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+

README

-This software have been developped by SDC team from iCube Laboratory.
-
-For installation refer to the "Install Guide MultiCube.pdf"

README.md

+## Demo Video
+
+![Video](https://icube-forge.unistra.fr/lafabregue/Mustic/-/wikis/uploads/f8acb00bfa0804a2388a513849d4f3c5/MultIcubeVIDEO.mp4)
+
+## MutIcube Install :<a id="install_guide"></a>
+
+### Requirements :<a id="requirements"></a>
+
+You will need java jre 1.8 or above (jdk is recommended) and git installed.
+
+Note that all commands are designed to work with unix bash.
+
+### Installation :<a id="install"></a>
+
+##### Create a MutIcube directory and clone the four git project in it : <a id="cloneGit"></a>
+```bash
+    mkdir MultIcube
+    cd MultIcube
+    git clone https://icube-forge.unistra.fr/lafabregue/MultiCubeTools.git
+    git clone https://icube-forge.unistra.fr/lafabregue/JCL.git
+    git clone https://icube-forge.unistra.fr/lafabregue/JSL.git
+    git clone https://icube-forge.unistra.fr/lafabregue/Mustic.git
+```
+
+##### Open your favourite java IDE but it is recommended to use eclipse. The following instruction will be based on eclipse interface.
+
+* Change your workspace to the MultiCube directory
+* Import the previous four projects into your IDE :
+    * Import > General > Projects from Folder or Archive
+    * Choose for each four projects the corresponding folder
+* For each projet change its build path :
+     * JCL : add project MultiCubeTools
+     * JSL : add project MultiCubeTools
+     * Mustic :
+        * add project MultiCubeTools
+        * add project JCL
+        * add project JSL
+        * add the directory « resources » as Class Folder in Libraries build path
+        * change the Order of importation of ressources in the Order and Export tab to have
+        the two highlighted libraries on top :
+
+![image 1](https://icube-forge.unistra.fr/lafabregue/Mustic/-/wikis/uploads/c243fa6d76b68f5f5b2c32d9186abc39/image1.png)
+
+* Add gdal external jars to the Mustic project :
+
+![image 2](https://icube-forge.unistra.fr/lafabregue/Mustic/-/wikis/uploads/002a0be48017c19cf0baef306a7ce4cc/image2.png)
+
+* Run the mustic project :
+Run > Java Application >
+choose «MultiCube - mustic » among the different Main class
+Use the Mustic/src/mustic/MultiCube.java if you don’t use eclipse
+* Change the Run Configuration :
+  * add the two following Environment variables :
+    * Name : GDAL_DATA => Value: *../MultiCubeTools/share/*
+    * ***for linux only :***
+    * Name : LD_LIBRARY_PATH => Value: *../MultiCubeTools/lib:./lib*
+  * ***for Windows and MacOS :***
+  * add the following VM argument : -Djava.library.path=../MultiCubeTools/lib:./lib
+  * it is also recommended to change the memory allocated, by adding the VM arguments :
+    * -Xms<your_min_memory_to_use>m -Xmx<your_max_memory_available>m
+
+On x64 unix platfrom you should normally be able to launch Mustic.
+But if you import a picture and still have an error, or you want to use the project on MacOS
+Windows, or x32 Unix you will have to change the dynamic libraries :
+* For Windows : copy paste content of MultiCubeTools/lib/Windows/xx, xx beeing 64 or 32
+depending of your architecture
+* For MacOS : copy paste content of MultiCubeTools/lib/MacOS
+
+If it does not fix your problem, you need to get the gdal binaries with java bidings :
+* for Windows, you can refer to :
+https://trac.osgeo.org/gdal/wiki/DownloadingGdalBinaries
+* for Linux, you need to compile GDAL with the –with-java option, make the gdal-*/swig/java
+sub-projet, and copy the resulting .so files and jar. For more details, you can refer to :
+https://github.com/VertNet/reproject/wiki/GDAL-Java-Bindings (note that now there only one
+.so file generated)
+* for MacOS, the homebrew build no longer support the –with-java option, you need to
+compile it yourself with the –with-java option, make the gdal-*/swig/java sub-projet, and
+copy the resulting .so files and jar. For more details, you can refer to :
+http://www.ecgs.lu/gilles/enabling-gdal-java-binding-for-geoserver-on-macos/
+

lib/libgdalconstjni.la

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lib/libgdaljni.la

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lib/libgnmjni.la

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-
-# Directory that this library needs to be installed in:
-libdir='/usr/local/lib'
-relink_command="(cd /home/baptiste/Downloads/gdal-2.2.2/swig/java; /bin/bash /home/baptiste/Downloads/gdal-2.2.2/libtool  --mode=relink g++ -std=gnu++11 osr_wrap.lo /home/baptiste/Downloads/gdal-2.2.2/libgdal.la -o libosrjni.la -rpath /usr/local/lib -no-undefined -version-info 23:1:3 @inst_prefix_dir@)"

src/mustic/gui/dialog/ConcatenateImagesDialog.java

@@ -16,8 +16,10 @@ import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JTextField;
 
+import org.gdal.gdal.Driver;
+import org.gdal.gdal.gdal;
+
 import mustic.utils.filters.ImageFileFilter;
-import otbAppWrapping.ExecCommand;
 
 public class ConcatenateImagesDialog extends JFrame {
 
@@ -166,7 +168,10 @@ public class ConcatenateImagesDialog extends JFrame {
 					index++;
 				}
 			}
-			ExecCommand.ConcatenateImages(il, path);
+			gdal.AllRegister();
+			
+			Driver driver = gdal.GetDriverByName("GTiff");
+//			gdal.Warp(dstDS, object_list_count, warpAppOptions);
 
