diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ImageUtil.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ImageUtil.java
index d8f2b1673ddb069a7e65e387f3455b0a7b45fa59..f85b8fbdedc1577e081efd92c57976a7161bfa84 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ImageUtil.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ImageUtil.java
@@ -191,13 +191,15 @@ public class ImageUtil
/**
* Loads the specified <var>page</var> from the image from the tiven </var>inputStream</var>.
* Supported images formats are GIF, JPG, PNG, and TIFF. The input stream will be closed after
- * loading. Note that only for TIFF files a <var>page</var> other than 0 may be specified.
+ * loading. Note that only for TIFF files a <var>page</var> other than 0 (or null which is
+ * equivalent) may be specified.
*
* @throws IllegalArgumentException if the input stream doesn't start with a magic number
* identifying supported image format.
*/
- public static BufferedImage loadImage(IContent content, int page)
+ public static BufferedImage loadImage(IContent content, Integer pageOrNull)
{
+ int page = pageOrNull == null ? 0 : pageOrNull.intValue();
InputStream markSupportingInputStream = content.getInputStream();
if (markSupportingInputStream.markSupported() == false)
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageDatasetLoaderFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageDatasetLoaderFactory.java
index 25b21d981f3c5335bfc0e8ada0ab66f2f91f20b8..a907afba38de28cccd5e725b87f0f5141f14963e 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageDatasetLoaderFactory.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageDatasetLoaderFactory.java
@@ -31,6 +31,13 @@ public class HCSImageDatasetLoaderFactory
private static final Map<String, IContentRepositoryFactory> repositoryFactories =
createFactories();
+ /** the loader has to be closed when it is not used any more to free database resources! */
+ public static final IImagingDatasetLoader create(File datasetRootDir, String datasetCode)
+ {
+ IContentRepository repository = createContentRepository(datasetRootDir);
+ return new ImagingDatasetLoader(DssScreeningUtils.getQuery(), datasetCode, repository);
+ }
+
private static Map<String, IContentRepositoryFactory> createFactories()
{
Map<String, IContentRepositoryFactory> factories =
@@ -39,16 +46,9 @@ public class HCSImageDatasetLoaderFactory
return factories;
}
- /** the loader has to be closed when it is not used any more to free database resources! */
- public static final IImagingDatasetLoader create(File datasetRootDir, String datasetCode)
- {
- return createImageDBLoader(datasetRootDir, datasetCode);
- }
-
- private static ImagingDatasetLoader createImageDBLoader(File datasetRootDir, String datasetCode)
+ public static IContentRepository createContentRepository(File datasetRootDir)
{
- IContentRepository repository = new ContentRepository(datasetRootDir, repositoryFactories);
- return new ImagingDatasetLoader(DssScreeningUtils.getQuery(), datasetCode, repository);
+ return new ContentRepository(datasetRootDir, repositoryFactories);
}
}
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 d27f9e8f21da655ebe7b9d5b76062dcef7c6f05c..2eeb96d4361310a0034fe8a47f82bc5dd291f12c 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 "009"; // changed in S96
+ return "010"; // changed in S102
}
}
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 4348e6bfb240f222da0de87272e88af4e43b8a5d..54268f601a0f8872d7cf39a45e82be92fd950218 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
