From 89fd557ff9de287113300b4da13d9a20c359a9c4 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Wed, 4 Jan 2012 10:06:14 +0000
Subject: [PATCH] LMS-2735 client API and facade clean up. Unit tests for new
functionality.
SVN: 24089
---
.../server/DssServiceRpcScreening.java | 163 ++++++++++--------
.../server/DssServiceRpcScreeningLogger.java | 22 +--
.../ImageRepresentationFormatFinder.java | 56 ++++++
.../server/logic/SimpleImageSetMetaData.java | 73 --------
.../server/logic/ZoomLevelFinder.java | 68 --------
.../api/v1/IDssServiceRpcScreening.java | 56 +++---
.../v1/IScreeningOpenbisServiceFacade.java | 44 +++--
.../api/v1/ScreeningOpenbisServiceFacade.java | 46 ++---
... => AbstractFormatSelectionCriterion.java} | 27 +--
.../api/v1/dto/ColorDepthCriterion.java | 10 +-
.../shared/api/v1/dto/FileTypeCriterion.java | 10 +-
...presentationFormatSelectionCriterion.java} | 13 +-
.../shared/api/v1/dto/IImageSetMetaData.java | 55 ------
.../api/v1/dto/ImageMetaDataIdCriterion.java | 42 -----
.../api/v1/dto/ImageRepresentationFormat.java | 26 ++-
.../shared/api/v1/dto/OriginalCriterion.java | 12 +-
.../shared/api/v1/dto/SizeCriterion.java | 119 +++++++------
.../basic/dto/ImageDatasetParameters.java | 13 --
.../shared/imaging/HCSDatasetLoader.java | 25 ---
.../server/DssServiceRpcScreeningTest.java | 152 +++++++++++++---
.../shared/api/v1/dto/SizeCriterionTest.java | 91 ++++++++++
21 files changed, 597 insertions(+), 526 deletions(-)
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/logic/ImageRepresentationFormatFinder.java
delete mode 100644 screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/logic/SimpleImageSetMetaData.java
delete mode 100644 screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/logic/ZoomLevelFinder.java
rename screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/{AbstractImageSelectionCriterion.java => AbstractFormatSelectionCriterion.java} (52%)
rename screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/{IImageSetSelectionCriterion.java => IImageRepresentationFormatSelectionCriterion.java} (64%)
delete mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/IImageSetMetaData.java
delete mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageMetaDataIdCriterion.java
create mode 100644 screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/SizeCriterionTest.java
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
index 72dc83707a7..fae3a3acc04 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
@@ -58,14 +58,14 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.IHierarchicalContentProvider;
import ch.systemsx.cisd.openbis.dss.generic.shared.IShareIdManager;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
-import ch.systemsx.cisd.openbis.dss.screening.server.logic.SimpleImageSetMetaData;
-import ch.systemsx.cisd.openbis.dss.screening.server.logic.ZoomLevelFinder;
+import ch.systemsx.cisd.openbis.dss.screening.server.logic.ImageRepresentationFormatFinder;
import ch.systemsx.cisd.openbis.dss.screening.shared.api.v1.IDssServiceRpcScreening;
import ch.systemsx.cisd.openbis.dss.screening.shared.api.v1.LoadImageConfiguration;
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.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.AbstractFormatSelectionCriterion;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetImageRepresentationFormats;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureInformation;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVector;
@@ -76,8 +76,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVector
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IDatasetIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IFeatureVectorDatasetIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IImageDatasetIdentifier;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IImageSetMetaData;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IImageSetSelectionCriterion;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IImageRepresentationFormatSelectionCriterion;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageChannel;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetMetadata;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageRepresentationFormat;
@@ -88,7 +87,6 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateImageRef
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.FeatureValue;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageDatasetParameters;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageSetMetaData;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.InternalImageChannel;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.InternalImageTransformationInfo;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
@@ -245,25 +243,6 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
}
}
- public List<Set<IImageSetMetaData>> listImageSetsMetadata(String sessionToken,
- List<? extends IImageDatasetIdentifier> imageDatasets)
- {
- List<Set<IImageSetMetaData>> sets = new ArrayList<Set<IImageSetMetaData>>();
- for (IImageDatasetIdentifier dataSet : imageDatasets)
- {
- String datasetCode = dataSet.getDatasetCode();
- IImagingDatasetLoader loader = createImageLoader(datasetCode);
- List<ImageSetMetaData> zoomLevels = loader.getImageParameters().getZoomLevels();
- Set<IImageSetMetaData> set = new HashSet<IImageSetMetaData>();
- for (ImageSetMetaData zoomLevel : zoomLevels)
- {
- set.add(new SimpleImageSetMetaData(zoomLevel));
- }
- sets.add(set);
- }
- return sets;
- }
-
private ImageDatasetMetadata extractImageMetadata(IImageDatasetIdentifier dataset,
IHierarchicalContent content)
{
@@ -537,41 +516,69 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
configuration.isOpenBisImageTransformationApplied(), imageLoadersMap);
}
+ public InputStream loadImages(String sessionToken, List<PlateImageReference> imageReferences,
+ final ImageRepresentationFormat format)
+ {
+ for (PlateImageReference plateImageReference : imageReferences)
+ {
+ if (plateImageReference.getDatasetCode().equals(format.getDataSetCode()) == false)
+ {
+ throw new UserFailureException(
+ "At least for one plate image reference the image representation format "
+ + "is unknown: Plate image reference: " + plateImageReference
+ + ", format: " + format);
+ }
+ }
+ IImageRepresentationFormatSelectionCriterion criterion =
+ new AbstractFormatSelectionCriterion()
+ {
+ private static final long serialVersionUID = 1L;
+
+ @Override
+ protected boolean accept(ImageRepresentationFormat availableFormat)
+ {
+ return format.getId() == availableFormat.getId();
+ }
+ };
+ return loadImages(sessionToken, imageReferences, criterion);
+ }
public InputStream loadImages(String sessionToken, List<PlateImageReference> imageReferences,
- IImageSetSelectionCriterion... criteria)
+ IImageRepresentationFormatSelectionCriterion... criteria)
{
- ZoomLevelFinder finder = new ZoomLevelFinder(criteria);
final Map<String, IImagingDatasetLoader> imageLoadersMap =
getImageDatasetsMap(sessionToken, imageReferences);
- Map<String, ImageSetMetaData> dataSetToZoomLevelMap = new HashMap<String, ImageSetMetaData>();
- for (Entry<String, IImagingDatasetLoader> entry : imageLoadersMap.entrySet())
+ Map<String, ImgImageDatasetDTO> imageDataSetMap =
+ createDataSetCodeToImageDataSetMap(imageReferences);
+ ImageRepresentationFormatFinder finder = new ImageRepresentationFormatFinder(criteria);
+ Map<String, ImageRepresentationFormat> dataSetToImageReferenceFormatMap =
+ new HashMap<String, ImageRepresentationFormat>();
+ for (Entry<String, ImgImageDatasetDTO> entry : imageDataSetMap.entrySet())
{
String dataSetCode = entry.getKey();
- IImagingDatasetLoader loader = entry.getValue();
- ImageDatasetParameters imageParameters = loader.getImageParameters();
- List<ImageSetMetaData> filteredZoomLevels =
- finder.find(imageParameters.getZoomLevels());
- if (filteredZoomLevels.isEmpty())
+ List<ImageRepresentationFormat> filteredFormats =
+ finder.find(getImageRepresentationFormats(entry.getValue()));
+ if (filteredFormats.isEmpty())
{
- throw new UserFailureException("No image set fitting criteria found for data set "
- + dataSetCode + ".");
+ throw new UserFailureException(
+ "No image representation format fitting criteria found for data set "
+ + dataSetCode + ".");
}
- if (filteredZoomLevels.size() > 1)
+ if (filteredFormats.size() > 1)
{
- throw new UserFailureException("To many image sets fitting criteria for data set "
- + dataSetCode + ": " + filteredZoomLevels);
+ throw new UserFailureException(
+ "To many image representation formats fitting criteria for data set "
+ + dataSetCode + ": " + filteredFormats);
}
- dataSetToZoomLevelMap.put(dataSetCode, filteredZoomLevels.get(0));
+ dataSetToImageReferenceFormatMap.put(dataSetCode, filteredFormats.get(0));
}
- List<IHierarchicalContentNode> imageContents =
- new ArrayList<IHierarchicalContentNode>();
+ List<IHierarchicalContentNode> imageContents = new ArrayList<IHierarchicalContentNode>();
for (PlateImageReference imageReference : imageReferences)
{
String datasetCode = imageReference.getDatasetCode();
IImagingDatasetLoader loader = imageLoadersMap.get(datasetCode);
- ImageSetMetaData zoomLevel = dataSetToZoomLevelMap.get(datasetCode);
- Size size = new Size(zoomLevel.getWidth(), zoomLevel.getHeight());
