.
@@ -63,12 +63,25 @@ public class StartDialogDescriptor extends WizardPanelDescriptor
private static final String KEY = "Start";
+
+ public static final String PUB0_URL = "https://doi.org/10.1016/j.ymeth.2016.09.016";
+
+ public static final String PUB0_TXT = "Tinevez JY, Perry N. Schindelin J, et al. "
+ + "'TrackMate: An open and extensible platform for single-particle tracking', "
+ + "Methods (2017).";
+
public static final String PUB1_URL = "https://doi.org/10.1038/s41592-022-01507-1";
- public static final String PUB1_TXT = "Ershov, D., Phan, MS., Pylvänäinen, J.W., Rigaud S.U., et al. "
- + "TrackMate 7: integrating state-of-the-art segmentation algorithms into tracking pipelines. "
- + "Nat Methods (2022). https://doi.org/10.1038/s41592-022-01507-1";
-
+ public static final String PUB1_TXT = "Ershov D, Phan MS, Pylvänäinen JW, Rigaud SU, et al. "
+ + "'TrackMate 7: integrating state-of-the-art segmentation algorithms into tracking pipelines' "
+ + "Nature Methods (2022).";
+
+ public static final String PUB2_URL = "https://doi.org/10.1002/cpz1.70369";
+
+ public static final String PUB2_TXT = "Anselmet M, et al. "
+ + "'Automated optimization of bacterial tracking pipelines with trackmate 8' "
+ + "Current Protocols (2026).";
+
private final Settings settings;
private final Logger logger;
@@ -89,12 +102,14 @@ public void aboutToDisplayPanel()
logger.log( welcomeMessage, Logger.BLUE_COLOR );
logger.log( "Please note that TrackMate is available through Fiji, and is based on a publication. "
+ "If you use it successfully for your research please be so kind to cite our work:\n" );
+ logger.log( PUB2_TXT + "\n", Logger.GREEN_COLOR );
+ logger.log( PUB2_URL + "\n", Logger.BLUE_COLOR );
+ logger.log( "and / or:\n" );
logger.log( PUB1_TXT + "\n", Logger.GREEN_COLOR );
logger.log( PUB1_URL + "\n", Logger.BLUE_COLOR );
logger.log( "and / or:\n" );
- logger.log( "Tinevez, JY.; Perry, N. & Schindelin, J. et al. (2017), 'TrackMate: An open and extensible platform for single-particle tracking.', "
- + "Methods 115: 80-90, PMID 27713081.\n", Logger.GREEN_COLOR );
- logger.log( "https://www.sciencedirect.com/science/article/pii/S1046202316303346\n", Logger.BLUE_COLOR );
+ logger.log( PUB0_TXT + "\n", Logger.GREEN_COLOR );
+ logger.log( PUB0_URL + "\n", Logger.BLUE_COLOR );
logger.log( "\nNumerical feature analyzers:\n", Logger.BLUE_COLOR );
logger.log( settings.toStringFeatureAnalyzersInfo() );
diff --git a/src/main/java/fiji/plugin/trackmate/io/TmGeffWriter.java b/src/main/java/fiji/plugin/trackmate/io/TmGeffWriter.java
deleted file mode 100644
index 98fd0909a..000000000
--- a/src/main/java/fiji/plugin/trackmate/io/TmGeffWriter.java
+++ /dev/null
@@ -1,256 +0,0 @@
-package fiji.plugin.trackmate.io;
-
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import org.jgrapht.graph.DefaultWeightedEdge;
-import org.mastodon.geff.GeffAxis;
-import org.mastodon.geff.GeffEdge;
-import org.mastodon.geff.GeffMetadata;
-import org.mastodon.geff.GeffNode;
-import org.mastodon.geff.PropMetadata;
-
-import fiji.plugin.trackmate.Dimension;
-import fiji.plugin.trackmate.FeatureModel;
-import fiji.plugin.trackmate.Model;
-import fiji.plugin.trackmate.Spot;
-import fiji.plugin.trackmate.Spot.SpotVisitor;
-import fiji.plugin.trackmate.SpotBase;
-import fiji.plugin.trackmate.SpotCollection;
-import fiji.plugin.trackmate.SpotRoi;
-import fiji.plugin.trackmate.TrackModel;
-import gnu.trove.map.TObjectIntMap;
-import gnu.trove.map.hash.TObjectIntHashMap;
-
-public class TmGeffWriter
-{
-
- public static void write( final Model model, final String zarrPath ) throws IOException
- {
-
- /*
- * Serialize spots
- */
- final SpotCollection spots = model.getSpots();
- final Map< String, Boolean > isInt = model.getFeatureModel().getSpotFeatureIsInt();
- final GeffSpotVisitor visitor = new GeffSpotVisitor( isInt );
- spots.iterable( true ).forEach( spot -> spot.accept( visitor ) );
-
- /*
- * Serialize edges
- */
- final TrackModel trackModel = model.getTrackModel();
- final Set< DefaultWeightedEdge > edges = trackModel.edgeSet();
- final FeatureModel fm = model.getFeatureModel();
-
- final List< GeffEdge > geffEdges = new ArrayList<>();
- int edgeId = 0;
- for ( final DefaultWeightedEdge edge : edges )
- {
- final Spot source = trackModel.getEdgeSource( edge );
- final Integer srcId = visitor.spotToId.get( source );
- final Spot target = trackModel.getEdgeTarget( edge );
- final Integer tgtId = visitor.spotToId.get( target );
- if ( srcId == null || tgtId == null )
- continue;
-
- final boolean swap = source.getFeature( Spot.FRAME ) > target.getFeature( Spot.FRAME );
- final GeffEdge edgeNode = new GeffEdge.Builder()
- .setId( edgeId++ )
- .setSourceNodeId( swap ? tgtId : srcId )
- .setTargetNodeId( swap ? srcId : tgtId )
- .setScore( trackModel.getEdgeWeight( edge ) )
- .setDistance( Math.sqrt( source.squareDistanceTo( target ) ) )
- .build();
-
- // Feature
- for ( final String edgeFeature : fm.getEdgeFeatures() )
- {
- final Double ef = fm.getEdgeFeature( edge, edgeFeature );
- if ( ef == null )
- continue;
- final Object val = ( fm.getEdgeFeatureIsInt().get( edgeFeature )
- ? ef.intValue()
- : ef.doubleValue() );
- edgeNode.setProp( edgeFeature, val );
- }
- geffEdges.add( edgeNode );
- }
-
- /*
- * Serialize tracks
- */
- // TODO -> nodes with a specific path.
-
- /*
- * Metadata
- */
-
- // Axes
- final List< GeffAxis > axes = buildAxes( model.getTimeUnits(), model.getSpaceUnits() );
- final GeffMetadata metadata = new GeffMetadata( "1.0.0", true, axes );
-
- // Spot features
- final Map< String, PropMetadata > nodePropsMetadata = new HashMap<>();
- for ( final String spotFeature : fm.getSpotFeatures() )
- {
- final String dType = isInt.get( spotFeature ) ? "int32" : "float64";
- final Dimension dimension = fm.getSpotFeatureDimensions().get( spotFeature );
- final String unit = dimension.units( model.getSpaceUnits(), model.getTimeUnits() );
- final String name = fm.getSpotFeatureNames().get( spotFeature );
- // Description stores short names.
- final String description = fm.getSpotFeatureShortNames().get( spotFeature );
- final PropMetadata propMetadata = new PropMetadata( spotFeature, dType, false, unit, name, description );
- nodePropsMetadata.put( spotFeature, propMetadata );
- }
- metadata.setNodePropsMetadata( nodePropsMetadata );
-
- // Edge features
- final Map< String, PropMetadata > edgePropsMetadata = new HashMap<>();
- for ( final String edgeFeature : fm.getEdgeFeatures() )
- {
- final String dType = fm.getEdgeFeatureIsInt().get( edgeFeature ) ? "int32" : "float64";
- final Dimension dimension = fm.getEdgeFeatureDimensions().get( edgeFeature );
- final String unit = dimension.units( model.getSpaceUnits(), model.getTimeUnits() );
- final String name = fm.getEdgeFeatureNames().get( edgeFeature );
- final String description = fm.getEdgeFeatureShortNames().get( edgeFeature );
- final PropMetadata propMetadata = new PropMetadata( edgeFeature, dType, false, unit, name, description );
- edgePropsMetadata.put( edgeFeature, propMetadata );
- }
- metadata.setEdgePropsMetadata( edgePropsMetadata );
-
- /*
- * Write to disk
- */
-
- GeffNode.writeToZarr( visitor.nodes, zarrPath, metadata );
- GeffEdge.writeToZarr( geffEdges, zarrPath, metadata );
- GeffMetadata.writeToZarr( metadata, zarrPath );
- }
-
- private static List< GeffAxis > buildAxes( final String timeUnit, final String spaceUnit )
- {
- return Arrays.asList(
- GeffAxis.createTimeAxis( GeffAxis.NAME_TIME, timeUnit, null, null ),
- GeffAxis.createSpaceAxis( GeffAxis.NAME_SPACE_X, normalizeSpaceUnit( spaceUnit ), null, null ),
- GeffAxis.createSpaceAxis( GeffAxis.NAME_SPACE_Y, normalizeSpaceUnit( spaceUnit ), null, null ),
- GeffAxis.createSpaceAxis( GeffAxis.NAME_SPACE_Z, normalizeSpaceUnit( spaceUnit ), null, null ) );
- }
-
- /**
- * Maps common unit abbreviations to OME-Zarr compliant names. See
- * https://ngff.openmicroscopy.org/latest/#axes-md for the valid set.
- */
- static String normalizeSpaceUnit( final String unit )
- {
- if ( unit == null || unit.isEmpty() )
- return "pixel";
- switch ( unit.trim() )
- {
- case "um":
- case "µm":
- case "μm":
- case "micron":
- case "microns":
- return "micrometer";
- case "nm":
- return "nanometer";
- case "mm":
- return "millimeter";
- case "cm":
- return "centimeter";
- case "m":
- return "meter";
- case "km":
- return "kilometer";
- case "pm":
- return "picometer";
- case "Å":
- return "angstrom";
- default:
- return unit;
- }
- }
-
- public static class GeffSpotVisitor implements SpotVisitor
- {
-
- /** Features not in the general prop, because they are the core node. */
- private static final Set< String > SLOP_PROPS = Set.of( "FRAME", "POSITION_X", "POSITION_Y", "POSITION_Z", "RADIUS" );
-
- private int geffId = 0;
-
- private final TObjectIntMap< Spot > spotToId = new TObjectIntHashMap< Spot >();
-
- private final List< GeffNode > nodes = new ArrayList<>();
-
- private final Map< String, Boolean > isInt;
-
- public GeffSpotVisitor( final Map< String, Boolean > isInt )
- {
- this.isInt = isInt;
- }
-
- private void serializeFeatures( final Spot spot, final GeffNode node )
- {
- final Map< String, Double > features = spot.getFeatures();
- for ( final Map.Entry< String, Double > entry : features.entrySet() )
- {
- final String name = entry.getKey();
- if ( SLOP_PROPS.contains( name ) )
- continue;
-
- final Object val = ( isInt.get( name ) ? entry.getValue().intValue() : entry.getValue() );
- node.setProp( name, val );
- }
- }
-
- @Override
- public void visit( final SpotBase spot )
- {
- final GeffNode node = new GeffNode.Builder()
- .id( geffId )
- .timepoint( spot.getFeature( Spot.FRAME ).intValue() )
- .x( spot.getDoublePosition( 0 ) )
- .y( spot.getDoublePosition( 1 ) )
- .z( spot.getDoublePosition( 2 ) )
- .radius( spot.getFeature( Spot.RADIUS ).doubleValue() )
- .build();
- serializeFeatures( spot, node );
- nodes.add( node );
- spotToId.put( spot, geffId++ );
- }
-
- @Override
- public void visit( final SpotRoi spot )
- {
- final int nPoints = spot.nPoints();
- final double[] polygonX = new double[ nPoints ];
- final double[] polygonY = new double[ nPoints ];
- for ( int i = 0; i < nPoints; i++ )
- {
- polygonX[ i ] = spot.x( i );
- polygonY[ i ] = spot.y( i );
- }
-
- final GeffNode node = new GeffNode.Builder()
- .id( geffId )
- .timepoint( spot.getFeature( Spot.FRAME ).intValue() )
- .x( spot.getDoublePosition( 0 ) )
- .y( spot.getDoublePosition( 1 ) )
- .z( spot.getDoublePosition( 2 ) )
- .radius( spot.getFeature( Spot.RADIUS ).doubleValue() )
- .polygonX( polygonX )
- .polygonY( polygonY )
- .build();
- serializeFeatures( spot, node );
- nodes.add( node );
- spotToId.put( spot, geffId++ );
- }
- }
-}
diff --git a/src/main/java/fiji/plugin/trackmate/io/geff/TmGeffReader.java b/src/main/java/fiji/plugin/trackmate/io/geff/TmGeffReader.java
new file mode 100644
index 000000000..383ff49b5
--- /dev/null
+++ b/src/main/java/fiji/plugin/trackmate/io/geff/TmGeffReader.java
@@ -0,0 +1,403 @@
+package fiji.plugin.trackmate.io.geff;
+import static fiji.plugin.trackmate.SpotCollection.VISIBILITY;
+import static fiji.plugin.trackmate.features.edges.EdgeTargetAnalyzer.SPOT_SOURCE_ID;
+import static fiji.plugin.trackmate.features.edges.EdgeTargetAnalyzer.SPOT_TARGET_ID;
+import static fiji.plugin.trackmate.features.track.TrackIndexAnalyzer.TRACK_ID;
+import static fiji.plugin.trackmate.io.TmXmlKeys.GUI_STATE_ELEMENT_KEY;
+import static fiji.plugin.trackmate.io.TmXmlKeys.LOG_ELEMENT_KEY;
+import static fiji.plugin.trackmate.io.geff.TmGeffWriter.NAME_PROP;
+import static fiji.plugin.trackmate.io.geff.TmGeffWriter.TRACKMATE_SPOT_ID_PROP;
+import static fiji.plugin.trackmate.io.geff.TmGeffWriter.TRACK_GEFF_NAME;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Paths;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.jgrapht.graph.DefaultWeightedEdge;
+import org.jgrapht.graph.SimpleWeightedGraph;
+import org.mastodon.geff.GeffAxis;
+import org.mastodon.geff.GeffEdge;
+import org.mastodon.geff.GeffMetadata;
+import org.mastodon.geff.GeffMetadata.RelatedObjects;
+import org.mastodon.geff.GeffNode;
+import org.mastodon.geff.VarlengthProperty;
+
+import fiji.plugin.trackmate.Dimension;
+import fiji.plugin.trackmate.FeatureModel;
+import fiji.plugin.trackmate.Model;
+import fiji.plugin.trackmate.Settings;
+import fiji.plugin.trackmate.Spot;
+import fiji.plugin.trackmate.SpotBase;
