protocol with autoselection fucusing rotation and split

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

+package feedback.fly.embryo.jobdistributors;
+
+
+import ij.gui.GenericDialog;
+import ij.gui.WaitForUserDialog;
+import ij.plugin.PlugIn;
+
+import automic.online.jobdistributors.JobDistributor_Abstract;
+import automic.online.jobs.common.Job_AutofocusInitOffset;
+import automic.parameters.ParameterCollection;
+import automic.parameters.gui.ParameterGuiManager;
+import automic.table.TableModel;
+import automic.table.TableProcessor;
+import feedback.fly.embryo.jobs.Job_FocusEmbryoAutoDatasetSplit;
+import feedback.fly.embryo.jobs.Job_RecordFinishDataset;
+import feedback.fly.embryo.jobs.Job_SelectMultipleEmbryosAutoRotation;
+
+
+public class JobDistributor_AutoSelectionMultiple_AFocus_Rotation_Split extends JobDistributor_Abstract implements PlugIn {
+	
+
+	
+	@Override
+	protected void fillJobList(){
+		
+		Job_AutofocusInitOffset job1=new Job_AutofocusInitOffset();
+		ParameterCollection job1Parameters=job1.createJobParameters();
+		job1Parameters.setUndefinedValuesFromDefaults();
+		ParameterGuiManager pgManager1=new ParameterGuiManager(job1Parameters);
+		try{
+			pgManager1.refineParametersViaDialog("Coverslip focusing");
+		}catch(Exception _ex){
+			new WaitForUserDialog("error in parameter values");
+		}
+		
+		job1.parseInputParameterValues(pgManager1.getParameterCollection());
+		
+		
+		super.addImageJob(job1,	"DE_1_",  "AFocus",	true);
+		
+		
+		Job_SelectMultipleEmbryosAutoRotation job2=new Job_SelectMultipleEmbryosAutoRotation();
+		ParameterCollection job2Parameters=job2.createJobParameters();
+		job2Parameters.setUndefinedValuesFromDefaults();
+		ParameterGuiManager pgManager2=new ParameterGuiManager(job2Parameters);
+		try{
+			pgManager2.refineParametersViaDialog("Parameters for embryo selection");
+		}catch(Exception _ex){
+			new WaitForUserDialog("error in parameter values");
+		}
+		
+		job2.parseInputParameterValues(pgManager2.getParameterCollection());
+		super.addImageJob(job2,	"DE_2_",  "LZ.Image",	true);
+		
+
+		Job_FocusEmbryoAutoDatasetSplit job3=new Job_FocusEmbryoAutoDatasetSplit();
+		ParameterCollection job3Parameters=job3.createJobParameters();
+		job3Parameters.setUndefinedValuesFromDefaults();
+		ParameterGuiManager pgManager3=new ParameterGuiManager(job3Parameters);
+		try{
+			pgManager3.refineParametersViaDialog("Parameters for embryo focusing");
+		}catch(Exception _ex){
+			new WaitForUserDialog("error in parameter values");
+		}
+		
+		job3.parseInputParameterValues(pgManager3.getParameterCollection());
+
+		
+		super.addImageJob(job3,	"TR1_1_",  "Focus.Image",	true);
+		
+		super.addImageJob(Job_RecordFinishDataset.class,	"TR2_1_", "Result.Image",	true);
+				
+	}
+	
+	@Override
+	protected TableModel constructTabModel(String _rpth){
+		TableModel outTbl=new TableModel(_rpth);
+
+		outTbl.addColumn("Date.Time");
+		
+		outTbl.addFileColumns("AFocus", "IMG");
+		outTbl.addFileColumns("LZ.Image", "IMG");
+		outTbl.addFileColumns("Focus.Image", "IMG");
+		outTbl.addFileColumns("Result.Image", "IMG");
+		
+		
+		
+		outTbl.addValueColumn("Zoom.X", "NUM");
+		outTbl.addValueColumn("Zoom.Y", "NUM");
+		outTbl.addValueColumn("Correction.X", "NUM");
+		outTbl.addValueColumn("Correction.Y", "NUM");
+		outTbl.addValueColumn("Rotation", "NUM");
+		outTbl.addValueColumn("Focus.Z", "NUM");
+
+		
+		
+		outTbl.addValueColumn("Success", "BOOL");
+		
+		outTbl.addRow(new Object[outTbl.getColumnCount()]);
+		return outTbl;
+	}
+	
+	@Override
+	protected TableProcessor configureTableProcessor(TableModel _tModel)throws Exception{
+		TableProcessor tProcessor=new TableProcessor(_tModel);
+		tProcessor.addFileColumns("Selected.Embryo.LZ", "ROI");
+		return tProcessor;
+	}
+
+	
+	
+	@Override
+	protected void putProtocolPreferencesToDialog(GenericDialog _dialog){
+	}
+
+	@Override
+	protected void getProtocolPreferencesFromDialog(GenericDialog _dialog){
+	}
+	
+	@Override
+	protected boolean showDialogInDebugRun(){
+		return false;
+	}
+
+
+	
+	@Override
+	protected void setDebugConfiguration(){
+		final String searchPath="C:/tempDat/AutoMic_test";
+		this.setGeneralOptions(searchPath, true, false);
+		this.fileExtension="lsm";
+		
+		
+	}
+}