+ ImageRepresentationFormat format = dataSetToImageReferenceFormatMap.get(datasetCode);
+ Size size = new Size(format.getWidth(), format.getHeight());
addImageContentTo(imageContents, loader, imageReference, size, null, false, false);
}
return new ConcatenatedContentInputStream(true, imageContents);
@@ -791,59 +798,71 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
public List<DatasetImageRepresentationFormats> listAvailableImageRepresentationFormats(
String sessionToken, List<? extends IDatasetIdentifier> imageDatasets)
{
- IImagingReadonlyQueryDAO queryInterface = getDAO();
ArrayList<DatasetImageRepresentationFormats> result =
new ArrayList<DatasetImageRepresentationFormats>(imageDatasets.size());
- // Get the database identifiers for the data sets
- String[] permIds = new String[imageDatasets.size()];
- for (int i = 0; i < imageDatasets.size(); ++i)
- {
- permIds[i] = imageDatasets.get(i).getPermId();
- }
- List<ImgImageDatasetDTO> primImageDatasets =
- queryInterface.listImageDatasetsByPermId(permIds);
-
- // Convert this to a hash map for faster indexing
- HashMap<String, ImgImageDatasetDTO> imageDataSetMap =
- new HashMap<String, ImgImageDatasetDTO>();
- for (ImgImageDatasetDTO primImageDataSet : primImageDatasets)
- {
- imageDataSetMap.put(primImageDataSet.getPermId(), primImageDataSet);
- }
+ Map<String, ImgImageDatasetDTO> imageDataSetMap =
+ createDataSetCodeToImageDataSetMap(imageDatasets);
// Not an efficient way to execute this query, but it reuses the queries at our disposal
for (IDatasetIdentifier imageDataset : imageDatasets)
{
- ImgImageDatasetDTO primImageDataSet = imageDataSetMap.get(imageDataset.getPermId());
+ String dataSetCode = imageDataset.getPermId();
+ ImgImageDatasetDTO primImageDataSet = imageDataSetMap.get(dataSetCode);
if (null == primImageDataSet)
{
List<ImageRepresentationFormat> emptyList = Collections.emptyList();
DatasetImageRepresentationFormats datasetResult =
new DatasetImageRepresentationFormats(imageDataset, emptyList);
result.add(datasetResult);
- continue;
+ } else
+ {
+ List<ImageRepresentationFormat> formats =
+ getImageRepresentationFormats(primImageDataSet);
+ DatasetImageRepresentationFormats datasetResult =
+ new DatasetImageRepresentationFormats(imageDataset, formats);
+ result.add(datasetResult);
}
- List<ImgImageZoomLevelDTO> zoomLevels =
- queryInterface.listImageZoomLevels(primImageDataSet.getId());
- List<ImageRepresentationFormat> formats =
- convertZoomLevelsToRepresentationFormats(zoomLevels);
- DatasetImageRepresentationFormats datasetResult =
- new DatasetImageRepresentationFormats(imageDataset, formats);
- result.add(datasetResult);
}
return result;
}
+ private List<ImageRepresentationFormat> getImageRepresentationFormats(ImgImageDatasetDTO imageDataSet)
+ {
+ List<ImgImageZoomLevelDTO> zoomLevels = getDAO().listImageZoomLevels(imageDataSet.getId());
+ return convertZoomLevelsToRepresentationFormats(imageDataSet.getPermId(), zoomLevels);
+ }
+
+ private Map<String, ImgImageDatasetDTO> createDataSetCodeToImageDataSetMap(
+ List<? extends IDatasetIdentifier> imageDatasets)
+ {
+ Set<String> permIds = new HashSet<String>();
+ for (IDatasetIdentifier identifier : imageDatasets)
+ {
+ permIds.add(identifier.getPermId());
+ }
+ List<ImgImageDatasetDTO> primImageDatasets =
+ getDAO().listImageDatasetsByPermId(permIds.toArray(new String[permIds.size()]));
+
+ // Convert this to a hash map for faster indexing
+ HashMap<String, ImgImageDatasetDTO> imageDataSetMap =
+ new HashMap<String, ImgImageDatasetDTO>();
+ for (ImgImageDatasetDTO primImageDataSet : primImageDatasets)
+ {
+ imageDataSetMap.put(primImageDataSet.getPermId(), primImageDataSet);
+ }
+ return imageDataSetMap;
+ }
+
private List<ImageRepresentationFormat> convertZoomLevelsToRepresentationFormats(
- List<ImgImageZoomLevelDTO> zoomLevels)
+ String dataSetCode, List<ImgImageZoomLevelDTO> zoomLevels)
{
ArrayList<ImageRepresentationFormat> results = new ArrayList<ImageRepresentationFormat>();
for (ImgImageZoomLevelDTO zoomLevel : zoomLevels)
{
ImageRepresentationFormat result =
- new ImageRepresentationFormat(zoomLevel.getIsOriginal(), zoomLevel.getWidth(),
- zoomLevel.getHeight(), zoomLevel.getColorDepth(),
+ new ImageRepresentationFormat(dataSetCode, zoomLevel.getId(), zoomLevel.getIsOriginal(),
+ zoomLevel.getWidth(), zoomLevel.getHeight(), zoomLevel.getColorDepth(),
zoomLevel.getFileType());
results.add(result);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningLogger.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningLogger.java
index 0573ed63ad5..3022f6bafbe 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningLogger.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningLogger.java
@@ -19,7 +19,6 @@ package ch.systemsx.cisd.openbis.dss.screening.server;
import java.io.InputStream;
import java.util.Arrays;
import java.util.List;
-import java.util.Set;
import ch.systemsx.cisd.base.image.IImageTransformerFactory;
import ch.systemsx.cisd.common.spring.IInvocationLoggerContext;
@@ -35,9 +34,9 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVector
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IDatasetIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IFeatureVectorDatasetIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IImageDatasetIdentifier;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IImageSetMetaData;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IImageSetSelectionCriterion;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IImageRepresentationFormatSelectionCriterion;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetMetadata;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageRepresentationFormat;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageSize;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.MicroscopyImageReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateImageReference;
@@ -202,13 +201,6 @@ public class DssServiceRpcScreeningLogger extends AbstractServerLogger implement
return null;
}
- public List<Set<IImageSetMetaData>> listImageSetsMetadata(String sessionToken,
- List<? extends IImageDatasetIdentifier> imageDatasets)
- {
- logAccess(sessionToken, "load_image_sets_metadata", "DATA_SETS(%s)", imageDatasets);
- return null;
- }
-
public void checkDatasetsAuthorizationForIDatasetIdentifier(String sessionToken,
List<? extends IDatasetIdentifier> featureDatasets)
{
@@ -248,7 +240,15 @@ public class DssServiceRpcScreeningLogger extends AbstractServerLogger implement
}
public InputStream loadImages(String sessionToken, List<PlateImageReference> imageReferences,
- IImageSetSelectionCriterion... criteria)
+ ImageRepresentationFormat format)
+ {
+ logAccess(sessionToken, "load_images", "IMAGE_REFERENCES(%s) FORMAT(%s)", imageReferences,
+ format);
+ return null;
+ }
+
+ public InputStream loadImages(String sessionToken, List<PlateImageReference> imageReferences,
+ IImageRepresentationFormatSelectionCriterion... criteria)
{
logAccess(sessionToken, "load_images", "IMAGE_REFERENCES(%s) CRITERIA(%s)",
imageReferences, Arrays.asList(criteria));
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/logic/ImageRepresentationFormatFinder.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/logic/ImageRepresentationFormatFinder.java
new file mode 100644
index 00000000000..9605ee80536
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/logic/ImageRepresentationFormatFinder.java
@@ -0,0 +1,56 @@
+/*
+ * 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.screening.server.logic;
+
+import java.util.List;
+
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IImageRepresentationFormatSelectionCriterion;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageRepresentationFormat;
+
+/**
+ * Find {@link ImageRepresentationFormat} instances which fulfill some criteria.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class ImageRepresentationFormatFinder
+{
+ private final IImageRepresentationFormatSelectionCriterion[] criteria;
+
+ public ImageRepresentationFormatFinder(IImageRepresentationFormatSelectionCriterion... criteria)
+ {
+ if (criteria == null || criteria.length == 0)
+ {
+ throw new UserFailureException("No criterion specified.");
+ }
+ this.criteria = criteria;
+ }
+
+ public List<ImageRepresentationFormat> find(List<ImageRepresentationFormat> formats)
+ {
+ List<ImageRepresentationFormat> filteredFormats = formats;
+ for (IImageRepresentationFormatSelectionCriterion criterion : criteria)
+ {
+ filteredFormats = criterion.getMatching(filteredFormats);
+ if (filteredFormats.size() == 1)
+ {
+ break;
+ }
+ }
+ return filteredFormats;
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/logic/SimpleImageSetMetaData.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/logic/SimpleImageSetMetaData.java
deleted file mode 100644
index faf8a8b4184..00000000000
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/logic/SimpleImageSetMetaData.java
+++ /dev/null
@@ -1,73 +0,0 @@
-/*
- * 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.screening.server.logic;
-
-import java.io.Serializable;
-
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IImageSetMetaData;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageSetMetaData;
-
-/**
- * Implementation of {@link IImageSetMetaData} which wraps a {@link ImageSetMetaData}.
