Added an release notes file

-- however still lots of bugs in there !

ch.psi.fda/.classpath

@@ -6,7 +6,6 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="src" path="target/generated-sources/xjc"/>
 	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>

ch.psi.fda/.settings/org.eclipse.core.resources.prefs

@@ -0,0 +1,3 @@
+eclipse.preferences.version=1
+encoding//src/main/java=UTF-8
+encoding//src/test/java=UTF-8

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/ReleaseNotes.md

@@ -0,0 +1,2 @@
+# 3.0.0
+  * Update the fda.properties file and replace ch.psi.fda.aq.data.baseDirectory with ch.psi.fda.aq.data.dir.

ch.psi.fda/pom.xml

@@ -3,107 +3,100 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>ch.psi</groupId>
 	<artifactId>fda</artifactId>
-	<version>2.0.0</version>
+	<version>2.4.3</version>
 
 	<dependencies>
+
+		<dependency>
+			<groupId>ch.psi</groupId>
+			<artifactId>ch.psi.fda.core</artifactId>
+			<version>2.3.0</version>
+		</dependency>
+
+		<!-- These 3 libraries are just needed for testing -->
+		<dependency>
+			<groupId>ch.psi.fda</groupId>
+			<artifactId>ch.psi.fda.xscan</artifactId>
+			<version>2.3.2</version>
+		</dependency>
+		<dependency>
+			<groupId>ch.psi</groupId>
+			<artifactId>ch.psi.fda.cdump</artifactId>
+			<version>2.3.0</version>
+		</dependency>
+		<dependency>
+			<groupId>ch.psi</groupId>
+			<artifactId>ch.psi.fda.fdaq</artifactId>
+			<version>2.3.0</version>
+		</dependency>
+
 		<dependency>
 			<groupId>ch.psi</groupId>
 			<artifactId>jcae</artifactId>
-			<version>2.1.11</version>
+			<version>2.4.1</version>
 		</dependency>
-		<!-- Plotting library -->
+
 		<dependency>
 			<groupId>ch.psi</groupId>
 			<artifactId>plot</artifactId>
-			<version>1.1.30</version>
-		</dependency>
-		<!-- Java SMB/CIFS library -->
-		<dependency>
-			<groupId>jcifs</groupId>
-			<artifactId>jcifs</artifactId>
-			<version>1.3.17</version>
+			<version>1.1.31</version>
 		</dependency>
 
-		<!-- JAXB implementation -->
-		<!-- <dependency> <groupId>com.sun.xml.bind</groupId> <artifactId>jaxb-impl</artifactId> 
-			<version>2.2.1</version> </dependency> <dependency> <groupId>com.sun.xml.bind</groupId> 
-			<artifactId>jaxb-xjc</artifactId> <version>2.2.1</version> </dependency> -->
-		<!-- Jython Library -->
 		<dependency>
-			<groupId>org.python</groupId>
-			<artifactId>jython</artifactId>
-			<!-- <artifactId>jython-standalone</artifactId> -->
-			<version>2.5.3</version>
+			<groupId>com.google.inject</groupId>
+			<artifactId>guice</artifactId>
+			<version>3.0</version>
 		</dependency>
-		<!-- CLI Libraries -->
+
+		<dependency>
+			<groupId>org.glassfish.jersey.containers</groupId>
+			<artifactId>jersey-container-grizzly2-http</artifactId>
+			<version>2.5.1</version>
+		</dependency>
+
+		<dependency>
+			<groupId>org.glassfish.jersey.media</groupId>
+			<artifactId>jersey-media-sse</artifactId>
+			<version>2.5.1</version>
+		</dependency>
+
+		<dependency>
+			<groupId>org.glassfish.jersey.media</groupId>
+			<artifactId>jersey-media-json-jackson</artifactId>
+			<version>2.5.1</version>
+		</dependency>
+
+		<dependency>
+			<groupId>org.jeromq</groupId>
+			<artifactId>jeromq</artifactId>
+			<version>0.2.0</version>
+		</dependency>
+
 		<dependency>
 			<groupId>org.apache.commons</groupId>
 			<artifactId>cli</artifactId>
 			<version>1.2</version>
 		</dependency>
+
 		<!-- Library to Read Matlab Files -->
 		<dependency>
 			<groupId>com.jmatio</groupId>
 			<artifactId>jmatio</artifactId>
 			<version>0.2u2psi1</version>
 		</dependency>
-		<!-- Mail Libraries -->
-		<dependency>
-			<groupId>javax.mail</groupId>
-			<artifactId>mail</artifactId>
-			<version>1.4.1</version>
-		</dependency>
 		<!-- Library for reading/writing XDR Format (MDA) -->
 		<dependency>
 			<groupId>org.freehep</groupId>
 			<artifactId>freehep-xdr</artifactId>
 			<version>2.0.4</version>
 		</dependency>
-		
-		<dependency>
-			<groupId>com.google.inject</groupId>
-			<artifactId>guice</artifactId>
-			<version>3.0</version>
-		</dependency>
-		
-		<dependency>
-			<groupId>com.google.guava</groupId>
-			<artifactId>guava</artifactId>
-			<version>14.0.1</version>
-		</dependency>
 
 		<dependency>
-			<scope>test</scope>
 			<groupId>junit</groupId>
 			<artifactId>junit</artifactId>
-			<version>4.11</version>
+			<version>4.8.2</version>
+			<scope>test</scope>
 		</dependency>
-		
-		<!-- For Testing NG functionality purposes -->
-		<dependency>
-			<groupId>org.glassfish.jersey.containers</groupId>
-			<artifactId>jersey-container-grizzly2-http</artifactId>
-			<version>2.0</version>
-		</dependency>
-
-		<dependency>
-			<groupId>org.glassfish.jersey.media</groupId>
-			<artifactId>jersey-media-sse</artifactId>
-			<version>2.0</version>
-		</dependency>
-
-		<dependency>
-			<groupId>org.glassfish.jersey.media</groupId>
-			<artifactId>jersey-media-json-jackson</artifactId>
-			<version>2.0</version>
-		</dependency>
-
-		<dependency>
-			<groupId>commons-cli</groupId>
-			<artifactId>commons-cli</artifactId>
-			<version>1.2</version>
-		</dependency>
-		
 	</dependencies>
 
 	<build>
@@ -112,15 +105,17 @@
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-compiler-plugin</artifactId>
 				<configuration>
+					<encoding>UTF-8</encoding>
 					<source>1.7</source>
 					<target>1.7</target>
 				</configuration>
 			</plugin>
-			<!-- Generate Javadoc Jar -->
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-javadoc-plugin</artifactId>
-				<version>2.8</version>
+				<configuration>
+					<additionalparam>-Xdoclint:none</additionalparam> <!-- Disable Java8 strict Javadoc checking -->
+				</configuration>
 				<executions>
 					<execution>
 						<id>attach-javadocs</id>
@@ -130,11 +125,9 @@
 					</execution>
 				</executions>
 			</plugin>
-			<!-- Generate Source Jar -->
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-source-plugin</artifactId>
-				<version>2.1.2</version>
 				<executions>
 					<execution>
 						<id>attach-sources</id>
@@ -144,101 +137,19 @@
 					</execution>
 				</executions>
 			</plugin>
-			<!-- Schema generation -->
-			<plugin>
-				<groupId>org.jvnet.jaxb2.maven2</groupId>
-				<artifactId>maven-jaxb2-plugin</artifactId>
-				<version>0.8.0</version>
-				<executions>
-					<execution>
-						<goals>
-							<goal>generate</goal>
-						</goals>
-					</execution>
-				</executions>
-				<configuration>
-					<generatePackage>ch.psi.fda.model.v1</generatePackage>
-				</configuration>
-			</plugin>
-			<!-- Schema Documentation Generation -->
-			<plugin>
-				<groupId>org.codehaus.mojo</groupId>
-				<artifactId>xml-maven-plugin</artifactId>
-				<version>1.0</version>
-				<executions>
-					<execution>
-						<phase>transform</phase>
-						<goals>
-							<goal>transform</goal>
-						</goals>
-					</execution>
-				</executions>
-				<configuration>
-					<transformationSets>
-						<transformationSet>
-							<!-- <outputDir>target</outputDir> -->
-							<dir>src/main/resources</dir>
-							<stylesheet>src/main/documentation/xs3p.xsl</stylesheet>
-							<fileMappers>
-								<fileMapper
-									implementation="org.codehaus.plexus.components.io.filemappers.RegExpFileMapper">
-									<pattern>\.xsd$</pattern>
-									<replacement>.html</replacement>
-								</fileMapper>
-							</fileMappers>
-						</transformationSet>
-					</transformationSets>
-				</configuration>
-			</plugin>
 		</plugins>
-		<pluginManagement>
-			<plugins>
-				<!--This plugin's configuration is used to store Eclipse m2e settings 
-					only. It has no influence on the Maven build itself. -->
-				<plugin>
-					<groupId>org.eclipse.m2e</groupId>
-					<artifactId>lifecycle-mapping</artifactId>
-					<version>1.0.0</version>
-					<configuration>
-						<lifecycleMappingMetadata>
-							<pluginExecutions>
-								<pluginExecution>
-									<pluginExecutionFilter>
-										<groupId>
-											org.jvnet.jaxb2.maven2
-										</groupId>
-										<artifactId>
-											maven-jaxb2-plugin
-										</artifactId>
-										<versionRange>
-											[0.8.0,)
-										</versionRange>
-										<goals>
-											<goal>generate</goal>
-										</goals>
-									</pluginExecutionFilter>
-									<action>
-										<ignore></ignore>
-									</action>
-								</pluginExecution>
-							</pluginExecutions>
-						</lifecycleMappingMetadata>
-					</configuration>
-				</plugin>
-			</plugins>
-		</pluginManagement>
 	</build>
 
 	<distributionManagement>
 		<snapshotRepository>
 			<id>i.snapshots</id>
 			<name>Artifactory Snapshots</name>
-			<url>http://yoke/artifactory/libs-snapshots-local</url>
+			<url>http://yoke.psi.ch:8081/artifactory/libs-snapshots-local</url>
 		</snapshotRepository>
 		<repository>
 			<id>i.releases</id>
 			<name>Atrifactory Releases</name>
-			<url>http://yoke/artifactory/libs-releases-local</url>
+			<url>http://yoke.psi.ch:8081/artifactory/libs-releases-local</url>
 		</repository>
 	</distributionManagement>
 </project>

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 $CLASSPATH -Djava.util.logging.config.file=${APPLICATION_HOME}/config/logging.properties $VM_ARGUMENTS ch.psi.fda.ui.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.ui.RemoteAcquisitionMain $ARGUMENTS

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

@@ -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.ui.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 $CLASSPATH -Djava.util.logging.config.file=${APPLICATION_HOME}/config/logging.properties $VM_ARGUMENTS ch.psi.fda.ui.VisualizationZMQMain $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 $CLASSPATH -Djava.util.logging.config.file=${APPLICATION_HOME}/config/logging.properties $VM_ARGUMENTS ch.psi.fda.ui.VisualizationMain $ARGUMENTS

ch.psi.fda/src/main/assembly/www/css/main.css

@@ -0,0 +1,22 @@
+
+
+/* ==========================================================================
+   Author's custom styles
+   ========================================================================== */
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+

ch.psi.fda/src/main/assembly/www/index.html

@@ -0,0 +1,222 @@
+<!DOCTYPE html>
+<!--[if lt IE 7]>      <html class="no-js lt-ie9 lt-ie8 lt-ie7"> <![endif]-->
+<!--[if IE 7]>         <html class="no-js lt-ie9 lt-ie8"> <![endif]-->
+<!--[if IE 8]>         <html class="no-js lt-ie9"> <![endif]-->
+<!--[if gt IE 8]><!-->
+<html class="no-js">
+<!--<![endif]-->
+<head>
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1">
+<title></title>
+<meta name="description" content="">
+<meta name="viewport" content="width=device-width">
+
+<link rel="stylesheet" href="css/bootstrap.min.css">
+<style>
+body {
+	padding-top: 60px;
+	padding-bottom: 40px;
+}
+</style>
+<link rel="stylesheet" href="css/bootstrap-responsive.min.css">
+<link rel="stylesheet" href="css/main.css">
+
+<script src="js/vendor/modernizr-2.6.2-respond-1.1.0.min.js"></script>
+<script src="js/jquery-2.0.0.min.js"></script>
+<script type='text/javascript'>
+	var base = '../hub';
+	var stream;
+
+	function getVersion() {
+		$.get(base+'/version', function(data) {
+			$('#version').empty();
+			$('#version').append(data)
+		});
+	}
+	
+	function getBeamlines() {
+		$.get(base, function(data) {
+			/* update beamlines selection */
+			
+			$('#selectionBeamline').empty();
+			for (var i in data){
+				beamline = data[i];
+				$('#selectionBeamline').append('<option value="'+beamline+'">'+beamline+'</option>')
+			}
+			/* $('#selectionBeamline')[0].selectedIndex=0; */
+			connectStream(data[0]);
+		});
+	}
+	
+	function updateKeys(beamline, keys){
+		keytag = $('#beamlineKeys');
+		keytag.empty();
+		table='<table class="table table-hover"><thead><tr><td>Key</td><td>Value</td></tr></thead><tbody>';
+		
+		for(k in keys){
+			table=table+'<tr><td>'+k+'</td><td>'+
+			'<div class="input-append">'+
+			'<input type="text" value="'+keys[k]+'" onchange="setKey(\''+beamline+'\',\''+k+'\',$(this).val())">'+
+			//'<button class="btn" type="button" onclick="setKey(\''+beamline+'\',\''+k+'\',$(this).prev().val())">Update</button>'+
+			'<button class="btn" type="button" onclick="deleteKey(\''+beamline+'\',\''+k+'\')">Delete</button>'+
+			'</div>'+
+			'</td></tr>';
+		}
+		
+		table = table+'<tr>'+
+			'<td><input id="keyToAdd" type="text" placeholder="Key"></td>'+
+			'<td><div class="input-append">'+
+			'<input id="valueToAdd"type="text" placeholder="Value">'+
+			'<button class="btn" type="button" onclick="setKey(\''+beamline+'\',$(\'#keyToAdd\').val(),$(\'#valueToAdd\').val())">Add</button>'+
+			'</div></td>'+
+			'</tr>';
+		
+		table = table+'</table></tbody>';
+		keytag.append(table);
+	}
+
+	function connectStream(beamline) {
+		closeStream();
+		stream = new EventSource(base + '/' + beamline + '/stream');
+		stream.onmessage = function(event) {
+			keys=JSON.parse(event.data)
+			updateKeys(beamline, keys);
+			
+		};
+		getKeys(beamline);
+	}
+
+	function closeStream() {
+		try {
+			stream.close();
+		} catch (e) {
+		}
+	}
+	
+	function getKeys(beamline){
+		$.get(base+'/'+beamline+'/keys', function(data) {
+			updateKeys(beamline, data );
+		});
+	}
+	
+	function setKey(beamline, key, value){
+		$.ajax({
+		    url: base+'/'+beamline+'/keys/'+key,
+		    type: 'PUT',
+		    data: value,
+		    success: function(result) {
+		    }
+		});
+	}
+	
+	function deleteKey(beamline, key){
+		$.ajax({
+		    url: base+'/'+beamline+'/keys/'+key,
+		    type: 'DELETE',
+		    success: function(result) {
+		    }
+		});
+	}
+	
+	function addBeamline(beamline){
+		getKeys(beamline); /*create beamline*/
+		getBeamlines();
+	}
+	
+	function deleteBeamline(beamline){
+		$.ajax({
+		    url: base+'/'+beamline,
+		    type: 'DELETE',
+		    success: function(result) {
+		    	getBeamlines(); /* Update beamline list */
+		    }
+		});
+		
+	}
+	
+</script>
+</head>
+<body>
+	<!-- <script>
+        var source = new EventSource('../server-sent-events/');
+        source.onmessage = function(e) {
+        	$('#messagefield') = e.data;
+        };
+        </script> -->
+
+	<!--[if lt IE 7]>
+            <p class="chromeframe">You are using an <strong>outdated</strong> browser. Please <a href="http://browsehappy.com/">upgrade your browser</a> or <a href="http://www.google.com/chromeframe/?redirect=true">activate Google Chrome Frame</a> to improve your experience.</p>
+        <![endif]-->
+
+	<!-- This code is taken from http://twitter.github.com/bootstrap/examples/hero.html -->
+
+	<div class="navbar navbar-inverse navbar-fixed-top">
+		<div class="navbar-inner">
+			<div class="container">
+				<a class="btn btn-navbar" data-toggle="collapse"
+					data-target=".nav-collapse"> <span class="icon-bar"></span> <span
+					class="icon-bar"></span> <span class="icon-bar"></span>
+				</a> <a class="brand" href="#">hub</a>
+			</div>
+		</div>
+	</div>
+
+	<div class="container">
+
+		<!-- Main hero unit for a primary marketing message or call to action -->
+		<!-- <div class="hero-unit">
+			<p>This is the central Hub administration page ...</p>
+		</div> -->
+
+		<!-- Example row of columns -->
+		<div class="row">
+			<div class="span5">
+				<h2>Key Group</h2>
+				<div>
+					<select id="selectionBeamline">
+						<!-- <option value="sydney">Sydney</option> -->
+					</select>
+				</div>
+				<div id="beamlineKeys"></div>
+			</div>
+		</div>
+		<div class="row">
+			<div class="span5">
+				<h2>Key Group Management</h2>
+				<div class="input-append">
+					  <input class="span2" id="appendedInputButton" placeholder="Key Group" type="text">
+					  <button id="addBeamlineBtn" class="btn" type="button" onclick="addBeamline($(this).prev().val());$(this).prev().val('')">Add</button>
+					  <button id="addBeamlineBtn" class="btn" type="button" onclick="deleteBeamline($(this).prev().prev().val());$(this).prev().prev().val('')">Delete</button>
+				</div>
+			</div>
+		</div>
+
+		<hr>
+
+		<footer>
+			<p>Hub - Version <span id='version'></span> - &copy; Paul Scherrer Institute 2013</p>
+		</footer>
+
+	</div>
+	<!-- /container -->
+
+	<script>
+		/* update beamlines */
+		getVersion();
+		getBeamlines();
+		$('#selectionBeamline').change(function(){connectStream($('#selectionBeamline').val())});
+	</script>
+
+	
+	<script>
+		window.jQuery
+				|| document
+						.write('<script src="js/vendor/jquery-1.9.1.min.js"><\/script>')
+	</script>
+
+	<script src="js/vendor/bootstrap.min.js"></script>
+
+	<script src="js/main.js"></script>
+</body>
+</html>

ch.psi.fda/src/main/assembly/www/js/main.js

@@ -0,0 +1 @@
+

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

@@ -1,299 +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.aq;
-
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.IOException;
-import java.text.SimpleDateFormat;
-import java.util.Date;
-import java.util.Properties;
-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 AcquisitionEngineConfiguration {
-	
-	
-	private static final Logger logger = Logger.getLogger(AcquisitionEngineConfiguration.class.getName());
-	private static final AcquisitionEngineConfiguration instance = new AcquisitionEngineConfiguration();
-	
-	private String otfChannelPrefix;
-	private String otfNfsServer;
-	private String otfNfsShare;
-	private String otfSmbShare;
-	private String otfScalerPrefix;
-	private boolean otfUseCrlogic;
-	private String otfCrlogicPrefix;
-	private boolean otfCrlogicKeepTmpFiles;
-	
-	/**
-	 * Base directory for data. The directory may contain date macros. The string may contain any @see java.text.SimpleDateFormat
-	 * patterns within ${ } brackets. The macros are resolved with the actual time while the get method
-	 * of this property is called.
-	 */
-	private String dataBaseDirectory = System.getProperty("user.home");
-	/**
-	 * Prefix of the data file. The prefix may contain date macros. The string may contain any @see java.text.SimpleDateFormat
-	 * patterns within ${ } brackets. The macros are resolved with the actual time while the get method
-	 * of this property is called.
-	 */
-	private String dataFilePrefix = "";
-	
-	/**
-	 * Maximum time for a actor move
-	 */
-	private Long actorMoveTimeout = 600000l; // 10 Minutes maximum move time 
-	
-	private String smptServer;
-	
-	/**
-	 * Default Constructor
-	 * The constructor will read the configuration from the /fda.properties file (resource) located in the classpath.
-	 */
-	private AcquisitionEngineConfiguration(){
-		loadConfiguration();
-	}
-	
-	/**
-	 * Get instance of this configuration
-	 * @return configuration
-	 */
-	public static AcquisitionEngineConfiguration getInstance(){
-		return(instance);
-	}
-	
-	/**
-	 * Load configuration from properties file
-	 */
-	private void loadConfiguration() {
-		String config = System.getProperty(ApplicationConfigurator.FDA_CONFIG_FILE_ARGUMENT);
-		
-		Properties properties = new Properties();
-		
-		if(config != null){
-			try {
-				properties.load(new FileReader(config));
-			} catch (FileNotFoundException e) {
-				throw new RuntimeException("Configuration file "+config+" not found", e);
-			} catch (IOException e) {
-				throw new RuntimeException("Cannot read configuration file "+config, e);
-			}
-		}
-		else{
-			logger.warning("No configfile specified !");
-		}
-		
-		// The defaults are set here
-		otfChannelPrefix = properties.getProperty(AcquisitionEngineConfiguration.class.getPackage().getName()+".otf.channelPrefix", "");
-		otfScalerPrefix = properties.getProperty(AcquisitionEngineConfiguration.class.getPackage().getName()+".otf.scalerPrefix", "");
-		otfNfsServer = properties.getProperty(AcquisitionEngineConfiguration.class.getPackage().getName()+".otf.nfsServer", "");
-		otfNfsShare = properties.getProperty(AcquisitionEngineConfiguration.class.getPackage().getName()+".otf.nfsShare", "");
-		otfSmbShare = properties.getProperty(AcquisitionEngineConfiguration.class.getPackage().getName()+".otf.smbShare", "");
-		otfUseCrlogic = new Boolean(properties.getProperty(AcquisitionEngineConfiguration.class.getPackage().getName()+".otf.useCrlogic", "false"));
-		otfCrlogicPrefix = properties.getProperty(AcquisitionEngineConfiguration.class.getPackage().getName()+".otf.crlogicPrefix", "");
-		otfCrlogicKeepTmpFiles = new Boolean(properties.getProperty(AcquisitionEngineConfiguration.class.getPackage().getName()+".otf.crlogicKeepTmpFiles", "false"));
-		
-		// Workaround
-//		dataBaseDirectory = properties.getProperty(AcquisitionEngineConfiguration.class.getPackage().getName()+".data.baseDirectory", ".");
-		if(System.getProperty(ApplicationConfigurator.FDA_HOME_ARGUMENT)!=null){
-			dataBaseDirectory = System.getProperty(ApplicationConfigurator.FDA_HOME_ARGUMENT)+"/data";
-		}
-		else{
-			dataBaseDirectory = "./data";
-		}
-		
-		dataFilePrefix = properties.getProperty(AcquisitionEngineConfiguration.class.getPackage().getName()+".data.filePrefix","");
-		
-		actorMoveTimeout = new Long(properties.getProperty(AcquisitionEngineConfiguration.class.getPackage().getName()+".actorMoveTimeout","600000"));
-		
-		smptServer= properties.getProperty(AcquisitionEngineConfiguration.class.getPackage().getName()+".notification.host","mail.psi.ch");
-		
-	}
-	
-	/**
-	 * Reload this configuration from the corresponding properties file
-	 * @throws IOException 
-	 */
-	public void reloadConfiguration() throws IOException{
-		loadConfiguration();
-	}
-
-	/**
-	 * @return the otfChannelPrefix
-	 */
-	public String getOtfChannelPrefix() {
-		return otfChannelPrefix;
-	}
-
-	/**
-	 * @return the otfScalerPrefix
-	 */
-	public String getOtfScalerPrefix() {
-		return otfScalerPrefix;
-	}
-
-	/**
-	 * @return the otfNfsServer
-	 */
-	public String getOtfNfsServer() {
-		return otfNfsServer;
-	}
-
-	/**
-	 * @return the otfNfsShare
-	 */
-	public String getOtfNfsShare() {
-		return otfNfsShare;
-	}
-
-	/**
-	 * @return the otfSmbShare
-	 */
-	public String getOtfSmbShare() {
-		return otfSmbShare;
-	}
-
-	/**
-	 * @return the otfUseCrlogic
-	 */
-	public boolean isOtfUseCrlogic() {
-		return otfUseCrlogic;
-	}
-
-	/**
-	 * @return the dataBaseDirectory
-	 */
-	public String getDataBaseDirectory() {
-		return dataBaseDirectory;
-	}
-
-	/**
-	 * @return the dataFilePrefix
-	 */
-	public String getDataFilePrefix() {
-		return dataFilePrefix;
-	}
-
-	/**
-	 * @return the smptServer
-	 */
-	public String getSmptServer() {
-		return smptServer;
-	}
-
-	
-	/**
-	 * @return the otfCrlogicPrefix
-	 */
-	public String getOtfCrlogicPrefix() {
-		return otfCrlogicPrefix;
-	}
-
-	/**
-	 * @return the otfCrlogicKeepTmpFiles
-	 */
-	public boolean isOtfCrlogicKeepTmpFiles() {
-		return otfCrlogicKeepTmpFiles;
-	}
-
-	/**
-	 * @return the actorMoveTimeout
-	 */
-	public Long getActorMoveTimeout() {
-		return actorMoveTimeout;
-	}
-
-	public String replaceMacros(String string, Date date, String name){
-		String newString = string;
-		
-		// Replace scan name macros
-		newString = newString.replaceAll("\\$\\{name\\}", name);
-		
-		
-		// Replace date macros
-		Pattern pattern = Pattern.compile("\\$\\{[a-z,A-Z,-,_,:]*\\}");
-        Matcher matcher = pattern.matcher(newString);
-        while(matcher.find()){
-        	String datePattern = matcher.group();
-        	datePattern = datePattern.replaceAll("\\$\\{", "");
-        	datePattern = datePattern.replaceAll("\\}", "");
-        	SimpleDateFormat datef = new SimpleDateFormat(datePattern);
-        	newString = matcher.replaceFirst(datef.format(date));
-        	matcher = pattern.matcher(newString);
-        }
-		return newString;
-	}
-
-	public void setOtfChannelPrefix(String otfChannelPrefix) {
-		this.otfChannelPrefix = otfChannelPrefix;
-	}
-
-	public void setOtfNfsServer(String otfNfsServer) {
-		this.otfNfsServer = otfNfsServer;
-	}
-
-	public void setOtfNfsShare(String otfNfsShare) {
-		this.otfNfsShare = otfNfsShare;
-	}
-
-	public void setOtfSmbShare(String otfSmbShare) {
-		this.otfSmbShare = otfSmbShare;
-	}
-
-	public void setOtfScalerPrefix(String otfScalerPrefix) {
-		this.otfScalerPrefix = otfScalerPrefix;
-	}
-
-	public void setOtfUseCrlogic(boolean otfUseCrlogic) {
-		this.otfUseCrlogic = otfUseCrlogic;
-	}
-
-	public void setOtfCrlogicPrefix(String otfCrlogicPrefix) {
-		this.otfCrlogicPrefix = otfCrlogicPrefix;
-	}
-
-	public void setOtfCrlogicKeepTmpFiles(boolean otfCrlogicKeepTmpFiles) {
-		this.otfCrlogicKeepTmpFiles = otfCrlogicKeepTmpFiles;
-	}
-
-	public void setDataBaseDirectory(String dataBaseDirectory) {
-		this.dataBaseDirectory = dataBaseDirectory;
-	}
-
-	public void setDataFilePrefix(String dataFilePrefix) {
-		this.dataFilePrefix = dataFilePrefix;
-	}
-
-	public void setActorMoveTimeout(Long actorMoveTimeout) {
-		this.actorMoveTimeout = actorMoveTimeout;
-	}
-
-	public void setSmptServer(String smptServer) {
-		this.smptServer = smptServer;
-	}
-	
-}

ch.psi.fda/src/main/java/ch/psi/fda/aq/ng/AcquisitionEngineNG.java

@@ -1,154 +0,0 @@
-/**
- * 
- * 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.aq.ng;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.concurrent.BlockingQueue;
-import java.util.concurrent.LinkedBlockingQueue;
-import java.util.concurrent.TimeoutException;
-import java.util.logging.Logger;
-
-import javax.script.ScriptEngine;
-import javax.script.ScriptEngineManager;
-import javax.script.ScriptException;
-
-import ch.psi.fda.aq.ng.rdescriptors.ProbeDescriptor;
-import ch.psi.fda.aq.ng.rdescriptors.ShellDescriptor;
-import ch.psi.fda.aq.ng.resources.ChannelProbeResource;
-import ch.psi.fda.aq.ng.resources.ShellResource;
-import ch.psi.fda.core.messages.Message;
-import ch.psi.jcae.Channel;
-import ch.psi.jcae.ChannelDescriptor;
-import ch.psi.jcae.ChannelException;
-import ch.psi.jcae.ChannelService;
-
-/**
- * @author ebner
- * 
- */
-public class AcquisitionEngineNG {
-	
-	private static final Logger logger = Logger.getLogger(AcquisitionEngineNG.class.getName());
-	
-	private ChannelService cservice;
-	private BlockingQueue<Message> outQueue;
-	
-	public AcquisitionEngineNG(ChannelService cservice) {
-		this.cservice = cservice;
-		this.outQueue = new LinkedBlockingQueue<Message>(1000); // Create bounded queue to prevent running out of memory ...
-		
-		// Workaround for Jython memory leak
-		// http://blog.hillbrecht.de/2009/07/11/jython-memory-leakout-of-memory-problem/
-		System.setProperty("python.options.internalTablesImpl", "weak");
-	}
-	
-	/**
-	 * Execute the specified script/logic while using the specified resources and paramters
-	 * @param resourceDescriptors
-	 * @param script
-	 * @param parameter
-	 */
-	public void execute(Map<String, ?> resourceDescriptors, String script, List<String> parameter){
-		
-		// TODO Remove debugging messages
-		// For debugging purpose only
-		logger.info("Resources to create: "+resourceDescriptors);
-		logger.info("Script to execute: "+script);
-		
-		try {
-			ScriptEngine engine = new ScriptEngineManager().getEngineByName("python");
-			
-			// Set logger
-			engine.put("logger", logger);
-			
-			// Set parameters
-			engine.put("parameter", parameter);
-			
-			// Create/retrieve and set resources
-			Map<String,?> resources = createResources(resourceDescriptors);
-			engine.put("resources", resources);
-			for(String k: resources.keySet()){ // For convenience make resources also available as variable named by the resource id
-				engine.put(k, resources.get(k));
-			}
-			
-			// Execute script
-			engine.eval(script);
-			
-			
-		} catch (ScriptException e) {
-			logger.info(e.getMessage());
-			throw new RuntimeException("Action failed while executing the Jython script",e);
-		}	
-	}
-	
-	/**
-	 * Create resources based on the passed rDescriptors
-	 * Supported descriptor types are:
-	 * ChannelDescriptor, ShellDescriptor, ProbeDescriptor
-	 * 
-	 * @param resourceDescriptors
-	 * @return
-	 */
-	private Map<String,?> createResources(Map<String, ?> resourceDescriptors){
-		Map<String,Object> resources = new HashMap<>();
-		for(String k: resourceDescriptors.keySet()){
-			if(resourceDescriptors.get(k) instanceof ChannelDescriptor){
-				ChannelDescriptor<?> descriptor = (ChannelDescriptor<?>)resourceDescriptors.get(k);
-				try {
-					resources.put(k, cservice.createChannel(descriptor));
-//					engine.put(k, cservice.createChannel(descriptor));
-				} catch (ChannelException | InterruptedException | TimeoutException e) {
-					throw new RuntimeException("Unable to create resource for channel: "+descriptor.getName(),e);
-				}
-			}
-			else if(resourceDescriptors.get(k) instanceof ShellDescriptor){
-				resources.put(k, new ShellResource());
-//				engine.put(k, new ShellResource());
-			}
-			else if(resourceDescriptors.get(k) instanceof ProbeDescriptor){
-				ProbeDescriptor descriptor = (ProbeDescriptor) resourceDescriptors.get(k);
-				List<Channel<?>> channels = new ArrayList<>();
-				
-				for(ChannelDescriptor<?> s: descriptor.getSensors()){
-					try {
-							channels.add(cservice.createChannel(s));
-							
-					} catch (ChannelException | InterruptedException | TimeoutException e) {
-						throw new RuntimeException("Unable to create resource for channel: "+s.getName(),e);
-					}
-				}
-				// TODO Remove workaround ...
-				resources.put(k, new ChannelProbeResource(channels, outQueue)); // Configure the probe to use the acquisitions out queue for writing data into
-//				engine.put(k, new ChannelProbeResource(channels, outQueue));
-			}
-			else{
-				throw new RuntimeException("Resource type not supported: "+resourceDescriptors.get(k).getClass().getName());
-			}
-		}
-		return resources;
-	}
-	
-	public BlockingQueue<Message> getOutQueue(){
-		return outQueue;
-	}
-
-}

ch.psi.fda/src/main/java/ch/psi/fda/aq/ng/AcquisitionEngineNGResource.java

@@ -1,173 +0,0 @@
-/**
- * 
- * 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.aq.ng;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import javax.inject.Inject;
-import javax.ws.rs.Consumes;
-import javax.ws.rs.GET;
-import javax.ws.rs.NotFoundException;
-import javax.ws.rs.POST;
-import javax.ws.rs.PUT;
-import javax.ws.rs.Path;
-import javax.ws.rs.PathParam;
-import javax.ws.rs.Produces;
-import javax.ws.rs.core.MediaType;
-
-import ch.psi.fda.aq.ng.rdescriptors.ShellDescriptor;
-import ch.psi.jcae.ChannelDescriptor;
-
-/**
- * @author ebner
- *
- */
-@Path("/")
-public class AcquisitionEngineNGResource {
-
-	@Inject
-	private AcquisitionEngineNG engine;
-	
-	@Inject
-	private LManager lmanager;
-	
-//	@PUT
-//	@Path("logic")
-//	public void execute(String logic){
-//		Map<String, ?> map = new HashMap<>();
-//		engine.execute(map, logic);
-//	}
-	
-	@GET
-	@Path("logic")
-	@Produces(MediaType.APPLICATION_JSON)
-	public Set<String> getLogics(){
-		return lmanager.getLogics();
-	}
-	
-	@PUT
-	@Path("logic/{id}")
-	public void setLogic(@PathParam("id") String id, String logic){
-		lmanager.addLogic(id, logic);
-	}
-	
-	@GET
-	@Path("logic/{id}")
-	public String getLogic(@PathParam("id") String id){
-		String logic = lmanager.getLogic(id);
-		if(logic==null){
-			throw new NotFoundException();
-		}
-		return logic;
-	}
-	
-	@POST
-	@Path("logic/{id}")
-	@Consumes(MediaType.APPLICATION_JSON)
-	public void executeLogic(@PathParam("id") String id, EDescriptor edescriptor){
-
-		// Before executing the logic first merge the default descriptors and provided descriptors
-		// Where the provided descriptors take precedence over the default onces.
-		Map<String, RDescriptor> rdesc = new HashMap<>();
-		rdesc.putAll(lmanager.getResources(id));
-		if (edescriptor.getResources() != null) {
-			rdesc.putAll(edescriptor.getResources());
-		}
-		
-		Map<String, ?> map = createResourceDescriptors(rdesc);
-		
-		List<String> parameters = new ArrayList<>();
-		if(edescriptor.getParameter()!=null){
-			parameters = edescriptor.getParameter();
-		}
-		
-		engine.execute(map, lmanager.getLogic(id), parameters);
-	}
-	
-	@PUT
-	@Path("logic/{id}/resources")
-	public void setLogicResources(@PathParam("id") String id, Map<String, RDescriptor> rprofile){
-		lmanager.addResources(id, rprofile);
-	}
-	
-	@GET
-	@Path("logic/{id}/resources")
-	public Map<String, RDescriptor> getLogicResources(@PathParam("id") String id){
-		Map<String, RDescriptor> rprofile = lmanager.getResources(id);
-		if(rprofile==null){
-			throw new NotFoundException();
-		}
-		return rprofile;
-	}
-	
-	/**
-	 * Create internal resource descriptors based on the rdescriptors passed to the method.
-	 * 
-	 * Currently following rdescriptor types are supported:
-	 *  - channel
-	 *  - shell
-	 * 
-	 * @param descriptor
-	 * @return
-	 */
-	private Map<String, ?> createResourceDescriptors(Map<String, RDescriptor> resourceDescriptors) {
-		Map<String, Object> map = new HashMap<>();
-
-		for (String k : resourceDescriptors.keySet()) {
-			RDescriptor r = resourceDescriptors.get(k);
-			if (r.getType().equals("channel")) {
-				Class<?> c;
-				switch (r.getParameter().get("type").toLowerCase()) {
-				case "double":
-					c = Double.class;
-					break;
-				case "integer":
-					c = Integer.class;
-					break;
-				case "boolean":
-					c = Boolean.class;
-					break;
-				case "String":
-					c = String.class;
-					break;
-				default:
-					c = String.class;
-				}
-				;
-				String name = r.getParameter().get("name");
-				boolean monitored = false;
-				if(r.getParameter().get("monitor")!=null){
-					monitored = new Boolean(r.getParameter().get("monitor"));
-				}
-
-				// Create channel descriptor
-				ChannelDescriptor<?> cd = new ChannelDescriptor<>(c, name, monitored);
-				map.put(k, cd);
-			}
-			else if (r.getType().equals("shell")) {
-				map.put(k, new ShellDescriptor());
-			}
-		}
-		return map;
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/aq/ng/EDescriptor.java

