resolve an issue when the well is the whole image

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

@@ -215,9 +215,14 @@ public class Job_SelectMultipleEmbryosAuto  extends Job_Default{
 		this.showDebug(_embryoImage, "Image for embryo segmentation", true);
 		
 		//exclude particles outside ROI by filling with 0
-		embryoProcessor.setColor(0);
-		embryoProcessor.fillOutside(wellRoi);
-		
+		long imageSize=embryoProcessor.getWidth()*embryoProcessor.getHeight();
+		embryoProcessor.setRoi(wellRoi);
+		long roiSize=(long)embryoProcessor.getStats().area;
+		embryoProcessor.setRoi((Roi)null);
+		if(roiSize<imageSize) {//check if there is any area on the image outside Roi
+			embryoProcessor.setColor(0);
+			embryoProcessor.fillOutside(wellRoi);
+		}
 		ImageProcessor maskProcessor=new MaximumFinder().findMaxima(embryoProcessor,watershedTolerance,embryoFluorThreshold,MaximumFinder.SEGMENTED,false,false);
 		
 		ImagePlus watershedMaskImage=new ImagePlus("Embryo Mask Image", maskProcessor);
@@ -309,7 +314,12 @@ public class Job_SelectMultipleEmbryosAuto  extends Job_Default{
 		//saveRoiForImage(newImgFile,saveRoi);
 		
 		this.setSharedValue("Zoom Points", selectedPoints);
-		this.setSharedValue("Zoom Counter", -1);
+		if(this.getSharedValue("Zoom Counter")==null) {
+			this.setSharedValue("Zoom Counter", -1);
+		}
+		if(this.getSharedValue("Table Row Counter")==null) {
+			this.setSharedValue("Table Row Counter", -1);
+		}
 		this.setSharedValue("Selected Embryo Rois", selectedEmbryoRois);
 	}
 	

src/main/java/feedback/fly/embryo/jobs/Job_SelectMultipleEmbryosManual3D.java

@@ -177,8 +177,12 @@ public class Job_SelectMultipleEmbryosManual3D  extends Job_Default{
 		
 		saveRoiForImage(newImgFile,saveRoi);
 		
-		this.setSharedValue("Zoom Counter", -1);
-		this.setSharedValue("Table Row Counter", -1);
+		if(this.getSharedValue("Zoom Counter")==null) {
+			this.setSharedValue("Zoom Counter", -1);
+		}
+		if(this.getSharedValue("Table Row Counter")==null) {
+			this.setSharedValue("Table Row Counter", -1);
+		}
 	}
 	
 	

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

+package jobdistributors.run.debug;
+
+import feedback.fly.embryo.jobdistributors.JobDistributor_AutoSelectionMultiple_AFocus_Rotation_Split;
+//import feedback.fly.embryo.jobdistributors.JobDistributor_ManualSelection3DMultiple_AFocus_Rotation_Split;
+import ij.IJ;
+import net.imagej.ImageJ;
+
+public class RunJobDistributor {
+	public static void main(String[] args) {
+		//Class<?> clazz = JobDistributor_ManualSelection3DMultiple_AFocus_Rotation_Split.class;
+		Class<?> clazz = JobDistributor_AutoSelectionMultiple_AFocus_Rotation_Split.class;
+
+		// start ImageJ
+		ImageJ ij2=new ImageJ();
+		ij2.ui().showUI();
+
+		//IJ.runPlugIn(clazz.getName(),"Debug run");
+		IJ.runPlugIn(clazz.getName(),"");
+	}
+}

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

-package jobdistributors.run.debug;
-
-import feedback.fly.embryo.jobdistributors.JobDistributor_ManualSelection3DMultiple_AFocus_Rotation_Split;
-import ij.IJ;
-import net.imagej.ImageJ;
-
-public class RunManualDistributorRotationSplit {
-	public static void main(String[] args) {
-		Class<?> clazz = JobDistributor_ManualSelection3DMultiple_AFocus_Rotation_Split.class;
-
-		// start ImageJ
-		ImageJ ij2=new ImageJ();
-		ij2.ui().showUI();
-
-		IJ.runPlugIn(clazz.getName(),"Debug run");
-		//IJ.runPlugIn(clazz.getName(),"");
-	}
-}