A B C D E F G H I L M O P R S T U V W
All Classes All Packages
All Classes All Packages
All Classes All Packages
A
- AccessException - Exception in fr.igred.omero.exception
-
Reports an error occurred while trying to pull out data from the server.
- AccessException(String, Throwable) - Constructor for exception fr.igred.omero.exception.AccessException
-
Constructs a new exception with the specified detail message and cause.
- AccessException(Throwable) - Constructor for exception fr.igred.omero.exception.AccessException
-
Constructs a new exception with a general message and the cause.
- add(AnnotationData) - Method in class fr.igred.omero.annotations.AnnotationList
-
Wraps the specified AnnotationData object and add it to the end of this list.
- add(ShapeData) - Method in class fr.igred.omero.roi.ShapeList
-
Wraps the specified ShapeData object and add it to the end of this list.
- addAndReplaceFile(Client, File) - Method in class fr.igred.omero.AnnotatableWrapper
-
Uploads a file, links it to the object and unlinks previous files with the same name, or deletes them if they're orphaned.
- addAndReplaceFile(Client, File, GenericRepositoryObjectWrapper.ReplacePolicy) - Method in class fr.igred.omero.AnnotatableWrapper
-
Uploads a file, links it to the object and unlinks or deletes previous files with the same name.
- addAndReplaceTable(Client, TableWrapper) - Method in class fr.igred.omero.AnnotatableWrapper
-
Adds a table to the object in OMERO and unlinks previous tables with the same name, or deletes them if they're orphaned.
- addAndReplaceTable(Client, TableWrapper, GenericRepositoryObjectWrapper.ReplacePolicy) - Method in class fr.igred.omero.AnnotatableWrapper
-
Adds a table to the object in OMERO and unlinks or deletes previous tables with the same name.
- addChild(FolderWrapper) - Method in class fr.igred.omero.repository.FolderWrapper
-
Adds a child folder to this folder.
- addChildren(Collection<? extends FolderWrapper>) - Method in class fr.igred.omero.repository.FolderWrapper
-
Adds children folders to this folder.
- addDataset(Client, DatasetWrapper) - Method in class fr.igred.omero.repository.ProjectWrapper
-
Adds a dataset to the project in OMERO.
- addDataset(Client, String, String) - Method in class fr.igred.omero.repository.ProjectWrapper
-
Adds a dataset to the project in OMERO.
- addFile(Client, File) - Method in class fr.igred.omero.AnnotatableWrapper
-
Uploads a file and links it to the object
- addFileAnnotation(Client, FileAnnotationWrapper) - Method in class fr.igred.omero.AnnotatableWrapper
-
Deprecated.Links a file annotation to the object. Use
AnnotatableWrapper.link(fr.igred.omero.Client, A)
instead. - addImage(Client, ImageWrapper) - Method in class fr.igred.omero.repository.DatasetWrapper
-
Adds a single image to the dataset in OMERO
- addImages(Client, ImageWrapper...) - Method in class fr.igred.omero.repository.FolderWrapper
-
Links images to the folder in OMERO.
- addImages(Client, List<? extends ImageWrapper>) - Method in class fr.igred.omero.repository.DatasetWrapper
-
Adds a list of image to the dataset in OMERO.
- addKeyValuePair(Client, String, String) - Method in class fr.igred.omero.AnnotatableWrapper
-
Adds a single Key-Value pair to the object.
- addMapAnnotation(Client, MapAnnotationWrapper) - Method in class fr.igred.omero.AnnotatableWrapper
-
Deprecated.Adds a List of Key-Value pair to the object. Use
AnnotatableWrapper.link(fr.igred.omero.Client, A)
instead.The list is contained in the map annotation.
- addPairKeyValue(Client, String, String) - Method in class fr.igred.omero.AnnotatableWrapper
-
Deprecated.Adds a single Key-Value pair to the object.
- addROI(Client, ROIWrapper) - Method in class fr.igred.omero.repository.FolderWrapper
-
Deprecated.Adds an ROI to the folder and associate it to the image id set(an image need to be associated)
- addROIs(Client, long, ROIWrapper...) - Method in class fr.igred.omero.repository.FolderWrapper
-
Adds ROIs to the folder and associate them to the provided image ID.
- addROIs(Client, ImageWrapper, ROIWrapper...) - Method in class fr.igred.omero.repository.FolderWrapper
-
Adds ROIs to the folder and associate them to the provided image.
- addRow(Object...) - Method in class fr.igred.omero.annotations.TableWrapper
-
Adds a row to the table.
- addRows(Client, ResultsTable, Long, List<? extends Roi>) - Method in class fr.igred.omero.annotations.TableWrapper
-
Adds rows from an ImageJ
ResultsTable
. - addRows(Client, ResultsTable, Long, List<? extends Roi>, String) - Method in class fr.igred.omero.annotations.TableWrapper
-
Adds rows from an ImageJ
ResultsTable
. - addShape(GenericShapeWrapper<?>) - Method in class fr.igred.omero.roi.ROIWrapper
-
Adds a ShapeData from a GenericShapeWrapper to the ROIData
- addShapes(List<? extends GenericShapeWrapper<?>>) - Method in class fr.igred.omero.roi.ROIWrapper
-
Adds ShapeData objects from a list of GenericShapeWrapper to the ROIData
- addTable(Client, TableWrapper) - Method in class fr.igred.omero.AnnotatableWrapper
-
Adds a table to the object in OMERO.
- addTag(Client, TagAnnotationWrapper) - Method in class fr.igred.omero.AnnotatableWrapper
-
Deprecated.Adds a tag to the object in OMERO, if possible. Use
AnnotatableWrapper.link(fr.igred.omero.Client, A)
instead. - addTag(Client, Long) - Method in class fr.igred.omero.AnnotatableWrapper
-
Adds a tag to the object in OMERO, if possible.
- addTag(Client, String, String) - Method in class fr.igred.omero.AnnotatableWrapper
-
Adds a newly created tag to the object in OMERO, if possible.
- addTags(Client, TagAnnotationWrapper...) - Method in class fr.igred.omero.AnnotatableWrapper
-
Deprecated.Adds multiple tag to the object in OMERO, if possible. Use
AnnotatableWrapper.link(Client, GenericAnnotationWrapper[])
instead. - addTags(Client, Long...) - Method in class fr.igred.omero.AnnotatableWrapper
-
Adds multiple tags by ID to the object in OMERO, if possible.
- AnnotatableWrapper<T extends DataObject> - Class in fr.igred.omero
-
Generic class containing a DataObject (or a subclass) object.
- AnnotatableWrapper(T) - Constructor for class fr.igred.omero.AnnotatableWrapper
-
Constructor of the class GenericRepositoryObjectWrapper.
- ANNOTATION_LINK - Static variable in class fr.igred.omero.repository.DatasetWrapper
-
Annotation link name for this type of object
- ANNOTATION_LINK - Static variable in class fr.igred.omero.repository.FolderWrapper
-
Annotation link name for this type of object
- ANNOTATION_LINK - Static variable in class fr.igred.omero.repository.ImageWrapper
-
Annotation link name for this type of object
- ANNOTATION_LINK - Static variable in class fr.igred.omero.repository.PlateAcquisitionWrapper
-
Annotation link name for this type of object
- ANNOTATION_LINK - Static variable in class fr.igred.omero.repository.PlateWrapper
-
Annotation link name for this type of object
- ANNOTATION_LINK - Static variable in class fr.igred.omero.repository.ProjectWrapper
-
Annotation link name for this type of object
- ANNOTATION_LINK - Static variable in class fr.igred.omero.repository.ScreenWrapper
-
Annotation link name for this type of object
- ANNOTATION_LINK - Static variable in class fr.igred.omero.repository.WellWrapper
-
Annotation link name for this type of object
- ANNOTATION_LINK - Static variable in class fr.igred.omero.roi.GenericShapeWrapper
-
Annotation link name for this type of object
- ANNOTATION_LINK - Static variable in class fr.igred.omero.roi.ROIWrapper
-
Annotation link name for this type of object
- annotationLinkType() - Method in class fr.igred.omero.AnnotatableWrapper
-
Returns the type of annotation link for this object.
- annotationLinkType() - Method in class fr.igred.omero.repository.DatasetWrapper
-
Returns the type of annotation link for this object.
- annotationLinkType() - Method in class fr.igred.omero.repository.FolderWrapper
-
Returns the type of annotation link for this object.
- annotationLinkType() - Method in class fr.igred.omero.repository.ImageWrapper
-
Returns the type of annotation link for this object.
- annotationLinkType() - Method in class fr.igred.omero.repository.PlateAcquisitionWrapper
-
Returns the type of annotation link for this object.
- annotationLinkType() - Method in class fr.igred.omero.repository.PlateWrapper
-
Returns the type of annotation link for this object.
- annotationLinkType() - Method in class fr.igred.omero.repository.ProjectWrapper
-
Returns the type of annotation link for this object.
- annotationLinkType() - Method in class fr.igred.omero.repository.ScreenWrapper
-
Returns the type of annotation link for this object.
- annotationLinkType() - Method in class fr.igred.omero.repository.WellWrapper
-
Returns the type of annotation link for this object.
- annotationLinkType() - Method in class fr.igred.omero.roi.GenericShapeWrapper
-
Returns the type of annotation link for this object.
- annotationLinkType() - Method in class fr.igred.omero.roi.ROIWrapper
-
Returns the type of annotation link for this object.
- AnnotationList - Class in fr.igred.omero.annotations
-
List of GenericAnnotationWrapper objects
- AnnotationList() - Constructor for class fr.igred.omero.annotations.AnnotationList
-
Constructs an empty list with an initial capacity of ten.
- AnnotationList(int) - Constructor for class fr.igred.omero.annotations.AnnotationList
-
Constructs an empty list with the specified initial capacity.
- apply(String, T) - Method in interface fr.igred.omero.exception.ExceptionHandler.ExceptionWrapper
- apply(T) - Method in interface fr.igred.omero.exception.ExceptionHandler.ThrowingConsumer
- apply(T) - Method in interface fr.igred.omero.exception.ExceptionHandler.ThrowingFunction
- areRequirementsAvailable() - Static method in class fr.igred.omero.util.LibraryChecker
-
Checks if the required libraries are available.
- ARROW - Static variable in class fr.igred.omero.roi.LineWrapper
-
String to use arrows as markers
- asChannelData() - Method in class fr.igred.omero.repository.ChannelWrapper
-
Deprecated.Returns the ChannelData contained. Use
GenericObjectWrapper.asDataObject()
instead. - asDataObject() - Method in class fr.igred.omero.GenericObjectWrapper
-
Returns the wrapped DataObject.
- asDatasetData() - Method in class fr.igred.omero.repository.DatasetWrapper
-
Deprecated.Returns the DatasetData contained. Use
GenericObjectWrapper.asDataObject()
instead. - asExperimenterData() - Method in class fr.igred.omero.meta.ExperimenterWrapper
-
Deprecated.Returns the ExperimenterData contained. Use
GenericObjectWrapper.asDataObject()
instead. - asFileAnnotationData() - Method in class fr.igred.omero.annotations.FileAnnotationWrapper
-
Deprecated.Gets the FileAnnotationData contained.
- asFolderData() - Method in class fr.igred.omero.repository.FolderWrapper
-
Deprecated.Gets the folder contained in the FolderWrapper. Use
GenericObjectWrapper.asDataObject()
instead. - asGroupData() - Method in class fr.igred.omero.meta.GroupWrapper
-
Deprecated.Returns the GroupData contained. Use
GenericObjectWrapper.asDataObject()
instead. - asImageData() - Method in class fr.igred.omero.repository.ImageWrapper
-
Deprecated.Returns the ImageData contained. Use
GenericObjectWrapper.asDataObject()
instead. - asMapAnnotationData() - Method in class fr.igred.omero.annotations.MapAnnotationWrapper
-
Deprecated.Gets the MapAnnotationData contained. Use
GenericObjectWrapper.asDataObject()
instead. - asPlaneInfoData() - Method in class fr.igred.omero.meta.PlaneInfoWrapper
-
Deprecated.Returns the PlaneInfoData contained. Use
GenericObjectWrapper.asDataObject()
instead. - asPlateAcquisitionData() - Method in class fr.igred.omero.repository.PlateAcquisitionWrapper
-
Deprecated.Returns the PlateAcquisitionData contained. Use
GenericObjectWrapper.asDataObject()
instead. - asPlateData() - Method in class fr.igred.omero.repository.PlateWrapper
-
Deprecated.Returns the PlateData contained. Use
GenericObjectWrapper.asDataObject()
instead. - asProjectData() - Method in class fr.igred.omero.repository.ProjectWrapper
-
Deprecated.Returns the ProjectData contained. Use
GenericObjectWrapper.asDataObject()
instead. - asROIData() - Method in class fr.igred.omero.roi.ROIWrapper
-
Deprecated.Returns the ROIData contained. Use
GenericObjectWrapper.asDataObject()
instead. - asScreenData() - Method in class fr.igred.omero.repository.ScreenWrapper
-
Deprecated.Returns the ScreenData contained. Use
GenericObjectWrapper.asDataObject()
instead. - asShapeData() - Method in class fr.igred.omero.roi.GenericShapeWrapper
-
Deprecated.Gets the ShapeData object contained.
- asTagAnnotationData() - Method in class fr.igred.omero.annotations.TagAnnotationWrapper
-
Deprecated.Gets the TagAnnotationData contained. Use
GenericObjectWrapper.asDataObject()
instead. - asWellData() - Method in class fr.igred.omero.repository.WellWrapper
-
Deprecated.Returns the WellData contained. Use
GenericObjectWrapper.asDataObject()
instead. - asWellSampleData() - Method in class fr.igred.omero.repository.WellSampleWrapper
-
Deprecated.Returns the WellSampleData contained. Use
GenericObjectWrapper.asDataObject()
instead.
B
- Bounds(PixelsWrapper.Coordinates, PixelsWrapper.Coordinates) - Constructor for class fr.igred.omero.repository.PixelsWrapper.Bounds
-
Bounds constructor.
- Browser - Class in fr.igred.omero
-
Abstract class to browse data on an OMERO server in a given
SecurityContext
and wrap DataObjects. - Browser(Gateway, SecurityContext, ExperimenterWrapper) - Constructor for class fr.igred.omero.Browser
-
Constructor of the Browser class.
C
- canAnnotate() - Method in class fr.igred.omero.GenericObjectWrapper
-
Returns
true
if the object can be annotatedfalse
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 infalse
otherwise, depending on permissions level. - canLink() - Method in class fr.igred.omero.GenericObjectWrapper
-
Returns
true
if the object can be linked e.g. - ChannelWrapper - Class in fr.igred.omero.repository
-
Class containing a ChannelData object.
