ome.formats
Class OMEROMetadataStoreClient

java.lang.Object
  extended by ome.formats.OMEROMetadataStoreClient
All Implemented Interfaces:
loci.formats.meta.IMinMaxStore, loci.formats.meta.MetadataStore, IObjectContainerStore

public class OMEROMetadataStoreClient
extends Object
implements loci.formats.meta.MetadataStore, loci.formats.meta.IMinMaxStore, IObjectContainerStore

Client side implementation of the Bio-Formats MetadataStore. It is responsible for handling metadata from Bio-Formats and maintaining communication with an OMERO server.

Author:
Brian Loranger, brain at lifesci.dundee.ac.uk, Chris Allan, callan at lifesci.dundee.ac.uk

Field Summary
static String OMERO_EMISSION_FILTER_SUFFIX
          Emission filter LSID suffix.
static String OMERO_EXCITATION_FILTER_SUFFIX
          Excitation filter LSID suffix.
 
Constructor Summary
OMEROMetadataStoreClient()
           
 
Method Summary
 omero.model.Dataset addDataset(String datasetName, String datasetDescription, omero.model.Project project)
           
 boolean addModelProcessor(ModelProcessor processor)
          Adds a model processor to the end of the processing chain.
 omero.model.Project addProject(String projectName, String projectDescription)
           
 void addReference(ome.util.LSID source, ome.util.LSID target)
          Adds a reference to the reference cache.
 omero.model.Screen addScreen(String screenName, String screenDescription)
           
static String byteArrayToHexString(byte[] in)
           
 void closeServices()
          Closes all stateful services.
 int countCachedContainers(Class<? extends omero.model.IObject> klass, int... indexes)
          Counts the number of containers the MetadataStore has of a given class and at a given index of the hierarchy if specified.
 int countCachedReferences(Class<? extends omero.model.IObject> source, Class<? extends omero.model.IObject> target)
          Counts the number of references the MetadataStore has between objects of two classes.
 void createRoot()
           
 void finalizePixelStore()
          Closes the active raw pixels store.
 Map<Class<? extends omero.model.IObject>,Map<String,omero.metadatastore.IObjectContainer>> getAuthoritativeContainerCache()
          Returns the current authoritative LSID container cache.
 omero.model.Channel getChannel(int imageIndex, int channelIndex)
           
 String getConfigValue(String key)
          Retrieves a configuration value from the IConfig service.
 Map<ome.util.LSID,omero.metadatastore.IObjectContainer> getContainerCache()
          Returns the current container cache.
 List<omero.model.Dataset> getDatasets(omero.model.Project p)
           
 List<omero.model.Dataset> getDatasetsWithoutProjects()
           
 int getDefaultGroupLevel()
          Retrieve teh default groups permission 'level'.
 String getDefaultGroupName()
          Retrieve the default group's name
 omero.model.Detector getDetector(int instrumentIndex, int detectorIndex)
           
 EnumerationProvider getEnumerationProvider()
          Retrieves the active enumeration provider.
 long getExperimenterID()
           
 omero.model.Filament getFilament(int instrumentIndex, int lightSourceIndex)
           
 List<String> getFilteredCompanionFiles()
          Returns the current set of filtered companion files that the Bio-Formats image reader contains.
 List<String> getFilteredSeriesCompanionFiles()
          Returns the current set of filtered companion files that the Bio-Formats image reader contains for the current series.
 omero.model.FilterSet getFilterSet(int instrumentIndex, int filterSetIndex)
           
 omero.model.ObjectiveSettings getImageObjectiveSettings(int imageIndex)
           
 omero.model.ImagingEnvironment getImagingEnvironment(int imageIndex)
           
 InstanceProvider getInstanceProvider()
          Retrieves the active enumeration provider.
 omero.metadatastore.IObjectContainer getIObjectContainer(Class<? extends omero.model.IObject> klass, LinkedHashMap<Index,Integer> indexes)
          Retrieves an IObject container for a given class and location within the OME-XML data model.
 List<omero.metadatastore.IObjectContainer> getIObjectContainers(Class<? extends omero.model.IObject> klass)
          Retrieves all IObject containers of a given class.
 omero.api.IQueryPrx getIQuery()
           
 ClientKeepAlive getKeepAlive()
          Returns clientKeepAlive created in store
 omero.model.Laser getLaser(int instrumentIndex, int lightSourceIndex)
           
 omero.model.LightEmittingDiode getLightEmittingDiode(int instrumentIndex, int lightSourceIndex)
           
 omero.model.Line getLine(int ROIIndex, int shapeIndex)
           
 omero.model.ListAnnotation getListAnnotation(int listAnnotationIndex)
           
 omero.model.LongAnnotation getLongAnnotation(int longAnnotationIndex)
           
 omero.model.Mask getMask(int ROIIndex, int shapeIndex)
           
 omero.model.MicrobeamManipulation getMicrobeamManipulation(int experimentIndex, int microbeamManipulationIndex)
           
 omero.model.LightSettings getMicrobeamManipulationLightSourceSettings(int experimentIndex, int microbeamManipulationIndex, int lightSourceSettingsIndex)
           
 List<ModelProcessor> getModelProcessors()
          Retrieves the current list of model processors the metadata store is using.
 omero.model.Objective getObjective(int instrumentIndex, int objectiveIndex)
           
 omero.model.OTF getOTF(int instrumentIndex, int OTFIndex)
           
 omero.model.Project getProject(long projectId)
           
 List<omero.model.Project> getProjects()
           
 loci.formats.IFormatReader getReader()
          Returns the current Bio-Formats reader that has been used to populate the container store.
 Map<ome.util.LSID,List<ome.util.LSID>> getReferenceCache()
          Returns the current reference cache.
 Map<String,String[]> getReferenceStringCache()
          Returns the current string based reference cache.
 long getRepositorySpace()
           
 Object getRoot()
           
 List<omero.model.Screen> getScreens()
           
 omero.api.ServiceFactoryPrx getServiceFactory()
          Returns the currently active service factory.
 omero.model.IObject getSourceObject(ome.util.LSID LSID)
          Retrieves an OMERO Blitz source object for a given LSID.
<T extends omero.model.IObject>
List<T>
getSourceObjects(Class<T> klass)
          Retrieves all OMERO Blitz source objects of a given class.
<T extends omero.model.IObject>
T
getTarget(Class<T> klass, long id)
          Helper method to retrieve an object from iQuery
 int[] getTileSize(Long pixId)
          Retrieves the suggested tile size for a pixels set.
 List<omero.model.Annotation> getUserSpecifiedAnnotations()
          Returns the user specified annotations.
 String getUserSpecifiedImageDescription()
          Returns the user specified image description.
 String getUserSpecifiedImageName()
          Returns the user specified image name.
 Double[] getUserSpecifiedPhysicalPixelSizes()
          Returns the user specified physical pixel sizes.
 String getUserSpecifiedPlateDescription()
          Returns the user specified plate description.
 String getUserSpecifiedPlateName()
          Returns the user specified plate name.
 omero.model.IObject getUserSpecifiedTarget()
          Returns the user specified linkage target (usually a Dataset for Images and a Screen for Plates).
 boolean hasReference(ome.util.LSID source, ome.util.LSID target)
          Checks to see if there is currently an active reference for two LSIDs.
 void initialize(client c)
          Initializes the MetadataStore with an already logged in, ready to go service factory.
 void initialize(omero.api.ServiceFactoryPrx serviceFactory)
          Initializes the MetadataStore with an already logged in, ready to go service factory.
 void initialize(String server, int port, String sessionKey)
          Initializes the MetadataStore by joining an existing session.
 void initialize(String server, int port, String sessionKey, boolean isSecure)
          Initializes the MetadataStore by joining an existing session.
 void initialize(String username, String password, String server, int port)
          Initializes the MetadataStore taking string parameters to feed to the OMERO Blitz client object.
 void initialize(String username, String password, String server, int port, boolean isSecure)
          Initializes the MetadataStore taking string parameters to feed to the OMERO Blitz client object.
 void initialize(String username, String password, String server, int port, long group, boolean isSecure)
          Initializes the MetadataStore taking string parameters to feed to the OMERO Blitz client object.
 boolean isEncryptedConnection()
           
 List<omero.grid.InteractiveProcessorPrx> launchProcessing()
           
 void logout()
          Destroys the sessionFactory and closes the client.
 void logVersionInfo(String clientVersion)
           
 Map<Long,String> mapUserGroups()
          Maps the user's groups for use by ScreenLogin.registerGroup() Also strips system groups from this map
 void ping()
          Pings all registered OMERO Blitz proxies.
 void populateMinMax()
          Sends all the minimums and maximums for all images processed so far to the server.
 void postProcess()
          Post processes the internal structure of the client side MetadataStore.
 void prepare(Map<Integer,omero.model.Image> existingMetadata)
          Prepares the metadata store using existing metadata that has been pre-registered by OMERO.fs.
 void preparePixelsStore(List<Long> pixelsIds)
          Prepares the server side RawPixelsStore.
 void removeIObjectContainer(ome.util.LSID lsid)
          Removes an IObject container from within the OME-XML data model store.
 void removeModelProcessor(ModelProcessor processor)
          Removes a model processor from use.
 void resetDefaultsAndGenerateThumbnails(List<Long> plateIds, List<Long> pixelsIds)
          Resets the defaults and generates thumbnails for a given set of Pixels IDs.
 List<omero.model.Pixels> saveToDB()
          Updates the server side MetadataStore with a list of our objects and references and saves them into the database.
 List<File> setArchive(boolean archive, boolean useMetadataFile)
          Populates archive flags on all images currently processed links relevant original metadata files as requested and performs graph logic to have the scaffolding in place for later original file upload.
 List<File> setArchiveScreeningDomain(boolean archive)
          Populates archive flags on all images currently processed links relevant original metadata files as requested and performs graph logic to have the scafolding in place for later original file upload if we are of the HCS domain.
 void setArcID(String id, int instrumentIndex, int lightSourceIndex)
           
 void setArcLotNumber(String lotNumber, int instrumentIndex, int lightSourceIndex)
           
 void setArcManufacturer(String manufacturer, int instrumentIndex, int lightSourceIndex)
           
 void setArcModel(String model, int instrumentIndex, int lightSourceIndex)
           
 void setArcPower(Double power, int instrumentIndex, int lightSourceIndex)
           
 void setArcSerialNumber(String serialNumber, int instrumentIndex, int lightSourceIndex)
           
 void setArcType(ome.xml.model.enums.ArcType type, int instrumentIndex, int lightSourceIndex)
           
 void setBinaryOnlyMetadataFile(String metadataFile)
           
 void setBinaryOnlyUUID(String uuid)
           
 void setBooleanAnnotationAnnotationRef(String annotation, int booleanAnnotationIndex, int annotationRefIndex)
           
 void setBooleanAnnotationDescription(String description, int booleanAnnotationIndex)
           
 void setBooleanAnnotationID(String id, int booleanAnnotationIndex)
           
 void setBooleanAnnotationNamespace(String namespace, int booleanAnnotationIndex)
           
 void setBooleanAnnotationValue(Boolean value, int booleanAnnotationIndex)
           
 void setChannelAcquisitionMode(ome.xml.model.enums.AcquisitionMode acquisitionMode, int imageIndex, int channelIndex)
           
 void setChannelAnnotationRef(String annotation, int imageIndex, int channelIndex, int annotationRefIndex)
           
 void setChannelColor(Integer color, int imageIndex, int channelIndex)
           
 void setChannelContrastMethod(ome.xml.model.enums.ContrastMethod contrastMethod, int imageIndex, int channelIndex)
           
 void setChannelEmissionWavelength(ome.xml.model.primitives.PositiveInteger emissionWavelength, int imageIndex, int channelIndex)
           
 void setChannelExcitationWavelength(ome.xml.model.primitives.PositiveInteger excitationWavelength, int imageIndex, int channelIndex)
          (non-Javadoc)
 void setChannelFilterSetRef(String filterSet, int imageIndex, int channelIndex)
           
 void setChannelFluor(String fluor, int imageIndex, int channelIndex)
           
 void setChannelGlobalMinMax(int channel, double minimum, double maximum, int series)
           
 void setChannelID(String id, int imageIndex, int channelIndex)
           
 void setChannelIlluminationType(ome.xml.model.enums.IlluminationType illuminationType, int imageIndex, int channelIndex)
           
 void setChannelLightSourceSettingsAttenuation(ome.xml.model.primitives.PercentFraction attenuation, int imageIndex, int channelIndex)
           
 void setChannelLightSourceSettingsID(String id, int imageIndex, int channelIndex)
           
 void setChannelLightSourceSettingsWavelength(ome.xml.model.primitives.PositiveInteger wavelength, int imageIndex, int channelIndex)
           
 void setChannelName(String name, int imageIndex, int channelIndex)
           
 void setChannelNDFilter(Double ndfilter, int imageIndex, int channelIndex)
           
 void setChannelOTFRef(String otf, int imageIndex, int channelIndex)
           
 void setChannelPinholeSize(Double pinholeSize, int imageIndex, int channelIndex)
           
 void setChannelPockelCellSetting(Integer pockelCellSetting, int imageIndex, int channelIndex)
           
 void setChannelSamplesPerPixel(ome.xml.model.primitives.PositiveInteger samplesPerPixel, int imageIndex, int channelIndex)
           
 void setCommentAnnotationAnnotationRef(String annotation, int commentAnnotationIndex, int annotationRefIndex)
           
 void setCommentAnnotationDescription(String description, int commentAnnotationIndex)
           
 void setCommentAnnotationID(String id, int commentAnnotationIndex)
           
 void setCommentAnnotationNamespace(String namespace, int commentAnnotationIndex)
           
 void setCommentAnnotationValue(String value, int commentAnnotationIndex)
           
 void setCurrentGroup(long groupID)
          Changes the default group of the currently logged in user.
 void setDatasetAnnotationRef(String annotation, int datasetIndex, int annotationRefIndex)
           
 void setDatasetDescription(String description, int datasetIndex)
           
 void setDatasetExperimenterRef(String experimenter, int datasetIndex)
           
 void setDatasetGroupRef(String group, int datasetIndex)
           
 void setDatasetID(String id, int datasetIndex)
           
 void setDatasetName(String name, int datasetIndex)
           
 void setDatasetProjectRef(String project, int datasetIndex, int projectRefIndex)
           
 void setDetectorAmplificationGain(Double amplificationGain, int instrumentIndex, int detectorIndex)
           
 void setDetectorGain(Double gain, int instrumentIndex, int detectorIndex)
           
 void setDetectorID(String id, int instrumentIndex, int detectorIndex)
           
 void setDetectorLotNumber(String lotNumber, int instrumentIndex, int detectorIndex)
           
 void setDetectorManufacturer(String manufacturer, int instrumentIndex, int detectorIndex)
           
 void setDetectorModel(String model, int instrumentIndex, int detectorIndex)
           
 void setDetectorOffset(Double offset, int instrumentIndex, int detectorIndex)
           
 void setDetectorSerialNumber(String serialNumber, int instrumentIndex, int detectorIndex)
           
 void setDetectorSettingsBinning(ome.xml.model.enums.Binning binning, int imageIndex, int channelIndex)
           
 void setDetectorSettingsGain(Double gain, int imageIndex, int channelIndex)
           
 void setDetectorSettingsID(String id, int imageIndex, int channelIndex)
           
 void setDetectorSettingsOffset(Double offset, int imageIndex, int channelIndex)
           
 void setDetectorSettingsReadOutRate(Double readOutRate, int imageIndex, int channelIndex)
           
 void setDetectorSettingsVoltage(Double voltage, int imageIndex, int channelIndex)
           
 void setDetectorType(ome.xml.model.enums.DetectorType type, int instrumentIndex, int detectorIndex)
           
 void setDetectorVoltage(Double voltage, int instrumentIndex, int detectorIndex)
           
 void setDetectorZoom(Double zoom, int instrumentIndex, int detectorIndex)
           
 void setDichroicID(String id, int instrumentIndex, int dichroicIndex)
           
 void setDichroicLotNumber(String lotNumber, int instrumentIndex, int dichroicIndex)
           
 void setDichroicManufacturer(String manufacturer, int instrumentIndex, int dichroicIndex)
           
 void setDichroicModel(String model, int instrumentIndex, int dichroicIndex)
           
 void setDichroicSerialNumber(String serialNumber, int instrumentIndex, int dichroicIndex)
           
 void setDoubleAnnotationAnnotationRef(String annotation, int doubleAnnotationIndex, int annotationRefIndex)
           
 void setDoubleAnnotationDescription(String description, int doubleAnnotationIndex)
           
 void setDoubleAnnotationID(String id, int doubleAnnotationIndex)
           
 void setDoubleAnnotationNamespace(String namespace, int doubleAnnotationIndex)
           
 void setDoubleAnnotationValue(Double value, int doubleAnnotationIndex)
           
 void setEllipseDescription(String description, int ROIIndex, int shapeIndex)
           
 void setEllipseFill(Integer fill, int ROIIndex, int shapeIndex)
           
 void setEllipseFontSize(ome.xml.model.primitives.NonNegativeInteger fontSize, int ROIIndex, int shapeIndex)
           
 void setEllipseID(String id, int ROIIndex, int shapeIndex)
           
 void setEllipseLabel(String label, int ROIIndex, int shapeIndex)
           
 void setEllipseName(String name, int ROIIndex, int shapeIndex)
           
 void setEllipseRadiusX(Double radiusX, int ROIIndex, int shapeIndex)
           
 void setEllipseRadiusY(Double radiusY, int ROIIndex, int shapeIndex)
           
 void setEllipseStroke(Integer stroke, int ROIIndex, int shapeIndex)
           
 void setEllipseStrokeDashArray(String strokeDashArray, int ROIIndex, int shapeIndex)
           
 void setEllipseStrokeWidth(Double strokeWidth, int ROIIndex, int shapeIndex)
           
 void setEllipseTheC(ome.xml.model.primitives.NonNegativeInteger theC, int ROIIndex, int shapeIndex)
           
 void setEllipseTheT(ome.xml.model.primitives.NonNegativeInteger theT, int ROIIndex, int shapeIndex)
           
 void setEllipseTheZ(ome.xml.model.primitives.NonNegativeInteger theZ, int ROIIndex, int shapeIndex)
           
 void setEllipseTransform(String transform, int ROIIndex, int shapeIndex)
           
 void setEllipseX(Double x, int ROIIndex, int shapeIndex)
           
 void setEllipseY(Double y, int ROIIndex, int shapeIndex)
           
 void setEncryptedConnection(boolean encryptedConnection)
           
 void setEnumerationProvider(EnumerationProvider enumProvider)
          Sets the active enumeration provider.
 void setExperimentDescription(String description, int experimentIndex)
           
 void setExperimenterAnnotationRef(String annotation, int experimenterIndex, int annotationRefIndex)
           
 void setExperimenterDisplayName(String displayName, int experimenterIndex)
           
 void setExperimenterEmail(String email, int experimenterIndex)
           
 void setExperimenterFirstName(String firstName, int experimenterIndex)
           
 void setExperimenterGroupRef(String group, int experimenterIndex, int groupRefIndex)
           
 void setExperimenterID(String id, int experimenterIndex)
           
 void setExperimenterInstitution(String institution, int experimenterIndex)
           
 void setExperimenterLastName(String lastName, int experimenterIndex)
           
 void setExperimenterMiddleName(String middleName, int experimenterIndex)
           
 void setExperimenterUserName(String userName, int experimenterIndex)
           
 void setExperimentExperimenterRef(String experimenter, int experimentIndex)
           
 void setExperimentID(String id, int experimentIndex)
           
 void setExperimentType(ome.xml.model.enums.ExperimentType type, int experimentIndex)
           
 void setFilamentID(String id, int instrumentIndex, int lightSourceIndex)
           
 void setFilamentLotNumber(String lotNumber, int instrumentIndex, int lightSourceIndex)
           
 void setFilamentManufacturer(String manufacturer, int instrumentIndex, int lightSourceIndex)
           
 void setFilamentModel(String model, int instrumentIndex, int lightSourceIndex)
           
 void setFilamentPower(Double power, int instrumentIndex, int lightSourceIndex)
           
 void setFilamentSerialNumber(String serialNumber, int instrumentIndex, int lightSourceIndex)
           
 void setFilamentType(ome.xml.model.enums.FilamentType type, int instrumentIndex, int lightSourceIndex)
           
 void setFileAnnotationAnnotationRef(String annotation, int fileAnnotationIndex, int annotationRefIndex)
           
 void setFileAnnotationBinaryFileFileName(String fileName, int fileAnnotationIndex)
           
 void setFileAnnotationBinaryFileMIMEType(String mimetype, int fileAnnotationIndex)
           
 void setFileAnnotationBinaryFileSize(ome.xml.model.primitives.NonNegativeLong size, int fileAnnotationIndex)
           
 void setFileAnnotationDescription(String description, int fileAnnotationIndex)
           
 void setFileAnnotationID(String id, int fileAnnotationIndex)
           
 void setFileAnnotationNamespace(String namespace, int fileAnnotationIndex)
           
 void setFilterFilterWheel(String filterWheel, int instrumentIndex, int filterIndex)
           
 void setFilterID(String id, int instrumentIndex, int filterIndex)
           
 void setFilterLotNumber(String lotNumber, int instrumentIndex, int filterIndex)
           
 void setFilterManufacturer(String manufacturer, int instrumentIndex, int filterIndex)
           
 void setFilterModel(String model, int instrumentIndex, int filterIndex)
           
 void setFilterSerialNumber(String serialNumber, int instrumentIndex, int filterIndex)
           
 void setFilterSetDichroicRef(String dichroic, int instrumentIndex, int filterSetIndex)
           
 void setFilterSetEmissionFilterRef(String emissionFilter, int instrumentIndex, int filterSetIndex, int emissionFilterRefIndex)
           
 void setFilterSetExcitationFilterRef(String excitationFilter, int instrumentIndex, int filterSetIndex, int excitationFilterRefIndex)
           
 void setFilterSetID(String id, int instrumentIndex, int filterSetIndex)
           
 void setFilterSetLotNumber(String lotNumber, int instrumentIndex, int filterSetIndex)
           
 void setFilterSetManufacturer(String manufacturer, int instrumentIndex, int filterSetIndex)
           
 void setFilterSetModel(String model, int instrumentIndex, int filterSetIndex)
           
 void setFilterSetSerialNumber(String serialNumber, int instrumentIndex, int filterSetIndex)
           
 void setFilterType(ome.xml.model.enums.FilterType type, int instrumentIndex, int filterIndex)
           
 void setGroupContact(String contact, int groupIndex)
           
 void setGroupDescription(String description, int groupIndex)
           
 void setGroupID(String id, int groupIndex)
           
 void setGroupLeader(String leader, int groupIndex)
           
 void setGroupName(String name, int groupIndex)
           
 void setImageAcquiredDate(String acquiredDate, int imageIndex)
           
 void setImageAnnotationRef(String annotation, int imageIndex, int annotationRefIndex)
           
 void setImageDatasetRef(String dataset, int imageIndex, int datasetRefIndex)
           
 void setImageDescription(String description, int imageIndex)
           
 void setImageExperimenterRef(String experimenter, int imageIndex)
           
 void setImageExperimentRef(String experiment, int imageIndex)
           
 void setImageGroupRef(String group, int imageIndex)
           
 void setImageID(String id, int imageIndex)
           
 void setImageInstrumentRef(String instrument, int imageIndex)
           
 void setImageMicrobeamManipulationRef(String microbeamManipulation, int imageIndex, int microbeamManipulationRefIndex)
           
