A B C D E F G H I L M O P R S T U V W
All Classes All Packages

A

AccessException - Exception in fr.igred.omero.exception

Reports an error occurred while trying to pull out data from the server.

AccessException(String, Throwable) - Constructor for exception fr.igred.omero.exception.AccessException

Constructs a new exception with the specified detail message and cause.

AccessException(Throwable) - Constructor for exception fr.igred.omero.exception.AccessException

Constructs a new exception with a general message and the cause.

addAndReplaceFile(Client, File) - Method in interface fr.igred.omero.Annotatable

Uploads a file, links it to the object and unlinks previous files with the same name, or deletes them if they're orphaned.

addAndReplaceFile(Client, File, ReplacePolicy) - Method in interface fr.igred.omero.Annotatable

Uploads a file, links it to the object and unlinks or deletes previous files with the same name.

addAndReplaceFile(Client, File, ReplacePolicy) - Method in class fr.igred.omero.AnnotatableWrapper

Uploads a file, links it to the object and unlinks or deletes previous files with the same name.

addAndReplaceTable(Client, Table) - Method in interface fr.igred.omero.Annotatable

Adds a table to the object in OMERO and unlinks previous tables with the same name, or deletes them if they're orphaned.

addAndReplaceTable(Client, Table, ReplacePolicy) - Method in interface fr.igred.omero.Annotatable

Adds a table to the object in OMERO and unlinks or deletes previous tables with the same name.

addAndReplaceTable(Client, Table, ReplacePolicy) - Method in class fr.igred.omero.AnnotatableWrapper

Adds a table to the object in OMERO and unlinks or deletes previous tables with the same name.

addChild(Folder) - Method in interface fr.igred.omero.containers.Folder

Adds a child folder to this folder.

addChild(Folder) - Method in class fr.igred.omero.containers.FolderWrapper

Adds a child folder to this folder.

addChildren(Collection<? extends Folder>) - Method in interface fr.igred.omero.containers.Folder

Adds children folders to this folder.

addChildren(Collection<? extends Folder>) - Method in class fr.igred.omero.containers.FolderWrapper

Adds children folders to this folder.

addDataset(Client, Dataset) - Method in interface fr.igred.omero.containers.Project

Adds a dataset to the project in OMERO.

addDataset(Client, String, String) - Method in interface fr.igred.omero.containers.Project

Adds a dataset to the project in OMERO.

addDataset(Client, String, String) - Method in class fr.igred.omero.containers.ProjectWrapper

Adds a dataset to the project in OMERO.

addFile(DataManager, File) - Method in interface fr.igred.omero.Annotatable

Uploads a file and links it to the object

addImage(Client, Image) - Method in interface fr.igred.omero.containers.Dataset

Adds a single image to the dataset in OMERO

addImages(Client, Iterable<? extends Image>) - Method in interface fr.igred.omero.containers.Dataset

Adds a list of image to the dataset in OMERO.

addImages(DataManager, Image...) - Method in interface fr.igred.omero.containers.Folder

Links images to the folder in OMERO.

addKeyValuePair(DataManager, String, String) - Method in interface fr.igred.omero.Annotatable

Adds a single Key-Value pair to the object.

addKeyValuePair(DataManager, String, String) - Method in class fr.igred.omero.AnnotatableWrapper

Adds a single Key-Value pair to the object.

addROIs(DataManager, long, ROI...) - Method in interface fr.igred.omero.containers.Folder

Adds ROIs to the folder and associate them to the provided image ID.

addROIs(DataManager, Image, ROI...) - Method in interface fr.igred.omero.containers.Folder

Adds ROIs to the folder and associate them to the provided image.

addRow(Object...) - Method in interface fr.igred.omero.annotations.Table

Adds a row to the table.

addRow(Object...) - Method in class fr.igred.omero.annotations.TableWrapper

Adds a row to the table.

addRows(Client, ResultsTable, Long, Collection<? extends Roi>) - Method in interface fr.igred.omero.annotations.Table

Adds rows from an ImageJ ResultsTable.

addRows(Client, ResultsTable, Long, Collection<? extends Roi>, String) - Method in interface fr.igred.omero.annotations.Table

Adds rows from an ImageJ ResultsTable.

addRows(Client, ResultsTable, Long, Collection<? extends Roi>, String) - Method in class fr.igred.omero.annotations.TableWrapper

Adds rows from an ImageJ ResultsTable.

addShape(Shape) - Method in interface fr.igred.omero.roi.ROI

Adds a Shape to the ROI.

addShape(Shape) - Method in class fr.igred.omero.roi.ROIWrapper

Adds a Shape to the ROI.

addShapes(Iterable<? extends Shape>) - Method in interface fr.igred.omero.roi.ROI

Adds shape objects from a list of shapes to the ROI.

addTable(DataManager, Table) - Method in interface fr.igred.omero.Annotatable

Adds a table to the object in OMERO.

addTag(DataManager, Long) - Method in interface fr.igred.omero.Annotatable

Adds a tag to the object in OMERO, if possible.

addTag(DataManager, Long) - Method in class fr.igred.omero.AnnotatableWrapper

Adds a tag to the object in OMERO, if possible.

addTag(DataManager, String, String) - Method in interface fr.igred.omero.Annotatable

Adds a newly created tag to the object in OMERO, if possible.

addTag(DataManager, String, String) - Method in class fr.igred.omero.AnnotatableWrapper

Adds a newly created tag to the object in OMERO, if possible.

addTags(DataManager, Long...) - Method in interface fr.igred.omero.Annotatable

Adds multiple tags by ID to the object in OMERO, if possible.

AdminManager - Interface in fr.igred.omero.client

Interface to handle admin functions on an OMERO server in a given SecurityContext.

Annotatable - Interface in fr.igred.omero

Interface to handle Annotatable Objects on OMERO.

AnnotatableWrapper<T extends DataObject> - Class in fr.igred.omero

Generic class containing an annotatable DataObject (or a subclass) object.

AnnotatableWrapper(T) - Constructor for class fr.igred.omero.AnnotatableWrapper

Constructor of the class RepositoryObjectWrapper.

Annotation - Interface in fr.igred.omero.annotations

Interface to handle Annotations on OMERO.

ANNOTATION_LINK - Static variable in class fr.igred.omero.containers.DatasetWrapper

Annotation link name for this type of object

ANNOTATION_LINK - Static variable in class fr.igred.omero.containers.FolderWrapper

Annotation link name for this type of object

ANNOTATION_LINK - Static variable in class fr.igred.omero.containers.ProjectWrapper

Annotation link name for this type of object

ANNOTATION_LINK - Static variable in class fr.igred.omero.core.ImageWrapper

Annotation link name for this type of object

ANNOTATION_LINK - Static variable in class fr.igred.omero.roi.ROIWrapper

Annotation link name for this type of object

ANNOTATION_LINK - Static variable in class fr.igred.omero.roi.ShapeWrapper

Annotation link name for this type of object

ANNOTATION_LINK - Static variable in class fr.igred.omero.screen.PlateAcquisitionWrapper

Annotation link name for this type of object

ANNOTATION_LINK - Static variable in class fr.igred.omero.screen.PlateWrapper

Annotation link name for this type of object

ANNOTATION_LINK - Static variable in class fr.igred.omero.screen.ScreenWrapper

Annotation link name for this type of object

ANNOTATION_LINK - Static variable in class fr.igred.omero.screen.WellWrapper

Annotation link name for this type of object

annotationLinkType() - Method in class fr.igred.omero.AnnotatableWrapper

Returns the type of annotation link for this object.

annotationLinkType() - Method in class fr.igred.omero.containers.DatasetWrapper

Returns the type of annotation link for this object.

annotationLinkType() - Method in class fr.igred.omero.containers.FolderWrapper

Returns the type of annotation link for this object.

annotationLinkType() - Method in class fr.igred.omero.containers.ProjectWrapper

Returns the type of annotation link for this object.

annotationLinkType() - Method in class fr.igred.omero.core.ImageWrapper

Returns the type of annotation link for this object.

annotationLinkType() - Method in class fr.igred.omero.roi.ROIWrapper

Returns the type of annotation link for this object.

annotationLinkType() - Method in class fr.igred.omero.roi.ShapeWrapper

Returns the type of annotation link for this object.

annotationLinkType() - Method in class fr.igred.omero.screen.PlateAcquisitionWrapper

Returns the type of annotation link for this object.

annotationLinkType() - Method in class fr.igred.omero.screen.PlateWrapper

Returns the type of annotation link for this object.

annotationLinkType() - Method in class fr.igred.omero.screen.ScreenWrapper

Returns the type of annotation link for this object.

annotationLinkType() - Method in class fr.igred.omero.screen.WellWrapper

Returns the type of annotation link for this object.

AnnotationWrapper<T extends AnnotationData> - Class in fr.igred.omero.annotations

Generic class containing an AnnotationData (or a subclass) object.

AnnotationWrapper(T) - Constructor for class fr.igred.omero.annotations.AnnotationWrapper

Constructor of the AnnotationWrapper class.

apply(String, T) - Method in interface fr.igred.omero.exception.ExceptionHandler.ExceptionWrapper

apply(T) - Method in interface fr.igred.omero.exception.ExceptionHandler.ThrowingConsumer

apply(T) - Method in interface fr.igred.omero.exception.ExceptionHandler.ThrowingFunction

areRequirementsAvailable() - Static method in class fr.igred.omero.util.LibraryChecker

Checks if the required libraries are available.

ARROW - Static variable in interface fr.igred.omero.roi.Line

String to use arrows as markers

asDataObject() - Method in interface fr.igred.omero.annotations.Annotation

Returns an AnnotationData corresponding to the handled object.

asDataObject() - Method in interface fr.igred.omero.annotations.FileAnnotation

Returns an FileAnnotationData corresponding to the handled object.

asDataObject() - Method in interface fr.igred.omero.annotations.MapAnnotation

Returns a MapAnnotationData corresponding to the handled object.

asDataObject() - Method in interface fr.igred.omero.annotations.RatingAnnotation

Returns a RatingAnnotationData corresponding to the handled object.

asDataObject() - Method in interface fr.igred.omero.annotations.TagAnnotation

Returns a TagAnnotationData corresponding to the handled object.

asDataObject() - Method in interface fr.igred.omero.annotations.TextualAnnotation

Returns a TextualAnnotationData corresponding to the handled object.

asDataObject() - Method in interface fr.igred.omero.containers.Dataset

Returns a DatasetData corresponding to the handled object.

asDataObject() - Method in interface fr.igred.omero.containers.Folder

Returns a DataObject (or a subclass) corresponding to the handled object.

asDataObject() - Method in interface fr.igred.omero.containers.Project

Returns a ProjectData corresponding to the handled object.

asDataObject() - Method in interface fr.igred.omero.core.Channel

Returns a ChannelData corresponding to the handled object.

asDataObject() - Method in interface fr.igred.omero.core.Image

Returns a ImageData corresponding to the handled object.

asDataObject() - Method in interface fr.igred.omero.core.Pixels

Returns a PixelsData corresponding to the handled object.

asDataObject() - Method in interface fr.igred.omero.core.PlaneInfo

Returns a PlaneInfoData corresponding to the handled object.

asDataObject() - Method in interface fr.igred.omero.meta.Experimenter

Returns an ExperimenterData corresponding to the handled object.

asDataObject() - Method in interface fr.igred.omero.meta.Group

Returns a GroupData corresponding to the handled object.

asDataObject() - Method in class fr.igred.omero.ObjectWrapper

Returns the wrapped DataObject.

asDataObject() - Method in interface fr.igred.omero.RemoteObject

Returns a DataObject (or a subclass) corresponding to the handled object.

asDataObject() - Method in interface fr.igred.omero.roi.Ellipse

Returns an EllipseData corresponding to the handled object.

asDataObject() - Method in interface fr.igred.omero.roi.Line

Returns an LineData corresponding to the handled object.

asDataObject() - Method in interface fr.igred.omero.roi.Mask

Returns an MaskData corresponding to the handled object.

asDataObject() - Method in interface fr.igred.omero.roi.Point

Returns an PointData corresponding to the handled object.

asDataObject() - Method in interface fr.igred.omero.roi.Polygon

Returns an PolygonData corresponding to the handled object.

asDataObject() - Method in interface fr.igred.omero.roi.Polyline

Returns an PolylineData corresponding to the handled object.

asDataObject() - Method in interface fr.igred.omero.roi.Rectangle

Returns an RectangleData corresponding to the handled object.

asDataObject() - Method in interface fr.igred.omero.roi.ROI

Returns a ROIData corresponding to the handled object.

asDataObject() - Method in interface fr.igred.omero.roi.Shape

Returns a ShapeData corresponding to the handled object.

asDataObject() - Method in interface fr.igred.omero.roi.Text

Returns an TextData corresponding to the handled object.

asDataObject() - Method in interface fr.igred.omero.screen.Plate

Returns an PlateData corresponding to the handled object.

asDataObject() - Method in interface fr.igred.omero.screen.PlateAcquisition

Returns an PlateAcquisitionData corresponding to the handled object.

asDataObject() - Method in interface fr.igred.omero.screen.Screen

Returns an ScreenData corresponding to the handled object.

asDataObject() - Method in interface fr.igred.omero.screen.Well

Returns a WellData corresponding to the handled object.

asDataObject() - Method in interface fr.igred.omero.screen.WellSample

Returns an WellSampleData corresponding to the handled object.

B

Bounds - Class in fr.igred.omero.util

Class containing 5D bounds coordinates

Bounds(Coordinates, Coordinates) - Constructor for class fr.igred.omero.util.Bounds

Bounds constructor.

Browser - Interface in fr.igred.omero.client

Interface to browse data on an OMERO server in a given SecurityContext.

C

canAnnotate() - Method in class fr.igred.omero.ObjectWrapper

Returns true if the object can be annotated false otherwise, depending on permissions level.

canAnnotate() - Method in interface fr.igred.omero.RemoteObject

Returns true if the object can be annotated false otherwise, depending on permissions level.

canChgrp() - Method in class fr.igred.omero.ObjectWrapper

Returns true if the object can be moved by the user currently logged in, false otherwise, depending on permissions level.

canChgrp() - Method in interface fr.igred.omero.RemoteObject

Returns true if the object can be moved by the user currently logged in, false otherwise, depending on permissions level.

canChown() - Method in class fr.igred.omero.ObjectWrapper

Returns true if the object can be given by the user currently logged in, false otherwise, depending on permissions level.

canChown() - Method in interface fr.igred.omero.RemoteObject

Returns true if the object can be given by the user currently logged in, false otherwise, depending on permissions level.

canDelete() - Method in class fr.igred.omero.ObjectWrapper

Returns true if the object can be deleted by the user currently logged in, false otherwise, depending on permissions level.

canDelete() - Method in interface fr.igred.omero.RemoteObject

Returns true if the object can be deleted by the user currently logged in, false otherwise, depending on permissions level.

canEdit() - Method in class fr.igred.omero.ObjectWrapper

Returns true if the object can be edited by the user currently logged in false otherwise, depending on permissions level.

canEdit() - Method in interface fr.igred.omero.RemoteObject

Returns true if the object can be edited by the user currently logged in false otherwise, depending on permissions level.

canLink() - Method in class fr.igred.omero.ObjectWrapper

Returns true if the object can be linked e.g.

canLink() - Method in interface fr.igred.omero.RemoteObject

Returns true if the object can be linked e.g.

Channel - Interface in fr.igred.omero.core

Interface to handle Channel information on OMERO.

ChannelWrapper - Class in fr.igred.omero.core

Class containing a ChannelData object.

ChannelWrapper(ChannelData) - Constructor for class fr.igred.omero.core.ChannelWrapper

Constructor of the class ChannelWrapper.

checkClass(String) - Static method in class fr.igred.omero.util.LibraryChecker

Checks whether the given class is available.

checkProperty(String) - Static method in interface fr.igred.omero.roi.ROI

Checks the provided property.

Client - Interface in fr.igred.omero.client

Client interface to connect to OMERO, browse through all the data accessible to the user and modify it.

computeMeanExposureTime(Iterable<? extends PlaneInfo>, int) - Static method in interface fr.igred.omero.core.PlaneInfo

Computes the mean exposure time for a given channel in a PlaneInfo collection.

computeMeanTimeInterval(Collection<? extends PlaneInfo>, int) - Static method in interface fr.igred.omero.core.PlaneInfo

Computes the mean time interval from the deltaT in a PlaneInfo collection.

connect(String, int, String) - Method in interface fr.igred.omero.client.ConnectionHandler

Connects to OMERO using a session ID.

connect(String, int, String, char[]) - Method in interface fr.igred.omero.client.ConnectionHandler

Connects the user to OMERO.

connect(String, int, String, char[], Long) - Method in interface fr.igred.omero.client.ConnectionHandler

Connects the user to OMERO.

connect(LoginCredentials) - Method in interface fr.igred.omero.client.ConnectionHandler

Connects the user to OMERO.

connect(LoginCredentials) - Method in class fr.igred.omero.client.GatewayWrapper

Connects the user to OMERO.

ConnectionHandler - Interface in fr.igred.omero.client

Interface to handle the connection to an OMERO server through a Gateway for a given user and in a specific SecurityContext.

ContainerLinked - Interface in fr.igred.omero

Interface to handle objects that can be linked to containers (projects, datasets) on OMERO.

Coordinates - Class in fr.igred.omero.util

Class containing 5D pixel coordinates

Coordinates(int, int, int, int, int) - Constructor for class fr.igred.omero.util.Coordinates

Coordinates constructor.

copyAnnotationLinks(Client, Annotatable) - Method in interface fr.igred.omero.Annotatable

Copies annotation links from some other object to this one.

copyFromIJRoi(Roi) - Method in class fr.igred.omero.roi.ShapeWrapper

Copies details from an ImageJ ROI (position, stroke color, stroke width).

copyToIJRoi(Roi) - Method in class fr.igred.omero.roi.ShapeWrapper

Copies details to an ImageJ ROI (name, position, stroke color, fill color, stroke width).

countAnnotationLinks(Browser) - Method in interface fr.igred.omero.annotations.Annotation

Returns the number of annotations links for this object.

createTable() - Method in interface fr.igred.omero.annotations.Table

Creates the corresponding TableData object.

createTable() - Method in class fr.igred.omero.annotations.TableWrapper

Creates the corresponding TableData object.

createTransformedAWTShape() - Method in interface fr.igred.omero.roi.Shape

Returns a new Shape defined by the geometry of the specified Shape after it has been transformed by the transform.

