All Superinterfaces:

Annotatable, ContainerLinked, ImageLinked, RemoteObject, RepositoryObject

All Known Implementing Classes:

DatasetWrapper
```
public interface Dataset
extends RepositoryObject, ContainerLinked
```
Interface to handle Datasets on OMERO.

Method Summary

All Methods Instance Methods Abstract Methods Default Methods
Modifier and Type	Method	Description
`default void`	`addImage(Client client, Image image)`	Adds a single image to the dataset in OMERO
`default void`	`addImages(Client client, java.lang.Iterable<? extends Image> images)`	Adds a list of image to the dataset in OMERO.
`DatasetData`	`asDataObject()`	Returns a `DatasetData` corresponding to the handled object.
`default java.util.List<Dataset>`	`getDatasets(Browser browser)`	Reloads and returns this dataset (updated from OMERO) as a singleton list.
`java.util.List<Image>`	`getImages()`	Gets all the images in the dataset (if it was properly loaded from OMERO).
`java.util.List<Image>`	`getImages(Browser browser)`	Gets all images in the dataset available from OMERO.
`default java.util.List<Image>`	`getImages(Browser browser, java.lang.String name)`	Gets all images in the dataset with a certain name from OMERO.
`default java.util.List<Image>`	`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>`	`getImagesTagged(Browser browser, TagAnnotation tag)`	Gets all images in the dataset tagged with a specified tag from OMERO.
`default java.util.List<Image>`	`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>`	`getImagesWithKey(Browser browser, java.lang.String key)`	Gets all images in the dataset with a certain key
`default java.util.List<Image>`	`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<Project>`	`getProjects(Browser browser)`	Retrieves the projects containing this dataset.
`default java.util.List<java.lang.Long>`	`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>`	`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>`	`importImage(Client client, java.lang.String path)`	Imports one image file to the dataset in OMERO.
`boolean`	`importImages(Client client, java.lang.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 java.util.List<Image>`	`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`	`setDescription(java.lang.String description)`	Sets the description of the dataset.
`void`	`setName(java.lang.String name)`	Sets the name of the dataset.

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, linkIfNotLinked, rate, unlink

Methods inherited from interface fr.igred.omero.RemoteObject
canAnnotate, canChgrp, canChown, canDelete, canEdit, canLink, getCreated, getGroupId, getId, getOwner, saveAndUpdate

Methods inherited from interface fr.igred.omero.RepositoryObject
getDescription, getName

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(java.lang.String name)
```
Sets the name of the dataset.

Parameters:

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

Throws:

java.lang.IllegalArgumentException - If the name is null.

setDescription
```
void setDescription(java.lang.String description)
```
Sets the description of the dataset.

Parameters:

description - The description of the dataset.

getProjects

default java.util.List<Project> getProjects(Browser browser)
                                     throws ServerException,
                                            ServiceException,
                                            AccessException,
                                            java.util.concurrent.ExecutionException

Retrieves the projects containing this dataset.

Specified by:: getProjects in interface ContainerLinked
Parameters:: browser - The data browser.
Returns:: See above.
Throws:: ServerException - Server error.; ServiceException - Cannot connect to OMERO.; AccessException - Cannot access data.; java.util.concurrent.ExecutionException - A Facility can't be retrieved or instantiated.

getDatasets
```
default java.util.List<Dataset> getDatasets(Browser browser)
                                     throws AccessException,
                                            ServiceException,
                                            java.util.concurrent.ExecutionException
```
Reloads and returns this dataset (updated from OMERO) as a singleton list.

Specified by:

getDatasets in interface ContainerLinked

Parameters:

browser - The data browser.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getImages
```
java.util.List<Image> getImages()
```
Gets all the images in the dataset (if it was properly loaded from OMERO).

Returns:

See above.

getImages
```
java.util.List<Image> getImages(Browser browser)
                         throws ServiceException,
                                AccessException,
                                java.util.concurrent.ExecutionException
```
Gets all images in the dataset available from OMERO.

Specified by:

getImages in interface ImageLinked

Parameters:

browser - The data browser.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getImages

default java.util.List<Image> getImages(Browser browser,
                                        java.lang.String name)
                                 throws ServiceException,
                                        AccessException,
                                        java.util.concurrent.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.; java.util.concurrent.ExecutionException - A Facility can't be retrieved or instantiated.

getImagesLike

default java.util.List<Image> getImagesLike(Browser browser,
                                            java.lang.String motif)
                                     throws ServiceException,
                                            AccessException,
                                            java.util.concurrent.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.; java.util.concurrent.ExecutionException - A Facility can't be retrieved or instantiated.

getImagesTagged

default java.util.List<Image> getImagesTagged(Browser browser,
                                              TagAnnotation tag)
                                       throws ServiceException,
                                              AccessException,
                                              ServerException,
                                              java.util.concurrent.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.; ServerException - Server error.; java.util.concurrent.ExecutionException - A Facility can't be retrieved or instantiated.

getImagesTagged

default java.util.List<Image> getImagesTagged(Browser browser,
                                              java.lang.Long tagId)
                                       throws ServiceException,
                                              AccessException,
                                              ServerException,
                                              java.util.concurrent.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.; ServerException - Server error.; java.util.concurrent.ExecutionException - A Facility can't be retrieved or instantiated.

getImagesWithKey

default java.util.List<Image> getImagesWithKey(Browser browser,
                                               java.lang.String key)
                                        throws ServiceException,
                                               AccessException,
                                               java.util.concurrent.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.; java.util.concurrent.ExecutionException - A Facility can't be retrieved or instantiated.

getImagesWithKeyValuePair

default java.util.List<Image> getImagesWithKeyValuePair(Browser browser,
                                                        java.lang.String key,
                                                        java.lang.String value)
                                                 throws ServiceException,
                                                        AccessException,
                                                        java.util.concurrent.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.; java.util.concurrent.ExecutionException - A Facility can't be retrieved or instantiated.

addImages
```
default void addImages(Client client,
                       java.lang.Iterable<? extends Image> images)
                throws ServiceException,
                       AccessException,
                       java.util.concurrent.ExecutionException
```
Adds a list of image to the dataset in OMERO.

Parameters:

client - The client handling the connection.

images - Image to add to the dataset.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

addImage
```
default void addImage(Client client,
                      Image image)
               throws ServiceException,
                      AccessException,
                      java.util.concurrent.ExecutionException
```
Adds a single image to the dataset in OMERO

Parameters:

client - The client handling the connection.

image - Image to add.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

removeImage
```
void removeImage(Client client,
                 Image image)
          throws ServiceException,
                 AccessException,
                 java.util.concurrent.ExecutionException,
                 ServerException,
                 java.lang.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.

