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.

add(AnnotationData) - Method in class fr.igred.omero.annotations.AnnotationList

Wraps the specified AnnotationData object and add it to the end of this list.

add(ShapeData) - Method in class fr.igred.omero.roi.ShapeList

Wraps the specified ShapeData object and add it to the end of this list.

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

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, GenericRepositoryObjectWrapper.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, TableWrapper) - Method in class fr.igred.omero.AnnotatableWrapper

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, TableWrapper, GenericRepositoryObjectWrapper.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(FolderWrapper) - Method in class fr.igred.omero.repository.FolderWrapper

Adds a child folder to this folder.

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

Adds children folders to this folder.

addDataset(Client, DatasetWrapper) - Method in class fr.igred.omero.repository.ProjectWrapper

Adds a dataset to the project in OMERO.

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

Adds a dataset to the project in OMERO.

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

Uploads a file and links it to the object

addFileAnnotation(Client, FileAnnotationWrapper) - Method in class fr.igred.omero.AnnotatableWrapper

Deprecated.

Links a file annotation to the object. Use AnnotatableWrapper.link(fr.igred.omero.Client, A) instead.

addImage(Client, ImageWrapper) - Method in class fr.igred.omero.repository.DatasetWrapper

Adds a single image to the dataset in OMERO

addImages(Client, ImageWrapper...) - Method in class fr.igred.omero.repository.FolderWrapper

Links images to the folder in OMERO.

addImages(Client, List<? extends ImageWrapper>) - Method in class fr.igred.omero.repository.DatasetWrapper

Adds a list of image to the dataset in OMERO.

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

Adds a single Key-Value pair to the object.

addMapAnnotation(Client, MapAnnotationWrapper) - Method in class fr.igred.omero.AnnotatableWrapper

Deprecated.

Adds a List of Key-Value pair to the object. Use AnnotatableWrapper.link(fr.igred.omero.Client, A) instead.

The list is contained in the map annotation.

addPairKeyValue(Client, String, String) - Method in class fr.igred.omero.AnnotatableWrapper

Deprecated.

Adds a single Key-Value pair to the object.

addROI(Client, ROIWrapper) - Method in class fr.igred.omero.repository.FolderWrapper

Deprecated.

Adds an ROI to the folder and associate it to the image id set(an image need to be associated)

addROIs(Client, long, ROIWrapper...) - Method in class fr.igred.omero.repository.FolderWrapper

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

addROIs(Client, ImageWrapper, ROIWrapper...) - Method in class fr.igred.omero.repository.FolderWrapper

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

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

Adds a row to the table.

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

Adds rows from an ImageJ ResultsTable.

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

Adds rows from an ImageJ ResultsTable.

addShape(GenericShapeWrapper<?>) - Method in class fr.igred.omero.roi.ROIWrapper

Adds a ShapeData from a GenericShapeWrapper to the ROIData

addShapes(List<? extends GenericShapeWrapper<?>>) - Method in class fr.igred.omero.roi.ROIWrapper

Adds ShapeData objects from a list of GenericShapeWrapper to the ROIData

addTable(Client, TableWrapper) - Method in class fr.igred.omero.AnnotatableWrapper

Adds a table to the object in OMERO.

addTag(Client, TagAnnotationWrapper) - Method in class fr.igred.omero.AnnotatableWrapper

Deprecated.

Adds a tag to the object in OMERO, if possible. Use AnnotatableWrapper.link(fr.igred.omero.Client, A) instead.

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

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

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

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

addTags(Client, TagAnnotationWrapper...) - Method in class fr.igred.omero.AnnotatableWrapper

Deprecated.

Adds multiple tag to the object in OMERO, if possible. Use AnnotatableWrapper.link(Client, GenericAnnotationWrapper[]) instead.

addTags(Client, Long...) - Method in class fr.igred.omero.AnnotatableWrapper

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

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

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

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

Constructor of the class GenericRepositoryObjectWrapper.

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

Annotation link name for this type of object

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

Annotation link name for this type of object

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

Annotation link name for this type of object

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

Annotation link name for this type of object

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

Annotation link name for this type of object

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

Annotation link name for this type of object

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

Annotation link name for this type of object

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

Annotation link name for this type of object

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

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

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

Returns the type of annotation link for this object.

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

Returns the type of annotation link for this object.

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

Returns the type of annotation link for this object.

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

Returns the type of annotation link for this object.

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

Returns the type of annotation link for this object.

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

Returns the type of annotation link for this object.

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

Returns the type of annotation link for this object.

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

Returns the type of annotation link for this object.

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

Returns the type of annotation link for this object.

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

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.

AnnotationList - Class in fr.igred.omero.annotations

List of GenericAnnotationWrapper objects

AnnotationList() - Constructor for class fr.igred.omero.annotations.AnnotationList

Constructs an empty list with an initial capacity of ten.

AnnotationList(int) - Constructor for class fr.igred.omero.annotations.AnnotationList

Constructs an empty list with the specified initial capacity.

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 class fr.igred.omero.roi.LineWrapper

String to use arrows as markers

asChannelData() - Method in class fr.igred.omero.repository.ChannelWrapper

Deprecated.

Returns the ChannelData contained. Use GenericObjectWrapper.asDataObject() instead.

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

Returns the wrapped DataObject.

asDatasetData() - Method in class fr.igred.omero.repository.DatasetWrapper

Deprecated.

Returns the DatasetData contained. Use GenericObjectWrapper.asDataObject() instead.

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

Deprecated.

Returns the ExperimenterData contained. Use GenericObjectWrapper.asDataObject() instead.

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

Deprecated.

Gets the FileAnnotationData contained.

asFolderData() - Method in class fr.igred.omero.repository.FolderWrapper

Deprecated.

Gets the folder contained in the FolderWrapper. Use GenericObjectWrapper.asDataObject() instead.

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

Deprecated.

Returns the GroupData contained. Use GenericObjectWrapper.asDataObject() instead.

asImageData() - Method in class fr.igred.omero.repository.ImageWrapper

Deprecated.

Returns the ImageData contained. Use GenericObjectWrapper.asDataObject() instead.

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

Deprecated.

Gets the MapAnnotationData contained. Use GenericObjectWrapper.asDataObject() instead.

asPlaneInfoData() - Method in class fr.igred.omero.meta.PlaneInfoWrapper

Deprecated.

Returns the PlaneInfoData contained. Use GenericObjectWrapper.asDataObject() instead.

asPlateAcquisitionData() - Method in class fr.igred.omero.repository.PlateAcquisitionWrapper

Deprecated.

Returns the PlateAcquisitionData contained. Use GenericObjectWrapper.asDataObject() instead.

asPlateData() - Method in class fr.igred.omero.repository.PlateWrapper

Deprecated.

Returns the PlateData contained. Use GenericObjectWrapper.asDataObject() instead.

asProjectData() - Method in class fr.igred.omero.repository.ProjectWrapper

Deprecated.

Returns the ProjectData contained. Use GenericObjectWrapper.asDataObject() instead.

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

Deprecated.

Returns the ROIData contained. Use GenericObjectWrapper.asDataObject() instead.

asScreenData() - Method in class fr.igred.omero.repository.ScreenWrapper

Deprecated.

Returns the ScreenData contained. Use GenericObjectWrapper.asDataObject() instead.

asShapeData() - Method in class fr.igred.omero.roi.GenericShapeWrapper

Deprecated.

Gets the ShapeData object contained.

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

Deprecated.

Gets the TagAnnotationData contained. Use GenericObjectWrapper.asDataObject() instead.

asWellData() - Method in class fr.igred.omero.repository.WellWrapper

Deprecated.

