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Commit c0c4f03d authored by Aliaksandr Halavatyi's avatar Aliaksandr Halavatyi
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Modifying the code to match updates in fly-reg

parent 2a5d5fd0
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pom.xml
View file @ c0c4f03d
...@@ -15,7 +15,7 @@ ...@@ -15,7 +15,7 @@
<groupId>embl.almf</groupId> <groupId>embl.almf</groupId>
<version>1.0.8-SNAPSHOT</version> <version>1.0.9-SNAPSHOT</version>
<name>Fly_Embryo_Feedback</name> <name>Fly_Embryo_Feedback</name>
<inceptionYear>2017</inceptionYear> <inceptionYear>2017</inceptionYear>
...@@ -100,13 +100,13 @@ ...@@ -100,13 +100,13 @@
<dependency> <dependency>
<groupId>embl.almf</groupId> <groupId>embl.almf</groupId>
<artifactId>AutoMicTools_</artifactId> <artifactId>AutoMicTools_</artifactId>
<version>1.1.17-SNAPSHOT</version> <version>1.1.20-SNAPSHOT</version>
</dependency> </dependency>
<dependency> <dependency>
<groupId>de.embl.cba</groupId> <groupId>de.embl.cba</groupId>
<artifactId>fly-reg</artifactId> <artifactId>fly-reg</artifactId>
<version>0.1.1</version> <version>0.1.3-SNAPSHOT</version>
</dependency> </dependency>
</dependencies> </dependencies>
...@@ -172,7 +172,7 @@ ...@@ -172,7 +172,7 @@
<plugin> <plugin>
<groupId>org.apache.maven.plugins</groupId> <groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId> <artifactId>maven-compiler-plugin</artifactId>
<version>3.5.1</version> <version>3.7.0</version>
<configuration> <configuration>
<source>1.8</source> <source>1.8</source>
<target>1.8</target> <target>1.8</target>
......
src/main/java/feedback/fly/embryo/jobs/Job_FocusEmbryoAutoDatasetSplit.java
View file @ c0c4f03d
...@@ -10,9 +10,10 @@ import automic.online.jobs.Job_Default; ...@@ -10,9 +10,10 @@ import automic.online.jobs.Job_Default;
import automic.parameters.ParameterCollection; import automic.parameters.ParameterCollection;
import automic.parameters.ParameterType; import automic.parameters.ParameterType;
import automic.table.TableModel; import automic.table.TableModel;
import automic.geom.Position3DWithRotation;
import de.embl.cba.flyreg.FlyEmbryoNerveCordRegistration; import de.embl.cba.flyreg.FlyEmbryoNerveCordRegistration;
import de.embl.cba.flyreg.FlyEmbryoRegistrationSettings; import de.embl.cba.flyreg.FlyEmbryoRegistrationSettings;
import de.embl.cba.morphometry.Utils;
import ij.IJ; import ij.IJ;
import net.imagej.ImageJ; import net.imagej.ImageJ;
import ij.ImagePlus; import ij.ImagePlus;
...@@ -27,10 +28,12 @@ import ij.process.ImageProcessor; ...@@ -27,10 +28,12 @@ import ij.process.ImageProcessor;
import loci.plugins.BF; import loci.plugins.BF;
import loci.plugins.in.ImporterOptions; import loci.plugins.in.ImporterOptions;
import net.imagej.ops.OpService; import net.imagej.ops.OpService;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.type.NativeType; import net.imglib2.type.NativeType;
import net.imglib2.type.numeric.RealType; import net.imglib2.type.numeric.RealType;
public class Job_FocusEmbryoAutoDatasetSplit extends Job_Default{ public class Job_FocusEmbryoAutoDatasetSplit extends Job_Default{
public static final String KEY_FOCUS_CHANNEL_INDEX="Focus channel index"; public static final String KEY_FOCUS_CHANNEL_INDEX="Focus channel index";
...@@ -40,13 +43,10 @@ public class Job_FocusEmbryoAutoDatasetSplit extends Job_Default{ ...@@ -40,13 +43,10 @@ public class Job_FocusEmbryoAutoDatasetSplit extends Job_Default{
private OpService opService=null; private static OpService opService=null;
private ImagePlus img=null; private ImagePlus img=null;
private Double selectedXPosition; Position3DWithRotation selectedPosition;
private Double selectedYPosition;
private Double selectedZPosition;
private Double rotation;
private Double halfLength; private Double halfLength;
...@@ -61,17 +61,15 @@ public class Job_FocusEmbryoAutoDatasetSplit extends Job_Default{ ...@@ -61,17 +61,15 @@ public class Job_FocusEmbryoAutoDatasetSplit extends Job_Default{
@Override @Override
public void initialise(String _fTag,String _colNm, boolean _visOnline){ public void initialise(String _fTag,String _colNm, boolean _visOnline){
super.initialise(_fTag, _colNm, _visOnline); super.initialise(_fTag, _colNm, _visOnline);
opService=new ImageJ().op(); if(opService==null)
