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

A

AccessException - Exception in fr.igred.omero.exception

Reports an error occurred while trying to pull out data from the server.

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

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

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

Constructs a new exception with a general message and the cause.

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

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

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

Add a dataset to the project in OMERO.

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

Add a dataset to the project in OMERO.

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

Links a file to the object

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

Adds a single image to the dataset in OMERO

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

Adds a list of image to the dataset in OMERO.

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

Adds a List of Key-Value pair to the object

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

Adds a single Key-Value pair to the object.

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

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

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

Adds a row to the table.

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

Adds rows from an ImageJ ResultsTable.

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

Adds a ShapeData from a GenericShapeWrapper to the ROIData

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

Adds ShapeData objects from a list of GenericShapeWrapper to the ROIData

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

Adds a table to the object in OMERO

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

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

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

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

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

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

addTag(Client, TagAnnotationData) - Method in class fr.igred.omero.repository.GenericRepositoryObjectWrapper

Private function.

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

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

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

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

ARROW - Static variable in class fr.igred.omero.roi.LineWrapper

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

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

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

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

Gets the folder contained in the FolderWrapper

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

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

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

Gets the MapAnnotationData contained.

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

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

Returns the ROIData contained.

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

Gets the ShapeData object contained.

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

Gets the TagAnnotationData contained.

B

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

Bounds constructor.

C

ChannelWrapper - Class in fr.igred.omero.repository

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

Constructor of the class ChannelWrapper.

Client - Class in fr.igred.omero

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

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

Constructor of the Client class.

compare(U, U) - Method in class fr.igred.omero.GenericObjectWrapper.SortById

Compare 2 ObjectWrappers.

compare(U, U) - Method in class fr.igred.omero.meta.ExperimenterWrapper.SortByLastName

Compare 2 ExperimenterWrappers.

compare(U, U) - Method in class fr.igred.omero.meta.GroupWrapper.SortByName

Compare 2 GroupWrappers.

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

Connects to OMERO using a session ID.

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

Connects the user to OMERO.

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

Connects the user to OMERO.

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

Connects the user to OMERO.

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

Coordinates constructor.

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

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

Returns a new Shape defined by the geometry of the specified Shape after it has been transformed by the transform.

D

data - Variable in class fr.igred.omero.GenericObjectWrapper

DatasetWrapper - Class in fr.igred.omero.repository

Class containing a DatasetData.

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

Constructor of the DatasetWrapper class

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

Constructor of the DatasetWrapper class

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

Deletes a table from OMERO

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

Deletes an object from OMERO.

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

Deletes a file from OMERO

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

Deletes a ShapeData from the ROIData.

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

Deletes a ShapeData from the ROIData.

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

Disconnects the user

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

Downloads the original files from the server.

E

EllipseWrapper - Class in fr.igred.omero.roi

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

Constructor of the EllipseWrapper class using a new empty EllipseData.

EllipseWrapper(double, double, double, double) - Constructor for class fr.igred.omero.roi.EllipseWrapper

Constructor of the EllipseWrapper class using a new EllipseData.

EllipseWrapper(EllipseData) - Constructor for class fr.igred.omero.roi.EllipseWrapper

Constructor of the EllipseWrapper class using a EllipseData.

ExceptionHandler - Class in fr.igred.omero.exception

Class with methods to handle OMERO exceptions

ExperimenterWrapper - Class in fr.igred.omero.meta

ExperimenterWrapper(ExperimenterData) - Constructor for class fr.igred.omero.meta.ExperimenterWrapper

Constructor of the class ExperimenterWrapper.

ExperimenterWrapper.SortByLastName<U extends ExperimenterWrapper> - Class in fr.igred.omero.meta

Class used to sort ExperimenterWrappers.

F

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

Finds objects on OMERO through a database query.

FolderWrapper - Class in fr.igred.omero.repository

Class containing a FolderData.

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

Constructor of the FolderWrapper class.

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

Constructor of the FolderWrapper class.

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

Constructor of the FolderWrapper class.

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

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

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

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

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

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

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

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

G

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

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

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

Constructor of the GenericAnnotationWrapper class.