@@ -470,13 +470,7 @@ public class ImageChannelsUtils
private static BufferedImage loadImage(AbsoluteImageReference imageReference)
{
- IContent content = imageReference.getContent();
-
- // extracts the correct page if necessary
- int page = (imageReference.tryGetPage() != null) ? imageReference.tryGetPage() : 0;
-
- BufferedImage image = ImageUtil.loadImage(content, page);
- return image;
+ return ImageUtil.loadImage(imageReference.getContent(), imageReference.tryGetPage());
}
/**
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 ee825310f453748da5ec15663e99dfcf35d83b24..bb7d43982d7e0a13a46bc5e049920a04dceb06c4 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
@@ -120,9 +120,8 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
public DssServiceRpcScreening(String storeRootDir)
{
- this(storeRootDir, null, QueryTool.getQuery(ServiceProvider.getDataSourceProvider()
- .getDataSource(ScreeningConstants.IMAGING_DATA_SOURCE),
- IImagingTransformerDAO.class), ServiceProvider.getOpenBISService(), null, true);
+ this(storeRootDir, null, DssScreeningUtils.createImagingTransformerDAO(), ServiceProvider
+ .getOpenBISService(), null, true);
}
DssServiceRpcScreening(String storeRootDir, IImagingReadonlyQueryDAO dao,
@@ -218,8 +217,8 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
{
final IImagingDatasetLoader imageAccessor =
createImageLoader(dataset.getDatasetCode(), datasetRoot);
- final Size imageSize = getImageSize(dataset, imageAccessor);
- final Size thumbnailSize = getThumbnailImageSize(dataset, imageAccessor);
+ final Size imageSize = getImageSize(dataset, imageAccessor, false);
+ final Size thumbnailSize = getImageSize(dataset, imageAccessor, true);
final ImageDatasetParameters params = imageAccessor.getImageParameters();
return new ImageDatasetMetadata(dataset, params.getChannelsCodes(),
params.getChannelsLabels(), params.getTileRowsNum(), params.getTileColsNum(),
@@ -228,96 +227,73 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
}
private static Size getImageSize(IImageDatasetIdentifier dataset,
- IImagingDatasetLoader imageAccessor)
+ IImagingDatasetLoader imageAccessor, boolean thumbnailsRequired)
{
- IContent imageFile = getAnyImagePath(imageAccessor, dataset);
+ IContent imageFile = getAnyImagePath(imageAccessor, dataset, thumbnailsRequired);
BufferedImage image = ImageUtil.loadImage(imageFile);
Size imageSize = new Size(image.getWidth(), image.getHeight());
return imageSize;
}
- /**
- * Returns the size of the thumbnails, or {@link NULL_SIZE}.
- */
- private static Size getThumbnailImageSize(IImageDatasetIdentifier dataset,
- IImagingDatasetLoader imageAccessor)
+ private static IContent getAnyImagePath(IImagingDatasetLoader imageAccessor,
+ IImageDatasetIdentifier dataset, boolean thumbnailsRequired)
{
- IContent imageFile = tryGetAnyThumbnailImagePath(imageAccessor, dataset);
- if (imageFile == null)
+ if (imageAccessor.getImageParameters().tryGetRowsNum() == null)
{
- return NULL_SIZE;
+ return getAnyMicroscopyImagePath(imageAccessor, dataset, thumbnailsRequired);
+ } else
+ {
+ return getAnyHCSImagePath(imageAccessor, dataset, thumbnailsRequired);
}
- final BufferedImage image = ImageUtil.loadImage(imageFile);
- final Size imageSize = new Size(image.getWidth(), image.getHeight());
- return imageSize;
}
- // TODO 2010-12-09, Tomasz Pylak: replace this code by choosing the dataset representative
- // Now it works only in HCS case.
