Update to pom-scijava 29.2.1

And update code accordingly.

This commit addresses the following issues:

* Account for Location-related backwards incompatibilities.
* Make the GetMetadata example GUI-free.
* Clean up the SwingExample.
* Slightly improve the WorkingWithModules example (but see #88).

howtos/pom.xml

@@ -8,7 +8,7 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>26.0.0</version>
+		<version>29.2.1</version>
 		<relativePath />
 	</parent>
 

howtos/src/main/java/howto/app/DisposeImageJ.java

@@ -25,7 +25,7 @@ public static void run() {
 		// do something with ImageJ
 
 		// dispose ImageJ
-		ij.context().dispose();
+		ij.dispose();
 	}
 
 	public static void main(String...args) { run(); }

howtos/src/main/java/howto/images/SaveImageCompressed.java

@@ -11,14 +11,17 @@
 import io.scif.config.SCIFIOConfig;
 import io.scif.formats.TIFFFormat;
 import io.scif.services.DatasetIOService;
+
+import java.io.IOException;
+import java.nio.file.Files;
+
 import net.imagej.Dataset;
 import net.imagej.DefaultDataset;
 import net.imagej.ImageJ;
 import net.imagej.ImgPlus;
 import net.imglib2.img.Img;
 
-import java.io.IOException;
-import java.nio.file.Files;
+import org.scijava.io.location.FileLocation;
 
 /**
  * How to save an image as LZW compressed TIFF
@@ -35,7 +38,7 @@ public static void run() throws IOException {
 		Img img = (Img) ij.io().open(Object.class.getResource("/blobs.png").getPath());
 
 		// create temporary path to save image to
-		String dest = Files.createTempFile("img", ".tif").toString();
+		FileLocation dest = new FileLocation(Files.createTempFile("img", ".tif").toFile());
 		System.out.println("Saving image to " + dest);
 
 		// create SCIFIO config to set compression algorithm
@@ -48,7 +51,7 @@ public static void run() throws IOException {
 		ij.get(DatasetIOService.class).save(dataset, dest, config);
 
 		// load and show saved image
-		Object savedImg = ij.io().open(dest);
+		Object savedImg = ij.io().open(dest.getFile().getAbsolutePath());
 		ij.ui().show("saved image", savedImg);
 	}
 

howtos/src/main/java/howto/metadata/GetMetadata.java

@@ -7,22 +7,19 @@
  */
 package howto.metadata;
 
-import java.io.IOException;
-
-import io.scif.services.FormatService;
+import io.scif.FieldPrinter;
 import io.scif.Format;
-import io.scif.FormatException;
 import io.scif.Metadata;
-import io.scif.FieldPrinter;
+import io.scif.services.FormatService;
 
-import net.imagej.ImageJ;
 import net.imagej.Dataset;
+import net.imagej.ImageJ;
 
 import org.scijava.ItemIO;
-import org.scijava.command.Command;
+import org.scijava.io.location.Location;
+import org.scijava.io.location.LocationService;
 import org.scijava.log.LogService;
 import org.scijava.plugin.Parameter;
-import org.scijava.plugin.Plugin;
 
 /**
  * This example illustrates how to access and display image metadata using the {@link FormatService} and
@@ -35,61 +32,62 @@
  * An optional {@code formatMetadata} method is included to (hopefully) make the text more readable.
  * </p>
  */
-@Plugin(type = Command.class, menuPath = "Image>Show Metadata")
-public class GetMetadata implements Command {
+public class GetMetadata {
 
     // -- Needed services --
 
     // for determining the Format of the input image
     @Parameter
     private FormatService formatService;
 
+    @Parameter
+    private LocationService locationService;
+
     // for logging errors
     @Parameter
     private LogService log;
 
     // -- Inputs and outputs to the command --
 
-    // input image
-    @Parameter
-    private Dataset img;
-
     // output metadata string
     @Parameter(label = "Metadata", type = ItemIO.OUTPUT)
     private String mString;
 
