diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..3d47f986c41db29ec6dc0d5036bf760b3a1cf366
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,6 @@
+.idea/
+target/
+.settings/
+*.iml
+.project
+.classpath
\ No newline at end of file
diff --git a/pom.xml b/pom.xml
new file mode 100644
index 0000000000000000000000000000000000000000..3932634b72ee13bfc34241cf35223a7458d513a8
--- /dev/null
+++ b/pom.xml
@@ -0,0 +1,101 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+
+ <!-- Inherited Icy Parent POM -->
+ <parent>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <artifactId>parent-pom-plugin</artifactId>
+ <version>1.0.3</version>
+ </parent>
+
+ <!-- Project Information -->
+ <artifactId>msd-track-processor</artifactId>
+ <version>1.1.1</version>
+
+ <packaging>jar</packaging>
+
+ <name>MSD Track Processor</name>
+ <description>Track Processor computing the MSD (Mean Square Displacement).</description>
+ <url>http://icy.bioimageanalysis.org/plugin/track-processor-msd/</url>
+ <inceptionYear>2020</inceptionYear>
+
+ <organization>
+ <name>Institut Pasteur</name>
+ <url>https://pasteur.fr</url>
+ </organization>
+
+ <licenses>
+ <license>
+ <name>GNU GPLv3</name>
+ <url>https://www.gnu.org/licenses/gpl-3.0.en.html</url>
+ <distribution>repo</distribution>
+ </license>
+ </licenses>
+
+ <developers>
+ <developer>
+ <id>sdallongeville</id>
+ <name>Stéphane Dallongeville</name>
+ <url>https://research.pasteur.fr/fr/member/stephane-dallongeville/</url>
+ <roles>
+ <role>founder</role>
+ <role>lead</role>
+ <role>architect</role>
+ <role>developer</role>
+ <role>debugger</role>
+ <role>tester</role>
+ <role>maintainer</role>
+ <role>support</role>
+ </roles>
+ </developer>
+ </developers>
+
+ <!-- Project properties -->
+ <properties>
+
+ </properties>
+
+ <!-- Project build configuration -->
+ <build>
+
+ </build>
+
+ <!-- List of project's dependencies -->
+ <dependencies>
+ <!-- The core of Icy -->
+ <dependency>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <artifactId>icy-kernel</artifactId>
+ </dependency>
+
+ <dependency>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <artifactId>jfreechart</artifactId>
+ <version>1.5.3</version>
+ </dependency>
+
+ <dependency>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <artifactId>spot-detection-utilities</artifactId>
+ <version>1.1.6</version>
+ </dependency>
+
+ <dependency>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <artifactId>distance-profiler</artifactId>
+ <version>1.0.0</version>
+ </dependency>
+ </dependencies>
+
+ <!-- Icy Maven repository (to find parent POM) -->
+ <repositories>
+ <repository>
+ <id>icy</id>
+ <name>Icy's Nexus</name>
+ <url>https://icy-nexus.pasteur.fr/repository/Icy/</url>
+ </repository>
+ </repositories>
+</project>
diff --git a/src/main/java/plugins/fab/trackmanager/processors/TrackProcessorMSD.java b/src/main/java/plugins/fab/trackmanager/processors/TrackProcessorMSD.java
new file mode 100644
index 0000000000000000000000000000000000000000..727c7f618d5dce1e690aa1e78ec6cae93e0b97e2
--- /dev/null
+++ b/src/main/java/plugins/fab/trackmanager/processors/TrackProcessorMSD.java
@@ -0,0 +1,532 @@
+package plugins.fab.trackmanager.processors;
+
+import java.awt.Graphics2D;
+import java.awt.Point;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyEvent;