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

ServerException - Server error.

java.lang.InterruptedException - If block(long) does not return.

importImages
```
boolean importImages(Client client,
                     java.lang.String... paths)
              throws ServiceException,
                     ServerException,
                     AccessException,
                     java.io.IOException,
                     java.util.concurrent.ExecutionException
```
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.

ServerException - Server error.

java.io.IOException - Cannot read file.

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

importImage

java.util.List<java.lang.Long> importImage(Client client,
                                           java.lang.String path)
                                    throws ServiceException,
                                           AccessException,
                                           ServerException,
                                           java.util.concurrent.ExecutionException

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.; ServerException - Server error.; java.util.concurrent.ExecutionException - A Facility can't be retrieved or instantiated.

replaceImages

default java.util.List<Image> replaceImages(Client client,
                                            java.util.Collection<? extends Image> oldImages,
                                            Image newImage)
                                     throws AccessException,
                                            ServiceException,
                                            java.util.concurrent.ExecutionException,
                                            ServerException,
                                            java.lang.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.; ServerException - Server error.; java.util.concurrent.ExecutionException - A Facility can't be retrieved or instantiated.; java.lang.InterruptedException - If block(long) does not return.

importAndReplaceImages

default java.util.List<java.lang.Long> importAndReplaceImages(Client client,
                                                              java.lang.String path,
                                                              ReplacePolicy policy)
                                                       throws ServiceException,
                                                              AccessException,
                                                              ServerException,
                                                              java.util.concurrent.ExecutionException,
                                                              java.lang.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.; ServerException - Server error.; java.util.concurrent.ExecutionException - A Facility can't be retrieved or instantiated.; java.lang.InterruptedException - If block(long) does not return.

importAndReplaceImages

default java.util.List<java.lang.Long> importAndReplaceImages(Client client,
                                                              java.lang.String path)
                                                       throws ServiceException,
                                                              AccessException,
                                                              ServerException,
                                                              java.util.concurrent.ExecutionException,
                                                              java.lang.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.; ServerException - Server error.; java.util.concurrent.ExecutionException - A Facility can't be retrieved or instantiated.; java.lang.InterruptedException - If block(long) does not return.

reload
```
void reload(Browser browser)
     throws ServiceException,
            AccessException,
            java.util.concurrent.ExecutionException
```
Reloads the dataset from OMERO.

Parameters:

browser - The data browser.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

Interface Dataset

Method Summary

Methods inherited from interface fr.igred.omero.Annotatable

Methods inherited from interface fr.igred.omero.RemoteObject

Methods inherited from interface fr.igred.omero.RepositoryObject

Method Detail

asDataObject

setName

setDescription

getProjects

getDatasets

getImages

getImages

getImages

getImagesLike

getImagesTagged

getImagesTagged

getImagesWithKey

getImagesWithKeyValuePair

addImages

addImage

removeImage

importImages

importImage

replaceImages

importAndReplaceImages

importAndReplaceImages

reload