D

data - Variable in class fr.igred.omero.ObjectWrapper

Wrapped object

DataManager - Interface in fr.igred.omero.client

Interface to add or remove data on an OMERO server in a given SecurityContext.

Dataset - Interface in fr.igred.omero.containers

Interface to handle Datasets on OMERO.

DatasetWrapper - Class in fr.igred.omero.containers

Class containing a DatasetData object.

DatasetWrapper(String, String) - Constructor for class fr.igred.omero.containers.DatasetWrapper

Constructor of the DatasetWrapper class

DatasetWrapper(DatasetData) - Constructor for class fr.igred.omero.containers.DatasetWrapper

Constructor of the DatasetWrapper class

delete(Table) - Method in interface fr.igred.omero.client.DataManager

Deletes a table from OMERO.

delete(RemoteObject) - Method in interface fr.igred.omero.client.DataManager

Deletes an object from OMERO.

delete(Collection<? extends RemoteObject>) - Method in interface fr.igred.omero.client.DataManager

Deletes multiple objects from OMERO.

delete(List<IObject>) - Method in interface fr.igred.omero.client.DataManager

Deletes multiple objects from OMERO.

delete(IObject) - Method in interface fr.igred.omero.client.DataManager

Deletes an object from OMERO.

DELETE - fr.igred.omero.util.ReplacePolicy

Delete all objects

DELETE_ORPHANED - fr.igred.omero.util.ReplacePolicy

Delete orphaned objects

deleteFile(Long) - Method in interface fr.igred.omero.client.DataManager

Deletes a file from OMERO

deleteShape(int) - Method in interface fr.igred.omero.roi.ROI

Deletes a shape from the ROI.

deleteShape(int) - Method in class fr.igred.omero.roi.ROIWrapper

Deletes a shape from the ROI.

deleteShape(ShapeData) - Method in interface fr.igred.omero.roi.ROI

Deletes a ShapeData from the ROI.

deleteShape(ShapeData) - Method in class fr.igred.omero.roi.ROIWrapper

Deletes a ShapeData from the ROI.

disconnect() - Method in interface fr.igred.omero.client.ConnectionHandler

Disconnects the user

disconnect() - Method in class fr.igred.omero.client.GatewayWrapper

Disconnects the user

distinct(Collection<? extends T>) - Static method in interface fr.igred.omero.RemoteObject

Only keeps objects with different IDs in a collection.

download(ConnectionHandler, String) - Method in interface fr.igred.omero.core.Image

Downloads the original files from the server.

download(ConnectionHandler, String) - Method in class fr.igred.omero.core.ImageWrapper

Downloads the original files from the server.

E

Ellipse - Interface in fr.igred.omero.roi

Interface to handle Ellipse shapes on OMERO.

EllipseWrapper - Class in fr.igred.omero.roi

Class containing an EllipseData.

EllipseWrapper() - Constructor for class fr.igred.omero.roi.EllipseWrapper

Constructor of the EllipseWrapper class using a new empty EllipseData.

EllipseWrapper(double, double, double, double) - Constructor for class fr.igred.omero.roi.EllipseWrapper

Constructor of the EllipseWrapper class using a new EllipseData.

EllipseWrapper(Roi) - Constructor for class fr.igred.omero.roi.EllipseWrapper

Constructor of the EllipseWrapper class using bounds from an ImageJ ROI.

EllipseWrapper(EllipseData) - Constructor for class fr.igred.omero.roi.EllipseWrapper

Constructor of the EllipseWrapper class using a EllipseData.

ExceptionHandler<T> - Class in fr.igred.omero.exception

Class to handle and convert OMERO exceptions.

ExceptionHandler(T, Exception) - Constructor for class fr.igred.omero.exception.ExceptionHandler

Private class constructor.

ExceptionHandler.ExceptionWrapper<T,E extends java.lang.Throwable> - Interface in fr.igred.omero.exception

ExceptionHandler.ThrowingConsumer<T,E extends java.lang.Throwable> - Interface in fr.igred.omero.exception

ExceptionHandler.ThrowingFunction<T,R,E extends java.lang.Throwable> - Interface in fr.igred.omero.exception

Experimenter - Interface in fr.igred.omero.meta

Interface to handle Experimenters on OMERO.

ExperimenterWrapper - Class in fr.igred.omero.meta

Class containing an ExperimenterData object.

ExperimenterWrapper(ExperimenterData) - Constructor for class fr.igred.omero.meta.ExperimenterWrapper

Constructor of the class ExperimenterWrapper.

F

FileAnnotation - Interface in fr.igred.omero.annotations

Interface to handle File Annotations on OMERO.

FileAnnotationWrapper - Class in fr.igred.omero.annotations

Class containing a FileAnnotationData object.

FileAnnotationWrapper(FileAnnotationData) - Constructor for class fr.igred.omero.annotations.FileAnnotationWrapper

Constructor of the AnnotationWrapper class.

findByQuery(String) - Method in interface fr.igred.omero.client.Browser

Finds objects on OMERO through a database query.

flatten(Collection<? extends Collection<? extends T>>) - Static method in interface fr.igred.omero.RemoteObject

Flattens a collection of collections and only keeps objects with different IDs.

Folder - Interface in fr.igred.omero.containers

Interface to handle Folders on OMERO.

FolderWrapper - Class in fr.igred.omero.containers

Class containing a FolderData object.

FolderWrapper(DataManager, String) - Constructor for class fr.igred.omero.containers.FolderWrapper

Constructor of the FolderWrapper class.

FolderWrapper(FolderData) - Constructor for class fr.igred.omero.containers.FolderWrapper

Constructor of the FolderWrapper class.

FolderWrapper(Folder) - Constructor for class fr.igred.omero.containers.FolderWrapper

Constructor of the FolderWrapper class.

fr.igred.omero - package fr.igred.omero

This package contains the main interfaces and abstract classes to handle OME Remote Objects.

fr.igred.omero.annotations - package fr.igred.omero.annotations

This package contains interfaces and classes for handling annotations.

fr.igred.omero.client - package fr.igred.omero.client

This package contains the client interfaces used to interact with an OMERO server and a class implementing them.

fr.igred.omero.containers - package fr.igred.omero.containers

This package contains interfaces and classes related to the hierarchical organization for images,

fr.igred.omero.core - package fr.igred.omero.core

This package contains interfaces and classes to handle images and their content, such as pixels, channels or planes.

fr.igred.omero.exception - package fr.igred.omero.exception

This package contains wrapper classes for exceptions and an exception handler.

fr.igred.omero.meta - package fr.igred.omero.meta

This package contains wrapper classes for users and groups.

fr.igred.omero.roi - package fr.igred.omero.roi

This package contains wrapper classes for OMERO shapes and ROIs.

fr.igred.omero.screen - package fr.igred.omero.screen

This package contains interfaces and classes related to the HCS organization, e.g.

fr.igred.omero.util - package fr.igred.omero.util

This package contains classes to handle 5D positions and boundaries as well as a utility class to check if the library requirements are available, and another one to convert DataObjects to Wrapper objects.

fromImageJ(Collection<? extends Roi>) - Static method in class fr.igred.omero.roi.ROIWrapper

Converts a collection of ImageJ ROIs to a list of OMERO ROIs

fromImageJ(Collection<? extends Roi>, String) - Static method in class fr.igred.omero.roi.ROIWrapper

Converts a collection of ImageJ ROIs to a list of OMERO ROIs

fromImageJ(Collection<? extends Roi>, String, Supplier<? extends ROI>, Function<? super Roi, ? extends Iterable<? extends Shape>>) - Static method in interface fr.igred.omero.roi.ROI

Converts a collection of ImageJ ROIs to a list of OMERO ROIs using the provided constructor and shape converter.

fromImageJ(Collection<? extends Roi>, Supplier<? extends ROI>, Function<? super Roi, Iterable<? extends Shape>>) - Static method in interface fr.igred.omero.roi.ROI

Converts an ImageJ list of ROIs to a list of OMERO ROIs using the provided constructor and shape converter.

G

GatewayWrapper - Class in fr.igred.omero.client

Allows the user to connect to OMERO and browse through all the data accessible to the user.

GatewayWrapper() - Constructor for class fr.igred.omero.client.GatewayWrapper

Constructor of the GatewayWrapper class.

GatewayWrapper(Gateway, SecurityContext, Experimenter) - Constructor for class fr.igred.omero.client.GatewayWrapper

Constructor of the GatewayWrapper class.

get() - Method in class fr.igred.omero.exception.ExceptionHandler

Returns the contained object.

getAcquisitionDate() - Method in interface fr.igred.omero.core.Image

Gets the ImageData acquisition date

getAcquisitionDate() - Method in class fr.igred.omero.core.ImageWrapper

Gets the ImageData acquisition date.

getAdminFacility() - Method in interface fr.igred.omero.client.AdminManager

Gets the AdminFacility to use admin specific function.

getAdminFacility() - Method in interface fr.igred.omero.client.Client

Gets the AdminFacility to use admin specific function.

getAllPixels(ConnectionHandler) - Method in interface fr.igred.omero.core.Pixels

Returns an array containing the value for each voxel

getAllPixels(ConnectionHandler, int[], int[], int[], int[], int[]) - Method in interface fr.igred.omero.core.Pixels

Returns an array containing the value for each voxel corresponding to the bounds

getAllPixels(ConnectionHandler, int[], int[], int[], int[], int[]) - Method in class fr.igred.omero.core.PixelsWrapper

Returns an array containing the value for each voxel corresponding to the bounds

getAlpha() - Method in interface fr.igred.omero.core.Channel

Gets the sRGB alpha value of the channel.

getAlpha() - Method in class fr.igred.omero.core.ChannelWrapper

Gets the sRGB alpha value of the channel.

getAlpha() - Method in interface fr.igred.omero.screen.Well

Returns the alpha component of the color associated to the well, or -1.

getAlpha() - Method in class fr.igred.omero.screen.WellWrapper

Returns the alpha component of the color associated to the well, or -1.

getAnnotationData(Browser) - Method in interface fr.igred.omero.Annotatable

Retrieves annotations linked to the object.

getAnnotations(Browser) - Method in interface fr.igred.omero.Annotatable

Retrieves annotations linked to the object (of known types).

getAnnotations(Browser) - Method in class fr.igred.omero.AnnotatableWrapper

Retrieves annotations linked to the object (of known types).

getAttachedFile() - Method in interface fr.igred.omero.annotations.FileAnnotation

Returns the file to upload to the server.

getAttachedFile() - Method in class fr.igred.omero.annotations.FileAnnotationWrapper

Returns the file to upload to the server.

getBlue() - Method in interface fr.igred.omero.core.Channel

Gets the sRGB blue value of the channel.

getBlue() - Method in class fr.igred.omero.core.ChannelWrapper

Gets the sRGB blue value of the channel.

getBlue() - Method in interface fr.igred.omero.screen.Well

Returns the blue component of the color associated to the well, or -1.

getBlue() - Method in class fr.igred.omero.screen.WellWrapper

Returns the blue component of the color associated to the well, or -1.

getBoundingBox() - Method in interface fr.igred.omero.roi.Shape

Returns a new Rectangle corresponding to the bounding box of the shape, once the related AffineTransform has been applied.

getBoundingBox() - Method in class fr.igred.omero.roi.ShapeWrapper

Returns a new Rectangle corresponding to the bounding box of the shape, once the related AffineTransform has been applied.

getBounds() - Method in interface fr.igred.omero.roi.ROI

Returns the 5D bounds containing the ROI.

getBrowseFacility() - Method in interface fr.igred.omero.client.Browser

Gets the BrowseFacility used to access the data from OMERO.

getBrowseFacility() - Method in interface fr.igred.omero.client.Client

Gets the BrowseFacility used to access the data from OMERO.

getC() - Method in interface fr.igred.omero.roi.Shape

Gets the channel.

getC() - Method in class fr.igred.omero.roi.ShapeWrapper

Gets the channel.

getC() - Method in class fr.igred.omero.util.Coordinates

Gets C coordinate.

getChannelColor(Client, int) - Method in interface fr.igred.omero.core.Image

Gets the current color of the channel

getChannelImportedColor(Browser, int) - Method in interface fr.igred.omero.core.Image

Gets the original color of the channel

getChannelLabeling() - Method in interface fr.igred.omero.core.Channel

Returns the label of the channel.

getChannelLabeling() - Method in class fr.igred.omero.core.ChannelWrapper

Returns the label of the channel.

getChannelName(Browser, int) - Method in interface fr.igred.omero.core.Image

Gets the name of the channel.

getChannels(Browser) - Method in interface fr.igred.omero.core.Image

Gets the image channels.

getChannels(Browser) - Method in class fr.igred.omero.core.ImageWrapper

Gets the image channels.

getChildren() - Method in interface fr.igred.omero.containers.Folder

Retrieves the children folders for this folder.

getChildren() - Method in class fr.igred.omero.containers.FolderWrapper

Retrieves the children folders for this folder.

getColor() - Method in interface fr.igred.omero.core.Channel

Gets the original channel color.

getColumn() - Method in interface fr.igred.omero.screen.Well

Returns the column used to indicate the location of the well on the grid.

getColumn() - Method in class fr.igred.omero.screen.WellWrapper

Returns the column used to indicate the location of the well on the grid.

getColumnCount() - Method in interface fr.igred.omero.annotations.Table

Returns the number of columns in the table.

getColumnCount() - Method in class fr.igred.omero.annotations.TableWrapper

Returns the number of columns in the table.

getColumnName(int) - Method in interface fr.igred.omero.annotations.Table

Returns the name of the column.

getColumnName(int) - Method in class fr.igred.omero.annotations.TableWrapper

Returns the name of the column.

getColumns() - Method in interface fr.igred.omero.annotations.Table

Gets the TableDataColumn which contains information on each column of the table

getColumns() - Method in class fr.igred.omero.annotations.TableWrapper

Gets the TableDataColumn which contains information on each column of the table

getColumnSequenceIndex() - Method in interface fr.igred.omero.screen.Plate

Returns the index indicating how to label a column.

getColumnSequenceIndex() - Method in class fr.igred.omero.screen.PlateWrapper

Returns the index indicating how to label a column.

getColumnType(int) - Method in interface fr.igred.omero.annotations.Table

Returns the type of the column.

getColumnType(int) - Method in class fr.igred.omero.annotations.TableWrapper

Returns the type of the column.

getContent() - Method in interface fr.igred.omero.annotations.MapAnnotation

Gets the List of Key-Value pairs contained in the map annotation.

getContent() - Method in class fr.igred.omero.annotations.MapAnnotationWrapper

Gets the List of Key-Value pairs contained in the map annotation.

getContentAsMap() - Method in interface fr.igred.omero.annotations.MapAnnotation

Gets the List of Key-Value pairs contained in the map annotation as a map.

getContentAsString() - Method in interface fr.igred.omero.annotations.FileAnnotation

Returns the absolute path to the file

getContentAsString() - Method in class fr.igred.omero.annotations.FileAnnotationWrapper

Returns the absolute path to the file

getCoordinates() - Method in interface fr.igred.omero.roi.Ellipse

Gets the coordinates of the MaskData shape.

getCoordinates() - Method in interface fr.igred.omero.roi.Line

Gets the coordinates of the LineData shape.

getCoordinates() - Method in interface fr.igred.omero.roi.Punctual

Gets the coordinates of the punctual shape.

getCoordinates() - Method in interface fr.igred.omero.roi.Rectangular

Gets the coordinates of the rectangular shape.

getCreated() - Method in class fr.igred.omero.ObjectWrapper

Gets the object creation date

getCreated() - Method in interface fr.igred.omero.RemoteObject

Gets the object creation date

getCtx() - Method in interface fr.igred.omero.client.AdminManager

Returns the current SecurityContext.

getCtx() - Method in interface fr.igred.omero.client.Browser

Returns the current SecurityContext.

getCtx() - Method in interface fr.igred.omero.client.ConnectionHandler

Returns the current SecurityContext.

getCtx() - Method in interface fr.igred.omero.client.DataManager

Returns the current SecurityContext.

getCtx() - Method in class fr.igred.omero.client.GatewayWrapper

Contains the permissions of the user in the group.

getCurrentGroupId() - Method in interface fr.igred.omero.client.ConnectionHandler

Gets the current group ID.

getCZT() - Method in interface fr.igred.omero.roi.Shape

Returns the C,Z,T positions as a comma-delimited String.

getData() - Method in interface fr.igred.omero.annotations.Table

Gets the value contained in the table

getData() - Method in class fr.igred.omero.annotations.TableWrapper

Gets the value contained in the table

getData(int, int) - Method in interface fr.igred.omero.annotations.Table

Gets a certain value of the table

getData(int, int) - Method in class fr.igred.omero.annotations.TableWrapper

Gets a certain value of the table

getDataset(Long) - Method in interface fr.igred.omero.client.Browser

Gets the dataset with the specified id from OMERO.

getDatasets() - Method in interface fr.igred.omero.client.Browser

Gets all datasets available from OMERO.

getDatasets() - Method in interface fr.igred.omero.containers.Project

Gets all the datasets in the project available from OMERO.

getDatasets() - Method in class fr.igred.omero.containers.ProjectWrapper

Gets all the datasets in the project available from OMERO.

getDatasets(Browser) - Method in class fr.igred.omero.annotations.AnnotationWrapper

Gets all datasets with this annotation from OMERO.

getDatasets(Browser) - Method in interface fr.igred.omero.ContainerLinked

Retrieves the datasets linked to this object, either directly, or through parents/children.

