cleaning procedures for line and frame acquisitions

pom.xml

@@ -14,7 +14,7 @@
 	 -->
 	<groupId>embl.almf</groupId>
 	<artifactId>AutoMicTools_</artifactId>
-	<version>1.1.16-SNAPSHOT</version>
+	<version>1.1.17-SNAPSHOT</version>
 
 	<name>plugins/AutoMicTools_.jar</name>
 	<description>Collection of tools for automated (feedback) microscopy data acquisition and analysis</description>

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

@@ -8,7 +8,6 @@ import automic.online.jobs.Job_Default;
 import automic.online.microscope.ZeissLSM800;
 import automic.utils.imagefiles.ImageOpenerWithBioformats;
 import automic.utils.roi.ROIManipulator2D;
-import ij.IJ;
 import ij.ImageJ;
 import ij.ImagePlus;
 import ij.ImageStack;
@@ -16,8 +15,6 @@ import ij.gui.Line;
 import ij.gui.Overlay;
 import ij.gui.ProfilePlot;
 import ij.gui.Roi;
-import imagescience.transform.Turn;
-import imagescience.image.Image;
 
 public class Job_AutofocusInit_ZenBlue  extends Job_Default{
 	//private static final Roi nullRoi=null;
@@ -44,6 +41,7 @@ public class Job_AutofocusInit_ZenBlue  extends Job_Default{
 		Exper_nm=Exper_nm.substring(0, Exper_nm.indexOf(fileTag));
 		this.setSharedValue("Experiment Name", Exper_nm);
 		TimeUnit.MILLISECONDS.sleep(1000);
+		ImageOpenerWithBioformats.turnLineScans=true;
 		img=ImageOpenerWithBioformats.openImage(newImgFile);
 		isLineScan=(img.getWidth()==1)||(img.getHeight()==1);
 	}
@@ -51,21 +49,51 @@ public class Job_AutofocusInit_ZenBlue  extends Job_Default{
 	@Override
 	protected void preProcessOffline()throws Exception{
 		//img=ImageOpenerWithBioformats.openImage(currentTable.getFile(curDInd, imgColumnNm, "IMG"));
+		ImageOpenerWithBioformats.turnLineScans=true;
 		img=ImageOpenerWithBioformats.openImage(newImgFile);
+		isLineScan=(img.getWidth()==1)||(img.getHeight()==1);
 	}
 	
 	
 	@Override
 	protected boolean runProcessing()throws Exception{
+		
+		if (isLineScan)
+			maxind=getFocusValueLine(img);
+		else {
+			maxind=getFocusValueFrameStack(img);
+		}
+
+		return true;
+		
+	}
+	
+	private int getFocusValueLine(ImagePlus _image) {
+
+		//find focus and send to the microscope macro
+		_image.setRoi(0,0,_image.getWidth(), _image.getHeight());
+		double [] vals=new ProfilePlot(_image,true).getProfile();
+		_image.setRoi((Roi)null);
+		int npoints=vals.length;
+		double maxv=0;
+		int max_id=-1;
+		for (int i=0;i<npoints;i++){
+			if (vals[i]>maxv){
+				max_id=i;
+				maxv=vals[i];
+			}
+		}
+		
+		return max_id;
+
+	}
+	
+	private int getFocusValueFrameStack(ImagePlus _image) {
 		//find focus and send to the microscope macro
-		//img.setRoi(0,0,img.getWidth(), img.getHeight());
-		//double [] vals=new ProfilePlot(img,true).getProfile();
-		//img.setRoi((Roi)null);
-		//int npoints=vals.length;
+		_image.setRoi((Roi)null);
 
-		/*
 		double maxv=0;
-		maxind=-1;
+		int max_id=-1;
 		
 		ImageStack stack=img.getStack();
 		int nSlices=stack.getSize();
@@ -74,40 +102,21 @@ public class Job_AutofocusInit_ZenBlue  extends Job_Default{
 		for (int i=0;i<nSlices;i++){
 			currentValue=stack.getProcessor(i+1).getStatistics().mean;
 			if (currentValue>maxv){
-				maxind=i;
+				max_id=i;
 				maxv=currentValue;
 			}
 		}
 		
-		//ln=new Line(0,maxind,img.getWidth(),maxind);
-		//ln.setStrokeColor(Color.ORANGE);
-		*/
-		
-		
-		//find focus and send to the microscope macro
-		img.setRoi(0,0,img.getWidth(), img.getHeight());
-		double [] vals=new ProfilePlot(img,true).getProfile();
-		img.setRoi((Roi)null);
-		int npoints=vals.length;
-		double maxv=0;
-		maxind=-1;
-		for (int i=0;i<npoints;i++){
-			if (vals[i]>maxv){
-				maxind=i;
-				maxv=vals[i];
-			}
-		}
+		return max_id;
 
-		return true;
-		
 	}
 	
+	
 	@Override
 	protected Overlay createOverlay(){
 		Overlay o=new Overlay();
 		
-		//if(isLineScan&&(maxind>0))
-		if(maxind>0)
+		if(isLineScan&&(maxind>0))
 			o.add(new Line(0, maxind, img.getWidth()-1, maxind));
 		return o;
 	}
@@ -115,18 +124,10 @@ public class Job_AutofocusInit_ZenBlue  extends Job_Default{
 	@Override 
 	public void visualise(int _xvis, int _yvis){
 		this.visualiseImg(img, getOverlay(), _xvis, _yvis);
-		/*
-		if (isLineScan) {
-			ImagePlus transformedImage=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");
-			this.visualiseImg(transformedImage, getOverlay(), _xvis, _yvis);
-		}else{
-			this.visualiseImg(img, getOverlay(), _xvis, _yvis);
-			if (maxind>0)
-				img.setSlice(maxind);
 
+		if ((!isLineScan) && (maxind>0)) {
+			img.setSlice(maxind);
 		}
-		*/
 	}