Uses of Class
fr.igred.omero.exception.ServiceException

Packages that use ServiceException

Package	Description
fr.igred.omero	This package contains the main interfaces and abstract classes to handle OME Remote Objects.
fr.igred.omero.annotations	This package contains interfaces and classes for handling annotations.
fr.igred.omero.client	This package contains the client interfaces used to interact with an OMERO server and a class implementing them.
fr.igred.omero.containers	This package contains interfaces and classes related to the hierarchical organization for images,
fr.igred.omero.core	This package contains interfaces and classes to handle images and their content, such as pixels, channels or planes.
fr.igred.omero.exception	This package contains wrapper classes for exceptions and an exception handler.
fr.igred.omero.roi	This package contains wrapper classes for OMERO shapes and ROIs.
fr.igred.omero.screen	This package contains interfaces and classes related to the HCS organization, e.g.

Uses of ServiceException in fr.igred.omero

Methods in fr.igred.omero that throw ServiceException

Modifier and Type	Method	Description
default long	Annotatable.addAndReplaceFile(Client client, java.io.File file)	Uploads a file, links it to the object and unlinks previous files with the same name, or deletes them if they're orphaned.
long	Annotatable.addAndReplaceFile(Client client, java.io.File file, ReplacePolicy policy)	Uploads a file, links it to the object and unlinks or deletes previous files with the same name.
long	AnnotatableWrapper.addAndReplaceFile(Client client, java.io.File file, ReplacePolicy policy)	Uploads a file, links it to the object and unlinks or deletes previous files with the same name.
default void	Annotatable.addAndReplaceTable(Client client, Table table)	Adds a table to the object in OMERO and unlinks previous tables with the same name, or deletes them if they're orphaned.
void	Annotatable.addAndReplaceTable(Client client, Table table, ReplacePolicy policy)	Adds a table to the object in OMERO and unlinks or deletes previous tables with the same name.
void	AnnotatableWrapper.addAndReplaceTable(Client client, Table table, ReplacePolicy policy)	Adds a table to the object in OMERO and unlinks or deletes previous tables with the same name.
void	Annotatable.addKeyValuePair(DataManager dm, java.lang.String key, java.lang.String value)	Adds a single Key-Value pair to the object.
void	AnnotatableWrapper.addKeyValuePair(DataManager dm, java.lang.String key, java.lang.String value)	Adds a single Key-Value pair to the object.
default void	Annotatable.addTable(DataManager dm, Table table)	Adds a table to the object in OMERO.
void	Annotatable.addTag(DataManager dm, java.lang.Long id)	Adds a tag to the object in OMERO, if possible.
void	Annotatable.addTag(DataManager dm, java.lang.String name, java.lang.String description)	Adds a newly created tag to the object in OMERO, if possible.
void	AnnotatableWrapper.addTag(DataManager dm, java.lang.Long id)	Adds a tag to the object in OMERO, if possible.
void	AnnotatableWrapper.addTag(DataManager dm, java.lang.String name, java.lang.String description)	Adds a newly created tag to the object in OMERO, if possible.
default void	Annotatable.addTags(DataManager dm, java.lang.Long... ids)	Adds multiple tags by ID to the object in OMERO, if possible.
default void	Annotatable.copyAnnotationLinks(Client client, Annotatable object)	Copies annotation links from some other object to this one.
default java.util.List<AnnotationData>	Annotatable.getAnnotationData(Browser browser)	Retrieves annotations linked to the object.
java.util.List<Annotation>	Annotatable.getAnnotations(Browser browser)	Retrieves annotations linked to the object (of known types).
java.util.List<Annotation>	AnnotatableWrapper.getAnnotations(Browser browser)	Retrieves annotations linked to the object (of known types).
java.util.List<Dataset>	ContainerLinked.getDatasets(Browser browser)	Retrieves the datasets linked to this object, either directly, or through parents/children.
java.util.List<FileAnnotation>	Annotatable.getFileAnnotations(Browser browser)	Returns the file annotations
java.util.List<FileAnnotation>	AnnotatableWrapper.getFileAnnotations(Browser browser)	Returns the file annotations
