- Gateway - Class in omero.gateway
-
A Gateway for simplifying access to an OMERO server
- Gateway(Logger) - Constructor for class omero.gateway.Gateway
-
Creates a new Gateway instance
- Gateway(Logger, CacheService) - Constructor for class omero.gateway.Gateway
-
Creates a new Gateway instance
- Gateway(Logger, CacheService, ExecutorService, boolean) - Constructor for class omero.gateway.Gateway
-
Creates a new Gateway instance
- GENERAL_ERROR - Static variable in class omero.gateway.model.SearchResultCollection
-
Some other error
- getAbsolutePath() - Method in class omero.gateway.model.FileData
-
Returns the absolute path.
- getAbsolutePaths() - Method in class omero.gateway.model.FilesetData
-
Returns the collections of absolute paths.
- getAcquisitionDate() - Method in class omero.gateway.model.ImageData
-
Returns the acquisition date.
- getAdminPrivileges(SecurityContext) - Method in class omero.gateway.facility.AdminFacility
-
Get the logged in user's admin privileges
(see omero.model.enums)
- getAdminPrivileges(SecurityContext, ExperimenterData) - Method in class omero.gateway.facility.AdminFacility
-
Get the admin privileges of a certain user
(see omero.model.enums)
- getAdminService(SecurityContext) - Method in class omero.gateway.Gateway
-
Returns the IAdminPrx service.
- getAdminService(SecurityContext, boolean) - Method in class omero.gateway.Gateway
-
Returns the IAdminPrx service.
- getAirPressure(UnitsPressure) - Method in class omero.gateway.model.ImageAcquisitionData
-
Returns the air pressure.
- getAllPixels() - Method in class omero.gateway.model.ImageData
-
Returns all the sets of pixels related to this image.
- getAlpha() - Method in class omero.gateway.model.WellData
-
Returns the alpha component of the color associated to the well,
or -1.
- getAmplificationGain() - Method in class omero.gateway.model.DetectorData
-
Returns the amplification gain of the detector.
- getAnnotatedObject(IObject) - Static method in class omero.gateway.util.ModelMapper
-
Returns the annotated IObject related to the specified annotation.
- getAnnotationObject(IObject) - Static method in class omero.gateway.util.ModelMapper
-
Returns the annotation represented by the specified link
- getAnnotations(SecurityContext, DataObject) - Method in class omero.gateway.facility.MetadataFacility
-
- getAnnotations(SecurityContext, DataObject, List<Class<? extends AnnotationData>>, List<Long>) - Method in class omero.gateway.facility.MetadataFacility
-
- getAnnotations(SecurityContext, List<? extends DataObject>, List<Class<? extends AnnotationData>>, List<Long>) - Method in class omero.gateway.facility.MetadataFacility
-
- getAnnotations() - Method in class omero.gateway.model.DatasetData
-
Returns the annotations related to this dataset.
- getAnnotations() - Method in class omero.gateway.model.ImageData
-
Returns the annotations
- getAnnotationsCounts() - Method in class omero.gateway.model.DatasetData
-
Returns the number of annotations linked to the object, key: id of the
user, value: number of annotation.
- getAnnotationsCounts() - Method in class omero.gateway.model.ImageData
-
Returns the number of annotations linked to the object, key: id of the
user, value: number of annotation.
- getAnnotationsCounts() - Method in class omero.gateway.model.PlateAcquisitionData
-
Returns the number of annotations linked to the object, key: id of the
user, value: number of annotation.
- getAnnotationsCounts() - Method in class omero.gateway.model.PlateData
-
Returns the number of annotations linked to the object, key: id of the
user, value: number of annotation.
- getAnnotationsCounts() - Method in class omero.gateway.model.ProjectData
-
Returns the number of annotations linked to the object, key: id of the
user, value: number of annotation.
- getAnnotationsCounts() - Method in class omero.gateway.model.ScreenData
-
Returns the number of annotations linked to the object, key: id of the
user, value: number of annotation.
- getAnnotationsCounts() - Method in class omero.gateway.model.WellData
-
Returns the number of annotations linked to the object, key: id of the
user, value: number of annotation.
- getApplicationName() - Method in class omero.gateway.LoginCredentials
-
- getArguments() - Method in class omero.gateway.LoginCredentials
-
Returns the arguments if set as a read-only list.
- getAttachedFile() - Method in class omero.gateway.model.FileAnnotationData
-
Returns the file to upload to the server.
- getAvailableAdminPrivileges(SecurityContext) - Method in class omero.gateway.facility.AdminFacility
-
Get all available admin privileges
- getAvailableGroups(SecurityContext, ExperimenterData) - Method in class omero.gateway.facility.BrowseFacility
-
Retrieves the groups visible by the current experimenter.
- getAvailableTables(SecurityContext, DataObject) - Method in class omero.gateway.facility.TablesFacility
-
Get all available tables for a the specified object
- getBit(byte[], int) - Method in class omero.gateway.model.MaskData
-
Sets the bit value in a byte array at position bit to be the value
value.
- getBlue() - Method in class omero.gateway.model.WellData
-
Returns the blue component of the color associated to the well,
or -1.
- getByGroup() - Method in class omero.gateway.model.SearchResultCollection
-
Get a perGroup map representation of the results
- getByGroup(Class<? extends DataObject>) - Method in class omero.gateway.model.SearchResultCollection
-
Get a perGroup map representation of the results, filtered by type
- getC() - Method in class omero.gateway.model.ShapeData
-
Returns the channel.
- getCacheService() - Method in class omero.gateway.Gateway
-
- getCalibratedMagnification() - Method in class omero.gateway.model.ObjectiveData
-
Returns the objective's calibrated magnification factor.
- getChannelData(SecurityContext, long) - Method in class omero.gateway.facility.MetadataFacility
-
- getChannelLabeling() - Method in class omero.gateway.model.ChannelData
-
Returns the label of the channel.
- getCheckVersion() - Method in class omero.gateway.LoginCredentials
-
Returns whether the version check is enabled
- getChildFromLink(IObject) - Static method in class omero.gateway.util.ModelMapper
-
Returns the child from the passed link.
- getCo2Percent() - Method in class omero.gateway.model.ImageAcquisitionData
-
Returns the Co2 level, this is a percent value in the interval [0, 1].
- getColor(int) - Static method in class omero.gateway.model.ShapeSettingsData
-
Creates a Color object from an RGBA integer value
- getColumn() - Method in class omero.gateway.model.WellData
-
Returns the column used to indicate the location of the well on the grid.
- getColumnIndex(Integer) - Method in class omero.gateway.model.TableResult
-
Returns the index of the column corresponding to the specified value.
- getColumns() - Method in class omero.gateway.model.TableData
-
Get the headers
- getColumnSequenceIndex() - Method in class omero.gateway.model.PlateData
-
Returns the index indicating how to label a column.
- getCompression() - Method in class omero.gateway.LoginCredentials
-
Returns the compression level.
- getCompression() - Method in class omero.gateway.SecurityContext
-
Get the compression level (A percentage compression level from 1.00
(100%) to 0.01 (1%) (the default is 85%))
- getConfigService(SecurityContext) - Method in class omero.gateway.Gateway
-
Returns the IConfigPrx service.
- getConnectionStatus() - Method in exception omero.gateway.exception.DSOutOfServiceException
-
- getConnector(SecurityContext) - Method in class omero.gateway.Gateway
-
- getConnector(SecurityContext, boolean, boolean) - Method in class omero.gateway.Gateway
-
Returns the connector corresponding to the passed context.
- getContent() - Method in class omero.gateway.model.AnnotationData
-
Returns the content of the annotation.
- getContent() - Method in class omero.gateway.model.BooleanAnnotationData
-
Returns the textual content of the annotation.
- getContent() - Method in class omero.gateway.model.DoubleAnnotationData
-
Returns the value.
- getContent() - Method in class omero.gateway.model.FileAnnotationData
-
Returns the original file.
- getContent() - Method in class omero.gateway.model.LongAnnotationData
-
Returns the rating value.
- getContent() - Method in class omero.gateway.model.MapAnnotationData
-
- getContent() - Method in class omero.gateway.model.RatingAnnotationData
-
Returns the rating value.
- getContent() - Method in class omero.gateway.model.TagAnnotationData
-
Returns the textual content of the annotation.
- getContent() - Method in class omero.gateway.model.TermAnnotationData
-
Returns the textual content of the annotation.
- getContent() - Method in class omero.gateway.model.TextualAnnotationData
-
Returns the textual content of the annotation.
- getContent() - Method in class omero.gateway.model.TimeAnnotationData
-
Returns the timestamp of the annotation.
- getContent() - Method in class omero.gateway.model.XMLAnnotationData
-
Returns the content of the annotation.
- getContentAsString() - Method in class omero.gateway.model.AnnotationData
-
Returns the content of the annotation as a String, which is
parsed on a Class-by-Class basis.
- getContentAsString() - Method in class omero.gateway.model.BooleanAnnotationData
-
Returns the textual content of the annotation.
- getContentAsString() - Method in class omero.gateway.model.DoubleAnnotationData
-
Returns the value as a string.
- getContentAsString() - Method in class omero.gateway.model.FileAnnotationData
-
Returns the absolute path to the file
- getContentAsString() - Method in class omero.gateway.model.LongAnnotationData
-
Returns the value as a string.
- getContentAsString() - Method in class omero.gateway.model.MapAnnotationData
-
- getContentAsString() - Method in class omero.gateway.model.RatingAnnotationData
-
Returns the rating value as a string.
- getContentAsString() - Method in class omero.gateway.model.TagAnnotationData
-
Returns the textual content of the annotation.
- getContentAsString() - Method in class omero.gateway.model.TermAnnotationData
-
Returns the textual content of the annotation.
- getContentAsString() - Method in class omero.gateway.model.TextualAnnotationData
-
Returns the textual content of the annotation.
- getContentAsString() - Method in class omero.gateway.model.TimeAnnotationData
-
Returns the time as a string.
- getContentAsString() - Method in class omero.gateway.model.XMLAnnotationData
-
Returns the textual content of the annotation.
- getContrastMethod() - Method in class omero.gateway.model.ChannelAcquisitionData
-
Returns the contrast method.
- getContrastMethod() - Method in class omero.gateway.model.ChannelData
-
Returns the contrast method.
- getContrastMethodAsEnum() - Method in class omero.gateway.model.ChannelData
-
Returns the contrast method enumeration value.
- getCorrection() - Method in class omero.gateway.model.ObjectiveData
-
Returns the correction value of the objective.
- getCorrectionCollar() - Method in class omero.gateway.model.ImageAcquisitionData
-
Returns the correction collar of the objective.
- getCreated() - Method in class omero.gateway.model.DataObject
-
Returns the creation time of the object.
- getCutIn(UnitsLength) - Method in class omero.gateway.model.FilterData
-
Returns the cut in value or null.
- getCutInTolerance(UnitsLength) - Method in class omero.gateway.model.FilterData
-
Returns the cut in tolerance value or null.
- getCutOut(UnitsLength) - Method in class omero.gateway.model.FilterData
-
Returns the cut out value or null.
- getCutOutTolerance(UnitsLength) - Method in class omero.gateway.model.FilterData
-
Returns the cut out tolerance value or null.
- getData() - Method in class omero.gateway.model.TableData
-
Get the data in form Object['column index']['row data']
- getData() - Method in class omero.gateway.model.TableResult
-
Returns the data.
- getDataObjects(int, Class<? extends DataObject>) - Method in class omero.gateway.model.SearchResultCollection
-
Get DataObjects filtered by scope and type
- getDataObjects() - Method in class omero.gateway.model.TagAnnotationData
-
Returns the collection of data objects related to this tag.
