From 8f8a1354c12cf624d0230149d03cdffefb2d97c5 Mon Sep 17 00:00:00 2001
From: gpawel <gpawel>
Date: Wed, 29 Aug 2012 10:15:30 +0000
Subject: [PATCH] SP-235 BIS-19: Processing plugin to generate and register
overview images
SVN: 26476
---
.../dss/etl/AbstractImageFileExtractor.java | 13 +-
.../dss/etl/Hdf5ThumbnailGenerator.java | 70 +++---
.../dss/etl/dto/RelativeImageFile.java | 7 +-
.../dto/api/impl/ImageDataSetInformation.java | 14 ++
.../dss/etl/dto/api/v1/ImageFileInfo.java | 31 ++-
.../api/v1/SimpleOverviewImageDataConfig.java | 14 ++
...ImagingDataSetRegistrationTransaction.java | 135 ++++++++---
.../etl/jython/JythonPlateDataSetHandler.java | 1 -
.../jython/SimpleImageDataSetRegistrator.java | 158 ++++++++++---
.../MarkerFileCreatingProcessingPlugin.java | 83 +++++++
.../dataaccess/IImagingReadonlyQueryDAO.java | 13 ++
.../ImgAcquiredImageEnrichedDTO.java | 213 ++++++++++++++++++
12 files changed, 650 insertions(+), 102 deletions(-)
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/plugins/MarkerFileCreatingProcessingPlugin.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgAcquiredImageEnrichedDTO.java
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageFileExtractor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageFileExtractor.java
index 517facb2e2e..145289ca196 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageFileExtractor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageFileExtractor.java
@@ -44,7 +44,6 @@ import ch.systemsx.cisd.openbis.dss.etl.dto.RelativeImageFile;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ThumbnailsInfo;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.Channel;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageFileInfo;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageIdentifier;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ChannelDescription;
@@ -472,8 +471,7 @@ abstract public class AbstractImageFileExtractor implements IImageFileExtractor
{
RelativeImageReference relativeImageRef =
new RelativeImageReference(imageInfo.getImageRelativePath(),
- getUniqueStringIdentifier(imageInfo.tryGetImageIdentifier()),
- colorComponentOrNull);
+ imageInfo.tryGetUniqueStringIdentifier(), colorComponentOrNull);
RelativeImageReference relativeThumbnailRef = null;
if (thumbnailFilePathsOrNull != null)
@@ -499,15 +497,6 @@ abstract public class AbstractImageFileExtractor implements IImageFileExtractor
relativeThumbnailRef);
}
- private static String getUniqueStringIdentifier(ImageIdentifier identifier)
- {
- if (identifier == null)
- {
- return null;
- }
- return identifier.getUniqueStringIdentifier();
- }
-
protected static Integer tryAsInt(String valueOrNull)
{
if (valueOrNull == null)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/Hdf5ThumbnailGenerator.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/Hdf5ThumbnailGenerator.java
index 5b2ba043d3f..53344e76af1 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/Hdf5ThumbnailGenerator.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/Hdf5ThumbnailGenerator.java
@@ -44,6 +44,7 @@ import ch.systemsx.cisd.common.hdf5.HDF5Container.IHDF5WriterClient;
import ch.systemsx.cisd.common.hdf5.IHDF5ContainerWriter;
import ch.systemsx.cisd.common.io.ByteArrayBasedContentNode;
import ch.systemsx.cisd.common.io.FileBasedContentNode;
+import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContent;
import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.common.process.ProcessExecutionHelper;
@@ -56,7 +57,6 @@ import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ThumbnailsInfo;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.Channel;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ChannelColorComponent;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageFileInfo;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageIdentifier;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageStorageConfiguraton;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ThumbnailsStorageFormat;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.transformations.ImageTransformation;
@@ -99,13 +99,14 @@ public class Hdf5ThumbnailGenerator implements IHDF5WriterClient
* imagesParentDirectory
* @param thumbnailFilePath absolute path to the file where thumbnails will be saved
* @param imageStorageConfiguraton describes how the thumbnails should be generated
+ * @param content
*/
public static void tryGenerateThumbnails(ImageDataSetStructure imageDataSetStructure,
File imagesParentDirectory, String thumbnailFilePath,
ImageStorageConfiguraton imageStorageConfiguraton,
String thumbnailPhysicalDatasetPermId,
ThumbnailsStorageFormat thumbnailsStorageFormatOrNull, ThumbnailsInfo thumbnailPaths,
- boolean registerOriginalImageAsThumbnail)
+ boolean registerOriginalImageAsThumbnail, IHierarchicalContent content)
{
if (thumbnailsStorageFormatOrNull != null)
{
@@ -121,7 +122,7 @@ public class Hdf5ThumbnailGenerator implements IHDF5WriterClient
new Hdf5ThumbnailGenerator(imageDataSetStructure, imagesParentDirectory,
thumbnailPhysicalDatasetPermId, thumbnailsStorageFormatOrNull,
imageLibrary, thumbnailPaths, registerOriginalImageAsThumbnail,
- operationLog);
+ content, operationLog);
container.runWriterClient(thumbnailsStorageFormatOrNull.isStoreCompressed(),
thumbnailsGenerator);
}
@@ -158,11 +159,13 @@ public class Hdf5ThumbnailGenerator implements IHDF5WriterClient
private final boolean registerOriginalImageAsThumbnail;
+ private IHierarchicalContent contentOrNull;
+
private Hdf5ThumbnailGenerator(ImageDataSetStructure imageDataSetStructure,
File imagesParentDirectory, String thumbnailPhysicalDatasetPermId,
ThumbnailsStorageFormat thumbnailsStorageFormat, ImageLibraryInfo imageLibraryOrNull,
ThumbnailsInfo thumbnailPathCollector, boolean registerOriginalImageAsThumbnail,
- Logger operationLog)
+ IHierarchicalContent contentOrNull, Logger operationLog)
{
this.imageDataSetStructure = imageDataSetStructure;
