Package ome.formats

Class OMEROMetadataStoreClient

  • All Implemented Interfaces:
    loci.formats.meta.IMinMaxStore, loci.formats.meta.MetadataStore, IObjectContainerStore, ome.xml.meta.BaseMetadata, ome.xml.meta.MetadataStore
    public class OMEROMetadataStoreClient
extends java.lang.Object
implements loci.formats.meta.MetadataStore, loci.formats.meta.IMinMaxStore, IObjectContainerStore
    Client side implementation of the Bio-Formats MetadataStore. It is responsible for handling metadata from Bio-Formats and maintaining communication with an OMERO server.

    • Constructor Detail

      • OMEROMetadataStoreClient

        public OMEROMetadataStoreClient()

    • Method Detail

      • getKeepAlive

        public ClientKeepAlive getKeepAlive()
        Returns clientKeepAlive created in store
        Returns:
        current ClientKeepAlive

      • logVersionInfo

        public void logVersionInfo​(java.lang.String clientVersion)
                    throws ServerError
        Throws:
        ServerError

      • getDefaultBatchSize

        public int getDefaultBatchSize()
        Returns:
        user-configured "omero.batch_size" or DEFAULTBATCHSIZE if none is set.

      • getDefaultBlockSize

        public int getDefaultBlockSize()
        Returns:
        user-configured "omero.block_size" or DEFAULTBLOCKSIZE if none is set.

      • getIQuery

        public IQueryPrx getIQuery()
        Returns:
        IQuery proxy

      • setEncryptedConnection

        public void setEncryptedConnection​(boolean encryptedConnection)

      • isEncryptedConnection

        public boolean isEncryptedConnection()

      • setGroup

        public java.lang.Long setGroup​(java.lang.Long groupID)
        Sets the id which will be used to set the call context for all services. If null, the call context will be left which will then use the context of the session.
        Parameters:
        groupID - the group ID to use for call contexts
        Returns:
        the previous group ID, may be null

      • initialize

        public void initialize​(ServiceFactoryPrx serviceFactory)
                throws ServerError
        Initializes the MetadataStore with an already logged in, ready to go service factory. When finished with this instance, close stateful services via closeServices().
        Parameters:
        serviceFactory - The factory. Mustn't be null.
        Throws:
        ServerError - if the services could not be initialized

      • initialize

        public void initialize​(client c)
                throws ServerError
        Initializes the MetadataStore with an already logged in, ready to go service factory. When finished with this instance, close stateful services via closeServices().
        Parameters:
        c - The client. Mustn't be null.
        Throws:
        ServerError - if the services could not be initialized

      • initialize

        public void initialize​(java.lang.String username,
                       java.lang.String password,
                       java.lang.String server,
                       int port)
                throws Glacier2.CannotCreateSessionException,
                       Glacier2.PermissionDeniedException,
                       ServerError
        Initializes the MetadataStore taking string parameters to feed to the OMERO Blitz client object. Using this method creates an unsecure session. When finished with this instance, close all resources via logout()
        Parameters:
        username - User's omename.
        password - User's password.
        server - Server hostname.
        port - Server port.
        Throws:
        Glacier2.CannotCreateSessionException - If there is a session error when creating the OMERO Blitz client object.
        Glacier2.PermissionDeniedException - If there is a problem logging the user in.
        ServerError - If there is a critical error communicating with the server.

      • initialize

        public void initialize​(java.lang.String username,
                       java.lang.String password,
                       java.lang.String server,
                       int port,
                       boolean isSecure)
                throws Glacier2.CannotCreateSessionException,
                       Glacier2.PermissionDeniedException,
                       ServerError
        Initializes the MetadataStore taking string parameters to feed to the OMERO Blitz client object. Using this method to create either secure or unsecure sessions. When finished with this instance, close all resources via logout()
        Parameters:
        username - User's omename.
        password - User's password.
        server - Server hostname.
        port - Server port.
        isSecure - is this session secure
        Throws:
        Glacier2.CannotCreateSessionException - If there is a session error when creating the OMERO Blitz client object.
        Glacier2.PermissionDeniedException - If there is a problem logging the user in.
        ServerError - If there is a critical error communicating with the server.

      • initialize

        public void initialize​(java.lang.String username,
                       java.lang.String password,
                       java.lang.String server,
                       int port,
                       java.lang.Long group,
                       boolean isSecure)
                throws Glacier2.CannotCreateSessionException,
                       Glacier2.PermissionDeniedException,
                       ServerError
        Initializes the MetadataStore taking string parameters to feed to the OMERO Blitz client object. Using this method to create either secure or unsecure sessions and sets the user's group to supplied group. When finished with this instance, close all resources via logout()
        Parameters:
        username - User's omename.
        password - User's password.
        server - Server hostname.
        port - Server port.
        group - User's current group.
        isSecure - is this session secure
        Throws:
        Glacier2.CannotCreateSessionException - If there is a session error when creating the OMERO Blitz client object.
        Glacier2.PermissionDeniedException - If there is a problem logging the user in.
        ServerError - If there is a critical error communicating with the server.

      • initialize

        public void initialize​(java.lang.String username,
                       java.lang.String password,
                       java.lang.String server,
                       int port,
                       java.lang.Long group,
                       boolean isSecure,
                       java.lang.Integer keepAliveRate)
                throws Glacier2.CannotCreateSessionException,
                       Glacier2.PermissionDeniedException,
                       ServerError
        Initializes the MetadataStore taking string parameters to feed to the OMERO Blitz client object. Using this method creates either secure or unsecure sessions and sets the user's group to supplied group. When finished with this instance, close all resources via logout()
        Parameters:
        username - User's omename.
        password - User's password.
        server - Server hostname.
        port - Server port.
        group - User's current group.
        isSecure - is this session secure
        keepAliveRate - Seconds. If null, then pinging will be deactivated.
        Throws:
        Glacier2.CannotCreateSessionException - If there is a session error when creating the OMERO Blitz client object.
        Glacier2.PermissionDeniedException - If there is a problem logging the user in.
        ServerError - If there is a critical error communicating with the server.

      • initialize

        public void initialize​(java.lang.String server,
                       int port,
                       java.lang.String sessionKey)
                throws Glacier2.CannotCreateSessionException,
                       Glacier2.PermissionDeniedException,
                       ServerError
        Initializes the MetadataStore by joining an existing session. Use this method only with unsecure sessions. When finished with this instance, close all resources via logout()
        Parameters:
        server - Server hostname.
        port - Server port.
        sessionKey - Bind session key.
        Throws:
        Glacier2.CannotCreateSessionException - if a session could not be created
        Glacier2.PermissionDeniedException - if the services may not be initialized
        ServerError - if the services could not be initialized

      • initialize

        public void initialize​(java.lang.String server,
                       int port,
                       java.lang.String sessionKey,
                       boolean isSecure)
                throws Glacier2.CannotCreateSessionException,
                       Glacier2.PermissionDeniedException,
                       ServerError
        Initializes the MetadataStore by joining an existing session. Use this method only with unsecure sessions. When finished with this instance, close all resources via logout()
        Parameters:
        server - Server hostname.
        port - Server port.
        sessionKey - Bind session key.
        isSecure - if a secure session should be created
        Throws:
        Glacier2.CannotCreateSessionException - if a session could not be created
        Glacier2.PermissionDeniedException - if the services may not be initialized
        ServerError - if the services could not be initialized

      • initialize

        public void initialize​(java.lang.String server,
                       int port,
                       java.lang.String sessionKey,
                       boolean isSecure,
                       java.lang.Integer keepAliveRate)
                throws Glacier2.CannotCreateSessionException,
                       Glacier2.PermissionDeniedException,
                       ServerError
        Initializes the MetadataStore by joining an existing session. Use this method only with unsecure sessions. When finished with this instance, close all resources via logout()
        Parameters:
        server - Server hostname.
        port - Server port.
        sessionKey - Bind session key.
        isSecure - if a secure session should be created
        keepAliveRate - Seconds. If null, then pinging will be deactivated.
        Throws:
        Glacier2.CannotCreateSessionException - if a session could not be created
        Glacier2.PermissionDeniedException - if the services may not be initialized
        ServerError - if the services could not be initialized

      • getServiceFactory

        public ServiceFactoryPrx getServiceFactory()
        Returns the currently active service factory.
        Returns:
        See above.

      • ping

        public void ping()
        Pings all registered OMERO Blitz proxies.

      • setCurrentLogFile

        public void setCurrentLogFile​(java.lang.String logFilename,
                              java.lang.String token)

      • setEnumerationProvider

        public void setEnumerationProvider​(EnumerationProvider enumProvider)
        Sets the active enumeration provider.
        Parameters:
        enumProvider - Enumeration provider to use.

      • getEnumerationProvider

        public EnumerationProvider getEnumerationProvider()
        Retrieves the active enumeration provider.
        Returns:
        See above.

      • setInstanceProvider

        public void setInstanceProvider​(InstanceProvider instanceProvider)
        Sets the active instance provider.
        Parameters:
        instanceProvider - the instance provider to use

      • getInstanceProvider

        public InstanceProvider getInstanceProvider()
        Retrieves the active instance provider.
        Returns:
        See above.

      • toRType

        public RInt toRType​(java.lang.Integer value)
        Transforms a Java type into the corresponding OMERO RType.
        Parameters:
        value - Java concrete type value.
        Returns:
        RType or null if value is null.

      • toRType

        public RInt toRType​(ome.xml.model.primitives.NonNegativeInteger value)
        Transforms a Java type into the corresponding OMERO RType.
        Parameters:
        value - Java concrete type value.
        Returns:
        RType or null if value is null.

      • toRType

        public RLong toRType​(ome.xml.model.primitives.NonNegativeLong value)
        Transforms a Java type into the corresponding OMERO RType.
        Parameters:
        value - Java concrete type value.
        Returns:
        RType or null if value is null.

      • toRType

        public RDouble toRType​(ome.xml.model.primitives.PositiveFloat value)
        Transforms a Java type into the corresponding OMERO RType.
        Parameters:
        value - Java concrete type value.
        Returns:
        RType or null if value is null.

      • toRType

        public RDouble toRType​(ome.xml.model.primitives.PercentFraction value)
        Transforms a Java type into the corresponding OMERO RType.
        Parameters:
        value - Java concrete type value.
        Returns:
        RType or null if value is null.

      • toRType

        public RLong toRType​(java.lang.Long value)
        Transforms a Java type into the corresponding OMERO RType.
        Parameters:
        value - Java concrete type value.
        Returns:
        RType or null if value is null.

      • toRType

        public RString toRType​(java.lang.String value)
        Transforms a Java type into the corresponding OMERO RType.
        Parameters:
        value - Java concrete type value.
        Returns:
        RType or null if value is null.

      • toRType

        public RBool toRType​(java.lang.Boolean value)
        Transforms a Java type into the corresponding OMERO RType.
        Parameters:
        value - Java concrete type value.
        Returns:
        RType or null if value is null.

      • toRType

        public RDouble toRType​(java.lang.Double value)
        Transforms a Java type into the corresponding OMERO RType.
        Parameters:
        value - Java concrete type value.
        Returns:
        RType or null if value is null.

      • toRType

        public RDouble toRType​(java.lang.Float value)
        Transforms a Java type into the corresponding OMERO RType.
        Parameters:
        value - Java concrete type value.
        Returns:
        RType or null if value is null.

      • toRType

        public RTime toRType​(ome.xml.model.primitives.Timestamp value)
        Transforms a Java type into the corresponding OMERO RType.
        Parameters:
        value - Java concrete type value.
        Returns:
        RType or null if value is null.

      • toRType

        public RString toRType​(ome.xml.model.enums.NamingConvention value)
        Transforms a Java type into the corresponding OMERO RType.
        Parameters:
        value - Java concrete type value.
        Returns:
        RType or null if value is null.

      • toRType

        public AffineTransform toRType​(ome.xml.model.AffineTransform schemaTransform)
        Transforms a Java type into the corresponding OMERO RType.
        Parameters:
        schemaTransform - Java concrete type value.
        Returns:
        RType or null if value is null.

      • toRType

        public RInt toRType​(ome.xml.model.primitives.Color value)
        Transforms a Java type into the corresponding OMERO RType.
        Parameters:
        value - Java concrete type value.
        Returns:
        RType or null if value is null.

      • prepare

        public void prepare​(java.util.Map<java.lang.Integer,​Image> existingMetadata)
        Prepares the metadata store using existing metadata that has been pre-registered by OMERO.fs. The expected graph should be fully loaded:
        • Image
        • Pixels
        NOTE: An execution of prepare() is only valid for a SINGLE importImage() execution. Following importImage() the existing metadata map will be reset regardless of success or failure.
        Parameters:
        existingMetadata - Map of imageIndex or series vs. populated Image source graph with the fetched objects defined above.

      • createRoot

        public void createRoot()
        Specified by:
        createRoot in interface ome.xml.meta.MetadataStore

      • getRoot

        public ome.xml.meta.MetadataRoot getRoot()
        Specified by:
        getRoot in interface ome.xml.meta.MetadataStore

      • getReader

        public loci.formats.IFormatReader getReader()
        Description copied from interface: IObjectContainerStore
        Returns the current Bio-Formats reader that has been used to populate the container store.
        Specified by:
        getReader in interface IObjectContainerStore
        Returns:
        See above.

      • setReader

        public void setReader​(loci.formats.IFormatReader reader)
        Description copied from interface: IObjectContainerStore
        Sets the Bio-Formats reader that will be used to populate the container store.
        Specified by:
        setReader in interface IObjectContainerStore
        Parameters:
        reader - Bio-Formats reader.

      • getUserSpecifiedImageName

        public java.lang.String getUserSpecifiedImageName()

      • setUserSpecifiedDescription

        public void setUserSpecifiedDescription​(java.lang.String description)
        Description copied from interface: IObjectContainerStore
        Sets the user specified image/plate description.
        Specified by:
        setUserSpecifiedDescription in interface IObjectContainerStore
        Parameters:
        description - user-specified image/plate description

      • setUserSpecifiedTarget

        public void setUserSpecifiedTarget​(IObject target)
        Description copied from interface: IObjectContainerStore
        Sets the user-specified linkage target (usually a Dataset for Images) and a Screen for Plates).
        Specified by:
        setUserSpecifiedTarget in interface IObjectContainerStore
        Parameters:
        target - user-specified linkage target

      • getUserSpecifiedPhysicalPixelSizes

        public java.lang.Double[] getUserSpecifiedPhysicalPixelSizes()
        Description copied from interface: IObjectContainerStore
        Returns the user specified physical pixel sizes.
        Specified by:
        getUserSpecifiedPhysicalPixelSizes in interface IObjectContainerStore
        Returns:
        An array of double[] { physicalSizeX, physicalSizeY, physicalSizeZ } as specified by the user. A value of null for any one index states the user has not made a choice for the size of that particular dimension.

      • setUserSpecifiedPhysicalPixelSizes

        public void setUserSpecifiedPhysicalPixelSizes​(java.lang.Double physicalSizeX,
                                               java.lang.Double physicalSizeY,
                                               java.lang.Double physicalSizeZ)
        Description copied from interface: IObjectContainerStore
        Sets the user specified physical pixel sizes. A value of null states the original file physical size for that dimension should be used.
        Specified by:
        setUserSpecifiedPhysicalPixelSizes in interface IObjectContainerStore
        Parameters:
        physicalSizeX - Physical pixel size width.
        physicalSizeY - Physical pixel height.
        physicalSizeZ - Physical pixel depth.

      • getModelProcessors

        public java.util.List<ModelProcessor> getModelProcessors()
        Retrieves the current list of model processors the metadata store is using.
        Returns:
        See above.

      • setModelProcessors

        public void setModelProcessors​(java.util.List<ModelProcessor> modelProcessors)
        Sets the current set of model processors.
        Parameters:
        modelProcessors - List of model processors to use.

      • removeModelProcessor

        public void removeModelProcessor​(ModelProcessor processor)
        Removes a model processor from use.
        Parameters:
        processor - Model processor to remove.

      • addModelProcessor

        public boolean addModelProcessor​(ModelProcessor processor)
        Adds a model processor to the end of the processing chain.
        Parameters:
        processor - Model processor to add.
        Returns:
        true as specified by Collection.add(Object)

      • addReference

        public void addReference​(ome.util.LSID source,
                         ome.util.LSID target)
        Adds a reference to the reference cache.
        Specified by:
        addReference in interface IObjectContainerStore
        Parameters:
        source - Source LSID to add.
        target - Target LSID to add.

      • getReferenceStringCache

        public java.util.Map<java.lang.String,​java.lang.String[]> getReferenceStringCache()
        Description copied from interface: IObjectContainerStore
        Returns the current string based reference cache. This is usually populated by a ReferenceProcessor instance.
        Specified by:
        getReferenceStringCache in interface IObjectContainerStore
        Returns:
        See above.

      • setReferenceStringCache

        public void setReferenceStringCache​(java.util.Map<java.lang.String,​java.lang.String[]> referenceStringCache)
        Description copied from interface: IObjectContainerStore
        Sets the string based reference cache for this container store. This is usually called by a ReferenceProcessor instance.
        Specified by:
        setReferenceStringCache in interface IObjectContainerStore
        Parameters:
        referenceStringCache - String based reference cache to use.

      • getSourceObject

        public IObject getSourceObject​(ome.util.LSID LSID)
        Description copied from interface: IObjectContainerStore
        Retrieves an OMERO Blitz source object for a given LSID.
        Specified by:
        getSourceObject in interface IObjectContainerStore
        Parameters:
        LSID - LSID to retrieve a source object for.
        Returns:
        See above.

      • getSourceObjects

        public <T extends IObject> java.util.List<T> getSourceObjects​(java.lang.Class<T> klass)
        Description copied from interface: IObjectContainerStore
        Retrieves all OMERO Blitz source objects of a given class.
        Specified by:
        getSourceObjects in interface IObjectContainerStore
        Parameters:
        klass - Class to retrieve source objects for.
        Returns:
        See above.

      • hasReference

        public boolean hasReference​(ome.util.LSID source,
                            ome.util.LSID target)
        Description copied from interface: IObjectContainerStore
        Checks to see if there is currently an active reference for two LSIDs.
        Specified by:
        hasReference in interface IObjectContainerStore
        Parameters:
        source - LSID of the source object.
        target - LSID of the target object.
        Returns:
        true if a reference exists, false otherwise.

      • setPixelsFile

        public void setPixelsFile​(long pixelsId,
                          java.lang.String file,
                          java.lang.String repo)
                   throws ServerError
        Sets the path, name and repo in the pixels table.
        Parameters:
        pixelsId - the ID of the Pixels object
        file - the file's filename, with path in the repository
        repo - the file's repository's UUID
        Throws:
        ServerError - in the event of a server error

      • setCurrentGroup

        public void setCurrentGroup​(long groupID)
                     throws ServerError
        Changes the default group of the currently logged in user.
        Parameters:
        groupID - The id of the group.
        Throws:
        ServerError - if the group could not be set or the services initialized accordingly

      • mapUserGroups

        public java.util.Map<java.lang.Long,​java.lang.String> mapUserGroups()
                                                                   throws ServerError
        Maps the user's groups for use by ScreenLogin.registerGroup() Also strips system groups from this map
        Returns:
        map of group id and name
        Throws:
        ServerError - if the groups could not be mapped

      • getDefaultGroupName

        public java.lang.String getDefaultGroupName()
                                     throws ServerError
        Retrieve the default group's name
        Returns:
        the name of the default group
        Throws:
        ServerError - if the default group could not be retrieved

      • getDefaultGroupLevel

        @Deprecated
public int getDefaultGroupLevel()
                         throws ServerError
        Deprecated.
        Retrieve the default group's permission 'level'.
        Returns:
        ImportEvent's group level
        Throws:
        ServerError - if the default group could not be retrieved

      • getRepositorySpace

        public long getRepositorySpace()
        Returns:
        repository space as a long

      • postProcess

        public void postProcess()
        Post processes the internal structure of the client side MetadataStore. Should be called before saveToDB(FilesetJobLink).

      • saveToDB

        public java.util.Map<java.lang.String,​java.util.List<IObject>> saveToDB​(FilesetJobLink link)
        Updates the server side MetadataStore with a list of our objects and references and saves them into the database.
        Parameters:
        link - the link to save to the database
        Returns:
        List of Pixels after database commit.

