creating ZenBlueCommander

pom.xml

@@ -8,7 +8,7 @@
 		<version>5.0</version> <relativePath /> </parent> -->
 	<groupId>embl.almf</groupId>
 	<artifactId>AutoMicTools_</artifactId>
-	<version>1.1.22-SNAPSHOT</version>
+	<version>1.1.23-SNAPSHOT</version>
 
 	<name>plugins/AutoMicTools_.jar</name>
 	<description>Collection of tools for automated (feedback) microscopy data acquisition and analysis</description>

src/main/java/automic/online/microscope/ZeissLSM800.java

@@ -4,7 +4,7 @@ import java.io.File;
 import java.io.Writer;
 import java.io.FileWriter;
 
-import com.eclipsesource.json.JsonArray;
+//import com.eclipsesource.json.JsonArray;
 import com.eclipsesource.json.JsonObject;
 import java.awt.Rectangle;
 
@@ -14,7 +14,8 @@ import ij.gui.OvalRoi;
 import ij.gui.Roi;
 import java.awt.Polygon;
 
-public abstract class ZeissLSM800 {
+@Deprecated
+public abstract class ZeissLSM800{
 	public static String FEEDBACK_POSTFIX="_feedback.json";
 	
 	public static final String JOB_KEY="Job";
@@ -64,6 +65,14 @@ public abstract class ZeissLSM800 {
 		if (_bleachRois!=null) {
 			for (Roi thisRoi:_bleachRois){
 				String roiKey=thisRoi.getName();
+				if(roiKey==null) {
+					int counter=0;
+					do {
+						counter++;
+						roiKey=String.format("R%04d", counter);
+					} while (jrois.names().contains(roiKey));
+				}
+				
 				JsonObject currentJRoi=new JsonObject();
 				int roiType=thisRoi.getType();
 				switch (roiType){