this.imagesParentDirectory = imagesParentDirectory;
@@ -171,6 +174,7 @@ public class Hdf5ThumbnailGenerator implements IHDF5WriterClient
this.imageLibraryOrNull = imageLibraryOrNull;
this.thumbnailPathCollector = thumbnailPathCollector;
this.registerOriginalImageAsThumbnail = registerOriginalImageAsThumbnail;
+ this.contentOrNull = contentOrNull;
this.logger = operationLog;
for (Channel ch : imageDataSetStructure.getChannels())
@@ -216,7 +220,7 @@ public class Hdf5ThumbnailGenerator implements IHDF5WriterClient
try
{
long start = System.currentTimeMillis();
- String imageIdOrNull = tryExtractImageID(image);
+ String imageIdOrNull = image.tryGetUniqueStringIdentifier();
List<ThumbnailData> thumbnailData =
generateThumbnail(bufferOutputStream, image, imageIdOrNull);
@@ -282,7 +286,7 @@ public class Hdf5ThumbnailGenerator implements IHDF5WriterClient
}
newImagePath.append("_c").append(channelCode);
- String imageIdOrNull = tryExtractImageID(plateImage);
+ String imageIdOrNull = plateImage.tryGetUniqueStringIdentifier();
if (imageIdOrNull != null)
{
newImagePath.append(imageIdOrNull);
@@ -295,12 +299,6 @@ public class Hdf5ThumbnailGenerator implements IHDF5WriterClient
return sb.length() > 0 ? "_" : "";
}
- private static String tryExtractImageID(ImageFileInfo image)
- {
- ImageIdentifier imageIdentifier = image.tryGetImageIdentifier();
- return imageIdentifier == null ? null : imageIdentifier.getUniqueStringIdentifier();
- }
-
private List<ThumbnailData> generateThumbnail(ByteArrayOutputStream bufferOutputStream,
ImageFileInfo img, String imageIdOrNull) throws IOException
{
@@ -323,7 +321,7 @@ public class Hdf5ThumbnailGenerator implements IHDF5WriterClient
{
final File imageFile =
new File(imagesParentDirectory, imageFileInfo.getImageRelativePath());
- Size originalSize = loadUnchangedImageDimension(imageFile, null);
+ Size originalSize = loadUnchangedImageDimension(imageFileInfo.getImageRelativePath(), null);
return Collections.singletonList(new ThumbnailData(
FileUtilities.loadToByteArray(imageFile), originalSize.getWidth(), originalSize
@@ -333,21 +331,29 @@ public class Hdf5ThumbnailGenerator implements IHDF5WriterClient
private List<ThumbnailData> generateThumbnailWithImageMagic(ImageFileInfo imageFileInfo)
throws IOException
{
- final File imageFile =
- new File(imagesParentDirectory, imageFileInfo.getImageRelativePath());
int width = thumbnailsStorageFormat.getMaxWidth();
int height = thumbnailsStorageFormat.getMaxHeight();
if (thumbnailsStorageFormat.getZoomLevel() != null)
{
- Size originalSize = loadUnchangedImageDimension(imageFile, null);
+ Size originalSize =
+ loadUnchangedImageDimension(imageFileInfo.getImageRelativePath(), null);
double zoomLevel = thumbnailsStorageFormat.getZoomLevel();
width = (int) Math.round(zoomLevel * originalSize.getWidth());
height = (int) Math.round(zoomLevel * originalSize.getHeight());
}
String size = width + "x" + height;
- String imageFilePath = imageFile.getPath();
+ String imageFilePath = null;
+ if (contentOrNull == null)
+ {
+ imageFilePath = new File(imageFilePath, imageFileInfo.getImageRelativePath()).getPath();
+ } else
+ {
+ imageFilePath =
+ contentOrNull.getNode(imageFileInfo.getImageRelativePath()).getFile().getPath();
+ }
+
List<String> params = new ArrayList<String>();
params.addAll(Arrays.asList(convertUtilityOrNull.getPath(), imageFilePath, "-scale", size));
List<String> additionalParams = thumbnailsStorageFormat.getImageMagicParams();
@@ -413,9 +419,7 @@ public class Hdf5ThumbnailGenerator implements IHDF5WriterClient
String imageIdOrNull, ByteArrayOutputStream bufferOutputStream) throws IOException
{
BufferedImage image =
- loadUnchangedImage(
- new File(imagesParentDirectory, imageFileInfo.getImageRelativePath()),
- imageIdOrNull);
+ loadUnchangedImage(imageFileInfo.getImageRelativePath(), imageIdOrNull);
int widht = thumbnailsStorageFormat.getMaxWidth();
int height = thumbnailsStorageFormat.getMaxHeight();
@@ -512,16 +516,30 @@ public class Hdf5ThumbnailGenerator implements IHDF5WriterClient
return null;
}
- private BufferedImage loadUnchangedImage(File imageFile, String imageIdOrNull)
+ private BufferedImage loadUnchangedImage(String imageRelativePath, String imageIdOrNull)
{
- return Utils.loadUnchangedImage(new FileBasedContentNode(imageFile), imageIdOrNull,
- imageLibraryOrNull);
+ if (contentOrNull == null)
+ {
+ return Utils.loadUnchangedImage(new FileBasedContentNode(new File(
+ imagesParentDirectory, imageRelativePath)), imageIdOrNull, imageLibraryOrNull);
+ } else
+ {
+ return Utils.loadUnchangedImage(contentOrNull.getNode(imageRelativePath),
+ imageIdOrNull, imageLibraryOrNull);
+ }
}
- private Size loadUnchangedImageDimension(File imageFile, String imageIdOrNull)
+ private Size loadUnchangedImageDimension(String imageRelativePath, String imageIdOrNull)
{
- return Utils.loadUnchangedImageSize(new FileBasedContentNode(imageFile), imageIdOrNull,
- imageLibraryOrNull);
+ if (contentOrNull == null)
+ {
+ return Utils.loadUnchangedImageSize(new FileBasedContentNode(new File(
+ imagesParentDirectory, imageRelativePath)), imageIdOrNull, imageLibraryOrNull);
+ } else
+ {
+ return Utils.loadUnchangedImageSize(contentOrNull.getNode(imageRelativePath),
+ imageIdOrNull, imageLibraryOrNull);
+ }
}
private Status createStatus(String thumbnailPath, IOException ex)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/RelativeImageFile.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/RelativeImageFile.java
index 051161ecac4..652abe2ac77 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/RelativeImageFile.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/RelativeImageFile.java
@@ -20,7 +20,6 @@ import java.io.Serializable;
import ch.systemsx.cisd.common.utilities.AbstractHashable;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageFileInfo;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageIdentifier;
/**
* Points to one image on the file system.
