OmeroBlitz API
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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

Used By

DoubleArrayArray
IntegerDoubleArrayMap
ShapeStats::max
ShapeStats::mean
ShapeStats::min
ShapeStats::stdDev
ShapeStats::sum
grid::DoubleColumn::values
grid::ImportSettings::userSpecifiedPixels
grid::MaskColumn::h
grid::MaskColumn::w
grid::MaskColumn::x
grid::MaskColumn::y
sequence<DoubleArray> DoubleArrayArray

Used By

DoubleArrayArrayArray
grid::DoubleArrayColumn::values
sequence<DoubleArrayArray> DoubleArrayArrayArray

Used By

MetadataStore::populateMinMax
[ "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.

Used By

PyramidService::getResolutionDescriptions
[ "java:type:java.util.ArrayList:java.util.List" ] sequence<model::Roi> RoiList

Used By

RoiResult::rois
[ "java:type:java.util.ArrayList:java.util.List" ] sequence<model::ScriptJob> ScriptJobList
[ "java:type:java.util.ArrayList" ] sequence<SearchMetadata> SearchMetadataList

Used By

Search::currentMetadataList
sequence<ServiceInterface*> ServiceList

Used By

ServiceFactory::keepAllAlive
[ "java:type:java.util.ArrayList:java.util.List" ] sequence<model::Session> SessionList

Used By

ISession::getMyOpenAgentSessions
ISession::getMyOpenClientSessions
ISession::getMyOpenSessions
IShare::getMemberShares
IShare::getMemberSharesFor
IShare::getOwnShares
IShare::getSharesOwnedBy
cmd::CurrentSessionsResponse::sessions
[ "java:type:java.util.ArrayList:java.util.List" ] sequence<model::Shape> ShapeList

Used By

IntShapeListMap
LongShapeListMap
StringShapeListMap
sequence<ShapeStats> ShapeStatsList

Used By

IRoi::getShapeStatsList
IRoi::getShapeStatsRestricted
RoiStats::perShape
sequence<short> ShortArray

Used By

ShortArrayArray
sequence<ShortArray> ShortArrayArray
sequence<string> StringArray

Used By

StringArrayArray
StringStringArrayMap
grid::JobParams::authors
grid::JobParams::institutions
grid::Repository::deletePaths
grid::StringColumn::values
model::Namespace::getKeywords
model::Namespace::keywords
model::Namespace::setKeywords
sequence<StringArray> StringArrayArray
[ "java:type:java.util.ArrayList:java.util.List" ] sequence<string> StringSet

Used By

FilePathNamingException::illegalNames
FilePathNamingException::illegalPrefixes
FilePathNamingException::illegalSuffixes
ILdap::searchByAttributes
ILdap::searchDnInGroups
IMetadata::countSpecifiedAnnotations
IMetadata::loadAnnotations
IMetadata::loadSpecifiedAnnotations
IMetadata::loadSpecifiedAnnotationsLinkedTo
ISession::getInputKeys
ISession::getOutputKeys
IShare::addGuests
IShare::createShare
IShare::getAllGuests
IShare::getAllUsers
IShare::removeGuests
ITimeline::countByPeriod
ITimeline::getByPeriod
ITimeline::getMostRecentAnnotationLinks
ITimeline::getMostRecentObjects
ITypes::getAnnotationTypes
ITypes::getEnumerationTypes
RoiOptions::shapes
Search::bySimilarTerms
Search::bySomeMustNone
Search::fetchAlso
Search::fetchAnnotations
Search::onlyAnnotatedWith
Search::onlyTypes
ServiceFactory::activeServices
cmd::Delete2::typesToIgnore
cmd::DiskUsage::classes
cmd::DiskUsage2::targetClasses
cmd::Duplicate::typesToDuplicate
cmd::Duplicate::typesToIgnore
cmd::Duplicate::typesToReference
cmd::FindChildren::stopBefore
cmd::FindChildren::typesOfChildren
cmd::FindParents::stopBefore
cmd::FindParents::typesOfParents
cmd::LegalGraphTargetsResponse::targets
cmd::SendEmailRequest::extra
cmd::SendEmailResponse::invalidemails
cmd::SkipHead::startFrom
cmd::graphs::ChildOption::excludeNs
cmd::graphs::ChildOption::excludeType
cmd::graphs::ChildOption::includeNs
cmd::graphs::ChildOption::includeType
grid::ImportLocation::usedFiles
grid::ImportProcess::verifyUpload
grid::JobParams::namespaces
grid::ManagedRepository::importPaths
grid::Param::namespaces
grid::RawAccessRequest::args
grid::Repository::list
model::Permissions::extendedRestrictions
sys::EventContext::adminPrivileges