- private static IContent getAnyImagePath(IImagingDatasetLoader imageAccessor,
- IImageDatasetIdentifier dataset)
+ private static IContent getAnyMicroscopyImagePath(IImagingDatasetLoader imageAccessor,
+ IImageDatasetIdentifier dataset, boolean thumbnailsRequired)
{
ImageDatasetParameters params = imageAccessor.getImageParameters();
- for (int row = 1; row <= params.tryGetRowsNum(); row++)
+ RequestedImageSize originalOrThumbnail = createOriginalOrThumbnail(thumbnailsRequired);
+ for (String channelCode : params.getChannelsCodes())
{
- for (int col = 1; col <= params.tryGetColsNum(); col++)
+ AbsoluteImageReference image =
+ imageAccessor.tryGetRepresentativeImage(channelCode, null, originalOrThumbnail);
+ if (image != null)
{
- for (int tileRow = 1; tileRow <= params.getTileRowsNum(); tileRow++)
- {
- for (int tileCol = 1; tileCol <= params.getTileColsNum(); tileCol++)
- {
- for (String channelCode : params.getChannelsCodes())
- {
- ImageChannelStackReference channelStackReference =
- ImageChannelStackReference.createHCSFromLocations(new Location(
- col, row), Location.createLocationFromRowAndColumn(
- tileRow, tileCol));
- AbsoluteImageReference image =
- imageAccessor.tryGetImage(channelCode, channelStackReference,
- RequestedImageSize.createOriginal());
- if (image != null)
- {
- return image.getContent();
- }
- }
- }
- }
+ return image.getContent();
}
}
throw new IllegalStateException("Cannot find any image in a dataset: " + dataset);
}
- // TODO 2010-12-09, Tomasz Pylak: replace this code by choosing the dataset representative
- // Now it works only in HCS case.
- private static IContent tryGetAnyThumbnailImagePath(IImagingDatasetLoader imageAccessor,
- IImageDatasetIdentifier dataset)
+ private static RequestedImageSize createOriginalOrThumbnail(boolean thumbnailsRequired)
+ {
+ // 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();
+ }
+
+ private static IContent getAnyHCSImagePath(IImagingDatasetLoader imageAccessor,
+ IImageDatasetIdentifier dataset, boolean thumbnailsRequired)
{
ImageDatasetParameters params = imageAccessor.getImageParameters();
+ RequestedImageSize originalOrThumbnail = createOriginalOrThumbnail(thumbnailsRequired);
for (int row = 1; row <= params.tryGetRowsNum(); row++)
{
for (int col = 1; col <= params.tryGetColsNum(); col++)
{
- for (int tileRow = 1; tileRow <= params.getTileRowsNum(); tileRow++)
+ for (String channelCode : params.getChannelsCodes())
{
- for (int tileCol = 1; tileCol <= params.getTileColsNum(); tileCol++)
+ AbsoluteImageReference image =
+ imageAccessor.tryGetRepresentativeImage(channelCode, new Location(col,
+ row), originalOrThumbnail);
+ if (image != null)
{
- for (String channelCode : params.getChannelsCodes())
- {
- ImageChannelStackReference channelStackReference =
- ImageChannelStackReference.createHCSFromLocations(new Location(
- col, row), Location.createLocationFromRowAndColumn(
- tileRow, tileCol));
- final IContent image =
- imageAccessor.tryGetThumbnail(channelCode,
- channelStackReference);
- // Either all images have a thumbnail or none has one.
- return image;
- }
+ return image.getContent();
}
}
}
}
- return null;
+ throw new IllegalStateException("Cannot find any image in a dataset: " + dataset);
}
public List<FeatureVectorDataset> loadFeatures(String sessionToken,
@@ -786,7 +762,8 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
{
if (isMergedChannel(channel))
{
- return getDAO().tryGetExperimentByPermId(experimentPermID).tryGetImageTransformerFactory();
+ return getDAO().tryGetExperimentByPermId(experimentPermID)
+ .tryGetImageTransformerFactory();
} else
{
return getDAO().tryGetChannelForExperimentPermId(experimentPermID, channel)
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 3eae016990a9e80953b8adb21da3edf07b5d9081..20e40fac3e176e2c354f02a7a813abc1db403637 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
@@ -23,6 +23,7 @@ import net.lemnik.eodsql.QueryTool;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingReadonlyQueryDAO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingTransformerDAO;
/**
* Utility methods for DSS.
@@ -32,7 +33,10 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImag
public class DssScreeningUtils
{
private static final IImagingReadonlyQueryDAO query = createQuery();
-
+
+ /**
+ * Returned query is reused and should NOT be closed.
