DefaultOMEROService (ImageJ2 Javadocs 0-SNAPSHOT API)

java.lang.Object
- org.scijava.AbstractContextual
- - org.scijava.plugin.AbstractRichPlugin
  - - org.scijava.service.AbstractService
    - - net.imagej.omero.DefaultOMEROService

All Implemented Interfaces:

Comparable<Prioritized>, ImageJService, OMEROService, Contextual, Disposable, Identifiable, Initializable, Locatable, Logged, Optional, HasPluginInfo, RichPlugin, SciJavaPlugin, Prioritized, Service, Versioned

Direct Known Subclasses:

LegacyOMEROService
```
public class DefaultOMEROService
extends AbstractService
implements OMEROService, Optional
```
Default ImageJ service for managing OMERO data conversion.

Author:

Curtis Rueden

Constructor Summary

Constructors
Constructor and Description

DefaultOMEROService()

Constructors
Constructor and Description
`DefaultOMEROService()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addROIMapping(Object roi, ROIData shape)` Add a mapping between a ROIs originating from ImageJ and an OMERO `ROIData`.
`void`	`clearROIMappings()` Removes all `Object` `ROIData` mappings.
`List<ROIData>`	`convertOMEROROI(TreeNode<?> dataNodeRois, Interval interval)` Converts the given `TreeNode` to `ROIData`.
`TableData`	`convertOMEROTable(Table<?,?> imageJTable)` Converts the given ImageJ table to an OMERO table, but does not save the table to the server.
`OMEROSession`	`createSession(OMEROLocation location)` Creates an OMEROSession.
`Dataset`	`downloadImage(client client, long imageID)` Downloads the image with the given image ID from OMERO, storing the result into a new ImageJ `Dataset`.
`ROITree`	`downloadROI(OMEROLocation credentials, long roiID)` Downloads the `ROIData` with the given `roiID` from OMERO, and returns it as a `ROITree`.
`ROITree`	`downloadROIs(OMEROLocation credentials, long imageID)` Downloads the ROIs associated with the given `imageID` from OMERO, and returns them as a `ROITree`.
`Table<?,?>`	`downloadTable(OMEROLocation credentials, long tableID)` Downloads the table with the given ID from OMERO, storing the result into a new ImageJ `Table`.
`List<Table<?,?>>`	`downloadTables(OMEROLocation credentials, long imageID)` Downloads all tables associated with the given image ID in OMERO.
`Param`	`getJobParam(ModuleItem<?> item)` Converts an ImageJ module parameter to an OMERO job parameter.
`ROIData`	`getROIMapping(Object key)` Retrieve the `ROIData` associated with this key.
`Set<Object>`	`getROIMappingKeys()` Returns all the keys for mapped ROIs.
`ROIData`	`getUpdatedServerROIData(long roiDataId)` Returns the most recently retrieved `ROIData` object with the given ID.
`RType`	`prototype(Class<?> type)` Creates an OMERO parameter prototype for the given Java class.
`void`	`removeROIMapping(Object key)` Removes the `Object` `ROIData` mapping associated with the given key from the stored ROIs.
`void`	`removeSession(OMEROSession session)` Remove the specified `OMEROSession` for the cache of stored sessions.
`OMEROSession`	`session()` Returns the `OMEROSession` related to the running thread.
`OMEROSession`	`session(OMEROLocation location)` Returns an `OMEROSession` using the given `OMEROLocation`.
`Object`	`toImageJ(client client, RType value, Class<?> type)` Converts an OMERO parameter value to an ImageJ value of the given type.
`Object`	`toOMERO(client client, Object value)` Converts an ImageJ parameter value to an OMERO parameter value.
`RType`	`toOMERO(Object value)` Converts an ImageJ parameter value to an OMERO parameter value.
`Collection<ROIData>`	`updateAndReturnROIs(OMEROLocation credentials, TreeNode<?> ijROIs, long imageID)` Converts the given `TreeNode` to OMERO ROI(s), creating new Objects on the server only for ROIs which didn't previously exist.
`long[]`	`updateROIs(OMEROLocation credentials, TreeNode<?> ijROIs, long imageID)` Converts the given `TreeNode` to OMERO ROIs(s).
`Collection<ROIData>`	`uploadAndReturnROIs(OMEROLocation credentials, TreeNode<?> ijROIs, long imageID)` Converts the given `TreeNode` to OMERO ROI(s), and uploads them all as new Objects to the server.
`long`	`uploadImage(client client, Dataset dataset)` Uploads the given ImageJ `Dataset`'s image to OMERO, returning the new image ID on the OMERO server.
`void`	`uploadImage(OMEROLocation credentials, Dataset image, boolean uploadROIs, TreeNode<?> rois, boolean updateROIs, boolean uploadTables, List<Table<?,?>> tables, String[] tableNames, long omeroDatasetID)` Uploads the given image to OMERO, and optionally uploads the given ROIs and tables.
`void`	`uploadImageAttachments(OMEROLocation credentials, long imageID, boolean uploadROIs, boolean updateROIs, boolean uploadTables, TreeNode<?> rois, List<Table<?,?>> tables, String[] tableNames)` Uploads the attachments to the OMERO server, and attaches them to the image associated with the given id.
`long[]`	`uploadROIs(OMEROLocation credentials, TreeNode<?> ijROIs, long imageID)` Converts the given `TreeNode` to OMERO ROI(s), uploads them to the OMEROServer, and attaches them to the image with the specified ID.
`long`	`uploadTable(OMEROLocation credentials, String name, Table<?,?> imageJTable, long imageID)` Uploads an ImageJ table to OMERO, returning the new table ID on the OMERO server.

