master to 25-multithreads-heavy-tasks · IdA Public / Zellige-core

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pom.xml

+13 −6

Original line number	Diff line number	Diff line
		@@ -6,7 +6,8 @@
		<parent>
		<groupId>org.scijava</groupId>
		<artifactId>pom-scijava</artifactId>
		<version>31.1.0</version>
		<version>39.0.0</version>
		<relativePath />
		</parent>

		<groupId>org.example</groupId>
		@@ -48,7 +49,13 @@
		</repository>
		</repositories>


		<build>
		<resources>
		<resource>
		<directory>src/main/resources</directory>
		</resource>
		</resources>
		<plugins>
		<plugin>
		<groupId>org.apache.maven.plugins</groupId>
		@@ -124,11 +131,11 @@
		<artifactId>imagej-legacy</artifactId>
		</dependency>

		<!-- https://mvnrepository.com/artifact/net.imglib2/imglib2-script -->
		<dependency>
		<groupId>net.imglib2</groupId>
		<artifactId>imglib2-script</artifactId>
		</dependency>
		<!-- <!– https://mvnrepository.com/artifact/net.imglib2/imglib2-script –>-->
		<!-- <dependency>-->
		<!-- <groupId>net.imglib2</groupId>-->
		<!-- <artifactId>imglib2-script</artifactId>-->
		<!-- </dependency>-->

		<!-- https://mvnrepository.com/artifact/net.imglib2/imglib2 -->
		<dependency>

src/main/java/fr/pasteur/ida/zellige/Main.java

+37 −106

Original line number	Diff line number	Diff line
		@@ -29,23 +29,49 @@
		package fr.pasteur.ida.zellige;


		import ch.qos.logback.classic.Level;
		import ch.qos.logback.classic.LoggerContext;
		import ch.qos.logback.classic.encoder.PatternLayoutEncoder;
		import ch.qos.logback.classic.spi.ILoggingEvent;
		import ch.qos.logback.core.FileAppender;
		import fr.pasteur.ida.zellige.element.ReferenceSurface;
		import fr.pasteur.ida.zellige.steps.construction.Construction;
		import fr.pasteur.ida.zellige.steps.construction.rounds.ConstructionParameters;
		import fr.pasteur.ida.zellige.steps.projection.DisplayParameters;
		import fr.pasteur.ida.zellige.steps.projection.ProjectionParameters;
		import fr.pasteur.ida.zellige.steps.projection.ReferenceSurfaceProjection;
		import fr.pasteur.ida.zellige.steps.selection.Selection;
		import fr.pasteur.ida.zellige.steps.selection.classification.ClassificationParameters;
		import fr.pasteur.ida.zellige.steps.selection.postTreatment.PostTreatmentParameters;
		import fr.pasteur.ida.zellige.steps.selection.pretreatment.PretreatmentParameters;
		import ij.IJ;
		import ij.ImageJ;
		import io.scif.img.IO;
		import io.scif.img.SCIFIOImgPlus;
		import fr.pasteur.ida.zellige.steps.selection.util.ArgumentCheck;
		import io.scif.img.ImgSaver;
		import net.imagej.Dataset;
		import net.imagej.ImageJ;
		import net.imagej.ImgPlus;
		import net.imglib2.RandomAccessibleInterval;
		import net.imglib2.display.ColorTable;
		import net.imglib2.img.Img;
		import net.imglib2.img.display.imagej.ImageJFunctions;
		import net.imglib2.type.NativeType;
		import net.imglib2.type.numeric.RealType;
		import net.imglib2.type.numeric.integer.UnsignedShortType;
		import net.imglib2.type.numeric.real.FloatType;
		import net.imglib2.view.Views;
		import org.apache.commons.io.FilenameUtils;
		import org.apache.commons.text.RandomStringGenerator;
		import org.slf4j.Logger;
		import org.slf4j.LoggerFactory;

		import java.awt.*;
		import java.nio.file.Files;
		import java.nio.file.Path;
		import java.nio.file.Paths;
		import java.util.ArrayList;
		import java.util.Arrays;
		import java.util.List;
		import java.util.stream.Collectors;
		import java.util.stream.Stream;

		import static fr.pasteur.ida.zellige.utils.Util.create4dimImage;


		/**
		@@ -54,108 +80,13 @@ import java.awt.*;
		public class Main
		{

		private final static Logger LOGGER = LoggerFactory.getLogger( Main.class );

		@SuppressWarnings( "unchecked" )
		public static < T extends RealType< T > & NativeType< T > > void main( String[] args ) throws Exception
		{
		// Launch ImageJ.
		ImageJ ij = new ImageJ();


		// Input of the image.
		final String imagePath =// "C:\\Users\\ctrebeau\\Desktop\\Zellige analysis\\files\\SNR\\snr_000\\multiSurfaces\\phantoms_snr0.mat.tif";
		args[ 0 ]; /* The image path goes here !!!! */
		LOGGER.debug( imagePath );
		/* JY version for opening files. */
		final SCIFIOImgPlus< ? > imgPlus = IO.openAll( imagePath ).get( 0 );

		final Img< T > stackImage = ( Img< T > ) imgPlus.getImg();


		/* User Parameters AKA arguments to run the program*/
		int amplitude = Integer.parseInt( args[ 1 ] );
		int otsu = Integer.parseInt( args[ 2 ] );
		int islandSize = Integer.parseInt( args[ 3 ] );
		int connexity = Integer.parseInt( args[ 4 ] );
		double sigmaXY = Double.parseDouble( args[ 5 ] );
		double sigmaZ = Double.parseDouble( args[ 6 ] );
		double startingOsSize1 = Double.parseDouble( args[ 7 ] );
		int overlap1 = Integer.parseInt( args[ 8 ] );
		double connexityRate1 = Double.parseDouble( args[ 9 ] );
		double startingOsSize2 = Double.parseDouble( args[ 10 ] );
		int overlap2 = Integer.parseInt( args[ 11 ] );
		double connexityRate2 = Double.parseDouble( args[ 12 ] );
		double surfaceMinSizeFactor = Double.parseDouble( args[ 13 ] );
		int delta = Integer.parseInt( args[ 14 ] );
		/* End of parameters. */


		// Fixed parameters for now...
		String filter = "GaussianBlur";
		double filterParameter = 2;


		/* Print parameters.*/
		LOGGER.debug( "Input image : " + imagePath );
		LOGGER.debug( "filter : " + filter );
		LOGGER.debug( "filter parameter : " + filterParameter );
		LOGGER.debug( "amplitude : " + amplitude );
		LOGGER.debug( "threshold : " + otsu );
		LOGGER.debug( "connexity : " + connexity );
		LOGGER.debug( "island size : " + islandSize );
		LOGGER.debug( "sigmaXY : " + sigmaXY );
		LOGGER.debug( "sigmaZ : " + sigmaZ );
		LOGGER.debug( "starting os size1 : " + startingOsSize1 );
		LOGGER.debug( "overlap1 :" + overlap1 );
		LOGGER.debug( "connexityRate1 :" + connexityRate1 );
		LOGGER.debug( "starting os size2 : " + startingOsSize2 );
		LOGGER.debug( "overlap2 :" + overlap2 );
		LOGGER.debug( "connexityRate2 :" + connexityRate2 );
		LOGGER.debug( "surface Minimum size factor : " + surfaceMinSizeFactor );
		LOGGER.debug( "delta : " + delta );
		LOGGER.debug( System.lineSeparator() );
		/* End of Print parameters.*/

		PretreatmentParameters pretreatmentParameters = new PretreatmentParameters( filter, filterParameter );
		ClassificationParameters classificationParameters = new ClassificationParameters( amplitude, otsu );
		PostTreatmentParameters postTreatmentParameters = new PostTreatmentParameters( sigmaXY, sigmaZ, islandSize, connexity );
		ProjectionParameters projectionParameters = new ProjectionParameters( delta, "MIP" );// no other method implemented yet.
		ConstructionParameters[] constructionParameters = new ConstructionParameters[]{
		new ConstructionParameters( startingOsSize1, overlap1, connexityRate1, surfaceMinSizeFactor ),
		new ConstructionParameters( startingOsSize2, overlap2, connexityRate2, surfaceMinSizeFactor ) };


		DisplayParameters displayParameters = new DisplayParameters(
		true,
		true,
		true,
		true,
		true, true );
		IJ.log( "Type: " + imgPlus.firstElement().getClass().toGenericString() );

		if ( stackImage.numDimensions() == 3 )// Is it a stack ?
		{
		ReferenceSurfaceExtraction< T > rse = new ReferenceSurfaceExtraction<>
		( stackImage, stackImage.factory() );
		rse.select( pretreatmentParameters, classificationParameters, postTreatmentParameters );
		rse.construct( constructionParameters );
		rse.project( projectionParameters, displayParameters );
		if ( ! GraphicsEnvironment.isHeadless() )
		{
		try
		{
		rse.project( projectionParameters, displayParameters );
		}
		catch ( Exception e )
		{
		LOGGER.debug( e.getMessage() );
		}
		}
		}
		else
		public static < T extends RealType< T > & NativeType< T > > void main( String [] args ) throws Exception
		{
		LOGGER.debug( " This image has to be a z-stack ! " );
		}
		String CSV_FILE ="doc/test.csv";
		ReferenceSurfaceExtraction.run( CSV_FILE );
		}

		}

src/main/java/fr/pasteur/ida/zellige/ReferenceSurfaceExtraction.java

+288 −47

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src/main/java/fr/pasteur/ida/zellige/command/Zellige.java

+3 −2

Original line number	Diff line number	Diff line
		@@ -50,18 +50,19 @@ public class Zellige extends ContextCommand
		.getPath( "" )
		.toAbsolutePath()
		.toString();
		// String imageFilePath = "C:\\Users\\ctrebeau\\Desktop\\channel_test.tif";
		String imageFilePath = "doc/Mouche.tif";

		// Launch ImageJ.
		ImageJ ij = new ImageJ();
		ij.launch( args );

		// Load the image.
		Object obj = ij.io().open( new File( currentFolder, imageFilePath ).getAbsolutePath() );
		Object obj = ij.io().open( new File( imageFilePath ).getAbsolutePath() );

		// Display it.
		ij.ui().show( obj );


		ij.command().run( Zellige.class, true );
		}

src/main/java/fr/pasteur/ida/zellige/element/Projection.java

+26 −29

Original line number	Diff line number	Diff line
		@@ -30,67 +30,64 @@ package fr.pasteur.ida.zellige.element;

		import net.imglib2.img.Img;
		import net.imglib2.type.NativeType;
		import net.imglib2.type.logic.BitType;
		import net.imglib2.type.numeric.RealType;
		import net.imglib2.type.numeric.integer.UnsignedShortType;

		public class Projection< T extends RealType< T > & NativeType< T > >
		{
		private final int offset;
		private final int deltaZ;
		private String method;
		private final ReferenceSurface<T> referenceSurface;
		private Img< T > projection;
		private Img< UnsignedShortType > extractedHeightMap;
		private Img< T > segmentedSurface;
		private Img< T > reduced3DSpace;
		private Img< BitType > segmentedSurfaceMask;
		private int index;
		private Img<T> subVolume;


		public Img< T > getSegmentedSurface()
		public Projection( int offset, int deltaZ, String method, ReferenceSurface< T > referenceSurface )
		{
		return segmentedSurface;
		this.offset = offset;
		this.deltaZ = deltaZ;
		this.method = method;
		this.referenceSurface = referenceSurface;
		}

		public void setSegmentedSurface( Img< T > segmentedSurface )
		public Img< T > get()
		{
		this.segmentedSurface = segmentedSurface;
		return projection;
		}

		public Img< UnsignedShortType > getExtractedHeightMap()
		public void setProjection( Img< T > projection )
		{
		return extractedHeightMap;
		this.projection = projection;
		}

		public void setExtractedHeightMap( Img< UnsignedShortType > extractedHeightMap )
		public Img< T > getSubVolume()
		{
		this.extractedHeightMap = extractedHeightMap;
		return subVolume;
		}

		public Img< T > get()
		public int getOffset()
		{
		return projection;
		return offset;
		}

		public void setProjection( Img< T > projection )
		public int getDeltaZ()
		{
		this.projection = projection;
		return deltaZ;
		}

		public Img< T > getReduced3DSpace()
		public String getMethod()
		{
		return reduced3DSpace;
		return method;
		}

		public void setReduced3DSpace( Img< T > reduced3DSpace )
		public void setSubVolume( Img< T > subVolume )
		{
		this.reduced3DSpace = reduced3DSpace;
		this.subVolume = subVolume;
		}

		public Img< BitType > getSegmentedSurfaceMask()
		public void setMethod( String method )
		{
		return segmentedSurfaceMask;
		this.method = method;
		}

		public void setSegmentedSurfaceMask( Img< BitType > segmentedSurfaceMask )
		{
		this.segmentedSurfaceMask = segmentedSurfaceMask;
		}
		}

src/main/java/fr/pasteur/ida/zellige/element/ReferenceSurface.java

+35 −8

Original line number	Diff line number	Diff line
		@@ -28,6 +28,7 @@
		*/
		package fr.pasteur.ida.zellige.element;

		import net.imglib2.RandomAccess;
		import net.imglib2.RandomAccessibleInterval;
		import net.imglib2.img.Img;
		import net.imglib2.img.ImgFactory;
		@@ -35,14 +36,18 @@ import net.imglib2.type.NativeType;
		import net.imglib2.type.numeric.RealType;
		import net.imglib2.type.numeric.integer.UnsignedShortType;

		import static fr.pasteur.ida.zellige.steps.Utils.setPositionAndGet;

		public class ReferenceSurface< T extends RealType< T > & NativeType< T > >
		{
		private final RandomAccessibleInterval< T > input;
		private final ImgFactory< T > factory;
		private final Img< UnsignedShortType > zMap;
		private final int index;
		private Projection< T > projection;
		private final String name;


		private final Img <T> rawProjection;

		public ReferenceSurface( RandomAccessibleInterval< T > input,
		ImgFactory< T > factory, Img< UnsignedShortType > zMap, int index )
		@@ -50,13 +55,35 @@ public class ReferenceSurface< T extends RealType< T > & NativeType< T > >
		this.input = input;
		this.factory = factory;
		this.zMap = zMap;
		this.projection = new Projection<>();
		this.rawProjection = factory.create(zMap);
		this.index = index;
		this.name = "Reference Surface n°" + (index + 1);
		setRawProjection();
		}

		public Projection< T > getProjection()
		/**
		* Creates the raw height map projection
		*/
		private void setRawProjection()
		{
		RandomAccess<T> projectionAccess = rawProjection.randomAccess();
		RandomAccess< UnsignedShortType > zMapAccess = zMap.randomAccess();
		RandomAccess <T > inputAccess = input.randomAccess();
		for ( int x = 0; x < zMap.dimension (0 ); x++ )
		{
		return projection;
		for ( int y = 0; y <zMap.dimension (1 ); y++ )
		{
		// Z value on Height Map
		int z = setPositionAndGet( zMapAccess, x, y ).getInteger();
		if( z > 0 )
		{
		// pixel value on input
		T value = setPositionAndGet( inputAccess, x, y, z - 1 );
		// Set value on projection
		setPositionAndGet( projectionAccess, x, y ).set( value );
		}
		}
		}
		}

		public RandomAccessibleInterval< T > getInput()
		@@ -74,14 +101,14 @@ public class ReferenceSurface< T extends RealType< T > & NativeType< T > >
		return zMap;
		}

		public int getIndex()
		public String getName()
		{
		return index;
		return name;
		}

		public void init()
		public int getIndex()
		{
		this.projection = new Projection<>();
		return index;
		}
		}

src/main/java/fr/pasteur/ida/zellige/element/Surface.java

+0 −37

Original line number	Diff line number	Diff line
		@@ -149,43 +149,6 @@ public class Surface
		return inCommon / ( double ) count;
		}

		public boolean isTheSameSurfaceAs( Surface other )
		{
		for ( int i = 0; i <= this.getHeight() - 1; i++ )
		{
		SurfaceLine refLine = this.get( i );
		if ( refLine != null )
		{
		SurfaceLine toTest = other.get( i );
		if ( toTest != null )
		{

		for ( int j = 0; j < refLine.getLength(); j++ )
		{
		Pixels refPixels = refLine.get( j );
		if ( refPixels != null )
		{
		Pixels pixelsToTest = toTest.get( j );
		if ( pixelsToTest != null )
		{
		// return false;
		// }
		if ( ! refPixels.equals( pixelsToTest ) )
		{
		return false;
		}
		}
		}
		}
		}

		}

		}
		return true;
		}


		/**
		* Checks if this object shares a majority of {@link Pixels} with another {@link Surface} object.
		*

src/main/java/fr/pasteur/ida/zellige/element/ose/AbstractOSE.java

+1 −5

Original line number	Diff line number	Diff line
		@@ -36,9 +36,7 @@ import java.util.ArrayList;
		public abstract class AbstractOSE extends ArrayList< Coordinate >
		{

		/* Not necessary for the program.*/
		private final OSEStartingStatus startingStatus;
		/-------------/

		/**
		* The visited status for the 1D and 2D reconstructions.
		@@ -62,10 +60,8 @@ public abstract class AbstractOSE extends ArrayList< Coordinate >
		*/
		public void set()
		{
		Integer j = startingStatus.get( this.size() );
		startingStatus.put( this.size(), ( j == null ) ? 1 : j + 1 );
		startingStatus.compute( this.size(), ( k, j ) -> ( j == null ) ? 1 : j + 1 );
		startingStatus.setOSCount();

		}

		/**

src/main/java/fr/pasteur/ida/zellige/element/ose/OSEList.java

+11 −1

Original line number	Diff line number	Diff line
		@@ -37,7 +37,6 @@ import java.util.Collection;
		public class OSEList extends ArrayList< AbstractOSE >
		{


		public OSEList()
		{
		}
		@@ -66,6 +65,10 @@ public class OSEList extends ArrayList< AbstractOSE >
		return add;
		}

