removed unused option

Updated Readme.md file

ch.psi.fda/Readme.md

@@ -0,0 +1,107 @@
+# Overview
+This package holds the core functionality of FDA.
+
+# Usage
+use -Djava.util.logging.config.file=logging.properties` to configure logging
+
+## Server
+
+The FDA server is started as follows:
+
+```
+./bin/server -h
+usage: fda
+ -h         Help
+ -p <arg>   Server port (default: 8080)
+ -s <arg>   Server address (default: localhost)
+```
+
+Start new scan:
+
+```
+curl -X PUT -d @scan1d.xml -H 'Content-Type:application/xml' http://localhost:8080/fda/scan
+```
+
+## Viewer
+
+```
+./bin/viewer -h
+usage: viewer
+ -h         Help
+ -p <arg>   Server port (default: 10000)
+ -s <arg>   Server address (default: localhost)
+ ```
+
+
+# Development
+When checking out the project from the repository there is the `target/generated-sources/xjc` folder missing.
+After checking out the project execute `mvn compile` to create the folder and the required classes. 
+
+To build project use `mvn clean install`.
+
+To upload the latest version to the central artifact repository use `mvn clean deploy`.
+Create Zip file via `mvn clean compile assembly:assembly`
+
+To use the FDA libary in an other project (like the GUI project) use:
+
+```
+<dependency>
+    <groupId>ch.psi</groupId>
+    <artifactId>fda</artifactId>
+    <version>x.x.x</version>
+</dependency>
+```
+
+## REST
+FDA offers a rest service to execute scans. There are 3 distinct service for fda scan, fdaq and cdump.
+
+### FDA Service
+
+Submit scan
+
+```
+PUT fda/{trackingId}
+Content-Type: application/xml
+<configuration>
+...
+</configuration>
+
+204 - Success
+
+```
+
+Stop/cancel scan
+
+```
+DELETE fda/{trackingId}
+
+204 - Success
+```
+
+Stop all scans
+
+```
+DELETE fda
+
+204 - Success
+```
+
+Check if scan is running
+
+```
+GET fda/{trackingId}/running
+
+200 - true/false
+```
+
+Wait for scan done (blocks until scan is done)
+
+```
+GET fda/{trackingId}/done
+
+204 - Success
+```
+
+# Notes
+## Upgrade FDA 1.x to 2.x
+In existing fda.properties file the following property need to be added: `ch.psi.fda.aq.data.dir=../data`

ch.psi.fda/pom.xml

@@ -3,41 +3,52 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>ch.psi</groupId>
 	<artifactId>fda</artifactId>
-	<version>1.1.41</version>
+	<version>2.1.1</version>
 
 	<dependencies>
-	
+
+		<dependency>
+			<groupId>ch.psi</groupId>
+			<artifactId>ch.psi.fda.core</artifactId>
+			<version>0.0.1-SNAPSHOT</version>
+		</dependency>
+
+		<dependency>
+			<groupId>ch.psi</groupId>
+			<artifactId>ch.psi.fda.cdump</artifactId>
+			<version>1.0.1</version>
+		</dependency>
+		<dependency>
+			<groupId>ch.psi</groupId>
+			<artifactId>ch.psi.fda.fdaq</artifactId>
+			<version>1.0.5</version>
+		</dependency>
+
 		<dependency>
 			<groupId>org.glassfish.jersey.containers</groupId>
 			<artifactId>jersey-container-grizzly2-http</artifactId>
-			<version>2.3.1</version>
+			<version>2.5.1</version>
 		</dependency>
 
 		<dependency>
 			<groupId>org.glassfish.jersey.media</groupId>
 			<artifactId>jersey-media-sse</artifactId>
-			<version>2.3.1</version>
+			<version>2.5.1</version>
 		</dependency>
 
 		<dependency>
 			<groupId>org.glassfish.jersey.media</groupId>
 			<artifactId>jersey-media-json-jackson</artifactId>
-			<version>2.3.1</version>
+			<version>2.5.1</version>
 		</dependency>
-	
-	
+
+
 		<dependency>
 			<groupId>org.jeromq</groupId>
 			<artifactId>jeromq</artifactId>
 			<version>0.2.0</version>
 		</dependency>
-	
-	
-		<dependency>
-			<groupId>com.google.guava</groupId>
-			<artifactId>guava</artifactId>
-			<version>15.0</version>
-		</dependency>
+
 		<dependency>
 			<groupId>ch.psi</groupId>
 			<artifactId>jcae</artifactId>
@@ -110,8 +121,7 @@
 					<target>1.7</target>
 				</configuration>
 			</plugin>
-			<!-- Generate Javadoc Jar -->
-			<plugin>
+			<!-- <plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-javadoc-plugin</artifactId>
 				<version>2.8</version>
@@ -123,8 +133,7 @@
 						</goals>
 					</execution>
 				</executions>
-			</plugin>
-			<!-- Generate Source Jar -->
+			</plugin> -->
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-source-plugin</artifactId>
@@ -219,23 +228,16 @@
 						</lifecycleMappingMetadata>
 					</configuration>
 				</plugin>
-				
 				<plugin>
-				<artifactId>maven-assembly-plugin</artifactId>
-				<configuration>
-					<finalName>${project.name}-${project.version}</finalName>
-					<appendAssemblyId>false</appendAssemblyId>
-					<archive>
-						<!-- <manifest>
-							<mainClass>ch.psi.fda.AcquisitionMain</mainClass>
-						</manifest> -->
-					</archive>
-					<descriptorRefs>
-						<descriptorRef>jar-with-dependencies</descriptorRef>
-					</descriptorRefs>
-				</configuration>
-			</plugin>
-				
+					<groupId>org.apache.maven.plugins</groupId>
+					<artifactId>maven-assembly-plugin</artifactId>
+					<configuration>
+						<descriptors>
+							<descriptor>src/main/assembly/assembly.xml</descriptor>
+						</descriptors>
+					</configuration>
+				</plugin>
+
 			</plugins>
 		</pluginManagement>
 	</build>

ch.psi.fda/src/main/assembly/assembly.xml

@@ -0,0 +1,54 @@
+<assembly xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2" 
+  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+  xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2 http://maven.apache.org/xsd/assembly-1.1.2.xsd">
+  
+  
+    <id>bin</id>
+    <!-- Generates a zip package containing the needed files -->
+    <formats>
+        <format>zip</format>
+    </formats>
+
+    <!-- Adds dependencies to zip package under lib directory -->
+    <dependencySets>
+        <dependencySet>
+            <outputDirectory>lib</outputDirectory>
+            <unpack>false</unpack>
+        </dependencySet>
+    </dependencySets>
+
+    <fileSets>
+        <!--  Adds startup scripts to the root directory of zip package -->
+        <fileSet>
+        	<fileMode>0755</fileMode>
+            <directory>src/main/assembly/bin</directory>
+            <outputDirectory>bin</outputDirectory>
+            <includes>
+                <include>*</include>
+            </includes>
+        </fileSet>
+        <!-- <fileSet>
+        	<directory>src/main/assembly/www</directory>
+            <outputDirectory>www</outputDirectory>
+            <includes>
+                <include>**/*</include>
+            </includes>
+        </fileSet> -->
+        <!-- <fileSet>
+        	<fileMode>0755</fileMode>
+        	<directory>src/main/assembly/var</directory>
+            <outputDirectory>var</outputDirectory>
+            <includes>
+                <include>**/*</include>
+            </includes>
+        </fileSet> -->
+        <!-- adds jar package to the root directory of zip package -->
+        <!-- <fileSet>
+            <directory>target</directory>
+            <outputDirectory></outputDirectory>
+            <includes>
+                <include>*.jar</include>
+            </includes>
+        </fileSet> -->
+    </fileSets>
+</assembly>

ch.psi.fda/src/main/assembly/bin/convert

@@ -0,0 +1,40 @@
+#!/bin/bash
+
+CURRENTDIR=`pwd`
+
+# Resolve symlinks
+BASEDIR=$0
+while [ -h "$BASEDIR" ]; do
+    ls=`ls -ld "$BASEDIR"`
+    link=`expr "$ls" : '^.*-> \(.*\)$' 2>/dev/null`
+    if expr "$link" : '^/' 2> /dev/null >/dev/null; then
+        BASEDIR="$link"
+    else
+        BASEDIR="`dirname "$BASEDIR"`/$link"
+    fi
+done
+BASEDIR=`dirname "$BASEDIR"`
+
+SCRIPTNAME=`basename ${0}`
+
+APPLICATION_HOME=$BASEDIR/../..
+
+LIB_DIR=`find $BASEDIR/../lib -name "*.jar"`
+LIB_DIR=`echo $LIB_DIR | sed -e 's/ /:/g'`
+
+CLASSPATH=${APPLICATION_HOME}/config/:$LIB_DIR
+
+ARGUMENTS=
+VM_ARGUMENTS=
+for i in $@
+do
+        if [ `expr $i : '-D.*'` != '0' ] ;then
+                # Extract VM options
+                VM_ARGUMENTS="$VM_ARGUMENTS $i"
+        else
+                ARGUMENTS="$ARGUMENTS $i"
+        fi
+done
+
+# Execute java
+java -Xmx1024m -XX:MaxPermSize=128m -cp $CLASSPATH -Dch.psi.fda.home=${APPLICATION_HOME} -Djava.util.logging.config.file=${APPLICATION_HOME}/config/logging.properties $VM_ARGUMENTS ch.psi.fda.ConversionMain $ARGUMENTS

ch.psi.fda/src/main/assembly/bin/scan

@@ -0,0 +1,40 @@
+#!/bin/bash
+
+CURRENTDIR=`pwd`
+
+# Resolve symlinks
+BASEDIR=$0
+while [ -h "$BASEDIR" ]; do
+    ls=`ls -ld "$BASEDIR"`
+    link=`expr "$ls" : '^.*-> \(.*\)$' 2>/dev/null`
+    if expr "$link" : '^/' 2> /dev/null >/dev/null; then
+        BASEDIR="$link"
+    else
+        BASEDIR="`dirname "$BASEDIR"`/$link"
+    fi
+done
+BASEDIR=`dirname "$BASEDIR"`
+
+SCRIPTNAME=`basename ${0}`
+
+APPLICATION_HOME=$BASEDIR/../..
+
+LIB_DIR=`find $BASEDIR/../lib -name "*.jar"`
+LIB_DIR=`echo $LIB_DIR | sed -e 's/ /:/g'`
+
+CLASSPATH=${APPLICATION_HOME}/config/:$LIB_DIR
+
+ARGUMENTS=
+VM_ARGUMENTS=
+for i in $@
+do
+        if [ `expr $i : '-D.*'` != '0' ] ;then
+                # Extract VM options
+                VM_ARGUMENTS="$VM_ARGUMENTS $i"
+        else
+                ARGUMENTS="$ARGUMENTS $i"
+        fi
+done
+
+# Execute java
+java -Xmx1024m -XX:MaxPermSize=128m -Dch.psi.fda.home=${APPLICATION_HOME} -Djava.util.logging.config.file=${APPLICATION_HOME}/config/logging.properties $VM_ARGUMENTS -cp $CLASSPATH ch.psi.fda.AcquisitionMain $ARGUMENTS

ch.psi.fda/src/main/assembly/bin/server

@@ -0,0 +1,42 @@
+#!/bin/bash
+
+CURRENTDIR=`pwd`
+
+# Resolve symlinks
+BASEDIR=$0
+while [ -h "$BASEDIR" ]; do
+    ls=`ls -ld "$BASEDIR"`
+    link=`expr "$ls" : '^.*-> \(.*\)$' 2>/dev/null`
+    if expr "$link" : '^/' 2> /dev/null >/dev/null; then
+        BASEDIR="$link"
+    else
+        BASEDIR="`dirname "$BASEDIR"`/$link"
+    fi
+done
+BASEDIR=`dirname "$BASEDIR"`
+
+SCRIPTNAME=`basename ${0}`
+
+APPLICATION_HOME=$BASEDIR/../..
+
+LIB_DIR=`find $BASEDIR/../lib -name "*.jar"`
+LIB_DIR=`echo $LIB_DIR | sed -e 's/ /:/g'`
+
+CLASSPATH=${APPLICATION_HOME}/config/:$LIB_DIR
+
+ARGUMENTS=
+VM_ARGUMENTS=
+for i in $@
+do
+        if [ `expr $i : '-D.*'` != '0' ] ;then
+                # Extract VM options
+                VM_ARGUMENTS="$VM_ARGUMENTS $i"
+        else
+                ARGUMENTS="$ARGUMENTS $i"
+        fi
+done
+
+
+#HUB_BASE=$BASEDIR/../
+#export HUB_BASE
+java $VM_ARGUMENTS -cp $CLASSPATH -Dch.psi.fda.home=${APPLICATION_HOME} -Djava.util.logging.config.file=${APPLICATION_HOME}/config/logging.properties ch.psi.fda.rest.FdaServer $ARGUMENTS

ch.psi.fda/src/main/assembly/bin/viewer

@@ -0,0 +1,40 @@
+#!/bin/bash
+
+CURRENTDIR=`pwd`
+
+# Resolve symlinks
+BASEDIR=$0
+while [ -h "$BASEDIR" ]; do
+    ls=`ls -ld "$BASEDIR"`
+    link=`expr "$ls" : '^.*-> \(.*\)$' 2>/dev/null`
+    if expr "$link" : '^/' 2> /dev/null >/dev/null; then
+        BASEDIR="$link"
+    else
+        BASEDIR="`dirname "$BASEDIR"`/$link"
+    fi
+done
+BASEDIR=`dirname "$BASEDIR"`
+
+SCRIPTNAME=`basename ${0}`
+
+APPLICATION_HOME=$BASEDIR/../..
+
+LIB_DIR=`find $BASEDIR/../lib -name "*.jar"`
+LIB_DIR=`echo $LIB_DIR | sed -e 's/ /:/g'`
+
+CLASSPATH=${APPLICATION_HOME}/config/:$LIB_DIR
+
+ARGUMENTS=
+VM_ARGUMENTS=
+for i in $@
+do
+        if [ `expr $i : '-D.*'` != '0' ] ;then
+                # Extract VM options
+                VM_ARGUMENTS="$VM_ARGUMENTS $i"
+        else
+                ARGUMENTS="$ARGUMENTS $i"
+        fi
+done
+
+# Execute java
+java -Xmx1024m -XX:MaxPermSize=128m -cp $CLASSPATH -Dch.psi.fda.home=${APPLICATION_HOME} -Djava.util.logging.config.file=${APPLICATION_HOME}/config/logging.properties $VM_ARGUMENTS ch.psi.fda.ViewerMain $ARGUMENTS

ch.psi.fda/src/main/assembly/bin/visualize

@@ -0,0 +1,40 @@
+#!/bin/bash
+
+CURRENTDIR=`pwd`
+
+# Resolve symlinks
+BASEDIR=$0
+while [ -h "$BASEDIR" ]; do
+    ls=`ls -ld "$BASEDIR"`
+    link=`expr "$ls" : '^.*-> \(.*\)$' 2>/dev/null`
+    if expr "$link" : '^/' 2> /dev/null >/dev/null; then
+        BASEDIR="$link"
+    else
+        BASEDIR="`dirname "$BASEDIR"`/$link"
+    fi
+done
+BASEDIR=`dirname "$BASEDIR"`
+
+SCRIPTNAME=`basename ${0}`
+
+APPLICATION_HOME=$BASEDIR/../..