- ChannelWrapper(ChannelData) - Constructor for class fr.igred.omero.repository.ChannelWrapper
-
Constructor of the class ChannelWrapper.
- checkClass(String) - Static method in class fr.igred.omero.util.LibraryChecker
-
Checks whether the given class is available.
- checkProperty(String) - Static method in class fr.igred.omero.roi.ROIWrapper
-
Checks the provided property.
- Client - Class in fr.igred.omero
-
Basic class, contains the gateway, the security context, and multiple facilities.
- Client() - Constructor for class fr.igred.omero.Client
-
Constructor of the Client class.
- Client(Gateway, SecurityContext, ExperimenterWrapper) - Constructor for class fr.igred.omero.Client
-
Constructor of the Client class.
- closeImport() - Method in class fr.igred.omero.GatewayWrapper
-
Closes the import store.
- computeMeanExposureTime(Iterable<? extends PlaneInfoWrapper>, int) - Static method in class fr.igred.omero.meta.PlaneInfoWrapper
-
Computes the mean exposure time for a given channel in a PlaneInfoWrapper collection.
- computeMeanTimeInterval(Collection<? extends PlaneInfoWrapper>, int) - Static method in class fr.igred.omero.meta.PlaneInfoWrapper
-
Computes the mean time interval from the deltaT in a PlaneInfoWrapper collection.
- connect(String, int, String) - Method in class fr.igred.omero.GatewayWrapper
-
Connects to OMERO using a session ID.
- connect(String, int, String, char[]) - Method in class fr.igred.omero.GatewayWrapper
-
Connects the user to OMERO.
- connect(String, int, String, char[], Long) - Method in class fr.igred.omero.GatewayWrapper
-
Connects the user to OMERO.
- connect(LoginCredentials) - Method in class fr.igred.omero.GatewayWrapper
-
Connects the user to OMERO.
- Coordinates(int, int, int, int, int) - Constructor for class fr.igred.omero.repository.PixelsWrapper.Coordinates
-
Coordinates constructor.
- copyAnnotationLinks(Client, AnnotatableWrapper<?>) - Method in class fr.igred.omero.AnnotatableWrapper
-
Copies annotation links from some other object to this one.
- copyAnnotationLinks(Client, GenericRepositoryObjectWrapper<?>) - Method in class fr.igred.omero.repository.GenericRepositoryObjectWrapper
-
Copies annotation links from some other object to this one.
- copyFromIJRoi(Roi) - Method in class fr.igred.omero.roi.GenericShapeWrapper
-
Copies details from an ImageJ ROI (position, stroke color, stroke width).
- copyToIJRoi(Roi) - Method in class fr.igred.omero.roi.GenericShapeWrapper
-
Copies details to an ImageJ ROI (name, position, stroke color, fill color, stroke width).
- countAnnotationLinks(Client) - Method in class fr.igred.omero.annotations.GenericAnnotationWrapper
-
Returns the number of annotations links for this object.
- createTable() - Method in class fr.igred.omero.annotations.TableWrapper
-
Creates the corresponding TableData object.
- createTransformedAWTShape() - Method in class fr.igred.omero.roi.GenericShapeWrapper
-
Returns a new
Shape
defined by the geometry of the specified Shape after it has been transformed by the transform.
D
- data - Variable in class fr.igred.omero.GenericObjectWrapper
-
Wrapped object
- DatasetWrapper - Class in fr.igred.omero.repository
-
Class containing a DatasetData object.
- DatasetWrapper(String, String) - Constructor for class fr.igred.omero.repository.DatasetWrapper
-
Constructor of the DatasetWrapper class
- DatasetWrapper(DatasetData) - Constructor for class fr.igred.omero.repository.DatasetWrapper
-
Constructor of the DatasetWrapper class
- delete(TableWrapper) - Method in class fr.igred.omero.Client
-
Deprecated.Deletes a table from OMERO.
- delete(Client, IObject) - Static method in class fr.igred.omero.GenericObjectWrapper
-
Deletes an object from OMERO.
- delete(GenericObjectWrapper<?>) - Method in class fr.igred.omero.Client
-
Deletes an object from OMERO.
- delete(Collection<? extends GenericObjectWrapper<?>>) - Method in class fr.igred.omero.Client
-
Deletes multiple objects from OMERO.
- DELETE - fr.igred.omero.repository.GenericRepositoryObjectWrapper.ReplacePolicy
-
Delete all objects
- DELETE_ORPHANED - fr.igred.omero.repository.GenericRepositoryObjectWrapper.ReplacePolicy
-
Delete orphaned objects
- deleteFile(Long) - Method in class fr.igred.omero.GatewayWrapper
-
Deletes a file from OMERO
- deleteFiles(Long...) - Method in class fr.igred.omero.GatewayWrapper
-
Deletes files from OMERO.
- deleteShape(int) - Method in class fr.igred.omero.roi.ROIWrapper
-
Deletes a shape from the ROI.
- deleteShape(ShapeData) - Method in class fr.igred.omero.roi.ROIWrapper
-
Deletes a ShapeData from the ROI.
- deleteTable(TableWrapper) - Method in class fr.igred.omero.Client
-
Deletes a table from OMERO.
- deleteTables(Collection<? extends TableWrapper>) - Method in class fr.igred.omero.Client
-
Deletes tables from OMERO.
- disconnect() - Method in class fr.igred.omero.GatewayWrapper
-
Disconnects the user
- distinct(Collection<? extends T>) - Static method in class fr.igred.omero.GenericObjectWrapper
-
Only keeps objects with different IDs in a collection.
- download(Client, String) - Method in class fr.igred.omero.repository.ImageWrapper
-
Downloads the original files from the server.
E
- EllipseWrapper - Class in fr.igred.omero.roi
-
Class containing an EllipseData.
- EllipseWrapper() - Constructor for class fr.igred.omero.roi.EllipseWrapper
-
Constructor of the EllipseWrapper class using a new empty EllipseData.
- EllipseWrapper(double, double, double, double) - Constructor for class fr.igred.omero.roi.EllipseWrapper
-
Constructor of the EllipseWrapper class using a new EllipseData.
- EllipseWrapper(Roi) - Constructor for class fr.igred.omero.roi.EllipseWrapper
-
Constructor of the EllipseWrapper class using bounds from an ImageJ ROI.
- EllipseWrapper(EllipseData) - Constructor for class fr.igred.omero.roi.EllipseWrapper
-
Constructor of the EllipseWrapper class using a EllipseData.
- ExceptionHandler<T> - Class in fr.igred.omero.exception
-
Class to handle and convert OMERO exceptions.
- ExceptionHandler(T, Exception) - Constructor for class fr.igred.omero.exception.ExceptionHandler
-
Private class constructor.
- ExceptionHandler.ExceptionWrapper<T,E extends Throwable> - Interface in fr.igred.omero.exception
- ExceptionHandler.ThrowingConsumer<T,E extends Throwable> - Interface in fr.igred.omero.exception
- ExceptionHandler.ThrowingFunction<T,R,E extends Throwable> - Interface in fr.igred.omero.exception
- ExperimenterWrapper - Class in fr.igred.omero.meta
-
Class containing an ExperimenterData object.
- ExperimenterWrapper(ExperimenterData) - Constructor for class fr.igred.omero.meta.ExperimenterWrapper
-
Constructor of the class ExperimenterWrapper.
F
- FileAnnotationWrapper - Class in fr.igred.omero.annotations
-
Class containing a FileAnnotationData object.
- FileAnnotationWrapper(FileAnnotationData) - Constructor for class fr.igred.omero.annotations.FileAnnotationWrapper
-
Constructor of the GenericAnnotationWrapper class.
- findByQuery(String) - Method in class fr.igred.omero.GatewayWrapper
-
Finds objects on OMERO through a database query.
- flatten(Collection<? extends Collection<? extends U>>) - Static method in class fr.igred.omero.GenericObjectWrapper
-
Flattens a collection of collections and only keeps objects with different IDs.
- FolderWrapper - Class in fr.igred.omero.repository
-
Class containing a FolderData object.
- FolderWrapper(Client, String) - Constructor for class fr.igred.omero.repository.FolderWrapper
-
Constructor of the FolderWrapper class.
- FolderWrapper(FolderData) - Constructor for class fr.igred.omero.repository.FolderWrapper
-
Constructor of the FolderWrapper class.
- FolderWrapper(Folder) - Constructor for class fr.igred.omero.repository.FolderWrapper
-
Constructor of the FolderWrapper class.
- fr.igred.omero - package fr.igred.omero
-
This package contains abstract wrapper classes for the OMERO Gateway and the basic OMERO object.
- fr.igred.omero.annotations - package fr.igred.omero.annotations
-
This package contains wrapper classes for annotations.
- fr.igred.omero.exception - package fr.igred.omero.exception
-
This package contains wrapper classes for exceptions and an exception handler.
- fr.igred.omero.meta - package fr.igred.omero.meta
-
This package contains wrapper classes for users, groups and planes information.
- fr.igred.omero.repository - package fr.igred.omero.repository
-
This package contains classes related to the hierarchical organization for images.
- fr.igred.omero.roi - package fr.igred.omero.roi
-
This package contains wrapper classes for OMERO shapes and ROIs.
- fr.igred.omero.util - package fr.igred.omero.util
-
This package contains a utility class used to check if the library requirements are available.
- fromImageJ(List<? extends Roi>) - Static method in class fr.igred.omero.roi.ROIWrapper
-
Converts an ImageJ list of ROIs to a list of OMERO ROIs
- fromImageJ(List<? extends Roi>, String) - Static method in class fr.igred.omero.roi.ROIWrapper
-
Converts an ImageJ list of ROIs to a list of OMERO ROIs
G
- GatewayWrapper - Class in fr.igred.omero
-
Basic class, contains the gateway, the security context, and multiple facilities.
- GatewayWrapper(Gateway, SecurityContext, ExperimenterWrapper) - Constructor for class fr.igred.omero.GatewayWrapper
-
Abstract constructor of the GatewayWrapper class.
- GenericAnnotationWrapper<T extends AnnotationData> - Class in fr.igred.omero.annotations
-
Generic class containing an AnnotationData (or a subclass) object.
- GenericAnnotationWrapper(T) - Constructor for class fr.igred.omero.annotations.GenericAnnotationWrapper
-
Constructor of the GenericAnnotationWrapper class.
- GenericObjectWrapper<T extends DataObject> - Class in fr.igred.omero
-
Generic class containing a DataObject (or a subclass) object.
- GenericObjectWrapper(T) - Constructor for class fr.igred.omero.GenericObjectWrapper
-
Constructor of the class GenericObjectWrapper.
- GenericRepositoryObjectWrapper<T extends DataObject> - Class in fr.igred.omero.repository
-
Generic class containing a DataObject (or a subclass) object.
- GenericRepositoryObjectWrapper(T) - Constructor for class fr.igred.omero.repository.GenericRepositoryObjectWrapper
-
Constructor of the class GenericRepositoryObjectWrapper.
- GenericRepositoryObjectWrapper.ReplacePolicy - Enum in fr.igred.omero.repository
-
Policy to specify how to handle objects when they are replaced.
- GenericShapeWrapper<T extends ShapeData> - Class in fr.igred.omero.roi
-
Generic class containing a ShapeData (or a subclass) object.
- GenericShapeWrapper(T) - Constructor for class fr.igred.omero.roi.GenericShapeWrapper
-
Constructor of the GenericShapeWrapper class using a ShapeData.
- get() - Method in class fr.igred.omero.exception.ExceptionHandler
-
Returns the contained object.
- getAcquisitionDate() - Method in class fr.igred.omero.repository.ImageWrapper
-
Gets the ImageData acquisition date
- getAdminFacility() - Method in class fr.igred.omero.GatewayWrapper
-
Gets the
AdminFacility
to use admin specific function. - getAllPixels(Client) - Method in class fr.igred.omero.repository.PixelsWrapper
-
Returns an array containing the value for each voxel
- getAllPixels(Client, int[], int[], int[], int[], int[]) - Method in class fr.igred.omero.repository.PixelsWrapper
-
Returns an array containing the value for each voxel corresponding to the bounds
- getAlpha() - Method in class fr.igred.omero.repository.ChannelWrapper
-
Gets the sRGB alpha value of the channel.
- getAlpha() - Method in class fr.igred.omero.repository.WellWrapper
-
Returns the alpha component of the color associated to the well, or
-1
. - getAnnotations(Client) - Method in class fr.igred.omero.AnnotatableWrapper
-
Retrieves annotations linked to the object (of known types).
- getAttachedFile() - Method in class fr.igred.omero.annotations.FileAnnotationWrapper
-
Returns the file to upload to the server.
- getBlue() - Method in class fr.igred.omero.repository.ChannelWrapper
-
Gets the sRGB blue value of the channel.
- getBlue() - Method in class fr.igred.omero.repository.WellWrapper
-
Returns the blue component of the color associated to the well, or
-1
. - getBoundingBox() - Method in class fr.igred.omero.roi.GenericShapeWrapper
-
Returns a new
RectangleWrapper
corresponding to the bounding box of the shape, once the relatedAffineTransform
has been applied. - getBounds() - Method in class fr.igred.omero.roi.ROIWrapper
-
Returns the 5D bounds containing the ROI.
- getBrowseFacility() - Method in class fr.igred.omero.GatewayWrapper
-
Gets the
BrowseFacility
used to access the data from OMERO. - getC() - Method in class fr.igred.omero.repository.PixelsWrapper.Coordinates
-
Gets C coordinate.
- getC() - Method in class fr.igred.omero.roi.GenericShapeWrapper
-
Gets the channel.
- getChannelColor(Client, int) - Method in class fr.igred.omero.repository.ImageWrapper
-
Gets the current color of the channel
- getChannelImportedColor(Client, int) - Method in class fr.igred.omero.repository.ImageWrapper
-
Gets the original color of the channel
- getChannelLabeling() - Method in class fr.igred.omero.repository.ChannelWrapper
-
Returns the label of the channel.
- getChannelName(Client, int) - Method in class fr.igred.omero.repository.ImageWrapper
-
Gets the name of the channel.
- getChannels(Client) - Method in class fr.igred.omero.repository.ImageWrapper
-
Gets the image channels.
- getChildren() - Method in class fr.igred.omero.repository.FolderWrapper
-
Retrieves the children folders for this folder.
- getColor() - Method in class fr.igred.omero.repository.ChannelWrapper
-
Gets the original channel color.