		/**
		*
		* @return the size of the OSE list
		*/
		public int getSize()
		{
		int size = 0;
		@@ -76,6 +79,9 @@ public class OSEList extends ArrayList< AbstractOSE >
		return size;
		}

		/**
		* Resets to false the visited status
		*/
		public void reset()
		{
		for ( AbstractOSE os : this )
		@@ -84,6 +90,10 @@ public class OSEList extends ArrayList< AbstractOSE >
		}
		}

		/**
		*
		* @return true if the OSE list contains a starting OSE
		*/
		public boolean containsAStart()
		{
		for ( AbstractOSE os : this )

src/main/java/fr/pasteur/ida/zellige/element/surfaceLine/SurfaceLine.java

+8 −7

Original line number	Diff line number	Diff line
		@@ -75,13 +75,14 @@ public abstract class SurfaceLine
		set( os );
		}


		public SurfaceLine( AbstractOSE os, int size )
		{
		this.dimension = new Pixels[ size] ;
		set( os );
		}

		/**
		*
		* @param os
		* @param overlap
		* @param connexity
		* @param surfaceLine
		* @return
		*/
		public SurfaceLine match2( AbstractOSE os, int overlap, double connexity, SurfaceLine surfaceLine )
		{
		int match = 0;

src/main/java/fr/pasteur/ida/zellige/element/surfaceLine/SurfaceLineX.java

+9 −8

Original line number	Diff line number	Diff line
		@@ -44,6 +44,15 @@ public class SurfaceLineX extends SurfaceLine
		this.setLine( os.get( 0 ).getY() );
		}

		/**
		* Tests if the OS matches the SurfaceLine instance and creates a new SurfaceLine object if so.
		*
		* @param os - the OS to test against the SurfaceLine instance.
		* @param direction - an integer witch indicates the line of the resulting SurfaceLine.
		* @param overlap - the minimum number of matching coordinates.
		* @param connexity - the minimum percentage of match between the OS and the current instance.
		* @return - a new SurfaceLine if there is a match, null otherwise.
		*/
		public SurfaceLine match( AbstractOSE os, int direction, int overlap, double connexity )
		{
		SurfaceLineX surfaceLineX = new SurfaceLineX( this.getLength(), this.getLine() + direction );
		@@ -61,12 +70,4 @@ public class SurfaceLineX extends SurfaceLine
		super(length, line );
		}

		public SurfaceLineX( AbstractOSE os, int size )
		{
		super( os , size);
		this.setLine( os.get( 0 ).getY() );
		}



		}

src/main/java/fr/pasteur/ida/zellige/element/surfaceLine/SurfaceLineY.java

+0 −2

Original line number	Diff line number	Diff line
		@@ -66,8 +66,6 @@ public class SurfaceLineY extends SurfaceLine
		* @param connexity - the minimum percentage of match between the OS and the current instance.
		* @return - a new SurfaceLine if there is a match, null otherwise.
		*/


		public SurfaceLine match( AbstractOSE os, int direction, int overlap, double connexity )
		{
		SurfaceLineY surfaceLineY = new SurfaceLineY( this.getLength(), this.getLine() + direction );

src/main/java/fr/pasteur/ida/zellige/gui/ChannelPanel.java

0 → 100644

+79 −0

Original line number	Diff line number	Diff line
		package fr.pasteur.ida.zellige.gui;

		import javafx.collections.FXCollections;
		import javafx.collections.ObservableList;
		import javafx.fxml.FXML;
		import javafx.fxml.FXMLLoader;
		import javafx.fxml.Initializable;
		import javafx.scene.control.*;
		import javafx.scene.layout.Pane;

		import java.io.IOException;
		import java.net.URL;
		import java.util.ResourceBundle;

		public class ChannelPanel extends Pane implements Initializable
		{
		@FXML
		private Spinner<Integer> deltaZ;

		@FXML
		private ChoiceBox<String> method;

		@FXML
		private Spinner<Integer> offset;

		@FXML
		private Button view;

		public ChannelPanel( )
		{
		FXMLLoader fxmlLoader = new FXMLLoader( ChannelPanel.class.getClassLoader().
		getResource( "fr.pasteur.ida.zellige.gui.view/ChannelProjection.fxml" ) );
		fxmlLoader.setRoot(this);
		fxmlLoader.setController( this );
		try
		{
		fxmlLoader.load();
		}
		catch ( IOException e )
		{
		e.printStackTrace();
		}
		}

		@Override
		public void initialize( URL url, ResourceBundle resourceBundle )
		{
		SpinnerValueFactory< Integer > valueFactory =
		new SpinnerValueFactory.IntegerSpinnerValueFactory( 0, 30, 1, 1 );
		deltaZ.setValueFactory( valueFactory );
		ObservableList< String > list = FXCollections.observableArrayList( "MIP", "Mean" );
		method.setItems( list );
		method.getSelectionModel().selectFirst();
		SpinnerValueFactory< Integer > valueFactory2 =
		new SpinnerValueFactory.IntegerSpinnerValueFactory( 0, 30, 0, 1 );
		offset.setValueFactory( valueFactory2 );

		}

		public Spinner< Integer > getDeltaZ()
		{
		return deltaZ;
		}

		public ChoiceBox< String > getMethod()
		{
		return method;
		}

		public Spinner< Integer > getOffset()
		{
		return offset;
		}

		public Button getView()
		{
		return view;
		}
		}

src/main/java/fr/pasteur/ida/zellige/gui/ChannelToolProperty.java

0 → 100644

+83 −0

Original line number	Diff line number	Diff line
		package fr.pasteur.ida.zellige.gui;

		import javafx.beans.property.*;
		import net.imglib2.img.Img;
		import net.imglib2.type.NativeType;
		import net.imglib2.type.numeric.RealType;

		public class ChannelToolProperty < T extends RealType< T > & NativeType< T > >
		{
		private final IntegerProperty deltaZ = new SimpleIntegerProperty();
		private final IntegerProperty offset = new SimpleIntegerProperty();
		private final StringProperty method = new SimpleStringProperty("");

		private final SimpleObjectProperty< Img< T > > subVolume = new SimpleObjectProperty<>();
		private final SimpleObjectProperty< Img< T > > projection = new SimpleObjectProperty<>();
		// private final SimpleObjectProperty< RandomAccessibleInterval<T> > reducedStack = new SimpleObjectProperty<>();
		// private final BooleanProperty parameterChanged = new SimpleBooleanProperty( true );
		// private final SimpleObjectProperty< RandomAccessibleInterval<T>> projection = new SimpleObjectProperty<>();

		public StringProperty getMethod()
		{
		return method;
		}

		public IntegerProperty getOffset()
		{
		return offset;
		}

		public IntegerProperty getDeltaZ()
		{
		return deltaZ;
		}

		// public void setProperties(int delta, int offset, String method)
		// {
		//
		// getDeltaZ().set( delta);
		// getOffset().set( offset );
		// getMethod().set( method );
		// }

		public ChannelToolProperty()
		{
		deltaZ.addListener(( observableValue, number, newValue ) ->
		{
		if (number.intValue() != newValue.intValue())
		{
		subVolume.set( null );
		projection.set( null );
		}
		});

		offset.addListener(( observableValue, number, newValue ) ->
		{
		if (number.intValue() != newValue.intValue())
		{
		subVolume.set( null );
		projection.set( null );
		}
		});

		method.addListener(( observableValue, number, newValue ) ->
		{
		if (! number.equals( newValue))
		{
		projection.set( null );
		}
		});
		}

		public SimpleObjectProperty< Img< T > > getSubVolume()
		{
		return subVolume;
		}

		public SimpleObjectProperty< Img< T > > getProjection()
		{
		return projection;
		}


		}

src/main/java/fr/pasteur/ida/zellige/gui/ConstructionDisplay.java

0 → 100644

+135 −0

Original line number	Diff line number	Diff line
		package fr.pasteur.ida.zellige.gui;

		import javafx.fxml.FXML;
		import javafx.fxml.FXMLLoader;

		import java.io.IOException;
		import javafx.scene.control.Button;
		import javafx.scene.control.Label;
		import javafx.scene.image.ImageView;
		import javafx.scene.layout.FlowPane;
		import javafx.scene.layout.VBox;

		public class ConstructionDisplay extends VBox
		{

		@FXML
		private Label surfaceNb;

		@FXML
		private FlowPane display;

		@FXML
		private Label log;

		@FXML
		private Button minus;

		@FXML
		private Button plus;



		private int surfaceNumber = 1;

		private int nbOfSurfaces;



		public ConstructionDisplay( )
		{
		FXMLLoader fxmlLoader = new FXMLLoader( ConstructionDisplay.class.getClassLoader().getResource(
		"fr.pasteur.ida.zellige.gui.view/ConstructionDisplay.fxml" ) );
		fxmlLoader.setRoot( this );
		fxmlLoader.setController( this );
		try
		{
		fxmlLoader.load();
		}
		catch ( IOException e )
		{
		e.printStackTrace();
		}
		}

		public void next()
		{
		if (surfaceNumber == nbOfSurfaces)
		{
		surfaceNumber = 1;
		}
		else
		{
		surfaceNumber++;
		}
		}

		public void previous()
		{
		if (surfaceNumber == 1)
		{
		surfaceNumber = nbOfSurfaces;
		}
		else
		{
		surfaceNumber--;
		}
		}
		public void set( ImageView image, int index )
		{
		display.getChildren().add( image );
		surfaceNb.setText( "Height map n°" + index );
		if ( nbOfSurfaces == 1 )
		{
		log.setText( "Extraction of " + nbOfSurfaces + " height map." );
		}
		else
		{
		log.setText( "Extraction of " + nbOfSurfaces + " height maps." );
		}


		}



		public void setNbOfSurfaces( int nbOfSurfaces )
		{
		this.nbOfSurfaces = nbOfSurfaces;
		}

		public Label getLog()
		{
		return log;
		}

		public Button getMinus()
		{
		return minus;
		}

		public Button getPlus()
		{
		return plus;
		}

		public int getSurfaceNumber()
		{
		return surfaceNumber;
		}

		public int getNbOfSurfaces()
		{
		return nbOfSurfaces;
		}

		public void setSurfaceNumber( int surfaceNumber )
		{
		this.surfaceNumber = surfaceNumber;
		}

		public FlowPane getDisplay()
		{
		return display;
		}
		}

src/main/java/fr/pasteur/ida/zellige/gui/ImageFXDisplay.java

+99 −45

Original line number	Diff line number	Diff line
		@@ -28,60 +28,50 @@
		*/
		package fr.pasteur.ida.zellige.gui;

		import javafx.scene.image.ImageView;
		import javafx.scene.image.PixelFormat;
		import javafx.scene.image.PixelWriter;
		import javafx.scene.image.WritableImage;
		import javafx.scene.image.*;
		import net.imglib2.Cursor;
		import net.imglib2.IterableInterval;
		import net.imglib2.type.logic.BitType;
		import net.imglib2.algorithm.stats.Normalize;
		import net.imglib2.img.Img;
		import net.imglib2.type.NativeType;
		import net.imglib2.type.numeric.RealType;
		import net.imglib2.util.ImgUtil;
		import org.slf4j.Logger;
		import org.slf4j.LoggerFactory;

		public class ImageFXDisplay
		{

		private final static Logger LOGGER = LoggerFactory.getLogger( ImageFXDisplay.class );

		private final IterableInterval< BitType > input;
		private final ImageView[] imageViews;
		private final int width;
		private final int height;
		private final int depth;


		public ImageFXDisplay( IterableInterval< BitType > input )
		public static < T extends RealType< T > & NativeType< T > > void setSelectedPixels( Img< T > input, ImageView[] imageViews )
		{
		this.input = input;

		width = ( int ) input.dimension( 0 );
		height = ( int ) input.dimension( 1 );
		depth = ( int ) input.dimension( 2 );
		this.imageViews = new ImageView[ depth ];

		}

		public void set()
		{
		int[] data2 = convert2( input );
		int width = ( int ) input.dimension( 0 );
		int height = ( int ) input.dimension( 1 );
		int depth = ( int ) input.dimension( 2 );
		int[] data = convertToBinary( input, width, height, depth );
		for ( int z = 0; z < depth; z++ )
		{
		WritableImage writableImage = new WritableImage( width, height );
		PixelWriter pixelWriter = writableImage.getPixelWriter();
		pixelWriter.setPixels( 0, 0, width, height, PixelFormat.getIntArgbInstance(), data2, height * width * z, width );
		this.imageViews[ z ] = new ImageView( writableImage );
		setImageViews( this.imageViews[ z ] );
		pixelWriter.setPixels( 0, 0, width, height, PixelFormat.getIntArgbInstance(), data, height * width * z, width );
		ImageView imageView = new ImageView( writableImage );
		setImageViews( imageView, width, height , 270);
		imageViews[ z ] = imageView;
		}

		LOGGER.debug( "Selected pixels ImageViews set." );
		}


		public int[] convert2( IterableInterval< BitType > input )
		public static < T extends RealType< T > & NativeType< T > > int[] convertToBinary( IterableInterval< T > input, int width, int height, int depth )
		{
		int[] data = new int[ height * width * depth ];
		Cursor< BitType > cursor = input.cursor();
		Cursor< T > cursor = input.cursor();
		int index = 0;
		System.out.println( 0xFFFFFFFF );
		while ( cursor.hasNext() )
		{
		cursor.fwd();
		if ( cursor.get().get() )
		if ( cursor.next().getRealFloat() > 0 )
		{
		data[ index++ ] = ( 0xFFFFFFFF );
		}
		@@ -89,37 +79,101 @@ public class ImageFXDisplay
		{
		data[ index++ ] = 0xFF000000;
		}


		}
		LOGGER.debug( "Selected pixels data converted for selected pixels display.");
		return data;
		}

		public ImageView[] getImageViews()
		public static < T extends RealType< T > & NativeType< T > > void setHM( Img< T > input, ImageView[] imageViews, int index )
		{
		return this.imageViews;
		int width = ( int ) input.dimension( 0 );
		int height = ( int ) input.dimension( 1 );
		int[] data = convertToGrays( normalize( input ), width, height );
		WritableImage writableImage = new WritableImage( width, height );
		PixelWriter pixelWriter = writableImage.getPixelWriter();
		pixelWriter.setPixels( 0, 0, width, height, PixelFormat.getIntArgbInstance(), data, 0, width );
		ImageView imageView = new ImageView( writableImage );
		setImageViews( imageView, width, height, 300 );
		imageViews[ index ] = imageView;
		LOGGER.debug( "Height Map ImageView set." );
		}

		public void setImageViews( ImageView imageView )
		public static < T extends RealType< T > & NativeType< T > > int[] convertToGrays( IterableInterval< T > input, int width, int height )
		{
		imageView.setPreserveRatio( true );
		setFit( imageView );
		int[] data = new int[ height * width ];
		Cursor< T > cursor = input.cursor();
		int index = 0;
		while ( cursor.hasNext() )
		{
		int value = ( int ) cursor.next().getRealFloat();

		data[ index++ ] = ( 255 ) << 24 \| ( 0xFF & value ) << 16 \| ( 0xFF & value ) << 8 \| ( 0xFF & value );
		}
		LOGGER.debug( "Height map data converted for construction display.");
		return data;
		}

		public static void setImageViews( ImageView imageView, int width, int height, int size )
		{
		imageView.setPreserveRatio( true );
		setFit( imageView, width, height , size);
		imageView.setSmooth( true );
		imageView.setCache( true );
		}

		public void setFit( ImageView imageView )
		public static void setFit( ImageView imageView, int width, int height, int size )
		{
		if ( width >= height )
		{
		imageView.setFitWidth( 254 );
		imageView.setFitWidth( size );
		}
		else
		{
		imageView.setFitHeight( 254 );
		imageView.setFitHeight( size );
		}
		}

		public static < T extends RealType< T > & NativeType< T > > Img< T > normalize( Img< T > input )
		{
		Img< T > normalizedImage = input.factory().create( input.dimensionsAsLongArray() );
		ImgUtil.copy( input, normalizedImage );
		T min = normalizedImage.firstElement().createVariable();
		min.setReal( 0 );
		T max = normalizedImage.firstElement().copy().createVariable();
		max.setReal( 255 );
		Normalize.normalize( normalizedImage, min, max );
		return normalizedImage;
		}

		/**
		* Creates a copy of an array of ImageView objects.
		*
		* Each ImageView in the new array is a separate instance
		* with the same image and properties as the original.
		*
		* @param original The original array of ImageView objects to copy.
		* @return A new array of ImageView objects with the same content.
		*/
		public static ImageView[] copyImageViewArray(ImageView[] original) {
		if (original == null) {
		return null;
		}

		ImageView[] copy = new ImageView[original.length];
		for (int i = 0; i < original.length; i++) {
		if (original[i] != null) {
		ImageView originalView = original[i];
		ImageView newView = new ImageView(originalView.getImage());

		// Optional: Copy some properties
		newView.setFitWidth(originalView.getFitWidth());
		newView.setFitHeight(originalView.getFitHeight());
		newView.setPreserveRatio(originalView.isPreserveRatio());
		newView.setSmooth(originalView.isSmooth());

		copy[i] = newView;
		}
		}
		return copy;
		}
		}

src/main/java/fr/pasteur/ida/zellige/gui/LogAppender.java

+1 −1

Original line number	Diff line number	Diff line
		@@ -51,7 +51,7 @@ public class LogAppender extends AppenderBase< ILoggingEvent >
		protected void append( ILoggingEvent iLoggingEvent )
		{
		String level = iLoggingEvent.getLevel().toString();
		if ( level.equals( Level.INFO.toString() ) )
		if ( level.equals( Level.INFO.toString()) && iLoggingEvent.getMarker().contains( "GUI" ))
		{
		logMessage.setValue( iLoggingEvent.getFormattedMessage() );
		}

src/main/java/fr/pasteur/ida/zellige/gui/MainAppFrame.java

+19 −12

Original line number	Diff line number	Diff line
		@@ -45,6 +45,8 @@ import org.scijava.log.LogService;
		import org.scijava.plugin.Parameter;
		import org.slf4j.Logger;
		import org.slf4j.LoggerFactory;
		import org.slf4j.Marker;
		import org.slf4j.MarkerFactory;

		import javax.swing.*;
		import java.awt.*;
		@@ -57,7 +59,7 @@ import java.util.ResourceBundle;
		public class MainAppFrame extends JFrame
		{

		private final static Logger LOGGER = LoggerFactory.getLogger( MainAppFrame.class );
		public static final Marker GUI_MARKER = MarkerFactory.getMarker("GUI");
		private ImageJ ij;
		private final ImageDisplayService image;
		@Parameter
		@@ -86,15 +88,21 @@ public class MainAppFrame extends JFrame
		*/
		public void setLogStatus()
		{
		LoggerContext lc = ( LoggerContext ) LoggerFactory.getILoggerFactory();
		PatternLayoutEncoder ple = new PatternLayoutEncoder();
		ple.setPattern( "%msg%n" );
		ple.setContext( lc );
		ple.start();
		LogAppender appender = new LogAppender();
		// Get the logger context
		LoggerContext context = ( LoggerContext ) LoggerFactory.getILoggerFactory();

