static void main( final String[] args )
 //		final String fn = "/Users/pietzsch/workspace/data/111010_weber_full.xml";
 //		final String fn = "/Volumes/projects/tomancak_lightsheet/Mette/ZeissZ1SPIM/Maritigrella/021013_McH2BsGFP_CAAX-mCherry/11-use/hdf5/021013_McH2BsGFP_CAAX-mCherry-11-use.xml";
 
-		final String fn = "/Users/Marwan/Downloads/drosophila_his-yfp/dataset.xml";
+//		final String fn = "/Users/Marwan/Downloads/drosophila_his-yfp/dataset.xml";
+
 		try
 		{
+			final String fn = args[0];
 			System.setProperty( "apple.laf.useScreenMenuBar", "true" );
 
 			final BigDataViewer bdv = open( fn, new File( fn ).getName(), new ProgressWriterConsole(), ViewerOptions.options() );
@@ -761,6 +763,8 @@ public static void main( final String[] args )
 		}
 		catch ( final Exception e )
 		{
+			if (args.length==0)
+				System.out.println("Please specify the input");
 			e.printStackTrace();
 		}
 	}