refactor: changed from observable Properties to raw values where binding was unnecessary

src/main/java/fr/pasteur/ida/zellige/gui/interactor/SelectionInteractor.java

@@ -31,7 +31,7 @@ public class SelectionInteractor
 
     public void runOtsuTask()
     {
-        OtsuThresholdingTask otsuTask = new OtsuThresholdingTask( model.pretreatedImgProperty(), model.imagesProperty().get().getOtsuImg(), model.otsuProperty().getValue().intValue() );
+        OtsuThresholdingTask otsuTask = new OtsuThresholdingTask( model.pretreatedImgProperty().get(), model.imagesProperty().get().getOtsuImg(), model.otsuProperty().getValue().intValue() );
         otsuTask.setOnSucceeded( workerStateEvent ->
                 model.selectedOtsuProperty().setValue( otsuTask.getValue() ) );
 //        otsuTask.setOnFailed( workerStateEvent -> LOGGER.debug( "Otsu classification has failed." ) );
@@ -40,14 +40,14 @@ public class SelectionInteractor
 
     public void runInterClassification()
     {
-        InterClassificationTask interClassificationTask = new InterClassificationTask( model.selectedAmplitudeProperty(), model.selectedOtsuProperty() );
+        InterClassificationTask interClassificationTask = new InterClassificationTask( model.selectedAmplitudeProperty().get(), model.selectedOtsuProperty().get() );
         interClassificationTask.setOnSucceeded( event -> model.interClassifiedImageProperty().setValue( interClassificationTask.getValue() ) );
         interClassificationTask.start();
     }
 
     public void runIslandSearch()
     {
-        IslandSearchTask islandSearchTask = new IslandSearchTask( model.interClassifiedImageProperty(), model.islandProperty() );
+        IslandSearchTask islandSearchTask = new IslandSearchTask( model.interClassifiedImageProperty().get(), model.islandProperty().get() );
         islandSearchTask.setOnSucceeded( workerStateEvent ->
                 model.islandSearchImageProperty().setValue( islandSearchTask.getValue() ) );
 //        islandSearchTask.setOnFailed( workerStateEvent -> LOGGER.debug( "FAILED" ) );
@@ -56,7 +56,10 @@ public class SelectionInteractor
 
     public void runSmoothing()
     {
-        SmoothingTask smoothingTask = new SmoothingTask( model.islandSearchImageProperty(), model.xyBlurProperty(), model.zBlurProperty() );
+        SmoothingTask smoothingTask = new SmoothingTask(
+                model.islandSearchImageProperty().get(),
+                model.xyBlurProperty().get(),
+                model.zBlurProperty().get() );
         smoothingTask.setOnSucceeded( event ->
                 model.selectedPixelsProperty().setValue( smoothingTask.getValue() ) );
         smoothingTask.start();

src/main/java/fr/pasteur/ida/zellige/gui/task/InterClassificationTask.java

@@ -29,7 +29,6 @@
 package fr.pasteur.ida.zellige.gui.task;
 
 import fr.pasteur.ida.zellige.steps.selection.classification.Classification;
-import javafx.beans.property.SimpleObjectProperty;
 import net.imglib2.img.Img;
 import net.imglib2.type.logic.BitType;
 import org.slf4j.Logger;
@@ -41,10 +40,10 @@ public class InterClassificationTask extends AbstractTask< Img< BitType > >
 {
 
     private final static Logger LOGGER = LoggerFactory.getLogger( InterClassificationTask.class );
-    private final SimpleObjectProperty< Img< BitType > > selectedAmplitude;
-    private final SimpleObjectProperty< Img< BitType > > selectedOtsu;
+    private final  Img< BitType >selectedAmplitude;
+    private final  Img< BitType >selectedOtsu;
 
-    public InterClassificationTask( SimpleObjectProperty< Img< BitType > > selectedAmplitude, SimpleObjectProperty< Img< BitType > > selectedOtsu )
+    public InterClassificationTask( Img< BitType > selectedAmplitude, Img< BitType > selectedOtsu )
     {
         this.selectedAmplitude = selectedAmplitude;
         this.selectedOtsu = selectedOtsu;
@@ -56,7 +55,7 @@ public class InterClassificationTask extends AbstractTask< Img< BitType > >
     {
 
         LOGGER.info(GUI_MARKER, "Computing inter-classification..." );
-        return Classification.interClassification( selectedAmplitude.getValue(), selectedAmplitude.getValue().factory(), selectedOtsu.getValue() );
+        return Classification.interClassification( selectedAmplitude, selectedAmplitude.factory(), selectedOtsu );
     }
 
 

src/main/java/fr/pasteur/ida/zellige/gui/task/IslandSearchTask.java

@@ -29,8 +29,6 @@
 package fr.pasteur.ida.zellige.gui.task;
 
 import fr.pasteur.ida.zellige.steps.selection.postTreatment.PostTreatment;
-import javafx.beans.property.IntegerProperty;
-import javafx.beans.property.SimpleObjectProperty;
 import net.imglib2.img.Img;
 import net.imglib2.type.logic.BitType;
 import org.slf4j.Logger;
@@ -42,10 +40,10 @@ public class IslandSearchTask extends AbstractTask< Img< BitType > >
 {
 
     private final static Logger LOGGER = LoggerFactory.getLogger( IslandSearchTask.class );
-    private final SimpleObjectProperty< Img< BitType > > image;
-    private final IntegerProperty islandSize;
+    private final  Img< BitType >  image;
+    private final int islandSize;
 
