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 0a2e1eb7e820999bb9af6544b37346af91c9df2b..0e504f5cd824656f7a71ea8baf80bf861ae2de2b 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
@@ -48,6 +48,8 @@ public class AbsoluteImageReference extends AbstractImageReference
private ChannelColorRGB channelColor;
+ private String singleChannelTransformationCodeOrNull;
+
/**
* @param contentNode is the original content before choosing the color component and the image
* ID
@@ -56,7 +58,7 @@ public class AbsoluteImageReference extends AbstractImageReference
String imageIdOrNull, ColorComponent colorComponentOrNull,
RequestedImageSize imageSize, ChannelColorRGB channelColor,
ImageTransfomationFactories imageTransfomationFactories,
- ImageLibraryInfo imageLibraryOrNull)
+ ImageLibraryInfo imageLibraryOrNull, String singleChannelTransformationCodeOrNull)
{
super(imageIdOrNull, colorComponentOrNull);
assert imageSize != null : "image size is null";
@@ -68,6 +70,7 @@ public class AbsoluteImageReference extends AbstractImageReference
this.channelColor = channelColor;
this.imageTransfomationFactories = imageTransfomationFactories;
this.imageLibraryOrNull = imageLibraryOrNull;
+ this.singleChannelTransformationCodeOrNull = singleChannelTransformationCodeOrNull;
}
/**
@@ -104,10 +107,10 @@ public class AbsoluteImageReference extends AbstractImageReference
}
return image;
}
-
+
/**
- * Returns the image size. Preferred method if only image size is needed because only the
- * header of an image file might be read to get the size.
+ * Returns the image size. Preferred method if only image size is needed because only the header
+ * of an image file might be read to get the size.
*/
public Size getUnchangedImageSize()
{
@@ -133,11 +136,16 @@ public class AbsoluteImageReference extends AbstractImageReference
return channelColor;
}
+ public String tryGetSingleChannelTransformationCode()
+ {
+ return singleChannelTransformationCodeOrNull;
+ }
+
public AbsoluteImageReference createWithoutColorComponent()
{
ColorComponent colorComponent = null;
return new AbsoluteImageReference(contentNode, uniqueId, tryGetImageID(), colorComponent,
- imageSize, channelColor, imageTransfomationFactories, imageLibraryOrNull);
-
+ imageSize, channelColor, imageTransfomationFactories, imageLibraryOrNull,
+ singleChannelTransformationCodeOrNull);
}
}
\ No newline at end of file
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 637641bf03caec39cf50925a98f19003d133af11..b5eff24ee1cb81dec96afbbc96bb01c6f187bcd0 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
@@ -30,15 +30,17 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.IImageDatasetLoa
public interface IImagingDatasetLoader extends IImageDatasetLoader
{
/**
- * @param channelCode The code fo the channel to get the image for
+ * @param channelCode The code for the channel to get the image for
* @param imageSize required image size, specified so that an image with the closest size to the
* required is returned (e.g. a thumbnail version if available). Note that this
* method does no image resizing and the result will most probably not have the
* required size.
+ * @param transformationCodeOrNull if transformed images are precomputed, they will be returned
* @return image (with original file content, page and color)
*/
AbsoluteImageReference tryGetImage(String channelCode,
- ImageChannelStackReference channelStackReference, RequestedImageSize imageSize);
+ ImageChannelStackReference channelStackReference, RequestedImageSize imageSize,
+ String transformationCodeOrNull);
/**
* Finds representative image of this data set. Returns <code>null</code> if no image was found.
@@ -55,9 +57,11 @@ public interface IImagingDatasetLoader extends IImageDatasetLoader
* required is returned (e.g. a thumbnail version if available). Note that this
* method does no image resizing and the result will most probably not have the
* required size.
+ * @param transformationCodeOrNull if transformed images are precomputed, they will be returned
*/
AbsoluteImageReference tryGetRepresentativeImage(String channelCode,
- Location wellLocationOrNull, RequestedImageSize imageSize);
+ Location wellLocationOrNull, RequestedImageSize imageSize,
+ String transformationCodeOrNull);
/**
* Tries to find a representative thumbnail of this data set. Returns <code>null</code> if no
@@ -73,9 +77,11 @@ public interface IImagingDatasetLoader extends IImageDatasetLoader
* @param wellLocationOrNull if not null the returned images are restricted to one well.
* Otherwise the dataset is assumed to have no container and spots.
* @param imageSize
+ * @param transformationCodeOrNull
*/
AbsoluteImageReference tryGetRepresentativeThumbnail(String channelCode,
- Location wellLocationOrNull, RequestedImageSize imageSize);
+ Location wellLocationOrNull, RequestedImageSize imageSize,
+ String transformationCodeOrNull);
/**
* Returns the stored thumbnail for the given parameters, or <code>null</code>, if no thumbnail
@@ -87,8 +93,10 @@ public interface IImagingDatasetLoader extends IImageDatasetLoader
* @param channelCode The code of the channel to get the thumbnail for.
* @param channelStackReference Specifies well and tile of the thumbnail.
* @param imageSize
+ * @param transformationCodeOrNull if transformed images are precomputed, they will be returned
*/
AbsoluteImageReference tryGetThumbnail(String channelCode,
- ImageChannelStackReference channelStackReference, RequestedImageSize imageSize);
+ ImageChannelStackReference channelStackReference, RequestedImageSize imageSize,
+ String transformationCodeOrNull);
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/IImagingLoaderStrategy.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/IImagingLoaderStrategy.java
index 40f037498eb797495bfe40c5d21cb5464f541485..7fd9a08ba06211318f4f6d4c954f6059e719f7f8 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/IImagingLoaderStrategy.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/IImagingLoaderStrategy.java
@@ -35,7 +35,8 @@ public interface IImagingLoaderStrategy extends IImageDatasetLoader
* @return image (with original file content, page and color)
*/
AbsoluteImageReference tryGetImage(String channelCode,
- ImageChannelStackReference channelStackReference, RequestedImageSize imageSize);
+ ImageChannelStackReference channelStackReference, RequestedImageSize imageSize,
+ String transformationCodeOrNull);
/**
* Finds representative image of this dataset in a given channel.
@@ -49,5 +50,6 @@ public interface IImagingLoaderStrategy extends IImageDatasetLoader
* required size.
