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 2c5f832622b408a95a9cba711f6932b3f7699db0..9283687317ce1d06fa8968fa5ec3bfd21d6ec768 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
@@ -21,7 +21,7 @@ import java.awt.image.BufferedImage;
import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContentNode;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageLibraryInfo;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageTransfomationFactories;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ChannelColorRGB;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColorRGB;
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.plugin.screening.shared.imaging.dataaccess.ColorComponent;
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 09960e8adea6d243afddc3163f95d71d4e13ad53..50712b186241894e88b8ab73fbe9a06d2b604d8b 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
@@ -41,9 +41,9 @@ import ch.systemsx.cisd.hcs.Geometry;
import ch.systemsx.cisd.hcs.Location;
import ch.systemsx.cisd.hcs.WellGeometry;
import ch.systemsx.cisd.openbis.dss.etl.dto.RelativeImageFile;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.Channel;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageFileInfo;
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.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;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageStorageProcessor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageStorageProcessor.java
index 7abd34affdcecf6f077d4e97bcc7176f1539b26f..b80f9824cdf8c95993fa60fbc8c521828dba5660 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageStorageProcessor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageStorageProcessor.java
@@ -61,15 +61,15 @@ import ch.systemsx.cisd.openbis.dss.etl.PlateStorageProcessor.DatasetOwnerInform
import ch.systemsx.cisd.openbis.dss.etl.PlateStorageProcessor.ImageDatasetOwnerInformation;
import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingQueryDAO;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageSeriesPoint;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.Channel;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColorComponent;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageFileInfo;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageStorageConfiguraton;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.OriginalDataStorageFormat;
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.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.ImageStorageConfiguraton;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.OriginalDataStorageFormat;
-import ch.systemsx.cisd.openbis.dss.etl.jython.JythonPlateDataSetHandler;
+import ch.systemsx.cisd.openbis.dss.etl.jython.v1.JythonPlateDataSetHandler;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ChannelDescription;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ComputeIntensityLevelTransformationsMaintenanceTask.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ComputeIntensityLevelTransformationsMaintenanceTask.java
index 3c3081c18534f5c21d0b15bdeaa2fdfbc356e3fc..4fe390990c2e22621a21e1d304d95b446191badf 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ComputeIntensityLevelTransformationsMaintenanceTask.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ComputeIntensityLevelTransformationsMaintenanceTask.java
@@ -37,9 +37,9 @@ import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.common.maintenance.IMaintenanceTask;
import ch.systemsx.cisd.common.properties.PropertyUtils;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.transformations.ImageTransformation;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.transformations.ImageTransformationBuffer;
-import ch.systemsx.cisd.openbis.dss.etl.jython.SimpleImageDataSetRegistrator;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.transformations.ImageTransformation;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.transformations.ImageTransformationBuffer;
+import ch.systemsx.cisd.openbis.dss.etl.jython.v1.SimpleImageDataSetRegistrator;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.IHierarchicalContentProvider;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/FlexibleHCSImageFileExtractor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/FlexibleHCSImageFileExtractor.java
index 5cf660cf96787875215162f16daf02ca4bbb4e6d..d8f88e347dec8efe55d9c25bfcf62b610898f2eb 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/FlexibleHCSImageFileExtractor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/FlexibleHCSImageFileExtractor.java
@@ -20,7 +20,7 @@ import java.io.File;
import java.util.Properties;
import ch.systemsx.cisd.openbis.dss.etl.dto.UnparsedImageFileInfo;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageFileInfo;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageFileInfo;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
/**
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageDatasetUploader.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageDatasetUploader.java
index 354e20f36421390c04b760c73dbbf28a882c1ac8..2f31e612b754cdae096e2c1a38ba3bac8730b849 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageDatasetUploader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageDatasetUploader.java
@@ -24,7 +24,7 @@ import ch.systemsx.cisd.openbis.dss.etl.ImagingDatabaseHelper.ExperimentWithChan
import ch.systemsx.cisd.openbis.dss.etl.ImagingDatabaseHelper.ImagingChannelsMap;
import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingQueryDAO;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageZoomLevel;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.Channel;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.Channel;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgImageZoomLevelDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgSpotDTO;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageFileExtractor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageFileExtractor.java
index dee8e2d5f3216df78c85b84e3779ff547b47cd15..f634e70062f72b9f0683539a1d43ed8d04598057 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageFileExtractor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageFileExtractor.java
@@ -25,7 +25,7 @@ import org.apache.commons.lang.StringUtils;
import ch.systemsx.cisd.common.properties.PropertyUtils;
import ch.systemsx.cisd.hcs.Location;
import ch.systemsx.cisd.openbis.dss.etl.dto.UnparsedImageFileInfo;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageFileInfo;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageFileInfo;
import ch.systemsx.cisd.openbis.generic.shared.basic.CodeNormalizer;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
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 643d466d9ee1778ee1b321595df7e92e21f7fe0d..bf73bdf98911b3803120a5c39bddfc24629d0396 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
@@ -52,14 +52,14 @@ import ch.systemsx.cisd.common.process.ProcessIOStrategy;
import ch.systemsx.cisd.common.process.ProcessResult;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageLibraryInfo;
import ch.systemsx.cisd.openbis.dss.etl.dto.RelativeImageFile;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.Channel;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColorComponent;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageFileInfo;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageStorageConfiguraton;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ThumbnailsStorageFormat;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ImageDataSetStructure;
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.ImageStorageConfiguraton;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ThumbnailsStorageFormat;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.transformations.ImageTransformation;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.transformations.ImageTransformation;
import ch.systemsx.cisd.openbis.dss.generic.server.images.ImageChannelsUtils;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImageFileExtractionResult.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImageFileExtractionResult.java
index d5a007aac581d25c1127509a1ada5efb3df0bf35..98bdf444582c2ce9e3190db2bc4c5468b166e862 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImageFileExtractionResult.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImageFileExtractionResult.java
@@ -20,7 +20,7 @@ import java.util.List;
import ch.systemsx.cisd.hcs.Geometry;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageLibraryInfo;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.Channel;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.Channel;
/**
* Class which contains the image extraction process results.
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImageValidator.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImageValidator.java
index 3c6c18cd58d4584c8825be5423c581c073e83e90..8b0c962cdd36f06589b36d5c138519a518d86cb7 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImageValidator.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImageValidator.java
@@ -29,7 +29,7 @@ import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.mail.IMailClient;
import ch.systemsx.cisd.hcs.Geometry;
import ch.systemsx.cisd.openbis.dss.etl.PlateStorageProcessor.DatasetOwnerInformation;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.Channel;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.Channel;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.plugin.screening.shared.dto.PlateDimension;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImagingDatabaseHelper.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImagingDatabaseHelper.java
index e73f63d36cbf7f3b92e2943bf6b911c0cd2a10fe..33773195aaa1ac229442455f0ee565c281859f7b 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImagingDatabaseHelper.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImagingDatabaseHelper.java
@@ -26,10 +26,10 @@ import java.util.Set;
import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingQueryDAO;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.Channel;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ChannelColor;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ChannelColorRGB;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.transformations.ImageTransformation;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.Channel;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColor;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColorRGB;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.transformations.ImageTransformation;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgChannelDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgContainerDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgExperimentDTO;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/MicroscopyBlackboxSeriesStorageProcessor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/MicroscopyBlackboxSeriesStorageProcessor.java
index ad15383454023188425bca50306aef473e040a81..d8e619e90a566b5ffd1019b637af1535c491ab9d 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/MicroscopyBlackboxSeriesStorageProcessor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/MicroscopyBlackboxSeriesStorageProcessor.java
@@ -31,7 +31,7 @@ import ch.systemsx.cisd.openbis.dss.etl.PlateStorageProcessor.ImageDatasetOwnerI
import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingQueryDAO;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageDatasetInfo;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageLibraryInfo;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageFileInfo;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageFileInfo;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ChannelDescription;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/MicroscopyImageDatasetUploader.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/MicroscopyImageDatasetUploader.java
index 7f01908efa342bf6fbd37bd5fc2f164d85bce3a7..002725fe625f39ddca0444e63679bba523fd70e9 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/MicroscopyImageDatasetUploader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/MicroscopyImageDatasetUploader.java
@@ -22,7 +22,7 @@ import java.util.Map;
import ch.systemsx.cisd.openbis.dss.etl.ImagingDatabaseHelper.ImagingChannelsMap;
import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingQueryDAO;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageZoomLevel;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.Channel;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.Channel;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgImageZoomLevelDTO;
/**
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/MicroscopyImageFileExtractor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/MicroscopyImageFileExtractor.java
index a4814547e474ed364dc74f4e534a89cedef023e5..dd97875a9a549e2f782d9b8786b71ff079ad22c5 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/MicroscopyImageFileExtractor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/MicroscopyImageFileExtractor.java
@@ -22,7 +22,7 @@ import java.util.Properties;
import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
import ch.systemsx.cisd.hcs.Location;
import ch.systemsx.cisd.openbis.dss.etl.dto.UnparsedImageFileInfo;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageFileInfo;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageFileInfo;
import ch.systemsx.cisd.openbis.generic.shared.basic.CodeNormalizer;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PlateGeometryOracle.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PlateGeometryOracle.java
index 58c3415cf68fbbad650f0a93146d9e89ed92a291..11346c45b0e8439725b8b47720d02b6e5fd80d9f 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PlateGeometryOracle.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PlateGeometryOracle.java
@@ -28,8 +28,8 @@ import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.shared.basic.string.StringUtils;
import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationDetails;
import ch.systemsx.cisd.hcs.Location;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageFileInfo;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ImageDataSetInformation;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageFileInfo;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedBasicOpenBISService;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.VocabularyTerm;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PlateStorageProcessor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PlateStorageProcessor.java
index 5364c9620b57a08d16a5c93f12ce2c9cf0e1f302..8229588f587c603b9dff3a6466612fb02ff6bb45 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PlateStorageProcessor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PlateStorageProcessor.java
@@ -31,10 +31,10 @@ import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingQueryDAO;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageDatasetInfo;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageLibraryInfo;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageZoomLevel;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ThumbnailsStorageFormat.FileFormat;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeatureVectorDataSetInformation;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ImageDataSetInformation;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ThumbnailsInfo;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ThumbnailsStorageFormat.FileFormat;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/TileGeometryOracle.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/TileGeometryOracle.java
index 5624c724a9089a1cf6ed5a86193c429905218f8a..c50bfe0f34b94ece1a07884466ed61ece70f32b9 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/TileGeometryOracle.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/TileGeometryOracle.java
@@ -25,7 +25,7 @@ import java.util.Map;
import java.util.Map.Entry;
import ch.systemsx.cisd.common.geometry.SpatialPoint;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.Location;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.Location;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry;
/**
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/ImageMetadataExtractor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/ImageMetadataExtractor.java
index 1318e501f4231a74378454026a47cd33146297e8..49454ba304e7a158e24713757af001b4482e9c97 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/ImageMetadataExtractor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/ImageMetadataExtractor.java
@@ -27,7 +27,7 @@ import ch.systemsx.cisd.imagereaders.ImageID;
import ch.systemsx.cisd.imagereaders.ImageReaderConstants;
import ch.systemsx.cisd.imagereaders.ImageReaderFactory;
import ch.systemsx.cisd.openbis.dss.etl.TileGeometryOracle;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.Location;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.Location;
/**
* @author Kaloyan Enimanev
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 6f1103cf731f12d82d136cd1fc08a6164ca73575..794d196d34d785f36a4d8c13f539baa170bb1220 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
@@ -35,7 +35,7 @@ import ch.systemsx.cisd.openbis.dss.etl.IImagingDatasetLoader;
import ch.systemsx.cisd.openbis.dss.etl.PrefixedImage;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageLibraryInfo;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageTransfomationFactories;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ChannelColorRGB;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColorRGB;
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.ImageChannelStackReference;
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.ImageChannelStackReference.HCSChannelStackByLocationReference;
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.ImageChannelStackReference.MicroscopyChannelStackByLocationReference;
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 e05a871f502b5cb5abfe79d54633208c5f6e6652..f552f0ada8e39a13f7776199c5ae65447d8dd59e 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
@@ -19,7 +19,7 @@ package ch.systemsx.cisd.openbis.dss.etl.dto;
import java.io.Serializable;
import ch.systemsx.cisd.common.reflection.AbstractHashable;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageFileInfo;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageFileInfo;
/**
* Points to one image on the file system.
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/UnparsedImageFileInfo.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/UnparsedImageFileInfo.java
index 6ae3e01cc00c44314681609fcb548b479d402967..38821a2c33a3430af8fae099b914323c0d953c35 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/UnparsedImageFileInfo.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/UnparsedImageFileInfo.java
@@ -1,7 +1,7 @@
package ch.systemsx.cisd.openbis.dss.etl.dto;
import ch.systemsx.cisd.common.reflection.AbstractHashable;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageFileInfo;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageFileInfo;
/**
* Intermediate DTO containing tokens from which image info {@link ImageFileInfo} can be extracted
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/BasicDataSetInformation.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/BasicDataSetInformation.java
new file mode 100644
index 0000000000000000000000000000000000000000..ad1f671874787924345f39b9b14ad9851a7d14e1
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/BasicDataSetInformation.java
@@ -0,0 +1,89 @@
+/*
+ * 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.dss.etl.dto.api;
+
+import java.util.Arrays;
+
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+import ch.systemsx.cisd.openbis.generic.shared.IServer;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
+
+/**
+ * Basic attributes of a dataset connected to a sample and optionally to one parent dataset.
+ *
+ * @author Tomasz Pylak
+ */
+public class BasicDataSetInformation extends DataSetInformation
+{
+ private static final long serialVersionUID = IServer.VERSION;
+
+ private String fileFormatTypeCode;
+
+ // marks if a dataset is measured or derived from measured data
+ private boolean isMeasured = true;
+
+ /** Sets code of the dataset type */
+ public void setDatasetTypeCode(String datasetTypeCode)
+ {
+ DataSetType dataSetType = new DataSetType();
+ dataSetType.setCode(datasetTypeCode);
+ super.setDataSetType(dataSetType);
+ }
+
+ /** Mandatory: sets file format code. */
+ public void setFileFormatCode(String fileFormatCode)
+ {
+ this.fileFormatTypeCode = fileFormatCode;
+ }
+
+ /**
+ * Sets attributes of the connected sample - optional.
+ * <p>
+ * Alternatively, call
+ * {@link ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSetUpdatable#setSample(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.ISampleImmutable)}
+ * on the object returned by
+ * {@link ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSetRegistrationTransaction#createNewDataSet()}.
+ */
+ public void setSample(String sampleSpaceCode, String sampleCode)
+ {
+ super.setSpaceCode(sampleSpaceCode);
+ super.setSampleCode(sampleCode);
+ }
+
+ /** attributes of the parent dataset - optional */
+ public void setParentDatasetCode(String parentDatasetCode)
+ {
+ super.setParentDataSetCodes(Arrays.asList(parentDatasetCode));
+ }
+
+ /** marks if a dataset is measured or derived from measured data */
+ public void setMeasured(boolean isMeasured)
+ {
+ this.isMeasured = isMeasured;
+ }
+
+ public String getFileFormatTypeCode()
+ {
+ return fileFormatTypeCode;
+ }
+
+ public boolean isMeasured()
+ {
+ return isMeasured;
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/Channel.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/Channel.java
new file mode 100644
index 0000000000000000000000000000000000000000..8a8465b4cffe1c7135338b0c4e7797fcadda8e25
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/Channel.java
@@ -0,0 +1,184 @@
+package ch.systemsx.cisd.openbis.dss.etl.dto.api;
+
+import java.awt.Color;
+import java.io.Serializable;
+
+import ch.systemsx.cisd.common.image.WavelengthColor;
+import ch.systemsx.cisd.common.reflection.AbstractHashable;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.transformations.ImageTransformation;
+
+/**
+ * A channel in which the image has been acquired.
+ * <p>
+ * Each channel has its <code>code</code> which uniquely identifies it in one experiment or dataset.
+ * </p>
+ *
+ * @author Tomasz Pylak
+ */
+public class Channel extends AbstractHashable implements Serializable
+{
+ private static final long serialVersionUID = 1L;
+
+ private final String code;
+
+ private final String label;
+
+ private String description;
+
+ private Integer wavelength;
+
+ private ChannelColorRGB channelColorOrNull;
+
+ private ImageTransformation[] availableTransformations = new ImageTransformation[0];
+
+ /**
+ * Constructs a channel with a specified code and label. The channel will be presented in a
+ * default color.
+ */
+ public Channel(String code, String label)
+ {
+ this(code, label, (ChannelColorRGB) null);
+ }
+
+ /**
+ * Constructs a channel with a specified code and label. The channel will be presented in a
+ * specified color.
+ */
+ public Channel(String code, String label, ChannelColor channelColorOrNull)
+ {
+ this(code, label, convertColor(channelColorOrNull));
+ }
+
+ /**
+ * Version of method for v1 channel color to keep backwards compatibility
+ */
+ public Channel(String code, String label,
+ ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ChannelColor channelColorOrNull)
+ {
+ this(code, label, channelColorOrNull.getIndependentChannelColor());
+ }
+
+ /**
+ * Constructs a channel with a specified code and label. The channel will be presented in a
+ * specified color.
+ */
+ public Channel(String code, String label, ChannelColorRGB channelColorOrNull)
+ {
+ assert code != null : "code is null";
+ assert label != null : "label is null";
+ this.label = label;
+ this.code = code;
+ this.channelColorOrNull = channelColorOrNull;
+ }
+
+ private static ChannelColorRGB convertColor(ChannelColor plainChannelColorOrNull)
+ {
+ if (plainChannelColorOrNull == null)
+ {
+ return null;
+ }
+ return plainChannelColorOrNull.getRGB();
+ }
+
+ public String getCode()
+ {
+ return code;
+ }
+
+ public String tryGetDescription()
+ {
+ return description;
+ }
+
+ public Integer tryGetWavelength()
+ {
+ return wavelength;
+ }
+
+ public String getLabel()
+ {
+ return label;
+ }
+
+ /**
+ * @return color for the specified channel which will be used to display merged channels images.
+ * null only during dataset registration when default color should be used, afterwards
+ * never null.
+ */
+ public ChannelColorRGB tryGetChannelColor()
+ {
+ return channelColorOrNull;
+ }
+
+ // never null, can be empty
+ public ImageTransformation[] getAvailableTransformations()
+ {
+ return availableTransformations;
+ }
+
+ // ------------------- setters -------------------
+
+ /** Sets the description of the channel. Optional. */
+ public void setDescription(String description)
+ {
+ this.description = description;
+ }
+
+ /** Sets the wavelength of the light (in nanometers) used to acquire this channel. Optional. */
+ public void setWavelength(Integer wavelength)
+ {
+ this.wavelength = wavelength;
+ }
+
+ /**
+ * Sets the wavelength of the light (in nanometers) used to acquire this channel.<br>
+ * Additionally sets the channel color. The color is calculated for display on a computer
+ * monitor on the basis of the given wavelength using Bruton's algorithm. See <a
+ * href="http://www.midnightkite.com/color.html">COLOR SCIENCE web page</a> for details.
+ * <p>
+ * Optional.
+ */
+ public void setWavelengthAndColor(Integer wavelength)
+ {
+ this.wavelength = wavelength;
+ Color color = WavelengthColor.getColorForWavelength(wavelength);
+ setChannelColorRGB(convertColor(color));
+ }
+
+ private ChannelColorRGB convertColor(Color color)
+ {
+ return new ChannelColorRGB(color.getRed(), color.getGreen(), color.getBlue());
+ }
+
+ /** Sets the plain color in which this channel will be displayed. */
+ public void setChannelColor(ChannelColor channelColor)
+ {
+ this.channelColorOrNull = convertColor(channelColor);
+ }
+
+ /** version of method for v1 ChannelColor kept for backwards compatibility */
+ public void setChannelColor(
+ ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ChannelColor channelColor)
+ {
+ setChannelColor(channelColor.getIndependentChannelColor());
+ }
+
+ /** Sets RGB color in which this channel will be displayed. */
+ public void setChannelColorRGB(ChannelColorRGB channelColor)
+ {
+ this.channelColorOrNull = channelColor;
+ }
+
+ /** Sets available transformations which can be applied to images of this channel on request. */
+ public void setAvailableTransformations(ImageTransformation[] transformations)
+ {
+ if (transformations == null)
+ {
+ this.availableTransformations = new ImageTransformation[0];
+ } else
+ {
+ this.availableTransformations = transformations;
+ }
+ }
+
+}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/ChannelColor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/ChannelColor.java
new file mode 100644
index 0000000000000000000000000000000000000000..ce01e320c95a9086a58130697c935834531f92f9
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/ChannelColor.java
@@ -0,0 +1,71 @@
+package ch.systemsx.cisd.openbis.dss.etl.dto.api;
+
+/**
+ * Allowed colors in which channels can be presented.
+ *
+ * @author Tomasz Pylak
+ */
+public enum ChannelColor
+{
+ BLUE(0), GREEN(1), RED(2), RED_GREEN(3), RED_BLUE(4), GREEN_BLUE(5);
+
+ private static final int MAX_COLOR = calcMaxColorIndex();
+
+ // If no mapping between channels and colors has been provided then channels get consecutive
+ // colors. This field determines the order in which colors are assigned.
+ // It is important for backward compatibility as well.
+ private final int orderIndex;
+
+ private ChannelColor(int orderIndex)
+ {
+ this.orderIndex = orderIndex;
+ }
+
+ private static int calcMaxColorIndex()
+ {
+ int max = 0;
+ for (ChannelColor color : values())
+ {
+ max = Math.max(max, color.getColorOrderIndex());
+ }
+ return max;
+ }
+
+ public int getColorOrderIndex()
+ {
+ return orderIndex;
+ }
+
+ public static ChannelColor createFromIndex(int colorIndex)
+ {
+ for (ChannelColor color : values())
+ {
+ if (color.getColorOrderIndex() == colorIndex % (MAX_COLOR + 1))
+ {
+ return color;
+ }
+ }
+ throw new IllegalStateException("Invalid color index: " + colorIndex + "!");
+ }
+
+ public ChannelColorRGB getRGB()
+ {
+ switch (this)
+ {
+ case RED:
+ return new ChannelColorRGB(255, 0, 0);
+ case GREEN:
+ return new ChannelColorRGB(0, 255, 0);
+ case BLUE:
+ return new ChannelColorRGB(0, 0, 255);
+ case RED_GREEN:
+ return new ChannelColorRGB(255, 255, 0);
+ case GREEN_BLUE:
+ return new ChannelColorRGB(0, 255, 255);
+ case RED_BLUE:
+ return new ChannelColorRGB(255, 0, 255);
+ default:
+ throw new IllegalStateException("unhandled enum " + this);
+ }
+ }
+}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/ChannelColorComponent.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/ChannelColorComponent.java
new file mode 100644
index 0000000000000000000000000000000000000000..76b5b29952eb23e7df40c60916ee6b64498cc03c
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/ChannelColorComponent.java
@@ -0,0 +1,45 @@
+/*
+ * 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.dss.etl.dto.api;
+
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ColorComponent;
+
+/**
+ * Color component of an image which constitutes one channel. Useful if the image consists of all
+ * channels merged together.
+ *
+ * @author Tomasz Pylak
+ */
+public enum ChannelColorComponent
+{
+ RED, GREEN, BLUE;
+
+ public static ColorComponent getColorComponent(ChannelColorComponent channelColorComponent)
+ {
+ switch (channelColorComponent)
+ {
+ case BLUE:
+ return ColorComponent.BLUE;
+ case GREEN:
+ return ColorComponent.GREEN;
+ case RED:
+ return ColorComponent.RED;
+ }
+
+ return null;
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/ChannelColorRGB.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/ChannelColorRGB.java
new file mode 100644
index 0000000000000000000000000000000000000000..5b659e00d0e3f70ee62d296666e6cd75819ef799
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/ChannelColorRGB.java
@@ -0,0 +1,101 @@
+/*
+ * 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.dss.etl.dto.api;
+
+import java.io.Serializable;
+
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
+
+/**
+ * RGB color components specify the color in which channel should be displayed.
+ *
+ * @author Tomasz Pylak
+ */
+public class ChannelColorRGB implements Serializable
+{
+ private static final long serialVersionUID = ServiceVersionHolder.VERSION;
+
+ private int r, g, b;
+
+ @SuppressWarnings("unused")
+ private ChannelColorRGB()
+ {
+ }
+
+ public ChannelColorRGB(int r, int g, int b)
+ {
+ assert r >= 0 && r <= 255 : "invalid color " + r;
+ assert g >= 0 && g <= 255 : "invalid color " + g;
+ assert b >= 0 && b <= 255 : "invalid color " + b;
+
+ this.r = r;
+ this.g = g;
+ this.b = b;
+ }
+
+ public int getR()
+ {
+ return r;
+ }
+
+ public int getG()
+ {
+ return g;
+ }
+
+ public int getB()
+ {
+ return b;
+ }
+
+ @Override
+ public String toString()
+ {
+ return "Color(r=" + r + ", g=" + g + ", b=" + b + ")";
+ }
+
+ @Override
+ public int hashCode()
+ {
+ final int prime = 31;
+ int result = 1;
+ result = prime * result + b;
+ result = prime * result + g;
+ result = prime * result + r;
+ return result;
+ }
+
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (this == obj)
+ return true;
+ if (obj == null)
+ return false;
+ if (getClass() != obj.getClass())
+ return false;
+ ChannelColorRGB other = (ChannelColorRGB) obj;
+ if (b != other.b)
+ return false;
+ if (g != other.g)
+ return false;
+ if (r != other.r)
+ return false;
+ return true;
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/IFeatureDefinition.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/IFeatureDefinition.java
similarity index 97%
rename from screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/IFeatureDefinition.java
rename to screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/IFeatureDefinition.java
index 4d52a964e47d252dbd131b2a7d6cce1407640601..57e2813b7fd925e3590e353bbc2eb1fe0c5956bd 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/IFeatureDefinition.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/IFeatureDefinition.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1;
+package ch.systemsx.cisd.openbis.dss.etl.dto.api;
/**
* An interface which allows to define values of one feature.
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/IFeaturesBuilder.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/IFeaturesBuilder.java
similarity index 94%
rename from screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/IFeaturesBuilder.java
rename to screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/IFeaturesBuilder.java
index e44605f40ab11e71919992b9e2fd5dea7ab62de2..229259ebf3f93562629efa750f67e31be0c0c866 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/IFeaturesBuilder.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/IFeaturesBuilder.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1;
+package ch.systemsx.cisd.openbis.dss.etl.dto.api;
/**
* Allows to define feature vectors of one image analysis dataset.
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/ImageFileInfo.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/ImageFileInfo.java
new file mode 100644
index 0000000000000000000000000000000000000000..d32a35aad31b517498a6a7f1cda20384903a90f5
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/ImageFileInfo.java
@@ -0,0 +1,183 @@
+package ch.systemsx.cisd.openbis.dss.etl.dto.api;
+
+import java.io.Serializable;
+
+import ch.systemsx.cisd.hcs.Location;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
+
+/**
+ * DTO with information about one image file
+ *
+ * @author Tomasz Pylak
+ */
+public class ImageFileInfo implements Serializable
+{
+ private static final long serialVersionUID = 1L;
+
+ private WellLocation wellLocationOrNull;
+
+ private Location tileLocation;
+
+ private String channelCode;
+
+ private final String imageRelativePath;
+
+ private Float timepointOrNull;
+
+ private Float depthOrNull;
+
+ private Integer seriesNumberOrNull;
+
+ private ImageIdentifier imageIdentifier;
+
+ private String uniqueImageIdentifier;
+
+ private String containerDataSetCode;
+
+ public ImageFileInfo(String channelCode, int tileRow, int tileColumn, String imageRelativePath)
+ {
+ assert channelCode != null;
+ assert imageRelativePath != null;
+
+ this.channelCode = channelCode;
+ this.imageRelativePath = imageRelativePath;
+ setTile(tileRow, tileColumn);
+ }
+
+ public String tryGetUniqueStringIdentifier()
+ {
+ if (imageIdentifier != null)
+ {
+ return imageIdentifier.getUniqueStringIdentifier();
+ } else if (uniqueImageIdentifier != null)
+ {
+ return uniqueImageIdentifier;
+ }
+
+ return null;
+ }
+
+ public Integer tryGetWellRow()
+ {
+ return wellLocationOrNull == null ? null : wellLocationOrNull.getRow();
+ }
+
+ public Integer tryGetWellColumn()
+ {
+ return wellLocationOrNull == null ? null : wellLocationOrNull.getColumn();
+ }
+
+ public WellLocation tryGetWellLocation()
+ {
+ return wellLocationOrNull;
+ }
+
+ public boolean hasWellLocation()
+ {
+ return wellLocationOrNull != null;
+ }
+
+ public int getTileRow()
+ {
+ return tileLocation.getY();
+ }
+
+ public int getTileColumn()
+ {
+ return tileLocation.getX();
+ }
+
+ public String getChannelCode()
+ {
+ return channelCode;
+ }
+
+ public String getImageRelativePath()
+ {
+ return imageRelativePath;
+ }
+
+ public Float tryGetTimepoint()
+ {
+ return timepointOrNull;
+ }
+
+ public Float tryGetDepth()
+ {
+ return depthOrNull;
+ }
+
+ public Integer tryGetSeriesNumber()
+ {
+ return seriesNumberOrNull;
+ }
+
+ // --- setters
+
+ public void setImageIdentifier(ImageIdentifier imageIdentifier)
+ {
+ this.imageIdentifier = imageIdentifier;
+ }
+
+ public void setWell(int row, int column)
+ {
+ this.wellLocationOrNull = new WellLocation(row, column);
+ }
+
+ /** @return true if well row and column could be parsed */
+ public boolean setWell(String wellText)
+ {
+ try
+ {
+ this.wellLocationOrNull = WellLocation.parseLocationStr(wellText);
+ } catch (Exception e)
+ {
+ // do nothing
+ }
+ return wellLocationOrNull != null;
+ }
+
+ public void setTile(int row, int column)
+ {
+ this.tileLocation = Location.createLocationFromRowAndColumn(row, column);
+ }
+
+ public void setTimepoint(Float value)
+ {
+ this.timepointOrNull = value;
+ }
+
+ public void setDepth(Float value)
+ {
+ this.depthOrNull = value;
+ }
+
+ public void setSeriesNumber(Integer value)
+ {
+ 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()
+ {
+ return "ImageFileInfo [well=" + wellLocationOrNull + ", tile=" + tileLocation
+ + ", channel=" + channelCode + ", path=" + imageRelativePath + ", timepoint="
+ + 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/ImageIdentifier.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/ImageIdentifier.java
new file mode 100644
index 0000000000000000000000000000000000000000..e5a71e6e446738f2864a41b5112634b16cb2c302
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/ImageIdentifier.java
@@ -0,0 +1,135 @@
+/*
+ * 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.dss.etl.dto.api;
+
+import java.io.Serializable;
+
+import ch.systemsx.cisd.imagereaders.ImageID;
+
+/**
+ * Immutable value class of an image ID based on series index, time series index, focal plane index,
+ * and color channel index. It will be used to identify images in a container image file format like
+ * multi-page TIFF.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class ImageIdentifier implements Comparable<ImageIdentifier>, Serializable
+{
+ private static final long serialVersionUID = 1L;
+
+ public static final ImageIdentifier NULL = new ImageIdentifier(0, 0, 0, 0);
+
+ private final int seriesIndex;
+
+ private final int timeSeriesIndex;
+
+ private final int focalPlaneIndex;
+
+ private final int colorChannelIndex;
+
+ /**
+ * Creates an instance for the specified series index, time series (or T) index, focal plane (or
+ * Z) index, color channel index.
+ */
+ public ImageIdentifier(int seriesIndex, int timeSeriesIndex, int focalPlaneIndex,
+ int colorChannelIndex)
+ {
+ this.seriesIndex = seriesIndex;
+ this.timeSeriesIndex = timeSeriesIndex;
+ this.focalPlaneIndex = focalPlaneIndex;
+ this.colorChannelIndex = colorChannelIndex;
+ }
+
+ public int getSeriesIndex()
+ {
+ return seriesIndex;
+ }
+
+ public int getTimeSeriesIndex()
+ {
+ return timeSeriesIndex;
+ }
+
+ public int getFocalPlaneIndex()
+ {
+ return focalPlaneIndex;
+ }
+
+ public int getColorChannelIndex()
+ {
+ return colorChannelIndex;
+ }
+
+ public String getUniqueStringIdentifier()
+ {
+ return new ImageID(getSeriesIndex(), getTimeSeriesIndex(), getFocalPlaneIndex(),
+ getColorChannelIndex()).getID();
+ }
+
+ @Override
+ public int compareTo(ImageIdentifier that)
+ {
+ int diff = seriesIndex - that.seriesIndex;
+ if (diff != 0)
+ {
+ return diff;
+ }
+ diff = timeSeriesIndex - that.timeSeriesIndex;
+ if (diff != 0)
+ {
+ return diff;
+ }
+ diff = focalPlaneIndex - that.focalPlaneIndex;
+ if (diff != 0)
+ {
+ return diff;
+ }
+ return colorChannelIndex - that.colorChannelIndex;
+ }
+
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj instanceof ImageIdentifier == false)
+ {
+ return false;
+ }
+ ImageIdentifier that = (ImageIdentifier) obj;
+ return seriesIndex == that.seriesIndex && timeSeriesIndex == that.timeSeriesIndex
+ && focalPlaneIndex == that.focalPlaneIndex
+ && colorChannelIndex == that.colorChannelIndex;
+ }
+
+ @Override
+ public int hashCode()
+ {
+ return ((((seriesIndex * 37) + timeSeriesIndex) * 37) + focalPlaneIndex) * 37
+ + colorChannelIndex;
+ }
+
+ @Override
+ public String toString()
+ {
+ return seriesIndex + "." + timeSeriesIndex + "." + focalPlaneIndex + "."
+ + colorChannelIndex;
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/ImageMetadata.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/ImageMetadata.java
new file mode 100644
index 0000000000000000000000000000000000000000..5198c5e9be1fbbe381d01649e75c8934561d5319
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/ImageMetadata.java
@@ -0,0 +1,160 @@
+package ch.systemsx.cisd.openbis.dss.etl.dto.api;
+
+import org.apache.commons.lang.StringUtils;
+
+
+/**
+ * Store well, channel and tile number to which an image belongs. Optionally stores
+ * timepoint/depth-scan/image series number.
+ *
+ * @author Tomasz Pylak
+ */
+public class ImageMetadata
+{
+ private String channelCode;
+
+ private int tileNumber;
+
+ private String well;
+
+ private Float timepointOrNull;
+
+ private Float depthOrNull;
+
+ private Integer seriesNumberOrNull;
+
+ private ImageIdentifier imageIdentifierOrNull;
+
+ public String getChannelCode()
+ {
+ return channelCode;
+ }
+
+ /** Sets channel code. */
+ public void setChannelCode(String channelCode)
+ {
+ this.channelCode = channelCode;
+ }
+
+ public int getTileNumber()
+ {
+ return tileNumber;
+ }
+
+ /** Sets tile number. It should start from 1. */
+ public void setTileNumber(int tileNumber)
+ {
+ this.tileNumber = tileNumber;
+ }
+
+ public String getWell()
+ {
+ return well;
+ }
+
+ /** Sets well code (example: "A1") */
+ public void setWell(String well)
+ {
+ this.well = well;
+ }
+
+ /** Sets the timepoint of the image. Optional. */
+ public void setTimepoint(Float value)
+ {
+ this.timepointOrNull = value;
+ }
+
+ /** Sets the depth at which the image has been scanned. Optional. */
+ public void setDepth(Float value)
+ {
+ this.depthOrNull = value;
+ }
+
+ /**
+ * Sets the integer series number of the image. Optional. Used to order images when there are no
+ * time or depth dimentions but there is a series of images for one well, channel and tile. Can
+ * be also used together with time and depth dimention.
+ */
+ public void setSeriesNumber(Integer value)
+ {
+ this.seriesNumberOrNull = value;
+ }
+
+ /**
+ * Sets the id of the image inside a container image file format. This is optional and not
+ * needed for image files which contain only one image.
+ */
+ public void setImageIdentifier(ImageIdentifier imageIdentifier)
+ {
+ imageIdentifierOrNull = imageIdentifier;
+ }
+
+ public Float tryGetTimepoint()
+ {
+ return timepointOrNull;
+ }
+
+ public Float tryGetDepth()
+ {
+ return depthOrNull;
+ }
+
+ public Integer tryGetSeriesNumber()
+ {
+ return seriesNumberOrNull;
+ }
+
+ public ImageIdentifier tryGetImageIdentifier()
+ {
+ return imageIdentifierOrNull;
+ }
+
+ /**
+ * Validates that tile number, channel and well (if argument is <code>false</code>) have been
+ * specified.
+ *
+ * @throws IllegalStateException if the object is not valid.
+ */
+ public void ensureValid(boolean isMicroscopy)
+ {
+ if (tileNumber <= 0)
+ {
+ throw new IllegalStateException("Tile number has to be > 0, but is " + tileNumber);
+ }
+ if (StringUtils.isBlank(channelCode))
+ {
+ throw new IllegalStateException("Channel code is not specified");
+ }
+ if (StringUtils.isBlank(well) && isMicroscopy == false)
+ {
+ throw new IllegalStateException("Well is not specified");
+ }
+ }
+
+ @Override
+ public String toString()
+ {
+ StringBuffer sb = new StringBuffer();
+ sb.append("ImageMetadata [channelCode=" + channelCode + ", tileNumber=" + tileNumber
+ + ", well=" + well);
+ if (timepointOrNull != null)
+ {
+ sb.append(", timepointOrNull =" + timepointOrNull);
+ }
+ if (depthOrNull != null)
+ {
+ sb.append(", depthOrNull=" + depthOrNull);
+ }
+ if (seriesNumberOrNull != null)
+ {
+ sb.append(", seriesNumberOrNull=" + seriesNumberOrNull);
+ }
+ if (imageIdentifierOrNull != null)
+ {
+ sb.append(", imageIdentifierOrNull=" + imageIdentifierOrNull);
+ }
+ sb.append("]");
+ return sb.toString();
+ }
+
+}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/ImageStorageConfiguraton.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/ImageStorageConfiguraton.java
new file mode 100644
index 0000000000000000000000000000000000000000..720abe63ca0337e451a2505724e80902e93c0912
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/ImageStorageConfiguraton.java
@@ -0,0 +1,205 @@
+/*
+ * 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.dss.etl.dto.api;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+
+import ch.systemsx.cisd.base.image.IImageTransformerFactory;
+import ch.systemsx.cisd.common.reflection.AbstractHashable;
+import ch.systemsx.cisd.openbis.dss.etl.dto.ImageLibraryInfo;
+
+/**
+ * Configuration of how images should be stored. By default:
+ * <UL>
+ * <LI>no thumbnails are generated</LI>
+ * <LI>original data are stored as they come (without additional compression).</LI>
+ * </UL>
+ *
+ * @author Tomasz Pylak
+ */
+public class ImageStorageConfiguraton extends AbstractHashable implements Serializable
+{
+ private static final long serialVersionUID = 1L;
+
+ /** Returns the default configuration. */
+ public static ImageStorageConfiguraton createDefault()
+ {
+ return new ImageStorageConfiguraton();
+ }
+
+ // --- State ----------
+
+ /** No thumbnails are generated by default. */
+ private List<ThumbnailsStorageFormat> thumbnailsStorageFormatsList =
+ new ArrayList<ThumbnailsStorageFormat>();
+
+ private OriginalDataStorageFormat originalDataStorageFormat =
+ OriginalDataStorageFormat.UNCHANGED;
+
+ /** No preferences by default, each storage processor decides by its own if it is not set. */
+ private Boolean storeChannelsOnExperimentLevelOrNull = null;
+
+ /**
+ * an image transformation to be applied before the image is stored.
+ */
+ private IImageTransformerFactory imageTransformerFactoryOrNull;
+
+ /**
+ * null by default, in this case some heuristics are used to find the right library to read the
+ * images, but it is slower and not all libraries are tried.
+ */
+ private ImageLibraryInfo imageLibraryOrNull = null;
+
+ // --- Getters & Setters ----------
+
+ /** @return null if no thumbnails should be generated */
+ public List<ThumbnailsStorageFormat> getThumbnailsStorageFormat()
+ {
+ return thumbnailsStorageFormatsList;
+ }
+
+ /** Set to null if no thumbnails should be generated. Overrides previous thumbnails settings. */
+ public void setThumbnailsStorageFormat(ThumbnailsStorageFormat thumbnailsStorageFormatOrNull)
+ {
+ thumbnailsStorageFormatsList.clear();
+ addThumbnailsStorageFormat(thumbnailsStorageFormatOrNull);
+
+ }
+
+ /**
+ * Adds new thumbnails setting to the list
+ */
+ public void addThumbnailsStorageFormat(ThumbnailsStorageFormat thumbnailsStorageFormatOrNull)
+ {
+ if (thumbnailsStorageFormatOrNull != null)
+ {
+ thumbnailsStorageFormatsList.add(thumbnailsStorageFormatOrNull);
+ }
+ }
+
+ /**
+ * Convenience method to switch on thumbnails generation with default settings. Overrides the
+ * results of {@link #setThumbnailsStorageFormat(ThumbnailsStorageFormat)}!.
+ */
+ public void switchOnThumbnailsGeneration()
+ {
+ thumbnailsStorageFormatsList.clear();
+ thumbnailsStorageFormatsList.add(new ThumbnailsStorageFormat());
+ }
+
+ public OriginalDataStorageFormat getOriginalDataStorageFormat()
+ {
+ return originalDataStorageFormat;
+ }
+
+ public void setOriginalDataStorageFormat(OriginalDataStorageFormat originalDataStorageFormat)
+ {
+ this.originalDataStorageFormat = originalDataStorageFormat;
+ }
+
+ public void setOriginalDataStorageFormat(
+ ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.OriginalDataStorageFormat originalDataStorageFormat)
+ {
+ this.originalDataStorageFormat =
+ originalDataStorageFormat.getIndependentOriginalDataStorageFormat();
+ }
+
+ /**
+ * Signalizes that the channels should be saved on experiment level rather than dataset level.
+ * Will be ignored in case of microscopy where all channels are always saved at dataset level.
+ */
+ public void setStoreChannelsOnExperimentLevel(boolean storeChannelsOnExperimentLevel)
+ {
+ this.storeChannelsOnExperimentLevelOrNull = storeChannelsOnExperimentLevel;
+ }
+
+ public Boolean getStoreChannelsOnExperimentLevel()
+ {
+ return storeChannelsOnExperimentLevelOrNull;
+ }
+
+ public IImageTransformerFactory getImageTransformerFactory()
+ {
+ return imageTransformerFactoryOrNull;
+ }
+
+ /**
+ * Allows for applying an image transformation on the fly when an image is fetched.
+ */
+ public void setImageTransformerFactory(IImageTransformerFactory transformerFactory)
+ {
+ this.imageTransformerFactoryOrNull = transformerFactory;
+ }
+
+ /** Sets the library which should be used to read the images. */
+ public void setImageLibrary(ImageLibraryInfo imageLibrary)
+ {
+ this.imageLibraryOrNull = imageLibrary;
+ }
+
+ /**
+ * @return library which should be used to read the images or null if the library is not
+ * specified.
+ */
+ public ImageLibraryInfo tryGetImageLibrary()
+ {
+ return imageLibraryOrNull;
+ }
+
+ @Override
+ public String toString()
+ {
+ final StringBuilder buffer = new StringBuilder(super.toString());
+ if (originalDataStorageFormat != OriginalDataStorageFormat.UNCHANGED)
+ {
+ appendNameAndObject(buffer, "original data storage format",
+ originalDataStorageFormat.toString());
+ }
+ if (thumbnailsStorageFormatsList.size() > 0)
+ {
+ for (ThumbnailsStorageFormat thumbnailsStorageFormat : thumbnailsStorageFormatsList)
+ {
+ appendNameAndObject(buffer, "thumbnails", thumbnailsStorageFormat.toString());
+ }
+ }
+ if (storeChannelsOnExperimentLevelOrNull != null)
+ {
+ appendNameAndObject(buffer, "store channels on experiment level",
+ storeChannelsOnExperimentLevelOrNull);
+ }
+ if (imageTransformerFactoryOrNull != null)
+ {
+ appendNameAndObject(buffer, "image transformation", "present");
+ }
+ if (imageLibraryOrNull != null)
+ {
+ appendNameAndObject(buffer, "image library", imageLibraryOrNull.toString());
+ }
+ return buffer.toString();
+ }
+
+ protected static final void appendNameAndObject(final StringBuilder buffer, final String name,
+ final Object object)
+ {
+ if (object != null)
+ {
+ buffer.append(name).append("::").append(object).append(";");
+ }
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/IntensityRange.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/IntensityRange.java
new file mode 100644
index 0000000000000000000000000000000000000000..bd3d95145432e17cf50b6a6007cb1e791ee9abcd
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/IntensityRange.java
@@ -0,0 +1,58 @@
+/*
+ * 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.etl.dto.api;
+
+/**
+ * The intensity range in a distribution of pixel values for a given symmetric quantile value.
+ *
+ * @author Bernd Rinn
+ */
+public class IntensityRange
+{
+ final int blackPoint;
+
+ final int whitePoint;
+
+ public IntensityRange(int blackPoint, int whitePoint)
+ {
+ this.blackPoint = blackPoint;
+ this.whitePoint = whitePoint;
+ }
+
+ /**
+ * The minimal level (black point).
+ */
+ public int getBlackPoint()
+ {
+ return blackPoint;
+ }
+
+ /**
+ * The maximal level (white point).
+ */
+ public int getWhitePoint()
+ {
+ return whitePoint;
+ }
+
+ @Override
+ public String toString()
+ {
+ return "MinMax [minLevel=" + blackPoint + ", maxLevel=" + whitePoint + "]";
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/Location.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/Location.java
new file mode 100644
index 0000000000000000000000000000000000000000..4650487b462c0b39162090c0490c0076fa279dbf
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/Location.java
@@ -0,0 +1,63 @@
+package ch.systemsx.cisd.openbis.dss.etl.dto.api;
+
+/**
+ * Auxiliary structure to store tile location on the well. The top left tile has coordinates (1,1).
+ *
+ * @author Tomasz Pylak
+ */
+public class Location
+{
+ private final int row, column;
+
+ /** Note: The top left tile has coordinates (1,1). */
+ public Location(int row, int column)
+ {
+ this.row = row;
+ this.column = column;
+ }
+
+ public int getRow()
+ {
+ return row;
+ }
+
+ public int getColumn()
+ {
+ return column;
+ }
+
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (this == obj)
+ {
+ return true;
+ }
+ if (obj == null)
+ {
+ return false;
+ }
+ if (getClass() != obj.getClass())
+ {
+ return false;
+ }
+ Location other = (Location) obj;
+ return column == other.column && row == other.row;
+ }
+
+ @Override
+ public int hashCode()
+ {
+ final int prime = 31;
+ int result = 1;
+ result = prime * result + column;
+ result = prime * result + row;
+ return result;
+ }
+
+ @Override
+ public String toString()
+ {
+ return "[" + row + ":" + column + "]";
+ }
+}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/OriginalDataStorageFormat.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/OriginalDataStorageFormat.java
new file mode 100644
index 0000000000000000000000000000000000000000..b7a67435b503e49d2af3c9b4aca5814efbb6d9b3
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/OriginalDataStorageFormat.java
@@ -0,0 +1,41 @@
+/*
+ * 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.dss.etl.dto.api;
+
+/**
+ * How original dataset data should be stored.
+ *
+ * @author Tomasz Pylak
+ */
+public enum OriginalDataStorageFormat
+{
+ /** original data are stored as they come (without additional compression) */
+ UNCHANGED,
+
+ /** original data are stored in one HDF5 container (uncompressed) */
+ HDF5,
+
+ /** original data are stored in one HDF5 container (compressed) */
+ HDF5_COMPRESSED;
+
+ public boolean isHdf5()
+ {
+ return this == OriginalDataStorageFormat.HDF5
+ || this == OriginalDataStorageFormat.HDF5_COMPRESSED;
+ }
+
+}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/SimpleImageContainerDataConfig.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/SimpleImageContainerDataConfig.java
new file mode 100644
index 0000000000000000000000000000000000000000..8b5baffe59cfd79350dcaeeca30d6ad246164bd6
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/SimpleImageContainerDataConfig.java
@@ -0,0 +1,70 @@
+/*
+ * 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.dss.etl.dto.api;
+
+import java.util.List;
+
+
+/**
+ * Subclass of {@link SimpleImageDataConfig} for container image files which creates
+ * {@link ImageMetadata} based on {@link ImageIdentifier} using the following simple mapping:
+ * <ul>
+ * <li>ImageMetadata.seriesNumber = ImageIdentifier.seriesIndex + 1
+ * <li>ImageMetadata.timePoint = ImageIdentifier.timeSeriesIndex
+ * <li>ImageMetadata.depth = ImageIdentifier.focalPlaneIndex
+ * <li>ImageMetadata.channelCode = 'CHANNEL-' + (ImageIdentifier.colorChannelIndex + 1)
+ * <li>ImageMetadata.tileNumber = 1
+ * </ul>
+ * ImageMetadata.well will be filled with return value of method
+ * {@link #tryToExtractWell(ImageIdentifier)}.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class SimpleImageContainerDataConfig extends SimpleImageDataConfig
+{
+
+ @Override
+ public ImageMetadata[] extractImagesMetadata(String imagePath,
+ List<ImageIdentifier> imageIdentifiers)
+ {
+ ImageMetadata[] metaData = new ImageMetadata[imageIdentifiers.size()];
+ for (int i = 0, n = imageIdentifiers.size(); i < n; i++)
+ {
+ ImageIdentifier imageIdentifier = imageIdentifiers.get(i);
+ ImageMetadata imageMetadata = new ImageMetadata();
+ imageMetadata.setImageIdentifier(imageIdentifier);
+ imageMetadata.setSeriesNumber(imageIdentifier.getSeriesIndex() + 1);
+ imageMetadata.setTimepoint(new Float(imageIdentifier.getTimeSeriesIndex()));
+ imageMetadata.setDepth(new Float(imageIdentifier.getFocalPlaneIndex()));
+ imageMetadata.setChannelCode("CHANNEL-" + (imageIdentifier.getColorChannelIndex() + 1));
+ imageMetadata.setWell(tryToExtractWell(imageIdentifier));
+ imageMetadata.setTileNumber(1);
+ metaData[i] = imageMetadata;
+ }
+ return metaData;
+ }
+
+ /**
+ * Tries to extract well from the specified image identifier. Default implementation returns
+ * <code>null</code>. In case of screening this method can be overridden.
