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

@@ -64,8 +64,8 @@ public class Main
 
 
         // 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 !!!! */
+        final String imagePath ="C:\\Users\\ctrebeau\\Desktop\\ramp_20_20.tif";
+               // args[ 0 ]; /* The image path goes here !!!! */
         LOGGER.debug( imagePath );
         /* JY version for opening files. */
         final SCIFIOImgPlus< ? > imgPlus = IO.openAll( imagePath ).get( 0 );

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

@@ -51,6 +51,7 @@ public class Zellige extends ContextCommand
                 .toAbsolutePath()
                 .toString();
         String imageFilePath = "doc/Mouche.tif";
+        String imageFilePath2 = "doc/multi-channel-test.tif";
 
         // Launch ImageJ.
         ImageJ ij = new ImageJ();
@@ -61,7 +62,8 @@ public class Zellige extends ContextCommand
 
         // Display it.
         ij.ui().show( obj );
-
+        /*obj = ij.io().open( new File( currentFolder, imageFilePath2 ).getAbsolutePath() );
+        ij.ui().show( obj );*/
         ij.command().run( Zellige.class, true );
     }
 

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

+package fr.pasteur.ida.zellige.gui.controller;
+
+public class ChannelController
+{
+
+
+}

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

@@ -42,10 +42,7 @@ import fr.pasteur.ida.zellige.gui.parameter.ConstructionParameter;
 import fr.pasteur.ida.zellige.gui.parameter.ProjectionParameter;
 import fr.pasteur.ida.zellige.gui.parameter.SelectionParameter;
 import fr.pasteur.ida.zellige.gui.parameter.ZelligeParameters;
-import fr.pasteur.ida.zellige.gui.task.AbstractTask;
-import fr.pasteur.ida.zellige.gui.task.ComputeClassificationImagesTask;
-import fr.pasteur.ida.zellige.gui.task.DisplayDatasetChoicesTask;
-import fr.pasteur.ida.zellige.gui.task.PretreatmentTask;
+import fr.pasteur.ida.zellige.gui.task.*;
 import javafx.application.Platform;
 import javafx.beans.property.SimpleBooleanProperty;
 import javafx.beans.property.SimpleObjectProperty;
@@ -53,13 +50,13 @@ import javafx.collections.FXCollections;
 import javafx.collections.ObservableList;
 import javafx.fxml.FXML;
 import javafx.fxml.Initializable;
-import javafx.scene.control.Alert;
-import javafx.scene.control.Button;
-import javafx.scene.control.ComboBox;
-import javafx.scene.control.Label;
+import javafx.scene.control.*;
 import javafx.stage.FileChooser;
+import javafx.util.StringConverter;
 import net.imagej.Dataset;
-import net.imagej.ImgPlus;
+import net.imagej.display.DefaultDatasetView;
+import net.imagej.display.DefaultImageDisplay;
+import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.img.Img;
 import net.imglib2.type.NativeType;
 import net.imglib2.type.numeric.RealType;
@@ -78,25 +75,31 @@ public class MainController< T extends RealType< T > & NativeType< T > > impleme
 {
 
     private final static Logger LOGGER = LoggerFactory.getLogger( MainController.class );
-    private final SimpleObjectProperty< Dataset > currentDataset = new SimpleObjectProperty<>();
+    private int targetChannel = 1;
+    private final SimpleObjectProperty< DefaultDatasetView > currentDataset = new SimpleObjectProperty<>();
+    private final SimpleObjectProperty< Img< T > > referenceImage = new SimpleObjectProperty<>();
     private final SimpleObjectProperty< ClassifiedImages< FloatType > > images = new SimpleObjectProperty<>();
     private final SimpleObjectProperty< Img< FloatType > > pretreatedImg = new SimpleObjectProperty<>();
     private final SimpleBooleanProperty disableGUI = new SimpleBooleanProperty();
     private final SimpleBooleanProperty changedParameters = new SimpleBooleanProperty();
+
+    AbstractTask< Img< FloatType > > pretreatmentTask = null;
+    @FXML
+    Spinner<Integer> channels;
     @FXML
-    ComboBox< Dataset > activeDatasets;
+    ComboBox< DefaultDatasetView > activeDatasets;
+    ComboBox< DefaultImageDisplay > x;
     @FXML
     private Button runButton;
     @FXML
     private ConstructionController< T > constructionController;
-
     @FXML
     private Label logInfo;
     private MainAppFrame mainAppFrame;
     @FXML
     private ProjectionController< T > projectionController;
     @FXML
-    private SelectionController< T > selectionController;
+    private SelectionController selectionController;
 
 
     MainModel< T > model;
@@ -107,7 +110,6 @@ public class MainController< T extends RealType< T > & NativeType< T > > impleme
         alert.setTitle( "Error alert" );
         alert.setHeaderText( exception.getMessage() );
         alert.showAndWait();
-       // throw new RuntimeException(exception);
     }
 