-    @Override
-    public void run() {
-        // we need the file path to determine the file format
-        final String filePath = img.getSource();
+    public static void run() throws Exception {
+      ImageJ ij = new ImageJ();
 
-        // catch any Format or IO exceptions
-        try {
+      // open a sample image
+      final Dataset img = ij.scifio().datasetIO().open("http://imagej.net/images/FluorescentCells.jpg");
 
-            // determine the Format based on the extension and, if necessary, the source data
-            Format format = formatService.getFormat(filePath);
+      // we need the file path to determine the file format
+      Location source = ij.get(LocationService.class).resolve(img.getSource());
 
-            // create an instance of the associated Parser and parse metadata from the image file
-            Metadata metadata = format.createParser().parse(filePath);
+      // catch any Format or IO exceptions
+      // determine the Format based on the extension and, if necessary, the source data
+      Format format = ij.scifio().format().getFormat(source);
 
-            // use FieldPrinter to traverse metadata tree and return as a String
-            String metadataTree = new FieldPrinter(metadata).toString();
+      // create an instance of the associated Parser and parse metadata from the image file
+      Metadata metadata = format.createParser().parse(source);
 
-            // (optional) remove some of the tree formatting to make the metadata easier to read
-            mString = formatMetadata(metadataTree);
-        }
-        catch (final FormatException | IOException e) {
-            log.error(e);
-        }
+      // use FieldPrinter to traverse metadata tree and return as a String
+      String metadataTree = new FieldPrinter(metadata).toString();
 
+      // (optional) remove some of the tree formatting to make the metadata easier to read
+      String mString = formatMetadata(metadataTree);
+
+      // print out our precious metadata!
+      ij.log().info(mString);
+
+      // close out our ImageJ
+      ij.dispose();
     }
 
     /**
      * This function makes the metadata easier to read by removing some of the tree formatting from FieldPrinter.
      * @param metadataTree raw metadata string returned by FieldPrinter().toString()
      * @return formatted version of metadataTree
      */
-    private String formatMetadata(String metadataTree) {
+    private static String formatMetadata(String metadataTree) {
 
         // remove ending braces | replace ", " between OME fields
         String tmp = metadataTree.replaceAll("(\\t+}\\n)|(,\\s)", "\n");
@@ -98,28 +96,5 @@ private String formatMetadata(String metadataTree) {
         return tmp.replaceAll("(\\t+\\{\\n)|(\\t+)", "");
     }
 
-    /**
-     * This main function serves for development purposes.
-     * It allows you to run the plugin immediately out of
-     * your integrated development environment (IDE).
-     *
-     * @param args unused
-     * @throws Exception
-     */
-    public static void main(final String... args) throws Exception {
-        // create the ImageJ application context with all available services
-        final ImageJ ij = new ImageJ();
-        ij.launch(args);
-
-        // open a sample image
-        final Dataset img = ij.scifio().datasetIO().open("http://imagej.net/images/FluorescentCells.jpg");
-
-        // show the image
-        ij.ui().show(img);
-
-        // invoke the plugin
-        ij.command().run(GetMetadata.class, true);
-
-    }
-
+    public static void main(String...args) throws Exception { run(); }
 }

maven-projects/add-two-datasets/pom.xml

@@ -8,7 +8,7 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>26.0.0</version>
+		<version>29.2.1</version>
 		<relativePath />
 	</parent>
 

maven-projects/custom-preprocessor-plugin/pom.xml

@@ -8,7 +8,7 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>26.0.0</version>
+		<version>29.2.1</version>
 		<relativePath />
 	</parent>
 

maven-projects/dynamic-commands/pom.xml

@@ -8,7 +8,7 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>26.0.0</version>
+		<version>29.2.1</version>
 		<relativePath />
 	</parent>
 

maven-projects/execute-commands/pom.xml

@@ -8,7 +8,7 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>26.0.0</version>
+		<version>29.2.1</version>
 		<relativePath />
 	</parent>
 

