Macro fixes

Modern/wrapperPlugins/pom.xml

@@ -181,7 +181,6 @@
         <dependency><!-- Needed for legacy UI. Do not remove. -->
             <groupId>net.imagej</groupId>
             <artifactId>imagej-legacy</artifactId>
-            <scope>runtime</scope>
             <optional>true</optional>
             <!-- Try removing after pom-scijava 29.x.x -->
             <exclusions>

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

@@ -29,6 +29,7 @@ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 import static org.bonej.wrapperPlugins.CommonMessages.NOT_8_BIT_BINARY_IMAGE;
 import static org.bonej.wrapperPlugins.CommonMessages.NO_IMAGE_OPEN;
 import static org.bonej.wrapperPlugins.CommonMessages.NO_SKELETONS;
+import static org.bonej.wrapperPlugins.wrapperUtils.Common.cancelMacroSafe;
 
 import ij.ImagePlus;
 import ij.ImageStack;
@@ -50,6 +51,7 @@ 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.bonej.wrapperPlugins.wrapperUtils.UsageReporter;
 import org.scijava.ItemIO;
 import org.scijava.ItemVisibility;
@@ -99,7 +101,7 @@ public class AnalyseSkeletonWrapper extends ContextCommand {
 		persist = false)
 	private ImagePlus inputImage;
 
-	@Parameter(visibility = ItemVisibility.MESSAGE, columns = 1)
+	@Parameter(visibility = ItemVisibility.MESSAGE, columns = 1, persist = false)
 	private String loopSection = "-- LOOPS --";
 
 	@Parameter(label = "Cycle pruning method",
@@ -108,7 +110,7 @@ public class AnalyseSkeletonWrapper extends ContextCommand {
 			"Shortest branch", "Lowest intensity voxel", "Lowest intensity branch" })
 	private String pruneCycleMethod = "None";
 
-	@Parameter(visibility = ItemVisibility.MESSAGE)
+	@Parameter(visibility = ItemVisibility.MESSAGE, persist = false)
 	private String endPointSection = "-- END-POINTS --";
 
 	@Parameter(label = "Prune ends",
@@ -117,10 +119,10 @@ public class AnalyseSkeletonWrapper extends ContextCommand {
 
 	@Parameter(label = "Exclude ROI from pruning",
 		description = "Exclude the current selection from pruning",
-		required = false, visibility = ItemVisibility.INVISIBLE)
+		required = false, visibility = ItemVisibility.INVISIBLE, persist = false)
 	private boolean excludeRoi;
 
-	@Parameter(visibility = ItemVisibility.MESSAGE)
+	@Parameter(visibility = ItemVisibility.MESSAGE, persist = false)
 	private String resultSection = "-- RESULTS AND OUTPUT --";
 
 	@Parameter(label = "Calculate largest shortest paths",
@@ -213,7 +215,7 @@ public void run() {
 		final SkeletonResult results = analyzeSkeleton_.run(pruneIndex, pruneEnds,
 				calculateShortestPaths, intensityImage, true, verbose, roi);
 		if (hasNoSkeletons(analyzeSkeleton_)) {
-			cancel(NO_SKELETONS);
+			cancelMacroSafe(this, NO_SKELETONS);
 			return;
 		}
 		showResults(results);
@@ -260,21 +262,21 @@ private boolean isValidIntensityImage(final Dataset dataset) {
 		// image
 		final int compositeChannelCount = dataset.getCompositeChannelCount();
 		if (compositeChannelCount != 1 || dataset.getValidBits() != 8) {
-			cancel("The intensity image needs to be 8-bit greyscale");
+			cancelMacroSafe(this, "The intensity image needs to be 8-bit greyscale");
 			return false;
 		}
 		if (AxisUtils.hasTimeDimensions(dataset)) {
-			cancel("The intensity image can't have a time dimension");
+			cancelMacroSafe(this, "The intensity image can't have a time dimension");
 			return false;
 		}
 		if (AxisUtils.hasChannelDimensions(dataset)) {
-			cancel("The intensity image can't have a channel dimension");
+			cancelMacroSafe(this, "The intensity image can't have a channel dimension");
 			return false;
 		}
 		if (AxisUtils.countSpatialDimensions(dataset) != inputImage
 			.getNDimensions())
 		{
-			cancel(
+			cancelMacroSafe(this,
 				"The intensity image should match the dimensionality of the input image");
 			return false;
 		}
@@ -312,17 +314,17 @@ private void openIntensityImage() {
 				return;
 			}
 			if (!convertService.supports(dataset, ImagePlus.class)) {
-				cancel("Intensity image could not be converted into an ImagePlus");
+				cancelMacroSafe(this, "Intensity image could not be converted into an ImagePlus");
 				return;
 			}
 			intensityImage = convertService.convert(dataset, ImagePlus.class);
 		}
 		catch (final FormatException e) {
-			cancel("Image format is not recognized");
+			cancelMacroSafe(this, "Image format is not recognized");
 			logService.trace(e);
 		}
 		catch (final IOException | NullPointerException e) {
-			cancel("An error occurred while opening the image");
+			cancelMacroSafe(this, "An error occurred while opening the image");
 			logService.trace(e);
 		}
 	}
@@ -433,7 +435,7 @@ private ImagePlus skeletonise(final ImagePlus inputImage) {
 	@SuppressWarnings("unused")
 	private void validateImage() {
 		if (inputImage == null) {
-			cancel(NO_IMAGE_OPEN);
+			cancelMacroSafe(this, NO_IMAGE_OPEN);
 			return;
 		}
 