Returns the WellData contained. Use GenericObjectWrapper.asDataObject() instead.

asWellSampleData() - Method in class fr.igred.omero.repository.WellSampleWrapper

Deprecated.

Returns the WellSampleData contained. Use GenericObjectWrapper.asDataObject() instead.

B

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

Bounds constructor.

Browser - Class in fr.igred.omero

Abstract class to browse data on an OMERO server in a given SecurityContext and wrap DataObjects.

Browser(Gateway, SecurityContext, ExperimenterWrapper) - Constructor for class fr.igred.omero.Browser

Constructor of the Browser class.

C

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

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

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

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.GenericObjectWrapper

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.GenericObjectWrapper

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.GenericObjectWrapper

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.GenericObjectWrapper

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

ChannelWrapper - Class in fr.igred.omero.repository

Class containing a ChannelData object.

ChannelWrapper(ChannelData) - Constructor for class fr.igred.omero.repository.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 class fr.igred.omero.roi.ROIWrapper

Checks the provided property.

Client - Class in fr.igred.omero

Basic class, contains the gateway, the security context, and multiple facilities.

Client() - Constructor for class fr.igred.omero.Client

Constructor of the Client class.

Client(Gateway, SecurityContext, ExperimenterWrapper) - Constructor for class fr.igred.omero.Client

Constructor of the Client class.

closeImport() - Method in class fr.igred.omero.GatewayWrapper

Closes the import store.

computeMeanExposureTime(Iterable<? extends PlaneInfoWrapper>, int) - Static method in class fr.igred.omero.meta.PlaneInfoWrapper

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

computeMeanTimeInterval(Collection<? extends PlaneInfoWrapper>, int) - Static method in class fr.igred.omero.meta.PlaneInfoWrapper

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

connect(String, int, String) - Method in class fr.igred.omero.GatewayWrapper

Connects to OMERO using a session ID.

connect(String, int, String, char[]) - Method in class fr.igred.omero.GatewayWrapper

Connects the user to OMERO.

connect(String, int, String, char[], Long) - Method in class fr.igred.omero.GatewayWrapper

Connects the user to OMERO.

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

Connects the user to OMERO.

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

Coordinates constructor.

copyAnnotationLinks(Client, AnnotatableWrapper<?>) - Method in class fr.igred.omero.AnnotatableWrapper

Copies annotation links from some other object to this one.

copyAnnotationLinks(Client, GenericRepositoryObjectWrapper<?>) - Method in class fr.igred.omero.repository.GenericRepositoryObjectWrapper

Copies annotation links from some other object to this one.

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

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

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

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

countAnnotationLinks(Client) - Method in class fr.igred.omero.annotations.GenericAnnotationWrapper

Returns the number of annotations links for this object.

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

Creates the corresponding TableData object.

createTransformedAWTShape() - Method in class fr.igred.omero.roi.GenericShapeWrapper

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.GenericObjectWrapper

Wrapped object

DatasetWrapper - Class in fr.igred.omero.repository

Class containing a DatasetData object.

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

Constructor of the DatasetWrapper class

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

Constructor of the DatasetWrapper class

delete(TableWrapper) - Method in class fr.igred.omero.Client

Deprecated.

Deletes a table from OMERO.

delete(Client, IObject) - Static method in class fr.igred.omero.GenericObjectWrapper

Deletes an object from OMERO.

delete(GenericObjectWrapper<?>) - Method in class fr.igred.omero.Client

Deletes an object from OMERO.

delete(Collection<? extends GenericObjectWrapper<?>>) - Method in class fr.igred.omero.Client

Deletes multiple objects from OMERO.

DELETE - fr.igred.omero.repository.GenericRepositoryObjectWrapper.ReplacePolicy

Delete all objects

DELETE_ORPHANED - fr.igred.omero.repository.GenericRepositoryObjectWrapper.ReplacePolicy

Delete orphaned objects

deleteFile(Long) - Method in class fr.igred.omero.GatewayWrapper

Deletes a file from OMERO

deleteFiles(Long...) - Method in class fr.igred.omero.GatewayWrapper

Deletes files from OMERO.

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

Deletes a shape from the ROI.

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

Deletes a ShapeData from the ROI.

deleteTable(TableWrapper) - Method in class fr.igred.omero.Client

Deletes a table from OMERO.

deleteTables(Collection<? extends TableWrapper>) - Method in class fr.igred.omero.Client

Deletes tables from OMERO.

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

Disconnects the user

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

Only keeps objects with different IDs in a collection.

download(Client, String) - Method in class fr.igred.omero.repository.ImageWrapper

Downloads the original files from the server.

E

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 Throwable> - Interface in fr.igred.omero.exception

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

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

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

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 GenericAnnotationWrapper class.

findByQuery(String) - Method in class fr.igred.omero.GatewayWrapper

Finds objects on OMERO through a database query.

flatten(Collection<? extends Collection<? extends U>>) - Static method in class fr.igred.omero.GenericObjectWrapper

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

FolderWrapper - Class in fr.igred.omero.repository

Class containing a FolderData object.

FolderWrapper(Client, String) - Constructor for class fr.igred.omero.repository.FolderWrapper

Constructor of the FolderWrapper class.

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

Constructor of the FolderWrapper class.

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

Constructor of the FolderWrapper class.

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

This package contains abstract wrapper classes for the OMERO Gateway and the basic OMERO object.

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

This package contains wrapper classes for annotations.

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, groups and planes information.

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

This package contains classes related to the hierarchical organization for images.

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

This package contains wrapper classes for OMERO shapes and ROIs.

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

This package contains a utility class used to check if the library requirements are available.

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

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

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

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

G

GatewayWrapper - Class in fr.igred.omero

Basic class, contains the gateway, the security context, and multiple facilities.

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

Abstract constructor of the GatewayWrapper class.

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

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

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

Constructor of the GenericAnnotationWrapper class.

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

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

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

Constructor of the class GenericObjectWrapper.

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

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

GenericRepositoryObjectWrapper(T) - Constructor for class fr.igred.omero.repository.GenericRepositoryObjectWrapper

Constructor of the class GenericRepositoryObjectWrapper.

GenericRepositoryObjectWrapper.ReplacePolicy - Enum in fr.igred.omero.repository

Policy to specify how to handle objects when they are replaced.

GenericShapeWrapper<T extends ShapeData> - Class in fr.igred.omero.roi

Generic class containing a ShapeData (or a subclass) object.

GenericShapeWrapper(T) - Constructor for class fr.igred.omero.roi.GenericShapeWrapper

Constructor of the GenericShapeWrapper class using a ShapeData.

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

Returns the contained object.

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

Gets the ImageData acquisition date

getAdminFacility() - Method in class fr.igred.omero.GatewayWrapper

Gets the AdminFacility to use admin specific function.

getAllPixels(Client) - Method in class fr.igred.omero.repository.PixelsWrapper

Returns an array containing the value for each voxel

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

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

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

Gets the sRGB alpha value of the channel.

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

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

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

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

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

Returns the file to upload to the server.

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

Gets the sRGB blue value of the channel.

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

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

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

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

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

Returns the 5D bounds containing the ROI.

getBrowseFacility() - Method in class fr.igred.omero.GatewayWrapper

Gets the BrowseFacility used to access the data from OMERO.

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

Gets C coordinate.

