New version

added datafile and filename to script actions

ch.psi.fda/.classpath

@@ -28,6 +28,10 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
 	<classpathentry kind="output" path="target/classes"/>
 </classpath>

ch.psi.fda/pom.xml

@@ -3,7 +3,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>ch.psi</groupId>
 	<artifactId>fda</artifactId>
-	<version>1.1.38</version>
+	<version>1.1.40</version>
 
 	<dependencies>
 		<dependency>

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

@@ -510,6 +510,12 @@ public class Acquisition {
 				}
 				
 				JythonManipulation manipulation = new JythonManipulation(sm.getId(), sm.getScript(), mapping, sm.isReturnArray());
+				
+				if(configuration.getData()!=null){ // Safety
+					manipulation.setVariable("FILENAME", configuration.getData().getFileName());
+					manipulation.setVariable("DATAFILE", datafile.getAbsoluteFile());
+				}
+				
 				this.manipulations.add(manipulation);
 			}
 		}
@@ -621,7 +627,9 @@ public class Acquisition {
 			}
 			else if(a instanceof ShellAction){
 				ShellAction sa = (ShellAction) a;
-				ch.psi.fda.core.actions.ShellAction action = new ch.psi.fda.core.actions.ShellAction(sa.getCommand());
+				String com = sa.getCommand().replaceAll("\\$\\{DATAFILE\\}", datafile.getAbsolutePath());
+				com = com.replaceAll("\\$\\{FILENAME\\}", datafile.getName().replaceAll("\\.\\w*$", ""));
+				ch.psi.fda.core.actions.ShellAction action = new ch.psi.fda.core.actions.ShellAction(com);
 				action.setCheckExitValue(sa.isCheckExitValue());
 				action.setExitValue(sa.getExitValue());
 				alist.add(action);
@@ -629,6 +637,9 @@ public class Acquisition {
 			else if(a instanceof ScriptAction){
 				
 				ScriptAction sa = (ScriptAction) a;
+				
+				// TODO set global variables DATAFILE and FILENAME
+				
 				// TODO create Jython Action
 				List<JythonParameterMappingChannel> mapping = new ArrayList<JythonParameterMappingChannel>();
 				for(ChannelParameterMapping ma: sa.getMapping()){
@@ -645,7 +656,11 @@ public class Acquisition {
 						logger.warning("Channel type ["+ma.getType()+"] is not supported for mapping");
 					}
 				}
-				alist.add(new ch.psi.fda.core.actions.JythonAction(sa.getScript(), mapping));
+				
+				ch.psi.fda.core.actions.JythonAction ja = new ch.psi.fda.core.actions.JythonAction(sa.getScript(), mapping);
+				ja.setVariable("FILENAME", datafile.getName().replaceAll("\\.\\w*$", ""));
+				ja.setVariable("DATAFILE", datafile.getAbsoluteFile());
+				alist.add(ja);
 			}
 		}
 		return(alist);

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

@@ -21,7 +21,9 @@ package ch.psi.fda.core.actions;
 
 import gov.aps.jca.CAException;
 
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 import java.util.logging.Logger;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
@@ -60,6 +62,8 @@ public class JythonAction implements Action {
 	 * Jython entry call
 	 */
 	private String jythonCall;
+	
+	private Map<String,Object> gvariables = new HashMap<String,Object>();
 		
 	public JythonAction(String script, List<JythonParameterMappingChannel> mapping){
 		
@@ -76,7 +80,12 @@ public class JythonAction implements Action {
 		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(" *, *");
+			if(matcher.group(1).matches(" *")){
+				functionParameters = new String[0];
+			}
+			else{
+				functionParameters = matcher.group(1).split(" *, *");
+			}
 		}
 		else{
 			throw new IllegalArgumentException("Cannot determine entry function: "+entryFunctionPattern);
@@ -112,7 +121,7 @@ public class JythonAction implements Action {
 		
 		StringBuffer buffer = new StringBuffer();
 		buffer.append(entryFunction);
-		buffer.append("(");
+		buffer.append("( "); // Need to have trailing space as otherwise there will be a problem if no paramters are specified
 		for(JythonParameterMappingChannel b: mapping){
 			// Create channel
 			
@@ -142,6 +151,15 @@ public class JythonAction implements Action {
 	 */
 	@Override
 	public void execute() {
+		
+		// Set global variables - WORKAROUND gvariables
+		// This block is not in initialization as we want to assure that all invocations
+		// of this manipulation will get the same value (i.e. to prevent inconsistent behaviour
+		// if variable was changed during an execution of the manipulation)
+		for(String k: gvariables.keySet()){
+			engine.put(k, gvariables.get(k));
+		}
+		
 		try {
 			engine.eval(jythonCall);
 		} catch (ScriptException e) {
@@ -166,4 +184,13 @@ public class JythonAction implements Action {
 		// Nothing to be done
 	}
 