		// Configure the log pattern
		PatternLayoutEncoder layout = new PatternLayoutEncoder();
		layout.setPattern( "%msg%n" );
		layout.setContext( context );
		layout.start();

		appender.setContext( lc );
		// Create and start the custom LogAppender
		LogAppender appender = new LogAppender();
		appender.setContext( context );
		appender.start();

		// Get the root logger and add the appender
		ch.qos.logback.classic.Logger logbackLogger =
		( ch.qos.logback.classic.Logger ) LoggerFactory.getLogger( Logger.ROOT_LOGGER_NAME );
		logbackLogger.addAppender( appender );
		@@ -102,7 +110,6 @@ public class MainAppFrame extends JFrame

		public MainAppFrame( Context context )
		{
		// this.ij = context.;
		this.image = context.getService( ImageDisplayService.class );
		this.logService = context.getService( LogService.class );
		this.setIconImages( ICONS );
		@@ -160,21 +167,19 @@ public class MainAppFrame extends JFrame
		{
		ResourceBundle bundle = ResourceBundle.getBundle( "gui" );// access to properties f
		FXMLLoader loader = new FXMLLoader( MainAppFrame.class.getClassLoader().getResource( "fr.pasteur.ida.zellige.gui.view/Main.fxml" ), bundle );

		VBox rootLayout = loader.load();

		// Get the controller and add an ImageJ context to it.
		MainController< T > controller = loader.getController();
		controller.setMainApp( this );


		// Show the scene containing the root layout.
		scene = new Scene( rootLayout );
		this.fxPanel.setScene( scene );

		// Resize the JFrame to the JavaFX scene
		this.setSize( ( int ) scene.getWidth() + 20, ( int ) scene.getHeight() + 50 );
		controller.initExtraction();
		// controller.initExtraction();
		}
		catch ( IOException e )
		{
		@@ -183,4 +188,6 @@ public class MainAppFrame extends JFrame
		}




		}

src/main/java/fr/pasteur/ida/zellige/gui/ParameterSlider.java

+14 −0

Original line number	Diff line number	Diff line
		@@ -29,7 +29,9 @@
		package fr.pasteur.ida.zellige.gui;

		import javafx.beans.NamedArg;
		import javafx.beans.binding.NumberExpressionBase;
		import javafx.beans.property.DoubleProperty;
		import javafx.beans.property.Property;
		import javafx.beans.property.StringProperty;
		import javafx.css.PseudoClass;
		import javafx.fxml.FXML;
		@@ -134,6 +136,8 @@ public abstract class ParameterSlider extends GridPane
		}




		public void enable()
		{
		this.getSlider().setDisable( false );
		@@ -186,6 +190,16 @@ public abstract class ParameterSlider extends GridPane
		{
		this.sliderProperty().set( value );
		}

		public Number getValue ()
		{
		return this.sliderProperty().getValue();
		}

		public String getName()
		{
		return name;
		}
		}

src/main/java/fr/pasteur/ida/zellige/gui/ParameterSliderInteger.java

+2 −0

Original line number	Diff line number	Diff line
		@@ -75,4 +75,6 @@ public class ParameterSliderInteger extends ParameterSlider
		}




		}

src/main/java/fr/pasteur/ida/zellige/gui/ProjectionProperties.java

0 → 100644

+29 −0

Original line number	Diff line number	Diff line
		package fr.pasteur.ida.zellige.gui;

		import javafx.beans.property.SimpleObjectProperty;
		import net.imglib2.img.Img;
		import net.imglib2.type.NativeType;
		import net.imglib2.type.numeric.RealType;

		import java.util.ArrayList;

		public class ProjectionProperties< T extends RealType< T > & NativeType< T > >
		{


		private final SimpleObjectProperty< ArrayList< ChannelToolProperty<T> > > properties = new SimpleObjectProperty<>(new ArrayList<>());

		public ProjectionProperties( int channels)
		{
		for ( int i = 0; i < channels; i++ )
		{
		getProperties().get().add( new ChannelToolProperty<>() );
		}

		}

		public SimpleObjectProperty< ArrayList< ChannelToolProperty <T>> > getProperties()
		{
		return properties;
		}
		}

src/main/java/fr/pasteur/ida/zellige/gui/ReferenceSurfacePanel.java

0 → 100644

+67 −0

Original line number	Diff line number	Diff line
		package fr.pasteur.ida.zellige.gui;

		import javafx.fxml.FXML;
		import javafx.fxml.FXMLLoader;
		import javafx.scene.control.Button;
		import javafx.scene.control.Tab;
		import javafx.scene.control.TabPane;
		import javafx.scene.layout.Pane;
		import net.imglib2.type.NativeType;
		import net.imglib2.type.numeric.RealType;

		import java.io.IOException;

		public class ReferenceSurfacePanel < T extends RealType< T > & NativeType< T > > extends Pane
		{

		@FXML
		private TabPane channelTools;



		@FXML
		private Button run;

		private final ProjectionProperties<T> projectionProperties;


		public ReferenceSurfacePanel( int channels)
		{
		FXMLLoader fxmlLoader = new FXMLLoader( ReferenceSurfacePanel.class.getClassLoader().
		getResource( "fr.pasteur.ida.zellige.gui.view/ReferenceSurfacePanel.fxml" ) );
		fxmlLoader.setRoot(this);
		fxmlLoader.setController( this );
		try
		{
		fxmlLoader.load();
		}
		catch ( IOException e )
		{
		e.printStackTrace();
		}
		for ( int i = 1; i <= channels; i++ )
		{
		Tab tab = new Tab( "C" + i );
		ChannelPanel pane = new ChannelPanel();
		tab.setContent( pane );
		getChannelTools().getTabs().add( tab );

		}
		projectionProperties =new ProjectionProperties<>( channels );
		}

		public TabPane getChannelTools()
		{
		return channelTools;
		}

		public Button getRun()
		{
		return run;
		}

		public ProjectionProperties< T > getProjectionProperties()
		{
		return projectionProperties;
		}
		}

src/main/java/fr/pasteur/ida/zellige/gui/ReferencesurfaceProjectionPane.java

0 → 100644

+5 −0

Original line number	Diff line number	Diff line
		package fr.pasteur.ida.zellige.gui;

		public class ReferencesurfaceProjectionPane
		{
		}

src/main/java/fr/pasteur/ida/zellige/gui/StepPanel.java

+17 −24

Original line number	Diff line number	Diff line
		@@ -39,32 +39,25 @@ import java.io.IOException;
		public class StepPanel extends VBox
		{

		private final String name;
		@FXML
		Label Label2;


		public StepPanel( @NamedArg( "name" ) String name )
		{
		this.name = name;
		FXMLLoader fxmlLoader = new FXMLLoader( StepPanel.class.getClassLoader().getResource(
		"fr.pasteur.ida.zellige.gui.view/StepPanel.fxml" ) );
		fxmlLoader.setRoot( this );
		fxmlLoader.setController( this );
		try
		{
		fxmlLoader.load();
		}
		catch ( IOException e )
		{
		e.printStackTrace();
		}
		}

		// public StepPanel( @NamedArg( "name" ) String name )
		// {
		// FXMLLoader fxmlLoader = new FXMLLoader( StepPanel.class.getClassLoader().getResource(
		// "fr.pasteur.ida.zellige.gui.view/StepPanel.fxml" ) );
		// fxmlLoader.setRoot( this );
		// fxmlLoader.setController( this );
		// try
		// {
		// fxmlLoader.load();
		// }
		// catch ( IOException e )
		// {
		// e.printStackTrace();
		// }
		// }



		@FXML
		public void initialize()
		{
		this.Label2.setText( name );
		}
		}

src/main/java/fr/pasteur/ida/zellige/gui/controller/BatchModeDialog.java

0 → 100644

+100 −0

Original line number	Diff line number	Diff line
		package fr.pasteur.ida.zellige.gui.controller;

		import fr.pasteur.ida.zellige.Main;
		import fr.pasteur.ida.zellige.ReferenceSurfaceExtraction;
		import javafx.fxml.FXML;
		import javafx.fxml.FXMLLoader;
		import javafx.fxml.Initializable;
		import javafx.scene.control.Button;
		import javafx.scene.control.TextField;
		import javafx.scene.layout.VBox;
		import javafx.stage.FileChooser;
		import javafx.stage.Stage;

		import java.io.File;
		import java.io.IOException;
		import java.net.URL;
		import java.util.ResourceBundle;

		public class BatchModeDialog extends VBox implements Initializable
		{
		@FXML
		private Button browse;

		@FXML
		private TextField filePathField; // TextField to display selected file path

		@FXML
		private Button run;

		public BatchModeDialog()
		{

		FXMLLoader fxmlLoader = new FXMLLoader( BatchModeDialog.class.getClassLoader().
		getResource( "fr.pasteur.ida.zellige.gui.view/BatchModeDialog.fxml" ) );
		fxmlLoader.setRoot(this);
		fxmlLoader.setController( this );
		try
		{
		fxmlLoader.load();
		}
		catch ( IOException e )
		{
		e.printStackTrace();
		}
		}



		private File selectedFile; // Store the selected file

		// Handle Browse Button Click
		@FXML
		private void handleBrowse() {
		FileChooser fileChooser = new FileChooser();
		fileChooser.setTitle("Select File");

		// Set file filter (optional)
		fileChooser.getExtensionFilters().add(new FileChooser.ExtensionFilter("Text Files", "*.csv"));

		// Open FileChooser
		Stage stage = (Stage) filePathField.getScene().getWindow();
		File file = fileChooser.showOpenDialog(stage);

		if (file != null) {
		selectedFile = file;
		filePathField.setText(file.getAbsolutePath());
		}
		}

		// Handle Run Button Click
		@FXML
		private void handleRun() throws Exception
		{
		if (selectedFile != null) {
		System.out.println("Running with file: " + selectedFile.getAbsolutePath());
		ReferenceSurfaceExtraction.run(selectedFile.getAbsolutePath());
		// Add logic to process the file
		} else {
		System.out.println("No file selected!");
		}
		}


		@Override
		public void initialize( URL url, ResourceBundle resourceBundle )
		{
		browse.setOnAction(e -> handleBrowse());
		run.setOnAction( e->
		{
		try
		{
		handleRun();
		}
		catch ( Exception ex )
		{
		throw new RuntimeException( ex );
		}
		} );
		}
		}

src/main/java/fr/pasteur/ida/zellige/gui/controller/ConstructionController.java

+205 −65

Original line number	Diff line number	Diff line
		@@ -28,14 +28,18 @@
		*/
		package fr.pasteur.ida.zellige.gui.controller;

		import fr.pasteur.ida.zellige.gui.ParameterSliderDouble;
		import fr.pasteur.ida.zellige.gui.ParameterSliderInteger;
		import fr.pasteur.ida.zellige.gui.*;
		import fr.pasteur.ida.zellige.gui.exception.NoParameterChangeException;
		import fr.pasteur.ida.zellige.gui.exception.NoPixelSelectionException;
		import fr.pasteur.ida.zellige.gui.interactor.ConstructionInteractor;
		import fr.pasteur.ida.zellige.gui.model.ConstructionModel;
		import fr.pasteur.ida.zellige.gui.parameter.ZelligeParameters;
		import javafx.beans.property.SimpleBooleanProperty;
		import javafx.beans.value.ChangeListener;
		import fr.pasteur.ida.zellige.gui.task.*;
		import javafx.beans.property.*;
		import javafx.fxml.FXML;
		import javafx.fxml.Initializable;
		import javafx.scene.control.Button;
		import javafx.scene.image.ImageView;
		import net.imglib2.type.NativeType;
		import net.imglib2.type.numeric.RealType;
		import org.slf4j.Logger;
		@@ -44,12 +48,17 @@ import org.slf4j.LoggerFactory;
		import java.net.URL;
		import java.util.ResourceBundle;

		import static fr.pasteur.ida.zellige.gui.MainAppFrame.GUI_MARKER;
		import static fr.pasteur.ida.zellige.gui.controller.MainController.showError;
		import static fr.pasteur.ida.zellige.gui.controller.MainController.showInfo;
		import static fr.pasteur.ida.zellige.gui.controller.SelectionController.setNextOutputToNull;

		public class ConstructionController< T extends RealType< T > & NativeType< T > > implements Initializable
		{
		private final static Logger LOGGER = LoggerFactory.getLogger( ConstructionController.class );

		private final SimpleBooleanProperty changedParameters = new SimpleBooleanProperty();
		private ConstructionModel< T > constructionModel;
		private MainController< T > parentController;

		@FXML
		private ParameterSliderDouble c1;
		@FXML
		@@ -64,102 +73,233 @@ public class ConstructionController< T extends RealType< T > & NativeType< T > >
		private ParameterSliderDouble st2;
		@FXML
		private ParameterSliderInteger surfaceSize;
		@FXML
		private ConstructionDisplay constructionDisplay;
		@FXML
		private Button run;

		private final ConstructionInteractor< T > interactor = new ConstructionInteractor<>( new ConstructionModel< T >() );

		@Override
		public void initialize( URL url, ResourceBundle resourceBundle )
		{
		// model
		constructionModel = new ConstructionModel<>();

		//link Model with View
		constructionModel.c1Property().bind( c1.sliderProperty() );
		constructionModel.r1Property().bind( r1.sliderProperty() );
		constructionModel.st1Property().bind( st1.sliderProperty() );
		constructionModel.c2Property().bind( c2.sliderProperty() );
		constructionModel.r2Property().bind( r2.sliderProperty() );
		constructionModel.st2Property().bind( st2.sliderProperty() );
		constructionModel.surfaceSizeProperty().bind( surfaceSize.sliderProperty() );

		/* Component */
		ChangeListener< ? super Number > firstRoundListener = ( observable, oldValue, newValue ) ->
		{
		constructionModel.firstRoundSurfacesProperty().setValue( null );
		changedParameters.setValue( true );
		};
		c1.sliderProperty().addListener( firstRoundListener );
		r1.sliderProperty().addListener( firstRoundListener );
		st1.sliderProperty().addListener( firstRoundListener );
		surfaceSize.sliderProperty().addListener( firstRoundListener );
		ChangeListener< ? super Number > secondRoundListener = ( observable, oldValue, newValue ) ->
		{
		changedParameters.setValue( true );
		constructionModel.secondRoundSurfacesProperty().setValue( null );
		};
		c2.sliderProperty().addListener( secondRoundListener );
		r2.sliderProperty().addListener( secondRoundListener );
		st2.sliderProperty().addListener( secondRoundListener );
		surfaceSize.sliderProperty().addListener( secondRoundListener );
		/* Component behaviour */
		constructionDisplay.getMinus().setOnAction( actionEvent ->
		{
		constructionDisplay.previous();
		setDisplay();
		} );
		constructionDisplay.getPlus().setOnAction( actionEvent ->
		{
		constructionDisplay.next();
		setDisplay();
		} );

		run.setOnAction( actionEvent ->
		{
		runConstruction();
		} );


		/* Results which depend on a parameter are set to null when modified*/
		resetResultFromChangedParameterValue( getModel().c1Property(), getModel().firstRoundSurfacesProperty(), "First round connexity" );
		resetResultFromChangedParameterValue( getModel().r1Property(), getModel().firstRoundSurfacesProperty(), "First round overlap" );
		resetResultFromChangedParameterValue( getModel().st1Property(), getModel().firstRoundSurfacesProperty(), "First round starting threshold" );
		resetResultFromChangedParameterValue( getModel().surfaceSizeProperty(), getModel().firstRoundSurfacesProperty(), "Surface minimum size" );

		resetResultFromChangedParameterValue( getModel().c2Property(), getModel().secondRoundSurfacesProperty(), "Second round connexity" );
		resetResultFromChangedParameterValue( getModel().r2Property(), getModel().secondRoundSurfacesProperty(), "Second round overlap" );
		resetResultFromChangedParameterValue( getModel().st2Property(), getModel().secondRoundSurfacesProperty(), "Second round starting threshold" );
		resetResultFromChangedParameterValue( getModel().surfaceSizeProperty(), getModel().secondRoundSurfacesProperty(), "Surface minimum size" );

		/* Results that depend on another result are set to null when the latter is null */
		setNextOutputToNull( getModel().firstRoundSurfacesProperty(), getModel().secondRoundSurfacesProperty() );
		setNextOutputToNull( getModel().secondRoundSurfacesProperty(), getModel().referenceSurfacesProperty() );
		setNextOutputToNull( getModel().referenceSurfacesProperty(), getModel().getImageViews() );