@@ -1,52 +0,0 @@
-/**
- * 
- * 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.aq.ng;
-
-import java.util.List;
-import java.util.Map;
-
-import javax.xml.bind.annotation.XmlRootElement;
-
-import org.codehaus.jackson.map.annotate.JsonSerialize;
-import org.codehaus.jackson.map.annotate.JsonSerialize.Inclusion;
-
-/**
- * Execution descriptor - Describes resources and parameters used to execute a logic
- */
-@XmlRootElement
-@JsonSerialize(include = Inclusion.NON_NULL) // Do not serialize NULL values
-public class EDescriptor {
-
-	private Map<String, RDescriptor> resources;
-	private List<String> parameter;
-	
-	public Map<String, RDescriptor> getResources() {
-		return resources;
-	}
-	public void setResources(Map<String, RDescriptor> resources) {
-		this.resources = resources;
-	}
-	public List<String> getParameter() {
-		return parameter;
-	}
-	public void setParameter(List<String> parameter) {
-		this.parameter = parameter;
-	}
-
-}

ch.psi.fda/src/main/java/ch/psi/fda/aq/ng/LManager.java

@@ -1,58 +0,0 @@
-/**
- * 
- * 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.aq.ng;
-
-import java.util.HashMap;
-import java.util.Map;
-import java.util.Set;
-
-/**
- * Logic Manager
- * Basically a map holding id->logic pairs
- * 
- * also holds default resource profiles for logics (rprofiles)
- */
-public class LManager {
-	private final Map<String, String> logics = new HashMap<>();
-	
-	/** Default resourses assigned to a logic */
-	private final Map<String, Map<String, RDescriptor>> resources = new HashMap<>();
-	
-	public void addLogic(String id, String logic){
-		logics.put(id, logic);
-		resources.put(id, new HashMap<String,RDescriptor>()); // No default resources attached to logic
-	}
-	
-	public void addResources(String id, Map<String, RDescriptor> lresources){
-		resources.put(id, lresources);
-	}
-	
-	public String getLogic(String id){
-		return logics.get(id);
-	}
-	
-	public Set<String> getLogics(){
-		return logics.keySet();
-	}
-	
-	public Map<String, RDescriptor> getResources(String id){
-		return resources.get(id);
-	}
-
-}

ch.psi.fda/src/main/java/ch/psi/fda/aq/ng/NGServer.java

@@ -1,119 +0,0 @@
-/**
- * 
- * 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.aq.ng;
-
-import java.net.InetAddress;
-import java.net.URI;
-import java.net.UnknownHostException;
-import java.util.concurrent.CountDownLatch;
-import java.util.logging.Logger;
-
-import javax.ws.rs.core.UriBuilder;
-import javax.ws.rs.core.UriBuilderException;
-
-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 org.glassfish.grizzly.http.server.HttpServer;
-import org.glassfish.grizzly.http.server.StaticHttpHandler;
-import org.glassfish.jersey.grizzly2.httpserver.GrizzlyHttpServerFactory;
-import org.glassfish.jersey.jackson.JacksonFeature;
-import org.glassfish.jersey.media.sse.SseFeature;
-import org.glassfish.jersey.server.ResourceConfig;
-
-import sun.misc.Signal;
-import sun.misc.SignalHandler;
-
-/**
- * @author ebner
- * 
- */
-@SuppressWarnings("restriction")
-public class NGServer {
-
-	private static final Logger logger = Logger.getLogger(NGServer.class.getName());
-
-	/**
-	 * @param args
-	 * @throws ParseException 
-	 * @throws UnknownHostException 
-	 * @throws UriBuilderException 
-	 * @throws IllegalArgumentException 
-	 */
-	public static void main(String[] args) throws ParseException, IllegalArgumentException, UriBuilderException, UnknownHostException {
-		// Option handling
-		int port = 8080;
-
-		Options options = new Options();
-		options.addOption("h", false, "Help");
-		options.addOption("p", true, "Server port (default: " + port + ")");
-
-		GnuParser parser = new GnuParser();
-		CommandLine line = parser.parse(options, args);
-
-		if (line.hasOption("p")) {
-			port = Integer.parseInt(line.getOptionValue("p"));
-		}
-		if (line.hasOption("h")) {
-			HelpFormatter f = new HelpFormatter();
-			f.printHelp("dae", options); // definition dae - http://www.urbandictionary.com/define.php?term=dae
-			return;
-		}
-
-		URI baseUri = UriBuilder.fromUri("http://" + InetAddress.getLocalHost().getHostName() + "/").port(port).build();
-
-		// final ResourceConfig resourceConfig = new
-		// ResourceConfig(ServerSentEventsResource.class, SseFeature.class);
-		ResourceConfig resourceConfig = new ResourceConfig(SseFeature.class, JacksonFeature.class);
-		resourceConfig.packages(AcquisitionEngineNGResource.class.getPackage().getName());
-		resourceConfig.register(new ResourceBinder());
-		HttpServer server = GrizzlyHttpServerFactory.createHttpServer(baseUri, resourceConfig);
-
-		// Static content
-		String home = System.getenv("DAE_BASE");
-		if (home == null) {
-			home = "src/main/assembly";
-		}
-		home = home + "/www";
-		server.getServerConfiguration().addHttpHandler(new StaticHttpHandler(home), "/static");
-
-		logger.info("dae started");
-		logger.info(String.format("Management interface available at %sstatic/", baseUri));
-		logger.info("Use ctrl+c to stop ...");
-
-		// Signal handling
-		final CountDownLatch latch = new CountDownLatch(1);
-		Signal.handle(new Signal("INT"), new SignalHandler() {
-			public void handle(Signal sig) {
-				latch.countDown();
-			}
-		});
-
-		// Wait for termination, i.e. wait for ctrl+c
-		try {
-			latch.await();
-		} catch (InterruptedException e) {
-		}
-
-		server.stop();
-	}
-
-}

ch.psi.fda/src/main/java/ch/psi/fda/aq/ng/RDescriptor.java

@@ -1,58 +0,0 @@
-/**
- * 
- * 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.aq.ng;
-
-import java.util.Map;
-
-import javax.xml.bind.annotation.XmlRootElement;
-
-import org.codehaus.jackson.map.annotate.JsonSerialize;
-import org.codehaus.jackson.map.annotate.JsonSerialize.Inclusion;
-
-/**
- * Resource descriptor - Used to identify and/or create resource on server
- */
-@XmlRootElement
-@JsonSerialize(include = Inclusion.NON_NULL) // Do not serialize NULL values
-public class RDescriptor {
-	
-	private String ref;
-	private String type;
-	private Map<String,String> parameter;
-	
-	public String getRef() {
-		return ref;
-	}
-	public void setRef(String ref) {
-		this.ref = ref;
-	}
-	public String getType() {
-		return type;
-	}
-	public void setType(String type) {
-		this.type = type;
-	}
-	public Map<String, String> getParameter() {
-		return parameter;
-	}
-	public void setParameter(Map<String, String> parameter) {
-		this.parameter = parameter;
-	}
-	
-}

ch.psi.fda/src/main/java/ch/psi/fda/aq/ng/ResourceBinder.java

@@ -1,31 +0,0 @@
-package ch.psi.fda.aq.ng;
-
-import org.glassfish.hk2.utilities.binding.AbstractBinder;
-//import org.glassfish.jersey.media.sse.SseBroadcaster;
-
-//import ch.psi.da.hub.model.Keystore;
-import ch.psi.jcae.impl.DefaultChannelService;
-
-public class ResourceBinder extends AbstractBinder {
-
-    @Override
-    protected void configure() {
-        // request scope binding
-//        bind(MyInjectablePerRequest.class).to(MyInjectablePerRequest.class).in(RequestScope.class);
-        // singleton binding
-//        bind(MyInjectableSingleton.class).in(Singleton.class);
-        // singleton instance binding
-    	
-//    	KeystoreSerializer serializer = new KeystoreSerializer();
-//    	Keystore keystore = serializer.deserialize();
-    	
-//        bind(new SseBroadcaster()).to(SseBroadcaster.class);
-//        bind(serializer).to(KeystoreSerializer.class);
-//        bind(new KeystoreBroadcaster()).to(KeystoreBroadcaster.class);
-//        bind(keystore).to(Keystore.class);
-    	
-    	bind(new AcquisitionEngineNG(new DefaultChannelService())).to(AcquisitionEngineNG.class);
-    	bind(new LManager()).to(LManager.class);
-    }
-
-}

ch.psi.fda/src/main/java/ch/psi/fda/aq/ng/ScanMapperNG.java

@@ -1,405 +0,0 @@
-/**
- * 
- * 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.aq.ng;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.UUID;
-import java.util.logging.Logger;
-
-import ch.psi.fda.aq.ng.rdescriptors.ProbeDescriptor;
-import ch.psi.fda.aq.ng.rdescriptors.ShellDescriptor;
-import ch.psi.fda.core.messages.ComponentMetadata;
-import ch.psi.fda.core.messages.DataMessageMetadata;
-import ch.psi.fda.model.v1.Action;
-import ch.psi.fda.model.v1.ArrayPositioner;
-import ch.psi.fda.model.v1.ChannelAction;
-import ch.psi.fda.model.v1.Configuration;
-import ch.psi.fda.model.v1.ContinuousDimension;
-import ch.psi.fda.model.v1.Dimension;
-import ch.psi.fda.model.v1.DiscreteStepDimension;
-import ch.psi.fda.model.v1.DiscreteStepPositioner;
-import ch.psi.fda.model.v1.FunctionPositioner;
-import ch.psi.fda.model.v1.LinearPositioner;
-import ch.psi.fda.model.v1.PseudoPositioner;
-import ch.psi.fda.model.v1.RegionPositioner;
-import ch.psi.fda.model.v1.Scan;
-import ch.psi.fda.model.v1.ScriptAction;
-import ch.psi.fda.model.v1.ShellAction;
-import ch.psi.jcae.ChannelDescriptor;
-import ch.psi.jcae.util.ComparatorAND;
-import ch.psi.jcae.util.ComparatorOR;
-import ch.psi.jcae.util.ComparatorREGEX;
-
-/**
- * Mapper to transform a FDA v1 xml into the new internal model
- * 
- */
-public class ScanMapperNG {
-	
-	// Reserved resource id's
-	private static final String PROBE_RESOURCE_ID = "probe";
-	private static final String SHELL_RESOURCE_ID = "shell";
-	// "logger" is also a special variable as it is bound to the logger of the application!
-	
-	private static final Logger logger = Logger.getLogger(ScanMapperNG.class.getName());
-
-	private static final String INDENT = "    ";
-
-	private StringBuilder script = new StringBuilder();
-	private Set<String> imports = new HashSet<>();
-	private Map<String, Object> resourceDescriptors = new HashMap<>();
-
-	private ProbeDescriptor probeDescriptor = new ProbeDescriptor();
-	private DataMessageMetadata dataMessageMetadata = new DataMessageMetadata();
-	
-	
-	private String indentation = "";
-
-	public void map(Configuration configuration) {
-		
-		// Clear object state
-		script = new StringBuilder();
-		imports = new HashSet<>();
-		resourceDescriptors = new HashMap<>();
-		probeDescriptor = new ProbeDescriptor();
-		
-		resourceDescriptors.put(PROBE_RESOURCE_ID, probeDescriptor);
-
-		Scan scan = configuration.getScan();
-		mapActions(scan.getPreAction());
-
-		// Bring the dimensions into the correct order and then map them
-		// to the script
-		List<Dimension> dimensions = new ArrayList<>();
-		int size = scan.getDimension().size();
-		for (int i = size - 1; i >= 0; i--) {
-			dimensions.add(scan.getDimension().get(i));
-		}
-		// Continuous dimensions are always at the very end
-		if (scan.getCdimension() != null) {
-			dimensions.add(scan.getCdimension());
-		}
-		mapDimensions(dimensions, 0);
-
-		// map
-		mapActions(scan.getPostAction());
-
-		// TODO CONSIDER TO PROVIDE RESOURCE MAP AND SCRIPT IN ONE OBJECT AS
-		// RETURN TYPE
-		// WOULD MAKE MORE SENSE
-	}
-
-	/**
-	 * Get the generated script
-	 * 
-	 * @return
-	 */
-	public String getScript() {
-		StringBuilder scriptlines = new StringBuilder();
-		for (String s : imports) {
-			scriptlines.append(s + "\n");
-		}
-		scriptlines.append(script);
-		return scriptlines.toString();
-	}
-	
-	/**
-	 * Get map of required resources
-	 * @return
-	 */
-	public Map<String, Object> getResourceDescriptors(){
-		return resourceDescriptors;
-	}
-
-	/**
-	 * TODO need to be moved somewhere else
-	 * @return
-	 */
-	public DataMessageMetadata getDataMessageMetadata(){
-		return dataMessageMetadata;
-	}
-	
-	private void mapDimensions(List<Dimension> dimensions, int index) {
-		
-		if(dimensions.size()<1){
-			logger.info("There are no dimensions to map");
-			return;
-		}
-		
-		Dimension dimension = dimensions.get(index);
-		if (dimension instanceof DiscreteStepDimension) {
-			DiscreteStepDimension d = (DiscreteStepDimension) dimension;
-
-			mapActions(d.getPreAction());
-			
-			List<String> actuators = new ArrayList<>();
-			
-			for(DiscreteStepPositioner positioner: d.getPositioner()){
-				Class<?> type = String.class;
-				switch (positioner.getType()) {
-				case "Integer":
-					type = Integer.class;
-					break;
-				case "Double":
-					type = Double.class;
-					break;
-				}
-				
-				String var = getChannelResourceVariable(positioner.getName(), type, false);
-				actuators.add(var);
-				
-				// Readback
-				if(positioner.getReadback()==null){
-					probeDescriptor.getSensors().add(new ChannelDescriptor<>(type, positioner.getName(), false));
-				}
-				else{
-					// Use readback
-					probeDescriptor.getSensors().add(new ChannelDescriptor<>(type, positioner.getReadback(), false));
-				}
-//				System.out.println(positioner.getId());
-				dataMessageMetadata.getComponents().add(new ComponentMetadata(positioner.getId(), (dimensions.size()-1-index)));
-				
-				// TODO Done resource
-				
-				
-				if(positioner instanceof LinearPositioner){
-					// Calculate steps and add it to position array
-					LinearPositioner lpositioner = (LinearPositioner) positioner;
-					boolean first = true;
-					StringBuffer b = new StringBuffer();
-					b.append("[");
-					for(double i=0;(lpositioner.getStart()+i*lpositioner.getStepSize())<=lpositioner.getEnd();i++){
-						if(first){
-							first=false;
-						}
-						else{
-							b.append(",");
-						}
-						b.append(String.format("%f", (lpositioner.getStart()+i*lpositioner.getStepSize())));
-					}
-					b.append("]");
-					script.append(indentation + var+"_positions="+b.toString()+"\n");
-				}
-				else if(positioner instanceof ArrayPositioner){
-					ArrayPositioner apositioner = (ArrayPositioner) positioner;
-					// Calculate positions
-					String[] positions = apositioner.getPositions().trim().split(" +");
-					boolean first = true;
-					StringBuffer b = new StringBuffer();
-					b.append("[");
-					for(String po: positions){
-						if(first){
-							first=false;
-						}
-						else{
-							b.append(",");
-						}
-						
-						b.append(getPythonValue(po, type));
-					}
-					b.append("]");
-					script.append(indentation + var+"_positions="+b.toString()+"\n");
-				}
-				else if(positioner instanceof FunctionPositioner){
-					// TODO take variable mappings into account !
-				}
-				else if(positioner instanceof PseudoPositioner){
-					// TODO implement
-				}
-				else if(positioner instanceof RegionPositioner){
-					// TODO implement
-				}
-			}
-			
-			// Create dimension loop
-			String v = getUniqueVariableName();
-			script.append(indentation + "for "+v+"_idx ,"+v+"_pos in enumerate("+actuators.get(0)+"_positions):\n");
-			indentation = indentation + INDENT;
-			
-			// Set all actuators of this dimension
-			for(String a: actuators){
-				script.append(indentation + a+".setValue("+a+"_positions["+v+"_idx])\n");
-			}
-			
-			// Add all actions executed between actuator and sensors
-			mapActions(d.getAction());
-
-			// TODO map guard and sensors
-			
-
-			// Check whether final dimension reached
-			if ((index + 1) < dimensions.size()) {
-				// Map next dimension
-				mapDimensions(dimensions, (index + 1));
-			}
-			else{
-				// Final dimension reached - readout probe
-				script.append(indentation + PROBE_RESOURCE_ID+".read()\n");
-			}
-
-			indentation = indentation.replaceFirst(INDENT, ""); // decrease indentation
-			
-			
-			script.append(indentation + PROBE_RESOURCE_ID+".delimiter("+(dimensions.size()-1-index)+", "+(d.isDataGroup()?"True":"False")+")\n");
-			// send delimiter for this dimension 
-			// if lowest dimension end of stream message
-			// if highest dimension no delimiter
-			if(index==0){
-				script.append(indentation + PROBE_RESOURCE_ID+".terminateStream()\n");
-			}
-			
-			mapActions(d.getPostAction());
-		} else if (dimension instanceof ContinuousDimension) {
-			// ContinuousDimension d = (ContinuousDimension) dimension;
-			// TODO Map continuous dimension
-		}
-
-	}
-
-	private void mapActions(List<Action> actions) {
-		for (Action action : actions) {
-			if (action instanceof ChannelAction) {
-				ChannelAction ca = (ChannelAction) action;
-				Class<?> type = String.class;
-				long waitTimeout=1800000; // Max wait timeout is 30 minutes
-				if(ca.getTimeout()!=null){
-					waitTimeout = ca.getTimeout().longValue()*1000; // wait timeout is currently in seconds
-				}
-				ca.getTimeout();
-				switch (ca.getType()) {
-				case "Integer":
-					type = Integer.class;
-					break;
-				case "Double":
-					type = Double.class;
-					break;
-				}
-				String var = getChannelResourceVariable(ca.getChannel(), type, false);
-				switch (ca.getOperation()) {
-				case "put":
-					if(ca.getTimeout()==null){
-						script.append(var+".setValue("+getPythonValue(ca.getValue(), type)+")\n");
-					} else {
-						imports.add("from java.util.concurrent import TimeUnit");
-						script.append(var+".setValueAsync("+getPythonValue(ca.getValue(), type)+").get("+ca.getTimeout()+", TimeUnit.MILLISECONDS)\n");
-					}
-					break;
-				case "putq":
-					script.append(var+".setValueNoWait("+getPythonValue(ca.getValue(), type)+")\n");
-					break;
-				case "wait":
-					script.append(var+".waitForValue("+getPythonValue(ca.getValue(), type)+", "+waitTimeout+")\n");
-					break;
-				case "waitREGEX":
-					imports.add("from"+ComparatorREGEX.class.getPackage().getName()+" import "+ComparatorREGEX.class.getName());
-					script.append(var+".waitForValue("+getPythonValue(ca.getValue(), type)+", "+ComparatorREGEX.class.getName()+"() "+waitTimeout+")\n");
-					break;
-				case "waitOR":
-					imports.add("from"+ComparatorOR.class.getPackage().getName()+" import "+ComparatorOR.class.getName());
-					script.append(var+".waitForValue("+getPythonValue(ca.getValue(), type)+", "+ComparatorOR.class.getName()+"() "+waitTimeout+")\n");
-					break;
-				case "waitAND":
-					imports.add("from"+ComparatorAND.class.getPackage().getName()+" import "+ComparatorAND.class.getName());
-					script.append(var+".waitForValue("+getPythonValue(ca.getValue(), type)+", "+ComparatorAND.class.getName()+"() "+waitTimeout+")\n");
-					break;
-				default:
-					logger.warning("Operation - "+ca.getOperation()+" - is not supported");
-					// TODO Eventually throw exception - have two modes one logging, one exception?
-					break;
-				}
-
-				// If delay is specified wait specified time
-				if (ca.getDelay() != null) {
-					imports.add("import time");
-					script.append("time.sleep(" + (ca.getDelay()) + ")\n");
-				}
-
-			} else if (action instanceof ShellAction) {
-				ShellAction saction = (ShellAction) action;
-				resourceDescriptors.put(SHELL_RESOURCE_ID, new ShellDescriptor());
-				// TODO Need to indicate that shell resource is required
-				script.append(indentation + String.format(SHELL_RESOURCE_ID+".execute('%s', %d, %s)\n", saction.getCommand(), saction.getExitValue(), saction.isCheckExitValue()?"True":"False"));
-			} else if (action instanceof ScriptAction) {
-				ScriptAction saction = (ScriptAction) action;
-
-				// TODO Need to indicate that that mapped resources are required
-				// Read script line by line and prepend the current indentation
-				// level
-				String[] lines = saction.getScript().split(System.getProperty("line.separator"));
-				for (String s : lines) {
-					script.append(indentation + s+"\n");
-				}
-				script.append(indentation + "\n");
-			}
-		}
-	}
-
-	/**
-	 * Get unique variable names that do not collide with others. (at least have
-	 * an extreme unlikeness to do so)
-	 * 
-	 * @return
-	 */
-	private String getUniqueVariableName() {
-		return "v" + UUID.randomUUID().toString().replaceAll("-", "");
-	}
-	
-	/**
-	 * Get the string representation for a variable in python
-	 * i.e. surrounds String with '', ensures that double has a . in the value, ...
-	 * @param value
-	 * @param type
-	 * @return
-	 */
-	private String getPythonValue(String value, Class<?> type){
-		if(type.equals(String.class)){
-			return "'"+value+"'";
-		}
-		else if(type.equals(Double.class)){
-			return String.format("%f", new Double(value));
-		}
-		else if(type.equals(Integer.class)){
-			return String.format("%d", new Integer(value));
-		}
-		return value.toString();
-	}
-
-	/**
-	 * Request resource
-	 * 
-	 * @param resourceId
-	 * @return variable name for resource
-	 * 
-	 *         TODO Eventually we need to add type of resource here to be able
-	 *         to generate the resource before the script is executed.
-	 */
-	private String getChannelResourceVariable(String channelName, Class<?> type, boolean monitor) {
-		// Right now each a new channel object will be created for each requirested channel resource (even it is the same channel)
-		// TODO Optimize the resource consumption by checking whether the resource already exists and return only one reference.
-		String varname = getUniqueVariableName();
-		resourceDescriptors.put(varname, new ChannelDescriptor<>(type, channelName, monitor));
-		return varname;
-	}
-
-}

ch.psi.fda/src/main/java/ch/psi/fda/aq/ng/rdescriptors/ProbeDescriptor.java

@@ -1,38 +0,0 @@
-/**
- * 
- * 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.aq.ng.rdescriptors;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import ch.psi.jcae.ChannelDescriptor;
-
-/**
- * @author ebner
- *
- */
-public class ProbeDescriptor {
-	
-	private List<ChannelDescriptor<?>> sensors = new ArrayList<>();
-	
-	public List<ChannelDescriptor<?>> getSensors(){
-		return sensors;
-	}
-
-}

ch.psi.fda/src/main/java/ch/psi/fda/aq/ng/rdescriptors/ShellDescriptor.java

@@ -1,28 +0,0 @@
-/**
- * 
- * 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.aq.ng.rdescriptors;
-
-/**
- * Resource descriptor of an operating system shell.
- * @author ebner
- *
- */
-public class ShellDescriptor {
-
-}

ch.psi.fda/src/main/java/ch/psi/fda/aq/ng/resources/ChannelProbeResource.java

@@ -1,94 +0,0 @@
-/**
- * 
- * 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.aq.ng.resources;
-
-import java.util.List;
-import java.util.concurrent.BlockingQueue;
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.TimeoutException;
-
-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.StreamDelimiterMessage;
-import ch.psi.jcae.Channel;
-import ch.psi.jcae.ChannelException;
-
-/**
- * @author ebner
- *
- */
-public class ChannelProbeResource {
-	
-	private final List<Channel<?>> channels;
-	private BlockingQueue<Message> queue;
-
-	public ChannelProbeResource(List<Channel<?>> channels, BlockingQueue<Message> queue){
-		this.channels = channels;
-		this.queue = queue;
-	}
-	
-	/**
-	 * Read configured channels and send out data message
-	 */
-	public void read(){
-		try{
-		DataMessage message = new DataMessage();
-			for(Channel<?> sensor: channels){
-				// Readout sensor
-				Object o = sensor.getValue();
-				// Add sensor data item to message
-				message.getData().add(o);
-			}
-			System.out.println("MESSAGE: "+message);
-			queue.put(message);
-		} catch (InterruptedException | TimeoutException | ChannelException | ExecutionException e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	/**
-	 * Send a stream delimiter message for the given index
-	 * @param index
-	 * @param iflag
-	 */
-	public void delimiter(int index, boolean iflag){
-		try {
-			StreamDelimiterMessage message = new StreamDelimiterMessage(index, iflag);
-			System.out.println(message);
-			queue.put(message);
-		} catch (InterruptedException e) {
-			throw new RuntimeException("Unable to send delimiter message", e);
-		}
-	}
-	
-	/**
-	 * Send end of stream message
-	 */
-	public void terminateStream(){
-		try {
-			EndOfStreamMessage message = new EndOfStreamMessage();
-			System.out.println(message);
-			queue.put(message);
-		} catch (InterruptedException e) {
-			throw new RuntimeException("Unable to send end of stream message", e);
-		}
-	}
-
-}

ch.psi.fda/src/main/java/ch/psi/fda/aq/ng/resources/ShellResource.java

@@ -1,73 +0,0 @@
-/**
- * 
- * 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.aq.ng.resources;
-
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.util.logging.Logger;
-
-/**
- * @author ebner
- *
- */
-public class ShellResource {
-	
-	private static final Logger logger = Logger.getLogger(ShellResource.class.getName());
-
-	/**
-	 * Execute script/command in shell
-	 * @param script
-	 */
-	public void execute(String script){
-		execute(script, 0, true);
-	}
-	
-	/**
-	 * Execute script/command in shell
-	 * @param script
-	 * @param returnValue
-	 * @param checkReturnValue
-	 */
-	public void execute(String script, int returnValue, boolean checkReturnValue){
-		ProcessBuilder pb = new ProcessBuilder(new String[]{"/bin/bash","-c",script});
-		pb.redirectErrorStream(true);
-
-		try {
-			Process p = pb.start();
-			int rvalue = p.waitFor();
-			
-			BufferedReader reader = new BufferedReader(new InputStreamReader(p.getInputStream()));
-			String line = null;
-			while((line=reader.readLine()) != null){
-				logger.info(line);
-			}
-			
-			// Check return value if need to be checked
-			if(checkReturnValue){
-				if(rvalue != returnValue){
-					throw new RuntimeException("Executing script "+script+" failed");
-				}
-			}
-		} catch (IOException | InterruptedException e) {
-			throw new RuntimeException("Unable to execute script", e);
-		}
-	}
-	
-}

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

@@ -1,46 +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;
-
-/**
- * @author ebner
- *
- */
-public interface Action {
-	
-	/**
-	 * Execute logic of the action
-	 */
-	public void execute() throws InterruptedException;
-	
-	/**
-	 * Abort the execution logic of the action
-	 */
-	public void abort();
-	
-	/**
-	 * Destroy action. 
-	 * Can be used for the cleanup of used resources of the action (e.g. to close connections, ...) if
-	 * this cannot be done automatically by the GarbageCollector.
-	 * 
-	 * After calling this method the action must not be executed any more!
-	 */
-	public void destroy();
-}

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

@@ -1,69 +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;
-
-import java.util.List;
-
-import ch.psi.fda.core.messages.DataQueue;
-
-/**
- * Loop of actions to accomplish a task. Depending on the loop
- * actions may be executed in a different way.
- * 
- * @author ebner
- *
- */
-public interface ActionLoop extends Action {
-	
-	/**
-	 * Prepare ActionLoop for execution.
-	 */
-	public void prepare();
-	
-	/**
-	 * Cleanup resources used by this ActionLoop while it was executed.
-	 */
-	public void cleanup();
-	
-	/**
-	 * Get the pre actions of the Loop
-	 * @return	pre actions
-	 */
-	public List<Action> getPreActions();
-	
-	/**
-	 * Get the post actions of the loop
-	 * @return post actions
-	 */
-	public List<Action> getPostActions();
-	
-	/**
-	 * @return is a datagroup
-	 */
-	public boolean isDataGroup();
-
-	/**
-	 * Set whether data of the loop belongs to a own data group
-	 * @param dataGroup
-	 */
-	public void setDataGroup(boolean dataGroup);
-	
-	public DataQueue getDataQueue();
-}

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

@@ -1,64 +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;
-
-/**
- * 
- * @author ebner
- *
- */
-public interface Actor {
-	/**
-	 * Set actor value
-	 */
-	public void set() throws InterruptedException;
-	
-	/**
-	 * Function to check whether the actor has a next set value
-	 * @return  Returns true if there is an actor value for the next iteration.
-	 * 			False if there is no actor value (i.e. this will be the last iteration in the ActionLoop)
-	 */
-	public boolean hasNext();
-	
-	/**
-	 * Initialize the actor to the start
-	 */
-	public void init();
-	
-	/**
-	 * Reverse the set values of the actor
-	 */
-	public void reverse();
-	
-	/**
-	 * Reset the actuator to its initial configuration
-	 */
-	public void reset();
-	
-	
-	/**
-	 * Destroy action. 
-	 * Can be used for the cleanup of used resources of the actor (e.g. to close connections, ...) if
-	 * this cannot be done automatically by the GarbageCollector.
-	 * 
-	 * After calling this method the actor must not be used any more!
-	 */
-	public void destroy();
-}

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

@@ -1,47 +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;
-
-import java.util.concurrent.Callable;
-
-/**
- * Callable used for parallel execution of the set method of an actor
- * @author ebner
- *
- */
-public class ActorSetCallable implements Callable<Object> {
-
-	// Callable actor
-	private Actor actor;
-	
-	public ActorSetCallable(Actor actor){
-		this.actor = actor;
-	}
-	
-	/* (non-Javadoc)
-	 * @see java.util.concurrent.Callable#call()
-	 */
-	@Override
-	public Object call() throws Exception {
-		actor.set();
-		return null;
-	}
-
-}

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

@@ -1,87 +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;
-
-/**
- * Singleton object for holing the core engine configuration
- * 
- * @author ebner
- */
-public class EngineConfiguration {
-
-	/**
-	 * Flag to indicate whether the engine should fail if there is an error while reading out a sensor.
-	 */
-	private boolean failOnSensorError = true;
-	
-	/**
-	 * Flag to indicate whether the set value of the actor should be verified after the set operation.
-	 * Having this flag on true will enable detecting for example that a motor hit the end switch or
-	 * did not move correctly.
-	 */
-	private boolean checkActorSet = true;
-	
-	/**
-	 * Singleton instance
-	 */
-	private final static EngineConfiguration instance = new EngineConfiguration(); 
-
-	
-	
-	private EngineConfiguration(){
-	}
-	
-	/**
-	 * Get singleton instance of this class
-	 * @return Engine configuration
-	 */
-	public static EngineConfiguration getInstance(){
-		return instance;
-	}
-
-	/**
-	 * @return the failOnSensorError
-	 */
-	public boolean isFailOnSensorError() {
-		return failOnSensorError;
-	}
-
-	/**
-	 * @param failOnSensorError the failOnSensorError to set
-	 */
-	public void setFailOnSensorError(boolean failOnSensorError) {
-		this.failOnSensorError = failOnSensorError;
-	}
-
-	/**
-	 * @return the checkActorSet
-	 */
-	public boolean isCheckActorSet() {
-		return checkActorSet;
-	}
-
-	/**
-	 * @param checkActorSet the checkActorSet to set
-	 */
-	public void setCheckActorSet(boolean checkActorSet) {
-		this.checkActorSet = checkActorSet;
-	}
-	
-}

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

@@ -1,53 +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;
-
-/**
- * Guard to protect specific activities. A guard can be used to check for environment changes while a
- * certain activity was executed. 
- * 
- * Example:
- * An Guard can be used to check whether an injection happened while the the detector were read. 
- * 
- * @author ebner
- *
- */
-public interface Guard {
-	
-	/**
-	 * Initialize guard object and its internal state.
-	 */
-	public void init();
-	
-	/**
-	 * Check the status of the guard.
-	 * @return	Returns true if the guard condition was not constrainted since the last init call. False otherwise.
-	 */
-	public boolean check();
-	
-	/**
-	 * Destroy guard. 
-	 * Can be used for the cleanup of used resources of the guard (e.g. to close connections, ...) if
-	 * this cannot be done automatically by the GarbageCollector.
-	 * 
-	 * After calling this method the guard must not be used any more!
-	 */
-	public void destroy();
-}

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

@@ -1,50 +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;
-
-/**
- * The sensor interface describes an entity that can be read out like a
- * simple channel or (image) detector. Depending on the sensor type the
- * returned data is of a certain type.
- * @author ebner
- *
- */
-public interface Sensor {
-	/**
-	 * Readout sensor. 
-	 * @return	Sensor value. The type of the returned value depends on the sensor type.
-	 */
-	public Object read() throws InterruptedException;
-	
-	/**
-	 * Get the global id of the sensor
-	 * @return	id of sensor
-	 */
-	public String getId();
-	
-	/**
-	 * Destroy sensor. 
-	 * Can be used for the cleanup of used resources of the sensor (e.g. to close connections, ...) if
-	 * this cannot be done automatically by the GarbageCollector.
-	 * 
-	 * After calling this method the sensor must not be used any more!
-	 */
-	public void destroy();
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/actions/ChannelAccessCondition.java

@@ -1,163 +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.actions;
-
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.TimeUnit;
-import java.util.concurrent.TimeoutException;
-import java.util.logging.Logger;
-
-import ch.psi.fda.core.Action;
-import ch.psi.jcae.Channel;
-import ch.psi.jcae.ChannelDescriptor;
-import ch.psi.jcae.ChannelException;
-import ch.psi.jcae.ChannelService;
-
-/**
- * Perform a put on the specified Channel Access channel. The put can be done
- * synchronous or asynchronously.
- * 
- * @author ebner
- * 
- */
-public class ChannelAccessCondition<E> implements Action {
-
-	// Get Logger
-	private static Logger logger = Logger.getLogger(ChannelAccessCondition.class.getName());
-
-	/**
-	 * Channel to set
-	 */
-	private final Channel<E> channel;
-	/**
-	 * Value to wait for
-	 */
-	private final E expectedValue;
-
-	private  Long timeout;
-
-	private volatile boolean abort = false;
-	private volatile Thread waitT = null;
-
-	/**
-	 * Constructor
-	 * 
-	 * @param channelName
-	 *            Name of the channel to set the value
-	 * @param expectedValue
-	 *            Value to wait for
-	 * @param timeout
-	 *            Timeout of the condition in milliseconds (null accepted - will
-	 *            take default wait timeout for channels
-	 *            ch.psi.jcae.ChannelBeanFactory.waitTimeout)
-	 * 
-	 * @throws IllegalArgumentException
-	 *             Unable to initialize channel, Timeout specified is not >=0
-	 */
-	@SuppressWarnings("unchecked")
-	public ChannelAccessCondition(ChannelService s, String channelName, E expectedValue, Long timeout) {
-
-		if (timeout != null && timeout <= 0) {
-			throw new IllegalArgumentException("Timeout must be > 0");
-		}
-
-		try {
-			this.channel = (Channel<E>) s.createChannel(new ChannelDescriptor<>(expectedValue.getClass(), channelName, false));
-		} catch (ChannelException | TimeoutException e) {
-			throw new IllegalArgumentException("Unable to initialize actuator channel [name:" + channelName + "]", e);
-		} catch (InterruptedException e) {
-			throw new RuntimeException("Unable to initialize actuator channel [name:" + channelName + "]", e);
-		}
-
-		this.expectedValue = expectedValue;
-
-		if (timeout == null) {
-			// this.timeout = channel.get.getWaitTimeout();
-			this.timeout=1L;
-		} else {
-			this.timeout = timeout;
-		}
-	}
-
-	/*
-	 * (non-Javadoc)
-	 * 
-	 * @see ch.psi.fda.core.Action#execute()
-	 */
-	/**
-	 * @throws InterruptedException
-	 * @throws RuntimeException
-	 *             Channel value did not reach expected value (within the
-	 *             specified timeout period)
-	 */
-	@Override
-	public void execute() throws InterruptedException {
-		abort = false;
-		logger.finest("Checking channel " + channel.getName() + " for value " + expectedValue + " [timeout: " + timeout + "]");
-		try {
-			waitT = Thread.currentThread();
-			channel.waitForValueAsync(expectedValue).get(timeout, TimeUnit.MILLISECONDS); // Workaround use
-															// 10seconds default
-															// set timeout to
-															// check several
-															// times whether the
-															// channel has
-															// reached the value
-		} catch (InterruptedException e) {
-			if (!abort) {
-				throw e;
-			}
-		} catch (ExecutionException | TimeoutException | ChannelException e) {
-			throw new RuntimeException("Channel [name:" + channel.getName() + "] did not reach expected value " + expectedValue + " ", e);
-		} finally {
-			waitT = null;
-		}
-	}
-
-	/*
-	 * (non-Javadoc)
-	 * 
-	 * @see ch.psi.fda.core.Action#abort()
-	 */
-	@Override
-	public void abort() {
-		abort = true;
-		if (waitT != null) {
-			waitT.interrupt();
-		}
-	}
-
-	/*
-	 * (non-Javadoc)
-	 * 
-	 * @see ch.psi.fda.core.Action#destroy()
-	 */
-	@Override
-	public void destroy() {
-		// Destroy channel
-			logger.finest("Destroy action channel: " + channel.getName());
-			try {
-				channel.destroy();
-			} catch (ChannelException e) {
-				throw new RuntimeException("Unable to destroy channel [" + channel.getName() + "]", e);
-			}
-	}
-
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/actions/ChannelAccessConditionAnd.java