+import java.awt.event.MouseEvent;
+import java.awt.geom.AffineTransform;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+import java.io.File;
+import java.io.IOException;
+
+import javax.swing.BoxLayout;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+
+import org.jfree.chart.ChartFactory;
+import org.jfree.chart.ChartPanel;
+import org.jfree.chart.JFreeChart;
+import org.jfree.chart.plot.PlotOrientation;
+import org.jfree.chart.plot.XYPlot;
+import org.jfree.chart.renderer.xy.XYItemRenderer;
+import org.jfree.data.xy.XYSeries;
+import org.jfree.data.xy.XYSeriesCollection;
+
+import icy.canvas.IcyCanvas;
+import icy.gui.util.GuiUtil;
+import icy.painter.Painter;
+import icy.preferences.GeneralPreferences;
+import icy.sequence.Sequence;
+import icy.util.StringUtil;
+import icy.util.XLSUtil;
+import jxl.write.WritableSheet;
+import jxl.write.WritableWorkbook;
+import jxl.write.WriteException;
+import plugins.fab.trackmanager.PluginTrackManagerProcessor;
+import plugins.fab.trackmanager.TrackSegment;
+import plugins.nchenouard.spot.Detection;
+
+/**
+ * @author Fabrice de Chaumont
+ */
+public class TrackProcessorMSD extends PluginTrackManagerProcessor implements ActionListener, Painter
+{
+ JFreeChart chart;
+ JCheckBox displayLegendCheckBox = new JCheckBox("Display legend.", false);
+ JCheckBox displayGraphInSequenceCheckBox = new JCheckBox("Display graph on sequence.", false);
+ JButton useRoiAsBoundsForChartButton = new JButton("place graph in ROI #1");
+ JCheckBox forceAllSequenceGraphWidthCheckBox = new JCheckBox("Force graph width.", false);
+ JCheckBox useRealScalesBox = new JCheckBox("use real scales", false);
+ JPanel chartpanel = new JPanel();
+ JTextField scaleTextField = new JTextField("1.0");
+ JButton exportButton = new JButton("export to console");
+ JButton exportExcelButton = new JButton("export to excel");
+
+ public TrackProcessorMSD()
+ {
+ panel.setLayout(new BoxLayout(panel, BoxLayout.PAGE_AXIS));
+ chartpanel.add(new ChartPanel(chart, 500, 300, 500, 300, 500, 300, false, false, true, true, true, true));
+ panel.add(GuiUtil.besidesPanel(chartpanel));
+ panel.add(GuiUtil.besidesPanel(useRealScalesBox));
+ useRealScalesBox.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ Compute();
+ }
+ });
+ panel.add(GuiUtil.besidesPanel(displayLegendCheckBox, forceAllSequenceGraphWidthCheckBox));
+ // panel.add( GuiUtil.besidesPanel( displayGraphInSequenceCheckBox , useRoiAsBoundsForChartButton ) );
+ // panel.add( GuiUtil.besidesPanel( new JLabel("Scale:") , scaleTextField ) );
+ exportButton.addActionListener(this);
+ exportExcelButton.addActionListener(this);
+ panel.add(GuiUtil.besidesPanel(exportButton, exportExcelButton));
+ useRoiAsBoundsForChartButton.addActionListener(this);
+ displayGraphInSequenceCheckBox.addActionListener(this);
+ displayLegendCheckBox.addActionListener(this);
+ forceAllSequenceGraphWidthCheckBox.addActionListener(this);
+ setName("Mean square displacement");
+ // trackPool.getDisplaySequence().addPainter( this );
+ }
+
+ @Override
+ public void Compute()
+ {
+ if (!super.isEnabled())
+ return;
+
+ XYSeriesCollection xyDataset = new XYSeriesCollection();
+
+ final Sequence seq = trackPool.getDisplaySequence();
+ final double tScale = (seq != null) ? seq.getTimeInterval() : 1d;