getDatasets(Browser) - Method in interface fr.igred.omero.containers.Dataset

Reloads and returns this dataset (updated from OMERO) as a singleton list.

getDatasets(Browser) - Method in interface fr.igred.omero.containers.Project

Reloads this project and retrieves the updated list of datasets contained in this project.

getDatasets(Browser) - Method in interface fr.igred.omero.core.Image

Retrieves the datasets containing this image

getDatasets(Experimenter) - Method in interface fr.igred.omero.client.Browser

Gets all datasets available from OMERO owned by a given user.

getDatasets(Long...) - Method in interface fr.igred.omero.client.Browser

Gets the datasets with the specified ids from OMERO.

getDatasets(String) - Method in interface fr.igred.omero.client.Browser

Gets all datasets with a certain name from OMERO.

getDatasets(String) - Method in interface fr.igred.omero.containers.Project

Gets the dataset with the specified name from OMERO

getDefaultGroup() - Method in interface fr.igred.omero.meta.Experimenter

Returns the default Group for this Experimenter

getDefaultGroup() - Method in class fr.igred.omero.meta.ExperimenterWrapper

Returns the default Group for this Experimenter

getDefaultSample() - Method in interface fr.igred.omero.screen.Plate

Returns the currently selected field or 0.

getDefaultSample() - Method in class fr.igred.omero.screen.PlateWrapper

Returns the currently selected field or 0.

getDeltaT() - Method in interface fr.igred.omero.core.PlaneInfo

Retrieves the plane deltaT.

getDeltaT() - Method in class fr.igred.omero.core.PlaneInfoWrapper

Retrieves the plane deltaT.

getDescription() - Method in interface fr.igred.omero.annotations.Annotation

Gets the annotation description.

getDescription() - Method in class fr.igred.omero.annotations.AnnotationWrapper

Gets the annotation description.

getDescription() - Method in class fr.igred.omero.containers.DatasetWrapper

Gets the DatasetData description

getDescription() - Method in class fr.igred.omero.containers.FolderWrapper

Gets the folder description

getDescription() - Method in class fr.igred.omero.containers.ProjectWrapper

Gets the project description.

getDescription() - Method in class fr.igred.omero.core.ImageWrapper

Gets the image description.

getDescription() - Method in interface fr.igred.omero.meta.Group

Returns the description of the group.

getDescription() - Method in class fr.igred.omero.meta.GroupWrapper

Returns the description of the group.

getDescription() - Method in interface fr.igred.omero.RepositoryObject

Gets the object description

getDescription() - Method in class fr.igred.omero.screen.PlateAcquisitionWrapper

Gets the plate acquisition description

getDescription() - Method in class fr.igred.omero.screen.PlateWrapper

Gets the plate description

getDescription() - Method in class fr.igred.omero.screen.ScreenWrapper

Gets the screen description

getDescription() - Method in class fr.igred.omero.screen.WellWrapper

Gets the object description

getDMFacility() - Method in interface fr.igred.omero.client.Client

Gets the DataManagerFacility to handle/write data on OMERO.

getDMFacility() - Method in interface fr.igred.omero.client.DataManager

Gets the DataManagerFacility to handle/write data on OMERO.

getElementsOf(Collection<? extends U>, Class<? extends V>) - Static method in interface fr.igred.omero.RemoteObject

Gets a list of elements of the specified class from a collection of RemoteObjects.

getEmail() - Method in interface fr.igred.omero.meta.Experimenter

Returns the e-mail of the experimenter.

getEmail() - Method in class fr.igred.omero.meta.ExperimenterWrapper

Returns the e-mail of the experimenter.

getEnd() - Method in class fr.igred.omero.util.Bounds

Gets size of bounds for each coordinate.

getEndTime() - Method in interface fr.igred.omero.screen.PlateAcquisition

Returns the time when the last image was collected.

getEndTime() - Method in class fr.igred.omero.screen.PlateAcquisitionWrapper

Returns the time when the last image was collected.

getExperimenters() - Method in interface fr.igred.omero.meta.Group

Returns the experimenters contained in this group.

getExperimenters() - Method in class fr.igred.omero.meta.GroupWrapper

Returns the experimenters contained in this group.

getExposureTime() - Method in interface fr.igred.omero.core.PlaneInfo

Retrieves the exposure time.

getExposureTime() - Method in class fr.igred.omero.core.PlaneInfoWrapper

Retrieves the exposure time.

getExternalIdentifier() - Method in interface fr.igred.omero.screen.Plate

Returns the external identifier of the plate.

getExternalIdentifier() - Method in class fr.igred.omero.screen.PlateWrapper

Returns the external identifier of the plate.

getFile(ConnectionHandler, String) - Method in interface fr.igred.omero.annotations.FileAnnotation

Returns the original file.

getFile(ConnectionHandler, String) - Method in class fr.igred.omero.annotations.FileAnnotationWrapper

Returns the original file.

getFileAnnotations(Browser) - Method in interface fr.igred.omero.Annotatable

Returns the file annotations

getFileAnnotations(Browser) - Method in class fr.igred.omero.AnnotatableWrapper

Returns the file annotations

getFileFormat() - Method in interface fr.igred.omero.annotations.FileAnnotation

Returns the format of the uploaded file.

getFileFormat() - Method in class fr.igred.omero.annotations.FileAnnotationWrapper

Returns the format of the uploaded file.

getFileId() - Method in interface fr.igred.omero.annotations.Table

Returns the fileId of the table.

getFileId() - Method in class fr.igred.omero.annotations.TableWrapper

Returns the fileId of the table.

getFileID() - Method in interface fr.igred.omero.annotations.FileAnnotation

Returns the ID of the file.

getFileID() - Method in class fr.igred.omero.annotations.FileAnnotationWrapper

Returns the ID of the file.

getFileKind() - Method in interface fr.igred.omero.annotations.FileAnnotation

Returns a user readable description of the file.

getFileKind() - Method in class fr.igred.omero.annotations.FileAnnotationWrapper

Returns a user readable description of the file.

getFileName() - Method in interface fr.igred.omero.annotations.FileAnnotation

Returns the name of the file.

getFileName() - Method in class fr.igred.omero.annotations.FileAnnotationWrapper

Returns the name of the file.

getFilePath() - Method in interface fr.igred.omero.annotations.FileAnnotation

Returns the absolute path to the file.

getFilePath() - Method in class fr.igred.omero.annotations.FileAnnotationWrapper

Returns the absolute path to the file.

getFilesetImages(Browser) - Method in interface fr.igred.omero.core.Image

Returns the list of images sharing the same fileset as the current image.

getFileSize() - Method in interface fr.igred.omero.annotations.FileAnnotation

Returns the size of the file.

getFileSize() - Method in class fr.igred.omero.annotations.FileAnnotationWrapper

Returns the size of the file.

getFill() - Method in interface fr.igred.omero.roi.Shape

Gets ShapeData fill color.

getFill() - Method in class fr.igred.omero.roi.ShapeWrapper

Gets ShapeData fill color.

getFirstName() - Method in interface fr.igred.omero.meta.Experimenter

Returns the first name of the experimenter.

getFirstName() - Method in class fr.igred.omero.meta.ExperimenterWrapper

Returns the first name of the experimenter.

getFolder(long) - Method in interface fr.igred.omero.client.Browser

Gets the folder with the specified ID from OMERO, fully loaded.

getFolders() - Method in interface fr.igred.omero.client.Browser

Gets all folders available from OMERO.

getFolders(Browser) - Method in interface fr.igred.omero.annotations.Annotation

Gets all folders with this annotation from OMERO.

getFolders(Browser) - Method in class fr.igred.omero.annotations.AnnotationWrapper

Gets all folders with this annotation from OMERO.

getFolders(Browser) - Method in interface fr.igred.omero.core.Image

Gets the list of folders linked to this image.

getFolders(Experimenter) - Method in interface fr.igred.omero.client.Browser

Gets all the folders owned by a given user from OMERO.

getFontSize() - Method in interface fr.igred.omero.roi.Shape

Gets ShapeData font size.

getFontSize() - Method in class fr.igred.omero.roi.ShapeWrapper

Gets ShapeData font size.

getGateway() - Method in interface fr.igred.omero.client.ConnectionHandler

Returns the Gateway used for the connection.

getGateway() - Method in class fr.igred.omero.client.GatewayWrapper

Returns the Gateway.

getGreen() - Method in interface fr.igred.omero.core.Channel

Gets the sRGB green value of the channel.

getGreen() - Method in class fr.igred.omero.core.ChannelWrapper

Gets the sRGB green value of the channel.

getGreen() - Method in interface fr.igred.omero.screen.Well

Returns the green component of the color associated to the well, or -1.

getGreen() - Method in class fr.igred.omero.screen.WellWrapper

Returns the green component of the color associated to the well, or -1.

getGroup(String) - Method in interface fr.igred.omero.client.AdminManager

Returns the group which matches the name.

getGroupId() - Method in class fr.igred.omero.ObjectWrapper

Gets the group ID

getGroupId() - Method in interface fr.igred.omero.RemoteObject

Gets the group ID

getGroups() - Method in interface fr.igred.omero.meta.Experimenter

Returns the groups the experimenter is a member of.

getGroups() - Method in class fr.igred.omero.meta.ExperimenterWrapper

Returns the groups the experimenter is a member of.

getHeight() - Method in class fr.igred.omero.roi.MaskWrapper

Returns the height of the rectangular shape.

getHeight() - Method in class fr.igred.omero.roi.RectangleWrapper

Returns the height untransformed rectangle.

getHeight() - Method in interface fr.igred.omero.roi.Rectangular

Returns the height of the rectangular shape.

getId() - Method in interface fr.igred.omero.annotations.Table

Returns the table ID.

getId() - Method in class fr.igred.omero.annotations.TableWrapper

Returns the table ID.

getId() - Method in interface fr.igred.omero.client.ConnectionHandler

Gets the user id.

getId() - Method in class fr.igred.omero.ObjectWrapper

Gets the object id

getId() - Method in interface fr.igred.omero.RemoteObject

Gets the object id

getImage() - Method in interface fr.igred.omero.screen.WellSample

Returns the image related to that sample if any.

getImage() - Method in class fr.igred.omero.screen.WellSampleWrapper

Returns the image related to that sample if any.

getImage(Long) - Method in interface fr.igred.omero.client.Browser

Returns the image with the specified ID from OMERO.

getImages() - Method in interface fr.igred.omero.client.Browser

Gets all images owned by the current user.

getImages() - Method in interface fr.igred.omero.containers.Dataset

Gets all the images in the dataset (if it was properly loaded from OMERO).

getImages() - Method in class fr.igred.omero.containers.DatasetWrapper

Gets all the images in the dataset (if it was properly loaded from OMERO).

getImages() - Method in interface fr.igred.omero.containers.Folder

Retrieves the images contained in this folder.

getImages() - Method in class fr.igred.omero.containers.FolderWrapper

Retrieves the images contained in this folder.

getImages() - Method in interface fr.igred.omero.screen.Well

Retrieves the images contained in this well.

getImages(Annotation) - Method in interface fr.igred.omero.client.Browser

Gets all images with the specified annotation from OMERO.

getImages(Browser) - Method in class fr.igred.omero.annotations.AnnotationWrapper

Gets all images with this annotation from OMERO.

getImages(Browser) - Method in interface fr.igred.omero.containers.Dataset

Gets all images in the dataset available from OMERO.

getImages(Browser) - Method in class fr.igred.omero.containers.DatasetWrapper

Gets all images in the dataset available from OMERO.

getImages(Browser) - Method in interface fr.igred.omero.containers.Folder

Retrieves the images contained in this folder.

getImages(Browser) - Method in interface fr.igred.omero.containers.Project

Gets all images in the project available from OMERO.

getImages(Browser) - Method in class fr.igred.omero.containers.ProjectWrapper

Gets all images in the project available from OMERO.

getImages(Browser) - Method in interface fr.igred.omero.core.Image

Returns this image, updated from OMERO, as a singleton list.

getImages(Browser) - Method in interface fr.igred.omero.ImageLinked

Retrieves the images linked to this object, either directly, or through parents/children.

getImages(Browser) - Method in interface fr.igred.omero.screen.Plate

Returns the images contained in the wells of this plate.

getImages(Browser) - Method in interface fr.igred.omero.screen.PlateAcquisition

Retrieves the images contained in the wells in the parent plate.

getImages(Browser) - Method in interface fr.igred.omero.screen.Screen

Retrieves the images contained in this screen.

getImages(Browser) - Method in interface fr.igred.omero.screen.Well

Reloads this well and retrieves the images it contains.

getImages(Browser) - Method in interface fr.igred.omero.screen.WellSample

Retrieves the image contained in this Well Sample as a singleton list.

getImages(Browser, String) - Method in interface fr.igred.omero.containers.Dataset

Gets all images in the dataset with a certain name from OMERO.

getImages(Browser, String) - Method in interface fr.igred.omero.containers.Project

Gets all images in the project with a certain name from OMERO.

getImages(Browser, String, String) - Method in interface fr.igred.omero.containers.Project

Gets all images with a certain name from datasets with the specified name inside this project on OMERO.

getImages(Long...) - Method in interface fr.igred.omero.client.Browser

Gets the images with the specified ids from OMERO

getImages(String) - Method in interface fr.igred.omero.client.Browser

Gets all images with a certain name from OMERO.

getImages(String, String, String) - Method in interface fr.igred.omero.client.Browser

Gets all images with the name specified inside projects and datasets with the given names.

getImagesLike(Browser, String) - Method in interface fr.igred.omero.containers.Dataset

Gets all images in the dataset with a certain motif in their name from OMERO.

getImagesLike(Browser, String) - Method in interface fr.igred.omero.containers.Project

Gets all images in the project with a certain motif in their name from OMERO.

getImagesLike(String) - Method in interface fr.igred.omero.client.Browser

Gets all images with a certain motif in their name from OMERO.

getImagesTagged(Browser, TagAnnotation) - Method in interface fr.igred.omero.containers.Dataset

Gets all images in the dataset tagged with a specified tag from OMERO.

getImagesTagged(Browser, TagAnnotation) - Method in interface fr.igred.omero.containers.Project

Gets all images in the project tagged with a specified tag from OMERO.

getImagesTagged(Browser, Long) - Method in interface fr.igred.omero.containers.Dataset

Gets all images in the dataset tagged with a specified tag from OMERO.

getImagesTagged(Browser, Long) - Method in interface fr.igred.omero.containers.Project

Gets all images in the project tagged with a specified tag from OMERO.

getImagesWithKey(Browser, String) - Method in interface fr.igred.omero.containers.Dataset

Gets all images in the dataset with a certain key

getImagesWithKey(Browser, String) - Method in interface fr.igred.omero.containers.Project

Gets all images in the project with a certain key

getImagesWithKey(String) - Method in interface fr.igred.omero.client.Browser

Gets all images with a certain key.

getImagesWithKeyValuePair(Browser, String, String) - Method in interface fr.igred.omero.containers.Dataset

Gets all images in the dataset with a certain key value pair from OMERO

getImagesWithKeyValuePair(Browser, String, String) - Method in interface fr.igred.omero.containers.Project

Gets all images in the project with a certain key value pair from OMERO.

getImagesWithKeyValuePair(String, String) - Method in interface fr.igred.omero.client.Browser

Gets all images with a certain key value pair from OMERO

getImportStore() - Method in interface fr.igred.omero.client.ConnectionHandler

Creates or recycles the import store.

getIndex() - Method in interface fr.igred.omero.core.Channel

Returns the channel index.

getIndex() - Method in class fr.igred.omero.core.ChannelWrapper

Returns the channel index.

getInstitution() - Method in interface fr.igred.omero.meta.Experimenter

Returns the institution where the experimenter works.

getInstitution() - Method in class fr.igred.omero.meta.ExperimenterWrapper

Returns the institution where the experimenter works.

getKeyValuePairs(Browser) - Method in interface fr.igred.omero.Annotatable

Gets the List of Key-Value pairs associated to an object.

getLabel() - Method in interface fr.igred.omero.screen.PlateAcquisition

Returns the label associated to the plate acquisition.

getLabel() - Method in class fr.igred.omero.screen.PlateAcquisitionWrapper

Returns the label associated to the plate acquisition.

getLastModified() - Method in interface fr.igred.omero.annotations.Annotation

Returns the time when the annotation was last modified.

getLastModified() - Method in class fr.igred.omero.annotations.AnnotationWrapper

Returns the time when the annotation was last modified.

getLastName() - Method in interface fr.igred.omero.meta.Experimenter

Returns the last name of the experimenter.

getLastName() - Method in class fr.igred.omero.meta.ExperimenterWrapper

Returns the last name of the experimenter.

getLeaders() - Method in interface fr.igred.omero.meta.Group

Returns the leaders of this group.

getLeaders() - Method in class fr.igred.omero.meta.GroupWrapper

Returns the leaders of this group.

getMapAnnotation(Long) - Method in interface fr.igred.omero.client.Browser

Gets a specific map annotation (key/value pairs) from the OMERO database.

getMapAnnotations() - Method in interface fr.igred.omero.client.Browser

Gets the list of map annotations available to the user.

getMapAnnotations(Browser) - Method in interface fr.igred.omero.Annotatable

Gets all map annotations linked to an object in OMERO, if possible.

getMapAnnotations(Browser) - Method in class fr.igred.omero.AnnotatableWrapper

Gets all map annotations linked to an object in OMERO, if possible.

getMapAnnotations(String) - Method in interface fr.igred.omero.client.Browser

Gets the list of map annotations with the specified key available to the user.

getMapAnnotations(String, String) - Method in interface fr.igred.omero.client.Browser

Gets the list of map annotations with the specified key and value available to the user.

getMask() - Method in interface fr.igred.omero.roi.Mask

Returns the mask as a byte array.

getMask() - Method in class fr.igred.omero.roi.MaskWrapper

Returns the mask as a byte array.

getMaskAsBinaryArray() - Method in interface fr.igred.omero.roi.Mask

Returns the mask image.

