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Merged
tinevez merged 3 commits into from
Nov 18, 2025
Merged

Acquaint to the new TrackMate v8 API #3

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2edf702
Update parent pom and dependencies
tinevez Jul 18, 2025
143918f
Adapt to the new TrackMate API.
tinevez Jul 18, 2025
f18b5b2
Update parent to pom-scijava 43.0.0 and TrackMate dep to 8.0.0
tinevez Nov 18, 2025
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6 changes: 3 additions & 3 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>37.0.0</version>
<version>43.0.0</version>
<relativePath />
</parent>

<groupId>sc.fiji</groupId>
<artifactId>TrackMate-MorphoLibJ</artifactId>
<version>1.2.2-SNAPSHOT</version>
<version>2.0.0-SNAPSHOT</version>

<name>TrackMate-MorphoLibJ</name>
<description>TrackMate detector based on the watershed segmentation tool in the MorphoLibJ plugin.</description>
Expand Down Expand Up @@ -84,7 +84,7 @@
<!-- NB: Deploy releases to the SciJava Maven repository. -->
<releaseProfiles>sign,deploy-to-scijava</releaseProfiles>

<TrackMate.version>7.10.2</TrackMate.version>
<TrackMate.version>8.0.0</TrackMate.version>
</properties>

<dependencies>
Expand Down
26 changes: 12 additions & 14 deletions src/main/java/fiji/plugin/trackmate/morpholibj/MorphoLibJDetectorConfigurationPanel.java
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Expand Up @@ -8,12 +8,12 @@
* it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 3 of the
* License, or (at your option) any later version.
*
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
*
* You should have received a copy of the GNU General Public
* License along with this program. If not, see
* <http://www.gnu.org/licenses/gpl-3.0.html>.
Expand All @@ -25,6 +25,7 @@
import static fiji.plugin.trackmate.detection.ThresholdDetectorFactory.KEY_SIMPLIFY_CONTOURS;
import static fiji.plugin.trackmate.gui.Fonts.BIG_FONT;
import static fiji.plugin.trackmate.gui.Fonts.SMALL_FONT;
import static fiji.plugin.trackmate.morpholibj.MorphoLibJDetectorFactory.ICON;
import static fiji.plugin.trackmate.morpholibj.MorphoLibJDetectorFactory.KEY_CONNECTIVITY;
import static fiji.plugin.trackmate.morpholibj.MorphoLibJDetectorFactory.KEY_TOLERANCE;

Expand All @@ -33,15 +34,13 @@
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.Insets;
import java.net.URL;
import java.text.DecimalFormat;
import java.text.NumberFormat;
import java.util.Arrays;
import java.util.HashMap;
import java.util.Map;
import java.util.Vector;

import javax.swing.ImageIcon;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JFormattedTextField;
Expand All @@ -64,8 +63,6 @@ public class MorphoLibJDetectorConfigurationPanel extends ConfigurationPanel

private static final NumberFormat THRESHOLD_FORMAT = new DecimalFormat( "#.##" );

protected static final ImageIcon ICON = new ImageIcon( getResource( "images/TrackMateMorphoLibJ-logo-100px.png" ) );

private static final String TITLE = MorphoLibJDetectorFactory.NAME;

private final JSlider sliderChannel;
Expand All @@ -80,9 +77,8 @@ public MorphoLibJDetectorConfigurationPanel( final Settings settings, final Mode
{
final GridBagLayout gridBagLayout = new GridBagLayout();
gridBagLayout.columnWidths = new int[] { 144, 0, 32 };
gridBagLayout.rowHeights = new int[] { 0, 84, 0, 27, 0, 0, 0 };
gridBagLayout.rowHeights = new int[] { 0, 84, 0, 27, 0, 0, 150 };
gridBagLayout.columnWeights = new double[] { 0.0, 1.0, 0.0 };
gridBagLayout.rowWeights = new double[] { 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0 };
setLayout( gridBagLayout );

final JLabel lblDetector = new JLabel( TITLE, ICON, JLabel.RIGHT );
Expand All @@ -107,7 +103,14 @@ public MorphoLibJDetectorConfigurationPanel( final Settings settings, final Mode
gbcLblHelptext.insets = new Insets( 5, 5, 5, 5 );
gbcLblHelptext.gridx = 0;
gbcLblHelptext.gridy = 1;
add( GuiUtils.textInScrollPanel( GuiUtils.infoDisplay( MorphoLibJDetectorFactory.INFO_TEXT ) ), gbcLblHelptext );
gbcLblHelptext.weighty = 1.;
add( GuiUtils.textInScrollPanel( GuiUtils.infoDisplay(
MorphoLibJDetectorFactory.INFO_TEXT.replace( "</html>", "" )
+ "<html>Online documentation: <br/>"
+ "<a href='" + MorphoLibJDetectorFactory.DOC_URL + "'>"
+ MorphoLibJDetectorFactory.DOC_URL
+ "</a></html>" ) ),
gbcLblHelptext );

