OmeroBlitz API

omero::api

Overview

module api

The omero::api module defines all the central verbs for working with OMERO.blitz.

Arguments and return values consist of those types defined in the other ice files available here. With no further custom code, it is possible to interoperate with OMERO.blitz simply via the definitions here. Start with the ServiceFactory definition at the end of this file.

Note: Using these types is significantly easier in combination with the JavaDocs of the OMERO.server, specifically the ome.api package. Where not further noted below, the follow mappings between ome.api argument types and omero::api argument types hold:

+-----------------------+------------------------+
|        ome.api        |      omero::api        |
+-----------------------+------------------------+
|java.lang.Class        |string                  |
+-----------------------+------------------------+
|java.util.Set          |java.util.List/vector   |
+-----------------------+------------------------+
|IPojo options (Map)    |omero::sys::ParamMap    |
+-----------------------+------------------------+
|If null needed         |omero::RType subclass   |
+-----------------------+------------------------+
|...                    |...                     |
+-----------------------+------------------------+

Class Index

ResolutionDescription
RoiOptions: Specifies filters used when querying the ROIs.
RoiResult: Returned by most search methods.
RoiStats: Container for ShapeStats, one with the combined values, and one per shape.
Save
SaveRsp
ShapePoints: Contains a discrete representation of the geometry of an omero::model::Shape.
ShapeStats: Contains arrays, one entry per channel, of the statistics for a given shape.

Interface Index

ClientCallback: Primary callback interface for interaction between client and server session (""ServiceFactory"").
Exporter: Stateful service for generating OME-XML or OME-TIFF from data stored in OMERO.
IAdmin: Administration interface providing access to admin-only functionality as well as JMX-based server access and selected user functions.
IConfig: Access to server configuration.
IContainer: Provides methods for dealing with the core Pojos of OME.
ILdap: Administration interface providing access to admin-only functionality as well as JMX-based server access and selected user functions.
IMetadata: Provides method to interact with acquisition metadata and annotations.
IPixels: Metadata gateway for the RenderingEngine and clients.
IProjection: Provides methods for performing projections of Pixels sets.
IQuery: Provides methods for directly querying object graphs.
IRenderingSettings: Provides method to apply rendering settings to a collection of images.
IRepositoryInfo: Provides methods for obtaining information for server repository disk space allocation.
IRoi: Interface for working with regions of interest.
IScript: Utility service for managing and launching scripts for execution by the Processor API.
ISession: model::Session creation service for OMERO.
IShare: Provides method for sharing - collaboration process for images, datasets, projects.
ITimeline: Service for the querying of OMERO metadata based on creation and modification time.
ITypes: Access to reflective type information.
IUpdate: Provides methods for directly updating object graphs.
JobHandle: Allows submission of asynchronous jobs.
MetadataStore: Server-side interface for import.
PyramidService
RawFileStore: Raw file gateway which provides access to the OMERO file repository.
RawPixelsStore: Binary data provider.
RenderingEngine: Defines a service to render a given pixels set.
Search: Central search interface, allowing Web2.0 style queries.
ServiceFactory: Starting point for all OMERO.blitz interaction.
ServiceInterface: Service marker similar to ome.api.ServiceInterface.
StatefulServiceInterface: Service marker for stateful services which permits the closing of a particular service before the destruction of the session.
ThumbnailStore: Provides methods for dealing with thumbnails.

Structure Index

LongPair

Sequence Index

AdminPrivilegeList
AnnotationList
BoolArray
ByteArray
ByteArrayArray
ChecksumAlgorithmList
DatasetList
DoubleArray
DoubleArrayArray
DoubleArrayArrayArray
EventContextList
EventList
EventLogList
ExperimenterGroupList
ExperimenterList
FloatArray
FloatArrayArray
FloatArrayArrayArray
IObjectList
ImageList
IntegerArray
IntegerArrayArray
IntegerArrayArrayArray
IntegerList
LogicalChannelList
LongArray
LongArrayArray
LongList
NamedValueList
OriginalFileList
PixelsList
PixelsTypeList
ProjectList
RTypeDictArray
ResolutionDescriptions: Description of the geometry of a single resolution level.
RoiList
ScriptJobList
SearchMetadataList
ServiceList
SessionList
ShapeList
ShapeStatsList
ShortArray
ShortArrayArray
StringArray
StringArrayArray
StringSet

Dictionary Index

BooleanIdListMap
BooleanLongListMap
IObjectListMap
IdBooleanLongListMapMap
IdListMap
IntShapeListMap
IntStringMap
IntegerDoubleArrayMap
IntegerIntegerArrayMap
LongAnnotationListMap
LongByteArrayMap
LongIObjectListMap
LongIntMap
LongPairIntMap
LongPairLongMap
LongPairToStringIntMap
LongPairToStringLongMap
LongPixelsMap
LongRoiResultMap
LongShapeListMap
LongStringMap
OriginalFileMap
SearchMetadata
StringIntMap
StringLongListMap
StringLongMap
StringRStringMap
StringRTypeMap
StringShapeListMap
StringStringArrayMap
StringStringMap
UserMap

