OmeroJava API
| Package | Description |
|---|---|
| omero.gateway | |
| omero.gateway.facility | |
| omero.gateway.rnd |
| Modifier and Type | Method and Description |
|---|---|
SecurityContext |
SecurityContext.copy()
Returns a copy of the security context.
|
| Modifier and Type | Method and Description |
|---|---|
Map<SecurityContext,Set<Long>> |
Gateway.getRenderingEngines()
Returns the rendering engines to re-activate.
|
| Modifier and Type | Method and Description |
|---|---|
void |
Gateway.closeConnector(SecurityContext ctx)
Close a connector for a certain
SecurityContext |
void |
Gateway.closeImport(SecurityContext ctx,
String userName)
Close Import for a certain user
|
void |
Gateway.closeService(SecurityContext ctx,
omero.api.StatefulServiceInterfacePrx svc)
Close a service
|
omero.api.RawPixelsStorePrx |
Gateway.createPixelsStore(SecurityContext ctx)
Create a
RawPixelsStorePrx |
omero.api.ThumbnailStorePrx |
Gateway.createThumbnailStore(SecurityContext ctx)
Create a
ThumbnailStorePrx |
omero.api.IAdminPrx |
Gateway.getAdminService(SecurityContext ctx)
Returns the
IAdminPrx service. |
omero.api.IAdminPrx |
Gateway.getAdminService(SecurityContext ctx,
boolean secure)
Returns the
IAdminPrx service. |
omero.api.IConfigPrx |
Gateway.getConfigService(SecurityContext ctx)
Returns the
IConfigPrx service. |
omero.gateway.Connector |
Gateway.getConnector(SecurityContext ctx)
Get a connector for a certain
SecurityContext |
omero.gateway.Connector |
Gateway.getConnector(SecurityContext ctx,
boolean recreate,
boolean permitNull)
Returns the connector corresponding to the passed context.
|
omero.api.ExporterPrx |
Gateway.getExporterService(SecurityContext ctx)
Returns the
ExporterPrx service. |
OMEROMetadataStoreClient |
Gateway.getImportStore(SecurityContext ctx)
Creates or recycles the import store.
|
OMEROMetadataStoreClient |
Gateway.getImportStore(SecurityContext ctx,
String userName)
Creates or recycles the import store.
|
omero.api.IMetadataPrx |
Gateway.getMetadataService(SecurityContext ctx)
Returns the
IMetadataPrx service. |
omero.api.IPixelsPrx |
Gateway.getPixelsService(SecurityContext ctx)
Returns the
IPixelsPrx service. |
omero.api.RawPixelsStorePrx |
Gateway.getPixelsStore(SecurityContext ctx)
Returns the
RawPixelsStorePrx service. |
omero.api.IContainerPrx |
Gateway.getPojosService(SecurityContext ctx)
Returns the
IContainerPrx service. |
omero.api.IProjectionPrx |
Gateway.getProjectionService(SecurityContext ctx)
Returns the
IProjectionPrx service. |
omero.api.IQueryPrx |
Gateway.getQueryService(SecurityContext ctx)
Returns the
IQueryPrx service. |
omero.api.RawFileStorePrx |
Gateway.getRawFileService(SecurityContext ctx)
Returns the
RawFileStorePrx service. |
omero.api.RenderingEnginePrx |
Gateway.getRenderingService(SecurityContext ctx,
long pixelsID)
Returns the
Rendering service. |
omero.api.IRenderingSettingsPrx |
Gateway.getRenderingSettingsService(SecurityContext ctx)
Returns the
IRenderingSettingsPrx service. |
omero.api.IRepositoryInfoPrx |
Gateway.getRepositoryService(SecurityContext ctx)
Returns the
IRepositoryInfoPrx service. |
omero.api.IRoiPrx |
Gateway.getROIService(SecurityContext ctx)
Returns the
IRoiPrx service. |
omero.api.IScriptPrx |
Gateway.getScriptService(SecurityContext ctx)
Returns the
IScriptPrx service. |
omero.api.SearchPrx |
