Realign dev branch with latest master branch

pom.xml

@@ -5,12 +5,12 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>40.0.0</version>
+		<version>42.0.0</version>
 	</parent>
 
 	<groupId>org.mastodon</groupId>
 	<artifactId>mastodon</artifactId>
-	<version>1.0.0-beta-35-SNAPSHOT</version>
+	<version>1.0.0-beta-36-SNAPSHOT</version>
 
 	<name>Mastodon</name>
 	<description>Mastodon – a large-scale tracking and track-editing framework for large, multi-view images.</description>

scripts/MastodonScriptExample.py

@@ -0,0 +1,77 @@
+#@ Context context
+
+from java.io import File
+
+from org.mastodon.mamut import WindowManager
+from org.mastodon.mamut.project import MamutProject
+from org.mastodon.tracking.mamut.trackmate import TrackMate
+from org.mastodon.tracking.mamut.trackmate import Settings
+from org.mastodon.tracking.mamut.detection import DoGDetectorMamut
+from org.mastodon.tracking.mamut.linking import SimpleSparseLAPLinkerMamut
+from org.mastodon.tracking.linking import LinkingUtils
+
+bdv_file = "/Users/tinevez/Development/Mastodon/mastodon/samples/datasethdf5.xml"
+project = MamutProject( None, File( bdv_file ) );
+
+# Open the project.
+wm = WindowManager( context )
+wm.getProjectManager().open( project )
+app_model = wm.getAppModel()
+
+# Get Mastodon model.
+model = app_model.getModel()
+selection_model = app_model.getSelectionModel()
+
+# Get image data.
+image_data = app_model.getSharedBdvData()
+
+# Configure TrackMate.
+
+# Detector settings.
+detector_settings = {
+	"MIN_TIMEPOINT" : 0,
+	"MAX_TIMEPOINT" : 1000,
+	"SETUP" : 0, 				# The channel or source in the BDV data.
+	"RADIUS" : 7., 			# The cell expected radius.
+	"THRESHOLD" : 200.	 		# Threshold on quality.
+}
+
+# Linker settings. There are too many, so we take the default and edit it.
+linker_settings = LinkingUtils.getDefaultLAPSettingsMap()
+linker_settings[ "MIN_TIMEPOINT" ] = 0
+linker_settings[ "MAX_TIMEPOINT" ] = 1000
+linker_settings[ "LINKING_MAX_DISTANCE" ] = 10.
+linker_settings[ "ALLOW_GAP_CLOSING" ] = True
+linker_settings[ "MAX_FRAME_GAP" ] = 2 
+
+# Create the settings objects.
+settings = Settings() \
+		.sources( image_data.getSources() ) \
+		.detector( DoGDetectorMamut ) \
+		.detectorSettings( detector_settings ) \
+		.linker( SimpleSparseLAPLinkerMamut ) \
+		.linkerSettings( linker_settings )
+
+trackmate = TrackMate( settings, model, selection_model )
+
+# We need to give a context to TrackMate.
+trackmate.setContext( context )
+
+# Run TrackMate.
+trackmate.run()
+if trackmate.isCanceled():
+	print( "Calculation was canceled. Reason: " + trackmate.getCancelReason() )
+elif not trackmate.isSuccessful():
+	print( "Calculation failed with error message:\n" + trackmate.getErrorMessage() )
+else:
+	print( "Calculation complete." );
+
+wm.createTrackScheme()
+wm.createBigDataViewer()
+
+# Compute features.
+
+
+
+
+wm.createTable( False )

src/main/java/org/mastodon/mamut/io/importer/trackmate/CommonTrackMateFeatureDeclarations.java

@@ -1,3 +1,31 @@
+/*-
+ * #%L
+ * Mastodon
+ * %%
+ * Copyright (C) 2014 - 2025 Tobias Pietzsch, Jean-Yves Tinevez
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
 package org.mastodon.mamut.io.importer.trackmate;
 
 import static org.mastodon.mamut.io.importer.trackmate.TrackMateXMLKeys.FEATURE_ATTRIBUTE;

src/main/java/org/mastodon/mamut/io/loader/util/mobie/OmeZarrMultiscalesAdapter.java

@@ -45,7 +45,6 @@
 public class OmeZarrMultiscalesAdapter implements JsonDeserializer< OmeZarrMultiscales >, JsonSerializer< OmeZarrMultiscales >
 {
 
-	@SuppressWarnings( "serial" )
 	@Override
     public OmeZarrMultiscales deserialize( final JsonElement json, final Type typeOfT, final JsonDeserializationContext context ) throws JsonParseException
     {