+
+LIB_DIR=`find $BASEDIR/../lib -name "*.jar"`
+LIB_DIR=`echo $LIB_DIR | sed -e 's/ /:/g'`
+
+CLASSPATH=${APPLICATION_HOME}/config/:$LIB_DIR
+
+ARGUMENTS=
+VM_ARGUMENTS=
+for i in $@
+do
+        if [ `expr $i : '-D.*'` != '0' ] ;then
+                # Extract VM options
+                VM_ARGUMENTS="$VM_ARGUMENTS $i"
+        else
+                ARGUMENTS="$ARGUMENTS $i"
+        fi
+done
+
+# Execute java
+java -Xmx1024m -XX:MaxPermSize=128m -cp $CLASSPATH -Dch.psi.fda.home=${APPLICATION_HOME} -Djava.util.logging.config.file=${APPLICATION_HOME}/config/logging.properties $VM_ARGUMENTS ch.psi.fda.VisualizationMain $ARGUMENTS

ch.psi.fda/src/main/java/ch/psi/fda/AcquisitionMain.java

@@ -26,7 +26,6 @@ import java.awt.event.WindowAdapter;
 import java.awt.event.WindowEvent;
 import java.io.File;
 import java.io.PrintWriter;
-import java.util.HashMap;
 import java.util.concurrent.Executors;
 import java.util.concurrent.atomic.AtomicInteger;
 import java.util.logging.Level;
@@ -91,8 +90,6 @@ public class AcquisitionMain {
 		boolean nogui = false;
 		String files[] = null;
 		
-		HashMap<String,String> varTable = new HashMap<String,String>();
-		
 		// Iterations option
 		OptionBuilder.hasArg();
         OptionBuilder.withArgName("iterations");
@@ -100,19 +97,11 @@ public class AcquisitionMain {
         OptionBuilder.withType(new Integer(1));
         Option o_iterations = OptionBuilder.create( "iterations");
         
-        // Variables option
-        OptionBuilder.hasArg();
-        OptionBuilder.withArgName("variables");
-        OptionBuilder.withDescription("Scan variables - variables are specified in the form var=value,var2=value2");
-        OptionBuilder.withType(new Integer(1));
-        Option o_variables = OptionBuilder.create( "variables");
-        
         Option o_autoclose = new Option( "autoclose", "Close down application after scan" );
         Option o_init = new Option( "initialize", "Initialize application directories and configuration files" );
         Option o_nogui = new Option( "nogui", "Do not show scan GUI" );
         
         Options options = new Options();
-        options.addOption(o_variables);
         options.addOption(o_iterations);
         options.addOption(o_autoclose);
         options.addOption(o_init);
@@ -142,19 +131,6 @@ public class AcquisitionMain {
             	iterations = Integer.parseInt(line.getOptionValue(o_iterations.getOpt()));
             }
 		
-			// Variables
-			if( line.hasOption(o_variables.getOpt()) ){
-				String variables = line.getOptionValue(o_variables.getOpt() );
-				String[] vars = variables.split(",");
-				for(String varp:vars){
-					String[] pair = varp.split("=");
-					if(pair.length!=2){
-						throw new ParseException("Variables are not specified the correct way. -variables var1=val1,var2=val2");
-					}
-					varTable.put(pair[0], pair[1]);
-				}
-			}
-			
 			// Autoclose option
             if( line.hasOption( o_autoclose.getOpt() ) ) {
                 autoclose = true;
@@ -175,7 +151,7 @@ public class AcquisitionMain {
         // Run application
         try{
         	for(String file: files){
-        		run(new File(file), iterations, autoclose, nogui, varTable);
+        		run(new File(file), iterations, autoclose, nogui);
         	}
         	
     		// Close application automatically if autoclose option is set (and visualizations are specified)
@@ -200,7 +176,7 @@ public class AcquisitionMain {
 	 * @param nogui			Flag whether to run the scan with a GUI
 	 * @param variables		Table of scan variables
 	 */
-	public static void run(File file, Integer iterations, boolean autoclose, boolean nogui, HashMap<String,String> variables){
+	public static void run(File file, Integer iterations, boolean autoclose, boolean nogui){
 		
 		// Initialize application
 		ApplicationConfigurator ac = new ApplicationConfigurator();

ch.psi.fda/src/main/java/ch/psi/fda/ConversionMain.java

@@ -38,14 +38,13 @@ import com.google.common.eventbus.EventBus;
 import ch.psi.fda.deserializer.DataDeserializer;
 import ch.psi.fda.deserializer.DataDeserializerMDA;
 import ch.psi.fda.deserializer.DataDeserializerTXT;
-import ch.psi.fda.serializer.DataSerializer;
-import ch.psi.fda.serializer.DataSerializerMAT;
-import ch.psi.fda.serializer.DataSerializerMAT2D;
-import ch.psi.fda.serializer.DataSerializerMAT2DZigZag;
-import ch.psi.fda.serializer.DataSerializerMDA;
-import ch.psi.fda.serializer.DataSerializerTXT;
-import ch.psi.fda.serializer.DataSerializerTXT2D;
-import ch.psi.fda.serializer.DataSerializerTXTSplit;
+import ch.psi.fda.serializer.SerializerMAT;
+import ch.psi.fda.serializer.SerializerMAT2D;
+import ch.psi.fda.serializer.SerializerMAT2DZigZag;
+import ch.psi.fda.serializer.SerializerMDA;
+import ch.psi.fda.serializer.SerializerTXT;
+import ch.psi.fda.serializer.SerializerTXT2D;
+import ch.psi.fda.serializer.SerializerTXTSplit;
 
 /**
  * Converter to convert the format of datafiles
@@ -98,34 +97,32 @@ public class ConversionMain {
 			throw new IllegalArgumentException("Reader of type "+reader+" not supported.");
 		}
 
-		DataSerializer serializer;
 		if(writer.equals(Writer.MAT)){
-			serializer = new DataSerializerMAT(output);
+			bus.register(new SerializerMAT(output));
 		}
 		else if(writer.equals(Writer.MAT_2D)){
-			serializer = new DataSerializerMAT2D(output);
+			bus.register(new SerializerMAT2D(output));
 		}
 		else if(writer.equals(Writer.TXT)){
-			serializer = new DataSerializerTXT(output, false);
+			bus.register(new SerializerTXT(output, false));
 		}
 		else if(writer.equals(Writer.TXT_2D)){
-			serializer = new DataSerializerTXT2D(output);
+			bus.register(new SerializerTXT2D(output));
 		}
 		else if(writer.equals(Writer.TXT_SPLIT)){
-			serializer = new DataSerializerTXTSplit(output);
+			bus.register(new SerializerTXTSplit(output));
 		}
 		else if(writer.equals(Writer.MDA)){
-			serializer = new DataSerializerMDA(output);
+			bus.register(new SerializerMDA(output));
 		}
 		else if(writer.equals(Writer.MAT_2D_Z)){
-			serializer = new DataSerializerMAT2DZigZag(output);
+			bus.register(new SerializerMAT2DZigZag(output));
 		}
 		else{
 			throw new IllegalArgumentException("Writer of type "+writer+" not supported.");
 		}
 
 		// Start conversion
-		bus.register(serializer);
 		deserializer.read();
 	}	
 	

ch.psi.fda/src/main/java/ch/psi/fda/ViewerMain.java

@@ -20,13 +20,9 @@
 package ch.psi.fda;
 
 import java.awt.FlowLayout;
+import java.awt.Label;
 import java.awt.event.WindowAdapter;
 import java.awt.event.WindowEvent;
-import java.io.ByteArrayInputStream;
-import java.io.IOException;
-import java.io.ObjectInput;
-import java.io.ObjectInputStream;
-import java.util.ArrayList;
 import java.util.List;
 import java.util.logging.Level;
 import java.util.logging.Logger;
@@ -37,15 +33,20 @@ import javax.swing.JScrollPane;
 import javax.swing.JTabbedPane;
 import javax.swing.ScrollPaneLayout;
 
-import org.jeromq.ZMQ;
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.GnuParser;
+import org.apache.commons.cli.HelpFormatter;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
 
 import com.google.common.eventbus.EventBus;
+import com.google.common.eventbus.Subscribe;
 
+import ch.psi.fda.aq.VisualizationMapper;
 import ch.psi.fda.gui.ScrollableFlowPanel;
-import ch.psi.fda.visualizer.SeriesDataFilter;
+import ch.psi.fda.model.v1.Visualization;
+import ch.psi.fda.rest.client.StreamClient;
 import ch.psi.fda.visualizer.Visualizer;
-import ch.psi.fda.visualizer.XYSeriesDataFilter;
-import ch.psi.plot.xy.LinePlot;
 
 /**
  * Visualize data according to the scan description
@@ -54,6 +55,13 @@ public class ViewerMain {
 
 	private static Logger logger = Logger.getLogger(ViewerMain.class.getName());
 	
+	private Visualizer visualizer;
+	private String source;;
+	
+	public ViewerMain(String source){
+		this.source = source;
+	}
+	
 	/**
 	 * Visualize data
 	 * @param configuration
@@ -62,32 +70,20 @@ public class ViewerMain {
 	 */
 	public void visualize() throws InterruptedException{
 		
-		List<SeriesDataFilter> filters = new ArrayList<>();
-		filters.add(new XYSeriesDataFilter("id0", "timestamp", new LinePlot("One")));
-		
-		Visualizer visualizer = new Visualizer(filters);
-		
-//		visualizer.setTerminateAtEOS(true);
-		// Adapt default visualizer behavior to optimize performance for visualization
-		visualizer.setUpdateAtStreamElement(true);
-		visualizer.setUpdateAtStreamDelimiter(true);
-		visualizer.setUpdateAtEndOfStream(true);
-		
-		JPanel opanel = new ScrollableFlowPanel();
+		final JPanel opanel = new ScrollableFlowPanel();
 		opanel.setLayout(new FlowLayout());
 
+		opanel.add(new Label());
+		
 		JScrollPane spane = new JScrollPane(opanel, ScrollPaneLayout.VERTICAL_SCROLLBAR_AS_NEEDED, ScrollPaneLayout.HORIZONTAL_SCROLLBAR_NEVER);
 		JTabbedPane tpane = new JTabbedPane();
 		tpane.addTab("Overview", spane);
 
-		for (JPanel p : visualizer.getPlotPanels()) {
-			opanel.add(p);
-		}
+		
 		
 		final JFrame frame = new JFrame();
 		frame.setSize(1200,800);
 		frame.add(tpane);
-//		frame.setDefaultCloseOperation(WindowConstants.EXIT_ON_CLOSE);
 		frame.addWindowListener(new WindowAdapter(){
 			@Override
 			public void windowClosing(WindowEvent we){
@@ -103,39 +99,39 @@ public class ViewerMain {
         });
 		
 		// Start receiving messages
-		EventBus bus = new EventBus();
-		bus.register(visualizer);
-		visualizer.configure();
+		final EventBus bus = new EventBus();
 		
-		ZMQ.Context context = ZMQ.context();
-		zmq.ZError.clear(); // Clear error code
-		ZMQ.Socket socket = context.socket(ZMQ.SUB);
-		socket.connect("tcp://emac:10000");
-		socket.subscribe(""); // SUBSCRIBE !
+		bus.register(new Object(){
+			@Subscribe
+			public void onMessage(List<Visualization> vis){
+				
+				logger.info("Build up new visualization");
+				
+				// De-register old visualizer
+				if(visualizer!=null){
+					bus.unregister(visualizer);
+				}
+				
+				visualizer = new Visualizer(VisualizationMapper.mapVisualizations(vis));
+				visualizer.setUpdateAtStreamElement(true);
+				visualizer.setUpdateAtStreamDelimiter(true);
+				visualizer.setUpdateAtEndOfStream(true);
+				
+				
+				opanel.removeAll();
+				for (JPanel p : visualizer.getPlotPanels()) {
+					opanel.add(p);
+				}
+				frame.repaint();
+				
+				bus.register(visualizer);
+				visualizer.configure();
+			}
+		});
 		
-		while(true){
-			byte[] content = null;
-//			String header = socket.recvStr(); // header
-			socket.recvStr(); // header
-			while(socket.hasReceiveMore()){
-				content = socket.recv();
-			}
-			if(content==null){ // we lost something discard read messages
-				logger.warning("Lost some message - discard and continue");
-				continue;
-			}
-			
-			try (
-					ByteArrayInputStream bis = new ByteArrayInputStream(content); 
-					ObjectInput in = new ObjectInputStream(bis);
-				) {
-				Object o = in.readObject();
-				bus.post(o);
-			} catch (IOException | ClassNotFoundException e) {
-				logger.log(Level.WARNING,"Unable to deserialize message",e);
-			}
-			
-		}
+		
+		
+		new StreamClient(bus).listen(source);
 	}	
 	
 	/**
@@ -147,9 +143,38 @@ public class ViewerMain {
 	 */
 	public static void main(String[] args) {
 		
+		int port = 10000;
+		String hostname = "localhost";
+		Options options = new Options();
+		options.addOption("h", false, "Help");
+		options.addOption("p", true, "Server port (default: "+port+")");
+		options.addOption("s", true, "Server address (default: "+hostname+")");
+
+		GnuParser parser = new GnuParser();
+		
+		try {
+			CommandLine line = parser.parse(options, args);
+			
+			if (line.hasOption("p")) {
+				port = Integer.parseInt(line.getOptionValue("p"));
+			}
+			if (line.hasOption("s")) {
+				hostname = line.getOptionValue("s");
+			}
+			if (line.hasOption("h")) {
+				HelpFormatter f = new HelpFormatter();
+				f.printHelp("viewer", options);
+				return;
+			}
+		} catch (ParseException e1) {
+			System.err.println("Wrong arguments: "+ e1.getMessage());
+			System.exit(-1);
+		}
+
+		
 		
 		try{
-			ViewerMain e = new ViewerMain();
+			ViewerMain e = new ViewerMain("tcp://"+hostname+":"+port);
 			e.visualize();
 		}
 		catch(Exception ee){

ch.psi.fda/src/main/java/ch/psi/fda/aq/Acquisition.java

@@ -106,7 +106,7 @@ import ch.psi.fda.model.v1.SimpleScalarDetector;
 import ch.psi.fda.model.v1.Timestamp;
 import ch.psi.fda.model.v1.Variable;
 import ch.psi.fda.model.v1.VariableParameterMapping;
-import ch.psi.fda.serializer.DataSerializerTXT;
+import ch.psi.fda.serializer.SerializerTXT;
 import ch.psi.jcae.Channel;
 import ch.psi.jcae.ChannelDescriptor;
 import ch.psi.jcae.ChannelException;
@@ -119,8 +119,6 @@ import ch.psi.jcae.util.ComparatorREGEX;
 /**
  * Data acquisition engine for performing scans
  * Mapping is specific to scan model version 1.0
- * @author ebner
- *
  */
 public class Acquisition {
 	
@@ -130,7 +128,7 @@ public class Acquisition {
 	
 	private ActionLoop actionLoop;
 	private Manipulator manipulator;
-	private DataSerializerTXT serializer;
+	private SerializerTXT serializer;
 	
 	private List<Manipulation> manipulations;
 	private volatile boolean active = false;
@@ -250,7 +248,7 @@ public class Acquisition {
 			b.register(this.manipulator);
 			
 			
-			this.serializer = new DataSerializerTXT(datafile, true);
+			this.serializer = new SerializerTXT(datafile, true);
 			bus.register(serializer);
 		}
 		else{
@@ -259,7 +257,7 @@ public class Acquisition {
 			mapScan(collector, smodel);
 //			col = collector;
 			
-			this.serializer = new DataSerializerTXT(datafile, true);
+			this.serializer = new SerializerTXT(datafile, true);
 			bus.register(serializer);
 		}
 	}
@@ -269,7 +267,13 @@ public class Acquisition {
 	 * @throws InterruptedException 
 	 */
 	public void execute() throws InterruptedException {
-
+		String hostname;
+		try {
+			hostname = InetAddress.getLocalHost().getHostName();
+		} catch (UnknownHostException e) {
+			hostname="unknown";
+		}
+		
 		try{
 			active = true;
 	
@@ -277,38 +281,16 @@ public class Acquisition {
 			actionLoop.execute();
 			actionLoop.cleanup();
 	
-			// Send notifications out to all recipients that want to have success notifications
-			try {
-				String hostname = InetAddress.getLocalHost().getHostName();
-				notificationAgent.sendNotification("Notification - FDA Execution Finished", "The execution of the FDA on '"+hostname+"' for file '"+datafile.getName()+"' finished successfully\n\nYou received this message because you are listed in the notification list for this data acquisition configuration.", false,true);
-			} catch (UnknownHostException e1) {
-				logger.log(Level.WARNING, "Unable to send notification", e1);
-			}
+			notificationAgent.sendNotification("Notification - FDA Execution Finished", "The execution of the FDA on '"+hostname+"' for file '"+datafile.getName()+"' finished successfully\n\nYou received this message because you are listed in the notification list for this data acquisition configuration.", false,true);
 		}
 		catch(RuntimeException e){
 			logger.log(Level.WARNING, "Execution failed: ", e);
-			
-			try {
-				String hostname = InetAddress.getLocalHost().getHostName();
-				notificationAgent.sendNotification("Notification - FDA Execution Failed", "The execution of the FDA failed on '"+hostname+"' for file '"+datafile.getName()+"'\n\nYou received this message because you are listed in the notification list for this data acquisition configuration.", true,false);
-			} catch (UnknownHostException e1) {
-				logger.log(Level.WARNING, "Unable to send notification", e1);
-			}
-			
+			notificationAgent.sendNotification("Notification - FDA Execution Failed", "The execution of the FDA failed on '"+hostname+"' for file '"+datafile.getName()+"'\n\nYou received this message because you are listed in the notification list for this data acquisition configuration.", true,false);
 			throw e;
 		}
 		catch(InterruptedException e){
 			logger.log(Level.WARNING, "Execution interrupted: ", e);
-			
-			// Execution got aborted.
