fr.igred.omero.core

Interface Image

All Superinterfaces:

Annotatable, RemoteObject, RepositoryObject

All Known Implementing Classes:

ImageWrapper

public interface Image
extends RepositoryObject, Annotatable

Interface to handle Images on OMERO.

Method Summary

Modifier and Type	Method and Description
ImageData	asDataObject() Returns a ImageData corresponding to the handled object.
List<File>	download(ConnectionHandler client, String path) Downloads the original files from the server.
Timestamp	getAcquisitionDate() Gets the ImageData acquisition date
default Color	getChannelColor(Client client, int index) Gets the current color of the channel, or the original if it cannot be retrieved.
default Color	getChannelImportedColor(Browser browser, int index) Gets the original color of the channel.
default String	getChannelName(Browser browser, int index) Gets the name of the channel.
List<Channel>	getChannels(Browser browser) Gets the image channels.
default List<RepositoryObject>	getChildren(Browser browser) Returns an empty list as images do not have children.
default List<Dataset>	getDatasets(Browser browser) Retrieves the datasets containing this image from OMERO.
default List<Image>	getFilesetImages(Browser browser) Returns the list of images sharing the same fileset as the current image.
default List<Folder>	getFolders(Browser browser) Gets the list of folders linked to this image.
default List<RepositoryObject>	getParents(Browser browser) Gets the object parents.
Pixels	getPixels() Gets the Pixels for this image.
default List<PlateAcquisition>	getPlateAcquisitions(Browser browser) Returns the plate acquisitions linked to this image.
default List<Plate>	getPlates(Browser browser) Retrieves the plates containing this image.
default List<Project>	getProjects(Browser browser) Retrieves the projects containing this image
List<Folder>	getROIFolders(DataManager dm) Gets the list of folders linked to the ROIs in this image.
List<ROI>	getROIs(DataManager dm) Gets all ROIs linked to the image in OMERO
default List<Screen>	getScreens(Browser browser) Retrieves the screens containing this image
BufferedImage	getThumbnail(ConnectionHandler client, int size) Retrieves the image thumbnail of the specified size.
default List<Well>	getWells(Browser browser) Retrieves the wells containing this image.
List<WellSample>	getWellSamples() Retrieves the well samples containing this image.
default List<WellSample>	getWellSamples(Browser browser) Retrieves the well samples containing this image and updates them from OMERO.
default boolean	isOrphaned(Browser browser) Checks if image is orphaned (not in a WellSample nor linked to a dataset).
void	reload(Browser browser) Reloads the image from OMERO.
List<ROI>	saveROIs(DataManager dm, Collection<? extends ROI> rois) Links ROIs to the image in OMERO.
default List<ROI>	saveROIs(DataManager dm, ROI... rois) Links ROIs to the image in OMERO.
void	setDescription(String description) Sets the description of the image.
void	setName(String name) Sets the name of the image.
default ij.ImagePlus	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
ij.ImagePlus	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 ij.ImagePlus	toImagePlus(Client client, ROI roi) Gets the imagePlus from the image generated from the ROI.

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

ImageData asDataObject()

Returns a ImageData corresponding to the handled object.

Specified by:

asDataObject in interface RemoteObject

Returns:

See above.

setName

void setName(String name)

Sets the name of the image.

Parameters:

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

Throws:

IllegalArgumentException - If the name is null.

setDescription

void setDescription(String description)

Sets the description of the image.

Parameters:

description - The description of the image.

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)

Returns an empty list as images do not have children.

Specified by:

getChildren in interface RepositoryObject

Parameters:

browser - The data browser.

Returns:

See above.

getAcquisitionDate

Timestamp getAcquisitionDate()

Gets the ImageData acquisition date

Returns:

acquisition date.

getProjects

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

Retrieves the projects containing this image

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.

getDatasets

default List<Dataset> getDatasets(Browser browser)
                           throws ServiceException,
                                  AccessException,
                                  ExecutionException

Retrieves the datasets containing this image 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.

getWellSamples

List<WellSample> getWellSamples()

Retrieves the well samples containing this image.

Returns:

See above

getWellSamples

default List<WellSample> getWellSamples(Browser browser)
                                 throws AccessException,
                                        ServiceException,
                                        ExecutionException

Retrieves the well samples containing this image and updates them 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.

getWells

default List<Well> getWells(Browser browser)
                     throws AccessException,
                            ServiceException,
                            ExecutionException

Retrieves the wells containing this image.

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.

getPlateAcquisitions

default List<PlateAcquisition> getPlateAcquisitions(Browser browser)
                                             throws AccessException,
                                                    ServiceException,
                                                    ExecutionException

Returns the plate acquisitions linked to this image.

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.

getPlates

default List<Plate> getPlates(Browser browser)
                       throws AccessException,
                              ServiceException,
                              ExecutionException

Retrieves the plates containing this image.

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.

getScreens

default List<Screen> getScreens(Browser browser)
                         throws AccessException,
                                ServiceException,
                                ExecutionException

Retrieves the screens containing this image

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.

isOrphaned

default boolean isOrphaned(Browser browser)
                    throws ServiceException,
                           AccessException

Checks if image is orphaned (not in a WellSample nor linked to a dataset).

