Index (Simple OMERO Client 5.8.3 API)

A B C D E F G H I L M O P R S T U
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(ShapeData) - Method in class fr.igred.omero.roi.ShapeList: Wraps the specified ShapeData object and add it to the end of this list.
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.repository.GenericRepositoryObjectWrapper: Links a file to the object
addImage(Client, ImageWrapper) - Method in class fr.igred.omero.repository.DatasetWrapper: Adds a single image to the dataset in OMERO
addImages(Client, List<ImageWrapper>) - Method in class fr.igred.omero.repository.DatasetWrapper: Adds a list of image to the dataset in OMERO.
addMapAnnotation(Client, MapAnnotationWrapper) - Method in class fr.igred.omero.repository.GenericRepositoryObjectWrapper: Adds a List of Key-Value pair to the object
addPairKeyValue(Client, String, String) - Method in class fr.igred.omero.repository.GenericRepositoryObjectWrapper: Adds a single Key-Value pair to the object.
addROI(Client, ROIWrapper) - Method in class fr.igred.omero.repository.FolderWrapper: Add an ROI to the folder and associate it to the image id set(an image need to be associated)
addRow(Object...) - Method in class fr.igred.omero.annotations.TableWrapper: Adds a row to the table.
addRows(Client, ResultsTable, Long, List<Roi>) - Method in class fr.igred.omero.annotations.TableWrapper: Adds rows from an ImageJ ResultsTable.
addRows(Client, ResultsTable, Long, List<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.repository.GenericRepositoryObjectWrapper: Adds a table to the object in OMERO
addTag(Client, TagAnnotationWrapper) - Method in class fr.igred.omero.repository.GenericRepositoryObjectWrapper: Adds a tag to the object in OMERO, if possible.
addTag(Client, Long) - Method in class fr.igred.omero.repository.GenericRepositoryObjectWrapper: Adds multiple tags to the object in OMERO, if possible.
addTag(Client, String, String) - Method in class fr.igred.omero.repository.GenericRepositoryObjectWrapper: Adds a newly created tag to the object in OMERO, if possible.
addTag(Client, TagAnnotationData) - Method in class fr.igred.omero.repository.FolderWrapper: Private function.
addTag(Client, TagAnnotationData) - Method in class fr.igred.omero.repository.GenericRepositoryObjectWrapper: Private function.
addTags(Client, TagAnnotationWrapper...) - Method in class fr.igred.omero.repository.GenericRepositoryObjectWrapper: Adds multiple tag to the object in OMERO, if possible.
addTags(Client, Long...) - Method in class fr.igred.omero.repository.GenericRepositoryObjectWrapper: Adds multiple tags by ID to the object in OMERO, if possible.
ANNOTATION_LINK - Static variable in class fr.igred.omero.repository.DatasetWrapper
ANNOTATION_LINK - Static variable in class fr.igred.omero.repository.FolderWrapper
ANNOTATION_LINK - Static variable in class fr.igred.omero.repository.ImageWrapper
ANNOTATION_LINK - Static variable in class fr.igred.omero.repository.ProjectWrapper
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.GenericRepositoryObjectWrapper: 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.ProjectWrapper: Returns the type of annotation link for this object
ARROW - Static variable in class fr.igred.omero.roi.LineWrapper
asChannelData() - Method in class fr.igred.omero.repository.ChannelWrapper
asDatasetData() - Method in class fr.igred.omero.repository.DatasetWrapper
asExperimenterData() - Method in class fr.igred.omero.meta.ExperimenterWrapper
asFolderData() - Method in class fr.igred.omero.repository.FolderWrapper: Gets the folder contained in the FolderWrapper
asGroupData() - Method in class fr.igred.omero.meta.GroupWrapper
asImageData() - Method in class fr.igred.omero.repository.ImageWrapper
asMapAnnotationData() - Method in class fr.igred.omero.annotations.MapAnnotationWrapper: Gets the MapAnnotationData contained.
asProjectData() - Method in class fr.igred.omero.repository.ProjectWrapper
asROIData() - Method in class fr.igred.omero.roi.ROIWrapper: Returns the ROIData contained.
asShapeData() - Method in class fr.igred.omero.roi.GenericShapeWrapper: Gets the ShapeData object contained.
asTagAnnotationData() - Method in class fr.igred.omero.annotations.TagAnnotationWrapper: Gets the TagAnnotationData contained.

