diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/controller/MainController.java b/src/main/java/fr/pasteur/ida/zellige/gui/controller/MainController.java
index 3b1f07e25c08487128e6f443514043416e56f4b8..1619f294cfc59ae86e0816e1a20fbd8c3bd60dbf 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/controller/MainController.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/controller/MainController.java
@@ -53,14 +53,14 @@ 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 net.imagej.Dataset;
import net.imagej.ImgPlus;
+import net.imglib2.RandomAccess;
+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.type.numeric.real.FloatType;
@@ -78,25 +78,30 @@ public class MainController< T extends RealType< T > & NativeType< T > > impleme
{
private final static Logger LOGGER = LoggerFactory.getLogger( MainController.class );
+ private int targetChannel = 1;
private final SimpleObjectProperty< Dataset > 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;
@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 +112,6 @@ 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
@@ -121,10 +125,10 @@ public class MainController< T extends RealType< T > & NativeType< T > > impleme
activeDatasets.getSelectionModel().selectedItemProperty().addListener( ( observableValue, oldValue, newValue ) ->
{
LOGGER.debug( "selectedItemProperty : old value = {}, new value = {} ", oldValue, newValue );
+ channels.setDisable( false );
if(newValue!= null && isValid( newValue ))
{
-
- setCurrentDataset( newValue );
+ currentDataset.setValue( newValue );
}
else
{
@@ -132,13 +136,23 @@ public class MainController< T extends RealType< T > & NativeType< T > > impleme
}
} );
+ channels.valueProperty().addListener( (observableValue, oldValue, newValue ) ->
+ {
+ if(!channels.isDisable())
+ {
+ setTargetChannel( newValue );
+ setReferenceImage( currentDataset.getValue() );
+ }
+ } );
+
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.getChannels(), 1 );
+ channels.setValueFactory( valueFactory );
+ setReferenceImage( currentDataset.getValue() );
}
else
{
@@ -147,6 +161,14 @@ 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 )
@@ -188,7 +210,6 @@ public class MainController< T extends RealType< T > & NativeType< T > > impleme
{
LOGGER.debug( "Active button" );
disableGUI.setValue( false );
-
}
} );
@@ -201,7 +222,6 @@ 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() );
@@ -238,13 +258,7 @@ 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()
{
@@ -266,16 +280,80 @@ 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( Dataset dataset )
{
- currentDataset.setValue( dataset );
- Img< T > input = ( ImgPlus< T > ) dataset.getImgPlus();
- constructionController.getConstructionModel().setInput( input );
- constructionController.getConstructionModel().setFactory( input.factory() );
+ Img< T > input = ( ImgPlus< T > ) dataset.getImgPlus();
+ if (getTargetChannel() == 0)
+ {
+ referenceImage.setValue( 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() );
+ }
+ }
+ }
+ referenceImage.setValue( output );
+ }
+ constructionController.getConstructionModel().setInput( referenceImage.getValue());
+ constructionController.getConstructionModel().setFactory(referenceImage.get().factory() );
}
+ 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 +450,15 @@ 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;
}
}