Mamut export and TrackMate import redux.

src/main/java/org/mastodon/revised/mamut/MainWindow.java

@@ -127,10 +127,22 @@ public MainWindow( final WindowManager windowManager )
 		button_gbc_left.gridy = gridy;
 		buttonsPanel.add( createProjectButton, button_gbc_left );
 
-		final JButton importButton = new JButton( actionMap.get( ProjectManager.IMPORT_TGMM ) );
-		importButton.setText( "import tgmm" );
+		final JButton importTgmmButton = new JButton( actionMap.get( ProjectManager.IMPORT_TGMM ) );
+		importTgmmButton.setText( "import tgmm" );
 		button_gbc_right.gridy = gridy;
-		buttonsPanel.add( importButton, button_gbc_right );
+		buttonsPanel.add( importTgmmButton, button_gbc_right );
+
+		++gridy;
+
+		final JButton importMamutButton = new JButton( actionMap.get( ProjectManager.IMPORT_MAMUT ) );
+		importMamutButton.setText( "import mamut" );
+		button_gbc_left.gridy = gridy;
+		buttonsPanel.add( importMamutButton, button_gbc_left );
+
+		final JButton exportMamutButton = new JButton( actionMap.get( ProjectManager.EXPORT_MAMUT ) );
+		exportMamutButton.setText( "export mamut" );
+		button_gbc_right.gridy = gridy;
+		buttonsPanel.add( exportMamutButton, button_gbc_right );
 
 		++gridy;
 
@@ -178,6 +190,8 @@ public static void addMenus( final ViewMenu menu, final ActionMap actionMap )
 						item( ProjectManager.SAVE_PROJECT ),
 						separator(),
 						item( ProjectManager.IMPORT_TGMM ),
+						item( ProjectManager.IMPORT_MAMUT ),
+						item( ProjectManager.EXPORT_MAMUT ),
 						separator(),
 						item( WindowManager.PREFERENCES_DIALOG )
 				),

src/main/java/org/mastodon/revised/mamut/MamutMenuBuilder.java

@@ -24,6 +24,8 @@ public class MamutMenuBuilder extends ViewMenuBuilder
 		menuTexts.put( ProjectManager.LOAD_PROJECT, "Load Project" );
 		menuTexts.put( ProjectManager.SAVE_PROJECT, "Save Project" );
 		menuTexts.put( ProjectManager.IMPORT_TGMM, "Import TGMM tracks" );
+		menuTexts.put( ProjectManager.IMPORT_MAMUT, "Import MaMuT project" );
+		menuTexts.put( ProjectManager.EXPORT_MAMUT, "Export MaMuT project" );
 
 		menuTexts.put( WindowManager.NEW_BDV_VIEW, "New Bdv" );
 		menuTexts.put( WindowManager.NEW_TRACKSCHEME_VIEW, "New Trackscheme" );

src/main/java/org/mastodon/revised/mamut/ProjectManager.java

@@ -13,6 +13,8 @@
 import org.mastodon.revised.bdv.overlay.ui.RenderSettingsManager;
 import org.mastodon.revised.mamut.feature.MamutFeatureComputerService;
 import org.mastodon.revised.model.mamut.Model;
+import org.mastodon.revised.model.mamut.trackmate.MamutExporter;
+import org.mastodon.revised.model.mamut.trackmate.TrackMateImporter;
 import org.mastodon.revised.model.tag.TagSetStructure;
 import org.mastodon.revised.trackscheme.display.style.TrackSchemeStyleManager;
 import org.mastodon.revised.ui.keymap.KeymapManager;
@@ -37,11 +39,15 @@ public class ProjectManager
 	public static final String LOAD_PROJECT = "load project";
 	public static final String SAVE_PROJECT = "save project";
 	public static final String IMPORT_TGMM = "import tgmm";
+	public static final String IMPORT_MAMUT = "import mamut";
+	public static final String EXPORT_MAMUT = "export mamut";
 
 	static final String[] CREATE_PROJECT_KEYS = new String[] { "not mapped" };
 	static final String[] LOAD_PROJECT_KEYS = new String[] { "not mapped" };
 	static final String[] SAVE_PROJECT_KEYS = new String[] { "not mapped" };
 	static final String[] IMPORT_TGMM_KEYS = new String[] { "not mapped" };
+	static final String[] IMPORT_MAMUT_KEYS = new String[] { "not mapped" };
+	static final String[] EXPORT_MAMUT_KEYS = new String[] { "not mapped" };
 
 	private final WindowManager windowManager;
 