      • getTarget

        public <T extends IObject> T getTarget​(java.lang.Class<T> klass,
                                       long id)
        Helper method to retrieve an object from iQuery
        Type Parameters:
        T - the kind of model object to retrieve
        Parameters:
        klass - the class of the model object
        id - the ID of the model object
        Returns:
        the model object

      • getProject

        public Project getProject​(long projectId)
        Parameters:
        projectId -
        Returns:
        project with given id

      • addDataset

        public Dataset addDataset​(java.lang.String datasetName,
                          java.lang.String datasetDescription,
                          Project project)
        Parameters:
        datasetName - the name of the dataset
        datasetDescription - the description of the dataset
        project - the project in which the dataset is (if any)
        Returns:
        the newly persisted dataset

      • getExperimenterID

        public long getExperimenterID()
        Returns:
        - experimenter id

      • getConfigValue

        public java.lang.String getConfigValue​(java.lang.String key)
        Retrieves a configuration value from the IConfig service.
        Parameters:
        key - Key for the string encoded value.
        Returns:
        String encoded configuration value.

      • getScreens

        public java.util.List<Screen> getScreens()
        Returns:
        the screens

      • getProjects

        public java.util.List<Project> getProjects()
        Returns:
        the projects

      • getDatasets

        public java.util.List<Dataset> getDatasets​(Project p)
        Parameters:
        p - the project whose datasets to get (null for orphaned datasets)
        Returns:
        the datasets

      • getDatasetsWithoutProjects

        public java.util.List<Dataset> getDatasetsWithoutProjects()
        Returns:
        the orphaned datasets

      • addProject

        public Project addProject​(java.lang.String projectName,
                          java.lang.String projectDescription)
        Parameters:
        projectName - the name of the project
        projectDescription - the description of the project
        Returns:
        the newly persisted project

      • addScreen

        public Screen addScreen​(java.lang.String screenName,
                        java.lang.String screenDescription)
        Parameters:
        screenName - the name of the screen
        screenDescription - the description of the screen
        Returns:
        the newly persisted screen

      • preparePixelsStore

        public void preparePixelsStore​(java.util.List<java.lang.Long> pixelsIds)
        Prepares the server side RawPixelsStore.
        Parameters:
        pixelsIds - List of Pixels IDs we'll be populating.

      • finalizePixelStore

        public void finalizePixelStore()
                        throws ServerError
        Closes the active raw pixels store. Finalizing any open server side resources. The call to close on the RawPixelsStorePrx may throw, in which case the current import should be considered failed, since the saving of the pixels server-side will have not completed successfully.
        Throws:
        ServerError - if the pixel store could not be finalized or a new one created
        See Also:
        Trac ticket #5594

      • getTileSize

        public int[] getTileSize​(java.lang.Long pixId)
                  throws ServerError
        Retrieves the suggested tile size for a pixels set.
        Parameters:
        pixId - Pixels set to write to.
        Returns:
        Width and height of the tile as an array.
        Throws:
        ServerError - If there is an error writing this tile to the server.

      • setTile

        public void setTile​(java.lang.Long pixId,
                    byte[] arrayBuf,
                    int z,
                    int c,
                    int t,
                    int x,
                    int y,
                    int w,
                    int h)
             throws ServerError
        Writes a tile of pixels to the server.
        Parameters:
        pixId - Pixels set to write to.
        arrayBuf - Byte array containing all pixels for this plane.
        z - Z offset within the Pixels set.
        c - Channel offset within the Pixels set.
        t - Timepoint offset within the Pixels set.
        x - X offset of the tile.
        y - Y offset of the tile.
        w - Width of the tile.
        h - Height of the tile.
        Throws:
        ServerError - If there is an error writing this tile to the server.
        See Also:
        setPlane(Long, byte[], int, int, int)

      • setPlane

        public void setPlane​(java.lang.Long pixId,
                     byte[] arrayBuf,
                     int z,
                     int c,
                     int t)
              throws ServerError
        Writes a plane to the server.
        Parameters:
        pixId - Pixels set to write to.
        arrayBuf - Byte array containing all pixels for this plane.
        z - Z offset within the Pixels set.
        c - Channel offset within the Pixels set.
        t - Timepoint offset within the Pixels set.
        Throws:
        ServerError - If there is an error writing this plane to the server.

      • setChannelGlobalMinMax

        public void setChannelGlobalMinMax​(int channel,
                                   double minimum,
                                   double maximum,
                                   int series)
        Specified by:
        setChannelGlobalMinMax in interface loci.formats.meta.IMinMaxStore

      • updatePixels

        public void updatePixels​(java.util.List<Pixels> pixelsList)
        Updates a list of Pixels.
        Parameters:
        pixelsList - List of Pixels to update.

      • populateMinMax

        public void populateMinMax()
        Sends all the minimums and maximums for all images processed so far to the server.

      • resetDefaultsAndGenerateThumbnails

        public void resetDefaultsAndGenerateThumbnails​(java.util.List<java.lang.Long> plateIds,
                                               java.util.List<java.lang.Long> pixelsIds)
        Resets the defaults and generates thumbnails for a given set of Pixels IDs.
        Parameters:
        plateIds - Set of Plate IDs to reset defaults and thumbnails for.
        pixelsIds - Set of Pixels IDs to reset defaults and thumbnails for.

      • getIObjectContainer

        public IObjectContainer getIObjectContainer​(java.lang.Class<? extends IObject> klass,
                                            java.util.LinkedHashMap<Index,​java.lang.Integer> indexes)
        Description copied from interface: IObjectContainerStore
        Retrieves an IObject container for a given class and location within the OME-XML data model. NOTE: The container will be created if it does not already exist.
        Specified by:
        getIObjectContainer in interface IObjectContainerStore
        Parameters:
        klass - Class to retrieve a container for.
        indexes - Indexes into the OME-XML data model.
        Returns:
        See above.

      • removeIObjectContainer

        public void removeIObjectContainer​(ome.util.LSID lsid)
        Description copied from interface: IObjectContainerStore
        Removes an IObject container from within the OME-XML data model store.
        Specified by:
        removeIObjectContainer in interface IObjectContainerStore
        Parameters:
        lsid - LSID of the container to remove.

      • getIObjectContainers

        public java.util.List<IObjectContainer> getIObjectContainers​(java.lang.Class<? extends IObject> klass)
        Description copied from interface: IObjectContainerStore
        Retrieves all IObject containers of a given class. NOTE: this will only return existing containers.
        Specified by:
        getIObjectContainers in interface IObjectContainerStore
        Parameters:
        klass - Class to retrieve containers for.
        Returns:
        See above.

      • countCachedContainers

        public int countCachedContainers​(java.lang.Class<? extends IObject> klass,
                                 int... indexes)
        Description copied from interface: IObjectContainerStore
        Counts the number of containers the MetadataStore has of a given class and at a given index of the hierarchy if specified.
        Specified by:
        countCachedContainers in interface IObjectContainerStore
        Parameters:
        klass - Class to count containers of.
        indexes - Indexes to use in the container count. For example, if klass is Image and indexes is int[] { 0 }; only containers that have an LSID of type Image and a first index of 0 will be counted.
        Returns:
        See above.

      • countCachedReferences

        public int countCachedReferences​(java.lang.Class<? extends IObject> source,
                                 java.lang.Class<? extends IObject> target)
        Description copied from interface: IObjectContainerStore
        Counts the number of references the MetadataStore has between objects of two classes.
        Specified by:
        countCachedReferences in interface IObjectContainerStore
        Parameters:
        source - Class of the source object. If null it is treated as a wild card, all references whose target match target will be counted.
        target - Class of the target object. If null it is treated as a wild card, all references whose source match source will be counted.
        Returns:
        See above.

      • setArcID

        public void setArcID​(java.lang.String id,
                     int instrumentIndex,
                     int lightSourceIndex)
        Specified by:
        setArcID in interface ome.xml.meta.MetadataStore

      • setArcLotNumber

        public void setArcLotNumber​(java.lang.String lotNumber,
                            int instrumentIndex,
                            int lightSourceIndex)
        Specified by:
        setArcLotNumber in interface ome.xml.meta.MetadataStore

      • setArcManufacturer

        public void setArcManufacturer​(java.lang.String manufacturer,
                               int instrumentIndex,
                               int lightSourceIndex)
        Specified by:
        setArcManufacturer in interface ome.xml.meta.MetadataStore

      • setArcModel

        public void setArcModel​(java.lang.String model,
                        int instrumentIndex,
                        int lightSourceIndex)
        Specified by:
        setArcModel in interface ome.xml.meta.MetadataStore

      • setArcPower

        public void setArcPower​(ome.units.quantity.Power power,
                        int instrumentIndex,
                        int lightSourceIndex)
        Specified by:
        setArcPower in interface ome.xml.meta.MetadataStore

      • setArcSerialNumber

        public void setArcSerialNumber​(java.lang.String serialNumber,
                               int instrumentIndex,
                               int lightSourceIndex)
        Specified by:
        setArcSerialNumber in interface ome.xml.meta.MetadataStore

      • setArcType

        public void setArcType​(ome.xml.model.enums.ArcType type,
                       int instrumentIndex,
                       int lightSourceIndex)
        Specified by:
        setArcType in interface ome.xml.meta.MetadataStore

      • setArcAnnotationRef

        public void setArcAnnotationRef​(java.lang.String annotation,
                                int instrumentIndex,
                                int lightSourceIndex,
                                int annotationRefIndex)
        Specified by:
        setArcAnnotationRef in interface ome.xml.meta.MetadataStore

      • setBooleanAnnotationID

        public void setBooleanAnnotationID​(java.lang.String id,
                                   int booleanAnnotationIndex)
        Specified by:
        setBooleanAnnotationID in interface ome.xml.meta.MetadataStore

      • setBooleanAnnotationNamespace

        public void setBooleanAnnotationNamespace​(java.lang.String namespace,
                                          int booleanAnnotationIndex)
        Specified by:
        setBooleanAnnotationNamespace in interface ome.xml.meta.MetadataStore

      • setBooleanAnnotationValue

        public void setBooleanAnnotationValue​(java.lang.Boolean value,
                                      int booleanAnnotationIndex)
        Specified by:
        setBooleanAnnotationValue in interface ome.xml.meta.MetadataStore

      • setBinaryOnlyUUID

        public void setBinaryOnlyUUID​(java.lang.String uuid)
        Specified by:
        setBinaryOnlyUUID in interface ome.xml.meta.MetadataStore

      • setBinaryOnlyMetadataFile

        public void setBinaryOnlyMetadataFile​(java.lang.String metadataFile)
        Specified by:
        setBinaryOnlyMetadataFile in interface ome.xml.meta.MetadataStore

      • getChannel

        public Channel getChannel​(int imageIndex,
                          int channelIndex)

      • setChannelID

        public void setChannelID​(java.lang.String id,
                         int imageIndex,
                         int channelIndex)
        Specified by:
        setChannelID in interface ome.xml.meta.MetadataStore

      • setChannelAcquisitionMode

        public void setChannelAcquisitionMode​(ome.xml.model.enums.AcquisitionMode acquisitionMode,
                                      int imageIndex,
                                      int channelIndex)
        Specified by:
        setChannelAcquisitionMode in interface ome.xml.meta.MetadataStore

      • setChannelColor

        public void setChannelColor​(ome.xml.model.primitives.Color color,
                            int imageIndex,
                            int channelIndex)
        Specified by:
        setChannelColor in interface ome.xml.meta.MetadataStore

      • setChannelContrastMethod

        public void setChannelContrastMethod​(ome.xml.model.enums.ContrastMethod contrastMethod,
                                     int imageIndex,
                                     int channelIndex)
        Specified by:
        setChannelContrastMethod in interface ome.xml.meta.MetadataStore

      • setChannelEmissionWavelength

        public void setChannelEmissionWavelength​(ome.units.quantity.Length emissionWavelength,
                                         int imageIndex,
                                         int channelIndex)
        Specified by:
        setChannelEmissionWavelength in interface ome.xml.meta.MetadataStore

      • setChannelExcitationWavelength

        public void setChannelExcitationWavelength​(ome.units.quantity.Length excitationWavelength,
                                           int imageIndex,
                                           int channelIndex)
        Specified by:
        setChannelExcitationWavelength in interface ome.xml.meta.MetadataStore
        See Also:
        MetadataStore.setChannelExcitationWavelength(Length, int, int)

      • setChannelFilterSetRef

        public void setChannelFilterSetRef​(java.lang.String filterSet,
                                   int imageIndex,
                                   int channelIndex)
        Specified by:
        setChannelFilterSetRef in interface ome.xml.meta.MetadataStore

      • setChannelFluor

        public void setChannelFluor​(java.lang.String fluor,
                            int imageIndex,
                            int channelIndex)
        Specified by:
        setChannelFluor in interface ome.xml.meta.MetadataStore

      • setChannelIlluminationType

        public void setChannelIlluminationType​(ome.xml.model.enums.IlluminationType illuminationType,
                                       int imageIndex,
                                       int channelIndex)
        Specified by:
        setChannelIlluminationType in interface ome.xml.meta.MetadataStore

      • setChannelNDFilter

        public void setChannelNDFilter​(java.lang.Double ndfilter,
                               int imageIndex,
                               int channelIndex)
        Specified by:
        setChannelNDFilter in interface ome.xml.meta.MetadataStore

      • setChannelName

        public void setChannelName​(java.lang.String name,
                           int imageIndex,
                           int channelIndex)
        Specified by:
        setChannelName in interface ome.xml.meta.MetadataStore

      • setChannelPinholeSize

        public void setChannelPinholeSize​(ome.units.quantity.Length pinholeSize,
                                  int imageIndex,
                                  int channelIndex)
        Specified by:
        setChannelPinholeSize in interface ome.xml.meta.MetadataStore

      • setChannelPockelCellSetting

        public void setChannelPockelCellSetting​(java.lang.Integer pockelCellSetting,
                                        int imageIndex,
                                        int channelIndex)
        Specified by:
        setChannelPockelCellSetting in interface ome.xml.meta.MetadataStore

      • setChannelSamplesPerPixel

        public void setChannelSamplesPerPixel​(ome.xml.model.primitives.PositiveInteger samplesPerPixel,
                                      int imageIndex,
                                      int channelIndex)
        Specified by:
        setChannelSamplesPerPixel in interface ome.xml.meta.MetadataStore

      • setChannelAnnotationRef

        public void setChannelAnnotationRef​(java.lang.String annotation,
                                    int imageIndex,
                                    int channelIndex,
                                    int annotationRefIndex)
        Specified by:
        setChannelAnnotationRef in interface ome.xml.meta.MetadataStore

      • setChannelLightSourceSettingsID

        public void setChannelLightSourceSettingsID​(java.lang.String id,
                                            int imageIndex,
                                            int channelIndex)
        Specified by:
        setChannelLightSourceSettingsID in interface ome.xml.meta.MetadataStore

      • setChannelLightSourceSettingsAttenuation

        public void setChannelLightSourceSettingsAttenuation​(ome.xml.model.primitives.PercentFraction attenuation,
                                                     int imageIndex,
                                                     int channelIndex)
        Specified by:
        setChannelLightSourceSettingsAttenuation in interface ome.xml.meta.MetadataStore

      • setChannelLightSourceSettingsWavelength

        public void setChannelLightSourceSettingsWavelength​(ome.units.quantity.Length wavelength,
                                                    int imageIndex,
                                                    int channelIndex)
        Specified by:
        setChannelLightSourceSettingsWavelength in interface ome.xml.meta.MetadataStore

      • setDatasetID

        public void setDatasetID​(java.lang.String id,
                         int datasetIndex)
        Specified by:
        setDatasetID in interface ome.xml.meta.MetadataStore

      • setDatasetAnnotationRef

        public void setDatasetAnnotationRef​(java.lang.String annotation,
                                    int datasetIndex,
                                    int annotationRefIndex)
        Specified by:
        setDatasetAnnotationRef in interface ome.xml.meta.MetadataStore

      • setDatasetDescription

        public void setDatasetDescription​(java.lang.String description,
                                  int datasetIndex)
        Specified by:
        setDatasetDescription in interface ome.xml.meta.MetadataStore

      • setDatasetExperimenterRef

        public void setDatasetExperimenterRef​(java.lang.String experimenter,
                                      int datasetIndex)
        Specified by:
        setDatasetExperimenterRef in interface ome.xml.meta.MetadataStore

      • setDatasetExperimenterGroupRef

        public void setDatasetExperimenterGroupRef​(java.lang.String group,
                                           int datasetIndex)
        Specified by:
        setDatasetExperimenterGroupRef in interface ome.xml.meta.MetadataStore

      • setDatasetName

        public void setDatasetName​(java.lang.String name,
                           int datasetIndex)
        Specified by:
        setDatasetName in interface ome.xml.meta.MetadataStore

      • getDetector

        public Detector getDetector​(int instrumentIndex,
                            int detectorIndex)
        Parameters:
        instrumentIndex - the instrument index
        detectorIndex - the detector index within the instrument
        Returns:
        the detector

      • setDetectorID

        public void setDetectorID​(java.lang.String id,
                          int instrumentIndex,
                          int detectorIndex)
        Specified by:
        setDetectorID in interface ome.xml.meta.MetadataStore

      • setDetectorAmplificationGain

        public void setDetectorAmplificationGain​(java.lang.Double amplificationGain,
                                         int instrumentIndex,
                                         int detectorIndex)
        Specified by:
        setDetectorAmplificationGain in interface ome.xml.meta.MetadataStore

      • setDetectorGain

        public void setDetectorGain​(java.lang.Double gain,
                            int instrumentIndex,
                            int detectorIndex)
        Specified by:
        setDetectorGain in interface ome.xml.meta.MetadataStore

      • setDetectorLotNumber

        public void setDetectorLotNumber​(java.lang.String lotNumber,
                                 int instrumentIndex,
                                 int detectorIndex)
        Specified by:
        setDetectorLotNumber in interface ome.xml.meta.MetadataStore

      • setDetectorManufacturer

        public void setDetectorManufacturer​(java.lang.String manufacturer,
                                    int instrumentIndex,
                                    int detectorIndex)
        Specified by:
        setDetectorManufacturer in interface ome.xml.meta.MetadataStore

      • setDetectorModel

        public void setDetectorModel​(java.lang.String model,
                             int instrumentIndex,
                             int detectorIndex)
        Specified by:
        setDetectorModel in interface ome.xml.meta.MetadataStore

      • setDetectorOffset

        public void setDetectorOffset​(java.lang.Double offset,
                              int instrumentIndex,
                              int detectorIndex)
        Specified by:
        setDetectorOffset in interface ome.xml.meta.MetadataStore

      • setDetectorSerialNumber

        public void setDetectorSerialNumber​(java.lang.String serialNumber,
                                    int instrumentIndex,
                                    int detectorIndex)
        Specified by:
        setDetectorSerialNumber in interface ome.xml.meta.MetadataStore

      • setDetectorType

        public void setDetectorType​(ome.xml.model.enums.DetectorType type,
                            int instrumentIndex,
                            int detectorIndex)
        Specified by:
        setDetectorType in interface ome.xml.meta.MetadataStore

      • setDetectorVoltage

        public void setDetectorVoltage​(ome.units.quantity.ElectricPotential voltage,
                               int instrumentIndex,
                               int detectorIndex)
        Specified by:
        setDetectorVoltage in interface ome.xml.meta.MetadataStore

      • setDetectorZoom

        public void setDetectorZoom​(java.lang.Double zoom,
                            int instrumentIndex,
                            int detectorIndex)
        Specified by:
        setDetectorZoom in interface ome.xml.meta.MetadataStore

      • setDetectorSettingsID

        public void setDetectorSettingsID​(java.lang.String id,
                                  int imageIndex,
                                  int channelIndex)
        Specified by:
        setDetectorSettingsID in interface ome.xml.meta.MetadataStore

      • setDetectorSettingsBinning

        public void setDetectorSettingsBinning​(ome.xml.model.enums.Binning binning,
                                       int imageIndex,
                                       int channelIndex)
        Specified by:
        setDetectorSettingsBinning in interface ome.xml.meta.MetadataStore

