LMS-2333 Extended API to allow downloading transformed images.

SVN: 21976

screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java

@@ -56,6 +56,7 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.IShareIdManager;
 import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
 import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
 import ch.systemsx.cisd.openbis.dss.screening.shared.api.v1.IDssServiceRpcScreening;
+import ch.systemsx.cisd.openbis.dss.screening.shared.api.v1.LoadImageConfiguration;
 import ch.systemsx.cisd.openbis.dss.shared.DssScreeningUtils;
 import ch.systemsx.cisd.openbis.generic.shared.basic.CodeNormalizer;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
@@ -101,7 +102,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
     /**
      * The minor version of this service.
      */
-    public static final int MINOR_VERSION = 7;
+    public static final int MINOR_VERSION = 8;
 
     /**
      * NULL_SIZE encodes for "no thumbnails available"
@@ -197,6 +198,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
         }
         try
         {
+            @SuppressWarnings("deprecation")
             Map<String, File> datasetRoots = getRootDirectories(sessionToken, datasetCodes);
             List<ImageDatasetMetadata> result = new ArrayList<ImageDatasetMetadata>();
             for (IImageDatasetIdentifier dataset : imageDatasets)
@@ -416,16 +418,26 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
         return loadImages(sessionToken, imageReferences, tryAsSize(thumbnailSizeOrNull), true);
     }
 
+    public InputStream loadImages(String sessionToken, List<PlateImageReference> imageReferences,
+            LoadImageConfiguration configuration)
+    {
+        final Map<String, IImagingDatasetLoader> imageLoadersMap =
+                getImageDatasetsMap(sessionToken, imageReferences);
+        return loadImages(imageReferences, tryAsSize(configuration.getDesiredImageSize()),
+                configuration.isDesiredImageFormatPng(),
+                configuration.isOpenBisImageTransformationApplied(), imageLoadersMap);
+    }
+
     private InputStream loadImages(String sessionToken, List<PlateImageReference> imageReferences,
             final Size sizeOrNull, final boolean convertToPng)
     {
         final Map<String, IImagingDatasetLoader> imageLoadersMap =
                 getImageDatasetsMap(sessionToken, imageReferences);
-        return loadImages(imageReferences, sizeOrNull, convertToPng, imageLoadersMap);
+        return loadImages(imageReferences, sizeOrNull, convertToPng, false, imageLoadersMap);
     }
 
     private InputStream loadImages(List<PlateImageReference> imageReferences,
-            final Size sizeOrNull, final boolean convertToPng,
+            final Size sizeOrNull, final boolean convertToPng, final boolean transform,
             final Map<String, IImagingDatasetLoader> imageLoadersMap)
     {
         final List<IContent> imageContents = new ArrayList<IContent>();
@@ -444,7 +456,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
                     public IContent getContent()
                     {
                         return tryGetImageContent(imageAccessor, channelStackRef, channelCode,
-                                sizeOrNull, convertToPng);
+                                sizeOrNull, convertToPng, transform);
                     }
                 }));
         }
@@ -494,7 +506,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
                 new HashMap<String, IImagingDatasetLoader>();
         imageLoadersMap.put(dataSetIdentifier.getDatasetCode(), imageAccessor);
 
-        return loadImages(imageReferences, size, true, imageLoadersMap);
+        return loadImages(imageReferences, size, true, false, imageLoadersMap);
     }
 
     public InputStream loadThumbnailImages(String sessionToken,
@@ -526,7 +538,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
                     public IContent getContent()
                     {
                         return tryGetImageContent(imageAccessor, channelStackRef, channelCode,
-                                sizeOrNull, true);
+                                sizeOrNull, true, false);
                     }
                 }));
         }
@@ -620,6 +632,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
     private IImagingDatasetLoader createImageLoader(IDatasetIdentifier dataSetIdentifier)
     {
         String datasetCode = dataSetIdentifier.getDatasetCode();
+        @SuppressWarnings("deprecation")
         File rootDir = getRootDirectory(datasetCode);
         IImagingDatasetLoader imageAccessor = createImageLoader(datasetCode, rootDir);
         return imageAccessor;
@@ -917,12 +930,12 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
 