     @Override
@@ -118,13 +120,30 @@ public class MainController< T extends RealType< T > & NativeType< T > > impleme
         activeDatasets.setOnMousePressed( event ->
                 setAndDisplayDatasetChoices() );// Update of the list of opened Fiji images
 
+        activeDatasets.setConverter( new StringConverter< DefaultDatasetView >()
+        {
+            @Override
+            public String toString( DefaultDatasetView defaultDatasetView )
+            {
+                if (defaultDatasetView!= null)
+                return defaultDatasetView.getData().getName();
+                return "";
+            }
+
+            @Override
+            public DefaultDatasetView fromString( String s )
+            {
+                return null;
+            }
+        } );
+
         activeDatasets.getSelectionModel().selectedItemProperty().addListener( ( observableValue, oldValue, newValue ) ->
         {
             LOGGER.debug( "selectedItemProperty : old value = {}, new value = {} ",  oldValue, newValue );
-            if(newValue!= null && isValid( newValue ))
+            channels.setDisable( false );
+            if(newValue!= null && isValid( newValue.getData() ))
             {
-
-                    setCurrentDataset( newValue );
+                currentDataset.setValue( newValue );
             }
             else
             {
@@ -132,13 +151,24 @@ public class MainController< T extends RealType< T > & NativeType< T > > impleme
             }
         } );
 
+        channels.valueProperty().addListener( (observableValue, oldValue, newValue ) ->
+        {
+            if(!channels.isDisable() && newValue!= getTargetChannel())
+            {
+                setTargetChannel( newValue );
+                setReferenceImage();
+            }
+        } );
+
         currentDataset.addListener( ( observableValue, dataset, t1 ) ->
         {
             if ( t1 != null )
             {
-                selectionController.disableParameters();
-                disableGUI.setValue( true );
-                runPretreatment( currentDataset.getValue() );
+                SpinnerValueFactory< Integer > valueFactory =
+                        new SpinnerValueFactory.IntegerSpinnerValueFactory( 1, (int) t1.getChannelCount(), 1 );
+                channels.setValueFactory( valueFactory );
+                setReferenceImage();
+                LOGGER.debug( "Current dataset Properties :{}", currentDataset.getValue().getData().getProperties() );
             }
             else
             {
@@ -147,6 +177,14 @@ public class MainController< T extends RealType< T > & NativeType< T > > impleme
             }
         } );
 
+        referenceImage.addListener(( observableValue, dataset, t1 ) ->
+        {
+            selectionController.disableParameters();
+            disableGUI.setValue( true );
+            LOGGER.debug("New reference image selected");
+            runPretreatment( referenceImage.getValue()  );
+        } );
+
         pretreatedImg.addListener( ( observable, oldValue, newValue ) ->
         {
             if ( newValue != null )
@@ -174,11 +212,15 @@ public class MainController< T extends RealType< T > & NativeType< T > > impleme
         /* Binding properties*/
         selectionController.getSelectionModel().pretreatedImgProperty().bind( pretreatedImg );
         selectionController.getSelectionModel().imagesProperty().bind( images );
-        constructionController.getConstructionModel().maximumsProperty().bind( selectionController.getSelectionModel().selectedPixelsProperty() );
-        projectionController.getModel().referenceSurfacesProperty().bind( constructionController.getConstructionModel().referenceSurfacesProperty() );
+        constructionController.getConstructionModel().maximumsProperty().bind(
+                selectionController.getSelectionModel().selectedPixelsProperty() );
+        projectionController.getModel().referenceSurfacesProperty().bind(
+                constructionController.getConstructionModel().referenceSurfacesProperty() );
         changedParameters.bindBidirectional( selectionController.changedParametersProperty() );
-        selectionController.changedParametersProperty().bindBidirectional( constructionController.changedParametersProperty() );
-        constructionController.changedParametersProperty().bindBidirectional( projectionController.changedParametersProperty() );
+        selectionController.changedParametersProperty().bindBidirectional(
+                constructionController.changedParametersProperty() );
+        constructionController.changedParametersProperty().bindBidirectional(
+                projectionController.changedParametersProperty() );
         disableGUI.bindBidirectional( selectionController.disableGUIProperty() );
 
         changedParameters.addListener( ( observable, oldValue, newValue ) ->
@@ -188,7 +230,6 @@ public class MainController< T extends RealType< T > & NativeType< T > > impleme
             {
                 LOGGER.debug( "Active button" );
                 disableGUI.setValue( false );
-
             }
         } );
 
