BigDataLoaderCmd: Improve network detection and misc improvements

Author: tferr

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

@@ -1362,7 +1362,7 @@ private void loadBookmarksFromFile(final File file) {
         try {
             model.populateFromFile(file);
         } catch (final Exception ex) {
-            guiUtils.error(ex.getMessage() + ".");
+            guiUtils.error(GuiUtils.friendlyErrorMessage(ex) + ".");
             SNTUtils.error("loadBookmarksFromFile() failure", ex);
         }
     }
@@ -1371,7 +1371,7 @@ private void loadBookmarksFromFile(final String filePathOrURL) {
         try {
             model.populateFromFile(filePathOrURL);
         } catch (final Exception ex) {
-            guiUtils.error(ex.getMessage() + ".");
+            guiUtils.error(GuiUtils.friendlyErrorMessage(ex) + ".");
             SNTUtils.error("loadBookmarksFromFile() failure", ex);
         }
     }

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

@@ -51,7 +51,6 @@
 import org.scijava.ui.swing.script.LanguageSupportService;
 import org.scijava.util.FileUtils;
 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;
@@ -60,6 +59,8 @@
 import java.awt.*;
 import java.io.*;
 import java.lang.reflect.InvocationTargetException;
+import java.net.InetSocketAddress;
+import java.net.Socket;
 import java.net.URI;
 import java.net.URISyntaxException;
 import java.net.URL;
@@ -74,8 +75,6 @@
 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;
 import java.util.regex.Pattern;
 
@@ -212,7 +211,7 @@ private static String stringForCSV(final String s) {
 		if (s.indexOf(',') >= 0 || s.indexOf(' ') >= 0) quote = true;
 		if (s.indexOf('"') >= 0) {
 			quote = true;
-			result = s.replaceAll("\"", "\"\"");
+			result = s.replace("\"", "\"\"");
 		}
 		if (quote) return "\"" + result + "\"";
 		else return result;
@@ -340,6 +339,35 @@ protected static boolean isValidURL(final String url) {
 		}
 	}
 
+	/**
+	 * Checks for whether {@code url}'s host can be reached, meant to be called before a real download/stream attempt
+	 * (e.g., {@link #downloadToTempFile}) so that a missing network connection surfaces as one clear message.
+	 * est-effort: only http(s) URLs are actually probed; any other scheme (e.g. a bare host-less URI) is assumed
+	 * reachable, deferring to the real caller
+	 *
+	 * @param url       the URL to check
+	 * @param timeoutMs connect timeout, in milliseconds
+	 * @return true if the host could be reached (or {@code url} is not a plain http(s) URL); false if
+	 * a connection could not be established within {@code timeoutMs}
+	 */
+	public static boolean isReachable(final String url, final int timeoutMs) {
+		try {
+			final URI uri = new URI(url);
+			final String scheme = uri.getScheme();
+			if (scheme == null || !(scheme.equalsIgnoreCase("http") || scheme.equalsIgnoreCase("https")))
+				return true; // not a plain HTTP(S) URL (e.g. s3://, gs://); nothing simple to probe here
+			final String host = uri.getHost();
+			if (host == null) return true; // no host to probe; let the real caller deal with it
+			final int port = uri.getPort() != -1 ? uri.getPort() : ("https".equalsIgnoreCase(scheme) ? 443 : 80);
+			try (final Socket socket = new Socket()) {
+				socket.connect(new InetSocketAddress(host, port), timeoutMs);
+				return true;
+			}
+		} catch (final Exception e) {
+			return false;
+		}
+	}
+
 	public static String formatDouble(final double value, final int digits) {
 		return (Double.isNaN(value)) ? "NaN" : getDecimalFormat(value, digits).format(value);
 	}
@@ -465,29 +493,6 @@ else if (time < 90000)
 						- TimeUnit.MINUTES.toSeconds(TimeUnit.MILLISECONDS.toMinutes(time)));
 	}
 
