Commit 119b5fee authored by balanche's avatar balanche

Merge with current master branch

parents 3b7e6baf b14022b0
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......@@ -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;
......
......@@ -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>();
......
......@@ -22,9 +22,9 @@ import javax.swing.JTextField;
import javax.swing.SpinnerNumberModel;
import javax.swing.text.NumberFormatter;
import multiCube.tools.image.ImageHelper;
import mustic.gui.MainFrame;
import mustic.utils.filters.ImageFileFilter;
import mustic.utils.image.ImageHelper;
import otbAppWrapping.ExecCommand;
public class WaterIndiceExtractionDialog extends JFrame {
......
......@@ -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;
......@@ -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()));
......
......@@ -56,7 +56,7 @@ import jcl.clustering.constraints.LabelConstraint;
import jcl.clustering.constraints.MustLinkConstraint;
import jcl.clustering.constraints.NbClusterConstraint;
import jcl.data.Data;
import jcl.data.DistanceModel;
import jcl.data.distance.DistanceModel;
import jcl.data.distance.DistanceParameter;
import jcl.weights.GlobalWeights;
import mustic.utils.image.ImageAddOn;
......@@ -1019,7 +1019,9 @@ public class ConstraintsSelectionFrame extends JFrame implements ImageAddOn {
}
public void refresh() {
container.updateUI();
if (container != null) {
container.updateUI();
}
imageDisplayer.refresh(false);
}
......
......@@ -22,15 +22,15 @@ import javax.swing.JTextField;
import jcl.data.Data;
import jcl.data.DataObject;
import jcl.data.DistanceModel;
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;
......
package mustic.gui.dialog.csv;
import java.awt.BorderLayout;
import java.awt.Dimension;
import java.awt.GridLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.FocusEvent;
import java.awt.event.FocusListener;
import java.io.File;
import java.io.FileNotFoundException;
import java.util.ArrayList;
import java.util.List;
import javax.swing.JButton;
import javax.swing.JFileChooser;
import javax.swing.JInternalFrame;
import javax.swing.JLabel;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JTextField;
import jcl.data.Data;
import jcl.data.DataObject;
import jcl.data.DistanceModel;
import jcl.data.SimpleData;
import jcl.data.attribute.AttributeMultiDimSequence;
<<<<<<< HEAD
import jcl.data.distance.DistanceParameter;
import jcl.weights.GlobalWeights;
=======
import multiCube.tools.image.ImageHelper;
>>>>>>> master
import mustic.gui.MainFrame;
import mustic.gui.dialog.Messages;
import mustic.utils.documentFilter.ToUpdateObject;
import mustic.utils.io.CSVUtils;
/**
* Dialog that allow the user to generate a Data from an arff file
*
* @author Baptiste LAFABREGUE
*
*/
public class CSVToDataDialog extends JInternalFrame implements ToUpdateObject {
private static final long serialVersionUID = 1L;
private JTextField textFile = new JTextField();
private JTextField textData = new JTextField();
private JTextField textSeparator = new JTextField();
public CSVToDataDialog() {
super();
JPanel mainPanel = new JPanel(new BorderLayout());
JPanel panel = new JPanel(new GridLayout(3, 2));
JPanel pInpout = new JPanel(new BorderLayout());
panel.add(new JLabel(Messages.getString("CSVToDataDialog.0")), BorderLayout.WEST); //$NON-NLS-1$
pInpout.add(this.textFile, BorderLayout.CENTER);
this.textFile.addFocusListener(new FocusListener() {
@Override
public void focusLost(FocusEvent e) {
updateOutputName();
}
@Override
public void focusGained(FocusEvent e) {
}
});
JButton buttonBrowse = new JButton("..."); //$NON-NLS-1$
buttonBrowse.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
JFileChooser fileChooser = new JFileChooser();
int returnVal = fileChooser
.showOpenDialog(CSVToDataDialog.this);
if (returnVal == JFileChooser.APPROVE_OPTION) {
CSVToDataDialog.this.textFile.setText(fileChooser
.getSelectedFile().getPath());
updateOutputName();
if (!fileChooser.getSelectedFile().getPath()
.endsWith(".csv")) { //$NON-NLS-1$
JOptionPane.showMessageDialog(CSVToDataDialog.this,