@@ -201,12 +242,10 @@ public class MainController< T extends RealType< T > & NativeType< T > > impleme
 
     public void initExtraction()
     {
-
         LOGGER.debug( "Init Extraction" );
-        Dataset dataset = mainAppFrame.getImage().getActiveDataset();
-        LOGGER.debug( dataset.getImgPlus().firstElement().getClass().toGenericString() );
-        LOGGER.debug( "Function getFrames() :{}", dataset.getFrames() );
-        LOGGER.debug( "Properties :{}", dataset.getImgPlus().getProperties() );
+        DefaultDatasetView dataset = ( DefaultDatasetView ) mainAppFrame.getImage().getActiveDatasetView();
+        LOGGER.debug( dataset.getData().firstElement().getClass().toGenericString() );
+        LOGGER.debug( "Function getFrames() :{}", dataset.getData().getFrames() );
         if ( dataset == null )
         {
             showError( new NoInputException() );
@@ -238,13 +277,7 @@ public class MainController< T extends RealType< T > & NativeType< T > > impleme
         LOGGER.debug( "###########################################---NEW RUN---###########################################" );
     }
 
-    private void runPretreatment( Dataset dataset )
-    {
-        AbstractTask< Img< FloatType > > task = new PretreatmentTask<>( dataset );
-        task.setOnSucceeded( workerStateEvent ->
-                pretreatedImg.setValue( task.getValue() ) );
-        task.start();
-    }
+
 
     public void setAndDisplayDatasetChoices()
     {
@@ -252,10 +285,9 @@ public class MainController< T extends RealType< T > & NativeType< T > > impleme
         displayTask.setOnSucceeded( workerStateEvent ->
         {
             LOGGER.debug( "Datasets displayed successfully" );
-            ObservableList< Dataset > list = FXCollections.observableArrayList( displayTask.getValue() );
+            ObservableList< DefaultDatasetView > list = FXCollections.observableArrayList( displayTask.getValue() );
             list.add( null );
             activeDatasets.setItems( list );
-
             LOGGER.debug( "item selected : list size = " + list.size() );
             if ( list.isEmpty() )
             {
@@ -266,15 +298,65 @@ public class MainController< T extends RealType< T > & NativeType< T > > impleme
         } );
         displayTask.start();
     }
+    private boolean isValid(Dataset dataset)
+    {
+        setTargetChannel( 1 );
+        channels.setDisable( false );
+        int numZ = ( int ) dataset.getDepth();
+        int numFrames = ( int ) dataset.getFrames();
+        int numChannels = (int) dataset.getChannels();
+        LOGGER.debug( "NUmber of dimensions: {}", dataset.numDimensions() );
+        LOGGER.debug( "NUmber of channels: {}", dataset.getChannels() );
+        LOGGER.debug( "Number of frames: {}", dataset.getFrames() );
+        if ( numFrames > 1 )
+        {
+            LOGGER.debug( "TimeLapseException" );
+            showError( new TimeLapseException() );
+            return false;
+        }
+        if ( numZ == 1 )
+        {
+            LOGGER.debug( "NoA3DStackException" );
+            showError( new NoA3DStackException() );
+            return false;
+        }
+        if (numChannels == 1)
+        {
+            channels.setDisable( true );
+            setTargetChannel( 0 );
+        }
+        LOGGER.debug( "The dataset is valid." );
+        return true;
+    }
 
-    @SuppressWarnings( "unchecked" )
-    public void setCurrentDataset( Dataset dataset )
+    public void setReferenceImage()
     {
-                currentDataset.setValue( dataset );
-                Img< T > input = ( ImgPlus< T > ) dataset.getImgPlus();
-                constructionController.getConstructionModel().setInput( input );
-                constructionController.getConstructionModel().setFactory( input.factory() );
+        LOGGER.debug( "Setting reference image" );
+        Img< T > input = ( Img< T > ) currentDataset.getValue().getData().getImgPlus();
+        ReferenceImageSettingTask< T > task = new ReferenceImageSettingTask<>( input, getTargetChannel() );
+        task.setOnSucceeded( workerStateEvent ->
+        {
+            referenceImage.set( task.getValue() );
+            constructionController.getConstructionModel().setInput( referenceImage.getValue() );
+            constructionController.getConstructionModel().setFactory( referenceImage.get().factory() );
+        } );
+        task.start();
+        LOGGER.debug("Setting is done.");
+
+
+    }
+    private void runPretreatment( RandomAccessibleInterval<T> input )
+    {
+//        ImageJFunctions.show(input , "pretreatment");
+        if (pretreatmentTask!= null)
+        {
+            pretreatmentTask.cancel();
+        }
+        pretreatmentTask = new PretreatmentTask<>( input );
+        pretreatmentTask.setOnSucceeded( workerStateEvent ->
+                pretreatedImg.setValue( pretreatmentTask.getValue() ) );
 
+        pretreatmentTask.start();
     }
 
     public void computeClassifiedImages()
@@ -372,26 +454,15 @@ public class MainController< T extends RealType< T > & NativeType< T > > impleme
         projectionController.setParameters( parameters );
     }
 
