Package ome.api

Interface IMetadata

  • All Superinterfaces:
    ServiceInterface
    public interface IMetadata
extends ServiceInterface
    Provides method to interact with acquisition metadata and annotations.
    Since:
    3.0-Beta4

    • Field Summary

      Fields 
      Modifier and Type Field Description
      static java.lang.String MOVIE_MPEG_NS
      The name space used to indicate that the FileAnnotation is an MPEG file.
      static java.lang.String MOVIE_QT_NS
      The name space used to indicate that the FileAnnotation is an QT file.
      static java.lang.String MOVIE_WMV_NS
      The name space used to indicate that the FileAnnotation is an WMV file.
      static java.lang.String NS_IMPORTER_ARCHIVED
      The name space indicating that the Boolean annotation indicated if an archived image is imported with the image.
      static java.lang.String NS_INSIGHT_RATING
      The name space indicating that the Long annotation is a rating annotation i.e.
      static java.lang.String NS_INSIGHT_TAG_SET
      The name space indicating that the tag is used a tag set.

    • Method Summary

      All Methods Instance Methods Abstract Methods 
      Modifier and Type Method Description
      java.lang.Long countAnnotationsUsedNotOwned​(java.lang.Class annotationType, long userID)
      Counts the number of annotation of a given type used by the specified user but not owned by the user.
      java.lang.Long countSpecifiedAnnotations​(java.lang.Class type, java.util.Set<java.lang.String> include, java.util.Set<java.lang.String> exclude, ome.parameters.Parameters options)
      Counts the number of annotation of a given type.
      java.util.Map<java.lang.Long,​java.lang.Long> getTaggedObjectsCount​(java.util.Set<java.lang.Long> tagIds, ome.parameters.Parameters options)
      Returns a map whose key is a tag's id and the value the number of Projects, Datasets, and Images linked to that tag.
      <A extends ome.model.annotations.Annotation>
      java.util.Set<A>      		 loadAnnotation​(java.util.Set<java.lang.Long> annotationIds)
      Loads the specified annotations.
      <T extends ome.model.IObject,​A extends ome.model.annotations.Annotation>
      java.util.Map<java.lang.Long,​java.util.Set<A>>      		 loadAnnotations​(java.lang.Class<T> nodeType, java.util.Set<java.lang.Long> rootNodeIds, java.util.Set<java.lang.String> annotationType, java.util.Set<java.lang.Long> annotatorIds, ome.parameters.Parameters options)
      Loads all the annotations of given types, that have been attached to the specified rootNodes for the specified annotatorIds.
      java.util.Set<ome.model.IObject> loadAnnotationsUsedNotOwned​(java.lang.Class annotationType, long userID)
      Loads the annotations of a given type used by the specified user but not owned by the user.
      java.util.Set<ome.model.core.LogicalChannel> loadChannelAcquisitionData​(java.util.Set<java.lang.Long> ids)
      Loads the logical channels and the acquisition metadata related to them.
      ome.model.acquisition.Instrument loadInstrument​(long id)
      Loads the instrument and its components i.e.
      java.util.Map<java.lang.Long,​java.util.Set<ome.model.IObject>> loadLogFiles​(java.lang.Class<? extends ome.model.IObject> rootNodeType, java.util.Set<java.lang.Long> ids)
      Find the original file IDs for the import logs corresponding to the given Image or Fileset IDs.
      <A extends ome.model.annotations.Annotation>
      java.util.Set<A>      		 loadSpecifiedAnnotations​(java.lang.Class type, java.util.Set<java.lang.String> include, java.util.Set<java.lang.String> exclude, ome.parameters.Parameters options)
      Loads all the annotations of a given type.
      <A extends ome.model.annotations.Annotation>
      java.util.Map<java.lang.Long,​java.util.Set<A>>      		 loadSpecifiedAnnotationsLinkedTo​(java.lang.Class type, java.util.Set<java.lang.String> include, java.util.Set<java.lang.String> exclude, java.lang.Class rootNodeType, java.util.Set<java.lang.Long> rootNodeIds, ome.parameters.Parameters options)
      Loads the annotations of a given type linked to the specified objects.
      java.util.Map<java.lang.Long,​java.util.Set<ome.model.IObject>> loadTagContent​(java.util.Set<java.lang.Long> tagIds, ome.parameters.Parameters options)
      Loads the Tag Set if the id is specified otherwise loads all the Tag Set.
      java.util.Set<ome.model.IObject> loadTagSets​(ome.parameters.Parameters options)
      Loads all the tag Sets.

