diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbsoluteImageReference.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbsoluteImageReference.java
index f648d1fdb730cb96d689525fd53b910bcdf7056a..7e2d3012d9b6c86f1d83028777c9b9420e03250d 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbsoluteImageReference.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbsoluteImageReference.java
@@ -16,6 +16,7 @@
package ch.systemsx.cisd.openbis.dss.etl;
+import ch.systemsx.cisd.base.image.IImageTransformerFactory;
import ch.systemsx.cisd.common.io.IContent;
import ch.systemsx.cisd.openbis.dss.generic.server.AbstractDatasetDownloadServlet.Size;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ColorComponent;
@@ -33,6 +34,10 @@ public class AbsoluteImageReference extends AbstractImageReference
private final Size thumbnailSizeOrNull;
+ private IImageTransformerFactory transformerFactory;
+
+ private IImageTransformerFactory transformerFactoryForMergedChannels;
+
/**
* @param content the content before choosing the color component and the page
*/
@@ -64,11 +69,36 @@ public class AbsoluteImageReference extends AbstractImageReference
return thumbnailSizeOrNull;
}
+ public final IImageTransformerFactory getTransformerFactory()
+ {
+ return transformerFactory;
+ }
+
+ public final IImageTransformerFactory getTransformerFactoryForMergedChannels()
+ {
+ return transformerFactoryForMergedChannels;
+ }
+
+ public final void setTransformerFactoryForMergedChannels(
+ IImageTransformerFactory transformerFactoryForMergedChannels)
+ {
+ this.transformerFactoryForMergedChannels = transformerFactoryForMergedChannels;
+ }
+
+ public final void setTransformerFactory(IImageTransformerFactory transformerFactory)
+ {
+ this.transformerFactory = transformerFactory;
+ }
+
public AbsoluteImageReference createWithoutColorComponent()
{
ColorComponent colorComponent = null;
- return new AbsoluteImageReference(content, uniqueId, tryGetPage(), colorComponent,
- thumbnailSizeOrNull);
+ AbsoluteImageReference ref =
+ new AbsoluteImageReference(content, uniqueId, tryGetPage(), colorComponent,
+ thumbnailSizeOrNull);
+ ref.setTransformerFactory(transformerFactory);
+ ref.setTransformerFactoryForMergedChannels(transformerFactoryForMergedChannels);
+ return ref;
}
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImagingDatabaseVersionHolder.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImagingDatabaseVersionHolder.java
index 1ee677222bd41d03ff5d06376d80ea51b1509d57..290ac0f99fe54ae9a7c259f8994a6612d83a1ca4 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImagingDatabaseVersionHolder.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImagingDatabaseVersionHolder.java
@@ -28,7 +28,7 @@ public class ImagingDatabaseVersionHolder implements IDatabaseVersionHolder
public String getDatabaseVersion()
{
- return "006"; // changed in S88
+ return "007"; // changed in S94
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ScreeningContainerDatasetInfoHelper.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ScreeningContainerDatasetInfoHelper.java
index d6e4edb7dbaeaf6b5853e446953d99add4658e67..fb279e1cbef6b2293a97bae2786b17fc1cde0c40 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ScreeningContainerDatasetInfoHelper.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ScreeningContainerDatasetInfoHelper.java
@@ -26,6 +26,7 @@ import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingQueryDAO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgChannelDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgContainerDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgDatasetDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgExperimentDTO;
/**
* Helper class for retrieving and/or creating entities associated with the screening container data
@@ -141,13 +142,13 @@ public class ScreeningContainerDatasetInfoHelper
ScreeningContainerDatasetInfo info)
{
String experimentPermId = info.getExperimentPermId();
- Long expId = dao.tryGetExperimentIdByPermId(experimentPermId);
- if (expId != null)
+ ImgExperimentDTO experiment = dao.tryGetExperimentByPermId(experimentPermId);
+ if (experiment != null)
{
- return new CreatedOrFetchedEntity(true, expId);
+ return new CreatedOrFetchedEntity(true, experiment.getId());
} else
{
- expId = dao.addExperiment(experimentPermId);
+ Long expId = dao.addExperiment(experimentPermId);
return new CreatedOrFetchedEntity(false, expId);
}
}
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 c6ce95b5e940ce1ec2288eae8d107cdf3f866f91..c65d486fc23f74ff63925ab332c9b694723df967 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
@@ -26,7 +26,10 @@ import ch.systemsx.cisd.openbis.dss.generic.server.AbstractDatasetDownloadServle
import ch.systemsx.cisd.openbis.dss.generic.server.images.ImageChannelStackReference;
import ch.systemsx.cisd.openbis.dss.generic.server.images.ImageChannelStackReference.LocationImageChannelStackReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.HCSDatasetLoader;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ColorComponent;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingReadonlyQueryDAO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgChannelDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgExperimentDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgImageDTO;
/**
@@ -65,10 +68,10 @@ public class HCSImageDatasetLoader extends HCSDatasetLoader implements IHCSImage
assert stackLocations.getWellLocation().getY() <= getContainer().getNumberOfRows();
}
- Long chosenChannelId =