- getDatasets(SecurityContext) - Method in class omero.gateway.facility.BrowseFacility
-
Loads all datasets
- getDatasets(SecurityContext, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility
-
Loads the datasets with the given ids
- getDatasets(SecurityContext, long) - Method in class omero.gateway.facility.BrowseFacility
-
Loads the datasets for a particular user
- getDatasets(SecurityContext, long, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility
-
Loads the datasets with the given ids which belong to a particular user
- getDatasets() - Method in class omero.gateway.model.ImageData
-
Returns the datasets containing this image.
- getDatasets() - Method in class omero.gateway.model.ProjectData
-
Returns the datasets contained in this project.
- getDataValue() - Method in class omero.gateway.model.DoubleAnnotationData
-
Returns the value.
- getDataValue() - Method in class omero.gateway.model.LongAnnotationData
-
Returns the value.
- getDateType() - Method in class omero.gateway.model.SearchParameters
-
- getDefaultGroup() - Method in class omero.gateway.model.ExperimenterData
-
Returns the default Group for this Experimenter
- getDefaultPixels() - Method in class omero.gateway.model.ImageData
-
Returns the default set of pixels.
- getDefaultSample() - Method in class omero.gateway.model.PlateData
-
Returns the currently selected field or 0.
- getDescription() - Method in class omero.gateway.model.AnnotationData
-
Retrieves the description of the
underlying Annotation instance.
- getDescription() - Method in class omero.gateway.model.DatasetData
-
Returns the description of the dataset.
- getDescription() - Method in class omero.gateway.model.FileAnnotationData
-
Returns the description of the annotation.
- getDescription() - Method in class omero.gateway.model.FileData
-
Returns the description of the file.
- getDescription() - Method in class omero.gateway.model.FolderData
-
Get the description of the Folder
- getDescription() - Method in class omero.gateway.model.GroupData
-
Returns the description of the group.
- getDescription() - Method in class omero.gateway.model.ImageData
-
Returns the description of the image.
- getDescription() - Method in class omero.gateway.model.PlateAcquisitionData
-
Returns the description of the plate acquisition.
- getDescription() - Method in class omero.gateway.model.PlateData
-
Returns the description of the plate.
- getDescription() - Method in class omero.gateway.model.ProjectData
-
Returns the description of the project.
- getDescription() - Method in class omero.gateway.model.ScreenData
-
Returns the description of the screen.
- getDescription() - Method in class omero.gateway.model.TableDataColumn
-
Get the description
- getDescription() - Method in class omero.gateway.model.XMLAnnotationData
-
Returns the description of the annotation.
- getDescription() - Method in class omero.gateway.util.TIFFFilter
-
Returns the description of the filter.
- getDetails() - Method in class omero.gateway.model.DataObject
-
Returns the details of the object.
- getDetector() - Method in class omero.gateway.model.ChannelAcquisitionData
-
Returns the detector used for that channel.
- getDetectorBinningAsEnum() - Method in class omero.gateway.model.ChannelAcquisitionData
-
Returns the binning enumeration value.
- getDetectors() - Method in class omero.gateway.model.InstrumentData
-
Returns the collection of detectors.
- getDetectorSettingsBinning() - Method in class omero.gateway.model.ChannelAcquisitionData
-
Returns the Binning factor.
- getDetectorSettingsGain() - Method in class omero.gateway.model.ChannelAcquisitionData
-
Returns the gain set on the detector.
- getDetectorSettingsOffset() - Method in class omero.gateway.model.ChannelAcquisitionData
-
Returns the offset set on the detector.
- getDetectorSettingsReadOutRate(UnitsFrequency) - Method in class omero.gateway.model.ChannelAcquisitionData
-
Returns the Read out rate set on the detector.
- getDetectorSettingsVoltage(UnitsElectricPotential) - Method in class omero.gateway.model.ChannelAcquisitionData
-
Returns the voltage set on the detector.
- getDichroic() - Method in class omero.gateway.model.FilterSetData
-
Returns the dichroic if any.
- getDichroic() - Method in class omero.gateway.model.LightPathData
-
Returns the dichroic if any.
- getDichroics() - Method in class omero.gateway.model.InstrumentData
-
Returns the collection of dichroics.
- getDisplayedFileName(String, Integer) - Static method in class omero.gateway.util.Utils
-
Returns the name to display for a file.
- getElement(int, Object) - Method in interface omero.gateway.cache.CacheService
-
Adds the specified element to the selected cache.
- getEmail() - Method in class omero.gateway.model.ExperimenterData
-
Returns the e-mail of the experimenter.
- getEmissionFilters() - Method in class omero.gateway.model.FilterSetData
-
Returns the collections of emission filters if any.
- getEmissionFilters() - Method in class omero.gateway.model.LightPathData
-
Returns the collections of emission filters if any.
- getEmissionWavelength(UnitsLength) - Method in class omero.gateway.model.ChannelData
-
Returns the emission wavelength of the channel.
- getEnd() - Method in class omero.gateway.model.SearchParameters
-
Returns the upper bound of the time interval.
- getEndTime() - Method in class omero.gateway.model.PlateAcquisitionData
-
Returns the time when the last image was collected.
- getError() - Method in class omero.gateway.model.SearchResultCollection
-
Get the error code
- getExcitationFilters() - Method in class omero.gateway.model.FilterSetData
-
Returns the collections of excitation filters if any.
- getExcitationFilters() - Method in class omero.gateway.model.LightPathData
-
Returns the collections of excitation filters if any.
- getExcitationWavelength(UnitsLength) - Method in class omero.gateway.model.ChannelData
-
Returns the excitation wavelength of the channel.
- getExperimenter() - Method in class omero.gateway.SecurityContext
-
Returns the id of the experimenter.
- getExperimenterData() - Method in class omero.gateway.SecurityContext
-
Returns the experimenter.
- getExperimenters() - Method in class omero.gateway.model.GroupData
-
Returns the experimenters contained in this group.
- getExporterService(SecurityContext) - Method in class omero.gateway.Gateway
-
Returns the ExporterPrx service.
- getExtendedMessage() - Method in exception omero.gateway.exception.RenderingServiceException
-
Prints the stack trace and returns it as a string.
- getExtension() - Method in class omero.gateway.util.TIFFFilter
-
Returns the extension of the filter.
- getExternalDescription() - Method in class omero.gateway.model.WellData
-
Returns the external description of the well.
- getExternalIdentifier() - Method in class omero.gateway.model.PlateData
-
Returns the external identifier of the plate.
- getFacility(Class<T>, Gateway) - Static method in class omero.gateway.facility.Facility
-
Get a reference to a certain Facility
- getFacility(Class<T>) - Method in class omero.gateway.Gateway
-
Get a
Facility to perform further operations with the server
- getFileFormat() - Method in class omero.gateway.model.FileAnnotationData
-
Returns the format of the uploaded file.
- getFileID() - Method in class omero.gateway.model.FileAnnotationData
-
Returns the id of the file.
- getFileID() - Method in class omero.gateway.model.ROIResult
-
Returns the id of the file.
- getFileKind() - Method in class omero.gateway.model.FileAnnotationData
-
Returns a user readable description of the file.
- getFileName() - Method in class omero.gateway.model.FileAnnotationData
-
Returns the name of the file.
- getFilePath() - Method in class omero.gateway.model.FileAnnotationData
-
Returns the absolute path to the file.
- getFilesetId() - Method in class omero.gateway.model.ImageData
-
Returns the ID of the fileset to which this image belongs.
- getFileSize() - Method in class omero.gateway.model.FileAnnotationData
-
Returns the size of the file.
- getFill() - Method in class omero.gateway.model.ShapeSettingsData
-
Returns the fill color.
- getFillRule() - Method in class omero.gateway.model.ShapeSettingsData
-
Returns the fill rule.
- getFilters() - Method in class omero.gateway.model.InstrumentData
-
Returns the collection of filters.
- getFilterSet() - Method in class omero.gateway.model.ChannelAcquisitionData
-
Returns the filter set or null.
- getFilterSet() - Method in class omero.gateway.model.OTFData
-
Returns the associated filter set.
- getFilterSets() - Method in class omero.gateway.model.InstrumentData
-
Returns the collection of filter sets.
- getFilterWheel() - Method in class omero.gateway.model.FilterData
-
Returns the wheel.
- getFirstName() - Method in class omero.gateway.model.ExperimenterData
-
Returns the first name of the experimenter.
- getFluor() - Method in class omero.gateway.model.ChannelData
-
Returns the Fluorophore used.
- getFolderAsContainerName(File) - Static method in class omero.gateway.util.Utils
-
Returns the name as container if option is on.
- getFolderPathString() - Method in class omero.gateway.model.FolderData
-
Returns the folder path as string
- getFolderPathString(char) - Method in class omero.gateway.model.FolderData
-
Returns the folder path as string using a custom path separator
- getFolders(SecurityContext) - Method in class omero.gateway.facility.BrowseFacility
-
Get all folders the logged in user has access to.
- getFolders(SecurityContext, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility
-
Get the folders for the given folder ids.
- getFolders(SecurityContext, long) - Method in class omero.gateway.facility.BrowseFacility
-
Get the folders which belong to the given user.
- getFolders() - Method in class omero.gateway.model.ROIData
-
Get the folders this ROI is part of
- getFolders() - Method in class omero.gateway.model.ROIResult
-
Get the available folders
- getFont() - Method in class omero.gateway.model.ShapeSettingsData
-
Get the style of the font for Shape.
- getFontFamily() - Method in class omero.gateway.model.ShapeSettingsData
-
Returns the stroke.
- getFontSize(UnitsLength) - Method in class omero.gateway.model.ShapeSettingsData
-
Returns the stroke.
- getFontStyle() - Method in class omero.gateway.model.ShapeSettingsData
-
Returns the font style.
- getFormat() - Method in class omero.gateway.model.ImageData
-
Returns the format of the image.
- getGain() - Method in class omero.gateway.model.DetectorData
-
Returns the gain of the detector.
- getGlobalMax() - Method in class omero.gateway.model.ChannelData
-
Returns the global maximum of the channel i.e.
- getGlobalMin() - Method in class omero.gateway.model.ChannelData
-
Returns the global minimum of the channel i.e.
- getGraphType(Class<? extends DataObject>) - Static method in class omero.gateway.util.PojoMapper
-
Returns the name of the data type which has to used for Graph actions,
see
Requests
- getGreen() - Method in class omero.gateway.model.WellData
-
Returns the green component of the color associated to the well,
or -1.
- getGridColumns() - Method in class omero.gateway.facility.TablesFacilityHelper
-
- getGroupID() - Method in class omero.gateway.LoginCredentials
-
Returns the OMERO group identifier.
- getGroupId() - Method in class omero.gateway.model.DataObject
-
Returns the id of the group.
- getGroupId() - Method in class omero.gateway.model.ExperimenterData
-
Overridden to return the id of the default group.
- getGroupId() - Method in class omero.gateway.model.GroupData
-
Overridden to return the id of the object.
- getGroupId() - Method in class omero.gateway.model.SearchParameters
-
- getGroupId() - Method in class omero.gateway.model.SearchResult
-
Get the group id of the object
- getGroupID() - Method in class omero.gateway.SecurityContext
-
Returns the identifier of the group.
- getGroups() - Method in class omero.gateway.model.ExperimenterData
-
Returns the groups the experimenter is a member of.
- getHeaders() - Method in class omero.gateway.model.TableResult
-
Returns the name of the columns.
- getHeadersDescription() - Method in class omero.gateway.model.TableResult
-
Returns the name of the columns.
- getHeight() - Method in class omero.gateway.model.MaskData
-
Returns the height of the mask.
- getHeight() - Method in class omero.gateway.model.RectangleData
-
Returns the height untransformed rectangle.
- getHierarchy(SecurityContext, Class, long) - Method in class omero.gateway.facility.BrowseFacility
-
Retrieves hierarchy trees rooted by a given node.
- getHierarchy(SecurityContext, Class, List<Long>, Parameters) - Method in class omero.gateway.facility.BrowseFacility
-
Retrieves hierarchy trees rooted by a given node i.e.
