diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractDssServiceRpc.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractDssServiceRpc.java
index 4ef88f85c215824b8fb921ed230481618e818e08..3a88d1913ef84c3a71a0b7ccfedaa7f5e6890af2 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractDssServiceRpc.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractDssServiceRpc.java
@@ -135,9 +135,9 @@ public abstract class AbstractDssServiceRpc
/**
* Asserts that specified data sets are all accessible by the user of the specified session.
*/
- protected void assertDatasetsAreAccessible(String sessionToken, List<String> dataSetCodes)
+ protected void checkDatasetsAuthorization(String sessionToken, List<String> dataSetCodes)
{
- if (areDatasetsAccessible(sessionToken, dataSetCodes) == false)
+ if (isSessionAuthorizedForDatasets(sessionToken, dataSetCodes) == false)
{
throw new IllegalArgumentException(
"User is not allowed to access at least one of the following data sets: "
@@ -153,7 +153,7 @@ public abstract class AbstractDssServiceRpc
* @param dataSetCodes The data set codes we want to check access for.
* @return True if all the data sets are accessible, false if one or more are not accessible.
*/
- protected boolean areDatasetsAccessible(String sessionToken, List<String> dataSetCodes)
+ protected boolean isSessionAuthorizedForDatasets(String sessionToken, List<String> dataSetCodes)
{
boolean access;
if (operationLog.isInfoEnabled())
@@ -201,7 +201,7 @@ public abstract class AbstractDssServiceRpc
protected Map<String, File> checkAccessAndGetRootDirectories(String sessionToken,
List<String> dataSetCodes) throws IllegalArgumentException
{
- if (areDatasetsAccessible(sessionToken, dataSetCodes) == false)
+ if (isSessionAuthorizedForDatasets(sessionToken, dataSetCodes) == false)
{
throw new IllegalArgumentException("Path does not exist.");
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/HCSImageDatasetLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/HCSImageDatasetLoader.java
index ec93ee30c00da85bb7930d8780050d4c53b995f2..4cf24d106f04f919137f3d8c4f9c51eb00eff352 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/HCSImageDatasetLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/HCSImageDatasetLoader.java
@@ -26,13 +26,21 @@ import javax.imageio.ImageIO;
import org.apache.commons.lang.StringUtils;
+import com.sun.media.jai.codec.ImageCodec;
+import com.sun.media.jai.codec.ImageEncoder;
+import com.sun.media.jai.codec.TIFFEncodeParam;
+
import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
import ch.systemsx.cisd.bds.hcs.Location;
+import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
+import ch.systemsx.cisd.common.io.ByteArrayBasedContent;
import ch.systemsx.cisd.common.io.IContent;
+import ch.systemsx.cisd.common.utilities.DataTypeUtil;
import ch.systemsx.cisd.openbis.dss.etl.AbsoluteImageReference;
import ch.systemsx.cisd.openbis.dss.etl.IContentRepository;
import ch.systemsx.cisd.openbis.dss.etl.IHCSImageDatasetLoader;
import ch.systemsx.cisd.openbis.dss.generic.server.AbstractDatasetDownloadServlet.Size;
+import ch.systemsx.cisd.openbis.dss.generic.server.images.ImageChannelsUtils;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.HCSDatasetLoader;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingQueryDAO;
@@ -106,6 +114,21 @@ public class HCSImageDatasetLoader extends HCSDatasetLoader implements IHCSImage
if (imageDTO != null)
{
content = contentRepository.getContent(imageDTO.getFilePath());
+ final InputStream is = content.getInputStream();
+ final String fileType = DataTypeUtil.tryToFigureOutFileTypeOf(is);
+ if (DataTypeUtil.isTiff(fileType) == false || imageDTO.getColorComponent() != null
+ || imageDTO.getPage() != null)
+ {
+ final int page = (imageDTO.getPage() != null) ? imageDTO.getPage() : 0;
+ BufferedImage image = ImageUtil.loadImage(is, fileType, page);
+ if (imageDTO.getColorComponent() != null)
+ {
+ image =
+ ImageChannelsUtils.transformToChannel(image, imageDTO
+ .getColorComponent());
+ }
+ content = asContent(image, fileType, content.getName(), content.getUniqueId());
+ }
}
}
if (content != null && imageDTO != null)
@@ -118,6 +141,29 @@ public class HCSImageDatasetLoader extends HCSDatasetLoader implements IHCSImage
}
}
+ private static IContent asContent(BufferedImage image, String fileType, String name, String id)
