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

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pom.xml

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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