 			JOptionPane.showMessageDialog(this, "Concatenation successful");
 

src/mustic/gui/dialog/CropDialog.java

@@ -6,13 +6,11 @@ import java.awt.geom.AffineTransform;
 import java.awt.image.AffineTransformOp;
 import java.awt.image.BufferedImage;
 import java.io.File;
-import java.io.IOException;
 
 import javax.swing.*;
 
 import mustic.gui.ImageSession;
 import mustic.gui.MainFrame;
-import mustic.io.Picture;
 import mustic.io.RawImage;
 
 public class CropDialog extends JInternalFrame {
@@ -58,7 +56,6 @@ public class CropDialog extends JInternalFrame {
 			int band = 0;
 
 			double[][][] dataSource = img.load(rec.x, rec.y, rec.width, rec.height);
-			this.setReplacer(img.getReplacer());
 			for (int x = 0; x < rec.width; x++) {
 				for (int y = 0; y < rec.height; y++) {
 					band = 0;

src/mustic/gui/dialog/MaskImportDialog.java

@@ -18,11 +18,11 @@ import javax.swing.JTextField;
 import jcl.data.mask.IntArrayMask;
 import jcl.data.mask.Mask;
 import jcl.data.mask.MultiIDIntArrayMask;
+import multiCube.tools.image.reader.GDALImageReaderWrapper;
+import multiCube.tools.image.reader.ReaderWrapper;
 import mustic.gui.dialog.Messages;
 import mustic.gui.panels.data.DataConstructPanel;
 import mustic.io.RawImage;
-import mustic.utils.image.reader.GDALImageReaderWrapper;
-import mustic.utils.image.reader.ReaderWrapper;
 import mustic.utils.io.CSVUtils;
 
 

src/mustic/gui/dialog/SequenceDialog.java

@@ -29,11 +29,9 @@ import javax.swing.JScrollPane;
 import javax.swing.event.ListSelectionEvent;
 import javax.swing.event.ListSelectionListener;
 
-import loci.formats.FormatException;
 import mustic.gui.ImageDesktopFrame;
 import mustic.gui.ImageSession;
 import mustic.gui.MainFrame;
-import mustic.io.PictureTool;
 import mustic.io.RawImage;
 import mustic.utils.documentFilter.ToUpdateObject;
 
@@ -297,11 +295,8 @@ public class SequenceDialog extends JDialog {
 	 * Return the list of image path constituting the selected sequence
 	 * 
 	 * @return the list of ordered file path
-	 * 
-	 * @throws FormatException 
-	 * 			if the images don't have the same dimensions
 	 */
-	public Vector<RawImage> getSequenceData() throws FormatException {
+	public Vector<RawImage> getSequenceData() {
 		int nb = this.dlmSeq.getSize();
 		Donnee donnee;
 		Vector<RawImage> paths = new Vector<RawImage>();
@@ -325,11 +320,8 @@ public class SequenceDialog extends JDialog {
 	 * Return the list of image sessions constituting the selected sequence
 	 * 
 	 * @return the list of ordered session
-	 * 
-	 * @throws FormatException 
-	 * 			if the images don't have the same dimensions
 	 */
-	public Vector<ImageSession> getSequenceSessions() throws FormatException {
+	public Vector<ImageSession> getSequenceSessions() {
 		int nb = this.dlmSeq.getSize();
 		Donnee donnee;
 		Vector<ImageSession> paths = new Vector<ImageSession>();

