From 8f8d36d81f81bac3ae5a98bb947cca9154d70c23 Mon Sep 17 00:00:00 2001
From: cramakri <cramakri>
Date: Tue, 20 Dec 2011 14:20:36 +0000
Subject: [PATCH] LMS-2700 Added API support for finding the image formats
available for an image
SVN: 24068
---
screening/.gitignore | 2 +
.../server/DssServiceRpcScreening.java | 67 ++++++++
.../server/DssServiceRpcScreeningLogger.java | 9 +
.../api/v1/IDssServiceRpcScreening.java | 13 ++
.../DatasetImageRepresentationFormats.java | 124 ++++++++++++++
.../api/v1/dto/ImageRepresentationFormat.java | 156 ++++++++++++++++++
6 files changed, 371 insertions(+)
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/DatasetImageRepresentationFormats.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageRepresentationFormat.java
diff --git a/screening/.gitignore b/screening/.gitignore
index ed41e31c465..dfaab234c0b 100644
--- a/screening/.gitignore
+++ b/screening/.gitignore
@@ -3,3 +3,5 @@
/.updater
/.dynamic_property_evaluator_queue
/tmp
+/dss-tmp
+/indices-screening
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 59e076ed698..72dc83707a7 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
@@ -22,6 +22,7 @@ import java.io.InputStream;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
+import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
@@ -65,6 +66,7 @@ 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.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;
@@ -78,6 +80,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IImageSetMeta
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IImageSetSelectionCriterion;
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;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageSize;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageTransformationInfo;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.MicroscopyImageReference;
@@ -103,6 +106,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgCo
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgFeatureDefDTO;
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;
/**
* Implementation of the screening API interface using RPC. The instance will be created in spring
@@ -784,6 +788,69 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
return createPlateImageReferences(imageAccessor, dataSetIdentifier, wellPositions, channels);
}
+ 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);
+ }
+
+ // 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());
+ if (null == primImageDataSet)
+ {
+ List<ImageRepresentationFormat> emptyList = Collections.emptyList();
+ DatasetImageRepresentationFormats datasetResult =
+ new DatasetImageRepresentationFormats(imageDataset, emptyList);
+ result.add(datasetResult);
+ continue;
+ }
+ 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> convertZoomLevelsToRepresentationFormats(
+ 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(),
+ zoomLevel.getFileType());
+ results.add(result);
+ }
+
+ return results;
+ }
+
private IImagingDatasetLoader createImageLoader(IDatasetIdentifier dataSetIdentifier)
{
final String datasetCode = dataSetIdentifier.getDatasetCode();
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 66ad5352016..0573ed63ad5 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
@@ -26,6 +26,7 @@ import ch.systemsx.cisd.common.spring.IInvocationLoggerContext;
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.generic.shared.AbstractServerLogger;
+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.FeatureVectorDataset;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetReference;
@@ -254,4 +255,12 @@ public class DssServiceRpcScreeningLogger extends AbstractServerLogger implement
return null;
}
+ public List<DatasetImageRepresentationFormats> listAvailableImageRepresentationFormats(
+ String sessionToken, List<? extends IDatasetIdentifier> imageDatasets)
+ {
+ logAccess(sessionToken, "list_available_image_representation_formats", "DATA_SETS(%s)",
+ imageDatasets);
+ return null;
+ }
+
}
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 3b06575c224..4f887d5b66a 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
@@ -29,6 +29,7 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.authorization.Da
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.authorization.PrivilegeLevel;
import ch.systemsx.cisd.openbis.dss.screening.shared.api.internal.authorization.DatasetIdentifierPredicate;
import ch.systemsx.cisd.openbis.dss.screening.shared.api.internal.authorization.SingleDataSetIdentifierPredicate;
+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.FeatureVectorDataset;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetReference;
@@ -393,4 +394,16 @@ public interface IDssServiceRpcScreening extends IRpcService
@AuthorizationGuard(guardClass = DatasetIdentifierPredicate.class)
List<? extends IImageDatasetIdentifier> imageDatasets);
+ /**
+ * Return image representation formats available for the specified image datasets.
+ *
+ * @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>.
+ */
+ @MinimalMinorVersion(10)
+ @DataSetAccessGuard
+ public List<DatasetImageRepresentationFormats> listAvailableImageRepresentationFormats(String sessionToken,
+ @AuthorizationGuard(guardClass = DatasetIdentifierPredicate.class)
+ List<? extends IDatasetIdentifier> imageDatasets);
+
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/DatasetImageRepresentationFormats.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/DatasetImageRepresentationFormats.java
new file mode 100644
index 00000000000..720f950a3be
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/DatasetImageRepresentationFormats.java
@@ -0,0 +1,124 @@
+/*
+ * 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;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+import org.apache.commons.lang.builder.ToStringBuilder;
+import org.apache.commons.lang.builder.ToStringStyle;
+
+/**
+ * A bean that lists all image representation formats available for a data set.
+ *
+ * @since 1.10
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class DatasetImageRepresentationFormats implements Serializable,
+ Comparable<DatasetImageRepresentationFormats>
+{
+ private static final long serialVersionUID = 1L;
+
+ private final IDatasetIdentifier dataset;
+
+ private final ArrayList<ImageRepresentationFormat> imageRepresentationFormats;
+
+ /**
+ * Constructor.