- getColumn() - Method in class fr.igred.omero.repository.WellWrapper
-
Returns the column used to indicate the location of the well on the grid.
- getColumnCount() - Method in class fr.igred.omero.annotations.TableWrapper
-
Returns the number of columns in the table.
- getColumnName(int) - Method in class fr.igred.omero.annotations.TableWrapper
-
Returns the name of the column.
- getColumns() - Method in class fr.igred.omero.annotations.TableWrapper
-
Gets the
TableDataColumn
which contains information on each column of the table - getColumnSequenceIndex() - Method in class fr.igred.omero.repository.PlateWrapper
-
Returns the index indicating how to label a column.
- getColumnType(int) - Method in class fr.igred.omero.annotations.TableWrapper
-
Returns the type of the column.
- getContent() - Method in class fr.igred.omero.annotations.MapAnnotationWrapper
-
Gets the List of NamedValue contained in the map annotation.
- getContentAsString() - Method in class fr.igred.omero.annotations.FileAnnotationWrapper
-
Returns the absolute path to the file
- getCoordinates() - Method in class fr.igred.omero.roi.EllipseWrapper
-
Gets the coordinates of the MaskData shape.
- getCoordinates() - Method in class fr.igred.omero.roi.LineWrapper
-
Gets the coordinates of the LineData shape.
- getCoordinates() - Method in class fr.igred.omero.roi.MaskWrapper
-
Gets the coordinates of the MaskData shape.
- getCoordinates() - Method in class fr.igred.omero.roi.PointWrapper
-
Gets the coordinates of the PointData shape.
- getCoordinates() - Method in class fr.igred.omero.roi.RectangleWrapper
-
Gets the coordinates of the RectangleData shape.
- getCoordinates() - Method in class fr.igred.omero.roi.TextWrapper
-
Gets the coordinates of the TextData shape.
- getCreated() - Method in class fr.igred.omero.GenericObjectWrapper
-
Gets the object creation date
- getCtx() - Method in class fr.igred.omero.GatewayWrapper
-
Contains the permissions of the user in the group.
- getCurrentGroupId() - Method in class fr.igred.omero.GatewayWrapper
-
Gets the current group ID.
- getData() - Method in class fr.igred.omero.annotations.TableWrapper
-
Gets the value contained in the table
- getData(int, int) - Method in class fr.igred.omero.annotations.TableWrapper
-
Gets a certain value of the table
- getDataset(Long) - Method in class fr.igred.omero.Browser
-
Gets the dataset with the specified id from OMERO.
- getDatasets() - Method in class fr.igred.omero.Browser
-
Gets all datasets available from OMERO.
- getDatasets() - Method in class fr.igred.omero.repository.ProjectWrapper
-
Gets all the datasets in the project available from OMERO.
- getDatasets(Client) - Method in class fr.igred.omero.annotations.GenericAnnotationWrapper
-
Gets all datasets with this annotation from OMERO.
- getDatasets(Client) - Method in class fr.igred.omero.repository.ImageWrapper
-
Retrieves the datasets containing this image
- getDatasets(ExperimenterWrapper) - Method in class fr.igred.omero.Browser
-
Gets all datasets available from OMERO owned by a given user.
- getDatasets(Long...) - Method in class fr.igred.omero.Browser
-
Gets the datasets with the specified ids from OMERO.
- getDatasets(String) - Method in class fr.igred.omero.Browser
-
Gets all datasets with a certain name from OMERO.
- getDatasets(String) - Method in class fr.igred.omero.repository.ProjectWrapper
-
Gets the dataset with the specified name from OMERO
- getDefaultGroup() - Method in class fr.igred.omero.meta.ExperimenterWrapper
-
Returns the default Group for this Experimenter
- getDefaultSample() - Method in class fr.igred.omero.repository.PlateWrapper
-
Returns the currently selected field or
0
. - getDeltaT() - Method in class fr.igred.omero.meta.PlaneInfoWrapper
-
Retrieves the plane deltaT.
- getDescription() - Method in class fr.igred.omero.annotations.GenericAnnotationWrapper
-
Retrieves the
description
of the underlyingAnnotationData
instance. - getDescription() - Method in class fr.igred.omero.meta.GroupWrapper
-
Returns the description of the group.
- getDescription() - Method in class fr.igred.omero.repository.DatasetWrapper
-
Gets the DatasetData description
- getDescription() - Method in class fr.igred.omero.repository.FolderWrapper
-
Gets the folder description
- getDescription() - Method in class fr.igred.omero.repository.GenericRepositoryObjectWrapper
-
Gets the object description
- getDescription() - Method in class fr.igred.omero.repository.ImageWrapper
-
Gets the ImageData description
- getDescription() - Method in class fr.igred.omero.repository.PlateAcquisitionWrapper
-
Gets the plate acquisition description
- getDescription() - Method in class fr.igred.omero.repository.PlateWrapper
-
Gets the plate description
- getDescription() - Method in class fr.igred.omero.repository.ProjectWrapper
-
Gets the project description
- getDescription() - Method in class fr.igred.omero.repository.ScreenWrapper
-
Gets the screen description
- getDescription() - Method in class fr.igred.omero.repository.WellWrapper
-
Gets the object description
- getDm() - Method in class fr.igred.omero.GatewayWrapper
-
Gets the
DataManagerFacility
to handle/write data on OMERO. - getElementsOf(Class<? extends T>) - Method in class fr.igred.omero.annotations.AnnotationList
-
Gets a list of elements from this list whose class is specified.
- getElementsOf(Class<? extends T>) - Method in class fr.igred.omero.roi.ShapeList
-
Gets a list of elements from this list whose class is specified.
- getEmail() - Method in class fr.igred.omero.meta.ExperimenterWrapper
-
Returns the e-mail of the experimenter.
- getEnd() - Method in class fr.igred.omero.repository.PixelsWrapper.Bounds
-
Gets size of bounds for each coordinate.
- getEndTime() - Method in class fr.igred.omero.repository.PlateAcquisitionWrapper
-
Returns the time when the last image was collected.
- getExperimenters() - Method in class fr.igred.omero.meta.GroupWrapper
-
Returns the experimenters contained in this group.
- getExposureTime() - Method in class fr.igred.omero.meta.PlaneInfoWrapper
-
Retrieves the exposure time.
- getExternalIdentifier() - Method in class fr.igred.omero.repository.PlateWrapper
-
Returns the external identifier of the plate.
- getFile(Client, String) - Method in class fr.igred.omero.annotations.FileAnnotationWrapper
-
Returns the original file.
- getFileAnnotations(Client) - Method in class fr.igred.omero.AnnotatableWrapper
-
Returns the file annotations
- getFileFormat() - Method in class fr.igred.omero.annotations.FileAnnotationWrapper
-
Returns the format of the uploaded file.
- getFileId() - Method in class fr.igred.omero.annotations.TableWrapper
-
Returns the fileId of the table.
- getFileID() - Method in class fr.igred.omero.annotations.FileAnnotationWrapper
-
Returns the ID of the file.
- getFileKind() - Method in class fr.igred.omero.annotations.FileAnnotationWrapper
-
Returns a user readable description of the file.
- getFileName() - Method in class fr.igred.omero.annotations.FileAnnotationWrapper
-
Returns the name of the file.
- getFilePath() - Method in class fr.igred.omero.annotations.FileAnnotationWrapper
-
Returns the absolute path to the file.
- getFilesetImages(Client) - Method in class fr.igred.omero.repository.ImageWrapper
-
Returns the list of images sharing the same fileset as the current image.
- getFileSize() - Method in class fr.igred.omero.annotations.FileAnnotationWrapper
-
Returns the size of the file.
- getFill() - Method in class fr.igred.omero.roi.GenericShapeWrapper
-
Gets ShapeData fill color.
- getFirstName() - Method in class fr.igred.omero.meta.ExperimenterWrapper
-
Returns the first name of the experimenter.
- getFolder(long) - Method in class fr.igred.omero.Browser
-
Gets the folder with the specified ID from OMERO, fully loaded.
- getFolder(Client, Long) - Method in class fr.igred.omero.repository.ImageWrapper
-
Deprecated.Gets the folder with the specified id on OMERO.
- getFolders() - Method in class fr.igred.omero.Browser
-
Gets all folders available from OMERO.
- getFolders(Client) - Method in class fr.igred.omero.annotations.GenericAnnotationWrapper
-
Gets all folders with this annotation from OMERO.
- getFolders(Client) - Method in class fr.igred.omero.repository.ImageWrapper
-
Gets the list of folders linked to this image.
- getFolders(ExperimenterWrapper) - Method in class fr.igred.omero.Browser
-
Gets all the folders owned by a given user from OMERO.
- getFontSize() - Method in class fr.igred.omero.roi.GenericShapeWrapper
-
Gets ShapeData font size.
- getGateway() - Method in class fr.igred.omero.GatewayWrapper
-
Returns the Gateway.
- getGreen() - Method in class fr.igred.omero.repository.ChannelWrapper
-
Gets the sRGB green value of the channel.
- getGreen() - Method in class fr.igred.omero.repository.WellWrapper
-
Returns the green component of the color associated to the well, or
-1
. - getGroup(String) - Method in class fr.igred.omero.Client
-
Returns the group which matches the name.
- getGroupId() - Method in class fr.igred.omero.GenericObjectWrapper
-
Gets the group ID
- getGroups() - Method in class fr.igred.omero.meta.ExperimenterWrapper
-
Returns the groups the experimenter is a member of.
- getHeight() - Method in class fr.igred.omero.roi.MaskWrapper
-
Returns the height of the mask.
- getHeight() - Method in class fr.igred.omero.roi.RectangleWrapper
-
Returns the height untransformed rectangle.
- getId() - Method in class fr.igred.omero.annotations.TableWrapper
-
Returns the table ID.
- getId() - Method in class fr.igred.omero.GatewayWrapper
-
Gets the user id.
- getId() - Method in class fr.igred.omero.GenericObjectWrapper
-
Gets the object id
- getImage() - Method in class fr.igred.omero.repository.WellSampleWrapper
-
Returns the image related to that sample if any.
- getImage(Long) - Method in class fr.igred.omero.Browser
-
Returns the image with the specified ID from OMERO.
- getImages() - Method in class fr.igred.omero.Browser
-
Gets all images owned by the current user.
- getImages() - Method in class fr.igred.omero.repository.FolderWrapper
-
Retrieves the images contained in this folder.
- getImages() - Method in class fr.igred.omero.repository.WellWrapper
-
Retrieves the images contained in this well.
- getImages(GenericAnnotationWrapper<?>) - Method in class fr.igred.omero.Browser
-
Gets all images with the specified annotation from OMERO.
- getImages(GenericAnnotationWrapper<?>) - Method in class fr.igred.omero.Client
-
Gets all images with the specified annotation from OMERO.
- getImages(Client) - Method in class fr.igred.omero.annotations.GenericAnnotationWrapper
-
Gets all images with this annotation from OMERO.
- getImages(Client) - Method in class fr.igred.omero.repository.DatasetWrapper
-
Gets all images in the dataset available from OMERO.
- getImages(Client) - Method in class fr.igred.omero.repository.FolderWrapper
-
Retrieves the images contained in this folder.
- getImages(Client) - Method in class fr.igred.omero.repository.PlateAcquisitionWrapper
-
Retrieves the images contained in the wells in the parent plate.
- getImages(Client) - Method in class fr.igred.omero.repository.PlateWrapper
-
Returns the images contained in the wells of this plate.
- getImages(Client) - Method in class fr.igred.omero.repository.ProjectWrapper
-
Gets all images in the project available from OMERO.
- getImages(Client) - Method in class fr.igred.omero.repository.ScreenWrapper
-
Retrieves the images contained in this screen.
- getImages(Client, String) - Method in class fr.igred.omero.repository.DatasetWrapper
-
Gets all images in the dataset with a certain name from OMERO.
- getImages(Client, String) - Method in class fr.igred.omero.repository.ProjectWrapper
-
Gets all images in the project with a certain name from OMERO.
- getImages(Client, String, String) - Method in class fr.igred.omero.repository.ProjectWrapper
-
Gets all images with a certain name from datasets with the specified name inside this project on OMERO.
- getImages(Long...) - Method in class fr.igred.omero.Browser
-
Gets the images with the specified ids from OMERO
- getImages(String) - Method in class fr.igred.omero.Browser
-
Gets all images with a certain name from OMERO.
- getImages(String, String, String) - Method in class fr.igred.omero.Browser
-
Gets all images with the name specified inside projects and datasets with the given names.
- getImages(String, String, String) - Method in class fr.igred.omero.Client
-
Gets all images with the name specified inside projects and datasets with the given names.
- getImagesKey(Client, String) - Method in class fr.igred.omero.repository.DatasetWrapper
-
Deprecated.Gets all images in the dataset with a certain key
- getImagesKey(Client, String) - Method in class fr.igred.omero.repository.ProjectWrapper
-
Deprecated.Gets all images in the project with a certain key
- getImagesKey(String) - Method in class fr.igred.omero.Browser
-
Deprecated.Gets all images with a certain key
- getImagesKey(String) - Method in class fr.igred.omero.Client
-
Deprecated.Gets all images with a certain key
- getImagesLike(Client, String) - Method in class fr.igred.omero.repository.DatasetWrapper
-
Gets all images in the dataset with a certain motif in their name from OMERO.
- getImagesLike(Client, String) - Method in class fr.igred.omero.repository.ProjectWrapper
-
Gets all images in the project with a certain motif in their name from OMERO.
- getImagesLike(String) - Method in class fr.igred.omero.Browser
-
Gets all images with a certain motif in their name from OMERO.
- getImagesPairKeyValue(Client, String, String) - Method in class fr.igred.omero.repository.DatasetWrapper
-
Deprecated.Gets all images in the dataset with a certain key value pair from OMERO
- getImagesPairKeyValue(Client, String, String) - Method in class fr.igred.omero.repository.ProjectWrapper
-
Deprecated.Gets all images in the project with a certain key value pair from OMERO.
- getImagesPairKeyValue(String, String) - Method in class fr.igred.omero.Browser
-
Deprecated.Gets all images with a certain key value pair from OMERO
- getImagesPairKeyValue(String, String) - Method in class fr.igred.omero.Client
-
Deprecated.Gets all images with a certain key value pair from OMERO
- getImagesTagged(TagAnnotationWrapper) - Method in class fr.igred.omero.Browser
-
Deprecated.Gets all images tagged with a specified tag from OMERO.
- getImagesTagged(Client, TagAnnotationWrapper) - Method in class fr.igred.omero.repository.DatasetWrapper
-
Gets all images in the dataset tagged with a specified tag from OMERO.
