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

Packages that use AccessException

Package	Description
fr.igred.omero	This package contains abstract wrapper classes for the OMERO Gateway and the basic OMERO object.
fr.igred.omero.annotations	This package contains wrapper classes for annotations.
fr.igred.omero.exception	This package contains wrapper classes for exceptions and an exception handler.
fr.igred.omero.meta	This package contains wrapper classes for users, groups and planes information.
fr.igred.omero.repository	This package contains classes related to the hierarchical organization for images.
fr.igred.omero.roi	This package contains wrapper classes for OMERO shapes and ROIs.

Uses of AccessException in fr.igred.omero

Methods in fr.igred.omero that throw AccessException

Modifier and Type	Method	Description
long	AnnotatableWrapper.addAndReplaceFile(Client client, 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	AnnotatableWrapper.addAndReplaceFile(Client client, File file, GenericRepositoryObjectWrapper.ReplacePolicy policy)	Uploads a file, links it to the object and unlinks or deletes previous files with the same name.
void	AnnotatableWrapper.addAndReplaceTable(Client client, TableWrapper 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	AnnotatableWrapper.addAndReplaceTable(Client client, TableWrapper table, GenericRepositoryObjectWrapper.ReplacePolicy policy)	Adds a table to the object in OMERO and unlinks or deletes previous tables with the same name.
void	AnnotatableWrapper.addFileAnnotation(Client client, FileAnnotationWrapper annotation)	Deprecated. Links a file annotation to the object.
void	AnnotatableWrapper.addKeyValuePair(Client client, String key, String value)	Adds a single Key-Value pair to the object.
void	AnnotatableWrapper.addMapAnnotation(Client client, MapAnnotationWrapper mapAnnotation)	Deprecated. Adds a List of Key-Value pair to the object.
void	AnnotatableWrapper.addPairKeyValue(Client client, String key, String value)	Deprecated. Adds a single Key-Value pair to the object.
void	AnnotatableWrapper.addTable(Client client, TableWrapper table)	Adds a table to the object in OMERO.
void	AnnotatableWrapper.addTag(Client client, TagAnnotationWrapper tag)	Deprecated. Adds a tag to the object in OMERO, if possible.
void	AnnotatableWrapper.addTag(Client client, Long id)	Adds a tag to the object in OMERO, if possible.
void	AnnotatableWrapper.addTag(Client client, String name, String description)	Adds a newly created tag to the object in OMERO, if possible.
void	AnnotatableWrapper.addTags(Client client, TagAnnotationWrapper... tags)	Deprecated. Adds multiple tag to the object in OMERO, if possible.
void	AnnotatableWrapper.addTags(Client client, Long... ids)	Adds multiple tags by ID to the object in OMERO, if possible.
void	AnnotatableWrapper.copyAnnotationLinks(Client client, AnnotatableWrapper<?> object)	Copies annotation links from some other object to this one.
void	Client.delete(TableWrapper table)	Deprecated. Deletes a table from OMERO.
void	Client.delete(GenericObjectWrapper<?> object)	Deletes an object from OMERO.
void	Client.delete(Collection<? extends GenericObjectWrapper<?>> objects)	Deletes multiple objects from OMERO.
void	GatewayWrapper.deleteFile(Long id)	Deletes a file from OMERO
void	GatewayWrapper.deleteFiles(Long... ids)	Deletes files from OMERO.
void	Client.deleteTable(TableWrapper table)	Deletes a table from OMERO.
void	Client.deleteTables(Collection<? extends TableWrapper> tables)	Deletes tables from OMERO.
AnnotationList	AnnotatableWrapper.getAnnotations(Client client)	Retrieves annotations linked to the object (of known types).
DatasetWrapper	Browser.getDataset(Long id)	Gets the dataset with the specified id from OMERO.
List<DatasetWrapper>	Browser.getDatasets()	Gets all datasets available from OMERO.
List<DatasetWrapper>	Browser.getDatasets(ExperimenterWrapper experimenter)	Gets all datasets available from OMERO owned by a given user.
List<DatasetWrapper>	Browser.getDatasets(Long... ids)	Gets the datasets with the specified ids from OMERO.
List<DatasetWrapper>	Browser.getDatasets(String name)	Gets all datasets with a certain name from OMERO.
