OMEROService (ImageJ2 Javadocs 0-SNAPSHOT API)

All Superinterfaces:

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

All Known Implementing Classes:

DefaultOMEROService, LegacyOMEROService
```
public interface OMEROService
extends ImageJService
```
Interface for ImageJ services that manage OMERO data conversion.

Author:

Curtis Rueden

Method Summary

All Methods Instance Methods Abstract 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 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

Method Detail

getJobParam
```
Param getJobParam(ModuleItem<?> item)
```
Converts an ImageJ module parameter to an OMERO job parameter.

prototype
```
RType prototype(Class<?> type)
```
Creates an OMERO parameter prototype for the given Java class.

toOMERO
```
RType toOMERO(Object value)
```
Converts an ImageJ parameter value to an OMERO parameter value.
This method only handles basic types, not image types; see toOMERO(omero.client, Object) for details.

toOMERO
```
Object toOMERO(client client,
               Object value)
        throws ServerError,
               IOException,
               Glacier2.PermissionDeniedException,
               Glacier2.CannotCreateSessionException,
               ExecutionException,
               DSOutOfServiceException,
               DSAccessException,
               NumberFormatException,
               URISyntaxException
```
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 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.

Throws:

DSAccessException

DSOutOfServiceException

ExecutionException

Glacier2.CannotCreateSessionException

Glacier2.PermissionDeniedException

ServerError

IOException

NumberFormatException

URISyntaxException

toImageJ

Object toImageJ(client client,
                RType value,
                Class<?> type)
         throws ServerError,
                IOException,
                Glacier2.PermissionDeniedException,
                Glacier2.CannotCreateSessionException,
                SecurityException,
                DSOutOfServiceException,
                ExecutionException,
                DSAccessException

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 downloadImage(omero.client, long) method will be used transparently to convert the OMERO image ID into such an object.

Throws:: ServerError; IOException; Glacier2.PermissionDeniedException; Glacier2.CannotCreateSessionException; SecurityException; DSOutOfServiceException; ExecutionException; DSAccessException

uploadImage

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

Uploads the given image to OMERO, and optionally uploads the given ROIs and tables. The ROIs can also optionally be updated on the server.

Throws:: ServerError; IOException; ExecutionException; DSOutOfServiceException; DSAccessException; Glacier2.PermissionDeniedException; Glacier2.CannotCreateSessionException

uploadImageAttachments

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

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.

Throws:: ExecutionException; DSOutOfServiceException; DSAccessException; ServerError; Glacier2.PermissionDeniedException; Glacier2.CannotCreateSessionException

downloadImage

Dataset downloadImage(client client,
                      long imageID)
               throws ServerError,
                      IOException

Downloads the image with the given image ID from OMERO, storing the result into a new ImageJ Dataset.

Throws:: ServerError; IOException

uploadImage

long uploadImage(client client,
                 Dataset dataset)
          throws ServerError,
                 IOException

Uploads the given ImageJ Dataset's image to OMERO, returning the new image ID on the OMERO server.

Throws:: ServerError; IOException

uploadTable

long uploadTable(OMEROLocation credentials,
                 String name,
                 Table<?,?> imageJTable,
                 long imageID)
          throws ServerError,
                 Glacier2.PermissionDeniedException,
                 Glacier2.CannotCreateSessionException,
                 ExecutionException,
                 DSOutOfServiceException,
                 DSAccessException

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.

Throws:: ServerError; Glacier2.PermissionDeniedException; Glacier2.CannotCreateSessionException; ExecutionException; DSOutOfServiceException; DSAccessException

convertOMEROTable
```
TableData convertOMEROTable(Table<?,?> imageJTable)
```
Converts the given ImageJ table to an OMERO table, but does not save the table to the server.

downloadTable

Table<?,?> downloadTable(OMEROLocation credentials,
                         long tableID)
                  throws ServerError,
                         Glacier2.PermissionDeniedException,
                         Glacier2.CannotCreateSessionException,
                         ExecutionException,
                         DSOutOfServiceException,
                         DSAccessException

Downloads the table with the given ID from OMERO, storing the result into a new ImageJ Table.