java.util.List<Image>	ImageLinked.getImages(Browser browser)	Retrieves the images linked to this object, either directly, or through parents/children.
default java.util.List<java.util.Map.Entry<java.lang.String,java.lang.String>>	Annotatable.getKeyValuePairs(Browser browser)	Gets the List of Key-Value pairs associated to an object.
java.util.List<MapAnnotation>	Annotatable.getMapAnnotations(Browser browser)	Gets all map annotations linked to an object in OMERO, if possible.
java.util.List<MapAnnotation>	AnnotatableWrapper.getMapAnnotations(Browser browser)	Gets all map annotations linked to an object in OMERO, if possible.
int	Annotatable.getMyRating(Browser browser)	Returns the user rating for this object (averaged if multiple ratings are linked).
int	AnnotatableWrapper.getMyRating(Browser browser)	Returns the user rating for this object (averaged if multiple ratings are linked).
java.util.List<PlateAcquisition>	HCSLinked.getPlateAcquisitions(Browser browser)	Returns the plate acquisitions linked to this object, either directly, or through parents/children.
java.util.List<Plate>	HCSLinked.getPlates(Browser browser)	Returns the plates linked to this object, either directly, or through parents/children.
java.util.List<Project>	ContainerLinked.getProjects(Browser browser)	Retrieves the projects linked to this object, either directly, or through parents/children.
java.util.List<Screen>	HCSLinked.getScreens(Browser browser)	Retrieves the screens linked to this object, either directly, or through parents/children.
Table	Annotatable.getTable(DataManager dm, java.lang.Long fileId)	Gets a certain table linked to the object in OMERO.
Table	AnnotatableWrapper.getTable(DataManager dm, java.lang.Long fileId)	Gets a certain table linked to the object in OMERO.
default java.util.List<Table>	Annotatable.getTables(DataManager dm)	Gets all tables linked to the object in OMERO.
java.util.List<TagAnnotation>	Annotatable.getTags(Browser browser)	Gets all tags linked to an object in OMERO, if possible.
java.util.List<TagAnnotation>	AnnotatableWrapper.getTags(Browser browser)	Gets all tags linked to an object in OMERO, if possible.
default java.util.List<java.lang.String>	Annotatable.getValues(Browser browser, java.lang.String key)	Gets the value from a Key-Value pair associated to the object.
java.util.List<Well>	HCSLinked.getWells(Browser browser)	Retrieves the wells linked to this object, either directly, or through parents/children.
protected static java.util.List<java.lang.Long>	RepositoryObjectWrapper.importImage(ConnectionHandler client, DataObject target, java.lang.String path)	Imports one image file to the target in OMERO.
protected static boolean	RepositoryObjectWrapper.importImages(ConnectionHandler client, DataObject target, java.lang.String... paths)	Imports all images candidates in the paths to the target in OMERO.
default <A extends Annotation> boolean	Annotatable.isLinked(Browser browser, A annotation)	Checks if a specific annotation is linked to the object.
default <A extends AnnotationData> void	Annotatable.link(DataManager dm, A annotation)	Attach an AnnotationData to this object.
default <A extends Annotation> void	Annotatable.link(DataManager dm, A annotation)	Adds an annotation to the object in OMERO, if possible.
default void	Annotatable.link(DataManager dm, Annotation... annotations)	Adds multiple annotations to the object in OMERO, if possible.
default void	Annotatable.linkIfNotLinked(Client client, Annotation... annotations)	Adds multiple annotations to the object in OMERO if they are not already linked.
void	Annotatable.rate(Client client, int rating)	Rates the object (using a rating annotation).
void	AnnotatableWrapper.rate(Client client, int rating)	Rates the object (using a rating annotation).
protected void	AnnotatableWrapper.removeLink(Client client, java.lang.String linkType, long childId)	Removes the link of the given type with the given child ID.
void	ObjectWrapper.saveAndUpdate(DataManager dm)	Saves and updates object.
void	RemoteObject.saveAndUpdate(DataManager dm)	Saves and updates object.
<A extends Annotation> void	Annotatable.unlink(Client client, A annotation)	Unlinks the given annotation from the current object.
<A extends Annotation> void	AnnotatableWrapper.unlink(Client client, A annotation)	Unlinks the given annotation from the current object.

