omero.gateway.facility

Class MetadataFacility

java.lang.Object

omero.gateway.facility.Facility

omero.gateway.facility.MetadataFacility

public class MetadataFacility
extends Facility

A Facility to access the metadata.

Since:

5.1

Method Summary

Modifier and Type	Method and Description
java.util.List<AnnotationData>	getAnnotations(SecurityContext ctx, DataObject object) Get all annotations for the given DataObject
java.util.List<AnnotationData>	getAnnotations(SecurityContext ctx, DataObject object, java.util.List<java.lang.Class<? extends AnnotationData>> annotationTypes, java.util.List<java.lang.Long> userIds) Get the annotations for the given DataObject
java.util.Map<DataObject,java.util.List<AnnotationData>>	getAnnotations(SecurityContext ctx, java.util.List<? extends DataObject> objects, java.util.List<java.lang.Class<? extends AnnotationData>> annotationTypes, java.util.List<java.lang.Long> userIds) Get the annotations for the given DataObjects
java.util.List<ChannelData>	getChannelData(SecurityContext ctx, long imageId) Get the ChannelData for a specific image
ImageAcquisitionData	getImageAcquisitionData(SecurityContext ctx, long imageId) Loads the ImageAcquisitionData for a specific image
java.util.List<java.lang.String>	getManagedRepositoriesPaths(SecurityContext ctx, ImageData img) Get the file paths of the image in the managed repository
void	getOriginalMetadata(SecurityContext ctx, long imageId, java.io.File output) Get the original metadata of an image and write it into a file
void	getOriginalMetadata(SecurityContext ctx, long imageId, java.lang.StringBuffer buffer) Get the original metadata of an image and write it a StringBuilder
java.util.List<java.lang.String>	getOriginalPaths(SecurityContext ctx, ImageData img) Get the original file paths where the image was imported from.
java.util.List<PlaneInfoData>	getPlaneInfos(SecurityContext ctx, PixelsData pix) Get the plane infos.

Methods inherited from class omero.gateway.facility.Facility

addPropertyChangeListener, clear, firePropertyChanged, firePropertyChanged, getFacility, logDebug, logError, logInfo, logWarn, removePropertyChangeListener

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

getImageAcquisitionData

public ImageAcquisitionData getImageAcquisitionData(SecurityContext ctx,
                                                    long imageId)
                                             throws DSOutOfServiceException,
                                                    DSAccessException

Loads the ImageAcquisitionData for a specific image

Parameters:

ctx - The SecurityContext

imageId - The imageId

Returns:

See above

Throws:

DSOutOfServiceException - If the connection is broken, or not logged in

DSAccessException - If an error occurred while trying to retrieve data from OMERO service.

getChannelData

public java.util.List<ChannelData> getChannelData(SecurityContext ctx,
                                                  long imageId)
                                           throws DSOutOfServiceException,
                                                  DSAccessException

Get the ChannelData for a specific image

Parameters:

ctx - The SecurityContext

imageId - The imageId to get the ChannelData for

Returns:

List of ChannelData

Throws:

DSOutOfServiceException - If the connection is broken, or not logged in

DSAccessException - If an error occurred while trying to retrieve data from OMERO service.

getAnnotations

public java.util.List<AnnotationData> getAnnotations(SecurityContext ctx,
                                                     DataObject object)
                                              throws DSOutOfServiceException,
                                                     DSAccessException

Get all annotations for the given DataObject

Parameters:

ctx - The SecurityContext

object - The DataObject to load the annotations for

Returns:

See above

Throws:

DSOutOfServiceException - If the connection is broken, or not logged in

DSAccessException - If an error occurred while trying to retrieve data from OMERO service.

getAnnotations

public java.util.List<AnnotationData> getAnnotations(SecurityContext ctx,
                                                     DataObject object,
                                                     java.util.List<java.lang.Class<? extends AnnotationData>> annotationTypes,
                                                     java.util.List<java.lang.Long> userIds)
                                              throws DSOutOfServiceException,
                                                     DSAccessException

Get the annotations for the given DataObject

Parameters:

ctx - The SecurityContext

object - The DataObject to load the annotations for

annotationTypes - The type of annotations to load (can be null)

userIds - Only load annotations of certain users (can be null, i. e. all users)

Returns:

See above

Throws:

DSOutOfServiceException - If the connection is broken, or not logged in

DSAccessException - If an error occurred while trying to retrieve data from OMERO service.

getAnnotations

public java.util.Map<DataObject,java.util.List<AnnotationData>> getAnnotations(SecurityContext ctx,
                                                                               java.util.List<? extends DataObject> objects,
                                                                               java.util.List<java.lang.Class<? extends AnnotationData>> annotationTypes,
                                                                               java.util.List<java.lang.Long> userIds)
                                                                        throws DSOutOfServiceException,
                                                                               DSAccessException

Get the annotations for the given DataObjects

Parameters:

ctx - The SecurityContext

objects - The DataObjects to load the annotations for (have to be all of the same type)

annotationTypes - The type of annotations to load (can be null)

userIds - Only load annotations of certain users (can be null, i. e. all users)

Returns:

Lists of AnnotationData mapped to the DataObject they are attached to.

Throws:

DSOutOfServiceException - If the connection is broken, or not logged in

DSAccessException - If an error occurred while trying to retrieve data from OMERO service.

getManagedRepositoriesPaths

public java.util.List<java.lang.String> getManagedRepositoriesPaths(SecurityContext ctx,
                                                                    ImageData img)
                                                             throws DSOutOfServiceException,
                                                                    DSAccessException

Get the file paths of the image in the managed repository

Parameters:

ctx - The SecurityContext

img - The image

Returns:

See above

Throws:

DSOutOfServiceException

DSAccessException

getOriginalPaths

public java.util.List<java.lang.String> getOriginalPaths(SecurityContext ctx,
                                                         ImageData img)
                                                  throws DSOutOfServiceException,
                                                         DSAccessException

Get the original file paths where the image was imported from.

Parameters:

ctx - The SecurityContext

img - The image

Returns:

See above

Throws:

DSOutOfServiceException

DSAccessException

getPlaneInfos

public java.util.List<PlaneInfoData> getPlaneInfos(SecurityContext ctx,
                                                   PixelsData pix)
                                            throws DSOutOfServiceException,
                                                   DSAccessException

Get the plane infos.

Parameters:

ctx - The SecurityContext

pix - The PixelsData

Returns:

See above

Throws:

DSOutOfServiceException

DSAccessException

getOriginalMetadata

public void getOriginalMetadata(SecurityContext ctx,
                                long imageId,
                                java.io.File output)
                         throws java.lang.Exception

Get the original metadata of an image and write it into a file

Parameters:

ctx - The SecurityContext

imageId - The image id

output - The output file

Throws:

java.lang.Throwable

java.lang.Exception

getOriginalMetadata

public void getOriginalMetadata(SecurityContext ctx,
                                long imageId,
                                java.lang.StringBuffer buffer)

Get the original metadata of an image and write it a StringBuilder

Parameters:

ctx - The SecurityContext

imageId - The image id

buffer - The buffer

Throws:

java.lang.Throwable