@@ -37,10 +36,8 @@ public class RelativeImageFile extends AbstractHashable implements Serializable
public static RelativeImageFile create(ImageFileInfo imageFileInfo)
{
- ImageIdentifier imageIdentifier = imageFileInfo.tryGetImageIdentifier();
- String imageIDOrNull =
- (imageIdentifier == null) ? null : imageIdentifier.getUniqueStringIdentifier();
- return new RelativeImageFile(imageFileInfo.getImageRelativePath(), imageIDOrNull);
+ return new RelativeImageFile(imageFileInfo.getImageRelativePath(),
+ imageFileInfo.tryGetUniqueStringIdentifier());
}
public RelativeImageFile(String imageRelativePath, String imageIDOrNull)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/ImageDataSetInformation.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/ImageDataSetInformation.java
index 3171778eced..a4f686564d2 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/ImageDataSetInformation.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/ImageDataSetInformation.java
@@ -51,6 +51,8 @@ public class ImageDataSetInformation extends BasicDataSetInformation
private boolean registerAsOverviewImageDataSet;
+ private boolean generateOverviewImagesFromRegisteredImages;
+
private int maximumImageWidth;
private int maximumImageHeight;
@@ -160,6 +162,18 @@ public class ImageDataSetInformation extends BasicDataSetInformation
this.registerAsOverviewImageDataSet = registerAsOverviewImageDataSet;
}
+ public boolean isGenerateOverviewImagesFromRegisteredImages()
+ {
+ return generateOverviewImagesFromRegisteredImages;
+ }
+
+ public void setGenerateOverviewImagesFromRegisteredImages(
+ boolean generateOverviewImagesFromRegisteredImages)
+ {
+ this.generateOverviewImagesFromRegisteredImages =
+ generateOverviewImagesFromRegisteredImages;
+ }
+
@Override
public String toString()
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ImageFileInfo.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ImageFileInfo.java
index 85c50c1d893..30ad9846389 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ImageFileInfo.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ImageFileInfo.java
@@ -30,6 +30,10 @@ public final class ImageFileInfo implements Serializable
private ImageIdentifier imageIdentifier;
+ private String uniqueImageIdentifier;
+
+ private String containerDataSetCode;
+
public ImageFileInfo(String channelCode, int tileRow, int tileColumn, String imageRelativePath)
{
assert channelCode != null;
@@ -40,10 +44,17 @@ public final class ImageFileInfo implements Serializable
setTile(tileRow, tileColumn);
}
- public ImageIdentifier tryGetImageIdentifier()
+ public String tryGetUniqueStringIdentifier()
{
- return imageIdentifier;
+ if (imageIdentifier != null)
+ {
+ return imageIdentifier.getUniqueStringIdentifier();
+ } else if (uniqueImageIdentifier != null)
+ {
+ return uniqueImageIdentifier;
+ }
+ return null;
}
public Integer tryGetWellRow()
@@ -146,6 +157,21 @@ public final class ImageFileInfo implements Serializable
this.seriesNumberOrNull = value;
}
+ public void setUniqueImageIdentifier(String uniqueImageIdentifier)
+ {
+ this.uniqueImageIdentifier = uniqueImageIdentifier;
+ }
+
+ public String getContainerDataSetCode()
+ {
+ return containerDataSetCode;
+ }
+
+ public void setContainerDataSetCode(String containerDataSetCode)
+ {
+ this.containerDataSetCode = containerDataSetCode;
+ }
+
@Override
public String toString()
{
@@ -154,5 +180,4 @@ public final class ImageFileInfo implements Serializable
+ timepointOrNull + ", depth=" + depthOrNull + ", seriesNumber="
+ seriesNumberOrNull + "]";
}
-
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/SimpleOverviewImageDataConfig.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/SimpleOverviewImageDataConfig.java
index f57b0ab05cb..3fe34cf6129 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/SimpleOverviewImageDataConfig.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/SimpleOverviewImageDataConfig.java
@@ -25,6 +25,8 @@ public class SimpleOverviewImageDataConfig extends SimpleImageDataConfig
{
private String containerDataSetCode;
+ private boolean generateOverviewImagesFromRegisteredImages;
+
public String getContainerDataSetCode()
{
return containerDataSetCode;
@@ -34,4 +36,16 @@ public class SimpleOverviewImageDataConfig extends SimpleImageDataConfig
{
this.containerDataSetCode = containerDataSetCode;
}
+
+ public boolean isGenerateOverviewImagesFromRegisteredImages()
+ {
+ return generateOverviewImagesFromRegisteredImages;
+ }
+
+ public void setGenerateOverviewImagesFromRegisteredImages(
+ boolean generateOverviewImagesFromRegisteredImages)
+ {
+ this.generateOverviewImagesFromRegisteredImages =
+ generateOverviewImagesFromRegisteredImages;
+ }
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/ImagingDataSetRegistrationTransaction.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/ImagingDataSetRegistrationTransaction.java
index ea1943f1aff..3e5f727c8d4 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/ImagingDataSetRegistrationTransaction.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/ImagingDataSetRegistrationTransaction.java
@@ -30,6 +30,7 @@ import java.util.Properties;
import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.io.FileBasedContentNode;
