delay time for opening is an additional parameter

src/main/java/feedback/fly/embryo/jobdistributors/JobDistributor_AutoSelectionMultiple_AFocus_Rotation.java

@@ -95,6 +95,7 @@ public class JobDistributor_AutoSelectionMultiple_AFocus_Rotation extends JobDis
 		
 		outTbl.addValueColumn("Zoom.X", "NUM");
 		outTbl.addValueColumn("Zoom.Y", "NUM");
+		outTbl.addValueColumn("Rotation", "NUM");
 		outTbl.addValueColumn("Focus.Z", "NUM");
 
 		
@@ -155,9 +156,9 @@ public class JobDistributor_AutoSelectionMultiple_AFocus_Rotation extends JobDis
 	
 	@Override
 	protected void setDebugConfiguration(){
-		final String searchPath="C:/tempDat/AutoFRAP_test";
+		final String searchPath="C:/tempDat/AutoMic_test";
 		this.setGeneralOptions(searchPath, true, false);
-		this.fileExtension="czi";
+		this.fileExtension="lsm";
 		
 		//manualTrackParameterCollectionSelect=new Job_SelectMultipleEmbryosAutoInit().createJobParameters();
 		//manualTrackParameterCollectionSelect.setUndefinedValuesFromDefaults();

src/main/java/feedback/fly/embryo/jobs/Job_SelectMultipleEmbryosAuto.java

@@ -44,6 +44,7 @@ public class Job_SelectMultipleEmbryosAuto  extends Job_Default{
 	
 
 	public static final String KEY_EMBRYO_MAX_COUNT="Maximal number of embryos from well";
+	public static final String KEY_WAIT_IMAGE_OPENING="Wait for image opening (milliseconds)";
 
 	
 	//private static final Roi nullRoi=null;
@@ -74,7 +75,8 @@ public class Job_SelectMultipleEmbryosAuto  extends Job_Default{
 	private double embryoMaxAR=10.0;
 	
 
-	private int embryoMaxCount;
+	private int embryoMaxCount=5;
+	private int imageOpeningTimeDelay=3000;
 	
 	
 	//private int initialLocationY;
@@ -96,7 +98,7 @@ public class Job_SelectMultipleEmbryosAuto  extends Job_Default{
 		Exper_nm=Exper_nm.substring(0, Exper_nm.indexOf(fileTag));
 		this.setSharedValue("Experiment Name", Exper_nm);
 		
-		TimeUnit.MILLISECONDS.sleep(2000);		
+		TimeUnit.MILLISECONDS.sleep(imageOpeningTimeDelay);		
 		//img=ImageOpenerWithBioformats.openImage(newImgFile);
 		img=openSelectedSlices(newImgFile);
 	}
@@ -291,9 +293,8 @@ public class Job_SelectMultipleEmbryosAuto  extends Job_Default{
 		jobCollection.addParameter(KEY_EMBRYO_MAX_AR, null, embryoMaxAR, ParameterType.DOUBLE_PARAMETER);
 
 		
-		
 		jobCollection.addParameter(KEY_EMBRYO_MAX_COUNT,null, 5, ParameterType.INT_PARAMETER);
-
+		jobCollection.addParameter(KEY_WAIT_IMAGE_OPENING,null, imageOpeningTimeDelay, ParameterType.INT_PARAMETER);
 		
 		return jobCollection;
 	}
@@ -316,9 +317,8 @@ public class Job_SelectMultipleEmbryosAuto  extends Job_Default{
 		this.embryoMaxAR=(Double)_jobParameterCollection.getParameterValue(KEY_EMBRYO_MAX_AR);
 		
 		
-		
-		
 		this.embryoMaxCount=(Integer)_jobParameterCollection.getParameterValue(KEY_EMBRYO_MAX_COUNT);
+		this.imageOpeningTimeDelay=(Integer)_jobParameterCollection.getParameterValue(KEY_WAIT_IMAGE_OPENING);
 	}
 	
 	@Override

src/main/java/feedback/fly/embryo/jobs/Job_SelectMultipleEmbryosAutoInit.java

 package feedback.fly.embryo.jobs;
 