 void setImageName(String name, int imageIndex)
           
 void setImageObjectiveSettingsCorrectionCollar(Double correctionCollar, int imageIndex)
           
 void setImageObjectiveSettingsID(String id, int imageIndex)
           
 void setImageObjectiveSettingsMedium(ome.xml.model.enums.Medium medium, int imageIndex)
           
 void setImageObjectiveSettingsRefractiveIndex(Double refractiveIndex, int imageIndex)
           
 void setImageROIRef(String roi, int imageIndex, int ROIRefIndex)
           
 void setImagingEnvironmentAirPressure(Double airPressure, int imageIndex)
           
 void setImagingEnvironmentCO2Percent(ome.xml.model.primitives.PercentFraction co2percent, int imageIndex)
           
 void setImagingEnvironmentHumidity(ome.xml.model.primitives.PercentFraction humidity, int imageIndex)
           
 void setImagingEnvironmentTemperature(Double temperature, int imageIndex)
           
 void setInstanceProvider(InstanceProvider instanceProvider)
          Sets the active instance provider.
 void setInstrumentID(String id, int instrumentIndex)
           
 void setLaserFrequencyMultiplication(ome.xml.model.primitives.PositiveInteger frequencyMultiplication, int instrumentIndex, int lightSourceIndex)
           
 void setLaserID(String id, int instrumentIndex, int lightSourceIndex)
           
 void setLaserLaserMedium(ome.xml.model.enums.LaserMedium laserMedium, int instrumentIndex, int lightSourceIndex)
           
 void setLaserLotNumber(String lotNumber, int instrumentIndex, int lightSourceIndex)
           
 void setLaserManufacturer(String manufacturer, int instrumentIndex, int lightSourceIndex)
           
 void setLaserModel(String model, int instrumentIndex, int lightSourceIndex)
           
 void setLaserPockelCell(Boolean pockelCell, int instrumentIndex, int lightSourceIndex)
           
 void setLaserPower(Double power, int instrumentIndex, int lightSourceIndex)
           
 void setLaserPulse(ome.xml.model.enums.Pulse pulse, int instrumentIndex, int lightSourceIndex)
           
 void setLaserPump(String pump, int instrumentIndex, int lightSourceIndex)
           
 void setLaserRepetitionRate(Double repetitionRate, int instrumentIndex, int lightSourceIndex)
           
 void setLaserSerialNumber(String serialNumber, int instrumentIndex, int lightSourceIndex)
           
 void setLaserTuneable(Boolean tuneable, int instrumentIndex, int lightSourceIndex)
           
 void setLaserType(ome.xml.model.enums.LaserType type, int instrumentIndex, int lightSourceIndex)
           
 void setLaserWavelength(ome.xml.model.primitives.PositiveInteger wavelength, int instrumentIndex, int lightSourceIndex)
           
 void setLightEmittingDiodeID(String id, int instrumentIndex, int lightSourceIndex)
           
 void setLightEmittingDiodeLotNumber(String lotNumber, int instrumentIndex, int lightSourceIndex)
           
 void setLightEmittingDiodeManufacturer(String manufacturer, int instrumentIndex, int lightSourceIndex)
           
 void setLightEmittingDiodeModel(String model, int instrumentIndex, int lightSourceIndex)
           
 void setLightEmittingDiodePower(Double power, int instrumentIndex, int lightSourceIndex)
           
 void setLightEmittingDiodeSerialNumber(String serialNumber, int instrumentIndex, int lightSourceIndex)
           
 void setLightPathDichroicRef(String dichroic, int imageIndex, int channelIndex)
           
 void setLightPathEmissionFilterRef(String emissionFilter, int imageIndex, int channelIndex, int emissionFilterRefIndex)
           
 void setLightPathExcitationFilterRef(String excitationFilter, int imageIndex, int channelIndex, int excitationFilterRefIndex)
           
 void setLineDescription(String description, int ROIIndex, int shapeIndex)
           
 void setLineFill(Integer fill, int ROIIndex, int shapeIndex)
           
 void setLineFontSize(ome.xml.model.primitives.NonNegativeInteger fontSize, int ROIIndex, int shapeIndex)
           
 void setLineID(String id, int ROIIndex, int shapeIndex)
           
 void setLineLabel(String label, int ROIIndex, int shapeIndex)
           
 void setLineName(String name, int ROIIndex, int shapeIndex)
           
 void setLineStroke(Integer stroke, int ROIIndex, int shapeIndex)
           
 void setLineStrokeDashArray(String strokeDashArray, int ROIIndex, int shapeIndex)
           
 void setLineStrokeWidth(Double strokeWidth, int ROIIndex, int shapeIndex)
           
 void setLineTheC(ome.xml.model.primitives.NonNegativeInteger theC, int ROIIndex, int shapeIndex)
           
 void setLineTheT(ome.xml.model.primitives.NonNegativeInteger theT, int ROIIndex, int shapeIndex)
           
 void setLineTheZ(ome.xml.model.primitives.NonNegativeInteger theZ, int ROIIndex, int shapeIndex)
           
 void setLineTransform(String transform, int ROIIndex, int shapeIndex)
           
 void setLineX1(Double x1, int ROIIndex, int shapeIndex)
           
 void setLineX2(Double x2, int ROIIndex, int shapeIndex)
           
 void setLineY1(Double y1, int ROIIndex, int shapeIndex)
           
 void setLineY2(Double y2, int ROIIndex, int shapeIndex)
           
 void setListAnnotationAnnotationRef(String annotation, int listAnnotationIndex, int annotationRefIndex)
           
 void setListAnnotationDescription(String description, int listAnnotationIndex)
           
 void setListAnnotationID(String id, int listAnnotationIndex)
           
 void setListAnnotationNamespace(String namespace, int listAnnotationIndex)
           
 void setLongAnnotationAnnotationRef(String annotation, int longAnnotationIndex, int annotationRefIndex)
           
 void setLongAnnotationDescription(String description, int longAnnotationIndex)
           
 void setLongAnnotationID(String id, int longAnnotationIndex)
           
 void setLongAnnotationNamespace(String namespace, int longAnnotationIndex)
           
 void setLongAnnotationValue(Long value, int longAnnotationIndex)
           
 void setMaskBinData(byte[] binData, int roiIndex, int shapeIndex)
           
 void setMaskDescription(String description, int ROIIndex, int shapeIndex)
           
 void setMaskFill(Integer fill, int ROIIndex, int shapeIndex)
           
 void setMaskFontSize(ome.xml.model.primitives.NonNegativeInteger fontSize, int ROIIndex, int shapeIndex)
           
 void setMaskHeight(Double height, int ROIIndex, int shapeIndex)
           
 void setMaskID(String id, int ROIIndex, int shapeIndex)
           
 void setMaskLabel(String label, int ROIIndex, int shapeIndex)
           
 void setMaskName(String name, int ROIIndex, int shapeIndex)
           
 void setMaskStroke(Integer stroke, int ROIIndex, int shapeIndex)
           
 void setMaskStrokeDashArray(String strokeDashArray, int ROIIndex, int shapeIndex)
           
 void setMaskStrokeWidth(Double strokeWidth, int ROIIndex, int shapeIndex)
           
 void setMaskTheC(ome.xml.model.primitives.NonNegativeInteger theC, int ROIIndex, int shapeIndex)
           
 void setMaskTheT(ome.xml.model.primitives.NonNegativeInteger theT, int ROIIndex, int shapeIndex)
           
 void setMaskTheZ(ome.xml.model.primitives.NonNegativeInteger theZ, int ROIIndex, int shapeIndex)
           
 void setMaskTransform(String transform, int ROIIndex, int shapeIndex)
           
 void setMaskWidth(Double width, int ROIIndex, int shapeIndex)
           
 void setMaskX(Double x, int ROIIndex, int shapeIndex)
           
 void setMaskY(Double y, int ROIIndex, int shapeIndex)
           
 void setMicrobeamManipulationDescription(String description, int experimentIndex, int microbeamManipulationIndex)
           
 void setMicrobeamManipulationExperimenterRef(String experimenter, int experimentIndex, int microbeamManipulationIndex)
           
 void setMicrobeamManipulationID(String id, int experimentIndex, int microbeamManipulationIndex)
           
 void setMicrobeamManipulationLightSourceSettingsAttenuation(ome.xml.model.primitives.PercentFraction attenuation, int experimentIndex, int microbeamManipulationIndex, int lightSourceSettingsIndex)
           
 void setMicrobeamManipulationLightSourceSettingsID(String id, int experimentIndex, int microbeamManipulationIndex, int lightSourceSettingsIndex)
           
 void setMicrobeamManipulationLightSourceSettingsWavelength(ome.xml.model.primitives.PositiveInteger wavelength, int experimentIndex, int microbeamManipulationIndex, int lightSourceSettingsIndex)
           
 void setMicrobeamManipulationROIRef(String roi, int experimentIndex, int microbeamManipulationIndex, int ROIRefIndex)
           
 void setMicrobeamManipulationType(ome.xml.model.enums.MicrobeamManipulationType type, int experimentIndex, int microbeamManipulationIndex)
           
 void setMicroscopeLotNumber(String lotNumber, int instrumentIndex)
           
 void setMicroscopeManufacturer(String manufacturer, int instrumentIndex)
           
 void setMicroscopeModel(String model, int instrumentIndex)
           
 void setMicroscopeSerialNumber(String serialNumber, int instrumentIndex)
           
 void setMicroscopeType(ome.xml.model.enums.MicroscopeType type, int instrumentIndex)
           
 void setModelProcessors(List<ModelProcessor> modelProcessors)
          Sets the current set of model processors.
 void setObjectiveCalibratedMagnification(Double calibratedMagnification, int instrumentIndex, int objectiveIndex)
           
 void setObjectiveCorrection(ome.xml.model.enums.Correction correction, int instrumentIndex, int objectiveIndex)
           
 void setObjectiveID(String id, int instrumentIndex, int objectiveIndex)
           
 void setObjectiveImmersion(ome.xml.model.enums.Immersion immersion, int instrumentIndex, int objectiveIndex)
           
 void setObjectiveIris(Boolean iris, int instrumentIndex, int objectiveIndex)
           
 void setObjectiveLensNA(Double lensNA, int instrumentIndex, int objectiveIndex)
           
 void setObjectiveLotNumber(String lotNumber, int instrumentIndex, int objectiveIndex)
           
 void setObjectiveManufacturer(String manufacturer, int instrumentIndex, int objectiveIndex)
           
 void setObjectiveModel(String model, int instrumentIndex, int objectiveIndex)
           
 void setObjectiveNominalMagnification(ome.xml.model.primitives.PositiveInteger nominalMagnification, int instrumentIndex, int objectiveIndex)
           
 void setObjectiveSerialNumber(String serialNumber, int instrumentIndex, int objectiveIndex)
           
 void setObjectiveWorkingDistance(Double workingDistance, int instrumentIndex, int objectiveIndex)
           
 void setOTFBinaryFileFileName(String fileName, int instrumentIndex, int OTFIndex)
           
 void setOTFBinaryFileMIMEType(String mimetype, int instrumentIndex, int OTFIndex)
           
 void setOTFBinaryFileSize(ome.xml.model.primitives.NonNegativeLong size, int instrumentIndex, int OTFIndex)
           
 void setOTFFilterSetRef(String filterSet, int instrumentIndex, int OTFIndex)
           
 void setOTFID(String id, int instrumentIndex, int OTFIndex)
           
 void setOTFObjectiveSettingsCorrectionCollar(Double correctionCollar, int instrumentIndex, int OTFIndex)
           
 void setOTFObjectiveSettingsID(String id, int instrumentIndex, int OTFIndex)
           
 void setOTFObjectiveSettingsMedium(ome.xml.model.enums.Medium medium, int instrumentIndex, int OTFIndex)
           
 void setOTFObjectiveSettingsRefractiveIndex(Double refractiveIndex, int instrumentIndex, int OTFIndex)
           
 void setOTFOpticalAxisAveraged(Boolean opticalAxisAveraged, int instrumentIndex, int OTFIndex)
           
 void setOTFSizeX(ome.xml.model.primitives.PositiveInteger sizeX, int instrumentIndex, int OTFIndex)
           
 void setOTFSizeY(ome.xml.model.primitives.PositiveInteger sizeY, int instrumentIndex, int OTFIndex)
           
 void setOTFType(ome.xml.model.enums.PixelType type, int instrumentIndex, int OTFIndex)
           
 void setPathDefinition(String definition, int ROIIndex, int shapeIndex)
           
 void setPathDescription(String description, int ROIIndex, int shapeIndex)
           
 void setPathFill(Integer fill, int ROIIndex, int shapeIndex)
           
 void setPathFontSize(ome.xml.model.primitives.NonNegativeInteger fontSize, int ROIIndex, int shapeIndex)
           
 void setPathID(String id, int ROIIndex, int shapeIndex)
           
 void setPathLabel(String label, int ROIIndex, int shapeIndex)
           
 void setPathName(String name, int ROIIndex, int shapeIndex)
           
 void setPathStroke(Integer stroke, int ROIIndex, int shapeIndex)
           
 void setPathStrokeDashArray(String strokeDashArray, int ROIIndex, int shapeIndex)
           
 void setPathStrokeWidth(Double strokeWidth, int ROIIndex, int shapeIndex)
           
 void setPathTheC(ome.xml.model.primitives.NonNegativeInteger theC, int ROIIndex, int shapeIndex)
           
 void setPathTheT(ome.xml.model.primitives.NonNegativeInteger theT, int ROIIndex, int shapeIndex)
           
 void setPathTheZ(ome.xml.model.primitives.NonNegativeInteger theZ, int ROIIndex, int shapeIndex)
           
 void setPathTransform(String transform, int ROIIndex, int shapeIndex)
           
 void setPixelsAnnotationRef(String annotation, int imageIndex, int annotationRefIndex)
           
 void setPixelsBinDataBigEndian(Boolean bigEndian, int imageIndex, int binDataIndex)
           
 void setPixelsDimensionOrder(ome.xml.model.enums.DimensionOrder dimensionOrder, int imageIndex)
           
 void setPixelsID(String id, int imageIndex)
           
 void setPixelsParams(long pixelsId, int series)
          Sets extended the properties on a pixel set.
 void setPixelsPhysicalSizeX(ome.xml.model.primitives.PositiveFloat physicalSizeX, int imageIndex)
           
 void setPixelsPhysicalSizeY(ome.xml.model.primitives.PositiveFloat physicalSizeY, int imageIndex)
           
 void setPixelsPhysicalSizeZ(ome.xml.model.primitives.PositiveFloat physicalSizeZ, int imageIndex)
           
 void setPixelsSizeC(ome.xml.model.primitives.PositiveInteger sizeC, int imageIndex)
           
 void setPixelsSizeT(ome.xml.model.primitives.PositiveInteger sizeT, int imageIndex)
           
 void setPixelsSizeX(ome.xml.model.primitives.PositiveInteger sizeX, int imageIndex)
           
 void setPixelsSizeY(ome.xml.model.primitives.PositiveInteger sizeY, int imageIndex)
           
 void setPixelsSizeZ(ome.xml.model.primitives.PositiveInteger sizeZ, int imageIndex)
           
 void setPixelsTimeIncrement(Double timeIncrement, int imageIndex)
           
 void setPixelsType(ome.xml.model.enums.PixelType type, int imageIndex)
           
 void setPlane(Long pixId, byte[] arrayBuf, int z, int c, int t)
          Writes a plane to the server.
 void setPlaneAnnotationRef(String annotation, int imageIndex, int planeIndex, int annotationRefIndex)
           
 void setPlaneDeltaT(Double deltaT, int imageIndex, int planeIndex)
           
 void setPlaneExposureTime(Double exposureTime, int imageIndex, int planeIndex)
           
 void setPlaneHashSHA1(String hashSHA1, int imageIndex, int planeIndex)
           
 void setPlanePositionX(Double positionX, int imageIndex, int planeIndex)
           
 void setPlanePositionY(Double positionY, int imageIndex, int planeIndex)
           
 void setPlanePositionZ(Double positionZ, int imageIndex, int planeIndex)
           
 void setPlaneTheC(ome.xml.model.primitives.NonNegativeInteger theC, int imageIndex, int planeIndex)
           
 void setPlaneTheT(ome.xml.model.primitives.NonNegativeInteger theT, int imageIndex, int planeIndex)
           
 void setPlaneTheZ(ome.xml.model.primitives.NonNegativeInteger theZ, int imageIndex, int planeIndex)
           
 void setPlateAcquisitionAnnotationRef(String annotation, int plateIndex, int plateAcquisitionIndex, int annotationRefIndex)
           
 void setPlateAcquisitionDescription(String description, int plateIndex, int plateAcquisitionIndex)
           
 void setPlateAcquisitionEndTime(String endTime, int plateIndex, int plateAcquisitionIndex)
           
 void setPlateAcquisitionID(String id, int plateIndex, int plateAcquisitionIndex)
           
 void setPlateAcquisitionMaximumFieldCount(ome.xml.model.primitives.PositiveInteger maximumFieldCount, int plateIndex, int plateAcquisitionIndex)
           
 void setPlateAcquisitionName(String name, int plateIndex, int plateAcquisitionIndex)
           
 void setPlateAcquisitionStartTime(String startTime, int plateIndex, int plateAcquisitionIndex)
           
 void setPlateAcquisitionWellSampleRef(String wellSample, int plateIndex, int plateAcquisitionIndex, int wellSampleRefIndex)
           
 void setPlateAnnotationRef(String annotation, int plateIndex, int annotationRefIndex)
           
 void setPlateColumnNamingConvention(ome.xml.model.enums.NamingConvention columnNamingConvention, int plateIndex)
           
 void setPlateColumns(ome.xml.model.primitives.PositiveInteger columns, int plateIndex)
           
 void setPlateDescription(String description, int plateIndex)
           
 void setPlateExternalIdentifier(String externalIdentifier, int plateIndex)
           
 void setPlateID(String id, int plateIndex)
           
 void setPlateName(String name, int plateIndex)
           
 void setPlateRowNamingConvention(ome.xml.model.enums.NamingConvention rowNamingConvention, int plateIndex)
           
 void setPlateRows(ome.xml.model.primitives.PositiveInteger rows, int plateIndex)
           
 void setPlateScreenRef(String screen, int plateIndex, int screenRefIndex)
           
 void setPlateStatus(String status, int plateIndex)
           
 void setPlateWellOriginX(Double wellOriginX, int plateIndex)
           
 void setPlateWellOriginY(Double wellOriginY, int plateIndex)
           
 void setPointDescription(String description, int ROIIndex, int shapeIndex)
           
 void setPointFill(Integer fill, int ROIIndex, int shapeIndex)
           
 void setPointFontSize(ome.xml.model.primitives.NonNegativeInteger fontSize, int ROIIndex, int shapeIndex)
           
 void setPointID(String id, int ROIIndex, int shapeIndex)
           
 void setPointLabel(String label, int ROIIndex, int shapeIndex)
           
 void setPointName(String name, int ROIIndex, int shapeIndex)
           
 void setPointStroke(Integer stroke, int ROIIndex, int shapeIndex)
           
 void setPointStrokeDashArray(String strokeDashArray, int ROIIndex, int shapeIndex)
           
 void setPointStrokeWidth(Double strokeWidth, int ROIIndex, int shapeIndex)
           
 void setPointTheC(ome.xml.model.primitives.NonNegativeInteger theC, int ROIIndex, int shapeIndex)
           
 void setPointTheT(ome.xml.model.primitives.NonNegativeInteger theT, int ROIIndex, int shapeIndex)
           
 void setPointTheZ(ome.xml.model.primitives.NonNegativeInteger theZ, int ROIIndex, int shapeIndex)
           
 void setPointTransform(String transform, int ROIIndex, int shapeIndex)
           
 void setPointX(Double x, int ROIIndex, int shapeIndex)
           
 void setPointY(Double y, int ROIIndex, int shapeIndex)
           
 void setPolylineClosed(Boolean closed, int ROIIndex, int shapeIndex)
           
 void setPolylineDescription(String description, int ROIIndex, int shapeIndex)
           
 void setPolylineFill(Integer fill, int ROIIndex, int shapeIndex)
           
 void setPolylineFontSize(ome.xml.model.primitives.NonNegativeInteger fontSize, int ROIIndex, int shapeIndex)
           
 void setPolylineID(String id, int ROIIndex, int shapeIndex)
           
 void setPolylineLabel(String label, int ROIIndex, int shapeIndex)
           
 void setPolylineName(String name, int ROIIndex, int shapeIndex)
           
 void setPolylinePoints(String points, int ROIIndex, int shapeIndex)
           
 void setPolylineStroke(Integer stroke, int ROIIndex, int shapeIndex)
           
 void setPolylineStrokeDashArray(String strokeDashArray, int ROIIndex, int shapeIndex)
           
 void setPolylineStrokeWidth(Double strokeWidth, int ROIIndex, int shapeIndex)
           
 void setPolylineTheC(ome.xml.model.primitives.NonNegativeInteger theC, int ROIIndex, int shapeIndex)
           
 void setPolylineTheT(ome.xml.model.primitives.NonNegativeInteger theT, int ROIIndex, int shapeIndex)
           
 void setPolylineTheZ(ome.xml.model.primitives.NonNegativeInteger theZ, int ROIIndex, int shapeIndex)
           
 void setPolylineTransform(String transform, int ROIIndex, int shapeIndex)
           
 void setProjectAnnotationRef(String annotation, int projectIndex, int annotationRefIndex)
           
 void setProjectDescription(String description, int projectIndex)
           
 void setProjectExperimenterRef(String experimenter, int projectIndex)
           
 void setProjectGroupRef(String group, int projectIndex)
           
 void setProjectID(String id, int projectIndex)
           
 void setProjectName(String name, int projectIndex)
           
 void setReader(loci.formats.IFormatReader reader)
          Sets the Bio-Formats reader that will be used to populate the container store.
 void setReagentAnnotationRef(String annotation, int screenIndex, int reagentIndex, int annotationRefIndex)
           
 void setReagentDescription(String description, int screenIndex, int reagentIndex)
           
 void setReagentID(String id, int screenIndex, int reagentIndex)
           
 void setReagentName(String name, int screenIndex, int reagentIndex)
           
 void setReagentReagentIdentifier(String reagentIdentifier, int screenIndex, int reagentIndex)
           
 void setRectangleDescription(String description, int ROIIndex, int shapeIndex)
           
 void setRectangleFill(Integer fill, int ROIIndex, int shapeIndex)
           
 void setRectangleFontSize(ome.xml.model.primitives.NonNegativeInteger fontSize, int ROIIndex, int shapeIndex)
           
 void setRectangleHeight(Double height, int ROIIndex, int shapeIndex)
           
 void setRectangleID(String id, int ROIIndex, int shapeIndex)
           
 void setRectangleLabel(String label, int ROIIndex, int shapeIndex)
           
 void setRectangleName(String name, int ROIIndex, int shapeIndex)
           
 void setRectangleStroke(Integer stroke, int ROIIndex, int shapeIndex)
           
 void setRectangleStrokeDashArray(String strokeDashArray, int ROIIndex, int shapeIndex)
           
 void setRectangleStrokeWidth(Double strokeWidth, int ROIIndex, int shapeIndex)
           
 void setRectangleTheC(ome.xml.model.primitives.NonNegativeInteger theC, int ROIIndex, int shapeIndex)
           
 void setRectangleTheT(ome.xml.model.primitives.NonNegativeInteger theT, int ROIIndex, int shapeIndex)
           