- getHistogram(SecurityContext, PixelsData, int[], int, int) - Method in class omero.gateway.facility.RawDataFacility
-
Get the histogram data for the given image, using default 256 bins and
the channels global min/max for the histogram range.
- getHistogram(SecurityContext, PixelsData, int[], int, boolean, PlaneDef) - Method in class omero.gateway.facility.RawDataFacility
-
Get the histogram data for the given image.
- getHistogram(int[], int, boolean, PlaneDef) - Method in class omero.gateway.rnd.DataSink
-
Get the histogram data for the given image.
- getHostname() - Method in class omero.gateway.ServerInformation
-
Return the hostname.
- getHQLEntityName(Class<? extends IObject>) - Static method in class omero.gateway.util.PojoMapper
-
Gets the type of an IObject class as String which can be used in HQL
queries.
- getHumidity() - Method in class omero.gateway.model.ImageAcquisitionData
-
Returns the humidity level, this is a value in the interval [0, 1].
- getId() - Method in class omero.gateway.model.DataObject
-
Returns the database id of the IObject or -1 if
null
- getIllumination() - Method in class omero.gateway.model.ChannelAcquisitionData
-
Returns the illumination.
- getIllumination() - Method in class omero.gateway.model.ChannelData
-
Returns the illumination.
- getIlluminationAsEnum() - Method in class omero.gateway.model.ChannelData
-
Returns the illumination enumeration value.
- getImage(SecurityContext, long) - Method in class omero.gateway.facility.BrowseFacility
-
Loads a image
- getImage(SecurityContext, long, ParametersI) - Method in class omero.gateway.facility.BrowseFacility
-
Loads a image
- getImage() - Method in class omero.gateway.model.PixelsData
-
Returns the image linked to this pixels' set.
- getImage() - Method in class omero.gateway.model.ROIData
-
Returns the image for the ROI.
- getImage() - Method in class omero.gateway.model.WellSampleData
-
Returns the image related to that sample if any.
- getImageAcquisitionData(SecurityContext, long) - Method in class omero.gateway.facility.MetadataFacility
-
- getImageIds() - Method in class omero.gateway.model.FilesetData
-
Returns the collection of images related to the file set.
- getImages(SecurityContext, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility
-
Loads the images with the given ids
- getImages(SecurityContext, Collection<Long>, ParametersI) - Method in class omero.gateway.facility.BrowseFacility
-
Loads the images with the given ids
- getImages(SecurityContext, long, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility
-
Loads the images for a particular user
- getImages() - Method in class omero.gateway.model.DatasetData
-
Returns a set of images contained in the dataset.
- getImagesForDatasets(SecurityContext, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility
-
Load all images belonging to particular datasets
- getImagesForProjects(SecurityContext, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility
-
Load all images belonging to particular projects
- getImagingEnvironmentId() - Method in class omero.gateway.model.ImageAcquisitionData
-
Returns the id of the StageLabel or -1
if not already linked to the image.
- getImmersion() - Method in class omero.gateway.model.ObjectiveData
-
Returns the immersion value of the objective.
- getImportStore(SecurityContext) - Method in class omero.gateway.Gateway
-
Creates or recycles the import store.
- getImportStore(SecurityContext, String) - Method in class omero.gateway.Gateway
-
Creates or recycles the import store.
- getIndex() - Method in exception omero.gateway.exception.RenderingServiceException
-
Returns the index.
- getIndex() - Method in class omero.gateway.model.ChannelData
-
Returns the channel's index.
- getIndex() - Method in class omero.gateway.model.ImageData
-
Returns the index of the image within the multi-images file.
- getIndex() - Method in class omero.gateway.model.TableDataColumn
-
Get the index
- getInserted() - Method in class omero.gateway.model.ImageData
-
Returns the insertion time of the image.
- getInstitution() - Method in class omero.gateway.model.ExperimenterData
-
Returns the institution where the experimenter works.
- getInstrumentId() - Method in class omero.gateway.model.ImageData
-
Returns the id of the instrument if any.
- getIterator() - Method in class omero.gateway.model.ROIData
-
Returns the iterator of the collection of the map.
- getKind() - Method in class omero.gateway.model.LightSourceData
-
Returns the kind of light source.
- getLabel() - Method in class omero.gateway.model.PlateAcquisitionData
-
Returns the label associated to the plate acquisition.
- getLabelName() - Method in class omero.gateway.model.ImageAcquisitionData
-
Returns the name of the stage label.
- getLaserFrequencyMultiplication() - Method in class omero.gateway.model.LightSourceData
-
Returns the frequency multiplication of the laser.
- getLaserMedium() - Method in class omero.gateway.model.LightSourceData
-
Returns the laser's medium.
- getLaserPockelCell() - Method in class omero.gateway.model.LightSourceData
-
Returns the pockel cell flag of the laser.
- getLaserPulse() - Method in class omero.gateway.model.LightSourceData
-
Returns the pulse of the laser.
- getLaserPump() - Method in class omero.gateway.model.LightSourceData
-
Returns the pump.
- getLaserRepetitionRate(UnitsFrequency) - Method in class omero.gateway.model.LightSourceData
-
Returns the repetition rate (Hz) if the laser is repetitive.
- getLaserTuneable() - Method in class omero.gateway.model.LightSourceData
-
Returns the value of the tuneable field or null
if no value set.
- getLaserWavelength(UnitsLength) - Method in class omero.gateway.model.LightSourceData
-
Returns the laser's wavelength.
- getLastModified() - Method in class omero.gateway.model.AnnotationData
-
Returns the time when the annotation was last modified.
- getLastName() - Method in class omero.gateway.model.ExperimenterData
-
Returns the last name of the experimenter.
- getLeaders() - Method in class omero.gateway.model.GroupData
-
Returns the experimenters contained in this group.
- getLensNA() - Method in class omero.gateway.model.ObjectiveData
-
Returns the objective's LensNA.
- getLightPath() - Method in class omero.gateway.model.ChannelAcquisitionData
-
Returns the light path or null.
- getLightSettingsAttenuation() - Method in class omero.gateway.model.ChannelAcquisitionData
-
Returns the attenuation of the light source, percent value
between 0 and 1.
- getLightSettingsWavelength(UnitsLength) - Method in class omero.gateway.model.ChannelAcquisitionData
-
Returns the wavelength of the light source.
- getLightSource() - Method in class omero.gateway.model.ChannelAcquisitionData
-
Returns the source of light.
- getLightSourceModel() - Method in class omero.gateway.model.LightSourceData
-
Returns the model of the light source.
- getLightSources() - Method in class omero.gateway.model.InstrumentData
-
Returns the collection of light sources.
- getLinkClass(Class<? extends DataObject>, Class<? extends DataObject>) - Static method in class omero.gateway.util.Links
-
Get the Link class for a certain child parent combination, e.g.
- getLoggedInUser() - Method in class omero.gateway.Gateway
-
Get the currently logged in user
- getLogger() - Method in class omero.gateway.Gateway
-
Provides access to the Logger
- getLookupTables(SecurityContext) - Method in class omero.gateway.facility.BrowseFacility
-
Get the available lookup tables
- getLotNumber() - Method in class omero.gateway.model.DetectorData
-
Returns the lot number of the detector.
- getLotNumber() - Method in class omero.gateway.model.DichroicData
-
Returns the lot number.
- getLotNumber() - Method in class omero.gateway.model.FilterData
-
Returns the lot number.
- getLotNumber() - Method in class omero.gateway.model.FilterSetData
-
Returns the lot number.
- getLotNumber() - Method in class omero.gateway.model.LightSourceData
-
Returns the lot of number the light source.
- getLotNumber() - Method in class omero.gateway.model.ObjectiveData
-
Returns the lot number of the detector.
- getManufacturer() - Method in class omero.gateway.model.DetectorData
-
Returns the manufacturer of the detector.
- getManufacturer() - Method in class omero.gateway.model.DichroicData
-
Returns the manufacturer.
- getManufacturer() - Method in class omero.gateway.model.FilterData
-
Returns the manufacturer.
- getManufacturer() - Method in class omero.gateway.model.FilterSetData
-
Returns the manufacturer.
- getManufacturer() - Method in class omero.gateway.model.LightSourceData
-
Returns the manufacturer of the light source.
- getManufacturer() - Method in class omero.gateway.model.ObjectiveData
-
Returns the manufacturer of the detector.
- getMarkerEnd() - Method in class omero.gateway.model.ShapeSettingsData
-
Returns the marker end.
- getMarkerStart() - Method in class omero.gateway.model.ShapeSettingsData
-
Returns the marker start.
- getMask() - Method in class omero.gateway.model.MaskData
-
Returns the mask as a byte array.
- getMaskAsBinaryArray() - Method in class omero.gateway.model.MaskData
-
Returns the mask image.
- getMaskAsBufferedImage() - Method in class omero.gateway.model.MaskData
-
Returns the mask image.
- getMaskPoints() - Method in class omero.gateway.model.PolygonData
-
Returns the points in the polygon.
- getMaximumFieldCount() - Method in class omero.gateway.model.PlateAcquisitionData
-
Returns the maximum number of fields in any well.
- getMedium() - Method in class omero.gateway.model.ImageAcquisitionData
-
Returns the medium of the objective.
- getMediumAsEnum() - Method in class omero.gateway.model.ImageAcquisitionData
-
Returns the medium enumeration value.
- getMembersOnly() - Method in class omero.gateway.model.GroupData
-
Returns the list of experimenters that are not owners of the group.
- getMetadataService(SecurityContext) - Method in class omero.gateway.Gateway
-
Returns the IMetadataPrx service.
- getMicroscopeLotNumber() - Method in class omero.gateway.model.InstrumentData
-
Returns the lot number of the microscope.
- getMicroscopeManufacturer() - Method in class omero.gateway.model.InstrumentData
-
Returns the model of the microscope.
- getMicroscopeModel() - Method in class omero.gateway.model.InstrumentData
-
Returns the model of the microscope.
- getMicroscopeSerialNumber() - Method in class omero.gateway.model.InstrumentData
-
Returns the serial number of the microscope.
- getMicroscopeType() - Method in class omero.gateway.model.InstrumentData
-
Returns the type of microscope.
- getMiddleName() - Method in class omero.gateway.model.ExperimenterData
-
Returns the middle name of the experimenter.
- getMIMEType() - Method in class omero.gateway.util.TIFFFilter
-
Returns the MIME type.
- getMode() - Method in class omero.gateway.model.ChannelAcquisitionData
-
Returns the mode.
- getMode() - Method in class omero.gateway.model.ChannelData
-
Returns the mode.
- getModeAsEnum() - Method in class omero.gateway.model.ChannelData
-
Returns the acquisition enumeration value.
- getModel() - Method in class omero.gateway.model.DetectorData
-
Returns the manufacturer of the detector.
- getModel() - Method in class omero.gateway.model.DichroicData
-
Returns the model.
- getModel() - Method in class omero.gateway.model.FilterData
-
Returns the model.
- getModel() - Method in class omero.gateway.model.FilterSetData
-
Returns the model.
- getModel() - Method in class omero.gateway.model.ObjectiveData
-
Returns the model of the objective.
- getModelType(String) - Static method in class omero.gateway.util.PojoMapper
-
- getModelType(Class<? extends DataObject>) - Static method in class omero.gateway.util.PojoMapper
-
Converts the specified POJO into the corresponding model class.
- getName() - Method in class omero.gateway.model.ChannelData
-
Returns the name of the channel.
- getName() - Method in class omero.gateway.model.DatasetData
-
Returns the name of the dataset.
- getName() - Method in class omero.gateway.model.FileData
-
Returns the name of the file.
- getName() - Method in class omero.gateway.model.FolderData
-
Get the name of the Folder
- getName() - Method in class omero.gateway.model.GroupData
-
Returns the name of the group.
- getName() - Method in class omero.gateway.model.ImageData
-
Returns the name of the image.