Uses of ServiceException in fr.igred.omero.annotations

Methods in fr.igred.omero.annotations that throw ServiceException

Modifier and Type	Method	Description
default void	Table.addRows(Client client, ResultsTable results, java.lang.Long imageId, java.util.Collection<? extends Roi> ijRois)	Adds rows from an ImageJ ResultsTable.
void	Table.addRows(Client client, ResultsTable results, java.lang.Long imageId, java.util.Collection<? extends Roi> ijRois, java.lang.String roiProperty)	Adds rows from an ImageJ ResultsTable.
void	TableWrapper.addRows(Client client, ResultsTable results, java.lang.Long imageId, java.util.Collection<? extends Roi> ijRois, java.lang.String roiProperty)	Adds rows from an ImageJ ResultsTable.
default int	Annotation.countAnnotationLinks(Browser browser)	Returns the number of annotations links for this object.
java.util.List<Dataset>	AnnotationWrapper.getDatasets(Browser browser)	Gets all datasets with this annotation from OMERO.
java.io.File	FileAnnotation.getFile(ConnectionHandler client, java.lang.String path)	Returns the original file.
java.io.File	FileAnnotationWrapper.getFile(ConnectionHandler client, java.lang.String path)	Returns the original file.
java.util.List<Folder>	Annotation.getFolders(Browser browser)	Gets all folders with this annotation from OMERO.
java.util.List<Folder>	AnnotationWrapper.getFolders(Browser browser)	Gets all folders with this annotation from OMERO.
java.util.List<Image>	AnnotationWrapper.getImages(Browser browser)	Gets all images with this annotation from OMERO.
java.util.List<PlateAcquisition>	AnnotationWrapper.getPlateAcquisitions(Browser browser)	Gets all plate acquisitions with this annotation from OMERO.
java.util.List<Plate>	AnnotationWrapper.getPlates(Browser browser)	Gets all plates with this annotation from OMERO.
java.util.List<Project>	AnnotationWrapper.getProjects(Browser browser)	Gets all projects with this annotation from OMERO.
java.util.List<Screen>	AnnotationWrapper.getScreens(Browser browser)	Gets all screens with this annotation from OMERO.
java.util.List<Well>	AnnotationWrapper.getWells(Browser browser)	Gets all wells with this annotation from OMERO.

Constructors in fr.igred.omero.annotations that throw ServiceException

Constructor	Description
TableWrapper(Client client, ResultsTable results, java.lang.Long imageId, java.util.Collection<? extends Roi> ijRois)	Constructor of the class TableWrapper.
TableWrapper(Client client, ResultsTable results, java.lang.Long imageId, java.util.Collection<? extends Roi> ijRois, java.lang.String roiProperty)	Constructor of the class TableWrapper.
TagAnnotationWrapper(DataManager dm, java.lang.String name, java.lang.String description)	Constructor of the TagAnnotationWrapper class.