-    private boolean isValid(Dataset dataset)
+    public int getTargetChannel()
     {
-        int numZ = ( int ) dataset.getDepth();
-        int numFrames = ( int ) dataset.getFrames();
-        LOGGER.debug( "NUmber of dimensions: {}", dataset.numDimensions() );
-        LOGGER.debug( "NUmber of channels: {}", dataset.getChannels() );
-        LOGGER.debug( "Number of frames: {}", dataset.getFrames() );
-        if ( numFrames > 1 )
-        {
-            LOGGER.debug( "TimeLapseException" );
-            showError( new TimeLapseException() );
-            return false;
-        }
-        if ( numZ == 1 )
-        {
-            LOGGER.debug( "NoA3DStackException" );
-            showError( new NoA3DStackException() );
-            return false;
-        }
-        return true;
+        return targetChannel;
+    }
+
+    public void setTargetChannel( int targetChannel )
+    {
+        LOGGER.debug( " targetChannel = {}", targetChannel);
+        this.targetChannel = targetChannel;
     }
 }
 

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

@@ -41,24 +41,19 @@ import javafx.geometry.Pos;
 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;
 
 import java.net.URL;
 import java.util.ResourceBundle;
 
-public class SelectionController< T extends RealType< T > & NativeType< T > > implements Initializable
+public class SelectionController implements Initializable
 {
     private final static Logger LOGGER = LoggerFactory.getLogger( SelectionController.class );
-
-
     private final SimpleBooleanProperty changedParameters = new SimpleBooleanProperty();
     private final SimpleBooleanProperty disableGUI = new SimpleBooleanProperty();
     private SelectionModel selectionModel;
-
     @FXML
     private ParameterSliderInteger amplitude;
     @FXML
@@ -301,21 +296,6 @@ public class SelectionController< T extends RealType< T > & NativeType< T > > im
         return otsu;
     }
 
-    public ParameterSliderInteger getXyBlur()
-    {
-        return xyBlur;
-    }
-
-    public ParameterSliderInteger getzBlur()
-    {
-        return zBlur;
-    }
-
-    public boolean isChangedParameters()
-    {
-        return changedParameters.get();
-    }
-
     public SimpleBooleanProperty changedParametersProperty()
     {
         return changedParameters;

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

@@ -32,11 +32,9 @@ import fr.pasteur.ida.zellige.element.Projection;
 import fr.pasteur.ida.zellige.element.ReferenceSurface;
 import fr.pasteur.ida.zellige.steps.projection.ReferenceSurfaceProjection;
 import javafx.beans.property.*;
-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 org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -157,6 +155,9 @@ public class ProjectionModel< T extends RealType< T > & NativeType< T > >
         showOutput();
     }
 
+
+
+
     public void showOutput()
     {
         if ( rawHM.get() && rawHMDisplay.getValue() )
@@ -199,13 +200,18 @@ public class ProjectionModel< T extends RealType< T > & NativeType< T > >
 
         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() ) );
+            if ( referenceSurface.getInput().numDimensions() == 3 )
+//            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() ) );
+            //Projection2.project(referenceSurface.getInput(), referenceSurface.getFactory(), )
+            {
+                System.out.println();
+            }
         }
         delta1Functions.setValue( true );
     }

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

+package fr.pasteur.ida.zellige.gui.task;
+
+import fr.pasteur.ida.zellige.steps.ChannelImageSelection;
+import net.imglib2.img.Img;
+import net.imglib2.type.NativeType;
+import net.imglib2.type.numeric.RealType;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class ChannelImageSelectionTask < T extends RealType< T > & NativeType< T > >extends AbstractTask< Img< T > >
+{
+    private final static Logger LOGGER = LoggerFactory.getLogger( ChannelImageSelectionTask.class );
+
+    private final Img<T> input;
+    private final int targetChannel;
+
+    public ChannelImageSelectionTask( Img<T> input, int targetChannel )
+    {
+        this.input = input;
+        this.targetChannel = targetChannel;
+    }
+
+    @Override
+    protected Img<T > call()
+    {
+        LOGGER.info( "Channel selection" );
+        return ChannelImageSelection.run( input, targetChannel );
+
+    }
+}

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

@@ -28,7 +28,7 @@
  */
 package fr.pasteur.ida.zellige.gui.task;
 
-import net.imagej.Dataset;
+import net.imagej.display.DefaultDatasetView;
 import net.imagej.display.ImageDisplay;
 import net.imagej.display.ImageDisplayService;
 import org.slf4j.Logger;
@@ -36,7 +36,7 @@ import org.slf4j.LoggerFactory;
 
 import java.util.ArrayList;
 
-public class DisplayDatasetChoicesTask extends AbstractTask< ArrayList< Dataset > >
+public class DisplayDatasetChoicesTask extends AbstractTask< ArrayList< DefaultDatasetView > >
 {
     private final static Logger LOGGER = LoggerFactory.getLogger( DisplayDatasetChoicesTask.class );
     private final ImageDisplayService imageDisplayService;
@@ -47,13 +47,13 @@ public class DisplayDatasetChoicesTask extends AbstractTask< ArrayList< Dataset
     }
 