- query.tryGetChannelIdByChannelCodeDatasetIdOrExperimentId(getDataset().getId(),
+ ImgChannelDTO channel =
+ query.tryGetChannelByChannelCodeDatasetIdOrExperimentId(getDataset().getId(),
getContainer().getExperimentId(), chosenChannelCode);
- if (chosenChannelId == null)
+ if (channel == null)
{
return null;
}
@@ -76,15 +79,21 @@ public class HCSImageDatasetLoader extends HCSDatasetLoader implements IHCSImage
long datasetId = getDataset().getId();
boolean thumbnailPrefered = thumbnailSizeOrNull != null;
ImgImageDTO imageDTO =
- tryGetImageDTO(channelStackReference, thumbnailPrefered, chosenChannelId, datasetId);
+ tryGetImageDTO(channelStackReference, thumbnailPrefered, channel.getId(), datasetId);
if (imageDTO == null)
{
return null;
}
String path = imageDTO.getFilePath();
IContent content = contentRepository.getContent(path);
- return new AbsoluteImageReference(content, path, imageDTO.getPage(), imageDTO
- .getColorComponent(), thumbnailSizeOrNull);
+ ColorComponent colorComponent = imageDTO.getColorComponent();
+ AbsoluteImageReference imgRef =
+ new AbsoluteImageReference(content, path, imageDTO.getPage(), colorComponent,
+ thumbnailSizeOrNull);
+ imgRef.setTransformerFactory(channel.getImageTransformerFactory());
+ ImgExperimentDTO experiment = query.tryGetExperimentById(getContainer().getExperimentId());
+ imgRef.setTransformerFactoryForMergedChannels(experiment.getImageTransformerFactory());
+ return imgRef;
}
private ImgImageDTO tryGetImageDTO(ImageChannelStackReference channelStackReference,
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/MergingImagesDownloadServlet.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/MergingImagesDownloadServlet.java
index d4605658f29074eb883fdf2ac53f3baa2b7fa9b6..c6bde9a3522cce4155067aa719776db77d56a2d1 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/MergingImagesDownloadServlet.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/MergingImagesDownloadServlet.java
@@ -21,6 +21,8 @@ import java.io.IOException;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.common.io.IContent;
+import ch.systemsx.cisd.openbis.dss.etl.HCSImageDatasetLoaderFactory;
+import ch.systemsx.cisd.openbis.dss.etl.IHCSImageDatasetLoader;
import ch.systemsx.cisd.openbis.dss.generic.server.images.ImageChannelsUtils;
import ch.systemsx.cisd.openbis.dss.generic.server.images.TileImageReference;
@@ -43,7 +45,9 @@ public class MergingImagesDownloadServlet extends AbstractImagesDownloadServlet
protected final ResponseContentStream createImageResponse(TileImageReference params,
File datasetRoot, String datasetCode) throws IOException, EnvironmentFailureException
{
- IContent image = ImageChannelsUtils.getImage(datasetRoot, datasetCode, params);
+ IHCSImageDatasetLoader imageAccessor =
+ HCSImageDatasetLoaderFactory.create(datasetRoot, datasetCode);
+ IContent image = ImageChannelsUtils.getImage(imageAccessor, params);
return createResponseContentStream(image.getInputStream(), image.getSize(),
ImageChannelsUtils.IMAGES_CONTENT_TYPE, image.tryGetName());
}
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 1360dd4c4e342c313e3ee29c789600d9f324b0db..67870306f2e194f2694ccb019d2c849f8a19907b 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
@@ -20,7 +20,6 @@ import java.awt.Color;
import java.awt.image.BufferedImage;
import java.awt.image.RenderedImage;
import java.io.ByteArrayOutputStream;
-import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
@@ -30,13 +29,13 @@ import javax.imageio.ImageIO;
import org.apache.log4j.Logger;
+import ch.systemsx.cisd.base.image.IImageTransformerFactory;
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.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.openbis.dss.etl.AbsoluteImageReference;
-import ch.systemsx.cisd.openbis.dss.etl.HCSImageDatasetLoaderFactory;
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.shared.utils.ImageUtil;
@@ -53,17 +52,25 @@ public class ImageChannelsUtils
static protected final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
ImageChannelsUtils.class);
- // MIME type of the images which are produced by thsi class
+ // MIME type of the images which are produced by this class
public static final String IMAGES_CONTENT_TYPE = "image/png";
/**
- * @return an image for the specified tile in the specified size and for the requested channel
- * or with all channels merged.
+ * Returns content of image for the specified tile in the specified size and for the requested
+ * channel or with all channels merged.
*/
- public static IContent getImage(File datasetRoot, String datasetCode, TileImageReference params)
+ public static IContent getImage(IHCSImageDatasetLoader imageAccessor, TileImageReference params)
{
- List<AbsoluteImageReference> images = getImageReferences(datasetRoot, datasetCode, params);
- return calculateImage(images);
+ List<AbsoluteImageReference> images = getImageReferences(imageAccessor, params);
+ if (images.size() > 1)
+ {
+ return mergeAllChannels(images);
+ } else
+ {
+ AbsoluteImageReference imageReference = images.get(0);
+ return calculateSingleImageContent(imageReference,
+ imageReference.getTransformerFactory(), true);
+ }
}
/**
@@ -76,19 +83,12 @@ public class ImageChannelsUtils
AbsoluteImageReference imageReference =
getImageReference(imageAccessor, channelStackReference, chosenChannelCode,
thumbnailSizeOrNull);
- return calculateSingleImageContent(imageReference, convertToPng);
+ return calculateSingleImageContent(imageReference, null, convertToPng);
}
- /**
- * @return file with the image for the chosen channel or images for all channels if they should
- * be merged.