opService=new ImageJ().op();
} }
@Override @Override
protected void cleanIterOutput(){ protected void cleanIterOutput(){
img=null; img=null;
selectedXPosition=null; selectedPosition=null;
selectedYPosition=null;
selectedYPosition=null;
rotation=null;
halfLength=null; halfLength=null;
} }
...@@ -155,61 +153,60 @@ public class Job_FocusEmbryoAutoDatasetSplit extends Job_Default{ ...@@ -155,61 +153,60 @@ public class Job_FocusEmbryoAutoDatasetSplit extends Job_Default{
//////code from Tischi //////code from Tischi
try{ try{
getEllipsoidParameters(imageToProcess,img); selectedPosition=getEllipsoidParameters(imageToProcess,img);
}catch (Exception _ex) { }catch (Exception _ex) {
return false; return false;
} }
//// ////
if (!correctXY) {
selectedPosition.setX(img.getWidth()/2.0);
selectedPosition.setX(img.getHeight()/2.0);
}
halfLength=img.getWidth()/3.0; halfLength=img.getWidth()/3.0;
if(rotation>90) double angle=selectedPosition.getAngle();
rotation=rotation-180; if(angle>90)
selectedPosition.setAngle(angle-180);
return true; return true;
} }
void getEllipsoidParameters(ImagePlus _imageProcess, ImagePlus _imageCalibration)throws Exception { static < T extends RealType< T > & NativeType< T > > Position3DWithRotation getEllipsoidParameters(ImagePlus _imageProcess, ImagePlus _imageCalibration)throws Exception {
final FlyEmbryoRegistrationSettings settings = new FlyEmbryoRegistrationSettings(); final FlyEmbryoRegistrationSettings settings = new FlyEmbryoRegistrationSettings();
settings.onlyComputeEllipsoidParameters = true; settings.onlyComputeEllipsoidParameters = true;
final FlyEmbryoNerveCordRegistration registration = new FlyEmbryoNerveCordRegistration( settings, opService ); final FlyEmbryoNerveCordRegistration<T> registration = new FlyEmbryoNerveCordRegistration<>( settings, opService );
final double[] calibration = Utils.getCalibration( _imageCalibration );
registration.run( _imageProcess,0); registration.run( _imageProcess,0);
final double[] centre = registration.getElliposidCentreInInputImagePixelUnits(); final double[] centre = registration.getElliposidCentreInInputImagePixelUnits();
final double[] angles = registration.getElliposidEulerAnglesInDegrees(); final double[] angles = registration.getElliposidEulerAnglesInDegrees();
if (correctXY) {
selectedXPosition = centre[0];
selectedYPosition = centre[1];
}else { return new Position3DWithRotation(centre[0], centre[1], centre[2], -angles[0]);
selectedXPosition=img.getWidth()/2.0;
selectedYPosition=img.getHeight()/2.0;
}
selectedZPosition = centre[2];
rotation=-angles[0];
} }
@Override @Override
protected Overlay createOverlay(){ protected Overlay createOverlay(){
Overlay o=new Overlay(); Overlay o=new Overlay();
if (selectedXPosition!=null) { if (selectedPosition!=null) {
Roi pointRoi=new PointRoi(selectedXPosition, selectedYPosition); double roiX=selectedPosition.getX();
pointRoi.setPosition((int)(selectedZPosition+1)); double roiY=selectedPosition.getY();
int roiZ=(int)(selectedPosition.getZ()+1);
Roi pointRoi=new PointRoi(roiX, roiY);
pointRoi.setPosition(roiZ);
o.add(pointRoi); o.add(pointRoi);
Double angleRadians=rotation/180*Math.PI; Double angleRadians=selectedPosition.getAngle()/180*Math.PI;
Roi lineRoi=new Arrow(selectedXPosition, selectedYPosition, selectedXPosition+halfLength*Math.cos(angleRadians), selectedYPosition-halfLength*Math.sin(angleRadians)); Roi lineRoi=new Arrow(roiX, roiY, roiX+halfLength*Math.cos(angleRadians), roiY-halfLength*Math.sin(angleRadians));
lineRoi.setStrokeColor(Color.PINK); lineRoi.setStrokeColor(Color.PINK);
lineRoi.setStrokeWidth(1); lineRoi.setStrokeWidth(1);
o.add(lineRoi); o.add(lineRoi);
...@@ -221,8 +218,8 @@ public class Job_FocusEmbryoAutoDatasetSplit extends Job_Default{ ...@@ -221,8 +218,8 @@ public class Job_FocusEmbryoAutoDatasetSplit extends Job_Default{
public void visualise(int _xvis, int _yvis){ public void visualise(int _xvis, int _yvis){
this.visualiseImg(img, getOverlay(), _xvis, _yvis); this.visualiseImg(img, getOverlay(), _xvis, _yvis);
if (selectedZPosition!=null) if (selectedPosition!=null)
img.setPosition((int)(selectedZPosition+1)); img.setPosition((int)(selectedPosition.getZ()+1));
} }