-			try {
-				String hostname = InetAddress.getLocalHost().getHostName();
-				notificationAgent.sendNotification("Notification - FDA Execution was aborted", "The execution of the FDA on '"+hostname+"' for file '"+datafile.getName()+"' was aborted\n\nYou received this message because you are listed in the notification list for this data acquisition configuration.", false, true);
-			} catch (UnknownHostException e1) {
-				logger.log(Level.WARNING, "Unable to send notification", e1);
-			}
-//			throw e;
-			
+			notificationAgent.sendNotification("Notification - FDA Execution was aborted", "The execution of the FDA on '"+hostname+"' for file '"+datafile.getName()+"' was aborted\n\nYou received this message because you are listed in the notification list for this data acquisition configuration.", false, true);
 		}
 		finally{
 			active = false;
@@ -340,10 +322,6 @@ public class Acquisition {
 		// Clear global variables Jython
 		jVariableDictionary.clear();
 		
-//		// Destroy the CA context
-//		cservice.destroy();
-//		logger.fine("ChannelService destroyed");
-		
 		// Remove log handler
 		if(logHandler!=null){
 			logger.fine("Close log handler");
@@ -352,15 +330,8 @@ public class Acquisition {
 		}
 	}
 
-	/**
-	 * Abort acquisition
-	 */
 	public void abort(){
-		
 		actionLoop.abort();
-//		if(acquisitionThread!=null){
-//			acquisitionThread.interrupt();
-//		}
 	}
 	
 	public String getDatafileName(){

ch.psi.fda/src/main/java/ch/psi/fda/aq/AcquisitionConfiguration.java

@@ -19,6 +19,7 @@
 
 package ch.psi.fda.aq;
 
+import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.FileReader;
 import java.io.IOException;
@@ -29,12 +30,6 @@ import java.util.logging.Logger;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
-import ch.psi.fda.install.ApplicationConfigurator;
-
-/**
- * @author ebner
- *
- */
 public class AcquisitionConfiguration {
 	
 	
@@ -77,27 +72,21 @@ public class AcquisitionConfiguration {
 	 * The constructor will read the configuration from the /fda.properties file (resource) located in the classpath.
 	 */
 	public AcquisitionConfiguration(){
-		loadConfiguration();
-	}
-	
-	
-	public void loadConfiguration(){
-		loadConfiguration(null);
+		loadConfiguration(System.getProperty(FDA_CONFIG_FILE));
 	}
 	
 	/**
 	 * Load configuration from properties file
 	 */
 	public void loadConfiguration(String file) {
-		if(file == null){
-			file = System.getProperty(FDA_CONFIG_FILE);
-		}
 		Properties properties = new Properties();
 		
+		File cfile = null;
 		// Only read in the property file if a file is specified
 		if(file != null){
+			cfile = new File(file);
 			try {
-				properties.load(new FileReader(file));
+				properties.load(new FileReader(cfile));
 			} catch (FileNotFoundException e) {
 				throw new RuntimeException("Configuration file "+file+" not found", e);
 			} catch (IOException e) {
@@ -118,16 +107,15 @@ public class AcquisitionConfiguration {
 		otfUseCrlogic = new Boolean(properties.getProperty(AcquisitionConfiguration.class.getPackage().getName()+".otf.useCrlogic", "false"));
 		otfCrlogicPrefix = properties.getProperty(AcquisitionConfiguration.class.getPackage().getName()+".otf.crlogicPrefix", "");
 		otfCrlogicKeepTmpFiles = new Boolean(properties.getProperty(AcquisitionConfiguration.class.getPackage().getName()+".otf.crlogicKeepTmpFiles", "false"));
+
 		
-		if(System.getProperty(ApplicationConfigurator.FDA_HOME_ARGUMENT)!=null){ // TODO remove
-			dataBaseDirectory = System.getProperty(ApplicationConfigurator.FDA_HOME_ARGUMENT)+"/data";
+		dataBaseDirectory = properties.getProperty(AcquisitionConfiguration.class.getPackage().getName()+".data.dir",".");
+		if(cfile!=null && dataBaseDirectory.matches("^\\.\\.?/.*")){ // if basedir starts with . or .. we assume the data directory to be relative to the directory of the configuration file
+			dataBaseDirectory = cfile.getParentFile().getAbsolutePath()+"/"+dataBaseDirectory; 
 		}
-		else{
-			dataBaseDirectory = "./data";
-		}
-		
 		dataFilePrefix = properties.getProperty(AcquisitionConfiguration.class.getPackage().getName()+".data.filePrefix","");
 		
+		
 		actorMoveTimeout = new Long(properties.getProperty(AcquisitionConfiguration.class.getPackage().getName()+".actorMoveTimeout","600000"));
 		
 		smptServer= properties.getProperty(AcquisitionConfiguration.class.getPackage().getName()+".notification.host","mail.psi.ch");

ch.psi.fda/src/main/java/ch/psi/fda/aq/Collector.java

@@ -25,11 +25,11 @@ import java.util.List;
 import com.google.common.eventbus.EventBus;
 import com.google.common.eventbus.Subscribe;
 
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.Metadata;
-import ch.psi.fda.core.messages.StreamDelimiterMessage;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Message;
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.EndOfStreamMessage;
+import ch.psi.fda.messages.Message;
+import ch.psi.fda.messages.Metadata;
+import ch.psi.fda.messages.StreamDelimiterMessage;
 
 /**
  * Collector class that is collecting and merging data from different Queues.

ch.psi.fda/src/main/java/ch/psi/fda/aq/Manipulator.java

@@ -26,9 +26,9 @@ import com.google.common.eventbus.EventBus;
 import com.google.common.eventbus.Subscribe;
 
 import ch.psi.fda.core.Manipulation;
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.Message;
-import ch.psi.fda.core.messages.Metadata;
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.Message;
+import ch.psi.fda.messages.Metadata;
 
 /**
  * Applies manipulations to the data stream

ch.psi.fda/src/main/java/ch/psi/fda/aq/VisualizationMapper.java

@@ -36,10 +36,6 @@ import ch.psi.fda.visualizer.XYZSeriesDataFilter;
 import ch.psi.plot.xyz.MatrixPlot;
 import ch.psi.plot.xyz.MatrixPlotData;
 
-/**
- * @author ebner
- *
- */
 public class VisualizationMapper {
 	
 	
@@ -69,6 +65,12 @@ public class VisualizationMapper {
 		return id;
 	}
 	
+	/**
+	 * Converts a list of visualizations into a list of data filters which can be applied to the data stream
+	 * 
+	 * @param vl
+	 * @return
+	 */
 	public static List<SeriesDataFilter> mapVisualizations(List<Visualization> vl){
 		List<SeriesDataFilter> filters = new ArrayList<SeriesDataFilter>();
 		

ch.psi.fda/src/main/java/ch/psi/fda/core/Manipulation.java

@@ -21,8 +21,8 @@ package ch.psi.fda.core;
 
 import java.util.List;
 
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.Metadata;
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.Metadata;
 
 public interface Manipulation {
 

ch.psi.fda/src/main/java/ch/psi/fda/core/loops/ActorSensorLoop.java

@@ -35,9 +35,9 @@ import ch.psi.fda.core.Actor;
 import ch.psi.fda.core.ActorSetCallable;
 import ch.psi.fda.core.Guard;
 import ch.psi.fda.core.Sensor;
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Metadata;
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.EndOfStreamMessage;
+import ch.psi.fda.messages.Metadata;
 
 /**
  * Loop of actions to accomplish a task or test.

ch.psi.fda/src/main/java/ch/psi/fda/core/loops/cr/CrlogicLoop.java

@@ -39,9 +39,9 @@ import com.google.common.eventbus.EventBus;
 import jcifs.smb.SmbFile;
 import ch.psi.fda.core.Action;
 import ch.psi.fda.core.ActionLoop;
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Metadata;
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.EndOfStreamMessage;
+import ch.psi.fda.messages.Metadata;
 import ch.psi.jcae.ChannelException;
 import ch.psi.jcae.ChannelService;
 

ch.psi.fda/src/main/java/ch/psi/fda/core/loops/cr/ParallelCrlogic.java

@@ -38,7 +38,7 @@ import com.google.common.eventbus.Subscribe;
 
 import ch.psi.fda.core.Action;
 import ch.psi.fda.core.ActionLoop;
-import ch.psi.fda.core.messages.Message;
+import ch.psi.fda.messages.Message;
 
 public class ParallelCrlogic implements ActionLoop {
 	

ch.psi.fda/src/main/java/ch/psi/fda/core/loops/cr/ParallelCrlogicStreamMerge.java

@@ -25,10 +25,10 @@ import java.util.concurrent.BlockingQueue;
 
 import com.google.common.eventbus.EventBus;
 
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Message;
-import ch.psi.fda.core.messages.Metadata;
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.EndOfStreamMessage;
+import ch.psi.fda.messages.Message;
+import ch.psi.fda.messages.Metadata;
 
 /**
  * Class to merge two data streams into one. The secondary queues data is added to the primary queues data.

ch.psi.fda/src/main/java/ch/psi/fda/core/loops/cr/ScrlogicLoop.java

@@ -32,9 +32,9 @@ import com.google.common.eventbus.EventBus;
 
 import ch.psi.fda.core.Action;
 import ch.psi.fda.core.ActionLoop;
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Metadata;
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.EndOfStreamMessage;
+import ch.psi.fda.messages.Metadata;
 import ch.psi.jcae.Channel;
 import ch.psi.jcae.impl.type.DoubleTimestamp;
 

ch.psi.fda/src/main/java/ch/psi/fda/core/loops/otf/OTFLoop.java

@@ -32,10 +32,10 @@ import com.google.common.eventbus.EventBus;
 import ch.psi.fda.core.Action;
 import ch.psi.fda.core.ActionLoop;
 import ch.psi.fda.core.Sensor;
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Metadata;
 import ch.psi.fda.core.sensors.TimestampSensor;
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.EndOfStreamMessage;
+import ch.psi.fda.messages.Metadata;
 
 /**
  * ActionLoop that is implementing the OTF Scan logic.

ch.psi.fda/src/main/java/ch/psi/fda/core/manipulator/JythonManipulation.java

@@ -33,12 +33,12 @@ import javax.script.ScriptEngineManager;
 import javax.script.ScriptException;
 
 import ch.psi.fda.core.Manipulation;
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.Metadata;
 import ch.psi.fda.core.scripting.JythonParameterMapping;
 import ch.psi.fda.core.scripting.JythonParameterMappingChannel;
 import ch.psi.fda.core.scripting.JythonParameterMappingGlobalVariable;
 import ch.psi.fda.core.scripting.JythonParameterMappingID;
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.Metadata;
 
 public class JythonManipulation implements Manipulation{
 

ch.psi.fda/src/main/java/ch/psi/fda/core/messages/ControlMessage.java

@@ -1,29 +0,0 @@
-/**
- * 
- * Copyright 2010 Paul Scherrer Institute. All rights reserved.
- * 
- * This code is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This code is distributed in the hope that it will be useful,
- * but without any warranty; without even the implied warranty of
- * merchantability or fitness for a particular purpose. See the
- * GNU Lesser General Public License for more details.
- * 
- * You should have received a copy of the GNU Lesser General Public License
- * along with this code. If not, see <http://www.gnu.org/licenses/>.
- * 
- */
-
-package ch.psi.fda.core.messages;
-
-
-/**
- * A control message that is not holding any data but
- * control information (like end of loop, etc.)
- */
-public abstract class ControlMessage extends Message{
-	private static final long serialVersionUID = 1L;
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/messages/DataMessage.java

@@ -1,105 +0,0 @@
-/**
- * 
- * Copyright 2010 Paul Scherrer Institute. All rights reserved.
- * 
- * This code is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This code is distributed in the hope that it will be useful,
- * but without any warranty; without even the implied warranty of
- * merchantability or fitness for a particular purpose. See the
- * GNU Lesser General Public License for more details.
- * 
- * You should have received a copy of the GNU Lesser General Public License
- * along with this code. If not, see <http://www.gnu.org/licenses/>.
- * 
- */
-
-package ch.psi.fda.core.messages;
-
-import java.util.ArrayList;
-import java.util.List;
-
-/**
- * Message holding data
- */
-public class DataMessage extends Message{
-	
-	private static final long serialVersionUID = 1L;
-	
-	private final List<Object> data;
-	private List<Metadata> metadata;
-	
-//	public DataMessage(){
-//		this.data = new ArrayList<Object>();
-//		this.metadata = new ArrayList<>();
-//	}
-//	
-	public DataMessage(List<Metadata> metadata){
-		this.data = new ArrayList<Object>();
-		this.metadata = metadata;
-	}
-	
-	public List<Object> getData(){
-		return(data);
-	}
-	public List<Metadata> getMetadata(){
-		return metadata;
-	}
-	public void setMetadata(List<Metadata> metadata){
-		this.metadata = metadata;
-	}
-	
-	// Utility functions
-	
-	@SuppressWarnings("unchecked")
-	public <T> T getData(String id){
-		int i=0;
-		for(Metadata m: metadata){
-			if(m.getId().equals(id)){
-				return (T) data.get(i);
-			}
-			i++;
-		}
-		throw new IllegalArgumentException("No data found for id: "+id);
-	}
-	
-	public Metadata getMetadata(String id){
-		for(Metadata m: metadata){
-			if(m.getId().equals(id)){
-				return m;
-			}
-		}
-		throw new IllegalArgumentException("No data found for id: "+id);
-	}
-	
-	@Override
-	public String toString() {
-		StringBuffer b = new StringBuffer();
-		b.append("Message [ ");
-		for (Object o : data) {
-			if (o.getClass().isArray()) {
-				// If the array object is of type double[] display its content
-				if (o instanceof double[]) {
-					double[] oa = (double[]) o;
-					b.append("[ ");
-					for (double o1 : oa) {
-						b.append(o1);
-						b.append(" ");
-					}
-					b.append("]");
-				} else {
-					b.append(o.toString());
-				}
-			} else {
-				b.append(o);
-			}
-			
-			b.append(" ");
-		}
-		b.append("]");
-		return b.toString();
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/messages/EndOfStreamMessage.java

@@ -1,52 +0,0 @@
-/**
- * 
- * Copyright 2010 Paul Scherrer Institute. All rights reserved.
- * 
- * This code is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This code is distributed in the hope that it will be useful,
- * but without any warranty; without even the implied warranty of
- * merchantability or fitness for a particular purpose. See the
- * GNU Lesser General Public License for more details.
- * 
- * You should have received a copy of the GNU Lesser General Public License
- * along with this code. If not, see <http://www.gnu.org/licenses/>.
- * 
- */
-
-package ch.psi.fda.core.messages;
-
-/**
- * Message that is send at the end of the action loop inside an ActionLoop implementation
- * of just to indicate that a particular stream has finished
- */
-public class EndOfStreamMessage extends ControlMessage {
-	
-	private static final long serialVersionUID = 1L;
-	
-	/**
-	 * Intersect flag - flag to indicate that stream should be intersected
-	 * after this message.
-	 */
-	private final boolean iflag;
-	
-	public EndOfStreamMessage(){
-		this(false);
-	}
-	
-	public EndOfStreamMessage(boolean iflag){
-		this.iflag = iflag;
-	}
-	
-	public boolean isIflag(){
-		return(iflag);
-	}
-
-	@Override
-	public String toString() {
-		return "Message[ c message: end of stream ]";
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/messages/Message.java

@@ -1,29 +0,0 @@
-/**
- * 
- * Copyright 2010 Paul Scherrer Institute. All rights reserved.
- * 
- * This code is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This code is distributed in the hope that it will be useful,
- * but without any warranty; without even the implied warranty of
- * merchantability or fitness for a particular purpose. See the
- * GNU Lesser General Public License for more details.
- * 
- * You should have received a copy of the GNU Lesser General Public License
- * along with this code. If not, see <http://www.gnu.org/licenses/>.
- * 
- */
-
-package ch.psi.fda.core.messages;
-
-import java.io.Serializable;
-
-/**
- * Message that can be put to the data queue
- */
-public abstract class Message implements Serializable{
-	private static final long serialVersionUID = 1L;
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/messages/Metadata.java

@@ -1,58 +0,0 @@
-/**
- * 
- * Copyright 2010 Paul Scherrer Institute. All rights reserved.
