Skip to content

Support 3D segmentation with TrackMate-Weka. #2

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Closed
tinevez wants to merge 15 commits into from
Closed

Support 3D segmentation with TrackMate-Weka. #2

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
15 commits
Select commit Hold shift + click to select a range
0d14629
Update parent to pom-scijava v34.1.0
tinevez Apr 17, 2023
957aad4
Temporary coupling to TrackMate v8.0.0-SNAPSHOT
tinevez Apr 17, 2023
30a60d3
Support 3D segmentation with WEKA.
tinevez Apr 17, 2023
b838aa5
Update interactive test.
tinevez Apr 17, 2023
f5329ac
Update parent-pom to scijava v37.0.0
tinevez Nov 29, 2023
25b0092
Fix missing smoothing scale.
tinevez Nov 29, 2023
678b387
Clean the test drives.
tinevez Nov 29, 2023
d686ce9
Change factory priority to have consistent detector menu ordering.
tinevez Dec 4, 2023
0bf9da3
Remove duplicate license file.
tinevez May 1, 2024
0633a9a
Add smoothing of spots.
tinevez May 1, 2024
079e202
Use the proba threshold widget.
tinevez May 1, 2024
6e9e6be
Tweak test drive.
tinevez May 1, 2024
3b928e9
Fix minor Eclipse warning.
tinevez May 1, 2024
9122135
Tweak adding elements to the config panel.
tinevez Jul 17, 2025
75f0b56
Merge branch 'v8' of github.com:trackmate-sc/TrackMate-Weka into v8
tinevez Jul 17, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
674 changes: 0 additions & 674 deletions LICENSE
View file
Open in desktop

This file was deleted.

4 changes: 2 additions & 2 deletions pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
<parent>
<groupId>org.scijava</groupId>
<artifactId>pom-scijava</artifactId>
<version>34.0.0</version>
<version>37.0.0</version>
<relativePath />
</parent>

Expand Down Expand Up @@ -86,7 +86,7 @@

<javaGeom.version>0.11.1</javaGeom.version>

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

<dependencies>
Expand Down
8 changes: 6 additions & 2 deletions src/main/java/fiji/plugin/trackmate/weka/WekaDetectionPreviewer.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,7 @@
package fiji.plugin.trackmate.weka;

import static fiji.plugin.trackmate.detection.DetectorKeys.KEY_TARGET_CHANNEL;
import static fiji.plugin.trackmate.detection.ThresholdDetectorFactory.KEY_SMOOTHING_SCALE;
import static fiji.plugin.trackmate.weka.WekaDetectorFactory.KEY_CLASSIFIER_FILEPATH;
import static fiji.plugin.trackmate.weka.WekaDetectorFactory.KEY_CLASS_INDEX;
import static fiji.plugin.trackmate.weka.WekaDetectorFactory.KEY_PROBA_THRESHOLD;
Expand Down Expand Up @@ -108,13 +109,16 @@ protected Pair< Model, Double > runPreviewDetection(
*/

final Map< String, Object > dsettings = new HashMap<>( detectorSettings );
@SuppressWarnings( "unchecked" )
final ImgPlus< T > img = TMUtils.rawWraps( settings.imp );
final int channel = ( Integer ) dsettings.get( KEY_TARGET_CHANNEL ) - 1;
final ImgPlus< T > input = TMUtils.hyperSlice( img, channel, frame );
final int classIndex = ( Integer ) dsettings.get( KEY_CLASS_INDEX );
final double probaThreshold = ( Double ) dsettings.get( KEY_PROBA_THRESHOLD );
final boolean simplify = true;
final Object smoothingObj = dsettings.get( KEY_SMOOTHING_SCALE );
final double smoothingScale = smoothingObj == null
? -1.
: ( ( Number ) smoothingObj ).doubleValue();

final boolean is3D = input.dimensionIndex( Axes.Z ) >= 0;
// First test to make sure we can read the classifier file.
Expand Down Expand Up @@ -180,7 +184,7 @@ protected Pair< Model, Double > runPreviewDetection(
}

logger.log( "Creating spots from probabilities." );
final List< Spot > spots = wekaRunner.getSpotsFromLastProbabilities( probaThreshold, simplify );
final List< Spot > spots = wekaRunner.getSpotsFromLastProbabilities( probaThreshold, simplify, smoothingScale );
if ( spots == null )
{
logger.error( "Problem creating spots: " + wekaRunner.getErrorMessage() );
Expand Down
8 changes: 6 additions & 2 deletions src/main/java/fiji/plugin/trackmate/weka/WekaDetector.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -59,20 +59,24 @@ public class WekaDetector< T extends RealType< T > & NativeType< T > > implement

private final boolean simplify;

private final double smoothingScale;

public WekaDetector(
final WekaRunner< T > runner,
final ImgPlus< T > img,
final Interval interval,
final int classIndex,
final double probaThreshold,
final boolean simplify )
final boolean simplify,
final double smoothingScale )
{
this.runner = runner;
this.img = img;
this.interval = DetectionUtils.squeeze( interval );
this.classIndex = classIndex;
this.probaThreshold = probaThreshold;
this.simplify = simplify;
this.smoothingScale = smoothingScale;
this.baseErrorMessage = BASE_ERROR_MESSAGE;
}

Expand All @@ -99,7 +103,7 @@ public boolean process()
return false;
}

spots = runner.getSpots( probabilities, TMUtils.getSpatialCalibration( img ), probaThreshold, simplify );
spots = runner.getSpots( probabilities, TMUtils.getSpatialCalibration( img ), probaThreshold, simplify, smoothingScale );
if ( spots == null )
{
System.err.println( "Problem creating spots: " + runner.getErrorMessage() );
Expand Down
Loading
Loading