Uses of Class
fr.igred.omero.Client

Packages that use Client

Package	Description
fr.igred.omero	This package contains abstract wrapper classes for the OMERO Gateway and the basic OMERO object.
fr.igred.omero.annotations	This package contains wrapper classes for annotations.
fr.igred.omero.repository	This package contains classes related to the hierarchical organization for images.
fr.igred.omero.roi	This package contains wrapper classes for OMERO shapes and ROIs.

Uses of Client in fr.igred.omero

Methods in fr.igred.omero that return Client

Modifier and Type	Method	Description
Client	Client.sudoGetUser(String username)	Gets the client associated with the username in the parameters.

Methods in fr.igred.omero with parameters of type Client

Modifier and Type	Method	Description
long	AnnotatableWrapper.addAndReplaceFile(Client client, File file)	Uploads a file, links it to the object and unlinks previous files with the same name, or deletes them if they're orphaned.
long	AnnotatableWrapper.addAndReplaceFile(Client client, File file, GenericRepositoryObjectWrapper.ReplacePolicy policy)	Uploads a file, links it to the object and unlinks or deletes previous files with the same name.
void	AnnotatableWrapper.addAndReplaceTable(Client client, TableWrapper table)	Adds a table to the object in OMERO and unlinks previous tables with the same name, or deletes them if they're orphaned.
void	AnnotatableWrapper.addAndReplaceTable(Client client, TableWrapper table, GenericRepositoryObjectWrapper.ReplacePolicy policy)	Adds a table to the object in OMERO and unlinks or deletes previous tables with the same name.
long	AnnotatableWrapper.addFile(Client client, File file)	Uploads a file and links it to the object
void	AnnotatableWrapper.addFileAnnotation(Client client, FileAnnotationWrapper annotation)	Deprecated. Links a file annotation to the object.
void	AnnotatableWrapper.addKeyValuePair(Client client, String key, String value)	Adds a single Key-Value pair to the object.
void	AnnotatableWrapper.addMapAnnotation(Client client, MapAnnotationWrapper mapAnnotation)	Deprecated. Adds a List of Key-Value pair to the object.
void	AnnotatableWrapper.addPairKeyValue(Client client, String key, String value)	Deprecated. Adds a single Key-Value pair to the object.
void	AnnotatableWrapper.addTable(Client client, TableWrapper table)	Adds a table to the object in OMERO.
void	AnnotatableWrapper.addTag(Client client, TagAnnotationWrapper tag)	Deprecated. Adds a tag to the object in OMERO, if possible.
void	AnnotatableWrapper.addTag(Client client, Long id)	Adds a tag to the object in OMERO, if possible.
void	AnnotatableWrapper.addTag(Client client, String name, String description)	Adds a newly created tag to the object in OMERO, if possible.
void	AnnotatableWrapper.addTags(Client client, TagAnnotationWrapper... tags)	Deprecated. Adds multiple tag to the object in OMERO, if possible.
void	AnnotatableWrapper.addTags(Client client, Long... ids)	Adds multiple tags by ID to the object in OMERO, if possible.
void	AnnotatableWrapper.copyAnnotationLinks(Client client, AnnotatableWrapper<?> object)	Copies annotation links from some other object to this one.
protected static void	GenericObjectWrapper.delete(Client client, IObject object)	Deletes an object from OMERO.
AnnotationList	AnnotatableWrapper.getAnnotations(Client client)	Retrieves annotations linked to the object (of known types).
List<FileAnnotationWrapper>	AnnotatableWrapper.getFileAnnotations(Client client)	Returns the file annotations
Map<String,String>	AnnotatableWrapper.getKeyValuePairs(Client client)	Gets the List of key-value pairs associated to an object as a map (no duplicate key should exist).
List<MapAnnotationWrapper>	AnnotatableWrapper.getMapAnnotations(Client client)	Gets all map annotations linked to an object in OMERO, if possible.
int	AnnotatableWrapper.getMyRating(Client client)	Returns the user rating for this object (averaged if multiple ratings are linked).
TableWrapper	AnnotatableWrapper.getTable(Client client, Long fileId)	Gets a certain table linked to the object in OMERO.
List<TableWrapper>	AnnotatableWrapper.getTables(Client client)	Gets all tables linked to the object in OMERO.
List<TagAnnotationWrapper>	AnnotatableWrapper.getTags(Client client)	Gets all tags linked to an object in OMERO, if possible.
String	AnnotatableWrapper.getValue(Client client, String key)	Gets the value from a Key-Value pair associated to the object.
<A extends GenericAnnotationWrapper<?>> boolean	AnnotatableWrapper.isLinked(Client client, A annotation)	Checks if a specific annotation is linked to the object.
protected <A extends AnnotationData> void	AnnotatableWrapper.link(Client client, A annotation)	Attach an AnnotationData to this object.
<A extends GenericAnnotationWrapper<?>> void	AnnotatableWrapper.link(Client client, A annotation)	Adds an annotation to the object in OMERO, if possible.
void	AnnotatableWrapper.link(Client client, GenericAnnotationWrapper<?>... annotations)	Adds multiple annotations to the object in OMERO, if possible.
void	AnnotatableWrapper.linkIfNotLinked(Client client, GenericAnnotationWrapper<?>... annotations)	Adds multiple annotations to the object in OMERO if they are not already linked.
void	AnnotatableWrapper.rate(Client client, int rating)	Rates the object (using a rating annotation).
protected void	AnnotatableWrapper.removeLink(Client client, String linkType, long childId)	Removes the link of the given type with the given child ID.
void	GenericObjectWrapper.saveAndUpdate(Client client)	Saves and updates object.
<A extends GenericAnnotationWrapper<?>> void	AnnotatableWrapper.unlink(Client client, A annotation)	Unlinks the given annotation from the current object.

