diff --git a/src/main/java/fr/pasteur/ida/zellige/Main.java b/src/main/java/fr/pasteur/ida/zellige/Main.java
index 1dfe551211cfecd9dc8d26ddba88b8ad3adab5a3..795b005cebdd16599caa5fd9932b2ae37e1b23d8 100644
--- a/src/main/java/fr/pasteur/ida/zellige/Main.java
+++ b/src/main/java/fr/pasteur/ida/zellige/Main.java
@@ -69,7 +69,7 @@ public class Main
// Input of the image.
- final String imagePath = "doc/Scan1_volume.tif";
+ final String imagePath = "doc/Scan1_volume_crop.tif";
//args[ 0 ]; /* The image path goes here !!!! */
//args[ 0 ]; /* The image path goes here !!!! */
LOGGER.debug( imagePath );
@@ -86,7 +86,7 @@ public class Main
.getPath( "" )
.toAbsolutePath()
.toString();
- String imageFilePath = "doc/Scan1_volume_crop.tif";
+ String imageFilePath = "doc/Cochlée1.tif";
Object obj = ij.io().
open( new File( currentFolder, imageFilePath ).getAbsolutePath() );
@@ -118,7 +118,7 @@ public class Main
- int bin = 4;//TODO order of arguments
+ int bin = 2;//TODO order of arguments
int amplitude = 10;
int otsu = 10;
int islandSize =5;
diff --git a/src/main/java/fr/pasteur/ida/zellige/ReferenceSurfaceExtraction.java b/src/main/java/fr/pasteur/ida/zellige/ReferenceSurfaceExtraction.java
index b8599c2460a50a46db2cf2cbd8ecfd0116014119..bc087d6b595a19e4a028fb92ce81178801cb957a 100644
--- a/src/main/java/fr/pasteur/ida/zellige/ReferenceSurfaceExtraction.java
+++ b/src/main/java/fr/pasteur/ida/zellige/ReferenceSurfaceExtraction.java
@@ -43,10 +43,12 @@ 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.exception.DataValidationException;
+import fr.pasteur.ida.zellige.steps.selection.exception.ImageTooLargeException;
import fr.pasteur.ida.zellige.steps.selection.exception.NoClassificationException;
import fr.pasteur.ida.zellige.steps.selection.postTreatment.PostTreatmentParameters;
import fr.pasteur.ida.zellige.steps.selection.pretreatment.PretreatmentParameters;
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;
@@ -64,8 +66,8 @@ public class ReferenceSurfaceExtraction< T extends RealType< T > & NativeType< T
private final static Logger LOGGER = LoggerFactory.getLogger( ReferenceSurfaceExtraction.class );
private final ArrayList< ReferenceSurface< T > > referenceSurfaces = new ArrayList<>();
- private final RandomAccessibleInterval< T > input;
- private final ImgFactory< T > factory;
+// private final RandomAccessibleInterval< T > input;
+// private final ImgFactory< T > factory;
private Pixels[][] maximums;
private final static double adequacy = 1;
@@ -85,12 +87,17 @@ public class ReferenceSurfaceExtraction< T extends RealType< T > & NativeType< T
private int SS_goodSurfaces;
private static final String derivativeMethod = FORWARD;
- public ReferenceSurfaceExtraction( RandomAccessibleInterval< T > input, ImgFactory< T > factory )
+// public ReferenceSurfaceExtraction( RandomAccessibleInterval< T > input, ImgFactory< T > factory )
+// {
+// this.input = input;
+// this.factory = factory;
+// }
+
+
+ public ReferenceSurfaceExtraction( )
{
- this.input = input;
- this.factory = factory;
- }
+ }
public static double getAdequacy()
{
return adequacy;
@@ -98,14 +105,21 @@ public class ReferenceSurfaceExtraction< T extends RealType< T > & NativeType< T
- public void select( PretreatmentParameters pretreatmentParameters, ClassificationParameters classificationParameters, PostTreatmentParameters postTreatmentParameters ) throws NoClassificationException, DataValidationException
+// public void select( PretreatmentParameters pretreatmentParameters, ClassificationParameters classificationParameters, PostTreatmentParameters postTreatmentParameters ) throws NoClassificationException, DataValidationException, ImageTooLargeException
+// {
+// /* First step : Pixel selection */
+// LOGGER.debug( "Running selection..." );
+// maximums = Selection.run( input, pretreatmentParameters, classificationParameters, postTreatmentParameters );
+// }
+
+ public void select( Img<T> input, PretreatmentParameters pretreatmentParameters, ClassificationParameters classificationParameters, PostTreatmentParameters postTreatmentParameters ) throws NoClassificationException, DataValidationException, ImageTooLargeException
{
/* First step : Pixel selection */
LOGGER.debug( "Running selection..." );
maximums = Selection.run( input, pretreatmentParameters, classificationParameters, postTreatmentParameters );
}
- public void construct( ConstructionParameters[] constructionParameters ) throws NoSurfaceFoundException
+ public void construct( RandomAccessibleInterval<T> input, ImgFactory<T> factory,ConstructionParameters[] constructionParameters ) throws NoSurfaceFoundException
{
LOGGER.debug( "Running construction..." );
/* First round construction*/
@@ -132,7 +146,40 @@ public class ReferenceSurfaceExtraction< T extends RealType< T > & NativeType< T
SS_OSConstructionProcessingTime = step2.getOSConstructionProcessingTime();
SS_SurfaceConstructionProcessingTime = step2.getConstructionProcessingTime();
/* Building reference surfaces */
- referenceSurfaces.addAll( ConstructionCompletion.run( input, factory, finalSurfaces ) );
+ referenceSurfaces.addAll( ConstructionCompletion.run( input, factory, finalSurfaces , 2) );
+// referenceSurfaceInstantiation( finalSurfaces );
+ LOGGER.debug( " Constructions of {} surfaces.", referenceSurfaces.size() );
+
+ }
+
+ public void construct( Img<T> input,ConstructionParameters[] constructionParameters ) throws NoSurfaceFoundException
+ {
+ LOGGER.debug( "Running construction..." );
+ /* First round construction*/
+ FirstRoundConstruction step1 = new FirstRoundConstruction( maximums, constructionParameters[ 0 ] );
+ step1.process();
+ ArrayList< Surface > tempSurfaces = step1.getSurfaces();
+ FS_startingOS_count = step1.getStartingOSCount();
+ FS_OS_count = step1.getOSCount();
+ FS_goodSurfaces = step1.getGoodSurfacesCount();
+ FS_smallSurfaces = step1.getSmallSurfacesCount();
+ FS_finalizedSurfaces = tempSurfaces.size();
+ FS_OSConstructionProcessingTime = step1.getOSConstructionProcessingTime();
+ FS_SurfaceConstructionProcessingTime = step1.getConstructionProcessingTime();
+ LOGGER.debug( "first round surfaces = " + tempSurfaces.size() );
+ /* Second round construction */
+ SecondRoundConstruction step2 =
+ new SecondRoundConstruction( tempSurfaces, constructionParameters[ 1 ] );
+ step2.process();
+ ArrayList< Surface > finalSurfaces = step2.getSurfaces();
+ SS_startingOS_count = step2.getStartingOSCount();
+ SS_OS_count = step2.getOSCount();
+ SS_goodSurfaces = step2.getGoodSurfacesCount();
+ SS_smallSurfaces = step2.getSmallSurfacesCount();
+ SS_OSConstructionProcessingTime = step2.getOSConstructionProcessingTime();
+ SS_SurfaceConstructionProcessingTime = step2.getConstructionProcessingTime();
+ /* Building reference surfaces */
+ referenceSurfaces.addAll( ConstructionCompletion.run( input, input.factory(), finalSurfaces, 2 ) );
// referenceSurfaceInstantiation( finalSurfaces );
LOGGER.debug( " Constructions of {} surfaces.", referenceSurfaces.size() );
@@ -140,7 +187,7 @@ public class ReferenceSurfaceExtraction< T extends RealType< T > & NativeType< T
public void project( ProjectionParameters projectionParameters, DisplayParameters displayParameters ) throws NoPossibleDisplayException
{
- LOGGER.debug( "Running projection..." );
+ LOGGER.debug( "Running projection1..." );
for ( ReferenceSurface< T > referenceSurface : referenceSurfaces )
{
referenceSurface.init();
diff --git a/src/main/java/fr/pasteur/ida/zellige/command/Zellige.java b/src/main/java/fr/pasteur/ida/zellige/command/Zellige.java
index 4bb0426aca7cb5fea923e121521219d93c27e308..37d50048c4693da277437302f62d9884e6897f6c 100644
--- a/src/main/java/fr/pasteur/ida/zellige/command/Zellige.java
+++ b/src/main/java/fr/pasteur/ida/zellige/command/Zellige.java
@@ -50,7 +50,7 @@ public class Zellige extends ContextCommand
.getPath( "" )
.toAbsolutePath()
.toString();
- String imageFilePath = "doc/Scan1_volume_crop.tif";
+ String imageFilePath = "doc/Cochlée1.tif";
// Launch ImageJ.
