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tineveztinevez
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Merge pull request #210 from fiji/auto-naming
Add an action that performs auto-naming of spots based on rules.
2 parents 401c767 + ed3699c commit f537640

10 files changed

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‎src/main/java/fiji/plugin/trackmate/action/autonaming/AutoNamingAction.java‎

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/*-
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* #%L
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* Fiji distribution of ImageJ for the life sciences.
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* %%
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* Copyright (C) 2010 - 2022 Fiji developers.
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* %%
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* This program is free software: you can redistribute it and/or modify
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* it under the terms of the GNU General Public License as
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* published by the Free Software Foundation, either version 3 of the
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* License, or (at your option) any later version.
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*
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* This program is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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*
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* You should have received a copy of the GNU General Public
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* License along with this program. If not, see
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* <http://www.gnu.org/licenses/gpl-3.0.html>.
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* #L%
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*/
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package fiji.plugin.trackmate.action.autonaming;
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import javax.swing.ImageIcon;
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import org.scijava.plugin.Plugin;
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import fiji.plugin.trackmate.SelectionModel;
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import fiji.plugin.trackmate.TrackMate;
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import fiji.plugin.trackmate.action.AbstractTMAction;
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import fiji.plugin.trackmate.action.TrackMateAction;
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import fiji.plugin.trackmate.action.TrackMateActionFactory;
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import fiji.plugin.trackmate.gui.Icons;
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import fiji.plugin.trackmate.gui.displaysettings.DisplaySettings;
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public class AutoNamingAction extends AbstractTMAction
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{
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public static final String INFO_TEXT = "<html>"
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+ "Rename individual spots based on auto-naming rules. "
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+ "All spot names are changed. There is no undo.</html>";
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@Override
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public void execute( final TrackMate trackmate, final SelectionModel selectionModel, final DisplaySettings displaySettings, final java.awt.Frame parent )
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{
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final AutoNamingController controller = new AutoNamingController( trackmate, logger );
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controller.show();
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}
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@Plugin( type = TrackMateActionFactory.class )
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public static class Factory implements TrackMateActionFactory
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{
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public static final String NAME = "Spot auto-naming";
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public static final String KEY = "AUTO_NAMING";
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@Override
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public String getInfoText()
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{
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return INFO_TEXT;
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}
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@Override
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public String getKey()
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{
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return KEY;
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}
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@Override
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public TrackMateAction create()
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{
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return new AutoNamingAction();
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}
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@Override
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public ImageIcon getIcon()
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{
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return Icons.PENCIL_ICON;
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}
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@Override
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public String getName()
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{
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return NAME;
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}
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}
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}

‎src/main/java/fiji/plugin/trackmate/action/autonaming/AutoNamingController.java‎

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/*-
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* #%L
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* Fiji distribution of ImageJ for the life sciences.
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* %%
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* Copyright (C) 2010 - 2022 Fiji developers.
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* %%
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* This program is free software: you can redistribute it and/or modify
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* it under the terms of the GNU General Public License as
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* published by the Free Software Foundation, either version 3 of the
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* License, or (at your option) any later version.
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*
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* This program is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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*
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* You should have received a copy of the GNU General Public
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* License along with this program. If not, see
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* <http://www.gnu.org/licenses/gpl-3.0.html>.
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* #L%
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*/
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package fiji.plugin.trackmate.action.autonaming;
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import java.util.ArrayList;
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import java.util.Collection;
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import javax.swing.JFrame;
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import javax.swing.JLabel;
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import fiji.plugin.trackmate.Logger;
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import fiji.plugin.trackmate.TrackMate;
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import fiji.plugin.trackmate.gui.GuiUtils;
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import fiji.plugin.trackmate.gui.Icons;
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import fiji.plugin.trackmate.util.EverythingDisablerAndReenabler;
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public class AutoNamingController
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{
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private final TrackMate trackmate;
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private final AutoNamingPanel gui;
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private final Logger logger;
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public AutoNamingController( final TrackMate trackmate, final Logger logger )
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{
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this.trackmate = trackmate;
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this.logger = logger;
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final Collection< AutoNamingRule > namingRules = new ArrayList<>( 3 );
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namingRules.add( new CopyTrackNameNamingRule() );
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namingRules.add( new DefaultAutoNamingRule( ".", "", false ) );
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namingRules.add( new DefaultAutoNamingRule( ".", "", true ) );
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this.gui = new AutoNamingPanel( namingRules );
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gui.btnRun.addActionListener( e -> run( ( ( AutoNamingRule ) gui.cmbboxRule.getSelectedItem() ) ) );
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}
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private void run( final AutoNamingRule autoNaming )
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{
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final EverythingDisablerAndReenabler disabler = new EverythingDisablerAndReenabler( gui, new Class[] { JLabel.class } );
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disabler.disable();
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new Thread( "TrackMateAutoNamingThread" )
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{
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@Override
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public void run()
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{
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try
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{
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logger.log( "Applying nameing rule: " + autoNaming.toString() + ".\n" );
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logger.setStatus( "Spot auto-naming" );
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AutoNamingPerformer.autoNameSpots( trackmate.getModel(), autoNaming );
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trackmate.getModel().notifyFeaturesComputed();
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logger.log( "Spot auto-naming done.\n" );
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}
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finally
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{
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disabler.reenable();
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}
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}
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}.start();
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}
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public void show()
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{
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if ( gui.getParent() != null && gui.getParent().isVisible() )
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return;
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final JFrame frame = new JFrame( "Spot auto-naming" );
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frame.setIconImage( Icons.TRACK_SCHEME_ICON.getImage() );
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frame.setSize( 500, 400 );
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frame.getContentPane().add( gui );
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GuiUtils.positionWindow( frame, trackmate.getSettings().imp.getCanvas() );
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frame.setVisible( true );
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}
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}