Methods inherited from class org.scijava.service.AbstractService
getContext, setContext, toString

Methods inherited from class org.scijava.plugin.AbstractRichPlugin
getInfo, getPriority, setInfo, setPriority

Methods inherited from class org.scijava.AbstractContextual
context

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.scijava.service.Service
initialize, registerEventHandlers

Methods inherited from interface org.scijava.plugin.RichPlugin
getIdentifier, log

Methods inherited from interface org.scijava.Contextual
context, getContext, setContext

Methods inherited from interface org.scijava.Prioritized
compareTo, getPriority, setPriority

Methods inherited from interface org.scijava.plugin.HasPluginInfo
getInfo, setInfo

Methods inherited from interface org.scijava.Locatable
getLocation

Methods inherited from interface org.scijava.Versioned
getVersion

Methods inherited from interface org.scijava.Disposable
dispose

- Constructor Detail
  - DefaultOMEROService
```
public DefaultOMEROService()
```
- Method Detail
  - getJobParam
```
public Param getJobParam(ModuleItem<?> item)
```
    Description copied from interface: OMEROService
    
    Converts an ImageJ module parameter to an OMERO job parameter.
    
    Specified by:
    
    getJobParam in interface OMEROService
  - prototype
```
public RType prototype(Class<?> type)
```
    Description copied from interface: OMEROService
    
    Creates an OMERO parameter prototype for the given Java class.
    
    Specified by:
    
    prototype in interface OMEROService
  - toOMERO
```
public RType toOMERO(Object value)
```
    Description copied from interface: OMEROService
    
    Converts an ImageJ parameter value to an OMERO parameter value.
    This method only handles basic types, not image types; see OMEROService.toOMERO(omero.client, Object) for details.
    
    Specified by:
    
    toOMERO in interface OMEROService
  - toOMERO
```
public Object toOMERO(client client,
                      Object value)
               throws ServerError,
                      IOException,
                      Glacier2.PermissionDeniedException,
                      Glacier2.CannotCreateSessionException,
                      ExecutionException,
                      DSOutOfServiceException,
                      DSAccessException,
                      NumberFormatException,
                      URISyntaxException
```
    Description copied from interface: OMEROService
    
    Converts an ImageJ parameter value to an OMERO parameter value.
    If the given object is an image type (i.e., Dataset, DatasetView or ImageDisplay) then the OMEROService.uploadImage(net.imagej.omero.OMEROLocation, net.imagej.Dataset, boolean, org.scijava.util.TreeNode<?>, boolean, boolean, java.util.List<org.scijava.table.Table<?, ?>>, java.lang.String[], long) method will be used transparently to convert the object into an OMERO image ID.
    
