fiji-plugin-morphometry for calculating embryo center and rotation in HZ focus job

README.md

@@ -17,7 +17,16 @@ Multichamber wide slide with fixed fly embryos stained with 3 dyes:
 
 # Log/updates
 
-2018-01-05 Tim and Alex
+## 2019-03
+
+Version of high-zoom focus job based on `fiji-plugin morphometry` from C. Tischer. It allows split to touching embryos and correctly calculate embryo center in XYZ anfd rotation angle.
+
+
+
+## ....
+
+## 2018-01-05 Tim and Alex
+
 - Configuring acquisition jobs manually.
 - Trying feedback experiments with manual selection procedures
 - X-Y coordinates are flipping, microscope additionally scans from right to left
\ No newline at end of file

pom.xml

@@ -94,7 +94,7 @@
 		<dependency>
 			<groupId>de.embl.cba</groupId>
 			<artifactId>fiji-plugin-morphometry</artifactId>
-			<version>0.4.03</version>
+			<version>0.4.04</version>
 		</dependency>
 		 
 	</dependencies>

src/main/java/feedback/fly/embryo/jobdistributors/JobDistributor_ManualSelection3DMultiple_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_SelectMultipleEmbryosManual3D;
+
+
+public class JobDistributor_ManualSelection3DMultiple_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_SelectMultipleEmbryosManual3D job2=new Job_SelectMultipleEmbryosManual3D();
+		ParameterCollection job2Parameters=job2.createJobParameters();
+		job2Parameters.setUndefinedValuesFromDefaults();
+		ParameterGuiManager pgManager2=new ParameterGuiManager(job2Parameters);
+		try{
+			pgManager2.refineParametersViaDialog("Parameters for manual 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("Focus.Z", "NUM");
+		outTbl.addValueColumn("Rotation", "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";
+		
+	}
+}