      • setDetectorSettingsGain

        public void setDetectorSettingsGain​(java.lang.Double gain,
                                    int imageIndex,
                                    int channelIndex)
        Specified by:
        setDetectorSettingsGain in interface ome.xml.meta.MetadataStore

      • setDetectorSettingsIntegration

        public void setDetectorSettingsIntegration​(ome.xml.model.primitives.PositiveInteger integration,
                                           int imageIndex,
                                           int channelIndex)
        Specified by:
        setDetectorSettingsIntegration in interface ome.xml.meta.MetadataStore

      • setDetectorSettingsOffset

        public void setDetectorSettingsOffset​(java.lang.Double offset,
                                      int imageIndex,
                                      int channelIndex)
        Specified by:
        setDetectorSettingsOffset in interface ome.xml.meta.MetadataStore

      • setDetectorSettingsReadOutRate

        public void setDetectorSettingsReadOutRate​(ome.units.quantity.Frequency readOutRate,
                                           int imageIndex,
                                           int channelIndex)
        Specified by:
        setDetectorSettingsReadOutRate in interface ome.xml.meta.MetadataStore

      • setDetectorSettingsVoltage

        public void setDetectorSettingsVoltage​(ome.units.quantity.ElectricPotential voltage,
                                       int imageIndex,
                                       int channelIndex)
        Specified by:
        setDetectorSettingsVoltage in interface ome.xml.meta.MetadataStore

      • setDetectorSettingsZoom

        public void setDetectorSettingsZoom​(java.lang.Double zoom,
                                    int imageIndex,
                                    int channelIndex)
        Specified by:
        setDetectorSettingsZoom in interface ome.xml.meta.MetadataStore

      • setDichroicID

        public void setDichroicID​(java.lang.String id,
                          int instrumentIndex,
                          int dichroicIndex)
        Specified by:
        setDichroicID in interface ome.xml.meta.MetadataStore

      • setDichroicLotNumber

        public void setDichroicLotNumber​(java.lang.String lotNumber,
                                 int instrumentIndex,
                                 int dichroicIndex)
        Specified by:
        setDichroicLotNumber in interface ome.xml.meta.MetadataStore

      • setDichroicManufacturer

        public void setDichroicManufacturer​(java.lang.String manufacturer,
                                    int instrumentIndex,
                                    int dichroicIndex)
        Specified by:
        setDichroicManufacturer in interface ome.xml.meta.MetadataStore

      • setDichroicModel

        public void setDichroicModel​(java.lang.String model,
                             int instrumentIndex,
                             int dichroicIndex)
        Specified by:
        setDichroicModel in interface ome.xml.meta.MetadataStore

      • setDichroicSerialNumber

        public void setDichroicSerialNumber​(java.lang.String serialNumber,
                                    int instrumentIndex,
                                    int dichroicIndex)
        Specified by:
        setDichroicSerialNumber in interface ome.xml.meta.MetadataStore

      • setDoubleAnnotationID

        public void setDoubleAnnotationID​(java.lang.String id,
                                  int doubleAnnotationIndex)
        Specified by:
        setDoubleAnnotationID in interface ome.xml.meta.MetadataStore

      • setDoubleAnnotationNamespace

        public void setDoubleAnnotationNamespace​(java.lang.String namespace,
                                         int doubleAnnotationIndex)
        Specified by:
        setDoubleAnnotationNamespace in interface ome.xml.meta.MetadataStore

      • setDoubleAnnotationValue

        public void setDoubleAnnotationValue​(java.lang.Double value,
                                     int doubleAnnotationIndex)
        Specified by:
        setDoubleAnnotationValue in interface ome.xml.meta.MetadataStore

      • setEllipseID

        public void setEllipseID​(java.lang.String id,
                         int ROIIndex,
                         int shapeIndex)
        Specified by:
        setEllipseID in interface ome.xml.meta.MetadataStore

      • setEllipseFillColor

        public void setEllipseFillColor​(ome.xml.model.primitives.Color fill,
                                int ROIIndex,
                                int shapeIndex)
        Specified by:
        setEllipseFillColor in interface ome.xml.meta.MetadataStore

      • setEllipseFontSize

        public void setEllipseFontSize​(ome.units.quantity.Length fontSize,
                               int ROIIndex,
                               int shapeIndex)
        Specified by:
        setEllipseFontSize in interface ome.xml.meta.MetadataStore

      • setEllipseText

        public void setEllipseText​(java.lang.String text,
                           int ROIIndex,
                           int shapeIndex)
        Specified by:
        setEllipseText in interface ome.xml.meta.MetadataStore

      • setEllipseRadiusX

        public void setEllipseRadiusX​(java.lang.Double radiusX,
                              int ROIIndex,
                              int shapeIndex)
        Specified by:
        setEllipseRadiusX in interface ome.xml.meta.MetadataStore

      • setEllipseRadiusY

        public void setEllipseRadiusY​(java.lang.Double radiusY,
                              int ROIIndex,
                              int shapeIndex)
        Specified by:
        setEllipseRadiusY in interface ome.xml.meta.MetadataStore

      • setEllipseStrokeColor

        public void setEllipseStrokeColor​(ome.xml.model.primitives.Color stroke,
                                  int ROIIndex,
                                  int shapeIndex)
        Specified by:
        setEllipseStrokeColor in interface ome.xml.meta.MetadataStore

      • setEllipseStrokeDashArray

        public void setEllipseStrokeDashArray​(java.lang.String strokeDashArray,
                                      int ROIIndex,
                                      int shapeIndex)
        Specified by:
        setEllipseStrokeDashArray in interface ome.xml.meta.MetadataStore

      • setEllipseStrokeWidth

        public void setEllipseStrokeWidth​(ome.units.quantity.Length strokeWidth,
                                  int ROIIndex,
                                  int shapeIndex)
        Specified by:
        setEllipseStrokeWidth in interface ome.xml.meta.MetadataStore

      • setEllipseTheC

        public void setEllipseTheC​(ome.xml.model.primitives.NonNegativeInteger theC,
                           int ROIIndex,
                           int shapeIndex)
        Specified by:
        setEllipseTheC in interface ome.xml.meta.MetadataStore

      • setEllipseTheT

        public void setEllipseTheT​(ome.xml.model.primitives.NonNegativeInteger theT,
                           int ROIIndex,
                           int shapeIndex)
        Specified by:
        setEllipseTheT in interface ome.xml.meta.MetadataStore

      • setEllipseTheZ

        public void setEllipseTheZ​(ome.xml.model.primitives.NonNegativeInteger theZ,
                           int ROIIndex,
                           int shapeIndex)
        Specified by:
        setEllipseTheZ in interface ome.xml.meta.MetadataStore

      • setEllipseTransform

        public void setEllipseTransform​(ome.xml.model.AffineTransform transform,
                                int ROIIndex,
                                int shapeIndex)
        Specified by:
        setEllipseTransform in interface ome.xml.meta.MetadataStore

      • setEllipseX

        public void setEllipseX​(java.lang.Double x,
                        int ROIIndex,
                        int shapeIndex)
        Specified by:
        setEllipseX in interface ome.xml.meta.MetadataStore

      • setEllipseY

        public void setEllipseY​(java.lang.Double y,
                        int ROIIndex,
                        int shapeIndex)
        Specified by:
        setEllipseY in interface ome.xml.meta.MetadataStore

      • setExperimentID

        public void setExperimentID​(java.lang.String id,
                            int experimentIndex)
        Specified by:
        setExperimentID in interface ome.xml.meta.MetadataStore

      • setExperimentDescription

        public void setExperimentDescription​(java.lang.String description,
                                     int experimentIndex)
        Specified by:
        setExperimentDescription in interface ome.xml.meta.MetadataStore

      • setExperimentExperimenterRef

        public void setExperimentExperimenterRef​(java.lang.String experimenter,
                                         int experimentIndex)
        Specified by:
        setExperimentExperimenterRef in interface ome.xml.meta.MetadataStore

      • setExperimentType

        public void setExperimentType​(ome.xml.model.enums.ExperimentType type,
                              int experimentIndex)
        Specified by:
        setExperimentType in interface ome.xml.meta.MetadataStore

      • setExperimenterID

        public void setExperimenterID​(java.lang.String id,
                              int experimenterIndex)
        Specified by:
        setExperimenterID in interface ome.xml.meta.MetadataStore

      • setExperimenterAnnotationRef

        public void setExperimenterAnnotationRef​(java.lang.String annotation,
                                         int experimenterIndex,
                                         int annotationRefIndex)
        Specified by:
        setExperimenterAnnotationRef in interface ome.xml.meta.MetadataStore

      • setExperimenterEmail

        public void setExperimenterEmail​(java.lang.String email,
                                 int experimenterIndex)
        Specified by:
        setExperimenterEmail in interface ome.xml.meta.MetadataStore

      • setExperimenterFirstName

        public void setExperimenterFirstName​(java.lang.String firstName,
                                     int experimenterIndex)
        Specified by:
        setExperimenterFirstName in interface ome.xml.meta.MetadataStore

      • setExperimenterInstitution

        public void setExperimenterInstitution​(java.lang.String institution,
                                       int experimenterIndex)
        Specified by:
        setExperimenterInstitution in interface ome.xml.meta.MetadataStore

      • setExperimenterLastName

        public void setExperimenterLastName​(java.lang.String lastName,
                                    int experimenterIndex)
        Specified by:
        setExperimenterLastName in interface ome.xml.meta.MetadataStore

      • setExperimenterMiddleName

        public void setExperimenterMiddleName​(java.lang.String middleName,
                                      int experimenterIndex)
        Specified by:
        setExperimenterMiddleName in interface ome.xml.meta.MetadataStore

      • setExperimenterUserName

        public void setExperimenterUserName​(java.lang.String userName,
                                    int experimenterIndex)
        Specified by:
        setExperimenterUserName in interface ome.xml.meta.MetadataStore

      • getFilament

        public Filament getFilament​(int instrumentIndex,
                            int lightSourceIndex)

      • setFilamentID

        public void setFilamentID​(java.lang.String id,
                          int instrumentIndex,
                          int lightSourceIndex)
        Specified by:
        setFilamentID in interface ome.xml.meta.MetadataStore

      • setFilamentLotNumber

        public void setFilamentLotNumber​(java.lang.String lotNumber,
                                 int instrumentIndex,
                                 int lightSourceIndex)
        Specified by:
        setFilamentLotNumber in interface ome.xml.meta.MetadataStore

      • setFilamentManufacturer

        public void setFilamentManufacturer​(java.lang.String manufacturer,
                                    int instrumentIndex,
                                    int lightSourceIndex)
        Specified by:
        setFilamentManufacturer in interface ome.xml.meta.MetadataStore

      • setFilamentModel

        public void setFilamentModel​(java.lang.String model,
                             int instrumentIndex,
                             int lightSourceIndex)
        Specified by:
        setFilamentModel in interface ome.xml.meta.MetadataStore

      • setFilamentPower

        public void setFilamentPower​(ome.units.quantity.Power power,
                             int instrumentIndex,
                             int lightSourceIndex)
        Specified by:
        setFilamentPower in interface ome.xml.meta.MetadataStore

      • setFilamentSerialNumber

        public void setFilamentSerialNumber​(java.lang.String serialNumber,
                                    int instrumentIndex,
                                    int lightSourceIndex)
        Specified by:
        setFilamentSerialNumber in interface ome.xml.meta.MetadataStore

      • setFilamentType

        public void setFilamentType​(ome.xml.model.enums.FilamentType type,
                            int instrumentIndex,
                            int lightSourceIndex)
        Specified by:
        setFilamentType in interface ome.xml.meta.MetadataStore

      • setFileAnnotationID

        public void setFileAnnotationID​(java.lang.String id,
                                int fileAnnotationIndex)
        Specified by:
        setFileAnnotationID in interface ome.xml.meta.MetadataStore

      • setFileAnnotationNamespace

        public void setFileAnnotationNamespace​(java.lang.String namespace,
                                       int fileAnnotationIndex)
        Specified by:
        setFileAnnotationNamespace in interface ome.xml.meta.MetadataStore

      • setFilterID

        public void setFilterID​(java.lang.String id,
                        int instrumentIndex,
                        int filterIndex)
        Specified by:
        setFilterID in interface ome.xml.meta.MetadataStore

      • setFilterFilterWheel

        public void setFilterFilterWheel​(java.lang.String filterWheel,
                                 int instrumentIndex,
                                 int filterIndex)
        Specified by:
        setFilterFilterWheel in interface ome.xml.meta.MetadataStore

      • setFilterLotNumber

        public void setFilterLotNumber​(java.lang.String lotNumber,
                               int instrumentIndex,
                               int filterIndex)
        Specified by:
        setFilterLotNumber in interface ome.xml.meta.MetadataStore

      • setFilterManufacturer

        public void setFilterManufacturer​(java.lang.String manufacturer,
                                  int instrumentIndex,
                                  int filterIndex)
        Specified by:
        setFilterManufacturer in interface ome.xml.meta.MetadataStore

      • setFilterModel

        public void setFilterModel​(java.lang.String model,
                           int instrumentIndex,
                           int filterIndex)
        Specified by:
        setFilterModel in interface ome.xml.meta.MetadataStore

      • setFilterSerialNumber

        public void setFilterSerialNumber​(java.lang.String serialNumber,
                                  int instrumentIndex,
                                  int filterIndex)
        Specified by:
        setFilterSerialNumber in interface ome.xml.meta.MetadataStore

      • setFilterType

        public void setFilterType​(ome.xml.model.enums.FilterType type,
                          int instrumentIndex,
                          int filterIndex)
        Specified by:
        setFilterType in interface ome.xml.meta.MetadataStore

      • getFilterSet

        public FilterSet getFilterSet​(int instrumentIndex,
                              int filterSetIndex)

      • setFilterSetID

        public void setFilterSetID​(java.lang.String id,
                           int instrumentIndex,
                           int filterSetIndex)
        Specified by:
        setFilterSetID in interface ome.xml.meta.MetadataStore

      • setFilterSetDichroicRef

        public void setFilterSetDichroicRef​(java.lang.String dichroic,
                                    int instrumentIndex,
                                    int filterSetIndex)
        Specified by:
        setFilterSetDichroicRef in interface ome.xml.meta.MetadataStore

      • setFilterSetEmissionFilterRef

        public void setFilterSetEmissionFilterRef​(java.lang.String emissionFilter,
                                          int instrumentIndex,
                                          int filterSetIndex,
                                          int emissionFilterRefIndex)
        Specified by:
        setFilterSetEmissionFilterRef in interface ome.xml.meta.MetadataStore

      • setFilterSetExcitationFilterRef

        public void setFilterSetExcitationFilterRef​(java.lang.String excitationFilter,
                                            int instrumentIndex,
                                            int filterSetIndex,
                                            int excitationFilterRefIndex)
        Specified by:
        setFilterSetExcitationFilterRef in interface ome.xml.meta.MetadataStore

      • setFilterSetLotNumber

        public void setFilterSetLotNumber​(java.lang.String lotNumber,
                                  int instrumentIndex,
                                  int filterSetIndex)
        Specified by:
        setFilterSetLotNumber in interface ome.xml.meta.MetadataStore

      • setFilterSetManufacturer

        public void setFilterSetManufacturer​(java.lang.String manufacturer,
                                     int instrumentIndex,
                                     int filterSetIndex)
        Specified by:
        setFilterSetManufacturer in interface ome.xml.meta.MetadataStore

      • setFilterSetModel

        public void setFilterSetModel​(java.lang.String model,
                              int instrumentIndex,
                              int filterSetIndex)
        Specified by:
        setFilterSetModel in interface ome.xml.meta.MetadataStore

      • setFilterSetSerialNumber

        public void setFilterSetSerialNumber​(java.lang.String serialNumber,
                                     int instrumentIndex,
                                     int filterSetIndex)
        Specified by:
        setFilterSetSerialNumber in interface ome.xml.meta.MetadataStore

      • setFolderAnnotationRef

        public void setFolderAnnotationRef​(java.lang.String annotation,
                                   int folderIndex,
                                   int annotationRefIndex)
        Specified by:
        setFolderAnnotationRef in interface ome.xml.meta.MetadataStore

      • setFolderDescription

        public void setFolderDescription​(java.lang.String description,
                                 int folderIndex)
        Specified by:
        setFolderDescription in interface ome.xml.meta.MetadataStore

      • setFolderFolderRef

        public void setFolderFolderRef​(java.lang.String folder,
                               int folderIndex,
                               int folderRefIndex)
        Specified by:
        setFolderFolderRef in interface ome.xml.meta.MetadataStore

      • setFolderID

        public void setFolderID​(java.lang.String id,
                        int folderIndex)
        Specified by:
        setFolderID in interface ome.xml.meta.MetadataStore

      • setFolderImageRef

        public void setFolderImageRef​(java.lang.String image,
                              int folderIndex,
                              int imageRefIndex)
        Specified by:
        setFolderImageRef in interface ome.xml.meta.MetadataStore

      • setFolderName

        public void setFolderName​(java.lang.String name,
                          int folderIndex)
        Specified by:
        setFolderName in interface ome.xml.meta.MetadataStore

      • setFolderROIRef

        public void setFolderROIRef​(java.lang.String roi,
                            int folderIndex,
                            int ROIRefIndex)
        Specified by:
        setFolderROIRef in interface ome.xml.meta.MetadataStore

      • setGenericExcitationSourceID

        public void setGenericExcitationSourceID​(java.lang.String id,
                                         int instrumentIndex,
                                         int lightSourceIndex)
        Specified by:
        setGenericExcitationSourceID in interface ome.xml.meta.MetadataStore

      • setGenericExcitationSourceLotNumber

        public void setGenericExcitationSourceLotNumber​(java.lang.String lotNumber,
                                                int instrumentIndex,
                                                int lightSourceIndex)
        Specified by:
        setGenericExcitationSourceLotNumber in interface ome.xml.meta.MetadataStore

      • setGenericExcitationSourceMap

        public void setGenericExcitationSourceMap​(java.util.List<ome.xml.model.MapPair> map,
                                          int instrumentIndex,
                                          int lightSourceIndex)
        Specified by:
        setGenericExcitationSourceMap in interface ome.xml.meta.MetadataStore

      • setGenericExcitationSourceManufacturer

        public void setGenericExcitationSourceManufacturer​(java.lang.String manufacturer,
                                                   int instrumentIndex,
                                                   int lightSourceIndex)
        Specified by:
        setGenericExcitationSourceManufacturer in interface ome.xml.meta.MetadataStore

      • setGenericExcitationSourceModel

        public void setGenericExcitationSourceModel​(java.lang.String model,
                                            int instrumentIndex,
                                            int lightSourceIndex)
        Specified by:
        setGenericExcitationSourceModel in interface ome.xml.meta.MetadataStore

      • setGenericExcitationSourcePower

        public void setGenericExcitationSourcePower​(ome.units.quantity.Power power,
                                            int instrumentIndex,
                                            int lightSourceIndex)
        Specified by:
        setGenericExcitationSourcePower in interface ome.xml.meta.MetadataStore

      • setGenericExcitationSourceSerialNumber

        public void setGenericExcitationSourceSerialNumber​(java.lang.String serialNumber,
                                                   int instrumentIndex,
                                                   int lightSourceIndex)
        Specified by:
        setGenericExcitationSourceSerialNumber in interface ome.xml.meta.MetadataStore

      • setExperimenterGroupID

        public void setExperimenterGroupID​(java.lang.String id,
                                   int groupIndex)
        Specified by:
        setExperimenterGroupID in interface ome.xml.meta.MetadataStore

      • setExperimenterGroupDescription

        public void setExperimenterGroupDescription​(java.lang.String description,
                                            int groupIndex)
        Specified by:
        setExperimenterGroupDescription in interface ome.xml.meta.MetadataStore

      • setExperimenterGroupLeader

        public void setExperimenterGroupLeader​(java.lang.String leader,
                                       int groupIndex,
                                       int leaderIndex)
        Specified by:
        setExperimenterGroupLeader in interface ome.xml.meta.MetadataStore

      • setExperimenterGroupName

        public void setExperimenterGroupName​(java.lang.String name,
                                     int groupIndex)
        Specified by:
        setExperimenterGroupName in interface ome.xml.meta.MetadataStore

      • setImageID

        public void setImageID​(java.lang.String id,
                       int imageIndex)
        Specified by:
        setImageID in interface ome.xml.meta.MetadataStore