Parameters:

browser - The data browser.

Returns:

true if the image is orphaned, false otherwise.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

getFilesetImages

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

Returns the list of images sharing the same fileset as the current image.

Parameters:

browser - The data browser.

Returns:

See above.

Throws:

AccessException - Cannot access data.

ServiceException - Cannot connect to OMERO.

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

saveROIs

List<ROI> saveROIs(DataManager dm,
                   Collection<? extends ROI> rois)
            throws ServiceException,
                   AccessException,
                   ExecutionException

Links ROIs to the image in OMERO.

DO NOT USE IT IF A SHAPE WAS DELETED !!!

Parameters:

dm - The data manager.

rois - ROIs to be added.

Returns:

The updated list of ROIs.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

saveROIs

default List<ROI> saveROIs(DataManager dm,
                           ROI... rois)
                    throws ServiceException,
                           AccessException,
                           ExecutionException

Links ROIs to the image in OMERO.

DO NOT USE IT IF A SHAPE WAS DELETED !!!

Parameters:

dm - The data manager.

rois - ROIs to be added.

Returns:

The updated list of ROIs.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getROIs

List<ROI> getROIs(DataManager dm)
           throws ServiceException,
                  AccessException,
                  ExecutionException

Gets all ROIs linked to the image in OMERO

Parameters:

dm - The data manager.

Returns:

List of ROIs linked to the image.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getROIFolders

List<Folder> getROIFolders(DataManager dm)
                    throws ServiceException,
                           AccessException,
                           ExecutionException

Gets the list of folders linked to the ROIs in this image.

Parameters:

dm - The data manager.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getFolders

default List<Folder> getFolders(Browser browser)
                         throws ServiceException,
                                AccessException,
                                ExecutionException

Gets the list of folders linked to this image.

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.

getPixels

Pixels getPixels()

Gets the Pixels for this image.

Returns:

See above.

toImagePlus

default ij.ImagePlus toImagePlus(Client client)
                          throws ServiceException,
                                 AccessException,
                                 ExecutionException

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

Parameters:

client - The client handling the connection.

Returns:

ImagePlus generated from the current image.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - If an error occurs while retrieving the plane data from the pixels source.

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

toImagePlus

ij.ImagePlus toImagePlus(Client client,
                         int[] xBounds,
                         int[] yBounds,
                         int[] cBounds,
                         int[] zBounds,
                         int[] tBounds)
                  throws ServiceException,
                         AccessException,
                         ExecutionException

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

Parameters:

client - The client handling the connection.

xBounds - Array containing the X bounds from which the pixels should be retrieved.

yBounds - Array containing the Y bounds from which the pixels should be retrieved.

cBounds - Array containing the C bounds from which the pixels should be retrieved.

zBounds - Array containing the Z bounds from which the pixels should be retrieved.

tBounds - Array containing the T bounds from which the pixels should be retrieved.

Returns:

an ImagePlus from the ij library.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - If an error occurs while retrieving the plane data from the pixels source.

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

toImagePlus

default ij.ImagePlus toImagePlus(Client client,
                                 ROI roi)
                          throws ServiceException,
                                 AccessException,
                                 ExecutionException

Gets the imagePlus from the image generated from the ROI.

Parameters:

client - The client handling the connection.

roi - The ROI.

Returns:

an ImagePlus from the ij library.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - If an error occurs while retrieving the plane data from the pixels source.

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

getChannels

List<Channel> getChannels(Browser browser)
                   throws ServiceException,
                          AccessException,
                          ExecutionException

Gets the image channels.

Parameters:

browser - The data browser.

Returns:

the channels.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getChannelName

default String getChannelName(Browser browser,
                              int index)
                       throws ServiceException,
                              AccessException,
                              ExecutionException

Gets the name of the channel.

Parameters:

browser - The data browser.

index - Channel number.

Returns:

name of the channel.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getChannelImportedColor

default Color getChannelImportedColor(Browser browser,
                                      int index)
                               throws ServiceException,
                                      AccessException,
                                      ExecutionException

Gets the original color of the channel.

Parameters:

browser - The data browser.

index - Channel number.

Returns:

Original color of the channel.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getChannelColor

default Color getChannelColor(Client client,
                              int index)
                       throws ServiceException,
                              AccessException,
                              ExecutionException

Gets the current color of the channel, or the original if it cannot be retrieved.

Parameters:

client - The client handling the connection.

index - Channel number.

Returns:

Color of the channel.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getThumbnail

BufferedImage getThumbnail(ConnectionHandler client,
                           int size)
                    throws ServiceException,
                           IOException,
                           AccessException

Retrieves the image thumbnail of the specified size.

If the image is not square, the size will be the longest side.

Parameters:

client - The client handling the connection.

size - The thumbnail size.

Returns:

The thumbnail as a BufferedImage.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

IOException - Cannot read thumbnail from store.

download

List<File> download(ConnectionHandler client,
                    String path)
             throws ServiceException,
                    AccessException,
                    ExecutionException

Downloads the original files from the server.

Parameters:

client - The client handling the connection.

path - Path to the file.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

reload

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

Reloads the image 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.