/*
* Channel selector.
Expand Down Expand Up @@ -301,9 +304,4 @@ public void setSettings( final Map< String, Object > settings )
@Override
public void clean()
{}

protected static URL getResource( final String name )
{
return MorphoLibJDetectorFactory.class.getClassLoader().getResource( name );
}
}
122 changes: 12 additions & 110 deletions src/main/java/fiji/plugin/trackmate/morpholibj/MorphoLibJDetectorFactory.java
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Expand Up @@ -8,12 +8,12 @@
* it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 3 of the
* License, or (at your option) any later version.
*
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
*
* You should have received a copy of the GNU General Public
* License along with this program. If not, see
* <http://www.gnu.org/licenses/gpl-3.0.html>.
Expand All @@ -24,29 +24,20 @@
import static fiji.plugin.trackmate.detection.DetectorKeys.DEFAULT_TARGET_CHANNEL;
import static fiji.plugin.trackmate.detection.DetectorKeys.KEY_TARGET_CHANNEL;
import static fiji.plugin.trackmate.detection.ThresholdDetectorFactory.KEY_SIMPLIFY_CONTOURS;
import static fiji.plugin.trackmate.io.IOUtils.readBooleanAttribute;
import static fiji.plugin.trackmate.io.IOUtils.readDoubleAttribute;
import static fiji.plugin.trackmate.io.IOUtils.readIntegerAttribute;
import static fiji.plugin.trackmate.io.IOUtils.writeAttribute;
import static fiji.plugin.trackmate.io.IOUtils.writeTargetChannel;
import static fiji.plugin.trackmate.util.TMUtils.checkMapKeys;
import static fiji.plugin.trackmate.util.TMUtils.checkParameter;

import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

import javax.swing.ImageIcon;

import org.jdom2.Element;
import org.scijava.Priority;
import org.scijava.plugin.Plugin;

import fiji.plugin.trackmate.Model;
import fiji.plugin.trackmate.Settings;
import fiji.plugin.trackmate.detection.SpotDetector;
import fiji.plugin.trackmate.detection.SpotDetectorFactory;
import fiji.plugin.trackmate.gui.GuiUtils;
import fiji.plugin.trackmate.gui.components.ConfigurationPanel;
import fiji.plugin.trackmate.util.TMUtils;
import net.imagej.ImgPlus;
Expand All @@ -57,11 +48,6 @@
@Plugin( type = SpotDetectorFactory.class, priority = Priority.LOW - 5. )
public class MorphoLibJDetectorFactory< T extends RealType< T > & NativeType< T > > implements SpotDetectorFactory< T >
{

/*
* CONSTANTS
*/

/**
* The key to the parameter that stores the tolerance value to use in
* morphological segmentation. Accepted values are doubles.
Expand Down Expand Up @@ -99,29 +85,14 @@ public class MorphoLibJDetectorFactory< T extends RealType< T > & NativeType< T
+ "also cite the MorphoLibJ paper: <a href=\"https://doi.org/10.1093/bioinformatics/btw413\">Legland, D.; Arganda-Carreras, I. & Andrey, P. (2016), "
+ "'MorphoLibJ: integrated library and plugins for mathematical morphology with ImageJ', "
+ "Bioinformatics (Oxford Univ Press) 32(22): 3532-3534.</a> "
+ "<p>"
+ "Documentation for this module "
+ "<a href=\"https://imagej.net/plugins/trackmate/trackmate-morpholibj\">on the ImageJ Wiki</a>."
+ "<p>"
+ "</html>";

/*
* FIELDS
*/

/** The image to operate on. Multiple frames, single channel. */
protected ImgPlus< T > img;

protected Map< String, Object > settings;
public static final String DOC_URL = "https://imagej.net/plugins/trackmate/trackmate-morpholibj";

protected String errorMessage;