      • setImageAcquisitionDate

        public void setImageAcquisitionDate​(ome.xml.model.primitives.Timestamp acquiredDate,
                                    int imageIndex)
        Specified by:
        setImageAcquisitionDate in interface ome.xml.meta.MetadataStore

      • setImageAnnotationRef

        public void setImageAnnotationRef​(java.lang.String annotation,
                                  int imageIndex,
                                  int annotationRefIndex)
        Specified by:
        setImageAnnotationRef in interface ome.xml.meta.MetadataStore

      • setImageDescription

        public void setImageDescription​(java.lang.String description,
                                int imageIndex)
        Specified by:
        setImageDescription in interface ome.xml.meta.MetadataStore

      • setImageExperimentRef

        public void setImageExperimentRef​(java.lang.String experiment,
                                  int imageIndex)
        Specified by:
        setImageExperimentRef in interface ome.xml.meta.MetadataStore

      • setImageExperimenterRef

        public void setImageExperimenterRef​(java.lang.String experimenter,
                                    int imageIndex)
        Specified by:
        setImageExperimenterRef in interface ome.xml.meta.MetadataStore

      • setImageExperimenterGroupRef

        public void setImageExperimenterGroupRef​(java.lang.String group,
                                         int imageIndex)
        Specified by:
        setImageExperimenterGroupRef in interface ome.xml.meta.MetadataStore

      • setImageInstrumentRef

        public void setImageInstrumentRef​(java.lang.String instrument,
                                  int imageIndex)
        Specified by:
        setImageInstrumentRef in interface ome.xml.meta.MetadataStore

      • setImageMicrobeamManipulationRef

        public void setImageMicrobeamManipulationRef​(java.lang.String microbeamManipulation,
                                             int imageIndex,
                                             int microbeamManipulationRefIndex)
        Specified by:
        setImageMicrobeamManipulationRef in interface ome.xml.meta.MetadataStore

      • setImageName

        public void setImageName​(java.lang.String name,
                         int imageIndex)
        Specified by:
        setImageName in interface ome.xml.meta.MetadataStore

      • setImageROIRef

        public void setImageROIRef​(java.lang.String roi,
                           int imageIndex,
                           int ROIRefIndex)
        Specified by:
        setImageROIRef in interface ome.xml.meta.MetadataStore

      • getObjectiveSettings

        public ObjectiveSettings getObjectiveSettings​(int imageIndex)

      • setObjectiveSettingsID

        public void setObjectiveSettingsID​(java.lang.String id,
                                   int imageIndex)
        Specified by:
        setObjectiveSettingsID in interface ome.xml.meta.MetadataStore

      • setObjectiveSettingsCorrectionCollar

        public void setObjectiveSettingsCorrectionCollar​(java.lang.Double correctionCollar,
                                                 int imageIndex)
        Specified by:
        setObjectiveSettingsCorrectionCollar in interface ome.xml.meta.MetadataStore

      • setObjectiveSettingsMedium

        public void setObjectiveSettingsMedium​(ome.xml.model.enums.Medium medium,
                                       int imageIndex)
        Specified by:
        setObjectiveSettingsMedium in interface ome.xml.meta.MetadataStore

      • setObjectiveSettingsRefractiveIndex

        public void setObjectiveSettingsRefractiveIndex​(java.lang.Double refractiveIndex,
                                                int imageIndex)
        Specified by:
        setObjectiveSettingsRefractiveIndex in interface ome.xml.meta.MetadataStore

      • getImagingEnvironment

        public ImagingEnvironment getImagingEnvironment​(int imageIndex)

      • setImagingEnvironmentAirPressure

        public void setImagingEnvironmentAirPressure​(ome.units.quantity.Pressure airPressure,
                                             int imageIndex)
        Specified by:
        setImagingEnvironmentAirPressure in interface ome.xml.meta.MetadataStore

      • setImagingEnvironmentCO2Percent

        public void setImagingEnvironmentCO2Percent​(ome.xml.model.primitives.PercentFraction co2percent,
                                            int imageIndex)
        Specified by:
        setImagingEnvironmentCO2Percent in interface ome.xml.meta.MetadataStore

      • setImagingEnvironmentHumidity

        public void setImagingEnvironmentHumidity​(ome.xml.model.primitives.PercentFraction humidity,
                                          int imageIndex)
        Specified by:
        setImagingEnvironmentHumidity in interface ome.xml.meta.MetadataStore

      • setImagingEnvironmentMap

        public void setImagingEnvironmentMap​(java.util.List<ome.xml.model.MapPair> map,
                                     int imageIndex)
        Specified by:
        setImagingEnvironmentMap in interface ome.xml.meta.MetadataStore

      • setImagingEnvironmentTemperature

        public void setImagingEnvironmentTemperature​(ome.units.quantity.Temperature temperature,
                                             int imageIndex)
        Specified by:
        setImagingEnvironmentTemperature in interface ome.xml.meta.MetadataStore

      • setInstrumentID

        public void setInstrumentID​(java.lang.String id,
                            int instrumentIndex)
        Specified by:
        setInstrumentID in interface ome.xml.meta.MetadataStore

      • getLaser

        public Laser getLaser​(int instrumentIndex,
                      int lightSourceIndex)

      • setLaserID

        public void setLaserID​(java.lang.String id,
                       int instrumentIndex,
                       int lightSourceIndex)
        Specified by:
        setLaserID in interface ome.xml.meta.MetadataStore

      • setLaserFrequencyMultiplication

        public void setLaserFrequencyMultiplication​(ome.xml.model.primitives.PositiveInteger frequencyMultiplication,
                                            int instrumentIndex,
                                            int lightSourceIndex)
        Specified by:
        setLaserFrequencyMultiplication in interface ome.xml.meta.MetadataStore

      • setLaserLaserMedium

        public void setLaserLaserMedium​(ome.xml.model.enums.LaserMedium laserMedium,
                                int instrumentIndex,
                                int lightSourceIndex)
        Specified by:
        setLaserLaserMedium in interface ome.xml.meta.MetadataStore

      • setLaserLotNumber

        public void setLaserLotNumber​(java.lang.String lotNumber,
                              int instrumentIndex,
                              int lightSourceIndex)
        Specified by:
        setLaserLotNumber in interface ome.xml.meta.MetadataStore

      • setLaserManufacturer

        public void setLaserManufacturer​(java.lang.String manufacturer,
                                 int instrumentIndex,
                                 int lightSourceIndex)
        Specified by:
        setLaserManufacturer in interface ome.xml.meta.MetadataStore

      • setLaserModel

        public void setLaserModel​(java.lang.String model,
                          int instrumentIndex,
                          int lightSourceIndex)
        Specified by:
        setLaserModel in interface ome.xml.meta.MetadataStore

      • setLaserPockelCell

        public void setLaserPockelCell​(java.lang.Boolean pockelCell,
                               int instrumentIndex,
                               int lightSourceIndex)
        Specified by:
        setLaserPockelCell in interface ome.xml.meta.MetadataStore

      • setLaserPower

        public void setLaserPower​(ome.units.quantity.Power power,
                          int instrumentIndex,
                          int lightSourceIndex)
        Specified by:
        setLaserPower in interface ome.xml.meta.MetadataStore

      • setLaserPulse

        public void setLaserPulse​(ome.xml.model.enums.Pulse pulse,
                          int instrumentIndex,
                          int lightSourceIndex)
        Specified by:
        setLaserPulse in interface ome.xml.meta.MetadataStore

      • setLaserPump

        public void setLaserPump​(java.lang.String pump,
                         int instrumentIndex,
                         int lightSourceIndex)
        Specified by:
        setLaserPump in interface ome.xml.meta.MetadataStore

      • setLaserRepetitionRate

        public void setLaserRepetitionRate​(ome.units.quantity.Frequency repetitionRate,
                                   int instrumentIndex,
                                   int lightSourceIndex)
        Specified by:
        setLaserRepetitionRate in interface ome.xml.meta.MetadataStore

      • setLaserSerialNumber

        public void setLaserSerialNumber​(java.lang.String serialNumber,
                                 int instrumentIndex,
                                 int lightSourceIndex)
        Specified by:
        setLaserSerialNumber in interface ome.xml.meta.MetadataStore

      • setLaserTuneable

        public void setLaserTuneable​(java.lang.Boolean tuneable,
                             int instrumentIndex,
                             int lightSourceIndex)
        Specified by:
        setLaserTuneable in interface ome.xml.meta.MetadataStore

      • setLaserType

        public void setLaserType​(ome.xml.model.enums.LaserType type,
                         int instrumentIndex,
                         int lightSourceIndex)
        Specified by:
        setLaserType in interface ome.xml.meta.MetadataStore

      • setLaserWavelength

        public void setLaserWavelength​(ome.units.quantity.Length wavelength,
                               int instrumentIndex,
                               int lightSourceIndex)
        Specified by:
        setLaserWavelength in interface ome.xml.meta.MetadataStore

      • getLightEmittingDiode

        public LightEmittingDiode getLightEmittingDiode​(int instrumentIndex,
                                                int lightSourceIndex)

      • setLightEmittingDiodeID

        public void setLightEmittingDiodeID​(java.lang.String id,
                                    int instrumentIndex,
                                    int lightSourceIndex)
        Specified by:
        setLightEmittingDiodeID in interface ome.xml.meta.MetadataStore

      • setLightEmittingDiodeLotNumber

        public void setLightEmittingDiodeLotNumber​(java.lang.String lotNumber,
                                           int instrumentIndex,
                                           int lightSourceIndex)
        Specified by:
        setLightEmittingDiodeLotNumber in interface ome.xml.meta.MetadataStore

      • setLightEmittingDiodeManufacturer

        public void setLightEmittingDiodeManufacturer​(java.lang.String manufacturer,
                                              int instrumentIndex,
                                              int lightSourceIndex)
        Specified by:
        setLightEmittingDiodeManufacturer in interface ome.xml.meta.MetadataStore

      • setLightEmittingDiodeModel

        public void setLightEmittingDiodeModel​(java.lang.String model,
                                       int instrumentIndex,
                                       int lightSourceIndex)
        Specified by:
        setLightEmittingDiodeModel in interface ome.xml.meta.MetadataStore

      • setLightEmittingDiodePower

        public void setLightEmittingDiodePower​(ome.units.quantity.Power power,
                                       int instrumentIndex,
                                       int lightSourceIndex)
        Specified by:
        setLightEmittingDiodePower in interface ome.xml.meta.MetadataStore

      • setLightEmittingDiodeSerialNumber

        public void setLightEmittingDiodeSerialNumber​(java.lang.String serialNumber,
                                              int instrumentIndex,
                                              int lightSourceIndex)
        Specified by:
        setLightEmittingDiodeSerialNumber in interface ome.xml.meta.MetadataStore

      • setLightPathDichroicRef

        public void setLightPathDichroicRef​(java.lang.String dichroic,
                                    int imageIndex,
                                    int channelIndex)
        Specified by:
        setLightPathDichroicRef in interface ome.xml.meta.MetadataStore

      • setLightPathEmissionFilterRef

        public void setLightPathEmissionFilterRef​(java.lang.String emissionFilter,
                                          int imageIndex,
                                          int channelIndex,
                                          int emissionFilterRefIndex)
        Specified by:
        setLightPathEmissionFilterRef in interface ome.xml.meta.MetadataStore

      • setLightPathExcitationFilterRef

        public void setLightPathExcitationFilterRef​(java.lang.String excitationFilter,
                                            int imageIndex,
                                            int channelIndex,
                                            int excitationFilterRefIndex)
        Specified by:
        setLightPathExcitationFilterRef in interface ome.xml.meta.MetadataStore

      • getLine

        public Line getLine​(int ROIIndex,
                    int shapeIndex)

      • setLineID

        public void setLineID​(java.lang.String id,
                      int ROIIndex,
                      int shapeIndex)
        Specified by:
        setLineID in interface ome.xml.meta.MetadataStore

      • setLineText

        public void setLineText​(java.lang.String text,
                        int ROIIndex,
                        int shapeIndex)
        Specified by:
        setLineText in interface ome.xml.meta.MetadataStore

      • setLineFillColor

        public void setLineFillColor​(ome.xml.model.primitives.Color fill,
                             int ROIIndex,
                             int shapeIndex)
        Specified by:
        setLineFillColor in interface ome.xml.meta.MetadataStore

      • setLineFontSize

        public void setLineFontSize​(ome.units.quantity.Length fontSize,
                            int ROIIndex,
                            int shapeIndex)
        Specified by:
        setLineFontSize in interface ome.xml.meta.MetadataStore

      • setLineStrokeColor

        public void setLineStrokeColor​(ome.xml.model.primitives.Color stroke,
                               int ROIIndex,
                               int shapeIndex)
        Specified by:
        setLineStrokeColor in interface ome.xml.meta.MetadataStore

      • setLineStrokeDashArray

        public void setLineStrokeDashArray​(java.lang.String strokeDashArray,
                                   int ROIIndex,
                                   int shapeIndex)
        Specified by:
        setLineStrokeDashArray in interface ome.xml.meta.MetadataStore

      • setLineStrokeWidth

        public void setLineStrokeWidth​(ome.units.quantity.Length strokeWidth,
                               int ROIIndex,
                               int shapeIndex)
        Specified by:
        setLineStrokeWidth in interface ome.xml.meta.MetadataStore

      • setLineTheC

        public void setLineTheC​(ome.xml.model.primitives.NonNegativeInteger theC,
                        int ROIIndex,
                        int shapeIndex)
        Specified by:
        setLineTheC in interface ome.xml.meta.MetadataStore

      • setLineTheT

        public void setLineTheT​(ome.xml.model.primitives.NonNegativeInteger theT,
                        int ROIIndex,
                        int shapeIndex)
        Specified by:
        setLineTheT in interface ome.xml.meta.MetadataStore

      • setLineTheZ

        public void setLineTheZ​(ome.xml.model.primitives.NonNegativeInteger theZ,
                        int ROIIndex,
                        int shapeIndex)
        Specified by:
        setLineTheZ in interface ome.xml.meta.MetadataStore

      • setLineTransform

        public void setLineTransform​(ome.xml.model.AffineTransform transform,
                             int ROIIndex,
                             int shapeIndex)
        Specified by:
        setLineTransform in interface ome.xml.meta.MetadataStore

      • setLineX1

        public void setLineX1​(java.lang.Double x1,
                      int ROIIndex,
                      int shapeIndex)
        Specified by:
        setLineX1 in interface ome.xml.meta.MetadataStore

      • setLineX2

        public void setLineX2​(java.lang.Double x2,
                      int ROIIndex,
                      int shapeIndex)
        Specified by:
        setLineX2 in interface ome.xml.meta.MetadataStore

      • setLineY1

        public void setLineY1​(java.lang.Double y1,
                      int ROIIndex,
                      int shapeIndex)
        Specified by:
        setLineY1 in interface ome.xml.meta.MetadataStore

      • setLineY2

        public void setLineY2​(java.lang.Double y2,
                      int ROIIndex,
                      int shapeIndex)
        Specified by:
        setLineY2 in interface ome.xml.meta.MetadataStore

      • getListAnnotation

        public ListAnnotation getListAnnotation​(int listAnnotationIndex)

      • setListAnnotationID

        public void setListAnnotationID​(java.lang.String id,
                                int listAnnotationIndex)
        Specified by:
        setListAnnotationID in interface ome.xml.meta.MetadataStore

      • setListAnnotationAnnotationRef

        public void setListAnnotationAnnotationRef​(java.lang.String annotation,
                                           int listAnnotationIndex,
                                           int annotationRefIndex)
        Specified by:
        setListAnnotationAnnotationRef in interface ome.xml.meta.MetadataStore

      • setListAnnotationNamespace

        public void setListAnnotationNamespace​(java.lang.String namespace,
                                       int listAnnotationIndex)
        Specified by:
        setListAnnotationNamespace in interface ome.xml.meta.MetadataStore

      • getLongAnnotation

        public LongAnnotation getLongAnnotation​(int longAnnotationIndex)

      • setLongAnnotationID

        public void setLongAnnotationID​(java.lang.String id,
                                int longAnnotationIndex)
        Specified by:
        setLongAnnotationID in interface ome.xml.meta.MetadataStore

      • setLongAnnotationNamespace

        public void setLongAnnotationNamespace​(java.lang.String namespace,
                                       int longAnnotationIndex)
        Specified by:
        setLongAnnotationNamespace in interface ome.xml.meta.MetadataStore

      • setLongAnnotationValue

        public void setLongAnnotationValue​(java.lang.Long value,
                                   int longAnnotationIndex)
        Specified by:
        setLongAnnotationValue in interface ome.xml.meta.MetadataStore

      • getMask

        public Mask getMask​(int ROIIndex,
                    int shapeIndex)

      • setMaskBinData

        public void setMaskBinData​(byte[] binData,
                           int roiIndex,
                           int shapeIndex)
        Specified by:
        setMaskBinData in interface ome.xml.meta.MetadataStore

      • setMaskBinDataBigEndian

        public void setMaskBinDataBigEndian​(java.lang.Boolean isBigEndian,
                                    int roiIndex,
                                    int shapeIndex)
        Specified by:
        setMaskBinDataBigEndian in interface ome.xml.meta.MetadataStore

      • setMaskBinDataCompression

        public void setMaskBinDataCompression​(ome.xml.model.enums.Compression compression,
                                      int roiIndex,
                                      int shapeIndex)
        Specified by:
        setMaskBinDataCompression in interface ome.xml.meta.MetadataStore

      • setMaskBinDataLength

        public void setMaskBinDataLength​(ome.xml.model.primitives.NonNegativeLong length,
                                 int roiIndex,
                                 int shapeIndex)
        Specified by:
        setMaskBinDataLength in interface ome.xml.meta.MetadataStore

      • setMaskText

        public void setMaskText​(java.lang.String description,
                        int ROIIndex,
                        int shapeIndex)
        Specified by:
        setMaskText in interface ome.xml.meta.MetadataStore

      • setMaskFillColor

        public void setMaskFillColor​(ome.xml.model.primitives.Color fill,
                             int ROIIndex,
                             int shapeIndex)
        Specified by:
        setMaskFillColor in interface ome.xml.meta.MetadataStore

      • setMaskFontSize

        public void setMaskFontSize​(ome.units.quantity.Length fontSize,
                            int ROIIndex,
                            int shapeIndex)
        Specified by:
        setMaskFontSize in interface ome.xml.meta.MetadataStore

      • setMaskID

        public void setMaskID​(java.lang.String id,
                      int ROIIndex,
                      int shapeIndex)
        Specified by:
        setMaskID in interface ome.xml.meta.MetadataStore

      • setMaskStrokeColor

        public void setMaskStrokeColor​(ome.xml.model.primitives.Color stroke,
                               int ROIIndex,
                               int shapeIndex)
        Specified by:
        setMaskStrokeColor in interface ome.xml.meta.MetadataStore

      • setMaskStrokeDashArray

        public void setMaskStrokeDashArray​(java.lang.String strokeDashArray,
                                   int ROIIndex,
                                   int shapeIndex)
        Specified by:
        setMaskStrokeDashArray in interface ome.xml.meta.MetadataStore

      • setMaskStrokeWidth

        public void setMaskStrokeWidth​(ome.units.quantity.Length strokeWidth,
                               int ROIIndex,
                               int shapeIndex)
        Specified by:
        setMaskStrokeWidth in interface ome.xml.meta.MetadataStore

      • setMaskTheC

        public void setMaskTheC​(ome.xml.model.primitives.NonNegativeInteger theC,
                        int ROIIndex,
                        int shapeIndex)
        Specified by:
        setMaskTheC in interface ome.xml.meta.MetadataStore

      • setMaskTheT

        public void setMaskTheT​(ome.xml.model.primitives.NonNegativeInteger theT,
                        int ROIIndex,
                        int shapeIndex)
        Specified by:
        setMaskTheT in interface ome.xml.meta.MetadataStore

      • setMaskTheZ

        public void setMaskTheZ​(ome.xml.model.primitives.NonNegativeInteger theZ,
                        int ROIIndex,
                        int shapeIndex)
        Specified by:
        setMaskTheZ in interface ome.xml.meta.MetadataStore