-	/**
-	 * Retrieves Sholl Analysis implementation date
-	 *
-	 * @return the implementation date or an empty strong if date could not be
-	 *         retrieved.
-	 */
-	public static String buildDate() {
-		String BUILD_DATE;
-		final Class<ShollUtils> clazz = ShollUtils.class;
-		final String className = clazz.getSimpleName() + ".class";
-		try {
-			final String classPath = clazz.getResource(className).toString();
-			final String manifestPath = classPath.substring(0, classPath.lastIndexOf("!") + 1) + "/META-INF/MANIFEST.MF";
-			final Manifest manifest = new Manifest(new URI(manifestPath).toURL().openStream());
-			final Attributes attr = manifest.getMainAttributes();
-			BUILD_DATE = attr.getValue("Implementation-Date");
-			BUILD_DATE = BUILD_DATE.substring(0, BUILD_DATE.lastIndexOf("T"));
-		} catch (final Exception ignored) {
-			BUILD_DATE = "";
-		}
-		return BUILD_DATE;
-	}
-
 	/**
 	 * Retrieves a list of reconstruction files stored in a common directory
 	 * matching the specified criteria.

src/main/java/sc/fiji/snt/gui/GuiUtils.java

@@ -143,6 +143,10 @@ public void error(final String msg, final String title) {
 		centeredDialog(msg, title, JOptionPane.ERROR_MESSAGE);
 	}
 
+	public void warning(final String msg) {
+		centeredDialog(msg, "SNT v" + SNTUtils.VERSION, JOptionPane.WARNING_MESSAGE);
+	}
+
 	/**
 	 * Returns the Last-Modified timestamp from a HEAD request, or -1 on failure.
 	 */
@@ -2508,6 +2512,26 @@ public static void errorPrompt(final String msg, final boolean centeredOnScreen)
 		guiUtils.error(msg, "SNT v" + SNTUtils.VERSION);
 	}
 
+	/**
+	 * Rewrites a common network-connectivity exception (unknown host, refused/timed-out connection)
+	 * into a short, user-facing message, instead of the exception's own message, which for e.g.
+	 * {@link java.net.UnknownHostException} is just the bare, unexplained hostname. Falls back to {@code
+	 * t.getMessage()} for anything else.
+	 *
+	 * @param t the exception to inspect (its cause chain is also walked)
+	 * @return a friendly message describing {@code t}
+	 */
+	public static String friendlyErrorMessage(final Throwable t) {
+		for (Throwable cause = t; cause != null; cause = cause.getCause()) {
+			if (cause instanceof java.net.UnknownHostException)
+				return "Could not reach '" + cause.getMessage() + "' - check your internet connection";
+			if (cause instanceof java.net.ConnectException || cause instanceof java.net.SocketTimeoutException)
+				return "Could not connect to the remote server - check your internet connection";
+		}
+        assert t != null;
+        return t.getMessage();
+	}
+
 	public static String[] availableLookAndFeels() {
 		return new String[] { LAF_LIGHT, LAF_LIGHT_INTJ, LAF_DARK, LAF_DARCULA };
 	}
@@ -3847,19 +3871,18 @@ public static JMenuItem openHelpURL(final String label, final String URL) {
 		}
 