+import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContent;
import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationDetails;
import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationService;
import ch.systemsx.cisd.etlserver.registrator.IDataSetRegistrationDetailsFactory;
@@ -59,6 +60,7 @@ import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ThumbnailsStorageFormat;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v2.IFeatureVectorDataSet;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v2.SimpleFeatureVectorDataConfig;
import ch.systemsx.cisd.openbis.dss.etl.featurevector.CsvFeatureVectorParser;
+import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IDataSetImmutable;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
@@ -242,7 +244,7 @@ public class ImagingDataSetRegistrationTransaction extends DataSetRegistrationTr
thumbnailDatasets.add(thumbnailDataset);
generateThumbnails(imageDataSetStructure, incomingDirectory, thumbnailDataset,
- thumbnailsStorageFormat, thumbnailsInfo, false);
+ thumbnailsStorageFormat, thumbnailsInfo, false, null);
containedDataSetCodes.add(thumbnailDataset.getDataSetCode());
}
imageDataSetInformation.setThumbnailsInfo(thumbnailsInfo);
@@ -271,7 +273,7 @@ public class ImagingDataSetRegistrationTransaction extends DataSetRegistrationTr
return containerDataset;
}
- public IDataSet createNewOverviewImageDataSet(
+ private IDataSet createNewOverviewImageDataSet(
DataSetRegistrationDetails<ImageDataSetInformation> imageRegistrationDetails)
{
ImageDataSetInformation imageDataSetInformation =
@@ -290,6 +292,8 @@ public class ImagingDataSetRegistrationTransaction extends DataSetRegistrationTr
container);
}
+ calculateBoundingBox(imageDataSetInformation, imageDataSetStructure, incomingDirectory);
+
SearchCriteria searchCriteria = new SearchCriteria();
SearchCriteria searchSubCriteria = new SearchCriteria();
searchSubCriteria.addMatchClause(MatchClause.createAttributeMatch(
@@ -302,8 +306,6 @@ public class ImagingDataSetRegistrationTransaction extends DataSetRegistrationTr
IDataSetImmutable exampleDataSet = containedDataSets.iterator().next();
- calculateBoundingBox(imageDataSetInformation, imageDataSetStructure, incomingDirectory);
-
imageDataSetStructure
.validateImageRepresentationGenerationParameters(imageDataSetInformation);
@@ -311,23 +313,73 @@ public class ImagingDataSetRegistrationTransaction extends DataSetRegistrationTr
List<String> containedDataSetCodes = new ArrayList<String>();
containedDataSetCodes.addAll(container.getContainedDataSetCodes());
- @SuppressWarnings("unchecked")
- DataSet<ImageDataSetInformation> thumbnailDataset =
- (DataSet<ImageDataSetInformation>) super.createNewDataSet(imageRegistrationDetails);
- thumbnailDataset.setFileFormatType(imageDataSetInformation.getFileFormatTypeCode());
- thumbnailDataset.setMeasuredData(false);
-
- generateThumbnails(imageDataSetStructure, incomingDirectory, thumbnailDataset,
- createThumbnailsStorageFormat(imageDataSetInformation), thumbnailsInfo, true);
- containedDataSetCodes.add(thumbnailDataset.getDataSetCode());
+ List<IDataSet> thumbnailDatasets = new ArrayList<IDataSet>();
+ if (imageDataSetInformation.isGenerateOverviewImagesFromRegisteredImages())
+ {
+ IHierarchicalContent content =
+ ServiceProvider.getHierarchicalContentProvider().asContent(containerCode);
+ try
+ {
+ imageDataSetStructure
+ .validateImageRepresentationGenerationParameters(imageDataSetInformation);
+
+ List<ThumbnailsStorageFormat> thumbnailsStorageFormatList =
+ imageDataSetStructure.getImageStorageConfiguraton()
+ .getThumbnailsStorageFormat();
+
+ boolean isFirst = true;
+ for (ThumbnailsStorageFormat thumbnailsStorageFormat : thumbnailsStorageFormatList)
+ {
+ IDataSet thumbnailDataset = null;
+ if (isFirst)
+ {
+ thumbnailDataset = super.createNewDataSet(imageRegistrationDetails);
+ isFirst = false;
+ } else
+ {
+ thumbnailDataset =
+ createThumbnailDataset(imageDataSetInformation,
+ thumbnailsStorageFormat);
+ }
+ thumbnailDatasets.add(thumbnailDataset);
+
+ generateThumbnails(imageDataSetStructure, incomingDirectory, thumbnailDataset,
+ thumbnailsStorageFormat, thumbnailsInfo, false, content);
+ containedDataSetCodes.add(thumbnailDataset.getDataSetCode());
+ }
+ } finally
+ {
+ if (content != null)
+ {
+ content.close();
+ }
+ }
+ } else
+ {
+ @SuppressWarnings("unchecked")
+ DataSet<ImageDataSetInformation> thumbnailDataset =
+ (DataSet<ImageDataSetInformation>) super
+ .createNewDataSet(imageRegistrationDetails);
+ thumbnailDataset.setFileFormatType(imageDataSetInformation.getFileFormatTypeCode());
+ thumbnailDataset.setMeasuredData(false);
+ thumbnailDatasets.add(thumbnailDataset);
+
+ generateThumbnails(imageDataSetStructure, incomingDirectory, thumbnailDataset,
+ createThumbnailsStorageFormat(imageDataSetInformation), thumbnailsInfo, true,
+ null);
+ containedDataSetCodes.add(thumbnailDataset.getDataSetCode());
+ }
imageDataSetInformation.setThumbnailsInfo(thumbnailsInfo);
- setSameDatasetOwner(exampleDataSet, thumbnailDataset);
+ for (IDataSet thumbnailDataset : thumbnailDatasets)
+ {
+ setSameDatasetOwner(exampleDataSet, thumbnailDataset);
+ }
container.setContainedDataSetCodes(containedDataSetCodes);