src/main/java/org/mastodon/mamut/launcher/NewFromUrlPanel.java

@@ -66,7 +66,7 @@
 import org.janelia.saalfeldlab.n5.metadata.N5ViewerMultichannelMetadata;
 import org.janelia.saalfeldlab.n5.ui.DatasetSelectorDialog;
 import org.janelia.saalfeldlab.n5.universe.N5Factory;
-import org.janelia.saalfeldlab.n5.universe.N5Factory.StorageFormat;
+import org.janelia.saalfeldlab.n5.universe.StorageFormat;
 import org.janelia.saalfeldlab.n5.universe.metadata.MultiscaleMetadata;
 import org.janelia.saalfeldlab.n5.universe.metadata.N5Metadata;
 import org.janelia.saalfeldlab.n5.universe.metadata.N5SingleScaleMetadata;
@@ -404,21 +404,14 @@ public N5Reader apply( final String n5UriOrPath )
 			String rootPath = null;
 			if ( n5UriOrPath.contains( "?" ) )
 			{
-				try
-				{
-					// need to strip off storage format for n5uri to correctly
-					// remove query;
-					final Pair< StorageFormat, URI > fmtUri = N5Factory.StorageFormat.parseUri( n5UriOrPath );
-					final StorageFormat format = fmtUri.getA();
-
-					final N5URI n5uri = new N5URI( URI.create( fmtUri.getB().toString() ) );
-					// add the format prefix back if it was present
-					rootPath = format == null ? n5uri.getContainerPath() : format.toString().toLowerCase() + ":" + n5uri.getContainerPath();
-				}
-				catch ( final URISyntaxException e )
-				{
-					messenger.accept( "The URI is not valid or credentials are missing: " + n5UriOrPath );
-				}
+				// need to strip off storage format for n5uri to correctly
+				// remove query;
+				final Pair< StorageFormat, URI > fmtUri = StorageFormat.parseUri( n5UriOrPath );
+				final StorageFormat format = fmtUri.getA();
+
+				final N5URI n5uri = new N5URI( URI.create( fmtUri.getB().toString() ) );
+				// add the format prefix back if it was present
+				rootPath = format == null ? n5uri.getContainerPath() : format.toString().toLowerCase() + ":" + n5uri.getContainerPath();
 			}
 
 			if ( rootPath == null )

src/main/java/org/mastodon/mamut/views/grapher/MamutViewGrapher.java

@@ -43,7 +43,6 @@
 import org.mastodon.ui.coloring.GraphColorGeneratorAdapter;
 import org.mastodon.ui.coloring.HasColorBarOverlay;
 import org.mastodon.ui.coloring.HasColoringModel;
-import org.mastodon.ui.commandfinder.CommandFinder;
 import org.mastodon.ui.keymap.KeyConfigContexts;
 import org.mastodon.views.context.ContextChooser;
 import org.mastodon.views.context.HasContextChooser;

src/main/java/org/mastodon/views/grapher/display/GrapherSidePanel.java

@@ -275,7 +275,7 @@ public JButton getBtnPlot()
 		return btnPlot;
 	}
 
-	public < V, E > void setFeatures(
+	public void setFeatures(
 			final Map< FeatureSpec< ?, V >, Feature< V > > vertexFeatures,
 			final Map< FeatureSpec< ?, E >, Feature< E > > edgeFeatures )
 	{
@@ -436,6 +436,7 @@ public FeatureProjectionSpec getFeatureProjectionSpec( final String projectionKe
 		return null;
 	}
 
+	@Override
 	public ContextChooser< V > getContextChooser()
 	{
 		return this.contextChooser;

src/main/java/org/mastodon/views/grapher/display/Plotable.java

@@ -1,3 +1,31 @@
+/*-
+ * #%L
+ * Mastodon
+ * %%
+ * Copyright (C) 2014 - 2025 Tobias Pietzsch, Jean-Yves Tinevez
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
 package org.mastodon.views.grapher.display;
 
 import org.mastodon.views.grapher.datagraph.ScreenTransform;

src/test/java/org/mastodon/StartMastodonDefaultProject.java

@@ -34,8 +34,8 @@ public class StartMastodonDefaultProject
 	public static void main( final String[] args )
 	{
 //		final String projectPath = "samples/MaMuT_Parhyale_small.mastodon";
-//		final String projectPath = "/Users/tinevez/Google Drive/Mastodon/Datasets/Remote/ParhyaleHawaiensis/MaMuT_Parhyale_demo-mamut.mastodon";
-		final String projectPath = "samples/drosophila_crop_LONG_NAME_LONGLONGLONG_SUPERLONG.mastodon";
+		final String projectPath = "/Users/tinevez/Library/CloudStorage/GoogleDrive-jeanyves.tinevez@gmail.com/My Drive/Mastodon/Datasets/Remote/BDV/Tribolium/CTC_TRIF_trainingVideo02_jy-GT-done.mastodon";
+//		final String projectPath = "samples/drosophila_crop_LONG_NAME_LONGLONGLONG_SUPERLONG.mastodon";
 //		final String projectPath = "samples/drosophila_crop.mastodon";
 		StartMastodonOnProject.launch( projectPath );
 	}

src/test/java/org/mastodon/graph/revised/CreateLargeModelExample.java

@@ -30,8 +30,6 @@
 
 import java.io.IOException;
 
-import org.mastodon.mamut.ProjectModel;
-import org.mastodon.mamut.WindowManager;
 import org.mastodon.mamut.io.importer.ModelImporter;
 import org.mastodon.mamut.io.project.MamutProject;
 import org.mastodon.mamut.model.Link;
@@ -184,11 +182,11 @@ public static void main( final String[] args ) throws IOException
 				( Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory() ) / 1e6d ) );
 
 
-		final Context context = new Context();
-		final SharedBigDataViewerData imagedata = SharedBigDataViewerData.fromDummyFilename( "x=1000 y=1000 z=100 sx=1 sy=1 sz=10 t=400.dummy" );
-		final MamutProject project = new MamutProject( "./large_model_example.mastodon" );
-		final ProjectModel appModel = ProjectModel.create( context, model, imagedata, project  );
-		final WindowManager wm = new WindowManager( appModel  );
+//		final Context context = new Context();
+//		final SharedBigDataViewerData imagedata = SharedBigDataViewerData.fromDummyFilename( "x=1000 y=1000 z=100 sx=1 sy=1 sz=10 t=400.dummy" );
+//		final MamutProject project = new MamutProject( "./large_model_example.mastodon" );
+//		final ProjectModel appModel = ProjectModel.create( context, model, imagedata, project  );
+//		final WindowManager wm = new WindowManager( appModel  );
 
 //		start = System.currentTimeMillis();
 //		wm.createBigDataViewer();