+ */
public static IImagingReadonlyQueryDAO getQuery()
{
return query;
@@ -52,4 +56,17 @@ public class DssScreeningUtils
ScreeningConstants.IMAGING_DATA_SOURCE);
return QueryTool.getQuery(dataSource, IImagingReadonlyQueryDAO.class);
}
+
+ /**
+ * Creates a new query each time when it is called. Returned query should be closed after all
+ * operations are done.
+ */
+ public static IImagingTransformerDAO createImagingTransformerDAO()
+ {
+ DataSource dataSource =
+ ServiceProvider.getDataSourceProvider().getDataSource(
+ ScreeningConstants.IMAGING_DATA_SOURCE);
+ return QueryTool.getQuery(dataSource, IImagingTransformerDAO.class);
+ }
+
}
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
index b1aa0de40a2d7579f58e2b6c05b3d3aa4bb60234..57253aea57ee33f622af4b9503a1ab7c4e72fc4a 100644
--- 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
@@ -22,18 +22,18 @@ 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 static final class Color
{
private int red;
+
private int green;
+
private int blue;
Color(int rgb)
@@ -42,26 +42,43 @@ public class ExampleImageTransformerFactory implements IImageTransformerFactory
green = (rgb >> 8) & 0xff;
blue = rgb & 0xff;
}
-
+
int getColor(char colorSymbol)
{
switch (colorSymbol)
{
- case 'r': return red;
- case 'g': return green;
- case 'b': return blue;
- default: return 0;
+ case 'r':
+ return red;
+ case 'g':
+ return green;
+ case 'b':
+ return blue;
+ default:
+ return 0;
}
}
}
-
+
private final String colorPattern;
-
+
+ private final int brightnessDelta;
+
public ExampleImageTransformerFactory(String colorPattern)
+ {
+ this(colorPattern, 0);
+ }
+
+ public ExampleImageTransformerFactory(int brightnessDelta)
+ {
+ this("rgb", brightnessDelta);
+ }
+
+ public ExampleImageTransformerFactory(String colorPattern, int brightnessDelta)
{
this.colorPattern = colorPattern;
+ this.brightnessDelta = brightnessDelta;
}
-
+
public IImageTransformer createTransformer()
{
return new IImageTransformer()
@@ -70,26 +87,29 @@ public class ExampleImageTransformerFactory implements IImageTransformerFactory
{
int width = input.getWidth();
int height = input.getHeight();
- BufferedImage output = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
+ 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);
Color color = new Color(rgb);
- output.setRGB(
- x,
- y,
- (color.getColor(colorPattern.charAt(0)) << 16)
- + (color.getColor(colorPattern.charAt(1)) << 8)
- + color.getColor(colorPattern.charAt(2)));
+ output.setRGB(x, y,
+ (calcNewColor(color, 0) << 16) + (calcNewColor(color, 1) << 8)
+ + calcNewColor(color, 2));
}
}
return output;
}
+
+ private int calcNewColor(Color color, int colorIndex)
+ {
+ return color.getColor(colorPattern.charAt(colorIndex)) + brightnessDelta;
+ }
};
}
-
+
@Override
public String toString()
