Update to pom-scijava-37.0.0

This includes changes for: - TrackMate 7.x - ImgLib2 6.x
fmi-faim · May 2, 2024 · 2153221 · 2153221
1 parent cbaf349
commit 2153221
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Showing 7 changed files with 80 additions and 114 deletions.
diff --git a/pom.xml b/pom.xml
@@ -5,13 +5,13 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>30.0.0</version>
+		<version>37.0.0</version>
 		<relativePath />
 	</parent>
 
 	<groupId>ch.fmi</groupId>
 	<artifactId>fmi-ij2-plugins</artifactId>
-	<version>0.8.2-SNAPSHOT</version>
+	<version>0.9.0-SNAPSHOT</version>
 
 	<name>ImageJ2 plugins for use in ImageJ and KNIME</name>
 	<description>A collection of plugins developed at the FMI Basel.</description>
@@ -79,8 +79,7 @@
 		<license.licenseName>lgpl_v3</license.licenseName>
 		<license.copyrightOwners>FMI Basel</license.copyrightOwners>
 
-		<TrackMate_extras.version>0.0.4</TrackMate_extras.version>
-		<fmi-trackmate-addons.version>0.1.2</fmi-trackmate-addons.version>
+		<fmi-trackmate-addons.version>0.7.0</fmi-trackmate-addons.version>
 
 		<!-- NB: Deploy releases to the SciJava Maven repository. -->
 		<releaseProfiles>sign,deploy-to-scijava</releaseProfiles>
@@ -132,12 +131,7 @@
 		</dependency>
 		<dependency>
 			<groupId>sc.fiji</groupId>
-			<artifactId>TrackMate_</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.scijava</groupId>
-			<artifactId>TrackMate_extras</artifactId>
-			<version>${TrackMate_extras.version}</version>
+			<artifactId>TrackMate</artifactId>
 		</dependency>
 		<dependency>
 			<groupId>gov.nist.math</groupId>

diff --git a/src/main/java/ch/fmi/AnisotropicDistanceMap.java b/src/main/java/ch/fmi/AnisotropicDistanceMap.java
@@ -29,8 +29,9 @@
 import net.imagej.ops.Ops;
 import net.imagej.ops.Ops.Image.DistanceTransform;
 import net.imagej.ops.convert.ConvertImages;
+import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.algorithm.morphology.distance.DistanceTransform.DISTANCE_TYPE;
-import net.imglib2.converter.read.ConvertedRandomAccessibleInterval;
+import net.imglib2.converter.Converters;
 import net.imglib2.img.Img;
 import net.imglib2.type.logic.BitType;
 import net.imglib2.type.numeric.RealType;
@@ -95,8 +96,8 @@ public void run() {
 			break;
 		case IMGLIB:
 			FloatType type = new FloatType();
-			ConvertedRandomAccessibleInterval<RealType<?>, FloatType> conv = new ConvertedRandomAccessibleInterval<>(
-					input, (s, t) -> t.set(s.getRealDouble() > 0.0 ? 100000000 : 0.0f),
+			RandomAccessibleInterval<FloatType> conv = Converters.convert(
+					(RandomAccessibleInterval<RealType<?>>) input, (s, t) -> t.set(s.getRealDouble() > 0.0 ? 100000000 : 0.0f),
 					type);
 			outImg = (Img<?>) ops.run(Ops.Create.Img.class, conv);
 			net.imglib2.algorithm.morphology.distance.DistanceTransform

diff --git a/src/main/java/ch/fmi/SpotImageGenerator.java b/src/main/java/ch/fmi/SpotImageGenerator.java
@@ -57,7 +57,7 @@ public class SpotImageGenerator implements Command {
 	private Double radius;
 
 	@Parameter(type = ItemIO.OUTPUT)
-	private ImgPlus<DoubleType> resultImg;
+	private ImgPlus<?> resultImg;
 
 	@SuppressWarnings("unchecked")
 	@Override
@@ -76,7 +76,7 @@ public void run() {
 		RandomAccessibleInterval<DoubleType> kernel = ops.create().kernelGauss(
 				radius * 2.0, 2);
 
-		resultImg = ImgPlus.wrap((Img<DoubleType>) ops.filter().convolve(img,
+		resultImg = ImgPlus.wrap((Img<?>) ops.filter().convolve(img,
 				kernel));
 	}
 

diff --git a/src/main/java/ch/fmi/TrackMateCollectionTracker.java b/src/main/java/ch/fmi/TrackMateCollectionTracker.java
@@ -21,25 +21,25 @@
  */
 package ch.fmi;
 