*/
AbsoluteImageReference tryGetRepresentativeImage(String channelCode,
- Location wellLocationOrNull, RequestedImageSize imageSize);
+ Location wellLocationOrNull, RequestedImageSize imageSize,
+ String transformationCodeOrNull);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImagingLoaderStrategyFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImagingLoaderStrategyFactory.java
index bacc108b641d08fbc653d4bd8c6c1817952efd03..5833749b01cabc84d23827e38af4d5c058e3293c 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImagingLoaderStrategyFactory.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImagingLoaderStrategyFactory.java
@@ -60,18 +60,19 @@ public class ImagingLoaderStrategyFactory
@Override
public AbsoluteImageReference tryGetImage(String channelCode,
ImageChannelStackReference channelStackReference,
- RequestedImageSize imageSize)
+ RequestedImageSize imageSize, String transformationCodeOrNull)
{
return this.imageAccessor.tryGetThumbnail(channelCode, channelStackReference,
- imageSize);
+ imageSize, transformationCodeOrNull);
}
@Override
public AbsoluteImageReference tryGetRepresentativeImage(String channelCode,
- Location wellLocationOrNull, RequestedImageSize imageSize)
+ Location wellLocationOrNull, RequestedImageSize imageSize,
+ String transformationCodeOrNull)
{
return imageAccessor.tryGetRepresentativeThumbnail(channelCode,
- wellLocationOrNull, imageSize);
+ wellLocationOrNull, imageSize, transformationCodeOrNull);
}
};
@@ -85,18 +86,19 @@ public class ImagingLoaderStrategyFactory
@Override
public AbsoluteImageReference tryGetImage(String channelCode,
ImageChannelStackReference channelStackReference,
- RequestedImageSize imageSize)
+ RequestedImageSize imageSize, String transformationCodeOrNull)
{
return this.imageAccessor.tryGetImage(channelCode, channelStackReference,
- imageSize);
+ imageSize, transformationCodeOrNull);
}
@Override
public AbsoluteImageReference tryGetRepresentativeImage(String channelCode,
- Location wellLocationOrNull, RequestedImageSize imageSize)
+ Location wellLocationOrNull, RequestedImageSize imageSize,
+ String transformationCodeOrNull)
{
return imageAccessor.tryGetRepresentativeImage(channelCode, wellLocationOrNull,
- imageSize);
+ imageSize, transformationCodeOrNull);
}
};
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PrefixedImage.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PrefixedImage.java
index 39a46c8becb2d62a37a613b80b755c409bf47c79..d88318df57a9cccc828ad09caa5eaf09263d36e2 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PrefixedImage.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PrefixedImage.java
@@ -30,12 +30,16 @@ public class PrefixedImage
private final String pathSuffix;
+ private final String singleChannelTransformationCodeOrNull;
+
private final ImgImageDTO image;
- public PrefixedImage(String pathPrefix, String pathSuffix, ImgImageDTO image)
+ public PrefixedImage(String pathPrefix, String pathSuffix,
+ String singleChannelTransformationCodeOrNull, ImgImageDTO image)
{
this.pathPrefix = pathPrefix;
this.pathSuffix = pathSuffix;
+ this.singleChannelTransformationCodeOrNull = singleChannelTransformationCodeOrNull;
this.image = image;
}
@@ -64,4 +68,8 @@ public class PrefixedImage
return image.tryGetImageTransformerFactory();
}
+ public String tryGetSingleChannelTransformationCode()
+ {
+ return singleChannelTransformationCodeOrNull;
+ }
}
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 60662bfa361bce92756287bd3611752e1623950f..693d53934181bd7a2b13cfc0705a39239884aa2c 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
@@ -18,8 +18,10 @@ package ch.systemsx.cisd.openbis.dss.etl.dataaccess;
import java.awt.image.BufferedImage;
import java.util.HashMap;
+import java.util.HashSet;
import java.util.List;
import java.util.Map;
+import java.util.Set;
import org.apache.commons.lang.StringUtils;
@@ -48,6 +50,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgIm
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgImageDatasetDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgImageTransformationDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgImageZoomLevelDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgImageZoomLevelTransformationEnrichedDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgSpotDTO;
/**
@@ -55,6 +58,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgSp
*
* @author Tomasz Pylak
* @author Piotr Buczek
+ * @author Pawel Glyzewski
*/
public class ImagingDatasetLoader extends HCSDatasetLoader implements IImagingDatasetLoader
{
@@ -91,7 +95,8 @@ public class ImagingDatasetLoader extends HCSDatasetLoader implements IImagingDa
*/
@Override
public AbsoluteImageReference tryGetImage(String chosenChannelCode,
- ImageChannelStackReference channelStackReference, RequestedImageSize imageSize)
+ ImageChannelStackReference channelStackReference, RequestedImageSize imageSize,
+ String singleChannelTransformationCodeOrNull)
{
if (StringUtils.isBlank(chosenChannelCode))
{
@@ -111,7 +116,8 @@ public class ImagingDatasetLoader extends HCSDatasetLoader implements IImagingDa
if (imageSize.isThumbnailRequired())
{
imageDTO =
- tryGetThumbnail(chosenChannelId, channelStackReference, datasetId, imageSize);
+ tryGetThumbnail(chosenChannelId, channelStackReference, datasetId, imageSize,
+ singleChannelTransformationCodeOrNull);
}
boolean thumbnailFetched = (imageDTO != null);
if (imageDTO == null)
@@ -124,7 +130,7 @@ public class ImagingDatasetLoader extends HCSDatasetLoader implements IImagingDa
{
imageDTO =
tryGetThumbnail(chosenChannelId, channelStackReference, datasetId,
- imageSize);
+ imageSize, singleChannelTransformationCodeOrNull);
thumbnailFetched = (imageDTO != null);
}
}
@@ -170,7 +176,8 @@ public class ImagingDatasetLoader extends HCSDatasetLoader implements IImagingDa