src/main/java/automic/online/microscope/ZenBlueCommander.java

+package automic.online.microscope;
+
+import java.io.File;
+import java.io.Writer;
+
+import java.io.FileWriter;
+
+//import com.eclipsesource.json.JsonArray;
+import com.eclipsesource.json.JsonObject;
+import java.awt.Rectangle;
+
+import automic.geom.Point3D;
+import automic.parameters.ParameterCollection;
+import automic.utils.FileUtils;
+import ij.gui.Roi;
+import java.awt.Polygon;
+
+public class ZenBlueCommander implements MicroscopeCommanderInterface{
+	public static String FEEDBACK_POSTFIX="_feedback.json";
+	
+	public static final String JOB_KEY="Job";
+	public static final String X_KEY="X";
+	public static final String Y_KEY="Y";
+	public static final String Z_KEY="Z";
+	public static final String WIDTH_KEY="WIDTH";
+	public static final String HEIGHT_KEY="HEIGHT";
+	
+	
+	public static final String XBLEACH_KEY="X_BLEACH";
+	public static final String YBLEACH_KEY="Y_BLEACH";
+	public static final String RADIUS_KEY="RADIUS";
+	
+	public static final String POSITIONS_KEY="POSITIONS";
+	public static final String ROIS_KEY="ROIS";
+	
+	public static final String ROITYPE_KEY="TYPE";
+	public static final String ROIPOSITION_KEY="";
+	
+	public static final String NO_JOB_NAME="None";
+	
+
+	@Override
+	public void parseSettings(ParameterCollection _microscopeSettings) {
+		
+	}
+	
+	@Override
+	public void connect() {
+		
+	}
+	
+	@Override
+	public void skipJobsInCurrentPosition() {
+		throw new RuntimeException("ZenBlueCommander.skipJobsInCurrentPosition(): method is not yet implamented");
+	}
+	
+	@Override
+	public void stopCommander() {}
+	
+	
+	@Override
+	public void submitJobPixels(File _sourceImageFile, String _jobNameToPerform, Point3D[] _positions,
+			Roi[] _bleachRois)throws Exception {
+
+		File decisionFile=getDecisionFile(_sourceImageFile);
+		JsonObject jObject=new JsonObject();
+
+		JsonObject jpositions=new JsonObject();
+		JsonObject jrois=new JsonObject();
+
+		
+		
+		if (_positions!=null) {
+			int nPositions=_positions.length;
+			for (int iPosition=0;iPosition<nPositions;iPosition++) {
+				String positionKey=String.format("Pos_%03d", iPosition+1);
+				JsonObject currentPosition=new JsonObject();
+				addValueIfNotNull(_positions[iPosition].getX(), X_KEY, currentPosition);
+				addValueIfNotNull(_positions[iPosition].getY(), Y_KEY, currentPosition);
+				addValueIfNotNull(_positions[iPosition].getZ(), Z_KEY, currentPosition);
+				jpositions.add(positionKey, currentPosition);
+			}
+		}
+
+		if (_bleachRois!=null) {
+			for (Roi thisRoi:_bleachRois){
+				String roiKey=thisRoi.getName();
+				JsonObject currentJRoi=new JsonObject();
+				int roiType=thisRoi.getType();
+				switch (roiType){
+					case Roi.OVAL:
+						
+						currentJRoi.add(ROITYPE_KEY, "OVAL");
+						Rectangle rect=thisRoi.getBounds();
+						currentJRoi.add(X_KEY, rect.x);
+						currentJRoi.add(Y_KEY, rect.y);
+						currentJRoi.add(WIDTH_KEY, rect.width);
+						currentJRoi.add(HEIGHT_KEY, rect.height);
+						
+						break;
+					case Roi.RECTANGLE:
+						currentJRoi.add(ROITYPE_KEY, "RECTANGLE");
+						rect=thisRoi.getBounds();
+						currentJRoi.add(X_KEY, rect.x);
+						currentJRoi.add(Y_KEY, rect.y);
+						currentJRoi.add(WIDTH_KEY, rect.width);
+						currentJRoi.add(HEIGHT_KEY, rect.height);
+
+						break;
+					case Roi.POLYGON: case Roi.TRACED_ROI:
+						currentJRoi.add(ROITYPE_KEY, "POLYGON");
+						Polygon poly=thisRoi.getPolygon();
+						JsonObject polygonJPositions=new JsonObject();
+						for (int iPosition=0;iPosition<poly.npoints;iPosition++) {
+							JsonObject thisJPosition=new JsonObject();
+							thisJPosition.add(X_KEY, poly.xpoints[iPosition]);
+							thisJPosition.add(Y_KEY, poly.ypoints[iPosition]);
+							
+							polygonJPositions.add(String.format("P_%03d", iPosition), thisJPosition);
+						}
+						
+						currentJRoi.add(POSITIONS_KEY, polygonJPositions);
+						break;
+					default:
+						throw new RuntimeException();
+				}
+					
+				
+				jrois.add(roiKey,currentJRoi);
+			}
+		}
+
+
+		jObject.add(JOB_KEY, _jobNameToPerform);
+		jObject.add(POSITIONS_KEY, jpositions);
+		jObject.add(ROIS_KEY, jrois);
+	
+	
+		writeJsonToFile(jObject, decisionFile);
+	}
+
+	@Override
+	public void submitJobPixels(File _sourceImageFile, String _jobNameToPerform, Point3D _position) 
+	throws Exception{
+		submitJobPixels(_sourceImageFile, _jobNameToPerform, new Point3D[] {_position},null);
+	}
+
+	
+	@Override
+	public void submitJobPixels(File _sourceImageFile, String _jobNameToPerform, Point3D[] _positions) 
+	throws Exception{
+		submitJobPixels(_sourceImageFile, _jobNameToPerform, _positions, null);
+	}
+	
+
+	
+	private static File getDecisionFile(File _sourceImageFile){
+		String newFileName=FileUtils.cutExtension(_sourceImageFile.getName())+FEEDBACK_POSTFIX;
+		return new File(_sourceImageFile.getParentFile(),newFileName);
+	}
+	
+	private static void writeJsonToFile(JsonObject _jObject,File _outputFile)throws Exception {
+		Writer jSonWriter=new FileWriter(_outputFile);
+		_jObject.writeTo(jSonWriter);
+		jSonWriter.close();
+	}
+	
+	private static void addValueIfNotNull(Double _value,String _key, JsonObject _jObject) {
+		if (_value==null)
+			return;
+		_jObject.add(_key, _value);
+	}
+	
+	private static Double getValueFromNonNullArray(double[] _array, int _index) {
+		if (_array==null)
+			return null;
+		return _array[_index];
+	}
+}