diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/IImagingDatasetLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/IImagingDatasetLoader.java
index 3757838a304d8f80807927236532116dd4fd1fdf..52c02e208ce337460fff81445ecc7ca5e571dd1a 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/IImagingDatasetLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/IImagingDatasetLoader.java
@@ -55,6 +55,17 @@ public interface IImagingDatasetLoader extends IImageDatasetLoader
AbsoluteImageReference tryGetRepresentativeImage(String channelCode,
Location wellLocationOrNull, RequestedImageSize imageSize);
+ /**
+ * Tries to find a representative thumbnail of this dataset in a given channel. Returns NULL if
+ * no thumbnail was found.
+ *
+ * @param channelCode channel code for which representative image is requested
+ * @param wellLocationOrNull if not null the returned images are restricted to one well.
+ * Otherwise the dataset is assumed to have no container and spots.
+ */
+ AbsoluteImageReference tryGetRepresentativeThumbnail(String channelCode,
+ Location wellLocationOrNull);
+
/**
* Returns the stored thumbnail for the given parameters, or <code>null</code>, if no thumbnail
* has been stored.
@@ -63,7 +74,7 @@ public interface IImagingDatasetLoader extends IImageDatasetLoader
* It will just plain give you the byte array that has been stored for the thumbnail.
*
* @param channelCode The code of the channel to get the thumbnail for.
- * @param channelStackReference Specifies well and tile of the thumbnail.
+ * @param channelStackReference Specifies well and tile of the thumbnail.
*/
IContent tryGetThumbnail(String channelCode, ImageChannelStackReference channelStackReference);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingDatasetLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingDatasetLoader.java
index 61d3b65910563964a2495f1708b271c342c1113b..336c98e63c3ca2babdd623d99b8ac7c3d037b729 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingDatasetLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingDatasetLoader.java
@@ -295,6 +295,37 @@ public class ImagingDatasetLoader extends HCSDatasetLoader implements IImagingDa
return createAbsoluteImageReference(imageDTO, channel, imageSize, useNativeImageLibrary);
}
+ private ImgImageDTO tryGetRepresentativeThumbnailImageDTO(long channelId,
+ Location wellLocationOrNull)
+ {
+ if (wellLocationOrNull == null)
+ {
+ return query.tryGetMicroscopyRepresentativeThumbnail(dataset.getId(), channelId);
+ } else
+ {
+ return query.tryGetHCSRepresentativeThumbnail(dataset.getId(), wellLocationOrNull,
+ channelId);
+ }
+ }
+
+ public AbsoluteImageReference tryGetRepresentativeThumbnail(String channelCode,
+ Location wellLocationOrNull)
+ {
+ ImgChannelDTO channel = tryLoadChannel(channelCode);
+ if (channel == null)
+ {
+ return null;
+ }
+ ImgImageDTO imageDTO =
+ tryGetRepresentativeThumbnailImageDTO(channel.getId(), wellLocationOrNull);
+ if (imageDTO == null)
+ {
+ return null;
+ }
+ return createAbsoluteImageReference(imageDTO, channel, new RequestedImageSize(
+ Size.NULL_SIZE, false), false);
+ }
+
public IContent tryGetThumbnail(String channelCode,
ImageChannelStackReference channelStackReference)
{
@@ -338,4 +369,5 @@ public class ImagingDatasetLoader extends HCSDatasetLoader implements IImagingDa
return null;
}
}
+
}
\ No newline at end of file
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 1bba06c2d246fa2802f8558c319f23826842490b..2ccee7a932e492e658d5f06fe922005026593e02 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
@@ -104,10 +104,6 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
*/
public static final int MINOR_VERSION = 8;
- /**
- * NULL_SIZE encodes for "no thumbnails available"
- */
- private final static Size NULL_SIZE = new Size(0, 0);
static
{
@@ -221,8 +217,8 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
{
final IImagingDatasetLoader imageAccessor =
createImageLoader(dataset.getDatasetCode(), datasetRoot);
- final Size imageSize = getImageSize(dataset, imageAccessor, false);
- final Size thumbnailSize = getImageSize(dataset, imageAccessor, true);
+ final Size imageSize = getOriginalImageSize(dataset, imageAccessor);
+ final Size thumbnailSize = getThumbnailImageSize(dataset, imageAccessor);
final ImageDatasetParameters params = imageAccessor.getImageParameters();
return new ImageDatasetMetadata(dataset, params.getChannelsCodes(),
params.getChannelsLabels(), params.getTileRowsNum(), params.getTileColsNum(),
@@ -230,31 +226,56 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
thumbnailSize.getHeight());
}
- private static Size getImageSize(IImageDatasetIdentifier dataset,
- IImagingDatasetLoader imageAccessor, boolean thumbnailsRequired)
+ private static Size getOriginalImageSize(IImageDatasetIdentifier dataset,
+ IImagingDatasetLoader imageAccessor)
{
- BufferedImage image = getAnyImage(imageAccessor, dataset, thumbnailsRequired);
+ BufferedImage image = getAnyImage(imageAccessor, dataset);
Size imageSize = new Size(image.getWidth(), image.getHeight());