src/mustic/gui/dialog/VegetationIndiceExtractionDialog.java

-package mustic.gui.dialog;
-
-import java.awt.BorderLayout;
-import java.awt.Dimension;
-import java.awt.GridLayout;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.io.File;
-
-import javax.swing.JButton;
-import javax.swing.JComboBox;
-import javax.swing.JFileChooser;
-import javax.swing.JFormattedTextField;
-import javax.swing.JFrame;
-import javax.swing.JLabel;
-import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-import javax.swing.JSpinner;
-import javax.swing.JTextField;
-import javax.swing.SpinnerNumberModel;
-import javax.swing.text.NumberFormatter;
-
-import mustic.utils.filters.ImageFileFilter;
-import otbAppWrapping.ExecCommand;
-
-public class VegetationIndiceExtractionDialog extends JFrame {
-
-	/**	 */
-	private static final long serialVersionUID = 1L;
-	
-	private JTextField				textInput	= new JTextField();
-	private JTextField				textOutput	= new JTextField();
-	private JComboBox<String>		indiceComboBox;
-	private JSpinner				spinnerRed;
-	private JSpinner				spinnerNir;
-
-	public VegetationIndiceExtractionDialog() {
-		super();
-
-		JPanel mainPanel = new JPanel(new BorderLayout());
-
-		JPanel panel = new JPanel(new GridLayout(5, 2));
-		JPanel pInput = new JPanel(new BorderLayout());
-
-		// Input browse
-		panel.add(new JLabel(Messages.getString("VegetationIndiceExtractionDialog.2")), BorderLayout.WEST); //$NON-NLS-1$
-		pInput.add(this.textInput, BorderLayout.CENTER);
-		JButton buttonBrowse = new JButton("..."); //$NON-NLS-1$
-		buttonBrowse.addActionListener(new ActionListener() {
-			@Override
-			public void actionPerformed(ActionEvent e) {
-				JFileChooser fileChooser = new JFileChooser();
-				ImageFileFilter filter = new ImageFileFilter();
-				fileChooser.addChoosableFileFilter(filter);
-				fileChooser.setFileFilter(filter);
-				int returnVal = fileChooser.showOpenDialog(VegetationIndiceExtractionDialog.this);
-				if (returnVal == JFileChooser.APPROVE_OPTION) {
-					if (fileChooser.getSelectedFile().getPath().endsWith(".tif")) //$NON-NLS-1$
-						VegetationIndiceExtractionDialog.this.textInput.setText(fileChooser.getSelectedFile().getPath());
-					else {
-						JOptionPane.showMessageDialog(VegetationIndiceExtractionDialog.this, Messages.getString("VegetationIndiceExtractionDialog.21"), Messages.getString("VegetationIndiceExtractionDialog.22"), //$NON-NLS-1$ //$NON-NLS-2$
-								JOptionPane.WARNING_MESSAGE);
-					}
-				}
-			}
-		});
-		pInput.add(buttonBrowse, BorderLayout.EAST);
-		panel.add(pInput);
-
-		
-		
-		// ComboBox
-		panel.add(new JLabel("Indice"));
-		String[] indices = new String[]{
-				"NDVI", "TNDVI", "RVI", "SAVI", "TSAVI", "MSAVI", "MSAVI2", "GEMI", "IPVI"
-		};
-		indiceComboBox = new JComboBox<String>(indices);
-		panel.add(indiceComboBox);
-		
-		// Red
-		panel.add(new JLabel(Messages.getString("VegetationIndiceExtractionDialog.4")), BorderLayout.WEST); //$NON-NLS-1$
-		JPanel pRed = new JPanel(new BorderLayout());
-		spinnerRed = new JSpinner();
-		spinnerRed.setModel(new SpinnerNumberModel(1, 1, 500, 1));
-		spinnerRed.setEditor(new JSpinner.NumberEditor(spinnerRed, "##"));
-		JFormattedTextField txtRed = ((JSpinner.NumberEditor) spinnerRed.getEditor()).getTextField();
-		((NumberFormatter) txtRed.getFormatter()).setAllowsInvalid(false);
-		pRed.add(spinnerRed);
-		panel.add(pRed);
-
-		// NIR
-		panel.add(new JLabel(Messages.getString("VegetationIndiceExtractionDialog.5")), BorderLayout.WEST); //$NON-NLS-1$
-		JPanel pNIR = new JPanel(new BorderLayout());
-		spinnerNir = new JSpinner();
-		spinnerNir.setModel(new SpinnerNumberModel(1, 1, 500, 1));
-		spinnerNir.setEditor(new JSpinner.NumberEditor(spinnerNir, "##"));
-		JFormattedTextField txtNir = ((JSpinner.NumberEditor) spinnerNir.getEditor()).getTextField();
-		((NumberFormatter) txtNir.getFormatter()).setAllowsInvalid(false);
-		pNIR.add(spinnerNir);
-		panel.add(pNIR);
-		
-		// Output Browse
-				panel.add(new JLabel(Messages.getString("VegetationIndiceExtractionDialog.3")), BorderLayout.WEST); //$NON-NLS-1$
-				JPanel pOutput = new JPanel(new BorderLayout());
-				pOutput.add(this.textOutput, BorderLayout.CENTER);
-				JButton buttonBrowse2 = new JButton("..."); //$NON-NLS-1$
-				buttonBrowse2.addActionListener(new ActionListener() {
-					@Override
-					public void actionPerformed(ActionEvent e) {
-						JFileChooser fileChooser = new JFileChooser();
-						if (!VegetationIndiceExtractionDialog.this.textInput.getText().isEmpty())
-							fileChooser.setSelectedFile(new File(VegetationIndiceExtractionDialog.this.textInput.getText().substring(0,
-									VegetationIndiceExtractionDialog.this.textInput.getText().indexOf(".tif"))
-									+"_"+indiceComboBox.getSelectedItem()+".tif"));
-						ImageFileFilter filter = new ImageFileFilter();
-						fileChooser.addChoosableFileFilter(filter);
-						fileChooser.setFileFilter(filter);
-						int returnVal = fileChooser.showSaveDialog(VegetationIndiceExtractionDialog.this);
-						if (returnVal == JFileChooser.APPROVE_OPTION) {
-
-							String path;
-							if (fileChooser.getSelectedFile().getPath().endsWith(".tif")) {
-								path = fileChooser.getSelectedFile().getPath();
-							} else {
-								path = fileChooser.getSelectedFile().getPath() + ".tif";
-							}
-
-							VegetationIndiceExtractionDialog.this.textOutput.setText(path);
-						}
-					}
-				});
-				pOutput.add(buttonBrowse2, BorderLayout.EAST);
-				panel.add(pOutput);
-
-		// Panel OK
-		this.textInput.setPreferredSize(new Dimension(200, 30));
-		JPanel panelButton = new JPanel();
-		JButton buttonOk = new JButton("Ok"); //$NON-NLS-1$
-		panelButton.add(buttonOk);
-
-		buttonOk.addActionListener(new ActionListener() {
-			@Override
-			public void actionPerformed(ActionEvent e) {
-				buttonOk_actionPerformed();
-			}
-		});
-
-		mainPanel.add(panel, BorderLayout.NORTH);
-		mainPanel.add(panelButton, BorderLayout.SOUTH);
-
-		this.setContentPane(mainPanel);
-		this.setTitle(Messages.getString("VegetationIndiceExtractionDialog.1")); //$NON-NLS-1$
-		this.setSize(350, 200);
-		this.setResizable(true);
-		this.setVisible(true);
-	}
-
-	protected void buttonOk_actionPerformed() {
-
-		try {
-			File temp = new File("temporary");
-			temp.mkdir();
-
-			String path;
-			if (textOutput.getText().endsWith(".tif")) {
-				path = textOutput.getText();
-			} else {
-				path = textOutput.getText() + ".tif";
-			}
-
-			ExecCommand.NdviExtraction(textInput.getText(), "temporary/vegetation.tif", (int) spinnerRed.getValue(), (int) spinnerNir.getValue(), (String) indiceComboBox.getSelectedItem());
-			ExecCommand.Rescale("temporary/vegetation.tif", path, 0, 255);
-
-			JOptionPane.showMessageDialog(this, "Vegetation indice extraction successful");
-
-			this.dispose();
-			setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
-			
-//			cccccccccccccc			JOptionPane.ERROR_MESSAGE);
-
-		} catch (Exception e) {
-			JOptionPane.showMessageDialog(this, "An error has occured", "Error", JOptionPane.ERROR_MESSAGE);
-			e.printStackTrace();
-		}
-		setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
-	}
-
-}