+import java.util.ArrayList;
+
 import com.google.common.primitives.Doubles;
 import com.google.common.primitives.Ints;
 
-import java.util.ArrayList;
+import org.scijava.ItemIO;
+import org.scijava.command.Command;
+import org.scijava.log.LogService;
+import org.scijava.plugin.Parameter;
+import org.scijava.plugin.Plugin;
 
 import fiji.plugin.trackmate.Model;
 import fiji.plugin.trackmate.Settings;
 import fiji.plugin.trackmate.Spot;
 import fiji.plugin.trackmate.TrackMate;
 import fiji.plugin.trackmate.TrackModel;
-import fiji.plugin.trackmate.tracking.LAPUtils;
 import fiji.plugin.trackmate.tracking.TrackerKeys;
-import fiji.plugin.trackmate.tracking.sparselap.SparseLAPTrackerFactory;
-
-import org.scijava.ItemIO;
-import org.scijava.command.Command;
-import org.scijava.log.LogService;
-import org.scijava.plugin.Parameter;
-import org.scijava.plugin.Plugin;
+import fiji.plugin.trackmate.tracking.jaqaman.LAPUtils;
+import fiji.plugin.trackmate.tracking.jaqaman.SparseLAPTrackerFactory;
 
 @Plugin(type = Command.class, headless = true, menuPath = "FMI>Track Spot Collection")
 public class TrackMateCollectionTracker implements Command {
@@ -130,7 +130,7 @@ public void run() {
 		settings.dt = frameInterval;
 
 		settings.trackerFactory = new SparseLAPTrackerFactory();
-		settings.trackerSettings = LAPUtils.getDefaultLAPSettingsMap();
+		settings.trackerSettings = LAPUtils.getDefaultSegmentSettingsMap();
 		settings.trackerSettings.put(TrackerKeys.KEY_LINKING_MAX_DISTANCE,
 				linkingMaxDistance);
 		settings.trackerSettings.put(TrackerKeys.KEY_GAP_CLOSING_MAX_DISTANCE,

diff --git a/src/main/java/ch/fmi/TrackMateSpotDetector.java b/src/main/java/ch/fmi/TrackMateSpotDetector.java
@@ -21,9 +21,18 @@
  */
 package ch.fmi;
 
+import java.util.ArrayList;
+
 import com.google.common.primitives.Doubles;
 import com.google.common.primitives.Ints;
 
+import org.scijava.ItemIO;
+import org.scijava.command.Command;
+import org.scijava.log.LogService;
+import org.scijava.plugin.Parameter;
+import org.scijava.plugin.Plugin;
+
+import ch.fmi.trackmate.features.MaxQualitySpotAnalyzerFactory;
 import fiji.plugin.trackmate.Model;
 import fiji.plugin.trackmate.Settings;
 import fiji.plugin.trackmate.Spot;
@@ -32,22 +41,13 @@
 import fiji.plugin.trackmate.detection.DetectorKeys;
 import fiji.plugin.trackmate.detection.LogDetectorFactory;
 import fiji.plugin.trackmate.features.FeatureFilter;
-import fiji.plugin.trackmate.features.spot.SpotContrastAnalyzerFactory;
-import fiji.plugin.trackmate.features.spot.SpotIntensityAnalyzerFactory;
-import fiji.plugin.trackmate.features.spot.SpotRadiusEstimatorFactory;
+import fiji.plugin.trackmate.features.spot.SpotContrastAndSNRAnalyzerFactory;
+import fiji.plugin.trackmate.features.spot.SpotIntensityMultiCAnalyzerFactory;
 import ij.ImagePlus;
 import ij.gui.Roi;
 import ij.plugin.filter.ThresholdToSelection;
 import ij.process.ImageProcessor;
 
-import java.util.ArrayList;
-
-import org.scijava.ItemIO;
-import org.scijava.command.Command;
-import org.scijava.log.LogService;
-import org.scijava.plugin.Parameter;
-import org.scijava.plugin.Plugin;
-
 @Plugin(type = Command.class, headless = true, menuPath = "FMI>Spot Detection (Subpixel localization)")
 public class TrackMateSpotDetector implements Command {
 	@Parameter
@@ -128,8 +128,7 @@ public void run() {
 			imp.setCalibration(null);
 		}
 
-		Settings settings = new Settings();
-		settings.setFrom(imp);
+		Settings settings = new Settings(imp);
 