		/* Properties*/
		constructionModel.maximumsProperty().addListener( ( observable, oldValue, newValue ) ->

		getModel().getDisableGUI().addListener( ( observable, oldValue, newValue ) ->
		{
		if ( newValue != null )
		if ( newValue )
		{
		LOGGER.debug( "Max is not null" );
		constructionModel.firstRound();
		disableParameters();
		}
		else
		{
		LOGGER.debug( "MAX is NULL" );
		constructionModel.firstRoundSurfacesProperty().setValue( null );
		enableParameters();
		}
		} );
		constructionModel.firstRoundSurfacesProperty().addListener( ( observableValue, surfaces, t1 ) ->

		getModel().firstRoundSurfacesProperty().addListener( ( observableValue, surfaces, newValue ) ->
		{
		if ( t1 == null )
		if ( newValue != null )
		{
		LOGGER.debug( "FIRST_ROUND_SURFACE is NULL" );
		constructionModel.secondRoundSurfacesProperty().setValue( null );
		interactor.secondRound();
		}
		} );
		getModel().secondRoundSurfacesProperty().addListener( ( observableValue, surfaces, newValue ) ->
		{
		if ( newValue != null )
		{
		interactor.constructionCompletion();
		}
		} );

		getModel().referenceSurfacesProperty().addListener( ( observableValue, surfaces, newValue ) ->
		{
		if (newValue!= null && ! newValue.isEmpty() )
		{
		computeImageFXDisplay();
		}
		else
		{
		constructionModel.secondRound();
		LOGGER.debug( "There is no SURFACE!!!" );
		}
		} );
		constructionModel.secondRoundSurfacesProperty().addListener( ( observableValue, surfaces, t1 ) ->
		}

		private void checkParameters()
		{
		setParameterValue( c1, getModel().c1Property() );
		setParameterValue( r1, getModel().r1Property() );
		setParameterValue( st1, getModel().st1Property() );
		setParameterValue( c2, getModel().c2Property() );
		setParameterValue( r2, getModel().r2Property() );
		setParameterValue( st2, getModel().st2Property() );
		setParameterValue( surfaceSize, getModel().surfaceSizeProperty() );
		}


		private void setParameterValue( ParameterSlider slider, Property< Number > property )
		{
		if ( t1 == null )
		if ( ! property.getValue().equals( slider.getValue() ) )
		{
		LOGGER.debug( "SECOND_ROUND_SURFACE is NULL" );
		constructionModel.referenceSurfacesProperty().setValue( null );
		LOGGER.debug( "model has changed with parameter {}, old value: {}, new value: {}", slider.getName(), property.getValue().doubleValue(), slider.getValue().doubleValue() );
		property.setValue( slider.getValue() );
		getModel().getParameterChanged().set( true );
		}
		}


		public void runConstruction()
		{
		checkParameters();
		if ( getModel().maximumsProperty().getValue() == null )
		{
		showError( new NoPixelSelectionException() );
		}
		else if ( ! getModel().getParameterChanged().getValue() && getModel().firstRoundSurfacesProperty().getValue() != null )
		{
		showInfo( new NoParameterChangeException() );
		}
		else
		{
		constructionModel.constructionCompletion();
		disableGUI( true );

		LOGGER.info(GUI_MARKER, "Running construction" );
		if ( getModel().maximumsProperty().getValue() != null )
		{
		if ( getModel().firstRoundSurfacesProperty().getValue() == null )
		{
		interactor.firstRound();
		}
		else if ( getModel().secondRoundSurfacesProperty().get() == null )
		{
		interactor.secondRound();
		}
		}
		}
		}


		public void computeImageFXDisplay()
		{
		ConstructionDisplayTask< T > task = new ConstructionDisplayTask<>( getModel().referenceSurfacesProperty().getValue() );
		task.setOnSucceeded( workerStateEvent ->
		{
		LOGGER.info(GUI_MARKER, "Construction display completed." );
		getModel().getImageViews().setValue( task.getValue() );
		ImageView[] imageViews = ImageFXDisplay.copyImageViewArray( task.getValue() );
		parentController.getProjectionController().getModel().getImageViews().set( imageViews );
		setDisplay();
		disableGUI( false );
		} );
		task.start();
		}

		public void setDisplay()
		{
		constructionDisplay.setNbOfSurfaces( getModel().referenceSurfacesProperty().get().size() );
		constructionDisplay.getDisplay().getChildren().clear();
		int index = constructionDisplay.getSurfaceNumber();
		ImageView i = getModel().getImageViews().getValue()[ index - 1 ];
		constructionDisplay.set( i, index );
		// setting of ZSlider

		disableGUI( false );
		}


		public ConstructionModel< T > getConstructionModel()
		public void resetResultFromChangedParameterValue( Property< Number > property, SimpleObjectProperty< ? > result, String parameterName )
		{
		property.addListener( ( observable, oldValue, newValue ) ->
		{
		if ( newValue != null )
		{
		LOGGER.info( "The {} parameter has been changed, old value:{}, new value: {}.", parameterName, oldValue, newValue );
		}
		if ( result.getValue() != null )
		{
		return constructionModel;
		result.set( null );
		}
		} );
		}

		public SimpleBooleanProperty changedParametersProperty()
		public void enableParameters()
		{
		return changedParameters;
		this.c1.enable();
		this.r1.enable();
		this.st1.enable();
		this.c2.enable();
		this.r2.enable();
		this.st2.enable();
		this.surfaceSize.enable();
		}

		public void disableParameters()
		{
		this.c1.disable();
		this.r1.disable();
		this.st1.disable();
		this.c2.disable();
		this.r2.disable();
		this.st2.disable();
		this.surfaceSize.disable();
		}


		public void setParameters( ZelligeParameters parameters )
		{
		st1.setValue( parameters.getSt1() );
		r1.setValue( parameters.getR1() );
		c1.setValue( parameters.getC1() );
		st2.setValue( parameters.getSt2() );
		r2.setValue( parameters.getR2() );
		c2.setValue( parameters.getC2() );
		surfaceSize.setValue( parameters.getSurfaceSize() );
		st1.setValue( parameters.getConstructionParameters()[0].getStartingSizeThreshold() );
		r1.setValue( parameters.getConstructionParameters()[0].getOverlap());
		c1.setValue( parameters.getConstructionParameters()[0].getConnexityRate() );
		st2.setValue( parameters.getConstructionParameters()[1].getStartingSizeThreshold() );
		r2.setValue( parameters.getConstructionParameters()[1].getOverlap());
		c2.setValue( parameters.getConstructionParameters()[1].getConnexityRate() );
		surfaceSize.setValue( parameters.getConstructionParameters()[0].getSurfaceMinSizeFactor() );
		}

		public ConstructionModel< T > getModel()
		{
		return interactor.getModel();
		}
		public void setParent( MainController< T > mainController )
		{
		parentController = mainController;
		}
		private void disableGUI( boolean value )
		{
		getModel().getDisableGUI().set( value );
		}
		}

src/main/java/fr/pasteur/ida/zellige/gui/controller/MainController.java

+200 −230

File changed.

Preview size limit exceeded, changes collapsed.

src/main/java/fr/pasteur/ida/zellige/gui/controller/PreprocessingController.java

0 → 100644

+303 −0

Original line number	Diff line number	Diff line
		package fr.pasteur.ida.zellige.gui.controller;

		import fr.pasteur.ida.zellige.gui.ReferenceSurfacePanel;
		import fr.pasteur.ida.zellige.gui.exception.NoA3DStackException;
		import fr.pasteur.ida.zellige.gui.exception.NoInputException;
		import fr.pasteur.ida.zellige.gui.exception.TimeLapseException;
		import fr.pasteur.ida.zellige.gui.interactor.PreprocessingInteractor;
		import fr.pasteur.ida.zellige.gui.model.PreprocessingModel;
		import fr.pasteur.ida.zellige.gui.parameter.ZelligeParameters;
		import fr.pasteur.ida.zellige.gui.task.DisplayDatasetChoicesTask;
		import javafx.beans.property.BooleanProperty;
		import javafx.beans.property.SimpleBooleanProperty;
		import javafx.collections.FXCollections;
		import javafx.collections.ObservableList;
		import javafx.fxml.FXML;
		import javafx.fxml.Initializable;
		import javafx.scene.control.*;
		import javafx.scene.layout.StackPane;
		import javafx.scene.paint.Color;
		import net.imagej.Dataset;
		import net.imagej.display.DatasetView;
		import net.imagej.display.ImageDisplayService;
		import net.imglib2.RandomAccessibleInterval;
		import net.imglib2.display.ColorTable;
		import net.imglib2.img.ImgFactory;
		import net.imglib2.type.NativeType;
		import net.imglib2.type.numeric.RealType;
		import net.imglib2.view.Views;
		import org.slf4j.Logger;
		import org.slf4j.LoggerFactory;

		import java.net.URL;
		import java.util.ArrayList;
		import java.util.ResourceBundle;

		import static fr.pasteur.ida.zellige.gui.controller.MainController.showError;
		import static fr.pasteur.ida.zellige.utils.Util.create4dimImage;


		public class PreprocessingController< T extends RealType< T > & NativeType< T > > implements Initializable
		{

		private final static Logger LOGGER = LoggerFactory.getLogger( PreprocessingController.class );

		private MainController< T > parentController;

		@FXML
		private ComboBox< Dataset > activeDatasets;

		@FXML
		private Spinner< Integer > binValue;

		@FXML
		private Spinner< Integer > channelValue;

		@FXML
		private Label fileInfo;

		@FXML
		private Label userAdvice;


		private final BooleanProperty disableGUI = new SimpleBooleanProperty( false );

		private final PreprocessingInteractor< T > interactor;

		public PreprocessingController()
		{
		PreprocessingModel< T > model = new PreprocessingModel<>();
		this.interactor = new PreprocessingInteractor<>( model );
		}

		@Override
		@SuppressWarnings( "unchecked" )
		public void initialize( URL url, ResourceBundle resourceBundle )
		{
		/* Controls */
		// Bin Spinner*/
		SpinnerValueFactory< Integer > valueFactory = new SpinnerValueFactory.IntegerSpinnerValueFactory( 1, 10, 5 );
		binValue.setValueFactory( valueFactory );

		// Channel spinner
		SpinnerValueFactory< Integer > valueFactory2 = new SpinnerValueFactory.IntegerSpinnerValueFactory( 1, 5, 1, 1 );
		channelValue.setValueFactory( valueFactory2 );
		//TODO : remove not necessary
		channelValue.valueProperty().addListener( ( observable, oldValue, newValue ) -> LOGGER.debug( "The Channel spinner has changed!" ) );

		// Control of the files comboBox*/
		activeDatasets.setOnMousePressed( event -> setAndDisplayDatasetChoices() );// Update of the list of opened Fiji images

		// If a new dataset is selected...
		activeDatasets.getSelectionModel().selectedItemProperty().addListener( ( observableValue, oldValue, newValue ) ->
		{
		LOGGER.debug( "selectedItemProperty : old value = {}, new value = {} ", oldValue, newValue );
		if ( newValue != null && checkFile( newValue ) )
		{
		int index = activeDatasets.getSelectionModel().getSelectedIndex();
		setColorTable( index );

		// Set number of channels
		getModel().getNbOfChannels().set( ( int ) newValue.getChannels() );
		//Set the channel spinner behaviour
		final SpinnerValueFactory< Integer > valueFactory3 = new SpinnerValueFactory.IntegerSpinnerValueFactory( 1, getModel().getNbOfChannels().get() );
		channelValue.setValueFactory( valueFactory3 );

		//set the input
		if ( getModel().getNbOfChannels().get() == 1 )
		{
		try
		{
		getModel().getInput().set( create4dimImage( newValue ) );
		}
		catch ( Exception e )
		{
		throw new RuntimeException( e );
		}
		}
		else
		{
		getModel().getInput().set( ( RandomAccessibleInterval< T > ) newValue.getImgPlus() );
		}
		// Set the input factory
		getModel().getFactory().setValue( ( ImgFactory< T > ) newValue.getImgPlus().factory() );

		// Sets the properties
		getModel().getParameterChanged().set( true );
		getModel().pretreatedImgProperty().setValue( null );

		// Update the default projection panel view
		StackPane stackPane = parentController.getProjectionController().getStackPane();
		stackPane.getChildren().clear();
		parentController.getProjectionController().getModel().getNumberOfChannels().set( getModel().getNbOfChannels().get() );
		ReferenceSurfacePanel panel = new ReferenceSurfacePanel( getModel().getNbOfChannels().get() );
		stackPane.getChildren().add( panel );
		}
		else
		{
		activeDatasets.getSelectionModel().selectLast(); //empty slot
		}
		} );

		disableGUI.addListener( ( observable, oldValue, newValue ) ->
		{
		if ( newValue )
		{
		disableParameters();
		}
		else
		{
		enableParameters();
		}
		} );

		/* Properties */
		getModel().getInput().addListener( ( observable, oldValue, newValue ) ->
		{
		if ( newValue != oldValue && newValue != null )
		{
		// Reset the input channel
		getModel().getInput_channel().set( null );
		}
		} );

		getModel().getInput_channel().addListener( ( observable, oldValue, newValue ) ->
		{
		if ( newValue != oldValue && newValue != null )
		{
		// Reset the input channel
		getModel().pretreatedImgProperty().set( null );
		}
		} );
		}

		public void setAndDisplayDatasetChoices()
		{
		DisplayDatasetChoicesTask displayTask = new DisplayDatasetChoicesTask( parentController.getMainAppFrame().getImage() );
		displayTask.setOnSucceeded( workerStateEvent ->
		{
		LOGGER.debug( "Datasets displayed successfully" );
		ObservableList< Dataset > list = FXCollections.observableArrayList( displayTask.getValue() );
		// list.add( null );
		activeDatasets.setItems( list );
		LOGGER.debug( "item selected : list size = {}", list.size() );
		if ( list.isEmpty() )
		{
		interactor.getModel().getInput().setValue( null );
		interactor.getModel().getFactory().setValue( null );
		LOGGER.debug( "CURRENT_DATASET is NULL" );
		showError( new NoInputException() );
		}
		} );
		displayTask.start();
		}

		/**
		* Finds and sets the input color tables.
		*
		* @param index the position of the input in the list of displayed datasets
		*/
		public void setColorTable( int index )
		{
		ImageDisplayService imageDisplayService = parentController.getMainAppFrame().getImage();
		DatasetView datasetView = ( DatasetView ) imageDisplayService.getImageDisplays().get( index ).get( 0 );
		ArrayList< ColorTable > colorTables = new ArrayList<>( datasetView.getColorTables() );
		getModel().getColors().set( colorTables );
		}


		private boolean checkFile( Dataset dataset )
		{
		int nbDim = dataset.numDimensions();
		int nbSlices = ( int ) dataset.getDepth();
		int nbFrames = ( int ) dataset.getFrames();
		int nbChannels = ( int ) dataset.getChannels();
		// int pixelNb = (int) 0; //TODO set the pixel nb and add user advice for binning ?

		// Set the file info label
		String advice = "You go girl!";
		fileInfo.setText( "Nb Channels: " + nbChannels + " Nb z-slices: " + nbSlices + " Nb time-points: " + nbFrames );
		userAdvice.setText( advice );
		userAdvice.setTextFill( Color.RED );
		LOGGER.debug( "NUmber of dimensions: {}", nbDim );
		LOGGER.debug( "NUmber of channels: {}", getModel().getNbOfChannels().get() );
		LOGGER.debug( "Number of frames: {}", nbFrames );

		if ( nbFrames > 1 )
		{
		LOGGER.debug( "TimeLapseException" );
		showError( new TimeLapseException() );
		return false;
		}
		if ( nbSlices == 1 )
		{
		LOGGER.debug( "NoA3DStackException" );
		showError( new NoA3DStackException() );
		return false;
		}
		return true;
		}

		public void checkParameters()
		{
		if ( ! ( getModel().binProperty().get() == binValue.valueProperty().get() ) )
		{
		getModel().getInput_channel().set( null );
		getModel().getParameterChanged().setValue( true );
		getModel().binProperty().set( binValue.getValue() );

		}
		if ( ! ( interactor.getModel().getChannel().get() == channelValue.valueProperty().get() ) )
		{
		getModel().getParameterChanged().setValue( true );
		getModel().getChannel().set( channelValue.getValue() - 1 );
		}
		// Set the input channel
		if ( getModel().getInput().get() == null )
		{
		showError( new NoInputException() );
		}
		else
		{
		getModel().getInput_channel().set( Views.hyperSlice( getModel().getInput().get(), 2, getModel().getChannel().get() ) );
		}
		}

		private void disableParameters()
		{
		binValue.setDisable( true );
		channelValue.setDisable( true );
		}

		private void enableParameters()
		{
		binValue.setDisable( false );
		channelValue.setDisable( false );
		}

		public PreprocessingInteractor< T > getInteractor()
		{
		return interactor;
		}

		public void setParent( MainController< T > mainController )
		{
		parentController = mainController;
		}

		public BooleanProperty getDisableGUI()
		{
		return disableGUI;
		}

		public PreprocessingModel< T > getModel()
		{
		return interactor.getModel();
		}

		public void setParameters( ZelligeParameters parameters )
		{
		binValue.getValueFactory().setValue( parameters.getPretreatmentParameters().getBin() );
		channelValue.getValueFactory().setValue( parameters.getPretreatmentParameters().getChannel() );
		}
		}
		No newline at end of file

src/main/java/fr/pasteur/ida/zellige/gui/controller/ProjectionController.java

+131 −164

Original line number	Diff line number	Diff line
		@@ -28,226 +28,193 @@
		*/
		package fr.pasteur.ida.zellige.gui.controller;

		import fr.pasteur.ida.zellige.gui.CheckBoxDisplay;
		import fr.pasteur.ida.zellige.gui.ChannelPanel;
		import fr.pasteur.ida.zellige.gui.ChannelToolProperty;
		import fr.pasteur.ida.zellige.gui.ProjectionProperties;
		import fr.pasteur.ida.zellige.gui.ReferenceSurfacePanel;
		import fr.pasteur.ida.zellige.gui.interactor.ProjectionInteractor;
		import fr.pasteur.ida.zellige.gui.model.ProjectionModel;
		import fr.pasteur.ida.zellige.gui.parameter.ZelligeParameters;
		import javafx.beans.property.BooleanProperty;
		import javafx.beans.property.SimpleBooleanProperty;
		import javafx.collections.FXCollections;
		import javafx.collections.ObservableList;
		import fr.pasteur.ida.zellige.steps.projection.ProjectionParameters;
		import javafx.beans.property.SimpleIntegerProperty;
		import javafx.fxml.FXML;
		import javafx.fxml.Initializable;
		import javafx.scene.control.ComboBox;
		import javafx.scene.control.Spinner;
		import javafx.scene.control.SpinnerValueFactory;
		import javafx.scene.Node;
		import javafx.scene.control.*;
		import javafx.scene.image.ImageView;
		import javafx.scene.layout.FlowPane;
		import javafx.scene.layout.StackPane;
		import net.imglib2.type.NativeType;
		import net.imglib2.type.numeric.RealType;
		import org.slf4j.Logger;
		import org.slf4j.LoggerFactory;

		import java.net.URL;
		import java.util.ArrayList;
		import java.util.ResourceBundle;

		public class ProjectionController< T extends RealType< T > & NativeType< T > > implements Initializable
		{

		private final static Logger LOGGER = LoggerFactory.getLogger( ProjectionController.class );
		private final SimpleBooleanProperty changedParameters = new SimpleBooleanProperty();
		@FXML
		private Spinner< Integer > delta1;
		@FXML
		private ComboBox< String > methodComboBox;
		@FXML
		private CheckBoxDisplay extractedHeightMap;
		@FXML
		private CheckBoxDisplay segmentedSurface;

		private MainController< T > parentController;