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/plugin/.gitignore b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/plugin/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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 b7b54fcb18c167147f1d7c32f2263b497025fb81..8e33b48e0187952cfac862318de230ca7fb53624 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
@@ -36,7 +36,8 @@ public interface IImagingReadonlyQueryDAO extends BaseQuery
public static final int FETCH_SIZE = 1000;
public static final String SQL_HCS_IMAGE =
- "select i.* from CHANNEL_STACKS, SPOTS, ACQUIRED_IMAGES, IMAGES as i "
+ "select i.*, ACQUIRED_IMAGES.image_transformer_factory as image_transformer_factory "
+ + "from CHANNEL_STACKS, SPOTS, ACQUIRED_IMAGES, IMAGES as i "
+ "where "
+ "ACQUIRED_IMAGES.CHANNEL_ID = ?{1} and CHANNEL_STACKS.DS_ID = ?{2} and "
+ "CHANNEL_STACKS.x = ?{3.x} and CHANNEL_STACKS.y = ?{3.y} and "
@@ -46,7 +47,8 @@ public interface IImagingReadonlyQueryDAO extends BaseQuery
+ "CHANNEL_STACKS.SPOT_ID = SPOTS.ID ";
public static final String SQL_MICROSCOPY_IMAGE =
- "select i.* from CHANNEL_STACKS, ACQUIRED_IMAGES, IMAGES as i "
+ "select i.*, ACQUIRED_IMAGES.image_transformer_factory as image_transformer_factory "
+ + "from CHANNEL_STACKS, ACQUIRED_IMAGES, IMAGES as i "
+ "where "
+ "ACQUIRED_IMAGES.CHANNEL_ID = ?{1} and CHANNEL_STACKS.DS_ID = ?{2} and "
+ "CHANNEL_STACKS.x = ?{3.x} and CHANNEL_STACKS.y = ?{3.y} and "
@@ -55,7 +57,8 @@ public interface IImagingReadonlyQueryDAO extends BaseQuery
+ "ACQUIRED_IMAGES.CHANNEL_STACK_ID = CHANNEL_STACKS.ID ";
public static final String SQL_HCS_IMAGE_REPRESENTATIVE =
- "select i.* from CHANNEL_STACKS, SPOTS, ACQUIRED_IMAGES, IMAGES as i "
+ "select i.*, ACQUIRED_IMAGES.image_transformer_factory as image_transformer_factory "
+ + "from CHANNEL_STACKS, SPOTS, ACQUIRED_IMAGES, IMAGES as i "
+ "where "
+ "CHANNEL_STACKS.is_representative = 'T' and "
+ "CHANNEL_STACKS.DS_ID = ?{1} and "
@@ -66,7 +69,8 @@ public interface IImagingReadonlyQueryDAO extends BaseQuery
+ "CHANNEL_STACKS.SPOT_ID = SPOTS.ID ";
public static final String SQL_MICROSCOPY_IMAGE_REPRESENTATIVE =
- "select i.* from CHANNEL_STACKS, ACQUIRED_IMAGES, IMAGES as i "
+ "select i.*, ACQUIRED_IMAGES.image_transformer_factory as image_transformer_factory "
+ + "from CHANNEL_STACKS, ACQUIRED_IMAGES, IMAGES as i "
+ "where "
+ "CHANNEL_STACKS.is_representative = 'T' and "
+ "CHANNEL_STACKS.DS_ID = ?{1} and "
@@ -117,6 +121,21 @@ public interface IImagingReadonlyQueryDAO extends BaseQuery
public ImgImageDTO tryGetHCSRepresentativeThumbnail(long datasetId, Location wellLocation,
long channelId);
+ /**
+ * @return all images of a given dataset and channel, every image is enriched with the
+ * information about the spot to which it belongs.