+ */
+ public String tryToExtractWell(ImageIdentifier imageIdentifier)
+ {
+ return null;
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/SimpleImageDataConfig.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/SimpleImageDataConfig.java
new file mode 100644
index 0000000000000000000000000000000000000000..e39c0e858bfbc83ae9afcda6fe847de4ee66522c
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/SimpleImageDataConfig.java
@@ -0,0 +1,988 @@
+/*
+ * 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.dss.etl.dto.api;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import ch.systemsx.cisd.base.image.IImageTransformerFactory;
+import ch.systemsx.cisd.common.shared.basic.string.StringUtils;
+import ch.systemsx.cisd.openbis.dss.etl.dto.ImageLibraryInfo;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.thumbnails.DefaultThumbnailsConfiguration;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.thumbnails.IThumbnailsConfiguration;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.thumbnails.ResolutionBasedThumbnailsConfiguration;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.thumbnails.ZoomLevelBasedThumbnailsConfiguration;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.transformations.ConvertToolImageTransformerFactory;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.transformations.ImageTransformation;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.transformations.ImageTransformationBuffer;
+import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
+import ch.systemsx.cisd.openbis.generic.shared.basic.CodeNormalizer;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
+
+/**
+ * Allows to configure extraction of images for a plate or microscopy sample.
+ *
+ * @author Tomasz Pylak
+ */
+abstract public class SimpleImageDataConfig
+{
+ // --- one of the following two methods has to be overridden -----------------
+
+ /**
+ * Extracts tile number, channel code and well code for a given relative path to a single image.
+ * This method should overridden to deal with files containing single images. It is ignored if
+ * {@link #extractImagesMetadata(String, List)} is overridden as well.
+ * <p>
+ * It will be called for each file found in the incoming directory which has the extension
+ * returned by {@link #getRecognizedImageExtensions()}.
+ * </p>
+ * To deal with image containers (like multi-page TIFF files) override
+ * {@link #extractImagesMetadata(String, List)} instead, otherwise leave that method unchanged.
+ */
+ public ImageMetadata extractImageMetadata(String imagePath)
+ {
+ throw new UnsupportedOperationException(
+ "One of the extractImageMetadata() methods has to be implemented.");
+ }
+
+ /**
+ * Returns meta-data for each image in the specified image container. This method should
+ * overridden to deal with container images (like multi-page TIFF files).
+ * <p>
+ * This implementation returns the result of {@link #extractImageMetadata(String)} wrapped in an
+ * array, image identifiers are ignored.
+ * </p>
+ *
+ * @param imagePath path to the single image or container of many images
+ * @param imageIdentifiers Identifiers of all images contained in the image file.
+ */
+ public ImageMetadata[] extractImagesMetadata(String imagePath,
+ List<ImageIdentifier> imageIdentifiers)
+ {
+
+ ImageMetadata imageMetadata = extractImageMetadata(imagePath);
+ return (imageMetadata != null) ? new ImageMetadata[]
+ { imageMetadata } : new ImageMetadata[0];
+ }
+
+ // --- methods which can be overridden -----------------
+
+ /**
+ * By default layouts all images in one row by returning (1, maxTileNumber) geometry.Can be
+ * overridden in subclasses.
+ *
+ * @param imageMetadataList a list of metadata for each encountered image
+ * @param maxTileNumber the biggest tile number among all encountered images
+ * @return the width and height of the matrix of tiles (a.k.a. fields or sides) in the well.
+ */
+ public Geometry getTileGeometry(List<? extends ImageMetadata> imageMetadataList,
+ int maxTileNumber)
+ {
+ return Geometry.createFromRowColDimensions(1, maxTileNumber);
+ }
+
+ /**
+ * For a given tile number and tiles geometry returns (x,y) which describes where the tile is
+ * located on the well. Can be overridden in subclasses.<br>
+ * Note: The top left tile has coordinates (1,1).
+ *
+ * @param tileNumber number of the tile extracted by {@link #extractImageMetadata}.
+ * @param tileGeometry the geometry of the well matrix returned by {@link #getTileGeometry}.
+ */
+ public Location getTileCoordinates(int tileNumber, Geometry tileGeometry)
+ {
+ int columns = tileGeometry.getWidth();
+ int row = ((tileNumber - 1) / columns) + 1;
+ int col = ((tileNumber - 1) % columns) + 1;
+ return new Location(row, col);
+ }
+
+ /**
+ * <p>
+ * Creates channel description for a given code. Can be overridden in subclasses.
+ * </p>
+ * By default the channel label will be equal to the code. Channel color returned by
+ * {@link #getChannelColor(String)} will be used.
+ */
+ public Channel createChannel(String channelCode)
+ {
+ ChannelColorRGB channelColorOrNull = tryGetChannelColor(channelCode.toUpperCase());
+ ImageTransformation[] availableTransformations =
+ getAvailableChannelTransformations(channelCode);
+ String label = channelCode;
+ String normalizedChannelCode = CodeNormalizer.normalize(channelCode);
+ Channel channel = new Channel(normalizedChannelCode, label, channelColorOrNull);
+ channel.setAvailableTransformations(availableTransformations);
+ return channel;
+ }
+
+ private ChannelColorRGB tryGetChannelColor(String channelCode)
+ {
+ ChannelColor channelColor = getChannelColor(channelCode);
+ ChannelColorRGB channelColorRGB = getChannelColorRGB(channelCode);
+ if (channelColorRGB != null && channelColor != null)
+ {
+ throw new IllegalStateException(String.format(
+ "Color for channel '%s' is specified in two ways: %s and %s", channelColor,
+ channelColorRGB));
+ }
+
+ if (channelColor != null)
+ {
+ return channelColor.getRGB();
+ } else
+ {
+ return channelColorRGB;
+ }
+ }
+
+ /**
+ * Sets available transformations which can be applied to images of the specified channel (on
+ * user's request).
+ * <p>
+ * Can be overridden in subclasses. The easiest way to create transformations is to use
+ * {@link ImageTransformationBuffer} class.
+ * <p>
+ * By default returns null.
+ */
+ public ImageTransformation[] getAvailableChannelTransformations(String channelCode)
+ {
+ return null;
+ }
+
+ /**
+ * Has the same effect as {@link #getChannelColorRGB(String)}, but can return only plain colors.
+ */
+ public ChannelColor getChannelColor(String channelCode)
+ {
+ return null;
+ }
+
+ /**
+ * Returns RGB color for the specified channel. It will be used to display merged channels
+ * images.
+ * <p>
+ * Can be overridden in subclasses. It is ignored if {@link #createChannel(String)} is
+ * overridden as well. One should not override {@link #getChannelColor(String)} and
+ * {@link #getChannelColorRGB(String)} at the same time.
+ * </p>
+ * By default returns null (the arbitrary color will be set).
+ */
+ public ChannelColorRGB getChannelColorRGB(String channelCode)
+ {
+ return null;
+ }
+
+ // --- auxiliary structures ----------------------------------------------
+
+ private String mainDatasetTypeCode;
+
+ private String fileFormatCode = ScreeningConstants.UNKNOWN_FILE_FORMAT;
+
+ private String plateCode;
+
+ private String spaceCode;
+
+ private boolean isMeasured = false;
+
+ private String[] recognizedImageExtensions = new String[]
+ { "tiff", "tif", "png", "gif", "jpg", "jpeg", "c01" };
+
+ private List<IThumbnailsConfiguration> imagePyramid = new ArrayList<IThumbnailsConfiguration>();
+
+ private int maxThumbnailWidthAndHeight = 256;
+
+ private boolean generateThumbnailsWithImageMagic = true;
+
+ private List<String> thumbnailsGenerationImageMagicParams = Collections.emptyList();
+
+ private boolean generateThumbnailsIn8BitHighQuality = false;
+
+ private double allowedMachineLoadDuringThumbnailsGeneration = 1.0;
+
+ private boolean storeChannelsOnExperimentLevel = false;
+
+ private OriginalDataStorageFormat originalDataStorageFormat =
+ OriginalDataStorageFormat.UNCHANGED;
+
+ private String convertTransformationCliArgumentsOrNull;
+
+ private ImageLibraryInfo imageLibraryInfoOrNull;
+
+ private boolean isMicroscopy;
+
+ // If null then no common intensity rescaling parameters are computed.
+ // If empty the computation will take place for all channels, otherwise only for specified
+ // channels.
+ private List<String> computeCommonIntensityRangeOfAllImagesForChannelsOrNull = null;
+
+ private float computeCommonIntensityRangeOfAllImagesThreshold =
+ ImageUtil.DEFAULT_IMAGE_OPTIMAL_RESCALING_FACTOR;
+
+ private String computeCommonIntensityRangeOfAllImagesLabel = "Optimal (series)";
+
+ private boolean computeCommonIntensityRangeOfAllImagesIsDefault = true;
+
+ private Map<String, IntensityRange> fixedIntensityRangeForAllImages;
+
+ private String thumbnailsFileFormat;
+
+ private List<Channel> channels;
+
+ private List<ChannelColorComponent> channelColorComponentsOrNull;
+
+ // --- getters & setters ----------------------------------------------
+
+ public ImageStorageConfiguraton getImageStorageConfiguration()
+ {
+ ImageStorageConfiguraton imageStorageConfiguraton =
+ ImageStorageConfiguraton.createDefault();
+ imageStorageConfiguraton
+ .setStoreChannelsOnExperimentLevel(isStoreChannelsOnExperimentLevel());
+ imageStorageConfiguraton.setOriginalDataStorageFormat(getOriginalDataStorageFormat());
+ for (IThumbnailsConfiguration thumbnailsConfiguration : imagePyramid)
+ {
+ imageStorageConfiguraton.addThumbnailsStorageFormat(thumbnailsConfiguration
+ .getThumbnailsStorageFormat(this));
+ }
+ if (false == StringUtils.isBlank(convertTransformationCliArgumentsOrNull))
+ {
+ IImageTransformerFactory convertTransformerFactory =
+ new ConvertToolImageTransformerFactory(convertTransformationCliArgumentsOrNull);
+ imageStorageConfiguraton.setImageTransformerFactory(convertTransformerFactory);
+
+ }
+ imageStorageConfiguraton.setImageLibrary(imageLibraryInfoOrNull);
+ return imageStorageConfiguraton;
+ }
+
+ public String getPlateSpace()
+ {
+ return spaceCode;
+ }
+
+ public String getPlateCode()
+ {
+ return plateCode;
+ }
+
+ public String[] getRecognizedImageExtensions()
+ {
+ return recognizedImageExtensions;
+ }
+
+ public boolean isGenerateThumbnails()
+ {
+ return imagePyramid.size() > 0;
+ }
+
+ public int getMaxThumbnailWidthAndHeight()
+ {
+ return maxThumbnailWidthAndHeight;
+ }
+
+ public double getAllowedMachineLoadDuringThumbnailsGeneration()
+ {
+ return allowedMachineLoadDuringThumbnailsGeneration;
+ }
+
+ public boolean isStoreChannelsOnExperimentLevel()
+ {
+ return storeChannelsOnExperimentLevel;
+ }
+
+ public OriginalDataStorageFormat getOriginalDataStorageFormat()
+ {
+ return originalDataStorageFormat;
+ }
+
+ public String tryGetConvertTransformationCliArguments()
+ {
+ return convertTransformationCliArgumentsOrNull;
+ }
+
+ public List<String> getComputeCommonIntensityRangeOfAllImagesForChannels()
+ {
+ return computeCommonIntensityRangeOfAllImagesForChannelsOrNull;
+ }
+
+ public float getComputeCommonIntensityRangeOfAllImagesThreshold()
+ {
+ return computeCommonIntensityRangeOfAllImagesThreshold;
+ }
+
+ public boolean isFixedIntensityRangeForAllImagesDefined()
+ {
+ return fixedIntensityRangeForAllImages != null;
+ }
+
+ public Map<String, IntensityRange> getFixedIntensityRangeForAllImages()
+ {
+ return fixedIntensityRangeForAllImages;
+ }
+
+ public String getComputeCommonIntensityRangeOfAllImagesLabel()
+ {
+ return computeCommonIntensityRangeOfAllImagesLabel;
+ }
+
+ public boolean isComputeCommonIntensityRangeOfAllImagesDefault()
+ {
+ return computeCommonIntensityRangeOfAllImagesIsDefault;
+ }
+
+ public List<Channel> getChannels()
+ {
+ return channels;
+ }
+
+ public List<ChannelColorComponent> getChannelColorComponentsOrNull()
+ {
+ return channelColorComponentsOrNull;
+ }
+
+ // ----- Setters -------------------------
+
+ /**
+ * Sets the existing plate to which the dataset should belong.
+ *
+ * @param spaceCode space where the plate for which the dataset has been acquired exist
+ * @param plateCode code of the plate to which the dataset will belong
+ */
+ public void setPlate(String spaceCode, String plateCode)
+ {
+ this.spaceCode = spaceCode;
+ this.plateCode = plateCode;
+ }
+
+ /**
+ * Only files with these extensions will be recognized as images (e.g. ["jpg", "png"]).<br>
+ * By default it is set to [ "tiff", "tif", "png", "gif", "jpg", "jpeg", "c01" ].
+ */
+ public void setRecognizedImageExtensions(String[] recognizedImageExtensions)
+ {
+ this.recognizedImageExtensions = recognizedImageExtensions;
+ }
+
+ /** Sets all channels available in the data set. */
+ public void setChannels(List<Channel> channels)
+ {
+ this.channels = channels;
+ }
+
+ /**
+ * Use this method if channels are encoded in color components of one image (or in other words:
+ * each image contains merged channels). For each channel you have to specify the corresponding
+ * color component of the image.
+ */
+ public void setChannels(List<Channel> channels,
+ List<ChannelColorComponent> channelColorComponents)
+ {
+ this.channels = channels;
+ channelColorComponentsOrNull = channelColorComponents;
+ }
+
+ /** should thumbnails be generated? False by default. */
+ public void setGenerateThumbnails(boolean generateThumbnails)
+ {
+ imagePyramid.clear();
+ imagePyramid.add(new DefaultThumbnailsConfiguration());
+ }
+
+ /**
+ * See {@link #setGenerateImageRepresentations}.
+ *
+ * @deprecated use {@link #setGenerateImageRepresentations} instead.
+ */
+ @Deprecated
+ public void setGenerateImagePyramid(IThumbnailsConfiguration[] elements)
+ {
+ setGenerateImageRepresentations(elements);
+ }
+
+ /**
+ * See {@link #setGenerateImageRepresentationsUsingScaleFactors}.
+ *
+ * @deprecated use {@link #setGenerateImageRepresentationsUsingScaleFactors} instead.
+ */
+ @Deprecated
+ public void setGenerateImagePyramidWithScaleFactors(double[] zoomLevels)
+ {
+ setGenerateImageRepresentationsUsingScaleFactors(zoomLevels);
+ }
+
+ /**
+ * See {@link #setGenerateImageRepresentationsUsingImageResolutions}.
+ *
+ * @deprecated use {@link #setGenerateImageRepresentationsUsingImageResolutions} instead.
+ */
+ @Deprecated
+ public void setGenerateImagePyramidWithImageResolution(String[] resolutions)
+ {
+ setGenerateImageRepresentationsUsingImageResolutions(resolutions);
+ }
+
+ /**
+ * Registers a request for alternate image representations to be generated based on the original
+ * image. The format of the alternate representations is specified by the
+ * {@link IThumbnailsConfiguration} formats argument.
+ *
+ * @param formats The formats of the image generated representations. One image representation
+ * will be created for each format.
+ */
+ public void setGenerateImageRepresentations(IThumbnailsConfiguration[] formats)
+ {
+ imagePyramid.clear();
+ imagePyramid.addAll(Arrays.asList(formats));
+ }
+
+ /**
+ * Registers a request for alternate image representations to be generated based on the original
+ * image. The alternate image representations vary with respect to resolution from the original
+ * image.
+ *
+ * @param scaleFactors The scale factors applied to the original resolution. Scale factors must
+ * be greater than 0.
+ */
+ public void setGenerateImageRepresentationsUsingScaleFactors(double[] scaleFactors)
+ {
+ imagePyramid.clear();
+ if (scaleFactors == null)
+ {
+ return;
+ }
+
+ // Verify the arguments
+ for (double scaleFactor : scaleFactors)
+ {
+ // This check is duplicated in addImageRepresentationUsingScale
+ if (scaleFactor <= 0)
+ {
+ throw new IllegalArgumentException(
+ "Scale factors for generated image representations must be greater than 0. "
+ + scaleFactor + " <= 0");
+ }
+ }
+ for (double scale : scaleFactors)
+ {
+ addGeneratedImageRepresentationWithScale(scale);
+ }
+ }
+
+ /**
+ * Registers a request for an alternate image representation to be generated based on the
+ * original image. The alternate image representations vary with respect to resolution from the
+ * original image.
+ *
+ * @param scale The scale factor applied to the original resolution. Scale factors must be
+ * greater than 0.
+ * @return The configuration for the image representation
+ */
+ public IThumbnailsConfiguration addGeneratedImageRepresentationWithScale(double scale)
+ {
+ if (scale <= 0)
+ {
+ throw new IllegalArgumentException(
+ "Scale factors for generated image representations must be greater than 0. "
+ + scale + " <= 0");
+ }
+ ZoomLevelBasedThumbnailsConfiguration imageRep =
+ new ZoomLevelBasedThumbnailsConfiguration(scale);
+ imagePyramid.add(imageRep);
+ return imageRep;
+ }
+
+ /**
+ * Registers a request for alternate image representations to be generated based on the original
+ * image. The alternate image representations vary with respect to resolution from the original
+ * image. By default, allow enlarging. Use
+ * {@link #setGenerateImageRepresentationsWithoutEnlargingUsingImageResolutions(String[])} to
+ * explicitly prevent enlarging.
+ *
+ * @param resolutions The resolutions
+ */
+ public void setGenerateImageRepresentationsUsingImageResolutions(String[] resolutions)
+ {
+ setGenerateImageRepresentationsUsingImageResolutions(resolutions, true);
+ }
+
+ /**
+ * Registers a request for alternate image representations to be generated based on the original
+ * image. The alternate image representations vary with respect to resolution from the original
+ * image. This method throws an exception if the requested resolution results in the image being
+ * enlarged. Use {@link #setGenerateImageRepresentationsUsingImageResolutions(String[])} to
+ * allow enlarging.
+ *
+ * @param resolutions The resolutions
+ */
+ public void setGenerateImageRepresentationsWithoutEnlargingUsingImageResolutions(
+ String[] resolutions)
+ {
+ setGenerateImageRepresentationsUsingImageResolutions(resolutions, false);
+ }
+
+ /**
+ * Registers a request for alternate image representations to be generated based on the original
+ * image. The alternate image representations vary with respect to resolution from the original
+ * image.
+ *
+ * @param resolutions The resolutions
+ * @param allowEnlarging If true, resolutions larger than the original size of the image are
+ * allowed
+ */
+ private void setGenerateImageRepresentationsUsingImageResolutions(String[] resolutions,
+ boolean allowEnlarging)
+ {
+ imagePyramid.clear();
+ if (resolutions != null)
+ {
+ for (String resolution : resolutions)
+ {
+ addGeneratedImageRepresentationWithResolution(resolution, allowEnlarging);
+ }
+ }
+ }
+
+ /**
+ * Registers a request for an alternate image representation to be generated based on the
+ * original image. The alternate image representations vary with respect to resolution from the
+ * original image. Enlarging is allowed. To prevent enlarging of the image, use
+ * {@link #addGeneratedImageRepresentationWithoutEnlargingWithResolution}.
+ *
+ * @param resolution The resolution of the representation.
+ * @return The configuration for the image representation.
+ */
+ public IThumbnailsConfiguration addGeneratedImageRepresentationWithResolution(String resolution)
+ {
+ return addGeneratedImageRepresentationWithResolution(resolution, true);
+ }
+
+ /**
+ * Registers a request for an alternate image representation to be generated based on the
+ * original image. The alternate image representations vary with respect to resolution from the
+ * original image. Enlarging is not allowed. To allow enlarging of the image, use
+ * {@link #addGeneratedImageRepresentationWithResolution}.
+ *
+ * @param resolution The resolution of the representation.
+ * @return The configuration for the image representation.
+ */
+ public IThumbnailsConfiguration addGeneratedImageRepresentationWithoutEnlargingWithResolution(
+ String resolution)
+ {
+ return addGeneratedImageRepresentationWithResolution(resolution, false);
+ }
+
+ /**
+ * Registers a request for an alternate image representation to be generated based on the
+ * original image. The alternate image representations vary with respect to resolution from the
+ * original image.
+ *
+ * @param resolution The resolution of the representation.
+ * @param allowEnlarging If true, the generated representation may be <b>larger</b> than the
+ * original image.
+ * @return The configuration for the image representation.
+ */
+ private IThumbnailsConfiguration addGeneratedImageRepresentationWithResolution(
+ String resolution, boolean allowEnlarging)
+ {
+ String[] dimension = resolution.split("x");
+ if (dimension.length != 2)
+ {
+ throw new IllegalArgumentException(
+ "Resolution must be specified in format width x height, e. g. '400x300', but was: '"
+ + resolution + "'");
+ }
+ int width = Integer.parseInt(dimension[0].trim());
+ int height = Integer.parseInt(dimension[1].trim());
+ ResolutionBasedThumbnailsConfiguration imageRep =
+ new ResolutionBasedThumbnailsConfiguration(width, height, allowEnlarging);
+ imagePyramid.add(imageRep);
+ return imageRep;
+ }
+
+ /** the maximal width and height of the generated thumbnails */
+ public void setMaxThumbnailWidthAndHeight(int maxThumbnailWidthAndHeight)
+ {
+ this.maxThumbnailWidthAndHeight = maxThumbnailWidthAndHeight;
+ }
+
+ /**
+ * Valid only if thumbnails generation is switched on. Set it to a value lower than 1 if you
+ * want only some of your processor cores to be used for thumbnails generation. Number of
+ * threads that are used for thumbnail generation will be equal to: this constant * number of
+ * processor cores.
+ */
+ public void setAllowedMachineLoadDuringThumbnailsGeneration(
+ double allowedMachineLoadDuringThumbnailsGeneration)
+ {
+ this.allowedMachineLoadDuringThumbnailsGeneration =
+ allowedMachineLoadDuringThumbnailsGeneration;
+ }
+
+ /**
+ * Decides if ImageMagic 'convert' utility will be used to generate thumbnails. True by default.
+ * <p>
+ * One should set this option to false and use the internal library if 'convert' tool is not
+ * installed or if many images are stored in one image container file.
+ */
+ public void setUseImageMagicToGenerateThumbnails(boolean generateWithImageMagic)
+ {
+ this.generateThumbnailsWithImageMagic = generateWithImageMagic;
+ }
+
+ public boolean getGenerateThumbnailsWithImageMagic()
+ {
+ return generateThumbnailsWithImageMagic;
+ }
+
+ /**
+ * Sets additional parameters which should be passed to ImageMagic 'convert' utility when it is
+ * used to generate thumbnails.
+ * <p>
+ * Example: pass "-contrast-stretch 2%" to discard 2% of brightest and darkest pixels in the
+ * thumbnails.
+ */
+ public void setThumbnailsGenerationImageMagicParams(String[] imageMagicParams)
+ {
+ this.thumbnailsGenerationImageMagicParams = Arrays.asList(imageMagicParams);
+ }
+
+ public List<String> getThumbnailsGenerationImageMagicParams()
+ {
+ return thumbnailsGenerationImageMagicParams;
+ }
+
+ /**
+ * If true and thumbnails generation is switched on, thumbnails will be generated with high
+ * quality.
+ * <p>
+ * Be careful: high quality means that the generation will take longer and the image will be
+ * converted to 8 bit color depth. This option is useful for segmentation images, images with 8
+ * bit color depth or when no 16 bit transformation has to be applied to the images.
+ */
+ public void setGenerateHighQuality8BitThumbnails(boolean highQualityThumbnails)
+ {
+ this.generateThumbnailsIn8BitHighQuality = highQualityThumbnails;
+ }
+
+ public boolean getGenerateThumbnailsIn8BitHighQuality()
+ {
+ return generateThumbnailsIn8BitHighQuality;
+ }
+
+ /**
+ * See {@link #setGenerateHighQuality8BitThumbnails}.
+ *
+ * @deprecated use {@link #setGenerateHighQuality8BitThumbnails} instead.
+ */
+ @Deprecated
+ public void setGenerateHighQualityThumbnails(boolean highQualityThumbnails)
+ {
+ this.generateThumbnailsIn8BitHighQuality = highQualityThumbnails;
+ }
+
+ /**
+ * <p>
+ * Can be used only for grayscale images, Useful when images do not use the whole available
+ * color depth of the format in which they are stored (e.g. 10 bits out of 12). By default
+ * switched off. Causes that the conversion to 8 bit color depth looses less information. At the
+ * same time allows to compare images of one dataset to each other.<br>
+ * Warning: causes that all images have to be analysed before registration, this is a costly
+ * operation!
+ * </p>
+ * <p>
+ * If isComputed is set to true all dataset images will be analysed and one range of pixel
+ * intensities used across all images will be computed (with 0.5% threshold). The result will be
+ * saved and it will be possible to apply on-the-fly transformation when browsing images.
+ * </p>
+ * <p>
+ * Example: let's assume that all plate images are saved as 12 bit grayscales. Each image has
+ * ability to use pixel intensities from 0 to 4095. In our example only a range of the available
+ * intensities is used, let's say from 1024 to 2048. Before the image is displayed to the user
+ * it has to be converted to 8-bit color depth (range of intensities from 0 to 255). Without
+ * taking the effectively used intensities into account the range 1024...2048 would be converted
+ * to a range of 64..128 and other intensities would be unused. Analysing the images allows to
+ * convert 1024...2048 range to the full 0..255 range.
+ * </p>
+ */
+ public void setComputeCommonIntensityRangeOfAllImagesForAllChannels()
+ {
+ this.computeCommonIntensityRangeOfAllImagesForChannelsOrNull = Collections.emptyList();
+ }
+
+ /**
+ * See {@link #setComputeCommonIntensityRangeOfAllImagesForAllChannels()}.
+ *
+ * @param channelCodesOrNull list of channel codes for which the optimal intensity rescaling
+ * parameters will be computed. If empty all channels will be analysed. If null
+ * nothing will be analysed (default behavior).
+ */
+ public void setComputeCommonIntensityRangeOfAllImagesForChannels(String[] channelCodesOrNull)
+ {
+ this.computeCommonIntensityRangeOfAllImagesForChannelsOrNull =
+ Arrays.asList(channelCodesOrNull);
+ }
+
+ /**
+ * Set the label of the transformation which will rescale dataset images intensities in an
+ * optimal and comparable way. Can be used if the default value is not appropriate.
+ * <p>
+ * See {@link #setComputeCommonIntensityRangeOfAllImagesForAllChannels()} for details.
+ */
+ public void setComputeCommonIntensityRangeOfAllImagesLabel(
+ String userFriendlyTransformationlabel)
+ {
+ this.computeCommonIntensityRangeOfAllImagesLabel = userFriendlyTransformationlabel;
+ }
+
+ /**
+ * Sets the threshold of intensities which should be ignored when computing common intensity
+ * range of all images. By default equal to 0.5%. Note that
+ * {@link #setComputeCommonIntensityRangeOfAllImagesForAllChannels()} or
+ * {@link #setComputeCommonIntensityRangeOfAllImagesForChannels(String[])} has to be called to
+ * switch on analysis.
+ *
+ * @param threshold value from 0 to 1. If set to e.g. 0.1 then 10% of brightest and darkest
+ * pixels will be ignored.
+ */
+ public void setComputeCommonIntensityRangeOfAllImagesThreshold(float threshold)
+ {
+ this.computeCommonIntensityRangeOfAllImagesThreshold = threshold;
+ }
+
+ /**
+ * Sets fixed levels for the common intensity range transformation for all images. If this one
+ * is set, the automatic level computation is switched off which may give big performance
+ * improvements. If the method
+ * {@link #setComputeCommonIntensityRangeOfAllImagesForChannels(String[])} is not called, will
+ * set the transformation for all channels.
+ */
+ public void setDefaultFixedIntensityRangeForAllImages(int minLevel, int maxLevel)
+ {
+ if (fixedIntensityRangeForAllImages == null)
+ {
+ fixedIntensityRangeForAllImages = new HashMap<String, IntensityRange>();
+ }
+ this.fixedIntensityRangeForAllImages.put(null, new IntensityRange(minLevel, maxLevel));
+ }
+
+ /**
+ * Add fixed levels for the common intensity range transformation of the given cannel for all
+ * images. If this one is set, the automatic level computation is switched off which can give
+ * big performance improvements.
+ * <p>
+ * Note: If {@link #setDefaultFixedIntensityRangeForAllImages(int, int)} is called as well, then
+ * the values provided here will overwrite the default values provided there for the channel
+ * <var>channelCode</var>. Otherwise, the common intensity transformation will only be computed
+ * for the channels where the levels have been set explicitly by this method.
+ */
+ public void addFixedIntensityRangeForAllImages(String channelCode, int minLevel, int maxLevel)
+ {
+ if (fixedIntensityRangeForAllImages == null)
+ {
+ fixedIntensityRangeForAllImages = new HashMap<String, IntensityRange>();
+ }
+ this.fixedIntensityRangeForAllImages.put(CodeNormalizer.normalize(channelCode),
+ new IntensityRange(minLevel, maxLevel));
+ }
+
+ /**
+ * Sets if the image transformation using common intensity range of all images should be the
+ * default choice when browsing images.
+ * <p>
+ * True by default, which means e.g. that the 'image optimal' transformation will not be
+ * automatically available for users. However one can still add it explicitly with a chosen
+ * threshold by redefining
+ * {@link SimpleImageDataConfig#getAvailableChannelTransformations(String)} method.
+ */
+ public void setComputeCommonIntensityRangeOfAllImagesIsDefault(boolean isDefault)
+ {
+ this.computeCommonIntensityRangeOfAllImagesIsDefault = isDefault;
+ }
+
+ /** Should all dataset in one experiment use the same channels? By default set to false. */
+ public void setStoreChannelsOnExperimentLevel(boolean storeChannelsOnExperimentLevel)
+ {
+ this.storeChannelsOnExperimentLevel = storeChannelsOnExperimentLevel;
+ }
+
+ /**
+ * Should the original data be stored in the original form or should we pack them into one
+ * container? Available values are {@link OriginalDataStorageFormat#UNCHANGED},
+ * {@link OriginalDataStorageFormat#HDF5}, {@link OriginalDataStorageFormat#HDF5_COMPRESSED}.
+ * The default is {@link OriginalDataStorageFormat#UNCHANGED}.
+ */
+ public void setOriginalDataStorageFormat(OriginalDataStorageFormat originalDataStorageFormat)
+ {
+ this.originalDataStorageFormat = originalDataStorageFormat;
+ }
+
+ public void setOriginalDataStorageFormat(
+ ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.OriginalDataStorageFormat originalDataStorageFormat)
+ {
+ this.originalDataStorageFormat =
+ originalDataStorageFormat.getIndependentOriginalDataStorageFormat();
+ }
+
+ /**
+ * Sets parameters for the 'convert' command line tool, which will be used to apply an image
+ * transformation on the fly when an image is fetched.
+ */
+ public void setConvertTransformationCliArguments(String convertTransformationCliArguments)
+ {
+ this.convertTransformationCliArgumentsOrNull = convertTransformationCliArguments;
+ }
+
+ /**
+ * Which image library and reader should be used to read the image? <br>
+ * Available libraries [readers]:<br>
+ * - IJ: [tiff]<br>
+ * - ImageIO: [jpg, bmp, jpeg, wbmp, png, gif]<br>
+ * - JAI: [pnm, jpeg, fpx, gif, tiff, wbmp, png, bmp]<br>
+ * - BioFormats: [ZipReader, APNGReader, JPEGReader, PGMReader, FitsReader, PCXReader,
+ * GIFReader, BMPReader, IPLabReader, IvisionReader, DeltavisionReader, MRCReader, GatanReader,
+ * GatanDM2Reader, ImarisReader, OpenlabRawReader, OMEXMLReader, LIFReader, AVIReader,
+ * PictReader, SDTReader, EPSReader, SlidebookReader, AliconaReader, MNGReader, KhorosReader,
+ * VisitechReader, LIMReader, PSDReader, InCellReader, L2DReader, FEIReader, NAFReader,
+ * MINCReader, QTReader, MRWReader, TillVisionReader, ARFReader, CellomicsReader, LiFlimReader,
+ * TargaReader, OxfordInstrumentsReader, VGSAMReader, HISReader, WATOPReader, SeikoReader,
+ * TopometrixReader, UBMReader, QuesantReader, BioRadGelReader, RHKReader,
+ * MolecularImagingReader, CellWorxReader, Ecat7Reader, VarianFDFReader, AIMReader, FakeReader,
+ * JEOLReader, NiftiReader, AnalyzeReader, APLReader, NRRDReader, ICSReader, PerkinElmerReader,
+ * AmiraReader, ScanrReader, BDReader, UnisokuReader, PDSReader, BioRadReader, FV1000Reader,
+ * ZeissZVIReader, IPWReader, ND2Reader, JPEG2000Reader, PCIReader, ImarisHDFReader,
+ * ZeissLSMReader, SEQReader, GelReader, ImarisTiffReader, FlexReader, SVSReader, ImaconReader,
+ * LEOReader, JPKReader, MIASReader, TCSReader, LeicaReader, NikonReader, FluoviewReader,
+ * PrairieReader, MetamorphReader, MicromanagerReader, ImprovisionTiffReader,
+ * MetamorphTiffReader, NikonTiffReader, OMETiffReader, PhotoshopTiffReader, FEITiffReader,
+ * SimplePCITiffReader, NikonElementsTiffReader, TiffDelegateReader, TextReader, BurleighReader,
+ * OpenlabReader, DicomReader, SMCameraReader, SBIGReader]
+ */
+ public void setImageLibrary(String imageLibraryName, String readerName)
+ {
+ this.imageLibraryInfoOrNull = new ImageLibraryInfo(imageLibraryName, readerName);
+ }
+
+ /**
+ * Sets the image library to be used for reading images. Available libraries are: IJ, ImageIO,
+ * JAI, and BioFormats. The first image file is used to determine the actual reader. Note, that
+ * all images are read with the same image reader.
+ */
+ public void setImageLibrary(String imageLibraryName)
+ {
+ this.imageLibraryInfoOrNull = new ImageLibraryInfo(imageLibraryName);
+ }
+
+ // --- predefined image dataset types
+
+ /**
+ * Sets dataset type to the one which should be used for storing raw images. Marks the dataset
+ * as a "measured" one.
+ */
+ public void setRawImageDatasetType()
+ {
+ setDataSetType(ScreeningConstants.DEFAULT_RAW_IMAGE_DATASET_TYPE);
+ setMeasuredData(true);
+ }
+
+ /**
+ * Sets dataset type to the one which should be used for storing overview images generated from
+ * raw images. Marks the dataset as a "derived" one.
+ */
+ public void setOverviewImageDatasetType()
+ {
+ setDataSetType(ScreeningConstants.DEFAULT_OVERVIEW_IMAGE_DATASET_TYPE);
+ setMeasuredData(false);
+ }
+
+ /**
+ * Sets dataset type to the one which should be used for storing overlay images. Marks the
+ * dataset as a "derived" one.
+ */
+ public void setSegmentationImageDatasetType()
+ {
+ setDataSetType(ScreeningConstants.DEFAULT_SEGMENTATION_IMAGE_DATASET_TYPE);
+ setMeasuredData(false);
+ }
+
+ // --- standard
+
+ /** Sets the type of the dataset. */
+ public void setDataSetType(String datasetTypeCode)
+ {
+ this.mainDatasetTypeCode = datasetTypeCode;
+ }
+
+ /** Sets the file type of the dataset. */
+ public void setFileFormatType(String fileFormatCode)
+ {
+ this.fileFormatCode = fileFormatCode;
+ }
+
+ /**
+ * Set whether the data is measured or not. By default false.
+ */
+ public void setMeasuredData(boolean isMeasured)
+ {
+ this.isMeasured = isMeasured;
+ }
+
+ /**
+ * Sets the microscopy flag which is by default <code>false</code>. This flag is used to check
+ * whether well in {@link ImageMetadata} is specified or not. In case of microscopy well is
+ * ignored. Otherwise it is mandatory.
+ */
+ public void setMicroscopyData(boolean isMicroscopy)
+ {
+ this.isMicroscopy = isMicroscopy;
+ }
+
+ public String getDataSetType()
+ {
+ return mainDatasetTypeCode;
+ }
+
+ public String getFileFormatType()
+ {
+ return fileFormatCode;
+ }
+
+ public boolean isMeasuredData()
+ {
+ return isMeasured;
+ }
+
+ public boolean isMicroscopyData()
+ {
+ return isMicroscopy;
+ }
+
+ public void setThumbnailsFileFormat(String thumbnailsFileFormat)
+ {
+ this.thumbnailsFileFormat = thumbnailsFileFormat;
+ }
+
+ public String getThumbnailsFileFormat()
+ {
+ return this.thumbnailsFileFormat;
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/SimpleOverviewImageDataConfig.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/SimpleOverviewImageDataConfig.java
new file mode 100644
index 0000000000000000000000000000000000000000..4934320a8c1f3c73241f4d09ad47c431e19b6037
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/SimpleOverviewImageDataConfig.java
@@ -0,0 +1,51 @@
+/*
+ * 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.etl.dto.api;
+
+/**
+ * * Allows to configure extraction of overview images for a plate or microscopy sample.
+ *
+ * @author Pawel Glyzewski
+ */
+public class SimpleOverviewImageDataConfig extends SimpleImageDataConfig
+{
+ private String containerDataSetCode;
+
+ private boolean generateOverviewImagesFromRegisteredImages;
+
+ public String getContainerDataSetCode()
+ {
+ return containerDataSetCode;
+ }
+
+ public void setContainerDataSetCode(String containerDataSetCode)
+ {
+ 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/dto/api/ThumbnailsStorageFormat.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/ThumbnailsStorageFormat.java
new file mode 100644
index 0000000000000000000000000000000000000000..f4c502ff7ebbdf659f6821605deebc7adb64e221
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/ThumbnailsStorageFormat.java
@@ -0,0 +1,332 @@
+/*
+ * 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.dss.etl.dto.api;
+
+import java.awt.image.BufferedImage;
+import java.io.OutputStream;
+import java.io.Serializable;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import ch.systemsx.cisd.common.reflection.AbstractHashable;
+import ch.systemsx.cisd.openbis.dss.Constants;
+import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
+
+/**
+ * Configuration parameters which describe how thumbnails should be generated.
+ *
+ * @author Tomasz Pylak
+ */
+public class ThumbnailsStorageFormat extends AbstractHashable implements Serializable
+{
+
+ private static final long serialVersionUID = 1L;
+
+ public enum FileFormat
+ {
+ PNG
+ {
+ @Override
+ public void writeImage(BufferedImage image, OutputStream stream)
+ {
+ ImageUtil.writeImageToPng(image, stream);
+ }
+
+ @Override
+ public String getFileExtension()
+ {
+ return "png";
+ }
+
+ @Override
+ public String getImageMagickParam()
+ {
+ return "png";
+ }
+ },
+ JPEG
+ {
+ @Override
+ public void writeImage(BufferedImage image, OutputStream stream)
+ {
+ ImageUtil.writeImageUsingImageIO(image, stream, "jpg");
+ }
+
+ @Override
+ public String getFileExtension()
+ {
+ return "jpg";
+ }
+
+ @Override
+ public String getImageMagickParam()
+ {
+ return "jpeg";
+ }
+ },
+ JPEG_2000
+ {
+ @Override
+ public void writeImage(BufferedImage image, OutputStream stream)
+ {
+ ImageUtil.writeImageUsingImageIO(image, stream, "jpeg 2000");
+ }
+
+ @Override
+ public String getFileExtension()
+ {
+ return "jp2";
+ }
+
+ @Override
+ public String getImageMagickParam()
+ {
+ return "jp2";
+ }
+ };
+
+ private static final Map<String, FileFormat> formats;
+ static
+ {
+ formats = new HashMap<String, ThumbnailsStorageFormat.FileFormat>();
+ for (FileFormat format : FileFormat.values())
+ {
+ formats.put(format.name().toUpperCase(), format);
+ }
+ formats.put("JP2", JPEG_2000);
+ formats.put("JPEG 2000", JPEG_2000);
+ formats.put("JPG", JPEG);
+ }
+
+ public abstract void writeImage(BufferedImage image, OutputStream stream);
+
+ public abstract String getFileExtension();
+
+ public abstract String getImageMagickParam();
+
+ public String getOpenBISFileType()
+ {
+ return getFileExtension().toUpperCase();
+ }
+
+ public static FileFormat getValue(String fileFormat)
+ {
+ return formats.get(fileFormat.toUpperCase());
+ }
+ }
+
+ /** Maximum default width and height of a thumbnail */
+ public static final int DEFAULT_THUMBNAIL_MAX_SIZE = 200;
+
+ /** Maximum default width and height of a thumbnail */
+ public static final boolean DEFAULT_COMPRESS_THUMBNAILS = false;
+
+ // ---
+
+ private int maxWidth = DEFAULT_THUMBNAIL_MAX_SIZE;
+
+ private int maxHeight = DEFAULT_THUMBNAIL_MAX_SIZE;
+
+ private boolean allowEnlarging = true;
+
+ private Double zoomLevel = null;
+
+ private boolean storeCompressed = DEFAULT_COMPRESS_THUMBNAILS;
+
+ private double allowedMachineLoadDuringGeneration = 1;
+
+ private boolean highQuality8Bit = false;
+
+ private boolean generateWithImageMagic = false;
+
+ private List<String> imageMagicParams = Collections.emptyList();
+
+ private String thumbnailsFileName;
+
+ private FileFormat fileFormat = FileFormat.PNG;
+
+ private final Map<String, String> transformations = new HashMap<String, String>();
+
+ /**
+ * Creates empty object which instructs that the thumbnails should be generated with default
+ * settings. Use setters to change default behaviour (you will probably not have to).
+ */
+ public ThumbnailsStorageFormat()
+ {
+ }
+
+ public int getMaxWidth()
+ {
+ return maxWidth;
+ }
+
+ public int getMaxHeight()
+ {
+ return maxHeight;
+ }
+
+ public boolean isStoreCompressed()
+ {
+ return storeCompressed;
+ }
+
+ public double getAllowedMachineLoadDuringGeneration()
+ {
+ return allowedMachineLoadDuringGeneration;
+ }
+
+ public boolean isHighQuality()
+ {
+ return highQuality8Bit;
+ }
+
+ public boolean isGenerateWithImageMagic()
+ {
+ return generateWithImageMagic;
+ }
+
+ public List<String> getImageMagicParams()
+ {
+ return imageMagicParams;
+ }
+
+ public boolean isAllowEnlarging()
+ {
+ return allowEnlarging;
+ }
+
+ // --- setters ---
+
+ /** Sets the maximum width of a thumbnail. */
+ public void setMaxWidth(int maxWidth)
+ {
+ this.maxWidth = maxWidth;
+ }
+
+ /** Sets the maximum height of a thumbnail. */
+ public void setMaxHeight(int maxHeight)
+ {
+ this.maxHeight = maxHeight;
+ }
+
+ /** Sets if each thumbnail should be additionally compressed (lostless) before it is stored. */
+ public void setStoreCompressed(boolean storeCompressed)
+ {
+ this.storeCompressed = storeCompressed;
+ }
+
+ /**
+ * Specify if this image representation is allowed to be larger than the original image.
+ */
+ public void setAllowEnlarging(boolean allowEnlarging)
+ {
+ this.allowEnlarging = allowEnlarging;
+ }
+
+ /**
+ * The number of threads which will be used during thumbnails generation will be equal to number
+ * of processor cores * machineLoad.
+ */
+ public void setAllowedMachineLoadDuringGeneration(double machineLoad)
+ {
+ this.allowedMachineLoadDuringGeneration = machineLoad;
+ }
+
+ /**
+ * Set to true if you want your thumbnails to be of higher quality. In such a case thumbnails
+ * generation during dataset registration will take longer. Recommended for overlay images.
+ */
+ public void setHighQuality(boolean highQuality)
+ {
+ this.highQuality8Bit = highQuality;
+ }
+
+ /**
+ * if true ImageMagic 'convert' utility should be installed and will be used to generate
+ * thumbnails. <br>
+ * Note: if images should be handled with a specific image library, it will be ignored for
+ * thumbnails generation if 'convert' is supposed to be used. Make sure that 'convert' can deal
+ * with your images in such a case.
+ */
+ public void setGenerateWithImageMagic(boolean generateWithImageMagic)
+ {
+ this.generateWithImageMagic = generateWithImageMagic;
+ }
+
+ /**
+ * Sets additional parameters which should be passed to ImageMagic 'convert' utility when it is
+ * used to generate thumbnails. Example: pass "-contrast-stretch 2%" to discard 2% of brightest
+ * and darkest pixels in the thumbnails.
