LMS-2700 Added API support for finding the image formats available for an image

SVN: 24068

screening/.gitignore

@@ -3,3 +3,5 @@
 /.updater
 /.dynamic_property_evaluator_queue
 /tmp
+/dss-tmp
+/indices-screening

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();

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;
+    }
+
 }

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);
+
 }

screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/DatasetImageRepresentationFormats.java

+/*
+ * 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();
+    }
+
+}

screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageRepresentationFormat.java

+/*
+ * 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();
+    }
+
+}