return imageSize;
}
+ private static Size getThumbnailImageSize(IImageDatasetIdentifier dataset,
+ IImagingDatasetLoader imageAccessor)
+ {
+ BufferedImage image = getAnyThumbnailImage(imageAccessor, dataset);
+ if (image != null)
+ {
+ return new Size(image.getWidth(), image.getHeight());
+ } else
+ {
+ return Size.NULL_SIZE;
+ }
+ }
+
private static BufferedImage getAnyImage(IImagingDatasetLoader imageAccessor,
- IImageDatasetIdentifier dataset, boolean thumbnailsRequired)
+ IImageDatasetIdentifier dataset)
{
if (imageAccessor.getImageParameters().tryGetRowsNum() == null)
{
- return getAnyMicroscopyImage(imageAccessor, dataset, thumbnailsRequired);
+ return getAnyMicroscopyImage(imageAccessor, dataset);
} else
{
- return getAnyHCSImage(imageAccessor, dataset, thumbnailsRequired);
+ return getAnyHCSImage(imageAccessor, dataset);
+ }
+ }
+
+ private static BufferedImage getAnyThumbnailImage(IImagingDatasetLoader imageAccessor,
+ IImageDatasetIdentifier dataset)
+ {
+ if (imageAccessor.getImageParameters().tryGetRowsNum() == null)
+ {
+ return getAnyMicroscopyThumbnail(imageAccessor, dataset);
+ } else
+ {
+ return getAnyHCSThumbnail(imageAccessor, dataset);
}
}
private static BufferedImage getAnyMicroscopyImage(IImagingDatasetLoader imageAccessor,
- IImageDatasetIdentifier dataset, boolean thumbnailsRequired)
+ IImageDatasetIdentifier dataset)
{
ImageDatasetParameters params = imageAccessor.getImageParameters();
- RequestedImageSize originalOrThumbnail = createOriginalOrThumbnail(thumbnailsRequired);
+ RequestedImageSize originalOrThumbnail = RequestedImageSize.createOriginal();
for (String channelCode : params.getChannelsCodes())
{
AbsoluteImageReference image =
@@ -267,19 +288,50 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
throw new IllegalStateException("Cannot find any image in a dataset: " + dataset);
}
- private static RequestedImageSize createOriginalOrThumbnail(boolean thumbnailsRequired)
+ private static BufferedImage getAnyMicroscopyThumbnail(IImagingDatasetLoader imageAccessor,
+ IImageDatasetIdentifier dataset)
+ {
+ ImageDatasetParameters params = imageAccessor.getImageParameters();
+ for (String channelCode : params.getChannelsCodes())
+ {
+ AbsoluteImageReference image =
+ imageAccessor.tryGetRepresentativeThumbnail(channelCode, null);
+ if (image != null)
+ {
+ return image.getImage();
+ }
+ }
+ return null;
+ }
+
+ private static BufferedImage getAnyHCSThumbnail(IImagingDatasetLoader imageAccessor,
+ IImageDatasetIdentifier dataset)
{
- // exact thumbnail size does not matter, we just want to mark that we do not want the
- // original image
- return thumbnailsRequired ? new RequestedImageSize(NULL_SIZE, false) : RequestedImageSize
- .createOriginal();
+ ImageDatasetParameters params = imageAccessor.getImageParameters();
+ for (int row = 1; row <= params.tryGetRowsNum(); row++)
+ {
+ for (int col = 1; col <= params.tryGetColsNum(); col++)
+ {
+ for (String channelCode : params.getChannelsCodes())
+ {
+ AbsoluteImageReference image =
+ imageAccessor.tryGetRepresentativeThumbnail(channelCode, new Location(
+ col, row));
+ if (image != null)
+ {
+ return image.getImage();
+ }
+ }
+ }
+ }
+ return null;
}
private static BufferedImage getAnyHCSImage(IImagingDatasetLoader imageAccessor,
- IImageDatasetIdentifier dataset, boolean thumbnailsRequired)
+ IImageDatasetIdentifier dataset)
{
ImageDatasetParameters params = imageAccessor.getImageParameters();
- RequestedImageSize originalOrThumbnail = createOriginalOrThumbnail(thumbnailsRequired);
+ RequestedImageSize originalOrThumbnail = RequestedImageSize.createOriginal();
for (int row = 1; row <= params.tryGetRowsNum(); row++)
{
for (int col = 1; col <= params.tryGetColsNum(); col++)
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 9b18f60695b436774b5c9d94b47389776eb08729..c659c22e0aa7264e3ca529507ebbab9c7dba3ba7 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
@@ -176,12 +176,7 @@ public class ImageDatasetMetadata implements Serializable
*/
public boolean hasThumbnails()
{
- return isInRange(thumbnailHeight, 0, height) && isInRange(thumbnailWidth, 0, width);
- }
-
- private boolean isInRange(int value, int lowerBound, int upperBound)
- {
- return lowerBound < value && value < upperBound;
+ return thumbnailHeight > 0 && thumbnailWidth > 0;
}
@Override
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacadeTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacadeTest.java
index b14cd12f54399f79b30b7b6f20e179954b75e9a9..d9f049aaadc135e4d9b8d3afff2e59483372a6e9 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacadeTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacadeTest.java
@@ -921,8 +921,8 @@ public class ScreeningOpenbisServiceFacadeTest extends AbstractFileSystemTestCas
ImageDatasetMetadata imgMetaData =
new ImageDatasetMetadata(imageDataSetId, Collections
- .<String> emptyList(),
- Collections.<String> emptyList(), 3, 3, 1024, 768, 1024, 768);
+ .<String> emptyList(), Collections.<String> emptyList(), 3, 3,
+ 1024, 768, 0, 0);
will(returnValue(Arrays.asList(imgMetaData)));
}