+ */
+ public void setImageMagicParams(List<String> imageMagicParams)
+ {
+ this.imageMagicParams = imageMagicParams;
+ }
+
+ public Double getZoomLevel()
+ {
+ return zoomLevel;
+ }
+
+ public void setZoomLevel(Double zoomLevel)
+ {
+ this.zoomLevel = zoomLevel;
+ }
+
+ public String getThumbnailsFileName()
+ {
+ return thumbnailsFileName == null ? Constants.HDF5_CONTAINER_THUMBNAILS_FILE_NAME
+ : thumbnailsFileName;
+ }
+
+ public void setThumbnailsFileName(String thumbnailsFileName)
+ {
+ this.thumbnailsFileName = thumbnailsFileName;
+ }
+
+ public void setFileFormat(String fileFormat)
+ {
+ FileFormat value = FileFormat.getValue(fileFormat);
+ if (value == null)
+ {
+ throw new IllegalArgumentException("File format '" + fileFormat + "' is unknown");
+ }
+ this.fileFormat = value;
+ }
+
+ public FileFormat getFileFormat()
+ {
+ return fileFormat;
+ }
+
+ public void setTransformations(Map<String, String> transformations)
+ {
+ this.transformations.putAll(transformations);
+ }
+
+ public String getTransformationCode(String channelCode)
+ {
+ return transformations.get(channelCode.toUpperCase());
+ }
+
+ public Map<String, String> getTransformations()
+ {
+ return transformations;
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/FeatureDefinition.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/FeatureDefinition.java
index 409ba08141fc91ba5d19f0efa5164aa3e64abaf0..3d8cc97d3948a89fabeab6d4f33c73b873e9155b 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/FeatureDefinition.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/FeatureDefinition.java
@@ -25,7 +25,7 @@ import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.IFeatureDefinition;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.IFeatureDefinition;
import ch.systemsx.cisd.openbis.dss.etl.featurevector.CanonicalFeatureVector;
import ch.systemsx.cisd.openbis.dss.etl.featurevector.FeatureValuesMap;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/FeatureVectorDataSetInformation.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/FeatureVectorDataSetInformation.java
index d1055fc2878570077fa39322baf3cd3a520faed3..4415f1b0ab1629faa3ccf7848771386150dbbc3a 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/FeatureVectorDataSetInformation.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/FeatureVectorDataSetInformation.java
@@ -22,7 +22,7 @@ import java.util.ArrayList;
import java.util.List;
import ch.systemsx.cisd.common.shared.basic.string.StringUtils;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.IFeatureDefinition;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.IFeatureDefinition;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.generic.shared.IServer;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/FeaturesBuilder.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/FeaturesBuilder.java
index 74ea5506fbb2e98260aca331b41c4d2f4996fea1..6011f108603faa8c1b50ea7c8b7ef7e6bdd6d959 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/FeaturesBuilder.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/FeaturesBuilder.java
@@ -20,8 +20,8 @@ import java.util.ArrayList;
import java.util.List;
import ch.systemsx.cisd.common.shared.basic.string.StringUtils;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.IFeatureDefinition;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.IFeaturesBuilder;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.IFeatureDefinition;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.IFeaturesBuilder;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgFeatureDefDTO;
/**
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 cc8817028732a712f8f17b3e9fa892fe7f554ba6..8c5d0b842526be8702980bb36c32eabfe2d83789 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
@@ -19,9 +19,9 @@ package ch.systemsx.cisd.openbis.dss.etl.dto.api.impl;
import java.io.File;
import java.util.List;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.BasicDataSetInformation;
-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.BasicDataSetInformation;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.Channel;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColorComponent;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.generic.shared.IServer;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/ImageDataSetStructure.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/ImageDataSetStructure.java
index 89b839f83334e8abf2e07b471e5e5e69a054aba7..d9a2e08f15fc92a6cb4387dcdcde7a2bc713221c 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/ImageDataSetStructure.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/ImageDataSetStructure.java
@@ -21,11 +21,11 @@ import java.util.List;
import ch.systemsx.cisd.common.collection.CollectionUtils;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
-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.ImageStorageConfiguraton;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ThumbnailsStorageFormat;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.Channel;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColorComponent;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageFileInfo;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageStorageConfiguraton;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ThumbnailsStorageFormat;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ToStringUtil;
/**
@@ -36,7 +36,7 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ToStringUtil;
*/
public class ImageDataSetStructure implements Serializable
{
-
+
private static final long serialVersionUID = 1L;
private List<ImageFileInfo> images;
@@ -122,8 +122,12 @@ public class ImageDataSetStructure implements Serializable
throw new IllegalArgumentException(
"There should be exactly one color component for each channel!");
}
+
this.channels = channels;
- this.channelColorComponentsOrNull = channelColorComponents;
+ // potentially necessary conversion of v1 ChanelColorComponent
+ this.channelColorComponentsOrNull =
+ ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ChannelColorComponent
+ .convertToIndependentChannelColorList(channelColorComponents);
}
/**
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/ThumbnailsInfo.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/ThumbnailsInfo.java
index 6c3c8c3f44466f29193d20c0b06c32f5cedb1a2d..18c79fc21fa5526dfbf43ed4b015d7773882210c 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/ThumbnailsInfo.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/ThumbnailsInfo.java
@@ -6,7 +6,7 @@ import java.util.Map;
import java.util.Set;
import ch.systemsx.cisd.openbis.dss.etl.dto.RelativeImageFile;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ThumbnailsStorageFormat.FileFormat;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ThumbnailsStorageFormat.FileFormat;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ToStringUtil;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ColorComponent;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/thumbnails/AbstractThumbnailsConfiguration.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/thumbnails/AbstractThumbnailsConfiguration.java
new file mode 100644
index 0000000000000000000000000000000000000000..cc300d2c7e04174e4dbcd8e205b0eeacda802940
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/thumbnails/AbstractThumbnailsConfiguration.java
@@ -0,0 +1,112 @@
+/*
+ * 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.dss.etl.dto.api.thumbnails;
+
+import java.util.HashMap;
+import java.util.Map;
+
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.SimpleImageDataConfig;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ThumbnailsStorageFormat;
+
+/**
+ * @author Pawel Glyzewski
+ */
+public abstract class AbstractThumbnailsConfiguration implements IThumbnailsConfiguration
+{
+ private String fileName;
+
+ private String fileFormat;
+
+ private Map<String, String> transformations = new HashMap<String, String>();
+
+ @Override
+ public ThumbnailsStorageFormat getThumbnailsStorageFormat(SimpleImageDataConfig config)
+ {
+ ThumbnailsStorageFormat thumbnailsStorageFormat = new ThumbnailsStorageFormat();
+ thumbnailsStorageFormat.setAllowedMachineLoadDuringGeneration(config
+ .getAllowedMachineLoadDuringThumbnailsGeneration());
+ thumbnailsStorageFormat.setThumbnailsFileName(getFileName());
+ thumbnailsStorageFormat.setMaxWidth(config.getMaxThumbnailWidthAndHeight());
+ thumbnailsStorageFormat.setMaxHeight(config.getMaxThumbnailWidthAndHeight());
+ thumbnailsStorageFormat.setGenerateWithImageMagic(config
+ .getGenerateThumbnailsWithImageMagic());
+ thumbnailsStorageFormat.setImageMagicParams(config
+ .getThumbnailsGenerationImageMagicParams());
+ thumbnailsStorageFormat.setHighQuality(config.getGenerateThumbnailsIn8BitHighQuality());
+ setFileFormat(thumbnailsStorageFormat, config.getThumbnailsFileFormat());
+ thumbnailsStorageFormat.setTransformations(transformations);
+ return thumbnailsStorageFormat;
+ }
+
+ protected abstract String getDefaultFileName();
+
+ @Override
+ public void setFileName(String fileName)
+ {
+ this.fileName = fileName;
+ }
+
+ public String getFileName()
+ {
+ if (fileName != null)
+ {
+ return fileName;
+ } else
+ {
+ return getDefaultFileName();
+ }
+ }
+
+ @Override
+ public void setFileFormat(String fileFormat)
+ {
+ this.fileFormat = fileFormat;
+ }
+
+ public String getFileFormat()
+ {
+ return this.fileFormat;
+ }
+
+ private void setFileFormat(ThumbnailsStorageFormat thumbnailsStorageFormat, String defaultValue)
+ {
+ if (fileFormat != null)
+ {
+ thumbnailsStorageFormat.setFileFormat(fileFormat);
+ } else if (defaultValue != null)
+ {
+ thumbnailsStorageFormat.setFileFormat(defaultValue);
+ }
+ }
+
+ @Override
+ public String setTransformation(String channelCode, String transformationCode)
+ {
+ return transformations.put(channelCode.toUpperCase(), transformationCode);
+ }
+
+ protected String getFirstTransformationCode()
+ {
+ if (transformations.size() == 0)
+ {
+ return "";
+ } else
+ {
+ return "_" + transformations.values().iterator().next();
+ }
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/thumbnails/DefaultThumbnailsConfiguration.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/thumbnails/DefaultThumbnailsConfiguration.java
new file mode 100644
index 0000000000000000000000000000000000000000..689e4b706539b081053de60efdaae0b2c3f92f0e
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/thumbnails/DefaultThumbnailsConfiguration.java
@@ -0,0 +1,31 @@
+/*
+ * 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.dss.etl.dto.api.thumbnails;
+
+import ch.systemsx.cisd.openbis.dss.Constants;
+
+/**
+ * @author Pawel Glyzewski
+ */
+public class DefaultThumbnailsConfiguration extends AbstractThumbnailsConfiguration
+{
+ @Override
+ protected String getDefaultFileName()
+ {
+ return Constants.HDF5_CONTAINER_THUMBNAILS_FILE_NAME;
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/thumbnails/IThumbnailsConfiguration.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/thumbnails/IThumbnailsConfiguration.java
similarity index 87%
rename from screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/thumbnails/IThumbnailsConfiguration.java
rename to screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/thumbnails/IThumbnailsConfiguration.java
index a4e23c1781ec507ff71d90a47be337a4dee3c698..87a2655c0ac8706de57e2cefd6da3cb080fe9382 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/thumbnails/IThumbnailsConfiguration.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/thumbnails/IThumbnailsConfiguration.java
@@ -14,10 +14,10 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.thumbnails;
+package ch.systemsx.cisd.openbis.dss.etl.dto.api.thumbnails;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.SimpleImageDataConfig;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ThumbnailsStorageFormat;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.SimpleImageDataConfig;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ThumbnailsStorageFormat;
/**
* @author Pawel Glyzewski
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/thumbnails/ResolutionBasedThumbnailsConfiguration.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/thumbnails/ResolutionBasedThumbnailsConfiguration.java
new file mode 100644
index 0000000000000000000000000000000000000000..dc0d16c563314489d520da6be79c0f04bb47fd5c
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/thumbnails/ResolutionBasedThumbnailsConfiguration.java
@@ -0,0 +1,62 @@
+/*
+ * 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.dss.etl.dto.api.thumbnails;
+
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.SimpleImageDataConfig;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ThumbnailsStorageFormat;
+
+/**
+ * @author Pawel Glyzewski
+ */
+public class ResolutionBasedThumbnailsConfiguration extends AbstractThumbnailsConfiguration
+{
+ private final int maxWidth;
+
+ private final int maxHeight;
+
+ private final boolean allowEnlarging;
+
+ public ResolutionBasedThumbnailsConfiguration(int maxWidth, int maxHeight)
+ {
+ this(maxWidth, maxHeight, true);
+ }
+
+ public ResolutionBasedThumbnailsConfiguration(int maxWidth, int maxHeight,
+ boolean allowEnlarging)
+ {
+ this.maxWidth = maxWidth;
+ this.maxHeight = maxHeight;
+ this.allowEnlarging = allowEnlarging;
+ }
+
+ @Override
+ public ThumbnailsStorageFormat getThumbnailsStorageFormat(SimpleImageDataConfig config)
+ {
+ ThumbnailsStorageFormat thumbnailsStorageFormat = super.getThumbnailsStorageFormat(config);
+ thumbnailsStorageFormat.setMaxWidth(maxWidth);
+ thumbnailsStorageFormat.setMaxHeight(maxHeight);
+ thumbnailsStorageFormat.setAllowEnlarging(allowEnlarging);
+ return thumbnailsStorageFormat;
+ }
+
+ @Override
+ protected String getDefaultFileName()
+ {
+ return String.format("thumbnails_%dx%d%s.h5ar", maxWidth, maxHeight,
+ getFirstTransformationCode());
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/thumbnails/ZoomLevelBasedThumbnailsConfiguration.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/thumbnails/ZoomLevelBasedThumbnailsConfiguration.java
new file mode 100644
index 0000000000000000000000000000000000000000..1e96d5c83c34ba996fb85700ff7d01e6a1653ecf
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/thumbnails/ZoomLevelBasedThumbnailsConfiguration.java
@@ -0,0 +1,48 @@
+/*
+ * 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.dss.etl.dto.api.thumbnails;
+
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.SimpleImageDataConfig;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ThumbnailsStorageFormat;
+
+/**
+ * @author Pawel Glyzewski
+ */
+public class ZoomLevelBasedThumbnailsConfiguration extends AbstractThumbnailsConfiguration
+{
+ private final double zoomLevel;
+
+ public ZoomLevelBasedThumbnailsConfiguration(double zoomLevel)
+ {
+ this.zoomLevel = zoomLevel;
+ }
+
+ @Override
+ public ThumbnailsStorageFormat getThumbnailsStorageFormat(SimpleImageDataConfig config)
+ {
+ ThumbnailsStorageFormat thumbnailsStorageFormat = super.getThumbnailsStorageFormat(config);
+ thumbnailsStorageFormat.setZoomLevel(zoomLevel);
+ return thumbnailsStorageFormat;
+ }
+
+ @Override
+ protected String getDefaultFileName()
+ {
+ return String.format("thumbnails_%.0fpct%s.h5ar", zoomLevel * 100.0,
+ getFirstTransformationCode());
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/transformations/AutoRescaleIntensityImageTransformerFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/transformations/AutoRescaleIntensityImageTransformerFactory.java
new file mode 100644
index 0000000000000000000000000000000000000000..97a16508fa1d5889151b569b7280a5e22bcc99f0
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/transformations/AutoRescaleIntensityImageTransformerFactory.java
@@ -0,0 +1,69 @@
+/*
+ * 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.dss.etl.dto.api.transformations;
+
+import java.awt.image.BufferedImage;
+
+
+import ch.systemsx.cisd.base.image.IImageTransformer;
+import ch.systemsx.cisd.base.image.IImageTransformerFactory;
+import ch.systemsx.cisd.base.annotation.JsonObject;
+import ch.systemsx.cisd.common.image.IntensityRescaling;
+import ch.systemsx.cisd.common.image.IntensityRescaling.Levels;
+
+/**
+ * Transformation performed by
+ * {@link IntensityRescaling#rescaleIntensityLevelTo8Bits(BufferedImage, Levels)} where levels are
+ * computed automatically by {@link IntensityRescaling#computeLevels(BufferedImage, float)}.
+ * <p>
+ * Warning: The serialized version of this class can be stored in the database for each image.
+ * Moving this class to a different package or changing it in a backward incompatible way would make
+ * all the saved transformations invalid.
+ *
+ * @author Tomasz Pylak
+ */
+@JsonObject("AutoRescaleIntensityImageTransformerFactory")
+public class AutoRescaleIntensityImageTransformerFactory implements IImageTransformerFactory
+{
+ private static final long serialVersionUID = 1L;
+
+ private final float threshold;
+
+ public AutoRescaleIntensityImageTransformerFactory(float threshold)
+ {
+ this.threshold = threshold;
+ }
+
+ @Override
+ public IImageTransformer createTransformer()
+ {
+ return new IImageTransformer()
+ {
+ @Override
+ public BufferedImage transform(BufferedImage image)
+ {
+ if (IntensityRescaling.isNotGrayscale(image))
+ {
+ return image;
+ }
+ Levels levels = IntensityRescaling.computeLevels(image, threshold);
+ return IntensityRescaling.rescaleIntensityLevelTo8Bits(image, levels);
+ }
+ };
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/BitShiftingImageTransformerFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/transformations/BitShiftingImageTransformerFactory.java
similarity index 95%
rename from screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/BitShiftingImageTransformerFactory.java
rename to screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/transformations/BitShiftingImageTransformerFactory.java
index 1209dc120ac0d3d86637977cc6247a90bc6fa951..5917b60a0cccfb203e84d975e8fece7aa15bae45 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/BitShiftingImageTransformerFactory.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/transformations/BitShiftingImageTransformerFactory.java
@@ -1,11 +1,10 @@
-package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.transformations;
+package ch.systemsx.cisd.openbis.dss.etl.dto.api.transformations;
import java.awt.image.BufferedImage;
-
+import ch.systemsx.cisd.base.annotation.JsonObject;
import ch.systemsx.cisd.base.image.IImageTransformer;
import ch.systemsx.cisd.base.image.IImageTransformerFactory;
-import ch.systemsx.cisd.base.annotation.JsonObject;
import ch.systemsx.cisd.common.image.IntensityRescaling;
/**
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/transformations/ConvertToolImageTransformer.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/transformations/ConvertToolImageTransformer.java
new file mode 100644
index 0000000000000000000000000000000000000000..9c061da84106894e4e64e2ee581ba8de67016789
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/transformations/ConvertToolImageTransformer.java
@@ -0,0 +1,269 @@
+/*
+ * 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.dss.etl.dto.api.transformations;
+
+import java.awt.image.BufferedImage;
+import java.io.BufferedReader;
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.OutputStream;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.concurrent.atomic.AtomicBoolean;
+
+import org.apache.log4j.Logger;
+
+import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
+import ch.systemsx.cisd.base.image.IStreamingImageTransformer;
+import ch.systemsx.cisd.base.utilities.OSUtilities;
+import ch.systemsx.cisd.common.concurrent.ConcurrencyUtilities;
+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.process.IProcessIOHandler;
+import ch.systemsx.cisd.common.process.ProcessExecutionHelper;
+import ch.systemsx.cisd.common.process.ProcessIOStrategy;
+import ch.systemsx.cisd.common.process.ProcessResult;
+import ch.systemsx.cisd.imagereaders.IImageReader;
+import ch.systemsx.cisd.imagereaders.ImageID;
+import ch.systemsx.cisd.imagereaders.ImageReaderConstants;
+import ch.systemsx.cisd.imagereaders.ImageReaderFactory;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.transformations.ConvertToolImageTransformerFactory.ToolChoice;
+import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
+
+/**
+ * An {@link IStreamingImageTransformer} using the convert command line tool for transformations.
+ *
+ * @author Kaloyan Enimanev
+ */
+public class ConvertToolImageTransformer implements IStreamingImageTransformer
+{
+
+ private static final String PNG = "png";
+
+ private static final File imageMagickConvertUtilityOrNull;
+
+ private static final File graphicsMagickUtilityOrNull;
+
+ static
+ {
+ imageMagickConvertUtilityOrNull = OSUtilities.findExecutable("convert");
+ graphicsMagickUtilityOrNull = OSUtilities.findExecutable("gm");
+ if (imageMagickConvertUtilityOrNull == null && graphicsMagickUtilityOrNull == null)
+ {
+ throw new ConfigurationFailureException(
+ "Neither ImageMagick 'convert' nor GraphisMagick 'gm' can be found"
+ + " on the system path. Requested image transformation is not available.");
+ }
+ }
+
+ private static final Logger machineLog = LogFactory.getLogger(LogCategory.MACHINE,
+ ConvertToolImageTransformer.class);
+
+ private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
+ ConvertToolImageTransformer.class);
+
+ private final byte[] buffer = new byte[ProcessExecutionHelper.RECOMMENDED_BUFFER_SIZE];
+
+ private final List<String> convertCliArguments;
+
+ private final boolean useGraphicsMagic;
+
+ protected ConvertToolImageTransformer(String arguments, ToolChoice choiceOrNull)
+ {
+ this.convertCliArguments = parseCommandArguments(arguments);
+ ToolChoice choice = (choiceOrNull == null ? ToolChoice.ENFORCE_IMAGEMAGICK : choiceOrNull);
+ switch (choice)
+ {
+ case ENFORCE_IMAGEMAGICK:
+ if (imageMagickConvertUtilityOrNull == null)
+ {
+ throw new ConfigurationFailureException(
+ "The ImageMagick 'convert' tool cannot be found on the system path."
+ + " Requested image transformation is not available.");
+ }
+ useGraphicsMagic = false;
+ break;
+ case ENFORCE_GRAPHICSMAGICK:
+ if (graphicsMagickUtilityOrNull == null)
+ {
+ throw new ConfigurationFailureException(
+ "The GraphicsMagic 'gm' tool cannot be found on the system path."
+ + " Requested image transformation is not available.");
+ }
+ useGraphicsMagic = true;
+ break;
+ case PREFER_IMAGEMAGICK:
+ useGraphicsMagic = (imageMagickConvertUtilityOrNull == null);
+ break;
+ case PREFER_GRAPHICSMAGICK:
+ useGraphicsMagic = (graphicsMagickUtilityOrNull != null);
+ break;
+ default:
+ throw new Error("Unknown ToolChoice " + choice + ".");
+ }
+ }
+
+ @Override
+ public BufferedImage transform(BufferedImage image)
+ {
+ try
+ {
+ byte[] input = ImageUtil.imageToPngFast(image);
+ byte[] output = transform(input);
+ return toBufferedImage(output);
+ } catch (IOException ioex)
+ {
+ throw CheckedExceptionTunnel.wrapIfNecessary(ioex);
+ }
+ }
+
+ @Override
+ public BufferedImage transform(InputStream input)
+ {
+ return toBufferedImage(transformToPNG(input));
+ }
+
+ @Override
+ public byte[] transformToPNG(InputStream input)
+ {
+ final ByteArrayOutputStream bos = new ByteArrayOutputStream();
+ transformToPNGStream(input, bos);
+ return bos.toByteArray();
+ }
+
+ @Override
+ public void transformToPNGStream(InputStream input, OutputStream output)
+ {
+ try
+ {
+ transform(input, output);
+ } catch (IOException ioex)
+ {
+ throw CheckedExceptionTunnel.wrapIfNecessary(ioex);
+ }
+ }
+
+ private BufferedImage toBufferedImage(byte[] output) throws ConfigurationFailureException
+ {
+ IImageReader imageReader =
+ ImageReaderFactory.tryGetReader(ImageReaderConstants.IMAGEIO_LIBRARY, PNG);
+ if (imageReader == null)
+ {
+ throw new ConfigurationFailureException("No ImageIO image readers available");
+ }
+ return imageReader.readImage(output, ImageID.NULL, null);
+ }
+
+ private byte[] transform(final byte[] input) throws IOException
+ {
+ final ByteArrayInputStream bis = new ByteArrayInputStream(input);
+ final ByteArrayOutputStream bos = new ByteArrayOutputStream();
+ transform(bis, bos);
+ return bos.toByteArray();
+ }
+
+ private void transform(final InputStream input, final OutputStream output) throws IOException
+ {
+
+ final List<String> errorLines = new ArrayList<String>();
+ ProcessIOStrategy customIOStrategy =
+ createCustomProcessIOStrategy(input, output, errorLines);
+
+ ProcessResult result =
+ ProcessExecutionHelper.run(getCommandLine(), operationLog, machineLog,
+ ConcurrencyUtilities.NO_TIMEOUT, customIOStrategy, false);
+
+ if (result.isOK() == false)
+ {
+ final String msg =
+ String.format(
+ "Error calling '%s'. Exit value: %d, I/O status: %s\nError output: %s",
+ getCommandLine().toString(), result.getExitValue(), result
+ .getProcessIOResult().getStatus(), errorLines.toString());
+ operationLog.warn(msg);
+ throw new IOException(msg);
+ }
+ }
+
+ private ProcessIOStrategy createCustomProcessIOStrategy(final InputStream input,
+ final OutputStream output, final List<String> errorLines)
+ {
+ return ProcessIOStrategy.createCustom(new IProcessIOHandler()
+ {
+
+ @Override
+ public void handle(AtomicBoolean processRunning, OutputStream stdin,
+ InputStream stdout, InputStream stderr) throws IOException
+ {
+ int n = 0;
+ final BufferedReader stdErrReader =
+ new BufferedReader(new InputStreamReader(stderr));
+ while (processRunning.get() && (-1 != (n = input.read(buffer))))
+ {
+ stdin.write(buffer, 0, n);
+ ProcessExecutionHelper.readBytesIfAvailable(stdout, output, buffer, -1,
+ false);
+ ProcessExecutionHelper.readTextIfAvailable(stdErrReader, errorLines, false);
+ }
+ stdin.flush();
+ stdin.close();
+
+ while (processRunning.get())
+ {
+ ProcessExecutionHelper.readBytesIfAvailable(stdout, output, buffer, -1,
+ false);
+ ProcessExecutionHelper.readTextIfAvailable(stdErrReader, errorLines, false);
+ }
+
+ ProcessExecutionHelper.readBytesIfAvailable(stdout, output, buffer, -1, false);
+ ProcessExecutionHelper.readTextIfAvailable(stdErrReader, errorLines, false);
+ }
+ });
+ }
+
+ private List<String> parseCommandArguments(String argsString)
+ {
+ String[] arguments = argsString.trim().split("\\s");
+ return Arrays.asList(arguments);
+ }
+
+ private List<String> getCommandLine()
+ {
+ ArrayList<String> result = new ArrayList<String>();
+ if (useGraphicsMagic)
+ {
+ result.add(graphicsMagickUtilityOrNull.getPath());
+ result.add("convert");
+ } else
+ {
+ result.add(imageMagickConvertUtilityOrNull.getPath());
+ }
+ result.addAll(convertCliArguments);
+ // use standard input to read image
+ result.add("-");
+ // use standard output to produce result
+ result.add("png:-");
+ return result;
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/transformations/ConvertToolImageTransformerFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/transformations/ConvertToolImageTransformerFactory.java
new file mode 100644
index 0000000000000000000000000000000000000000..df3e6e75f22ccbce3b00565312ca44c7e5b7ec6a
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/transformations/ConvertToolImageTransformerFactory.java
@@ -0,0 +1,68 @@
+/*
+ * 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.dss.etl.dto.api.transformations;
+
+import ch.systemsx.cisd.base.image.IStreamingImageTransformerFactory;
+
+/**
+ * A {@link IStreamingImageTransformerFactory} that constructs {@link ConvertToolImageTransformer}
+ * instances.
+ * <p>
+ * Warning: The serialized version of this class can be stored in the database for each image.
+ * Moving this class to a different package or changing it in a backward incompatible way would make
+ * all the saved transformations invalid.
+ *
+ * @author Kaloyan Enimanev
+ */
+public class ConvertToolImageTransformerFactory implements IStreamingImageTransformerFactory
+{
+ private static final long serialVersionUID = 1L;
+
+ private final String convertCliArguments;
+
+ private final ToolChoice choice;
+
+ /**
+ * An enum to choose which of the two tools, ImageMagick or GraphicsMagick, to prefer or to
+ * enforce.
+ */
+ public enum ToolChoice
+ {
+ ENFORCE_IMAGEMAGICK, ENFORCE_GRAPHICSMAGICK, PREFER_IMAGEMAGICK, PREFER_GRAPHICSMAGICK
+ }
+
+ /**
+ * Constructs the factory with {@link ToolChoice#PREFER_IMAGEMAGICK}.
+ */
+ public ConvertToolImageTransformerFactory(String convertCliArguments)
+ {
+ this(convertCliArguments, ToolChoice.ENFORCE_IMAGEMAGICK);
+ }
+
+ public ConvertToolImageTransformerFactory(String convertCliArguments, ToolChoice choice)
+ {
+ this.convertCliArguments = convertCliArguments;
+ this.choice = choice;
+ }
+
+ @Override
+ public ConvertToolImageTransformer createTransformer()
+ {
+ return new ConvertToolImageTransformer(convertCliArguments, choice);
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/transformations/ImageTransformation.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/transformations/ImageTransformation.java
new file mode 100644
index 0000000000000000000000000000000000000000..f9d41ef5b5839e6be5b4483ef48229df19fbd36e
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/transformations/ImageTransformation.java
@@ -0,0 +1,139 @@
+/*
+ * 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.dss.etl.dto.api.transformations;
+
+import java.io.Serializable;
+
+import ch.systemsx.cisd.base.image.IImageTransformerFactory;
+import ch.systemsx.cisd.openbis.generic.shared.basic.CodeNormalizer;
+
+/**
+ * Describes image transformation, contains user friendly label and description.
+ *
+ * @author Tomasz Pylak
+ */
+public class ImageTransformation implements Serializable
+{
+
+ private static final long serialVersionUID = 1L;
+
+ private String code;
+
+ private String label;
+
+ // can be null
+ private String description;
+
+ private boolean isDefault;
+
+ private final IImageTransformerFactory imageTransformerFactory;
+
+ private final boolean isEditable;
+
+ public ImageTransformation(String code, String label, String description,
+ IImageTransformerFactory imageTransformerFactory)
+ {
+ assert code != null : "code is null";
+ assert label != null : " label is null";
+ assert imageTransformerFactory != null : "imageTransformerFactory is null";
+
+ this.code = CodeNormalizer.normalize(code);
+ this.label = label;
+ this.description = description;
+ this.isDefault = false;
+ this.imageTransformerFactory = imageTransformerFactory;
+ this.isEditable = false; // will be used later for ImageViewer transformations
+ }
+
+ public String getCode()
+ {
+ return code;
+ }
+
+ public String getLabel()
+ {
+ return label;
+ }
+
+ public String getDescription()
+ {
+ return description;
+ }
+
+ public boolean isDefault()
+ {
+ return isDefault;
+ }
+
+ public IImageTransformerFactory getImageTransformerFactory()
+ {
+ return imageTransformerFactory;
+ }
+
+ public boolean isEditable()
+ {
+ return isEditable;
+ }
+
+ // ----------- setters
+
+ public void setCode(String code)
+ {
+ this.code = code;
+ }
+
+ public void setLabel(String label)
+ {
+ this.label = label;
+ }
+
+ public void setDescription(String description)
+ {
+ this.description = description;
+ }
+
+ /**
+ * Calling with true makes this transformation a default user's choice and makes the
+ * 'hard-coded' default unavailable. This transformation will become the first one on the list
+ * automatically.
+ * <p>
+ * Marking more then one transformation as a default for one channel will make it impossible to
+ * register a dataset.
+ * </p>
+ * <p>
+ * If no transformation on the list will be marked as default then a 'hard-coded' default
+ * transformation will become available.
+ * </p>
+ */
+ public void setDefault(boolean isDefault)
+ {
+ this.isDefault = isDefault;
+ }
+
+ @Override
+ public String toString()
+ {
+ StringBuffer sb = new StringBuffer();
+ sb.append("ImageTransformation [code=" + code + ", label=" + label);
+ if (description != null)
+ {
+ sb.append(", description=" + description);
+ }
+ sb.append(", isDefault=" + isDefault + "]");
+ return sb.toString();
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/transformations/ImageTransformationBuffer.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/transformations/ImageTransformationBuffer.java
new file mode 100644
index 0000000000000000000000000000000000000000..0ec4f470f3b12c9a31dfeb92e417e8bc3164605b
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/transformations/ImageTransformationBuffer.java
@@ -0,0 +1,465 @@
+/*
+ * 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.dss.etl.dto.api.transformations;
+
+import java.text.DecimalFormat;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import ch.rinn.restrictions.Private;
+import ch.systemsx.cisd.base.image.IImageTransformerFactory;
+import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
+import ch.systemsx.cisd.common.shared.basic.string.StringUtils;
+
+/**
+ * Utility class to construct various kinds of image transformations.
+ *
+ * @author Tomasz Pylak
+ */
+public class ImageTransformationBuffer
+{
+ private static final String PREDEFINED_TRANSFORMATIONS_CODE_PREFIX = "_";
+
+ private final List<ImageTransformation> imageTransformations;
+
+ public ImageTransformationBuffer()
+ {
+ this.imageTransformations = new ArrayList<ImageTransformation>();
+ }
+
+ /**
+ * Appends a single transformation and returns it. Note that code of each added transformation
+ * should be unique.
+ */
+ public ImageTransformation append(ImageTransformation transformation)
+ {
+ appendAll(transformation);
+ return transformation;
+ }
+
+ /**
+ * Appends any specified transformations. Note that code of each added transformation should be
+ * unique.
+ */
+ public void appendAll(ImageTransformation... transformations)
+ {
+ for (ImageTransformation transformation : transformations)
+ {
+ imageTransformations.add(transformation);
+ }
+ ensureTransformationCodesUnique();
+ }
+
+ // returns a set of used transformation codes
+ private Set<String> ensureTransformationCodesUnique()
+ {
+ Set<String> usedTransformationCodes = new HashSet<String>();
+ for (ImageTransformation transformation : imageTransformations)
+ {
+ String code = transformation.getCode();
+ if (usedTransformationCodes.contains(code))
+ {
+ throw new IllegalArgumentException("Two transformations have the same code: "
+ + code);
+ }
+ usedTransformationCodes.add(code);
+ }
+ return usedTransformationCodes;
+ }
+
+ private void ensureOnlyOneDefault()
+ {
+ ImageTransformation defaultTansf = null;
+ for (ImageTransformation transformation : imageTransformations)
+ {
+ if (transformation.isDefault())
+ {
+ if (defaultTansf == null)
+ {
+ defaultTansf = transformation;
+ } else
+ {
+ throw ConfigurationFailureException.fromTemplate(
+ "Only one image transformation can be default, but two were found: '%s' and "
+ + "'%s'.", defaultTansf.getLabel(), transformation.getLabel());
+ }
+ }
+ }
+ }
+
+ /** @returns all appended transformations */
+ public ImageTransformation[] getTransformations()
+ {
+ // codes of transformations could be changed after they have been added
+ ensureTransformationCodesUnique();
+ ensureOnlyOneDefault();
+ return imageTransformations.toArray(new ImageTransformation[imageTransformations.size()]);
+ }
+
+ // -------------- bit shifting transformations ---------------------
+
+ /**
+ * Appends transformations which extracts a range of grayscale image colors by choosing 8
+ * consecutive bits. All shifts which make sense for 12 bit images will be appended (from 0 to
+ * 4).
+ *
+ * @return appended transformations. They can be used to e.g. modify their label or description.
+ */
+ public ImageTransformation[] appendAllBitShiftsFor12BitGrayscale()
+ {
+ return appendAllAvailableGrayscaleBitShifts(12);
+ }
+
+ /**
+ * Appends transformations which extracts a range of grayscale image colors by choosing 8
+ * consecutive bits. All shifts which make sense for 16 bit images will be appended (from 0 to
+ * 8).
+ *
+ * @return appended transformations. They can be used to e.g. modify their label or description.
+ */
+ public ImageTransformation[] appendAllBitShiftsFor16BitGrayscale()
+ {
+ return appendAllAvailableGrayscaleBitShifts(16);
+ }
+
+ private ImageTransformation[] appendAllAvailableGrayscaleBitShifts(int totalNumberOfBits)
+ {
+ int transformationsNumber = totalNumberOfBits - 8 + 1;
+ ImageTransformation[] transformations = new ImageTransformation[transformationsNumber];
+ for (int i = 0; i < transformationsNumber; i++)
+ {
+ transformations[i] = appendGrayscaleBitShifting(i);
+ }
+ return transformations;
+ }
+
+ /**
+ * Appends transformation which extracts a range of grayscale image colors by choosing 8
+ * consecutive bits starting from the specified one.
+ *
+ * @return appended transformation. It can be used to e.g. modify its label or description.
+ */
+ public ImageTransformation appendGrayscaleBitShifting(int shiftBits)
+ {
+ return append(createGrayscaleBitShifting(shiftBits));
+ }
+
+ /**
+ * Creates a transformation which extracts a range of grayscale image colors by choosing 8
+ * consecutive bits, staring from the specified one.
+ * <p>
+ * This method is useful when one wants to modify the default code, label or description
+ * afterwards.
+ */
+ private static ImageTransformation createGrayscaleBitShifting(int shiftBits)
+ {
+ if (shiftBits < 0)
+ {
+ throw new IllegalArgumentException(
+ "Cannot create an image transformation which shifts by a negative number of bits");
+ }
+ String label = createBitShiftingTransformationLabel(shiftBits);
+ String code = createBitShiftingTransformationCode(shiftBits);
+ String description = createBitShiftingTransformationDescription(shiftBits);
+
+ IImageTransformerFactory factory = new BitShiftingImageTransformerFactory(shiftBits);
+ return new ImageTransformation(code, label, description, factory);
+ }
+
+ private static String createBitShiftingTransformationCode(int shiftBits)
+ {
+ return PREDEFINED_TRANSFORMATIONS_CODE_PREFIX + "BIT_SHIFTING_" + shiftBits;
+ }
+
+ private static String createBitShiftingTransformationDescription(int shiftBits)
+ {
+ return String.format(
+ "Shows a range of grayscale image colors by visualising only 8 consecutive bits from %d to %d. "
+ + "Useful for extracting information from 12 and 16 bit images.",
+ shiftBits, shiftBits + 7);
+ }
+
+ private static String createBitShiftingTransformationLabel(int shiftBits)
+ {
+ return String.format("Show bits %d-%d", shiftBits, shiftBits + 7);
+ }
+
+ // -----------------------------
+
+ /**
+ * Appends transformation which converts grayscale image pixel intensities from the range
+ * [blackPointIntensity, whitePointIntensity] to 8 bit color depth. Useful to compare images of
+ * higher color depth with each other when they do not use the whole range of available
+ * intensities.
+ *
+ * @return appended transformation. It can be used to e.g. modify its label or description.
+ */
+ public ImageTransformation appendRescaleGrayscaleIntensity(int blackPointIntensity,
+ int whitePointIntensity)
+ {
+ return appendRescaleGrayscaleIntensity(blackPointIntensity, whitePointIntensity, null);
+ }
+
+ /**
+ * See {@link #appendRescaleGrayscaleIntensity(int, int)}.
+ * <p>
+ * Additionally sets the label of the transformation.
+ *
+ * @return appended transformation. It can be used to e.g. modify its label or description.
+ */
+ public ImageTransformation appendRescaleGrayscaleIntensity(int blackPointIntensity,
+ int whitePointIntensity, String userFriendlyLabelOrNull)
+ {
+ return append(createRescaleGrayscaleIntensity(blackPointIntensity, whitePointIntensity,
+ userFriendlyLabelOrNull));
+ }
+
+ /**
+ * Creates a transformation which converts grayscale image pixel intensities from the range
+ * [blackPointIntensity, whitePointIntensity] to 8 bit color depth.
+ * <p>
+ * This method is useful when one wants to modify the default code, label or description
+ * afterwards.
+ *
+ * @param userFriendlyLabelOrNull label of the transformation. If null a default label is
+ * assigned.
+ */
+ public static ImageTransformation createRescaleGrayscaleIntensity(int blackPointIntensity,
+ int whitePointIntensity, String userFriendlyLabelOrNull)
+ {
+ if (blackPointIntensity > whitePointIntensity || blackPointIntensity < 0
+ || whitePointIntensity < 0)
+ {
+ throw new IllegalArgumentException(String.format(
+ "Cannot create an image transformation because the range "
+ + "of intensities is invalid: [%d, %d]", blackPointIntensity,
+ whitePointIntensity));
+ }
+ String label = createIntensityRangeTransformationLabel(userFriendlyLabelOrNull);
+ String code =
+ createIntensityRangeTransformationCode(blackPointIntensity, whitePointIntensity);
+ String description =
+ createIntensityRangeTransformationDescription(blackPointIntensity,
+ whitePointIntensity);
+
+ IImageTransformerFactory factory =
+ new IntensityRangeImageTransformerFactory(blackPointIntensity, whitePointIntensity);
+ return new ImageTransformation(code, label, description, factory);
+ }
+
+ private static String createIntensityRangeTransformationCode(int blackPointIntensity,
+ int whitePointIntensity)
+ {
+ return PREDEFINED_TRANSFORMATIONS_CODE_PREFIX + "INTENSITY_LEVEL_" + blackPointIntensity
+ + "_" + whitePointIntensity;
+ }
+
+ private static String createIntensityRangeTransformationDescription(int blackPointIntensity,
+ int whitePointIntensity)
+ {
+ return String
+ .format("Transforms grayscale image by converting intensities of its pixels "
+ + "which are in the range [%d, %d] to 8 bit color depth. "
+ + "The range of intensities is usually calculated by processing a series of 12 or 16 bit images, "
+ + "then the transformation becomes useful to compare these images with each other in 8 bit color depth, "
+ + "especially when they use only a small part of available intensities range.",
+ blackPointIntensity, whitePointIntensity);
+ }
+
+ private static String createIntensityRangeTransformationLabel(String labelOrNull)
+ {
+ return labelOrNull != null ? labelOrNull : "Fixed rescaling";
+ }
+
+ // --------------------------
+
+ /**
+ * Appends transformation which converts each single grayscale image to 8 bit color depth and
+ * rescales pixels intensities so that the darkest pixel will become black and the brightest
+ * will become white.
+ * <p>
+ * Note that by default openBIS applies this transformation with threshold 0 if it deals with
+ * grayscale image where color depth is bigger then 8 bit. So calling this method with parameter
+ * 0 is not necessary.
+ * </p>
+ *
+ * @param threshold value form 0 to 1, it specifies the percentage of darkest and brightest
+ * pixels which will be ignored (they will all become black or white).
+ * @return appended transformation. It can be used to e.g. modify its label or description.
+ */
+ public ImageTransformation appendAutoRescaleGrayscaleIntensity(float threshold)
+ {
+ return appendAutoRescaleGrayscaleIntensity(threshold, null);
+ }
+
+ /**
+ * See {@link #appendAutoRescaleGrayscaleIntensity(float)}.
+ * <p>
+ * Additionally sets the label of the transformation.
+ *
+ * @return appended transformation. It can be used to e.g. modify its label or description.
+ */
+ public ImageTransformation appendAutoRescaleGrayscaleIntensity(float threshold,
+ String userFriendlyLabelOrNull)
+ {
+ return append(createAutoRescaleGrayscaleIntensity(threshold, userFriendlyLabelOrNull));
+ }
+
+ /**
+ * Creates a transformation which converts each single grayscale image to 8 bit color depth and
+ * rescales pixels intensities so that the darkest pixel will become black and the brightest
+ * will become white (with some threshold margin).
+ * <p>
+ * This method is useful when one wants to modify the default code, label or description
+ * afterwards.
+ *
+ * @param threshold value form 0 to 1, it specifies the percentage of darkest and brightest
+ * pixels which will be ignored (they will all become black or white).
+ * @param userFriendlyLabelOrNull label of the transformation. If null a default label is
+ * assigned.
+ */
+ private static ImageTransformation createAutoRescaleGrayscaleIntensity(float threshold,
+ String userFriendlyLabelOrNull)
+ {
+ if (threshold < 0 || threshold > 1)
+ {
+ throw new IllegalArgumentException(
+ "Invalid value of the threshold, should be between 0 and 1, but is: "
+ + threshold);
+ }
+ String label =
+ createAutoRescaleIntensityTransformationLabel(userFriendlyLabelOrNull, threshold);
+ String code = createAutoRescaleIntensityTransformationCode(threshold);
+ String description = createAutoRescaleIntensityTransformationDescription(threshold);
+
+ IImageTransformerFactory factory =
+ new AutoRescaleIntensityImageTransformerFactory(threshold);
+ return new ImageTransformation(code, label, description, factory);
+ }
+
+ private static String createAutoRescaleIntensityTransformationCode(float threshold)
+ {
+ return PREDEFINED_TRANSFORMATIONS_CODE_PREFIX + "AUTO_INTENSITY_LEVEL_" + (threshold * 100);
+ }
+
+ private static String createAutoRescaleIntensityTransformationDescription(float threshold)
+ {
+ return String
+ .format("Creates a transformation which converts each single grayscale image to 8 bit color depth and "
+ + "rescales pixels intensities so that the darkest pixel will become black and the brightest "
+ + "will become white (threshold margin: %s).",
+ new DecimalFormat("#.###").format(threshold));
+ }
+
+ @Private
+ static String createAutoRescaleIntensityTransformationLabel(String labelOrNull, float threshold)
+ {
+ String thresholdPercentage = new DecimalFormat("##.#").format(threshold * 100);
+ return labelOrNull != null ? labelOrNull : String.format("Optimal (image, %s%% cut)",
+ thresholdPercentage);
+ }
+
+ // --------------------------
+
+ /**
+ * Allows to transform the images with ImageMagic convert tool (which has to be installed and
+ * accessible). Convert will be called with the specified parameters.
+ *
+ * @return appended transformation. It can be used to e.g. modify its label or description.
+ */
+ public ImageTransformation appendImageMagicConvert(String convertCliArguments)
+ {
+ return appendImageMagicConvert(convertCliArguments, null);
+ }
+
+ /**
+ * See {@link #appendImageMagicConvert(String)}.
+ * <p>
+ * Additionally sets the label of the transformation.
+ *
+ * @return appended transformation. It can be used to e.g. modify its label or description.
+ */
+ public ImageTransformation appendImageMagicConvert(String convertCliArguments,
+ String userFriendlyLabelOrNull)
+ {
+ return append(createImageMagicConvert(convertCliArguments,
+ generateUniqueConvertTransformationCode(), userFriendlyLabelOrNull));
+ }
+
+ /**
+ * Creates a transformation which converts the images with ImageMagic convert tool.
+ * <p>
+ * This method is useful when one wants to modify the default code, label or description
+ * afterwards.
+ *
+ * @param userFriendlyLabelOrNull label of the transformation. If null a default label is
+ * assigned.
+ */
+ private static ImageTransformation createImageMagicConvert(String convertCliArguments,
+ String transformationCode, String userFriendlyLabelOrNull)
+ {
+ if (StringUtils.isBlank(convertCliArguments))
+ {
+ throw new IllegalArgumentException(
+ "No argument has been specified for the 'convert' command");
+ }
+ if (StringUtils.isBlank(transformationCode))
+ {
+ throw new IllegalArgumentException("Transformation has not been specified");
+ }
+ String label =
+ createImageMagicConvertTransformationLabel(convertCliArguments,
+ userFriendlyLabelOrNull);
+ String description = createImageMagicConvertTransformationDescription(convertCliArguments);
+
+ IImageTransformerFactory factory =
+ new ConvertToolImageTransformerFactory(convertCliArguments);
+ return new ImageTransformation(transformationCode, label, description, factory);
+ }
+
+ private static String createImageMagicConvertTransformationDescription(
+ String convertCliArguments)
+ {
+ return String.format("Transforms images with ImageMagic tool by calling: 'convert %s ...'",
+ convertCliArguments);
+ }
+
+ private static String createImageMagicConvertTransformationLabel(String convertCliArguments,
+ String labelOrNull)
+ {
+ return labelOrNull != null ? labelOrNull : String.format("Convert (%s)",
+ convertCliArguments);
+ }
+
+ private String generateUniqueConvertTransformationCode()
+ {
+ int i = 1;
+ Set<String> usedTransformationCodes = ensureTransformationCodesUnique();
+ while (usedTransformationCodes.contains(getConvertTransformationCode(i)))
+ {
+ i++;
+ }
+ return getConvertTransformationCode(i);
+ }
+
+ private static String getConvertTransformationCode(int seqNumber)
+ {
+ return PREDEFINED_TRANSFORMATIONS_CODE_PREFIX + "CONVERT_" + seqNumber;
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/transformations/IntensityRangeImageTransformerFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/transformations/IntensityRangeImageTransformerFactory.java
new file mode 100644
index 0000000000000000000000000000000000000000..abae0a567e4596951435e42cf330d206290e1547
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/transformations/IntensityRangeImageTransformerFactory.java
@@ -0,0 +1,82 @@
+/*
+ * 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.dss.etl.dto.api.transformations;
+
+import java.awt.image.BufferedImage;
+
+
+import ch.systemsx.cisd.base.image.IImageTransformer;
+import ch.systemsx.cisd.base.image.IImageTransformerFactory;
+
+import ch.systemsx.cisd.base.annotation.JsonObject;
+import ch.systemsx.cisd.common.image.IntensityRescaling;
+import ch.systemsx.cisd.common.image.IntensityRescaling.Levels;
+
+/**
+ * Transformation performed by
+ * {@link IntensityRescaling#rescaleIntensityLevelTo8Bits(BufferedImage, Levels)}.
+ * <p>
+ * Warning: The serialized version of this class can be stored in the database for each image.
+ * Moving this class to a different package or changing it in a backward incompatible way would make
+ * all the saved transformations invalid.
+ *
+ * @author Tomasz Pylak
+ */
+@JsonObject("IntensityRangeImageTransformerFactory")
+public class IntensityRangeImageTransformerFactory implements IImageTransformerFactory
+{
+ private static final long serialVersionUID = 1L;
+
+ private final int blackPointIntensity;
+
+ private final int whitePointIntensity;
+
+ public IntensityRangeImageTransformerFactory(int blackPointIntensity, int whitePointIntensity)
+ {
+ this.blackPointIntensity = blackPointIntensity;
+ this.whitePointIntensity = whitePointIntensity;
+ }
+
+ public int getBlackPointIntensity()
+ {
+ return blackPointIntensity;
+ }
+
+ public int getWhitePointIntensity()
+ {
+ return whitePointIntensity;
+ }
+
+ @Override
+ public IImageTransformer createTransformer()
+ {
+ return new IImageTransformer()
+ {
+ @Override
+ public BufferedImage transform(BufferedImage image)
+ {
+ if (IntensityRescaling.isNotGrayscale(image))
+ {
+ return image;
+ }
+ Levels levels = new Levels(blackPointIntensity, whitePointIntensity);
+ return IntensityRescaling.rescaleIntensityLevelTo8Bits(image, levels);
+ }
+ };
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/utils/DropboxUtils.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/utils/DropboxUtils.java
new file mode 100644
index 0000000000000000000000000000000000000000..2746b4ca1913026d2e7e8b1cb9591d36d6af670e
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/utils/DropboxUtils.java
@@ -0,0 +1,63 @@
+/*
+ * 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.dss.etl.dto.api.utils;
+
+import java.util.Collection;
+import java.util.Map;
+
+import ch.systemsx.cisd.common.geometry.SpatialPoint;
+import ch.systemsx.cisd.openbis.dss.etl.TileGeometryOracle;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.Location;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.PlateUtils;
+
+/**
+ * @author Tomasz Pylak
+ */
+public class DropboxUtils
+{
+ /**
+ * Translates a row number into letter code. Thus, 1 -> A, 2 -> B, 26 -> Z, 27 -> AA, 28 -> AB,
+ * etc.
+ */
+ public static String translateRowNumberIntoLetterCode(int rowNumber)
+ {
+ return PlateUtils.translateRowNumberIntoLetterCode(rowNumber);
+ }
+
+ /**
+ * Figures the tile geometry based on all locations present in the it.
+ */
+ public static Geometry figureGeometry(Collection<Location> tileLocations)
+ {
+ return TileGeometryOracle.figureGeometry(tileLocations);
+ }
+
+ /**
+ * Tries to figure out tile locations based on their spatial coordinates.
+ * <p>
+ * Two spatial points (x1, y1) and (x2, y2) are assumed lie in the same tile when abs(x1-x2) <
+ * epsilon and abs(y1-y2) < epsilon.
+ *
+ * @param epsilon see the javadoc of the method
+ */
+ public static Map<Integer/* tile number */, Location> tryFigureLocations(
+ Map<Integer/* tile number */, SpatialPoint> tileToSpatialPointMap, double epsilon)
+ {
+ return TileGeometryOracle.tryFigureLocations(tileToSpatialPointMap, epsilon);
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/BasicDataSetInformation.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/BasicDataSetInformation.java
index 99bcf07c6308dcf4cd84a876fa3c836c976150d9..a25f0eae3e3282f0844b136360b9debfb17749ea 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/BasicDataSetInformation.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/BasicDataSetInformation.java
@@ -16,74 +16,15 @@
package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1;
-import java.util.Arrays;
-
-import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-import ch.systemsx.cisd.openbis.generic.shared.IServer;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
-
/**
- * Basic attributes of a dataset connected to a sample and optionally to one parent dataset.
+ * This class is obsolete, and should not be used. Use
+ * {@link ch.systemsx.cisd.openbis.dss.etl.dto.api.BasicDataSetInformation} instead
*
- * @author Tomasz Pylak
+ * @author Jakub Straszewski
*/
-public class BasicDataSetInformation extends DataSetInformation
+public class BasicDataSetInformation extends
+ ch.systemsx.cisd.openbis.dss.etl.dto.api.BasicDataSetInformation
{
- private static final long serialVersionUID = IServer.VERSION;
-
- private String fileFormatTypeCode;
-
- // marks if a dataset is measured or derived from measured data
- private boolean isMeasured = true;
-
- /** Sets code of the dataset type */
- public void setDatasetTypeCode(String datasetTypeCode)
- {
- DataSetType dataSetType = new DataSetType();
- dataSetType.setCode(datasetTypeCode);
- super.setDataSetType(dataSetType);
- }
-
- /** Mandatory: sets file format code. */
- public void setFileFormatCode(String fileFormatCode)
- {
- this.fileFormatTypeCode = fileFormatCode;
- }
-
- /**
- * Sets attributes of the connected sample - optional.
- * <p>
- * Alternatively, call
- * {@link ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSetUpdatable#setSample(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.ISampleImmutable)}
- * on the object returned by
- * {@link ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSetRegistrationTransaction#createNewDataSet()}.
- */
- public void setSample(String sampleSpaceCode, String sampleCode)
- {
- super.setSpaceCode(sampleSpaceCode);
- super.setSampleCode(sampleCode);
- }
-
- /** attributes of the parent dataset - optional */
- public void setParentDatasetCode(String parentDatasetCode)
- {
- super.setParentDataSetCodes(Arrays.asList(parentDatasetCode));
- }
-
- /** marks if a dataset is measured or derived from measured data */
- public void setMeasured(boolean isMeasured)
- {
- this.isMeasured = isMeasured;
- }
-
- public String getFileFormatTypeCode()
- {
- return fileFormatTypeCode;
- }
-
- public boolean isMeasured()
- {
- return isMeasured;
- }
+ private static final long serialVersionUID = 1L;
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/Channel.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/Channel.java
index 43fab945b936660c6c30087bc832221792675ef5..2e5551425c10e71e97e8be90ebe7450e54b57cca 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/Channel.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/Channel.java
@@ -1,168 +1,35 @@
package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1;
-import java.awt.Color;
-import java.io.Serializable;
-
-import ch.systemsx.cisd.common.image.WavelengthColor;
-import ch.systemsx.cisd.common.reflection.AbstractHashable;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.transformations.ImageTransformation;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColorRGB;
/**
- * A channel in which the image has been acquired.
- * <p>
- * Each channel has its <code>code</code> which uniquely identifies it in one experiment or dataset.
- * </p>
+ * This class is obsolete, and should not be used. Use
+ * {@link ch.systemsx.cisd.openbis.dss.etl.dto.api.Channel} instead
*
- * @author Tomasz Pylak
+ * @author Jakub Straszewski
*/
-public final class Channel extends AbstractHashable implements Serializable
+public final class Channel extends ch.systemsx.cisd.openbis.dss.etl.dto.api.Channel
{
private static final long serialVersionUID = 1L;
- private final String code;
-
- private final String label;
-
- private String description;
-
- private Integer wavelength;
-
- private ChannelColorRGB channelColorOrNull;
-
- private ImageTransformation[] availableTransformations = new ImageTransformation[0];
-
- /**
- * Constructs a channel with a specified code and label. The channel will be presented in a
- * default color.
- */
- public Channel(String code, String label)
+ public Channel(String code, String label,
+ ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColor channelColorOrNull)
{
- this(code, label, (ChannelColorRGB) null);
+ super(code, label, channelColorOrNull);
}
- /**
- * Constructs a channel with a specified code and label. The channel will be presented in a
- * specified color.
- */
public Channel(String code, String label, ChannelColor channelColorOrNull)
{
- this(code, label, convertColor(channelColorOrNull));
+ super(code, label, channelColorOrNull);
}
- /**
- * Constructs a channel with a specified code and label. The channel will be presented in a
- * specified color.
- */
public Channel(String code, String label, ChannelColorRGB channelColorOrNull)
{
- assert code != null : "code is null";
- assert label != null : "label is null";
- this.label = label;
- this.code = code;
- this.channelColorOrNull = channelColorOrNull;
- }
-
- private static ChannelColorRGB convertColor(ChannelColor plainChannelColorOrNull)
- {
- if (plainChannelColorOrNull == null)
- {
- return null;
- }
- return plainChannelColorOrNull.getRGB();
- }
-
- public String getCode()
- {
- return code;
- }
-
- public String tryGetDescription()
- {
- return description;
- }
-
- public Integer tryGetWavelength()
- {
- return wavelength;
- }
-
- public String getLabel()
- {
- return label;
- }
-
- /**
- * @return color for the specified channel which will be used to display merged channels images.
- * null only during dataset registration when default color should be used, afterwards
- * never null.
- */
- public ChannelColorRGB tryGetChannelColor()
- {
- return channelColorOrNull;
- }
-
- // never null, can be empty
- public ImageTransformation[] getAvailableTransformations()
- {
- return availableTransformations;
+ super(code, label, channelColorOrNull);
}
- // ------------------- setters -------------------
-
- /** Sets the description of the channel. Optional. */
- public void setDescription(String description)
- {
- this.description = description;
- }
-
- /** Sets the wavelength of the light (in nanometers) used to acquire this channel. Optional. */
- public void setWavelength(Integer wavelength)
- {
- this.wavelength = wavelength;
- }
-
- /**
- * Sets the wavelength of the light (in nanometers) used to acquire this channel.<br>
- * Additionally sets the channel color. The color is calculated for display on a computer
- * monitor on the basis of the given wavelength using Bruton's algorithm. See <a
- * href="http://www.midnightkite.com/color.html">COLOR SCIENCE web page</a> for details.