+ *
+ * @param dataSet
+ * @param formats
+ */
+ public DatasetImageRepresentationFormats(IDatasetIdentifier dataSet,
+ List<ImageRepresentationFormat> formats)
+ {
+ super();
+ this.dataset = dataSet;
+ this.imageRepresentationFormats = new ArrayList<ImageRepresentationFormat>(formats);
+ }
+
+ /**
+ * The data set the formats relate to.
+ */
+ public IDatasetIdentifier getDataset()
+ {
+ return dataset;
+ }
+
+ /**
+ * @return An immutable list containing the image representation formats for this data set.
+ */
+ public List<ImageRepresentationFormat> getImageRepresentationFormats()
+ {
+ return Collections.unmodifiableList(imageRepresentationFormats);
+ }
+
+ @Override
+ public int hashCode()
+ {
+ final int prime = 31;
+ int result = 1;
+ result = prime * result + ((dataset == null) ? 0 : dataset.hashCode());
+ return result;
+ }
+
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (this == obj)
+ {
+ return true;
+ }
+ if (obj == null)
+ {
+ return false;
+ }
+ if (getClass() != obj.getClass())
+ {
+ return false;
+ }
+ DatasetImageRepresentationFormats other = (DatasetImageRepresentationFormats) obj;
+ if (dataset == null)
+ {
+ if (other.dataset != null)
+ {
+ return false;
+ }
+ } else if (dataset.equals(other.dataset) == false)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ public int compareTo(DatasetImageRepresentationFormats o)
+ {
+ return dataset.getDatasetCode().compareTo(o.getDataset().getDatasetCode());
+ }
+
+ @Override
+ public String toString()
+ {
+ ToStringBuilder builder = new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE);
+ builder.append(dataset);
+ builder.append(imageRepresentationFormats);
+ return builder.toString();
+ }
+
+}
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
new file mode 100644
index 00000000000..ef49a97f580
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageRepresentationFormat.java
@@ -0,0 +1,156 @@
+/*
+ * 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;
+
+import java.io.Serializable;
+
+import org.apache.commons.lang.builder.EqualsBuilder;
+import org.apache.commons.lang.builder.HashCodeBuilder;
+import org.apache.commons.lang.builder.ToStringBuilder;
+import org.apache.commons.lang.builder.ToStringStyle;
+
+/**
+ * An image representation format is made up of its dimensions, bit depth, and file format.
+ *
+ * @since 1.10
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class ImageRepresentationFormat implements Serializable
+{
+ private static final long serialVersionUID = 1L;
+
+ private boolean original;
+
+ private Integer width;
+
+ private Integer height;
+
+ private Integer colorDepth;
+
+ private String fileType;
+
+ /**
+ * Constructor.
+ *
+ * @param original
+ * @param width
+ * @param height
+ * @param colorDepth
+ * @param fileType
+ */
+ public ImageRepresentationFormat(boolean original, Integer width, Integer height,
+ Integer colorDepth, String fileType)
+ {
+ super();
+ this.original = original;
+ this.width = width;
+ this.height = height;
+ this.colorDepth = colorDepth;
+ this.fileType = fileType;
+ }
+
+ /**
+ * @return True if the format is the original format of the underlying image.
+ */
+ public boolean isOriginal()
+ {
+ return original;
+ }
+
+ /**
+ * @return The width of the image.
+ */
+ public Integer getWidth()
+ {
+ return width;
+ }
+
+ /**
+ * @return The height of the image.
+ */
+ public Integer getHeight()
+ {
+ return height;
+ }
+
+ /**
+ * @return The number of bits of color of the image.
+ */
+ public Integer getColorDepth()
+ {
+ return colorDepth;
+ }
+
+ /**
+ * @return The file type of the image.
+ */
+ public String getFileType()
+ {
+ return fileType;
+ }
+
+ @Override
+ public int hashCode()
+ {
+ HashCodeBuilder builder = new HashCodeBuilder();
+ builder.append(original);
+ builder.append(width);
+ builder.append(height);
+ builder.append(colorDepth);
+ builder.append(fileType);
+ return builder.toHashCode();
+ }
+
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (this == obj)
+ {
+ return true;
+ }
+ if (obj == null)
+ {
+ return false;
+ }
+ if (getClass() != obj.getClass())
+ {
+ return false;
+ }
+
+ ImageRepresentationFormat other = (ImageRepresentationFormat) obj;
+ EqualsBuilder builder = new EqualsBuilder();
+ builder.append(original, other.original);
+ builder.append(width, other.width);
+ builder.append(height, other.height);
+ builder.append(colorDepth, other.colorDepth);
+ builder.append(fileType, other.fileType);
+ return builder.isEquals();
+ }
+
+ @Override
+ public String toString()
+ {
+ ToStringBuilder builder = new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE);
+ builder.append(original);
+ builder.append(width);
+ builder.append(height);
+ builder.append(colorDepth);
+ builder.append(fileType);
+ return builder.toString();
+ }
+
+}
--
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