- * @throw {@link EnvironmentFailureException} when image does not exist
- */
- private static List<AbsoluteImageReference> getImageReferences(File datasetRoot,
- String datasetCode, TileImageReference params)
+ private static List<AbsoluteImageReference> getImageReferences(
+ IHCSImageDatasetLoader imageAccessor, TileImageReference params)
{
- IHCSImageDatasetLoader imageAccessor =
- HCSImageDatasetLoaderFactory.create(datasetRoot, datasetCode);
List<AbsoluteImageReference> images = new ArrayList<AbsoluteImageReference>();
Size thumbnailSizeOrNull = params.tryGetThumbnailSize();
@@ -111,24 +111,13 @@ public class ImageChannelsUtils
return images;
}
- private static IContent calculateImage(List<AbsoluteImageReference> images)
- {
- if (images.size() > 1)
- {
- return mergeAllChannels(images);
- } else
- {
- return calculateSingleImageContent(images.get(0), true);
- }
- }
-
private static IContent calculateSingleImageContent(AbsoluteImageReference imageReference,
- boolean convertToPng)
+ IImageTransformerFactory transformerFactoryOrNull, boolean convertToPng)
{
final IContent content;
if (convertToPng || imageReference.tryGetColorComponent() != null)
{
- final BufferedImage image = calculateSingleImage(imageReference);
+ final BufferedImage image = transform(calculateSingleImage(imageReference), transformerFactoryOrNull);
long start = operationLog.isDebugEnabled() ? System.currentTimeMillis() : 0;
content = createPngContent(image, imageReference.getContent().tryGetName());
@@ -138,7 +127,14 @@ public class ImageChannelsUtils
}
} else
{
- content = imageReference.getContent();
+ if (transformerFactoryOrNull != null)
+ {
+ BufferedImage img = transform(loadImage(imageReference), transformerFactoryOrNull);
+ content = createPngContent(img, imageReference.getContent().tryGetName());
+ } else
+ {
+ content = imageReference.getContent();
+ }
}
return content;
@@ -146,15 +142,9 @@ public class ImageChannelsUtils
private static BufferedImage calculateSingleImage(AbsoluteImageReference imageReference)
{
- IContent content = imageReference.getContent();
-
- InputStream inputStream = content.getInputStream();
-
- // extracts the correct page if necessary
- int page = (imageReference.tryGetPage() != null) ? imageReference.tryGetPage() : 0;
long start = operationLog.isDebugEnabled() ? System.currentTimeMillis() : 0;
- BufferedImage image = ImageUtil.loadImage(inputStream, page);
+ BufferedImage image = loadImage(imageReference);
if (operationLog.isDebugEnabled())
{
operationLog.debug("Load original image: " + (System.currentTimeMillis() - start));
@@ -186,6 +176,18 @@ public class ImageChannelsUtils
return image;
}
+ private static BufferedImage loadImage(AbsoluteImageReference imageReference)
+ {
+ IContent content = imageReference.getContent();
+ InputStream inputStream = content.getInputStream();
+
+ // extracts the correct page if necessary
+ int page = (imageReference.tryGetPage() != null) ? imageReference.tryGetPage() : 0;
+
+ BufferedImage image = ImageUtil.loadImage(inputStream, page);
+ return image;
+ }
+
private static IContent mergeAllChannels(List<AbsoluteImageReference> imageReferences)
{
AbsoluteImageReference allChannelsImageReference =
@@ -193,13 +195,25 @@ public class ImageChannelsUtils
if (allChannelsImageReference != null)
{
// all channels are on an image in one file, no pixel-level operations needed
- return calculateSingleImageContent(allChannelsImageReference, true);
+ return calculateSingleImageContent(allChannelsImageReference,
+ allChannelsImageReference.getTransformerFactoryForMergedChannels(), true);
} else
{
List<BufferedImage> images = calculateSingleImages(imageReferences);
BufferedImage mergedImage = mergeChannels(images);
- return createPngContent(mergedImage, null);
+ IImageTransformerFactory transformerFactory =
+ imageReferences.get(0).getTransformerFactoryForMergedChannels();
+ return createPngContent(transform(mergedImage, transformerFactory), null);
+ }
+ }
+
+ private static BufferedImage transform(BufferedImage input, IImageTransformerFactory factoryOrNull)
+ {
+ if (factoryOrNull == null)
+ {
+ return input;
}
+ return factoryOrNull.createTransformer().transform(input);
}
private static List<BufferedImage> calculateSingleImages(
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 9d6194321e71be37f3cc8beda6f8745ab5e7f226..c6540ff4516922bfc2e80169d55795fa91a63daf 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
@@ -26,8 +26,11 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
+import net.lemnik.eodsql.QueryTool;
+
import org.springframework.remoting.httpinvoker.HttpInvokerServiceExporter;
+import ch.systemsx.cisd.base.image.IImageTransformerFactory;
import ch.systemsx.cisd.bds.hcs.Location;
import ch.systemsx.cisd.common.api.RpcServiceInterfaceVersionDTO;
import ch.systemsx.cisd.common.api.server.RpcServiceNameServer;
@@ -69,8 +72,10 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.FeatureVectorLoa
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.FeatureVectorLoader.IMetadataProvider;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.FeatureVectorLoader.WellFeatureCollection;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingReadonlyQueryDAO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingTransformerDAO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgDatasetDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgFeatureDefDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.TransformerFactoryMapper;
/**
* Implementation of the screening API interface using RPC. The instance will be created in spring
@@ -86,20 +91,30 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
* The minor version of this service.