- * <p>
- * Optional.
- */
- public void setWavelengthAndColor(Integer wavelength)
- {
- this.wavelength = wavelength;
- Color color = WavelengthColor.getColorForWavelength(wavelength);
- setChannelColorRGB(convertColor(color));
- }
-
- private ChannelColorRGB convertColor(Color color)
- {
- return new ChannelColorRGB(color.getRed(), color.getGreen(), color.getBlue());
- }
-
- /** Sets the plain color in which this channel will be displayed. */
- public void setChannelColor(ChannelColor channelColor)
- {
- this.channelColorOrNull = convertColor(channelColor);
- }
-
- /** Sets RGB color in which this channel will be displayed. */
- public void setChannelColorRGB(ChannelColorRGB channelColor)
- {
- this.channelColorOrNull = channelColor;
- }
-
- /** Sets available transformations which can be applied to images of this channel on request. */
- public void setAvailableTransformations(ImageTransformation[] transformations)
+ public Channel(String code, String label)
{
- if (transformations == null)
- {
- this.availableTransformations = new ImageTransformation[0];
- } else
- {
- this.availableTransformations = transformations;
- }
+ super(code, label);
}
-
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ChannelColor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ChannelColor.java
index 275b0fcfd15fd91c1fafa17fa936afa7a257fa8d..e1fbb8b140ff9e6c6a687560921c5a2aabc2e994 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ChannelColor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ChannelColor.java
@@ -1,9 +1,10 @@
package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1;
/**
- * Allowed colors in which channels can be presented.
+ * This class is obsolete, and should not be used. Use
+ * {@link ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColor} instead
*
- * @author Tomasz Pylak
+ * @author Jakub Straszewski
*/
public enum ChannelColor
{
@@ -68,4 +69,25 @@ public enum ChannelColor
throw new IllegalStateException("unhandled enum " + this);
}
}
+
+ public ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColor getIndependentChannelColor()
+ {
+ switch (this)
+ {
+ case RED:
+ return ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColor.RED;
+ case GREEN:
+ return ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColor.GREEN;
+ case BLUE:
+ return ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColor.BLUE;
+ case RED_GREEN:
+ return ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColor.RED_GREEN;
+ case GREEN_BLUE:
+ return ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColor.GREEN_BLUE;
+ case RED_BLUE:
+ return ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColor.RED_BLUE;
+ default:
+ throw new IllegalStateException("unhandled enum " + this);
+ }
+ }
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ChannelColorComponent.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ChannelColorComponent.java
index 3d536df7dbaf6271038ed430b1fdcf49159c0935..48ed465546a3c64371d507426a1c2fc4360b2aa6 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ChannelColorComponent.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ChannelColorComponent.java
@@ -16,18 +16,61 @@
package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1;
+import java.util.LinkedList;
+import java.util.List;
+
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ColorComponent;
/**
- * Color component of an image which constitutes one channel. Useful if the image consists of all
- * channels merged together.
+ * This class is obsolete, and should not be used. Use
+ * {@link ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColorComponent} instead
*
- * @author Tomasz Pylak
+ * @author Jakub Straszewski
*/
public enum ChannelColorComponent
{
RED, GREEN, BLUE;
+ public ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColorComponent getIndependentChannelColorComponent()
+ {
+ switch (this)
+ {
+ case BLUE:
+ return ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColorComponent.BLUE;
+ case GREEN:
+ return ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColorComponent.GREEN;
+ case RED:
+ return ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColorComponent.RED;
+ }
+ return null;
+ }
+
+ /**
+ * Gets the list of enums which are either of this type or of the version independent
+ * CahnnelColorComponent. Returns the list of the independent type
+ */
+ public static List<ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColorComponent> convertToIndependentChannelColorList(
+ List<?> inputList)
+ {
+ List<ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColorComponent> results =
+ new LinkedList<ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColorComponent>();
+ for (Object o : inputList)
+ {
+ if (o instanceof ChannelColorComponent)
+ {
+ results.add(((ChannelColorComponent) o).getIndependentChannelColorComponent());
+ } else if (o instanceof ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColorComponent)
+ {
+ results.add((ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColorComponent) o);
+ } else
+ {
+ throw new IllegalArgumentException(
+ "List items must be of one of ChannelColorComponent types.");
+ }
+ }
+ return results;
+ }
+
public static ColorComponent getColorComponent(ChannelColorComponent channelColorComponent)
{
switch (channelColorComponent)
@@ -39,7 +82,6 @@ public enum ChannelColorComponent
case RED:
return ColorComponent.RED;
}
-
return null;
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ChannelColorRGB.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ChannelColorRGB.java
index 55d3e8bb53a33ceb57c4dd1eb3af8b4de12905a6..cdb75551fb0804854f97c57a8d1760df53d120f7 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ChannelColorRGB.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ChannelColorRGB.java
@@ -16,86 +16,20 @@
package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1;
-import java.io.Serializable;
-
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
-
/**
- * RGB color components specify the color in which channel should be displayed.
+ * This class is obsolete, and should not be used. Use
+ * {@link ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColorRGB} instead
*
- * @author Tomasz Pylak
+ * @author Jakub Straszewski
*/
-public class ChannelColorRGB implements Serializable
+public class ChannelColorRGB extends ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColorRGB
{
- private static final long serialVersionUID = ServiceVersionHolder.VERSION;
-
- private int r, g, b;
- @SuppressWarnings("unused")
- private ChannelColorRGB()
- {
- }
+ private static final long serialVersionUID = 1L;
public ChannelColorRGB(int r, int g, int b)
{
- assert r >= 0 && r <= 255 : "invalid color " + r;
- assert g >= 0 && g <= 255 : "invalid color " + g;
- assert b >= 0 && b <= 255 : "invalid color " + b;
-
- this.r = r;
- this.g = g;
- this.b = b;
- }
-
- public int getR()
- {
- return r;
- }
-
- public int getG()
- {
- return g;
- }
-
- public int getB()
- {
- return b;
- }
-
- @Override
- public String toString()
- {
- return "Color(r=" + r + ", g=" + g + ", b=" + b + ")";
- }
-
- @Override
- public int hashCode()
- {
- final int prime = 31;
- int result = 1;
- result = prime * result + b;
- result = prime * result + g;
- result = prime * result + r;
- return result;
- }
-
- @Override
- public boolean equals(Object obj)
- {
- if (this == obj)
- return true;
- if (obj == null)
- return false;
- if (getClass() != obj.getClass())
- return false;
- ChannelColorRGB other = (ChannelColorRGB) obj;
- if (b != other.b)
- return false;
- if (g != other.g)
- return false;
- if (r != other.r)
- return false;
- return true;
+ super(r, g, b);
}
-}
+}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/FeatureListDataConfig.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/FeatureListDataConfig.java
new file mode 100644
index 0000000000000000000000000000000000000000..50cf00b1b5341f8e5c923c4e33154259dd1e76e2
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/FeatureListDataConfig.java
@@ -0,0 +1,79 @@
+/*
+ * 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.etl.dto.api.v1;
+
+import java.util.Collection;
+
+import ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSetUpdatable;
+
+/**
+ * The builder class for creation of feature lists.
+ *
+ * @author Jakub Straszewski
+ */
+public class FeatureListDataConfig
+{
+ /**
+ * The name of this feature grouping.
+ */
+ private String name;
+
+ /**
+ * The list of features for this grouping
+ */
+ private Collection<String> featureList;
+
+ /**
+ * The feature vector container data set to which this list should be assigned
+ */
+ private IDataSetUpdatable containerDataSet;
+
+ public FeatureListDataConfig()
+ {
+ }
+
+ public String getName()
+ {
+ return name;
+ }
+
+ public void setName(String name)
+ {
+ this.name = name;
+ }
+
+ public Collection<String> getFeatureList()
+ {
+ return featureList;
+ }
+
+ public void setFeatureList(Collection<String> featureList)
+ {
+ this.featureList = featureList;
+ }
+
+ public IDataSetUpdatable getContainerDataSet()
+ {
+ return containerDataSet;
+ }
+
+ public void setContainerDataSet(IDataSetUpdatable containerDataSet)
+ {
+ this.containerDataSet = containerDataSet;
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/IFeatureVectorDataSet.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/IFeatureVectorDataSet.java
new file mode 100644
index 0000000000000000000000000000000000000000..22b85622f5d8f4fec1277fb657457a99ab0b48d4
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/IFeatureVectorDataSet.java
@@ -0,0 +1,32 @@
+/*
+ * 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.etl.dto.api.v1;
+
+import ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSet;
+
+/**
+ * Extension of {@link IDataSet} specific for feature vector data sets.
+ *
+ * @author Franz-Josef Elmer
+ */
+public interface IFeatureVectorDataSet extends IDataSet
+{
+ /**
+ * Sets the analysis procedure used to create the feature vectors.
+ */
+ public void setAnalysisProcedure(String analysisProcedure);
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/IImagingDataSetRegistrationTransaction.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/IImagingDataSetRegistrationTransaction.java
index 244d911060bb4cffdf45bb393ed7087778de2c33..ba5c1d7997aceeb50bb108da87095784efbe28fb 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/IImagingDataSetRegistrationTransaction.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/IImagingDataSetRegistrationTransaction.java
@@ -21,6 +21,7 @@ import java.io.File;
import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationDetails;
import ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSet;
import ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSetRegistrationTransaction;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.SimpleImageDataConfig;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ImageDataSetInformation;
/**
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/IImagingDatasetFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/IImagingDatasetFactory.java
index 26ca7ebfbdc72e788f9e4be403f90a3fdde0245f..126b9502fc4a35195e7ea3ec7cb6f42bc6a7fe09 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/IImagingDatasetFactory.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/IImagingDatasetFactory.java
@@ -23,6 +23,8 @@ import java.util.Properties;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationDetails;
import ch.systemsx.cisd.etlserver.registrator.v1.DataSetRegistrationService;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.IFeaturesBuilder;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.SimpleImageDataConfig;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeatureVectorDataSetInformation;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ImageDataSetInformation;
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 ab3150afc013e8e013f4ea195afcf7b2422789bd..db8cc9b0fd40c8b09c2c20b82c9e2f8c387bda87 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
@@ -1,183 +1,18 @@
package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1;
-import java.io.Serializable;
-
-import ch.systemsx.cisd.hcs.Location;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
-
/**
- * DTO with information about one image file
+ * This class is obsolete, and should not be used. Use
+ * {@link ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageFileInfo} instead
*
- * @author Tomasz Pylak
+ * @author Jakub Straszewski
*/
-public final class ImageFileInfo implements Serializable
+public final class ImageFileInfo extends ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageFileInfo
{
- private static final long serialVersionUID = 1L;
-
- private WellLocation wellLocationOrNull;
-
- private Location tileLocation;
-
- private String channelCode;
-
- private final String imageRelativePath;
-
- private Float timepointOrNull;
-
- private Float depthOrNull;
-
- private Integer seriesNumberOrNull;
-
- private ImageIdentifier imageIdentifier;
- private String uniqueImageIdentifier;
-
- private String containerDataSetCode;
+ private static final long serialVersionUID = 1L;
public ImageFileInfo(String channelCode, int tileRow, int tileColumn, String imageRelativePath)
{
- assert channelCode != null;
- assert imageRelativePath != null;
-
- this.channelCode = channelCode;
- this.imageRelativePath = imageRelativePath;
- setTile(tileRow, tileColumn);
- }
-
- public String tryGetUniqueStringIdentifier()
- {
- if (imageIdentifier != null)
- {
- return imageIdentifier.getUniqueStringIdentifier();
- } else if (uniqueImageIdentifier != null)
- {
- return uniqueImageIdentifier;
- }
-
- return null;
- }
-
- public Integer tryGetWellRow()
- {
- return wellLocationOrNull == null ? null : wellLocationOrNull.getRow();
- }
-
- public Integer tryGetWellColumn()
- {
- return wellLocationOrNull == null ? null : wellLocationOrNull.getColumn();
- }
-
- public WellLocation tryGetWellLocation()
- {
- return wellLocationOrNull;
- }
-
- public boolean hasWellLocation()
- {
- return wellLocationOrNull != null;
- }
-
- public int getTileRow()
- {
- return tileLocation.getY();
- }
-
- public int getTileColumn()
- {
- return tileLocation.getX();
- }
-
- public String getChannelCode()
- {
- return channelCode;
- }
-
- public String getImageRelativePath()
- {
- return imageRelativePath;
- }
-
- public Float tryGetTimepoint()
- {
- return timepointOrNull;
- }
-
- public Float tryGetDepth()
- {
- return depthOrNull;
- }
-
- public Integer tryGetSeriesNumber()
- {
- return seriesNumberOrNull;
- }
-
- // --- setters
-
- public void setImageIdentifier(ImageIdentifier imageIdentifier)
- {
- this.imageIdentifier = imageIdentifier;
- }
-
- public void setWell(int row, int column)
- {
- this.wellLocationOrNull = new WellLocation(row, column);
- }
-
- /** @return true if well row and column could be parsed */
- public boolean setWell(String wellText)
- {
- try
- {
- this.wellLocationOrNull = WellLocation.parseLocationStr(wellText);
- } catch (Exception e)
- {
- // do nothing
- }
- return wellLocationOrNull != null;
- }
-
- public void setTile(int row, int column)
- {
- this.tileLocation = Location.createLocationFromRowAndColumn(row, column);
- }
-
- public void setTimepoint(Float value)
- {
- this.timepointOrNull = value;
- }
-
- public void setDepth(Float value)
- {
- this.depthOrNull = value;
- }
-
- public void setSeriesNumber(Integer value)
- {
- 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()
- {
- return "ImageFileInfo [well=" + wellLocationOrNull + ", tile=" + tileLocation
- + ", channel=" + channelCode + ", path=" + imageRelativePath + ", timepoint="
- + timepointOrNull + ", depth=" + depthOrNull + ", seriesNumber="
- + seriesNumberOrNull + "]";
+ super(channelCode, tileRow, tileColumn, imageRelativePath);
}
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ImageIdentifier.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ImageIdentifier.java
index ce63badb1431b49939cc5d02fec6c3c2fc68228c..b11302b2353e9809a98347cd9c9abc9e337679ca 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ImageIdentifier.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ImageIdentifier.java
@@ -16,120 +16,20 @@
package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1;
-import java.io.Serializable;
-
-import ch.systemsx.cisd.imagereaders.ImageID;
-
/**
- * Immutable value class of an image ID based on series index, time series index, focal plane index,
- * and color channel index. It will be used to identify images in a container image file format like
- * multi-page TIFF.
+ * This class is obsolete, and should not be used. Use
+ * {@link ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageIdentifier} instead
*
- * @author Franz-Josef Elmer
+ * @author Jakub Straszewski
*/
-public class ImageIdentifier implements Comparable<ImageIdentifier>, Serializable
+public class ImageIdentifier extends ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageIdentifier
{
- private static final long serialVersionUID = 1L;
-
- public static final ImageIdentifier NULL = new ImageIdentifier(0, 0, 0, 0);
-
- private final int seriesIndex;
- private final int timeSeriesIndex;
-
- private final int focalPlaneIndex;
-
- private final int colorChannelIndex;
+ private static final long serialVersionUID = 1L;
- /**
- * Creates an instance for the specified series index, time series (or T) index, focal plane (or
- * Z) index, color channel index.
- */
public ImageIdentifier(int seriesIndex, int timeSeriesIndex, int focalPlaneIndex,
int colorChannelIndex)
{
- this.seriesIndex = seriesIndex;
- this.timeSeriesIndex = timeSeriesIndex;
- this.focalPlaneIndex = focalPlaneIndex;
- this.colorChannelIndex = colorChannelIndex;
- }
-
- public int getSeriesIndex()
- {
- return seriesIndex;
- }
-
- public int getTimeSeriesIndex()
- {
- return timeSeriesIndex;
- }
-
- public int getFocalPlaneIndex()
- {
- return focalPlaneIndex;
- }
-
- public int getColorChannelIndex()
- {
- return colorChannelIndex;
- }
-
- public String getUniqueStringIdentifier()
- {
- return new ImageID(getSeriesIndex(), getTimeSeriesIndex(), getFocalPlaneIndex(),
- getColorChannelIndex()).getID();
- }
-
- @Override
- public int compareTo(ImageIdentifier that)
- {
- int diff = seriesIndex - that.seriesIndex;
- if (diff != 0)
- {
- return diff;
- }
- diff = timeSeriesIndex - that.timeSeriesIndex;
- if (diff != 0)
- {
- return diff;
- }
- diff = focalPlaneIndex - that.focalPlaneIndex;
- if (diff != 0)
- {
- return diff;
- }
- return colorChannelIndex - that.colorChannelIndex;
- }
-
- @Override
- public boolean equals(Object obj)
- {
- if (obj == this)
- {
- return true;
- }
- if (obj instanceof ImageIdentifier == false)
- {
- return false;
- }
- ImageIdentifier that = (ImageIdentifier) obj;
- return seriesIndex == that.seriesIndex && timeSeriesIndex == that.timeSeriesIndex
- && focalPlaneIndex == that.focalPlaneIndex
- && colorChannelIndex == that.colorChannelIndex;
- }
-
- @Override
- public int hashCode()
- {
- return ((((seriesIndex * 37) + timeSeriesIndex) * 37) + focalPlaneIndex) * 37
- + colorChannelIndex;
+ super(seriesIndex, timeSeriesIndex, focalPlaneIndex, colorChannelIndex);
}
-
- @Override
- public String toString()
- {
- return seriesIndex + "." + timeSeriesIndex + "." + focalPlaneIndex + "."
- + colorChannelIndex;
- }
-
-}
+}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ImageMetadata.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ImageMetadata.java
index f85739f2229b98fb6ccb0d004c86e3a71156c583..54089767f9f973dd9301d15271667196a99b8b92 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ImageMetadata.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ImageMetadata.java
@@ -1,159 +1,11 @@
package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1;
-import org.apache.commons.lang.StringUtils;
-
/**
- * Store well, channel and tile number to which an image belongs. Optionally stores
- * timepoint/depth-scan/image series number.
+ * This class is obsolete, and should not be used. Use
+ * {@link ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageMetadata} instead
*
- * @author Tomasz Pylak
+ * @author Jakub Straszewski
*/
-public class ImageMetadata
+public class ImageMetadata extends ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageMetadata
{
- private String channelCode;
-
- private int tileNumber;
-
- private String well;
-
- private Float timepointOrNull;
-
- private Float depthOrNull;
-
- private Integer seriesNumberOrNull;
-
- private ImageIdentifier imageIdentifierOrNull;
-
- public String getChannelCode()
- {
- return channelCode;
- }
-
- /** Sets channel code. */
- public void setChannelCode(String channelCode)
- {
- this.channelCode = channelCode;
- }
-
- public int getTileNumber()
- {
- return tileNumber;
- }
-
- /** Sets tile number. It should start from 1. */
- public void setTileNumber(int tileNumber)
- {
- this.tileNumber = tileNumber;
- }
-
- public String getWell()
- {
- return well;
- }
-
- /** Sets well code (example: "A1") */
- public void setWell(String well)
- {
- this.well = well;
- }
-
- /** Sets the timepoint of the image. Optional. */
- public void setTimepoint(Float value)
- {
- this.timepointOrNull = value;
- }
-
- /** Sets the depth at which the image has been scanned. Optional. */
- public void setDepth(Float value)
- {
- this.depthOrNull = value;
- }
-
- /**
- * Sets the integer series number of the image. Optional. Used to order images when there are no
- * time or depth dimentions but there is a series of images for one well, channel and tile. Can
- * be also used together with time and depth dimention.
- */
- public void setSeriesNumber(Integer value)
- {
- this.seriesNumberOrNull = value;
- }
-
- /**
- * Sets the id of the image inside a container image file format. This is optional and not
- * needed for image files which contain only one image.
- */
- public void setImageIdentifier(ImageIdentifier imageIdentifier)
- {
- imageIdentifierOrNull = imageIdentifier;
- }
-
- public Float tryGetTimepoint()
- {
- return timepointOrNull;
- }
-
- public Float tryGetDepth()
- {
- return depthOrNull;
- }
-
- public Integer tryGetSeriesNumber()
- {
- return seriesNumberOrNull;
- }
-
- public ImageIdentifier tryGetImageIdentifier()
- {
- return imageIdentifierOrNull;
- }
-
- /**
- * Validates that tile number, channel and well (if argument is <code>false</code>) have been
- * specified.
- *
- * @throws IllegalStateException if the object is not valid.
- */
- public void ensureValid(boolean isMicroscopy)
- {
- if (tileNumber <= 0)
- {
- throw new IllegalStateException("Tile number has to be > 0, but is " + tileNumber);
- }
- if (StringUtils.isBlank(channelCode))
- {
- throw new IllegalStateException("Channel code is not specified");
- }
- if (StringUtils.isBlank(well) && isMicroscopy == false)
- {
- throw new IllegalStateException("Well is not specified");
- }
- }
-
- @Override
- public String toString()
- {
- StringBuffer sb = new StringBuffer();
- sb.append("ImageMetadata [channelCode=" + channelCode + ", tileNumber=" + tileNumber
- + ", well=" + well);
- if (timepointOrNull != null)
- {
- sb.append(", timepointOrNull =" + timepointOrNull);
- }
- if (depthOrNull != null)
- {
- sb.append(", depthOrNull=" + depthOrNull);
- }
- if (seriesNumberOrNull != null)
- {
- sb.append(", seriesNumberOrNull=" + seriesNumberOrNull);
- }
- if (imageIdentifierOrNull != null)
- {
- sb.append(", imageIdentifierOrNull=" + imageIdentifierOrNull);
- }
- sb.append("]");
- return sb.toString();
- }
-
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ImageStorageConfiguraton.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ImageStorageConfiguraton.java
index 5caa8a84cd36e88f6c54573ecb04b9df79a0d944..ffc0ddf3cae1bb2da4bc3d0214d63520ef76dec7 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ImageStorageConfiguraton.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ImageStorageConfiguraton.java
@@ -16,183 +16,15 @@
package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1;
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
-
-import ch.systemsx.cisd.base.image.IImageTransformerFactory;
-import ch.systemsx.cisd.common.reflection.AbstractHashable;
-import ch.systemsx.cisd.openbis.dss.etl.dto.ImageLibraryInfo;
-
/**
- * Configuration of how images should be stored. By default:
- * <UL>
- * <LI>no thumbnails are generated</LI>
- * <LI>original data are stored as they come (without additional compression).</LI>
- * </UL>
+ * This class is obsolete, and should not be used. Use
+ * {@link ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageStorageConfiguraton} instead
*
- * @author Tomasz Pylak
+ * @author Jakub Straszewski
*/
-public class ImageStorageConfiguraton extends AbstractHashable implements Serializable
+public class ImageStorageConfiguraton extends
+ ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageStorageConfiguraton
{
- private static final long serialVersionUID = 1L;
-
- /** Returns the default configuration. */
- public static ImageStorageConfiguraton createDefault()
- {
- return new ImageStorageConfiguraton();
- }
-
- // --- State ----------
-
- /** No thumbnails are generated by default. */
- private List<ThumbnailsStorageFormat> thumbnailsStorageFormatsList =
- new ArrayList<ThumbnailsStorageFormat>();
-
- private OriginalDataStorageFormat originalDataStorageFormat =
- OriginalDataStorageFormat.UNCHANGED;
-
- /** No preferences by default, each storage processor decides by its own if it is not set. */
- private Boolean storeChannelsOnExperimentLevelOrNull = null;
-
- /**
- * an image transformation to be applied before the image is stored.
- */
- private IImageTransformerFactory imageTransformerFactoryOrNull;
-
- /**
- * null by default, in this case some heuristics are used to find the right library to read the
- * images, but it is slower and not all libraries are tried.
- */
- private ImageLibraryInfo imageLibraryOrNull = null;
-
- // --- Getters & Setters ----------
-
- /** @return null if no thumbnails should be generated */
- public List<ThumbnailsStorageFormat> getThumbnailsStorageFormat()
- {
- return thumbnailsStorageFormatsList;
- }
-
- /** Set to null if no thumbnails should be generated. Overrides previous thumbnails settings. */
- public void setThumbnailsStorageFormat(ThumbnailsStorageFormat thumbnailsStorageFormatOrNull)
- {
- thumbnailsStorageFormatsList.clear();
- addThumbnailsStorageFormat(thumbnailsStorageFormatOrNull);
- }
-
- /**
- * Adds new thumbnails setting to the list
- */
- public void addThumbnailsStorageFormat(ThumbnailsStorageFormat thumbnailsStorageFormatOrNull)
- {
- if (thumbnailsStorageFormatOrNull != null)
- {
- thumbnailsStorageFormatsList.add(thumbnailsStorageFormatOrNull);
- }
- }
-
- /**
- * Convenience method to switch on thumbnails generation with default settings. Overrides the
- * results of {@link #setThumbnailsStorageFormat(ThumbnailsStorageFormat)}!.
- */
- public void switchOnThumbnailsGeneration()
- {
- thumbnailsStorageFormatsList.clear();
- thumbnailsStorageFormatsList.add(new ThumbnailsStorageFormat());
- }
-
- public OriginalDataStorageFormat getOriginalDataStorageFormat()
- {
- return originalDataStorageFormat;
- }
-
- public void setOriginalDataStorageFormat(OriginalDataStorageFormat originalDataStorageFormat)
- {
- this.originalDataStorageFormat = originalDataStorageFormat;
- }
-
- /**
- * Signalizes that the channels should be saved on experiment level rather than dataset level.
- * Will be ignored in case of microscopy where all channels are always saved at dataset level.
- */
- public void setStoreChannelsOnExperimentLevel(boolean storeChannelsOnExperimentLevel)
- {
- this.storeChannelsOnExperimentLevelOrNull = storeChannelsOnExperimentLevel;
- }
-
- public Boolean getStoreChannelsOnExperimentLevel()
- {
- return storeChannelsOnExperimentLevelOrNull;
- }
-
- public IImageTransformerFactory getImageTransformerFactory()
- {
- return imageTransformerFactoryOrNull;
- }
-
- /**
- * Allows for applying an image transformation on the fly when an image is fetched.
- */
- public void setImageTransformerFactory(IImageTransformerFactory transformerFactory)
- {
- this.imageTransformerFactoryOrNull = transformerFactory;
- }
-
- /** Sets the library which should be used to read the images. */
- public void setImageLibrary(ImageLibraryInfo imageLibrary)
- {
- this.imageLibraryOrNull = imageLibrary;
- }
-
- /**
- * @return library which should be used to read the images or null if the library is not
- * specified.
- */
- public ImageLibraryInfo tryGetImageLibrary()
- {
- return imageLibraryOrNull;
- }
-
- @Override
- public String toString()
- {
- final StringBuilder buffer = new StringBuilder(super.toString());
- if (originalDataStorageFormat != OriginalDataStorageFormat.UNCHANGED)
- {
- appendNameAndObject(buffer, "original data storage format",
- originalDataStorageFormat.toString());
- }
- if (thumbnailsStorageFormatsList.size() > 0)
- {
- for (ThumbnailsStorageFormat thumbnailsStorageFormat : thumbnailsStorageFormatsList)
- {
- appendNameAndObject(buffer, "thumbnails", thumbnailsStorageFormat.toString());
- }
- }
- if (storeChannelsOnExperimentLevelOrNull != null)
- {
- appendNameAndObject(buffer, "store channels on experiment level",
- storeChannelsOnExperimentLevelOrNull);
- }
- if (imageTransformerFactoryOrNull != null)
- {
- appendNameAndObject(buffer, "image transformation", "present");
- }
- if (imageLibraryOrNull != null)
- {
- appendNameAndObject(buffer, "image library", imageLibraryOrNull.toString());
- }
- return buffer.toString();
- }
-
- protected static final void appendNameAndObject(final StringBuilder buffer, final String name,
- final Object object)
- {
- if (object != null)
- {
- buffer.append(name).append("::").append(object).append(";");
- }
- }
-}
+ private static final long serialVersionUID = 1L;
+}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/IntensityRange.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/IntensityRange.java
index e74cb9f4fbdcc71e67af5b6e66500afb330307c0..213361f4a46ef5fe607744ec9f151e86698bfafd 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/IntensityRange.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/IntensityRange.java
@@ -17,42 +17,16 @@
package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1;
/**
- * The intensity range in a distribution of pixel values for a given symmetric quantile value.
- *
- * @author Bernd Rinn
+ * This class is obsolete, and should not be used. Use
+ * {@link ch.systemsx.cisd.openbis.dss.etl.dto.api.IntensityRange} instead
+ *
+ * @author Jakub Straszewski
*/
-public class IntensityRange
+public class IntensityRange extends ch.systemsx.cisd.openbis.dss.etl.dto.api.IntensityRange
{
- final int blackPoint;
-
- final int whitePoint;
public IntensityRange(int blackPoint, int whitePoint)
{
- this.blackPoint = blackPoint;
- this.whitePoint = whitePoint;
- }
-
- /**
- * The minimal level (black point).
- */
- public int getBlackPoint()
- {
- return blackPoint;
- }
-
- /**
- * The maximal level (white point).
- */
- public int getWhitePoint()
- {
- return whitePoint;
- }
-
- @Override
- public String toString()
- {
- return "MinMax [minLevel=" + blackPoint + ", maxLevel=" + whitePoint + "]";
+ super(blackPoint, whitePoint);
}
-
-}
+}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/Location.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/Location.java
index eb3049f0e712dd57dc542f62bb0e32a8dd3af597..4b764d6da1c3ecb648bcb4f50ccb8505c1a42cbc 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/Location.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/Location.java
@@ -1,63 +1,16 @@
package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1;
/**
- * Auxiliary structure to store tile location on the well. The top left tile has coordinates (1,1).
+ * This class is obsolete, and should not be used. Use
+ * {@link ch.systemsx.cisd.openbis.dss.etl.dto.api.Location} instead
*
- * @author Tomasz Pylak
+ * @author Jakub Straszewski
*/
-public class Location
+public class Location extends ch.systemsx.cisd.openbis.dss.etl.dto.api.Location
{
- private final int row, column;
- /** Note: The top left tile has coordinates (1,1). */
public Location(int row, int column)
{
- this.row = row;
- this.column = column;
- }
-
- public int getRow()
- {
- return row;
- }
-
- public int getColumn()
- {
- return column;
- }
-
- @Override
- public boolean equals(Object obj)
- {
- if (this == obj)
- {
- return true;
- }
- if (obj == null)
- {
- return false;
- }
- if (getClass() != obj.getClass())
- {
- return false;
- }
- Location other = (Location) obj;
- return column == other.column && row == other.row;
- }
-
- @Override
- public int hashCode()
- {
- final int prime = 31;
- int result = 1;
- result = prime * result + column;
- result = prime * result + row;
- return result;
- }
-
- @Override
- public String toString()
- {
- return "[" + row + ":" + column + "]";
+ super(row, column);
}
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/OriginalDataStorageFormat.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/OriginalDataStorageFormat.java
index 26182aec37773073d5b4bc6f27bcbff4e353932a..7324346157b57e0ca0ef05753906a99b4cfdac9f 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/OriginalDataStorageFormat.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/OriginalDataStorageFormat.java
@@ -37,4 +37,18 @@ public enum OriginalDataStorageFormat
return this == OriginalDataStorageFormat.HDF5
|| this == OriginalDataStorageFormat.HDF5_COMPRESSED;
}
+
+ public ch.systemsx.cisd.openbis.dss.etl.dto.api.OriginalDataStorageFormat getIndependentOriginalDataStorageFormat()
+ {
+ switch (this)
+ {
+ case HDF5:
+ return ch.systemsx.cisd.openbis.dss.etl.dto.api.OriginalDataStorageFormat.HDF5;
+ case HDF5_COMPRESSED:
+ return ch.systemsx.cisd.openbis.dss.etl.dto.api.OriginalDataStorageFormat.HDF5_COMPRESSED;
+ case UNCHANGED:
+ return ch.systemsx.cisd.openbis.dss.etl.dto.api.OriginalDataStorageFormat.UNCHANGED;
+ }
+ return null; // impossible
+ }
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/SimpleFeatureVectorDataConfig.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/SimpleFeatureVectorDataConfig.java
new file mode 100644
index 0000000000000000000000000000000000000000..ddb2f14475de7265c277cdd8cd25c1b4dc49c876
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/SimpleFeatureVectorDataConfig.java
@@ -0,0 +1,65 @@
+/*
+ * 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.etl.dto.api.v1;
+
+import java.util.Properties;
+
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.IFeaturesBuilder;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeaturesBuilder;
+
+/**
+ * Configuration for creating a feature vector data set.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class SimpleFeatureVectorDataConfig
+{
+ private Properties properties;
+ private IFeaturesBuilder featuresBuilder;
+
+ /**
+ * Creates an instance with undefined properties assuming that the {@link FeaturesBuilder} is
+ * used to create the feature vectors.
+ */
+ public SimpleFeatureVectorDataConfig()
+ {
+ }
+
+ /**
+ * Creates an instance for the specified properties object which is used to configure parsing of
+ * a feature vector file.
+ */
+ public SimpleFeatureVectorDataConfig(Properties properties)
+ {
+ this.properties = properties;
+ }
+
+ public IFeaturesBuilder getFeaturesBuilder()
+ {
+ if (featuresBuilder == null)
+ {
+ featuresBuilder = new FeaturesBuilder();
+ }
+ return featuresBuilder;
+ }
+
+ public Properties getProperties()
+ {
+ return properties;
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/SimpleImageContainerDataConfig.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/SimpleImageContainerDataConfig.java
index a426593cbfe295ec5d809f7f2b6b939fa521e9ed..18d40e6fe8820a6a34ea169e67dd7b71010f9062 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/SimpleImageContainerDataConfig.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/SimpleImageContainerDataConfig.java
@@ -16,54 +16,13 @@
package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1;
-import java.util.List;
-
/**
- * Subclass of {@link SimpleImageDataConfig} for container image files which creates
- * {@link ImageMetadata} based on {@link ImageIdentifier} using the following simple mapping:
- * <ul>
- * <li>ImageMetadata.seriesNumber = ImageIdentifier.seriesIndex + 1
- * <li>ImageMetadata.timePoint = ImageIdentifier.timeSeriesIndex
- * <li>ImageMetadata.depth = ImageIdentifier.focalPlaneIndex
- * <li>ImageMetadata.channelCode = 'CHANNEL-' + (ImageIdentifier.colorChannelIndex + 1)
- * <li>ImageMetadata.tileNumber = 1
- * </ul>
- * ImageMetadata.well will be filled with return value of method
- * {@link #tryToExtractWell(ImageIdentifier)}.
+ * This class is obsolete, and should not be used. Use
+ * {@link ch.systemsx.cisd.openbis.dss.etl.dto.api.SimpleImageContainerDataConfig} instead
*
- * @author Franz-Josef Elmer
+ * @author Jakub Straszewski
*/
-public class SimpleImageContainerDataConfig extends SimpleImageDataConfig
+public class SimpleImageContainerDataConfig extends
+ ch.systemsx.cisd.openbis.dss.etl.dto.api.SimpleImageContainerDataConfig
{
-
- @Override
- public ImageMetadata[] extractImagesMetadata(String imagePath,
- List<ImageIdentifier> imageIdentifiers)
- {
- ImageMetadata[] metaData = new ImageMetadata[imageIdentifiers.size()];
- for (int i = 0, n = imageIdentifiers.size(); i < n; i++)
- {
- ImageIdentifier imageIdentifier = imageIdentifiers.get(i);
- ImageMetadata imageMetadata = new ImageMetadata();
- imageMetadata.setImageIdentifier(imageIdentifier);
- imageMetadata.setSeriesNumber(imageIdentifier.getSeriesIndex() + 1);
- imageMetadata.setTimepoint(new Float(imageIdentifier.getTimeSeriesIndex()));
- imageMetadata.setDepth(new Float(imageIdentifier.getFocalPlaneIndex()));
- imageMetadata.setChannelCode("CHANNEL-" + (imageIdentifier.getColorChannelIndex() + 1));
- imageMetadata.setWell(tryToExtractWell(imageIdentifier));
- imageMetadata.setTileNumber(1);
- metaData[i] = imageMetadata;
- }
- return metaData;
- }
-
- /**
- * Tries to extract well from the specified image identifier. Default implementation returns
- * <code>null</code>. In case of screening this method can be overridden.
- */
- public String tryToExtractWell(ImageIdentifier imageIdentifier)
- {
- return null;
- }
-
-}
+}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/SimpleImageDataConfig.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/SimpleImageDataConfig.java
index 83783da72cf29aad9856b0c136a9ba1ed8a5c5e7..21131836b6a61fb24ce4ea26fb99edf734d60480 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/SimpleImageDataConfig.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/SimpleImageDataConfig.java
@@ -16,966 +16,13 @@
package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import ch.systemsx.cisd.base.image.IImageTransformerFactory;
-import ch.systemsx.cisd.common.shared.basic.string.StringUtils;
-import ch.systemsx.cisd.openbis.dss.etl.dto.ImageLibraryInfo;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.thumbnails.DefaultThumbnailsConfiguration;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.thumbnails.IThumbnailsConfiguration;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.thumbnails.ResolutionBasedThumbnailsConfiguration;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.thumbnails.ZoomLevelBasedThumbnailsConfiguration;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.transformations.ConvertToolImageTransformerFactory;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.transformations.ImageTransformation;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.transformations.ImageTransformationBuffer;
-import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
-import ch.systemsx.cisd.openbis.generic.shared.basic.CodeNormalizer;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
-
/**
- * Allows to configure extraction of images for a plate or microscopy sample.
+ * This class is obsolete, and should not be used. Use
+ * {@link ch.systemsx.cisd.openbis.dss.etl.dto.api.SimpleImageDataConfig} instead
*
- * @author Tomasz Pylak
+ * @author Jakub Straszewski
*/
-abstract public class SimpleImageDataConfig
+abstract public class SimpleImageDataConfig extends
+ ch.systemsx.cisd.openbis.dss.etl.dto.api.SimpleImageDataConfig
{
- // --- one of the following two methods has to be overridden -----------------
-
- /**
- * Extracts tile number, channel code and well code for a given relative path to a single image.
- * This method should overridden to deal with files containing single images. It is ignored if
- * {@link #extractImagesMetadata(String, List)} is overridden as well.
- * <p>
- * It will be called for each file found in the incoming directory which has the extension
- * returned by {@link #getRecognizedImageExtensions()}.
- * </p>
- * To deal with image containers (like multi-page TIFF files) override
- * {@link #extractImagesMetadata(String, List)} instead, otherwise leave that method unchanged.
- */
- public ImageMetadata extractImageMetadata(String imagePath)
- {
- throw new UnsupportedOperationException(
- "One of the extractImageMetadata() methods has to be implemented.");
- }
-
- /**
- * Returns meta-data for each image in the specified image container. This method should
- * overridden to deal with container images (like multi-page TIFF files).
- * <p>
- * This implementation returns the result of {@link #extractImageMetadata(String)} wrapped in an
- * array, image identifiers are ignored.
- * </p>
- *
- * @param imagePath path to the single image or container of many images
- * @param imageIdentifiers Identifiers of all images contained in the image file.
- */
- public ImageMetadata[] extractImagesMetadata(String imagePath,
- List<ImageIdentifier> imageIdentifiers)
- {
-
- ImageMetadata imageMetadata = extractImageMetadata(imagePath);
- return (imageMetadata != null) ? new ImageMetadata[]
- { imageMetadata } : new ImageMetadata[0];
- }
-
- // --- methods which can be overridden -----------------
-
- /**
- * By default layouts all images in one row by returning (1, maxTileNumber) geometry.Can be
- * overridden in subclasses.
- *
- * @param imageMetadataList a list of metadata for each encountered image
- * @param maxTileNumber the biggest tile number among all encountered images
- * @return the width and height of the matrix of tiles (a.k.a. fields or sides) in the well.
- */
- public Geometry getTileGeometry(List<? extends ImageMetadata> imageMetadataList,
- int maxTileNumber)
- {
- return Geometry.createFromRowColDimensions(1, maxTileNumber);
- }
-
- /**
- * For a given tile number and tiles geometry returns (x,y) which describes where the tile is
- * located on the well. Can be overridden in subclasses.<br>
- * Note: The top left tile has coordinates (1,1).
- *
- * @param tileNumber number of the tile extracted by {@link #extractImageMetadata}.
- * @param tileGeometry the geometry of the well matrix returned by {@link #getTileGeometry}.
- */
- public Location getTileCoordinates(int tileNumber, Geometry tileGeometry)
- {
- int columns = tileGeometry.getWidth();
- int row = ((tileNumber - 1) / columns) + 1;
- int col = ((tileNumber - 1) % columns) + 1;
- return new Location(row, col);
- }
-
- /**
- * <p>
- * Creates channel description for a given code. Can be overridden in subclasses.
- * </p>
- * By default the channel label will be equal to the code. Channel color returned by
- * {@link #getChannelColor(String)} will be used.
- */
- public Channel createChannel(String channelCode)
- {
- ChannelColorRGB channelColorOrNull = tryGetChannelColor(channelCode.toUpperCase());
- ImageTransformation[] availableTransformations =
- getAvailableChannelTransformations(channelCode);
- String label = channelCode;
- String normalizedChannelCode = CodeNormalizer.normalize(channelCode);
- Channel channel = new Channel(normalizedChannelCode, label, channelColorOrNull);
- channel.setAvailableTransformations(availableTransformations);
- return channel;
- }
-
- private ChannelColorRGB tryGetChannelColor(String channelCode)
- {
- ChannelColor channelColor = getChannelColor(channelCode);
- ChannelColorRGB channelColorRGB = getChannelColorRGB(channelCode);
- if (channelColorRGB != null && channelColor != null)
- {
- throw new IllegalStateException(String.format(
- "Color for channel '%s' is specified in two ways: %s and %s", channelColor,
- channelColorRGB));
- }
-
- if (channelColor != null)
- {
- return channelColor.getRGB();
- } else
- {
- return channelColorRGB;
- }
- }
-
- /**
- * Sets available transformations which can be applied to images of the specified channel (on
- * user's request).
- * <p>
- * Can be overridden in subclasses. The easiest way to create transformations is to use
- * {@link ImageTransformationBuffer} class.
- * <p>
- * By default returns null.
- */
- public ImageTransformation[] getAvailableChannelTransformations(String channelCode)
- {
- return null;
- }
-
- /**
- * Has the same effect as {@link #getChannelColorRGB(String)}, but can return only plain colors.
- */
- public ChannelColor getChannelColor(String channelCode)
- {
- return null;
- }
-
- /**
- * Returns RGB color for the specified channel. It will be used to display merged channels
- * images.
- * <p>
- * Can be overridden in subclasses. It is ignored if {@link #createChannel(String)} is
- * overridden as well. One should not override {@link #getChannelColor(String)} and
- * {@link #getChannelColorRGB(String)} at the same time.
- * </p>
- * By default returns null (the arbitrary color will be set).
- */
- public ChannelColorRGB getChannelColorRGB(String channelCode)
- {
- return null;
- }
-
- // --- auxiliary structures ----------------------------------------------
-
- private String mainDatasetTypeCode;
-
- private String fileFormatCode = ScreeningConstants.UNKNOWN_FILE_FORMAT;
-
- private String plateCode;
-
- private String spaceCode;
-
- private boolean isMeasured = false;
-
- private String[] recognizedImageExtensions = new String[]
- { "tiff", "tif", "png", "gif", "jpg", "jpeg", "c01" };
-
- private List<IThumbnailsConfiguration> imagePyramid = new ArrayList<IThumbnailsConfiguration>();
-
- private int maxThumbnailWidthAndHeight = 256;
-
- private boolean generateThumbnailsWithImageMagic = true;
-
- private List<String> thumbnailsGenerationImageMagicParams = Collections.emptyList();
-
- private boolean generateThumbnailsIn8BitHighQuality = false;
-
- private double allowedMachineLoadDuringThumbnailsGeneration = 1.0;
-
- private boolean storeChannelsOnExperimentLevel = false;
-
- private OriginalDataStorageFormat originalDataStorageFormat =
- OriginalDataStorageFormat.UNCHANGED;
-
- private String convertTransformationCliArgumentsOrNull;
-
- private ImageLibraryInfo imageLibraryInfoOrNull;
-
- private boolean isMicroscopy;
-
- // If null then no common intensity rescaling parameters are computed.
- // If empty the computation will take place for all channels, otherwise only for specified
- // channels.
- private List<String> computeCommonIntensityRangeOfAllImagesForChannelsOrNull = null;
-
- private float computeCommonIntensityRangeOfAllImagesThreshold =
- ImageUtil.DEFAULT_IMAGE_OPTIMAL_RESCALING_FACTOR;
-
- private String computeCommonIntensityRangeOfAllImagesLabel = "Optimal (series)";
-
- private boolean computeCommonIntensityRangeOfAllImagesIsDefault = true;
-
- private Map<String, IntensityRange> fixedIntensityRangeForAllImages;
-
- private String thumbnailsFileFormat;
-
- private List<Channel> channels;
-
- private List<ChannelColorComponent> channelColorComponentsOrNull;
-
- // --- getters & setters ----------------------------------------------
-
- public ImageStorageConfiguraton getImageStorageConfiguration()
- {
- ImageStorageConfiguraton imageStorageConfiguraton =
- ImageStorageConfiguraton.createDefault();
- imageStorageConfiguraton
- .setStoreChannelsOnExperimentLevel(isStoreChannelsOnExperimentLevel());
- imageStorageConfiguraton.setOriginalDataStorageFormat(getOriginalDataStorageFormat());
- for (IThumbnailsConfiguration thumbnailsConfiguration : imagePyramid)
- {
- imageStorageConfiguraton.addThumbnailsStorageFormat(thumbnailsConfiguration
- .getThumbnailsStorageFormat(this));
- }
- if (false == StringUtils.isBlank(convertTransformationCliArgumentsOrNull))
- {
- IImageTransformerFactory convertTransformerFactory =
- new ConvertToolImageTransformerFactory(convertTransformationCliArgumentsOrNull);
- imageStorageConfiguraton.setImageTransformerFactory(convertTransformerFactory);
-
- }
- imageStorageConfiguraton.setImageLibrary(imageLibraryInfoOrNull);
- return imageStorageConfiguraton;
- }
-
- public String getPlateSpace()
- {
- return spaceCode;
- }
-
- public String getPlateCode()
- {
- return plateCode;
- }
-
- public String[] getRecognizedImageExtensions()
- {
- return recognizedImageExtensions;
- }
-
- public boolean isGenerateThumbnails()
- {
- return imagePyramid.size() > 0;
- }
-
- public int getMaxThumbnailWidthAndHeight()
- {
- return maxThumbnailWidthAndHeight;
- }
-
- public double getAllowedMachineLoadDuringThumbnailsGeneration()
- {
- return allowedMachineLoadDuringThumbnailsGeneration;
- }
-
- public boolean isStoreChannelsOnExperimentLevel()
- {
- return storeChannelsOnExperimentLevel;
- }
-
- public OriginalDataStorageFormat getOriginalDataStorageFormat()
- {
- return originalDataStorageFormat;
- }
-
- public String tryGetConvertTransformationCliArguments()
- {
- return convertTransformationCliArgumentsOrNull;
- }
-
- public List<String> getComputeCommonIntensityRangeOfAllImagesForChannels()
- {
- return computeCommonIntensityRangeOfAllImagesForChannelsOrNull;
- }
-
- public float getComputeCommonIntensityRangeOfAllImagesThreshold()
- {
- return computeCommonIntensityRangeOfAllImagesThreshold;
- }
-
- public boolean isFixedIntensityRangeForAllImagesDefined()
- {
- return fixedIntensityRangeForAllImages != null;
- }
-
- public Map<String, IntensityRange> getFixedIntensityRangeForAllImages()
- {
- return fixedIntensityRangeForAllImages;
- }
-
- public String getComputeCommonIntensityRangeOfAllImagesLabel()
- {
- return computeCommonIntensityRangeOfAllImagesLabel;
- }
-
- public boolean isComputeCommonIntensityRangeOfAllImagesDefault()
- {
- return computeCommonIntensityRangeOfAllImagesIsDefault;
- }
-
- public List<Channel> getChannels()
- {
- return channels;
- }
-
- public List<ChannelColorComponent> getChannelColorComponentsOrNull()
- {
- return channelColorComponentsOrNull;
- }
-
- // ----- Setters -------------------------
-
- /**
- * Sets the existing plate to which the dataset should belong.
- *
- * @param spaceCode space where the plate for which the dataset has been acquired exist
- * @param plateCode code of the plate to which the dataset will belong
- */
- public void setPlate(String spaceCode, String plateCode)
- {
- this.spaceCode = spaceCode;
- this.plateCode = plateCode;
- }
-
- /**
- * Only files with these extensions will be recognized as images (e.g. ["jpg", "png"]).<br>
- * By default it is set to [ "tiff", "tif", "png", "gif", "jpg", "jpeg", "c01" ].
- */
- public void setRecognizedImageExtensions(String[] recognizedImageExtensions)
- {
- this.recognizedImageExtensions = recognizedImageExtensions;
- }
-
- /** Sets all channels available in the data set. */
- public void setChannels(List<Channel> channels)
- {
- this.channels = channels;
- }
-
- /**
- * Use this method if channels are encoded in color components of one image (or in other words:
- * each image contains merged channels). For each channel you have to specify the corresponding
- * color component of the image.
- */
- public void setChannels(List<Channel> channels,
- List<ChannelColorComponent> channelColorComponents)
- {
- this.channels = channels;
- channelColorComponentsOrNull = channelColorComponents;
- }
-
- /** should thumbnails be generated? False by default. */
- public void setGenerateThumbnails(boolean generateThumbnails)
- {
- imagePyramid.clear();
- imagePyramid.add(new DefaultThumbnailsConfiguration());
- }
-
- /**
- * See {@link #setGenerateImageRepresentations}.
- *
- * @deprecated use {@link #setGenerateImageRepresentations} instead.
- */
- @Deprecated
- public void setGenerateImagePyramid(IThumbnailsConfiguration[] elements)
- {
- setGenerateImageRepresentations(elements);
- }
-
- /**
- * See {@link #setGenerateImageRepresentationsUsingScaleFactors}.
- *
- * @deprecated use {@link #setGenerateImageRepresentationsUsingScaleFactors} instead.
- */
- @Deprecated
- public void setGenerateImagePyramidWithScaleFactors(double[] zoomLevels)
- {
- setGenerateImageRepresentationsUsingScaleFactors(zoomLevels);
- }
-
- /**
- * See {@link #setGenerateImageRepresentationsUsingImageResolutions}.
- *
- * @deprecated use {@link #setGenerateImageRepresentationsUsingImageResolutions} instead.
