fr.igred.omero.core

Class ImageWrapper

java.lang.Object

fr.igred.omero.ObjectWrapper<T>

fr.igred.omero.AnnotatableWrapper<ImageData>

fr.igred.omero.core.ImageWrapper

All Implemented Interfaces:

Annotatable, Image, RemoteObject, RepositoryObject

public class ImageWrapper
extends AnnotatableWrapper<ImageData>
implements Image

Class containing an ImageData.

Wraps function calls to the ImageData contained.

Field Summary

Fields

Modifier and Type	Field and Description
static String	ANNOTATION_LINK Annotation link name for this type of object

Fields inherited from class fr.igred.omero.ObjectWrapper

data

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
protected String	annotationLinkType() Returns the type of annotation link for this object.
List<File>	download(ConnectionHandler client, String path) Downloads the original files from the server.
Timestamp	getAcquisitionDate() Gets the ImageData acquisition date.
List<Channel>	getChannels(Browser browser) Gets the image channels.
String	getDescription() Gets the image description.
String	getName() Gets the image name.
Pixels	getPixels() Gets the Pixels for 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
BufferedImage	getThumbnail(ConnectionHandler client, int size) Retrieves the image thumbnail of the specified size.
List<WellSample>	getWellSamples() Retrieves the well samples containing this image.
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.
void	setDescription(String description) Sets the description of the image.
void	setName(String name) Sets the name of the image.
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.

Methods inherited from class fr.igred.omero.AnnotatableWrapper

addAndReplaceFile, addAndReplaceTable, addKeyValuePair, addTag, addTag, getAnnotations, getFileAnnotations, getMapAnnotations, getMyRating, getTable, getTags, rate, removeLink, unlink

Methods inherited from class fr.igred.omero.ObjectWrapper

asDataObject, canAnnotate, canChgrp, canChown, canDelete, canEdit, canLink, 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

Methods inherited from interface fr.igred.omero.core.Image

asDataObject, getChannelColor, getChannelImportedColor, getChannelName, getChildren, getDatasets, getFilesetImages, getFolders, getParents, getPlateAcquisitions, getPlates, getProjects, getScreens, getWells, getWellSamples, isOrphaned, saveROIs, toImagePlus, toImagePlus

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

Field Detail

ANNOTATION_LINK

public static final String ANNOTATION_LINK

Annotation link name for this type of object

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 image name.

Specified by:

getName in interface RepositoryObject

Returns:

See above.

setName

public void setName(String name)

Sets the name of the image.

Specified by:

setName in interface Image

Parameters:

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

Throws:

IllegalArgumentException - If the name is null.

getDescription

public String getDescription()

Gets the image description.

Specified by:

getDescription in interface RepositoryObject

Returns:

See above.

setDescription

public void setDescription(String description)

Sets the description of the image.

Specified by:

setDescription in interface Image

Parameters:

description - The description of the image.

getAcquisitionDate

public Timestamp getAcquisitionDate()

Gets the ImageData acquisition date.

Specified by:

getAcquisitionDate in interface Image

Returns:

acquisition date.

getWellSamples

public List<WellSample> getWellSamples()

Retrieves the well samples containing this image.

Specified by:

getWellSamples in interface 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.

saveROIs

public 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 !!!

Specified by:

saveROIs in interface Image

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

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

Gets all ROIs linked to the image in OMERO

Specified by:

getROIs in interface Image

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

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

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

Specified by:

getROIFolders in interface 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.

getPixels

public Pixels getPixels()

Gets the Pixels for this image.

Specified by:

getPixels in interface Image

Returns:

See above.

toImagePlus

public 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.

Specified by:

toImagePlus in interface Image

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.

getChannels

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

Gets the image channels.

Specified by:

getChannels in interface Image

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.

getThumbnail

public 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.

Specified by:

getThumbnail in interface Image

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

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

Downloads the original files from the server.

Specified by:

download in interface Image

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

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

Reloads the image from OMERO.

Specified by:

reload in interface Image

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.