    In the case of Tables, it will be converted to a TableData.
    
    Specified by:
    
    toOMERO in interface OMEROService
    
    Throws:
    
    Glacier2.PermissionDeniedException
    
    Glacier2.CannotCreateSessionException
    
    ExecutionException
    
    DSOutOfServiceException
    
    DSAccessException
    
    ServerError
    
    IOException
    
    NumberFormatException
    
    URISyntaxException
  - toImageJ
```
public Object toImageJ(client client,
                       RType value,
                       Class<?> type)
                throws ServerError,
                       IOException,
                       Glacier2.PermissionDeniedException,
                       Glacier2.CannotCreateSessionException,
                       SecurityException,
                       DSOutOfServiceException,
                       ExecutionException,
                       DSAccessException
```
    Description copied from interface: OMEROService
    
    Converts an OMERO parameter value to an ImageJ value of the given type.
    If the requested type is an image type (i.e., Dataset, DatasetView or ImageDisplay) then the OMEROService.downloadImage(omero.client, long) method will be used transparently to convert the OMERO image ID into such an object.
    
    Specified by:
    
    toImageJ in interface OMEROService
    
    Throws:
    
    ServerError
    
    IOException
    
    Glacier2.PermissionDeniedException
    
    Glacier2.CannotCreateSessionException
    
    SecurityException
    
    DSOutOfServiceException
    
    ExecutionException
    
    DSAccessException
  - uploadImage
```
public void uploadImage(OMEROLocation credentials,
                        Dataset image,
                        boolean uploadROIs,
                        TreeNode<?> rois,
                        boolean updateROIs,
                        boolean uploadTables,
                        List<Table<?,?>> tables,
                        String[] tableNames,
                        long omeroDatasetID)
                 throws ServerError,
                        IOException,
                        ExecutionException,
                        DSOutOfServiceException,
                        DSAccessException,
                        Glacier2.PermissionDeniedException,
                        Glacier2.CannotCreateSessionException
```
    Description copied from interface: OMEROService
    
    Uploads the given image to OMERO, and optionally uploads the given ROIs and tables. The ROIs can also optionally be updated on the server.
    
    Specified by:
    
    uploadImage in interface OMEROService
    
    Throws:
    
    ServerError
    
    IOException
    
    ExecutionException
    
    DSOutOfServiceException
    
    DSAccessException
    
    Glacier2.PermissionDeniedException
    
    Glacier2.CannotCreateSessionException
  - uploadImageAttachments
```
public void uploadImageAttachments(OMEROLocation credentials,
                                   long imageID,
                                   boolean uploadROIs,
                                   boolean updateROIs,
                                   boolean uploadTables,
                                   TreeNode<?> rois,
                                   List<Table<?,?>> tables,
                                   String[] tableNames)
                            throws ExecutionException,
                                   DSOutOfServiceException,
                                   DSAccessException,
                                   ServerError,
                                   Glacier2.PermissionDeniedException,
                                   Glacier2.CannotCreateSessionException
```
    Description copied from interface: OMEROService
    
    Uploads the attachments to the OMERO server, and attaches them to the image associated with the given id. In order to update ROIs these ROIs must exist on the given image in OMERO.
    
    Specified by:
    
    uploadImageAttachments in interface OMEROService
    
    Throws:
    
    ExecutionException
    
    DSOutOfServiceException
    
    DSAccessException
    
    ServerError
    
    Glacier2.PermissionDeniedException
    
    Glacier2.CannotCreateSessionException
  - downloadImage
```
public Dataset downloadImage(client client,
                             long imageID)
                      throws ServerError,
                             IOException
```
    Description copied from interface: OMEROService
    
    Downloads the image with the given image ID from OMERO, storing the result into a new ImageJ Dataset.
    
