UI tweaks

Legacy/bonej/pom.xml

@@ -13,7 +13,7 @@
 
     <name>BoneJ legacy plugins</name>
     <description>Mavenized version of the BoneJ1 plugins</description>
-    <url>https://imagej.github.io/plugins/bonej</url>
+    <url>https://imagej.net/plugins/bonej</url>
     <inceptionYear>2015</inceptionYear>
     <organization>
         <name>Royal Veterinary College</name>

Legacy/bonej/src/main/java/org/bonej/plugins/Moments.java

@@ -166,6 +166,7 @@ public void run(final String arg) {
 		gd.addCheckbox("Show axes (3D)", true);
 		gd.addCheckbox("Record unit vectors", false);
 		gd.addDialogListener(this);
+		gd.addHelp("https://imagej.net/plugins/bonej#moments-of-inertia");
 		gd.showDialog();
 		if (gd.wasCanceled()) {
 			return;

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.github.io/plugins/bonej#particle-analyser");
+		gd.addHelp("https://imagej.net/plugins/bonej#particle-analyser");
 		gd.addDialogListener(this);
 		gd.showDialog();
 		if (gd.wasCanceled()) {

Legacy/bonej/src/main/java/org/bonej/plugins/Purify.java

@@ -99,6 +99,7 @@ public void run(final String arg) {
 		final GenericDialog gd = new GenericDialog("Setup");
 		gd.addCheckbox("Performance Log", false);
 		gd.addCheckbox("Make_copy", true);
+		gd.addHelp("https://imagej.net/plugins/bonej#purify");
 		gd.showDialog();
 		if (gd.wasCanceled()) return;
 		final boolean showPerformance = gd.getNextBoolean();

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.github.io/plugins/bonej#usage-reporting");
+		dialog.addHelp("https://imagej.net/plugins/bonej#usage-reporting");
 		dialog.showDialog();
 		if (dialog.wasCanceled()) {
 			Prefs.set(OPTOUTKEY, false);

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.github.io/plugins/bonej#slice-geometry");
+		gd.addHelp("https://imagej.net/plugins/bonej#slice-geometry");
 		gd.addDialogListener(this);
 		gd.showDialog();
 		final String bone = gd.getNextChoice();

Legacy/bonej/src/main/java/org/bonej/plugins/SphereFitter.java

@@ -128,6 +128,7 @@ public void run(final String arg) {
 		gd.addCheckbox("Add_to_ROI_Manager", false);
 		gd.addCheckbox("Clear_ROI_Manager", false);
 		gd.addDialogListener(this);
+		gd.addHelp("https://imagej.net/plugins/bonej#fit-sphere");
 		gd.showDialog();
 		if (gd.wasCanceled()) {
 			return;

Legacy/bonej/src/main/resources/plugins.config

@@ -29,9 +29,9 @@
 ###
 # Author: Michael Doube
 
-Plugins>BoneJ>Analyze, "Calibrate SCANCO", org.bonej.plugins.DensityCalibrator("scanco")
-Plugins>BoneJ>Analyze, "Orientation", org.bonej.plugins.Orienteer
-Plugins>BoneJ>Analyze, "Particle Analyser", org.bonej.plugins.ParticleCounter
+Plugins>BoneJ>Analyse, "Calibrate SCANCO", org.bonej.plugins.DensityCalibrator("scanco")
+Plugins>BoneJ>Analyse, "Orientation", org.bonej.plugins.Orienteer
+Plugins>BoneJ>Analyse, "Particle Analyser", org.bonej.plugins.ParticleCounter
 
 Plugins>BoneJ>Connectivity, "Connectivity", org.bonej.plugins.Connectivity 
 

Legacy/util/pom.xml

@@ -13,7 +13,7 @@
 
     <name>BoneJ legacy utilities</name>
     <description>Utility classes for BoneJ1 plugins</description>
-    <url>https://imagej.github.io/plugins/bonej</url>
+    <url>https://imagej.net/plugins/bonej</url>
     <inceptionYear>2015</inceptionYear>
     <organization>
         <name>Royal Veterinary College</name>