- getImagesTagged(Client, TagAnnotationWrapper) - Method in class fr.igred.omero.repository.ProjectWrapper
-
Gets all images in the project tagged with a specified tag from OMERO.
- getImagesTagged(Client, Long) - Method in class fr.igred.omero.repository.DatasetWrapper
-
Gets all images in the dataset tagged with a specified tag from OMERO.
- getImagesTagged(Client, Long) - Method in class fr.igred.omero.repository.ProjectWrapper
-
Gets all images in the project tagged with a specified tag from OMERO.
- getImagesTagged(Long) - Method in class fr.igred.omero.Browser
-
Deprecated.Gets all images tagged with a specified tag from OMERO.
- getImagesWithKey(Client, String) - Method in class fr.igred.omero.repository.DatasetWrapper
-
Gets all images in the dataset with a certain key
- getImagesWithKey(Client, String) - Method in class fr.igred.omero.repository.ProjectWrapper
-
Gets all images in the project with a certain key
- getImagesWithKey(String) - Method in class fr.igred.omero.Browser
-
Gets all images with a certain key.
- getImagesWithKeyValuePair(Client, String, String) - Method in class fr.igred.omero.repository.DatasetWrapper
-
Gets all images in the dataset with a certain key value pair from OMERO
- getImagesWithKeyValuePair(Client, String, String) - Method in class fr.igred.omero.repository.ProjectWrapper
-
Gets all images in the project with a certain key value pair from OMERO.
- getImagesWithKeyValuePair(String, String) - Method in class fr.igred.omero.Browser
-
Gets all images with a certain key value pair from OMERO
- getImportStore() - Method in class fr.igred.omero.GatewayWrapper
-
Creates or recycles the import store.
- getIndex() - Method in class fr.igred.omero.repository.ChannelWrapper
-
Returns the channel index.
- getInstitution() - Method in class fr.igred.omero.meta.ExperimenterWrapper
-
Returns the institution where the experimenter works.
- getKeyValuePairs(Client) - Method in class fr.igred.omero.AnnotatableWrapper
-
Gets the List of key-value pairs associated to an object as a map (no duplicate key should exist).
- getLabel() - Method in class fr.igred.omero.repository.PlateAcquisitionWrapper
-
Returns the label associated to the plate acquisition.
- getLastModified() - Method in class fr.igred.omero.annotations.GenericAnnotationWrapper
-
Returns the time when the annotation was last modified.
- getLastName() - Method in class fr.igred.omero.meta.ExperimenterWrapper
-
Returns the last name of the experimenter.
- getLeaders() - Method in class fr.igred.omero.meta.GroupWrapper
-
Returns the leaders of this group.
- getMapAnnotation(Long) - Method in class fr.igred.omero.Browser
-
Gets a specific map annotation (key/value pairs) from the OMERO database.
- getMapAnnotations() - Method in class fr.igred.omero.Browser
-
Gets the list of map annotations available to the user.
- getMapAnnotations(Client) - Method in class fr.igred.omero.AnnotatableWrapper
-
Gets all map annotations linked to an object in OMERO, if possible.
- getMapAnnotations(String) - Method in class fr.igred.omero.Browser
-
Gets the list of map annotations with the specified key available to the user.
- getMapAnnotations(String, String) - Method in class fr.igred.omero.Browser
-
Gets the list of map annotations with the specified key and value available to the user.
- getMask() - Method in class fr.igred.omero.roi.MaskWrapper
-
Returns the mask as a byte array.
- getMaskAsBinaryArray() - Method in class fr.igred.omero.roi.MaskWrapper
-
Returns the mask image.
- getMaskPoints() - Method in class fr.igred.omero.roi.PolygonWrapper
-
Returns the points in the polygon.
- getMaximumFieldCount() - Method in class fr.igred.omero.repository.PlateAcquisitionWrapper
-
Returns the maximum number of fields in any well.
- getMeanExposureTime(int) - Method in class fr.igred.omero.repository.PixelsWrapper
-
Computes the mean exposure time for a given channel from the planes exposureTime.
- getMeanTimeInterval() - Method in class fr.igred.omero.repository.PixelsWrapper
-
Computes the mean time interval from the planes deltaTs.
- getMembersOnly() - Method in class fr.igred.omero.meta.GroupWrapper
-
Returns the list of experimenters that are not owners of the group.
- getMetadata() - Method in class fr.igred.omero.GatewayWrapper
-
Gets the
MetadataFacility
used to retrieve annotations from OMERO. - getMiddleName() - Method in class fr.igred.omero.meta.ExperimenterWrapper
-
Returns the middle name of the experimenter.
- getMinPosition(Collection<? extends PlaneInfoWrapper>, Function<? super PlaneInfoWrapper, ? extends Length>, Unit<Length>) - Static method in class fr.igred.omero.meta.PlaneInfoWrapper
-
Retrieves the min value for the specified getter in a PlaneInfoWrapper collection.
- getMyRating(Client) - Method in class fr.igred.omero.AnnotatableWrapper
-
Returns the user rating for this object (averaged if multiple ratings are linked).
- getName() - Method in class fr.igred.omero.annotations.TableWrapper
-
Returns the name of the table.
- getName() - Method in class fr.igred.omero.annotations.TagAnnotationWrapper
-
Gets the name of the TagData.
- getName() - Method in class fr.igred.omero.meta.GroupWrapper
-
Returns the name of the group.
- getName() - Method in class fr.igred.omero.repository.ChannelWrapper
-
Returns the name of the channel.
- getName() - Method in class fr.igred.omero.repository.DatasetWrapper
-
Gets the DatasetData name
- getName() - Method in class fr.igred.omero.repository.FolderWrapper
-
Gets the name of the folder
- getName() - Method in class fr.igred.omero.repository.GenericRepositoryObjectWrapper
-
Gets the object name.
- getName() - Method in class fr.igred.omero.repository.ImageWrapper
-
Gets the ImageData name
- getName() - Method in class fr.igred.omero.repository.PlateAcquisitionWrapper
-
Gets the plate acquisition name.
- getName() - Method in class fr.igred.omero.repository.PlateWrapper
-
Gets the plate name.
- getName() - Method in class fr.igred.omero.repository.ProjectWrapper
-
Gets the ProjectData name
- getName() - Method in class fr.igred.omero.repository.ScreenWrapper
-
Gets the screen name.
- getName() - Method in class fr.igred.omero.repository.WellWrapper
-
Gets the object name.
- getName() - Method in class fr.igred.omero.roi.ROIWrapper
-
Gets the ROI name.
- getNameSpace() - Method in class fr.igred.omero.annotations.GenericAnnotationWrapper
-
Retrieves the
AnnotationData
namespace of the underlyingAnnotationData
instance. - getOriginalMimetype() - Method in class fr.igred.omero.annotations.FileAnnotationWrapper
-
Returns the format of the original file.
- getOwner() - Method in class fr.igred.omero.GenericObjectWrapper
-
Gets the owner ID
- getParent() - Method in class fr.igred.omero.repository.FolderWrapper
-
Retrieves the parent folders for this folder.
- getPermissionsLevel() - Method in class fr.igred.omero.meta.GroupWrapper
-
Returns the permissions level.
- getPixels() - Method in class fr.igred.omero.repository.ImageWrapper
-
Gets the Pixels for this image.
- getPixelSizeX() - Method in class fr.igred.omero.repository.PixelsWrapper
-
Gets the size of a single image pixel on the X axis.
- getPixelSizeY() - Method in class fr.igred.omero.repository.PixelsWrapper
-
Gets the size of a single image pixel on the Y axis.
- getPixelSizeZ() - Method in class fr.igred.omero.repository.PixelsWrapper
-
Gets the size of a single image pixel on the Z axis.
- getPixelType() - Method in class fr.igred.omero.repository.PixelsWrapper
-
Gets the pixel type.
- getPlanesInfo() - Method in class fr.igred.omero.repository.PixelsWrapper
-
Retrieves the planes information (which need to be
loaded
first). - getPlate() - Method in class fr.igred.omero.repository.WellWrapper
-
Returns the plate containing this Well.
- getPlate(Long) - Method in class fr.igred.omero.Browser
-
Gets the plate with the specified id from OMERO.
- getPlateAcquisitions() - Method in class fr.igred.omero.repository.PlateWrapper
-
Returns the plate acquisitions related to this plate.
- getPlateAcquisitions(Client) - Method in class fr.igred.omero.annotations.GenericAnnotationWrapper
-
Gets all plate acquisitions with this annotation from OMERO.
- getPlateAcquisitions(Client) - Method in class fr.igred.omero.repository.ImageWrapper
-
Returns the plate acquisitions linked to this image.
- getPlateAcquisitions(Client) - Method in class fr.igred.omero.repository.ScreenWrapper
-
Returns the plate acquisitions linked to this object, either directly, or through parents/children.
- getPlateAcquisitions(Client) - Method in class fr.igred.omero.repository.WellSampleWrapper
-
Returns the plate acquisitions linked to the parent Well.
- getPlateAcquisitions(Client) - Method in class fr.igred.omero.repository.WellWrapper
-
Refreshes this well and returns the plate acquisitions linked to it.
- getPlates() - Method in class fr.igred.omero.Browser
-
Gets all plates available from OMERO.
- getPlates() - Method in class fr.igred.omero.repository.ScreenWrapper
-
Returns the plates contained in this screen.
- getPlates(Client) - Method in class fr.igred.omero.annotations.GenericAnnotationWrapper
-
Gets all plates with this annotation from OMERO.
- getPlates(Client) - Method in class fr.igred.omero.repository.ImageWrapper
-
Retrieves the plates containing this image.
- getPlates(Client) - Method in class fr.igred.omero.repository.PlateAcquisitionWrapper
-
Returns the (updated) parent plate as a singleton list.
- getPlates(Client) - Method in class fr.igred.omero.repository.WellSampleWrapper
-
Returns the plates containing the parent Well.
- getPlates(ExperimenterWrapper) - Method in class fr.igred.omero.Browser
-
Gets all plates available from OMERO owned by a given user.
- getPlates(Long...) - Method in class fr.igred.omero.Browser
-
Gets the plates with the specified ids from OMERO.
- getPlates(String) - Method in class fr.igred.omero.repository.ScreenWrapper
-
Returns the plates contained in this screen, with the specified name.
- getPlateType() - Method in class fr.igred.omero.repository.PlateWrapper
-
Returns the type of plate e.g.
- getPoints() - Method in class fr.igred.omero.roi.PolygonWrapper
-
Returns the points in the Polygon.
- getPoints() - Method in class fr.igred.omero.roi.PolylineWrapper
-
Returns the points in the Polyline.
- getPositionX() - Method in class fr.igred.omero.meta.PlaneInfoWrapper
-
Retrieves the X stage position.
- getPositionX() - Method in class fr.igred.omero.repository.PixelsWrapper
-
Retrieves the X stage position.
- getPositionX(UnitsLength) - Method in class fr.igred.omero.repository.WellSampleWrapper
-
Returns the position X.
- getPositionY() - Method in class fr.igred.omero.meta.PlaneInfoWrapper
-
Retrieves the Y stage position.
- getPositionY() - Method in class fr.igred.omero.repository.PixelsWrapper
-
Retrieves the Y stage position.
- getPositionY(UnitsLength) - Method in class fr.igred.omero.repository.WellSampleWrapper
-
Returns the position Y.
- getPositionZ() - Method in class fr.igred.omero.meta.PlaneInfoWrapper
-
Retrieves the Z stage position.
- getPositionZ() - Method in class fr.igred.omero.repository.PixelsWrapper
-
Retrieves the Z stage position.
- getProject(Long) - Method in class fr.igred.omero.Browser
-
Gets the project with the specified id from OMERO.
- getProjects() - Method in class fr.igred.omero.Browser
-
Gets all projects available from OMERO.
- getProjects(Client) - Method in class fr.igred.omero.annotations.GenericAnnotationWrapper
-
Gets all projects with this annotation from OMERO.
- getProjects(Client) - Method in class fr.igred.omero.repository.DatasetWrapper
-
Retrieves the projects containing this dataset.
- getProjects(Client) - Method in class fr.igred.omero.repository.ImageWrapper
-
Retrieves the projects containing this image
- getProjects(ExperimenterWrapper) - Method in class fr.igred.omero.Browser
-
Gets all projects available from OMERO owned by a given user.
- getProjects(Long...) - Method in class fr.igred.omero.Browser
-
Gets the projects with the specified ids from OMERO.
- getProjects(String) - Method in class fr.igred.omero.Browser
-
Gets all projects with a certain name from OMERO.
- getProtocolDescription() - Method in class fr.igred.omero.repository.ScreenWrapper
-
Returns the description of the protocol.
- getProtocolIdentifier() - Method in class fr.igred.omero.repository.ScreenWrapper
-
Returns the identifier of the protocol.
- getQueryService() - Method in class fr.igred.omero.GatewayWrapper
-
Returns the
IQueryPrx
used to find objects on OMERO. - getRadiusX() - Method in class fr.igred.omero.roi.EllipseWrapper
-
Returns the radius along the X-axis.
- getRadiusY() - Method in class fr.igred.omero.roi.EllipseWrapper
-
Returns the radius along the Y-axis.
- getRating() - Method in class fr.igred.omero.annotations.RatingAnnotationWrapper
-
Returns the rating value.
- getRawPixels(Client, int) - Method in class fr.igred.omero.repository.PixelsWrapper
-
Returns an array containing the raw values for each voxel for each planes
- getRawPixels(Client, int[], int[], int[], int[], int[], int) - Method in class fr.igred.omero.repository.PixelsWrapper
-
Returns an array containing the raw values for each voxel for each plane corresponding to the bounds
- getReagentSetDescription() - Method in class fr.igred.omero.repository.ScreenWrapper
-
Returns the description of the reagent set.
- getReagentSetIdentifier() - Method in class fr.igred.omero.repository.ScreenWrapper
-
Returns the identifier of the Reagent set.
- getRed() - Method in class fr.igred.omero.repository.ChannelWrapper
-
Gets the sRGB red value of the channel.
- getRed() - Method in class fr.igred.omero.repository.WellWrapper
-
Returns the red component of the color associated to the well, or
-1
. - getRefPlateId() - Method in class fr.igred.omero.repository.PlateAcquisitionWrapper
-
Returns the id of the plate of reference.
- getRoiFacility() - Method in class fr.igred.omero.GatewayWrapper
-
Gets the
ROIFacility
used to manipulate ROIs from OMERO. - getROIFolders(Client) - Method in class fr.igred.omero.repository.ImageWrapper
-
Gets the list of folders linked to the ROIs in this image.