    Specified by:
    
    downloadImage in interface OMEROService
    
    Throws:
    
    ServerError
    
    IOException
  - uploadImage
```
public long uploadImage(client client,
                        Dataset dataset)
                 throws ServerError,
                        IOException
```
    Description copied from interface: OMEROService
    
    Uploads the given ImageJ Dataset's image to OMERO, returning the new image ID on the OMERO server.
    
    Specified by:
    
    uploadImage in interface OMEROService
    
    Throws:
    
    ServerError
    
    IOException
  - uploadTable
```
public long uploadTable(OMEROLocation credentials,
                        String name,
                        Table<?,?> imageJTable,
                        long imageID)
                 throws ServerError,
                        Glacier2.PermissionDeniedException,
                        Glacier2.CannotCreateSessionException,
                        ExecutionException,
                        DSOutOfServiceException,
                        DSAccessException
```
    Description copied from interface: OMEROService
    
    Uploads an ImageJ table to OMERO, returning the new table ID on the OMERO server. Tables must be attached to a DataObject, thus the given image ID must be valid or this method will throw an exception.
    
    Specified by:
    
    uploadTable in interface OMEROService
    
    Throws:
    
    ServerError
    
    Glacier2.PermissionDeniedException
    
    Glacier2.CannotCreateSessionException
    
    ExecutionException
    
    DSOutOfServiceException
    
    DSAccessException
  - convertOMEROTable
```
public TableData convertOMEROTable(Table<?,?> imageJTable)
```
    Description copied from interface: OMEROService
    
    Converts the given ImageJ table to an OMERO table, but does not save the table to the server.
    
    Specified by:
    
    convertOMEROTable in interface OMEROService
  - downloadTable
```
public Table<?,?> downloadTable(OMEROLocation credentials,
                                long tableID)
                         throws ServerError,
                                Glacier2.PermissionDeniedException,
                                Glacier2.CannotCreateSessionException,
                                ExecutionException,
                                DSOutOfServiceException,
                                DSAccessException
```
    Description copied from interface: OMEROService
    
    Downloads the table with the given ID from OMERO, storing the result into a new ImageJ Table.
    
    Specified by:
    
    downloadTable in interface OMEROService
    
    Throws:
    
    ServerError
    
    Glacier2.PermissionDeniedException
    
    Glacier2.CannotCreateSessionException
    
    ExecutionException
    
    DSOutOfServiceException
    
    DSAccessException
  - downloadTables
```
public List<Table<?,?>> downloadTables(OMEROLocation credentials,
                                       long imageID)
                                throws ExecutionException,
                                       DSOutOfServiceException,
                                       DSAccessException,
                                       ServerError,
                                       Glacier2.PermissionDeniedException,
                                       Glacier2.CannotCreateSessionException
```
    Description copied from interface: OMEROService
    
    Downloads all tables associated with the given image ID in OMERO.
    
    Specified by:
    
    downloadTables in interface OMEROService
    
    Throws:
    
    ExecutionException
    
    DSOutOfServiceException
    
    DSAccessException
    
    ServerError
    
    Glacier2.PermissionDeniedException
    
    Glacier2.CannotCreateSessionException
  - downloadROIs
```
public ROITree downloadROIs(OMEROLocation credentials,
                            long imageID)
                     throws ServerError,
                            Glacier2.PermissionDeniedException,
                            Glacier2.CannotCreateSessionException,
                            ExecutionException,
                            DSOutOfServiceException,
                            DSAccessException
```
    Description copied from interface: OMEROService
    
    Downloads the ROIs associated with the given imageID from OMERO, and returns them as a ROITree.
    
    Specified by:
    
    downloadROIs in interface OMEROService
    
    Throws:
    
    ServerError
    
    Glacier2.PermissionDeniedException
    
    Glacier2.CannotCreateSessionException
    
    ExecutionException
    
    DSOutOfServiceException
    
    DSAccessException
  - downloadROI
```
public ROITree downloadROI(OMEROLocation credentials,
                           long roiID)
                    throws DSOutOfServiceException,
                           DSAccessException,
                           ExecutionException
```
    Description copied from interface: OMEROService
    
    Downloads the ROIData with the given roiID from OMERO, and returns it as a ROITree.
    