@@ -1,159 +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.actions;
-
-import java.util.Comparator;
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.TimeoutException;
-import java.util.logging.Logger;
-
-import ch.psi.fda.core.Action;
-import ch.psi.jcae.Channel;
-import ch.psi.jcae.ChannelDescriptor;
-import ch.psi.jcae.ChannelException;
-import ch.psi.jcae.ChannelService;
-
-/**
- * Perform a put on the specified Channel Access channel. The put can be done synchronous or
- * asynchronously.
- * @author ebner
- *
- */
-public class ChannelAccessConditionAnd<E extends Integer> implements Action {
-
-	// Get Logger
-	private static Logger logger = Logger.getLogger(ChannelAccessConditionAnd.class.getName());
-	
-	/**
-	 * Channel to set
-	 */
-	private final Channel<E> channel;
-	/**
-	 * Value to wait for
-	 */
-	private final E expectedValue;
-	
-	private final Long timeout;
-	
-	private volatile boolean abort = false;
-	private volatile Thread waitT = null;
-	
-	/**
-	 * Constructor
-	 * @param channelName		Name of the channel to set the value
-	 * @param expectedValue		Value to wait for
-	 * @param timeout			Timeout of the condition in milliseconds (null accepted - will take default wait timeout for channels ch.psi.jcae.ChannelBeanFactory.waitTimeout)
-	 * 
-	 * @throws	IllegalArgumentException	Unable to initialize channel,
-	 * 										Timeout specified is not >=0
-	 */
-	@SuppressWarnings("unchecked")
-	public ChannelAccessConditionAnd(ChannelService s, String channelName, E expectedValue, Long timeout){
-
-		if(timeout !=null && timeout<=0){
-			throw new IllegalArgumentException("Timeout must be > 0");
-		}
-		
-		try {
-			this.channel = s.createChannel(new ChannelDescriptor<>( (Class<E>) expectedValue.getClass(), channelName, false));
-		} catch (ChannelException | TimeoutException e) {
-			// Convert Exception into unchecked RuntimeException
-			throw new IllegalArgumentException("Unable to initialize actuator channel [name:"+channelName+"]",e);
-		} catch (InterruptedException e) {
-			throw new RuntimeException("Unable to initialize actuator channel [name:"+channelName+"]",e);
-		}
-		
-		this.expectedValue = expectedValue;
-		
-		if(timeout==null){
-//			this.timeout = channel.getWaitTimeout();
-			this.timeout = 0L;
-		}
-		else{
-			this.timeout = timeout;
-		}
-	}
-
-	
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#execute()
-	 */
-	/**
-	 * @throws InterruptedException 
-	 * @throws RuntimeException		Channel value did not reach expected value (within the specified timeout period)
-	 */
-	@Override
-	public void execute() throws InterruptedException {
-		abort=false;
-		logger.finest("Checking channel "+channel.getName()+" for value "+expectedValue+" [timeout: "+timeout+"]" );
-		try{
-			waitT = Thread.currentThread();
-			channel.waitForValue(expectedValue, new Comparator<E>() {
-
-				@Override
-				public int compare(E o1, E o2) {
-					int one = o1;
-					int two = o2;
-					if((one & two) != 0){
-						return 0;
-					}
-					return 1;
-				}
-			}
-			, timeout); // Workaround use 10seconds default set timeout to check several times whether the channel has reached the value
-		} catch (ChannelException | ExecutionException e) {
-			throw new RuntimeException("Channel [name:"+channel.getName()+"] did not reach expected value "+expectedValue+" ", e);
-		} catch(InterruptedException e){
-			if(!abort){
-				throw e;
-			}
-		}
-		finally{
-			waitT=null;
-		}
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#abort()
-	 */
-	@Override
-	public void abort() {
-		abort=true;
-		if(waitT!=null){
-			waitT.interrupt();
-		}
-	}
-
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#destroy()
-	 */
-	@Override
-	public void destroy() {
-		// Destroy channel
-		try {
-			logger.finest("Destroy action channel: "+channel.getName());
-			channel.destroy();
-		} catch (ChannelException e) {
-			throw new RuntimeException("Unable to destroy channel ["+channel.getName()+"]",e);
-		}
-	}
-
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/actions/ChannelAccessConditionOr.java

@@ -1,159 +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.actions;
-
-import java.util.Comparator;
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.TimeoutException;
-import java.util.logging.Logger;
-
-import ch.psi.fda.core.Action;
-import ch.psi.jcae.Channel;
-import ch.psi.jcae.ChannelDescriptor;
-import ch.psi.jcae.ChannelException;
-import ch.psi.jcae.ChannelService;
-
-/**
- * Perform a put on the specified Channel Access channel. The put can be done synchronous or
- * asynchronously.
- * @author ebner
- *
- */
-public class ChannelAccessConditionOr<E extends Integer> implements Action {
-
-	// Get Logger
-	private static Logger logger = Logger.getLogger(ChannelAccessConditionOr.class.getName());
-	
-	/**
-	 * Channel to set
-	 */
-	private final Channel<E> channel;
-	/**
-	 * Value to wait for
-	 */
-	private final E expectedValue;
-	
-	private final Long timeout;
-	
-	private volatile boolean abort = false;
-	private volatile Thread waitT = null;
-	
-	/**
-	 * Constructor
-	 * @param channelName		Name of the channel to set the value
-	 * @param expectedValue		Value to wait for
-	 * @param timeout			Timeout of the condition in milliseconds (null accepted - will take default wait timeout for channels ch.psi.jcae.ChannelBeanFactory.waitTimeout)
-	 * 
-	 * @throws	IllegalArgumentException	Unable to initialize channel,
-	 * 										Timeout specified is not >=0
-	 */
-	@SuppressWarnings("unchecked")
-	public ChannelAccessConditionOr(ChannelService s, String channelName, E expectedValue, Long timeout){
-
-		if(timeout !=null && timeout<=0){
-			throw new IllegalArgumentException("Timeout must be > 0");
-		}
-		
-		try {
-			this.channel = s.createChannel(new ChannelDescriptor<>( (Class<E>) expectedValue.getClass(), channelName, false));
-		} catch (ChannelException | TimeoutException e) {
-			// Convert Exception into unchecked RuntimeException
-			throw new IllegalArgumentException("Unable to initialize actuator channel [name:"+channelName+"]",e);
-		} catch (InterruptedException e) {
-			throw new RuntimeException("Unable to initialize actuator channel [name:"+channelName+"]",e);
-		}
-		
-		this.expectedValue = expectedValue;
-		
-		if(timeout==null){
-//			this.timeout = channel.getWaitTimeout();
-			this.timeout = 0L;
-		}
-		else{
-			this.timeout = timeout;
-		}
-	}
-
-	
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#execute()
-	 */
-	/**
-	 * @throws InterruptedException 
-	 * @throws RuntimeException		Channel value did not reach expected value (within the specified timeout period)
-	 */
-	@Override
-	public void execute() throws InterruptedException {
-		abort=false;
-		logger.finest("Checking channel "+channel.getName()+" for value "+expectedValue+" [timeout: "+timeout+"]" );
-		try{
-			waitT = Thread.currentThread();
-			channel.waitForValue(expectedValue, new Comparator<E>() {
-
-				@Override
-				public int compare(E o1, E o2) {
-					int one = o1;
-					int two = o2;
-					if((one | two) != 0){
-						return 0;
-					}
-					return 1;
-				}
-			}
-			, timeout); // Workaround use 10seconds default set timeout to check several times whether the channel has reached the value
-		} catch (ChannelException | ExecutionException e) {
-			throw new RuntimeException("Channel [name:"+channel.getName()+"] did not reach expected value "+expectedValue+" ", e);
-		} catch(InterruptedException e){
-			if(!abort){
-				throw e;
-			}
-		}
-		finally{
-			waitT=null;
-		}
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#abort()
-	 */
-	@Override
-	public void abort() {
-		abort=true;
-		if(waitT!=null){
-			waitT.interrupt();
-		}
-	}
-
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#destroy()
-	 */
-	@Override
-	public void destroy() {
-		// Destroy channel
-		try {
-			logger.finest("Destroy action channel: "+channel.getName());
-			channel.destroy();
-		} catch (ChannelException e) {
-			throw new RuntimeException("Unable to destroy channel ["+channel.getName()+"]",e);
-		}
-	}
-
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/actions/ChannelAccessConditionRegex.java

@@ -1,153 +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.actions;
-
-import java.util.Comparator;
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.TimeoutException;
-import java.util.logging.Logger;
-
-import ch.psi.fda.core.Action;
-import ch.psi.jcae.Channel;
-import ch.psi.jcae.ChannelDescriptor;
-import ch.psi.jcae.ChannelException;
-import ch.psi.jcae.ChannelService;
-
-/**
- * Perform a put on the specified Channel Access channel. The put can be done synchronous or
- * asynchronously.
- * @author ebner
- *
- */
-public class ChannelAccessConditionRegex<E extends String> implements Action {
-
-	// Get Logger
-	private static Logger logger = Logger.getLogger(ChannelAccessConditionRegex.class.getName());
-	
-	/**
-	 * Channel to set
-	 */
-	private final Channel<E> channel;
-	/**
-	 * Value to wait for
-	 */
-	private final E expectedValue;
-	
-	private final Long timeout;
-	
-	private volatile boolean abort = false;
-	private volatile Thread waitT = null;
-	
-	/**
-	 * Constructor
-	 * @param channelName		Name of the channel to set the value
-	 * @param expectedValue		Value to wait for
-	 * @param timeout			Timeout of the condition in milliseconds (null accepted - will take default wait timeout for channels ch.psi.jcae.ChannelBeanFactory.waitTimeout)
-	 * 
-	 * @throws	IllegalArgumentException	Unable to initialize channel,
-	 * 										Timeout specified is not >=0
-	 */
-	@SuppressWarnings("unchecked")
-	public ChannelAccessConditionRegex(ChannelService s, String channelName, E expectedValue, Long timeout){
-
-		if(timeout !=null && timeout<=0){
-			throw new IllegalArgumentException("Timeout must be > 0");
-		}
-		
-		try {
-			this.channel = s.createChannel(new ChannelDescriptor<>( (Class<E>) expectedValue.getClass(), channelName, false));
-		} catch (ChannelException | TimeoutException e) {
-			// Convert Exception into unchecked RuntimeException
-			throw new IllegalArgumentException("Unable to initialize actuator channel [name:"+channelName+"]",e);
-		} catch (InterruptedException e) {
-			throw new RuntimeException("Unable to initialize actuator channel [name:"+channelName+"]",e);
-		}
-		
-		this.expectedValue = expectedValue;
-		
-		if(timeout==null){
-//			this.timeout = channel.getWaitTimeout();
-			this.timeout = 0L;
-		}
-		else{
-			this.timeout = timeout;
-		}
-	}
-
-	
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#execute()
-	 */
-	/**
-	 * @throws InterruptedException 
-	 * @throws RuntimeException		Channel value did not reach expected value (within the specified timeout period)
-	 */
-	@Override
-	public void execute() throws InterruptedException {
-		abort=false;
-		logger.finest("Checking channel "+channel.getName()+" for value "+expectedValue+" [timeout: "+timeout+"]" );
-		try{
-			waitT = Thread.currentThread();
-			channel.waitForValue(expectedValue, new Comparator<E>() {
-
-				@Override
-				public int compare(E o1, E o2) {
-					return o1.matches(o2) ? 0:1;
-				}
-			}, timeout); // Workaround use 10seconds default set timeout to check several times whether the channel has reached the value
-		} catch (ChannelException | ExecutionException e) {
-			throw new RuntimeException("Channel [name:"+channel.getName()+"] did not reach expected value "+expectedValue+" ", e);
-		} catch(InterruptedException e){
-			if(!abort){
-				throw e;
-			}
-		}
-		finally{
-			waitT=null;
-		}
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#abort()
-	 */
-	@Override
-	public void abort() {
-		abort=true;
-		if(waitT!=null){
-			waitT.interrupt();
-		}
-	}
-
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#destroy()
-	 */
-	@Override
-	public void destroy() {
-		// Destroy channel
-		try {
-			logger.finest("Destroy action channel: "+channel.getName());
-			channel.destroy();
-		} catch (ChannelException e) {
-			throw new RuntimeException("Unable to destroy channel ["+channel.getName()+"]",e);
-		}
-	}
-
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/actions/ChannelAccessPut.java

@@ -1,146 +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.actions;
-
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.TimeUnit;
-import java.util.concurrent.TimeoutException;
-import java.util.logging.Logger;
-
-import ch.psi.fda.core.Action;
-import ch.psi.jcae.Channel;
-import ch.psi.jcae.ChannelDescriptor;
-import ch.psi.jcae.ChannelException;
-import ch.psi.jcae.ChannelService;
-
-/**
- * Perform a put on the specified Channel Access channel. The put can be done synchronous or
- * asynchronously.
- * @author ebner
- *
- */
-public class ChannelAccessPut<E> implements Action {
-	
-	// Get Logger
-	private static Logger logger = Logger.getLogger(ChannelAccessPut.class.getName());
-
-	/**
-	 * Channel to set
-	 */
-	private final Channel<E> channel;
-	/**
-	 * Value to set
-	 */
-	private final E value;
-	/**
-	 * Put mode, true = fire and forget, false = wait for response
-	 */
-	private final boolean asynchronous;
-	
-	private final Long timeout;
-	
-	/**
-	 * Constructor
-	 * @param channelName		Name of the channel to set the value
-	 * @param value				Value to set
-	 * @param asynchronous		Flag whether to set the value synchronous (wait for response) or asynchronously (fire and forget)
-	 * @param timeout			Timeout used for set operation (time that set need to come back)
-	 * 
-	 * @throws	IllegalArgumentException	Unable to initialize channel
-	 */
-	@SuppressWarnings("unchecked")
-	public ChannelAccessPut(ChannelService s, String channelName, E value, boolean asynchronous, Long timeout){
-
-		try {
-			this.channel = s.createChannel(new ChannelDescriptor<>((Class<E>)value.getClass(), channelName, false));
-		} catch (ChannelException | TimeoutException e) {
-			// Convert Exception into unchecked RuntimeException
-			throw new IllegalArgumentException("Unable to initialize actuator channel [name:"+channelName+"]",e);
-		} catch (InterruptedException e) {
-			throw new RuntimeException("Unable to initialize actuator channel [name:"+channelName+"]",e);
-		}
-		
-		this.value = value;
-		this.asynchronous = asynchronous;
-		this.timeout = timeout;
-	}
-	
-	/**
-	 * Additional constructor for convenience. This constructor defaults the operation type to synchronous put.
-	 * @param channelName		Name of the channel to set the value
-	 * @param value				Value to set
-	 * 
-	 * @throws	RuntimeException	Unable to initialize channel
-	 */
-	public ChannelAccessPut(ChannelService s, String channelName, E value){
-		this(s, channelName, value, false, null);
-	}
-	
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#execute()
-	 */
-	/**
-	 * @throws InterruptedException 
-	 * @throws RuntimeException		Cannot set value on channel
-	 */
-	@Override
-	public void execute() throws InterruptedException {
-		logger.finest("Put to channel: "+channel.getName()+ " asynchronous: "+asynchronous);
-		try{
-			if(asynchronous){
-				channel.setValueNoWait(value);
-			}
-			else{
-				if(timeout==null){
-					channel.setValue(value);
-				}
-				else{
-					channel.setValueAsync(value).get(timeout, TimeUnit.MILLISECONDS);
-				}
-			}
-		} catch (ChannelException | ExecutionException | TimeoutException e) {
-			// Convert Exception into unchecked RuntimeException
-			throw new RuntimeException("Unable to set channel [name:"+channel.getName()+"] to value "+value, e);
-		}
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#abort()
-	 */
-	@Override
-	public void abort() {
-		// This action cannot be aborted, therefore this method is not implemented
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#destroy()
-	 */
-	@Override
-	public void destroy() {
-		// Destroy channel
-		try {
-			logger.finest("Destroy action channel: "+channel.getName());
-			channel.destroy();
-		} catch (ChannelException e) {
-			throw new RuntimeException("Unable to destroy channel ["+channel.getName()+"]",e);
-		}
-	}
-
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/actions/Delay.java

@@ -1,74 +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.actions;
-
-import ch.psi.fda.core.Action;
-
-/**
- * Wait a specific time until executing the next action ...
- * @author ebner
- *
- */
-public class Delay implements Action {
-
-	/**
-	 * Time to wait
-	 */
-	private final long time;
-	
-	/**
-	 * Constructor
-	 * @param time		Time to wait (in milliseconds)
-	 */
-	public Delay(long time){
-		
-		// Check if delay time is positive and >0
-		if(time<=0){
-			throw new IllegalArgumentException("Wait time must be >0");
-		}
-		
-		this.time = time;
-	}
-	
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#execute()
-	 */
-	@Override
-	public void execute() throws InterruptedException {
-		Thread.sleep(time);
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#abort()
-	 */
-	@Override
-	public void abort() {
-		// Not implemented because not needed
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#destroy()
-	 */
-	@Override
-	public void destroy() {
-		// Nothing to be done
-	}
-
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/actions/JythonAction.java

@@ -1,170 +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.actions;
-
-import java.util.List;
-import java.util.concurrent.TimeoutException;
-import java.util.logging.Logger;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import javax.script.ScriptEngine;
-import javax.script.ScriptEngineManager;
-import javax.script.ScriptException;
-
-import ch.psi.fda.core.Action;
-import ch.psi.fda.core.scripting.JythonParameterMapping;
-import ch.psi.fda.core.scripting.JythonParameterMappingChannel;
-import ch.psi.jcae.Channel;
-import ch.psi.jcae.ChannelDescriptor;
-import ch.psi.jcae.ChannelException;
-import ch.psi.jcae.ChannelService;
-
-/**
- * @author ebner
- *
- */
-public class JythonAction implements Action {
-
-	// Get Logger
-	private static Logger logger = Logger.getLogger(JythonAction.class.getName());
-	
-	/**
-	 * Pattern of the entry function of the jython script
-	 */
-	private static final String entryFunction = "process";
-	private static final String entryFunctionPattern = "def "+entryFunction+"\\((.*)\\):";
-	
-	/**
-	 * Script engine of the manipulator
-	 */
-	private ScriptEngine engine;
-	
-	/**
-	 * Jython entry call
-	 */
-	private String jythonCall;
-		
-	public JythonAction(ChannelService s, String script, List<JythonParameterMappingChannel> mapping){
-		
-		// Workaround for Jython memory leak 
-		// http://blog.hillbrecht.de/2009/07/11/jython-memory-leakout-of-memory-problem/
-		System.setProperty("python.options.internalTablesImpl","weak");
-		
-		// Create new script engine
-		this.engine = new ScriptEngineManager().getEngineByName("python");
-		
-		// Determine script entry function and the function parameters
-		Pattern pattern = Pattern.compile(entryFunctionPattern);
-		Matcher matcher = pattern.matcher(script);
-		String[] functionParameters = null;
-		if(matcher.find() && matcher.groupCount()==1){
-			logger.finest("Entry function '"+entryFunctionPattern+"' found - Identified parameters: "+matcher.group(1));
-			functionParameters = matcher.group(1).split(" *, *");
-		}
-		else{
-			throw new IllegalArgumentException("Cannot determine entry function: "+entryFunctionPattern);
-		}
-		
-		// Check whether all function parameters have a mapping
-		for(int i=0;i<functionParameters.length; i++){
-			String p = functionParameters[i];
-			p = p.trim();
-			boolean found = false;
-			for(JythonParameterMapping pm: mapping){
-				if(pm.getVariable().equals(p)){
-					found=true;
-					break;
-				}
-			}
-			if(!found){
-				throw new IllegalArgumentException("No mapping compontent found for parameter "+p);
-			}
-		}
-		
-		// Check whether more mappings are specified than function parameters
-		if(functionParameters.length<mapping.size()){
-			throw new IllegalArgumentException("More mappings than function parameters are specified");
-		}
-		
-		// Load manipulation script
-		try {
-			engine.eval(script);
-		} catch (ScriptException e) {
-			throw new RuntimeException("Unable to load manipulation script", e);
-		}
-		
-		StringBuffer buffer = new StringBuffer();
-		buffer.append(entryFunction);
-		buffer.append("(");
-		for(JythonParameterMappingChannel b: mapping){
-			// Create channel
-			
-			Channel<?> cb;
-			try {
-				cb = s.createChannel(new ChannelDescriptor<>(b.getType(), b.getChannel(), true));
-			} catch (TimeoutException | ChannelException e) {
-				throw new IllegalArgumentException("Unable to establish channel: "+b.getChannel(), e);
-			} catch (InterruptedException e) {
-				throw new RuntimeException("Unable to establish channel: "+b.getChannel(), e);
-			}
-			
-			// Assign channel bean to variable
-			engine.put(b.getVariable(), cb);
-			
-			buffer.append(b.getVariable());
-			buffer.append(",");
-		}
-		buffer.setCharAt(buffer.length()-1, ')');
-		
-		jythonCall = buffer.toString();
-	}
-	
-	
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#execute()
-	 */
-	@Override
-	public void execute() {
-		try {
-			engine.eval(jythonCall);
-		} catch (ScriptException e) {
-			throw new RuntimeException("Action failed while executing the Jython script",e);
-		}		
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#abort()
-	 */
-	@Override
-	public void abort() {
-		// TODO need to find a way to abort script execution
-	}
-
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#destroy()
-	 */
-	@Override
-	public void destroy() {
-		// Nothing to be done
-	}
-
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/actions/ShellAction.java

@@ -1,174 +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.actions;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.util.logging.Level;
-import java.util.logging.Logger;
-
-import ch.psi.fda.core.Action;
-
-/**
- * Action that executes a specified script when it is executed.
- * @author ebner
- *
- */
-public class ShellAction implements Action{
-	
-	// Get Logger
-	private static Logger logger = Logger.getLogger(ShellAction.class.getName());
-
-	private volatile Process process;
-	private volatile boolean abort = false;
-	private boolean checkExitValue = true;
-	private int exitValue = 0;
-	
-	/**
-	 * Name (full path if it is not in the system path) of the script to execute when
-	 * the execute() function of this action is invoked.
-	 */
-	private final String script;
-	
-	/**
-	 * Constructor
-	 * @param script	Name of the script to execute when this action is invoked
-	 * 
-	 * @throws IllegalArgumentException		Specified script does not exist
-	 */
-	public ShellAction(String script){
-		String[] scri = script.split("[ ,\t]");
-		File s = new File(scri[0]);
-		if(!s.exists()){
-			throw new IllegalArgumentException("Script "+script+" does not exist.");
-		}
-		this.script = script;
-	}
-	
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#execute()
-	 */
-	/**
-	 * @throws InterruptedException 
-	 * @throws RuntimeException		Script did not exit with 0,
-	 * 								Execution was interrupted,
-	 * 								IO problem occurred 
-	 */
-	@Override
-	public void execute() throws InterruptedException {
-		try{
-			abort = false;
-			logger.fine("Execute script "+script);
-			process = Runtime.getRuntime().exec(new String[]{"/bin/bash","-c",script});
-			int exitVal = process.waitFor();
-			
-			// Log output of the shell script if loglevel is finest
-			if(logger.isLoggable(Level.FINEST)){
-				logger.finest("STDOUT [BEGIN]");
-				// TODO The readout of the stream should be in parallel to the processing of the script! I.e. the output appears in the log as it is generated by the script!
-				BufferedReader reader = new BufferedReader(new InputStreamReader(process.getInputStream()));
-				String line = null;
-				while((line=reader.readLine()) != null){
-					logger.finest(line);
-				}
-				logger.finest("STDOUT [END]");
-				
-				logger.finest("STDERR [BEGIN]");
-				// TODO The readout of the stream should be in parallel to the processing of the script! I.e. the output appears in the log as it is generated by the script!
-				reader = new BufferedReader(new InputStreamReader(process.getErrorStream()));
-				line = null;
-				while((line=reader.readLine()) != null){
-					logger.finest(line);
-				}
-				logger.finest("STDERR [END]");
-			}
-			
-			logger.fine("Script ["+script+"] return value: "+exitVal);
-			
-			if(abort){
-				throw new RuntimeException("Script ["+script+"] was aborted");
-			}
-			else{
-				// Check script exit value to 0 if != 0 then throw an runtime exception
-				if(checkExitValue && exitVal != exitValue){
-					throw new RuntimeException("Script ["+script+"] returned with an exit value not equal to 0");
-				}
-			}
-			process = null; // Ensure that the process is null
-		}
-		catch(IOException e){
-			// Convert Exception into unchecked RuntimeException
-			throw new RuntimeException("Unable to execute script: "+script,e);
-		}
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#abort()
-	 */
-	@Override
-	public void abort() {
-		abort=true;
-		// This action cannot be aborted, therefore this function is not implemented.
-		if(process!=null){
-			// Terminate process via kill
-			process.destroy();
-		}
-	}
-
-	
-	
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#destroy()
-	 */
-	@Override
-	public void destroy() {
-		// Nothing to be done
-	}
-
-	/**
-	 * @return the checkExitValue
-	 */
-	public boolean isCheckExitValue() {
-		return checkExitValue;
-	}
-
-	/**
-	 * @param checkExitValue the checkExitValue to set
-	 */
-	public void setCheckExitValue(boolean checkExitValue) {
-		this.checkExitValue = checkExitValue;
-	}
-
-	/**
-	 * @return the exitValue
-	 */
-	public int getExitValue() {
-		return exitValue;
-	}
-
-	/**
-	 * @param exitValue the exitValue to set
-	 */
-	public void setExitValue(int exitValue) {
-		this.exitValue = exitValue;
-	}	
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/actors/ChannelAccessFunctionActuator.java

@@ -1,353 +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.actors;
-
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.TimeUnit;
-import java.util.concurrent.TimeoutException;
-import java.util.logging.Logger;
-
-import ch.psi.fda.core.Actor;
-import ch.psi.fda.core.EngineConfiguration;
-import ch.psi.jcae.Channel;
-import ch.psi.jcae.ChannelDescriptor;
-import ch.psi.jcae.ChannelException;
-import ch.psi.jcae.ChannelService;
-
-/**
- * This actuator sets an Channel Access channel from a start to an end value by doing discrete steps.
- * @author ebner
- *
- */
-public class ChannelAccessFunctionActuator<T> implements Actor {
-	
-	// Get Logger
-	private static Logger logger = Logger.getLogger(ChannelAccessFunctionActuator.class.getName());
-
-	private boolean asynchronous = false;
-	
-	/**
-	 * Start value of the actuator
-	 */
-	private double start;
-	
-	/**
-	 * End value of the actuator
-	 */
-	private double end;
-	
-	/**
-	 * Step size of the move
-	 */
-	private double stepSize;
-	
-	/**
-	 * Move direction (start&lt;end = 1, start&gt;end = -1)
-	 */
-	private int direction;
-	
-	/**
-	 * Execution count of actuator. This variable is used to minimize the floating point
-	 * rounding errors for calculating the next step. 
-	 */
-	private int count;
-	
-	/**
-	 * Flag that indicates whether there is a next set value for the Actor
-	 */
-	private boolean next;
-	
-	/**
-	 * Value to set at next @see ch.psi.fda.engine.Actor#set() call
-	 */
-	private double value;
-	
-	/**
-	 * Level of accuracy the positioner need to have (e.g. if a positioner is set to 1 the readback set value
-	 * of the positioner need to have at lease 1+/-accuracy) 
-	 * Default is stepSize/2 
-	 */
-	private double accuracy;
-	
-	/**
-	 * Channel Access channel of the actuator
-	 */
-	private Channel<Double> channel;
-	
-	/**
-	 * Channel Access channel of the actuator
-	 */
-	private Channel<T> doneChannel = null;
-	
-	private final T doneValue;
-	private final long doneDelay;
-	
-	private final double originalStart;
-	private final double originalEnd;
-	private final int originalDirection;
-	
-	
-	/**
-	 * Move timeout
-	 */
-	private Long timeout;
-	
-	private final Function function;
-	
-	/**
-	 * Constructor - Initialize actor
-	 * @param channelName
-	 * @param start
-	 * @param end
-	 * @param stepSize
-	 * @param timeout 	Maximum move time (in milliseconds)
-	 */
-	public ChannelAccessFunctionActuator(ChannelService s, String channelName, Function function, double start, double end, double stepSize, Long timeout){
-		this(s, channelName, null, null, 0, function, start, end, stepSize, timeout);
-	}
-	
-	/**
-	 * Constructor
-	 * @param channelName
-	 * @param doneChannelName	If null actor will not wait (for this channel) to continue
-	 * @param doneValue
-	 * @param doneDelay			Delay in seconds before checking the done channel
-	 * @param start
-	 * @param end
-	 * @param stepSize
-	 * @param timeout			Maximum move time (in milliseconds)
-	 */
-	@SuppressWarnings("unchecked")
-	public ChannelAccessFunctionActuator(ChannelService s, String channelName, String doneChannelName, T doneValue, double doneDelay,  Function function, double start, double end, double stepSize, Long timeout){
-		
-		this.doneValue = doneValue;
-		this.doneDelay = (long) Math.floor((doneDelay*1000));
-		this.start = start;
-		this.end = end;
-		
-		if(stepSize <= 0){
-			throw new IllegalArgumentException("Step size ["+stepSize+"] must be > 0");
-		}
-		this.stepSize = stepSize;
-		
-		this.accuracy = stepSize/2;
-		
-		// Validate and save timeout parameter
-		if(timeout!=null && timeout<=0){
-			throw new IllegalArgumentException("Timeout must be >0 or null");
-		}
-		else{
-			this.timeout = timeout;
-		}
-		
-		if(function==null){
-			throw new IllegalArgumentException("Function must not be null");
-		}
-		this.function = function;
-		
-		
-		init();
-		
-		// Save original settings
-		this.originalStart = start;
-		this.originalEnd = end;
-		this.originalDirection = direction;
-		
-		
-		// Initialize/create Channel Access channel
-		try {
-			channel = s.createChannel(new ChannelDescriptor<>(Double.class, channelName, false));
-		} catch (ChannelException | TimeoutException e) {
-			// Convert Exception into unchecked RuntimeException
-			throw new IllegalArgumentException("Unable to initialize actuator channel [name:"+channelName+"]",e);
-		} catch (InterruptedException e) {
-			throw new RuntimeException("Unable to initialize actuator channel [name:"+channelName+"]",e);
-		}
-		if(doneChannelName != null){
-			try {
-				doneChannel = s.createChannel(new ChannelDescriptor<>((Class<T>)doneValue.getClass(), doneChannelName, false));
-			} catch (ChannelException | TimeoutException e) {
-				// Convert Exception into unchecked RuntimeException
-				throw new IllegalArgumentException("Unable to initialize actuator channel [name:"+doneChannelName+"]",e);
-			} catch (InterruptedException e) {
-				throw new RuntimeException("Unable to initialize actuator channel [name:"+doneChannelName+"]",e);
-			}
-		}
-	}
-	
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.engine.Actor#set()
-	 */
-	@Override
-	public void set() throws InterruptedException {
-		
-		// Throw an IllegalStateException in the case that set is called although there is no next step.
-		if(!next){
-			throw new IllegalStateException("The actuator does not have any next step.");
-		}
-		
-		// Set actuator channel
-		logger.finest("Set actuator channel "+channel.getName()+" to value: "+value);
-		try {
-			double fvalue = function.calculate(value);
-			
-			if(!asynchronous){
-				if(timeout==null){
-					channel.setValue(fvalue);
-				}
-				else{
-					channel.setValueAsync(fvalue).get(timeout, TimeUnit.MILLISECONDS); 
-				}
-			}
-			else{
-				channel.setValueNoWait(fvalue);
-			}
-			
-			if(doneChannel != null){
-				Thread.sleep(doneDelay);
-				doneChannel.waitForValue(doneValue); 
-			}
-			
-			// Check whether the set value is really on the value that was set before.
-			if(EngineConfiguration.getInstance().isCheckActorSet()){
-				double c = channel.getValue(true);
-				double a = Math.abs( c - fvalue ); 
-				if ( a > accuracy ){
-					throw new RuntimeException("Actor could not be set to the value "+fvalue+" The readback of the set value does not match the value that was set [value: "+c+" delta: "+a+" accuracy: "+accuracy+"]");
-				}
-			}
-			
-		} catch (ChannelException | ExecutionException | TimeoutException e) {
-			// Convert Exception into unchecked RuntimeException
-			throw new RuntimeException("Unable to move actuator [channel: "+channel.getName()+"] to value "+value,e);
-		}
-		
-		
-		count++;
-		double nextValue = start+(count*stepSize*direction); // Done like this to keep floating point rounding errors minimal
-		
-		if((direction==1&&nextValue<=end)||(direction==-1&nextValue>=end)){
-			
-			// Apply function
-//			nextValue = function.calculate(nextValue);
-			
-			logger.fine("Next actor value: "+nextValue);
-			value=nextValue;
-			this.next = true;
-		}
-		else{
-			// There is no next set value
-			this.next = false;
-		}
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.engine.Actor#hasNext()
-	 */
-	@Override
-	public boolean hasNext() {
-		return next;
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Actor#init()
-	 */
-	@Override
-	public void init() {
-		this.count = 0;
-		
-		// Determine move direction
-		this.direction = 1;
-		if(start>end){
-			direction=-1; // Move in negative direction
-		}
-		
-		
-		// Set first set value to the start value
-		this.value = start;
-		this.next = true;
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Actor#reverse()
-	 */
-	@Override
-	public synchronized void reverse() {
-		double oldStart = start;
-		this.start = this.end;
-		this.end = oldStart;
-		
-		// Determine move direction
-		this.direction = 1;
-		if(this.start>this.end){
-			direction=-1; // Move in negative direction
-		}
-		
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Actor#reset()
-	 */
-	@Override
-	public void reset() {
-		this.start = this.originalStart;
-		this.end = this.originalEnd;
-		this.direction = this.originalDirection;
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Actor#destroy()
-	 */
-	@Override
-	public void destroy() {
-		// Destroy channel
-		try {
-			logger.finest("Destroy actor channel: "+channel.getName());
-			channel.destroy();
-		} catch (ChannelException e) {
-			throw new RuntimeException("Unable to destroy channel ["+channel.getName()+"]",e);
-		}
-		
-		// Destroy done channel if exists
-		if(doneChannel != null){
-			try {
-				logger.finest("Destroy actor done channel: "+doneChannel.getName());
-				doneChannel.destroy();
-			} catch (ChannelException e) {
-				throw new RuntimeException("Unable to destroy channel ["+channel.getName()+"]",e);
-			}
-		}
-	}
-
-	/**
-	 * @return the asynchronous
-	 */
-	public boolean isAsynchronous() {
-		return asynchronous;
-	}
-
-	/**
-	 * @param asynchronous the asynchronous to set
-	 */
-	public void setAsynchronous(boolean asynchronous) {
-		this.asynchronous = asynchronous;
-	}
-
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/actors/ChannelAccessLinearActuator.java

@@ -1,332 +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.actors;
-
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.TimeUnit;
-import java.util.concurrent.TimeoutException;
-import java.util.logging.Logger;
-
-import ch.psi.fda.core.Actor;
-import ch.psi.fda.core.EngineConfiguration;
-import ch.psi.jcae.Channel;
-import ch.psi.jcae.ChannelDescriptor;
-import ch.psi.jcae.ChannelException;
-import ch.psi.jcae.ChannelService;
-
-/**
- * This actuator sets an Channel Access channel from a start to an end value by doing discrete steps.
- * @author ebner
- *
- */
-public class ChannelAccessLinearActuator<T> implements Actor {
-	
-	// Get Logger
-	private static Logger logger = Logger.getLogger(ChannelAccessLinearActuator.class.getName());
-
-	private boolean asynchronous = false;
-	
-	/**
-	 * Start value of the actuator
-	 */
-	private double start;
-	
-	/**
-	 * End value of the actuator
-	 */
-	private double end;
-	
-	/**
-	 * Step size of the move
-	 */
-	private double stepSize;
-	
-	/**
-	 * Move direction (start&lt;end = 1, start&gt;end = -1)
-	 */
-	private int direction;
-	
-	/**
-	 * Execution count of actuator. This variable is used to minimize the floating point
-	 * rounding errors for calculating the next step. 
-	 */
-	private int count;
-	
-	/**
-	 * Flag that indicates whether there is a next set value for the Actor
-	 */
-	private boolean next;
-	
-	/**
-	 * Value to set at next @see ch.psi.fda.engine.Actor#set() call
-	 */
-	private double value;
-	
-	/**
-	 * Level of accuracy the positioner need to have (e.g. if a positioner is set to 1 the readback set value
-	 * of the positioner need to have at lease 1+/-accuracy) 
-	 * Default is stepSize/2 
-	 */
-	private double accuracy;
-	
-	/**
-	 * Channel Access channel of the actuator
-	 */
-	private Channel<Double> channel;
-	
-	/**
-	 * Channel Access channel of the actuator
-	 */
-	private Channel<T> doneChannel = null;
-	
-	private final T doneValue;
-	private final long doneDelay;
-	
-	private final double originalStart;
-	private final double originalEnd;
-	private final int originalDirection;
-	
-	
-	/**
-	 * Move timeout
-	 */
-	private Long timeout;
-	
-	
-	/**
-	 * Constructor
-	 * @param channelName
-	 * @param doneChannelName	If null actor will not wait (for this channel) to continue
-	 * @param doneValue
-	 * @param doneDelay			Delay in seconds before checking the done channel
-	 * @param start
-	 * @param end
-	 * @param stepSize
-	 * @param timeout			Maximum move time (in milliseconds)
-	 */
-	@SuppressWarnings("unchecked")
-	public ChannelAccessLinearActuator(ChannelService s, String channelName, String doneChannelName, T doneValue, double doneDelay,  double start, double end, double stepSize, Long timeout){
-		
-		this.doneValue = doneValue;
-		this.doneDelay = (long) Math.floor((doneDelay*1000));
-		this.start = start;
-		this.end = end;
-		
-		if(stepSize <= 0){
-			throw new IllegalArgumentException("Step size ["+stepSize+"] must be > 0");
-		}
-		this.stepSize = stepSize;
-		
-		this.accuracy = stepSize/2;
-		
-		// Validate and save timeout parameter
-		if(timeout!=null && timeout<=0){
-			throw new IllegalArgumentException("Timeout must be >0 or null");
-		}
-		else{
-			this.timeout = timeout;
-		}
-		
-		
-		init();
-		
-		// Save original settings
-		this.originalStart = start;
-		this.originalEnd = end;
-		this.originalDirection = direction;
-		
-		
-		// Initialize/create Channel Access channel
-		try {
-			channel = s.createChannel(new ChannelDescriptor<>(Double.class, channelName, false));
-		} catch (ChannelException | TimeoutException e) {
-			// Convert Exception into unchecked RuntimeException
-			throw new IllegalArgumentException("Unable to initialize actuator channel [name:"+channelName+"]",e);
-		} catch (InterruptedException e) {
-			throw new RuntimeException("Unable to initialize actuator channel [name:"+channelName+"]",e);
-		}
-		if(doneChannelName != null){
-			try {
-				doneChannel = s.createChannel(new ChannelDescriptor<>((Class<T>) doneValue.getClass(), doneChannelName, false));
-			} catch (ChannelException | TimeoutException e) {
-				// Convert Exception into unchecked RuntimeException
-				throw new IllegalArgumentException("Unable to initialize actuator channel [name:"+doneChannelName+"]",e);
-			} catch (InterruptedException e) {
-				throw new RuntimeException("Unable to initialize actuator channel [name:"+doneChannelName+"]",e);
-			}
-		}
-	}
-	
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.engine.Actor#set()
-	 */
-	@Override
-	public void set() throws InterruptedException {
-		
-		// Throw an IllegalStateException in the case that set is called although there is no next step.
-		if(!next){
-			throw new IllegalStateException("The actuator does not have any next step.");
-		}
-		
-		// Set actuator channel
-		logger.finest("Set actuator channel "+channel.getName()+" to value: "+value);
-		try {
-			
-			if(!asynchronous){
-				if(timeout==null){
-					channel.setValue(value);
-				}
-				else{
-					channel.setValueAsync(value).get(timeout, TimeUnit.MILLISECONDS); 
-				}
-			}
-			else{
-				channel.setValueNoWait(value);
-			}
-			
-			if(doneChannel != null){
-				Thread.sleep(doneDelay);
-				doneChannel.waitForValue(doneValue); 
-			}
-			
-			// Check whether the set value is really on the value that was set before.
-			if(EngineConfiguration.getInstance().isCheckActorSet()){
-				double c = channel.getValue(true);
-				double a = Math.abs( c - value ); 
-				if ( a > accuracy ){
-					throw new RuntimeException("Actor could not be set to the value "+value+" The readback of the set value does not match the value that was set [value: "+c+" delta: "+a+" accuracy: "+accuracy+"]");
-				}
-			}
-			
-		} catch (ChannelException | TimeoutException | ExecutionException e) {
-			// Convert Exception into unchecked RuntimeException
-			throw new RuntimeException("Unable to move actuator [channel: "+channel.getName()+"] to value "+value,e);
-		}
-		
-		
-		count++;
-		double nextValue = start+(count*stepSize*direction); // Done like this to keep floating point rounding errors minimal
-		
-		if((direction==1&&nextValue<=end)||(direction==-1&nextValue>=end)){
-			logger.fine("Next actor value: "+nextValue);
-			value=nextValue;
-			this.next = true;
-		}
-		else{
-			// There is no next set value
-			this.next = false;
-		}
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.engine.Actor#hasNext()
-	 */
-	@Override
-	public boolean hasNext() {
-		return next;
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Actor#init()
-	 */
-	@Override
-	public void init() {
-		this.count = 0;
-		
-		// Determine move direction
-		this.direction = 1;
-		if(start>end){
-			direction=-1; // Move in negative direction
-		}
-		
-		
-		// Set first set value to the start value
-		this.value = start;
-		this.next = true;
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Actor#reverse()
-	 */
-	@Override
-	public synchronized void reverse() {
-		double oldStart = start;
-		this.start = this.end;
-		this.end = oldStart;
-		
-		// Determine move direction
-		this.direction = 1;
-		if(this.start>this.end){
-			direction=-1; // Move in negative direction
-		}
-		
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Actor#reset()
-	 */
-	@Override
-	public void reset() {
-		this.start = this.originalStart;
-		this.end = this.originalEnd;
-		this.direction = this.originalDirection;
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Actor#destroy()
-	 */
-	@Override
-	public void destroy() {
-		// Destroy channel
-		try {
-			logger.finest("Destroy actor channel: "+channel.getName());
-			channel.destroy();
-		} catch (ChannelException e) {
-			throw new RuntimeException("Unable to destroy channel ["+channel.getName()+"]",e);
-		}
-		
-		// Destroy done channel if exists
-		if(doneChannel != null){
-			try {
-				logger.finest("Destroy actor done channel: "+doneChannel.getName());
-				doneChannel.destroy();
-			} catch (ChannelException e) {
-				throw new RuntimeException("Unable to destroy channel ["+channel.getName()+"]",e);
-			}
-		}
-	}
-
-	/**
-	 * @return the asynchronous
-	 */
-	public boolean isAsynchronous() {
-		return asynchronous;
-	}
-
-	/**
-	 * @param asynchronous the asynchronous to set
-	 */
-	public void setAsynchronous(boolean asynchronous) {
-		this.asynchronous = asynchronous;
-	}
-	
-	
-
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/actors/ChannelAccessTableActuator.java