- getName() - Method in class omero.gateway.model.PlateAcquisitionData
-
Returns the name of the plate acquisition.
- getName() - Method in class omero.gateway.model.PlateData
-
Returns the name of the plate.
- getName() - Method in class omero.gateway.model.ProjectData
-
Returns the name of the project.
- getName() - Method in class omero.gateway.model.ScreenData
-
Returns the name of the screen.
- getName() - Method in class omero.gateway.model.TableDataColumn
-
Get the header
- getNameSpace() - Method in class omero.gateway.model.AnnotationData
-
Retrieves the nameSpace of the underlying
Annotation instance.
- getNDFilter() - Method in class omero.gateway.model.ChannelData
-
Returns the ND filter wavelength of the channel.
- getNominalMagnification() - Method in class omero.gateway.model.ObjectiveData
-
Returns the objective's nominal magnification factor.
- getNumberOfRows() - Method in class omero.gateway.model.TableData
-
- getObject() - Method in class omero.gateway.model.SearchResult
-
Get the found object
- getObjectId() - Method in class omero.gateway.model.SearchResult
-
Get the Id of the found object
- getObjective() - Method in class omero.gateway.model.ImageAcquisitionData
-
Returns the objective used to capture the image.
- getObjective() - Method in class omero.gateway.model.OTFData
-
Returns the associated objective.
- getObjectives() - Method in class omero.gateway.model.InstrumentData
-
Returns the collection of objectives.
- getObjectiveSettingsId() - Method in class omero.gateway.model.ImageAcquisitionData
-
Returns the id of the Objective settings or -1
if not already linked to the image.
- getOffset() - Method in class omero.gateway.model.DetectorData
-
Returns the offset of the detector.
- getOffset() - Method in class omero.gateway.model.TableData
-
Get the row offset (if this
TableData represents only a subset of
the original table)
- getOriginalFileId() - Method in class omero.gateway.model.TableData
-
Get the original file id
- getOriginalMimetype() - Method in class omero.gateway.model.FileAnnotationData
-
Returns the format of the original file.
- getOrphanedImages(SecurityContext, long) - Method in class omero.gateway.facility.BrowseFacility
-
Get orphaned images for a certain user
- getOTF() - Method in class omero.gateway.model.ChannelAcquisitionData
-
Returns the OTF used for that channel.
- getOTF() - Method in class omero.gateway.model.InstrumentData
-
Returns the collection of OTFs.
- getOwner() - Method in class omero.gateway.model.DataObject
-
Returns the owner of the object.
- getParentFilePath() - Method in class omero.gateway.model.ImageData
-
Returns the path to the file hosting the image.
- getParentFolder() - Method in class omero.gateway.model.FolderData
-
Get the the parent folder
- getParentFromLink(IObject) - Static method in class omero.gateway.util.ModelMapper
-
Returns the child from the passed link.
- getPassword() - Method in class omero.gateway.UserCredentials
-
Returns the password.
- getPath() - Method in class omero.gateway.model.FileData
-
Returns the (relative) path of the file.
- getPath() - Method in class omero.gateway.model.OTFData
-
Returns the path.
- getPathToFile() - Method in class omero.gateway.model.ImageData
-
Returns the path to the file.
- getPermissions() - Method in class omero.gateway.model.DataObject
-
Returns the permission of the object.
- getPermissionsLevel() - Method in class omero.gateway.model.PermissionData
-
Returns the permissions level.
- getPinholeSize(UnitsLength) - Method in class omero.gateway.model.ChannelData
-
Returns the pin hole size of the channel.
- getPixelSizeX(UnitsLength) - Method in class omero.gateway.model.PixelsData
-
Returns the dimension of a pixel along the X-axis.
- getPixelSizeY(UnitsLength) - Method in class omero.gateway.model.PixelsData
-
Returns the dimension of a pixel along the Y-axis.
- getPixelSizeZ(UnitsLength) - Method in class omero.gateway.model.PixelsData
-
Returns the dimension of a pixel along the Z-axis
Note: Do not use the returned Length object to modify the
pixel size, use the setPixelSizeZ method instead.
- getPixelsService(SecurityContext) - Method in class omero.gateway.Gateway
-
Returns the IPixelsPrx service.
- getPixelsStore(SecurityContext) - Method in class omero.gateway.Gateway
-
Returns the RawPixelsStorePrx service.
- getPixelsType() - Method in class omero.gateway.model.OTFData
-
Returns the pixels type.
- getPixelType() - Method in class omero.gateway.model.PixelsData
-
Returns the pixels type.
- getPixelValue(int, int) - Method in class omero.gateway.rnd.Plane2D
-
Returns the pixels value at the point specified by the x-coordinate
and y-coordinate.
- getPixelValues() - Method in class omero.gateway.rnd.Plane2D
-
Returns the pixels values
- getPlane(SecurityContext, PixelsData, int, int, int) - Method in class omero.gateway.facility.RawDataFacility
-
Extracts a 2D plane from the pixels set.
- getPlane(int, int, int) - Method in class omero.gateway.rnd.DataSink
-
Extracts a 2D plane from the pixels set this object is working for.
- getPlaneCount() - Method in class omero.gateway.model.ROIData
-
- getPlate() - Method in class omero.gateway.model.WellData
-
Returns the plate containing this Well.
- getPlateAcquisitions() - Method in class omero.gateway.model.PlateData
-
Returns the plate acquisitions related to this plate.
- getPlates(SecurityContext) - Method in class omero.gateway.facility.BrowseFacility
-
Loads all plates
- getPlates(SecurityContext, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility
-
Loads the plates with the given ids
- getPlates(SecurityContext, long) - Method in class omero.gateway.facility.BrowseFacility
-
Loads the plates for a particular user
- getPlates(SecurityContext, long, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility
-
Loads the plates with the given ids which belong to a particular user
- getPlates() - Method in class omero.gateway.model.ScreenData
-
Returns the plates contained in this screen.
- getPlateType() - Method in class omero.gateway.model.PlateData
-
Returns the type of plate e.g.
- getPockelCell() - Method in class omero.gateway.model.ChannelData
-
Returns the Pockel cell settings.
- getPoints() - Method in class omero.gateway.model.PolygonData
-
Returns the points in the polygon.
- getPoints() - Method in class omero.gateway.model.PolylineData
-
Returns the points in the Polyline.
- getPojosService(SecurityContext) - Method in class omero.gateway.Gateway
-
Returns the IContainerPrx service.
- getPojoType(Class<? extends IObject>) - Static method in class omero.gateway.util.PojoMapper
-
- getPort() - Method in class omero.gateway.ServerInformation
-
Return the port
- getPositionX(UnitsLength) - Method in class omero.gateway.model.ImageAcquisitionData
-
Returns the x-coordinate in the frame microscope.
- getPositionX(UnitsLength) - Method in class omero.gateway.model.WellSampleData
-
Returns the position X.
- getPositionY(UnitsLength) - Method in class omero.gateway.model.ImageAcquisitionData
-
Returns the y-coordinate in the frame microscope.
- getPositionY(UnitsLength) - Method in class omero.gateway.model.WellSampleData
-
Returns the position Y.
- getPositionZ(UnitsLength) - Method in class omero.gateway.model.ImageAcquisitionData
-
Returns the z-coordinate in the frame microscope.
- getPower(UnitsPower) - Method in class omero.gateway.model.LightSourceData
-
Returns the power of the light source.
- getProjectionService(SecurityContext) - Method in class omero.gateway.Gateway
-
Returns the IProjectionPrx service.
- getProjects(SecurityContext) - Method in class omero.gateway.facility.BrowseFacility
-
Get all projects
- getProjects(SecurityContext, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility
-
Get the projects for the given project ids
- getProjects(SecurityContext, long) - Method in class omero.gateway.facility.BrowseFacility
-
Get the projects of a certain user
- getProjects(SecurityContext, long, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility
-
Get the projects for the given project ids which belong to a certain user
- getProjects() - Method in class omero.gateway.model.DatasetData
-
Returns a set of projects containing the dataset.
- getPropertyChangeListeners() - Method in class omero.gateway.Gateway
-
Get the PropertyChangeListeners
- getProtocolDescription() - Method in class omero.gateway.model.ScreenData
-
Returns the description of the protocol.
- getProtocolIdentifier() - Method in class omero.gateway.model.ScreenData
-
Returns the identifier of the protocol.
- getQuery() - Method in class omero.gateway.model.SearchParameters
-
Returns the query terms to search for
- getQueryService(SecurityContext) - Method in class omero.gateway.Gateway
-
Returns the IQueryPrx service.
- getRadiusX() - Method in class omero.gateway.model.EllipseData
-
Returns the radius along the X-axis.
- getRadiusY() - Method in class omero.gateway.model.EllipseData
-
Returns the radius along the Y-axis.
- getRating() - Method in class omero.gateway.model.RatingAnnotationData
-
Returns the rating value.
- getRawFileService(SecurityContext) - Method in class omero.gateway.Gateway
-
Returns the RawFileStorePrx service.
- getRawValue(int) - Method in class omero.gateway.rnd.Plane2D
-
Returns the raw data value at the given offset
- getReagentsCounts() - Method in class omero.gateway.model.WellData
-
Returns the number of reagents linked to the object, key: id of the user,
value: number of annotation.
- getReagentSetDescripion() - Method in class omero.gateway.model.ScreenData
-
Returns the description of the reagent set.
- getReagentSetIdentifier() - Method in class omero.gateway.model.ScreenData
-
Returns the identifier of the Reagent set.
- getRed() - Method in class omero.gateway.model.WellData
-
Returns the red component of the color associated to the well,
or -1.
- getReference() - Method in class omero.gateway.model.ImageData
-
Returns the reference to the file to register.
- getRefPlateId() - Method in class omero.gateway.model.PlateAcquisitionData
-
Returns the id of the plate of reference.
- getRefractiveIndex() - Method in class omero.gateway.model.ImageAcquisitionData
-
Returns the refractive index of the objective.
- getRenderingEngines() - Method in class omero.gateway.Gateway
-
Returns the rendering engines to re-activate.
- getRenderingService(SecurityContext, long) - Method in class omero.gateway.Gateway
-
Returns the Rendering service.
- getRenderingSettingsService(SecurityContext) - Method in class omero.gateway.Gateway
-
Returns the IRenderingSettingsPrx service.
- getRepositoryService(SecurityContext) - Method in class omero.gateway.Gateway
-
Returns the IRepositoryInfoPrx service.
- getResult() - Method in class omero.gateway.model.ROIResult
-
Returns the result.
- getResults(int, Class<? extends DataObject>) - Method in class omero.gateway.model.SearchResultCollection
-
Get all results of a certain scope and/or type
- getRGBA(Color) - Static method in class omero.gateway.model.ShapeSettingsData
-
Returns the Color's RGBA value as integer
- getROI() - Method in class omero.gateway.util.ROIComponent
-
Returns all the ROI in the component as a list.
- getROI() - Method in class omero.gateway.util.UploadMask
-
Returns the ROIs created from uploading the images.
- getROICoordinate() - Method in class omero.gateway.model.ShapeData
-
Returns the ROICoordinate for the ShapeData.
- getROICount(SecurityContext, long) - Method in class omero.gateway.facility.ROIFacility
-
Get the number of ROIs for an image (-1
in case of error)
- getROIFolders(SecurityContext, long) - Method in class omero.gateway.facility.ROIFacility
-
Get all ROI folders for a certain image
- getROIs() - Method in class omero.gateway.model.ROIResult
-
Returns the collection of ROIs.
- getROIService(SecurityContext) - Method in class omero.gateway.Gateway
-
Returns the IRoiPrx service.
- getRow() - Method in class omero.gateway.model.WellData
-
Returns the row used to indicate the location of the well on the grid.
- getRowSequenceIndex() - Method in class omero.gateway.model.PlateData
-
Returns the index indicating how to label a row.
- getScope() - Method in class omero.gateway.model.SearchParameters
-
Returns the scope of the search.