*/
public static final int MINOR_VERSION = 3;
+
+ static
+ {
+ QueryTool.getTypeMap().put(IImageTransformerFactory.class, new TransformerFactoryMapper());
+ }
// this dao will hold one connection to the database
private IImagingReadonlyQueryDAO dao;
+ private final IImagingTransformerDAO transformerDAO;
+
public DssServiceRpcScreening(String storeRootDir)
{
- this(storeRootDir, null, ServiceProvider.getOpenBISService(), true);
+ this(storeRootDir, null, QueryTool.getQuery(ServiceProvider.getDataSourceProvider()
+ .getDataSource(ScreeningConstants.IMAGING_DATA_SOURCE),
+ IImagingTransformerDAO.class), ServiceProvider.getOpenBISService(), true);
}
- DssServiceRpcScreening(String storeRootDir, IImagingReadonlyQueryDAO dao,
+ DssServiceRpcScreening(String storeRootDir, IImagingReadonlyQueryDAO dao, IImagingTransformerDAO transformerDAO,
IEncapsulatedOpenBISService service, boolean registerAtNameService)
{
super(service);
this.dao = dao;
+ this.transformerDAO = transformerDAO;
setStoreDirectory(new File(storeRootDir));
if (registerAtNameService)
{
@@ -354,6 +369,78 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
}
return new ConcatenatedContentInputStream(true, imageContents);
}
+
+
+
+ public void saveImageTransformerFactory(String sessionToken, List<IDatasetIdentifier> dataSetIdentifiers,
+ String channel, IImageTransformerFactory transformerFactory)
+ {
+ List<String> experimentPermIDs = getExperimentPermIDs(sessionToken, dataSetIdentifiers);
+ for (String experimentPermID : experimentPermIDs)
+ {
+ if (ScreeningConstants.MERGED_CHANNELS.equals(channel))
+ {
+ if (operationLog.isInfoEnabled())
+ {
+ operationLog.info("save image transformer factory " + transformerFactory
+ + " for experiment " + experimentPermID);
+ }
+ transformerDAO
+ .saveTransformerFactoryForExperiment(experimentPermID, transformerFactory);
+ } else
+ {
+ if (operationLog.isInfoEnabled())
+ {
+ operationLog
+ .info("save image transformer factory " + transformerFactory
+ + " for experiment " + experimentPermID + " and channel '"
+ + channel + "'.");
+ }
+ transformerDAO.saveTransformerFactoryForChannel(experimentPermID, channel,
+ transformerFactory);
+ }
+ }
+ transformerDAO.commit();
+ }
+
+ public IImageTransformerFactory getImageTransformerFactory(String sessionToken,
+ List<IDatasetIdentifier> dataSetIdentifiers, String channel)
+ {
+ List<String> experimentPermIDs = getExperimentPermIDs(sessionToken, dataSetIdentifiers);
+ if (experimentPermIDs.isEmpty())
+ {
+ throw new UserFailureException("No data set identifers specified.");
+ }
+ if (experimentPermIDs.size() > 1)
+ {
+ throw new UserFailureException("All data sets have to belong to the same experiment: "
+ + dataSetIdentifiers);
+ }
+ String experimentPermID = experimentPermIDs.get(0);
+ if (ScreeningConstants.MERGED_CHANNELS.equals(channel))
+ {
+ return getDAO().tryGetExperimentByPermId(experimentPermID).getImageTransformerFactory();
+ }
+ return getDAO().tryGetChannelByChannelCodeAndExperimentPermId(experimentPermID, channel)
+ .getImageTransformerFactory();
+ }
+
+ private List<String> getExperimentPermIDs(String sessionToken,
+ List<IDatasetIdentifier> dataSetIdentifiers)
+ {
+ List<String> experimentPermIDs = new ArrayList<String>();
+ for (IDatasetIdentifier dataSetIdentifier : dataSetIdentifiers)
+ {
+ ExternalData dataSet =
+ getOpenBISService().tryGetDataSet(sessionToken, dataSetIdentifier.getDatasetCode());
+ if (dataSet == null)
+ {
+ throw new UserFailureException("Unkown data set " + dataSetIdentifier);
+ }
+ experimentPermIDs.add(dataSet.getExperiment().getPermId());
+ }
+ return experimentPermIDs;
+ }
private List<PlateImageReference> createPlateImageReferences(
IHCSImageDatasetLoader imageAccessor, IDatasetIdentifier dataSetIdentifier,
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 bb1395d28636340ee0eb52f66896e8f74ed489ad..b9bd891562c70428bfd43823e647265d3d692a32 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
@@ -19,6 +19,7 @@ package ch.systemsx.cisd.openbis.dss.screening.shared.api.v1;
import java.io.InputStream;
import java.util.List;
+import ch.systemsx.cisd.base.image.IImageTransformerFactory;
import ch.systemsx.cisd.common.api.IRpcService;
import ch.systemsx.cisd.common.api.MinimalMinorVersion;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.authorization.AuthorizationGuard;
@@ -166,7 +167,21 @@ public interface IDssServiceRpcScreening extends IRpcService
String sessionToken,
@AuthorizationGuard(guardClass = SingleDataSetIdentifierPredicate.class) IDatasetIdentifier dataSetIdentifier,
List<WellPosition> wellPositions, String channel, ImageSize thumbnailSizeOrNull);
+
+ @MinimalMinorVersion(4)
+ @DataSetAccessGuard
+ public void saveImageTransformerFactory(
+ String sessionToken,
+ @AuthorizationGuard(guardClass = DatasetIdentifierPredicate.class) List<IDatasetIdentifier> dataSetIdentifiers,
+ String channel, IImageTransformerFactory transformerFactory);
+ @MinimalMinorVersion(4)
+ @DataSetAccessGuard
+ public IImageTransformerFactory getImageTransformerFactory(
+ String sessionToken,
+ @AuthorizationGuard(guardClass = DatasetIdentifierPredicate.class) List<IDatasetIdentifier> dataSetIdentifiers,
+ String channel);
+
/**
* For a given set of image data sets, provide all image channels that have been acquired and
* the available (natural) image size(s).