Gateway.getSearchService(SecurityContext ctx)
Returns the
SearchPrx service. |
omero.grid.SharedResourcesPrx |
Gateway.getSharedResources(SecurityContext ctx)
Returns the
SharedResourcesPrx service. |
omero.api.ThumbnailStorePrx |
Gateway.getThumbnailService(SecurityContext ctx)
Returns the
ThumbnailStorePrx service. |
omero.api.ITypesPrx |
Gateway.getTypesService(SecurityContext ctx)
Returns the
ITypesPrx service. |
omero.api.IUpdatePrx |
Gateway.getUpdateService(SecurityContext ctx)
Returns the
IUpdatePrx service. |
omero.api.IUpdatePrx |
Gateway.getUpdateService(SecurityContext ctx,
String userName)
Returns the
IUpdatePrx service. |
ExperimenterData |
Gateway.getUserDetails(SecurityContext ctx,
String name)
Get the user details of a certain user
|
boolean |
Gateway.isAlive(SecurityContext ctx)
Checks if there is a
Connector for a particular
SecurityContext |
ProcessCallbackI |
Gateway.runScript(SecurityContext ctx,
long scriptID,
Map<String,omero.RType> parameters)
Run a script on the server
|
void |
Gateway.shutDownDerivedConnector(SecurityContext ctx)
Shuts down the connectors created while creating/importing data for other
users.
|
void |
Gateway.shutdownRenderingEngine(SecurityContext ctx,
long pixelsID)
Shuts down the rendering engine
|
CmdCallbackI |
Gateway.submit(SecurityContext ctx,
List<omero.cmd.Request> commands,
SecurityContext target)
Executes the commands.
|
CmdCallbackI |
Gateway.submit(SecurityContext ctx,
omero.cmd.Request cmd)
Directly submit a
Request to the server |
| Modifier and Type | Method and Description |
|---|---|
void |
DataManagerFacility.addImagesToDataset(SecurityContext ctx,
Collection<ImageData> images,
DatasetData ds)
Adds the
ImageDatas to the given DatasetData |
void |
DataManagerFacility.addImageToDataset(SecurityContext ctx,
ImageData image,
DatasetData ds)
Adds the
ImageData to the given DatasetData |
Map<FolderData,Collection<ROIData>> |
ROIFacility.addRoisToFolders(SecurityContext ctx,
long imageID,
Collection<ROIData> roiList,
Collection<FolderData> folders)
Adds ROIs to Folders
|
Map<FolderData,Collection<ROIData>> |
ROIFacility.addRoisToFolders(SecurityContext ctx,
long imageID,
Collection<ROIData> roiList,
Collection<FolderData> folders,
boolean removeFromOtherFolders)
Adds ROIs to Folders
|
TableData |
TablesFacility.addTable(SecurityContext ctx,
DataObject target,
String name,
TableData data)
Adds a new table with the provided data
|
<T extends AnnotationData> |
DataManagerFacility.attachAnnotation(SecurityContext ctx,
T annotation,
DataObject target)
Create/attach an
AnnotationData to a given DataObject |
Future<FileAnnotationData> |
DataManagerFacility.attachFile(SecurityContext ctx,
File file,
String mimetype,
String description,
String namespace,
DataObject target)
Attaches a
File to a DataObject |
DatasetData |
DataManagerFacility.createDataset(SecurityContext ctx,
DatasetData dataset,
ProjectData project)
Creates the
DatasetData on the server and attaches it
to the ProjectData (if not null) (if the
project doesn't exist on the server yet, it will be created, too) |
ExperimenterData |
AdminFacility.createExperimenter(SecurityContext ctx,
ExperimenterData exp,
String username,
String password,
List<GroupData> groups,
boolean isAdmin,
boolean isGroupOwner)
Creates an experimenter and returns it.