B

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

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
ChannelWrapper(ChannelData) - Constructor for class fr.igred.omero.repository.ChannelWrapper: Constructor of the class ChannelWrapper.
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.
compare(U, U) - Method in class fr.igred.omero.GenericObjectWrapper.SortById: Compare 2 ObjectWrappers.
compare(U, U) - Method in class fr.igred.omero.meta.ExperimenterWrapper.SortByLastName: Compare 2 ExperimenterWrappers.
compare(U, U) - Method in class fr.igred.omero.meta.GroupWrapper.SortByName: Compare 2 GroupWrappers.
connect(String, int, String) - Method in class fr.igred.omero.Client: Connects to OMERO using a session ID.
connect(String, int, String, char[]) - Method in class fr.igred.omero.Client: Connects the user to OMERO.
connect(String, int, String, char[], Long) - Method in class fr.igred.omero.Client: Connects the user to OMERO.
connect(LoginCredentials) - Method in class fr.igred.omero.Client: Connects the user to OMERO.
Coordinates(int, int, int, int, int) - Constructor for class fr.igred.omero.repository.PixelsWrapper.Coordinates: Coordinates constructor.
createTable() - Method in class fr.igred.omero.annotations.TableWrapper
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
DatasetWrapper - Class in fr.igred.omero.repository: Class containing a DatasetData.
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.
deleteFile(Long) - Method in class fr.igred.omero.Client: Deletes a file from OMERO
deleteShape(int) - Method in class fr.igred.omero.roi.ROIWrapper: Deletes a ShapeData from the ROIData.
deleteShape(ShapeData) - Method in class fr.igred.omero.roi.ROIWrapper: Deletes a ShapeData from the ROIData.
disconnect() - Method in class fr.igred.omero.Client: Disconnects the user
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
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(EllipseData) - Constructor for class fr.igred.omero.roi.EllipseWrapper: Constructor of the EllipseWrapper class using a EllipseData.
ExceptionHandler - Class in fr.igred.omero.exception: Class with methods to handle OMERO exceptions
ExperimenterWrapper - Class in fr.igred.omero.meta
ExperimenterWrapper(ExperimenterData) - Constructor for class fr.igred.omero.meta.ExperimenterWrapper: Constructor of the class ExperimenterWrapper.
ExperimenterWrapper.SortByLastName<U extends ExperimenterWrapper> - Class in fr.igred.omero.meta: Class used to sort ExperimenterWrappers.

F

FileAnnotationWrapper - Class in fr.igred.omero.annotations
FileAnnotationWrapper(FileAnnotationData) - Constructor for class fr.igred.omero.annotations.FileAnnotationWrapper: Constructor of the GenericAnnotationWrapper class.
findByQuery(String) - Method in class fr.igred.omero.Client: Finds objects on OMERO through a database query.
FolderWrapper - Class in fr.igred.omero.repository: Class containing a FolderData.
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
fr.igred.omero.annotations - package fr.igred.omero.annotations
fr.igred.omero.exception - package fr.igred.omero.exception
fr.igred.omero.meta - package fr.igred.omero.meta
fr.igred.omero.repository - package fr.igred.omero.repository
fr.igred.omero.roi - package fr.igred.omero.roi
fromImageJ(List<Roi>) - Static method in class fr.igred.omero.roi.ROIWrapper: Converts an ImageJ list of ROIs to a list of OMERO ROIs
fromImageJ(List<Roi>, String) - Static method in class fr.igred.omero.roi.ROIWrapper: Converts an ImageJ list of ROIs to a list of OMERO ROIs