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

+package feedback.fly.embryo.jobs;
+
+import java.awt.Color;
+import java.io.File;
+import java.util.concurrent.TimeUnit;
+
+
+import automic.online.microscope.ZeissKeys;
+import automic.online.jobs.Job_Default;
+import automic.parameters.ParameterCollection;
+import automic.parameters.ParameterType;
+import automic.table.TableModel;
+import de.embl.cba.morphometry.ImageIO;
+import de.embl.cba.morphometry.Utils;
+import de.embl.cba.morphometry.drosophila.registration.DrosophilaRegistrationSettings;
+import de.embl.cba.morphometry.drosophila.registration.DrosophilaSingleChannelRegistration;
+import ij.IJ;
+import net.imagej.ImageJ;
+import ij.ImagePlus;
+import ij.gui.Arrow;
+import ij.gui.Overlay;
+import ij.gui.PointRoi;
+import ij.gui.Roi;
+import loci.plugins.BF;
+import loci.plugins.in.ImporterOptions;
+import net.imagej.ops.OpService;
+import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.type.NativeType;
+import net.imglib2.type.numeric.RealType;
+
+public class Job_FocusEmbryoAutoDatasetSplit  extends Job_Default{
+
+	public static final String KEY_FOCUS_CHANNEL_INDEX="Focus channel index";
+	public static final String KEY_WAIT_IMAGE_OPENING="Wait for image opening (milliseconds)";
+	public static final String KEY_FOCUS_OFFSET="Focus offset";
+
+	
+	
+	private OpService opService=null;
+	private ImagePlus img=null;
+	
+	private Double selectedXPosition;
+	private Double selectedYPosition;
+	private Double selectedZPosition;
+	private Double rotation;
+	private Double halfLength;
+
+	
+	private int targetChannel=1;
+	private int imageOpeningTimeDelay=3000;
+	private int focusOffset=0;
+
+	@Override	
+	public void initialise(String _fTag,String _colNm, boolean _visOnline){
+		super.initialise(_fTag, _colNm, _visOnline);
+		opService=new ImageJ().op();
+	}
+
+	
+	@Override
+	protected void cleanIterOutput(){
+		img=null;
+		selectedXPosition=null;
+		selectedYPosition=null;
+		selectedYPosition=null;
+		rotation=null;
+		halfLength=null;
+	}
+	
+	@Override
+	protected void preProcessOnline()throws Exception{
+		int zoomCounter=(int)this.getSharedValue("Zoom Counter");
+		int tableRowCounter=(int)this.getSharedValue("Table Row Counter");
+		zoomCounter++;
+		tableRowCounter++;
+		
+		String Exper_nm=(String)getSharedValue("Experiment Name");// newImgFile.getName();
+		String rootPath=currentTable.getRootPath();
+		File experimentTableFile=new File(rootPath,"summary_"+Exper_nm+".txt");
+		TableModel experimentTable=new TableModel(experimentTableFile);
+		while(experimentTable.getBooleanValue(tableRowCounter, "Success")==false) {
+			tableRowCounter++;
+		}
+
+		experimentTable.setFileAbsolutePath(newImgFile, tableRowCounter, imgColumnNm, "IMG");
+		
+		
+		experimentTable.writeNewFile("summary_"+Exper_nm+".txt", true);
+		
+		TimeUnit.MILLISECONDS.sleep(imageOpeningTimeDelay);
+		img=openSelectedSlices(newImgFile);
+		
+		this.setSharedValue("Zoom Counter", zoomCounter);
+		this.setSharedValue("Table Row Counter", tableRowCounter);
+	}
+	
+	@Override
+	protected void preProcessOffline()throws Exception{
+		//img=ImageOpenerWithBioformats.openImage(currentTable.getFile(curDInd, imgColumnNm, "IMG"));
+		img=openSelectedSlices(currentTable.getFile(curDInd, imgColumnNm, "IMG"));
+	}
+	
+	
+	private ImagePlus openSelectedSlices(File _imageFile)throws Exception{
+		ImporterOptions options = new ImporterOptions();
+		options.setAutoscale(true);
+		options.setId(_imageFile.getAbsolutePath());
+		options.setCBegin(0, targetChannel-1);
+		options.setCEnd(0, targetChannel-1);
+		
+		return BF.openImagePlus(options)[0];
+	}
+	@Override
+	protected boolean runProcessing()throws Exception{
+		
+		
+		
+		
+		this.showDebug(img, "Original Image", false);
+		
+		
+		//new WaitForUserDialog ("Select Shift Point").show();
+
+
+		this.showDebug(img, "Original Image", false);
+
+		//////code from Tischi
+		
+		getEllipsoidParameters(img);
+
+		////
+		
+		halfLength=img.getWidth()/3.0;
+		if(rotation>90)
+			rotation=rotation-180;
+		
+		return true;
+		
+	}
+	
+	private < T extends RealType< T > & NativeType< T > >
+	void getEllipsoidParameters(ImagePlus _image)throws Exception {
+
+
+
+		final DrosophilaRegistrationSettings settings =
+				new DrosophilaRegistrationSettings();
+		settings.onlyComputeEllipsoidParameters = true;
+
+
+		double w=img.getCalibration().pixelWidth/settings.registrationResolution;
+		double h=img.getCalibration().pixelHeight/settings.registrationResolution;
+		double d=img.getCalibration().pixelDepth/settings.registrationResolution;
+
+		
+		RandomAccessibleInterval< T > images =
+				ImageIO.getChannelImages( _image );