createImageTransfomationFactories(image, channel);
ImageLibraryInfo imageLibrary = tryGetImageLibrary(dataset, useNativeImageLibrary);
return new AbsoluteImageReference(contentNode, path, image.getImageID(), colorComponent,
- imageSize, getColor(channel), imageTransfomationFactories, imageLibrary);
+ imageSize, getColor(channel), imageTransfomationFactories, imageLibrary,
+ image.tryGetSingleChannelTransformationCode());
}
private static ChannelColorRGB getColor(ImgChannelDTO channel)
@@ -307,7 +314,7 @@ public class ImagingDatasetLoader extends HCSDatasetLoader implements IImagingDa
+ channelStackReference;
image = query.tryGetImage(channelId, channelStackId, datasetId);
}
- return checkAccessability("", "", image);
+ return checkAccessability("", "", null, image);
}
private static ImgImageZoomLevelDTO selectBestZoomLevel(ImgImageZoomLevelDTO current,
@@ -363,13 +370,15 @@ public class ImagingDatasetLoader extends HCSDatasetLoader implements IImagingDa
private PrefixedImage tryGetThumbnail(long channelId,
ImageChannelStackReference channelStackReference, long datasetId,
- RequestedImageSize imageSize)
+ RequestedImageSize imageSize, String singleChannelTransformationCodeOrNullOrNull)
{
HCSChannelStackByLocationReference hcsRef = channelStackReference.tryGetHCSChannelStack();
MicroscopyChannelStackByLocationReference micRef =
channelStackReference.tryGetMicroscopyChannelStack();
ImgImageDTO image;
- String[] pathPrefixAndSuffix = findPathPrefixAndSuffix(datasetId, imageSize);
+ String[] pathPrefixAndSuffix =
+ findPathPrefixAndSuffix(datasetId, channelId, imageSize,
+ singleChannelTransformationCodeOrNullOrNull);
if (hcsRef != null)
{
@@ -386,22 +395,61 @@ public class ImagingDatasetLoader extends HCSDatasetLoader implements IImagingDa
+ channelStackReference;
image = query.tryGetThumbnail(channelId, channelStackId, datasetId);
}
- return checkAccessability(pathPrefixAndSuffix[0], pathPrefixAndSuffix[1], image);
+ return checkAccessability(pathPrefixAndSuffix[0], pathPrefixAndSuffix[1],
+ pathPrefixAndSuffix[2], image);
}
- private String[] findPathPrefixAndSuffix(long datasetId, RequestedImageSize imageSize)
+ private String[] findPathPrefixAndSuffix(long datasetId, long channelId,
+ RequestedImageSize imageSize, String singleChannelTransformationCodeOrNull)
{
String[] ret = new String[]
- { "", "" };
+ { "", "", null };
ImgImageZoomLevelDTO bestZoomLevel = null;
List<ImgImageZoomLevelDTO> zoomLevels = query.listImageZoomLevels(datasetId);
if (zoomLevels != null && zoomLevels.size() > 0)
{
- for (ImgImageZoomLevelDTO zoomLevel : zoomLevels)
+ if (singleChannelTransformationCodeOrNull != null)
{
- if (false == zoomLevel.getIsOriginal())
+ List<ImgImageZoomLevelTransformationEnrichedDTO> zoomLevelTransformations =
+ query.findImageZoomLevelTransformations(datasetId, channelId,
+ singleChannelTransformationCodeOrNull);
+
+ if (false == zoomLevelTransformations.isEmpty())
+ {
+
+ Set<Long> zoomLevelsWithTransformedImages = new HashSet<Long>();
+ for (ImgImageZoomLevelTransformationEnrichedDTO zoomLevelTransformation : zoomLevelTransformations)
+ {
+ zoomLevelsWithTransformedImages.add(zoomLevelTransformation
+ .getImageZoomLevelId());
+ }
+
+ for (ImgImageZoomLevelDTO zoomLevel : zoomLevels)
+ {
+ if (false == zoomLevel.getIsOriginal()
+ && zoomLevelsWithTransformedImages.contains(zoomLevel.getId()))
+ {
+ bestZoomLevel =
+ selectBestZoomLevel(bestZoomLevel, zoomLevel, imageSize);
+ }
+ }
+ }
+
+ if (bestZoomLevel != null)
{
- bestZoomLevel = selectBestZoomLevel(bestZoomLevel, zoomLevel, imageSize);
+ ret[2] = singleChannelTransformationCodeOrNull;
+ }
+ }
+
+ if (bestZoomLevel == null)
+ {
+ zoomLevels = query.listImageZoomLevelsWithNoTransformations(datasetId);
+ for (ImgImageZoomLevelDTO zoomLevel : zoomLevels)
+ {
+ if (false == zoomLevel.getIsOriginal())
+ {
+ bestZoomLevel = selectBestZoomLevel(bestZoomLevel, zoomLevel, imageSize);
+ }
}
}
@@ -426,14 +474,14 @@ public class ImagingDatasetLoader extends HCSDatasetLoader implements IImagingDa
}
private PrefixedImage checkAccessability(String pathPrefix, String pathSuffix,
- ImgImageDTO imageOrNull)
+ String singleChannelTransformationCodeOrNull, ImgImageDTO imageOrNull)
{
if (imageOrNull == null)
{
return null;
}
return isFileAccessible(pathPrefix, pathSuffix, imageOrNull) ? new PrefixedImage(
- pathPrefix, pathSuffix, imageOrNull) : null;
+ pathPrefix, pathSuffix, singleChannelTransformationCodeOrNull, imageOrNull) : null;
}
private boolean isFileAccessible(String pathPrefix, String pathSuffix, ImgImageDTO image)
@@ -492,7 +540,7 @@ public class ImagingDatasetLoader extends HCSDatasetLoader implements IImagingDa
query.tryGetHCSRepresentativeImage(datasetId, wellLocationOrNull, channelId);
}
}
- return checkAccessability("", "", image);
+ return checkAccessability("", "", null, image);
}
@Override
@@ -508,7 +556,8 @@ public class ImagingDatasetLoader extends HCSDatasetLoader implements IImagingDa
{
AbsoluteImageReference image =
tryGetRepresentativeImage(channelCode,
- new Location(well.getColumn(), well.getRow()), originalOrThumbnail);
+ new Location(well.getColumn(), well.getRow()), originalOrThumbnail,
+ null);
if (image != null)
{
return image;
@@ -520,7 +569,8 @@ public class ImagingDatasetLoader extends HCSDatasetLoader implements IImagingDa
@Override
public AbsoluteImageReference tryGetRepresentativeImage(String channelCode,
- Location wellLocationOrNull, RequestedImageSize imageSize)
+ Location wellLocationOrNull, RequestedImageSize imageSize,
+ String singleChannelTransformationCodeOrNull)
{
ImgChannelDTO channel = tryLoadChannel(channelCode);
if (channel == null)
@@ -539,10 +589,13 @@ public class ImagingDatasetLoader extends HCSDatasetLoader implements IImagingDa
}
private PrefixedImage tryGetRepresentativeThumbnailImageDTO(long channelId,
- Location wellLocationOrNull, RequestedImageSize imageSize)