G

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.
GenericObjectWrapper.SortById<U extends GenericObjectWrapper<?>> - Class in fr.igred.omero: Class used to sort wrappers.
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.
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.
getAcquisitionDate() - Method in class fr.igred.omero.repository.ImageWrapper: Gets the ImageData acquisition date
getAdminFacility() - Method in class fr.igred.omero.Client: Gets the AdminFacility linked to the gateway to use admin specific function.
getAllPixels(Client) - Method in class fr.igred.omero.repository.PixelsWrapper: Returns an array containing the value for each voxels
getAllPixels(Client, int[], int[], int[], int[], int[]) - Method in class fr.igred.omero.repository.PixelsWrapper: Returns an array containing the value for each voxels corresponding to the bounds
getAlpha() - Method in class fr.igred.omero.repository.ChannelWrapper: Gets the sRGB alpha value of the channel.
getAttachedFile() - Method in class fr.igred.omero.annotations.FileAnnotationWrapper
getBlue() - Method in class fr.igred.omero.repository.ChannelWrapper: Gets the sRGB blue value of the channel.
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.Client: 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
getColor() - Method in class fr.igred.omero.repository.ChannelWrapper: Gets the original channel color.
getColumnCount() - Method in class fr.igred.omero.annotations.TableWrapper
getColumnName(int) - Method in class fr.igred.omero.annotations.TableWrapper
getColumns() - Method in class fr.igred.omero.annotations.TableWrapper: Gets the TableDataColumn which contains information on each column of the table
getColumnType(int) - Method in class fr.igred.omero.annotations.TableWrapper
getContent() - Method in class fr.igred.omero.annotations.MapAnnotationWrapper: Gets the List of NamedValue contained in the MapAnnotationData.
getContentAsString() - Method in class fr.igred.omero.annotations.FileAnnotationWrapper
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.Client: Contains the permissions of the user in the group.
getCurrentGroupId() - Method in class fr.igred.omero.Client: 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.Client: Gets the dataset with the specified id from OMERO.
getDatasets() - Method in class fr.igred.omero.Client: Gets all the 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 tag from OMERO.
getDatasets(String) - Method in class fr.igred.omero.Client: 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
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.ProjectWrapper: Gets the project description
getDm() - Method in class fr.igred.omero.Client: Gets the DataManagerFacility to handle/write data on OMERO.
getElementsOf(Class<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.
getExperimenters() - Method in class fr.igred.omero.meta.GroupWrapper: Returns the experimenters contained in this group.
getFile(Client, String) - Method in class fr.igred.omero.annotations.FileAnnotationWrapper
getFileAnnotations(Client) - Method in class fr.igred.omero.repository.GenericRepositoryObjectWrapper: Returns the file annotations
getFileFormat() - Method in class fr.igred.omero.annotations.FileAnnotationWrapper
getFileId() - Method in class fr.igred.omero.annotations.TableWrapper
getFileID() - Method in class fr.igred.omero.annotations.FileAnnotationWrapper
getFileKind() - Method in class fr.igred.omero.annotations.FileAnnotationWrapper
getFileName() - Method in class fr.igred.omero.annotations.FileAnnotationWrapper
getFilePath() - Method in class fr.igred.omero.annotations.FileAnnotationWrapper
getFileSize() - Method in class fr.igred.omero.annotations.FileAnnotationWrapper
getFirstName() - Method in class fr.igred.omero.meta.ExperimenterWrapper: Returns the first name of the experimenter.
getFolder(Client, Long) - Method in class fr.igred.omero.repository.ImageWrapper: Gets the folder with the specified id on OMERO.
getFolders(Client) - Method in class fr.igred.omero.repository.ImageWrapper: Gets the list of Folder linked to the image Associate the folder to the image
getFontSize() - Method in class fr.igred.omero.roi.GenericShapeWrapper: Gets ShapeData font size
getGateway() - Method in class fr.igred.omero.Client
getGreen() - Method in class fr.igred.omero.repository.ChannelWrapper: Gets the sRGB green value of the channel.
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
getId() - Method in class fr.igred.omero.Client: Gets the user id.
getId() - Method in class fr.igred.omero.GenericObjectWrapper: Gets the object id
getImage(Long) - Method in class fr.igred.omero.Client: Returns an ImageWrapper that contains the image with the specified id from OMERO.
getImages() - Method in class fr.igred.omero.Client: Gets all images available from OMERO.
getImages(Client) - Method in class fr.igred.omero.annotations.GenericAnnotationWrapper: Gets all images with this tag 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.ProjectWrapper: Gets all images in the project available from OMERO.
getImages(Client, String) - Method in class fr.igred.omero.repository.DatasetWrapper: Gets all images in the dataset with a certain from OMERO.
getImages(Client, String) - Method in class fr.igred.omero.repository.ProjectWrapper: Gets all images in the project with a certain from OMERO.
