Collaboration Tools

pom.xml

@@ -46,6 +46,22 @@
 			<artifactId>mpicbg</artifactId>
 		</dependency>
 
+		<dependency>
+			<groupId>org.eclipse.jgit</groupId>
+			<artifactId>org.eclipse.jgit</artifactId>
+			<version>5.13.2.202306221912-r</version>
+		</dependency>
+		<!-- SSH support for JGit based on Apache MINA sshd - not sure if this is needed -->
+		<dependency>
+			<groupId>org.eclipse.jgit</groupId>
+			<artifactId>org.eclipse.jgit.ssh.apache</artifactId>
+			<version>5.13.2.202306221912-r</version>
+		</dependency>
+		<dependency>
+			<groupId>org.eclipse.jgit</groupId>
+			<artifactId>org.eclipse.jgit.ui</artifactId>
+			<version>5.13.2.202306221912-r</version>
+		</dependency>
 		<!-- Test dependencies -->
 		<dependency>
 			<groupId>junit</groupId>

src/main/java/org/mastodon/mamut/tomancak/collaboration/CommitMessageDialog.java

@@ -0,0 +1,60 @@
+package org.mastodon.mamut.tomancak.collaboration;
+
+import java.awt.KeyboardFocusManager;
+
+import javax.swing.JDialog;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
+
+import net.miginfocom.swing.MigLayout;
+
+/**
+ * A dialog that asks the user to enter a commit message.
+ * The dialog can be closed by using the mouse to clock OK or Cancel,
+ * by pressing CTRL-ENTER or ESCAPE, or by pressing TAB and ENTER.
+ */
+public class CommitMessageDialog
+{
+
+	/**
+	 * Show a dialog that asks the user to enter a commit message.
+	 *
+	 * @return The commit message as a String, or null if the dialog was cancelled.
+	 */
+	public static String showDialog()
+	{
+		JTextArea textArea = new JTextArea( 5, 40 );
+
+		// Make the tab key move focus to the next component and shift-tab to the previous.
+		textArea.setFocusTraversalKeys( KeyboardFocusManager.FORWARD_TRAVERSAL_KEYS, null );
+		textArea.setFocusTraversalKeys( KeyboardFocusManager.BACKWARD_TRAVERSAL_KEYS, null );
+
+		JPanel panel = new JPanel();
+		panel.setLayout( new MigLayout( "insets dialog" ) );
+		panel.add( new JLabel( "Save point message:" ), "wrap" );
+		panel.add( new JScrollPane( textArea ), "wrap" );
+		panel.add( new JLabel( "Please describe briefly the changes since the last save point!" ) );
+
+		// Show a JOptionPane, where the TextArea has focus when the dialog is shown.
+		JOptionPane optionPane = new JOptionPane( panel, JOptionPane.PLAIN_MESSAGE, JOptionPane.OK_CANCEL_OPTION )
+		{
+			@Override
+			public void selectInitialValue()
+			{
+				super.selectInitialValue();
+				textArea.requestFocusInWindow();
+			}
+		};
+		JDialog dialog = optionPane.createDialog( "Add Save Point (commit)" );
+		dialog.setVisible( true );
+		dialog.dispose();
+		Object result = optionPane.getValue();
+		if ( result instanceof Integer && ( int ) result == JOptionPane.OK_OPTION )
+			return textArea.getText();
+		else
+			return null;
+	}
+}

