Merge branch 'v8' of github.com:trackmate-sc/TrackMate into v8

trackmate-sc · Mar 28, 2024 · 721182c · 721182c
2 parents 3ea93bf + 2dd870e
commit 721182c
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Showing 4 changed files with 30 additions and 23 deletions.
diff --git a/pom.xml b/pom.xml
@@ -148,7 +148,8 @@
 
  <fontchooser.version>2.5.2</fontchooser.version>
  <javaGeom.version>0.11.1</javaGeom.version>
- <imglib2.version>6.1.0</imglib2.version>
+ <imglib2-mesh.version>1.0.0</imglib2-mesh.version>
+ <bigvolumeviewer.version>0.3.1</bigvolumeviewer.version>
  </properties>
 
  <dependencies>
@@ -160,7 +161,12 @@
  <dependency>
  <groupId>sc.fiji</groupId>
  <artifactId>labkit-ui</artifactId>
- <version>0.3.12-SNAPSHOT</version>
+ <exclusions>
+ <exclusion>
+ <groupId>net.imagej</groupId>
+ <artifactId>imagej-legacy</artifactId>
+ </exclusion>
+ </exclusions>
  </dependency>
 
  <!-- ImageJ dependencies -->
@@ -175,7 +181,7 @@
  <dependency>
  <groupId>net.imglib2</groupId>
  <artifactId>imglib2-mesh</artifactId>
- <version>1.0.0-SNAPSHOT</version>
+ <version>${imglib2-mesh.version}</version>
  </dependency>
  <dependency>
  <groupId>net.imagej</groupId>
@@ -184,18 +190,26 @@
  <dependency>
  <groupId>sc.fiji</groupId>
  <artifactId>bigvolumeviewer</artifactId>
- <version>0.3.1</version>
- </dependency>
- <dependency>
- <groupId>org.jogamp.jogl</groupId>
- <artifactId>jogl-all-main</artifactId>
- <version>2.3.2</version>
- </dependency>
- <dependency>
- <groupId>org.jogamp.gluegen</groupId>
- <artifactId>gluegen-rt-main</artifactId>
- <version>2.3.2</version>
- </dependency> 
+ <version>${bigvolumeviewer.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.jogamp.jogl</groupId>
+ <artifactId>jogl-all</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.jogamp.gluegen</groupId>
+ <artifactId>gluegen-rt</artifactId>
+ </dependency> 
+ <dependency>
+ <groupId>org.jogamp.gluegen</groupId>
+ <artifactId>gluegen-rt</artifactId>
+ <classifier>${scijava.natives.classifier.gluegen}</classifier>
+ </dependency>
+ <dependency>
+ <groupId>org.jogamp.jogl</groupId>
+ <artifactId>jogl-all</artifactId>
+ <classifier>${scijava.natives.classifier.jogl}</classifier>
+ </dependency>
 
  <!-- ImgLib2 dependencies -->
  <dependency>

diff --git a/src/main/java/fiji/plugin/trackmate/detection/MaskUtils.java b/src/main/java/fiji/plugin/trackmate/detection/MaskUtils.java
@@ -164,8 +164,6 @@ public static final long getThreshold( final Histogram1d< ? > hist )
  * the type of the input image. Must be real, scalar.
  * @param input
  * the input image.
- * @param interval
- * the interval in the input image to analyze.
  * @param threshold
  * the threshold to apply to the input image.
  * @param numThreads

diff --git a/src/main/java/fiji/plugin/trackmate/detection/SpotMeshUtils.java b/src/main/java/fiji/plugin/trackmate/detection/SpotMeshUtils.java
@@ -106,12 +106,6 @@ public class SpotMeshUtils
  * @param simplify
  * if <code>true</code> the meshes will be post-processed to be
  * smoother and contain less points.
- * @param smoothingScale
- * if strictly larger than 0, the input will be smoothed before
- * creating the contour, resulting in smoother contours. The
- * scale value sets the (Gaussian) filter radius and is specified
- * in physical units. If 0 or lower than 0, no smoothing is
- * applied.
  * @param qualityImage
  * the image in which to read the quality value.
  * @return a list of spots, with meshes.

diff --git a/src/main/java/fiji/plugin/trackmate/util/TMUtils.java b/src/main/java/fiji/plugin/trackmate/util/TMUtils.java
@@ -949,6 +949,7 @@ public static double standardDeviation( final DoubleArray data )
  * Returns a string of the name of the image without the extension, with the
  * full path
  * 
+ * @param settings A {@link Settings} object referencing the image
  * @return full name of the image without the extension
  */
  public static String getImagePathWithoutExtension( final Settings settings )