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

Gets the channel.

getChannelColor(Client, int) - Method in class fr.igred.omero.repository.ImageWrapper

Gets the current color of the channel

getChannelImportedColor(Client, int) - Method in class fr.igred.omero.repository.ImageWrapper

Gets the original color of the channel

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

Returns the label of the channel.

getChannelName(Client, int) - Method in class fr.igred.omero.repository.ImageWrapper

Gets the name of the channel.

getChannels(Client) - Method in class fr.igred.omero.repository.ImageWrapper

Gets the image channels.

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

Retrieves the children folders for this folder.

getColor() - Method in class fr.igred.omero.repository.ChannelWrapper

Gets the original channel color.

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

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

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

Returns the number of columns in the table.

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

Returns the name of the column.

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

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

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

Returns the index indicating how to label a column.

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

Returns the type of the column.

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

Gets the List of NamedValue contained in the map annotation.

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

Returns the absolute path to the file

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

Gets the coordinates of the MaskData shape.

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

Gets the coordinates of the LineData shape.

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

Gets the coordinates of the MaskData shape.

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

Gets the coordinates of the PointData shape.

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

Gets the coordinates of the RectangleData shape.

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

Gets the coordinates of the TextData shape.

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

Gets the object creation date

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

Contains the permissions of the user in the group.

getCurrentGroupId() - Method in class fr.igred.omero.GatewayWrapper

Gets the current group ID.

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

Gets the value contained in the table

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

Gets a certain value of the table

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

Gets the dataset with the specified id from OMERO.

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

Gets all datasets available from OMERO.

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

Gets all the datasets in the project available from OMERO.

getDatasets(Client) - Method in class fr.igred.omero.annotations.GenericAnnotationWrapper

Gets all datasets with this annotation from OMERO.

getDatasets(Client) - Method in class fr.igred.omero.repository.ImageWrapper

Retrieves the datasets containing this image

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

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

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

Gets the datasets with the specified ids from OMERO.

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

Gets all datasets with a certain name from OMERO.

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

Gets the dataset with the specified name from OMERO

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

Returns the default Group for this Experimenter

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

Returns the currently selected field or 0.

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

Retrieves the plane deltaT.

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

Retrieves the description of the underlying AnnotationData instance.

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

Returns the description of the group.

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

Gets the DatasetData description

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

Gets the folder description

getDescription() - Method in class fr.igred.omero.repository.GenericRepositoryObjectWrapper

Gets the object description

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

Gets the ImageData description

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

Gets the plate acquisition description

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

Gets the plate description

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

Gets the project description

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

Gets the screen description

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

Gets the object description

getDm() - Method in class fr.igred.omero.GatewayWrapper

Gets the DataManagerFacility to handle/write data on OMERO.

getElementsOf(Class<? extends T>) - Method in class fr.igred.omero.annotations.AnnotationList

Gets a list of elements from this list whose class is specified.

getElementsOf(Class<? extends T>) - Method in class fr.igred.omero.roi.ShapeList

Gets a list of elements from this list whose class is specified.

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

Returns the e-mail of the experimenter.

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

Gets size of bounds for each coordinate.

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

Returns the time when the last image was collected.

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

Returns the experimenters contained in this group.

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

Retrieves the exposure time.

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

Returns the external identifier of the plate.

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

Returns the original file.

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

Returns the file annotations

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

Returns the format of the uploaded file.

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

Returns the fileId of the table.

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

Returns the ID of the file.

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

Returns a user readable description of the file.

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

Returns the name of the file.

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

Returns the absolute path to the file.

getFilesetImages(Client) - Method in class fr.igred.omero.repository.ImageWrapper

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

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

Returns the size of the file.

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

Gets ShapeData fill color.

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

Returns the first name of the experimenter.

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

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

getFolder(Client, Long) - Method in class fr.igred.omero.repository.ImageWrapper

Deprecated.

Gets the folder with the specified id on OMERO.

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

Gets all folders available from OMERO.

getFolders(Client) - Method in class fr.igred.omero.annotations.GenericAnnotationWrapper

Gets all folders with this annotation from OMERO.

getFolders(Client) - Method in class fr.igred.omero.repository.ImageWrapper

Gets the list of folders linked to this image.

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

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

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

Gets ShapeData font size.

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

Returns the Gateway.

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

Gets the sRGB green value of the channel.

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

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

getGroup(String) - Method in class fr.igred.omero.Client

Returns the group which matches the name.

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

Gets the group ID

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 mask.

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

Returns the height untransformed rectangle.

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

Returns the table ID.

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

Gets the user id.

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

Gets the object id

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

Returns the image related to that sample if any.

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

Returns the image with the specified ID from OMERO.

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

Gets all images owned by the current user.

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

Retrieves the images contained in this folder.

getImages() - Method in class fr.igred.omero.repository.WellWrapper

Retrieves the images contained in this well.

getImages(GenericAnnotationWrapper<?>) - Method in class fr.igred.omero.Browser

Gets all images with the specified annotation from OMERO.

getImages(GenericAnnotationWrapper<?>) - Method in class fr.igred.omero.Client

Gets all images with the specified annotation from OMERO.

getImages(Client) - Method in class fr.igred.omero.annotations.GenericAnnotationWrapper

Gets all images with this annotation from OMERO.

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

Gets all images in the dataset available from OMERO.

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

Retrieves the images contained in this folder.

getImages(Client) - Method in class fr.igred.omero.repository.PlateAcquisitionWrapper

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

getImages(Client) - Method in class fr.igred.omero.repository.PlateWrapper

Returns the images contained in the wells of this plate.

getImages(Client) - Method in class fr.igred.omero.repository.ProjectWrapper

Gets all images in the project available from OMERO.

getImages(Client) - Method in class fr.igred.omero.repository.ScreenWrapper

Retrieves the images contained in this screen.

getImages(Client, String) - Method in class fr.igred.omero.repository.DatasetWrapper

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

getImages(Client, String) - Method in class fr.igred.omero.repository.ProjectWrapper

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

getImages(Client, String, String) - Method in class fr.igred.omero.repository.ProjectWrapper

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

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

Gets the images with the specified ids from OMERO

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

Gets all images with a certain name from OMERO.

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

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

getImages(String, String, String) - Method in class fr.igred.omero.Client

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

getImagesKey(Client, String) - Method in class fr.igred.omero.repository.DatasetWrapper

Deprecated.

Gets all images in the dataset with a certain key

getImagesKey(Client, String) - Method in class fr.igred.omero.repository.ProjectWrapper

Deprecated.

Gets all images in the project with a certain key

getImagesKey(String) - Method in class fr.igred.omero.Browser

Deprecated.

Gets all images with a certain key

getImagesKey(String) - Method in class fr.igred.omero.Client

Deprecated.

Gets all images with a certain key

getImagesLike(Client, String) - Method in class fr.igred.omero.repository.DatasetWrapper

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

getImagesLike(Client, String) - Method in class fr.igred.omero.repository.ProjectWrapper

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

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

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

getImagesPairKeyValue(Client, String, String) - Method in class fr.igred.omero.repository.DatasetWrapper

Deprecated.

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

getImagesPairKeyValue(Client, String, String) - Method in class fr.igred.omero.repository.ProjectWrapper

Deprecated.

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

getImagesPairKeyValue(String, String) - Method in class fr.igred.omero.Browser

Deprecated.

Gets all images with a certain key value pair from OMERO

getImagesPairKeyValue(String, String) - Method in class fr.igred.omero.Client

Deprecated.

Gets all images with a certain key value pair from OMERO

getImagesTagged(TagAnnotationWrapper) - Method in class fr.igred.omero.Browser

Deprecated.