- *
- * @author Franz-Josef Elmer
- */
-public class SimpleImageSetMetaData implements IImageSetMetaData, Serializable
-{
- private static final long serialVersionUID = 1L;
-
- private final Geometry size;
- private final ImageSetMetaData metaData;
-
- public SimpleImageSetMetaData(ImageSetMetaData zoomLevel)
- {
- this.metaData = zoomLevel;
- size = Geometry.createFromCartesianDimensions(zoomLevel.getWidth(), zoomLevel.getHeight());
- }
-
- public ImageSetMetaData getMetaData()
- {
- return metaData;
- }
-
- public long getId()
- {
- return metaData.getId();
- }
-
- public boolean isOriginal()
- {
- return metaData.isOriginal();
- }
-
- public Geometry getSize()
- {
- return size;
- }
-
- public Integer getColorDepth()
- {
- return metaData.getColorDepth();
- }
-
- public String getFileType()
- {
- return metaData.getFileType();
- }
-
-}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/logic/ZoomLevelFinder.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/logic/ZoomLevelFinder.java
deleted file mode 100644
index 0aed5879119..00000000000
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/logic/ZoomLevelFinder.java
+++ /dev/null
@@ -1,68 +0,0 @@
-/*
- * 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.screening.server.logic;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IImageSetMetaData;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IImageSetSelectionCriterion;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageSetMetaData;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgImageZoomLevelDTO;
-
-/**
- * Find {@link ImgImageZoomLevelDTO} instances which fulfill some criteria.
- *
- * @author Franz-Josef Elmer
- */
-public class ZoomLevelFinder
-{
- private final IImageSetSelectionCriterion[] criteria;
-
- public ZoomLevelFinder(IImageSetSelectionCriterion... criteria)
- {
- this.criteria = criteria;
- }
-
- public List<ImageSetMetaData> find(List<ImageSetMetaData> zoomLevels)
- {
- List<ImageSetMetaData> filteredLevels = zoomLevels;
- for (IImageSetSelectionCriterion criterion : criteria)
- {
- if (filteredLevels.size() == 1)
- {
- break;
- }
- List<IImageSetMetaData> adaptedFilteredLevels = new ArrayList<IImageSetMetaData>();
- for (ImageSetMetaData level : filteredLevels)
- {
- adaptedFilteredLevels.add(new SimpleImageSetMetaData(level));
- }
- adaptedFilteredLevels = criterion.getMatching(adaptedFilteredLevels);
- filteredLevels = new ArrayList<ImageSetMetaData>();
- for (IImageSetMetaData adaptedFilteredLevel : adaptedFilteredLevels)
- {
- if (adaptedFilteredLevel instanceof SimpleImageSetMetaData)
- {
- filteredLevels.add(((SimpleImageSetMetaData) adaptedFilteredLevel)
- .getMetaData());
- }
- }
- }
- return filteredLevels;
- }
-}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/shared/api/v1/IDssServiceRpcScreening.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/shared/api/v1/IDssServiceRpcScreening.java
index 4f887d5b66a..b1c0ab7d94d 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/shared/api/v1/IDssServiceRpcScreening.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/shared/api/v1/IDssServiceRpcScreening.java
@@ -18,7 +18,6 @@ package ch.systemsx.cisd.openbis.dss.screening.shared.api.v1;
import java.io.InputStream;
import java.util.List;
-import java.util.Set;
import ch.systemsx.cisd.base.image.IImageTransformerFactory;
import ch.systemsx.cisd.common.api.IRpcService;
@@ -38,9 +37,9 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVector
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IDatasetIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IFeatureVectorDatasetIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IImageDatasetIdentifier;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IImageSetMetaData;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IImageSetSelectionCriterion;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IImageRepresentationFormatSelectionCriterion;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetMetadata;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageRepresentationFormat;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageSize;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.MicroscopyImageReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateImageReference;
@@ -267,21 +266,42 @@ public interface IDssServiceRpcScreening extends IRpcService
/**
* Provides images for the specified list of image references (specified by data set code, well
- * position, channel and tile) and image selection criteria. These criteria are applied to the
- * {@link IImageSetMetaData} sets of each data set. Beside of the set of original images a data
- * set can have other image sets like thumbnails of various sizes. The provided array of
- * {@link IImageSetSelectionCriterion} are applied one after another onto the set of
- * {@link IImageSetMetaData} until its size is reduced to one.
+ * position, channel and tile) and specified image representation format. The
+ * {@link ImageRepresentationFormat} argument should be an object returned by
+ * {@link #listAvailableImageRepresentationFormats(String, List)}. This method assumes that all
+ * image references belong to the same data set which has image representations of specified
+ * format.
*
- * @throws UserFailureException if for one data set the filtered {@link IImageSetMetaData} set
- * has size zero or greater than one.
+ * @throws UserFailureException if the specified format refers to an image representations
+ * unknown by at least one plate image reference.
+ * @since 1.10
*/
@MinimalMinorVersion(10)
@DataSetAccessGuard
public InputStream loadImages(String sessionToken,
@AuthorizationGuard(guardClass = DatasetIdentifierPredicate.class)
- List<PlateImageReference> imageReferences, IImageSetSelectionCriterion... criteria);
+ List<PlateImageReference> imageReferences, ImageRepresentationFormat format);
+ /**
+ * Provides images for the specified list of image references (specified by data set code, well
+ * position, channel and tile) and image selection criteria. These criteria are applied to the
+ * {@link ImageRepresentationFormat} sets of each data set. Beside of the set of original images
+ * a data set can have other image representations like thumbnails of various sizes. The
+ * provided array of {@link IImageRepresentationFormatSelectionCriterion} are applied one after
+ * another onto the set of {@link ImageRepresentationFormat} until its size is reduced to one.
+ *
+ * @throws UserFailureException if no criterion has been specified (i.e. <code>criteria</code>
+ * is an empty array) or if for at least one data set the filtered
+ * {@link ImageRepresentationFormat} set has size zero or greater than one.
+ * @since 1.10
+ */
+ @MinimalMinorVersion(10)
+ @DataSetAccessGuard
+ public InputStream loadImages(String sessionToken,
+ @AuthorizationGuard(guardClass = DatasetIdentifierPredicate.class)
+ List<PlateImageReference> imageReferences,
+ IImageRepresentationFormatSelectionCriterion... criteria);
+
/**
* Provide thumbnail images for specified microscopy data set. If no thumbnails are stored on
* the server, this method will return an empty stream. Images of all tiles are delivered.
@@ -384,21 +404,11 @@ public interface IDssServiceRpcScreening extends IRpcService
List<? extends IImageDatasetIdentifier> imageDatasets);
/**
- * Returns for each of the specified image data sets the meta data of available image sets.
- *
- * @since 1.10
- */
- @MinimalMinorVersion(10)
- @DataSetAccessGuard
- public List<Set<IImageSetMetaData>> listImageSetsMetadata(String sessionToken,
- @AuthorizationGuard(guardClass = DatasetIdentifierPredicate.class)
- List<? extends IImageDatasetIdentifier> imageDatasets);
-
- /**
- * Return image representation formats available for the specified image datasets.
+ * Return image representation formats available for the specified image data sets.
*
* @param imageDatasets The image data sets for which the representation formats are requested.
* @return A list with one entry for each in <b>imageDatasets</b>.