+ Location wellLocationOrNull, RequestedImageSize imageSize,
+ String singleChannelTransformationCodeOrNull)
{
long datasetId = getDataset().getId();
- String[] pathPrefixAndSuffix = findPathPrefixAndSuffix(datasetId, imageSize);
+ String[] pathPrefixAndSuffix =
+ findPathPrefixAndSuffix(datasetId, channelId, imageSize,
+ singleChannelTransformationCodeOrNull);
ImgImageDTO image;
if (wellLocationOrNull == null)
@@ -554,7 +607,8 @@ public class ImagingDatasetLoader extends HCSDatasetLoader implements IImagingDa
query.tryGetHCSRepresentativeThumbnail(dataset.getId(), wellLocationOrNull,
channelId);
}
- return checkAccessability(pathPrefixAndSuffix[0], pathPrefixAndSuffix[1], image);
+ return checkAccessability(pathPrefixAndSuffix[0], pathPrefixAndSuffix[1],
+ pathPrefixAndSuffix[2], image);
}
@Override
@@ -568,7 +622,7 @@ public class ImagingDatasetLoader extends HCSDatasetLoader implements IImagingDa
{
AbsoluteImageReference image =
tryGetRepresentativeThumbnail(channelCode, new Location(well.getColumn(),
- well.getRow()), null);
+ well.getRow()), null, null);
if (image != null)
{
return image;
@@ -580,7 +634,8 @@ public class ImagingDatasetLoader extends HCSDatasetLoader implements IImagingDa
@Override
public AbsoluteImageReference tryGetRepresentativeThumbnail(String channelCode,
- Location wellLocationOrNull, RequestedImageSize imageSize)
+ Location wellLocationOrNull, RequestedImageSize imageSize,
+ String singleChannelTransformationCodeOrNull)
{
ImgChannelDTO channel = tryLoadChannel(channelCode);
if (channel == null)
@@ -589,7 +644,7 @@ public class ImagingDatasetLoader extends HCSDatasetLoader implements IImagingDa
}
PrefixedImage imageDTO =
tryGetRepresentativeThumbnailImageDTO(channel.getId(), wellLocationOrNull,
- imageSize);
+ imageSize, singleChannelTransformationCodeOrNull);
if (imageDTO == null)
{
return null;
@@ -600,7 +655,8 @@ public class ImagingDatasetLoader extends HCSDatasetLoader implements IImagingDa
@Override
public AbsoluteImageReference tryGetThumbnail(String channelCode,
- ImageChannelStackReference channelStackReference, RequestedImageSize imageSize)
+ ImageChannelStackReference channelStackReference, RequestedImageSize imageSize,
+ String singleChannelTransformationCodeOrNull)
{
if (StringUtils.isBlank(channelCode))
{
@@ -616,7 +672,8 @@ public class ImagingDatasetLoader extends HCSDatasetLoader implements IImagingDa
long datasetId = getDataset().getId();
final PrefixedImage thumbnailDTO =
- tryGetThumbnail(channel.getId(), channelStackReference, datasetId, imageSize);
+ tryGetThumbnail(channel.getId(), channelStackReference, datasetId, imageSize,
+ singleChannelTransformationCodeOrNull);
if (thumbnailDTO == null)
{
return null;
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 a7e1177fb0e5b615d7b0056cda8a0ab4b88c266d..506391bd1bdbfdead2c6ede63e2346a477bbae9c 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
@@ -69,7 +69,7 @@ public class MergingImagesDownloadServlet extends AbstractImagesDownloadServlet
{
Size thumbnailSize = tryGetThumbnailSize(resolution);
return ImageChannelsUtils.getRepresentativeImageStream(datasetRoot, datasetCode, null,
- thumbnailSize);
+ thumbnailSize, null);
}
private static Size tryGetThumbnailSize(ImageResolutionKind resolution)
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 d52e984085ea23c8d066bd1b432d8e73484ba08f..f3b06d50201765ffd0e91e389f85fb65e7d2d599 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
@@ -81,17 +81,23 @@ public class ImageChannelsUtils
private final RequestedImageSize imageSizeLimit;
+ private final String singleChannelTransformationCodeOrNull;
+
@Private
- ImageChannelsUtils(IImagingLoaderStrategy imageLoaderStrategy, RequestedImageSize imageSizeLimit)
+ ImageChannelsUtils(IImagingLoaderStrategy imageLoaderStrategy,
+ RequestedImageSize imageSizeLimit, String singleChannelTransformationCodeOrNull)
{
this.imageLoaderStrategy = imageLoaderStrategy;
this.imageSizeLimit = imageSizeLimit;
+ this.singleChannelTransformationCodeOrNull = singleChannelTransformationCodeOrNull;
}
@Private
- ImageChannelsUtils(IImagingLoaderStrategy imageLoaderStrategy, Size imageSizeLimitOrNull)
+ ImageChannelsUtils(IImagingLoaderStrategy imageLoaderStrategy, Size imageSizeLimitOrNull,
+ String singleChannelTransformationCodeOrNull)
{
- this(imageLoaderStrategy, new RequestedImageSize(imageSizeLimitOrNull, false));
+ this(imageLoaderStrategy, new RequestedImageSize(imageSizeLimitOrNull, false),
+ singleChannelTransformationCodeOrNull);
}
/**
@@ -123,7 +129,8 @@ public class ImageChannelsUtils
// NOTE: never merges the overlays, draws each channel separately (merging looses
// transparency and is slower)
List<ImageWithReference> overlayImages =
- getSingleImagesSkipNonExisting(overlayChannels, overlaySize, contentProvider);
+ getSingleImagesSkipNonExisting(overlayChannels, overlaySize,
+ params.tryGetSingleChannelTransformationCode(), contentProvider);
for (ImageWithReference overlayImage : overlayImages)
{
if (image != null)
@@ -144,10 +151,12 @@ public class ImageChannelsUtils
private static List<ImageWithReference> getSingleImagesSkipNonExisting(
DatasetAcquiredImagesReference imagesReference, RequestedImageSize imageSize,
+ String singleChannelTransformationCodeOrNull,
IHierarchicalContentProvider contentProvider)
{
ImageChannelsUtils utils =
- createImageChannelsUtils(imagesReference, contentProvider, imageSize);
+ createImageChannelsUtils(imagesReference, contentProvider, imageSize,
+ singleChannelTransformationCodeOrNull);
boolean mergeAllChannels = utils.isMergeAllChannels(imagesReference);
List<AbsoluteImageReference> imageContents =
utils.fetchImageContents(imagesReference, mergeAllChannels, true);
@@ -197,7 +206,8 @@ public class ImageChannelsUtils
IHierarchicalContentProvider contentProvider, RequestedImageSize imageSizeLimit)