Modern/ops/pom.xml

@@ -13,7 +13,7 @@
 
     <name>BoneJ2 Ops</name>
     <description>Ops created for BoneJ2</description>
-    <url>https://imagej.github.io/plugins/bonej</url>
+    <url>https://imagej.net/plugins/bonej</url>
     <inceptionYear>2015</inceptionYear>
     <organization>
         <name>Royal Veterinary College</name>

Modern/utilities/pom.xml

@@ -13,7 +13,7 @@
 
     <name>BoneJ2 utilities</name>
     <description>Utility methods for BoneJ2</description>
-    <url>https://imagej.github.io/plugins/bonej</url>
+    <url>https://imagej.net/plugins/bonej</url>
     <inceptionYear>2015</inceptionYear>
     <organization>
         <name>Royal Veterinary College</name>

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.
     </description>
-    <url>https://imagej.github.io/plugins/bonej</url>
+    <url>https://imagej.net/plugins/bonej</url>
     <inceptionYear>2015</inceptionYear>
     <organization>
         <name>Royal Veterinary College</name>

Modern/wrapperPlugins/src/main/java/org/bonej/wrapperPlugins/AnalyseSkeletonWrapper.java

@@ -80,6 +80,7 @@ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 import org.bonej.utilities.AxisUtils;
 import org.bonej.utilities.ImagePlusUtil;
 import org.bonej.utilities.SharedTable;
+import org.bonej.wrapperPlugins.wrapperUtils.Common;
 import org.scijava.ItemIO;
 import org.scijava.ItemVisibility;
 import org.scijava.app.StatusService;
@@ -88,13 +89,15 @@ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 import org.scijava.io.IOService;
 import org.scijava.io.location.FileLocation;
 import org.scijava.log.LogService;
+import org.scijava.platform.PlatformService;
 import org.scijava.plugin.Parameter;
 import org.scijava.plugin.Plugin;
 import org.scijava.table.DefaultGenericTable;
 import org.scijava.table.DoubleColumn;
 import org.scijava.table.IntColumn;
 import org.scijava.table.PrimitiveColumn;
 import org.scijava.ui.UIService;
+import org.scijava.widget.Button;
 import org.scijava.widget.ChoiceWidget;
 import org.scijava.widget.FileWidget;
 
@@ -150,6 +153,9 @@ public class AnalyseSkeletonWrapper extends BoneJCommand {
 		description = "Show skeleton images labelled with their IDs",
 		required = false)
 	private boolean displaySkeletons;
+
+	@Parameter(label = "Help", description = "More about Analyse Skeleton", callback = "showHelpPage")
+	private Button button;
 
 	/**
 	 * Additional analysis details in a {@link DefaultGenericTable}, null if
@@ -189,7 +195,10 @@ public class AnalyseSkeletonWrapper extends BoneJCommand {
 
 	@Parameter
 	private StatusService statusService;
-
+
+	@Parameter
+	private PlatformService platformService;
+
 	private ImagePlus intensityImage;
 
 	@Override
@@ -231,6 +240,11 @@ public void run() {
 		}
 		reportUsage();
 	}
+
+	@SuppressWarnings("unused")
+	private void showHelpPage() {
+		Common.showHelpPage("#analyse-skeleton", platformService, uiService, logService);
+	}
 
 	private boolean hasNoSkeletons(final AnalyzeSkeleton_ analyzeSkeleton_) {
 		final Graph[] graphs = analyzeSkeleton_.getGraphs();

Modern/wrapperPlugins/src/main/java/org/bonej/wrapperPlugins/AnisotropyWrapper.java

@@ -100,6 +100,7 @@ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 import org.bonej.utilities.ElementUtil;
 import org.bonej.utilities.SharedTable;
 import org.bonej.utilities.Visualiser;
+import org.bonej.wrapperPlugins.wrapperUtils.Common;
 import org.bonej.wrapperPlugins.wrapperUtils.HyperstackUtils.Subspace;
 import org.joml.Matrix3d;
 import org.joml.Matrix4d;
@@ -112,10 +113,12 @@ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 import org.scijava.app.StatusService;
 import org.scijava.command.Command;
 import org.scijava.log.LogService;
+import org.scijava.platform.PlatformService;
 import org.scijava.plugin.Parameter;
 import org.scijava.plugin.Plugin;
 import org.scijava.ui.DialogPrompt.Result;
 import org.scijava.ui.UIService;
+import org.scijava.widget.Button;
 import org.scijava.widget.NumberWidget;
 