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/shared/DssScreeningUtils.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/shared/DssScreeningUtils.java
index 325a99a7c663e1244e8224e9c6379df398fa00d5..3eae016990a9e80953b8adb21da3edf07b5d9081 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/shared/DssScreeningUtils.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/shared/DssScreeningUtils.java
@@ -32,7 +32,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImag
public class DssScreeningUtils
{
private static final IImagingReadonlyQueryDAO query = createQuery();
-
+
public static IImagingReadonlyQueryDAO getQuery()
{
return query;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ExampleImageTransformerFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ExampleImageTransformerFactory.java
new file mode 100644
index 0000000000000000000000000000000000000000..bbe6c0d9dc58b1ba2fcbdd1b63cbdf09ff0896c2
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ExampleImageTransformerFactory.java
@@ -0,0 +1,81 @@
+/*
+ * Copyright 2010 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.plugin.screening.client.api.v1;
+
+import java.awt.image.BufferedImage;
+
+import ch.systemsx.cisd.base.image.IImageTransformer;
+import ch.systemsx.cisd.base.image.IImageTransformerFactory;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class ExampleImageTransformerFactory implements IImageTransformerFactory
+{
+ private static final long serialVersionUID = 1L;
+
+ private final int indexOfRed;
+ private final int indexOfGreen;
+ private final int indexOfBlue;
+
+ public ExampleImageTransformerFactory(String colorPattern)
+ {
+ indexOfRed = colorPattern.indexOf('r');
+ indexOfGreen = colorPattern.indexOf('g');
+ indexOfBlue = colorPattern.indexOf('b');
+ }
+
+ public IImageTransformer createTransformer()
+ {
+ return new IImageTransformer()
+ {
+ public BufferedImage transform(BufferedImage input)
+ {
+ int width = input.getWidth();
+ int height = input.getHeight();
+ BufferedImage output = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
+ for (int x = 0; x < width; x++)
+ {
+ for (int y = 0; y < height; y++)
+ {
+ int rgb = input.getRGB(x, y);
+ int blue = (rgb >> 16) & 0xff;
+ int green = (rgb >> 8) & 0xff;
+ int red = rgb & 0xff;
+ output.setRGB(x, y, shift(red, indexOfRed) + shift(green, indexOfGreen)
+ + shift(blue, indexOfBlue));
+ }
+ }
+ return output;
+ }
+ };
+ }
+
+ private int shift(int color, int position)
+ {
+ return color << (8 * (2 - position));
+ }
+
+ @Override
+ public String toString()
+ {
+ return getClass().getSimpleName() + "[" + indexOfRed + "." + indexOfGreen + "." + indexOfBlue + "]";
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/IScreeningOpenbisServiceFacade.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/IScreeningOpenbisServiceFacade.java
index 2cb44013e12003fa2d9e1b44d547ad3a7710b0ff..8731c64f3fe508c656acf95b48a8e2452592ac32 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/IScreeningOpenbisServiceFacade.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/IScreeningOpenbisServiceFacade.java
@@ -19,6 +19,7 @@ package ch.systemsx.cisd.openbis.plugin.screening.client.api.v1;
import java.io.IOException;
import java.util.List;
+import ch.systemsx.cisd.base.image.IImageTransformerFactory;
import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade.IImageOutputStreamProvider;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDataset;
@@ -263,6 +264,22 @@ public interface IScreeningOpenbisServiceFacade
public List<byte[]> loadImages(IDatasetIdentifier dataSetIdentifier,
List<WellPosition> wellPositions, String channel, ImageSize thumbnailSizeOrNull)
throws IOException;
+
+ /**
+ * Saves the specified transformer factory for the specified channel and the experiment to
+ * which the specified data sets belong.
+ */
+ public void saveImageTransformerFactory(List<IDatasetIdentifier> dataSetIdentifiers, String channel,
+ IImageTransformerFactory transformerFactory);
+
+ /**
+ * Returns the transformer factory for the specified channel and the experiment to which
+ * the specified data sets belong.
+ *
+ * @return <code>null</code> if such a factory has been defined yet.
+ */
+ public IImageTransformerFactory getImageTransformerFactoryOrNull(
+ List<IDatasetIdentifier> dataSetIdentifiers, String channel);
/**
* For a given set of image data sets, provide all image channels that have been acquired and
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ImageViewer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ImageViewer.java
index a9ecceeef0ab053c18575f17c432c9be156d4c75..526ed5b8b9f3443edd31fd0c67e585f1cde02600 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ImageViewer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ImageViewer.java
@@ -18,7 +18,6 @@ package ch.systemsx.cisd.openbis.plugin.screening.client.api.v1;
import java.awt.Container;
import java.util.ArrayList;
-import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
@@ -29,8 +28,7 @@ import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JPanel;
-import org.apache.commons.lang.StringUtils;
-
+import ch.systemsx.cisd.base.image.IImageTransformerFactory;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DataSetCodeAndWellPositions;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IDatasetIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageSize;
@@ -44,15 +42,14 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition;
*/
public class ImageViewer
{
- public static void main(String[] args)
+ public static void main(String[] args) throws Exception
{
String serviceURL = args[0];
String sessionToken = args[1];
- long experimentID = Long.parseLong(args[2]);
- String channel = args[3];
+ String channel = args[2];
Map<String, DataSetCodeAndWellPositions> dataSets =
new HashMap<String, DataSetCodeAndWellPositions>();
- for (int i = 4; i < args.length; i++)
+ for (int i = 3; i < args.length; i++)
{
DataSetCodeAndWellPositions dw = new DataSetCodeAndWellPositions(args[i]);
dataSets.put(dw.getDataSetCode(), dw);
@@ -69,9 +66,9 @@ public class ImageViewer
{
IScreeningOpenbisServiceFacade facade =
ScreeningOpenbisServiceFacadeFactory.tryCreate(sessionToken, serviceURL);
- List<IDatasetIdentifier> dsIdentifier =
+ List<IDatasetIdentifier> dsIdentifiers =
facade.getDatasetIdentifiers(new ArrayList<String>(dataSets.keySet()));
- for (IDatasetIdentifier identifier : dsIdentifier)
+ for (IDatasetIdentifier identifier : dsIdentifiers)
{
content.add(new JLabel("Images for data set " + identifier.getDatasetCode()));
JPanel imagePanel = new JPanel();
@@ -86,9 +83,14 @@ public class ImageViewer
imagePanel.add(new JLabel(new ImageIcon(bytes)));
}
}
+ String pattern = channel.equals("Merged Channels") ? "brg" : "gbr";
+ facade.saveImageTransformerFactory(dsIdentifiers, channel, new ExampleImageTransformerFactory(pattern));
+ IImageTransformerFactory factory = facade.getImageTransformerFactoryOrNull(dsIdentifiers, channel);
+ System.out.println("Image Transformer Factory: " + factory);
} catch (Exception ex)
{
content.add(new JLabel(ex.toString()));
+ throw ex;
}
frame.pack();
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java
index 47ccad7a181a161f110f71ed7b9ee2d1a6000adc..cc19b2ba29628c7a2e04cda2c143ba7f513e52aa 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java
@@ -14,6 +14,7 @@ import java.util.Map;
import java.util.Set;
import java.util.Map.Entry;
+import ch.systemsx.cisd.base.image.IImageTransformerFactory;
import ch.systemsx.cisd.common.api.MinimalMinorVersion;
import ch.systemsx.cisd.common.api.client.ServiceFinder;
import ch.systemsx.cisd.common.io.ConcatenatedFileOutputStreamWriter;
@@ -565,6 +566,26 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
return result;
}
+ public void saveImageTransformerFactory(List<IDatasetIdentifier> dataSetIdentifiers, String channel,
+ IImageTransformerFactory transformerFactory)
+ {
+ Map<String, List<IDatasetIdentifier>> map = getReferencesPerDss(dataSetIdentifiers);
+ Set<Entry<String, List<IDatasetIdentifier>>> entrySet = map.entrySet();
+ for (Entry<String, List<IDatasetIdentifier>> entry : entrySet)
+ {
+ String serverUrl = entry.getKey();
+ IDssServiceRpcScreening service = dssServiceCache.createDssService(serverUrl).getService();
+ service.saveImageTransformerFactory(sessionToken, entry.getValue(), channel, transformerFactory);
+ }
+ }
+
+ public IImageTransformerFactory getImageTransformerFactoryOrNull(
+ List<IDatasetIdentifier> dataSetIdentifiers, String channel)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
/**
* For a given set of image data sets, provide all image channels that have been acquired and
* the available (natural) image size(s).