|
GroupData |
AdminFacility.createGroup(SecurityContext ctx,
GroupData groupData,
ExperimenterData owner,
int permissions)
Creates a group and returns it.
|
CmdCallbackI |
DataManagerFacility.delete(SecurityContext ctx,
omero.model.IObject object)
Deletes the specified object asynchronously
|
CmdCallbackI |
DataManagerFacility.delete(SecurityContext ctx,
List<omero.model.IObject> objects)
Deletes the specified objects asynchronously
|
CmdCallbackI |
DataManagerFacility.deleteFolders(SecurityContext ctx,
Collection<FolderData> folders,
boolean includeSubFolders,
boolean includeContent)
Delete Folders (asynchronous)
|
omero.cmd.Response |
DataManagerFacility.deleteObject(SecurityContext ctx,
omero.model.IObject object)
Deprecated.
Use the asynchronous method
DataManagerFacility.delete(SecurityContext, IObject) instead |
omero.cmd.Response |
DataManagerFacility.deleteObjects(SecurityContext ctx,
List<omero.model.IObject> objects)
Deprecated.
Use the asynchronous method
DataManagerFacility.delete(SecurityContext, List) instead |
List<File> |
TransferFacility.downloadImage(SecurityContext context,
String targetPath,
long imageId)
Downloads the original file of an image from the server.
|
omero.model.IObject |
BrowseFacility.findIObject(SecurityContext ctx,
omero.model.IObject o)
Retrieves an updated version of the specified object.
|
omero.model.IObject |
BrowseFacility.findIObject(SecurityContext ctx,
String klassName,
long id)
Retrieves an updated version of the specified object.
|
omero.model.IObject |
BrowseFacility.findIObject(SecurityContext ctx,
String klassName,
long id,
boolean allGroups)
Retrieves an updated version of the specified object.
|
<T extends DataObject> |
BrowseFacility.findObject(SecurityContext ctx,
Class<T> klass,
long id)
Retrieves an updated version of the specified object.
|
<T extends DataObject> |
BrowseFacility.findObject(SecurityContext ctx,
Class<T> klass,
long id,
boolean allGroups)
Retrieves an updated version of the specified object.
|
DataObject |
BrowseFacility.findObject(SecurityContext ctx,
String pojoName,
long id)
Retrieves an updated version of the specified object.
|
DataObject |
BrowseFacility.findObject(SecurityContext ctx,
String pojoName,
long id,
boolean allGroups)
Retrieves an updated version of the specified object.
|
List<AnnotationData> |
MetadataFacility.getAnnotations(SecurityContext ctx,
DataObject object)
Get all annotations for the given
DataObject |
List<AnnotationData> |
MetadataFacility.getAnnotations(SecurityContext ctx,
DataObject object,
List<Class<? extends AnnotationData>> annotationTypes,
List<Long> userIds)
Get the annotations for the given
DataObject |
Map<DataObject,List<AnnotationData>> |
MetadataFacility.getAnnotations(SecurityContext ctx,
List<? extends DataObject> objects,
List<Class<? extends AnnotationData>> annotationTypes,
List<Long> userIds)
Get the annotations for the given
DataObjects |
Set<GroupData> |
BrowseFacility.getAvailableGroups(SecurityContext ctx,
ExperimenterData user)
Retrieves the groups visible by the current experimenter.
|
Collection<FileAnnotationData> |
TablesFacility.getAvailableTables(SecurityContext ctx,
DataObject parent)
Get all available tables for a the specified object
|
List<ChannelData> |
MetadataFacility.getChannelData(SecurityContext ctx,
long imageId)
Get the
ChannelData for a specific image |
Collection<DatasetData> |
BrowseFacility.getDatasets(SecurityContext ctx)
Loads all datasets
|
Collection<DatasetData> |
BrowseFacility.getDatasets(SecurityContext ctx,
Collection<Long> ids)
Loads the datasets with the given ids
|
Collection<DatasetData> |
BrowseFacility.getDatasets(SecurityContext ctx,
long ownerId)
Loads the datasets for a particular user
|
Collection<DatasetData> |
BrowseFacility.getDatasets(SecurityContext ctx,
long ownerId,
Collection<Long> ids)
Loads the datasets with the given ids which belong to a particular user
|
Collection<FolderData> |
BrowseFacility.getFolders(SecurityContext ctx)
Get all folders the logged in user has access to.