Gets all images tagged with a specified tag from OMERO.

getImagesTagged(Client, TagAnnotationWrapper) - Method in class fr.igred.omero.repository.DatasetWrapper

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

getImagesTagged(Client, TagAnnotationWrapper) - Method in class fr.igred.omero.repository.ProjectWrapper

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

getImagesTagged(Client, Long) - Method in class fr.igred.omero.repository.DatasetWrapper

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

getImagesTagged(Client, Long) - Method in class fr.igred.omero.repository.ProjectWrapper

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

getImagesTagged(Long) - Method in class fr.igred.omero.Browser

Deprecated.

Gets all images tagged with a specified tag from OMERO.

getImagesWithKey(Client, String) - Method in class fr.igred.omero.repository.DatasetWrapper

Gets all images in the dataset with a certain key

getImagesWithKey(Client, String) - Method in class fr.igred.omero.repository.ProjectWrapper

Gets all images in the project with a certain key

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

Gets all images with a certain key.

getImagesWithKeyValuePair(Client, String, String) - Method in class fr.igred.omero.repository.DatasetWrapper

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

getImagesWithKeyValuePair(Client, String, String) - Method in class fr.igred.omero.repository.ProjectWrapper

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

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

Gets all images with a certain key value pair from OMERO

getImportStore() - Method in class fr.igred.omero.GatewayWrapper

Creates or recycles the import store.

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

Returns the channel index.

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

Returns the institution where the experimenter works.

getKeyValuePairs(Client) - Method in class fr.igred.omero.AnnotatableWrapper

Gets the List of key-value pairs associated to an object as a map (no duplicate key should exist).

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

Returns the label associated to the plate acquisition.

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

Returns the time when the annotation was last modified.

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

Returns the last name of the experimenter.

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

Returns the leaders of this group.

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

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

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

Gets the list of map annotations available to the user.

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

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

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

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

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

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

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

Returns the mask as a byte array.

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

Returns the mask image.

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

Returns the points in the polygon.

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

Returns the maximum number of fields in any well.

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

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

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

Computes the mean time interval from the planes deltaTs.

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

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

getMetadata() - Method in class fr.igred.omero.GatewayWrapper

Gets the MetadataFacility used to retrieve annotations from OMERO.

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

Returns the middle name of the experimenter.

getMinPosition(Collection<? extends PlaneInfoWrapper>, Function<? super PlaneInfoWrapper, ? extends Length>, Unit<Length>) - Static method in class fr.igred.omero.meta.PlaneInfoWrapper

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

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

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

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

Returns the name of the table.

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

Gets the name of the TagData.

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

Returns the name of the group.

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

Returns the name of the channel.

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

Gets the DatasetData name

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

Gets the name of the folder

getName() - Method in class fr.igred.omero.repository.GenericRepositoryObjectWrapper

Gets the object name.

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

Gets the ImageData name

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

Gets the plate acquisition name.

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

Gets the plate name.

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

Gets the ProjectData name

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

Gets the screen name.

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

Gets the object name.

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

Gets the ROI name.

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

Retrieves the AnnotationData namespace of the underlying AnnotationData instance.

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

Returns the format of the original file.

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

Gets the owner ID

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

Retrieves the parent folders for this folder.

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

Returns the permissions level.

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

Gets the Pixels for this image.

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

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

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

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

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

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

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

Gets the pixel type.

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

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

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

Returns the plate containing this Well.

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

Gets the plate with the specified id from OMERO.

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

Returns the plate acquisitions related to this plate.

getPlateAcquisitions(Client) - Method in class fr.igred.omero.annotations.GenericAnnotationWrapper

Gets all plate acquisitions with this annotation from OMERO.

getPlateAcquisitions(Client) - Method in class fr.igred.omero.repository.ImageWrapper

Returns the plate acquisitions linked to this image.

getPlateAcquisitions(Client) - Method in class fr.igred.omero.repository.ScreenWrapper

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

getPlateAcquisitions(Client) - Method in class fr.igred.omero.repository.WellSampleWrapper

Returns the plate acquisitions linked to the parent Well.

getPlateAcquisitions(Client) - Method in class fr.igred.omero.repository.WellWrapper

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

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

Gets all plates available from OMERO.

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

Returns the plates contained in this screen.

getPlates(Client) - Method in class fr.igred.omero.annotations.GenericAnnotationWrapper

Gets all plates with this annotation from OMERO.

getPlates(Client) - Method in class fr.igred.omero.repository.ImageWrapper

Retrieves the plates containing this image.

getPlates(Client) - Method in class fr.igred.omero.repository.PlateAcquisitionWrapper

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

getPlates(Client) - Method in class fr.igred.omero.repository.WellSampleWrapper

Returns the plates containing the parent Well.

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

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

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

Gets the plates with the specified ids from OMERO.

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

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

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

Returns the type of plate e.g.

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

Returns the points in the Polygon.

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

Returns the points in the Polyline.

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

Retrieves the X stage position.

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

Retrieves the X stage position.

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

Returns the position X.

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

Retrieves the Y stage position.

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

Retrieves the Y stage position.

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

Returns the position Y.

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

Retrieves the Z stage position.

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

Retrieves the Z stage position.

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

Gets the project with the specified id from OMERO.

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

Gets all projects available from OMERO.

getProjects(Client) - Method in class fr.igred.omero.annotations.GenericAnnotationWrapper

Gets all projects with this annotation from OMERO.

getProjects(Client) - Method in class fr.igred.omero.repository.DatasetWrapper

Retrieves the projects containing this dataset.

getProjects(Client) - Method in class fr.igred.omero.repository.ImageWrapper

Retrieves the projects containing this image

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

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

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

Gets the projects with the specified ids from OMERO.

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

Gets all projects with a certain name from OMERO.

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

Returns the description of the protocol.

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

Returns the identifier of the protocol.

getQueryService() - Method in class fr.igred.omero.GatewayWrapper

Returns the IQueryPrx used to find objects on OMERO.

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

Returns the radius along the X-axis.

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

Returns the radius along the Y-axis.

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

Returns the rating value.

getRawPixels(Client, int) - Method in class fr.igred.omero.repository.PixelsWrapper

Returns an array containing the raw values for each voxel for each planes

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

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

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

Returns the description of the reagent set.

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

Returns the identifier of the Reagent set.

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

Gets the sRGB red value of the channel.

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

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

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

Returns the id of the plate of reference.

getRoiFacility() - Method in class fr.igred.omero.GatewayWrapper

Gets the ROIFacility used to manipulate ROIs from OMERO.

getROIFolders(Client) - Method in class fr.igred.omero.repository.ImageWrapper

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

getROIs(Client) - Method in class fr.igred.omero.repository.FolderWrapper

Deprecated.

Gets the ROI contained in the folder associated with the image id set (an image need to be associated)

getROIs(Client) - Method in class fr.igred.omero.repository.ImageWrapper

Gets all ROIs linked to the image in OMERO

getROIs(Client, long) - Method in class fr.igred.omero.repository.FolderWrapper

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

getROIs(Client, ImageWrapper) - Method in class fr.igred.omero.repository.FolderWrapper

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

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

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

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

Returns the number of rows in the table.

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

Returns the index indicating how to label a row.

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

Gets the screen with the specified id from OMERO.