- * 
- * This code is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This code is distributed in the hope that it will be useful,
- * but without any warranty; without even the implied warranty of
- * merchantability or fitness for a particular purpose. See the
- * GNU Lesser General Public License for more details.
- * 
- * You should have received a copy of the GNU Lesser General Public License
- * along with this code. If not, see <http://www.gnu.org/licenses/>.
- * 
- */
-
-package ch.psi.fda.core.messages;
-
-import java.io.Serializable;
-
-/**
- * Metadata of a component of a message. Each component has a global id.
- * Optionally the component can also belong to a dimension. However, depending on the 
- * view the number of the dimension might vary. Therefore the dimension number
- * might change during the lifetime of a message (component).
- */
-public class Metadata implements Serializable{
-
-	private static final long serialVersionUID = 1L;
-
-	private final String id;
-	private int dimension;
-	
-	public Metadata(String id){
-		this.id = id;
-		this.dimension = 0;
-	}
-	
-	public Metadata(String id, int dimension){
-		this.id = id;
-		this.dimension = dimension;
-	}
-
-	public void setDimension(int dimension){
-		this.dimension = dimension;
-	}
-	
-	public int getDimension() {
-		return dimension;
-	}
-
-	public String getId() {
-		return id;
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/messages/StreamDelimiterMessage.java

@@ -1,67 +0,0 @@
-/**
- * 
- * Copyright 2010 Paul Scherrer Institute. All rights reserved.
- * 
- * This code is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This code is distributed in the hope that it will be useful,
- * but without any warranty; without even the implied warranty of
- * merchantability or fitness for a particular purpose. See the
- * GNU Lesser General Public License for more details.
- * 
- * You should have received a copy of the GNU Lesser General Public License
- * along with this code. If not, see <http://www.gnu.org/licenses/>.
- * 
- */
-
-package ch.psi.fda.core.messages;
-
-/**
- * Message that is send at the end of the action loop inside an ActionLoop implementation
- */
-public class StreamDelimiterMessage extends ControlMessage{
-	private static final long serialVersionUID = 1L;
-	/**
-	 * Number of the dimension this delimiter belongs to.
-	 */
-	private final int number;
-	
-	/**
-	 * Intersect flag - flag to indicate that stream should be intersected
-	 * after this message.
-	 */
-	private final boolean iflag;
-	
-	/**
-	 * @param number	Number of the dimension this delimiter belongs to
-	 */
-	public StreamDelimiterMessage(int number){
-		this(number, false);
-	}
-	
-	/**
-	 * @param number
-	 * @param iflag		Flag to indicate that data is grouped
-	 */
-	public StreamDelimiterMessage(int number, boolean iflag){
-		this.number = number;
-		this.iflag = iflag;
-	}
-
-	public int getNumber() {
-		return number;
-	}
-	
-	public boolean isIflag(){
-		return iflag;
-	}
-	
-	@Override
-	public String toString() {
-		// TODO Auto-generated method stub
-		return "Message [ c message: delimiter dimension "+number+" ]";
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/deserializer/DataDeserializerMDA.java

@@ -13,11 +13,11 @@ import java.util.logging.Logger;
 
 import com.google.common.eventbus.EventBus;
 
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Message;
-import ch.psi.fda.core.messages.Metadata;
-import ch.psi.fda.core.messages.StreamDelimiterMessage;
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.EndOfStreamMessage;
+import ch.psi.fda.messages.Message;
+import ch.psi.fda.messages.Metadata;
+import ch.psi.fda.messages.StreamDelimiterMessage;
 
 /**
  * Deserializer MDA file

ch.psi.fda/src/main/java/ch/psi/fda/deserializer/DataDeserializerTXT.java

@@ -29,10 +29,10 @@ import java.util.logging.Logger;
 
 import com.google.common.eventbus.EventBus;
 
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.Metadata;
-import ch.psi.fda.core.messages.StreamDelimiterMessage;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.EndOfStreamMessage;
+import ch.psi.fda.messages.Metadata;
+import ch.psi.fda.messages.StreamDelimiterMessage;
 
 /**
  * Deserializer for text files

ch.psi.fda/src/main/java/ch/psi/fda/install/ApplicationConfigurator.java

@@ -81,15 +81,8 @@ public class ApplicationConfigurator {
 		createApplicationHome();
 		createDefaultConfigurationFiles();
 		
-		// Configure used packages / e.g. via setting system/environment parameters, etc.
-		// Set logging configuration -Djava.util.logging=... 
-		String property = System.getProperty("java.util.logging.config.file");
-		if(property==null){
-			System.setProperty("java.util.logging.config.file", loggingProperties.getAbsolutePath());
-		}
-		
 		// Set FDA configuration argument -Dch.psi.fda.config.file=... 
-		property = System.getProperty(AcquisitionConfiguration.FDA_CONFIG_FILE);
+		String property = System.getProperty(AcquisitionConfiguration.FDA_CONFIG_FILE);
 		if(property==null){
 			System.setProperty(AcquisitionConfiguration.FDA_CONFIG_FILE, fdaProperties.getAbsolutePath());
 		}
@@ -237,7 +230,7 @@ public class ApplicationConfigurator {
 				BufferedWriter writer = new BufferedWriter(new FileWriter(fdaProperties));
 				PrintWriter w = new PrintWriter(writer);
 				
-	//			w.println("ch.psi.fda.aq.data.baseDirectory="+datadir.getAbsolutePath());
+				w.println("ch.psi.fda.aq.data.dir=../data");
 				w.println("ch.psi.fda.aq.data.filePrefix=${yyyy_MM}/${yyyyMMdd}/${yyyyMMddHHmmss}_${name}/${yyyyMMddHHmm}_");
 				
 				w.println();

ch.psi.fda/src/main/java/ch/psi/fda/rest/AcquisitionEngine.java

@@ -18,18 +18,18 @@
  */
 package ch.psi.fda.rest;
 
-import java.util.UUID;
-import java.util.concurrent.BlockingQueue;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.concurrent.CancellationException;
+import java.util.concurrent.ExecutionException;
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;
-import java.util.concurrent.LinkedBlockingQueue;
-import java.util.logging.Logger;
+import java.util.concurrent.Future;
+import java.util.concurrent.TimeUnit;
+import java.util.concurrent.TimeoutException;
 
 import javax.inject.Inject;
 
-import com.google.common.eventbus.EventBus;
-
-import ch.psi.fda.aq.Acquisition;
 import ch.psi.fda.aq.AcquisitionConfiguration;
 import ch.psi.fda.model.v1.Configuration;
 import ch.psi.jcae.ChannelService;
@@ -39,69 +39,18 @@ import ch.psi.jcae.ChannelService;
  */
 public class AcquisitionEngine {
 	
-	private static final Logger logger = Logger.getLogger(AcquisitionEngine.class.getName());
-
-	private AcquisitionConfiguration config;
-	private ChannelService cservice;
-	private final ZMQDataService dservice;
+	private final AcquisitionConfiguration config;
+	private final ChannelService cService;
+	private final ZMQDataService zmqService;
 	
-	/**
-	 * Variable holding the current acquisition
-	 */
-	private volatile Acquisition acquisition;
-	private volatile ExecutionRequest currentRequest;
-	
-	private ExecutorService eservice;
-	
-	
-	private BlockingQueue<ExecutionRequest> requests = new LinkedBlockingQueue<>();
+	private final ExecutorService eservice = Executors.newSingleThreadExecutor();
+	private final Map<String, Future<?>> erequests = new HashMap<>();
 	
 	@Inject
-	public AcquisitionEngine(ChannelService cservice, ZMQDataService dservice, AcquisitionConfiguration config) {
-		this.dservice = dservice;
-		this.cservice = cservice;
+	public AcquisitionEngine(ChannelService cService, ZMQDataService zmqService, AcquisitionConfiguration config) {
+		this.zmqService = zmqService;
+		this.cService = cService;
 		this.config = config;
-
-		// Start main execution loop 
-		eservice = Executors.newSingleThreadExecutor();
-		eservice.execute(new Runnable() {
-			@Override
-			public void run() {
-				try {
-					while (!Thread.currentThread().isInterrupted()) {
-						try {
-							ExecutionRequest r = requests.take();
-
-							logger.info("Execute - " + r.getTrackingId());
-
-							EventBus ebus = new EventBus();
-							// Provide tracking id to data service and register the service to the event bus
-							AcquisitionEngine.this.dservice.setTrackingId(r.getTrackingId()); 
-							ebus.register(AcquisitionEngine.this.dservice);
-
-							synchronized (AcquisitionEngine.this) { // synchronize access to acquisition object via the AcquisitionEngine object
-								acquisition = new Acquisition(AcquisitionEngine.this.cservice, AcquisitionEngine.this.config);
-								currentRequest = r;
-							}
-							acquisition.initalize(ebus, r.getConfiguration());
-							acquisition.execute();
-							logger.info("" + r.getTrackingId() + " done");
-							
-							// Cleanup
-							ebus.unregister(AcquisitionEngine.this.dservice);
-						} finally {
-							acquisition.destroy();
-							
-							synchronized (AcquisitionEngine.this) {
-								acquisition = null;
-								currentRequest = null;
-							}
-						}
-					}
-				} catch (InterruptedException e) {
-				}
-			}
-		});
 	}
 	
 	/**
@@ -111,27 +60,30 @@ public class AcquisitionEngine {
 	 * @param configuration
 	 * @return
 	 */
-	public String submit(Configuration configuration){
-		ExecutionRequest r = new ExecutionRequest(UUID.randomUUID().toString(), configuration);
-		try{
-			requests.put(r);
-		} catch (InterruptedException e) {
+	public void submit(String trackingId, Configuration configuration){
+
+		if(erequests.keySet().contains(trackingId) && !erequests.get(trackingId).isDone()){ // Allow finished tracking ids to be reused for new scans
+			throw new IllegalArgumentException("A request with tracking ID "+trackingId+" is already submitted");
 		}
-		return r.getTrackingId();
+		
+		AcquisitionJob job = new AcquisitionJob(cService, zmqService, config, trackingId, configuration);
+		Future<?> future = eservice.submit(job);
+		erequests.put(trackingId, future);
 	}
 	
 	
-	/**
-	 * Terminate the currently executed request
-	 */
-	public void terminate(){
-		synchronized(this){
-			if(acquisition==null){
-				return;
+	public void terminateAll() {
+		for(Future<?> f: erequests.values()){
+			f.cancel(true);
+		}
+		
+		for(Future<?> f: erequests.values()){
+			try{
+				f.get(10, TimeUnit.SECONDS);
+			}
+			catch(CancellationException | InterruptedException | ExecutionException | TimeoutException e){
+				// Nothing to be done here
 			}
-			
-			logger.info("Stop current acquisition");
-			acquisition.abort();
 		}
 	}
 	
@@ -142,29 +94,38 @@ public class AcquisitionEngine {
 	 */
 	public void terminate(String trackingId){
 		
-		// If request is currently executed terminate it
-		if(currentRequest.getTrackingId().equals(trackingId)){
-			terminate();
-			return;
+		final Future<?> f = erequests.get(trackingId);
+		if(f==null){
+			throw new IllegalArgumentException("There is no request running/pending with tracking id "+trackingId);
 		}
-		
-		// Remove request from request queue
-		ExecutionRequest rremove = null;
-		for(ExecutionRequest r:requests){
-			if(r.getTrackingId().equals(trackingId)){
-				rremove = r; // We have to split the filtering and termination as we otherwise get a concurrent access exception.
-				break;
-			}
+		f.cancel(true);
+		try{
+			f.get(10, TimeUnit.SECONDS);
 		}
-		if(rremove!=null){
-			boolean b = requests.remove(rremove);
-			// There is a chance that between the upper loop and here the request
-			// already got dequeued. This check ensures that the requests got removed
-			// if not it got dequeued and therefore we have to terminate the current
-			// execution.
-			if(!b){ 
-				terminate();
-			}
+		catch(CancellationException | InterruptedException | ExecutionException | TimeoutException e){
+			// Nothing to be done here
 		}
 	}
+
+	public boolean isActive(String trackingId) {
+		Future<?> f = erequests.get(trackingId);
+		if(f==null){
+			throw new IllegalArgumentException("There is no request for tracking id "+trackingId);
+		}
+		return !f.isDone();
+	}
+	
+	/**
+	 * Wait for the termination of the scan request
+	 * @param trackingId
+	 * @throws ExecutionException 
+	 * @throws InterruptedException 
+	 */
+	public void wait(String trackingId) throws InterruptedException, ExecutionException{
+		Future<?> f = erequests.get(trackingId);
+		if(f==null){
+			throw new IllegalArgumentException("There is no request for tracking id "+trackingId);
+		}
+		f.get();
+	}
 }

ch.psi.fda/src/main/java/ch/psi/fda/rest/AcquisitionJob.java

@@ -0,0 +1,80 @@
+/**
+ * 
+ * Copyright 2014 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ * 
+ * This code is distributed in the hope that it will be useful, but without any
+ * warranty; without even the implied warranty of merchantability or fitness for
+ * a particular purpose. See the GNU Lesser General Public License for more
+ * details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+package ch.psi.fda.rest;
+
+import java.util.logging.Logger;
+
+import ch.psi.fda.aq.Acquisition;
+import ch.psi.fda.aq.AcquisitionConfiguration;
+import ch.psi.fda.model.v1.Configuration;
+import ch.psi.jcae.ChannelService;
+
+import com.google.common.eventbus.EventBus;
+
+public class AcquisitionJob implements Runnable {
+
+	private static final Logger logger = Logger.getLogger(AcquisitionJob.class.getName());
+
+	private final AcquisitionConfiguration config;
+	private final ChannelService cService;
+	private final ZMQDataService zmqService;
+
+	private final String trackingId;
+	private final Configuration configuration;
+
+	public AcquisitionJob(ChannelService cService, ZMQDataService zmqService, AcquisitionConfiguration config, String trackingId, Configuration configuration) {
+		this.zmqService = zmqService;
+		this.cService = cService;
+		this.config = config;
+
+		this.trackingId = trackingId;
+		this.configuration = configuration;
+	}
+
+	@Override
+	public void run() {
+
+		Acquisition acquisition = null;
+		try {
+
+			logger.info("Execute - " + trackingId);
+
+			EventBus ebus = new EventBus();
+			zmqService.setTrackingId(trackingId);
+			ebus.register(zmqService);
+
+			// Post visualization configuration
+			ebus.post(configuration.getVisualization());
+			
+			acquisition = new Acquisition(cService, config);
+			acquisition.initalize(ebus, configuration);
+			acquisition.execute();
+			logger.info("" + trackingId + " done");
+
+			// Cleanup
+			ebus.unregister(zmqService);
+		} catch (InterruptedException e) {
+			logger.info("Execution of "+trackingId+ " was interrupted");
+		} finally {
+			if(acquisition!=null){
+				acquisition.destroy();
+			}
+		}
+	}
+}

ch.psi.fda/src/main/java/ch/psi/fda/rest/CdumpEngine.java

@@ -0,0 +1,99 @@
+/**
+ * 
+ * Copyright 2014 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ * 
+ * This code is distributed in the hope that it will be useful, but without any
+ * warranty; without even the implied warranty of merchantability or fitness for
+ * a particular purpose. See the GNU Lesser General Public License for more
+ * details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+package ch.psi.fda.rest;
+
+import java.io.File;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+
+import javax.inject.Inject;
+
+import ch.psi.fda.cdump.Cdump;
+import ch.psi.fda.cdump.CdumpConfiguration;
+import ch.psi.fda.rest.model.CdumpRequest;
+import ch.psi.fda.serializer.SerializerTXT;
+import ch.psi.jcae.ChannelService;
+
+import com.google.common.eventbus.AsyncEventBus;
+import com.google.common.eventbus.EventBus;
+
+public class CdumpEngine {
+
+	private Cdump cdump;
+	private EventBus bus;
+	
+	private ZMQDataService zmqService;
+	private ChannelService cservice;
+	private CdumpConfiguration configuration;
+	
+	private boolean stream = false;
+	
+	private ExecutorService eservice;
+	
+	
+	@Inject
+	public CdumpEngine(ChannelService cservice, ZMQDataService zmqService, CdumpConfiguration configuration){
+		this.cservice = cservice;
+		this.zmqService = zmqService;
+		this.configuration = configuration;
+		
+		eservice = Executors.newSingleThreadExecutor();
+	}
+	
+	
+	public void acquire(String trackingId, final CdumpRequest request){
+		if(cdump!=null){
+			throw new IllegalStateException("Cdump is already running");
+		}
+		
+		bus = new AsyncEventBus(Executors.newSingleThreadExecutor());
+		cdump = new Cdump(cservice,bus,configuration);
+
+		SerializerTXT serializer = new SerializerTXT(new File(request.getFilename()));
+		serializer.setShowDimensionHeader(false);
+		bus.register(serializer);
+		
+		stream = (request.getStream()!=null && request.getStream().getIds().length>0) ;
+		if(stream){
+			// Stream data via ZMQ
+			zmqService.setTrackingId(trackingId);
+			// TODO set id filter !!!