- return thumbnailDataset;
+ return thumbnailDatasets.iterator().next();
}
private static ThumbnailsStorageFormat createThumbnailsStorageFormat(
@@ -349,15 +401,45 @@ public class ImagingDataSetRegistrationTransaction extends DataSetRegistrationTr
ImageLibraryInfo imageLibrary =
imageDataSetStructure.getImageStorageConfiguraton().tryGetImageLibrary();
List<ImageFileInfo> images = imageDataSetStructure.getImages();
- for (ImageFileInfo imageFileInfo : images)
- {
- File file = new File(incomingDirectory, imageFileInfo.getImageRelativePath());
- Size size =
- Utils.loadUnchangedImageSize(new FileBasedContentNode(file), null, imageLibrary);
- imageDataSetInformation.setMaximumImageWidth(Math.max(
- imageDataSetInformation.getMaximumImageWidth(), size.getWidth()));
- imageDataSetInformation.setMaximumImageHeight(Math.max(
- imageDataSetInformation.getMaximumImageHeight(), size.getHeight()));
+
+ if (imageDataSetInformation.isGenerateOverviewImagesFromRegisteredImages())
+ {
+ IHierarchicalContent content =
+ ServiceProvider.getHierarchicalContentProvider().asContent(
+ imageDataSetInformation.getContainerDatasetPermId());
+ try
+ {
+ for (ImageFileInfo imageFileInfo : images)
+ {
+ Size size =
+ Utils.loadUnchangedImageSize(
+ content.getNode(imageFileInfo.getImageRelativePath()), null,
+ imageLibrary);
+ imageDataSetInformation.setMaximumImageWidth(Math.max(
+ imageDataSetInformation.getMaximumImageWidth(), size.getWidth()));
+ imageDataSetInformation.setMaximumImageHeight(Math.max(
+ imageDataSetInformation.getMaximumImageHeight(), size.getHeight()));
+ }
+ } finally
+ {
+ if (content != null)
+ {
+ content.close();
+ }
+ }
+ } else
+ {
+ for (ImageFileInfo imageFileInfo : images)
+ {
+ File file = new File(incomingDirectory, imageFileInfo.getImageRelativePath());
+ Size size =
+ Utils.loadUnchangedImageSize(new FileBasedContentNode(file), null,
+ imageLibrary);
+ imageDataSetInformation.setMaximumImageWidth(Math.max(
+ imageDataSetInformation.getMaximumImageWidth(), size.getWidth()));
+ imageDataSetInformation.setMaximumImageHeight(Math.max(
+ imageDataSetInformation.getMaximumImageHeight(), size.getHeight()));
+ }
}
}
@@ -369,7 +451,7 @@ public class ImagingDataSetRegistrationTransaction extends DataSetRegistrationTr
private void generateThumbnails(ImageDataSetStructure imageDataSetStructure,
File incomingDirectory, IDataSet thumbnailDataset,
ThumbnailsStorageFormat thumbnailsStorageFormatOrNull, ThumbnailsInfo thumbnailPaths,
- boolean registerOriginalImageAsThumbnail)
+ boolean registerOriginalImageAsThumbnail, IHierarchicalContent content)
{
String thumbnailFile;
if (thumbnailsStorageFormatOrNull == null)
@@ -386,7 +468,7 @@ public class ImagingDataSetRegistrationTransaction extends DataSetRegistrationTr
Hdf5ThumbnailGenerator.tryGenerateThumbnails(imageDataSetStructure, incomingDirectory,
thumbnailFile, imageDataSetStructure.getImageStorageConfiguraton(),
thumbnailDataset.getDataSetCode(), thumbnailsStorageFormatOrNull, thumbnailPaths,
- registerOriginalImageAsThumbnail);
+ registerOriginalImageAsThumbnail, content);
enhanceWithResolution(thumbnailDataset, thumbnailPaths);
}
@@ -643,5 +725,4 @@ public class ImagingDataSetRegistrationTransaction extends DataSetRegistrationTr
return null;
}
}
-
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonPlateDataSetHandler.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonPlateDataSetHandler.java
index 045573b617b..6a3c1368dfe 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonPlateDataSetHandler.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonPlateDataSetHandler.java
@@ -21,7 +21,6 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
*/
public class JythonPlateDataSetHandler extends JythonTopLevelDataSetHandler<DataSetInformation>
{
-
private final String originalDirName;
public JythonPlateDataSetHandler(TopLevelDataSetRegistratorGlobalState globalState)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/SimpleImageDataSetRegistrator.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/SimpleImageDataSetRegistrator.java
index f40870e744f..1b7f57f4531 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/SimpleImageDataSetRegistrator.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/SimpleImageDataSetRegistrator.java
@@ -52,6 +52,7 @@ import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ImageDataSetInformation;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ImageDataSetStructure;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.Channel;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ChannelColorComponent;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ChannelColorRGB;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageFileInfo;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageIdentifier;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageMetadata;
@@ -63,10 +64,16 @@ import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.transformations.ImageTransfor
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.transformations.ImageTransformationBuffer;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
+import ch.systemsx.cisd.openbis.dss.shared.DssScreeningUtils;