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

Gets all screens available from OMERO.

getScreens(Client) - Method in class fr.igred.omero.annotations.GenericAnnotationWrapper

Gets all screens with this annotation from OMERO.

getScreens(Client) - Method in class fr.igred.omero.repository.ImageWrapper

Retrieves the screens containing this image

getScreens(Client) - Method in class fr.igred.omero.repository.PlateAcquisitionWrapper

Retrieves the screens containing the parent plates.

getScreens(Client) - Method in class fr.igred.omero.repository.PlateWrapper

Retrieves the screens containing this plate.

getScreens(Client) - Method in class fr.igred.omero.repository.WellSampleWrapper

Returns the screens containing the parent Well.

getScreens(Client) - Method in class fr.igred.omero.repository.WellWrapper

Refreshes this well and retrieves the screens containing it.

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

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

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

Gets the screens with the specified ids from OMERO.

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 class fr.igred.omero.GatewayWrapper

Get the ID of the current session

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

Returns the list of shapes contained in the ROIData.

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

Gets size of bounds for each coordinate.

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

Gets the size of the image on the C axis

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

Gets the size of the image on the T axis

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

Gets the size of the image on the X axis

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

Gets the size of the image on the Y axis

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

Gets the size of the image on the Z axis

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

Gets starting coordinates.

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

Returns the time when the first image was collected.

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

Returns the time at which the field was acquired.

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

Returns the status of the plate.

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

Returns the status of the well.

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

Gets the ShapeData stroke color.

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

Gets T coordinate.

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

Sets the time-point.

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

Gets a certain table linked to the object in OMERO.

getTables(Client) - Method in class fr.igred.omero.AnnotatableWrapper

Gets all tables linked to the object in OMERO.

getTablesFacility() - Method in class fr.igred.omero.GatewayWrapper

Gets the TablesFacility used to manipulate tables on OMERO.

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

Gets a specific tag from the OMERO database.

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

Gets the list of tag annotations available to the user.

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

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

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

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

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.GenericShapeWrapper

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 class fr.igred.omero.roi.TextWrapper

Gets the text on the ShapeData.

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

Retrieves the plane channel index.

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

Retrieves the plane time index.

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

Retrieves the plane slice index.

getThumbnail(Client, int) - Method in class fr.igred.omero.repository.ImageWrapper

Retrieves the image thumbnail of the specified size.

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

Gets the time increment between time points.

getUser() - Method in class fr.igred.omero.GatewayWrapper

Returns the current user.

getUser(String) - Method in class fr.igred.omero.Client

Returns the user which matches the username.

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

Returns the last name of the experimenter.

getValue(Client, String) - Method in class fr.igred.omero.AnnotatableWrapper

Gets the value from a Key-Value pair associated to the object.

getWell(Client) - Method in class fr.igred.omero.repository.WellSampleWrapper

Retrieves the well containing this well sample

getWell(Long) - Method in class fr.igred.omero.Browser

Gets the well with the specified id from OMERO.

getWellOriginX(UnitsLength) - Method in class fr.igred.omero.repository.PlateWrapper

Returns the x-coordinate in 2D-space of the well.

getWellOriginY(UnitsLength) - Method in class fr.igred.omero.repository.PlateWrapper

Returns the y-coordinate in 2D-space of the well.

getWells() - Method in class fr.igred.omero.Browser

Gets all wells available from OMERO.

getWells(Client) - Method in class fr.igred.omero.annotations.GenericAnnotationWrapper

Gets all wells with this annotation from OMERO.

getWells(Client) - Method in class fr.igred.omero.repository.ImageWrapper

Retrieves the wells containing this image.

getWells(Client) - Method in class fr.igred.omero.repository.PlateAcquisitionWrapper

Retrieves the wells contained in the parent plate.

getWells(Client) - Method in class fr.igred.omero.repository.PlateWrapper

Gets all wells in the plate available from OMERO.

getWells(Client) - Method in class fr.igred.omero.repository.ScreenWrapper

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

getWells(ExperimenterWrapper) - Method in class fr.igred.omero.Browser

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

getWells(Long...) - Method in class fr.igred.omero.Browser

Gets the wells with the specified ids from OMERO.

getWellSamples() - Method in class fr.igred.omero.repository.WellWrapper

Returns the well samples linked to the well.

getWellType() - Method in class fr.igred.omero.repository.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 mask.

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

Returns the width untransformed rectangle.

getX() - Method in class fr.igred.omero.repository.PixelsWrapper.Coordinates

Gets X coordinate.

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 top-left corner of the mask.

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

Returns the x-coordinate of the shape.

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

Returns the x-coordinate of the shape.

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

Returns the x-coordinate of the shape.

getX1() - Method in class fr.igred.omero.roi.LineWrapper

Returns the x-coordinate of the starting 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 class fr.igred.omero.repository.PixelsWrapper.Coordinates

Gets Y coordinate.

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 top-left corner of the mask.

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

Returns the y coordinate of the shape.

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

Returns the y coordinate of the shape.

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

Returns the y coordinate of the shape.

getY1() - Method in class fr.igred.omero.roi.LineWrapper

Returns the y-coordinate of the starting 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 class fr.igred.omero.repository.PixelsWrapper.Coordinates

Gets Z coordinate.

getZ() - Method in class fr.igred.omero.roi.GenericShapeWrapper

Gets the z-section.

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 OMEROServerError if ServerError was caught

handleException(Throwable, String) - Static method in class fr.igred.omero.exception.ExceptionHandler

Deprecated.

Helper method to convert an exception from:

• DSAccessException to AccessException
• DSOutOfServiceException to ServiceException
• ServerError to OMEROServerError

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

Throws: ServiceException if DSOutOfServiceException was caught AccessException if DSAccessException was caught

handleServiceOrAccess(Throwable, String) - Static method in class fr.igred.omero.exception.ExceptionHandler

Deprecated.

Helper method to convert an exception from:

• DSOutOfServiceException to ServiceException
• DSAccessException to AccessException

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

Throws: ServiceException if DSOutOfServiceException was caught OMEROServerError if ServerError was caught

handleServiceOrServer(Throwable, String) - Static method in class fr.igred.omero.exception.ExceptionHandler

Deprecated.

Helper method to convert an exception from:

• DSOutOfServiceException to ServiceException
• ServerError to OMEROServerError

hasRGBA() - Method in class fr.igred.omero.repository.ChannelWrapper

Returns whether the channel contains all the RGBA values or not.

I

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

Default IJ property to store ROI local labels / indices.

ijIDProperty(String) - Static method in class fr.igred.omero.roi.ROIWrapper

Returns the ID property corresponding to the input local index/label property (appends "_ID" to said property).

ijNameProperty(String) - Static method in class fr.igred.omero.roi.ROIWrapper

Returns the ID property corresponding to the input local index/label property (appends "_NAME" to said property).

ImageWrapper - Class in fr.igred.omero.repository

Class containing an ImageData.

ImageWrapper(ImageData) - Constructor for class fr.igred.omero.repository.ImageWrapper

Constructor of the class ImageWrapper

importAndReplaceImages(Client, String) - Method in class fr.igred.omero.repository.DatasetWrapper

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, GenericRepositoryObjectWrapper.ReplacePolicy) - Method in class fr.igred.omero.repository.DatasetWrapper

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 class fr.igred.omero.repository.DatasetWrapper

Imports one image file to the dataset in OMERO.

importImage(GatewayWrapper, String) - Method in class fr.igred.omero.repository.ScreenWrapper

Imports one image file to the screen in OMERO.

importImage(GatewayWrapper, DataObject, String) - Static method in class fr.igred.omero.repository.GenericRepositoryObjectWrapper

Imports one image file to the target in OMERO.

importImages(Client, int, String...) - Method in class fr.igred.omero.repository.DatasetWrapper

Imports all images candidates in the paths to the dataset in OMERO.

importImages(Client, String...) - Method in class fr.igred.omero.repository.DatasetWrapper

Imports all images candidates in the paths to the dataset in OMERO.

importImages(GatewayWrapper, int, String...) - Method in class fr.igred.omero.repository.ScreenWrapper

Imports all images candidates in the paths to the screen in OMERO.

importImages(GatewayWrapper, String...) - Method in class fr.igred.omero.repository.ScreenWrapper

Imports all images candidates in the paths to the screen in OMERO.

importImages(GatewayWrapper, DataObject, int, String...) - Static method in class fr.igred.omero.repository.GenericRepositoryObjectWrapper

Imports all images candidates in the paths to the target in OMERO.