src/mustic/gui/dialog/WaterIndiceExtractionDialog.java

-package mustic.gui.dialog;
-
-import java.awt.BorderLayout;
-import java.awt.Dimension;
-import java.awt.FlowLayout;
-import java.awt.GridLayout;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.io.File;
-import java.util.Vector;
-
-import javax.swing.JButton;
-import javax.swing.JComboBox;
-import javax.swing.JFileChooser;
-import javax.swing.JFormattedTextField;
-import javax.swing.JFrame;
-import javax.swing.JLabel;
-import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-import javax.swing.JSpinner;
-import javax.swing.JTextField;
-import javax.swing.SpinnerNumberModel;
-import javax.swing.text.NumberFormatter;
-
-import mustic.gui.MainFrame;
-import mustic.utils.filters.ImageFileFilter;
-import mustic.utils.image.ImageHelper;
-import otbAppWrapping.ExecCommand;
-
-public class WaterIndiceExtractionDialog extends JFrame {
-
-	/**	 */
-	private static final long serialVersionUID = 1L;
-
-	private Vector<JTextField>	textInput	= new Vector<JTextField>();
-	private JPanel				inPanel;
-	private JTextField			textOutput	= new JTextField();
-	private JComboBox<String>	indiceComboBox;
-	private JSpinner			spinnerBand1;
-	private JSpinner			spinnerBand2;
-	private JSpinner			spinnerBand3;
-	private JSpinner			spinnerBand4;
-	private JSpinner			spinnerBand5;
-	private JLabel 				labelBand1;
-	private JLabel 				labelBand2;
-	private JLabel 				labelBand3;
-	private JLabel 				labelBand4;
-	private JLabel 				labelBand5;
-
-	public WaterIndiceExtractionDialog() {
-		super();
-		
-		JPanel subPanel1 = new JPanel(new BorderLayout());
-		JPanel subPanel2 = new JPanel(new BorderLayout());
-		JPanel mainPanel = new JPanel(new BorderLayout());
-
-		inPanel = new JPanel(new GridLayout(0, 2));
-		addImageInputPanel();
-		
-		JButton addButton = new JButton(Messages.getString("ConcatenateImagesDialog.7"));
-		addButton.addActionListener(new ActionListener() {
-			@Override
-			public void actionPerformed(ActionEvent e) {
-				addImageInputPanel();
-			}
-		});
-		JPanel addPanel = new JPanel(new FlowLayout(FlowLayout.CENTER));
-		addPanel.add(addButton);
-		JPanel inSubPanel = new JPanel(new BorderLayout());
-		inSubPanel.add(inPanel, BorderLayout.NORTH);
-		inSubPanel.add(addPanel, BorderLayout.SOUTH);
-		subPanel1.add(inSubPanel, BorderLayout.NORTH);
-
-		JPanel indicePanel = new JPanel(new GridLayout(0, 2));
-		// ComboBox
-		indicePanel.add(new JLabel("Indice"));
-		String[] indices = new String[]{
-				"NDWI", "NDWI2", "MNDWI", "NDPI", "NDTI", "AWEIsh", "AWEInsh", "WI"
-		};
-		indiceComboBox = new JComboBox<String>(indices);
-		indiceComboBox.addActionListener(new ActionListener() {
-			
-			@Override
-			public void actionPerformed(ActionEvent e) {
-				setIndiceLabel();
-				
-			}
-		});
-		indicePanel.add(indiceComboBox);
-		
-		
-		
-		// FirstBand
-		labelBand1 = new JLabel("NIR");
-		indicePanel.add(labelBand1, BorderLayout.WEST); //$NON-NLS-1$
-		JPanel pBand1 = new JPanel(new BorderLayout());
-		spinnerBand1 = new JSpinner();
-		spinnerBand1.setModel(new SpinnerNumberModel(1, 1, 500, 1));
-		spinnerBand1.setEditor(new JSpinner.NumberEditor(spinnerBand1, "##"));
-		JFormattedTextField txtBand1 = ((JSpinner.NumberEditor) spinnerBand1.getEditor()).getTextField();
-		((NumberFormatter) txtBand1.getFormatter()).setAllowsInvalid(false);
-		pBand1.add(spinnerBand1);
-		indicePanel.add(pBand1);
-
-		// SecondBand
-		labelBand2 = new JLabel("MIR");
-		indicePanel.add(labelBand2, BorderLayout.WEST); //$NON-NLS-1$
-		JPanel pBand2 = new JPanel(new BorderLayout());
-		spinnerBand2 = new JSpinner();
-		spinnerBand2.setModel(new SpinnerNumberModel(1, 1, 500, 1));
-		spinnerBand2.setEditor(new JSpinner.NumberEditor(spinnerBand2, "##"));
-		JFormattedTextField txtBand2 = ((JSpinner.NumberEditor) spinnerBand2.getEditor()).getTextField();
-		((NumberFormatter) txtBand2.getFormatter()).setAllowsInvalid(false);
-		pBand2.add(spinnerBand2);
-		indicePanel.add(pBand2);
-		
-		// ThirdBand
-		labelBand3 = new JLabel("_");
-		indicePanel.add(labelBand3, BorderLayout.WEST); //$NON-NLS-1$
-		JPanel pBand3 = new JPanel(new BorderLayout());
-		spinnerBand3 = new JSpinner();
-		spinnerBand3.setModel(new SpinnerNumberModel(1, 1, 500, 1));
-		spinnerBand3.setEditor(new JSpinner.NumberEditor(spinnerBand3, "##"));
-		JFormattedTextField txtBand3 = ((JSpinner.NumberEditor) spinnerBand3.getEditor()).getTextField();
-		((NumberFormatter) txtBand3.getFormatter()).setAllowsInvalid(false);
-		pBand3.add(spinnerBand3);
-		indicePanel.add(pBand3);
-		
-		// FourthBand
-		labelBand4 = new JLabel("_");
-		indicePanel.add(labelBand4, BorderLayout.WEST); //$NON-NLS-1$
-		JPanel pBand4 = new JPanel(new BorderLayout());
-		spinnerBand4 = new JSpinner();
-		spinnerBand4.setModel(new SpinnerNumberModel(1, 1, 500, 1));
-		spinnerBand4.setEditor(new JSpinner.NumberEditor(spinnerBand4, "##"));
-		JFormattedTextField txtBand4 = ((JSpinner.NumberEditor) spinnerBand4.getEditor()).getTextField();
-		((NumberFormatter) txtBand4.getFormatter()).setAllowsInvalid(false);
-		pBand4.add(spinnerBand4);
-		indicePanel.add(pBand4);
-		
-		// FifthBand
-		labelBand5 = new JLabel("_");
