SNTUtils: Add convenience helper to start SNT in stream mode

Author: tferr

src/main/java/sc/fiji/snt/SNTUtils.java

@@ -31,6 +31,7 @@
 import org.scijava.Context;
 import org.scijava.app.StatusService;
 import org.scijava.batch.BatchService;
+import org.scijava.command.CommandModule;
 import org.scijava.command.CommandService;
 import org.scijava.convert.ConvertService;
 import org.scijava.display.DisplayService;
@@ -52,6 +53,7 @@
 import org.scijava.util.VersionUtils;
 import sc.fiji.snt.analysis.sholl.ShollUtils;
 import sc.fiji.snt.gui.GuiUtils;
+import sc.fiji.snt.gui.cmds.BigDataLoaderCmd;
 import sc.fiji.snt.util.BoundingBox;
 import sc.fiji.snt.viewer.Viewer3D;
 
@@ -68,7 +70,10 @@
 import java.text.SimpleDateFormat;
 import java.util.List;
 import java.util.*;
+import java.util.concurrent.ExecutionException;
+import java.util.concurrent.Future;
 import java.util.concurrent.TimeUnit;
+import java.util.concurrent.TimeoutException;
 import java.util.jar.Attributes;
 import java.util.jar.Manifest;
 import java.util.regex.Matcher;
@@ -715,25 +720,47 @@ private static List<Class<? extends Service>> requiredServices() {
 	}
 
 	/**
-	 * Convenience method to start up SNT's GUI.
-	 * 
+	 * Convenience method to start up SNT's GUI in 'standard' mode.
+	 *
 	 * @return a reference to the {@link SNT} instance just started.s
 	 */
 	public static SNT startApp() {
+		return startApp(false);
+	}
+
+	/**
+	 * Convenience method to start up SNT's GUI.
+	 * @param streamMode If {@code true} SNT is initialized in stream (big data) mode, otherwise in 'standard' mode.
+	 * @return a reference to the {@link SNT} instance just started.s
+	 */
+	public static SNT startApp(final boolean streamMode) {
 		GuiUtils.setLookAndFeel(); // needs to be called here to set L&F of image's contextual menu!?
 		if (context == null && ij.IJ.getInstance() == null) {
-			new ImageJ().ui().showUI();
+			new ImageJ().ui().showUI(); // ImageJ ui needs to be displayed for proper display of scijava prompts
 		}
-		setIsLoading(true);
-		final PathAndFillManager pathAndFillManager = new PathAndFillManager();
-		final SNT snt = new SNT(getContext(), pathAndFillManager);
-		snt.initialize(null);
-		try {
-			javax.swing.SwingUtilities.invokeAndWait(snt::startUI);
-		} catch (final InvocationTargetException | InterruptedException e) {
-			e.printStackTrace();
+
+		if (streamMode) {
+			final Future<CommandModule> future = getContext().getService(CommandService.class).run(BigDataLoaderCmd.class,
+					true, (Map<String, Object>) null);
+			try {
+				future.get(30, TimeUnit.SECONDS);
+			} catch (final InterruptedException | ExecutionException | TimeoutException e) {
+				error("SNTUTils.startApp(true) failed", e);
+			}
+			return getInstance();
+
+        } else {
+			setIsLoading(true);
+			final PathAndFillManager pathAndFillManager = new PathAndFillManager();
+			final SNT snt = new SNT(getContext(), pathAndFillManager);
+			snt.initialize(null);
+			try {
+				javax.swing.SwingUtilities.invokeAndWait(snt::startUI);
+			} catch (final InvocationTargetException | InterruptedException e) {
+				e.printStackTrace();
+			}
+			return snt;
 		}
-		return snt;
 	}
 }
 

src/main/java/sc/fiji/snt/gui/cmds/BigDataLoaderCmd.java

@@ -97,7 +97,8 @@ and big data formats with lazy loading (N5, Zarr, HDF5, OME-TIFF,
     File img2File;
 
     @Parameter(required = false, label = "Reconstruction(s)",
-            description = "Optional.\nEither a single file (TRACES, SWC, JSON), or a folder containing reconstruction files.")
+            description = "Optional.\nEither a single file (TRACES, SWC, JSON), or a\n" +
+                    "folder/.zip archive of several such files.")
     File recFiles;
 
     @Parameter(required = false, label = "Markers",

src/main/java/sc/fiji/snt/gui/cmds/SNTLoaderCmd.java

@@ -108,7 +108,7 @@ public class SNTLoaderCmd extends DynamicCommand {
 	@Override
 	public void initialize() {
 		if (sntService != null && sntService.isActive() && sntService.getUI() != null) {
-			exit("SNT seems to be already running.");
+			exit("SNT seems to be already running. Please close the current instance and re-run.");
 			return;
 		}
 		// TODO: load defaults from prefService?
@@ -382,8 +382,10 @@ private boolean validateImageDimensions() {
 
 	private void exit(final String msg) {
 		SNTUtils.setIsLoading(false);
-		if (msg != null && !msg.isEmpty())
-			cancel(msg);
+		if (msg != null && !msg.isEmpty()) {
+			GuiUtils.errorPrompt(msg, true);
+		}
+		cancel("");
 	}
 
 	/*

src/test/java/sc/fiji/snt/demo/StartImageJAndSNTDemo.java

@@ -43,9 +43,9 @@ public class StartImageJAndSNTDemo {
     public static void main(final String[] args) throws InterruptedException, InvocationTargetException {
 
         // 1. Start ImageJ and SNT
-        final SNT snt = SNTUtils.startApp();
-        // 2. Load a demo dataset (File> Load Demo Dataset...> Demo 03)
-        snt.getUI().runCommand("Load Demo Dataset...", "3");
+        final SNT snt = SNTUtils.startApp(false); // false: 'Regular' mode for traditional images; true: 'Stream' (big data) mode
+        // 2. Load a demo dataset (File> Load Demo Dataset...> Demo 04)
+        snt.getUI().runCommand("Load Demo Dataset...", "4");
 
 	}
 }