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

Returns true if the experimenter is active, false otherwise.

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

Checks if the table is complete

isConnected() - Method in class fr.igred.omero.GatewayWrapper

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 class fr.igred.omero.meta.ExperimenterWrapper

Returns true if the user is connected via LDAP.

isLinked(Client, A) - Method in class fr.igred.omero.AnnotatableWrapper

Checks if a specific annotation is linked to the object.

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 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(Client) - Method in class fr.igred.omero.repository.ImageWrapper

Checks if image is orphaned (not in a WellSample nor linked to a dataset).

L

LEVEL_FIVE - Static variable in class fr.igred.omero.annotations.RatingAnnotationWrapper

Indicates the object is rated with five stars.

LEVEL_FOUR - Static variable in class fr.igred.omero.annotations.RatingAnnotationWrapper

Indicates the object is rated with four stars.

LEVEL_ONE - Static variable in class fr.igred.omero.annotations.RatingAnnotationWrapper

Indicates the object is rated with one star.

LEVEL_THREE - Static variable in class fr.igred.omero.annotations.RatingAnnotationWrapper

Indicates the object is rated with three stars.

LEVEL_TWO - Static variable in class fr.igred.omero.annotations.RatingAnnotationWrapper

Indicates the object is rated with two stars.

LEVEL_ZERO - Static variable in class fr.igred.omero.annotations.RatingAnnotationWrapper

Indicates the object is not rated.

LibraryChecker - Class in fr.igred.omero.util

Utility methods to check if required libraries/classes are available

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(Client, A) - Method in class fr.igred.omero.AnnotatableWrapper

Attach an AnnotationData to this object.

link(Client, A) - Method in class fr.igred.omero.repository.FolderWrapper

Adds an annotation to the object in OMERO, if possible.

link(Client, A) - Method in class fr.igred.omero.repository.PlateAcquisitionWrapper

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

link(Client, A) - Method in class fr.igred.omero.roi.GenericShapeWrapper

Attach an AnnotationData to this object.

link(Client, A) - Method in class fr.igred.omero.roi.ROIWrapper

Attach an AnnotationData to this object.

link(Client, GenericAnnotationWrapper<?>...) - Method in class fr.igred.omero.AnnotatableWrapper

Adds multiple annotations to the object in OMERO, if possible.

linkIfNotLinked(Client, GenericAnnotationWrapper<?>...) - Method in class fr.igred.omero.AnnotatableWrapper

Adds multiple annotations to the object in OMERO if they are not already linked.

loadFolders(Long...) - Method in class fr.igred.omero.Browser

Gets the folders with the specified IDs from OMERO (fully loaded).

loadPlanesInfo(Client) - Method in class fr.igred.omero.repository.PixelsWrapper

Loads the planes information.

M

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(List<NamedValue>) - 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.

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.repository.PixelsWrapper

Size of tiles when retrieving pixels

O

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.

OMEROServerError - Exception in fr.igred.omero.exception

Reports an error occurred on the server.

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

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

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

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

P

PERMISSIONS_GROUP_READ - Static variable in class fr.igred.omero.meta.GroupWrapper

Indicates that the group is Group i.e.

PERMISSIONS_GROUP_READ_LINK - Static variable in class fr.igred.omero.meta.GroupWrapper

Indicates that the group is Group i.e.

PERMISSIONS_GROUP_READ_WRITE - Static variable in class fr.igred.omero.meta.GroupWrapper

Indicates that the group is Group i.e.

PERMISSIONS_PRIVATE - Static variable in class fr.igred.omero.meta.GroupWrapper

Indicates that the group is Private i.e.

PERMISSIONS_PUBLIC_READ - Static variable in class fr.igred.omero.meta.GroupWrapper

Indicates that the group is Public i.e.

PERMISSIONS_PUBLIC_READ_WRITE - Static variable in class fr.igred.omero.meta.GroupWrapper

Indicates that the group is Public i.e.

PixelsWrapper - Class in fr.igred.omero.repository

Class containing a PixelData object.

PixelsWrapper(PixelsData) - Constructor for class fr.igred.omero.repository.PixelsWrapper

Constructor of the PixelsWrapper class

PixelsWrapper.Bounds - Class in fr.igred.omero.repository

Class containing 5D bounds coordinates

PixelsWrapper.Coordinates - Class in fr.igred.omero.repository

Class containing 5D pixel coordinates

PlaneInfoWrapper - Class in fr.igred.omero.meta

PlaneInfoWrapper(PlaneInfoData) - Constructor for class fr.igred.omero.meta.PlaneInfoWrapper

Constructor of the class PlaneInfoWrapper.

PlateAcquisitionWrapper - Class in fr.igred.omero.repository

Class containing a PlateAcquisitionData object.

PlateAcquisitionWrapper(PlateAcquisitionData) - Constructor for class fr.igred.omero.repository.PlateAcquisitionWrapper

Constructor of the class PlateAcquisitionWrapper.

PlateWrapper - Class in fr.igred.omero.repository

Class containing a PlateData object.

PlateWrapper(PlateData) - Constructor for class fr.igred.omero.repository.PlateWrapper

Constructor of the class PlateWrapper.

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.

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.

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.

ProjectWrapper - Class in fr.igred.omero.repository

Class containing a ProjectData object.

ProjectWrapper(Client, String, String) - Constructor for class fr.igred.omero.repository.ProjectWrapper

Constructor of the ProjectWrapper class.

ProjectWrapper(ProjectData) - Constructor for class fr.igred.omero.repository.ProjectWrapper

Constructor of the ProjectWrapper class.

R

rate(Client, int) - Method in class fr.igred.omero.AnnotatableWrapper

Rates the object (using a rating annotation).

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.

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.

refresh(Client) - Method in class fr.igred.omero.repository.DatasetWrapper

Reloads the dataset from OMERO.

refresh(Client) - Method in class fr.igred.omero.repository.PlateWrapper

Reloads the plate from OMERO.

refresh(Client) - Method in class fr.igred.omero.repository.ProjectWrapper

Reloads the project from OMERO.

refresh(Client) - Method in class fr.igred.omero.repository.WellWrapper

Reloads the well from OMERO.

refresh(GatewayWrapper) - Method in class fr.igred.omero.repository.ScreenWrapper

Reloads the screen from OMERO.

reload(Client) - Method in class fr.igred.omero.repository.FolderWrapper

Reloads the folder from OMERO, to update all links.

removeDataset(Client, DatasetWrapper) - Method in class fr.igred.omero.repository.ProjectWrapper

Removes a dataset from the project in OMERO.

removeImage(Client, ImageWrapper) - Method in class fr.igred.omero.repository.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 ImageWrapper>, ImageWrapper) - Method in class fr.igred.omero.repository.DatasetWrapper

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).

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.

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 GenericShapeWrapper<?>>) - 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 class fr.igred.omero.GatewayWrapper

Saves an object on OMERO.

saveAndUpdate(Client) - Method in class fr.igred.omero.GenericObjectWrapper

Saves and updates object.

saveAs(String, char) - Method in class fr.igred.omero.annotations.TableWrapper

Saves the current table as a character-delimited text file.