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

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

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

Constructor of the class GenericObjectWrapper.

GenericObjectWrapper.SortById<U extends GenericObjectWrapper<?>> - Class in fr.igred.omero

Class used to sort wrappers.

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

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

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

Constructor of the class GenericRepositoryObjectWrapper.

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

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

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

Constructor of the GenericShapeWrapper class using a ShapeData.

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

Gets the ImageData acquisition date

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

Gets the AdminFacility linked to the gateway to use admin specific function.

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

Returns an array containing the value for each voxels

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

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

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

Gets the sRGB alpha value of the channel.

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

Gets the sRGB blue value of the channel.

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

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

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

Returns the 5D bounds containing the ROI.

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

Gets the BrowseFacility used to access the data from OMERO.

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

Gets C coordinate.

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

Gets the channel.

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

Gets the current color of the channel

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

Gets the original color of the channel

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

Returns the label of the channel.

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

Gets the name of the channel

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

Gets the image channels

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

Gets the original channel color.

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

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

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

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

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

getConfig() - Method in class fr.igred.omero.Client

Gets a copy of the importation config for the user.

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

Gets the List of NamedValue contained in the MapAnnotationData.

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

Gets the coordinates of the MaskData shape.

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

Gets the coordinates of the LineData shape.

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

Gets the coordinates of the MaskData shape.

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

Gets the coordinates of the PointData shape.

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

Gets the coordinates of the RectangleData shape.

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

Gets the coordinates of the TextData shape.

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

Gets the object creation date

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

Contains the permissions of the user in the group.

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

Gets the current group ID.

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

Gets the value contained in the table

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

Gets a certain value of the table

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

Gets the dataset with the specified id from OMERO.

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

Gets all the datasets available from OMERO.

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

Gets all the datasets in the project available from OMERO.

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

Gets all datasets with this tag from OMERO.

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

Gets all datasets with a certain name from OMERO.

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

Gets the dataset with the specified name from OMERO

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

Returns the default Group for this Experimenter

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

Retrieves the description of the underlying AnnotationData instance.

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

Returns the description of the group.

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

Gets the DatasetData description

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

Gets the folder description

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

Gets the ImageData description

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

Gets the project description

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

Gets the DataManagerFacility to handle/write data on OMERO.

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

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

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

Returns the e-mail of the experimenter.

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

Gets size of bounds for each coordinate.

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

Returns the experimenters contained in this group.

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

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

Returns the first name of the experimenter.

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

Gets the folder with the specified id on OMERO.

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

Gets the list of Folder linked to the image Associate the folder to the image

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

Gets ShapeData font size

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

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

Gets the sRGB green value of the channel.

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

Returns the group which matches the name.

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

Gets the group ID

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

Returns the groups the experimenter is a member of.

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

Returns the height of the mask.

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

Returns the height untransformed rectangle.

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

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

Gets the user id.

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

Gets the object id

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

Returns an ImageWrapper that contains the image with the specified id from OMERO.

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

Gets all images available from OMERO.

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

Gets all images with this tag from OMERO.

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

Gets all images in the dataset available from OMERO.

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

Gets all images in the project available from OMERO.

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

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

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

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

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

Gets all images with a certain from OMERO.

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

Gets all images in the dataset with a certain key

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

Gets all images in the project with a certain key

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

Gets all images with a certain key

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

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

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

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

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

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

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

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

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

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

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

Gets all images with a certain key value pair from OMERO

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

Gets all images tagged with a specified tag from OMERO.

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

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

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

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

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

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

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

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

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

Gets all images tagged with a specified tag from OMERO.

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

Returns the channel index.

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

Returns the institution where the experimenter works.

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

Gets the List of NamedValue (Key-Value pair) associated to an object.

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

Returns the time when the annotation was last modified.

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

Returns the last name of the experimenter.

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

Returns the leaders of this group.

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

Returns the mask as a byte array.

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

Returns the mask image.

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

Returns the points in the polygon.

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

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

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

Gets the MetadataFacility used to manipulate annotations from OMERO.

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

Returns the middle name of the experimenter.

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

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

Gets the name of the TagData.