+ * @since 1.10
*/
@MinimalMinorVersion(10)
@DataSetAccessGuard
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/IScreeningOpenbisServiceFacade.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/IScreeningOpenbisServiceFacade.java
index 98aa555ea67..e5d8f0c887a 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/IScreeningOpenbisServiceFacade.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/IScreeningOpenbisServiceFacade.java
@@ -20,7 +20,6 @@ import java.io.File;
import java.io.IOException;
import java.util.List;
import java.util.Map;
-import java.util.Set;
import ch.systemsx.cisd.base.image.IImageTransformerFactory;
import ch.systemsx.cisd.common.api.retry.Retry;
@@ -44,10 +43,10 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVector
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IDatasetIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IFeatureVectorDatasetIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IImageDatasetIdentifier;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IImageSetMetaData;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IImageSetSelectionCriterion;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IImageRepresentationFormatSelectionCriterion;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetMetadata;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageRepresentationFormat;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageSize;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.MaterialIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.MaterialTypeIdentifier;
@@ -770,20 +769,36 @@ public interface IScreeningOpenbisServiceFacade
/**
* Provides images for the specified list of image references (specified by data set code, well
- * position, channel and tile) and image selection criteria. These criteria are applied to the
- * {@link IImageSetMetaData} sets of each data set. Beside of the set of original images a data
- * set can have other image sets like thumbnails of various sizes. The provided array of
- * {@link IImageSetSelectionCriterion} are applied one after another onto the set of
- * {@link IImageSetMetaData} until its size is reduced to one.
+ * position, channel and tile) and specified image representation format. The
+ * {@link ImageRepresentationFormat} argument should be an object returned by
+ * {@link #listAvailableImageRepresentationFormats(List)}. This method assumes that all image
+ * references belong to the same data set which has image representations of specified format.
*
* @param plateImageHandler Handler for the delivered images.
- * @throws UserFailureException if for one data set the filtered {@link IImageSetMetaData} set
- * has size zero or greater than one.
+ * @throws UserFailureException if the specified format refers to an image representations
+ * unknown by at least one plate image reference.
*/
public void loadImages(List<PlateImageReference> imageReferences,
- IPlateImageHandler plateImageHandler, IImageSetSelectionCriterion... criteria)
+ IPlateImageHandler plateImageHandler, ImageRepresentationFormat format)
throws IOException;
+ /**
+ * Provides images for the specified list of image references (specified by data set code, well
+ * position, channel and tile) and image selection criteria. These criteria are applied to the
+ * {@link ImageRepresentationFormat} sets of each data set. Beside of the set of original images
+ * a data set can have other image representations like thumbnails of various sizes. The
+ * provided array of {@link IImageRepresentationFormatSelectionCriterion} are applied one after
+ * another onto the set of {@link ImageRepresentationFormat} until its size is reduced to one.
+ *
+ * @param plateImageHandler Handler for the delivered images.
+ * @throws UserFailureException if no criterion has been specified (i.e. <code>criteria</code>
+ * is an empty array) or if for at least one data set the filtered
+ * {@link ImageRepresentationFormat} set has size zero or greater than one.
+ */
+ public void loadImages(List<PlateImageReference> imageReferences,
+ IPlateImageHandler plateImageHandler,
+ IImageRepresentationFormatSelectionCriterion... criteria) throws IOException;
+
/**
* Loads the PNG-encoded image for the specified <var>imageReference</var>.
* <p>
@@ -852,13 +867,6 @@ public interface IScreeningOpenbisServiceFacade
public List<ImageDatasetMetadata> listImageMetadata(
List<? extends IImageDatasetIdentifier> imageDatasets);
- /**
- * Returns for each of the specified image data sets the meta data of available image sets.
- */
- @Retry
- public List<Set<IImageSetMetaData>> listImageSetsMetadata(
- List<? extends IImageDatasetIdentifier> imageDatasets);
-
/**
* For a given list of <var>plates</var>, return the mapping of plate wells to materials
* contained in each well.
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java
index dc796a8cd0d..6e78202370a 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java
@@ -70,10 +70,10 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IDatasetIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IFeatureVectorDatasetIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IImageDatasetIdentifier;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IImageSetMetaData;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IImageSetSelectionCriterion;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IImageRepresentationFormatSelectionCriterion;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetMetadata;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageRepresentationFormat;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageSize;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.MaterialIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.MaterialTypeIdentifier;
@@ -1609,24 +1609,6 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
return result;
}
- public List<Set<IImageSetMetaData>> listImageSetsMetadata(
- List<? extends IImageDatasetIdentifier> imageDatasets)
- {
- final List<Set<IImageSetMetaData>> list = new ArrayList<Set<IImageSetMetaData>>();
- metaDataMultiplexer.process(imageDatasets, new IReferenceHandler<IImageDatasetIdentifier>()
- {
- public void handle(DssServiceRpcScreeningHolder dssService,
- List<IImageDatasetIdentifier> references)
- {
- checkDSSMinimalMinorVersion(dssService, "listImageSetsMetadata", List.class);
- List<Set<IImageSetMetaData>> sets =
- dssService.getService().listImageSetsMetadata(sessionToken, references);
- list.addAll(sets);
- }
- });
- return list;
- }
-
public List<PlateWellMaterialMapping> listPlateMaterialMapping(
List<? extends PlateIdentifier> plates,
MaterialTypeIdentifier materialTypeIdentifierOrNull)
@@ -1833,9 +1815,29 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
});
}
+ public void loadImages(final List<PlateImageReference> imageReferences,
+ final IPlateImageHandler plateImageHandler, final ImageRepresentationFormat format)
+ throws IOException
+ {
+ plateImageReferencesMultiplexer.process(imageReferences,
+ new IReferenceHandler<PlateImageReference>()
+ {
+ public void handle(DssServiceRpcScreeningHolder dssService,
+ List<PlateImageReference> references)
+ {
+ checkDSSMinimalMinorVersion(dssService, "loadImages", List.class,
+ ImageRepresentationFormat.class);
+ final InputStream stream =
+ dssService.getService().loadImages(sessionToken, references,
+ format);
+ processImagesStreamUnchecked(plateImageHandler, references, stream);
+ }
+ });
+ }
+
public void loadImages(List<PlateImageReference> imageReferences,
final IPlateImageHandler plateImageHandler,
- final IImageSetSelectionCriterion... criteria) throws IOException
+ final IImageRepresentationFormatSelectionCriterion... criteria) throws IOException
{
plateImageReferencesMultiplexer.process(imageReferences,
new IReferenceHandler<PlateImageReference>()
@@ -1844,7 +1846,7 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
List<PlateImageReference> references)
{
checkDSSMinimalMinorVersion(dssService, "loadImages", List.class,
- IImageSetSelectionCriterion[].class);
+ IImageRepresentationFormatSelectionCriterion[].class);
final InputStream stream =
dssService.getService().loadImages(sessionToken, references,
criteria);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/AbstractImageSelectionCriterion.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/AbstractFormatSelectionCriterion.java
similarity index 52%
rename from screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/AbstractImageSelectionCriterion.java
rename to screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/AbstractFormatSelectionCriterion.java
index 5396f41386c..b4c3fce8253 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/AbstractImageSelectionCriterion.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/AbstractFormatSelectionCriterion.java
@@ -20,32 +20,35 @@ import java.util.ArrayList;
import java.util.List;
/**
- * Abstract super class of {@link IImageSetSelectionCriterion} which accepting matching
- * {@link IImageSetMetaData} instance individually.
- *
+ * Abstract super class of {@link IImageRepresentationFormatSelectionCriterion} which accepting
+ * matching {@link ImageRepresentationFormat} instance individually.
+ *
* @author Franz-Josef Elmer
*/
-public abstract class AbstractImageSelectionCriterion implements IImageSetSelectionCriterion
+public abstract class AbstractFormatSelectionCriterion implements
+ IImageRepresentationFormatSelectionCriterion
{
private static final long serialVersionUID = 1L;
- public List<IImageSetMetaData> getMatching(List<IImageSetMetaData> imageMetaData)
+ public List<ImageRepresentationFormat> getMatching(
+ List<ImageRepresentationFormat> imageRepresentationFormats)
{
- List<IImageSetMetaData> filteredMetaData = new ArrayList<IImageSetMetaData>();
- for (IImageSetMetaData metaData : imageMetaData)
+ List<ImageRepresentationFormat> filteredMetaData =
+ new ArrayList<ImageRepresentationFormat>();
+ for (ImageRepresentationFormat format : imageRepresentationFormats)
{
- if (accept(metaData))
+ if (accept(format))
{
- filteredMetaData.add(metaData);
+ filteredMetaData.add(format);
}
}
return filteredMetaData;
}
-
+
/**
- * Returns <code>true</code> if the specified {@link IImageSetMetaData} instance is
+ * Returns <code>true</code> if the specified {@link ImageRepresentationFormat} instance is
* accepted by this criterion.
