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Support 3D segmentation with TrackMate-MorphoLibJ. #1

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Support 3D segmentation with TrackMate-MorphoLibJ. #1

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9e14a8b
Update parent to pom-scijava v34.1.0
tinevez Apr 17, 2023
1e1e20c
Temporary coupling to TrackMate v8.0.0-SNAPSHOT
tinevez Apr 17, 2023
38ba4f5
Interactive test for 3D segmentation with MorphoLibJ.
tinevez Apr 20, 2023
ca31685
Add temporary dependency to imagej-mesh.
tinevez May 15, 2023
d9d5a9f
Declare that the detector can do 3D shapes.
tinevez May 15, 2023
7b00d84
Fix interactive test.
tinevez May 15, 2023
82dc647
Update parent to pom-scijava v37.0.0
tinevez Dec 2, 2023
c7c676a
Depend on imglib2-mesh v1.0.0-SNAPSHOT
tinevez Dec 2, 2023
e54510a
Add smoothing scale.
tinevez Dec 2, 2023
ad24329
Add an option to remove largest object.
tinevez Dec 2, 2023
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9 changes: 6 additions & 3 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,6 @@
<groupId>org.scijava</groupId>
<artifactId>pom-scijava</artifactId>
<version>37.0.0</version>
<relativePath />
</parent>

<groupId>sc.fiji</groupId>
Expand Down Expand Up @@ -84,7 +83,7 @@
<!-- 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-SNAPSHOT</TrackMate.version>
</properties>

<dependencies>
Expand Down Expand Up @@ -118,7 +117,11 @@
<groupId>org.scijava</groupId>
<artifactId>scijava-common</artifactId>
</dependency>

<dependency>
<groupId>net.imglib2</groupId>
<artifactId>imglib2-mesh</artifactId>
<version>1.0.0-SNAPSHOT</version>
</dependency>
<!-- Other dependencies -->
<dependency>
<groupId>fr.inra.ijpb</groupId>
Expand Down
25 changes: 21 additions & 4 deletions src/main/java/fiji/plugin/trackmate/morpholibj/MorphoLibJDetector.java
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Original file line number Diff line number Diff line change
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 @@ -33,6 +33,7 @@
import ij.ImageStack;
import ij.plugin.Duplicator;
import inra.ijpb.binary.BinaryImages;
import inra.ijpb.label.LabelImages;
import inra.ijpb.morphology.MinimaAndMaxima3D;
import inra.ijpb.watershed.Watershed;
import net.imagej.ImgPlus;
Expand Down Expand Up @@ -64,16 +65,24 @@ public class MorphoLibJDetector< T extends RealType< T > & NativeType< T > > imp

private final boolean simplify;

private final double smoothingScale;

private final boolean removeLargestObject;

public MorphoLibJDetector(
final ImgPlus< T > img,
final Interval interval,
final double tolerance,
final Connectivity connectivity,
final boolean simplify )
final boolean removeLargestObject,
final boolean simplify,
final double smoothingScale )
{
this.img = img;
this.tolerance = tolerance;
this.connectivity = connectivity;
this.removeLargestObject = removeLargestObject;
this.smoothingScale = smoothingScale;
this.interval = DetectionUtils.squeeze( interval );
this.simplify = simplify;
this.baseErrorMessage = BASE_ERROR_MESSAGE;
Expand Down Expand Up @@ -109,11 +118,19 @@ public boolean process()
final ImageStack labeledMinima = BinaryImages.componentsLabeling( regionalMinima, conn, 32 );
final ImageStack resultStack = Watershed.computeWatershed( imposedMinima, labeledMinima, conn, dams );

if ( removeLargestObject )
LabelImages.removeLargestLabel( resultStack );

final ImagePlus resultImage = new ImagePlus( "watershed", resultStack );
final Img< T > labelImage = ImageJFunctions.wrap( resultImage );
final double[] calibration = TMUtils.getSpatialCalibration( img );

final LabelImageDetector< T > lbldetector = new LabelImageDetector<>( labelImage, interval, calibration, simplify );
final LabelImageDetector< T > lbldetector = new LabelImageDetector<>(
labelImage,
interval,
calibration,
simplify,
smoothingScale );
if ( !lbldetector.checkInput() || !lbldetector.process() )
{
errorMessage = baseErrorMessage + lbldetector.getErrorMessage();
Expand Down
103 changes: 87 additions & 16 deletions src/main/java/fiji/plugin/trackmate/morpholibj/MorphoLibJDetectorConfigurationPanel.java
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Original file line number Diff line number Diff line change
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 @@ -23,9 +23,11 @@

