diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
index 33456d2040c53c7b24a46677a980b3d942ae4cba..1bba06c2d246fa2802f8558c319f23826842490b 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
+++ b/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);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningLogger.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningLogger.java
index e5f6a474cfbfbc6975cde0a231b7e3f0c70ab433..c8f8b6ac31f24264b188b98877a21a54a2ac0e0d 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningLogger.java
+++ b/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;
+ }
+
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/shared/api/v1/IDssServiceRpcScreening.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/shared/api/v1/IDssServiceRpcScreening.java
index 0bde2cd6a4862200c08a8709ec6d77c01e5bfa15..ab7883f06651d1402e8e4178490d3fda5d106506 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/shared/api/v1/IDssServiceRpcScreening.java
+++ b/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.
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/shared/api/v1/LoadImageConfiguration.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/shared/api/v1/LoadImageConfiguration.java
new file mode 100644
index 0000000000000000000000000000000000000000..769f472d0354472d75cfc5dab0c2b06740e31d8d
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/shared/api/v1/LoadImageConfiguration.java
@@ -0,0 +1,125 @@
+/*
+ * 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 + "]";
+ }
+
+}