*/
- protected abstract boolean accept(IImageSetMetaData imageMetaData);
+ protected abstract boolean accept(ImageRepresentationFormat format);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ColorDepthCriterion.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ColorDepthCriterion.java
index 2f5d6332677..0ae6932fe6d 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ColorDepthCriterion.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ColorDepthCriterion.java
@@ -25,12 +25,14 @@ import java.util.Set;
*
* @author Franz-Josef Elmer
*/
-public class ColorDepthCriterion extends AbstractImageSelectionCriterion
+public class ColorDepthCriterion extends AbstractFormatSelectionCriterion
{
+ private static final long serialVersionUID = 1L;
+
private final Set<Integer> colorDepth;
/**
- * Creates an instance which allows all images with specified color depths.
+ * Creates an instance which allows all image representation formats with specified color depths.
*/
public ColorDepthCriterion(Integer... colorDepths)
{
@@ -38,9 +40,9 @@ public class ColorDepthCriterion extends AbstractImageSelectionCriterion
}
@Override
- protected boolean accept(IImageSetMetaData imageMetaData)
+ protected boolean accept(ImageRepresentationFormat format)
{
- return colorDepth.contains(imageMetaData.getColorDepth());
+ return colorDepth.contains(format.getColorDepth());
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/FileTypeCriterion.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/FileTypeCriterion.java
index 7ca3e4a72fb..9d001d303ef 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/FileTypeCriterion.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/FileTypeCriterion.java
@@ -25,12 +25,14 @@ import java.util.Set;
*
* @author Franz-Josef Elmer
*/
-public class FileTypeCriterion extends AbstractImageSelectionCriterion
+public class FileTypeCriterion extends AbstractFormatSelectionCriterion
{
+ private static final long serialVersionUID = 1L;
+
private final Set<String> fileTypes;
/**
- * Creates an instance which accepts all images of specified file types.
+ * Creates an instance which accepts all image representation formats of specified file types.
*/
public FileTypeCriterion(String... fileTypes)
{
@@ -38,9 +40,9 @@ public class FileTypeCriterion extends AbstractImageSelectionCriterion
}
@Override
- protected boolean accept(IImageSetMetaData imageMetaData)
+ protected boolean accept(ImageRepresentationFormat format)
{
- return fileTypes.contains(imageMetaData.getFileType());
+ return fileTypes.contains(format.getFileType());
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/IImageSetSelectionCriterion.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/IImageRepresentationFormatSelectionCriterion.java
similarity index 64%
rename from screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/IImageSetSelectionCriterion.java
rename to screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/IImageRepresentationFormatSelectionCriterion.java
index c4e73f568f9..3895733af55 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/IImageSetSelectionCriterion.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/IImageRepresentationFormatSelectionCriterion.java
@@ -20,15 +20,16 @@ import java.io.Serializable;
import java.util.List;
/**
- * Interface of an image selection criterion based on {@link IImageSetMetaData}.
- *
+ * Interface of an image selection criterion based on {@link ImageRepresentationFormat}.
+ *
* @author Franz-Josef Elmer
*/
-public interface IImageSetSelectionCriterion extends Serializable
+public interface IImageRepresentationFormatSelectionCriterion extends Serializable
{
/**
- * Returns all {@link IImageSetMetaData} objects from the specified list which fulfill this
- * criterion.
+ * Returns all {@link ImageRepresentationFormat} objects from the specified list which fulfill
+ * this criterion.
*/
- public List<IImageSetMetaData> getMatching(List<IImageSetMetaData> imageMetaData);
+ public List<ImageRepresentationFormat> getMatching(
+ List<ImageRepresentationFormat> imageRepresentationFormats);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/IImageSetMetaData.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/IImageSetMetaData.java
deleted file mode 100644
index f049eb105da..00000000000
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/IImageSetMetaData.java
+++ /dev/null
@@ -1,55 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto;
-
-/**
- * Interface for meta data of image sets.
- *
- * @author Franz-Josef Elmer
- */
-public interface IImageSetMetaData
-{
- /**
- * Returns the unique id of this image set meta data.
- */
- public long getId();
-
- /**
- * Returns <code>true</code> if this image set contains the original images.
- */
- public boolean isOriginal();
-
- /**
- * Returns the size of all images in the set.
- */
- public Geometry getSize();
-
- /**
- * Returns the color depth (if known) of all images in the set.
- *
- * @return <code>null</code> if color depth is unknown.
- */
- public Integer getColorDepth();
-
- /**
- * Returns the file type (if known) of all images in the set.
- *
- * @return <code>null</code> if file type is unknown.
- */
- public String getFileType();
-
-}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageMetaDataIdCriterion.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageMetaDataIdCriterion.java
deleted file mode 100644
index 970cd1fb3eb..00000000000
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageMetaDataIdCriterion.java
+++ /dev/null
@@ -1,42 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto;
-
-/**
- * Criterion based on the ID of an {@link IImageSetMetaData} object.
- *
- * @author Franz-Josef Elmer
- */
-public class ImageMetaDataIdCriterion extends AbstractImageSelectionCriterion
-{
- private final long imageMetaDataId;
-
- /**
- * Creates an instance based on the specified ID.
- */
- public ImageMetaDataIdCriterion(long imageMetaDataId)
- {
- this.imageMetaDataId = imageMetaDataId;
- }
-
- @Override
- protected boolean accept(IImageSetMetaData imageMetaData)
- {
- return imageMetaDataId == imageMetaData.getId();
- }
-
-}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageRepresentationFormat.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageRepresentationFormat.java
index ef49a97f580..704919eb47d 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageRepresentationFormat.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageRepresentationFormat.java
@@ -33,6 +33,10 @@ public class ImageRepresentationFormat implements Serializable
{
private static final long serialVersionUID = 1L;
+ private final String dataSetCode;
+
+ private final long id;
+
private boolean original;
private Integer width;
@@ -46,16 +50,20 @@ public class ImageRepresentationFormat implements Serializable
/**
* Constructor.
*
+ * @param dataSetCode
+ * @param id
* @param original
* @param width
* @param height
* @param colorDepth
* @param fileType
*/
- public ImageRepresentationFormat(boolean original, Integer width, Integer height,
+ public ImageRepresentationFormat(String dataSetCode, long id, boolean original, Integer width, Integer height,
Integer colorDepth, String fileType)
{
super();
+ this.dataSetCode = dataSetCode;
+ this.id = id;
this.original = original;
this.width = width;
this.height = height;
@@ -63,6 +71,22 @@ public class ImageRepresentationFormat implements Serializable
this.fileType = fileType;
}
+ /**
+ * Returns the data set code to which this image representation format belongs.
+ */
+ public String getDataSetCode()
+ {
+ return dataSetCode;
+ }
+
+ /**
+ * Return the ID of this image representation format.
+ */
+ public long getId()
+ {
+ return id;
+ }
+
/**
* @return True if the format is the original format of the underlying image.
*/
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/OriginalCriterion.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/OriginalCriterion.java
index af8314eba28..42cc82755e9 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/OriginalCriterion.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/OriginalCriterion.java
@@ -17,18 +17,20 @@
package ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto;
/**
- * Criterion which filters image meta data concerning whether they are original or not.
+ * Criterion which filters image representation formats concerning whether they are original or not.
*
* @author Franz-Josef Elmer
*/
-public class OriginalCriterion extends AbstractImageSelectionCriterion
+public class OriginalCriterion extends AbstractFormatSelectionCriterion
{
+ private static final long serialVersionUID = 1L;
+
private final boolean original;
/**
* Creates an instance based on the specified flag. If the flag is <code>true</code>
* all original images fulfill this criterion. If the flag is <code>false</code> all
- * images which are not original (e.g. thumbnails) fullfil this criterion.
+ * images which are not original (e.g. thumbnails) fulfill this criterion.
*/
public OriginalCriterion(boolean original)
{
@@ -36,9 +38,9 @@ public class OriginalCriterion extends AbstractImageSelectionCriterion
}
@Override
- protected boolean accept(IImageSetMetaData imageMetaData)
+ protected boolean accept(ImageRepresentationFormat format)
{
- return imageMetaData.isOriginal() == original;
+ return format.isOriginal() == original;
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/SizeCriterion.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/SizeCriterion.java
index c8cbcedc26e..3324974d4e4 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/SizeCriterion.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/SizeCriterion.java
@@ -26,128 +26,143 @@ import java.util.List;
*
* @author Franz-Josef Elmer
*/
-public class SizeCriterion implements IImageSetSelectionCriterion
+public class SizeCriterion implements IImageRepresentationFormatSelectionCriterion
{
private static final long serialVersionUID = 1L;
public static enum Type
{
/**
- * Picks that image set where the image size is the largest one which just fits into
- * a bounding box specified by width and height.
+ * Picks that format where the image size is the largest one which just fits into a
+ * bounding box specified by width and height.