-		indicePanel.add(labelBand5, BorderLayout.WEST); //$NON-NLS-1$
-		JPanel pBand5 = new JPanel(new BorderLayout());
-		spinnerBand5 = new JSpinner();
-		spinnerBand5.setModel(new SpinnerNumberModel(1, 1, 500, 1));
-		spinnerBand5.setEditor(new JSpinner.NumberEditor(spinnerBand5, "##"));
-		JFormattedTextField txtBand5 = ((JSpinner.NumberEditor) spinnerBand5.getEditor()).getTextField();
-		((NumberFormatter) txtBand5.getFormatter()).setAllowsInvalid(false);
-		pBand5.add(spinnerBand5);
-		indicePanel.add(pBand5);
-		
-		subPanel1.add(indicePanel, BorderLayout.SOUTH);
-		setIndiceLabel();
-		
-		// Output Browse
-		JPanel outPanel = new JPanel(new BorderLayout());
-		outPanel.add(new JLabel(Messages.getString("WaterIndiceExtractionDialog.3")), BorderLayout.WEST); //$NON-NLS-1$
-		outPanel.add(this.textOutput, BorderLayout.CENTER);
-		JButton buttonBrowse2 = new JButton("..."); //$NON-NLS-1$
-		buttonBrowse2.addActionListener(new ActionListener() {
-			@Override
-			public void actionPerformed(ActionEvent e) {
-				JFileChooser fileChooser = new JFileChooser(MainFrame.getInstance().getCurrentDirectory());
-				if (WaterIndiceExtractionDialog.this.textInput.size() > 0 &&
-						!WaterIndiceExtractionDialog.this.textInput.get(0).getText().isEmpty()) {
-					fileChooser.setSelectedFile(new File(WaterIndiceExtractionDialog.this.textInput.get(0).getText().substring(0,
-							WaterIndiceExtractionDialog.this.textInput.get(0).getText().indexOf(".tif"))
-							+"_"+indiceComboBox.getSelectedItem()+".tif"));
-				}
-				ImageFileFilter filter = new ImageFileFilter();
-				fileChooser.addChoosableFileFilter(filter);
-				fileChooser.setFileFilter(filter);
-				int returnVal = fileChooser.showSaveDialog(WaterIndiceExtractionDialog.this);
-				if (returnVal == JFileChooser.APPROVE_OPTION) {
-					MainFrame.getInstance().setCurrentDirectory(fileChooser.getCurrentDirectory());
-
-					String path;
-					if (fileChooser.getSelectedFile().getPath().endsWith(".tif")) {
-						path = fileChooser.getSelectedFile().getPath();
-					} else {
-						path = fileChooser.getSelectedFile().getPath() + ".tif";
-					}
-
-					WaterIndiceExtractionDialog.this.textOutput.setText(path);
-				}
-			}
-		});
-		outPanel.add(buttonBrowse2, BorderLayout.EAST);
-		
-		subPanel2.add(subPanel1, BorderLayout.NORTH);
-		subPanel2.add(outPanel, BorderLayout.SOUTH);
-		
-		// Panel OK
-		JPanel panelButton = new JPanel();
-		JButton buttonOk = new JButton("Ok"); //$NON-NLS-1$
-		panelButton.add(buttonOk);
-
-		buttonOk.addActionListener(new ActionListener() {
-			@Override
-			public void actionPerformed(ActionEvent e) {
-				buttonOk_actionPerformed();
-			}
-		});
-
-		mainPanel.add(subPanel2, BorderLayout.CENTER);
-		mainPanel.add(panelButton, BorderLayout.SOUTH);
-		
-		this.setContentPane(mainPanel);
-		this.setTitle(Messages.getString("WaterIndiceExtractionDialog.1")); //$NON-NLS-1$
-		this.setSize(350, 350);
-		this.setResizable(true);
-		this.setVisible(true);
-	}
-	
-	private void addImageInputPanel() {
-		JPanel pInput = new JPanel(new BorderLayout());
-		
-		final JTextField txtField = new JTextField();
-		//txtField.setPreferredSize(new Dimension(200, 30));
-		textInput.add(txtField);
-		// Input browse
-		inPanel.add(new JLabel(Messages.getString("WaterIndiceExtractionDialog.2")), BorderLayout.WEST); //$NON-NLS-1$
-		pInput.add(this.textInput.get(textInput.size()-1), BorderLayout.CENTER);
-		JButton buttonBrowse = new JButton("..."); //$NON-NLS-1$
-		buttonBrowse.addActionListener(new ActionListener() {
-			@Override
-			public void actionPerformed(ActionEvent e) {
-				JFileChooser fileChooser = new JFileChooser(MainFrame.getInstance().getCurrentDirectory());
-				ImageFileFilter filter = new ImageFileFilter();
-				fileChooser.addChoosableFileFilter(filter);
-				fileChooser.setFileFilter(filter);
-				int returnVal = fileChooser.showOpenDialog(WaterIndiceExtractionDialog.this);
-				if (returnVal == JFileChooser.APPROVE_OPTION) {
-					MainFrame.getInstance().setCurrentDirectory(fileChooser.getCurrentDirectory());
-					txtField.setText(fileChooser.getSelectedFile().getPath());
-				}
-			}
-		});
-		pInput.add(buttonBrowse, BorderLayout.EAST);
-		inPanel.add(pInput);
-		inPanel.updateUI();
-	}
-
-	protected void buttonOk_actionPerformed() {
-
-		try {
-			String path;
-			if (textOutput.getText().endsWith(".tif")) { //$NON-NLS-1$
-				path = textOutput.getText();
-			} else {
-				path = textOutput.getText() + ".tif"; //$NON-NLS-1$
-			}
-			for(int i = 0 ; i < textInput.size() ; i++) {
-				File f = new File(textInput.get(i).getText());
-				if (f.exists() && !f.isDirectory()) {
-					String currentPath = path;
-					currentPath = currentPath.replaceAll("\\*", ImageHelper.stripExtension(f.getName()));
-					if (indiceComboBox.getSelectedIndex() <= 4) {
-						ExecCommand.WaterExtraction(textInput.get(i).getText(), currentPath, (int) spinnerBand1.getValue(),
-								(int) spinnerBand2.getValue(), (String)indiceComboBox.getSelectedItem());
-					} else {
-						switch ((String)indiceComboBox.getSelectedItem())
-						{
-						case "AWEIsh":  //$NON-NLS-1$
-							ExecCommand.BandMath(new String[]{textInput.get(i).getText()}, currentPath, 