import ch.systemsx.cisd.openbis.generic.shared.basic.CodeNormalizer;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.FileFormatType;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingReadonlyQueryDAO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgAcquiredImageEnrichedDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgChannelDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgImageDatasetDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgImageTransformationDTO;
/**
* Allows to prepare the image dataset which should be registered easily using the specified
@@ -166,6 +173,19 @@ public class SimpleImageDataSetRegistrator
DataSetRegistrationDetails<ImageDataSetInformation> registrationDetails =
imageDatasetFactory.createDataSetRegistrationDetails();
ImageDataSetInformation imageDataset = registrationDetails.getDataSetInformation();
+
+ if (simpleImageConfig instanceof SimpleOverviewImageDataConfig)
+ {
+ SimpleOverviewImageDataConfig simpleOverviewImageConfig =
+ (SimpleOverviewImageDataConfig) simpleImageConfig;
+
+ imageDataset.setContainerDatasetPermId(simpleOverviewImageConfig
+ .getContainerDataSetCode());
+ imageDataset.setGenerateOverviewImagesFromRegisteredImages(simpleOverviewImageConfig
+ .isGenerateOverviewImagesFromRegisteredImages());
+ imageDataset.setRegisterAsOverviewImageDataSet(true);
+ }
+
setImageDataset(incoming, imageDataset);
List<Channel> channels = simpleImageConfig.getChannels();
if (channels != null)
@@ -181,16 +201,6 @@ public class SimpleImageDataSetRegistrator
}
}
- if (simpleImageConfig instanceof SimpleOverviewImageDataConfig)
- {
- SimpleOverviewImageDataConfig simpleOverviewImageConfig =
- (SimpleOverviewImageDataConfig) simpleImageConfig;
-
- imageDataset.setContainerDatasetPermId(simpleOverviewImageConfig
- .getContainerDataSetCode());
- imageDataset.setRegisterAsOverviewImageDataSet(true);
- }
-
setRegistrationDetails(registrationDetails, imageDataset);
return registrationDetails;
}
@@ -620,30 +630,43 @@ public class SimpleImageDataSetRegistrator
dataset.setSample(simpleImageConfig.getPlateSpace(), simpleImageConfig.getPlateCode());
dataset.setIncomingDirectory(incoming);
- ImageDataSetStructure imageStruct = createImageDataSetStructure(incoming);
+ ImageDataSetStructure imageStruct = createImageDataSetStructure(incoming, dataset);
dataset.setImageDataSetStructure(imageStruct);
}
- private ImageDataSetStructure createImageDataSetStructure(File incoming)
+ private ImageDataSetStructure createImageDataSetStructure(File incoming,
+ ImageDataSetInformation dataset)
{
- List<File> imageFiles = extractImageFiles(incoming);
- IImageReader imageReaderOrNull = tryCreateAndSaveImageReader(imageFiles);
- List<ImageTokensWithPath> imageTokensList =
- parseImageTokens(imageFiles, incoming, imageReaderOrNull);
-
- int maxTileNumber = getMaxTileNumber(imageTokensList);
- Geometry tileGeometry = simpleImageConfig.getTileGeometry(imageTokensList, maxTileNumber);
- List<ImageFileInfo> images = createImageInfos(imageTokensList, tileGeometry);
- List<Channel> channels = getAvailableChannels(images);
-
- if (simpleImageConfig.isFixedIntensityRangeForAllImagesDefined())
- {
- computeAndAppendCommonFixedIntensityRangeTransformation(images, incoming, channels,
- imageReaderOrNull);
+ List<ImageFileInfo> images = null;
+ List<Channel> channels = null;
+ Geometry tileGeometry = null;
+ if (dataset.isGenerateOverviewImagesFromRegisteredImages())
+ {
+ images = new ArrayList<ImageFileInfo>();
+ channels = new ArrayList<Channel>();
+ tileGeometry = extractImageFileInfos(dataset, images, channels);
} else
{
- computeAndAppendCommonIntensityRangeTransformation(images, incoming, channels,
- imageReaderOrNull);
+ List<File> imageFiles = extractImageFiles(incoming);
+ IImageReader imageReaderOrNull = tryCreateAndSaveImageReader(imageFiles);
+ List<ImageTokensWithPath> imageTokensList =
+ parseImageTokens(imageFiles, incoming, imageReaderOrNull);
+
+ int maxTileNumber = getMaxTileNumber(imageTokensList);
+ tileGeometry = simpleImageConfig.getTileGeometry(imageTokensList, maxTileNumber);
+
+ images = createImageInfos(imageTokensList, tileGeometry);
+ channels = getAvailableChannels(images);
+
+ if (simpleImageConfig.isFixedIntensityRangeForAllImagesDefined())
+ {
+ computeAndAppendCommonFixedIntensityRangeTransformation(images, incoming, channels,
+ imageReaderOrNull);
+ } else
+ {
+ computeAndAppendCommonIntensityRangeTransformation(images, incoming, channels,
+ imageReaderOrNull);
+ }
}
ImageDataSetStructure imageStruct = new ImageDataSetStructure();
@@ -656,6 +679,85 @@ public class SimpleImageDataSetRegistrator
return imageStruct;
}
+ private Geometry extractImageFileInfos(ImageDataSetInformation dataset,
+ List<ImageFileInfo> images, List<Channel> channels)
+ {
+ IImagingReadonlyQueryDAO query = DssScreeningUtils.getQuery();
+
+ List<ImgImageDatasetDTO> containers =
+ DssScreeningUtils.getQuery().listImageDatasetsByPermId(
+ dataset.getContainerDatasetPermId());
+
+ for (ImgImageDatasetDTO container : containers)
+ {
+ List<ImgAcquiredImageEnrichedDTO> acquiredImages =
+ query.listAllEnrichedAcquiredImagesForDataSet(container.getId());
+ for (ImgAcquiredImageEnrichedDTO acquiredImage : acquiredImages)
+ {