getMaskAsBinaryArray() - Method in class fr.igred.omero.roi.MaskWrapper

Returns the mask image.

getMaskPoints() - Method in interface fr.igred.omero.roi.Polygon

Returns the points in the polygon.

getMaskPoints() - Method in class fr.igred.omero.roi.PolygonWrapper

Returns the points in the polygon.

getMaximumFieldCount() - Method in interface fr.igred.omero.screen.PlateAcquisition

Returns the maximum number of fields in any well.

getMaximumFieldCount() - Method in class fr.igred.omero.screen.PlateAcquisitionWrapper

Returns the maximum number of fields in any well.

getMeanExposureTime(int) - Method in interface fr.igred.omero.core.Pixels

Computes the mean exposure time for a given channel from the planes exposureTime.

getMeanExposureTime(int) - Method in class fr.igred.omero.core.PixelsWrapper

Computes the mean exposure time for a given channel from the planes exposureTime.

getMeanTimeInterval() - Method in interface fr.igred.omero.core.Pixels

Computes the mean time interval from the planes deltaTs.

getMeanTimeInterval() - Method in class fr.igred.omero.core.PixelsWrapper

Computes the mean time interval from the planes deltaTs.

getMembersOnly() - Method in interface fr.igred.omero.meta.Group

Returns the list of experimenters that are not owners of the group.

getMembersOnly() - Method in class fr.igred.omero.meta.GroupWrapper

Returns the list of experimenters that are not owners of the group.

getMetadataFacility() - Method in interface fr.igred.omero.client.Browser

Gets the MetadataFacility used to retrieve annotations from OMERO.

getMetadataFacility() - Method in interface fr.igred.omero.client.Client

Gets the MetadataFacility used to retrieve annotations from OMERO.

getMiddleName() - Method in interface fr.igred.omero.meta.Experimenter

Returns the middle name of the experimenter.

getMiddleName() - Method in class fr.igred.omero.meta.ExperimenterWrapper

Returns the middle name of the experimenter.

getMinPosition(Collection<? extends PlaneInfo>, Function<? super PlaneInfo, ? extends Length>, Unit<Length>) - Static method in interface fr.igred.omero.core.PlaneInfo

Retrieves the min value for the specified getter in a PlaneInfo collection.

getMyRating(Browser) - Method in interface fr.igred.omero.Annotatable

Returns the user rating for this object (averaged if multiple ratings are linked).

getMyRating(Browser) - Method in class fr.igred.omero.AnnotatableWrapper

Returns the user rating for this object (averaged if multiple ratings are linked).

getName() - Method in interface fr.igred.omero.annotations.Table

Returns the name of the table.

getName() - Method in class fr.igred.omero.annotations.TableWrapper

Returns the name of the table.

getName() - Method in interface fr.igred.omero.annotations.TagAnnotation

Gets the name of the tag.

getName() - Method in class fr.igred.omero.annotations.TagAnnotationWrapper

Gets the name of the TagData.

getName() - Method in class fr.igred.omero.containers.DatasetWrapper

Gets the DatasetData name

getName() - Method in class fr.igred.omero.containers.FolderWrapper

Gets the name of the folder

getName() - Method in class fr.igred.omero.containers.ProjectWrapper

Gets the project name.

getName() - Method in interface fr.igred.omero.core.Channel

Returns the name of the channel.

getName() - Method in class fr.igred.omero.core.ChannelWrapper

Returns the name of the channel.

getName() - Method in class fr.igred.omero.core.ImageWrapper

Gets the image name.

getName() - Method in interface fr.igred.omero.meta.Group

Returns the name of the group.

getName() - Method in class fr.igred.omero.meta.GroupWrapper

Returns the name of the group.

getName() - Method in interface fr.igred.omero.RepositoryObject

Gets the object name.

getName() - Method in interface fr.igred.omero.roi.ROI

Gets the ROI name.

getName() - Method in class fr.igred.omero.roi.ROIWrapper

Gets the ROI name.

getName() - Method in class fr.igred.omero.screen.PlateAcquisitionWrapper

Gets the plate acquisition name.

getName() - Method in class fr.igred.omero.screen.PlateWrapper

Gets the plate name.

getName() - Method in class fr.igred.omero.screen.ScreenWrapper

Gets the screen name.

getName() - Method in class fr.igred.omero.screen.WellWrapper

Gets the object name.

getNameSpace() - Method in interface fr.igred.omero.annotations.Annotation

Retrieves the annotation namespace.

getNameSpace() - Method in class fr.igred.omero.annotations.AnnotationWrapper

Retrieves the annotation namespace.

getOriginalMimetype() - Method in interface fr.igred.omero.annotations.FileAnnotation

Returns the format of the original file.

getOriginalMimetype() - Method in class fr.igred.omero.annotations.FileAnnotationWrapper

Returns the format of the original file.

getOwner() - Method in class fr.igred.omero.ObjectWrapper

Gets the owner ID

getOwner() - Method in interface fr.igred.omero.RemoteObject

Gets the owner ID

getParent() - Method in interface fr.igred.omero.containers.Folder

Retrieves the parent folders for this folder.

getParent() - Method in class fr.igred.omero.containers.FolderWrapper

Retrieves the parent folders for this folder.

getPermissionsLevel() - Method in interface fr.igred.omero.meta.Group

Returns the permissions level.

getPermissionsLevel() - Method in class fr.igred.omero.meta.GroupWrapper

Returns the permissions level.

getPixels() - Method in interface fr.igred.omero.core.Image

Gets the Pixels for this image.

getPixels() - Method in class fr.igred.omero.core.ImageWrapper

Gets the Pixels for this image.

getPixelSizeX() - Method in interface fr.igred.omero.core.Pixels

Gets the size of a single image pixel on the X axis.

getPixelSizeX() - Method in class fr.igred.omero.core.PixelsWrapper

Gets the size of a single image pixel on the X axis.

getPixelSizeY() - Method in interface fr.igred.omero.core.Pixels

Gets the size of a single image pixel on the Y axis.

getPixelSizeY() - Method in class fr.igred.omero.core.PixelsWrapper

Gets the size of a single image pixel on the Y axis.

getPixelSizeZ() - Method in interface fr.igred.omero.core.Pixels

Gets the size of a single image pixel on the Z axis.

getPixelSizeZ() - Method in class fr.igred.omero.core.PixelsWrapper

Gets the size of a single image pixel on the Z axis.

getPixelType() - Method in interface fr.igred.omero.core.Pixels

Gets the pixel type.

getPixelType() - Method in class fr.igred.omero.core.PixelsWrapper

Gets the pixel type.

getPlanesInfo() - Method in interface fr.igred.omero.core.Pixels

Retrieves the planes information (which need to be loaded first).

getPlanesInfo() - Method in class fr.igred.omero.core.PixelsWrapper

Retrieves the planes information (which need to be loaded first).

getPlate() - Method in interface fr.igred.omero.screen.Well

Returns the plate containing this Well.

getPlate() - Method in class fr.igred.omero.screen.WellWrapper

Returns the plate containing this Well.

getPlate(Long) - Method in interface fr.igred.omero.client.Browser

Gets the plate with the specified id from OMERO.

getPlateAcquisitions() - Method in interface fr.igred.omero.screen.Plate

Returns the plate acquisitions related to this plate.

getPlateAcquisitions() - Method in class fr.igred.omero.screen.PlateWrapper

Returns the plate acquisitions related to this plate.

getPlateAcquisitions(Browser) - Method in class fr.igred.omero.annotations.AnnotationWrapper

Gets all plate acquisitions with this annotation from OMERO.

getPlateAcquisitions(Browser) - Method in interface fr.igred.omero.core.Image

Returns the plate acquisitions linked to this image.

getPlateAcquisitions(Browser) - Method in interface fr.igred.omero.HCSLinked

Returns the plate acquisitions linked to this object, either directly, or through parents/children.

getPlateAcquisitions(Browser) - Method in interface fr.igred.omero.screen.Plate

Reloads this plate and returns the related plate acquisitions.

getPlateAcquisitions(Browser) - Method in interface fr.igred.omero.screen.PlateAcquisition

Returns this plate acquisitions as a singleton list.

getPlateAcquisitions(Browser) - Method in interface fr.igred.omero.screen.Screen

Returns the plate acquisitions linked to this object, either directly, or through parents/children.

getPlateAcquisitions(Browser) - Method in interface fr.igred.omero.screen.Well

Refreshes this well and returns the plate acquisitions linked to it.

getPlateAcquisitions(Browser) - Method in interface fr.igred.omero.screen.WellSample

Returns the plate acquisitions linked to the parent Well.

getPlates() - Method in interface fr.igred.omero.client.Browser

Gets all plates available from OMERO.

getPlates() - Method in interface fr.igred.omero.screen.Screen

Returns the plates contained in this screen.

getPlates() - Method in class fr.igred.omero.screen.ScreenWrapper

Returns the plates contained in this screen.

getPlates(Browser) - Method in class fr.igred.omero.annotations.AnnotationWrapper

Gets all plates with this annotation from OMERO.

getPlates(Browser) - Method in interface fr.igred.omero.core.Image

Retrieves the plates containing this image.

getPlates(Browser) - Method in interface fr.igred.omero.HCSLinked

Returns the plates linked to this object, either directly, or through parents/children.

getPlates(Browser) - Method in interface fr.igred.omero.screen.Plate

Reloads and returns this plate as a singleton list.

getPlates(Browser) - Method in interface fr.igred.omero.screen.PlateAcquisition

Returns the (updated) parent plate as a singleton list.

getPlates(Browser) - Method in interface fr.igred.omero.screen.Screen

Reloads this screen and returns the updated list of plates linked to this screen.

getPlates(Browser) - Method in interface fr.igred.omero.screen.Well

Reloads this well and returns the plate containing it.

getPlates(Browser) - Method in interface fr.igred.omero.screen.WellSample

Returns the plates containing the parent Well.

getPlates(Experimenter) - Method in interface fr.igred.omero.client.Browser

Gets all plates available from OMERO owned by a given user.

getPlates(Long...) - Method in interface fr.igred.omero.client.Browser

Gets the plates with the specified ids from OMERO.

getPlates(String) - Method in interface fr.igred.omero.screen.Screen

Returns the plates contained in this screen, with the specified name.

getPlateType() - Method in interface fr.igred.omero.screen.Plate

Returns the type of plate e.g.

getPlateType() - Method in class fr.igred.omero.screen.PlateWrapper

Returns the type of plate e.g.

getPoints() - Method in interface fr.igred.omero.roi.Polygonal

Returns the points in the polygonal shape.

getPoints() - Method in class fr.igred.omero.roi.PolygonWrapper

Returns the points in the polygonal shape.

getPoints() - Method in class fr.igred.omero.roi.PolylineWrapper

Returns the points in the Polyline.

getPositionX() - Method in interface fr.igred.omero.core.Pixels

Retrieves the X stage position.

getPositionX() - Method in class fr.igred.omero.core.PixelsWrapper

Retrieves the X stage position.

getPositionX() - Method in interface fr.igred.omero.core.PlaneInfo

Retrieves the X stage position.

getPositionX() - Method in class fr.igred.omero.core.PlaneInfoWrapper

Retrieves the X stage position.

getPositionX(UnitsLength) - Method in interface fr.igred.omero.screen.WellSample

Returns the position X.

getPositionX(UnitsLength) - Method in class fr.igred.omero.screen.WellSampleWrapper

Returns the position X.

getPositionY() - Method in interface fr.igred.omero.core.Pixels

Retrieves the Y stage position.

getPositionY() - Method in class fr.igred.omero.core.PixelsWrapper

Retrieves the Y stage position.

getPositionY() - Method in interface fr.igred.omero.core.PlaneInfo

Retrieves the Y stage position.

getPositionY() - Method in class fr.igred.omero.core.PlaneInfoWrapper

Retrieves the Y stage position.

getPositionY(UnitsLength) - Method in interface fr.igred.omero.screen.WellSample

Returns the position Y.

getPositionY(UnitsLength) - Method in class fr.igred.omero.screen.WellSampleWrapper

Returns the position Y.

getPositionZ() - Method in interface fr.igred.omero.core.Pixels

Retrieves the Z stage position.

getPositionZ() - Method in class fr.igred.omero.core.PixelsWrapper

Retrieves the Z stage position.

getPositionZ() - Method in interface fr.igred.omero.core.PlaneInfo

Retrieves the Z stage position.

getPositionZ() - Method in class fr.igred.omero.core.PlaneInfoWrapper

Retrieves the Z stage position.

getProject(Long) - Method in interface fr.igred.omero.client.Browser

Gets the project with the specified id from OMERO.

getProjects() - Method in interface fr.igred.omero.client.Browser

Gets all projects available from OMERO.

getProjects(Browser) - Method in class fr.igred.omero.annotations.AnnotationWrapper

Gets all projects with this annotation from OMERO.

getProjects(Browser) - Method in interface fr.igred.omero.ContainerLinked

Retrieves the projects linked to this object, either directly, or through parents/children.

getProjects(Browser) - Method in interface fr.igred.omero.containers.Dataset

Retrieves the projects containing this dataset.

getProjects(Browser) - Method in interface fr.igred.omero.containers.Project

Reloads and returns this project as a singleton list.

getProjects(Browser) - Method in interface fr.igred.omero.core.Image

Retrieves the projects containing this image.

getProjects(Experimenter) - Method in interface fr.igred.omero.client.Browser

Gets all projects available from OMERO owned by a given user.

getProjects(Long...) - Method in interface fr.igred.omero.client.Browser

Gets the projects with the specified ids from OMERO.

getProjects(String) - Method in interface fr.igred.omero.client.Browser

Gets all projects with a certain name from OMERO.

getProtocolDescription() - Method in interface fr.igred.omero.screen.Screen

Returns the description of the protocol.

getProtocolDescription() - Method in class fr.igred.omero.screen.ScreenWrapper

Returns the description of the protocol.

getProtocolIdentifier() - Method in interface fr.igred.omero.screen.Screen

Returns the identifier of the protocol.

getProtocolIdentifier() - Method in class fr.igred.omero.screen.ScreenWrapper

Returns the identifier of the protocol.

getQueryService() - Method in interface fr.igred.omero.client.Browser

Returns the IQueryPrx used to find objects on OMERO.

getQueryService() - Method in interface fr.igred.omero.client.Client

Returns the IQueryPrx used to find objects on OMERO.

getRadiusX() - Method in interface fr.igred.omero.roi.Ellipse

Returns the radius along the X-axis.

getRadiusX() - Method in class fr.igred.omero.roi.EllipseWrapper

Returns the radius along the X-axis.

getRadiusY() - Method in interface fr.igred.omero.roi.Ellipse

Returns the radius along the Y-axis.

getRadiusY() - Method in class fr.igred.omero.roi.EllipseWrapper

Returns the radius along the Y-axis.

getRating() - Method in interface fr.igred.omero.annotations.RatingAnnotation

Returns the rating value.

getRating() - Method in class fr.igred.omero.annotations.RatingAnnotationWrapper

Returns the rating value.

getRawPixels(ConnectionHandler, int) - Method in interface fr.igred.omero.core.Pixels

Returns an array containing the raw values for each voxel of each plane.

getRawPixels(ConnectionHandler, int[], int[], int[], int[], int[], int) - Method in interface fr.igred.omero.core.Pixels

Returns an array containing the raw values for each voxel for each plane corresponding to the bounds

getRawPixels(ConnectionHandler, int[], int[], int[], int[], int[], int) - Method in class fr.igred.omero.core.PixelsWrapper

Returns an array containing the raw values for each voxel for each plane corresponding to the bounds

getReagentSetDescription() - Method in interface fr.igred.omero.screen.Screen

Returns the description of the reagent set.

getReagentSetDescription() - Method in class fr.igred.omero.screen.ScreenWrapper

Returns the description of the reagent set.

getReagentSetIdentifier() - Method in interface fr.igred.omero.screen.Screen

Returns the identifier of the Reagent set.

getReagentSetIdentifier() - Method in class fr.igred.omero.screen.ScreenWrapper

Returns the identifier of the Reagent set.

getRed() - Method in interface fr.igred.omero.core.Channel

Gets the sRGB red value of the channel.

getRed() - Method in class fr.igred.omero.core.ChannelWrapper

Gets the sRGB red value of the channel.

getRed() - Method in interface fr.igred.omero.screen.Well

Returns the red component of the color associated to the well, or -1.

getRed() - Method in class fr.igred.omero.screen.WellWrapper

Returns the red component of the color associated to the well, or -1.

getRefPlateId() - Method in interface fr.igred.omero.screen.PlateAcquisition

Returns the id of the plate of reference.

getRefPlateId() - Method in class fr.igred.omero.screen.PlateAcquisitionWrapper

Returns the id of the plate of reference.

getRoiFacility() - Method in interface fr.igred.omero.client.Client

Gets the ROIFacility used to manipulate ROIs from OMERO.

getRoiFacility() - Method in interface fr.igred.omero.client.DataManager

Gets the ROIFacility used to manipulate ROIs from OMERO.

getROIFolders(DataManager) - Method in interface fr.igred.omero.core.Image

Gets the list of folders linked to the ROIs in this image.

getROIFolders(DataManager) - Method in class fr.igred.omero.core.ImageWrapper

Gets the list of folders linked to the ROIs in this image.

getROIs(DataManager) - Method in interface fr.igred.omero.core.Image

Gets all ROIs linked to the image in OMERO

getROIs(DataManager) - Method in class fr.igred.omero.core.ImageWrapper

Gets all ROIs linked to the image in OMERO

getROIs(DataManager, long) - Method in interface fr.igred.omero.containers.Folder

Gets the ROIs contained in the folder associated with the provided image ID.

getROIs(DataManager, long) - Method in class fr.igred.omero.containers.FolderWrapper

Gets the ROIs contained in the folder associated with the provided image ID.

getROIs(DataManager, Image) - Method in interface fr.igred.omero.containers.Folder

Gets the ROIs contained in the folder associated with the provided image.