     private IContent tryGetImageContent(IImagingDatasetLoader imageAccessor,
             final ImageChannelStackReference channelStackReference, String channelCode,
-            Size thumbnailSizeOrNull, boolean convertToPng)
+            Size thumbnailSizeOrNull, boolean convertToPng, boolean transform)
     {
         try
         {
             return ImageChannelsUtils.getImage(imageAccessor, channelStackReference, channelCode,
-                    thumbnailSizeOrNull, convertToPng);
+                    thumbnailSizeOrNull, convertToPng, transform);
         } catch (EnvironmentFailureException e)
         {
             operationLog.error("Error reading image.", e);
@@ -987,6 +1000,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
 
     private IImagingDatasetLoader createImageLoader(String datasetCode)
     {
+        @SuppressWarnings("deprecation")
         File datasetRoot = getRootDirectory(datasetCode);
         return createImageLoader(datasetCode, datasetRoot);
     }

screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningLogger.java

@@ -22,6 +22,7 @@ import java.util.List;
 import ch.systemsx.cisd.base.image.IImageTransformerFactory;
 import ch.systemsx.cisd.common.spring.IInvocationLoggerContext;
 import ch.systemsx.cisd.openbis.dss.screening.shared.api.v1.IDssServiceRpcScreening;
+import ch.systemsx.cisd.openbis.dss.screening.shared.api.v1.LoadImageConfiguration;
 import ch.systemsx.cisd.openbis.generic.shared.AbstractServerLogger;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDataset;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetReference;
@@ -217,4 +218,12 @@ public class DssServiceRpcScreeningLogger extends AbstractServerLogger implement
         return null;
     }
 
+    public InputStream loadImages(String sessionToken, List<PlateImageReference> imageReferences,
+            LoadImageConfiguration configuration)
+    {
+        logAccess(sessionToken, "load_images", "IMAGE_REFERENCES(%s) CONFIGURATION(%s)",
+                imageReferences, configuration);
+        return null;
+    }
+
 }

screening/source/java/ch/systemsx/cisd/openbis/dss/screening/shared/api/v1/IDssServiceRpcScreening.java

@@ -233,6 +233,39 @@ public interface IDssServiceRpcScreening extends IRpcService
             @AuthorizationGuard(guardClass = SingleDataSetIdentifierPredicate.class) IDatasetIdentifier dataSetIdentifier,
             String channel, ImageSize thumbnailSizeOrNull);
 
+    /**
+     * Provide images for a given list of image references (specified by data set code, well
+     * position, channel and tile). The result is encoded into one stream, which consist of multiple
+     * blocks in a format: (<block-size><block-of-bytes>), where block-size is the block size in
+     * bytes encoded as one long number. The number of blocks is equal to the number of specified
+     * references and the order of blocks corresponds to the order of image references. If
+     * <code>convertToPng==true</code>, the images will be converted to PNG format before being
+     * shipped, otherwise they will be shipped in the format that they are stored on the server.
+     * 
+     * @since 1.3
+     */
+
+    /**
+     * Provide images for a given list of image references (specified by data set code, well
+     * position, channel and tile). The format and properties of the returned images are configured
+     * by the configuration.
+     * <p>
+     * The options are described in {@link LoadImageConfiguration}.
+     * <p>
+     * The encoding of the result is described in
+     * {@link IDssServiceRpcScreening#loadImages(String, List)}.
+     * 
+     * @see IDssServiceRpcScreening#loadImages(String, List)
+     * @see LoadImageConfiguration
+     * @since 1.8
+     */
+    @MinimalMinorVersion(8)
+    @DataSetAccessGuard
+    public InputStream loadImages(
+            String sessionToken,
+            @AuthorizationGuard(guardClass = DatasetIdentifierPredicate.class) List<PlateImageReference> imageReferences,
+            LoadImageConfiguration configuration);
+
     /**
      * Provide thumbnail images for specified microscopy data set. If no thumbnails are stored on
      * the server, this method will return an empty stream. Images of all tiles are delivered.