*/
LARGEST_IN_BOUNDING_BOX()
{
@Override
- void filter(int width, int height, List<IImageSetMetaData> imageMetaData,
- List<IImageSetMetaData> filteredImageMetaData)
+ void filter(int width, int height, List<ImageRepresentationFormat> formats,
+ List<ImageRepresentationFormat> filteredFormats)
{
- List<IImageSetMetaData> smallerMetaData = new ArrayList<IImageSetMetaData>();
- INSIDE_BOUNDING_BOX.filter(width, height, imageMetaData, smallerMetaData);
- if (smallerMetaData.isEmpty() == false)
+ List<ImageRepresentationFormat> smallerFormats =
+ new ArrayList<ImageRepresentationFormat>();
+ INSIDE_BOUNDING_BOX.filter(width, height, formats, smallerFormats);
+ if (smallerFormats.isEmpty() == false)
{
- Collections.sort(smallerMetaData, SIZE_COMPARATOR);
- filteredImageMetaData.add(smallerMetaData.get(smallerMetaData.size() - 1));
+ Collections.sort(smallerFormats, SIZE_COMPARATOR);
+ filteredFormats.add(smallerFormats.get(smallerFormats.size() - 1));
}
}
},
/**
- * Picks all image sets where the image size is inside a bounding box specified by width and
+ * Picks all formats where the image size is inside a bounding box specified by width and
* height.
*/
INSIDE_BOUNDING_BOX
{
@Override
- void filter(int width, int height, List<IImageSetMetaData> imageMetaData,
- List<IImageSetMetaData> filteredImageMetaData)
+ void filter(int width, int height, List<ImageRepresentationFormat> formats,
+ List<ImageRepresentationFormat> filteredFormats)
{
- for (IImageSetMetaData metaData : imageMetaData)
+ for (ImageRepresentationFormat format : formats)
{
- Geometry size = metaData.getSize();
- if (size.getWidth() <= width && size.getHeight() <= height)
+ if (getWidth(format) <= width && getHeight(format) <= height)
{
- filteredImageMetaData.add(metaData);
+ filteredFormats.add(format);
}
}
}
},
/**
- * Picks that image set where the image size is the smallest one covering a bounding box
+ * Picks that format where the image size is the smallest one covering a bounding box
* specified by width and height.
*/
SMALLEST_COVERING_BOUNDING_BOX
{
@Override
- void filter(int width, int height, List<IImageSetMetaData> imageMetaData,
- List<IImageSetMetaData> filteredImageMetaData)
+ void filter(int width, int height, List<ImageRepresentationFormat> formats,
+ List<ImageRepresentationFormat> filteredFormats)
{
- List<IImageSetMetaData> largerMetaData = new ArrayList<IImageSetMetaData>();
- COVERING_BOUNDING_BOX.filter(width, height, imageMetaData, largerMetaData);
- if (largerMetaData.isEmpty() == false)
+ List<ImageRepresentationFormat> largerFormats =
+ new ArrayList<ImageRepresentationFormat>();
+ COVERING_BOUNDING_BOX.filter(width, height, formats, largerFormats);
+ if (largerFormats.isEmpty() == false)
{
- Collections.sort(largerMetaData, SIZE_COMPARATOR);
- filteredImageMetaData.add(largerMetaData.get(0));
+ Collections.sort(largerFormats, SIZE_COMPARATOR);
+ filteredFormats.add(largerFormats.get(0));
}
}
},
/**
- * Picks all image sets where the image size covers a bounding box specified by width and
+ * Picks all formats where the image size covers a bounding box specified by width and
* height.
*/
COVERING_BOUNDING_BOX
{
@Override
- void filter(int width, int height, List<IImageSetMetaData> imageMetaData,
- List<IImageSetMetaData> filteredImageMetaData)
+ void filter(int width, int height, List<ImageRepresentationFormat> formats,
+ List<ImageRepresentationFormat> filteredFormats)
{
- for (IImageSetMetaData metaData : imageMetaData)
+ for (ImageRepresentationFormat format : formats)
{
- Geometry size = metaData.getSize();
- if (size.getWidth() >= width && size.getHeight() >= height)
+ if (getWidth(format) >= width && getHeight(format) >= height)
{
- filteredImageMetaData.add(metaData);
+ filteredFormats.add(format);
}
}
}
},
/**
- * Picks all image sets where the image size is exactly as specified by width and height.
+ * Picks all formats where the image size is exactly as specified by width and height.
*/
EXACTLY
{
@Override
- void filter(int width, int height, List<IImageSetMetaData> imageMetaData,
- List<IImageSetMetaData> filteredImageMetaData)
+ void filter(int width, int height, List<ImageRepresentationFormat> formats,
+ List<ImageRepresentationFormat> filteredFormats)
{
- for (IImageSetMetaData metaData : imageMetaData)
+ for (ImageRepresentationFormat format : formats)
{
- Geometry size = metaData.getSize();
- if (size.getWidth() == width && size.getHeight() == height)
+ if (getWidth(format) == width && getHeight(format) == height)
{
- filteredImageMetaData.add(metaData);
+ filteredFormats.add(format);
}
}
}
};
- abstract void filter(int width, int height, List<IImageSetMetaData> imageMetaData,
- List<IImageSetMetaData> filteredImageMetaData);
+ abstract void filter(int width, int height, List<ImageRepresentationFormat> formats,
+ List<ImageRepresentationFormat> filteredFormats);
}
- private static final Comparator<IImageSetMetaData> SIZE_COMPARATOR =
- new Comparator<IImageSetMetaData>()
+ private static final Comparator<ImageRepresentationFormat> SIZE_COMPARATOR =
+ new Comparator<ImageRepresentationFormat>()
{
- public int compare(IImageSetMetaData i1, IImageSetMetaData i2)
+ public int compare(ImageRepresentationFormat i1, ImageRepresentationFormat i2)
{
- return area(i1.getSize()) - area(i2.getSize());
+ return area(i1) - area(i2);
}
- private int area(Geometry geometry)
+ private int area(ImageRepresentationFormat format)
{
- return geometry.getWidth() * geometry.getHeight();
+ return mapNull(format.getWidth()) * mapNull(format.getHeight());
}
+
};
+ private static int getWidth(ImageRepresentationFormat format)
+ {
+ return mapNull(format.getWidth());
+ }
+
+ private static int getHeight(ImageRepresentationFormat format)
+ {
+ return mapNull(format.getHeight());
+ }
+
+ private static int mapNull(Integer number)
+ {
+ return number == null ? 0 : number.intValue();
+ }
+
private final int width;
private final int height;
@@ -168,11 +183,13 @@ public class SizeCriterion implements IImageSetSelectionCriterion
this.type = type;
}
- public List<IImageSetMetaData> getMatching(List<IImageSetMetaData> imageMetaData)
+ public List<ImageRepresentationFormat> getMatching(
+ List<ImageRepresentationFormat> imageRepresentationFormats)
{
- List<IImageSetMetaData> filteredMetaData = new ArrayList<IImageSetMetaData>();
- type.filter(width, height, imageMetaData, filteredMetaData);
- return filteredMetaData;
+ List<ImageRepresentationFormat> filteredFormats =
+ new ArrayList<ImageRepresentationFormat>();
+ type.filter(width, height, imageRepresentationFormats, filteredFormats);
+ return filteredFormats;
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageDatasetParameters.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageDatasetParameters.java
index 4d5b577bcf3..e185875d656 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageDatasetParameters.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageDatasetParameters.java
@@ -21,7 +21,6 @@ import java.util.ArrayList;
import java.util.List;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgImageZoomLevelDTO;
/**
* Describes the images in the dataset: tiles geometry, channels, dataset code and plate geometry if
@@ -51,8 +50,6 @@ public class ImageDatasetParameters implements Serializable
private String mergedChannelTransformerFactorySignatureOrNull;
- private List<ImageSetMetaData> zoomLevels;
-
public Integer tryGetRowsNum()
{
return rowsNumOrNull;
@@ -197,14 +194,4 @@ public class ImageDatasetParameters implements Serializable
mergedChannelTransformerFactorySignatureOrNull;
}
- public List<ImageSetMetaData> getZoomLevels()
- {
- return zoomLevels;
- }
-
- public void setZoomLevels(List<ImageSetMetaData> zoomLevels)
- {
- this.zoomLevels = zoomLevels;
- }
-
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/HCSDatasetLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/HCSDatasetLoader.java
index 17b351c5e7d..05acbdd419c 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/HCSDatasetLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/HCSDatasetLoader.java
@@ -30,7 +30,6 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.utils.GroupByMap;
import ch.systemsx.cisd.openbis.generic.shared.basic.utils.IGroupKeyExtractor;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelStack;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageDatasetParameters;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageSetMetaData;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.InternalImageChannel;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.InternalImageTransformationInfo;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
@@ -41,7 +40,6 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgCo
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgExperimentDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgImageDatasetDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgImageTransformationDTO;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgImageZoomLevelDTO;
/**
* Helper class for easy handling of HCS image dataset standard structure with no code for handling
@@ -209,32 +207,9 @@ public class HCSDatasetLoader implements IImageDatasetLoader
params.setIsMultidimensional(dataset.getIsMultidimensional());
params.setMergedChannelTransformerFactorySignature(mergedChannelTransformerFactorySignatureOrNull);
params.setInternalChannels(convertChannels());
- params.setZoomLevels(translate(query.listImageZoomLevels(dataset.getId())));
return params;
}
- private List<ImageSetMetaData> translate(List<ImgImageZoomLevelDTO> zoomLevels)
- {
- List<ImageSetMetaData> result = new ArrayList<ImageSetMetaData>();
- for (ImgImageZoomLevelDTO zoomLevel : zoomLevels)
- {
- ImageSetMetaData metaData = new ImageSetMetaData();
- metaData.setId(zoomLevel.getId());
- metaData.setOriginal(zoomLevel.getIsOriginal());
- metaData.setWidth(mapNullTo0(zoomLevel.getWidth()));
- metaData.setHeight(mapNullTo0(zoomLevel.getHeight()));
- metaData.setColorDepth(zoomLevel.getColorDepth());
- metaData.setFileType(zoomLevel.getFileType());
- result.add(metaData);
- }
- return result;
- }
-
- private int mapNullTo0(Integer n)
- {
- return n == null ? 0 : n;
- }
-
private List<InternalImageChannel> convertChannels()
{
List<InternalImageChannel> convertedChannels = new ArrayList<InternalImageChannel>();
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 82d53dd2270..de6851a0702 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
@@ -70,9 +70,12 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtilTest;
import ch.systemsx.cisd.openbis.dss.screening.shared.api.v1.IDssServiceRpcScreening;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSet;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.DataSetBuilder;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.ExperimentBuilder;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetImageRepresentationFormats;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureInformation;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVector;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDataset;
@@ -80,6 +83,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVector
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IDatasetIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IFeatureVectorDatasetIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageSize;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.OriginalCriterion;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateImageReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageDatasetParameters;
@@ -98,6 +102,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgFe
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgFeatureVocabularyTermDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgImageDatasetDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgImageTransformationDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgImageZoomLevelDTO;
/**
* Test cases for the {@link DssServiceRpcScreening}.