+ images.add(createImageFileInfo(container, acquiredImage));
+ }
+
+ List<ImgChannelDTO> channelDTOs = query.getChannelsByDatasetId(container.getId());
+ for (ImgChannelDTO channelDTO : channelDTOs)
+ {
+ Channel channel = createChannel(query, channelDTO);
+
+ channels.add(channel);
+ }
+
+ return Geometry.createFromRowColDimensions(container.getFieldNumberOfRows(),
+ container.getFieldNumberOfColumns());
+ }
+
+ return null;
+ }
+
+ private Channel createChannel(IImagingReadonlyQueryDAO query, ImgChannelDTO channelDTO)
+ {
+ Channel channel =
+ new Channel(channelDTO.getCode(), channelDTO.getLabel(), new ChannelColorRGB(
+ channelDTO.getRedColorComponent(), channelDTO.getGreenColorComponent(),
+ channelDTO.getBlueColorComponent()));
+ channel.setDescription(channelDTO.getDescription());
+ channel.setWavelength(channelDTO.getWavelength());
+
+ List<ImgImageTransformationDTO> transformationDTOs =
+ query.listImageTransformations(channelDTO.getId());
+ ImageTransformation[] transformations = new ImageTransformation[transformationDTOs.size()];
+ int counter = 0;
+ for (ImgImageTransformationDTO transformationDTO : transformationDTOs)
+ {
+ ImageTransformation transformation =
+ new ImageTransformation(transformationDTO.getCode(),
+ transformationDTO.getLabel(), transformationDTO.getDescription(),
+ transformationDTO.getImageTransformerFactory());
+ transformations[counter++] = transformation;
+ }
+ channel.setAvailableTransformations(transformations);
+
+ return channel;
+ }
+
+ private ImageFileInfo createImageFileInfo(ImgImageDatasetDTO container,
+ ImgAcquiredImageEnrichedDTO acquiredImage)
+ {
+ ImageFileInfo img =
+ new ImageFileInfo(acquiredImage.getChannelCode(), acquiredImage.getTileRow(),
+ acquiredImage.getTileColumn(), acquiredImage.getImageFilePath());
+ img.setTimepoint(acquiredImage.getT());
+ img.setDepth(acquiredImage.getZ());
+ img.setSeriesNumber(acquiredImage.getSeriesNumber());
+
+ if (acquiredImage.getSpotRow() != null && acquiredImage.getSpotColumn() != null)
+ {
+ img.setWell(acquiredImage.getSpotRow(), acquiredImage.getSpotColumn());
+ }
+ img.setUniqueImageIdentifier(acquiredImage.getImageIdOrNull());
+ img.setContainerDataSetCode(container.getPermId());
+
+ return img;
+ }
+
private <T extends DataSetInformation> void setRegistrationDetails(
DataSetRegistrationDetails<T> registrationDetails, T dataset)
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/plugins/MarkerFileCreatingProcessingPlugin.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/plugins/MarkerFileCreatingProcessingPlugin.java
new file mode 100644
index 00000000000..6d6e826fac3
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/plugins/MarkerFileCreatingProcessingPlugin.java
@@ -0,0 +1,83 @@
+/*
+ * Copyright 2012 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.dss.screening.server.plugins;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.List;
+import java.util.Properties;
+
+import org.apache.log4j.Logger;
+
+import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
+import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
+import ch.systemsx.cisd.common.logging.LogCategory;
+import ch.systemsx.cisd.common.logging.LogFactory;
+import ch.systemsx.cisd.common.utilities.PropertyUtils;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.IProcessingPluginTask;
+import ch.systemsx.cisd.openbis.dss.generic.shared.DataSetProcessingContext;
+import ch.systemsx.cisd.openbis.dss.generic.shared.ProcessingStatus;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
+
+/**
+ * A processing plugin that create a marker file (named with the dataset code) in specified
+ * location.
+ *
+ * @author Pawel Glyzewski
+ */
+public class MarkerFileCreatingProcessingPlugin implements IProcessingPluginTask
+{
+ private static final String OUTPUT_DIR = "output-dir";
+
+ private static final long serialVersionUID = 1L;
+
+ private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
+ MarkerFileCreatingProcessingPlugin.class);
+
+ private final File outputDirectory;
+
+ public MarkerFileCreatingProcessingPlugin(Properties properties, File storeRoot)
+ {
+ String directoryPath = PropertyUtils.getMandatoryProperty(properties, OUTPUT_DIR);
+ this.outputDirectory = new File(directoryPath);
+ if (false == outputDirectory.exists() || false == outputDirectory.isDirectory())
+ {
+ throw new ConfigurationFailureException("'" + OUTPUT_DIR + "' (" + directoryPath
+ + ") should point to an existing directory.");
+ }
+ }
+
+ @Override
+ public ProcessingStatus process(List<DatasetDescription> datasets,
+ DataSetProcessingContext context)
+ {
+ for (DatasetDescription dataset : datasets)
+ {
+ File markerFile = new File(outputDirectory, dataset.getDataSetCode());
+ try
+ {
+ markerFile.createNewFile();
+ } catch (IOException ex)
+ {
+ CheckedExceptionTunnel.unwrapIfNecessary(ex);
+ }
+ }
+
+ operationLog.info("Processing done.");
+ return null;
+ }
+}
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 b0913373434..a9d7027bdc2 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
@@ -243,6 +243,19 @@ public interface IImagingReadonlyQueryDAO extends BaseQuery
// lists all acquired images available for given dataset