{
ImageChannelsUtils imageChannelsUtils =
- createImageChannelsUtils(imageChannels, contentProvider, imageSizeLimit);
+ createImageChannelsUtils(imageChannels, contentProvider, imageSizeLimit,
+ singleChannelTransformationCodeOrNull);
boolean useMergedChannelsTransformation =
imageChannelsUtils.isMergeAllChannels(imageChannels);
ImageTransformationParams transformationInfo =
@@ -209,12 +219,13 @@ public class ImageChannelsUtils
private static ImageChannelsUtils createImageChannelsUtils(
DatasetAcquiredImagesReference imageChannels,
- IHierarchicalContentProvider contentProvider, RequestedImageSize imageSizeLimit)
+ IHierarchicalContentProvider contentProvider, RequestedImageSize imageSizeLimit,
+ String singleChannelTransformationCodeOrNull)
{
IImagingDatasetLoader imageAccessor = createImageAccessor(imageChannels, contentProvider);
return new ImageChannelsUtils(
ImagingLoaderStrategyFactory.createImageLoaderStrategy(imageAccessor),
- imageSizeLimit);
+ imageSizeLimit, singleChannelTransformationCodeOrNull);
}
@Private
@@ -249,7 +260,7 @@ public class ImageChannelsUtils
imagesReference.getChannelStackReference();
AbsoluteImageReference image =
imageLoaderStrategy.tryGetImage(channelCode, channelStackReference,
- imageSizeLimit);
+ imageSizeLimit, singleChannelTransformationCodeOrNull);
if (image == null && skipNonExisting == false)
{
throw createImageNotFoundException(channelStackReference, channelCode);
@@ -288,13 +299,14 @@ public class ImageChannelsUtils
*/
public static ResponseContentStream getRepresentativeImageStream(
IHierarchicalContent dataSetRoot, String datasetCode, Location wellLocationOrNull,
- Size imageSizeLimitOrNull)
+ Size imageSizeLimitOrNull, String singleChannelTransformationCodeOrNull)
{
IImagingDatasetLoader imageAccessor = createDatasetLoader(dataSetRoot, datasetCode);
List<AbsoluteImageReference> imageReferences =
new ImageChannelsUtils(
ImagingLoaderStrategyFactory.createImageLoaderStrategy(imageAccessor),
- imageSizeLimitOrNull).getRepresentativeImageReferences(wellLocationOrNull);
+ imageSizeLimitOrNull, singleChannelTransformationCodeOrNull)
+ .getRepresentativeImageReferences(wellLocationOrNull);
BufferedImage image =
calculateBufferedImage(imageReferences, new ImageTransformationParams(true, true,
null));
@@ -354,7 +366,8 @@ public class ImageChannelsUtils
: chosenChannelCode);
ImageChannelsUtils imageChannelsUtils =
- new ImageChannelsUtils(imageLoaderStrategy, imageSizeLimitOrNull);
+ new ImageChannelsUtils(imageLoaderStrategy, imageSizeLimitOrNull,
+ singleChannelImageTransformationCodeOrNull);
boolean mergeAllChannels = imageChannelsUtils.isMergeAllChannels(imagesReference);
List<AbsoluteImageReference> imageContents =
imageChannelsUtils.fetchImageContents(imagesReference, mergeAllChannels, false);
@@ -429,7 +442,7 @@ public class ImageChannelsUtils
{
AbsoluteImageReference image =
imageLoaderStrategy.tryGetRepresentativeImage(channelCode, wellLocationOrNull,
- imageSizeLimit);
+ imageSizeLimit, singleChannelTransformationCodeOrNull);
if (image != null)
{
return image;
@@ -553,11 +566,13 @@ public class ImageChannelsUtils
{
return resultImage;
}
- IImageTransformerFactory channelLevelTransformationOrNull;
+ IImageTransformerFactory channelLevelTransformationOrNull = null;
if (transformationInfo.isUseMergedChannelsTransformation())
{
channelLevelTransformationOrNull = transfomations.tryGetForMerged();
- } else
+ } else if (transformationInfo.tryGetSingleChannelTransformationCode() != null
+ && (false == transformationInfo.tryGetSingleChannelTransformationCode().equals(
+ imageReference.tryGetSingleChannelTransformationCode())))
{
channelLevelTransformationOrNull =
transfomations.tryGetForChannel(transformationInfo
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 27e32e49eea12512a2b3bfdad451ed297fe492ce..47c456e23cb3017de9e772207c5b85545063f6af 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
@@ -414,11 +414,13 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
IImageDatasetIdentifier dataset)
{
ImageDatasetParameters params = imageAccessor.getImageParameters();
+
RequestedImageSize originalOrThumbnail = RequestedImageSize.createOriginal();
for (String channelCode : params.getChannelsCodes())
{
AbsoluteImageReference image =
- imageAccessor.tryGetRepresentativeImage(channelCode, null, originalOrThumbnail);
+ imageAccessor.tryGetRepresentativeImage(channelCode, null, originalOrThumbnail,
+ null);
if (image != null)
{
return image.getUnchangedImage();
@@ -434,7 +436,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
for (String channelCode : params.getChannelsCodes())
{
AbsoluteImageReference image =
- imageAccessor.tryGetRepresentativeThumbnail(channelCode, null, null);
+ imageAccessor.tryGetRepresentativeThumbnail(channelCode, null, null, null);
if (image != null)
{
return image.getUnchangedImage();
@@ -584,9 +586,11 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
{
return loadImages(sessionToken, imageReferences, null, null, convertToPng);
}
-
+
@Override
- public List<String> loadImagesBase64(String sessionToken, List<PlateImageReference> imageReferences, boolean convertToPng) {
+ public List<String> loadImagesBase64(String sessionToken,
+ List<PlateImageReference> imageReferences, boolean convertToPng)
+ {
InputStream stream = loadImages(sessionToken, imageReferences, convertToPng);
@@ -596,8 +600,10 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
List<String> result = new ArrayList<String>();
try
{
- for (byte[] bytes = extractNextImage(imagesWriter); bytes.length > 0; bytes = extractNextImage(imagesWriter)) {
- result.add(Base64.encodeBytes(bytes));
+ for (byte[] bytes = extractNextImage(imagesWriter); bytes.length > 0; bytes =
+ extractNextImage(imagesWriter))
+ {
+ result.add(Base64.encodeBytes(bytes));
}
} catch (IOException ex)
{