+			bus.register(zmqService);
+		}
+		
+		eservice.execute(new Runnable() {
+			@Override
+			public void run() {
+				cdump.acquire(request.getSamplingRate());
+			}
+		});
+	}
+	
+	
+	public void stop(){
+		cdump.stop();
+		cdump = null;
+		bus.unregister(zmqService);
+	}
+	
+	
+	public boolean isActive(){
+		return cdump!=null;
+	}
+}

ch.psi.fda/src/main/java/ch/psi/fda/rest/FdaServer.java

@@ -18,22 +18,24 @@ import org.glassfish.jersey.jackson.JacksonFeature;
 import org.glassfish.jersey.server.ResourceConfig;
 import org.glassfish.grizzly.http.server.HttpServer;
 
+import ch.psi.fda.install.ApplicationConfigurator;
 import sun.misc.Signal;
 import sun.misc.SignalHandler;
 
 @SuppressWarnings("restriction")
-public class RestServer {
+public class FdaServer {
 	
-	private static final Logger logger = Logger.getLogger(RestServer.class.getName());
+	private static final Logger logger = Logger.getLogger(FdaServer.class.getName());
 
 	public static void main(String[] args) throws IOException, ParseException {
 
-		// Option handling
 		int port = 8080;
+		String hostname = InetAddress.getLocalHost().getHostName();
 
 		Options options = new Options();
 		options.addOption("h", false, "Help");
 		options.addOption("p", true, "Server port (default: "+port+")");
+		options.addOption("s", true, "Server address (default: "+hostname+")");
 
 		GnuParser parser = new GnuParser();
 		CommandLine line = parser.parse(options, args);
@@ -41,35 +43,44 @@ public class RestServer {
 		if (line.hasOption("p")) {
 			port = Integer.parseInt(line.getOptionValue("p"));
 		}
+		if (line.hasOption("s")) {
+			hostname = line.getOptionValue("s");
+		}
 		if (line.hasOption("h")) {
 			HelpFormatter f = new HelpFormatter();
-			f.printHelp("broker", options);
+			f.printHelp("fda", options);
 			return;
 		}
 
-		URI baseUri = UriBuilder.fromUri("http://" + InetAddress.getLocalHost().getHostName() + "/").port(port).build();
+		// set the correct environment variable based on ch.psi.fda.home variable
+		ApplicationConfigurator ac = new ApplicationConfigurator();
+		ac.initializeApplication();
+		
+		URI baseUri = UriBuilder.fromUri("http://" + hostname + "/").port(port).build();
 
-		
-//		Broker broker = createBroker(config);
-		
-		
 		ResourceBinder binder = new ResourceBinder();
 		
-		ResourceConfig resourceConfig = new ResourceConfig(JacksonFeature.class);
-		resourceConfig.packages(RestServer.class.getPackage().getName()+".services"); // Services are located in services package
+		ResourceConfig resourceConfig = new ResourceConfig();
+		resourceConfig.packages(FdaServer.class.getPackage().getName()+".services"); // Services are located in services package
 		resourceConfig.register(binder);
+		
+		resourceConfig.register(JacksonFeature.class);
+		
+		
 		HttpServer server = GrizzlyHttpServerFactory.createHttpServer(baseUri, resourceConfig);
 
+		
+		
 		// Static content
-//		String home = System.getenv("BROKER_BASE");
+//		String home = System.getenv("FDA_BASE");
 //		if (home == null) {
 //			home = "src/main/assembly";
 //		}
 //		home = home + "/www";
 //		server.getServerConfiguration().addHttpHandler(new StaticHttpHandler(home), "/static");
-
-		logger.info("Broker started");
 //		logger.info(String.format("Management interface available at %sstatic/", baseUri));
+
+		logger.info("Server started");
 		logger.info("Use ctrl+c to stop ...");
 
 		// Signal handling
@@ -89,10 +100,9 @@ public class RestServer {
 			latch.await();
 		} catch (InterruptedException e) {
 		}
-
-		server.stop();
-		
-//		broker.terminate();
 		
+		server.shutdownNow();
+		logger.info("Server terminated");
+		System.exit(0); // TODO need to shutdown ChannelService correctly !!!!
 	}
 }

ch.psi.fda/src/main/java/ch/psi/fda/rest/FdaqEngine.java

@@ -0,0 +1,90 @@
+/**
+ * 
+ * Copyright 2014 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ * 
+ * This code is distributed in the hope that it will be useful, but without any
+ * warranty; without even the implied warranty of merchantability or fitness for
+ * a particular purpose. See the GNU Lesser General Public License for more
+ * details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+package ch.psi.fda.rest;
+
+import java.io.File;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+
+import javax.inject.Inject;
+
+import ch.psi.fda.fdaq.FdaqConfiguration;
+import ch.psi.fda.fdaq.FdaqService;
+import ch.psi.fda.rest.model.FdaqRequest;
+import ch.psi.fda.serializer.SerializerTXT;
+
+import com.google.common.eventbus.AsyncEventBus;
+import com.google.common.eventbus.EventBus;
+
+/**
+ * 
+ */
+public class FdaqEngine {
+
+	private FdaqService fdaq;
+	private EventBus bus;
+	private ZMQDataService zmqService;
+	private boolean stream = false;
+	
+	private ExecutorService eservice;
+	
+	@Inject
+	public FdaqEngine(ZMQDataService zmqService){
+		this.zmqService = zmqService;
+		
+		eservice = Executors.newSingleThreadExecutor();
+	}
+	
+	public void acquire(String trackingId, FdaqRequest request){
+		
+		if(fdaq!=null && fdaq.isRunning()){
+			throw new IllegalStateException("FDAQ is already running");
+		}
+		
+		bus = new AsyncEventBus(Executors.newSingleThreadExecutor());
+		fdaq = new FdaqService(bus, new FdaqConfiguration());
+
+		SerializerTXT serializer = new SerializerTXT(new File(request.getFilename()));
+		serializer.setShowDimensionHeader(false);
+		bus.register(serializer);
+		
+		stream = (request.getStream()!=null && request.getStream().getIds().length>0) ;
+		if(stream){
+			// Stream data via ZMQ
+			zmqService.setTrackingId(trackingId);
+			// TODO Set id filter !!!!
+			bus.register(zmqService);
+		}
+		
+		
+		eservice.execute(new Runnable() {
+			@Override
+			public void run() {
+				fdaq.acquire();
+			}
+		});
+	}
+	
+	public void stop(){
+		fdaq.stop();
+		bus.unregister(zmqService);
+
+		// TODO check whether serializer also needs to be unregistered ...
+	}
+}

ch.psi.fda/src/main/java/ch/psi/fda/rest/ResourceBinder.java

@@ -1,11 +1,13 @@
 package ch.psi.fda.rest;
 
 
+
 import javax.inject.Singleton;
 
 import org.glassfish.hk2.utilities.binding.AbstractBinder;
 
 import ch.psi.fda.aq.AcquisitionConfiguration;
+import ch.psi.fda.cdump.CdumpConfiguration;
 import ch.psi.jcae.ChannelService;
 import ch.psi.jcae.impl.DefaultChannelService;
 
@@ -15,8 +17,14 @@ public class ResourceBinder extends AbstractBinder {
     protected void configure() {
     	bind(DefaultChannelService.class).to(ChannelService.class).in(Singleton.class);
     	bind(AcquisitionConfiguration.class).to(AcquisitionConfiguration.class).in(Singleton.class);
+    	
     	bind(AcquisitionEngine.class).to(AcquisitionEngine.class).in(Singleton.class);
-    	bind(ZMQDataService.class).to(ZMQDataService.class).in(Singleton.class);
+    	bind(FdaqEngine.class).to(FdaqEngine.class).in(Singleton.class);
+   
+    	// ZMQ data service singleton
+    	bind(new ZMQDataService(10000)).to(ZMQDataService.class);
+    	
+    	bind(CdumpEngine.class).to(CdumpEngine.class).in(Singleton.class);
+    	bind(CdumpConfiguration.class).to(CdumpConfiguration.class).in(Singleton.class);
     }
-
 }

ch.psi.fda/src/main/java/ch/psi/fda/rest/ZMQDataService.java

@@ -21,12 +21,14 @@ package ch.psi.fda.rest;
 import java.io.ByteArrayOutputStream;
 import java.io.IOException;
 import java.io.ObjectOutputStream;
+import java.util.List;
 import java.util.logging.Level;
 import java.util.logging.Logger;
 
 import org.jeromq.ZMQ;
 
-import ch.psi.fda.core.messages.Message;
+import ch.psi.fda.messages.Message;
+import ch.psi.fda.model.v1.Visualization;
 
 import com.google.common.eventbus.Subscribe;
 
@@ -39,13 +41,15 @@ public class ZMQDataService {
 	private static final Logger logger = Logger.getLogger(ZMQDataService.class.getName());
 	
 	private final int bufferSize = 5;
+	private final int port;
 	
 	private ZMQ.Context context;
 	private ZMQ.Socket socket;
 	
 	private String trackingId;
 	
-	public ZMQDataService(){
+	public ZMQDataService(int port){
+		this.port = port;
 		initialize();
 	}
 
@@ -54,7 +58,7 @@ public class ZMQDataService {
 		zmq.ZError.clear(); // Clear error code
 		socket = context.socket(ZMQ.PUB);
 		socket.setHWM(bufferSize);
-		socket.bind("tcp://*:10000");
+		socket.bind("tcp://*:"+port);
 	}
 	
 	public void terminate(){
@@ -65,8 +69,8 @@ public class ZMQDataService {
 	
 	@Subscribe
 	public void onMessage(Message m) {
-		logger.info(m.toString());
-		socket.sendMore("{\"trackingId\":\"" + trackingId + "\"}");
+		logger.fine(m.toString());
+		socket.sendMore("{\"htype\": [\"fda-2.1\"], \"trackingId\":\"" + trackingId + "\"}");
 		try (
 				ByteArrayOutputStream b = new ByteArrayOutputStream(); 
 				ObjectOutputStream o = new ObjectOutputStream(b);
@@ -78,6 +82,20 @@ public class ZMQDataService {
 		}
 	}
 	
+	@Subscribe
+	public void onMessage(List<Visualization> vis){
+		logger.fine("Sending plotting filters");
+		socket.sendMore("{\"htype\": [\"fda-plot-2.1\"], \"trackingId\":\"" + trackingId + "\"}");
+		try (
+				ByteArrayOutputStream b = new ByteArrayOutputStream(); 
+				ObjectOutputStream o = new ObjectOutputStream(b);
+			) {
+			o.writeObject(vis);
+			socket.send(b.toByteArray());
+		} catch (IOException e) {
+			logger.log(Level.WARNING, "Unable to serialize message", e);
+		}
+	}
 	
 	public void setTrackingId(String id){
 		trackingId = id;

ch.psi.fda/src/main/java/ch/psi/fda/rest/client/ControlClient.java

@@ -0,0 +1,57 @@
+/**
+ * 
+ * Copyright 2013 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ * 
+ * This code is distributed in the hope that it will be useful, but without any
+ * warranty; without even the implied warranty of merchantability or fitness for
+ * a particular purpose. See the GNU Lesser General Public License for more
+ * details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+package ch.psi.fda.rest.client;
+
+import javax.ws.rs.client.Client;
+import javax.ws.rs.client.ClientBuilder;
+import javax.ws.rs.client.Entity;
+import javax.ws.rs.client.WebTarget;
+import javax.ws.rs.core.MediaType;
+import javax.xml.bind.JAXBElement;
+import javax.xml.namespace.QName;
+
+import org.glassfish.jersey.jackson.JacksonFeature;
+
+import ch.psi.fda.model.v1.Configuration;
+
+public class ControlClient {
+	
+	private Client client = ClientBuilder.newClient().register(JacksonFeature.class);
+	private WebTarget target = client.target("http://emac:8080").path("fda");
+	 
+
+	 
+	public String acquire(String trackingId, Configuration c){
+		// Wrap configuration in JAXBElement as there is no @XmlRootElement available within the generated Configuration class
+		JAXBElement<Configuration> jaxbElement = new JAXBElement<>(new QName("ROOT"), Configuration.class, c);
+		return target.path(trackingId).request().put(Entity.entity(jaxbElement, MediaType.APPLICATION_XML), String.class);
+	}
+	
+	public void terminate(String trackingId){
+		target.path(trackingId).request().delete();
+	}
+	
+	public void terminateAll(){
+		target.request().delete();
+	}
+	
+	public boolean isActive(String trackingId){
+		return target.path(trackingId).path("running").request().get(Boolean.class);
+	}
+}

ch.psi.fda/src/main/java/ch/psi/fda/rest/client/RemoteAcquisitionMain.java

@@ -0,0 +1,315 @@
+/**
+ * 
+ * Copyright 2010 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ * 
+ * This code is distributed in the hope that it will be useful, but without any
+ * warranty; without even the implied warranty of merchantability or fitness for
+ * a particular purpose. See the GNU Lesser General Public License for more
+ * details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
+package ch.psi.fda.rest.client;
+
+import java.awt.FlowLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.io.File;
+import java.io.PrintWriter;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.UUID;
+import java.util.concurrent.Executors;
+import java.util.concurrent.atomic.AtomicInteger;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+import javax.swing.JFrame;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JSplitPane;
+import javax.swing.JTabbedPane;
+import javax.swing.ScrollPaneLayout;
+
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.CommandLineParser;
+import org.apache.commons.cli.GnuParser;
+import org.apache.commons.cli.HelpFormatter;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.OptionBuilder;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
+
+import com.google.common.eventbus.AsyncEventBus;
+import com.google.common.eventbus.EventBus;
+
+import sun.misc.Signal;
+import sun.misc.SignalHandler;
+import ch.psi.fda.aq.VisualizationMapper;
+import ch.psi.fda.gui.ProgressPanel;
+import ch.psi.fda.gui.ScrollableFlowPanel;
+import ch.psi.fda.model.ModelManager;
+import ch.psi.fda.model.v1.Configuration;
+import ch.psi.fda.model.v1.Data;
+import ch.psi.fda.visualizer.Visualizer;
+
+@SuppressWarnings("restriction")
+public class RemoteAcquisitionMain {
+
+	private static Logger logger = Logger.getLogger(RemoteAcquisitionMain.class.getName());
+
+	StreamClient streamClient = null;
+	private String trackingId;
+	
+	/**
+	 * Main Program Process exit code: -1 if wrong number of arguments are
+	 * passed Process exit code: 3 if aborted via Ctrl+C
+	 * 
+	 * @param args
+	 *            Arguments of the program
+	 */
+	public static void main(String[] args) {
+
+		String scriptname = "fda_scan";
+
+		Integer iterations = null;
+		boolean nogui = false;
+		List<File> files = new ArrayList<>();
+
+		OptionBuilder.hasArg();
+		OptionBuilder.withArgName("iterations");
+		OptionBuilder.withDescription("Number of iterations");
+		OptionBuilder.withType(new Integer(1));
+		Option o_iterations = OptionBuilder.create("iterations");
+
+		Option o_nogui = new Option("nogui", "Do not show scan GUI");
+
+		Options options = new Options();
+		options.addOption(o_iterations);
+		options.addOption(o_nogui);
+
+		CommandLineParser parser = new GnuParser();
+		try {
+			CommandLine line = parser.parse(options, args);
+
+			if (line.getArgs().length < 1) {
+				throw new ParseException("One argument is required");
+			}
+
+			if (line.hasOption(o_iterations.getOpt())) {
+				iterations = Integer.parseInt(line.getOptionValue(o_iterations.getOpt()));
+			}
+
+			if (line.hasOption(o_nogui.getOpt())) {
+				nogui = true;
+			}
+
+			for (String f : line.getArgs()) {
+				File file = new File(f);
+				if (!file.exists()) {
+					throw new RuntimeException("File " + file.getAbsolutePath() + " does not exist");
+				}
+				files.add(file);
+			}
+
+		} catch (ParseException e) {
+			System.err.println(e.getMessage());
+			HelpFormatter formatter = new HelpFormatter();
+			formatter.printUsage(new PrintWriter(System.out, true), HelpFormatter.DEFAULT_WIDTH, scriptname, options);
+			System.exit(-1);
+		}
+
+		try {
+			for (File file : files) {
+				RemoteAcquisitionMain m = new RemoteAcquisitionMain();
+				m.execute(file, iterations, nogui);
+			}
+		} catch (Exception ee) {
+			logger.log(Level.SEVERE, "Acquisition failed due to: ", ee);
+			System.exit(-1);
+		}
+	}
+
+	
+	/**
+	 * Execute the given scan on the server
+	 * @param file
+	 * @param iterations
+	 * @param nogui
+	 */
+	public void execute(File file, Integer iterations, boolean nogui) {
+
+		trackingId = UUID.randomUUID().toString(); 
+		logger.info("TrackingID of job: " + trackingId);
+		
+		
+		Configuration c;
+		try {
+			c = ModelManager.unmarshall(file);
+		} catch (Exception e) {
+			throw new RuntimeException("Unable to deserialize configuration: " + e.getMessage(), e);
+		}
+
+		// Set data file name
+		// Determine name used for the data file
+		String name = file.getName();
+		name = name.replaceAll("\\.xml$", "");
+
+		if (c.getData() != null) {
+			Data data = c.getData();
+			// Only update filename if no name is specified in xml file
+			if (data.getFileName() == null) {
+				data.setFileName(name);
+			}
+		} else {
+			Data data = new Data();
+			data.setFileName(name);
+			c.setData(data);
+		}
+
+		// Override number of executions
+		if (iterations != null) {
+			c.setNumberOfExecution(iterations);
+		}
+		// Fix configuration if iterations is specified with 0 and no iterations
+		// option is specified
+		if (c.getNumberOfExecution() == 0) {
+			c.setNumberOfExecution(1);
+		}
+
+