      • setMaskTransform

        public void setMaskTransform​(ome.xml.model.AffineTransform transform,
                             int ROIIndex,
                             int shapeIndex)
        Specified by:
        setMaskTransform in interface ome.xml.meta.MetadataStore

      • setMaskX

        public void setMaskX​(java.lang.Double x,
                     int ROIIndex,
                     int shapeIndex)
        Specified by:
        setMaskX in interface ome.xml.meta.MetadataStore

      • setMaskY

        public void setMaskY​(java.lang.Double y,
                     int ROIIndex,
                     int shapeIndex)
        Specified by:
        setMaskY in interface ome.xml.meta.MetadataStore

      • setMaskHeight

        public void setMaskHeight​(java.lang.Double height,
                          int ROIIndex,
                          int shapeIndex)
        Specified by:
        setMaskHeight in interface ome.xml.meta.MetadataStore

      • setMaskWidth

        public void setMaskWidth​(java.lang.Double width,
                         int ROIIndex,
                         int shapeIndex)
        Specified by:
        setMaskWidth in interface ome.xml.meta.MetadataStore

      • getMicrobeamManipulation

        public MicrobeamManipulation getMicrobeamManipulation​(int experimentIndex,
                                                      int microbeamManipulationIndex)

      • setMicrobeamManipulationID

        public void setMicrobeamManipulationID​(java.lang.String id,
                                       int experimentIndex,
                                       int microbeamManipulationIndex)
        Specified by:
        setMicrobeamManipulationID in interface ome.xml.meta.MetadataStore

      • setMicrobeamManipulationDescription

        public void setMicrobeamManipulationDescription​(java.lang.String description,
                                                int experimentIndex,
                                                int microbeamManipulationIndex)
        Specified by:
        setMicrobeamManipulationDescription in interface ome.xml.meta.MetadataStore

      • setMicrobeamManipulationExperimenterRef

        public void setMicrobeamManipulationExperimenterRef​(java.lang.String experimenter,
                                                    int experimentIndex,
                                                    int microbeamManipulationIndex)
        Specified by:
        setMicrobeamManipulationExperimenterRef in interface ome.xml.meta.MetadataStore

      • setMicrobeamManipulationROIRef

        public void setMicrobeamManipulationROIRef​(java.lang.String roi,
                                           int experimentIndex,
                                           int microbeamManipulationIndex,
                                           int ROIRefIndex)
        Specified by:
        setMicrobeamManipulationROIRef in interface ome.xml.meta.MetadataStore

      • setMicrobeamManipulationType

        public void setMicrobeamManipulationType​(ome.xml.model.enums.MicrobeamManipulationType type,
                                         int experimentIndex,
                                         int microbeamManipulationIndex)
        Specified by:
        setMicrobeamManipulationType in interface ome.xml.meta.MetadataStore

      • getMicrobeamManipulationLightSourceSettings

        public LightSettings getMicrobeamManipulationLightSourceSettings​(int experimentIndex,
                                                                 int microbeamManipulationIndex,
                                                                 int lightSourceSettingsIndex)

      • setMicrobeamManipulationLightSourceSettingsID

        public void setMicrobeamManipulationLightSourceSettingsID​(java.lang.String id,
                                                          int experimentIndex,
                                                          int microbeamManipulationIndex,
                                                          int lightSourceSettingsIndex)
        Specified by:
        setMicrobeamManipulationLightSourceSettingsID in interface ome.xml.meta.MetadataStore

      • setMicrobeamManipulationLightSourceSettingsAttenuation

        public void setMicrobeamManipulationLightSourceSettingsAttenuation​(ome.xml.model.primitives.PercentFraction attenuation,
                                                                   int experimentIndex,
                                                                   int microbeamManipulationIndex,
                                                                   int lightSourceSettingsIndex)
        Specified by:
        setMicrobeamManipulationLightSourceSettingsAttenuation in interface ome.xml.meta.MetadataStore

      • setMicrobeamManipulationLightSourceSettingsWavelength

        public void setMicrobeamManipulationLightSourceSettingsWavelength​(ome.units.quantity.Length wavelength,
                                                                  int experimentIndex,
                                                                  int microbeamManipulationIndex,
                                                                  int lightSourceSettingsIndex)
        Specified by:
        setMicrobeamManipulationLightSourceSettingsWavelength in interface ome.xml.meta.MetadataStore

      • setMicroscopeLotNumber

        public void setMicroscopeLotNumber​(java.lang.String lotNumber,
                                   int instrumentIndex)
        Specified by:
        setMicroscopeLotNumber in interface ome.xml.meta.MetadataStore

      • setMicroscopeManufacturer

        public void setMicroscopeManufacturer​(java.lang.String manufacturer,
                                      int instrumentIndex)
        Specified by:
        setMicroscopeManufacturer in interface ome.xml.meta.MetadataStore

      • setMicroscopeModel

        public void setMicroscopeModel​(java.lang.String model,
                               int instrumentIndex)
        Specified by:
        setMicroscopeModel in interface ome.xml.meta.MetadataStore

      • setMicroscopeSerialNumber

        public void setMicroscopeSerialNumber​(java.lang.String serialNumber,
                                      int instrumentIndex)
        Specified by:
        setMicroscopeSerialNumber in interface ome.xml.meta.MetadataStore

      • setMicroscopeType

        public void setMicroscopeType​(ome.xml.model.enums.MicroscopeType type,
                              int instrumentIndex)
        Specified by:
        setMicroscopeType in interface ome.xml.meta.MetadataStore

      • getObjective

        public Objective getObjective​(int instrumentIndex,
                              int objectiveIndex)

      • setObjectiveCalibratedMagnification

        public void setObjectiveCalibratedMagnification​(java.lang.Double calibratedMagnification,
                                                int instrumentIndex,
                                                int objectiveIndex)
        Specified by:
        setObjectiveCalibratedMagnification in interface ome.xml.meta.MetadataStore

      • setObjectiveCorrection

        public void setObjectiveCorrection​(ome.xml.model.enums.Correction correction,
                                   int instrumentIndex,
                                   int objectiveIndex)
        Specified by:
        setObjectiveCorrection in interface ome.xml.meta.MetadataStore

      • setObjectiveID

        public void setObjectiveID​(java.lang.String id,
                           int instrumentIndex,
                           int objectiveIndex)
        Specified by:
        setObjectiveID in interface ome.xml.meta.MetadataStore

      • setObjectiveImmersion

        public void setObjectiveImmersion​(ome.xml.model.enums.Immersion immersion,
                                  int instrumentIndex,
                                  int objectiveIndex)
        Specified by:
        setObjectiveImmersion in interface ome.xml.meta.MetadataStore

      • setObjectiveIris

        public void setObjectiveIris​(java.lang.Boolean iris,
                             int instrumentIndex,
                             int objectiveIndex)
        Specified by:
        setObjectiveIris in interface ome.xml.meta.MetadataStore

      • setObjectiveLensNA

        public void setObjectiveLensNA​(java.lang.Double lensNA,
                               int instrumentIndex,
                               int objectiveIndex)
        Specified by:
        setObjectiveLensNA in interface ome.xml.meta.MetadataStore

      • setObjectiveLotNumber

        public void setObjectiveLotNumber​(java.lang.String lotNumber,
                                  int instrumentIndex,
                                  int objectiveIndex)
        Specified by:
        setObjectiveLotNumber in interface ome.xml.meta.MetadataStore

      • setObjectiveManufacturer

        public void setObjectiveManufacturer​(java.lang.String manufacturer,
                                     int instrumentIndex,
                                     int objectiveIndex)
        Specified by:
        setObjectiveManufacturer in interface ome.xml.meta.MetadataStore

      • setObjectiveModel

        public void setObjectiveModel​(java.lang.String model,
                              int instrumentIndex,
                              int objectiveIndex)
        Specified by:
        setObjectiveModel in interface ome.xml.meta.MetadataStore

      • setObjectiveNominalMagnification

        public void setObjectiveNominalMagnification​(java.lang.Double nominalMagnification,
                                             int instrumentIndex,
                                             int objectiveIndex)
        Specified by:
        setObjectiveNominalMagnification in interface ome.xml.meta.MetadataStore

      • setObjectiveSerialNumber

        public void setObjectiveSerialNumber​(java.lang.String serialNumber,
                                     int instrumentIndex,
                                     int objectiveIndex)
        Specified by:
        setObjectiveSerialNumber in interface ome.xml.meta.MetadataStore

      • setObjectiveWorkingDistance

        public void setObjectiveWorkingDistance​(ome.units.quantity.Length workingDistance,
                                        int instrumentIndex,
                                        int objectiveIndex)
        Specified by:
        setObjectiveWorkingDistance in interface ome.xml.meta.MetadataStore

      • setPixelsID

        public void setPixelsID​(java.lang.String id,
                        int imageIndex)
        Specified by:
        setPixelsID in interface ome.xml.meta.MetadataStore

      • setPixelsBigEndian

        public void setPixelsBigEndian​(java.lang.Boolean value,
                               int index)
        Specified by:
        setPixelsBigEndian in interface ome.xml.meta.MetadataStore

      • setPixelsBinData

        public void setPixelsBinData​(byte[] binData,
                             int imageIndex,
                             int binDataIndex)
        Specified by:
        setPixelsBinData in interface ome.xml.meta.MetadataStore

      • setPixelsBinDataBigEndian

        public void setPixelsBinDataBigEndian​(java.lang.Boolean bigEndian,
                                      int imageIndex,
                                      int binDataIndex)
        Specified by:
        setPixelsBinDataBigEndian in interface ome.xml.meta.MetadataStore

      • setPixelsBinDataCompression

        public void setPixelsBinDataCompression​(ome.xml.model.enums.Compression compression,
                                        int imageIndex,
                                        int binDataIndex)
        Specified by:
        setPixelsBinDataCompression in interface ome.xml.meta.MetadataStore

      • setPixelsBinDataLength

        public void setPixelsBinDataLength​(ome.xml.model.primitives.NonNegativeLong length,
                                   int imageIndex,
                                   int binDataIndex)
        Specified by:
        setPixelsBinDataLength in interface ome.xml.meta.MetadataStore

      • setPixelsDimensionOrder

        public void setPixelsDimensionOrder​(ome.xml.model.enums.DimensionOrder dimensionOrder,
                                    int imageIndex)
        Specified by:
        setPixelsDimensionOrder in interface ome.xml.meta.MetadataStore

      • setPixelsInterleaved

        public void setPixelsInterleaved​(java.lang.Boolean value,
                                 int index)
        Specified by:
        setPixelsInterleaved in interface ome.xml.meta.MetadataStore

      • setPixelsPhysicalSizeX

        public void setPixelsPhysicalSizeX​(ome.units.quantity.Length physicalSizeX,
                                   int imageIndex)
        Specified by:
        setPixelsPhysicalSizeX in interface ome.xml.meta.MetadataStore

      • setPixelsPhysicalSizeY

        public void setPixelsPhysicalSizeY​(ome.units.quantity.Length physicalSizeY,
                                   int imageIndex)
        Specified by:
        setPixelsPhysicalSizeY in interface ome.xml.meta.MetadataStore

      • setPixelsPhysicalSizeZ

        public void setPixelsPhysicalSizeZ​(ome.units.quantity.Length physicalSizeZ,
                                   int imageIndex)
        Specified by:
        setPixelsPhysicalSizeZ in interface ome.xml.meta.MetadataStore

      • setPixelsSignificantBits

        public void setPixelsSignificantBits​(ome.xml.model.primitives.PositiveInteger value,
                                     int imageIndex)
        Specified by:
        setPixelsSignificantBits in interface ome.xml.meta.MetadataStore

      • setPixelsSizeC

        public void setPixelsSizeC​(ome.xml.model.primitives.PositiveInteger sizeC,
                           int imageIndex)
        Specified by:
        setPixelsSizeC in interface ome.xml.meta.MetadataStore

      • setPixelsSizeT

        public void setPixelsSizeT​(ome.xml.model.primitives.PositiveInteger sizeT,
                           int imageIndex)
        Specified by:
        setPixelsSizeT in interface ome.xml.meta.MetadataStore

      • setPixelsSizeX

        public void setPixelsSizeX​(ome.xml.model.primitives.PositiveInteger sizeX,
                           int imageIndex)
        Specified by:
        setPixelsSizeX in interface ome.xml.meta.MetadataStore

      • setPixelsSizeY

        public void setPixelsSizeY​(ome.xml.model.primitives.PositiveInteger sizeY,
                           int imageIndex)
        Specified by:
        setPixelsSizeY in interface ome.xml.meta.MetadataStore

      • setPixelsSizeZ

        public void setPixelsSizeZ​(ome.xml.model.primitives.PositiveInteger sizeZ,
                           int imageIndex)
        Specified by:
        setPixelsSizeZ in interface ome.xml.meta.MetadataStore

      • setPixelsTimeIncrement

        public void setPixelsTimeIncrement​(ome.units.quantity.Time timeIncrement,
                                   int imageIndex)
        Specified by:
        setPixelsTimeIncrement in interface ome.xml.meta.MetadataStore

      • setPixelsType

        public void setPixelsType​(ome.xml.model.enums.PixelType type,
                          int imageIndex)
        Specified by:
        setPixelsType in interface ome.xml.meta.MetadataStore

      • setPlaneAnnotationRef

        public void setPlaneAnnotationRef​(java.lang.String annotation,
                                  int imageIndex,
                                  int planeIndex,
                                  int annotationRefIndex)
        Specified by:
        setPlaneAnnotationRef in interface ome.xml.meta.MetadataStore

      • setPlaneDeltaT

        public void setPlaneDeltaT​(ome.units.quantity.Time deltaT,
                           int imageIndex,
                           int planeIndex)
        Specified by:
        setPlaneDeltaT in interface ome.xml.meta.MetadataStore

      • setPlaneExposureTime

        public void setPlaneExposureTime​(ome.units.quantity.Time exposureTime,
                                 int imageIndex,
                                 int planeIndex)
        Specified by:
        setPlaneExposureTime in interface ome.xml.meta.MetadataStore

      • setPlaneHashSHA1

        public void setPlaneHashSHA1​(java.lang.String hashSHA1,
                             int imageIndex,
                             int planeIndex)
        Specified by:
        setPlaneHashSHA1 in interface ome.xml.meta.MetadataStore

      • setPlanePositionX

        public void setPlanePositionX​(ome.units.quantity.Length positionX,
                              int imageIndex,
                              int planeIndex)
        Specified by:
        setPlanePositionX in interface ome.xml.meta.MetadataStore

      • setPlanePositionY

        public void setPlanePositionY​(ome.units.quantity.Length positionY,
                              int imageIndex,
                              int planeIndex)
        Specified by:
        setPlanePositionY in interface ome.xml.meta.MetadataStore

      • setPlanePositionZ

        public void setPlanePositionZ​(ome.units.quantity.Length positionZ,
                              int imageIndex,
                              int planeIndex)
        Specified by:
        setPlanePositionZ in interface ome.xml.meta.MetadataStore

      • setPlaneTheC

        public void setPlaneTheC​(ome.xml.model.primitives.NonNegativeInteger theC,
                         int imageIndex,
                         int planeIndex)
        Specified by:
        setPlaneTheC in interface ome.xml.meta.MetadataStore

      • setPlaneTheT

        public void setPlaneTheT​(ome.xml.model.primitives.NonNegativeInteger theT,
                         int imageIndex,
                         int planeIndex)
        Specified by:
        setPlaneTheT in interface ome.xml.meta.MetadataStore

      • setPlaneTheZ

        public void setPlaneTheZ​(ome.xml.model.primitives.NonNegativeInteger theZ,
                         int imageIndex,
                         int planeIndex)
        Specified by:
        setPlaneTheZ in interface ome.xml.meta.MetadataStore

      • setPlateAcquisitionAnnotationRef

        public void setPlateAcquisitionAnnotationRef​(java.lang.String annotation,
                                             int plateIndex,
                                             int plateAcquisitionIndex,
                                             int annotationRefIndex)
        Specified by:
        setPlateAcquisitionAnnotationRef in interface ome.xml.meta.MetadataStore

      • setPlateAcquisitionDescription

        public void setPlateAcquisitionDescription​(java.lang.String description,
                                           int plateIndex,
                                           int plateAcquisitionIndex)
        Specified by:
        setPlateAcquisitionDescription in interface ome.xml.meta.MetadataStore

      • setPlateAcquisitionEndTime

        public void setPlateAcquisitionEndTime​(ome.xml.model.primitives.Timestamp endTime,
                                       int plateIndex,
                                       int plateAcquisitionIndex)
        Specified by:
        setPlateAcquisitionEndTime in interface ome.xml.meta.MetadataStore

      • setPlateAcquisitionID

        public void setPlateAcquisitionID​(java.lang.String id,
                                  int plateIndex,
                                  int plateAcquisitionIndex)
        Specified by:
        setPlateAcquisitionID in interface ome.xml.meta.MetadataStore

      • setPlateAcquisitionMaximumFieldCount

        public void setPlateAcquisitionMaximumFieldCount​(ome.xml.model.primitives.PositiveInteger maximumFieldCount,
                                                 int plateIndex,
                                                 int plateAcquisitionIndex)
        Specified by:
        setPlateAcquisitionMaximumFieldCount in interface ome.xml.meta.MetadataStore

      • setPlateAcquisitionName

        public void setPlateAcquisitionName​(java.lang.String name,
                                    int plateIndex,
                                    int plateAcquisitionIndex)
        Specified by:
        setPlateAcquisitionName in interface ome.xml.meta.MetadataStore

      • setPlateAcquisitionStartTime

        public void setPlateAcquisitionStartTime​(ome.xml.model.primitives.Timestamp startTime,
                                         int plateIndex,
                                         int plateAcquisitionIndex)
        Specified by:
        setPlateAcquisitionStartTime in interface ome.xml.meta.MetadataStore

      • setPlateAcquisitionWellSampleRef

        public void setPlateAcquisitionWellSampleRef​(java.lang.String wellSample,
                                             int plateIndex,
                                             int plateAcquisitionIndex,
                                             int wellSampleRefIndex)
        Specified by:
        setPlateAcquisitionWellSampleRef in interface ome.xml.meta.MetadataStore

      • setPlateAnnotationRef

        public void setPlateAnnotationRef​(java.lang.String annotation,
                                  int plateIndex,
                                  int annotationRefIndex)
        Specified by:
        setPlateAnnotationRef in interface ome.xml.meta.MetadataStore

      • setPlateColumnNamingConvention

        public void setPlateColumnNamingConvention​(ome.xml.model.enums.NamingConvention columnNamingConvention,
                                           int plateIndex)
        Specified by:
        setPlateColumnNamingConvention in interface ome.xml.meta.MetadataStore

      • setPlateColumns

        public void setPlateColumns​(ome.xml.model.primitives.PositiveInteger columns,
                            int plateIndex)
        Specified by:
        setPlateColumns in interface ome.xml.meta.MetadataStore

      • setPlateDescription

        public void setPlateDescription​(java.lang.String description,
                                int plateIndex)
        Specified by:
        setPlateDescription in interface ome.xml.meta.MetadataStore

      • setPlateExternalIdentifier

        public void setPlateExternalIdentifier​(java.lang.String externalIdentifier,
                                       int plateIndex)
        Specified by:
        setPlateExternalIdentifier in interface ome.xml.meta.MetadataStore

      • setPlateID

        public void setPlateID​(java.lang.String id,
                       int plateIndex)
        Specified by:
        setPlateID in interface ome.xml.meta.MetadataStore

      • setPlateName

        public void setPlateName​(java.lang.String name,
                         int plateIndex)
        Specified by:
        setPlateName in interface ome.xml.meta.MetadataStore

      • setPlateRowNamingConvention

        public void setPlateRowNamingConvention​(ome.xml.model.enums.NamingConvention rowNamingConvention,
                                        int plateIndex)
        Specified by:
        setPlateRowNamingConvention in interface ome.xml.meta.MetadataStore

      • setPlateRows

        public void setPlateRows​(ome.xml.model.primitives.PositiveInteger rows,
                         int plateIndex)
        Specified by:
        setPlateRows in interface ome.xml.meta.MetadataStore

      • setPlateStatus

        public void setPlateStatus​(java.lang.String status,
                           int plateIndex)
        Specified by:
        setPlateStatus in interface ome.xml.meta.MetadataStore