-									" im1b"+ (int) spinnerBand2.getValue() + //$NON-NLS-1$
-									"+2.5*im1b"+ (int) spinnerBand1.getValue() + //$NON-NLS-1$
-									"-1.5*(im1b"+ (int) spinnerBand3.getValue() + //$NON-NLS-1$
-									"+im1b"+ (int) spinnerBand4.getValue() + //$NON-NLS-1$
-									")-0.25*im1b"+ (int) spinnerBand5.getValue()); //$NON-NLS-1$
-							break;
-						case "AWEInsh":  //$NON-NLS-1$
-							ExecCommand.BandMath(new String[]{textInput.get(i).getText()}, currentPath, 
-									"4*(im1b"+ (int) spinnerBand1.getValue() + //$NON-NLS-1$
-									"-im1b"+ (int) spinnerBand3.getValue() + //$NON-NLS-1$
-									")-(0.25*im1b"+ (int) spinnerBand2.getValue() + //$NON-NLS-1$
-									"+2.75*im1b"+ (int) spinnerBand4.getValue() +")"); //$NON-NLS-1$
-							break;
-						case "WI": 
-							labelBand1.setText("Red");
-							labelBand2.setText("Green");
-							labelBand3.setText("PIR");
-							labelBand4.setText("MIR1");
-							labelBand5.setText("MIR2");
-							spinnerBand3.setEnabled(true);
-							spinnerBand4.setEnabled(true);
-							spinnerBand5.setEnabled(true);
-							ExecCommand.BandMath(new String[]{textInput.get(i).getText()}, currentPath, 
-									"1.7204+171*im1b"+ (int) spinnerBand2.getValue() + //$NON-NLS-1$
-									"+3*im1b"+ (int) spinnerBand1.getValue() + //$NON-NLS-1$
-									"-70*im1b"+ (int) spinnerBand3.getValue() + //$NON-NLS-1$
-									"-45*im1b"+ (int) spinnerBand4.getValue() + //$NON-NLS-1$
-									"-71*im1b"+ (int) spinnerBand5.getValue()); //$NON-NLS-1$
-							break;
-						}
-					}
-				}
-			}
-			//ExecCommand.Rescale("temporary/water.tif", path);
-
-			JOptionPane.showMessageDialog(this, "Water Indice Extraction successful");
-
-			this.dispose();
-			setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
-
-//			File Water = new File(path);
-//			boolean imageOuvre = MainFrame.getInstance().openSession(Water);
-//			if (!imageOuvre)
-//				JOptionPane.showMessageDialog(MainFrame.getInstance(), Messages.getString("MainFrame.151"), Messages.getString("MainFrame.152"), //$NON-NLS-1$ //$NON-NLS-2$
-//						JOptionPane.ERROR_MESSAGE);
-
-		} catch (Exception e) {
-			JOptionPane.showMessageDialog(this, "An error has occured", "Error", JOptionPane.ERROR_MESSAGE);
-			e.printStackTrace();
-		}
-		setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
-	}
-	
-	protected void setIndiceLabel(){
-
-		switch ((String)indiceComboBox.getSelectedItem())
-		{
-			case "NDWI":  //$NON-NLS-1$
-				labelBand1.setText("NIR");
-				labelBand2.setText("MIR");
-				labelBand3.setText("_");
-				labelBand4.setText("_");
-				labelBand5.setText("_");
-				spinnerBand3.setEnabled(false);
-				spinnerBand3.setValue(1);
-				spinnerBand4.setEnabled(false);
-				spinnerBand4.setValue(1);
-				spinnerBand5.setEnabled(false);
-				spinnerBand5.setValue(1);
-				
-				break;
-			case "NDWI2":  //$NON-NLS-1$
-				labelBand1.setText("Green");
-				labelBand2.setText("NIR");
-				labelBand3.setText("_"); //$NON-NLS-1$
-				labelBand4.setText("_"); //$NON-NLS-1$
-				labelBand5.setText("_"); //$NON-NLS-1$
-				spinnerBand3.setEnabled(false);
-				spinnerBand3.setValue(1);
-				spinnerBand4.setEnabled(false);
-				spinnerBand4.setValue(1);
-				spinnerBand5.setEnabled(false);
-				spinnerBand5.setValue(1);
-				break;
-			case "MNDWI":  //$NON-NLS-1$
-				labelBand1.setText("Green");
-				labelBand2.setText("MIR");
-				labelBand3.setText("_"); //$NON-NLS-1$
-				labelBand4.setText("_"); //$NON-NLS-1$
-				labelBand5.setText("_"); //$NON-NLS-1$
-				spinnerBand3.setEnabled(false);
-				spinnerBand3.setValue(1);
-				spinnerBand4.setEnabled(false);
-				spinnerBand4.setValue(1);
-				spinnerBand5.setEnabled(false);
-				spinnerBand5.setValue(1);
-				break;
-			case "NDPI":  //$NON-NLS-1$
-				labelBand1.setText("MIR");
-				labelBand2.setText("Green");
-				labelBand3.setText("_"); //$NON-NLS-1$
-				labelBand4.setText("_"); //$NON-NLS-1$
-				labelBand5.setText("_"); //$NON-NLS-1$
-				spinnerBand3.setEnabled(false);
-				spinnerBand3.setValue(1);
-				spinnerBand4.setEnabled(false);
-				spinnerBand4.setValue(1);
-				spinnerBand5.setEnabled(false);
-				spinnerBand5.setValue(1);
-				break;
-			case "AWEIsh":  //$NON-NLS-1$
-				labelBand1.setText("Green");
-				labelBand2.setText("Blue");
-				labelBand3.setText("PIR");
-				labelBand4.setText("MIR1");
-				labelBand5.setText("MIR2");
-				spinnerBand3.setEnabled(true);
-				spinnerBand4.setEnabled(true);
-				spinnerBand5.setEnabled(true);
-				break;
-			case "AWEInsh":  //$NON-NLS-1$
-				labelBand1.setText("Green");
-				labelBand2.setText("PIR");
-				labelBand3.setText("MIR1");
-				labelBand4.setText("MIR2");
-				labelBand5.setText("_"); //$NON-NLS-1$
-				spinnerBand3.setEnabled(true);
-				spinnerBand4.setEnabled(true);
-				spinnerBand5.setEnabled(false);
-				spinnerBand5.setValue(1);
-				break;
-			case "WI":  //$NON-NLS-1$
-				labelBand1.setText("Green");
-				labelBand2.setText("Blue");
-				labelBand3.setText("PIR");
-				labelBand4.setText("MIR1");
-				labelBand5.setText("MIR2");
-				spinnerBand3.setEnabled(true);
-				spinnerBand4.setEnabled(true);
-				spinnerBand5.setEnabled(true);
-				break;
-				
-		}
-		
-		
-	}
-
-}

