fr.igred.omero.containers

Interface Dataset

All Superinterfaces:

Annotatable, RemoteObject, RepositoryObject

All Known Implementing Classes:

DatasetWrapper

public interface Dataset
extends RepositoryObject, Annotatable

Interface to handle Datasets on OMERO.

Method Summary

Modifier and Type	Method and Description
default void	addImage(DataManager dm, Image image) Adds a single image to the dataset in OMERO
default void	addImages(DataManager dm, Iterable<? extends Image> images) Adds multiple images to the dataset in OMERO.
DatasetData	asDataObject() Returns a DatasetData corresponding to the handled object.
default List<RepositoryObject>	getChildren(Browser browser) Gets the object children.
List<Image>	getImages() Gets all the images in the dataset (if it was properly loaded from OMERO).
List<Image>	getImages(Browser browser) Gets all images in the dataset available from OMERO.
default List<Image>	getImages(Browser browser, String name) Gets all images in the dataset with a certain name from OMERO.
default List<Image>	getImagesLike(Browser browser, String motif) Gets all images in the dataset with a certain motif in their name from OMERO.
default List<Image>	getImagesTagged(Browser browser, Long tagId) Gets all images in the dataset tagged with a specified tag from OMERO.
default List<Image>	getImagesTagged(Browser browser, TagAnnotation tag) Gets all images in the dataset tagged with a specified tag from OMERO.
default List<Image>	getImagesWithKey(Browser browser, String key) Gets all images in the dataset with a certain key
default List<Image>	getImagesWithKeyValuePair(Browser browser, String key, String value) Gets all images in the dataset with a certain key value pair from OMERO
default List<RepositoryObject>	getParents(Browser browser) Gets the object parents.
default List<Project>	getProjects(Browser browser) Retrieves the projects containing this dataset.
default List<Long>	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.
default List<Long>	importAndReplaceImages(Client client, 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.
List<Long>	importImage(ConnectionHandler client, String path) Imports one image file to the dataset in OMERO.
boolean	importImages(ConnectionHandler client, String... paths) Imports all images candidates in the paths to the dataset in OMERO.
void	reload(Browser browser) Reloads the dataset from OMERO.
void	removeImage(Client client, Image image) Removes an image from the dataset in OMERO.
default List<Image>	replaceImages(Client client, 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	setDescription(String description) Sets the description of the dataset.
void	setName(String name) Sets the name of the dataset.

Methods inherited from interface fr.igred.omero.RepositoryObject

getDescription, getName

Methods inherited from interface fr.igred.omero.Annotatable

addAndReplaceFile, addAndReplaceFile, addAndReplaceTable, addAndReplaceTable, addFile, addKeyValuePair, addTable, addTag, addTag, addTags, copyAnnotationLinks, getAnnotationData, getAnnotations, getFileAnnotations, getKeyValuePairs, getMapAnnotations, getMyRating, getTable, getTables, getTags, getValues, isLinked, link, link, link, linkIfNotLinked, rate, unlink

Methods inherited from interface fr.igred.omero.RemoteObject

canAnnotate, canChgrp, canChown, canDelete, canEdit, canLink, distinct, flatten, getCreated, getElementsOf, getGroupId, getId, getOwner, getUpdated, saveAndUpdate

Method Detail

asDataObject

DatasetData asDataObject()

Returns a DatasetData corresponding to the handled object.

Specified by:

asDataObject in interface RemoteObject

Returns:

See above.

setName

void setName(String name)

Sets the name of the dataset.

Parameters:

name - The name of the dataset. Mustn't be null.

Throws:

IllegalArgumentException - If the name is null.

setDescription

void setDescription(String description)

Sets the description of the dataset.

Parameters:

description - The description of the dataset.

getParents

default List<RepositoryObject> getParents(Browser browser)
                                   throws AccessException,
                                          ServiceException,
                                          ExecutionException

Gets the object parents.

Specified by:

getParents in interface RepositoryObject

Parameters:

browser - The data browser.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

getChildren

default List<RepositoryObject> getChildren(Browser browser)
                                    throws AccessException,
                                           ServiceException,
                                           ExecutionException

Gets the object children.

Specified by:

getChildren in interface RepositoryObject

Parameters:

browser - The data browser.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

getProjects

default List<Project> getProjects(Browser browser)
                           throws ServiceException,
                                  AccessException,
                                  ExecutionException

Retrieves the projects containing this dataset.

Parameters:

browser - The data browser.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

getImages

List<Image> getImages()

Gets all the images in the dataset (if it was properly loaded from OMERO).

Returns:

See above.

getImages

List<Image> getImages(Browser browser)
               throws ServiceException,
                      AccessException,
                      ExecutionException

Gets all images in the dataset available from OMERO.