+
+		RandomAccessibleInterval< T > image =
+				ImageIO.getChannelImage( images, 0  );
+
+		final DrosophilaSingleChannelRegistration registration = new DrosophilaSingleChannelRegistration( settings, opService );
+
+		final double[] calibration = Utils.getCalibration( _image );
+
+		registration.run( image, calibration );
+		
+		final double[] centre = registration.getElliposidCentreInInputImagePixelUnits();
+		final double[] angles = registration.getElliposidEulerAnglesInDegrees();
+		
+		selectedXPosition = centre[0];
+		selectedYPosition = centre[1];
+		selectedZPosition = centre[2];
+		rotation=-angles[0];
+
+	}
+	
+	@Override
+	protected Overlay createOverlay(){
+		Overlay o=new Overlay();
+		
+		Roi pointRoi=new PointRoi(selectedXPosition, selectedYPosition);
+		pointRoi.setPosition((int)(selectedZPosition+1));
+		o.add(pointRoi);
+		
+		Double angleRadians=rotation/180*Math.PI;
+		Roi lineRoi=new Arrow(selectedXPosition, selectedYPosition, selectedXPosition+halfLength*Math.cos(angleRadians), selectedYPosition-halfLength*Math.sin(angleRadians));
+		lineRoi.setStrokeColor(Color.PINK);
+		lineRoi.setStrokeWidth(1);
+		o.add(lineRoi);
+		
+		return o;
+	}
+	
+	@Override 
+	public void visualise(int _xvis, int _yvis){
+		
+		this.visualiseImg(img, getOverlay(), _xvis, _yvis);
+		if (selectedZPosition!=null)
+			img.setPosition((int)(selectedZPosition+1));
+
+	}
+	
+	
+	@Override
+	public void  postProcessSuccess()throws Exception{
+		
+		ZeissKeys.submitCommandsToMicroscope("trigger2", ""+selectedXPosition,""+selectedYPosition,""+selectedZPosition,""+rotation,"","","","","");
+		
+
+		int tableRowCounter=(int)this.getSharedValue("Table Row Counter");
+		
+		String Exper_nm=(String)getSharedValue("Experiment Name");// newImgFile.getName();
+		File experimentTableFile=new File(currentTable.getRootPath(),"summary_"+Exper_nm+".txt");
+		TableModel experimentTable=new TableModel(experimentTableFile);
+
+		experimentTable.setNumericValue(selectedXPosition, tableRowCounter, "Correction.X");
+		experimentTable.setNumericValue(selectedYPosition, tableRowCounter, "Correction.Y");
+		experimentTable.setNumericValue(selectedZPosition, tableRowCounter, "Focus.Z");
+		experimentTable.setNumericValue(rotation, tableRowCounter, "Rotation");
+
+		experimentTable.writeNewFile("summary_"+Exper_nm+".txt", true);
+		
+		saveRoisForImage(newImgFile,getOverlay().toArray());
+		
+		
+	}
+	
+	@Override
+	public void  postProcessFail()throws Exception{
+		ZeissKeys.submitCommandsToMicroscope("nothing",null,null,null,null,null,null,null,null, "Suitable object is not found");
+		
+		int tableRowCounter=(int)this.getSharedValue("Table Row Counter");
+		
+		String Exper_nm=(String)getSharedValue("Experiment Name");// newImgFile.getName();
+		File experimentTableFile=new File(currentTable.getRootPath(),"summary_"+Exper_nm+".txt");
+		TableModel experimentTable=new TableModel(experimentTableFile);
+
+		experimentTable.setBooleanValue(false, tableRowCounter, "Success");
+		experimentTable.writeNewFile("summary_"+Exper_nm+".txt", true);
+	}
+	
+	protected void postProcessOffline(){
+		try {
+			this.showDebug(img, "Image with overlay", true,getOverlay());
+		}catch (Exception ex){
+			IJ.error("Error during offline visualisation");
+		}
+	}
+
+
+	
+	@Override
+	public ParameterCollection createJobParameters(){
+		ParameterCollection jobCollection=new ParameterCollection();
+		
+		jobCollection.addParameter(KEY_FOCUS_CHANNEL_INDEX,	null, targetChannel, 		ParameterType.INT_PARAMETER);
+		jobCollection.addParameter(KEY_WAIT_IMAGE_OPENING,	null, imageOpeningTimeDelay,ParameterType.INT_PARAMETER);
+		jobCollection.addParameter(KEY_FOCUS_OFFSET,		null, focusOffset,			ParameterType.INT_PARAMETER);
+
+		
+		return jobCollection;
+	}
+
+	@Override
+	public void parseInputParameterValues(ParameterCollection _jobParameterCollection){
+		this.targetChannel=			(Integer)_jobParameterCollection.getParameterValue(KEY_FOCUS_CHANNEL_INDEX);
+		this.imageOpeningTimeDelay=	(Integer)_jobParameterCollection.getParameterValue(KEY_WAIT_IMAGE_OPENING);
+		this.focusOffset=			(Integer)_jobParameterCollection.getParameterValue(KEY_FOCUS_OFFSET);
+
+	}
+	
+	/**
+	 * offline debugging
+	 * @param args unsused
+	 */
+	public static void main(String[] args)throws Exception{
+		// start ImageJ
+		new ImageJ().ui().showUI();
+		
+		String tblPth="C:\\tempDat\\Crocker-lab\\Test_protocol_update_20181109";
+		String tblFnm="summary_test8_m.txt";
+		Job_FocusEmbryoAutoDatasetSplit testJob=new Job_FocusEmbryoAutoDatasetSplit();
+		testJob.initialise(null, "Focus.Image", false);
+		testJob.testJobMicTable(3, tblPth, tblFnm);
+	}
+	
+}