@@ -606,14 +612,13 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
return result;
}
-
- private byte[] extractNextImage(ConcatenatedFileOutputStreamWriter imagesWriter) throws IOException
+ private byte[] extractNextImage(ConcatenatedFileOutputStreamWriter imagesWriter)
+ throws IOException
{
ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
imagesWriter.writeNextBlock(outputStream);
return outputStream.toByteArray();
}
-
@Override
public InputStream loadImages(String sessionToken, List<PlateImageReference> imageReferences,
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/HCSImageResolutionLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/HCSImageResolutionLoader.java
index f3bde24dbd8e085f53785773b422bb6c5a3ce333..ecbece555df538306342d7cf78adcb20c27f1bed 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/HCSImageResolutionLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/HCSImageResolutionLoader.java
@@ -66,7 +66,8 @@ public class HCSImageResolutionLoader implements IImageResolutionLoader
@Override
public List<ImageResolution> getImageResolutions()
{
- List<ImgImageZoomLevelDTO> zoomLevels = query.listImageZoomLevels(dataset.getId());
+ List<ImgImageZoomLevelDTO> zoomLevels =
+ query.listImageZoomLevelsWithNoTransformations(dataset.getId());
if (zoomLevels == null || zoomLevels.isEmpty())
{
@@ -85,5 +86,4 @@ public class HCSImageResolutionLoader implements IImageResolutionLoader
return resolutions;
}
}
-
}
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 6d7a44b70920d5440245f2fa72410a1e55d48cb4..f6eec6d11ca3783ecb1aa3fe045e66c4d62f89a6 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
@@ -248,10 +248,19 @@ public interface IImagingReadonlyQueryDAO extends BaseQuery
@Select(sql = "select * from IMAGE_ZOOM_LEVELS zoom where zoom.CONTAINER_DATASET_ID = ?{1}", fetchSize = FETCH_SIZE)
public List<ImgImageZoomLevelDTO> listImageZoomLevels(long datasetId);
+ @Select(sql = "select * from IMAGE_ZOOM_LEVELS zoom where zoom.CONTAINER_DATASET_ID = ?{1} "
+ + "and ID not in (select ZOOM_LEVEL_ID from IMAGE_ZOOM_LEVEL_TRANSFORMATIONS)", fetchSize = FETCH_SIZE)
+ public List<ImgImageZoomLevelDTO> listImageZoomLevelsWithNoTransformations(long datasetId);
+
@Select(sql = SQL_ZOOM_LEVEL_TRANSFORMATIONS_ENRICHED + " and zl.container_dataset_id = ?{1}", fetchSize = FETCH_SIZE)
public List<ImgImageZoomLevelTransformationEnrichedDTO> listImageZoomLevelTransformations(
long datasetId);
+ @Select(sql = SQL_ZOOM_LEVEL_TRANSFORMATIONS_ENRICHED
+ + " and zl.container_dataset_id = ?{1} and izlt.channel_id = ?{2} and it.code = ?{3}", fetchSize = FETCH_SIZE)
+ public List<ImgImageZoomLevelTransformationEnrichedDTO> findImageZoomLevelTransformations(
+ long datasetId, long channelId, String transformationCode);
+
@Select(sql = "select * from IMAGE_ZOOM_LEVELS zoom where zoom.physical_dataset_perm_id = ?{1} and zoom.is_original")
public List<ImgImageZoomLevelDTO> listOriginalImageZoomLevelsByPermId(String datasetPermId);
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/ImageSizeFeedingMaintenanceTaskTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/ImageSizeFeedingMaintenanceTaskTest.java
index ee580e11d5050e3fb829820110689e141d6b1a70..17f415dcc4247b49dc5ef257616c3ea3f92b2123 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/ImageSizeFeedingMaintenanceTaskTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/ImageSizeFeedingMaintenanceTaskTest.java
@@ -42,23 +42,22 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgIm
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgImageZoomLevelDTO;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class ImageSizeFeedingMaintenanceTaskTest extends AssertJUnit
{
private static final long CONTAINER_ID = 42L;
-
+
private static final class MockAbsoluteImageReference extends AbsoluteImageReference
{
private final int width;
+
private final int height;
public MockAbsoluteImageReference(int width, int height)
{
super(null, null, null, null, new RequestedImageSize(null, false), null,
- new ImageTransfomationFactories(), null);
+ new ImageTransfomationFactories(), null, null);
this.width = width;
this.height = height;
}
@@ -73,18 +72,29 @@ public class ImageSizeFeedingMaintenanceTaskTest extends AssertJUnit
return new Size(width, height);
}
}
-
+
private BufferedAppender logRecorder;
+
private Mockery context;
+
private IImagingQueryDAO dao;
+
private IEncapsulatedOpenBISService service;
+
private IHierarchicalContentProvider contentProvider;
+
private ImageSizeFeedingMaintenanceTask maintenanceTask;
+
private IHierarchicalContent ds1Content;
+
private IHierarchicalContent ds2Content;
+
private IHierarchicalContent ds3Content;
+
private IImagingDatasetLoader imageLoader1;
+
private IImagingDatasetLoader imageLoader2;
+
private IImagingDatasetLoader imageLoader3;
@BeforeMethod
@@ -101,7 +111,8 @@ public class ImageSizeFeedingMaintenanceTaskTest extends AssertJUnit
imageLoader1 = context.mock(IImagingDatasetLoader.class, "ds1-loader");
imageLoader2 = context.mock(IImagingDatasetLoader.class, "ds2-loader");
imageLoader3 = context.mock(IImagingDatasetLoader.class, "ds3-loader");
- final Map<String, IImagingDatasetLoader> loaderMap = new HashMap<String, IImagingDatasetLoader>();
+ final Map<String, IImagingDatasetLoader> loaderMap =
+ new HashMap<String, IImagingDatasetLoader>();
loaderMap.put("ds1", imageLoader1);
loaderMap.put("ds2", imageLoader2);
loaderMap.put("ds3", imageLoader3);
@@ -121,14 +132,14 @@ public class ImageSizeFeedingMaintenanceTaskTest extends AssertJUnit
};
assertEquals(true, maintenanceTask.requiresDataStoreLock());
}
-
+
@AfterMethod
public void tearDown()
{
logRecorder.reset();
context.assertIsSatisfied();
}
-
+
@Test
public void testNonMatchingOrUnknownDataSets()
{
@@ -139,25 +150,25 @@ public class ImageSizeFeedingMaintenanceTaskTest extends AssertJUnit