maven-projects/execute-commands/src/main/java/ExecuteCommands.java

@@ -158,7 +158,7 @@ public static Dataset invokeWithArgs(final ImageJ ij) {
 	 */
 	public static Dataset invokeWithMap(final ImageJ ij) {
 		// populate the map of input parameters
-		final Map<String, Object> inputMap = new HashMap<String, Object>();
+		final Map<String, Object> inputMap = new HashMap<>();
 		inputMap.put("inputFile", new File("sample-image.fake"));
 		// execute asynchronously using the command service
 		final Future<CommandModule> future =

maven-projects/ij2-image-plus/pom.xml

@@ -8,7 +8,7 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>26.0.0</version>
+		<version>29.2.1</version>
 		<relativePath />
 	</parent>
 

maven-projects/listen-to-events/pom.xml

@@ -8,7 +8,7 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>26.0.0</version>
+		<version>29.2.1</version>
 		<relativePath />
 	</parent>
 

maven-projects/simple-commands/pom.xml

@@ -8,7 +8,7 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>26.0.0</version>
+		<version>29.2.1</version>
 		<relativePath />
 	</parent>
 

maven-projects/swing-example/pom.xml

@@ -8,7 +8,7 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>26.0.0</version>
+		<version>29.2.1</version>
 		<relativePath />
 	</parent>
 

maven-projects/swing-example/src/main/java/DeconvolutionCommand.java

@@ -66,7 +66,8 @@ public void run() {
 		}
 
 		log.info("starting deconvolution");
-		deconvolved = ops.deconvolve().richardsonLucy(imgFloat, psf, numIterations);
+		final Img<FloatType> deconvolved = ops.create().img(imgFloat);
+		ops.deconvolve().richardsonLucy(deconvolved, imgFloat, psf, numIterations);
 		log.info("finished deconvolution");
 
 	}

maven-projects/swing-example/src/main/java/DeconvolutionCommandSwing.java

@@ -8,66 +8,37 @@
 
 import javax.swing.SwingUtilities;
 
-import net.imagej.ops.OpService;
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.type.numeric.real.FloatType;
 
+import org.scijava.Context;
 import org.scijava.ItemIO;
-import org.scijava.app.StatusService;
 import org.scijava.command.Command;
-import org.scijava.command.CommandService;
-import org.scijava.log.LogService;
 import org.scijava.plugin.Parameter;
 import org.scijava.plugin.Plugin;
-import org.scijava.thread.ThreadService;
-import org.scijava.ui.UIService;
 
 @Plugin(type = Command.class, headless = true,
 	menuPath = "Deconvolution>Deconvolution Swing")
 public class DeconvolutionCommandSwing implements Command {
 
 	@Parameter
-	OpService ops;
+	private Context ctx;
 
-	@Parameter
-	LogService log;
-
-	@Parameter
-	UIService ui;
-
-	@Parameter
-	CommandService cmd;
-
-	@Parameter
-	StatusService status;
-
-	@Parameter
-	ThreadService thread;
+	@Parameter(type = ItemIO.OUTPUT)
+	private RandomAccessibleInterval<FloatType> deconvolved;
 
 	private static DeconvolutionDialog dialog = null;
 
-	@Parameter(type = ItemIO.OUTPUT)
-	RandomAccessibleInterval<FloatType> deconvolved;
-
 	/**
 	 * show a dialog and give the dialog access to required IJ2 Services
 	 */
 	@Override
 	public void run() {
-
 		SwingUtilities.invokeLater(() -> {
 			if (dialog == null) {
-				dialog = new DeconvolutionDialog();
+				dialog = new DeconvolutionDialog(ctx);
 			}
 			dialog.setVisible(true);
-
-			dialog.setOps(ops);
-			dialog.setLog(log);
-			dialog.setStatus(status);
-			dialog.setCommand(cmd);
-			dialog.setThread(thread);
-			dialog.setUi(ui);
-
 		});
 	}
 }