List<FileAnnotationWrapper>	AnnotatableWrapper.getFileAnnotations(Client client)	Returns the file annotations
FolderWrapper	Browser.getFolder(long id)	Gets the folder with the specified ID from OMERO, fully loaded.
List<FolderWrapper>	Browser.getFolders()	Gets all folders available from OMERO.
List<FolderWrapper>	Browser.getFolders(ExperimenterWrapper experimenter)	Gets all the folders owned by a given user from OMERO.
GroupWrapper	Client.getGroup(String groupName)	Returns the group which matches the name.
List<GroupWrapper>	Client.getGroups()	Returns all the groups on OMERO.
ImageWrapper	Browser.getImage(Long id)	Returns the image with the specified ID from OMERO.
List<ImageWrapper>	Browser.getImages()	Gets all images owned by the current user.
abstract List<ImageWrapper>	Browser.getImages(GenericAnnotationWrapper<?> annotation)	Gets all images with the specified annotation from OMERO.
List<ImageWrapper>	Browser.getImages(Long... ids)	Gets the images with the specified ids from OMERO
List<ImageWrapper>	Browser.getImages(String name)	Gets all images with a certain name from OMERO.
abstract List<ImageWrapper>	Browser.getImages(String projectName, String datasetName, String imageName)	Gets all images with the name specified inside projects and datasets with the given names.
List<ImageWrapper>	Client.getImages(GenericAnnotationWrapper<?> annotation)	Gets all images with the specified annotation from OMERO.
List<ImageWrapper>	Client.getImages(String projectName, String datasetName, String imageName)	Gets all images with the name specified inside projects and datasets with the given names.
abstract List<ImageWrapper>	Browser.getImagesKey(String key)	Deprecated. Gets all images with a certain key
List<ImageWrapper>	Client.getImagesKey(String key)	Deprecated. Gets all images with a certain key
List<ImageWrapper>	Browser.getImagesLike(String motif)	Gets all images with a certain motif in their name from OMERO.
abstract List<ImageWrapper>	Browser.getImagesPairKeyValue(String key, String value)	Deprecated. Gets all images with a certain key value pair from OMERO
List<ImageWrapper>	Client.getImagesPairKeyValue(String key, String value)	Deprecated. Gets all images with a certain key value pair from OMERO
List<ImageWrapper>	Browser.getImagesTagged(TagAnnotationWrapper tag)	Deprecated. Gets all images tagged with a specified tag from OMERO.
List<ImageWrapper>	Browser.getImagesTagged(Long tagId)	Deprecated. Gets all images tagged with a specified tag from OMERO.
List<ImageWrapper>	Browser.getImagesWithKey(String key)	Gets all images with a certain key.
List<ImageWrapper>	Browser.getImagesWithKeyValuePair(String key, String value)	Gets all images with a certain key value pair from OMERO
Map<String,String>	AnnotatableWrapper.getKeyValuePairs(Client client)	Gets the List of key-value pairs associated to an object as a map (no duplicate key should exist).
MapAnnotationWrapper	Browser.getMapAnnotation(Long id)	Gets a specific map annotation (key/value pairs) from the OMERO database.
List<MapAnnotationWrapper>	AnnotatableWrapper.getMapAnnotations(Client client)	Gets all map annotations linked to an object in OMERO, if possible.
int	AnnotatableWrapper.getMyRating(Client client)	Returns the user rating for this object (averaged if multiple ratings are linked).
List<DatasetWrapper>	Browser.getOrphanedDatasets()	Gets all orphaned datasets available from OMERO owned by the current user.
List<DatasetWrapper>	Browser.getOrphanedDatasets(ExperimenterWrapper experimenter)	Gets all orphaned datasets available from OMERO owned by a given user.
List<ImageWrapper>	Browser.getOrphanedImages()	Gets all orphaned images owned by the current user.
List<ImageWrapper>	Browser.getOrphanedImages(ExperimenterWrapper experimenter)	Gets all orphaned images owned by the specified user.
List<PlateWrapper>	Browser.getOrphanedPlates()	Gets all orphaned plates available from OMERO for the current user.
List<PlateWrapper>	Browser.getOrphanedPlates(ExperimenterWrapper experimenter)	Gets all orphaned plates available from OMERO owned by a given user.
PlateWrapper	Browser.getPlate(Long id)	Gets the plate with the specified id from OMERO.
List<PlateWrapper>	Browser.getPlates()	Gets all plates available from OMERO.
