Better handling of failed connections - 3 attempts then returns null

Also adds a meaningful message when the connection fails Adds logger in OmeroHelper Decreases init time when reading Omero dataset - get rid of rawPixStore.getResolutionDescriptions() call fix #28
BIOP · Sep 17, 2024 · 17fb9ee · 17fb9ee
1 parent 54437e1
commit 17fb9ee
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Showing 4 changed files with 44 additions and 30 deletions.
diff --git a/src/main/java/ch/epfl/biop/bdv/img/omero/OmeroHelper.java b/src/main/java/ch/epfl/biop/bdv/img/omero/OmeroHelper.java
@@ -40,6 +40,8 @@
 import org.scijava.Context;
 import org.scijava.command.CommandModule;
 import org.scijava.command.CommandService;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import java.lang.reflect.Field;
 import java.net.MalformedURLException;
@@ -53,6 +55,8 @@
 
 public class OmeroHelper {
 
+	protected static final Logger logger = LoggerFactory.getLogger(OmeroHelper.class);
+
 	/**
 	 * OMERO connection with credentials and simpleLogger
 	 * 
@@ -134,31 +138,40 @@ public static UnitsLength getUnitsLengthFromString(String unit_string) {
 
 	public static OMEROSession getGatewayAndSecurityContext(Context context, String host) throws Exception {
 		OMEROService omeroService = context.getService(OMEROService.class);
-
 		OMEROServer server = new OMEROServer(host, 4064);
-
-		OMEROSession omeroSession;
 		try {
-			omeroSession = omeroService.session(server);
+			return omeroService.session(server);
 		} catch (Exception e) {
-			System.err.println("The OMERO session for "+host+" needs to be initialized");
+			logger.info("The OMERO session for "+host+" needs to be initialized");
 			CommandService command = context.getService(CommandService.class);
 			boolean success = false;
-			Exception error;
-			try {
-				OmeroConnectCommand.message_in = "Please enter your "+host+" credentials:";
-				CommandModule module = command.run(OmeroConnectCommand.class, true, "host", host).get();
-				success = (Boolean) module.getOutput("success");
-				omeroSession = (OMEROSession) module.getOutput("omeroSession");
-				error = (DSOutOfServiceException) module.getOutput("error");
-			} catch (Exception commandException) {
-				commandException.printStackTrace();
-				omeroSession = null;
-				error = commandException;
+			int iAttempt = 0;
+			int nAttempts = 3;
+			String lastErrorMessage = "";
+			while ((iAttempt<nAttempts) && (!success)) {
+				iAttempt++;
+				Exception error;
+				try {
+					if (lastErrorMessage.isEmpty()) {
+						OmeroConnectCommand.message_in = "<html>Please enter your " + host + " credentials:</html>";
+					} else {
+						OmeroConnectCommand.message_in = "<html>Error:"+lastErrorMessage+"<br> Please re-enter your " + host + " credentials ("+iAttempt+"/"+nAttempts+"):</html>";
+					}
+					CommandModule module = command.run(OmeroConnectCommand.class, true, "host", host).get();
+					success = (Boolean) module.getOutput("success");
+					OMEROSession omeroSession = (OMEROSession) module.getOutput("omeroSession");
+					if (success) return omeroSession;
+					error = (Exception) module.getOutput("error");
+					if (error!=null) {
+						lastErrorMessage = error.getMessage();
+					}
+				} catch (Exception commandException) {
+					error = commandException;
+				}
+				if ((!success) && (iAttempt == nAttempts)) throw error;
 			}
-			if ((!success)&&(error!=null)) throw error;
 		}
-		return omeroSession;
+		return null;
 	}
 
 	/**

diff --git a/src/main/java/ch/epfl/biop/bdv/img/omero/OmeroOpener.java b/src/main/java/ch/epfl/biop/bdv/img/omero/OmeroOpener.java
@@ -175,7 +175,10 @@ public OmeroOpener(
 			exception = e;
 		}
 
-		if (exception != null) throw exception;
+		if (exception != null) {
+			// avoid asking again and again connection credentials
+			throw exception;
+		}
 
 		this.gateway = session.getGateway();
 		this.securityContext = session.getSecurityContext();
@@ -230,22 +233,19 @@ public OmeroOpener(
 			} else {
 				tileSize = new HashMap<>();
 				logger.debug("Get image size and tile sizes...");
-				Instant start = Instant.now();
-				ResolutionDescription[] resDesc = rawPixStore.getResolutionDescriptions();
-				Instant finish = Instant.now();
-				logger.debug("Done! Time elapsed : " + Duration.between(start,
-					finish));
 				int tileSizeX = rawPixStore.getTileSize()[0];
 				int tileSizeY = rawPixStore.getTileSize()[1];
+				int bytesWidth = rawPixStore.getByteWidth();
 
 				for (int level = 0; level < this.nMipmapLevels; level++) {
 					int[] sizes = new int[3];
-					sizes[0] = resDesc[level].sizeX;
-					sizes[1] = resDesc[level].sizeY;
+                    rawPixStore.setResolutionLevel(this.nMipmapLevels - level - 1);
+					sizes[0] = rawPixStore.getRowSize() / bytesWidth;
+					sizes[1] = (int) ( (rawPixStore.getPlaneSize() / sizes[0]) / bytesWidth );
 					sizes[2] = pixels.getSizeZ();
 					int[] tileSizes = new int[2];
-					tileSizes[0] = Math.min(tileSizeX, resDesc[this.nMipmapLevels - 1].sizeX);
-					tileSizes[1] = Math.min(tileSizeY, resDesc[this.nMipmapLevels - 1].sizeY);
+					tileSizes[0] = Math.min(tileSizeX, sizes[0]);
+					tileSizes[1] = Math.min(tileSizeY, sizes[1]);
 					imageSize.put(level, sizes);
 					tileSize.put(level, tileSizes);
 				}

diff --git a/src/main/java/ch/epfl/biop/bdv/img/omero/command/OmeroConnectCommand.java b/src/main/java/ch/epfl/biop/bdv/img/omero/command/OmeroConnectCommand.java
@@ -79,7 +79,7 @@ public void run() {
             password = "";
             logger.info("Session active : " + omeroSession.getGateway().isConnected());
             omeroSession.getSecurityContext().setServerInformation(new ServerInformation(host));
-            success = true;
+            success = omeroSession.getGateway().isConnected();
         } catch (Exception e) {
             error = e;
             logger.error(e.getMessage());

diff --git a/src/test/java/ch/epfl/biop/SimpleIJLaunch.java b/src/test/java/ch/epfl/biop/SimpleIJLaunch.java
@@ -30,9 +30,10 @@ public class SimpleIJLaunch {
 	static public void main(String... args) {
 		// Arrange
 		// create the ImageJ application context with all available services
+
+		//DebugTools.enableLogging("INFO");
 		final ImageJ ij = new ImageJ();
 		DebugTools.enableLogging("DEBUG");
-		//DebugTools.enableLogging("INFO");
 		//SwingUtilities.invokeAndWait(() ->);
 		//System.out.println("bf version = "+VersionUtils.getVersion(ZeissCZIReader.class));
 		ij.ui().showUI();