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

Returns the name of the group.

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

Returns the name of the channel.

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

Gets the DatasetData name

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

Gets the name of the folder

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

Gets the ImageData name

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

Gets the ProjectData name

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

Retrieves the AnnotationData namespace of the underlying AnnotationData instance.

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

Gets the owner ID

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

Gets the PixelsWrapper of the image

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

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

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

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

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

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

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

Gets the pixel type.

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

Returns the points in the Polygon.

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

Returns the points in the Polyline.

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

Gets the project with the specified id from OMERO.

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

Gets all projects available from OMERO.

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

Gets all projects with this tag from OMERO.

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

Gets all projects with a certain name from OMERO.

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

Returns the radius along the X-axis.

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

Returns the radius along the Y-axis.

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

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

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

Returns an array containing the raw values for each voxels for each planes corresponding to the bounds

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

Gets the sRGB red value of the channel.

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

Gets the ROIFacility used to manipulate ROI from OMERO.

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

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

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

Gets all ROIs linked to the image in OMERO

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

getSessionId() - Method in class fr.igred.omero.Client

Get the ID of the current session

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

Returns the list of shapes contained in the ROIData

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

Gets size of bounds for each coordinate.

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

Gets the size of the image on the C axis

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

Gets the size of the image on the T axis

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

Gets the size of the image on the X axis

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

Gets the size of the image on the Y axis

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

Gets the size of the image on the Z axis

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

Gets starting coordinates.

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

Sets ShapeData stroke color

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

Gets T coordinate.

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

Sets the time-point.

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

Gets a certain table linked to the object in OMERO

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

Gets all table linked to the object in OMERO.

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

Gets the TablesFacility used to manipulate table from OMERO.

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

Gets a specific tag from the OMERO database

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

Gets the list of TagAnnotationWrapper available to the user

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

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

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

Gets the list of TagAnnotationWrapper with the specified name available to the user

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

Gets the text on the ShapeData.

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

Gets the text on the ShapeData.

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

Gets the text on the ShapeData.

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

Gets the text on the ShapeData.

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

Gets the text on the ShapeData.

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

Gets the text on the ShapeData.

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

Gets the text on the ShapeData.

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

Gets the text on the ShapeData.

getText() - Method in class fr.igred.omero.roi.ShapeWrapper

Gets the text on the ShapeData.

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

Gets the text on the ShapeData.

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

Retrieves the image thumbnail of the specified size.

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

Returns the current user.

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

Returns the user which matches the username.

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

Returns the last name of the experimenter.

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

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

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

Returns the width of the mask.

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

Returns the width untransformed rectangle.

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

Gets X coordinate.

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

Returns the x-coordinate of the center of the ellipse.

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

Returns the x-coordinate of the top-left corner of the mask.

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

Returns the x-coordinate of the shape.

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

Returns the x-coordinate of the shape.

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

Returns the x-coordinate of the shape.

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

Returns the x-coordinate of the starting point of an untransformed line.

getX2() - Method in class fr.igred.omero.roi.LineWrapper

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

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

Gets Y coordinate.

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

Returns the y-coordinate of the center of the ellipse.

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

Returns the y-coordinate of the top-left corner of the mask.

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

Returns the y coordinate of the shape.

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

Returns the y coordinate of the shape.

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

Returns the y coordinate of the shape.

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

Returns the y-coordinate of the starting point of an untransformed line.

getY2() - Method in class fr.igred.omero.roi.LineWrapper

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

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

Gets Z coordinate.

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

Gets the z-section.

GroupWrapper - Class in fr.igred.omero.meta

GroupWrapper(GroupData) - Constructor for class fr.igred.omero.meta.GroupWrapper

Constructor of the class GroupWrapper.

GroupWrapper.SortByName<U extends GroupWrapper> - Class in fr.igred.omero.meta

Class used to sort GroupWrappers.

H

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

Helper method to convert an exception from: DSAccessException to AccessException DSOutOfServiceException to ServiceException ServerError to OMEROServerError

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

Helper method to convert an exception from: DSOutOfServiceException to ServiceException DSAccessException to AccessException

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

Helper method to convert an exception from: DSOutOfServiceException to ServiceException ServerError to OMEROServerError

I

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

ImageWrapper - Class in fr.igred.omero.repository

Class containing an ImageData.