    • Field Detail

      • NS_INSIGHT_TAG_SET

        static final java.lang.String NS_INSIGHT_TAG_SET
        The name space indicating that the tag is used a tag set.
        See Also:
        Constant Field Values

      • NS_INSIGHT_RATING

        static final java.lang.String NS_INSIGHT_RATING
        The name space indicating that the Long annotation is a rating annotation i.e. an integer in the interval [0, 5].
        See Also:
        Constant Field Values

      • NS_IMPORTER_ARCHIVED

        static final java.lang.String NS_IMPORTER_ARCHIVED
        The name space indicating that the Boolean annotation indicated if an archived image is imported with the image.
        See Also:
        Constant Field Values

      • MOVIE_MPEG_NS

        static final java.lang.String MOVIE_MPEG_NS
        The name space used to indicate that the FileAnnotation is an MPEG file.
        See Also:
        Constant Field Values

      • MOVIE_QT_NS

        static final java.lang.String MOVIE_QT_NS
        The name space used to indicate that the FileAnnotation is an QT file.
        See Also:
        Constant Field Values

      • MOVIE_WMV_NS

        static final java.lang.String MOVIE_WMV_NS
        The name space used to indicate that the FileAnnotation is an WMV file.
        See Also:
        Constant Field Values

    • Method Detail

      • loadChannelAcquisitionData

        java.util.Set<ome.model.core.LogicalChannel> loadChannelAcquisitionData​(java.util.Set<java.lang.Long> ids)
        Loads the logical channels and the acquisition metadata related to them.
        Parameters:
        ids - The collection of logical channel's ids. Mustn't be null.
        Returns:
        The collection of loaded logical channels.

      • loadAnnotations

        <T extends ome.model.IObject,​A extends ome.model.annotations.Annotation> java.util.Map<java.lang.Long,​java.util.Set<A>> loadAnnotations​(java.lang.Class<T> nodeType,
                                                                                                                                                    java.util.Set<java.lang.Long> rootNodeIds,
                                                                                                                                                    java.util.Set<java.lang.String> annotationType,
                                                                                                                                                    java.util.Set<java.lang.Long> annotatorIds,
                                                                                                                                                    ome.parameters.Parameters options)
        Loads all the annotations of given types, that have been attached to the specified rootNodes for the specified annotatorIds. If no types specified, all annotations will be loaded. This method looks for the annotations that have been attached to each of the specified objects. It then maps each rootNodeId onto the set of annotations that were found for that node. If no annotations were found for that node, then the entry will be null. Otherwise it will be a Set containing Annotation objects.
        Parameters:
        nodeType - The type of the nodes the annotations are linked to. Mustn't be null.
        rootNodeIds - Ids of the objects of type rootNodeType. Mustn't be null.
        annotationType - The types of annotation to retrieve. If null all annotations will be loaded. String of the type ome.model.annotations.*.
        annotatorIds - Ids of the users for whom annotations should be retrieved. If null, all annotations returned.
        options -
        Returns:
        A map whose key is rootNodeId and value the Set of all annotations for that node or null.

      • loadSpecifiedAnnotations

        <A extends ome.model.annotations.Annotation> java.util.Set<A> loadSpecifiedAnnotations​(java.lang.Class type,
                                                                                       java.util.Set<java.lang.String> include,
                                                                                       java.util.Set<java.lang.String> exclude,
                                                                                       ome.parameters.Parameters options)
        Loads all the annotations of a given type. It is possible to filter the annotations by including or excluding name spaces set on the annotations.
        Parameters:
        type - The type of annotations to load.
        include - Include the annotations with the specified name spaces.
        exclude - Exclude the annotations with the specified name spaces.
        options - The POJO options.
        Returns:
        A collection of found annotations.

      • loadTagContent

        java.util.Map<java.lang.Long,​java.util.Set<ome.model.IObject>> loadTagContent​(java.util.Set<java.lang.Long> tagIds,
                                                                                    ome.parameters.Parameters options)
        Loads the Tag Set if the id is specified otherwise loads all the Tag Set.
        Parameters:
        tagIds - The id of the tag to load or -1.
        options - The POJO options.
        Returns:
        Map whose key is a Tag/Tag Set and the value either a Map or a list of related DataObject.