‎src/main/java/fiji/plugin/trackmate/action/autonaming/AutoNamingPanel.java‎

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package fiji.plugin.trackmate.action.autonaming;
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import java.awt.GridBagConstraints;
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import java.awt.GridBagLayout;
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import java.awt.Insets;
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import java.util.Collection;
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import java.util.Vector;
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import javax.swing.BorderFactory;
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import javax.swing.JButton;
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import javax.swing.JComboBox;
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import javax.swing.JLabel;
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import javax.swing.JPanel;
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import javax.swing.SwingConstants;
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import fiji.plugin.trackmate.gui.Fonts;
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public class AutoNamingPanel extends JPanel
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{
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private static final long serialVersionUID = 1L;
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final JComboBox< AutoNamingRule > cmbboxRule;
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final JButton btnRun;
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public AutoNamingPanel( final Collection< AutoNamingRule > namingRules )
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{
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setBorder( BorderFactory.createEmptyBorder( 5, 5, 5, 5 ) );
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final GridBagLayout gridBagLayout = new GridBagLayout();
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gridBagLayout.columnWidths = new int[] { 0, 0, 0 };
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gridBagLayout.rowHeights = new int[] { 0, 0, 0, 0, 0, 0 };
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gridBagLayout.columnWeights = new double[] { 1.0, 1.0, Double.MIN_VALUE };
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gridBagLayout.rowWeights = new double[] { 0.0, 1.0, 0.0, 1.0, 0.0, Double.MIN_VALUE };
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setLayout( gridBagLayout );
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final JLabel lblTitle = new JLabel( "Auto naming spots" );
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lblTitle.setFont( Fonts.BIG_FONT );
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lblTitle.setHorizontalAlignment( SwingConstants.CENTER );
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final GridBagConstraints gbcLblTitle = new GridBagConstraints();
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gbcLblTitle.gridwidth = 2;
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gbcLblTitle.insets = new Insets( 0, 0, 5, 0 );
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gbcLblTitle.fill = GridBagConstraints.HORIZONTAL;
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gbcLblTitle.gridx = 0;
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gbcLblTitle.gridy = 0;
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add( lblTitle, gbcLblTitle );
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final JLabel lblDoc = new JLabel( AutoNamingAction.INFO_TEXT );
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lblDoc.setFont( Fonts.SMALL_FONT );
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final GridBagConstraints gbcLblDoc = new GridBagConstraints();
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gbcLblDoc.gridwidth = 2;
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gbcLblDoc.insets = new Insets( 0, 0, 5, 0 );
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gbcLblDoc.fill = GridBagConstraints.BOTH;
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gbcLblDoc.gridx = 0;
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gbcLblDoc.gridy = 1;
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add( lblDoc, gbcLblDoc );
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final JLabel lblRule = new JLabel( "Naming rule" );
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lblRule.setFont( Fonts.SMALL_FONT );
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final GridBagConstraints gbcLblRule = new GridBagConstraints();
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gbcLblRule.anchor = GridBagConstraints.EAST;
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gbcLblRule.insets = new Insets( 0, 0, 5, 5 );
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gbcLblRule.gridx = 0;
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gbcLblRule.gridy = 2;
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add( lblRule, gbcLblRule );
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cmbboxRule = new JComboBox<>( new Vector<>( namingRules ) );
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cmbboxRule.setFont( Fonts.SMALL_FONT );
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final GridBagConstraints gbcCmbboxRule = new GridBagConstraints();
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gbcCmbboxRule.insets = new Insets( 0, 0, 5, 0 );
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gbcCmbboxRule.fill = GridBagConstraints.HORIZONTAL;
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gbcCmbboxRule.gridx = 1;
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gbcCmbboxRule.gridy = 2;
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add( cmbboxRule, gbcCmbboxRule );
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final JLabel lblRuleInfo = new JLabel();
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lblRuleInfo.setFont( Fonts.SMALL_FONT );
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final GridBagConstraints gbcLblRuleInfo = new GridBagConstraints();
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gbcLblRuleInfo.fill = GridBagConstraints.BOTH;
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gbcLblRuleInfo.insets = new Insets( 0, 0, 5, 0 );
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gbcLblRuleInfo.gridwidth = 2;
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gbcLblRuleInfo.gridx = 0;
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gbcLblRuleInfo.gridy = 3;
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add( lblRuleInfo, gbcLblRuleInfo );
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btnRun = new JButton( "Run" );
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final GridBagConstraints gbcBtnRun = new GridBagConstraints();
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gbcBtnRun.anchor = GridBagConstraints.EAST;
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gbcBtnRun.gridx = 1;
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gbcBtnRun.gridy = 4;
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add( btnRun, gbcBtnRun );
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/*
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* Listeners.
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*/
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cmbboxRule.addActionListener( e -> lblRuleInfo.setText( ( ( AutoNamingRule ) cmbboxRule.getSelectedItem() ).getInfoText() ) );
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cmbboxRule.setSelectedIndex( 0 );
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}
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}