+ */
+ @Select("select i.*, ai.image_transformer_factory as image_transformer_factory, "
+ +"s.id as spot_id, ai.id as acquired_image_id "
+ + " from data_sets d "
+ + " join channel_stacks cs on cs.ds_id = d.id "
+ + " join spots s on cs.spot_id = s.id "
+ + " join acquired_images ai on ai.channel_stack_id = cs.id "
+ + " join channels ch on ai.channel_id = ch.id "
+ + " join images i on i.id = ai.img_id "
+ + " where d.perm_id = ?{1} and ch.code = upper(?{2}) and s.id is NOT NULL")
+ public List<ImgImageEnrichedDTO> listHCSImages(String datasetPermId, String channelCode);
+
// ---------------- Microscopy ---------------------------------
/**
@@ -168,7 +187,8 @@ public interface IImagingReadonlyQueryDAO extends BaseQuery
// ---------------- Generic ---------------------------------
/** @return an image for the specified channel and channel stack or null */
- @Select("select i.* from IMAGES as i "
+ @Select("select i.*, ACQUIRED_IMAGES.image_transformer_factory as image_transformer_factory "
+ + "from IMAGES as i "
+ "join ACQUIRED_IMAGES on ACQUIRED_IMAGES.IMG_ID = i.ID "
+ "join CHANNEL_STACKS on ACQUIRED_IMAGES.CHANNEL_STACK_ID = CHANNEL_STACKS.ID "
+ "where "
@@ -179,7 +199,8 @@ public interface IImagingReadonlyQueryDAO extends BaseQuery
public ImgImageDTO tryGetImage(long channelId, Long channelStackId, long datasetId);
/** @return a thumbnail for the specified chanel and channel stack or null */
- @Select("select i.* from IMAGES as i "
+ @Select("select i.*, ACQUIRED_IMAGES.image_transformer_factory as image_transformer_factory "
+ + "from IMAGES as i "
+ "join ACQUIRED_IMAGES on ACQUIRED_IMAGES.THUMBNAIL_ID = i.ID "
+ "join CHANNEL_STACKS on ACQUIRED_IMAGES.CHANNEL_STACK_ID = CHANNEL_STACKS.ID "
+ "where "
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
index f08a89140afb2167a9ee472cd45558577ac3a4aa..c9c45d9061666f7b934565fa8b501bb3c489789f 100644
--- 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
@@ -36,9 +36,10 @@ public interface IImagingTransformerDAO extends TransactionQuery
{ TransformerFactoryMapper.class, TypeMapper.class /* default */})
public void saveTransformerFactoryForDataset(long datasetId, IImageTransformerFactory factory);
- @Update(sql = "update images set image_transformer_factory = ?{2} where id = ?{1}", parameterBindings =
+ @Update(sql = "update acquired_images set image_transformer_factory = ?{2} where id = ?{1}", parameterBindings =
{ TransformerFactoryMapper.class, TypeMapper.class /* default */})
- public void saveTransformerFactoryForImage(long imageId, IImageTransformerFactory factory);
+ public void saveTransformerFactoryForImage(long acquiredImageId,
+ IImageTransformerFactory factory);
@Update(sql = "update channels set image_transformer_factory = ?{3} "
+ "where code = ?{2} and exp_id = ?{1}", parameterBindings =
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgImageDTO.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgImageDTO.java
index b3ccb8a864939d6876adee4b3734121a8a6a083f..631b59795552e9f4139732f9e5243c63f9398819 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgImageDTO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgImageDTO.java
@@ -34,9 +34,8 @@ public class ImgImageDTO extends AbstractImageTransformerFactoryHolder
@ResultColumn("COLOR")
private String colorComponentOrNull;
-
- @SuppressWarnings("unused")
- private ImgImageDTO()
+
+ protected ImgImageDTO()
{
// All Data-Object classes must have a default constructor.
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgImageEnrichedDTO.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgImageEnrichedDTO.java
new file mode 100644
index 0000000000000000000000000000000000000000..4c9c20d7415ac2c32816790ebe88608750cbdc8b
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgImageEnrichedDTO.java
@@ -0,0 +1,57 @@
+/*
+ * Copyright 2011 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.ResultColumn;
+
+/**
+ * HCS image with additional information about the spot and acquired image id.
+ *
+ * @author Tomasz Pylak
+ */
+public class ImgImageEnrichedDTO extends ImgImageDTO
+{
+ @ResultColumn("spot_id")
+ private long spotId;
+
+ @ResultColumn("acquired_image_id")
+ private long acquiredImageId;
+
+ @SuppressWarnings("unused")
+ private ImgImageEnrichedDTO()
+ {
+ // All Data-Object classes must have a default constructor.