Dictionaries

dictionary<bool, sys::LongList> BooleanIdListMap

Used By

IRenderingSettings::applySettingsToDataset
IRenderingSettings::applySettingsToImages
IRenderingSettings::applySettingsToProject
IRenderingSettings::applySettingsToSet
dictionary<bool, LongList> BooleanLongListMap

Used By

IdBooleanLongListMapMap
dictionary<string, IObjectList> IObjectListMap

Used By

ITimeline::getByPeriod
ITimeline::getMostRecentObjects
ITypes::getEnumerationsWithEntries
MetadataStore::saveToDB
dictionary<long, BooleanLongListMap> IdBooleanLongListMapMap

Used By

IContainer::getImagesBySplitFilesets
dictionary<string, ::Ice::LongSeq> IdListMap

Used By

IShare::getContentMap
dictionary<int, ShapeList> IntShapeListMap

Used By

RoiResult::byT
RoiResult::byZ
dictionary<int, string> IntStringMap

Used By

ChecksumValidationException::failingChecksums
dictionary<int, DoubleArray> IntegerDoubleArrayMap

Used By

RawPixelsStore::findMinMax
dictionary<int, IntegerArray> IntegerIntegerArrayMap

Used By

RawPixelsStore::getHistogram
dictionary<long, AnnotationList> LongAnnotationListMap

Used By

IMetadata::loadSpecifiedAnnotationsLinkedTo
dictionary<long, ByteArray> LongByteArrayMap
dictionary<long, IObjectList> LongIObjectListMap

Used By

IMetadata::loadAnnotations
IMetadata::loadLogFiles
IMetadata::loadTagContent
dictionary<long, int> LongIntMap

Used By

RenderingEngine::setOverlays
dictionary<LongPair, int> LongPairIntMap

Used By

cmd::DiskUsage2Response::totalFileCount
cmd::DiskUsageResponse::totalFileCount
dictionary<LongPair, long> LongPairLongMap

Used By

cmd::DiskUsage2Response::totalBytesUsed
cmd::DiskUsageResponse::totalBytesUsed
dictionary<LongPair, StringIntMap> LongPairToStringIntMap

Used By

cmd::DiskUsage2Response::fileCountByReferer
cmd::DiskUsageResponse::fileCountByReferer
dictionary<LongPair, StringLongMap> LongPairToStringLongMap

Used By

cmd::DiskUsage2Response::bytesUsedByReferer
cmd::DiskUsageResponse::bytesUsedByReferer
dictionary<long, model::Pixels> LongPixelsMap
dictionary<long, RoiResult> LongRoiResultMap

Used By

IRoi::getMeasuredRoisMap
dictionary<long, ShapeList> LongShapeListMap
dictionary<long, string> LongStringMap
dictionary<string, model::OriginalFile> OriginalFileMap
dictionary<string, model::Annotation> SearchMetadata

Used By

SearchMetadataList
Search::currentMetadata
dictionary<string, int> StringIntMap

Used By

LongPairToStringIntMap
metadatastore::IObjectContainer::indexes
dictionary<string, LongList> StringLongListMap

Used By

IContainer::getImagesBySplitFilesets
cmd::Chgrp2Response::deletedObjects
cmd::Chgrp2Response::includedObjects
cmd::Chmod2Response::deletedObjects
cmd::Chmod2Response::includedObjects
cmd::Chown2Response::deletedObjects
cmd::Chown2Response::includedObjects
cmd::Delete2Response::deletedObjects
cmd::DiskUsage::objects
cmd::DuplicateResponse::duplicates
cmd::FoundChildren::children
cmd::FoundParents::parents
cmd::GraphQuery::targetObjects
dictionary<string, long> StringLongMap

Used By

LongPairToStringLongMap
ITimeline::countByPeriod
dictionary<string, RString> StringRStringMap
dictionary<string, RType> StringRTypeMap
dictionary<string, ShapeList> StringShapeListMap
dictionary<string, StringArray> StringStringArrayMap

Used By

MetadataStore::updateReferences
dictionary<string, string> StringStringMap

Used By

IConfig::getClientConfigDefaults
IConfig::getClientConfigValues
IConfig::getConfigDefaults
IConfig::getConfigValues
model::Experimenter::getConfigAsMap
model::ExperimenterGroup::getConfigAsMap
model::GenericExcitationSource::getMapAsMap
model::ImagingEnvironment::getMapAsMap
model::MapAnnotation::getMapValueAsMap
model::MetadataImportJob::getVersionInfoAsMap
model::UploadJob::getVersionInfoAsMap
dictionary<string, model::Experimenter> UserMap

Used By

IShare::getActiveConnections
IShare::getPastConnections

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