- */
- @Deprecated
- public void setGenerateImagePyramidWithImageResolution(String[] resolutions)
- {
- setGenerateImageRepresentationsUsingImageResolutions(resolutions);
- }
-
- /**
- * Registers a request for alternate image representations to be generated based on the original
- * image. The format of the alternate representations is specified by the
- * {@link IThumbnailsConfiguration} formats argument.
- *
- * @param formats The formats of the image generated representations. One image representation
- * will be created for each format.
- */
- public void setGenerateImageRepresentations(IThumbnailsConfiguration[] formats)
- {
- imagePyramid.clear();
- imagePyramid.addAll(Arrays.asList(formats));
- }
-
- /**
- * Registers a request for alternate image representations to be generated based on the original
- * image. The alternate image representations vary with respect to resolution from the original
- * image.
- *
- * @param scaleFactors The scale factors applied to the original resolution. Scale factors must
- * be greater than 0.
- */
- public void setGenerateImageRepresentationsUsingScaleFactors(double[] scaleFactors)
- {
- imagePyramid.clear();
- if (scaleFactors == null)
- {
- return;
- }
-
- // Verify the arguments
- for (double scaleFactor : scaleFactors)
- {
- // This check is duplicated in addImageRepresentationUsingScale
- if (scaleFactor <= 0)
- {
- throw new IllegalArgumentException(
- "Scale factors for generated image representations must be greater than 0. "
- + scaleFactor + " <= 0");
- }
- }
- for (double scale : scaleFactors)
- {
- addGeneratedImageRepresentationWithScale(scale);
- }
- }
-
- /**
- * Registers a request for an alternate image representation to be generated based on the
- * original image. The alternate image representations vary with respect to resolution from the
- * original image.
- *
- * @param scale The scale factor applied to the original resolution. Scale factors must be
- * greater than 0.
- * @return The configuration for the image representation
- */
- public IThumbnailsConfiguration addGeneratedImageRepresentationWithScale(double scale)
- {
- if (scale <= 0)
- {
- throw new IllegalArgumentException(
- "Scale factors for generated image representations must be greater than 0. "
- + scale + " <= 0");
- }
- ZoomLevelBasedThumbnailsConfiguration imageRep =
- new ZoomLevelBasedThumbnailsConfiguration(scale);
- imagePyramid.add(imageRep);
- return imageRep;
- }
-
- /**
- * Registers a request for alternate image representations to be generated based on the original
- * image. The alternate image representations vary with respect to resolution from the original
- * image. By default, allow enlarging. Use
- * {@link #setGenerateImageRepresentationsWithoutEnlargingUsingImageResolutions(String[])} to
- * explicitly prevent enlarging.
- *
- * @param resolutions The resolutions
- */
- public void setGenerateImageRepresentationsUsingImageResolutions(String[] resolutions)
- {
- setGenerateImageRepresentationsUsingImageResolutions(resolutions, true);
- }
-
- /**
- * Registers a request for alternate image representations to be generated based on the original
- * image. The alternate image representations vary with respect to resolution from the original
- * image. This method throws an exception if the requested resolution results in the image being
- * enlarged. Use {@link #setGenerateImageRepresentationsUsingImageResolutions(String[])} to
- * allow enlarging.
- *
- * @param resolutions The resolutions
- */
- public void setGenerateImageRepresentationsWithoutEnlargingUsingImageResolutions(
- String[] resolutions)
- {
- setGenerateImageRepresentationsUsingImageResolutions(resolutions, false);
- }
-
- /**
- * Registers a request for alternate image representations to be generated based on the original
- * image. The alternate image representations vary with respect to resolution from the original
- * image.
- *
- * @param resolutions The resolutions
- * @param allowEnlarging If true, resolutions larger than the original size of the image are
- * allowed
- */
- private void setGenerateImageRepresentationsUsingImageResolutions(String[] resolutions,
- boolean allowEnlarging)
- {
- imagePyramid.clear();
- if (resolutions != null)
- {
- for (String resolution : resolutions)
- {
- addGeneratedImageRepresentationWithResolution(resolution, allowEnlarging);
- }
- }
- }
-
- /**
- * Registers a request for an alternate image representation to be generated based on the
- * original image. The alternate image representations vary with respect to resolution from the
- * original image. Enlarging is allowed. To prevent enlarging of the image, use
- * {@link #addGeneratedImageRepresentationWithoutEnlargingWithResolution}.
- *
- * @param resolution The resolution of the representation.
- * @return The configuration for the image representation.
- */
- public IThumbnailsConfiguration addGeneratedImageRepresentationWithResolution(String resolution)
- {
- return addGeneratedImageRepresentationWithResolution(resolution, true);
- }
-
- /**
- * Registers a request for an alternate image representation to be generated based on the
- * original image. The alternate image representations vary with respect to resolution from the
- * original image. Enlarging is not allowed. To allow enlarging of the image, use
- * {@link #addGeneratedImageRepresentationWithResolution}.
- *
- * @param resolution The resolution of the representation.
- * @return The configuration for the image representation.
- */
- public IThumbnailsConfiguration addGeneratedImageRepresentationWithoutEnlargingWithResolution(
- String resolution)
- {
- return addGeneratedImageRepresentationWithResolution(resolution, false);
- }
-
- /**
- * Registers a request for an alternate image representation to be generated based on the
- * original image. The alternate image representations vary with respect to resolution from the
- * original image.
- *
- * @param resolution The resolution of the representation.
- * @param allowEnlarging If true, the generated representation may be <b>larger</b> than the
- * original image.
- * @return The configuration for the image representation.
- */
- private IThumbnailsConfiguration addGeneratedImageRepresentationWithResolution(
- String resolution, boolean allowEnlarging)
- {
- String[] dimension = resolution.split("x");
- if (dimension.length != 2)
- {
- throw new IllegalArgumentException(
- "Resolution must be specified in format width x height, e. g. '400x300', but was: '"
- + resolution + "'");
- }
- int width = Integer.parseInt(dimension[0].trim());
- int height = Integer.parseInt(dimension[1].trim());
- ResolutionBasedThumbnailsConfiguration imageRep =
- new ResolutionBasedThumbnailsConfiguration(width, height, allowEnlarging);
- imagePyramid.add(imageRep);
- return imageRep;
- }
-
- /** the maximal width and height of the generated thumbnails */
- public void setMaxThumbnailWidthAndHeight(int maxThumbnailWidthAndHeight)
- {
- this.maxThumbnailWidthAndHeight = maxThumbnailWidthAndHeight;
- }
-
- /**
- * Valid only if thumbnails generation is switched on. Set it to a value lower than 1 if you
- * want only some of your processor cores to be used for thumbnails generation. Number of
- * threads that are used for thumbnail generation will be equal to: this constant * number of
- * processor cores.
- */
- public void setAllowedMachineLoadDuringThumbnailsGeneration(
- double allowedMachineLoadDuringThumbnailsGeneration)
- {
- this.allowedMachineLoadDuringThumbnailsGeneration =
- allowedMachineLoadDuringThumbnailsGeneration;
- }
-
- /**
- * Decides if ImageMagic 'convert' utility will be used to generate thumbnails. True by default.
- * <p>
- * One should set this option to false and use the internal library if 'convert' tool is not
- * installed or if many images are stored in one image container file.
- */
- public void setUseImageMagicToGenerateThumbnails(boolean generateWithImageMagic)
- {
- this.generateThumbnailsWithImageMagic = generateWithImageMagic;
- }
-
- public boolean getGenerateThumbnailsWithImageMagic()
- {
- return generateThumbnailsWithImageMagic;
- }
-
- /**
- * Sets additional parameters which should be passed to ImageMagic 'convert' utility when it is
- * used to generate thumbnails.
- * <p>
- * Example: pass "-contrast-stretch 2%" to discard 2% of brightest and darkest pixels in the
- * thumbnails.
- */
- public void setThumbnailsGenerationImageMagicParams(String[] imageMagicParams)
- {
- this.thumbnailsGenerationImageMagicParams = Arrays.asList(imageMagicParams);
- }
-
- public List<String> getThumbnailsGenerationImageMagicParams()
- {
- return thumbnailsGenerationImageMagicParams;
- }
-
- /**
- * If true and thumbnails generation is switched on, thumbnails will be generated with high
- * quality.
- * <p>
- * Be careful: high quality means that the generation will take longer and the image will be
- * converted to 8 bit color depth. This option is useful for segmentation images, images with 8
- * bit color depth or when no 16 bit transformation has to be applied to the images.
- */
- public void setGenerateHighQuality8BitThumbnails(boolean highQualityThumbnails)
- {
- this.generateThumbnailsIn8BitHighQuality = highQualityThumbnails;
- }
-
- public boolean getGenerateThumbnailsIn8BitHighQuality()
- {
- return generateThumbnailsIn8BitHighQuality;
- }
-
- /**
- * See {@link #setGenerateHighQuality8BitThumbnails}.
- *
- * @deprecated use {@link #setGenerateHighQuality8BitThumbnails} instead.
- */
- @Deprecated
- public void setGenerateHighQualityThumbnails(boolean highQualityThumbnails)
- {
- this.generateThumbnailsIn8BitHighQuality = highQualityThumbnails;
- }
-
- /**
- * <p>
- * Can be used only for grayscale images, Useful when images do not use the whole available
- * color depth of the format in which they are stored (e.g. 10 bits out of 12). By default
- * switched off. Causes that the conversion to 8 bit color depth looses less information. At the
- * same time allows to compare images of one dataset to each other.<br>
- * Warning: causes that all images have to be analysed before registration, this is a costly
- * operation!
- * </p>
- * <p>
- * If isComputed is set to true all dataset images will be analysed and one range of pixel
- * intensities used across all images will be computed (with 0.5% threshold). The result will be
- * saved and it will be possible to apply on-the-fly transformation when browsing images.
- * </p>
- * <p>
- * Example: let's assume that all plate images are saved as 12 bit grayscales. Each image has
- * ability to use pixel intensities from 0 to 4095. In our example only a range of the available
- * intensities is used, let's say from 1024 to 2048. Before the image is displayed to the user
- * it has to be converted to 8-bit color depth (range of intensities from 0 to 255). Without
- * taking the effectively used intensities into account the range 1024...2048 would be converted
- * to a range of 64..128 and other intensities would be unused. Analysing the images allows to
- * convert 1024...2048 range to the full 0..255 range.
- * </p>
- */
- public void setComputeCommonIntensityRangeOfAllImagesForAllChannels()
- {
- this.computeCommonIntensityRangeOfAllImagesForChannelsOrNull = Collections.emptyList();
- }
-
- /**
- * See {@link #setComputeCommonIntensityRangeOfAllImagesForAllChannels()}.
- *
- * @param channelCodesOrNull list of channel codes for which the optimal intensity rescaling
- * parameters will be computed. If empty all channels will be analysed. If null
- * nothing will be analysed (default behavior).
- */
- public void setComputeCommonIntensityRangeOfAllImagesForChannels(String[] channelCodesOrNull)
- {
- this.computeCommonIntensityRangeOfAllImagesForChannelsOrNull =
- Arrays.asList(channelCodesOrNull);
- }
-
- /**
- * Set the label of the transformation which will rescale dataset images intensities in an
- * optimal and comparable way. Can be used if the default value is not appropriate.
- * <p>
- * See {@link #setComputeCommonIntensityRangeOfAllImagesForAllChannels()} for details.
- */
- public void setComputeCommonIntensityRangeOfAllImagesLabel(
- String userFriendlyTransformationlabel)
- {
- this.computeCommonIntensityRangeOfAllImagesLabel = userFriendlyTransformationlabel;
- }
-
- /**
- * Sets the threshold of intensities which should be ignored when computing common intensity
- * range of all images. By default equal to 0.5%. Note that
- * {@link #setComputeCommonIntensityRangeOfAllImagesForAllChannels()} or
- * {@link #setComputeCommonIntensityRangeOfAllImagesForChannels(String[])} has to be called to
- * switch on analysis.
- *
- * @param threshold value from 0 to 1. If set to e.g. 0.1 then 10% of brightest and darkest
- * pixels will be ignored.
- */
- public void setComputeCommonIntensityRangeOfAllImagesThreshold(float threshold)
- {
- this.computeCommonIntensityRangeOfAllImagesThreshold = threshold;
- }
-
- /**
- * Sets fixed levels for the common intensity range transformation for all images. If this one
- * is set, the automatic level computation is switched off which may give big performance
- * improvements. If the method
- * {@link #setComputeCommonIntensityRangeOfAllImagesForChannels(String[])} is not called, will
- * set the transformation for all channels.
- */
- public void setDefaultFixedIntensityRangeForAllImages(int minLevel, int maxLevel)
- {
- if (fixedIntensityRangeForAllImages == null)
- {
- fixedIntensityRangeForAllImages = new HashMap<String, IntensityRange>();
- }
- this.fixedIntensityRangeForAllImages.put(null, new IntensityRange(minLevel, maxLevel));
- }
-
- /**
- * Add fixed levels for the common intensity range transformation of the given cannel for all
- * images. If this one is set, the automatic level computation is switched off which can give
- * big performance improvements.
- * <p>
- * Note: If {@link #setDefaultFixedIntensityRangeForAllImages(int, int)} is called as well, then
- * the values provided here will overwrite the default values provided there for the channel
- * <var>channelCode</var>. Otherwise, the common intensity transformation will only be computed
- * for the channels where the levels have been set explicitly by this method.
- */
- public void addFixedIntensityRangeForAllImages(String channelCode, int minLevel, int maxLevel)
- {
- if (fixedIntensityRangeForAllImages == null)
- {
- fixedIntensityRangeForAllImages = new HashMap<String, IntensityRange>();
- }
- this.fixedIntensityRangeForAllImages.put(CodeNormalizer.normalize(channelCode),
- new IntensityRange(minLevel, maxLevel));
- }
-
- /**
- * Sets if the image transformation using common intensity range of all images should be the
- * default choice when browsing images.
- * <p>
- * True by default, which means e.g. that the 'image optimal' transformation will not be
- * automatically available for users. However one can still add it explicitly with a chosen
- * threshold by redefining
- * {@link SimpleImageDataConfig#getAvailableChannelTransformations(String)} method.
- */
- public void setComputeCommonIntensityRangeOfAllImagesIsDefault(boolean isDefault)
- {
- this.computeCommonIntensityRangeOfAllImagesIsDefault = isDefault;
- }
-
- /** Should all dataset in one experiment use the same channels? By default set to false. */
- public void setStoreChannelsOnExperimentLevel(boolean storeChannelsOnExperimentLevel)
- {
- this.storeChannelsOnExperimentLevel = storeChannelsOnExperimentLevel;
- }
-
- /**
- * Should the original data be stored in the original form or should we pack them into one
- * container? Available values are {@link OriginalDataStorageFormat#UNCHANGED},
- * {@link OriginalDataStorageFormat#HDF5}, {@link OriginalDataStorageFormat#HDF5_COMPRESSED}.
- * The default is {@link OriginalDataStorageFormat#UNCHANGED}.
- */
- public void setOriginalDataStorageFormat(OriginalDataStorageFormat originalDataStorageFormat)
- {
- this.originalDataStorageFormat = originalDataStorageFormat;
- }
-
- /**
- * Sets parameters for the 'convert' command line tool, which will be used to apply an image
- * transformation on the fly when an image is fetched.
- */
- public void setConvertTransformationCliArguments(String convertTransformationCliArguments)
- {
- this.convertTransformationCliArgumentsOrNull = convertTransformationCliArguments;
- }
-
- /**
- * Which image library and reader should be used to read the image? <br>
- * Available libraries [readers]:<br>
- * - IJ: [tiff]<br>
- * - ImageIO: [jpg, bmp, jpeg, wbmp, png, gif]<br>
- * - JAI: [pnm, jpeg, fpx, gif, tiff, wbmp, png, bmp]<br>
- * - BioFormats: [ZipReader, APNGReader, JPEGReader, PGMReader, FitsReader, PCXReader,
- * GIFReader, BMPReader, IPLabReader, IvisionReader, DeltavisionReader, MRCReader, GatanReader,
- * GatanDM2Reader, ImarisReader, OpenlabRawReader, OMEXMLReader, LIFReader, AVIReader,
- * PictReader, SDTReader, EPSReader, SlidebookReader, AliconaReader, MNGReader, KhorosReader,
- * VisitechReader, LIMReader, PSDReader, InCellReader, L2DReader, FEIReader, NAFReader,
- * MINCReader, QTReader, MRWReader, TillVisionReader, ARFReader, CellomicsReader, LiFlimReader,
- * TargaReader, OxfordInstrumentsReader, VGSAMReader, HISReader, WATOPReader, SeikoReader,
- * TopometrixReader, UBMReader, QuesantReader, BioRadGelReader, RHKReader,
- * MolecularImagingReader, CellWorxReader, Ecat7Reader, VarianFDFReader, AIMReader, FakeReader,
- * JEOLReader, NiftiReader, AnalyzeReader, APLReader, NRRDReader, ICSReader, PerkinElmerReader,
- * AmiraReader, ScanrReader, BDReader, UnisokuReader, PDSReader, BioRadReader, FV1000Reader,
- * ZeissZVIReader, IPWReader, ND2Reader, JPEG2000Reader, PCIReader, ImarisHDFReader,
- * ZeissLSMReader, SEQReader, GelReader, ImarisTiffReader, FlexReader, SVSReader, ImaconReader,
- * LEOReader, JPKReader, MIASReader, TCSReader, LeicaReader, NikonReader, FluoviewReader,
- * PrairieReader, MetamorphReader, MicromanagerReader, ImprovisionTiffReader,
- * MetamorphTiffReader, NikonTiffReader, OMETiffReader, PhotoshopTiffReader, FEITiffReader,
- * SimplePCITiffReader, NikonElementsTiffReader, TiffDelegateReader, TextReader, BurleighReader,
- * OpenlabReader, DicomReader, SMCameraReader, SBIGReader]
- */
- public void setImageLibrary(String imageLibraryName, String readerName)
- {
- this.imageLibraryInfoOrNull = new ImageLibraryInfo(imageLibraryName, readerName);
- }
-
- /**
- * Sets the image library to be used for reading images. Available libraries are: IJ, ImageIO,
- * JAI, and BioFormats. The first image file is used to determine the actual reader. Note, that
- * all images are read with the same image reader.
- */
- public void setImageLibrary(String imageLibraryName)
- {
- this.imageLibraryInfoOrNull = new ImageLibraryInfo(imageLibraryName);
- }
-
- // --- predefined image dataset types
-
- /**
- * Sets dataset type to the one which should be used for storing raw images. Marks the dataset
- * as a "measured" one.
- */
- public void setRawImageDatasetType()
- {
- setDataSetType(ScreeningConstants.DEFAULT_RAW_IMAGE_DATASET_TYPE);
- setMeasuredData(true);
- }
-
- /**
- * Sets dataset type to the one which should be used for storing overview images generated from
- * raw images. Marks the dataset as a "derived" one.
- */
- public void setOverviewImageDatasetType()
- {
- setDataSetType(ScreeningConstants.DEFAULT_OVERVIEW_IMAGE_DATASET_TYPE);
- setMeasuredData(false);
- }
-
- /**
- * Sets dataset type to the one which should be used for storing overlay images. Marks the
- * dataset as a "derived" one.
- */
- public void setSegmentationImageDatasetType()
- {
- setDataSetType(ScreeningConstants.DEFAULT_SEGMENTATION_IMAGE_DATASET_TYPE);
- setMeasuredData(false);
- }
-
- // --- standard
-
- /** Sets the type of the dataset. */
- public void setDataSetType(String datasetTypeCode)
- {
- this.mainDatasetTypeCode = datasetTypeCode;
- }
-
- /** Sets the file type of the dataset. */
- public void setFileFormatType(String fileFormatCode)
- {
- this.fileFormatCode = fileFormatCode;
- }
-
- /**
- * Set whether the data is measured or not. By default false.
- */
- public void setMeasuredData(boolean isMeasured)
- {
- this.isMeasured = isMeasured;
- }
-
- /**
- * Sets the microscopy flag which is by default <code>false</code>. This flag is used to check
- * whether well in {@link ImageMetadata} is specified or not. In case of microscopy well is
- * ignored. Otherwise it is mandatory.
- */
- public void setMicroscopyData(boolean isMicroscopy)
- {
- this.isMicroscopy = isMicroscopy;
- }
-
- public String getDataSetType()
- {
- return mainDatasetTypeCode;
- }
-
- public String getFileFormatType()
- {
- return fileFormatCode;
- }
-
- public boolean isMeasuredData()
- {
- return isMeasured;
- }
-
- public boolean isMicroscopyData()
- {
- return isMicroscopy;
- }
-
- public void setThumbnailsFileFormat(String thumbnailsFileFormat)
- {
- this.thumbnailsFileFormat = thumbnailsFileFormat;
- }
-
- public String getThumbnailsFileFormat()
- {
- return this.thumbnailsFileFormat;
- }
-}
+}
\ 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 3fe34cf61299aae241ece223042ef454e6760b46..f6d3a3f9db57c184c8e039907df7689720f221dc 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
@@ -17,35 +17,12 @@
package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1;
/**
- * * Allows to configure extraction of overview images for a plate or microscopy sample.
+ * This class is obsolete, and should not be used. Use
+ * {@link ch.systemsx.cisd.openbis.dss.etl.dto.api.SimpleOverviewImageDataConfig} instead
*
- * @author Pawel Glyzewski
+ * @author Jakub Straszewski
*/
-public class SimpleOverviewImageDataConfig extends SimpleImageDataConfig
+public class SimpleOverviewImageDataConfig extends
+ ch.systemsx.cisd.openbis.dss.etl.dto.api.SimpleOverviewImageDataConfig
{
- private String containerDataSetCode;
-
- private boolean generateOverviewImagesFromRegisteredImages;
-
- public String getContainerDataSetCode()
- {
- return containerDataSetCode;
- }
-
- public void setContainerDataSetCode(String containerDataSetCode)
- {
- this.containerDataSetCode = containerDataSetCode;
- }
-
- public boolean isGenerateOverviewImagesFromRegisteredImages()
- {
- return generateOverviewImagesFromRegisteredImages;
- }
-
- public void setGenerateOverviewImagesFromRegisteredImages(
- boolean generateOverviewImagesFromRegisteredImages)
- {
- this.generateOverviewImagesFromRegisteredImages =
- generateOverviewImagesFromRegisteredImages;
- }
-}
+}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ThumbnailsStorageFormat.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ThumbnailsStorageFormat.java
index a9fc82c84b2d7bfb5c6b257bf5752fb51e5a7717..53e40f036110c3b850d75a33eff3052fcc74f907 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ThumbnailsStorageFormat.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ThumbnailsStorageFormat.java
@@ -16,317 +16,15 @@
package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1;
-import java.awt.image.BufferedImage;
-import java.io.OutputStream;
-import java.io.Serializable;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import ch.systemsx.cisd.common.reflection.AbstractHashable;
-import ch.systemsx.cisd.openbis.dss.Constants;
-import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
-
/**
- * Configuration parameters which describe how thumbnails should be generated.
+ * This class is obsolete, and should not be used. Use
+ * {@link ch.systemsx.cisd.openbis.dss.etl.dto.api.ThumbnailsStorageFormat} instead
*
- * @author Tomasz Pylak
+ * @author Jakub Straszewski
*/
-public class ThumbnailsStorageFormat extends AbstractHashable implements Serializable
+public class ThumbnailsStorageFormat extends
+ ch.systemsx.cisd.openbis.dss.etl.dto.api.ThumbnailsStorageFormat
{
private static final long serialVersionUID = 1L;
-
- public enum FileFormat
- {
- PNG
- {
- @Override
- public void writeImage(BufferedImage image, OutputStream stream)
- {
- ImageUtil.writeImageToPng(image, stream);
- }
-
- @Override
- public String getFileExtension()
- {
- return "png";
- }
-
- @Override
- public String getImageMagickParam()
- {
- return "png";
- }
- },
- JPEG
- {
- @Override
- public void writeImage(BufferedImage image, OutputStream stream)
- {
- ImageUtil.writeImageUsingImageIO(image, stream, "jpg");
- }
-
- @Override
- public String getFileExtension()
- {
- return "jpg";
- }
-
- @Override
- public String getImageMagickParam()
- {
- return "jpeg";
- }
- },
- JPEG_2000
- {
- @Override
- public void writeImage(BufferedImage image, OutputStream stream)
- {
- ImageUtil.writeImageUsingImageIO(image, stream, "jpeg 2000");
- }
-
- @Override
- public String getFileExtension()
- {
- return "jp2";
- }
-
- @Override
- public String getImageMagickParam()
- {
- return "jp2";
- }
- };
-
- private static final Map<String, FileFormat> formats;
- static
- {
- formats = new HashMap<String, ThumbnailsStorageFormat.FileFormat>();
- for (FileFormat format : FileFormat.values())
- {
- formats.put(format.name().toUpperCase(), format);
- }
- formats.put("JP2", JPEG_2000);
- formats.put("JPEG 2000", JPEG_2000);
- formats.put("JPG", JPEG);
- }
-
- public abstract void writeImage(BufferedImage image, OutputStream stream);
-
- public abstract String getFileExtension();
-
- public abstract String getImageMagickParam();
-
- public String getOpenBISFileType()
- {
- return getFileExtension().toUpperCase();
- }
-
- public static FileFormat getValue(String fileFormat)
- {
- return formats.get(fileFormat.toUpperCase());
- }
- }
-
- /** Maximum default width and height of a thumbnail */
- public static final int DEFAULT_THUMBNAIL_MAX_SIZE = 200;
-
- /** Maximum default width and height of a thumbnail */
- public static final boolean DEFAULT_COMPRESS_THUMBNAILS = false;
-
- // ---
-
- private int maxWidth = DEFAULT_THUMBNAIL_MAX_SIZE;
-
- private int maxHeight = DEFAULT_THUMBNAIL_MAX_SIZE;
-
- private boolean allowEnlarging = true;
-
- private Double zoomLevel = null;
-
- private boolean storeCompressed = DEFAULT_COMPRESS_THUMBNAILS;
-
- private double allowedMachineLoadDuringGeneration = 1;
-
- private boolean highQuality8Bit = false;
-
- private boolean generateWithImageMagic = false;
-
- private List<String> imageMagicParams = Collections.emptyList();
-
- private String thumbnailsFileName;
-
- private FileFormat fileFormat = FileFormat.PNG;
-
- private final Map<String, String> transformations = new HashMap<String, String>();
-
- /**
- * Creates empty object which instructs that the thumbnails should be generated with default
- * settings. Use setters to change default behaviour (you will probably not have to).
- */
- public ThumbnailsStorageFormat()
- {
- }
-
- public int getMaxWidth()
- {
- return maxWidth;
- }
-
- public int getMaxHeight()
- {
- return maxHeight;
- }
-
- public boolean isStoreCompressed()
- {
- return storeCompressed;
- }
-
- public double getAllowedMachineLoadDuringGeneration()
- {
- return allowedMachineLoadDuringGeneration;
- }
-
- public boolean isHighQuality()
- {
- return highQuality8Bit;
- }
-
- public boolean isGenerateWithImageMagic()
- {
- return generateWithImageMagic;
- }
-
- public List<String> getImageMagicParams()
- {
- return imageMagicParams;
- }
-
- public boolean isAllowEnlarging()
- {
- return allowEnlarging;
- }
-
- // --- setters ---
-
- /** Sets the maximum width of a thumbnail. */
- public void setMaxWidth(int maxWidth)
- {
- this.maxWidth = maxWidth;
- }
-
- /** Sets the maximum height of a thumbnail. */
- public void setMaxHeight(int maxHeight)
- {
- this.maxHeight = maxHeight;
- }
-
- /** Sets if each thumbnail should be additionally compressed (lostless) before it is stored. */
- public void setStoreCompressed(boolean storeCompressed)
- {
- this.storeCompressed = storeCompressed;
- }
-
- /**
- * Specify if this image representation is allowed to be larger than the original image.
- */
- public void setAllowEnlarging(boolean allowEnlarging)
- {
- this.allowEnlarging = allowEnlarging;
- }
-
- /**
- * The number of threads which will be used during thumbnails generation will be equal to number
- * of processor cores * machineLoad.
- */
- public void setAllowedMachineLoadDuringGeneration(double machineLoad)
- {
- this.allowedMachineLoadDuringGeneration = machineLoad;
- }
-
- /**
- * Set to true if you want your thumbnails to be of higher quality. In such a case thumbnails
- * generation during dataset registration will take longer. Recommended for overlay images.
- */
- public void setHighQuality(boolean highQuality)
- {
- this.highQuality8Bit = highQuality;
- }
-
- /**
- * if true ImageMagic 'convert' utility should be installed and will be used to generate
- * thumbnails. <br>
- * Note: if images should be handled with a specific image library, it will be ignored for
- * thumbnails generation if 'convert' is supposed to be used. Make sure that 'convert' can deal
- * with your images in such a case.
- */
- public void setGenerateWithImageMagic(boolean generateWithImageMagic)
- {
- this.generateWithImageMagic = generateWithImageMagic;
- }
-
- /**
- * Sets additional parameters which should be passed to ImageMagic 'convert' utility when it is
- * used to generate thumbnails. Example: pass "-contrast-stretch 2%" to discard 2% of brightest
- * and darkest pixels in the thumbnails.
- */
- public void setImageMagicParams(List<String> imageMagicParams)
- {
- this.imageMagicParams = imageMagicParams;
- }
-
- public Double getZoomLevel()
- {
- return zoomLevel;
- }
-
- public void setZoomLevel(Double zoomLevel)
- {
- this.zoomLevel = zoomLevel;
- }
-
- public String getThumbnailsFileName()
- {
- return thumbnailsFileName == null ? Constants.HDF5_CONTAINER_THUMBNAILS_FILE_NAME
- : thumbnailsFileName;
- }
-
- public void setThumbnailsFileName(String thumbnailsFileName)
- {
- this.thumbnailsFileName = thumbnailsFileName;
- }
-
- public void setFileFormat(String fileFormat)
- {
- FileFormat value = FileFormat.getValue(fileFormat);
- if (value == null)
- {
- throw new IllegalArgumentException("File format '" + fileFormat + "' is unknown");
- }
- this.fileFormat = value;
- }
-
- public FileFormat getFileFormat()
- {
- return fileFormat;
- }
-
- public void setTransformations(Map<String, String> transformations)
- {
- this.transformations.putAll(transformations);
- }
-
- public String getTransformationCode(String channelCode)
- {
- return transformations.get(channelCode.toUpperCase());
- }
-
- public Map<String, String> getTransformations()
- {
- return transformations;
- }
-}
+}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/FeatureVectorContainerDataSet.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/impl/FeatureVectorContainerDataSet.java
similarity index 97%
rename from screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/FeatureVectorContainerDataSet.java
rename to screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/impl/FeatureVectorContainerDataSet.java
index 39fc5a09711862de1692e4fe90e343569fe5814b..4107b3b13cb44a6560f03e639821a80c8e1ef711 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/FeatureVectorContainerDataSet.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/impl/FeatureVectorContainerDataSet.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.etl.dto.api.impl;
+package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.impl;
import static ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants.ANALYSIS_PROCEDURE;
@@ -24,7 +24,7 @@ import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationDetails;
import ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSet;
import ch.systemsx.cisd.etlserver.registrator.api.v1.impl.DataSet;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v2.IFeatureVectorDataSet;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.IFeatureVectorDataSet;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IExperimentImmutable;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.ISampleImmutable;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/FeatureVectorDataSet.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/impl/FeatureVectorDataSet.java
similarity index 96%
rename from screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/FeatureVectorDataSet.java
rename to screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/impl/FeatureVectorDataSet.java
index 0597293943e8008b78a56259e3ae8c2938ef3ea7..f432b51b95de3d34a4a813164044efbdce668783 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/FeatureVectorDataSet.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/impl/FeatureVectorDataSet.java
@@ -14,14 +14,15 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.etl.dto.api.impl;
+package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.impl;
import java.io.File;
import java.util.List;
import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationDetails;
import ch.systemsx.cisd.etlserver.registrator.api.v1.impl.DataSet;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v2.IFeatureVectorDataSet;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeatureVectorDataSetInformation;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.IFeatureVectorDataSet;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IDataSetImmutable;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IExperimentImmutable;
@@ -30,8 +31,6 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.ISampleImmuta
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class FeatureVectorDataSet extends DataSet<FeatureVectorDataSetInformation> implements
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/ImageContainerDataSet.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/impl/ImageContainerDataSet.java
similarity index 97%
rename from screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/ImageContainerDataSet.java
rename to screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/impl/ImageContainerDataSet.java
index 20944b729310f5aca62374767b5494732a0b8772..0c29e2bb6b284f1e35267fc359a803e130363a7d 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/ImageContainerDataSet.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/impl/ImageContainerDataSet.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.etl.dto.api.impl;
+package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.impl;
import java.io.File;
import java.util.Collections;
@@ -24,6 +24,7 @@ import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationDetails;
import ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSet;
import ch.systemsx.cisd.etlserver.registrator.api.v1.impl.DataSet;
import ch.systemsx.cisd.openbis.dss.etl.PlateGeometryOracle;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ImageDataSetInformation;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.IImageDataSet;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IExperimentImmutable;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/thumbnails/AbstractThumbnailsConfiguration.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/thumbnails/AbstractThumbnailsConfiguration.java
index f034defe2e45f5192fd9a079c9ee25163f5f4808..310d4e93c1a7a7845d46ed043a187576c0a994cb 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/thumbnails/AbstractThumbnailsConfiguration.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/thumbnails/AbstractThumbnailsConfiguration.java
@@ -16,97 +16,14 @@
package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.thumbnails;
-import java.util.HashMap;
-import java.util.Map;
-
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.SimpleImageDataConfig;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ThumbnailsStorageFormat;
-
/**
- * @author Pawel Glyzewski
+ * This class is obsolete, and should not be used. Use
+ * {@link ch.systemsx.cisd.openbis.dss.etl.dto.api.thumbnails.AbstractThumbnailsConfiguration}
+ * instead
+ *
+ * @author Jakub Straszewski
*/
-public abstract class AbstractThumbnailsConfiguration implements IThumbnailsConfiguration
+public abstract class AbstractThumbnailsConfiguration extends
+ ch.systemsx.cisd.openbis.dss.etl.dto.api.thumbnails.AbstractThumbnailsConfiguration
{
- private String fileName;
-
- private String fileFormat;
-
- private Map<String, String> transformations = new HashMap<String, String>();
-
- @Override
- public ThumbnailsStorageFormat getThumbnailsStorageFormat(SimpleImageDataConfig config)
- {
- ThumbnailsStorageFormat thumbnailsStorageFormat = new ThumbnailsStorageFormat();
- thumbnailsStorageFormat.setAllowedMachineLoadDuringGeneration(config
- .getAllowedMachineLoadDuringThumbnailsGeneration());
- thumbnailsStorageFormat.setThumbnailsFileName(getFileName());
- thumbnailsStorageFormat.setMaxWidth(config.getMaxThumbnailWidthAndHeight());
- thumbnailsStorageFormat.setMaxHeight(config.getMaxThumbnailWidthAndHeight());
- thumbnailsStorageFormat.setGenerateWithImageMagic(config
- .getGenerateThumbnailsWithImageMagic());
- thumbnailsStorageFormat.setImageMagicParams(config
- .getThumbnailsGenerationImageMagicParams());
- thumbnailsStorageFormat.setHighQuality(config.getGenerateThumbnailsIn8BitHighQuality());
- setFileFormat(thumbnailsStorageFormat, config.getThumbnailsFileFormat());
- thumbnailsStorageFormat.setTransformations(transformations);
- return thumbnailsStorageFormat;
- }
-
- protected abstract String getDefaultFileName();
-
- @Override
- public void setFileName(String fileName)
- {
- this.fileName = fileName;
- }
-
- public String getFileName()
- {
- if (fileName != null)
- {
- return fileName;
- } else
- {
- return getDefaultFileName();
- }
- }
-
- @Override
- public void setFileFormat(String fileFormat)
- {
- this.fileFormat = fileFormat;
- }
-
- public String getFileFormat()
- {
- return this.fileFormat;
- }
-
- private void setFileFormat(ThumbnailsStorageFormat thumbnailsStorageFormat, String defaultValue)
- {
- if (fileFormat != null)
- {
- thumbnailsStorageFormat.setFileFormat(fileFormat);
- } else if (defaultValue != null)
- {
- thumbnailsStorageFormat.setFileFormat(defaultValue);
- }
- }
-
- @Override
- public String setTransformation(String channelCode, String transformationCode)
- {
- return transformations.put(channelCode.toUpperCase(), transformationCode);
- }
-
- protected String getFirstTransformationCode()
- {
- if (transformations.size() == 0)
- {
- return "";
- } else
- {
- return "_" + transformations.values().iterator().next();
- }
- }
-}
+}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/thumbnails/DefaultThumbnailsConfiguration.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/thumbnails/DefaultThumbnailsConfiguration.java
index 531b8c8ea962a761091907ab1743cb89a322bc85..f835ac5d0aae67859d46a1c9c1657b11a8e2e4b6 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/thumbnails/DefaultThumbnailsConfiguration.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/thumbnails/DefaultThumbnailsConfiguration.java
@@ -16,16 +16,14 @@
package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.thumbnails;
-import ch.systemsx.cisd.openbis.dss.Constants;
-
/**
- * @author Pawel Glyzewski
+ * This class is obsolete, and should not be used. Use
+ * {@link ch.systemsx.cisd.openbis.dss.etl.dto.api.thumbnails.DefaultThumbnailsConfiguration}
+ * instead
+ *
+ * @author Jakub Straszewski
*/
-public class DefaultThumbnailsConfiguration extends AbstractThumbnailsConfiguration
+public class DefaultThumbnailsConfiguration extends
+ ch.systemsx.cisd.openbis.dss.etl.dto.api.thumbnails.DefaultThumbnailsConfiguration
{
- @Override
- protected String getDefaultFileName()
- {
- return Constants.HDF5_CONTAINER_THUMBNAILS_FILE_NAME;
- }
-}
+}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/thumbnails/ResolutionBasedThumbnailsConfiguration.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/thumbnails/ResolutionBasedThumbnailsConfiguration.java
index 4c464ba1ab8f165888af4d26bc1b7973b7f76265..1a255a8ac177d1845fedf57259e913a8b8f84ecb 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/thumbnails/ResolutionBasedThumbnailsConfiguration.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/thumbnails/ResolutionBasedThumbnailsConfiguration.java
@@ -16,47 +16,25 @@
package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.thumbnails;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.SimpleImageDataConfig;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ThumbnailsStorageFormat;
-
/**
- * @author Pawel Glyzewski
+ * This class is obsolete, and should not be used. Use
+ * {@link ch.systemsx.cisd.openbis.dss.etl.dto.api.thumbnails.ResolutionBasedThumbnailsConfiguration}
+ * instead
+ *
+ * @author Jakub Straszewski
*/
-public class ResolutionBasedThumbnailsConfiguration extends AbstractThumbnailsConfiguration
+public class ResolutionBasedThumbnailsConfiguration extends
+ ch.systemsx.cisd.openbis.dss.etl.dto.api.thumbnails.ResolutionBasedThumbnailsConfiguration
{
- private final int maxWidth;
-
- private final int maxHeight;
-
- private final boolean allowEnlarging;
- public ResolutionBasedThumbnailsConfiguration(int maxWidth, int maxHeight)
- {
- this(maxWidth, maxHeight, true);
- }
-
- public ResolutionBasedThumbnailsConfiguration(int maxWidth, int maxHeight,
+ private ResolutionBasedThumbnailsConfiguration(int maxWidth, int maxHeight,
boolean allowEnlarging)
{
- this.maxWidth = maxWidth;
- this.maxHeight = maxHeight;
- this.allowEnlarging = allowEnlarging;
- }
-
- @Override
- public ThumbnailsStorageFormat getThumbnailsStorageFormat(SimpleImageDataConfig config)
- {
- ThumbnailsStorageFormat thumbnailsStorageFormat = super.getThumbnailsStorageFormat(config);
- thumbnailsStorageFormat.setMaxWidth(maxWidth);
- thumbnailsStorageFormat.setMaxHeight(maxHeight);
- thumbnailsStorageFormat.setAllowEnlarging(allowEnlarging);
- return thumbnailsStorageFormat;
+ super(maxWidth, maxHeight, allowEnlarging);
}
- @Override
- protected String getDefaultFileName()
+ private ResolutionBasedThumbnailsConfiguration(int maxWidth, int maxHeight)
{
- return String.format("thumbnails_%dx%d%s.h5ar", maxWidth, maxHeight,
- getFirstTransformationCode());
+ super(maxWidth, maxHeight);
}
-}
+}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/thumbnails/ZoomLevelBasedThumbnailsConfiguration.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/thumbnails/ZoomLevelBasedThumbnailsConfiguration.java
index 4930e0052fd5e16d81d9467e70081b1a80a9d84c..89bcb1f7ce6083ecb9932d928a69eb96dca11134 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/thumbnails/ZoomLevelBasedThumbnailsConfiguration.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/thumbnails/ZoomLevelBasedThumbnailsConfiguration.java
@@ -16,33 +16,19 @@
package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.thumbnails;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.SimpleImageDataConfig;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ThumbnailsStorageFormat;
-
/**
- * @author Pawel Glyzewski
+ * This class is obsolete, and should not be used. Use
+ * {@link ch.systemsx.cisd.openbis.dss.etl.dto.api.thumbnails.ZoomLevelBasedThumbnailsConfiguration}
+ * instead
+ *
+ * @author Jakub Straszewski
*/
-public class ZoomLevelBasedThumbnailsConfiguration extends AbstractThumbnailsConfiguration
+public class ZoomLevelBasedThumbnailsConfiguration extends
+ ch.systemsx.cisd.openbis.dss.etl.dto.api.thumbnails.ZoomLevelBasedThumbnailsConfiguration
{
- private final double zoomLevel;
-
- public ZoomLevelBasedThumbnailsConfiguration(double zoomLevel)
- {
- this.zoomLevel = zoomLevel;
- }
-
- @Override
- public ThumbnailsStorageFormat getThumbnailsStorageFormat(SimpleImageDataConfig config)
- {
- ThumbnailsStorageFormat thumbnailsStorageFormat = super.getThumbnailsStorageFormat(config);
- thumbnailsStorageFormat.setZoomLevel(zoomLevel);
- return thumbnailsStorageFormat;
- }
- @Override
- protected String getDefaultFileName()
+ private ZoomLevelBasedThumbnailsConfiguration(double zoomLevel)
{
- return String.format("thumbnails_%.0fpct%s.h5ar", zoomLevel * 100.0,
- getFirstTransformationCode());
+ super(zoomLevel);
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/AutoRescaleIntensityImageTransformerFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/AutoRescaleIntensityImageTransformerFactory.java
index fa5b8cba044597275159b834df3a795b879e4077..831d4c40b7cebeb340c116a593cd989d11c8b1c6 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/AutoRescaleIntensityImageTransformerFactory.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/AutoRescaleIntensityImageTransformerFactory.java
@@ -16,54 +16,22 @@
package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.transformations;
-import java.awt.image.BufferedImage;
-
-
-import ch.systemsx.cisd.base.image.IImageTransformer;
-import ch.systemsx.cisd.base.image.IImageTransformerFactory;
-import ch.systemsx.cisd.base.annotation.JsonObject;
-import ch.systemsx.cisd.common.image.IntensityRescaling;
-import ch.systemsx.cisd.common.image.IntensityRescaling.Levels;
-
/**
- * Transformation performed by
- * {@link IntensityRescaling#rescaleIntensityLevelTo8Bits(BufferedImage, Levels)} where levels are
- * computed automatically by {@link IntensityRescaling#computeLevels(BufferedImage, float)}.
- * <p>
- * Warning: The serialized version of this class can be stored in the database for each image.
- * Moving this class to a different package or changing it in a backward incompatible way would make
- * all the saved transformations invalid.
+ * This class is obsolete, and should not be used. Use
+ * {@link ch.systemsx.cisd.openbis.dss.etl.dto.api.transformations.AutoRescaleIntensityImageTransformerFactory}
+ * instead
*
- * @author Tomasz Pylak
+ * @author Jakub Straszewski
*/
-@JsonObject("AutoRescaleIntensityImageTransformerFactory")
-public class AutoRescaleIntensityImageTransformerFactory implements IImageTransformerFactory
+public class AutoRescaleIntensityImageTransformerFactory
+ extends
+ ch.systemsx.cisd.openbis.dss.etl.dto.api.transformations.AutoRescaleIntensityImageTransformerFactory
{
private static final long serialVersionUID = 1L;
- private final float threshold;
-
public AutoRescaleIntensityImageTransformerFactory(float threshold)
{
- this.threshold = threshold;
- }
-
- @Override
- public IImageTransformer createTransformer()
- {
- return new IImageTransformer()
- {
- @Override
- public BufferedImage transform(BufferedImage image)
- {
- if (IntensityRescaling.isNotGrayscale(image))
- {
- return image;
- }
- Levels levels = IntensityRescaling.computeLevels(image, threshold);
- return IntensityRescaling.rescaleIntensityLevelTo8Bits(image, levels);
- }
- };
+ super(threshold);
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/ConvertToolImageTransformer.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/ConvertToolImageTransformer.java
index fd2eeac9d7f87488e9623a7bd30c81e721e7976b..5c046ca8dd022e75ef8ea60f0225420725dd51b7 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/ConvertToolImageTransformer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/ConvertToolImageTransformer.java
@@ -16,254 +16,22 @@
package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.transformations;
-import java.awt.image.BufferedImage;
-import java.io.BufferedReader;
-import java.io.ByteArrayInputStream;
-import java.io.ByteArrayOutputStream;
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.OutputStream;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-import java.util.concurrent.atomic.AtomicBoolean;
-
-import org.apache.log4j.Logger;
-
-import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
-import ch.systemsx.cisd.base.image.IStreamingImageTransformer;
-import ch.systemsx.cisd.base.utilities.OSUtilities;
-import ch.systemsx.cisd.common.concurrent.ConcurrencyUtilities;
-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.process.IProcessIOHandler;
-import ch.systemsx.cisd.common.process.ProcessExecutionHelper;
-import ch.systemsx.cisd.common.process.ProcessIOStrategy;
-import ch.systemsx.cisd.common.process.ProcessResult;
-import ch.systemsx.cisd.imagereaders.IImageReader;
-import ch.systemsx.cisd.imagereaders.ImageID;
-import ch.systemsx.cisd.imagereaders.ImageReaderConstants;
-import ch.systemsx.cisd.imagereaders.ImageReaderFactory;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.transformations.ConvertToolImageTransformerFactory.ToolChoice;
-import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.transformations.ConvertToolImageTransformerFactory.ToolChoice;
/**
- * An {@link IStreamingImageTransformer} using the convert command line tool for transformations.
+ * This class is obsolete, and should not be used. Use
+ * {@link ch.systemsx.cisd.openbis.dss.etl.dto.api.transformations.ConvertToolImageTransformer}
+ * instead
*
- * @author Kaloyan Enimanev
+ * @author Jakub Straszewski
*/
-public class ConvertToolImageTransformer implements IStreamingImageTransformer
+public class ConvertToolImageTransformer extends
+ ch.systemsx.cisd.openbis.dss.etl.dto.api.transformations.ConvertToolImageTransformer
{
- private static final String PNG = "png";
-
- private static final File imageMagickConvertUtilityOrNull;
-
- private static final File graphicsMagickUtilityOrNull;
-
- static
- {
- imageMagickConvertUtilityOrNull = OSUtilities.findExecutable("convert");
- graphicsMagickUtilityOrNull = OSUtilities.findExecutable("gm");
- if (imageMagickConvertUtilityOrNull == null && graphicsMagickUtilityOrNull == null)
- {
- throw new ConfigurationFailureException(
- "Neither ImageMagick 'convert' nor GraphisMagick 'gm' can be found"
- + " on the system path. Requested image transformation is not available.");
- }
- }
-
- private static final Logger machineLog = LogFactory.getLogger(LogCategory.MACHINE,
- ConvertToolImageTransformer.class);
-
- private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
- ConvertToolImageTransformer.class);
-
- private final byte[] buffer = new byte[ProcessExecutionHelper.RECOMMENDED_BUFFER_SIZE];
-
- private final List<String> convertCliArguments;
-
- private final boolean useGraphicsMagic;
-
ConvertToolImageTransformer(String arguments, ToolChoice choiceOrNull)
{
- this.convertCliArguments = parseCommandArguments(arguments);
- ToolChoice choice = (choiceOrNull == null ? ToolChoice.ENFORCE_IMAGEMAGICK : choiceOrNull);
- switch (choice)
- {
- case ENFORCE_IMAGEMAGICK:
- if (imageMagickConvertUtilityOrNull == null)
- {
- throw new ConfigurationFailureException(
- "The ImageMagick 'convert' tool cannot be found on the system path."
- + " Requested image transformation is not available.");
- }
- useGraphicsMagic = false;
- break;
- case ENFORCE_GRAPHICSMAGICK:
- if (graphicsMagickUtilityOrNull == null)
- {
- throw new ConfigurationFailureException(
- "The GraphicsMagic 'gm' tool cannot be found on the system path."