+		EventBus b = new AsyncEventBus(Executors.newSingleThreadExecutor());
+		final ControlClient client = new ControlClient();
+		 
+
+		
+		if (!nogui && c.getVisualization().size() > 0) {
+		
+			streamClient = new StreamClient(b);
+
+			Visualizer visualizer = new Visualizer(VisualizationMapper.mapVisualizations(c.getVisualization()));
+			visualizer.configure();
+			b.register(visualizer);
+
+			// If there is a continuous dimension only update plot at the end of a line
+			if (c.getScan() != null && c.getScan().getCdimension() != null) {
+				visualizer.setUpdateAtStreamElement(false);
+				visualizer.setUpdateAtStreamDelimiter(true);
+				visualizer.setUpdateAtEndOfStream(true);
+			}
+
+			JPanel opanel = new ScrollableFlowPanel();
+			opanel.setLayout(new FlowLayout());
+
+			JScrollPane spane = new JScrollPane(opanel, ScrollPaneLayout.VERTICAL_SCROLLBAR_AS_NEEDED, ScrollPaneLayout.HORIZONTAL_SCROLLBAR_NEVER);
+			JTabbedPane tpane = new JTabbedPane();
+			tpane.addTab("Overview", spane);
+
+			for (JPanel p : visualizer.getPlotPanels()) {
+				opanel.add(p);
+			}
+
+			final JFrame frame = new JFrame("FDA: " + file);
+			frame.setSize(1200, 800);
+
+			final ProgressPanel progressPanel = new ProgressPanel();
+			progressPanel.addActionListener(new ActionListener() {
+
+				@Override
+				public void actionPerformed(ActionEvent e) {
+					try {
+						client.terminate(trackingId);
+					} catch (Exception e1) {
+						logger.log(Level.SEVERE, "Exception occured while aborting scan", e1);
+					} finally {
+						progressPanel.done();
+					}
+
+				}
+			});
+
+			JSplitPane splitPane = new JSplitPane();
+			splitPane.setLeftComponent(progressPanel);
+			splitPane.setRightComponent(tpane);
+
+			frame.add(splitPane);
+			frame.addWindowListener(new WindowAdapter() {
+				@Override
+				public void windowClosing(WindowEvent we) {
+					client.terminate(trackingId);
+
+					int count = 0;
+					while (client.isActive(trackingId)) {
+						if (count == 10) {
+							break;
+						}
+
+						try {
+							Thread.sleep(100);
+						} catch (InterruptedException e) {
+						}
+						count++;
+					}
+
+					System.exit(0);
+				}
+			});
+			frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); // .DO_NOTHING_ON_CLOSE);
+
+			java.awt.EventQueue.invokeLater(new Runnable() {
+				public void run() {
+					frame.setVisible(true);
+				}
+			});
+		}
+
+		
+		
+		Signal.handle(new Signal("INT"), new SignalHandler() {
+
+			private AtomicInteger signalCount = new AtomicInteger(0);
+
+			@Override
+			public void handle(Signal signal) {
+
+				logger.finest("Received signal: " + signal);
+
+				try{
+					client.terminate(trackingId);
+				}
+				catch(Exception e){
+					logger.log(Level.WARNING, "Stopping scan failed with exception", e);
+				}
+				
+				if (signalCount.incrementAndGet() > 1) {
+					logger.info("Terminate application");
+					System.exit(2);
+				}
+			}
+		});
+
+		
+		
+		if(streamClient!=null){
+			streamClient.filterTrackingId(trackingId);
+			Executors.newSingleThreadExecutor().execute(new Runnable() {
+				@Override
+				public void run() {
+					streamClient.listen("tcp://emac:10000");
+				}
+			});
+		}
+		
+		client.acquire(trackingId, c);
+	}
+}

ch.psi.fda/src/main/java/ch/psi/fda/rest/client/StreamClient.java

@@ -0,0 +1,98 @@
+/**
+ * 
+ * Copyright 2013 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ * 
+ * This code is distributed in the hope that it will be useful, but without any
+ * warranty; without even the implied warranty of merchantability or fitness for
+ * a particular purpose. See the GNU Lesser General Public License for more
+ * details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+package ch.psi.fda.rest.client;
+
+import java.io.ByteArrayInputStream;
+import java.io.IOException;
+import java.io.ObjectInput;
+import java.io.ObjectInputStream;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+import org.codehaus.jackson.JsonFactory;
+import org.codehaus.jackson.map.ObjectMapper;
+import org.codehaus.jackson.type.TypeReference;
+import org.jeromq.ZMQ;
+
+import com.google.common.eventbus.EventBus;
+
+public class StreamClient {
+
+	private static final Logger logger = Logger.getLogger(StreamClient.class.getName());
+	private ObjectMapper mapper = new ObjectMapper(new JsonFactory());
+	
+	
+	private final EventBus bus;
+	private String trackingIdFilter = null;
+
+	public StreamClient(EventBus bus) {
+		this.bus = bus;
+	}
+	
+	public void listen(String endpoint) {
+		ZMQ.Context context = ZMQ.context();
+		zmq.ZError.clear(); // Clear error code
+		ZMQ.Socket socket = context.socket(ZMQ.SUB);
+		socket.connect(endpoint);
+		socket.subscribe(""); // SUBSCRIBE !
+
+		while (true) {
+			String tid = null;
+			
+			byte[] content = null;
+			byte[] header = socket.recv(); // header
+			if(trackingIdFilter!=null){
+				try {
+					Map<String,Object> m = mapper.readValue(header, new TypeReference<HashMap<String,Object>>(){});
+					tid = (String) m.get("trackingId");
+				} catch (IOException e) {
+				}
+			}
+			while (socket.hasReceiveMore()) {
+				content = socket.recv();
+			}
+			if (content == null) { // we lost something discard read messages
+				logger.warning("Lost some message - discard and continue");
+				continue;
+			}
+
+			if(tid!=null && !tid.matches(trackingIdFilter)){
+				continue;
+			}
+			
+			try (ByteArrayInputStream bis = new ByteArrayInputStream(content); ObjectInput in = new ObjectInputStream(bis);) {
+				Object o = in.readObject();
+				bus.post(o);
+			} catch (IOException | ClassNotFoundException e) {
+				logger.log(Level.WARNING, "Unable to deserialize message", e);
+			}
+
+		}
+	}
+
+	public String getTrackingIdFilter() {
+		return trackingIdFilter;
+	}
+
+	public void filterTrackingId(String trackingId) {
+		this.trackingIdFilter = trackingId;
+	}
+}

ch.psi.fda/src/main/java/ch/psi/fda/rest/model/CdumpRequest.java

@@ -0,0 +1,48 @@
+/**
+ * 
+ * Copyright 2014 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ * 
+ * This code is distributed in the hope that it will be useful, but without any
+ * warranty; without even the implied warranty of merchantability or fitness for
+ * a particular purpose. See the GNU Lesser General Public License for more
+ * details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+package ch.psi.fda.rest.model;
+
+import javax.xml.bind.annotation.XmlRootElement;
+
+@XmlRootElement
+public class CdumpRequest {
+	private String filename;
+	private Stream stream;
+	
+	private String samplingRate;
+
+	public String getFilename() {
+		return filename;
+	}
+	public void setFilename(String filename) {
+		this.filename = filename;
+	}
+	public Stream getStream() {
+		return stream;
+	}
+	public void setStream(Stream stream) {
+		this.stream = stream;
+	}
+	public String getSamplingRate() {
+		return samplingRate;
+	}
+	public void setSamplingRate(String samplingRate) {
+		this.samplingRate = samplingRate;
+	}
+}

ch.psi.fda/src/main/java/ch/psi/fda/rest/model/ERequest.java

@@ -0,0 +1,74 @@
+/**
+ * 
+ * Copyright 2014 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ * 
+ * This code is distributed in the hope that it will be useful, but without any
+ * warranty; without even the implied warranty of merchantability or fitness for
+ * a particular purpose. See the GNU Lesser General Public License for more
+ * details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+package ch.psi.fda.rest.model;
+
+import javax.xml.bind.annotation.XmlRootElement;
+
+import org.codehaus.jackson.map.annotate.JsonDeserialize;
+
+/**
+ * Execution request
+ */
+@XmlRootElement
+@JsonDeserialize(using = ERequestJsonDeserializer.class)
+public class ERequest {
+	
+	/**
+	 * List of ids to stream
+	 */
+	private Stream stream;
+	
+	/**
+	 * Execution type: scan, fdaq, cdump
+	 */
+	private String etype;
+	
+	/**
+	 * Json string holding the executions' configuration. It will interpreted differently based on the specified etype
+	 * 
+	 * Use adapter ???? https://www.google.ch/url?sa=t&rct=j&q=&esrc=s&source=web&cd=6&cad=rja&ved=0CFgQFjAF&url=http%3A%2F%2Fblog.bdoughan.com%2F2012%2F01%2Fjaxb-and-inhertiance-using-xmladapter.html&ei=GfrMUtzTNsGp7AbykYDQDw&usg=AFQjCNG3xDZKYLYV6Ez-EvvJe_AIYE5EHA&sig2=ND5Epp90O-FWrJI4T3zyCw&bvm=bv.58187178,d.ZGU
+	 */
+	private String configuration;
+
+	public Stream getStream() {
+		return stream;
+	}
+
+	public void setStream(Stream stream) {
+		this.stream = stream;
+	}
+
+	public String getEtype() {
+		return etype;
+	}
+
+	public void setEtype(String etype) {
+		this.etype = etype;
+	}
+
+	public String getConfiguration() {
+		return configuration;
+	}
+
+	public void setConfiguration(String configuration) {
+		this.configuration = configuration;
+	}
+	
+	
+}

ch.psi.fda/src/main/java/ch/psi/fda/rest/model/ERequestJsonDeserializer.java

@@ -0,0 +1,30 @@
+package ch.psi.fda.rest.model;
+
+import java.io.IOException;
+
+import org.codehaus.jackson.JsonNode;
+import org.codehaus.jackson.JsonParser;
+import org.codehaus.jackson.JsonProcessingException;
+import org.codehaus.jackson.map.DeserializationContext;
+import org.codehaus.jackson.map.JsonDeserializer;
+
+class ERequestJsonDeserializer extends JsonDeserializer<ERequest> {
+
+    @Override
+    public ERequest deserialize(JsonParser jp, DeserializationContext ctxt) throws IOException, JsonProcessingException {
+    	
+    	ERequest request = new ERequest();
+    	
+    	JsonNode node = jp.readValueAsTree();
+    	request.setEtype(node.get("etype").asText());
+    	request.setStream(jp.getCodec().treeToValue(node.get("stream"), Stream.class));
+
+    	request.setConfiguration(node.get("configuration").toString());
+    	
+//        Class<? extends ERe> concreteType = determineConcreteType(node); //Implement 
+//        return jp.getCodec().treeToValue(node, concreteType);
+//    	
+//        return jp.readValueAsTree().toString();
+    	return request;
+    }
+}

ch.psi.fda/src/main/java/ch/psi/fda/rest/model/FdaqRequest.java

@@ -0,0 +1,40 @@
+/**
+ * 
+ * Copyright 2014 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ * 
+ * This code is distributed in the hope that it will be useful, but without any
+ * warranty; without even the implied warranty of merchantability or fitness for
+ * a particular purpose. See the GNU Lesser General Public License for more
+ * details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+package ch.psi.fda.rest.model;
+
+import javax.xml.bind.annotation.XmlRootElement;
+
+@XmlRootElement
+public class FdaqRequest {
+	private String filename;
+	private Stream stream;
+
+	public String getFilename() {
+		return filename;
+	}
+	public void setFilename(String filename) {
+		this.filename = filename;
+	}
+	public Stream getStream() {
+		return stream;
+	}
+	public void setStream(Stream stream) {
+		this.stream = stream;
+	}
+}

ch.psi.fda/src/main/java/ch/psi/fda/rest/model/Stream.java

@@ -0,0 +1,31 @@
+/**
+ * 
+ * Copyright 2014 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ * 
+ * This code is distributed in the hope that it will be useful, but without any
+ * warranty; without even the implied warranty of merchantability or fitness for
+ * a particular purpose. See the GNU Lesser General Public License for more
+ * details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+package ch.psi.fda.rest.model;
+
+public class Stream {
+	private String[] ids;
+
+	public String[] getIds() {
+		return ids;
+	}
+
+	public void setIds(String[] ids) {
+		this.ids = ids;
+	}
+}

ch.psi.fda/src/main/java/ch/psi/fda/rest/services/CDUMPService.java

@@ -0,0 +1,63 @@
+/**
+ * 
+ * Copyright 2013 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ * 
+ * This code is distributed in the hope that it will be useful, but without any
+ * warranty; without even the implied warranty of merchantability or fitness for
+ * a particular purpose. See the GNU Lesser General Public License for more
+ * details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
+package ch.psi.fda.rest.services;
+
+import javax.inject.Inject;
+import javax.ws.rs.Consumes;
+import javax.ws.rs.DELETE;
+import javax.ws.rs.GET;
+import javax.ws.rs.PUT;
+import javax.ws.rs.Path;
+import javax.ws.rs.PathParam;
+import javax.ws.rs.core.MediaType;
+
+import ch.psi.fda.rest.CdumpEngine;
+import ch.psi.fda.rest.model.CdumpRequest;
+
+@Path("cdump")
+public class CDUMPService {
+
+	@Inject
+	private CdumpEngine cdumpE;
+	
+	@PUT
+	@Path("{trackingId}")
+	@Consumes({MediaType.APPLICATION_JSON, MediaType.APPLICATION_XML})
+	public void execute(@PathParam("trackingId") String trackingId, CdumpRequest request) throws InterruptedException{
+		cdumpE.acquire(trackingId, request);
+	}
+	
+	@DELETE
+	@Path("{trackingId}")
+	public void stop(@PathParam("trackingId") String trackingId){
+		terminateAll();
+	}
+	
+	@DELETE
+	public void terminateAll(){
+		cdumpE.stop();
+	}
+	
+	@GET
+	public boolean isActive(){
+		return cdumpE.isActive();
+	}
+	
+}

ch.psi.fda/src/main/java/ch/psi/fda/rest/services/FDAQService.java

@@ -19,31 +19,40 @@
 
 package ch.psi.fda.rest.services;
 
+
 import javax.inject.Inject;
 import javax.ws.rs.Consumes;
 import javax.ws.rs.DELETE;
-import javax.ws.rs.POST;
+import javax.ws.rs.PUT;
 import javax.ws.rs.Path;
+import javax.ws.rs.PathParam;
 import javax.ws.rs.core.MediaType;
 
-import ch.psi.fda.model.v1.Configuration;
-import ch.psi.fda.rest.AcquisitionEngine;
 
-@Path("fda")
-public class ScanService {
+import ch.psi.fda.fdaq.FdaqService;
+import ch.psi.fda.rest.model.FdaqRequest;
+
+@Path("fdaq")
+public class FDAQService {
 
 	@Inject
-	private AcquisitionEngine aengine;
+	private FdaqService fdaq;
 	
-	@POST
+	@PUT
+	@Path("{trackingId}")
 	@Consumes({MediaType.APPLICATION_JSON, MediaType.APPLICATION_XML})
-//	@Produces({MediaType.APPLICATION_JSON, MediaType.APPLICATION_XML})
-	public String execute(Configuration configuration) throws InterruptedException{
-		return aengine.submit(configuration);
+	public void execute(@PathParam("trackingId") String trackingId, FdaqRequest request) throws InterruptedException {
+		fdaq.acquire();
 	}
 	
 	@DELETE
-	public void stop(){
-		aengine.terminate();
+	@Path("{trackingId}")
+	public void stop(@PathParam("trackingId") String trackingId) {
+		terminateAll();
+	}
+	
+	@DELETE
+	public void terminateAll(){
+		fdaq.stop();
 	}
 }

ch.psi.fda/src/main/java/ch/psi/fda/rest/services/FDAService.java

@@ -0,0 +1,72 @@
+/**
+ * 
+ * Copyright 2013 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ * 
+ * This code is distributed in the hope that it will be useful, but without any
+ * warranty; without even the implied warranty of merchantability or fitness for
+ * a particular purpose. See the GNU Lesser General Public License for more
+ * details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
+package ch.psi.fda.rest.services;
+
+import java.util.concurrent.ExecutionException;
+
+import javax.inject.Inject;
+import javax.ws.rs.Consumes;
+import javax.ws.rs.DELETE;
+import javax.ws.rs.GET;
+import javax.ws.rs.PUT;
+import javax.ws.rs.Path;
+import javax.ws.rs.PathParam;
+import javax.ws.rs.core.MediaType;
+
+import ch.psi.fda.model.v1.Configuration;
+import ch.psi.fda.rest.AcquisitionEngine;
+
+@Path("fda")
+public class FDAService {
+
+	@Inject
+	private AcquisitionEngine aengine;
+	
+	@PUT
+	@Path("{trackingId}")
+	@Consumes({MediaType.APPLICATION_JSON, MediaType.APPLICATION_XML})
+	public void execute(@PathParam("trackingId") String trackingId, Configuration configuration) throws InterruptedException{
+		aengine.submit(trackingId, configuration);
+	}
+	
+	@DELETE
+	@Path("{trackingId}")
+	public void stop(@PathParam("trackingId") String trackingId){
+		aengine.terminate(trackingId);
+	}
+	
+	@DELETE
+	public void terminateAll(){
+		aengine.terminateAll();
+	}
+	
+	@GET
+	@Path("{trackingId}/running")
+	public boolean isActive(@PathParam("trackingId") String trackingId){
+		return aengine.isActive(trackingId);
+	}
+	
+	@GET
+	@Path("{trackingId}/done")
+	public void wait(@PathParam("trackingId") String trackingId) throws InterruptedException, ExecutionException{
+		aengine.wait(trackingId);
+	}
+	
+}

ch.psi.fda/src/main/java/ch/psi/fda/serializer/DataSerializer.java

@@ -1,23 +0,0 @@
-/**
- * 
- * Copyright 2010 Paul Scherrer Institute. All rights reserved.