Messages.getString("CSVToDataDialog.3"), //$NON-NLS-1$
Messages.getString("CSVToDataDialog.4"), //$NON-NLS-1$
JOptionPane.WARNING_MESSAGE);
}
}
}
});
pInpout.add(buttonBrowse, BorderLayout.EAST);
panel.add(pInpout);
JPanel pSeparator = new JPanel(new BorderLayout());
panel.add(new JLabel(Messages.getString("CSVToDataDialog.2")), BorderLayout.WEST); //$NON-NLS-1$
pSeparator.add(this.textSeparator, BorderLayout.CENTER);
panel.add(pSeparator);
this.textSeparator.setText(";");
JPanel pOutpout = new JPanel(new BorderLayout());
panel.add(new JLabel(Messages.getString("CSVToDataDialog.5")), BorderLayout.WEST); //$NON-NLS-1$
pOutpout.add(this.textData, BorderLayout.CENTER);
panel.add(pOutpout);
this.textFile.setPreferredSize(new Dimension(200, 30));
JPanel panelButton = new JPanel();
JButton buttonOk = new JButton(Messages.getString("CSVToDataDialog.7")); //$NON-NLS-1$
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("CSVToDataDialog.8")); //$NON-NLS-1$
this.setSize(300, 180);
this.setResizable(true);
this.setMaximizable(true);
this.setIconifiable(true);
this.setClosable(true);
this.setVisible(true);
this.requestFocus();
}
private void updateOutputName() {
if (this.textData.getText() != null && this.textData.getText() != "") { //$NON-NLS-1$
// we don't update if there is already a value
return;
}
if (this.textFile.getText() != null && this.textFile.getText() != "") { //$NON-NLS-1$
this.textData.setText(ImageHelper.extractFileName(
ImageHelper.stripExtension(this.textData.getText())));
}
}
protected void buttonOk_actionPerformed() {
try {
List<DataObject> result = new ArrayList<DataObject>();
Data data = null;
CSVUtils reader = null;
try {
File file = new File(this.textFile.getText());
reader = new CSVUtils(file, this.textSeparator.getText().charAt(0));
List<String> line;
while((line = reader.readNext()) != null) {
extractObjectFromLine(result, line);
}
} catch (FileNotFoundException e) {
e.printStackTrace();
result = null;
}
if(result != null) {
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(
ImageHelper.stripExtension(this.textData.getText())));
}
data.setDataName(this.textData.getText());
MainFrame.getInstance().createDataSession(data);
JOptionPane.showMessageDialog(this,
Messages.getString("CSVToDataDialog.151") + this.textData.getText() //$NON-NLS-1$
+ " " + Messages.getString("CSVToDataDialog.152"), //$NON-NLS-1$
Messages.getString("CSVToDataDialog.16"), //$NON-NLS-1$
JOptionPane.INFORMATION_MESSAGE);
} else {
JOptionPane.showMessageDialog(this,
Messages.getString("CSVToDataDialog.41"), //$NON-NLS-1$
Messages.getString("CSVToDataDialog.4"), //$NON-NLS-1$
JOptionPane.WARNING_MESSAGE);
}
this.dispose();
} catch (Exception e) {
JOptionPane.showMessageDialog(this,
Messages.getString("CSVToDataDialog.41"), //$NON-NLS-1$
Messages.getString("CSVToDataDialog.4"), //$NON-NLS-1$
JOptionPane.WARNING_MESSAGE);
e.printStackTrace();
}
}
/**
* Construct a DataObject from a set of Strings and add it to a List
* @param list
* the list to add the DataObject to
* @param line
* the line to interpret
*/
private void extractObjectFromLine(List<DataObject> list, List<String> line) {
DataObject obj = new DataObject(1);
double[][] seq = new double[line.size()][];
for (int i = 0 ; i < line.size() ; i++) {
seq[i] = new double[1];
seq[i][0] = Double.parseDouble(line.get(i));
}
obj.setAttribute(0, new AttributeMultiDimSequence(seq));
list.add(obj);
}
@Override
public void update(String s) {
}
}
......@@ -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;
/**
......
......@@ -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);
data = new SimpleData(result, null, null);
DistanceModel distanceModel = DistanceModel.generateDefaultModel(
data.getOneDataObject(), new GlobalWeights(data.getOneDataObject()));
DistanceParameter[][] distanceParameters = DistanceModel
.generateDefaultDistanceParameters(1, distanceModel, data);
data.setDistanceModel(distanceModel, distanceParameters);
data.setDataName(this.textData.getText());
MainFrame.getInstance().createDataSession(data);
......