List<PlateWrapper>	Browser.getPlates(ExperimenterWrapper experimenter)	Gets all plates available from OMERO owned by a given user.
List<PlateWrapper>	Browser.getPlates(Long... ids)	Gets the plates with the specified ids from OMERO.
ProjectWrapper	Browser.getProject(Long id)	Gets the project with the specified id from OMERO.
List<ProjectWrapper>	Browser.getProjects()	Gets all projects available from OMERO.
List<ProjectWrapper>	Browser.getProjects(ExperimenterWrapper experimenter)	Gets all projects available from OMERO owned by a given user.
List<ProjectWrapper>	Browser.getProjects(Long... ids)	Gets the projects with the specified ids from OMERO.
List<ProjectWrapper>	Browser.getProjects(String name)	Gets all projects with a certain name from OMERO.
List<RatingAnnotationWrapper>	AnnotatableWrapper.getRatings(Client client)	Returns all the ratings from all users for this object.
ScreenWrapper	Browser.getScreen(Long id)	Gets the screen with the specified id from OMERO.
List<ScreenWrapper>	Browser.getScreens()	Gets all screens available from OMERO.
List<ScreenWrapper>	Browser.getScreens(ExperimenterWrapper experimenter)	Gets all screens available from OMERO owned by a given user.
List<ScreenWrapper>	Browser.getScreens(Long... ids)	Gets the screens with the specified ids from OMERO.
TableWrapper	AnnotatableWrapper.getTable(Client client, Long fileId)	Gets a certain table linked to the object in OMERO.
List<TableWrapper>	AnnotatableWrapper.getTables(Client client)	Gets all tables linked to the object in OMERO.
List<TagAnnotationWrapper>	AnnotatableWrapper.getTags(Client client)	Gets all tags linked to an object in OMERO, if possible.
ExperimenterWrapper	Client.getUser(String username)	Returns the user which matches the username.
String	AnnotatableWrapper.getValue(Client client, String key)	Gets the value from a Key-Value pair associated to the object.
WellWrapper	Browser.getWell(Long id)	Gets the well with the specified id from OMERO.
List<WellWrapper>	Browser.getWells()	Gets all wells available from OMERO.
List<WellWrapper>	Browser.getWells(ExperimenterWrapper experimenter)	Gets all wells available from OMERO owned by a given user.
List<WellWrapper>	Browser.getWells(Long... ids)	Gets the wells with the specified ids from OMERO.
<A extends GenericAnnotationWrapper<?>> boolean	AnnotatableWrapper.isLinked(Client client, A annotation)	Checks if a specific annotation is linked to the object.
protected <A extends AnnotationData> void	AnnotatableWrapper.link(Client client, A annotation)	Attach an AnnotationData to this object.
<A extends GenericAnnotationWrapper<?>> void	AnnotatableWrapper.link(Client client, A annotation)	Adds an annotation to the object in OMERO, if possible (and if it's not a TagSet).
void	AnnotatableWrapper.link(Client client, GenericAnnotationWrapper<?>... annotations)	Adds multiple annotations to the object in OMERO, if possible.
void	AnnotatableWrapper.linkIfNotLinked(Client client, GenericAnnotationWrapper<?>... annotations)	Adds multiple annotations to the object in OMERO if they are not already linked.
List<FolderWrapper>	Browser.loadFolders(Long... ids)	Gets the folders with the specified IDs from OMERO (fully loaded).
void	AnnotatableWrapper.rate(Client client, int rating)	Rates the object (using a rating annotation).
protected void	AnnotatableWrapper.removeLink(Client client, String linkType, long childId)	Removes the link of the given type with the given child ID.
protected void	AnnotatableWrapper.removeLinks(Client client, String linkType, Collection<Long> childIds)	Removes the link of the given type with the given child IDs.
IObject	GatewayWrapper.save(IObject object)	Saves an object on OMERO.
void	GenericObjectWrapper.saveAndUpdate(Client client)	Saves and updates object.
Client	Client.sudoGetUser(String username)	Gets the client associated with the username in the parameters.
<A extends GenericAnnotationWrapper<?>> void	AnnotatableWrapper.unlink(Client client, A annotation)	Unlinks the given annotation from the current object.
<A extends GenericAnnotationWrapper<?>> void	AnnotatableWrapper.unlink(Client client, Collection<A> annotations)	Unlinks the given annotations from the current object.