- getScopeId() - Method in class omero.gateway.model.SearchResult
-
The Id of the search scope, e.g.
- getScreens(SecurityContext) - Method in class omero.gateway.facility.BrowseFacility
-
Loads all screens
- getScreens(SecurityContext, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility
-
Loads the screens with the given ids
- getScreens(SecurityContext, long) - Method in class omero.gateway.facility.BrowseFacility
-
Loads the screens for a particular user
- getScreens(SecurityContext, long, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility
-
Loads the screens with the given ids which belong to a particular user
- getScreens() - Method in class omero.gateway.model.PlateData
-
Returns a set of screens containing the plate.
- getScriptService(SecurityContext) - Method in class omero.gateway.Gateway
-
Returns the IScriptPrx service.
- getSearchService(SecurityContext) - Method in class omero.gateway.Gateway
-
Returns the SearchPrx service.
- getSerialNumber() - Method in class omero.gateway.model.DetectorData
-
Returns the serial number of the detector.
- getSerialNumber() - Method in class omero.gateway.model.DichroicData
-
Returns the serial number.
- getSerialNumber() - Method in class omero.gateway.model.FilterData
-
Returns the serial number.
- getSerialNumber() - Method in class omero.gateway.model.FilterSetData
-
Returns the serial number.
- getSerialNumber() - Method in class omero.gateway.model.LightSourceData
-
Returns the serial number of the light source.
- getSerialNumber() - Method in class omero.gateway.model.ObjectiveData
-
Returns the serial number of the objective.
- getSeries() - Method in class omero.gateway.model.ImageData
-
Returns the series.
- getServer() - Method in class omero.gateway.LoginCredentials
-
Returns the server information.
- getServerFileMimetype() - Method in class omero.gateway.model.FileAnnotationData
-
Returns the file format as defined by the specification, corresponding to
the file extension.
- getServerInformation() - Method in class omero.gateway.SecurityContext
-
- getServerVersion() - Method in class omero.gateway.Gateway
-
Get the version of the server the Gateway is connected to
- getSessionId(ExperimenterData) - Method in class omero.gateway.Gateway
-
Get the ID of the current session
- getShapeCount() - Method in class omero.gateway.model.ROIData
-
Returns the number of shapes in the ROI.
- getShapes() - Method in class omero.gateway.model.ROIData
-
Returns a list of all shapes.
- getShapes(int, int) - Method in class omero.gateway.model.ROIData
-
Returns a list of shapes on a given plane, including
shapes which are not specifically attached to the plane
(span over all z planes and/or timepoints).
- getShapes(int, int, boolean) - Method in class omero.gateway.model.ROIData
-
Returns a list of shapes on a given plane.
- getShapeSettings() - Method in class omero.gateway.model.ShapeData
-
Returns the settings associated to the shape.
- getShapesInRange(ROICoordinate, ROICoordinate) - Method in class omero.gateway.model.ROIData
-
- getSharedResources(SecurityContext) - Method in class omero.gateway.Gateway
-
Returns the SharedResourcesPrx service.
- getSizeC() - Method in class omero.gateway.model.PixelsData
-
Returns the number of channels.
- getSizeT() - Method in class omero.gateway.model.PixelsData
-
Returns the number of time-points.
- getSizeX() - Method in class omero.gateway.model.OTFData
-
Returns the size along the X-axis.
- getSizeX() - Method in class omero.gateway.model.PixelsData
-
Returns the number of pixels along the X-axis.
- getSizeY() - Method in class omero.gateway.model.OTFData
-
Returns the size along the Y-axis.
- getSizeY() - Method in class omero.gateway.model.PixelsData
-
Returns the number of pixels along the Y-axis.
- getSizeZ() - Method in class omero.gateway.model.PixelsData
-
Returns the number of pixels along the Z-axis.
- getStageLabelId() - Method in class omero.gateway.model.ImageAcquisitionData
-
Returns the id of the StageLabel or -1
if not already linked to the image.
- getStart() - Method in class omero.gateway.model.SearchParameters
-
Returns the lower bound of the time interval.
- getStartTime() - Method in class omero.gateway.model.PlateAcquisitionData
-
Returns the time when the first image was collected.
- getStartTime() - Method in class omero.gateway.model.WellSampleData
-
Returns the time at which the field was acquired.
- getStatus() - Method in class omero.gateway.model.PlateData
-
Returns the status of the plate.
- getStatus() - Method in class omero.gateway.model.WellData
-
Returns the status of the well.
- getStringRepresentation() - Method in enum omero.gateway.model.SearchScope
-
Get a String representation of this scope which can be used in a
lucene search
- getStringRepresentation(Collection<SearchScope>) - Static method in enum omero.gateway.model.SearchScope
-
Get a String representation of the given scopes which can be used in a
lucence search
- getStringSeparator(String) - Static method in class omero.gateway.util.Utils
-
Returns the separator or null.
- getStroke() - Method in class omero.gateway.model.ShapeSettingsData
-
Returns the color of the stroke.
- getStrokeDashArray() - Method in class omero.gateway.model.ShapeSettingsData
-
Returns the stroke dashes.
- getStrokeWidth(UnitsLength) - Method in class omero.gateway.model.ShapeSettingsData
-
Returns the stroke's width (or 1 px if it's not set or less than or equals to 0)
- getT() - Method in class omero.gateway.model.ShapeData
-
Returns the time-point.
- getTable(SecurityContext, long) - Method in class omero.gateway.facility.TablesFacility
-
- getTable(SecurityContext, long, long, long, int...) - Method in class omero.gateway.facility.TablesFacility
-
Load data from a table
- getTable(SecurityContext, long, List<Long>) - Method in class omero.gateway.facility.TablesFacility
-
Load data from a table
- getTable(SecurityContext, long, long...) - Method in class omero.gateway.facility.TablesFacility
-
Load data from a table
- getTable(SecurityContext, long, long, long, long...) - Method in class omero.gateway.facility.TablesFacility
-
Load data from a table
- getTableID() - Method in class omero.gateway.model.TableResult
-
Returns the id of the table.
- getTableInfo(SecurityContext, long) - Method in class omero.gateway.facility.TablesFacility
-
Get basic information about a table.
- getTagDescription() - Method in class omero.gateway.model.TagAnnotationData
-
Returns the description of the tag.
- getTagDescriptions() - Method in class omero.gateway.model.TagAnnotationData
-
Returns the descriptions linked to that tag.
- getTags() - Method in class omero.gateway.model.TagAnnotationData
-
Returns the collection of tags related to this tag.
- getTagValue() - Method in class omero.gateway.model.TagAnnotationData
-
Returns the text of the tag.
- getTemperature(UnitsTemperature) - Method in class omero.gateway.model.ImageAcquisitionData
-
Returns the temperature.
- getTerm() - Method in class omero.gateway.model.TermAnnotationData
-
Returns the term.
- getTermDescription() - Method in class omero.gateway.model.TermAnnotationData
-
Returns the description of the term.
- getText() - Method in class omero.gateway.model.EllipseData
-
Returns the text of the shape.
- getText() - Method in class omero.gateway.model.LineData
-
Returns the text of the shape.
- getText() - Method in class omero.gateway.model.MaskData
-
Returns the text of the shape.
- getText() - Method in class omero.gateway.model.PointData
-
Returns the text of the shape.
- getText() - Method in class omero.gateway.model.PolygonData
-
Returns the text of the shape.
- getText() - Method in class omero.gateway.model.PolylineData
-
Returns the text of the shape.
- getText() - Method in class omero.gateway.model.RectangleData
-
Returns the text of the shape.
- getText() - Method in class omero.gateway.model.TextData
-
Returns the text of the shape.
- getText() - Method in class omero.gateway.model.TextualAnnotationData
-
Returns the text of this annotation.
- getText() - Method in class omero.gateway.model.XMLAnnotationData
-
Returns the text of this annotation.
- getThumbnailService(SecurityContext) - Method in class omero.gateway.Gateway
-
Returns the ThumbnailStorePrx service.
- getTile(SecurityContext, PixelsData, int, int, int, int, int, int, int) - Method in class omero.gateway.facility.RawDataFacility
-
Extracts a 2D tile from the pixels set
- getTile(int, int, int, int, int, int, int) - Method in class omero.gateway.rnd.DataSink
-
Extracts a 2D tile from the pixels set this object is working for.
- getTime() - Method in class omero.gateway.model.TimeAnnotationData
-
Returns the time value.
- getTimePoint() - Method in class omero.gateway.model.ROICoordinate
-
Returns the timepoint.
- getTransform() - Method in class omero.gateway.model.ShapeData
-
Returns the transformation.
- getTransmittance() - Method in class omero.gateway.model.FilterData
-
Returns the cut out tolerance value or -1.
- getType() - Method in class omero.gateway.model.DetectorData
-
Returns the type of the detector.
- getType() - Method in class omero.gateway.model.FilterData
-
Returns the type.
- getType() - Method in class omero.gateway.model.LightSourceData
-
Returns the type of light.
- getType() - Method in class omero.gateway.model.SearchResult
-
Get the type (class) of objects to search for see
DataObject
- getType() - Method in class omero.gateway.model.TableDataColumn
-
Get the data type
- getTypes() - Method in class omero.gateway.model.SearchParameters
-
Returns the types to search on.
- getTypesService(SecurityContext) - Method in class omero.gateway.Gateway
-
Returns the ITypesPrx service.
- getUpdated() - Method in class omero.gateway.model.DataObject
-
Returns the updated time of the object.
- getUpdateService(SecurityContext) - Method in class omero.gateway.Gateway
-
Returns the IUpdatePrx service.
- getUpdateService(SecurityContext, String) - Method in class omero.gateway.Gateway
-
Returns the IUpdatePrx service.
- getUsedFilePaths() - Method in class omero.gateway.model.FilesetData
-
Returns the collection of file paths used for importing the files
(in case of in-place imports these are the targets of the (sym)links)
- getUser() - Method in class omero.gateway.LoginCredentials
-
Returns the credentials.
- getUserDetails(SecurityContext, String) - Method in class omero.gateway.Gateway
-
Get the user details of a certain user
- getUserId() - Method in class omero.gateway.model.SearchParameters
-
- getUserImages(SecurityContext) - Method in class omero.gateway.facility.BrowseFacility
-
Loads all images of the logged in user
- getUserName() - Method in class omero.gateway.model.ExperimenterData
-
Returns the last name of the experimenter.
- getUsername() - Method in class omero.gateway.UserCredentials
-
Returns the user name (or session ID, if it was set before instead of an
username)
- getUuid() - Method in class omero.gateway.model.ROIData
-
Get the UUID
- getValue() - Method in class omero.gateway.model.BooleanAnnotationData
-
Returns the text of this annotation.
- getVersion() - Method in class omero.gateway.model.DataObject
-
Returns the version of the object if the object is immutable,
false otherwise.
- getVoltage(UnitsElectricPotential) - Method in class omero.gateway.model.DetectorData
-
Returns the voltage of the detector.
- getWellOriginX(UnitsLength) - Method in class omero.gateway.model.PlateData
-
Returns the x-coordinate in 2D-space of the well.
- getWellOriginY(UnitsLength) - Method in class omero.gateway.model.PlateData
-
Returns the y-coordinate in 2D-space of the well.
- getWells(SecurityContext, Collection<Long>) - Method in class omero.gateway.facility.BrowseFacility
-
Loads the wells
- getWells(SecurityContext, long) - Method in class omero.gateway.facility.BrowseFacility
-
Loads the wells for a given plate
- getWellSamples() - Method in class omero.gateway.model.WellData
-
Returns the well samples linked to the well.
- getWellType() - Method in class omero.gateway.model.WellData
-
Returns a human readable identifier for the screening status e.g.
- getWidth() - Method in class omero.gateway.model.MaskData
-
Returns the width of the mask.
- getWidth() - Method in class omero.gateway.model.RectangleData
-
Returns the width untransformed rectangle.