- getROIs(Client) - Method in class fr.igred.omero.repository.FolderWrapper
-
Deprecated.Gets the ROI contained in the folder associated with the image id set (an image need to be associated)
- getROIs(Client) - Method in class fr.igred.omero.repository.ImageWrapper
-
Gets all ROIs linked to the image in OMERO
- getROIs(Client, long) - Method in class fr.igred.omero.repository.FolderWrapper
-
Gets the ROIs contained in the folder associated with the provided image ID.
- getROIs(Client, ImageWrapper) - Method in class fr.igred.omero.repository.FolderWrapper
-
Gets the ROIs contained in the folder associated with the provided image.
- getRow() - Method in class fr.igred.omero.repository.WellWrapper
-
Returns the row used to indicate the location of the well on the grid.
- getRowCount() - Method in class fr.igred.omero.annotations.TableWrapper
-
Returns the number of rows in the table.
- getRowSequenceIndex() - Method in class fr.igred.omero.repository.PlateWrapper
-
Returns the index indicating how to label a row.
- getScreen(Long) - Method in class fr.igred.omero.Browser
-
Gets the screen with the specified id from OMERO.
- getScreens() - Method in class fr.igred.omero.Browser
-
Gets all screens available from OMERO.
- getScreens(Client) - Method in class fr.igred.omero.annotations.GenericAnnotationWrapper
-
Gets all screens with this annotation from OMERO.
- getScreens(Client) - Method in class fr.igred.omero.repository.ImageWrapper
-
Retrieves the screens containing this image
- getScreens(Client) - Method in class fr.igred.omero.repository.PlateAcquisitionWrapper
-
Retrieves the screens containing the parent plates.
- getScreens(Client) - Method in class fr.igred.omero.repository.PlateWrapper
-
Retrieves the screens containing this plate.
- getScreens(Client) - Method in class fr.igred.omero.repository.WellSampleWrapper
-
Returns the screens containing the parent Well.
- getScreens(Client) - Method in class fr.igred.omero.repository.WellWrapper
-
Refreshes this well and retrieves the screens containing it.
- getScreens(ExperimenterWrapper) - Method in class fr.igred.omero.Browser
-
Gets all screens available from OMERO owned by a given user.
- getScreens(Long...) - Method in class fr.igred.omero.Browser
-
Gets the screens with the specified ids from OMERO.
- getServerFileMimetype() - Method in class fr.igred.omero.annotations.FileAnnotationWrapper
-
Returns the file format as defined by the specification, corresponding to the file extension.
- getSessionId() - Method in class fr.igred.omero.GatewayWrapper
-
Get the ID of the current session
- getShapes() - Method in class fr.igred.omero.roi.ROIWrapper
-
Returns the list of shapes contained in the ROIData.
- getSize() - Method in class fr.igred.omero.repository.PixelsWrapper.Bounds
-
Gets size of bounds for each coordinate.
- getSizeC() - Method in class fr.igred.omero.repository.PixelsWrapper
-
Gets the size of the image on the C axis
- getSizeT() - Method in class fr.igred.omero.repository.PixelsWrapper
-
Gets the size of the image on the T axis
- getSizeX() - Method in class fr.igred.omero.repository.PixelsWrapper
-
Gets the size of the image on the X axis
- getSizeY() - Method in class fr.igred.omero.repository.PixelsWrapper
-
Gets the size of the image on the Y axis
- getSizeZ() - Method in class fr.igred.omero.repository.PixelsWrapper
-
Gets the size of the image on the Z axis
- getStart() - Method in class fr.igred.omero.repository.PixelsWrapper.Bounds
-
Gets starting coordinates.
- getStartTime() - Method in class fr.igred.omero.repository.PlateAcquisitionWrapper
-
Returns the time when the first image was collected.
- getStartTime() - Method in class fr.igred.omero.repository.WellSampleWrapper
-
Returns the time at which the field was acquired.
- getStatus() - Method in class fr.igred.omero.repository.PlateWrapper
-
Returns the status of the plate.
- getStatus() - Method in class fr.igred.omero.repository.WellWrapper
-
Returns the status of the well.
- getStroke() - Method in class fr.igred.omero.roi.GenericShapeWrapper
-
Gets the ShapeData stroke color.
- getT() - Method in class fr.igred.omero.repository.PixelsWrapper.Coordinates
-
Gets T coordinate.
- getT() - Method in class fr.igred.omero.roi.GenericShapeWrapper
-
Sets the time-point.
- getTable(Client, Long) - Method in class fr.igred.omero.AnnotatableWrapper
-
Gets a certain table linked to the object in OMERO.
- getTables(Client) - Method in class fr.igred.omero.AnnotatableWrapper
-
Gets all tables linked to the object in OMERO.
- getTablesFacility() - Method in class fr.igred.omero.GatewayWrapper
-
Gets the
TablesFacility
used to manipulate tables on OMERO. - getTag(Long) - Method in class fr.igred.omero.Browser
-
Gets a specific tag from the OMERO database.
- getTags() - Method in class fr.igred.omero.Browser
-
Gets the list of tag annotations available to the user.
- getTags(Client) - Method in class fr.igred.omero.AnnotatableWrapper
-
Gets all tags linked to an object in OMERO, if possible.
- getTags(String) - Method in class fr.igred.omero.Browser
-
Gets the list of tag annotations with the specified name available to the user.
- getText() - Method in class fr.igred.omero.annotations.TextualAnnotationWrapper
-
Returns the text of this annotation.
- getText() - Method in class fr.igred.omero.roi.EllipseWrapper
-
Gets the text on the ShapeData.
- getText() - Method in class fr.igred.omero.roi.GenericShapeWrapper
-
Gets the text on the ShapeData.
- getText() - Method in class fr.igred.omero.roi.LineWrapper
-
Gets the text on the ShapeData.
- getText() - Method in class fr.igred.omero.roi.MaskWrapper
-
Gets the text on the ShapeData.
- getText() - Method in class fr.igred.omero.roi.PointWrapper
-
Gets the text on the ShapeData.
- getText() - Method in class fr.igred.omero.roi.PolygonWrapper
-
Gets the text on the ShapeData.
- getText() - Method in class fr.igred.omero.roi.PolylineWrapper
-
Gets the text on the ShapeData.
- getText() - Method in class fr.igred.omero.roi.RectangleWrapper
-
Gets the text on the ShapeData.
- getText() - Method in class fr.igred.omero.roi.TextWrapper
-
Gets the text on the ShapeData.
- getTheC() - Method in class fr.igred.omero.meta.PlaneInfoWrapper
-
Retrieves the plane channel index.
- getTheT() - Method in class fr.igred.omero.meta.PlaneInfoWrapper
-
Retrieves the plane time index.
- getTheZ() - Method in class fr.igred.omero.meta.PlaneInfoWrapper
-
Retrieves the plane slice index.
- getThumbnail(Client, int) - Method in class fr.igred.omero.repository.ImageWrapper
-
Retrieves the image thumbnail of the specified size.
- getTimeIncrement() - Method in class fr.igred.omero.repository.PixelsWrapper
-
Gets the time increment between time points.
- getUser() - Method in class fr.igred.omero.GatewayWrapper
-
Returns the current user.
- getUser(String) - Method in class fr.igred.omero.Client
-
Returns the user which matches the username.
- getUserName() - Method in class fr.igred.omero.meta.ExperimenterWrapper
-
Returns the last name of the experimenter.
- getValue(Client, String) - Method in class fr.igred.omero.AnnotatableWrapper
-
Gets the value from a Key-Value pair associated to the object.
- getWell(Client) - Method in class fr.igred.omero.repository.WellSampleWrapper
-
Retrieves the well containing this well sample
- getWell(Long) - Method in class fr.igred.omero.Browser
-
Gets the well with the specified id from OMERO.
- getWellOriginX(UnitsLength) - Method in class fr.igred.omero.repository.PlateWrapper
-
Returns the x-coordinate in 2D-space of the well.
- getWellOriginY(UnitsLength) - Method in class fr.igred.omero.repository.PlateWrapper
-
Returns the y-coordinate in 2D-space of the well.
- getWells() - Method in class fr.igred.omero.Browser
-
Gets all wells available from OMERO.
- getWells(Client) - Method in class fr.igred.omero.annotations.GenericAnnotationWrapper
-
Gets all wells with this annotation from OMERO.
- getWells(Client) - Method in class fr.igred.omero.repository.ImageWrapper
-
Retrieves the wells containing this image.
- getWells(Client) - Method in class fr.igred.omero.repository.PlateAcquisitionWrapper
-
Retrieves the wells contained in the parent plate.
- getWells(Client) - Method in class fr.igred.omero.repository.PlateWrapper
-
Gets all wells in the plate available from OMERO.
- getWells(Client) - Method in class fr.igred.omero.repository.ScreenWrapper
-
Retrieves the wells linked to this object, either directly, or through parents/children.
- getWells(ExperimenterWrapper) - Method in class fr.igred.omero.Browser
-
Gets all wells available from OMERO owned by a given user.
- getWells(Long...) - Method in class fr.igred.omero.Browser
-
Gets the wells with the specified ids from OMERO.
- getWellSamples() - Method in class fr.igred.omero.repository.WellWrapper
-
Returns the well samples linked to the well.
- getWellType() - Method in class fr.igred.omero.repository.WellWrapper
-
Returns a human-readable identifier for the screening status e.g.
- getWidth() - Method in class fr.igred.omero.roi.MaskWrapper
-
Returns the width of the mask.
- getWidth() - Method in class fr.igred.omero.roi.RectangleWrapper
-
Returns the width untransformed rectangle.
- getX() - Method in class fr.igred.omero.repository.PixelsWrapper.Coordinates
-
Gets X coordinate.
- getX() - Method in class fr.igred.omero.roi.EllipseWrapper
-
Returns the x-coordinate of the center of the ellipse.
- getX() - Method in class fr.igred.omero.roi.MaskWrapper
-
Returns the x-coordinate of the top-left corner of the mask.
- getX() - Method in class fr.igred.omero.roi.PointWrapper
-
Returns the x-coordinate of the shape.
- getX() - Method in class fr.igred.omero.roi.RectangleWrapper
-
Returns the x-coordinate of the shape.
- getX() - Method in class fr.igred.omero.roi.TextWrapper
-
Returns the x-coordinate of the shape.
- getX1() - Method in class fr.igred.omero.roi.LineWrapper
-
Returns the x-coordinate of the starting point of an untransformed line.
- getX2() - Method in class fr.igred.omero.roi.LineWrapper
-
Returns the x-coordinate of the end point of an untransformed line.
- getY() - Method in class fr.igred.omero.repository.PixelsWrapper.Coordinates
-
Gets Y coordinate.
- getY() - Method in class fr.igred.omero.roi.EllipseWrapper
-
Returns the y-coordinate of the center of the ellipse.
- getY() - Method in class fr.igred.omero.roi.MaskWrapper
-
Returns the y-coordinate of the top-left corner of the mask.
- getY() - Method in class fr.igred.omero.roi.PointWrapper
-
Returns the y coordinate of the shape.
- getY() - Method in class fr.igred.omero.roi.RectangleWrapper
-
Returns the y coordinate of the shape.
- getY() - Method in class fr.igred.omero.roi.TextWrapper
-
Returns the y coordinate of the shape.
- getY1() - Method in class fr.igred.omero.roi.LineWrapper
-
Returns the y-coordinate of the starting point of an untransformed line.
- getY2() - Method in class fr.igred.omero.roi.LineWrapper
-
Returns the y-coordinate of the end point of an untransformed line.
- getZ() - Method in class fr.igred.omero.repository.PixelsWrapper.Coordinates
-
Gets Z coordinate.
- getZ() - Method in class fr.igred.omero.roi.GenericShapeWrapper
-
Gets the z-section.
- GroupWrapper - Class in fr.igred.omero.meta
-
Class containing a GroupData object.
- GroupWrapper(GroupData) - Constructor for class fr.igred.omero.meta.GroupWrapper
-
Constructor of the class GroupWrapper.
H
- handleException(String) - Method in class fr.igred.omero.exception.ExceptionHandler
-
Throws:
AccessException
ifDSAccessException
was caughtServiceException
ifDSOutOfServiceException
was caughtOMEROServerError
ifServerError
was caught - handleException(Throwable, String) - Static method in class fr.igred.omero.exception.ExceptionHandler
-
Deprecated.Helper method to convert an exception from:
- DSAccessException to AccessException
- DSOutOfServiceException to ServiceException
- ServerError to OMEROServerError
- handleServiceOrAccess(String) - Method in class fr.igred.omero.exception.ExceptionHandler
-
Throws:
ServiceException
ifDSOutOfServiceException
was caughtAccessException
ifDSAccessException
was caught - handleServiceOrAccess(Throwable, String) - Static method in class fr.igred.omero.exception.ExceptionHandler
-
Deprecated.Helper method to convert an exception from:
- DSOutOfServiceException to ServiceException
- DSAccessException to AccessException
- handleServiceOrServer(String) - Method in class fr.igred.omero.exception.ExceptionHandler
-
Throws:
ServiceException
ifDSOutOfServiceException
was caughtOMEROServerError
ifServerError
was caught - handleServiceOrServer(Throwable, String) - Static method in class fr.igred.omero.exception.ExceptionHandler
-
Deprecated.Helper method to convert an exception from:
- DSOutOfServiceException to ServiceException
- ServerError to OMEROServerError
- hasRGBA() - Method in class fr.igred.omero.repository.ChannelWrapper
-
Returns whether the channel contains all the RGBA values or not.
I
- IJ_PROPERTY - Static variable in class fr.igred.omero.roi.ROIWrapper
-
Default IJ property to store ROI local labels / indices.
- ijIDProperty(String) - Static method in class fr.igred.omero.roi.ROIWrapper
-
Returns the ID property corresponding to the input local index/label property (appends "_ID" to said property).
- ijNameProperty(String) - Static method in class fr.igred.omero.roi.ROIWrapper
-
Returns the ID property corresponding to the input local index/label property (appends "_NAME" to said property).
- ImageWrapper - Class in fr.igred.omero.repository
-
Class containing an ImageData.
- ImageWrapper(ImageData) - Constructor for class fr.igred.omero.repository.ImageWrapper
-
Constructor of the class ImageWrapper
- importAndReplaceImages(Client, String) - Method in class fr.igred.omero.repository.DatasetWrapper
-
Imports one image file to the dataset in OMERO and replace older images sharing the same name after copying their annotations and ROIs, and concatenating the descriptions (on new lines) by unlinking them.