Uses of AccessException in fr.igred.omero.annotations

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

Modifier and Type	Method	Description
void	TableWrapper.addRows(Client client, ResultsTable results, Long imageId, List<? extends Roi> ijRois)	Adds rows from an ImageJ ResultsTable.
void	TableWrapper.addRows(Client client, ResultsTable results, Long imageId, List<? extends Roi> ijRois, String roiProperty)	Adds rows from an ImageJ ResultsTable.
List<DatasetWrapper>	GenericAnnotationWrapper.getDatasets(Client client)	Gets all datasets with this annotation from OMERO.
List<FolderWrapper>	GenericAnnotationWrapper.getFolders(Client client)	Gets all folders with this annotation from OMERO.
List<ImageWrapper>	GenericAnnotationWrapper.getImages(Client client)	Gets all images with this annotation from OMERO.
List<PlateWrapper>	GenericAnnotationWrapper.getPlates(Client client)	Gets all plates with this annotation from OMERO.
List<ProjectWrapper>	GenericAnnotationWrapper.getProjects(Client client)	Gets all projects with this annotation from OMERO.
List<ScreenWrapper>	GenericAnnotationWrapper.getScreens(Client client)	Gets all screens with this annotation from OMERO.
List<TagAnnotationWrapper>	TagSetWrapper.getTags(Browser browser)	Reloads the tag set and returns the corresponding list of tags.
List<WellWrapper>	GenericAnnotationWrapper.getWells(Client client)	Gets all wells with this annotation from OMERO.
void	TagSetWrapper.link(Client dm, TagAnnotationWrapper tag)	Links a tag to this tag set.
void	TagSetWrapper.link(Client dm, TagAnnotationWrapper... tags)	Links multiple tags to this tag set.
void	TagSetWrapper.reload(Browser browser)	Reloads the tag set from OMERO.

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

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

Uses of AccessException in fr.igred.omero.exception

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

Modifier and Type	Method	Description
ExceptionHandler<T>	ExceptionHandler.handleException(String message)	Deprecated. Throws: AccessException if DSAccessException was caught ServiceException if DSOutOfServiceException was caught The appropriate exception if ServerError was caught (see ExceptionHandler.handleOMEROException(java.lang.Throwable, java.lang.String))
static void	ExceptionHandler.handleException(Throwable t, String message)	Deprecated. Helper method to convert an exception from: DSAccessException to AccessException DSOutOfServiceException to ServiceException ServerError to OMEROServerError
ExceptionHandler<T>	ExceptionHandler.handleOMEROException(String message)	Throws: AccessException if DSAccessException was caught ServiceException if DSOutOfServiceException was caught The appropriate exception if ServerError was caught (see ExceptionHandler.handleOMEROException(java.lang.Throwable, java.lang.String))
static void	ExceptionHandler.handleOMEROException(Throwable throwable, String message)	Checks the cause of an exception on OMERO and throws: ServiceException if the cause was: SessionException AuthenticationException ResourceError AccessException if the cause was: SecurityViolation Anything else
ExceptionHandler<T>	ExceptionHandler.handleServerAndService(String message)	Checks if a ServerError or a DSOutOfService was thrown and handles the exception according to the cause.
ExceptionHandler<T>	ExceptionHandler.handleServiceOrAccess(String message)	Deprecated. Throws: ServiceException if DSOutOfServiceException was caught AccessException if DSAccessException was caught
static void	ExceptionHandler.handleServiceOrAccess(Throwable t, String message)	Deprecated. Helper method to convert an exception from: DSOutOfServiceException to ServiceException DSAccessException to AccessException