@@ -1,317 +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.actors;
-
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.TimeUnit;
-import java.util.concurrent.TimeoutException;
-import java.util.logging.Logger;
-
-import ch.psi.fda.core.Actor;
-import ch.psi.fda.core.EngineConfiguration;
-import ch.psi.jcae.Channel;
-import ch.psi.jcae.ChannelDescriptor;
-import ch.psi.jcae.ChannelException;
-import ch.psi.jcae.ChannelService;
-
-/**
- * This actuator sets an Channel Access channel by using the positions from the given table.
- * @author ebner
- *
- */
-public class ChannelAccessTableActuator<T> implements Actor {
-	
-	// Get Logger
-	private static Logger logger = Logger.getLogger(ChannelAccessTableActuator.class.getName());
-
-	private boolean asynchronous = false;
-	
-	/**
-	 * Position table
-	 */
-	private final double[] table;
-	
-	/**
-	 * Level of accuracy the positioner need to have (e.g. if a positioner is set to 1 the readback set value
-	 * of the positioner need to have at lease 1+/-accuracy)
-	 */
-	private double accuracy = 0.1;
-	
-	/**
-	 * Execution count of actuator. This variable is used to minimize the floating point
-	 * rounding errors for calculating the next step. 
-	 */
-	private int count;
-	
-	/**
-	 * Flag that indicates whether there is a next set value for the Actor
-	 */
-	private boolean next;
-
-	
-	/**
-	 * Channel Access channel of the actuator
-	 */
-	private Channel<Double> channel;
-	
-	/**
-	 * Channel Access channel of the actuator
-	 */
-	private Channel<T> doneChannel = null;
-	
-	private final T doneValue;
-	private final long doneDelay;
-	
-	/**
-	 * Flag that indicates whether the actor moves in the positive direction 
-	 */
-	private boolean positiveDirection = true;
-	private final boolean originalPositiveDirection;
-	
-	/**
-	 * Maximum move time (in milliseconds)
-	 */
-	private Long timeout = null;
-	
-	
-	/**
-	 * Constructor - Initialize actor
-	 * @param channelName	Name of the channel to set
-	 * @param table			Position table with the explicit positions for each step
-	 * @param timeout		Maximum move time (in milliseconds)
-	 */
-	public ChannelAccessTableActuator(ChannelService s, String channelName, double[] table, Long timeout){
-		this(s, channelName, null, null, 0, table, timeout);
-	}
-	
-	/**
-	 * Constructor
-	 * @param channelName
-	 * @param doneChannelName
-	 * @param doneValue
-	 * @param doneDelay
-	 * @param table
-	 * @param timeout		Maximum move time (in milliseconds)
-	 */
-	@SuppressWarnings("unchecked")
-	public ChannelAccessTableActuator(ChannelService s, String channelName, String doneChannelName, T doneValue, double doneDelay, double[] table, Long timeout){
-		
-		this.doneValue = doneValue;
-		this.doneDelay = (long) Math.floor((doneDelay*1000));
-		
-		if(table==null){
-			throw new IllegalArgumentException("Null table is not accepted");
-		}
-		if(table.length==0){
-			throw new IllegalArgumentException("Position table need to have at least one position");
-		}
-		
-		this.table = table;
-		
-		// Validate and save timeout parameter
-		if(timeout!=null && timeout<=0){
-			throw new IllegalArgumentException("Timeout must be >0 or null");
-		}
-		else{
-			this.timeout = timeout;
-		}
-		
-		init();
-		
-		// Save the initial direction
-		this.originalPositiveDirection = positiveDirection;
-		
-		// Initialize/create Channel Access channel
-		try {
-			channel = s.createChannel(new ChannelDescriptor<>(Double.class, channelName, false));
-		} catch (ChannelException | TimeoutException e) {
-			// Convert Exception into unchecked RuntimeException
-			throw new IllegalArgumentException("Unable to initialize actuator channel [name:"+channelName+"]",e);
-		} catch (InterruptedException e) {
-			throw new RuntimeException("Unable to initialize actuator channel [name:"+channelName+"]",e);
-		}
-		
-		if(doneChannelName != null){
-			try {
-				doneChannel = s.createChannel(new ChannelDescriptor<>((Class<T>)doneValue.getClass(), doneChannelName, false));
-			} catch (ChannelException | TimeoutException e) {
-				// Convert Exception into unchecked RuntimeException
-				throw new IllegalArgumentException("Unable to initialize actuator channel [name:"+doneChannelName+"]",e);
-			} catch (InterruptedException e) {
-				throw new RuntimeException("Unable to initialize actuator channel [name:"+doneChannelName+"]",e);
-			}
-		}
-	}
-	
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.engine.Actor#set()
-	 */
-	@Override
-	public void set() throws InterruptedException {
-		
-		// Throw an IllegalStateException in the case that set is called although there is no next step.
-		if(!next){
-			throw new IllegalStateException("The actuator does not have any next step.");
-		}
-		
-		// Set actuator channel
-		logger.finest("Set actuator channel "+channel.getName()+" to value: "+table[count]);
-		try {
-			if(!asynchronous){
-				if(timeout==null){
-					channel.setValue(table[count]);
-				}
-				else{
-					channel.setValueAsync(table[count]).get(timeout, TimeUnit.MILLISECONDS);
-				}
-			}
-			else{
-				channel.setValueNoWait(table[count]);
-			}
-			
-			
-			if(doneChannel != null){
-				Thread.sleep(doneDelay);
-				doneChannel.waitForValue(doneValue); 
-			}
-			
-			// Check whether the set value is really on the value that was set before.
-			if(doneChannel==null && !asynchronous && EngineConfiguration.getInstance().isCheckActorSet()){
-				if ( Math.abs( channel.getValue() - table[count] ) > accuracy ){
-					throw new RuntimeException("Actor could not be set to the value "+table[count]+" The readback of the set value does not match the value that was set");
-				}
-			}
-			
-		} catch (ChannelException | ExecutionException | TimeoutException e) {
-			// Convert Exception into unchecked RuntimeException
-			throw new RuntimeException("Move actuator [channel: "+channel.getName()+"] to value "+table[count],e);
-		}
-		
-		if(positiveDirection){
-			count++;
-			if(count<table.length){
-				this.next = true;
-			}
-			else{
-				// There is no next set value
-				this.next = false;
-			}
-		}
-		else{
-			count--;
-			if(count>=0){
-				this.next = true;
-			}
-			else{
-				// There is no next set value
-				this.next = false;
-			}
-		}
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.engine.Actor#hasNext()
-	 */
-	@Override
-	public boolean hasNext() {
-		return next;
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Actor#init()
-	 */
-	@Override
-	public void init() {
-		
-		// Set first set value to the start value
-		if(positiveDirection){
-			this.count = 0; // Set count to the first element
-		}
-		else{
-			this.count = table.length-1; // Set count to the last element
-		}
-		
-		if(table.length>0){
-			this.next = true;
-		}
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Actor#reverse()
-	 */
-	@Override
-	public void reverse() {
-		if(positiveDirection){
-			positiveDirection=false;
-		}
-		else{
-			positiveDirection=true;
-		}
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Actor#reset()
-	 */
-	@Override
-	public void reset() {
-		this.positiveDirection = this.originalPositiveDirection;
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Actor#destroy()
-	 */
-	@Override
-	public void destroy() {
-		// Destroy channel
-		try {
-			logger.finest("Destroy actor channel: "+channel.getName());
-			channel.destroy();
-		} catch (ChannelException e) {
-			throw new RuntimeException("Unable to destroy channel ["+channel.getName()+"]",e);
-		}
-		
-		// Destroy done channel if exists
-		if(doneChannel != null){
-			try {
-				logger.finest("Destroy actor done channel: "+doneChannel.getName());
-				doneChannel.destroy();
-			} catch (ChannelException e) {
-				throw new RuntimeException("Unable to destroy channel ["+channel.getName()+"]",e);
-			}
-		}
-	}
-
-	/**
-	 * @return the asynchronous
-	 */
-	public boolean isAsynchronous() {
-		return asynchronous;
-	}
-
-	/**
-	 * @param asynchronous the asynchronous to set
-	 */
-	public void setAsynchronous(boolean asynchronous) {
-		this.asynchronous = asynchronous;
-	}
-	
-	
-
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/actors/ComplexActuator.java

@@ -1,261 +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.actors;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.logging.Logger;
-
-import ch.psi.fda.core.Action;
-import ch.psi.fda.core.Actor;
-
-/**
- * Complex actuator that consists of a list of other actuators. The steps of this actor are composed out of the
- * steps of the actors that this actuator consists of.
- * First all the steps of the first actor are used, after that the steps of the next actor are done.
- * Before the first step of an actor pre actions are available and after the last step of an actor a post action is available.
- * 
- * @author ebner
- *
- */
-public class ComplexActuator implements Actor {
-
-	// Get Logger
-	private static Logger logger = Logger.getLogger(ComplexActuator.class.getName());
-	
-	/**
-	 * List of actors this actor is made of
-	 */
-	private final List<Actor> actors;
-	
-	/**
-	 * Actions that are executed directly before the first step of this actor
-	 */
-	private final List<Action> preActions;
-	
-	/**
-	 * Actions that are executed directly after the last step of this actor
-	 */
-	private final List<Action> postActions;
-	
-	/**
-	 * Flag that indicates whether there is a next set value for the Actor
-	 */
-	private boolean next;
-	
-	/**
-	 * Index of the actor currently used
-	 */
-	private int actualActorCount;
-	
-	/**
-	 * Actor currently used to perform steps
-	 */
-	private Actor actualActor;
-	
-	/**
-	 * Flag to indicate the first set() execution of this actor.
-	 * This flag is used to decide whether to execute the pre actions.
-	 */
-	private boolean firstrun;
-	
-	/**
-	 * Constructor
-	 */
-	public ComplexActuator(){
-		this.actors = new ArrayList<Actor>();
-		this.preActions = new ArrayList<Action>();
-		this.postActions = new ArrayList<Action>();
-		
-		this.next = false;
-		this.actualActorCount = 0;
-		
-		this.firstrun = true;
-	}
-	
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Actor#set()
-	 */
-	@Override
-	public void set() throws InterruptedException {
-		// Throw an IllegalStateException in the case that set is called although there is no next step.
-		if(!next){
-			throw new IllegalStateException("The actuator does not have any next step.");
-		}
-		
-		// PRE actions
-		if(firstrun){
-			this.firstrun = false;
-			
-			// Execute pre actions
-			logger.finest("Execute pre actions");
-			for(Action action: preActions){
-				action.execute();
-			}
-		}
-		
-		actualActor.set(); // If the actor has no next step then something is wrong in the init/next step logic
-		
-		// If the last point of the actual actuator is set take the next actuator in the list if there is one available
-		while(!actualActor.hasNext()&&actualActorCount<actors.size()){
-			actualActorCount++;
-			if(actualActorCount<actors.size()){
-				actualActor = actors.get(actualActorCount);
-			}
-			else{
-				break;
-			}
-		}
-		
-		if(actualActor.hasNext()){
-			this.next = true;
-		}
-		else{
-			this.next = false;
-			
-			// Execute post actions
-			logger.finest("Execute post actions");
-			for(Action action: postActions){
-				action.execute();
-			}
-		}
-		
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Actor#hasNext()
-	 */
-	@Override
-	public boolean hasNext() {
-		return next;
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Actor#init()
-	 */
-	@Override
-	public void init() {
-		
-		// Initialize all actors this actor consist of
-		for(Actor a: actors){
-			a.init();
-		}
-		
-		// Set the actual actor to the first actor in the list
-		actualActorCount=0;
-		if(actualActorCount<actors.size()){
-			actualActor = actors.get(actualActorCount);
-			
-			// Check whether the actor has a next step, if not increase to the next one
-			// This is needed because the first actor might not have any step ... (very unlikely but bad things happens some time)
-			while(!actualActor.hasNext()&&actualActorCount<actors.size()){
-				actualActorCount++;
-				if(actualActorCount<actors.size()){
-					actualActor = actors.get(actualActorCount);
-				}
-				else{
-					break;
-				}
-			}
-			
-			if(actualActor.hasNext()){
-				this.next = true;
-			}
-			else{
-				this.next = false;
-			}
-			
-		}
-		else{
-			actualActor=null;
-			this.next=false;
-		}
-		
-		this.firstrun = true;
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Actor#reverse()
-	 */
-	@Override
-	public void reverse() {
-		// Reverse all actors this actor consist of
-		for(Actor a: actors){
-			a.reverse();
-		}
-	}
-	
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Actor#reset()
-	 */
-	@Override
-	public void reset() {
-		// Reset all actors this actor consist of
-		for(Actor a: actors){
-			a.reset();
-		}
-	}
-	
-	/**
-	 * Get the list of actors of this ComplexActor
-	 * @return the actors
-	 */
-	public List<Actor> getActors() {
-		return actors;
-	}
-
-	/**
-	 * @return the preActions
-	 */
-	public List<Action> getPreActions() {
-		return preActions;
-	}
-
-	/**
-	 * @return the postActions
-	 */
-	public List<Action> getPostActions() {
-		return postActions;
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Actor#destroy()
-	 */
-	@Override
-	public void destroy() {
-		// Destroy preActions
-		for(Action a: preActions){
-			a.destroy();
-		}
-		
-		// Destroy actors
-		for(Actor a: actors){
-			a.destroy();
-		}
-		
-		// Destroy postActions
-		for(Action a: postActions){
-			a.destroy();
-		}
-	}
-
-	
-	
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/actors/Function.java

@@ -1,28 +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.actors;
-
-/**
- * @author ebner
- *
- */
-public interface Function {
-	public double calculate(double parameter);
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/actors/JythonFunction.java

@@ -1,114 +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.actors;
-
-import java.util.Map;
-import java.util.logging.Logger;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import javax.script.ScriptEngine;
-import javax.script.ScriptEngineManager;
-import javax.script.ScriptException;
-
-import ch.psi.fda.core.scripting.JythonGlobalVariable;
-
-/**
- * @author ebner
- *
- */
-public class JythonFunction implements Function {
-	
-	// Get Logger
-	private static final Logger logger = Logger.getLogger(JythonFunction.class.getName());
-
-	public static final String ENTRY_FUNCTION_NAME = "calculate";
-	private static final String ENTRY_FUNCTION_PATTERN = "def "+ENTRY_FUNCTION_NAME+"\\((.*)\\):";
-	
-	/**
-	 * Script engine of the manipulator
-	 */
-	private ScriptEngine engine;
-	
-	private String additionalParameter = "";
-	
-	
-	public JythonFunction(String script, Map<String, JythonGlobalVariable> map){
-		// Create new script engine
-		this.engine = new ScriptEngineManager().getEngineByName("python");
-		
-		// Determine script entry function and the function parameters
-		String[] parameter;
-		Pattern pattern = Pattern.compile(ENTRY_FUNCTION_PATTERN);
-		Matcher matcher = pattern.matcher(script);
-		if(matcher.find() && matcher.groupCount()==1){
-			if(!matcher.group(1).trim().equals("")){
-				logger.finest("Entry function '"+ENTRY_FUNCTION_PATTERN+"' found - Identified parameters: "+matcher.group(1));
-				parameter = matcher.group(1).split(" *, *");
-			}
-			else{
-				parameter = new String[0];
-			}
-		}
-		else{
-			throw new IllegalArgumentException("Cannot determine entry function: "+ENTRY_FUNCTION_PATTERN);
-		}
-		
-		// Check whether all parameters are mapped
-		StringBuilder b = new StringBuilder();
-		for(int i=1;i<parameter.length; i++){ // Starting at 1 because first argument is implicit.
-			if(!map.containsKey(parameter[i])){
-				throw new IllegalArgumentException("Function parameter "+parameter[i]+" is not mapped");
-			}
-			b.append(",");
-			b.append(parameter[i]);
-		}
-		additionalParameter = b.toString();
-		
-		// Set variables in Jython engine
-		for(String k: map.keySet()){
-			engine.put(k, map.get(k));
-		}
-		
-		// Load manipulation script
-		try {
-			engine.eval(script);
-		} catch (ScriptException e) {
-			throw new RuntimeException("Unable to load manipulation script", e);
-		}
-	}
-	
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.actors.Function#calculate(double)
-	 */
-	@Override
-	public double calculate(double parameter) {
-		logger.fine("Function called");
-		
-		try {
-			logger.info("calculate( "+parameter+""+additionalParameter+" )");
-			return ((Double) engine.eval("calculate( "+parameter+""+additionalParameter+" )"));
-		} catch (ScriptException e) {
-			throw new RuntimeException("Calculating actuator step failed while executing the Jython script",e);
-		}
-		
-	}
-
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/actors/OTFActuator.java

@@ -1,188 +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.actors;
-
-import ch.psi.fda.core.Actor;
-
-/**
- * Special actuator for the OTFLoop. This type of actor must not be used in any other
- * type of loop than OTFLoop. If it is used it will, depending on the loop, immediately stop the loop
- * as it no single step.
- * @author ebner
- *
- */
-public class OTFActuator implements Actor {
-
-	/**
-	 * Name of the motor channel
-	 */
-	private final String name;
-	
-	/**
-	 * Channel name of the encoder;
-	 */
-	private final String readback;
-	
-	private  double start;
-	private  double end;
-	private final double stepSize;
-	private final double integrationTime;
-	
-	private final String id;
-	
-	/**
-	 * Additional backlash for the motor
-	 */
-	private final double additionalBacklash;
-	
-	
-	public OTFActuator(String id, String name, String readback, double start, double end, double stepSize, double integrationTime, double additionalBacklash){
-		this.id = id;
-		this.name = name;
-		this.readback = readback;
-		this.start = start;
-		this.end = end;
-		this.stepSize = stepSize;
-		this.integrationTime = integrationTime;
-		this.additionalBacklash = additionalBacklash;
-	}
-	
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Actor#set()
-	 */
-	@Override
-	public void set() {
-		// Do nothing
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Actor#hasNext()
-	 */
-	@Override
-	public boolean hasNext() {
-		return false;
-	}
-
-	
-	
-	/**
-	 * @return the name
-	 */
-	public String getName() {
-		return name;
-	}
-
-	/**
-	 * @return the readback
-	 */
-	public String getReadback() {
-		return readback;
-	}
-
-	/**
-	 * @return the start
-	 */
-	public double getStart() {
-		return start;
-	}
-
-	/**
-	 * @return the end
-	 */
-	public double getEnd() {
-		return end;
-	}
-
-	/**
-	 * @return the stepSize
-	 */
-	public double getStepSize() {
-		return stepSize;
-	}
-
-	/**
-	 * @return the integrationTime
-	 */
-	public double getIntegrationTime() {
-		return integrationTime;
-	}
-
-	/**
-	 * @return the additionalBacklash
-	 */
-	public double getAdditionalBacklash() {
-		return additionalBacklash;
-	}
-
-	/**
-	 * @return the id
-	 */
-	public String getId() {
-		return id;
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Actor#init()
-	 */
-	@Override
-	public void init() {
-		// Not implemented
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Actor#reverse()
-	 */
-	@Override
-	public void reverse() {
-		// Not implemented
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Actor#reset()
-	 */
-	@Override
-	public void reset() {
-		// Not implemented
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Actor#destroy()
-	 */
-	@Override
-	public void destroy() {
-		// Nothing to be done
-		
-	}
-
-	/**
-	 * @param start the start to set
-	 */
-	public void setStart(double start) {
-		this.start = start;
-	}
-
-	/**
-	 * @param end the end to set
-	 */
-	public void setEnd(double end) {
-		this.end = end;
-	}
-	
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/actors/PseudoActuatorSensor.java

@@ -1,135 +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.actors;
-
-import ch.psi.fda.core.Actor;
-import ch.psi.fda.core.Sensor;
-
-/**
- * Pseudo actor that is literally doing nothing for n times
- * @author ebner
- *
- */
-public class PseudoActuatorSensor implements Actor, Sensor {
-
-	/**
-	 * Execution count of actuator.
-	 */
-	private int count;
-	
-	/**
-	 * Number of counts for this actuator
-	 */
-	private final int counts;
-	
-	private final String id;
-	
-	/**
-	 * Constructor
-	 * @param counts
-	 * @param id		Id of the Actor/Sensor
-	 */
-	public PseudoActuatorSensor(String id, int counts){
-		if(counts < 1){
-			throw new IllegalArgumentException("Count ["+counts+"] must be > 0");
-		}
-		this.id = id;
-		this.counts = counts;
-		
-		init();
-	}
-	
-	
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Actor#set()
-	 */
-	@Override
-	public void set() {
-		
-		// Throw an IllegalStateException in the case that set is called although there is no next step.
-		if(!hasNext()){
-			throw new IllegalStateException("The actuator does not have any next step.");
-		}
-		
-		count++;
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Actor#hasNext()
-	 */
-	@Override
-	public boolean hasNext() {
-		return (count<counts);
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Actor#init()
-	 */
-	@Override
-	public void init() {
-		count=0; // Set count back to 0
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Actor#reverse()
-	 */
-	@Override
-	public void reverse() {
-		// Not implemented
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Actor#reset()
-	 */
-	@Override
-	public void reset() {
-		// NOt implemented
-	}
-
-	
-	// Sensor implementation
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Sensor#read()
-	 */
-	@Override
-	public Object read() {
-		return new Double(count); // Return actual count
-	}
-
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Sensor#getId()
-	 */
-	@Override
-	public String getId() {
-		return this.id;
-	}
-
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Actor#destroy()
-	 */
-	@Override
-	public void destroy() {
-		// Nothing to be done
-	}
-
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/collector/Collector.java

@@ -1,165 +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.collector;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.concurrent.BlockingQueue;
-import java.util.concurrent.LinkedBlockingQueue;
-import java.util.logging.Logger;
-
-import ch.psi.fda.core.messages.ComponentMetadata;
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.DataMessageMetadata;
-import ch.psi.fda.core.messages.DataQueue;
-import ch.psi.fda.core.messages.StreamDelimiterMessage;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Message;
-
-/**
- * Collector class that is collecting and merging data from different Queues.
- * @author ebner
- *
- */
-public class Collector implements Runnable{
-	
-	// Get Logger
-	private static Logger logger = Logger.getLogger(Collector.class.getName());
-	
-	/**
-	 * List of queues and their metadata this collector is responsible to readout.
-	 * The logic is as follows:
-	 * Read out the last queue until the first queue in the list has the EndOfLoopMessage.
-	 */
-	private List<DataQueue> queues;
-	
-	/**
-	 * Outgoing queue of this collector
-	 */
-	private BlockingQueue<Message> outQueue;
-	
-	/**
-	 * Constructor
-	 */
-	public Collector(){
-		queues = new ArrayList<DataQueue>();
-		outQueue = new LinkedBlockingQueue<Message>(1000); // Create bounded queue to prevent running out of memory ...
-	}
-	
-	/* (non-Javadoc)
-	 * @see java.lang.Runnable#run()
-	 */
-	@Override
-	public void run() {
-		
-		if(queues.size()>0){
-			try{
-				readQueue(0, null);
-			}
-			catch(InterruptedException e){
-				// Readout aborted through interrupt
-			}
-		}
-		else{
-			// No queue registered for reading
-		}
-		
-		try {
-			
-			outQueue.put(new EndOfStreamMessage());
-			
-		} catch (InterruptedException e) {
-			// TODO Stop loop and exit logic instead of throwing an Exception
-			throw new RuntimeException("Unable to terminate stream with and End of Stream Message",e);
-		}
-		
-		logger.info("END");
-		
-	}
-
-	
-	private void readQueue(int index, DataMessage m) throws InterruptedException{
-		
-		BlockingQueue<Message> q = queues.get(index).getQueue();
-		
-		// Read Message
-		Message message = q.take();
-		while(message instanceof DataMessage){
-			// Create new data message 
-			DataMessage dm = new DataMessage();
-			if(m!=null){
-				dm.getData().addAll(m.getData());
-			}
-			
-			dm.getData().addAll(((DataMessage)message).getData());
-			
-			if(index<(queues.size()-1)){
-				readQueue(index+1, dm);
-			}
-			else{
-				// Write message to outgoing queue
-				outQueue.put(dm);
-			}
-			
-			// Read next message
-			message = q.take();
-		}
-		
-		if(message instanceof EndOfStreamMessage){
-			// Translate EndOfStream to StreamDelimiter message
-			StreamDelimiterMessage ddm = new StreamDelimiterMessage(queues.size()-1-index, ((EndOfStreamMessage)message).isIflag());
-			// Write message to outgoing queue
-			outQueue.put(ddm);
-		}
-	}
-	
-
-	/**
-	 * @return the queues
-	 */
-	public List<DataQueue> getQueues() {
-		return queues;
-	}
-	
-	
-	/**
-	 * Get the outgoing data queue.
-	 * Attention, only call this method after all ingoing queues were registered! Otherwise the data returned
-	 * by this method is not accurate.
-	 * @return	output queue of collector
-	 */
-	public DataQueue getOutQueue(){
-		DataMessageMetadata dataMessageMetadata = new DataMessageMetadata();
-		dataMessageMetadata.getComponents();
-		
-		// Generate new combined metadata and add dimension information to the components
-		int nq = queues.size();
-		for(int i=0;i<nq;i++){
-			DataQueue q = queues.get(i);
-			for(ComponentMetadata cm: q.getDataMessageMetadata().getComponents()){
-				// The dimension number is the number of queues minus the index of the current queue minus 1 (because dimension index starts at 0)
-				dataMessageMetadata.getComponents().add(new ComponentMetadata(cm.getId(), nq-i-1));
-			}
-		}
-		
-		return(new DataQueue(outQueue, dataMessageMetadata));
-	}
-
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/collector/DataDispatcher.java

@@ -1,88 +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.collector;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import ch.psi.fda.core.messages.DataQueue;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Message;
-
-/**
- * Serialize data received by a DataQueue
- * @author ebner
- *
- */
-public class DataDispatcher implements Runnable{
-	
-	private DataQueue queue;
-	private List<DataQueue> outQueues;
-	
-	public DataDispatcher(DataQueue queue){
-		this.queue = queue;
-		this.outQueues = new ArrayList<DataQueue>();
-	}
-
-	/* (non-Javadoc)
-	 * @see java.lang.Runnable#run()
-	 */
-	@Override
-	public void run() {
-		try{
-
-			// TODO Need to synchronize message metadata
-//			for(DataQueue q: outQueues){
-//			}
-			
-			// Dispatch Messages
-			Message message = queue.getQueue().take();
-			while(!(message instanceof EndOfStreamMessage)){
-				
-				// Clone message ...
-				for(DataQueue q: outQueues){
-					q.getQueue().put(message);
-				}
-				
-				// Read next message
-				message = queue.getQueue().take();
-			}
-			
-			// Write end of stream message
-			for(DataQueue q: outQueues){
-				q.getQueue().put(message);
-			}
-			
-		} catch (InterruptedException e) {
-			// TODO Stop loop and exit logic instead of throwing an Exception
-			throw new RuntimeException("Data serializer was interrupted while writing data to file",e);
-		} 
-	}
-
-	/**
-	 * @return the outQueues
-	 */
-	public List<DataQueue> getOutQueues() {
-		return outQueues;
-	}
-	
-	
-	
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/guard/ChannelAccessGuard.java

@@ -1,118 +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.guard;
-
-import java.beans.PropertyChangeEvent;
-import java.beans.PropertyChangeListener;
-import java.util.List;
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.TimeoutException;
-import java.util.logging.Level;
-import java.util.logging.Logger;
-
-import ch.psi.fda.core.Guard;
-import ch.psi.jcae.ChannelException;
-
-/**
- * Guard checking channels to meet a certain condition
- * @author ebner
- *
- */
-public class ChannelAccessGuard implements Guard {
-
-	
-	// Get Logger
-	private static Logger logger = Logger.getLogger(ChannelAccessGuard.class.getName());
-	
-	/**
-	 * Flag to indicate whether a guard condition failed since the last init call
-	 * true: all conditions met, false: at least one condition failed
-	 */
-	private boolean check = true;
-	
-	private final List<ChannelAccessGuardCondition> conditions;
-	
-	/**
-	 * Constructor
-	 * @param conditions
-	 */
-	public ChannelAccessGuard(List<ChannelAccessGuardCondition> conditions){
-
-		this.conditions = conditions;
-		
-		// Create channel that contribute to the status of the guard
-		for(final ChannelAccessGuardCondition condition: conditions){
-			condition.getChannel().addPropertyChangeListener(new PropertyChangeListener() {		
-				@Override
-				public void propertyChange(PropertyChangeEvent evt) {
-					if(! evt.getNewValue().equals(condition.getValue())){
-						check=false;
-					}
-				}
-			});
-		}
-	}
-	
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Guard#init()
-	 */
-	@Override
-	public void init() {
-		check = true;
-		
-		// Check one time if all conditions are met
-		for(ChannelAccessGuardCondition condition: conditions){
-			try{
-				if(! (condition.getChannel().getValue(true)).equals(condition.getValue()) ){
-					check=false;
-					// Early exit
-					break;
-				}
-			}
-			catch(ChannelException | TimeoutException | ExecutionException e){
-				logger.log(Level.WARNING, "Unable ", e);
-				check=false;
-			} catch (InterruptedException e) {
-				throw new RuntimeException("Guard interrupted ",e);
-			}
-		}
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Guard#check()
-	 */
-	@Override
-	public boolean check() {
-		return check;
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Guard#destroy()
-	 */
-	@Override
-	public void destroy() {
-		// Destroy Guard Conditions
-		for(ChannelAccessGuardCondition condition: conditions){
-			condition.destroy();
-		}
-		
-	}
-
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/guard/ChannelAccessGuardCondition.java

@@ -1,98 +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.guard;
-
-import java.util.concurrent.TimeoutException;
-import java.util.logging.Logger;
-
-import ch.psi.jcae.Channel;
-import ch.psi.jcae.ChannelDescriptor;
-import ch.psi.jcae.ChannelException;
-import ch.psi.jcae.ChannelService;
-
-/**
- * Channel and condition that need to be met. 
- * @author ebner
- *
- */
-public class ChannelAccessGuardCondition {
-	
-	// Get Logger
-	private static Logger logger = Logger.getLogger(ChannelAccessGuardCondition.class.getName());
-	
-	/**
-	 * Channel name
-	 */
-	private final Channel<?> channel;
-	
-	/**
-	 * Value of the channel to meet condition
-	 */
-	private final Object value;
-
-	/**
-	 * Constructor
-	 * @param channel	Name of the channel that contributes to a guard
-	 * @param value
-	 */
-	public ChannelAccessGuardCondition(ChannelService s, String channel, Object value){
-		try {
-			this.channel = s.createChannel(new ChannelDescriptor<>(value.getClass(), channel, true));
-		} catch (ChannelException | TimeoutException e) {
-			// Convert Exception into unchecked RuntimeException
-			throw new IllegalArgumentException("Unable to initialize actuator channel [name:"+channel+"]",e);
-		} catch (InterruptedException e) {
-			throw new RuntimeException("Unable to initialize actuator channel [name:"+channel+"]",e);
-		}
-		this.value = value;
-	}
-	
-	/**
-	 * @return the channel
-	 */
-	public Channel<?> getChannel() {
-		return channel;
-	}
-
-	/**
-	 * @return the value
-	 */
-	public Object getValue() {
-		return value;
-	}
-	
-	/**
-	 * Destroy guard condition. 
-	 * Can be used for the cleanup of used resources of the guard condition (e.g. to close connections, ...) if
-	 * this cannot be done automatically by the GarbageCollector.
-	 * 
-	 * After calling this method the guard condition must not be used any more!
-	 */
-	public void destroy(){
-		// Destroy channel
-		try {
-			logger.finest("Destroy guard condition channel: "+channel.getName());
-			channel.destroy();
-		} catch (ChannelException e) {
-			throw new RuntimeException("Unable to destroy channel ["+channel.getName()+"]",e);
-		}
-	}
-	
-}