Uses of ServiceException in fr.igred.omero.client

Methods in fr.igred.omero.client that throw ServiceException

Modifier and Type	Method	Description
default void	ConnectionHandler.connect(java.lang.String hostname, int port, java.lang.String sessionId)	Connects to OMERO using a session ID.
default void	ConnectionHandler.connect(java.lang.String hostname, int port, java.lang.String username, char[] password)	Connects the user to OMERO.
default void	ConnectionHandler.connect(java.lang.String hostname, int port, java.lang.String username, char[] password, java.lang.Long groupID)	Connects the user to OMERO.
void	ConnectionHandler.connect(LoginCredentials credentials)	Connects the user to OMERO.
void	GatewayWrapper.connect(LoginCredentials credentials)	Connects the user to OMERO.
default void	DataManager.delete(Table table)	Deletes a table from OMERO.
default void	DataManager.delete(RemoteObject object)	Deletes an object from OMERO.
default void	DataManager.delete(java.util.Collection<? extends RemoteObject> objects)	Deletes multiple objects from OMERO.
default void	DataManager.delete(java.util.List<IObject> objects)	Deletes multiple objects from OMERO.
default void	DataManager.delete(IObject object)	Deletes an object from OMERO.
default void	DataManager.deleteFile(java.lang.Long id)	Deletes a file from OMERO
default java.util.List<IObject>	Browser.findByQuery(java.lang.String query)	Finds objects on OMERO through a database query.
default Dataset	Browser.getDataset(java.lang.Long id)	Gets the dataset with the specified id from OMERO.
default java.util.List<Dataset>	Browser.getDatasets()	Gets all datasets available from OMERO.
default java.util.List<Dataset>	Browser.getDatasets(Experimenter experimenter)	Gets all datasets available from OMERO owned by a given user.
default java.util.List<Dataset>	Browser.getDatasets(java.lang.Long... ids)	Gets the datasets with the specified ids from OMERO.
default java.util.List<Dataset>	Browser.getDatasets(java.lang.String name)	Gets all datasets with a certain name from OMERO.
default Folder	Browser.getFolder(long id)	Gets the folder with the specified ID from OMERO, fully loaded.
default java.util.List<Folder>	Browser.getFolders()	Gets all folders available from OMERO.
default java.util.List<Folder>	Browser.getFolders(Experimenter experimenter)	Gets all the folders owned by a given user from OMERO.
default Group	AdminManager.getGroup(java.lang.String groupName)	Returns the group which matches the name.
default Image	Browser.getImage(java.lang.Long id)	Returns the image with the specified ID from OMERO.
default java.util.List<Image>	Browser.getImages()	Gets all images owned by the current user.
default java.util.List<Image>	Browser.getImages(Annotation annotation)	Gets all images with the specified annotation from OMERO.
default java.util.List<Image>	Browser.getImages(java.lang.Long... ids)	Gets the images with the specified ids from OMERO
default java.util.List<Image>	Browser.getImages(java.lang.String name)	Gets all images with a certain name from OMERO.
default java.util.List<Image>	Browser.getImages(java.lang.String projectName, java.lang.String datasetName, java.lang.String imageName)	Gets all images with the name specified inside projects and datasets with the given names.
default java.util.List<Image>	Browser.getImagesLike(java.lang.String motif)	Gets all images with a certain motif in their name from OMERO.
default java.util.List<Image>	Browser.getImagesWithKey(java.lang.String key)	Gets all images with a certain key.
default java.util.List<Image>	Browser.getImagesWithKeyValuePair(java.lang.String key, java.lang.String value)	Gets all images with a certain key value pair from OMERO
default OMEROMetadataStoreClient	ConnectionHandler.getImportStore()	Creates or recycles the import store.
