LMS-2502 image transformations: minor refactoring

SVN: 22933

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

@@ -40,7 +40,6 @@ import ch.systemsx.cisd.common.filesystem.FileUtilities;
 import ch.systemsx.cisd.common.logging.LogCategory;
 import ch.systemsx.cisd.common.logging.LogFactory;
 import ch.systemsx.cisd.common.utilities.PropertyUtils;
-import ch.systemsx.cisd.imagereaders.ImageID;
 import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.Channel;
 import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageFileInfo;
 import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageIdentifier;
@@ -472,7 +471,8 @@ abstract public class AbstractImageFileExtractor implements IImageFileExtractor
     {
         RelativeImageReference relativeImageRef =
                 new RelativeImageReference(imageInfo.getImageRelativePath(),
-                        getImageID(imageInfo.tryGetImageIdentifier()), colorComponentOrNull);
+                        getUniqueStringIdentifier(imageInfo.tryGetImageIdentifier()),
+                        colorComponentOrNull);
         Location wellLoc = null;
         if (imageInfo.hasWellLocation())
         {
@@ -486,15 +486,14 @@ abstract public class AbstractImageFileExtractor implements IImageFileExtractor
         return new AcquiredSingleImage(wellLoc, tileLoc, channelCode, imageInfo.tryGetTimepoint(),
                 imageInfo.tryGetDepth(), imageInfo.tryGetSeriesNumber(), relativeImageRef);
     }
-    
-    private static String getImageID(ImageIdentifier identifier)
+
+    private static String getUniqueStringIdentifier(ImageIdentifier identifier)
     {
         if (identifier == null)
         {
             return null;
         }
-        return new ImageID(identifier.getSeriesIndex(), identifier.getTimeSeriesIndex(),
-                identifier.getFocalPlaneIndex(), identifier.getColorChannelIndex()).getID();
+        return identifier.getUniqueStringIdentifier();
     }
 
     protected static Integer tryAsInt(String valueOrNull)

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

@@ -190,7 +190,7 @@ class Hdf5ThumbnailGenerator implements IHDF5WriterClient
     private byte[] generateThumbnailInternally(File imageFile, String imageIdOrNull,
             ByteArrayOutputStream bufferOutputStream) throws IOException
     {
-        BufferedImage image = loadImage(imageFile, imageIdOrNull);
+        BufferedImage image = loadUnchangedImage(imageFile, imageIdOrNull);
         BufferedImage thumbnail =
                 ImageUtil.rescale(image, thumbnailsStorageFormat.getMaxWidth(),
                         thumbnailsStorageFormat.getMaxHeight(), false,
@@ -199,10 +199,10 @@ class Hdf5ThumbnailGenerator implements IHDF5WriterClient
         return bufferOutputStream.toByteArray();
     }
 
-    private BufferedImage loadImage(File imageFile, String imageIdOrNull)
+    private BufferedImage loadUnchangedImage(File imageFile, String imageIdOrNull)
     {
-        return AbsoluteImageReference.loadUnchangedImage(new FileBasedContent(imageFile), imageIdOrNull,
-                imageLibraryOrNull);
+        return AbsoluteImageReference.loadUnchangedImage(new FileBasedContent(imageFile),
+                imageIdOrNull, imageLibraryOrNull);
     }
 
     private Status createStatus(String thumbnailPath, IOException ex)

screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ImageIdentifier.java

@@ -16,6 +16,8 @@
 
 package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1;
 
+import ch.systemsx.cisd.imagereaders.ImageID;
+
 /**
  * Immutable value class of an image ID based on series index, time series index, focal plane index,
  * and color channel index. It will be used to identify images in a container image file format like
@@ -26,7 +28,7 @@ package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1;
 public class ImageIdentifier implements Comparable<ImageIdentifier>
 {
     public static final ImageIdentifier NULL = new ImageIdentifier(0, 0, 0, 0);
-    
+
     private final int seriesIndex;
 
     private final int timeSeriesIndex;
@@ -34,7 +36,7 @@ public class ImageIdentifier implements Comparable<ImageIdentifier>
     private final int focalPlaneIndex;
 
     private final int colorChannelIndex;
-    
+
     /**
      * Creates an instance for the specified series index, time series (or T) index, focal plane (or
      * Z) index, color channel index.
@@ -68,6 +70,12 @@ public class ImageIdentifier implements Comparable<ImageIdentifier>
         return colorChannelIndex;
     }
 
+    public String getUniqueStringIdentifier()
+    {
+        return new ImageID(getSeriesIndex(), getTimeSeriesIndex(), getFocalPlaneIndex(),
+                getColorChannelIndex()).getID();
+    }
+
     public int compareTo(ImageIdentifier that)
     {
         int diff = seriesIndex - that.seriesIndex;