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellContentDialog.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellContentDialog.java
index 79c2c12c819b723208b12e9e5e06c2ab733678c7..8e042e4cc8f936977edd0a7cba6b5ca21557a944 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellContentDialog.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellContentDialog.java
@@ -412,8 +412,6 @@ public class WellContentDialog extends Dialog
viewContext.getModel().getSessionContext()
.getSessionID();
urlParams.addParameter("session", sessionToken);
- urlParams.addParameter(ParameterNames.EXPERIMENT_ID,
- experimentCriteria.getExperimentId());
if (selectionProvider != null)
{
urlParams.addParameter(ParameterNames.CHANNEL, selectionProvider
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/ImageViewerLaunchServlet.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/ImageViewerLaunchServlet.java
index 03ae3ba93779d5fb99947b717819a050719c1c9f..4b0890f015337e8ee0c8a45195f751cee7d01865 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/ImageViewerLaunchServlet.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/ImageViewerLaunchServlet.java
@@ -86,7 +86,6 @@ public class ImageViewerLaunchServlet extends AbstractServlet
+ " <application-desc main-class='${main-class}'>\n"
+ " <argument>${service-URL}</argument>\n"
+ " <argument>${session-id}</argument>\n"
- + " <argument>${experiment-id}</argument>\n"
+ " <argument>${channel}</argument>\n"
+ "${data-set-and-wells-arguments}\n"
+ " </application-desc>\n" + "</jnlp>\n");
@@ -114,7 +113,6 @@ public class ImageViewerLaunchServlet extends AbstractServlet
template.bind("main-class", getMainClass());
template.bind("service-URL", basicURL);
template.bind("session-id", getSessionToken(request));
- template.bind("experiment-id", getParam(request, ParameterNames.EXPERIMENT_ID));
template.bind("channel", getParam(request, ParameterNames.CHANNEL));
StringBuilder builder = new StringBuilder();
for (String dataSetAndWells : getParams(request, ParameterNames.DATA_SET_AND_WELLS))
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/AbstractImageTransformerFactoryHolder.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/AbstractImageTransformerFactoryHolder.java
new file mode 100644
index 0000000000000000000000000000000000000000..c93bc26675043cc8bcc717b98b24cc401838164b
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/AbstractImageTransformerFactoryHolder.java
@@ -0,0 +1,55 @@
+/*
+ * Copyright 2010 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.plugin.screening.shared.imaging.dataaccess;
+
+import org.apache.commons.lang.SerializationUtils;
+
+import net.lemnik.eodsql.ResultColumn;
+
+import ch.systemsx.cisd.base.image.IImageTransformerFactory;
+import ch.systemsx.cisd.common.utilities.AbstractHashable;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+abstract class AbstractImageTransformerFactoryHolder extends AbstractHashable
+{
+ @ResultColumn("IMAGE_TRANSFORMER_FACTORY")
+ private byte[] serializedImageTransformerFactory;
+
+ public final byte[] getSerializedImageTransformerFactory()
+ {
+ return serializedImageTransformerFactory;
+ }
+
+ public final void setSerializedImageTransformerFactory(byte[] serializedImageTransformerFactory)
+ {
+ this.serializedImageTransformerFactory = serializedImageTransformerFactory;
+ }
+
+ public IImageTransformerFactory getImageTransformerFactory()
+ {
+ if (serializedImageTransformerFactory == null)
+ {
+ return null;
+ }
+ return (IImageTransformerFactory) SerializationUtils.deserialize(serializedImageTransformerFactory);
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingReadonlyQueryDAO.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingReadonlyQueryDAO.java
index 2e7b6ba7b7b0151f62a492c63fb4928b81322fb2..7e59b00c86bbcb049975715dc627776fec55ec45 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingReadonlyQueryDAO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingReadonlyQueryDAO.java
@@ -89,9 +89,12 @@ public interface IImagingReadonlyQueryDAO extends BaseQuery
// simple getters
- @Select("select ID from EXPERIMENTS where PERM_ID = ?{1}")
- public Long tryGetExperimentIdByPermId(String experimentPermId);
+ @Select("select * from EXPERIMENTS where PERM_ID = ?{1}")
+ public ImgExperimentDTO tryGetExperimentByPermId(String experimentPermId);
+ @Select("select * from EXPERIMENTS where ID = ?{1}")
+ public ImgExperimentDTO tryGetExperimentById(long experimentId);
+
@Select("select ID from CONTAINERS where PERM_ID = ?{1}")
public Long tryGetContainerIdPermId(String containerPermId);
@@ -127,8 +130,13 @@ public interface IImagingReadonlyQueryDAO extends BaseQuery
@Select(sql = "select * from FEATURE_VALUES where FD_ID = ?{1.id} order by T_in_SEC, Z_in_M", resultSetBinding = FeatureVectorDataObjectBinding.class)
public List<ImgFeatureValuesDTO> getFeatureValues(ImgFeatureDefDTO featureDef);
- @Select("select ID from CHANNELS where (DS_ID = ?{1} or EXP_ID = ?{2}) and CODE = upper(?{3})")
- public Long tryGetChannelIdByChannelCodeDatasetIdOrExperimentId(long id, long experimentId,
+ @Select("select * from CHANNELS where (DS_ID = ?{1} or EXP_ID = ?{2}) and CODE = upper(?{3})")
+ public ImgChannelDTO tryGetChannelByChannelCodeDatasetIdOrExperimentId(long id, long experimentId,
String chosenChannelCode);
-
+
+ @Select("select * from channels where code = ?{2} and "
+ + "exp_id in (select id from experiments where perm_id = ?{1})")