- * 
- * This code is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This code is distributed in the hope that it will be useful,
- * but without any warranty; without even the implied warranty of
- * merchantability or fitness for a particular purpose. See the
- * GNU Lesser General Public License for more details.
- * 
- * You should have received a copy of the GNU Lesser General Public License
- * along with this code. If not, see <http://www.gnu.org/licenses/>.
- * 
- */
-
-package ch.psi.fda.serializer;
-
-public interface DataSerializer {
-}

ch.psi.fda/src/main/java/ch/psi/fda/serializer/DataSerializerTXT.java

@@ -1,197 +0,0 @@
-/**
- * 
- * Copyright 2010 Paul Scherrer Institute. All rights reserved.
- * 
- * This code is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- * 
- * This code is distributed in the hope that it will be useful,
- * but without any warranty; without even the implied warranty of
- * merchantability or fitness for a particular purpose. See the
- * GNU Lesser General Public License for more details.
- * 
- * You should have received a copy of the GNU Lesser General Public License
- * along with this code. If not, see <http://www.gnu.org/licenses/>.
- * 
- */
-
-package ch.psi.fda.serializer;
-
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.util.logging.Logger;
-
-import com.google.common.eventbus.Subscribe;
-
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Message;
-import ch.psi.fda.core.messages.Metadata;
-import ch.psi.fda.core.messages.StreamDelimiterMessage;
-
-/**
- * Serialize data received by a DataQueue
- */
-public class DataSerializerTXT implements DataSerializer{
-	
-	private static final Logger logger = Logger.getLogger(DataSerializerTXT.class.getName());
-	
-	private File file;
-	
-	private boolean appendSuffix = true;
-
-	
-	private boolean first = true;
-	private File outfile;
-	
-	private int icount;
-	private String basename;
-	private String extension;
-	private boolean newfile;
-	private boolean dataInBetween;
-	private BufferedWriter writer;
-	private StringBuffer b;
-	private StringBuffer b1;
-	
-	
-	/**
-	 * @param metadata
-	 * @param file
-	 * @param appendSuffix	Flag whether to append a _0000 suffix after the original file name
-	 */
-	public DataSerializerTXT(File file, boolean appendSuffix){
-		this.file = file;
-		this.appendSuffix = appendSuffix;
-	}
-
-	@Subscribe
-	public void onMessage(Message message){
-		try{
-		if(first){
-			first=false;
-			// Write header
-						
-						
-						
-						icount = 0;
-						newfile = true;
-						dataInBetween = false;
-						writer = null;
-						
-						// Get basename of the file
-						basename = this.file.getAbsolutePath(); // Determine file name
-						extension = basename.replaceAll("^.*\\.", ""); // Determine extension
-						basename = basename.replaceAll("\\."+extension+"$", "");
-		}
-		
-		if(message instanceof DataMessage){
-			dataInBetween = true;
-			if(newfile){
-				
-				b = new StringBuffer();
-				b1 = new StringBuffer();
-				b.append("#");
-				b1.append("#");
-				for(Metadata c: ((DataMessage) message).getMetadata()){
-
-					b.append(c.getId());
-					b.append("\t");
-					
-					b1.append(c.getDimension());
-					b1.append("\t");
-				}
-				b.setCharAt(b.length()-1, '\n');
-				b1.setCharAt(b1.length()-1, '\n');
-				
-				// Open new file and write header
-				// Construct file name
-				if(appendSuffix){
-					outfile = new File(String.format("%s_%04d.%s", basename, icount, extension));
-				}
-				else{
-					outfile = new File(String.format("%s.%s", basename, extension));
-				}
-				
-				// Open file
-				logger.fine("Open new data file: "+outfile.getAbsolutePath());
-				writer = new BufferedWriter(new FileWriter(outfile));
-				
-				// Write header
-				writer.write(b.toString());
-				writer.write(b1.toString());
-				
-				newfile=false;
-			}
-			
-			// Write message to file - each message will result in one line
-			DataMessage m = (DataMessage) message;
-			StringBuffer buffer = new StringBuffer();
-			for(Object o: m.getData()){
-				if(o.getClass().isArray()){
-					// If the array object is of type double[] display its content
-					if(o instanceof double[]){
-						double[] oa = (double[]) o;
-						for(double o1 : oa){
-							buffer.append(o1);
-							buffer.append(" "); // Use space instead of tab
-						}
-						buffer.replace(buffer.length()-1,buffer.length()-1 , "\t"); // Replace last space with tab
-					}
-					else if(o instanceof Object[]){
-						// TODO need to be recursive ...
-						Object[] oa = (Object[])o;
-						for(Object o1 : oa){
-							buffer.append(o1);
-							buffer.append(" "); // Use space instead of tab
-						}
-						buffer.replace(buffer.length()-1,buffer.length()-1 , "\t"); // Replace last space with tab
-					}
-					else{
-						buffer.append("-"); // Not supported
-					}
-				}
-				else{
-					buffer.append(o);
-					buffer.append("\t");
-				}
-			}
-			
-			if(buffer.length()>0){
-				buffer.deleteCharAt(buffer.length()-1); // Remove last character (i.e. \t)
-				buffer.append("\n"); // Append newline
-			}
-			writer.write(buffer.toString());
-		}
-		else if(message instanceof StreamDelimiterMessage){
-			StreamDelimiterMessage m = (StreamDelimiterMessage) message;
-			logger.info("Delimiter - number: "+m.getNumber()+" iflag: "+m.isIflag());
-			if(m.isIflag() && appendSuffix){
-				// Only increase iflag counter if there was data in between
-				// subsequent StreamDelimiterMessages.
-				if(dataInBetween){
-					icount++;
-				}
-				dataInBetween = false;
-				
-				// Set flag to open new file
-				newfile = true;
-				
-				// Close file
-				writer.close();
-			}
-		}
-		else if (message instanceof EndOfStreamMessage){
-			if(writer!=null){
-				// Close file
-				writer.close(); //If the stream was closed previously this has no effect
-			}
-		}
-		} catch (IOException e) {
-			throw new RuntimeException("Data serializer had a problem writing to the specified file",e);
-		}
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/serializer/SerializerMAT.java

@@ -29,15 +29,15 @@ import com.jmatio.io.MatFileWriter;
 import com.jmatio.types.MLArray;
 import com.jmatio.types.MLDouble;
 
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Message;
-import ch.psi.fda.core.messages.Metadata;
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.EndOfStreamMessage;
+import ch.psi.fda.messages.Message;
+import ch.psi.fda.messages.Metadata;
 
 /**
  * Serialize data received by a DataQueue into a Matlab file
  */
-public class DataSerializerMAT implements DataSerializer{
+public class SerializerMAT {
 	
 	private File file;
 	
@@ -49,7 +49,7 @@ public class DataSerializerMAT implements DataSerializer{
 	 * @param queue	Data queue holding the data to serialize
 	 * @param file	Name of the Matlab file to serialize the data to
 	 */
-	public DataSerializerMAT(File file){
+	public SerializerMAT(File file){
 		this.file = file;
 	}
 

ch.psi.fda/src/main/java/ch/psi/fda/serializer/SerializerMAT2D.java

@@ -30,18 +30,18 @@ import com.jmatio.io.MatFileWriter;
 import com.jmatio.types.MLArray;
 import com.jmatio.types.MLDouble;
 
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.Metadata;
-import ch.psi.fda.core.messages.StreamDelimiterMessage;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Message;
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.EndOfStreamMessage;
+import ch.psi.fda.messages.Message;
+import ch.psi.fda.messages.Metadata;
+import ch.psi.fda.messages.StreamDelimiterMessage;
 
 /**
  * Serialize data received by a DataQueue into a Matlab file
  */
-public class DataSerializerMAT2D implements DataSerializer{
+public class SerializerMAT2D {
 
-	private static final Logger logger = Logger.getLogger(DataSerializerMAT2D.class.getName());
+	private static final Logger logger = Logger.getLogger(SerializerMAT2D.class.getName());
 	
 	private File file;
 	private boolean appendSuffix = false;
@@ -61,7 +61,7 @@ public class DataSerializerMAT2D implements DataSerializer{
 	 * @param queue	Data queue holding the data to serialize
 	 * @param file	Name of the Matlab file to serialize the data to
 	 */
-	public DataSerializerMAT2D(File file){
+	public SerializerMAT2D(File file){
 		this.file = file;
 		
 		

ch.psi.fda/src/main/java/ch/psi/fda/serializer/SerializerMAT2DZigZag.java

@@ -31,18 +31,18 @@ import com.jmatio.io.MatFileWriter;
 import com.jmatio.types.MLArray;
 import com.jmatio.types.MLDouble;
 
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.Metadata;
-import ch.psi.fda.core.messages.StreamDelimiterMessage;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Message;
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.EndOfStreamMessage;
+import ch.psi.fda.messages.Message;
+import ch.psi.fda.messages.Metadata;
+import ch.psi.fda.messages.StreamDelimiterMessage;
 
 /**
  * Serialize data received by a DataQueue into a Matlab file
  */
-public class DataSerializerMAT2DZigZag implements DataSerializer{
+public class SerializerMAT2DZigZag {
 	
-	private static final Logger logger = Logger.getLogger(DataSerializerMAT2DZigZag.class.getName());
+	private static final Logger logger = Logger.getLogger(SerializerMAT2DZigZag.class.getName());
 	
 	private List<Metadata> metadata;
 	private File file;
@@ -66,7 +66,7 @@ public class DataSerializerMAT2DZigZag implements DataSerializer{
 	 * @param queue	Data queue holding the data to serialize
 	 * @param file	Name of the Matlab file to serialize the data to
 	 */
-	public DataSerializerMAT2DZigZag(File file){
+	public SerializerMAT2DZigZag(File file){
 		this.file = file;
 		
 		

ch.psi.fda/src/main/java/ch/psi/fda/serializer/SerializerMDA.java

@@ -32,20 +32,20 @@ import java.util.logging.Logger;
 
 import com.google.common.eventbus.Subscribe;
 
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Message;
-import ch.psi.fda.core.messages.Metadata;
-import ch.psi.fda.core.messages.StreamDelimiterMessage;
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.EndOfStreamMessage;
+import ch.psi.fda.messages.Message;
+import ch.psi.fda.messages.Metadata;
+import ch.psi.fda.messages.StreamDelimiterMessage;
 
 /**
  * Serialize data received by a DataQueue
  * 
  * http://www.aps.anl.gov/bcda/synApps/sscan/saveData_fileFormat.txt
  */
-public class DataSerializerMDA implements DataSerializer{
+public class SerializerMDA {
 	
-	private static final Logger logger = Logger.getLogger(DataSerializerMDA.class.getName());
+	private static final Logger logger = Logger.getLogger(SerializerMDA.class.getName());
 	
 	private File file;
 	
@@ -59,7 +59,7 @@ public class DataSerializerMDA implements DataSerializer{
 	private HashMap<Integer,List<String>> idMap;
 	private int numberOfDimensions;
 	
-	public DataSerializerMDA(File file){
+	public SerializerMDA(File file){
 		this.file = file;
 	}
 

ch.psi.fda/src/main/java/ch/psi/fda/serializer/SerializerTXT2D.java

@@ -28,16 +28,16 @@ import java.util.List;
 
 import com.google.common.eventbus.Subscribe;
 
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.Metadata;
-import ch.psi.fda.core.messages.StreamDelimiterMessage;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Message;
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.EndOfStreamMessage;
+import ch.psi.fda.messages.Message;
+import ch.psi.fda.messages.Metadata;
+import ch.psi.fda.messages.StreamDelimiterMessage;
 
 /**
  * Serialize data received by a DataQueue into a Matlab file
  */
-public class DataSerializerTXT2D implements DataSerializer{
+public class SerializerTXT2D {
 	
 	private File file;
 	private boolean appendSuffix = false;
@@ -56,7 +56,7 @@ public class DataSerializerTXT2D implements DataSerializer{
 	 * @param queue	Data queue holding the data to serialize
 	 * @param file	Name of the Matlab file to serialize the data to
 	 */
-	public DataSerializerTXT2D(File file){
+	public SerializerTXT2D(File file){
 		this.file = file;
 	}
 

ch.psi.fda/src/main/java/ch/psi/fda/serializer/SerializerTXTSplit.java

@@ -28,15 +28,15 @@ import java.util.List;
 
 import com.google.common.eventbus.Subscribe;
 
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.Metadata;
-import ch.psi.fda.core.messages.StreamDelimiterMessage;
-import ch.psi.fda.core.messages.Message;
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.Message;
+import ch.psi.fda.messages.Metadata;
+import ch.psi.fda.messages.StreamDelimiterMessage;
 
 /**
  * Serialize data received by a DataQueue
  */
-public class DataSerializerTXTSplit implements DataSerializer {
+public class SerializerTXTSplit {
 
 	private File file;
 
@@ -47,7 +47,7 @@ public class DataSerializerTXTSplit implements DataSerializer {
 	private List<String> header;
 	private List<String> data;
 
-	public DataSerializerTXTSplit(File file) {
+	public SerializerTXTSplit(File file) {
 		this.file = file;
 	}
 

ch.psi.fda/src/main/java/ch/psi/fda/visualizer/Visualizer.java

@@ -29,9 +29,9 @@ import javax.swing.SwingUtilities;
 
 import com.google.common.eventbus.Subscribe;
 
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.StreamDelimiterMessage;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.EndOfStreamMessage;
+import ch.psi.fda.messages.StreamDelimiterMessage;
 import ch.psi.plot.Plot;
 import ch.psi.plot.xy.LinePlot;
 import ch.psi.plot.xy.XYSeriesCollectionP;

ch.psi.fda/src/main/resources/xjb.xjb

@@ -0,0 +1,9 @@
+<jxb:bindings version="1.0"