+import fiji.plugin.trackmate.SpotCollection;
+import fiji.plugin.trackmate.SpotRoi;
+import fiji.plugin.trackmate.features.edges.EdgeTargetAnalyzer;
+import fiji.plugin.trackmate.features.edges.EdgeTimeLocationAnalyzer;
+import fiji.plugin.trackmate.gui.displaysettings.DisplaySettings;
+import fiji.plugin.trackmate.gui.displaysettings.DisplaySettingsIO;
+import fiji.plugin.trackmate.io.json.SettingsIO;
+import gnu.trove.map.TIntObjectMap;
+import gnu.trove.map.TObjectIntMap;
+import gnu.trove.map.hash.TIntObjectHashMap;
+import gnu.trove.map.hash.TObjectIntHashMap;
+import ij.IJ;
+import ij.ImagePlus;
+
+public class TmGeffReader
+{
+
+ private final String geffPath;
+
+ private GeffMetadata metadata;
+
+ public TmGeffReader( final String geffPath )
+ {
+ this.geffPath = geffPath;
+ }
+
+ public String getLog()
+ {
+ if ( null == metadata )
+ metadata = GeffMetadata.readFromZarr( geffPath );
+
+ @SuppressWarnings( "unchecked" )
+ final Map< String, Object > trackmateMD = ( Map< String, Object > ) metadata.getExtra().get( "trackmate" );
+ final String log = ( String ) trackmateMD.get( LOG_ELEMENT_KEY );
+ return log;
+ }
+
+ public String getGUIState()
+ {
+ if ( null == metadata )
+ metadata = GeffMetadata.readFromZarr( geffPath );
+
+ @SuppressWarnings( "unchecked" )
+ final Map< String, Object > trackmateMD = ( Map< String, Object > ) metadata.getExtra().get( "trackmate" );
+ final String guiState = ( String ) trackmateMD.get( GUI_STATE_ELEMENT_KEY );
+ return guiState;
+ }
+
+ @SuppressWarnings( "unchecked" )
+ public DisplaySettings getDisplaySettings()
+ {
+ if ( null == metadata )
+ metadata = GeffMetadata.readFromZarr( geffPath );
+
+ final Map< String, Object > trackmateMD = ( Map< String, Object > ) metadata.getExtra().get( "trackmate" );
+ final Map< String, Object > displaySettingsJson = ( Map< String, Object > ) trackmateMD.get( "displaySettings" );
+ return DisplaySettingsIO.fromJsonTree( displaySettingsJson );
+ }
+
+ public synchronized ImagePlus readImage()
+ {
+ if ( null == metadata )
+ metadata = GeffMetadata.readFromZarr( geffPath );
+
+ final RelatedObjects relatedObjects = metadata.getRelatedObjects();
+ if ( null == relatedObjects )
+ return null;
+
+ final List< String > imagePaths = relatedObjects.getImagePaths();
+ for ( final String imagePath : imagePaths )
+ {
+ final File imageFile = new File( new File( geffPath ).getParent(), imagePath );
+ if ( !imageFile.exists() || !imageFile.canRead() )
+ continue;
+
+ final ImagePlus imp = IJ.openImage( imageFile.getAbsolutePath() );
+ if ( null == imp )
+ continue;
+ return imp;
+ }
+ return null;
+ }
+
+ @SuppressWarnings( "unchecked" )
+ public synchronized Settings readSettings( final ImagePlus imp )
+ {
+ if ( null == metadata )
+ metadata = GeffMetadata.readFromZarr( geffPath );
+
+ final Map< String, Object > trackmateMD = ( Map< String, Object > ) metadata.getExtra().get( "trackmate" );
+ final Map< String, Object > settingsJson = ( Map< String, Object > ) trackmateMD.get( "settings" );
+
+ final Settings settings = new Settings( imp );
+ SettingsIO.updateFromJsonTree( settingsJson, settings );
+ return settings;
+ }
+
+ public synchronized Model getModel() throws IOException
+ {
+ final Model model = new Model();
+
+ if ( null == metadata )
+ metadata = GeffMetadata.readFromZarr( geffPath );
+
+ // Units
+ final boolean is2D = readUnits( model );
+
+ // Spots
+ final TIntObjectMap< Spot > spotIdMap = new TIntObjectHashMap<>();
+ final TObjectIntMap< Spot > spotTrackIDMap = new TObjectIntHashMap<>();
+ readSpots( model, is2D, spotIdMap, spotTrackIDMap );
+
+ // Read edges and tracks
+ readEdgesAndTracks( model, spotIdMap, spotTrackIDMap );
+
+ // Read feature declarations
+ readFeatureDeclarations( model.getFeatureModel() );
+
+ return model;
+ }
+
+ @SuppressWarnings( "unchecked" )
+ private void readFeatureDeclarations( final FeatureModel featureModel )
+ {
+ final Map< String, Object > trackmateMD = ( Map< String, Object > ) metadata.getExtra().get( "trackmate" );
+ final Map< String, Object > featureDeclarations = ( Map< String, Object > ) trackmateMD.get( "featureDeclarations" );
+
+ // Spot features
+ final List< String > spotFeatures = ( List< String > ) featureDeclarations.get( "spotFeatures" );
+ final Map< String, String > spotFeatureNames = ( Map< String, String > ) featureDeclarations.get( "spotFeatureNames" );
+ final Map< String, String > spotFeatureShortNames = ( Map< String, String > ) featureDeclarations.get( "spotFeatureShortNames" );
+ final Map< String, String > spotFeatureDimensionsStr = ( Map< String, String > ) featureDeclarations.get( "spotFeatureDimensions" );
+ final Map< String, Dimension > spotFeatureDimensions = new HashMap<>();
+ for ( final String feature : spotFeatureDimensionsStr.keySet() )
+ {
+ final String dimStr = spotFeatureDimensionsStr.get( feature );
+ final Dimension dim = Dimension.valueOf( dimStr );
+ spotFeatureDimensions.put( feature, dim );
+ }
+ final Map< String, Boolean > spotFeatureIsInt = ( Map< String, Boolean > ) featureDeclarations.get( "spotFeatureIsInt" );
+ featureModel.declareSpotFeatures( spotFeatures, spotFeatureNames, spotFeatureShortNames, spotFeatureDimensions, spotFeatureIsInt );
+
+ // Edge features
+ final List< String > edgeFeatures = ( List< String > ) featureDeclarations.get( "edgeFeatures" );
+ final Map< String, String > edgeFeatureNames = ( Map< String, String > ) featureDeclarations.get( "edgeFeatureNames" );
+ final Map< String, String > edgeFeatureShortNames = ( Map< String, String > ) featureDeclarations.get( "edgeFeatureShortNames" );
+ final Map< String, String > edgeFeatureDimensionsStr = ( Map< String, String > ) featureDeclarations.get( "edgeFeatureDimensions" );
+ final Map< String, Dimension > edgeFeatureDimensions = new HashMap<>();
+ for ( final String feature : edgeFeatureDimensionsStr.keySet() )
+ {
+ final String dimStr = edgeFeatureDimensionsStr.get( feature );
+ final Dimension dim = Dimension.valueOf( dimStr );
+ edgeFeatureDimensions.put( feature, dim );
+ }
+ final Map< String, Boolean > edgeFeatureIsInt = ( Map< String, Boolean > ) featureDeclarations.get( "edgeFeatureIsInt" );
+ featureModel.declareEdgeFeatures( edgeFeatures, edgeFeatureNames, edgeFeatureShortNames, edgeFeatureDimensions, edgeFeatureIsInt );
+
+ // Track features
+ final List< String > trackFeatures = ( List< String > ) featureDeclarations.get( "trackFeatures" );
+ final Map< String, String > trackFeatureNames = ( Map< String, String > ) featureDeclarations.get( "trackFeatureNames" );
+ final Map< String, String > trackFeatureShortNames = ( Map< String, String > ) featureDeclarations.get( "trackFeatureShortNames" );
+ final Map< String, String > trackFeatureDimensionsStr = ( Map< String, String > ) featureDeclarations.get( "trackFeatureDimensions" );
+ final Map< String, Dimension > trackFeatureDimensions = new HashMap<>();
+ for ( final String feature : trackFeatureDimensionsStr.keySet() )
+ {
+ final String dimStr = trackFeatureDimensionsStr.get( feature );
+ final Dimension dim = Dimension.valueOf( dimStr );
+ trackFeatureDimensions.put( feature, dim );
+ }
+ final Map< String, Boolean > trackFeatureIsInt = ( Map< String, Boolean > ) featureDeclarations.get( "trackFeatureIsInt" );
+ featureModel.declareTrackFeatures( trackFeatures, trackFeatureNames, trackFeatureShortNames, trackFeatureDimensions, trackFeatureIsInt );
+ }
+
+ private void readEdgesAndTracks( final Model model, final TIntObjectMap< Spot > spotIdMap, final TObjectIntMap< Spot > spotTrackIDMap )
+ {
+ // Load files
+ final String geffTracksPath = Paths.get( geffPath, TRACK_GEFF_NAME ).toString();
+ final List< GeffEdge > edges = GeffEdge.readFromZarr( geffPath, metadata );
+ final GeffMetadata trackMetadata = GeffMetadata.readFromZarr( geffTracksPath );
+ final List< GeffNode > tracks = GeffNode.readFromZarr( geffTracksPath, trackMetadata );
+
+ final FeatureModel fm = model.getFeatureModel();
+ final SimpleWeightedGraph< Spot, DefaultWeightedEdge > graph = new SimpleWeightedGraph<>( DefaultWeightedEdge.class );
+ final Map< Integer, Set< Spot > > connectedVertexSet = new HashMap<>();
+ final Map< Integer, Set< DefaultWeightedEdge > > connectedEdgeSet = new HashMap<>();
+
+ for ( final GeffEdge edge : edges )
+ {
+ // Connectivity
+ final int sid = edge.getSourceNodeId();
+ final Spot source = spotIdMap.get( sid );
+ final int tid = edge.getTargetNodeId();
+ final Spot target = spotIdMap.get( tid );
+
+ graph.addVertex( source );
+ graph.addVertex( target );
+ final DefaultWeightedEdge e = graph.addEdge( source, target );
+
+ // Put back source and target with TrackMate Spot ID
+ fm.putEdgeFeature( e, SPOT_SOURCE_ID, Double.valueOf( source.ID() ) );
+ fm.putEdgeFeature( e, SPOT_TARGET_ID, Double.valueOf( target.ID() ) );
+
+ // We did not serialize Z features for the 2D case, but we need to
+ // put them back when reading, because the feature model expects
+ // them to be there. These default values will be overwritten if the
+ // edge has a Z feature value.
+ fm.putEdgeFeature( e, EdgeTimeLocationAnalyzer.Z_LOCATION, Double.valueOf( 0. ) );
+
+ // Other Features
+ final Map< String, Object > props = edge.getProps();
+ for ( final String feature : props.keySet() )
+ fm.putEdgeFeature( e, feature, ( ( Number ) props.get( feature ) ).doubleValue() );
+
+ // Put back edge weight
+ final Double weight = fm.getEdgeFeature( e, EdgeTargetAnalyzer.EDGE_COST );
+ graph.setEdgeWeight( e, weight );
+
+ // Track ID
+ final int trackID = spotTrackIDMap.get( source );
+ final Set< Spot > trackSpots = connectedVertexSet.computeIfAbsent( trackID, k -> new HashSet<>() );
+ trackSpots.add( source );
+ trackSpots.add( target );
+ connectedEdgeSet.computeIfAbsent( trackID, k -> new HashSet<>() ).add( e );
+ }
+
+ // Track visibility, name and feature values
+ final Map< Integer, Boolean > visibility = new HashMap<>( connectedEdgeSet.size() );
+ final Map< Integer, String > savedTrackNames = new HashMap<>();
+ for ( final GeffNode track : tracks )
+ {
+ final int trackID = track.getId();
+
+ // Visibility
+ final Integer val = ( Integer ) track.getProp( VISIBILITY );
+ final boolean isVisible = val > 0;
+ visibility.put( trackID, isVisible );
+
+ // Name
+ final VarlengthProperty nameProperty = track.getVarlengthProperty( NAME_PROP );
+ final Object[] bytes = nameProperty.getData();
+ final String name = fromByteArray( bytes );
+ savedTrackNames.put( trackID, name );
+
+ // Features
+ final Map< String, Object > props = track.getProps();
+ for ( final String feature : props.keySet() )
+ {
+ if ( feature.equals( VISIBILITY ) || feature.equals( NAME_PROP ) )
+ continue;
+ fm.putTrackFeature( trackID, feature, ( ( Number ) props.get( feature ) ).doubleValue() );
+ }
+ }
+
+ // Rebuild track model
+ model.getTrackModel().from( graph, connectedVertexSet, connectedEdgeSet, visibility, savedTrackNames );
+ }
+
+ private boolean readUnits( final Model model )
+ {
+ final GeffAxis[] geffAxes = metadata.getGeffAxes();
+ String spaceUnits = null;
+ String timeUnits = null;
+ int spaceDim = 0;
+ for ( final GeffAxis axis : geffAxes )
+ {
+ if ( spaceUnits == null && axis.getType().equals( GeffAxis.TYPE_SPACE ) )
+ {
+ spaceUnits = axis.getUnit();
+ spaceDim++;
+ }
+
+ if ( timeUnits == null && axis.getType().equals( GeffAxis.TYPE_TIME ) )
+ timeUnits = axis.getUnit();
+ }
+ model.setPhysicalUnits( spaceUnits, timeUnits );
+ final boolean is2D = spaceDim < 3;
+ return is2D;
+ }
+
+ private TIntObjectMap< Spot > readSpots(
+ final Model model,
+ final boolean is2D,
+ final TIntObjectMap< Spot > spotIdMap,
+ final TObjectIntMap< Spot > spotTrackIDMap ) throws IOException
+ {
+ // Where is stored the track ID?
+ final String trackIdProp = metadata.getTrackNodeProps().get( "lineage" );
+
+ final List< GeffNode > geffNodes = GeffNode.readFromZarr( geffPath, metadata );
+ final SpotCollection spots = model.getSpots();
+ for ( final GeffNode node : geffNodes )
+ {
+ // Read its internal ID if present
+ int trackmateId;
+ final Object idObj = node.getProps().get( TRACKMATE_SPOT_ID_PROP );
+ if ( null != idObj && idObj instanceof Integer )
+ trackmateId = ( Integer ) idObj;
+ else
+ trackmateId = Spot.IDcounter.incrementAndGet();
+
+ // Frame
+ final int frame = node.getT();
+
+ // Deserialize
+ Spot spot = null;
+
+ // Is it a mesh?
+ // TODO
+
+ // Is it a polygon?