......@@ -28,10 +28,11 @@ import jcl.learning.methods.monostrategy.SingleClassification;
import jcl.learning.methods.monostrategy.ahc.LearningResultAHC;
import jcl.learning.methods.monostrategy.ahc.ParametersAHC;
import jcl.utils.exceptions.JCLFormatException;
import jcl.utils.exceptions.MethodNotImplementedException;
import jcl.utils.io.JCLModelExchange;
import jsl.Segmentation;
import jsl.regionalisation.vectorisation.Filters;
import multiCube.tools.image.tiff.TiffUtils;
import multiCube.tools.util.exceptions.MethodNotImplementedException;
import mustic.gui.*;
import mustic.gui.dialog.FilterDialog;
import mustic.gui.dialog.classifier.ConstraintsSelectionFrame;
......@@ -52,7 +53,6 @@ import mustic.utils.image.viewer.ClusteringImageViewer;
import mustic.utils.image.viewer.GDALPyramidImageViewer;
import mustic.utils.image.viewer.ImageViewer;
import mustic.utils.image.viewer.MultiResolutionClusterMap;
import mustic.utils.io.tiff.TiffUtils;
import org.apache.batik.svggen.SVGGraphics2DIOException;
......@@ -72,90 +72,90 @@ public class ImageResultPanel extends ResultPanel implements TreeSelectionListen
private MultiResolutionClusterMap clusterMap = null;
protected File currentDirectory = null;
protected File currentDirectory = null;
/** Coordinates of the current position of the top left corner
* of the screen image in the original image */
private Point currentTopLeft = new Point(0,0);
private Point currentTopLeft = new Point(0,0);
/** l'image contenant les donnees d'origine */
private BufferedImage data;
private BufferedImage data;
/** l'image contenant les donnees d'origine */
protected BufferedImage data_zoomed;
protected BufferedImage data_zoomed;
/** panel that displays the image */
protected ZoomBoxPanel displayPanel = null;
protected ZoomBoxPanel displayPanel = null;
/** the list of add on that the displayer has subscribed to */
private Vector<ImageAddOn> imageAddOns = new Vector<ImageAddOn>();
private Vector<ImageAddOn> imageAddOns = new Vector<ImageAddOn>();
/** the parent session */
private ImageManager imageManager = null;
private ImageManager imageManager = null;
private ImageData imgData;
private ImageData imgData;
protected JInternalFrame jif_saveResult = new JInternalFrame();
protected JInternalFrame jif_saveResult = new JInternalFrame();
protected JLayeredPane lpane = new JLayeredPane();
protected JLayeredPane lpane = new JLayeredPane();
/** width of the screen image */
private int lastWidth = 0;
private int lastWidth = 0;
/** height of the screen image */
private int lastHeight = 0;
private int lastHeight = 0;
protected int[] map = null;
protected int[] map = null;
/** classification */
// protected Classification classification;
/** image initiale */
/** record the position of the mouse when it has been pressed */
private Point mousePressedCoordinates = null;
private Point mousePressedCoordinates = null;
// protected RawImage mRawImage;
// protected RawImage mRawImage;
/** zoom level */
protected double mZoomRate = 1.0f;
protected double mZoomRate = 1.0f;
/** zoom step */
private double mZoomStep = 0.7f;
private double mZoomStep = 0.7f;
// clusters' opacity
// up to 0 - 1
private float opacity = 1;
private float opacity = 1;
private float opacityCluster = 1;
private float opacityCluster = 1;
/** */
protected JPanel panelResSave = new JPanel();
protected JPanel panelResSave = new JPanel();
/** offset between the panel and the actual displayed image */
private Point screenOffset = new Point(0,0);
private Point screenOffset = new Point(0,0);
protected ClusteringResult result;
protected ClusteringResult result;
protected boolean[] resultSave = null;
protected boolean[] resultSave = null;
private ROIImage roi = null;
private ROIImage roi = null;
protected int rx = 0;
protected int rx = 0;
protected int ry = 0;
protected int ry = 0;
private float scaleFactor = 1.0f;
private float scaleFactor = 1.0f;
/** */
protected JToolBar tools = new JToolBar();
protected JToolBar tools = new JToolBar();
protected JButton vectorise = new JButton("Segmentation");
protected JButton vectorise = new JButton("Segmentation");
/** the viewer that allows to reader the image */
private ImageViewer viewer = null;
private ClusteringImageViewer viewer = null;
/** */
protected BufferedImage zoomed;
protected BufferedImage zoomed = null;
/**
*
......@@ -1679,8 +1679,14 @@ public class ImageResultPanel extends ResultPanel implements TreeSelectionListen
@Override
public BufferedImage getBirdViewImage(double zoomFactor) {
// we want the original image in the birdview so we hide every clusters
viewer.disableClustersDisplay();
BufferedImage result = viewer.getScreenImage(0, 0, (int) (viewer.getRealImageWidth()*zoomFactor),
(int) (viewer.getRealImageHeight()*zoomFactor), zoomFactor, false);
viewer.enableClustersDisplay();
return result;
}
......
......@@ -5,7 +5,10 @@ import java.awt.event.ActionEvent;
import javax.swing.JComboBox;
import javax.swing.JLabel;
import jcl.data.distance.DistanceModel;
import jcl.data.distance.DistanceParameter;
import jcl.learning.LearningParameters;
import jcl.weights.GlobalWeights;
import mustic.gui.ImageDesktopFrame;
import mustic.gui.MainFrame;
import mustic.io.ImageData;
......@@ -79,7 +82,13 @@ class RemoteSensingClassifierDialog extends ClassifierDialog {
if (this.bidouille == null) {
img = MainFrame.getInstance().getDesktop().getAllImageDesktopFrames()[this.dataBox
.getSelectedIndex()].getImageSession().getRawImage();
this.bidouille = new ImageData(img);
this.bidouille = new ImageData(img, null, null);
DistanceModel distanceModel = DistanceModel.generateDefaultModel(
this.bidouille.getOneDataObject(), new GlobalWeights(this.bidouille.getOneDataObject()));
DistanceParameter[][] distanceParameters = DistanceModel
.generateDefaultDistanceParameters(1, distanceModel, this.bidouille);
this.bidouille.setDistanceModel(distanceModel, distanceParameters);
}
LearningParameters params = this.classifiersPanel
......
......@@ -17,10 +17,10 @@ import javax.xml.parsers.SAXParserFactory;
import jcl.Classification;
import jcl.data.Data;
import jcl.data.DataObject;
import jcl.data.DistanceModel;