+
+ if (useRealScalesBox.isSelected())
+ {
+ for (TrackSegment ts : trackPool.getTrackSegmentList())
+ {
+ XYSeries series = new XYSeries("Track " + trackPool.getTrackIndex(ts));
+
+ if (ts.isAllDetectionEnabled())
+ {
+ double[] msd = scaledMeanSquaredDisplacement(seq, ts);
+
+ for (int i = 0; i < msd.length; i++)
+ series.add(i * tScale, msd[i]);
+
+ xyDataset.addSeries(series);
+ }
+ }
+ }
+ else
+ {
+ for (TrackSegment ts : trackPool.getTrackSegmentList())
+ {
+ XYSeries series = new XYSeries("Track " + trackPool.getTrackIndex(ts));
+
+ if (ts.isAllDetectionEnabled())
+ {
+ double[] msd = scaledMeanSquaredDisplacement(null, ts);
+
+ for (int i = 0; i < msd.length; i++)
+ series.add(i, msd[i]);
+
+ xyDataset.addSeries(series);
+ }
+ }
+ }
+ String TitleString = "";
+ String TitleString2 = "";
+ String TitleString3 = "";
+
+ if (displayLegendCheckBox.isSelected())
+ {
+ if (useRealScalesBox.isSelected())
+ {
+ TitleString = "Mean Square Displacement";
+ TitleString2 = "Delta (s)";
+ TitleString3 = "MSD (um^2)";
+ }
+ else
+ {
+ TitleString = "Mean Square Displacement";
+ TitleString2 = "Delta (frame)";
+ TitleString3 = "MSD (pixel^2)";
+ }
+ }
+
+ chart = ChartFactory.createXYLineChart(TitleString, // chart title
+ TitleString2, // x axis label
+ TitleString3, // y axis label
+ xyDataset, // data
+ PlotOrientation.VERTICAL, displayLegendCheckBox.isSelected(), // include legend
+ true, // tooltips
+ false // urls
+ );
+
+ if (forceAllSequenceGraphWidthCheckBox.isSelected())
+ {
+ XYSeries series = new XYSeries("");
+ series.add(trackPool.getLastDetectionTimePoint(), 0);
+ xyDataset.addSeries(series);
+ }
+
+ chartpanel.removeAll();
+
+ if (chart != null)
+ {
+ // replace default chart colors by detection colors (taken from t=0)
+ XYItemRenderer renderer = ((XYPlot) chart.getPlot()).getRenderer();
+ for (TrackSegment ts : trackPool.getTrackSegmentList())
+ renderer.setSeriesPaint(trackPool.getTrackIndex(ts), ts.getFirstDetection().getColor());
+ }
+ chartpanel.add(new ChartPanel(chart, 400, 300, 400, 300, 400, 300, false, false, true, true, true, true));
+
+ chartpanel.updateUI();
+ panel.updateUI();
+
+ }
+
+ /** Export to console and optionaly in xls */
+ private void exportMSD(boolean xlsExport)
+ {
+ WritableWorkbook workbook = null;
+ WritableSheet page = null;
+ String outputName;
+
+ if ((trackPool.getDisplaySequence() == null)
+ || StringUtil.isEmpty(trackPool.getDisplaySequence().getFilename()))
+ outputName = GeneralPreferences.getResultFolder() + "Tracks";
+ else
+ outputName = trackPool.getDisplaySequence().getFilename();
+
+ outputName += ".msd.xls";
+
+ if (xlsExport)
+ {
+ try
+ {
+ workbook = XLSUtil.createWorkbook(new File(outputName));
+ }
+ catch (IOException e)
+ {
+ e.printStackTrace();
+ }
+
+ }
+
+ if (workbook != null)
+ page = XLSUtil.createNewPage(workbook, "results");
+
+ final Sequence seq = trackPool.getDisplaySequence();
+ final double tScale = (seq != null) ? seq.getTimeInterval() : 1d;
+
+ if (useRealScalesBox.isSelected())
+ {
+ int cnt = 0;
+ int row = 0;
+ for (TrackSegment ts : trackPool.getTrackSegmentList())
+ {
+ if (ts.isAllDetectionEnabled())
+ {
+ System.out.println("track " + cnt);
+
+ if (page != null)
+ XLSUtil.setCellString(page, 0, row, "track " + cnt);
+