+ final double[] polygonX = node.getPolygonX();
+ final double[] polygonY = node.getPolygonY();
+ if ( polygonX != null && polygonY != null && polygonX.length > 0 && polygonY.length > 0 )
+ {
+ // Put coords relative to center
+ final double x = node.getX();
+ final double y = node.getY();
+ for ( int i = 0; i < polygonX.length; i++ )
+ {
+ polygonX[ i ] -= x;
+ polygonY[ i ] -= y;
+ }
+ spot = new SpotRoi( trackmateId, polygonX, polygonY );
+ spot.setPosition( x, 0 );
+ spot.setPosition( y, 1 );
+ }
+ else
+ {
+ spot = new SpotBase( trackmateId );
+ spot.setPosition( node.getX(), 0 );
+ spot.setPosition( node.getY(), 1 );
+ }
+ spot.putFeature( Spot.RADIUS, node.getRadius() );
+ spot.setPosition( is2D ? 0. : node.getZ(), 2 );
+ spots.add( spot, frame );
+ spotIdMap.put( node.getId(), spot );
+ spotTrackIDMap.put( spot, ( ( Number ) node.getProp( trackIdProp ) ).intValue() );
+
+ // Features
+ final Set< String > SKIP_FEATURES = Set.of( TRACKMATE_SPOT_ID_PROP, TRACK_ID, Spot.RADIUS, Spot.POSITION_X, Spot.POSITION_Y, Spot.POSITION_Z );
+ final Map< String, Object > props = node.getProps();
+ for ( final Map.Entry< String, Object > entry : props.entrySet() )
+ {
+ final String key = entry.getKey();
+ final Object value = entry.getValue();
+ if ( SKIP_FEATURES.contains( key ) )
+ continue;
+ spot.putFeature( key, ( ( Number ) value ).doubleValue() );
+ }
+
+ // Names
+ final VarlengthProperty nameProperty = node.getVarlengthProperty( NAME_PROP );
+ final Object[] bytes = nameProperty.getData();
+ final String name = fromByteArray( bytes );
+ spot.setName( name );
+
+ }
+ return spotIdMap;
+ }
+
+ private static final String fromByteArray( final Object[] bytes )
+ {
+ final byte[] recoveredBytes0 = new byte[ bytes.length ];
+ for ( int i = 0; i < bytes.length; i++ )
+ recoveredBytes0[ i ] = ( ( Integer ) bytes[ i ] ).byteValue();
+ return new String( recoveredBytes0, java.nio.charset.StandardCharsets.UTF_8 );
+ }
+}
diff --git a/src/main/java/fiji/plugin/trackmate/io/geff/TmGeffWriter.java b/src/main/java/fiji/plugin/trackmate/io/geff/TmGeffWriter.java
new file mode 100644
index 000000000..924c32998
--- /dev/null
+++ b/src/main/java/fiji/plugin/trackmate/io/geff/TmGeffWriter.java
@@ -0,0 +1,542 @@
+package fiji.plugin.trackmate.io.geff;
+
+import static fiji.plugin.trackmate.Spot.FRAME;
+import static fiji.plugin.trackmate.Spot.POSITION_X;
+import static fiji.plugin.trackmate.Spot.POSITION_Y;
+import static fiji.plugin.trackmate.Spot.POSITION_Z;
+import static fiji.plugin.trackmate.Spot.RADIUS;
+import static fiji.plugin.trackmate.SpotCollection.VISIBILITY;
+import static fiji.plugin.trackmate.features.edges.EdgeTargetAnalyzer.SPOT_SOURCE_ID;
+import static fiji.plugin.trackmate.features.edges.EdgeTargetAnalyzer.SPOT_TARGET_ID;
+import static fiji.plugin.trackmate.features.edges.EdgeTimeLocationAnalyzer.Z_LOCATION;
+import static fiji.plugin.trackmate.features.track.TrackDurationAnalyzer.TRACK_START;
+import static fiji.plugin.trackmate.features.track.TrackIndexAnalyzer.TRACK_ID;
+import static fiji.plugin.trackmate.features.track.TrackMotilityAnalyzer.TRACK_MAX_DISTANCE_TRAVELED;
+import static fiji.plugin.trackmate.io.TmXmlKeys.GUI_STATE_ELEMENT_KEY;
+import static fiji.plugin.trackmate.io.TmXmlKeys.LOG_ELEMENT_KEY;
+import static fiji.plugin.trackmate.io.TmXmlKeys.PLUGIN_VERSION_ATTRIBUTE_NAME;
+
+import java.io.IOException;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.jgrapht.graph.DefaultWeightedEdge;
+import org.mastodon.geff.GeffAxis;
+import org.mastodon.geff.GeffEdge;
+import org.mastodon.geff.GeffMetadata;
+import org.mastodon.geff.GeffMetadata.DisplayHints;
+import org.mastodon.geff.GeffMetadata.RelatedObjects;
+import org.mastodon.geff.GeffNode;
+import org.mastodon.geff.GeffNode.Builder;
+import org.mastodon.geff.PropMetadata;
+import org.mastodon.geff.VarlengthProperty;
+
+import com.google.gson.JsonElement;
+
+import fiji.plugin.trackmate.Dimension;
+import fiji.plugin.trackmate.FeatureModel;
+import fiji.plugin.trackmate.Model;
+import fiji.plugin.trackmate.Settings;
+import fiji.plugin.trackmate.Spot;
+import fiji.plugin.trackmate.Spot.SpotVisitor;
+import fiji.plugin.trackmate.SpotBase;
+import fiji.plugin.trackmate.SpotCollection;
+import fiji.plugin.trackmate.SpotRoi;
+import fiji.plugin.trackmate.TrackMate;
+import fiji.plugin.trackmate.TrackModel;
+import fiji.plugin.trackmate.detection.DetectionUtils;
+import fiji.plugin.trackmate.features.FeatureUtils;
+import fiji.plugin.trackmate.features.track.TrackLocationAnalyzer;
+import fiji.plugin.trackmate.gui.displaysettings.DisplaySettings;
+import fiji.plugin.trackmate.gui.displaysettings.DisplaySettings.TrackMateObject;
+import fiji.plugin.trackmate.gui.displaysettings.DisplaySettingsIO;
+import fiji.plugin.trackmate.io.json.FeatureModelIO;
+import fiji.plugin.trackmate.io.json.SettingsIO;
+import fiji.plugin.trackmate.util.TMUtils;
+import gnu.trove.map.TObjectIntMap;
+import gnu.trove.map.hash.TObjectIntHashMap;
+
+public class TmGeffWriter
+{
+
+ private static final String GEFF_VERSION = "1.0.0";
+
+ static final String TRACKMATE_SPOT_ID_PROP = "trackmate_spot_id";
+
+ static final String NAME_PROP = "name";
+
+ static final String TRACK_GEFF_NAME = "tracks.geff";
+
+ private final String geffPath;
+
+ private final GeffMetadata metadata;
+
+ private final GeffMetadata trackMetadata;
+
+ private final List< GeffNode > geffNodes = new ArrayList<>();
+
+ private final List< GeffEdge > geffEdges = new ArrayList<>();
+
+ private final List< GeffNode > geffTrackNodes = new ArrayList<>();
+
+ private final Map< String, Object > trackmateInfo;
+
+ public TmGeffWriter( final String zarrPath )
+ {
+ this.geffPath = zarrPath;
+ this.metadata = new GeffMetadata( GEFF_VERSION, true );
+ this.trackMetadata = new GeffMetadata( GEFF_VERSION, true );
+ this.trackmateInfo = new HashMap<>();
+ final Map< String, Object > extra = Map.of( "trackmate", trackmateInfo );
+ metadata.setExtra( extra );
+ trackmateInfo.put( PLUGIN_VERSION_ATTRIBUTE_NAME, TrackMate.PLUGIN_NAME_VERSION );
+ }
+
+ public void appendModel( final Model model )
+ {
+ final String spaceUnits = model.getSpaceUnits();
+ final String timeUnits = model.getTimeUnits();
+ final boolean is2D = DetectionUtils.is2D( model );
+
+ /*
+ * Serialize spots
+ */
+ final SpotCollection spots = model.getSpots();
+ final GeffSpotVisitor visitor = new GeffSpotVisitor( is2D, model.getTrackModel(), model.getFeatureModel().getSpotFeatureIsInt() );
+ spots.iterable( false ).forEach( spot -> spot.accept( visitor ) );
+
+ /*
+ * Serialize edges
+ */
+ final TrackModel trackModel = model.getTrackModel();
+ final Set< DefaultWeightedEdge > edges = trackModel.edgeSet();
+ final FeatureModel fm = model.getFeatureModel();
+
+ int edgeId = 0;
+ for ( final DefaultWeightedEdge edge : edges )
+ {
+ final Spot source = trackModel.getEdgeSource( edge );
+ final Integer srcId = visitor.spotToId.get( source );
+ final Spot target = trackModel.getEdgeTarget( edge );
+ final Integer tgtId = visitor.spotToId.get( target );
+ if ( srcId == null || tgtId == null )
+ continue;
+
+ final boolean swap = source.getFeature( FRAME ) > target.getFeature( FRAME );
+ final GeffEdge edgeNode = new GeffEdge.Builder()
+ .setId( edgeId++ )
+ .setSourceNodeId( swap ? tgtId : srcId )
+ .setTargetNodeId( swap ? srcId : tgtId )
+ .build();
+
+ // Feature
+ for ( final String edgeFeature : fm.getEdgeFeatures() )
+ {
+ if ( edgeFeature.equals( SPOT_SOURCE_ID ) || edgeFeature.equals( SPOT_TARGET_ID ) )
+ continue;
+ if ( is2D && edgeFeature.equals( Z_LOCATION ) )
+ continue;
+
+ final Double ef = fm.getEdgeFeature( edge, edgeFeature );
+ edgeNode.setProp( edgeFeature, ef );
+ }
+ geffEdges.add( edgeNode );
+ }
+
+ /*
+ * Metadata
+ */
+
+ // Axes
+ final List< GeffAxis > axes = buildAxes( spaceUnits, timeUnits, is2D, model );
+ metadata.setGeffAxes( axes );
+
+ // Display hints
+ DisplayHints displayHints = new DisplayHints()
+ .displayHorizontal( POSITION_X )
+ .displayVertical( POSITION_Y )
+ .displayTime( FRAME );
+ if ( !is2D )
+ displayHints = displayHints.displayDepth( POSITION_Z );
+ metadata.setDisplayHints( displayHints );
+
+ // Spot features
+
+ // First, determine what spot features have an actual value.
+ final Set< String > spotFeaturesWithValue = new HashSet<>();
+ for ( final Spot spot : spots.iterable( false ) )
+ spotFeaturesWithValue.addAll( spot.getFeatures().keySet() );
+
+ // Then add only those to the metadata.
+ final Map< String, Boolean > isInt = fm.getSpotFeatureIsInt();
+ final Map< String, PropMetadata > nodePropsMetadata = new HashMap<>();
+ for ( final String spotFeature : spotFeaturesWithValue )
+ {
+ if ( is2D && spotFeature.equals( POSITION_Z ) )
+ continue;
+ if ( spotFeature.equals( RADIUS ) || spotFeature.equals( TRACK_ID ) )
+ continue;
+
+ final String dType = isInt.get( spotFeature ) ? "int32" : "float64";
+ final Dimension dimension = fm.getSpotFeatureDimensions().get( spotFeature );
+ final String unit = dimension.units( spaceUnits, timeUnits );
+ final String name = fm.getSpotFeatureNames().get( spotFeature );
+ final PropMetadata propMetadata = new PropMetadata( spotFeature, dType, false, unit, name, null );
+ nodePropsMetadata.put( spotFeature, propMetadata );
+ }
+ // Add the TRACKMATE_ID feature
+ final PropMetadata trackmateIdPropMetadata = new PropMetadata( TRACKMATE_SPOT_ID_PROP, "int32", false, null, "TrackMate ID", "The TrackMate internal ID of spots" );
+ nodePropsMetadata.put( TRACKMATE_SPOT_ID_PROP, trackmateIdPropMetadata );
+ // Add the 'radius' feature -> mandatory for GEFF
+ final PropMetadata radiusPropMetadata = new PropMetadata( "radius", "float64", false, spaceUnits, "Radius", "The radius of the spot" );
+ nodePropsMetadata.put( "radius", radiusPropMetadata );
+ // Spot name property
+ nodePropsMetadata.put( NAME_PROP, new PropMetadata( NAME_PROP, "uint8", true, null, "Spot name", "The name of the spot" ) );
+ // Add the TRACK_ID feature -> map it to the GEFF 'lineage' property
+ final PropMetadata trackIdPropMetadata = new PropMetadata( TRACK_ID, "int32", false, null, "Track ID", "The TrackMate track ID of the spot" );
+ nodePropsMetadata.put( TRACK_ID, trackIdPropMetadata );
+ final Map< String, String > trackNodePros = Map.of( "lineage", TRACK_ID );
+ metadata.setTrackNodeProps( trackNodePros );
+
+ metadata.setNodePropsMetadata( nodePropsMetadata );
+
+ // Edge features
+
+ // First, determine what edge features have an actual value.
+ final Set< String > edgeFeaturesWithValue = new HashSet<>();
+ for ( final DefaultWeightedEdge edge : edges )
+ {
+ for ( final String edgeFeature : fm.getEdgeFeatures() )
+ {
+ final Double ef = fm.getEdgeFeature( edge, edgeFeature );
+ if ( ef != null )
+ edgeFeaturesWithValue.add( edgeFeature );
+ }
+ }
+
+ final Map< String, PropMetadata > edgePropsMetadata = new HashMap<>();
+ for ( final String edgeFeature : edgeFeaturesWithValue )
+ {
+ if ( edgeFeature.equals( SPOT_SOURCE_ID ) || edgeFeature.equals( SPOT_TARGET_ID ) )
+ continue;
+ if ( is2D && edgeFeature.equals( Z_LOCATION ) )
+ continue;
+
+ final String dType = fm.getEdgeFeatureIsInt().get( edgeFeature ) ? "int32" : "float64";
+ final Dimension dimension = fm.getEdgeFeatureDimensions().get( edgeFeature );
+ final String unit = dimension.units( spaceUnits, timeUnits );
+ final String name = fm.getEdgeFeatureNames().get( edgeFeature );
+ final PropMetadata propMetadata = new PropMetadata( edgeFeature, dType, false, unit, name, null );
+ edgePropsMetadata.put( edgeFeature, propMetadata );
+ }
+ metadata.setEdgePropsMetadata( edgePropsMetadata );
+
+ // Feature declarations
+ trackmateInfo.put( "featureDeclarations", FeatureModelIO.toJsonTree( fm ) );
+
+ /*
+ * Tracks feature values -> on a sub GEFF file (geffception) that has no
+ * edges, only nodes.
+ */
+
+ for ( final Integer trackID : trackModel.trackIDs( false ) )
+ {
+ final double xt = fm.getTrackFeature( trackID, TrackLocationAnalyzer.X_LOCATION );
+ final double yt = fm.getTrackFeature( trackID, TrackLocationAnalyzer.Y_LOCATION );
+ final int tt = fm.getTrackFeature( trackID, TRACK_START ).intValue();
+ final double radius = fm.getTrackFeature( trackID, TRACK_MAX_DISTANCE_TRAVELED ) / 2.;
+
+ final GeffNode.Builder builder = new GeffNode.Builder()
+ .id( trackID )
+ .timepoint( tt )
+ .x( xt )
+ .y( yt )
+ .radius( radius );
+ if ( !is2D )
+ {
+ final double zt = fm.getTrackFeature( trackID, TrackLocationAnalyzer.Z_LOCATION );
+ builder.z( zt );
+ }
+ final GeffNode trackNode = builder.build();
+
+ // Track features
+ for ( final String trackFeature : fm.getTrackFeatures() )
+ {
+ Object val;
+ if ( fm.getTrackFeatureIsInt().get( trackFeature ) )
+ val = Integer.valueOf( fm.getTrackFeature( trackID, trackFeature ).intValue() );
+ else
+ val = fm.getTrackFeature( trackID, trackFeature );
+ trackNode.setProp( trackFeature, val );
+ }
+ // Track visibility property
+ final Integer visibility = trackModel.isVisible( trackID ) ? 1 : 0;
+ trackNode.setProp( VISIBILITY, visibility );
+ // Add the 'radius' feature -> mandatory for GEFF
+ final PropMetadata trackRadiusPropMetadata = new PropMetadata( "radius", "float64", false, spaceUnits, "Radius", "The radius of excursion of the track" );
+ nodePropsMetadata.put( "radius", trackRadiusPropMetadata );
+ // Track name -> variable length property
+ final String trackName = trackModel.name( trackID );
+ final Object[] bytes = toByteArray( trackName );
+ trackNode.setVarlengthProperty( NAME_PROP, new VarlengthProperty( NAME_PROP, "uint8", bytes ) );
+
+ geffTrackNodes.add( trackNode );
+ }
+
+ /*
+ * Tracks metadata
+ */
+
+ // Axes
+ final List< GeffAxis > trackAxes = buildTrackAxes( spaceUnits, timeUnits, is2D, model );
+ trackMetadata.setGeffAxes( trackAxes );
+
+ // Display hints
+ DisplayHints trackDisplayHints = new DisplayHints()
+ .displayHorizontal( TrackLocationAnalyzer.X_LOCATION )
+ .displayVertical( TrackLocationAnalyzer.Y_LOCATION )
+ .displayTime( TRACK_START );
+ if ( !is2D )
+ trackDisplayHints = trackDisplayHints.displayDepth( TrackLocationAnalyzer.Z_LOCATION );
+ trackMetadata.setDisplayHints( trackDisplayHints );
+
+ // Track features
+
+ // First, determine what track features have an actual value.
+ final Set< String > trackFeaturesWithValue = new HashSet<>();
+ for ( final DefaultWeightedEdge edge : edges )
+ {
+ for ( final String trackFeature : fm.getTrackFeatures() )
+ {
+ final Double ef = fm.getEdgeFeature( edge, trackFeature );
+ if ( ef != null )
+ trackFeaturesWithValue.add( trackFeature );
+ }
+ }
+
+ // Then add only those to the metadata.
