creating autofocus jobs for commander

pom.xml

@@ -8,7 +8,7 @@
 		<version>5.0</version> <relativePath /> </parent> -->
 	<groupId>embl.almf</groupId>
 	<artifactId>AutoMicTools_</artifactId>
-	<version>1.1.24-SNAPSHOT</version>
+	<version>1.1.25-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_Commander.java

+package automic.online.jobs.common;
+
+import java.io.File;
+import java.util.concurrent.TimeUnit;
+
+import automic.geom.Point3D;
+import automic.online.jobs.Job_Default;
+import automic.utils.imagefiles.ImageOpenerWithBioformats;
+import automic.utils.roi.ROIManipulator2D;
+import ij.ImageJ;
+import ij.ImagePlus;
+import ij.ImageStack;
+import ij.gui.Line;
+import ij.gui.Overlay;
+import ij.gui.ProfilePlot;
+import ij.gui.Roi;
+
+public class Job_AutofocusInit_Commander  extends Job_Default{
+	//private static final Roi nullRoi=null;
+	private ImagePlus img=null;
+	int maxind=-1;
+	int zSubmit=-1;
+	Boolean isLineScan=null;
+	
+	@Override
+	protected void cleanIterOutput(){
+		img=null;
+		isLineScan=null;
+	}
+	
+	@Override
+	protected void preProcessOnline()throws Exception{
+		super.clearSharedData();
+		currentTable.cleanRecord(curDInd);
+		//change the root path of the table to experiment folder
+		currentTable.setRootPath(newImgFile.getParentFile().getParent());
+		//
+		currentTable.setFileAbsolutePath(newImgFile, curDInd, imgColumnNm, "IMG");
+		
+		String Exper_nm=newImgFile.getName();
+		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.getNSlices()==1);
+	}
+	
+	@Override
+	protected void preProcessOffline()throws Exception{
+		//img=ImageOpenerWithBioformats.openImage(currentTable.getFile(curDInd, imgColumnNm, "IMG"));
+		ImageOpenerWithBioformats.turnLineScans=true;
+		img=ImageOpenerWithBioformats.openImage(newImgFile);
+		isLineScan=(img.getNSlices()==1);
+	}
+	
+	
+	@Override
+	protected boolean runProcessing()throws Exception{
+		
+		if (isLineScan) {
+			maxind=getFocusValueLine(img);
+			zSubmit=img.getHeight()-maxind-1;
+		}else {
+			maxind=getFocusValueFrameStack(img);
+			zSubmit=maxind;
+		}
+
+		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
+		_image.setRoi((Roi)null);
+
+		double maxv=0;
+		int max_id=-1;
+		
+		ImageStack stack=img.getStack();
+		int nSlices=stack.getSize();
+		
+		double currentValue;
+		for (int i=0;i<nSlices;i++){
+			currentValue=stack.getProcessor(i+1).getStatistics().mean;
+			if (currentValue>maxv){
+				max_id=i;
+				maxv=currentValue;
+			}
+		}
+		
+		return max_id;
+
+	}
+	
+	
+	@Override
+	protected Overlay createOverlay(){
+		Overlay o=new Overlay();
+		
+		if(isLineScan&&(maxind>0))
+			o.add(new Line(0, maxind, img.getWidth()-1, maxind));
+		return o;
+	}
+	
+	@Override 
+	public void visualise(int _xvis, int _yvis){
+		this.visualiseImg(img, getOverlay(), _xvis, _yvis);
+
+		if ((!isLineScan) && (maxind>0)) {
+			img.setSlice(maxind);
+		}
+	}
+	
+	
+	@Override
+	public void  postProcessSuccess()throws Exception{
+		this.microscopeCommander.submitJobPixels(newImgFile, "spindle-LZ", new Point3D(null,null,(double)zSubmit));
+		Roi[] rs=getOverlay().toArray();
+		if (!ROIManipulator2D.isEmptyRoiArr(rs))
+			saveRoisForImage(newImgFile,rs);
+	}
+
+	@Override
+	public void  postProcessOffline()throws Exception{
+		this.microscopeCommander.submitJobPixels(newImgFile, "spindle-LZ", new Point3D(null,null,(double)zSubmit));
+		Roi[] rs=getOverlay().toArray();
+		if (!ROIManipulator2D.isEmptyRoiArr(rs))
+			saveRoisForImage(newImgFile,rs);
+		this.visualise(1000, 100);
+	}
+
+	
+	/**
+	 * offline debugging
+	 * @param args unsused
+	 */
+	public static void main(String[] args)throws Exception{
+		// start ImageJ
+		new ImageJ();
+		
+		Job_AutofocusInit_Commander testJob=new Job_AutofocusInit_Commander();
+		testJob.initialise(null, "AFocus", false);
+		testJob.testImageFile(new File("X:\\group\\Aliaksandr\\User_data\\Marco_Cosenza\\test-AF-update\\AF--W0000--P0001-T0001.czi"));
+		//testJob.testJobMicTable(0, tblPth, tblFnm);
+	}
+	
+}