ImageJ ij = new ImageJ();
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/PreprocessingPanel.java b/src/main/java/fr/pasteur/ida/zellige/gui/PreprocessingPanel.java
new file mode 100644
index 0000000000000000000000000000000000000000..9a6599bd2649a44ecb3171b75f0d771160c58fc0
--- /dev/null
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/PreprocessingPanel.java
@@ -0,0 +1,71 @@
+/*-
+ * #%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;
+
+import javafx.beans.NamedArg;
+import javafx.fxml.FXML;
+import javafx.fxml.FXMLLoader;
+import javafx.scene.control.Label;
+import javafx.scene.control.Spinner;
+import javafx.scene.layout.HBox;
+import javafx.scene.layout.VBox;
+
+import java.io.IOException;
+
+public class PreprocessingPanel extends HBox
+{
+
+
+
+
+
+ public PreprocessingPanel( )
+ {
+ FXMLLoader fxmlLoader = new FXMLLoader( PreprocessingPanel.class.getClassLoader().getResource(
+ "fr.pasteur.ida.zellige.gui.view/PreprocessingPanel.fxml" ) );
+ fxmlLoader.setRoot( this );
+ fxmlLoader.setController( this );
+ try
+ {
+ fxmlLoader.load();
+ }
+ catch ( IOException e )
+ {
+ e.printStackTrace();
+ }
+ }
+
+ @FXML
+ public void initialize()
+ {
+
+ }
+
+
+}
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 0cb8622c376ff0048978f80fe2f551e3bf93850b..267530c10293dc85544162291ccd146143ac1f85 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
@@ -34,18 +34,13 @@ import fr.pasteur.ida.zellige.gui.MainAppFrame;
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.model.ConstructionModel;
-import fr.pasteur.ida.zellige.gui.model.MainModel;
-import fr.pasteur.ida.zellige.gui.model.ProjectionModel;
+import fr.pasteur.ida.zellige.gui.model.*;
import fr.pasteur.ida.zellige.gui.model.SelectionModel;
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;
@@ -53,10 +48,7 @@ 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;
@@ -85,18 +77,24 @@ public class MainController< T extends RealType< T > & NativeType< T > > impleme
private final SimpleBooleanProperty changedParameters = new SimpleBooleanProperty();
@FXML
ComboBox< Dataset > activeDatasets;
+
@FXML
private Button runButton;
+
+
+ @FXML
+ private PreprocessingController< T > preprocessingController;
+ @FXML
+ private SelectionController< T > selectionController;
@FXML
private ConstructionController< T > constructionController;
+ @FXML
+ private ProjectionController< T > projectionController;
+
@FXML
private Label logInfo;
private MainAppFrame mainAppFrame;
- @FXML
- private ProjectionController< T > projectionController;
- @FXML
- private SelectionController< T > selectionController;
MainModel< T > model;
@@ -107,24 +105,30 @@ public class MainController< T extends RealType< T > & NativeType< T > > impleme
alert.setTitle( "Error alert" );
alert.setHeaderText( exception.getMessage() );
alert.showAndWait();
- // throw new RuntimeException(exception);
+ // throw new RuntimeException(exception);
}
@Override
public void initialize( URL url, ResourceBundle resourceBundle )
{
- model = new MainModel<>( selectionController.getSelectionModel(), constructionController.getConstructionModel(), projectionController.getModel() );
+
+
+ model = new MainModel<>( preprocessingController.getModel(), selectionController.getModel(), constructionController.getConstructionModel(), projectionController.getModel() );
+
+
+
+
/* Control of the files comboBox*/
activeDatasets.setOnMousePressed( event ->
setAndDisplayDatasetChoices() );// Update of the list of opened Fiji images
activeDatasets.getSelectionModel().selectedItemProperty().addListener( ( observableValue, oldValue, newValue ) ->
{
- LOGGER.debug( "selectedItemProperty : old value = {}, new value = {} ", oldValue, newValue );
- if(newValue!= null && isValid( newValue ))
+ LOGGER.debug( "selectedItemProperty : old value = {}, new value = {} ", oldValue, newValue );
+ if ( newValue != null && isValid( newValue ) )
{
- setCurrentDataset( newValue );
+ setCurrentDataset( newValue );
}
else
{
@@ -132,6 +136,8 @@ public class MainController< T extends RealType< T > & NativeType< T > > impleme
}
} );
+
+
currentDataset.addListener( ( observableValue, dataset, t1 ) ->
{
if ( t1 != null )
@@ -147,6 +153,7 @@ public class MainController< T extends RealType< T > & NativeType< T > > impleme
}
} );
+
pretreatedImg.addListener( ( observable, oldValue, newValue ) ->
{
if ( newValue != null )
@@ -163,6 +170,7 @@ public class MainController< T extends RealType< T > & NativeType< T > > impleme
disableGUI.addListener( ( observable, oldValue, newValue ) ->
runButton.setDisable( newValue ) );
+
// run button initialization
runButton.setOnAction( actionEvent ->
{
@@ -172,9 +180,11 @@ 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() );
+ preprocessingController.getModel().currentDatasetProperty().bind( currentDataset );
+ preprocessingController.getModel().pretreatedImgProperty().bind( pretreatedImg );
+ selectionController.getModel().pretreatedImgProperty().bind( pretreatedImg );
+ selectionController.getModel().imagesProperty().bind( images );
+ constructionController.getConstructionModel().maximumsProperty().bind( selectionController.getModel().selectedPixelsProperty() );
projectionController.getModel().referenceSurfacesProperty().bind( constructionController.getConstructionModel().referenceSurfacesProperty() );
changedParameters.bindBidirectional( selectionController.changedParametersProperty() );
selectionController.changedParametersProperty().bindBidirectional( constructionController.changedParametersProperty() );
@@ -201,26 +211,28 @@ 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() );
+
if ( dataset == null )
{
showError( new NoInputException() );
return;
}
+ LOGGER.debug( dataset.getImgPlus().firstElement().getClass().toGenericString() );
+ LOGGER.debug( "Function getFrames() :{}", dataset.getFrames() );
+ LOGGER.debug( "Properties :{}", dataset.getImgPlus().getProperties() );
activeDatasets.getItems().add( dataset );
LOGGER.debug( "Init Extraction completed" );
}
+
+
public void run2()
{
- if ( selectionController.getSelectionModel().selectedPixelsProperty().getValue() != null )
+ if ( selectionController.getModel().selectedPixelsProperty().getValue() != null )
{
if ( constructionController.getConstructionModel().referenceSurfacesProperty().getValue() != null )
{
@@ -233,14 +245,19 @@ public class MainController< T extends RealType< T > & NativeType< T > > impleme
}
else
{
- selectionController.getSelectionModel().runPixelSelection();
+ selectionController.runPixelSelection();
}
LOGGER.debug( "###########################################---NEW RUN---###########################################" );
}
+ private void runPreprocessing( Dataset dataset )
+ {
+ // AbstractTask< Img<T> > task = new BinningTask<>( pr )
+ }
+
private void runPretreatment( Dataset dataset )
{
- AbstractTask< Img< FloatType > > task = new PretreatmentTask<>( dataset);//TODO default value to change
+ AbstractTask< Img< FloatType > > task = new PreprocessingTask<>( dataset, 2, 2 );//TODO default value to change
task.setOnSucceeded( workerStateEvent ->
pretreatedImg.setValue( task.getValue() ) );
task.start();
@@ -268,12 +285,12 @@ public class MainController< T extends RealType< T > & NativeType< T > > impleme
}
@SuppressWarnings( "unchecked" )
- public void setCurrentDataset( Dataset dataset )
+ public void setCurrentDataset( Dataset dataset ) // TODO modify for channel selection
{
- currentDataset.setValue( dataset );
- Img< T > input = ( ImgPlus< T > ) dataset.getImgPlus();
- constructionController.getConstructionModel().setInput( input );
- constructionController.getConstructionModel().setFactory( input.factory() );
+ currentDataset.setValue( dataset );
+ Img< T > input = ( ImgPlus< T > ) dataset.getImgPlus();
+ constructionController.getConstructionModel().setInput( input );
+ constructionController.getConstructionModel().setFactory( input.factory() );
}
@@ -316,7 +333,7 @@ public class MainController< T extends RealType< T > & NativeType< T > > impleme
ConstructionParameter cp = build( model.getConstructionModel() );
ProjectionParameter pp = build( model.getProjectionModel() );
- ZelligeParameters.serialize( new ZelligeParameters( sp, cp, pp ), file );
+ ZelligeParameters.serialize( new ZelligeParameters( 2, sp, cp, pp ), file );
}
}
@@ -372,7 +389,7 @@ public class MainController< T extends RealType< T > & NativeType< T > > impleme
projectionController.setParameters( parameters );
}
- private boolean isValid(Dataset dataset)
+ private boolean isValid( Dataset dataset )
{
int numZ = ( int ) dataset.getDepth();
int numFrames = ( int ) dataset.getFrames();
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/controller/PreprocessingController.java b/src/main/java/fr/pasteur/ida/zellige/gui/controller/PreprocessingController.java
new file mode 100644
index 0000000000000000000000000000000000000000..78f3212bede7ca12b262e889d914ed48ae1d2cc4
--- /dev/null
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/controller/PreprocessingController.java
@@ -0,0 +1,72 @@
+package fr.pasteur.ida.zellige.gui.controller;
+
+import fr.pasteur.ida.zellige.gui.PreprocessingPanel;
+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.model.PreprocessingModel;
+import fr.pasteur.ida.zellige.gui.task.DisplayDatasetChoicesTask;
+import javafx.collections.FXCollections;
+import javafx.collections.ObservableList;
+import javafx.fxml.FXML;
+import javafx.fxml.FXMLLoader;
+import javafx.fxml.Initializable;
+import javafx.scene.control.ComboBox;
+import javafx.scene.control.Spinner;
+import javafx.scene.control.SpinnerValueFactory;
+import net.imagej.Dataset;
+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.ResourceBundle;
+