+	/**
+	 * Workaround to put variables into the jython engine.
+	 * @param name
+	 * @param value
+	 */
+	public void setVariable(String name, Object value){
+		gvariables.put(name, value);
+	}
+	
 }

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

@@ -21,7 +21,9 @@ package ch.psi.fda.core.manipulator;
 
 import gov.aps.jca.CAException;
 
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 import java.util.logging.Level;
 import java.util.logging.Logger;
 import java.util.regex.Matcher;
@@ -102,6 +104,10 @@ public class JythonManipulation implements Manipulation{
 	 */
 	private String jythonCall;
 	
+	
+	private Map<String,Object> gvariables = new HashMap<String,Object>();
+	
+	
 	public JythonManipulation(String id, String script, List<JythonParameterMapping> mapping){
 		this(id, script, mapping, false);
 	}
@@ -232,12 +238,19 @@ public class JythonManipulation implements Manipulation{
 		buffer.setCharAt(buffer.length()-1, ')');
 		
 		jythonCall = buffer.toString();
-		
 	}
 	
 	@Override
 	public Object execute(DataMessage message){
 		
+		// Set global variables - WORKAROUND gvariables
+		// This block is not in initialization as we want to assure that all invocations
+		// of this manipulation will get the same value (i.e. to prevent inconsistent behaviour
+		// if variable was changed during an execution of the manipulation)
+		for(String k: gvariables.keySet()){
+			engine.put(k, gvariables.get(k));
+		}
+		
 		// Manipulate data
 		for(int i=0;i<parameterIndex.length;i++){
 			if(parameterIndex[i] != null){
@@ -261,7 +274,8 @@ public class JythonManipulation implements Manipulation{
 					return(((Integer)r).doubleValue());
 				}
 				else{
-					return Double.NaN;
+//					return Double.NaN;
+					return r;
 				}
 			}
 		} catch (ScriptException e) {
@@ -270,4 +284,13 @@ public class JythonManipulation implements Manipulation{
 			return Double.NaN;
 		}
 	}
+	
+	/**
+	 * Workaround to put variables into the jython engine.
+	 * @param name
+	 * @param value
+	 */
+	public void setVariable(String name, Object value){
+		gvariables.put(name, value);
+	}
 }

ch.psi.fda/src/main/java/ch/psi/fda/model/ModelManager.java

@@ -47,6 +47,7 @@ import org.xml.sax.SAXException;
 import org.xml.sax.SAXParseException;
 
 import ch.psi.fda.model.v1.Configuration;
+import ch.psi.fda.model.v1.Data;
 
 /**
  * Manage the serialization and deserialization of the model
@@ -111,6 +112,15 @@ public class ModelManager {
 		
 		try{
 			Configuration model = (Configuration) u.unmarshal(bsource, Configuration.class).getValue();
+
+			// Ensure that the filename inside the xml file is always the file name
+			Data d = model.getData();
+			if(d==null){
+				d = new Data();
+				model.setData(d);
+			}
+			d.setFileName(file.getName().replaceAll("\\.xml$", ""));
+			
 			return (model);
 		}
 		catch(UnmarshalException e){
@@ -142,6 +152,15 @@ public class ModelManager {
 		
 		try{
 			Configuration model = (Configuration) u.unmarshal(new StreamSource(file), Configuration.class).getValue();
+			
+			// Ensure that the filename inside the xml file is always the file name
+			Data d = model.getData();
+			if(d==null){
+				d = new Data();
+				model.setData(d);
+			}
+			d.setFileName(file.getName().replaceAll("\\.xml$", ""));
+			
 			return (model);
 		}
 		catch(UnmarshalException e){
@@ -173,6 +192,14 @@ public class ModelManager {
 		Schema schema = sf.newSchema(new Source[]{s}); // Use schema reference provided in XML
 		m.setSchema(schema);
 		
+		// Set scan name equal to file name
+		Data d = model.getData();
+		if(d==null){
+			d = new Data();
+			model.setData(d);
+		}
+		d.setFileName(file.getName().replaceAll("\\.xml$", ""));
+		
 		m.marshal( new JAXBElement<Configuration>(qname, Configuration.class, model ), file);
 	}
 }