Sequences

[ "java:type:java.util.ArrayList:java.util.List" ] sequence<model::AdminPrivilege> AdminPrivilegeList

Used By

IAdmin::createRestrictedSystemUser
IAdmin::createRestrictedSystemUserWithPassword
IAdmin::getAdminPrivileges
IAdmin::getAdminsWithPrivileges
IAdmin::getCurrentAdminPrivileges
IAdmin::setAdminPrivileges

[ "java:type:java.util.ArrayList:java.util.List" ] sequence<model::Annotation> AnnotationList

Used By

LongAnnotationListMap
IMetadata::loadAnnotation
IMetadata::loadSpecifiedAnnotations
IRoi::getRoiMeasurements
IShare::getComments
Search::byAnnotatedWith
grid::ImportSettings::userSpecifiedAnnotationList

sequence<bool> BoolArray

Used By

grid::BoolColumn::values
model::Permissions::restrictions

sequence<byte> ByteArray

Used By

ByteArrayArray
LongByteArrayMap

sequence<ByteArray> ByteArrayArray

Used By

grid::MaskColumn::bytes

[ "java:type:java.util.ArrayList:java.util.List" ] sequence<model::ChecksumAlgorithm> ChecksumAlgorithmList

Used By

grid::ManagedRepository::listChecksumAlgorithms
grid::ManagedRepository::suggestChecksumAlgorithm

[ "java:type:java.util.ArrayList:java.util.List" ] sequence<model::Dataset> DatasetList

sequence<double> DoubleArray

[ "java:type:java.util.ArrayList:java.util.List" ] sequence<sys::EventContext> EventContextList

Used By

cmd::CurrentSessionsResponse::contexts

[ "java:type:java.util.ArrayList:java.util.List" ] sequence<model::Event> EventList

[ "java:type:java.util.ArrayList:java.util.List" ] sequence<model::EventLog> EventLogList

Used By

ITimeline::getEventLogsByPeriod

[ "java:type:java.util.ArrayList:java.util.List" ] sequence<model::ExperimenterGroup> ExperimenterGroupList

Used By

IAdmin::addGroups
IAdmin::containedGroups
IAdmin::createExperimenter
IAdmin::createExperimenterWithPassword
IAdmin::lookupGroups
IAdmin::removeGroups
ILdap::discoverGroups

[ "java:type:java.util.ArrayList:java.util.List" ] sequence<model::Experimenter> ExperimenterList

Used By

IAdmin::addGroupOwners
IAdmin::containedExperimenters
IAdmin::getAdminsWithPrivileges
IAdmin::lookupExperimenters
IAdmin::removeGroupOwners
ILdap::discover
ILdap::searchAll
ILdap::searchByAttribute
ILdap::searchByAttributes
IShare::addUsers
IShare::createShare
IShare::getAllMembers
IShare::removeUsers

sequence<float> FloatArray

Used By

FloatArrayArray

sequence<FloatArray> FloatArrayArray

Used By

FloatArrayArrayArray
grid::FloatArrayColumn::values

sequence<FloatArrayArray> FloatArrayArrayArray

[ "java:type:java.util.ArrayList:java.util.List" ] sequence<model::IObject> IObjectList

Used By

IObjectListMap
LongIObjectListMap
IAdmin::moveToCommonSpace
IContainer::createDataObjects
IContainer::findContainerHierarchies
IContainer::link
IContainer::loadContainerHierarchy
IContainer::retrieveCollection
IContainer::unlink
IContainer::updateDataObjects
IMetadata::loadAnnotationsUsedNotOwned
IMetadata::loadTagSets
IPixels::getAllEnumerations
IPixels::retrieveAllRndSettings
IQuery::findAll
IQuery::findAllByExample
IQuery::findAllByFullText
IQuery::findAllByQuery
IQuery::findAllByString
IScript::getUserScripts
IScript::validateScript
IShare::addObjects
IShare::createShare
IShare::getContentSubList
IShare::getContents
IShare::getEvents
IShare::removeObjects
ITimeline::getMostRecentAnnotationLinks
ITimeline::getMostRecentShareCommentLinks
ITypes::allEnumerations
ITypes::getOriginalEnumerations
ITypes::updateEnumerations
IUpdate::saveAndReturnArray
IUpdate::saveAndReturnIds
IUpdate::saveArray
IUpdate::saveCollection
RenderingEngine::getAvailableFamilies
RenderingEngine::getAvailableModels
RenderingEngine::getCodomainMapContext
Search::results
ServiceFactory::getSecurityContexts
grid::ImportResponse::objects