@@ -59,6 +65,10 @@ public class ProjectManager
 
 	private final AbstractNamedAction importTgmmAction;
 
+	private final AbstractNamedAction importMamutAction;
+
+	private final AbstractNamedAction exportMamutAction;
+
 	public ProjectManager( final WindowManager windowManager )
 	{
 		this.windowManager = windowManager;
@@ -69,6 +79,8 @@ public ProjectManager( final WindowManager windowManager )
 		loadProjectAction = new RunnableAction( LOAD_PROJECT, this::loadProject );
 		saveProjectAction = new RunnableAction( SAVE_PROJECT, this::saveProject );
 		importTgmmAction = new RunnableAction( IMPORT_TGMM, this::importTgmm );
+		importMamutAction = new RunnableAction( IMPORT_MAMUT, this::importMamut );
+		exportMamutAction = new RunnableAction( EXPORT_MAMUT, this::exportMamut );
 
 		updateEnabledActions();
 	}
@@ -78,6 +90,7 @@ private void updateEnabledActions()
 		final boolean projectOpen = ( project != null );
 		saveProjectAction.setEnabled( projectOpen );
 		importTgmmAction.setEnabled( projectOpen );
+		exportMamutAction.setEnabled( projectOpen );
 	}
 
 	/**
@@ -93,6 +106,8 @@ public void install( final Actions actions )
 		actions.namedAction( loadProjectAction, LOAD_PROJECT_KEYS );
 		actions.namedAction( saveProjectAction, SAVE_PROJECT_KEYS );
 		actions.namedAction( importTgmmAction, IMPORT_TGMM_KEYS );
+		actions.namedAction( importMamutAction, IMPORT_MAMUT_KEYS );
+		actions.namedAction( exportMamutAction, EXPORT_MAMUT_KEYS );
 	}
 
 	public synchronized void createProject()
@@ -176,11 +191,26 @@ public synchronized void saveProject()
 		}
 	}
 
+	public synchronized void saveProject( final File projectFolder ) throws IOException
+	{
+		if ( project == null )
+			return;
+
+		project.setProjectFolder( projectFolder );
+		new MamutProjectIO().save( project );
+
+		final Model model = windowManager.getAppModel().getModel();
+		model.saveRaw( project );
+
+		updateEnabledActions();
+	}
+
 	/**
 	 * Open a project. If {@code project.getProjectFolder() == null} this is a new project and data structures are initialized as empty.
 	 * The image data {@code project.getDatasetXmlFile()} must always be set.
 	 *
 	 * @param project
+	 *
 	 * @throws IOException
 	 * @throws SpimDataException
 	 */
@@ -257,29 +287,83 @@ public synchronized void open( final MamutProject project ) throws IOException,
 		updateEnabledActions();
 	}
 
-	public synchronized void saveProject( final File projectFolder ) throws IOException
+	public synchronized void importTgmm()
 	{
 		if ( project == null )
 			return;
 
-		project.setProjectFolder( projectFolder );
-		new MamutProjectIO().save( project );
+		final MamutAppModel appModel = windowManager.getAppModel();
+		tgmmImportDialog.showImportDialog( appModel.getSharedBdvData().getSpimData(), appModel.getModel() );
 
