option in embryo focusing job to ignore xy positions from calculations

pom.xml

@@ -15,7 +15,7 @@
 	
 
 	<groupId>embl.almf</groupId>
-	<version>1.0.6-snapshot</version>
+	<version>1.0.7-SNAPSHOT</version>
 
 	<name>Fly_Embryo_Feedback</name>
 	<inceptionYear>2017</inceptionYear>

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

@@ -16,10 +16,14 @@ import de.embl.cba.morphometry.Utils;
 import ij.IJ;
 import net.imagej.ImageJ;
 import ij.ImagePlus;
+import ij.ImageStack;
+import ij.Prefs;
 import ij.gui.Arrow;
 import ij.gui.Overlay;
 import ij.gui.PointRoi;
 import ij.gui.Roi;
+import ij.plugin.ImageCalculator;
+import ij.process.ImageProcessor;
 import loci.plugins.BF;
 import loci.plugins.in.ImporterOptions;
 import net.imagej.ops.OpService;
@@ -32,6 +36,7 @@ public class Job_FocusEmbryoAutoDatasetSplit  extends Job_Default{
 	public static final String KEY_FOCUS_CHANNEL_INDEX="Focus channel index";
 	public static final String KEY_WAIT_IMAGE_OPENING="Wait for image opening (milliseconds)";
 	public static final String KEY_FOCUS_OFFSET="Focus offset";
+	public static final String KEY_CORRECT_XY="Correct XY";
 
 	
 	
@@ -48,6 +53,10 @@ public class Job_FocusEmbryoAutoDatasetSplit  extends Job_Default{
 	private int targetChannel=1;
 	private int imageOpeningTimeDelay=3000;
 	private int focusOffset=0;
+	private boolean makeBinary=false;
+	private int thresholdValue=300;
+	private boolean correctXY=true;
+	
 
 	@Override	
 	public void initialise(String _fTag,String _colNm, boolean _visOnline){
@@ -115,18 +124,38 @@ public class Job_FocusEmbryoAutoDatasetSplit  extends Job_Default{
 		
 		
 		
-		this.showDebug(img, "Original Image", false);
+		this.showDebug(img, "Original Image", true);
 		
+		ImagePlus imageToProcess=null;
+		if (makeBinary) {
+			Prefs.blackBackground = true;
+			ImageStack originalStack=img.getStack();
+			ImageStack binaryStack=new ImageStack(originalStack.getWidth(),originalStack.getHeight());
+			int nSlices=originalStack.getSize();
+			for (int iSlice=1;iSlice<=nSlices;iSlice++) {
+				ImageProcessor originalSlice=originalStack.getProcessor(iSlice);
+				originalSlice.setThreshold(thresholdValue, Double.MAX_VALUE, originalSlice.getLutUpdateMode());
+				binaryStack.addSlice(originalSlice.createMask());
+			}
+			imageToProcess=new ImagePlus("Image to process", binaryStack);
+			IJ.run(imageToProcess, "Divide...", "value=255 stack");
+			ImageCalculator ic=new ImageCalculator();
+			imageToProcess = ic.run("Multiply create stack", img, imageToProcess);
+
+
+		}else {
+			imageToProcess=img;
+		}
 		
 		//new WaitForUserDialog ("Select Shift Point").show();
 
 
-		this.showDebug(img, "Original Image", false);
+		this.showDebug(imageToProcess, "ImageToProcess", true);
 
 		//////code from Tischi
 		
 		try{
-			getEllipsoidParameters(img);
+			getEllipsoidParameters(imageToProcess,img);
 		}catch (Exception _ex) {
 			return false;
 		}
@@ -141,7 +170,7 @@ public class Job_FocusEmbryoAutoDatasetSplit  extends Job_Default{
 		
 	}
 	
-	void getEllipsoidParameters(ImagePlus _image)throws Exception {
+	void getEllipsoidParameters(ImagePlus _imageProcess, ImagePlus _imageCalibration)throws Exception {
 		
 
 		final FlyEmbryoRegistrationSettings settings = new FlyEmbryoRegistrationSettings();
@@ -149,15 +178,22 @@ public class Job_FocusEmbryoAutoDatasetSplit  extends Job_Default{
 
 		final FlyEmbryoSingleChannelRegistration registration = new FlyEmbryoSingleChannelRegistration( settings, opService );
 
-		final double[] calibration = Utils.getCalibration( _image );
+		final double[] calibration = Utils.getCalibration( _imageCalibration );
 
-		registration.run( _image,0);
+		registration.run( _imageProcess,0);
 		
 		final double[] centre = registration.getElliposidCentreInInputImagePixelUnits();
 		final double[] angles = registration.getElliposidEulerAnglesInDegrees();
 		
-		selectedXPosition = centre[0];
-		selectedYPosition = centre[1];
+		if (correctXY) {
+			selectedXPosition = centre[0];
+			selectedYPosition = centre[1];
+
+		}else {
+			selectedXPosition=img.getWidth()/2.0;
+			selectedYPosition=img.getHeight()/2.0;
+			
+		}
 		selectedZPosition = centre[2];
 		rotation=-angles[0];
 		
@@ -246,6 +282,7 @@ public class Job_FocusEmbryoAutoDatasetSplit  extends Job_Default{
 		jobCollection.addParameter(KEY_FOCUS_CHANNEL_INDEX,	null, targetChannel, 		ParameterType.INT_PARAMETER);
 		jobCollection.addParameter(KEY_WAIT_IMAGE_OPENING,	null, imageOpeningTimeDelay,ParameterType.INT_PARAMETER);
 		jobCollection.addParameter(KEY_FOCUS_OFFSET,		null, focusOffset,			ParameterType.INT_PARAMETER);
+		jobCollection.addParameter(KEY_CORRECT_XY,		    null, correctXY,			ParameterType.BOOL_PARAMETER);
 
 		
 		return jobCollection;
@@ -256,6 +293,7 @@ public class Job_FocusEmbryoAutoDatasetSplit  extends Job_Default{
 		this.targetChannel=			(Integer)_jobParameterCollection.getParameterValue(KEY_FOCUS_CHANNEL_INDEX);
 		this.imageOpeningTimeDelay=	(Integer)_jobParameterCollection.getParameterValue(KEY_WAIT_IMAGE_OPENING);
 		this.focusOffset=			(Integer)_jobParameterCollection.getParameterValue(KEY_FOCUS_OFFSET);
+		this.correctXY=				(Boolean)_jobParameterCollection.getParameterValue(KEY_CORRECT_XY);
 
 	}
 	
@@ -267,11 +305,11 @@ public class Job_FocusEmbryoAutoDatasetSplit  extends Job_Default{
 		// start ImageJ
 		new ImageJ().ui().showUI();
 		
-		String tblPth="X:\\group\\Aliaksandr\\User_data\\Crocker-fly-feedback\\03082019_march_test";
-		String tblFnm="summary_test03_.txt";
+		String tblPth="C:\\tempdat\\Raquel\\Raquel-LSM880_15042021_finok";
+		String tblFnm="summary_Test1_.txt";
 		Job_FocusEmbryoAutoDatasetSplit testJob=new Job_FocusEmbryoAutoDatasetSplit();
 		testJob.initialise(null, "Focus.Image", false);
-		testJob.testJobMicTable(11, tblPth, tblFnm);
+		testJob.testJobMicTable(3, tblPth, tblFnm);
 	}
 	
 }