 		public static JMenuItem showHelpOnCountingSpines(final boolean streamMode, final Action postDialogAction) {
-
 			final JMenuItem mi = new JMenuItem("Spine/Varicosity Analysis Help", IconFactory.menuIcon(GLYPH.QUESTION));
 			mi.addActionListener(e -> {
 				if (postDialogAction == null) {
 					GuiUtils.showHTMLDialog(spineHelpMsg(streamMode), "Annotating Spines/Varicosities");
-				} else if (new GuiUtils().yesNoHTMLDialog(spineHelpMsg(streamMode), "Annotating Spines/Varicosities",
-						"Pause SNT & Start Manual Annotation", "Dismiss")) {
+				} else {
 					String actionName = (String) postDialogAction.getValue(Action.NAME);
-					if (actionName == null) {
-						actionName = "Proceed";
+					if (actionName == null) actionName = "Proceed";
+					if (new GuiUtils().yesNoHTMLDialog(spineHelpMsg(streamMode), "Annotating Spines/Varicosities",
+							actionName, "Dismiss")) {
+						final ActionEvent event = new ActionEvent(GuiUtils.class, ActionEvent.ACTION_PERFORMED, actionName);
+						postDialogAction.actionPerformed(event);
 					}
-					final ActionEvent event = new ActionEvent(GuiUtils.class, ActionEvent.ACTION_PERFORMED, actionName);
-					postDialogAction.actionPerformed(event);
 				}
 			});
 			return mi;

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

@@ -58,7 +58,9 @@
 import java.io.File;
 import java.util.ArrayList;
 import java.util.Collection;
+import java.util.LinkedHashMap;
 import java.util.List;
+import java.util.Map;
 import java.util.Objects;
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;
@@ -83,6 +85,7 @@ and big data formats with lazy loading (N5, Zarr, HDF5, OME-TIFF,
             the entire file into memory.""";
 
     private static final int GL_MAX_3D_TEXTURE_SIZE = 0x8073; // OpenGL constant
+    private static final int REACHABILITY_TIMEOUT_MS = 4000;
     private static final String ABORT = "Abort";
     private static final String DOWNSAMPLE = "Downsample to fit";
     private static final String CONVERT = "Show me how to convert to multi-resolution pyramid image";
@@ -147,7 +150,7 @@ private void loadDemo() {
         // fine to declare URL as file even though File collapses "//" -> "/": restoreUrlScheme() already handles that
         img1File = new File("https://ome-zarr-scivis.s3.us-east-1.amazonaws.com/v0.4/96x0/marmoset_neurons.ome.zarr");
         img2File = null;
-        recFiles = new File("https://raw.githubusercontent.com/morphonets/misc/680ac2a9b2cb1dfe85c0b64f17fed816e3da1647/dataset-demos/marmoset_neurons/autotracings.traces");;
+        recFiles = new File("https://raw.githubusercontent.com/morphonets/misc/680ac2a9b2cb1dfe85c0b64f17fed816e3da1647/dataset-demos/marmoset_neurons/autotracings.traces");
         markerFile = new File("https://raw.githubusercontent.com/morphonets/misc/680ac2a9b2cb1dfe85c0b64f17fed816e3da1647/dataset-demos/marmoset_neurons/soma_detections.csv");
         viewerType = "Big Data Viewer (BDV): Interactive reslicing";
         tracingEnabled = true;
@@ -198,7 +201,6 @@ private void putOrRemove(final String key, final File file) {
 
     @Override
     public void run() {
-        SNTUtils.setDebugMode(true);
         if (img1File == null) {
             error("Main volume is required.");
             return;
@@ -212,6 +214,7 @@ public void run() {
             error("No volume files specified.");
             return;
         }
+        if (!checkReachable(filePaths)) return; // single friendly dialog if any remote field is unreachable
         final boolean threeD = viewerType != null && viewerType.toLowerCase().contains("bvv");
         final boolean tracer = tracingEnabled;
 