src/main/java/org/mastodon/mamut/tomancak/collaboration/ErrorDialog.java

@@ -0,0 +1,71 @@
+package org.mastodon.mamut.tomancak.collaboration;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Frame;
+import java.awt.event.ItemEvent;
+
+import javax.swing.JCheckBox;
+import javax.swing.JDialog;
+import javax.swing.JOptionPane;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
+import javax.swing.SwingUtilities;
+
+import org.apache.commons.lang3.exception.ExceptionUtils;
+
+/**
+ * A dialog that shows an exception message and stack trace.
+ * The stack trace is hidden by default and can be shown by
+ * clicking on "details".
+ */
+public class ErrorDialog
+{
+
+	public static void showErrorMessage( String title, Exception exception )
+	{
+		SwingUtilities.invokeLater( () -> showDialog( null, title + " (Error)", exception ) );
+	}
+
+	private static void showDialog( Frame parent, String title, Exception exception )
+	{
+		String message = "\nThere was a problem:\n\n  " + exception.getMessage() + "\n\n";
+		final JScrollPane scrollPane = initScrollPane( exception );
+		final JCheckBox checkBox = new JCheckBox( "show details" );
+		checkBox.setForeground( Color.BLUE );
+		Object[] objects = { message, checkBox, scrollPane };
+		JOptionPane pane = new JOptionPane( objects, JOptionPane.ERROR_MESSAGE );
+		JDialog dialog = pane.createDialog( parent, title );
+		dialog.setResizable( true );
+		checkBox.addItemListener( event -> {
+			boolean visible = event.getStateChange() == ItemEvent.SELECTED;
+			scrollPane.setVisible( visible );
+			scrollPane.setPreferredSize( visible ? null : new Dimension( 0, 0 ) );
+			dialog.pack();
+		} );
+		dialog.setModal( true );
+		dialog.pack();
+		dialog.setVisible( true );
+		dialog.dispose();
+	}
+
+	private static JScrollPane initScrollPane( Exception exception )
+	{
+		String stackTrace = ExceptionUtils.getStackTrace( exception );
+		int lines = Math.min( 20, countLines( stackTrace ) );
+		JTextArea textArea = new JTextArea( stackTrace, lines, 70 );
+		textArea.setForeground( new Color( 0x880000 ) );
+		textArea.setEditable( false );
+		textArea.setFont( new Font( Font.MONOSPACED, Font.PLAIN, textArea.getFont().getSize() ) );
+		final JScrollPane scrollPane = new JScrollPane( textArea );
+		scrollPane.setVisible( false );
+		return scrollPane;
+	}
+
+	private static int countLines( String str )
+	{
+		String[] lines = str.split( "\r\n|\r|\n" );
+		return lines.length;
+	}
+}

src/main/java/org/mastodon/mamut/tomancak/collaboration/FixGraphInconsistenciesPlugin.java

