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

A

AccessException - Exception in fr.igred.omero.exception
Reports an error occurred while trying to pull out data from the server.
AccessException(String, Throwable) - Constructor for exception fr.igred.omero.exception.AccessException
Constructs a new exception with the specified detail message and cause.
AccessException(Throwable) - Constructor for exception fr.igred.omero.exception.AccessException
Constructs a new exception with a general message and the cause.
add(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<? extends 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
Protected function.
addTag(Client, TagAnnotationData) - Method in class fr.igred.omero.repository.PlateAcquisitionWrapper
Protected 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.PlateAcquisitionWrapper
 
ANNOTATION_LINK - Static variable in class fr.igred.omero.repository.PlateWrapper
 
ANNOTATION_LINK - Static variable in class fr.igred.omero.repository.ProjectWrapper
 
ANNOTATION_LINK - Static variable in class fr.igred.omero.repository.ScreenWrapper
 
ANNOTATION_LINK - Static variable in class fr.igred.omero.repository.WellWrapper
 
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.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
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.
asPlateAcquisitionData() - Method in class fr.igred.omero.repository.PlateAcquisitionWrapper
 
asPlateData() - Method in class fr.igred.omero.repository.PlateWrapper
 
asProjectData() - Method in class fr.igred.omero.repository.ProjectWrapper
 
asROIData() - Method in class fr.igred.omero.roi.ROIWrapper
Returns the ROIData contained.
asScreenData() - Method in class fr.igred.omero.repository.ScreenWrapper
 
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.
asWellData() - Method in class fr.igred.omero.repository.WellWrapper
 
asWellSampleData() - Method in class fr.igred.omero.repository.WellSampleWrapper
 

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.
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.
copy(Roi) - Method in class fr.igred.omero.roi.GenericShapeWrapper
Copies details from an ImageJ ROI (position, stroke color, stroke width).
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.GatewayWrapper
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.GatewayWrapper
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(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 - 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.

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.GatewayWrapper
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
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 and groups.
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.
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) - Constructor for class fr.igred.omero.GatewayWrapper
Abstract constructor of the GatewayWrapper class.
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.
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.GatewayWrapper
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 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.
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.
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
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
 
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
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
 
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.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.Client
Gets the dataset with the specified id from OMERO.
getDatasets() - Method in class fr.igred.omero.Client
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 tag from OMERO.
getDatasets(Long...) - Method in class fr.igred.omero.Client
Gets the datasets with the specified ids 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
getDefaultSample() - Method in class fr.igred.omero.repository.PlateWrapper
Returns the currently selected field or 0.
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.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.
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
 
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.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
 
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.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 owned by the current user.
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(Long...) - Method in class fr.igred.omero.Client
Gets the images with the specified ids 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.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.repository.GenericRepositoryObjectWrapper
Gets the List of NamedValue (Key-Value pair) associated to an object.
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.
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.
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 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.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.
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.
getPlate() - Method in class fr.igred.omero.repository.WellWrapper
Returns the plate containing this Well.
getPlate(Long) - Method in class fr.igred.omero.Client
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.
getPlates() - Method in class fr.igred.omero.Client
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 tag from OMERO.
getPlates(Long...) - Method in class fr.igred.omero.Client
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(UnitsLength) - Method in class fr.igred.omero.repository.WellSampleWrapper
Returns the position X.
getPositionY(UnitsLength) - Method in class fr.igred.omero.repository.WellSampleWrapper
Returns the position Y.
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(Long...) - Method in class fr.igred.omero.Client
Gets the projects with the specified ids from OMERO.
getProjects(String) - Method in class fr.igred.omero.Client
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.
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 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 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
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
 
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.Client
Gets the screen with the specified id from OMERO.
getScreens() - Method in class fr.igred.omero.Client
Gets all screens available from OMERO.
getScreens(Client) - Method in class fr.igred.omero.annotations.GenericAnnotationWrapper
Gets all screens with this tag from OMERO.
getScreens(Long...) - Method in class fr.igred.omero.Client
Gets the screens with the specified ids from OMERO.
getServerFileMimetype() - Method in class fr.igred.omero.annotations.FileAnnotationWrapper
 
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
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 tables linked to the object in OMERO.
getTablesFacility() - Method in class fr.igred.omero.GatewayWrapper
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.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.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.repository.GenericRepositoryObjectWrapper
Gets the value from a Key-Value pair associated to the object
getWell(Long) - Method in class fr.igred.omero.Client
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.Client
Gets all wells available from OMERO.
getWells(Client) - Method in class fr.igred.omero.annotations.GenericAnnotationWrapper
Gets all wells with this tag from OMERO.
getWells(Client) - Method in class fr.igred.omero.repository.PlateWrapper
Gets all wells in the plate available from OMERO.
getWells(Long...) - Method in class fr.igred.omero.Client
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
 
GroupWrapper(GroupData) - Constructor for class fr.igred.omero.meta.GroupWrapper
Constructor of the class GroupWrapper.

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.GatewayWrapper
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(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.

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
PlateAcquisitionWrapper - Class in fr.igred.omero.repository
 
PlateAcquisitionWrapper(PlateAcquisitionData) - Constructor for class fr.igred.omero.repository.PlateAcquisitionWrapper
Constructor of the class PlateAcquisitionWrapper.
PlateWrapper - Class in fr.igred.omero.repository
 
PlateWrapper(PlateData) - Constructor for class fr.igred.omero.repository.PlateWrapper
Constructor of the class PlateWrapper.
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(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
 
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
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(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
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(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
Links a ROI to the image in OMERO
ScreenWrapper - Class in fr.igred.omero.repository
 
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(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 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.
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.
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
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.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.
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.
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.
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.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
 
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<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(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
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<? 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.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.

W

WellSampleWrapper - Class in fr.igred.omero.repository
 
WellSampleWrapper(WellSampleData) - Constructor for class fr.igred.omero.repository.WellSampleWrapper
Constructor of the class WellSampleWrapper.
WellWrapper - Class in fr.igred.omero.repository
 
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 a ObjectWrapper list, sorted by sorter.
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