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

@@ -1,590 +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.loops;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.concurrent.BlockingQueue;
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.Executors;
-import java.util.concurrent.Future;
-import java.util.concurrent.LinkedBlockingQueue;
-import java.util.logging.Logger;
-
-import ch.psi.fda.core.Action;
-import ch.psi.fda.core.ActionLoop;
-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.ComponentMetadata;
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.DataMessageMetadata;
-import ch.psi.fda.core.messages.DataQueue;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Message;
-
-/**
- * Loop of actions to accomplish a task or test.
- * @author ebner
- *
- */
-public class ActorSensorLoop implements ActionLoop {
-	
-	// Get Logger
-	private static Logger logger = Logger.getLogger(ActorSensorLoop.class.getName());
-	
-	/**
-	 * Flag to indicate whether the data of this loop will be grouped
-	 * According to this flag the dataGroup flag in EndOfStream will be set.
-	 */
-	private boolean dataGroup = false;
-	
-	/**
-	 * List of additional action loops that are executed at the end of each
-	 * iteration of the loop
-	 */
-	private List<ActionLoop> actionLoops;
-	/**
-	 * List of actions that are executed at the beginning of the loop.
-	 */
-	private List<Action> preActions;
-	/**
-	 * List of actions that are executed at the end of the loop.
-	 */
-	private List<Action> postActions;
-	
-	/**
-	 * List of actions that are executed before the actors are set
-	 */
-	private List<Action> preActorActions;
-	
-	/**
-	 * List of actions that are executed after all actors have been set
-	 */
-	private List<Action> postActorActions;
-	
-	/**
-	 * List of actions that are executed before the sensors are read out
-	 */
-	private List<Action> preSensorActions;
-	/**
-	 * List of actions that are executed after all sensors have been read out
-	 */
-	private List<Action> postSensorActions;
-	
-	/**
-	 * List of actors of this loop
-	 */
-	private List<Actor> actors;
-	
-	/**
-	 * List of sensors of this loop
-	 */
-	private List<Sensor> sensors;
-	
-	/**
-	 * Data queue sensor data is posted to. A message consists of a list of data objects
-	 * that are read out of the sensors of this loop.
-	 */
-	private BlockingQueue<Message> dataQueue;
-	
-	/**
-	 * Guard used to check whether the environment was ok while reading out the sensors
-	 */
-	private Guard guard = null;
-	
-	private volatile boolean loop = false;
-	private volatile boolean abort = false;
-	
-	private final boolean zigZag;
-	
-	private List<ActorSetCallable> pactors;
-	
-	
-	/**
-	 * Default constructor
-	 */
-	public ActorSensorLoop(){
-		this(false);
-	}
-	
-	/**
-	 * Create instance of the 
-	 */
-	public ActorSensorLoop(boolean zigZag){
-		this.zigZag = zigZag;
-		this.actionLoops = new ArrayList<ActionLoop>();
-		this.preActions = new ArrayList<Action>();
-		this.postActions = new ArrayList<Action>();
-		this.preActorActions = new ArrayList<Action>();
-		this.postActorActions = new ArrayList<Action>();
-		this.preSensorActions = new ArrayList<Action>();
-		this.postSensorActions = new ArrayList<Action>();
-		
-		this.actors = new ArrayList<Actor>();
-		this.pactors = new ArrayList<ActorSetCallable>();
-		this.sensors = new ArrayList<Sensor>();
-		
-		this.dataQueue = new LinkedBlockingQueue<Message>(1000);
-	}
-	
-	
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.engine.ActionLoop#execute()
-	 */
-	/**
-	 * Executes the actor sensor loop. The actor sensor loop is build up as follows:
-	 * preActions
-	 * loop{
-	 *  check actors - abort if there are no new steps
-	 *  pre actor actions
-	 *  set actors
-	 *  post actor actions
-	 *  pre sensor actions
-	 *  read sensors
-	 *  post sensor actions
-	 *  execute additional registered action loops
-	 * }
-	 * postActions
-	 * @throws InterruptedException 
-	 */
-	@Override
-	public void execute() throws InterruptedException {
-		abort = false;
-		
-		/**
-		 * Thread pool for parallel execution of tasks
-		 */
-		ExecutorService executorService = Executors.newCachedThreadPool();
-		
-		loop = true;
-		
-		// Execute pre actions
-		for(Action action: preActions){
-			action.execute();
-		}
-		
-		// Initialize actors of Loop
-		for(Actor actor: actors){
-			actor.init();
-		}
-		
-		// Variable to store the last guard status
-		boolean guardOK=true;
-		
-		try{
-			
-			// Execute loop logic
-			while(loop){
-				
-				if(guardOK){
-					
-					
-					// If actors are defined for the loop check whether all of them
-					// have a next step defined if there is no actor defined only run this loop once
-					if(actors.size()>0){
-						// Check whether the actors of this loop have a next step. If not 
-						// abort the loop
-						boolean hasNext = true;
-						for(Actor actor: actors){
-							if(!actor.hasNext()){
-								hasNext=false;
-								break; // Stop actor check loop
-							}
-						}
-						
-						// If not all actors have a next step abort the loop
-						if(!hasNext){
-							break; // Stop action loop
-						}
-					}
-					else{
-						// No actors defined, only run loop once
-						loop = false;
-					}
-		
-					
-					
-					// Execute pre actor actions
-					for(Action action: preActorActions){
-						action.execute();
-					}
-					
-					if(abort){ // End loop if abort was issued
-						break;
-					}
-					
-					// Set actors
-	//				for(Actor actor: actors){
-	//					actor.set();
-	//				}
-					// Parallel set of the actors
-					try {
-						for (Future<Object> f : executorService.invokeAll(pactors)) {
-						    f.get(); //Blocks until the async set() is finished
-						}
-					} catch (ExecutionException e) {
-						throw new RuntimeException("Setting the actors failed",e);
-					}
-					
-					// Execute post actor actions
-					for(Action action: postActorActions){
-						action.execute();
-					}
-					
-					if(abort){ // End loop if abort was issued
-						break;
-					}
-				
-				}
-				
-				if(guard!=null){
-					// Initialize guard
-					guard.init();
-					guardOK=guard.check();
-					
-					// Wait until guard is ok
-					while(!guardOK){
-						logger.info("Waiting for guard condition(s) to be met");
-						// Sleep 100 milliseconds before next check
-						Thread.sleep(1000);
-						
-						// Check whether the loop is not aborted, if it is aborted
-						// break the wait loop (afterwards also the loop loop is aborted)
-						if(!loop){
-							break;
-						}
-						
-						guard.init();
-						guardOK=guard.check();
-					}
-					
-					// If loop is aborted proceed to next iteration an abort loop
-					if(!loop){
-						continue;
-					}
-				}
-				
-				// Execute pre sensor actions
-				for(Action action: preSensorActions){
-					action.execute();
-				}
-				
-				if(abort){ // End loop if abort was issued
-					break;
-				}
-				
-				// Read sensors
-				DataMessage message = new DataMessage();
-				for(Sensor sensor: sensors){
-					// Readout sensor
-					Object o = sensor.read();
-					// Add sensor data item to message
-					message.getData().add(o);
-				}
-				
-				// Execute post sensor actions
-				for(Action action: postSensorActions){
-					action.execute();
-				}
-				
-				if(abort){ // End loop if abort was issued
-					break;
-				}
-				
-				// Check guard if one is registered
-				if(guard!=null){
-					guardOK=guard.check();
-				}
-				
-				if(guardOK){
-				
-					// Post a message with the sensor data
-					dataQueue.put(message);
-					
-					// Loop all configured ActionLoop objects
-					for(ActionLoop actionLoop: actionLoops){
-						actionLoop.execute();
-					}
-				}
-			}
-			
-			// Execute post actions
-			for(Action action: postActions){
-				action.execute();
-			}
-		
-		}
-		finally{
-			// Ensure that data stream is terminated ...
-			
-			// Issue end of loop control message
-			// Set iflag of the EndOfStreamMessage according to dataGroup flag of this loop
-			dataQueue.put(new EndOfStreamMessage(dataGroup));
-		}
-		
-		if(zigZag){
-			// Reverse actors for the next run
-			for(Actor actor: actors){
-				actor.reverse();
-			}
-		}
-		
-		executorService.shutdownNow();
-		
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.engine.ActionLoop#abort()
-	 */
-	@Override
-	public void abort(){
-		abort = true;
-		loop = false;
-		
-		// To abort all wait actions interrupt this thread
-		for(Action a: preSensorActions){
-			a.abort();
-		}
-		
-		// Recursively abort all registered action loops
-		for(ActionLoop actionLoop: actionLoops){
-			actionLoop.abort();
-		}
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.ActionLoop#prepare()
-	 */
-	@Override
-	public void prepare() {
-		// Put in prepare code here
-		
-		// Create callable for all actors
-		pactors.clear();
-		for(final Actor a: actors){
-			pactors.add(new ActorSetCallable(a));
-		}
-		
-		// Reset all actuators
-		for(Actor a: actors){
-			a.reset();
-		}
-		
-		// Recursively call prepare() method of all registered action loops
-		for(ActionLoop actionLoop: actionLoops){
-			actionLoop.prepare();
-		}
-	}
-
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.ActionLoop#cleanup()
-	 */
-	@Override
-	public void cleanup() {
-		// Put in cleanup code here
-		
-		// Recursively call cleanup() method of all registered action loops
-		for(ActionLoop actionLoop: actionLoops){
-			actionLoop.cleanup();
-		}
-	}
-	
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#destroy()
-	 */
-	@Override
-	public void destroy() {
-
-		// Call destroy method of sub components
-		for(Action a: preActions){
-			logger.finest("Destroy pre-action");
-			a.destroy();
-		}
-		
-		for(Action a: postActions){
-			logger.finest("Destroy post-action");
-			a.destroy();
-		}
-		
-		for(Action a: preActorActions){
-			logger.finest("Destroy pre-actor action");
-			a.destroy();
-		}
-		
-		for(Action a: postActorActions){
-			logger.finest("Destroy post-actor action");
-			a.destroy();
-		}
-		
-		for(Action a: preSensorActions){
-			logger.finest("Destroy pre-sensor action");
-			a.destroy();
-		}
-		
-		for(Action a: postSensorActions){
-			logger.finest("Destroy post-sensor action");
-			a.destroy();
-		}
-		
-		for(Actor a: actors){
-			logger.finest("Destroy actor");
-			a.destroy();
-		}
-		
-		for(Sensor s: sensors){
-			logger.finest("Destroy sensor");
-			s.destroy();
-		}
-		
-		if(guard != null){
-			logger.finest("Destroy guard");
-			guard.destroy();
-		}
-		
-		// Recursively call cleanup() method of all registered action loops
-		for(ActionLoop actionLoop: actionLoops){
-			logger.finest("Destroy action loop");
-			actionLoop.destroy();
-		}
-	}
-	
-	
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.ActionLoop#getPreActions()
-	 */
-	@Override
-	public List<Action> getPreActions() {
-		return preActions;
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.ActionLoop#getPostActions()
-	 */
-	@Override
-	public List<Action> getPostActions() {
-		return postActions;
-	}
-	
-
-	/**
-	 * The structure of the data message depends on the sensors registered at this loop 
-	 * at the time this method is called.
-	 * @return the data queue and the metadata of the data messages
-	 */
-	public DataQueue getDataQueue() {
-		DataMessageMetadata m = new DataMessageMetadata();
-		
-		// Build up data message metadata based on the sensors currently registered.
-		for(Sensor s: sensors){
-			m.getComponents().add(new ComponentMetadata(s.getId()));
-		}
-		return new DataQueue(dataQueue, m);
-	}
-	
-	// Getter functions for variable parts
-	
-	/**
-	 * @return the actionLoops
-	 */
-	public List<ActionLoop> getActionLoops() {
-		return actionLoops;
-	}
-	
-
-	/**
-	 * @return the preActorActions
-	 */
-	public List<Action> getPreActorActions() {
-		return preActorActions;
-	}
-
-
-	/**
-	 * @return the postActorActions
-	 */
-	public List<Action> getPostActorActions() {
-		return postActorActions;
-	}
-
-
-	/**
-	 * @return the preSensorActions
-	 */
-	public List<Action> getPreSensorActions() {
-		return preSensorActions;
-	}
-
-
-	/**
-	 * @return the postSensorActions
-	 */
-	public List<Action> getPostSensorActions() {
-		return postSensorActions;
-	}
-
-
-	/**
-	 * @return the actors
-	 */
-	public List<Actor> getActors() {
-		return actors;
-	}
-
-
-	/**
-	 * @return the sensors
-	 */
-	public List<Sensor> getSensors() {
-		return sensors;
-	}
-
-	/**
-	 * @return the guard
-	 */
-	public Guard getGuard() {
-		return guard;
-	}
-
-	/**
-	 * @param guard the guard to set
-	 */
-	public void setGuard(Guard guard) {
-		this.guard = guard;
-	}
-
-	/**
-	 * @return the dataGroup
-	 */
-	public boolean isDataGroup() {
-		return dataGroup;
-	}
-
-	/**
-	 * @param dataGroup the dataGroup to set
-	 */
-	public void setDataGroup(boolean dataGroup) {
-		this.dataGroup = dataGroup;
-	}
-
-}

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

@@ -1,162 +0,0 @@
-/**
- * 
- * Copyright 2012 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.loops;
-
-import java.io.File;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.net.MalformedURLException;
-
-import jcifs.smb.SmbFile;
-
-/**
- * @author ebner
- *
- */
-public class DistributedFile {
-
-	private SmbFile smbfile = null;
-	private File file = null;
-	
-	public DistributedFile(SmbFile file){
-		this.smbfile = file;
-	}
-	
-	public DistributedFile(File file){
-		this.file = file;
-	}
-	
-	public DistributedFile(String url) throws MalformedURLException{
-		if(url.startsWith("smb://")){
-			smbfile = new SmbFile(url);
-		}
-		else {
-			file = new File(url);
-		}
-	}
-
-	
-	public String getCanonicalPath() throws IOException{
-		if(smbfile!=null){
-			return(smbfile.getCanonicalPath());
-		}
-		else{
-			return file.getCanonicalPath();
-		}
-	}
-
-
-	/**
-	 * @return
-	 * @throws IOException 
-	 */
-	public boolean exists() throws IOException {
-		if(smbfile!=null){
-			return(smbfile.exists());
-		}
-		else{
-			return file.exists();
-		}
-	}
-
-
-	/**
-	 * @return
-	 */
-	public boolean isDirectory() throws IOException {
-		if(smbfile!=null){
-			return(smbfile.isDirectory());
-		}
-		else{
-			return file.isDirectory();
-		}
-	}
-
-
-	/**
-	 * @return
-	 */
-	public DistributedFile[] listFiles() throws IOException {
-		if(smbfile!=null){
-			SmbFile[] files = smbfile.listFiles();
-			DistributedFile[] dfiles = new DistributedFile[files.length];
-			for(int i=0;i<files.length;i++){
-				dfiles[i] = new DistributedFile(files[i]);
-			}
-			return(dfiles);
-		}
-		else{
-			File[] files = file.listFiles();
-			DistributedFile[] dfiles = new DistributedFile[files.length];
-			for(int i=0;i<files.length;i++){
-				dfiles[i] = new DistributedFile(files[i]);
-			}
-			return(dfiles);
-		}
-	}
-
-	/**
-	 * @return
-	 */
-	public String getName() {
-		if(smbfile!=null){
-			return(smbfile.getName());
-		}
-		else{
-			return file.getName();
-		}
-	}
-
-	/**
-	 * @return
-	 */
-	public boolean isFile() throws IOException {
-		if(smbfile!=null){
-			return(smbfile.isFile());
-		}
-		else{
-			return file.isFile();
-		}
-	}
-
-	/**
-	 * 
-	 */
-	public void delete() throws IOException {
-		if(smbfile!=null){
-			smbfile.delete();
-		}
-		else{
-			file.delete();
-		}
-	}
-
-	/**
-	 * @return
-	 */
-	public InputStreamReader getInputStream() throws IOException {
-		if(smbfile!=null){
-			return(new InputStreamReader(smbfile.getInputStream()));
-		}
-		else{
-			return new FileReader(file);
-		}
-	}
-}

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

@@ -1,801 +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.loops;
-
-import java.util.List;
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.TimeoutException;
-
-import ch.psi.jcae.Channel;
-import ch.psi.jcae.ChannelException;
-import ch.psi.jcae.annotation.CaChannel;
-
-/**
- * Bean holding all OTF channels and functionality
- * @author ebner
- *
- */
-public class OTFBean {
-
-	public enum Status { SETUP, INACTIVE, INITIALIZE, ACTIVE, STOP, FAULT, ERROR };
-	public enum Command { NONE, START, STOP };
-	
-	private long timeoutMotorOk = 8000;
-	private long commandTimeout = 20000; // Maximum time until a command should take effect
-
-	@CaChannel(type=String.class, name ="${PREFIX}:UMOT")
-	private Channel<String> motor;
-	
-	@CaChannel(type=String.class, name="${PREFIX}:MENC")
-	private Channel<String> encoder;
-	
-	@CaChannel(type=Double.class, name="${PREFIX}:UBEG")
-	private Channel<Double> begin;
-	
-	@CaChannel(type=Double.class, name="${PREFIX}:UBEG.DRVL")
-	private Channel<Double> beginMin;
-	
-	@CaChannel(type=Double.class, name="${PREFIX}:UBEG.DRVH")
-	private Channel<Double> beginMax;
-	
-	@CaChannel(type=Double.class, name="${PREFIX}:UEND")
-	private Channel<Double> end;
-	
-	@CaChannel(type=Double.class, name="${PREFIX}:UEND.DRVL")
-	private Channel<Double> endMin;
-	
-	@CaChannel(type=Double.class, name="${PREFIX}:UEND.DRVH")
-	private Channel<Double> endMax;
-	
-	@CaChannel(type=Double.class, name="${PREFIX}:USSIZ")
-	private Channel<Double> stepSize;
-	
-	@CaChannel(type=Double.class, name="${PREFIX}:USSIZ.DRVL")
-	private Channel<Double> stepSizeMin;
-	
-	@CaChannel(type=Double.class, name="${PREFIX}:UITIM")
-	private Channel<Double> integrationTime;
-	
-	@CaChannel(type=Double.class, name="${PREFIX}:UITIM.DRVL")
-	private Channel<Double> integrationTimeMin;
-	
-	@CaChannel(type=Double.class, name="${PREFIX}:UITIM.DRVH")
-	private Channel<Double> integrationTimeMax;
-	
-	@CaChannel(type=Double.class, name="${PREFIX}:UBCL")
-	private Channel<Double> userBacklash;
-	
-	@CaChannel(type=String.class, name="${PREFIX}:NFSSE")
-	private Channel<String> nfsServer;
-	
-	@CaChannel(type=String.class, name="${PREFIX}:NFSSH")
-	private Channel<String> nfsShare;
-	
-	@CaChannel(type=String.class, name="${PREFIX}:DFNAM")
-	private Channel<String> fileName;
-	
-	@CaChannel(type=String.class, name="${PREFIX}:FFORM")
-	private Channel<String> fileNameFormat;
-	
-	@CaChannel(type=Integer.class, name="${PREFIX}:FCNT")
-	private Channel<Integer> fileCount;
-	
-	@CaChannel(type=Integer.class, name="${PREFIX}:FCNT.B")
-	private Channel<Integer> resetFileCounter;
-	
-	@CaChannel(type=Boolean.class, name="${PREFIX}:FAPPE")
-	private Channel<Boolean> appendFile;
-
-	@CaChannel(type=Boolean.class, name="${PREFIX}:FUSE")
-	private Channel<Boolean> fileNameGeneration;
-	
-	@CaChannel(type=Boolean.class, name="${PREFIX}:UZIGZ")
-	private Channel<Boolean> zigZag;
-	
-	@CaChannel(type=Integer.class, name="${PREFIX}:UCOM")
-	private Channel<Integer> command;
-	
-	@CaChannel(type=Boolean.class, name="${PREFIX}:SCRU", monitor=true)
-	private Channel<Boolean> scanRunning;
-	
-	@CaChannel(type=Boolean.class, name="${PREFIX}:MUENC")
-	private Channel<Boolean> useEncoder;
-	
-	@CaChannel(type=String.class, name={"${PREFIX}:CTM0","${PREFIX}:CTM1","${PREFIX}:CTM2","${PREFIX}:CTM3","${PREFIX}:CTM4","${PREFIX}:CTM5","${PREFIX}:CTM6","${PREFIX}:CTM7"})
-	private List<Channel<String>> monitoredChannels;
-	
-	@CaChannel(type=Boolean.class, name="${PREFIX}:OTF", monitor=true)
-	private Channel<Boolean> running;
-	
-	@CaChannel(type=Integer.class, name="${PREFIX}:USTAT", monitor=true)
-	private Channel<Integer> status;
-	
-	@CaChannel(type=Boolean.class, name="${PREFIX}:MOK", monitor=true)
-	private Channel<Boolean> motorOk;
-	
-	@CaChannel(type=Boolean.class, name="${PREFIX}:EOK", monitor=true)
-	private Channel<Boolean> encoderOk;
-	
-	@CaChannel(type=String.class, name="${PREFIX}:MSG")
-	private Channel<String> message;
-
-	/**
-	 * Get the trigger name that can be used by the sscan record to trigger an OTFScan
-	 * @return	Name of the trigger that can be used by sscan record
-	 */
-	public String getSScanTriggerName(){
-		return(running.getName());
-	}
-
-	/**
-	 * Start OTF scan
-	 */
-	public void start() {
-		try{
-		if(getStatus().equals(Status.INACTIVE)){
-			
-			// Send START command
-			this.command.setValue(Command.START.ordinal());
-			
-			// Wait until OtF logic is active
-			this.scanRunning.waitForValue(true, commandTimeout);
-		}
-		else{
-			throw new RuntimeException("Cannot start scan, status is not INACTIVE.\nThe current status is: "+getStatus()+" . The OTF logic need to be recovered manually [Message: "+getMessage()+"]");
-		}
-		}
-		catch(Exception e){
-			throw new RuntimeException("Unable to start OTF scan.",e);
-		}
-	}
-	
-	/**
-	 * Abort scan
-	 */
-	public void abort() {
-		try{
-			// Send STOP command
-			this.command.setValue(Command.STOP.ordinal());
-	
-			// Do not wait for put to return
-			this.running.setValueNoWait(false);
-		}
-		catch(Exception e){
-			throw new RuntimeException("Unable to abort OTF logic" ,e);
-		}
-	}
-	
-	/**
-	 * Stop OTF scan
-	 * @throws Exception
-	 */
-	public void stop() throws Exception{
-		if(!getStatus().equals(Status.INACTIVE) || !getStatus().equals(Status.FAULT)){
-			
-			// Send STOP command
-			this.command.setValue(Command.STOP.ordinal());
-
-			// Wait until logic is stopped
-			status.waitForValue(Status.INACTIVE.ordinal(), commandTimeout);
-		}
-		
-	}
-
-	/**
-	 * Wait until scan has stopped
-	 * @throws InterruptedException 
-	 */
-	public void waitUntilStopped() throws InterruptedException {
-		try {
-			scanRunning.waitForValue(false); // Use of default wait timeout
-			
-			// Check whether the status is INACTIVE otherwise get messge from OTF and throw an exception
-			if(status.getValue() != Status.INACTIVE.ordinal()){
-				throw new RuntimeException("OTFSCAN failed with message: "+message.getValue());
-			}
-			
-		} catch (ChannelException | ExecutionException | TimeoutException e) {
-			throw new RuntimeException("An error occurred while waiting for the OTF logic to finish.", e);
-		}
-	}
-	
-	/**
-	 * Wait until scan has stopped
-	 * @param waitTimeout
-	 * @throws InterruptedException 
-	 */
-	public void waitUntilStopped(Long waitTimeout) throws InterruptedException {
-		try {
-			scanRunning.waitForValue(false, waitTimeout);
-			
-			// Check whether the status is INACTIVE otherwise get messge from OTF and throw an exception
-			if(status.getValue() != Status.INACTIVE.ordinal()){
-				throw new RuntimeException("OTFSCAN failed with message: "+message.getValue());
-			}
-			
-		} catch (ChannelException | ExecutionException | TimeoutException e) {
-			throw new RuntimeException("An error occurred while waiting for the OTF logic to finish.", e);
-		}
-		
-		
-		
-	}
-	
-	/**
-	 * Reset OTFScan records to defaults
-	 * @throws TimeoutException, ChannelException, ExecutionException
-	 * @throws InterruptedException 
-	 */
-	public void resetToDefaults() throws ChannelException , ExecutionException , TimeoutException, InterruptedException{
-		setMonitoredChannels(new String[]{});
-		setMotor("");
-		begin.setValue(0d);
-		end.setValue(0d);
-		stepSize.setValue(0d);
-		integrationTime.setValue(0d);
-		zigZag.setValue(false);
-		setAppendFile(false);
-		setFileNameGeneration(true);
-		setFileName("");
-		setFileNameFormat("%06d.txt");
-		resetFileCounter();
-		
-		setUserBacklash(0d);
-		
-//		setNfsServer("");
-//		setNfsShare("");
-		
-		waitUntilMotorNotOk(timeoutMotorOk);
-	}
-
-	/**
-	 * Get motor of the OTFScan axis
-	 * @return	Name of the OTF motor
-	 * @throws ExecutionException 
-	 * @throws TimeoutException 
-	 * @throws TimeoutException, ChannelException, ExecutionException
-	 */
-	public String getMotor() throws ChannelException, InterruptedException, TimeoutException, ExecutionException {
-		return(this.motor.getValue());
-	}
-	
-	/**
-	 * Set motor of the OTFScan axis
-	 * @param motor
-	 * @throws ChannelException 
-	 * @throws ExecutionException 
-	 * @throws TimeoutException, ChannelException, ExecutionException
-	 */
-	public void setMotor(String motor) throws  InterruptedException, ExecutionException, ChannelException {
-		this.motor.setValue(motor);
-	}
-	
-	/**
-	 * Get encoder of the OTFScan axis
-	 * @return	Name of the used encoder
-	 * @throws ExecutionException 
-	 * @throws ChannelException 
-	 * @throws TimeoutException 
-	 * @throws TimeoutException, ChannelException, ExecutionException
-	 */
-	public String getEncoder() throws InterruptedException, TimeoutException, ChannelException, ExecutionException {
-		return(this.encoder.getValue());
-	}
-	
-	/**
-	 * Set encoder to use of the OTFScan axis
-	 * @param encoder
-	 * @throws ChannelException 
-	 * @throws ExecutionException 
-	 * @throws TimeoutException, ChannelException, ExecutionException
-	 */
-	public void setEncoder(String encoder) throws  InterruptedException, ExecutionException, ChannelException {
-		this.encoder.setValue(encoder);
-	}
-	
-	/**
-	 * Get begin position of the scan
-	 * @return Begin position scan
-	 * @throws ExecutionException 
-	 * @throws ChannelException 
-	 * @throws TimeoutException 
-	 * @throws TimeoutException, ChannelException, ExecutionException
-	 */
-	public Double getBegin() throws InterruptedException, TimeoutException, ChannelException, ExecutionException {
-		return(this.begin.getValue());
-	}
-	
-	/**
-	 * Set begin position of scan
-	 * @param begin
-	 * @throws ExecutionException 
-	 * @throws ChannelException 
-	 * @throws TimeoutException 
-	 * @throws Exception
-	 */
-	public void setBegin(Double begin) throws InterruptedException, TimeoutException, ChannelException, ExecutionException {
-		
-		if(begin==null){
-			throw new IllegalArgumentException("Begin position must not be null");
-		}
-		
-		if(begin < beginMin.getValue() || begin > beginMax.getValue()){
-			throw new IllegalArgumentException("Cannot set begin value to "+begin+ ". Value is outside range [min: "+beginMin.getValue()+" max: "+beginMax.getValue()+"]");
-		}
-		
-		this.begin.setValue(begin);
-	}
-	
-	/**
-	 * Get minimum value of the begin position
-	 * @return	Min value for begin
-	 * @throws ExecutionException 
-	 * @throws ChannelException 
-	 * @throws TimeoutException 
-	 * @throws TimeoutException, ChannelException, ExecutionException
-	 */
-	public Double getMinBegin() throws InterruptedException, TimeoutException, ChannelException, ExecutionException {
-		return(this.beginMin.getValue());
-	}
-	
-	/**
-	 * Get maximum value of the begin position
-	 * @return	Max value for begin
-	 * @throws ExecutionException 
-	 * @throws ChannelException 
-	 * @throws TimeoutException 
-	 * @throws TimeoutException, ChannelException, ExecutionException
-	 */
-	public Double getMaxBegin() throws InterruptedException, TimeoutException, ChannelException, ExecutionException {
-		return(this.beginMax.getValue());
-	}
-	
-	/**
-	 * Get end position of the scan
-	 * @return End position scan
-	 * @throws ExecutionException 
-	 * @throws ChannelException 
-	 * @throws TimeoutException 
-	 * @throws TimeoutException, ChannelException, ExecutionException
-	 */
-	public Double getEnd() throws InterruptedException, TimeoutException, ChannelException, ExecutionException {
-		return(this.end.getValue());
-	}
-	
-	/**
-	 * Set end positon of scan
-	 * @param end
-	 * @throws ExecutionException 
-	 * @throws ChannelException 
-	 * @throws TimeoutException 
-	 * @throws TimeoutException, ChannelException, ExecutionException
-	 */
-	public void setEnd(Double end) throws InterruptedException, TimeoutException, ChannelException, ExecutionException {
-		
-		if(end==null){
-			throw new IllegalArgumentException("End position must not be null");
-		}
-		
-		if(end < endMin.getValue() || end > endMax.getValue()){
-			throw new IllegalArgumentException("Cannot set end value to "+end+ ". Value is outside range [min: "+endMin.getValue()+" max: "+endMax.getValue()+"]");
-		}
-		
-		this.end.setValue(end);
-	}
-	
-	/**
-	 * Get minimum value of end position
-	 * @return	Min value for end
-	 * @throws ExecutionException 
-	 * @throws ChannelException 
-	 * @throws TimeoutException 
-	 * @throws TimeoutException, ChannelException, ExecutionException
-	 */
-	public Double getMinEnd() throws InterruptedException, TimeoutException, ChannelException, ExecutionException {
-		return(this.endMin.getValue());
-	}
-	/**
-	 * Get maximum value of end position
-	 * @return 	Max value for end
-	 * @throws TimeoutException, ChannelException, ExecutionException
-	 */
-	public Double getMaxEnd() throws TimeoutException, ChannelException, ExecutionException, InterruptedException {
-		return(this.endMax.getValue());
-	}
-	
-	/**
-	 * Get scan step size
-	 * @return Step size
-	 * @throws TimeoutException, ChannelException, ExecutionException
-	 */
-	public Double getStepSize() throws TimeoutException, ChannelException, ExecutionException, InterruptedException {
-		return(this.stepSize.getValue());
-	}
-	
-	/**
-	 * Set step size of scan
-	 * @param stepSize
-	 * @throws TimeoutException, ChannelException, ExecutionException
-	 */
-	public void setStepSize(Double stepSize) throws TimeoutException, ChannelException, ExecutionException, InterruptedException {
-
-		if(integrationTime==null){
-			throw new IllegalArgumentException("Step size must not be null");
-		}
-		
-		// Check if step size is greater than min step size
-		if(stepSizeMin.getValue() != 0 && stepSize < stepSizeMin.getValue()){
-			throw new IllegalArgumentException("Step size value ["+stepSize+"] is less than minimum step size ["+stepSizeMin.getValue()+"]!");
-		}
-		
-		this.stepSize.setValue(stepSize);
-
-		// TODO WORKAROUND - Wait to "ensure" that step size related fields are updated (i.e. min/max integration time)
-		Thread.sleep(1);
-	}
-	
-	/**
-	 * Get minimum integration time
-	 * @return	Min value for step size
-	 * @throws TimeoutException, ChannelException, ExecutionException
-	 */
-	public double getMinStepSize() throws TimeoutException, ChannelException, ExecutionException, InterruptedException {
-		return(this.stepSizeMin.getValue());
-	}
-	
-	/**
-	 * Get scan integration time (time that is spend in one step)
-	 * @return	Integration time
-	 * @throws TimeoutException, ChannelException, ExecutionException
-	 */
-	public Double getIntegrationTime() throws TimeoutException, ChannelException, ExecutionException, InterruptedException {
-		return(this.integrationTime.getValue());
-	}
-
-	/**
-	 * Set integration time of scan
-	 * @param integrationTime
-	 * @throws TimeoutException, ChannelException, ExecutionException
-	 */
-	public void setIntegrationTime(Double integrationTime) throws TimeoutException, ChannelException, ExecutionException, InterruptedException {
-		
-		if(integrationTime==null){
-			throw new IllegalArgumentException("Integration time must not be null");
-		}
-		
-		// Check range (if limit is set to 0 then limit is not set)
-		double min = integrationTimeMin.getValue();
-		double max = integrationTimeMax.getValue();
-		if(min!= 0 && max!= 0){
-			if(integrationTime < min || integrationTime > max){
-				throw new IllegalArgumentException("Integration time ["+integrationTime+"] is outside range [min: "+min+" max: "+max+"]");
-			}
-		}
-		else {
-			if(min!= 0 && integrationTime<min){
-				throw new IllegalArgumentException("Integration time ["+integrationTime+"] is outside range [min: "+min+" max: - ]");
-			}
-			else if(max!= 0 && integrationTime>max){
-				throw new IllegalArgumentException("Integration time ["+integrationTime+"] is outside range [min: -  max: "+max+"]");
-			}
-		}
-		
-		this.integrationTime.setValue(integrationTime);
-	}
-	
-	/**
-	 * Get minimum integration time
-	 * @return	Min value for integration time
-	 * @throws TimeoutException, ChannelException, ExecutionException
-	 */
-	public Double getMinIntegrationTime() throws TimeoutException, ChannelException, ExecutionException, InterruptedException {
-		return(this.integrationTimeMin.getValue());
-	}
-	/**
-	 * Get maximum integration time
-	 * @return	Max value for integration time
-	 * @throws TimeoutException, ChannelException, ExecutionException
-	 */
-	public Double getMaxIntegrationTime() throws TimeoutException, ChannelException, ExecutionException, InterruptedException {
-		return(this.integrationTimeMax.getValue());
-	}
-	
-	/**
-	 * Get additional user defined backlash
-	 * @return	User backlash
-	 * @throws TimeoutException, ChannelException, ExecutionException 
-	 */
-	public Double getUserBacklash() throws TimeoutException, ChannelException, ExecutionException, InterruptedException {
-		return(this.userBacklash.getValue());
-	}
-
-	/**
-	 * Set additional user defined backlash
-	 * @param userBacklash
-	 * @throws TimeoutException, ChannelException, ExecutionException
-	 */
-	public void setUserBacklash(Double userBacklash) throws TimeoutException, ChannelException, ExecutionException, InterruptedException {
-		if(userBacklash==null){
-			throw new IllegalArgumentException("User backlash must not be null");
-		}
-		
-		this.userBacklash.setValue(userBacklash);
-	}
-	
-	/**
-	 * Get the current NFS server the data is written to
-	 * @return	Name of NFS server
-	 * @throws TimeoutException, ChannelException, ExecutionException
-	 */
-	public String getNfsServer() throws TimeoutException, ChannelException, ExecutionException, InterruptedException {
-		return(this.nfsServer.getValue());
-	}
-	
-	/**
-	 * Set name of the NFS server the data is written to
-	 * @param nfsServer
-	 * @throws TimeoutException, ChannelException, ExecutionException
-	 */
-	public void setNfsServer(String nfsServer) throws TimeoutException, ChannelException, ExecutionException, InterruptedException {
-		this.nfsServer.setValue(nfsServer);
-	}
-	
-	/**
-	 * Get the NFS share the data is written to
-	 * @return	Name of NFS share
-	 * @throws TimeoutException, ChannelException, ExecutionException
-	 */
-	public String getNfsShare() throws TimeoutException, ChannelException, ExecutionException, InterruptedException {
-		return(this.nfsShare.getValue());
-	}
-	
-	/**
-	 * Set name of the NFS share the data is written to
-	 * @param nfsShare
-	 * @throws TimeoutException, ChannelException, ExecutionException
-	 */
-	public void setNfsShare(String nfsShare) throws TimeoutException, ChannelException, ExecutionException, InterruptedException {
-		this.nfsShare.setValue(nfsShare);
-	}
-	
-	/**
-	 * Get the name of the data file
-	 * @return	Name of data file name
-	 * @throws TimeoutException, ChannelException, ExecutionException
-	 */
-	public String getFileName() throws TimeoutException, ChannelException, ExecutionException, InterruptedException {
-		return(this.fileName.getValue());
-	}
-
-	/**
-	 * Set name of the data file
-	 * @param filename
-	 * @throws TimeoutException, ChannelException, ExecutionException
-	 */
-	public void setFileName(String filename) throws TimeoutException, ChannelException, ExecutionException, InterruptedException {
-		this.fileName.setValue(filename);
-	}
-	
-	/**
-	 * Get File name formate
-	 * @return	Get format for file name
-	 * @throws TimeoutException, ChannelException, ExecutionException
-	 */
-	public String getFileNameFormat() throws TimeoutException, ChannelException, ExecutionException, InterruptedException {
-		return(this.fileNameFormat.getValue());
-	}
-	
-	/**
-	 * Set file name formate of the data file
-	 * @param fileNameFormat
-	 * @throws Exception
-	 */
-	public void setFileNameFormat(String fileNameFormat) throws TimeoutException, ChannelException, ExecutionException, InterruptedException {
-		this.fileNameFormat.setValue(fileNameFormat);
-	}
-	
-	/**
-	 * Get value of the IOC based file name counter
-	 * @return	File counter
-	 * @throws TimeoutException, ChannelException, ExecutionException
-	 */
-	public int getFileCounter() throws TimeoutException, ChannelException, ExecutionException, InterruptedException {
-		return(this.fileCount.getValue());
-	}
-	
-	/**
-	 * Reset the IOC based file counter
-	 * @throws TimeoutException, ChannelException, ExecutionException
-	 */
-	public void resetFileCounter() throws TimeoutException, ChannelException, ExecutionException, InterruptedException {
-		this.resetFileCounter.setValue(1);
-	}
-	
-	/**
-	 * Get if append file option is activated
-	 * @return	Append file flag
-	 * @throws TimeoutException, ChannelException, ExecutionException
-	 */
-	public boolean isAppendFile() throws TimeoutException, ChannelException, ExecutionException, InterruptedException {
-		return(this.appendFile.getValue());
-	}
-	
-	/**
-	 * Set whether to append the specified file if the file exists
-	 * @param append
-	 * @throws TimeoutException, ChannelException, ExecutionException
-	 */
-	public void setAppendFile(boolean append) throws TimeoutException, ChannelException, ExecutionException, InterruptedException {
-		this.appendFile.setValue(append);
-	}
-	
-	/**
-	 * Get if file name generation is on or off
-	 * @return	File name generation flag
-	 * @throws TimeoutException, ChannelException, ExecutionException
-	 */
-	public boolean isFileNameGeneration() throws TimeoutException, ChannelException, ExecutionException, InterruptedException {
-		return(this.fileNameGeneration.getValue());
-	}
-	
-	/**
-	 * Set Whether the file name should be generated out of the file name format and the file counter
-	 * @param generation
-	 * @throws TimeoutException, ChannelException, ExecutionException
-	 */
-	public void setFileNameGeneration(boolean generation) throws TimeoutException, ChannelException, ExecutionException, InterruptedException {
-		this.fileNameGeneration.setValue(generation);
-	}
-	
-	/**
-	 * Get if ZigZag scan option is on or off
-	 * @return	ZigZag flag
-	 * @throws TimeoutException, ChannelException, ExecutionException
-	 */
-	public boolean isZigZag() throws TimeoutException, ChannelException, ExecutionException, InterruptedException {
-		return(this.zigZag.getValue());
-	}
-	
-	/**
-	 * Set ZigZag scan mode on/off
-	 * @param zigZag	ZigZag mode on = true, ZigZag mode off = false
-	 * @throws TimeoutException, ChannelException, ExecutionException
-	 */
-	public void setZigZag(boolean zigZag) throws TimeoutException, ChannelException, ExecutionException, InterruptedException {
-		this.zigZag.setValue(zigZag);
-	}
-	
-	/**
-	 * Get whether encoder is used
-	 */
-	public boolean isUseEncoder() throws TimeoutException, ChannelException, ExecutionException, InterruptedException {
-		return(this.useEncoder.getValue());
-	}
-	
-	/**
-	 * Set flag to use encoder
-	 * @throws TimeoutException, ChannelException, ExecutionException
-	 */
-	public void setUseEncoder(boolean flag) throws TimeoutException, ChannelException, ExecutionException, InterruptedException {
-		this.useEncoder.setValue(flag);
-	}
-	
-	/**
-	 * Get the channels that are currently monitored by the OTFScan logic
-	 * @return	Names of the monitored channels
-	 * @throws TimeoutException, ChannelException, ExecutionException
-	 */
-	public String[] getMonitoredChannels() throws TimeoutException, ChannelException, ExecutionException, InterruptedException {
-		String[] values = new String[this.monitoredChannels.size()];
-		
-		for(int i=0; i<this.monitoredChannels.size();i++){
-			values[i] = monitoredChannels.get(i).getValue();
-		}
-		
-		return(values);
-	}
-	
-	/**
-	 * Set the channels that need to be monitored.
-	 * Note: As OTF only supports 8 channels to be monitored, only the first 8 
-	 * values of the passed channelNames are considered.
-	 * @param values	Array of channel names to be monitored
-	 * @throws TimeoutException, ChannelException, ExecutionException
-	 */
-	public void setMonitoredChannels(String[] values) throws TimeoutException, ChannelException, ExecutionException, InterruptedException {
-		
-		if(values.length>monitoredChannels.size()){
-			throw new IllegalArgumentException("Only up to "+monitoredChannels.size()+" monitored channels are supported by OTF");
-		}
-		
-		for(int i=0; i<this.monitoredChannels.size(); i++){
-			if(values != null && i<values.length){
-				this.monitoredChannels.get(i).setValue(values[i]);
-			}
-			else{
-				this.monitoredChannels.get(i).setValue("");
-			}
-		}
-	}
-	
-	/**
-	 * Returns whether an scan is running
-	 * @return	Running flag
-	 * @throws TimeoutException, ChannelException, ExecutionException 
-	 */
-	public boolean isRunning() throws TimeoutException, ChannelException, ExecutionException, InterruptedException {
-		return(running.getValue());
-	}
-	
-	/**
-	 * Get status of the scan
-	 * @return Status of the scan
-	 * @throws TimeoutException, ChannelException, ExecutionException 
-	 */
-	public Status getStatus() throws TimeoutException, ChannelException, ExecutionException, InterruptedException {
-		return(Status.values()[this.status.getValue()]);
-	}
-	
-	/**
-	 * Get the (error) message from the OTF records
-	 * @return	Message from OTF C logic
-	 * @throws TimeoutException, ChannelException, ExecutionException
-	 */
-	public String getMessage() throws TimeoutException, ChannelException, ExecutionException, InterruptedException {
-		return(message.getValue());
-	}
-	
-	/**
-	 * Check whether the specified motor is recognized as ok (i.e. it is registered as OTFScan motor)
-	 * @return	Flag whether motor is ok
-	 * @throws TimeoutException, ChannelException, ExecutionException 
-	 */
-	public boolean isMotorOk() throws TimeoutException, ChannelException, ExecutionException, InterruptedException {
-		return(motorOk.getValue());
-	}
-	
-	/**
-	 * Wait until the motor flag goes to ok
-	 * @param timeout	Timout in milliseconds
-	 * 
-	 * @throws TimeoutException, ChannelException, ExecutionException	If motor ok flag does not switch to ok within the specified timeout
-	 */
-	public void waitUntilMotorOk(long timeout) throws TimeoutException, ChannelException, ExecutionException, InterruptedException {
-		motorOk.waitForValue(true, timeout);
-	}
-	
-	/**
-	 * Wait until the motor flag goes to not ok
-	 * @param timeout	Timout in milliseconds
-	 * 
-	 * @throws TimeoutException, ChannelException, ExecutionException	If motor ok flag does not switch to ok within the specified timeout
-	 */
-	public void waitUntilMotorNotOk(long timeout) throws TimeoutException, ChannelException, ExecutionException, InterruptedException {
-		motorOk.waitForValue(false, timeout);
-	}
-	
-	
-	public void waitUntilEncoderOk(long timeout) throws TimeoutException, ChannelException, ExecutionException, InterruptedException {
-		if(!useEncoder.getValue()){
-			return;
-		}
-		encoderOk.waitForValue(true, timeout);
-	}
-}