+ {
+ final ByteArrayOutputStream out = new ByteArrayOutputStream();
+ final TIFFEncodeParam param = new TIFFEncodeParam();
+ param.setLittleEndian(true);
+ if (DataTypeUtil.isJpeg(fileType))
+ {
+ param.setCompression(TIFFEncodeParam.COMPRESSION_JPEG_TTN2);
+ } else
+ {
+ param.setCompression(TIFFEncodeParam.COMPRESSION_DEFLATE);
+ }
+ final ImageEncoder enc = ImageCodec.createImageEncoder("tiff", out, param);
+ try
+ {
+ enc.encode(image);
+ return new ByteArrayBasedContent(out.toByteArray(), name, id);
+ } catch (IOException ex)
+ {
+ throw EnvironmentFailureException.fromTemplate("Cannot encode image.", ex);
+ }
+ }
+
private static final class ThumbnailContent implements IContent
{
private final IContent content;
@@ -166,6 +212,7 @@ public class HCSImageDatasetLoader extends HCSDatasetLoader implements IHCSImage
{
return content.getUniqueId();
}
+
}
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtils.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtils.java
index 649a762c2f5c223fc1c142fdbe51584a53b59c67..c0a27640060a339101572332e3b0db8b9cb2b195 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtils.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtils.java
@@ -18,7 +18,9 @@ package ch.systemsx.cisd.openbis.dss.generic.server.images;
import java.awt.Color;
import java.awt.image.BufferedImage;
+import java.awt.image.RenderedImage;
import java.io.File;
+import java.io.InputStream;
import java.util.ArrayList;
import java.util.List;
@@ -82,9 +84,18 @@ public class ImageChannelsUtils
*/
public static BufferedImage mergeImageChannels(TileImageReference params,
List<AbsoluteImageReference> imageReferences)
+ {
+ return mergeImageChannels(imageReferences, params.isMergeAllChannels());
+ }
+
+ /**
+ * Creates an images of the specified tile and with requested channels merged.<br>
+ */
+ public static BufferedImage mergeImageChannels(List<AbsoluteImageReference> imageReferences,
+ boolean mergeChannels)
{
BufferedImage resultImage;
- if (params.isMergeAllChannels())
+ if (mergeChannels)
{
resultImage = mergeAllChannels(imageReferences);
} else
@@ -93,16 +104,26 @@ public class ImageChannelsUtils
+ "but more have been specified: " + imageReferences;
AbsoluteImageReference imageReference = imageReferences.get(0);
- resultImage = selectSingleChannel(params, imageReference);
+ resultImage = selectSingleChannel(imageReference);
}
return resultImage;
}
- private static BufferedImage selectSingleChannel(TileImageReference params,
- AbsoluteImageReference imageReference)
+ /**
+ * Reads the given content and selects a single channel from it.
+ */
+ public static BufferedImage selectSingleChannel(AbsoluteImageReference imageReference)
+ {
+ return selectSingleChannel(imageReference.getContent().getInputStream(), imageReference
+ .tryGetColorComponent());
+ }
+
+ /**
+ * Reads the given content and selects a single channel from it.
+ */
+ public static BufferedImage selectSingleChannel(InputStream input, ColorComponent colorComponent)
{
- BufferedImage image = ImageUtil.loadImage(imageReference.getContent().getInputStream());
- ColorComponent colorComponent = imageReference.tryGetColorComponent();
+ BufferedImage image = ImageUtil.loadImage(input);
if (colorComponent == null)
{
// TODO 2010-06-15 Izabela Adamczyk: We have to select a single channel from the (most
@@ -238,7 +259,10 @@ public class ImageChannelsUtils
}
}
- private static BufferedImage transformToChannel(BufferedImage bufferedImage,
+ /**
+ * Transforms the given <var>bufferedImage</var> as
+ */
+ public static BufferedImage transformToChannel(BufferedImage bufferedImage,
ColorComponent colorComponent)
{
BufferedImage newImage = createNewImage(bufferedImage);
@@ -256,7 +280,7 @@ public class ImageChannelsUtils
return newImage;
}
- private static BufferedImage createNewImage(BufferedImage bufferedImage)
+ private static BufferedImage createNewImage(RenderedImage bufferedImage)
{
BufferedImage newImage =
new BufferedImage(bufferedImage.getWidth(), bufferedImage.getHeight(),
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 f1970227f39756dbdca595dd1e62c1a748fa24c9..c1c0e96785444139a13915207f5215d4bbbe4d96 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
@@ -77,7 +77,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
/**
* The minor version of this service.