      • setPlateWellOriginX

        public void setPlateWellOriginX​(ome.units.quantity.Length wellOriginX,
                                int plateIndex)
        Specified by:
        setPlateWellOriginX in interface ome.xml.meta.MetadataStore

      • setPlateWellOriginY

        public void setPlateWellOriginY​(ome.units.quantity.Length wellOriginY,
                                int plateIndex)
        Specified by:
        setPlateWellOriginY in interface ome.xml.meta.MetadataStore

      • setPointText

        public void setPointText​(java.lang.String text,
                         int ROIIndex,
                         int shapeIndex)
        Specified by:
        setPointText in interface ome.xml.meta.MetadataStore

      • setPointFillColor

        public void setPointFillColor​(ome.xml.model.primitives.Color fill,
                              int ROIIndex,
                              int shapeIndex)
        Specified by:
        setPointFillColor in interface ome.xml.meta.MetadataStore

      • setPointFontSize

        public void setPointFontSize​(ome.units.quantity.Length fontSize,
                             int ROIIndex,
                             int shapeIndex)
        Specified by:
        setPointFontSize in interface ome.xml.meta.MetadataStore

      • setPointID

        public void setPointID​(java.lang.String id,
                       int ROIIndex,
                       int shapeIndex)
        Specified by:
        setPointID in interface ome.xml.meta.MetadataStore

      • setPointStrokeColor

        public void setPointStrokeColor​(ome.xml.model.primitives.Color stroke,
                                int ROIIndex,
                                int shapeIndex)
        Specified by:
        setPointStrokeColor in interface ome.xml.meta.MetadataStore

      • setPointStrokeDashArray

        public void setPointStrokeDashArray​(java.lang.String strokeDashArray,
                                    int ROIIndex,
                                    int shapeIndex)
        Specified by:
        setPointStrokeDashArray in interface ome.xml.meta.MetadataStore

      • setPointStrokeWidth

        public void setPointStrokeWidth​(ome.units.quantity.Length strokeWidth,
                                int ROIIndex,
                                int shapeIndex)
        Specified by:
        setPointStrokeWidth in interface ome.xml.meta.MetadataStore

      • setPointTheC

        public void setPointTheC​(ome.xml.model.primitives.NonNegativeInteger theC,
                         int ROIIndex,
                         int shapeIndex)
        Specified by:
        setPointTheC in interface ome.xml.meta.MetadataStore

      • setPointTheT

        public void setPointTheT​(ome.xml.model.primitives.NonNegativeInteger theT,
                         int ROIIndex,
                         int shapeIndex)
        Specified by:
        setPointTheT in interface ome.xml.meta.MetadataStore

      • setPointTheZ

        public void setPointTheZ​(ome.xml.model.primitives.NonNegativeInteger theZ,
                         int ROIIndex,
                         int shapeIndex)
        Specified by:
        setPointTheZ in interface ome.xml.meta.MetadataStore

      • setPointTransform

        public void setPointTransform​(ome.xml.model.AffineTransform transform,
                              int ROIIndex,
                              int shapeIndex)
        Specified by:
        setPointTransform in interface ome.xml.meta.MetadataStore

      • setPointX

        public void setPointX​(java.lang.Double x,
                      int ROIIndex,
                      int shapeIndex)
        Specified by:
        setPointX in interface ome.xml.meta.MetadataStore

      • setPointY

        public void setPointY​(java.lang.Double y,
                      int ROIIndex,
                      int shapeIndex)
        Specified by:
        setPointY in interface ome.xml.meta.MetadataStore

      • setPolylineID

        public void setPolylineID​(java.lang.String id,
                          int ROIIndex,
                          int shapeIndex)
        Specified by:
        setPolylineID in interface ome.xml.meta.MetadataStore

      • setPolylineText

        public void setPolylineText​(java.lang.String text,
                            int ROIIndex,
                            int shapeIndex)
        Specified by:
        setPolylineText in interface ome.xml.meta.MetadataStore

      • setPolylineFillColor

        public void setPolylineFillColor​(ome.xml.model.primitives.Color fill,
                                 int ROIIndex,
                                 int shapeIndex)
        Specified by:
        setPolylineFillColor in interface ome.xml.meta.MetadataStore

      • setPolylineFontSize

        public void setPolylineFontSize​(ome.units.quantity.Length fontSize,
                                int ROIIndex,
                                int shapeIndex)
        Specified by:
        setPolylineFontSize in interface ome.xml.meta.MetadataStore

      • setPolylinePoints

        public void setPolylinePoints​(java.lang.String points,
                              int ROIIndex,
                              int shapeIndex)
        Specified by:
        setPolylinePoints in interface ome.xml.meta.MetadataStore

      • setPolylineStrokeColor

        public void setPolylineStrokeColor​(ome.xml.model.primitives.Color stroke,
                                   int ROIIndex,
                                   int shapeIndex)
        Specified by:
        setPolylineStrokeColor in interface ome.xml.meta.MetadataStore

      • setPolylineStrokeDashArray

        public void setPolylineStrokeDashArray​(java.lang.String strokeDashArray,
                                       int ROIIndex,
                                       int shapeIndex)
        Specified by:
        setPolylineStrokeDashArray in interface ome.xml.meta.MetadataStore

      • setPolylineStrokeWidth

        public void setPolylineStrokeWidth​(ome.units.quantity.Length strokeWidth,
                                   int ROIIndex,
                                   int shapeIndex)
        Specified by:
        setPolylineStrokeWidth in interface ome.xml.meta.MetadataStore

      • setPolylineTheC

        public void setPolylineTheC​(ome.xml.model.primitives.NonNegativeInteger theC,
                            int ROIIndex,
                            int shapeIndex)
        Specified by:
        setPolylineTheC in interface ome.xml.meta.MetadataStore

      • setPolylineTheT

        public void setPolylineTheT​(ome.xml.model.primitives.NonNegativeInteger theT,
                            int ROIIndex,
                            int shapeIndex)
        Specified by:
        setPolylineTheT in interface ome.xml.meta.MetadataStore

      • setPolylineTheZ

        public void setPolylineTheZ​(ome.xml.model.primitives.NonNegativeInteger theZ,
                            int ROIIndex,
                            int shapeIndex)
        Specified by:
        setPolylineTheZ in interface ome.xml.meta.MetadataStore

      • setPolylineTransform

        public void setPolylineTransform​(ome.xml.model.AffineTransform transform,
                                 int ROIIndex,
                                 int shapeIndex)
        Specified by:
        setPolylineTransform in interface ome.xml.meta.MetadataStore

      • setProjectID

        public void setProjectID​(java.lang.String id,
                         int projectIndex)
        Specified by:
        setProjectID in interface ome.xml.meta.MetadataStore

      • setProjectAnnotationRef

        public void setProjectAnnotationRef​(java.lang.String annotation,
                                    int projectIndex,
                                    int annotationRefIndex)
        Specified by:
        setProjectAnnotationRef in interface ome.xml.meta.MetadataStore

      • setProjectDescription

        public void setProjectDescription​(java.lang.String description,
                                  int projectIndex)
        Specified by:
        setProjectDescription in interface ome.xml.meta.MetadataStore

      • setProjectExperimenterRef

        public void setProjectExperimenterRef​(java.lang.String experimenter,
                                      int projectIndex)
        Specified by:
        setProjectExperimenterRef in interface ome.xml.meta.MetadataStore

      • setProjectExperimenterGroupRef

        public void setProjectExperimenterGroupRef​(java.lang.String group,
                                           int projectIndex)
        Specified by:
        setProjectExperimenterGroupRef in interface ome.xml.meta.MetadataStore

      • setProjectName

        public void setProjectName​(java.lang.String name,
                           int projectIndex)
        Specified by:
        setProjectName in interface ome.xml.meta.MetadataStore

      • setROIID

        public void setROIID​(java.lang.String id,
                     int ROIIndex)
        Specified by:
        setROIID in interface ome.xml.meta.MetadataStore

      • setROIAnnotationRef

        public void setROIAnnotationRef​(java.lang.String annotation,
                                int ROIIndex,
                                int annotationRefIndex)
        Specified by:
        setROIAnnotationRef in interface ome.xml.meta.MetadataStore

      • setROIDescription

        public void setROIDescription​(java.lang.String description,
                              int ROIIndex)
        Specified by:
        setROIDescription in interface ome.xml.meta.MetadataStore

      • setROIName

        public void setROIName​(java.lang.String name,
                       int ROIIndex)
        Specified by:
        setROIName in interface ome.xml.meta.MetadataStore

      • setReagentID

        public void setReagentID​(java.lang.String id,
                         int screenIndex,
                         int reagentIndex)
        Specified by:
        setReagentID in interface ome.xml.meta.MetadataStore

      • setReagentAnnotationRef

        public void setReagentAnnotationRef​(java.lang.String annotation,
                                    int screenIndex,
                                    int reagentIndex,
                                    int annotationRefIndex)
        Specified by:
        setReagentAnnotationRef in interface ome.xml.meta.MetadataStore

      • setReagentDescription

        public void setReagentDescription​(java.lang.String description,
                                  int screenIndex,
                                  int reagentIndex)
        Specified by:
        setReagentDescription in interface ome.xml.meta.MetadataStore

      • setReagentName

        public void setReagentName​(java.lang.String name,
                           int screenIndex,
                           int reagentIndex)
        Specified by:
        setReagentName in interface ome.xml.meta.MetadataStore

      • setReagentReagentIdentifier

        public void setReagentReagentIdentifier​(java.lang.String reagentIdentifier,
                                        int screenIndex,
                                        int reagentIndex)
        Specified by:
        setReagentReagentIdentifier in interface ome.xml.meta.MetadataStore

      • setRectangleID

        public void setRectangleID​(java.lang.String id,
                           int ROIIndex,
                           int shapeIndex)
        Specified by:
        setRectangleID in interface ome.xml.meta.MetadataStore

      • setRectangleText

        public void setRectangleText​(java.lang.String description,
                             int ROIIndex,
                             int shapeIndex)
        Specified by:
        setRectangleText in interface ome.xml.meta.MetadataStore

      • setRectangleFillColor

        public void setRectangleFillColor​(ome.xml.model.primitives.Color fill,
                                  int ROIIndex,
                                  int shapeIndex)
        Specified by:
        setRectangleFillColor in interface ome.xml.meta.MetadataStore

      • setRectangleFontSize

        public void setRectangleFontSize​(ome.units.quantity.Length fontSize,
                                 int ROIIndex,
                                 int shapeIndex)
        Specified by:
        setRectangleFontSize in interface ome.xml.meta.MetadataStore

      • setRectangleHeight

        public void setRectangleHeight​(java.lang.Double height,
                               int ROIIndex,
                               int shapeIndex)
        Specified by:
        setRectangleHeight in interface ome.xml.meta.MetadataStore

      • setRectangleStrokeColor

        public void setRectangleStrokeColor​(ome.xml.model.primitives.Color stroke,
                                    int ROIIndex,
                                    int shapeIndex)
        Specified by:
        setRectangleStrokeColor in interface ome.xml.meta.MetadataStore

      • setRectangleStrokeDashArray

        public void setRectangleStrokeDashArray​(java.lang.String strokeDashArray,
                                        int ROIIndex,
                                        int shapeIndex)
        Specified by:
        setRectangleStrokeDashArray in interface ome.xml.meta.MetadataStore

      • setRectangleStrokeWidth

        public void setRectangleStrokeWidth​(ome.units.quantity.Length strokeWidth,
                                    int ROIIndex,
                                    int shapeIndex)
        Specified by:
        setRectangleStrokeWidth in interface ome.xml.meta.MetadataStore

      • setRectangleTheC

        public void setRectangleTheC​(ome.xml.model.primitives.NonNegativeInteger theC,
                             int ROIIndex,
                             int shapeIndex)
        Specified by:
        setRectangleTheC in interface ome.xml.meta.MetadataStore

      • setRectangleTheT

        public void setRectangleTheT​(ome.xml.model.primitives.NonNegativeInteger theT,
                             int ROIIndex,
                             int shapeIndex)
        Specified by:
        setRectangleTheT in interface ome.xml.meta.MetadataStore

      • setRectangleTheZ

        public void setRectangleTheZ​(ome.xml.model.primitives.NonNegativeInteger theZ,
                             int ROIIndex,
                             int shapeIndex)
        Specified by:
        setRectangleTheZ in interface ome.xml.meta.MetadataStore

      • setRectangleTransform

        public void setRectangleTransform​(ome.xml.model.AffineTransform transform,
                                  int ROIIndex,
                                  int shapeIndex)
        Specified by:
        setRectangleTransform in interface ome.xml.meta.MetadataStore

      • setRectangleWidth

        public void setRectangleWidth​(java.lang.Double width,
                              int ROIIndex,
                              int shapeIndex)
        Specified by:
        setRectangleWidth in interface ome.xml.meta.MetadataStore

      • setRectangleX

        public void setRectangleX​(java.lang.Double x,
                          int ROIIndex,
                          int shapeIndex)
        Specified by:
        setRectangleX in interface ome.xml.meta.MetadataStore

      • setRectangleY

        public void setRectangleY​(java.lang.Double y,
                          int ROIIndex,
                          int shapeIndex)
        Specified by:
        setRectangleY in interface ome.xml.meta.MetadataStore

      • setRoot

        public void setRoot​(ome.xml.meta.MetadataRoot root)
        Specified by:
        setRoot in interface ome.xml.meta.MetadataStore

      • setScreenID

        public void setScreenID​(java.lang.String id,
                        int screenIndex)
        Specified by:
        setScreenID in interface ome.xml.meta.MetadataStore

      • setScreenAnnotationRef

        public void setScreenAnnotationRef​(java.lang.String annotation,
                                   int screenIndex,
                                   int annotationRefIndex)
        Specified by:
        setScreenAnnotationRef in interface ome.xml.meta.MetadataStore

      • setScreenDescription

        public void setScreenDescription​(java.lang.String description,
                                 int screenIndex)
        Specified by:
        setScreenDescription in interface ome.xml.meta.MetadataStore

      • setScreenName

        public void setScreenName​(java.lang.String name,
                          int screenIndex)
        Specified by:
        setScreenName in interface ome.xml.meta.MetadataStore

      • setScreenPlateRef

        public void setScreenPlateRef​(java.lang.String plate,
                              int screenIndex,
                              int plateRefIndex)
        Specified by:
        setScreenPlateRef in interface ome.xml.meta.MetadataStore

      • setScreenProtocolDescription

        public void setScreenProtocolDescription​(java.lang.String protocolDescription,
                                         int screenIndex)
        Specified by:
        setScreenProtocolDescription in interface ome.xml.meta.MetadataStore

      • setScreenProtocolIdentifier

        public void setScreenProtocolIdentifier​(java.lang.String protocolIdentifier,
                                        int screenIndex)
        Specified by:
        setScreenProtocolIdentifier in interface ome.xml.meta.MetadataStore

      • setScreenReagentSetDescription

        public void setScreenReagentSetDescription​(java.lang.String reagentSetDescription,
                                           int screenIndex)
        Specified by:
        setScreenReagentSetDescription in interface ome.xml.meta.MetadataStore

      • setScreenReagentSetIdentifier

        public void setScreenReagentSetIdentifier​(java.lang.String reagentSetIdentifier,
                                          int screenIndex)
        Specified by:
        setScreenReagentSetIdentifier in interface ome.xml.meta.MetadataStore

      • setScreenType

        public void setScreenType​(java.lang.String type,
                          int screenIndex)
        Specified by:
        setScreenType in interface ome.xml.meta.MetadataStore

      • setStageLabelName

        public void setStageLabelName​(java.lang.String name,
                              int imageIndex)
        Specified by:
        setStageLabelName in interface ome.xml.meta.MetadataStore

      • setStageLabelX

        public void setStageLabelX​(ome.units.quantity.Length x,
                           int imageIndex)
        Specified by:
        setStageLabelX in interface ome.xml.meta.MetadataStore

      • setStageLabelY

        public void setStageLabelY​(ome.units.quantity.Length y,
                           int imageIndex)
        Specified by:
        setStageLabelY in interface ome.xml.meta.MetadataStore

      • setStageLabelZ

        public void setStageLabelZ​(ome.units.quantity.Length z,
                           int imageIndex)
        Specified by:
        setStageLabelZ in interface ome.xml.meta.MetadataStore

      • setCommentAnnotationID

        public void setCommentAnnotationID​(java.lang.String id,
                                   int commentAnnotationIndex)
        Specified by:
        setCommentAnnotationID in interface ome.xml.meta.MetadataStore

      • setCommentAnnotationNamespace

        public void setCommentAnnotationNamespace​(java.lang.String namespace,
                                          int commentAnnotationIndex)
        Specified by:
        setCommentAnnotationNamespace in interface ome.xml.meta.MetadataStore

      • setCommentAnnotationAnnotator

        public void setCommentAnnotationAnnotator​(java.lang.String value,
                                          int index)
        Specified by:
        setCommentAnnotationAnnotator in interface ome.xml.meta.MetadataStore

      • setCommentAnnotationValue

        public void setCommentAnnotationValue​(java.lang.String value,
                                      int commentAnnotationIndex)
        Specified by:
        setCommentAnnotationValue in interface ome.xml.meta.MetadataStore

      • setLabelID

        public void setLabelID​(java.lang.String id,
                       int ROIIndex,
                       int shapeIndex)
        Specified by:
        setLabelID in interface ome.xml.meta.MetadataStore

      • setLabelText

        public void setLabelText​(java.lang.String text,
                         int ROIIndex,
                         int shapeIndex)
        Specified by:
        setLabelText in interface ome.xml.meta.MetadataStore

      • setLabelFillColor

        public void setLabelFillColor​(ome.xml.model.primitives.Color fill,
                              int ROIIndex,
                              int shapeIndex)
        Specified by:
        setLabelFillColor in interface ome.xml.meta.MetadataStore

      • setLabelFontSize

        public void setLabelFontSize​(ome.units.quantity.Length fontSize,
                             int ROIIndex,
                             int shapeIndex)
        Specified by:
        setLabelFontSize in interface ome.xml.meta.MetadataStore

      • setLabelStrokeColor

        public void setLabelStrokeColor​(ome.xml.model.primitives.Color stroke,
                                int ROIIndex,
                                int shapeIndex)
        Specified by:
        setLabelStrokeColor in interface ome.xml.meta.MetadataStore

      • setLabelStrokeDashArray

        public void setLabelStrokeDashArray​(java.lang.String strokeDashArray,
                                    int ROIIndex,
                                    int shapeIndex)
        Specified by:
        setLabelStrokeDashArray in interface ome.xml.meta.MetadataStore

      • setLabelStrokeWidth

        public void setLabelStrokeWidth​(ome.units.quantity.Length strokeWidth,
                                int ROIIndex,
                                int shapeIndex)
        Specified by:
        setLabelStrokeWidth in interface ome.xml.meta.MetadataStore

      • setLabelTheC

        public void setLabelTheC​(ome.xml.model.primitives.NonNegativeInteger theC,
                         int ROIIndex,
                         int shapeIndex)
        Specified by:
        setLabelTheC in interface ome.xml.meta.MetadataStore

      • setLabelTheT

        public void setLabelTheT​(ome.xml.model.primitives.NonNegativeInteger theT,
                         int ROIIndex,
                         int shapeIndex)
        Specified by:
        setLabelTheT in interface ome.xml.meta.MetadataStore

      • setLabelTheZ

        public void setLabelTheZ​(ome.xml.model.primitives.NonNegativeInteger theZ,
                         int ROIIndex,
                         int shapeIndex)
        Specified by:
        setLabelTheZ in interface ome.xml.meta.MetadataStore

      • setLabelTransform

        public void setLabelTransform​(ome.xml.model.AffineTransform transform,
                              int ROIIndex,
                              int shapeIndex)
        Specified by:
        setLabelTransform in interface ome.xml.meta.MetadataStore

      • setLabelX

        public void setLabelX​(java.lang.Double x,
                      int ROIIndex,
                      int shapeIndex)
        Specified by:
        setLabelX in interface ome.xml.meta.MetadataStore

      • setLabelY

        public void setLabelY​(java.lang.Double y,
                      int ROIIndex,
                      int shapeIndex)
        Specified by:
        setLabelY in interface ome.xml.meta.MetadataStore