@@ -442,16 +444,16 @@ private void validateImage() {
 		{
 			// AnalyzeSkeleton_ and Skeletonize_ cast to byte[], anything else than
 			// 8-bit will crash
-			cancel(NOT_8_BIT_BINARY_IMAGE);
+			cancelMacroSafe(this, NOT_8_BIT_BINARY_IMAGE);
 			return;
 		}
 
 		if (inputImage.getNChannels() > 1) {
-			cancel(HAS_CHANNEL_DIMENSIONS + ". Please split the channels.");
+			cancelMacroSafe(this, HAS_CHANNEL_DIMENSIONS + ". Please split the channels.");
 			return;
 		}
 		if (inputImage.getNFrames() > 1) {
-			cancel(HAS_TIME_DIMENSIONS + ". Please split the hyperstack.");
+			cancelMacroSafe(this, HAS_TIME_DIMENSIONS + ". Please split the hyperstack.");
 		}
 	}
 

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

@@ -29,6 +29,7 @@ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 import static org.bonej.wrapperPlugins.CommonMessages.NOT_3D_IMAGE;
 import static org.bonej.wrapperPlugins.CommonMessages.NOT_BINARY;
 import static org.bonej.wrapperPlugins.CommonMessages.NO_IMAGE_OPEN;
+import static org.bonej.wrapperPlugins.wrapperUtils.Common.cancelMacroSafe;
 import static org.scijava.ui.DialogPrompt.MessageType.WARNING_MESSAGE;
 import static org.scijava.ui.DialogPrompt.OptionType.OK_CANCEL_OPTION;
 import static org.scijava.ui.DialogPrompt.Result.OK_OPTION;
@@ -364,12 +365,12 @@ private Ellipsoid milEllipsoid(final RandomAccessibleInterval<BitType> interval)
 		try {
 			pointCloud = runDirectionsInParallel(interval);
 			if (pointCloud.size() < Quadric.MIN_DATA) {
-				cancel("Anisotropy could not be calculated - too few points");
+				cancelMacroSafe(this, "Anisotropy could not be calculated - too few points");
 				return null;
 			}
 			final Optional<Ellipsoid> ellipsoid = fitEllipsoid(pointCloud);
 			if (!ellipsoid.isPresent()) {
-				cancel("Anisotropy could not be calculated - ellipsoid fitting failed");
+				cancelMacroSafe(this, "Anisotropy could not be calculated - ellipsoid fitting failed");
 				return null;
 			}
 			if (displayMILVectors) {
@@ -379,7 +380,7 @@ private Ellipsoid milEllipsoid(final RandomAccessibleInterval<BitType> interval)
 		}
 		catch (final ExecutionException | InterruptedException e) {
 			logService.trace(e.getMessage());
-			cancel("The plug-in was interrupted");
+			cancelMacroSafe(this, "The plug-in was interrupted");
 		}
 		return null;
 	}
@@ -441,15 +442,15 @@ private void shutdownAndAwaitTermination(final ExecutorService executor) {
 	@SuppressWarnings("unused")
 	private void validateImage() {
 		if (inputImage == null) {
-			cancel(NO_IMAGE_OPEN);
+			cancelMacroSafe(this, NO_IMAGE_OPEN);
 			return;
 		}
 		if (AxisUtils.countSpatialDimensions(inputImage) != 3) {
-			cancel(NOT_3D_IMAGE);
+			cancelMacroSafe(this, NOT_3D_IMAGE);
 			return;
 		}
 		if (!ElementUtil.isBinary(inputImage)) {
-			cancel(NOT_BINARY);
+			cancelMacroSafe(this, NOT_BINARY);
 			return;
 		}
 		if (!isSpatialCalibrationsIsotropic(inputImage, 0.01, unitService) &&