      • loadTagSets

        java.util.Set<ome.model.IObject> loadTagSets​(ome.parameters.Parameters options)
        Loads all the tag Sets. Returns a collection of AnnotationAnnotatioLink objects and, if the orphan parameters is true, the TagAnnotation object. Note that the difference between a Tag Set and a Tag is made using the name space NS_INSIGHT_TAG_SET.
        Parameters:
        options - The POJO options.
        Returns:
        See above.

      • getTaggedObjectsCount

        java.util.Map<java.lang.Long,​java.lang.Long> getTaggedObjectsCount​(java.util.Set<java.lang.Long> tagIds,
                                                                         ome.parameters.Parameters options)
        Returns a map whose key is a tag's id and the value the number of Projects, Datasets, and Images linked to that tag.
        Parameters:
        tagIds - The collection of ids.
        options - The POJO options.
        Returns:
        See above.

      • countSpecifiedAnnotations

        java.lang.Long countSpecifiedAnnotations​(java.lang.Class type,
                                         java.util.Set<java.lang.String> include,
                                         java.util.Set<java.lang.String> exclude,
                                         ome.parameters.Parameters options)
        Counts the number of annotation of a given type.
        Parameters:
        type - The type of annotations to load.
        include - The collection of name space, one of the constants defined by this class.
        exclude - The collection of name space, one of the constants defined by this class.
        options - The POJO options.
        Returns:
        See above.

      • loadAnnotation

        <A extends ome.model.annotations.Annotation> java.util.Set<A> loadAnnotation​(java.util.Set<java.lang.Long> annotationIds)
        Loads the specified annotations.
        Parameters:
        annotationIds - The collection of annotation's ids.
        Returns:
        See above.

      • loadInstrument

        ome.model.acquisition.Instrument loadInstrument​(long id)
        Loads the instrument and its components i.e. detectors, objectives, etc.
        Parameters:
        id - The id of the instrument to load.
        Returns:
        See above

      • countAnnotationsUsedNotOwned

        java.lang.Long countAnnotationsUsedNotOwned​(java.lang.Class annotationType,
                                            long userID)
        Counts the number of annotation of a given type used by the specified user but not owned by the user.
        Parameters:
        annotationType - The type of annotations to load.
        userID - The identifier of the user.
        Returns:
        See above.

      • loadAnnotationsUsedNotOwned

        java.util.Set<ome.model.IObject> loadAnnotationsUsedNotOwned​(java.lang.Class annotationType,
                                                             long userID)
        Loads the annotations of a given type used by the specified user but not owned by the user.
        Parameters:
        annotationType - The type of annotations to load.
        userID - The identifier of the user.
        Returns:
        See above.

      • loadSpecifiedAnnotationsLinkedTo

        <A extends ome.model.annotations.Annotation> java.util.Map<java.lang.Long,​java.util.Set<A>> loadSpecifiedAnnotationsLinkedTo​(java.lang.Class type,
                                                                                                                                   java.util.Set<java.lang.String> include,
                                                                                                                                   java.util.Set<java.lang.String> exclude,
                                                                                                                                   java.lang.Class rootNodeType,
                                                                                                                                   java.util.Set<java.lang.Long> rootNodeIds,
                                                                                                                                   ome.parameters.Parameters options)
        Loads the annotations of a given type linked to the specified objects. It is possible to filter the annotations by including or excluding name spaces set on the annotations. This method looks for the annotations that have been attached to each of the specified objects. It then maps each rootNodeId onto the set of annotations that were found for that node. If no annotations were found for that node, the map will not contain an entry for that node. Otherwise it will be a Set containing Annotation objects. The rootNodeType supported are: Project, Dataset, Image, Pixels, Screen, Plate, PlateAcquisition, Well, Fileset.
        Parameters:
        type - The type of annotations to load.
        include - Include the annotations with the specified name spaces.
        exclude - Exclude the annotations with the specified name spaces.
        rootNodeType - The type of objects the annotations are linked to.
        rootNodeIds - The identifiers of the objects.
        options - The POJO options.
        Returns:
        A collection of found annotations.

      • loadLogFiles

        java.util.Map<java.lang.Long,​java.util.Set<ome.model.IObject>> loadLogFiles​(java.lang.Class<? extends ome.model.IObject> rootNodeType,
                                                                                  java.util.Set<java.lang.Long> ids)
        Find the original file IDs for the import logs corresponding to the given Image or Fileset IDs.
        Parameters:
        rootNodeType - the root node type, may be Image or Fileset
        ids - the IDs of the entities for which the import log original file IDs are required
        Returns:
        the original file IDs of the import logs