@@ -122,12 +127,14 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
private static final String DATASET_CODE = "ds1";
+ private static final String DATASET_CODE2 = "ds2";
+
private static final String CHANNEL_CODE = "GFP";
private static final String EXPERIMENT_PERM_ID = "exp-123";
private static final long EXPERIMENT_ID = 333;
-
+
private static final String URL1 = "url1";
private static final String SESSION_TOKEN = "session";
@@ -175,7 +182,7 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
contentProvider = context.mock(IHierarchicalContentProvider.class);
transformerFactory = new ImageTransformerFactory();
featureVectorDatasetIdentifier1 = create(DATASET_CODE);
- featureVectorDatasetIdentifier2 = create("ds2");
+ featureVectorDatasetIdentifier2 = create(DATASET_CODE2);
final ImageDatasetParameters imageParameters = new ImageDatasetParameters();
imageParameters.setRowsNum(7);
imageParameters.setColsNum(4);
@@ -262,7 +269,7 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
public void testListAvailableFeatureNames()
{
prepareAssetDataSetsAreAccessible();
- prepareLockDataSet("ds1", "ds2");
+ prepareLockDataSet("ds1", DATASET_CODE2);
long[] dataSetIDs = new long[]
{ 1, 2 };
@@ -286,7 +293,7 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
public void testListAvailableFeatures()
{
prepareAssetDataSetsAreAccessible();
- prepareLockDataSet("ds1", "ds2");
+ prepareLockDataSet("ds1", DATASET_CODE2);
long[] dataSetIDs = new long[]
{ 1, 2 };
@@ -323,9 +330,9 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
public void testLoadFeatures()
{
prepareAssetDataSetsAreAccessible();
- prepareLockDataSet("ds1", "ds2");
+ prepareLockDataSet("ds1", DATASET_CODE2);
FeatureVectorDatasetReference r1 = createFeatureVectorDatasetReference(DATASET_CODE);
- FeatureVectorDatasetReference r2 = createFeatureVectorDatasetReference("ds2");
+ FeatureVectorDatasetReference r2 = createFeatureVectorDatasetReference(DATASET_CODE2);
String[][] featureCodesPerDataset = new String[][]
{
{ "F1", "F2" } };
@@ -429,15 +436,117 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
"UNKNOWN"));
}
+ @Test
+ public void testListAvailableImageRepresentationFormats()
+ {
+ prepareLockDataSet(DATASET_CODE, DATASET_CODE2);
+ prepareAssetDataSetsAreAccessible(DATASET_CODE, DATASET_CODE2);
+ context.checking(new Expectations()
+ {
+ {
+ one(dao).listImageDatasetsByPermId(new String[]
+ { DATASET_CODE, DATASET_CODE2 });
+ ImgImageDatasetDTO ds1 =
+ new ImgImageDatasetDTO(DATASET_CODE, null, null, null, false, null,
+ null);
+ ds1.setId(42);
+ will(returnValue(Arrays.asList(ds1)));
+
+ one(dao).listImageZoomLevels(42L);
+ ImgImageZoomLevelDTO level1 =
+ new ImgImageZoomLevelDTO("i1", true, "r1", 10, 20, 8, "png", 102);
+ ImgImageZoomLevelDTO level2 =
+ new ImgImageZoomLevelDTO("i2", false, "r2", 11, 21, 16, "blub", 103);
+ will(returnValue(Arrays.asList(level1, level2)));
+ }
+ });
+
+ DatasetIdentifier id1 = new DatasetIdentifier(DATASET_CODE, URL1);
+ DatasetIdentifier id2 = new DatasetIdentifier(DATASET_CODE2, URL1);
+ List<DatasetIdentifier> dataSetIdentifiers = Arrays.asList(id1, id2);
+ List<DatasetImageRepresentationFormats> formats =
+ screeningService.listAvailableImageRepresentationFormats(SESSION_TOKEN,
+ dataSetIdentifiers);
+
+ assertEquals("[DatasetImageRepresentationFormats[ds1,["
+ + "ImageRepresentationFormat[true,10,20,8,png], "
+ + "ImageRepresentationFormat[false,11,21,16,blub]]], "
+ + "DatasetImageRepresentationFormats[ds2,[]]]", formats.toString());
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testLoadImagesByCriteria() throws IOException
+ {
+ prepareLockDataSet(DATASET_CODE, DATASET_CODE);
+ prepareAssetDataSetsAreAccessible(DATASET_CODE, DATASET_CODE);
+ DatasetIdentifier id1 = new DatasetIdentifier(DATASET_CODE, URL1);
+ prepareGetExperimentPermIDs(id1);
+ PlateImageReference plateRef1 = new PlateImageReference(1, 1, 0, CHANNEL_CODE, id1);
+ PlateImageReference plateRef2 = new PlateImageReference(1, 2, 1, CHANNEL_CODE, id1);
+ context.checking(new Expectations()
+ {
+ {
+ one(dao).listImageDatasetsByPermId(new String[]
+ { DATASET_CODE });
+ ImgImageDatasetDTO ds1 =
+ new ImgImageDatasetDTO(DATASET_CODE, null, null, null, false, null,
+ null);
+ ds1.setId(42);
+ will(returnValue(Arrays.asList(ds1)));
+
+ one(dao).listImageZoomLevels(42L);
+ ImgImageZoomLevelDTO level1 =
+ new ImgImageZoomLevelDTO("i1", true, "r1", 10, 20, null, null, 102);
+ ImgImageZoomLevelDTO level2 =
+ new ImgImageZoomLevelDTO("i2", false, "r2", 11, 21, null, null, 103);
+ will(returnValue(Arrays.asList(level1, level2)));
+
+ RequestedImageSize thumbnailSize =
+ new RequestedImageSize(new Size(10, 20), false);
+ one(imageLoader).tryGetImage(
+ CHANNEL_CODE,
+ ImageChannelStackReference.createHCSFromLocations(new Location(1, 1),
+ new Location(1, 1)), thumbnailSize);
+ will(returnValue(new AbsoluteImageReference(image("img1.jpg"), "img1", null,
+ null, thumbnailSize, createBlueColor(),
+ new ImageTransfomationFactories(), null)));
+
+ one(imageLoader).tryGetImage(
+ CHANNEL_CODE,
+ ImageChannelStackReference.createHCSFromLocations(new Location(2, 1),
+ new Location(2, 1)), thumbnailSize);
+ will(returnValue(new AbsoluteImageReference(image("img1.png"), "img1", null,
+ null, thumbnailSize, createBlueColor(),
+ new ImageTransfomationFactories(), null)));
+
+ }
+ });
+
+
+ InputStream stream = screeningService.loadImages(SESSION_TOKEN,
+ Arrays.asList(plateRef1, plateRef2),
+ new OriginalCriterion(true));
+
+ ConcatenatedFileOutputStreamWriter imagesWriter =
+ new ConcatenatedFileOutputStreamWriter(stream);
+ BufferedImage image1 = extractNextImage(imagesWriter);
+ assertEquals("4x4", image1.getWidth() + "x" + image1.getHeight());
+ BufferedImage image2 = extractNextImage(imagesWriter);
+ assertEquals("4x4", image2.getWidth() + "x" + image2.getHeight());
+ stream.close();
+ context.assertIsSatisfied();
+ }
+
@Test
public void testGetImageTransformerFactoryForChannel()
{
final DatasetIdentifier ds1 = new DatasetIdentifier(DATASET_CODE, "url1");
- final DatasetIdentifier ds2 = new DatasetIdentifier("ds2", "url1");
+ final DatasetIdentifier ds2 = new DatasetIdentifier(DATASET_CODE2, "url1");
final String channel = "dapi";