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

Saves the ROI.

saveROI(Client, ROIWrapper) - Method in class fr.igred.omero.repository.ImageWrapper

Deprecated.

Links a ROI to the image in OMERO

DO NOT USE IT IF A SHAPE WAS DELETED !!!

saveROIs(Client, ROIWrapper...) - Method in class fr.igred.omero.repository.ImageWrapper

Links ROIs to the image in OMERO.

saveROIs(Client, Collection<? extends ROIWrapper>) - Method in class fr.igred.omero.repository.ImageWrapper

Links ROIs to the image in OMERO.

ScreenWrapper - Class in fr.igred.omero.repository

Class containing a ScreenData object.

ScreenWrapper(Client, String, String) - Constructor for class fr.igred.omero.repository.ScreenWrapper

Constructor of the ProjectWrapper class.

ScreenWrapper(ScreenData) - Constructor for class fr.igred.omero.repository.ScreenWrapper

Constructor of the class ScreenWrapper.

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 class fr.igred.omero.repository.WellWrapper

Sets the alpha component of the color associated to the well.

setBlue(Integer) - Method in class fr.igred.omero.repository.WellWrapper

Sets the blue component of the color associated to the well.

setC(int) - Method in class fr.igred.omero.roi.GenericShapeWrapper

Sets the channel.

setColumn(int, String, Class<?>) - Method in class fr.igred.omero.annotations.TableWrapper

Sets the information about a certain column.

setContent(List<NamedValue>) - Method in class fr.igred.omero.annotations.MapAnnotationWrapper

Sets the content of the map annotation.

setCoordinates(double[]) - Method in class fr.igred.omero.roi.EllipseWrapper

Sets the coordinates of the EllipseData shape.

setCoordinates(double[]) - Method in class fr.igred.omero.roi.LineWrapper

Sets the coordinates of the LineData shape.

setCoordinates(double[]) - Method in class fr.igred.omero.roi.MaskWrapper

Sets the coordinates of the MaskData shape.

setCoordinates(double[]) - Method in class fr.igred.omero.roi.PointWrapper

Sets the coordinates of the PointData shape.

setCoordinates(double[]) - Method in class fr.igred.omero.roi.RectangleWrapper

Sets the coordinates of the RectangleData shape.

setCoordinates(double[]) - Method in class fr.igred.omero.roi.TextWrapper

Sets the coordinates of the TextData object.

setCoordinates(double, double) - Method in class fr.igred.omero.roi.PointWrapper

Sets the coordinates the PointData shape.

setCoordinates(double, double) - Method in class fr.igred.omero.roi.TextWrapper

Sets the coordinates of the TextData shape.

setCoordinates(double, double, double, double) - Method in class fr.igred.omero.roi.EllipseWrapper

Sets the coordinates of the EllipseData shape.

setCoordinates(double, double, double, double) - Method in class fr.igred.omero.roi.LineWrapper

Sets the coordinates of the LineData shape.

setCoordinates(double, double, double, double) - Method in class fr.igred.omero.roi.MaskWrapper

Sets the coordinates of the MaskData shape.

setCoordinates(double, double, double, double) - Method in class fr.igred.omero.roi.RectangleWrapper

Sets the coordinates of the RectangleData shape.

setCZT(int, int, int) - Method in class fr.igred.omero.roi.GenericShapeWrapper

Sets the channel, z-section and time-point at once.

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

Deprecated.

Changes the wrapped data.

setDefaultSample(int) - Method in class fr.igred.omero.repository.PlateWrapper

Sets the default sample.

setDescription(String) - Method in class fr.igred.omero.annotations.GenericAnnotationWrapper

Sets the description of the underlying AnnotationData instance.

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

Sets the description of the group.

setDescription(String) - Method in class fr.igred.omero.repository.DatasetWrapper

Sets the description of the dataset.

setDescription(String) - Method in class fr.igred.omero.repository.FolderWrapper

Sets the description of the folder.

setDescription(String) - Method in class fr.igred.omero.repository.ImageWrapper

Sets the description of the image.

setDescription(String) - Method in class fr.igred.omero.repository.PlateAcquisitionWrapper

Sets the description of the plate acquisition.

setDescription(String) - Method in class fr.igred.omero.repository.PlateWrapper

Sets the description of the plate.

setDescription(String) - Method in class fr.igred.omero.repository.ProjectWrapper

Sets the description of the project.

setDescription(String) - Method in class fr.igred.omero.repository.ScreenWrapper

Sets the description of the screen.

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

Sets the e-mail of the experimenter.

setExternalIdentifier(String) - Method in class fr.igred.omero.repository.PlateWrapper

Sets the external identifier.

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

Sets the fileId of the table.

setFill(Color) - Method in class fr.igred.omero.roi.GenericShapeWrapper

Sets the ShapeData fill color.

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

Sets the first name of the experimenter.

setFontSize(double) - Method in class fr.igred.omero.roi.GenericShapeWrapper

Sets ShapeData font size.

setGreen(Integer) - Method in class fr.igred.omero.repository.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 an untransformed mask.

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

Sets the height of an untransformed rectangle.

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

Sets the id of the table.

setImage(long) - Method in class fr.igred.omero.repository.FolderWrapper

Deprecated.

Sets the image associated to the folder

setImage(ImageWrapper) - Method in class fr.igred.omero.repository.FolderWrapper

Deprecated.

Sets the image associated to the folder

setImage(ImageWrapper) - Method in class fr.igred.omero.repository.WellSampleWrapper

Sets the image linked to this well sample.

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

Sets the image linked to the ROI.

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

Sets the institution where the experimenter works.

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

Sets the last name of the experimenter.

setMask(boolean[][]) - Method in class fr.igred.omero.roi.MaskWrapper

Sets the mask

setMask(byte[]) - Method in class fr.igred.omero.roi.MaskWrapper

Sets the mask image.

setMask(int[][]) - Method in class fr.igred.omero.roi.MaskWrapper

Sets the mask

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

Sets the middle name of the experimenter.

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

Sets the name of the table.

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

Sets the name of the TagData.

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

Sets the name of the group.

setName(String) - Method in class fr.igred.omero.repository.ChannelWrapper

Sets the name of the channel.

setName(String) - Method in class fr.igred.omero.repository.DatasetWrapper

Sets the name of the dataset.

setName(String) - Method in class fr.igred.omero.repository.FolderWrapper

Sets the name of the folder.

setName(String) - Method in class fr.igred.omero.repository.ImageWrapper

Sets the name of the image.

setName(String) - Method in class fr.igred.omero.repository.PlateAcquisitionWrapper

Sets the name of the plate acquisition.

setName(String) - Method in class fr.igred.omero.repository.PlateWrapper

Sets the name of the plate.

setName(String) - Method in class fr.igred.omero.repository.ProjectWrapper

Sets the name of the project.

setName(String) - Method in class fr.igred.omero.repository.ScreenWrapper

Sets the name of the screen.

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

Sets the ROI name.

setNameSpace(String) - Method in class fr.igred.omero.annotations.GenericAnnotationWrapper

Sets the name space of the underlying AnnotationData instance.

setParent(FolderWrapper) - Method in class fr.igred.omero.repository.FolderWrapper

Sets the parent folder for this folder.

setPoints(List<Point2D.Double>) - Method in class fr.igred.omero.roi.PolygonWrapper

Sets the points in the polyline.

setPoints(List<Point2D.Double>) - Method in class fr.igred.omero.roi.PolylineWrapper

Sets the points in the polyline.

setProtocolDescription(String) - Method in class fr.igred.omero.repository.ScreenWrapper

Sets the description of the protocol.

setProtocolIdentifier(String) - Method in class fr.igred.omero.repository.ScreenWrapper

Sets the identifier of the protocol.