Uses of AccessException in fr.igred.omero.meta

Methods in fr.igred.omero.meta that throw AccessException

Modifier and Type	Method	Description
boolean	ExperimenterWrapper.isAdmin(Client client)	Returns true if the user is a full admin.

Uses of AccessException in fr.igred.omero.repository

Methods in fr.igred.omero.repository that throw AccessException

Modifier and Type	Method	Description
DatasetWrapper	ProjectWrapper.addDataset(Client client, DatasetWrapper dataset)	Adds a dataset to the project in OMERO.
DatasetWrapper	ProjectWrapper.addDataset(Client client, String name, String description)	Creates a dataset and adds it to the project in OMERO.
void	DatasetWrapper.addImage(Client client, ImageWrapper image)	Adds a single image to the dataset in OMERO
void	DatasetWrapper.addImages(Client client, List<? extends ImageWrapper> images)	Adds a list of image to the dataset in OMERO.
void	FolderWrapper.addImages(Client client, ImageWrapper... images)	Links images to the folder in OMERO.
void	FolderWrapper.addROI(Client client, ROIWrapper roi)	Deprecated. Adds an ROI to the folder and associate it to the image id set(an image need to be associated)
void	FolderWrapper.addROIs(Client client, long imageId, ROIWrapper... rois)	Adds ROIs to the folder and associate them to the provided image ID.
void	FolderWrapper.addROIs(Client client, ImageWrapper image, ROIWrapper... rois)	Adds ROIs to the folder and associate them to the provided image.
void	GenericRepositoryObjectWrapper.copyAnnotationLinks(Client client, GenericRepositoryObjectWrapper<?> object)	Copies annotation links from some other object to this one.
List<File>	ImageWrapper.download(Client client, String path)	Downloads the original files from the server.
double[][][][][]	PixelsWrapper.getAllPixels(Client client)	Returns an array containing the value for each voxel
double[][][][][]	PixelsWrapper.getAllPixels(Client client, int[] xBounds, int[] yBounds, int[] cBounds, int[] zBounds, int[] tBounds)	Returns an array containing the value for each voxel corresponding to the bounds
Color	ImageWrapper.getChannelColor(Client client, int index)	Gets the current color of the channel
Color	ImageWrapper.getChannelImportedColor(Client client, int index)	Gets the original color of the channel
String	ImageWrapper.getChannelName(Client client, int index)	Gets the name of the channel.
List<ChannelWrapper>	ImageWrapper.getChannels(Client client)	Gets the image channels.
List<DatasetWrapper>	ImageWrapper.getDatasets(Client client)	Retrieves the datasets containing this image
List<ImageWrapper>	ImageWrapper.getFilesetImages(Client client)	Returns the list of images sharing the same fileset as the current image.
List<FolderWrapper>	ImageWrapper.getFolders(Client client)	Gets the list of folders linked to this image.
List<ImageWrapper>	DatasetWrapper.getImages(Client client)	Gets all images in the dataset available from OMERO.
List<ImageWrapper>	DatasetWrapper.getImages(Client client, String name)	Gets all images in the dataset with a certain name from OMERO.
List<ImageWrapper>	FolderWrapper.getImages(Client client)	Retrieves the images contained in this folder.
List<ImageWrapper>	PlateAcquisitionWrapper.getImages(Client client)	Retrieves the images contained in the wells in the parent plate.
List<ImageWrapper>	PlateWrapper.getImages(Client client)	Returns the images contained in the wells of this plate.
List<ImageWrapper>	ProjectWrapper.getImages(Client client)	Gets all images in the project available from OMERO.
List<ImageWrapper>	ProjectWrapper.getImages(Client client, String name)	Gets all images in the project with a certain name from OMERO.
