From 9962bf705fcd5bb82fe79da76bd975ed62b92d37 Mon Sep 17 00:00:00 2001 From: Raniere Silva Date: Fri, 23 Apr 2021 13:31:16 +0800 Subject: [PATCH 1/4] Update links in CONTRIBUTING.md --- CONTRIBUTING.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 0f0625470..38d7bf5be 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -2,14 +2,14 @@ ## Prerequisites * Familiarize yourself with GitHub -* [Java 8]() (newer version is fine, but the project still uses 1.8 bytecode) -* [Maven](https://imagej.net/Maven) -* [Git](https://imagej.net/Git) +* [Java 8](https://openjdk.java.net/) (newer version is fine, but the project still uses 1.8 bytecode) +* [Maven](https://imagej.github.io/develop/maven) +* [GitHub](https://imagej.github.io/develop/github) and Git * Preferrably an IDE such as [Eclipse](https://www.eclipse.org), [IntelliJ](https://www.jetbrains.com/idea/) or [NetBeans](https://netbeans.org) * Eclipse requires the m2e-egit connector to be installed so that you can seamlessly import your BoneJ2 fork from GitHub, but the version in the marketplace is often too old: you may need to [install it from the repository](https://stackoverflow.com/questions/51359823/m2e-egit-connector-for-scm-on-eclipse-photon-failure). ## Getting started -1) Create a [fork](https://imagej.net/How_to_contribute_to_an_existing_plugin_or_library) +1) Create a [fork](https://imagej.github.io/develop/improving-the-code) 2) [Synchronize](https://help.github.com/articles/syncing-a-fork/) your fork 3) Create a topic branch for your fix / new feature, e.g. `fix-issue-#1` From c0a8cd23f9d08456958948e32b9185f0c82dc66d Mon Sep 17 00:00:00 2001 From: Raniere Silva Date: Fri, 23 Apr 2021 13:45:32 +0800 Subject: [PATCH 2/4] Update URL in Java code --- Legacy/bonej/src/main/java/org/bonej/plugins/Connectivity.java | 2 +- .../bonej/src/main/java/org/bonej/plugins/ParticleCounter.java | 2 +- .../bonej/src/main/java/org/bonej/plugins/ReporterOptions.java | 2 +- Legacy/bonej/src/main/java/org/bonej/plugins/SliceGeometry.java | 2 +- .../bonej/wrapperPlugins/wrapperUtils/UsageReporterOptions.java | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/Legacy/bonej/src/main/java/org/bonej/plugins/Connectivity.java b/Legacy/bonej/src/main/java/org/bonej/plugins/Connectivity.java index 89cadb16e..621f8ed26 100644 --- a/Legacy/bonej/src/main/java/org/bonej/plugins/Connectivity.java +++ b/Legacy/bonej/src/main/java/org/bonej/plugins/Connectivity.java @@ -114,7 +114,7 @@ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE *

*

* Several of the methods are based on Ignacio Arganda-Carreras's - * Skeletonize3D_ plugin: + * Skeletonize3D_ plugin: * Skeletonize3D homepage *

* diff --git a/Legacy/bonej/src/main/java/org/bonej/plugins/ParticleCounter.java b/Legacy/bonej/src/main/java/org/bonej/plugins/ParticleCounter.java index 2a3f9427b..f0b9fe84b 100644 --- a/Legacy/bonej/src/main/java/org/bonej/plugins/ParticleCounter.java +++ b/Legacy/bonej/src/main/java/org/bonej/plugins/ParticleCounter.java @@ -194,7 +194,7 @@ public void run(final String arg) { gd.addChoice("Surface colours", items, items[0]); gd.addNumericField("Split value", 0, 3, 7, units + "³"); gd.addNumericField("Volume_resampling", 2, 0); - gd.addHelp("https://imagej.net/BoneJ#Particle_Analyser"); + gd.addHelp("https://imagej.github.io/plugins/bonej#particle-analyser"); gd.addDialogListener(this); gd.showDialog(); if (gd.wasCanceled()) { diff --git a/Legacy/bonej/src/main/java/org/bonej/plugins/ReporterOptions.java b/Legacy/bonej/src/main/java/org/bonej/plugins/ReporterOptions.java index 940d8f09e..0453bdad4 100644 --- a/Legacy/bonej/src/main/java/org/bonej/plugins/ReporterOptions.java +++ b/Legacy/bonej/src/main/java/org/bonej/plugins/ReporterOptions.java @@ -78,7 +78,7 @@ public void run(final String arg) { "and promote BoneJ to funders."); dialog.addMessage("If you agree to participate please hit OK\n" + "otherwise, cancel. For more information click Help."); - dialog.addHelp("https://imagej.net/BoneJ2#Usage_reporting"); + dialog.addHelp("https://imagej.github.io/plugins/bonej#usage-reporting"); dialog.showDialog(); if (dialog.wasCanceled()) { Prefs.set(OPTOUTKEY, false); diff --git a/Legacy/bonej/src/main/java/org/bonej/plugins/SliceGeometry.java b/Legacy/bonej/src/main/java/org/bonej/plugins/SliceGeometry.java index fc180d325..d83f386d8 100644 --- a/Legacy/bonej/src/main/java/org/bonej/plugins/SliceGeometry.java +++ b/Legacy/bonej/src/main/java/org/bonej/plugins/SliceGeometry.java @@ -274,7 +274,7 @@ else if (roi.getType() != Roi.RECTANGLE) { gd.addCheckbox("Partial_volume_compensation", false); gd.addNumericField("Background", thresholds[0], 1, 6, pixUnits + " "); gd.addNumericField("Foreground", thresholds[1], 1, 6, pixUnits + " "); - gd.addHelp("https://imagej.net/BoneJ2#Slice_geometry"); + gd.addHelp("https://imagej.github.io/plugins/bonej#slice-geometry"); gd.addDialogListener(this); gd.showDialog(); final String bone = gd.getNextChoice(); diff --git a/Modern/wrapperPlugins/src/main/java/org/bonej/wrapperPlugins/wrapperUtils/UsageReporterOptions.java b/Modern/wrapperPlugins/src/main/java/org/bonej/wrapperPlugins/wrapperUtils/UsageReporterOptions.java index 2558145fb..75bada01a 100644 --- a/Modern/wrapperPlugins/src/main/java/org/bonej/wrapperPlugins/wrapperUtils/UsageReporterOptions.java +++ b/Modern/wrapperPlugins/src/main/java/org/bonej/wrapperPlugins/wrapperUtils/UsageReporterOptions.java @@ -149,7 +149,7 @@ public void run() { @SuppressWarnings("unused") private void showHelpPage() { try { - platformService.open(new URL("https://imagej.net/BoneJ2#Usage_reporting")); + platformService.open(new URL("https://imagej.github.io/plugins/bonej#usage-reporting")); } catch (final IOException e) { uiService.showDialog("Something went wrong while opening the help page. Please try again."); logService.trace(e); From a791d861b9ad29aa464586ecf2535c520d92e5bc Mon Sep 17 00:00:00 2001 From: Raniere Silva Date: Fri, 23 Apr 2021 13:35:21 +0800 Subject: [PATCH 3/4] Update */pom.xml --- Legacy/bonej/pom.xml | 8 ++++---- Legacy/util/pom.xml | 8 ++++---- Modern/ops/pom.xml | 8 ++++---- Modern/utilities/pom.xml | 6 +++--- Modern/wrapperPlugins/pom.xml | 8 ++++---- pom.xml | 8 ++++---- 6 files changed, 23 insertions(+), 23 deletions(-) diff --git a/Legacy/bonej/pom.xml b/Legacy/bonej/pom.xml index 3b9339b74..36022d164 100644 --- a/Legacy/bonej/pom.xml +++ b/Legacy/bonej/pom.xml @@ -13,7 +13,7 @@ BoneJ legacy plugins Mavenized version of the BoneJ1 plugins - https://imagej.net/BoneJ_experimental + https://imagej.github.io/plugins/bonej 2015 Royal Veterinary College @@ -49,17 +49,17 @@ Richard Domander - https://imagej.net/User:Rdom + https://imagej.github.io/users/rimadoma rimadoma Curtis Rueden - https://imagej.net/User:Rueden + https://imagej.github.io/users/ctrueden ctrueden Mark Hiner - https://imagej.net/User:Hinerm + https://imagej.github.io/users/hinerm hinerm diff --git a/Legacy/util/pom.xml b/Legacy/util/pom.xml index d9f88dd3b..81790e5d4 100644 --- a/Legacy/util/pom.xml +++ b/Legacy/util/pom.xml @@ -13,7 +13,7 @@ BoneJ legacy utilities Utility classes for BoneJ1 plugins - https://imagej.net/BoneJ_experimental + https://imagej.github.io/plugins/bonej 2015 Royal Veterinary College @@ -49,17 +49,17 @@ Richard Domander - https://imagej.net/User:Rdom + https://imagej.github.io/users/rimadoma rimadoma Curtis Rueden - https://imagej.net/User:Rueden + https://imagej.github.io/users/ctrueden ctrueden Mark Hiner - https://imagej.net/User:Hinerm + https://imagej.github.io/users/hinerm hinerm diff --git a/Modern/ops/pom.xml b/Modern/ops/pom.xml index d1bfdac87..f64840b00 100644 --- a/Modern/ops/pom.xml +++ b/Modern/ops/pom.xml @@ -13,7 +13,7 @@ BoneJ2 Ops Ops created for BoneJ2 - https://imagej.net/BoneJ_experimental + https://imagej.github.io/plugins/bonej 2015 Royal Veterinary College @@ -64,17 +64,17 @@ Richard Domander - https://imagej.net/User:Rdom + https://imagej.github.io/users/rimadoma rimadoma Curtis Rueden - https://imagej.net/User:Rueden + https://imagej.github.io/users/ctrueden ctrueden Mark