src/mustic/gui/dialog/arff/ArffToDataDialog.java

@@ -23,6 +23,9 @@ import jcl.data.Data;
 import jcl.data.DataObject;
 import jcl.data.SimpleData;
 import jcl.data.attribute.AttributeMultiDimSequence;
+import jcl.data.distance.DistanceModel;
+import jcl.data.distance.DistanceParameter;
+import jcl.weights.GlobalWeights;
 import mustic.gui.MainFrame;
 import mustic.gui.dialog.Messages;
 import mustic.gui.dialog.SequenceDialog;
@@ -138,7 +141,7 @@ public class ArffToDataDialog extends JInternalFrame implements ToUpdateObject {
 		}
 	}
 
-	@SuppressWarnings({ "unchecked", "deprecation" })
+	@SuppressWarnings({ "unchecked" })
 	protected void buttonOk_actionPerformed() {
 		try {
 			Object[] result = DataArffExchange.arffToData(this.textFile.getText());
@@ -212,16 +215,23 @@ public class ArffToDataDialog extends JInternalFrame implements ToUpdateObject {
 					// test if we have one or multiples images
 					if (sequenceFiles.size() > 1) {
 						data = new ImageData(new ImportedImageSampler(sequenceFilesPath, 
-								(List<DataObject>) result[1], (List<Integer>) result[0]), sequenceFiles);
+								(List<DataObject>) result[1], (List<Integer>) result[0]), sequenceFiles, null, null);
 					} else {
 						data = new ImageData(new ImportedImageSampler(sequenceFilesPath.get(0), 
-								(List<DataObject>) result[1], (List<Integer>) result[0]), sequenceFiles.get(0));
+								(List<DataObject>) result[1], (List<Integer>) result[0]), sequenceFiles.get(0),
+								null, null);
 					}
 					