default MapAnnotation	Browser.getMapAnnotation(java.lang.Long id)	Gets a specific map annotation (key/value pairs) from the OMERO database.
default java.util.List<MapAnnotation>	Browser.getMapAnnotations()	Gets the list of map annotations available to the user.
default java.util.List<MapAnnotation>	Browser.getMapAnnotations(java.lang.String key)	Gets the list of map annotations with the specified key available to the user.
default java.util.List<MapAnnotation>	Browser.getMapAnnotations(java.lang.String key, java.lang.String value)	Gets the list of map annotations with the specified key and value available to the user.
default Plate	Browser.getPlate(java.lang.Long id)	Gets the plate with the specified id from OMERO.
default java.util.List<Plate>	Browser.getPlates()	Gets all plates available from OMERO.
default java.util.List<Plate>	Browser.getPlates(Experimenter experimenter)	Gets all plates available from OMERO owned by a given user.
default java.util.List<Plate>	Browser.getPlates(java.lang.Long... ids)	Gets the plates with the specified ids from OMERO.
default Project	Browser.getProject(java.lang.Long id)	Gets the project with the specified id from OMERO.
default java.util.List<Project>	Browser.getProjects()	Gets all projects available from OMERO.
default java.util.List<Project>	Browser.getProjects(Experimenter experimenter)	Gets all projects available from OMERO owned by a given user.
default java.util.List<Project>	Browser.getProjects(java.lang.Long... ids)	Gets the projects with the specified ids from OMERO.
default java.util.List<Project>	Browser.getProjects(java.lang.String name)	Gets all projects with a certain name from OMERO.
omero.api.IQueryPrx	Browser.getQueryService()	Returns the IQueryPrx used to find objects on OMERO.
default omero.api.IQueryPrx	Client.getQueryService()	Returns the IQueryPrx used to find objects on OMERO.
default Screen	Browser.getScreen(java.lang.Long id)	Gets the screen with the specified id from OMERO.
default java.util.List<Screen>	Browser.getScreens()	Gets all screens available from OMERO.
default java.util.List<Screen>	Browser.getScreens(Experimenter experimenter)	Gets all screens available from OMERO owned by a given user.
default java.util.List<Screen>	Browser.getScreens(java.lang.Long... ids)	Gets the screens with the specified ids from OMERO.
default java.lang.String	ConnectionHandler.getSessionId()	Get the ID of the current session
default TagAnnotation	Browser.getTag(java.lang.Long id)	Gets a specific tag from the OMERO database.
default java.util.List<TagAnnotation>	Browser.getTags()	Gets the list of tag annotations available to the user.
default java.util.List<TagAnnotation>	Browser.getTags(java.lang.String name)	Gets the list of tag annotations with the specified name available to the user.
default Experimenter	AdminManager.getUser(java.lang.String username)	Returns the user which matches the username.
default Well	Browser.getWell(java.lang.Long id)	Gets the well with the specified id from OMERO.
default java.util.List<Well>	Browser.getWells()	Gets all wells available from OMERO.
default java.util.List<Well>	Browser.getWells(Experimenter experimenter)	Gets all wells available from OMERO owned by a given user.
default java.util.List<Well>	Browser.getWells(java.lang.Long... ids)	Gets the wells with the specified ids from OMERO.
default java.util.List<Folder>	Browser.loadFolders(java.lang.Long... ids)	Gets the folders with the specified IDs from OMERO (fully loaded).
default IObject	DataManager.save(IObject object)	Saves an object on OMERO.
Client	Client.sudo(java.lang.String username)	Gets the client associated with the username in the parameters.
ConnectionHandler	ConnectionHandler.sudo(java.lang.String username)	Returns a ConnectionHandler associated with the given username.
Client	GatewayWrapper.sudo(java.lang.String username)	Returns a Client associated with the given username.