 void setRectangleTheZ(ome.xml.model.primitives.NonNegativeInteger theZ, int ROIIndex, int shapeIndex)
           
 void setRectangleTransform(String transform, int ROIIndex, int shapeIndex)
           
 void setRectangleWidth(Double width, int ROIIndex, int shapeIndex)
           
 void setRectangleX(Double x, int ROIIndex, int shapeIndex)
           
 void setRectangleY(Double y, int ROIIndex, int shapeIndex)
           
 void setReferenceStringCache(Map<String,String[]> referenceStringCache)
          Sets the string based reference cache for this container store.
 void setROIAnnotationRef(String annotation, int ROIIndex, int annotationRefIndex)
           
 void setROIDescription(String description, int ROIIndex)
           
 void setROIID(String id, int ROIIndex)
           
 void setROIName(String name, int ROIIndex)
           
 void setROINamespace(String namespace, int ROIIndex)
           
 void setRoot(Object root)
           
 void setScreenAnnotationRef(String annotation, int screenIndex, int annotationRefIndex)
           
 void setScreenDescription(String description, int screenIndex)
           
 void setScreenID(String id, int screenIndex)
           
 void setScreenName(String name, int screenIndex)
           
 void setScreenPlateRef(String plate, int screenIndex, int plateRefIndex)
           
 void setScreenProtocolDescription(String protocolDescription, int screenIndex)
           
 void setScreenProtocolIdentifier(String protocolIdentifier, int screenIndex)
           
 void setScreenReagentSetDescription(String reagentSetDescription, int screenIndex)
           
 void setScreenReagentSetIdentifier(String reagentSetIdentifier, int screenIndex)
           
 void setScreenType(String type, int screenIndex)
           
 void setStageLabelName(String name, int imageIndex)
           
 void setStageLabelX(Double x, int imageIndex)
           
 void setStageLabelY(Double y, int imageIndex)
           
 void setStageLabelZ(Double z, int imageIndex)
           
 void setTagAnnotationAnnotationRef(String annotation, int tagAnnotationIndex, int annotationRefIndex)
           
 void setTagAnnotationDescription(String description, int tagAnnotationIndex)
           
 void setTagAnnotationID(String id, int tagAnnotationIndex)
           
 void setTagAnnotationNamespace(String namespace, int tagAnnotationIndex)
           
 void setTagAnnotationValue(String value, int tagAnnotationIndex)
           
 void setTermAnnotationAnnotationRef(String annotation, int termAnnotationIndex, int annotationRefIndex)
           
 void setTermAnnotationDescription(String description, int termAnnotationIndex)
           
 void setTermAnnotationID(String id, int termAnnotationIndex)
           
 void setTermAnnotationNamespace(String namespace, int termAnnotationIndex)
           
 void setTermAnnotationValue(String value, int termAnnotationIndex)
           
 void setTextDescription(String description, int ROIIndex, int shapeIndex)
           
 void setTextFill(Integer fill, int ROIIndex, int shapeIndex)
           
 void setTextFontSize(ome.xml.model.primitives.NonNegativeInteger fontSize, int ROIIndex, int shapeIndex)
           
 void setTextID(String id, int ROIIndex, int shapeIndex)
           
 void setTextLabel(String label, int ROIIndex, int shapeIndex)
           
 void setTextName(String name, int ROIIndex, int shapeIndex)
           
 void setTextStroke(Integer stroke, int ROIIndex, int shapeIndex)
           
 void setTextStrokeDashArray(String strokeDashArray, int ROIIndex, int shapeIndex)
           
 void setTextStrokeWidth(Double strokeWidth, int ROIIndex, int shapeIndex)
           
 void setTextTheC(ome.xml.model.primitives.NonNegativeInteger theC, int ROIIndex, int shapeIndex)
           
 void setTextTheT(ome.xml.model.primitives.NonNegativeInteger theT, int ROIIndex, int shapeIndex)
           
 void setTextTheZ(ome.xml.model.primitives.NonNegativeInteger theZ, int ROIIndex, int shapeIndex)
           
 void setTextTransform(String transform, int ROIIndex, int shapeIndex)
           
 void setTextValue(String value, int ROIIndex, int shapeIndex)
           
 void setTextX(Double x, int ROIIndex, int shapeIndex)
           
 void setTextY(Double y, int ROIIndex, int shapeIndex)
           
 void setTiffDataFirstC(ome.xml.model.primitives.NonNegativeInteger firstC, int imageIndex, int tiffDataIndex)
           
 void setTiffDataFirstT(ome.xml.model.primitives.NonNegativeInteger firstT, int imageIndex, int tiffDataIndex)
           
 void setTiffDataFirstZ(ome.xml.model.primitives.NonNegativeInteger firstZ, int imageIndex, int tiffDataIndex)
           
 void setTiffDataIFD(ome.xml.model.primitives.NonNegativeInteger ifd, int imageIndex, int tiffDataIndex)
           
 void setTiffDataPlaneCount(ome.xml.model.primitives.NonNegativeInteger planeCount, int imageIndex, int tiffDataIndex)
           
 void setTile(Long pixId, byte[] arrayBuf, int z, int c, int t, int x, int y, int w, int h)
          Writes a tile of pixels to the server.
 void setTimestampAnnotationAnnotationRef(String annotation, int timestampAnnotationIndex, int annotationRefIndex)
           
 void setTimestampAnnotationDescription(String description, int timestampAnnotationIndex)
           
 void setTimestampAnnotationID(String id, int timestampAnnotationIndex)
           
 void setTimestampAnnotationNamespace(String namespace, int timestampAnnotationIndex)
           
 void setTimestampAnnotationValue(String value, int timestampAnnotationIndex)
           
 void setTransmittanceRangeCutIn(ome.xml.model.primitives.PositiveInteger cutIn, int instrumentIndex, int filterIndex)
           
 void setTransmittanceRangeCutInTolerance(ome.xml.model.primitives.NonNegativeInteger cutInTolerance, int instrumentIndex, int filterIndex)
           
 void setTransmittanceRangeCutOut(ome.xml.model.primitives.PositiveInteger cutOut, int instrumentIndex, int filterIndex)
           
 void setTransmittanceRangeCutOutTolerance(ome.xml.model.primitives.NonNegativeInteger cutOutTolerance, int instrumentIndex, int filterIndex)
           
 void setTransmittanceRangeTransmittance(ome.xml.model.primitives.PercentFraction transmittance, int instrumentIndex, int filterIndex)
           
 void setUserSpecifiedAnnotations(List<omero.model.Annotation> annotations)
          Sets the user specified image annotations.
 void setUserSpecifiedImageDescription(String description)
          Sets the user specified image description.
 void setUserSpecifiedImageName(String name)
          Sets the user specified image name.
 void setUserSpecifiedPhysicalPixelSizes(Double physicalSizeX, Double physicalSizeY, Double physicalSizeZ)
          Sets the user specified physical pixel sizes.
 void setUserSpecifiedPlateDescription(String description)
          Sets the user specified plate description.
 void setUserSpecifiedPlateName(String name)
          Sets the user specified plate name.
 void setUserSpecifiedTarget(omero.model.IObject target)
          Sets the user specified linkage target (usually a Dataset for Images and a Screen for Plates).
 void setUUID(String uuid)
           
 void setUUIDFileName(String fileName, int imageIndex, int tiffDataIndex)
           
 void setUUIDValue(String fileName, int imageIndex, int tiffDataIndex)
           
 void setWellAnnotationRef(String annotation, int plateIndex, int wellIndex, int annotationRefIndex)
           
 void setWellColor(Integer color, int plateIndex, int wellIndex)
           
 void setWellColumn(ome.xml.model.primitives.NonNegativeInteger column, int plateIndex, int wellIndex)
           
 void setWellExternalDescription(String externalDescription, int plateIndex, int wellIndex)
           
 void setWellExternalIdentifier(String externalIdentifier, int plateIndex, int wellIndex)
           
 void setWellID(String id, int plateIndex, int wellIndex)
           
 void setWellReagentRef(String reagent, int plateIndex, int wellIndex)
           
 void setWellRow(ome.xml.model.primitives.NonNegativeInteger row, int plateIndex, int wellIndex)
           
 void setWellSampleAnnotationRef(String annotation, int plateIndex, int wellIndex, int wellSampleIndex, int annotationRefIndex)
           
 void setWellSampleID(String id, int plateIndex, int wellIndex, int wellSampleIndex)
           
 void setWellSampleImageRef(String image, int plateIndex, int wellIndex, int wellSampleIndex)
           
 void setWellSampleIndex(ome.xml.model.primitives.NonNegativeInteger index, int plateIndex, int wellIndex, int wellSampleIndex)
           
 void setWellSamplePositionX(Double positionX, int plateIndex, int wellIndex, int wellSampleIndex)
           
 void setWellSamplePositionY(Double positionY, int plateIndex, int wellIndex, int wellSampleIndex)
           
 void setWellSampleTimepoint(String timepoint, int plateIndex, int wellIndex, int wellSampleIndex)
           
 void setWellStatus(String status, int plateIndex, int wellIndex)
           
 void setXMLAnnotationAnnotationRef(String annotation, int XMLAnnotationIndex, int annotationRefIndex)
           
 void setXMLAnnotationDescription(String description, int XMLAnnotationIndex)
           
 void setXMLAnnotationID(String id, int XMLAnnotationIndex)
           
 void setXMLAnnotationNamespace(String namespace, int XMLAnnotationIndex)
           
 void setXMLAnnotationValue(String value, int XMLAnnotationIndex)
           
 omero.RBool toRType(Boolean value)
          Transforms a Java type into the corresponding OMERO RType.
 omero.RDouble toRType(Double value)
          Transforms a Java type into the corresponding OMERO RType.
 omero.RDouble toRType(Float value)
          Transforms a Java type into the corresponding OMERO RType.
 omero.RInt toRType(Integer value)
          Transforms a Java type into the corresponding OMERO RType.
 omero.RLong toRType(Long value)
          Transforms a Java type into the corresponding OMERO RType.
 omero.RString toRType(ome.xml.model.enums.NamingConvention value)
          Transforms a Java type into the corresponding OMERO RType.
 omero.RInt toRType(ome.xml.model.primitives.NonNegativeInteger value)
          Transforms a Java type into the corresponding OMERO RType.
 omero.RLong toRType(ome.xml.model.primitives.NonNegativeLong value)
          Transforms a Java type into the corresponding OMERO RType.
 omero.RDouble toRType(ome.xml.model.primitives.PercentFraction value)
          Transforms a Java type into the corresponding OMERO RType.
 omero.RDouble toRType(ome.xml.model.primitives.PositiveFloat value)
          Transforms a Java type into the corresponding OMERO RType.
 omero.RString toRType(String value)
          Transforms a Java type into the corresponding OMERO RType.
 omero.RTime toRType(Timestamp value)
          Transforms a Java type into the corresponding OMERO RType.
 void updatePixels(List<omero.model.Pixels> pixelsList)
          Updates a list of Pixels.
 void writeFilesToFileStore(List<File> files, Map<String,omero.model.OriginalFile> originalFileMap)
          Writes binary original file data to the OMERO server.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

OMERO_EMISSION_FILTER_SUFFIX

public static final String OMERO_EMISSION_FILTER_SUFFIX
Emission filter LSID suffix.

See Also:
Constant Field Values

OMERO_EXCITATION_FILTER_SUFFIX

public static final String OMERO_EXCITATION_FILTER_SUFFIX
Excitation filter LSID suffix.

See Also:
Constant Field Values
Constructor Detail

OMEROMetadataStoreClient

public OMEROMetadataStoreClient()
Method Detail

getKeepAlive

public ClientKeepAlive getKeepAlive()
Returns clientKeepAlive created in store

Returns:
current ClientKeepAlive

logVersionInfo

public void logVersionInfo(String clientVersion)
                    throws omero.ServerError
Throws:
omero.ServerError

getIQuery

public omero.api.IQueryPrx getIQuery()
Returns:
IQuery proxy

setEncryptedConnection

public void setEncryptedConnection(boolean encryptedConnection)

isEncryptedConnection

public boolean isEncryptedConnection()

initialize

public void initialize(omero.api.ServiceFactoryPrx serviceFactory)
                throws omero.ServerError
Initializes the MetadataStore with an already logged in, ready to go service factory. When finished with this instance, close stateful services via closeServices().

Parameters:
serviceFactory - The factory. Mustn't be null.
Throws:
omero.ServerError

initialize

public void initialize(client c)
                throws omero.ServerError
Initializes the MetadataStore with an already logged in, ready to go service factory. When finished with this instance, close stateful services via closeServices().

Parameters:
c - The client. Mustn't be null.
Throws:
omero.ServerError

initialize

public void initialize(String username,
                       String password,
                       String server,
                       int port)
                throws Glacier2.CannotCreateSessionException,
                       Glacier2.PermissionDeniedException,
                       omero.ServerError
Initializes the MetadataStore taking string parameters to feed to the OMERO Blitz client object. Using this method creates an unsecure session. When finished with this instance, close all resources via logout()

Parameters:
username - User's omename.
password - User's password.
server - Server hostname.
port - Server port.
Throws:
Glacier2.CannotCreateSessionException - If there is a session error when creating the OMERO Blitz client object.
Glacier2.PermissionDeniedException - If there is a problem logging the user in.
omero.ServerError - If there is a critical error communicating with the server.

initialize

public void initialize(String username,
                       String password,
                       String server,
                       int port,
                       boolean isSecure)
                throws Glacier2.CannotCreateSessionException,
                       Glacier2.PermissionDeniedException,
                       omero.ServerError
Initializes the MetadataStore taking string parameters to feed to the OMERO Blitz client object. Using this method to create either secure or unsecure sessions. When finished with this instance, close all resources via logout()

Parameters:
username - User's omename.
password - User's password.
server - Server hostname.
port - Server port.
isSecure - is this session secure
Throws:
Glacier2.CannotCreateSessionException - If there is a session error when creating the OMERO Blitz client object.
Glacier2.PermissionDeniedException - If there is a problem logging the user in.
omero.ServerError - If there is a critical error communicating with the server.

initialize

public void initialize(String username,
                       String password,
                       String server,
                       int port,
                       long group,
                       boolean isSecure)
                throws Glacier2.CannotCreateSessionException,
                       Glacier2.PermissionDeniedException,
                       omero.ServerError
Initializes the MetadataStore taking string parameters to feed to the OMERO Blitz client object. Using this method to create either secure or unsecure sessions and sets the user's group to supplied group. When finished with this instance, close all resources via logout()

Parameters:
username - User's omename.
password - User's password.
server - Server hostname.
port - Server port.
group - User's current group.
isSecure - is this session secure
Throws:
Glacier2.CannotCreateSessionException - If there is a session error when creating the OMERO Blitz client object.
Glacier2.PermissionDeniedException - If there is a problem logging the user in.
omero.ServerError - If there is a critical error communicating with the server.

initialize

public void initialize(String server,
                       int port,
                       String sessionKey)
                throws Glacier2.CannotCreateSessionException,
                       Glacier2.PermissionDeniedException,
                       omero.ServerError
Initializes the MetadataStore by joining an existing session. Use this method only with unsecure sessions. When finished with this instance, close all resources via logout()

Parameters:
server - Server hostname.
port - Server port.
sessionKey - Bind session key.
Throws:
Glacier2.CannotCreateSessionException
Glacier2.PermissionDeniedException
omero.ServerError

initialize

public void initialize(String server,
                       int port,
                       String sessionKey,
                       boolean isSecure)
                throws Glacier2.CannotCreateSessionException,
                       Glacier2.PermissionDeniedException,
                       omero.ServerError
Initializes the MetadataStore by joining an existing session. Use this method only with unsecure sessions. When finished with this instance, close all resources via logout()

Parameters:
server - Server hostname.
port - Server port.
sessionKey - Bind session key.
Throws:
Glacier2.CannotCreateSessionException
Glacier2.PermissionDeniedException
omero.ServerError

getServiceFactory

public omero.api.ServiceFactoryPrx getServiceFactory()
Returns the currently active service factory.

Returns:
See above.

ping

public void ping()
Pings all registered OMERO Blitz proxies.


setEnumerationProvider

public void setEnumerationProvider(EnumerationProvider enumProvider)
Sets the active enumeration provider.

Parameters:
enumProvider - Enumeration provider to use.

getEnumerationProvider

public EnumerationProvider getEnumerationProvider()
Retrieves the active enumeration provider.

Returns:
See above.

setInstanceProvider

public void setInstanceProvider(InstanceProvider instanceProvider)
Sets the active instance provider.

Parameters:
enumProvider - Enumeration provider to use.

getInstanceProvider

public InstanceProvider getInstanceProvider()
Retrieves the active enumeration provider.

Returns:
See above.

toRType

public omero.RInt toRType(Integer value)
Transforms a Java type into the corresponding OMERO RType.

Parameters:
value - Java concrete type value.
Returns:
RType or null if value is null.

toRType

public omero.RInt toRType(ome.xml.model.primitives.NonNegativeInteger value)
Transforms a Java type into the corresponding OMERO RType.

Parameters:
value - Java concrete type value.
Returns:
RType or null if value is null.

toRType

public omero.RLong toRType(ome.xml.model.primitives.NonNegativeLong value)
Transforms a Java type into the corresponding OMERO RType.

Parameters:
value - Java concrete type value.
Returns:
RType or null if value is null.

toRType

public omero.RDouble toRType(ome.xml.model.primitives.PositiveFloat value)
Transforms a Java type into the corresponding OMERO RType.

Parameters:
value - Java concrete type value.
Returns:
RType or null if value is null.

toRType

public omero.RDouble toRType(ome.xml.model.primitives.PercentFraction value)
Transforms a Java type into the corresponding OMERO RType.

Parameters:
value - Java concrete type value.
Returns:
RType or null if value is null.

toRType

public omero.RLong toRType(Long value)
Transforms a Java type into the corresponding OMERO RType.

Parameters:
value - Java concrete type value.
Returns:
RType or null if value is null.

toRType

public omero.RString toRType(String value)
Transforms a Java type into the corresponding OMERO RType.

Parameters:
value - Java concrete type value.
Returns:
RType or null if value is null.

toRType

public omero.RBool toRType(Boolean value)
Transforms a Java type into the corresponding OMERO RType.

Parameters:
value - Java concrete type value.
Returns:
RType or null if value is null.

toRType

public omero.RDouble toRType(Double value)
Transforms a Java type into the corresponding OMERO RType.

Parameters:
value - Java concrete type value.
Returns:
RType or null if value is null.

toRType

public omero.RDouble toRType(Float value)
Transforms a Java type into the corresponding OMERO RType.

Parameters:
value - Java concrete type value.
Returns:
RType or null if value is null.

toRType

public omero.RTime toRType(Timestamp value)
Transforms a Java type into the corresponding OMERO RType.

Parameters:
value - Java concrete type value.
Returns:
RType or null if value is null.

toRType

public omero.RString toRType(ome.xml.model.enums.NamingConvention value)
Transforms a Java type into the corresponding OMERO RType.

Parameters:
value - Java concrete type value.
Returns:
RType or null if value is null.

closeServices

public void closeServices()
Closes all stateful services. This method should be preferred over logout() when initialized via an client or a ServiceFactoryPrx instance.

See Also:
initialize(client), initialize(ServiceFactoryPrx)

logout

public void logout()
Destroys the sessionFactory and closes the client. This method should not be called when initialized via an client or a ServiceFactoryPrx instance. * @see #initialize(client)

See Also:
initialize(ServiceFactoryPrx), closeServices()

prepare

public void prepare(Map<Integer,omero.model.Image> existingMetadata)
Prepares the metadata store using existing metadata that has been pre-registered by OMERO.fs. The expected graph should be fully loaded: NOTE: An execution of prepare() is only valid for a SINGLE importImage() execution. Following importImage() the existing metadata map will be reset regardless of success or failure.

Parameters:
existingMetadata - Map of imageIndex or series vs. populated Image source graph with the fetched objects defined above.

createRoot

public void createRoot()
Specified by:
createRoot in interface loci.formats.meta.MetadataStore

getRoot

public Object getRoot()
Specified by:
getRoot in interface loci.formats.meta.MetadataStore

getReader

public loci.formats.IFormatReader getReader()
Description copied from interface: IObjectContainerStore
Returns the current Bio-Formats reader that has been used to populate the container store.

Specified by:
getReader in interface IObjectContainerStore
Returns:
See above.

setReader

public void setReader(loci.formats.IFormatReader reader)
Description copied from interface: IObjectContainerStore
Sets the Bio-Formats reader that will be used to populate the container store.

Specified by:
setReader in interface IObjectContainerStore
Parameters:
reader - Bio-Formats reader.

getUserSpecifiedAnnotations

public List<omero.model.Annotation> getUserSpecifiedAnnotations()
Description copied from interface: IObjectContainerStore
Returns the user specified annotations.

Specified by:
getUserSpecifiedAnnotations in interface IObjectContainerStore
Returns:
See above.

setUserSpecifiedAnnotations

public void setUserSpecifiedAnnotations(List<omero.model.Annotation> annotations)
Description copied from interface: IObjectContainerStore
Sets the user specified image annotations.

Specified by:
setUserSpecifiedAnnotations in interface IObjectContainerStore
Parameters:
annotations - user specified annotations

getUserSpecifiedPlateName

public String getUserSpecifiedPlateName()
Description copied from interface: IObjectContainerStore
Returns the user specified plate name.

Specified by:
getUserSpecifiedPlateName in interface IObjectContainerStore
Returns:
See above.

setUserSpecifiedPlateName

public void setUserSpecifiedPlateName(String name)
Description copied from interface: IObjectContainerStore
Sets the user specified plate name.

Specified by:
setUserSpecifiedPlateName in interface IObjectContainerStore
Parameters:
name - user specified plate name

getUserSpecifiedPlateDescription

public String getUserSpecifiedPlateDescription()
Description copied from interface: IObjectContainerStore
Returns the user specified plate description.

Specified by:
getUserSpecifiedPlateDescription in interface IObjectContainerStore
Returns:
See above.

setUserSpecifiedPlateDescription

public void setUserSpecifiedPlateDescription(String description)
Description copied from interface: IObjectContainerStore
Sets the user specified plate description.

Specified by:
setUserSpecifiedPlateDescription in interface IObjectContainerStore

getUserSpecifiedImageName

public String getUserSpecifiedImageName()
Description copied from interface: IObjectContainerStore
Returns the user specified image name.

Specified by:
getUserSpecifiedImageName in interface IObjectContainerStore
Returns:
See above.

setUserSpecifiedImageName

public void setUserSpecifiedImageName(String name)
Description copied from interface: IObjectContainerStore
Sets the user specified image name.

Specified by:
setUserSpecifiedImageName in interface IObjectContainerStore
Parameters:
name - user specified image name

getUserSpecifiedImageDescription

public String getUserSpecifiedImageDescription()
Description copied from interface: IObjectContainerStore
Returns the user specified image description.

Specified by:
getUserSpecifiedImageDescription in interface IObjectContainerStore
Returns:
See above.

setUserSpecifiedImageDescription

public void setUserSpecifiedImageDescription(String description)
Description copied from interface: IObjectContainerStore
Sets the user specified image description.

Specified by:
setUserSpecifiedImageDescription in interface IObjectContainerStore

getUserSpecifiedTarget

public omero.model.IObject getUserSpecifiedTarget()
Description copied from interface: IObjectContainerStore
Returns the user specified linkage target (usually a Dataset for Images and a Screen for Plates).