|
Collection<FolderData> |
BrowseFacility.getFolders(SecurityContext ctx,
Collection<Long> ids)
Get the folders for the given folder ids.
|
Collection<FolderData> |
BrowseFacility.getFolders(SecurityContext ctx,
long userId)
Get the folders which belong to the given user.
|
Collection<DataObject> |
BrowseFacility.getHierarchy(SecurityContext ctx,
Class rootType,
List<Long> rootIDs,
omero.sys.Parameters options)
Retrieves hierarchy trees rooted by a given node.
|
Collection<DataObject> |
BrowseFacility.getHierarchy(SecurityContext ctx,
Class rootType,
long userId)
Retrieves hierarchy trees rooted by a given node.
|
Map<Integer,int[]> |
RawDataFacility.getHistogram(SecurityContext ctx,
PixelsData pixels,
int[] channels,
int binCount,
boolean globalRange,
omero.romio.PlaneDef plane)
Get the histogram data for the given image.
|
Map<Integer,int[]> |
RawDataFacility.getHistogram(SecurityContext ctx,
PixelsData pixels,
int[] channels,
int z,
int t)
Get the histogram data for the given image, using default 256 bins and
the channels global min/max for the histogram range.
|
ImageData |
BrowseFacility.getImage(SecurityContext ctx,
long id)
Loads a image
|
ImageData |
BrowseFacility.getImage(SecurityContext ctx,
long id,
ParametersI params)
Loads a image
|
ImageAcquisitionData |
MetadataFacility.getImageAcquisitionData(SecurityContext ctx,
long imageId)
Loads the
ImageAcquisitionData for a specific image |
Collection<ImageData> |
BrowseFacility.getImages(SecurityContext ctx,
Collection<Long> ids)
Loads the images with the given ids
|
Collection<ImageData> |
BrowseFacility.getImages(SecurityContext ctx,
Collection<Long> ids,
ParametersI params)
Loads the images with the given ids
|
Collection<ImageData> |
BrowseFacility.getImages(SecurityContext ctx,
long ownerId,
Collection<Long> ids)
Loads the images for a particular user
|
Collection<ImageData> |
BrowseFacility.getImagesForDatasets(SecurityContext ctx,
Collection<Long> datasetIds)
Load all images belonging to particular datasets
|
Collection<ImageData> |
BrowseFacility.getImagesForProjects(SecurityContext ctx,
Collection<Long> projectIds)
Load all images belonging to particular projects
|
Collection<String> |
BrowseFacility.getLookupTables(SecurityContext ctx)
Get the available lookup tables
|
Collection<ImageData> |
BrowseFacility.getOrphanedImages(SecurityContext ctx,
long userID)
Get orphaned images for a certain user
|
Plane2D |
RawDataFacility.getPlane(SecurityContext ctx,
PixelsData pixels,
int z,
int t,
int c)
Extracts a 2D plane from the pixels set.
|
Plane2D |
RawDataFacility.getPlane(SecurityContext ctx,
PixelsData pixels,
int z,
int t,
int c,
boolean close)
Deprecated.
