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 a2919f628bad39ee44f3aa8e67b5dd81622eefdd..a449cc6340a29fa3229d9badc5421e43a57361be 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
@@ -89,18 +89,19 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
{
// Register the service with the name server
RpcServiceInterfaceVersionDTO ifaceVersion =
- new RpcServiceInterfaceVersionDTO("screening-dss",
- "/rmi-datastore-server-screening-api-v1", getMajorVersion(),
- getMinorVersion());
+ new RpcServiceInterfaceVersionDTO("screening-dss",
+ "/rmi-datastore-server-screening-api-v1", getMajorVersion(),
+ getMinorVersion());
HttpInvokerServiceExporter nameServiceExporter =
- ServiceProvider.getRpcNameServiceExporter();
- RpcServiceNameServer nameServer = (RpcServiceNameServer) nameServiceExporter.getService();
+ ServiceProvider.getRpcNameServiceExporter();
+ RpcServiceNameServer nameServer =
+ (RpcServiceNameServer) nameServiceExporter.getService();
nameServer.addSupportedInterfaceVersion(ifaceVersion);
-
+
operationLog.info("[rpc] Started DSS RPC screening service V1.");
}
}
-
+
// ------------------ impl -----------------
public List<String> listAvailableFeatureNames(String sessionToken,
@@ -153,11 +154,10 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
HCSImageDatasetLoaderFactory.create(datasetRoot, dataset.getDatasetCode());
IContent imageFile = getAnyImagePath(imageAccessor, dataset);
Geometry wellGeometry = imageAccessor.getWellGeometry();
- int channelsNumber = imageAccessor.getChannelCount();
int tilesNumber = wellGeometry.getColumns() * wellGeometry.getRows();
BufferedImage image = ImageUtil.loadImage(imageFile.getInputStream());
- return new ImageDatasetMetadata(dataset, channelsNumber, tilesNumber, image.getWidth(),
- image.getHeight());
+ return new ImageDatasetMetadata(dataset, imageAccessor.getChannelsNames(), tilesNumber,
+ image.getWidth(), image.getHeight());
}
private static IContent getAnyImagePath(IHCSImageDatasetLoader imageAccessor,
@@ -199,7 +199,8 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
private FeatureVectorDataset createFeatureVectorDataset(String sessionToken,
FeatureVectorDatasetReference dataset, List<String> featureNames)
{
- FeatureTableBuilder builder = new FeatureTableBuilder(featureNames, getDAO(), getOpenBISService());
+ FeatureTableBuilder builder =
+ new FeatureTableBuilder(featureNames, getDAO(), getOpenBISService());
builder.addFeatureVectorsOfDataSet(dataset.getDatasetCode());
List<String> existingFeatureNames = builder.getFeatureNames();
List<FeatureTableRow> featureTableRows = builder.getFeatureTableRows();
@@ -361,7 +362,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
{
return 0;
}
-
+
private List<ImgFeatureDefDTO> getFeatureDefinitions(IDatasetIdentifier identifier)
{
ImgDatasetDTO dataSet = getDAO().tryGetDatasetByPermId(identifier.getDatasetCode());
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 461b00c6ff1e5c6fd82d478ab17c55dd80641315..75577297c6d662a5065f7970d36b0e9ab729135a 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
@@ -245,6 +245,11 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
* Saves images for a given list of image references (given by data set code, well position,
* channel and tile) in the provided output streams. Output streams will not be closed
* automatically.<br>
+ * <p>
+ * If there is an image reference specified which is not referring to the existing image on the
+ * server, nothing will be written to the output stream returned by the output streams provider.
+ * No exception will be thrown.
+ * </p>
* The number of image references has to be the same as the number of files.
*
* @throws IOException when reading images from the server or writing them to the output streams
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageDatasetMetadata.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageDatasetMetadata.java
index 920945a051fb1116d5a0e60d5f865da5aba1d3f8..517b00b9d44f04d769739cc2991f9407e222bc53 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageDatasetMetadata.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageDatasetMetadata.java
@@ -1,6 +1,7 @@
package ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto;
import java.io.Serializable;
+import java.util.List;
/**
* Metadata information about images in a specified dataset.
@@ -15,17 +16,20 @@ public class ImageDatasetMetadata implements Serializable
private final int channelsNumber;
+ private final List<String> channelNames;
+
private final int tilesNumber;
private final int width;
private final int height;
- public ImageDatasetMetadata(IImageDatasetIdentifier dataset, int channelsNumber,
+ public ImageDatasetMetadata(IImageDatasetIdentifier dataset, List<String> channelNames,
int tilesNumber, int width, int height)
{
this.imageDataset = dataset;
- this.channelsNumber = channelsNumber;
+ this.channelNames = channelNames;
+ this.channelsNumber = channelNames.size();
this.tilesNumber = tilesNumber;
this.width = width;
this.height = height;
@@ -45,6 +49,14 @@ public class ImageDatasetMetadata implements Serializable
return channelsNumber;
}
+ /**
+ * names of channels in which images have been acquired for the described dataset
+ */
+ public List<String> getChannelNames()
+ {
+ return channelNames;
+ }
+
/**
* number of image tiles (aka fields) into which each well is splited
*/
@@ -68,7 +80,7 @@ public class ImageDatasetMetadata implements Serializable
@Override
public String toString()
{
- return "Dataset " + imageDataset + " has " + channelsNumber + " channels, " + tilesNumber
+ return "Dataset " + imageDataset + " has [" + channelNames + "] channels, " + tilesNumber
+ " tiles. Images resolution: " + width + "x" + height;
}
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/IHCSDatasetLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/IHCSDatasetLoader.java
index 16fa7369b7dff1b6b994d88c66945a9523d053b0..14feaf5983a7729e1bf4b7cfd70ef7146b3812e5 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/IHCSDatasetLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/IHCSDatasetLoader.java
@@ -35,8 +35,6 @@ public interface IHCSDatasetLoader
Geometry getWellGeometry();
- int getChannelCount();
-
List<String> getChannelsNames();
}
\ No newline at end of file