Specified by:
getUserSpecifiedTarget in interface IObjectContainerStore
Returns:
See above.

setUserSpecifiedTarget

public void setUserSpecifiedTarget(omero.model.IObject target)
Description copied from interface: IObjectContainerStore
Sets the user specified linkage target (usually a Dataset for Images and a Screen for Plates).

Specified by:
setUserSpecifiedTarget in interface IObjectContainerStore

getUserSpecifiedPhysicalPixelSizes

public Double[] getUserSpecifiedPhysicalPixelSizes()
Description copied from interface: IObjectContainerStore
Returns the user specified physical pixel sizes.

Specified by:
getUserSpecifiedPhysicalPixelSizes in interface IObjectContainerStore
Returns:
An array of double[] { physicalSizeX, physicalSizeY, physicalSizeZ } as specified by the user. A value of null for any one index states the user has not made a choice for the size of that particular dimension.

setUserSpecifiedPhysicalPixelSizes

public void setUserSpecifiedPhysicalPixelSizes(Double physicalSizeX,
                                               Double physicalSizeY,
                                               Double physicalSizeZ)
Description copied from interface: IObjectContainerStore
Sets the user specified physical pixel sizes. A value of null states the original file physical size for that dimension should be used.

Specified by:
setUserSpecifiedPhysicalPixelSizes in interface IObjectContainerStore
Parameters:
physicalSizeX - Physical pixel size width.
physicalSizeY - Physical pixel height.
physicalSizeZ - Physical pixel depth.

getModelProcessors

public List<ModelProcessor> getModelProcessors()
Retrieves the current list of model processors the metadata store is using.

Returns:
See above.

setModelProcessors

public void setModelProcessors(List<ModelProcessor> modelProcessors)
Sets the current set of model processors.

Parameters:
modelProcessors - List of model processors to use.

removeModelProcessor

public void removeModelProcessor(ModelProcessor processor)
Removes a model processor from use.

Parameters:
processor - Model processor to remove.

addModelProcessor

public boolean addModelProcessor(ModelProcessor processor)
Adds a model processor to the end of the processing chain.

Parameters:
processor - Model processor to add.
Returns:
true as specified by Collection.add(E).

getContainerCache

public Map<ome.util.LSID,omero.metadatastore.IObjectContainer> getContainerCache()
Description copied from interface: IObjectContainerStore
Returns the current container cache.

Specified by:
getContainerCache in interface IObjectContainerStore
Returns:
See above.

getReferenceCache

public Map<ome.util.LSID,List<ome.util.LSID>> getReferenceCache()
Description copied from interface: IObjectContainerStore
Returns the current reference cache.

Specified by:
getReferenceCache in interface IObjectContainerStore
Returns:
See above.

getAuthoritativeContainerCache

public Map<Class<? extends omero.model.IObject>,Map<String,omero.metadatastore.IObjectContainer>> getAuthoritativeContainerCache()
Description copied from interface: IObjectContainerStore
Returns the current authoritative LSID container cache. This container cache records the explicitly set LSID to container references.

Specified by:
getAuthoritativeContainerCache in interface IObjectContainerStore
Returns:
See above.

addReference

public void addReference(ome.util.LSID source,
                         ome.util.LSID target)
Adds a reference to the reference cache.

Specified by:
addReference in interface IObjectContainerStore
Parameters:
source - Source LSID to add.
target - Target LSID to add.

getReferenceStringCache

public Map<String,String[]> getReferenceStringCache()
Description copied from interface: IObjectContainerStore
Returns the current string based reference cache. This is usually populated by a ReferenceProcessor instance.

Specified by:
getReferenceStringCache in interface IObjectContainerStore
Returns:
See above.

setReferenceStringCache

public void setReferenceStringCache(Map<String,String[]> referenceStringCache)
Description copied from interface: IObjectContainerStore
Sets the string based reference cache for this container store. This is usually called by a ReferenceProcessor instance.

Specified by:
setReferenceStringCache in interface IObjectContainerStore
Parameters:
referenceStringCache - String based reference cache to use.

getSourceObject

public omero.model.IObject getSourceObject(ome.util.LSID LSID)
Description copied from interface: IObjectContainerStore
Retrieves an OMERO Blitz source object for a given LSID.

Specified by:
getSourceObject in interface IObjectContainerStore
Parameters:
LSID - LSID to retrieve a source object for.
Returns:
See above.

getSourceObjects

public <T extends omero.model.IObject> List<T> getSourceObjects(Class<T> klass)
Description copied from interface: IObjectContainerStore
Retrieves all OMERO Blitz source objects of a given class.

Specified by:
getSourceObjects in interface IObjectContainerStore
Parameters:
klass - Class to retrieve source objects for.
Returns:
See above.

hasReference

public boolean hasReference(ome.util.LSID source,
                            ome.util.LSID target)
Description copied from interface: IObjectContainerStore
Checks to see if there is currently an active reference for two LSIDs.

Specified by:
hasReference in interface IObjectContainerStore
Parameters:
source - LSID of the source object.
target - LSID of the target object.
Returns:
true if a reference exists, false otherwise.

setArchiveScreeningDomain

public List<File> setArchiveScreeningDomain(boolean archive)
Populates archive flags on all images currently processed links relevant original metadata files as requested and performs graph logic to have the scafolding in place for later original file upload if we are of the HCS domain.

Parameters:
archive - Whether or not the user requested the original files to be archived.
Returns:
A list of the temporary metadata files created on local disk.

setArchive

public List<File> setArchive(boolean archive,
                             boolean useMetadataFile)
Populates archive flags on all images currently processed links relevant original metadata files as requested and performs graph logic to have the scaffolding in place for later original file upload.

Parameters:
archive - Whether or not the user requested the original files to be archived.
useMetadataFile - Whether or not to dump all metadata to a flat file annotation on the server.
Returns:
A list of the temporary metadata files created on local disk.

getFilteredCompanionFiles

public List<String> getFilteredCompanionFiles()
Returns the current set of filtered companion files that the Bio-Formats image reader contains.

Returns:
See above.
See Also:
getFilteredSeriesCompanionFiles()

getFilteredSeriesCompanionFiles

public List<String> getFilteredSeriesCompanionFiles()
Returns the current set of filtered companion files that the Bio-Formats image reader contains for the current series.

Returns:
See above.
See Also:
getFilteredCompanionFiles()

writeFilesToFileStore

public void writeFilesToFileStore(List<File> files,
                                  Map<String,omero.model.OriginalFile> originalFileMap)
Writes binary original file data to the OMERO server.

Parameters:
files - Files to populate against an original file list.
originalFileMap - Map of absolute path against original file objects that we are to populate.

setPixelsParams

public void setPixelsParams(long pixelsId,
                            int series)
Sets extended the properties on a pixel set.

Parameters:
pixelsId - The pixels set identifier.
series - The series number to populate.

setCurrentGroup

public void setCurrentGroup(long groupID)
                     throws omero.ServerError
Changes the default group of the currently logged in user.

Parameters:
groupID - The id of the group.
Throws:
Exception - If an error occurred while trying to retrieve data from OMERO service.
omero.ServerError

mapUserGroups

public Map<Long,String> mapUserGroups()
                               throws omero.ServerError
Maps the user's groups for use by ScreenLogin.registerGroup() Also strips system groups from this map

Returns:
map of group id & name
Throws:
omero.ServerError

getDefaultGroupName

public String getDefaultGroupName()
                           throws omero.ServerError
Retrieve the default group's name

Returns:
name
Throws:
omero.ServerError

getDefaultGroupLevel

public int getDefaultGroupLevel()
                         throws omero.ServerError
Retrieve teh default groups permission 'level'.

Returns:
ImportEvent's group level
Throws:
omero.ServerError

getRepositorySpace

public long getRepositorySpace()
Returns:
repository space as a long

postProcess

public void postProcess()
Post processes the internal structure of the client side MetadataStore. Should be called before saveToDB().


saveToDB

public List<omero.model.Pixels> saveToDB()
Updates the server side MetadataStore with a list of our objects and references and saves them into the database.

Returns:
List of Pixels after database commit.

launchProcessing

public List<omero.grid.InteractiveProcessorPrx> launchProcessing()

getTarget

public <T extends omero.model.IObject> T getTarget(Class<T> klass,
                                                   long id)
Helper method to retrieve an object from iQuery

Type Parameters:
T -
Parameters:
klass -
id -
Returns:

getProject

public omero.model.Project getProject(long projectId)
Parameters:
projectId -
Returns:

addDataset

public omero.model.Dataset addDataset(String datasetName,
                                      String datasetDescription,
                                      omero.model.Project project)
Parameters:
datasetName -
datasetDescription -
project -
Returns:

getExperimenterID

public long getExperimenterID()
Returns:
- experimenter id

getConfigValue

public String getConfigValue(String key)
Retrieves a configuration value from the IConfig service.

Parameters:
key - Key for the string encoded value.
Returns:
String encoded configuration value.

getScreens

public List<omero.model.Screen> getScreens()
Returns:

getProjects

public List<omero.model.Project> getProjects()
Returns:

getDatasets

public List<omero.model.Dataset> getDatasets(omero.model.Project p)
Parameters:
p -
Returns:

getDatasetsWithoutProjects

public List<omero.model.Dataset> getDatasetsWithoutProjects()
Returns:

addProject

public omero.model.Project addProject(String projectName,
                                      String projectDescription)
Parameters:
projectName -
projectDescription -
Returns:

addScreen

public omero.model.Screen addScreen(String screenName,
                                    String screenDescription)
Parameters:
screenName -
screenDescription -
Returns:

preparePixelsStore

public void preparePixelsStore(List<Long> pixelsIds)
Prepares the server side RawPixelsStore.

Parameters:
pixelsIds - List of Pixels IDs we'll be populating.

finalizePixelStore

public void finalizePixelStore()
                        throws omero.ServerError
Closes the active raw pixels store. Finalizing any open server side resources. The call to close on the RawPixelsStorePrx may throw, in which case the current import should be considered failed, since the saving of the pixels server-side will have not completed successfully.

Throws:
omero.ServerError
See Also:
ticket:5594

getTileSize

public int[] getTileSize(Long pixId)
                  throws omero.ServerError
Retrieves the suggested tile size for a pixels set.

Parameters:
pixId - Pixels set to write to.
Returns:
Width and height of the tile as an array.
Throws:
omero.ServerError - If there is an error writing this tile to the server.

setTile

public void setTile(Long pixId,
                    byte[] arrayBuf,
                    int z,
                    int c,
                    int t,
                    int x,
                    int y,
                    int w,
                    int h)
             throws omero.ServerError
Writes a tile of pixels to the server.

Parameters:
pixId - Pixels set to write to.
arrayBuf - Byte array containing all pixels for this plane.
z - Z offset within the Pixels set.
c - Channel offset within the Pixels set.
t - Timepoint offset within the Pixels set.
x - X offset of the tile.
y - Y offset of the tile.
w - Width of the tile.
h - Height of the tile.
Throws:
omero.ServerError - If there is an error writing this tile to the server.
See Also:
setPlane(Long, byte[], int, int, int)

setPlane

public void setPlane(Long pixId,
                     byte[] arrayBuf,
                     int z,
                     int c,
                     int t)
              throws omero.ServerError
Writes a plane to the server.

Parameters:
pixId - Pixels set to write to.
arrayBuf - Byte array containing all pixels for this plane.
z - Z offset within the Pixels set.
c - Channel offset within the Pixels set.
t - Timepoint offset within the Pixels set.
Throws:
omero.ServerError - If there is an error writing this plane to the server.

setChannelGlobalMinMax

public void setChannelGlobalMinMax(int channel,
                                   double minimum,
                                   double maximum,
                                   int series)
Specified by:
setChannelGlobalMinMax in interface loci.formats.meta.IMinMaxStore

updatePixels

public void updatePixels(List<omero.model.Pixels> pixelsList)
Updates a list of Pixels.

Parameters:
pixelsList - List of Pixels to update.

byteArrayToHexString

public static String byteArrayToHexString(byte[] in)
Parameters:
in -
Returns:

populateMinMax

public void populateMinMax()
Sends all the minimums and maximums for all images processed so far to the server.


resetDefaultsAndGenerateThumbnails

public void resetDefaultsAndGenerateThumbnails(List<Long> plateIds,
                                               List<Long> pixelsIds)
Resets the defaults and generates thumbnails for a given set of Pixels IDs.

Parameters:
plateIds - Set of Plate IDs to reset defaults and thumbnails for.
pixelsIds - Set of Pixels IDs to reset defaults and thumbnails for.

getIObjectContainer

public omero.metadatastore.IObjectContainer getIObjectContainer(Class<? extends omero.model.IObject> klass,
                                                                LinkedHashMap<Index,Integer> indexes)
Description copied from interface: IObjectContainerStore
Retrieves an IObject container for a given class and location within the OME-XML data model. NOTE: The container will be created if it does not already exist.

Specified by:
getIObjectContainer in interface IObjectContainerStore
Parameters:
klass - Class to retrieve a container for.
indexes - Indexes into the OME-XML data model.
Returns:
See above.

removeIObjectContainer

public void removeIObjectContainer(ome.util.LSID lsid)
Description copied from interface: IObjectContainerStore
Removes an IObject container from within the OME-XML data model store.

Specified by:
removeIObjectContainer in interface IObjectContainerStore
Parameters:
lsid - LSID of the container to remove.

getIObjectContainers

public List<omero.metadatastore.IObjectContainer> getIObjectContainers(Class<? extends omero.model.IObject> klass)
Description copied from interface: IObjectContainerStore
Retrieves all IObject containers of a given class. NOTE: this will only return existing containers.

Specified by:
getIObjectContainers in interface IObjectContainerStore
Parameters:
klass - Class to retrieve containers for.
Returns:
See above.

countCachedContainers

public int countCachedContainers(Class<? extends omero.model.IObject> klass,
                                 int... indexes)
Description copied from interface: IObjectContainerStore
Counts the number of containers the MetadataStore has of a given class and at a given index of the hierarchy if specified.

Specified by:
countCachedContainers in interface IObjectContainerStore
Parameters:
klass - Class to count containers of.
indexes - Indexes to use in the container count. For example, if klass is Image and indexes is int[] { 0 }; only containers that have an LSID of type Image and a first index of 0 will be counted.
Returns:
See above.

countCachedReferences

public int countCachedReferences(Class<? extends omero.model.IObject> source,
                                 Class<? extends omero.model.IObject> target)
Description copied from interface: IObjectContainerStore
Counts the number of references the MetadataStore has between objects of two classes.

Specified by:
countCachedReferences in interface IObjectContainerStore
Parameters:
source - Class of the source object. If null it is treated as a wild card, all references whose target match target will be counted.
target - Class of the target object. If null it is treated as a wild card, all references whose source match source will be counted.
Returns:
See above.

setArcID

public void setArcID(String id,
                     int instrumentIndex,
                     int lightSourceIndex)
Specified by:
setArcID in interface loci.formats.meta.MetadataStore

setArcLotNumber

public void setArcLotNumber(String lotNumber,
                            int instrumentIndex,
                            int lightSourceIndex)
Specified by:
setArcLotNumber in interface loci.formats.meta.MetadataStore

setArcManufacturer

public void setArcManufacturer(String manufacturer,
                               int instrumentIndex,
                               int lightSourceIndex)
Specified by:
setArcManufacturer in interface loci.formats.meta.MetadataStore

setArcModel

public void setArcModel(String model,
                        int instrumentIndex,
                        int lightSourceIndex)
Specified by:
setArcModel in interface loci.formats.meta.MetadataStore

setArcPower

public void setArcPower(Double power,
                        int instrumentIndex,
                        int lightSourceIndex)
Specified by:
setArcPower in interface loci.formats.meta.MetadataStore

setArcSerialNumber

public void setArcSerialNumber(String serialNumber,
                               int instrumentIndex,
                               int lightSourceIndex)
Specified by:
setArcSerialNumber in interface loci.formats.meta.MetadataStore

setArcType

public void setArcType(ome.xml.model.enums.ArcType type,
                       int instrumentIndex,
                       int lightSourceIndex)
Specified by:
setArcType in interface loci.formats.meta.MetadataStore

setBooleanAnnotationID

public void setBooleanAnnotationID(String id,
                                   int booleanAnnotationIndex)
Specified by:
setBooleanAnnotationID in interface loci.formats.meta.MetadataStore

setBooleanAnnotationNamespace

public void setBooleanAnnotationNamespace(String namespace,
                                          int booleanAnnotationIndex)
Specified by:
setBooleanAnnotationNamespace in interface loci.formats.meta.MetadataStore

setBooleanAnnotationValue

public void setBooleanAnnotationValue(Boolean value,
                                      int booleanAnnotationIndex)
Specified by:
setBooleanAnnotationValue in interface loci.formats.meta.MetadataStore

setBinaryOnlyUUID

public void setBinaryOnlyUUID(String uuid)
Specified by:
setBinaryOnlyUUID in interface loci.formats.meta.MetadataStore

setBinaryOnlyMetadataFile

public void setBinaryOnlyMetadataFile(String metadataFile)
Specified by:
setBinaryOnlyMetadataFile in interface loci.formats.meta.MetadataStore

getChannel

public omero.model.Channel getChannel(int imageIndex,
                                      int channelIndex)

setChannelID

public void setChannelID(String id,
                         int imageIndex,
                         int channelIndex)
Specified by:
setChannelID in interface loci.formats.meta.MetadataStore

setChannelAcquisitionMode

public void setChannelAcquisitionMode(ome.xml.model.enums.AcquisitionMode acquisitionMode,
                                      int imageIndex,
                                      int channelIndex)
Specified by:
setChannelAcquisitionMode in interface loci.formats.meta.MetadataStore

setChannelColor

public void setChannelColor(Integer color,
                            int imageIndex,
                            int channelIndex)
Specified by:
setChannelColor in interface loci.formats.meta.MetadataStore

setChannelContrastMethod

public void setChannelContrastMethod(ome.xml.model.enums.ContrastMethod contrastMethod,
                                     int imageIndex,
                                     int channelIndex)
Specified by:
setChannelContrastMethod in interface loci.formats.meta.MetadataStore

setChannelEmissionWavelength

public void setChannelEmissionWavelength(ome.xml.model.primitives.PositiveInteger emissionWavelength,
                                         int imageIndex,
                                         int channelIndex)
Specified by:
setChannelEmissionWavelength in interface loci.formats.meta.MetadataStore

setChannelExcitationWavelength

public void setChannelExcitationWavelength(ome.xml.model.primitives.PositiveInteger excitationWavelength,
                                           int imageIndex,
                                           int channelIndex)
(non-Javadoc)

Specified by:
setChannelExcitationWavelength in interface loci.formats.meta.MetadataStore
See Also:
MetadataStore.setChannelExcitationWavelength(ome.xml.model.primitives.PositiveInteger, int, int)

setChannelFilterSetRef

public void setChannelFilterSetRef(String filterSet,
                                   int imageIndex,
                                   int channelIndex)
Specified by:
setChannelFilterSetRef in interface loci.formats.meta.MetadataStore

setChannelFluor

public void setChannelFluor(String fluor,
                            int imageIndex,
                            int channelIndex)
Specified by:
setChannelFluor in interface loci.formats.meta.MetadataStore

setChannelIlluminationType

public void setChannelIlluminationType(ome.xml.model.enums.IlluminationType illuminationType,
                                       int imageIndex,
                                       int channelIndex)
Specified by:
setChannelIlluminationType in interface loci.formats.meta.MetadataStore

setChannelNDFilter

public void setChannelNDFilter(Double ndfilter,
                               int imageIndex,
                               int channelIndex)
Specified by:
setChannelNDFilter in interface loci.formats.meta.MetadataStore

setChannelName

public void setChannelName(String name,
                           int imageIndex,
                           int channelIndex)
Specified by:
setChannelName in interface loci.formats.meta.MetadataStore

setChannelOTFRef

public void setChannelOTFRef(String otf,
                             int imageIndex,
                             int channelIndex)
Specified by:
setChannelOTFRef in interface loci.formats.meta.MetadataStore

setChannelPinholeSize

public void setChannelPinholeSize(Double pinholeSize,
                                  int imageIndex,
                                  int channelIndex)
Specified by:
setChannelPinholeSize in interface loci.formats.meta.MetadataStore

setChannelPockelCellSetting

public void setChannelPockelCellSetting(Integer pockelCellSetting,
                                        int imageIndex,
                                        int channelIndex)
Specified by:
setChannelPockelCellSetting in interface loci.formats.meta.MetadataStore

setChannelSamplesPerPixel

public void setChannelSamplesPerPixel(ome.xml.model.primitives.PositiveInteger samplesPerPixel,
                                      int imageIndex,
                                      int channelIndex)
Specified by:
setChannelSamplesPerPixel in interface loci.formats.meta.MetadataStore

setChannelAnnotationRef

public void setChannelAnnotationRef(String annotation,
                                    int imageIndex,
                                    int channelIndex,
                                    int annotationRefIndex)
Specified by:
setChannelAnnotationRef in interface loci.formats.meta.MetadataStore

setChannelLightSourceSettingsID

public void setChannelLightSourceSettingsID(String id,
                                            int imageIndex,
                                            int channelIndex)
Specified by:
setChannelLightSourceSettingsID in interface loci.formats.meta.MetadataStore

setChannelLightSourceSettingsAttenuation

public void setChannelLightSourceSettingsAttenuation(ome.xml.model.primitives.PercentFraction attenuation,
                                                     int imageIndex,
                                                     int channelIndex)
Specified by:
setChannelLightSourceSettingsAttenuation in interface loci.formats.meta.MetadataStore

setChannelLightSourceSettingsWavelength

public void setChannelLightSourceSettingsWavelength(ome.xml.model.primitives.PositiveInteger wavelength,
                                                    int imageIndex,
                                                    int channelIndex)
Specified by:
setChannelLightSourceSettingsWavelength in interface loci.formats.meta.MetadataStore

setDatasetID

public void setDatasetID(String id,
                         int datasetIndex)
Specified by:
setDatasetID in interface loci.formats.meta.MetadataStore

setDatasetAnnotationRef

public void setDatasetAnnotationRef(String annotation,
                                    int datasetIndex,
                                    int annotationRefIndex)
Specified by:
setDatasetAnnotationRef in interface loci.formats.meta.MetadataStore

setDatasetDescription

public void setDatasetDescription(String description,
                                  int datasetIndex)
Specified by:
setDatasetDescription in interface loci.formats.meta.MetadataStore

setDatasetExperimenterRef

public void setDatasetExperimenterRef(String experimenter,
                                      int datasetIndex)
Specified by:
setDatasetExperimenterRef in interface loci.formats.meta.MetadataStore

setDatasetGroupRef

public void setDatasetGroupRef(String group,
                               int datasetIndex)
Specified by:
setDatasetGroupRef in interface loci.formats.meta.MetadataStore

setDatasetName

public void setDatasetName(String name,
                           int datasetIndex)
Specified by:
setDatasetName in interface loci.formats.meta.MetadataStore

setDatasetProjectRef

public void setDatasetProjectRef(String project,
                                 int datasetIndex,
                                 int projectRefIndex)
Specified by:
setDatasetProjectRef in interface loci.formats.meta.MetadataStore

getDetector

public omero.model.Detector getDetector(int instrumentIndex,
                                        int detectorIndex)
Parameters:
instrumentIndex -
detectorIndex -
Returns:

setDetectorID

public void setDetectorID(String id,
                          int instrumentIndex,
                          int detectorIndex)
Specified by:
setDetectorID in interface loci.formats.meta.MetadataStore