Use getPlane(SecurityContext, PixelsData, z, t, c) instead
|
Collection<PlateData> |
BrowseFacility.getPlates(SecurityContext ctx)
Loads all plates
|
Collection<PlateData> |
BrowseFacility.getPlates(SecurityContext ctx,
Collection<Long> ids)
Loads the plates with the given ids
|
Collection<PlateData> |
BrowseFacility.getPlates(SecurityContext ctx,
long ownerId)
Loads the plates for a particular user
|
Collection<PlateData> |
BrowseFacility.getPlates(SecurityContext ctx,
long ownerId,
Collection<Long> ids)
Loads the plates with the given ids which belong to a particular user
|
Collection<ProjectData> |
BrowseFacility.getProjects(SecurityContext ctx)
Get all projects
|
Collection<ProjectData> |
BrowseFacility.getProjects(SecurityContext ctx,
Collection<Long> ids)
Get the projects for the given project ids
|
Collection<ProjectData> |
BrowseFacility.getProjects(SecurityContext ctx,
long ownerId)
Get the projects of a certain user
|
Collection<ProjectData> |
BrowseFacility.getProjects(SecurityContext ctx,
long ownerId,
Collection<Long> ids)
Get the projects for the given project ids which belong to a certain user
|
int |
ROIFacility.getROICount(SecurityContext ctx,
long imageId)
Get the number of ROIs for an image (
-1
in case of error) |
Collection<FolderData> |
ROIFacility.getROIFolders(SecurityContext ctx,
long imageId)
Get all ROI folders for a certain image
|
Collection<ScreenData> |
BrowseFacility.getScreens(SecurityContext ctx)
Loads all screens
|
Collection<ScreenData> |
BrowseFacility.getScreens(SecurityContext ctx,
Collection<Long> ids)
Loads the screens with the given ids
|
Collection<ScreenData> |
BrowseFacility.getScreens(SecurityContext ctx,
long ownerId)
Loads the screens for a particular user
|
Collection<ScreenData> |
BrowseFacility.getScreens(SecurityContext ctx,
long ownerId,
Collection<Long> ids)
Loads the screens with the given ids which belong to a particular user
|
TableData |
TablesFacility.getTable(SecurityContext ctx,
long fileId)
Load the data from a table (Note: limited to
TablesFacility.DEFAULT_MAX_ROWS_TO_FETCH number of rows) |
TableData |
TablesFacility.getTable(SecurityContext ctx,
long fileId,
List<Long> rows)
Load data from a table
|
TableData |
TablesFacility.getTable(SecurityContext ctx,
long fileId,
long... rows)
Load data from a table
|
TableData |
TablesFacility.getTable(SecurityContext ctx,
long fileId,
long rowFrom,
long rowTo,
int... columns)
Load data from a table
|
TableData |
TablesFacility.getTable(SecurityContext ctx,
long fileId,
long rowFrom,
long rowTo,
long... columns)
Load data from a table
|
TableData |
TablesFacility.getTableInfo(SecurityContext ctx,
long fileId)
Get basic information about a table.
|
Plane2D |
RawDataFacility.getTile(SecurityContext ctx,
PixelsData pixels,
int z,
int t,
int c,
int x,
int y,
int w,
int h)
Extracts a 2D tile from the pixels set
|
Collection<ImageData> |
BrowseFacility.getUserImages(SecurityContext ctx)
Loads all images of the logged in user
|
Collection<WellData> |
BrowseFacility.getWells(SecurityContext ctx,
Collection<Long> wellIds)
Loads the wells
|
Collection<WellData> |
BrowseFacility.getWells(SecurityContext ctx,
long plateId)
Loads the wells for a given plate
|
Collection<FolderData> |
BrowseFacility.loadFolders(SecurityContext ctx,
Collection<Long> ids)
Loads the folders for the given Ids.
|
Set<DataObject> |
BrowseFacility.loadHierarchy(SecurityContext ctx,
Class rootType,
List<Long> rootIDs,
omero.sys.Parameters options)
Deprecated.
Please use the more generic method
BrowseFacility.getHierarchy(SecurityContext, Class, long) |
Set<DataObject> |
BrowseFacility.loadHierarchy(SecurityContext ctx,
Class rootType,
long userId)
Deprecated.
