SP-958 BIS-557 include filename in error message in some known image-reading error scenarios

SVN: 29953

screening/source/java/ch/systemsx/cisd/openbis/dss/etl/Hdf5ThumbnailGenerator.java

@@ -39,6 +39,7 @@ import ch.systemsx.cisd.common.concurrent.ITaskExecutor;
 import ch.systemsx.cisd.common.concurrent.ParallelizedExecutor;
 import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
 import ch.systemsx.cisd.common.exceptions.Status;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
 import ch.systemsx.cisd.common.filesystem.FileUtilities;
 import ch.systemsx.cisd.common.logging.LogCategory;
 import ch.systemsx.cisd.common.logging.LogFactory;
@@ -534,14 +535,20 @@ public class Hdf5ThumbnailGenerator implements IHDF5WriterClient
 
     private BufferedImage loadUnchangedImage(String imageRelativePath, String imageIdOrNull)
     {
-        if (contentOrNull == null)
+        try
         {
-            return Utils.loadUnchangedImage(new FileBasedContentNode(new File(
-                    imagesParentDirectory, imageRelativePath)), imageIdOrNull, imageLibraryOrNull);
-        } else
+            if (contentOrNull == null)
+            {
+                return Utils.loadUnchangedImage(new FileBasedContentNode(new File(
+                        imagesParentDirectory, imageRelativePath)), imageIdOrNull, imageLibraryOrNull);
+            } else
+            {
+                return Utils.loadUnchangedImage(contentOrNull.getNode(imageRelativePath),
+                        imageIdOrNull, imageLibraryOrNull);
+            }
+        } catch (Exception ex)
         {
-            return Utils.loadUnchangedImage(contentOrNull.getNode(imageRelativePath),
-                    imageIdOrNull, imageLibraryOrNull);
+            throw new UserFailureException("Failed to load image " + imageRelativePath, ex);
         }
     }
 

screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/ImagingDataSetRegistrationTransaction.java

@@ -499,17 +499,22 @@ public class ImagingDataSetRegistrationTransaction extends DataSetRegistrationTr
     private void setBoundingBox(ImageDataSetInformation imageDataSetInformation,
             IHierarchicalContentNode content, ImageLibraryInfo imageLibrary)
     {
-        Size size = Utils.loadUnchangedImageSize(content, null, imageLibrary);
-        imageDataSetInformation.setMaximumImageWidth(Math.max(
-                imageDataSetInformation.getMaximumImageWidth(), size.getWidth()));
-        imageDataSetInformation.setMaximumImageHeight(Math.max(
-                imageDataSetInformation.getMaximumImageHeight(), size.getHeight()));
-        if (imageDataSetInformation.getColorDepth() == null)
-        {
-            imageDataSetInformation.setColorDepth(Utils.loadUnchangedImageColorDepth(content, null,
-                    imageLibrary));
+        try
+        {
+            Size size = Utils.loadUnchangedImageSize(content, null, imageLibrary);
+            imageDataSetInformation.setMaximumImageWidth(Math.max(
+                    imageDataSetInformation.getMaximumImageWidth(), size.getWidth()));
+            imageDataSetInformation.setMaximumImageHeight(Math.max(
+                    imageDataSetInformation.getMaximumImageHeight(), size.getHeight()));
+            if (imageDataSetInformation.getColorDepth() == null)
+            {
+                imageDataSetInformation.setColorDepth(Utils.loadUnchangedImageColorDepth(content, null,
+                        imageLibrary));
+            }
+        } catch (Exception ex)
+        {
+            throw new UserFailureException("Error ocured when calculating bounding box of " + content.getRelativePath(), ex);
         }
-
     }
 
     private File prependOriginalDirectory(String directoryPath)

screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/SimpleImageDataSetRegistrator.java

@@ -258,15 +258,21 @@ public class SimpleImageDataSetRegistrator
 
         for (File imageFile : imageFiles)
         {
-            File file = new File(imageFile.getPath());
-            List<ImageIdentifier> identifiers = getImageIdentifiers(imageReaderOrNull, file);
-            String imageRelativePath = FileUtilities.getRelativeFilePath(incomingDirectory, file);
-            ImageMetadata[] imageTokens =
-                    simpleImageConfig.extractImagesMetadata(imageRelativePath, identifiers);
-            for (ImageMetadata imageToken : imageTokens)
+            try
             {
-                imageToken.ensureValid(simpleImageConfig.isMicroscopyData());
-                imageTokensList.add(new ImageTokensWithPath(imageToken, imageRelativePath));
+                File file = new File(imageFile.getPath());
+                List<ImageIdentifier> identifiers = getImageIdentifiers(imageReaderOrNull, file);
+                String imageRelativePath = FileUtilities.getRelativeFilePath(incomingDirectory, file);
+                ImageMetadata[] imageTokens =
+                        simpleImageConfig.extractImagesMetadata(imageRelativePath, identifiers);
+                for (ImageMetadata imageToken : imageTokens)
+                {
+                    imageToken.ensureValid(simpleImageConfig.isMicroscopyData());
+                    imageTokensList.add(new ImageTokensWithPath(imageToken, imageRelativePath));
+                }
+            } catch (Exception ex)
+            {
+                throw new UserFailureException("Error ocured when processing image " + imageFile.getPath(), ex);
             }
         }
         if (imageTokensList.isEmpty())
@@ -589,20 +595,26 @@ public class SimpleImageDataSetRegistrator
 
         for (File imageFile : imageFiles)
         {
-            List<ImageIdentifier> imageIdentifiers = getImageIdentifiers(readerOrNull, imageFile);
-            for (ImageIdentifier imageIdentifier : imageIdentifiers)
+            try
             {
-                BufferedImage image =
-                        loadUnchangedImage(imageFile, imageIdentifier, libraryName, readerName);
-                if (IntensityRescaling.isNotGrayscale(image))
+                List<ImageIdentifier> imageIdentifiers = getImageIdentifiers(readerOrNull, imageFile);
+                for (ImageIdentifier imageIdentifier : imageIdentifiers)
                 {
-                    operationLog
-                            .warn(String
-                                    .format("Intensity range cannot be computed because image '%s' is not in grayscale.",
-                                            imageFile.getPath()));
-                    return null;
+                    BufferedImage image =
+                            loadUnchangedImage(imageFile, imageIdentifier, libraryName, readerName);
+                    if (IntensityRescaling.isNotGrayscale(image))
+                    {
+                        operationLog
+                                .warn(String
+                                        .format("Intensity range cannot be computed because image '%s' is not in grayscale.",
+                                                imageFile.getPath()));
+                        return null;
+                    }
+                    IntensityRescaling.addToLevelStats(histogram, image);
                 }
-                IntensityRescaling.addToLevelStats(histogram, image);
+            } catch (Exception ex)
+            {
+                throw new UserFailureException("Error ocured when processing image " + imageFile.getPath(), ex);
             }
         }
         return IntensityRescaling.computeLevels(histogram, threshold);