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

@@ -26,6 +26,7 @@ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 import static org.bonej.wrapperPlugins.CommonMessages.NOT_3D_IMAGE;
 import static org.bonej.wrapperPlugins.CommonMessages.NOT_BINARY;
 import static org.bonej.wrapperPlugins.CommonMessages.NO_IMAGE_OPEN;
+import static org.bonej.wrapperPlugins.wrapperUtils.Common.cancelMacroSafe;
 import static org.scijava.ui.DialogPrompt.MessageType.INFORMATION_MESSAGE;
 
 import java.util.List;
@@ -213,17 +214,17 @@ private void subspaceConnectivity(final String label,
 	@SuppressWarnings("unused")
 	private void validateImage() {
 		if (inputImage == null) {
-			cancel(NO_IMAGE_OPEN);
+			cancelMacroSafe(this, NO_IMAGE_OPEN);
 			return;
 		}
 
 		if (AxisUtils.countSpatialDimensions(inputImage) != 3) {
-			cancel(NOT_3D_IMAGE);
+			cancelMacroSafe(this, NOT_3D_IMAGE);
 			return;
 		}
 
 		if (!ElementUtil.isBinary(inputImage)) {
-			cancel(NOT_BINARY);
+			cancelMacroSafe(this, NOT_BINARY);
 		}
 	}
 	// endregion

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

@@ -26,6 +26,7 @@ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 import static org.bonej.wrapperPlugins.CommonMessages.NOT_BINARY;
 import static org.bonej.wrapperPlugins.CommonMessages.NO_IMAGE_OPEN;
 import static org.bonej.wrapperPlugins.CommonMessages.WEIRD_SPATIAL;
+import static org.bonej.wrapperPlugins.wrapperUtils.Common.cancelMacroSafe;
 
 import java.util.List;
 import java.util.stream.Collectors;
@@ -178,17 +179,17 @@ private void prepareResultDisplay() {
 	@SuppressWarnings("unused")
 	private void validateImage() {
 		if (inputImage == null) {
-			cancel(NO_IMAGE_OPEN);
+			cancelMacroSafe(this, NO_IMAGE_OPEN);
 			return;
 		}
 
 		if (!ElementUtil.isBinary(inputImage)) {
-			cancel(NOT_BINARY);
+			cancelMacroSafe(this, NOT_BINARY);
 		}
 
 		final long spatialDimensions = AxisUtils.countSpatialDimensions(inputImage);
 		if (spatialDimensions < 2 || spatialDimensions > 3) {
-			cancel(WEIRD_SPATIAL);
+			cancelMacroSafe(this, WEIRD_SPATIAL);
 		}
 	}
 	// endregion

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

@@ -26,6 +26,7 @@ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 import static net.imagej.ops.stats.regression.leastSquares.Quadric.MIN_DATA;
 import static org.bonej.wrapperPlugins.CommonMessages.NOT_3D_IMAGE;
 import static org.bonej.wrapperPlugins.CommonMessages.NO_IMAGE_OPEN;
+import static org.bonej.wrapperPlugins.wrapperUtils.Common.cancelMacroSafe;
 