getImages(String) - Method in class fr.igred.omero.Client: Gets all images with a certain from OMERO.
getImagesKey(Client, String) - Method in class fr.igred.omero.repository.DatasetWrapper: Gets all images in the dataset with a certain key
getImagesKey(Client, String) - Method in class fr.igred.omero.repository.ProjectWrapper: Gets all images in the project with a certain key
getImagesKey(String) - Method in class fr.igred.omero.Client: 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.Client: Gets all images with a certain motif in their name from OMERO.
getImagesPairKeyValue(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
getImagesPairKeyValue(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.
getImagesPairKeyValue(String, String) - Method in class fr.igred.omero.Client: Gets all images with a certain key value pair from OMERO
getImagesTagged(TagAnnotationWrapper) - Method in class fr.igred.omero.Client: 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.Client: Gets all images tagged with a specified tag from OMERO.
getImportStore() - Method in class fr.igred.omero.Client: 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.repository.GenericRepositoryObjectWrapper: Gets the List of NamedValue (Key-Value pair) associated to an object.
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.
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.
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.Client: Gets the MetadataFacility used to manipulate annotations from OMERO.
getMiddleName() - Method in class fr.igred.omero.meta.ExperimenterWrapper: Returns the middle name of the experimenter.
getName() - Method in class fr.igred.omero.annotations.TableWrapper
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.ProjectWrapper: Gets the ProjectData 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
getOwner() - Method in class fr.igred.omero.GenericObjectWrapper: Gets the owner ID
getPermissionsLevel() - Method in class fr.igred.omero.meta.GroupWrapper: Returns the permissions level.
getPixels() - Method in class fr.igred.omero.repository.ImageWrapper: Gets the PixelsWrapper of the 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.
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.
getProject(Long) - Method in class fr.igred.omero.Client: Gets the project with the specified id from OMERO.
getProjects() - Method in class fr.igred.omero.Client: Gets all projects available from OMERO.
getProjects(Client) - Method in class fr.igred.omero.annotations.GenericAnnotationWrapper: Gets all projects with this tag from OMERO.
getProjects(String) - Method in class fr.igred.omero.Client: Gets all projects with a certain name from 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.
getRawPixels(Client, int) - Method in class fr.igred.omero.repository.PixelsWrapper: Returns an array containing the raw values for each voxels 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 voxels for each planes corresponding to the bounds
getRed() - Method in class fr.igred.omero.repository.ChannelWrapper: Gets the sRGB red value of the channel.
getRoiFacility() - Method in class fr.igred.omero.Client: Gets the ROIFacility used to manipulate ROI from OMERO.
getROIs(Client) - Method in class fr.igred.omero.repository.FolderWrapper: 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
getRowCount() - Method in class fr.igred.omero.annotations.TableWrapper
getServerFileMimetype() - Method in class fr.igred.omero.annotations.FileAnnotationWrapper
getSessionId() - Method in class fr.igred.omero.Client: 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.
getStroke() - Method in class fr.igred.omero.roi.GenericShapeWrapper: Sets 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.repository.GenericRepositoryObjectWrapper: Gets a certain table linked to the object in OMERO
getTables(Client) - Method in class fr.igred.omero.repository.GenericRepositoryObjectWrapper: Gets all table linked to the object in OMERO.
getTablesFacility() - Method in class fr.igred.omero.Client: Gets the TablesFacility used to manipulate table from OMERO.
getTag(Long) - Method in class fr.igred.omero.Client: Gets a specific tag from the OMERO database
getTags() - Method in class fr.igred.omero.Client: Gets the list of TagAnnotationWrapper available to the user
getTags(Client) - Method in class fr.igred.omero.repository.GenericRepositoryObjectWrapper: Gets all tag linked to an object in OMERO, if possible.
getTags(String) - Method in class fr.igred.omero.Client: Gets the list of TagAnnotationWrapper with the specified name available to the user
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.ShapeWrapper: Gets the text on the ShapeData.
getText() - Method in class fr.igred.omero.roi.TextWrapper: Gets the text on the ShapeData.
getThumbnail(Client, int) - Method in class fr.igred.omero.repository.ImageWrapper: Retrieves the image thumbnail of the specified size.
getUser() - Method in class fr.igred.omero.Client: 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.repository.GenericRepositoryObjectWrapper: Gets the value from a Key-Value pair associated to the object
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
GroupWrapper(GroupData) - Constructor for class fr.igred.omero.meta.GroupWrapper: Constructor of the class GroupWrapper.
GroupWrapper.SortByName<U extends GroupWrapper> - Class in fr.igred.omero.meta: Class used to sort GroupWrappers.