-		final Model model = windowManager.getAppModel().getModel();
-		model.saveRaw( project );
+		updateEnabledActions();
+	}
+
+	public synchronized void importMamut()
+	{
+		final Component parent = null; // TODO
+		final File file = FileChooser.chooseFile(
+				parent,
+				null,
+				new XmlFileFilter(),
+				"Import MaMuT Project",
+				FileChooser.DialogType.LOAD );
+		if ( file == null )
+			return;
+
+		try
+		{
+			final TrackMateImporter importer = new TrackMateImporter( file );
+			open( importer.createProject() );
+			importer.readModel( windowManager.getAppModel().getModel() );
+		}
+		catch ( final IOException | SpimDataException e )
+		{
+			e.printStackTrace();
+		}
 
 		updateEnabledActions();
 	}
 
-	public void importTgmm()
+	public synchronized void exportMamut()
 	{
 		if ( project == null )
 			return;
 
-		final MamutAppModel appModel = windowManager.getAppModel();
-		tgmmImportDialog.showImportDialog( appModel.getSharedBdvData().getSpimData(), appModel.getModel() );
+		final String filename = getProprosedMamutExportFileName( project );
 
-		updateEnabledActions();
+		final Component parent = null; // TODO
+		final File file = FileChooser.chooseFile(
+				parent,
+				filename,
+				new XmlFileFilter(),
+				"Export As MaMuT Project",
+				FileChooser.DialogType.SAVE );
+		if ( file == null )
+			return;
+
+		try
+		{
+			MamutExporter.export( file, windowManager.getAppModel().getModel(), project );
+		}
+		catch ( final IOException e )
+		{
+			e.printStackTrace();
+		}
+	}
+
+	private static String getProprosedMamutExportFileName( final MamutProject project )
+	{
+		final File pf = project.getProjectFolder();
+		if ( pf != null )
+		{
+			return new File( pf.getParentFile(), pf.getName() + "_mamut.xml" ).getAbsolutePath();
+		}
+		else
+		{
+			final File f = project.getDatasetXmlFile();
+			final String fn = f.getName();
+			return new File( f.getParentFile(), fn.substring( 0, fn.length() - ".xml".length() ) + "_mamut.xml" ).getAbsolutePath();
+		}
 	}
 
 	private static String getProposedProjectFolder( final MamutProject project )