- + " Requested image transformation is not available.");
- }
- useGraphicsMagic = true;
- break;
- case PREFER_IMAGEMAGICK:
- useGraphicsMagic = (imageMagickConvertUtilityOrNull == null);
- break;
- case PREFER_GRAPHICSMAGICK:
- useGraphicsMagic = (graphicsMagickUtilityOrNull != null);
- break;
- default:
- throw new Error("Unknown ToolChoice " + choice + ".");
- }
- }
-
- @Override
- public BufferedImage transform(BufferedImage image)
- {
- try
- {
- byte[] input = ImageUtil.imageToPngFast(image);
- byte[] output = transform(input);
- return toBufferedImage(output);
- } catch (IOException ioex)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(ioex);
- }
- }
-
- @Override
- public BufferedImage transform(InputStream input)
- {
- return toBufferedImage(transformToPNG(input));
- }
-
- @Override
- public byte[] transformToPNG(InputStream input)
- {
- final ByteArrayOutputStream bos = new ByteArrayOutputStream();
- transformToPNGStream(input, bos);
- return bos.toByteArray();
- }
-
- @Override
- public void transformToPNGStream(InputStream input, OutputStream output)
- {
- try
- {
- transform(input, output);
- } catch (IOException ioex)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(ioex);
- }
- }
-
- private BufferedImage toBufferedImage(byte[] output) throws ConfigurationFailureException
- {
- IImageReader imageReader =
- ImageReaderFactory.tryGetReader(ImageReaderConstants.IMAGEIO_LIBRARY, PNG);
- if (imageReader == null)
- {
- throw new ConfigurationFailureException("No ImageIO image readers available");
- }
- return imageReader.readImage(output, ImageID.NULL, null);
- }
-
- private byte[] transform(final byte[] input) throws IOException
- {
- final ByteArrayInputStream bis = new ByteArrayInputStream(input);
- final ByteArrayOutputStream bos = new ByteArrayOutputStream();
- transform(bis, bos);
- return bos.toByteArray();
- }
-
- private void transform(final InputStream input, final OutputStream output) throws IOException
- {
-
- final List<String> errorLines = new ArrayList<String>();
- ProcessIOStrategy customIOStrategy =
- createCustomProcessIOStrategy(input, output, errorLines);
-
- ProcessResult result =
- ProcessExecutionHelper.run(getCommandLine(), operationLog, machineLog,
- ConcurrencyUtilities.NO_TIMEOUT, customIOStrategy, false);
-
- if (result.isOK() == false)
- {
- final String msg =
- String.format(
- "Error calling '%s'. Exit value: %d, I/O status: %s\nError output: %s",
- getCommandLine().toString(), result.getExitValue(), result
- .getProcessIOResult().getStatus(), errorLines.toString());
- operationLog.warn(msg);
- throw new IOException(msg);
- }
- }
-
- private ProcessIOStrategy createCustomProcessIOStrategy(final InputStream input,
- final OutputStream output, final List<String> errorLines)
- {
- return ProcessIOStrategy.createCustom(new IProcessIOHandler()
- {
-
- @Override
- public void handle(AtomicBoolean processRunning, OutputStream stdin,
- InputStream stdout, InputStream stderr) throws IOException
- {
- int n = 0;
- final BufferedReader stdErrReader =
- new BufferedReader(new InputStreamReader(stderr));
- while (processRunning.get() && (-1 != (n = input.read(buffer))))
- {
- stdin.write(buffer, 0, n);
- ProcessExecutionHelper.readBytesIfAvailable(stdout, output, buffer, -1,
- false);
- ProcessExecutionHelper.readTextIfAvailable(stdErrReader, errorLines, false);
- }
- stdin.flush();
- stdin.close();
-
- while (processRunning.get())
- {
- ProcessExecutionHelper.readBytesIfAvailable(stdout, output, buffer, -1,
- false);
- ProcessExecutionHelper.readTextIfAvailable(stdErrReader, errorLines, false);
- }
-
- ProcessExecutionHelper.readBytesIfAvailable(stdout, output, buffer, -1, false);
- ProcessExecutionHelper.readTextIfAvailable(stdErrReader, errorLines, false);
- }
- });
- }
-
- private List<String> parseCommandArguments(String argsString)
- {
- String[] arguments = argsString.trim().split("\\s");
- return Arrays.asList(arguments);
- }
-
- private List<String> getCommandLine()
- {
- ArrayList<String> result = new ArrayList<String>();
- if (useGraphicsMagic)
- {
- result.add(graphicsMagickUtilityOrNull.getPath());
- result.add("convert");
- } else
- {
- result.add(imageMagickConvertUtilityOrNull.getPath());
- }
- result.addAll(convertCliArguments);
- // use standard input to read image
- result.add("-");
- // use standard output to produce result
- result.add("png:-");
- return result;
+ super(arguments, choiceOrNull);
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/ConvertToolImageTransformerFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/ConvertToolImageTransformerFactory.java
index 99377947d6d0dafe04b4c710c8e3d103b267c158..9b63be17052c007b657a1eff51fca562cdd38e00 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/ConvertToolImageTransformerFactory.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/ConvertToolImageTransformerFactory.java
@@ -16,53 +16,26 @@
package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.transformations;
-import ch.systemsx.cisd.base.image.IStreamingImageTransformerFactory;
-
/**
- * A {@link IStreamingImageTransformerFactory} that constructs {@link ConvertToolImageTransformer}
- * instances.
- * <p>
- * Warning: The serialized version of this class can be stored in the database for each image.
- * Moving this class to a different package or changing it in a backward incompatible way would make
- * all the saved transformations invalid.
+ * This class is obsolete, and should not be used. Use
+ * {@link ch.systemsx.cisd.openbis.dss.etl.dto.api.transformations.ConvertToolImageTransformerFactory}
+ * instead
*
- * @author Kaloyan Enimanev
+ * @author Jakub Straszewski
*/
-public class ConvertToolImageTransformerFactory implements IStreamingImageTransformerFactory
+public class ConvertToolImageTransformerFactory extends
+ ch.systemsx.cisd.openbis.dss.etl.dto.api.transformations.ConvertToolImageTransformerFactory
{
- private static final long serialVersionUID = 1L;
-
- private final String convertCliArguments;
- private final ToolChoice choice;
-
- /**
- * An enum to choose which of the two tools, ImageMagick or GraphicsMagick, to prefer or to
- * enforce.
- */
- public enum ToolChoice
- {
- ENFORCE_IMAGEMAGICK, ENFORCE_GRAPHICSMAGICK, PREFER_IMAGEMAGICK, PREFER_GRAPHICSMAGICK
- }
+ private static final long serialVersionUID = 1L;
- /**
- * Constructs the factory with {@link ToolChoice#PREFER_IMAGEMAGICK}.
- */
public ConvertToolImageTransformerFactory(String convertCliArguments)
{
- this(convertCliArguments, ToolChoice.ENFORCE_IMAGEMAGICK);
+ super(convertCliArguments);
}
public ConvertToolImageTransformerFactory(String convertCliArguments, ToolChoice choice)
{
- this.convertCliArguments = convertCliArguments;
- this.choice = choice;
+ super(convertCliArguments, choice);
}
-
- @Override
- public ConvertToolImageTransformer createTransformer()
- {
- return new ConvertToolImageTransformer(convertCliArguments, choice);
- }
-
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/ImageTransformation.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/ImageTransformation.java
index 6c67458d0e8c110a62ea232439eb1b3d9ec1559e..c997281bd2c056528104aeffd41ec441fc974dba 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/ImageTransformation.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/ImageTransformation.java
@@ -16,124 +16,24 @@
package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.transformations;
-import java.io.Serializable;
-
import ch.systemsx.cisd.base.image.IImageTransformerFactory;
-import ch.systemsx.cisd.openbis.generic.shared.basic.CodeNormalizer;
/**
- * Describes image transformation, contains user friendly label and description.
+ * This class is obsolete, and should not be used. Use
+ * {@link ch.systemsx.cisd.openbis.dss.etl.dto.api.transformations.ImageTransformation} instead
*
- * @author Tomasz Pylak
+ * @author Jakub Straszewski
*/
-public class ImageTransformation implements Serializable
+public class ImageTransformation extends
+ ch.systemsx.cisd.openbis.dss.etl.dto.api.transformations.ImageTransformation
{
-
- private static final long serialVersionUID = 1L;
-
- private String code;
-
- private String label;
-
- // can be null
- private String description;
-
- private boolean isDefault;
- private final IImageTransformerFactory imageTransformerFactory;
-
- private final boolean isEditable;
+ private static final long serialVersionUID = 1L;
public ImageTransformation(String code, String label, String description,
IImageTransformerFactory imageTransformerFactory)
{
- assert code != null : "code is null";
- assert label != null : " label is null";
- assert imageTransformerFactory != null : "imageTransformerFactory is null";
-
- this.code = CodeNormalizer.normalize(code);
- this.label = label;
- this.description = description;
- this.isDefault = false;
- this.imageTransformerFactory = imageTransformerFactory;
- this.isEditable = false; // will be used later for ImageViewer transformations
- }
-
- public String getCode()
- {
- return code;
- }
-
- public String getLabel()
- {
- return label;
- }
-
- public String getDescription()
- {
- return description;
- }
-
- public boolean isDefault()
- {
- return isDefault;
+ super(code, label, description, imageTransformerFactory);
}
- public IImageTransformerFactory getImageTransformerFactory()
- {
- return imageTransformerFactory;
- }
-
- public boolean isEditable()
- {
- return isEditable;
- }
-
- // ----------- setters
-
- public void setCode(String code)
- {
- this.code = code;
- }
-
- public void setLabel(String label)
- {
- this.label = label;
- }
-
- public void setDescription(String description)
- {
- this.description = description;
- }
-
- /**
- * Calling with true makes this transformation a default user's choice and makes the
- * 'hard-coded' default unavailable. This transformation will become the first one on the list
- * automatically.
- * <p>
- * Marking more then one transformation as a default for one channel will make it impossible to
- * register a dataset.
- * </p>
- * <p>
- * If no transformation on the list will be marked as default then a 'hard-coded' default
- * transformation will become available.
- * </p>
- */
- public void setDefault(boolean isDefault)
- {
- this.isDefault = isDefault;
- }
-
- @Override
- public String toString()
- {
- StringBuffer sb = new StringBuffer();
- sb.append("ImageTransformation [code=" + code + ", label=" + label);
- if (description != null)
- {
- sb.append(", description=" + description);
- }
- sb.append(", isDefault=" + isDefault + "]");
- return sb.toString();
- }
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/ImageTransformationBuffer.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/ImageTransformationBuffer.java
index 3d4ff923983d1d297e08c7b3d388c776b9d8e83a..5cac3799a3a327913bbfca91189a99fe3bfaa1d8 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/ImageTransformationBuffer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/ImageTransformationBuffer.java
@@ -16,450 +16,14 @@
package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.transformations;
-import java.text.DecimalFormat;
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import ch.rinn.restrictions.Private;
-import ch.systemsx.cisd.base.image.IImageTransformerFactory;
-import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
-import ch.systemsx.cisd.common.shared.basic.string.StringUtils;
-
/**
- * Utility class to construct various kinds of image transformations.
+ * This class is obsolete, and should not be used. Use
+ * {@link ch.systemsx.cisd.openbis.dss.etl.dto.api.transformations.ImageTransformationBuffer}
+ * instead
*
- * @author Tomasz Pylak
+ * @author Jakub Straszewski
*/
-public class ImageTransformationBuffer
+public class ImageTransformationBuffer extends
+ ch.systemsx.cisd.openbis.dss.etl.dto.api.transformations.ImageTransformationBuffer
{
- private static final String PREDEFINED_TRANSFORMATIONS_CODE_PREFIX = "_";
-
- private final List<ImageTransformation> imageTransformations;
-
- public ImageTransformationBuffer()
- {
- this.imageTransformations = new ArrayList<ImageTransformation>();
- }
-
- /**
- * Appends a single transformation and returns it. Note that code of each added transformation
- * should be unique.
- */
- public ImageTransformation append(ImageTransformation transformation)
- {
- appendAll(transformation);
- return transformation;
- }
-
- /**
- * Appends any specified transformations. Note that code of each added transformation should be
- * unique.
- */
- public void appendAll(ImageTransformation... transformations)
- {
- for (ImageTransformation transformation : transformations)
- {
- imageTransformations.add(transformation);
- }
- ensureTransformationCodesUnique();
- }
-
- // returns a set of used transformation codes
- private Set<String> ensureTransformationCodesUnique()
- {
- Set<String> usedTransformationCodes = new HashSet<String>();
- for (ImageTransformation transformation : imageTransformations)
- {
- String code = transformation.getCode();
- if (usedTransformationCodes.contains(code))
- {
- throw new IllegalArgumentException("Two transformations have the same code: "
- + code);
- }
- usedTransformationCodes.add(code);
- }
- return usedTransformationCodes;
- }
-
- private void ensureOnlyOneDefault()
- {
- ImageTransformation defaultTansf = null;
- for (ImageTransformation transformation : imageTransformations)
- {
- if (transformation.isDefault())
- {
- if (defaultTansf == null)
- {
- defaultTansf = transformation;
- } else
- {
- throw ConfigurationFailureException.fromTemplate(
- "Only one image transformation can be default, but two were found: '%s' and "
- + "'%s'.", defaultTansf.getLabel(), transformation.getLabel());
- }
- }
- }
- }
-
- /** @returns all appended transformations */
- public ImageTransformation[] getTransformations()
- {
- // codes of transformations could be changed after they have been added
- ensureTransformationCodesUnique();
- ensureOnlyOneDefault();
- return imageTransformations.toArray(new ImageTransformation[imageTransformations.size()]);
- }
-
- // -------------- bit shifting transformations ---------------------
-
- /**
- * Appends transformations which extracts a range of grayscale image colors by choosing 8
- * consecutive bits. All shifts which make sense for 12 bit images will be appended (from 0 to
- * 4).
- *
- * @return appended transformations. They can be used to e.g. modify their label or description.
- */
- public ImageTransformation[] appendAllBitShiftsFor12BitGrayscale()
- {
- return appendAllAvailableGrayscaleBitShifts(12);
- }
-
- /**
- * Appends transformations which extracts a range of grayscale image colors by choosing 8
- * consecutive bits. All shifts which make sense for 16 bit images will be appended (from 0 to
- * 8).
- *
- * @return appended transformations. They can be used to e.g. modify their label or description.
- */
- public ImageTransformation[] appendAllBitShiftsFor16BitGrayscale()
- {
- return appendAllAvailableGrayscaleBitShifts(16);
- }
-
- private ImageTransformation[] appendAllAvailableGrayscaleBitShifts(int totalNumberOfBits)
- {
- int transformationsNumber = totalNumberOfBits - 8 + 1;
- ImageTransformation[] transformations = new ImageTransformation[transformationsNumber];
- for (int i = 0; i < transformationsNumber; i++)
- {
- transformations[i] = appendGrayscaleBitShifting(i);
- }
- return transformations;
- }
-
- /**
- * Appends transformation which extracts a range of grayscale image colors by choosing 8
- * consecutive bits starting from the specified one.
- *
- * @return appended transformation. It can be used to e.g. modify its label or description.
- */
- public ImageTransformation appendGrayscaleBitShifting(int shiftBits)
- {
- return append(createGrayscaleBitShifting(shiftBits));
- }
-
- /**
- * Creates a transformation which extracts a range of grayscale image colors by choosing 8
- * consecutive bits, staring from the specified one.
- * <p>
- * This method is useful when one wants to modify the default code, label or description
- * afterwards.
- */
- private static ImageTransformation createGrayscaleBitShifting(int shiftBits)
- {
- if (shiftBits < 0)
- {
- throw new IllegalArgumentException(
- "Cannot create an image transformation which shifts by a negative number of bits");
- }
- String label = createBitShiftingTransformationLabel(shiftBits);
- String code = createBitShiftingTransformationCode(shiftBits);
- String description = createBitShiftingTransformationDescription(shiftBits);
-
- IImageTransformerFactory factory = new BitShiftingImageTransformerFactory(shiftBits);
- return new ImageTransformation(code, label, description, factory);
- }
-
- private static String createBitShiftingTransformationCode(int shiftBits)
- {
- return PREDEFINED_TRANSFORMATIONS_CODE_PREFIX + "BIT_SHIFTING_" + shiftBits;
- }
-
- private static String createBitShiftingTransformationDescription(int shiftBits)
- {
- return String.format(
- "Shows a range of grayscale image colors by visualising only 8 consecutive bits from %d to %d. "
- + "Useful for extracting information from 12 and 16 bit images.",
- shiftBits, shiftBits + 7);
- }
-
- private static String createBitShiftingTransformationLabel(int shiftBits)
- {
- return String.format("Show bits %d-%d", shiftBits, shiftBits + 7);
- }
-
- // -----------------------------
-
- /**
- * Appends transformation which converts grayscale image pixel intensities from the range
- * [blackPointIntensity, whitePointIntensity] to 8 bit color depth. Useful to compare images of
- * higher color depth with each other when they do not use the whole range of available
- * intensities.
- *
- * @return appended transformation. It can be used to e.g. modify its label or description.
- */
- public ImageTransformation appendRescaleGrayscaleIntensity(int blackPointIntensity,
- int whitePointIntensity)
- {
- return appendRescaleGrayscaleIntensity(blackPointIntensity, whitePointIntensity, null);
- }
-
- /**
- * See {@link #appendRescaleGrayscaleIntensity(int, int)}.
- * <p>
- * Additionally sets the label of the transformation.
- *
- * @return appended transformation. It can be used to e.g. modify its label or description.
- */
- public ImageTransformation appendRescaleGrayscaleIntensity(int blackPointIntensity,
- int whitePointIntensity, String userFriendlyLabelOrNull)
- {
- return append(createRescaleGrayscaleIntensity(blackPointIntensity, whitePointIntensity,
- userFriendlyLabelOrNull));
- }
-
- /**
- * Creates a transformation which converts grayscale image pixel intensities from the range
- * [blackPointIntensity, whitePointIntensity] to 8 bit color depth.
- * <p>
- * This method is useful when one wants to modify the default code, label or description
- * afterwards.
- *
- * @param userFriendlyLabelOrNull label of the transformation. If null a default label is
- * assigned.
- */
- public static ImageTransformation createRescaleGrayscaleIntensity(int blackPointIntensity,
- int whitePointIntensity, String userFriendlyLabelOrNull)
- {
- if (blackPointIntensity > whitePointIntensity || blackPointIntensity < 0
- || whitePointIntensity < 0)
- {
- throw new IllegalArgumentException(String.format(
- "Cannot create an image transformation because the range "
- + "of intensities is invalid: [%d, %d]", blackPointIntensity,
- whitePointIntensity));
- }
- String label = createIntensityRangeTransformationLabel(userFriendlyLabelOrNull);
- String code =
- createIntensityRangeTransformationCode(blackPointIntensity, whitePointIntensity);
- String description =
- createIntensityRangeTransformationDescription(blackPointIntensity,
- whitePointIntensity);
-
- IImageTransformerFactory factory =
- new IntensityRangeImageTransformerFactory(blackPointIntensity, whitePointIntensity);
- return new ImageTransformation(code, label, description, factory);
- }
-
- private static String createIntensityRangeTransformationCode(int blackPointIntensity,
- int whitePointIntensity)
- {
- return PREDEFINED_TRANSFORMATIONS_CODE_PREFIX + "INTENSITY_LEVEL_" + blackPointIntensity
- + "_" + whitePointIntensity;
- }
-
- private static String createIntensityRangeTransformationDescription(int blackPointIntensity,
- int whitePointIntensity)
- {
- return String
- .format("Transforms grayscale image by converting intensities of its pixels "
- + "which are in the range [%d, %d] to 8 bit color depth. "
- + "The range of intensities is usually calculated by processing a series of 12 or 16 bit images, "
- + "then the transformation becomes useful to compare these images with each other in 8 bit color depth, "
- + "especially when they use only a small part of available intensities range.",
- blackPointIntensity, whitePointIntensity);
- }
-
- private static String createIntensityRangeTransformationLabel(String labelOrNull)
- {
- return labelOrNull != null ? labelOrNull : "Fixed rescaling";
- }
-
- // --------------------------
-
- /**
- * Appends transformation which converts each single grayscale image to 8 bit color depth and
- * rescales pixels intensities so that the darkest pixel will become black and the brightest
- * will become white.
- * <p>
- * Note that by default openBIS applies this transformation with threshold 0 if it deals with
- * grayscale image where color depth is bigger then 8 bit. So calling this method with parameter
- * 0 is not necessary.
- * </p>
- *
- * @param threshold value form 0 to 1, it specifies the percentage of darkest and brightest
- * pixels which will be ignored (they will all become black or white).
- * @return appended transformation. It can be used to e.g. modify its label or description.
- */
- public ImageTransformation appendAutoRescaleGrayscaleIntensity(float threshold)
- {
- return appendAutoRescaleGrayscaleIntensity(threshold, null);
- }
-
- /**
- * See {@link #appendAutoRescaleGrayscaleIntensity(float)}.
- * <p>
- * Additionally sets the label of the transformation.
- *
- * @return appended transformation. It can be used to e.g. modify its label or description.
- */
- public ImageTransformation appendAutoRescaleGrayscaleIntensity(float threshold,
- String userFriendlyLabelOrNull)
- {
- return append(createAutoRescaleGrayscaleIntensity(threshold, userFriendlyLabelOrNull));
- }
-
- /**
- * Creates a transformation which converts each single grayscale image to 8 bit color depth and
- * rescales pixels intensities so that the darkest pixel will become black and the brightest
- * will become white (with some threshold margin).
- * <p>
- * This method is useful when one wants to modify the default code, label or description
- * afterwards.
- *
- * @param threshold value form 0 to 1, it specifies the percentage of darkest and brightest
- * pixels which will be ignored (they will all become black or white).
- * @param userFriendlyLabelOrNull label of the transformation. If null a default label is
- * assigned.
- */
- private static ImageTransformation createAutoRescaleGrayscaleIntensity(float threshold,
- String userFriendlyLabelOrNull)
- {
- if (threshold < 0 || threshold > 1)
- {
- throw new IllegalArgumentException(
- "Invalid value of the threshold, should be between 0 and 1, but is: "
- + threshold);
- }
- String label =
- createAutoRescaleIntensityTransformationLabel(userFriendlyLabelOrNull, threshold);
- String code = createAutoRescaleIntensityTransformationCode(threshold);
- String description = createAutoRescaleIntensityTransformationDescription(threshold);
-
- IImageTransformerFactory factory =
- new AutoRescaleIntensityImageTransformerFactory(threshold);
- return new ImageTransformation(code, label, description, factory);
- }
-
- private static String createAutoRescaleIntensityTransformationCode(float threshold)
- {
- return PREDEFINED_TRANSFORMATIONS_CODE_PREFIX + "AUTO_INTENSITY_LEVEL_" + (threshold * 100);
- }
-
- private static String createAutoRescaleIntensityTransformationDescription(float threshold)
- {
- return String
- .format("Creates a transformation which converts each single grayscale image to 8 bit color depth and "
- + "rescales pixels intensities so that the darkest pixel will become black and the brightest "
- + "will become white (threshold margin: %s).",
- new DecimalFormat("#.###").format(threshold));
- }
-
- @Private
- static String createAutoRescaleIntensityTransformationLabel(String labelOrNull, float threshold)
- {
- String thresholdPercentage = new DecimalFormat("##.#").format(threshold * 100);
- return labelOrNull != null ? labelOrNull : String.format("Optimal (image, %s%% cut)",
- thresholdPercentage);
- }
-
- // --------------------------
-
- /**
- * Allows to transform the images with ImageMagic convert tool (which has to be installed and
- * accessible). Convert will be called with the specified parameters.
- *
- * @return appended transformation. It can be used to e.g. modify its label or description.
- */
- public ImageTransformation appendImageMagicConvert(String convertCliArguments)
- {
- return appendImageMagicConvert(convertCliArguments, null);
- }
-
- /**
- * See {@link #appendImageMagicConvert(String)}.
- * <p>
- * Additionally sets the label of the transformation.
- *
- * @return appended transformation. It can be used to e.g. modify its label or description.
- */
- public ImageTransformation appendImageMagicConvert(String convertCliArguments,
- String userFriendlyLabelOrNull)
- {
- return append(createImageMagicConvert(convertCliArguments,
- generateUniqueConvertTransformationCode(), userFriendlyLabelOrNull));
- }
-
- /**
- * Creates a transformation which converts the images with ImageMagic convert tool.
- * <p>
- * This method is useful when one wants to modify the default code, label or description
- * afterwards.
- *
- * @param userFriendlyLabelOrNull label of the transformation. If null a default label is
- * assigned.
- */
- private static ImageTransformation createImageMagicConvert(String convertCliArguments,
- String transformationCode, String userFriendlyLabelOrNull)
- {
- if (StringUtils.isBlank(convertCliArguments))
- {
- throw new IllegalArgumentException(
- "No argument has been specified for the 'convert' command");
- }
- if (StringUtils.isBlank(transformationCode))
- {
- throw new IllegalArgumentException("Transformation has not been specified");
- }
- String label =
- createImageMagicConvertTransformationLabel(convertCliArguments,
- userFriendlyLabelOrNull);
- String description = createImageMagicConvertTransformationDescription(convertCliArguments);
-
- IImageTransformerFactory factory =
- new ConvertToolImageTransformerFactory(convertCliArguments);
- return new ImageTransformation(transformationCode, label, description, factory);
- }
-
- private static String createImageMagicConvertTransformationDescription(
- String convertCliArguments)
- {
- return String.format("Transforms images with ImageMagic tool by calling: 'convert %s ...'",
- convertCliArguments);
- }
-
- private static String createImageMagicConvertTransformationLabel(String convertCliArguments,
- String labelOrNull)
- {
- return labelOrNull != null ? labelOrNull : String.format("Convert (%s)",
- convertCliArguments);
- }
-
- private String generateUniqueConvertTransformationCode()
- {
- int i = 1;
- Set<String> usedTransformationCodes = ensureTransformationCodesUnique();
- while (usedTransformationCodes.contains(getConvertTransformationCode(i)))
- {
- i++;
- }
- return getConvertTransformationCode(i);
- }
-
- private static String getConvertTransformationCode(int seqNumber)
- {
- return PREDEFINED_TRANSFORMATIONS_CODE_PREFIX + "CONVERT_" + seqNumber;
- }
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/IntensityRangeImageTransformerFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/IntensityRangeImageTransformerFactory.java
index 4c588dd0b97c041f007a3176fd14bdbce02677e3..41567f4d910252106a4df6990b59a2d0cafd8863 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/IntensityRangeImageTransformerFactory.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/IntensityRangeImageTransformerFactory.java
@@ -16,67 +16,22 @@
package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.transformations;
-import java.awt.image.BufferedImage;
-
-
-import ch.systemsx.cisd.base.image.IImageTransformer;
-import ch.systemsx.cisd.base.image.IImageTransformerFactory;
-
-import ch.systemsx.cisd.base.annotation.JsonObject;
-import ch.systemsx.cisd.common.image.IntensityRescaling;
-import ch.systemsx.cisd.common.image.IntensityRescaling.Levels;
-
/**
- * Transformation performed by
- * {@link IntensityRescaling#rescaleIntensityLevelTo8Bits(BufferedImage, Levels)}.
- * <p>
- * Warning: The serialized version of this class can be stored in the database for each image.
- * Moving this class to a different package or changing it in a backward incompatible way would make
- * all the saved transformations invalid.
+ * This class is obsolete, and should not be used. Use
+ * {@link ch.systemsx.cisd.openbis.dss.etl.dto.api.transformations.IntensityRangeImageTransformerFactory}
+ * instead
*
- * @author Tomasz Pylak
+ * @author Jakub Straszewski
*/
-@JsonObject("IntensityRangeImageTransformerFactory")
-public class IntensityRangeImageTransformerFactory implements IImageTransformerFactory
+public class IntensityRangeImageTransformerFactory
+ extends
+ ch.systemsx.cisd.openbis.dss.etl.dto.api.transformations.IntensityRangeImageTransformerFactory
{
private static final long serialVersionUID = 1L;
- private final int blackPointIntensity;
-
- private final int whitePointIntensity;
-
public IntensityRangeImageTransformerFactory(int blackPointIntensity, int whitePointIntensity)
{
- this.blackPointIntensity = blackPointIntensity;
- this.whitePointIntensity = whitePointIntensity;
- }
-
- public int getBlackPointIntensity()
- {
- return blackPointIntensity;
- }
-
- public int getWhitePointIntensity()
- {
- return whitePointIntensity;
- }
-
- @Override
- public IImageTransformer createTransformer()
- {
- return new IImageTransformer()
- {
- @Override
- public BufferedImage transform(BufferedImage image)
- {
- if (IntensityRescaling.isNotGrayscale(image))
- {
- return image;
- }
- Levels levels = new Levels(blackPointIntensity, whitePointIntensity);
- return IntensityRescaling.rescaleIntensityLevelTo8Bits(image, levels);
- }
- };
+ super(blackPointIntensity, whitePointIntensity);
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/utils/DropboxUtils.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/utils/DropboxUtils.java
index 2a2c55d1325008401bd72ab907af9d604bcc26d8..6885a2a6b54a371d073a3f680adcef4d50317b9f 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/utils/DropboxUtils.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/utils/DropboxUtils.java
@@ -16,48 +16,12 @@
package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.utils;
-import java.util.Collection;
-import java.util.Map;
-
-import ch.systemsx.cisd.common.geometry.SpatialPoint;
-import ch.systemsx.cisd.openbis.dss.etl.TileGeometryOracle;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.Location;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.PlateUtils;
-
/**
- * @author Tomasz Pylak
+ * This class is obsolete, and should not be used. Use
+ * {@link ch.systemsx.cisd.openbis.dss.etl.dto.api.utils.DropboxUtils} instead
+ *
+ * @author Jakub Straszewski
*/
-public class DropboxUtils
+public class DropboxUtils extends ch.systemsx.cisd.openbis.dss.etl.dto.api.utils.DropboxUtils
{
- /**
- * Translates a row number into letter code. Thus, 1 -> A, 2 -> B, 26 -> Z, 27 -> AA, 28 -> AB,
- * etc.
- */
- public static String translateRowNumberIntoLetterCode(int rowNumber)
- {
- return PlateUtils.translateRowNumberIntoLetterCode(rowNumber);
- }
-
- /**
- * Figures the tile geometry based on all locations present in the it.
- */
- public static Geometry figureGeometry(Collection<Location> tileLocations)
- {
- return TileGeometryOracle.figureGeometry(tileLocations);
- }
-
- /**
- * Tries to figure out tile locations based on their spatial coordinates.
- * <p>
- * Two spatial points (x1, y1) and (x2, y2) are assumed lie in the same tile when abs(x1-x2) <
- * epsilon and abs(y1-y2) < epsilon.
- *
- * @param epsilon see the javadoc of the method
- */
- public static Map<Integer/* tile number */, Location> tryFigureLocations(
- Map<Integer/* tile number */, SpatialPoint> tileToSpatialPointMap, double epsilon)
- {
- return TileGeometryOracle.tryFigureLocations(tileToSpatialPointMap, epsilon);
- }
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v2/FeatureListDataConfig.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v2/FeatureListDataConfig.java
index 24cefa209aea33c830e958fc40154aa32c2354ef..362eadb658235909f656e0266caf90e0e637b4f9 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v2/FeatureListDataConfig.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v2/FeatureListDataConfig.java
@@ -18,7 +18,7 @@ package ch.systemsx.cisd.openbis.dss.etl.dto.api.v2;
import java.util.Collection;
-import ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSetUpdatable;
+import ch.systemsx.cisd.etlserver.registrator.api.v2.IDataSetUpdatable;
/**
* The builder class for creation of feature lists.
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v2/IFeatureVectorDataSet.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v2/IFeatureVectorDataSet.java
index d042b0639c7ec4ae3c41150a528313782f917c25..d6a72dca6c6f7f9e92d9169afdc85c2e69026471 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v2/IFeatureVectorDataSet.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v2/IFeatureVectorDataSet.java
@@ -16,11 +16,11 @@
package ch.systemsx.cisd.openbis.dss.etl.dto.api.v2;
-import ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSet;
+import ch.systemsx.cisd.etlserver.registrator.api.v2.IDataSet;
/**
* Extension of {@link IDataSet} specific for feature vector data sets.
- *
+ *
* @author Franz-Josef Elmer
*/
public interface IFeatureVectorDataSet extends IDataSet
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v2/IImageDataSet.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v2/IImageDataSet.java
new file mode 100644
index 0000000000000000000000000000000000000000..6cbf0bacff479fa3eab189c3fad27f718e506f07
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v2/IImageDataSet.java
@@ -0,0 +1,60 @@
+/*
+ * 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.dss.etl.dto.api.v2;
+
+import java.util.List;
+
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.etlserver.registrator.api.v2.IDataSet;
+
+/**
+ * Container image dataset which contains original and thumbnail physical datasets.
+ *
+ * @author Tomasz Pylak
+ */
+public interface IImageDataSet extends IDataSet
+{
+ IDataSet getOriginalDataset();
+
+ List<IDataSet> getThumbnailDatasets();
+
+ /** Sets analysis procedure. Makes sense only for segmentation datasets. */
+ void setAnalysisProcedure(String analysisProcedure);
+
+ /**
+ * If this method is called the contained data sets (original data set and thumbnails) will
+ * automatically linked to the sample specified by
+ * {@link IDataSet#setSample(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISampleImmutable)}
+ * . By default there will be no such links.
+ *
+ * @deprecated this method is for backwards compatibility only
+ */
+ @Deprecated
+ void establishSampleLinkForContainedDataSets();
+
+ /**
+ * Utility method to find out the plate geometry by looking for which wells images are
+ * available.
+ *
+ * @return a constant which can be used as a vocabulary term value for $PLATE_GEOMETRY property
+ * of a plate/
+ * @throws UserFailureException if all available geometries in openBIS are too small (there is a
+ * well outside).
+ */
+ String figureGeometry();
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v2/IImagingDataSetRegistrationTransactionV2.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v2/IImagingDataSetRegistrationTransactionV2.java
index ca39a0e38935bf6b35b3f6c5e6465f6bbadb01da..65686d7eaf89a4c19812e26a81798f88c06855ba 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v2/IImagingDataSetRegistrationTransactionV2.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v2/IImagingDataSetRegistrationTransactionV2.java
@@ -18,11 +18,10 @@ package ch.systemsx.cisd.openbis.dss.etl.dto.api.v2;
import java.io.File;
-import ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSet;
+import ch.systemsx.cisd.etlserver.registrator.api.v2.IDataSet;
import ch.systemsx.cisd.etlserver.registrator.api.v2.IDataSetRegistrationTransactionV2;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.SimpleImageDataConfig;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeaturesBuilder;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.IImageDataSet;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.SimpleImageDataConfig;
/**
* Extension of {@link IDataSetRegistrationTransactionV2} for screening.
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v2/IImagingDatasetFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v2/IImagingDatasetFactory.java
new file mode 100644
index 0000000000000000000000000000000000000000..8053996a4c7aceb7801a1347ee000bee39efbe93
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v2/IImagingDatasetFactory.java
@@ -0,0 +1,111 @@
+/*
+ * 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.dss.etl.dto.api.v2;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.Properties;
+
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationDetails;
+import ch.systemsx.cisd.etlserver.registrator.v2.DataSetRegistrationService;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.IFeaturesBuilder;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.SimpleImageDataConfig;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeatureVectorDataSetInformation;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ImageDataSetInformation;
+
+/**
+ * Factory for defining image and feature vector datasets.
+ *
+ * @author Tomasz Pylak
+ */
+public interface IImagingDatasetFactory
+{
+ /**
+ * Creates image dataset details. Used if <br>
+ * 1. more then one dataset is created in one transaction and using
+ * {@link #registerImageDataset} is not sufficient or <br>
+ * 2. {@link SimpleImageDataConfig} is not sufficient to describe the dataset and further
+ * modifications on the dataset detail object are required.
+ */
+ @Deprecated
+ DataSetRegistrationDetails<ImageDataSetInformation> createImageRegistrationDetails(
+ SimpleImageDataConfig imageDataSet, File incomingDatasetFolder);
+
+ /**
+ * A convenience method to register the specified image dataset in a separate transaction.
+ *
+ * @param imageDataSet simple dataset specification
+ */
+ boolean registerImageDataset(SimpleImageDataConfig imageDataSet, File incomingDatasetFolder,
+ DataSetRegistrationService<ImageDataSetInformation> service);
+
+ /**
+ * A convenience method to register the specified image dataset in a separate transaction.
+ *
+ * @param imageDatasetDetails advanced dataset specification
+ */
+ @Deprecated
+ boolean registerImageDataset(
+ DataSetRegistrationDetails<ImageDataSetInformation> imageDatasetDetails,
+ File incomingDatasetFolder, DataSetRegistrationService<ImageDataSetInformation> service);
+
+ /**
+ * Allows to define feature vectors of one image analysis dataset. Used to define a dataset
+ * details with {@link #createFeatureVectorDatasetDetails(IFeaturesBuilder)}.
+ */
+ IFeaturesBuilder createFeaturesBuilder();
+
+ /**
+ * Creates feature vector dataset details by using the specified builder.
+ */
+ DataSetRegistrationDetails<FeatureVectorDataSetInformation> createFeatureVectorDatasetDetails(
+ IFeaturesBuilder featureBuilder);
+
+ /**
+ * Creates feature vector dataset details by parsing the specified CSV file.
+ * <p>
+ * CSV format can be configured with following properties:
+ *
+ * <pre>
+ * # Separator character between headers and row cells.
+ * separator = ,
+ * ignore-comments = true
+ * # Header of the column denoting the row of a well.
+ * well-name-row = row
+ * # Header of the column denoting the column of a well.
+ * well-name-col = col
+ * well-name-col-is-alphanum = true
+ * </pre>
+ *
+ * @throws IOException if file cannot be parsed
+ */
+ DataSetRegistrationDetails<FeatureVectorDataSetInformation> createFeatureVectorDatasetDetails(
+ String csvFilePath, Properties properties) throws IOException;
+
+ /**
+ * Utility method to find out the plate geometry by looking for which wells images are
+ * available.
+ *
+ * @return a constant which can be used as a vocabulary term value for $PLATE_GEOMETRY property
+ * of a plate/
+ * @throws UserFailureException if all available geometries in openBIS are too small (there is a
+ * well outside).
+ */
+ String figureGeometry(DataSetRegistrationDetails<ImageDataSetInformation> registrationDetails);
+
+}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v2/SimpleFeatureVectorDataConfig.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v2/SimpleFeatureVectorDataConfig.java
index 548c2765c753d76014d22e23e40d33a5835a8b6d..4389e9fca7cb52c0dfa9a9dfc5b8524de42b3a46 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v2/SimpleFeatureVectorDataConfig.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v2/SimpleFeatureVectorDataConfig.java
@@ -18,8 +18,8 @@ package ch.systemsx.cisd.openbis.dss.etl.dto.api.v2;
import java.util.Properties;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.IFeaturesBuilder;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeaturesBuilder;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.IFeaturesBuilder;
/**
* Configuration for creating a feature vector data set.
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v2/impl/FeatureVectorContainerDataSet.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v2/impl/FeatureVectorContainerDataSet.java
new file mode 100644
index 0000000000000000000000000000000000000000..3047aa608fef028eb0ed5b30a40cfa5665b83cfa
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v2/impl/FeatureVectorContainerDataSet.java
@@ -0,0 +1,155 @@
+/*
+ * 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.etl.dto.api.v2.impl;
+
+import static ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants.ANALYSIS_PROCEDURE;
+
+import java.io.File;
+
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationDetails;
+import ch.systemsx.cisd.etlserver.registrator.api.v2.IDataSet;
+import ch.systemsx.cisd.etlserver.registrator.api.v2.impl.DataSet;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v2.IFeatureVectorDataSet;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IExperimentImmutable;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISampleImmutable;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
+
+/**
+ * @author jakubs
+ */
+public class FeatureVectorContainerDataSet extends DataSet<DataSetInformation> implements
+ IFeatureVectorDataSet
+{
+
+ /**
+ * @param registrationDetails
+ * @param dataSetFolder
+ * @param service
+ */
+ public FeatureVectorContainerDataSet(
+ DataSetRegistrationDetails<? extends DataSetInformation> registrationDetails,
+ File dataSetFolder, IEncapsulatedOpenBISService service)
+ {
+ super(registrationDetails, dataSetFolder, service);
+ }
+
+ private FeatureVectorDataSet originalDataset;
+
+ public IDataSet getOriginalDataset()
+ {
+ return originalDataset;
+ }
+
+ public void setOriginalDataSet(FeatureVectorDataSet mainDataSet)
+ {
+ this.originalDataset = mainDataSet;
+ }
+
+ @Override
+ public void setAnalysisProcedure(String analysisProcedure)
+ {
+ getRegistrationDetails().getDataSetInformation().getDataSetProperties()
+ .add(new NewProperty(ANALYSIS_PROCEDURE, analysisProcedure));
+ }
+
+ @Override
+ public void setSample(ISampleImmutable sampleOrNull)
+ {
+ super.setSample(sampleOrNull);
+ if (originalDataset != null)
+ {
+ originalDataset.setSample(sampleOrNull);
+ // calling this line assures, that the sample in the contained dataset will not be kept.
+ originalDataset.getRegistrationDetails().getDataSetInformation().setLinkSample(false);
+ }
+ }
+
+ @Override
+ public void setExperiment(IExperimentImmutable experimentOrNull)
+ {
+ super.setExperiment(experimentOrNull);
+ if (originalDataset != null)
+ {
+ originalDataset.setExperiment(experimentOrNull);
+ }
+ }
+
+ @Override
+ public void setPropertyValue(String propertyCode, String propertyValue)
+ {
+ getRegistrationDetails().setPropertyValue(propertyCode, propertyValue);
+ }
+
+ @Override
+ public File getDataSetStagingFolder()
+ {
+ return originalDataset.getDataSetStagingFolder();
+ }
+
+ public static String getContainerAnalysisType(String dataSetTypeCode)
+ {
+ if (!isHCSAnalysisDataSetType(dataSetTypeCode))
+ {
+ throw UserFailureException
+ .fromTemplate(
+ "Feature vector data set type should conform to the HCS_ANALYSIS_* pattern, but was %s",
+ dataSetTypeCode);
+
+ }
+
+ String containerDatasetTypeCode =
+ ScreeningConstants.HCS_ANALYSIS_PREFIX
+ + ScreeningConstants.IMAGE_CONTAINER_DATASET_TYPE_MARKER
+ + dataSetTypeCode
+ .substring(ScreeningConstants.HCS_ANALYSIS_PREFIX.length());
+
+ return containerDatasetTypeCode;
+ }
+
+ private static boolean isHCSAnalysisDataSetType(String mainDatasetTypeCode)
+ {
+ String prefix = ScreeningConstants.HCS_ANALYSIS_PREFIX;
+ if (mainDatasetTypeCode.startsWith(prefix))
+ {
+ if (mainDatasetTypeCode
+ .contains(ScreeningConstants.IMAGE_CONTAINER_DATASET_TYPE_MARKER))
+ {
+ throw UserFailureException
+ .fromTemplate(
+ "The specified analysis dataset type '%s' should not be of container type, but contains '%s' in the type code.",
+ mainDatasetTypeCode,
+ ScreeningConstants.IMAGE_CONTAINER_DATASET_TYPE_MARKER);
+ }
+ return true;
+ } else
+ {
+ return false;
+ }
+ }
+
+ @Override
+ public void setDataSetType(String dataSetTypeCode)
+ {
+ originalDataset.setDataSetType(dataSetTypeCode);
+
+ super.setDataSetType(getContainerAnalysisType(dataSetTypeCode));
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v2/impl/FeatureVectorDataSet.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v2/impl/FeatureVectorDataSet.java
new file mode 100644
index 0000000000000000000000000000000000000000..25d2ccaa59754f8eac1a0361d9c7257cd1098375
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v2/impl/FeatureVectorDataSet.java
@@ -0,0 +1,278 @@
+/*
+ * 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.etl.dto.api.v2.impl;
+
+import java.io.File;
+import java.util.List;
+
+import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationDetails;
+import ch.systemsx.cisd.etlserver.registrator.api.v2.impl.DataSet;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeatureVectorDataSetInformation;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v2.IFeatureVectorDataSet;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IDataSetImmutable;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IExperimentImmutable;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IExternalDataManagementSystemImmutable;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISampleImmutable;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType;
+
+/**
+ * @author Franz-Josef Elmer
+ */
+public class FeatureVectorDataSet extends DataSet<FeatureVectorDataSetInformation> implements
+ IFeatureVectorDataSet
+{
+ private final DataSet<FeatureVectorDataSetInformation> dataSet;
+
+ public FeatureVectorDataSet(DataSet<FeatureVectorDataSetInformation> dataSet,
+ IEncapsulatedOpenBISService service)
+ {
+ super(dataSet.getRegistrationDetails(), dataSet.getDataSetStagingFolder(), service);
+ this.dataSet = dataSet;
+ }
+
+ @Override
+ public void setAnalysisProcedure(String analysisProcedure)
+ {
+ dataSet.getRegistrationDetails().getDataSetInformation()
+ .setAnalysisProcedure(analysisProcedure);
+ }
+
+ @Override
+ public boolean equals(Object obj)
+ {
+ return dataSet.equals(obj);
+ }
+
+ @Override
+ public DataSetRegistrationDetails<? extends FeatureVectorDataSetInformation> getRegistrationDetails()
+ {
+ return dataSet.getRegistrationDetails();
+ }
+
+ @Override
+ public File getDataSetStagingFolder()
+ {
+ return dataSet.getDataSetStagingFolder();
+ }
+
+ @Override
+ public String getDataSetCode()
+ {
+ return dataSet.getDataSetCode();
+ }
+
+ @Override
+ public IExperimentImmutable getExperiment()
+ {
+ return dataSet.getExperiment();
+ }
+
+ @Override
+ public ISampleImmutable getSample()
+ {
+ return dataSet.getSample();
+ }
+
+ @Override
+ public String getFileFormatType()
+ {
+ return dataSet.getFileFormatType();
+ }
+
+ @Override
+ public int getSpeedHint()
+ {
+ return dataSet.getSpeedHint();
+ }
+
+ @Override
+ public String getDataSetType()
+ {
+ return dataSet.getDataSetType();
+ }
+
+ @Override
+ public DataSetType getDataSetTypeWithPropertyTypes()
+ {
+ return dataSet.getDataSetTypeWithPropertyTypes();
+ }
+
+ @Override
+ public String getPropertyValue(String propertyCode)
+ {
+ return dataSet.getPropertyValue(propertyCode);
+ }
+
+ @Override
+ public List<String> getAllPropertyCodes()
+ {
+ return dataSet.getAllPropertyCodes();
+ }
+
+ @Override
+ public List<String> getParentDatasets()
+ {
+ return dataSet.getParentDatasets();
+ }
+
+ @Override
+ public List<String> getContainedDataSetCodes()
+ {
+ return dataSet.getContainedDataSetCodes();
+ }
+
+ @Override
+ public List<IDataSetImmutable> getChildrenDataSets()
+ {
+ return dataSet.getChildrenDataSets();
+ }
+
+ @Override
+ public String getContainerDataSet()
+ {
+ return dataSet.getContainerDataSet();
+ }
+
+ @Override
+ public IExternalDataManagementSystemImmutable getExternalDataManagementSystem()
+ {
+ return dataSet.getExternalDataManagementSystem();
+ }
+
+ @Override
+ public String getExternalCode()
+ {
+ return dataSet.getExternalCode();
+ }
+
+ @Override
+ public int hashCode()
+ {
+ return dataSet.hashCode();
+ }
+
+ @Override
+ public void setExperiment(IExperimentImmutable experiment)
+ {
+ dataSet.setExperiment(experiment);
+ }
+
+ @Override
+ public void setSample(ISampleImmutable sampleOrNull)
+ {
+ dataSet.setSample(sampleOrNull);
+ }
+
+ @Override
+ public void setFileFormatType(String fileFormatTypeCode)
+ {
+ dataSet.setFileFormatType(fileFormatTypeCode);
+ }
+
+ @Override
+ public boolean isMeasuredData()
+ {
+ return dataSet.isMeasuredData();
+ }
+
+ @Override
+ public void setMeasuredData(boolean measuredData)
+ {
+ dataSet.setMeasuredData(measuredData);
+ }
+
+ @Override
+ public void setSpeedHint(int speedHint)
+ {
+ dataSet.setSpeedHint(speedHint);
+ }
+
+ @Override
+ public void setDataSetType(String dataSetTypeCode)
+ {
+ dataSet.setDataSetType(dataSetTypeCode);
+ }
+
+ @Override
+ public void setPropertyValue(String propertyCode, String propertyValue)
+ {
+ dataSet.setPropertyValue(propertyCode, propertyValue);
+ }
+
+ @Override
+ public void setParentDatasets(List<String> parentDatasetCodes)
+ {
+ dataSet.setParentDatasets(parentDatasetCodes);
+ }
+
+ @Override
+ public boolean isContainerDataSet()
+ {
+ return dataSet.isContainerDataSet();
+ }
+
+ @Override
+ public void setContainedDataSetCodes(List<String> containedDataSetCodes)
+ {
+ dataSet.setContainedDataSetCodes(containedDataSetCodes);
+ }
+
+ @Override
+ public boolean isContainedDataSet()
+ {
+ return dataSet.isContainedDataSet();
+ }
+
+ @Override
+ public void setExternalDataManagementSystem(
+ IExternalDataManagementSystemImmutable externalDataManagementSystem)
+ {
+ dataSet.setExternalDataManagementSystem(externalDataManagementSystem);
+ }
+
+ @Override
+ public boolean isLinkDataSet()
+ {
+ return dataSet.isLinkDataSet();
+ }
+
+ @Override
+ public void setExternalCode(String externalCode)
+ {
+ dataSet.setExternalCode(externalCode);
+ }
+
+ @Override
+ public boolean isNoFileDataSet()
+ {
+ return dataSet.isNoFileDataSet();
+ }
+
+ @Override
+ public String toString()
+ {
+ return dataSet.toString();
+ }
+
+ @Override
+ public File tryDataSetContents()
+ {
+ return dataSet.tryDataSetContents();
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v2/impl/ImageContainerDataSet.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v2/impl/ImageContainerDataSet.java
new file mode 100644
index 0000000000000000000000000000000000000000..640b56105908a5da1932250802a5b4742f0f1b17
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v2/impl/ImageContainerDataSet.java
@@ -0,0 +1,141 @@
+/*
+ * 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.dss.etl.dto.api.v2.impl;
+
+import java.io.File;
+import java.util.Collections;
+import java.util.List;
+
+import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationDetails;
+import ch.systemsx.cisd.etlserver.registrator.api.v2.IDataSet;
+import ch.systemsx.cisd.etlserver.registrator.api.v2.impl.DataSet;
+import ch.systemsx.cisd.openbis.dss.etl.PlateGeometryOracle;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ImageDataSetInformation;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v2.IImageDataSet;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IExperimentImmutable;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISampleImmutable;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
+
+/**
+ * Represents an image data set for the registration API.