setDetectorAmplificationGain

public void setDetectorAmplificationGain(Double amplificationGain,
                                         int instrumentIndex,
                                         int detectorIndex)
Specified by:
setDetectorAmplificationGain in interface loci.formats.meta.MetadataStore

setDetectorGain

public void setDetectorGain(Double gain,
                            int instrumentIndex,
                            int detectorIndex)
Specified by:
setDetectorGain in interface loci.formats.meta.MetadataStore

setDetectorLotNumber

public void setDetectorLotNumber(String lotNumber,
                                 int instrumentIndex,
                                 int detectorIndex)
Specified by:
setDetectorLotNumber in interface loci.formats.meta.MetadataStore

setDetectorManufacturer

public void setDetectorManufacturer(String manufacturer,
                                    int instrumentIndex,
                                    int detectorIndex)
Specified by:
setDetectorManufacturer in interface loci.formats.meta.MetadataStore

setDetectorModel

public void setDetectorModel(String model,
                             int instrumentIndex,
                             int detectorIndex)
Specified by:
setDetectorModel in interface loci.formats.meta.MetadataStore

setDetectorOffset

public void setDetectorOffset(Double offset,
                              int instrumentIndex,
                              int detectorIndex)
Specified by:
setDetectorOffset in interface loci.formats.meta.MetadataStore

setDetectorSerialNumber

public void setDetectorSerialNumber(String serialNumber,
                                    int instrumentIndex,
                                    int detectorIndex)
Specified by:
setDetectorSerialNumber in interface loci.formats.meta.MetadataStore

setDetectorType

public void setDetectorType(ome.xml.model.enums.DetectorType type,
                            int instrumentIndex,
                            int detectorIndex)
Specified by:
setDetectorType in interface loci.formats.meta.MetadataStore

setDetectorVoltage

public void setDetectorVoltage(Double voltage,
                               int instrumentIndex,
                               int detectorIndex)
Specified by:
setDetectorVoltage in interface loci.formats.meta.MetadataStore

setDetectorZoom

public void setDetectorZoom(Double zoom,
                            int instrumentIndex,
                            int detectorIndex)
Specified by:
setDetectorZoom in interface loci.formats.meta.MetadataStore

setDetectorSettingsID

public void setDetectorSettingsID(String id,
                                  int imageIndex,
                                  int channelIndex)
Specified by:
setDetectorSettingsID in interface loci.formats.meta.MetadataStore

setDetectorSettingsBinning

public void setDetectorSettingsBinning(ome.xml.model.enums.Binning binning,
                                       int imageIndex,
                                       int channelIndex)
Specified by:
setDetectorSettingsBinning in interface loci.formats.meta.MetadataStore

setDetectorSettingsGain

public void setDetectorSettingsGain(Double gain,
                                    int imageIndex,
                                    int channelIndex)
Specified by:
setDetectorSettingsGain in interface loci.formats.meta.MetadataStore

setDetectorSettingsOffset

public void setDetectorSettingsOffset(Double offset,
                                      int imageIndex,
                                      int channelIndex)
Specified by:
setDetectorSettingsOffset in interface loci.formats.meta.MetadataStore

setDetectorSettingsReadOutRate

public void setDetectorSettingsReadOutRate(Double readOutRate,
                                           int imageIndex,
                                           int channelIndex)
Specified by:
setDetectorSettingsReadOutRate in interface loci.formats.meta.MetadataStore

setDetectorSettingsVoltage

public void setDetectorSettingsVoltage(Double voltage,
                                       int imageIndex,
                                       int channelIndex)
Specified by:
setDetectorSettingsVoltage in interface loci.formats.meta.MetadataStore

setDichroicID

public void setDichroicID(String id,
                          int instrumentIndex,
                          int dichroicIndex)
Specified by:
setDichroicID in interface loci.formats.meta.MetadataStore

setDichroicLotNumber

public void setDichroicLotNumber(String lotNumber,
                                 int instrumentIndex,
                                 int dichroicIndex)
Specified by:
setDichroicLotNumber in interface loci.formats.meta.MetadataStore

setDichroicManufacturer

public void setDichroicManufacturer(String manufacturer,
                                    int instrumentIndex,
                                    int dichroicIndex)
Specified by:
setDichroicManufacturer in interface loci.formats.meta.MetadataStore

setDichroicModel

public void setDichroicModel(String model,
                             int instrumentIndex,
                             int dichroicIndex)
Specified by:
setDichroicModel in interface loci.formats.meta.MetadataStore

setDichroicSerialNumber

public void setDichroicSerialNumber(String serialNumber,
                                    int instrumentIndex,
                                    int dichroicIndex)
Specified by:
setDichroicSerialNumber in interface loci.formats.meta.MetadataStore

setDoubleAnnotationID

public void setDoubleAnnotationID(String id,
                                  int doubleAnnotationIndex)
Specified by:
setDoubleAnnotationID in interface loci.formats.meta.MetadataStore

setDoubleAnnotationNamespace

public void setDoubleAnnotationNamespace(String namespace,
                                         int doubleAnnotationIndex)
Specified by:
setDoubleAnnotationNamespace in interface loci.formats.meta.MetadataStore

setDoubleAnnotationValue

public void setDoubleAnnotationValue(Double value,
                                     int doubleAnnotationIndex)
Specified by:
setDoubleAnnotationValue in interface loci.formats.meta.MetadataStore

setEllipseID

public void setEllipseID(String id,
                         int ROIIndex,
                         int shapeIndex)
Specified by:
setEllipseID in interface loci.formats.meta.MetadataStore

setEllipseDescription

public void setEllipseDescription(String description,
                                  int ROIIndex,
                                  int shapeIndex)
Specified by:
setEllipseDescription in interface loci.formats.meta.MetadataStore

setEllipseFill

public void setEllipseFill(Integer fill,
                           int ROIIndex,
                           int shapeIndex)
Specified by:
setEllipseFill in interface loci.formats.meta.MetadataStore

setEllipseFontSize

public void setEllipseFontSize(ome.xml.model.primitives.NonNegativeInteger fontSize,
                               int ROIIndex,
                               int shapeIndex)
Specified by:
setEllipseFontSize in interface loci.formats.meta.MetadataStore

setEllipseLabel

public void setEllipseLabel(String label,
                            int ROIIndex,
                            int shapeIndex)
Specified by:
setEllipseLabel in interface loci.formats.meta.MetadataStore

setEllipseName

public void setEllipseName(String name,
                           int ROIIndex,
                           int shapeIndex)
Specified by:
setEllipseName in interface loci.formats.meta.MetadataStore

setEllipseRadiusX

public void setEllipseRadiusX(Double radiusX,
                              int ROIIndex,
                              int shapeIndex)
Specified by:
setEllipseRadiusX in interface loci.formats.meta.MetadataStore

setEllipseRadiusY

public void setEllipseRadiusY(Double radiusY,
                              int ROIIndex,
                              int shapeIndex)
Specified by:
setEllipseRadiusY in interface loci.formats.meta.MetadataStore

setEllipseStroke

public void setEllipseStroke(Integer stroke,
                             int ROIIndex,
                             int shapeIndex)
Specified by:
setEllipseStroke in interface loci.formats.meta.MetadataStore

setEllipseStrokeDashArray

public void setEllipseStrokeDashArray(String strokeDashArray,
                                      int ROIIndex,
                                      int shapeIndex)
Specified by:
setEllipseStrokeDashArray in interface loci.formats.meta.MetadataStore

setEllipseStrokeWidth

public void setEllipseStrokeWidth(Double strokeWidth,
                                  int ROIIndex,
                                  int shapeIndex)
Specified by:
setEllipseStrokeWidth in interface loci.formats.meta.MetadataStore

setEllipseTheC

public void setEllipseTheC(ome.xml.model.primitives.NonNegativeInteger theC,
                           int ROIIndex,
                           int shapeIndex)
Specified by:
setEllipseTheC in interface loci.formats.meta.MetadataStore

setEllipseTheT

public void setEllipseTheT(ome.xml.model.primitives.NonNegativeInteger theT,
                           int ROIIndex,
                           int shapeIndex)
Specified by:
setEllipseTheT in interface loci.formats.meta.MetadataStore

setEllipseTheZ

public void setEllipseTheZ(ome.xml.model.primitives.NonNegativeInteger theZ,
                           int ROIIndex,
                           int shapeIndex)
Specified by:
setEllipseTheZ in interface loci.formats.meta.MetadataStore

setEllipseTransform

public void setEllipseTransform(String transform,
                                int ROIIndex,
                                int shapeIndex)
Specified by:
setEllipseTransform in interface loci.formats.meta.MetadataStore

setEllipseX

public void setEllipseX(Double x,
                        int ROIIndex,
                        int shapeIndex)
Specified by:
setEllipseX in interface loci.formats.meta.MetadataStore

setEllipseY

public void setEllipseY(Double y,
                        int ROIIndex,
                        int shapeIndex)
Specified by:
setEllipseY in interface loci.formats.meta.MetadataStore

setExperimentID

public void setExperimentID(String id,
                            int experimentIndex)
Specified by:
setExperimentID in interface loci.formats.meta.MetadataStore

setExperimentDescription

public void setExperimentDescription(String description,
                                     int experimentIndex)
Specified by:
setExperimentDescription in interface loci.formats.meta.MetadataStore

setExperimentExperimenterRef

public void setExperimentExperimenterRef(String experimenter,
                                         int experimentIndex)
Specified by:
setExperimentExperimenterRef in interface loci.formats.meta.MetadataStore

setExperimentType

public void setExperimentType(ome.xml.model.enums.ExperimentType type,
                              int experimentIndex)
Specified by:
setExperimentType in interface loci.formats.meta.MetadataStore

setExperimenterID

public void setExperimenterID(String id,
                              int experimenterIndex)
Specified by:
setExperimenterID in interface loci.formats.meta.MetadataStore

setExperimenterAnnotationRef

public void setExperimenterAnnotationRef(String annotation,
                                         int experimenterIndex,
                                         int annotationRefIndex)
Specified by:
setExperimenterAnnotationRef in interface loci.formats.meta.MetadataStore

setExperimenterDisplayName

public void setExperimenterDisplayName(String displayName,
                                       int experimenterIndex)
Specified by:
setExperimenterDisplayName in interface loci.formats.meta.MetadataStore

setExperimenterEmail

public void setExperimenterEmail(String email,
                                 int experimenterIndex)
Specified by:
setExperimenterEmail in interface loci.formats.meta.MetadataStore

setExperimenterFirstName

public void setExperimenterFirstName(String firstName,
                                     int experimenterIndex)
Specified by:
setExperimenterFirstName in interface loci.formats.meta.MetadataStore

setExperimenterGroupRef

public void setExperimenterGroupRef(String group,
                                    int experimenterIndex,
                                    int groupRefIndex)
Specified by:
setExperimenterGroupRef in interface loci.formats.meta.MetadataStore

setExperimenterInstitution

public void setExperimenterInstitution(String institution,
                                       int experimenterIndex)
Specified by:
setExperimenterInstitution in interface loci.formats.meta.MetadataStore

setExperimenterLastName

public void setExperimenterLastName(String lastName,
                                    int experimenterIndex)
Specified by:
setExperimenterLastName in interface loci.formats.meta.MetadataStore

setExperimenterMiddleName

public void setExperimenterMiddleName(String middleName,
                                      int experimenterIndex)
Specified by:
setExperimenterMiddleName in interface loci.formats.meta.MetadataStore

setExperimenterUserName

public void setExperimenterUserName(String userName,
                                    int experimenterIndex)
Specified by:
setExperimenterUserName in interface loci.formats.meta.MetadataStore

getFilament

public omero.model.Filament getFilament(int instrumentIndex,
                                        int lightSourceIndex)

setFilamentID

public void setFilamentID(String id,
                          int instrumentIndex,
                          int lightSourceIndex)
Specified by:
setFilamentID in interface loci.formats.meta.MetadataStore

setFilamentLotNumber

public void setFilamentLotNumber(String lotNumber,
                                 int instrumentIndex,
                                 int lightSourceIndex)
Specified by:
setFilamentLotNumber in interface loci.formats.meta.MetadataStore

setFilamentManufacturer

public void setFilamentManufacturer(String manufacturer,
                                    int instrumentIndex,
                                    int lightSourceIndex)
Specified by:
setFilamentManufacturer in interface loci.formats.meta.MetadataStore

setFilamentModel

public void setFilamentModel(String model,
                             int instrumentIndex,
                             int lightSourceIndex)
Specified by:
setFilamentModel in interface loci.formats.meta.MetadataStore

setFilamentPower

public void setFilamentPower(Double power,
                             int instrumentIndex,
                             int lightSourceIndex)
Specified by:
setFilamentPower in interface loci.formats.meta.MetadataStore

setFilamentSerialNumber

public void setFilamentSerialNumber(String serialNumber,
                                    int instrumentIndex,
                                    int lightSourceIndex)
Specified by:
setFilamentSerialNumber in interface loci.formats.meta.MetadataStore

setFilamentType

public void setFilamentType(ome.xml.model.enums.FilamentType type,
                            int instrumentIndex,
                            int lightSourceIndex)
Specified by:
setFilamentType in interface loci.formats.meta.MetadataStore

setFileAnnotationID

public void setFileAnnotationID(String id,
                                int fileAnnotationIndex)
Specified by:
setFileAnnotationID in interface loci.formats.meta.MetadataStore

setFileAnnotationNamespace

public void setFileAnnotationNamespace(String namespace,
                                       int fileAnnotationIndex)
Specified by:
setFileAnnotationNamespace in interface loci.formats.meta.MetadataStore

setFileAnnotationBinaryFileFileName

public void setFileAnnotationBinaryFileFileName(String fileName,
                                                int fileAnnotationIndex)
Specified by:
setFileAnnotationBinaryFileFileName in interface loci.formats.meta.MetadataStore

setFileAnnotationBinaryFileMIMEType

public void setFileAnnotationBinaryFileMIMEType(String mimetype,
                                                int fileAnnotationIndex)
Specified by:
setFileAnnotationBinaryFileMIMEType in interface loci.formats.meta.MetadataStore

setFileAnnotationBinaryFileSize

public void setFileAnnotationBinaryFileSize(ome.xml.model.primitives.NonNegativeLong size,
                                            int fileAnnotationIndex)
Specified by:
setFileAnnotationBinaryFileSize in interface loci.formats.meta.MetadataStore

setFilterID

public void setFilterID(String id,
                        int instrumentIndex,
                        int filterIndex)
Specified by:
setFilterID in interface loci.formats.meta.MetadataStore

setFilterFilterWheel

public void setFilterFilterWheel(String filterWheel,
                                 int instrumentIndex,
                                 int filterIndex)
Specified by:
setFilterFilterWheel in interface loci.formats.meta.MetadataStore

setFilterLotNumber

public void setFilterLotNumber(String lotNumber,
                               int instrumentIndex,
                               int filterIndex)
Specified by:
setFilterLotNumber in interface loci.formats.meta.MetadataStore

setFilterManufacturer

public void setFilterManufacturer(String manufacturer,
                                  int instrumentIndex,
                                  int filterIndex)
Specified by:
setFilterManufacturer in interface loci.formats.meta.MetadataStore

setFilterModel

public void setFilterModel(String model,
                           int instrumentIndex,
                           int filterIndex)
Specified by:
setFilterModel in interface loci.formats.meta.MetadataStore

setFilterSerialNumber

public void setFilterSerialNumber(String serialNumber,
                                  int instrumentIndex,
                                  int filterIndex)
Specified by:
setFilterSerialNumber in interface loci.formats.meta.MetadataStore

setFilterType

public void setFilterType(ome.xml.model.enums.FilterType type,
                          int instrumentIndex,
                          int filterIndex)
Specified by:
setFilterType in interface loci.formats.meta.MetadataStore

getFilterSet

public omero.model.FilterSet getFilterSet(int instrumentIndex,
                                          int filterSetIndex)

setFilterSetID

public void setFilterSetID(String id,
                           int instrumentIndex,
                           int filterSetIndex)
Specified by:
setFilterSetID in interface loci.formats.meta.MetadataStore

setFilterSetDichroicRef

public void setFilterSetDichroicRef(String dichroic,
                                    int instrumentIndex,
                                    int filterSetIndex)
Specified by:
setFilterSetDichroicRef in interface loci.formats.meta.MetadataStore

setFilterSetEmissionFilterRef

public void setFilterSetEmissionFilterRef(String emissionFilter,
                                          int instrumentIndex,
                                          int filterSetIndex,
                                          int emissionFilterRefIndex)
Specified by:
setFilterSetEmissionFilterRef in interface loci.formats.meta.MetadataStore

setFilterSetExcitationFilterRef

public void setFilterSetExcitationFilterRef(String excitationFilter,
                                            int instrumentIndex,
                                            int filterSetIndex,
                                            int excitationFilterRefIndex)
Specified by:
setFilterSetExcitationFilterRef in interface loci.formats.meta.MetadataStore

setFilterSetLotNumber

public void setFilterSetLotNumber(String lotNumber,
                                  int instrumentIndex,
                                  int filterSetIndex)
Specified by:
setFilterSetLotNumber in interface loci.formats.meta.MetadataStore

setFilterSetManufacturer

public void setFilterSetManufacturer(String manufacturer,
                                     int instrumentIndex,
                                     int filterSetIndex)
Specified by:
setFilterSetManufacturer in interface loci.formats.meta.MetadataStore

setFilterSetModel

public void setFilterSetModel(String model,
                              int instrumentIndex,
                              int filterSetIndex)
Specified by:
setFilterSetModel in interface loci.formats.meta.MetadataStore

setFilterSetSerialNumber

public void setFilterSetSerialNumber(String serialNumber,
                                     int instrumentIndex,
                                     int filterSetIndex)
Specified by:
setFilterSetSerialNumber in interface loci.formats.meta.MetadataStore

setGroupID

public void setGroupID(String id,
                       int groupIndex)
Specified by:
setGroupID in interface loci.formats.meta.MetadataStore

setGroupContact

public void setGroupContact(String contact,
                            int groupIndex)
Specified by:
setGroupContact in interface loci.formats.meta.MetadataStore

setGroupDescription

public void setGroupDescription(String description,
                                int groupIndex)
Specified by:
setGroupDescription in interface loci.formats.meta.MetadataStore

setGroupLeader

public void setGroupLeader(String leader,
                           int groupIndex)
Specified by:
setGroupLeader in interface loci.formats.meta.MetadataStore

setGroupName

public void setGroupName(String name,
                         int groupIndex)
Specified by:
setGroupName in interface loci.formats.meta.MetadataStore

setImageID

public void setImageID(String id,
                       int imageIndex)
Specified by:
setImageID in interface loci.formats.meta.MetadataStore

setImageAcquiredDate

public void setImageAcquiredDate(String acquiredDate,
                                 int imageIndex)
Specified by:
setImageAcquiredDate in interface loci.formats.meta.MetadataStore

setImageAnnotationRef

public void setImageAnnotationRef(String annotation,
                                  int imageIndex,
                                  int annotationRefIndex)
Specified by:
setImageAnnotationRef in interface loci.formats.meta.MetadataStore

setImageDatasetRef

public void setImageDatasetRef(String dataset,
                               int imageIndex,
                               int datasetRefIndex)
Specified by:
setImageDatasetRef in interface loci.formats.meta.MetadataStore

setImageDescription

public void setImageDescription(String description,
                                int imageIndex)
Specified by:
setImageDescription in interface loci.formats.meta.MetadataStore

setImageExperimentRef

public void setImageExperimentRef(String experiment,
                                  int imageIndex)
Specified by:
setImageExperimentRef in interface loci.formats.meta.MetadataStore

setImageExperimenterRef

public void setImageExperimenterRef(String experimenter,
                                    int imageIndex)
Specified by:
setImageExperimenterRef in interface loci.formats.meta.MetadataStore

setImageGroupRef

public void setImageGroupRef(String group,
                             int imageIndex)
Specified by:
setImageGroupRef in interface loci.formats.meta.MetadataStore

setImageInstrumentRef

public void setImageInstrumentRef(String instrument,
                                  int imageIndex)
Specified by:
setImageInstrumentRef in interface loci.formats.meta.MetadataStore

setImageMicrobeamManipulationRef

public void setImageMicrobeamManipulationRef(String microbeamManipulation,
                                             int imageIndex,
                                             int microbeamManipulationRefIndex)
Specified by:
setImageMicrobeamManipulationRef in interface loci.formats.meta.MetadataStore

setImageName

public void setImageName(String name,
                         int imageIndex)
Specified by:
setImageName in interface loci.formats.meta.MetadataStore

setImageROIRef

public void setImageROIRef(String roi,
                           int imageIndex,
                           int ROIRefIndex)
Specified by:
setImageROIRef in interface loci.formats.meta.MetadataStore

getImageObjectiveSettings

public omero.model.ObjectiveSettings getImageObjectiveSettings(int imageIndex)

setImageObjectiveSettingsID

public void setImageObjectiveSettingsID(String id,
                                        int imageIndex)
Specified by:
setImageObjectiveSettingsID in interface loci.formats.meta.MetadataStore

setImageObjectiveSettingsCorrectionCollar

public void setImageObjectiveSettingsCorrectionCollar(Double correctionCollar,
                                                      int imageIndex)
Specified by:
setImageObjectiveSettingsCorrectionCollar in interface loci.formats.meta.MetadataStore

setImageObjectiveSettingsMedium

public void setImageObjectiveSettingsMedium(ome.xml.model.enums.Medium medium,
                                            int imageIndex)
Specified by:
setImageObjectiveSettingsMedium in interface loci.formats.meta.MetadataStore

setImageObjectiveSettingsRefractiveIndex

public void setImageObjectiveSettingsRefractiveIndex(Double refractiveIndex,
                                                     int imageIndex)
Specified by:
setImageObjectiveSettingsRefractiveIndex in interface loci.formats.meta.MetadataStore

getImagingEnvironment

public omero.model.ImagingEnvironment getImagingEnvironment(int imageIndex)

setImagingEnvironmentAirPressure

public void setImagingEnvironmentAirPressure(Double airPressure,
                                             int imageIndex)
Specified by:
setImagingEnvironmentAirPressure in interface loci.formats.meta.MetadataStore

setImagingEnvironmentCO2Percent

public void setImagingEnvironmentCO2Percent(ome.xml.model.primitives.PercentFraction co2percent,
                                            int imageIndex)
Specified by:
setImagingEnvironmentCO2Percent in interface loci.formats.meta.MetadataStore

setImagingEnvironmentHumidity

public void setImagingEnvironmentHumidity(ome.xml.model.primitives.PercentFraction humidity,
                                          int imageIndex)
Specified by:
setImagingEnvironmentHumidity in interface loci.formats.meta.MetadataStore

setImagingEnvironmentTemperature

public void setImagingEnvironmentTemperature(Double temperature,
                                             int imageIndex)
Specified by:
setImagingEnvironmentTemperature in interface loci.formats.meta.MetadataStore

setInstrumentID

public void setInstrumentID(String id,
                            int instrumentIndex)
Specified by:
setInstrumentID in interface loci.formats.meta.MetadataStore

getLaser

public omero.model.Laser getLaser(int instrumentIndex,
                                  int lightSourceIndex)

setLaserID

public void setLaserID(String id,
                       int instrumentIndex,
                       int lightSourceIndex)
Specified by:
setLaserID in interface loci.formats.meta.MetadataStore

