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