Hiner - https://imagej.net/User:Hinerm + https://imagej.github.io/users/hinerm hinerm diff --git a/Modern/utilities/pom.xml b/Modern/utilities/pom.xml index e9eb57a7a..358a4c2fc 100644 --- a/Modern/utilities/pom.xml +++ b/Modern/utilities/pom.xml @@ -13,7 +13,7 @@ BoneJ2 utilities Utility methods for BoneJ2 - https://imagej.net/BoneJ_experimental + https://imagej.github.io/plugins/bonej 2015 Royal Veterinary College @@ -64,12 +64,12 @@ Richard Domander - https://imagej.net/User:Rdom + https://imagej.github.io/users/rimadoma rimadoma Curtis Rueden - https://imagej.net/User:Rueden + https://imagej.github.io/users/ctrueden ctrueden diff --git a/Modern/wrapperPlugins/pom.xml b/Modern/wrapperPlugins/pom.xml index d015d637b..cb3b2c222 100644 --- a/Modern/wrapperPlugins/pom.xml +++ b/Modern/wrapperPlugins/pom.xml @@ -16,7 +16,7 @@ The Domain Presentation Layer (DPL) of BoneJ2, i.e. the commands that wrap the needed ops, and present results for skeletal biologists. - https://imagej.net/BoneJ_experimental + https://imagej.github.io/plugins/bonej 2015 Royal Veterinary College @@ -67,17 +67,17 @@ Richard Domander - https://imagej.net/User:Rdom + https://imagej.github.io/users/rimadoma rimadoma Curtis Rueden - https://imagej.net/User:Rueden + https://imagej.github.io/users/ctrueden ctrueden Mark Hiner - https://imagej.net/User:Hinerm + https://imagej.github.io/users/hinerm hinerm diff --git a/pom.xml b/pom.xml index d9106a225..aadd31b75 100644 --- a/pom.xml +++ b/pom.xml @@ -16,7 +16,7 @@ BoneJ Parent POM Parent POM for BoneJ components - https://imagej.net/BoneJ2 + https://imagej.github.io/plugins/bonej 2016 Royal Veterinary College @@ -67,18 +67,18 @@ Richard Domander - https://imagej.net/User:Rdom + https://imagej.github.io/users/rimadoma rimadoma founder Curtis Rueden - https://imagej.net/User:Rueden + https://imagej.github.io/users/ctrueden ctrueden Mark Hiner - https://imagej.net/User:Hinerm + https://imagej.github.io/users/hinerm hinerm From b628d9d138b8f20c4578fb71de4818a9e4c6602b Mon Sep 17 00:00:00 2001 From: Raniere Silva Date: Fri, 23 Apr 2021 15:19:19 +0800 Subject: [PATCH 4/4] Update link in README --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 36758c0c8..5b913f3a0 100644 --- a/README.md +++ b/README.md @@ -14,7 +14,7 @@ BoneJ is a collection of Fiji/ImageJ plug-ins for skeletal biology. It provides For legacy ImageJ1 plug-ins, which are no longer maintained, please visit https://bonej.org/legacy. ## Overview -The code is in two main modules: `Legacy` and `Modern`. The code in `Legacy` is originally from [BoneJ1](https://bonej.org/legacy), but it has been refactored to manage its dependencies via Maven. Unlike BoneJ1, the plug-ins in `Legacy` work with Java 8 and the latest version of [Fiji](https://imagej.net/Fiji). However some of them still depend on [3D_Viewer](https://github.com/fiji/3D_Viewer), which is known to have issues with the latest versions of MacOS (see the [forum](https://forum.image.sc)). +The code is in two main modules: `Legacy` and `Modern`. The code in `Legacy` is originally from [BoneJ1](https://bonej.org/legacy), but it has been refactored to manage its dependencies via Maven. Unlike BoneJ1, the plug-ins in `Legacy` work with Java 8 and the latest version of [Fiji](https://imagej.github.io/fiji/). However some of them still depend on [3D_Viewer](https://github.com/fiji/3D_Viewer), which is known to have issues with the latest versions of MacOS (see the [forum](https://forum.image.sc)). The main development happens in the `Modern` module. It hosts the modernized versions of BoneJ plug-ins, which fully comply with the current ImageJ API. Our goal is that as code matures, `Modern` hosts only "thin" wrapper plug-ins. They should be responsible only for interacting with the user, and collecting and displaying results. The wrappers call algorithms from the [Ops framework](https://imagej.net/ImageJ_Ops), specialised algorithms from BoneJ's own `Ops`, and utility code from `imagej-common`, `scifio` and other such core libraries.