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Commit 7cba4d6a authored by Aliaksandr Halavatyi's avatar Aliaksandr Halavatyi
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remove obsolete auto selection job

parent 3213af56
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src/main/java/feedback/fly/embryo/jobs/Job_SelectMultipleEmbryosAuto.java deleted 100644 → 0
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package feedback.fly.embryo.jobs;
import java.awt.Color;
import java.awt.geom.Point2D;
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.utils.ArrIndUtils;
import automic.utils.DebugVisualiserSettings;
import automic.utils.roi.ParticleFilterer;
import automic.utils.roi.ROIManipulator2D;
import ij.IJ;
import ij.ImageJ;
import ij.ImagePlus;
import ij.gui.Overlay;
import ij.gui.Roi;
import ij.plugin.Duplicator;
import ij.plugin.filter.MaximumFinder;
import ij.plugin.filter.ParticleAnalyzer;
import ij.plugin.filter.RankFilters;
import ij.plugin.frame.RoiManager;
import ij.process.ImageProcessor;
import loci.plugins.BF;
import loci.plugins.in.ImporterOptions;
public class Job_SelectMultipleEmbryosAuto extends Job_Default{
public static final String KEY_WELL_CHANNEL_INDEX="LZ well (brightfield) channel index";
public static final String KEY_WELL_CHANNEL_THRESHOLD="LZ well (brightfield) channel threshold";
public static final String KEY_EMBRYO_CHANNEL_INDEX="LZ embryo (fluorescence) channel index";
public static final String KEY_EMBRYO_CHANNEL_FILTER_RADIUS="LZ embryo (fluorescence) channel filter radius";
public static final String KEY_EMBRYO_CHANNEL_THRESHOLD="LZ embryo (fluorescence) channel threshold";
public static final String KEY_WATERSHED_TOLERANCE="Watershed tolerance";
public static final String KEY_EMBRYO_MIN_SIZE="Embryo minimal size (pixels)";
public static final String KEY_EMBRYO_MAX_SIZE="Embryo maximal size (pixels)";
public static final String KEY_EMBRYO_MIN_INTENSITY="Embryo minimal intensity";
public static final String KEY_EMBRYO_MAX_INTENSITY="Embryo maximal intensity";
public static final String KEY_EMBRYO_MIN_AR="Embryo minimal aspect ratio";
public static final String KEY_EMBRYO_MAX_AR="Embryo maximal aspect ratio";
public static final String KEY_EMBRYO_MAX_COUNT="Maximal number of embryos from well";
public static final String KEY_WAIT_IMAGE_OPENING="Wait for image opening (milliseconds)";
//private static final Roi nullRoi=null;
protected ImagePlus img=null;
//private Roi selectedPointsRoi;
//private Integer selectedXPosition;
//private Integer selectedYPosition;
private Point2D.Double[] selectedPoints;
private Roi wellRoi;
private Roi[] embryoRois;
private Roi[] selectedEmbryoRois;
//private boolean selectionMade=false;
//private boolean invert_Z;
private int wellBrightFieldChannel=2;
private int wellBrightFieldThreshold=10;
private int embryoFluorChannel=1;
private double embryoFluorFilterRadius=5.0;
private int embryoFluorThreshold=70;
private double watershedTolerance=100.0;
private int embryoMinSize=500;
private int embryoMaxSize=10000;
private double embryoMinIntensity=50.0;
private double embryoMaxIntensity=256.0;
private double embryoMinAR=1.8;
private double embryoMaxAR=10.0;
private int embryoMaxCount=5;
private int imageOpeningTimeDelay=3000;
//private int initialLocationY;
@Override
protected void cleanIterOutput(){
img=null;
selectedPoints=null;
wellRoi=null;
embryoRois=null;
selectedEmbryoRois=null;
}
@Override
protected void preProcessOnline()throws Exception{
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(imageOpeningTimeDelay);
//img=ImageOpenerWithBioformats.openImage(newImgFile);
img=openSelectedSlices(newImgFile);
}
@Override
protected void preProcessOffline()throws Exception{
//img=ImageOpenerWithBioformats.openImage(currentTable.getFile(curDInd, imgColumnNm, "IMG"));
img=openSelectedSlices(newImgFile);
}
protected ImagePlus openSelectedSlices(File _imageFile)throws Exception{
ImporterOptions options = new ImporterOptions();
options.setAutoscale(true);
options.setId(_imageFile.getAbsolutePath());
return BF.openImagePlus(options)[0];