Throws:: ServerError; Glacier2.PermissionDeniedException; Glacier2.CannotCreateSessionException; ExecutionException; DSOutOfServiceException; DSAccessException

downloadTables

List<Table<?,?>> downloadTables(OMEROLocation credentials,
                                long imageID)
                         throws ExecutionException,
                                DSOutOfServiceException,
                                DSAccessException,
                                ServerError,
                                Glacier2.PermissionDeniedException,
                                Glacier2.CannotCreateSessionException

Downloads all tables associated with the given image ID in OMERO.

Throws:: ExecutionException; DSOutOfServiceException; DSAccessException; ServerError; Glacier2.PermissionDeniedException; Glacier2.CannotCreateSessionException

downloadROIs

ROITree downloadROIs(OMEROLocation credentials,
                     long imageID)
              throws ServerError,
                     Glacier2.PermissionDeniedException,
                     Glacier2.CannotCreateSessionException,
                     ExecutionException,
                     DSOutOfServiceException,
                     DSAccessException

Downloads the ROIs associated with the given imageID from OMERO, and returns them as a ROITree.

Throws:: ServerError; Glacier2.PermissionDeniedException; Glacier2.CannotCreateSessionException; ExecutionException; DSOutOfServiceException; DSAccessException

downloadROI

ROITree downloadROI(OMEROLocation credentials,
                    long roiID)
             throws DSOutOfServiceException,
                    DSAccessException,
                    ExecutionException

Downloads the ROIData with the given roiID from OMERO, and returns it as a ROITree.

Throws:: DSOutOfServiceException; DSAccessException; ExecutionException

uploadROIs

long[] uploadROIs(OMEROLocation credentials,
                  TreeNode<?> ijROIs,
                  long imageID)
           throws ExecutionException,
                  DSOutOfServiceException,
                  DSAccessException

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.

Throws:: ExecutionException; DSOutOfServiceException; DSAccessException

updateROIs

long[] updateROIs(OMEROLocation credentials,
                  TreeNode<?> ijROIs,
                  long imageID)
           throws ExecutionException,
                  DSOutOfServiceException,
                  DSAccessException

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.

Throws:: ExecutionException; DSOutOfServiceException; DSAccessException

uploadAndReturnROIs

Collection<ROIData> uploadAndReturnROIs(OMEROLocation credentials,
                                        TreeNode<?> ijROIs,
                                        long imageID)
                                 throws ExecutionException,
                                        DSOutOfServiceException,
                                        DSAccessException

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.

Throws:: ExecutionException; DSOutOfServiceException; DSAccessException

updateAndReturnROIs

Collection<ROIData> updateAndReturnROIs(OMEROLocation credentials,
                                        TreeNode<?> ijROIs,
                                        long imageID)
                                 throws ExecutionException,
                                        DSOutOfServiceException,
                                        DSAccessException

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.

Throws:: ExecutionException; DSOutOfServiceException; DSAccessException

convertOMEROROI
```
List<ROIData> convertOMEROROI(TreeNode<?> dataNodeRois,
                              Interval interval)
```
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.

getUpdatedServerROIData
```
ROIData getUpdatedServerROIData(long roiDataId)
```
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.

addROIMapping

void addROIMapping(Object roi,
                   ROIData shape)

Add a mapping between a ROIs originating from ImageJ and an OMERO ROIData.

getROIMapping
```
ROIData getROIMapping(Object key)
```
Retrieve the ROIData associated with this key. Returns null if there's no mapping.

getROIMappingKeys
```
Set<Object> getROIMappingKeys()
```
Returns all the keys for mapped ROIs.

removeROIMapping
```
void removeROIMapping(Object key)
```
Removes the Object ROIData mapping associated with the given key from the stored ROIs.

clearROIMappings
```
void clearROIMappings()
```
Removes all Object ROIData mappings.

session
```
OMEROSession session(OMEROLocation location)
```
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.

Parameters:

location - OMEROLocation

Returns:

OMEROSession

session
```
OMEROSession session()
```
Returns the OMEROSession related to the running thread.

Returns:

the OMEROSession with the current thread

createSession
```
OMEROSession createSession(OMEROLocation location)
```
Creates an OMEROSession. This does not cache the session nor does it associate this session with the thread.

Parameters:

location - OMEROLocation to be used to create the session

Returns:

a new OMEROSession

removeSession
```
void removeSession(OMEROSession session)
```
Remove the specified OMEROSession for the cache of stored sessions.

Parameters:

session - The session to be removed

Interface OMEROService

Method Summary

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

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