+ final Map< String, Boolean > trackIsInt = fm.getTrackFeatureIsInt();
+ final Map< String, PropMetadata > trackNodePropsMetadata = new HashMap<>();
+ for ( final String trackFeature : trackFeaturesWithValue )
+ {
+ if ( is2D && trackFeature.equals( TrackLocationAnalyzer.Z_LOCATION ) )
+ continue;
+
+ final String dType = trackIsInt.get( trackFeature ) ? "int32" : "float64";
+ final Dimension dimension = fm.getSpotFeatureDimensions().get( trackFeature );
+ final String unit = dimension.units( spaceUnits, timeUnits );
+ final String name = fm.getSpotFeatureNames().get( trackFeature );
+ final PropMetadata propMetadata = new PropMetadata( trackFeature, dType, false, unit, name, null );
+ trackNodePropsMetadata.put( trackFeature, propMetadata );
+ }
+ // Track visibility property
+ trackNodePropsMetadata.put( VISIBILITY, new PropMetadata( VISIBILITY, "int32", false, null, Spot.FEATURE_NAMES.get( VISIBILITY ), "Whether the track is visible in the display" ) );
+ // Track name property
+ trackNodePropsMetadata.put( NAME_PROP, new PropMetadata( NAME_PROP, "uint8", true, null, "Track name", "The name of the track" ) );
+
+ trackMetadata.setNodePropsMetadata( trackNodePropsMetadata );
+ }
+
+ public void appendSettings( final Settings settings )
+ {
+ // All settings
+ final JsonElement settingsJson = SettingsIO.toJsonTree( settings );
+ trackmateInfo.put( "settings", settingsJson );
+
+ // Path to the image
+ String imagePathStr = TMUtils.getImagePathWithoutExtension( settings );
+ if ( settings.imageFileName != null && !settings.imageFileName.isEmpty() )
+ imagePathStr = imagePathStr + "." + settings.imageFileName.substring( settings.imageFileName.lastIndexOf( '.' ) + 1 );
+
+ // Make it relative to the save path
+ final Path imagePath = Paths.get( imagePathStr ).toAbsolutePath().normalize();
+ final Path savePath = Paths.get( geffPath ).toAbsolutePath().normalize();
+ metadata.setRelatedObjects( new RelatedObjects().image( savePath.getParent().relativize( imagePath ).toString() ) );
+ }
+
+ public void appendLog( final String log )
+ {
+ trackmateInfo.put( LOG_ELEMENT_KEY, log );
+ }
+
+ public void appendDisplaySettings( final DisplaySettings ds )
+ {
+ final JsonElement json = DisplaySettingsIO.toJsonTree( ds );
+ trackmateInfo.put( "displaySettings", json );
+ }
+
+ public void appendGUIState( final String currentPanelIdentifier )
+ {
+ trackmateInfo.put( GUI_STATE_ELEMENT_KEY, currentPanelIdentifier );
+ }
+
+ public void write() throws IOException
+ {
+ // Core GEFF
+ GeffNode.writeToZarr( geffNodes, geffPath, metadata );
+ GeffEdge.writeToZarr( geffEdges, geffPath, metadata );
+ GeffMetadata.writeToZarr( metadata, geffPath );
+
+ // Track GEFF
+ final String geffTracksPath = Paths.get( geffPath, TRACK_GEFF_NAME ).toString();
+ GeffNode.writeToZarr( geffTrackNodes, geffTracksPath, trackMetadata );
+ // Required to be a valid GEFF:
+ GeffEdge.writeToZarr( new ArrayList<>(), geffTracksPath, trackMetadata );
+ GeffMetadata.writeToZarr( trackMetadata, geffTracksPath );
+ }
+
+ private class GeffSpotVisitor implements SpotVisitor
+ {
+
+ /** Features not in the general prop, because they are the core node. */
+ private static final Set< String > SKIP_PROPS = Set.of( FRAME, POSITION_X, POSITION_Y, POSITION_Z, RADIUS, TRACK_ID );
+
+ private int geffId = 0;
+
+ private final TObjectIntMap< Spot > spotToId = new TObjectIntHashMap< Spot >();
+
+ private final boolean is2d;
+
+ private final TrackModel trackModel;
+
+ private final Map< String, Boolean > isInt;
+
+ public GeffSpotVisitor( final boolean is2d, final TrackModel trackModel, final Map< String, Boolean > isInt )
+ {
+ this.is2d = is2d;
+ this.trackModel = trackModel;
+ this.isInt = isInt;
+ }
+
+ private void serializeFeatures( final Spot spot, final GeffNode node )
+ {
+ final Map< String, Double > features = spot.getFeatures();
+ for ( final String feature : features.keySet() )
+ {
+ if ( SKIP_PROPS.contains( feature ) )
+ continue;
+
+ final Double obj = spot.getFeature( feature );
+ final Object val;
+ if ( isInt.get( feature ) )
+ val = Integer.valueOf( obj.intValue() );
+ else
+ val = obj;
+ node.setProp( feature, val );
+ }
+
+ // Spot ID
+ node.setProp( TRACKMATE_SPOT_ID_PROP, spot.ID() );
+ // Track ID -> will be mapped to the 'lineage' GEFF property
+ final Integer trackID = trackModel.trackIDOf( spot );
+ if ( trackID != null )
+ node.setProp( TRACK_ID, trackID.intValue() );
+ // Name -> variable length property
+ final String name = spot.getName();
+ if ( name != null )
+ {
+ final Object[] bytes = toByteArray( name );
+ node.setVarlengthProperty( NAME_PROP, new VarlengthProperty( NAME_PROP, "uint8", bytes ) );
+ }
+ }
+
+ @Override
+ public void visit( final SpotBase spot )
+ {
+ final Builder builder = new GeffNode.Builder()
+ .id( geffId )
+ .timepoint( spot.getFeature( FRAME ).intValue() )
+ .x( spot.getDoublePosition( 0 ) )
+ .y( spot.getDoublePosition( 1 ) )
+ .radius( spot.getFeature( RADIUS ).doubleValue() );
+ if ( !is2d )
+ builder.z( spot.getDoublePosition( 2 ) );
+
+ final GeffNode node = builder.build();
+ serializeFeatures( spot, node );
+ geffNodes.add( node );
+ spotToId.put( spot, geffId++ );
+ }
+
+ @Override
+ public void visit( final SpotRoi spot )
+ {
+ final int nPoints = spot.nPoints();
+ final double[] polygonX = new double[ nPoints ];
+ final double[] polygonY = new double[ nPoints ];
+ for ( int i = 0; i < nPoints; i++ )
+ {
+ polygonX[ i ] = spot.x( i );
+ polygonY[ i ] = spot.y( i );
+ }
+
+ final GeffNode node = new GeffNode.Builder()
+ .id( geffId )
+ .timepoint( spot.getFeature( FRAME ).intValue() )
+ .x( spot.getDoublePosition( 0 ) )
+ .y( spot.getDoublePosition( 1 ) ) // No Z <- 2D
+ .radius( spot.getFeature( RADIUS ).doubleValue() )
+ .polygonX( polygonX )
+ .polygonY( polygonY )
+ .build();
+ serializeFeatures( spot, node );
+ geffNodes.add( node );
+ spotToId.put( spot, geffId++ );
+ }
+ }
+
+ private static final Object[] toByteArray( final String name )
+ {
+ final byte[] bytes = name.getBytes( java.nio.charset.StandardCharsets.UTF_8 );
+ final Object[] data = new Object[ bytes.length ];
+ for ( int i = 0; i < bytes.length; i++ )
+ data[ i ] = bytes[ i ] & 0xFF;
+ return data;
+ }
+
+ private static final List< GeffAxis > buildAxes( final String spaceUnit, final String timeUnit, final boolean is2d, final Model model )
+ {
+ final String[] spaceFeatures = is2d
+ ? new String[] { POSITION_X, POSITION_Y }
+ : new String[] { POSITION_X, POSITION_Y, POSITION_Z };
+ return axesOf( TrackMateObject.SPOTS, spaceFeatures, FRAME, spaceUnit, timeUnit, model );
+ }
+
+ private static final List< GeffAxis > buildTrackAxes( final String spaceUnit, final String timeUnit, final boolean is2d, final Model model )
+ {
+ final String[] spaceFeatures = is2d
+ ? new String[] { TrackLocationAnalyzer.X_LOCATION, TrackLocationAnalyzer.Y_LOCATION }
+ : new String[] { TrackLocationAnalyzer.X_LOCATION, TrackLocationAnalyzer.Y_LOCATION, TrackLocationAnalyzer.Z_LOCATION };
+ return axesOf( TrackMateObject.TRACKS, spaceFeatures, TRACK_START, spaceUnit, timeUnit, model );
+ }
+
+ private static final List< GeffAxis > axesOf(
+ final TrackMateObject obj,
+ final String[] spaceFeatures,
+ final String timeFeature,
+ final String spaceUnit,
+ final String timeUnit,
+ final Model model )
+ {
+ final String su = spaceUnit;
+ final String tu = timeUnit;
+
+ final List< GeffAxis > axes = new ArrayList<>();
+
+ final double[] minMaxT = FeatureUtils.autoMinMax( model, obj, timeFeature, false );
+ axes.add( GeffAxis.createTimeAxis( timeFeature, tu, minMaxT[ 0 ], minMaxT[ 1 ] ) );
+
+ for ( final String spaceFeature : spaceFeatures )
+ {
+ final double[] minMaxX = FeatureUtils.autoMinMax( model, obj, spaceFeature, false );
+ axes.add( GeffAxis.createSpaceAxis( spaceFeature, su, minMaxX[ 0 ], minMaxX[ 1 ] ) );
+ }
+ return axes;
+ }
+}
diff --git a/src/main/java/fiji/plugin/trackmate/io/json/FeatureModelIO.java b/src/main/java/fiji/plugin/trackmate/io/json/FeatureModelIO.java
new file mode 100644
index 000000000..ac195fcb5
--- /dev/null
+++ b/src/main/java/fiji/plugin/trackmate/io/json/FeatureModelIO.java
@@ -0,0 +1,22 @@
+package fiji.plugin.trackmate.io.json;
+
+import com.google.gson.Gson;
+import com.google.gson.GsonBuilder;
+import com.google.gson.JsonElement;
+
+import fiji.plugin.trackmate.FeatureModel;
+
+public class FeatureModelIO
+{
+ private static Gson getGson()
+ {
+ return new GsonBuilder()
+ .setPrettyPrinting()
+ .create();
+ }
+
+ public static JsonElement toJsonTree( final FeatureModel featureModel )
+ {
+ return getGson().toJsonTree( featureModel );
+ }
+}
diff --git a/src/main/java/fiji/plugin/trackmate/io/json/SettingsIO.java b/src/main/java/fiji/plugin/trackmate/io/json/SettingsIO.java
new file mode 100644
index 000000000..aebc2740a
--- /dev/null
+++ b/src/main/java/fiji/plugin/trackmate/io/json/SettingsIO.java
@@ -0,0 +1,249 @@
+package fiji.plugin.trackmate.io.json;
+
+import java.awt.Rectangle;
+import java.io.IOException;
+import java.util.Map;
+
+import com.google.gson.Gson;
+import com.google.gson.GsonBuilder;
+import com.google.gson.InstanceCreator;
+import com.google.gson.JsonElement;
+import com.google.gson.TypeAdapter;
+import com.google.gson.stream.JsonReader;
+import com.google.gson.stream.JsonToken;
+import com.google.gson.stream.JsonWriter;
+
+import fiji.plugin.trackmate.Settings;
+import fiji.plugin.trackmate.TrackMateModule;
+import fiji.plugin.trackmate.detection.SpotDetectorFactoryBase;
+import fiji.plugin.trackmate.features.edges.EdgeAnalyzer;
+import fiji.plugin.trackmate.features.spot.SpotAnalyzerFactoryBase;
+import fiji.plugin.trackmate.features.track.TrackAnalyzer;
+import fiji.plugin.trackmate.providers.AbstractProvider;
+import fiji.plugin.trackmate.providers.DetectorProvider;
+import fiji.plugin.trackmate.providers.EdgeAnalyzerProvider;
+import fiji.plugin.trackmate.providers.Spot2DMorphologyAnalyzerProvider;
+import fiji.plugin.trackmate.providers.Spot3DMorphologyAnalyzerProvider;
+import fiji.plugin.trackmate.providers.SpotAnalyzerProvider;
+import fiji.plugin.trackmate.providers.TrackAnalyzerProvider;
+import fiji.plugin.trackmate.providers.TrackerProvider;
+import fiji.plugin.trackmate.tracking.SpotTrackerFactory;
+import ij.gui.Roi;
+
+public class SettingsIO
+{
+
+ private static Gson getGson( final int nChannels, final Settings updateTarget )
+ {
+ final GsonBuilder builder = new GsonBuilder()
+ .setPrettyPrinting()
+ .serializeSpecialFloatingPointValues()
+ .registerTypeHierarchyAdapter( Roi.class, new RoiTypeAdapter() )
+ .registerTypeHierarchyAdapter( SpotDetectorFactoryBase.class, new SpotDetectorTypeAdapter() )
+ .registerTypeHierarchyAdapter( SpotTrackerFactory.class, new SpotTrackerTypeAdapter() )
+ .registerTypeHierarchyAdapter( SpotAnalyzerFactoryBase.class, new SpotAnalyzerAdapter( nChannels ) )
+ .registerTypeHierarchyAdapter( EdgeAnalyzer.class, new EdgeAnalyserTypeAdapter() )
+ .registerTypeHierarchyAdapter( TrackAnalyzer.class, new TrackAnalyserTypeAdapter() );
+ if ( updateTarget != null )
+ builder.registerTypeAdapter( Settings.class, ( InstanceCreator< Settings > ) type -> updateTarget );
+ return builder.create();
+ }
+
+ public static JsonElement toJsonTree( final Settings settings )
+ {
+ final int nChannels = ( settings.imp == null ) ? 1 : settings.imp.getNChannels();
+ return getGson( nChannels, null ).toJsonTree( settings );
+ }
+
+ public static void updateFromJsonTree( final Map< String, Object > settingsJson, final Settings updateTarget )
+ {
+ final int nChannels = ( updateTarget.imp == null ) ? 1 : updateTarget.imp.getNChannels();
+ final Gson gson = getGson( nChannels, updateTarget );
+ final JsonElement tree = gson.toJsonTree( settingsJson );
+ gson.fromJson( tree, Settings.class );
+
+ /*
+ * Post-processing: Since we are dealing with a Map< String, Object >
+ * settingsJson that is re returned by the N5Reader, we have some issues
+ * with the Json tree. All numbers are deserialized as doubles, and we
+ * need to convert some of them back to integers, particularly for the
+ * detector and tracker settings. We do this by using the default
+ * settings maps as a template, using the default value types to
+ * properly case numbers.
+ */
+ final Map< String, Object > detectorDS = updateTarget.detectorFactory.getDefaultSettings();
+ for ( final String key : detectorDS.keySet() )
+ {
+ final Object val = updateTarget.detectorSettings.get( key );
+ if ( val instanceof Double && detectorDS.get( key ) instanceof Integer )
+ updateTarget.detectorSettings.put( key, ( ( Double ) val ).intValue() );
+ }
+
+ final Map< String, Object > trackerDS = updateTarget.trackerFactory.getDefaultSettings();
+ for ( final String key : trackerDS.keySet() )
+ {
+ final Object val = updateTarget.trackerSettings.get( key );
+ if ( val instanceof Double && trackerDS.get( key ) instanceof Integer )
+ updateTarget.trackerSettings.put( key, ( ( Double ) val ).intValue() );
+ }
+ }
+
+ private static class FactoryTypeAdapter< T extends TrackMateModule > extends TypeAdapter< T >
+ {
+
+ private final AbstractProvider< T > provider;
+
+ public FactoryTypeAdapter( final AbstractProvider< T > provider )
+ {
+ this.provider = provider;
+ }
+
+ @Override
+ public void write( final JsonWriter out, final T value ) throws IOException
+ {
+ out.value( value.getKey() );
+ }
+
+ @Override
+ public T read( final JsonReader in ) throws IOException
+ {
+ return provider.getFactory( in.nextString() );
+ }
+ }
+
+ @SuppressWarnings( "rawtypes" )
+ private static class SpotDetectorTypeAdapter extends FactoryTypeAdapter< SpotDetectorFactoryBase >
+ {
+
+ public SpotDetectorTypeAdapter()
+ {
+ super( new DetectorProvider() );
+ }
+
+ }
+
+ private static class SpotTrackerTypeAdapter extends FactoryTypeAdapter< SpotTrackerFactory >
+ {
+
+ public SpotTrackerTypeAdapter()
+ {
+ super( new TrackerProvider() );
+ }
+ }
+
+ private static class SpotAnalyzerAdapter extends TypeAdapter< SpotAnalyzerFactoryBase< ? > >
+ {
+
+ private final SpotAnalyzerProvider spotAnalyzerProvider;
+
+ private final Spot2DMorphologyAnalyzerProvider spot2dMorphologyAnalyzerProvider;
+
+ private final Spot3DMorphologyAnalyzerProvider spot3dMorphologyAnalyzerProvider;
+
+ public SpotAnalyzerAdapter( final int nChannels )
+ {
+ spotAnalyzerProvider = new SpotAnalyzerProvider( nChannels );
+ spot2dMorphologyAnalyzerProvider = new Spot2DMorphologyAnalyzerProvider( nChannels );
+ spot3dMorphologyAnalyzerProvider = new Spot3DMorphologyAnalyzerProvider( nChannels );
+ }
+
+ @Override
+ public void write( final JsonWriter out, final SpotAnalyzerFactoryBase< ? > value ) throws IOException
+ {
+ out.value( value.getKey() );
+ }
+
+ @Override
+ public SpotAnalyzerFactoryBase< ? > read( final JsonReader in ) throws IOException
+ {
+ // Try each provider in turn
+ final String key = in.nextString();
+ SpotAnalyzerFactoryBase< ? > factory = spotAnalyzerProvider.getFactory( key );
+ if ( factory != null )
+ return factory;
+ factory = spot2dMorphologyAnalyzerProvider.getFactory( key );
+ if ( factory != null )
+ return factory;
+ factory = spot3dMorphologyAnalyzerProvider.getFactory( key );
+ if ( factory != null )
+ return factory;
+ return null;
+ }
+ }
+
+ private static class EdgeAnalyserTypeAdapter extends FactoryTypeAdapter< EdgeAnalyzer >
+ {
+
+ public EdgeAnalyserTypeAdapter()
+ {
+ super( new EdgeAnalyzerProvider() );
+ }
+ }
+
+ private static class TrackAnalyserTypeAdapter extends FactoryTypeAdapter< TrackAnalyzer >
+ {
+
+ public TrackAnalyserTypeAdapter()
+ {
+ super( new TrackAnalyzerProvider() );
+ }
+ }
+
+ private static class RoiTypeAdapter extends TypeAdapter< Roi >
+ {
+
+ // We serialize only the bounding-box.
