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Update to pom-scijava-37.0.0 #20

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May 2, 2024
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Update to pom-scijava-37.0.0 #20

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14 changes: 4 additions & 10 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -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>
Expand Down Expand Up @@ -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>
Expand Down Expand Up @@ -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>
Expand Down
7 changes: 4 additions & 3 deletions src/main/java/ch/fmi/AnisotropicDistanceMap.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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
Expand Down
4 changes: 2 additions & 2 deletions src/main/java/ch/fmi/SpotImageGenerator.java
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Expand Up @@ -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
Expand All @@ -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));
}

Expand Down
20 changes: 10 additions & 10 deletions src/main/java/ch/fmi/TrackMateCollectionTracker.java
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Expand Up @@ -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 {
Expand Down Expand Up @@ -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,
Expand Down
41 changes: 17 additions & 24 deletions src/main/java/ch/fmi/TrackMateSpotDetector.java
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Expand Up @@ -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;
Expand All @@ -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
Expand Down Expand Up @@ -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<>();
Expand All @@ -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) {
Expand All @@ -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

Expand All @@ -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());
Expand All @@ -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
Expand Down
50 changes: 20 additions & 30 deletions src/main/java/ch/fmi/TrackMateWrapper.java
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Expand Up @@ -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;
Expand All @@ -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
Expand Down Expand Up @@ -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;

Expand All @@ -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<>();

Expand All @@ -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());

Expand Down Expand Up @@ -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();
Expand All @@ -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"));
}
}

Expand All @@ -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
Expand Down
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