Autofocus with offset job moved to AutoMicTools

src/main/java/feedback/fly/embryo/jobdistributors/JobDistributor_AutoSelectionMultiple_AFocus.java

@@ -7,12 +7,12 @@ import ij.gui.WaitForUserDialog;
 import ij.plugin.PlugIn;
 
 import automic.online.jobdistributors.JobDistributor_Abstract;
+import automic.online.jobs.common.Job_AutofocusInitOffset;
 import automic.online.jobs.common.Job_RecordFinish;
 import automic.parameters.ParameterCollection;
 import automic.parameters.gui.ParameterGuiManager;
 import automic.table.TableModel;
 import automic.table.TableProcessor;
-import feedback.fly.embryo.jobs.Job_AutofocusInitOffset;
 import feedback.fly.embryo.jobs.Job_FocusEmbryoAuto;
 import feedback.fly.embryo.jobs.Job_SelectMultipleEmbryosAuto;
 

src/main/java/feedback/fly/embryo/jobdistributors/JobDistributor_AutoSelectionMultiple_AFocus_Rotation.java

@@ -7,12 +7,12 @@ import ij.gui.WaitForUserDialog;
 import ij.plugin.PlugIn;
 
 import automic.online.jobdistributors.JobDistributor_Abstract;
+import automic.online.jobs.common.Job_AutofocusInitOffset;
 import automic.online.jobs.common.Job_RecordFinish;
 import automic.parameters.ParameterCollection;
 import automic.parameters.gui.ParameterGuiManager;
 import automic.table.TableModel;
 import automic.table.TableProcessor;
-import feedback.fly.embryo.jobs.Job_AutofocusInitOffset;
 import feedback.fly.embryo.jobs.Job_FocusEmbryoAutoRotation;
 import feedback.fly.embryo.jobs.Job_SelectMultipleEmbryosAutoRotation;
 

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

-package feedback.fly.embryo.jobs;
-
-import java.awt.Color;
-
-import automic.online.microscope.ZeissKeys;
-import automic.online.jobs.Job_Default;
-import automic.parameters.ParameterCollection;
-import automic.parameters.ParameterType;
-import automic.utils.imagefiles.ImageOpenerWithBioformats;
-import ij.IJ;
-import ij.ImageJ;
-import ij.ImagePlus;
-import ij.gui.Line;
-import ij.gui.Overlay;
-import ij.gui.ProfilePlot;
-import ij.gui.Roi;
-import ij.plugin.MontageMaker;
-
-public class Job_AutofocusInitOffset  extends Job_Default{
-	public static final String KEY_FOCUS_SLICE_OFFSET="Slice offset";
-	
-	
-	int sliceOffset=2000;
-	
-	
-	//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.cleanRecord(curDInd);
-		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);
-		
-		img=ImageOpenerWithBioformats.openImage(newImgFile);
-		img=new MontageMaker().makeMontage2(img, 1, img.getNSlices(), 1.0, 1, img.getNSlices(), 1, 0, false);
-		
-	}
-	
-	@Override
-	protected void preProcessOffline()throws Exception{
-		img=ImageOpenerWithBioformats.openImage(currentTable.getFile(curDInd, imgColumnNm, "IMG"));
-		img=new MontageMaker().makeMontage2(img, 1, img.getNSlices(), 1.0, 1, img.getNSlices(), 1, 0, false);
-	}
-	
-	
-	@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;
-		for (int i=0;i<npoints;i++){
-			if (vals[i]>maxv){
-				maxind=i;
-				maxv=vals[i];
-			}
-		}
-		IJ.log("maxind: "+maxind);
-		ln=new Line(0,maxind,img.getWidth(),maxind);
-		ln.setStrokeColor(Color.ORANGE);
-		
-		return true;
-		
-	}
-	
-	@Override
-	protected Overlay createOverlay(){
-		return (ln!=null)?new Overlay(ln):new Overlay();
-	}
-	
-	@Override 
-	public void visualise(int _xvis, int _yvis){
-		this.visualiseImg(img, getOverlay(), _xvis, _yvis);
-	}
-	
-	
-	@Override
-	public void  postProcessSuccess()throws Exception{
-		ZeissKeys.submitCommandsToMicroscope("focus", ""+(img.getWidth()-1)/2.0,"0",""+(maxind+sliceOffset),"","","","","");
-		saveRoiForImage(newImgFile,ln);
-	}
-	
-	@Override
-	public ParameterCollection createJobParameters(){
-		ParameterCollection jobCollection=new ParameterCollection();
-		
-		jobCollection.addParameter(KEY_FOCUS_SLICE_OFFSET, null, sliceOffset, ParameterType.INT_PARAMETER);
-		
-		return jobCollection;
-	}
-
-	@Override
-	public void parseInputParameterValues(ParameterCollection _jobParameterCollection){
-		this.sliceOffset=(Integer)_jobParameterCollection.getParameterValue(KEY_FOCUS_SLICE_OFFSET);
-	}
-
-	
-	/**
-	 * offline debugging
-	 * @param args unsused
-	 */
-	public static void main(String[] args)throws Exception{
-		// start ImageJ
-		new ImageJ();
-		
-		String tblPth="D:/tempDat/Crocker_group/fly feedback files 20180410/ttt";
-		String tblFnm="summary_test05_.txt";
-		Job_AutofocusInitOffset testJob=new Job_AutofocusInitOffset();
-		testJob.initialise(null, "AFocus", false);
-		testJob.testJobMicTable(0, tblPth, tblFnm);
-		
-		System.out.print("test end");
-	}
-	
-}