Please use the more generic method
BrowseFacility.getHierarchy(SecurityContext, Class, List, Parameters) |
ROIResult |
ROIFacility.loadROI(SecurityContext ctx,
long roiId)
Loads the ROI
|
List<ROIResult> |
ROIFacility.loadROIs(SecurityContext ctx,
long imageID)
Loads the ROI related to the specified image.
|
List<ROIResult> |
ROIFacility.loadROIs(SecurityContext ctx,
long imageID,
List<Long> measurements)
Loads the ROI related to the specified image.
|
List<ROIResult> |
ROIFacility.loadROIs(SecurityContext ctx,
long imageID,
List<Long> measurements,
long userID)
Loads the ROI related to the specified image.
|
List<ROIResult> |
ROIFacility.loadROIsByPlane(SecurityContext ctx,
long imageID,
int z,
int t)
Loads the ROI related to the specified image.
|
Collection<ROIResult> |
ROIFacility.loadROIsForFolder(SecurityContext ctx,
long imageId,
long folderId)
Get all ROIs which are part of a certain folder
|
ExperimenterData |
AdminFacility.lookupExperimenter(SecurityContext ctx,
String name)
Returns the experimenter corresponding to the passed name or
null. |
GroupData |
AdminFacility.lookupGroup(SecurityContext ctx,
String name)
Returns the group corresponding to the passed name or
null. |
long[] |
TablesFacility.query(SecurityContext ctx,
long fileId,
String condition)
Perform a query on the table
|
long[] |
TablesFacility.query(SecurityContext ctx,
long fileId,
String condition,
long start,
long stop,
long step)
Perform a query on the table
|
void |
ROIFacility.removeRoisFromFolders(SecurityContext ctx,
long imageID,
Collection<ROIData> roiList,
Collection<FolderData> folders)
Remove the ROIs from the folders
|
DataObject |
DataManagerFacility.saveAndReturnObject(SecurityContext ctx,
DataObject object)
Updates the specified object.
|
DataObject |
DataManagerFacility.saveAndReturnObject(SecurityContext ctx,
DataObject object,
String userName)
Updates the specified object.
|
omero.model.IObject |
DataManagerFacility.saveAndReturnObject(SecurityContext ctx,
omero.model.IObject object)
Updates the specified object.
|
omero.model.IObject |
DataManagerFacility.saveAndReturnObject(SecurityContext ctx,
omero.model.IObject object,
Map options)
Updates the specified object.
|
omero.model.IObject |
DataManagerFacility.saveAndReturnObject(SecurityContext ctx,
omero.model.IObject object,
Map options,
String userName)
Updates the specified object.
|
omero.model.IObject |
DataManagerFacility.saveAndReturnObject(SecurityContext ctx,
omero.model.IObject object,
String userName)
Updates the specified object.
|
List<omero.model.IObject> |
DataManagerFacility.saveAndReturnObject(SecurityContext ctx,
List<omero.model.IObject> objects,
Map options,
String userName)
Updates the specified object.
|
Collection<ROIData> |
ROIFacility.saveROIs(SecurityContext ctx,
long imageID,
Collection<ROIData> roiList)
Save the ROI for the image to the server.
|
Collection<ROIData> |
ROIFacility.saveROIs(SecurityContext ctx,
long imageID,
long userID,
Collection<ROIData> roiList)
Save the ROI for the image to the server.
|
SearchResultCollection |
SearchFacility.search(SecurityContext ctx,
SearchParameters context)
Searches for data.
|
omero.model.IObject |
DataManagerFacility.updateObject(SecurityContext ctx,
omero.model.IObject object,
omero.sys.Parameters options)
Updates the specified object.
|
List<omero.model.IObject> |
DataManagerFacility.updateObjects(SecurityContext ctx,
List<omero.model.IObject> objects,
omero.sys.Parameters options)
Updates the specified
IObjects and returned the updated
IObjects. |
| Constructor and Description |
|---|
DataSink(SecurityContext ctx,
PixelsData source,
Gateway gw)
Creates a new instance.
|
OmeroJava API
Version: 5.3.3-ice35-b63
Copyright © 2017 The University of Dundee & Open Microscopy Environment. All Rights Reserved.