getRow() - Method in interface fr.igred.omero.screen.Well

Returns the row used to indicate the location of the well on the grid.

getRow() - Method in class fr.igred.omero.screen.WellWrapper

Returns the row used to indicate the location of the well on the grid.

getRowCount() - Method in interface fr.igred.omero.annotations.Table

Returns the number of rows in the table.

getRowCount() - Method in class fr.igred.omero.annotations.TableWrapper

Returns the number of rows in the table.

getRowSequenceIndex() - Method in interface fr.igred.omero.screen.Plate

Returns the index indicating how to label a row.

getRowSequenceIndex() - Method in class fr.igred.omero.screen.PlateWrapper

Returns the index indicating how to label a row.

getScreen(Long) - Method in interface fr.igred.omero.client.Browser

Gets the screen with the specified id from OMERO.

getScreens() - Method in interface fr.igred.omero.client.Browser

Gets all screens available from OMERO.

getScreens(Browser) - Method in class fr.igred.omero.annotations.AnnotationWrapper

Gets all screens with this annotation from OMERO.

getScreens(Browser) - Method in interface fr.igred.omero.core.Image

Retrieves the screens containing this image

getScreens(Browser) - Method in interface fr.igred.omero.HCSLinked

Retrieves the screens linked to this object, either directly, or through parents/children.

getScreens(Browser) - Method in interface fr.igred.omero.screen.Plate

Retrieves the screens containing this plate.

getScreens(Browser) - Method in interface fr.igred.omero.screen.PlateAcquisition

Retrieves the screens containing the parent plates.

getScreens(Browser) - Method in interface fr.igred.omero.screen.Screen

Reloads and returns this screen as a singleton list.

getScreens(Browser) - Method in interface fr.igred.omero.screen.Well

Refreshes this well and retrieves the screens containing it.

getScreens(Browser) - Method in interface fr.igred.omero.screen.WellSample

Returns the screens containing the parent Well.

getScreens(Experimenter) - Method in interface fr.igred.omero.client.Browser

Gets all screens available from OMERO owned by a given user.

getScreens(Long...) - Method in interface fr.igred.omero.client.Browser

Gets the screens with the specified ids from OMERO.

getServerFileMimetype() - Method in interface fr.igred.omero.annotations.FileAnnotation

Returns the file format as defined by the specification, corresponding to the file extension.

getServerFileMimetype() - Method in class fr.igred.omero.annotations.FileAnnotationWrapper

Returns the file format as defined by the specification, corresponding to the file extension.

getSessionId() - Method in interface fr.igred.omero.client.ConnectionHandler

Get the ID of the current session

getShapes() - Method in interface fr.igred.omero.roi.ROI

Returns the list of shapes contained in the ROI.

getShapes() - Method in class fr.igred.omero.roi.ROIWrapper

Returns the list of shapes contained in the ROI.

getSize() - Method in class fr.igred.omero.util.Bounds

Gets size of bounds for each coordinate.

getSizeC() - Method in interface fr.igred.omero.core.Pixels

Gets the size of the image on the C axis

getSizeC() - Method in class fr.igred.omero.core.PixelsWrapper

Gets the size of the image on the C axis

getSizeT() - Method in interface fr.igred.omero.core.Pixels

Gets the size of the image on the T axis

getSizeT() - Method in class fr.igred.omero.core.PixelsWrapper

Gets the size of the image on the T axis

getSizeX() - Method in interface fr.igred.omero.core.Pixels

Gets the size of the image on the X axis

getSizeX() - Method in class fr.igred.omero.core.PixelsWrapper

Gets the size of the image on the X axis

getSizeY() - Method in interface fr.igred.omero.core.Pixels

Gets the size of the image on the Y axis

getSizeY() - Method in class fr.igred.omero.core.PixelsWrapper

Gets the size of the image on the Y axis

getSizeZ() - Method in interface fr.igred.omero.core.Pixels

Gets the size of the image on the Z axis

getSizeZ() - Method in class fr.igred.omero.core.PixelsWrapper

Gets the size of the image on the Z axis

getStart() - Method in class fr.igred.omero.util.Bounds

Gets starting coordinates.

getStartTime() - Method in interface fr.igred.omero.screen.PlateAcquisition

Returns the time when the first image was collected.

getStartTime() - Method in class fr.igred.omero.screen.PlateAcquisitionWrapper

Returns the time when the first image was collected.

getStartTime() - Method in interface fr.igred.omero.screen.WellSample

Returns the time at which the field was acquired.

getStartTime() - Method in class fr.igred.omero.screen.WellSampleWrapper

Returns the time at which the field was acquired.

getStatus() - Method in interface fr.igred.omero.screen.Plate

Returns the status of the plate.

getStatus() - Method in class fr.igred.omero.screen.PlateWrapper

Returns the status of the plate.

getStatus() - Method in interface fr.igred.omero.screen.Well

Returns the status of the well.

getStatus() - Method in class fr.igred.omero.screen.WellWrapper

Returns the status of the well.

getStroke() - Method in interface fr.igred.omero.roi.Shape

Gets the ShapeData stroke color.

getStroke() - Method in class fr.igred.omero.roi.ShapeWrapper

Gets the ShapeData stroke color.

getT() - Method in interface fr.igred.omero.roi.Shape

Sets the time-point.

getT() - Method in class fr.igred.omero.roi.ShapeWrapper

Sets the time-point.

getT() - Method in class fr.igred.omero.util.Coordinates

Gets T coordinate.

getTable(DataManager, Long) - Method in interface fr.igred.omero.Annotatable

Gets a certain table linked to the object in OMERO.

getTable(DataManager, Long) - Method in class fr.igred.omero.AnnotatableWrapper

Gets a certain table linked to the object in OMERO.

getTables(DataManager) - Method in interface fr.igred.omero.Annotatable

Gets all tables linked to the object in OMERO.

getTablesFacility() - Method in interface fr.igred.omero.client.Client

Gets the TablesFacility used to manipulate tables on OMERO.

getTablesFacility() - Method in interface fr.igred.omero.client.DataManager

Gets the TablesFacility used to manipulate tables on OMERO.

getTag(Long) - Method in interface fr.igred.omero.client.Browser

Gets a specific tag from the OMERO database.

getTags() - Method in interface fr.igred.omero.client.Browser

Gets the list of tag annotations available to the user.

getTags(Browser) - Method in interface fr.igred.omero.Annotatable

Gets all tags linked to an object in OMERO, if possible.

getTags(Browser) - Method in class fr.igred.omero.AnnotatableWrapper

Gets all tags linked to an object in OMERO, if possible.

getTags(String) - Method in interface fr.igred.omero.client.Browser

Gets the list of tag annotations with the specified name available to the user.

getText() - Method in interface fr.igred.omero.annotations.TextualAnnotation

Returns the text of this annotation.

getText() - Method in class fr.igred.omero.annotations.TextualAnnotationWrapper

Returns the text of this annotation.

getText() - Method in class fr.igred.omero.roi.EllipseWrapper

Gets the text on the ShapeData.

getText() - Method in class fr.igred.omero.roi.LineWrapper

Gets the text on the ShapeData.

getText() - Method in class fr.igred.omero.roi.MaskWrapper

Gets the text on the ShapeData.

getText() - Method in class fr.igred.omero.roi.PointWrapper

Gets the text on the ShapeData.

getText() - Method in class fr.igred.omero.roi.PolygonWrapper

Gets the text on the ShapeData.

getText() - Method in class fr.igred.omero.roi.PolylineWrapper

Gets the text on the ShapeData.

getText() - Method in class fr.igred.omero.roi.RectangleWrapper

Gets the text on the ShapeData.

getText() - Method in interface fr.igred.omero.roi.Shape

Gets the text on the ShapeData.

getText() - Method in class fr.igred.omero.roi.TextWrapper

Gets the text on the ShapeData.

getTheC() - Method in interface fr.igred.omero.core.PlaneInfo

Retrieves the plane channel index.

getTheC() - Method in class fr.igred.omero.core.PlaneInfoWrapper

Retrieves the plane channel index.

getTheT() - Method in interface fr.igred.omero.core.PlaneInfo

Retrieves the plane time index.

getTheT() - Method in class fr.igred.omero.core.PlaneInfoWrapper

Retrieves the plane time index.

getTheZ() - Method in interface fr.igred.omero.core.PlaneInfo

Retrieves the plane slice index.

getTheZ() - Method in class fr.igred.omero.core.PlaneInfoWrapper

Retrieves the plane slice index.

getThumbnail(ConnectionHandler, int) - Method in interface fr.igred.omero.core.Image

Retrieves the image thumbnail of the specified size.

getThumbnail(ConnectionHandler, int) - Method in class fr.igred.omero.core.ImageWrapper

Retrieves the image thumbnail of the specified size.

getTimeIncrement() - Method in interface fr.igred.omero.core.Pixels

Gets the time increment between time points.

getTimeIncrement() - Method in class fr.igred.omero.core.PixelsWrapper

Gets the time increment between time points.

getUser() - Method in interface fr.igred.omero.client.ConnectionHandler

Returns the current user.

getUser() - Method in class fr.igred.omero.client.GatewayWrapper

Returns the current user.

getUser(String) - Method in interface fr.igred.omero.client.AdminManager

Returns the user which matches the username.

getUserName() - Method in interface fr.igred.omero.meta.Experimenter

Returns the last name of the experimenter.

getUserName() - Method in class fr.igred.omero.meta.ExperimenterWrapper

Returns the last name of the experimenter.

getValues(Browser, String) - Method in interface fr.igred.omero.Annotatable

Gets the value from a Key-Value pair associated to the object.

getWell(Browser) - Method in interface fr.igred.omero.screen.WellSample

Retrieves the well containing this well sample.

getWell(Long) - Method in interface fr.igred.omero.client.Browser

Gets the well with the specified id from OMERO.

getWellOriginX(UnitsLength) - Method in interface fr.igred.omero.screen.Plate

Returns the x-coordinate in 2D-space of the well.

getWellOriginX(UnitsLength) - Method in class fr.igred.omero.screen.PlateWrapper

Returns the x-coordinate in 2D-space of the well.

getWellOriginY(UnitsLength) - Method in interface fr.igred.omero.screen.Plate

Returns the y-coordinate in 2D-space of the well.

getWellOriginY(UnitsLength) - Method in class fr.igred.omero.screen.PlateWrapper

Returns the y-coordinate in 2D-space of the well.

getWells() - Method in interface fr.igred.omero.client.Browser

Gets all wells available from OMERO.

getWells(Browser) - Method in class fr.igred.omero.annotations.AnnotationWrapper

Gets all wells with this annotation from OMERO.

getWells(Browser) - Method in interface fr.igred.omero.core.Image

Retrieves the wells containing this image.

getWells(Browser) - Method in interface fr.igred.omero.HCSLinked

Retrieves the wells linked to this object, either directly, or through parents/children.

getWells(Browser) - Method in interface fr.igred.omero.screen.Plate

Gets all wells in the plate available from OMERO.

getWells(Browser) - Method in interface fr.igred.omero.screen.PlateAcquisition

Retrieves the wells contained in the parent plate.

getWells(Browser) - Method in class fr.igred.omero.screen.PlateWrapper

Gets all wells in the plate available from OMERO.

getWells(Browser) - Method in interface fr.igred.omero.screen.Screen

Retrieves the wells linked to this object, either directly, or through parents/children.

getWells(Browser) - Method in interface fr.igred.omero.screen.Well

Reloads this well and returns it as a singleton list.

getWells(Browser) - Method in interface fr.igred.omero.screen.WellSample

Retrieves the well containing this Well Sample as a singleton list.

getWells(Experimenter) - Method in interface fr.igred.omero.client.Browser

Gets all wells available from OMERO owned by a given user.

getWells(Long...) - Method in interface fr.igred.omero.client.Browser

Gets the wells with the specified ids from OMERO.

getWellSamples() - Method in interface fr.igred.omero.screen.Well

Returns the well samples linked to the well.

getWellSamples() - Method in class fr.igred.omero.screen.WellWrapper

Returns the well samples linked to the well.

getWellType() - Method in interface fr.igred.omero.screen.Well

Returns a human-readable identifier for the screening status e.g.

getWellType() - Method in class fr.igred.omero.screen.WellWrapper

Returns a human-readable identifier for the screening status e.g.

getWidth() - Method in class fr.igred.omero.roi.MaskWrapper

Returns the width of the rectangular shape.

getWidth() - Method in class fr.igred.omero.roi.RectangleWrapper

Returns the width untransformed rectangle.

getWidth() - Method in interface fr.igred.omero.roi.Rectangular

Returns the width of the rectangular shape.

getX() - Method in interface fr.igred.omero.roi.Ellipse

Returns the x-coordinate of the center of the ellipse.

getX() - Method in class fr.igred.omero.roi.EllipseWrapper

Returns the x-coordinate of the center of the ellipse.

getX() - Method in class fr.igred.omero.roi.MaskWrapper

Returns the x-coordinate of the rectangular shape.

getX() - Method in class fr.igred.omero.roi.PointWrapper

Returns the x-coordinate of the punctual shape.

getX() - Method in interface fr.igred.omero.roi.Punctual

Returns the x-coordinate of the punctual shape.

getX() - Method in class fr.igred.omero.roi.RectangleWrapper

Returns the x-coordinate of the shape.

getX() - Method in interface fr.igred.omero.roi.Rectangular

Returns the x-coordinate of the rectangular shape.

getX() - Method in class fr.igred.omero.roi.TextWrapper

Returns the x-coordinate of the shape.

getX() - Method in class fr.igred.omero.util.Coordinates

Gets X coordinate.

getX1() - Method in interface fr.igred.omero.roi.Line

Returns the x-coordinate of the starting point of an untransformed line.

getX1() - Method in class fr.igred.omero.roi.LineWrapper

Returns the x-coordinate of the starting point of an untransformed line.

getX2() - Method in interface fr.igred.omero.roi.Line

Returns the x-coordinate of the end point of an untransformed line.

getX2() - Method in class fr.igred.omero.roi.LineWrapper

Returns the x-coordinate of the end point of an untransformed line.

getY() - Method in interface fr.igred.omero.roi.Ellipse

Returns the y-coordinate of the center of the ellipse.

getY() - Method in class fr.igred.omero.roi.EllipseWrapper

Returns the y-coordinate of the center of the ellipse.

getY() - Method in class fr.igred.omero.roi.MaskWrapper

Returns the y coordinate of the rectangular shape.

getY() - Method in class fr.igred.omero.roi.PointWrapper

Returns the y coordinate of the punctual shape.

getY() - Method in interface fr.igred.omero.roi.Punctual

Returns the y coordinate of the punctual shape.

getY() - Method in class fr.igred.omero.roi.RectangleWrapper

Returns the y coordinate of the shape.

getY() - Method in interface fr.igred.omero.roi.Rectangular

Returns the y coordinate of the rectangular shape.

getY() - Method in class fr.igred.omero.roi.TextWrapper

Returns the y coordinate of the shape.

getY() - Method in class fr.igred.omero.util.Coordinates

Gets Y coordinate.

getY1() - Method in interface fr.igred.omero.roi.Line

Returns the y-coordinate of the starting point of an untransformed line.

getY1() - Method in class fr.igred.omero.roi.LineWrapper

Returns the y-coordinate of the starting point of an untransformed line.

getY2() - Method in interface fr.igred.omero.roi.Line

Returns the y-coordinate of the end point of an untransformed line.

getY2() - Method in class fr.igred.omero.roi.LineWrapper

Returns the y-coordinate of the end point of an untransformed line.

getZ() - Method in interface fr.igred.omero.roi.Shape

Gets the z-section.

getZ() - Method in class fr.igred.omero.roi.ShapeWrapper

Gets the z-section.

getZ() - Method in class fr.igred.omero.util.Coordinates

Gets Z coordinate.

Group - Interface in fr.igred.omero.meta

Interface to handle Groups on OMERO.

GroupWrapper - Class in fr.igred.omero.meta

Class containing a GroupData object.

GroupWrapper(GroupData) - Constructor for class fr.igred.omero.meta.GroupWrapper

Constructor of the class GroupWrapper.

H

handleException(String) - Method in class fr.igred.omero.exception.ExceptionHandler

Throws: AccessException if DSAccessException was caught ServiceException if DSOutOfServiceException was caught ServerException if ServerError was caught

handleServiceOrAccess(String) - Method in class fr.igred.omero.exception.ExceptionHandler

Throws: ServiceException if DSOutOfServiceException was caught AccessException if DSAccessException was caught

handleServiceOrServer(String) - Method in class fr.igred.omero.exception.ExceptionHandler

Throws: ServiceException if DSOutOfServiceException was caught ServerException if ServerError was caught

hasRGBA() - Method in interface fr.igred.omero.core.Channel

Returns whether the channel contains all the RGBA values or not.

hasRGBA() - Method in class fr.igred.omero.core.ChannelWrapper

Returns whether the channel contains all the RGBA values or not.

HCSLinked - Interface in fr.igred.omero

Interface to handle objects that can be linked to HCS objects (screens, plates, wells) on OMERO.

I

IJ_PROPERTY - Static variable in interface fr.igred.omero.roi.ROI

Default IJ property to store ROI local labels / indices.

ijIDProperty(String) - Static method in interface fr.igred.omero.roi.ROI

Returns the ID property corresponding to the input local index/label property (appends "_ID" to said property).

ijNameProperty(String) - Static method in interface fr.igred.omero.roi.ROI

Returns the ID property corresponding to the input local index/label property (appends "_NAME" to said property).

Image - Interface in fr.igred.omero.core

Interface to handle Images on OMERO.

ImageLinked - Interface in fr.igred.omero

Interface to handle objects that can be linked to images (tags, containers, HCS, folders).

ImageWrapper - Class in fr.igred.omero.core

Class containing an ImageData.

