Implemented KalmanTrackerFF for fast flows as a separate method

trackmate-sc · May 19, 2024 · fe8b0fd · fe8b0fd
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diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -0,0 +1,3 @@
+{
+    "java.configuration.updateBuildConfiguration": "interactive"
+}
diff --git a/src/main/java/fiji/plugin/trackmate/gui/components/tracker/KalmanTrackerFFConfigPanel.java b/src/main/java/fiji/plugin/trackmate/gui/components/tracker/KalmanTrackerFFConfigPanel.java
@@ -0,0 +1,204 @@
+/*-
+ * #%L
+ * TrackMate: your buddy for everyday tracking.
+ * %%
+ * Copyright (C) 2010 - 2024 TrackMate developers.
+ * %%
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation, either version 3 of the
+ * License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public
+ * License along with this program.  If not, see
+ * <http://www.gnu.org/licenses/gpl-3.0.html>.
+ * #L%
+ */
+package fiji.plugin.trackmate.gui.components.tracker;
+
+import static fiji.plugin.trackmate.gui.Fonts.BIG_FONT;
+import static fiji.plugin.trackmate.gui.Fonts.FONT;
+import static fiji.plugin.trackmate.gui.Fonts.TEXTFIELD_DIMENSION;
+import static fiji.plugin.trackmate.tracking.TrackerKeys.KEY_GAP_CLOSING_MAX_FRAME_GAP;
+import static fiji.plugin.trackmate.tracking.TrackerKeys.KEY_LINKING_MAX_DISTANCE;
+import static fiji.plugin.trackmate.tracking.TrackerKeys.KEY_KALMAN_SEARCH_RADIUS;
+import static fiji.plugin.trackmate.tracking.TrackerKeys.KEY_EXPECTED_MOVEMENT;
+
+import java.awt.Font;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
+import java.util.HashMap;
+import java.util.Map;
+
+import javax.swing.JFormattedTextField;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.SwingConstants;
+import javax.swing.JTextField;
+
+import fiji.plugin.trackmate.gui.GuiUtils;
+import fiji.plugin.trackmate.gui.components.ConfigurationPanel;
+
+public class KalmanTrackerFFConfigPanel extends ConfigurationPanel
+{
+	private static final long serialVersionUID = 1L;
+
+	private final JFormattedTextField tfInitSearchRadius;
+
+	private final JFormattedTextField tfSearchRadius;
+
+	private final JFormattedTextField tfMaxFrameGap;
+
+	private final JTextField tfExpectedMovement;
+
+	public KalmanTrackerFFConfigPanel( final String trackerName, final String infoText, final String spaceUnits )
+	{
+		setLayout( null );
+
+		final JLabel lbl1 = new JLabel( "Settings for tracker:" );
+		lbl1.setBounds( 6, 6, 288, 16 );
+		lbl1.setFont( FONT );
+		add( lbl1 );
+
+		final JLabel lblTrackerName = new JLabel( trackerName );
+		lblTrackerName.setFont( BIG_FONT );
+		lblTrackerName.setHorizontalAlignment( SwingConstants.CENTER );
+		lblTrackerName.setBounds( 6, 34, 288, 32 );
+		add( lblTrackerName );
+
+		final JLabel lblTrackerDescription = new JLabel( "<tracker description>" );
+		lblTrackerDescription.setFont( FONT.deriveFont( Font.ITALIC ) );
+		lblTrackerDescription.setVerticalAlignment( SwingConstants.TOP );
+		lblTrackerDescription.setBounds( 6, 81, 288, 175 );
+		lblTrackerDescription.setText( infoText
+				.replace( "<br>", "" )
+				.replace( "<p>", "<p align=\"justify\">" )
+				.replace( "<html>", "<html><p align=\"justify\">" ) );
+		add( lblTrackerDescription );
+
+		final JLabel lblInitSearchRadius = new JLabel( "Initial search radius:" );
+		lblInitSearchRadius.setFont( FONT );
+		lblInitSearchRadius.setBounds( 6, 348, 173, 16 );
+		add( lblInitSearchRadius );
+
+		final JLabel lblSearchRadius = new JLabel( "Search radius:" );
+		lblSearchRadius.setFont( FONT );
+		lblSearchRadius.setBounds( 6, 376, 173, 16 );
+		add( lblSearchRadius );
+
+		final JLabel lblMaxFrameGap = new JLabel( "Max frame gap:" );
+		lblMaxFrameGap.setFont( FONT );
+		lblMaxFrameGap.setBounds( 6, 404, 173, 16 );
+		add( lblMaxFrameGap );
+
+		tfInitSearchRadius = new JFormattedTextField( 15. );
+		tfInitSearchRadius.setHorizontalAlignment( SwingConstants.CENTER );
+		tfInitSearchRadius.setFont( FONT );
+		tfInitSearchRadius.setBounds( 167, 348, 60, 28 );
+		add( tfInitSearchRadius );
+		tfInitSearchRadius.setSize( TEXTFIELD_DIMENSION );
+
+		tfSearchRadius = new JFormattedTextField( 15. );
+		tfSearchRadius.setHorizontalAlignment( SwingConstants.CENTER );
+		tfSearchRadius.setFont( FONT );
+		tfSearchRadius.setBounds( 167, 376, 60, 28 );
+		add( tfSearchRadius );
+		tfSearchRadius.setSize( TEXTFIELD_DIMENSION );
+