+
+
+public class PreprocessingController < T extends RealType< T > & NativeType< T > > implements Initializable
+{
+
+ private final static Logger LOGGER = LoggerFactory.getLogger( PreprocessingController.class );
+
+ @FXML
+ private Spinner<Integer> bin;
+
+
+ private PreprocessingModel model;
+
+ public PreprocessingController()
+ {
+ FXMLLoader fxmlLoader = new FXMLLoader( PreprocessingPanel.class.getClassLoader().getResource(
+ "fr.pasteur.ida.zellige.gui.view/PreprocessingPanel.fxml" ) );
+ fxmlLoader.setRoot( this );
+ fxmlLoader.setController( this );
+
+ }
+
+
+ @Override
+ public void initialize( URL url, ResourceBundle resourceBundle )
+ {
+ //Model
+ model = new PreprocessingModel();
+
+ //link Model with View
+ model.binProperty().bind(bin.valueProperty()); // link between model and controller
+
+ /* Control of the bin Spinner*/
+ SpinnerValueFactory< Integer > valueFactory =
+ new SpinnerValueFactory.IntegerSpinnerValueFactory( 1, 10, 1 );
+ bin.setValueFactory( valueFactory );
+
+ bin.valueProperty().addListener( ( observableValue, number, newValue ) ->
+ model.runPreprocessingTask());
+
+ }
+
+ public PreprocessingModel getModel()
+ {
+ return model;
+ }
+}
\ No newline at end of file
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/controller/SelectionController.java b/src/main/java/fr/pasteur/ida/zellige/gui/controller/SelectionController.java
index 31fdbf2e31543a891fcb414b2d9e7951084c7357..a00d308a8a3dc5fedb80a11fc10315d0f959c16f 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/controller/SelectionController.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/controller/SelectionController.java
@@ -32,7 +32,7 @@ import fr.pasteur.ida.zellige.gui.ParameterSliderInteger;
import fr.pasteur.ida.zellige.gui.ZSlicesSlider;
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.SimpleBooleanProperty;
import javafx.beans.value.ChangeListener;
import javafx.fxml.FXML;
@@ -57,7 +57,7 @@ public class SelectionController< T extends RealType< T > & NativeType< T > > im
private final SimpleBooleanProperty changedParameters = new SimpleBooleanProperty();
private final SimpleBooleanProperty disableGUI = new SimpleBooleanProperty();
- private SelectionModel selectionModel;
+ private SelectionModel model;
@FXML
private ParameterSliderInteger amplitude;
@@ -78,25 +78,25 @@ public class SelectionController< T extends RealType< T > & NativeType< T > > im
public void initialize( URL url, ResourceBundle resourceBundle )
{
// model
- selectionModel = new SelectionModel();
+ model = 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 );
+ model.amplitudeProperty().bind( amplitude.sliderProperty() );
+ model.otsuProperty().bind( otsu.sliderProperty() );
+ model.islandProperty().bind( island.sliderProperty() );
+ model.xyBlurProperty().bind( xyBlur.sliderProperty() );
+ model.zBlurProperty().bind( zBlur.sliderProperty() );
+ model.disableGUIProperty().bindBidirectional( disableGUI );
/* JavaFx Components */
/* Amplitude slider initialization */
amplitude.sliderProperty().addListener( ( observableValue, number, newValue ) ->
{
- if ( amplitude.hasChanged( newValue ) && selectionModel.selectedAmplitudeProperty().getValue() != null )
+ if ( amplitude.hasChanged( newValue ) && model.selectedAmplitudeProperty().getValue() != null )
{
disableGUI.setValue( true );
- selectionModel.runAmplitudeTask();
+ runAmplitudeTask();
changedParameters.setValue( true );
}
} );
@@ -104,10 +104,10 @@ public class SelectionController< T extends RealType< T > & NativeType< T > > im
/* Otsu slider initialization */
otsu.sliderProperty().addListener( ( observableValue, number, newValue ) ->
{
- if ( otsu.hasChanged( newValue ) && selectionModel.selectedOtsuProperty().getValue() != null )
+ if ( otsu.hasChanged( newValue ) && model.selectedOtsuProperty().getValue() != null )
{
disableGUI.setValue( true );
- selectionModel.runOtsuTask();
+ runOtsuTask();
changedParameters.setValue( true );
}
} );
@@ -116,7 +116,7 @@ public class SelectionController< T extends RealType< T > & NativeType< T > > im
{
if ( island.hasChanged( t1 ) )
{
- selectionModel.setIslandSearchImage( null );
+ model.setIslandSearchImage( null );
changedParameters.setValue( true );
}
} );
@@ -125,7 +125,7 @@ public class SelectionController< T extends RealType< T > & NativeType< T > > im
{
if ( xyBlur.hasChanged( newValue ) )
{
- selectionModel.setSelectedPixels( null );
+ model.setSelectedPixels( null );
changedParameters.setValue( true );
}
} );
@@ -133,7 +133,7 @@ public class SelectionController< T extends RealType< T > & NativeType< T > > im
{
if ( zBlur.hasChanged( newValue ) )
{
- selectionModel.setSelectedPixels( null );
+ model.setSelectedPixels( null );
changedParameters.setValue( true );
}
} );
@@ -162,73 +162,139 @@ public class SelectionController< T extends RealType< T > & NativeType< T > > im
enableParameters();
}
} );
- selectionModel.imagesProperty().addListener( ( observableValue, classifiedImages, t1 ) ->
+ model.imagesProperty().addListener( ( observableValue, classifiedImages, t1 ) ->
{
if ( t1 != null )
{
- selectionModel.runAmplitudeTask();
- selectionModel.runOtsuTask();
+ runAmplitudeTask();
+ runOtsuTask();
}
else
{
LOGGER.debug( "IMAGES is NULL" );
- selectionModel.selectedAmplitudeProperty().setValue( null );
- selectionModel.selectedOtsuProperty().setValue( null );
- selectionModel.interClassifiedImageProperty().setValue( null );
+ model.selectedAmplitudeProperty().setValue( null );
+ model.selectedOtsuProperty().setValue( null );
+ model.interClassifiedImageProperty().setValue( null );
}
} );
ChangeListener< Img< BitType > > listener = ( observableValue, bitTypeClassifiedImages, t1 ) ->
{
- if ( selectionModel.selectedAmplitudeProperty().getValue() != null && selectionModel.selectedOtsuProperty().getValue() != null )
+ if ( model.selectedAmplitudeProperty().getValue() != null && model.selectedOtsuProperty().getValue() != null )
{
- selectionModel.runInterClassification();
+ runInterClassification();
LOGGER.debug( "Inter classification" );
}
else
{
LOGGER.debug( "SELECTED_AMPLITUDE or SELECTED_OTSU is NULL" );
- selectionModel.interClassifiedImageProperty().setValue( null );
+ model.interClassifiedImageProperty().setValue( null );
}
};
- selectionModel.selectedAmplitudeProperty().addListener( listener );
- selectionModel.selectedOtsuProperty().addListener( listener );
+ model.selectedAmplitudeProperty().addListener( listener );
+ model.selectedOtsuProperty().addListener( listener );
- selectionModel.interClassifiedImageProperty().addListener( ( observable, oldValue, newValue ) ->
+ model.interClassifiedImageProperty().addListener( ( observable, oldValue, newValue ) ->
{
LOGGER.info( "Computing double classification..." );
if ( newValue != null )
{
computeImageFXDisplay();
}
- selectionModel.islandSearchImageProperty().setValue( null );
+ model.islandSearchImageProperty().setValue( null );
} );
- selectionModel.islandSearchImageProperty().addListener( ( observableValue, bitTypes, t1 ) ->
+ model.islandSearchImageProperty().addListener( ( observableValue, bitTypes, t1 ) ->
{
if ( t1 == null )
{
LOGGER.debug( "ISLAND_SEARCH is NULL" );
- selectionModel.selectedPixelsProperty().setValue( null );
+ model.selectedPixelsProperty().setValue( null );
}
else
{
- selectionModel.runSmoothing();
+ runSmoothing();
}
} );
}
+ public void runAmplitudeTask()
+ {
+ AmplitudeThresholdingTask amplitudeTask = new AmplitudeThresholdingTask( model.imagesProperty().get().getAmplitudeImg(), model.amplitudeProperty().getValue().intValue() );
+ amplitudeTask.setOnSucceeded( workerStateEvent ->
+ {
+ model.selectedAmplitudeProperty().setValue( amplitudeTask.getValue() );
+ disableGUI.setValue( false );
+ } );
+ amplitudeTask.setOnFailed( workerStateEvent -> LOGGER.debug( "Amplitude classification has failed." ) );
+ amplitudeTask.start();
+ }
+
+ public void runOtsuTask()
+ {
+ OtsuThresholdingTask otsuTask = new OtsuThresholdingTask( model.pretreatedImgProperty(), model.imagesProperty().get().getOtsuImg(), model.otsuProperty().getValue().intValue() );
+ otsuTask.setOnSucceeded( workerStateEvent ->
+ {
+ model.selectedOtsuProperty().setValue( otsuTask.getValue() );
+ disableGUI.setValue( false );
+ } );
+ otsuTask.setOnFailed( workerStateEvent -> LOGGER.debug( "Otsu classification has failed." ) );
+ otsuTask.start();
+ }
+
+ public void runInterClassification()
+ {
+ InterClassificationTask interClassificationTask = new InterClassificationTask( model.selectedAmplitudeProperty(), model.selectedOtsuProperty() );
+ interClassificationTask.setOnSucceeded( event -> model.interClassifiedImageProperty().setValue( interClassificationTask.getValue() ) );
+ interClassificationTask.start();
+ }
+
+
+ public void runIslandSearch()
+ {
+ IslandSearchTask islandSearchTask = new IslandSearchTask( model.interClassifiedImageProperty(), model.islandProperty() );
+ 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(), model.xyBlurProperty(), model.zBlurProperty() );
+ smoothingTask.setOnSucceeded( event ->
+ {
+ model.selectedPixelsProperty().setValue( smoothingTask.getValue() );
+ LOGGER.debug( "max is set" );
+ } );
+ smoothingTask.start();
+ }
+
+ public void runPixelSelection()
+ {
+ if ( model.islandSearchImageProperty().getValue() == null )
+ {
+ LOGGER.debug( "Island search image is NULL" );
+ runIslandSearch();
+ }
+ else if ( model.selectedPixelsProperty().getValue() == null )
+ {
+ LOGGER.debug( "Island search image is not NULL" );
+ runSmoothing();
+ }
+ }
+
public void computeImageFXDisplay()
{
- ImageFXDisplayTask imageFXDisplayTask = new ImageFXDisplayTask( selectionModel.interClassifiedImageProperty() );