{
one(service).listDataSets();
will(returnValue(Arrays.asList(ds0, ds1)));
-
+
one(contentProvider).asContent(ds1.getDataSetCode());
will(returnValue(ds1Content));
-
+
one(dao).tryGetImageDatasetByPermId(ds1.getDataSetCode());
will(returnValue(null));
-
+
one(ds1Content).close();
}
});
-
+
maintenanceTask.execute();
-
+
assertEquals("Scan 2 data sets.\n"
+ "0 original image sizes and 0 thumbnail image sizes are added to the database.",
logRecorder.getLogContent());
context.assertIsSatisfied();
}
-
+
@Test
public void testImageDataSets()
{
@@ -173,7 +184,8 @@ public class ImageSizeFeedingMaintenanceTaskTest extends AssertJUnit
will(returnValue(Arrays.asList(ds1, ds2, ds3)));
}
});
- prepareListZoomLevels(ds1, ds1Content, new ImgImageZoomLevelDTO("", true, "", 1, 2, null, null, 12));
+ prepareListZoomLevels(ds1, ds1Content, new ImgImageZoomLevelDTO("", true, "", 1, 2, null,
+ null, 12));
prepareListZoomLevels(ds2, ds2Content);
prepareForTryFindAnyOriginal(ds2, imageLoader2, new MockAbsoluteImageReference(144, 89));
prepareForAddZoomLevel(zoomLevelRecorder);
@@ -186,20 +198,21 @@ public class ImageSizeFeedingMaintenanceTaskTest extends AssertJUnit
prepareForCommit();
maintenanceTask.execute();
-
+
List<ImgImageZoomLevelDTO> zoomLevels = zoomLevelRecorder.getRecordedObjects();
assertEquals("Scan 3 data sets.\n" + "Original size 144x89 added for data set ds2\n"
+ "Thumbnail size 21x34 added for data set ds3\n"
+ "1 original image sizes and 1 thumbnail image sizes are added to the database.",
logRecorder.getLogContent());
- assertEquals("[ImgImageZoomLevelDTO{physicalDatasetPermId=ds2,isOriginal=true,"
- + "containerDatasetId=99715,rootPath=,width=144,height=89,colorDepth=<null>,fileType=<null>,id=0}, "
- + "ImgImageZoomLevelDTO{physicalDatasetPermId=ds3,isOriginal=false,"
- + "containerDatasetId=99716,rootPath=,width=21,height=34,colorDepth=<null>,fileType=<null>,id=0}]",
+ assertEquals(
+ "[ImgImageZoomLevelDTO{physicalDatasetPermId=ds2,isOriginal=true,"
+ + "containerDatasetId=99715,rootPath=,width=144,height=89,colorDepth=<null>,fileType=<null>,id=0}, "
+ + "ImgImageZoomLevelDTO{physicalDatasetPermId=ds3,isOriginal=false,"
+ + "containerDatasetId=99716,rootPath=,width=21,height=34,colorDepth=<null>,fileType=<null>,id=0}]",
zoomLevels.toString());
context.assertIsSatisfied();
}
-
+
@Test
public void testExceptionHandling()
{
@@ -222,22 +235,22 @@ public class ImageSizeFeedingMaintenanceTaskTest extends AssertJUnit
prepareForAddZoomLevel(zoomLevelRecorder);
prepareForTryFindAnyThumbnail(ds2, imageLoader2, new MockAbsoluteImageReference(-13, 0));
prepareForRollback();
-
+
maintenanceTask.execute();
-
+
List<ImgImageZoomLevelDTO> zoomLevels = zoomLevelRecorder.getRecordedObjects();
- assertEquals("Scan 2 data sets.\n" +
- "2 exceptions occured:\n" +
- "Data set ds1: java.lang.RuntimeException: Negative width: -1\n" +
- "Data set ds2: java.lang.RuntimeException: Negative width: -13\n" +
- "0 original image sizes and 0 thumbnail image sizes are added to the database.",
+ assertEquals("Scan 2 data sets.\n" + "2 exceptions occured:\n"
+ + "Data set ds1: java.lang.RuntimeException: Negative width: -1\n"
+ + "Data set ds2: java.lang.RuntimeException: Negative width: -13\n"
+ + "0 original image sizes and 0 thumbnail image sizes are added to the database.",
logRecorder.getLogContent());
- assertEquals("[ImgImageZoomLevelDTO{physicalDatasetPermId=ds2,isOriginal=true,"
- + "containerDatasetId=99715,rootPath=,width=1,height=2,colorDepth=<null>,fileType=<null>,id=0}]",
+ assertEquals(
+ "[ImgImageZoomLevelDTO{physicalDatasetPermId=ds2,isOriginal=true,"
+ + "containerDatasetId=99715,rootPath=,width=1,height=2,colorDepth=<null>,fileType=<null>,id=0}]",
zoomLevels.toString());
context.assertIsSatisfied();
}
-
+
private void prepareListZoomLevels(final SimpleDataSetInformationDTO dataSet,
final IHierarchicalContent content, final ImgImageZoomLevelDTO... zoomLevels)
{
@@ -256,8 +269,7 @@ public class ImageSizeFeedingMaintenanceTaskTest extends AssertJUnit
will(returnValue(imageDataSet));
one(dao).listImageZoomLevels(imageDataSet.getId());
- will(returnValue(Arrays
- .asList(zoomLevels)));
+ will(returnValue(Arrays.asList(zoomLevels)));
one(content).close();
}
@@ -276,7 +288,6 @@ public class ImageSizeFeedingMaintenanceTaskTest extends AssertJUnit
});
}
-
private void prepareForTryFindAnyThumbnail(final SimpleDataSetInformationDTO dataSet,
final IImagingDatasetLoader loader, final AbsoluteImageReference thumbnailOrNull)
{
@@ -288,7 +299,7 @@ public class ImageSizeFeedingMaintenanceTaskTest extends AssertJUnit
}
});
}
-
+
private void prepareForAddZoomLevel(
final RecordingMatcher<ImgImageZoomLevelDTO> zoomLevelRecorder)
{
@@ -309,17 +320,17 @@ public class ImageSizeFeedingMaintenanceTaskTest extends AssertJUnit
}
});
}
-
+
private void prepareForRollback()
{
context.checking(new Expectations()
- {
{
- one(dao).rollback();
- }
- });
+ {
+ one(dao).rollback();
+ }
+ });
}
-
+
private SimpleDataSetInformationDTO dataSet(String code, String type)
{
SimpleDataSetInformationDTO dataSet = new SimpleDataSetInformationDTO();
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtilsTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtilsTest.java
index 7549757e7620a59ace41bf36ed5b4ae602d17d70..5c5eac15af02071fb4094e41af7380cbfe66efb3 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtilsTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtilsTest.java
@@ -53,8 +53,8 @@ import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.ImageTransformatio
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.RequestedImageSize;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtilTest;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.InternalImageChannel;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageDatasetParameters;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.InternalImageChannel;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.InternalImageTransformationInfo;