H

handleException(Throwable, String) - Static method in class fr.igred.omero.exception.ExceptionHandler: Helper method to convert an exception from: DSAccessException to AccessException DSOutOfServiceException to ServiceException ServerError to OMEROServerError
handleServiceOrAccess(Throwable, String) - Static method in class fr.igred.omero.exception.ExceptionHandler: Helper method to convert an exception from: DSOutOfServiceException to ServiceException DSAccessException to AccessException
handleServiceOrServer(Throwable, String) - Static method in class fr.igred.omero.exception.ExceptionHandler: Helper method to convert an exception from: DSOutOfServiceException to ServiceException ServerError to OMEROServerError

I

IJ_PROPERTY - Static variable in class fr.igred.omero.roi.ROIWrapper: Default IJ property to store ROI local IDs / indices.
ijIDProperty(String) - Static method in class fr.igred.omero.roi.ROIWrapper: Returns ID property corresponding to input local ID property (appends "_ID" 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
importImage(Client, String) - Method in class fr.igred.omero.repository.DatasetWrapper: Imports one image candidate 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.
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.Client: Check if the client is still connected to the server
isLDAP() - Method in class fr.igred.omero.meta.ExperimenterWrapper: Returns true if the user is connected via LDAP.
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

L

LineWrapper - Class in fr.igred.omero.roi
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(LineData) - Constructor for class fr.igred.omero.roi.LineWrapper: Constructor of the LineWrapper class using a LineData.

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
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

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
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
PointWrapper - Class in fr.igred.omero.roi
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
PolygonWrapper() - Constructor for class fr.igred.omero.roi.PolygonWrapper: Constructor of the PolygonWrapper class using a new empty LineData.
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
PolylineWrapper() - Constructor for class fr.igred.omero.roi.PolylineWrapper: Constructor of the RectangleWrapper class using a new empty LineData.
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
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