		@FXML
		private CheckBoxDisplay reduced3DSpace;
		private StackPane stackPane;

		@FXML
		private CheckBoxDisplay segmentedSurfaceMask;
		private FlowPane display;

		@FXML
		private CheckBoxDisplay projection;
		private Button displayRS;

		@FXML
		private CheckBoxDisplay rawHeightMap;
		private Label log;

		@FXML
		private Spinner< Integer > delta2;
		private ChoiceBox< String > referenceSurfacesList;

		private ProjectionModel< T > model;
		private final SimpleIntegerProperty currentIndex = new SimpleIntegerProperty( 0 );
		private final ProjectionInteractor< T > interactor;

		@Override
		public void initialize( URL url, ResourceBundle resourceBundle )
		public ProjectionController()
		{
		// Model
		model = new ProjectionModel<>();

		//link Model with View
		model.methodProperty().bind( methodComboBox.valueProperty() );
		model.delta1Property().bind( delta1.valueProperty() );
		model.delta2Property().bind( delta2.valueProperty() );
		bindCheckBox( model.rawHMProperty(), model.rawHMDisplayProperty(), rawHeightMap );
		bindCheckBox( model.projectionProperty(), model.projectionDisplayProperty(), projection );
		bindCheckBox( model.extractedHMProperty(), model.extractedHMDisplayProperty(), extractedHeightMap );
		bindCheckBox( model.reduced3DspaceProperty(), model.reduced3DspaceDisplayProperty(), reduced3DSpace );
		bindCheckBox( model.segmentedSurfaceProperty(), model.segmentedSurfaceDisplayProperty(), segmentedSurface );
		bindCheckBox( model.segmentedSurfaceMaskProperty(), model.segmentedSurfaceMaskDisplayProperty(), segmentedSurfaceMask );


		/* Components*/
		SpinnerValueFactory< Integer > valueFactory =
		new SpinnerValueFactory.IntegerSpinnerValueFactory( 1, 30, 0 );
		delta1.setValueFactory( valueFactory );
		ObservableList< String > list = FXCollections.observableArrayList( "MIP", "Mean" );
		methodComboBox.setItems( list );
		methodComboBox.getSelectionModel().selectFirst();
		SpinnerValueFactory< Integer > valueFactory2 =
		new SpinnerValueFactory.IntegerSpinnerValueFactory( 1, 30, 0 );
		delta2.setValueFactory( valueFactory2 );

		delta1.valueProperty().addListener( ( observableValue, integer, t1 ) ->
		{
		model.delta1FunctionsProperty().setValue( false );
		resetDisplayMode();
		changedParameters.setValue( true );
		} );
		ProjectionModel< T > model = new ProjectionModel<>();
		this.interactor = new ProjectionInteractor<>( model );
		}

		delta2.valueProperty().addListener( ( observableValue, integer, t1 ) ->
		@Override
		public void initialize( URL url, ResourceBundle resourceBundle )
		{
		model.delta2FunctionsProperty().setValue( false );
		segmentedSurfaceMask.enable();
		changedParameters.setValue( true );
		} );


		projection.selectedProperty().addListener( ( observableValue, aBoolean, t1 ) ->
		getModel().getImageViews().addListener( ( observableValue, number, newValue ) ->
		{
		if ( model.delta1FunctionsProperty().getValue() && t1 && projection.isNotDisplayed() )
		if ( newValue != null )
		{

		model.showProjections();
		getModel().getReferenceSurfaces().
		set( parentController.getConstructionController().getModel().referenceSurfacesProperty().get() );
		}
		} );
		}
		);

		rawHeightMap.selectedProperty().addListener( ( observableValue, aBoolean, t1 ) ->
		// Listening of the reference surface choiceBox
		referenceSurfacesList.getSelectionModel().selectedIndexProperty().addListener( ( observableValue, number, newValue ) ->
		{
		if ( model.delta1FunctionsProperty().getValue() && t1 && rawHeightMap.isNotDisplayed() )
		if ( newValue.intValue() != -1 )
		{
		model.showRawHeightMap();

		currentIndex.set( newValue.intValue() );
		LOGGER.debug( "Checking Reference surface n°{}", currentIndex.get() );
		setDisplay();
		setProjectionPane();
		}
		} );
		extractedHeightMap.selectedProperty().addListener( ( observableValue, aBoolean, t1 ) ->
		{
		if ( model.delta1FunctionsProperty().getValue() && t1 && extractedHeightMap.isNotDisplayed() )
		{

		model.showExtractedHeightMaps();
		}
		} );
		reduced3DSpace.selectedProperty().addListener( ( observableValue, aBoolean, t1 ) ->
		getModel().getReferenceSurfaces().addListener( ( observableValue, number, newValue ) ->
		{
		if ( model.delta1FunctionsProperty().getValue() && t1 && reduced3DSpace.isNotDisplayed() )
		if ( newValue != null )
		{

		model.showReduced3DSpace();
		}
		} );
		segmentedSurface.selectedProperty().addListener( ( observableValue, aBoolean, t1 ) ->
		listsInitialization();
		// Removes default projection pane
		stackPane.getChildren().clear();
		int channels = parentController.getPreprocessingController().getModel().getNbOfChannels().get();
		for ( int i = 0; i < getModel().getReferenceSurfaces().get().size(); i++ )
		{
		if ( model.delta1FunctionsProperty().getValue() && t1 && segmentedSurface.isNotDisplayed() )
		// sets a new projection panel according to the input channel number.
		ReferenceSurfacePanel< T > panel = new ReferenceSurfacePanel<>( channels );
		// Adding properties to each reference surfaces
		getModel().getProjectionProperties().get().add( panel.getProjectionProperties() );
		stackPane.getChildren().add( panel );
		panel.getRun().setOnAction( actionEvent ->
		{

		model.showSegmentedSurface();
		}
		interactor.setParameters( panel );
		interactor.runProjection( currentIndex.get() );
		} );
		segmentedSurfaceMask.selectedProperty().addListener( ( observableValue, aBoolean, t1 ) ->
		for ( int j = 0; j < panel.getChannelTools().getTabs().size(); j++ )
		{
		if ( model.delta2FunctionsProperty().getValue() && t1 && segmentedSurfaceMask.isNotDisplayed() )
		final int channel = j;
		ChannelPanel channelPanel = ( ChannelPanel ) panel.getChannelTools().getTabs().get( j ).getContent();
		channelPanel.getView().setOnAction( actionEvent ->
		{

		model.showSegmentedSurfaceMask();
		LOGGER.debug( "The view button has been pressed" );
		interactor.setParameters( currentIndex.intValue(),
		channel, channelPanel.getDeltaZ().getValue(),
		channelPanel.getOffset().getValue(), channelPanel.getMethod().getValue() );
		interactor.runSubVolume( currentIndex.intValue(), channel );
		} );
		}
		}
		referenceSurfacesList.getSelectionModel().selectFirst();
		}
		});

		// Model Properties
		model.referenceSurfacesProperty().addListener( ( observableValue, referenceSurfaces1, t1 ) ->
		{
		if ( t1 == null )
		{
		model.delta1FunctionsProperty().setValue( false );
		LOGGER.debug( "REFERENCE_SURFACES is NULL" );

		/* Components*/
		displayRS.setOnAction( actionEvent -> interactor.displayHM( currentIndex.intValue() ) );
		}
		else

		public void setDisplay()
		{
		LOGGER.info( "Extraction of {} surfaces", model.referenceSurfacesProperty().getValue().size() );
		LOGGER.debug( "Compute output delta1" );
		model.setOutputDelta1();
		resetDisplayMode();
		display.getChildren().clear();
		ImageView i = getModel().getImageViews().getValue()[ currentIndex.get() ];
		display.getChildren().add( i );
		// setting of ZSlider
		}
		} );

		model.delta1FunctionsProperty().addListener( ( observableValue, aBoolean, t1 ) ->
		public void setProjectionPane()
		{
		if ( ! t1 )
		int length = stackPane.getChildren().size();
		for ( int i = 0; i < length; i++ )
		{
		LOGGER.debug( "DELTA1_FUNCTIONS is NULL" );
		model.delta2FunctionsProperty().setValue( false );
		Node node = stackPane.getChildren().get( i );
		node.setVisible( i == currentIndex.get() );
		}
		else
		{
		LOGGER.debug( "Compute output delta2" );
		model.setOutputDelta2();
		LOGGER.debug( "Displaying channel panel n°{}\n", ( currentIndex.get() + 1 ) );
		}
		} );

		model.delta2FunctionsProperty().addListener( ( observable, oldValue, newValue ) ->

		private void listsInitialization()
		{
		if ( newValue )
		ArrayList< String > names = new ArrayList<>();
		if ( ! getModel().getReferenceSurfaces().get().isEmpty() )
		{
		model.showOutput();
		}
		else
		getModel().getReferenceSurfaces().get().forEach( rf ->
		{
		LOGGER.debug( "DELTA2_FUNCTIONS is NULL" );
		}
		// Creates the names
		names.add( rf.getName() );
		} );
		// Clears the ChoiceBox
		referenceSurfacesList.getItems().clear();
		// Fills the ChoiceBox
		referenceSurfacesList.getItems().addAll( names );
		// Display the first reference surface
		// display.getChildren().clear();
		// display.getChildren().add( getModel().getImageViews().get()[ 0 ] );


		}
		}


		private void resetDisplayMode()
		public void setParent( MainController< T > mainController )
		{
		extractedHeightMap.enable();
		projection.enable();
		segmentedSurface.enable();
		rawHeightMap.enable();
		reduced3DSpace.enable();
		segmentedSurfaceMask.enable();


		parentController = mainController;
		}

		public SimpleBooleanProperty changedParametersProperty()
		{
		return changedParameters;
		}

		public ProjectionModel< T > getModel()
		{
		return model;
		return interactor.getModel();
		}


		private void bindCheckBox( BooleanProperty selected, BooleanProperty notDisplayed, CheckBoxDisplay checkBox )
		public StackPane getStackPane()
		{
		selected.bind( checkBox.selectedProperty() );
		notDisplayed.bindBidirectional( checkBox.notDisplayedProperty() );
		return stackPane;
		}

		public void setParameters( ZelligeParameters parameters )
		{
		delta1.getValueFactory().setValue( parameters.getDelta1() );
		delta2.getValueFactory().setValue( parameters.getDelta2() );
		methodComboBox.getSelectionModel().select( parameters.getMethod() );
		ArrayList< ProjectionParameters > projectionParameters = parameters.getProjectionParameters();
		//TODO Dynamic loading ?
		}
		}

src/main/java/fr/pasteur/ida/zellige/gui/controller/SelectionController.java

+218 −124

Original line number	Diff line number	Diff line
		@@ -28,21 +28,25 @@
		*/
		package fr.pasteur.ida.zellige.gui.controller;

		import fr.pasteur.ida.zellige.gui.ParameterSlider;
		import fr.pasteur.ida.zellige.gui.ParameterSliderInteger;
		import fr.pasteur.ida.zellige.gui.ZSlicesSlider;
		import fr.pasteur.ida.zellige.gui.exception.NoParameterChangeException;
		import fr.pasteur.ida.zellige.gui.interactor.SelectionInteractor;
		import fr.pasteur.ida.zellige.gui.model.SelectionModel;
		import fr.pasteur.ida.zellige.gui.parameter.ZelligeParameters;
		import fr.pasteur.ida.zellige.gui.task.ImageFXDisplayTask;
		import fr.pasteur.ida.zellige.gui.task.*;
		import javafx.beans.property.DoubleProperty;
		import javafx.beans.property.IntegerProperty;
		import javafx.beans.property.SimpleBooleanProperty;
		import javafx.beans.value.ChangeListener;
		import javafx.beans.property.SimpleObjectProperty;
		import javafx.fxml.FXML;
		import javafx.fxml.Initializable;
		import javafx.geometry.Pos;
		import javafx.scene.control.Button;
		import javafx.scene.image.ImageView;
		import javafx.scene.layout.FlowPane;
		import net.imglib2.img.Img;
		import net.imglib2.type.NativeType;
		import net.imglib2.type.logic.BitType;
		import net.imglib2.type.numeric.RealType;
		import org.slf4j.Logger;
		import org.slf4j.LoggerFactory;
		@@ -50,14 +54,19 @@ import org.slf4j.LoggerFactory;
		import java.net.URL;
		import java.util.ResourceBundle;

		import static fr.pasteur.ida.zellige.gui.MainAppFrame.GUI_MARKER;
		import static fr.pasteur.ida.zellige.gui.controller.MainController.showInfo;


		public class SelectionController< T extends RealType< T > & NativeType< T > > implements Initializable
		{
		private final static Logger LOGGER = LoggerFactory.getLogger( SelectionController.class );


		private final SimpleBooleanProperty changedParameters = new SimpleBooleanProperty();
		//private final SimpleBooleanProperty changedParameters = new SimpleBooleanProperty();
		private final SimpleBooleanProperty disableGUI = new SimpleBooleanProperty();
		private SelectionModel selectionModel;

		private MainController< T > parentController;

		@FXML
		private ParameterSliderInteger amplitude;
		@@ -73,180 +82,234 @@ public class SelectionController< T extends RealType< T > & NativeType< T > > im
		private ParameterSliderInteger zBlur;
		@FXML
		private ZSlicesSlider zSlices;
		@FXML
		private Button run;

		private final SelectionInteractor interactor = new SelectionInteractor( new SelectionModel() );


		@Override
		public void initialize( URL url, ResourceBundle resourceBundle )
		{
		// model
		selectionModel = new SelectionModel();

		//link Model with View
		selectionModel.amplitudeProperty().bind( amplitude.sliderProperty() );
		selectionModel.otsuProperty().bind( otsu.sliderProperty() );
		selectionModel.islandProperty().bind( island.sliderProperty() );
		selectionModel.xyBlurProperty().bind( xyBlur.sliderProperty() );
		selectionModel.zBlurProperty().bind( zBlur.sliderProperty() );
		selectionModel.disableGUIProperty().bindBidirectional( disableGUI );
		/* JavaFx Components */

		/* Amplitude slider initialization */
		// Update the log when a slider is used
		parameterListening( amplitude, "Amplitude" );
		parameterListening( otsu, "Otsu" );
		parameterListening(island, "Island Search" );
		parameterListening( xyBlur, "XY Blur" );
		parameterListening( zBlur, "Z Blur" );

		amplitude.sliderProperty().addListener( ( observableValue, number, newValue ) ->
		stack.setAlignment( Pos.CENTER );

		// section Slider initialization
		zSlices.getSlider().valueProperty().addListener( ( observableValue, number, newValue ) ->
		{
		if ( amplitude.hasChanged( newValue ) && selectionModel.selectedAmplitudeProperty().getValue() != null )
		int newZValue = newValue.intValue();
		if ( zSlices.hasChanged( newZValue ) )
		{
		disableGUI.setValue( true );
		selectionModel.runAmplitudeTask();
		changedParameters.setValue( true );
		LOGGER.debug( "Slice n° {} is displayed.", newZValue );
		refreshDisplay( newZValue );
		}
		} );

		/* Otsu slider initialization */
		otsu.sliderProperty().addListener( ( observableValue, number, newValue ) ->
		run.setOnAction( actionEvent ->
		{
		if ( otsu.hasChanged( newValue ) && selectionModel.selectedOtsuProperty().getValue() != null )

		run();
		} );

