/*
*------------------------------------------------------------------------------
* Copyright (C) 2015-2016 University of Dundee. All rights reserved.
*
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along
* with this program; if not, write to the Free Software Foundation, Inc.,
* 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
*------------------------------------------------------------------------------
*/
package omero.gateway.facility;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.concurrent.ExecutionException;
import java.util.Arrays;
import omero.api.IMetadataPrx;
import omero.gateway.Gateway;
import omero.gateway.SecurityContext;
import omero.gateway.exception.DSAccessException;
import omero.gateway.exception.DSOutOfServiceException;
import omero.model.Channel;
import omero.model.IObject;
import omero.model.Pixels;
import omero.sys.ParametersI;
import omero.gateway.model.AnnotationData;
import omero.gateway.model.ChannelData;
import omero.gateway.model.DataObject;
import omero.gateway.model.ImageAcquisitionData;
import omero.gateway.model.ImageData;
import omero.gateway.util.PojoMapper;
/**
* A {@link Facility} to access the metadata.
* @author Dominik Lindner <a
* href="mailto:d.lindner@dundee.ac.uk">d.lindner@dundee.ac.uk</a>
* @since 5.1
*/
public class MetadataFacility extends Facility {
private BrowseFacility browse;
/**
* Creates a new instance.
*
* @param gateway Reference to the gateway.
* @throws ExecutionException
*/
MetadataFacility(Gateway gateway) throws ExecutionException {
super(gateway);
this.browse = gateway.getFacility(BrowseFacility.class);
}
/**
* Loads the {@link ImageAcquisitionData} for a specific image
*
* @param ctx
* The {@link SecurityContext}
* @param imageId
* The imageId
* @return See above
* @throws DSOutOfServiceException
* If the connection is broken, or not logged in
* @throws DSAccessException
* If an error occurred while trying to retrieve data from OMERO
* service.
*/
public ImageAcquisitionData getImageAcquisitionData(SecurityContext ctx,
long imageId) throws DSOutOfServiceException, DSAccessException {
ParametersI params = new ParametersI();
params.acquisitionData();
ImageData img = browse.getImage(ctx, imageId, params);
return new ImageAcquisitionData(img.asImage());
}
/**
* Get the {@link ChannelData} for a specific image
*
* @param ctx
* The {@link SecurityContext}
* @param imageId
* The imageId to get the ChannelData for
* @return List of ChannelData
* @throws DSOutOfServiceException
* If the connection is broken, or not logged in
* @throws DSAccessException
* If an error occurred while trying to retrieve data from OMERO
* service.
*/
public List<ChannelData> getChannelData(SecurityContext ctx, long imageId)
throws DSOutOfServiceException, DSAccessException {
List<ChannelData> result = new ArrayList<ChannelData>();
try {
ImageData img = browse.getImage(ctx, imageId);
long pixelsId = img.getDefaultPixels().getId();
Pixels pixels = gateway.getPixelsService(ctx)
.retrievePixDescription(pixelsId);
List<Channel> l = pixels.copyChannels();
for (int i = 0; i < l.size(); i++)
result.add(new ChannelData(i, l.get(i)));
} catch (Throwable t) {
handleException(this, t, "Cannot load channel data.");
}
return result;
}
/**
* Get all annotations for the given {@link DataObject}
* @param ctx The {@link SecurityContext}
* @param object The {@link DataObject} to load the annotations for
* @return See above
* @throws DSOutOfServiceException
* If the connection is broken, or not logged in
* @throws DSAccessException
* If an error occurred while trying to retrieve data from OMERO
* service.
*/
public List<AnnotationData> getAnnotations(SecurityContext ctx,
DataObject object) throws DSOutOfServiceException,
DSAccessException {
return getAnnotations(ctx, object, null, null);
}
/**
* Get the annotations for the given {@link DataObject}
*
* @param ctx
* The {@link SecurityContext}
* @param object
* The {@link DataObject} to load the annotations for
* @param annotationTypes
* The type of annotations to load (can be <code>null</code>)
* @param userIds
* Only load annotations of certain users (can be
* <code>null</code>, i. e. all users)
* @return See above
* @throws DSOutOfServiceException
* If the connection is broken, or not logged in
* @throws DSAccessException
* If an error occurred while trying to retrieve data from OMERO
* service.
*/
public List<AnnotationData> getAnnotations(SecurityContext ctx,
DataObject object,
List<Class<? extends AnnotationData>> annotationTypes,
List<Long> userIds) throws DSOutOfServiceException,
DSAccessException {
Map<DataObject, List<AnnotationData>> result = getAnnotations(ctx,
Arrays.asList(new DataObject[] { object }), annotationTypes,
userIds);
return result.get(object);
}
/**
* Get the annotations for the given {@link DataObject}s
*
* @param ctx
* The {@link SecurityContext}
* @param objects
* The {@link DataObject}s to load the annotations for (have to
* be all of the same type)
* @param annotationTypes
* The type of annotations to load (can be <code>null</code>)
* @param userIds
* Only load annotations of certain users (can be
* <code>null</code>, i. e. all users)
* @return Lists of {@link AnnotationData} mapped to the {@link DataObject}
* they are attached to.
* @throws DSOutOfServiceException
* If the connection is broken, or not logged in
* @throws DSAccessException
* If an error occurred while trying to retrieve data from OMERO
* service.
*/
public Map<DataObject, List<AnnotationData>> getAnnotations(
SecurityContext ctx, List<? extends DataObject> objects,
List<Class<? extends AnnotationData>> annotationTypes,
List<Long> userIds) throws DSOutOfServiceException,
DSAccessException {
Map<DataObject, List<AnnotationData>> result = new HashMap<DataObject, List<AnnotationData>>();
String type = null;
List<Long> ids = new ArrayList<Long>();
for (DataObject obj : objects) {
if (type == null)
type = PojoMapper.getModelType(obj.getClass()).getName();
else if (!type.equals(PojoMapper.getModelType(obj.getClass())
.getName()))
throw new IllegalArgumentException(
"All objects have to be the same type");
ids.add(obj.getId());
}
try {
IMetadataPrx proxy = gateway.getMetadataService(ctx);
List<String> annoTypes = null;
if (annotationTypes != null) {
annoTypes = new ArrayList<String>(annotationTypes.size());
for (Class c : annotationTypes)
annoTypes.add(PojoMapper.getModelType(c).getName());
}
Map<Long, List<IObject>> annos = proxy.loadAnnotations(type, ids,
annoTypes, userIds, null);
for (Entry<Long, List<IObject>> e : annos.entrySet()) {
long id = e.getKey();
DataObject dobj = null;
for (DataObject o : objects) {
if (o.getId() == id) {
dobj = o;
break;
}
}
List<AnnotationData> list = new ArrayList<AnnotationData>();
for (IObject a : e.getValue()) {
list.add((AnnotationData) PojoMapper.asDataObject(a));
}
result.put(dobj, list);
}
} catch (Throwable t) {
handleException(this, t, "Cannot get annotations.");
}
return result;
}
}