Package fr.igred.omero.repository

Class ImageWrapper

java.lang.Object

fr.igred.omero.GenericObjectWrapper<T>

fr.igred.omero.repository.GenericRepositoryObjectWrapper<ImageData>

fr.igred.omero.repository.ImageWrapper

public class ImageWrapper
extends GenericRepositoryObjectWrapper<ImageData>

Class containing an ImageData.

Implements function using the ImageData contained

Nested Class Summary

Nested classes/interfaces inherited from class fr.igred.omero.repository.GenericRepositoryObjectWrapper

GenericRepositoryObjectWrapper.ReplacePolicy

Field Summary

Fields

Modifier and Type	Field	Description
static String	ANNOTATION_LINK

Fields inherited from class fr.igred.omero.GenericObjectWrapper

data

Constructor Summary

Constructors

Constructor	Description
ImageWrapper(ImageData image)	Constructor of the class ImageWrapper

Method Summary

Modifier and Type	Method	Description
protected String	annotationLinkType()	Returns the type of annotation link for this object
ImageData	asImageData()
List<File>	download(Client client, String path)	Downloads the original files from the server.
Timestamp	getAcquisitionDate()	Gets the ImageData acquisition date
Color	getChannelColor(Client client, int index)	Gets the current color of the channel
Color	getChannelImportedColor(Client client, int index)	Gets the original color of the channel
String	getChannelName(Client client, int index)	Gets the name of the channel
List<ChannelWrapper>	getChannels(Client client)	Gets the image channels
List<DatasetWrapper>	getDatasets(Client client)	Retrieves the datasets containing this image
String	getDescription()	Gets the ImageData description
List<ImageWrapper>	getFilesetImages(Client client)	Returns the list of images sharing the same fileset as the current image.
FolderWrapper	getFolder(Client client, Long folderId)	Gets the folder with the specified id on OMERO.
List<FolderWrapper>	getFolders(Client client)	Gets the list of Folder linked to the image Associate the folder to the image
String	getName()	Gets the ImageData name
PixelsWrapper	getPixels()	Gets the PixelsWrapper of the image
List<ProjectWrapper>	getProjects(Client client)	Retrieves the projects containing this image
List<ROIWrapper>	getROIs(Client client)	Gets all ROIs linked to the image in OMERO
BufferedImage	getThumbnail(Client client, int size)	Retrieves the image thumbnail of the specified size.
boolean	isOrphaned(Client client)	Checks if image is orphaned (not in a WellSample nor linked to a dataset).
void	saveROI(Client client, ROIWrapper roi)	Links a ROI 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.
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
ImagePlus	toImagePlus(Client client, int[] xBound, int[] yBound, int[] cBound, int[] zBound, int[] tBound)	Gets the imagePlus generated from the image from OMERO corresponding to the bound
ImagePlus	toImagePlus(Client client, ROIWrapper roi)	Gets the imagePlus from the image generated from the ROI.

Methods inherited from class fr.igred.omero.repository.GenericRepositoryObjectWrapper

addAndReplaceFile, addAndReplaceFile, addFile, addFileAnnotation, addMapAnnotation, addPairKeyValue, addTable, addTag, addTag, addTag, addTag, addTags, addTags, copyAnnotationLinks, getFileAnnotations, getKeyValuePairs, getMapAnnotations, getTable, getTables, getTags, getValue, removeLink, unlink

Methods inherited from class fr.igred.omero.GenericObjectWrapper

canAnnotate, canChgrp, canChown, canDelete, canEdit, canLink, delete, distinct, getCreated, getGroupId, getId, getOwner, saveAndUpdate, toString, wrap, wrap

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

ANNOTATION_LINK

public static final String ANNOTATION_LINK

See Also:

Constant Field Values

Constructor Detail

ImageWrapper

public ImageWrapper(ImageData image)

Constructor of the class ImageWrapper

Parameters:

image - The image contained in the ImageWrapper.

Method Detail

getName

public String getName()

Gets the ImageData name

Specified by:

getName in class GenericRepositoryObjectWrapper<ImageData>

Returns:

name.

setName

public 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.

asImageData

public ImageData asImageData()

Returns:

ImageData contained.

getDescription

public String getDescription()

Gets the ImageData description

Specified by:

getDescription in class GenericRepositoryObjectWrapper<ImageData>

Returns:

description.

setDescription

public void setDescription(String description)

Sets the description of the image.