     @Override
-    protected ArrayList< Dataset > call()
+    protected ArrayList< DefaultDatasetView > call()
     {
         ArrayList< ImageDisplay > imageDisplays = ( ArrayList< ImageDisplay > ) imageDisplayService.getImageDisplays();
-        ArrayList< Dataset > tempDatasets = new ArrayList<>( imageDisplays.size() );
+        ArrayList< DefaultDatasetView > tempDatasets = new ArrayList<>( imageDisplays.size() );
         for ( ImageDisplay imageDisplay : imageDisplays )
         {
-            tempDatasets.add( imageDisplayService.getActiveDataset( imageDisplay ) );
+            tempDatasets.add( ( DefaultDatasetView ) imageDisplayService.getActiveDatasetView( imageDisplay ) );
         }
         LOGGER.debug( "Available datasets updated." );
         return tempDatasets;

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

@@ -29,8 +29,7 @@
 package fr.pasteur.ida.zellige.gui.task;
 
 import fr.pasteur.ida.zellige.steps.selection.pretreatment.Pretreatment;
-import net.imagej.Dataset;
-import net.imagej.ImgPlus;
+import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.img.Img;
 import net.imglib2.type.NativeType;
 import net.imglib2.type.numeric.RealType;
@@ -40,21 +39,18 @@ import org.slf4j.LoggerFactory;
 
 public class PretreatmentTask< T extends RealType< T > & NativeType< T > > extends AbstractTask< Img< FloatType > >
 {
-
     private final static Logger LOGGER = LoggerFactory.getLogger( PretreatmentTask.class );
-    private final Dataset dataset;
+    private final RandomAccessibleInterval<T> input;
 
-    public PretreatmentTask( Dataset dataset )
+    public PretreatmentTask( RandomAccessibleInterval<T> input )
     {
-        this.dataset = dataset;
+        this.input = input;
     }
 
     @Override
-    @SuppressWarnings( "unchecked" )
     protected Img< FloatType > call()
     {
         LOGGER.info( "Computing pretreatment..." );
-        ImgPlus< T > input = ( ImgPlus< T > ) dataset.getImgPlus();
         Img< FloatType > pretreatedImg = Pretreatment.run( input );
         LOGGER.debug( "Done." );
         return pretreatedImg;

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

+package fr.pasteur.ida.zellige.gui.task;
+
+import fr.pasteur.ida.zellige.steps.ChannelImageSelection;
+import net.imglib2.img.Img;
+import net.imglib2.type.NativeType;
+import net.imglib2.type.numeric.RealType;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class ReferenceImageSettingTask < T extends RealType< T > & NativeType< T > > extends AbstractTask< Img<T>  >
+{
+    private final static Logger LOGGER = LoggerFactory.getLogger( ReferenceImageSettingTask.class );
+    private final Img<T> input;
+    private final int targetChannel;
+
+
+    public ReferenceImageSettingTask( Img< T > input, int targetChannel )
+    {
+        this.input = input;
+        this.targetChannel = targetChannel;
+    }
+
+
+    @Override
+    protected Img<T> call()
+    {
+
+        return ChannelImageSelection.run( input, targetChannel );
+    }
+
+}