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.detection.ThresholdDetectorFactory.KEY_SMOOTHING_SCALE;
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.KEY_CONNECTIVITY;
import static fiji.plugin.trackmate.morpholibj.MorphoLibJDetectorFactory.KEY_REMOVE_LARGEST_OBJECT;
import static fiji.plugin.trackmate.morpholibj.MorphoLibJDetectorFactory.KEY_TOLERANCE;

import java.awt.Dimension;
Expand Down Expand Up @@ -55,6 +57,7 @@
import fiji.plugin.trackmate.detection.SpotDetectorFactoryBase;
import fiji.plugin.trackmate.gui.GuiUtils;
import fiji.plugin.trackmate.gui.components.ConfigurationPanel;
import fiji.plugin.trackmate.gui.components.PanelSmoothContour;
import fiji.plugin.trackmate.util.DetectionPreview;

public class MorphoLibJDetectorConfigurationPanel extends ConfigurationPanel
Expand All @@ -72,12 +75,18 @@ public class MorphoLibJDetectorConfigurationPanel extends ConfigurationPanel

private final JFormattedTextField ftfTolerance;

private final JComboBox< Connectivity > cmbboxConnectivity;

private final JCheckBox chkboxRemoveLargest;

private final JCheckBox chkboxSimplify;
private final PanelSmoothContour smoothingPanel;

private final JComboBox< Connectivity > cmbboxConnectivity;

public MorphoLibJDetectorConfigurationPanel( final Settings settings, final Model model )
{
int gridy = 0;

final GridBagLayout gridBagLayout = new GridBagLayout();
gridBagLayout.columnWidths = new int[] { 144, 0, 32 };
gridBagLayout.rowHeights = new int[] { 0, 84, 0, 27, 0, 0, 0 };
Expand All @@ -93,41 +102,46 @@ public MorphoLibJDetectorConfigurationPanel( final Settings settings, final Mode
gbcLblDetector.insets = new Insets( 5, 5, 5, 0 );
gbcLblDetector.fill = GridBagConstraints.HORIZONTAL;
gbcLblDetector.gridx = 0;
gbcLblDetector.gridy = 0;
gbcLblDetector.gridy = gridy;
add( lblDetector, gbcLblDetector );

/*
* Help text.
*/

gridy++;

final GridBagConstraints gbcLblHelptext = new GridBagConstraints();
gbcLblHelptext.anchor = GridBagConstraints.NORTH;
gbcLblHelptext.fill = GridBagConstraints.BOTH;
gbcLblHelptext.gridwidth = 3;
gbcLblHelptext.insets = new Insets( 5, 5, 5, 5 );
gbcLblHelptext.gridx = 0;
gbcLblHelptext.gridy = 1;
gbcLblHelptext.gridy = gridy;
add( GuiUtils.textInScrollPanel( GuiUtils.infoDisplay( MorphoLibJDetectorFactory.INFO_TEXT ) ), gbcLblHelptext );

/*
* Channel selector.
*/


gridy++;

final JLabel lblSegmentInChannel = new JLabel( "Segment in channel:" );
lblSegmentInChannel.setFont( SMALL_FONT );
final GridBagConstraints gbcLblSegmentInChannel = new GridBagConstraints();
gbcLblSegmentInChannel.anchor = GridBagConstraints.EAST;
gbcLblSegmentInChannel.insets = new Insets( 5, 5, 5, 5 );
gbcLblSegmentInChannel.gridx = 0;
gbcLblSegmentInChannel.gridy = 2;
gbcLblSegmentInChannel.gridy = gridy;
add( lblSegmentInChannel, gbcLblSegmentInChannel );

sliderChannel = new JSlider();
final GridBagConstraints gbcSliderChannel = new GridBagConstraints();
gbcSliderChannel.fill = GridBagConstraints.HORIZONTAL;
gbcSliderChannel.insets = new Insets( 5, 5, 5, 5 );
gbcSliderChannel.gridx = 1;
gbcSliderChannel.gridy = 2;
gbcSliderChannel.gridy = gridy;
add( sliderChannel, gbcSliderChannel );