ImageWrapper(ImageData) - Constructor for class fr.igred.omero.core.ImageWrapper

Constructor of the class ImageWrapper

importAndReplaceImages(Client, String) - Method in interface fr.igred.omero.containers.Dataset

Imports one image file to the dataset in OMERO and replace older images sharing the same name after copying their annotations and ROIs, and concatenating the descriptions (on new lines) by unlinking them.

importAndReplaceImages(Client, String, ReplacePolicy) - Method in interface fr.igred.omero.containers.Dataset

Imports one image file to the dataset in OMERO and replace older images sharing the same name after copying their annotations and ROIs, and concatenating the descriptions (on new lines) by unlinking or even deleting them.

importImage(Client, String) - Method in interface fr.igred.omero.containers.Dataset

Imports one image file to the dataset in OMERO.

importImage(Client, String) - Method in class fr.igred.omero.containers.DatasetWrapper

Imports one image file to the dataset in OMERO.

importImage(Client, String) - Method in interface fr.igred.omero.screen.Screen

Imports one image file to the screen in OMERO.

importImage(Client, String) - Method in class fr.igred.omero.screen.ScreenWrapper

Imports one image file to the screen in OMERO.

importImage(ConnectionHandler, DataObject, String) - Static method in class fr.igred.omero.RepositoryObjectWrapper

Imports one image file to the target in OMERO.

importImages(Client, String...) - Method in interface fr.igred.omero.containers.Dataset

Imports all images candidates in the paths to the dataset in OMERO.

importImages(Client, String...) - Method in class fr.igred.omero.containers.DatasetWrapper

Imports all images candidates in the paths to the dataset in OMERO.

importImages(Client, String...) - Method in interface fr.igred.omero.screen.Screen

Imports all images candidates in the paths to the screen in OMERO.

importImages(Client, String...) - Method in class fr.igred.omero.screen.ScreenWrapper

Imports all images candidates in the paths to the screen in OMERO.

importImages(ConnectionHandler, DataObject, String...) - Static method in class fr.igred.omero.RepositoryObjectWrapper

Imports all images candidates in the paths to the target in OMERO.

isActive() - Method in interface fr.igred.omero.meta.Experimenter

Returns true if the experimenter is active, false otherwise.

isActive() - Method in class fr.igred.omero.meta.ExperimenterWrapper

Returns true if the experimenter is active, false otherwise.

isComplete() - Method in interface fr.igred.omero.annotations.Table

Checks if the table is complete

isComplete() - Method in class fr.igred.omero.annotations.TableWrapper

Checks if the table is complete

isConnected() - Method in interface fr.igred.omero.client.ConnectionHandler

Check if the client is still connected to the server

isFormatsAPIAvailable() - Static method in class fr.igred.omero.util.LibraryChecker

Checks if formats-api is available.

isLDAP() - Method in interface fr.igred.omero.meta.Experimenter

Returns true if the user is connected via LDAP.

isLDAP() - Method in class fr.igred.omero.meta.ExperimenterWrapper

Returns true if the user is connected via LDAP.

isLinked(Browser, A) - Method in interface fr.igred.omero.Annotatable

Checks if a specific annotation is linked to the object.

isMemberOfGroup(long) - Method in interface fr.igred.omero.meta.Experimenter

Checks if supplied group id matches any group to which the current experimenter belongs to.

isMemberOfGroup(long) - Method in class fr.igred.omero.meta.ExperimenterWrapper

Checks if supplied group id matches any group to which the current experimenter belongs to.

isMovieFile() - Method in interface fr.igred.omero.annotations.FileAnnotation

Returns true if it is a movie file.

isMovieFile() - Method in class fr.igred.omero.annotations.FileAnnotationWrapper

Returns true if it is a movie file.

isOMECommonAvailable() - Static method in class fr.igred.omero.util.LibraryChecker

Checks if ome-common is available.

isOMEROBlitzAvailable() - Static method in class fr.igred.omero.util.LibraryChecker

Checks if OMERO Blitz is available.

isOMEROGatewayAvailable() - Static method in class fr.igred.omero.util.LibraryChecker

Checks if the omero-gateway is available.

isOMEROModelAvailable() - Static method in class fr.igred.omero.util.LibraryChecker

Checks if the omero-model is available.

isOMEXMLAvailable() - Static method in class fr.igred.omero.util.LibraryChecker

Checks if the omero-model is available.

isOrphaned(Browser) - Method in interface fr.igred.omero.core.Image

Checks if image is orphaned (not in a WellSample nor linked to a dataset).

L

LEVEL_FIVE - Static variable in interface fr.igred.omero.annotations.RatingAnnotation

Indicates the object is rated with five stars.

LEVEL_FOUR - Static variable in interface fr.igred.omero.annotations.RatingAnnotation

Indicates the object is rated with four stars.

LEVEL_ONE - Static variable in interface fr.igred.omero.annotations.RatingAnnotation

Indicates the object is rated with one star.

LEVEL_THREE - Static variable in interface fr.igred.omero.annotations.RatingAnnotation

Indicates the object is rated with three stars.

LEVEL_TWO - Static variable in interface fr.igred.omero.annotations.RatingAnnotation

Indicates the object is rated with two stars.

LEVEL_ZERO - Static variable in interface fr.igred.omero.annotations.RatingAnnotation

Indicates the object is not rated.

LibraryChecker - Class in fr.igred.omero.util

Utility methods to check if required libraries/classes are available

Line - Interface in fr.igred.omero.roi

Interface to handle Line shapes on OMERO.

LineWrapper - Class in fr.igred.omero.roi

Class containing an LineData.

LineWrapper() - Constructor for class fr.igred.omero.roi.LineWrapper

Constructor of the RectangleWrapper class using a new empty LineData.

LineWrapper(double, double, double, double) - Constructor for class fr.igred.omero.roi.LineWrapper

Constructor of the RectangleWrapper class using a new LineData.

LineWrapper(Line) - Constructor for class fr.igred.omero.roi.LineWrapper

Constructor of the LineWrapper class using an ImageJ Line ROI.

LineWrapper(LineData) - Constructor for class fr.igred.omero.roi.LineWrapper

Constructor of the LineWrapper class using a LineData.

link(DataManager, A) - Method in interface fr.igred.omero.Annotatable

Attach an AnnotationData to this object.

link(DataManager, A) - Method in interface fr.igred.omero.containers.Folder

Attach an AnnotationData to this object.

link(DataManager, A) - Method in interface fr.igred.omero.roi.ROI

Attach an AnnotationData to this object.

link(DataManager, A) - Method in interface fr.igred.omero.roi.Shape

Attach an AnnotationData to this object.

link(DataManager, A) - Method in interface fr.igred.omero.screen.PlateAcquisition

Attach an AnnotationData to this object.

link(DataManager, A) - Method in class fr.igred.omero.screen.PlateAcquisitionWrapper

Adds a tag to the object in OMERO, if possible.

link(DataManager, Annotation...) - Method in interface fr.igred.omero.Annotatable

Adds multiple annotations to the object in OMERO, if possible.

linkIfNotLinked(Client, Annotation...) - Method in interface fr.igred.omero.Annotatable

Adds multiple annotations to the object in OMERO if they are not already linked.

loadFolders(Long...) - Method in interface fr.igred.omero.client.Browser

Gets the folders with the specified IDs from OMERO (fully loaded).

loadPlanesInfo(Browser) - Method in interface fr.igred.omero.core.Pixels

Loads the planes information.

loadPlanesInfo(Browser) - Method in class fr.igred.omero.core.PixelsWrapper

Loads the planes information.

M

MapAnnotation - Interface in fr.igred.omero.annotations

Interface to handle Map Annotations on OMERO.

MapAnnotationWrapper - Class in fr.igred.omero.annotations

Class containing a MapAnnotationData, a MapAnnotationData contains a list of NamedValue(Key-Value pair).

MapAnnotationWrapper() - Constructor for class fr.igred.omero.annotations.MapAnnotationWrapper

Constructor of the MapAnnotationWrapper class.

MapAnnotationWrapper(Collection<? extends Map.Entry<String, String>>) - Constructor for class fr.igred.omero.annotations.MapAnnotationWrapper

Constructor of the MapAnnotationWrapper class.

MapAnnotationWrapper(MapAnnotationData) - Constructor for class fr.igred.omero.annotations.MapAnnotationWrapper

Constructor of the MapAnnotationWrapper class.

Mask - Interface in fr.igred.omero.roi

Interface to handle Mask shapes on OMERO.

MaskWrapper - Class in fr.igred.omero.roi

Class containing an MaskData.

MaskWrapper() - Constructor for class fr.igred.omero.roi.MaskWrapper

Constructor of the MaskWrapper class using a new empty MaskData.

MaskWrapper(double, double, double, double, byte[]) - Constructor for class fr.igred.omero.roi.MaskWrapper

Constructor of the MaskWrapper class using a new MaskData.

MaskWrapper(MaskData) - Constructor for class fr.igred.omero.roi.MaskWrapper

Constructor of the MaskWrapper class using a MaskData.

MAX_DIST - Static variable in class fr.igred.omero.core.PixelsWrapper

Size of tiles when retrieving pixels

O

ObjectWrapper<T extends DataObject> - Class in fr.igred.omero

Generic class containing a DataObject (or a subclass) object.

ObjectWrapper(T) - Constructor for class fr.igred.omero.ObjectWrapper

Constructor of the class ObjectWrapper.

of(I, ExceptionHandler.ThrowingFunction<? super I, ? extends R, ? extends Exception>) - Static method in class fr.igred.omero.exception.ExceptionHandler

Creates an ExceptionHandler from an object and a function.

ofConsumer(I, ExceptionHandler.ThrowingConsumer<? super I, ? extends Exception>) - Static method in class fr.igred.omero.exception.ExceptionHandler

Creates an ExceptionHandler from an object and a function with no return value.

P

PERMISSIONS_GROUP_READ - Static variable in interface fr.igred.omero.meta.Group

Indicates that the group is Group i.e.

PERMISSIONS_GROUP_READ_LINK - Static variable in interface fr.igred.omero.meta.Group

Indicates that the group is Group i.e.

PERMISSIONS_GROUP_READ_WRITE - Static variable in interface fr.igred.omero.meta.Group

Indicates that the group is Group i.e.

PERMISSIONS_PRIVATE - Static variable in interface fr.igred.omero.meta.Group

Indicates that the group is Private i.e.

PERMISSIONS_PUBLIC_READ - Static variable in interface fr.igred.omero.meta.Group

Indicates that the group is Public i.e.

PERMISSIONS_PUBLIC_READ_WRITE - Static variable in interface fr.igred.omero.meta.Group

Indicates that the group is Public i.e.

Pixels - Interface in fr.igred.omero.core

Interface to handle Pixels on OMERO.

PixelsWrapper - Class in fr.igred.omero.core

Class containing a PixelData object.

PixelsWrapper(PixelsData) - Constructor for class fr.igred.omero.core.PixelsWrapper

Constructor of the PixelsWrapper class

PlaneInfo - Interface in fr.igred.omero.core

Interface to handle PlaneInfo on OMERO.

PlaneInfoWrapper - Class in fr.igred.omero.core

PlaneInfoWrapper(PlaneInfoData) - Constructor for class fr.igred.omero.core.PlaneInfoWrapper

Constructor of the class PlaneInfoWrapper.

Plate - Interface in fr.igred.omero.screen

Interface to handle Plates on OMERO.

PlateAcquisition - Interface in fr.igred.omero.screen

Interface to handle Plate Acquisitions on OMERO.

PlateAcquisitionWrapper - Class in fr.igred.omero.screen

Class containing a PlateAcquisitionData object.

PlateAcquisitionWrapper(PlateAcquisitionData) - Constructor for class fr.igred.omero.screen.PlateAcquisitionWrapper

Constructor of the class PlateAcquisitionWrapper.

PlateWrapper - Class in fr.igred.omero.screen

Class containing a PlateData object.

PlateWrapper(PlateData) - Constructor for class fr.igred.omero.screen.PlateWrapper

Constructor of the class PlateWrapper.

Point - Interface in fr.igred.omero.roi

Interface to handle Point shapes on OMERO.

PointWrapper - Class in fr.igred.omero.roi

Class containing an PointData.

PointWrapper() - Constructor for class fr.igred.omero.roi.PointWrapper

Constructor of the PointWrapper class using a new empty PointData.

PointWrapper(double, double) - Constructor for class fr.igred.omero.roi.PointWrapper

Constructor of the PointWrapper class using a new empty ShapeData.

PointWrapper(PointData) - Constructor for class fr.igred.omero.roi.PointWrapper

Constructor of the PointWrapper class using a PointData.

Polygon - Interface in fr.igred.omero.roi

Interface to handle Polygon shapes on OMERO.

Polygonal - Interface in fr.igred.omero.roi

Interface for polygonal shapes.

PolygonWrapper - Class in fr.igred.omero.roi

Class containing an PolygonData.

PolygonWrapper() - Constructor for class fr.igred.omero.roi.PolygonWrapper

Constructor of the PolygonWrapper class using a new empty LineData.

PolygonWrapper(Roi) - Constructor for class fr.igred.omero.roi.PolygonWrapper

Constructor of the PolygonWrapper class using an ImageJ PolygonRoi.

PolygonWrapper(List<Point2D.Double>) - Constructor for class fr.igred.omero.roi.PolygonWrapper

Constructor of the PolygonWrapper class using a new LineData.

PolygonWrapper(PolygonData) - Constructor for class fr.igred.omero.roi.PolygonWrapper

Constructor of the PolygonWrapper class using a PolygonData.

Polyline - Interface in fr.igred.omero.roi

Interface to handle Polyline shapes on OMERO.

PolylineWrapper - Class in fr.igred.omero.roi

Class containing an PolylineData.

PolylineWrapper() - Constructor for class fr.igred.omero.roi.PolylineWrapper

Constructor of the RectangleWrapper class using a new empty LineData.

PolylineWrapper(Roi) - Constructor for class fr.igred.omero.roi.PolylineWrapper

Constructor of the PolylineWrapper class using an ImageJ PolygonRoi.

PolylineWrapper(List<Point2D.Double>) - Constructor for class fr.igred.omero.roi.PolylineWrapper

Constructor of the RectangleWrapper class using a new LineData.

PolylineWrapper(PolylineData) - Constructor for class fr.igred.omero.roi.PolylineWrapper

Constructor of the PolylineWrapper class using a PolylineData.

Project - Interface in fr.igred.omero.containers

Interface to handle Projects on OMERO.

ProjectWrapper - Class in fr.igred.omero.containers

Class containing a ProjectData object.

ProjectWrapper(DataManager, String, String) - Constructor for class fr.igred.omero.containers.ProjectWrapper

Constructor of the ProjectWrapper class.

ProjectWrapper(ProjectData) - Constructor for class fr.igred.omero.containers.ProjectWrapper

Constructor of the ProjectWrapper class.

Punctual - Interface in fr.igred.omero.roi

Interface for punctual shapes.

R

rate(Client, int) - Method in interface fr.igred.omero.Annotatable

Rates the object (using a rating annotation).

rate(Client, int) - Method in class fr.igred.omero.AnnotatableWrapper

Rates the object (using a rating annotation).

RatingAnnotation - Interface in fr.igred.omero.annotations

Interface to handle Rating Annotations on OMERO.

RatingAnnotationWrapper - Class in fr.igred.omero.annotations

Class containing a RatingAnnotationData object.

RatingAnnotationWrapper(int) - Constructor for class fr.igred.omero.annotations.RatingAnnotationWrapper

Creates a new Textual Annotation with the provided text.

RatingAnnotationWrapper(RatingAnnotationData) - Constructor for class fr.igred.omero.annotations.RatingAnnotationWrapper

Constructor of the RatingAnnotationWrapper class.

Rectangle - Interface in fr.igred.omero.roi

Interface to handle Rectangle shapes on OMERO.

RectangleWrapper - Class in fr.igred.omero.roi

Class containing an RectangleData.

RectangleWrapper() - Constructor for class fr.igred.omero.roi.RectangleWrapper

Constructor of the RectangleWrapper class using a new empty RectangleData.

RectangleWrapper(double, double, double, double) - Constructor for class fr.igred.omero.roi.RectangleWrapper

Constructor of the RectangleWrapper class using a new RectangleData.

RectangleWrapper(Roi) - Constructor for class fr.igred.omero.roi.RectangleWrapper

Constructor of the RectangleWrapper class using bounds from an ImageJ ROI.

RectangleWrapper(RectangleData) - Constructor for class fr.igred.omero.roi.RectangleWrapper

Constructor of the RectangleWrapper class using a RectangleData.

Rectangular - Interface in fr.igred.omero.roi

Interface for rectangular shapes.

reload(Browser) - Method in interface fr.igred.omero.containers.Dataset

Reloads the dataset from OMERO.

reload(Browser) - Method in class fr.igred.omero.containers.DatasetWrapper

Reloads the dataset from OMERO.

reload(Browser) - Method in interface fr.igred.omero.containers.Folder

Reloads the folder from OMERO, to update all links.

reload(Browser) - Method in class fr.igred.omero.containers.FolderWrapper

Reloads the folder from OMERO, to update all links.

reload(Browser) - Method in interface fr.igred.omero.containers.Project

Reloads the project from OMERO.

reload(Browser) - Method in class fr.igred.omero.containers.ProjectWrapper

Reloads the project from OMERO.

reload(Browser) - Method in interface fr.igred.omero.screen.Plate

Reloads the plate from OMERO.

reload(Browser) - Method in class fr.igred.omero.screen.PlateWrapper

Reloads the plate from OMERO.

reload(Browser) - Method in interface fr.igred.omero.screen.Screen

Reloads the screen from OMERO.

reload(Browser) - Method in class fr.igred.omero.screen.ScreenWrapper

Reloads the screen from OMERO.

reload(Browser) - Method in interface fr.igred.omero.screen.Well

Reloads the well from OMERO.

reload(Browser) - Method in class fr.igred.omero.screen.WellWrapper

Reloads the well from OMERO.