 /**
@@ -194,6 +197,9 @@ public class AnisotropyWrapper<T extends RealType<T> & NativeType<T>> extends Bo
 			description = "Show the vectors of the mean intercept lengths",
 			required = false)
 	private boolean displayMILVectors;
+
+	@Parameter(label = "Help", description = "More about Anisotropy", callback = "showHelpPage")
+	private Button button;
 
 	@Parameter
 	private LogService logService;
@@ -205,6 +211,8 @@ public class AnisotropyWrapper<T extends RealType<T> & NativeType<T>> extends Bo
 	private UIService uiService;
 	@Parameter
 	private UnitService unitService;
+	@Parameter
+	private PlatformService platformService;
 	private static BinaryHybridCFI1<Vector3d, Quaterniondc, Vector3d> rotateOp;
 	private double milLength;
 
@@ -229,6 +237,11 @@ public void run() {
 		resultsTable = SharedTable.getTable();
 		reportUsage();
 	}
+
+	@SuppressWarnings("unused")
+	private void showHelpPage() {
+		Common.showHelpPage("#anisotropy", platformService, uiService, logService);
+	}
 
 	// region -- Helper methods --
 	private void calculateMILLength(final RandomAccessibleInterval<BitType> interval) {

Modern/wrapperPlugins/src/main/java/org/bonej/wrapperPlugins/EllipsoidFactorWrapper.java

@@ -118,9 +118,11 @@ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 import org.scijava.app.StatusService;
 import org.scijava.command.Command;
 import org.scijava.log.LogService;
+import org.scijava.platform.PlatformService;
 import org.scijava.plugin.Parameter;
 import org.scijava.plugin.Plugin;
 import org.scijava.ui.UIService;
+import org.scijava.widget.Button;
 
 import sc.fiji.skeletonize3D.Skeletonize3D_;
 
@@ -166,6 +168,8 @@ public class EllipsoidFactorWrapper extends BoneJCommand {
 	@SuppressWarnings("unused")
     @Parameter
 	private UnitService unitService;
+	@Parameter
+	private PlatformService platformService;
 	//main input image
 	@SuppressWarnings("unused")
 	@Parameter(validater = "validateImage")
@@ -213,7 +217,9 @@ public class EllipsoidFactorWrapper extends BoneJCommand {
 	private List<ImgPlus> ellipsoidFactorOutputImages;
 	@Parameter(label = "Seed Points", type = ItemIO.OUTPUT)
 	private ImgPlus<ByteType> seedPointImage;// 0=not a seed, 1=medial seed
-
+	@Parameter(label = "Help", description = "More about Ellipsoid Factor", callback = "showHelpPage")
+	private Button button;
+
 	private ImgPlus<BitType> inputAsBitType;
 
 	@Override
@@ -341,6 +347,11 @@ public void run() {
 		statusService.showStatus("Ellipsoid Factor completed");
 		reportUsage();
 	}
+
+	@SuppressWarnings("unused")
+	private void showHelpPage() {
+		Common.showHelpPage("#ellipsoid-factor", platformService, uiService, logService);
+	}
 
 	private List<ImgPlus> divideOutput(final List<ImgPlus> outputList, final int repetitions) {
 		final List<ImgPlus> divided = new ArrayList<>();

Modern/wrapperPlugins/src/main/java/org/bonej/wrapperPlugins/FractalDimensionWrapper.java

@@ -81,15 +81,20 @@ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 import org.apache.commons.math3.stat.regression.SimpleRegression;
 import org.bonej.utilities.ElementUtil;
 import org.bonej.utilities.SharedTable;
+import org.bonej.wrapperPlugins.wrapperUtils.Common;
 import org.bonej.wrapperPlugins.wrapperUtils.HyperstackUtils.Subspace;
 import org.scijava.ItemIO;
 import org.scijava.app.StatusService;
 import org.scijava.command.Command;
+import org.scijava.log.LogService;
+import org.scijava.platform.PlatformService;
 import org.scijava.plugin.Parameter;
 import org.scijava.plugin.Plugin;
 import org.scijava.table.DefaultGenericTable;
 import org.scijava.table.DoubleColumn;
 import org.scijava.table.GenericTable;
+import org.scijava.ui.UIService;
+import org.scijava.widget.Button;
 import org.scijava.widget.NumberWidget;
 
