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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
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
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.
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
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
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
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
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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