		/* Properties */
		// Set the linked output to null when the related parameter value has changed.
		resetOutputFromParameter( getModel().selectedAmplitudeProperty(), getModel().amplitudeProperty() );
		resetOutputFromParameter( getModel().selectedOtsuProperty(), getModel().otsuProperty() );
		resetOutputFromParameter( getModel().islandSearchImageProperty(), getModel().islandProperty() );
		resetOutputFromParameter( getModel().selectedPixelsProperty(), getModel().zBlurProperty() );
		resetOutputFromParameter( getModel().selectedPixelsProperty(), getModel().xyBlurProperty() );


		disableGUI.addListener( ( observable, oldValue, newValue ) ->
		{
		disableGUI.setValue( true );
		selectionModel.runOtsuTask();
		changedParameters.setValue( true );
		if ( newValue )
		{
		disableParameters();
		}
		else
		{
		enableParameters();
		}
		} );

		island.getSlider().valueProperty().addListener( ( observableValue, number, t1 ) ->
		/* Chain reaction : if one parameter value is changed the following outputs are reset. */
		setNextOutputToNull( getModel().pretreatedImgProperty(), getModel().imagesProperty() );

		setNextOutputToNull( getModel().imagesProperty(), getModel().selectedAmplitudeProperty() );
		setNextOutputToNull( getModel().imagesProperty(), getModel().selectedOtsuProperty() );

		setNextOutputToNull( getModel().selectedAmplitudeProperty(), getModel().interClassifiedImageProperty() );
		setNextOutputToNull( getModel().selectedOtsuProperty(), getModel().interClassifiedImageProperty() );

		setNextOutputToNull( getModel().interClassifiedImageProperty(), getModel().islandSearchImageProperty() );


		setNextOutputToNull( getModel().islandSearchImageProperty(), getModel().selectedPixelsProperty() );

		setNextOutputToNull( getModel().selectedPixelsProperty(), getModel().imageViewsProperty() );

		getModel().pretreatedImgProperty().addListener( ( observableValue, number, newValue ) ->
		{
		if ( island.hasChanged( t1 ) )
		LOGGER.debug( "Pretreated image value update." );
		if ( getModel().pretreatedImgProperty().getValue() != null )
		{
		selectionModel.setIslandSearchImage( null );
		changedParameters.setValue( true );
		LOGGER.debug( " Update value is valid : starting computing classified images" );
		interactor.computeClassifiedImages();
		}
		} );

		xyBlur.sliderProperty().addListener( ( observable, oldValue, newValue ) ->
		getModel().imagesProperty().addListener( ( observableValue, number, newValue ) ->
		{
		if ( xyBlur.hasChanged( newValue ) )
		if ( newValue != null )
		{
		selectionModel.setSelectedPixels( null );
		changedParameters.setValue( true );

		interactor.runAmplitudeTask();
		interactor.runOtsuTask();
		}
		} );
		zBlur.sliderProperty().addListener( ( observable, oldValue, newValue ) ->

		getModel().selectedAmplitudeProperty().addListener( ( observableValue, number, newValue ) ->
		{
		if ( zBlur.hasChanged( newValue ) )
		if ( newValue != null && getModel().selectedOtsuProperty().getValue() != null )
		{
		selectionModel.setSelectedPixels( null );
		changedParameters.setValue( true );
		interactor.runInterClassification();
		}
		} );
		stack.setAlignment( Pos.CENTER );

		// section Slider initialization
		zSlices.getSlider().valueProperty().addListener( ( observableValue, number, newValue ) ->
		getModel().selectedOtsuProperty().addListener( ( observableValue, number, newValue ) ->
		{
		int newZValue = newValue.intValue();
		if ( zSlices.hasChanged( newZValue ) )
		if ( newValue != null && getModel().selectedAmplitudeProperty().getValue() != null )
		{
		refreshDisplay( newZValue );
		interactor.runInterClassification();
		}
		} );

		/* Properties */

		disableGUI.addListener( ( observable, oldValue, newValue ) ->
		getModel().interClassifiedImageProperty().addListener( ( observableValue, number, newValue ) ->
		{
		if ( newValue )
		if ( newValue != null )
		{
		disableParameters();
		interactor.runIslandSearch();
		}
		else
		} );

		getModel().islandSearchImageProperty().addListener( ( observableValue, number, newValue ) ->
		{
		enableParameters();
		if ( newValue != null )
		{
		interactor.runSmoothing();
		}
		} );
		selectionModel.imagesProperty().addListener( ( observableValue, classifiedImages, t1 ) ->

		getModel().selectedPixelsProperty().addListener( ( observableValue, number, newValue ) ->
		{
		if ( t1 != null )
		if ( newValue != null )
		{
		selectionModel.runAmplitudeTask();
		selectionModel.runOtsuTask();
		computeImageFXDisplay();
		}
		else
		{
		LOGGER.debug( "IMAGES is NULL" );
		selectionModel.selectedAmplitudeProperty().setValue( null );
		selectionModel.selectedOtsuProperty().setValue( null );
		selectionModel.interClassifiedImageProperty().setValue( null );
		} );
		}

		} );
		ChangeListener< Img< BitType > > listener = ( observableValue, bitTypeClassifiedImages, t1 ) ->


		public void run()
		{
		if ( selectionModel.selectedAmplitudeProperty().getValue() != null && selectionModel.selectedOtsuProperty().getValue() != null )
		parentController.getPreprocessingController().checkParameters();
		checkParameters();
		if (! parentController.getPreprocessingController().getInteractor().getModel().getParameterChanged().get() && ! getModel().getParameterChanged().get())
		{
		selectionModel.runInterClassification();
		LOGGER.debug( "Inter classification" );
		showInfo( new NoParameterChangeException() );
		}
		else
		{
		LOGGER.debug( "SELECTED_AMPLITUDE or SELECTED_OTSU is NULL" );
		selectionModel.interClassifiedImageProperty().setValue( null );
		if ( getModel().pretreatedImgProperty().getValue() == null )
		{
		disableGUI.setValue( true );
		parentController.getPreprocessingController().getInteractor().runPreprocessing();
		}

		};

		selectionModel.selectedAmplitudeProperty().addListener( listener );
		selectionModel.selectedOtsuProperty().addListener( listener );


		selectionModel.interClassifiedImageProperty().addListener( ( observable, oldValue, newValue ) ->
		else if ( getModel().selectedAmplitudeProperty().getValue() == null \|\| getModel().selectedOtsuProperty().getValue() == null )
		{
		LOGGER.info( "Computing double classification..." );
		if ( newValue != null )
		disableGUI.setValue( true );
		if ( getModel().selectedAmplitudeProperty().getValue() == null )
		{
		computeImageFXDisplay();
		interactor.runAmplitudeTask();
		}
		selectionModel.islandSearchImageProperty().setValue( null );
		} );

		selectionModel.islandSearchImageProperty().addListener( ( observableValue, bitTypes, t1 ) ->
		if ( getModel().selectedOtsuProperty().getValue() == null )
		{
		if ( t1 == null )
		interactor.runOtsuTask();
		}
		}
		else if (getModel().islandSearchImageProperty().getValue() == null )
		{
		LOGGER.debug( "ISLAND_SEARCH is NULL" );
		selectionModel.selectedPixelsProperty().setValue( null );
		disableGUI.setValue( true );
		interactor.runIslandSearch();
		}
		else
		else if ( getModel().selectedPixelsProperty().getValue() == null )
		{
		selectionModel.runSmoothing();
		disableGUI.setValue( true );
		interactor.runSmoothing();
		}
		}
		} );
		}

		private void checkParameters()
		{
		setParameterValue( amplitude, getModel().amplitudeProperty() );
		setParameterValue( otsu, getModel().otsuProperty() ) ;
		setParameterValue( island, getModel().islandProperty() );
		setParameterValue( xyBlur, getModel().xyBlurProperty() );
		setParameterValue( zBlur, getModel().zBlurProperty() ) ;
		}




		private void setParameterValue( ParameterSlider slider, IntegerProperty property)
		{
		if ( !property.getValue().equals( slider.getValue()))
		{
		LOGGER.debug( "model has changed with parameter {}", slider.getName() );
		property.setValue( slider.getValue() );
		getModel().getParameterChanged().set( true );
		}
		}

		public void computeImageFXDisplay()
		{
		ImageFXDisplayTask imageFXDisplayTask = new ImageFXDisplayTask( selectionModel.interClassifiedImageProperty() );
		imageFXDisplayTask.setOnSucceeded( workerStateEvent ->
		SelectionDisplayTask selectionDisplayTask = new SelectionDisplayTask( getModel().selectedPixelsProperty().getValue() );
		selectionDisplayTask.setOnSucceeded( workerStateEvent ->
		{
		LOGGER.info( "Double classification done." );
		selectionModel.imageViewsProperty().setValue( imageFXDisplayTask.getValue() );
		LOGGER.info( GUI_MARKER,"Double classification done!!!!!." );
		getModel().imageViewsProperty().setValue( selectionDisplayTask.getValue() );
		setDisplay();
		} );
		imageFXDisplayTask.start();
		selectionDisplayTask.start();
		}

		public void setDisplay()
		{
		stack.getChildren().clear();
		ImageView i = selectionModel.imageViewsProperty().getValue()[ zSlices.getUserValue() ];
		ImageView i = getModel().imageViewsProperty().getValue()[ zSlices.getUserValue() ];

		stack.getChildren().add( i );

		// setting of ZSlider
		this.setSliceNumber( ( int ) selectionModel.pretreatedImgProperty().getValue().dimension( 2 ) );
		this.setSliceNumber( ( int ) getModel().pretreatedImgProperty().getValue().dimension( 2 ) );
		int width = ( int ) i.boundsInParentProperty().get().getWidth();
		this.zSlices.getSlider().setMaxWidth( width );
		this.zSlices.getSlider().setVisible( true );

		// reset everything
		disableGUI.setValue( false );
		getModel().getParameterChanged().set( false );
		parentController.getPreprocessingController().getModel().getParameterChanged().set( false );
		}


		@@ -258,7 +321,7 @@ public class SelectionController< T extends RealType< T > & NativeType< T > > im
		public void refreshDisplay( int value )
		{
		this.stack.getChildren().clear();// Removal of previous slice
		ImageView i = selectionModel.imageViewsProperty().getValue()[ value ];
		ImageView i = getModel().imageViewsProperty().getValue()[ value ];
		stack.getChildren().add( i ); // display of selected z slice
		}

		@@ -269,20 +332,27 @@ public class SelectionController< T extends RealType< T > & NativeType< T > > im

		public void set()
		{
		this.setSliceNumber( ( int ) selectionModel.pretreatedImgProperty().getValue().dimension( 2 ) );
		this.setSliceNumber( ( int ) getModel().pretreatedImgProperty().getValue().dimension( 2 ) );
		}

		public void enableParameters()
		{
		this.amplitude.enable();
		this.otsu.enable();

		this.island.enable();
		this.zBlur.enable();
		this.xyBlur.enable();
		this.stack.setVisible( true );
		}

		public void disableParameters()
		{
		this.amplitude.disable();
		this.otsu.disable();
		this.island.disable();
		this.zBlur.disable();
		this.xyBlur.disable();
		this.stack.setVisible( false );
		}


		@@ -301,42 +371,66 @@ public class SelectionController< T extends RealType< T > & NativeType< T > > im
		return otsu;
		}

		public ParameterSliderInteger getXyBlur()
		public SimpleBooleanProperty disableGUIProperty()
		{
		return xyBlur;
		return disableGUI;
		}

		public ParameterSliderInteger getzBlur()
		public SelectionModel getModel()
		{
		return zBlur;
		return interactor.getModel();
		}

		public boolean isChangedParameters()



		public void setParameters( ZelligeParameters parameters )
		{
		return changedParameters.get();
		amplitude.setValue( parameters.getSelectionParameters().getAmplitude() );
		otsu.setValue( parameters.getSelectionParameters().getOtsu() );
		island.setValue( parameters.getSelectionParameters().getIsland() );
		xyBlur.setValue( parameters.getSelectionParameters().getXyBlur() );
		zBlur.setValue( parameters.getSelectionParameters().getzBlur() );
		}

		public SimpleBooleanProperty changedParametersProperty()
		public void setParent( MainController< T > mainController )
		{
		return changedParameters;
		parentController = mainController;
		}

		public SimpleBooleanProperty disableGUIProperty()
		public static void setNextOutputToNull( SimpleObjectProperty< ? > property, SimpleObjectProperty< ? > nextOutput )
		{
		return disableGUI;
		property.addListener( ( observable, oldValue, newValue ) ->
		{
		if ( newValue != oldValue && newValue == null )
		{
		LOGGER.debug( "Next output set to null...." );
		nextOutput.set( null );
		}
		} );
		}

		public SelectionModel getSelectionModel()
		private void parameterListening( ParameterSlider slider, String parameterName )
		{
		return selectionModel;
		slider.sliderProperty().addListener( ( observable, oldValue, newValue ) ->
		{
		if ( slider.hasChanged( newValue ) && newValue != null )
		{
		LOGGER.debug( "The {} parameter has been changed, new value: {}.", parameterName, newValue );
		}
		} );
		}

		public void setParameters( ZelligeParameters parameters )

		public void resetOutputFromParameter( SimpleObjectProperty< ? > result, IntegerProperty property )
		{
		amplitude.setValue( parameters.getAmplitude() );
		otsu.setValue( parameters.getOtsu() );
		island.setValue( parameters.getIsland() );
		xyBlur.setValue( parameters.getXyBlur() );
		zBlur.setValue( parameters.getzBlur() );
		property.addListener( ( observable, oldValue, newValue ) ->
		result.set( null ) );
		}


		public SimpleBooleanProperty getDisableGUI()
		{
		return disableGUI;
		}
		}

src/main/java/fr/pasteur/ida/zellige/gui/controller/Utils.java

0 → 100644

+12 −0

Original line number	Diff line number	Diff line
		package fr.pasteur.ida.zellige.gui.controller;

		import javafx.beans.property.Property;

		public class Utils
		{

		public static void setPropertyValue ( Property<Number> controllerProperty, Property<Number> modelProperty )
		{
		modelProperty.setValue( controllerProperty.getValue());
		}
		}

src/main/java/fr/pasteur/ida/zellige/gui/exception/NoInputException.java

+3 −1

Original line number	Diff line number	Diff line
		@@ -31,7 +31,9 @@ package fr.pasteur.ida.zellige.gui.exception;
		public class NoInputException extends Exception
		{

		final String message = " No 3D stack loaded on ImageJ";
		final String message = "Oops! No Image Loaded\n" +
		"Before running the program, please load an image on Zellige (Input File) .\n" +
		"We need it to work our magic! ✨ ";

		@Override
		public String getMessage()

src/main/java/fr/pasteur/ida/zellige/gui/exception/NoParameterChangeException.java

0 → 100644

+13 −0

Original line number	Diff line number	Diff line
		package fr.pasteur.ida.zellige.gui.exception;

		public class NoParameterChangeException extends Exception
		{

		final String message = " No parameter has been modify !";

		@Override
		public String getMessage()
		{
		return message;
		}
		}

src/main/java/fr/pasteur/ida/zellige/gui/exception/NoPixelSelectionException.java

0 → 100644

+13 −0

Original line number	Diff line number	Diff line
		package fr.pasteur.ida.zellige.gui.exception;

		public class NoPixelSelectionException extends Exception
		{

		final String message = " No Pixel Selection previously performed, please select pixels first (//TODO : new message) ";

		@Override
		public String getMessage()
		{
		return message;
		}
		}

src/main/java/fr/pasteur/ida/zellige/gui/exception/NoSelectedInputException.java

0 → 100644

+13 −0

Original line number	Diff line number	Diff line
		package fr.pasteur.ida.zellige.gui.exception;

		public class NoSelectedInputException extends Exception
		{

		final String message = " Please select a file!";

		@Override
		public String getMessage()
		{
		return message;
		}
		}

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

0 → 100644

+99 −0

Original line number	Diff line number	Diff line
		package fr.pasteur.ida.zellige.gui.interactor;

		import fr.pasteur.ida.zellige.element.ReferenceSurface;
		import fr.pasteur.ida.zellige.element.Surface;
		import fr.pasteur.ida.zellige.gui.model.ConstructionModel;
		import fr.pasteur.ida.zellige.gui.task.AbstractTask;
		import fr.pasteur.ida.zellige.gui.task.ConstructionCompletionTask;
		import fr.pasteur.ida.zellige.gui.task.RunFirstConstructionTask;
		import fr.pasteur.ida.zellige.gui.task.RunSecondConstructionTask;
		import fr.pasteur.ida.zellige.steps.construction.exception.FirstRoundConstructionException;
		import fr.pasteur.ida.zellige.steps.construction.exception.SecondRoundConstructionException;
		import net.imglib2.type.NativeType;
		import net.imglib2.type.numeric.RealType;
		import org.slf4j.Logger;
		import org.slf4j.LoggerFactory;

		import java.util.ArrayList;

		import static fr.pasteur.ida.zellige.gui.MainAppFrame.GUI_MARKER;
		import static fr.pasteur.ida.zellige.gui.controller.MainController.showError;

		public class ConstructionInteractor< T extends RealType< T > & NativeType< T > >

		{

		Logger LOGGER = LoggerFactory.getLogger( ConstructionInteractor.class );

		private final ConstructionModel< T > model;

		public ConstructionInteractor( ConstructionModel< T > model )
		{
		this.model = model;
		}

		public void firstRound()
		{
		AbstractTask< ArrayList< Surface > > firstRoundTask =
		new RunFirstConstructionTask(
		model.maximumsProperty().get(),
		model.st1Property().get(),
		model.r1Property().get(),
		model.c1Property().get(),
		model.surfaceSizeProperty().get() / 100.0 );
		firstRoundTask.setOnSucceeded( workerStateEvent ->
		{
		model.firstRoundSurfacesProperty().setValue( firstRoundTask.getValue() );
		if ( firstRoundTask.getValue() == null )
		{
		model.getDisableGUI().set( false );
		showError( new FirstRoundConstructionException() );
		}
		} );
		firstRoundTask.start();
		}

		public void secondRound()
		{
		LOGGER.info( GUI_MARKER,"Computing second round construction..." );
		if ( model.firstRoundSurfacesProperty().getValue() != null )
		{
		AbstractTask< ArrayList< Surface > > secondRoundTask = new RunSecondConstructionTask(
		model.firstRoundSurfacesProperty().getValue(),
		model.st2Property().get(),
		model.r2Property().get(),
		model.c2Property().get(),
		model.surfaceSizeProperty().get() / 100.0 );
		secondRoundTask.setOnSucceeded( workerStateEvent ->
		{
		model.secondRoundSurfacesProperty().setValue( secondRoundTask.getValue() );
		if ( secondRoundTask.getValue() == null )
		{
		model.getDisableGUI().set( false );
		showError( new SecondRoundConstructionException() );
		}
		else
		{
		LOGGER.info(GUI_MARKER, "Second round construction done." );
		}
		} );

		secondRoundTask.start();
		}
		}


		public void constructionCompletion()
		{

		AbstractTask< ArrayList< ReferenceSurface< T > > > constructionCompletionTask = new ConstructionCompletionTask<>( model.getInput().getValue(), model.getFactory().getValue(), model.secondRoundSurfacesProperty().get() , model.getBin().get());
		constructionCompletionTask.setOnSucceeded( workerStateEvent ->
		model.referenceSurfacesProperty().setValue( constructionCompletionTask.getValue() ) );
		constructionCompletionTask.start();
		}