setLaserFrequencyMultiplication

public void setLaserFrequencyMultiplication(ome.xml.model.primitives.PositiveInteger frequencyMultiplication,
                                            int instrumentIndex,
                                            int lightSourceIndex)
Specified by:
setLaserFrequencyMultiplication in interface loci.formats.meta.MetadataStore

setLaserLaserMedium

public void setLaserLaserMedium(ome.xml.model.enums.LaserMedium laserMedium,
                                int instrumentIndex,
                                int lightSourceIndex)
Specified by:
setLaserLaserMedium in interface loci.formats.meta.MetadataStore

setLaserLotNumber

public void setLaserLotNumber(String lotNumber,
                              int instrumentIndex,
                              int lightSourceIndex)
Specified by:
setLaserLotNumber in interface loci.formats.meta.MetadataStore

setLaserManufacturer

public void setLaserManufacturer(String manufacturer,
                                 int instrumentIndex,
                                 int lightSourceIndex)
Specified by:
setLaserManufacturer in interface loci.formats.meta.MetadataStore

setLaserModel

public void setLaserModel(String model,
                          int instrumentIndex,
                          int lightSourceIndex)
Specified by:
setLaserModel in interface loci.formats.meta.MetadataStore

setLaserPockelCell

public void setLaserPockelCell(Boolean pockelCell,
                               int instrumentIndex,
                               int lightSourceIndex)
Specified by:
setLaserPockelCell in interface loci.formats.meta.MetadataStore

setLaserPower

public void setLaserPower(Double power,
                          int instrumentIndex,
                          int lightSourceIndex)
Specified by:
setLaserPower in interface loci.formats.meta.MetadataStore

setLaserPulse

public void setLaserPulse(ome.xml.model.enums.Pulse pulse,
                          int instrumentIndex,
                          int lightSourceIndex)
Specified by:
setLaserPulse in interface loci.formats.meta.MetadataStore

setLaserPump

public void setLaserPump(String pump,
                         int instrumentIndex,
                         int lightSourceIndex)
Specified by:
setLaserPump in interface loci.formats.meta.MetadataStore

setLaserRepetitionRate

public void setLaserRepetitionRate(Double repetitionRate,
                                   int instrumentIndex,
                                   int lightSourceIndex)
Specified by:
setLaserRepetitionRate in interface loci.formats.meta.MetadataStore

setLaserSerialNumber

public void setLaserSerialNumber(String serialNumber,
                                 int instrumentIndex,
                                 int lightSourceIndex)
Specified by:
setLaserSerialNumber in interface loci.formats.meta.MetadataStore

setLaserTuneable

public void setLaserTuneable(Boolean tuneable,
                             int instrumentIndex,
                             int lightSourceIndex)
Specified by:
setLaserTuneable in interface loci.formats.meta.MetadataStore

setLaserType

public void setLaserType(ome.xml.model.enums.LaserType type,
                         int instrumentIndex,
                         int lightSourceIndex)
Specified by:
setLaserType in interface loci.formats.meta.MetadataStore

setLaserWavelength

public void setLaserWavelength(ome.xml.model.primitives.PositiveInteger wavelength,
                               int instrumentIndex,
                               int lightSourceIndex)
Specified by:
setLaserWavelength in interface loci.formats.meta.MetadataStore

getLightEmittingDiode

public omero.model.LightEmittingDiode getLightEmittingDiode(int instrumentIndex,
                                                            int lightSourceIndex)

setLightEmittingDiodeID

public void setLightEmittingDiodeID(String id,
                                    int instrumentIndex,
                                    int lightSourceIndex)
Specified by:
setLightEmittingDiodeID in interface loci.formats.meta.MetadataStore

setLightEmittingDiodeLotNumber

public void setLightEmittingDiodeLotNumber(String lotNumber,
                                           int instrumentIndex,
                                           int lightSourceIndex)
Specified by:
setLightEmittingDiodeLotNumber in interface loci.formats.meta.MetadataStore

setLightEmittingDiodeManufacturer

public void setLightEmittingDiodeManufacturer(String manufacturer,
                                              int instrumentIndex,
                                              int lightSourceIndex)
Specified by:
setLightEmittingDiodeManufacturer in interface loci.formats.meta.MetadataStore

setLightEmittingDiodeModel

public void setLightEmittingDiodeModel(String model,
                                       int instrumentIndex,
                                       int lightSourceIndex)
Specified by:
setLightEmittingDiodeModel in interface loci.formats.meta.MetadataStore

setLightEmittingDiodePower

public void setLightEmittingDiodePower(Double power,
                                       int instrumentIndex,
                                       int lightSourceIndex)
Specified by:
setLightEmittingDiodePower in interface loci.formats.meta.MetadataStore

setLightEmittingDiodeSerialNumber

public void setLightEmittingDiodeSerialNumber(String serialNumber,
                                              int instrumentIndex,
                                              int lightSourceIndex)
Specified by:
setLightEmittingDiodeSerialNumber in interface loci.formats.meta.MetadataStore

setLightPathDichroicRef

public void setLightPathDichroicRef(String dichroic,
                                    int imageIndex,
                                    int channelIndex)
Specified by:
setLightPathDichroicRef in interface loci.formats.meta.MetadataStore

setLightPathEmissionFilterRef

public void setLightPathEmissionFilterRef(String emissionFilter,
                                          int imageIndex,
                                          int channelIndex,
                                          int emissionFilterRefIndex)
Specified by:
setLightPathEmissionFilterRef in interface loci.formats.meta.MetadataStore

setLightPathExcitationFilterRef

public void setLightPathExcitationFilterRef(String excitationFilter,
                                            int imageIndex,
                                            int channelIndex,
                                            int excitationFilterRefIndex)
Specified by:
setLightPathExcitationFilterRef in interface loci.formats.meta.MetadataStore

getLine

public omero.model.Line getLine(int ROIIndex,
                                int shapeIndex)

setLineID

public void setLineID(String id,
                      int ROIIndex,
                      int shapeIndex)
Specified by:
setLineID in interface loci.formats.meta.MetadataStore

setLineDescription

public void setLineDescription(String description,
                               int ROIIndex,
                               int shapeIndex)
Specified by:
setLineDescription in interface loci.formats.meta.MetadataStore

setLineFill

public void setLineFill(Integer fill,
                        int ROIIndex,
                        int shapeIndex)
Specified by:
setLineFill in interface loci.formats.meta.MetadataStore

setLineFontSize

public void setLineFontSize(ome.xml.model.primitives.NonNegativeInteger fontSize,
                            int ROIIndex,
                            int shapeIndex)
Specified by:
setLineFontSize in interface loci.formats.meta.MetadataStore

setLineLabel

public void setLineLabel(String label,
                         int ROIIndex,
                         int shapeIndex)
Specified by:
setLineLabel in interface loci.formats.meta.MetadataStore

setLineName

public void setLineName(String name,
                        int ROIIndex,
                        int shapeIndex)
Specified by:
setLineName in interface loci.formats.meta.MetadataStore

setLineStroke

public void setLineStroke(Integer stroke,
                          int ROIIndex,
                          int shapeIndex)
Specified by:
setLineStroke in interface loci.formats.meta.MetadataStore

setLineStrokeDashArray

public void setLineStrokeDashArray(String strokeDashArray,
                                   int ROIIndex,
                                   int shapeIndex)
Specified by:
setLineStrokeDashArray in interface loci.formats.meta.MetadataStore

setLineStrokeWidth

public void setLineStrokeWidth(Double strokeWidth,
                               int ROIIndex,
                               int shapeIndex)
Specified by:
setLineStrokeWidth in interface loci.formats.meta.MetadataStore

setLineTheC

public void setLineTheC(ome.xml.model.primitives.NonNegativeInteger theC,
                        int ROIIndex,
                        int shapeIndex)
Specified by:
setLineTheC in interface loci.formats.meta.MetadataStore

setLineTheT

public void setLineTheT(ome.xml.model.primitives.NonNegativeInteger theT,
                        int ROIIndex,
                        int shapeIndex)
Specified by:
setLineTheT in interface loci.formats.meta.MetadataStore

setLineTheZ

public void setLineTheZ(ome.xml.model.primitives.NonNegativeInteger theZ,
                        int ROIIndex,
                        int shapeIndex)
Specified by:
setLineTheZ in interface loci.formats.meta.MetadataStore

setLineTransform

public void setLineTransform(String transform,
                             int ROIIndex,
                             int shapeIndex)
Specified by:
setLineTransform in interface loci.formats.meta.MetadataStore

setLineX1

public void setLineX1(Double x1,
                      int ROIIndex,
                      int shapeIndex)
Specified by:
setLineX1 in interface loci.formats.meta.MetadataStore

setLineX2

public void setLineX2(Double x2,
                      int ROIIndex,
                      int shapeIndex)
Specified by:
setLineX2 in interface loci.formats.meta.MetadataStore

setLineY1

public void setLineY1(Double y1,
                      int ROIIndex,
                      int shapeIndex)
Specified by:
setLineY1 in interface loci.formats.meta.MetadataStore

setLineY2

public void setLineY2(Double y2,
                      int ROIIndex,
                      int shapeIndex)
Specified by:
setLineY2 in interface loci.formats.meta.MetadataStore

getListAnnotation

public omero.model.ListAnnotation getListAnnotation(int listAnnotationIndex)

setListAnnotationID

public void setListAnnotationID(String id,
                                int listAnnotationIndex)
Specified by:
setListAnnotationID in interface loci.formats.meta.MetadataStore

setListAnnotationAnnotationRef

public void setListAnnotationAnnotationRef(String annotation,
                                           int listAnnotationIndex,
                                           int annotationRefIndex)
Specified by:
setListAnnotationAnnotationRef in interface loci.formats.meta.MetadataStore

setListAnnotationNamespace

public void setListAnnotationNamespace(String namespace,
                                       int listAnnotationIndex)
Specified by:
setListAnnotationNamespace in interface loci.formats.meta.MetadataStore

getLongAnnotation

public omero.model.LongAnnotation getLongAnnotation(int longAnnotationIndex)

setLongAnnotationID

public void setLongAnnotationID(String id,
                                int longAnnotationIndex)
Specified by:
setLongAnnotationID in interface loci.formats.meta.MetadataStore

setLongAnnotationNamespace

public void setLongAnnotationNamespace(String namespace,
                                       int longAnnotationIndex)
Specified by:
setLongAnnotationNamespace in interface loci.formats.meta.MetadataStore

setLongAnnotationValue

public void setLongAnnotationValue(Long value,
                                   int longAnnotationIndex)
Specified by:
setLongAnnotationValue in interface loci.formats.meta.MetadataStore

getMask

public omero.model.Mask getMask(int ROIIndex,
                                int shapeIndex)

setMaskBinData

public void setMaskBinData(byte[] binData,
                           int roiIndex,
                           int shapeIndex)
Specified by:
setMaskBinData in interface loci.formats.meta.MetadataStore

setMaskDescription

public void setMaskDescription(String description,
                               int ROIIndex,
                               int shapeIndex)
Specified by:
setMaskDescription in interface loci.formats.meta.MetadataStore

setMaskFill

public void setMaskFill(Integer fill,
                        int ROIIndex,
                        int shapeIndex)
Specified by:
setMaskFill in interface loci.formats.meta.MetadataStore

setMaskFontSize

public void setMaskFontSize(ome.xml.model.primitives.NonNegativeInteger fontSize,
                            int ROIIndex,
                            int shapeIndex)
Specified by:
setMaskFontSize in interface loci.formats.meta.MetadataStore

setMaskID

public void setMaskID(String id,
                      int ROIIndex,
                      int shapeIndex)
Specified by:
setMaskID in interface loci.formats.meta.MetadataStore

setMaskLabel

public void setMaskLabel(String label,
                         int ROIIndex,
                         int shapeIndex)
Specified by:
setMaskLabel in interface loci.formats.meta.MetadataStore

setMaskName

public void setMaskName(String name,
                        int ROIIndex,
                        int shapeIndex)
Specified by:
setMaskName in interface loci.formats.meta.MetadataStore

setMaskStroke

public void setMaskStroke(Integer stroke,
                          int ROIIndex,
                          int shapeIndex)
Specified by:
setMaskStroke in interface loci.formats.meta.MetadataStore

setMaskStrokeDashArray

public void setMaskStrokeDashArray(String strokeDashArray,
                                   int ROIIndex,
                                   int shapeIndex)
Specified by:
setMaskStrokeDashArray in interface loci.formats.meta.MetadataStore

setMaskStrokeWidth

public void setMaskStrokeWidth(Double strokeWidth,
                               int ROIIndex,
                               int shapeIndex)
Specified by:
setMaskStrokeWidth in interface loci.formats.meta.MetadataStore

setMaskTheC

public void setMaskTheC(ome.xml.model.primitives.NonNegativeInteger theC,
                        int ROIIndex,
                        int shapeIndex)
Specified by:
setMaskTheC in interface loci.formats.meta.MetadataStore

setMaskTheT

public void setMaskTheT(ome.xml.model.primitives.NonNegativeInteger theT,
                        int ROIIndex,
                        int shapeIndex)
Specified by:
setMaskTheT in interface loci.formats.meta.MetadataStore

setMaskTheZ

public void setMaskTheZ(ome.xml.model.primitives.NonNegativeInteger theZ,
                        int ROIIndex,
                        int shapeIndex)
Specified by:
setMaskTheZ in interface loci.formats.meta.MetadataStore

setMaskTransform

public void setMaskTransform(String transform,
                             int ROIIndex,
                             int shapeIndex)
Specified by:
setMaskTransform in interface loci.formats.meta.MetadataStore

setMaskX

public void setMaskX(Double x,
                     int ROIIndex,
                     int shapeIndex)
Specified by:
setMaskX in interface loci.formats.meta.MetadataStore

setMaskY

public void setMaskY(Double y,
                     int ROIIndex,
                     int shapeIndex)
Specified by:
setMaskY in interface loci.formats.meta.MetadataStore

setMaskHeight

public void setMaskHeight(Double height,
                          int ROIIndex,
                          int shapeIndex)
Specified by:
setMaskHeight in interface loci.formats.meta.MetadataStore

setMaskWidth

public void setMaskWidth(Double width,
                         int ROIIndex,
                         int shapeIndex)
Specified by:
setMaskWidth in interface loci.formats.meta.MetadataStore

getMicrobeamManipulation

public omero.model.MicrobeamManipulation getMicrobeamManipulation(int experimentIndex,
                                                                  int microbeamManipulationIndex)

setMicrobeamManipulationID

public void setMicrobeamManipulationID(String id,
                                       int experimentIndex,
                                       int microbeamManipulationIndex)
Specified by:
setMicrobeamManipulationID in interface loci.formats.meta.MetadataStore

setMicrobeamManipulationDescription

public void setMicrobeamManipulationDescription(String description,
                                                int experimentIndex,
                                                int microbeamManipulationIndex)
Specified by:
setMicrobeamManipulationDescription in interface loci.formats.meta.MetadataStore

setMicrobeamManipulationExperimenterRef

public void setMicrobeamManipulationExperimenterRef(String experimenter,
                                                    int experimentIndex,
                                                    int microbeamManipulationIndex)
Specified by:
setMicrobeamManipulationExperimenterRef in interface loci.formats.meta.MetadataStore

setMicrobeamManipulationROIRef

public void setMicrobeamManipulationROIRef(String roi,
                                           int experimentIndex,
                                           int microbeamManipulationIndex,
                                           int ROIRefIndex)
Specified by:
setMicrobeamManipulationROIRef in interface loci.formats.meta.MetadataStore

setMicrobeamManipulationType

public void setMicrobeamManipulationType(ome.xml.model.enums.MicrobeamManipulationType type,
                                         int experimentIndex,
                                         int microbeamManipulationIndex)
Specified by:
setMicrobeamManipulationType in interface loci.formats.meta.MetadataStore

getMicrobeamManipulationLightSourceSettings

public omero.model.LightSettings getMicrobeamManipulationLightSourceSettings(int experimentIndex,
                                                                             int microbeamManipulationIndex,
                                                                             int lightSourceSettingsIndex)

setMicrobeamManipulationLightSourceSettingsID

public void setMicrobeamManipulationLightSourceSettingsID(String id,
                                                          int experimentIndex,
                                                          int microbeamManipulationIndex,
                                                          int lightSourceSettingsIndex)
Specified by:
setMicrobeamManipulationLightSourceSettingsID in interface loci.formats.meta.MetadataStore

setMicrobeamManipulationLightSourceSettingsAttenuation

public void setMicrobeamManipulationLightSourceSettingsAttenuation(ome.xml.model.primitives.PercentFraction attenuation,
                                                                   int experimentIndex,
                                                                   int microbeamManipulationIndex,
                                                                   int lightSourceSettingsIndex)
Specified by:
setMicrobeamManipulationLightSourceSettingsAttenuation in interface loci.formats.meta.MetadataStore

setMicrobeamManipulationLightSourceSettingsWavelength

public void setMicrobeamManipulationLightSourceSettingsWavelength(ome.xml.model.primitives.PositiveInteger wavelength,
                                                                  int experimentIndex,
                                                                  int microbeamManipulationIndex,
                                                                  int lightSourceSettingsIndex)
Specified by:
setMicrobeamManipulationLightSourceSettingsWavelength in interface loci.formats.meta.MetadataStore

setMicroscopeLotNumber

public void setMicroscopeLotNumber(String lotNumber,
                                   int instrumentIndex)
Specified by:
setMicroscopeLotNumber in interface loci.formats.meta.MetadataStore

setMicroscopeManufacturer

public void setMicroscopeManufacturer(String manufacturer,
                                      int instrumentIndex)
Specified by:
setMicroscopeManufacturer in interface loci.formats.meta.MetadataStore

setMicroscopeModel

public void setMicroscopeModel(String model,
                               int instrumentIndex)
Specified by:
setMicroscopeModel in interface loci.formats.meta.MetadataStore

setMicroscopeSerialNumber

public void setMicroscopeSerialNumber(String serialNumber,
                                      int instrumentIndex)
Specified by:
setMicroscopeSerialNumber in interface loci.formats.meta.MetadataStore

setMicroscopeType

public void setMicroscopeType(ome.xml.model.enums.MicroscopeType type,
                              int instrumentIndex)
Specified by:
setMicroscopeType in interface loci.formats.meta.MetadataStore

getOTF

public omero.model.OTF getOTF(int instrumentIndex,
                              int OTFIndex)

setOTFID

public void setOTFID(String id,
                     int instrumentIndex,
                     int OTFIndex)
Specified by:
setOTFID in interface loci.formats.meta.MetadataStore

setOTFBinaryFileFileName

public void setOTFBinaryFileFileName(String fileName,
                                     int instrumentIndex,
                                     int OTFIndex)
Specified by:
setOTFBinaryFileFileName in interface loci.formats.meta.MetadataStore

setOTFBinaryFileMIMEType

public void setOTFBinaryFileMIMEType(String mimetype,
                                     int instrumentIndex,
                                     int OTFIndex)
Specified by:
setOTFBinaryFileMIMEType in interface loci.formats.meta.MetadataStore

setOTFBinaryFileSize

public void setOTFBinaryFileSize(ome.xml.model.primitives.NonNegativeLong size,
                                 int instrumentIndex,
                                 int OTFIndex)
Specified by:
setOTFBinaryFileSize in interface loci.formats.meta.MetadataStore

setOTFFilterSetRef

public void setOTFFilterSetRef(String filterSet,
                               int instrumentIndex,
                               int OTFIndex)
Specified by:
setOTFFilterSetRef in interface loci.formats.meta.MetadataStore

setOTFOpticalAxisAveraged

public void setOTFOpticalAxisAveraged(Boolean opticalAxisAveraged,
                                      int instrumentIndex,
                                      int OTFIndex)
Specified by:
setOTFOpticalAxisAveraged in interface loci.formats.meta.MetadataStore

setOTFSizeX

public void setOTFSizeX(ome.xml.model.primitives.PositiveInteger sizeX,
                        int instrumentIndex,
                        int OTFIndex)
Specified by:
setOTFSizeX in interface loci.formats.meta.MetadataStore

setOTFSizeY

public void setOTFSizeY(ome.xml.model.primitives.PositiveInteger sizeY,
                        int instrumentIndex,
                        int OTFIndex)
Specified by:
setOTFSizeY in interface loci.formats.meta.MetadataStore

setOTFType

public void setOTFType(ome.xml.model.enums.PixelType type,
                       int instrumentIndex,
                       int OTFIndex)
Specified by:
setOTFType in interface loci.formats.meta.MetadataStore

setOTFObjectiveSettingsID

public void setOTFObjectiveSettingsID(String id,
                                      int instrumentIndex,
                                      int OTFIndex)
Specified by:
setOTFObjectiveSettingsID in interface loci.formats.meta.MetadataStore

setOTFObjectiveSettingsCorrectionCollar

public void setOTFObjectiveSettingsCorrectionCollar(Double correctionCollar,
                                                    int instrumentIndex,
                                                    int OTFIndex)
Specified by:
setOTFObjectiveSettingsCorrectionCollar in interface loci.formats.meta.MetadataStore

setOTFObjectiveSettingsMedium

public void setOTFObjectiveSettingsMedium(ome.xml.model.enums.Medium medium,
                                          int instrumentIndex,
                                          int OTFIndex)
Specified by:
setOTFObjectiveSettingsMedium in interface loci.formats.meta.MetadataStore

setOTFObjectiveSettingsRefractiveIndex

public void setOTFObjectiveSettingsRefractiveIndex(Double refractiveIndex,
                                                   int instrumentIndex,
                                                   int OTFIndex)
Specified by:
setOTFObjectiveSettingsRefractiveIndex in interface loci.formats.meta.MetadataStore

getObjective

public omero.model.Objective getObjective(int instrumentIndex,
                                          int objectiveIndex)

setObjectiveCalibratedMagnification

public void setObjectiveCalibratedMagnification(Double calibratedMagnification,
                                                int instrumentIndex,
                                                int objectiveIndex)
Specified by:
setObjectiveCalibratedMagnification in interface loci.formats.meta.MetadataStore

setObjectiveCorrection

public void setObjectiveCorrection(ome.xml.model.enums.Correction correction,
                                   int instrumentIndex,
                                   int objectiveIndex)
Specified by:
setObjectiveCorrection in interface loci.formats.meta.MetadataStore

setObjectiveID

public void setObjectiveID(String id,
                           int instrumentIndex,
                           int objectiveIndex)
Specified by:
setObjectiveID in interface loci.formats.meta.MetadataStore

setObjectiveImmersion

public void setObjectiveImmersion(ome.xml.model.enums.Immersion immersion,
                                  int instrumentIndex,
                                  int objectiveIndex)
Specified by:
setObjectiveImmersion in interface loci.formats.meta.MetadataStore

setObjectiveIris

public void setObjectiveIris(Boolean iris,
                             int instrumentIndex,
                             int objectiveIndex)
Specified by:
setObjectiveIris in interface loci.formats.meta.MetadataStore

setObjectiveLensNA

public void setObjectiveLensNA(Double lensNA,
                               int instrumentIndex,
                               int objectiveIndex)
Specified by:
setObjectiveLensNA in interface loci.formats.meta.MetadataStore

setObjectiveLotNumber

public void setObjectiveLotNumber(String lotNumber,
                                  int instrumentIndex,
                                  int objectiveIndex)
Specified by:
setObjectiveLotNumber in interface loci.formats.meta.MetadataStore

setObjectiveManufacturer

public void setObjectiveManufacturer(String manufacturer,
                                     int instrumentIndex,
                                     int objectiveIndex)
Specified by:
setObjectiveManufacturer in interface loci.formats.meta.MetadataStore