src/main/java/fr/pasteur/ida/zellige/steps/ChannelImageSelection.java

+package fr.pasteur.ida.zellige.steps;
+
+import net.imagej.display.DefaultDatasetView;
+import net.imglib2.RandomAccess;
+import net.imglib2.display.ColorTable;
+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 java.util.List;
+
+
+public class ChannelImageSelection< T extends RealType< T > & NativeType< T > >
+{
+
+    private final static Logger LOGGER = LoggerFactory.getLogger( ChannelImageSelection.class );
+    private final static int GRAYS = 0;
+    private final static int RED = 1;
+    private final static int BLUE = 2;
+    private final static int GREEN = 3;
+    private final static int CYAN = 4;
+    private final static int MAGENTA = 5;
+    private final static int YELLOW = 6;
+    private final int targetChannel;
+    private final Img<T> input;
+
+    public static < T extends RealType< T > & NativeType< T > > Img< T > run( Img<T> input, int targetChannel )
+    {
+        ChannelImageSelection< T > channelImageSelection = new ChannelImageSelection<>( input, targetChannel);
+
+        return channelImageSelection.run();
+    }
+
+    /**
+     *
+     * @param input
+     * @param targetChannel
+     */
+    public ChannelImageSelection( Img<T> input, int targetChannel )
+    {
+        this.targetChannel = targetChannel;
+        this.input = input;
+        LOGGER.debug( " running...." );
+    }
+
+    public Img< T > run()
+    {
+        if ( getTargetChannel() == 0 )
+        {
+            return input;
+        }
+        else
+        {
+            Img< T > output = input.factory().create( input.dimension( 0 ), input.dimension( 1 ), input.dimension( 3 ) );
+            RandomAccess< T > randomAccess = input.randomAccess();
+            RandomAccess< T > randomAccess1 = output.randomAccess();
+            for ( int x = 0; x < ( int ) input.dimension( 0 ); x++ )
+            {
+                for ( int y = 0; y < ( int ) input.dimension( 1 ); y++ )
+                {
+                    for ( int z = 0; z < ( int ) input.dimension( 3 ); z++ )
+                    {
+                        randomAccess.setPositionAndGet( x, y, getTargetChannel() - 1, z );
+                        randomAccess1.setPosition( new int[]{ x, y, z } );
+                        randomAccess1.get().set( randomAccess.get() );
+                    }
+                }
+            }
+            return output;
+        }
+    }
+
+    public int getTargetChannel()
+    {
+        return targetChannel;
+    }
+
+
+    /**
+     *
+      * @param defaultDatasetView the input image
+     * @return an int array of colors
+     */
+    private static int[] getColors( DefaultDatasetView defaultDatasetView )
+    {
+        return getColors( defaultDatasetView.getColorTables() );
+    }
+
+    private static int [] getColors( List<ColorTable> colorTables)
+    {
+        int[] colors = new int[ colorTables.size() ];
+        if (colors.length == 1)
+        {
+            colors[0] = GRAYS;
+            return colors;
+        }
+        for ( int i = 0; i <colorTables.size(); i++ )
+        {
+            colors[i]= getColor(  colorTables.get( i ));
+        }
+        return colors;
+    }
+
+    private static int getColor( ColorTable colorTable )
+    {
+        int R = colorTable.get( 0, 255 );
+        int G = colorTable.get( 1, 255 );
+        int B = colorTable.get( 2, 255 );
+        if ( R== 0)
+        {
+           if (G == 0)
+           {
+               return BLUE; // BLUE
+           }
+           else
+           {
+               if (B == 0)
+               {
+                   return  GREEN; // GREEN
+               }
+               return CYAN ; // CYAN
+           }
+        }
+        else
+        {
+            if (G == 0)
+            {
+                if (B == 0)
+                {
+                    return  RED; // RED
+                }
+                return MAGENTA ; // MAGENTA
+            }
+            else
+            {
+                if (B == 0)
+                {
+                    return  YELLOW; // YELLOW
+                }
+                return GRAYS ; // GRAYS
+            }
+        }
+    }
+}

src/main/java/fr/pasteur/ida/zellige/steps/Utils.java

@@ -74,6 +74,12 @@ public class Utils
         setPosition( randomAccess, u, v );
         randomAccess.setPosition( z, 2 );
     }
+    public static < T extends RealType< T > & NativeType< T > > T setPosition( RandomAccess< T > randomAccess, int u, int v, int channel, int z)
+    {
+        setPosition( randomAccess, u, v, channel );
+        randomAccess.setPosition( z, 3 );
+        return randomAccess.get();
+    }
 
 
     public static < T extends RealType< T > & NativeType< T > > T setPositionAndGet( RandomAccess< T > randomAccess, int u, int v )
@@ -87,4 +93,6 @@ public class Utils
         setPosition( randomAccess, u, v, z );
         return randomAccess.get();
     }
+
+
 }

src/main/java/fr/pasteur/ida/zellige/steps/projection/ReferenceSurfaceProjection.java

@@ -6,13 +6,13 @@
  * %%
  * 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
@@ -85,6 +85,67 @@ public class ReferenceSurfaceProjection< T extends RealType< T > & NativeType< T
     }
 