}
@Override
protected boolean runProcessing()throws Exception{
this.showDebug(img, "original image", true);
wellRoi=getWellRoi(new Duplicator().run(img, wellBrightFieldChannel, wellBrightFieldChannel, 1, 1, 1, 1));
if (wellRoi==null)
return false;
identifyEmbryos(new Duplicator().run(img, embryoFluorChannel, embryoFluorChannel, 1, 1, 1, 1));
if (embryoRois==null) return false;
if (embryoRois.length<1) return false;
if (embryoRois.length<=embryoMaxCount){
selectedEmbryoRois=embryoRois;
}
else{
int[] selectedIndexes=ArrIndUtils.getRandomIndexes(embryoRois.length, embryoMaxCount);
selectedEmbryoRois=new Roi[embryoMaxCount];
for (int i=0;i<embryoMaxCount;i++)
selectedEmbryoRois[i]=embryoRois[selectedIndexes[i]];
}
for (Roi r:selectedEmbryoRois)
r.setStrokeColor(Color.cyan);
double x,y;
selectedPoints=new Point2D.Double[selectedEmbryoRois.length];
for (int i=0;i<selectedEmbryoRois.length;i++){
x=selectedEmbryoRois[i].getContourCentroid()[0];
y=selectedEmbryoRois[i].getContourCentroid()[1];
selectedPoints[i]=new Point2D.Double(x, y);
}
return true;
}
private Roi getWellRoi(ImagePlus _2dimage)throws Exception{
IJ.setThreshold(_2dimage, wellBrightFieldThreshold, Double.MAX_VALUE);
RoiManager rm=ROIManipulator2D.getEmptyRm();
ParticleAnalyzer pAnalyzer=new ParticleAnalyzer(ParticleAnalyzer.ADD_TO_MANAGER|ParticleAnalyzer.SHOW_NONE|ParticleAnalyzer.FOUR_CONNECTED,
0,
null,
_2dimage.getWidth()*_2dimage.getHeight()/5, Double.MAX_VALUE, 0.0, 1.0);
pAnalyzer.analyze(_2dimage);
if (rm.getCount()<1)
return null;
Roi[] segmentedRegions=rm.getRoisAsArray();
Roi identifiedWellRoi=ROIManipulator2D.selBiggestRoi(_2dimage, segmentedRegions);
identifiedWellRoi.setStrokeColor(Color.MAGENTA);
this.showDebug(_2dimage, "Well segmentation", false, new Overlay(identifiedWellRoi));
return identifiedWellRoi;
}
private void identifyEmbryos(ImagePlus _embryoImage)throws Exception {
new RankFilters().rank(_embryoImage.getProcessor(), embryoFluorFilterRadius, RankFilters.MEDIAN);
this.showDebug(_embryoImage, "Image for embryo segmentation", true);
ImageProcessor maskProcessor=new MaximumFinder().findMaxima(_embryoImage.getProcessor(),watershedTolerance,embryoFluorThreshold,MaximumFinder.SEGMENTED,false,false);
ImagePlus watershedMaskImage=new ImagePlus("Embryo Mask Image", maskProcessor);
this.showDebug(watershedMaskImage, "Watershed mask", true);
IJ.setThreshold(watershedMaskImage, 125, 255);
RoiManager rm=ROIManipulator2D.getEmptyRm();
ParticleAnalyzer pAnalyzer=new ParticleAnalyzer(ParticleAnalyzer.ADD_TO_MANAGER|ParticleAnalyzer.SHOW_NONE|ParticleAnalyzer.FOUR_CONNECTED|ParticleAnalyzer.EXCLUDE_EDGE_PARTICLES,
0,
null,
embryoMinSize, embryoMaxSize, 0.0, 1.0);
pAnalyzer.analyze(watershedMaskImage);
if (rm.getCount()<1)
return;
Roi[] identifiedRois=rm.getRoisAsArray();
ParticleFilterer embryoFilter=new ParticleFilterer(_embryoImage.getProcessor(), identifiedRois);
embryoFilter.filterInRoi(wellRoi);
embryoFilter.filterThr(ParticleFilterer.MEAN, embryoMinIntensity, embryoMaxIntensity);
embryoFilter.filterThr(ParticleFilterer.ASPECT_RATIO, embryoMinAR, embryoMaxAR);
embryoRois=embryoFilter.getPassedRois();
if (embryoRois==null)
return;
for (Roi r:embryoRois)
r.setStrokeColor(Color.yellow);
this.showDebug(_embryoImage, "Segmented embryos", true,this.createOverlay());
return;
}
@Override
protected Overlay createOverlay(){
Overlay o=new Overlay();
if (wellRoi!=null)
o.add(wellRoi);
if (embryoRois!=null)
for (Roi r:embryoRois){
o.add(r);
}
return o;
}
@Override
public void visualise(int _xvis, int _yvis){
img.setDisplayMode(IJ.COMPOSITE);
this.visualiseImg(img, getOverlay(), _xvis, _yvis);
img.setC(embryoFluorChannel);
}
@Override
public void postProcessSuccess()throws Exception{
//PointRoi saveRoi=null;
//form comma-separated strings with coordinates
String xstr="", ystr="",zstr="";
// submit 3d points in future
for (int i=0;i<selectedEmbryoRois.length;i++){
if (i>0){
xstr+=";";
ystr+=";";
zstr+=";";
}
xstr+=selectedPoints[i].x;
ystr+=selectedPoints[i].y;
zstr+="0";
}
ZeissKeys.submitCommandsToMicroscope("trigger1", xstr,ystr,zstr,"","","","","");