      • setTiffDataFirstC

        public void setTiffDataFirstC​(ome.xml.model.primitives.NonNegativeInteger firstC,
                              int imageIndex,
                              int tiffDataIndex)
        Specified by:
        setTiffDataFirstC in interface ome.xml.meta.MetadataStore

      • setTiffDataFirstT

        public void setTiffDataFirstT​(ome.xml.model.primitives.NonNegativeInteger firstT,
                              int imageIndex,
                              int tiffDataIndex)
        Specified by:
        setTiffDataFirstT in interface ome.xml.meta.MetadataStore

      • setTiffDataFirstZ

        public void setTiffDataFirstZ​(ome.xml.model.primitives.NonNegativeInteger firstZ,
                              int imageIndex,
                              int tiffDataIndex)
        Specified by:
        setTiffDataFirstZ in interface ome.xml.meta.MetadataStore

      • setTiffDataIFD

        public void setTiffDataIFD​(ome.xml.model.primitives.NonNegativeInteger ifd,
                           int imageIndex,
                           int tiffDataIndex)
        Specified by:
        setTiffDataIFD in interface ome.xml.meta.MetadataStore

      • setTiffDataPlaneCount

        public void setTiffDataPlaneCount​(ome.xml.model.primitives.NonNegativeInteger planeCount,
                                  int imageIndex,
                                  int tiffDataIndex)
        Specified by:
        setTiffDataPlaneCount in interface ome.xml.meta.MetadataStore

      • setTimestampAnnotationID

        public void setTimestampAnnotationID​(java.lang.String id,
                                     int timestampAnnotationIndex)
        Specified by:
        setTimestampAnnotationID in interface ome.xml.meta.MetadataStore

      • setTimestampAnnotationNamespace

        public void setTimestampAnnotationNamespace​(java.lang.String namespace,
                                            int timestampAnnotationIndex)
        Specified by:
        setTimestampAnnotationNamespace in interface ome.xml.meta.MetadataStore

      • setTimestampAnnotationValue

        public void setTimestampAnnotationValue​(ome.xml.model.primitives.Timestamp value,
                                        int timestampAnnotationIndex)
        Specified by:
        setTimestampAnnotationValue in interface ome.xml.meta.MetadataStore

      • setTransmittanceRangeCutIn

        public void setTransmittanceRangeCutIn​(ome.units.quantity.Length cutIn,
                                       int instrumentIndex,
                                       int filterIndex)
        Specified by:
        setTransmittanceRangeCutIn in interface ome.xml.meta.MetadataStore

      • setTransmittanceRangeCutInTolerance

        public void setTransmittanceRangeCutInTolerance​(ome.units.quantity.Length cutInTolerance,
                                                int instrumentIndex,
                                                int filterIndex)
        Specified by:
        setTransmittanceRangeCutInTolerance in interface ome.xml.meta.MetadataStore

      • setTransmittanceRangeCutOut

        public void setTransmittanceRangeCutOut​(ome.units.quantity.Length cutOut,
                                        int instrumentIndex,
                                        int filterIndex)
        Specified by:
        setTransmittanceRangeCutOut in interface ome.xml.meta.MetadataStore

      • setTransmittanceRangeCutOutTolerance

        public void setTransmittanceRangeCutOutTolerance​(ome.units.quantity.Length cutOutTolerance,
                                                 int instrumentIndex,
                                                 int filterIndex)
        Specified by:
        setTransmittanceRangeCutOutTolerance in interface ome.xml.meta.MetadataStore

      • setTransmittanceRangeTransmittance

        public void setTransmittanceRangeTransmittance​(ome.xml.model.primitives.PercentFraction transmittance,
                                               int instrumentIndex,
                                               int filterIndex)
        Specified by:
        setTransmittanceRangeTransmittance in interface ome.xml.meta.MetadataStore

      • setUUID

        public void setUUID​(java.lang.String uuid)
        Specified by:
        setUUID in interface ome.xml.meta.MetadataStore

      • setUUIDFileName

        public void setUUIDFileName​(java.lang.String fileName,
                            int imageIndex,
                            int tiffDataIndex)
        Specified by:
        setUUIDFileName in interface ome.xml.meta.MetadataStore

      • setUUIDValue

        public void setUUIDValue​(java.lang.String fileName,
                         int imageIndex,
                         int tiffDataIndex)
        Specified by:
        setUUIDValue in interface ome.xml.meta.MetadataStore

      • setWellID

        public void setWellID​(java.lang.String id,
                      int plateIndex,
                      int wellIndex)
        Specified by:
        setWellID in interface ome.xml.meta.MetadataStore

      • setWellAnnotationRef

        public void setWellAnnotationRef​(java.lang.String annotation,
                                 int plateIndex,
                                 int wellIndex,
                                 int annotationRefIndex)
        Specified by:
        setWellAnnotationRef in interface ome.xml.meta.MetadataStore

      • setWellColor

        public void setWellColor​(ome.xml.model.primitives.Color color,
                         int plateIndex,
                         int wellIndex)
        Specified by:
        setWellColor in interface ome.xml.meta.MetadataStore

      • setWellColumn

        public void setWellColumn​(ome.xml.model.primitives.NonNegativeInteger column,
                          int plateIndex,
                          int wellIndex)
        Specified by:
        setWellColumn in interface ome.xml.meta.MetadataStore

      • setWellExternalDescription

        public void setWellExternalDescription​(java.lang.String externalDescription,
                                       int plateIndex,
                                       int wellIndex)
        Specified by:
        setWellExternalDescription in interface ome.xml.meta.MetadataStore

      • setWellExternalIdentifier

        public void setWellExternalIdentifier​(java.lang.String externalIdentifier,
                                      int plateIndex,
                                      int wellIndex)
        Specified by:
        setWellExternalIdentifier in interface ome.xml.meta.MetadataStore

      • setWellReagentRef

        public void setWellReagentRef​(java.lang.String reagent,
                              int plateIndex,
                              int wellIndex)
        Specified by:
        setWellReagentRef in interface ome.xml.meta.MetadataStore

      • setWellRow

        public void setWellRow​(ome.xml.model.primitives.NonNegativeInteger row,
                       int plateIndex,
                       int wellIndex)
        Specified by:
        setWellRow in interface ome.xml.meta.MetadataStore

      • setWellSampleID

        public void setWellSampleID​(java.lang.String id,
                            int plateIndex,
                            int wellIndex,
                            int wellSampleIndex)
        Specified by:
        setWellSampleID in interface ome.xml.meta.MetadataStore

      • setWellSampleImageRef

        public void setWellSampleImageRef​(java.lang.String image,
                                  int plateIndex,
                                  int wellIndex,
                                  int wellSampleIndex)
        Specified by:
        setWellSampleImageRef in interface ome.xml.meta.MetadataStore

      • setWellSampleIndex

        public void setWellSampleIndex​(ome.xml.model.primitives.NonNegativeInteger index,
                               int plateIndex,
                               int wellIndex,
                               int wellSampleIndex)
        Specified by:
        setWellSampleIndex in interface ome.xml.meta.MetadataStore

      • setWellSamplePositionX

        public void setWellSamplePositionX​(ome.units.quantity.Length positionX,
                                   int plateIndex,
                                   int wellIndex,
                                   int wellSampleIndex)
        Specified by:
        setWellSamplePositionX in interface ome.xml.meta.MetadataStore

      • setWellSamplePositionY

        public void setWellSamplePositionY​(ome.units.quantity.Length positionY,
                                   int plateIndex,
                                   int wellIndex,
                                   int wellSampleIndex)
        Specified by:
        setWellSamplePositionY in interface ome.xml.meta.MetadataStore

      • setWellSampleTimepoint

        public void setWellSampleTimepoint​(ome.xml.model.primitives.Timestamp timepoint,
                                   int plateIndex,
                                   int wellIndex,
                                   int wellSampleIndex)
        Specified by:
        setWellSampleTimepoint in interface ome.xml.meta.MetadataStore

      • setXMLAnnotationID

        public void setXMLAnnotationID​(java.lang.String id,
                               int XMLAnnotationIndex)
        Specified by:
        setXMLAnnotationID in interface ome.xml.meta.MetadataStore

      • setXMLAnnotationNamespace

        public void setXMLAnnotationNamespace​(java.lang.String namespace,
                                      int XMLAnnotationIndex)
        Specified by:
        setXMLAnnotationNamespace in interface ome.xml.meta.MetadataStore

      • setXMLAnnotationValue

        public void setXMLAnnotationValue​(java.lang.String value,
                                  int XMLAnnotationIndex)
        Specified by:
        setXMLAnnotationValue in interface ome.xml.meta.MetadataStore

      • setXMLAnnotationAnnotator

        public void setXMLAnnotationAnnotator​(java.lang.String value,
                                      int index)
        Specified by:
        setXMLAnnotationAnnotator in interface ome.xml.meta.MetadataStore

      • setXMLAnnotationAnnotationRef

        public void setXMLAnnotationAnnotationRef​(java.lang.String annotation,
                                          int XMLAnnotationIndex,
                                          int annotationRefIndex)
        Specified by:
        setXMLAnnotationAnnotationRef in interface ome.xml.meta.MetadataStore

      • setXMLAnnotationDescription

        public void setXMLAnnotationDescription​(java.lang.String description,
                                        int XMLAnnotationIndex)
        Specified by:
        setXMLAnnotationDescription in interface ome.xml.meta.MetadataStore

      • setBooleanAnnotationAnnotationRef

        public void setBooleanAnnotationAnnotationRef​(java.lang.String annotation,
                                              int booleanAnnotationIndex,
                                              int annotationRefIndex)
        Specified by:
        setBooleanAnnotationAnnotationRef in interface ome.xml.meta.MetadataStore

      • setBooleanAnnotationDescription

        public void setBooleanAnnotationDescription​(java.lang.String description,
                                            int booleanAnnotationIndex)
        Specified by:
        setBooleanAnnotationDescription in interface ome.xml.meta.MetadataStore

      • setBooleanAnnotationAnnotator

        public void setBooleanAnnotationAnnotator​(java.lang.String value,
                                          int index)
        Specified by:
        setBooleanAnnotationAnnotator in interface ome.xml.meta.MetadataStore

      • setCommentAnnotationAnnotationRef

        public void setCommentAnnotationAnnotationRef​(java.lang.String annotation,
                                              int commentAnnotationIndex,
                                              int annotationRefIndex)
        Specified by:
        setCommentAnnotationAnnotationRef in interface ome.xml.meta.MetadataStore

      • setCommentAnnotationDescription

        public void setCommentAnnotationDescription​(java.lang.String description,
                                            int commentAnnotationIndex)
        Specified by:
        setCommentAnnotationDescription in interface ome.xml.meta.MetadataStore

      • setDoubleAnnotationAnnotationRef

        public void setDoubleAnnotationAnnotationRef​(java.lang.String annotation,
                                             int doubleAnnotationIndex,
                                             int annotationRefIndex)
        Specified by:
        setDoubleAnnotationAnnotationRef in interface ome.xml.meta.MetadataStore

      • setDoubleAnnotationDescription

        public void setDoubleAnnotationDescription​(java.lang.String description,
                                           int doubleAnnotationIndex)
        Specified by:
        setDoubleAnnotationDescription in interface ome.xml.meta.MetadataStore

      • setDoubleAnnotationAnnotator

        public void setDoubleAnnotationAnnotator​(java.lang.String value,
                                         int index)
        Specified by:
        setDoubleAnnotationAnnotator in interface ome.xml.meta.MetadataStore

      • setFileAnnotationAnnotationRef

        public void setFileAnnotationAnnotationRef​(java.lang.String annotation,
                                           int fileAnnotationIndex,
                                           int annotationRefIndex)
        Specified by:
        setFileAnnotationAnnotationRef in interface ome.xml.meta.MetadataStore

      • setFileAnnotationDescription

        public void setFileAnnotationDescription​(java.lang.String description,
                                         int fileAnnotationIndex)
        Specified by:
        setFileAnnotationDescription in interface ome.xml.meta.MetadataStore

      • setFileAnnotationAnnotator

        public void setFileAnnotationAnnotator​(java.lang.String value,
                                       int index)
        Specified by:
        setFileAnnotationAnnotator in interface ome.xml.meta.MetadataStore

      • setListAnnotationDescription

        public void setListAnnotationDescription​(java.lang.String description,
                                         int listAnnotationIndex)
        Specified by:
        setListAnnotationDescription in interface ome.xml.meta.MetadataStore

      • setListAnnotationAnnotator

        public void setListAnnotationAnnotator​(java.lang.String value,
                                       int index)
        Specified by:
        setListAnnotationAnnotator in interface ome.xml.meta.MetadataStore

      • setLongAnnotationAnnotationRef

        public void setLongAnnotationAnnotationRef​(java.lang.String annotation,
                                           int longAnnotationIndex,
                                           int annotationRefIndex)
        Specified by:
        setLongAnnotationAnnotationRef in interface ome.xml.meta.MetadataStore

      • setLongAnnotationDescription

        public void setLongAnnotationDescription​(java.lang.String description,
                                         int longAnnotationIndex)
        Specified by:
        setLongAnnotationDescription in interface ome.xml.meta.MetadataStore

      • setLongAnnotationAnnotator

        public void setLongAnnotationAnnotator​(java.lang.String value,
                                       int XMLAnnotationIndex)
        Specified by:
        setLongAnnotationAnnotator in interface ome.xml.meta.MetadataStore

      • setMapAnnotationAnnotationRef

        public void setMapAnnotationAnnotationRef​(java.lang.String annotation,
                                          int mapAnnotationIndex,
                                          int annotationRefIndex)
        Specified by:
        setMapAnnotationAnnotationRef in interface ome.xml.meta.MetadataStore

      • setMapAnnotationAnnotator

        public void setMapAnnotationAnnotator​(java.lang.String annotator,
                                      int mapAnnotationIndex)
        Specified by:
        setMapAnnotationAnnotator in interface ome.xml.meta.MetadataStore

      • setMapAnnotationDescription

        public void setMapAnnotationDescription​(java.lang.String description,
                                        int mapAnnotationIndex)
        Specified by:
        setMapAnnotationDescription in interface ome.xml.meta.MetadataStore

      • setMapAnnotationID

        public void setMapAnnotationID​(java.lang.String id,
                               int mapAnnotationIndex)
        Specified by:
        setMapAnnotationID in interface ome.xml.meta.MetadataStore

      • setMapAnnotationNamespace

        public void setMapAnnotationNamespace​(java.lang.String namespace,
                                      int mapAnnotationIndex)
        Specified by:
        setMapAnnotationNamespace in interface ome.xml.meta.MetadataStore

      • setMapAnnotationValue

        public void setMapAnnotationValue​(java.util.List<ome.xml.model.MapPair> value,
                                  int mapAnnotationIndex)
        Specified by:
        setMapAnnotationValue in interface ome.xml.meta.MetadataStore

      • setTagAnnotationAnnotationRef

        public void setTagAnnotationAnnotationRef​(java.lang.String annotation,
                                          int tagAnnotationIndex,
                                          int annotationRefIndex)
        Specified by:
        setTagAnnotationAnnotationRef in interface ome.xml.meta.MetadataStore

      • setTagAnnotationDescription

        public void setTagAnnotationDescription​(java.lang.String description,
                                        int tagAnnotationIndex)
        Specified by:
        setTagAnnotationDescription in interface ome.xml.meta.MetadataStore

      • setTagAnnotationID

        public void setTagAnnotationID​(java.lang.String id,
                               int tagAnnotationIndex)
        Specified by:
        setTagAnnotationID in interface ome.xml.meta.MetadataStore

      • setTagAnnotationNamespace

        public void setTagAnnotationNamespace​(java.lang.String namespace,
                                      int tagAnnotationIndex)
        Specified by:
        setTagAnnotationNamespace in interface ome.xml.meta.MetadataStore

      • setTagAnnotationAnnotator

        public void setTagAnnotationAnnotator​(java.lang.String value,
                                      int index)
        Specified by:
        setTagAnnotationAnnotator in interface ome.xml.meta.MetadataStore

      • setTagAnnotationValue

        public void setTagAnnotationValue​(java.lang.String value,
                                  int tagAnnotationIndex)
        Specified by:
        setTagAnnotationValue in interface ome.xml.meta.MetadataStore

      • setTermAnnotationAnnotationRef

        public void setTermAnnotationAnnotationRef​(java.lang.String annotation,
                                           int termAnnotationIndex,
                                           int annotationRefIndex)
        Specified by:
        setTermAnnotationAnnotationRef in interface ome.xml.meta.MetadataStore

      • setTermAnnotationDescription

        public void setTermAnnotationDescription​(java.lang.String description,
                                         int termAnnotationIndex)
        Specified by:
        setTermAnnotationDescription in interface ome.xml.meta.MetadataStore

      • setTermAnnotationID

        public void setTermAnnotationID​(java.lang.String id,
                                int termAnnotationIndex)
        Specified by:
        setTermAnnotationID in interface ome.xml.meta.MetadataStore

      • setTermAnnotationNamespace

        public void setTermAnnotationNamespace​(java.lang.String namespace,
                                       int termAnnotationIndex)
        Specified by:
        setTermAnnotationNamespace in interface ome.xml.meta.MetadataStore

      • setTermAnnotationAnnotator

        public void setTermAnnotationAnnotator​(java.lang.String value,
                                       int index)
        Specified by:
        setTermAnnotationAnnotator in interface ome.xml.meta.MetadataStore

      • setTermAnnotationValue

        public void setTermAnnotationValue​(java.lang.String value,
                                   int termAnnotationIndex)
        Specified by:
        setTermAnnotationValue in interface ome.xml.meta.MetadataStore

      • setTimestampAnnotationAnnotationRef

        public void setTimestampAnnotationAnnotationRef​(java.lang.String annotation,
                                                int timestampAnnotationIndex,
                                                int annotationRefIndex)
        Specified by:
        setTimestampAnnotationAnnotationRef in interface ome.xml.meta.MetadataStore

      • setTimestampAnnotationDescription

        public void setTimestampAnnotationDescription​(java.lang.String description,
                                              int timestampAnnotationIndex)
        Specified by:
        setTimestampAnnotationDescription in interface ome.xml.meta.MetadataStore

      • setTimestampAnnotationAnnotator

        public void setTimestampAnnotationAnnotator​(java.lang.String value,
                                            int index)
        Specified by:
        setTimestampAnnotationAnnotator in interface ome.xml.meta.MetadataStore

      • setPlateFieldIndex

        public void setPlateFieldIndex​(ome.xml.model.primitives.NonNegativeInteger fieldIndex,
                               int plateIndex)
        Specified by:
        setPlateFieldIndex in interface ome.xml.meta.MetadataStore

      • setBinaryFileBinData

        public void setBinaryFileBinData​(byte[] binData,
                                 int fileAnnotationIndex)
        Specified by:
        setBinaryFileBinData in interface ome.xml.meta.MetadataStore

      • setBinaryFileBinDataBigEndian

        public void setBinaryFileBinDataBigEndian​(java.lang.Boolean isBigEndian,
                                          int fileAnnotationIndex)
        Specified by:
        setBinaryFileBinDataBigEndian in interface ome.xml.meta.MetadataStore

      • setBinaryFileBinDataCompression

        public void setBinaryFileBinDataCompression​(ome.xml.model.enums.Compression compression,
                                            int fileAnnotationIndex)
        Specified by:
        setBinaryFileBinDataCompression in interface ome.xml.meta.MetadataStore

      • setBinaryFileBinDataLength

        public void setBinaryFileBinDataLength​(ome.xml.model.primitives.NonNegativeLong length,
                                       int fileAnnotationIndex)
        Specified by:
        setBinaryFileBinDataLength in interface ome.xml.meta.MetadataStore

      • setBinaryFileFileName

        public void setBinaryFileFileName​(java.lang.String fileName,
                                  int fileAnnotationIndex)
        Specified by:
        setBinaryFileFileName in interface ome.xml.meta.MetadataStore

      • setBinaryFileMIMEType

        public void setBinaryFileMIMEType​(java.lang.String mimeType,
                                  int fileAnnotationIndex)
        Specified by:
        setBinaryFileMIMEType in interface ome.xml.meta.MetadataStore