RemoteObject - Interface in fr.igred.omero

Generic interface to handle OMERO objects.

removeDataset(Client, Dataset) - Method in interface fr.igred.omero.containers.Project

Removes a dataset from the project in OMERO.

removeDataset(Client, Dataset) - Method in class fr.igred.omero.containers.ProjectWrapper

Removes a dataset from the project in OMERO.

removeImage(Client, Image) - Method in interface fr.igred.omero.containers.Dataset

Removes an image from the dataset in OMERO.

removeImage(Client, Image) - Method in class fr.igred.omero.containers.DatasetWrapper

Removes an image from the dataset in OMERO.

removeLink(Client, String, long) - Method in class fr.igred.omero.AnnotatableWrapper

Removes the link of the given type with the given child ID.

replaceImages(Client, Collection<? extends Image>, Image) - Method in interface fr.igred.omero.containers.Dataset

Replaces (and unlinks) a collection of images from this dataset by a new image, after copying their annotations and ROIs, and concatenating the descriptions (on new lines).

ReplacePolicy - Enum in fr.igred.omero.util

Policy to specify how to handle objects when they are replaced.

RepositoryObject - Interface in fr.igred.omero

Interface to handle Repository Objects on OMERO.

RepositoryObjectWrapper<T extends DataObject> - Class in fr.igred.omero

Generic class containing a DataObject (or a subclass) object.

RepositoryObjectWrapper(T) - Constructor for class fr.igred.omero.RepositoryObjectWrapper

Constructor of the class RepositoryObjectWrapper.

rethrow() - Method in class fr.igred.omero.exception.ExceptionHandler

Rethrows exception if one was caught (to not swallow it).

rethrow(Class<E>) - Method in class fr.igred.omero.exception.ExceptionHandler

Throws an exception from the specified type, if one was caught.

rethrow(Class<E>, ExceptionHandler.ExceptionWrapper<? super E, ? extends F>, String) - Method in class fr.igred.omero.exception.ExceptionHandler

Throws an exception converted from the specified type, if one was caught.

ROI - Interface in fr.igred.omero.roi

Interface to handle ROIs on OMERO.

ROIWrapper - Class in fr.igred.omero.roi

Class containing a ROIData object.

ROIWrapper() - Constructor for class fr.igred.omero.roi.ROIWrapper

Constructor of the ROIWrapper class.

ROIWrapper(Iterable<? extends Shape>) - Constructor for class fr.igred.omero.roi.ROIWrapper

Constructor of the ROIWrapper class.

ROIWrapper(ROIData) - Constructor for class fr.igred.omero.roi.ROIWrapper

Constructor of the ROIWrapper class.

S

save(IObject) - Method in interface fr.igred.omero.client.DataManager

Saves an object on OMERO.

saveAndUpdate(DataManager) - Method in class fr.igred.omero.ObjectWrapper

Saves and updates object.

saveAndUpdate(DataManager) - Method in interface fr.igred.omero.RemoteObject

Saves and updates object.

saveAs(String, char) - Method in interface fr.igred.omero.annotations.Table

Saves the current table as a character-delimited text file.

saveAs(String, char) - Method in class fr.igred.omero.annotations.TableWrapper

Saves the current table as a character-delimited text file.

saveROI(DataManager) - Method in interface fr.igred.omero.roi.ROI

Saves the ROI.

saveROI(DataManager) - Method in class fr.igred.omero.roi.ROIWrapper

Saves the ROI.

saveROIs(DataManager, ROI...) - Method in interface fr.igred.omero.core.Image

Links ROIs to the image in OMERO.

saveROIs(DataManager, Collection<? extends ROI>) - Method in interface fr.igred.omero.core.Image

Links ROIs to the image in OMERO.

saveROIs(DataManager, Collection<? extends ROI>) - Method in class fr.igred.omero.core.ImageWrapper

Links ROIs to the image in OMERO.

Screen - Interface in fr.igred.omero.screen

Interface to handle Screens on OMERO.

ScreenWrapper - Class in fr.igred.omero.screen

Class containing a ScreenData object.

ScreenWrapper(DataManager, String, String) - Constructor for class fr.igred.omero.screen.ScreenWrapper

Constructor of the ProjectWrapper class.

ScreenWrapper(ScreenData) - Constructor for class fr.igred.omero.screen.ScreenWrapper

Constructor of the class ScreenWrapper.

ServerException - Exception in fr.igred.omero.exception

Reports an error occurred on the server.

ServerException(String, Throwable) - Constructor for exception fr.igred.omero.exception.ServerException

Constructs a new exception with the specified cause and detailed message.

ServerException(Throwable) - Constructor for exception fr.igred.omero.exception.ServerException

Constructs a new exception with the specified cause and detailed message.

ServiceException - Exception in fr.igred.omero.exception

Reports an error occurred while trying to access the OMERO service.

ServiceException(String, Throwable, ConnectionStatus) - Constructor for exception fr.igred.omero.exception.ServiceException

Constructs a new exception with the specified cause and a generic message.

ServiceException(String, DSOutOfServiceException) - Constructor for exception fr.igred.omero.exception.ServiceException

Constructs a new exception with the specified cause and a generic message.

ServiceException(Throwable, ConnectionStatus) - Constructor for exception fr.igred.omero.exception.ServiceException

Constructs a new exception with the specified cause and a generic message.

setAlpha(Integer) - Method in interface fr.igred.omero.screen.Well

Sets the alpha component of the color associated to the well.

setAlpha(Integer) - Method in class fr.igred.omero.screen.WellWrapper

Sets the alpha component of the color associated to the well.

setBlue(Integer) - Method in interface fr.igred.omero.screen.Well

Sets the blue component of the color associated to the well.

setBlue(Integer) - Method in class fr.igred.omero.screen.WellWrapper

Sets the blue component of the color associated to the well.

setC(int) - Method in interface fr.igred.omero.roi.Shape

Sets the channel.

setC(int) - Method in class fr.igred.omero.roi.ShapeWrapper

Sets the channel.

setColumn(int, String, Class<?>) - Method in interface fr.igred.omero.annotations.Table

Sets the information about a certain column.

setColumn(int, String, Class<?>) - Method in class fr.igred.omero.annotations.TableWrapper

Sets the information about a certain column.

setContent(Collection<? extends Map.Entry<String, String>>) - Method in interface fr.igred.omero.annotations.MapAnnotation

Sets the content of the map annotation.

setContent(Collection<? extends Map.Entry<String, String>>) - Method in class fr.igred.omero.annotations.MapAnnotationWrapper

Sets the content of the map annotation.

setCoordinates(double[]) - Method in interface fr.igred.omero.roi.Ellipse

Sets the coordinates of the EllipseData shape.

setCoordinates(double[]) - Method in interface fr.igred.omero.roi.Line

Sets the coordinates of the LineData shape.

setCoordinates(double[]) - Method in interface fr.igred.omero.roi.Punctual

Sets the coordinates of the punctual shape.

setCoordinates(double[]) - Method in interface fr.igred.omero.roi.Rectangular

Sets the coordinates of the rectangular shape.

setCoordinates(double, double) - Method in interface fr.igred.omero.roi.Punctual

Sets the coordinates the punctual shape.

setCoordinates(double, double, double, double) - Method in interface fr.igred.omero.roi.Ellipse

Sets the coordinates of the EllipseData shape.

setCoordinates(double, double, double, double) - Method in interface fr.igred.omero.roi.Line

Sets the coordinates of the LineData shape.

setCoordinates(double, double, double, double) - Method in interface fr.igred.omero.roi.Rectangular

Sets the coordinates of the rectangular shape.

setCZT(int, int, int) - Method in interface fr.igred.omero.roi.Shape

Sets the channel, z-section and time-point at once.

setDefaultSample(int) - Method in interface fr.igred.omero.screen.Plate

Sets the default sample.

setDefaultSample(int) - Method in class fr.igred.omero.screen.PlateWrapper

Sets the default sample.

setDescription(String) - Method in interface fr.igred.omero.annotations.Annotation

Sets the description of the underlying AnnotationData instance.

setDescription(String) - Method in class fr.igred.omero.annotations.AnnotationWrapper

Sets the description of the underlying AnnotationData instance.

setDescription(String) - Method in interface fr.igred.omero.containers.Dataset

Sets the description of the dataset.

setDescription(String) - Method in class fr.igred.omero.containers.DatasetWrapper

Sets the description of the dataset.

setDescription(String) - Method in interface fr.igred.omero.containers.Folder

Sets the description of the folder.

setDescription(String) - Method in class fr.igred.omero.containers.FolderWrapper

Sets the description of the folder.

setDescription(String) - Method in interface fr.igred.omero.containers.Project

Sets the description of the project.

setDescription(String) - Method in class fr.igred.omero.containers.ProjectWrapper

Sets the description of the project.

setDescription(String) - Method in interface fr.igred.omero.core.Image

Sets the description of the image.

setDescription(String) - Method in class fr.igred.omero.core.ImageWrapper

Sets the description of the image.

setDescription(String) - Method in interface fr.igred.omero.meta.Group

Sets the description of the group.

setDescription(String) - Method in class fr.igred.omero.meta.GroupWrapper

Sets the description of the group.

setDescription(String) - Method in interface fr.igred.omero.screen.Plate

Sets the description of the plate.

setDescription(String) - Method in interface fr.igred.omero.screen.PlateAcquisition

Sets the description of the plate acquisition.

setDescription(String) - Method in class fr.igred.omero.screen.PlateAcquisitionWrapper

Sets the description of the plate acquisition.

setDescription(String) - Method in class fr.igred.omero.screen.PlateWrapper

Sets the description of the plate.

setDescription(String) - Method in interface fr.igred.omero.screen.Screen

Sets the description of the screen.

setDescription(String) - Method in class fr.igred.omero.screen.ScreenWrapper

Sets the description of the screen.

setEmail(String) - Method in interface fr.igred.omero.meta.Experimenter

Sets the e-mail of the experimenter.

setEmail(String) - Method in class fr.igred.omero.meta.ExperimenterWrapper

Sets the e-mail of the experimenter.

setExternalIdentifier(String) - Method in interface fr.igred.omero.screen.Plate

Sets the external identifier.

setExternalIdentifier(String) - Method in class fr.igred.omero.screen.PlateWrapper

Sets the external identifier.

setFileId(Long) - Method in interface fr.igred.omero.annotations.Table

Sets the fileId of the table.

setFileId(Long) - Method in class fr.igred.omero.annotations.TableWrapper

Sets the fileId of the table.

setFill(Color) - Method in interface fr.igred.omero.roi.Shape

Sets the ShapeData fill color.

setFill(Color) - Method in class fr.igred.omero.roi.ShapeWrapper

Sets the ShapeData fill color.

setFirstName(String) - Method in interface fr.igred.omero.meta.Experimenter

Sets the first name of the experimenter.

setFirstName(String) - Method in class fr.igred.omero.meta.ExperimenterWrapper

Sets the first name of the experimenter.

setFontSize(double) - Method in interface fr.igred.omero.roi.Shape

Sets ShapeData font size.

setFontSize(double) - Method in class fr.igred.omero.roi.ShapeWrapper

Sets ShapeData font size.

setGreen(Integer) - Method in interface fr.igred.omero.screen.Well

Sets the green component of the color associated to the well.

setGreen(Integer) - Method in class fr.igred.omero.screen.WellWrapper

Sets the green component of the color associated to the well.

setHeight(double) - Method in class fr.igred.omero.roi.MaskWrapper

Sets the height of the rectangular shape.

setHeight(double) - Method in class fr.igred.omero.roi.RectangleWrapper

Sets the height of an untransformed rectangle.

setHeight(double) - Method in interface fr.igred.omero.roi.Rectangular

Sets the height of the rectangular shape.

setId(Long) - Method in interface fr.igred.omero.annotations.Table

Sets the id of the table.

setId(Long) - Method in class fr.igred.omero.annotations.TableWrapper

Sets the ID of the table.

setImage(Image) - Method in interface fr.igred.omero.roi.ROI

Sets the image linked to the ROI.

setImage(Image) - Method in class fr.igred.omero.roi.ROIWrapper

Sets the image linked to the ROI.

setImage(Image) - Method in interface fr.igred.omero.screen.WellSample

Sets the image linked to this well sample.

setImage(Image) - Method in class fr.igred.omero.screen.WellSampleWrapper

Sets the image linked to this well sample.

setInstitution(String) - Method in interface fr.igred.omero.meta.Experimenter

Sets the institution where the experimenter works.

setInstitution(String) - Method in class fr.igred.omero.meta.ExperimenterWrapper

Sets the institution where the experimenter works.

setLastName(String) - Method in interface fr.igred.omero.meta.Experimenter

Sets the last name of the experimenter.

setLastName(String) - Method in class fr.igred.omero.meta.ExperimenterWrapper

Sets the last name of the experimenter.

setMask(boolean[][]) - Method in interface fr.igred.omero.roi.Mask

Sets the mask

setMask(boolean[][]) - Method in class fr.igred.omero.roi.MaskWrapper

Sets the mask

setMask(byte[]) - Method in interface fr.igred.omero.roi.Mask

Sets the mask image.

setMask(byte[]) - Method in class fr.igred.omero.roi.MaskWrapper

Sets the mask image.

setMask(int[][]) - Method in interface fr.igred.omero.roi.Mask

Sets the mask

setMask(int[][]) - Method in class fr.igred.omero.roi.MaskWrapper

Sets the mask

setMiddleName(String) - Method in interface fr.igred.omero.meta.Experimenter

Sets the middle name of the experimenter.

setMiddleName(String) - Method in class fr.igred.omero.meta.ExperimenterWrapper

Sets the middle name of the experimenter.

setName(String) - Method in interface fr.igred.omero.annotations.Table

Sets the name of the table.

setName(String) - Method in class fr.igred.omero.annotations.TableWrapper

Sets the name of the table.

setName(String) - Method in interface fr.igred.omero.annotations.TagAnnotation

Sets the name of the tag.

setName(String) - Method in class fr.igred.omero.annotations.TagAnnotationWrapper

Sets the name of the TagData.

setName(String) - Method in interface fr.igred.omero.containers.Dataset

Sets the name of the dataset.

setName(String) - Method in class fr.igred.omero.containers.DatasetWrapper

Sets the name of the dataset.

setName(String) - Method in interface fr.igred.omero.containers.Folder

Sets the name of the folder.

setName(String) - Method in class fr.igred.omero.containers.FolderWrapper

Sets the name of the folder.

setName(String) - Method in interface fr.igred.omero.containers.Project

Sets the name of the project.

setName(String) - Method in class fr.igred.omero.containers.ProjectWrapper

Sets the name of the project.

setName(String) - Method in interface fr.igred.omero.core.Channel

Sets the name of the channel.

setName(String) - Method in class fr.igred.omero.core.ChannelWrapper

Sets the name of the channel.

setName(String) - Method in interface fr.igred.omero.core.Image

Sets the name of the image.

setName(String) - Method in class fr.igred.omero.core.ImageWrapper

Sets the name of the image.

setName(String) - Method in interface fr.igred.omero.meta.Group

Sets the name of the group.

setName(String) - Method in class fr.igred.omero.meta.GroupWrapper

Sets the name of the group.

setName(String) - Method in interface fr.igred.omero.roi.ROI

Sets the ROI name.

setName(String) - Method in class fr.igred.omero.roi.ROIWrapper

Sets the ROI name.

setName(String) - Method in interface fr.igred.omero.screen.Plate

Sets the name of the plate.

setName(String) - Method in interface fr.igred.omero.screen.PlateAcquisition

Sets the name of the plate acquisition.

setName(String) - Method in class fr.igred.omero.screen.PlateAcquisitionWrapper

Sets the name of the plate acquisition.

setName(String) - Method in class fr.igred.omero.screen.PlateWrapper

Sets the name of the plate.

setName(String) - Method in interface fr.igred.omero.screen.Screen

Sets the name of the screen.

setName(String) - Method in class fr.igred.omero.screen.ScreenWrapper

Sets the name of the screen.

setNameSpace(String) - Method in interface fr.igred.omero.annotations.Annotation

Sets the annotation namespace.

setNameSpace(String) - Method in class fr.igred.omero.annotations.AnnotationWrapper

Sets the annotation namespace.

setParent(Folder) - Method in interface fr.igred.omero.containers.Folder

Sets the parent folder for this folder.

setParent(Folder) - Method in class fr.igred.omero.containers.FolderWrapper

Sets the parent folder for this folder.

setPoints(List<Point2D.Double>) - Method in interface fr.igred.omero.roi.Polygonal

Sets the points in the polygonal shape.

setPoints(List<Point2D.Double>) - Method in class fr.igred.omero.roi.PolygonWrapper

Sets the points in the polygonal shape.

setPoints(List<Point2D.Double>) - Method in class fr.igred.omero.roi.PolylineWrapper

Sets the points in the polyline.

setProtocolDescription(String) - Method in interface fr.igred.omero.screen.Screen

Sets the description of the protocol.

setProtocolDescription(String) - Method in class fr.igred.omero.screen.ScreenWrapper

Sets the description of the protocol.

setProtocolIdentifier(String) - Method in interface fr.igred.omero.screen.Screen

Sets the identifier of the protocol.

setProtocolIdentifier(String) - Method in class fr.igred.omero.screen.ScreenWrapper

Sets the identifier of the protocol.

setRadiusX(double) - Method in interface fr.igred.omero.roi.Ellipse

Sets the radius along the X-axis.

setRadiusX(double) - Method in class fr.igred.omero.roi.EllipseWrapper

Sets the radius along the X-axis.

setRadiusY(double) - Method in interface fr.igred.omero.roi.Ellipse

Sets the radius along the Y-axis.

setRadiusY(double) - Method in class fr.igred.omero.roi.EllipseWrapper

Sets the radius along the Y-axis.

setRating(int) - Method in interface fr.igred.omero.annotations.RatingAnnotation

Sets the rating value.

setRating(int) - Method in class fr.igred.omero.annotations.RatingAnnotationWrapper

Sets the rating value.

setReagentSetDescription(String) - Method in interface fr.igred.omero.screen.Screen

Sets the identifier of the reagent.

setReagentSetDescription(String) - Method in class fr.igred.omero.screen.ScreenWrapper