List<ImageWrapper>	ProjectWrapper.getImages(Client client, String datasetName, String imageName)	Gets all images with a certain name from datasets with the specified name inside this project on OMERO.
List<ImageWrapper>	ScreenWrapper.getImages(Client client)	Retrieves the images contained in this screen.
List<ImageWrapper>	DatasetWrapper.getImagesKey(Client client, String key)	Deprecated. Gets all images in the dataset with a certain key
List<ImageWrapper>	ProjectWrapper.getImagesKey(Client client, String key)	Deprecated. Gets all images in the project with a certain key
List<ImageWrapper>	DatasetWrapper.getImagesLike(Client client, String motif)	Gets all images in the dataset with a certain motif in their name from OMERO.
List<ImageWrapper>	ProjectWrapper.getImagesLike(Client client, String motif)	Gets all images in the project with a certain motif in their name from OMERO.
List<ImageWrapper>	DatasetWrapper.getImagesPairKeyValue(Client client, String key, String value)	Deprecated. Gets all images in the dataset with a certain key value pair from OMERO
List<ImageWrapper>	ProjectWrapper.getImagesPairKeyValue(Client client, String key, String value)	Deprecated. Gets all images in the project with a certain key value pair from OMERO.
List<ImageWrapper>	DatasetWrapper.getImagesTagged(Client client, TagAnnotationWrapper tag)	Gets all images in the dataset tagged with a specified tag from OMERO.
List<ImageWrapper>	DatasetWrapper.getImagesTagged(Client client, Long tagId)	Gets all images in the dataset tagged with a specified tag from OMERO.
List<ImageWrapper>	ProjectWrapper.getImagesTagged(Client client, TagAnnotationWrapper tag)	Gets all images in the project tagged with a specified tag from OMERO.
List<ImageWrapper>	ProjectWrapper.getImagesTagged(Client client, Long tagId)	Gets all images in the project tagged with a specified tag from OMERO.
List<ImageWrapper>	DatasetWrapper.getImagesWithKey(Client client, String key)	Gets all images in the dataset with a certain key
List<ImageWrapper>	ProjectWrapper.getImagesWithKey(Client client, String key)	Gets all images in the project with a certain key
List<ImageWrapper>	DatasetWrapper.getImagesWithKeyValuePair(Client client, String key, String value)	Gets all images in the dataset with a certain key value pair from OMERO
List<ImageWrapper>	ProjectWrapper.getImagesWithKeyValuePair(Client client, String key, String value)	Gets all images in the project with a certain key value pair from OMERO.
List<PlateAcquisitionWrapper>	ImageWrapper.getPlateAcquisitions(Client client)	Returns the plate acquisitions linked to this image.
List<PlateAcquisitionWrapper>	ScreenWrapper.getPlateAcquisitions(Client client)	Returns the plate acquisitions linked to this object, either directly, or through parents/children.
List<PlateAcquisitionWrapper>	WellSampleWrapper.getPlateAcquisitions(Client client)	Returns the plate acquisitions linked to the parent Well.
List<PlateAcquisitionWrapper>	WellWrapper.getPlateAcquisitions(Client client)	Refreshes this well and returns the plate acquisitions linked to it.
List<PlateWrapper>	ImageWrapper.getPlates(Client client)	Retrieves the plates containing this image.
List<PlateWrapper>	PlateAcquisitionWrapper.getPlates(Client client)	Returns the (updated) parent plate as a singleton list.
List<PlateWrapper>	WellSampleWrapper.getPlates(Client client)	Returns the plates containing the parent Well.
List<ProjectWrapper>	DatasetWrapper.getProjects(Client client)	Retrieves the projects containing this dataset.
List<ProjectWrapper>	ImageWrapper.getProjects(Client client)	Retrieves the projects containing this image
byte[][][][]	PixelsWrapper.getRawPixels(Client client, int bpp)	Returns an array containing the raw values for each voxel for each planes