+
+ @Override
+ public void write( final JsonWriter out, final Roi roi ) throws IOException
+ {
+ if ( roi == null )
+ {
+ out.nullValue();
+ return;
+ }
+ final Rectangle bounds = roi.getBounds();
+ out.beginObject();
+ out.name( "x" ).value( bounds.x );
+ out.name( "y" ).value( bounds.y );
+ out.name( "width" ).value( bounds.width );
+ out.name( "height" ).value( bounds.height );
+ out.endObject();
+ }
+
+ @Override
+ public Roi read( final JsonReader in ) throws IOException
+ {
+ if ( in.peek() == JsonToken.NULL )
+ {
+ in.nextNull();
+ return null;
+ }
+ int x = 0, y = 0, width = 0, height = 0;
+ in.beginObject();
+ while ( in.hasNext() )
+ {
+ switch ( in.nextName() )
+ {
+ case "x":
+ x = in.nextInt();
+ break;
+ case "y":
+ y = in.nextInt();
+ break;
+ case "width":
+ width = in.nextInt();
+ break;
+ case "height":
+ height = in.nextInt();
+ break;
+ default:
+ in.skipValue();
+ break;
+ }
+ }
+ in.endObject();
+ return new Roi( x, y, width, height );
+ }
+ }
+}
diff --git a/src/main/java/fiji/plugin/trackmate/tracking/TrackerKeys.java b/src/main/java/fiji/plugin/trackmate/tracking/TrackerKeys.java
index 4016f4282..e87b376cd 100644
--- a/src/main/java/fiji/plugin/trackmate/tracking/TrackerKeys.java
+++ b/src/main/java/fiji/plugin/trackmate/tracking/TrackerKeys.java
@@ -251,13 +251,4 @@ public class TrackerKeys
/** A default value for the {@value #KEY_CUTOFF_PERCENTILE} parameter. */
public static final double DEFAULT_CUTOFF_PERCENTILE = 0.9d;
- /**
- * Key for the parameter that stores the blocking value: cost for
- * non-physical, forbidden links. Expected values are {@link Double}s, and
- * are typically very large.
- */
- public static final String KEY_BLOCKING_VALUE = "BLOCKING_VALUE";
-
- /** A default value for the {@value #KEY_BLOCKING_VALUE} parameter. */
- public static final double DEFAULT_BLOCKING_VALUE = Double.POSITIVE_INFINITY;
}
diff --git a/src/main/java/fiji/plugin/trackmate/tracking/jaqaman/LAPUtils.java b/src/main/java/fiji/plugin/trackmate/tracking/jaqaman/LAPUtils.java
index 09a714ed3..5fa66ab92 100644
--- a/src/main/java/fiji/plugin/trackmate/tracking/jaqaman/LAPUtils.java
+++ b/src/main/java/fiji/plugin/trackmate/tracking/jaqaman/LAPUtils.java
@@ -25,7 +25,6 @@
import static fiji.plugin.trackmate.tracking.TrackerKeys.DEFAULT_ALLOW_TRACK_MERGING;
import static fiji.plugin.trackmate.tracking.TrackerKeys.DEFAULT_ALLOW_TRACK_SPLITTING;
import static fiji.plugin.trackmate.tracking.TrackerKeys.DEFAULT_ALTERNATIVE_LINKING_COST_FACTOR;
-import static fiji.plugin.trackmate.tracking.TrackerKeys.DEFAULT_BLOCKING_VALUE;
import static fiji.plugin.trackmate.tracking.TrackerKeys.DEFAULT_CUTOFF_PERCENTILE;
import static fiji.plugin.trackmate.tracking.TrackerKeys.DEFAULT_GAP_CLOSING_FEATURE_PENALTIES;
import static fiji.plugin.trackmate.tracking.TrackerKeys.DEFAULT_GAP_CLOSING_MAX_DISTANCE;
@@ -38,7 +37,6 @@
import static fiji.plugin.trackmate.tracking.TrackerKeys.KEY_ALLOW_TRACK_MERGING;
import static fiji.plugin.trackmate.tracking.TrackerKeys.KEY_ALLOW_TRACK_SPLITTING;
import static fiji.plugin.trackmate.tracking.TrackerKeys.KEY_ALTERNATIVE_LINKING_COST_FACTOR;
-import static fiji.plugin.trackmate.tracking.TrackerKeys.KEY_BLOCKING_VALUE;
import static fiji.plugin.trackmate.tracking.TrackerKeys.KEY_CUTOFF_PERCENTILE;
import static fiji.plugin.trackmate.tracking.TrackerKeys.KEY_GAP_CLOSING_FEATURE_PENALTIES;
import static fiji.plugin.trackmate.tracking.TrackerKeys.KEY_GAP_CLOSING_MAX_DISTANCE;
@@ -158,7 +156,6 @@ public static final Map< String, Object > getDefaultSegmentSettingsMap()
settings.put( KEY_MERGING_MAX_DISTANCE, DEFAULT_MERGING_MAX_DISTANCE );
settings.put( KEY_MERGING_FEATURE_PENALTIES, new HashMap<>( DEFAULT_MERGING_FEATURE_PENALTIES ) );
// Others
- settings.put( KEY_BLOCKING_VALUE, DEFAULT_BLOCKING_VALUE );
settings.put( KEY_ALTERNATIVE_LINKING_COST_FACTOR, DEFAULT_ALTERNATIVE_LINKING_COST_FACTOR );
settings.put( KEY_CUTOFF_PERCENTILE, DEFAULT_CUTOFF_PERCENTILE );
// return
@@ -294,7 +291,6 @@ public static final boolean checkSettingsValidity( final Map< String, Object > s
// Others
ok = ok & checkParameter( settings, KEY_CUTOFF_PERCENTILE, Double.class, errorHolder );
ok = ok & checkParameter( settings, KEY_ALTERNATIVE_LINKING_COST_FACTOR, Double.class, errorHolder );
- ok = ok & checkParameter( settings, KEY_BLOCKING_VALUE, Double.class, errorHolder );
// Check keys
final List< String > mandatoryKeys = new ArrayList<>();
@@ -311,7 +307,6 @@ public static final boolean checkSettingsValidity( final Map< String, Object > s
mandatoryKeys.add( KEY_MERGING_MAX_DISTANCE );
mandatoryKeys.add( KEY_ALTERNATIVE_LINKING_COST_FACTOR );
mandatoryKeys.add( KEY_CUTOFF_PERCENTILE );
- mandatoryKeys.add( KEY_BLOCKING_VALUE );
final List< String > optionalKeys = new ArrayList<>();
if ( linking )
{
diff --git a/src/main/java/fiji/plugin/trackmate/tracking/jaqaman/SegmentTracker.java b/src/main/java/fiji/plugin/trackmate/tracking/jaqaman/SegmentTracker.java
index a1fe2ea77..fcd20cba1 100644
--- a/src/main/java/fiji/plugin/trackmate/tracking/jaqaman/SegmentTracker.java
+++ b/src/main/java/fiji/plugin/trackmate/tracking/jaqaman/SegmentTracker.java
@@ -25,7 +25,6 @@
import static fiji.plugin.trackmate.tracking.TrackerKeys.KEY_ALLOW_TRACK_MERGING;
import static fiji.plugin.trackmate.tracking.TrackerKeys.KEY_ALLOW_TRACK_SPLITTING;
import static fiji.plugin.trackmate.tracking.TrackerKeys.KEY_ALTERNATIVE_LINKING_COST_FACTOR;
-import static fiji.plugin.trackmate.tracking.TrackerKeys.KEY_BLOCKING_VALUE;
import static fiji.plugin.trackmate.tracking.TrackerKeys.KEY_CUTOFF_PERCENTILE;
import static fiji.plugin.trackmate.tracking.TrackerKeys.KEY_GAP_CLOSING_FEATURE_PENALTIES;
import static fiji.plugin.trackmate.tracking.TrackerKeys.KEY_GAP_CLOSING_MAX_DISTANCE;
@@ -278,7 +277,6 @@ private static final boolean checkSettingsValidity( final Map< String, Object >
optionalKeys.add( KEY_GAP_CLOSING_FEATURE_PENALTIES );
optionalKeys.add( KEY_SPLITTING_FEATURE_PENALTIES );
optionalKeys.add( KEY_MERGING_FEATURE_PENALTIES );
- optionalKeys.add( KEY_BLOCKING_VALUE );
ok = ok & checkMapKeys( settings, mandatoryKeys, optionalKeys, str );
return ok;
diff --git a/src/main/java/fiji/plugin/trackmate/tracking/jaqaman/SegmentTrackerFactory.java b/src/main/java/fiji/plugin/trackmate/tracking/jaqaman/SegmentTrackerFactory.java
index ba9d6e215..c4a710f68 100644
--- a/src/main/java/fiji/plugin/trackmate/tracking/jaqaman/SegmentTrackerFactory.java
+++ b/src/main/java/fiji/plugin/trackmate/tracking/jaqaman/SegmentTrackerFactory.java
@@ -31,7 +31,6 @@
import static fiji.plugin.trackmate.tracking.TrackerKeys.KEY_ALLOW_TRACK_MERGING;
import static fiji.plugin.trackmate.tracking.TrackerKeys.KEY_ALLOW_TRACK_SPLITTING;
import static fiji.plugin.trackmate.tracking.TrackerKeys.KEY_ALTERNATIVE_LINKING_COST_FACTOR;
-import static fiji.plugin.trackmate.tracking.TrackerKeys.KEY_BLOCKING_VALUE;
import static fiji.plugin.trackmate.tracking.TrackerKeys.KEY_CUTOFF_PERCENTILE;
import static fiji.plugin.trackmate.tracking.TrackerKeys.KEY_GAP_CLOSING_FEATURE_PENALTIES;
import static fiji.plugin.trackmate.tracking.TrackerKeys.KEY_GAP_CLOSING_MAX_DISTANCE;
@@ -109,7 +108,6 @@ public String marshal( final Map< String, Object > settings, final Element eleme
// Others
ok = ok & writeAttribute( settings, element, KEY_CUTOFF_PERCENTILE, Double.class, str );
ok = ok & writeAttribute( settings, element, KEY_ALTERNATIVE_LINKING_COST_FACTOR, Double.class, str );
- ok = ok & writeAttribute( settings, element, KEY_BLOCKING_VALUE, Double.class, str );
if ( !ok )
return str.toString();
@@ -188,7 +186,6 @@ public boolean unmarshallSegment( final Element element, final Map< String, Obje
// Others
ok = ok & readDoubleAttribute( element, settings, KEY_CUTOFF_PERCENTILE, errorHolder );
ok = ok & readDoubleAttribute( element, settings, KEY_ALTERNATIVE_LINKING_COST_FACTOR, errorHolder );
- ok = ok & readDoubleAttribute( element, settings, KEY_BLOCKING_VALUE, errorHolder );
return ok;
}
diff --git a/src/test/java/fiji/plugin/trackmate/io/TmGeffWriterTestDrive.java b/src/test/java/fiji/plugin/trackmate/io/TmGeffWriterTestDrive.java
deleted file mode 100644
index 579a6c8a0..000000000
--- a/src/test/java/fiji/plugin/trackmate/io/TmGeffWriterTestDrive.java
+++ /dev/null
@@ -1,28 +0,0 @@
-package fiji.plugin.trackmate.io;
-
-import java.io.File;
-import java.io.IOException;
-
-import fiji.plugin.trackmate.Model;
-
-public class TmGeffWriterTestDrive
-{
-
- public static void main( final String[] args ) throws IOException
- {
- final String path = "samples/FakeTracks.xml";
- final TmXmlReader reader = new TmXmlReader( new File( path ) );
- if ( !reader.isReadingOk() )
- {
- System.err.println( reader.getErrorMessage() );
- return;
- }
- final String savePath = path.replace( ".xml", ".geff" );
-
- final Model model = reader.getModel();
-
- System.out.println( "Writing to " + savePath );
- TmGeffWriter.write( model, savePath );
- System.out.println( "Done." );
- }
-}
diff --git a/src/test/java/fiji/plugin/trackmate/io/geff/GeffTestBase.java b/src/test/java/fiji/plugin/trackmate/io/geff/GeffTestBase.java
new file mode 100644
index 000000000..c07cc0d06
--- /dev/null
+++ b/src/test/java/fiji/plugin/trackmate/io/geff/GeffTestBase.java
@@ -0,0 +1,54 @@
+package fiji.plugin.trackmate.io.geff;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+/**
+ * Base class for GEFF tests. Sets up the native library path for blosc
+ * before any test code runs, covering all platforms and environments
+ * (Eclipse, Maven, CI) without requiring manual run configuration.
+ */
+public abstract class GeffTestBase
+{
+ static
+ {
+ setupJnaLibraryPath();
+ }
+
+ /**
+ * Prepends common blosc installation directories to {@code jna.library.path}
+ * so JNA can find {@code libblosc} regardless of the execution environment.
+ *
+ * Priority order matters: more specific paths (Apple Silicon Homebrew) come
+ * before more generic ones so the correct architecture is always preferred.
+ */
+ private static void setupJnaLibraryPath()
+ {
+ final String[] candidates = {
+ "/opt/homebrew/lib", // macOS Apple Silicon (Homebrew)
+ "/usr/local/lib", // macOS Intel (Homebrew) or manual install
+ "/usr/lib", // Linux generic
+ "/usr/lib/x86_64-linux-gnu", // Ubuntu / Debian x86_64
+ "/usr/lib/aarch64-linux-gnu", // Ubuntu / Debian ARM64
+ };
+
+ // Start from whatever is already set (e.g. by Maven Surefire -D flags)
+ final String existing = System.getProperty( "jna.library.path", "" );
+ final List< String > paths = new ArrayList<>(
+ Arrays.asList( existing.split( File.pathSeparator ) ) );
+ paths.removeIf( String::isEmpty );
+
+ for ( final String candidate : candidates )
+ {
+ final File dir = new File( candidate );
+ if ( dir.isDirectory() && !paths.contains( candidate ) )
+ paths.add( candidate );
+ }
+
+ final String joined = String.join( File.pathSeparator, paths );
+ System.setProperty( "jna.library.path", joined );
+ System.out.println( "[GeffTestBase] jna.library.path = " + joined );
+ }
+}
diff --git a/src/test/java/fiji/plugin/trackmate/io/geff/GeffTestDeserializationTest.java b/src/test/java/fiji/plugin/trackmate/io/geff/GeffTestDeserializationTest.java
new file mode 100644
index 000000000..c23297c29
--- /dev/null
+++ b/src/test/java/fiji/plugin/trackmate/io/geff/GeffTestDeserializationTest.java
@@ -0,0 +1,444 @@
+package fiji.plugin.trackmate.io.geff;
+
+import static org.assertj.core.api.Assertions.assertThat;
+
+import java.io.File;
+import java.util.HashMap;
+import java.util.LinkedHashMap;
+import java.util.Map;
+import java.util.Set;
+import java.util.stream.Collectors;
+
+import org.assertj.core.presentation.StandardRepresentation;
+import org.jgrapht.graph.DefaultWeightedEdge;
+import org.junit.BeforeClass;
+import org.junit.Rule;
+import org.junit.Test;
+import org.junit.rules.TemporaryFolder;
+
+import fiji.plugin.trackmate.FeatureModel;
+import fiji.plugin.trackmate.Model;
+import fiji.plugin.trackmate.Settings;
+import fiji.plugin.trackmate.Spot;
+import fiji.plugin.trackmate.SpotCollection;
+import fiji.plugin.trackmate.SpotRoi;
+import fiji.plugin.trackmate.TrackModel;
+import fiji.plugin.trackmate.gui.displaysettings.DisplaySettings;
+import fiji.plugin.trackmate.io.TmXmlReader;
+
+/**
+ * Tests that check that a TrackMate model, settings etc, can be written and
+ * read to / from a GEFF file, and that the resulting objects are identical.