+ ImageFXDisplayTask imageFXDisplayTask = new ImageFXDisplayTask( model.interClassifiedImageProperty() );
imageFXDisplayTask.setOnSucceeded( workerStateEvent ->
{
LOGGER.info( "Double classification done." );
- selectionModel.imageViewsProperty().setValue( imageFXDisplayTask.getValue() );
+ model.imageViewsProperty().setValue( imageFXDisplayTask.getValue() );
setDisplay();
} );
imageFXDisplayTask.start();
@@ -237,12 +303,12 @@ public class SelectionController< T extends RealType< T > & NativeType< T > > im
public void setDisplay()
{
stack.getChildren().clear();
- ImageView i = selectionModel.imageViewsProperty().getValue()[ zSlices.getUserValue() ];
+ ImageView i = model.imageViewsProperty().getValue()[ zSlices.getUserValue() ];
stack.getChildren().add( i );
// setting of ZSlider
- this.setSliceNumber( ( int ) selectionModel.pretreatedImgProperty().getValue().dimension( 2 ) );
+ this.setSliceNumber( ( int ) model.pretreatedImgProperty().getValue().dimension( 2 ) );
int width = ( int ) i.boundsInParentProperty().get().getWidth();
this.zSlices.getSlider().setMaxWidth( width );
this.zSlices.getSlider().setVisible( true );
@@ -258,7 +324,7 @@ 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 = model.imageViewsProperty().getValue()[ value ];
stack.getChildren().add( i ); // display of selected z slice
}
@@ -269,7 +335,7 @@ public class SelectionController< T extends RealType< T > & NativeType< T > > im
public void set()
{
- this.setSliceNumber( ( int ) selectionModel.pretreatedImgProperty().getValue().dimension( 2 ) );
+ this.setSliceNumber( ( int ) model.pretreatedImgProperty().getValue().dimension( 2 ) );
}
public void enableParameters()
@@ -326,9 +392,9 @@ public class SelectionController< T extends RealType< T > & NativeType< T > > im
return disableGUI;
}
- public SelectionModel getSelectionModel()
+ public SelectionModel getModel()
{
- return selectionModel;
+ return model;
}
public void setParameters( ZelligeParameters parameters )
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/model/MainModel.java b/src/main/java/fr/pasteur/ida/zellige/gui/model/MainModel.java
index 0277933bda39614dfeda5e0bf3687c908be56437..30e8989a4332a9e4588f794376c26002d81c58bd 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/model/MainModel.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/model/MainModel.java
@@ -33,18 +33,25 @@ import net.imglib2.type.numeric.RealType;
public class MainModel< T extends RealType< T > & NativeType< T > >
{
-
+ private final PreprocessingModel 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 preprocessingModel, SelectionModel selectionModel, ConstructionModel< T > constructionModel, ProjectionModel< T > projectionModel )
{
+ this.preprocessingModel = preprocessingModel;
this.selectionModel = selectionModel;
this.constructionModel = constructionModel;
this.projectionModel = projectionModel;
}
+
+ public PreprocessingModel getPreprocessingModel()
+ {
+ return preprocessingModel;
+ }
+
public SelectionModel getSelectionModel()
{
return selectionModel;
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/model/PreprocessingModel.java b/src/main/java/fr/pasteur/ida/zellige/gui/model/PreprocessingModel.java
new file mode 100644
index 0000000000000000000000000000000000000000..cd571811dc0058256fa3a0e2b6c4b75381a139c3
--- /dev/null
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/model/PreprocessingModel.java
@@ -0,0 +1,71 @@
+package fr.pasteur.ida.zellige.gui.model;
+
+import fr.pasteur.ida.zellige.gui.task.AbstractTask;
+import fr.pasteur.ida.zellige.gui.task.PreprocessingTask;
+import javafx.beans.property.IntegerProperty;
+import javafx.beans.property.SimpleIntegerProperty;
+import javafx.beans.property.SimpleObjectProperty;
+import net.imagej.Dataset;
+import net.imglib2.img.Img;
+import net.imglib2.type.numeric.real.FloatType;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class PreprocessingModel
+{
+ private final static Logger LOGGER = LoggerFactory.getLogger( PreprocessingModel.class );
+
+ private final IntegerProperty bin;
+ private final SimpleObjectProperty< Dataset > currentDataset = new SimpleObjectProperty<>();
+ private final SimpleObjectProperty< Img< FloatType > > pretreatedImg = new SimpleObjectProperty<>();
+
+ public PreprocessingModel()
+ {
+ this.bin = new SimpleIntegerProperty();
+ }
+
+ public void runBinningTask()
+ {
+
+ }
+
+ public void runPreprocessingTask()
+ {
+ AbstractTask< Img< FloatType > > task = new PreprocessingTask<>(currentDataset.get(), 2, getBin() );
+ task.setOnSucceeded( workerStateEvent ->
+ pretreatedImg.setValue( task.getValue() ) );
+ task.start();
+ }
+
+ public int getBin()
+ {
+ return bin.get();
+ }
+
+ public IntegerProperty binProperty()
+ {
+ return bin;
+ }
+
+ public Dataset getCurrentDataset()
+ {
+ return currentDataset.get();
+ }
+
+ public Img< FloatType > getPretreatedImg()
+ {
+ return pretreatedImg.get();
+ }
+
+ public SimpleObjectProperty< Img< FloatType > > pretreatedImgProperty()
+ {
+ return pretreatedImg;
+ }
+
+ public SimpleObjectProperty< Dataset > currentDatasetProperty()
+ {
+ return currentDataset;
+
+
+ }
+}
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/model/SelectionModel.java b/src/main/java/fr/pasteur/ida/zellige/gui/model/SelectionModel.java
index b703deff5be5cbd0bc21fb34881aa919a3cb8a2e..7a7b4284c3e28a07095843fa6850fea9c7936e7e 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/model/SelectionModel.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/model/SelectionModel.java
@@ -69,69 +69,71 @@ public class SelectionModel
zBlur = new SimpleDoubleProperty();
}
- public void runAmplitudeTask()
- {
- AmplitudeThresholdingTask amplitudeTask = new AmplitudeThresholdingTask( images, amplitude.getValue().intValue() );
- amplitudeTask.setOnSucceeded( workerStateEvent ->
- {
- selectedAmplitude.setValue( amplitudeTask.getValue() );
- disableGUI.setValue( false );
- } );
- amplitudeTask.start();
- }
-
- public void runOtsuTask()
- {
- OtsuThresholdingTask otsuTask = new OtsuThresholdingTask( pretreatedImg, images, otsu.getValue().intValue() );
- otsuTask.setOnSucceeded( workerStateEvent ->
- {
- selectedOtsu.setValue( otsuTask.getValue() );
- disableGUI.setValue( false );
- } );
- otsuTask.start();
- }
-
- public void runInterClassification()
- {
- InterClassificationTask interClassificationTask = new InterClassificationTask( selectedAmplitude, selectedOtsu );
- interClassificationTask.setOnSucceeded( event -> interClassifiedImage.setValue( interClassificationTask.getValue() ) );
- interClassificationTask.start();
- }
-
-
- public void runIslandSearch()
- {
- IslandSearchTask islandSearchTask = new IslandSearchTask( interClassifiedImage, island );
- islandSearchTask.setOnSucceeded( workerStateEvent ->
- islandSearchImage.setValue( islandSearchTask.getValue() ) );
- islandSearchTask.setOnFailed( workerStateEvent -> LOGGER.debug( "FAILED" ) );
- islandSearchTask.start();
- }
-
- public void runSmoothing()
- {
- SmoothingTask smoothingTask = new SmoothingTask( islandSearchImage, xyBlur, zBlur );
- smoothingTask.setOnSucceeded( event ->
- {
- selectedPixels.setValue( smoothingTask.getValue() );
- LOGGER.debug( "max is set" );
- } );
- smoothingTask.start();
- }
-
- public void runPixelSelection()
- {
- if ( islandSearchImage.getValue() == null )
- {
- LOGGER.debug( "Island search image is NULL" );
- runIslandSearch();
- }
- else if ( selectedPixelsProperty().getValue() == null )
- {
- LOGGER.debug( "Island search image is not NULL" );
- runSmoothing();
- }
- }
+// public void runAmplitudeTask()
+// {
+// AmplitudeThresholdingTask amplitudeTask = new AmplitudeThresholdingTask( images, amplitude.getValue().intValue() );
+// amplitudeTask.setOnSucceeded( workerStateEvent ->
+// {
+// selectedAmplitude.setValue( amplitudeTask.getValue() );
+// disableGUI.setValue( false );
+// } );
+// amplitudeTask.setOnFailed( workerStateEvent -> LOGGER.debug( "Amplitude classification has failed." ) );
+// amplitudeTask.start();
+// }
+//
+// public void runOtsuTask()
+// {
+// OtsuThresholdingTask otsuTask = new OtsuThresholdingTask( pretreatedImg, images, otsu.getValue().intValue() );
+// otsuTask.setOnSucceeded( workerStateEvent ->
+// {
+// selectedOtsu.setValue( otsuTask.getValue() );
+// disableGUI.setValue( false );
+// } );
+// otsuTask.setOnFailed( workerStateEvent -> LOGGER.debug( "Otsu classification has failed." ) );
+// otsuTask.start();
+// }
+//
+// public void runInterClassification()
+// {
+// InterClassificationTask interClassificationTask = new InterClassificationTask( selectedAmplitude, selectedOtsu );
+// interClassificationTask.setOnSucceeded( event -> interClassifiedImage.setValue( interClassificationTask.getValue() ) );
+// interClassificationTask.start();
+// }
+//
+//
+// public void runIslandSearch()
+// {
+// IslandSearchTask islandSearchTask = new IslandSearchTask( interClassifiedImage, island );
+// islandSearchTask.setOnSucceeded( workerStateEvent ->
+// islandSearchImage.setValue( islandSearchTask.getValue() ) );
+// islandSearchTask.setOnFailed( workerStateEvent -> LOGGER.debug( "FAILED" ) );
+// islandSearchTask.start();
+// }
+//
+// public void runSmoothing()
+// {
+// SmoothingTask smoothingTask = new SmoothingTask( islandSearchImage, xyBlur, zBlur );
+// smoothingTask.setOnSucceeded( event ->
+// {
+// selectedPixels.setValue( smoothingTask.getValue() );
+// LOGGER.debug( "max is set" );
+// } );
+// smoothingTask.start();
+// }
+//
+// public void runPixelSelection()
+// {
+// if ( islandSearchImage.getValue() == null )
+// {
+// LOGGER.debug( "Island search image is NULL" );
+// runIslandSearch();
+// }
+// else if ( selectedPixelsProperty().getValue() == null )
+// {