-    public IslandSearchTask( SimpleObjectProperty< Img< BitType > > image, IntegerProperty islandSize )
+    public IslandSearchTask( Img< BitType > image, int islandSize )
     {
         this.image = image;
         this.islandSize = islandSize;
@@ -55,7 +53,7 @@ public class IslandSearchTask extends AbstractTask< Img< BitType > >
     protected Img< BitType > call()
     {
         LOGGER.info( GUI_MARKER,"Computing Island Search..." );
-        Img< BitType > img = PostTreatment.runIslandSearch( image.getValue(), islandSize.intValue() );
+        Img< BitType > img = PostTreatment.runIslandSearch( image, islandSize );
         LOGGER.info( GUI_MARKER,"Task's end." );
         return img;
 //        return iSImage;

src/main/java/fr/pasteur/ida/zellige/gui/task/OtsuThresholdingTask.java

@@ -29,7 +29,6 @@
 package fr.pasteur.ida.zellige.gui.task;
 
 import fr.pasteur.ida.zellige.steps.selection.classification.OtsuClassification;
-import javafx.beans.property.SimpleObjectProperty;
 import net.imglib2.img.Img;
 import net.imglib2.type.logic.BitType;
 import net.imglib2.type.numeric.real.FloatType;
@@ -42,12 +41,12 @@ public class OtsuThresholdingTask extends AbstractTask< Img< BitType > >
 {
 
     private final static Logger LOGGER = LoggerFactory.getLogger( OtsuThresholdingTask.class );
-    private final SimpleObjectProperty< Img< FloatType > > pretreatedImage;
+    private final Img< FloatType >  pretreatedImage;
     private final  Img<FloatType> input;
     private final int otsuThreshold;
 
 
-    public OtsuThresholdingTask( SimpleObjectProperty< Img< FloatType > > pretreatedImage, Img<FloatType> input, int otsuThreshold )
+    public OtsuThresholdingTask( Img< FloatType > pretreatedImage, Img<FloatType> input, int otsuThreshold )
     {
         this.pretreatedImage = pretreatedImage;
         this.input = input;
@@ -58,7 +57,7 @@ public class OtsuThresholdingTask extends AbstractTask< Img< BitType > >
     protected Img< BitType > call()
     {
         LOGGER.info( GUI_MARKER,"Computing otsu thresholding..." );
-        Img< BitType > output = OtsuClassification.applyLocalThreshold( pretreatedImage.getValue(), input, otsuThreshold );
+        Img< BitType > output = OtsuClassification.applyLocalThreshold( pretreatedImage, input, otsuThreshold );
         LOGGER.info( GUI_MARKER,"Amplitude thresholds computed..." );
         return  output;
     }

src/main/java/fr/pasteur/ida/zellige/gui/task/SmoothingTask.java

@@ -29,8 +29,6 @@
 package fr.pasteur.ida.zellige.gui.task;
 
 import fr.pasteur.ida.zellige.steps.selection.postTreatment.PostTreatment;
-import javafx.beans.property.IntegerProperty;
-import javafx.beans.property.SimpleObjectProperty;
 import net.imglib2.img.Img;
 import net.imglib2.type.logic.BitType;
 import net.imglib2.type.numeric.real.FloatType;
@@ -43,11 +41,11 @@ public class SmoothingTask extends AbstractTask<Img < FloatType >>
 {
 
     private final static Logger LOGGER = LoggerFactory.getLogger( SmoothingTask.class );
-    private final SimpleObjectProperty< Img< BitType > > islandSearchImage;
-    private final IntegerProperty sigmaXY;
-    private final IntegerProperty sigmaZ;
+    private final  Img< BitType >  islandSearchImage;
+    private final int sigmaXY;
+    private final int sigmaZ;
 
-    public SmoothingTask( SimpleObjectProperty< Img< BitType > > islandSearchImage, IntegerProperty sigmaXY, IntegerProperty sigmaZ )
+    public SmoothingTask( Img< BitType > islandSearchImage, int sigmaXY, int sigmaZ )
     {
         this.islandSearchImage = islandSearchImage;
         this.sigmaXY = sigmaXY;
@@ -58,6 +56,6 @@ public class SmoothingTask extends AbstractTask<Img < FloatType >>
     protected Img<FloatType> call() throws Exception
     {
         LOGGER.info( GUI_MARKER,"Computing first smoothing..." );
-        return PostTreatment.runSmoothing( islandSearchImage.getValue(), sigmaXY.intValue(), sigmaZ.intValue() );
+        return PostTreatment.runSmoothing( islandSearchImage, sigmaXY, sigmaZ );
     }
 }