 /**
@@ -147,6 +152,9 @@ public class FractalDimensionWrapper<T extends RealType<T> & NativeType<T>> exte
 	@Parameter(label = "Show points",
 		description = "Show (log(size), -log(count)) points", required = false)
 	private boolean showPoints;
+
+	@Parameter(label = "Help", description = "More about Fractal Dimension", callback = "showHelpPage")
+	private Button button;
 
 	/**
 	 * Table containing the (-log(size), log(count)) points for each 3D subspace
@@ -158,6 +166,12 @@ public class FractalDimensionWrapper<T extends RealType<T> & NativeType<T>> exte
 	private OpService opService;
 	@Parameter
 	private StatusService statusService;
+	@Parameter
+	private LogService logService;
+	@Parameter
+	private UIService uiService;
+	@Parameter
+	private PlatformService platformService;
 
 	private BinaryHybridCF<RandomAccessibleInterval<BitType>, Boolean, RandomAccessibleInterval<BitType>> hollowOp;
 	private UnaryFunctionOp<RandomAccessibleInterval<BitType>, List<ValuePair<DoubleType, DoubleType>>> boxCountOp;
@@ -194,6 +208,12 @@ public void run() {
 		resultsTable = SharedTable.getTable();
 		reportUsage();
 	}
+
+	@SuppressWarnings("unused")
+	private void showHelpPage() {
+		Common.showHelpPage("#fractal-dimension", platformService, uiService, logService);
+	}
+
 
 	// region -- Helper methods --
 	private void writePoints(final String headerSuffix,

Modern/wrapperPlugins/src/main/java/org/bonej/wrapperPlugins/IntertrabecularAngleWrapper.java

@@ -83,11 +83,14 @@ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 import org.scijava.ItemIO;
 import org.scijava.app.StatusService;
 import org.scijava.command.Command;
+import org.scijava.log.LogService;
+import org.scijava.platform.PlatformService;
 import org.scijava.plugin.Parameter;
 import org.scijava.plugin.Plugin;
 import org.scijava.table.DoubleColumn;
 import org.scijava.table.Table;
 import org.scijava.ui.UIService;
+import org.scijava.widget.Button;
 import org.scijava.widget.NumberWidget;
 
 import sc.fiji.analyzeSkeleton.AnalyzeSkeleton_;
@@ -166,6 +169,7 @@ public class IntertrabecularAngleWrapper extends BoneJCommand {
 		description = "Print the percentage of each of the type of edges that were culled after calling analyseSkeleton",
 		required = false, persistKey = "ITA_print_culled_edges")
 	private boolean printCulledEdgePercentages;
+
 	/**
 	 * The ITA edge-end coordinates in a {@link Table}, null if there are no
 	 * results
@@ -174,10 +178,16 @@ public class IntertrabecularAngleWrapper extends BoneJCommand {
 	private ResultsTable centroidTable;
 	@Parameter(type = ItemIO.OUTPUT, label = "Edge culling percentages")
 	private ResultsTable culledEdgePercentagesTable;
+	@Parameter(label = "Help", description = "More about Intertrabecular Angles", callback = "showHelpPage")
+	private Button button;
 	@Parameter
 	private StatusService statusService;
 	@Parameter
 	private UIService uiService;
+	@Parameter
+	private LogService logService;
+	@Parameter
+	private PlatformService platformService;
 
 	private double[] coefficients;
 	private boolean anisotropyWarned;
@@ -219,6 +229,11 @@ public void run() {
 		printCulledEdgePercentages(pruningResult.b);
 		reportUsage();
 	}
+
+	@SuppressWarnings("unused")
+	private void showHelpPage() {
+		Common.showHelpPage("#inter-trabecular-angles", platformService, uiService, logService);
+	}
 
 	private void addResults(final Map<Integer, DoubleStream> anglesMap) {
 		final String label = inputImage.getTitle();