- getWorkingDistance(UnitsLength) - Method in class omero.gateway.model.ObjectiveData
-
Returns the working distance.
- getX() - Method in class omero.gateway.model.EllipseData
-
Returns the x-coordinate of the center of the ellipse.
- getX() - Method in class omero.gateway.model.MaskData
-
Returns the x-coordinate of the top-left corner of the mask.
- getX() - Method in class omero.gateway.model.PointData
-
Returns the x-coordinate of the shape.
- getX() - Method in class omero.gateway.model.RectangleData
-
Returns the x-coordinate of the top-left corner of an untransformed
rectangle.
- getX() - Method in class omero.gateway.model.TextData
-
Returns the x-coordinate text field.
- getX1() - Method in class omero.gateway.model.LineData
-
Returns the x-coordinate of the starting point of an untransformed line.
- getX2() - Method in class omero.gateway.model.LineData
-
Returns the x-coordinate of the end point of an untransformed line.
- getY() - Method in class omero.gateway.model.EllipseData
-
Returns the y-coordinate of the center of the ellipse.
- getY() - Method in class omero.gateway.model.MaskData
-
Returns the y-coordinate of the top-left corner of the mask.
- getY() - Method in class omero.gateway.model.PointData
-
Returns the y coordinate of the shape.
- getY() - Method in class omero.gateway.model.RectangleData
-
Returns the y-coordinate of the top-left corner of an
untransformed rectangle.
- getY() - Method in class omero.gateway.model.TextData
-
Returns the y-coordinate text field.
- getY1() - Method in class omero.gateway.model.LineData
-
Returns the y-coordinate of the starting point of an untransformed line.
- getY2() - Method in class omero.gateway.model.LineData
-
Returns the y-coordinate of the end point of an untransformed line.
- getZ() - Method in class omero.gateway.model.ShapeData
-
Returns the z-section.
- getZoom() - Method in class omero.gateway.model.DetectorData
-
Returns the offset of the detector.
- getZSection() - Method in class omero.gateway.model.ROICoordinate
-
Returns the z-section.
- GROUP_EXPERIMENTER_MAP - Static variable in class omero.gateway.model.ExperimenterData
-
Identifies the ExperimenterI.GROUPEXPERIMENTERMAP field.
- GROUP_EXPERIMENTER_MAP - Static variable in class omero.gateway.model.GroupData
-
Identifies the ExperimenterGroupI.GROUPEXPERIMENTERMAP field.
- GroupData - Class in omero.gateway.model
-
The data that makes up an OME Group along with the various members of
the Group
- GroupData() - Constructor for class omero.gateway.model.GroupData
-
Creates a new instance.
- GroupData(ExperimenterGroup) - Constructor for class omero.gateway.model.GroupData
-
Creates a new instance.
- GUEST - Static variable in class omero.gateway.model.GroupData
-
Identifies the Guest group.
- saveAndReturnObject(SecurityContext, IObject, Map) - Method in class omero.gateway.facility.DataManagerFacility
-
Updates the specified object.
- saveAndReturnObject(SecurityContext, DataObject) - Method in class omero.gateway.facility.DataManagerFacility
-
Updates the specified object.
- saveAndReturnObject(SecurityContext, IObject) - Method in class omero.gateway.facility.DataManagerFacility
-
Updates the specified object.
- saveAndReturnObject(SecurityContext, IObject, Map, String) - Method in class omero.gateway.facility.DataManagerFacility
-
Updates the specified object.
- saveAndReturnObject(SecurityContext, DataObject, String) - Method in class omero.gateway.facility.DataManagerFacility
-
Updates the specified object.
- saveAndReturnObject(SecurityContext, IObject, String) - Method in class omero.gateway.facility.DataManagerFacility
-
Updates the specified object.
- saveAndReturnObject(SecurityContext, List<IObject>, Map, String) - Method in class omero.gateway.facility.DataManagerFacility
-
Updates the specified object.
- saveROIs(SecurityContext, long, Collection<ROIData>) - Method in class omero.gateway.facility.ROIFacility
-
Save the ROI for the image to the server.
- saveROIs(SecurityContext, long, long, Collection<ROIData>) - Method in class omero.gateway.facility.ROIFacility
-
Save the ROI for the image to the server.
- SCREEN_LINKS - Static variable in class omero.gateway.model.PlateData
-
Identifies the PlateI.SCREENLINKS field.
- ScreenData - Class in omero.gateway.model
-
The data that makes up an OME Screen along with links to its
contained Plates and the Experimenter that owns this Screen.
- ScreenData() - Constructor for class omero.gateway.model.ScreenData
-
Creates a new instance.
- ScreenData(Screen) - Constructor for class omero.gateway.model.ScreenData
-
Creates a new instance.
- search(SecurityContext, SearchParameters) - Method in class omero.gateway.facility.SearchFacility
-
Searches for data.
- SearchFacility - Class in omero.gateway.facility
-
- SearchParameters - Class in omero.gateway.model
-
- SearchParameters(Set<SearchScope>, List<Class<? extends DataObject>>, String) - Constructor for class omero.gateway.model.SearchParameters
-
Creates a new instance.
- SearchResult - Class in omero.gateway.model
-
Encapsulates a single object found by a search together with the search scope
(name, description, etc.) it was found with.
- SearchResult() - Constructor for class omero.gateway.model.SearchResult
-
Create a new instance
- SearchResult(int, Class<? extends DataObject>, long, long) - Constructor for class omero.gateway.model.SearchResult
-
Create a new instance
- SearchResultCollection - Class in omero.gateway.model
-
Holds the results of a search; a collection of
SearchResults
- SearchResultCollection() - Constructor for class omero.gateway.model.SearchResultCollection
-
- SearchScope - Enum in omero.gateway.model
-
Defines the scope of a search, i.e.
- SecurityContext - Class in omero.gateway
-
Hosts information required to access correct connector.
- SecurityContext(long) - Constructor for class omero.gateway.SecurityContext
-
Creates a new instance.
- ServerInformation - Class in omero.gateway
-
Holds hostname and port of an OMERO server
- ServerInformation() - Constructor for class omero.gateway.ServerInformation
-
Creates an empty instance
- ServerInformation(String, int) - Constructor for class omero.gateway.ServerInformation
-
Creates a new instance
- setAdminPrivileges(SecurityContext, ExperimenterData, Collection<String>) - Method in class omero.gateway.facility.AdminFacility
-
Set the admin privileges of a certain user
(see omero.model.enums)
- setAirPressure(Pressure) - Method in class omero.gateway.model.ImageAcquisitionData
-
Sets the air pressure.
- setAllPixels(List<PixelsData>) - Method in class omero.gateway.model.ImageData
-
Sets the set of pixels related to this image.
- setAlpha(Integer) - Method in class omero.gateway.model.WellData
-
Sets the alpha component of the color associated to the well.
- setAnnotations(Set) - Method in class omero.gateway.model.DatasetData
-
Sets the annotations related to this dataset.
- setAnnotations(Set) - Method in class omero.gateway.model.ImageData
-
Sets the image's annotations.
- setApplicationName(String) - Method in class omero.gateway.LoginCredentials
-
Set the application name
- setBit(byte[], int, int) - Method in class omero.gateway.model.MaskData
-
Sets the bit value in a byte array at position bit to be the value
value.
- setBlue(Integer) - Method in class omero.gateway.model.WellData
-
Sets the blue component of the color associated to the well.
- setC(int) - Method in class omero.gateway.model.ShapeData
-
Sets the channel.
- setCacheEntries(int, int) - Method in interface omero.gateway.cache.CacheService
-
Resets the number of items in memory of the cache,
when a new cache is created or deleted.
- setCheckNetwork(boolean) - Method in class omero.gateway.LoginCredentials
-
Enable/Disable network checks
- setCheckVersion(boolean) - Method in class omero.gateway.LoginCredentials
-
Enable/Disable version check
- setClientObject(boolean) - Method in class omero.gateway.model.ShapeData
-
Sets to true if the object one that has been created client
side, false otherwise.
- setClientSide(boolean) - Method in class omero.gateway.model.ROIData
-
Sets the flag indicating if the object is a client-side object or not.
- setCo2Percent(double) - Method in class omero.gateway.model.ImageAcquisitionData
-
Sets the co2 level.
- setCompleted() - Method in class omero.gateway.model.TableData
-
- setCompression(float) - Method in class omero.gateway.LoginCredentials
-
Sets the compression level
- setCompression(float) - Method in class omero.gateway.SecurityContext
-
Set the compression level
- setContent(Object) - Method in class omero.gateway.model.AnnotationData
-
Sets the annotation value.
- setContent(Object) - Method in class omero.gateway.model.BooleanAnnotationData
-
Sets the text annotation.
- setContent(Object) - Method in class omero.gateway.model.DoubleAnnotationData
-
Sets the text annotation.
- setContent(Object) - Method in class omero.gateway.model.FileAnnotationData
-
Sets the text annotation.
- setContent(Object) - Method in class omero.gateway.model.LongAnnotationData
-
Sets the text annotation.
- setContent(Object) - Method in class omero.gateway.model.MapAnnotationData
-
- setContent(Object) - Method in class omero.gateway.model.RatingAnnotationData
-
Sets the text annotation.
- setContent(Object) - Method in class omero.gateway.model.TagAnnotationData
-
Sets the text annotation.
- setContent(Object) - Method in class omero.gateway.model.TermAnnotationData
-
Sets the text annotation.
- setContent(Object) - Method in class omero.gateway.model.TextualAnnotationData
-
Sets the text annotation.
- setContent(Object) - Method in class omero.gateway.model.TimeAnnotationData
-
Sets the time annotation.
- setContent(Object) - Method in class omero.gateway.model.XMLAnnotationData
-
Sets the annotation.
- setContrastMethod(ContrastMethod) - Method in class omero.gateway.model.ChannelData
-
Sets the contrast method value.
- setCorrectionCollar(double) - Method in class omero.gateway.model.ImageAcquisitionData
-
Sets the correction of the objective.
- setDataObjects(Set<DataObject>) - Method in class omero.gateway.model.TagAnnotationData
-
Sets the collection of data objects related to that tag.
- setDatasets(Set) - Method in class omero.gateway.model.ImageData
-
Sets the datasets containing the image.
- setDatasets(Set<DatasetData>) - Method in class omero.gateway.model.ProjectData
-
Sets the datasets contained in this project.
- setDataValue(double) - Method in class omero.gateway.model.DoubleAnnotationData
-
Sets the rating value.
- setDataValue(long) - Method in class omero.gateway.model.LongAnnotationData
-
Sets the rating value.
- setDateType(int) - Method in class omero.gateway.model.SearchParameters
-
- setDefaultPixels(PixelsData) - Method in class omero.gateway.model.ImageData
-
Sets the default set of pixels.
- setDefaultSample(int) - Method in class omero.gateway.model.PlateData
-
Sets the default sample.
- setDescription(String) - Method in class omero.gateway.model.AnnotationData
-
Sets the description of the underlying Annotation instance.
- setDescription(String) - Method in class omero.gateway.model.DatasetData
-
Sets the description of the dataset.
- setDescription(String) - Method in class omero.gateway.model.FileAnnotationData
-
Sets the description of the annotation.
- setDescription(String) - Method in class omero.gateway.model.FileData
-
Sets the description.
- setDescription(String) - Method in class omero.gateway.model.FolderData
-
Set the description of the Folder
- setDescription(String) - Method in class omero.gateway.model.GroupData
-
Sets the name of the group.
- setDescription(String) - Method in class omero.gateway.model.ImageData
-
Sets the description of the image.
- setDescription(String) - Method in class omero.gateway.model.PlateAcquisitionData
-
Sets the name of the acquisition.
- setDescription(String) - Method in class omero.gateway.model.PlateData
-
Sets the description of the plate.
- setDescription(String) - Method in class omero.gateway.model.ProjectData
-
Sets the description of the project.