final JLabel labelChannel = new JLabel( "1" );
Expand All @@ -136,7 +150,7 @@ public MorphoLibJDetectorConfigurationPanel( final Settings settings, final Mode
final GridBagConstraints gbcLabelChannel = new GridBagConstraints();
gbcLabelChannel.insets = new Insets( 5, 5, 5, 0 );
gbcLabelChannel.gridx = 2;
gbcLabelChannel.gridy = 2;
gbcLabelChannel.gridy = gridy;
add( labelChannel, gbcLabelChannel );

sliderChannel.addChangeListener( l -> labelChannel.setText( "" + sliderChannel.getValue() ) );
Expand All @@ -145,13 +159,15 @@ public MorphoLibJDetectorConfigurationPanel( final Settings settings, final Mode
* Tolerance
*/

gridy++;

final JLabel lblTolerance = new JLabel( "Tolerance:" );
lblTolerance.setFont( SMALL_FONT );
final GridBagConstraints gbcLblTolerance = new GridBagConstraints();
gbcLblTolerance.anchor = GridBagConstraints.EAST;
gbcLblTolerance.insets = new Insets( 5, 5, 5, 5 );
gbcLblTolerance.gridx = 0;
gbcLblTolerance.gridy = 3;
gbcLblTolerance.gridy = gridy;
add( lblTolerance, gbcLblTolerance );

ftfTolerance = new JFormattedTextField( THRESHOLD_FORMAT );
Expand All @@ -161,22 +177,24 @@ public MorphoLibJDetectorConfigurationPanel( final Settings settings, final Mode
final GridBagConstraints gbcTolerance = new GridBagConstraints();
gbcTolerance.gridwidth = 2;
gbcTolerance.fill = GridBagConstraints.HORIZONTAL;
gbcTolerance.insets = new Insets( 5, 5, 5, 0 );
gbcTolerance.insets = new Insets( 5, 5, 5, 5 );
gbcTolerance.gridx = 1;
gbcTolerance.gridy = 3;
gbcTolerance.gridy = gridy;
add( ftfTolerance, gbcTolerance );

/*
* Connectivity.
*/

gridy++;

final JLabel lblConnectivity = new JLabel( "Connectivity:" );
lblConnectivity.setFont( new Font( "Arial", Font.PLAIN, 10 ) );
final GridBagConstraints gbcLblConnectivity = new GridBagConstraints();
gbcLblConnectivity.anchor = GridBagConstraints.EAST;
gbcLblConnectivity.insets = new Insets( 0, 5, 5, 5 );
gbcLblConnectivity.gridx = 0;
gbcLblConnectivity.gridy = 4;
gbcLblConnectivity.gridy = gridy;
add( lblConnectivity, gbcLblConnectivity );

this.cmbboxConnectivity = new JComboBox<>( new Vector<>( Arrays.asList( Connectivity.values() ) ) );
Expand All @@ -187,41 +205,84 @@ public MorphoLibJDetectorConfigurationPanel( final Settings settings, final Mode
gbcCmbboxConnectivity.insets = new Insets( 0, 5, 5, 0 );
gbcCmbboxConnectivity.fill = GridBagConstraints.HORIZONTAL;
gbcCmbboxConnectivity.gridx = 1;
gbcCmbboxConnectivity.gridy = 4;
gbcCmbboxConnectivity.gridy = gridy;
add( cmbboxConnectivity, gbcCmbboxConnectivity );

/*
* Remove largest object.
*/

gridy++;

final JLabel lblRemoveLargest = new JLabel( "Remove largest object:" );
lblRemoveLargest.setFont( SMALL_FONT );
final GridBagConstraints gbcLblRemoveLargest = new GridBagConstraints();
gbcLblRemoveLargest.anchor = GridBagConstraints.EAST;
gbcLblRemoveLargest.insets = new Insets( 0, 5, 5, 5 );
gbcLblRemoveLargest.gridx = 0;
gbcLblRemoveLargest.gridy = gridy;
add( lblRemoveLargest, gbcLblRemoveLargest );

this.chkboxRemoveLargest = new JCheckBox();
final GridBagConstraints gbcChkboxRemoveLargest = new GridBagConstraints();
gbcChkboxRemoveLargest.anchor = GridBagConstraints.WEST;
gbcChkboxRemoveLargest.insets = new Insets( 0, 5, 5, 5 );
gbcChkboxRemoveLargest.gridx = 1;
gbcChkboxRemoveLargest.gridy = gridy;
add( chkboxRemoveLargest, gbcChkboxRemoveLargest );

