fill pixels with 0 out of the well area on Low-zoom image

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

@@ -88,9 +88,9 @@ public class Job_SelectMultipleEmbryosAutoRotation  extends Job_Default{
 	
 	private double embryoMinAR=1.8;
 	private double embryoMaxAR=10.0;
-	private double embryoMinCircularity=0.0;
+	private double embryoMinCircularity=0.3;
 	private double embryoMaxCircularity=1.0;
-	private double embryoMinSolidity=0.0;
+	private double embryoMinSolidity=0.7;
 	private double embryoMaxSolidity=1.0;
 
 	
@@ -204,10 +204,15 @@ public class Job_SelectMultipleEmbryosAutoRotation  extends Job_Default{
 	}
 	
 	private void identifyEmbryos(ImagePlus _embryoImage)throws Exception {
-		new RankFilters().rank(_embryoImage.getProcessor(), embryoFluorFilterRadius, RankFilters.MEDIAN);
+		ImageProcessor embryoProcessor = _embryoImage.getProcessor();
+		new RankFilters().rank(embryoProcessor, embryoFluorFilterRadius, RankFilters.MEDIAN);
 		this.showDebug(_embryoImage, "Image for embryo segmentation", true);
 		
-		ImageProcessor maskProcessor=new MaximumFinder().findMaxima(_embryoImage.getProcessor(),watershedTolerance,embryoFluorThreshold,MaximumFinder.SEGMENTED,false,false);
+		//exclude particles outside ROI by filling with 0
+		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);
 
@@ -228,7 +233,7 @@ public class Job_SelectMultipleEmbryosAutoRotation  extends Job_Default{
 		Roi[] identifiedRois=rm.getRoisAsArray();
 		
 		ParticleFilterer embryoFilter=new ParticleFilterer(_embryoImage.getProcessor(), identifiedRois);
-		embryoFilter.filterInRoi(wellRoi);
+		//embryoFilter.filterInRoi(wellRoi); exclude particles outside ROI by filling with 0 before
 		embryoFilter.filterThr(ParticleFilterer.MEAN, embryoMinMeanIntensity, embryoMaxMeanIntensity);
 		embryoFilter.filterThr(ParticleFilterer.MEDIAN, embryoMinMedianIntensity, embryoMaxMedianIntensity);
 		embryoFilter.filterThr(ParticleFilterer.ASPECT_RATIO, embryoMinAR, embryoMaxAR);
@@ -330,7 +335,6 @@ public class Job_SelectMultipleEmbryosAutoRotation  extends Job_Default{
 		jobCollection.addParameter(KEY_EMBRYO_MIN_SOLIDITY, null, embryoMinSolidity, ParameterType.DOUBLE_PARAMETER);
 		jobCollection.addParameter(KEY_EMBRYO_MAX_SOLIDITY, null, embryoMaxSolidity, 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);
@@ -381,8 +385,8 @@ public class Job_SelectMultipleEmbryosAutoRotation  extends Job_Default{
 		// start ImageJ
 		new ImageJ();
 		
-		String tblPth="Z:/halavaty/temp/20180622 auto test";
-		String tblFnm="summary_test09_.txt";
+		String tblPth="X:\\group\\ALMFstuff\\Aliaksandr\\Crocker-fly-feedback\\20181";
+		String tblFnm="summary_test01_.txt";
 		Job_SelectMultipleEmbryosAutoRotation testJob=new Job_SelectMultipleEmbryosAutoRotation();
 		testJob.initialise(null, "LZ.Image", false);
 		testJob.testJobMicTable(0, tblPth, tblFnm);

src/main/java/feedback/fly/embryo/jobtests/Embryo_Selection_Tester.java

@@ -7,7 +7,7 @@ import ij.plugin.PlugIn;
 import automic.online.jobs.TestJobGui;
 
 import automic.utils.Utils;
-import feedback.fly.embryo.jobs.Job_SelectMultipleEmbryosAuto;
+import feedback.fly.embryo.jobs.Job_SelectMultipleEmbryosAutoRotation;
 
 
 
@@ -23,7 +23,7 @@ public class Embryo_Selection_Tester implements PlugIn {
 //		}
 		
 		try{
-			TestJobGui jobTester=new TestJobGui(Job_SelectMultipleEmbryosAuto.class, "LZ.Image");
+			TestJobGui jobTester=new TestJobGui(Job_SelectMultipleEmbryosAutoRotation.class, "LZ.Image");
 			jobTester.initialiseGui();
 			jobTester.runTest();
 		}catch (Exception e){