Parameters:

description - The description of the image.

getAcquisitionDate

public Timestamp getAcquisitionDate()

Gets the ImageData acquisition date

Returns:

acquisition date.

annotationLinkType

protected String annotationLinkType()

Returns the type of annotation link for this object

Specified by:

annotationLinkType in class GenericRepositoryObjectWrapper<ImageData>

Returns:

See above.

getProjects

public List<ProjectWrapper> getProjects(Client client)
                                 throws OMEROServerError,
                                        ServiceException,
                                        AccessException,
                                        ExecutionException

Retrieves the projects containing this image

Parameters:

client - The client handling the connection.

Returns:

See above.

Throws:

OMEROServerError - Server error.

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getDatasets

public List<DatasetWrapper> getDatasets(Client client)
                                 throws OMEROServerError,
                                        ServiceException,
                                        AccessException,
                                        ExecutionException

Retrieves the datasets containing this image

Parameters:

client - The client handling the connection.

Returns:

See above.

Throws:

OMEROServerError - Server error.

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

isOrphaned

public boolean isOrphaned(Client client)
                   throws ServiceException,
                          OMEROServerError

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

Parameters:

client - The client handling the connection.

Returns:

true if the image is orphaned, false otherwise.

Throws:

ServiceException - Cannot connect to OMERO.

OMEROServerError - Server error.

getFilesetImages

public List<ImageWrapper> getFilesetImages(Client client)
                                    throws AccessException,
                                           ServiceException,
                                           ExecutionException,
                                           OMEROServerError

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

Parameters:

client - The client handling the connection.

Returns:

See above.

Throws:

AccessException - Cannot access data.

ServiceException - Cannot connect to OMERO.

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

OMEROServerError - Server error.

saveROI

public void saveROI(Client client,
                    ROIWrapper roi)
             throws ServiceException,
                    AccessException,
                    ExecutionException

Links a ROI to the image in OMERO

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

Parameters:

client - The client handling the connection.

roi - ROI to be added.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getROIs

public List<ROIWrapper> getROIs(Client client)
                         throws ServiceException,
                                AccessException,
                                ExecutionException

Gets all ROIs linked to the image in OMERO

Parameters:

client - The client handling the connection.

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.

getFolders

public List<FolderWrapper> getFolders(Client client)
                               throws ServiceException,
                                      AccessException,
                                      ExecutionException

Gets the list of Folder linked to the image Associate the folder to the image

Parameters:

client - The client handling the connection.

Returns:

List of FolderWrapper containing the folder.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getFolder

public FolderWrapper getFolder(Client client,
                               Long folderId)
                        throws ServiceException,
                               OMEROServerError

Gets the folder with the specified id on OMERO.

Parameters:

client - The client handling the connection.

folderId - ID of the folder.

Returns:

The folder if it exists.

Throws:

ServiceException - Cannot connect to OMERO.

OMEROServerError - Server error.

NoSuchElementException - Folder does not exist.

getPixels

public PixelsWrapper getPixels()

Gets the PixelsWrapper of the image

Returns:

Contains the PixelsData associated with the image.

toImagePlus

public 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

public ImagePlus toImagePlus(Client client,
                             int[] xBound,
                             int[] yBound,
                             int[] cBound,
                             int[] zBound,
                             int[] tBound)
                      throws ServiceException,
                             AccessException,
                             ExecutionException

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

Parameters:

client - The client handling the connection.

xBound - Array containing the X bound from which the pixels should be retrieved.

yBound - Array containing the Y bound from which the pixels should be retrieved.

cBound - Array containing the C bound from which the pixels should be retrieved.

zBound - Array containing the Z bound from which the pixels should be retrieved.

tBound - Array containing the T bound 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

public ImagePlus toImagePlus(Client client,
                             ROIWrapper 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

public List<ChannelWrapper> getChannels(Client client)
                                 throws ServiceException,
                                        AccessException,
                                        ExecutionException

Gets the image channels

Parameters:

client - The client handling the connection.

Returns:

the channels.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getChannelName

public String getChannelName(Client client,
                             int index)
                      throws ServiceException,
                             AccessException,
                             ExecutionException

Gets the name of the channel

Parameters:

client - The client handling the connection.

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

public Color getChannelImportedColor(Client client,
                                     int index)
                              throws ServiceException,
                                     AccessException,
                                     ExecutionException

Gets the original color of the channel

Parameters:

client - The client handling the connection.

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

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

Gets the current color of the channel

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

public BufferedImage getThumbnail(Client client,
                                  int size)
                           throws ServiceException,
                                  OMEROServerError,
                                  IOException

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.

OMEROServerError - Server error.

IOException - Cannot read thumbnail from store.

download

public List<File> download(Client client,
                           String path)
                    throws OMEROServerError,
                           ServiceException,
                           AccessException

Downloads the original files from the server.

Parameters:

client - The client handling the connection.

path - Path to the file.

Returns:

See above.

Throws:

OMEROServerError - Server error.

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.