From f890a1a867d6fef69094623f82bbbc2b1a471657 Mon Sep 17 00:00:00 2001 From: Curtis Rueden Date: Thu, 28 Mar 2024 13:08:42 -0500 Subject: [PATCH 1/3] Keep imagej-legacy out of the dependency tree This works around a test failure in TrackMatePluginTest caused by the original ImageJ classes being loaded too soon. There are other ways of working around this problem, such as creating a SciJava context more eagerly, but it's a distraction from the business of testing TrackMate, and anyway we don't need imagej-legacy on the classpath. The only reason labkit-ui has imagej-legacy as a dependency is for one line of code, which can be refactored to avoid it, so hopefully the exclusion will be able to disappear later after labkit-ui is updated. --- pom.xml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/pom.xml b/pom.xml index 90aa45511..b46cb35c2 100644 --- a/pom.xml +++ b/pom.xml @@ -161,6 +161,12 @@ sc.fiji labkit-ui 0.3.12-SNAPSHOT + + + net.imagej + imagej-legacy + + From 65bcd7b1f251e240ccce9f9ff671e6fe2ad2650f Mon Sep 17 00:00:00 2001 From: Curtis Rueden Date: Thu, 28 Mar 2024 13:18:25 -0500 Subject: [PATCH 2/3] POM: fix the dependencies * Avoid SNAPSHOT versions. * Factor out version pins to properties. * Avoid jogamp *-main uber-JARs. --- pom.xml | 38 +++++++++++++++++++++++--------------- 1 file changed, 23 insertions(+), 15 deletions(-) diff --git a/pom.xml b/pom.xml index b46cb35c2..6ae15cd1c 100644 --- a/pom.xml +++ b/pom.xml @@ -148,7 +148,8 @@ 2.5.2 0.11.1 - 6.1.0 + 1.0.0 + 0.3.1 @@ -160,7 +161,6 @@ sc.fiji labkit-ui - 0.3.12-SNAPSHOT net.imagej @@ -181,7 +181,7 @@ net.imglib2 imglib2-mesh - 1.0.0-SNAPSHOT + ${imglib2-mesh.version} net.imagej @@ -190,18 +190,26 @@ sc.fiji bigvolumeviewer - 0.3.1 - - - org.jogamp.jogl - jogl-all-main - 2.3.2 - - - org.jogamp.gluegen - gluegen-rt-main - 2.3.2 - + ${bigvolumeviewer.version} + + + org.jogamp.jogl + jogl-all + + + org.jogamp.gluegen + gluegen-rt + + + org.jogamp.gluegen + gluegen-rt + ${scijava.natives.classifier.gluegen} + + + org.jogamp.jogl + jogl-all + ${scijava.natives.classifier.jogl} + From 2dd870e040071a653e48a2d1fc5fa3259b0f2a37 Mon Sep 17 00:00:00 2001 From: Curtis Rueden Date: Thu, 28 Mar 2024 13:24:22 -0500 Subject: [PATCH 3/3] Fix Javadoc errors --- .../java/fiji/plugin/trackmate/detection/MaskUtils.java | 2 -- .../java/fiji/plugin/trackmate/detection/SpotMeshUtils.java | 6 ------ src/main/java/fiji/plugin/trackmate/util/TMUtils.java | 1 + 3 files changed, 1 insertion(+), 8 deletions(-) diff --git a/src/main/java/fiji/plugin/trackmate/detection/MaskUtils.java b/src/main/java/fiji/plugin/trackmate/detection/MaskUtils.java index ca2977323..72b71f7a1 100644 --- 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 index 0cfb3bdda..3c3cac760 100644 --- 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 true 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 index 5abc5a3c3..0dc59712a 100644 --- 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 )