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

@@ -141,7 +141,22 @@ public class Visualizer {
 	//						XYSeriesP series = ((LinePlot) xyfilter.getPlot()).getData().getSeries(xyfilter.getCount()); // TODO Does not work with multiple series filter per plot !!!!
 							XYSeriesP series = xyfilter.getActualSeries(); // TODO Does not work with multiple series filter per plot !!!!
 	//						series.add((Double) m.getData().get(xyfilter.getIndexX()), (Double) m.getData().get(xyfilter.getIndexY()));
-							series.add((Double) m.getData().get(xyfilter.getIndexX()), (Double) m.getData().get(xyfilter.getIndexY()), updateAtStreamElement);
+							
+							
+							// There might be other values than double in the data, therefore we have to check for it
+							Object dX = m.getData().get(xyfilter.getIndexX());
+							Object dY = m.getData().get(xyfilter.getIndexY());
+							Double dataX = Double.NaN;
+							Double dataY = Double.NaN;
+							if(dX instanceof Double){
+								dataX = (Double) dX;
+							}
+							if(dY instanceof Double){
+								dataY = (Double) dY;
+							}
+							
+							// Add Data to the series
+							series.add(dataX , dataY, updateAtStreamElement);
 						}
 						if(filter instanceof XYSeriesArrayDataFilter){
 							final XYSeriesArrayDataFilter xyfilter = (XYSeriesArrayDataFilter) filter;

ch.psi.fda/src/test/java/ch/psi/fda/model/ModelManagerTest.java

@@ -75,6 +75,8 @@ public class ModelManagerTest {
 		URL url = this.getClass().getClassLoader().getResource("home/scans/templates/scan1d.xml");
 		Configuration c = ModelManager.unmarshall(new File(new URI(url.toString())));
 		logger.info(""+c.getData().getFormat());
+		
+		logger.info("FILENAME: "+c.getData().getFileName());
 	}
 
 	/**
@@ -106,7 +108,7 @@ public class ModelManagerTest {
 		Scan s = new Scan();
 		c.setScan(s);
 		
-		ModelManager.marshall(c, new File(tmpDirectory+"/scan.xml"));
+		ModelManager.marshall(c, new File(tmpDirectory+"/scan1234.xml"));
 		
 	}
 

ch.psi.fda/src/test/resources/home/scans/templates/scan1d-shell.xml

@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<configuration numberOfExecution="0" xmlns="http://www.psi.ch/~ebner/models/scan/1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.psi.ch/~ebner/models/scan/1.0 ../../src/model-v1.xsd">
+<!-- 
+1D Scan reading out scalar channels and the timestamp for each point
+ -->
+  <data format="txt"/>
+  <scan id="">
+    <preAction xsi:type="ShellAction" command="/bin/echo hello ${DATAFILE} ${FILENAME}"/>
+    <preAction xsi:type="ScriptAction">
+  		<script>
+def process( ):
+    print "filename __ %s" % FILENAME
+    print "data __ %s" % DATAFILE
+  		</script>
+  	</preAction>
+  </scan>
+</configuration>

ch.psi.fda/src/test/resources/home/scans/templates/scan1d_manipulationNoDouble.xml

@@ -0,0 +1,44 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<configuration numberOfExecution="0" xmlns="http://www.psi.ch/~ebner/models/scan/1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.psi.ch/~ebner/models/scan/1.0 ../../src/model-v1.xsd">
+<!-- 
+1D Scan reading out scalar channels and the timestamp for each point
+ -->
+  <data format="txt"/>
+  <scan id="">
+    <dimension zigzag="true">
+    	<positioner id="id0" name="MTEST-HW3:MOT1" settlingTime="0.1" xsi:type="LinearPositioner">
+    		<start>0.0</start>
+        	<end>8.0</end>
+        	<stepSize>0.5</stepSize>
+    	</positioner>
+    	<detector id="idD0" xsi:type="ScalarDetector" name="MTEST-HW3:MOT1.RRBV"/>
+    	<detector id="idD1" xsi:type="ScalarDetector" name="MTEST-HW3:MOT1.RBV"/>
+    	<detector xsi:type="Timestamp" id="timestamp"/>
+    </dimension>
+    
+    <manipulation id="man1" xsi:type="ScriptManipulation">
+		<mapping xsi:type="IDParameterMapping" variable="a" refid="idD1"/>
+    	<script>
+def process(a):
+    return [1,a]
+    	</script>
+    </manipulation>
+    <manipulation id="man2" xsi:type="ScriptManipulation">
+		<mapping xsi:type="IDParameterMapping" variable="a" refid="man1"/>
+    	<script>
+def process(a):
+    print a[1]
+    print FILENAME
+    return 1.0
+    	</script>
+    </manipulation>
+  </scan>
+
+
+
+	<visualization title="Line Plot One" xsi:type="LinePlot" x="id0" y="idD0"/>
+	<visualization title="Line Plot Two" xsi:type="LinePlot" x="id0" y="idD1"/>
+	<visualization title="Line Plot Two" xsi:type="LinePlot" x="id0" y="man1"/>
+	<visualization title="Line Plot Two" xsi:type="LinePlot" x="id0" y="man2"/>
+	<visualization xsi:type="LinePlot" x="id0" y="timestamp" title="Timestamp" />
+</configuration>