+ */
+public class GeffTestDeserializationTest extends GeffTestBase
+{
+
+ /**
+ * A TrackMate XML file generated with TrackMate v8, containing only
+ * 'SpotBase' spots.
+ */
+ static final String SPOT_BASE_PATH = GeffTestDeserializationTest.class
+ .getResource( "FakeTracks.xml" )
+ .getFile();
+
+ /**
+ * A TrackMate XML file generated with TrackMate v8, containing only
+ * 'SpotRoi' spots.
+ */
+ static final String SPOT_ROI_PATH = GeffTestDeserializationTest.class
+ .getResource( "MAX_Merged.xml" )
+ .getFile();
+
+ /**
+ * A TrackMate XML file generated with TrackMate v8, containing 'SpotBase
+ * and 'SpotRoi' spots.
+ */
+ static final String SPOT_MIXED_PATH = GeffTestDeserializationTest.class
+ .getResource( "MAX_Merged-mixed.xml" )
+ .getFile();
+
+ @Test
+ public void testSpotBaseSerialization() throws Exception
+ {
+ testModelSerialization( SPOT_BASE_PATH );
+ }
+
+ @Test
+ public void testSpotRoiSerialization() throws Exception
+ {
+ testModelSerialization( SPOT_ROI_PATH );
+ }
+
+ @Test
+ public void testSpotMixedSerialization() throws Exception
+ {
+ testModelSerialization( SPOT_MIXED_PATH );
+ }
+
+ /**
+ * JUnit 4 rule that creates a temporary folder that is guaranteed to exist
+ * and be writable, and is automatically deleted after each test.
+ */
+ @Rule
+ public TemporaryFolder temporaryFolder = new TemporaryFolder();
+
+ protected void testModelSerialization( final String path ) throws Exception
+ {
+ final TmXmlReader reader = new TmXmlReader( new File( path ) );
+ if ( !reader.isReadingOk() )
+ throw new Exception( reader.getErrorMessage() );
+
+ final Model initialModel = reader.getModel();
+ final Settings initialSettings = reader.readSettings( null );
+ final DisplaySettings initialDisplaySettings = reader.getDisplaySettings();
+ final String initialLog = reader.getLog();
+ final String initialGUIState = reader.getGUIState();
+
+ final String geffFile = new File( temporaryFolder.getRoot(), "test.geff" ).getAbsolutePath();
+ final TmGeffWriter geffWriter = new TmGeffWriter( geffFile );
+ geffWriter.appendModel( initialModel );
+ geffWriter.appendSettings( initialSettings );
+ geffWriter.appendDisplaySettings( initialDisplaySettings );
+ geffWriter.appendLog( initialLog );
+ geffWriter.appendGUIState( initialGUIState );
+ geffWriter.write();
+
+ final TmGeffReader geffReader = new TmGeffReader( geffFile );
+
+ final Model readBackModel = geffReader.getModel();
+ testModelEquality( initialModel, readBackModel );
+
+ final Settings readBackSettings = geffReader.readSettings( null );
+ testSettingsEquality( initialSettings, readBackSettings );
+
+ final DisplaySettings readBackDisplaySettings = geffReader.getDisplaySettings();
+ testDisplaySettingsEquality( initialDisplaySettings, readBackDisplaySettings );
+
+ final String readBackLog = geffReader.getLog();
+ assertThat( readBackLog )
+ .as( "TrackMate log" )
+ .isEqualTo( initialLog );
+
+ final String readBackGUIState = geffReader.getGUIState();
+ assertThat( readBackGUIState )
+ .as( "TrackMate GUI state" )
+ .isEqualTo( initialGUIState );
+ }
+
+ private void testDisplaySettingsEquality( final DisplaySettings initialDisplaySettings, final DisplaySettings readBackDisplaySettings )
+ {
+ assertThat( initialDisplaySettings )
+ .withRepresentation( new StandardRepresentation()
+ {
+ @Override
+ public String toStringOf( final Object obj )
+ {
+ if ( obj instanceof final DisplaySettings ds )
+ return String.format( "DisplaySettings[%d]", ds.hashCode() );
+ return super.toStringOf( obj );
+ }
+ } )
+ .usingRecursiveComparison()
+ .isEqualTo( readBackDisplaySettings );
+ }
+
+ private void testSettingsEquality( final Settings initialSettings, final Settings readBackSettings )
+ {
+
+ assertThat( initialSettings )
+ .withRepresentation( new StandardRepresentation()
+ {
+ @Override
+ public String toStringOf( final Object obj )
+ {
+ if ( obj instanceof final Settings s )
+ return String.format( "Settings[%d]", s.hashCode() );
+ return super.toStringOf( obj );
+ }
+ } )
+ .usingRecursiveComparison()
+ .isEqualTo( readBackSettings );
+ }
+
+ private void testModelEquality( final Model initialModel, final Model readBackModel )
+ {
+ assertThat( initialModel )
+ .withRepresentation( new StandardRepresentation()
+ {
+ @Override
+ public String toStringOf( final Object obj )
+ {
+ if ( obj instanceof final Model m )
+ return String.format( "Model[%d]", m.hashCode() );
+ return super.toStringOf( obj );
+ }
+ } )
+ .usingRecursiveComparison()
+ .withEqualsForType(
+ // Used to pair spots in sets.
+ ( a, b ) -> a.ID() == b.ID(), Spot.class )
+ .ignoringFields(
+ // Treated separately
+ "spots",
+ "featureModel",
+ "trackModel",
+ // Listeners
+ "modelChangeListeners",
+ // Utils
+ "logger",
+ // Transaction state fields
+ "updateLevel",
+ "spotsAdded",
+ "spotsRemoved",
+ "spotsMoved",
+ "spotsUpdated",
+ "eventCache" )
+ .isEqualTo( readBackModel );
+
+ /*
+ * SpotCollection
+ */
+
+ compareSpotCollections( initialModel.getSpots(), readBackModel.getSpots() );
+
+ /*
+ * Feature model
+ */
+
+ assertThat( initialModel.getFeatureModel() )
+ .withRepresentation( new StandardRepresentation()
+ {
+ @Override
+ public String toStringOf( final Object obj )
+ {
+ if ( obj instanceof final FeatureModel fm )
+ return String.format( "FeatureModel[%d]", fm.hashCode() );
+ return super.toStringOf( obj );
+ }
+ } )
+ .usingRecursiveComparison()
+ .ignoringFields(
+ "model", // Transient
+ "edgeFeatureValues" ) // Treated separately )
+ .isEqualTo( readBackModel.getFeatureModel() );
+
+ // Compare edge feature values separately, because the keys are
+ // DefaultWeightedEdge objects
+ compareEdgeFeatureValues( initialModel, readBackModel );
+
+ /*
+ * Track model
+ */
+
+ compareTrackModels( initialModel.getTrackModel(), readBackModel.getTrackModel() );
+ }
+
+ private static void compareSpotCollections( final SpotCollection actual, final SpotCollection expected )
+ {
+ // Same frames
+ assertThat( actual.keySet() )
+ .as( "SpotCollection frames" )
+ .containsExactlyInAnyOrderElementsOf( expected.keySet() );
+
+ actual.keySet().forEach( frame -> {
+
+ final Iterable< Spot > actualSpots = actual.iterable( frame, false );
+ final Iterable< Spot > expectedSpots = expected.iterable( frame, false );
+
+ // Same number of spots per frame
+ assertThat( actualSpots )
+ .as( "number of spots in frame %d", frame )
+ .hasSameSizeAs( expectedSpots );
+
+ // Build ID -> Spot lookup for expected
+ final Map< Integer, Spot > expectedById = new HashMap<>();
+ expectedSpots.forEach( s -> expectedById.put( s.ID(), s ) );
+
+ actualSpots.forEach( actualSpot -> {
+
+ // Spot exists in expected
+ final Spot expectedSpot = expectedById.get( actualSpot.ID() );
+ assertThat( expectedSpot )
+ .as( "Spot ID=%d missing in frame %d", actualSpot.ID(), frame )
+ .isNotNull();
+
+ // Delegate to single-spot comparison
+ assertSpotEquals( actualSpot, expectedSpot );
+ } );
+ } );
+ }
+
+ private static void assertSpotEquals( final Spot actual, final Spot expected )
+ {
+ // 1. Check same implementation type
+ assertThat( actual.getClass() )
+ .as( "Spot ID=%d implementation type", actual.ID() )
+ .isEqualTo( expected.getClass() );
+
+ // 2. Basic identity
+ assertThat( actual.ID() )
+ .as( "Spot ID" )
+ .isEqualTo( expected.ID() );
+
+ assertThat( actual.getName() )
+ .as( "Spot ID=%d name", actual.ID() )
+ .isEqualTo( expected.getName() );
+
+ // 3. Feature keys
+ assertThat( actual.getFeatures().keySet() )
+ .as( "Spot ID=%d feature keys", actual.ID() )
+ .containsExactlyInAnyOrderElementsOf(
+ expected.getFeatures().keySet() );
+
+ // 4. Feature values
+ assertThat( actual.getFeatures() )
+ .as( "Spot ID=%d feature values", actual.ID() )
+ .allSatisfy( ( key, value ) -> assertThat( value )
+ .as( "Spot ID=%d feature '%s'", actual.ID(), key )
+ .isEqualTo(
+ expected.getFeatures().getOrDefault( key, Double.NaN ) ) );
+
+ // 5. SpotRoi-specific: polygon coordinates
+ if ( actual instanceof SpotRoi )
+ assertSpotRoiEquals( ( SpotRoi ) actual, ( SpotRoi ) expected );
+ }
+
+ private static void assertSpotRoiEquals( final SpotRoi actual, final SpotRoi expected )
+ {
+ // Number of polygon vertices
+ assertThat( actual.nPoints() )
+ .as( "SpotRoi ID=%d number of polygon points", actual.ID() )
+ .isEqualTo( expected.nPoints() );
+
+ // X coordinates of polygon vertices (relative to center)
+ for ( int i = 0; i < actual.nPoints(); i++ )
+ {
+ final int idx = i; // for lambda capture
+ assertThat( actual.xr( i ) )
+ .as( "SpotRoi ID=%d polygon x[%d]", actual.ID(), idx )
+ .isEqualTo( expected.xr( i ) );
+
+ assertThat( actual.yr( i ) )
+ .as( "SpotRoi ID=%d polygon y[%d]", actual.ID(), idx )
+ .isEqualTo( expected.yr( i ) );
+ }
+ }
+
+ private void compareTrackModels( final TrackModel actual, final TrackModel expected )
+ {
+ // 1. All spots in the graph (including isolated ones)
+ assertThat( actual.vertexSet().stream()
+ .map( s -> s.ID() )
+ .collect( Collectors.toSet() ) )
+ .as( "TrackModel: spot IDs" )
+ .containsExactlyInAnyOrderElementsOf(
+ expected.vertexSet().stream()
+ .map( s -> s.ID() )
+ .collect( Collectors.toSet() ) );
+
+ // 2. Edge topology and weights
+ final Map< String, Double > actualEdges = buildEdgeWeightMap( actual );
+ final Map< String, Double > expectedEdges = buildEdgeWeightMap( expected );
+
+ assertThat( actualEdges.keySet() )
+ .as( "TrackModel: edges" )
+ .containsExactlyInAnyOrderElementsOf( expectedEdges.keySet() );
+
+ assertThat( actualEdges )
+ .as( "TrackModel: edge weights" )
+ .allSatisfy( ( edgeKey, weight ) -> assertThat( weight )
+ .as( "weight of edge [%s]", edgeKey )
+ .isEqualTo( expectedEdges.get( edgeKey ) ) );
+
+ // 3. Track structure, visibility and names
+ compareTracks( actual, expected );
+ }
+
+ /**
+ * Build "srcID->tgtID" -> weight map, independent of edge object identity.
+ */
+ private static Map< String, Double > buildEdgeWeightMap( final TrackModel model )
+ {
+ final Map< String, Double > map = new LinkedHashMap<>();
+ model.edgeSet().forEach( e -> {
+ final String key = model.getEdgeSource( e ).ID() + "->" + model.getEdgeTarget( e ).ID();
+ map.put( key, model.getEdgeWeight( e ) );
+ } );
+ return map;
+ }
+
+ /** Compare tracks matched by spot content, not by track ID. */
+ private static void compareTracks( final TrackModel actual, final TrackModel expected )
+ {
+ final Set< Integer > actualTrackIDs = actual.trackIDs( false );
+ final Set< Integer > expectedTrackIDs = expected.trackIDs( false );
+
+ assertThat( actualTrackIDs )
+ .as( "TrackModel: identical tracks IDs" )
+ .isEqualTo( expectedTrackIDs );
+
+ actualTrackIDs.forEach( actualTID -> {
+
+ // Visibility
+ assertThat( actual.isVisible( actualTID ) )
+ .as( "visibility of track ID: [%d]", actualTID )
+ .isEqualTo( expected.isVisible( actualTID ) );
+
+ // Name
+ assertThat( actual.name( actualTID ) )
+ .as( "name of track ID: [%d]", actualTID )
+ .isEqualTo( expected.name( actualTID ) );
+ } );
+ }
+
+ private void compareEdgeFeatureValues( final Model m1, final Model m2 )
+ {
+ final FeatureModel fm1 = m1.getFeatureModel();
+ final FeatureModel fm2 = m2.getFeatureModel();
+
+ // If so, iterate edges from the track model instead:
+ m1.getTrackModel().edgeSet().forEach( edge -> {
+ final int sId = m1.getTrackModel().getEdgeSource( edge ).ID();
+ final int tId = m1.getTrackModel().getEdgeTarget( edge ).ID();
+
+ // Find matching edge in readback model
+ final DefaultWeightedEdge matchedEdge = m2.getTrackModel().edgeSet().stream()
+ .filter( e -> m2.getTrackModel().getEdgeSource( e ).ID() == sId
+ && m2.getTrackModel().getEdgeTarget( e ).ID() == tId )
+ .findFirst()
+ .orElseThrow( () -> new AssertionError( "No matching edge for ID" + sId + " -> ID" + tId ) );
+
+ // Compare feature by feature
+ fm1.getEdgeFeatures()
+ .forEach( featureKey -> {
+ final Double actual = fm1.getEdgeFeature( edge, featureKey );
+ final Double expected = fm2.getEdgeFeature( matchedEdge, featureKey );
+
+ // Both null is ok.