+ public ImgChannelDTO tryGetChannelByChannelCodeAndExperimentPermId(String experimentPermId,
+ String chosenChannelCode);
+
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingTransformerDAO.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingTransformerDAO.java
new file mode 100644
index 0000000000000000000000000000000000000000..fdb0e86cbe15c9ce953463da47565fef1d848886
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingTransformerDAO.java
@@ -0,0 +1,42 @@
+/*
+ * Copyright 2010 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.plugin.screening.shared.imaging.dataaccess;
+
+import net.lemnik.eodsql.TransactionQuery;
+import net.lemnik.eodsql.TypeMapper;
+import net.lemnik.eodsql.Update;
+
+import ch.systemsx.cisd.base.image.IImageTransformerFactory;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public interface IImagingTransformerDAO extends TransactionQuery
+{
+ @Update(sql = "update experiments set image_transformer_factory = ?{2} where perm_id = ?{1}", parameterBindings =
+ { TransformerFactoryMapper.class, TypeMapper.class/* default */ })
+ public void saveTransformerFactoryForExperiment(String experimentPermID,
+ IImageTransformerFactory factory);
+
+ @Update(sql = "update channels set image_transformer_factory = ?{3} "
+ + "where code = ?{2} and exp_id in (select id from experiments where perm_id = ?{1})", parameterBindings =
+ { TransformerFactoryMapper.class, TypeMapper.class/* default */, TypeMapper.class /* default */ })
+ public void saveTransformerFactoryForChannel(String experimentPermID, String channel,
+ IImageTransformerFactory factory);
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgChannelDTO.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgChannelDTO.java
index 0072348e2b147f3cf0b72817ed59e82666d48a83..dc9a6216900861ae79c6dc88bf1a724f98f6224f 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgChannelDTO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgChannelDTO.java
@@ -19,12 +19,10 @@ package ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess;
import net.lemnik.eodsql.AutoGeneratedKeys;
import net.lemnik.eodsql.ResultColumn;
-import ch.systemsx.cisd.common.utilities.AbstractHashable;
-
/**
* @author Tomasz Pylak
*/
-public class ImgChannelDTO extends AbstractHashable
+public class ImgChannelDTO extends AbstractImageTransformerFactoryHolder
{
@AutoGeneratedKeys
private long id;
@@ -48,7 +46,7 @@ public class ImgChannelDTO extends AbstractHashable
// can be null if datasetId is not null
@ResultColumn("EXP_ID")
private Long experimentIdOrNull;
-
+
public static ImgChannelDTO createDatasetChannel(String code, String descriptionOrNull,
Integer wavelengthOrNull, long datasetId, String label)
{
@@ -151,4 +149,5 @@ public class ImgChannelDTO extends AbstractHashable
this.experimentIdOrNull = experimentId;
}
+
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgExperimentDTO.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgExperimentDTO.java
new file mode 100644
index 0000000000000000000000000000000000000000..c7c24ff4d96f91731ebc08d7a8819000eff65782
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgExperimentDTO.java
@@ -0,0 +1,55 @@
+/*
+ * Copyright 2010 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.plugin.screening.shared.imaging.dataaccess;
+
+import net.lemnik.eodsql.AutoGeneratedKeys;
+import net.lemnik.eodsql.ResultColumn;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class ImgExperimentDTO extends AbstractImageTransformerFactoryHolder
+{
+ @AutoGeneratedKeys
+ private long id;
+
+ @ResultColumn("PERM_ID")
+ private String permId;
+
+ public long getId()
+ {
+ return id;
+ }
+
+ public void setId(long id)
+ {
+ this.id = id;
+ }
+
+ public String getPermId()
+ {
+ return permId;
+ }
+
+ public void setPermId(String permId)
+ {
+ this.permId = permId;
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/TransformerFactoryMapper.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/TransformerFactoryMapper.java
new file mode 100644
index 0000000000000000000000000000000000000000..88dbf938cb41bac1c2b86a42b6eafef0dc3c9709
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/TransformerFactoryMapper.java
@@ -0,0 +1,55 @@
+/*
+ * Copyright 2010 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.plugin.screening.shared.imaging.dataaccess;
+
+import java.io.Serializable;
+import java.sql.PreparedStatement;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+
+import ch.systemsx.cisd.base.image.IImageTransformerFactory;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.SerializableObjectMapper;
+
+import net.lemnik.eodsql.TypeMapper;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class TransformerFactoryMapper implements TypeMapper<IImageTransformerFactory>
+{
+ private final TypeMapper<Serializable> serializableObjectMapper = new SerializableObjectMapper();
+
+ public IImageTransformerFactory get(ResultSet results, int column) throws SQLException
+ {
+ return (IImageTransformerFactory) serializableObjectMapper.get(results, column);
+ }
+
+ public void set(ResultSet results, int column, IImageTransformerFactory obj)
+ throws SQLException
+ {
+ serializableObjectMapper.set(results, column, obj);
+ }
+
+ public void set(PreparedStatement statement, int column, IImageTransformerFactory obj)
+ throws SQLException
+ {
+ serializableObjectMapper.set(statement, column, obj);
+ }
+
+}
diff --git a/screening/source/sql/postgresql/007/schema-007.sql b/screening/source/sql/postgresql/007/schema-007.sql