‎src/main/java/fiji/plugin/trackmate/action/autonaming/AutoNamingPerformer.java‎

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package fiji.plugin.trackmate.action.autonaming;
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import java.util.ArrayList;
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import java.util.Collection;
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import java.util.List;
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import java.util.Set;
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import java.util.stream.Collectors;
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import org.jgrapht.Graphs;
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import org.jgrapht.graph.DefaultEdge;
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import org.jgrapht.graph.SimpleDirectedGraph;
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import org.jgrapht.traverse.DepthFirstIterator;
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import fiji.plugin.trackmate.Model;
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import fiji.plugin.trackmate.Spot;
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import fiji.plugin.trackmate.TrackModel;
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import fiji.plugin.trackmate.graph.ConvexBranchesDecomposition;
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import fiji.plugin.trackmate.graph.ConvexBranchesDecomposition.TrackBranchDecomposition;
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import fiji.plugin.trackmate.graph.TimeDirectedNeighborIndex;
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public class AutoNamingPerformer
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{
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public static void autoNameSpots( final Model model, final AutoNamingRule rule )
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{
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final TimeDirectedNeighborIndex neighborIndex = model.getTrackModel().getDirectedNeighborIndex();
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for ( final Integer trackID : model.getTrackModel().unsortedTrackIDs( true ) )
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{
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final TrackBranchDecomposition branchDecomposition = ConvexBranchesDecomposition.processTrack( trackID, model.getTrackModel(), neighborIndex, true, false );
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final SimpleDirectedGraph< List< Spot >, DefaultEdge > branchGraph = ConvexBranchesDecomposition.buildBranchGraph( branchDecomposition );
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processTrack( rule, model.getTrackModel(), branchGraph );
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}
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}
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private static void processTrack(
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final AutoNamingRule rule,
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final TrackModel model,
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final SimpleDirectedGraph< List< Spot >, DefaultEdge > graph )
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{
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// Find the roots. Might be several.
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final List< List< Spot > > roots = graph.vertexSet().stream()
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.filter( key -> graph.incomingEdgesOf( key ).size() == 0 )
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.collect( Collectors.toList() );
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for ( final List< Spot > root : roots )
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{
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// Name the spots in the root branch.
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final Spot first = root.get( 0 );
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rule.nameRoot( first, model );
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// Other spots in the root branch.
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Spot predecessor = first;
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for ( int i = 1; i < root.size(); i++ )
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{
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final Spot current = root.get( i );
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rule.nameSpot( current, predecessor );
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predecessor = current;
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}
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// Iterate through branch, settings the name of children.
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final DepthFirstIterator< List< Spot >, DefaultEdge > it = new DepthFirstIterator<>( graph, root );
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while ( it.hasNext() )
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{
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final List< Spot > currentBranch = it.next();
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// Collect children branches.
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final List< List< Spot > > childrenBranches = new ArrayList<>();
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final Set< DefaultEdge > edges = graph.outgoingEdgesOf( currentBranch );
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for ( final DefaultEdge edge : edges )
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{
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final List< Spot > cb = Graphs.getOppositeVertex( graph, edge, currentBranch );
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childrenBranches.add( cb );
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}
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// Build siblings spots (first one of the children branch.
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final Collection< Spot > siblings = new ArrayList<>( childrenBranches.size() );
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for ( final List< Spot > cb : childrenBranches )
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siblings.add( cb.get( 0 ) );
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// Collect mother spot (last one of current branch).
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final Spot mother = currentBranch.get( currentBranch.size() - 1 );
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// Name the branch first spots.
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rule.nameBranches( mother, siblings );
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// Name the spots inside each branch.
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for ( final List< Spot > cb : childrenBranches )
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{
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Spot parent = cb.get( 0 );
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for ( int i = 1; i < cb.size(); i++ )
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{
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final Spot current = cb.get( i );
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rule.nameSpot( current, parent );
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parent = current;
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}
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}
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}
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}
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}
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}

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