		public ConstructionModel< T > getModel()
		{
		return model;
		}
		}

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

0 → 100644

+49 −0

Original line number	Diff line number	Diff line
		package fr.pasteur.ida.zellige.gui.interactor;

		import fr.pasteur.ida.zellige.gui.exception.NoSelectedInputException;
		import fr.pasteur.ida.zellige.gui.model.PreprocessingModel;
		import fr.pasteur.ida.zellige.gui.task.AbstractTask;
		import fr.pasteur.ida.zellige.gui.task.PreprocessingTask;
		import net.imglib2.img.Img;
		import net.imglib2.type.NativeType;
		import net.imglib2.type.numeric.RealType;
		import net.imglib2.type.numeric.real.FloatType;

		import static fr.pasteur.ida.zellige.gui.controller.MainController.showError;

		public class PreprocessingInteractor < T extends RealType< T > & NativeType< T > >
		{
		private final PreprocessingModel<T> model;

		public PreprocessingInteractor( PreprocessingModel<T> model )
		{
		this.model = model;
		}


		public boolean runPreprocessing()
		{
		if (model.getInput_channel() == null )
		{
		showError( new NoSelectedInputException() );
		return false;
		}
		else
		{
		// if ( model.getParameterChanged().get() ) // if parameters has been modified
		{
		AbstractTask< Img< FloatType > > task = new PreprocessingTask<>(model.getInput_channel().getValue(), 2, model.binProperty().get() );
		task.setOnSucceeded( workerStateEvent ->
		model.pretreatedImgProperty().set( task.getValue() ) );
		task.start();
		return true;
		}
		}
		// return true;
		}

		public PreprocessingModel <T> getModel()
		{
		return model;
		}
		}

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

0 → 100644

+127 −0

Original line number	Diff line number	Diff line
		package fr.pasteur.ida.zellige.gui.interactor;

		import fr.pasteur.ida.zellige.element.ReferenceSurface;
		import fr.pasteur.ida.zellige.gui.ChannelPanel;
		import fr.pasteur.ida.zellige.gui.ChannelToolProperty;
		import fr.pasteur.ida.zellige.gui.ProjectionProperties;
		import fr.pasteur.ida.zellige.gui.ReferenceSurfacePanel;
		import fr.pasteur.ida.zellige.gui.model.ProjectionModel;
		import fr.pasteur.ida.zellige.gui.task.ProjectionTask;
		import fr.pasteur.ida.zellige.gui.task.SubVolumeTask;
		import fr.pasteur.ida.zellige.steps.projection.ReferenceSurfaceProjection;
		import ij.IJ;
		import net.imagej.ImgPlus;
		import net.imglib2.RandomAccessibleInterval;
		import net.imglib2.img.Img;
		import net.imglib2.img.display.imagej.ImageJFunctions;
		import net.imglib2.type.NativeType;
		import net.imglib2.type.numeric.RealType;
		import net.imglib2.view.Views;
		import org.scijava.Context;
		import org.slf4j.Logger;
		import org.slf4j.LoggerFactory;

		public class ProjectionInteractor< T extends RealType< T > & NativeType< T > >
		{
		private final static Logger LOGGER = LoggerFactory.getLogger( ProjectionInteractor.class );
		private final ProjectionModel< T > model;

		public ProjectionInteractor( ProjectionModel< T > model )
		{
		this.model = model;
		}

		public void runProjection( int index )
		{
		ReferenceSurface< T > referenceSurface = model.getReferenceSurfaces().get().get( index );
		ProjectionProperties< T > properties = model.getProjectionProperties().get().get( index );
		ProjectionTask< T > task = new ProjectionTask<>( referenceSurface, properties );
		task.setOnSucceeded( workerStateEvent ->
		{
		LOGGER.debug( "The projection has succeed!" );
		// Wraps the projection inside an ImgPlus to display the colors if necessary.
		ImgPlus< T > imgPlus = ReferenceSurfaceProjection.setColorsAndName( task.getValue(), getModel().getColors().get(), "" );
		Context context = ( Context ) IJ.runPlugIn( "org.scijava.Context", "" );
		net.imagej.ImageJ ij = new net.imagej.ImageJ( context );
		ij.ui().show( imgPlus );
		//TODO find a way to retrieve ij instance
		} );
		task.setOnFailed( workerStateEvent -> LOGGER.debug( "The projection has failed!" ) );
		task.start();
		}

		public void runSubVolume( int index, int channel )
		{
		// Selection of the reference surface
		ReferenceSurface< T > referenceSurface = model.getReferenceSurfaces().get().get( index );
		// Selection of the properties associated
		ProjectionProperties< T > properties = model.getProjectionProperties().get().get( index );
		RandomAccessibleInterval< T > input = Views.hyperSlice( referenceSurface.getInput(), 2, channel );
		ChannelToolProperty< T > channelToolProperty = properties.getProperties().get().get( channel );
		if ( channelToolProperty.getSubVolume().get() == null )
		{
		int delta = channelToolProperty.getDeltaZ().get();
		int offset = channelToolProperty.getOffset().get();
		SubVolumeTask< T > task = new SubVolumeTask<>( input, referenceSurface.getFactory(), referenceSurface.getzMap(), delta, offset );
		task.setOnSucceeded( workerStateEvent ->
		{
		Img< T > subVolume = task.getValue();
		channelToolProperty.getSubVolume().set( subVolume );
		LOGGER.debug( "SubVolume dimensions:{}.", subVolume.dimensionsAsLongArray() );
		String title = String.format( "SubVolume_RS_%d_channel_%d", ( index + 1 ), ( channel + 1 ) );
		ImageJFunctions.show( subVolume, title );
		} );
		task.setOnFailed( workerStateEvent -> LOGGER.debug( "The subVolume task has failed!" ) );
		task.start();
		}
		}

		public void displayHM( int index )
		{
		ReferenceSurface< T > referenceSurface = model.getReferenceSurfaces().get().get( index );
		ImageJFunctions.show( referenceSurface.getzMap() );
		}

		public void setParameters( ReferenceSurfacePanel< T > panel )
		{
		for ( int channel = 0; channel < panel.getChannelTools().getTabs().size(); channel++ )
		{
		ChannelPanel channelPanel = ( ChannelPanel ) panel.getChannelTools().getTabs().get( channel ).getContent();
		ChannelToolProperty< T > channelToolProperty = panel.getProjectionProperties().getProperties().get().get( channel );
		setParameters( channelToolProperty, channelPanel.getDeltaZ().getValue(), channelPanel.getOffset().getValue(), channelPanel.getMethod().getValue() );
		}
		}


		public void setParameters( ChannelToolProperty< T > channelToolProperty, int delta, int offset, String method )
		{

		if ( delta != channelToolProperty.getDeltaZ().get() )
		{
		channelToolProperty.getDeltaZ().set( delta );
		}
		if ( offset != channelToolProperty.getOffset().get() )
		{
		channelToolProperty.getOffset().set( offset );
		}
		if ( ! method.equals( channelToolProperty.getMethod().get() ) )
		{
		channelToolProperty.getMethod().set( method );
		}
		}

		public void setParameters( final int index, int channel, int delta, int offset, String method )
		{
		ProjectionProperties< T > projectionProperties = getModel().getProjectionProperties().get().get( index );
		ChannelToolProperty< T > channelToolProperty = projectionProperties.getProperties().get().get( channel );
		setParameters( channelToolProperty, delta, offset, method );
		}


		public ProjectionModel< T > getModel()
		{
		return model;
		}


		}

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

0 → 100644

+72 −0

Original line number	Diff line number	Diff line
		package fr.pasteur.ida.zellige.gui.interactor;

		import fr.pasteur.ida.zellige.gui.model.SelectionModel;
		import fr.pasteur.ida.zellige.gui.task.*;

		public class SelectionInteractor
		{

		private final SelectionModel model;

		public SelectionInteractor( SelectionModel model )
		{
		this.model = model;
		}

		public void computeClassifiedImages()
		{
		ComputeClassificationImagesTask classifiedImagesTask = new ComputeClassificationImagesTask( model.pretreatedImgProperty().getValue() );
		classifiedImagesTask.setOnSucceeded( workerStateEvent -> model.imagesProperty().set( classifiedImagesTask.getValue() ) );
		classifiedImagesTask.start();
		}

		public void runAmplitudeTask()
		{
		AmplitudeThresholdingTask amplitudeTask = new AmplitudeThresholdingTask( model.imagesProperty().get().getAmplitudeImg(), model.amplitudeProperty().getValue().intValue() );
		amplitudeTask.setOnSucceeded( workerStateEvent ->
		model.selectedAmplitudeProperty().setValue( amplitudeTask.getValue() ) );
		// amplitudeTask.setOnFailed( workerStateEvent -> LOGGER.debug( "Amplitude classification has failed." ) );
		amplitudeTask.start();
		}

		public void runOtsuTask()
		{
		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." ) );
		otsuTask.start();
		}

		public void runInterClassification()
		{
		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().get(), model.islandProperty().get() );
		islandSearchTask.setOnSucceeded( workerStateEvent ->
		model.islandSearchImageProperty().setValue( islandSearchTask.getValue() ) );
		// islandSearchTask.setOnFailed( workerStateEvent -> LOGGER.debug( "FAILED" ) );
		islandSearchTask.start();
		}

		public void runSmoothing()
		{
		SmoothingTask smoothingTask = new SmoothingTask(
		model.islandSearchImageProperty().get(),
		model.xyBlurProperty().get(),
		model.zBlurProperty().get() );
		smoothingTask.setOnSucceeded( event ->
		model.selectedPixelsProperty().setValue( smoothingTask.getValue() ) );
		smoothingTask.start();
		}

		public SelectionModel getModel()
		{
		return model;
		}
		}

src/main/java/fr/pasteur/ida/zellige/gui/model/ConstructionModel.java

+37 −78

Original line number	Diff line number	Diff line
		@@ -28,24 +28,20 @@
		*/
		package fr.pasteur.ida.zellige.gui.model;

		import fr.pasteur.ida.zellige.element.Pixels;
		import fr.pasteur.ida.zellige.element.ReferenceSurface;
		import fr.pasteur.ida.zellige.element.Surface;
		import fr.pasteur.ida.zellige.gui.ZDoubleProperty;
		import fr.pasteur.ida.zellige.gui.controller.MainController;
		import fr.pasteur.ida.zellige.gui.task.AbstractTask;
		import fr.pasteur.ida.zellige.gui.task.ConstructionCompletionTask;
		import fr.pasteur.ida.zellige.gui.task.RunFirstConstructionTask;
		import fr.pasteur.ida.zellige.gui.task.RunSecondConstructionTask;
		import fr.pasteur.ida.zellige.steps.construction.exception.FirstRoundConstructionException;
		import fr.pasteur.ida.zellige.steps.construction.exception.SecondRoundConstructionException;
		import javafx.beans.property.IntegerProperty;
		import javafx.beans.property.SimpleBooleanProperty;
		import javafx.beans.property.SimpleIntegerProperty;
		import javafx.beans.property.SimpleObjectProperty;
		import javafx.scene.image.ImageView;
		import net.imglib2.RandomAccessibleInterval;
		import net.imglib2.img.Img;
		import net.imglib2.img.ImgFactory;
		import net.imglib2.type.NativeType;
		import net.imglib2.type.numeric.RealType;
		import net.imglib2.type.numeric.real.FloatType;
		import org.slf4j.Logger;
		import org.slf4j.LoggerFactory;

		@@ -56,6 +52,7 @@ public class ConstructionModel< T extends RealType< T > & NativeType< T > >

		private final static Logger LOGGER = LoggerFactory.getLogger( ConstructionModel.class );

		private final IntegerProperty bin;
		private final ZDoubleProperty c1;
		private final ZDoubleProperty c2;
		private final IntegerProperty r1;
		@@ -65,13 +62,18 @@ public class ConstructionModel< T extends RealType< T > & NativeType< T > >
		private final ZDoubleProperty surfaceSize;
		private final SimpleObjectProperty< ArrayList< Surface > > firstRoundSurfaces = new SimpleObjectProperty<>();
		private final SimpleObjectProperty< ArrayList< Surface > > secondRoundSurfaces = new SimpleObjectProperty<>();
		private final SimpleObjectProperty< ArrayList< ReferenceSurface< T > > > referenceSurfaces = new SimpleObjectProperty<>();
		private final SimpleObjectProperty< Pixels[][] > maximums = new SimpleObjectProperty<>();
		private RandomAccessibleInterval< T > input;
		private ImgFactory< T > factory;
		private final SimpleObjectProperty< ArrayList< ReferenceSurface< T > > > referenceSurfaces = new SimpleObjectProperty<>(new ArrayList<>());
		private final SimpleObjectProperty< Img< FloatType > >maximums = new SimpleObjectProperty<>();
		private final SimpleObjectProperty< RandomAccessibleInterval <T> > channelInput = new SimpleObjectProperty<>();
		private final SimpleObjectProperty< RandomAccessibleInterval <T> > input = new SimpleObjectProperty<>();
		private final SimpleObjectProperty< ImgFactory< T >> factory = new SimpleObjectProperty<>();
		private final SimpleObjectProperty< ImageView[] > imageViews = new SimpleObjectProperty<>();
		private final SimpleBooleanProperty parameterChanged = new SimpleBooleanProperty(false);
		private final SimpleBooleanProperty disableGUI = new SimpleBooleanProperty();

		public ConstructionModel()
		{
		bin = new SimpleIntegerProperty();
		c1 = new ZDoubleProperty();
		c2 = new ZDoubleProperty();
		r1 = new SimpleIntegerProperty();
		@@ -81,64 +83,12 @@ public class ConstructionModel< T extends RealType< T > & NativeType< T > >
		surfaceSize = new ZDoubleProperty();
		}

		public void firstRound()
		{
		LOGGER.info( "Computing first round construction..." );
		AbstractTask< ArrayList< Surface > > firstRoundTask = new RunFirstConstructionTask( maximums.getValue(), st1.doubleValue(), r1.intValue(), c1.doubleValue(), surfaceSize.doubleValue() / 100.0 );
		firstRoundTask.setOnSucceeded( workerStateEvent ->
		{
		firstRoundSurfaces.setValue( firstRoundTask.getValue() );
		if ( firstRoundTask.getValue() == null )
		{
		LOGGER.info( "" ); //TODO write right message
		MainController.showError( new FirstRoundConstructionException() );
		}
		} );
		LOGGER.info( "First round construction done." );
		firstRoundTask.start();
		}


		public void secondRound()
		{
		LOGGER.info( "Computing second round construction..." );
		AbstractTask< ArrayList< Surface > > secondRoundTask = new RunSecondConstructionTask( firstRoundSurfacesProperty().getValue(), st2.getValue(), r2.intValue(), c2.doubleValue(), surfaceSize.doubleValue() / 100.0 );
		secondRoundTask.setOnSucceeded( workerStateEvent ->
		{
		secondRoundSurfacesProperty().setValue( secondRoundTask.getValue() );
		if ( secondRoundTask.getValue() == null )
		{
		LOGGER.info( "" ); //TODO write right message
		MainController.showError( new SecondRoundConstructionException() );
		}
		} );
		LOGGER.info( "Second round construction done." );
		secondRoundTask.start();
		}

		public void runConstruction()
		{
		LOGGER.debug( "Run construction" );
		if ( firstRoundSurfacesProperty().getValue() == null )
		{
		firstRound();
		}
		else if ( secondRoundSurfaces.getValue() == null )
		{
		secondRound();
		}
		}


		public void constructionCompletion()
		public IntegerProperty getBin()
		{
		AbstractTask< ArrayList< ReferenceSurface< T > > > constructionCompletionTask = new ConstructionCompletionTask<>( input, factory, secondRoundSurfaces.getValue() );
		constructionCompletionTask.setOnSucceeded( workerStateEvent ->
		referenceSurfacesProperty().setValue( constructionCompletionTask.getValue() ) );
		constructionCompletionTask.start();
		return bin;
		}


		public ZDoubleProperty c1Property()
		{
		return c1;
		@@ -189,34 +139,43 @@ public class ConstructionModel< T extends RealType< T > & NativeType< T > >
		return referenceSurfaces;
		}

		public void setInput( RandomAccessibleInterval< T > input )
		public SimpleBooleanProperty getParameterChanged()
		{
		return parameterChanged;
		}

		public SimpleObjectProperty< RandomAccessibleInterval< T > > getChannelInput()
		{
		this.input = input;
		return channelInput;
		}

		public SimpleObjectProperty< RandomAccessibleInterval< T > > getInput()
		{
		return input;
		}

		public void setFactory( ImgFactory< T > factory )
		public SimpleObjectProperty< ImgFactory< T > > getFactory()
		{
		this.factory = factory;
		return factory;
		}

		public double getC1()
		public SimpleObjectProperty< Img<FloatType> > maximumsProperty()
		{
		return c1.get();
		return maximums;
		}

		public RandomAccessibleInterval< T > getInput()
		public SimpleObjectProperty< ImageView[] > getImageViews()
		{
		return input;
		return imageViews;
		}

		public ImgFactory< T > getFactory()
		public SimpleBooleanProperty getDisableGUI()
		{
		return factory;
		return disableGUI;
		}

		public SimpleObjectProperty< Pixels[][] > maximumsProperty()
		public int getSurfaceMax()
		{
		return maximums;
		return ( int ) (input.get().dimension( 0 )* input.get().dimension( 1 )/ (bin.get() * bin.get()));
		}
		}

src/main/java/fr/pasteur/ida/zellige/gui/model/MainModel.java

+12 −4

Original line number	Diff line number	Diff line
		@@ -33,18 +33,26 @@ import net.imglib2.type.numeric.RealType;

		public class MainModel< T extends RealType< T > & NativeType< T > >
		{

		private final PreprocessingModel< T > preprocessingModel;
		private final SelectionModel selectionModel;
		private final ConstructionModel< T > constructionModel;
		private final ProjectionModel< T > projectionModel;

		public MainModel( SelectionModel selectionModel, ConstructionModel< T > constructionModel, ProjectionModel< T > projectionModel )