- setDescription(String) - Method in class omero.gateway.model.ScreenData
-
Sets the description of the screen.
- setDescription(String) - Method in class omero.gateway.model.TableDataColumn
-
Set the description
- setDescription(String) - Method in class omero.gateway.model.XMLAnnotationData
-
Sets the description of the annotation.
- setDetectorSettingBinning(Binning) - Method in class omero.gateway.model.ChannelAcquisitionData
-
Sets the detector's binning.
- setDetectorSettingOffset(double) - Method in class omero.gateway.model.ChannelAcquisitionData
-
Sets the detector's setting offset.
- setDetectorSettingsGain(double) - Method in class omero.gateway.model.ChannelAcquisitionData
-
Sets the detector setting's gain.
- setDetectorSettingsReadOutRate(Frequency) - Method in class omero.gateway.model.ChannelAcquisitionData
-
Sets the detector setting's read out rate.
- setDetectorSettingsVoltage(ElectricPotential) - Method in class omero.gateway.model.ChannelAcquisitionData
-
Sets the detector setting's voltage.
- setDirty(boolean) - Method in class omero.gateway.model.DataObject
-
Sets to true if the value has been modified,
otherwise.
- setDirty(boolean) - Method in class omero.gateway.model.ShapeData
-
Sets to true if the figure been changed from the server
side version, false otherwise.
- setEmail(String) - Method in class omero.gateway.model.ExperimenterData
-
Sets the e-mail of the experimenter.
- setEmissionWavelength(Length) - Method in class omero.gateway.model.ChannelData
-
Sets the emission wavelength.
- setEncryption(boolean) - Method in class omero.gateway.LoginCredentials
-
Enable/Disable encryption
- setError(int) - Method in class omero.gateway.model.SearchResultCollection
-
Set the error state
- setExcitationWavelength(Length) - Method in class omero.gateway.model.ChannelData
-
Sets the excitation wavelength.
- setExperimenter(ExperimenterData) - Method in class omero.gateway.SecurityContext
-
Sets the experimenter
- setExperimenters(Set<ExperimenterData>) - Method in class omero.gateway.model.GroupData
-
Sets the experimenters contained in this group.
- setExternalDescription(String) - Method in class omero.gateway.model.WellData
-
Sets the external description of the well.
- setExternalIdentifier(String) - Method in class omero.gateway.model.PlateData
-
Sets the external identifier.
- setFill(Color) - Method in class omero.gateway.model.ShapeSettingsData
-
Set the fill color.
- setFillRule(String) - Method in class omero.gateway.model.ShapeSettingsData
-
Set the fill rule.
- setFirstName(String) - Method in class omero.gateway.model.ExperimenterData
-
Sets the first name of the experimenter.
- setFluor(String) - Method in class omero.gateway.model.ChannelData
-
Sets the fluor.
- setFolder(Folder) - Method in class omero.gateway.model.FolderData
-
Set the Folder
- setFolders(Collection<FolderData>) - Method in class omero.gateway.model.ROIResult
-
Sets the available folders
- setFontFamily(String) - Method in class omero.gateway.model.ShapeSettingsData
-
Returns the stroke.
- setFontSize(Length) - Method in class omero.gateway.model.ShapeSettingsData
-
Set the size of the font.
- setFontStyle(String) - Method in class omero.gateway.model.ShapeSettingsData
-
Sets the style of the font.
- setGreen(Integer) - Method in class omero.gateway.model.WellData
-
Sets the green component of the color associated to the well.
- setGroupAnnotate(boolean) - Method in class omero.gateway.model.PermissionData
-
Sets to true if the group has annotate access,
false otherwise.
- setGroupID(long) - Method in class omero.gateway.LoginCredentials
-
Sets the groupID to use for the connection
- setGroupId(long) - Method in class omero.gateway.model.SearchParameters
-
- setGroupId(long) - Method in class omero.gateway.model.SearchResult
-
Set the group id of the object
- setGroupRead(boolean) - Method in class omero.gateway.model.PermissionData
-
Sets to true if the group has read access,
false otherwise.
- setGroups(List<GroupData>) - Method in class omero.gateway.model.ExperimenterData
-
Sets the groups the experimenter is a member of.
- setGroupWrite(boolean) - Method in class omero.gateway.model.PermissionData
-
Sets to true if the group has write access,
false otherwise.
- setHeight(double) - Method in class omero.gateway.model.MaskData
-
Sets the height of an untransformed mask.
- setHeight(double) - Method in class omero.gateway.model.RectangleData
-
Sets the height of an untransformed rectangle.
- setHostname(String) - Method in class omero.gateway.ServerInformation
-
Set the hostname
- setHumidity(double) - Method in class omero.gateway.model.ImageAcquisitionData
-
Sets the humidity.
- setId(long) - Method in class omero.gateway.model.DataObject
-
Sets the database id.
- setIdMatch(boolean) - Method in class omero.gateway.model.SearchResult
-
Set to true if this result is an ID match.
- setIllumination(Illumination) - Method in class omero.gateway.model.ChannelData
-
Sets the illumination value.
- setImage(ImageData) - Method in class omero.gateway.model.PixelsData
-
Sets the image linked to this pixels' set.
- setImage(Image) - Method in class omero.gateway.model.ROIData
-
Sets the image for the ROI.
- setImage(ImageData) - Method in class omero.gateway.model.WellSampleData
-
Sets the image linked to this well sample.
- setImages(Set<ImageData>) - Method in class omero.gateway.model.DatasetData
-
Sets the images contained in this dataset.
- setIndex(int) - Method in exception omero.gateway.exception.RenderingServiceException
-
Sets the index indicating if the error occurred due to a network
failure.
- setIndex(int) - Method in class omero.gateway.model.TableDataColumn
-
Set the index
- setIndexes(Map<Integer, Integer>) - Method in class omero.gateway.model.TableResult
-
Sets the indexes.
- setInstitution(String) - Method in class omero.gateway.model.ExperimenterData
-
Sets the institution where the experimenter works.
- setLabelName(String) - Method in class omero.gateway.model.ImageAcquisitionData
-
Sets the name of the stage label.
- setLastName(String) - Method in class omero.gateway.model.ExperimenterData
-
Sets the last name of the experimenter.
- setLightSettingsAttenuation(double) - Method in class omero.gateway.model.ChannelAcquisitionData
-
Sets the attenuation of the light settings.
- setLightSettingsWavelength(Length) - Method in class omero.gateway.model.ChannelAcquisitionData
-
Sets the wavelength of the light source.
- setLightSource(LightSourceData) - Method in class omero.gateway.model.ChannelAcquisitionData
-
Sets the light source associated to the settings.
- setMarkerEnd(String) - Method in class omero.gateway.model.ShapeSettingsData
-
Sets the marker end.
- setMarkerStart(String) - Method in class omero.gateway.model.ShapeSettingsData
-
Sets the marker start.
- setMask(byte[]) - Method in class omero.gateway.model.MaskData
-
Sets the mask image.
- setMask(BufferedImage) - Method in class omero.gateway.model.MaskData
-
Sets the mask from the bufferedImage.
- setMask(int[]) - Method in class omero.gateway.model.MaskData
-
Set the mask
- setMask(int[][]) - Method in class omero.gateway.model.MaskData
-
Set the mask
- setMask(boolean[]) - Method in class omero.gateway.model.MaskData
-
Set the mask
- setMask(boolean[][]) - Method in class omero.gateway.model.MaskData
-
Set the mask
- setMedium(Medium) - Method in class omero.gateway.model.ImageAcquisitionData
-
Sets the medium of the objective.
- setMiddleName(String) - Method in class omero.gateway.model.ExperimenterData
-
Sets the middle name of the experimenter.
- setMode(AcquisitionMode) - Method in class omero.gateway.model.ChannelData
-
Sets the acquisition mode value.
- setName(String) - Method in class omero.gateway.model.ChannelData
-
Sets the name of the logical channel.
- setName(String) - Method in class omero.gateway.model.DatasetData
-
Sets the name of the dataset.
- setName(String) - Method in class omero.gateway.model.FolderData
-
Set the name of the Folder
- setName(String) - Method in class omero.gateway.model.GroupData
-
Sets the name of the group.
- setName(String) - Method in class omero.gateway.model.ImageData
-
Sets the name of the image.
- setName(String) - Method in class omero.gateway.model.PlateAcquisitionData
-
Sets the name of the acquisition.
- setName(String) - Method in class omero.gateway.model.PlateData
-
Sets the name of the plate.
- setName(String) - Method in class omero.gateway.model.ProjectData
-
Sets the name of the project.
- setName(String) - Method in class omero.gateway.model.ScreenData
-
Sets the name of the screen.
- setName(String) - Method in class omero.gateway.model.TableDataColumn
-
Set the header
- setNameSpace(String) - Method in class omero.gateway.model.AnnotationData
-
Sets the name space of the underlying Annotation instance.
- setNDFilter(double) - Method in class omero.gateway.model.ChannelData
-
Sets the ND filter.
- setNumberOfRows(long) - Method in class omero.gateway.model.TableData
-
Set the total number of rows in the original table
- setObject(DataObject) - Method in class omero.gateway.model.SearchResult
-
Set the found object
- setObjectId(long) - Method in class omero.gateway.model.SearchResult
-
Set the Id of the found object
- setObjects(IObject, DataObject, DataObject) - Static method in class omero.gateway.util.Links
-
Set the parent, child or both of an existing link
- setOffset(long) - Method in class omero.gateway.model.TableData
-
Set the row offset (if this
TableData represents only a subset of
the original table)
- setOriginalFileId(long) - Method in class omero.gateway.model.TableData
-
Set the originalfile id
- setParentFilePath(String, int) - Method in class omero.gateway.model.ImageData
-
Sets the path to the file hosting the image.
- setParentFolder(Folder) - Method in class omero.gateway.model.FolderData
-
Set the the parent folder
- setPassword(String) - Method in class omero.gateway.UserCredentials
-
Sets the password
- setPathToFile(String) - Method in class omero.gateway.model.ImageData
-
Sets the path to the file.
- setPinholeSize(Length) - Method in class omero.gateway.model.ChannelData
-
Sets the pinhole size.
- setPixelSizeX(Length) - Method in class omero.gateway.model.PixelsData
-
Sets the dimension of a pixel along the X-axis
- setPixelSizeY(Length) - Method in class omero.gateway.model.PixelsData
-
Sets the dimension of a pixel along the Y-axis.
- setPixelSizeZ(Length) - Method in class omero.gateway.model.PixelsData
-
Sets the dimension of a pixel along the Z-axis
- setPlateAcquisition(Set<PlateAcquisitionData>) - Method in class omero.gateway.model.PlateData
-
Sets the plate acquisition linked to the plate.
- setPlates(Set<PlateData>) - Method in class omero.gateway.model.ScreenData
-
Sets the plates contained in this screen.
- setPockelCell(int) - Method in class omero.gateway.model.ChannelData
-
Sets the pockel cell.
- setPoints(List<Point2D.Double>) - Method in class omero.gateway.model.PolygonData
-
Sets the points in the polygon.
- setPoints(List<Point2D.Double>) - Method in class omero.gateway.model.PolylineData
-
Sets the points in the polyline.
- setPort(int) - Method in class omero.gateway.ServerInformation
-
Set the port
- setPositionX(Length) - Method in class omero.gateway.model.ImageAcquisitionData
-
Sets the x-position.
- setPositionY(Length) - Method in class omero.gateway.model.ImageAcquisitionData
-
Sets the y-position.
- setPositionZ(Length) - Method in class omero.gateway.model.ImageAcquisitionData
-
Sets the z-position.
- setProjects(Set<ProjectData>) - Method in class omero.gateway.model.DatasetData
-
Sets the projects containing the dataset.
- setProtocolDescription(String) - Method in class omero.gateway.model.ScreenData
-
Sets the description of the protocol.