RectangleWrapper - Class in fr.igred.omero.roi
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(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: Refreshes the wrapped dataset.
refresh(Client) - Method in class fr.igred.omero.repository.ProjectWrapper: Refreshes the wrapped project.
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.repository.GenericRepositoryObjectWrapper: Removes the link of the given type with the given child ID.
ROIWrapper - Class in fr.igred.omero.roi: Class containing a ROIData
ROIWrapper() - Constructor for class fr.igred.omero.roi.ROIWrapper: Constructor of the ROIWrapper class.
ROIWrapper(List<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.Client: 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: Links a ROI to the image in OMERO
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(Throwable, ConnectionStatus) - Constructor for exception fr.igred.omero.exception.ServiceException: Constructs a new exception with the specified cause and a generic message.
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 MapAnnotationData.
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: Changes the wrapped data.
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.ProjectWrapper: Sets the description of the project.
setEmail(String) - Method in class fr.igred.omero.meta.ExperimenterWrapper: Sets the e-mail of the experimenter.
setFileId(Long) - Method in class fr.igred.omero.annotations.TableWrapper: Sets the fileId of the table.
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
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: Sets the image associated to the folder
setImage(ImageWrapper) - Method in class fr.igred.omero.repository.FolderWrapper: Sets the image associated to the folder
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.ProjectWrapper: Sets the name of the project.
setNameSpace(String) - Method in class fr.igred.omero.annotations.GenericAnnotationWrapper: Sets the name space of the underlying AnnotationData instance.
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.
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.
setRowCount(int) - Method in class fr.igred.omero.annotations.TableWrapper: Sets the number of row in the table.
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.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.ShapeWrapper: 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.
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
ShapeWrapper - Class in fr.igred.omero.roi
ShapeWrapper(ShapeData) - Constructor for class fr.igred.omero.roi.ShapeWrapper: Constructor of the ShapeWrapper class using a ShapeData.
SortById() - Constructor for class fr.igred.omero.GenericObjectWrapper.SortById
SortByLastName() - Constructor for class fr.igred.omero.meta.ExperimenterWrapper.SortByLastName
SortByName() - Constructor for class fr.igred.omero.meta.GroupWrapper.SortByName
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.Client: 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<Roi>) - Constructor for class fr.igred.omero.annotations.TableWrapper: Constructor of the class TableWrapper.
TableWrapper(Client, ResultsTable, Long, List<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
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.
TextWrapper - Class in fr.igred.omero.roi
TextWrapper() - Constructor for class fr.igred.omero.roi.TextWrapper: Constructor of the TextWrapper class using a new empty ShapeData.
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.ShapeWrapper: Converts the shape to an Shape.
toAWTShape() - Method in class fr.igred.omero.roi.TextWrapper: Converts the shape to an Shape.
toAWTTransform() - Method in class fr.igred.omero.roi.GenericShapeWrapper: Converts AffineTransform to AffineTransform.
toImageJ() - Method in class fr.igred.omero.roi.EllipseWrapper: Converts shape to ImageJ ROI.
toImageJ() - Method in class fr.igred.omero.roi.GenericShapeWrapper: Converts shape to ImageJ ROI.
toImageJ() - Method in class fr.igred.omero.roi.LineWrapper: Converts shape to ImageJ ROI.
toImageJ() - Method in class fr.igred.omero.roi.MaskWrapper: Converts shape to ImageJ ROI.
toImageJ() - Method in class fr.igred.omero.roi.PointWrapper: Converts shape to ImageJ ROI.
toImageJ() - Method in class fr.igred.omero.roi.RectangleWrapper: Converts shape to ImageJ ROI.
toImageJ() - Method in class fr.igred.omero.roi.ROIWrapper: Convert ROI to ImageJ list of 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: Convert ROI to ImageJ list of ROIs.
toImageJ(List<ROIWrapper>) - Static method in class fr.igred.omero.roi.ROIWrapper: Converts an OMERO list of ROIs to a list of ImageJ ROIs
toImageJ(List<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.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.repository.GenericRepositoryObjectWrapper: Unlinks the given annotation from the current object.
unlinkAllROI(Client) - Method in class fr.igred.omero.repository.FolderWrapper: Unlink all ROI, associated to the image set, in the folder.
unlinkROI(Client, ROIWrapper) - Method in class fr.igred.omero.repository.FolderWrapper: Unlink an ROI, associated to the image set, in the folder.

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