byte[][][][]	PixelsWrapper.getRawPixels(Client client, int[] xBounds, int[] yBounds, int[] cBounds, int[] zBounds, int[] tBounds, int bpp)	Returns an array containing the raw values for each voxel for each plane corresponding to the bounds
List<FolderWrapper>	ImageWrapper.getROIFolders(Client client)	Gets the list of folders linked to the ROIs in this image.
List<ROIWrapper>	FolderWrapper.getROIs(Client client)	Deprecated. Gets the ROI contained in the folder associated with the image id set (an image need to be associated)
List<ROIWrapper>	FolderWrapper.getROIs(Client client, long imageId)	Gets the ROIs contained in the folder associated with the provided image ID.
List<ROIWrapper>	FolderWrapper.getROIs(Client client, ImageWrapper image)	Gets the ROIs contained in the folder associated with the provided image.
List<ROIWrapper>	ImageWrapper.getROIs(Client client)	Gets all ROIs linked to the image in OMERO
List<ScreenWrapper>	ImageWrapper.getScreens(Client client)	Retrieves the screens containing this image
List<ScreenWrapper>	PlateAcquisitionWrapper.getScreens(Client client)	Retrieves the screens containing the parent plates.
List<ScreenWrapper>	PlateWrapper.getScreens(Client client)	Retrieves the screens containing this plate.
List<ScreenWrapper>	WellSampleWrapper.getScreens(Client client)	Returns the screens containing the parent Well.
List<ScreenWrapper>	WellWrapper.getScreens(Client client)	Refreshes this well and retrieves the screens containing it.
WellWrapper	WellSampleWrapper.getWell(Client client)	Retrieves the well containing this well sample
List<WellWrapper>	ImageWrapper.getWells(Client client)	Retrieves the wells containing this image.
List<WellWrapper>	PlateAcquisitionWrapper.getWells(Client client)	Retrieves the wells contained in the parent plate.
List<WellWrapper>	PlateWrapper.getWells(Client client)	Gets all wells in the plate available from OMERO.
List<WellWrapper>	ScreenWrapper.getWells(Client client)	Retrieves the wells linked to this object, either directly, or through parents/children.
List<WellSampleWrapper>	ImageWrapper.getWellSamples(Client client)	Retrieves the well samples containing this image and updates them from OMERO.
List<WellSampleWrapper>	PlateAcquisitionWrapper.getWellSamples(Browser browser)	Retrieves the well samples for this plate acquisition from OMERO and updates the object.
List<Long>	DatasetWrapper.importAndReplaceImages(Client client, 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.
List<Long>	DatasetWrapper.importAndReplaceImages(Client client, String path, GenericRepositoryObjectWrapper.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.
List<Long>	DatasetWrapper.importImage(Client client, String path)	Imports one image file to the dataset in OMERO.
List<Long>	ScreenWrapper.importImage(GatewayWrapper client, String path)	Imports one image file to the screen in OMERO.
boolean	DatasetWrapper.importImages(Client client, int threads, String... paths)	Imports all images candidates in the paths to the dataset in OMERO.
boolean	DatasetWrapper.importImages(Client client, String... paths)	Imports all images candidates in the paths to the dataset in OMERO.
boolean	ScreenWrapper.importImages(GatewayWrapper client, int threads, String... paths)	Imports all images candidates in the paths to the screen in OMERO.
boolean	ScreenWrapper.importImages(GatewayWrapper client, String... paths)	Imports all images candidates in the paths to the screen in OMERO.
protected <A extends AnnotationData> void	FolderWrapper.link(Client client, A annotation)	Adds an annotation to the object in OMERO, if possible.
protected <A extends AnnotationData> void	PlateAcquisitionWrapper.link(Client client, A annotation)	Adds a tag to the object in OMERO, if possible.