+ double[] msd = scaledMeanSquaredDisplacement(seq, ts);
+ for (int i = 0; i < msd.length; i++)
+ {
+ System.out.println((i * tScale) + "\t" + msd[i]);
+ // System.out.println(i + "\t" + msd[i]);
+
+ if (page != null)
+ XLSUtil.setCellNumber(page, i + 1, row, msd[i]);
+ }
+
+ cnt++;
+ row++;
+ }
+ }
+ }
+ else
+ {
+ int cnt = 0;
+ int row = 0;
+
+ for (TrackSegment ts : trackPool.getTrackSegmentList())
+ {
+ if (ts.isAllDetectionEnabled())
+ {
+ System.out.println("track " + cnt);
+
+ if (page != null)
+ XLSUtil.setCellString(page, 0, row, "track " + cnt);
+
+ double[] msd = scaledMeanSquaredDisplacement(null, ts);
+ // double[] msd = meanSquaredDisplacement(ts);
+
+ for (int i = 0; i < msd.length; i++)
+ {
+ System.out.println(i + "\t" + msd[i]);
+
+ if (page != null)
+ XLSUtil.setCellNumber(page, i + 1, row, msd[i]);
+ }
+
+ cnt++;
+ row++;
+ }
+ }
+ }
+
+ if (workbook != null)
+ {
+ try
+ {
+ XLSUtil.saveAndClose(workbook);
+ }
+ catch (WriteException e)
+ {
+ e.printStackTrace();
+ }
+ catch (IOException e)
+ {
+ e.printStackTrace();
+ }
+ }
+ }
+
+ Rectangle2D chartRectangleInSequence = new Rectangle2D.Float(250, 20 + 260 * 0, 490, 240);
+
+ JLabel outLabel = new JLabel();
+
+ private double[] scaledMeanSquaredDisplacement(Sequence seq, TrackSegment ts)
+ {
+ final double sx, sy, sz;
+
+ if (seq != null)
+ {
+ sx = seq.getPixelSizeX();
+ sy = seq.getPixelSizeY();
+ sz = seq.getPixelSizeZ();
+ }
+ else
+ {
+ sx = 1d;
+ sy = 1d;
+ sz = 1d;
+ }
+
+ int nMSD = ts.getDetectionList().size();
+ // double[] dt_n = new double[nMSD];
+ double[] msd = new double[nMSD];
+
+ for (int t = 1; t < nMSD; t++)
+ {
+ msd[t] = 0d;
+ for (int j = 1; j <= t; j++)
+ msd[t] += scaledSquaredDistance(ts.getDetectionAt(0), ts.getDetectionAt(j), sx, sy, sz);
+
+ msd[t] /= t;
+ }
+
+ // for (int dt = 1; dt < nMSD; dt++)
+ // {
+ // for (int j = 0; (j + dt) < nMSD; j += dt)
+ // {
+ // msd[dt] += scaledSquaredDistance(ts.getDetectionAt(j), ts.getDetectionAt(j + dt), sx, sy, sz);
+ // dt_n[dt]++;
+ // }
+ // }
+ //
+ // for (int dt = 1; dt < nMSD; dt++)
+ // msd[dt] = (dt_n[dt] != 0) ? msd[dt] / dt_n[dt] : 0;
+
+ return msd;
+ }
+
+ // mean squared displacement
+ private double[] meanSquaredDisplacement(TrackSegment ts)
+ {
+ int nMSD = ts.getDetectionList().size();
+
+ double[] dt_n = new double[nMSD];
+ double[][] msd = new double[nMSD][2];
+
+ for (int dt = 1; dt < nMSD; dt++)
+ {
+ msd[dt][0] = dt * 1;
+
+ for (int j = 0; j + dt < ts.getDetectionList().size(); j += dt)
+ {
+ msd[dt][1] += squaredDistance(ts.getDetectionAt(j), ts.getDetectionAt(j + dt));
+ dt_n[dt]++;
+ }
+ }
+
+ for (int dt = 1; dt < nMSD; dt++)
+ msd[dt][1] = (dt_n[dt] != 0) ? msd[dt][1] / dt_n[dt] : 0;
+
+ double[] resultmsd = new double[nMSD];
+ resultmsd[0] = 0;
+ for (int dt = 1; dt < nMSD; dt++)
+ resultmsd[dt] = msd[dt][1];
+
+ return resultmsd;
+
+ }
+
+ private static double squaredDistance(Detection d1, Detection d2)
+ {
+ return scaledSquaredDistance(d1, d2, 1d, 1d, 1d);
+ }
+
+ private static double scaledSquaredDistance(Detection d1, Detection d2, double sx, double sy, double sz)
+ {
+ return Math.pow((d1.getX() - d2.getX()) * sx, 2) + Math.pow((d1.getY() - d2.getY()) * sy, 2)
+ + Math.pow((d1.getZ() - d2.getZ()) * sz, 2);
+ }
+