Uses of ServiceException in fr.igred.omero.containers

Methods in fr.igred.omero.containers that throw ServiceException

Modifier and Type	Method	Description
default Dataset	Project.addDataset(Client client, Dataset dataset)	Adds a dataset to the project in OMERO.
Dataset	Project.addDataset(Client client, java.lang.String name, java.lang.String description)	Adds a dataset to the project in OMERO.
Dataset	ProjectWrapper.addDataset(Client client, java.lang.String name, java.lang.String description)	Adds a dataset to the project in OMERO.
default void	Dataset.addImage(Client client, Image image)	Adds a single image to the dataset in OMERO
default void	Dataset.addImages(Client client, java.lang.Iterable<? extends Image> images)	Adds a list of image to the dataset in OMERO.
default void	Folder.addImages(DataManager dm, Image... images)	Links images to the folder in OMERO.
default void	Folder.addROIs(DataManager dm, long imageId, ROI... rois)	Adds ROIs to the folder and associate them to the provided image ID.
default void	Folder.addROIs(DataManager dm, Image image, ROI... rois)	Adds ROIs to the folder and associate them to the provided image.
default java.util.List<Dataset>	Dataset.getDatasets(Browser browser)	Reloads and returns this dataset (updated from OMERO) as a singleton list.
default java.util.List<Dataset>	Project.getDatasets(Browser browser)	Reloads this project and retrieves the updated list of datasets contained in this project.
java.util.List<Image>	Dataset.getImages(Browser browser)	Gets all images in the dataset available from OMERO.
default java.util.List<Image>	Dataset.getImages(Browser browser, java.lang.String name)	Gets all images in the dataset with a certain name from OMERO.
java.util.List<Image>	DatasetWrapper.getImages(Browser browser)	Gets all images in the dataset available from OMERO.
default java.util.List<Image>	Folder.getImages(Browser browser)	Retrieves the images contained in this folder.
java.util.List<Image>	Project.getImages(Browser browser)	Gets all images in the project available from OMERO.
default java.util.List<Image>	Project.getImages(Browser browser, java.lang.String name)	Gets all images in the project with a certain name from OMERO.
default java.util.List<Image>	Project.getImages(Browser browser, java.lang.String datasetName, java.lang.String imageName)	Gets all images with a certain name from datasets with the specified name inside this project on OMERO.
java.util.List<Image>	ProjectWrapper.getImages(Browser browser)	Gets all images in the project available from OMERO.
default java.util.List<Image>	Dataset.getImagesLike(Browser browser, java.lang.String motif)	Gets all images in the dataset with a certain motif in their name from OMERO.
default java.util.List<Image>	Project.getImagesLike(Browser browser, java.lang.String motif)	Gets all images in the project with a certain motif in their name from OMERO.
default java.util.List<Image>	Dataset.getImagesTagged(Browser browser, TagAnnotation tag)	Gets all images in the dataset tagged with a specified tag from OMERO.
default java.util.List<Image>	Dataset.getImagesTagged(Browser browser, java.lang.Long tagId)	Gets all images in the dataset tagged with a specified tag from OMERO.
default java.util.List<Image>	Project.getImagesTagged(Browser browser, TagAnnotation tag)	Gets all images in the project tagged with a specified tag from OMERO.
default java.util.List<Image>	Project.getImagesTagged(Browser browser, java.lang.Long tagId)	Gets all images in the project tagged with a specified tag from OMERO.
default java.util.List<Image>	Dataset.getImagesWithKey(Browser browser, java.lang.String key)	Gets all images in the dataset with a certain key
default java.util.List<Image>	Project.getImagesWithKey(Browser browser, java.lang.String key)	Gets all images in the project with a certain key
default java.util.List<Image>	Dataset.getImagesWithKeyValuePair(Browser browser, java.lang.String key, java.lang.String value)	Gets all images in the dataset with a certain key value pair from OMERO
default java.util.List<Image>	Project.getImagesWithKeyValuePair(Browser browser, java.lang.String key, java.lang.String value)	Gets all images in the project with a certain key value pair from OMERO.
default java.util.List<Project>	Dataset.getProjects(Browser browser)	Retrieves the projects containing this dataset.
default java.util.List<Project>	Project.getProjects(Browser browser)	Reloads and returns this project as a singleton list.
java.util.List<ROI>	Folder.getROIs(DataManager dm, long imageId)	Gets the ROIs contained in the folder associated with the provided image ID.
default java.util.List<ROI>	Folder.getROIs(DataManager dm, Image image)	Gets the ROIs contained in the folder associated with the provided image.
java.util.List<ROI>	FolderWrapper.getROIs(DataManager dm, long imageId)	Gets the ROIs contained in the folder associated with the provided image ID.
default java.util.List<java.lang.Long>	Dataset.importAndReplaceImages(Client client, java.lang.String path)	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.
default java.util.List<java.lang.Long>	Dataset.importAndReplaceImages(Client client, java.lang.String path, ReplacePolicy policy)	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.
java.util.List<java.lang.Long>	Dataset.importImage(Client client, java.lang.String path)	Imports one image file to the dataset in OMERO.
java.util.List<java.lang.Long>	DatasetWrapper.importImage(Client client, java.lang.String path)	Imports one image file to the dataset in OMERO.
boolean	Dataset.importImages(Client client, java.lang.String... paths)	Imports all images candidates in the paths to the dataset in OMERO.
boolean	DatasetWrapper.importImages(Client client, java.lang.String... paths)	Imports all images candidates in the paths to the dataset in OMERO.
default <A extends AnnotationData> void	Folder.link(DataManager dm, A annotation)	Attach an AnnotationData to this object.
void	Dataset.reload(Browser browser)	Reloads the dataset from OMERO.
void	DatasetWrapper.reload(Browser browser)	Reloads the dataset from OMERO.
void	Folder.reload(Browser browser)	Reloads the folder from OMERO, to update all links.
void	FolderWrapper.reload(Browser browser)	Reloads the folder from OMERO, to update all links.
void	Project.reload(Browser browser)	Reloads the project from OMERO.
void	ProjectWrapper.reload(Browser browser)	Reloads the project from OMERO.
void	Project.removeDataset(Client client, Dataset dataset)	Removes a dataset from the project in OMERO.
void	ProjectWrapper.removeDataset(Client client, Dataset dataset)	Removes a dataset from the project in OMERO.
void	Dataset.removeImage(Client client, Image image)	Removes an image from the dataset in OMERO.
void	DatasetWrapper.removeImage(Client client, Image image)	Removes an image from the dataset in OMERO.
default java.util.List<Image>	Dataset.replaceImages(Client client, java.util.Collection<? extends Image> oldImages, Image newImage)	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).
void	Folder.unlinkAllROIs(DataManager dm)	Unlink all ROIs associated to this folder.
default void	Folder.unlinkAllROIs(DataManager dm, long imageId)	Unlink all ROIs associated to the provided image ID from the folder.
default void	Folder.unlinkAllROIs(DataManager dm, Image image)	Unlink all ROIs associated to the provided image from the folder.
void	FolderWrapper.unlinkAllROIs(DataManager dm)	Unlink all ROIs associated to this folder.
default void	Folder.unlinkROIs(DataManager dm, ROI... rois)	Unlink ROIs from the folder.