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

Constructor of the class ImageWrapper

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

Imports one image candidate in the paths to the dataset in OMERO.

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

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

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

Returns true if the experimenter is active, false otherwise.

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

Checks if the table is complete

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

Returns true if the user is connected via LDAP.

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

Checks if supplied group id matches any group to which the current experimenter belongs to.

L

LineWrapper - Class in fr.igred.omero.roi

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

Constructor of the RectangleWrapper class using a new empty LineData.

LineWrapper(double, double, double, double) - Constructor for class fr.igred.omero.roi.LineWrapper

Constructor of the RectangleWrapper class using a new LineData.

LineWrapper(LineData) - Constructor for class fr.igred.omero.roi.LineWrapper

Constructor of the LineWrapper class using a LineData.

M

MapAnnotationWrapper - Class in fr.igred.omero.annotations

Class containing a MapAnnotationData, a MapAnnotationData contains a list of NamedValue(Key-Value pair).

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

Constructor of the MapAnnotationWrapper class.

MapAnnotationWrapper(List<NamedValue>) - Constructor for class fr.igred.omero.annotations.MapAnnotationWrapper

Constructor of the MapAnnotationWrapper class.

MapAnnotationWrapper(MapAnnotationData) - Constructor for class fr.igred.omero.annotations.MapAnnotationWrapper

Constructor of the MapAnnotationWrapper class.

MaskWrapper - Class in fr.igred.omero.roi

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

Constructor of the MaskWrapper class using a new empty MaskData.

MaskWrapper(double, double, double, double, byte[]) - Constructor for class fr.igred.omero.roi.MaskWrapper

Constructor of the MaskWrapper class using a new MaskData.

MaskWrapper(MaskData) - Constructor for class fr.igred.omero.roi.MaskWrapper

Constructor of the MaskWrapper class using a MaskData.

MAX_DIST - Static variable in class fr.igred.omero.repository.PixelsWrapper

Size of tiles when retrieving pixels

O

OMEROServerError - Exception in fr.igred.omero.exception

Reports an error occurred on the server.

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

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

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

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

P

PixelsWrapper - Class in fr.igred.omero.repository

Class containing a PixelData

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

Constructor of the PixelsWrapper class

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

Class containing 5D bounds coordinates

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

Class containing 5D pixel coordinates

PointWrapper - Class in fr.igred.omero.roi

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

Constructor of the PointWrapper class using a new empty PointData.

PointWrapper(double, double) - Constructor for class fr.igred.omero.roi.PointWrapper

Constructor of the PointWrapper class using a new empty ShapeData.

PointWrapper(PointData) - Constructor for class fr.igred.omero.roi.PointWrapper

Constructor of the PointWrapper class using a PointData.

PolygonWrapper - Class in fr.igred.omero.roi

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

Constructor of the PolygonWrapper class using a new empty LineData.

PolygonWrapper(List<Point2D.Double>) - Constructor for class fr.igred.omero.roi.PolygonWrapper

Constructor of the PolygonWrapper class using a new LineData.

PolygonWrapper(PolygonData) - Constructor for class fr.igred.omero.roi.PolygonWrapper

Constructor of the PolygonWrapper class using a PolygonData.

PolylineWrapper - Class in fr.igred.omero.roi

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

Constructor of the RectangleWrapper class using a new empty LineData.

PolylineWrapper(List<Point2D.Double>) - Constructor for class fr.igred.omero.roi.PolylineWrapper

Constructor of the RectangleWrapper class using a new LineData.

PolylineWrapper(PolylineData) - Constructor for class fr.igred.omero.roi.PolylineWrapper

Constructor of the PolylineWrapper class using a PolylineData.

ProjectWrapper - Class in fr.igred.omero.repository

Class containing a ProjectData

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

Constructor of the ProjectWrapper class.

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

Constructor of the ProjectWrapper class.