+ super();
+ }
+
+ public ImgImageEnrichedDTO(long id, String filePath, Integer pageOrNull,
+ ColorComponent colorComponentOrNull)
+ {
+ super(id, filePath, pageOrNull, colorComponentOrNull);
+ }
+
+ public long getSpotId()
+ {
+ return spotId;
+ }
+
+ public long getAcquiredImageId()
+ {
+ return acquiredImageId;
+ }
+
+}
diff --git a/screening/source/sql/postgresql/010/schema-010.sql b/screening/source/sql/postgresql/010/schema-010.sql
index 681a48e7475b37745e2c199da0d840ea246cb176..d8cf0ea92b11a5dce9049cb6b03c1275b207b23f 100644
--- a/screening/source/sql/postgresql/010/schema-010.sql
+++ b/screening/source/sql/postgresql/010/schema-010.sql
@@ -139,7 +139,6 @@ CREATE TABLE IMAGES (
PATH FILE_PATH NOT NULL,
PAGE INTEGER,
COLOR COLOR_COMPONENT,
- IMAGE_TRANSFORMER_FACTORY BYTEA,
PRIMARY KEY (ID)
);
@@ -149,6 +148,7 @@ CREATE TABLE ACQUIRED_IMAGES (
IMG_ID TECH_ID NOT NULL,
THUMBNAIL_ID TECH_ID,
+ IMAGE_TRANSFORMER_FACTORY BYTEA,
CHANNEL_STACK_ID TECH_ID NOT NULL,
CHANNEL_ID TECH_ID NOT NULL,
diff --git a/screening/source/sql/postgresql/migration/migration-009-010.sql b/screening/source/sql/postgresql/migration/migration-009-010.sql
index db3cf424f7c9734a1cbd670781f515b4eb433799..d182ca8cbc82a1dcdbb4268b9e2d864ab9e920fe 100644
--- a/screening/source/sql/postgresql/migration/migration-009-010.sql
+++ b/screening/source/sql/postgresql/migration/migration-009-010.sql
@@ -1,3 +1,3 @@
-- Migration from 009 to 010
-ALTER TABLE images ADD COLUMN image_transformer_factory BYTEA;
\ No newline at end of file
+ALTER TABLE acquired_images ADD COLUMN image_transformer_factory BYTEA;
\ No newline at end of file
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 d7fae52662e581161656470db6b75aa8ef98ccfc..e3428dd866627daf9c57d35ea079856af0a09a90 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
@@ -39,6 +39,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgCh
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.ImgImageDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgImageEnrichedDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgSpotDTO;
/**
@@ -224,7 +225,7 @@ public class ImagingQueryDAOTest extends AbstractDBTest
addAcquiredImage(imageId1, channelStackId, datasetChannelId1);
addAcquiredImage(imageId2, channelStackId, experimentChannelId2);
- testGetHCSImage(datasetId, channelStackId, datasetChannelId1, experimentChannelId2);
+ testGetHCSImage(datasetId, channelStackId, datasetChannelId1, experimentChannelId2, spotId);
testListChannelStacksAndSpots(datasetId, channelStackId, spotId);
}
@@ -251,7 +252,7 @@ public class ImagingQueryDAOTest extends AbstractDBTest
}
private void testGetHCSImage(final long datasetId, final long channelStackId,
- final long channelId1, final long channelId2)
+ final long channelId1, final long channelId2, long spotId)
{
Location tileLocation = new Location(X_TILE_COLUMN, Y_TILE_ROW);
Location wellLocation = new Location(X_WELL_COLUMN, Y_WELL_ROW);
@@ -283,6 +284,10 @@ public class ImagingQueryDAOTest extends AbstractDBTest
ImgImageDTO image2bis = dao.tryGetImage(channelId2, channelStackId, datasetId);
assertEquals(image2, image2bis);
+
+ List<ImgImageEnrichedDTO> allImages = dao.listHCSImages(DS_PERM_ID, DS_CHANNEL);
+ assertEquals(1, allImages.size());
+ assertEquals(spotId, allImages.get(0).getSpotId());
}
private void testChannelMethods(final long experimentId, final long datasetId,