+		tfMaxFrameGap = new JFormattedTextField( 2 );
+		tfMaxFrameGap.setHorizontalAlignment( SwingConstants.CENTER );
+		tfMaxFrameGap.setFont( FONT );
+		tfMaxFrameGap.setBounds( 167, 404, 60, 28 );
+		add( tfMaxFrameGap );
+		tfMaxFrameGap.setSize( TEXTFIELD_DIMENSION );
+
+		tfExpectedMovement = new JTextField("0;0;0"); // Initialize with default value
+        tfExpectedMovement.setHorizontalAlignment(SwingConstants.CENTER);
+        tfExpectedMovement.setFont(FONT);
+        tfExpectedMovement.setBounds(167, 432, 100, 28); // Adjust position as needed
+        add(tfExpectedMovement);
+
+        // Adding input validation
+        tfExpectedMovement.addFocusListener(new FocusAdapter() {
+            @Override
+            public void focusLost(FocusEvent e) {
+                if (!validateExpectedMovementInput(tfExpectedMovement.getText())) {
+                    JOptionPane.showMessageDialog(null, "Invalid input. Please enter a semicolon-separated list of three numbers (e.g., '123;0;0').", "Invalid Input", JOptionPane.ERROR_MESSAGE);
+                    tfExpectedMovement.setText(String.format("%.1f;%.1f;%.1f", 0, 0, 0));
+                }
+            }
+        });
+
+		final JLabel lblSpaceUnits1 = new JLabel( spaceUnits );
+		lblSpaceUnits1.setFont( FONT );
+		lblSpaceUnits1.setBounds( 219, 348, 51, 16 );
+		add( lblSpaceUnits1 );
+
+		final JLabel lblSpaceUnits2 = new JLabel( spaceUnits );
+		lblSpaceUnits2.setFont( FONT );
+		lblSpaceUnits2.setBounds( 219, 376, 51, 16 );
+		add( lblSpaceUnits2 );
+
+		final JLabel lblFrameUnits = new JLabel( "frames" );
+		lblFrameUnits.setFont( FONT );
+		lblFrameUnits.setBounds( 219, 404, 51, 16 );
+		add( lblFrameUnits );
+
+		// Select text-fields content on focus.
+		GuiUtils.selectAllOnFocus( tfInitSearchRadius );
+		GuiUtils.selectAllOnFocus( tfMaxFrameGap );
+		GuiUtils.selectAllOnFocus( tfSearchRadius );
+		GuiUtils.selectAllOnFocus( tfExpectedMovement );
+	}
+
+	private boolean validateExpectedMovementInput(String input) {
+        String[] parts = input.split(";");
+        if (parts.length != 3)
+            return false;
+        try {
+            for (String part : parts) {
+                Double.parseDouble(part.trim());
+            }
+        } catch (NumberFormatException e) {
+            return false;
+        }
+        return true;
+    }
+
+	@Override
+	public void setSettings( final Map< String, Object > settings )
+	{
+		tfInitSearchRadius.setValue( settings.get( KEY_LINKING_MAX_DISTANCE ) );
+		tfSearchRadius.setValue( settings.get( KEY_KALMAN_SEARCH_RADIUS ) );
+		tfMaxFrameGap.setValue( settings.get( KEY_GAP_CLOSING_MAX_FRAME_GAP ) );
+		double[] expectedMovementArray = (double[]) settings.get( KEY_EXPECTED_MOVEMENT );
+        tfExpectedMovement.setText( expectedMovementArray[0] + ";" + expectedMovementArray[1] + ";" + expectedMovementArray[2] );
+	}
+
+	@Override
+	public Map< String, Object > getSettings()
+	{
+		final Map< String, Object > settings = new HashMap<>();
+		settings.put( KEY_LINKING_MAX_DISTANCE, ( ( Number ) tfInitSearchRadius.getValue() ).doubleValue() );
+		settings.put( KEY_KALMAN_SEARCH_RADIUS, ( ( Number ) tfSearchRadius.getValue() ).doubleValue() );
+		settings.put( KEY_GAP_CLOSING_MAX_FRAME_GAP, ( ( Number ) tfMaxFrameGap.getValue() ).intValue() );
+
+		String[] parts = tfExpectedMovement.getText().split(";");
+        double[] expectedMovement = new double[3];
+        for (int i = 0; i < parts.length; i++) {
+            expectedMovement[i] = Double.parseDouble(parts[i].trim());
+        }
+        settings.put(KEY_EXPECTED_MOVEMENT, expectedMovement);
+
+		return settings;
+	}
+
+	@Override
+	public void clean()
+	{}
+}
diff --git a/src/main/java/fiji/plugin/trackmate/tracking/TrackerKeys.java b/src/main/java/fiji/plugin/trackmate/tracking/TrackerKeys.java
@@ -100,6 +100,13 @@ public class TrackerKeys
 
 	/** A default value for the {@value #KEY_KALMAN_SEARCH_RADIUS} parameter. */
 	public static final double DEFAULT_KALMAN_SEARCH_RADIUS = 20.0;
+
+	/** Search radius for the Kalman tracker - Fast Flow. */
+	public static final String KEY_EXPECTED_MOVEMENT = "EXPECTED_MOVEMENT";
+
+	/** A default value for the {@value #KEY_EXPECTED_MOVEMENT} parameter. */
+	public static final double[] DEFAULT_EXPECTED_MOVEMENT = {0.0, 0.0, 0.0};
+
 
 	/**
 	 * Key for the parameter specifying whether we allow the detection of