screening/source/java/ch/systemsx/cisd/openbis/dss/screening/shared/api/v1/LoadImageConfiguration.java

+/*
+ * Copyright 2011 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.dss.screening.shared.api.v1;
+
+import java.io.Serializable;
+
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageSize;
+
+/**
+ * A DTO for transmitting information about how the images should be loaded. The parameters that can
+ * be controlled include image size, format (PNG or original), and the application of image
+ * transformations stored in openBIS.
+ * <p>
+ * The default configuration is to retrieve images in their original size and format (i.e., not
+ * converted to PNG), without the openBIS image transformation applied.
+ * <p>
+ * Providing a non-null desired size will instruct the image loader to return images that maintain
+ * the aspect ratio of the original and fit in the desired size.
+ * 
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class LoadImageConfiguration implements Serializable
+{
+    private static final long serialVersionUID = 1L;
+
+    private ImageSize desiredImageSizeOrNull = null;
+
+    private boolean desiredImageFormatPng = false;
+
+    private boolean openBisImageTransformationApplied = false;
+
+    /**
+     * The desired size of the image. Null if the original size is requested.
+     * <p>
+     * The actual size of the returned image will have the same aspect ratio as the original, and
+     * thus might not be exactly the same as the desired size, but will fit in the desired size.
+     * 
+     * @return The desired size of the image or null if the original size is to be returned.
+     */
+    public ImageSize getDesiredImageSize()
+    {
+        return desiredImageSizeOrNull;
+    }
+
+    /**
+     * Set the desired size of the image.
+     * <p>
+     * The actual size of the returned image will have the same aspect ratio as the original, and
+     * thus might not be exactly the same as the desired size, but will fit in the desired size.
+     * 
+     * @param desiredImageSizeOrNull Pass in the desired size or null if you want the image to have
+     *            its original size.
+     */
+    public void setDesiredImageSize(ImageSize desiredImageSizeOrNull)
+    {
+        this.desiredImageSizeOrNull = desiredImageSizeOrNull;
+    }
+
+    /**
+     * Should the image be converted from its original format to PNG?
+     * 
+     * @return True if the image should be converted to PNG; false if it should be left in its
+     *         original format.
+     */
+    public boolean isDesiredImageFormatPng()
+    {
+        return desiredImageFormatPng;
+    }
+
+    /**
+     * Set whether the image should be converted from its original format to PNG.
+     * 
+     * @param desiredImageFormatPng Pass in true if the image should be converted to PNG; false if
+     *            it should be left in its original format.
+     */
+    public void setDesiredImageFormatPng(boolean desiredImageFormatPng)
+    {
+        this.desiredImageFormatPng = desiredImageFormatPng;
+    }
+
+    /**
+     * Should the image transformation stored in openBIS be applied to the image?
+     * 
+     * @return True if the image transformation should be applied; false if the original image
+     *         should be returned.
+     */
+    public boolean isOpenBisImageTransformationApplied()
+    {
+        return openBisImageTransformationApplied;
+    }
+
+    /**
+     * Set whether the image transformation stored in openBIS should be applied.
+     * 
+     * @param openBisImageTransformationApplied Pass in true if the transformation should be
+     *            applied; false otherwise.
+     */
+    public void setOpenBisImageTransformationApplied(boolean openBisImageTransformationApplied)
+    {
+        this.openBisImageTransformationApplied = openBisImageTransformationApplied;
+    }
+
+    @Override
+    public String toString()
+    {
+        return "LoadImageConfiguration [desiredImageSizeOrNull=" + desiredImageSizeOrNull
+                + ", desiredImageFormatPng=" + desiredImageFormatPng
+                + ", openBisImageTransformationApplied=" + openBisImageTransformationApplied + "]";
+    }
+
+}