- importAndReplaceImages(Client, String, GenericRepositoryObjectWrapper.ReplacePolicy) - Method in class fr.igred.omero.repository.DatasetWrapper
-
Imports one image file to the dataset in OMERO and replace older images sharing the same name after copying their annotations and ROIs, and concatenating the descriptions (on new lines) by unlinking or even deleting them.
- importImage(Client, String) - Method in class fr.igred.omero.repository.DatasetWrapper
-
Imports one image file to the dataset in OMERO.
- importImage(GatewayWrapper, String) - Method in class fr.igred.omero.repository.ScreenWrapper
-
Imports one image file to the screen in OMERO.
- importImage(GatewayWrapper, DataObject, String) - Static method in class fr.igred.omero.repository.GenericRepositoryObjectWrapper
-
Imports one image file to the target in OMERO.
- importImages(Client, int, String...) - Method in class fr.igred.omero.repository.DatasetWrapper
-
Imports all images candidates in the paths to the dataset in OMERO.
- importImages(Client, String...) - Method in class fr.igred.omero.repository.DatasetWrapper
-
Imports all images candidates in the paths to the dataset in OMERO.
- importImages(GatewayWrapper, int, String...) - Method in class fr.igred.omero.repository.ScreenWrapper
-
Imports all images candidates in the paths to the screen in OMERO.
- importImages(GatewayWrapper, String...) - Method in class fr.igred.omero.repository.ScreenWrapper
-
Imports all images candidates in the paths to the screen in OMERO.
- importImages(GatewayWrapper, DataObject, int, String...) - Static method in class fr.igred.omero.repository.GenericRepositoryObjectWrapper
-
Imports all images candidates in the paths to the target in OMERO.
- isActive() - Method in class fr.igred.omero.meta.ExperimenterWrapper
-
Returns
true
if the experimenter is active,false
otherwise. - isComplete() - Method in class fr.igred.omero.annotations.TableWrapper
-
Checks if the table is complete
- isConnected() - Method in class fr.igred.omero.GatewayWrapper
-
Check if the client is still connected to the server
- isFormatsAPIAvailable() - Static method in class fr.igred.omero.util.LibraryChecker
-
Checks if formats-api is available.
- isLDAP() - Method in class fr.igred.omero.meta.ExperimenterWrapper
-
Returns
true
if the user is connected via LDAP. - isLinked(Client, A) - Method in class fr.igred.omero.AnnotatableWrapper
-
Checks if a specific annotation is linked to the object.
- isMemberOfGroup(long) - Method in class fr.igred.omero.meta.ExperimenterWrapper
-
Checks if supplied group id matches any group to which the current experimenter belongs to.
- isMovieFile() - Method in class fr.igred.omero.annotations.FileAnnotationWrapper
-
Returns
true
if it is a movie file. - isOMECommonAvailable() - Static method in class fr.igred.omero.util.LibraryChecker
-
Checks if ome-common is available.
- isOMEROBlitzAvailable() - Static method in class fr.igred.omero.util.LibraryChecker
-
Checks if OMERO Blitz is available.
- isOMEROGatewayAvailable() - Static method in class fr.igred.omero.util.LibraryChecker
-
Checks if the omero-gateway is available.
- isOMEROModelAvailable() - Static method in class fr.igred.omero.util.LibraryChecker
-
Checks if the omero-model is available.
- isOMEXMLAvailable() - Static method in class fr.igred.omero.util.LibraryChecker
-
Checks if the omero-model is available.
- isOrphaned(Client) - Method in class fr.igred.omero.repository.ImageWrapper
-
Checks if image is orphaned (not in a WellSample nor linked to a dataset).
L
- LEVEL_FIVE - Static variable in class fr.igred.omero.annotations.RatingAnnotationWrapper
-
Indicates the object is rated with five stars.
- LEVEL_FOUR - Static variable in class fr.igred.omero.annotations.RatingAnnotationWrapper
-
Indicates the object is rated with four stars.
- LEVEL_ONE - Static variable in class fr.igred.omero.annotations.RatingAnnotationWrapper
-
Indicates the object is rated with one star.
- LEVEL_THREE - Static variable in class fr.igred.omero.annotations.RatingAnnotationWrapper
-
Indicates the object is rated with three stars.
- LEVEL_TWO - Static variable in class fr.igred.omero.annotations.RatingAnnotationWrapper
-
Indicates the object is rated with two stars.
- LEVEL_ZERO - Static variable in class fr.igred.omero.annotations.RatingAnnotationWrapper
-
Indicates the object is not rated.
- LibraryChecker - Class in fr.igred.omero.util
-
Utility methods to check if required libraries/classes are available
- LineWrapper - Class in fr.igred.omero.roi
-
Class containing an LineData.
- LineWrapper() - Constructor for class fr.igred.omero.roi.LineWrapper
-
Constructor of the RectangleWrapper class using a new empty LineData.
- LineWrapper(double, double, double, double) - Constructor for class fr.igred.omero.roi.LineWrapper
-
Constructor of the RectangleWrapper class using a new LineData.
- LineWrapper(Line) - Constructor for class fr.igred.omero.roi.LineWrapper
-
Constructor of the LineWrapper class using an ImageJ Line ROI.
- LineWrapper(LineData) - Constructor for class fr.igred.omero.roi.LineWrapper
-
Constructor of the LineWrapper class using a LineData.
- link(Client, A) - Method in class fr.igred.omero.AnnotatableWrapper
-
Attach an
AnnotationData
to this object. - link(Client, A) - Method in class fr.igred.omero.repository.FolderWrapper
-
Adds an annotation to the object in OMERO, if possible.
- link(Client, A) - Method in class fr.igred.omero.repository.PlateAcquisitionWrapper
-
Adds a tag to the object in OMERO, if possible.
- link(Client, A) - Method in class fr.igred.omero.roi.GenericShapeWrapper
-
Attach an
AnnotationData
to this object. - link(Client, A) - Method in class fr.igred.omero.roi.ROIWrapper
-
Attach an
AnnotationData
to this object. - link(Client, GenericAnnotationWrapper<?>...) - Method in class fr.igred.omero.AnnotatableWrapper
-
Adds multiple annotations to the object in OMERO, if possible.
- linkIfNotLinked(Client, GenericAnnotationWrapper<?>...) - Method in class fr.igred.omero.AnnotatableWrapper
-
Adds multiple annotations to the object in OMERO if they are not already linked.
- loadFolders(Long...) - Method in class fr.igred.omero.Browser
-
Gets the folders with the specified IDs from OMERO (fully loaded).
- loadPlanesInfo(Client) - Method in class fr.igred.omero.repository.PixelsWrapper
-
Loads the planes information.
M
- MapAnnotationWrapper - Class in fr.igred.omero.annotations
-
Class containing a MapAnnotationData, a MapAnnotationData contains a list of NamedValue(Key-Value pair).
- MapAnnotationWrapper() - Constructor for class fr.igred.omero.annotations.MapAnnotationWrapper
-
Constructor of the MapAnnotationWrapper class.
- MapAnnotationWrapper(List<NamedValue>) - Constructor for class fr.igred.omero.annotations.MapAnnotationWrapper
-
Constructor of the MapAnnotationWrapper class.
- MapAnnotationWrapper(MapAnnotationData) - Constructor for class fr.igred.omero.annotations.MapAnnotationWrapper
-
Constructor of the MapAnnotationWrapper class.
- MaskWrapper - Class in fr.igred.omero.roi
-
Class containing an MaskData.
- MaskWrapper() - Constructor for class fr.igred.omero.roi.MaskWrapper
-
Constructor of the MaskWrapper class using a new empty MaskData.
- MaskWrapper(double, double, double, double, byte[]) - Constructor for class fr.igred.omero.roi.MaskWrapper
-
Constructor of the MaskWrapper class using a new MaskData.
- MaskWrapper(MaskData) - Constructor for class fr.igred.omero.roi.MaskWrapper
-
Constructor of the MaskWrapper class using a MaskData.
- MAX_DIST - Static variable in class fr.igred.omero.repository.PixelsWrapper
-
Size of tiles when retrieving pixels
O
- of(I, ExceptionHandler.ThrowingFunction<? super I, ? extends R, ? extends Exception>) - Static method in class fr.igred.omero.exception.ExceptionHandler
-
Creates an ExceptionHandler from an object and a function.
- ofConsumer(I, ExceptionHandler.ThrowingConsumer<? super I, ? extends Exception>) - Static method in class fr.igred.omero.exception.ExceptionHandler
-
Creates an ExceptionHandler from an object and a function with no return value.
- OMEROServerError - Exception in fr.igred.omero.exception
-
Reports an error occurred on the server.
- OMEROServerError(String, Throwable) - Constructor for exception fr.igred.omero.exception.OMEROServerError
-
Constructs a new exception with the specified cause and detailed message.
- OMEROServerError(Throwable) - Constructor for exception fr.igred.omero.exception.OMEROServerError
-
Constructs a new exception with the specified cause and detailed message.
P
- PERMISSIONS_GROUP_READ - Static variable in class fr.igred.omero.meta.GroupWrapper
-
Indicates that the group is
Group
i.e. - PERMISSIONS_GROUP_READ_LINK - Static variable in class fr.igred.omero.meta.GroupWrapper
-
Indicates that the group is
Group
i.e. - PERMISSIONS_GROUP_READ_WRITE - Static variable in class fr.igred.omero.meta.GroupWrapper
-
Indicates that the group is
Group
i.e. - PERMISSIONS_PRIVATE - Static variable in class fr.igred.omero.meta.GroupWrapper
-
Indicates that the group is
Private
i.e. - PERMISSIONS_PUBLIC_READ - Static variable in class fr.igred.omero.meta.GroupWrapper
-
Indicates that the group is
Public
i.e. - PERMISSIONS_PUBLIC_READ_WRITE - Static variable in class fr.igred.omero.meta.GroupWrapper
-
Indicates that the group is
Public
i.e. - PixelsWrapper - Class in fr.igred.omero.repository
-
Class containing a PixelData object.
- PixelsWrapper(PixelsData) - Constructor for class fr.igred.omero.repository.PixelsWrapper
-
Constructor of the PixelsWrapper class
- PixelsWrapper.Bounds - Class in fr.igred.omero.repository
-
Class containing 5D bounds coordinates
- PixelsWrapper.Coordinates - Class in fr.igred.omero.repository
-
Class containing 5D pixel coordinates
- PlaneInfoWrapper - Class in fr.igred.omero.meta
- PlaneInfoWrapper(PlaneInfoData) - Constructor for class fr.igred.omero.meta.PlaneInfoWrapper
-
Constructor of the class PlaneInfoWrapper.
- PlateAcquisitionWrapper - Class in fr.igred.omero.repository
-
Class containing a PlateAcquisitionData object.
- PlateAcquisitionWrapper(PlateAcquisitionData) - Constructor for class fr.igred.omero.repository.PlateAcquisitionWrapper
-
Constructor of the class PlateAcquisitionWrapper.
- PlateWrapper - Class in fr.igred.omero.repository
-
Class containing a PlateData object.
- PlateWrapper(PlateData) - Constructor for class fr.igred.omero.repository.PlateWrapper
-
Constructor of the class PlateWrapper.
- PointWrapper - Class in fr.igred.omero.roi
-
Class containing an PointData.
- PointWrapper() - Constructor for class fr.igred.omero.roi.PointWrapper
-
Constructor of the PointWrapper class using a new empty PointData.
- PointWrapper(double, double) - Constructor for class fr.igred.omero.roi.PointWrapper
-
Constructor of the PointWrapper class using a new empty ShapeData.
- PointWrapper(PointData) - Constructor for class fr.igred.omero.roi.PointWrapper
-
Constructor of the PointWrapper class using a PointData.
- PolygonWrapper - Class in fr.igred.omero.roi
-
Class containing an PolygonData.
- PolygonWrapper() - Constructor for class fr.igred.omero.roi.PolygonWrapper
-
Constructor of the PolygonWrapper class using a new empty LineData.
- PolygonWrapper(Roi) - Constructor for class fr.igred.omero.roi.PolygonWrapper
-
Constructor of the PolygonWrapper class using an ImageJ PolygonRoi.
- PolygonWrapper(List<Point2D.Double>) - Constructor for class fr.igred.omero.roi.PolygonWrapper
-
Constructor of the PolygonWrapper class using a new LineData.
- PolygonWrapper(PolygonData) - Constructor for class fr.igred.omero.roi.PolygonWrapper
-
Constructor of the PolygonWrapper class using a PolygonData.
- PolylineWrapper - Class in fr.igred.omero.roi
-
Class containing an PolylineData.
- PolylineWrapper() - Constructor for class fr.igred.omero.roi.PolylineWrapper
-
Constructor of the RectangleWrapper class using a new empty LineData.
- PolylineWrapper(Roi) - Constructor for class fr.igred.omero.roi.PolylineWrapper
-
Constructor of the PolylineWrapper class using an ImageJ PolygonRoi.
- PolylineWrapper(List<Point2D.Double>) - Constructor for class fr.igred.omero.roi.PolylineWrapper
-
Constructor of the RectangleWrapper class using a new LineData.
- PolylineWrapper(PolylineData) - Constructor for class fr.igred.omero.roi.PolylineWrapper
-
Constructor of the PolylineWrapper class using a PolylineData.
- ProjectWrapper - Class in fr.igred.omero.repository
-
Class containing a ProjectData object.
- ProjectWrapper(Client, String, String) - Constructor for class fr.igred.omero.repository.ProjectWrapper
-
Constructor of the ProjectWrapper class.
- ProjectWrapper(ProjectData) - Constructor for class fr.igred.omero.repository.ProjectWrapper
-
Constructor of the ProjectWrapper class.
R
- rate(Client, int) - Method in class fr.igred.omero.AnnotatableWrapper
-
Rates the object (using a rating annotation).
- RatingAnnotationWrapper - Class in fr.igred.omero.annotations
-
Class containing a RatingAnnotationData object.
- RatingAnnotationWrapper(int) - Constructor for class fr.igred.omero.annotations.RatingAnnotationWrapper
-
Creates a new Textual Annotation with the provided text.
- RatingAnnotationWrapper(RatingAnnotationData) - Constructor for class fr.igred.omero.annotations.RatingAnnotationWrapper
-
Constructor of the RatingAnnotationWrapper class.
- RectangleWrapper - Class in fr.igred.omero.roi
-
Class containing an RectangleData.
- RectangleWrapper() - Constructor for class fr.igred.omero.roi.RectangleWrapper
-
Constructor of the RectangleWrapper class using a new empty RectangleData.
- RectangleWrapper(double, double, double, double) - Constructor for class fr.igred.omero.roi.RectangleWrapper
-
Constructor of the RectangleWrapper class using a new RectangleData.