/**
@@ -180,8 +180,8 @@ public class ImageChannelsUtilsTest extends AssertJUnit
{
allowing(loader).getImageParameters();
ImageDatasetParameters imgParams = new ImageDatasetParameters();
- imgParams.setInternalChannels(Arrays.asList(new InternalImageChannel(CHANNEL, CHANNEL, null,
- null, new ArrayList<InternalImageTransformationInfo>())));
+ imgParams.setInternalChannels(Arrays.asList(new InternalImageChannel(CHANNEL,
+ CHANNEL, null, null, new ArrayList<InternalImageTransformationInfo>())));
will(returnValue(imgParams));
RequestedImageSize requestedSize =
@@ -189,7 +189,7 @@ public class ImageChannelsUtilsTest extends AssertJUnit
.createOriginal() : absoluteImageReferenceOrNull
.getRequestedSize();
one(loader).tryGetImage(imageRef.getChannelCodes(null).get(0),
- imageRef.getChannelStackReference(), requestedSize);
+ imageRef.getChannelStackReference(), requestedSize, null);
will(returnValue(absoluteImageReferenceOrNull));
}
});
@@ -247,14 +247,14 @@ public class ImageChannelsUtilsTest extends AssertJUnit
RequestedImageSize imageSize)
{
return new AbsoluteImageReference(image(fileName), "id42", null, null, imageSize,
- new ChannelColorRGB(0, 0, 255), new ImageTransfomationFactories(), null);
+ new ChannelColorRGB(0, 0, 255), new ImageTransfomationFactories(), null, null);
}
private ImageChannelsUtils createImageChannelsUtils(Size thumbnailSizeOrNull)
{
return new ImageChannelsUtils(
ImagingLoaderStrategyFactory.createImageLoaderStrategy(loader),
- new RequestedImageSize(thumbnailSizeOrNull, false));
+ new RequestedImageSize(thumbnailSizeOrNull, false), null);
}
public void assertPNG(IHierarchicalContentNode image)
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 071f8b119872e9dc52e356bc62d96bb33310bff4..23ef9d1d9a69ae595751a12a79e3e4bc1dd1d28d 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
@@ -279,8 +279,8 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
{ 1, 2 };
String[][] featureCodesPerDataset = new String[][]
{
- { "f1", "f2" },
- { "f2", "f3" } };
+ { "f1", "f2" },
+ { "f2", "f3" } };
prepareListAnalysisDatasets(dataSetIDs);
prepareGetFeatureDefinitions(dataSetIDs, featureCodesPerDataset);
@@ -304,16 +304,16 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
FeatureInformation[][] featureCodesPerDataset =
new FeatureInformation[][]
{
- {
- new FeatureInformation("f1", "Feature 1",
- "The first feature."),
- new FeatureInformation("f2", "Feature 2",
- "The second feature.") },
- {
- new FeatureInformation("f2", "Feature 2",
- "The second feature."),
- new FeatureInformation("f3", "Feature 3",
- "The third feature.") } };
+ {
+ new FeatureInformation("f1", "Feature 1",
+ "The first feature."),
+ new FeatureInformation("f2", "Feature 2",
+ "The second feature.") },
+ {
+ new FeatureInformation("f2", "Feature 2",
+ "The second feature."),
+ new FeatureInformation("f3", "Feature 3",
+ "The third feature.") } };
prepareListAnalysisDatasets(dataSetIDs);
prepareGetFeatureDefinitions(dataSetIDs, featureCodesPerDataset);
@@ -339,12 +339,12 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
FeatureVectorDatasetReference r2 = createFeatureVectorDatasetReference(DATASET_CODE2);
String[][] featureCodesPerDataset = new String[][]
{
- { "F1", "F2" } };
+ { "F1", "F2" } };
prepareLoadFeatures(new long[]
{ 1 }, featureCodesPerDataset);
featureCodesPerDataset = new String[][]
{
- { "F2" } };
+ { "F2" } };
prepareLoadFeatures(new long[]
{ 2 }, featureCodesPerDataset);
@@ -393,17 +393,17 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
one(imageLoader).tryGetImage(
channel,
ImageChannelStackReference.createHCSFromLocations(new Location(3, 1),
- new Location(1, 1)), thumbnailSize);
+ new Location(1, 1)), thumbnailSize, null);
will(returnValue(new AbsoluteImageReference(image("img1.jpg"), "img1", null,
null, thumbnailSize, createBlueColor(),
- new ImageTransfomationFactories(), null)));
+ new ImageTransfomationFactories(), null, null)));
one(imageLoader).tryGetImage(
channel,
ImageChannelStackReference.createHCSFromLocations(new Location(3, 1),
- new Location(2, 1)), thumbnailSize);
+ new Location(2, 1)), thumbnailSize, null);
will(returnValue(new AbsoluteImageReference(image("img1.gif"), "img1", null,
null, thumbnailSize, createBlueColor(),
- new ImageTransfomationFactories(), null)));
+ new ImageTransfomationFactories(), null, null)));
}
});
@@ -538,18 +538,18 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
one(imageLoader).tryGetImage(
CHANNEL_CODE,
ImageChannelStackReference.createHCSFromLocations(new Location(1, 1),
- new Location(1, 1)), thumbnailSize);
+ new Location(1, 1)), thumbnailSize, null);
will(returnValue(new AbsoluteImageReference(image("img1.jpg"), "img1", null,
null, thumbnailSize, createBlueColor(),
- new ImageTransfomationFactories(), null)));
+ new ImageTransfomationFactories(), null, null)));
one(imageLoader).tryGetImage(
CHANNEL_CODE,
ImageChannelStackReference.createHCSFromLocations(new Location(2, 1),
- new Location(2, 1)), thumbnailSize);
+ new Location(2, 1)), thumbnailSize, null);
will(returnValue(new AbsoluteImageReference(image("img1.png"), "img1", null,
null, thumbnailSize, createBlueColor(),
- new ImageTransfomationFactories(), null)));
+ new ImageTransfomationFactories(), null, null)));
}
});
@@ -826,8 +826,8 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
new PlateFeatureValues(NativeTaggedArray
.toByteArray(new MDFloatArray(new float[][]
{
- { 3.5f * dataSetId + offset },
- { 1.25f * dataSetId + offset } })));
+ { 3.5f * dataSetId + offset },
+ { 1.25f * dataSetId + offset } })));
ImgFeatureValuesDTO value =
new ImgFeatureValuesDTO(0.0, 0.0, matrixValues, 0L);
value.setFeatureDefId(featureDefIds[featureDefIx]);