[ "java:type:java.util.ArrayList:java.util.List" ] sequence<model::Image> ImageList

Used By

IContainer::getImages
IContainer::getImagesByOptions
IContainer::getUserImages

sequence<int> IntegerArray

Used By

IntegerArrayArray
IntegerIntegerArrayMap
IRoi::getShapeStatsRestricted
RawPixelsStore::findMinMax
RawPixelsStore::getHistogram
ShapePoints::x
ShapePoints::y
grid::MaskColumn::theT
grid::MaskColumn::theZ

sequence<IntegerArray> IntegerArrayArray

Used By

IntegerArrayArrayArray
grid::JobParams::authorsInstitutions

sequence<IntegerArrayArray> IntegerArrayArrayArray

[ "java:type:java.util.ArrayList:java.util.List" ] sequence<int> IntegerList

Used By

FilePathNamingException::illegalCodePoints

[ "java:type:java.util.ArrayList:java.util.List" ] sequence<model::LogicalChannel> LogicalChannelList

Used By

IMetadata::loadChannelAcquisitionData

sequence<long> LongArray

Used By

LongArrayArray
ShapeStats::channelIds
ShapeStats::pointsCount
grid::Data::rowNumbers
grid::DatasetColumn::values
grid::FileColumn::values
grid::ImageColumn::values
grid::LongColumn::values
grid::MaskColumn::imageId
grid::PlateColumn::values
grid::RoiColumn::values
grid::Table::getWhereList
grid::Table::read
grid::Table::readCoordinates
grid::Table::slice
grid::WellColumn::values

sequence<LongArray> LongArrayArray

Used By

grid::LongArrayColumn::values

[ "java:type:java.util.ArrayList:java.util.List" ] sequence<long> LongList

Used By

BooleanLongListMap
StringLongListMap
IAdmin::getLeaderOfGroupIds
IAdmin::getMemberOfGroupIds
IRoi::getMeasuredRoisMap
IRoi::getShapeStatsList
IRoi::getShapeStatsRestricted
cmd::Chown2::targetUsers
cmd::FindPyramidsResponse::pyramidFiles
cmd::ManageImageBinariesResponse::archivedFiles
cmd::SendEmailResponse::invalidusers
cmd::UsedFilesResponse::binaryFilesOtherSeries
cmd::UsedFilesResponse::binaryFilesThisSeries
cmd::UsedFilesResponse::companionFilesOtherSeries
cmd::UsedFilesResponse::companionFilesThisSeries
cmd::UsedFilesResponsePreFs::archivedFiles
cmd::UsedFilesResponsePreFs::companionFiles
cmd::UsedFilesResponsePreFs::originalMetadataFiles
grid::ManagedRepository::setChecksumAlgorithm
grid::ManagedRepository::verifyChecksums
grid::ProcessorCallback::responseRunning
romio::PlaneDefWithMasks::shapeIds

[ "java:type:java.util.ArrayList:java.util.List" ] sequence<model::NamedValue> NamedValueList

Used By

model::Experimenter::config
model::Experimenter::getConfig
model::Experimenter::setConfig
model::ExperimenterGroup::config
model::ExperimenterGroup::getConfig
model::ExperimenterGroup::setConfig
model::GenericExcitationSource::getMap
model::GenericExcitationSource::map
model::GenericExcitationSource::setMap
model::ImagingEnvironment::getMap
model::ImagingEnvironment::map
model::ImagingEnvironment::setMap
model::MapAnnotation::getMapValue
model::MapAnnotation::mapValue
model::MapAnnotation::setMapValue
model::MetadataImportJob::getVersionInfo
model::MetadataImportJob::setVersionInfo
model::MetadataImportJob::versionInfo
model::UploadJob::getVersionInfo
model::UploadJob::setVersionInfo
model::UploadJob::versionInfo

[ "java:type:java.util.ArrayList:java.util.List" ] sequence<model::OriginalFile> OriginalFileList

Used By

IAdmin::getMyUserPhotos
IScript::getScripts
IScript::getScriptsByMimetype
IScript::getUserScripts
grid::Repository::listFiles
grid::RepositoryMap::descriptions

[ "java:type:java.util.ArrayList:java.util.List" ] sequence<model::Pixels> PixelsList

Used By

grid::ImportResponse::pixels

[ "java:type:java.util.ArrayList:java.util.List" ] sequence<model::PixelsType> PixelsTypeList

[ "java:type:java.util.ArrayList:java.util.List" ] sequence<model::Project> ProjectList

sequence<RTypeDict> RTypeDictArray

Used By

cmd::CurrentSessionsResponse::data

sequence<ResolutionDescription> ResolutionDescriptions

Description of the geometry of a single resolution level. Initially this contains simply the sizeX/sizeY so that the client can calculate percentages. Eventually, this may also include columns, rows, etc.