/*
* METHODS
*/
public static final ImageIcon ICON = new ImageIcon( GuiUtils.getResource( "images/TrackMateMorphoLibJ-logo-64px.png", MorphoLibJDetectorFactory.class ) );

@Override
public SpotDetector< T > getDetector( final Interval interval, final int frame )
public SpotDetector< T > getDetector( final ImgPlus< T > img, final Map< String, Object > settings, final Interval interval, final int frame )
{
final int channel = ( Integer ) settings.get( KEY_TARGET_CHANNEL ) - 1;
final ImgPlus< T > input = TMUtils.hyperSlice( img, channel, frame );
Expand All @@ -138,54 +109,6 @@ public SpotDetector< T > getDetector( final Interval interval, final int frame )
return detector;
}

@Override
public boolean setTarget( final ImgPlus< T > img, final Map< String, Object > settings )
{
this.img = img;
this.settings = settings;
return checkSettings( settings );
}

@Override
public String getErrorMessage()
{
return errorMessage;
}

@Override
public boolean marshall( final Map< String, Object > settings, final Element element )
{
final StringBuilder errorHolder = new StringBuilder();
boolean ok = writeTargetChannel( settings, element, errorHolder );
ok = ok && writeAttribute( settings, element, KEY_TOLERANCE, Double.class, errorHolder );
ok = ok && writeAttribute( settings, element, KEY_CONNECTIVITY, Integer.class, errorHolder );
ok = ok && writeAttribute( settings, element, KEY_SIMPLIFY_CONTOURS, Boolean.class, errorHolder );

if ( !ok )
errorMessage = errorHolder.toString();

return ok;
}

@Override
public boolean unmarshall( final Element element, final Map< String, Object > settings )
{
settings.clear();
final StringBuilder errorHolder = new StringBuilder();
boolean ok = true;
ok = ok && readIntegerAttribute( element, settings, KEY_TARGET_CHANNEL, errorHolder );
ok = ok && readDoubleAttribute( element, settings, KEY_TOLERANCE, errorHolder );
ok = ok && readIntegerAttribute( element, settings, KEY_CONNECTIVITY, errorHolder );
ok = ok && readBooleanAttribute( element, settings, KEY_SIMPLIFY_CONTOURS, errorHolder );

if ( !ok )
{
errorMessage = errorHolder.toString();
return false;
}
return checkSettings( settings );
}

@Override
public ConfigurationPanel getDetectorConfigurationPanel( final Settings settings, final Model model )
{
Expand All @@ -204,36 +127,21 @@ public Map< String, Object > getDefaultSettings()
}

@Override
public boolean checkSettings( final Map< String, Object > settings )
public String getInfoText()
{
boolean ok = true;
final StringBuilder errorHolder = new StringBuilder();
ok = ok & checkParameter( settings, KEY_TARGET_CHANNEL, Integer.class, errorHolder );
ok = ok & checkParameter( settings, KEY_TOLERANCE, Double.class, errorHolder );
ok = ok & checkParameter( settings, KEY_CONNECTIVITY, Integer.class, errorHolder );
ok = ok & checkParameter( settings, KEY_SIMPLIFY_CONTOURS, Boolean.class, errorHolder );
final List< String > mandatoryKeys = new ArrayList<>();
mandatoryKeys.add( KEY_TARGET_CHANNEL );
mandatoryKeys.add( KEY_TOLERANCE );
mandatoryKeys.add( KEY_CONNECTIVITY );
mandatoryKeys.add( KEY_SIMPLIFY_CONTOURS );
ok = ok & checkMapKeys( settings, mandatoryKeys, null, errorHolder );
if ( !ok )
errorMessage = errorHolder.toString();

return ok;
return INFO_TEXT;
}

@Override
public String getInfoText()
public ImageIcon getIcon()
{
return INFO_TEXT;
return ICON;
}

@Override
public ImageIcon getIcon()
public String getUrl()
{
return null;
return DOC_URL;
}

@Override
Expand All @@ -253,10 +161,4 @@ public boolean has2Dsegmentation()
{
return true;
}

@Override
public MorphoLibJDetectorFactory< T > copy()
{
return new MorphoLibJDetectorFactory<>();
}
}
Binary file added src/main/resources/images/TrackMateMorphoLibJ-logo-64px.png
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