@@ -220,20 +223,30 @@ public void run() {
             return;
         }
 
+        AbstractBigViewer viewer = null;
         try {
             SNTUtils.setIsLoading(true);
             if (tracer && threeD)
-                runBvvWithTracing(filePaths);
+                viewer = runBvvWithTracing(filePaths);
             else if (tracer)
-                runBdvWithTracing(filePaths);
+                viewer = runBdvWithTracing(filePaths);
             else if (threeD)
-                runBvv(filePaths);
+                viewer = runBvv(filePaths);
             else
-                runBdv(filePaths);
-            SNTUtils.setIsLoading(false);
+                viewer = runBdv(filePaths);
         } catch (final Exception e) {
             SNTUtils.setIsLoading(false); // hide splashscreen behind error dialog
-            error("An error occurred: " + e.getMessage());
+            error("An error occurred: " + GuiUtils.friendlyErrorMessage(e));
+        } finally {
+            SNTUtils.setIsLoading(false);
+            if (viewer != null && viewer.getViewerFrame() != null && BoundingBox.UNSET_SPACING_UNIT.equals(viewer.getPhysicalUnit())) {
+                AbstractBigViewer finalViewer = viewer;
+                SwingUtilities.invokeLater(() -> {
+                    new GuiUtils(finalViewer.getViewerFrame()).warning(
+                            "<HTML>Spatial calibration values appear to be invalid.<br>" +
+                                    "To adjust them, right-click the scale bar button in <i>Scene Controls</i>.");
+                });
+            }
         }
     }
 
@@ -252,6 +265,29 @@ private static String toPathString(final File f) {
                 : f.getAbsolutePath();
     }
 
+    /**
+     * @return true if every remote field is reachable (or none are remote); false if the run was
+     *         aborted because at least one was not
+     */
+    private boolean checkReachable(final String[] filePaths) {
+        final LinkedHashMap<String, String> byLabel = new LinkedHashMap<>();
+        if (filePaths.length > 0) byLabel.put("Main volume", filePaths[0]);
+        if (filePaths.length > 1) byLabel.put("Secondary volume", filePaths[1]);
+        if (recFiles != null) byLabel.put("Reconstruction(s)", toPathString(recFiles));
+        if (markerFile != null) byLabel.put("Markers", toPathString(markerFile));
+        final List<String> unreachable = new ArrayList<>();
+        for (final Map.Entry<String, String> entry : byLabel.entrySet()) {
+            final String path = entry.getValue();
+            if (SpimDataUtils.isRemoteUrl(path) && !SNTUtils.isReachable(path, REACHABILITY_TIMEOUT_MS))
+                unreachable.add(entry.getKey() + ": " + path);
+        }
+        if (unreachable.isEmpty()) return true;
+        error("<HTML>No internet access. Could not reach:<br>&nbsp;&nbsp;"
+                + String.join("<br>&nbsp;&nbsp;", unreachable)
+                + "<br>Please check your connection and try again.");
+        return false;
+    }
+
     /** True if path is an existing .n5/.zarr directory, or a remote URL to one. */
     private static boolean isN5OrZarrDir(final String path) {
         if (SpimDataUtils.isRemoteUrl(path)) {
@@ -311,15 +347,16 @@ private static DatasetSelectorDialog getDatasetSelectorDialog(final String n5Zar
     }
 
     /** Resolves sources, enforces GPU texture limits, then opens BVV. */
-    private void runBvv(final String[] filePaths) {
+    private AbstractBigViewer runBvv(final String[] filePaths) {
         final int maxTexSize = queryMaxTexture3DSize();
         SNTUtils.log("BVV: GL_MAX_3D_TEXTURE_SIZE = " + maxTexSize);
         final ResolvedSources resolved = resolveBvvSources(filePaths, maxTexSize);
-        if (resolved == null) return; // user chose Abort (oversized image or non-pyramidal dataset)
+        if (resolved == null) return null; // user chose Abort (oversized image or non-pyramidal dataset)
         final Bvv bvv = new Bvv();
         addSourcesToBvv(bvv, resolved);
         loadReconstructions(bvv);
         loadMarkers(bvv);
+        return bvv;
     }
 