+ // public static double getScaledDistance(double x1, double y1, double z1, double x2, double y2, double z2)
+ // {
+ // return Math.sqrt((x1 - x2) * (x1 - x2) + (y1 - y2) * (y1 - y2) + (z1 - z2) * (z1 - z2));
+ // }
+ //
+ // public static double getDistance(double x1, double y1, double z1, double x2, double y2, double z2)
+ // {
+ // return Math.sqrt((x1 - x2) * (x1 - x2) + (y1 - y2) * (y1 - y2) + (z1 - z2) * (z1 - z2));
+ // }
+ //
+ // public double getDistance(Detection d1, Detection d2)
+ // {
+ // return getDistance(d1.getX(), d1.getY(), d1.getZ(), d2.getX(), d2.getY(), d2.getZ());
+ // }
+
+ @Override
+ public void Close()
+ {
+ Sequence sequence = trackPool.getDisplaySequence();
+ if (sequence != null)
+ {
+ sequence.removePainter(this);
+ }
+ }
+
+ public void actionPerformed(ActionEvent e)
+ {
+
+ // if ( e.getSource() == useRoiAsBoundsForChartButton )
+ // {
+ // Shape shape = (Shape) trackPool.getDisplaySequence().getROIs().get( 0 );
+ // chartRectangleInSequence = (Rectangle2D) shape.getBounds2D().clone();
+ // }
+ if (e.getSource() == exportButton)
+ {
+ exportMSD(false);
+ }
+
+ if (e.getSource() == exportExcelButton)
+ {
+ exportMSD(true);
+ }
+
+ trackPool.fireTrackEditorProcessorChange();
+
+ }
+
+ public void keyPressed(Point p, KeyEvent e)
+ {
+
+ }
+
+ public void mouseClick(Point p, MouseEvent e)
+ {
+
+ }
+
+ public void mouseDrag(Point p, MouseEvent e)
+ {
+
+ }
+
+ public void mouseMove(Point p, MouseEvent e)
+ {
+
+ }
+
+ @Override
+ public void displaySequenceChanged()
+ {
+
+ }
+
+ @Override
+ public void paint(Graphics2D g, Sequence sequence, IcyCanvas canvas)
+ {
+
+ double scale = Double.parseDouble(scaleTextField.getText());
+ double minX = chartRectangleInSequence.getCenterX();
+ double minY = chartRectangleInSequence.getCenterY();
+
+ Rectangle2D transformedChartRectangleInSequence = (Rectangle2D) chartRectangleInSequence.clone();
+ transformedChartRectangleInSequence.setRect((-chartRectangleInSequence.getWidth() / 2) * (1d / scale),
+ (-chartRectangleInSequence.getHeight() / 2) * (1d / scale),
+ chartRectangleInSequence.getWidth() * (1d / scale),
+ chartRectangleInSequence.getHeight() * (1d / scale));
+
+ Graphics2D g2 = (Graphics2D) g;
+
+ AffineTransform transform = g2.getTransform();
+ g2.scale(scale, scale);
+ g2.translate(minX * (1d / scale), minY * (1d / scale));
+
+ if (displayGraphInSequenceCheckBox.isSelected())
+ chart.draw((Graphics2D) g, transformedChartRectangleInSequence);
+
+ g2.setTransform(transform);
+
+ // if ( displayGraphInSequenceCheckBox.isSelected() )
+ // chart.draw( (Graphics2D)g , chartRectangleInSequence );
+
+ }
+
+ @Override
+ public void mousePressed(MouseEvent e, Point2D imagePoint, IcyCanvas canvas)
+ {
+
+ }
+
+ @Override
+ public void mouseReleased(MouseEvent e, Point2D imagePoint, IcyCanvas canvas)
+ {
+
+ }
+
+ @Override
+ public void mouseClick(MouseEvent e, Point2D imagePoint, IcyCanvas canvas)
+ {
+
+ }
+
+ @Override
+ public void mouseMove(MouseEvent e, Point2D imagePoint, IcyCanvas canvas)
+ {
+
+ }
+
+ @Override
+ public void mouseDrag(MouseEvent e, Point2D imagePoint, IcyCanvas canvas)
+ {
+
+ }
+
+ @Override
+ public void keyPressed(KeyEvent e, Point2D imagePoint, IcyCanvas canvas)
+ {
+
+ }
+
+ @Override
+ public void keyReleased(KeyEvent e, Point2D imagePoint, IcyCanvas canvas)
+ {
+
+ }
+
+}