From a3e9a7b9ecf7faa16e6e2aedd8ad710a12adc65a Mon Sep 17 00:00:00 2001 From: Jean-Yves Tinevez Date: Thu, 25 Jul 2024 17:19:02 +0200 Subject: [PATCH 1/9] Don't crash when saving with an image without an associated on-disk location Fix #303 Reported by @jiyuuchc --- src/main/java/fiji/plugin/trackmate/util/TMUtils.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/fiji/plugin/trackmate/util/TMUtils.java b/src/main/java/fiji/plugin/trackmate/util/TMUtils.java index 0550f0adb..cd4c2ee05 100644 --- a/src/main/java/fiji/plugin/trackmate/util/TMUtils.java +++ b/src/main/java/fiji/plugin/trackmate/util/TMUtils.java @@ -745,7 +745,7 @@ public static File proposeTrackMateSaveFile( final Settings settings, final Logg */ settings.imageFolder = settings.imp.getOriginalFileInfo().directory; } - else if ( !settings.imageFolder.isEmpty() ) + else if ( null != settings.imageFolder && !settings.imageFolder.isEmpty() ) { final String absolutePath = FileSystems.getDefault().getPath( settings.imageFolder ).normalize().toAbsolutePath().toString(); folder = new File( absolutePath ); From 61f65e83f433eabea46802bbd4d307882ac34e60 Mon Sep 17 00:00:00 2001 From: tpietzsch Date: Fri, 5 Apr 2024 20:07:27 +0200 Subject: [PATCH 2/9] POM: Bump parent to pom-scijava-38.0.1 --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index b282df815..1932439f5 100644 --- a/pom.xml +++ b/pom.xml @@ -5,7 +5,7 @@ org.scijava pom-scijava - 37.0.0 + 38.0.1 From a503933bbd32e65428ca71688aaafc41d78848f1 Mon Sep 17 00:00:00 2001 From: tpietzsch Date: Wed, 28 Aug 2024 13:45:29 +0200 Subject: [PATCH 3/9] POM: Bump dependency versions imglib2 -> 7.1.0 imglib2-realtransform -> 4.0.3 imglib2-roi -> 0.15.0 imglib2-cache -> 1.0.0-beta-18 imglib2-algorithm -> 0.15.3 imglib2-ij -> 2.0.2 bigdataviewer-core -> 10.6.0 --- pom.xml | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 1932439f5..a9a31241f 100644 --- a/pom.xml +++ b/pom.xml @@ -147,7 +147,14 @@ 2.5.2 0.11.1 - 6.1.0 + + 7.1.0 + 4.0.3 + 0.15.0 + 1.0.0-beta-18 + 0.15.3 + 2.0.2 + 10.6.0 From 5e0af5215b0fc681a7dda0563dcc6ee58bf0c00d Mon Sep 17 00:00:00 2001 From: tpietzsch Date: Fri, 5 Apr 2024 20:11:37 +0200 Subject: [PATCH 4/9] Addapt API changes introduced by https://github.com/imglib/imglib2-roi/pull/71 --- src/main/java/fiji/plugin/trackmate/detection/MaskUtils.java | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/main/java/fiji/plugin/trackmate/detection/MaskUtils.java b/src/main/java/fiji/plugin/trackmate/detection/MaskUtils.java index 53cf70fd8..2786afec3 100644 --- a/src/main/java/fiji/plugin/trackmate/detection/MaskUtils.java +++ b/src/main/java/fiji/plugin/trackmate/detection/MaskUtils.java @@ -33,6 +33,7 @@ import ij.gui.PolygonRoi; import ij.measure.Measurements; import ij.process.FloatPolygon; +import net.imglib2.Cursor; import net.imglib2.Interval; import net.imglib2.RandomAccess; import net.imglib2.RandomAccessible; @@ -280,7 +281,7 @@ public static < R extends IntegerType< R > > List< Spot > fromLabeling( while ( iterator.hasNext() ) { final LabelRegion< Integer > region = iterator.next(); - final LabelRegionCursor cursor = region.localizingCursor(); + final Cursor< Void > cursor = region.inside().localizingCursor(); final int[] cursorPos = new int[ labeling.numDimensions() ]; final long[] sum = new long[ 3 ]; while ( cursor.hasNext() ) @@ -358,7 +359,7 @@ public static < T extends RealType< T >, R extends RealType< R > > List< Spot > while ( iterator.hasNext() ) { final LabelRegion< Integer > region = iterator.next(); - final LabelRegionCursor cursor = region.localizingCursor(); + final Cursor< Void > cursor = region.inside().localizingCursor(); final int[] cursorPos = new int[ labeling.numDimensions() ]; final long[] sum = new long[ 3 ]; double quality = Double.NEGATIVE_INFINITY; From 514d5dbab6461223e775b78bde0adc9da62ad125 Mon Sep 17 00:00:00 2001 From: tpietzsch Date: Fri, 5 Apr 2024 20:12:08 +0200 Subject: [PATCH 5/9] Adapt API changes introduced by https://github.com/imglib/imglib2/pull/333 --- .../tracking/kdtree/NearestNeighborFlagSearchOnKDTree.java | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/main/java/fiji/plugin/trackmate/tracking/kdtree/NearestNeighborFlagSearchOnKDTree.java b/src/main/java/fiji/plugin/trackmate/tracking/kdtree/NearestNeighborFlagSearchOnKDTree.java index b5e639341..98a5e00dd 100644 --- a/src/main/java/fiji/plugin/trackmate/tracking/kdtree/NearestNeighborFlagSearchOnKDTree.java +++ b/src/main/java/fiji/plugin/trackmate/tracking/kdtree/NearestNeighborFlagSearchOnKDTree.java @@ -28,6 +28,8 @@ import net.imglib2.Sampler; import net.imglib2.neighborsearch.NearestNeighborSearch; + +// TODO: revise for new KDTree implementation, where KDTreeNode are reusable proxies. public class NearestNeighborFlagSearchOnKDTree< T > implements NearestNeighborSearch< FlagNode< T > > { @@ -78,8 +80,8 @@ protected void searchNode( final KDTreeNode< FlagNode< T > > current ) final boolean leftIsNearBranch = axisDiff < 0; // search the near branch - final KDTreeNode< FlagNode< T > > nearChild = leftIsNearBranch ? current.left : current.right; - final KDTreeNode< FlagNode< T > > awayChild = leftIsNearBranch ? current.right : current.left; + final KDTreeNode< FlagNode< T > > nearChild = leftIsNearBranch ? current.left() : current.right(); + final KDTreeNode< FlagNode< T > > awayChild = leftIsNearBranch ? current.right() : current.left(); if ( nearChild != null ) searchNode( nearChild ); From f513e17e48eb0a5704a9ca1246571d24af045688 Mon Sep 17 00:00:00 2001 From: Curtis Rueden Date: Thu, 29 Aug 2024 14:03:53 -0500 Subject: [PATCH 6/9] POM: bump minor version digit New public method: fiji.plugin.trackmate.util.cli.CondaPathConfigCommand.test() --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index a9a31241f..325819489 100644 --- a/pom.xml +++ b/pom.xml @@ -11,7 +11,7 @@ sc.fiji TrackMate - 7.13.3-SNAPSHOT + 7.14.0-SNAPSHOT TrackMate TrackMate plugin for Fiji. From 580032583eb9ad53f1ee79b3ea4690710a16e404 Mon Sep 17 00:00:00 2001 From: Curtis Rueden Date: Thu, 29 Aug 2024 14:04:55 -0500 Subject: [PATCH 7/9] Make the license-maven-plugin happy --- src/main/java/fiji/plugin/trackmate/io/TmXmlReader.java | 4 ++-- src/main/java/fiji/plugin/trackmate/util/cli/CLIUtils.java | 4 ++-- .../fiji/plugin/trackmate/util/cli/CondaCLIConfigurator.java | 4 ++-- .../plugin/trackmate/util/cli/CondaPathConfigCommand.java | 4 ++-- 4 files changed, 8 insertions(+), 8 deletions(-) diff --git a/src/main/java/fiji/plugin/trackmate/io/TmXmlReader.java b/src/main/java/fiji/plugin/trackmate/io/TmXmlReader.java index 9f5faf46e..267ce5d41 100644 --- a/src/main/java/fiji/plugin/trackmate/io/TmXmlReader.java +++ b/src/main/java/fiji/plugin/trackmate/io/TmXmlReader.java @@ -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 * . diff --git a/src/main/java/fiji/plugin/trackmate/util/cli/CLIUtils.java b/src/main/java/fiji/plugin/trackmate/util/cli/CLIUtils.java index f6c1adf7c..a0b306cd5 100644 --- a/src/main/java/fiji/plugin/trackmate/util/cli/CLIUtils.java +++ b/src/main/java/fiji/plugin/trackmate/util/cli/CLIUtils.java @@ -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 * . diff --git a/src/main/java/fiji/plugin/trackmate/util/cli/CondaCLIConfigurator.java b/src/main/java/fiji/plugin/trackmate/util/cli/CondaCLIConfigurator.java index e8a20114d..371c7728c 100644 --- a/src/main/java/fiji/plugin/trackmate/util/cli/CondaCLIConfigurator.java +++ b/src/main/java/fiji/plugin/trackmate/util/cli/CondaCLIConfigurator.java @@ -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 * . diff --git a/src/main/java/fiji/plugin/trackmate/util/cli/CondaPathConfigCommand.java b/src/main/java/fiji/plugin/trackmate/util/cli/CondaPathConfigCommand.java index dc044ad44..19de2a760 100644 --- a/src/main/java/fiji/plugin/trackmate/util/cli/CondaPathConfigCommand.java +++ b/src/main/java/fiji/plugin/trackmate/util/cli/CondaPathConfigCommand.java @@ -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 * . From 0bca9bc89dd4b61d8e313b3daa4fe6034098315b Mon Sep 17 00:00:00 2001 From: Curtis Rueden Date: Thu, 29 Aug 2024 14:05:40 -0500 Subject: [PATCH 8/9] Bump to next development cycle Signed-off-by: Curtis Rueden --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 325819489..4cfd04dec 100644 --- a/pom.xml +++ b/pom.xml @@ -11,7 +11,7 @@ sc.fiji TrackMate - 7.14.0-SNAPSHOT + 7.14.1-SNAPSHOT TrackMate TrackMate plugin for Fiji. From 476d646e91ac524f83808162714244138800f8a1 Mon Sep 17 00:00:00 2001 From: Jean-Yves Tinevez Date: Mon, 28 Oct 2024 16:47:47 +0100 Subject: [PATCH 9/9] Update parent to pom-scijava v39.0.0 --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 4cfd04dec..03b803051 100644 --- a/pom.xml +++ b/pom.xml @@ -5,7 +5,7 @@ org.scijava pom-scijava - 38.0.1 + 39.0.0