prepareAssetDataSetsAreAccessible();
prepareGetExperimentPermIDs(ds1, ds2);
- prepareLockDataSet("ds1", "ds2");
+ prepareLockDataSet("ds1", DATASET_CODE2);
context.checking(new Expectations()
{
{
@@ -471,10 +580,10 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
public void testGetImageTransformerFactoryForExperiment()
{
final DatasetIdentifier ds1 = new DatasetIdentifier(DATASET_CODE, "url1");
- final DatasetIdentifier ds2 = new DatasetIdentifier("ds2", "url1");
+ final DatasetIdentifier ds2 = new DatasetIdentifier(DATASET_CODE2, "url1");
prepareAssetDataSetsAreAccessible();
prepareGetExperimentPermIDs(ds1, ds2);
- prepareLockDataSet("ds1", "ds2");
+ prepareLockDataSet("ds1", DATASET_CODE2);
context.checking(new Expectations()
{
{
@@ -500,9 +609,9 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
public void testSaveImageTransformerFactoryForDatasetChannelFailedDueToInvalidAuthorization()
{
final DatasetIdentifier ds1 = new DatasetIdentifier(DATASET_CODE, "url1");
- final DatasetIdentifier ds2 = new DatasetIdentifier("ds2", "url1");
+ final DatasetIdentifier ds2 = new DatasetIdentifier(DATASET_CODE2, "url1");
final String channel = "dapi";
- prepareLockDataSet(DATASET_CODE, "ds2");
+ prepareLockDataSet(DATASET_CODE, DATASET_CODE2);
context.checking(new Expectations()
{
{
@@ -529,9 +638,9 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
public void testSaveImageTransformerFactoryForDatasetChannel()
{
final DatasetIdentifier ds1 = new DatasetIdentifier(DATASET_CODE, "url1");
- final DatasetIdentifier ds2 = new DatasetIdentifier("ds2", "url1");
+ final DatasetIdentifier ds2 = new DatasetIdentifier(DATASET_CODE2, "url1");
final String channel = "dapi";
- prepareLockDataSet(DATASET_CODE, "ds2");
+ prepareLockDataSet(DATASET_CODE, DATASET_CODE2);
prepareAssetDataSetsAreAccessible();
context.checking(new Expectations()
{
@@ -545,7 +654,7 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
one(dao).tryGetImageDatasetByPermId(DATASET_CODE);
will(returnValue(dataset));
- one(dao).tryGetImageDatasetByPermId("ds2");
+ one(dao).tryGetImageDatasetByPermId(DATASET_CODE2);
will(returnValue(dataset));
allowing(dao).hasDatasetChannels(DATASET_CODE);
@@ -633,15 +742,16 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
context.checking(new Expectations()
{
{
- DataSet dataSet = new DataSet();
- Experiment experiment = new Experiment();
- experiment.setPermId(EXPERIMENT_PERM_ID);
- experiment.setId(EXPERIMENT_ID);
- dataSet.setExperiment(experiment);
+ Experiment experiment =
+ new ExperimentBuilder().id(EXPERIMENT_ID).permID(EXPERIMENT_PERM_ID)
+ .getExperiment();
for (DatasetIdentifier datasetIdentifier : dataSetIdentifiers)
{
one(service).tryGetDataSet(SESSION_TOKEN,
datasetIdentifier.getDatasetCode());
+ DataSet dataSet =
+ new DataSetBuilder().code(datasetIdentifier.getDatasetCode())
+ .experiment(experiment).type("HCS_IMAGE").getDataSet();
will(returnValue(dataSet));
}
}
@@ -853,7 +963,7 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
private void prepareAssetDataSetsAreAccessible()
{
- prepareAssetDataSetsAreAccessible("ds1", "ds2");
+ prepareAssetDataSetsAreAccessible("ds1", DATASET_CODE2);
}
private void prepareAssetDataSetsAreAccessible(final String... dsCodes)
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/SizeCriterionTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/SizeCriterionTest.java
new file mode 100644
index 00000000000..130a228f5e9
--- /dev/null
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/SizeCriterionTest.java
@@ -0,0 +1,91 @@
+/*
+ * Copyright 2012 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto;
+
+import java.util.Arrays;
+import java.util.List;
+
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
+
+/**
+ * @author Franz-Josef Elmer
+ */
+public class SizeCriterionTest extends AssertJUnit
+{
+ @Test
+ public void testMatchingExactly()
+ {
+ SizeCriterion criterion = new SizeCriterion(10, 20, SizeCriterion.Type.EXACTLY);
+ List<ImageRepresentationFormat> result =
+ criterion
+ .getMatching(Arrays.asList(format(10, 20), format(10, 21), format(11, 20)));
+ assertEquals("[ImageRepresentationFormat[true,10,20,8,png]]", result.toString());
+ }
+
+ @Test
+ public void testMatchingCoveringBoundingBox()
+ {
+ SizeCriterion criterion =
+ new SizeCriterion(10, 20, SizeCriterion.Type.COVERING_BOUNDING_BOX);
+ List<ImageRepresentationFormat> result =
+ criterion.getMatching(Arrays.asList(format(10, 20), format(10, 21), format(11, 20),
+ format(9, 20), format(10, 19)));
+ assertEquals("[ImageRepresentationFormat[true,10,20,8,png], "
+ + "ImageRepresentationFormat[true,10,21,8,png], "
+ + "ImageRepresentationFormat[true,11,20,8,png]]", result.toString());
+ }
+
+ @Test
+ public void testMatchingSamllestCoveringBoundingBox()
+ {
+ SizeCriterion criterion =
+ new SizeCriterion(10, 20, SizeCriterion.Type.SMALLEST_COVERING_BOUNDING_BOX);
+ List<ImageRepresentationFormat> result =
+ criterion.getMatching(Arrays.asList(format(20, 20), format(9, 21), format(21, 20)));
+ assertEquals("[ImageRepresentationFormat[true,20,20,8,png]]", result.toString());
+ }
+
+ @Test
+ public void testMatchingInsideBoundingBox()
+ {
+ SizeCriterion criterion =
+ new SizeCriterion(10, 20, SizeCriterion.Type.INSIDE_BOUNDING_BOX);
+ List<ImageRepresentationFormat> result =
+ criterion.getMatching(Arrays.asList(format(10, 20), format(10, 21), format(11, 20),
+ format(9, 20), format(10, 19)));
+ assertEquals("[ImageRepresentationFormat[true,10,20,8,png], "
+ + "ImageRepresentationFormat[true,9,20,8,png], "
+ + "ImageRepresentationFormat[true,10,19,8,png]]", result.toString());
+ }
+
+ @Test
+ public void testMatchingLargestInBoundingBox()
+ {
+ SizeCriterion criterion =
+ new SizeCriterion(10, 20, SizeCriterion.Type.LARGEST_IN_BOUNDING_BOX);
+ List<ImageRepresentationFormat> result =
+ criterion.getMatching(Arrays.asList(format(10, 21), format(1, 2),
+ format(9, 20), format(10, 19)));
+ assertEquals("[ImageRepresentationFormat[true,10,19,8,png]]", result.toString());
+ }
+
+ private ImageRepresentationFormat format(Integer width, Integer height)
+ {
+ return new ImageRepresentationFormat("ds1", 1, true, width, height, 8, "png");
+ }
+}
--
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