    Specified by:
    
    downloadROI in interface OMEROService
    
    Throws:
    
    DSOutOfServiceException
    
    DSAccessException
    
    ExecutionException
  - uploadROIs
```
public long[] uploadROIs(OMEROLocation credentials,
                         TreeNode<?> ijROIs,
                         long imageID)
                  throws ExecutionException,
                         DSOutOfServiceException,
                         DSAccessException
```
    Description copied from interface: OMEROService
    
    Converts the given TreeNode to OMERO ROI(s), uploads them to the OMEROServer, and attaches them to the image with the specified ID. All ROIs are uploaded as new Objects, regardless of their origin.
    
    Specified by:
    
    uploadROIs in interface OMEROService
    
    Throws:
    
    ExecutionException
    
    DSOutOfServiceException
    
    DSAccessException
  - updateROIs
```
public long[] updateROIs(OMEROLocation credentials,
                         TreeNode<?> ijROIs,
                         long imageID)
                  throws ExecutionException,
                         DSOutOfServiceException,
                         DSAccessException
```
    Description copied from interface: OMEROService
    
    Converts the given TreeNode to OMERO ROIs(s). ROIs which originated from OMERO are updated on the server, and new ROIs are uploaded. The ids of the new ROI objects is returned.
    
    Specified by:
    
    updateROIs in interface OMEROService
    
    Throws:
    
    ExecutionException
    
    DSOutOfServiceException
    
    DSAccessException
  - uploadAndReturnROIs
```
public Collection<ROIData> uploadAndReturnROIs(OMEROLocation credentials,
                                               TreeNode<?> ijROIs,
                                               long imageID)
                                        throws ExecutionException,
                                               DSOutOfServiceException,
                                               DSAccessException
```
    Description copied from interface: OMEROService
    
    Converts the given TreeNode to OMERO ROI(s), and uploads them all as new Objects to the server. The new OMERO objects are then returned.
    
    Specified by:
    
    uploadAndReturnROIs in interface OMEROService
    
    Throws:
    
    ExecutionException
    
    DSOutOfServiceException
    
    DSAccessException
  - updateAndReturnROIs
```
public Collection<ROIData> updateAndReturnROIs(OMEROLocation credentials,
                                               TreeNode<?> ijROIs,
                                               long imageID)
                                        throws ExecutionException,
                                               DSOutOfServiceException,
                                               DSAccessException
```
    Description copied from interface: OMEROService
    
    Converts the given TreeNode to OMERO ROI(s), creating new Objects on the server only for ROIs which didn't previously exist. ROIs which originated from OMERO are updated on the server. A collection of the new ROI objects is returned.
    
    Specified by:
    
    updateAndReturnROIs in interface OMEROService
    
    Throws:
    
    ExecutionException
    
    DSOutOfServiceException
    
    DSAccessException
  - convertOMEROROI
```
public List<ROIData> convertOMEROROI(TreeNode<?> dataNodeRois,
                                     Interval interval)
```
    Description copied from interface: OMEROService
    
    Converts the given TreeNode to ROIData. If an interval is provided it will be used to convert unbounded MaskPredicates to ROIData. If the interval is null, then unbounded MaskPredicates cannot be converted to ROIData and an exception is thrown.
    
    Specified by:
    
    convertOMEROROI in interface OMEROService
  - getUpdatedServerROIData
```
public ROIData getUpdatedServerROIData(long roiDataId)
```
    Description copied from interface: OMEROService
    
    Returns the most recently retrieved ROIData object with the given ID. If no such mapping exists null is returned.
    When a ROIData object is updated and the new version uploaded to the OMERO server, previous ROIData objects become "locked" and subsequent attempts to update and upload new versions of them to OMERO will result in OptimisticLockException. Therefore, pairings of the id and the update OMERO server ROIData object must be stored.
    
