Embryo focusing using mean intensity value rather then CV

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

@@ -137,7 +137,7 @@ public class Job_FocusEmbryoAuto  extends Job_Default{
 		for (int sliceIndex=1; sliceIndex<=nSlices; sliceIndex++){
 			currentProcessor=imStack.getProcessor(sliceIndex);
 			currentStatistics=currentProcessor.getStatistics();
-			focusValues[sliceIndex-1]=currentValue=currentStatistics.stdDev/currentStatistics.mean;//currentStatistics.mean;
+			focusValues[sliceIndex-1]=currentValue=currentStatistics.mean;//currentStatistics.stdDev/currentStatistics.mean;
 			if(currentValue>maxValue){
 				maxValue=currentValue;
 				maxSliceIndex=sliceIndex;

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

@@ -97,7 +97,7 @@ public class Job_FocusEmbryoAutoDataset  extends Job_Default{
 		//ImageWindow.setNextLocation(initialLocationX,initialLocationY);
 		//img=new Duplicator().run(img, 3, 4, 1, img.getNSlices(), 1, 1);
 		
-
+		this.showDebug(img, "Original Image", false);
 		
 		
 		//new WaitForUserDialog ("Select Shift Point").show();
@@ -135,7 +135,7 @@ public class Job_FocusEmbryoAutoDataset  extends Job_Default{
 		for (int sliceIndex=1; sliceIndex<=nSlices; sliceIndex++){
 			currentProcessor=imStack.getProcessor(sliceIndex);
 			currentStatistics=currentProcessor.getStatistics();
-			focusValues[sliceIndex-1]=currentValue=currentStatistics.stdDev/currentStatistics.mean;//currentStatistics.mean;
+			focusValues[sliceIndex-1]=currentValue=currentStatistics.mean;//currentStatistics.stdDev/currentStatistics.mean;//
 			if(currentValue>maxValue){
 				maxValue=currentValue;
 				maxSliceIndex=sliceIndex;
@@ -225,8 +225,8 @@ public class Job_FocusEmbryoAutoDataset  extends Job_Default{
 		// start ImageJ
 		new ImageJ();
 		
-		String tblPth="C:/tempDat/AutoFRAP_test";
-		String tblFnm="summary_TEST14_.txt";
+		String tblPth="C:\\tempDat\\Crocker-lab\\Test_protocol_update_20181109";
+		String tblFnm="summary_test8_m.txt";
 		Job_FocusEmbryoAutoDataset testJob=new Job_FocusEmbryoAutoDataset();
 		testJob.initialise(null, "Focus.Image", false);
 		testJob.testJobMicTable(0, tblPth, tblFnm);