 import ij.ImagePlus;
 import ij.measure.Calibration;
@@ -113,8 +114,8 @@ public class FitEllipsoidWrapper extends ContextCommand {
 	@Override
 	public void run() {
 		if (!initPointROIs()) {
-			cancel("Please populate ROI Manager with at least " + MIN_DATA +
-				" point ROIs");
+			cancelMacroSafe(this, "Please populate ROI Manager with at least "
+					+ MIN_DATA + " point ROIs");
 			return;
 		}
 		statusService.showStatus("Fit ellipsoid: solving ellipsoid equation");
@@ -126,7 +127,7 @@ public void run() {
 		final Optional<Ellipsoid> result = (Optional<Ellipsoid>) opService.run(
 			QuadricToEllipsoid.class, quadric);
 		if (!result.isPresent()) {
-			cancel("Can't fit ellipsoid to points.\n" +
+			cancelMacroSafe(this, "Can't fit ellipsoid to points.\n" +
 				"Try adding more point ROIs to the ROI Manager and try again.");
 			return;
 		}
@@ -181,11 +182,11 @@ private boolean initPointROIs() {
 	@SuppressWarnings("unused")
 	private void validateImage() {
 		if (inputImage == null) {
-			cancel(NO_IMAGE_OPEN);
+			cancelMacroSafe(this, NO_IMAGE_OPEN);
 			return;
 		}
 		if (!ImagePlusUtil.is3D(inputImage)) {
-			cancel(NOT_3D_IMAGE);
+			cancelMacroSafe(this, NOT_3D_IMAGE);
 			return;
 		}
 		if (!Common.warnAnisotropy(inputImage, uiService)) {

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

@@ -25,6 +25,7 @@ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 
 import static org.bonej.wrapperPlugins.CommonMessages.NOT_BINARY;
 import static org.bonej.wrapperPlugins.CommonMessages.NO_IMAGE_OPEN;
+import static org.bonej.wrapperPlugins.wrapperUtils.Common.cancelMacroSafe;
 
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -322,11 +323,11 @@ private WeightedObservedPoints toWeightedObservedPoints(
 	@SuppressWarnings("unused")
 	private void validateImage() {
 		if (inputImage == null) {
-			cancel(NO_IMAGE_OPEN);
+			cancelMacroSafe(this, NO_IMAGE_OPEN);
 			return;
 		}
 		if (!ElementUtil.isBinary(inputImage)) {
-			cancel(NOT_BINARY);
+			cancelMacroSafe(this, NOT_BINARY);
 		}
 	}
 

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

@@ -28,6 +28,7 @@ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 import static org.bonej.wrapperPlugins.CommonMessages.HAS_TIME_DIMENSIONS;
 import static org.bonej.wrapperPlugins.CommonMessages.NOT_8_BIT_BINARY_IMAGE;
 import static org.bonej.wrapperPlugins.CommonMessages.NO_SKELETONS;
+import static org.bonej.wrapperPlugins.wrapperUtils.Common.cancelMacroSafe;
 import static org.scijava.ui.DialogPrompt.MessageType.WARNING_MESSAGE;
 
 import ij.ImagePlus;
@@ -180,7 +181,7 @@ public void run() {
 		statusService.showProgress(0, PROGRESS_STEPS);
 		final Graph[] graphs = analyzeSkeleton(skeleton);
 		if (graphs == null || graphs.length == 0) {
-			cancel(NO_SKELETONS);
+			cancelMacroSafe(this, NO_SKELETONS);
 			return;
 		}
 		warnMultipleGraphs(graphs);
@@ -226,7 +227,7 @@ private void addResults(final Map<Integer, DoubleStream> anglesMap) {
 			anglesTable = SharedTable.getTable();
 		}
 		else {
-			cancel(NO_RESULTS_MSG);
+			cancelMacroSafe(this, NO_RESULTS_MSG);
 		}
 	}
 
@@ -277,23 +278,23 @@ private List<Vertex> filterBoundaryVertices(
 	@SuppressWarnings("unused")
 	private void imageValidater() {
 		if (inputImage == null) {
-			cancel(CommonMessages.NO_IMAGE_OPEN);
+			cancelMacroSafe(this, CommonMessages.NO_IMAGE_OPEN);
 			return;
 		}
 		if (inputImage.getBitDepth() != 8 || !ImagePlusUtil.isBinaryColour(
 			inputImage))
 		{
-			cancel(NOT_8_BIT_BINARY_IMAGE);
+			cancelMacroSafe(this, NOT_8_BIT_BINARY_IMAGE);
 			return;
 		}
 
 		if (inputImage.getNChannels() > 1) {
-			cancel(HAS_CHANNEL_DIMENSIONS + ". Please split the channels.");
+			cancelMacroSafe(this, HAS_CHANNEL_DIMENSIONS + ". Please split the channels.");
 			return;
 		}
 
 		if (inputImage.getNFrames() > 1) {
-			cancel(HAS_TIME_DIMENSIONS + ". Please split the hyperstack.");
+			cancelMacroSafe(this, HAS_TIME_DIMENSIONS + ". Please split the hyperstack.");
 		}
 		// Without anisotropyWarned the warning is shown twice
 		if (!anisotropyWarned) {