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

@@ -1,533 +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.loops;
-
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.net.MalformedURLException;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.concurrent.BlockingQueue;
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.LinkedBlockingQueue;
-import java.util.concurrent.TimeoutException;
-import java.util.logging.Logger;
-
-//import jcifs.smb.SmbException;
-//import jcifs.smb.SmbFile;
-
-
-
-
-
-
-
-import ch.psi.fda.core.Action;
-import ch.psi.fda.core.ActionLoop;
-import ch.psi.fda.core.Sensor;
-import ch.psi.fda.core.actors.OTFActuator;
-import ch.psi.fda.core.messages.ComponentMetadata;
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.DataMessageMetadata;
-import ch.psi.fda.core.messages.DataQueue;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Message;
-import ch.psi.fda.core.sensors.MillisecondTimestampSensor;
-import ch.psi.fda.core.sensors.OTFNamedChannelSensor;
-import ch.psi.fda.core.sensors.OTFReadbackSensor;
-import ch.psi.fda.core.sensors.OTFScalerChannelSensor;
-import ch.psi.jcae.ChannelException;
-import ch.psi.jcae.ChannelService;
-
-/**
- * ActionLoop that is implementing the OTF Scan logic.
- * While executing the loop a full OTF scan procedure is executed.
- * @author ebner
- *
- */
-public class OTFLoop implements ActionLoop {
-	
-	// Get Logger
-	private static Logger logger = Logger.getLogger(OTFLoop.class.getName());
-	
-	/**
-	 * Flag to indicate whether the data of this loop will be grouped
-	 * According to this flag the dataGroup flag in EndOfStream will be set.
-	 */
-	private boolean dataGroup = false;
-	
-	// Constants
-	/**
-	 * Maximum number of monitored channels
-	 */
-	private static final int numberOfMonitoredChannels = 8;
-	/**
-	 * Maximum number of Scaler channels
-	 */
-	private static final int numberOfScalerChannels = 16;
-	
-	/**
-	 * Default timeout (in milliseconds) for wait operations
-	 */
-	private long timeout = 8000;
-	
-	/**
-	 * Name of the NFS server to place the data of the OTF logic
-	 */
-	private final String server;
-	/**
-	 * Share on the NFS server to put the OTF data on to
-	 */
-	private final String share;
-	/**
-	 * SMB share  to access the data written by the OTF C logic
-	 */
-	private final String smbShare;
-	
-	/**
-	 * Flag whether the actor of this loop should move in zig zag mode
-	 */
-	private final boolean zigZag;
-	
-	/**
-	 * Bean holding all OTF channels and functionality.
-	 */
-	private OTFBean obean;
-
-	/**
-	 * List of actions that are executed at the beginning of the loop.
-	 */
-	private List<Action> preActions;
-	/**
-	 * List of actions that are executed at the end of the loop.
-	 */
-	private List<Action> postActions;
-	
-	/**
-	 * Special OTF Actuator
-	 */
-	private OTFActuator actor = null;
-	
-	/**
-	 * List of sensors of this loop
-	 */
-	private List<Sensor> sensors;
-	
-	
-	private List<Integer> dataIndexes;
-	
-	/**
-	 * Execution count of this loop. This count is used to determine the 
-	 * file name of the OTF file.
-	 */
-	private int executionCount;
-	
-	/**
-	 * Data queue sensor data is posted to. A message consists of a list of data objects
-	 * that are read out of the sensors of this loop.
-	 */
-	private BlockingQueue<Message> dataQueue;
-	
-	/**
-	 * Flag that indicates that the loop was requested to abort.
-	 */
-	private volatile boolean abort = false;
-	
-	private ChannelService cservice;
-	
-	/**
-	 * Constructor
-	 * @param channelPrefix	Prefix of the OTF related records, e.g. MTEST-HW3-OTF
-	 * @param server		NFS server the OTF C Logic should put its data to
-	 * @param share			Share on NFS server to put the OTF C Logic data
-	 * @param smbShare		SMB share to get the data written by the OTF C Logic
-	 * @param zigZag		Operate loop in zig zag mode
-	 */
-	public OTFLoop(ChannelService s, String channelPrefix, String server, String share, String smbShare, boolean zigZag){
-		cservice = s;
-		// Initialize connection to the OTF records
-		try {
-			this.obean = new OTFBean();
-			Map<String,String> m = new HashMap<>();
-			m.put("PREFIX", channelPrefix);
-			s.createAnnotatedChannels(obean, m);
-		} catch (ChannelException | TimeoutException e) {
-			throw new IllegalArgumentException("Unable to connect to the OTF channels",e);
-		} catch (InterruptedException e) {
-			throw new RuntimeException("Unable to connect to the OTF channels",e);
-		}
-		
-		// Store loop configuration
-		this.server = server;
-		this.share = share;
-		this.smbShare = smbShare;
-		this.zigZag = zigZag;
-		
-		// Initialize lists used by the loop
-		this.preActions = new ArrayList<Action>();
-		this.postActions = new ArrayList<Action>();
-		this.sensors = new ArrayList<Sensor>();
-		
-		this.dataQueue = new LinkedBlockingQueue<Message>(2000);
-	}
-	
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#execute()
-	 */
-	@Override
-	public void execute() throws InterruptedException {
-		
-		// Execute pre actions
-		for(Action action: preActions){
-			action.execute();
-		}
-		
-		// Start scan
-		obean.start();
-		
-		// Wait for end of scan
-		obean.waitUntilStopped();
-		
-		// Read data from file
-		collectData();
-
-		// Execute post actions
-		for(Action action: postActions){
-			action.execute();
-		}
-		
-		
-		// Issue end of loop control message
-		dataQueue.put(new EndOfStreamMessage(dataGroup));
-		
-		// Increase execution count
-		executionCount++;
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#abort()
-	 */
-	@Override
-	public void abort() {
-		// Abort otf scan logic
-		obean.abort();
-		
-		abort=true;
-	}
-	
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.ActionLoop#prepare()
-	 */
-	@Override
-	public void prepare() {
-		executionCount = 0;
-		
-		// Set abort flag to false
-		abort=false;
-		
-		// Check whether actor is set for the loop
-		if(actor == null){
-			throw new IllegalStateException("No actor specified for this loop");
-		}
-		
-		// list with all monitored channels
-		List<String> monitoredChannels = new ArrayList<String>();
-		dataIndexes = new ArrayList<Integer>();
-		int channelCount =0;
-		for(Sensor s: sensors){
-			if(s instanceof OTFNamedChannelSensor){
-				// Monitored channel
-				OTFNamedChannelSensor so = (OTFNamedChannelSensor) s;
-				if(channelCount>=numberOfMonitoredChannels){
-					throw new IllegalArgumentException("Only up to "+numberOfMonitoredChannels+" channels can be monitored by OTF");
-				}
-				
-				monitoredChannels.add(so.getName());
-				dataIndexes.add(2+numberOfScalerChannels+channelCount);
-				
-				
-				channelCount++;
-			}
-			else if (s instanceof OTFScalerChannelSensor){
-				OTFScalerChannelSensor so = (OTFScalerChannelSensor) s;
-				if(so.getIndex()>=numberOfScalerChannels){
-					throw new IllegalArgumentException("Scaler index must be between 0<=index<"+numberOfScalerChannels);
-				}
-				dataIndexes.add(2+so.getIndex()); // scalers follow directly after the readback
-			}
-			else if (s instanceof MillisecondTimestampSensor){
-				dataIndexes.add(2+numberOfScalerChannels+numberOfMonitoredChannels);
-			}
-			else if (s instanceof OTFReadbackSensor){
-				dataIndexes.add(1);
-			}
-			else{
-				throw new IllegalArgumentException("Sensor type "+s.getClass()+" is not supported by this loop");
-			}
-		}
-		
-		// Set OTF parameters
-		try{
-			obean.resetToDefaults();
-			
-			// Set actor properties
-			obean.setMotor(actor.getName());
-			obean.waitUntilMotorOk(timeout);
-	
-			obean.setBegin(actor.getStart());
-			obean.setEnd(actor.getEnd());
-			obean.setStepSize(actor.getStepSize());
-			obean.setIntegrationTime(actor.getIntegrationTime());
-			
-			// Override encoder if specified
-			if(actor.getReadback()!=null){
-				obean.setUseEncoder(true);
-				obean.setEncoder(actor.getReadback());
-				obean.waitUntilEncoderOk(timeout);
-			}
-			
-			// Set user backlash
-			obean.setUserBacklash(actor.getAdditionalBacklash());
-			
-			
-			// NFS settings
-			obean.setNfsServer(server);
-			obean.setNfsShare(share);
-			
-			obean.setFileNameGeneration(true);
-			obean.setAppendFile(false);
-			obean.setZigZag(zigZag); // Set ZigZag because there might be iterations
-			obean.setFileNameFormat("%06d"); // Force an update of the filename/counter by setting file format twice with different values
-			obean.setFileNameFormat("%06d.txt");
-	    	
-			
-			
-			// Set monitored channels
-			obean.setMonitoredChannels(monitoredChannels.toArray(new String[monitoredChannels.size()]));
-		}
-		catch(ChannelException | ExecutionException | TimeoutException e){
-			throw new RuntimeException("Unable to set OTF configuration parameters",e);
-		} catch (InterruptedException e) {
-			throw new RuntimeException("Unable to set OTF configuration parameters",e);
-		}
-		
-		
-		// Cleanup temporary directory
-		try{
-			DistributedFile tmpDir = new DistributedFile(smbShare);
-			if( !tmpDir.exists() || !tmpDir.isDirectory() ){
-				throw new RuntimeException("Cannot access OTF temporary directory "+tmpDir.getCanonicalPath());
-			}
-			DistributedFile[] files = tmpDir.listFiles();
-	
-			for(int i=0;i<files.length;i++){
-				// Only delete item if it is not a directory and if it matches the given pattern.
-				if(files[i].isFile() && files[i].getName().matches("[0-9]+.txt")){
-					files[i].delete();
-					logger.fine("Delete file: "+files[i].getName());
-				}
-			}
-		}
-		catch(MalformedURLException e){
-			throw new RuntimeException(e);
-		} catch (IOException e) {
-			throw new RuntimeException("Unable to access share (temporary files)",e);
-		}
-		
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.ActionLoop#cleanup()
-	 */
-	@Override
-	public void cleanup() {
-		// TODO Auto-generated method stub
-		
-	}
-	
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#destroy()
-	 */
-	@Override
-	public void destroy() {
-		// Close all connections used by the OTFBean
-		try {
-			cservice.destroyAnnotatedChannels(obean);
-		} catch (ChannelException e) {
-			throw new RuntimeException("Unable to destroy channels",e);
-		}		
-	}
-	
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.ActionLoop#getPreActions()
-	 */
-	@Override
-	public List<Action> getPreActions() {
-		return preActions;
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.ActionLoop#getPostActions()
-	 */
-	@Override
-	public List<Action> getPostActions() {
-		return postActions;
-	}
-
-	/**
-	 * The structure of the data message depends on the sensors registered at this loop 
-	 * at the time this method is called.
-	 * @return the data queue and the metadata of the data messages
-	 */
-	public DataQueue getDataQueue() {
-		DataMessageMetadata m = new DataMessageMetadata();
-		
-		// Build up data message metadata based on the sensors currently registered.
-		for(Sensor s: sensors){
-			m.getComponents().add(new ComponentMetadata(s.getId()));
-		}
-		return new DataQueue(dataQueue, m);
-	}
-	
-	/**
-	 * Collect data written by the OTFScan logic
-	 * @param dataSet
-	 * @param tmpFile
-	 */
-	private void collectData() {
-		try{
-			final int timestampIndex = 2+numberOfScalerChannels+numberOfMonitoredChannels;
-			
-			DistributedFile tmpFile = new DistributedFile(smbShare +"/"+ String.format("%06d.txt", executionCount));
-			logger.fine("Collect data from "+tmpFile.getCanonicalPath());
-
-			DistributedFile lockfile = new DistributedFile(tmpFile.getCanonicalPath() + ".lock");
-			
-			logger.fine("Wait until file is written [lock file: "+lockfile.getCanonicalPath()+"]");
-			// Wait until file is created
-			while ((!tmpFile.exists()) || lockfile.exists()) {
-				Thread.sleep(500);
-				if(abort){
-					// If abort is issued while waiting for data immediately return without
-					// trying to read the data
-					return;
-				}
-			}
-				
-			logger.fine("Read file " + tmpFile.getCanonicalPath());
-			InputStreamReader inreader = tmpFile.getInputStream();
-			BufferedReader in = new BufferedReader(inreader);
-			String line;
-			boolean firstline = true;
-			while (true) {
-				line = in.readLine();
-					if (line == null) {
-						break;
-				} else {
-					if(line.matches("^\\[.*")){
-						// Skip header lines
-					}
-					else{
-						if(firstline){
-							firstline=false;
-							continue;
-						}
-						
-						DataMessage message = new DataMessage();
-						// Add data to dataset
-						String[] tokens = line.split("\t");
-
-						for(Integer i: dataIndexes){
-							try{
-								if(i == timestampIndex) {
-									// Calculate time in milliseconds
-									Double seconds = new Double(tokens[i]);
-									Double nanoseconds = new Double(tokens[i+1]);
-									
-									Double v = seconds*1000+Math.floor(nanoseconds*0.000001);
-									message.getData().add(v);
-								}
-								else {
-									
-									message.getData().add(new Double(tokens[i]));
-								}
-							}
-							catch(NumberFormatException e){
-									logger.warning("Cannot parse component ["+tokens[i]+"] from source file - will add 0 for this component");
-									message.getData().add(new Double(0));
-							}
-						}
-						dataQueue.put(message);
-					}
-				}
-			}
-			in.close();
-			inreader.close();
-		} catch(InterruptedException e){
-			throw new RuntimeException("An interrupt occured while waiting for the file to show up",e);
-		} catch (IOException e) {
-			throw new RuntimeException("An IO Exception occured while reading the OTF data file",e);
-		}
-	}
-	
-	
-	// Getter functions for variable parts
-
-
-	
-	/**
-	 * @return the sensors
-	 */
-	public List<Sensor> getSensors() {
-		return sensors;
-	}
-	
-	/**
-	 * @return the actor
-	 */
-	public OTFActuator getActor() {
-		return actor;
-	}
-
-	/**
-	 * @param actor the actor to set
-	 */
-	public void setActor(OTFActuator actor) {
-		this.actor = actor;
-	}
-
-	/**
-	 * @return the dataGroup
-	 */
-	public boolean isDataGroup() {
-		return dataGroup;
-	}
-
-	/**
-	 * @param dataGroup the dataGroup to set
-	 */
-	public void setDataGroup(boolean dataGroup) {
-		this.dataGroup = dataGroup;
-	}
-	
-}

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

@@ -1,157 +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.loops.cr;
-
-import ch.psi.jcae.Channel;
-import ch.psi.jcae.annotation.CaChannel;
-
-/**
- * @author ebner
- *
- */
-public class CrlogicChannelsTemplate {
-
-	/**
-	 * Status of the OTFSCAN IOC logic
-	 */
-	public enum Status { SETUP, INACTIVE, INITIALIZE, ACTIVE, STOP, FAULT, ERROR };
-	
-	/**
-	 * Ticks per second - IOC setting
-	 * ATTENTION - This field must only be set bu the IOC - ATTENTION
-	 */
-	@CaChannel(type=Integer.class, name ="${PREFIX}:TPS")
-	private Channel<Integer> ticksPerSecond;
-
-	/**
-	 * Status of the OTFSCAN IOC logic
-	 */
-	@CaChannel(type=String.class, name ="${PREFIX}:STATUS")
-	private Channel<String> status;
-	
-	/**
-	 * Message from the OTFSCAN IOC logic
-	 */
-	@CaChannel(type=String.class, name ="${PREFIX}:MSG")
-	private Channel<String> message;
-
-	/**
-	 * IOC ticks between data acquisition interrupts
-	 */
-	@CaChannel(type=Integer.class, name ="${PREFIX}:TBINT")
-	private Channel<Integer> ticksBetweenInterrupts;
-
-	/**
-	 * Name or ip address of the NFS server to save the data to
-	 * (depending on the IOC setup)
-	 */
-	@CaChannel(type=String.class, name ="${PREFIX}:NFSSE")
-	private Channel<String> nfsServer;
-	
-	/**
-	 * Name of the NFS share on the NFS server
-	 */
-	@CaChannel(type=String.class, name ="${PREFIX}:NFSSH")
-	private Channel<String> nfsShare;
-
-	/**
-	 * Name of the data file
-	 */
-	@CaChannel(type=String.class, name ="${PREFIX}:DFNAM")
-	private Channel<String> dataFile;
-	
-	/**
-	 * Flag to identify whether the data file should be appended
-	 */
-	@CaChannel(type=Boolean.class, name ="${PREFIX}:FAPPE")
-	private Channel<Boolean> appendFile;
-
-	
-	/**
-	 * Readout resources
-	 */
-	@CaChannel(type=String[].class, name ="${PREFIX}:RRES")
-	private Channel<String[]> readoutResources;
-	
-	
-	/**
-	 * @return the ticksPerSecond
-	 */
-	public Channel<Integer> getTicksPerSecond() {
-		return ticksPerSecond;
-	}
-
-	/**
-	 * @return the status
-	 */
-	public Channel<String> getStatus() {
-		return status;
-	}
-
-	/**
-	 * @return the message
-	 */
-	public Channel<String> getMessage() {
-		return message;
-	}
-
-	/**
-	 * @return the ticksBetweenInterrupts
-	 */
-	public Channel<Integer> getTicksBetweenInterrupts() {
-		return ticksBetweenInterrupts;
-	}
-
-	/**
-	 * @return the nfsServer
-	 */
-	public Channel<String> getNfsServer() {
-		return nfsServer;
-	}
-
-	/**
-	 * @return the nfsShare
-	 */
-	public Channel<String> getNfsShare() {
-		return nfsShare;
-	}
-
-	/**
-	 * @return the dataFile
-	 */
-	public Channel<String> getDataFile() {
-		return dataFile;
-	}
-
-	/**
-	 * @return the appendFile
-	 */
-	public Channel<Boolean> getAppendFile() {
-		return appendFile;
-	}
-
-	/**
-	 * @return the readoutResources
-	 */
-	public Channel<String[]> getReadoutResources() {
-		return readoutResources;
-	}
-	
-}

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

@@ -1,47 +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.loops.cr;
-
-/**
- * @author ebner
- *
- */
-public class CrlogicDeltaDataFilter {
-
-	private Double lastValue = null;
-	
-	public void reset(){
-		lastValue = null;
-	}
-	
-	public Double delta(Double value){
-		
-		Double lvalue = lastValue;
-		lastValue = value;
-		
-		if(lvalue==null){
-			return Double.NaN;
-		}
-		else{
-			// Return delta
-			return(value-lvalue);
-		}
-	}
-}

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

@@ -1,908 +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.loops.cr;
-
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.concurrent.BlockingQueue;
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.LinkedBlockingQueue;
-import java.util.concurrent.Semaphore;
-import java.util.concurrent.TimeUnit;
-import java.util.concurrent.TimeoutException;
-import java.util.logging.Logger;
-
-import jcifs.smb.SmbFile;
-import ch.psi.fda.core.Action;
-import ch.psi.fda.core.ActionLoop;
-import ch.psi.fda.core.Sensor;
-import ch.psi.fda.core.actors.OTFActuator;
-import ch.psi.fda.core.messages.ComponentMetadata;
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.DataMessageMetadata;
-import ch.psi.fda.core.messages.DataQueue;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Message;
-import ch.psi.fda.core.sensors.MillisecondTimestampSensor;
-import ch.psi.fda.core.sensors.OTFNamedChannelSensor;
-import ch.psi.fda.core.sensors.OTFScalerChannelSensor;
-import ch.psi.jcae.ChannelException;
-import ch.psi.jcae.ChannelService;
-
-/**
- * @author ebner
- * 
- * While using Crlogic the IOC system clock rate should/must be set to 1000 (default 60)
- * 
- * sysClkRateSet 1000
- *
- */
-public class CrlogicLoop implements ActionLoop {
-	
-	// Get Logger
-	private static final Logger logger = Logger.getLogger(CrlogicLoop.class.getName());
-	
-	/**
-	 * Flag to indicate whether the data of this loop will be grouped
-	 * According to this flag the dataGroup flag in EndOfStream will be set.
-	 */
-	private boolean dataGroup = false;
-	
-	private boolean keepTmpFiles = false;
-	
-	private BlockingQueue<String> readQueue = new LinkedBlockingQueue<String>();
-	private volatile boolean stopReadoutThread = false;
-	private Thread readoutThread;
-	
-	// Constants
-	
-	/**
-	 * Default timeout (in milliseconds) for wait operations
-	 */
-	private long startStopTimeout = 8000;
-	
-	/**
-	 * Name of the NFS server to place the data of the OTF logic
-	 */
-	private final String server;
-	/**
-	 * Share on the NFS server to put the OTF data on to
-	 */
-	private final String share;
-	/**
-	 * SMB share  to access the data written by the OTF C logic
-	 */
-	private final String smbShare;
-	
-	/**
-	 * Flag whether the actor of this loop should move in zig zag mode
-	 */
-	private final boolean zigZag;
-	
-	boolean useReadback;
-	boolean useEncoder;
-	
-	/**
-	 * List of actions that are executed at the beginning of the loop.
-	 */
-	private List<Action> preActions;
-	/**
-	 * List of actions that are executed at the end of the loop.
-	 */
-	private List<Action> postActions;
-	
-	/**
-	 * Prefix for the CRLOGIC channels
-	 */
-	private String prefix;
-	
-	private CrlogicChannelsTemplate template;
-	private MotorChannelsTemplate motortemplate;
-	
-	/**
-	 * Semaphore to ensure that data is read in correct sequence
-	 */
-	private Semaphore semaphore = new Semaphore(1);
-	
-	/**
-	 * Special OTF Actuator
-	 */
-	private OTFActuator actuator = null;
-	
-	/**
-	 * List of sensors of this loop
-	 */
-	private List<Sensor> sensors;
-	
-	private List<String> readoutResources;
-	private Map<Integer, CrlogicDeltaDataFilter> scalerIndices;
-	private CrlogicRangeDataFilter crlogicDataFilter;
-	
-	/**
-	 * Data queue sensor data is posted to. A message consists of a list of data objects
-	 * that are read out of the sensors of this loop.
-	 */
-	private BlockingQueue<Message> dataQueue;
-	
-	/**
-	 * Abort status
-	 */
-	private boolean abort = false;
-	private boolean abortForce = false;
-	private Thread executionThread = null;
-	
-	private ChannelService cservice;
-	public CrlogicLoop(ChannelService s, String prefix, String server, String share, String smbShare, boolean zigZag){
-		cservice = s;
-		this.prefix = prefix;
-		this.server = server;
-		this.share = share;
-		this.smbShare = smbShare;
-		this.zigZag = zigZag;
-		
-		// Initialize lists used by the loop
-		this.preActions = new ArrayList<Action>();
-		this.postActions = new ArrayList<Action>();
-		this.sensors = new ArrayList<Sensor>();
-		this.readoutResources = new ArrayList<String>();
-		this.scalerIndices = new HashMap<Integer, CrlogicDeltaDataFilter>();
-		
-		this.crlogicDataFilter = new CrlogicRangeDataFilter();
-		this.dataQueue = new LinkedBlockingQueue<Message>(2000);
-	}
-	
-		
-	/**
-	 * Collect data from share
-	 * @param tmpFileName	Name of the temporary file
-	 * @throws InterruptedException 
-	 * @throws IOException 
-	 */
-	private void collectData(String tmpDir, String tmpFileName) throws InterruptedException, IOException {
-		semaphore.acquire();
-		if (tmpDir.startsWith("smb:")) {
-
-			SmbFile tmpFile = new SmbFile(tmpDir, tmpFileName);
-			logger.info("Collect data from " + tmpFile.getCanonicalPath());
-
-			SmbFile lockfile = new SmbFile(tmpFile.getCanonicalPath() + ".lock");
-
-			logger.info("Wait until file is written [lock file: " + lockfile.getCanonicalPath() + "]");
-			// Wait until file is created
-			while ((!tmpFile.exists()) || lockfile.exists()) {
-				try{
-					Thread.sleep(100);
-				}
-				catch(InterruptedException e){
-					abort=true;
-				}
-				 if(abort){
-					 // If abort is issued while waiting for data immediately return without
-					 // trying to read the data
-					 return;
-				 }
-			}
-
-			InputStreamReader inreader = new InputStreamReader(tmpFile.getInputStream());
-			BufferedReader in = new BufferedReader(inreader);
-			String line;
-			boolean firstline = true;
-			int linecount=0;
-			int mcounter=0;
-			
-//			boolean wasInRangeBefore = false;
-			boolean discardAnyway = false;
-			
-			while (true) {
-				line = in.readLine();
-				linecount++;
-				if (line == null) {
-					break;
-				} else {
-					// if(line.matches("^\\[.*")){
-					if (line.matches("^ *#.*")) {
-						// Skip header/comment lines
-//						logger.info("HEADER: " + line);
-					} else {
-						if (firstline) {
-							firstline = false;
-							continue;
-						}
-
-//						logger.info(line);
-
-						// Write into queue
-						DataMessage message = new DataMessage();
-						String[] tokens = line.split("\t");
-						boolean use = true;
-						
-						for(int i=0;i<tokens.length;i++){
-							String t = tokens[i];
-							Double val;
-							
-							if(i==0){
-								Double raw = new Double(t);
-								
-								if(useEncoder){
-									val = crlogicDataFilter.calculatePositionMotorUseEncoder(raw);
-								}
-								else if(useReadback){
-									val = crlogicDataFilter.calculatePositionMotorUseReadback(raw);
-								}
-								else{
-									val = crlogicDataFilter.calculatePositionMotor(raw);
-								}
-								
-								// Check whether data is within the configured range - otherwise drop data
-								use = crlogicDataFilter.filter(val);
-//								if(!use){
-//									break;
-//								}
-							}
-							else if(scalerIndices.containsKey(i)){
-								CrlogicDeltaDataFilter f = scalerIndices.get(i); 
-								val = f.delta(new Double(t));
-							}
-							else{
-								val = new Double(t);
-							}
-							
-							
-							message.getData().add(val);
-						}
-						
-						// Does not work if zigzag, ... 
-//						// Use this to filter out motor retry movements at the end of the scan
-//						wasInRangeBefore = wasInRangeBefore | use;
-//						if(!use && wasInRangeBefore){
-//							discardAnyway=true;
-//							// Optimization - terminate read loop once range is left
-//							logger.info("Terminate read loop because point is outside range");
-//							break;
-//						}
-						
-						// Filter data
-						if(use && !discardAnyway){
-							dataQueue.put(message);
-							mcounter++;
-						}
-						
-						
-					}
-				}
-			}
-			in.close();
-			inreader.close();
-			
-			logger.info("Lines read: "+linecount+" Messages generated (after filtering): "+mcounter);
-			
-			// Remove temporary file
-			if(!keepTmpFiles){
-				tmpFile.delete();
-			}
-		}
-		else{
-			// TODO - File in local file system
-		}
-		
-		// Issue end of loop control message
-		dataQueue.put(new EndOfStreamMessage(dataGroup));
-		semaphore.release();
-	}
-	
-	
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#execute()
-	 */
-	@Override
-	public void execute() throws InterruptedException {
-		try{
-		
-			double stepSize = actuator.getStepSize();
-			double start = actuator.getStart();
-			double end = actuator.getEnd();
-			double integrationTime = actuator.getIntegrationTime();
-			double ubacklash = actuator.getAdditionalBacklash();
-			
-			// Set values for the datafilter
-			crlogicDataFilter.setStart(actuator.getStart());
-			crlogicDataFilter.setEnd(actuator.getEnd());
-			
-			// Reset data filter
-			for(Integer k: scalerIndices.keySet()){
-				scalerIndices.get(k).reset();
-			}
-			
-			synchronized(this){
-				// Set abort state to false
-				abort = false;
-				abortForce = false;
-			
-			// Set execution thread to current thread
-				executionThread = Thread.currentThread();
-			}
-			
-			
-			// TODO each actuator will result in an additional sensor (at the beginning)
-			// Dependent on actuator settings (readback use encoder, ...)
-			
-			
-			// TODO filename generation?
-			final String tmpFileName = "tmp-"+System.currentTimeMillis()+".txt";
-			
-			Long timeout = 600000l; // 10 minutes move timeout
-			
-			// Check if logic is inactive, otherwise return early
-			if(!template.getStatus().getValue().equals(CrlogicChannelsTemplate.Status.INACTIVE.toString())){
-				logger.info("CRLOGIC is not inactive!");
-				// TODO Decide what to do in this situation
-				
-				if(template.getStatus().getValue().equals(CrlogicChannelsTemplate.Status.FAULT.toString())){
-					// If in fault show message and recover
-					logger.info("CRLOGIC in FAULT state");
-					logger.info("Error message: "+template.getMessage().getValue());
-					logger.info("Recover logic and set it to INACTIVE");
-					template.getStatus().setValue(CrlogicChannelsTemplate.Status.INACTIVE.toString());
-				}
-				else if(template.getStatus().getValue().equals(CrlogicChannelsTemplate.Status.ACTIVE.toString())){
-					template.getStatus().setValue(CrlogicChannelsTemplate.Status.STOP.toString());
-					template.getStatus().waitForValue(CrlogicChannelsTemplate.Status.INACTIVE.toString(), startStopTimeout);
-				}
-				else{
-					throw new RuntimeException("CRLOGIC is not inactive");
-				}
-			}
-			
-			
-			logger.info("Set parameters");
-			template.getNfsServer().setValue(server);
-			template.getNfsShare().setValue(share);
-			template.getDataFile().setValue(tmpFileName);
-			
-			int tps = template.getTicksPerSecond().getValue();
-			logger.info("Ticks per second: "+tps);
-			
-			logger.info("Set readout resources");
-			
-			template.getReadoutResources().setValue(readoutResources.toArray(new String[readoutResources.size()]));
-			
-			
-			
-			// Set ticks between interrupt to integration time
-			int ticks = (int)(tps*integrationTime);
-			template.getTicksBetweenInterrupts().setValue(ticks);
-			
-			// Prepare motor
-			double totalTimeSeconds = Math.abs((end-start)/stepSize*integrationTime);
-			int hours = (int) Math.floor(totalTimeSeconds/60/60);
-			int minutes = (int) Math.floor(totalTimeSeconds/60-hours*60);
-			int seconds = (int) Math.floor(totalTimeSeconds-hours*60*60-minutes*60);
-			
-			logger.info("Estimated time: "+hours+":"+minutes+":"+seconds);
-			
-			int direction = 1;
-			if(end-start<0){
-				direction = -1;
-			}
-			
-			double motorBaseSpeed = motortemplate.getBaseSpeed().getValue();
-			double motorHighLimit = motortemplate.getHighLimit().getValue();
-			double motorLowLimit = motortemplate.getLowLimit().getValue();
-			double motorBacklash = motortemplate.getBacklashDistance().getValue();
-			
-			boolean respectMotorMinSpeed = false; // if false set min speed to 0
-			double motorMinSpeed = 0;
-			if(respectMotorMinSpeed){
-				motorMinSpeed = motorBaseSpeed;
-			}
-			
-			// Check user parameters
-			// TODO start and end values must be between the motor high and low value - otherwise fail
-			if(start>motorHighLimit || start<motorLowLimit){
-				// Start value is outside motor high and/or low value
-				logger.info("Start value is outside motor high and/or low value");
-				throw new IllegalArgumentException("Start value is outside motor high and/or low value");
-			}
-			if(end>motorHighLimit || end<motorLowLimit){
-				// End value is outside motor high and/or low value
-				logger.info("End value is outside motor high and/or low value");
-				throw new IllegalArgumentException("End value is outside motor high and/or low value");
-			}
-			// TODO Check minimum step size
-			int minimumTicks = 10;
-			double minStepSize = motorMinSpeed*(minimumTicks/tps);
-			if(stepSize<minStepSize){
-				// Step size is too small
-				logger.info("Step size is too small");
-				throw new IllegalArgumentException("Step size is too small");
-			}
-			// TODO Check integration time
-			if(motorMinSpeed>0){
-				double maxIntegrationTime = stepSize/motorMinSpeed;
-				if(integrationTime>maxIntegrationTime){
-					logger.info("Integration time is too big");
-					// Integration time is too big
-					throw new IllegalArgumentException("Integration time is too big");
-				}
-			}
-			double motorMaxSpeed = motortemplate.getVelocity().getValue();
-			double minIntegrationTime = Math.min( (stepSize/motorMaxSpeed), ((double)minimumTicks/(double)tps) );
-			if(integrationTime<minIntegrationTime){
-				// Integration time is too small
-				logger.info("Integration time is too small [min integration time: "+minIntegrationTime+"]");
-				throw new IllegalArgumentException("Integration time is too small [min integration time: "+minIntegrationTime+"]");
-			}
-			
-			
-			// TODO Calculate and set motor speed, backlash, etc.
-			double motorSpeed = stepSize/integrationTime;
-			double backlash = (0.5*motorSpeed*motortemplate.getAccelerationTime().getValue())+motorBacklash+ubacklash;
-			double realEnd = end+(backlash*direction);
-			double realStart = start-(backlash*direction);
-	
-			
-			// Move to start
-			logger.info("Move motor to start ["+realStart+"]");
-			motortemplate.getSetValue().setValueAsync(realStart).get(timeout, TimeUnit.MILLISECONDS); // Will block until move is done
-			
-			
-			// Set motor paramters
-			// Backup settings
-			logger.info("Backup motor settings");
-			double backupSpeed = motortemplate.getVelocity().getValue();
-			double backupBacklash = motorBacklash;
-			double backupMinSpeed = motorBaseSpeed;
-			
-			try{
-				// Set motor settings
-				logger.info("Update motor settings");
-//				if(!respectMotorMinSpeed){
-//					motortemplate.getBaseSpeed().setValue(0d);
-//				}
-				// Set base speed as fast as possible but not faster than the original base speed.
-				double base = motorBaseSpeed;
-				if(motorSpeed<base){
-					base = motorSpeed;
-				}
-				motortemplate.getBaseSpeed().setValue(base);
-				motortemplate.getVelocity().setValue(motorSpeed);
-				motortemplate.getBacklashDistance().setValue(0d);
-				
-				
-				// Execute pre actions
-				for(Action action: preActions){
-					action.execute();
-				}
-				
-				
-				// Start crlogic logic
-				logger.info("Start CRLOGIC");
-				template.getStatus().setValue(CrlogicChannelsTemplate.Status.INITIALIZE.toString());
-				try{
-					template.getStatus().waitForValue(CrlogicChannelsTemplate.Status.ACTIVE.toString(), startStopTimeout);
-				}
-				catch(ChannelException e){
-					logger.info( "Failed to start CRLOGIC. Logic in status: "+template.getStatus().getValue() );
-					if(template.getStatus().getValue().equals(CrlogicChannelsTemplate.Status.FAULT.toString())){
-						logger.info("Error message: "+template.getMessage().getValue());
-					}
-					// Recover to inactive
-					template.getStatus().setValue(CrlogicChannelsTemplate.Status.INACTIVE.toString());
-					// TODO Improve error handling
-					throw new RuntimeException("Failed to start CRLOGIC. Logic in status: "+template.getStatus().getValue()+ " Error message: "+template.getMessage().getValue(), e);
-					
-				}
-
-				// Move motor(s) to end / wait until motor is stopped
-				logger.info("Move motor to end ["+realEnd+"]");
-				try{
-					motortemplate.getSetValue().setValueAsync(realEnd).get(timeout, TimeUnit.MILLISECONDS); // Will block until move is done
-				}
-				catch (InterruptedException e) {
-					if(abort & (!abortForce)){
-						// Abort motor move 
-						motortemplate.getCommand().setValue(MotorChannelsTemplate.Commands.Stop.ordinal());
-						motortemplate.getCommand().setValue(MotorChannelsTemplate.Commands.Go.ordinal());
-					}
-					else{
-						throw e;
-					}
-				}
-				logger.info("Motor reached end position");
-				
-				// Stop crlogic logic
-				logger.info("Stop CRLOGIC");
-				template.getStatus().setValue(CrlogicChannelsTemplate.Status.STOP.toString());
-				// Wait until stopped
-				logger.info("Wait until stopped");
-				try{
-					template.getStatus().waitForValue(CrlogicChannelsTemplate.Status.INACTIVE.toString(), startStopTimeout);
-				}
-				catch(ChannelException | ExecutionException e){
-					logger.info( "Failed to stop CRLOGIC. Logic in status: "+template.getStatus().getValue() );
-					// TODO Improve error handling
-					throw new RuntimeException("Failed to stop CRLOGIC.  Logic in status: "+template.getStatus().getValue(), e);
-				}
-				logger.info("CRLOGIC is now stopped");
-				
-				
-				// Execute post actions
-				for(Action action: postActions){
-					action.execute();
-				}
-				
-				
-			}
-			finally{
-				logger.info("Restore motor settings");
-				motortemplate.getBaseSpeed().setValue(backupMinSpeed);
-				motortemplate.getVelocity().setValue(backupSpeed);
-				motortemplate.getBacklashDistance().setValue(backupBacklash);
-			}
-			
-			// Request read of data file
-			readQueue.put(tmpFileName);
-			
-//			// Read data
-//			Thread t = new Thread(new Runnable() {
-//				
-//				@Override
-//				public void run() {
-//					try {
-//						collectData(smbShare, tmpFileName);
-//					} catch (InterruptedException e) {
-//						throw new RuntimeException("Unable to read CRLOGIC raw data file",e);
-//					} catch (IOException e) {
-//						throw new RuntimeException("Unable to read CRLOGIC raw data file",e);
-//					}
-//				}
-//			});
-//			t.start();
-			
-			if(zigZag){
-				// Swap start and end
-				double aend = actuator.getEnd();
-				actuator.setEnd(actuator.getStart());
-				actuator.setStart(aend);
-			}
-			
-			synchronized(this){
-				executionThread = null;
-			}
-		}
-		catch(ChannelException | ExecutionException | TimeoutException e){
-			throw new RuntimeException("Unable to execute crloop", e);
-		}
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#abort()
-	 */
-	@Override
-	public void abort() {
-		abort(false);
-	}
-	
-	/**
-	 * Abort logic
-	 * @param force
-	 */
-	public synchronized void abort(boolean force){
-		abort = true;
-		abortForce = force;
-		
-		// executionThread variable guarded by "this"
-		if(executionThread != null){
-			executionThread.interrupt();
-		}
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#destroy()
-	 */
-	@Override
-	public void destroy() {
-		stopReadoutThread = true;
-		readoutThread.interrupt();
-		// TODO eventually interrupt readout thread
-		
-		try {
-			
-			cservice.destroyAnnotatedChannels(template);
-			cservice.destroyAnnotatedChannels(motortemplate);
-			template = null;
-			motortemplate = null;
-			
-		} catch (Exception e) {
-			throw new RuntimeException("Unable to destroy CrlogicLoop", e);
-		}
-		
-		
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.ActionLoop#prepare()
-	 */
-	@Override
-	public void prepare() {
-		
-		stopReadoutThread = false;
-		// Start readout Thread
-		readoutThread = new Thread(new Runnable() {
-			
-			@Override
-			public void run() {
-				while(!stopReadoutThread){
-					String file;
-					try {
-						file = readQueue.take();
-					} catch (InterruptedException e) {
-						break;
-					}
-					// TODO Read file and 
-					try {
-						collectData(smbShare, file);
-					} catch (InterruptedException e) {
-						throw new RuntimeException("Unable to read CRLOGIC raw data file",e);
-					} catch (IOException e) {
-						throw new RuntimeException("Unable to read CRLOGIC raw data file",e);
-					}
-					
-				}
-				
-			}
-		});
-		readoutThread.start();
-		
-		try{
-			// Connect crlogic channels
-			template = new CrlogicChannelsTemplate();
-			logger.info("Connect channels");
-			Map<String, String> m = new HashMap<>();
-			m.put("PREFIX", prefix);
-			cservice.createAnnotatedChannels(template, m);
-			
-			// Connect motor channels
-			motortemplate = new MotorChannelsTemplate();
-			m = new HashMap<>();
-			m.put("PREFIX", actuator.getName());
-			cservice.createAnnotatedChannels(motortemplate, m);
-			
-			useReadback = motortemplate.getUseReadback().getValue();
-			useEncoder = motortemplate.getUseEncoder().getValue();
-			
-			logger.info("Motor type: "+ MotorChannelsTemplate.Type.values()[motortemplate.getType().getValue()]);
-			logger.info("Motor use readback: "+useReadback);
-			logger.info("Motor use encoder: "+useEncoder);
-			
-			// TODO build up list of readout resources (based on sensors)
-			readoutResources.clear();
-			// first sensor is the actuator
-			
-			// Determine mode of motor
-			if((!useReadback) && (!useEncoder)){
-				// Open loop
-				if(actuator.getReadback()!=null){
-					throw new IllegalArgumentException("Readback not supported if motor is configured in open loop");
-				}
-				else{
-					readoutResources.add(actuator.getName());
-				}
-				
-			}
-			else if(useReadback && (!useEncoder)){
-				String readback;
-				// use readback link
-				if(actuator.getReadback()!=null){
-					// Use specified readback
-					readback = (actuator.getReadback());
-				}
-				else{
-					// Set resouce to readback link
-					readback = (motortemplate.getReadbackLink().getValue());
-					readback = readback.replaceAll(" +.*", ""); // remove NPP etc at the end
-				}
-				
-				readoutResources.add(readback);
-				
-				// Fill readback encoder settings
-				// Connect to encoder
-				EncoderChannelsTemplate encodertemplate = new EncoderChannelsTemplate();
-				m = new HashMap<>();
-				m.put("PREFIX", readback);
-				cservice.createAnnotatedChannels(encodertemplate, m);
-				
-				// Read encoder settings
-				if(encodertemplate.getDirection().getValue()==EncoderChannelsTemplate.Direction.Positive.ordinal()){
-					crlogicDataFilter.setEncoderDirection(1);
-				}
-				else{
-					crlogicDataFilter.setEncoderDirection(-1);
-				}
-				crlogicDataFilter.setEncoderOffset(encodertemplate.getOffset().getValue());
-				crlogicDataFilter.setEncoderResolution(encodertemplate.getResolution().getValue());
-				
-				// Disconnect from encoder
-				cservice.destroyAnnotatedChannels(encodertemplate);
-				
-			}
-			else if (useEncoder && (!useReadback)){
-				// use readback link
-				if(actuator.getReadback()!=null){
-					throw new IllegalArgumentException("Readback not supported if motor is configured to use encoder");
-				}
-				else{
-					// Set resouce to readback link
-					readoutResources.add(actuator.getName()+"_ENC");
-				}
-			}
-			else{
-				throw new IllegalArgumentException("Motor configuration not supportet: use readback - "+useReadback+" use encoder - "+useEncoder);
-			}
-			
-			// Fill Motor specific settings
-			if(motortemplate.getDirection().getValue()==MotorChannelsTemplate.Direction.Positive.ordinal()){
-				crlogicDataFilter.setMotorDirection(1);
-			}
-			else{
-				crlogicDataFilter.setMotorDirection(-1);
-			}
-			crlogicDataFilter.setMotorEncoderResolution(motortemplate.getEncoderResolution().getValue());
-			crlogicDataFilter.setMotorOffset(motortemplate.getOffset().getValue());
-			crlogicDataFilter.setMotorReadbackResolution(motortemplate.getReadbackResolution().getValue());
-			crlogicDataFilter.setMotorResolution(motortemplate.getMotorResolution().getValue());
-			
-			// Clear all indices
-			scalerIndices.clear();
-			
-			int c = 1; // We start at 1 because the actuator right now is an implicit sensor 
-			for(Sensor s: sensors){
-					if(s instanceof OTFNamedChannelSensor){
-						// Monitored channel (MUST be configured MODULE ID'S)
-						OTFNamedChannelSensor so = (OTFNamedChannelSensor) s;
-						readoutResources.add(so.getName());
-					}
-					else if (s instanceof OTFScalerChannelSensor){
-						OTFScalerChannelSensor so = (OTFScalerChannelSensor) s;
-						readoutResources.add("SCALER"+so.getIndex());
-						scalerIndices.put(c, new CrlogicDeltaDataFilter());
-					}
-					else if (s instanceof MillisecondTimestampSensor){
-						readoutResources.add("TIMESTAMP");
-					}
-					else{
-						throw new IllegalArgumentException("Sensor type "+s.getClass()+" is not supported by this loop");
-					}
-					c++;
-			}
-			
-			// Workaround - somehow one has to add an empty thing to the value otherwise the c logic 
-			// does not pick up the end
-			readoutResources.add("");
-		}
-		catch(Exception e){
-			throw new RuntimeException("Unable to prepare crloop: ",e);
-		}
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.ActionLoop#cleanup()
-	 */
-	@Override
-	public void cleanup() {
-		// TODO Auto-generated method stub
-		
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.ActionLoop#getPreActions()
-	 */
-	@Override
-	public List<Action> getPreActions() {
-		return preActions;
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.ActionLoop#getPostActions()
-	 */
-	@Override
-	public List<Action> getPostActions() {
-		return postActions;
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.ActionLoop#isDataGroup()
-	 */
-	@Override
-	public boolean isDataGroup() {
-		// TODO Auto-generated method stub
-		return dataGroup;
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.ActionLoop#setDataGroup(boolean)
-	 */
-	@Override
-	public void setDataGroup(boolean dataGroup) {
-		this.dataGroup = dataGroup;
-	}
-	
-	/**
-	 * @return the sensors
-	 */
-	public List<Sensor> getSensors() {
-		return sensors;
-	}
-	
-	/**
-	 * @return the actor
-	 */
-	public OTFActuator getActor() {
-		return actuator;
-	}
-
-	/**
-	 * @param actor the actor to set
-	 */
-	public void setActor(OTFActuator actor) {
-		this.actuator = actor;
-	}
-
-	/**
-	 * The structure of the data message depends on the sensors registered at this loop 
-	 * at the time this method is called.
-	 * @return the data queue and the metadata of the data messages
-	 */
-	public DataQueue getDataQueue() {
-		DataMessageMetadata m = new DataMessageMetadata();
-		
-		// Build up data message metadata based on the sensors currently registered.
-		m.getComponents().add(new ComponentMetadata(actuator.getId()));
-		for(Sensor s: sensors){
-			m.getComponents().add(new ComponentMetadata(s.getId()));
-		}
-		return new DataQueue(dataQueue, m);
-	}
-
-
-	/**
-	 * @return the keepTmpFiles
-	 */
-	public boolean isKeepTmpFiles() {
-		return keepTmpFiles;
-	}
-
-
-	/**
-	 * @param keepTmpFiles the keepTmpFiles to set
-	 */
-	public void setKeepTmpFiles(boolean keepTmpFiles) {
-		this.keepTmpFiles = keepTmpFiles;
-	}
-	
-	
-	
-}