-import java.util.concurrent.TimeUnit;
-
 import ij.ImageJ;
 
 public class Job_SelectMultipleEmbryosAutoInit  extends Job_SelectMultipleEmbryosAuto{
@@ -11,15 +9,7 @@ public class Job_SelectMultipleEmbryosAutoInit  extends Job_SelectMultipleEmbryo
 	protected void preProcessOnline()throws Exception{
 		super.clearSharedData();
 		currentTable.cleanRecord(curDInd);
-		currentTable.setFileAbsolutePath(newImgFile, curDInd, imgColumnNm, "IMG");
-		
-		String Exper_nm=newImgFile.getName();
-		Exper_nm=Exper_nm.substring(0, Exper_nm.indexOf(fileTag));
-		this.setSharedValue("Experiment Name", Exper_nm);
-		
-		TimeUnit.MILLISECONDS.sleep(2000);		
-		//img=ImageOpenerWithBioformats.openImage(newImgFile);
-		img=openSelectedSlices(newImgFile);
+		super.preProcessOnline();
 	}
 	
 	/**

src/main/java/feedback/fly/embryo/jobs/Job_SelectMultipleEmbryosAutoRotation.java

@@ -45,6 +45,7 @@ public class Job_SelectMultipleEmbryosAutoRotation  extends Job_Default{
 	
 
 	public static final String KEY_EMBRYO_MAX_COUNT="Maximal number of embryos from well";
+	public static final String KEY_WAIT_IMAGE_OPENING="Wait for image opening (milliseconds)";
 
 	
 	//private static final Roi nullRoi=null;
@@ -76,6 +77,7 @@ public class Job_SelectMultipleEmbryosAutoRotation  extends Job_Default{
 	private double embryoMaxAR=10.0;
 
 	private int embryoMaxCount=5;
+	private int imageOpeningTimeDelay=3000;
 	
 	
 	@Override
@@ -96,7 +98,7 @@ public class Job_SelectMultipleEmbryosAutoRotation  extends Job_Default{
 		Exper_nm=Exper_nm.substring(0, Exper_nm.indexOf(fileTag));
 		this.setSharedValue("Experiment Name", Exper_nm);
 		
-		TimeUnit.MILLISECONDS.sleep(2000);		
+		TimeUnit.MILLISECONDS.sleep(imageOpeningTimeDelay);		
 		//img=ImageOpenerWithBioformats.openImage(newImgFile);
 		img=openSelectedSlices(newImgFile);
 	}
@@ -298,6 +300,7 @@ public class Job_SelectMultipleEmbryosAutoRotation  extends Job_Default{
 		jobCollection.addParameter(KEY_EMBRYO_MAX_AR, null, embryoMaxAR, ParameterType.DOUBLE_PARAMETER);
 
 		jobCollection.addParameter(KEY_EMBRYO_MAX_COUNT,null, embryoMaxCount, ParameterType.INT_PARAMETER);
+		jobCollection.addParameter(KEY_WAIT_IMAGE_OPENING,null, imageOpeningTimeDelay, ParameterType.INT_PARAMETER);
 
 		
 		return jobCollection;
@@ -320,6 +323,7 @@ public class Job_SelectMultipleEmbryosAutoRotation  extends Job_Default{
 		this.embryoMaxAR=(Double)_jobParameterCollection.getParameterValue(KEY_EMBRYO_MAX_AR);
 		
 		this.embryoMaxCount=(Integer)_jobParameterCollection.getParameterValue(KEY_EMBRYO_MAX_COUNT);
+		this.imageOpeningTimeDelay=(Integer)_jobParameterCollection.getParameterValue(KEY_WAIT_IMAGE_OPENING);
 	}
 	
 	@Override

src/test/java/jobdistributors/run/debug/RunAutoDistributorRotation.java

+package jobdistributors.run.debug;
+
+import feedback.fly.embryo.jobdistributors.JobDistributor_AutoSelectionMultiple_AFocus_Rotation;
+import ij.IJ;
+import ij.ImageJ;
+
+public class RunAutoDistributorRotation {
+	public static void main(String[] args) {
+		Class<?> clazz = JobDistributor_AutoSelectionMultiple_AFocus_Rotation.class;
+
+		// start ImageJ
+		new ImageJ();
+
+		IJ.runPlugIn(clazz.getName(),"Debug run");
+		//IJ.runPlugIn(clazz.getName(),"");
+	}
+}