setObjectiveModel

public void setObjectiveModel(String model,
                              int instrumentIndex,
                              int objectiveIndex)
Specified by:
setObjectiveModel in interface loci.formats.meta.MetadataStore

setObjectiveNominalMagnification

public void setObjectiveNominalMagnification(ome.xml.model.primitives.PositiveInteger nominalMagnification,
                                             int instrumentIndex,
                                             int objectiveIndex)
Specified by:
setObjectiveNominalMagnification in interface loci.formats.meta.MetadataStore

setObjectiveSerialNumber

public void setObjectiveSerialNumber(String serialNumber,
                                     int instrumentIndex,
                                     int objectiveIndex)
Specified by:
setObjectiveSerialNumber in interface loci.formats.meta.MetadataStore

setObjectiveWorkingDistance

public void setObjectiveWorkingDistance(Double workingDistance,
                                        int instrumentIndex,
                                        int objectiveIndex)
Specified by:
setObjectiveWorkingDistance in interface loci.formats.meta.MetadataStore

setPathDefinition

public void setPathDefinition(String definition,
                              int ROIIndex,
                              int shapeIndex)
Specified by:
setPathDefinition in interface loci.formats.meta.MetadataStore

setPathDescription

public void setPathDescription(String description,
                               int ROIIndex,
                               int shapeIndex)
Specified by:
setPathDescription in interface loci.formats.meta.MetadataStore

setPathFill

public void setPathFill(Integer fill,
                        int ROIIndex,
                        int shapeIndex)
Specified by:
setPathFill in interface loci.formats.meta.MetadataStore

setPathFontSize

public void setPathFontSize(ome.xml.model.primitives.NonNegativeInteger fontSize,
                            int ROIIndex,
                            int shapeIndex)
Specified by:
setPathFontSize in interface loci.formats.meta.MetadataStore

setPathID

public void setPathID(String id,
                      int ROIIndex,
                      int shapeIndex)
Specified by:
setPathID in interface loci.formats.meta.MetadataStore

setPathLabel

public void setPathLabel(String label,
                         int ROIIndex,
                         int shapeIndex)
Specified by:
setPathLabel in interface loci.formats.meta.MetadataStore

setPathName

public void setPathName(String name,
                        int ROIIndex,
                        int shapeIndex)
Specified by:
setPathName in interface loci.formats.meta.MetadataStore

setPathStroke

public void setPathStroke(Integer stroke,
                          int ROIIndex,
                          int shapeIndex)
Specified by:
setPathStroke in interface loci.formats.meta.MetadataStore

setPathStrokeDashArray

public void setPathStrokeDashArray(String strokeDashArray,
                                   int ROIIndex,
                                   int shapeIndex)
Specified by:
setPathStrokeDashArray in interface loci.formats.meta.MetadataStore

setPathStrokeWidth

public void setPathStrokeWidth(Double strokeWidth,
                               int ROIIndex,
                               int shapeIndex)
Specified by:
setPathStrokeWidth in interface loci.formats.meta.MetadataStore

setPathTheC

public void setPathTheC(ome.xml.model.primitives.NonNegativeInteger theC,
                        int ROIIndex,
                        int shapeIndex)
Specified by:
setPathTheC in interface loci.formats.meta.MetadataStore

setPathTheT

public void setPathTheT(ome.xml.model.primitives.NonNegativeInteger theT,
                        int ROIIndex,
                        int shapeIndex)
Specified by:
setPathTheT in interface loci.formats.meta.MetadataStore

setPathTheZ

public void setPathTheZ(ome.xml.model.primitives.NonNegativeInteger theZ,
                        int ROIIndex,
                        int shapeIndex)
Specified by:
setPathTheZ in interface loci.formats.meta.MetadataStore

setPathTransform

public void setPathTransform(String transform,
                             int ROIIndex,
                             int shapeIndex)
Specified by:
setPathTransform in interface loci.formats.meta.MetadataStore

setPixelsID

public void setPixelsID(String id,
                        int imageIndex)
Specified by:
setPixelsID in interface loci.formats.meta.MetadataStore

setPixelsAnnotationRef

public void setPixelsAnnotationRef(String annotation,
                                   int imageIndex,
                                   int annotationRefIndex)
Specified by:
setPixelsAnnotationRef in interface loci.formats.meta.MetadataStore

setPixelsBinDataBigEndian

public void setPixelsBinDataBigEndian(Boolean bigEndian,
                                      int imageIndex,
                                      int binDataIndex)
Specified by:
setPixelsBinDataBigEndian in interface loci.formats.meta.MetadataStore

setPixelsDimensionOrder

public void setPixelsDimensionOrder(ome.xml.model.enums.DimensionOrder dimensionOrder,
                                    int imageIndex)
Specified by:
setPixelsDimensionOrder in interface loci.formats.meta.MetadataStore

setPixelsPhysicalSizeX

public void setPixelsPhysicalSizeX(ome.xml.model.primitives.PositiveFloat physicalSizeX,
                                   int imageIndex)
Specified by:
setPixelsPhysicalSizeX in interface loci.formats.meta.MetadataStore

setPixelsPhysicalSizeY

public void setPixelsPhysicalSizeY(ome.xml.model.primitives.PositiveFloat physicalSizeY,
                                   int imageIndex)
Specified by:
setPixelsPhysicalSizeY in interface loci.formats.meta.MetadataStore

setPixelsPhysicalSizeZ

public void setPixelsPhysicalSizeZ(ome.xml.model.primitives.PositiveFloat physicalSizeZ,
                                   int imageIndex)
Specified by:
setPixelsPhysicalSizeZ in interface loci.formats.meta.MetadataStore

setPixelsSizeC

public void setPixelsSizeC(ome.xml.model.primitives.PositiveInteger sizeC,
                           int imageIndex)
Specified by:
setPixelsSizeC in interface loci.formats.meta.MetadataStore

setPixelsSizeT

public void setPixelsSizeT(ome.xml.model.primitives.PositiveInteger sizeT,
                           int imageIndex)
Specified by:
setPixelsSizeT in interface loci.formats.meta.MetadataStore

setPixelsSizeX

public void setPixelsSizeX(ome.xml.model.primitives.PositiveInteger sizeX,
                           int imageIndex)
Specified by:
setPixelsSizeX in interface loci.formats.meta.MetadataStore

setPixelsSizeY

public void setPixelsSizeY(ome.xml.model.primitives.PositiveInteger sizeY,
                           int imageIndex)
Specified by:
setPixelsSizeY in interface loci.formats.meta.MetadataStore

setPixelsSizeZ

public void setPixelsSizeZ(ome.xml.model.primitives.PositiveInteger sizeZ,
                           int imageIndex)
Specified by:
setPixelsSizeZ in interface loci.formats.meta.MetadataStore

setPixelsTimeIncrement

public void setPixelsTimeIncrement(Double timeIncrement,
                                   int imageIndex)
Specified by:
setPixelsTimeIncrement in interface loci.formats.meta.MetadataStore

setPixelsType

public void setPixelsType(ome.xml.model.enums.PixelType type,
                          int imageIndex)
Specified by:
setPixelsType in interface loci.formats.meta.MetadataStore

setPlaneAnnotationRef

public void setPlaneAnnotationRef(String annotation,
                                  int imageIndex,
                                  int planeIndex,
                                  int annotationRefIndex)
Specified by:
setPlaneAnnotationRef in interface loci.formats.meta.MetadataStore

setPlaneDeltaT

public void setPlaneDeltaT(Double deltaT,
                           int imageIndex,
                           int planeIndex)
Specified by:
setPlaneDeltaT in interface loci.formats.meta.MetadataStore

setPlaneExposureTime

public void setPlaneExposureTime(Double exposureTime,
                                 int imageIndex,
                                 int planeIndex)
Specified by:
setPlaneExposureTime in interface loci.formats.meta.MetadataStore

setPlaneHashSHA1

public void setPlaneHashSHA1(String hashSHA1,
                             int imageIndex,
                             int planeIndex)
Specified by:
setPlaneHashSHA1 in interface loci.formats.meta.MetadataStore

setPlanePositionX

public void setPlanePositionX(Double positionX,
                              int imageIndex,
                              int planeIndex)
Specified by:
setPlanePositionX in interface loci.formats.meta.MetadataStore

setPlanePositionY

public void setPlanePositionY(Double positionY,
                              int imageIndex,
                              int planeIndex)
Specified by:
setPlanePositionY in interface loci.formats.meta.MetadataStore

setPlanePositionZ

public void setPlanePositionZ(Double positionZ,
                              int imageIndex,
                              int planeIndex)
Specified by:
setPlanePositionZ in interface loci.formats.meta.MetadataStore

setPlaneTheC

public void setPlaneTheC(ome.xml.model.primitives.NonNegativeInteger theC,
                         int imageIndex,
                         int planeIndex)
Specified by:
setPlaneTheC in interface loci.formats.meta.MetadataStore

setPlaneTheT

public void setPlaneTheT(ome.xml.model.primitives.NonNegativeInteger theT,
                         int imageIndex,
                         int planeIndex)
Specified by:
setPlaneTheT in interface loci.formats.meta.MetadataStore

setPlaneTheZ

public void setPlaneTheZ(ome.xml.model.primitives.NonNegativeInteger theZ,
                         int imageIndex,
                         int planeIndex)
Specified by:
setPlaneTheZ in interface loci.formats.meta.MetadataStore

setPlateAcquisitionAnnotationRef

public void setPlateAcquisitionAnnotationRef(String annotation,
                                             int plateIndex,
                                             int plateAcquisitionIndex,
                                             int annotationRefIndex)
Specified by:
setPlateAcquisitionAnnotationRef in interface loci.formats.meta.MetadataStore

setPlateAcquisitionDescription

public void setPlateAcquisitionDescription(String description,
                                           int plateIndex,
                                           int plateAcquisitionIndex)
Specified by:
setPlateAcquisitionDescription in interface loci.formats.meta.MetadataStore

setPlateAcquisitionEndTime

public void setPlateAcquisitionEndTime(String endTime,
                                       int plateIndex,
                                       int plateAcquisitionIndex)
Specified by:
setPlateAcquisitionEndTime in interface loci.formats.meta.MetadataStore

setPlateAcquisitionID

public void setPlateAcquisitionID(String id,
                                  int plateIndex,
                                  int plateAcquisitionIndex)
Specified by:
setPlateAcquisitionID in interface loci.formats.meta.MetadataStore

setPlateAcquisitionMaximumFieldCount

public void setPlateAcquisitionMaximumFieldCount(ome.xml.model.primitives.PositiveInteger maximumFieldCount,
                                                 int plateIndex,
                                                 int plateAcquisitionIndex)
Specified by:
setPlateAcquisitionMaximumFieldCount in interface loci.formats.meta.MetadataStore

setPlateAcquisitionName

public void setPlateAcquisitionName(String name,
                                    int plateIndex,
                                    int plateAcquisitionIndex)
Specified by:
setPlateAcquisitionName in interface loci.formats.meta.MetadataStore

setPlateAcquisitionStartTime

public void setPlateAcquisitionStartTime(String startTime,
                                         int plateIndex,
                                         int plateAcquisitionIndex)
Specified by:
setPlateAcquisitionStartTime in interface loci.formats.meta.MetadataStore

setPlateAcquisitionWellSampleRef

public void setPlateAcquisitionWellSampleRef(String wellSample,
                                             int plateIndex,
                                             int plateAcquisitionIndex,
                                             int wellSampleRefIndex)
Specified by:
setPlateAcquisitionWellSampleRef in interface loci.formats.meta.MetadataStore

setPlateAnnotationRef

public void setPlateAnnotationRef(String annotation,
                                  int plateIndex,
                                  int annotationRefIndex)
Specified by:
setPlateAnnotationRef in interface loci.formats.meta.MetadataStore

setPlateColumnNamingConvention

public void setPlateColumnNamingConvention(ome.xml.model.enums.NamingConvention columnNamingConvention,
                                           int plateIndex)
Specified by:
setPlateColumnNamingConvention in interface loci.formats.meta.MetadataStore

setPlateColumns

public void setPlateColumns(ome.xml.model.primitives.PositiveInteger columns,
                            int plateIndex)
Specified by:
setPlateColumns in interface loci.formats.meta.MetadataStore

setPlateDescription

public void setPlateDescription(String description,
                                int plateIndex)
Specified by:
setPlateDescription in interface loci.formats.meta.MetadataStore

setPlateExternalIdentifier

public void setPlateExternalIdentifier(String externalIdentifier,
                                       int plateIndex)
Specified by:
setPlateExternalIdentifier in interface loci.formats.meta.MetadataStore

setPlateID

public void setPlateID(String id,
                       int plateIndex)
Specified by:
setPlateID in interface loci.formats.meta.MetadataStore

setPlateName

public void setPlateName(String name,
                         int plateIndex)
Specified by:
setPlateName in interface loci.formats.meta.MetadataStore

setPlateRowNamingConvention

public void setPlateRowNamingConvention(ome.xml.model.enums.NamingConvention rowNamingConvention,
                                        int plateIndex)
Specified by:
setPlateRowNamingConvention in interface loci.formats.meta.MetadataStore

setPlateRows

public void setPlateRows(ome.xml.model.primitives.PositiveInteger rows,
                         int plateIndex)
Specified by:
setPlateRows in interface loci.formats.meta.MetadataStore

setPlateScreenRef

public void setPlateScreenRef(String screen,
                              int plateIndex,
                              int screenRefIndex)
Specified by:
setPlateScreenRef in interface loci.formats.meta.MetadataStore

setPlateStatus

public void setPlateStatus(String status,
                           int plateIndex)
Specified by:
setPlateStatus in interface loci.formats.meta.MetadataStore

setPlateWellOriginX

public void setPlateWellOriginX(Double wellOriginX,
                                int plateIndex)
Specified by:
setPlateWellOriginX in interface loci.formats.meta.MetadataStore

setPlateWellOriginY

public void setPlateWellOriginY(Double wellOriginY,
                                int plateIndex)
Specified by:
setPlateWellOriginY in interface loci.formats.meta.MetadataStore

setPointDescription

public void setPointDescription(String description,
                                int ROIIndex,
                                int shapeIndex)
Specified by:
setPointDescription in interface loci.formats.meta.MetadataStore

setPointFill

public void setPointFill(Integer fill,
                         int ROIIndex,
                         int shapeIndex)
Specified by:
setPointFill in interface loci.formats.meta.MetadataStore

setPointFontSize

public void setPointFontSize(ome.xml.model.primitives.NonNegativeInteger fontSize,
                             int ROIIndex,
                             int shapeIndex)
Specified by:
setPointFontSize in interface loci.formats.meta.MetadataStore

setPointID

public void setPointID(String id,
                       int ROIIndex,
                       int shapeIndex)
Specified by:
setPointID in interface loci.formats.meta.MetadataStore

setPointLabel

public void setPointLabel(String label,
                          int ROIIndex,
                          int shapeIndex)
Specified by:
setPointLabel in interface loci.formats.meta.MetadataStore

setPointName

public void setPointName(String name,
                         int ROIIndex,
                         int shapeIndex)
Specified by:
setPointName in interface loci.formats.meta.MetadataStore

setPointStroke

public void setPointStroke(Integer stroke,
                           int ROIIndex,
                           int shapeIndex)
Specified by:
setPointStroke in interface loci.formats.meta.MetadataStore

setPointStrokeDashArray

public void setPointStrokeDashArray(String strokeDashArray,
                                    int ROIIndex,
                                    int shapeIndex)
Specified by:
setPointStrokeDashArray in interface loci.formats.meta.MetadataStore

setPointStrokeWidth

public void setPointStrokeWidth(Double strokeWidth,
                                int ROIIndex,
                                int shapeIndex)
Specified by:
setPointStrokeWidth in interface loci.formats.meta.MetadataStore

setPointTheC

public void setPointTheC(ome.xml.model.primitives.NonNegativeInteger theC,
                         int ROIIndex,
                         int shapeIndex)
Specified by:
setPointTheC in interface loci.formats.meta.MetadataStore

setPointTheT

public void setPointTheT(ome.xml.model.primitives.NonNegativeInteger theT,
                         int ROIIndex,
                         int shapeIndex)
Specified by:
setPointTheT in interface loci.formats.meta.MetadataStore

setPointTheZ

public void setPointTheZ(ome.xml.model.primitives.NonNegativeInteger theZ,
                         int ROIIndex,
                         int shapeIndex)
Specified by:
setPointTheZ in interface loci.formats.meta.MetadataStore

setPointTransform

public void setPointTransform(String transform,
                              int ROIIndex,
                              int shapeIndex)
Specified by:
setPointTransform in interface loci.formats.meta.MetadataStore

setPointX

public void setPointX(Double x,
                      int ROIIndex,
                      int shapeIndex)
Specified by:
setPointX in interface loci.formats.meta.MetadataStore

setPointY

public void setPointY(Double y,
                      int ROIIndex,
                      int shapeIndex)
Specified by:
setPointY in interface loci.formats.meta.MetadataStore

setPolylineID

public void setPolylineID(String id,
                          int ROIIndex,
                          int shapeIndex)
Specified by:
setPolylineID in interface loci.formats.meta.MetadataStore

setPolylineClosed

public void setPolylineClosed(Boolean closed,
                              int ROIIndex,
                              int shapeIndex)
Specified by:
setPolylineClosed in interface loci.formats.meta.MetadataStore

setPolylineDescription

public void setPolylineDescription(String description,
                                   int ROIIndex,
                                   int shapeIndex)
Specified by:
setPolylineDescription in interface loci.formats.meta.MetadataStore

setPolylineFill

public void setPolylineFill(Integer fill,
                            int ROIIndex,
                            int shapeIndex)
Specified by:
setPolylineFill in interface loci.formats.meta.MetadataStore

setPolylineFontSize

public void setPolylineFontSize(ome.xml.model.primitives.NonNegativeInteger fontSize,
                                int ROIIndex,
                                int shapeIndex)
Specified by:
setPolylineFontSize in interface loci.formats.meta.MetadataStore

setPolylineLabel

public void setPolylineLabel(String label,
                             int ROIIndex,
                             int shapeIndex)
Specified by:
setPolylineLabel in interface loci.formats.meta.MetadataStore

setPolylineName

public void setPolylineName(String name,
                            int ROIIndex,
                            int shapeIndex)
Specified by:
setPolylineName in interface loci.formats.meta.MetadataStore

setPolylinePoints

public void setPolylinePoints(String points,
                              int ROIIndex,
                              int shapeIndex)
Specified by:
setPolylinePoints in interface loci.formats.meta.MetadataStore

setPolylineStroke

public void setPolylineStroke(Integer stroke,
                              int ROIIndex,
                              int shapeIndex)
Specified by:
setPolylineStroke in interface loci.formats.meta.MetadataStore

setPolylineStrokeDashArray

public void setPolylineStrokeDashArray(String strokeDashArray,
                                       int ROIIndex,
                                       int shapeIndex)
Specified by:
setPolylineStrokeDashArray in interface loci.formats.meta.MetadataStore

setPolylineStrokeWidth

public void setPolylineStrokeWidth(Double strokeWidth,
                                   int ROIIndex,
                                   int shapeIndex)
Specified by:
setPolylineStrokeWidth in interface loci.formats.meta.MetadataStore

setPolylineTheC

public void setPolylineTheC(ome.xml.model.primitives.NonNegativeInteger theC,
                            int ROIIndex,
                            int shapeIndex)
Specified by:
setPolylineTheC in interface loci.formats.meta.MetadataStore

setPolylineTheT

public void setPolylineTheT(ome.xml.model.primitives.NonNegativeInteger theT,
                            int ROIIndex,
                            int shapeIndex)
Specified by:
setPolylineTheT in interface loci.formats.meta.MetadataStore

setPolylineTheZ

public void setPolylineTheZ(ome.xml.model.primitives.NonNegativeInteger theZ,
                            int ROIIndex,
                            int shapeIndex)
Specified by:
setPolylineTheZ in interface loci.formats.meta.MetadataStore

setPolylineTransform

public void setPolylineTransform(String transform,
                                 int ROIIndex,
                                 int shapeIndex)
Specified by:
setPolylineTransform in interface loci.formats.meta.MetadataStore

setProjectID

public void setProjectID(String id,
                         int projectIndex)
Specified by:
setProjectID in interface loci.formats.meta.MetadataStore

setProjectAnnotationRef

public void setProjectAnnotationRef(String annotation,
                                    int projectIndex,
                                    int annotationRefIndex)
Specified by:
setProjectAnnotationRef in interface loci.formats.meta.MetadataStore

setProjectDescription

public void setProjectDescription(String description,
                                  int projectIndex)
Specified by:
setProjectDescription in interface loci.formats.meta.MetadataStore

setProjectExperimenterRef

public void setProjectExperimenterRef(String experimenter,
                                      int projectIndex)
Specified by:
setProjectExperimenterRef in interface loci.formats.meta.MetadataStore

setProjectGroupRef

public void setProjectGroupRef(String group,
                               int projectIndex)
Specified by:
setProjectGroupRef in interface loci.formats.meta.MetadataStore

setProjectName

public void setProjectName(String name,
                           int projectIndex)
Specified by:
setProjectName in interface loci.formats.meta.MetadataStore

setROIID

public void setROIID(String id,
                     int ROIIndex)
Specified by:
setROIID in interface loci.formats.meta.MetadataStore

setROIAnnotationRef

public void setROIAnnotationRef(String annotation,
                                int ROIIndex,
                                int annotationRefIndex)
Specified by:
setROIAnnotationRef in interface loci.formats.meta.MetadataStore

setROIDescription

public void setROIDescription(String description,
                              int ROIIndex)
Specified by:
setROIDescription in interface loci.formats.meta.MetadataStore

setROIName

public void setROIName(String name,
                       int ROIIndex)
Specified by:
setROIName in interface loci.formats.meta.MetadataStore

setROINamespace

public void setROINamespace(String namespace,
                            int ROIIndex)
Specified by:
setROINamespace in interface loci.formats.meta.MetadataStore

setReagentID

public void setReagentID(String id,
                         int screenIndex,
                         int reagentIndex)
Specified by:
setReagentID in interface loci.formats.meta.MetadataStore

setReagentAnnotationRef

public void setReagentAnnotationRef(String annotation,
                                    int screenIndex,
                                    int reagentIndex,
                                    int annotationRefIndex)
Specified by:
setReagentAnnotationRef in interface loci.formats.meta.MetadataStore

setReagentDescription

public void setReagentDescription(String description,
                                  int screenIndex,
                                  int reagentIndex)
Specified by:
setReagentDescription in interface loci.formats.meta.MetadataStore

setReagentName

public void setReagentName(String name,
                           int screenIndex,
                           int reagentIndex)
Specified by:
setReagentName in interface loci.formats.meta.MetadataStore

setReagentReagentIdentifier

public void setReagentReagentIdentifier(String reagentIdentifier,
                                        int screenIndex,
                                        int reagentIndex)
Specified by:
setReagentReagentIdentifier in interface loci.formats.meta.MetadataStore

setRectangleID

public void setRectangleID(String id,
                           int ROIIndex,
                           int shapeIndex)
Specified by:
setRectangleID in interface loci.formats.meta.MetadataStore

setRectangleDescription

public void setRectangleDescription(String description,
                                    int ROIIndex,
                                    int shapeIndex)
Specified by:
setRectangleDescription in interface loci.formats.meta.MetadataStore

setRectangleFill

public void setRectangleFill(Integer fill,
                             int ROIIndex,
                             int shapeIndex)
Specified by:
setRectangleFill in interface loci.formats.meta.MetadataStore