+xmlns:jxb="http://java.sun.com/xml/ns/jaxb"
+xmlns:xs="http://www.w3.org/2001/XMLSchema">
+
+<jxb:globalBindings>
+  <jxb:serializable uid="1"/>
+</jxb:globalBindings>
+
+</jxb:bindings>

ch.psi.fda/src/test/java/ch/psi/fda/aq/CollectorTest.java

@@ -33,11 +33,11 @@ import com.google.common.eventbus.EventBus;
 import com.google.common.eventbus.Subscribe;
 
 import ch.psi.fda.aq.Collector;
-import ch.psi.fda.core.messages.ControlMessage;
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Message;
-import ch.psi.fda.core.messages.Metadata;
+import ch.psi.fda.messages.ControlMessage;
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.EndOfStreamMessage;
+import ch.psi.fda.messages.Message;
+import ch.psi.fda.messages.Metadata;
 
 public class CollectorTest {
 

ch.psi.fda/src/test/java/ch/psi/fda/aq/ManipulatorTest.java

@@ -40,13 +40,13 @@ import ch.psi.fda.TestChannels;
 import ch.psi.fda.aq.Manipulator;
 import ch.psi.fda.core.Manipulation;
 import ch.psi.fda.core.manipulator.JythonManipulation;
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Message;
-import ch.psi.fda.core.messages.Metadata;
 import ch.psi.fda.core.scripting.JythonParameterMapping;
 import ch.psi.fda.core.scripting.JythonParameterMappingChannel;
 import ch.psi.fda.core.scripting.JythonParameterMappingID;
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.EndOfStreamMessage;
+import ch.psi.fda.messages.Message;
+import ch.psi.fda.messages.Metadata;
 import ch.psi.jcae.Channel;
 import ch.psi.jcae.ChannelDescriptor;
 import ch.psi.jcae.ChannelException;

ch.psi.fda/src/test/java/ch/psi/fda/core/loops/ActorSensorLoopTest.java

@@ -44,8 +44,8 @@ import ch.psi.fda.core.actors.ChannelAccessLinearActuator;
 import ch.psi.fda.core.guard.ChannelAccessGuard;
 import ch.psi.fda.core.guard.ChannelAccessGuardCondition;
 import ch.psi.fda.core.loops.ActorSensorLoop;
-import ch.psi.fda.core.messages.Message;
 import ch.psi.fda.core.sensors.ChannelAccessSensor;
+import ch.psi.fda.messages.Message;
 import ch.psi.jcae.Channel;
 import ch.psi.jcae.ChannelDescriptor;
 import ch.psi.jcae.ChannelException;

ch.psi.fda/src/test/java/ch/psi/fda/core/loops/OTFLoopTest.java

@@ -39,10 +39,10 @@ import ch.psi.fda.core.loops.otf.OTFLoop;
 import ch.psi.fda.core.loops.otf.OTFNamedChannelSensor;
 import ch.psi.fda.core.loops.otf.OTFScalerChannelSensor;
 import ch.psi.fda.core.loops.otf.TemplateOTF;
-import ch.psi.fda.core.messages.ControlMessage;
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.Message;
 import ch.psi.fda.core.sensors.TimestampSensor;
+import ch.psi.fda.messages.ControlMessage;
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.Message;
 import ch.psi.jcae.Channel;
 import ch.psi.jcae.ChannelDescriptor;
 import ch.psi.jcae.ChannelException;

ch.psi.fda/src/test/java/ch/psi/fda/core/loops/cr/ParallelCrlogicStreamMergeTest.java

@@ -32,10 +32,10 @@ import org.junit.Test;
 import com.google.common.eventbus.EventBus;
 import com.google.common.eventbus.Subscribe;
 
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Message;
-import ch.psi.fda.core.messages.Metadata;
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.EndOfStreamMessage;
+import ch.psi.fda.messages.Message;
+import ch.psi.fda.messages.Metadata;
 
 public class ParallelCrlogicStreamMergeTest {
 	

ch.psi.fda/src/test/java/ch/psi/fda/core/loops/cr/ParallelCrlogicTest.java

@@ -34,7 +34,7 @@ import org.junit.Test;
 import com.google.common.eventbus.Subscribe;
 
 import ch.psi.fda.TestConfiguration;
-import ch.psi.fda.core.messages.Message;
+import ch.psi.fda.messages.Message;
 import ch.psi.jcae.Channel;
 import ch.psi.jcae.ChannelDescriptor;
 import ch.psi.jcae.ChannelException;

ch.psi.fda/src/test/java/ch/psi/fda/core/loops/cr/ScrlogicLoopTest.java

@@ -32,7 +32,7 @@ import org.junit.Test;
 
 import com.google.common.eventbus.Subscribe;
 
-import ch.psi.fda.core.messages.Message;
+import ch.psi.fda.messages.Message;
 import ch.psi.jcae.Channel;
 import ch.psi.jcae.ChannelDescriptor;
 import ch.psi.jcae.ChannelException;

ch.psi.fda/src/test/java/ch/psi/fda/deserializer/DataDeserializerMDATest.java

@@ -31,10 +31,10 @@ import org.junit.Test;
 import com.google.common.eventbus.EventBus;
 import com.google.common.eventbus.Subscribe;
 
-import ch.psi.fda.core.messages.ControlMessage;
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.Message;
-import ch.psi.fda.core.messages.Metadata;
+import ch.psi.fda.messages.ControlMessage;
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.Message;
+import ch.psi.fda.messages.Metadata;
 
 /**
  * @author ebner

ch.psi.fda/src/test/java/ch/psi/fda/deserializer/DataDeserializerTest.java

@@ -31,11 +31,11 @@ import org.junit.Test;
 import com.google.common.eventbus.EventBus;
 import com.google.common.eventbus.Subscribe;
 
-import ch.psi.fda.core.messages.ControlMessage;
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.Message;
 import ch.psi.fda.deserializer.DataDeserializer;
 import ch.psi.fda.deserializer.DataDeserializerTXT;
+import ch.psi.fda.messages.ControlMessage;
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.Message;
 
 public class DataDeserializerTest {
 	

ch.psi.fda/src/test/java/ch/psi/fda/serializer/SerializerTest.java

@@ -29,19 +29,18 @@ import org.junit.Test;
 
 import com.google.common.eventbus.EventBus;
 
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.Metadata;
-import ch.psi.fda.core.messages.StreamDelimiterMessage;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.serializer.DataSerializer;
-import ch.psi.fda.serializer.DataSerializerMAT;
-import ch.psi.fda.serializer.DataSerializerMAT2D;
-import ch.psi.fda.serializer.DataSerializerTXT;
-import ch.psi.fda.serializer.DataSerializerTXT2D;
-import ch.psi.fda.serializer.DataSerializerTXTSplit;
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.EndOfStreamMessage;
+import ch.psi.fda.messages.Metadata;
+import ch.psi.fda.messages.StreamDelimiterMessage;
+import ch.psi.fda.serializer.SerializerMAT;
+import ch.psi.fda.serializer.SerializerMAT2D;
+import ch.psi.fda.serializer.SerializerTXT;
+import ch.psi.fda.serializer.SerializerTXT2D;
+import ch.psi.fda.serializer.SerializerTXTSplit;
 
 
-public class DataSerializerTest {
+public class SerializerTest {
 
 	private static final String tmpDirectory = "target/tmp";
 	
@@ -147,79 +146,79 @@ public class DataSerializerTest {
 	}
 
 	/**
-	 * Test method for {@link ch.psi.fda.serializer.DataSerializerTXT#run()}.
+	 * Test method for {@link ch.psi.fda.serializer.SerializerTXT#run()}.
 	 * @throws InterruptedException 
 	 */
 	@Test
 	public void testRunTXT() throws InterruptedException {
-		DataSerializer serializer = new DataSerializerTXT(new File(tmpDirectory+"/test.txt"), true);
+		SerializerTXT serializer = new SerializerTXT(new File(tmpDirectory+"/test.txt"), true);
 		bus.register(serializer);
 		generate1DData();
 	}
 
 	/**
-	 * Test method for {@link ch.psi.fda.serializer.DataSerializerTXT#run()}.
+	 * Test method for {@link ch.psi.fda.serializer.SerializerTXT#run()}.
 	 * @throws InterruptedException 
 	 */
 	@Test
 	public void testRunMAT() throws InterruptedException {
 		
-		DataSerializer serializer = new DataSerializerMAT(new File(tmpDirectory+"/test.mat"));
+		SerializerMAT serializer = new SerializerMAT(new File(tmpDirectory+"/test.mat"));
 		bus.register(serializer);
 		generate1DData();
 	}
 	
 	/**
-	 * Test method for {@link ch.psi.fda.serializer.DataSerializerTXT#run()}.
+	 * Test method for {@link ch.psi.fda.serializer.SerializerTXT#run()}.
 	 * @throws InterruptedException 
 	 */
 	@Test
 	public void testRunMAT2D() throws InterruptedException {
-		DataSerializer serializer = new DataSerializerMAT2D(new File(tmpDirectory+"/test-2d.mat"));
+		SerializerMAT2D serializer = new SerializerMAT2D(new File(tmpDirectory+"/test-2d.mat"));
 		bus.register(serializer);
 		generate2DData();
 	}
 	
 	/**
-	 * Test method for {@link ch.psi.fda.serializer.DataSerializerTXT#run()}.
+	 * Test method for {@link ch.psi.fda.serializer.SerializerTXT#run()}.
 	 * @throws InterruptedException 
 	 */
 	@Test
 	public void testRunTXT2D() throws InterruptedException {
-		DataSerializer serializer = new DataSerializerTXT2D(new File(tmpDirectory+"/test-2d.txt"));
+		SerializerTXT2D serializer = new SerializerTXT2D(new File(tmpDirectory+"/test-2d.txt"));
 		bus.register(serializer);
 		generate2DData();
 	}
 	
 	/**
-	 * Test method for {@link ch.psi.fda.serializer.DataSerializerTXT#run()}.
+	 * Test method for {@link ch.psi.fda.serializer.SerializerTXT#run()}.
 	 * @throws InterruptedException 
 	 */
 	@Test
 	public void testRunSplitTXT() throws InterruptedException {
-		DataSerializer serializer = new DataSerializerTXTSplit(new File(tmpDirectory+"/test-2d-split.txt"));
+		SerializerTXTSplit serializer = new SerializerTXTSplit(new File(tmpDirectory+"/test-2d-split.txt"));
 		bus.register(serializer);
 		generate2DData();
 	}
 	
 	/**
-	 * Test method for {@link ch.psi.fda.serializer.DataSerializerMDA#run()}.
+	 * Test method for {@link ch.psi.fda.serializer.SerializerMDA#run()}.
 	 * @throws InterruptedException 
 	 */
 	@Test
 	public void testRun2D() throws InterruptedException {
-		DataSerializer serializer = new DataSerializerMDA(new File(tmpDirectory+"/test-2d.mda"));
+		SerializerMDA serializer = new SerializerMDA(new File(tmpDirectory+"/test-2d.mda"));
 		bus.register(serializer);
 		generate2DData();
 	}
 
 	/**
-	 * Test method for {@link ch.psi.fda.serializer.DataSerializerMDA#run()}.
+	 * Test method for {@link ch.psi.fda.serializer.SerializerMDA#run()}.
 	 * @throws InterruptedException 
 	 */
 	@Test
 	public void testRun3D() throws InterruptedException {
-		DataSerializer serializer = new DataSerializerMDA(new File(tmpDirectory+"/test-3d.mda"));
+		SerializerMDA serializer = new SerializerMDA(new File(tmpDirectory+"/test-3d.mda"));
 		bus.register(serializer);
 		generate3DData();
 	}

ch.psi.fda/src/test/java/ch/psi/fda/visualizer/DataVisualizerTest.java

@@ -33,10 +33,10 @@ import org.junit.Test;
 
 import com.google.common.eventbus.EventBus;
 
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.Metadata;
-import ch.psi.fda.core.messages.StreamDelimiterMessage;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
+import ch.psi.fda.messages.DataMessage;
+import ch.psi.fda.messages.EndOfStreamMessage;
+import ch.psi.fda.messages.Metadata;
+import ch.psi.fda.messages.StreamDelimiterMessage;
 import ch.psi.plot.xy.LinePlot;
 import ch.psi.plot.xyz.MatrixPlotData;
 

ch.psi.fda/src/test/resources/home/config/fda.properties

@@ -1,4 +1,5 @@
 # Serialization properties
+ch.psi.fda.aq.data.dir=../data
 ch.psi.fda.aq.data.filePrefix=${yyyy_MM}/${yyyyMMdd}/${yyyyMMddHHmmss}_${name}/${yyyyMMddHHmm}_
 
 # OTF scan related configuration

ch.psi.fda/src/test/resources/home/config/jcae.properties

@@ -1,4 +1,4 @@
-ch.psi.jcae.ContextFactory.addressList=129.129.130.255 129.129.130.37 129.129.145.26 129.129.130.77
+ch.psi.jcae.ContextFactory.addressList=129.129.130.188 129.129.130.255 129.129.130.37 129.129.145.26 129.129.130.88 129.129.130.142
 ch.psi.jcae.ChannelFactory.timeout=2000
 ch.psi.jcae.ChannelFactory.retries=4
 ch.psi.jcae.ChannelBeanFactory.timeout=10000

ch.psi.fda/src/test/resources/home/config/logging.properties

@@ -1,9 +1,8 @@
 # Specify the handlers to create in the root logger
-##handlers = java.util.logging.ConsoleHandler, java.util.logging.FileHandler
 handlers = java.util.logging.ConsoleHandler
 
 # Set the default logging level for the root logger
-.level=ALL
+.level=INFO
 
 # Set the default logging level for new ConsoleHandler instances
 java.util.logging.ConsoleHandler.level=ALL
@@ -11,22 +10,5 @@ java.util.logging.ConsoleHandler.level=ALL
 # Set the default formatter for new ConsoleHandler instances
 java.util.logging.ConsoleHandler.formatter = java.util.logging.SimpleFormatter
 
-# Set the default logging level for new FileHandler instances
-##java.util.logging.FileHandler.level=ALL
-
-# Set the default formatter for new ConsoleHandler instances
-##java.util.logging.FileHandler.formatter=java.util.logging.SimpleFormatter
-
-# Naming of the output file:
-##java.util.logging.FileHandler.pattern=/Users/ebner/Workspace/Eclipse/workspace-xasec/ch.psi.x10/resources/logs/fda-%u.%g.log
-
-# Limiting size of output file in bytes (10000kb):
-##java.util.logging.FileHandler.limit=10000000
-
-# Number of output files to cycle through, by appending an
-# integer to the base file name:
-##java.util.logging.FileHandler.count=10
-
 # Set the default logging level for the logger named com.mycompany
-ch.psi.fda.level=ALL
-com.cosylab.epics.level=ALL
+ch.psi.level=ALL

ch.psi.fda/src/test/resources/jcae.properties

@@ -1,4 +0,0 @@
-# Test properties file
-ch.psi.jcae.ContextFactory.addressList=129.129.130.255 129.129.130.37 129.129.145.26 129.129.130.88 129.129.130.142
-
-ch.psi.jcae.ChannelBeanFactory.retries=4

ch.psi.fda/src/test/resources/logging.properties

@@ -1,14 +0,0 @@
-# Specify the handlers to create in the root logger
-handlers = java.util.logging.ConsoleHandler
-
-# Set the default logging level for the root logger
-.level=INFO
-
-# Set the default logging level for new ConsoleHandler instances
-java.util.logging.ConsoleHandler.level=ALL
-
-# Set the default formatter for new ConsoleHandler instances
-java.util.logging.ConsoleHandler.formatter = java.util.logging.SimpleFormatter
-
-# Set the default logging level for the logger named com.mycompany
-ch.psi.level=ALL