Sets the identifier of the reagent.

setReagentSetIdentifier(String) - Method in interface fr.igred.omero.screen.Screen

Sets the identifier of the reagent.

setReagentSetIdentifier(String) - Method in class fr.igred.omero.screen.ScreenWrapper

Sets the identifier of the reagent.

setRed(Integer) - Method in interface fr.igred.omero.screen.Well

Sets the red component of the color associated to the well.

setRed(Integer) - Method in class fr.igred.omero.screen.WellWrapper

Sets the red component of the color associated to the well.

setRefPlateId(long) - Method in interface fr.igred.omero.screen.PlateAcquisition

Sets the id of the plate this plate acquisition is for.

setRefPlateId(long) - Method in class fr.igred.omero.screen.PlateAcquisitionWrapper

Sets the id of the plate this plate acquisition is for.

setRowCount(int) - Method in interface fr.igred.omero.annotations.Table

Sets the number of row in the table.

setRowCount(int) - Method in class fr.igred.omero.annotations.TableWrapper

Sets the number of row in the table.

setStatus(String) - Method in interface fr.igred.omero.screen.Plate

Sets the status.

setStatus(String) - Method in class fr.igred.omero.screen.PlateWrapper

Sets the status.

setStatus(String) - Method in interface fr.igred.omero.screen.Well

Sets the status of the well.

setStatus(String) - Method in class fr.igred.omero.screen.WellWrapper

Sets the status of the well.

setStroke(Color) - Method in interface fr.igred.omero.roi.Shape

Sets ShapeData stroke color.

setStroke(Color) - Method in class fr.igred.omero.roi.ShapeWrapper

Sets ShapeData stroke color.

setT(int) - Method in interface fr.igred.omero.roi.Shape

Sets the time-point.

setT(int) - Method in class fr.igred.omero.roi.ShapeWrapper

Sets the time-point.

setText(String) - Method in interface fr.igred.omero.annotations.TextualAnnotation

Sets the text.

setText(String) - Method in class fr.igred.omero.annotations.TextualAnnotationWrapper

Sets the text.

setText(String) - Method in class fr.igred.omero.roi.EllipseWrapper

Sets the text on the ShapeData.

setText(String) - Method in class fr.igred.omero.roi.LineWrapper

Sets the text on the ShapeData.

setText(String) - Method in class fr.igred.omero.roi.MaskWrapper

Sets the text on the ShapeData.

setText(String) - Method in class fr.igred.omero.roi.PointWrapper

Sets the text on the ShapeData.

setText(String) - Method in class fr.igred.omero.roi.PolygonWrapper

Sets the text on the ShapeData.

setText(String) - Method in class fr.igred.omero.roi.PolylineWrapper

Sets the text on the ShapeData.

setText(String) - Method in class fr.igred.omero.roi.RectangleWrapper

Sets the text on the ShapeData.

setText(String) - Method in interface fr.igred.omero.roi.Shape

Sets the text on the ShapeData.

setText(String) - Method in class fr.igred.omero.roi.TextWrapper

Sets the text on the ShapeData.

setTransform(double, double, double, double, double, double) - Method in interface fr.igred.omero.roi.Shape

Sets the transform to the matrix specified by the 6 double precision values.

setTransform(double, double, double, double, double, double) - Method in class fr.igred.omero.roi.ShapeWrapper

Sets the transform to the matrix specified by the 6 double precision values.

setTransform(AffineTransform) - Method in interface fr.igred.omero.roi.Shape

Sets the transform from a AffineTransform.

setWellType(String) - Method in interface fr.igred.omero.screen.Well

Sets a human-readable identifier for the screening status e.g.

setWellType(String) - Method in class fr.igred.omero.screen.WellWrapper

Sets a human-readable identifier for the screening status e.g.

setWidth(double) - Method in class fr.igred.omero.roi.MaskWrapper

Sets width of the rectangular shape.

setWidth(double) - Method in class fr.igred.omero.roi.RectangleWrapper

Sets width of an untransformed rectangle.

setWidth(double) - Method in interface fr.igred.omero.roi.Rectangular

Sets width of the rectangular shape.

setX(double) - Method in interface fr.igred.omero.roi.Ellipse

Sets the x-coordinate of the center of the ellipse.

setX(double) - Method in class fr.igred.omero.roi.EllipseWrapper

Sets the x-coordinate of the center of the ellipse.

setX(double) - Method in class fr.igred.omero.roi.MaskWrapper

Sets the x-coordinate of the rectangular shape.

setX(double) - Method in class fr.igred.omero.roi.PointWrapper

Sets the x-coordinate of the punctual shape.

setX(double) - Method in interface fr.igred.omero.roi.Punctual

Sets the x-coordinate of the punctual shape.

setX(double) - Method in class fr.igred.omero.roi.RectangleWrapper

Sets the x-coordinate of the shape.

setX(double) - Method in interface fr.igred.omero.roi.Rectangular

Sets the x-coordinate of the rectangular shape.

setX(double) - Method in class fr.igred.omero.roi.TextWrapper

Sets the x-coordinate of the shape.

setX1(double) - Method in interface fr.igred.omero.roi.Line

Set the x-coordinate of the starting point of an untransformed line.

setX1(double) - Method in class fr.igred.omero.roi.LineWrapper

Set the x-coordinate of the starting point of an untransformed line.

setX2(double) - Method in interface fr.igred.omero.roi.Line

Set the x-coordinate of the end point of an untransformed line.

setX2(double) - Method in class fr.igred.omero.roi.LineWrapper

Set the x-coordinate of the end point of an untransformed line.

setY(double) - Method in interface fr.igred.omero.roi.Ellipse

Sets the y-coordinate of the center of the ellipse.

setY(double) - Method in class fr.igred.omero.roi.EllipseWrapper

Sets the y-coordinate of the center of the ellipse.

setY(double) - Method in class fr.igred.omero.roi.MaskWrapper

Sets the y-coordinate of the rectangular shape.

setY(double) - Method in class fr.igred.omero.roi.PointWrapper

Sets the y-coordinate of the punctual shape.

setY(double) - Method in interface fr.igred.omero.roi.Punctual

Sets the y-coordinate of the punctual shape.

setY(double) - Method in class fr.igred.omero.roi.RectangleWrapper

Sets the y-coordinate of the shape.

setY(double) - Method in interface fr.igred.omero.roi.Rectangular

Sets the y-coordinate of the rectangular shape.

setY(double) - Method in class fr.igred.omero.roi.TextWrapper

Sets the y-coordinate of the shape.

setY1(double) - Method in interface fr.igred.omero.roi.Line

Set the y-coordinate of the starting point of an untransformed line.

setY1(double) - Method in class fr.igred.omero.roi.LineWrapper

Set the y-coordinate of the starting point of an untransformed line.

setY2(double) - Method in interface fr.igred.omero.roi.Line

Set the y-coordinate of the end point of an untransformed line.

setY2(double) - Method in class fr.igred.omero.roi.LineWrapper

Set the y-coordinate of the end point of an untransformed line.

setZ(int) - Method in interface fr.igred.omero.roi.Shape

Sets the z-section.

setZ(int) - Method in class fr.igred.omero.roi.ShapeWrapper

Sets the z-section.

Shape - Interface in fr.igred.omero.roi

Generic interface to handle Shape objects.

ShapeWrapper<T extends ShapeData> - Class in fr.igred.omero.roi

Generic class containing a ShapeData (or a subclass) object.

ShapeWrapper(T) - Constructor for class fr.igred.omero.roi.ShapeWrapper

Constructor of the ShapeWrapper class using a ShapeData.

sudo(String) - Method in interface fr.igred.omero.client.Client

Gets the client associated with the username in the parameters.

sudo(String) - Method in interface fr.igred.omero.client.ConnectionHandler

Returns a ConnectionHandler associated with the given username.

sudo(String) - Method in class fr.igred.omero.client.GatewayWrapper

Returns a Client associated with the given username.

switchGroup(long) - Method in interface fr.igred.omero.client.ConnectionHandler

Change the current group used by the current user;

switchGroup(long) - Method in class fr.igred.omero.client.GatewayWrapper

Change the current group used by the current user;

T

Table - Interface in fr.igred.omero.annotations

Interface to create and handle a Table in OMERO.

TableWrapper - Class in fr.igred.omero.annotations

Class containing the information to create a Table in OMERO.

TableWrapper(int, String) - Constructor for class fr.igred.omero.annotations.TableWrapper

Constructor of the class TableWrapper

TableWrapper(Client, ResultsTable, Long, Collection<? extends Roi>) - Constructor for class fr.igred.omero.annotations.TableWrapper

Constructor of the class TableWrapper.

TableWrapper(Client, ResultsTable, Long, Collection<? extends Roi>, String) - Constructor for class fr.igred.omero.annotations.TableWrapper

Constructor of the class TableWrapper.

TableWrapper(TableData) - Constructor for class fr.igred.omero.annotations.TableWrapper

Constructor of the class TableWrapper.

TagAnnotation - Interface in fr.igred.omero.annotations

Interface to handle Tag Annotations on OMERO.

TagAnnotationWrapper - Class in fr.igred.omero.annotations

Class containing a TagAnnotationData object.

TagAnnotationWrapper(DataManager, String, String) - Constructor for class fr.igred.omero.annotations.TagAnnotationWrapper

Constructor of the TagAnnotationWrapper class.

TagAnnotationWrapper(TagAnnotationData) - Constructor for class fr.igred.omero.annotations.TagAnnotationWrapper

Constructor of the TagAnnotationWrapper class.

Text - Interface in fr.igred.omero.roi

Interface to handle Text shapes on OMERO.

TextualAnnotation - Interface in fr.igred.omero.annotations

Interface to handle Textual Annotations on OMERO.

TextualAnnotationWrapper - Class in fr.igred.omero.annotations

Class containing a TextualAnnotationData object.

TextualAnnotationWrapper(String) - Constructor for class fr.igred.omero.annotations.TextualAnnotationWrapper

Creates a new Textual Annotation with the provided text.

TextualAnnotationWrapper(TextualAnnotationData) - Constructor for class fr.igred.omero.annotations.TextualAnnotationWrapper

Constructor of the TextualAnnotationWrapper class.

TextWrapper - Class in fr.igred.omero.roi

Class containing an TextData.

TextWrapper() - Constructor for class fr.igred.omero.roi.TextWrapper

Constructor of the TextWrapper class using a new empty ShapeData.

TextWrapper(TextRoi) - Constructor for class fr.igred.omero.roi.TextWrapper

Constructor of the TextWrapper class using an ImageJ TextRoi.

TextWrapper(String, double, double) - Constructor for class fr.igred.omero.roi.TextWrapper

Creates a new instance of the TextWrapper, sets the centre and major, minor axes.

TextWrapper(TextData) - Constructor for class fr.igred.omero.roi.TextWrapper

Constructor of the TextWrapper class using a TextData.

toAWTShape() - Method in interface fr.igred.omero.roi.Ellipse

Converts the shape to an Shape.

toAWTShape() - Method in interface fr.igred.omero.roi.Line

Converts the shape to an Shape.

toAWTShape() - Method in interface fr.igred.omero.roi.Mask

Converts the shape to an Shape.

toAWTShape() - Method in interface fr.igred.omero.roi.Point

Converts the shape to an Shape.

toAWTShape() - Method in interface fr.igred.omero.roi.Polygon

Converts the shape to an Shape.

toAWTShape() - Method in interface fr.igred.omero.roi.Polyline

Converts the shape to an Shape.

toAWTShape() - Method in interface fr.igred.omero.roi.Rectangle

Converts the shape to an Shape.

toAWTShape() - Method in interface fr.igred.omero.roi.Shape

Converts the shape to an Shape.

toAWTShape() - Method in interface fr.igred.omero.roi.Text

Converts the shape to an Shape.

toAWTTransform() - Method in interface fr.igred.omero.roi.Shape

Converts AffineTransform to AffineTransform.

toAWTTransform() - Method in class fr.igred.omero.roi.ShapeWrapper

Converts AffineTransform to AffineTransform.

toImageJ() - Method in class fr.igred.omero.roi.EllipseWrapper

Converts shape to ImageJ ROI.

toImageJ() - Method in class fr.igred.omero.roi.LineWrapper

Converts shape to ImageJ ROI.

toImageJ() - Method in class fr.igred.omero.roi.MaskWrapper

Converts shape to ImageJ ROI.

toImageJ() - Method in class fr.igred.omero.roi.PointWrapper

Converts shape to ImageJ ROI.

toImageJ() - Method in class fr.igred.omero.roi.RectangleWrapper

Converts shape to ImageJ ROI.

toImageJ() - Method in interface fr.igred.omero.roi.ROI

Converts the ROI to a list of ImageJ ROIs.

toImageJ() - Method in interface fr.igred.omero.roi.Shape

Converts shape to ImageJ ROI.

toImageJ() - Method in class fr.igred.omero.roi.ShapeWrapper

Converts shape to ImageJ ROI.

toImageJ() - Method in class fr.igred.omero.roi.TextWrapper

Converts shape to ImageJ ROI.

toImageJ(String) - Method in interface fr.igred.omero.roi.ROI

Converts the ROI to a list of ImageJ ROIs.

toImageJ(Collection<? extends ROI>) - Static method in interface fr.igred.omero.roi.ROI

Converts a collection of OMERO ROIs to a list of ImageJ ROIs.

toImageJ(Collection<? extends ROI>, String) - Static method in interface fr.igred.omero.roi.ROI

Converts a collection of OMERO ROIs to a list of ImageJ ROIs.

toImageJ(Collection<? extends ROI>, String, boolean) - Static method in interface fr.igred.omero.roi.ROI

Converts a collection of OMERO ROIs to a list of ImageJ ROIs.

toImagePlus(Client) - Method in interface fr.igred.omero.core.Image

Generates the ImagePlus from the ij library corresponding to the image from OMERO WARNING : you need to include the ij library to use this function

toImagePlus(Client, int[], int[], int[], int[], int[]) - Method in interface fr.igred.omero.core.Image

Gets the imagePlus generated from the image from OMERO corresponding to the bound.

toImagePlus(Client, int[], int[], int[], int[], int[]) - Method in class fr.igred.omero.core.ImageWrapper

Gets the imagePlus generated from the image from OMERO corresponding to the bound.

toImagePlus(Client, ROI) - Method in interface fr.igred.omero.core.Image

Gets the imagePlus from the image generated from the ROI.

toString() - Method in class fr.igred.omero.annotations.TableWrapper

Overridden to return the name of the class and the object id.

toString() - Method in class fr.igred.omero.client.GatewayWrapper

Overridden to return the host name, the group ID, the username and the connection status.

toString() - Method in class fr.igred.omero.exception.ExceptionHandler

toString() - Method in class fr.igred.omero.ObjectWrapper

Overridden to return the name of the class and the object id.

toString() - Method in class fr.igred.omero.util.Bounds

toString() - Method in class fr.igred.omero.util.Coordinates

truncateRow() - Method in interface fr.igred.omero.annotations.Table

Deletes all unused row in the table

truncateRow() - Method in class fr.igred.omero.annotations.TableWrapper

Deletes all unused row in the table

U

unlink(Client, A) - Method in interface fr.igred.omero.Annotatable

Unlinks the given annotation from the current object.

unlink(Client, A) - Method in class fr.igred.omero.AnnotatableWrapper

Unlinks the given annotation from the current object.

UNLINK - fr.igred.omero.util.ReplacePolicy

Unlink objects only

unlinkAllROIs(DataManager) - Method in interface fr.igred.omero.containers.Folder

Unlink all ROIs associated to this folder.

unlinkAllROIs(DataManager) - Method in class fr.igred.omero.containers.FolderWrapper

Unlink all ROIs associated to this folder.

unlinkAllROIs(DataManager, long) - Method in interface fr.igred.omero.containers.Folder

Unlink all ROIs associated to the provided image ID from the folder.

unlinkAllROIs(DataManager, Image) - Method in interface fr.igred.omero.containers.Folder

Unlink all ROIs associated to the provided image from the folder.

unlinkROIs(DataManager, ROI...) - Method in interface fr.igred.omero.containers.Folder

Unlink ROIs from the folder.

V

valueOf(String) - Static method in enum fr.igred.omero.util.ReplacePolicy

Returns the enum constant of this type with the specified name.

values() - Static method in enum fr.igred.omero.util.ReplacePolicy

Returns an array containing the constants of this enum type, in the order they are declared.

W

Well - Interface in fr.igred.omero.screen

Interface to handle Wells on OMERO.

WellSample - Interface in fr.igred.omero.screen

Interface to handle Well Samples on OMERO.

WellSampleWrapper - Class in fr.igred.omero.screen

Class containing a WellSampleData object.

WellSampleWrapper(WellSampleData) - Constructor for class fr.igred.omero.screen.WellSampleWrapper

Constructor of the class WellSampleWrapper.

WellWrapper - Class in fr.igred.omero.screen

Class containing a WellData object.

WellWrapper(WellData) - Constructor for class fr.igred.omero.screen.WellWrapper

Constructor of the class WellWrapper.

wrap(Collection<U>, Function<? super U, ? extends V>) - Static method in class fr.igred.omero.ObjectWrapper

Converts a DataObject list to a ObjectWrapper list, sorted by sorter.

wrap(Collection<U>, Function<? super U, ? extends V>, Function<? super V, ? extends W>) - Static method in class fr.igred.omero.ObjectWrapper

Converts a DataObject list to an ObjectWrapper list, sorted by sorter.

wrap(T) - Static method in class fr.igred.omero.util.Wrapper

Converts (wraps) a ShapeData object to a Shape object.

wrapAnnotatableObject(T) - Static method in class fr.igred.omero.util.Wrapper

Converts (wraps) a DataObject object to an Annotatable object.

Wrapper - Class in fr.igred.omero.util

Utility class to convert DataObjects dynamically.

wrapRepositoryObject(T) - Static method in class fr.igred.omero.util.Wrapper

Converts (wraps) a DataObject object to a Repository object.

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