 				} else {
 					// if no images is associated we create a SimpleData
-					data = new SimpleData((List<DataObject>) result[1]);
+					data = new SimpleData((List<DataObject>) result[1], null, null);
 				}
+
+				DistanceModel distanceModel = DistanceModel.generateDefaultModel(
+						data.getOneDataObject(), new GlobalWeights(data.getOneDataObject()));
+				DistanceParameter[][] distanceParameters = DistanceModel
+						.generateDefaultDistanceParameters(1, distanceModel, data);		
+				data.setDistanceModel(distanceModel, distanceParameters);
 				
 				if (this.textData.getText().length() == 0) {
 					this.textData.setText(DataArffExchange.getRelationName(this.textFile.getText()));

src/mustic/gui/dialog/classifier/ConstraintsSelectionFrame.java

@@ -56,6 +56,9 @@ import jcl.clustering.constraints.LabelConstraint;
 import jcl.clustering.constraints.MustLinkConstraint;
 import jcl.clustering.constraints.NbClusterConstraint;
 import jcl.data.Data;
+import jcl.data.distance.DistanceModel;
+import jcl.data.distance.DistanceParameter;
+import jcl.weights.GlobalWeights;
 import mustic.utils.image.ImageAddOn;
 import mustic.utils.image.ImageDisplayer;
 import mustic.utils.tools.ProgressPropertyChangeListener;
@@ -161,11 +164,15 @@ public class ConstraintsSelectionFrame extends JFrame implements ImageAddOn {
 		this.imageDisplayer = imgDisplayer;
 		
 		this.constraintsContainer = constraintsContainer;
-
+		
 		if (data != null) {
 			// case of Data provided
-			minDistance = data.getEstimatedMinDistance();
-			maxDistance = data.getEstimatedMaxDistance();
+			DistanceModel model = DistanceModel.generateDefaultModel(data.getOneDataObject(), 
+					new GlobalWeights(data.getOneDataObject()));
+			DistanceParameter[][] parameters = DistanceModel.generateDefaultDistanceParameters(1,model, data);
+			
+			minDistance = data.getEstimatedMinDistance(model, parameters[0]);
+			maxDistance = data.getEstimatedMaxDistance(model, parameters[0]);
 			this.data = data;
 		} else {
 			// otherwise we base our estimation on the image
@@ -1012,7 +1019,9 @@ public class ConstraintsSelectionFrame extends JFrame implements ImageAddOn {
 	}
 	
 	public void refresh() {
-		container.updateUI();
+		if (container != null) {
+			container.updateUI();
+		}
 		imageDisplayer.refresh(false);
 	}
 

src/mustic/gui/dialog/csv/CSVToDataDialog.java

@@ -24,10 +24,13 @@ import jcl.data.Data;
 import jcl.data.DataObject;
 import jcl.data.SimpleData;
 import jcl.data.attribute.AttributeMultiDimSequence;
+import jcl.data.distance.DistanceModel;
+import jcl.data.distance.DistanceParameter;
+import jcl.weights.GlobalWeights;
+import multiCube.tools.image.ImageHelper;
 import mustic.gui.MainFrame;
 import mustic.gui.dialog.Messages;
 import mustic.utils.documentFilter.ToUpdateObject;
-import mustic.utils.image.ImageHelper;
 import mustic.utils.io.CSVUtils;
 
 
@@ -140,7 +143,6 @@ public class CSVToDataDialog extends JInternalFrame implements ToUpdateObject {
 		}
 	}
 
-	@SuppressWarnings({"deprecation"})
 	protected void buttonOk_actionPerformed() {
 		try {
 			List<DataObject> result = new ArrayList<DataObject>();
@@ -160,7 +162,11 @@ public class CSVToDataDialog extends JInternalFrame implements ToUpdateObject {
 			}
 			
 			if(result != null) {
-					data = new SimpleData(result);
+				data = new SimpleData(result, null, null);
+				DistanceModel model = DistanceModel.generateDefaultModel(data.getOneDataObject(), 
+						new GlobalWeights(data.getOneDataObject()));
+				DistanceParameter[][] parameters = DistanceModel.generateDefaultDistanceParameters(1,model, data);
+				data.setDistanceModel(model, parameters);
 				
 				if (this.textData.getText().length() == 0) {
 					this.textData.setText(ImageHelper.extractFileName(

src/mustic/gui/dialog/ogr/DataToOGRDialog.java

@@ -20,10 +20,10 @@ import javax.swing.JPanel;
 import javax.swing.JTextField;
 
 import jcl.data.Data;
+import multiCube.tools.image.ImageHelper;
 import mustic.gui.DataDesktopFrame;
 import mustic.gui.MainFrame;
 import mustic.gui.dialog.Messages;
-import mustic.utils.image.ImageHelper;
 import mustic.utils.io.dataExchange.DataOGRExchange;
 
 /**

src/mustic/gui/dialog/ogr/OGRToDataDialog.java

@@ -21,6 +21,9 @@ import javax.swing.text.PlainDocument;
 import jcl.data.Data;
 import jcl.data.DataObject;
 import jcl.data.SimpleData;
+import jcl.data.distance.DistanceModel;
+import jcl.data.distance.DistanceParameter;
+import jcl.weights.GlobalWeights;
 import mustic.gui.MainFrame;
 import mustic.gui.dialog.Messages;
 import mustic.utils.documentFilter.BasicIntDocumentFilter;
@@ -158,7 +161,13 @@ public class OGRToDataDialog extends JInternalFrame implements ToUpdateObject {
 			
 			if(result != null) {
 				
-				data = new SimpleData(result