 		// TODO make detector choice optional
 		settings.detectorFactory = new LogDetectorFactory<>();
@@ -142,9 +141,8 @@ public void run() {
 				DetectorKeys.KEY_RADIUS, spotSize);
 		settings.detectorSettings.put( //
 				DetectorKeys.KEY_THRESHOLD, spotThreshold);
-		settings.addSpotAnalyzerFactory(new SpotIntensityAnalyzerFactory<>());
-		settings.addSpotAnalyzerFactory(new SpotRadiusEstimatorFactory<>());
-		settings.addSpotAnalyzerFactory(new SpotContrastAnalyzerFactory<>());
+		settings.addSpotAnalyzerFactory(new SpotIntensityMultiCAnalyzerFactory<>());
+		settings.addSpotAnalyzerFactory(new SpotContrastAndSNRAnalyzerFactory<>());
 		settings.addSpotAnalyzerFactory(new MaxQualitySpotAnalyzerFactory<>());
 
 		if (filterMaxQuality) {
@@ -165,7 +163,6 @@ public void run() {
 		ArrayList<Double> qualityList = new ArrayList<>();
 		ArrayList<Double> totalIntensityList = new ArrayList<>();
 		ArrayList<Double> meanIntensityList = new ArrayList<>();
-		ArrayList<Double> estDiameterList = new ArrayList<>();
 		ArrayList<Double> contrastList = new ArrayList<>();
 		// TODO add other outputs
 
@@ -183,15 +180,12 @@ public void run() {
 				qualityList.add(spot.getFeature(Spot.QUALITY));
 				totalIntensityList
 						.add(spot
-								.getFeature(SpotIntensityAnalyzerFactory.TOTAL_INTENSITY));
+								.getFeature("TOTAL_INTENSITY_CH1"));
 				meanIntensityList
 						.add(spot
-								.getFeature(SpotIntensityAnalyzerFactory.MEAN_INTENSITY));
-				estDiameterList
-						.add(spot
-								.getFeature(SpotRadiusEstimatorFactory.ESTIMATED_DIAMETER));
+								.getFeature("MEAN_INTENSITY_CH1"));
 				contrastList.add(spot
-						.getFeature(SpotContrastAnalyzerFactory.KEY));
+						.getFeature("CONTRAST_CH1"));
 			}
 		} else {
 			log.warn(trackmate.getErrorMessage());
@@ -207,7 +201,6 @@ public void run() {
 		quality = Doubles.toArray(qualityList);
 		totalIntensity = Doubles.toArray(totalIntensityList);
 		meanIntensity = Doubles.toArray(meanIntensityList);
-		estDiameter = Doubles.toArray(estDiameterList);
 		contrast = Doubles.toArray(contrastList);
 
 		// Return summary values

diff --git a/src/main/java/ch/fmi/TrackMateWrapper.java b/src/main/java/ch/fmi/TrackMateWrapper.java
@@ -21,8 +21,17 @@
  */
 package ch.fmi;
 
+import java.util.ArrayList;
+
 import com.google.common.primitives.Doubles;
 
+import org.scijava.ItemIO;
+import org.scijava.command.Command;
+import org.scijava.log.LogService;
+import org.scijava.plugin.Parameter;
+import org.scijava.plugin.Plugin;
+
+import ch.fmi.trackmate.features.MaxQualitySpotAnalyzerFactory;
 import fiji.plugin.trackmate.FeatureModel;
 import fiji.plugin.trackmate.Model;
 import fiji.plugin.trackmate.Settings;
@@ -32,26 +41,17 @@
 import fiji.plugin.trackmate.detection.DetectorKeys;
 import fiji.plugin.trackmate.detection.LogDetectorFactory;
 import fiji.plugin.trackmate.features.FeatureFilter;
-import fiji.plugin.trackmate.features.spot.SpotContrastAnalyzerFactory;
-import fiji.plugin.trackmate.features.spot.SpotIntensityAnalyzerFactory;
-import fiji.plugin.trackmate.features.spot.SpotRadiusEstimatorFactory;
+import fiji.plugin.trackmate.features.spot.SpotContrastAndSNRAnalyzerFactory;
+import fiji.plugin.trackmate.features.spot.SpotIntensityMultiCAnalyzerFactory;
 import fiji.plugin.trackmate.features.track.TrackDurationAnalyzer;
-import fiji.plugin.trackmate.tracking.LAPUtils;
 import fiji.plugin.trackmate.tracking.TrackerKeys;
-import fiji.plugin.trackmate.tracking.sparselap.SparseLAPTrackerFactory;
+import fiji.plugin.trackmate.tracking.jaqaman.LAPUtils;
+import fiji.plugin.trackmate.tracking.jaqaman.SparseLAPTrackerFactory;
 import ij.ImagePlus;
 import ij.gui.Roi;
 import ij.plugin.filter.ThresholdToSelection;
 import ij.process.ImageProcessor;
 