- RectangleWrapper(Roi) - Constructor for class fr.igred.omero.roi.RectangleWrapper
-
Constructor of the RectangleWrapper class using bounds from an ImageJ ROI.
- RectangleWrapper(RectangleData) - Constructor for class fr.igred.omero.roi.RectangleWrapper
-
Constructor of the RectangleWrapper class using a RectangleData.
- refresh(Client) - Method in class fr.igred.omero.repository.DatasetWrapper
-
Reloads the dataset from OMERO.
- refresh(Client) - Method in class fr.igred.omero.repository.PlateWrapper
-
Reloads the plate from OMERO.
- refresh(Client) - Method in class fr.igred.omero.repository.ProjectWrapper
-
Reloads the project from OMERO.
- refresh(Client) - Method in class fr.igred.omero.repository.WellWrapper
-
Reloads the well from OMERO.
- refresh(GatewayWrapper) - Method in class fr.igred.omero.repository.ScreenWrapper
-
Reloads the screen from OMERO.
- reload(Client) - Method in class fr.igred.omero.repository.FolderWrapper
-
Reloads the folder from OMERO, to update all links.
- removeDataset(Client, DatasetWrapper) - Method in class fr.igred.omero.repository.ProjectWrapper
-
Removes a dataset from the project in OMERO.
- removeImage(Client, ImageWrapper) - Method in class fr.igred.omero.repository.DatasetWrapper
-
Removes an image from the dataset in OMERO.
- removeLink(Client, String, long) - Method in class fr.igred.omero.AnnotatableWrapper
-
Removes the link of the given type with the given child ID.
- replaceImages(Client, Collection<? extends ImageWrapper>, ImageWrapper) - Method in class fr.igred.omero.repository.DatasetWrapper
-
Replaces (and unlinks) a collection of images from this dataset by a new image, after copying their annotations and ROIs, and concatenating the descriptions (on new lines).
- rethrow() - Method in class fr.igred.omero.exception.ExceptionHandler
-
Rethrows exception if one was caught (to not swallow it).
- rethrow(Class<E>) - Method in class fr.igred.omero.exception.ExceptionHandler
-
Throws an exception from the specified type, if one was caught.
- rethrow(Class<E>, ExceptionHandler.ExceptionWrapper<? super E, ? extends F>, String) - Method in class fr.igred.omero.exception.ExceptionHandler
-
Throws an exception converted from the specified type, if one was caught.
- ROIWrapper - Class in fr.igred.omero.roi
-
Class containing a ROIData object.
- ROIWrapper() - Constructor for class fr.igred.omero.roi.ROIWrapper
-
Constructor of the ROIWrapper class.
- ROIWrapper(Iterable<? extends GenericShapeWrapper<?>>) - Constructor for class fr.igred.omero.roi.ROIWrapper
-
Constructor of the ROIWrapper class.
- ROIWrapper(ROIData) - Constructor for class fr.igred.omero.roi.ROIWrapper
-
Constructor of the ROIWrapper class.
S
- save(IObject) - Method in class fr.igred.omero.GatewayWrapper
-
Saves an object on OMERO.
- saveAndUpdate(Client) - Method in class fr.igred.omero.GenericObjectWrapper
-
Saves and updates object.
- saveAs(String, char) - Method in class fr.igred.omero.annotations.TableWrapper
-
Saves the current table as a character-delimited text file.
- saveROI(Client) - Method in class fr.igred.omero.roi.ROIWrapper
-
Saves the ROI.
- saveROI(Client, ROIWrapper) - Method in class fr.igred.omero.repository.ImageWrapper
-
Deprecated.Links a ROI to the image in OMERO
DO NOT USE IT IF A SHAPE WAS DELETED !!!
- saveROIs(Client, ROIWrapper...) - Method in class fr.igred.omero.repository.ImageWrapper
-
Links ROIs to the image in OMERO.
- saveROIs(Client, Collection<? extends ROIWrapper>) - Method in class fr.igred.omero.repository.ImageWrapper
-
Links ROIs to the image in OMERO.
- ScreenWrapper - Class in fr.igred.omero.repository
-
Class containing a ScreenData object.
- ScreenWrapper(Client, String, String) - Constructor for class fr.igred.omero.repository.ScreenWrapper
-
Constructor of the ProjectWrapper class.
- ScreenWrapper(ScreenData) - Constructor for class fr.igred.omero.repository.ScreenWrapper
-
Constructor of the class ScreenWrapper.
- ServiceException - Exception in fr.igred.omero.exception
-
Reports an error occurred while trying to access the OMERO service.
- ServiceException(String, Throwable, ConnectionStatus) - Constructor for exception fr.igred.omero.exception.ServiceException
-
Constructs a new exception with the specified cause and a generic message.
- ServiceException(String, DSOutOfServiceException) - Constructor for exception fr.igred.omero.exception.ServiceException
-
Constructs a new exception with the specified cause and a generic message.
- ServiceException(Throwable, ConnectionStatus) - Constructor for exception fr.igred.omero.exception.ServiceException
-
Constructs a new exception with the specified cause and a generic message.
- setAlpha(Integer) - Method in class fr.igred.omero.repository.WellWrapper
-
Sets the alpha component of the color associated to the well.
- setBlue(Integer) - Method in class fr.igred.omero.repository.WellWrapper
-
Sets the blue component of the color associated to the well.
- setC(int) - Method in class fr.igred.omero.roi.GenericShapeWrapper
-
Sets the channel.
- setColumn(int, String, Class<?>) - Method in class fr.igred.omero.annotations.TableWrapper
-
Sets the information about a certain column.
- setContent(List<NamedValue>) - Method in class fr.igred.omero.annotations.MapAnnotationWrapper
-
Sets the content of the map annotation.
- setCoordinates(double[]) - Method in class fr.igred.omero.roi.EllipseWrapper
-
Sets the coordinates of the EllipseData shape.
- setCoordinates(double[]) - Method in class fr.igred.omero.roi.LineWrapper
-
Sets the coordinates of the LineData shape.
- setCoordinates(double[]) - Method in class fr.igred.omero.roi.MaskWrapper
-
Sets the coordinates of the MaskData shape.
- setCoordinates(double[]) - Method in class fr.igred.omero.roi.PointWrapper
-
Sets the coordinates of the PointData shape.
- setCoordinates(double[]) - Method in class fr.igred.omero.roi.RectangleWrapper
-
Sets the coordinates of the RectangleData shape.
- setCoordinates(double[]) - Method in class fr.igred.omero.roi.TextWrapper
-
Sets the coordinates of the TextData object.
- setCoordinates(double, double) - Method in class fr.igred.omero.roi.PointWrapper
-
Sets the coordinates the PointData shape.
- setCoordinates(double, double) - Method in class fr.igred.omero.roi.TextWrapper
-
Sets the coordinates of the TextData shape.
- setCoordinates(double, double, double, double) - Method in class fr.igred.omero.roi.EllipseWrapper
-
Sets the coordinates of the EllipseData shape.
- setCoordinates(double, double, double, double) - Method in class fr.igred.omero.roi.LineWrapper
-
Sets the coordinates of the LineData shape.
- setCoordinates(double, double, double, double) - Method in class fr.igred.omero.roi.MaskWrapper
-
Sets the coordinates of the MaskData shape.
- setCoordinates(double, double, double, double) - Method in class fr.igred.omero.roi.RectangleWrapper
-
Sets the coordinates of the RectangleData shape.
- setCZT(int, int, int) - Method in class fr.igred.omero.roi.GenericShapeWrapper
-
Sets the channel, z-section and time-point at once.
- setData(ROIData) - Method in class fr.igred.omero.roi.ROIWrapper
-
Deprecated.Changes the wrapped data.
- setDefaultSample(int) - Method in class fr.igred.omero.repository.PlateWrapper
-
Sets the default sample.
- setDescription(String) - Method in class fr.igred.omero.annotations.GenericAnnotationWrapper
-
Sets the description of the underlying
AnnotationData
instance. - setDescription(String) - Method in class fr.igred.omero.meta.GroupWrapper
-
Sets the description of the group.
- setDescription(String) - Method in class fr.igred.omero.repository.DatasetWrapper
-
Sets the description of the dataset.
- setDescription(String) - Method in class fr.igred.omero.repository.FolderWrapper
-
Sets the description of the folder.
- setDescription(String) - Method in class fr.igred.omero.repository.ImageWrapper
-
Sets the description of the image.
- setDescription(String) - Method in class fr.igred.omero.repository.PlateAcquisitionWrapper
-
Sets the description of the plate acquisition.
- setDescription(String) - Method in class fr.igred.omero.repository.PlateWrapper
-
Sets the description of the plate.
- setDescription(String) - Method in class fr.igred.omero.repository.ProjectWrapper
-
Sets the description of the project.
- setDescription(String) - Method in class fr.igred.omero.repository.ScreenWrapper
-
Sets the description of the screen.
- setEmail(String) - Method in class fr.igred.omero.meta.ExperimenterWrapper
-
Sets the e-mail of the experimenter.
- setExternalIdentifier(String) - Method in class fr.igred.omero.repository.PlateWrapper
-
Sets the external identifier.
- setFileId(Long) - Method in class fr.igred.omero.annotations.TableWrapper
-
Sets the fileId of the table.
- setFill(Color) - Method in class fr.igred.omero.roi.GenericShapeWrapper
-
Sets the ShapeData fill color.
- setFirstName(String) - Method in class fr.igred.omero.meta.ExperimenterWrapper
-
Sets the first name of the experimenter.
- setFontSize(double) - Method in class fr.igred.omero.roi.GenericShapeWrapper
-
Sets ShapeData font size.
- setGreen(Integer) - Method in class fr.igred.omero.repository.WellWrapper
-
Sets the green component of the color associated to the well.
- setHeight(double) - Method in class fr.igred.omero.roi.MaskWrapper
-
Sets the height of an untransformed mask.
- setHeight(double) - Method in class fr.igred.omero.roi.RectangleWrapper
-
Sets the height of an untransformed rectangle.
- setId(Long) - Method in class fr.igred.omero.annotations.TableWrapper
-
Sets the id of the table.
- setImage(long) - Method in class fr.igred.omero.repository.FolderWrapper
-
Deprecated.Sets the image associated to the folder
- setImage(ImageWrapper) - Method in class fr.igred.omero.repository.FolderWrapper
-
Deprecated.Sets the image associated to the folder
- setImage(ImageWrapper) - Method in class fr.igred.omero.repository.WellSampleWrapper
-
Sets the image linked to this well sample.
- setImage(ImageWrapper) - Method in class fr.igred.omero.roi.ROIWrapper
-
Sets the image linked to the ROI.
- setInstitution(String) - Method in class fr.igred.omero.meta.ExperimenterWrapper
-
Sets the institution where the experimenter works.
- setLastName(String) - Method in class fr.igred.omero.meta.ExperimenterWrapper
-
Sets the last name of the experimenter.
- setMask(boolean[][]) - Method in class fr.igred.omero.roi.MaskWrapper
-
Sets the mask
- setMask(byte[]) - Method in class fr.igred.omero.roi.MaskWrapper
-
Sets the mask image.
- setMask(int[][]) - Method in class fr.igred.omero.roi.MaskWrapper
-
Sets the mask
- setMiddleName(String) - Method in class fr.igred.omero.meta.ExperimenterWrapper
-
Sets the middle name of the experimenter.
- setName(String) - Method in class fr.igred.omero.annotations.TableWrapper
-
Sets the name of the table.
- setName(String) - Method in class fr.igred.omero.annotations.TagAnnotationWrapper
-
Sets the name of the TagData.
- setName(String) - Method in class fr.igred.omero.meta.GroupWrapper
-
Sets the name of the group.
- setName(String) - Method in class fr.igred.omero.repository.ChannelWrapper
-
Sets the name of the channel.
- setName(String) - Method in class fr.igred.omero.repository.DatasetWrapper
-
Sets the name of the dataset.
- setName(String) - Method in class fr.igred.omero.repository.FolderWrapper
-
Sets the name of the folder.
- setName(String) - Method in class fr.igred.omero.repository.ImageWrapper
-
Sets the name of the image.
- setName(String) - Method in class fr.igred.omero.repository.PlateAcquisitionWrapper
-
Sets the name of the plate acquisition.
- setName(String) - Method in class fr.igred.omero.repository.PlateWrapper
-
Sets the name of the plate.
- setName(String) - Method in class fr.igred.omero.repository.ProjectWrapper
-
Sets the name of the project.
- setName(String) - Method in class fr.igred.omero.repository.ScreenWrapper
-
Sets the name of the screen.
- setName(String) - Method in class fr.igred.omero.roi.ROIWrapper
-
Sets the ROI name.
- setNameSpace(String) - Method in class fr.igred.omero.annotations.GenericAnnotationWrapper
-
Sets the name space of the underlying
AnnotationData
instance. - setParent(FolderWrapper) - Method in class fr.igred.omero.repository.FolderWrapper
-
Sets the parent folder for this folder.
- setPoints(List<Point2D.Double>) - Method in class fr.igred.omero.roi.PolygonWrapper
-
Sets the points in the polyline.
- setPoints(List<Point2D.Double>) - Method in class fr.igred.omero.roi.PolylineWrapper
-
Sets the points in the polyline.
- setProtocolDescription(String) - Method in class fr.igred.omero.repository.ScreenWrapper
-
Sets the description of the protocol.
- setProtocolIdentifier(String) - Method in class fr.igred.omero.repository.ScreenWrapper
-
Sets the identifier of the protocol.
- setRadiusX(double) - Method in class fr.igred.omero.roi.EllipseWrapper
-
Sets the radius along the X-axis.
- setRadiusY(double) - Method in class fr.igred.omero.roi.EllipseWrapper
-
Sets the radius along the Y-axis.
- setRating(int) - Method in class fr.igred.omero.annotations.RatingAnnotationWrapper
-
Sets the rating value.
- setReagentSetDescription(String) - Method in class fr.igred.omero.repository.ScreenWrapper
-
Sets the identifier of the reagent.
- setReagentSetIdentifier(String) - Method in class fr.igred.omero.repository.ScreenWrapper
-
Sets the identifier of the reagent.
- setRed(Integer) - Method in class fr.igred.omero.repository.WellWrapper
-
Sets the red component of the color associated to the well.
- setRefPlateId(long) - Method in class fr.igred.omero.repository.PlateAcquisitionWrapper
-
Sets the id of the plate this plate acquisition is for.
- setRowCount(int) - Method in class fr.igred.omero.annotations.TableWrapper
-
Sets the number of row in the table.