setRectangleFontSize

public void setRectangleFontSize(ome.xml.model.primitives.NonNegativeInteger fontSize,
                                 int ROIIndex,
                                 int shapeIndex)
Specified by:
setRectangleFontSize in interface loci.formats.meta.MetadataStore

setRectangleHeight

public void setRectangleHeight(Double height,
                               int ROIIndex,
                               int shapeIndex)
Specified by:
setRectangleHeight in interface loci.formats.meta.MetadataStore

setRectangleLabel

public void setRectangleLabel(String label,
                              int ROIIndex,
                              int shapeIndex)
Specified by:
setRectangleLabel in interface loci.formats.meta.MetadataStore

setRectangleName

public void setRectangleName(String name,
                             int ROIIndex,
                             int shapeIndex)
Specified by:
setRectangleName in interface loci.formats.meta.MetadataStore

setRectangleStroke

public void setRectangleStroke(Integer stroke,
                               int ROIIndex,
                               int shapeIndex)
Specified by:
setRectangleStroke in interface loci.formats.meta.MetadataStore

setRectangleStrokeDashArray

public void setRectangleStrokeDashArray(String strokeDashArray,
                                        int ROIIndex,
                                        int shapeIndex)
Specified by:
setRectangleStrokeDashArray in interface loci.formats.meta.MetadataStore

setRectangleStrokeWidth

public void setRectangleStrokeWidth(Double strokeWidth,
                                    int ROIIndex,
                                    int shapeIndex)
Specified by:
setRectangleStrokeWidth in interface loci.formats.meta.MetadataStore

setRectangleTheC

public void setRectangleTheC(ome.xml.model.primitives.NonNegativeInteger theC,
                             int ROIIndex,
                             int shapeIndex)
Specified by:
setRectangleTheC in interface loci.formats.meta.MetadataStore

setRectangleTheT

public void setRectangleTheT(ome.xml.model.primitives.NonNegativeInteger theT,
                             int ROIIndex,
                             int shapeIndex)
Specified by:
setRectangleTheT in interface loci.formats.meta.MetadataStore

setRectangleTheZ

public void setRectangleTheZ(ome.xml.model.primitives.NonNegativeInteger theZ,
                             int ROIIndex,
                             int shapeIndex)
Specified by:
setRectangleTheZ in interface loci.formats.meta.MetadataStore

setRectangleTransform

public void setRectangleTransform(String transform,
                                  int ROIIndex,
                                  int shapeIndex)
Specified by:
setRectangleTransform in interface loci.formats.meta.MetadataStore

setRectangleWidth

public void setRectangleWidth(Double width,
                              int ROIIndex,
                              int shapeIndex)
Specified by:
setRectangleWidth in interface loci.formats.meta.MetadataStore

setRectangleX

public void setRectangleX(Double x,
                          int ROIIndex,
                          int shapeIndex)
Specified by:
setRectangleX in interface loci.formats.meta.MetadataStore

setRectangleY

public void setRectangleY(Double y,
                          int ROIIndex,
                          int shapeIndex)
Specified by:
setRectangleY in interface loci.formats.meta.MetadataStore

setRoot

public void setRoot(Object root)
Specified by:
setRoot in interface loci.formats.meta.MetadataStore

setScreenID

public void setScreenID(String id,
                        int screenIndex)
Specified by:
setScreenID in interface loci.formats.meta.MetadataStore

setScreenAnnotationRef

public void setScreenAnnotationRef(String annotation,
                                   int screenIndex,
                                   int annotationRefIndex)
Specified by:
setScreenAnnotationRef in interface loci.formats.meta.MetadataStore

setScreenDescription

public void setScreenDescription(String description,
                                 int screenIndex)
Specified by:
setScreenDescription in interface loci.formats.meta.MetadataStore

setScreenName

public void setScreenName(String name,
                          int screenIndex)
Specified by:
setScreenName in interface loci.formats.meta.MetadataStore

setScreenPlateRef

public void setScreenPlateRef(String plate,
                              int screenIndex,
                              int plateRefIndex)
Specified by:
setScreenPlateRef in interface loci.formats.meta.MetadataStore

setScreenProtocolDescription

public void setScreenProtocolDescription(String protocolDescription,
                                         int screenIndex)
Specified by:
setScreenProtocolDescription in interface loci.formats.meta.MetadataStore

setScreenProtocolIdentifier

public void setScreenProtocolIdentifier(String protocolIdentifier,
                                        int screenIndex)
Specified by:
setScreenProtocolIdentifier in interface loci.formats.meta.MetadataStore

setScreenReagentSetDescription

public void setScreenReagentSetDescription(String reagentSetDescription,
                                           int screenIndex)
Specified by:
setScreenReagentSetDescription in interface loci.formats.meta.MetadataStore

setScreenReagentSetIdentifier

public void setScreenReagentSetIdentifier(String reagentSetIdentifier,
                                          int screenIndex)
Specified by:
setScreenReagentSetIdentifier in interface loci.formats.meta.MetadataStore

setScreenType

public void setScreenType(String type,
                          int screenIndex)
Specified by:
setScreenType in interface loci.formats.meta.MetadataStore

setStageLabelName

public void setStageLabelName(String name,
                              int imageIndex)
Specified by:
setStageLabelName in interface loci.formats.meta.MetadataStore

setStageLabelX

public void setStageLabelX(Double x,
                           int imageIndex)
Specified by:
setStageLabelX in interface loci.formats.meta.MetadataStore

setStageLabelY

public void setStageLabelY(Double y,
                           int imageIndex)
Specified by:
setStageLabelY in interface loci.formats.meta.MetadataStore

setStageLabelZ

public void setStageLabelZ(Double z,
                           int imageIndex)
Specified by:
setStageLabelZ in interface loci.formats.meta.MetadataStore

setCommentAnnotationID

public void setCommentAnnotationID(String id,
                                   int commentAnnotationIndex)
Specified by:
setCommentAnnotationID in interface loci.formats.meta.MetadataStore

setCommentAnnotationNamespace

public void setCommentAnnotationNamespace(String namespace,
                                          int commentAnnotationIndex)
Specified by:
setCommentAnnotationNamespace in interface loci.formats.meta.MetadataStore

setCommentAnnotationValue

public void setCommentAnnotationValue(String value,
                                      int commentAnnotationIndex)
Specified by:
setCommentAnnotationValue in interface loci.formats.meta.MetadataStore

setTextID

public void setTextID(String id,
                      int ROIIndex,
                      int shapeIndex)
Specified by:
setTextID in interface loci.formats.meta.MetadataStore

setTextDescription

public void setTextDescription(String description,
                               int ROIIndex,
                               int shapeIndex)
Specified by:
setTextDescription in interface loci.formats.meta.MetadataStore

setTextFill

public void setTextFill(Integer fill,
                        int ROIIndex,
                        int shapeIndex)
Specified by:
setTextFill in interface loci.formats.meta.MetadataStore

setTextFontSize

public void setTextFontSize(ome.xml.model.primitives.NonNegativeInteger fontSize,
                            int ROIIndex,
                            int shapeIndex)
Specified by:
setTextFontSize in interface loci.formats.meta.MetadataStore

setTextLabel

public void setTextLabel(String label,
                         int ROIIndex,
                         int shapeIndex)
Specified by:
setTextLabel in interface loci.formats.meta.MetadataStore

setTextName

public void setTextName(String name,
                        int ROIIndex,
                        int shapeIndex)
Specified by:
setTextName in interface loci.formats.meta.MetadataStore

setTextStroke

public void setTextStroke(Integer stroke,
                          int ROIIndex,
                          int shapeIndex)
Specified by:
setTextStroke in interface loci.formats.meta.MetadataStore

setTextStrokeDashArray

public void setTextStrokeDashArray(String strokeDashArray,
                                   int ROIIndex,
                                   int shapeIndex)
Specified by:
setTextStrokeDashArray in interface loci.formats.meta.MetadataStore

setTextStrokeWidth

public void setTextStrokeWidth(Double strokeWidth,
                               int ROIIndex,
                               int shapeIndex)
Specified by:
setTextStrokeWidth in interface loci.formats.meta.MetadataStore

setTextTheC

public void setTextTheC(ome.xml.model.primitives.NonNegativeInteger theC,
                        int ROIIndex,
                        int shapeIndex)
Specified by:
setTextTheC in interface loci.formats.meta.MetadataStore

setTextTheT

public void setTextTheT(ome.xml.model.primitives.NonNegativeInteger theT,
                        int ROIIndex,
                        int shapeIndex)
Specified by:
setTextTheT in interface loci.formats.meta.MetadataStore

setTextTheZ

public void setTextTheZ(ome.xml.model.primitives.NonNegativeInteger theZ,
                        int ROIIndex,
                        int shapeIndex)
Specified by:
setTextTheZ in interface loci.formats.meta.MetadataStore

setTextTransform

public void setTextTransform(String transform,
                             int ROIIndex,
                             int shapeIndex)
Specified by:
setTextTransform in interface loci.formats.meta.MetadataStore

setTextValue

public void setTextValue(String value,
                         int ROIIndex,
                         int shapeIndex)
Specified by:
setTextValue in interface loci.formats.meta.MetadataStore

setTextX

public void setTextX(Double x,
                     int ROIIndex,
                     int shapeIndex)
Specified by:
setTextX in interface loci.formats.meta.MetadataStore

setTextY

public void setTextY(Double y,
                     int ROIIndex,
                     int shapeIndex)
Specified by:
setTextY in interface loci.formats.meta.MetadataStore

setTiffDataFirstC

public void setTiffDataFirstC(ome.xml.model.primitives.NonNegativeInteger firstC,
                              int imageIndex,
                              int tiffDataIndex)
Specified by:
setTiffDataFirstC in interface loci.formats.meta.MetadataStore

setTiffDataFirstT

public void setTiffDataFirstT(ome.xml.model.primitives.NonNegativeInteger firstT,
                              int imageIndex,
                              int tiffDataIndex)
Specified by:
setTiffDataFirstT in interface loci.formats.meta.MetadataStore

setTiffDataFirstZ

public void setTiffDataFirstZ(ome.xml.model.primitives.NonNegativeInteger firstZ,
                              int imageIndex,
                              int tiffDataIndex)
Specified by:
setTiffDataFirstZ in interface loci.formats.meta.MetadataStore

setTiffDataIFD

public void setTiffDataIFD(ome.xml.model.primitives.NonNegativeInteger ifd,
                           int imageIndex,
                           int tiffDataIndex)
Specified by:
setTiffDataIFD in interface loci.formats.meta.MetadataStore

setTiffDataPlaneCount

public void setTiffDataPlaneCount(ome.xml.model.primitives.NonNegativeInteger planeCount,
                                  int imageIndex,
                                  int tiffDataIndex)
Specified by:
setTiffDataPlaneCount in interface loci.formats.meta.MetadataStore

setTimestampAnnotationID

public void setTimestampAnnotationID(String id,
                                     int timestampAnnotationIndex)
Specified by:
setTimestampAnnotationID in interface loci.formats.meta.MetadataStore

setTimestampAnnotationNamespace

public void setTimestampAnnotationNamespace(String namespace,
                                            int timestampAnnotationIndex)
Specified by:
setTimestampAnnotationNamespace in interface loci.formats.meta.MetadataStore

setTimestampAnnotationValue

public void setTimestampAnnotationValue(String value,
                                        int timestampAnnotationIndex)
Specified by:
setTimestampAnnotationValue in interface loci.formats.meta.MetadataStore

setTransmittanceRangeCutIn

public void setTransmittanceRangeCutIn(ome.xml.model.primitives.PositiveInteger cutIn,
                                       int instrumentIndex,
                                       int filterIndex)
Specified by:
setTransmittanceRangeCutIn in interface loci.formats.meta.MetadataStore

setTransmittanceRangeCutInTolerance

public void setTransmittanceRangeCutInTolerance(ome.xml.model.primitives.NonNegativeInteger cutInTolerance,
                                                int instrumentIndex,
                                                int filterIndex)
Specified by:
setTransmittanceRangeCutInTolerance in interface loci.formats.meta.MetadataStore

setTransmittanceRangeCutOut

public void setTransmittanceRangeCutOut(ome.xml.model.primitives.PositiveInteger cutOut,
                                        int instrumentIndex,
                                        int filterIndex)
Specified by:
setTransmittanceRangeCutOut in interface loci.formats.meta.MetadataStore

setTransmittanceRangeCutOutTolerance

public void setTransmittanceRangeCutOutTolerance(ome.xml.model.primitives.NonNegativeInteger cutOutTolerance,
                                                 int instrumentIndex,
                                                 int filterIndex)
Specified by:
setTransmittanceRangeCutOutTolerance in interface loci.formats.meta.MetadataStore

setTransmittanceRangeTransmittance

public void setTransmittanceRangeTransmittance(ome.xml.model.primitives.PercentFraction transmittance,
                                               int instrumentIndex,
                                               int filterIndex)
Specified by:
setTransmittanceRangeTransmittance in interface loci.formats.meta.MetadataStore

setUUID

public void setUUID(String uuid)
Specified by:
setUUID in interface loci.formats.meta.MetadataStore

setUUIDFileName

public void setUUIDFileName(String fileName,
                            int imageIndex,
                            int tiffDataIndex)
Specified by:
setUUIDFileName in interface loci.formats.meta.MetadataStore

setUUIDValue

public void setUUIDValue(String fileName,
                         int imageIndex,
                         int tiffDataIndex)
Specified by:
setUUIDValue in interface loci.formats.meta.MetadataStore

setWellID

public void setWellID(String id,
                      int plateIndex,
                      int wellIndex)
Specified by:
setWellID in interface loci.formats.meta.MetadataStore

setWellAnnotationRef

public void setWellAnnotationRef(String annotation,
                                 int plateIndex,
                                 int wellIndex,
                                 int annotationRefIndex)
Specified by:
setWellAnnotationRef in interface loci.formats.meta.MetadataStore

setWellColor

public void setWellColor(Integer color,
                         int plateIndex,
                         int wellIndex)
Specified by:
setWellColor in interface loci.formats.meta.MetadataStore

setWellColumn

public void setWellColumn(ome.xml.model.primitives.NonNegativeInteger column,
                          int plateIndex,
                          int wellIndex)
Specified by:
setWellColumn in interface loci.formats.meta.MetadataStore

setWellExternalDescription

public void setWellExternalDescription(String externalDescription,
                                       int plateIndex,
                                       int wellIndex)
Specified by:
setWellExternalDescription in interface loci.formats.meta.MetadataStore

setWellExternalIdentifier

public void setWellExternalIdentifier(String externalIdentifier,
                                      int plateIndex,
                                      int wellIndex)
Specified by:
setWellExternalIdentifier in interface loci.formats.meta.MetadataStore

setWellReagentRef

public void setWellReagentRef(String reagent,
                              int plateIndex,
                              int wellIndex)
Specified by:
setWellReagentRef in interface loci.formats.meta.MetadataStore

setWellRow

public void setWellRow(ome.xml.model.primitives.NonNegativeInteger row,
                       int plateIndex,
                       int wellIndex)
Specified by:
setWellRow in interface loci.formats.meta.MetadataStore

setWellStatus

public void setWellStatus(String status,
                          int plateIndex,
                          int wellIndex)
Specified by:
setWellStatus in interface loci.formats.meta.MetadataStore

setWellSampleID

public void setWellSampleID(String id,
                            int plateIndex,
                            int wellIndex,
                            int wellSampleIndex)
Specified by:
setWellSampleID in interface loci.formats.meta.MetadataStore

setWellSampleAnnotationRef

public void setWellSampleAnnotationRef(String annotation,
                                       int plateIndex,
                                       int wellIndex,
                                       int wellSampleIndex,
                                       int annotationRefIndex)
Specified by:
setWellSampleAnnotationRef in interface loci.formats.meta.MetadataStore

setWellSampleImageRef

public void setWellSampleImageRef(String image,
                                  int plateIndex,
                                  int wellIndex,
                                  int wellSampleIndex)
Specified by:
setWellSampleImageRef in interface loci.formats.meta.MetadataStore

setWellSampleIndex

public void setWellSampleIndex(ome.xml.model.primitives.NonNegativeInteger index,
                               int plateIndex,
                               int wellIndex,
                               int wellSampleIndex)
Specified by:
setWellSampleIndex in interface loci.formats.meta.MetadataStore

setWellSamplePositionX

public void setWellSamplePositionX(Double positionX,
                                   int plateIndex,
                                   int wellIndex,
                                   int wellSampleIndex)
Specified by:
setWellSamplePositionX in interface loci.formats.meta.MetadataStore

setWellSamplePositionY

public void setWellSamplePositionY(Double positionY,
                                   int plateIndex,
                                   int wellIndex,
                                   int wellSampleIndex)
Specified by:
setWellSamplePositionY in interface loci.formats.meta.MetadataStore

setWellSampleTimepoint

public void setWellSampleTimepoint(String timepoint,
                                   int plateIndex,
                                   int wellIndex,
                                   int wellSampleIndex)
Specified by:
setWellSampleTimepoint in interface loci.formats.meta.MetadataStore

setXMLAnnotationID

public void setXMLAnnotationID(String id,
                               int XMLAnnotationIndex)
Specified by:
setXMLAnnotationID in interface loci.formats.meta.MetadataStore

setXMLAnnotationNamespace

public void setXMLAnnotationNamespace(String namespace,
                                      int XMLAnnotationIndex)
Specified by:
setXMLAnnotationNamespace in interface loci.formats.meta.MetadataStore

setXMLAnnotationValue

public void setXMLAnnotationValue(String value,
                                  int XMLAnnotationIndex)
Specified by:
setXMLAnnotationValue in interface loci.formats.meta.MetadataStore

setBooleanAnnotationAnnotationRef

public void setBooleanAnnotationAnnotationRef(String annotation,
                                              int booleanAnnotationIndex,
                                              int annotationRefIndex)
Specified by:
setBooleanAnnotationAnnotationRef in interface loci.formats.meta.MetadataStore

setBooleanAnnotationDescription

public void setBooleanAnnotationDescription(String description,
                                            int booleanAnnotationIndex)
Specified by:
setBooleanAnnotationDescription in interface loci.formats.meta.MetadataStore

setCommentAnnotationAnnotationRef

public void setCommentAnnotationAnnotationRef(String annotation,
                                              int commentAnnotationIndex,
                                              int annotationRefIndex)
Specified by:
setCommentAnnotationAnnotationRef in interface loci.formats.meta.MetadataStore

setCommentAnnotationDescription

public void setCommentAnnotationDescription(String description,
                                            int commentAnnotationIndex)
Specified by:
setCommentAnnotationDescription in interface loci.formats.meta.MetadataStore

setDoubleAnnotationAnnotationRef

public void setDoubleAnnotationAnnotationRef(String annotation,
                                             int doubleAnnotationIndex,
                                             int annotationRefIndex)
Specified by:
setDoubleAnnotationAnnotationRef in interface loci.formats.meta.MetadataStore

setDoubleAnnotationDescription

public void setDoubleAnnotationDescription(String description,
                                           int doubleAnnotationIndex)
Specified by:
setDoubleAnnotationDescription in interface loci.formats.meta.MetadataStore

setFileAnnotationAnnotationRef

public void setFileAnnotationAnnotationRef(String annotation,
                                           int fileAnnotationIndex,
                                           int annotationRefIndex)
Specified by:
setFileAnnotationAnnotationRef in interface loci.formats.meta.MetadataStore

setFileAnnotationDescription

public void setFileAnnotationDescription(String description,
                                         int fileAnnotationIndex)
Specified by:
setFileAnnotationDescription in interface loci.formats.meta.MetadataStore

setListAnnotationDescription

public void setListAnnotationDescription(String description,
                                         int listAnnotationIndex)
Specified by:
setListAnnotationDescription in interface loci.formats.meta.MetadataStore

setLongAnnotationAnnotationRef

public void setLongAnnotationAnnotationRef(String annotation,
                                           int longAnnotationIndex,
                                           int annotationRefIndex)
Specified by:
setLongAnnotationAnnotationRef in interface loci.formats.meta.MetadataStore

setLongAnnotationDescription

public void setLongAnnotationDescription(String description,
                                         int longAnnotationIndex)
Specified by:
setLongAnnotationDescription in interface loci.formats.meta.MetadataStore

setTagAnnotationAnnotationRef

public void setTagAnnotationAnnotationRef(String annotation,
                                          int tagAnnotationIndex,
                                          int annotationRefIndex)
Specified by:
setTagAnnotationAnnotationRef in interface loci.formats.meta.MetadataStore

setTagAnnotationDescription

public void setTagAnnotationDescription(String description,
                                        int tagAnnotationIndex)
Specified by:
setTagAnnotationDescription in interface loci.formats.meta.MetadataStore

setTagAnnotationID

public void setTagAnnotationID(String id,
                               int tagAnnotationIndex)
Specified by:
setTagAnnotationID in interface loci.formats.meta.MetadataStore

setTagAnnotationNamespace

public void setTagAnnotationNamespace(String namespace,
                                      int tagAnnotationIndex)
Specified by:
setTagAnnotationNamespace in interface loci.formats.meta.MetadataStore

setTagAnnotationValue

public void setTagAnnotationValue(String value,
                                  int tagAnnotationIndex)
Specified by:
setTagAnnotationValue in interface loci.formats.meta.MetadataStore

setTermAnnotationAnnotationRef

public void setTermAnnotationAnnotationRef(String annotation,
                                           int termAnnotationIndex,
                                           int annotationRefIndex)
Specified by:
setTermAnnotationAnnotationRef in interface loci.formats.meta.MetadataStore

setTermAnnotationDescription

public void setTermAnnotationDescription(String description,
                                         int termAnnotationIndex)
Specified by:
setTermAnnotationDescription in interface loci.formats.meta.MetadataStore

setTermAnnotationID

public void setTermAnnotationID(String id,
                                int termAnnotationIndex)
Specified by:
setTermAnnotationID in interface loci.formats.meta.MetadataStore

setTermAnnotationNamespace

public void setTermAnnotationNamespace(String namespace,
                                       int termAnnotationIndex)
Specified by:
setTermAnnotationNamespace in interface loci.formats.meta.MetadataStore

setTermAnnotationValue

public void setTermAnnotationValue(String value,
                                   int termAnnotationIndex)
Specified by:
setTermAnnotationValue in interface loci.formats.meta.MetadataStore

setTimestampAnnotationAnnotationRef

public void setTimestampAnnotationAnnotationRef(String annotation,
                                                int timestampAnnotationIndex,
                                                int annotationRefIndex)
Specified by:
setTimestampAnnotationAnnotationRef in interface loci.formats.meta.MetadataStore

setTimestampAnnotationDescription

public void setTimestampAnnotationDescription(String description,
                                              int timestampAnnotationIndex)
Specified by:
setTimestampAnnotationDescription in interface loci.formats.meta.MetadataStore

setXMLAnnotationAnnotationRef

public void setXMLAnnotationAnnotationRef(String annotation,
                                          int XMLAnnotationIndex,
                                          int annotationRefIndex)
Specified by:
setXMLAnnotationAnnotationRef in interface loci.formats.meta.MetadataStore

setXMLAnnotationDescription

public void setXMLAnnotationDescription(String description,
                                        int XMLAnnotationIndex)
Specified by:
setXMLAnnotationDescription in interface loci.formats.meta.MetadataStore


OmeroJava Api

Version: 4.3.3-00d1137e-b2894

Copyright © 2009 The University of Dundee. All Rights Reserved.