-import java.util.ArrayList;
-
-import org.scijava.ItemIO;
-import org.scijava.command.Command;
-import org.scijava.log.LogService;
-import org.scijava.plugin.Parameter;
-import org.scijava.plugin.Plugin;
-
 @Plugin(type = Command.class, headless = true, menuPath = "FMI>Track Spots (Subpixel localization)")
 public class TrackMateWrapper implements Command {
 	@Parameter
@@ -125,9 +125,6 @@ public class TrackMateWrapper implements Command {
 	@Parameter(type = ItemIO.OUTPUT)
 	private double[] radius;
 
-	@Parameter(type = ItemIO.OUTPUT)
-	private double[] estDiameter;
-
 	@Parameter(type = ItemIO.OUTPUT)
 	private double[] contrast;
 
@@ -143,9 +140,8 @@ public void run() {
 
 		// Create TrackMate instance with settings
 		Model model = new Model();
-		Settings settings = new Settings();
+		Settings settings = new Settings(imp);
 
-		settings.setFrom(imp);
 		settings.dt = frameInterval;
 		settings.detectorFactory = new LogDetectorFactory<>();
 
@@ -164,16 +160,15 @@ public void run() {
 		}
 
 		settings.trackerFactory = new SparseLAPTrackerFactory();
-		settings.trackerSettings = LAPUtils.getDefaultLAPSettingsMap();
+		settings.trackerSettings = LAPUtils.getDefaultSegmentSettingsMap();
 		settings.trackerSettings.put(TrackerKeys.KEY_LINKING_MAX_DISTANCE,
 				linkingMaxDistance);
 		settings.trackerSettings.put(TrackerKeys.KEY_GAP_CLOSING_MAX_DISTANCE,
 				closingMaxDistance);
 		settings.trackerSettings.put(TrackerKeys.KEY_GAP_CLOSING_MAX_FRAME_GAP,
 				frameGap);
-		settings.addSpotAnalyzerFactory(new SpotIntensityAnalyzerFactory<>());
-		settings.addSpotAnalyzerFactory(new SpotRadiusEstimatorFactory<>());
-		settings.addSpotAnalyzerFactory(new SpotContrastAnalyzerFactory<>());
+		settings.addSpotAnalyzerFactory(new SpotIntensityMultiCAnalyzerFactory<>());
+		settings.addSpotAnalyzerFactory(new SpotContrastAndSNRAnalyzerFactory<>());
 		settings.addSpotAnalyzerFactory(new MaxQualitySpotAnalyzerFactory<>());
 		settings.addTrackAnalyzer(new TrackDurationAnalyzer());
 
@@ -204,7 +199,6 @@ public void run() {
 		ArrayList<Double> totalIntensityList = new ArrayList<>();
 		ArrayList<Double> meanIntensityList = new ArrayList<>();
 		ArrayList<Double> radiusList = new ArrayList<>();
-		ArrayList<Double> diameterList = new ArrayList<>();
 		ArrayList<Double> contrastList = new ArrayList<>();
 
 		TrackModel trackModel = model.getTrackModel();
@@ -223,16 +217,13 @@ public void run() {
 				zList.add(spot.getDoublePosition(2));
 				totalIntensityList
 						.add(spot
-								.getFeature(SpotIntensityAnalyzerFactory.TOTAL_INTENSITY));
+								.getFeature("TOTAL_INTENSITY_CH1"));
 				meanIntensityList
 						.add(spot
-								.getFeature(SpotIntensityAnalyzerFactory.MEAN_INTENSITY));
+								.getFeature("MEAN_INTENSITY_CH1"));
 				radiusList.add(spot.getFeature(Spot.RADIUS));
-				diameterList
-						.add(spot
-								.getFeature(SpotRadiusEstimatorFactory.ESTIMATED_DIAMETER));
 				contrastList.add(spot
-						.getFeature(SpotContrastAnalyzerFactory.KEY));
+						.getFeature("CONTRAST_CH1"));
 			}
 		}
 
@@ -257,7 +248,6 @@ public void run() {
 		totalIntensity = Doubles.toArray(totalIntensityList);
 		meanIntensity = Doubles.toArray(meanIntensityList);
 		radius = Doubles.toArray(radiusList);
-		estDiameter = Doubles.toArray(diameterList);
 		contrast = Doubles.toArray(contrastList);
 
 		// Return summary values