+// LOGGER.debug( "Island search image is not NULL" );
+// runSmoothing();
+// }
+// }
public double getAmplitude()
{
@@ -183,37 +185,17 @@ public class SelectionModel
return xyBlur;
}
- public double getzBlur()
- {
- return zBlur.get();
- }
-
public DoubleProperty zBlurProperty()
{
return zBlur;
}
- public boolean isDisableGUI()
- {
- return disableGUI.get();
- }
-
- public void setDisableGUI( boolean disableGUI )
- {
- this.disableGUI.set( disableGUI );
- }
-
public SimpleBooleanProperty disableGUIProperty()
{
return disableGUI;
}
- public Pixels[][] getSelectedPixels()
- {
- return selectedPixels.get();
- }
-
public void setSelectedPixels( Pixels[][] selectedPixels )
{
this.selectedPixels.set( selectedPixels );
@@ -239,11 +221,6 @@ public class SelectionModel
return images;
}
- public Img< BitType > getIslandSearchImage()
- {
- return islandSearchImage.get();
- }
-
public void setIslandSearchImage( Img< BitType > islandSearchImage )
{
this.islandSearchImage.set( islandSearchImage );
@@ -254,71 +231,26 @@ public class SelectionModel
return islandSearchImage;
}
- public Img< FloatType > getPretreatedImg()
- {
- return pretreatedImg.get();
- }
-
- public void setPretreatedImg( Img< FloatType > pretreatedImg )
- {
- this.pretreatedImg.set( pretreatedImg );
- }
-
public SimpleObjectProperty< Img< FloatType > > pretreatedImgProperty()
{
return pretreatedImg;
}
- public Img< BitType > getSelectedAmplitude()
- {
- return selectedAmplitude.get();
- }
-
- public void setSelectedAmplitude( Img< BitType > selectedAmplitude )
- {
- this.selectedAmplitude.set( selectedAmplitude );
- }
-
public SimpleObjectProperty< Img< BitType > > selectedAmplitudeProperty()
{
return selectedAmplitude;
}
- public Img< BitType > getSelectedOtsu()
- {
- return selectedOtsu.get();
- }
-
- public void setSelectedOtsu( Img< BitType > selectedOtsu )
- {
- this.selectedOtsu.set( selectedOtsu );
- }
-
public SimpleObjectProperty< Img< BitType > > selectedOtsuProperty()
{
return selectedOtsu;
}
- public Img< BitType > getInterClassifiedImage()
- {
- return interClassifiedImage.get();
- }
-
- public void setInterClassifiedImage( Img< BitType > interClassifiedImage )
- {
- this.interClassifiedImage.set( interClassifiedImage );
- }
-
public SimpleObjectProperty< Img< BitType > > interClassifiedImageProperty()
{
return interClassifiedImage;
}
- public ImageView[] getImageViews()
- {
- return imageViews.get();
- }
-
public SimpleObjectProperty< ImageView[] > imageViewsProperty()
{
return imageViews;
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/parameter/SelectionParameter.java b/src/main/java/fr/pasteur/ida/zellige/gui/parameter/SelectionParameter.java
index 4dccfcb4a8c3ba2ef8b666322ac7ca7112c2f38f..b065e90147f4aa5f0303258801980b9fd9de22d9 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/parameter/SelectionParameter.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/parameter/SelectionParameter.java
@@ -72,3 +72,5 @@ public class SelectionParameter
return zBlur;
}
}
+
+// TODO verify why the amplitude and otsu parameters are Double property instead of IntegerProperty
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/parameter/ZelligeParameters.java b/src/main/java/fr/pasteur/ida/zellige/gui/parameter/ZelligeParameters.java
index 3e247c73265b20797d84176bb9d8e2b3dcd44c61..088d589a670eeb488b9d91b8ee25739c538f331f 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/parameter/ZelligeParameters.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/parameter/ZelligeParameters.java
@@ -42,6 +42,7 @@ import java.util.stream.Stream;
public class ZelligeParameters
{
+ private final int bin;
//selection
private final int amplitude;
private final int otsu;
@@ -62,26 +63,27 @@ public class ZelligeParameters
private final String method;
- public ZelligeParameters( SelectionParameter sp, ConstructionParameter cp, ProjectionParameter pp )
+ public ZelligeParameters( int bin, SelectionParameter sp, ConstructionParameter cp, ProjectionParameter pp )
{
+ this.bin = bin;
// selection
- amplitude = sp.getAmplitude();
- otsu = sp.getOtsu();
- island = sp.getIsland();
- xyBlur = sp.getXyBlur();
- zBlur = sp.getzBlur();
+ this.amplitude = sp.getAmplitude();
+ this.otsu = sp.getOtsu();
+ this.island = sp.getIsland();
+ this.xyBlur = sp.getXyBlur();
+ this.zBlur = sp.getzBlur();
// construction
- c1 = cp.getC1();
- r1 = cp.getR1();
- st1 = cp.getSt1();
- c2 = cp.getC2();
- r2 = cp.getR2();
- st2 = cp.getSt2();
- surfaceSize = cp.getSurfaceSize();
+ this.c1 = cp.getC1();
+ this.r1 = cp.getR1();
+ this.st1 = cp.getSt1();
+ this.c2 = cp.getC2();
+ this.r2 = cp.getR2();
+ this.st2 = cp.getSt2();
+ this.surfaceSize = cp.getSurfaceSize();
// projection
- delta1 = pp.getDelta1();
- delta2 = pp.getDelta2();
- method = pp.getMethod();
+ this.delta1 = pp.getDelta1();
+ this.delta2 = pp.getDelta2();
+ this.method = pp.getMethod();
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/task/AmplitudeThresholdingTask.java b/src/main/java/fr/pasteur/ida/zellige/gui/task/AmplitudeThresholdingTask.java
index 69b7d4f5803b90ec7f6b0354c397c7b851811a1b..3077ef1a745392068aee21911bcaf58473fbff9a 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/task/AmplitudeThresholdingTask.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/task/AmplitudeThresholdingTask.java
@@ -28,9 +28,7 @@
*/
package fr.pasteur.ida.zellige.gui.task;
-import fr.pasteur.ida.zellige.gui.ClassifiedImages;
import fr.pasteur.ida.zellige.steps.selection.classification.AmplitudeClassification;
-import javafx.beans.property.SimpleObjectProperty;
import net.imglib2.img.Img;
import net.imglib2.type.logic.BitType;
import net.imglib2.type.numeric.real.FloatType;
@@ -41,13 +39,13 @@ public class AmplitudeThresholdingTask extends AbstractTask< Img< BitType > >
{
private final static Logger LOGGER = LoggerFactory.getLogger( AmplitudeThresholdingTask.class );
- private final SimpleObjectProperty< ClassifiedImages< FloatType > > images;
+ private final Img<FloatType> input;
private final int amplitudeThreshold;
- public AmplitudeThresholdingTask( SimpleObjectProperty< ClassifiedImages< FloatType > > images, int amplitudeThreshold )
+ public AmplitudeThresholdingTask( Img<FloatType> input, int amplitudeThreshold )
{
- this.images = images;
+ this.input = input;
this.amplitudeThreshold = amplitudeThreshold;
}
@@ -55,6 +53,8 @@ public class AmplitudeThresholdingTask extends AbstractTask< Img< BitType > >
protected Img< BitType > call()
{
LOGGER.info( "Computing amplitude thresholding..." );
- return AmplitudeClassification.applyThreshold( images.getValue().getAmplitudeImg(), amplitudeThreshold );
+ Img< BitType > output = AmplitudeClassification.applyThreshold( input, amplitudeThreshold );
+ LOGGER.info( "Amplitude thresholds computed..." );
+ return output;
}
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/task/BinningTask.java b/src/main/java/fr/pasteur/ida/zellige/gui/task/BinningTask.java
new file mode 100644
index 0000000000000000000000000000000000000000..df3517509a9abd19f2d7ba3e1db277c51be8c502
--- /dev/null
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/task/BinningTask.java
@@ -0,0 +1,30 @@
+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;
+
+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( "Binning" );
+ Img<T> binnedImage = Binning.run( input, bin );
+ LOGGER.info( "Image binned !" );
+ return binnedImage;
+ }
+}
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/task/ConstructionCompletionTask.java b/src/main/java/fr/pasteur/ida/zellige/gui/task/ConstructionCompletionTask.java
index d3aee6782fbef6509413403dc3501977acd199ef..3afab1e1a2dff87144780ae704f66ef145b2831c 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/task/ConstructionCompletionTask.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/task/ConstructionCompletionTask.java
@@ -59,7 +59,7 @@ public class ConstructionCompletionTask< T extends RealType< T > & NativeType< T
protected ArrayList< ReferenceSurface< T > > call()
{
LOGGER.info( "Processing construction completion..." );
- return ConstructionCompletion.run( input, factory, finalSurfaces );
+ return ConstructionCompletion.run( input, factory, finalSurfaces , 2);
}
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/task/OtsuThresholdingTask.java b/src/main/java/fr/pasteur/ida/zellige/gui/task/OtsuThresholdingTask.java
index 9709e35eabf951d8fa312194620b3ccf64443ce8..982b55216e4ffd06211191c26ff462b66d88f358 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/task/OtsuThresholdingTask.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/task/OtsuThresholdingTask.java
@@ -28,7 +28,6 @@
*/
package fr.pasteur.ida.zellige.gui.task;
-import fr.pasteur.ida.zellige.gui.ClassifiedImages;
import fr.pasteur.ida.zellige.steps.selection.classification.OtsuClassification;
import javafx.beans.property.SimpleObjectProperty;
import net.imglib2.img.Img;
@@ -42,14 +41,14 @@ public class OtsuThresholdingTask extends AbstractTask< Img< BitType > >
private final static Logger LOGGER = LoggerFactory.getLogger( OtsuThresholdingTask.class );
private final SimpleObjectProperty< Img< FloatType > > pretreatedImage;
- private final SimpleObjectProperty< ClassifiedImages< FloatType > > images;
+ private final Img<FloatType> input;
private final int otsuThreshold;
- public OtsuThresholdingTask( SimpleObjectProperty< Img< FloatType > > pretreatedImage, SimpleObjectProperty< ClassifiedImages< FloatType > > images, int otsuThreshold )
+ public OtsuThresholdingTask( SimpleObjectProperty< Img< FloatType > > pretreatedImage, Img<FloatType> input, int otsuThreshold )
{
this.pretreatedImage = pretreatedImage;
- this.images = images;
+ this.input = input;
this.otsuThreshold = otsuThreshold;