- setStatus(String) - Method in class fr.igred.omero.repository.PlateWrapper
-
Sets the status.
- setStatus(String) - Method in class fr.igred.omero.repository.WellWrapper
-
Sets the status of the well.
- setStroke(Color) - Method in class fr.igred.omero.roi.GenericShapeWrapper
-
Sets ShapeData stroke color.
- setT(int) - Method in class fr.igred.omero.roi.GenericShapeWrapper
-
Sets the time-point.
- setText(String) - Method in class fr.igred.omero.annotations.TextualAnnotationWrapper
-
Sets the text.
- setText(String) - Method in class fr.igred.omero.roi.EllipseWrapper
-
Sets the text on the ShapeData.
- setText(String) - Method in class fr.igred.omero.roi.GenericShapeWrapper
-
Sets the text on the ShapeData.
- setText(String) - Method in class fr.igred.omero.roi.LineWrapper
-
Sets the text on the ShapeData.
- setText(String) - Method in class fr.igred.omero.roi.MaskWrapper
-
Sets the text on the ShapeData.
- setText(String) - Method in class fr.igred.omero.roi.PointWrapper
-
Sets the text on the ShapeData.
- setText(String) - Method in class fr.igred.omero.roi.PolygonWrapper
-
Sets the text on the ShapeData.
- setText(String) - Method in class fr.igred.omero.roi.PolylineWrapper
-
Sets the text on the ShapeData.
- setText(String) - Method in class fr.igred.omero.roi.RectangleWrapper
-
Sets the text on the ShapeData.
- setText(String) - Method in class fr.igred.omero.roi.TextWrapper
-
Sets the text on the ShapeData.
- setTransform(double, double, double, double, double, double) - Method in class fr.igred.omero.roi.GenericShapeWrapper
-
Sets the transform to the matrix specified by the 6 double precision values.
- setTransform(AffineTransform) - Method in class fr.igred.omero.roi.GenericShapeWrapper
-
Sets the transform from a
AffineTransform
. - setWellType(String) - Method in class fr.igred.omero.repository.WellWrapper
-
Sets a human-readable identifier for the screening status e.g.
- setWidth(double) - Method in class fr.igred.omero.roi.MaskWrapper
-
Sets the width of an untransformed mask.
- setWidth(double) - Method in class fr.igred.omero.roi.RectangleWrapper
-
Sets width of an untransformed rectangle.
- setX(double) - Method in class fr.igred.omero.roi.EllipseWrapper
-
Sets the x-coordinate of the center of the ellipse.
- setX(double) - Method in class fr.igred.omero.roi.MaskWrapper
-
Sets the x-coordinate top-left corner of an untransformed mask.
- setX(double) - Method in class fr.igred.omero.roi.PointWrapper
-
Sets the x-coordinate of the shape.
- setX(double) - Method in class fr.igred.omero.roi.RectangleWrapper
-
Sets the x-coordinate of the shape.
- setX(double) - Method in class fr.igred.omero.roi.TextWrapper
-
Sets the x-coordinate of the shape.
- setX1(double) - Method in class fr.igred.omero.roi.LineWrapper
-
Set the x-coordinate of the starting point of an untransformed line.
- setX2(double) - Method in class fr.igred.omero.roi.LineWrapper
-
Set the x-coordinate of the end point of an untransformed line.
- setY(double) - Method in class fr.igred.omero.roi.EllipseWrapper
-
Sets the y-coordinate of the center of the ellipse.
- setY(double) - Method in class fr.igred.omero.roi.MaskWrapper
-
Sets the y-coordinate top-left corner of an untransformed mask.
- setY(double) - Method in class fr.igred.omero.roi.PointWrapper
-
Sets the y-coordinate of the shape.
- setY(double) - Method in class fr.igred.omero.roi.RectangleWrapper
-
Sets the y-coordinate of the shape.
- setY(double) - Method in class fr.igred.omero.roi.TextWrapper
-
Sets the y-coordinate of the shape.
- setY1(double) - Method in class fr.igred.omero.roi.LineWrapper
-
Set the y-coordinate of the starting point of an untransformed line.
- setY2(double) - Method in class fr.igred.omero.roi.LineWrapper
-
Set the y-coordinate of the end point of an untransformed line.
- setZ(int) - Method in class fr.igred.omero.roi.GenericShapeWrapper
-
Sets the z-section.
- ShapeList - Class in fr.igred.omero.roi
-
List of GenericShapeWrapper objects
- ShapeList() - Constructor for class fr.igred.omero.roi.ShapeList
-
Constructs an empty list with an initial capacity of ten.
- ShapeList(int) - Constructor for class fr.igred.omero.roi.ShapeList
-
Constructs an empty list with the specified initial capacity.
- sudoGetUser(String) - Method in class fr.igred.omero.Client
-
Gets the client associated with the username in the parameters.
- switchGroup(long) - Method in class fr.igred.omero.GatewayWrapper
-
Change the current group used by the current user;
T
- TableWrapper - Class in fr.igred.omero.annotations
-
Class containing the information to create a Table in OMERO.
- TableWrapper(int, String) - Constructor for class fr.igred.omero.annotations.TableWrapper
-
Constructor of the class TableWrapper
- TableWrapper(Client, ResultsTable, Long, List<? extends Roi>) - Constructor for class fr.igred.omero.annotations.TableWrapper
-
Constructor of the class TableWrapper.
- TableWrapper(Client, ResultsTable, Long, List<? extends Roi>, String) - Constructor for class fr.igred.omero.annotations.TableWrapper
-
Constructor of the class TableWrapper.
- TableWrapper(TableData) - Constructor for class fr.igred.omero.annotations.TableWrapper
-
Constructor of the class TableWrapper.
- TagAnnotationWrapper - Class in fr.igred.omero.annotations
-
Class containing a TagAnnotationData object.
- TagAnnotationWrapper(Client, String, String) - Constructor for class fr.igred.omero.annotations.TagAnnotationWrapper
-
Constructor of the TagAnnotationWrapper class.
- TagAnnotationWrapper(TagAnnotationData) - Constructor for class fr.igred.omero.annotations.TagAnnotationWrapper
-
Constructor of the TagAnnotationWrapper class.
- TextualAnnotationWrapper - Class in fr.igred.omero.annotations
-
Class containing a TextualAnnotationData object.
- TextualAnnotationWrapper(String) - Constructor for class fr.igred.omero.annotations.TextualAnnotationWrapper
-
Creates a new Textual Annotation with the provided text.
- TextualAnnotationWrapper(TextualAnnotationData) - Constructor for class fr.igred.omero.annotations.TextualAnnotationWrapper
-
Constructor of the TextualAnnotationWrapper class.
- TextWrapper - Class in fr.igred.omero.roi
-
Class containing an TextData.
- TextWrapper() - Constructor for class fr.igred.omero.roi.TextWrapper
-
Constructor of the TextWrapper class using a new empty ShapeData.
- TextWrapper(TextRoi) - Constructor for class fr.igred.omero.roi.TextWrapper
-
Constructor of the TextWrapper class using an ImageJ TextRoi.
- TextWrapper(String, double, double) - Constructor for class fr.igred.omero.roi.TextWrapper
-
Creates a new instance of the TextWrapper, sets the centre and major, minor axes.
- TextWrapper(TextData) - Constructor for class fr.igred.omero.roi.TextWrapper
-
Constructor of the TextWrapper class using a TextData.
- toAWTShape() - Method in class fr.igred.omero.roi.EllipseWrapper
-
Converts the shape to an
Shape
. - toAWTShape() - Method in class fr.igred.omero.roi.GenericShapeWrapper
-
Converts the shape to an
Shape
. - toAWTShape() - Method in class fr.igred.omero.roi.LineWrapper
-
Converts the shape to an
Shape
. - toAWTShape() - Method in class fr.igred.omero.roi.MaskWrapper
-
Converts the shape to an
Shape
. - toAWTShape() - Method in class fr.igred.omero.roi.PointWrapper
-
Converts the shape to an
Shape
. - toAWTShape() - Method in class fr.igred.omero.roi.PolygonWrapper
-
Converts the shape to an
Shape
. - toAWTShape() - Method in class fr.igred.omero.roi.PolylineWrapper
-
Converts the shape to an
Shape
. - toAWTShape() - Method in class fr.igred.omero.roi.RectangleWrapper
-
Converts the shape to an
Shape
. - toAWTShape() - Method in class fr.igred.omero.roi.TextWrapper
-
Converts the shape to an
Shape
. - toAWTTransform() - Method in class fr.igred.omero.roi.GenericShapeWrapper
-
Converts
AffineTransform
toAffineTransform
. - toImageJ() - Method in class fr.igred.omero.roi.EllipseWrapper
-
Converts shape to ImageJ ROI.
- toImageJ() - Method in class fr.igred.omero.roi.GenericShapeWrapper
-
Converts shape to ImageJ ROI.
- toImageJ() - Method in class fr.igred.omero.roi.LineWrapper
-
Converts shape to ImageJ ROI.
- toImageJ() - Method in class fr.igred.omero.roi.MaskWrapper
-
Converts shape to ImageJ ROI.
- toImageJ() - Method in class fr.igred.omero.roi.PointWrapper
-
Converts shape to ImageJ ROI.
- toImageJ() - Method in class fr.igred.omero.roi.RectangleWrapper
-
Converts shape to ImageJ ROI.
- toImageJ() - Method in class fr.igred.omero.roi.ROIWrapper
-
Converts the ROI to a list of ImageJ ROIs.
- toImageJ() - Method in class fr.igred.omero.roi.TextWrapper
-
Converts shape to ImageJ ROI.
- toImageJ(String) - Method in class fr.igred.omero.roi.ROIWrapper
-
Converts the ROI to a list of ImageJ ROIs.
- toImageJ(Collection<? extends ROIWrapper>, String, boolean) - Static method in class fr.igred.omero.roi.ROIWrapper
-
Converts an OMERO list of ROIs to a list of ImageJ ROIs
- toImageJ(List<? extends ROIWrapper>) - Static method in class fr.igred.omero.roi.ROIWrapper
-
Converts an OMERO list of ROIs to a list of ImageJ ROIs
- toImageJ(List<? extends ROIWrapper>, String) - Static method in class fr.igred.omero.roi.ROIWrapper
-
Converts an OMERO list of ROIs to a list of ImageJ ROIs
- toImagePlus(Client) - Method in class fr.igred.omero.repository.ImageWrapper
-
Generates the ImagePlus from the ij library corresponding to the image from OMERO WARNING : you need to include the ij library to use this function
- toImagePlus(Client, int[], int[], int[], int[], int[]) - Method in class fr.igred.omero.repository.ImageWrapper
-
Gets the imagePlus generated from the image from OMERO corresponding to the bound.
- toImagePlus(Client, ROIWrapper) - Method in class fr.igred.omero.repository.ImageWrapper
-
Gets the imagePlus from the image generated from the ROI.
- toString() - Method in class fr.igred.omero.annotations.TableWrapper
-
Overridden to return the name of the class and the object id.
- toString() - Method in class fr.igred.omero.exception.ExceptionHandler
- toString() - Method in class fr.igred.omero.GatewayWrapper
-
Overridden to return the host name, the group ID, the username and the connection status.
- toString() - Method in class fr.igred.omero.GenericObjectWrapper
-
Overridden to return the name of the class and the object id.
- truncateRow() - Method in class fr.igred.omero.annotations.TableWrapper
-
Deletes all unused row in the table
U
- unlink(Client, A) - Method in class fr.igred.omero.AnnotatableWrapper
-
Unlinks the given annotation from the current object.
- UNLINK - fr.igred.omero.repository.GenericRepositoryObjectWrapper.ReplacePolicy
-
Unlink objects only
- unlinkAllROI(Client) - Method in class fr.igred.omero.repository.FolderWrapper
-
Deprecated.Unlink all ROI, associated to the image set, in the folder. ROIs are now linked to the image directly
- unlinkAllROIs(Client) - Method in class fr.igred.omero.repository.FolderWrapper
-
Unlink all ROIs associated to this folder.
- unlinkAllROIs(Client, long) - Method in class fr.igred.omero.repository.FolderWrapper
-
Unlink all ROIs associated to the provided image ID from the folder.
- unlinkAllROIs(Client, ImageWrapper) - Method in class fr.igred.omero.repository.FolderWrapper
-
Unlink all ROIs associated to the provided image from the folder.
- unlinkROI(Client, ROIWrapper) - Method in class fr.igred.omero.repository.FolderWrapper
-
Deprecated.Unlink an ROI, associated to the image set, in the folder. The ROI is now linked to the image directly.
- unlinkROIs(Client, ROIWrapper...) - Method in class fr.igred.omero.repository.FolderWrapper
-
Unlink ROIs from the folder.
V
- valueOf(String) - Static method in enum fr.igred.omero.repository.GenericRepositoryObjectWrapper.ReplacePolicy
-
Returns the enum constant of this type with the specified name.
- values() - Static method in enum fr.igred.omero.repository.GenericRepositoryObjectWrapper.ReplacePolicy
-
Returns an array containing the constants of this enum type, in the order they are declared.
W
- WellSampleWrapper - Class in fr.igred.omero.repository
-
Class containing a WellSampleData object.
- WellSampleWrapper(WellSampleData) - Constructor for class fr.igred.omero.repository.WellSampleWrapper
-
Constructor of the class WellSampleWrapper.
- WellWrapper - Class in fr.igred.omero.repository
-
Class containing a WellData object.
- WellWrapper(WellData) - Constructor for class fr.igred.omero.repository.WellWrapper
-
Constructor of the class WellWrapper.
- wrap(Collection<U>, Function<? super U, ? extends V>) - Static method in class fr.igred.omero.GenericObjectWrapper
-
Converts a DataObject list to a ObjectWrapper list, sorted by
sorter
. - wrap(Collection<U>, Function<? super U, ? extends V>, Function<? super V, ? extends W>) - Static method in class fr.igred.omero.GenericObjectWrapper
-
Converts a DataObject list to an ObjectWrapper list, sorted by
sorter
. - wrap(T) - Static method in class fr.igred.omero.util.Wrapper
-
Converts (wraps) a ShapeData object to a Shape object.
- wrapAnnotatableObject(T) - Static method in class fr.igred.omero.util.Wrapper
-
Converts (wraps) a DataObject object to an Annotatable object.
- Wrapper - Class in fr.igred.omero.util
-
Utility class to convert DataObjects dynamically.
- wrapRepositoryObject(T) - Static method in class fr.igred.omero.util.Wrapper
-
Converts (wraps) a DataObject object to a Repository object.
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