    Specified by:
    
    getUpdatedServerROIData in interface OMEROService
  - addROIMapping
```
public void addROIMapping(Object roi,
                          ROIData shape)
```
    Description copied from interface: OMEROService
    
    Add a mapping between a ROIs originating from ImageJ and an OMERO ROIData.
    
    Specified by:
    
    addROIMapping in interface OMEROService
  - getROIMapping
```
public ROIData getROIMapping(Object key)
```
    Description copied from interface: OMEROService
    
    Retrieve the ROIData associated with this key. Returns null if there's no mapping.
    
    Specified by:
    
    getROIMapping in interface OMEROService
  - getROIMappingKeys
```
public Set<Object> getROIMappingKeys()
```
    Description copied from interface: OMEROService
    
    Returns all the keys for mapped ROIs.
    
    Specified by:
    
    getROIMappingKeys in interface OMEROService
  - removeROIMapping
```
public void removeROIMapping(Object key)
```
    Description copied from interface: OMEROService
    
    Removes the Object ROIData mapping associated with the given key from the stored ROIs.
    
    Specified by:
    
    removeROIMapping in interface OMEROService
  - clearROIMappings
```
public void clearROIMappings()
```
    Description copied from interface: OMEROService
    
    Removes all Object ROIData mappings.
    
    Specified by:
    
    clearROIMappings in interface OMEROService
  - session
```
public OMEROSession session(OMEROLocation location)
```
    Description copied from interface: OMEROService
    
    Returns an OMEROSession using the given OMEROLocation. If a session with this location already exists it is returned, if not a new one is created.
    
    Specified by:
    
    session in interface OMEROService
    
    Parameters:
    
    location - OMEROLocation
    
    Returns:
    
    OMEROSession
  - session
```
public OMEROSession session()
```
    Description copied from interface: OMEROService
    
    Returns the OMEROSession related to the running thread.
    
    Specified by:
    
    session in interface OMEROService
    
    Returns:
    
    the OMEROSession with the current thread
  - createSession
```
public OMEROSession createSession(OMEROLocation location)
```
    Description copied from interface: OMEROService
    
    Creates an OMEROSession. This does not cache the session nor does it associate this session with the thread.
    
    Specified by:
    
    createSession in interface OMEROService
    
    Parameters:
    
    location - OMEROLocation to be used to create the session
    
    Returns:
    
    a new OMEROSession
  - removeSession
```
public void removeSession(OMEROSession session)
```
    Description copied from interface: OMEROService
    
    Remove the specified OMEROSession for the cache of stored sessions.
    
    Specified by:
    
    removeSession in interface OMEROService
    
    Parameters:
    
    session - The session to be removed

Class DefaultOMEROService

Constructor Summary

Method Summary

Methods inherited from class org.scijava.service.AbstractService

Methods inherited from class org.scijava.plugin.AbstractRichPlugin

Methods inherited from class org.scijava.AbstractContextual

Methods inherited from class java.lang.Object

Methods inherited from interface org.scijava.service.Service

Methods inherited from interface org.scijava.plugin.RichPlugin

Methods inherited from interface org.scijava.Contextual

Methods inherited from interface org.scijava.Prioritized

Methods inherited from interface org.scijava.plugin.HasPluginInfo

Methods inherited from interface org.scijava.Locatable

Methods inherited from interface org.scijava.Versioned

Methods inherited from interface org.scijava.Disposable

Constructor Detail

DefaultOMEROService

Method Detail

getJobParam

prototype

toOMERO

toOMERO

toImageJ

uploadImage

uploadImageAttachments

downloadImage

uploadImage

uploadTable

convertOMEROTable

downloadTable

downloadTables

downloadROIs

downloadROI

uploadROIs

updateROIs

uploadAndReturnROIs

updateAndReturnROIs

convertOMEROROI

getUpdatedServerROIData

addROIMapping

getROIMapping

getROIMappingKeys

removeROIMapping

clearROIMappings

session

session

createSession

removeSession