}
@@ -57,6 +56,8 @@ public class OtsuThresholdingTask extends AbstractTask< Img< BitType > >
protected Img< BitType > call()
{
LOGGER.info( "Computing otsu thresholding..." );
- return OtsuClassification.applyLocalThreshold( pretreatedImage.getValue(), images.getValue().getOtsuImg(), otsuThreshold );
+ Img< BitType > output = OtsuClassification.applyLocalThreshold( pretreatedImage.getValue(), input, otsuThreshold );
+ LOGGER.info( "Amplitude thresholds computed..." );
+ return output;
}
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/gui/task/PretreatmentTask.java b/src/main/java/fr/pasteur/ida/zellige/gui/task/PreprocessingTask.java
similarity index 86%
rename from src/main/java/fr/pasteur/ida/zellige/gui/task/PretreatmentTask.java
rename to src/main/java/fr/pasteur/ida/zellige/gui/task/PreprocessingTask.java
index bbb6fb4ee955e89579ecee899efdd15dd1b7b7b1..596a54ce78ec7bb3bb6566600824094ccda38cc8 100644
--- a/src/main/java/fr/pasteur/ida/zellige/gui/task/PretreatmentTask.java
+++ b/src/main/java/fr/pasteur/ida/zellige/gui/task/PreprocessingTask.java
@@ -38,15 +38,19 @@ import net.imglib2.type.numeric.real.FloatType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
-public class PretreatmentTask< T extends RealType< T > & NativeType< T > > extends AbstractTask< Img< FloatType > >
+public class PreprocessingTask< T extends RealType< T > & NativeType< T > > extends AbstractTask< Img< FloatType > >
{
- private final static Logger LOGGER = LoggerFactory.getLogger( PretreatmentTask.class );
+ private final static Logger LOGGER = LoggerFactory.getLogger( PreprocessingTask.class );
private final Dataset dataset;
+ private final double radius;
+ private final int bin;
- public PretreatmentTask( Dataset dataset )
+ public PreprocessingTask( Dataset dataset, double radius, int bin)
{
this.dataset = dataset;
+ this.radius = radius;
+ this.bin = bin;
}
@Override
@@ -55,7 +59,7 @@ public class PretreatmentTask< T extends RealType< T > & NativeType< T > > exten
{
LOGGER.info( "Computing pretreatment..." );
ImgPlus< T > input = ( ImgPlus< T > ) dataset.getImgPlus();
- Img< FloatType > pretreatedImg = Pretreatment.run( input );
+ Img< FloatType > pretreatedImg = Pretreatment.run( input, radius, bin );
LOGGER.debug( "Done." );
return pretreatedImg;
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/steps/construction/ConstructionCompletion.java b/src/main/java/fr/pasteur/ida/zellige/steps/construction/ConstructionCompletion.java
index b779899a33f457be5f46bb60aacdb88a2a42e71c..72aa7276356ca7359013a2515326e23f8d6ab0eb 100644
--- a/src/main/java/fr/pasteur/ida/zellige/steps/construction/ConstructionCompletion.java
+++ b/src/main/java/fr/pasteur/ida/zellige/steps/construction/ConstructionCompletion.java
@@ -61,18 +61,19 @@ public class ConstructionCompletion< T extends RealType< T > & NativeType< T > >
private final static Logger LOGGER = LoggerFactory.getLogger( ConstructionCompletion.class );
private final ArrayList< ReferenceSurface< T > > referenceSurfaces;
+ private final int bin;
-
- public ConstructionCompletion()
+ public ConstructionCompletion( int bin)
{
this.referenceSurfaces = new ArrayList<>();
+ this.bin = bin;
}
public static < T extends RealType< T > & NativeType< T > > ArrayList< ReferenceSurface< T > > run(
- RandomAccessibleInterval< T > input, ImgFactory< T > factory, ArrayList< Surface > surfaces )
+ RandomAccessibleInterval< T > input, ImgFactory< T > factory, ArrayList< Surface > surfaces, int bin )
{
- ConstructionCompletion< T > completion = new ConstructionCompletion<>();
+ ConstructionCompletion< T > completion = new ConstructionCompletion<>( bin );
completion.referenceSurfaceInstantiation( input, factory, surfaces );
return completion.getReferenceSurfaces();
}
@@ -84,7 +85,11 @@ public class ConstructionCompletion< T extends RealType< T > & NativeType< T > >
for ( Surface surface : finalSurfaces )
{
Img< UnsignedShortType > processedZMap = processedZMap( surface );
-
+ if (bin > 1)
+ {
+ processedZMap = Unbinning.run( processedZMap, bin );
+ LOGGER.info("Height map unbinned");
+ }
ReferenceSurface< T > referenceSurface = new ReferenceSurface<>( input, factory, processedZMap, index++ );
referenceSurfaces.add( referenceSurface );
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/steps/projection/ReferenceSurfaceProjection.java b/src/main/java/fr/pasteur/ida/zellige/steps/projection/ReferenceSurfaceProjection.java
index 6e6bbc70de4f82d99674c63b14a33cf7788984c0..bdd7f55a61bace62d3c5daeee4d40dc5c75bc3dd 100644
--- a/src/main/java/fr/pasteur/ida/zellige/steps/projection/ReferenceSurfaceProjection.java
+++ b/src/main/java/fr/pasteur/ida/zellige/steps/projection/ReferenceSurfaceProjection.java
@@ -396,11 +396,11 @@ public class ReferenceSurfaceProjection< T extends RealType< T > & NativeType< T
projectionType.equals( "Minimum Intensity" ) )
{
referenceSurface.getProjection().setExtractedHeightMap( getProjectionHeightMap( referenceSurface, projectionType, delta ) );
- referenceSurface.getProjection().setReduced3DSpace( getExtractedHeightMapSubStack( referenceSurface, delta ) );
+// referenceSurface.getProjection().setReduced3DSpace( getExtractedHeightMapSubStack( referenceSurface, delta ) );
referenceSurface.getProjection().setProjection( projection1( referenceSurface, projectionType ) );
- referenceSurface.getProjection().setSegmentedSurface( getSegmentedSurface( referenceSurface.getProjection().getExtractedHeightMap(),
- referenceSurface.getInput(),
- referenceSurface.getFactory() ) );
+// referenceSurface.getProjection().setSegmentedSurface( getSegmentedSurface( referenceSurface.getProjection().getExtractedHeightMap(),
+// referenceSurface.getInput(),
+// referenceSurface.getFactory() ) );
}
else
{
diff --git a/src/main/java/fr/pasteur/ida/zellige/steps/selection/Selection.java b/src/main/java/fr/pasteur/ida/zellige/steps/selection/Selection.java
index e88cd6a27d7fcf5a949ed8dccf2c5e9c572a1953..de99155bc69b544cbcc8601e203ad32f7a8eb733 100644
--- a/src/main/java/fr/pasteur/ida/zellige/steps/selection/Selection.java
+++ b/src/main/java/fr/pasteur/ida/zellige/steps/selection/Selection.java
@@ -57,7 +57,7 @@ public class Selection< T extends RealType< T > & NativeType< T > >
{
private final static Logger LOGGER = LoggerFactory.getLogger( Selection.class );
- private final double radius;
+ private final PretreatmentParameters pretreatmentParameters;
private final ClassificationParameters classificationParameters;
private final PostTreatmentParameters postTreatmentParameters;
private final RandomAccessibleInterval< T > input;
@@ -70,14 +70,15 @@ public class Selection< T extends RealType< T > & NativeType< T > >
public Selection( PretreatmentParameters pretreatmentParameters, ClassificationParameters classificationParameters, PostTreatmentParameters postTreatmentParameters,
RandomAccessibleInterval< T > input )
{
- this.radius = pretreatmentParameters.getParameter();
+ this.pretreatmentParameters = pretreatmentParameters;
this.classificationParameters = classificationParameters;
this.postTreatmentParameters = postTreatmentParameters;
this.input = input;
+ //this.factory = factory;
}
public static < T extends RealType< T > & NativeType< T > > Pixels[][]
- run( RandomAccessibleInterval< T > input, PretreatmentParameters pretreatmentParameters, ClassificationParameters classificationParameters, PostTreatmentParameters postTreatmentParameters ) throws NoClassificationException, DataValidationException
+ run( RandomAccessibleInterval< T > input, PretreatmentParameters pretreatmentParameters, ClassificationParameters classificationParameters, PostTreatmentParameters postTreatmentParameters ) throws NoClassificationException, DataValidationException, ImageTooLargeException
{
LOGGER.debug( "Starting process..." );
Selection< T > selection = new Selection<>( pretreatmentParameters, classificationParameters, postTreatmentParameters, input );
@@ -86,6 +87,35 @@ public class Selection< T extends RealType< T > & NativeType< T > >
return selection.output;
}
+ /**
+ * @throws NoClassificationException if the no classification was performed
+ * @throws DataValidationException if one of the input parameters is not valid
+ */
+ public void run() throws NoClassificationException, DataValidationException, ImageTooLargeException
+ {
+
+ /* Pretreatment of the image.*/
+ Img< FloatType > pretreatedImage = Pretreatment.run( input, pretreatmentParameters.getRadius() , pretreatmentParameters.getBin() );
+ if (pretreatedImage != null)
+ {
+ /* Classification. */
+ Img< BitType > classifiedPixel = Classification.run( pretreatedImage, pretreatedImage.factory(), classificationParameters );
+ amplitudePT = AmplitudeClassification.getProcessingTime();
+ otsuPT = OtsuClassification.getProcessingTime();
+ /* PostTreatment and output*/
+ output = PostTreatment.run( classifiedPixel, postTreatmentParameters );
+ islandSearchPT = IslandSearch.getProcessingTime();
+ }
+ else
+ {
+ throw new ImageTooLargeException();
+ }
+ }
+
+ public Pixels[][] getOutput()
+ {
+ return output;
+ }
public static Logger getLOGGER()
{
@@ -106,26 +136,4 @@ public class Selection< T extends RealType< T > & NativeType< T > >
{
return islandSearchPT;
}
-
- /**
- * @throws NoClassificationException if the no classification was performed
- * @throws DataValidationException if one of the input parameters is not valid
- */
- public void run() throws NoClassificationException, DataValidationException
- {
- /* Pretreatment of the image.*/
- Img< FloatType > pretreatedImage = Pretreatment.run( input, radius );
- /* Classification. */
- Img< BitType > classifiedPixel = Classification.run( pretreatedImage, pretreatedImage.factory(), classificationParameters );