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

Sets the radius along the X-axis.

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

Sets the radius along the Y-axis.

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

Sets the rating value.

setReagentSetDescription(String) - Method in class fr.igred.omero.repository.ScreenWrapper

Sets the identifier of the reagent.

setReagentSetIdentifier(String) - Method in class fr.igred.omero.repository.ScreenWrapper

Sets the identifier of the reagent.

setRed(Integer) - Method in class fr.igred.omero.repository.WellWrapper

Sets the red component of the color associated to the well.

setRefPlateId(long) - Method in class fr.igred.omero.repository.PlateAcquisitionWrapper

Sets the id of the plate this plate acquisition is for.

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

Sets the number of row in the table.

setStatus(String) - Method in class fr.igred.omero.repository.PlateWrapper

Sets the status.

setStatus(String) - Method in class fr.igred.omero.repository.WellWrapper

Sets the status of the well.

setStroke(Color) - Method in class fr.igred.omero.roi.GenericShapeWrapper

Sets ShapeData stroke color.

setT(int) - Method in class fr.igred.omero.roi.GenericShapeWrapper

Sets the time-point.

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.GenericShapeWrapper

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 class fr.igred.omero.roi.TextWrapper

Sets the text on the ShapeData.

setTransform(double, double, double, double, double, double) - Method in class fr.igred.omero.roi.GenericShapeWrapper

Sets the transform to the matrix specified by the 6 double precision values.

setTransform(AffineTransform) - Method in class fr.igred.omero.roi.GenericShapeWrapper

Sets the transform from a AffineTransform.

setWellType(String) - Method in class fr.igred.omero.repository.WellWrapper

Sets a human-readable identifier for the screening status e.g.

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

Sets the width of an untransformed mask.

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

Sets width of an untransformed rectangle.

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 top-left corner of an untransformed mask.

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

Sets the x-coordinate of the shape.

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

Sets the x-coordinate of the shape.

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

Sets the x-coordinate of the shape.

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 class fr.igred.omero.roi.LineWrapper

Set the x-coordinate of the end point of an untransformed line.

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 top-left corner of an untransformed mask.

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

Sets the y-coordinate of the shape.

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

Sets the y-coordinate of the shape.

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

Sets the y-coordinate of the shape.

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 class fr.igred.omero.roi.LineWrapper

Set the y-coordinate of the end point of an untransformed line.

setZ(int) - Method in class fr.igred.omero.roi.GenericShapeWrapper

Sets the z-section.

ShapeList - Class in fr.igred.omero.roi

List of GenericShapeWrapper objects

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

Constructs an empty list with an initial capacity of ten.

ShapeList(int) - Constructor for class fr.igred.omero.roi.ShapeList

Constructs an empty list with the specified initial capacity.

sudoGetUser(String) - Method in class fr.igred.omero.Client

Gets the client associated with the username in the parameters.

switchGroup(long) - Method in class fr.igred.omero.GatewayWrapper

Change the current group used by the current user;

T

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, List<? extends Roi>) - Constructor for class fr.igred.omero.annotations.TableWrapper

Constructor of the class TableWrapper.

TableWrapper(Client, ResultsTable, Long, List<? 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.

TagAnnotationWrapper - Class in fr.igred.omero.annotations

Class containing a TagAnnotationData object.

TagAnnotationWrapper(Client, 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.

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 class fr.igred.omero.roi.EllipseWrapper

Converts the shape to an Shape.

toAWTShape() - Method in class fr.igred.omero.roi.GenericShapeWrapper

Converts the shape to an Shape.

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

Converts the shape to an Shape.

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

Converts the shape to an Shape.

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

Converts the shape to an Shape.

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

Converts the shape to an Shape.

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

Converts the shape to an Shape.

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

Converts the shape to an Shape.

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

Converts the shape to an Shape.

toAWTTransform() - Method in class fr.igred.omero.roi.GenericShapeWrapper

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.GenericShapeWrapper

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 class fr.igred.omero.roi.ROIWrapper

Converts the ROI to a list of ImageJ ROIs.

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

Converts shape to ImageJ ROI.

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

Converts the ROI to a list of ImageJ ROIs.

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

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

toImageJ(List<? extends ROIWrapper>) - Static method in class fr.igred.omero.roi.ROIWrapper

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

toImageJ(List<? extends ROIWrapper>, String) - Static method in class fr.igred.omero.roi.ROIWrapper

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

toImagePlus(Client) - Method in class fr.igred.omero.repository.ImageWrapper

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 class fr.igred.omero.repository.ImageWrapper

Gets the imagePlus generated from the image from OMERO corresponding to the bound.

toImagePlus(Client, ROIWrapper) - Method in class fr.igred.omero.repository.ImageWrapper

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.exception.ExceptionHandler

toString() - Method in class fr.igred.omero.GatewayWrapper

Overridden to return the host name, the group ID, the username and the connection status.

toString() - Method in class fr.igred.omero.GenericObjectWrapper

Overridden to return the name of the class and the object id.

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

Deletes all unused row in the table

U

unlink(Client, A) - Method in class fr.igred.omero.AnnotatableWrapper

Unlinks the given annotation from the current object.

UNLINK - fr.igred.omero.repository.GenericRepositoryObjectWrapper.ReplacePolicy

Unlink objects only

unlinkAllROI(Client) - Method in class fr.igred.omero.repository.FolderWrapper

Deprecated.

Unlink all ROI, associated to the image set, in the folder. ROIs are now linked to the image directly

unlinkAllROIs(Client) - Method in class fr.igred.omero.repository.FolderWrapper

Unlink all ROIs associated to this folder.

unlinkAllROIs(Client, long) - Method in class fr.igred.omero.repository.FolderWrapper

Unlink all ROIs associated to the provided image ID from the folder.

unlinkAllROIs(Client, ImageWrapper) - Method in class fr.igred.omero.repository.FolderWrapper

Unlink all ROIs associated to the provided image from the folder.

unlinkROI(Client, ROIWrapper) - Method in class fr.igred.omero.repository.FolderWrapper

Deprecated.

Unlink an ROI, associated to the image set, in the folder. The ROI is now linked to the image directly.

unlinkROIs(Client, ROIWrapper...) - Method in class fr.igred.omero.repository.FolderWrapper

Unlink ROIs from the folder.

V

valueOf(String) - Static method in enum fr.igred.omero.repository.GenericRepositoryObjectWrapper.ReplacePolicy

Returns the enum constant of this type with the specified name.

values() - Static method in enum fr.igred.omero.repository.GenericRepositoryObjectWrapper.ReplacePolicy

Returns an array containing the constants of this enum type, in the order they are declared.

W

WellSampleWrapper - Class in fr.igred.omero.repository

Class containing a WellSampleData object.

WellSampleWrapper(WellSampleData) - Constructor for class fr.igred.omero.repository.WellSampleWrapper

Constructor of the class WellSampleWrapper.

WellWrapper - Class in fr.igred.omero.repository

Class containing a WellData object.

WellWrapper(WellData) - Constructor for class fr.igred.omero.repository.WellWrapper

Constructor of the class WellWrapper.

wrap(Collection<U>, Function<? super U, ? extends V>) - Static method in class fr.igred.omero.GenericObjectWrapper

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.GenericObjectWrapper

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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