+ if ( actual == null && expected == null )
+ return;
+
+ assertThat( actual )
+ .as( "feature '%s' on edge (ID%d -> ID%d)", featureKey, sId, tId )
+ .isEqualTo( expected );
+ } );
+ } );
+ }
+
+ @BeforeClass
+ public static void checkBlosc()
+ {
+ System.out.println( "[GeffCompatSpotBaseTest] Checking that blosc is loadable..." );
+ System.out.println( "jna.library.path = " + System.getProperty( "jna.library.path" ) );
+ System.out.println( "java.library.path = " + System.getProperty( "java.library.path" ) );
+ try
+ {
+ new org.janelia.saalfeldlab.n5.blosc.BloscCompression();
+ System.out.println( "blosc loaded successfully" );
+ }
+ catch ( final Throwable t )
+ {
+ System.err.println( "blosc load failed: " + t.getMessage() );
+ }
+ }
+}
diff --git a/src/test/java/fiji/plugin/trackmate/io/geff/TmGeffIODemo.java b/src/test/java/fiji/plugin/trackmate/io/geff/TmGeffIODemo.java
new file mode 100644
index 000000000..c670379ad
--- /dev/null
+++ b/src/test/java/fiji/plugin/trackmate/io/geff/TmGeffIODemo.java
@@ -0,0 +1,176 @@
+package fiji.plugin.trackmate.io.geff;
+
+import static fiji.plugin.trackmate.gui.Icons.TRACKMATE_ICON;
+
+import java.awt.Color;
+import java.io.File;
+import java.io.IOException;
+
+import javax.swing.JFrame;
+
+import org.apache.commons.io.FileUtils;
+
+import fiji.plugin.trackmate.Logger;
+import fiji.plugin.trackmate.Model;
+import fiji.plugin.trackmate.SelectionModel;
+import fiji.plugin.trackmate.Settings;
+import fiji.plugin.trackmate.TrackMate;
+import fiji.plugin.trackmate.features.edges.EdgeAnalyzer;
+import fiji.plugin.trackmate.features.spot.SpotAnalyzerFactoryBase;
+import fiji.plugin.trackmate.features.track.TrackAnalyzer;
+import fiji.plugin.trackmate.gui.GuiUtils;
+import fiji.plugin.trackmate.gui.components.LogPanel;
+import fiji.plugin.trackmate.gui.displaysettings.DisplaySettings;
+import fiji.plugin.trackmate.gui.wizard.TrackMateWizardSequence;
+import fiji.plugin.trackmate.gui.wizard.WizardSequence;
+import fiji.plugin.trackmate.gui.wizard.descriptors.LogPanelDescriptor2;
+import fiji.plugin.trackmate.gui.wizard.descriptors.StartDialogDescriptor;
+import fiji.plugin.trackmate.io.TmXmlReader;
+import fiji.plugin.trackmate.util.TMUtils;
+import fiji.plugin.trackmate.visualization.TrackMateModelView;
+import fiji.plugin.trackmate.visualization.hyperstack.HyperStackDisplayer;
+import ij.ImagePlus;
+
+public class TmGeffIODemo
+{
+
+ public static void main( final String[] args ) throws IOException
+ {
+ final String path = GeffTestDeserializationTest.SPOT_MIXED_PATH;
+ System.out.println( "Reading from " + path );
+ final TmXmlReader reader = new TmXmlReader( new File( path ) );
+ if ( !reader.isReadingOk() )
+ {
+ System.err.println( reader.getErrorMessage() );
+ return;
+ }
+ System.out.println( "Done." );
+ final String savePath = path.replace( ".xml", ".geff" );
+
+ final Model model = reader.getModel();
+ final ImagePlus imp = reader.readImage();
+ final Settings settings = reader.readSettings( imp );
+
+ System.out.println( "Deleting previous " + savePath );
+ FileUtils.deleteDirectory( new File( savePath ) );
+ System.out.println( "Done." );
+
+ System.out.println( "Writing to " + savePath );
+
+ final TmGeffWriter geffWriter = new TmGeffWriter( savePath );
+ geffWriter.appendModel( model );
+ geffWriter.appendSettings( settings );
+ geffWriter.appendDisplaySettings( reader.getDisplaySettings() );
+ geffWriter.appendLog( reader.getLog() );
+ geffWriter.appendGUIState( reader.getGUIState() );
+ geffWriter.write();
+
+ System.out.println( "Done." );
+
+ System.out.println( "Reading the model back from " + savePath );
+ readBack( savePath );
+ }
+
+ private static void readBack( final String savePath ) throws IOException
+ {
+ final TmGeffReader geffReader = new TmGeffReader( savePath );
+
+ // Model
+ final Model model = geffReader.getModel();
+
+ // Image
+ final ImagePlus imp = geffReader.readImage();
+
+ // Settings
+ final Settings settings = geffReader.readSettings( imp );
+
+ /*
+ * Declare the analyzers that are in the settings to the model. This is
+ * required when we are loading a file that does not have the analyzer
+ * presents at runtime declared in the settings section of the file.
+ */
+ for ( final SpotAnalyzerFactoryBase< ? > analyzer : settings.getSpotAnalyzerFactories() )
+ model.getFeatureModel().declareSpotFeatures(
+ analyzer.getFeatures(),
+ analyzer.getFeatureNames(),
+ analyzer.getFeatureShortNames(),
+ analyzer.getFeatureDimensions(),
+ analyzer.getIsIntFeature() );
+
+ for ( final EdgeAnalyzer analyzer : settings.getEdgeAnalyzers() )
+ model.getFeatureModel().declareEdgeFeatures(
+ analyzer.getFeatures(),
+ analyzer.getFeatureNames(),
+ analyzer.getFeatureShortNames(),
+ analyzer.getFeatureDimensions(),
+ analyzer.getIsIntFeature() );
+ for ( final TrackAnalyzer analyzer : settings.getTrackAnalyzers() )
+ model.getFeatureModel().declareTrackFeatures(
+ analyzer.getFeatures(),
+ analyzer.getFeatureNames(),
+ analyzer.getFeatureShortNames(),
+ analyzer.getFeatureDimensions(),
+ analyzer.getIsIntFeature() );
+
+ // Display settings
+ final DisplaySettings displaySettings = geffReader.getDisplaySettings();
+
+ // GUI state
+ final String panelIdentifier = geffReader.getGUIState();
+
+ // Log
+ final String log = geffReader.getLog();
+
+ // Put them together in a TrackMate instance.
+ final TrackMate trackmate = new TrackMate( model, settings );
+ final SelectionModel selectionModel = new SelectionModel( model );
+
+ // Main view.
+ final TrackMateModelView displayer = new HyperStackDisplayer( model, selectionModel, settings.imp, displaySettings );
+ displayer.render();
+
+ // Wizard.
+ final WizardSequence sequence = new TrackMateWizardSequence( trackmate, selectionModel, displaySettings );
+ sequence.setCurrent( panelIdentifier );
+ final JFrame frame = sequence.run( "From GEFF: " + savePath );
+ frame.setIconImage( TRACKMATE_ICON.getImage() );
+ GuiUtils.positionWindow( frame, settings.imp.getWindow() );
+
+ // Text
+ final LogPanelDescriptor2 logDescriptor = ( LogPanelDescriptor2 ) sequence.logDescriptor();
+ final LogPanel logPanel = ( LogPanel ) logDescriptor.getPanelComponent();
+ final Logger logger2 = logPanel.getLogger();
+
+ logger2.log( "Session log saved in the file:\n"
+ + "--------------------\n"
+ + log
+ + "--------------------\n",
+ Color.GRAY );
+
+ final String warning = "";
+ if ( !warning.isEmpty() )
+ {
+ logger2.log( "Warnings occurred during reading the file:\n"
+ + "--------------------\n"
+ + warning
+ + "--------------------\n",
+ Color.ORANGE.darker() );
+ }
+ logger2.log( "File loaded on " + TMUtils.getCurrentTimeString() + '\n', Logger.BLUE_COLOR );
+ final String welcomeMessage = TrackMate.PLUGIN_NAME_STR + " v" + TrackMate.PLUGIN_NAME_VERSION + '\n';
+ // Log GUI processing start
+ logger2.log( welcomeMessage, Logger.BLUE_COLOR );
+ logger2.log( "Please note that TrackMate is available through Fiji, and is based on a publication. "
+ + "If you use it successfully for your research please be so kind to cite our work:\n" );
+ logger2.log( StartDialogDescriptor.PUB2_TXT + "\n", Logger.GREEN_COLOR );
+ logger2.log( StartDialogDescriptor.PUB2_URL + "\n", Logger.BLUE_COLOR );
+ logger2.log( "and / or:\n" );
+ logger2.log( StartDialogDescriptor.PUB1_TXT + "\n", Logger.GREEN_COLOR );
+ logger2.log( StartDialogDescriptor.PUB1_URL + "\n", Logger.BLUE_COLOR );
+ logger2.log( "and / or:\n" );
+ logger2.log( StartDialogDescriptor.PUB0_TXT + "\n", Logger.GREEN_COLOR );
+ logger2.log( StartDialogDescriptor.PUB0_URL + "\n", Logger.BLUE_COLOR );
+
+ frame.setVisible( true );
+ }
+}
diff --git a/src/test/resources/fiji/plugin/trackmate/io/geff/FakeTracks.xml b/src/test/resources/fiji/plugin/trackmate/io/geff/FakeTracks.xml
new file mode 100644
index 000000000..28992be52
--- /dev/null
+++ b/src/test/resources/fiji/plugin/trackmate/io/geff/FakeTracks.xml
@@ -0,0 +1,757 @@
+
+
+ Session log saved in the file:
+--------------------
+TrackMate v8.1.6 started on:
+Thu, 23 Jul 2026 09:44:18
+Please note that TrackMate is available through iji, and is based on a publication. If you use it successfully for your research please be so kind to cite our work:
+rshov, D., Phan, MS., Pylvänäinen, J.W., Rigaud S.U., et al. TrackMate 7: integrating state-of-the-art segmentation algorithms into tracking pipelines. Nat Methods (2022). https://doi.org/10.1038/s41592-022-01507-1
+https://doi.org/10.1038/s41592-022-01507-1
+and / or:
+Tinevez, JY.; Perry, N. & Schindelin, J. et al. (2017), 'TrackMate: An open and extensible platform for single-particle tracking.', Methods 115: 80-90, PMID 27713081.
+https://www.sciencedirect.com/science/article/pii/S1046202316303346
+
+Numerical feature analyzers:
+Spot feature analyzers:
+ - Manual spot color provides: Spot color; is manual.
+ - Spot intensity provides: Mean ch1, Median ch1, Min ch1, Max ch1, Sum ch1, Std ch1.
+ - xTrack probabilities provides: P stuck, P diffusive; is manual.
+ - Spot contrast and SNR provides: Ctrst ch1, SNR ch1.
+dge feature analyzers:
+ - Directional change provides: γ rate.
+ - dge speed provides: Speed, Disp.
+ - dge target provides: Source ID, Target ID, Cost.
+ - dge location provides: dge T, dge X, dge Y, dge Z.
+ - Manual edge color provides: dge color; is manual.
+Track feature analyzers:
+ - Branching analyzer provides: N spots, N gaps, N splits, N merges, N complex, Lgst gap.
+ - Track duration provides: Duration, Track start, Track stop, Track disp.
+ - Track index provides: Index, ID.
+ - Track location provides: Track X, Track Y, Track Z.
+ - Track speed provides: Mean sp., Max speed, Min speed, Med. speed, Std speed.
+ - Track quality provides: Mean Q.
+ - Track motility analysis provides: Total dist., Max dist., Cfn. ratio, Mn. v. line, wd. progr., Mn. γ rate.
+
+Image region of interest:
+Image data:
+or the image named: akeTracks.tif.
+Matching file akeTracks.tif in folder: /Users/tinevez/Development/TrackMateWS/TrackMate/samples/
+Geometry:
+ X = 6 - 122, dx = 1.00000
+ Y = 1 - 125, dy = 1.00000
+ Z = 0 - 0, dz = 1.00000
+ T = 0 - 49, dt = 1.00000
+
+Configured detector LoG detector with settings:
+ - target channel: 1
+ - threshold: 0.0
+ - radius: 2.5
+ - do subpixel localization: true
+ - do median filtering: false
+
+Starting detection process using 12 threads.
+Detection processes 12 frames simultaneously and allocates 1 thread per frame.
+ound 19359 spots.
+Detection done in 0.3 s.
+
+Computing spot quality histogram...
+Initial thresholding with a quality threshold above 19.0 ...
+Starting initial filtering process.
+Retained 233 spots out of 19359.
+
+Calculating spot features...
+Calculating features done in 0.0 s.
+
+Performing spot filtering on the following features:
+ - on Quality above 60.0
+Kept 84 spots out of 233.
+
+Configured tracker LAP Tracker with settings:
+ - max frame gap: 2
+ - alternative linking cost factor: 1.05
+ - linking feature penalties:
+ - linking max distance: 15.0
+ - gap closing max distance: 15.0
+ - merging feature penalties:
+ - splitting max distance: 15.0
+ - blocking value: Infinity
+ - allow gap closing: true
+ - allow track splitting: false
+ - allow track merging: false
+ - merging max distance: 15.0
+ - splitting feature penalties:
+ - cutoff percentile: 0.9
+ - gap closing feature penalties:
+
+Starting tracking process.
+Tracking done in 0.0 s.
+ound 4 tracks.
+ - avg size: 21.0 spots.
+ - min size: 10 spots.
+ - max size: 42 spots.
+
+Configured tracker LAP Tracker with settings:
+ - max frame gap: 2
+ - alternative linking cost factor: 1.05
+ - linking feature penalties:
+ - linking max distance: 15.0
+ - gap closing max distance: 15.0
+ - merging feature penalties:
+ - splitting max distance: 15.0
+ - blocking value: Infinity
+ - allow gap closing: true
+ - allow track splitting: true
+ - allow track merging: false
+ - merging max distance: 15.0
+ - splitting feature penalties:
+ - cutoff percentile: 0.9
+ - gap closing feature penalties:
+
+Starting tracking process.
+Tracking done in 0.0 s.
+ound 2 tracks.
+ - avg size: 42.0 spots.
+ - min size: 10 spots.
+ - max size: 74 spots.
+
+Calculating features done in 0.0 s.
+
+Performing track filtering on the following features:
+ - on Number of spots in track above 40.0
+Kept 1 spots out of 2.
+Saving data...
+Computing edge features:
+ - Directional change in 0 ms.
+ - dge speed in 1 ms.
+ - dge target in 0 ms.
+ - dge location in 1 ms.
+Computation done in 3 ms.
+Computing track features:
+ - Branching analyzer in 0 ms.
+ - Track duration in 1 ms.
+ - Track index in 0 ms.
+ - Track location in 0 ms.
+ - Track speed in 0 ms.
+ - Track quality in 0 ms.
+ - Track motility analysis in 0 ms.
+Computation done in 1 ms.
+--------------------
+ile loaded on Thu, 23 Jul 2026 09:45:19
+TrackMate v8.1.6
+Please note that TrackMate is available through iji, and is based on a publication. If you use it successfully for your research please be so kind to cite our work:
+rshov, D., Phan, MS., Pylvänäinen, J.W., Rigaud S.U., et al. TrackMate 7: integrating state-of-the-art segmentation algorithms into tracking pipelines. Nat Methods (2022). https://doi.org/10.1038/s41592-022-01507-1
+https://doi.org/10.1038/s41592-022-01507-1
+and / or:
+Tinevez, JY.; Perry, N. & Schindelin, J. et al. (2017), 'TrackMate: An open and extensible platform for single-particle tracking.', Methods 115: 80-90, PMID 27713081.
+https://www.sciencedirect.com/science/article/pii/S1046202316303346
+
+Performing track filtering on the following features:
+ - on Number of spots in track above -1.3
+Kept 2 spots out of 2.
+
+Performing track filtering on the following features:
+ - on Number of spots in track above 40.0
+Kept 1 spots out of 2.
+Saving data...
+Computing edge features:
+ - Directional change in 2 ms.
+ - dge speed in 0 ms.
+ - dge target in 2 ms.
+ - dge location in 2 ms.
+Computation done in 8 ms.
+Computing track features:
+ - Branching analyzer in 0 ms.
+ - Track duration in 0 ms.
+ - Track index in 0 ms.
+ - Track location in 0 ms.
+ - Track speed in 0 ms.
+ - Track quality in 3 ms.
+ - Track motility analysis in 0 ms.
+Computation done in 4 ms.