- amplitudePT = AmplitudeClassification.getProcessingTime();
- otsuPT = OtsuClassification.getProcessingTime();
- /* PostTreatment and output*/
- output = PostTreatment.run( classifiedPixel, postTreatmentParameters );
- islandSearchPT = IslandSearch.getProcessingTime();
- }
-
- public Pixels[][] getOutput()
- {
- return output;
- }
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/steps/selection/pretreatment/Binning.java b/src/main/java/fr/pasteur/ida/zellige/steps/selection/pretreatment/Binning.java
deleted file mode 100644
index 4b1d14a4887cebd5318294f68a259c98a607c482..0000000000000000000000000000000000000000
--- a/src/main/java/fr/pasteur/ida/zellige/steps/selection/pretreatment/Binning.java
+++ /dev/null
@@ -1,228 +0,0 @@
-package fr.pasteur.ida.zellige.steps.selection.pretreatment;
-
-import io.scif.img.ImgOpener;
-import net.imagej.ImageJ;
-import net.imglib2.*;
-import net.imglib2.algorithm.util.Grids;
-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;
-import net.imglib2.view.IntervalView;
-import net.imglib2.view.Views;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.Executors;
-import java.util.stream.Collectors;
-
-public class Binning< T extends RealType< T > & NativeType< T > >
-{
-
- private final static Logger LOGGER = LoggerFactory.getLogger( Binning.class );
- private final Img< T > input;
-
-
- private int bin = 2;
-
- public ArrayList< Img< T > > getOutputs()
- {
- return outputs;
- }
-
- private final ArrayList< Img< T > > outputs;
-
-
- public static < T extends RealType< T > & NativeType< T > > ArrayList< Img< T > > binning( Img< T > input, int bin )
- {
- Binning< T > binning = new Binning<>( input, bin );
- final int numberOfChunks = Runtime.getRuntime().availableProcessors() / 2;
-
- final List< Integer > chunks = new ArrayList<>();
- for ( int i = 0; i < input.dimension( 2 ); i++ )
- {
- chunks.add( i );
- }
- final List< Runnable > runnables =
- chunks.stream()
- .map( chunk -> new PixelAttribution<>( input, binning.getOutputs(), chunk ) )
- .collect( Collectors.toList() );
-
- final ExecutorService executorService = Executors.newFixedThreadPool( numberOfChunks );
- runnables.forEach( executorService::submit );
- for ( int i = 0; i < binning.getOutputs().size(); i++ )
- {
- ImageJFunctions.show( binning.getOutputs().get( i ), "output " + i );
- }
-
- return binning.getOutputs();
- }
-
-
- public Binning( Img< T > input, int bin )
- {
- this.bin = bin;
- this.input = input;
- outputs = new ArrayList<>( bin );
- int[] dimensions = new int[]{ ( int ) input.dimension( 0 ) / ( bin / 2 ), ( int ) input.dimension( 1 ) / ( bin / 2 ), 1, 1, ( int ) input.dimension( 2 ) }; // X and Y dimensions are divided by the bin value
- for ( int i = 0; i < this.bin; i++ )
- {
- outputs.add( i, input.factory().create( dimensions ) );
- }
- }
-
-
- public Binning( Img< T > input )
- {
- this.input = input;
- outputs = new ArrayList<>( bin );
- int[] dimensions = new int[]{ ( int ) input.dimension( 0 ) / ( bin / 2 ), ( int ) input.dimension( 1 ) / ( bin / 2 ), 1, 1, ( int ) input.dimension( 2 ) }; // X and Y dimensions are divided by the bin value
- for ( int i = 0; i < this.bin; i++ )
- {
- outputs.add( i, input.factory().create( dimensions ) );
- }
- }
-
- public void run()
- {
- int[] dimensions = new int[]{ ( int ) input.dimension( 0 ) / ( bin / 2 ), ( int ) input.dimension( 1 ) / ( bin / 2 ), 1, 1, ( int ) input.dimension( 2 ) }; // X and Y dimensions are divided by the bin value
- for ( int i = 0; i < this.bin; i++ )
- {
- outputs.add( i, input.factory().create( dimensions ) );
- }
-
- for ( int Z = 0; Z < input.dimension( 2 ); Z++ )// iteration section by section
- {
- pixelAttribution1( input, Z );
- }
-
- for ( int i = 0; i < outputs.size(); i++ )
- {
- ImageJFunctions.show( outputs.get( i ), "output " + i );
- }
- }
-
- private void pixelAttribution1( Img< T > input, int sliceNUmber )
- {
- IntervalView< T > slice = Views.hyperSlice( input, 2, sliceNUmber );
- ArrayList< Cursor< T > > cursors = new ArrayList<>( this.bin );
- for ( int i = 0; i < outputs.size(); i++ )
- {
- cursors.add( i, Views.hyperSlice( outputs.get( i ), 2, sliceNUmber ).cursor() );
- }
- pixelAttribution1( slice, cursors );
- }
-
- private void pixelAttribution1( IntervalView< T > slice, ArrayList< Cursor< T > > cursors )
- {
-
- List< Interval > intervals = Grids.collectAllContainedIntervals( slice.dimensionsAsLongArray(), new int[]{ 2, 2 } ); // section split into grid
- for ( Interval interval : intervals ) // iteration over each grid
- {
- pixelAttribution1( slice, interval, cursors );
- }
- }
-
- private void pixelAttribution1( IntervalView< T > slice, Interval interval, ArrayList< Cursor< T > > cursors )
- {
- IntervalView< T > viewGrid = Views.offsetInterval( slice, interval );
- Cursor< T > viewGridCursor = viewGrid.cursor();
- assignPixel1( viewGridCursor, cursors );
- }
-
- private void assignPixel1( Cursor< T > gridCursor, ArrayList< Cursor< T > > cursors )
- {
- for ( Cursor< T > cursor : cursors )
- {
- assignPixel( gridCursor, cursor );
- }
- }
-
- private void assignPixel( Cursor< T > gridCursor, Cursor< T > outputCursor )
- {
- gridCursor.fwd();
- outputCursor.fwd();
- outputCursor.get().set( gridCursor.get() );
- }
-
-
- private static final class PixelAttribution< T extends RealType< T > & NativeType< T > > implements Runnable
- {
- private final Img< T > input;
- private final ArrayList< Img< T > > outputs;
- private final int sliceNUmber;
-
- private PixelAttribution( final Img< T > input, ArrayList< Img< T > > outputs, int sliceNumber )
- {
- this.input = input;
- this.outputs = outputs;
- this.sliceNUmber = sliceNumber;
- }
-
- @Override
- public void run()
- {
- IntervalView< T > slice = Views.hyperSlice( input, 2, sliceNUmber );
- ArrayList< Cursor< T > > cursors = new ArrayList<>( this.outputs.size() );
- for ( int i = 0; i < outputs.size(); i++ )
- {
- cursors.add( i, Views.hyperSlice( outputs.get( i ), 2, sliceNUmber ).cursor() );
- }
- pixelAttribution( slice, cursors );
- }
-
- private void pixelAttribution( IntervalView< T > slice, ArrayList< Cursor< T > > cursors )
- {
-
- List< Interval > intervals = Grids.collectAllContainedIntervals( slice.dimensionsAsLongArray(), new int[]{ 2, 2 } ); // section split into grid
- for ( Interval interval : intervals ) // iteration over each grid
- {
- pixelAttribution( slice, interval, cursors );
- }
- }
-
- private void pixelAttribution( IntervalView< T > slice, Interval interval, ArrayList< Cursor< T > > cursors )
- {
- IntervalView< T > viewGrid = Views.offsetInterval( slice, interval );
- Cursor< T > viewGridCursor = viewGrid.cursor();
- assignPixel( viewGridCursor, cursors );
- }
-
- private void assignPixel( Cursor< T > gridCursor, ArrayList< Cursor< T > > cursors )
- {
- for ( Cursor< T > cursor : cursors )
- {
- assignPixel( gridCursor, cursor );
- }
- }
-
- private void assignPixel( Cursor< T > gridCursor, Cursor< T > outputCursor )
- {
- gridCursor.fwd();
- outputCursor.fwd();
- outputCursor.get().set( gridCursor.get() );
- }
- }
-
-
- public static void main( String[] args )
- {
- ImageJ ij = new ImageJ();
- ij.launch( args );
- final ImgOpener io = new ImgOpener();
- final Img< FloatType > kernel = ( Img< FloatType > ) io.openImgs( "doc/Scan1_volume_Supercrop.tif" ).get( 0 );
- ImageJFunctions.show( kernel, "original" );
- Binning< FloatType > b = new Binning<>( kernel, 4 );
- double time1 = System.currentTimeMillis();
- Binning.binning( kernel, 4 );
- double time2 = System.currentTimeMillis();
- b.run();
- double time3 = System.currentTimeMillis();
- LOGGER.debug( "Single thread time = {}", (time3 - time2) / 1000 );
- LOGGER.debug( "Multithreading time = {}", (time2 - time1 )/ 1000 );
- }
-}
diff --git a/src/main/java/fr/pasteur/ida/zellige/steps/selection/pretreatment/Pretreatment.java b/src/main/java/fr/pasteur/ida/zellige/steps/selection/pretreatment/Pretreatment.java
index d803581738f93fe12bcbc9ce4ff8bfeee3cebdaa..3562d86ad3e82d95629d3125ac356ed57f1b4aaf 100644
--- a/src/main/java/fr/pasteur/ida/zellige/steps/selection/pretreatment/Pretreatment.java
+++ b/src/main/java/fr/pasteur/ida/zellige/steps/selection/pretreatment/Pretreatment.java
@@ -50,7 +50,6 @@ import org.slf4j.LoggerFactory;
import static fr.pasteur.ida.zellige.steps.Utils.setPosition;
import static fr.pasteur.ida.zellige.steps.Utils.setPositionAndGet;
-import static fr.pasteur.ida.zellige.steps.selection.pretreatment.PretreatmentParameters.getBin;
public class Pretreatment< T extends RealType< T > & NativeType< T > >
{
@@ -58,32 +57,34 @@ public class Pretreatment< T extends RealType< T > & NativeType< T > >
public static < T extends RealType< T > & NativeType< T > > Img< FloatType >
- run( Img< T > input, double radius )
+ run( RandomAccessibleInterval< T > input, double radius, int bin )
{
Pretreatment< T > pretreatment = new Pretreatment<>();
- return pretreatment.runSteps( input, radius );
+ return pretreatment.runSteps( input, radius, bin );
}
- public static < T extends RealType< T > & NativeType< T > > Img< FloatType >
- run( Img< T > input )
- {
- return run( input, 2 );
- }
- private Img< FloatType > runSteps( Img< T > input, double radius )
+ private Img< FloatType > runSteps( RandomAccessibleInterval< T > input, double radius, int bin )
{
LOGGER.debug( "Starting process..." );
+ Img< FloatType > output;
try
{
- Img< T > temp = Binning.run( input, getBin() ); // Binning op
- if (temp == null)
+ if (bin == 1)
{
- throw new BinningFailedException();
+ output = gaussianBlurFilterDenoising( input, radius );
+ }
+ else
+ {
+ Img< T > temp = Binning.run( input, bin ); // Binning op
+ if (temp == null)
+ {