     /**
@@ -333,7 +370,7 @@ private void runBvv(final String[] filePaths) {
      * manual tracing still works (segment tracing only needs spacing, which defaults to 1 regardless
      * of a loaded image), but A* has nothing real to search until an image is loaded via the SNTUI.
      */
-    private void runBvvWithTracing(final String[] filePaths) {
+    private AbstractBigViewer runBvvWithTracing(final String[] filePaths) {
         final int maxTexSize = queryMaxTexture3DSize();
         SNTUtils.log("BVV: GL_MAX_3D_TEXTURE_SIZE = " + maxTexSize);
         // Resolve the primary volume (img1File, i.e. filePaths[0]) exactly once: startTracingSNT() needs
@@ -342,11 +379,12 @@ private void runBvvWithTracing(final String[] filePaths) {
         // discovery a second time for an unchanged path
         final TracingSetup setup = startTracingSNT(img1File);
         final ResolvedSources resolved = resolveBvvSources(filePaths, maxTexSize, setup.primarySource());
-        if (resolved == null) return; // user chose Abort (oversized image or non-pyramidal dataset)
+        if (resolved == null) return null; // user chose Abort (oversized image or non-pyramidal dataset)
         final Bvv bvv = new Bvv(setup.snt());
         addSourcesToBvv(bvv, resolved);
         loadReconstructions(bvv);
         loadMarkers(bvv);
+        return bvv;
     }
 
     /** Holds the outcome of {@link #resolveBvvSources(String[], int, Object)}. */
@@ -591,7 +629,7 @@ private static void applyWorldOriginOffset(final SNT snt, final bdv.viewer.Sourc
     }
 
     /** Resolves sources (no texture-size constraint) then opens BDV. */
-    private void runBdv(final String[] filePaths) {
+    private AbstractBigViewer runBdv(final String[] filePaths) {
         final Bdv bdv = new Bdv();
         final List<String> deferredPaths = new ArrayList<>(); // need the interactive dialog
         for (final String path : filePaths) {
@@ -620,10 +658,11 @@ private void runBdv(final String[] filePaths) {
             datasetDialog(path, bdv);
         loadReconstructions(bdv);
         loadMarkers(bdv);
+        return bdv;
     }
 
     /** BDV counterpart to runBvvWithTracing(final String[] filePaths); */
-    private void runBdvWithTracing(final String[] filePaths) {
+    private AbstractBigViewer runBdvWithTracing(final String[] filePaths) {
         final TracingSetup setup = startTracingSNT(img1File);
         final Bdv bdv = new Bdv(setup.snt());
         final List<String> deferredPaths = new ArrayList<>(); // need the interactive dialog
@@ -657,6 +696,7 @@ private void runBdvWithTracing(final String[] filePaths) {
             datasetDialog(path, bdv);
         loadReconstructions(bdv);
         loadMarkers(bdv);
+        return bdv;
     }
 
     private void loadMarkers(final AbstractBigViewer viewer) {
@@ -698,11 +738,11 @@ private void loadReconstructions(final AbstractBigViewer viewer) {
         if (SpimDataUtils.isRemoteUrl(path)) {
             // fileAvailable()/getReconstructionFiles() below are local-filesystem-only checks. Tree.listFromFile()
             // already knows how to handle a remote URL directly (a single reconstruction file is streamed, a .zip is
-            // downloaded/extracted and treated as a irectory), so route straight through it instead for this case
+            // downloaded/extracted and treated as a directory), so route straight through it instead for this case
             try {
                 trees.addAll(Tree.listFromFile(path));
             } catch (final IllegalArgumentException e) {
-                error("Could not load reconstructions from " + path + ": " + e.getMessage());
+                error("Could not load reconstructions from " + path + ": " + GuiUtils.friendlyErrorMessage(e));
                 return;
             }
             if (trees.isEmpty()) {

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

@@ -236,8 +236,7 @@ private void tracesFileChanged() {
 	public void run() {
 
 		SNTUtils.setIsLoading(true);
-		final boolean noImg = IMAGE_NONE.equals(imageChoice) || (IMAGE_FILE.equals(
-			imageChoice) && imageFile == null);
+		final boolean noImg = IMAGE_NONE.equals(imageChoice) || (IMAGE_FILE.equals(imageChoice) && imageFile == null);
 
 		if (noImg) {
 			final PathAndFillManager pathAndFillManager = new PathAndFillManager();