src/main/java/org/mastodon/revised/model/mamut/ModelUtils.java

@@ -0,0 +1,144 @@
+package org.mastodon.revised.model.mamut;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.mastodon.revised.model.feature.Feature;
+import org.mastodon.revised.model.feature.FeatureModel;
+import org.mastodon.revised.model.feature.FeatureProjection;
+
+public class ModelUtils
+{
+
+	public static final String dump( final Model model )
+	{
+		final ModelGraph graph = model.getGraph();
+		final FeatureModel featureModel = model.getFeatureModel();
+
+		final StringBuilder str = new StringBuilder();
+		str.append( "Model " + model.toString() + "\n" );
+
+		/*
+		 * Collect spot feature headers.
+		 */
+
+		final Map< String, FeatureProjection< Spot > > sfs = new LinkedHashMap<>();
+		final Set< Feature< ?, ? > > set1 = featureModel.getFeatureSet( Spot.class );
+		final List< Feature< ?, ? > > spotFeatures = set1 == null ? new ArrayList<>() : new ArrayList<>( set1 );
+		spotFeatures.sort( ( f1, f2 ) -> f1.getKey().compareTo( f2.getKey() ) );
+		for ( final Feature< ?, ? > feature : spotFeatures )
+		{
+			@SuppressWarnings( "unchecked" )
+			final Feature< Spot, ? > sf = ( Feature< Spot, ? > ) feature;
+			final Map< String, FeatureProjection< Spot > > projections = sf.getProjections();
+			sfs.putAll( projections );
+		}
+
+		/*
+		 * Loop over all spots.
+		 */
+
+		str.append( "Spots:\n" );
+		final String h1a = String.format( "%9s  %9s  %6s  %9s  %9s  %9s",
+				"Id", "Label", "Frame", "X", "Y", "Z" );
+		str.append( h1a );
+
+		final int[] spotColumnHeaderWidth = new int[ sfs.size() ];
+		int i = 0;
+		for ( final String pn : sfs.keySet() )
+		{
+			spotColumnHeaderWidth[ i ] = pn.length() + 2;
+			str.append( String.format( "  %" + spotColumnHeaderWidth[ i ] + "s", pn ) );
+			i++;
+		}
+
+		str.append( '\n' );
+		final char[] sline = new char[ h1a.length() + Arrays.stream( spotColumnHeaderWidth ).sum() + 2 * spotColumnHeaderWidth.length ];
+		Arrays.fill( sline, '-' );
+		str.append( sline );
+		str.append( '\n' );
+
+		for ( final Spot spot : graph.vertices() )
+		{
+			final String h1b = String.format( "%9d  %9s  %6d  %9.1f  %9.1f  %9.1f",
+					spot.getInternalPoolIndex(), spot.getLabel(), spot.getTimepoint(),
+					spot.getDoublePosition( 0 ), spot.getDoublePosition( 1 ), spot.getDoublePosition( 2 ) );
+
+			str.append( h1b );
+			i = 0;
+			for ( final String pn : sfs.keySet() )
+			{
+				if ( sfs.get( pn ).isSet( spot ) )
+					str.append( String.format( "  %" + spotColumnHeaderWidth[ i ] + ".1f", sfs.get( pn ).value( spot ) ) );
+				else
+					str.append( String.format( "  %" + spotColumnHeaderWidth[ i ] + "s", "unset" ) );
+				i++;
+			}
+			str.append( '\n' );
+		}
+
+		/*
+		 * Collect link feature headers.
+		 */
+
+		final Map< String, FeatureProjection< Link > > lfs = new LinkedHashMap<>();
+		final Set< Feature< ?, ? > > set2 = featureModel.getFeatureSet( Link.class );
+		final List< Feature< ?, ? > > linkFeatures = set2 == null ? new ArrayList<>() : new ArrayList<>( set2 );
+		linkFeatures.sort( ( f1, f2 ) -> f1.getKey().compareTo( f2.getKey() ) );
+		for ( final Feature< ?, ? > feature : linkFeatures )
+		{
+			@SuppressWarnings( "unchecked" )
+			final Feature< Link, ? > lf = ( Feature< Link, ? > ) feature;
+			final Map< String, FeatureProjection< Link > > projections = lf.getProjections();
+			lfs.putAll( projections );
+		}
+
+		/*
+		 * Loop over all links.
+		 */
+
+		str.append( "Links:\n" );
+		final String h2a = String.format( "%9s  %9s  %9s", "Id", "Source Id", "Target Id" );
+		str.append( h2a );
+
+		final int[] linkColumnHeaderWidth = new int[ lfs.size() ];
+		i = 0;
+		for ( final String pn : lfs.keySet() )
+		{
+			linkColumnHeaderWidth[ i ] = pn.length() + 2;
+			str.append( String.format( "  %" + linkColumnHeaderWidth[ i ] + "s", pn ) );
+			i++;
+		}
+
+		str.append( '\n' );
+		final char[] lline = new char[ h2a.length() + Arrays.stream( linkColumnHeaderWidth ).sum() + 2 * linkColumnHeaderWidth.length ];
+		Arrays.fill( lline, '-' );
+		str.append( lline );
+		str.append( '\n' );
+
+		final Spot ref = graph.vertexRef();
+		for ( final Link link : graph.edges() )
+		{
+			final String h1b = String.format( "%9d  %9d  %9d", link.getInternalPoolIndex(),
+					link.getSource( ref ).getInternalPoolIndex(), link.getTarget( ref ).getInternalPoolIndex() );
+			str.append( h1b );
+			i = 0;
+			for ( final String pn : lfs.keySet() )
+			{
+				if ( lfs.get( pn ).isSet( link ) )
+					str.append( String.format( "  %" + linkColumnHeaderWidth[ i ] + ".1f", lfs.get( pn ).value( link ) ) );
+				else
+					str.append( String.format( "  %" + linkColumnHeaderWidth[ i ] + "s", "unset" ) );
+				i++;
+			}
+			str.append( '\n' );
+		}
+
+		return str.toString();
+	}
+
+}