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

@@ -1,274 +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.loops.cr;
-
-/**
- * @author ebner
- *
- */
-public class CrlogicRangeDataFilter {
-
-	private double motorResolution = 1;
-	private int motorDirection = 1;
-	private double motorOffset = 0;
-	private double motorReadbackResolution = 1;
-	private double motorEncoderResolution = 1;
-	
-	private double encoderOffset = 0;
-	private double encoderResolution = 1;
-	private int encoderDirection = 1;
-	
-	private double start = 0;
-	private double end = 0;
-	private boolean positive = true;
-	
-	/**
-	 * Marker whether the value was equal
-	 */
-	private boolean wasEqualBefore = false;
-	
-	/**
-	 * @return the motorResolution
-	 */
-	public double getMotorResolution() {
-		return motorResolution;
-	}
-
-	/**
-	 * @param motorResolution the motorResolution to set
-	 */
-	public void setMotorResolution(double motorResolution) {
-		this.motorResolution = motorResolution;
-	}
-
-	/**
-	 * @return the motorDirection
-	 */
-	public int getMotorDirection() {
-		return motorDirection;
-	}
-
-	/**
-	 * @param motorDirection the motorDirection to set
-	 */
-	public void setMotorDirection(int motorDirection) {
-		this.motorDirection = motorDirection;
-	}
-
-	/**
-	 * @return the motorOffset
-	 */
-	public double getMotorOffset() {
-		return motorOffset;
-	}
-
-	/**
-	 * @param motorOffset the motorOffset to set
-	 */
-	public void setMotorOffset(double motorOffset) {
-		this.motorOffset = motorOffset;
-	}
-
-	/**
-	 * @return the motorReadbackResolution
-	 */
-	public double getMotorReadbackResolution() {
-		return motorReadbackResolution;
-	}
-
-	/**
-	 * @param motorReadbackResolution the motorReadbackResolution to set
-	 */
-	public void setMotorReadbackResolution(double motorReadbackResolution) {
-		this.motorReadbackResolution = motorReadbackResolution;
-	}
-
-	/**
-	 * @return the motorEncoderResolution
-	 */
-	public double getMotorEncoderResolution() {
-		return motorEncoderResolution;
-	}
-
-	/**
-	 * @param motorEncoderResolution the motorEncoderResolution to set
-	 */
-	public void setMotorEncoderResolution(double motorEncoderResolution) {
-		this.motorEncoderResolution = motorEncoderResolution;
-	}
-
-	/**
-	 * @return the encoderOffset
-	 */
-	public double getEncoderOffset() {
-		return encoderOffset;
-	}
-
-	/**
-	 * @param encoderOffset the encoderOffset to set
-	 */
-	public void setEncoderOffset(double encoderOffset) {
-		this.encoderOffset = encoderOffset;
-	}
-
-	/**
-	 * @return the encoderResolution
-	 */
-	public double getEncoderResolution() {
-		return encoderResolution;
-	}
-
-	/**
-	 * @param encoderResolution the encoderResolution to set
-	 */
-	public void setEncoderResolution(double encoderResolution) {
-		this.encoderResolution = encoderResolution;
-	}
-
-	/**
-	 * @return the encoderDirection
-	 */
-	public int getEncoderDirection() {
-		return encoderDirection;
-	}
-
-	/**
-	 * @param encoderDirection the encoderDirection to set
-	 */
-	public void setEncoderDirection(int encoderDirection) {
-		this.encoderDirection = encoderDirection;
-	}
-
-	
-	/**
-	 * @return the start
-	 */
-	public double getStart() {
-		return start;
-	}
-
-	/**
-	 * @param start the start to set
-	 */
-	public void setStart(double start) {
-		this.start = start;
-		if(start<=end){
-			positive=true;
-		}
-		else{
-			positive=false;
-		}
-	}
-
-	/**
-	 * @return the end
-	 */
-	public double getEnd() {
-		return end;
-	}
-
-	/**
-	 * @param end the end to set
-	 */
-	public void setEnd(double end) {
-		this.end = end;
-		if(end>=start){
-			positive=true;
-		}
-		else{
-			positive=false;
-		}
-	}
-	
-	/**
-	 * Calculate real position
-	 * @param raw
-	 * @return
-	 */
-	public double calculatePositionMotor(double raw){
-		return(((raw * motorResolution * motorReadbackResolution)/motorDirection)+motorOffset);
-	}
-	
-	/**
-	 * Calculate real motor position using the readback link
-	 * @param raw
-	 * @return
-	 */
-	public double calculatePositionMotorUseReadback(double raw){
-		return((((raw - encoderOffset) * encoderResolution * encoderDirection * motorReadbackResolution) / motorDirection) + motorOffset);
-	}
-	
-	/**
-	 * Calculate real motor position using encoder
-	 * @param raw
-	 * @return
-	 */
-	public double calculatePositionMotorUseEncoder(double raw){
-		return(raw * motorEncoderResolution * motorReadbackResolution/motorDirection + motorOffset);
-	}
-	
-	/**
-	 * Filter whether value is with the range
-	 * @param value
-	 * @return
-	 */
-	public boolean filter(Double value){
-		if(positive){
-			if(start<=value && value<=end){
-				
-				// If motor is very accurete and user backlash==null it might be that value is exactly 
-				// the end value. To prevent that unnecessary data is captured execute this check
-				if(wasEqualBefore){
-					wasEqualBefore=false; // Reset flag
-					return false;
-				}
-				
-				// Check whether was equal
-				if(value==end){
-					wasEqualBefore=true;
-				}
-				
-				return true;
-			}
-			else{
-				return false;
-			}
-		}
-		else{
-			if(end<=value && value <=start){
-				
-				if(wasEqualBefore){
-					wasEqualBefore=false; // Reset flag
-					return false;
-				}
-				
-				// Check whether was equal
-				if(value==start){
-					wasEqualBefore=true;
-				}
-				
-				return true;
-			}
-			else{
-				return false;
-			}
-		}
-	}
-}

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

@@ -1,73 +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.loops.cr;
-
-import ch.psi.jcae.Channel;
-import ch.psi.jcae.annotation.CaChannel;
-
-/**
- * @author ebner
- *
- */
-public class EncoderChannelsTemplate {
-	
-	/**
-	 * Resolution	- $(P)$(E)_SCL
-	 */
-	@CaChannel(type=Double.class, name="${PREFIX}_SCL")
-	private Channel<Double> resolution;
-
-	/**
-	 * Offset	- $(P)$(E)_OFF
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}_OFF")
-	private Channel<Double> offset;
-
-	/**
-	 * Direction	- $(P)$(E)_DIR
-	 */
-	public enum Direction {Negative, Positive};
-	@CaChannel(type=Integer.class, name ="${PREFIX}_DIR")
-	private Channel<Integer> direction;
-
-	
-	/**
-	 * @return the resolution
-	 */
-	public Channel<Double> getResolution() {
-		return resolution;
-	}
-
-	/**
-	 * @return the offset
-	 */
-	public Channel<Double> getOffset() {
-		return offset;
-	}
-
-	/**
-	 * @return the direction
-	 */
-	public Channel<Integer> getDirection() {
-		return direction;
-	}
-	
-	
-}

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

@@ -1,652 +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.loops.cr;
-
-import ch.psi.jcae.Channel;
-import ch.psi.jcae.annotation.CaChannel;
-
-/**
- * @author ebner
- *
- */
-public class MotorChannelsTemplate {
-
-	public enum Type {SOFT_CHANNEL, MOTOR_SIMULATION, OMS_VME58, OMS_MAXv};
-	
-	/**
-	 * ## Drive section ##
-	 * # User coordinates #
-	 */
-	
-	/**
-	 * .HLM	High limit	- double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.HLM")
-	private Channel<Double> highLimit;
-	
-	/**
-	 * .LLM	Low limit	- double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.LLM")
-	private Channel<Double> lowLimit;
-	
-	/**
-	 * .RBV	Readback value	- double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.RBV", monitor=true)
-	private Channel<Double> readbackValue;
-	
-	/**
-	 * .VAL	Set value	- double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.VAL", monitor=true)
-	private Channel<Double> setValue;
-
-	/**
-	 * .RLV	Relative move value	- double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.RLV")
-	private Channel<Double> relativeMoveValue;
-	
-	/**
-	 * .TWV	Teak value	- double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.TWV")
-	private Channel<Double> tweakValue;
-	
-	/**
-	 * .TWR	Tweak reverse - move left	- int
-	 */
-	@CaChannel(type=Integer.class, name ="${PREFIX}.TWR")
-	private Channel<Integer> tweakReverse;
-	
-	/**
-	 * .TWF	Tweak forward - move right	- int
-	 */
-	@CaChannel(type=Integer.class, name ="${PREFIX}.TWF")
-	private Channel<Integer> tweakForward;
-	
-	/**
-	 * .JOGR	Jog reverse	- int
-	 */
-	@CaChannel(type=Integer.class, name ="${PREFIX}.JOGR")
-	private Channel<Integer> jogReverse;
-	
-	/**
-	 * .JOGF	Jog forward	- int
-	 */
-	@CaChannel(type=Integer.class, name ="${PREFIX}.JOGF")
-	private Channel<Integer> jogForward;
-	
-	/**
-	 * .HOMR	Home reverse	- int
-	 */
-	@CaChannel(type=Integer.class, name ="${PREFIX}.HOMR")
-	private Channel<Integer> homeReverse;
-	
-	/**
-	 * .HOMF	Home forward	- int
-	 */
-	@CaChannel(type=Integer.class, name ="${PREFIX}.HOMF")
-	private Channel<Integer> homeForward;
-
-	/**
-	 * .EGU	Engineering unit	- String
-	 */
-	@CaChannel(type=String.class, name ="${PREFIX}.EGU")
-	private Channel<String> engineeringUnit;
-
-	/**
-	 * .DTYP	Type	- String (e.g. "OMS MAXv") see enum Type
-	 */
-	@CaChannel(type=Integer.class, name ="${PREFIX}.DTYP")
-	private Channel<Integer> type;
-	
-	/**
-	 * .DESC	Description	- String
-	 */
-	@CaChannel(type=String.class, name ="${PREFIX}.DESC")
-	private Channel<String> description;
-
-	
-	/**
-	 * # Dial coordinates #
-	 */
-	
-	/**
-	 * .DHLM	Dial high limit	- double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.DHLM")
-	private Channel<Double> dialHighLimit;
-	
-	/**
-	 * .DLLM	Dial low limit	- double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.DLLM")
-	private Channel<Double> dialLowLimit;
-	
-	/**
-	 * .DRBV	Dial readback value	- double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.DRBV", monitor=true)
-	private Channel<Double> dialReadbackValue;
-	
-	/**
-	 * .DVAL	Dial set value	- double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.DVAL", monitor=true)
-	private Channel<Double> dialSetValue;
-
-	/**
-	 * .RVAL	Raw value	- int
-	 */
-	@CaChannel(type=Integer.class, name ="${PREFIX}.RVAL", monitor=true)
-	private Channel<Integer> rawValue;
-	
-	/**
-	 * .RRBV	Raw readback value	- int
-	 */
-	@CaChannel(type=Integer.class, name ="${PREFIX}.RRBV", monitor=true)
-	private Channel<Integer> rawReadbackValue;
-
-	/**
-	 * .SPMG	Stop/Pause/Move/Go	- (0:"Stop", 1:"Pause", 2:"Move", 3:"Go")	- 3
-	 */
-	public enum Commands { Stop, Pause, Move, Go };
-	@CaChannel(type=Integer.class, name ="${PREFIX}.SPMG")
-	private Channel<Integer> command;
-	
-
-	/**
-	 * ## Calibration section ##
-	 */
-	
-	/**
-	 * .SET	Set/Use Switch	- (0:"Use", 1:"Set")	- 0
-	 */
-	public enum Calibration {Use, Set};
-	@CaChannel(type=Integer.class, name ="${PREFIX}.SET")
-	private Channel<Integer> calibration;
-	
-	/**
-	 * .OFF	User offset (EGU)	- double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.OFF")
-	private Channel<Double> offset;
-	
-	/**
-	 * .FOFF	Offset-Freeze Switch	- (0:"Variable", 1:"Frozen") - 1
-	 */
-	public enum OffsetMode {Variable, Frozen};
-	@CaChannel(type=Integer.class, name ="${PREFIX}.FOFF")
-	private Channel<Integer> offsetMode;
-	
-	/**
-	 * .DIR	User direction	- (0:"Pos", 1:"Neg")
-	 */
-	public enum Direction {Positive, Negative};
-	@CaChannel(type=Integer.class, name ="${PREFIX}.DIR")
-	private Channel<Integer> direction;
-
-	
-	/**
-	 * ## Dynamics ##
-	 */
-	
-	/**
-	 * .VELO	Velocity (EGU/s)	- double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.VELO")
-	private Channel<Double> velocity;
-	
-	/**
-	 * .BVEL	Backlash velocity (EGU/s) - double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.BVEL")
-	private Channel<Double> backlashVelocity;
-	
-	/**
-	 * .VBAS	Base speed (EGU/s) - double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.VBAS")
-	private Channel<Double> baseSpeed;
-	
-	/**
-	 * .ACCL	Acceleration time / seconds to velocity	- double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.ACCL")
-	private Channel<Double> accelerationTime;
-	
-	/**
-	 * .BACC	Backlash acceleration time / seconds to velocity	- double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.BACC")
-	private Channel<Double> backlashAccelerationTime;
-	
-	/**
-	 * .BDST	Backlash distance (EGU)	- double 
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.BDST")
-	private Channel<Double> backlashDistance;
-	
-	/**
-	 * .FRAC	Move fraction	- double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.FRAC")
-	private Channel<Double> moveFracion;
-	
-
-	/**
-	 * ## Resolution ##
-	 */
-	
-	/**
-	 * .MRES	Motor resolution	- double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.MRES")
-	private Channel<Double> motorResolution;
-	
-	/**
-	 * .ERES	Encoder resolution	- double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.ERES")
-	private Channel<Double> encoderResolution;
-	
-	/**
-	 * .RRES	Readback resolution	- double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.RRES")
-	private Channel<Double> readbackResolution;
-	
-	/**
-	 * .RDBD	Retry deadband (EGU)	- double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.RDBD")
-	private Channel<Double> retryDeadband;
-	
-	/**
-	 * .RTRY	Max retry count	- int
-	 */
-	@CaChannel(type=Integer.class, name ="${PREFIX}.RTRY")
-	private Channel<Integer> maxRetryCount;
-	
-	/**
-	 * .RCNT	Retry count	- int
-	 */
-	@CaChannel(type=Integer.class, name ="${PREFIX}.RCNT", monitor=true)
-	private Channel<Integer> retryCount;
-	
-	/**
-	 * .UEIP	Use encoder (if present) - (0:"No", 1:"Yes")
-	 */
-	@CaChannel(type=Boolean.class, name ="${PREFIX}.UEIP")
-	private Channel<Boolean> useEncoder;
-	
-	/**
-	 * .URIP	Use readback link (if present)	- (0:"No", 1:"Yes")
-	 */
-	@CaChannel(type=Boolean.class, name ="${PREFIX}.URIP")
-	private Channel<Boolean> useReadback;
-	
-	/**
-	 * .DLY	Readback delay (s)	- double
-	 */
-	@CaChannel(type=Double.class, name ="${PREFIX}.DLY")
-	private Channel<Double> readbackDelay;
-	
-	/**
-	 * .RDBL	Readback link	- String
-	 */
-	@CaChannel(type=String.class, name ="${PREFIX}.RDBL")
-	private Channel<String> readbackLink;
-	
-	/**
-	 * .OMSL	Output mode select	- (0:"supervisory", 1:"closed_loop")
-	 */
-	public enum OutputMode {Supervisory, Closed_Loop};
-	@CaChannel(type=Integer.class, name ="${PREFIX}.OMSL")
-	private Channel<Integer> outputMode;
-	
-	/**
-	 * ## Status ## 
-	 */
-	
-	/**
-	 * .DMOV	Done move	- int
-	 */
-	@CaChannel(type=Boolean.class, name ="${PREFIX}.DMOV", monitor=true)
-	private Channel<Boolean> moveDone;
-
-	/**
-	 * @return the highLimit
-	 */
-	public Channel<Double> getHighLimit() {
-		return highLimit;
-	}
-
-	/**
-	 * @return the lowLimit
-	 */
-	public Channel<Double> getLowLimit() {
-		return lowLimit;
-	}
-
-	/**
-	 * @return the readbackValue
-	 */
-	public Channel<Double> getReadbackValue() {
-		return readbackValue;
-	}
-
-	/**
-	 * @return the setValue
-	 */
-	public Channel<Double> getSetValue() {
-		return setValue;
-	}
-
-	/**
-	 * @return the relativeMoveValue
-	 */
-	public Channel<Double> getRelativeMoveValue() {
-		return relativeMoveValue;
-	}
-
-	/**
-	 * @return the tweakValue
-	 */
-	public Channel<Double> getTweakValue() {
-		return tweakValue;
-	}
-
-	/**
-	 * @return the tweakReverse
-	 */
-	public Channel<Integer> getTweakReverse() {
-		return tweakReverse;
-	}
-
-	/**
-	 * @return the tweakForward
-	 */
-	public Channel<Integer> getTweakForward() {
-		return tweakForward;
-	}
-
-	/**
-	 * @return the jogReverse
-	 */
-	public Channel<Integer> getJogReverse() {
-		return jogReverse;
-	}
-
-	/**
-	 * @return the jogForward
-	 */
-	public Channel<Integer> getJogForward() {
-		return jogForward;
-	}
-
-	/**
-	 * @return the homeReverse
-	 */
-	public Channel<Integer> getHomeReverse() {
-		return homeReverse;
-	}
-
-	/**
-	 * @return the homeForward
-	 */
-	public Channel<Integer> getHomeForward() {
-		return homeForward;
-	}
-
-	/**
-	 * @return the engineeringUnit
-	 */
-	public Channel<String> getEngineeringUnit() {
-		return engineeringUnit;
-	}
-
-	/**
-	 * @return the type
-	 */
-	public Channel<Integer> getType() {
-		return type;
-	}
-
-	/**
-	 * @return the description
-	 */
-	public Channel<String> getDescription() {
-		return description;
-	}
-
-	/**
-	 * @return the dialHighLimit
-	 */
-	public Channel<Double> getDialHighLimit() {
-		return dialHighLimit;
-	}
-
-	/**
-	 * @return the dialLowLimit
-	 */
-	public Channel<Double> getDialLowLimit() {
-		return dialLowLimit;
-	}
-
-	/**
-	 * @return the dialReadbackValue
-	 */
-	public Channel<Double> getDialReadbackValue() {
-		return dialReadbackValue;
-	}
-
-	/**
-	 * @return the dialSetValue
-	 */
-	public Channel<Double> getDialSetValue() {
-		return dialSetValue;
-	}
-
-	/**
-	 * @return the rawValue
-	 */
-	public Channel<Integer> getRawValue() {
-		return rawValue;
-	}
-
-	/**
-	 * @return the rawReadbackValue
-	 */
-	public Channel<Integer> getRawReadbackValue() {
-		return rawReadbackValue;
-	}
-
-	/**
-	 * @return the command
-	 */
-	public Channel<Integer> getCommand() {
-		return command;
-	}
-
-	/**
-	 * @return the calibration
-	 */
-	public Channel<Integer> getCalibration() {
-		return calibration;
-	}
-
-	/**
-	 * @return the userOffset
-	 */
-	public Channel<Double> getOffset() {
-		return offset;
-	}
-
-	/**
-	 * @return the offsetMode
-	 */
-	public Channel<Integer> getOffsetMode() {
-		return offsetMode;
-	}
-
-	/**
-	 * @return the direction
-	 */
-	public Channel<Integer> getDirection() {
-		return direction;
-	}
-
-	/**
-	 * @return the velocity
-	 */
-	public Channel<Double> getVelocity() {
-		return velocity;
-	}
-
-	/**
-	 * @return the backlashVelocity
-	 */
-	public Channel<Double> getBacklashVelocity() {
-		return backlashVelocity;
-	}
-
-	/**
-	 * @return the baseSpeed
-	 */
-	public Channel<Double> getBaseSpeed() {
-		return baseSpeed;
-	}
-
-	/**
-	 * @return the accelerationTime
-	 */
-	public Channel<Double> getAccelerationTime() {
-		return accelerationTime;
-	}
-
-	/**
-	 * @return the backlashAccelerationTime
-	 */
-	public Channel<Double> getBacklashAccelerationTime() {
-		return backlashAccelerationTime;
-	}
-
-	/**
-	 * @return the backlashDistance
-	 */
-	public Channel<Double> getBacklashDistance() {
-		return backlashDistance;
-	}
-
-	/**
-	 * @return the moveFracion
-	 */
-	public Channel<Double> getMoveFracion() {
-		return moveFracion;
-	}
-
-	/**
-	 * @return the motorResolution
-	 */
-	public Channel<Double> getMotorResolution() {
-		return motorResolution;
-	}
-
-	/**
-	 * @return the encoderResolution
-	 */
-	public Channel<Double> getEncoderResolution() {
-		return encoderResolution;
-	}
-
-	/**
-	 * @return the readbackResolution
-	 */
-	public Channel<Double> getReadbackResolution() {
-		return readbackResolution;
-	}
-
-	/**
-	 * @return the retryDeadband
-	 */
-	public Channel<Double> getRetryDeadband() {
-		return retryDeadband;
-	}
-
-	/**
-	 * @return the maxRetryCount
-	 */
-	public Channel<Integer> getMaxRetryCount() {
-		return maxRetryCount;
-	}
-
-	/**
-	 * @return the retryCount
-	 */
-	public Channel<Integer> getRetryCount() {
-		return retryCount;
-	}
-
-	/**
-	 * @return the useEncoder
-	 */
-	public Channel<Boolean> getUseEncoder() {
-		return useEncoder;
-	}
-
-	/**
-	 * @return the useReadback
-	 */
-	public Channel<Boolean> getUseReadback() {
-		return useReadback;
-	}
-
-	/**
-	 * @return the readbackDelay
-	 */
-	public Channel<Double> getReadbackDelay() {
-		return readbackDelay;
-	}
-
-	/**
-	 * @return the readbackLink
-	 */
-	public Channel<String> getReadbackLink() {
-		return readbackLink;
-	}
-
-	/**
-	 * @return the outputMode
-	 */
-	public Channel<Integer> getOutputMode() {
-		return outputMode;
-	}
-
-	/**
-	 * @return the moveDone
-	 */
-	public Channel<Boolean> getMoveDone() {
-		return moveDone;
-	}
-	
-}

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

@@ -1,268 +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.loops.cr;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.concurrent.Callable;
-import java.util.concurrent.CyclicBarrier;
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.Executors;
-import java.util.concurrent.Future;
-import java.util.concurrent.TimeUnit;
-import java.util.logging.Level;
-import java.util.logging.Logger;
-
-import ch.psi.fda.core.Action;
-import ch.psi.fda.core.ActionLoop;
-import ch.psi.fda.core.messages.DataQueue;
-import ch.psi.fda.core.sensors.MillisecondTimestampSensor;
-
-/**
- * @author ebner
- *
- */
-public class ParallelCrlogic implements ActionLoop {
-	
-	// Get Logger
-	private static final Logger logger = Logger.getLogger(ParallelCrlogic.class.getName());
-
-	/**
-	 * Flag to indicate whether the data of this loop will be grouped
-	 * According to this flag the dataGroup flag in EndOfStream will be set.
-	 */
-	private boolean dataGroup = false;
-	
-	private CrlogicLoop crlogic;
-	private ScrlogicLoop scrlogic;
-	
-	/**
-	 * List of actions that are executed at the beginning of the loop.
-	 */
-	private List<Action> preActions;
-	/**
-	 * List of actions that are executed at the end of the loop.
-	 */
-	private List<Action> postActions;
-	
-	private ParallelCrlogicStreamMerge merger;
-	
-	
-	public ParallelCrlogic(CrlogicLoop crlogic, ScrlogicLoop scrlogic){
-		
-		if(crlogic==null){
-			throw new IllegalArgumentException("No Crloop specified");
-		}
-		if(scrlogic==null){
-			throw new IllegalArgumentException("No Scrloop specified");
-		}
-		
-		this.crlogic = crlogic;
-		// Add timestamp to sensor at the beginning of the sensor list as this is required for merging the data
-		// Timestamp will be at the second position of a message in the queue!
-		this.crlogic.getSensors().add(0, new MillisecondTimestampSensor("tmp_timestamp"));
-		this.scrlogic = scrlogic;
-		
-		// Initialize lists used by the loop
-		this.preActions = new ArrayList<Action>();
-		this.postActions = new ArrayList<Action>();
-		
-		this.merger = new ParallelCrlogicStreamMerge(crlogic.getDataQueue(), scrlogic.getDataQueue());
-	}
-	
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.logic.Logic#prepare()
-	 */
-	@Override
-	public void prepare() {
-		// TODO Auto-generated method stub
-		
-	}
-	
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.logic.Logic#execute()
-	 */
-	@Override
-	public void execute() throws InterruptedException {
-		
-		// Execute pre actions
-		for(Action action: preActions){
-			action.execute();
-		}
-		
-		
-		ExecutorService service = Executors.newFixedThreadPool(3); // 2 for the parallel data acquisition and 1 for the merger thread
-		final CyclicBarrier b = new CyclicBarrier(2);
-		
-		List<Future<Boolean>> list = new ArrayList<Future<Boolean>>();
-		
-		// Start a thread for each logic
-		logger.info("Submit logic");
-		Future<Boolean> f = service.submit(new Callable<Boolean>(){
-			@Override
-			public Boolean call() throws Exception {
-				
-				// Prepare logic
-				crlogic.prepare();
-				
-				// Ensure that really all parallel logics start in parallel
-				b.await();
-				
-				// Execute the logic of this path
-				crlogic.execute();
-	
-				// Need to stop the scrlogic logic (otherwise it would keep going to take data)
-				scrlogic.abort();
-				return true;
-			}});
-		list.add(f);
-		
-		//Start a thread for the scrlogic
-		logger.info("Submit logic");
-		f = service.submit(new Callable<Boolean>(){
-			@Override
-			public Boolean call() throws Exception {
-				
-				// Prepare logic
-				scrlogic.prepare();
-				
-				// Ensure that really all parallel logics start in parallel
-				b.await();
-				
-				// Execute the logic of this path
-				scrlogic.execute(); // This actually just starts the collection ...
-				return true;
-			}});
-		list.add(f);
-		
-		
-//		// Start data merge thread
-//		logger.info("Start data merge");
-//		f = service.submit(new Callable<Boolean>(){
-//			@Override
-//			public Boolean call() throws Exception {
-//				
-//				merger.merge();
-//				return true;
-//			}});
-//		list.add(f);
-		
-		
-		for(Future<Boolean> bf: list){
-			// Wait for completion of the thread
-			try {
-				bf.get();
-			} catch (ExecutionException e) {
-				logger.log(Level.WARNING, "Something went wrong while waiting for crthreads to finish");
-				throw new RuntimeException(e);
-			}
-		}
-		
-		merger.merge();
-		
-		// Wait until all threads have finished
-		service.shutdown();
-		service.awaitTermination(1, TimeUnit.MINUTES);
-		
-		
-		// Execute post actions
-		for(Action action: postActions){
-			action.execute();
-		}
-		
-	}
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#abort()
-	 */
-	@Override
-	public void abort() {
-		// TODO Auto-generated method stub
-		
-	}
-
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.Action#destroy()
-	 */
-	@Override
-	public void destroy() {
-		crlogic.destroy();
-		scrlogic.destroy();
-	}
-
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.ActionLoop#cleanup()
-	 */
-	@Override
-	public void cleanup() {
-		// TODO Auto-generated method stub
-		
-	}
-
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.ActionLoop#getPreActions()
-	 */
-	@Override
-	public List<Action> getPreActions() {
-		return preActions;
-	}
-
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.ActionLoop#getPostActions()
-	 */
-	@Override
-	public List<Action> getPostActions() {
-		return postActions;
-	}
-
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.ActionLoop#isDataGroup()
-	 */
-	@Override
-	public boolean isDataGroup() {
-		return dataGroup;
-	}
-
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.ActionLoop#setDataGroup(boolean)
-	 */
-	@Override
-	public void setDataGroup(boolean dataGroup) {
-		this.dataGroup = dataGroup;
-	}
-
-
-	/* (non-Javadoc)
-	 * @see ch.psi.fda.core.ActionLoop#getDataQueue()
-	 */
-	@Override
-	public DataQueue getDataQueue() {
-		return(merger.getDataQueue());
-	}
-	
-}