*/
- private static final int MINOR_VERSION = 1;
+ public static final int MINOR_VERSION = 1;
private IImagingQueryDAO dao;
@@ -114,7 +114,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
public List<String> listAvailableFeatureNames(String sessionToken,
List<? extends IFeatureVectorDatasetIdentifier> featureDatasets)
{
- assertDataSetsAreAccessible(sessionToken, featureDatasets);
+ checkDatasetsAuthorizationForIDatasetIdentifier(sessionToken, featureDatasets);
List<String> result = new ArrayList<String>(); // keep the order
for (IFeatureVectorDatasetIdentifier identifier : featureDatasets)
{
@@ -135,6 +135,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
public List<ImageDatasetMetadata> listImageMetadata(String sessionToken,
List<? extends IImageDatasetIdentifier> imageDatasets)
{
+ checkDatasetsAuthorizationForIDatasetIdentifier(sessionToken, imageDatasets);
ArrayList<String> datasetCodes = new ArrayList<String>();
for (IImageDatasetIdentifier dataset : imageDatasets)
{
@@ -194,7 +195,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
public List<FeatureVectorDataset> loadFeatures(String sessionToken,
List<FeatureVectorDatasetReference> featureDatasets, List<String> featureNames)
{
- assertDataSetsAreAccessible(sessionToken, featureDatasets);
+ checkDatasetsAuthorizationForIDatasetIdentifier(sessionToken, featureDatasets);
List<FeatureVectorDataset> result = new ArrayList<FeatureVectorDataset>();
for (FeatureVectorDatasetReference dataset : featureDatasets)
{
@@ -224,7 +225,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
String sessionToken, List<FeatureVectorDatasetWellReference> datasetWellReferences,
List<String> featureNames)
{
- assertDataSetsAreAccessible(sessionToken, datasetWellReferences);
+ checkDatasetsAuthorizationForIDatasetIdentifier(sessionToken, datasetWellReferences);
final FeatureTableBuilder builder =
createFeatureTableBuilder(datasetWellReferences, featureNames);
return createFeatureVectorList(builder);
@@ -265,26 +266,19 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
public InputStream loadImages(String sessionToken, List<PlateImageReference> imageReferences)
{
- Map<String, IHCSImageDatasetLoader> imageLoadersMap =
+ checkDatasetsAuthorizationForIDatasetIdentifier(sessionToken, imageReferences);
+ final Map<String, IHCSImageDatasetLoader> imageLoadersMap =
getImageDatasetsMap(sessionToken, imageReferences);
- List<IContent> imageFiles = new ArrayList<IContent>();
+ final List<IContent> imageFiles = new ArrayList<IContent>();
try
{
for (PlateImageReference imageReference : imageReferences)
{
- IHCSImageDatasetLoader imageAccessor =
+ final IHCSImageDatasetLoader imageAccessor =
imageLoadersMap.get(imageReference.getDatasetCode());
assert imageAccessor != null : "imageAccessor not found for: " + imageReference;
- AbsoluteImageReference image = tryGetImage(imageAccessor, imageReference);
- if (image == null
- || (image.tryGetColorComponent() != null || image.tryGetPage() != null))
- {
- // TODO 2010-06-01, Tomasz Pylak: support paging/merged channels images in API
- imageFiles.add(null);
- } else
- {
- imageFiles.add(image.getContent());
- }
+ final AbsoluteImageReference imageRef = tryGetImage(imageAccessor, imageReference);
+ imageFiles.add((imageRef == null) ? null : imageRef.getContent());
}
} finally
{
@@ -340,6 +334,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
.getChannel(), null);
} catch (EnvironmentFailureException e)
{
+ operationLog.error("Error reading image.", e);
return null; // no image found
}
}
@@ -412,7 +407,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
return getDAO().listFeatureDefsByDataSetId(dataSet.getId());
}
- private void assertDataSetsAreAccessible(String sessionToken,
+ private void checkDatasetsAuthorizationForIDatasetIdentifier(String sessionToken,
List<? extends IDatasetIdentifier> identifiers)
{
List<String> dataSetCodes = new ArrayList<String>();
@@ -420,7 +415,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
{
dataSetCodes.add(identifier.getDatasetCode());
}
- assertDatasetsAreAccessible(sessionToken, dataSetCodes);
+ checkDatasetsAuthorization(sessionToken, dataSetCodes);
}
private IImagingQueryDAO getDAO()