saveRoisForImage(newImgFile, getOverlay().toArray());
//saveRoiForImage(newImgFile,saveRoi);
this.setSharedValue("Zoom Points", selectedPoints);
this.setSharedValue("Zoom Counter", -1);
this.setSharedValue("Selected Embryo Rois", selectedEmbryoRois);
}
@Override
public ParameterCollection createJobParameters(){
ParameterCollection jobCollection=new ParameterCollection();
jobCollection.addParameter(KEY_WELL_CHANNEL_INDEX, null, wellBrightFieldChannel, ParameterType.INT_PARAMETER);
jobCollection.addParameter(KEY_WELL_CHANNEL_THRESHOLD, null, wellBrightFieldThreshold, ParameterType.INT_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_CHANNEL_INDEX, null, embryoFluorChannel, ParameterType.INT_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_CHANNEL_FILTER_RADIUS, null, embryoFluorFilterRadius, ParameterType.DOUBLE_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_CHANNEL_THRESHOLD, null, embryoFluorThreshold, ParameterType.INT_PARAMETER);
jobCollection.addParameter(KEY_WATERSHED_TOLERANCE, null, watershedTolerance, ParameterType.DOUBLE_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_MIN_SIZE, null, embryoMinSize, ParameterType.INT_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_MAX_SIZE, null, embryoMaxSize, ParameterType.INT_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_MIN_INTENSITY, null, embryoMinIntensity, ParameterType.DOUBLE_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_MAX_INTENSITY, null, embryoMaxIntensity, ParameterType.DOUBLE_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_MIN_AR, null, embryoMinAR, ParameterType.DOUBLE_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_MAX_AR, null, embryoMaxAR, ParameterType.DOUBLE_PARAMETER);
jobCollection.addParameter(KEY_EMBRYO_MAX_COUNT,null, 5, ParameterType.INT_PARAMETER);
jobCollection.addParameter(KEY_WAIT_IMAGE_OPENING,null, imageOpeningTimeDelay, ParameterType.INT_PARAMETER);
return jobCollection;
}
@Override
public void parseInputParameterValues(ParameterCollection _jobParameterCollection){
this.wellBrightFieldChannel=(Integer)_jobParameterCollection.getParameterValue(KEY_WELL_CHANNEL_INDEX);
this.wellBrightFieldThreshold=(Integer)_jobParameterCollection.getParameterValue(KEY_WELL_CHANNEL_THRESHOLD);
this.embryoFluorChannel=(Integer)_jobParameterCollection.getParameterValue(KEY_EMBRYO_CHANNEL_INDEX);
this.embryoFluorFilterRadius=(Double)_jobParameterCollection.getParameterValue(KEY_EMBRYO_CHANNEL_FILTER_RADIUS);
this.embryoFluorThreshold=(Integer)_jobParameterCollection.getParameterValue(KEY_EMBRYO_CHANNEL_THRESHOLD);
this.watershedTolerance=(Double)_jobParameterCollection.getParameterValue(KEY_WATERSHED_TOLERANCE);
this.embryoMinSize=(Integer)_jobParameterCollection.getParameterValue(KEY_EMBRYO_MIN_SIZE);
this.embryoMaxSize=(Integer)_jobParameterCollection.getParameterValue(KEY_EMBRYO_MAX_SIZE);
this.embryoMinIntensity=(Double)_jobParameterCollection.getParameterValue(KEY_EMBRYO_MIN_INTENSITY);
this.embryoMaxIntensity=(Double)_jobParameterCollection.getParameterValue(KEY_EMBRYO_MAX_INTENSITY);
this.embryoMinAR=(Double)_jobParameterCollection.getParameterValue(KEY_EMBRYO_MIN_AR);
this.embryoMaxAR=(Double)_jobParameterCollection.getParameterValue(KEY_EMBRYO_MAX_AR);
this.embryoMaxCount=(Integer)_jobParameterCollection.getParameterValue(KEY_EMBRYO_MAX_COUNT);
this.imageOpeningTimeDelay=(Integer)_jobParameterCollection.getParameterValue(KEY_WAIT_IMAGE_OPENING);
}
@Override
protected DebugVisualiserSettings getDebugVisualiserSettings(){
return new DebugVisualiserSettings(-1, 10,10,2);
}
/**
* offline debugging
* @param args unsused
*/
public static void main(String[] args)throws Exception{
// start ImageJ
new ImageJ();
String tblPth="X:\\group\\ALMFstuff\\Aliaksandr\\User_data\\Crocker-fly-feedback\\03082019_march_test";
String tblFnm="summary_test03_.txt";
Job_SelectMultipleEmbryosAuto testJob=new Job_SelectMultipleEmbryosAuto();
testJob.initialise(null, "LZ.Image", false);
testJob.testJobMicTable(0, tblPth, tblFnm);
}
}
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