/*
* Simplify.
*/

gridy++;

final JLabel lblSimplify = new JLabel( "Simplify contours:" );
lblSimplify.setFont( SMALL_FONT );
final GridBagConstraints gbcLblSimplify = new GridBagConstraints();
gbcLblSimplify.anchor = GridBagConstraints.EAST;
gbcLblSimplify.insets = new Insets( 0, 5, 5, 5 );
gbcLblSimplify.gridx = 0;
gbcLblSimplify.gridy = 5;
gbcLblSimplify.gridy = gridy;
add( lblSimplify, gbcLblSimplify );

this.chkboxSimplify = new JCheckBox();
final GridBagConstraints gbcChkboxSimplify = new GridBagConstraints();
gbcChkboxSimplify.anchor = GridBagConstraints.WEST;
gbcChkboxSimplify.insets = new Insets( 0, 5, 5, 5 );
gbcChkboxSimplify.gridx = 1;
gbcChkboxSimplify.gridy = 5;
gbcChkboxSimplify.gridy = gridy;
add( chkboxSimplify, gbcChkboxSimplify );

/*
* Smoothing scale.
*/

gridy++;

smoothingPanel = new PanelSmoothContour( -1., model.getSpaceUnits() );
smoothingPanel.setFont( SMALL_FONT );
final GridBagConstraints gbcSmoothingPanel = new GridBagConstraints();
gbcSmoothingPanel.gridwidth = 3;
gbcSmoothingPanel.fill = GridBagConstraints.HORIZONTAL;
gbcSmoothingPanel.insets = new Insets( 0, 5, 5, 5 );
gbcSmoothingPanel.gridx = 0;
gbcSmoothingPanel.gridy = gridy;
add( smoothingPanel, gbcSmoothingPanel );

/*
* Logger.
*/

gridy++;

final GridBagConstraints gbcBtnPreview = new GridBagConstraints();
gbcBtnPreview.fill = GridBagConstraints.HORIZONTAL;
gbcBtnPreview.gridwidth = 3;
gbcBtnPreview.fill = GridBagConstraints.BOTH;
gbcBtnPreview.insets = new Insets( 5, 5, 5, 5 );
gbcBtnPreview.gridx = 0;
gbcBtnPreview.gridy = 6;
gbcBtnPreview.gridy = gridy;

final DetectionPreview detectionPreview = DetectionPreview.create()
.model( model )
Expand Down Expand Up @@ -283,9 +344,15 @@ public Map< String, Object > getSettings()
final Connectivity connectivity = ( Connectivity ) cmbboxConnectivity.getSelectedItem();
settings.put( KEY_CONNECTIVITY, connectivity.getConnectivity() );

final boolean removeLargestObject = chkboxRemoveLargest.isSelected();
settings.put( KEY_REMOVE_LARGEST_OBJECT, removeLargestObject );

final boolean simplify = chkboxSimplify.isSelected();
settings.put( KEY_SIMPLIFY_CONTOURS, simplify );

final double scale = smoothingPanel.getScale();
settings.put( KEY_SMOOTHING_SCALE, scale );

return settings;
}

Expand All @@ -295,7 +362,11 @@ public void setSettings( final Map< String, Object > settings )
sliderChannel.setValue( ( Integer ) settings.get( KEY_TARGET_CHANNEL ) );
ftfTolerance.setValue( settings.get( KEY_TOLERANCE ) );
cmbboxConnectivity.setSelectedItem( Connectivity.valueFor( ( int ) settings.get( KEY_CONNECTIVITY ) ) );
chkboxRemoveLargest.setSelected( ( boolean ) settings.get( KEY_REMOVE_LARGEST_OBJECT ) );
chkboxSimplify.setSelected( ( boolean ) settings.get( KEY_SIMPLIFY_CONTOURS ) );
final Object scaleObj = settings.get( KEY_SMOOTHING_SCALE );
final double scale = scaleObj == null ? -1. : ( ( Number ) scaleObj ).doubleValue();
smoothingPanel.setScale( scale );
}

@Override
Expand Down
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