Constructors in fr.igred.omero.containers that throw ServiceException

Constructor	Description
FolderWrapper(DataManager dm, java.lang.String name)	Constructor of the FolderWrapper class.
ProjectWrapper(DataManager dm, java.lang.String name, java.lang.String description)	Constructor of the ProjectWrapper class.

Uses of ServiceException in fr.igred.omero.core

Methods in fr.igred.omero.core that throw ServiceException

Modifier and Type	Method	Description
java.util.List<java.io.File>	Image.download(ConnectionHandler client, java.lang.String path)	Downloads the original files from the server.
java.util.List<java.io.File>	ImageWrapper.download(ConnectionHandler client, java.lang.String path)	Downloads the original files from the server.
default java.awt.Color	Image.getChannelColor(Client client, int index)	Gets the current color of the channel
default java.awt.Color	Image.getChannelImportedColor(Browser browser, int index)	Gets the original color of the channel
default java.lang.String	Image.getChannelName(Browser browser, int index)	Gets the name of the channel.
java.util.List<Channel>	Image.getChannels(Browser browser)	Gets the image channels.
java.util.List<Channel>	ImageWrapper.getChannels(Browser browser)	Gets the image channels.
default java.util.List<Dataset>	Image.getDatasets(Browser browser)	Retrieves the datasets containing this image
default java.util.List<Image>	Image.getFilesetImages(Browser browser)	Returns the list of images sharing the same fileset as the current image.
default java.util.List<Folder>	Image.getFolders(Browser browser)	Gets the list of folders linked to this image.
default java.util.List<Image>	Image.getImages(Browser browser)	Returns this image, updated from OMERO, as a singleton list.
default java.util.List<PlateAcquisition>	Image.getPlateAcquisitions(Browser browser)	Returns the plate acquisitions linked to this image.
default java.util.List<Plate>	Image.getPlates(Browser browser)	Retrieves the plates containing this image.
default java.util.List<Project>	Image.getProjects(Browser browser)	Retrieves the projects containing this image.
java.util.List<Folder>	Image.getROIFolders(DataManager dm)	Gets the list of folders linked to the ROIs in this image.
java.util.List<Folder>	ImageWrapper.getROIFolders(DataManager dm)	Gets the list of folders linked to the ROIs in this image.
java.util.List<ROI>	Image.getROIs(DataManager dm)	Gets all ROIs linked to the image in OMERO
java.util.List<ROI>	ImageWrapper.getROIs(DataManager dm)	Gets all ROIs linked to the image in OMERO
default java.util.List<Screen>	Image.getScreens(Browser browser)	Retrieves the screens containing this image
java.awt.image.BufferedImage	Image.getThumbnail(ConnectionHandler client, int size)	Retrieves the image thumbnail of the specified size.
java.awt.image.BufferedImage	ImageWrapper.getThumbnail(ConnectionHandler client, int size)	Retrieves the image thumbnail of the specified size.
default java.util.List<Well>	Image.getWells(Browser browser)	Retrieves the wells containing this image.
default boolean	Image.isOrphaned(Browser browser)	Checks if image is orphaned (not in a WellSample nor linked to a dataset).
void	Pixels.loadPlanesInfo(Browser browser)	Loads the planes information.
void	PixelsWrapper.loadPlanesInfo(Browser browser)	Loads the planes information.
default java.util.List<ROI>	Image.saveROIs(DataManager dm, ROI... rois)	Links ROIs to the image in OMERO.
java.util.List<ROI>	Image.saveROIs(DataManager dm, java.util.Collection<? extends ROI> rois)	Links ROIs to the image in OMERO.
java.util.List<ROI>	ImageWrapper.saveROIs(DataManager dm, java.util.Collection<? extends ROI> rois)	Links ROIs to the image in OMERO.
default ImagePlus	Image.toImagePlus(Client client)	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
ImagePlus	Image.toImagePlus(Client client, int[] xBounds, int[] yBounds, int[] cBounds, int[] zBounds, int[] tBounds)	Gets the imagePlus generated from the image from OMERO corresponding to the bound.
default ImagePlus	Image.toImagePlus(Client client, ROI roi)	Gets the imagePlus from the image generated from the ROI.
ImagePlus	ImageWrapper.toImagePlus(Client client, int[] xBounds, int[] yBounds, int[] cBounds, int[] zBounds, int[] tBounds)	Gets the imagePlus generated from the image from OMERO corresponding to the bound.

Uses of ServiceException in fr.igred.omero.exception

Methods in fr.igred.omero.exception that throw ServiceException

Modifier and Type	Method	Description
ExceptionHandler<T>	ExceptionHandler.handleException(java.lang.String message)	Throws: AccessException if DSAccessException was caught ServiceException if DSOutOfServiceException was caught ServerException if ServerError was caught
ExceptionHandler<T>	ExceptionHandler.handleServiceOrAccess(java.lang.String message)	Throws: ServiceException if DSOutOfServiceException was caught AccessException if DSAccessException was caught
ExceptionHandler<T>	ExceptionHandler.handleServiceOrServer(java.lang.String message)	Throws: ServiceException if DSOutOfServiceException was caught ServerException if ServerError was caught

Uses of ServiceException in fr.igred.omero.roi

Methods in fr.igred.omero.roi that throw ServiceException

Modifier and Type	Method	Description
default <A extends AnnotationData> void	ROI.link(DataManager dm, A annotation)	Attach an AnnotationData to this object.
default <A extends AnnotationData> void	Shape.link(DataManager dm, A annotation)	Attach an AnnotationData to this object.
void	ROI.saveROI(DataManager dm)	Saves the ROI.
void	ROIWrapper.saveROI(DataManager dm)	Saves the ROI.