...@@ -230,7 +227,7 @@ public class Job_FocusEmbryoAutoDatasetSplit extends Job_Default{ ...@@ -230,7 +227,7 @@ public class Job_FocusEmbryoAutoDatasetSplit extends Job_Default{
@Override @Override
public void postProcessSuccess()throws Exception{ public void postProcessSuccess()throws Exception{
ZeissKeys.submitCommandsToMicroscope("trigger2", ""+selectedXPosition,""+selectedYPosition,""+selectedZPosition,""+rotation,"","","","",""); ZeissKeys.submitCommandsToMicroscope("trigger2", ""+selectedPosition.getX(),""+selectedPosition.getY(),""+selectedPosition.getZ(),""+selectedPosition.getAngle(),"","","","","");
int tableRowCounter=(int)this.getSharedValue("Table Row Counter"); int tableRowCounter=(int)this.getSharedValue("Table Row Counter");
...@@ -239,10 +236,10 @@ public class Job_FocusEmbryoAutoDatasetSplit extends Job_Default{ ...@@ -239,10 +236,10 @@ public class Job_FocusEmbryoAutoDatasetSplit extends Job_Default{
File experimentTableFile=new File(currentTable.getRootPath(),"summary_"+Exper_nm+".txt"); File experimentTableFile=new File(currentTable.getRootPath(),"summary_"+Exper_nm+".txt");
TableModel experimentTable=new TableModel(experimentTableFile); TableModel experimentTable=new TableModel(experimentTableFile);
experimentTable.setNumericValue(selectedXPosition, tableRowCounter, "Correction.X"); experimentTable.setNumericValue(selectedPosition.getX(), tableRowCounter, "Correction.X");
experimentTable.setNumericValue(selectedYPosition, tableRowCounter, "Correction.Y"); experimentTable.setNumericValue(selectedPosition.getY(), tableRowCounter, "Correction.Y");
experimentTable.setNumericValue(selectedZPosition, tableRowCounter, "Focus.Z"); experimentTable.setNumericValue(selectedPosition.getZ(), tableRowCounter, "Focus.Z");
experimentTable.setNumericValue(rotation, tableRowCounter, "Rotation"); experimentTable.setNumericValue(selectedPosition.getAngle(), tableRowCounter, "Rotation");
experimentTable.writeNewFile("summary_"+Exper_nm+".txt", true); experimentTable.writeNewFile("summary_"+Exper_nm+".txt", true);
......
src/main/java/feedback/fly/embryo/jobs/Job_SelectMultipleEmbryosAuto.java
View file @ c0c4f03d
...@@ -11,14 +11,12 @@ import automic.parameters.ParameterCollection; ...@@ -11,14 +11,12 @@ import automic.parameters.ParameterCollection;
import automic.parameters.ParameterType; import automic.parameters.ParameterType;
import automic.utils.ArrIndUtils; import automic.utils.ArrIndUtils;
import automic.utils.DebugVisualiserSettings; import automic.utils.DebugVisualiserSettings;
import automic.utils.FileUtils;
import automic.utils.roi.ParticleFilterer; import automic.utils.roi.ParticleFilterer;
import automic.utils.roi.ROIManipulator2D; import automic.utils.roi.ROIManipulator2D;
import ij.IJ; import ij.IJ;
import ij.ImageJ; import ij.ImageJ;
import ij.ImagePlus; import ij.ImagePlus;
import ij.gui.Overlay; import ij.gui.Overlay;
import ij.gui.PointRoi;
import ij.gui.Roi; import ij.gui.Roi;
import ij.plugin.Duplicator; import ij.plugin.Duplicator;
import ij.plugin.ZProjector; import ij.plugin.ZProjector;
......
src/test/java/algorithm/tests/FindEmbryoOrientationTischi.java
View file @ c0c4f03d
...@@ -6,7 +6,6 @@ import java.io.File; ...@@ -6,7 +6,6 @@ import java.io.File;
import de.embl.cba.flyreg.FlyEmbryoNerveCordRegistration; import de.embl.cba.flyreg.FlyEmbryoNerveCordRegistration;
import de.embl.cba.flyreg.FlyEmbryoRegistrationSettings; import de.embl.cba.flyreg.FlyEmbryoRegistrationSettings;
//import de.embl.cba.flyreg.FlyEmbryoSingleChannelRegistration;
import ij.ImagePlus; import ij.ImagePlus;
import loci.plugins.BF; import loci.plugins.BF;
...@@ -33,7 +32,7 @@ public class FindEmbryoOrientationTischi { ...@@ -33,7 +32,7 @@ public class FindEmbryoOrientationTischi {
final FlyEmbryoRegistrationSettings settings = new FlyEmbryoRegistrationSettings(); final FlyEmbryoRegistrationSettings settings = new FlyEmbryoRegistrationSettings();
settings.onlyComputeEllipsoidParameters = true; settings.onlyComputeEllipsoidParameters = true;
final FlyEmbryoNerveCordRegistration registration = new FlyEmbryoNerveCordRegistration( settings, opService ); final FlyEmbryoNerveCordRegistration<T> registration = new FlyEmbryoNerveCordRegistration<>( settings, opService );
registration.run(imagePlus, 0); registration.run(imagePlus, 0);
......
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