Parameters:

browser - The data browser.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

getImages

default List<Image> getImages(Browser browser,
                              String name)
                       throws ServiceException,
                              AccessException,
                              ExecutionException

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

Parameters:

browser - The data browser.

name - Name searched.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

getImagesLike

default List<Image> getImagesLike(Browser browser,
                                  String motif)
                           throws ServiceException,
                                  AccessException,
                                  ExecutionException

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

Parameters:

browser - The data browser.

motif - Motif searched in an image name.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

getImagesTagged

default List<Image> getImagesTagged(Browser browser,
                                    TagAnnotation tag)
                             throws ServiceException,
                                    AccessException,
                                    ExecutionException

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

Parameters:

browser - The data browser.

tag - TagAnnotation containing the tag researched.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

getImagesTagged

default List<Image> getImagesTagged(Browser browser,
                                    Long tagId)
                             throws ServiceException,
                                    AccessException,
                                    ExecutionException

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

Parameters:

browser - The data browser.

tagId - ID of the tag researched.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

getImagesWithKey

default List<Image> getImagesWithKey(Browser browser,
                                     String key)
                              throws ServiceException,
                                     AccessException,
                                     ExecutionException

Gets all images in the dataset with a certain key

Parameters:

browser - The data browser.

key - Name of the key researched.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

getImagesWithKeyValuePair

default List<Image> getImagesWithKeyValuePair(Browser browser,
                                              String key,
                                              String value)
                                       throws ServiceException,
                                              AccessException,
                                              ExecutionException

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

Parameters:

browser - The data browser.

key - Name of the key researched.

value - Value associated with the key.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

addImages

default void addImages(DataManager dm,
                       Iterable<? extends Image> images)
                throws ServiceException,
                       AccessException,
                       ExecutionException

Adds multiple images to the dataset in OMERO.

Parameters:

dm - The data manager.

images - Image to add to the dataset.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

addImage

default void addImage(DataManager dm,
                      Image image)
               throws ServiceException,
                      AccessException,
                      ExecutionException

Adds a single image to the dataset in OMERO

Parameters:

dm - The data manager.

image - Image to add.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

removeImage

void removeImage(Client client,
                 Image image)
          throws ServiceException,
                 AccessException,
                 ExecutionException,
                 InterruptedException

Removes an image from the dataset in OMERO.

Parameters:

client - The client handling the connection.

image - Image to remove.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

InterruptedException - If block(long) does not return.

importImages

boolean importImages(ConnectionHandler client,
                     String... paths)
              throws ServiceException,
                     AccessException,
                     IOException

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

Parameters:

client - The client handling the connection.

paths - Paths to the image files on the computer.

Returns:

If the import did not exit because of an error.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

IOException - Cannot read file.

importImage

List<Long> importImage(ConnectionHandler client,
                       String path)
                throws ServiceException,
                       AccessException,
                       IOException

Imports one image file to the dataset in OMERO.

Parameters:

client - The client handling the connection.

path - Path to the image file on the computer.

Returns:

The list of IDs of the newly imported images.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

IOException - Cannot read file.

replaceImages

default List<Image> replaceImages(Client client,
                                  Collection<? extends Image> oldImages,
                                  Image newImage)
                           throws AccessException,
                                  ServiceException,
                                  ExecutionException,
                                  InterruptedException

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).

Parameters:

client - The client handling the connection.

oldImages - The list of old images to replace.

newImage - The new image.

Returns:

The list of images that became orphaned once replaced.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

InterruptedException - If block(long) does not return.

importAndReplaceImages

default List<Long> importAndReplaceImages(Client client,
                                          String path,
                                          ReplacePolicy policy)
                                   throws ServiceException,
                                          AccessException,
                                          IOException,
                                          ExecutionException,
                                          InterruptedException

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.

Parameters:

client - The client handling the connection.

path - Path to the image on the computer.

policy - Whether older images should be unlinked, deleted or deleted only if they become orphaned.

Returns:

The list of IDs of the newly imported images.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

IOException - Cannot read file.

ExecutionException - A Facility can't be retrieved or instantiated.

InterruptedException - If block(long) does not return.

importAndReplaceImages

default List<Long> importAndReplaceImages(Client client,
                                          String path)
                                   throws ServiceException,
                                          AccessException,
                                          IOException,
                                          ExecutionException,
                                          InterruptedException

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.

Parameters:

client - The client handling the connection.

path - Path to the image on the computer.

Returns:

The list of IDs of the newly imported images.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

IOException - Cannot read file.

ExecutionException - A Facility can't be retrieved or instantiated.

InterruptedException - If block(long) does not return.

reload

void reload(Browser browser)
     throws ServiceException,
            AccessException,
            ExecutionException

Reloads the dataset from OMERO.

Specified by:

reload in interface RepositoryObject

Parameters:

browser - The data browser.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.