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

+package automic.online.jobs.common;
+
+import java.io.File;
+import java.util.concurrent.TimeUnit;
+
+import automic.geom.Point3D;
+import automic.online.jobs.Job_Default;
+import automic.utils.imagefiles.ImageOpenerWithBioformats;
+import automic.utils.roi.ROIManipulator2D;
+import ij.ImageJ;
+import ij.ImagePlus;
+import ij.ImageStack;
+import ij.gui.Overlay;
+import ij.gui.Roi;
+
+public class Job_Autofocus_Commander  extends Job_Default{
+	//private static final Roi nullRoi=null;
+	private ImagePlus img=null;
+	int maxind=-1;
+	Roi ln=null;
+	
+	@Override
+	protected void cleanIterOutput(){
+		img=null;
+		ln=null;
+	}
+	
+	@Override
+	protected void preProcessOnline()throws Exception{
+		super.clearSharedData();
+		currentTable.setFileAbsolutePath(newImgFile, curDInd, imgColumnNm, "IMG");
+		
+		String Exper_nm=newImgFile.getName();
+		Exper_nm=Exper_nm.substring(0, Exper_nm.indexOf(fileTag));
+		this.setSharedValue("Experiment Name", Exper_nm);
+		TimeUnit.MILLISECONDS.sleep(1000);
+		img=ImageOpenerWithBioformats.openImage(newImgFile);
+		
+	}
+	
+	@Override
+	protected void preProcessOffline()throws Exception{
+		//img=ImageOpenerWithBioformats.openImage(currentTable.getFile(curDInd, imgColumnNm, "IMG"));
+		img=ImageOpenerWithBioformats.openImage(newImgFile);
+	}
+	
+	
+	@Override
+	protected boolean runProcessing()throws Exception{
+		//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;
+		
+		ImageStack stack=img.getStack();
+		int nSlices=stack.getSize();
+		
+		double currentValue;
+		for (int i=0;i<nSlices;i++){
+			currentValue=stack.getProcessor(i+1).getStatistics().mean;
+			if (currentValue>maxv){
+				maxind=i;
+				maxv=currentValue;
+			}
+		}
+		
+		//ln=new Line(0,maxind,img.getWidth(),maxind);
+		//ln.setStrokeColor(Color.ORANGE);
+		
+		return true;
+		
+	}
+	
+	@Override
+	protected Overlay createOverlay(){
+		return new Overlay();
+	}
+	
+	@Override 
+	public void visualise(int _xvis, int _yvis){
+		this.visualiseImg(img, getOverlay(), _xvis, _yvis);
+		if (maxind>0)
+			img.setSlice(maxind);
+	}
+	
+	
+	@Override
+	public void  postProcessSuccess()throws Exception{
+		this.microscopeCommander.submitJobPixels(newImgFile, "spindle-LZ", new Point3D(null,null,(double)maxind));
+		Roi[] rs=getOverlay().toArray();
+		if (!ROIManipulator2D.isEmptyRoiArr(rs))
+			saveRoisForImage(newImgFile,rs);
+	}
+
+	@Override
+	public void  postProcessOffline()throws Exception{
+		this.microscopeCommander.submitJobPixels(newImgFile, "spindle-LZ", new Point3D(null,null,(double)maxind));
+		Roi[] rs=getOverlay().toArray();
+		if (!ROIManipulator2D.isEmptyRoiArr(rs))
+			saveRoisForImage(newImgFile,rs);
+	}
+
+	
+	/**
+	 * offline debugging
+	 * @param args unsused
+	 */
+	public static void main(String[] args)throws Exception{
+		// start ImageJ
+		new ImageJ();
+		
+		Job_Autofocus_Commander testJob=new Job_Autofocus_Commander();
+		testJob.initialise(null, "AFocus", false);
+		testJob.testImageFile(new File("W:\\halavaty\\Tobias-LSM800-data\\20190219-183148\\AF\\AF--W0000--P0001-T0001.czi"));
+		//testJob.testJobMicTable(0, tblPth, tblFnm);
+	}
+	
+}