@@ -0,0 +1,144 @@
+package org.mastodon.mamut.tomancak.collaboration;
+
+import org.mastodon.collection.RefCollection;
+import org.mastodon.collection.RefCollections;
+import org.mastodon.collection.RefList;
+import org.mastodon.collection.RefSet;
+import org.mastodon.collection.ref.RefArrayList;
+import org.mastodon.collection.ref.RefSetImp;
+import org.mastodon.mamut.model.Link;
+import org.mastodon.mamut.model.Model;
+import org.mastodon.mamut.model.ModelGraph;
+import org.mastodon.mamut.model.Spot;
+import org.mastodon.mamut.plugin.MamutPlugin;
+import org.mastodon.mamut.tomancak.collaboration.utils.ActionDescriptions;
+import org.mastodon.mamut.tomancak.collaboration.utils.BasicDescriptionProvider;
+import org.mastodon.mamut.tomancak.collaboration.utils.BasicMamutPlugin;
+import org.mastodon.ui.keymap.CommandDescriptionProvider;
+import org.mastodon.ui.keymap.KeyConfigContexts;
+import org.scijava.plugin.Plugin;
+
+@Plugin( type = MamutPlugin.class )
+public class FixGraphInconsistenciesPlugin extends BasicMamutPlugin
+{
+
+	private static final ActionDescriptions< FixGraphInconsistenciesPlugin > actionDescriptions = new ActionDescriptions<>( FixGraphInconsistenciesPlugin.class );
+
+	static
+	{
+		actionDescriptions.addActionDescription(
+				"[mastodon-tomancak] fix graph inconsistencies",
+				"Plugins > Trees Management > Fix Graph Inconsistencies",
+				"Flip reversed edges",
+				FixGraphInconsistenciesPlugin::fixGraphInconsistencies );
+	}
+
+	public < T > FixGraphInconsistenciesPlugin()
+	{
+		super( actionDescriptions );
+	}
+
+	private void fixGraphInconsistencies()
+	{
+		Model model = getAppModel().getModel();
+		ModelGraph graph = model.getGraph();
+		flipBackwardsEdges( graph );
+		removeDoubleEdges( graph );
+		removeSameTimepointEdge( graph );
+		printWarnings( graph );
+	}
+
+	private static void printWarnings( ModelGraph graph )
+	{
+		for ( Spot spot : graph.vertices() )
+		{
+			if ( spot.incomingEdges().size() > 1 )
+				System.out.println( "More than one parent: " + spot.getLabel() );
+
+			if ( spot.outgoingEdges().size() > 2 )
+				System.out.println( "More than two children: " + spot.getLabel() );
+		}
+	}
+
+	private static void removeSameTimepointEdge( ModelGraph graph )
+	{
+		RefCollection< Link > backwardEdge = RefCollections.createRefList( graph.edges() );
+		Spot sourceRef = graph.vertexRef();
+		Spot targetRef = graph.vertexRef();
+		for ( Link edge : graph.edges() )
+		{
+			Spot source = edge.getSource( sourceRef );
+			Spot target = edge.getTarget( targetRef );
+			if ( source.getTimepoint() == target.getTimepoint() )
+				backwardEdge.add( edge );
+		}
+		for ( Link edge : backwardEdge )
+		{
+			Spot source = edge.getSource( sourceRef );
+			Spot target = edge.getTarget( targetRef );
+			System.out.println( "Remove same timepoint edge " + source.getLabel() + " -> " + target.getLabel() );
+			graph.remove( edge );
+		}
+	}
+
+	private static void removeDoubleEdges( ModelGraph graph )
+	{
+		Spot ref1 = graph.vertexRef();
+		Spot ref2 = graph.vertexRef();
+		RefSet< Spot > sources = new RefSetImp<>( graph.vertices().getRefPool() );
+		RefList< Link > doubleEdge = new RefArrayList<>( graph.edges().getRefPool() );
+		for ( Spot spot : graph.vertices() )
+		{
+			if ( spot.incomingEdges().size() > 1 )
+			{
+				for ( Link link : spot.incomingEdges() )
+				{
+					Spot source = link.getSource( ref1 );
+					if ( sources.contains( source ) )
+						doubleEdge.add( link );
+					else
+						sources.add( source );
+				}
+				sources.clear();
+			}
+		}
+		for ( Link link : doubleEdge )
+		{
+			Spot source = link.getSource( ref1 );
+			Spot target = link.getTarget( ref2 );
+			System.out.println( "Remove duplicated edge: " + source.getLabel() + " -> " + target.getLabel() );
+			graph.remove( link );
+		}
+	}
+
+	private static void flipBackwardsEdges( ModelGraph graph )
+	{
+		RefCollection< Link > backwardEdge = RefCollections.createRefList( graph.edges() );
+		Spot sourceRef = graph.vertexRef();
+		Spot targetRef = graph.vertexRef();
+		for ( Link edge : graph.edges() )
+		{
+			Spot source = edge.getSource( sourceRef );
+			Spot target = edge.getTarget( targetRef );
+			if ( source.getTimepoint() > target.getTimepoint() )
+				backwardEdge.add( edge );
+		}
+		for ( Link edge : backwardEdge )
+		{
+			Spot source = edge.getSource( sourceRef );
+			Spot target = edge.getTarget( targetRef );
+			System.out.println( "Flip backwards edge " + source.getLabel() + " -> " + target.getLabel() );
+			graph.remove( edge );
+			graph.addEdge( source, target ).init();
+		}
+	}
+
+	@Plugin( type = CommandDescriptionProvider.class )
+	public static class DescriptionProvider extends BasicDescriptionProvider
+	{
+		public DescriptionProvider()
+		{
+			super( actionDescriptions, KeyConfigContexts.MASTODON, KeyConfigContexts.TRACKSCHEME );
+		}
+	}
+}