+ *
+ * @author Tomasz Pylak
+ */
+public class ImageContainerDataSet extends DataSet<DataSetInformation> implements IImageDataSet
+{
+ private DataSet<ImageDataSetInformation> originalDataset;
+
+ private List<IDataSet> thumbnailDatasets = Collections.emptyList();
+
+ private boolean establishSampleLinkForContainedDataSets = false;
+
+ public ImageContainerDataSet(
+ DataSetRegistrationDetails<? extends DataSetInformation> registrationDetails,
+ File dataSetFolder, IEncapsulatedOpenBISService service)
+ {
+ super(registrationDetails, dataSetFolder, service);
+ }
+
+ @Override
+ public void setAnalysisProcedure(String analysisProcedure)
+ {
+ setPropertyValue(ScreeningConstants.ANALYSIS_PROCEDURE, analysisProcedure);
+ }
+
+ @Override
+ public void establishSampleLinkForContainedDataSets()
+ {
+ establishSampleLinkForContainedDataSets = true;
+ }
+
+ public boolean sampleLinkForContainedDataSetsShouldBeEstablished()
+ {
+ return establishSampleLinkForContainedDataSets;
+ }
+
+ @Override
+ public DataSet<ImageDataSetInformation> getOriginalDataset()
+ {
+ return originalDataset;
+ }
+
+ public void setOriginalDataset(DataSet<ImageDataSetInformation> originalDataset)
+ {
+ this.originalDataset = originalDataset;
+ }
+
+ @Override
+ public List<IDataSet> getThumbnailDatasets()
+ {
+ return thumbnailDatasets;
+ }
+
+ public void setThumbnailDatasets(List<IDataSet> thumbnailDatasets)
+ {
+ this.thumbnailDatasets = thumbnailDatasets;
+ }
+
+ @Override
+ public void setSample(ISampleImmutable sampleOrNull)
+ {
+ super.setSample(sampleOrNull);
+ if (originalDataset != null)
+ {
+ originalDataset.setSample(sampleOrNull);
+ originalDataset.getRegistrationDetails().getDataSetInformation()
+ .setLinkSample(establishSampleLinkForContainedDataSets);
+ }
+ for (IDataSet thumbnailDataset : thumbnailDatasets)
+ {
+ thumbnailDataset.setSample(sampleOrNull);
+ if (thumbnailDataset instanceof DataSet)
+ {
+ ((DataSet<?>) thumbnailDataset).getRegistrationDetails().getDataSetInformation()
+ .setLinkSample(establishSampleLinkForContainedDataSets);
+ }
+ }
+ }
+
+ @Override
+ public void setExperiment(IExperimentImmutable experimentOrNull)
+ {
+ super.setExperiment(experimentOrNull);
+ if (originalDataset != null)
+ {
+ originalDataset.setExperiment(experimentOrNull);
+ }
+ for (IDataSet thumbnailDataset : thumbnailDatasets)
+ {
+ thumbnailDataset.setExperiment(experimentOrNull);
+ }
+ }
+
+ @Override
+ public String figureGeometry()
+ {
+ return PlateGeometryOracle.figureGeometry(getImageRegistrationDetails(), service);
+ }
+
+ @SuppressWarnings("unchecked")
+ private DataSetRegistrationDetails<ImageDataSetInformation> getImageRegistrationDetails()
+ {
+ return (DataSetRegistrationDetails<ImageDataSetInformation>) originalDataset
+ .getRegistrationDetails();
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/HCSImageFileExtractor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/HCSImageFileExtractor.java
index 652ca1e0ee7db4112fd202f6c73098a6861bbc0f..0d48ced8df4d9eea846a73e2e37ffc7cdf558c2a 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/HCSImageFileExtractor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/HCSImageFileExtractor.java
@@ -31,7 +31,7 @@ import org.apache.commons.lang.StringUtils;
import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.openbis.dss.etl.AbstractImageFileExtractor;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageFileInfo;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageFileInfo;
import ch.systemsx.cisd.openbis.dss.etl.dynamix.WellLocationMappingUtils.DynamixWellPosition;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/FeatureVectorContainerDataSetRegistrationFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v1/FeatureVectorContainerDataSetRegistrationFactory.java
similarity index 93%
rename from screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/FeatureVectorContainerDataSetRegistrationFactory.java
rename to screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v1/FeatureVectorContainerDataSetRegistrationFactory.java
index f4a239ea7372d57ff3581db2fe0e251841920f15..579cab4043f326eddde309f452474751f31deb5e 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/FeatureVectorContainerDataSetRegistrationFactory.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v1/FeatureVectorContainerDataSetRegistrationFactory.java
@@ -14,13 +14,13 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.etl.jython;
+package ch.systemsx.cisd.openbis.dss.etl.jython.v1;
import java.io.File;
import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationDetails;
import ch.systemsx.cisd.etlserver.registrator.v1.AbstractDataSetRegistrationDetailsFactory;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeatureVectorContainerDataSet;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.impl.FeatureVectorContainerDataSet;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
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/v1/ImagingDataSetRegistrationTransaction.java
similarity index 97%
rename from screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/ImagingDataSetRegistrationTransaction.java
rename to screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v1/ImagingDataSetRegistrationTransaction.java
index 9a2faaae1ba2eda45711b332ddef41223a385833..4f42ec225f200da84a2b8f7ca23315737785eb69 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/v1/ImagingDataSetRegistrationTransaction.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.etl.jython;
+package ch.systemsx.cisd.openbis.dss.etl.jython.v1;
import static ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants.MICROSCOPY_CONTAINER_TYPE_SUBSTRING;
import static ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants.MICROSCOPY_IMAGE_TYPE_SUBSTRING;
@@ -32,36 +32,35 @@ import java.util.Properties;
import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.common.io.FileBasedContentNode;
-import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContent;
import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationDetails;
import ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSet;
import ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSetUpdatable;
import ch.systemsx.cisd.etlserver.registrator.api.v1.impl.DataSet;
import ch.systemsx.cisd.etlserver.registrator.api.v1.impl.DataSetRegistrationTransaction;
-import ch.systemsx.cisd.etlserver.registrator.recovery.AutoRecoverySettings;
import ch.systemsx.cisd.etlserver.registrator.v1.DataSetRegistrationService;
import ch.systemsx.cisd.etlserver.registrator.v1.IDataSetRegistrationDetailsFactory;
+import ch.systemsx.cisd.openbis.common.io.FileBasedContentNode;
+import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContent;
import ch.systemsx.cisd.openbis.dss.Constants;
import ch.systemsx.cisd.openbis.dss.etl.Hdf5ThumbnailGenerator;
import ch.systemsx.cisd.openbis.dss.etl.Utils;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageLibraryInfo;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageFileInfo;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.SimpleImageDataConfig;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ThumbnailsStorageFormat;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeatureDefinition;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeatureVectorContainerDataSet;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeatureVectorDataSet;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeatureVectorDataSetInformation;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeaturesBuilder;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ImageContainerDataSet;
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.impl.ThumbnailsInfo;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.FeatureListDataConfig;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.IImageDataSet;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.IImagingDataSetRegistrationTransaction;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageFileInfo;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.SimpleImageDataConfig;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ThumbnailsStorageFormat;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v2.FeatureListDataConfig;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v2.SimpleFeatureVectorDataConfig;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.SimpleFeatureVectorDataConfig;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.impl.FeatureVectorContainerDataSet;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.impl.FeatureVectorDataSet;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.impl.ImageContainerDataSet;
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;
@@ -73,12 +72,6 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchCl
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchSubCriteria;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
-/**
- *
- *
- * @author jakubs
- */
-
/**
* Imaging-specific transaction. Handles image datasets in a special way, other datasets are
* registered using a standard procedure.
@@ -104,10 +97,10 @@ public class ImagingDataSetRegistrationTransaction extends DataSetRegistrationTr
File workingDirectory, File stagingDirectory,
DataSetRegistrationService<DataSetInformation> registrationService,
IDataSetRegistrationDetailsFactory<DataSetInformation> registrationDetailsFactory,
- String originalDirName, AutoRecoverySettings autoRecoverySettings)
+ String originalDirName)
{
super(rollBackStackParentFolder, workingDirectory, stagingDirectory, registrationService,
- registrationDetailsFactory, autoRecoverySettings);
+ registrationDetailsFactory);
assert registrationDetailsFactory instanceof JythonPlateDatasetFactory : "JythonPlateDatasetFactory expected, but got: "
+ registrationDetailsFactory.getClass().getCanonicalName();
@@ -207,8 +200,8 @@ public class ImagingDataSetRegistrationTransaction extends DataSetRegistrationTr
"Setting of container dataset for feature list data set is obligatory");
}
- if (false == container.getDataSetType()
- .startsWith(ScreeningConstants.HCS_ANALYSIS_ANY_CONTAINER_DATASET_TYPE_PREFIX))
+ if (false == container.getDataSetType().startsWith(
+ ScreeningConstants.HCS_ANALYSIS_ANY_CONTAINER_DATASET_TYPE_PREFIX))
{
throw new UserFailureException(
"Container for feature list must be of HCS_ANALYSIS_CONTAINER.* type");
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonImageContainerDataSetRegistrationFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v1/JythonImageContainerDataSetRegistrationFactory.java
similarity index 93%
rename from screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonImageContainerDataSetRegistrationFactory.java
rename to screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v1/JythonImageContainerDataSetRegistrationFactory.java
index 47b0a25953158f7b41f11cc36845cd2c054abb08..843ce453207c48b97bdcaa517c499f48a4a2d6c7 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonImageContainerDataSetRegistrationFactory.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v1/JythonImageContainerDataSetRegistrationFactory.java
@@ -14,13 +14,13 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.etl.jython;
+package ch.systemsx.cisd.openbis.dss.etl.jython.v1;
import java.io.File;
import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationDetails;
import ch.systemsx.cisd.etlserver.registrator.v1.AbstractDataSetRegistrationDetailsFactory;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ImageContainerDataSet;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.impl.ImageContainerDataSet;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonImageDataSetRegistrationFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v1/JythonImageDataSetRegistrationFactory.java
similarity index 96%
rename from screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonImageDataSetRegistrationFactory.java
rename to screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v1/JythonImageDataSetRegistrationFactory.java
index 5054968787ea0c8a2e0da289b74610b65cfe3ddd..6c688efa466f82498f1ccce89f7e0aa70ef9e38b 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonImageDataSetRegistrationFactory.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v1/JythonImageDataSetRegistrationFactory.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.etl.jython;
+package ch.systemsx.cisd.openbis.dss.etl.jython.v1;
import ch.systemsx.cisd.etlserver.registrator.v1.AbstractDataSetRegistrationDetailsFactory;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ImageDataSetInformation;
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/v1/JythonPlateDataSetHandler.java
similarity index 93%
rename from screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonPlateDataSetHandler.java
rename to screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v1/JythonPlateDataSetHandler.java
index 66f033aa6a7da72eeec680864507b3b0d1bbe5b6..c0a8573482a60995ff58d302c9b2e8e895a03057 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/v1/JythonPlateDataSetHandler.java
@@ -1,4 +1,4 @@
-package ch.systemsx.cisd.openbis.dss.etl.jython;
+package ch.systemsx.cisd.openbis.dss.etl.jython.v1;
import java.io.File;
@@ -8,7 +8,6 @@ import ch.systemsx.cisd.etlserver.ITopLevelDataSetRegistratorDelegate;
import ch.systemsx.cisd.etlserver.TopLevelDataSetRegistratorGlobalState;
import ch.systemsx.cisd.etlserver.registrator.DataSetFile;
import ch.systemsx.cisd.etlserver.registrator.api.v1.impl.DataSetRegistrationTransaction;
-import ch.systemsx.cisd.etlserver.registrator.recovery.AutoRecoverySettings;
import ch.systemsx.cisd.etlserver.registrator.v1.DataSetRegistrationService;
import ch.systemsx.cisd.etlserver.registrator.v1.IDataSetRegistrationDetailsFactory;
import ch.systemsx.cisd.etlserver.registrator.v1.JythonTopLevelDataSetHandler;
@@ -62,7 +61,7 @@ public class JythonPlateDataSetHandler extends JythonTopLevelDataSetHandler<Data
{
return new ImagingDataSetRegistrationTransaction(rollBackStackParentFolder,
workingDirectory, stagingDirectory, this, registrationDetailsFactory,
- originalDirName, AutoRecoverySettings.DO_NOT_USE_AUTO_RECOVERY);
+ originalDirName);
}
};
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonPlateDataSetHandlerUtils.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v1/JythonPlateDataSetHandlerUtils.java
similarity index 96%
rename from screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonPlateDataSetHandlerUtils.java
rename to screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v1/JythonPlateDataSetHandlerUtils.java
index 627f002be3b4e1bcb0896380d7880654633d6762..764153a9f02251af48ec8b54fcc4b3b6c5a240bc 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonPlateDataSetHandlerUtils.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v1/JythonPlateDataSetHandlerUtils.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.etl.jython;
+package ch.systemsx.cisd.openbis.dss.etl.jython.v1;
import java.util.Properties;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonPlateDatasetFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v1/JythonPlateDatasetFactory.java
similarity index 98%
rename from screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonPlateDatasetFactory.java
rename to screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v1/JythonPlateDatasetFactory.java
index 44ec309f1c9052c4421b9d7dcfa7f9a76a0e3e2d..ba0c549122fbe50e6421f12956d4649d76f79ea9 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonPlateDatasetFactory.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v1/JythonPlateDatasetFactory.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.etl.jython;
+package ch.systemsx.cisd.openbis.dss.etl.jython.v1;
import java.io.File;
import java.io.IOException;
@@ -30,13 +30,13 @@ import ch.systemsx.cisd.etlserver.registrator.v1.IDataSetRegistrationDetailsFact
import ch.systemsx.cisd.etlserver.registrator.v1.AbstractOmniscientTopLevelDataSetRegistrator.OmniscientTopLevelDataSetRegistratorState;
import ch.systemsx.cisd.etlserver.registrator.v1.JythonTopLevelDataSetHandler.ProgrammableDropboxObjectFactory;
import ch.systemsx.cisd.openbis.dss.etl.PlateGeometryOracle;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.IFeaturesBuilder;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.SimpleImageDataConfig;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeatureDefinition;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeatureVectorDataSetInformation;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeaturesBuilder;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ImageDataSetInformation;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.IFeaturesBuilder;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.IImagingDatasetFactory;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.SimpleImageDataConfig;
import ch.systemsx.cisd.openbis.dss.etl.featurevector.CsvFeatureVectorParser;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
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/v1/SimpleImageDataSetRegistrator.java
similarity index 96%
rename from screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/SimpleImageDataSetRegistrator.java
rename to screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v1/SimpleImageDataSetRegistrator.java
index 185f28781de8620459747784f51d036fbdcb2fbb..766a48c7533e8a5208bf90c8cae748779d673735 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/v1/SimpleImageDataSetRegistrator.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.etl.jython;
+package ch.systemsx.cisd.openbis.dss.etl.jython.v1;
import java.awt.image.BufferedImage;
import java.io.File;
@@ -48,20 +48,20 @@ import ch.systemsx.cisd.imagereaders.IImageReader;
import ch.systemsx.cisd.imagereaders.ImageID;
import ch.systemsx.cisd.imagereaders.ImageReaderFactory;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageLibraryInfo;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.Channel;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColorComponent;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColorRGB;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageFileInfo;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageIdentifier;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageMetadata;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.IntensityRange;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.Location;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.SimpleImageDataConfig;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.SimpleOverviewImageDataConfig;
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;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.IntensityRange;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.Location;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.SimpleImageDataConfig;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.SimpleOverviewImageDataConfig;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.transformations.ImageTransformation;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.transformations.ImageTransformationBuffer;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.transformations.ImageTransformation;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.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;
@@ -449,9 +449,9 @@ public class SimpleImageDataSetRegistrator
private List<Channel> findChannelsToComputeFixedCommonIntensityRange(List<Channel> channels)
{
- final Map<String, ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.IntensityRange> map =
+ final Map<String, ch.systemsx.cisd.openbis.dss.etl.dto.api.IntensityRange> map =
simpleImageConfig.getFixedIntensityRangeForAllImages();
- final ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.IntensityRange defaultLevelOrNull =
+ final ch.systemsx.cisd.openbis.dss.etl.dto.api.IntensityRange defaultLevelOrNull =
map.get(null);
if (defaultLevelOrNull != null)
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/FeatureVectorContainerDataSetRegistrationFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/FeatureVectorContainerDataSetRegistrationFactory.java
new file mode 100644
index 0000000000000000000000000000000000000000..a70321d7e37bccbdff157e84c6b9603a69a99fa2
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/FeatureVectorContainerDataSetRegistrationFactory.java
@@ -0,0 +1,56 @@
+/*
+ * 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.etl.jython.v2;
+
+import java.io.File;
+
+import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationDetails;
+import ch.systemsx.cisd.etlserver.registrator.v2.AbstractDataSetRegistrationDetailsFactory;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v2.impl.FeatureVectorContainerDataSet;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+
+/**
+ * Factory class that creates FeatureVectorContainerDataSet
+ *
+ * @author jakubs
+ */
+public class FeatureVectorContainerDataSetRegistrationFactory extends
+ AbstractDataSetRegistrationDetailsFactory<DataSetInformation>
+{
+
+ public FeatureVectorContainerDataSetRegistrationFactory(
+ ch.systemsx.cisd.etlserver.registrator.v2.AbstractOmniscientTopLevelDataSetRegistrator.OmniscientTopLevelDataSetRegistratorState registratorState,
+ DataSetInformation userProvidedDataSetInformationOrNull)
+ {
+ super(registratorState, userProvidedDataSetInformationOrNull);
+ }
+
+ @Override
+ public FeatureVectorContainerDataSet createDataSet(
+ DataSetRegistrationDetails<DataSetInformation> registrationDetails, File stagingFile)
+ {
+ IEncapsulatedOpenBISService service = registratorState.getGlobalState().getOpenBisService();
+ return new FeatureVectorContainerDataSet(registrationDetails, stagingFile, service);
+ }
+
+ @Override
+ protected DataSetInformation createDataSetInformation()
+ {
+ return new DataSetInformation();
+ }
+}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/ImagingDataSetRegistrationTransaction.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/ImagingDataSetRegistrationTransaction.java
new file mode 100644
index 0000000000000000000000000000000000000000..f3032202f8e9ebaf20660d22193bd012953a2527
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/ImagingDataSetRegistrationTransaction.java
@@ -0,0 +1,799 @@
+/*
+ * 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.etl.jython.v2;
+
+import static ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants.MICROSCOPY_CONTAINER_TYPE_SUBSTRING;
+import static ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants.MICROSCOPY_IMAGE_TYPE_SUBSTRING;
+
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Properties;
+
+import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationDetails;
+import ch.systemsx.cisd.etlserver.registrator.api.v2.IDataSet;
+import ch.systemsx.cisd.etlserver.registrator.api.v2.IDataSetUpdatable;
+import ch.systemsx.cisd.etlserver.registrator.api.v2.impl.DataSet;
+import ch.systemsx.cisd.etlserver.registrator.api.v2.impl.DataSetRegistrationTransaction;
+import ch.systemsx.cisd.etlserver.registrator.v2.DataSetRegistrationService;
+import ch.systemsx.cisd.etlserver.registrator.v2.IDataSetRegistrationDetailsFactory;
+import ch.systemsx.cisd.openbis.common.io.FileBasedContentNode;
+import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContent;
+import ch.systemsx.cisd.openbis.dss.Constants;
+import ch.systemsx.cisd.openbis.dss.etl.Hdf5ThumbnailGenerator;
+import ch.systemsx.cisd.openbis.dss.etl.Utils;
+import ch.systemsx.cisd.openbis.dss.etl.dto.ImageLibraryInfo;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageFileInfo;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.SimpleImageDataConfig;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ThumbnailsStorageFormat;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeatureDefinition;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeatureVectorDataSetInformation;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeaturesBuilder;
+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.impl.ThumbnailsInfo;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v2.FeatureListDataConfig;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v2.IImageDataSet;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v2.SimpleFeatureVectorDataConfig;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v2.impl.FeatureVectorContainerDataSet;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v2.impl.FeatureVectorDataSet;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v2.impl.ImageContainerDataSet;
+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.v2.IDataSetImmutable;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClause;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClauseAttribute;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchSubCriteria;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
+
+/**
+ * Imaging-specific transaction. Handles image datasets in a special way, other datasets are
+ * registered using a standard procedure.
+ * <p>
+ * Note that this transaction is not parametrized by a concrete {@link DataSetInformation} subclass.
+ * It has to deal with {@link ImageDataSetInformation}, {@link FeatureVectorDataSetInformation} and
+ * {@link DataSetInformation} at the same time.
+ */
+@SuppressWarnings("rawtypes")
+public class ImagingDataSetRegistrationTransaction extends DataSetRegistrationTransaction
+{
+ private final IDataSetRegistrationDetailsFactory<ImageDataSetInformation> imageDatasetFactory;
+
+ private final IDataSetRegistrationDetailsFactory<DataSetInformation> imageContainerDatasetFactory;
+
+ private final String originalDirName;
+
+ private final JythonPlateDatasetFactory factory;
+
+ @SuppressWarnings("unchecked")
+ public ImagingDataSetRegistrationTransaction(File rollBackStackParentFolder,
+ File workingDirectory, File stagingDirectory,
+ DataSetRegistrationService<DataSetInformation> registrationService,
+ IDataSetRegistrationDetailsFactory<DataSetInformation> registrationDetailsFactory,
+ String originalDirName)
+ {
+ super(rollBackStackParentFolder, workingDirectory, stagingDirectory, registrationService,
+ registrationDetailsFactory);
+
+ assert registrationDetailsFactory instanceof JythonPlateDatasetFactory : "JythonPlateDatasetFactory expected, but got: "
+ + registrationDetailsFactory.getClass().getCanonicalName();
+
+ factory = (JythonPlateDatasetFactory) registrationDetailsFactory;
+ this.imageDatasetFactory = factory.imageDatasetFactory;
+ this.imageContainerDatasetFactory = factory.imageContainerDatasetFactory;
+ this.originalDirName = originalDirName;
+ }
+
+ public JythonPlateDatasetFactory getFactory()
+ {
+ return factory;
+ }
+
+ public IImageDataSet createNewImageDataSet(SimpleImageDataConfig imageDataSet,
+ File incomingFolderWithImages)
+ {
+ DataSetRegistrationDetails<ImageDataSetInformation> details =
+ SimpleImageDataSetRegistrator.createImageDatasetDetails(imageDataSet,
+ incomingFolderWithImages, imageDatasetFactory);
+ return createNewImageDataSet(details);
+ }
+
+ public IDataSet createNewOverviewImageDataSet(SimpleImageDataConfig imageDataSet,
+ File incomingFolderWithImages)
+ {
+ DataSetRegistrationDetails<ImageDataSetInformation> details =
+ SimpleImageDataSetRegistrator.createImageDatasetDetails(imageDataSet,
+ incomingFolderWithImages, imageDatasetFactory);
+ return createNewOverviewImageDataSet(details);
+ }
+
+ public IDataSet createNewFeatureListDataSet(FeatureListDataConfig config)
+ {
+ IDataSet dataSet = createNewDataSet();
+
+ dataSet.setDataSetType(ScreeningConstants.ANALYSIS_FEATURE_LIST);
+
+ IDataSetUpdatable container = config.getContainerDataSet();
+
+ verifyFeatureVectorContainer(container);
+
+ addNewDataSetToContainer(dataSet, container);
+
+ dataSet.setExperiment(container.getExperiment());
+
+ storeFeatureListInDataset(config, dataSet);
+
+ return dataSet;
+ }
+
+ private void storeFeatureListInDataset(FeatureListDataConfig config, IDataSet dataSet)
+ {
+ try
+ {
+ File directory =
+ new File(getIncoming().getParentFile().getAbsolutePath(),
+ ScreeningConstants.ANALYSIS_FEATURE_LIST_TOP_LEVEL_DIRECTORY_NAME);
+ directory.mkdirs();
+
+ File file = new File(directory, config.getName());
+ file.createNewFile();
+
+ BufferedWriter bw = new BufferedWriter(new FileWriter(file));
+
+ for (String feature : config.getFeatureList())
+ {
+ bw.append(feature);
+ bw.newLine();
+ }
+
+ bw.close();
+
+ moveFile(directory.getAbsolutePath(), dataSet);
+
+ } catch (IOException ex)
+ {
+ throw CheckedExceptionTunnel.wrapIfNecessary(ex);
+ }
+ }
+
+ private void addNewDataSetToContainer(IDataSet dataSet, IDataSetUpdatable container)
+ {
+ List<String> contained = new LinkedList<String>(container.getContainedDataSetCodes());
+ contained.add(dataSet.getDataSetCode());
+ container.setContainedDataSetCodes(contained);
+ }
+
+ private void verifyFeatureVectorContainer(IDataSetUpdatable container)
+ {
+ if (container == null)
+ {
+ throw new UserFailureException(
+ "Setting of container dataset for feature list data set is obligatory");
+ }
+
+ if (false == container.getDataSetType().startsWith(
+ ScreeningConstants.HCS_ANALYSIS_ANY_CONTAINER_DATASET_TYPE_PREFIX))
+ {
+ throw new UserFailureException(
+ "Container for feature list must be of HCS_ANALYSIS_CONTAINER.* type");
+ }
+ }
+
+ /**
+ * Creates new container dataset which contains one feature vector dataset.
+ */
+ public FeatureVectorContainerDataSet createNewFeatureVectorDataSet(
+ SimpleFeatureVectorDataConfig featureDataSetConfig, File featureVectorFileOrNull)
+ {
+ DataSetRegistrationDetails<FeatureVectorDataSetInformation> registrationDetails =
+ createFeatureVectorDataSetRegistrationDetails(featureDataSetConfig,
+ featureVectorFileOrNull);
+ return createFeatureVectorDataSet(registrationDetails);
+ }
+
+ private FeatureVectorContainerDataSet createFeatureVectorDataSet(
+ DataSetRegistrationDetails<FeatureVectorDataSetInformation> registrationDetails)
+ {
+ @SuppressWarnings("unchecked")
+ DataSet<FeatureVectorDataSetInformation> dataSet =
+ (DataSet<FeatureVectorDataSetInformation>) super
+ .createNewDataSet(registrationDetails);
+
+ FeatureVectorDataSet featureDataset =
+ new FeatureVectorDataSet(dataSet, getGlobalState().getOpenBisService());
+
+ // create container
+ FeatureVectorContainerDataSet containerDataset =
+ createFeatureVectorContainerDataSet(featureDataset);
+
+ registrationDetails.getDataSetInformation().setContainerDatasetPermId(
+ containerDataset.getDataSetCode());
+
+ return containerDataset;
+ }
+
+ private DataSetRegistrationDetails<FeatureVectorDataSetInformation> createFeatureVectorDataSetRegistrationDetails(
+ SimpleFeatureVectorDataConfig featureDataSetConfig, File featureVectorFileOrNull)
+ {
+ List<FeatureDefinition> featureDefinitions;
+ Properties properties = featureDataSetConfig.getProperties();
+ if (properties == null)
+ {
+ featureDefinitions =
+ ((FeaturesBuilder) featureDataSetConfig.getFeaturesBuilder())
+ .getFeatureDefinitionValuesList();
+ } else
+ {
+ try
+ {
+ featureDefinitions =
+ CsvFeatureVectorParser.parse(featureVectorFileOrNull, properties);
+ } catch (IOException ex)
+ {
+ throw CheckedExceptionTunnel.wrapIfNecessary(ex);
+ }
+ }
+ DataSetRegistrationDetails<FeatureVectorDataSetInformation> registrationDetails =
+ factory.createFeatureVectorRegistrationDetails(featureDefinitions);
+ return registrationDetails;
+ }
+
+ /**
+ * Creates container dataset which contains dataset with original images (created on the fly).
+ * If thumbnails are required they are generated and moved to a thumbnail dataset which becomes
+ * a part of the container as well.
+ * <p>
+ * The original images dataset is special - it contains description of what should be saved in
+ * imaging database by the storage processor.
+ *
+ * @return container dataset.
+ */
+ public IImageDataSet createNewImageDataSet(
+ DataSetRegistrationDetails<ImageDataSetInformation> imageRegistrationDetails)
+ {
+ ImageDataSetInformation imageDataSetInformation =
+ imageRegistrationDetails.getDataSetInformation();
+ ImageDataSetStructure imageDataSetStructure =
+ imageDataSetInformation.getImageDataSetStructure();
+ File incomingDirectory = imageDataSetInformation.getIncomingDirectory();
+ List<String> containedDataSetCodes = new ArrayList<String>();
+
+ // Compute the bounding box of the images -- needs to happen before thumbnail
+ // generation, since thumbnails may want to know the bounding box
+ calculateBoundingBox(imageDataSetInformation, imageDataSetStructure, incomingDirectory);
+
+ // create thumbnails dataset if needed
+ List<IDataSet> thumbnailDatasets = new ArrayList<IDataSet>();
+ boolean generateThumbnails = imageDataSetStructure.areThumbnailsGenerated();
+ if (generateThumbnails)
+ {
+ imageDataSetStructure
+ .validateImageRepresentationGenerationParameters(imageDataSetInformation);
+
+ List<ThumbnailsStorageFormat> thumbnailsStorageFormatList =
+ imageDataSetStructure.getImageStorageConfiguraton()
+ .getThumbnailsStorageFormat();
+
+ ThumbnailsInfo thumbnailsInfo = new ThumbnailsInfo();
+ for (ThumbnailsStorageFormat thumbnailsStorageFormat : thumbnailsStorageFormatList)
+ {
+ IDataSet thumbnailDataset =
+ createThumbnailDataset(imageDataSetInformation, thumbnailsStorageFormat);
+ thumbnailDatasets.add(thumbnailDataset);
+
+ generateThumbnails(imageDataSetStructure, incomingDirectory, thumbnailDataset,
+ thumbnailsStorageFormat, thumbnailsInfo, false, null);
+ containedDataSetCodes.add(thumbnailDataset.getDataSetCode());
+ }
+ imageDataSetInformation.setThumbnailsInfo(thumbnailsInfo);
+ }
+
+ // create main dataset (with original images)
+ @SuppressWarnings("unchecked")
+ DataSet<ImageDataSetInformation> mainDataset =
+ (DataSet<ImageDataSetInformation>) super.createNewDataSet(imageRegistrationDetails);
+ containedDataSetCodes.add(mainDataset.getDataSetCode());
+
+ for (IDataSet thumbnailDataset : thumbnailDatasets)
+ {
+ setSameDatasetOwner(mainDataset, thumbnailDataset);
+ }
+ ImageContainerDataSet containerDataset =
+ createImageContainerDataset(mainDataset, imageDataSetInformation,
+ containedDataSetCodes);
+ containerDataset.setOriginalDataset(mainDataset);
+ for (IDataSet thumbnailDataset : thumbnailDatasets)
+ {
+ containerDataset.setThumbnailDatasets(Arrays.asList(thumbnailDataset));
+ }
+ imageDataSetInformation.setContainerDatasetPermId(containerDataset.getDataSetCode());
+
+ return containerDataset;
+ }
+
+ @SuppressWarnings("unchecked")
+ private IDataSet createNewOverviewImageDataSet(
+ DataSetRegistrationDetails<ImageDataSetInformation> imageRegistrationDetails)
+ {
+ ImageDataSetInformation imageDataSetInformation =
+ imageRegistrationDetails.getDataSetInformation();
+ ImageDataSetStructure imageDataSetStructure =
+ imageDataSetInformation.getImageDataSetStructure();
+ File incomingDirectory = imageDataSetInformation.getIncomingDirectory();
+
+ String containerCode = imageDataSetInformation.tryGetContainerDatasetPermId();
+
+ IDataSetUpdatable container = getDataSetForUpdate(containerCode);
+
+ if (container == null || false == container.isContainerDataSet())
+ {
+ throw UserFailureException.fromTemplate("Container data set %s coudn't be found.",
+ container);
+ }
+
+ calculateBoundingBox(imageDataSetInformation, imageDataSetStructure, incomingDirectory);
+
+ SearchCriteria searchCriteria = new SearchCriteria();
+ SearchCriteria searchSubCriteria = new SearchCriteria();
+ searchSubCriteria.addMatchClause(MatchClause.createAttributeMatch(
+ MatchClauseAttribute.CODE, containerCode));
+ searchCriteria.addSubCriteria(SearchSubCriteria
+ .createDataSetContainerCriteria(searchSubCriteria));
+
+ List<IDataSetImmutable> containedDataSets =
+ getSearchService().searchForDataSets(searchCriteria);
+
+ IDataSetImmutable exampleDataSet = containedDataSets.iterator().next();
+
+ imageDataSetStructure
+ .validateImageRepresentationGenerationParameters(imageDataSetInformation);
+
+ ThumbnailsInfo thumbnailsInfo = new ThumbnailsInfo();
+ List<String> containedDataSetCodes = new ArrayList<String>();
+ containedDataSetCodes.addAll(container.getContainedDataSetCodes());
+
+ 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);
+ thumbnailDataset.setFileFormatType(thumbnailsStorageFormat.getFileFormat()
+ .getOpenBISFileType());
+ thumbnailDataset.setMeasuredData(false);
+ 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
+ {
+ 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);
+
+ for (IDataSet thumbnailDataset : thumbnailDatasets)
+ {
+ setSameDatasetOwner(exampleDataSet, thumbnailDataset);
+ }
+
+ container.setContainedDataSetCodes(containedDataSetCodes);
+
+ return thumbnailDatasets.iterator().next();
+ }
+
+ private static ThumbnailsStorageFormat createThumbnailsStorageFormat(
+ ImageDataSetInformation imageDataSetInformation)
+ {
+ ThumbnailsStorageFormat thumbnailsStorageFormat = new ThumbnailsStorageFormat();
+
+ thumbnailsStorageFormat.setFileFormat(imageDataSetInformation.getFileFormatTypeCode());
+ thumbnailsStorageFormat.setThumbnailsFileName(String.format("thumbnails_%dx%d.h5ar",
+ imageDataSetInformation.getMaximumImageWidth(),
+ imageDataSetInformation.getMaximumImageHeight()));
+
+ return thumbnailsStorageFormat;
+ }
+
+ private void calculateBoundingBox(ImageDataSetInformation imageDataSetInformation,
+ ImageDataSetStructure imageDataSetStructure, File incomingDirectory)
+ {
+ ImageLibraryInfo imageLibrary =
+ imageDataSetStructure.getImageStorageConfiguraton().tryGetImageLibrary();
+ List<ImageFileInfo> images = imageDataSetStructure.getImages();
+
+ if (imageDataSetInformation.isGenerateOverviewImagesFromRegisteredImages())
+ {
+ IHierarchicalContent content =
+ ServiceProvider.getHierarchicalContentProvider().asContent(
+ imageDataSetInformation.tryGetContainerDatasetPermId());
+ 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()));
+ }
+ }
+ }
+
+ private File prependOriginalDirectory(String directoryPath)
+ {
+ return new File(originalDirName + File.separator + directoryPath);
+ }
+
+ private void generateThumbnails(ImageDataSetStructure imageDataSetStructure,
+ File incomingDirectory, IDataSet thumbnailDataset,
+ ThumbnailsStorageFormat thumbnailsStorageFormatOrNull, ThumbnailsInfo thumbnailPaths,
+ boolean registerOriginalImageAsThumbnail, IHierarchicalContent content)
+ {
+ String thumbnailFile;
+ if (thumbnailsStorageFormatOrNull == null)
+ {
+ thumbnailFile =
+ createNewFile(thumbnailDataset, Constants.HDF5_CONTAINER_THUMBNAILS_FILE_NAME);
+ } else
+ {
+ thumbnailFile =
+ createNewFile(thumbnailDataset,
+ thumbnailsStorageFormatOrNull.getThumbnailsFileName());
+ }
+
+ Hdf5ThumbnailGenerator.tryGenerateThumbnails(imageDataSetStructure, incomingDirectory,
+ thumbnailFile, imageDataSetStructure.getImageStorageConfiguraton(),
+ thumbnailDataset.getDataSetCode(), thumbnailsStorageFormatOrNull, thumbnailPaths,
+ registerOriginalImageAsThumbnail, content);
+ enhanceWithResolution(thumbnailDataset, thumbnailPaths);
+ }
+
+ private static void enhanceWithResolution(IDataSet thumbnailDataset,
+ ThumbnailsInfo thumbnailPaths)
+ {
+ Size size = thumbnailPaths.tryGetDimension(thumbnailDataset.getDataSetCode());
+ if (size != null)
+ {
+ thumbnailDataset.setPropertyValue(ScreeningConstants.RESOLUTION, size.getWidth() + "x"
+ + size.getHeight());
+ }
+ }
+
+ private IDataSet createThumbnailDataset(DataSetInformation imageDataSetInformation,
+ ThumbnailsStorageFormat thumbnailsStorageFormat)
+ {
+ String thumbnailsDatasetTypeCode = findThumbnailsDatasetTypeCode(imageDataSetInformation);
+ IDataSet thumbnailDataset = createNewDataSet(thumbnailsDatasetTypeCode);
+ thumbnailDataset.setFileFormatType(thumbnailsStorageFormat.getFileFormat()
+ .getOpenBISFileType());
+ thumbnailDataset.setMeasuredData(false);
+
+ return thumbnailDataset;
+ }
+
+ private ImageContainerDataSet createImageContainerDataset(IDataSet mainDataset,
+ DataSetInformation imageDataSetInformation, List<String> containedDataSetCodes)
+ {
+ String containerDatasetTypeCode = findContainerDatasetTypeCode(imageDataSetInformation);
+ @SuppressWarnings("unchecked")
+ ImageContainerDataSet containerDataset =
+ (ImageContainerDataSet) createNewDataSet(imageContainerDatasetFactory,
+ containerDatasetTypeCode);
+ setSameDatasetOwner(mainDataset, containerDataset);
+ moveDatasetRelations(mainDataset, containerDataset);
+
+ containerDataset.setContainedDataSetCodes(containedDataSetCodes);
+ return containerDataset;
+ }
+
+ private FeatureVectorContainerDataSet createFeatureVectorContainerDataSet(
+ FeatureVectorDataSet mainDataset)
+ {
+ String containerDatasetTypeCode =
+ FeatureVectorContainerDataSet
+ .getContainerAnalysisType(mainDataset.getDataSetType());
+
+ @SuppressWarnings("unchecked")
+ FeatureVectorContainerDataSet containerDataSet =
+ (FeatureVectorContainerDataSet) createNewDataSet(
+ factory.featureVectorContainerDatasetFactory, containerDatasetTypeCode);
+ containerDataSet.setContainedDataSetCodes(Collections.singletonList(mainDataset
+ .getDataSetCode()));
+
+ containerDataSet.setOriginalDataSet(mainDataset);
+
+ return containerDataSet;
+ }
+
+ // Copies properties and relations to datasets from the main dataset to the container and
+ // resets them in the main dataset.
+ private static void moveDatasetRelations(IDataSet mainDataset, IDataSet containerDataset)
+ {
+ containerDataset.setParentDatasets(mainDataset.getParentDatasets());
+ mainDataset.setParentDatasets(Collections.<String> emptyList());
+
+ for (String propertyCode : mainDataset.getAllPropertyCodes())
+ {
+ containerDataset.setPropertyValue(propertyCode,
+ mainDataset.getPropertyValue(propertyCode));
+ mainDataset.setPropertyValue(propertyCode, null);
+ }
+ }
+
+ private static boolean isHCSImageDataSetType(String mainDatasetTypeCode)
+ {
+ String prefix = ScreeningConstants.HCS_IMAGE_DATASET_TYPE_PREFIX;
+ if (mainDatasetTypeCode.startsWith(prefix))
+ {
+ if (mainDatasetTypeCode
+ .contains(ScreeningConstants.IMAGE_CONTAINER_DATASET_TYPE_MARKER))
+ {
+ throw UserFailureException
+ .fromTemplate(
+ "The specified image dataset type '%s' should not be of container type, but contains '%s' in the type code.",
+ mainDatasetTypeCode,
+ ScreeningConstants.IMAGE_CONTAINER_DATASET_TYPE_MARKER);
+ }
+ return true;
+ } else
+ {
+ return false;
+ }
+ }
+
+ private static boolean isMicroscopyImageDataSetType(String dataSetTypeCode)
+ {
+ return dataSetTypeCode.contains(MICROSCOPY_IMAGE_TYPE_SUBSTRING)
+ && false == dataSetTypeCode.contains(MICROSCOPY_CONTAINER_TYPE_SUBSTRING);
+ }
+
+ private static String findContainerDatasetTypeCode(DataSetInformation imageDataSetInformation)
+ {
+ String dataSetTypeCode = imageDataSetInformation.getDataSetType().getCode().toUpperCase();
+ String prefix = ScreeningConstants.HCS_IMAGE_DATASET_TYPE_PREFIX;
+ if (isHCSImageDataSetType(dataSetTypeCode))
+ {
+ return prefix + ScreeningConstants.IMAGE_CONTAINER_DATASET_TYPE_MARKER
+ + dataSetTypeCode.substring(prefix.length());
+ } else if (isMicroscopyImageDataSetType(dataSetTypeCode))
+ {
+ return dataSetTypeCode.replace(MICROSCOPY_IMAGE_TYPE_SUBSTRING,
+ MICROSCOPY_CONTAINER_TYPE_SUBSTRING);
+ } else
+ {
+ throw UserFailureException
+ .fromTemplate(
+ "The image dataset type '%s' is neither standard HCS type (starts with '%s') nor a microscopy type (contains '%s').",
+ dataSetTypeCode, prefix,
+ ScreeningConstants.MICROSCOPY_IMAGE_SAMPLE_TYPE_PATTERN);
+ }
+ }
+
+ private static String findThumbnailsDatasetTypeCode(DataSetInformation imageDataSetInformation)
+ {
+ String dataSetTypeCode = imageDataSetInformation.getDataSetType().getCode().toUpperCase();
+
+ if (isHCSImageDataSetType(dataSetTypeCode))
+ {
+ return ScreeningConstants.HCS_IMAGE_DATASET_TYPE_PREFIX
+ + ScreeningConstants.IMAGE_THUMBNAIL_DATASET_TYPE_MARKER;
+ } else if (isMicroscopyImageDataSetType(dataSetTypeCode))
+ {
+ return dataSetTypeCode.replace(ScreeningConstants.MICROSCOPY_IMAGE_TYPE_SUBSTRING,
+ ScreeningConstants.MICROSCOPY_THUMBNAIL_TYPE_SUBSTRING);
+ } else
+ {
+ throw UserFailureException
+ .fromTemplate(
+ "The image dataset type '%s' is neither standard HCS type (starts with '%s') nor a microscopy type (contains '%s').",
+ dataSetTypeCode, ScreeningConstants.HCS_IMAGE_DATASET_TYPE_PREFIX,
+ ScreeningConstants.MICROSCOPY_IMAGE_SAMPLE_TYPE_PATTERN);
+ }
+ }
+
+ private static void setSameDatasetOwner(IDataSetImmutable templateDataset,
+ IDataSet destinationDataset)
+ {
+ destinationDataset.setExperiment(templateDataset.getExperiment());
+ destinationDataset.setSample(templateDataset.getSample());
+
+ }
+
+ @SuppressWarnings(
+ { "cast", "unchecked" })
+ @Override
+ public IDataSet createNewDataSet(DataSetRegistrationDetails registrationDetails)
+ {
+ if (registrationDetails.getDataSetInformation() instanceof ImageDataSetInformation)
+ {
+ DataSetRegistrationDetails<ImageDataSetInformation> imageRegistrationDetails =
+ (DataSetRegistrationDetails<ImageDataSetInformation>) registrationDetails;
+ return createNewImageDataSet(imageRegistrationDetails);
+ } else if (registrationDetails.getDataSetInformation() instanceof FeatureVectorDataSetInformation)
+ {
+ DataSetRegistrationDetails<FeatureVectorDataSetInformation> featureRegistrationDetails =
+ (DataSetRegistrationDetails<FeatureVectorDataSetInformation>) registrationDetails;
+ return createFeatureVectorDataSet(featureRegistrationDetails);
+ } else
+ {
+ return super.createNewDataSet(registrationDetails);
+ }
+ }
+
+ /**
+ * If we are dealing with the image dataset container then the move operation is delegated to
+ * the original dataset. Otherwise a default implementation is used.
+ */
+ @Override
+ public String moveFile(String src, IDataSet dst)
+ {
+ System.out.println("MF:" + src);
+
+ return moveFile(src, dst, new File(src).getName());
+ }
+
+ /**
+ * If we are dealing with the image dataset container then the move operation is delegated to
+ * the original dataset. Otherwise a default implementation is used.