index 84614f313a73e15e7bdb082b0dcf4a39d709b5e1..2c2af9c2a051c8f17ff33229f64184a67653fd61 100644
--- a/screening/source/sql/postgresql/007/schema-007.sql
+++ b/screening/source/sql/postgresql/007/schema-007.sql
@@ -24,7 +24,7 @@ CREATE DOMAIN BOOLEAN_CHAR AS BOOLEAN DEFAULT FALSE;
CREATE TABLE EXPERIMENTS (
ID BIGSERIAL NOT NULL,
PERM_ID CODE NOT NULL,
- IMAGE_TRANSFORMATION_FACTORY BYTEA,
+ IMAGE_TRANSFORMER_FACTORY BYTEA,
PRIMARY KEY (ID),
UNIQUE (PERM_ID)
@@ -87,7 +87,7 @@ CREATE TABLE CHANNELS (
LABEL NAME NOT NULL,
DESCRIPTION DESCRIPTION,
WAVELENGTH INTEGER,
- IMAGE_TRANSFORMATION_FACTORY BYTEA,
+ IMAGE_TRANSFORMER_FACTORY BYTEA,
DS_ID TECH_ID,
EXP_ID TECH_ID,
diff --git a/screening/source/sql/postgresql/migration/migration-006-007.sql b/screening/source/sql/postgresql/migration/migration-006-007.sql
index 4ea38cfa3d65dfa3db65d51e8f1c15b42bdda7ab..d555348bc3ef43089a6251f9243d9c029bd02e7b 100644
--- a/screening/source/sql/postgresql/migration/migration-006-007.sql
+++ b/screening/source/sql/postgresql/migration/migration-006-007.sql
@@ -1,4 +1,4 @@
-- Migration from 006 to 007
-ALTER TABLE CHANNELS ADD COLUMN IMAGE_TRANSFORMATION_FACTORY BYTEA;
-ALTER TABLE EXPERIMENTS ADD COLUMN IMAGE_TRANSFORMATION_FACTORY BYTEA,
+ALTER TABLE CHANNELS ADD COLUMN IMAGE_TRANSFORMER_FACTORY BYTEA;
+ALTER TABLE EXPERIMENTS ADD COLUMN IMAGE_TRANSFORMER_FACTORY BYTEA;
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingQueryDAOTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingQueryDAOTest.java
index 3f4539f4e48242955d5aca9863469b69af354eca..a01629d43d027a6466ad8d225df3d41a476864be 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingQueryDAOTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingQueryDAOTest.java
@@ -191,8 +191,8 @@ public class ImagingQueryDAOTest extends AbstractDBTest
// test get id of first channel
assertEquals(
channels.get(0).getId(),
- dao.tryGetChannelIdByChannelCodeDatasetIdOrExperimentId(datasetId, experimentId,
- "dsChannel").intValue());
+ dao.tryGetChannelByChannelCodeDatasetIdOrExperimentId(datasetId, experimentId,
+ "dsChannel").getId());
List<ImgChannelDTO> experimentChannels = dao.getChannelsByExperimentId(experimentId);
assertEquals(1, experimentChannels.size());
@@ -217,7 +217,7 @@ public class ImagingQueryDAOTest extends AbstractDBTest
final String permId = EXP_PERM_ID;
final long experimentId = dao.addExperiment(permId);
- assertEquals(Long.valueOf(experimentId), dao.tryGetExperimentIdByPermId(permId));
+ assertEquals(experimentId, dao.tryGetExperimentByPermId(permId).getId());
return experimentId;
}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/genedata/FeatureStorageProcessorTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/genedata/FeatureStorageProcessorTest.java
index dfddca565e7280a29d7dd1cbdba540c602c284a7..9a6297cb4890f2d689a47379a33fca6c4729cfdd 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/genedata/FeatureStorageProcessorTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/genedata/FeatureStorageProcessorTest.java
@@ -43,6 +43,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.plugin.screening.shared.dto.PlateDimensionParser;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgDatasetDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgExperimentDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgFeatureDefDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgFeatureValuesDTO;
@@ -84,8 +85,10 @@ public class FeatureStorageProcessorTest extends AbstractFileSystemTestCase
context.checking(new Expectations()
{
{
- one(dao).tryGetExperimentIdByPermId(EXPERIMENT_PERM_ID);
- will(returnValue((long) 1));
+ one(dao).tryGetExperimentByPermId(EXPERIMENT_PERM_ID);
+ ImgExperimentDTO exp = new ImgExperimentDTO();
+ exp.setId(1);
+ will(returnValue(exp));
one(dao).tryGetContainerIdPermId(CONTAINER_PERM_ID);
will(returnValue((long) 1));
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java
index 1dcd92e90d7b98279e9f2ec5f3ad0311ba5963b6..1fc67af76c5ba43ecf1d9134bb081f877c0e1dc3 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java
@@ -44,6 +44,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVector
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IFeatureVectorDatasetIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.dto.PlateFeatureValues;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingReadonlyQueryDAO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingTransformerDAO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgContainerDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgDatasetDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgFeatureDefDTO;
@@ -70,16 +71,19 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
private DssServiceRpcScreening screeningService;
+ private IImagingTransformerDAO transformerDAO;
+
@BeforeMethod
public void beforeMethod()
{
context = new Mockery();
service = context.mock(IEncapsulatedOpenBISService.class);
dao = context.mock(IImagingReadonlyQueryDAO.class);
+ transformerDAO = context.mock(IImagingTransformerDAO.class);
featureVectorDatasetIdentifier1 = create("ds1");
featureVectorDatasetIdentifier2 = create("ds2");
- screeningService = new DssServiceRpcScreening("targets", dao, service, false);
+ screeningService = new DssServiceRpcScreening("targets", dao, transformerDAO, service, false);
}
private IFeatureVectorDatasetIdentifier create(final String dataSetCode)