void	PixelsWrapper.loadPlanesInfo(Client client)	Loads the planes information.
void	GenericRepositoryObjectWrapper.refresh(Client client)	Deprecated. Reloads the object from OMERO.
void	ScreenWrapper.refresh(GatewayWrapper client)	Deprecated. Reloads the screen from OMERO.
void	DatasetWrapper.reload(Browser browser)	Reloads the dataset from OMERO.
void	FolderWrapper.reload(Browser browser)	Reloads the folder from OMERO, to update all links.
void	FolderWrapper.reload(Client client)	Deprecated. Reloads the folder from OMERO, to update all links.
void	GenericRepositoryObjectWrapper.reload(Browser browser)	Reloads the object from OMERO.
void	ImageWrapper.reload(Browser browser)	Reloads the image from OMERO.
void	PlateAcquisitionWrapper.reload(Browser browser)	Reloads the plate acquisition from OMERO.
void	PlateWrapper.reload(Browser browser)	Reloads the plate from OMERO.
void	ProjectWrapper.reload(Browser browser)	Reloads the project from OMERO.
void	ScreenWrapper.reload(Browser browser)	Reloads the screen from OMERO.
void	WellSampleWrapper.reload(Browser browser)	Reloads the well sample from OMERO.
void	WellWrapper.reload(Browser browser)	Reloads the well from OMERO.
void	ProjectWrapper.removeDataset(Client client, DatasetWrapper dataset)	Removes a dataset from the project in OMERO.
void	DatasetWrapper.removeImage(Client client, ImageWrapper image)	Removes an image from the dataset in OMERO.
List<ImageWrapper>	DatasetWrapper.replaceImages(Client client, Collection<? extends ImageWrapper> oldImages, ImageWrapper 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	ImageWrapper.saveROI(Client client, ROIWrapper roi)	Deprecated. Links a ROI to the image in OMERO
List<ROIWrapper>	ImageWrapper.saveROIs(Client client, ROIWrapper... rois)	Links ROIs to the image in OMERO.
List<ROIWrapper>	ImageWrapper.saveROIs(Client client, Collection<? extends ROIWrapper> rois)	Links ROIs to the image in OMERO.
ImagePlus	ImageWrapper.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	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.
ImagePlus	ImageWrapper.toImagePlus(Client client, ROIWrapper roi)	Gets the imagePlus from the image generated from the ROI.
void	FolderWrapper.unlinkAllROI(Client client)	Deprecated. Unlink all ROI, associated to the image set, in the folder.
void	FolderWrapper.unlinkAllROIs(Client client)	Unlink all ROIs associated to this folder.
void	FolderWrapper.unlinkAllROIs(Client client, long imageId)	Unlink all ROIs associated to the provided image ID from the folder.
void	FolderWrapper.unlinkAllROIs(Client client, ImageWrapper image)	Unlink all ROIs associated to the provided image from the folder.
void	FolderWrapper.unlinkROI(Client client, ROIWrapper roi)	Deprecated. Unlink an ROI, associated to the image set, in the folder.
void	FolderWrapper.unlinkROIs(Client client, ROIWrapper... rois)	Unlink ROIs from the folder.
void	FolderWrapper.unlinkROIs(Client client, Collection<? extends ROIWrapper> rois)	Unlink ROIs from the folder.

Constructors in fr.igred.omero.repository that throw AccessException

Constructor	Description
ProjectWrapper(Client client, String name, String description)	Constructor of the ProjectWrapper class.
ScreenWrapper(Client client, String name, String description)	Constructor of the ScreenWrapper class.

Uses of AccessException in fr.igred.omero.roi

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

Modifier and Type	Method	Description
<A extends AnnotationData> void	GenericShapeWrapper.link(Client client, A annotation)	Attach an AnnotationData to this object.
protected <A extends AnnotationData> void	ROIWrapper.link(Client client, A annotation)	Attach an AnnotationData to this object.