+ */
+ @Override
+ public String moveFile(String src, IDataSet dst, String dstInDataset)
+ {
+ System.out.println("MF3:" + dstInDataset);
+
+ ImageContainerDataSet imageContainerDataset = tryAsImageContainerDataset(dst);
+
+ if (imageContainerDataset != null)
+ {
+ String destination = getDestinationInOriginal(dstInDataset);
+ DataSet<ImageDataSetInformation> originalDataset =
+ imageContainerDataset.getOriginalDataset();
+ if (originalDataset == null)
+ {
+ throw new UserFailureException(
+ "Cannot move the files because the original dataset is missing: " + src);
+ }
+ originalDataset.getRegistrationDetails().getDataSetInformation()
+ .setDatasetRelativeImagesFolderPath(new File(destination));
+
+ return super.moveFile(src, originalDataset, destination);
+ }
+
+ FeatureVectorContainerDataSet featureContainer = tryAsFeatureVectorContainerDataset(dst);
+ if (featureContainer != null)
+ {
+ IDataSet originalDataSet = featureContainer.getOriginalDataset();
+
+ if (originalDataSet == null)
+ {
+ throw new UserFailureException(
+ "Cannot move the files because the original dataset is missing: " + src);
+ }
+
+ return super.moveFile(src, originalDataSet, dstInDataset);
+ }
+
+ return super.moveFile(src, dst, dstInDataset);
+ }
+
+ private String getDestinationInOriginal(String dstInDataset)
+ {
+ String destination = dstInDataset;
+ if (destination.startsWith(originalDirName) == false)
+ {
+ destination = prependOriginalDirectory(destination).getPath();
+ }
+ return destination;
+ }
+
+ private static FeatureVectorContainerDataSet tryAsFeatureVectorContainerDataset(IDataSet dataset)
+ {
+ if (dataset instanceof FeatureVectorContainerDataSet)
+ {
+ return (FeatureVectorContainerDataSet) dataset;
+ }
+ return null;
+ }
+
+ private static ImageContainerDataSet tryAsImageContainerDataset(IDataSet dataset)
+ {
+ if (dataset instanceof ImageContainerDataSet)
+ {
+ return (ImageContainerDataSet) dataset;
+ } else
+ {
+ return null;
+ }
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/ImagingDataSetRegistrationTransactionV2Delegate.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/ImagingDataSetRegistrationTransactionV2Delegate.java
index 9f524cfb849a55c73d84499c567edc04e25434f8..535108642ae3c228c53ad0d3f7716ec64d93edee 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/ImagingDataSetRegistrationTransactionV2Delegate.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/ImagingDataSetRegistrationTransactionV2Delegate.java
@@ -22,34 +22,33 @@ import net.lemnik.eodsql.DynamicTransactionQuery;
import ch.systemsx.cisd.etlserver.TopLevelDataSetRegistratorGlobalState;
import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationContext;
-import ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSet;
-import ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSetUpdatable;
-import ch.systemsx.cisd.etlserver.registrator.api.v1.IExperiment;
-import ch.systemsx.cisd.etlserver.registrator.api.v1.IExperimentUpdatable;
-import ch.systemsx.cisd.etlserver.registrator.api.v1.IMaterial;
-import ch.systemsx.cisd.etlserver.registrator.api.v1.IMetaproject;
-import ch.systemsx.cisd.etlserver.registrator.api.v1.IProject;
-import ch.systemsx.cisd.etlserver.registrator.api.v1.ISample;
-import ch.systemsx.cisd.etlserver.registrator.api.v1.ISpace;
-import ch.systemsx.cisd.etlserver.registrator.api.v1.IVocabulary;
-import ch.systemsx.cisd.etlserver.registrator.api.v1.IVocabularyTerm;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.IImageDataSet;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.SimpleImageDataConfig;
+import ch.systemsx.cisd.etlserver.registrator.api.v2.IDataSet;
+import ch.systemsx.cisd.etlserver.registrator.api.v2.IDataSetUpdatable;
+import ch.systemsx.cisd.etlserver.registrator.api.v2.IExperiment;
+import ch.systemsx.cisd.etlserver.registrator.api.v2.IExperimentUpdatable;
+import ch.systemsx.cisd.etlserver.registrator.api.v2.IMaterial;
+import ch.systemsx.cisd.etlserver.registrator.api.v2.IMetaproject;
+import ch.systemsx.cisd.etlserver.registrator.api.v2.IProject;
+import ch.systemsx.cisd.etlserver.registrator.api.v2.ISample;
+import ch.systemsx.cisd.etlserver.registrator.api.v2.ISpace;
+import ch.systemsx.cisd.etlserver.registrator.api.v2.IVocabulary;
+import ch.systemsx.cisd.etlserver.registrator.api.v2.IVocabularyTerm;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.SimpleImageDataConfig;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v2.FeatureListDataConfig;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v2.IFeatureVectorDataSet;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v2.IImageDataSet;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v2.IImagingDataSetRegistrationTransactionV2;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v2.SimpleFeatureVectorDataConfig;
-import ch.systemsx.cisd.openbis.dss.etl.jython.ImagingDataSetRegistrationTransaction;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IDataSetImmutable;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IExperimentImmutable;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IExternalDataManagementSystemImmutable;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IMaterialImmutable;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IProjectImmutable;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.ISampleImmutable;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.ISearchService;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.ISpaceImmutable;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IVocabularyImmutable;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.authorization.IAuthorizationService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IDataSetImmutable;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IExperimentImmutable;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IExternalDataManagementSystemImmutable;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IMaterialImmutable;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IProjectImmutable;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISampleImmutable;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISearchService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISpaceImmutable;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IVocabularyImmutable;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.authorization.IAuthorizationService;
/**
* @author Jakub Straszewski
@@ -148,8 +147,7 @@ public class ImagingDataSetRegistrationTransactionV2Delegate implements
}
@Override
- public ISample createNewSampleWithGeneratedCode(String spaceCode,
- String sampleTypeCode)
+ public ISample createNewSampleWithGeneratedCode(String spaceCode, String sampleTypeCode)
{
return transaction.createNewSampleWithGeneratedCode(spaceCode, sampleTypeCode);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/JythonImageContainerDataSetRegistrationFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/JythonImageContainerDataSetRegistrationFactory.java
new file mode 100644
index 0000000000000000000000000000000000000000..075d56b230812432a6ce9353bd0a1921d1022ad4
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/JythonImageContainerDataSetRegistrationFactory.java
@@ -0,0 +1,54 @@
+/*
+ * 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.etl.jython.v2;
+
+import java.io.File;
+
+import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationDetails;
+import ch.systemsx.cisd.etlserver.registrator.v2.AbstractDataSetRegistrationDetailsFactory;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v2.impl.ImageContainerDataSet;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+
+/**
+ * @author jakubs
+ */
+public class JythonImageContainerDataSetRegistrationFactory extends
+ AbstractDataSetRegistrationDetailsFactory<DataSetInformation>
+{
+
+ public JythonImageContainerDataSetRegistrationFactory(
+ ch.systemsx.cisd.etlserver.registrator.v2.AbstractOmniscientTopLevelDataSetRegistrator.OmniscientTopLevelDataSetRegistratorState registratorState,
+ DataSetInformation userProvidedDataSetInformationOrNull)
+ {
+ super(registratorState, userProvidedDataSetInformationOrNull);
+ }
+
+ @Override
+ public ImageContainerDataSet createDataSet(
+ DataSetRegistrationDetails<DataSetInformation> registrationDetails, File stagingFile)
+ {
+ IEncapsulatedOpenBISService service = registratorState.getGlobalState().getOpenBisService();
+ return new ImageContainerDataSet(registrationDetails, stagingFile, service);
+ }
+
+ @Override
+ protected DataSetInformation createDataSetInformation()
+ {
+ return new DataSetInformation();
+ }
+}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/JythonImageDataSetRegistrationFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/JythonImageDataSetRegistrationFactory.java
new file mode 100644
index 0000000000000000000000000000000000000000..2ff12a87b10749d6e4fcf2dfeda81632c3a12cef
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/JythonImageDataSetRegistrationFactory.java
@@ -0,0 +1,42 @@
+/*
+ * 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.etl.jython.v2;
+
+import ch.systemsx.cisd.etlserver.registrator.v2.AbstractDataSetRegistrationDetailsFactory;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ImageDataSetInformation;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+
+/**
+ * @author jakubs
+ */
+public class JythonImageDataSetRegistrationFactory extends
+ AbstractDataSetRegistrationDetailsFactory<ImageDataSetInformation>
+{
+
+ public JythonImageDataSetRegistrationFactory(
+ ch.systemsx.cisd.etlserver.registrator.v2.AbstractOmniscientTopLevelDataSetRegistrator.OmniscientTopLevelDataSetRegistratorState registratorState,
+ DataSetInformation userProvidedDataSetInformationOrNull)
+ {
+ super(registratorState, userProvidedDataSetInformationOrNull);
+ }
+
+ @Override
+ protected ImageDataSetInformation createDataSetInformation()
+ {
+ return new ImageDataSetInformation();
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/JythonPlateDataSetHandlerUtils.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/JythonPlateDataSetHandlerUtils.java
new file mode 100644
index 0000000000000000000000000000000000000000..e89cf3e04cc124880e8a4349556211c4f8b235c8
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/JythonPlateDataSetHandlerUtils.java
@@ -0,0 +1,48 @@
+/*
+ * 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.etl.jython.v2;
+
+import java.util.Properties;
+
+import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
+import ch.systemsx.cisd.common.filesystem.FileUtilities;
+import ch.systemsx.cisd.common.properties.PropertyUtils;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
+
+/**
+ *
+ *
+ * @author jakubs
+ */
+public class JythonPlateDataSetHandlerUtils
+{
+ private static final String ORIGINAL_DIRNAME_KEY = "image-datasets-original-dir-name";
+
+ public static String parseOriginalDir(Properties threadProperties)
+ {
+ String originalDir =
+ PropertyUtils.getProperty(threadProperties, ORIGINAL_DIRNAME_KEY,
+ ScreeningConstants.ORIGINAL_DATA_DIR);
+ if (false == FileUtilities.isValidFileName(originalDir))
+ {
+ throw ConfigurationFailureException.fromTemplate(
+ "Invalid folder name specified in '%s': '%s'.", ORIGINAL_DIRNAME_KEY,
+ originalDir);
+ }
+ return originalDir;
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/JythonPlateDataSetHandlerV2.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/JythonPlateDataSetHandlerV2.java
index d8953d16315aa1a294c38b4e16e4d14d456e9175..757015700954ea983c638dbb66670b8d80870893 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/JythonPlateDataSetHandlerV2.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/JythonPlateDataSetHandlerV2.java
@@ -23,17 +23,12 @@ import ch.systemsx.cisd.common.jython.PythonInterpreter;
import ch.systemsx.cisd.etlserver.ITopLevelDataSetRegistratorDelegate;
import ch.systemsx.cisd.etlserver.TopLevelDataSetRegistratorGlobalState;
import ch.systemsx.cisd.etlserver.registrator.DataSetFile;
-import ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSetRegistrationTransaction;
-import ch.systemsx.cisd.etlserver.registrator.api.v1.impl.DataSetRegistrationTransaction;
import ch.systemsx.cisd.etlserver.registrator.api.v2.IDataSetRegistrationTransactionV2;
import ch.systemsx.cisd.etlserver.registrator.api.v2.JythonDataSetRegistrationServiceV2;
import ch.systemsx.cisd.etlserver.registrator.api.v2.JythonTopLevelDataSetHandlerV2;
-import ch.systemsx.cisd.etlserver.registrator.recovery.AutoRecoverySettings;
-import ch.systemsx.cisd.etlserver.registrator.v1.DataSetRegistrationService;
-import ch.systemsx.cisd.etlserver.registrator.v1.IDataSetRegistrationDetailsFactory;
-import ch.systemsx.cisd.openbis.dss.etl.jython.ImagingDataSetRegistrationTransaction;
-import ch.systemsx.cisd.openbis.dss.etl.jython.JythonPlateDataSetHandlerUtils;
-import ch.systemsx.cisd.openbis.dss.etl.jython.JythonPlateDatasetFactory;
+import ch.systemsx.cisd.etlserver.registrator.api.v2.impl.DataSetRegistrationTransaction;
+import ch.systemsx.cisd.etlserver.registrator.v2.DataSetRegistrationService;
+import ch.systemsx.cisd.etlserver.registrator.v2.IDataSetRegistrationDetailsFactory;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
/**
@@ -77,7 +72,7 @@ public class JythonPlateDataSetHandlerV2 extends JythonTopLevelDataSetHandlerV2<
{
@SuppressWarnings("unchecked")
@Override
- protected DataSetRegistrationTransaction<DataSetInformation> createV2DatasetRegistrationTransaction(
+ protected DataSetRegistrationTransaction<DataSetInformation> createTransaction(
File rollBackStackParentFolder,
File workingDirectory,
File stagingDirectory,
@@ -85,14 +80,14 @@ public class JythonPlateDataSetHandlerV2 extends JythonTopLevelDataSetHandlerV2<
{
return new ImagingDataSetRegistrationTransaction(rollBackStackParentFolder,
workingDirectory, stagingDirectory, this, registrationDetailsFactory,
- originalDirName, AutoRecoverySettings.USE_AUTO_RECOVERY);
+ originalDirName);
}
};
}
@Override
protected IDataSetRegistrationTransactionV2 wrapTransaction(
- IDataSetRegistrationTransaction transaction)
+ DataSetRegistrationTransaction<DataSetInformation> transaction)
{
return new ImagingDataSetRegistrationTransactionV2Delegate(
(ImagingDataSetRegistrationTransaction) transaction);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/JythonPlateDatasetFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/JythonPlateDatasetFactory.java
new file mode 100644
index 0000000000000000000000000000000000000000..972213024b940ce9f714d300ede92bb6e63895e1
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/JythonPlateDatasetFactory.java
@@ -0,0 +1,222 @@
+/*
+ * 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.etl.jython.v2;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.List;
+import java.util.Properties;
+
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationDetails;
+import ch.systemsx.cisd.etlserver.registrator.api.v2.IDataSet;
+import ch.systemsx.cisd.etlserver.registrator.api.v2.JythonTopLevelDataSetHandlerV2.ProgrammableDropboxObjectFactory;
+import ch.systemsx.cisd.etlserver.registrator.api.v2.impl.DataSetRegistrationTransaction;
+import ch.systemsx.cisd.etlserver.registrator.v2.AbstractOmniscientTopLevelDataSetRegistrator.OmniscientTopLevelDataSetRegistratorState;
+import ch.systemsx.cisd.etlserver.registrator.v2.DataSetRegistrationService;
+import ch.systemsx.cisd.etlserver.registrator.v2.IDataSetRegistrationDetailsFactory;
+import ch.systemsx.cisd.openbis.dss.etl.PlateGeometryOracle;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.IFeaturesBuilder;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.SimpleImageDataConfig;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeatureDefinition;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeatureVectorDataSetInformation;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeaturesBuilder;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ImageDataSetInformation;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v2.IImagingDatasetFactory;
+import ch.systemsx.cisd.openbis.dss.etl.featurevector.CsvFeatureVectorParser;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
+
+/**
+ * @author jakubs
+ */
+
+public class JythonPlateDatasetFactory extends ProgrammableDropboxObjectFactory<DataSetInformation>
+ implements IImagingDatasetFactory
+{
+ final IDataSetRegistrationDetailsFactory<ImageDataSetInformation> imageDatasetFactory;
+
+ final IDataSetRegistrationDetailsFactory<DataSetInformation> imageContainerDatasetFactory;
+
+ final IDataSetRegistrationDetailsFactory<DataSetInformation> featureVectorContainerDatasetFactory;
+
+ final IDataSetRegistrationDetailsFactory<FeatureVectorDataSetInformation> featureVectorDatasetFactory;
+
+ public JythonPlateDatasetFactory(OmniscientTopLevelDataSetRegistratorState registratorState,
+ DataSetInformation userProvidedDataSetInformationOrNull)
+ {
+ super(registratorState, userProvidedDataSetInformationOrNull);
+ this.imageContainerDatasetFactory =
+ new JythonImageContainerDataSetRegistrationFactory(this.registratorState,
+ this.userProvidedDataSetInformationOrNull);
+ this.imageDatasetFactory =
+ new JythonImageDataSetRegistrationFactory(this.registratorState,
+ this.userProvidedDataSetInformationOrNull);
+ this.featureVectorDatasetFactory =
+ new ProgrammableDropboxObjectFactory<FeatureVectorDataSetInformation>(
+ this.registratorState, this.userProvidedDataSetInformationOrNull)
+ {
+ @Override
+ protected FeatureVectorDataSetInformation createDataSetInformation()
+ {
+ return new FeatureVectorDataSetInformation();
+ }
+ };
+
+ this.featureVectorContainerDatasetFactory =
+ new FeatureVectorContainerDataSetRegistrationFactory(this.registratorState,
+ this.userProvidedDataSetInformationOrNull);
+ }
+
+ /** By default a standard dataset is created. */
+ @Override
+ protected DataSetInformation createDataSetInformation()
+ {
+ return new DataSetInformation();
+ }
+
+ @Override
+ public DataSetRegistrationDetails<ImageDataSetInformation> createImageRegistrationDetails(
+ SimpleImageDataConfig imageDataSet, File incomingDatasetFolder)
+ {
+ return SimpleImageDataSetRegistrator.createImageDatasetDetails(imageDataSet,
+ incomingDatasetFolder, imageDatasetFactory);
+ }
+
+ /** a simple method to register the described image dataset in a separate transaction */
+ @Override
+ public boolean registerImageDataset(SimpleImageDataConfig imageDataSet,
+ File incomingDatasetFolder, DataSetRegistrationService<ImageDataSetInformation> service)
+ {
+ DataSetRegistrationDetails<ImageDataSetInformation> imageDatasetDetails =
+ createImageRegistrationDetails(imageDataSet, incomingDatasetFolder);
+ return registerImageDataset(imageDatasetDetails, incomingDatasetFolder, service);
+ }
+
+ @Override
+ public boolean registerImageDataset(
+ DataSetRegistrationDetails<ImageDataSetInformation> imageDatasetDetails,
+ File incomingDatasetFolder, DataSetRegistrationService<ImageDataSetInformation> service)
+ {
+ DataSetRegistrationTransaction<ImageDataSetInformation> transaction =
+ service.transaction(incomingDatasetFolder,
+ service.getDataSetRegistrationDetailsFactory());
+ IDataSet newDataset = transaction.createNewDataSet(imageDatasetDetails);
+ transaction.moveFile(incomingDatasetFolder.getPath(), newDataset);
+ return transaction.commit();
+ }
+
+ /**
+ * @return a constant which can be used as a vocabulary term value for $PLATE_GEOMETRY property
+ * of a plate/
+ * @throws UserFailureException if all available geometries in openBIS are too small (there is a
+ * well outside).
+ */
+ @Override
+ public String figureGeometry(
+ DataSetRegistrationDetails<ImageDataSetInformation> registrationDetails)
+ {
+ IEncapsulatedOpenBISService openBisService =
+ registratorState.getGlobalState().getOpenBisService();
+ return PlateGeometryOracle.figureGeometry(registrationDetails, openBisService);
+ }
+
+ // ----
+
+ @Override
+ public IFeaturesBuilder createFeaturesBuilder()
+ {
+ return new FeaturesBuilder();
+ }
+
+ @Override
+ public DataSetRegistrationDetails<FeatureVectorDataSetInformation> createFeatureVectorDatasetDetails(
+ IFeaturesBuilder featureBuilder)
+ {
+ FeaturesBuilder myFeatureBuilder = (FeaturesBuilder) featureBuilder;
+ List<FeatureDefinition> featureDefinitions =
+ myFeatureBuilder.getFeatureDefinitionValuesList();
+ return createFeatureVectorRegistrationDetails(featureDefinitions);
+ }
+
+ /**
+ * Parses the feature vectors from the specified CSV file. CSV format can be configured with
+ * following properties:
+ *
+ * <pre>
+ * # Separator character between headers and row cells.
+ * separator = ,
+ * ignore-comments = true
+ * # Header of the column denoting the row of a well.
+ * well-name-row = row
+ * # Header of the column denoting the column of a well.
+ * well-name-col = col
+ * well-name-col-is-alphanum = true
+ * </pre>
+ *
+ * @throws IOException if file cannot be parsed
+ */
+ @Override
+ public DataSetRegistrationDetails<FeatureVectorDataSetInformation> createFeatureVectorDatasetDetails(
+ String csvFilePath, Properties properties) throws IOException
+ {
+ List<FeatureDefinition> featureDefinitions =
+ CsvFeatureVectorParser.parse(new File(csvFilePath), properties);
+ return createFeatureVectorRegistrationDetails(featureDefinitions);
+ }
+
+ public DataSetRegistrationDetails<FeatureVectorDataSetInformation> createFeatureVectorRegistrationDetails(
+ List<FeatureDefinition> featureDefinitions)
+ {
+ DataSetRegistrationDetails<FeatureVectorDataSetInformation> registrationDetails =
+ featureVectorDatasetFactory.createDataSetRegistrationDetails();
+ FeatureVectorDataSetInformation featureVectorDataSet =
+ registrationDetails.getDataSetInformation();
+ featureVectorDataSet.setFeatures(featureDefinitions);
+ registrationDetails.setDataSetType(ScreeningConstants.DEFAULT_ANALYSIS_WELL_DATASET_TYPE);
+ registrationDetails.setMeasuredData(false);
+ return registrationDetails;
+ }
+
+ // -------- backward compatibility methods
+
+ /**
+ * This method exists just for backward compatibility. It used to have the second parameter,
+ * which is now ignored.
+ *
+ * @deprecated use {@link #createFeatureVectorDatasetDetails(IFeaturesBuilder)} instead.
+ */
+ @Deprecated
+ public DataSetRegistrationDetails<FeatureVectorDataSetInformation> createFeatureVectorRegistrationDetails(
+ IFeaturesBuilder featureBuilder, Object incomingDatasetFolder)
+ {
+ return createFeatureVectorDatasetDetails(featureBuilder);
+ }
+
+ /**
+ * @deprecated Changed to {@link #createFeatureVectorDatasetDetails(String, Properties)} due to
+ * naming convention change.
+ */
+ @Deprecated
+ public DataSetRegistrationDetails<FeatureVectorDataSetInformation> createFeatureVectorRegistrationDetails(
+ String csvFilePath, Properties properties) throws IOException
+ {
+ return createFeatureVectorDatasetDetails(csvFilePath, properties);
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/SimpleImageDataSetRegistrator.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/SimpleImageDataSetRegistrator.java
new file mode 100644
index 0000000000000000000000000000000000000000..c028b44596367f2758d04fa0a480c9a6d8745b8d
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/SimpleImageDataSetRegistrator.java
@@ -0,0 +1,772 @@
+/*
+ * 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.dss.etl.jython.v2;
+
+import java.awt.image.BufferedImage;
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.apache.commons.io.FilenameUtils;
+import org.apache.log4j.Logger;
+
+import ch.rinn.restrictions.Private;
+import ch.systemsx.cisd.common.collection.CollectionUtils;
+import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.common.filesystem.FileOperations;
+import ch.systemsx.cisd.common.filesystem.FileUtilities;
+import ch.systemsx.cisd.common.image.IntensityRescaling;
+import ch.systemsx.cisd.common.image.IntensityRescaling.Levels;
+import ch.systemsx.cisd.common.image.IntensityRescaling.PixelHistogram;
+import ch.systemsx.cisd.common.logging.LogCategory;
+import ch.systemsx.cisd.common.logging.LogFactory;
+import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationDetails;
+import ch.systemsx.cisd.etlserver.registrator.v2.IDataSetRegistrationDetailsFactory;
+import ch.systemsx.cisd.imagereaders.IImageReader;
+import ch.systemsx.cisd.imagereaders.ImageID;
+import ch.systemsx.cisd.imagereaders.ImageReaderFactory;
+import ch.systemsx.cisd.openbis.common.io.FileBasedContentNode;
+import ch.systemsx.cisd.openbis.dss.etl.dto.ImageLibraryInfo;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.Channel;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColorComponent;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColorRGB;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageFileInfo;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageIdentifier;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageMetadata;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.IntensityRange;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.Location;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.SimpleImageDataConfig;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.SimpleOverviewImageDataConfig;
+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.transformations.ImageTransformation;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.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
+ * {@link SimpleImageDataConfig}.
+ *
+ * @author Tomasz Pylak
+ */
+public class SimpleImageDataSetRegistrator
+{
+ public static final String OPTIMAL_DATASET_INTENSITY_RESCALING_DESCRIPTION =
+ "Optimal intensity rescaling for a series of images. "
+ + "It allows to compare images of one plate's dataset to each other."
+ + "At the same time it causes that the conversion to 8 bit color depth looses less information, "
+ + "especially when images use only a small part of available intensities range.";
+
+ @Private
+ static interface IImageReaderFactory
+ {
+ IImageReader tryGetReader(String libraryName, String readerName);
+
+ IImageReader tryGetReaderForFile(String libraryName, String fileName);
+ }
+
+ private static class ImageTokensWithPath extends ImageMetadata
+ {
+ /** path relative to the incoming dataset directory */
+ private String imageRelativePath;
+
+ public ImageTokensWithPath(ImageMetadata imageTokens, String imageRelativePath)
+ {
+ setWell(imageTokens.getWell());
+ setChannelCode(imageTokens.getChannelCode());
+ setTileNumber(imageTokens.getTileNumber());
+ setDepth(imageTokens.tryGetDepth());
+ setTimepoint(imageTokens.tryGetTimepoint());
+ setSeriesNumber(imageTokens.tryGetSeriesNumber());
+ setImageIdentifier(imageTokens.tryGetImageIdentifier());
+ this.imageRelativePath = imageRelativePath;
+ }
+
+ public String getImagePath()
+ {
+ return imageRelativePath;
+ }
+ }
+
+ public static DataSetRegistrationDetails<ImageDataSetInformation> createImageDatasetDetails(
+ SimpleImageDataConfig simpleImageConfig, File incoming,
+ IDataSetRegistrationDetailsFactory<ImageDataSetInformation> factory)
+ {
+ return createImageDatasetDetails(simpleImageConfig, incoming, factory,
+ new IImageReaderFactory()
+ {
+ @Override
+ public IImageReader tryGetReaderForFile(String libraryName, String fileName)
+ {
+ return ImageReaderFactory.tryGetReaderForFile(libraryName, fileName);
+ }
+
+ @Override
+ public IImageReader tryGetReader(String libraryName, String readerName)
+ {
+ return ImageReaderFactory.tryGetReader(libraryName, readerName);
+ }
+ });
+ }
+
+ @Private
+ static DataSetRegistrationDetails<ImageDataSetInformation> createImageDatasetDetails(
+ SimpleImageDataConfig simpleImageConfig, File incoming,
+ IDataSetRegistrationDetailsFactory<ImageDataSetInformation> factory,
+ IImageReaderFactory readerFactory)
+ {
+ SimpleImageDataSetRegistrator registrator =
+ new SimpleImageDataSetRegistrator(simpleImageConfig, readerFactory);
+ return registrator.createImageDatasetDetails(incoming, factory);
+ }
+
+ final static Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
+ SimpleImageDataSetRegistrator.class);
+
+ private final SimpleImageDataConfig simpleImageConfig;
+
+ private final IImageReaderFactory readerFactory;
+
+ private SimpleImageDataSetRegistrator(SimpleImageDataConfig simpleImageConfig,
+ IImageReaderFactory readerFactory)
+ {
+ this.simpleImageConfig = simpleImageConfig;
+ this.readerFactory = readerFactory;
+ }
+
+ private DataSetRegistrationDetails<ImageDataSetInformation> createImageDatasetDetails(
+ File incoming,
+ IDataSetRegistrationDetailsFactory<ImageDataSetInformation> imageDatasetFactory)
+ {
+ 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)
+ {
+ List<ChannelColorComponent> channelColorComponentsOrNull =
+ simpleImageConfig.getChannelColorComponentsOrNull();
+ if (channelColorComponentsOrNull == null)
+ {
+ imageDataset.setChannels(channels);
+ } else
+ {
+ imageDataset.setChannels(channels, channelColorComponentsOrNull);
+ }
+ }
+
+ setRegistrationDetails(registrationDetails, imageDataset);
+ return registrationDetails;
+ }
+
+ /**
+ * Finds all images in the directory.
+ */
+ private List<File> listImageFiles(final File incoming)
+ {
+ String[] extensions = simpleImageConfig.getRecognizedImageExtensions();
+ if (incoming.isFile())
+ {
+ List<File> list = new ArrayList<File>();
+ if (extensionMatches(incoming, extensions))
+ {
+ list.add(incoming);
+ }
+ return list;
+ } else
+ {
+ return FileOperations.getInstance().listFiles(incoming, extensions, true);
+ }
+ }
+
+ private boolean extensionMatches(final File incoming, String[] extensions)
+ {
+ if (extensions == null || extensions.length == 0)
+ {
+ return true;
+ }
+ String fileExt = FilenameUtils.getExtension(incoming.getName());
+ if (fileExt == null)
+ {
+ fileExt = "";
+ }
+ for (String ext : extensions)
+ {
+ if (ext.equalsIgnoreCase(fileExt))
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ /**
+ * Tokenizes file names of all images in the directory.
+ */
+ protected List<ImageTokensWithPath> parseImageTokens(List<File> imageFiles,
+ File incomingDirectory, IImageReader imageReaderOrNull)
+ {
+ List<ImageTokensWithPath> imageTokensList = new ArrayList<ImageTokensWithPath>();
+
+ for (File imageFile : imageFiles)
+ {
+ File file = new File(imageFile.getPath());
+ List<ImageIdentifier> identifiers = getImageIdentifiers(imageReaderOrNull, file);
+ String imageRelativePath = FileUtilities.getRelativeFilePath(incomingDirectory, file);
+ ImageMetadata[] imageTokens =
+ simpleImageConfig.extractImagesMetadata(imageRelativePath, identifiers);
+ for (ImageMetadata imageToken : imageTokens)
+ {
+ imageToken.ensureValid(simpleImageConfig.isMicroscopyData());
+ imageTokensList.add(new ImageTokensWithPath(imageToken, imageRelativePath));
+ }
+ }
+ if (imageTokensList.isEmpty())
+ {
+ throw UserFailureException
+ .fromTemplate(
+ "No image tokens could be parsed from incoming directory '%s' for extensions %s!",
+ incomingDirectory.getPath(),
+ CollectionUtils.abbreviate(
+ simpleImageConfig.getRecognizedImageExtensions(), -1));
+ }
+ return imageTokensList;
+ }
+
+ private List<File> extractImageFiles(File incoming)
+ {
+ List<File> imageFiles = listImageFiles(incoming);
+ if (imageFiles.isEmpty())
+ {
+ throw UserFailureException.fromTemplate(
+ "Incoming directory '%s' contains no images with extensions %s!", incoming
+ .getPath(), CollectionUtils.abbreviate(
+ simpleImageConfig.getRecognizedImageExtensions(), -1));
+ }
+ return imageFiles;
+ }
+
+ // this method can have a side effect - it autodetects the image reader if only the library is
+ // specified
+ private IImageReader tryCreateAndSaveImageReader(List<File> imageFiles)
+ {
+ IImageReader readerOrNull = null;
+ ImageLibraryInfo imageLibraryInfoOrNull = tryGetImageLibrary();
+ if (imageLibraryInfoOrNull != null)
+ {
+ readerOrNull = tryCreateImageReader(imageFiles, imageLibraryInfoOrNull);
+ if (readerOrNull != null)
+ {
+ // NOTE: ugly side effect which is used later on
+ // if (null == imageLibraryInfoOrNull.getReaderName())
+ // {
+ imageLibraryInfoOrNull.setReaderName(readerOrNull.getName());
+ // }
+ } else
+ {
+ throw ConfigurationFailureException.fromTemplate(
+ "Cannot find any reader for '%s' library.", imageLibraryInfoOrNull);
+ }
+ }
+ return readerOrNull;
+ }
+
+ private IImageReader tryCreateImageReader(List<File> imageFiles,
+ ImageLibraryInfo imageLibraryInfo)
+ {
+ if (imageFiles.isEmpty())
+ {
+ return null;
+ }
+ File imageFile = imageFiles.get(0);
+ String libraryName = imageLibraryInfo.getName();
+ String readerNameOrNull = imageLibraryInfo.getReaderName();
+ if (readerNameOrNull != null)
+ {
+ return readerFactory.tryGetReader(libraryName, readerNameOrNull);
+ } else
+ {
+ return readerFactory.tryGetReaderForFile(libraryName, imageFile.getPath());
+ }
+ }
+
+ private ImageLibraryInfo tryGetImageLibrary()
+ {
+ return simpleImageConfig.getImageStorageConfiguration().tryGetImageLibrary();
+ }
+
+ private static List<ImageIdentifier> getImageIdentifiers(IImageReader readerOrNull,
+ File imageFile)
+ {
+ List<ImageIdentifier> ids = new ArrayList<ImageIdentifier>();
+ if (readerOrNull == null)
+ {
+ ids.add(ImageIdentifier.NULL);
+ } else
+ {
+ List<ImageID> imageIDs = readerOrNull.getImageIDs(imageFile);
+ for (ImageID imageID : imageIDs)
+ {
+ ids.add(new ImageIdentifier(imageID.getSeriesIndex(), imageID.getTimeSeriesIndex(),
+ imageID.getFocalPlaneIndex(), imageID.getColorChannelIndex()));
+ }
+ }
+ Collections.sort(ids);
+ return ids;
+ }
+
+ /**
+ * Creates ImageFileInfo for a given path to an image.
+ */
+ protected ImageFileInfo createImageInfo(ImageTokensWithPath imageTokens, Geometry tileGeometry)
+ {
+ Location tileCoords =
+ simpleImageConfig.getTileCoordinates(imageTokens.getTileNumber(), tileGeometry);
+ ImageFileInfo img =
+ new ImageFileInfo(imageTokens.getChannelCode(), tileCoords.getRow(),
+ tileCoords.getColumn(), imageTokens.getImagePath());
+ img.setTimepoint(imageTokens.tryGetTimepoint());
+ img.setDepth(imageTokens.tryGetDepth());
+ img.setSeriesNumber(imageTokens.tryGetSeriesNumber());
+ img.setWell(imageTokens.getWell());
+ img.setImageIdentifier(imageTokens.tryGetImageIdentifier());
+ return img;
+ }
+
+ /**
+ * @param imageTokensList list of ImageTokens for each image
+ * @param tileGeometry describes the matrix of tiles (aka fields or sides) in the well
+ */
+ protected List<ImageFileInfo> createImageInfos(List<ImageTokensWithPath> imageTokensList,
+ Geometry tileGeometry)
+ {
+ List<ImageFileInfo> images = new ArrayList<ImageFileInfo>();
+ for (ImageTokensWithPath imageTokens : imageTokensList)
+ {
+ ImageFileInfo image = createImageInfo(imageTokens, tileGeometry);
+ images.add(image);
+ }
+ return images;
+ }
+
+ private List<Channel> getAvailableChannels(List<ImageFileInfo> images)
+ {
+ Set<String> channelCodes = new LinkedHashSet<String>();
+ for (ImageFileInfo image : images)
+ {
+ channelCodes.add(image.getChannelCode());
+ }
+ List<Channel> channels = new ArrayList<Channel>();
+ for (String channelCode : channelCodes)
+ {
+ Channel channel = simpleImageConfig.createChannel(channelCode);
+ channels.add(channel);
+ }
+ return channels;
+ }
+
+ private static int getMaxTileNumber(List<ImageTokensWithPath> imageTokensList)
+ {
+ int max = 0;
+ for (ImageMetadata imageTokens : imageTokensList)
+ {
+ max = Math.max(max, imageTokens.getTileNumber());
+ }
+ return max;
+ }
+
+ // -------------------
+
+ private void computeAndAppendCommonFixedIntensityRangeTransformation(
+ List<ImageFileInfo> images, File incomingDir, List<Channel> channels,
+ IImageReader readerOrNull)
+ {
+ final List<Channel> channelsForComputation =
+ findChannelsToComputeFixedCommonIntensityRange(channels);
+ final Map<String, IntensityRange> map =
+ simpleImageConfig.getFixedIntensityRangeForAllImages();
+ final IntensityRange defaultLevelsOrNull = map.get(null);
+ for (Channel channel : channelsForComputation)
+ {
+ final IntensityRange levelsOrNull = map.get(channel.getCode());
+ final Levels intensityRange =
+ levelsOrNull == null ? new Levels(defaultLevelsOrNull.getBlackPoint(),
+ defaultLevelsOrNull.getWhitePoint()) : new Levels(
+ levelsOrNull.getBlackPoint(), levelsOrNull.getWhitePoint());
+ operationLog.info(String.format(
+ "Set intensity range for channel '%s' to fixed value: %s "
+ + "(incoming directory '%s').", channel.getCode(),
+ intensityRange.toString(), incomingDir.getName()));
+ appendCommonIntensityRangeTransformation(channel, intensityRange);
+ }
+ }
+
+ private List<Channel> findChannelsToComputeFixedCommonIntensityRange(List<Channel> channels)
+ {
+ final Map<String, ch.systemsx.cisd.openbis.dss.etl.dto.api.IntensityRange> map =
+ simpleImageConfig.getFixedIntensityRangeForAllImages();
+ final ch.systemsx.cisd.openbis.dss.etl.dto.api.IntensityRange defaultLevelOrNull =
+ map.get(null);
+ if (defaultLevelOrNull != null)
+ {
+ return channels;
+ }
+ final Set<String> channelCodesSet = map.keySet();
+ List<Channel> chosenChannels = new ArrayList<Channel>();
+ for (Channel channel : channels)
+ {
+ if (channelCodesSet.contains(channel.getCode()))
+ {
+ chosenChannels.add(channel);
+ }
+ }
+ return chosenChannels;
+ }
+
+ private void computeAndAppendCommonIntensityRangeTransformation(List<ImageFileInfo> images,
+ File incomingDir, List<Channel> channels, IImageReader readerOrNull)
+ {
+ final List<Channel> channelsForComputation =
+ tryFindChannelsToComputeCommonIntensityRange(channels);
+ if (channelsForComputation == null)
+ {
+ return;
+ }
+ for (Channel channel : channelsForComputation)
+ {
+ final String channelCode = channel.getCode();
+ final List<File> imagePaths = chooseChannelImages(images, incomingDir, channelCode);
+ operationLog.info(String.format("Computing intensity range for channel '%s'. "
+ + "Found %d images for the channel in incoming directory '%s'.", channelCode,
+ imagePaths.size(), incomingDir.getName()));
+ final Levels intensityRange;
+ intensityRange =
+ tryComputeCommonIntensityRange(readerOrNull, imagePaths,
+ simpleImageConfig.getComputeCommonIntensityRangeOfAllImagesThreshold());
+ if (intensityRange != null)
+ {
+ operationLog.info(String.format(
+ "Computed intensity range for channel '%s': %s (incoming directory '%s').",
+ channelCode, intensityRange.toString(), incomingDir.getName()));
+ appendCommonIntensityRangeTransformation(channel, intensityRange);
+ } else
+ {
+ operationLog
+ .warn(String
+ .format("Transformation cannot be generated for channel '%s' (incoming directory '%s').",
+ channelCode, incomingDir.getName()));
+ }
+ }
+ }
+
+ private void appendCommonIntensityRangeTransformation(Channel channel, Levels intensityRange)
+ {
+ ImageTransformationBuffer buffer = new ImageTransformationBuffer();
+ // append first
+ String label = simpleImageConfig.getComputeCommonIntensityRangeOfAllImagesLabel();
+ ImageTransformation imageTransformation =
+ buffer.appendRescaleGrayscaleIntensity(intensityRange.getMinLevel(),
+ intensityRange.getMaxLevel(), label);
+ imageTransformation.setDescription(OPTIMAL_DATASET_INTENSITY_RESCALING_DESCRIPTION);
+ boolean isDefault = simpleImageConfig.isComputeCommonIntensityRangeOfAllImagesDefault();
+ imageTransformation.setDefault(isDefault);
+ buffer.appendAll(channel.getAvailableTransformations());
+
+ channel.setAvailableTransformations(buffer.getTransformations());
+ }
+
+ private static List<File> chooseChannelImages(List<ImageFileInfo> images, File incomingDir,
+ String channelCode)
+ {
+ String normalizedChannelCode = CodeNormalizer.normalize(channelCode);
+ List<File> channelImages = new ArrayList<File>();
+ for (ImageFileInfo imageFileInfo : images)
+ {
+ String imageChannelCode = CodeNormalizer.normalize(imageFileInfo.getChannelCode());
+ if (imageChannelCode.equals(normalizedChannelCode))
+ {
+ channelImages.add(new File(incomingDir, imageFileInfo.getImageRelativePath()));
+ }
+ }
+ return channelImages;
+ }
+
+ private List<Channel> tryFindChannelsToComputeCommonIntensityRange(List<Channel> channels)
+ {
+ List<String> channelCodes =
+ simpleImageConfig.getComputeCommonIntensityRangeOfAllImagesForChannels();
+ if (channelCodes == null)
+ {
+ return null;
+ }
+ if (channelCodes.isEmpty())
+ {
+ return channels;
+ }
+
+ Set<String> channelCodesSet = createNormalizedCodesSet(channelCodes);
+ List<Channel> chosenChannels = new ArrayList<Channel>();
+ for (Channel channel : channels)
+ {
+ if (channelCodesSet.contains(channel.getCode()))
+ {
+ chosenChannels.add(channel);
+ }
+ }
+ return chosenChannels;
+ }
+
+ private static Set<String> createNormalizedCodesSet(Collection<String> channelCodes)
+ {
+ final Set<String> normalizedCodes = new HashSet<String>();
+ for (String code : channelCodes)
+ {
+ normalizedCodes.add(CodeNormalizer.normalize(code));
+ }
+ return normalizedCodes;
+ }
+
+ /**
+ * Computes common intensity range for a list of files.
+ *
+ * @return calculated levels or null if calculation couldn't succeed because some images where
+ * not in gray scale
+ */
+ public static Levels tryComputeCommonIntensityRange(IImageReader readerOrNull,
+ List<File> imageFiles, float threshold)
+ {
+ String libraryName = (readerOrNull == null) ? null : readerOrNull.getLibraryName();
+ String readerName = (readerOrNull == null) ? null : readerOrNull.getName();
+ PixelHistogram histogram = new PixelHistogram();
+
+ for (File imageFile : imageFiles)
+ {
+ List<ImageIdentifier> imageIdentifiers = getImageIdentifiers(readerOrNull, imageFile);
+ for (ImageIdentifier imageIdentifier : imageIdentifiers)
+ {
+ BufferedImage image =
+ loadUnchangedImage(imageFile, imageIdentifier, libraryName, readerName);
+ if (IntensityRescaling.isNotGrayscale(image))
+ {
+ operationLog
+ .warn(String
+ .format("Intensity range cannot be computed because image '%s' is not in grayscale.",
+ imageFile.getPath()));
+ return null;
+ }
+ IntensityRescaling.addToLevelStats(histogram, image);
+ }
+ }
+ return IntensityRescaling.computeLevels(histogram, threshold);
+ }
+
+ private static BufferedImage loadUnchangedImage(File imageFile,
+ ImageIdentifier imageIdentifier, String libraryName, String readerName)
+ {
+ String imageStringIdentifier = imageIdentifier.getUniqueStringIdentifier();
+ return ImageUtil.loadUnchangedImage(new FileBasedContentNode(imageFile),
+ imageStringIdentifier, libraryName, readerName, null);
+ }
+
+ // -------------------
+ /**
+ * Extracts all images from the incoming directory.
+ *
+ * @param incoming - folder with images
+ * @param dataset - here the result will be stored
+ */
+ protected void setImageDataset(File incoming, ImageDataSetInformation dataset)
+ {
+ dataset.setDatasetTypeCode(simpleImageConfig.getDataSetType());
+ dataset.setFileFormatCode(simpleImageConfig.getFileFormatType());
+ dataset.setMeasured(simpleImageConfig.isMeasuredData());
+
+ dataset.setSample(simpleImageConfig.getPlateSpace(), simpleImageConfig.getPlateCode());
+ dataset.setIncomingDirectory(incoming);
+
+ ImageDataSetStructure imageStruct = createImageDataSetStructure(incoming, dataset);
+ dataset.setImageDataSetStructure(imageStruct);
+ }
+
+ private ImageDataSetStructure createImageDataSetStructure(File incoming,
+ ImageDataSetInformation dataset)
+ {
+ 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
+ {
+ 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();
+ imageStruct.setImages(images);
+ imageStruct.setChannels(channels);
+ imageStruct.setTileGeometry(tileGeometry.getNumberOfRows(),
+ tileGeometry.getNumberOfColumns());
+
+ imageStruct.setImageStorageConfiguraton(simpleImageConfig.getImageStorageConfiguration());
+ return imageStruct;
+ }
+
+ private Geometry extractImageFileInfos(DataSetInformation dataset, List<ImageFileInfo> images,
+ List<Channel> channels)
+ {
+ IImagingReadonlyQueryDAO query = DssScreeningUtils.getQuery();
+
+ List<ImgImageDatasetDTO> containers =
+ DssScreeningUtils.getQuery().listImageDatasetsByPermId(
+ dataset.tryGetContainerDatasetPermId());
+
+ 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)
+ {
+ registrationDetails.setDataSetInformation(dataset);
+ registrationDetails.setFileFormatType(new FileFormatType(simpleImageConfig
+ .getFileFormatType()));
+ registrationDetails.setDataSetType(new DataSetType(simpleImageConfig.getDataSetType()));
+ registrationDetails.setMeasuredData(simpleImageConfig.isMeasuredData());
+
+ }
+
+}
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 f8dcf80438f4a7c533188bb834396409b56c114d..e1b839ff3e4b4b7c045ba01d236992906662e51f 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
@@ -44,7 +44,7 @@ import ch.systemsx.cisd.openbis.dss.etl.IImagingDatasetLoader;
import ch.systemsx.cisd.openbis.dss.etl.IImagingLoaderStrategy;
import ch.systemsx.cisd.openbis.dss.etl.ImagingLoaderStrategyFactory;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageTransfomationFactories;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ChannelColorRGB;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColorRGB;
import ch.systemsx.cisd.openbis.dss.generic.server.ResponseContentStream;
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.DatasetAcquiredImagesReference;
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.ImageChannelStackReference;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/plugins/jython/ScreeningJythonIngestionService.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/plugins/jython/ScreeningJythonIngestionService.java
index bc481d0ced2f016c9eb91b205c2be94ba3739978..0a9572465444efcd6ed03c09b65e2d10c5f81888 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/plugins/jython/ScreeningJythonIngestionService.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/plugins/jython/ScreeningJythonIngestionService.java
@@ -21,16 +21,15 @@ import java.util.Properties;
import ch.systemsx.cisd.common.action.IDelegatedActionWithResult;
import ch.systemsx.cisd.etlserver.registrator.DataSetFile;
-import ch.systemsx.cisd.etlserver.registrator.api.v1.impl.DataSetRegistrationTransaction;
-import ch.systemsx.cisd.etlserver.registrator.recovery.AutoRecoverySettings;
+import ch.systemsx.cisd.etlserver.registrator.api.v2.impl.DataSetRegistrationTransaction;
import ch.systemsx.cisd.etlserver.registrator.v2.AbstractOmniscientTopLevelDataSetRegistrator.NoOpDelegate;
import ch.systemsx.cisd.etlserver.registrator.v2.DataSetRegistrationService;
import ch.systemsx.cisd.etlserver.registrator.v2.IDataSetRegistrationDetailsFactory;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v2.IImagingDataSetRegistrationTransactionV2;
-import ch.systemsx.cisd.openbis.dss.etl.jython.ImagingDataSetRegistrationTransaction;
-import ch.systemsx.cisd.openbis.dss.etl.jython.JythonPlateDataSetHandlerUtils;
-import ch.systemsx.cisd.openbis.dss.etl.jython.JythonPlateDatasetFactory;
+import ch.systemsx.cisd.openbis.dss.etl.jython.v2.ImagingDataSetRegistrationTransaction;
import ch.systemsx.cisd.openbis.dss.etl.jython.v2.ImagingDataSetRegistrationTransactionV2Delegate;
+import ch.systemsx.cisd.openbis.dss.etl.jython.v2.JythonPlateDataSetHandlerUtils;
+import ch.systemsx.cisd.openbis.dss.etl.jython.v2.JythonPlateDatasetFactory;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.jython.IPluginScriptRunnerFactory;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.jython.JythonIngestionService;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
@@ -85,8 +84,7 @@ public class ScreeningJythonIngestionService extends JythonIngestionService
return new ImagingDataSetRegistrationTransaction(
rollBackStackParentFolder, workingDirectory, stagingDirectory,
this, factory,
- JythonPlateDataSetHandlerUtils.parseOriginalDir(properties),
- AutoRecoverySettings.DO_NOT_USE_AUTO_RECOVERY);
+ JythonPlateDataSetHandlerUtils.parseOriginalDir(properties));
}
};
return service;
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/ImagingChannelsCreatorTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/ImagingChannelsCreatorTest.java
index 56d2af34acc16f8836be81428ca1bb6f445e0b24..f36578d6ee2794ce36f6b8eec7288a3a80deb7b5 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/ImagingChannelsCreatorTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/ImagingChannelsCreatorTest.java
@@ -24,9 +24,9 @@ import org.testng.annotations.Test;
import ch.rinn.restrictions.Friend;
import ch.systemsx.cisd.openbis.dss.etl.ImagingDatabaseHelper.ImagingChannelsCreator;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.Channel;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ChannelColor;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ChannelColorRGB;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.Channel;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColor;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColorRGB;
/**
* Test of {@link ImagingChannelsCreator}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/TileGeometryOracleTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/TileGeometryOracleTest.java
index dce9f3dc262629200b9f46b120cdb16b5c2195f8..04b3f36289338c0b3d64f227c88003de24c22d60 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/TileGeometryOracleTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/TileGeometryOracleTest.java
@@ -23,7 +23,7 @@ import org.testng.AssertJUnit;
import org.testng.annotations.Test;
import ch.systemsx.cisd.common.geometry.SpatialPoint;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.Location;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.Location;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry;
/**
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/ImageMetadataExtractorTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/ImageMetadataExtractorTest.java
index fa199d9329e8d34d6f86b86fbb6618191941122e..b3db6c9f92cd08666167e338cc23ab4c265a919e 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/ImageMetadataExtractorTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/ImageMetadataExtractorTest.java
@@ -29,7 +29,7 @@ import org.testng.annotations.Test;
import com.csvreader.CsvReader;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.Location;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.Location;
/**
* @author Kaloyan Enimanev
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ChannelColorTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ChannelColorTest.java
index 9f14f9af3b0a3748c5b107cb9ad7941f51e35b8c..a1da1f2eeee26b70c229497d7a2263c25492b5d9 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ChannelColorTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ChannelColorTest.java
@@ -23,7 +23,7 @@ import org.testng.AssertJUnit;
import org.testng.annotations.Test;
import ch.systemsx.cisd.common.test.AssertionUtil;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ChannelColor;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColor;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelColor;
/**
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 68400f219919c41ed89bce0a50fd2e3dd06b63e1..f6e928b8217152bedfdb6a4ede5715a7f40939bf 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
@@ -33,7 +33,7 @@ import org.testng.annotations.Test;
import ch.systemsx.cisd.base.image.IImageTransformerFactory;
import ch.systemsx.cisd.common.test.AssertionUtil;
import ch.systemsx.cisd.hcs.Location;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ChannelColorRGB;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColorRGB;
import ch.systemsx.cisd.openbis.generic.shared.basic.CodeNormalizer;
import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ExampleImageTransformerFactory;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.AbstractDBTest;
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ChannelColorComponentTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/ChannelColorComponentTest.java
similarity index 91%
rename from screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ChannelColorComponentTest.java
rename to screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/ChannelColorComponentTest.java
index 963cb1aeb944f62388beee52dfb8b0d36c8c53ba..7385de4f751d2298280822cd16f869c37d72976a 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ChannelColorComponentTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/ChannelColorComponentTest.java
@@ -14,11 +14,11 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1;
+package ch.systemsx.cisd.openbis.dss.etl.dto.api;
import org.testng.annotations.Test;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ChannelColorComponent;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColorComponent;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ColorComponent;
/**
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/ConvertToolImageTransformerTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/transformations/ConvertToolImageTransformerTest.java
similarity index 93%
rename from screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/ConvertToolImageTransformerTest.java
rename to screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/transformations/ConvertToolImageTransformerTest.java
index 070d7de5ec82a56449ac325df7db1d5e1856becb..ecb3efca5bbae3eae841a9153283a6461f19bab5 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/ConvertToolImageTransformerTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/transformations/ConvertToolImageTransformerTest.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.transformations;
+package ch.systemsx.cisd.openbis.dss.etl.dto.api.transformations;
import java.awt.image.BufferedImage;
import java.io.File;
@@ -23,6 +23,7 @@ import org.testng.AssertJUnit;
import org.testng.annotations.Test;
import ch.systemsx.cisd.base.image.IImageTransformer;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.transformations.ConvertToolImageTransformerFactory;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtilTest;
/**
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/ImageTransformationBufferTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/transformations/ImageTransformationBufferTest.java
similarity index 89%
rename from screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/ImageTransformationBufferTest.java
rename to screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/transformations/ImageTransformationBufferTest.java
index f0acbf746fa547850d87d4431a9aecf311869477..25ffe09e40151eda924d32a28a8b1aaa9497632c 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/ImageTransformationBufferTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/transformations/ImageTransformationBufferTest.java
@@ -14,12 +14,13 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.transformations;
+package ch.systemsx.cisd.openbis.dss.etl.dto.api.transformations;
import org.testng.AssertJUnit;
import org.testng.annotations.Test;
import ch.rinn.restrictions.Friend;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.transformations.ImageTransformationBuffer;
/**
* Test of {@link ImageTransformationBuffer}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/jython/FeatureVectorContainerDataSetTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/jython/v1/FeatureVectorContainerDataSetTest.java
similarity index 92%
rename from screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/jython/FeatureVectorContainerDataSetTest.java
rename to screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/jython/v1/FeatureVectorContainerDataSetTest.java
index ad86354329499324b0ae667cf8a58030d6954589..cc91242711051faa0d03e78c676234b7357ce38b 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/jython/FeatureVectorContainerDataSetTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/jython/v1/FeatureVectorContainerDataSetTest.java
@@ -14,13 +14,13 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.etl.jython;
+package ch.systemsx.cisd.openbis.dss.etl.jython.v1;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeatureVectorContainerDataSet;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.impl.FeatureVectorContainerDataSet;
/**
* @author Jakub Straszewski
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/jython/SimpleImageDataSetRegistratorTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/jython/v1/SimpleImageDataSetRegistratorTest.java
similarity index 96%
rename from screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/jython/SimpleImageDataSetRegistratorTest.java
rename to screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/jython/v1/SimpleImageDataSetRegistratorTest.java
index 218bcaaa4f95bd3a3d0781458956637a4344dbd9..334fac275d8e3d9a6138dba0337ce078d9e9ae75 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/jython/SimpleImageDataSetRegistratorTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/jython/v1/SimpleImageDataSetRegistratorTest.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.etl.jython;
+package ch.systemsx.cisd.openbis.dss.etl.jython.v1;
import java.io.File;
import java.util.Arrays;
@@ -33,13 +33,13 @@ import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationDetails;
import ch.systemsx.cisd.etlserver.registrator.v1.IDataSetRegistrationDetailsFactory;
import ch.systemsx.cisd.imagereaders.IImageReader;
import ch.systemsx.cisd.imagereaders.ImageID;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.Channel;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColor;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageFileInfo;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.SimpleImageContainerDataConfig;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ImageDataSetInformation;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.Channel;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ChannelColor;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageFileInfo;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.SimpleImageContainerDataConfig;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.transformations.IntensityRangeImageTransformerFactory;
-import ch.systemsx.cisd.openbis.dss.etl.jython.SimpleImageDataSetRegistrator.IImageReaderFactory;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.transformations.IntensityRangeImageTransformerFactory;
+import ch.systemsx.cisd.openbis.dss.etl.jython.v1.SimpleImageDataSetRegistrator.IImageReaderFactory;
/**
* @author Franz-Josef Elmer
@@ -252,8 +252,7 @@ public class SimpleImageDataSetRegistratorTest extends AbstractFileSystemTestCas
configData.setImageLibrary("MyLibrary");
assertFalse(configData.isFixedIntensityRangeForAllImagesDefined());
configData.setDefaultFixedIntensityRangeForAllImages(99, 1001);
- configData.addFixedIntensityRangeForAllImages("channel-4", 51,
- 1017);
+ configData.addFixedIntensityRangeForAllImages("channel-4", 51, 1017);
assertTrue(configData.isFixedIntensityRangeForAllImagesDefined());
DataSetRegistrationDetails<ImageDataSetInformation> actualDetails =
SimpleImageDataSetRegistrator.createImageDatasetDetails(configData, incoming,
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 59837cb8769828d332be3b18f486ceb60e4131d9..ceac2fb6ed1281fd3d4483b6d0375af8deb60e68 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
@@ -46,7 +46,7 @@ import ch.systemsx.cisd.openbis.dss.etl.AbsoluteImageReference;
import ch.systemsx.cisd.openbis.dss.etl.IImagingDatasetLoader;
import ch.systemsx.cisd.openbis.dss.etl.ImagingLoaderStrategyFactory;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageTransfomationFactories;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ChannelColorRGB;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColorRGB;
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.DatasetAcquiredImagesReference;
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.ImageChannelStackReference;
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.ImageTransformationParams;
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 cbc2f8a27ac41fd13e0ff36a4b1088a30984613d..580e746d64afca3a7ac9bdd24b421c964b87100e 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
@@ -55,7 +55,7 @@ import ch.systemsx.cisd.hcs.Location;
import ch.systemsx.cisd.openbis.dss.etl.AbsoluteImageReference;
import ch.systemsx.cisd.openbis.dss.etl.IImagingDatasetLoader;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageTransfomationFactories;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ChannelColorRGB;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColorRGB;
import ch.systemsx.cisd.openbis.dss.generic.server.DatasetSessionAuthorizer;
import ch.systemsx.cisd.openbis.dss.generic.server.DssServiceRpcAuthorizationAdvisor;
import ch.systemsx.cisd.openbis.dss.generic.server.DssServiceRpcAuthorizationAdvisor.DssServiceRpcAuthorizationMethodInterceptor;
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/plugins/jython/ScreeningJythonBasedAggregationServiceReportingPluginTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/plugins/jython/ScreeningJythonBasedAggregationServiceReportingPluginTest.java
index eea0a932da28e6df424f89b06615f3d94bc35572..fa39be1827a104d1fc98cac46de3a87a4a948136 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/plugins/jython/ScreeningJythonBasedAggregationServiceReportingPluginTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/plugins/jython/ScreeningJythonBasedAggregationServiceReportingPluginTest.java
@@ -32,9 +32,9 @@ import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.jython.JythonBasedAggregationServiceReportingPluginTest.ParametersBuilder;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.IReportingPluginTask;
import ch.systemsx.cisd.openbis.dss.generic.shared.DataSetProcessingContext;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IDataSourceQueryService;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.ISearchService;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.authorization.IAuthorizationService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.IDataSourceQueryService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISearchService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.authorization.IAuthorizationService;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ExperimentIdentifier;