debugging autofocus with LineScan

pom.xml

@@ -14,7 +14,7 @@
 	 -->
 	<groupId>embl.almf</groupId>
 	<artifactId>AutoMicTools_</artifactId>
-	<version>1.1.14-SNAPSHOT</version>
+	<version>1.1.15-SNAPSHOT</version>
 
 	<name>plugins/AutoMicTools_.jar</name>
 	<description>Collection of tools for automated (feedback) microscopy data acquisition and analysis</description>
@@ -290,11 +290,6 @@
 				<artifactId>imglib2-meta</artifactId>
 				<version>2.0.0-beta-26</version>
 			</dependency>
-			<dependency>
-				<groupId>ome</groupId>
-				<artifactId>bioformats_package</artifactId>
-				<version>6.0.0</version>
-			</dependency>
 			<dependency>
 				<groupId>com.github.mcib3d</groupId>
 				<artifactId>mcib3d-core</artifactId>
@@ -320,7 +315,12 @@
   				<artifactId>ilastik4ij</artifactId>
   				<version>1.7.2</version>
 			</dependency>
-			 			
+
+			<dependency>
+				<groupId>ome</groupId>
+				<artifactId>bioformats_package</artifactId>
+				<version>6.5.0</version>
+			</dependency>
 		</dependencies>
 	</dependencyManagement>
 

src/main/java/automic/online/jobs/common/Job_AutofocusInit_ZenBlue.java

@@ -157,7 +157,7 @@ public class Job_AutofocusInit_ZenBlue  extends Job_Default{
 		
 		Job_AutofocusInit_ZenBlue testJob=new Job_AutofocusInit_ZenBlue();
 		testJob.initialise(null, "AFocus", false);
-		testJob.testImageFile(new File("X:\\group\\Aliaksandr\\tmp\\AF--W0000--P0001-T0001.czi"));
+		testJob.testImageFile(new File("X:\\group\\Aliaksandr\\test-Tobias-auto-20200724\\20200724-150541\\AF\\AF--W0000--P0001-T0001.czi"));
 		//testJob.testJobMicTable(0, tblPth, tblFnm);
 	}
 	

src/main/java/automic/online/jobs/common/Job_Autofocus_ZenBlue.java

@@ -92,7 +92,7 @@ public class Job_Autofocus_ZenBlue  extends Job_Default{
 	
 	@Override
 	public void  postProcessSuccess()throws Exception{
-		ZeissLSM800.submitJobPixels(newImgFile, "spindle-LZ", new Point3D[]{new Point3D(null,null,(double)maxind)});
+		ZeissLSM800.submitJobPixels(newImgFile, "spindle-LZ", new Point3D(null,null,(double)maxind));
 		Roi[] rs=getOverlay().toArray();
 		if (!ROIManipulator2D.isEmptyRoiArr(rs))
 			saveRoisForImage(newImgFile,rs);
@@ -100,7 +100,7 @@ public class Job_Autofocus_ZenBlue  extends Job_Default{
 
 	@Override
 	public void  postProcessOffline()throws Exception{
-		ZeissLSM800.submitJobPixels(newImgFile, "spindle-LZ", new Point3D[]{new Point3D(null,null,(double)maxind)});
+		ZeissLSM800.submitJobPixels(newImgFile, "spindle-LZ", new Point3D(null,null,(double)maxind));
 		Roi[] rs=getOverlay().toArray();
 		if (!ROIManipulator2D.isEmptyRoiArr(rs))
 			saveRoisForImage(newImgFile,rs);

src/main/java/automic/utils/imagefiles/ImageOpenerWithBioformats.java

@@ -80,7 +80,7 @@ public class ImageOpenerWithBioformats {
 		ImagePlus img=imgs[0];
 		
 		if(turnLineScans&&((img.getWidth()==1)||(img.getHeight()==1))) {
-			img=new Turn().run(Image.wrap(img), 0, 0, 1).imageplus();//img.duplicate();
+			img=new Turn().run(Image.wrap(img), 0, 0, -1).imageplus();//img.duplicate();
 			//IJ.run(transformedImage, "TransformJ Turn", "z-angle=0 y-angle=0 x-angle=90");
 		}