+
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+ {
+ "name": "CurrentDisplaySettings",
+ "spotUniformColor": "204, 51, 204, 255",
+ "spotColorByType": "TRACKS",
+ "spotColorByFeature": "TRACK_INDEX",
+ "spotDisplayRadius": 1.0,
+ "spotDisplayedAsRoi": true,
+ "spotMin": 0.0,
+ "spotMax": 10.0,
+ "spotShowName": true,
+ "trackMin": 0.0,
+ "trackMax": 10.0,
+ "trackColorByType": "TRACKS",
+ "trackColorByFeature": "TRACK_INDEX",
+ "trackUniformColor": "204, 204, 51, 255",
+ "undefinedValueColor": "0, 0, 0, 255",
+ "missingValueColor": "89, 89, 89, 255",
+ "highlightColor": "51, 230, 51, 255",
+ "trackDisplayMode": "FULL",
+ "colormap": "Jet",
+ "limitZDrawingDepth": false,
+ "drawingZDepth": 10.0,
+ "fadeTracks": true,
+ "fadeTrackRange": 30,
+ "useAntialiasing": true,
+ "spotVisible": true,
+ "trackVisible": true,
+ "font": {
+ "name": "Arial",
+ "style": 1,
+ "size": 12
+ },
+ "lineThickness": 1.0,
+ "selectionLineThickness": 4.0,
+ "trackschemeBackgroundColor1": "128, 128, 128, 255",
+ "trackschemeBackgroundColor2": "192, 192, 192, 255",
+ "trackschemeForegroundColor": "0, 0, 0, 255",
+ "trackschemeDecorationColor": "0, 0, 0, 255",
+ "trackschemeFillBox": false,
+ "spotFilled": false,
+ "spotTransparencyAlpha": 1.0
+}
+
diff --git a/src/test/resources/fiji/plugin/trackmate/io/geff/MAX_Merged-mixed.xml b/src/test/resources/fiji/plugin/trackmate/io/geff/MAX_Merged-mixed.xml
new file mode 100644
index 000000000..b44b0d4d8
--- /dev/null
+++ b/src/test/resources/fiji/plugin/trackmate/io/geff/MAX_Merged-mixed.xml
@@ -0,0 +1,532 @@
+
+
+ Session log saved in the file:
+--------------------
+TrackMate v8.1.6 started on:
+ri, 24 Jul 2026 10:16:29
+Please note that TrackMate is available through iji, and is based on a publication. If you use it successfully for your research please be so kind to cite our work:
+rshov, D., Phan, MS., Pylvänäinen, J.W., Rigaud S.U., et al. TrackMate 7: integrating state-of-the-art segmentation algorithms into tracking pipelines. Nat Methods (2022). https://doi.org/10.1038/s41592-022-01507-1
+https://doi.org/10.1038/s41592-022-01507-1
+and / or:
+Tinevez, JY.; Perry, N. & Schindelin, J. et al. (2017), 'TrackMate: An open and extensible platform for single-particle tracking.', Methods 115: 80-90, PMID 27713081.
+https://www.sciencedirect.com/science/article/pii/S1046202316303346
+
+Numerical feature analyzers:
+Spot feature analyzers:
+ - Manual spot color provides: Spot color; is manual.
+ - Spot intensity provides: Mean ch1, Median ch1, Min ch1, Max ch1, Sum ch1, Std ch1, Mean ch2, Median ch2, Min ch2, Max ch2, Sum ch2, Std ch2.
+ - xTrack probabilities provides: P stuck, P diffusive; is manual.
+ - Spot contrast and SNR provides: Ctrst ch1, SNR ch1, Ctrst ch2, SNR ch2.
+dge feature analyzers:
+ - Directional change provides: γ rate.
+ - dge speed provides: Speed, Disp.
+ - dge target provides: Source ID, Target ID, Cost.
+ - dge location provides: dge T, dge X, dge Y, dge Z.
+ - Manual edge color provides: dge color; is manual.
+Track feature analyzers:
+ - Branching analyzer provides: N spots, N gaps, N splits, N merges, N complex, Lgst gap.
+ - Track duration provides: Duration, Track start, Track stop, Track disp.
+ - Track index provides: Index, ID.
+ - Track location provides: Track X, Track Y, Track Z.
+ - Track speed provides: Mean sp., Max speed, Min speed, Med. speed, Std speed.
+ - Track quality provides: Mean Q.
+ - Track motility analysis provides: Total dist., Max dist., Cfn. ratio, Mn. v. line, wd. progr., Mn. γ rate.
+
+Image region of interest:
+Image data:
+or the image named: MAX_Merged.tif.
+Matching file MAX_Merged.tif in folder: /Users/tinevez/Development/TrackMateWS/TrackMate/samples/
+Geometry:
+ X = 0 - 239, dx = 0.198467
+ Y = 0 - 294, dy = 0.198467
+ Z = 0 - 0, dz = 1.00000
+ T = 0 - 16, dt = 2.00000
+
+Configured detector Mask detector with settings:
+ - target channel: 2
+ - simplify contours: true
+
+Starting detection process using 12 threads.
+Detection processes 12 frames simultaneously and allocates 1 thread per frame.
+ound 78 spots.
+Detection done in 0.1 s.
+
+Computing spot quality histogram...
+Initial thresholding with a quality threshold above 19.0 ...
+Starting initial filtering process.
+Retained 78 spots out of 78.
+
+Adding morphology analyzers...
+ - Spot fit 2D ellipse provides: l. x0, l. y0, l. long axis, l. sh. axis, l. angle, l. a.r.
+ - Spot 2D shape descriptors provides: Area, Perim., Circ., Solidity, Shape index.
+
+Calculating spot features...
+Calculating features done in 0.1 s.
+
+Performing spot filtering on the following features:
+ - on Area above 0.5
+Kept 78 spots out of 78.
+
+Configured tracker LAP Tracker with settings:
+ - max frame gap: 2
+ - alternative linking cost factor: 1.05
+ - linking feature penalties:
+ - linking max distance: 15.0
+ - gap closing max distance: 15.0
+ - merging feature penalties:
+ - splitting max distance: 15.0
+ - blocking value: Infinity
+ - allow gap closing: true
+ - allow track splitting: true
+ - allow track merging: false
+ - merging max distance: 15.0
+ - splitting feature penalties:
+ - cutoff percentile: 0.9
+ - gap closing feature penalties:
+
+Starting tracking process.
+Tracking done in 0.0 s.
+ound 3 tracks.
+ - avg size: 25.7 spots.
+ - min size: 20 spots.
+ - max size: 32 spots.
+
+Calculating features done in 0.0 s.
+
+Performing track filtering on the following features:
+No feature threshold set, kept the 3 tracks.
+Saving data...
+Computing edge features:
+ - Directional change in 1 ms.
+ - dge speed in 1 ms.
+ - dge target in 1 ms.
+ - dge location in 1 ms.
+Computation done in 4 ms.
+Computing track features:
+ - Branching analyzer in 0 ms.
+ - Track duration in 0 ms.
+ - Track index in 0 ms.
+ - Track location in 0 ms.
+ - Track speed in 0 ms.
+ - Track quality in 1 ms.
+ - Track motility analysis in 0 ms.
+Computation done in 2 ms.
+--------------------
+ile loaded on ri, 24 Jul 2026 10:56:11
+TrackMate v8.1.6
+Please note that TrackMate is available through iji, and is based on a publication. If you use it successfully for your research please be so kind to cite our work:
+rshov, D., Phan, MS., Pylvänäinen, J.W., Rigaud S.U., et al. TrackMate 7: integrating state-of-the-art segmentation algorithms into tracking pipelines. Nat Methods (2022). https://doi.org/10.1038/s41592-022-01507-1
+https://doi.org/10.1038/s41592-022-01507-1
+and / or:
+Tinevez, JY.; Perry, N. & Schindelin, J. et al. (2017), 'TrackMate: An open and extensible platform for single-particle tracking.', Methods 115: 80-90, PMID 27713081.
+https://www.sciencedirect.com/science/article/pii/S1046202316303346
+Saving data...
+Computing edge features:
+ - Directional change in 1 ms.
+ - dge speed in 0 ms.
+ - dge target in 1 ms.
+ - dge location in 1 ms.
+Computation done in 5 ms.
+Computing track features:
+ - Branching analyzer in 1 ms.
+ - Track duration in 0 ms.
+ - Track index in 0 ms.
+ - Track location in 0 ms.
+ - Track speed in 1 ms.
+ - Track quality in 0 ms.
+ - Track motility analysis in 0 ms.
+Computation done in 2 ms.
+
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+ {
+ "name": "CurrentDisplaySettings",
+ "spotUniformColor": "204, 51, 204, 255",
+ "spotColorByType": "TRACKS",
+ "spotColorByFeature": "TRACK_INDEX",
+ "spotDisplayRadius": 1.0,
+ "spotDisplayedAsRoi": true,
+ "spotMin": 0.0,
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+ "undefinedValueColor": "0, 0, 0, 255",
+ "missingValueColor": "89, 89, 89, 255",
+ "highlightColor": "51, 230, 51, 255",
+ "trackDisplayMode": "LOCAL_BACKWARD",
+ "colormap": "Jet",
+ "limitZDrawingDepth": false,
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+ "fadeTracks": true,
+ "fadeTrackRange": 30,
+ "useAntialiasing": true,
+ "spotVisible": true,
+ "trackVisible": true,
+ "font": {
+ "name": "Arial",
+ "style": 1,
+ "size": 12
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+ "lineThickness": 2.0,
+ "selectionLineThickness": 4.0,
+ "trackschemeBackgroundColor1": "128, 128, 128, 255",
+ "trackschemeBackgroundColor2": "192, 192, 192, 255",
+ "trackschemeForegroundColor": "0, 0, 0, 255",
+ "trackschemeDecorationColor": "0, 0, 0, 255",
+ "trackschemeFillBox": false,
+ "spotFilled": false,
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+}
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diff --git a/src/test/resources/fiji/plugin/trackmate/io/geff/MAX_Merged.xml b/src/test/resources/fiji/plugin/trackmate/io/geff/MAX_Merged.xml
new file mode 100644
index 000000000..918ae2e3f
--- /dev/null
+++ b/src/test/resources/fiji/plugin/trackmate/io/geff/MAX_Merged.xml
@@ -0,0 +1,492 @@
+
+
+ TrackMate v8.1.6 started on:
+ri, 24 Jul 2026 10:16:29
+Please note that TrackMate is available through iji, and is based on a publication. If you use it successfully for your research please be so kind to cite our work:
+rshov, D., Phan, MS., Pylvänäinen, J.W., Rigaud S.U., et al. TrackMate 7: integrating state-of-the-art segmentation algorithms into tracking pipelines. Nat Methods (2022). https://doi.org/10.1038/s41592-022-01507-1
+https://doi.org/10.1038/s41592-022-01507-1
+and / or:
+Tinevez, JY.; Perry, N. & Schindelin, J. et al. (2017), 'TrackMate: An open and extensible platform for single-particle tracking.', Methods 115: 80-90, PMID 27713081.
+https://www.sciencedirect.com/science/article/pii/S1046202316303346
+
+Numerical feature analyzers:
+Spot feature analyzers:
+ - Manual spot color provides: Spot color; is manual.
+ - Spot intensity provides: Mean ch1, Median ch1, Min ch1, Max ch1, Sum ch1, Std ch1, Mean ch2, Median ch2, Min ch2, Max ch2, Sum ch2, Std ch2.
+ - xTrack probabilities provides: P stuck, P diffusive; is manual.
+ - Spot contrast and SNR provides: Ctrst ch1, SNR ch1, Ctrst ch2, SNR ch2.
+dge feature analyzers:
+ - Directional change provides: γ rate.
+ - dge speed provides: Speed, Disp.
+ - dge target provides: Source ID, Target ID, Cost.
+ - dge location provides: dge T, dge X, dge Y, dge Z.
+ - Manual edge color provides: dge color; is manual.
+Track feature analyzers:
+ - Branching analyzer provides: N spots, N gaps, N splits, N merges, N complex, Lgst gap.
+ - Track duration provides: Duration, Track start, Track stop, Track disp.
+ - Track index provides: Index, ID.
+ - Track location provides: Track X, Track Y, Track Z.
+ - Track speed provides: Mean sp., Max speed, Min speed, Med. speed, Std speed.
+ - Track quality provides: Mean Q.
+ - Track motility analysis provides: Total dist., Max dist., Cfn. ratio, Mn. v. line, wd. progr., Mn. γ rate.
+
+Image region of interest:
+Image data:
+or the image named: MAX_Merged.tif.
+Matching file MAX_Merged.tif in folder: /Users/tinevez/Development/TrackMateWS/TrackMate/samples/
+Geometry:
+ X = 0 - 239, dx = 0.198467
+ Y = 0 - 294, dy = 0.198467
+ Z = 0 - 0, dz = 1.00000
+ T = 0 - 16, dt = 2.00000
+
+Configured detector Mask detector with settings:
+ - target channel: 2
+ - simplify contours: true
+
+Starting detection process using 12 threads.
+Detection processes 12 frames simultaneously and allocates 1 thread per frame.
+ound 78 spots.
+Detection done in 0.1 s.
+
+Computing spot quality histogram...
+Initial thresholding with a quality threshold above 19.0 ...
+Starting initial filtering process.
+Retained 78 spots out of 78.
+
+Adding morphology analyzers...
+ - Spot fit 2D ellipse provides: l. x0, l. y0, l. long axis, l. sh. axis, l. angle, l. a.r.
+ - Spot 2D shape descriptors provides: Area, Perim., Circ., Solidity, Shape index.
+
+Calculating spot features...
+Calculating features done in 0.1 s.
+
+Performing spot filtering on the following features:
+ - on Area above 0.5
+Kept 78 spots out of 78.
+
+Configured tracker LAP Tracker with settings:
+ - max frame gap: 2
+ - alternative linking cost factor: 1.05
+ - linking feature penalties:
+ - linking max distance: 15.0
+ - gap closing max distance: 15.0
+ - merging feature penalties:
+ - splitting max distance: 15.0
+ - blocking value: Infinity
+ - allow gap closing: true
+ - allow track splitting: true
+ - allow track merging: false
+ - merging max distance: 15.0
+ - splitting feature penalties:
+ - cutoff percentile: 0.9
+ - gap closing feature penalties:
+
+Starting tracking process.
+Tracking done in 0.0 s.
+ound 3 tracks.
+ - avg size: 25.7 spots.
+ - min size: 20 spots.
+ - max size: 32 spots.
+
+Calculating features done in 0.0 s.
+
+Performing track filtering on the following features:
+No feature threshold set, kept the 3 tracks.
+Saving data...
+Computing edge features:
+ - Directional change in 1 ms.
+ - dge speed in 1 ms.
+ - dge target in 1 ms.
+ - dge location in 1 ms.
+Computation done in 4 ms.
+Computing track features:
+ - Branching analyzer in 0 ms.
+ - Track duration in 0 ms.
+ - Track index in 0 ms.
+ - Track location in 0 ms.
+ - Track speed in 0 ms.
+ - Track quality in 1 ms.
+ - Track motility analysis in 0 ms.
+Computation done in 2 ms.
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+ "trackMax": 10.0,
+ "trackColorByType": "TRACKS",
+ "trackColorByFeature": "TRACK_INDEX",
+ "trackUniformColor": "204, 204, 51, 255",
+ "undefinedValueColor": "0, 0, 0, 255",
+ "missingValueColor": "89, 89, 89, 255",
+ "highlightColor": "51, 230, 51, 255",
+ "trackDisplayMode": "LOCAL_BACKWARD",
+ "colormap": "Jet",
+ "limitZDrawingDepth": false,
+ "drawingZDepth": 10.0,
+ "fadeTracks": true,
+ "fadeTrackRange": 30,
+ "useAntialiasing": true,
+ "spotVisible": true,
+ "trackVisible": true,
+ "font": {
+ "name": "Arial",
+ "style": 1,
+ "size": 12
+ },
+ "lineThickness": 2.0,
+ "selectionLineThickness": 4.0,
+ "trackschemeBackgroundColor1": "128, 128, 128, 255",
+ "trackschemeBackgroundColor2": "192, 192, 192, 255",
+ "trackschemeForegroundColor": "0, 0, 0, 255",
+ "trackschemeDecorationColor": "0, 0, 0, 255",
+ "trackschemeFillBox": false,
+ "spotFilled": false,
+ "spotTransparencyAlpha": 1.0
+}
+