public List<ImgAcquiredImageDTO> listAllAcquiredImagesForDataSet(long datasetId);
+ @Select("select ai.ID as ID, ai.IMAGE_TRANSFORMER_FACTORY as IMAGE_TRANSFORMER_FACTORY, ai.IMG_ID as IMG_ID, ai.CHANNEL_STACK_ID as CHANNEL_STACK_ID, ai.CHANNEL_ID as CHANNEL_ID, "
+ + " s.X as SPOT_X, s.Y as SPOT_Y, i.path as IMAGE_PATH, i.IMAGE_ID as IMAGE_ID, i.color as IMAGE_COLOR, "
+ + " th.path as THUMBNAIL_PATH, th.IMAGE_ID as THUMBNAIL_IMAGE_ID, th.color as THUMBNAIL_COLOR, "
+ + " ch.code as CHANNEL_CODE, cs.X as X, cs.Y as Y, cs.Z_in_M as Z_in_M, cs.T_in_SEC as T_in_SEC, cs.SERIES_NUMBER as SERIES_NUMBER "
+ + "from acquired_images ai "
+ + " join images i on ai.img_id = i.id "
+ + " left outer join images th on ai.thumbnail_id = th.id "
+ + " left outer join channels ch on ai.channel_id = ch.id "
+ + " left outer join channel_stacks cs on ai.channel_stack_id = cs.id "
+ + " left outer join spots s on cs.spot_id = s.id "
+ + "where ch.ds_id = ?{1} or cs.ds_id = ?{1}")
+ public List<ImgAcquiredImageEnrichedDTO> listAllEnrichedAcquiredImagesForDataSet(long datasetId);
+
// simple getters
@Select("select * from IMAGE_DATA_SETS where PERM_ID = ?{1}")
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgAcquiredImageEnrichedDTO.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgAcquiredImageEnrichedDTO.java
new file mode 100644
index 00000000000..0d70a8994f9
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgAcquiredImageEnrichedDTO.java
@@ -0,0 +1,213 @@
+/*
+ * Copyright 2012 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;
+
+/**
+ * @author Pawel Glyzewski
+ */
+public class ImgAcquiredImageEnrichedDTO extends ImgAcquiredImageDTO
+{
+ @ResultColumn("SPOT_X")
+ private Integer spotColumn;
+
+ // position in the container, one-based (e.g. well row, 1 is the first row)
+ @ResultColumn("SPOT_Y")
+ private Integer spotRow;
+
+ @ResultColumn("IMAGE_PATH")
+ private String imageFilePath;
+
+ @ResultColumn("IMAGE_ID")
+ private String imageIdOrNull;
+
+ @ResultColumn("IMAGE_COLOR")
+ private String imageColorComponentOrNull;
+
+ @ResultColumn("THUMBNAIL_PATH")
+ private String filePath;
+
+ @ResultColumn("THUMBNAIL_IMAGE_ID")
+ private String thumbnailImageIdOrNull;
+
+ @ResultColumn("THUMBNAIL_COLOR")
+ private String thumbnailColorComponentOrNull;
+
+ @ResultColumn("CHANNEL_CODE")
+ private String channelCode;
+
+ // x and y are kind of a two dimensional sequence number, (e.g. tile column)
+ @ResultColumn("X")
+ private Integer tileColumn;
+
+ // x and y are kind of a two dimensional sequence number, (e.g. tile row, 1 is the first row)
+ // Some use case may only use x and leave y alone.
+ @ResultColumn("Y")
+ private Integer tileRow;
+
+ // can be null
+ @ResultColumn("Z_in_M")
+ private Float z;
+
+ // can be null
+ @ResultColumn("T_in_SEC")
+ private Float t;
+
+ @ResultColumn("SERIES_NUMBER")
+ private Integer seriesNumber;
+
+ public Integer getSpotColumn()
+ {
+ return spotColumn;
+ }
+
+ public void setSpotColumn(Integer spotColumn)
+ {
+ this.spotColumn = spotColumn;
+ }
+
+ public Integer getSpotRow()
+ {
+ return spotRow;
+ }
+
+ public void setSpotRow(Integer spotRow)
+ {
+ this.spotRow = spotRow;
+ }
+
+ public String getImageFilePath()
+ {
+ return imageFilePath;
+ }
+
+ public void setImageFilePath(String imageFilePath)
+ {
+ this.imageFilePath = imageFilePath;
+ }
+
+ public String getImageIdOrNull()
+ {
+ return imageIdOrNull;
+ }
+
+ public void setImageIdOrNull(String imageIdOrNull)
+ {
+ this.imageIdOrNull = imageIdOrNull;
+ }
+
+ public String getImageColorComponentOrNull()
+ {
+ return imageColorComponentOrNull;
+ }
+
+ public void setImageColorComponentOrNull(String imageColorComponentOrNull)
+ {
+ this.imageColorComponentOrNull = imageColorComponentOrNull;
+ }
+
+ public String getFilePath()
+ {
+ return filePath;
+ }
+
+ public void setFilePath(String filePath)
+ {
+ this.filePath = filePath;
+ }
+
+ public String getThumbnailImageIdOrNull()
+ {
+ return thumbnailImageIdOrNull;
+ }
+
+ public void setThumbnailImageIdOrNull(String thumbnailImageIdOrNull)
+ {
+ this.thumbnailImageIdOrNull = thumbnailImageIdOrNull;
+ }
+
+ public String getThumbnailColorComponentOrNull()
+ {
+ return thumbnailColorComponentOrNull;
+ }
+
+ public void setThumbnailColorComponentOrNull(String thumbnailColorComponentOrNull)
+ {
+ this.thumbnailColorComponentOrNull = thumbnailColorComponentOrNull;
+ }
+
+ public String getChannelCode()
+ {
+ return channelCode;
+ }
+
+ public void setChannelCode(String channelCode)
+ {
+ this.channelCode = channelCode;
+ }
+
+ public Integer getTileColumn()
+ {
+ return tileColumn;
+ }
+
+ public void setTileColumn(Integer tileColumn)
+ {
+ this.tileColumn = tileColumn;
+ }
+
+ public Integer getTileRow()
+ {
+ return tileRow;
+ }
+
+ public void setTileRow(Integer tileRow)
+ {
+ this.tileRow = tileRow;
+ }
+
+ public Float getZ()
+ {
+ return z;
+ }
+
+ public void setZ(Float z)
+ {
+ this.z = z;
+ }
+
+ public Float getT()
+ {
+ return t;
+ }
+
+ public void setT(Float t)
+ {
+ this.t = t;
+ }
+
+ public Integer getSeriesNumber()
+ {
+ return seriesNumber;
+ }
+
+ public void setSeriesNumber(Integer seriesNumber)
+ {
+ this.seriesNumber = seriesNumber;
+ }
+}
--
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