      • setBinaryFileSize

        public void setBinaryFileSize​(ome.xml.model.primitives.NonNegativeLong size,
                              int fileAnnotationIndex)
        Specified by:
        setBinaryFileSize in interface ome.xml.meta.MetadataStore

      • setDatasetImageRef

        public void setDatasetImageRef​(java.lang.String image,
                               int datasetIndex,
                               int imageRefIndex)
        Specified by:
        setDatasetImageRef in interface ome.xml.meta.MetadataStore

      • setEllipseFillRule

        public void setEllipseFillRule​(ome.xml.model.enums.FillRule fillRule,
                               int ROIIndex,
                               int shapeIndex)
        Specified by:
        setEllipseFillRule in interface ome.xml.meta.MetadataStore

      • setEllipseFontFamily

        public void setEllipseFontFamily​(ome.xml.model.enums.FontFamily fontFamily,
                                 int ROIIndex,
                                 int shapeIndex)
        Specified by:
        setEllipseFontFamily in interface ome.xml.meta.MetadataStore

      • setEllipseFontStyle

        public void setEllipseFontStyle​(ome.xml.model.enums.FontStyle fontStyle,
                                int ROIIndex,
                                int shapeIndex)
        Specified by:
        setEllipseFontStyle in interface ome.xml.meta.MetadataStore

      • setEllipseLocked

        public void setEllipseLocked​(java.lang.Boolean locked,
                             int ROIIndex,
                             int shapeIndex)
        Specified by:
        setEllipseLocked in interface ome.xml.meta.MetadataStore

      • setExperimenterGroupAnnotationRef

        public void setExperimenterGroupAnnotationRef​(java.lang.String annotation,
                                              int experimenterGroupIndex,
                                              int annotationRefIndex)
        Specified by:
        setExperimenterGroupAnnotationRef in interface ome.xml.meta.MetadataStore

      • setExperimenterGroupExperimenterRef

        public void setExperimenterGroupExperimenterRef​(java.lang.String experimenter,
                                                int experimenterGroupIndex,
                                                int experimenterRefIndex)
        Specified by:
        setExperimenterGroupExperimenterRef in interface ome.xml.meta.MetadataStore

      • setLabelFillRule

        public void setLabelFillRule​(ome.xml.model.enums.FillRule fillRule,
                             int ROIIndex,
                             int shapeIndex)
        Specified by:
        setLabelFillRule in interface ome.xml.meta.MetadataStore

      • setLabelFontFamily

        public void setLabelFontFamily​(ome.xml.model.enums.FontFamily fontFamily,
                               int ROIIndex,
                               int shapeIndex)
        Specified by:
        setLabelFontFamily in interface ome.xml.meta.MetadataStore

      • setLabelFontStyle

        public void setLabelFontStyle​(ome.xml.model.enums.FontStyle fontStyle,
                              int ROIIndex,
                              int shapeIndex)
        Specified by:
        setLabelFontStyle in interface ome.xml.meta.MetadataStore

      • setLabelLocked

        public void setLabelLocked​(java.lang.Boolean locked,
                           int ROIIndex,
                           int shapeIndex)
        Specified by:
        setLabelLocked in interface ome.xml.meta.MetadataStore

      • setLineFillRule

        public void setLineFillRule​(ome.xml.model.enums.FillRule fillRule,
                            int ROIIndex,
                            int shapeIndex)
        Specified by:
        setLineFillRule in interface ome.xml.meta.MetadataStore

      • setLineFontFamily

        public void setLineFontFamily​(ome.xml.model.enums.FontFamily fontFamily,
                              int ROIIndex,
                              int shapeIndex)
        Specified by:
        setLineFontFamily in interface ome.xml.meta.MetadataStore

      • setLineFontStyle

        public void setLineFontStyle​(ome.xml.model.enums.FontStyle fontStyle,
                             int ROIIndex,
                             int shapeIndex)
        Specified by:
        setLineFontStyle in interface ome.xml.meta.MetadataStore

      • setLineLocked

        public void setLineLocked​(java.lang.Boolean locked,
                          int ROIIndex,
                          int shapeIndex)
        Specified by:
        setLineLocked in interface ome.xml.meta.MetadataStore

      • setLineMarkerEnd

        public void setLineMarkerEnd​(ome.xml.model.enums.Marker markerEnd,
                             int ROIIndex,
                             int shapeIndex)
        Specified by:
        setLineMarkerEnd in interface ome.xml.meta.MetadataStore

      • setLineMarkerStart

        public void setLineMarkerStart​(ome.xml.model.enums.Marker markerStart,
                               int ROIIndex,
                               int shapeIndex)
        Specified by:
        setLineMarkerStart in interface ome.xml.meta.MetadataStore

      • setMaskFillRule

        public void setMaskFillRule​(ome.xml.model.enums.FillRule fillRule,
                            int ROIIndex,
                            int shapeIndex)
        Specified by:
        setMaskFillRule in interface ome.xml.meta.MetadataStore

      • setMaskFontFamily

        public void setMaskFontFamily​(ome.xml.model.enums.FontFamily fontFamily,
                              int ROIIndex,
                              int shapeIndex)
        Specified by:
        setMaskFontFamily in interface ome.xml.meta.MetadataStore

      • setMaskFontStyle

        public void setMaskFontStyle​(ome.xml.model.enums.FontStyle fontStyle,
                             int ROIIndex,
                             int shapeIndex)
        Specified by:
        setMaskFontStyle in interface ome.xml.meta.MetadataStore

      • setMaskLocked

        public void setMaskLocked​(java.lang.Boolean locked,
                          int ROIIndex,
                          int shapeIndex)
        Specified by:
        setMaskLocked in interface ome.xml.meta.MetadataStore

      • setPointFillRule

        public void setPointFillRule​(ome.xml.model.enums.FillRule fillRule,
                             int ROIIndex,
                             int shapeIndex)
        Specified by:
        setPointFillRule in interface ome.xml.meta.MetadataStore

      • setPointFontFamily

        public void setPointFontFamily​(ome.xml.model.enums.FontFamily fontFamily,
                               int ROIIndex,
                               int shapeIndex)
        Specified by:
        setPointFontFamily in interface ome.xml.meta.MetadataStore

      • setPointFontStyle

        public void setPointFontStyle​(ome.xml.model.enums.FontStyle fontStyle,
                              int ROIIndex,
                              int shapeIndex)
        Specified by:
        setPointFontStyle in interface ome.xml.meta.MetadataStore

      • setPointLocked

        public void setPointLocked​(java.lang.Boolean locked,
                           int ROIIndex,
                           int shapeIndex)
        Specified by:
        setPointLocked in interface ome.xml.meta.MetadataStore

      • setPolygonFillColor

        public void setPolygonFillColor​(ome.xml.model.primitives.Color fillColor,
                                int ROIIndex,
                                int shapeIndex)
        Specified by:
        setPolygonFillColor in interface ome.xml.meta.MetadataStore

      • setPolygonFillRule

        public void setPolygonFillRule​(ome.xml.model.enums.FillRule fillRule,
                               int ROIIndex,
                               int shapeIndex)
        Specified by:
        setPolygonFillRule in interface ome.xml.meta.MetadataStore

      • setPolygonFontFamily

        public void setPolygonFontFamily​(ome.xml.model.enums.FontFamily fontFamily,
                                 int ROIIndex,
                                 int shapeIndex)
        Specified by:
        setPolygonFontFamily in interface ome.xml.meta.MetadataStore

      • setPolygonFontSize

        public void setPolygonFontSize​(ome.units.quantity.Length fontSize,
                               int ROIIndex,
                               int shapeIndex)
        Specified by:
        setPolygonFontSize in interface ome.xml.meta.MetadataStore

      • setPolygonFontStyle

        public void setPolygonFontStyle​(ome.xml.model.enums.FontStyle fontStyle,
                                int ROIIndex,
                                int shapeIndex)
        Specified by:
        setPolygonFontStyle in interface ome.xml.meta.MetadataStore

      • setPolygonID

        public void setPolygonID​(java.lang.String id,
                         int ROIIndex,
                         int shapeIndex)
        Specified by:
        setPolygonID in interface ome.xml.meta.MetadataStore

      • setPolygonLocked

        public void setPolygonLocked​(java.lang.Boolean locked,
                             int ROIIndex,
                             int shapeIndex)
        Specified by:
        setPolygonLocked in interface ome.xml.meta.MetadataStore

      • setPolygonStrokeColor

        public void setPolygonStrokeColor​(ome.xml.model.primitives.Color strokeColor,
                                  int ROIIndex,
                                  int shapeIndex)
        Specified by:
        setPolygonStrokeColor in interface ome.xml.meta.MetadataStore

      • setPolygonStrokeDashArray

        public void setPolygonStrokeDashArray​(java.lang.String strokeDashArray,
                                      int ROIIndex,
                                      int shapeIndex)
        Specified by:
        setPolygonStrokeDashArray in interface ome.xml.meta.MetadataStore

      • setPolygonStrokeWidth

        public void setPolygonStrokeWidth​(ome.units.quantity.Length strokeWidth,
                                  int ROIIndex,
                                  int shapeIndex)
        Specified by:
        setPolygonStrokeWidth in interface ome.xml.meta.MetadataStore

      • setPolygonText

        public void setPolygonText​(java.lang.String text,
                           int ROIIndex,
                           int shapeIndex)
        Specified by:
        setPolygonText in interface ome.xml.meta.MetadataStore

      • setPolygonTheC

        public void setPolygonTheC​(ome.xml.model.primitives.NonNegativeInteger theC,
                           int ROIIndex,
                           int shapeIndex)
        Specified by:
        setPolygonTheC in interface ome.xml.meta.MetadataStore

      • setPolygonTheT

        public void setPolygonTheT​(ome.xml.model.primitives.NonNegativeInteger theT,
                           int ROIIndex,
                           int shapeIndex)
        Specified by:
        setPolygonTheT in interface ome.xml.meta.MetadataStore

      • setPolygonTheZ

        public void setPolygonTheZ​(ome.xml.model.primitives.NonNegativeInteger theZ,
                           int ROIIndex,
                           int shapeIndex)
        Specified by:
        setPolygonTheZ in interface ome.xml.meta.MetadataStore

      • setPolygonTransform

        public void setPolygonTransform​(ome.xml.model.AffineTransform transform,
                                int ROIIndex,
                                int shapeIndex)
        Specified by:
        setPolygonTransform in interface ome.xml.meta.MetadataStore

      • setPolygonPoints

        public void setPolygonPoints​(java.lang.String points,
                             int ROIIndex,
                             int shapeIndex)
        Specified by:
        setPolygonPoints in interface ome.xml.meta.MetadataStore

      • setPolylineFillRule

        public void setPolylineFillRule​(ome.xml.model.enums.FillRule fillRule,
                                int ROIIndex,
                                int shapeIndex)
        Specified by:
        setPolylineFillRule in interface ome.xml.meta.MetadataStore

      • setPolylineFontFamily

        public void setPolylineFontFamily​(ome.xml.model.enums.FontFamily fontFamily,
                                  int ROIIndex,
                                  int shapeIndex)
        Specified by:
        setPolylineFontFamily in interface ome.xml.meta.MetadataStore

      • setPolylineFontStyle

        public void setPolylineFontStyle​(ome.xml.model.enums.FontStyle fontStyle,
                                 int ROIIndex,
                                 int shapeIndex)
        Specified by:
        setPolylineFontStyle in interface ome.xml.meta.MetadataStore

      • setPolylineLocked

        public void setPolylineLocked​(java.lang.Boolean locked,
                              int ROIIndex,
                              int shapeIndex)
        Specified by:
        setPolylineLocked in interface ome.xml.meta.MetadataStore

      • setPolylineMarkerEnd

        public void setPolylineMarkerEnd​(ome.xml.model.enums.Marker markerEnd,
                                 int ROIIndex,
                                 int shapeIndex)
        Specified by:
        setPolylineMarkerEnd in interface ome.xml.meta.MetadataStore

      • setPolylineMarkerStart

        public void setPolylineMarkerStart​(ome.xml.model.enums.Marker markerStart,
                                   int ROIIndex,
                                   int shapeIndex)
        Specified by:
        setPolylineMarkerStart in interface ome.xml.meta.MetadataStore

      • setProjectDatasetRef

        public void setProjectDatasetRef​(java.lang.String dataset,
                                 int projectIndex,
                                 int datasetRefIndex)
        Specified by:
        setProjectDatasetRef in interface ome.xml.meta.MetadataStore

      • setRectangleFillRule

        public void setRectangleFillRule​(ome.xml.model.enums.FillRule fillRule,
                                 int ROIIndex,
                                 int shapeIndex)
        Specified by:
        setRectangleFillRule in interface ome.xml.meta.MetadataStore

      • setRectangleFontFamily

        public void setRectangleFontFamily​(ome.xml.model.enums.FontFamily fontFamily,
                                   int ROIIndex,
                                   int shapeIndex)
        Specified by:
        setRectangleFontFamily in interface ome.xml.meta.MetadataStore

      • setRectangleFontStyle

        public void setRectangleFontStyle​(ome.xml.model.enums.FontStyle fontStyle,
                                  int ROIIndex,
                                  int shapeIndex)
        Specified by:
        setRectangleFontStyle in interface ome.xml.meta.MetadataStore

      • setRectangleLocked

        public void setRectangleLocked​(java.lang.Boolean locked,
                               int ROIIndex,
                               int shapeIndex)
        Specified by:
        setRectangleLocked in interface ome.xml.meta.MetadataStore

      • setWellType

        public void setWellType​(java.lang.String type,
                        int plateIndex,
                        int wellIndex)
        Specified by:
        setWellType in interface ome.xml.meta.MetadataStore

      • setRightsRightsHeld

        public void setRightsRightsHeld​(java.lang.String value)
        Specified by:
        setRightsRightsHeld in interface ome.xml.meta.MetadataStore

      • setRightsRightsHolder

        public void setRightsRightsHolder​(java.lang.String value)
        Specified by:
        setRightsRightsHolder in interface ome.xml.meta.MetadataStore

      • setDetectorAnnotationRef

        public void setDetectorAnnotationRef​(java.lang.String annotation,
                                     int instrumentIndex,
                                     int detectorIndex,
                                     int annotationRefIndex)
        Specified by:
        setDetectorAnnotationRef in interface ome.xml.meta.MetadataStore

      • setDichroicAnnotationRef

        public void setDichroicAnnotationRef​(java.lang.String annotation,
                                     int instrumentIndex,
                                     int dichroicIndex,
                                     int annotationRefIndex)
        Specified by:
        setDichroicAnnotationRef in interface ome.xml.meta.MetadataStore

      • setEllipseAnnotationRef

        public void setEllipseAnnotationRef​(java.lang.String annotation,
                                    int ROIIndex,
                                    int shapeIndex,
                                    int annotationRefIndex)
        Specified by:
        setEllipseAnnotationRef in interface ome.xml.meta.MetadataStore

      • setFilamentAnnotationRef

        public void setFilamentAnnotationRef​(java.lang.String annotation,
                                     int instrumentIndex,
                                     int lightSourceIndex,
                                     int annotationRefIndex)
        Specified by:
        setFilamentAnnotationRef in interface ome.xml.meta.MetadataStore

      • setFilterAnnotationRef

        public void setFilterAnnotationRef​(java.lang.String annotation,
                                   int instrumentIndex,
                                   int filterIndex,
                                   int annotationRefIndex)
        Specified by:
        setFilterAnnotationRef in interface ome.xml.meta.MetadataStore

      • setGenericExcitationSourceAnnotationRef

        public void setGenericExcitationSourceAnnotationRef​(java.lang.String annotation,
                                                    int instrumentIndex,
                                                    int lightSourceIndex,
                                                    int annotationRefIndex)
        Specified by:
        setGenericExcitationSourceAnnotationRef in interface ome.xml.meta.MetadataStore

      • setInstrumentAnnotationRef

        public void setInstrumentAnnotationRef​(java.lang.String annotation,
                                       int instrumentIndex,
                                       int annotationRefIndex)
        Specified by:
        setInstrumentAnnotationRef in interface ome.xml.meta.MetadataStore

      • setLabelAnnotationRef

        public void setLabelAnnotationRef​(java.lang.String annotation,
                                  int ROIIndex,
                                  int shapeIndex,
                                  int annotationRefIndex)
        Specified by:
        setLabelAnnotationRef in interface ome.xml.meta.MetadataStore

      • setLaserAnnotationRef

        public void setLaserAnnotationRef​(java.lang.String annotation,
                                  int instrumentIndex,
                                  int lightSourceIndex,
                                  int annotationRefIndex)
        Specified by:
        setLaserAnnotationRef in interface ome.xml.meta.MetadataStore

      • setLightEmittingDiodeAnnotationRef

        public void setLightEmittingDiodeAnnotationRef​(java.lang.String annotation,
                                               int instrumentIndex,
                                               int lightSourceIndex,
                                               int annotationRefIndex)
        Specified by:
        setLightEmittingDiodeAnnotationRef in interface ome.xml.meta.MetadataStore

      • setLightPathAnnotationRef

        public void setLightPathAnnotationRef​(java.lang.String annotation,
                                      int imageIndex,
                                      int channelIndex,
                                      int annotationRefIndex)
        Specified by:
        setLightPathAnnotationRef in interface ome.xml.meta.MetadataStore

      • setLineAnnotationRef

        public void setLineAnnotationRef​(java.lang.String annotation,
                                 int ROIIndex,
                                 int shapeIndex,
                                 int annotationRefIndex)
        Specified by:
        setLineAnnotationRef in interface ome.xml.meta.MetadataStore

      • setMaskAnnotationRef

        public void setMaskAnnotationRef​(java.lang.String annotation,
                                 int ROIIndex,
                                 int shapeIndex,
                                 int annotationRefIndex)
        Specified by:
        setMaskAnnotationRef in interface ome.xml.meta.MetadataStore

      • setObjectiveAnnotationRef

        public void setObjectiveAnnotationRef​(java.lang.String annotation,
                                      int instrumentIndex,
                                      int objectiveIndex,
                                      int annotationRefIndex)
        Specified by:
        setObjectiveAnnotationRef in interface ome.xml.meta.MetadataStore

      • setPointAnnotationRef

        public void setPointAnnotationRef​(java.lang.String annotation,
                                  int ROIIndex,
                                  int shapeIndex,
                                  int annotationRefIndex)
        Specified by:
        setPointAnnotationRef in interface ome.xml.meta.MetadataStore

      • setPolygonAnnotationRef

        public void setPolygonAnnotationRef​(java.lang.String annotation,
                                    int ROIIndex,
                                    int shapeIndex,
                                    int annotationRefIndex)
        Specified by:
        setPolygonAnnotationRef in interface ome.xml.meta.MetadataStore

      • setPolylineAnnotationRef

        public void setPolylineAnnotationRef​(java.lang.String annotation,
                                     int ROIIndex,
                                     int shapeIndex,
                                     int annotationRefIndex)
        Specified by:
        setPolylineAnnotationRef in interface ome.xml.meta.MetadataStore

      • setRectangleAnnotationRef

        public void setRectangleAnnotationRef​(java.lang.String annotation,
                                      int ROIIndex,
                                      int shapeIndex,
                                      int annotationRefIndex)
        Specified by:
        setRectangleAnnotationRef in interface ome.xml.meta.MetadataStore

      • ignoreMissing

        protected void ignoreMissing​(java.lang.String method,
                             java.lang.Object... args)
        Called when a property is missing from the OMERO model (WARN).

      • ignoreUnneeded

        protected void ignoreUnneeded​(java.lang.String method,
                              java.lang.Object... args)
        Called when a property is not needed in OMERO since the data can be gotten elsewhere, as in directly from the file itself (DEBUG).

      • ignoreUnsupported

        protected void ignoreUnsupported​(java.lang.String method,
                                 java.lang.Object... args)
        Called when a property is not expected in a file to be imported. log.warn is used to signal to the user that something is being missed (WARN).

      • ignoreInsecure

        protected void ignoreInsecure​(java.lang.String method,
                              java.lang.Object... args)
        Called when saving a property to OMERO would result in a SecurityViolation (DEBUG). These are logged at debug since there's nothing the user need worry about.

      • ignoreAnnotator

        protected void ignoreAnnotator​(java.lang.String method,
                               java.lang.Object... args)
        For all cases of an annotator being ignore (WARN).