		public MainModel( PreprocessingModel< T > preprocessingModel, SelectionModel selectionModel, ConstructionModel< T > constructionModel, ProjectionModel< T > projectionModel )
		{
		this.preprocessingModel = preprocessingModel;
		this.selectionModel = selectionModel;
		this.constructionModel = constructionModel;
		this.projectionModel = projectionModel;
		}


		public PreprocessingModel< T > getPreprocessingModel()
		{
		return preprocessingModel;
		}

		public SelectionModel getSelectionModel()
		{
		return selectionModel;

src/main/java/fr/pasteur/ida/zellige/gui/model/PreprocessingModel.java

0 → 100644

+84 −0

Original line number	Diff line number	Diff line
		package fr.pasteur.ida.zellige.gui.model;

		import javafx.beans.property.IntegerProperty;
		import javafx.beans.property.SimpleBooleanProperty;
		import javafx.beans.property.SimpleIntegerProperty;
		import javafx.beans.property.SimpleObjectProperty;
		import net.imglib2.RandomAccessibleInterval;
		import net.imglib2.display.ColorTable;
		import net.imglib2.img.Img;
		import net.imglib2.img.ImgFactory;
		import net.imglib2.type.NativeType;
		import net.imglib2.type.numeric.RealType;
		import net.imglib2.type.numeric.real.FloatType;

		import java.util.ArrayList;

		public class PreprocessingModel< T extends RealType< T > & NativeType< T > >
		{

		private final IntegerProperty bin = new SimpleIntegerProperty();

		private final IntegerProperty channel = new SimpleIntegerProperty();

		private final IntegerProperty nbOfChannels = new SimpleIntegerProperty();

		private final SimpleObjectProperty< RandomAccessibleInterval<T> > input = new SimpleObjectProperty<>();

		private final SimpleObjectProperty< RandomAccessibleInterval<T> > input_channel = new SimpleObjectProperty<>();

		private final SimpleObjectProperty< ImgFactory< T > > factory = new SimpleObjectProperty<>();

		private final SimpleObjectProperty< Img< FloatType > > pretreatedImg = new SimpleObjectProperty<>();

		private final SimpleBooleanProperty parameterChanged = new SimpleBooleanProperty(false);

		private final SimpleObjectProperty< ArrayList< ColorTable > > colors = new SimpleObjectProperty<>(new ArrayList<>());

		public IntegerProperty binProperty()
		{
		return bin;
		}

		public SimpleObjectProperty< Img< FloatType > > pretreatedImgProperty()
		{
		return pretreatedImg;
		}

		public IntegerProperty getChannel()
		{
		return channel;
		}

		public SimpleBooleanProperty getParameterChanged()
		{
		return parameterChanged;
		}

		public SimpleObjectProperty< ImgFactory< T > > getFactory()
		{
		return factory;
		}

		public SimpleObjectProperty< RandomAccessibleInterval< T > > getInput()
		{
		return input;
		}

		public IntegerProperty getNbOfChannels()
		{
		return nbOfChannels;
		}

		public SimpleObjectProperty< ArrayList<ColorTable > > getColors()
		{
		return colors;
		}

		public SimpleObjectProperty< RandomAccessibleInterval< T > > getInput_channel()
		{
		return input_channel;
		}


		}

src/main/java/fr/pasteur/ida/zellige/gui/model/ProjectionModel.java

+19 −282

Original line number	Diff line number	Diff line
		@@ -28,311 +28,48 @@
		*/
		package fr.pasteur.ida.zellige.gui.model;

		import fr.pasteur.ida.zellige.element.Projection;
		import fr.pasteur.ida.zellige.element.ReferenceSurface;
		import fr.pasteur.ida.zellige.steps.projection.ReferenceSurfaceProjection;
		import fr.pasteur.ida.zellige.gui.ProjectionProperties;
		import javafx.beans.property.*;
		import net.imglib2.img.Img;
		import net.imglib2.img.display.imagej.ImageJFunctions;
		import javafx.scene.image.ImageView;
		import net.imglib2.display.ColorTable;
		import net.imglib2.type.NativeType;
		import net.imglib2.type.numeric.RealType;
		import net.imglib2.type.numeric.integer.UnsignedShortType;
		import org.slf4j.Logger;
		import org.slf4j.LoggerFactory;

		import java.util.ArrayList;

		public class ProjectionModel< T extends RealType< T > & NativeType< T > >
		{
		private final static Logger LOGGER = LoggerFactory.getLogger( ProjectionModel.class );
		private final SimpleObjectProperty< ArrayList< ReferenceSurface< T > > > referenceSurfaces;
		private final SimpleBooleanProperty delta1Functions;
		private final SimpleBooleanProperty delta2Functions;
		private final IntegerProperty delta1;
		private final IntegerProperty delta2;

		private final StringProperty method;
		private final SimpleObjectProperty< ArrayList< ReferenceSurface< T > > > referenceSurfaces = new SimpleObjectProperty<>( new ArrayList<>() );
		private final SimpleObjectProperty< ArrayList< ProjectionProperties< T > > > projectionProperties = new SimpleObjectProperty<>( new ArrayList<>() );
		private final SimpleObjectProperty< ImageView[] > imageViews = new SimpleObjectProperty<>();

		private final SimpleIntegerProperty numberOfChannels = new SimpleIntegerProperty();

		private final BooleanProperty rawHM;
		private final BooleanProperty projection;
		private final BooleanProperty extractedHM;
		private final BooleanProperty reduced3Dspace;
		private final BooleanProperty segmentedSurface;
		private final BooleanProperty segmentedSurfaceMask;

		private final BooleanProperty rawHMDisplay;
		private final BooleanProperty projectionDisplay;
		private final BooleanProperty extractedHMDisplay;
		private final BooleanProperty reduced3DspaceDisplay;
		private final BooleanProperty segmentedSurfaceDisplay;
		private final BooleanProperty segmentedSurfaceMaskDisplay;

		public ProjectionModel()
		{
		this.referenceSurfaces = new SimpleObjectProperty<>();
		this.delta1Functions = new SimpleBooleanProperty( false );
		this.delta2Functions = new SimpleBooleanProperty( false );
		this.method = new SimpleStringProperty();
		this.delta1 = new SimpleIntegerProperty();
		this.delta2 = new SimpleIntegerProperty();
		this.rawHM = new SimpleBooleanProperty();
		this.projection = new SimpleBooleanProperty();
		this.extractedHM = new SimpleBooleanProperty();
		this.reduced3Dspace = new SimpleBooleanProperty();
		this.segmentedSurface = new SimpleBooleanProperty();
		this.segmentedSurfaceMask = new SimpleBooleanProperty();
		this.rawHMDisplay = new SimpleBooleanProperty( true );
		this.projectionDisplay = new SimpleBooleanProperty( true );
		this.extractedHMDisplay = new SimpleBooleanProperty( true );
		this.reduced3DspaceDisplay = new SimpleBooleanProperty( true );
		this.segmentedSurfaceDisplay = new SimpleBooleanProperty( true );
		this.segmentedSurfaceMaskDisplay = new SimpleBooleanProperty( true );
		}

		public void showSegmentedSurfaceMask()
		{
		for ( ReferenceSurface< T > referenceSurface : referenceSurfaces.getValue() )
		{
		ImageJFunctions.show( referenceSurface.getProjection().getSegmentedSurfaceMask(), "Surface_mask_" + referenceSurface.getIndex() );
		}
		}

		public void showSegmentedSurface()
		{

		for ( ReferenceSurface< T > referenceSurface : referenceSurfaces.getValue() )
		{
		ImageJFunctions.show( referenceSurface.getProjection().getSegmentedSurface(), "Segmented_surface_" + referenceSurface.getIndex() );
		}
		}

		public void showReduced3DSpace()
		{

		for ( ReferenceSurface< T > referenceSurface : referenceSurfaces.getValue() )
		{
		ImageJFunctions.show( referenceSurface.getProjection().getReduced3DSpace(), "Reduced_3D_space_" + referenceSurface.getIndex() );
		}
		}

		public void showExtractedHeightMaps()
		{
		for ( ReferenceSurface< T > referenceSurface : referenceSurfaces.getValue() )
		{
		ImageJFunctions.show( referenceSurface.getProjection().getExtractedHeightMap(), "Extracted_HM_" + referenceSurface.getIndex() );
		}
		}

		public void showRawHeightMap()
		{
		for ( ReferenceSurface< T > referenceSurface : referenceSurfaces.getValue() )
		{
		ImageJFunctions.show( referenceSurface.getzMap(), "Raw_HM_" + referenceSurface.getIndex() );
		}
		}

		public void showProjections()
		{
		for ( ReferenceSurface< T > referenceSurface : referenceSurfaces.getValue() )
		{
		ImageJFunctions.show( referenceSurface.getProjection().get(), "Projection_" + referenceSurface.getIndex() );
		}
		}

		public void runProjection()
		{

		LOGGER.debug( "Starting projections ! " );
		if ( ! delta1Functions.getValue() )
		{
		LOGGER.debug( "Output with delta1 " );
		setOutputDelta1();
		}
		if ( ! delta2Functions.getValue() )
		{
		LOGGER.debug( "Output with delta2 " );
		setOutputDelta2();
		}
		showOutput();
		}

		public void showOutput()
		{
		if ( rawHM.get() && rawHMDisplay.getValue() )
		{
		showRawHeightMap();
		rawHMDisplay.setValue( false );
		}
		if ( projection.get() && projectionDisplay.get() )
		{
		showProjections();
		projectionDisplay.setValue( false );
		}

		if ( extractedHM.get() && extractedHMDisplay.get() )
		{
		showExtractedHeightMaps();
		extractedHMDisplay.setValue( false );
		}
		if ( segmentedSurface.get() && segmentedSurfaceDisplay.get() )
		{
		showSegmentedSurface();
		segmentedSurface.setValue( false );
		}

		if ( reduced3Dspace.get() && reduced3DspaceDisplay.get() )
		{
		showReduced3DSpace();
		reduced3DspaceDisplay.setValue( false );
		}
		if ( segmentedSurfaceMask.get() && segmentedSurfaceMaskDisplay.get() )
		{
		showSegmentedSurfaceMask();
		segmentedSurfaceMask.setValue( false );
		}

		}

		public void setOutputDelta1()
		{

		for ( ReferenceSurface< T > referenceSurface : referenceSurfaces.getValue() )
		{
		Projection< T > projection = referenceSurface.getProjection();
		Img< UnsignedShortType > extractedHeightMap = ReferenceSurfaceProjection.getProjectionHeightMap( referenceSurface, method.get(), delta1.intValue() );
		projection.setExtractedHeightMap( extractedHeightMap );
		projection.setProjection( ReferenceSurfaceProjection.projection1( referenceSurface, this.method.get() ) );

		projection.setSegmentedSurface( ReferenceSurfaceProjection.getSegmentedSurface( extractedHeightMap, referenceSurface.getInput(), referenceSurface.getFactory() ) );
		projection.setReduced3DSpace( ReferenceSurfaceProjection.getExtractedHeightMapSubStack( referenceSurface, delta1.intValue() ) );
		}
		delta1Functions.setValue( true );
		}

		public void setOutputDelta2()
		{

		for ( ReferenceSurface< T > referenceSurface : referenceSurfaces.getValue() )
		{

		Projection< T > projection = referenceSurface.getProjection();
		projection.setSegmentedSurfaceMask( ReferenceSurfaceProjection.getSegmentedSurfaceMask( projection.getSegmentedSurface(), delta2.intValue() ) );

		}
		delta2Functions.setValue( true );
		}


		public ArrayList< ReferenceSurface< T > > getReferenceSurfaces()
		{
		return referenceSurfaces.get();
		}

		public SimpleObjectProperty< ArrayList< ReferenceSurface< T > > > referenceSurfacesProperty()
		private final SimpleObjectProperty<ArrayList< ColorTable >> colors = new SimpleObjectProperty<>();
		public SimpleObjectProperty< ArrayList< ReferenceSurface< T > > > getReferenceSurfaces()
		{
		return referenceSurfaces;
		}

		public SimpleBooleanProperty delta1FunctionsProperty()
		{
		return delta1Functions;
		}

		public SimpleBooleanProperty delta2FunctionsProperty()
		{
		return delta2Functions;
		}

		public IntegerProperty delta1Property()
		{
		return delta1;
		}

		public IntegerProperty delta2Property()
		{
		return delta2;
		}

		public BooleanProperty rawHMProperty()
		{
		return rawHM;
		}

		public boolean isProjection()
		{
		return projection.get();
		}

		public BooleanProperty projectionProperty()
		public SimpleObjectProperty< ImageView[] > getImageViews()
		{
		return projection;
		return imageViews;
		}

		public BooleanProperty extractedHMProperty()
		{
		return extractedHM;
		}

		public BooleanProperty reduced3DspaceProperty()
		{
		return reduced3Dspace;
		}

		public BooleanProperty segmentedSurfaceProperty()
		{
		return segmentedSurface;
		}

		public BooleanProperty segmentedSurfaceMaskProperty()
		{
		return segmentedSurfaceMask;
		}

		public String getMethod()
		{
		return method.get();
		}

		public void setMethod( String method )
		{
		this.method.set( method );
		}

		public StringProperty methodProperty()
		{
		return method;
		}


		public BooleanProperty rawHMDisplayProperty()
		{
		return rawHMDisplay;
		}

		public BooleanProperty projectionDisplayProperty()
		{
		return projectionDisplay;
		}

		public BooleanProperty extractedHMDisplayProperty()
		{
		return extractedHMDisplay;
		}


		public BooleanProperty reduced3DspaceDisplayProperty()
		public SimpleIntegerProperty getNumberOfChannels()
		{
		return reduced3DspaceDisplay;
		return numberOfChannels;
		}

		public BooleanProperty segmentedSurfaceDisplayProperty()
		public SimpleObjectProperty< ArrayList< ProjectionProperties< T > > > getProjectionProperties()
		{
		return segmentedSurfaceDisplay;
		return projectionProperties;
		}

		public BooleanProperty segmentedSurfaceMaskDisplayProperty()
		public SimpleObjectProperty< ArrayList< ColorTable > > getColors()
		{
		return segmentedSurfaceMaskDisplay;
		return colors;
		}
		}

src/main/java/fr/pasteur/ida/zellige/gui/model/SelectionModel.java

+27 −185

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src/main/java/fr/pasteur/ida/zellige/gui/parameter/ConstructionParameter.java

deleted100644 → 0

+0 −90

Original line number	Diff line number	Diff line
		/*-
		* #%L
		* Zellige
		* %%
		* Copyright (C) 2020 - 2023 Institut Pasteur
		* %%
		* Redistribution and use in source and binary forms, with or without
		* modification, are permitted provided that the following conditions are met:
		*
		* 1. Redistributions of source code must retain the above copyright notice,
		* this list of conditions and the following disclaimer.
		* 2. Redistributions in binary form must reproduce the above copyright notice,
		* this list of conditions and the following disclaimer in the documentation
		* and/or other materials provided with the distribution.
		*
		* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
		* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
		* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
		* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
		* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
		* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
		* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
		* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
		* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
		* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
		* POSSIBILITY OF SUCH DAMAGE.
		* #L%
		*/
		package fr.pasteur.ida.zellige.gui.parameter;

		import fr.pasteur.ida.zellige.gui.ZDoubleProperty;
		import javafx.beans.property.IntegerProperty;

		public class ConstructionParameter
		{

		private final double c1;
		private final int r1;
		private final double st1;
		private final double c2;
		private final int r2;
		private final double st2;
		private final int surfaceSize;

		public ConstructionParameter( ZDoubleProperty c1, IntegerProperty r1, ZDoubleProperty st1, ZDoubleProperty c2, IntegerProperty r2, ZDoubleProperty st2, ZDoubleProperty surfaceSize )
		{
		this.c1 = c1.value();
		this.r1 = r1.intValue();
		this.st1 = st1.value();
		this.c2 = c2.value();
		this.r2 = r2.intValue();
		this.st2 = st2.value();
		this.surfaceSize = surfaceSize.intValue();
		}

		public double getC1()
		{
		return c1;
		}

		public int getR1()
		{
		return r1;
		}

		public double getSt1()
		{
		return st1;
		}

		public double getC2()
		{
		return c2;
		}

		public int getR2()
		{
		return r2;
		}

		public double getSt2()
		{
		return st2;
		}

		public int getSurfaceSize()
		{
		return surfaceSize;
		}
		}

src/main/java/fr/pasteur/ida/zellige/gui/parameter/ProjectionParameter.java

deleted100644 → 0

+0 −62

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src/main/java/fr/pasteur/ida/zellige/gui/parameter/SelectionParameter.java

deleted100644 → 0

+0 −74

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src/main/java/fr/pasteur/ida/zellige/gui/parameter/ZelligeParameters.java

+23 −100

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

+9 −7

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

0 → 100644

+32 −0

Original line number	Diff line number	Diff line
		package fr.pasteur.ida.zellige.gui.task;

		import fr.pasteur.ida.zellige.steps.selection.util.Binning;
		import net.imglib2.RandomAccessibleInterval;
		import net.imglib2.img.Img;
		import net.imglib2.type.NativeType;
		import net.imglib2.type.numeric.RealType;
		import org.slf4j.Logger;
		import org.slf4j.LoggerFactory;

		import static fr.pasteur.ida.zellige.gui.MainAppFrame.GUI_MARKER;

		public class BinningTask < T extends RealType< T > & NativeType< T > > extends AbstractTask<Img<T>>
		{
		private final static Logger LOGGER = LoggerFactory.getLogger( BinningTask.class );
		private final int bin;
		private final RandomAccessibleInterval<T> input;

		public BinningTask( int bin, RandomAccessibleInterval< T > input )
		{
		this.bin = bin;
		this.input = input;
		}

		@Override
		protected Img<T> call() {
		LOGGER.info( GUI_MARKER,"Binning" );
		Img<T> binnedImage = Binning.run( input, bin );
		LOGGER.info( GUI_MARKER,"Image binned !" );
		return binnedImage;
		}
		}