 
+    public static < T extends RealType< T > & NativeType< T > > Img< T > getReducedStack( ReferenceSurface< T > referenceSurface,
+                                                                                          int offset, int deltaZ, int channel )
+    {
+        RandomAccessibleInterval< T > input = referenceSurface.getInput();
+        RandomAccessibleInterval< UnsignedShortType > zMap = referenceSurface.getzMap();
+        //The stack slice number depends on the user "deltaZ" parameter.
+        Img< T > reducedStack = referenceSurface.getFactory().create( input.dimension( 0 ), input.dimension( 1 ), deltaZ * 2L + 1 );
+        RandomAccess< T > inputAccess = input.randomAccess();
+        RandomAccess< UnsignedShortType > zMapAccess = zMap.randomAccess();
+        RandomAccess< T > outputAccess = reducedStack.randomAccess();
+
+        for ( int x = 0; x <= input.dimension( 0 ) - 1; x++ )
+        {
+            zMapAccess.setPosition( x, 0 );
+            for ( int y = 0; y <= input.dimension( 1 ) - 1; y++ )
+            {
+                zMapAccess.setPosition( y, 1 );
+                int zMapValue = zMapAccess.get().getInteger() - 1;// ImageJ can not display negative values.
+                if ( zMapValue != - 1 ) // a surface pixel has been found at that position
+                {
+                    int startIndex = Math.max( zMapValue + offset - deltaZ, 0 );
+                    int stopIndex = Math.min( ( zMapValue + offset + deltaZ ), ( int ) input.dimension( 2 ) - 1 );
+                    int Z = deltaZ;
+                    for ( int z = zMapValue; z >= startIndex; z-- )
+                    {
+                        setPosition( outputAccess, x, y, Z );
+                        setPosition( inputAccess, x, y, channel, z );
+                        outputAccess.get().set( inputAccess.get() );
+                        Z--;
+                    }
+                    //second loop for plus delta
+                    Z = deltaZ + 1;
+                    for ( int z = zMapValue + 1; z <= stopIndex; z++ )
+                    {
+                        setPosition( outputAccess, x, y, Z );
+                        setPosition( inputAccess, x, y, z );
+                        outputAccess.get().set( inputAccess.get() );
+                        Z++;
+                    }
+                }
+                else
+                {
+                    for ( int z = 0; z <= reducedStack.dimension( 2 ) - 1; z++ )
+                    {
+                        setPosition( outputAccess, x, y, z );
+                        outputAccess.get().setReal( 0 );
+                    }
+                }
+            }
+        }
+        return reducedStack;
+    }
+
+
+    public static < T extends RealType< T > & NativeType< T > > Img< T > projection( RandomAccessibleInterval< T > reducedStack, ImgFactory< T > factory, String method )
+    {
+        Img< T > projection = factory.create( reducedStack.dimension( 0 ), reducedStack.dimension( 1 ), 1 );
+        return projection;
+    }
+
+
     /**
      * @param referenceSurface the considered referenceSurface
      * @param method           the desired user projection method
@@ -221,7 +282,7 @@ public class ReferenceSurfaceProjection< T extends RealType< T > & NativeType< T
 
 
     public static < T extends RealType< T > & NativeType< T > > Img< T > getSegmentedSurface
-    ( Img< UnsignedShortType > extractedHeightMap, RandomAccessibleInterval< T > originalInput, ImgFactory< T > factory )
+            ( Img< UnsignedShortType > extractedHeightMap, RandomAccessibleInterval< T > originalInput, ImgFactory< T > factory )
     {
         Img< T > segmentedSurface = factory.create( originalInput );
         RandomAccess< T > surfaceAccess = segmentedSurface.randomAccess();
@@ -629,6 +690,15 @@ public class ReferenceSurfaceProjection< T extends RealType< T > & NativeType< T
         }
 
     }
+
+    public static < T extends RealType< T > & NativeType< T > > void channelProjection(
+            final RandomAccessibleInterval<T> inputChannel,
+            final RandomAccessibleInterval< T > outputChannel,
+            final RandomAccessibleInterval< UnsignedShortType > referenceSurface,
+            final int offset, final int deltaZ )
+    {
+
+    }
 }
 
 