src/main/resources/plugins.config

@@ -11,5 +11,6 @@ Plugins>Auto Mic Tools>Fly Embryo Screen, "Automated selection of multiple embry
 Plugins>Auto Mic Tools>Fly Embryo Screen, "Automated selection of multiple embryos with reflection autofocus", feedback.fly.embryo.jobdistributors.JobDistributor_AutoSelectionMultiple_AFocus
 Plugins>Auto Mic Tools>Fly Embryo Screen, "Automated selection of multiple embryos with reflection autofocus and embryo rotation", feedback.fly.embryo.jobdistributors.JobDistributor_AutoSelectionMultiple_AFocus_Rotation
 Plugins>Auto Mic Tools>Fly Embryo Screen, "Manual selection of multiple embryos with reflection autofocus and embryo rotation", feedback.fly.embryo.jobdistributors.JobDistributor_ManualSelection3DMultiple_AFocus_Rotation
+Plugins>Auto Mic Tools>Fly Embryo Screen, "Manual selection of multiple embryos with reflection autofocus, embryo rotation and split", feedback.fly.embryo.jobdistributors.JobDistributor_ManualSelection3DMultiple_AFocus_Rotation_Split
 Plugins>Auto Mic Tools>Fly Embryo Screen,"-"
 Plugins>Auto Mic Tools>Fly Embryo Screen, "Test segmentation parameters", feedback.fly.embryo.jobtests.Embryo_Selection_Tester

src/test/java/algorithm/tests/FindEmbryoOrientationTischi.java

@@ -25,7 +25,7 @@ public class FindEmbryoOrientationTischi {
 	public static < T extends RealType< T > & NativeType< T > >
 	void main(String[] args) throws Exception{
 		final ImageJ ij = new ImageJ();
-		//ij.ui().showUI();
+		ij.ui().showUI();
 
 		final OpService opService = ij.op();
 
@@ -33,7 +33,8 @@ public class FindEmbryoOrientationTischi {
 		System.out.println(new File(inputPath).exists());			
 
 		final ImagePlus imagePlus = BF.openImagePlus(inputPath)[0];
-
+		imagePlus.show();
+		
 		final DrosophilaRegistrationSettings settings =
 				new DrosophilaRegistrationSettings();
 		settings.onlyComputeEllipsoidParameters = true;
@@ -49,11 +50,17 @@ public class FindEmbryoOrientationTischi {
 		final double[] calibration = Utils.getCalibration( imagePlus );
 
 		registration.run( image, calibration );
+		
+		final double[] centre = registration.getElliposidCentreInInputImagePixelUnits();
+		final double[] angles = registration.getElliposidEulerAnglesInDegrees();
 
-		final EllipsoidMLJ ellipsoidParameters = registration.getEllipsoidParameters();
+		System.out.println(String.format("X:%f; Y: %f; z: %f", centre[0], centre[1], centre[2]));
+		System.out.println(String.format("A1:%f; A2: %f; A3: %f", angles[0], angles[1], angles[2]));
+		
+		//final EllipsoidMLJ ellipsoidParameters = registration.getEllipsoidParameters();
 
-		Logger.log( ellipsoidParameters.toString() );
+		//Logger.log( ellipsoidParameters.toString() );
 
-		final AffineTransform3D alignmentTransform =EllipsoidsMLJ.createAlignmentTransform( ellipsoidParameters );		
+		//final AffineTransform3D alignmentTransform =EllipsoidsMLJ.createAlignmentTransform( ellipsoidParameters );		
 	}
 }

src/test/java/jobdistributors/run/debug/RunManualDistributorRotation.java → src/test/java/jobdistributors/run/debug/RunManualDistributorRotationSplit.java

 package jobdistributors.run.debug;
 
-import feedback.fly.embryo.jobdistributors.JobDistributor_ManualSelection3DMultiple_AFocus_Rotation;
+import feedback.fly.embryo.jobdistributors.JobDistributor_ManualSelection3DMultiple_AFocus_Rotation_Split;
 import ij.IJ;
-import ij.ImageJ;
+import net.imagej.ImageJ;
 
-public class RunManualDistributorRotation {
+public class RunManualDistributorRotationSplit {
 	public static void main(String[] args) {
-		Class<?> clazz = JobDistributor_ManualSelection3DMultiple_AFocus_Rotation.class;
+		Class<?> clazz = JobDistributor_ManualSelection3DMultiple_AFocus_Rotation_Split.class;
 
 		// start ImageJ
-		new ImageJ();
+		ImageJ ij2=new ImageJ();
+		ij2.ui().showUI();
 
 		IJ.runPlugIn(clazz.getName(),"Debug run");
 		//IJ.runPlugIn(clazz.getName(),"");