Uses of ServiceException in fr.igred.omero.screen

Methods in fr.igred.omero.screen that throw ServiceException

Modifier and Type	Method	Description
default java.util.List<Image>	Plate.getImages(Browser browser)	Returns the images contained in the wells of this plate.
default java.util.List<Image>	PlateAcquisition.getImages(Browser browser)	Retrieves the images contained in the wells in the parent plate.
default java.util.List<Image>	Screen.getImages(Browser browser)	Retrieves the images contained in this screen.
default java.util.List<Image>	Well.getImages(Browser browser)	Reloads this well and retrieves the images it contains.
default java.util.List<PlateAcquisition>	Plate.getPlateAcquisitions(Browser browser)	Reloads this plate and returns the related plate acquisitions.
default java.util.List<PlateAcquisition>	Screen.getPlateAcquisitions(Browser browser)	Returns the plate acquisitions linked to this object, either directly, or through parents/children.
default java.util.List<PlateAcquisition>	Well.getPlateAcquisitions(Browser browser)	Refreshes this well and returns the plate acquisitions linked to it.
default java.util.List<PlateAcquisition>	WellSample.getPlateAcquisitions(Browser browser)	Returns the plate acquisitions linked to the parent Well.
default java.util.List<Plate>	Plate.getPlates(Browser browser)	Reloads and returns this plate as a singleton list.
default java.util.List<Plate>	PlateAcquisition.getPlates(Browser browser)	Returns the (updated) parent plate as a singleton list.
default java.util.List<Plate>	Screen.getPlates(Browser browser)	Reloads this screen and returns the updated list of plates linked to this screen.
default java.util.List<Plate>	Well.getPlates(Browser browser)	Reloads this well and returns the plate containing it.
default java.util.List<Plate>	WellSample.getPlates(Browser browser)	Returns the plates containing the parent Well.
default java.util.List<Screen>	Plate.getScreens(Browser browser)	Retrieves the screens containing this plate.
default java.util.List<Screen>	PlateAcquisition.getScreens(Browser browser)	Retrieves the screens containing the parent plates.
default java.util.List<Screen>	Screen.getScreens(Browser browser)	Reloads and returns this screen as a singleton list.
default java.util.List<Screen>	Well.getScreens(Browser browser)	Refreshes this well and retrieves the screens containing it.
default java.util.List<Screen>	WellSample.getScreens(Browser browser)	Returns the screens containing the parent Well.
default Well	WellSample.getWell(Browser browser)	Retrieves the well containing this well sample.
java.util.List<Well>	Plate.getWells(Browser browser)	Gets all wells in the plate available from OMERO.
default java.util.List<Well>	PlateAcquisition.getWells(Browser browser)	Retrieves the wells contained in the parent plate.
java.util.List<Well>	PlateWrapper.getWells(Browser browser)	Gets all wells in the plate available from OMERO.
default java.util.List<Well>	Screen.getWells(Browser browser)	Retrieves the wells linked to this object, either directly, or through parents/children.
default java.util.List<Well>	Well.getWells(Browser browser)	Reloads this well and returns it as a singleton list.
default java.util.List<Well>	WellSample.getWells(Browser browser)	Retrieves the well containing this Well Sample as a singleton list.
java.util.List<java.lang.Long>	Screen.importImage(Client client, java.lang.String path)	Imports one image file to the screen in OMERO.
java.util.List<java.lang.Long>	ScreenWrapper.importImage(Client client, java.lang.String path)	Imports one image file to the screen in OMERO.
boolean	Screen.importImages(Client client, java.lang.String... paths)	Imports all images candidates in the paths to the screen in OMERO.
boolean	ScreenWrapper.importImages(Client client, java.lang.String... paths)	Imports all images candidates in the paths to the screen in OMERO.
default <A extends AnnotationData> void	PlateAcquisition.link(DataManager dm, A annotation)	Attach an AnnotationData to this object.
<A extends AnnotationData> void	PlateAcquisitionWrapper.link(DataManager dm, A annotation)	Adds a tag to the object in OMERO, if possible.
void	Plate.reload(Browser browser)	Reloads the plate from OMERO.
void	PlateWrapper.reload(Browser browser)	Reloads the plate from OMERO.
void	Screen.reload(Browser browser)	Reloads the screen from OMERO.
void	ScreenWrapper.reload(Browser browser)	Reloads the screen from OMERO.
void	Well.reload(Browser browser)	Reloads the well from OMERO.
void	WellWrapper.reload(Browser browser)	Reloads the well from OMERO.

Constructors in fr.igred.omero.screen that throw ServiceException

Constructor	Description
ScreenWrapper(DataManager dm, java.lang.String name, java.lang.String description)	Constructor of the ProjectWrapper class.