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

@@ -1,169 +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.loops.cr;
-
-import java.util.List;
-import java.util.concurrent.BlockingQueue;
-import java.util.concurrent.LinkedBlockingQueue;
-
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.DataMessageMetadata;
-import ch.psi.fda.core.messages.DataQueue;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Message;
-
-/**
- * @author ebner
- *
- */
-public class ParallelCrlogicStreamMerge {
-
-	private BlockingQueue<Message> dataQueue;
-	
-	private DataQueue primaryQueue;
-	private DataQueue secondaryQueue;
-	
-	/**
-	 * Class to merge two data streams into one. The secondary queues data is added to the primary queues data.
-	 * The resulting queue therefor will hold the same amount of elements as the primary queue does.
-	 * The datagroup flag set in the end of stream message will be set according to the flag set in the primary queue.
-	 * 
-	 * @param pqueue	Primary/master queue
-	 * @param squeue	Secondary queue
-	 */
-	public ParallelCrlogicStreamMerge(DataQueue pqueue, DataQueue squeue){
-		this.primaryQueue = pqueue;
-		this.secondaryQueue = squeue;
-		
-		this.dataQueue = new LinkedBlockingQueue<Message>();
-	}
-	
-	/**
-	 * Merge the streams based on the timestamp
-	 * @throws InterruptedException 
-	 */
-	public void merge() throws InterruptedException{
-		
-		// Actual data of the secondary queue
-		List<Object> currData = null;
-		
-		// Take first element of the primary queue (wait until message is available)
-		Message m = primaryQueue.getQueue().take();
-		
-		while(! (m instanceof EndOfStreamMessage)){
-			
-			if(m instanceof DataMessage){
-				
-				DataMessage dm = (DataMessage) m;
-				
-				// Get and remove merge timestamp from the data of the message 
-				Double timestamp = (Double) dm.getData().remove(1);
-				long milliseconds = (long) (timestamp*1000);
-				long nanoOffset = (long)((timestamp*1000-milliseconds)*1000000);
-				
-//				System.out.println("timestamp: "+new Date(milliseconds)+" "+milliseconds+" ."+nanoOffset);
-				
-				while(true){
-					// Assumption: the secondary Queue holds at least the data up to the 
-					// timestamp of the primary queue
-					Message mess = secondaryQueue.getQueue().peek();
-//					Message mess = secondaryQueue.getQueue().take();
-					
-					if(mess instanceof EndOfStreamMessage){
-						break;
-					}
-					
-					if(mess == null){
-						break;
-					}
-					
-					if(mess instanceof DataMessage){
-						// Check whether timestamp of the next message is bigger than the timestamp of the 
-						// message from the primary queue - if the timestamp is bigger do not take message out of the queue
-						DataMessage msCheck = (DataMessage) mess;
-						
-//						System.out.println("Mess: "+mess);
-						
-						long currMilliCheck = ((Double) msCheck.getData().get(0)).longValue();
-						long currNanoCheck = ((Double) msCheck.getData().get(1)).longValue();
-	
-						// Check
-						if(currMilliCheck>milliseconds || (currMilliCheck==milliseconds && currNanoCheck>nanoOffset)){
-							break;
-						}
-						
-						DataMessage ms = (DataMessage) secondaryQueue.getQueue().take();
-						
-//						System.out.println("Ms: "+ms);
-						
-						currData = ms.getData();
-						// Remove timestamps
-						currData.remove(0);
-						currData.remove(0);
-					}
-					else{
-						// No DataMessage
-						break;
-					}
-				}
-				
-				// Add data to primary data queue message and put it into the out queue
-				dm.getData().addAll(currData);
-				
-				dataQueue.add(dm);
-			}
-			
-			
-			m = primaryQueue.getQueue().take();
-		}
-		
-		// Add the end of stream message of the primary queue
-		dataQueue.add(m);
-		
-		// Clear all remaining messages in secondary queue  
-		secondaryQueue.getQueue().clear();
-	}
-	
-	
-	/**
-	 * The structure of the data message depends on the sensors registered at this loop 
-	 * at the time this method is called.
-	 * @return the data queue and the metadata of the data messages
-	 */
-	public DataQueue getDataQueue() {
-		DataMessageMetadata m = new DataMessageMetadata();
-		
-		DataMessageMetadata pqm = primaryQueue.getDataMessageMetadata();
-		m.getComponents().add(pqm.getComponents().get(0)); // add first component (this is the actuator)
-		// Skip the next component as this is the timestamp used to merge the data
-		for(int i=2;i<pqm.getComponents().size();i++){
-			m.getComponents().add(pqm.getComponents().get(i));
-		}
-		
-		DataMessageMetadata sqm = secondaryQueue.getDataMessageMetadata();
-		// Skip first two components of the message as this is the timestamp
-		for(int i=2;i<sqm.getComponents().size();i++){
-			m.getComponents().add(sqm.getComponents().get(i));
-		}
-		
-		return new DataQueue(dataQueue, m);
-	}
-	
-}

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

@@ -1,405 +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.loops.cr;
-
-import gov.aps.jca.Monitor;
-
-import java.beans.PropertyChangeEvent;
-import java.beans.PropertyChangeListener;
-import java.util.ArrayList;
-import java.util.Date;
-import java.util.List;
-import java.util.concurrent.BlockingQueue;
-import java.util.concurrent.CountDownLatch;
-import java.util.concurrent.LinkedBlockingQueue;
-import java.util.concurrent.TimeoutException;
-import java.util.logging.Level;
-import java.util.logging.Logger;
-
-import ch.psi.fda.core.Action;
-import ch.psi.fda.core.ActionLoop;
-import ch.psi.fda.core.Sensor;
-import ch.psi.fda.core.messages.ComponentMetadata;
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.DataMessageMetadata;
-import ch.psi.fda.core.messages.DataQueue;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Message;
-import ch.psi.fda.core.sensors.ChannelAccessDoubleSensor;
-import ch.psi.jcae.Channel;
-import ch.psi.jcae.ChannelDescriptor;
-import ch.psi.jcae.ChannelException;
-import ch.psi.jcae.ChannelService;
-import ch.psi.jcae.impl.type.DoubleTimestamp;
-
-/**
- * @author ebner
- * 
- *         Assumptions: - The delay between the monitor writing the value to the
- *         monitor queue and the readout of all the queues is sufficient to
- *         prevent the situation that some monitors of events close to each
- *         other on different IOC's have not arrived yet. - The sequence of
- *         monitors fired for one channel is according to the sequence of the
- *         causes. No monitor package is overtaking an other package on the
- *         network.
- * 
- *         - No monitor events are lost on the network (while using monitors you
- *         cannot guarantee this)
- * 
- *         The data queue returned by this logic includes two items for the
- *         timestamp and nanoseconds offset. These two items are the first two
- *         items of a message The id's are: crTimestampMilliseconds
- *         crTimestampOffsetNanoseconds
- */
-public class ScrlogicLoop implements ActionLoop {
-
-	private static String ID_TIMESTAMP_MILLISECONDS = "crTimestampMilliseconds";
-	private static String ID_TIMESTAMP_OFFSET_NANOSECONDS = "crTimestampOffsetNanoseconds";
-
-	// Get Logger
-	private static final Logger logger = Logger.getLogger(ScrlogicLoop.class.getName());
-
-
-	/**
-	 * Data queue sensor data is posted to. A message consists of a list of data
-	 * objects that are read out of the sensors of this loop.
-	 */
-	private final BlockingQueue<Message> dataQueue = new LinkedBlockingQueue<Message>();
-
-	private boolean dataGroup = false;
-	private final List<Action> preActions = new ArrayList<Action>();
-	private final List<Action> postActions = new ArrayList<Action>();
-
-	/**
-	 * Sensors to read out
-	 */
-//	private List<Sensor> sensors;
-
-	/**
-	 * List of monitors that were attached to the sensor channels (i.e
-	 * workaround)
-	 */
-	private final List<PropertyChangeListener> monitors = new ArrayList<>();
-
-	/**
-	 * List of blocking queues that hold the data for one sensor (channel)
-	 */
-	private final List<BlockingQueue<TimestampedValue>> queues = new ArrayList<BlockingQueue<TimestampedValue>>();
-
-	private CountDownLatch latch;
-
-	private List<Channel<DoubleTimestamp>> sensors = new ArrayList<>();
-	private List<String> sensorIds = new ArrayList<>();
-	private ChannelService cservice;
-	
-	public ScrlogicLoop(ChannelService s, List<Sensor> sensors) {
-		try{
-		for(Sensor ss: sensors){
-			this.sensors.add(s.createChannel(new ChannelDescriptor<DoubleTimestamp>(DoubleTimestamp.class, ((ChannelAccessDoubleSensor)ss).getChannel().getName(), true)));
-			sensorIds.add(ss.getId());
-		}
-		this.cservice = s;
-		} catch (ChannelException | InterruptedException | TimeoutException e) {
-			throw new RuntimeException(e);
-		}
-	}
-
-	/*
-	 * (non-Javadoc)
-	 * 
-	 * @see ch.psi.fda.core.Action#execute()
-	 */
-	@Override
-	public void execute() throws InterruptedException {
-
-		// Clear all queues
-		queues.clear();
-		latch = new CountDownLatch(1);
-
-			// Attach monitors to the channels (this is actually a workaround)
-			for (Channel<DoubleTimestamp> sensor : sensors) {
-//				if (sensor instanceof ChannelAccessDoubleSensor) {
-//					ChannelAccessDoubleSensor s = (ChannelAccessDoubleSensor) sensor;
-//					Channel<Double> b = s.getChannel();
-					// Create data queue for the channel
-					final BlockingQueue<TimestampedValue> q = new LinkedBlockingQueue<TimestampedValue>();
-					queues.add(q);
-					
-					PropertyChangeListener b = new PropertyChangeListener() {
-						
-						@Override
-						public void propertyChange(PropertyChangeEvent evt) {
-							DoubleTimestamp value = (DoubleTimestamp) evt.getNewValue();
-							q.add(new TimestampedValue(value.getValue(), value.getTimestamp().getTime(), value.getNanosecondOffset()));
-						}
-					};
-
-					sensor.addPropertyChangeListener("value", b);
-					
-					monitors.add(b);
-//				}
-			}
-
-		logger.info("Start data acquisition");
-
-		latch.await();
-
-		// Remove monitors
-		try{
-			for (int i = 0; i < sensors.size(); i++) {
-				Channel<DoubleTimestamp> sensor = sensors.get(i);
-				sensor.removePropertyChangeListener(monitors.get(i));
-			}
-		}
-		finally{
-			// Clear all monitors in the list
-			monitors.clear();
-		}
-
-		// Merge data
-		merge();
-
-		// Clear data queues
-		for (BlockingQueue<TimestampedValue> q : queues) {
-			q.clear();
-		}
-		queues.clear();
-
-		// Put end of stream to the queue
-		dataQueue.add(new EndOfStreamMessage(dataGroup));
-		
-	}
-
-	/*
-	 * (non-Javadoc)
-	 * 
-	 * @see ch.psi.fda.core.Action#abort()
-	 */
-	@Override
-	public void abort() {
-		latch.countDown();
-	}
-
-	/*
-	 * (non-Javadoc)
-	 * 
-	 * @see ch.psi.fda.core.Action#destroy()
-	 */
-	@Override
-	public void destroy() {
-		// Destroy all sensors
-		for (Channel<DoubleTimestamp> s : sensors) {
-			try {
-				s.destroy();
-			} catch (ChannelException e) {
-				throw new RuntimeException(e);
-			}
-		}
-		sensors.clear();
-	}
-
-	/*
-	 * (non-Javadoc)
-	 * 
-	 * @see ch.psi.fda.core.ActionLoop#prepare()
-	 */
-	@Override
-	public void prepare() {
-		// do nothing
-	}
-
-	/*
-	 * (non-Javadoc)
-	 * 
-	 * @see ch.psi.fda.core.ActionLoop#cleanup()
-	 */
-	@Override
-	public void cleanup() {
-		// Do nothing
-	}
-
-	/*
-	 * (non-Javadoc)
-	 * 
-	 * @see ch.psi.fda.core.ActionLoop#getPreActions()
-	 */
-	@Override
-	public List<Action> getPreActions() {
-		return preActions;
-	}
-
-	/*
-	 * (non-Javadoc)
-	 * 
-	 * @see ch.psi.fda.core.ActionLoop#getPostActions()
-	 */
-	@Override
-	public List<Action> getPostActions() {
-		return postActions;
-	}
-
-	/*
-	 * (non-Javadoc)
-	 * 
-	 * @see ch.psi.fda.core.ActionLoop#isDataGroup()
-	 */
-	@Override
-	public boolean isDataGroup() {
-		return dataGroup;
-	}
-
-	/*
-	 * (non-Javadoc)
-	 * 
-	 * @see ch.psi.fda.core.ActionLoop#setDataGroup(boolean)
-	 */
-	@Override
-	public void setDataGroup(boolean dataGroup) {
-		this.dataGroup = dataGroup;
-	}
-
-	/**
-	 * The structure of the data message depends on the sensors registered at
-	 * this loop at the time this method is called.
-	 * 
-	 * @return the data queue and the metadata of the data messages
-	 */
-	public DataQueue getDataQueue() {
-		DataMessageMetadata m = new DataMessageMetadata();
-
-		// Build up data message metadata based on the channels registered.
-		m.getComponents().add(new ComponentMetadata(ID_TIMESTAMP_MILLISECONDS));
-		m.getComponents().add(
-				new ComponentMetadata(ID_TIMESTAMP_OFFSET_NANOSECONDS));
-		for (String id : sensorIds) {
-			m.getComponents().add(new ComponentMetadata(id));
-		}
-		return new DataQueue(dataQueue, m);
-	}
-
-	private boolean hasNext(){
-		for (int i = 0; i < queues.size(); i++) {
-			if(!queues.get(i).isEmpty()){
-				return true;
-			}
-		}
-		return false;
-	}
-	
-	/**
-	 * Merge data collected by different monitor
-	 * 
-	 * @throws InterruptedException
-	 */
-	private void merge() throws InterruptedException {
-
-		// Array to hold temporary channel values
-		TimestampedValue[] cvalues = new TimestampedValue[queues.size()];
-		TimestampedValueComparator comparator = new TimestampedValueComparator();
-
-		// Oldest value written
-		TimestampedValue globalOldest = null;
-		List<Integer> indexes = new ArrayList<Integer>();
-
-		while (hasNext()) {
-
-//			semaphore.acquire();
-			Thread.sleep(10); // Ensure that close by monitors have time to
-								// catch up / also ensure context switch
-
-			// Oldest value of this run
-			TimestampedValue oldest = null;
-			// Queue index of the oldest value of this run
-			indexes.clear();
-
-			// Find oldest element in any of the queues
-			for (int i = 0; i < queues.size(); i++) {
-
-				BlockingQueue<TimestampedValue> q = queues.get(i);
-				TimestampedValue ttcheck = q.peek();
-
-				if (ttcheck != null) {
-					if (oldest == null) {
-						// Update the oldest variable with current element
-						oldest = ttcheck;
-						indexes.clear();
-						indexes.add(i);
-					} else if (comparator.compare(ttcheck, oldest) < 0) { 
-						// Check whether timestamp is less (older) than the current oldest timestamp.
-						oldest = ttcheck;
-						indexes.clear();
-						indexes.add(i);
-					} else if (comparator.compare(ttcheck, oldest) == 0) {
-						// SAME TIMESTAMP
-						indexes.add(i);
-					} else {
-					}
-				}
-			}
-
-			// logger.info("Index: "+index+" Permits: "+semaphore.availablePermits());
-			// System.out.println("indexes: "+indexes.size());
-
-			if (indexes.size() > 0) {
-				long timestamp = 0l;
-				long nanoOffset = 0l;
-
-				for (Integer index : indexes) {
-					// Get next older value
-					cvalues[index] = queues.get(index).poll();
-
-					if (globalOldest != null) {
-						if (comparator.compare(cvalues[index], globalOldest) >= 0) {
-							// Update the global oldest variable
-							globalOldest = cvalues[index];
-							timestamp = cvalues[index].getTimestamp();
-							nanoOffset = cvalues[index].getNanosecondsOffset();
-						} else {
-							// Monitors did not fire in sequence (an newer
-							// monitor overtook an older (from an other IOC))
-							logger.warning("Timestamped value out of sequence - discard value !!!!");
-							// Continue with next value ...
-							continue;
-						}
-					} else {
-						globalOldest = cvalues[index];
-					}
-				}
-
-				// Assemble data message ...
-				DataMessage message = new DataMessage();
-
-				message.getData().add(new Double(timestamp));
-				message.getData().add(new Double(nanoOffset));
-
-				for (int y = 0; y < cvalues.length; y++) {
-					if (cvalues[y] != null) {
-						message.getData().add(new Double(cvalues[y].getValue()));
-					} else {
-						message.getData().add(Double.NaN);
-					}
-				}
-//				System.out.println(message);
-				dataQueue.add(message);
-			}
-
-		}
-	}
-}

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

@@ -1,81 +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.loops.cr;
-
-/**
- * @author ebner
- *
- */
-public class TimestampedValue {
-
-	private Double value;
-	private long timestamp;
-	private long nanosecondsOffset;
-	
-	public TimestampedValue(Double value, long timestamp, long nanosecondsOffset){
-		this.value = value;
-		this.timestamp = timestamp;
-		this.nanosecondsOffset = nanosecondsOffset;
-	}
-
-	/**
-	 * @return the value
-	 */
-	public Double getValue() {
-		return value;
-	}
-
-	/**
-	 * @param value the value to set
-	 */
-	public void setValue(Double value) {
-		this.value = value;
-	}
-
-	/**
-	 * @return the timestamp
-	 */
-	public long getTimestamp() {
-		return timestamp;
-	}
-
-	/**
-	 * @param timestamp the timestamp to set
-	 */
-	public void setTimestamp(long timestamp) {
-		this.timestamp = timestamp;
-	}
-
-	/**
-	 * @return the nanosecondsOffset
-	 */
-	public long getNanosecondsOffset() {
-		return nanosecondsOffset;
-	}
-
-	/**
-	 * @param nanosecondsOffset the nanosecondsOffset to set
-	 */
-	public void setNanosecondsOffset(long nanosecondsOffset) {
-		this.nanosecondsOffset = nanosecondsOffset;
-	}
-	
-	
-}

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

@@ -1,45 +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.loops.cr;
-
-import java.util.Comparator;
-
-/**
- * @author ebner
- *
- */
-public class TimestampedValueComparator implements Comparator<TimestampedValue> {
-
-	@Override
-	public int compare(TimestampedValue o1, TimestampedValue o2) {
-		if (o1.getTimestamp() < o2.getTimestamp()) {
-			return -1;
-		} else if (o1.getTimestamp() > o2.getTimestamp()) {
-			return 1;
-		} else if (o1.getTimestamp() == o2.getTimestamp()) {
-			if (o1.getNanosecondsOffset() < o2.getNanosecondsOffset()) {
-				return -1;
-			} else if (o1.getNanosecondsOffset() > o2.getNanosecondsOffset()) {
-				return 1;
-			}
-		}
-		return 0;
-	}
-}

ch.psi.fda/src/main/java/ch/psi/fda/core/loops/cr/VSC16ScalerChannelsTemplate.java

@@ -1,103 +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.loops.cr;
-
-import java.util.List;
-
-import ch.psi.jcae.Channel;
-import ch.psi.jcae.annotation.CaChannel;
-
-/**
- * @author ebner
- *
- */
-public class VSC16ScalerChannelsTemplate {
-
-	
-	public enum Command {Done, Count};
-	/**
-	 * Command
-	 */
-	@CaChannel(type=Integer.class, name ="${PREFIX}.CNT")
-	private Channel<Integer> command;
-	
-	
-	public enum Mode {OneShot, AutoCount};
-	/**
-	 * Count mode
-	 */
-	@CaChannel(type=Integer.class, name ="${PREFIX}.CONT")
-	private Channel<Integer> mode;
-	
-	/**
-	 * Channel description
-	 */
-	@CaChannel(type=Boolean.class, name={"${PREFIX}.NM1", "${PREFIX}.NM2", "${PREFIX}.NM3", "${PREFIX}.NM4", "${PREFIX}.NM5", "${PREFIX}.NM6", "${PREFIX}.NM7", "${PREFIX}.NM8", "${PREFIX}.NM9", "${PREFIX}.NM10", "${PREFIX}.NM11", "${PREFIX}.NM12", "${PREFIX}.NM13", "${PREFIX}.NM14", "${PREFIX}.NM15", "${PREFIX}.NM16"})
-	private List<Channel<Boolean>> channelDescription;
-	
-	/**
-	 * Channel gate
-	 */
-	@CaChannel(type=Boolean.class, name={"${PREFIX}.G1", "${PREFIX}.G2", "${PREFIX}.G3", "${PREFIX}.G4", "${PREFIX}.G5", "${PREFIX}.G6", "${PREFIX}.G7", "${PREFIX}.G8", "${PREFIX}.G9", "${PREFIX}.G10", "${PREFIX}.G11", "${PREFIX}.G12", "${PREFIX}.G13", "${PREFIX}.G14", "${PREFIX}.G15", "${PREFIX}.G16"})
-	private List<Channel<Boolean>> channelGate;
-	
-	/**
-	 * Channel preset count
-	 * If gate is on scaler will only count until this value
-	 */
-	@CaChannel(type=Integer.class, name={"${PREFIX}.PR1", "${PREFIX}.PR2", "${PREFIX}.PR3", "${PREFIX}.PR4", "${PREFIX}.PR5", "${PREFIX}.PR6", "${PREFIX}.PR7", "${PREFIX}.PR8", "${PREFIX}.PR9", "${PREFIX}.PR10", "${PREFIX}.PR11", "${PREFIX}.PR12", "${PREFIX}.PR13", "${PREFIX}.PR14", "${PREFIX}.PR15", "${PREFIX}.PR16"})
-	private List<Channel<Integer>> channelPresetCount;
-
-	/**
-	 * @return the command
-	 */
-	public Channel<Integer> getCommand() {
-		return command;
-	}
-
-	/**
-	 * @return the mode
-	 */
-	public Channel<Integer> getMode() {
-		return mode;
-	}
-
-	/**
-	 * @return the channelDescription
-	 */
-	public List<Channel<Boolean>> getChannelDescription() {
-		return channelDescription;
-	}
-
-	/**
-	 * @return the channelGate
-	 */
-	public List<Channel<Boolean>> getChannelGate() {
-		return channelGate;
-	}
-
-	/**
-	 * @return the channelPresetCount
-	 */
-	public List<Channel<Integer>> getChannelPresetCount() {
-		return channelPresetCount;
-	}
-	
-}

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

@@ -1,276 +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.manipulator;
-
-import java.util.List;
-import java.util.concurrent.TimeoutException;
-import java.util.logging.Level;
-import java.util.logging.Logger;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import javax.script.ScriptEngine;
-import javax.script.ScriptEngineManager;
-import javax.script.ScriptException;
-
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.DataMessageMetadata;
-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.jcae.Channel;
-import ch.psi.jcae.ChannelDescriptor;
-import ch.psi.jcae.ChannelException;
-import ch.psi.jcae.ChannelService;
-
-/**
- * Manipulation
- * @author ebner
- */
-public class JythonManipulation implements Manipulation{
-
-	
-	// Get Logger
-	private static Logger logger = Logger.getLogger(JythonManipulation.class.getName());
-	
-	/**
-	 * Pattern of the entry function of the jython script
-	 */
-	private static final String entryFunction = "process";
-	private static final String entryFunctionPattern = "def "+entryFunction+"\\((.*)\\):";
-	
-	/**
-	 * Code of the manipulation. The script need to implement a function of the type:
-	 * <code>
-	 * def process():
-	 *     # ... your code
-	 *     return value
-	 * </code>
-	 * 
-	 * The number of parameters of the script are not limited. So <code>process(a)</code> is valid
-	 * as well as <code>process(a,b,c,d,e,f)</code>.
-	 * However for each parameter there need to be a mapping inside the mapping list! If there is no
-	 * mapping inside the Manipulator evaluating this Manipulation will throw an Exception.
-	 */
-	private final String script;
-	
-	/**
-	 * Id of the resulting component
-	 */
-	private final String id;
-	
-	/**
-	 * Mapping of components to manipulation code variables
-	 */
-	private final List<JythonParameterMapping> mapping;
-
-	private final boolean returnArray;
-	
-	/**
-	 * Script engine of the manipulator
-	 */
-	private ScriptEngine engine;
-	/**
-	 * Component index of the script parameter. The sequence of the indexes in this array correspond to the script
-	 * parameter position, i.e. the first index corresponds to the first parameter.
-	 */
-	private Integer[] parameterIndex;
-	/**
-	 * Parameter array of the entry function
-	 */
-	private String[] parameter;
-	private ChannelService cservice;
-	
-	/**
-	 * Jython entry call
-	 */
-	private String jythonCall;
-	
-	public JythonManipulation(ChannelService s, String id, String script, List<JythonParameterMapping> mapping){
-		this(s, id, script, mapping, false);
-	}
-	
-	/**
-	 * Constructor
-	 * @param id
-	 * @param script
-	 * @param mapping
-	 */
-	public JythonManipulation(ChannelService s, String id, String script, List<JythonParameterMapping> mapping, boolean returnArray){
-		this.id = id;
-		this.script = script;
-		this.mapping = mapping;
-		this.returnArray = returnArray;
-		this.cservice = s;
-	}
-	
-	/**
-	 * @return the script
-	 */
-	public String getScript() {
-		return script;
-	}
-
-	/**
-	 * @return the mapping
-	 */
-	public List<JythonParameterMapping> getMapping() {
-		return mapping;
-	}
-
-
-	@Override
-	public String getId() {
-		return id;
-	}
-	
-
-	@Override
-	public void initialize(DataMessageMetadata metadata){
-		
-		// Workaround for Jython memory leak 
-		// http://blog.hillbrecht.de/2009/07/11/jython-memory-leakout-of-memory-problem/
-		System.setProperty("python.options.internalTablesImpl","weak");
-		
-		// Create new script engine
-		this.engine = new ScriptEngineManager().getEngineByName("python");
-		
-		// Determine script entry function and the function parameters
-		Pattern pattern = Pattern.compile(entryFunctionPattern);
-		Matcher matcher = pattern.matcher(this.script);
-		if(matcher.find() && matcher.groupCount()==1){
-			if(!matcher.group(1).trim().equals("")){
-				logger.finest("Entry function '"+entryFunctionPattern+"' found - Identified parameters: "+matcher.group(1));
-				parameter = matcher.group(1).split(" *, *");
-			}
-			else{
-				parameter = new String[0];
-			}
-		}
-		else{
-			throw new IllegalArgumentException("Cannot determine entry function: "+entryFunctionPattern);
-		}
-		
-		// Load manipulation script
-		try {
-			engine.eval(this.script);
-		} catch (ScriptException e) {
-			throw new RuntimeException("Unable to load manipulation script", e);
-		}
-		
-		// Determine component index of the needed parameters
-		// If the component index of the parameter cannot be determined an IllegalArgumentException is thrown
-		parameterIndex = new Integer[parameter.length];
-		for(int i=0;i<parameter.length; i++){
-			String p = parameter[i];
-			p = p.trim();
-			boolean found = false;
-			
-			for(JythonParameterMapping jpm: this.mapping){
-				if(jpm.getVariable().equals(p)){
-					if(jpm instanceof JythonParameterMappingID){
-						JythonParameterMappingID pm = (JythonParameterMappingID)jpm;
-						// Mapping for parameter found, determine index of the corresponding component
-						parameterIndex[i] = metadata.getIndex(pm.getRefid());
-					}
-					else if (jpm instanceof JythonParameterMappingChannel){
-						JythonParameterMappingChannel pm = (JythonParameterMappingChannel)jpm;
-						parameterIndex[i] = null;
-						
-						Channel<?> cb;
-						try {
-							cb = cservice.createChannel(new ChannelDescriptor<>(pm.getType(), pm.getChannel(), true));
-						} catch (ChannelException | TimeoutException e) {
-							throw new IllegalArgumentException("Unable to establish channel: "+pm.getChannel(), e);
-						} catch (InterruptedException e) {
-							throw new RuntimeException("Unable to establish channel: "+pm.getChannel(), e);
-						}
-						
-						engine.put(pm.getVariable(), cb);
-					}
-					else if (jpm instanceof JythonParameterMappingGlobalVariable){
-						JythonParameterMappingGlobalVariable pm = (JythonParameterMappingGlobalVariable)jpm;
-						parameterIndex[i] = null;
-						
-						engine.put(pm.getVariable(), pm.getGlobalVariable());
-					}
-					found=true;
-					break;
-				}
-			}
-			// If there is no mapping nothing can be found
-			// If there are mappings everything need to be found
-			if(!found){
-				throw new IllegalArgumentException("No mapping compontent found for parameter "+p);
-			}
-		}
-		
-		StringBuffer buffer = new StringBuffer();
-		buffer.append(entryFunction);
-		buffer.append("(");
-		
-		for(String p: parameter){
-			buffer.append(p);
-			buffer.append(",");
-		}
-		
-		buffer.setCharAt(buffer.length()-1, ')');
-		
-		jythonCall = buffer.toString();
-		
-	}
-	
-	@Override
-	public Object execute(DataMessage message){
-		
-		// Manipulate data
-		for(int i=0;i<parameterIndex.length;i++){
-			if(parameterIndex[i] != null){
-				engine.put(parameter[i], message.getData().get(parameterIndex[i]));
-			}
-		}
-		
-		try {
-			if(returnArray){
-				return((double[]) engine.eval(jythonCall));
-			}
-			else{
-				// Due to the typeless nature of Python an Integer of Float/Double might be returned from the 
-				// Python code (e.g. depending on the factors in a calculation)
-				// Always return the return value to a double. If this cannot be done return NaN
-				Object r = engine.eval(jythonCall);
-				if(r instanceof Double){
-					return((Double) r);
-				}
-				else if( r instanceof Integer){
-					return(((Integer)r).doubleValue());
-				}
-				else{
-					return Double.NaN;
-				}
-			}
-		} catch (ScriptException e) {
-//			throw new RuntimeException("Data manipulaton [id: "+id+"] failed while executing the manipulation script",e);
-			logger.log(Level.WARNING, "Data manipulaton [id: "+id+"] failed while executing the manipulation script");
-			return Double.NaN;
-		}
-	}
-}

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

@@ -1,49 +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.manipulator;
-
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.DataMessageMetadata;
-
-/**
- * @author ebner
- *
- */
-public interface Manipulation {
-
-	/**
-	 * Get the id of the manipulation
-	 * @return	id of manipulation
-	 */
-	public String getId();
-	
-	/**
-	 * Initialize the manipulation
-	 * @param metadata	Metadata of the incomming data message
-	 */
-	public void initialize(DataMessageMetadata metadata);
-	
-	/**
-	 * Execute the manipulation on the passed data message
-	 * @param message Message to manipulate
-	 * @return	Result of the manipulation
-	 */
-	public Object execute(DataMessage message);
-}

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

@@ -1,123 +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.manipulator;
-
-import java.util.List;
-import java.util.concurrent.LinkedBlockingQueue;
-
-import ch.psi.fda.core.messages.ComponentMetadata;
-import ch.psi.fda.core.messages.DataMessage;
-import ch.psi.fda.core.messages.DataMessageMetadata;
-import ch.psi.fda.core.messages.DataQueue;
-import ch.psi.fda.core.messages.EndOfStreamMessage;
-import ch.psi.fda.core.messages.Message;
-
-/**
- * @author ebner
- *
- */
-public class Manipulator implements Runnable{
-	
-	/**
-	 * Outgoing data queue
-	 */
-	private final DataQueue outQueue;
-	
-	/**
-	 * Incomming data queue
-	 */
-	private final DataQueue queue;
-	
-	/**
-	 * List of manipulations
-	 */
-	private final List<Manipulation> manipulations;
-	
-	/**
-	 * Constructor
-	 * @param queue
-	 * @param manipulations
-	 */
-	// TODO need to support multiple (a list of) manipulation(s)
-	public Manipulator(DataQueue queue, List<Manipulation> manipulations){
-
-		this.manipulations = manipulations;
-		
-		// Create outgoing data metadata
-		DataMessageMetadata dmetadata = queue.getDataMessageMetadata().clone();
-		
-		// Initialize manipulations and create outgoing metadata
-		for(Manipulation manipulation: this.manipulations){
-			// Initialize manipulation
-//			manipulation.initialize(queue.getDataMessageMetadata());
-			manipulation.initialize(dmetadata);
-			
-			// Add manipulation id to metadata
-			dmetadata.getComponents().add(new ComponentMetadata(manipulation.getId(),0)); // Calculated component always belongs to lowes dimension
-		}
-		
-		this.queue = queue;
-		this.outQueue = new DataQueue(new LinkedBlockingQueue<Message>(1000) , dmetadata ); // Create bounded queue to prevent running out of memory ...
-	}
-
-	/**
-	 * @return the outQueue
-	 */
-	public DataQueue getOutQueue() {
-		return outQueue;
-	}
-
-	/* (non-Javadoc)
-	 * @see java.lang.Runnable#run()
-	 */
-	@Override
-	public void run() {
-		try{
-			
-			// Dispatch Messages
-			Message message = queue.getQueue().take();
-			while(!(message instanceof EndOfStreamMessage)){
-				if(message instanceof DataMessage){
-					DataMessage dm = (DataMessage) message;
-					
-					for(Manipulation manipulation: manipulations){
-						dm.getData().add(manipulation.execute(dm));
-					}
-				}
-				
-				// Put message to outgoing queue ...
-				outQueue.getQueue().put(message);
-				
-				// Read next message
-				message = queue.getQueue().take();
-			}
-			
-			// Write end of stream message
-			outQueue.getQueue().put(message);
-
-			
-		} catch (InterruptedException e) {
-			// TODO Stop loop and exit logic instead of throwing an Exception
-			throw new RuntimeException("Data manipulator was interrupted while writing data to file",e);
-		}
-	}
-	
-	
-}

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

@@ -1,82 +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;
-
-/**
- * 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).
- * 
- * @author ebner
- *
- */
-public class ComponentMetadata {
-	/**
-	 * Global id of the component
-	 */
-	private final String id;
-	
-	/**
-	 * Dimension of the component (optional)
-	 */
-	private final int dimension;
-	
-	/**
-	 * Default constructor - Create component metadata
-	 * @param id	Global id of the component
-	 */
-	public ComponentMetadata(String id){
-		this.id = id;
-		this.dimension = 0;
-	}
-	
-	/**
-	 * Constructor that initializes id and the dimension number
-	 * @param id
-	 * @param dimension
-	 */
-	public ComponentMetadata(String id, int dimension){
-		this.id = id;
-		this.dimension = dimension;
-	}
-
-	/**
-	 * @return the dimension
-	 */
-	public int getDimension() {
-		return dimension;
-	}
-
-	/**
-	 * @return the id
-	 */
-	public String getId() {
-		return id;
-	}
-	
-	/* (non-Javadoc)
-	 * @see java.lang.Object#toString()
-	 */
-	@Override
-	public String toString() {
-		return "Component Metadata[id="+id+" dimension="+dimension+"]";
-	}
-}

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.)
- * @author ebner
- *
- */
-public abstract class ControlMessage extends Message {
-}

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

@@ -1,83 +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
- * @author ebner
- *
- */
-public class DataMessage extends Message {
-	
-	/**
-	 * Data payload of the message
-	 */
-	private List<Object> data;
-	
-	/**
-	 * Constructor - Create message object with data payload
-	 */
-	public DataMessage(){
-		this.data = new ArrayList<Object>();
-	}
-	
-	/**
-	 * Get data object of the message
-	 * @return Data object of the message
-	 */
-	public List<Object> getData(){
-		return(data);
-	}
-	
-	
-	/* (non-Javadoc)
-	 * @see java.lang.Object#toString()
-	 */
-	@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/DataMessageMetadata.java

@@ -1,81 +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;
-
-/**
- * Structure to hold the metadata of a component of a message.
- * @author ebner
- *
- */
-public class DataMessageMetadata {
-
-	/**
-	 * List of the metadata of the message components
-	 */
-	private List<ComponentMetadata> components;
-	
-	/**
-	 * Default constructor
-	 */
-	public DataMessageMetadata(){
-		components = new ArrayList<ComponentMetadata>();
-	}
-
-	/**
-	 * @return the list of component metadata of a message described by this object.
-	 */
-	public List<ComponentMetadata> getComponents() {
-		return components;
-	}
-	
-	/**
-	 * Get the index of the component with the specified Id
-	 * @param componentId	Id of the component to look for
-	 * @return Index of the component
-	 * @throws IllegalArgumentException	There is no component with the specified Id
-	 */
-	public int getIndex(String componentId) throws IllegalArgumentException {
-		for(int i=0;i<components.size();i++){
-			ComponentMetadata c =components.get(i);
-			if(c.getId().equals(componentId)){
-				return(i);
-			}
-		}
-		throw new IllegalArgumentException("There is no message component with Id "+ componentId);
-	}
-	
-	/**
-	 * Clone data structure
-	 * @return Cloned data structure
-	 */
-	public DataMessageMetadata clone(){
-		DataMessageMetadata metadata = new DataMessageMetadata();
-		
-		for(int i=0;i<components.size();i++){
-			ComponentMetadata c =components.get(i);
-			metadata.getComponents().add(new ComponentMetadata(c.getId(), c.getDimension()));
-		}
-		
-		return(metadata);
-	}
-}

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

@@ -1,66 +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.concurrent.BlockingQueue;
-
-
-/**
- * Container holding for holding a queue and the metadata of the 
- * data messages of that queue.
- * @author ebner
- *
- */
-public class DataQueue {
-	
-	/**
-	 * Queue serving the messages
-	 */
-	private final BlockingQueue<Message> queue;
-	/**
-	 * Metadata of the data messages of the queue
-	 */
-	private final DataMessageMetadata dataMessageMetadata;
-	
-	/**
-	 * Constructor
-	 * @param queue		Data queue
-	 * @param dataMessageMetadata	Metadata of the data messages of the queue
-	 */
-	public DataQueue(BlockingQueue<Message> queue, DataMessageMetadata dataMessageMetadata){
-		this.queue = queue;
-		this.dataMessageMetadata = dataMessageMetadata;
-	}
-
-	/**
-	 * @return the queue
-	 */
-	public BlockingQueue<Message> getQueue() {
-		return queue;
-	}
-
-	/**
-	 * @return the metadata
-	 */
-	public DataMessageMetadata getDataMessageMetadata() {
-		return dataMessageMetadata;
-	}
-	
-}

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

@@ -1,59 +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
- * @author ebner
- *
- */
-public class EndOfStreamMessage extends ControlMessage{
-	
-	
-	/**
-	 * 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;
-	}
-	
-	/**
-	 * @return the iflag
-	 */
-	public boolean isIflag(){
-		return(iflag);
-	}
-	
-	/* (non-Javadoc)
-	 * @see java.lang.Object#toString()
-	 */
-	@Override
-	public String toString() {
-		return "Message[ c message: end of stream ]";
-	}
-}