src/main/resources/fr.pasteur.ida.zellige.gui.view/Main.fxml

 <?xml version="1.0" encoding="UTF-8"?>
 
 <!--suppress JavaFxDefaultTag, JavaFxUnresolvedFxIdReference -->
+
 <?import javafx.geometry.Insets?>
 <?import javafx.scene.control.*?>
 <?import javafx.scene.image.Image?>
 <?import javafx.scene.image.ImageView?>
 <?import javafx.scene.layout.*?>
 <?import javafx.scene.text.Font?>
-<VBox xmlns:fx="http://javafx.com/fxml" maxHeight="1.7976931348623157E308" maxWidth="1.7976931348623157E308"
-      minHeight="-Infinity" minWidth="-Infinity" prefHeight="786.0" prefWidth="866.0" spacing="5.0"
-      stylesheets="@theme2.css" xmlns="http://javafx.com/javafx"
-      fx:controller="fr.pasteur.ida.zellige.gui.controller.MainController">
+<VBox maxHeight="1.7976931348623157E308" maxWidth="1.7976931348623157E308" minHeight="-Infinity" minWidth="-Infinity" prefHeight="786.0" prefWidth="866.0" spacing="5.0" stylesheets="@theme2.css" xmlns="http://javafx.com/javafx/19" xmlns:fx="http://javafx.com/fxml/1" fx:controller="fr.pasteur.ida.zellige.gui.controller.MainController">
     <padding>
-        <Insets left="10.0" right="10.0" top="5.0"/>
+        <Insets left="10.0" right="10.0" top="5.0" />
     </padding>
-    <HBox alignment="CENTER_LEFT" prefHeight="26.0" prefWidth="774.0" spacing="5.0" VBox.vgrow="ALWAYS">
+    <HBox alignment="CENTER_LEFT" prefHeight="26.0" prefWidth="759.0" spacing="5.0" VBox.vgrow="ALWAYS">
         <padding>
-            <Insets left="10.0"/>
+            <Insets left="10.0" />
         </padding>
-        <HBox alignment="CENTER_LEFT" prefHeight="45.0" prefWidth="494.0">
+        <HBox alignment="CENTER_LEFT" prefHeight="26.0" prefWidth="483.0">
             <children>
                 <Label prefHeight="12.0" prefWidth="71.0" text="File : ">
                     <font>
-                        <Font size="14.0"/>
+                        <Font size="14.0" />
                     </font>
                 </Label>
-                <ComboBox fx:id="activeDatasets" minHeight="-Infinity" minWidth="-Infinity" prefHeight="26.0"
-                          prefWidth="262.0"/>
+                <ComboBox fx:id="activeDatasets" minHeight="-Infinity" minWidth="-Infinity" prefHeight="26.0" prefWidth="401.0" />
             </children>
         </HBox>
-        <HBox alignment="CENTER_RIGHT" prefHeight="45.0" prefWidth="333.0" spacing="10.0">
+      <HBox prefHeight="26.0" prefWidth="83.0">
+         <children>
+            <Label text="Channel" />
+            <Spinner fx:id="channels" prefHeight="21.0" prefWidth="42.0" />
+         </children>
+      </HBox>
+        <HBox alignment="CENTER_RIGHT" prefHeight="26.0" prefWidth="151.0" spacing="10.0">
             <children>
-                <Button mnemonicParsing="false" onAction="#loadParameters" text="Load parameters">
+                <Button mnemonicParsing="false" onAction="#loadParameters" text="Load">
                     <graphic>
                         <ImageView fitHeight="15.0" fitWidth="22.0" pickOnBounds="true" preserveRatio="true">
                             <image>
-                                <Image url="@/icons/script_add.png"/>
+                                <Image url="@/icons/script_add.png" />
                             </image>
                         </ImageView>
                     </graphic>
                 </Button>
-                <Button mnemonicParsing="false" onAction="#saveParameters" text="Save Parameters">
+                <Button mnemonicParsing="false" onAction="#saveParameters" text="Save">
                     <graphic>
                         <ImageView fitHeight="15.0" fitWidth="26.0" pickOnBounds="true" preserveRatio="true">
                             <image>
-                                <Image url="@../icons/script_save.png"/>
+                                <Image url="@../icons/script_save.png" />
                             </image>
                         </ImageView>
                     </graphic>
@@ -52,23 +55,18 @@
             </children>
         </HBox>
     </HBox>
-    <fx:include fx:id="selection" maxHeight="1.7976931348623157E308" maxWidth="1.7976931348623157E308"
-                minHeight="-Infinity" minWidth="-Infinity" source="Selection.fxml" VBox.vgrow="ALWAYS"/>
+    <fx:include fx:id="selection" maxHeight="1.7976931348623157E308" maxWidth="1.7976931348623157E308" minHeight="-Infinity" minWidth="-Infinity" source="Selection.fxml" VBox.vgrow="ALWAYS" />
     <HBox alignment="CENTER_LEFT" prefHeight="319.0" prefWidth="700.0" spacing="5.0">
-        <fx:include fx:id="construction" maxHeight="1.7976931348623157E308" maxWidth="1.7976931348623157E308"
-                    minHeight="-Infinity" minWidth="-Infinity" source="Construction.fxml" HBox.hgrow="ALWAYS"/>
-        <fx:include fx:id="projection" maxHeight="1.7976931348623157E308" maxWidth="1.7976931348623157E308"
-                    minHeight="-Infinity" minWidth="-Infinity" source="Projection.fxml" HBox.hgrow="ALWAYS"/>
+        <fx:include fx:id="construction" maxHeight="1.7976931348623157E308" maxWidth="1.7976931348623157E308" minHeight="-Infinity" minWidth="-Infinity" source="Construction.fxml" HBox.hgrow="ALWAYS" />
+        <fx:include fx:id="projection" maxHeight="1.7976931348623157E308" maxWidth="1.7976931348623157E308" minHeight="-Infinity" minWidth="-Infinity" source="Projection.fxml" HBox.hgrow="ALWAYS" />
     </HBox>
     <StackPane prefHeight="51.0" prefWidth="747.0" VBox.vgrow="ALWAYS">
         <BorderPane prefHeight="27.0" prefWidth="846.0">
             <left>
-                <Label fx:id="logInfo" alignment="CENTER" prefHeight="32.0" prefWidth="418.0"
-                       BorderPane.alignment="CENTER"/>
+                <Label fx:id="logInfo" alignment="CENTER" prefHeight="32.0" prefWidth="418.0" BorderPane.alignment="CENTER" />
             </left>
             <center>
-                <Button fx:id="runButton" disable="true" mnemonicParsing="false" text="Run Zellige !"
-                        BorderPane.alignment="TOP_CENTER"/>
+                <Button fx:id="runButton" disable="true" mnemonicParsing="false" text="Run Zellige !" BorderPane.alignment="TOP_CENTER" />
             </center>
         </BorderPane>
     </StackPane>