+ throw new BinningFailedException();
+ }
+ output = gaussianBlurFilterDenoising( temp, radius ); // Filtering op
}
- Img< FloatType > output = gaussianBlurFilterDenoising( temp, radius ); // Filtering op
-
// The denoised image is normalized between 0 and 255
output = normalizeImage( output, output.factory() ); // normalizing op
return output;
diff --git a/src/main/java/fr/pasteur/ida/zellige/steps/selection/pretreatment/PretreatmentParameters.java b/src/main/java/fr/pasteur/ida/zellige/steps/selection/pretreatment/PretreatmentParameters.java
index ca379a6609bed849815769a083c960fce02d7d78..dd154d432fd2e7c229ca694c699db5f197856fc1 100644
--- a/src/main/java/fr/pasteur/ida/zellige/steps/selection/pretreatment/PretreatmentParameters.java
+++ b/src/main/java/fr/pasteur/ida/zellige/steps/selection/pretreatment/PretreatmentParameters.java
@@ -35,14 +35,17 @@ public class PretreatmentParameters
public static final String GAUSSIAN_BLUR = "GaussianBlur";
public static final String NOT_IMPLEMENTED = "not implemented";
private final String method;
- private final double parameter;
+ private final double radius;
+ private int bin = 8;
- public PretreatmentParameters( String method, double parameter ) throws DataValidationException
+
+ public PretreatmentParameters( String method, double radius, int bin ) throws DataValidationException
{
- this.checkParameters( method, parameter );
+ this.checkParameters( method, radius );
this.method = method;
- this.parameter = parameter;
+ this.radius = radius;
+ this.bin = bin;
}
/**
@@ -92,8 +95,16 @@ public class PretreatmentParameters
return method;
}
- public double getParameter()
+ public double getRadius()
+ {
+ return radius;
+ }
+
+ public int getBin()
{
- return parameter;
+ return bin;
}
+
+
+
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/steps/selection/util/Binning.java b/src/main/java/fr/pasteur/ida/zellige/steps/selection/util/Binning.java
index 97b1e5e60e9c2c64cccb8b345ab3a766c0baecdc..37cdd269cf1bae3bd7c99813b6b1e316c431aa0a 100644
--- a/src/main/java/fr/pasteur/ida/zellige/steps/selection/util/Binning.java
+++ b/src/main/java/fr/pasteur/ida/zellige/steps/selection/util/Binning.java
@@ -48,10 +48,6 @@ public class Binning< T extends RealType< T > & NativeType< T > >
public static < T extends RealType< T > & NativeType< T > > Img< T >
run( final RandomAccessibleInterval< T > input, int bin )
{
- if ( bin == 1 )
- {
- return null;
- }
LOGGER.debug( "Staring process...." );
double startTime = System.currentTimeMillis();
final int threads = Runtime.getRuntime().availableProcessors() / 2;
diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/test/ZelligePipelineAnalyse.java b/src/main/java/fr/pasteur/ida/zellige/utils/test/ZelligePipelineAnalyse.java
index 604778b85f53e2c572b787c39934aa72c60ab99b..13f5b24164e78e134a9045cba98e91ff5a6286f2 100644
--- a/src/main/java/fr/pasteur/ida/zellige/utils/test/ZelligePipelineAnalyse.java
+++ b/src/main/java/fr/pasteur/ida/zellige/utils/test/ZelligePipelineAnalyse.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
@@ -65,10 +65,9 @@ public class ZelligePipelineAnalyse< T extends RealType< T > & NativeType< T >,
long startTime = System.currentTimeMillis();
ImgFactory< R > factory = tested.factory();
- extraction = new ReferenceSurfaceExtraction<>( tested, factory
- );
+ extraction = new ReferenceSurfaceExtraction<>();
long extractionStartTime = System.currentTimeMillis();
- extraction.select( parameters.getPretreatmentParameters(), parameters.getClassificationParameters(), parameters.getPostTreatmentParameters() );
+ extraction.select(tested, parameters.getPretreatmentParameters(), parameters.getClassificationParameters(), parameters.getPostTreatmentParameters() );
long extractionStopTime = System.currentTimeMillis();
selectionProcessingTime = extractionStopTime - extractionStartTime;
LOGGER.debug( "Extraction processing time : {} ms", selectionProcessingTime );
@@ -78,7 +77,7 @@ public class ZelligePipelineAnalyse< T extends RealType< T > & NativeType< T >,
try
{
extractionStartTime = System.currentTimeMillis();
- extraction.construct( parameters.getConstructionParameters() );
+ extraction.construct(tested, factory, parameters.getConstructionParameters() );
stopTime = System.currentTimeMillis();
constructionProcessingTime = stopTime - extractionStartTime;
LOGGER.debug( "Construction processing time : {} ms", constructionProcessingTime );
diff --git a/src/main/resources/fr.pasteur.ida.zellige.gui.view/Main.fxml b/src/main/resources/fr.pasteur.ida.zellige.gui.view/Main.fxml
index b22f97166fbc38cef4cce29a62376af30f8fe166..3fecfe8052272a00fa97cdf5dae651e117b7ba7a 100644
--- a/src/main/resources/fr.pasteur.ida.zellige.gui.view/Main.fxml
+++ b/src/main/resources/fr.pasteur.ida.zellige.gui.view/Main.fxml
@@ -1,41 +1,45 @@
<?xml version="1.0" encoding="UTF-8"?>
<!--suppress JavaFxDefaultTag, JavaFxUnresolvedFxIdReference -->
+
<?import javafx.geometry.Insets?>
-<?import javafx.scene.control.*?>
+<?import javafx.scene.control.Button?>
+<?import javafx.scene.control.ComboBox?>
+<?import javafx.scene.control.Label?>
<?import javafx.scene.image.Image?>
<?import javafx.scene.image.ImageView?>
-<?import javafx.scene.layout.*?>
+<?import javafx.scene.layout.BorderPane?>
+<?import javafx.scene.layout.HBox?>
+<?import javafx.scene.layout.StackPane?>
+<?import javafx.scene.layout.VBox?>
<?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/23.0.1" 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" maxHeight="-Infinity" maxWidth="-Infinity" minHeight="-Infinity" minWidth="-Infinity" prefHeight="30.0" prefWidth="846.0" 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="266.0">
<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="262.0" />
</children>
</HBox>
- <HBox alignment="CENTER_RIGHT" prefHeight="45.0" prefWidth="333.0" spacing="10.0">
+ <fx:include fx:id="preprocessing" prefHeight="30.0" prefWidth="200.0" source="testBin.fxml" />
+ <HBox alignment="CENTER_RIGHT" prefHeight="26.0" prefWidth="383.0" spacing="10.0">
<children>
<Button mnemonicParsing="false" onAction="#loadParameters" text="Load parameters">
<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>
@@ -44,7 +48,7 @@
<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 +56,18 @@
</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>
diff --git a/src/main/resources/fr.pasteur.ida.zellige.gui.view/StepPanel.fxml b/src/main/resources/fr.pasteur.ida.zellige.gui.view/StepPanel.fxml
index b49b698657c34246376cdc01c912fcea90b2cca6..07460b8f5f77f18b4e781ae1cdaabe4d5d5eee0e 100644
--- a/src/main/resources/fr.pasteur.ida.zellige.gui.view/StepPanel.fxml
+++ b/src/main/resources/fr.pasteur.ida.zellige.gui.view/StepPanel.fxml
@@ -6,8 +6,10 @@
<?import javafx.scene.control.Separator?>
<?import javafx.scene.layout.VBox?>
<?import java.lang.String?>
-<fx:root xmlns:fx="http://javafx.com/fxml" maxHeight="1.7976931348623157E308" maxWidth="1.7976931348623157E308"
- minHeight="-Infinity" minWidth="-Infinity" prefHeight="303.0" prefWidth="322.0" stylesheets="@theme2.css"
+<fx:root xmlns:fx="http://javafx.com/fxml" maxHeight="1.7976931348623157E308"
+ maxWidth="1.7976931348623157E308"
+ minHeight="-Infinity" minWidth="-Infinity" prefHeight="303.0"
+ prefWidth="322.0" stylesheets="@theme2.css"
type="VBox" xmlns="http://javafx.com/javafx">
<children>
<Label fx:id="Label2" alignment="CENTER_RIGHT" contentDisplay="RIGHT" maxHeight="-Infinity" maxWidth="-Infinity"
diff --git a/src/test/java/fr/pasteur/ida/zellige/behavior/StartingOSESameSurfaceTest.java b/src/test/java/fr/pasteur/ida/zellige/behavior/StartingOSESameSurfaceTest.java
index 8ec2228443fab09c0535e87d5cb67cf703a75674..89c27cd1bdb83c8a4838b34bdbdc179f153f7f70 100644
--- a/src/test/java/fr/pasteur/ida/zellige/behavior/StartingOSESameSurfaceTest.java
+++ b/src/test/java/fr/pasteur/ida/zellige/behavior/StartingOSESameSurfaceTest.java
@@ -39,6 +39,7 @@ import fr.pasteur.ida.zellige.steps.construction.rounds.surface.SurfaceConstruct
import fr.pasteur.ida.zellige.steps.selection.Selection;
import fr.pasteur.ida.zellige.steps.selection.classification.ClassificationParameters;
import fr.pasteur.ida.zellige.steps.selection.exception.DataValidationException;
+import fr.pasteur.ida.zellige.steps.selection.exception.ImageTooLargeException;
import fr.pasteur.ida.zellige.steps.selection.exception.NoClassificationException;
import fr.pasteur.ida.zellige.steps.selection.postTreatment.PostTreatmentParameters;
import fr.pasteur.ida.zellige.steps.selection.pretreatment.PretreatmentParameters;
@@ -64,7 +65,7 @@ public class StartingOSESameSurfaceTest
@Ignore
@DisplayName( "Two starting OSE from the same surface don't necessarily produce the exact same surface" )
@Test
- < T extends RealType< T > & NativeType< T > > void TwoStartingOSEFromTheSameSurface_whenUseForStartASurface_DonTProduceTheExactSameSurface() throws DataValidationException, NoClassificationException
+ < T extends RealType< T > & NativeType< T > > void TwoStartingOSEFromTheSameSurface_whenUseForStartASurface_DonTProduceTheExactSameSurface() throws DataValidationException, NoClassificationException, ImageTooLargeException
{
/* Parameters*/
int amplitude = 5;
@@ -83,7 +84,7 @@ public class StartingOSESameSurfaceTest
@SuppressWarnings( "unchecked" )
final Img< T > source = ( Img< T > ) imgPlus.getImg();
- Pixels[][] maximums = Selection.run( source, source.factory(), pretreatmentParameters, classificationParameters, postTreatmentParameters );
+ Pixels[][] maximums = Selection.run( source, pretreatmentParameters, classificationParameters, postTreatmentParameters );
OSEListArray oseLists = OseConstructionXZ.run( maximums, startingSizeThreshold );
int width = maximums[ 0 ].length;