- setProtocolIdentifier(String) - Method in class omero.gateway.model.ScreenData
-
Sets the identifier of the protocol.
- setRadiusX(double) - Method in class omero.gateway.model.EllipseData
-
Sets the radius along the X-axis.
- setRadiusY(double) - Method in class omero.gateway.model.EllipseData
-
Sets the radius along the Y-axis.
- setRating(int) - Method in class omero.gateway.model.RatingAnnotationData
-
Sets the rating value.
- setReadOnly(boolean) - Method in class omero.gateway.model.ShapeData
-
Sets to true if the object is a read-only object,
false otherwise.
- setReagentSetDescripion(String) - Method in class omero.gateway.model.ScreenData
-
Sets the identifier of the reagent.
- setReagentSetIdentifier(String) - Method in class omero.gateway.model.ScreenData
-
Sets the identifier of the reagent.
- setRed(Integer) - Method in class omero.gateway.model.WellData
-
Sets the red component of the color associated to the well.
- setReference(OriginalFile) - Method in class omero.gateway.model.ImageData
-
Sets the reference to the file to register.
- setRefPlateId(long) - Method in class omero.gateway.model.PlateAcquisitionData
-
Sets the id of the plate this plate acquisition is for.
- setRefractiveIndex(double) - Method in class omero.gateway.model.ImageAcquisitionData
-
Sets the refractive index of the objective.
- setRegisteredFile(OriginalFile) - Method in class omero.gateway.model.FileData
-
Sets the registered file.
- setRegisteredFile(Image) - Method in class omero.gateway.model.ImageData
-
Sets the registered file.
- setRepositoryPath(String) - Method in class omero.gateway.model.FileData
-
Sets the path to the parent.
- setResult(Object) - Method in class omero.gateway.model.ROIResult
-
Sets the results.
- setROICoordinate(ROICoordinate) - Method in class omero.gateway.model.ShapeData
-
Sets the ROICoordinate for the ShapeData.
- setScopeId(int) - Method in class omero.gateway.model.SearchResult
-
Set the id of the search scope, e.g.
- setScreens(Set<ScreenData>) - Method in class omero.gateway.model.PlateData
-
Sets the screens containing the plate.
- setServerInformation(ServerInformation) - Method in class omero.gateway.SecurityContext
-
- setShapeSettings(Shape) - Method in class omero.gateway.model.ShapeData
-
Set the settings associated to the shape.
- setSizeC(int) - Method in class omero.gateway.model.PixelsData
-
Sets the number of channels.
- setSizeT(int) - Method in class omero.gateway.model.PixelsData
-
Sets the number of time-points.
- setSizeX(int) - Method in class omero.gateway.model.PixelsData
-
Sets the number of pixels along the X-axis.
- setSizeY(int) - Method in class omero.gateway.model.PixelsData
-
Sets the number of pixels along the Y-axis.
- setSizeZ(int) - Method in class omero.gateway.model.PixelsData
-
Sets the number of pixels along the Z-axis.
- setStatus(String) - Method in class omero.gateway.model.PlateData
-
Sets the status.
- setStatus(String) - Method in class omero.gateway.model.WellData
-
Sets the status of the well.
- setStroke(Color) - Method in class omero.gateway.model.ShapeSettingsData
-
Set the stroke color.
- setStrokeDashArray(double[]) - Method in class omero.gateway.model.ShapeSettingsData
-
Set the stroke dashes.
- setStrokeWidth(Length) - Method in class omero.gateway.model.ShapeSettingsData
-
Set the stroke width.
- setT(int) - Method in class omero.gateway.model.ShapeData
-
Sets the time-point.
- setTableID(long) - Method in class omero.gateway.model.TableResult
-
Sets the id of the table.
- setTagDescription(String) - Method in class omero.gateway.model.TagAnnotationData
-
Sets the description of the tag.
- setTagDescriptions(List<TextualAnnotationData>) - Method in class omero.gateway.model.TagAnnotationData
-
Sets the tag's descriptions.
- setTagValue(String) - Method in class omero.gateway.model.TagAnnotationData
-
Sets the value of the tag.
- setTemperature(Temperature) - Method in class omero.gateway.model.ImageAcquisitionData
-
Sets the temperature.
- setTerm(String) - Method in class omero.gateway.model.TermAnnotationData
-
Sets the term.
- setTermDescription(String) - Method in class omero.gateway.model.TermAnnotationData
-
Sets the description of the tag.
- setText(String) - Method in class omero.gateway.model.EllipseData
-
Sets the text of the shape.
- setText(String) - Method in class omero.gateway.model.LineData
-
Sets the text of the shape.
- setText(String) - Method in class omero.gateway.model.MaskData
-
Sets the text of the shape.
- setText(String) - Method in class omero.gateway.model.PointData
-
Sets the text of the shape.
- setText(String) - Method in class omero.gateway.model.PolygonData
-
Sets the text of the shape.
- setText(String) - Method in class omero.gateway.model.PolylineData
-
Sets the text of the shape.
- setText(String) - Method in class omero.gateway.model.RectangleData
-
Sets the text of the shape.
- setText(String) - Method in class omero.gateway.model.TextData
-
Sets the text of the shape.
- setText(String) - Method in class omero.gateway.model.TextualAnnotationData
-
Sets the text.
- setText(String) - Method in class omero.gateway.model.XMLAnnotationData
-
Sets the text value.
- setTimeInterval(Timestamp, Timestamp, int) - Method in class omero.gateway.model.SearchParameters
-
Sets the time interval.
- settings - Variable in class omero.gateway.model.ShapeData
-
The representation of the shape.
- setTransform(AffineTransform) - Method in class omero.gateway.model.ShapeData
-
Sets the Affine transform of the shape.
- setType(Class<? extends DataObject>) - Method in class omero.gateway.model.SearchResult
-
Set the type (class) of objects to search for see
DataObject
- setType(Class<?>) - Method in class omero.gateway.model.TableDataColumn
-
Set the data type
- setUserId(long) - Method in class omero.gateway.model.SearchParameters
-
- setUsername(String) - Method in class omero.gateway.UserCredentials
-
Sets the username (or session ID)
- setUserRead(boolean) - Method in class omero.gateway.model.PermissionData
-
Sets to true if the user has read access,
false otherwise.
- setUserWrite(boolean) - Method in class omero.gateway.model.PermissionData
-
Sets to true if the user has write access,
false otherwise.
- setUuid(String) - Method in class omero.gateway.model.ROIData
-
Set the UUID
- setValue(boolean) - Method in class omero.gateway.model.BooleanAnnotationData
-
Returns the text.
- setValue(IObject) - Method in class omero.gateway.model.DataObject
-
Sets the IObject.
- setVersion(int) - Method in class omero.gateway.model.DataObject
-
Sets the version of the object if it is immutable.
- setWellSamples(List<WellSampleData>) - Method in class omero.gateway.model.WellData
-
Sets the well samples linked to the well.
- setWellType(String) - Method in class omero.gateway.model.WellData
-
Sets a human readable identifier for the screening status e.g.
- setWidth(double) - Method in class omero.gateway.model.MaskData
-
Sets the width of an untransformed mask.
- setWidth(double) - Method in class omero.gateway.model.RectangleData
-
Sets width of an untransformed rectangle.
- setWorldRead(boolean) - Method in class omero.gateway.model.PermissionData
-
Sets to true if the world has read access,
false otherwise.
- setWorldWrite(boolean) - Method in class omero.gateway.model.PermissionData
-
Sets to true if the world has write access,
false otherwise.
- setX(double) - Method in class omero.gateway.model.EllipseData
-
Sets the x-coordinate of the center of the ellipse.
- setX(double) - Method in class omero.gateway.model.MaskData
-
Sets the x-coordinate top-left corner of an untransformed mask.
- setX(double) - Method in class omero.gateway.model.PointData
-
set the x-coordinate of the shape.
- setX(double) - Method in class omero.gateway.model.RectangleData
-
Sets the x-coordinate of the top-left corner of an
untransformed rectangle.
- setX(double) - Method in class omero.gateway.model.TextData
-
Sets the x-coordinate of the text field.
- setX1(double) - Method in class omero.gateway.model.LineData
-
Set the x-coordinate of the starting point of an untransformed line.
- setX2(double) - Method in class omero.gateway.model.LineData
-
Set the x-coordinate of the end point of an untransformed line.
- setY(double) - Method in class omero.gateway.model.EllipseData
-
Sets the y-coordinate of the center of the ellipse.
- setY(double) - Method in class omero.gateway.model.MaskData
-
Sets the y-coordinate top-left corner of an untransformed mask.
- setY(double) - Method in class omero.gateway.model.PointData
-
set the y-coordinate of the shape.
- setY(double) - Method in class omero.gateway.model.RectangleData
-
Sets the y-coordinate of the top-left corner of an untransformed
rectangle.
- setY(double) - Method in class omero.gateway.model.TextData
-
Sets the y-coordinate of the text field.
- setY1(double) - Method in class omero.gateway.model.LineData
-
Set the y-coordinate of the starting point of an untransformed line.
- setY2(double) - Method in class omero.gateway.model.LineData
-
Set the y-coordinate of the end point of an untransformed line.
- setZ(int) - Method in class omero.gateway.model.ShapeData
-
Sets the z-section.
- ShapeData - Class in omero.gateway.model
-
Hosts a shape.
- ShapeData(Shape, boolean) - Constructor for class omero.gateway.model.ShapeData
-
Creates a new instance.
- ShapeData(Shape) - Constructor for class omero.gateway.model.ShapeData
-
Creates a new instance.
- ShapeSettingsData - Class in omero.gateway.model
-
Stores the settings related to a given shape.
- shutDown() - Method in interface omero.gateway.cache.CacheService
-
Shuts the cache down.
- shutDownDerivedConnector(SecurityContext) - Method in class omero.gateway.Gateway
-
Shuts down the connectors created while creating/importing data for other
users.
- shutdownRenderingEngine(SecurityContext, long) - Method in class omero.gateway.Gateway
-
Shuts down the rendering engine
- skipHead() - Static method in class omero.gateway.util.Requests
-
- SkipHeadBuilder() - Constructor for class omero.gateway.util.Requests.SkipHeadBuilder
-
Instantiate a new SkipHead and initialize its collection containers.
- splitString(String) - Static method in class omero.gateway.util.Utils
-
Returns the partial name of the image's name
- startFrom(Iterable<String>) - Method in class omero.gateway.util.Requests.SkipHeadBuilder
-
- startFrom(Class<? extends IObject>...) - Method in class omero.gateway.util.Requests.SkipHeadBuilder
-
- startFrom(String...) - Method in class omero.gateway.util.Requests.SkipHeadBuilder
-
- stopBefore(Iterable<String>) - Method in class omero.gateway.util.Requests.FindChildrenBuilder
-
- stopBefore(Class<? extends IObject>...) - Method in class omero.gateway.util.Requests.FindChildrenBuilder
-
- stopBefore(String...) - Method in class omero.gateway.util.Requests.FindChildrenBuilder
-
- stopBefore(Iterable<String>) - Method in class omero.gateway.util.Requests.FindParentsBuilder
-
- stopBefore(Class<? extends IObject>...) - Method in class omero.gateway.util.Requests.FindParentsBuilder
-
- stopBefore(String...) - Method in class omero.gateway.util.Requests.FindParentsBuilder
-
- subfolderCount() - Method in class omero.gateway.model.FolderData
-
Get the number of sub folders
- submit(Callable<T>) - Method in class omero.gateway.Gateway
-
Submits an async task
- submit(SecurityContext, List<Request>, SecurityContext) - Method in class omero.gateway.Gateway
-
Executes the commands.
- submit(SecurityContext, Request) - Method in class omero.gateway.Gateway
-
Directly submit a Request to the server
- sudo() - Method in class omero.gateway.SecurityContext
-
Indicates to create a session for another user.
- SYSTEM - Static variable in class omero.gateway.model.GroupData
-
Identifies the System group.