R

RectangleWrapper - Class in fr.igred.omero.roi

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

Constructor of the RectangleWrapper class using a new empty RectangleData.

RectangleWrapper(double, double, double, double) - Constructor for class fr.igred.omero.roi.RectangleWrapper

Constructor of the RectangleWrapper class using a new RectangleData.

RectangleWrapper(RectangleData) - Constructor for class fr.igred.omero.roi.RectangleWrapper

Constructor of the RectangleWrapper class using a RectangleData.

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

Refreshes the wrapped project.

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

Refreshes the wrapped project.

ROIWrapper - Class in fr.igred.omero.roi

Class containing a ROIData

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

Constructor of the ROIWrapper class.

ROIWrapper(List<GenericShapeWrapper<?>>) - Constructor for class fr.igred.omero.roi.ROIWrapper

Constructor of the ROIWrapper class.

ROIWrapper(ROIData) - Constructor for class fr.igred.omero.roi.ROIWrapper

Constructor of the ROIWrapper class.

S

save(IObject) - Method in class fr.igred.omero.Client

Saves an object on OMERO.

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

Saves and updates object.

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

Saves the ROI.

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

Links a ROI to the image in OMERO

ServiceException - Exception in fr.igred.omero.exception

Reports an error occurred while trying to access the OMERO service.

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

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

ServiceException(Throwable, ConnectionStatus) - Constructor for exception fr.igred.omero.exception.ServiceException

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

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

Sets the channel.

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

Sets the information about a certain column.

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

Sets the content of the MapAnnotationData.

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

Sets the coordinates of the EllipseData shape.

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

Sets the coordinates of the LineData shape.

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

Sets the coordinates of the MaskData shape.

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

Sets the coordinates of the PointData shape.

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

Sets the coordinates of the RectangleData shape.

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

Sets the coordinates of the TextData object.

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

Sets the coordinates the PointData shape.

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

Sets the coordinates of the TextData shape.

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

Sets the coordinates of the EllipseData shape.

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

Sets the coordinates of the LineData shape.

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

Sets the coordinates of the MaskData shape.

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

Sets the coordinates of the RectangleData shape.

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

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

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

Changes the wrapped data.

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

Sets the description of the underlying AnnotationData instance.

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

Sets the description of the group.

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

Sets the description of the dataset.

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

Sets the description of the folder.

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

Sets the description of the image.

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

Sets the description of the project.

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

Sets the e-mail of the experimenter.

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

Sets the fileId of the table.

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

Sets the first name of the experimenter.

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

Sets ShapeData font size

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

Sets the height of an untransformed mask.

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

Sets the height of an untransformed rectangle.

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

Sets the id of the table.

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

Sets the image associated to the folder

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

Sets the image linked to the ROI.

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

Sets the image associated to the folder

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

Sets the institution where the experimenter works.

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

Sets the last name of the experimenter.

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

Sets the mask

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

Sets the mask image.

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

Sets the mask

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

Sets the middle name of the experimenter.

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

Sets the name of the table.

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

Sets the name of the TagData.

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

Sets the name of the group.

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

Sets the name of the channel.

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

Sets the name of the dataset.

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

Sets the name of the folder.

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

Sets the name of the image.

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

Sets the name of the project.

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

Sets the name space of the underlying AnnotationData instance.

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

Sets the points in the polyline.

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

Sets the points in the polyline.

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

Sets the radius along the X-axis.

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

Sets the radius along the Y-axis.

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

Sets the number of row in the table.

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

Sets ShapeData stroke color

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

Sets the time-point.

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

Sets the text on the ShapeData.

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

Sets the text on the ShapeData.

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

Sets the text on the ShapeData.

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

Sets the text on the ShapeData.

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

Sets the text on the ShapeData.

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

Sets the text on the ShapeData.

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

Sets the text on the ShapeData.

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

Sets the text on the ShapeData.

setText(String) - Method in class fr.igred.omero.roi.ShapeWrapper

Sets the text on the ShapeData.

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

Sets the text on the ShapeData.

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

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

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

Sets the transform from a AffineTransform.

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

Sets the width of an untransformed mask.

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

Sets width of an untransformed rectangle.

