Package fr.igred.omero.repository

Class ImageWrapper

java.lang.Object

fr.igred.omero.GenericObjectWrapper<T>

fr.igred.omero.AnnotatableWrapper<T>

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

fr.igred.omero.repository.ImageWrapper

public class ImageWrapper
extends GenericRepositoryObjectWrapper<ImageData>

Class containing an ImageData.

Wraps function calls to 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	Annotation link name for this type of object
static String	IJ_ID_PROPERTY	Default IJ property to store image ID.

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()	Deprecated. Returns the ImageData contained.
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)	Deprecated. Gets the folder with the specified id on OMERO.
List<FolderWrapper>	getFolders(Client client)	Gets the list of folders linked to this image.
String	getFormat()	Returns the format of the image.
String	getName()	Gets the ImageData name
PixelsWrapper	getPixels()	Gets the Pixels for this image.
List<PlateAcquisitionWrapper>	getPlateAcquisitions(Client client)	Returns the plate acquisitions linked to this image.
List<PlateWrapper>	getPlates(Client client)	Retrieves the plates containing this image.
List<ProjectWrapper>	getProjects(Client client)	Retrieves the projects containing this image
List<FolderWrapper>	getROIFolders(Client client)	Gets the list of folders linked to the ROIs in this image.
List<ROIWrapper>	getROIs(Client client)	Gets all ROIs linked to the image in OMERO
List<ScreenWrapper>	getScreens(Client client)	Retrieves the screens containing this image
BufferedImage	getThumbnail(Client client, int size)	Retrieves the image thumbnail of the specified size.
List<WellWrapper>	getWells(Client client)	Retrieves the wells containing this image.
List<WellSampleWrapper>	getWellSamples()	Retrieves the well samples containing this image.
List<WellSampleWrapper>	getWellSamples(Client client)	Retrieves the well samples containing this image and updates them from OMERO.
boolean	isOrphaned(Client client)	Checks if image is orphaned (not in a WellSample nor linked to a dataset).
void	reload(Browser browser)	Reloads the image from OMERO.
void	saveROI(Client client, ROIWrapper roi)	Deprecated. Links a ROI to the image in OMERO
List<ROIWrapper>	saveROIs(Client client, ROIWrapper... rois)	Links ROIs to the image in OMERO.
List<ROIWrapper>	saveROIs(Client client, Collection<? extends ROIWrapper> 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.
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[] xBounds, int[] yBounds, int[] cBounds, int[] zBounds, int[] tBounds)	Gets the ImagePlus from the image within the specified boundaries.
ImagePlus	toImagePlus(Client client, PixelsWrapper.Bounds bounds)	Gets the ImagePlus from the image within the specified boundaries.
ImagePlus	toImagePlus(Client client, ROIWrapper roi)	Gets the ImagePlus from the image, but only inside the ROI.

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

copyAnnotationLinks, importImage, importImages, refresh

Methods inherited from class fr.igred.omero.AnnotatableWrapper

addAndReplaceFile, addAndReplaceFile, addAndReplaceTable, addAndReplaceTable, addFile, addFileAnnotation, addKeyValuePair, addMapAnnotation, addPairKeyValue, addTable, addTag, addTag, addTag, addTags, addTags, copyAnnotationLinks, getAnnotations, getFileAnnotations, getKeyValuePairs, getMapAnnotations, getMyRating, getRatings, getTable, getTables, getTags, getValue, isLinked, link, link, linkIfNotLinked, rate, removeLink, removeLinks, unlink, unlink

Methods inherited from class fr.igred.omero.GenericObjectWrapper

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

Annotation link name for this type of object

See Also:

Constant Field Values

IJ_ID_PROPERTY

public static final String IJ_ID_PROPERTY

Default IJ property to store image ID.

See Also:

Constant Field Values

Constructor Detail

ImageWrapper

public ImageWrapper(ImageData image)

Constructor of the class ImageWrapper

Parameters:

image - The image to wrap 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

@Deprecated
public ImageData asImageData()

Deprecated.

Returns the ImageData contained. Use GenericObjectWrapper.asDataObject() instead.

Returns:

See above.

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.

getFormat

public String getFormat()

Returns the format of the image.

Returns:

See above.

annotationLinkType

protected String annotationLinkType()

Returns the type of annotation link for this object.

Specified by:

annotationLinkType in class AnnotatableWrapper<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.

getWellSamples

public List<WellSampleWrapper> getWellSamples()

Retrieves the well samples containing this image.

Returns:

See above

getWellSamples

public List<WellSampleWrapper> getWellSamples(Client client)
                                       throws AccessException,
                                              ServiceException,
                                              ExecutionException

Retrieves the well samples containing this image and updates them from OMERO.

Parameters:

client - 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

public List<WellWrapper> getWells(Client client)
                           throws AccessException,
                                  ServiceException,
                                  ExecutionException

Retrieves the wells containing this image.

Parameters:

client - The client handling the connection.

Returns:

See above

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getPlateAcquisitions

public List<PlateAcquisitionWrapper> getPlateAcquisitions(Client client)
                                                   throws AccessException,
                                                          ServiceException,
                                                          ExecutionException

Returns the plate acquisitions linked to this image.

Parameters:

client - The client handling the connection.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getPlates

public List<PlateWrapper> getPlates(Client client)
                             throws AccessException,
                                    ServiceException,
                                    ExecutionException

Retrieves the plates containing this image.

Parameters:

client - The client handling the connection.

Returns:

See above

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getScreens

public List<ScreenWrapper> getScreens(Client client)
                               throws AccessException,
                                      ServiceException,
                                      ExecutionException,
                                      OMEROServerError

Retrieves the screens containing this image

Parameters:

client - The client handling the connection.

Returns:

See above

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

OMEROServerError - Server error.

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.

saveROIs

public List<ROIWrapper> saveROIs(Client client,
                                 Collection<? extends ROIWrapper> rois)
                          throws ServiceException,
                                 AccessException,
                                 ExecutionException

Links ROIs to the image in OMERO.

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

Parameters:

client - The client handling the connection.

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

public List<ROIWrapper> saveROIs(Client client,
                                 ROIWrapper... rois)
                          throws ServiceException,
                                 AccessException,
                                 ExecutionException

Links ROIs to the image in OMERO.

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

Parameters:

client - 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.

saveROI

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

Deprecated.

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.

getROIFolders

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

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

Parameters:

client - The client handling the connection.

Returns:

See above.

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,
                                      OMEROServerError

Gets the list of folders linked to this image.

Parameters:

client - The client handling the connection.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

OMEROServerError - Server error.

getFolder

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

Deprecated.

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 Pixels for this image.

Returns:

See above.

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[] xBounds,
                             int[] yBounds,
                             int[] cBounds,
                             int[] zBounds,
                             int[] tBounds)
                      throws ServiceException,
                             AccessException,
                             ExecutionException

Gets the ImagePlus from the image within the specified boundaries.

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

public ImagePlus toImagePlus(Client client,
                             ROIWrapper roi)
                      throws ServiceException,
                             AccessException,
                             ExecutionException

Gets the ImagePlus from the image, but only inside 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.

toImagePlus

public ImagePlus toImagePlus(Client client,
                             PixelsWrapper.Bounds bounds)
                      throws ServiceException,
                             AccessException,
                             ExecutionException

Gets the ImagePlus from the image within the specified boundaries.

Parameters:

client - The client handling the connection.

bounds - The bounds.

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.

reload

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

Reloads the image from OMERO.

Overrides:

reload in class GenericRepositoryObjectWrapper<ImageData>

Parameters:

browser - The data browser.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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