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

Sets the x-coordinate of the center of the ellipse.

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

Sets the x-coordinate top-left corner of an untransformed mask.

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

Sets the x-coordinate of the shape.

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

Sets the x-coordinate of the shape.

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

Sets the x-coordinate of the shape.

setX1(double) - Method in class fr.igred.omero.roi.LineWrapper

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

setX2(double) - Method in class fr.igred.omero.roi.LineWrapper

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

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

Sets the y-coordinate of the center of the ellipse.

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

Sets the y-coordinate top-left corner of an untransformed mask.

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

Sets the y-coordinate of the shape.

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

Sets the y-coordinate of the shape.

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

Sets the y-coordinate of the shape.

setY1(double) - Method in class fr.igred.omero.roi.LineWrapper

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

setY2(double) - Method in class fr.igred.omero.roi.LineWrapper

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

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

Sets the z-section.

ShapeList - Class in fr.igred.omero.roi

List of GenericShapeWrapper objects

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

ShapeWrapper - Class in fr.igred.omero.roi

ShapeWrapper(ShapeData) - Constructor for class fr.igred.omero.roi.ShapeWrapper

Constructor of the ShapeWrapper class using a ShapeData.

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

SortByLastName() - Constructor for class fr.igred.omero.meta.ExperimenterWrapper.SortByLastName

SortByName() - Constructor for class fr.igred.omero.meta.GroupWrapper.SortByName

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

Gets the client associated with the username in the parameters.

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

Change the current group used by the current user;

T

TableWrapper - Class in fr.igred.omero.annotations

Class containing the information to create a Table in OMERO.

TableWrapper(int, String) - Constructor for class fr.igred.omero.annotations.TableWrapper

Constructor of the class TableWrapper

TableWrapper(Client, ResultsTable, Long, List<Roi>, String) - Constructor for class fr.igred.omero.annotations.TableWrapper

Constructor of the class TableWrapper.

TableWrapper(TableData) - Constructor for class fr.igred.omero.annotations.TableWrapper

Constructor of the class TableWrapper.

TagAnnotationWrapper - Class in fr.igred.omero.annotations

Class containing a TagAnnotationData

TagAnnotationWrapper(Client, String, String) - Constructor for class fr.igred.omero.annotations.TagAnnotationWrapper

Constructor of the TagAnnotationWrapper class.

TagAnnotationWrapper(TagAnnotationData) - Constructor for class fr.igred.omero.annotations.TagAnnotationWrapper

Constructor of the TagAnnotationWrapper class.

TextWrapper - Class in fr.igred.omero.roi

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

Constructor of the TextWrapper class using a new empty ShapeData.

TextWrapper(String, double, double) - Constructor for class fr.igred.omero.roi.TextWrapper

Creates a new instance of the TextWrapper, sets the centre and major, minor axes.

TextWrapper(TextData) - Constructor for class fr.igred.omero.roi.TextWrapper

Constructor of the TextWrapper class using a TextData.

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

Converts the shape to an Shape.

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

Converts the shape to an Shape.

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

Converts the shape to an Shape.

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

Converts the shape to an Shape.

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

Converts the shape to an Shape.

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

Converts the shape to an Shape.

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

Converts the shape to an Shape.

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

Converts the shape to an Shape.

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

Converts the shape to an Shape.

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

Converts the shape to an Shape.

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

Converts AffineTransform to AffineTransform.

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

Converts shape to ImageJ ROI.

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

Converts shape to ImageJ ROI.

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

Converts shape to ImageJ ROI.

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

Converts shape to ImageJ ROI.

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

Converts shape to ImageJ ROI.

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

Converts shape to ImageJ ROI.

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

Convert ROI to ImageJ list of ROIs.

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

Converts shape to ImageJ ROI.

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

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

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

Generates the ImagePlus from the ij library corresponding to the image from OMERO WARNING : you need to include the ij library to use this function

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

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

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

Gets the imagePlus from the image generated from the ROI.

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

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

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

Deletes all unused row in the table

U

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

Unlink all ROI, associated to the image set, in the folder.

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

Unlink an ROI, associated to the image set, in the folder.

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