Uses of Client in fr.igred.omero.annotations

Methods in fr.igred.omero.annotations with parameters of type Client

Modifier and Type	Method	Description
void	TableWrapper.addRows(Client client, ResultsTable results, Long imageId, List<? extends Roi> ijRois)	Adds rows from an ImageJ ResultsTable.
void	TableWrapper.addRows(Client client, ResultsTable results, Long imageId, List<? extends Roi> ijRois, String roiProperty)	Adds rows from an ImageJ ResultsTable.
int	GenericAnnotationWrapper.countAnnotationLinks(Client client)	Returns the number of annotations links for this object.
List<DatasetWrapper>	GenericAnnotationWrapper.getDatasets(Client client)	Gets all datasets with this annotation from OMERO.
File	FileAnnotationWrapper.getFile(Client client, String path)	Returns the original file.
List<FolderWrapper>	GenericAnnotationWrapper.getFolders(Client client)	Gets all folders with this annotation from OMERO.
List<ImageWrapper>	GenericAnnotationWrapper.getImages(Client client)	Gets all images with this annotation from OMERO.
List<PlateAcquisitionWrapper>	GenericAnnotationWrapper.getPlateAcquisitions(Client client)	Gets all plate acquisitions with this annotation from OMERO.
List<PlateWrapper>	GenericAnnotationWrapper.getPlates(Client client)	Gets all plates with this annotation from OMERO.
List<ProjectWrapper>	GenericAnnotationWrapper.getProjects(Client client)	Gets all projects with this annotation from OMERO.
List<ScreenWrapper>	GenericAnnotationWrapper.getScreens(Client client)	Gets all screens with this annotation from OMERO.
List<WellWrapper>	GenericAnnotationWrapper.getWells(Client client)	Gets all wells with this annotation from OMERO.

Constructors in fr.igred.omero.annotations with parameters of type Client

Constructor	Description
TableWrapper(Client client, ResultsTable results, Long imageId, List<? extends Roi> ijRois)	Constructor of the class TableWrapper.
TableWrapper(Client client, ResultsTable results, Long imageId, List<? extends Roi> ijRois, String roiProperty)	Constructor of the class TableWrapper.
TagAnnotationWrapper(Client client, String name, String description)	Constructor of the TagAnnotationWrapper class.

Uses of Client in fr.igred.omero.repository

Methods in fr.igred.omero.repository with parameters of type Client

Modifier and Type	Method	Description
DatasetWrapper	ProjectWrapper.addDataset(Client client, DatasetWrapper dataset)	Adds a dataset to the project in OMERO.
DatasetWrapper	ProjectWrapper.addDataset(Client client, String name, String description)	Adds a dataset to the project in OMERO.
void	DatasetWrapper.addImage(Client client, ImageWrapper image)	Adds a single image to the dataset in OMERO
void	DatasetWrapper.addImages(Client client, List<? extends ImageWrapper> images)	Adds a list of image to the dataset in OMERO.
void	FolderWrapper.addImages(Client client, ImageWrapper... images)	Links images to the folder in OMERO.
void	FolderWrapper.addROI(Client client, ROIWrapper roi)	Deprecated. Adds an ROI to the folder and associate it to the image id set(an image need to be associated)
void	FolderWrapper.addROIs(Client client, long imageId, ROIWrapper... rois)	Adds ROIs to the folder and associate them to the provided image ID.
void	FolderWrapper.addROIs(Client client, ImageWrapper image, ROIWrapper... rois)	Adds ROIs to the folder and associate them to the provided image.
void	GenericRepositoryObjectWrapper.copyAnnotationLinks(Client client, GenericRepositoryObjectWrapper<?> object)	Copies annotation links from some other object to this one.
List<File>	ImageWrapper.download(Client client, String path)	Downloads the original files from the server.
double[][][][][]	PixelsWrapper.getAllPixels(Client client)	Returns an array containing the value for each voxel
double[][][][][]	PixelsWrapper.getAllPixels(Client client, int[] xBounds, int[] yBounds, int[] cBounds, int[] zBounds, int[] tBounds)	Returns an array containing the value for each voxel corresponding to the bounds
Color	ImageWrapper.getChannelColor(Client client, int index)	Gets the current color of the channel
Color	ImageWrapper.getChannelImportedColor(Client client, int index)	Gets the original color of the channel
String	ImageWrapper.getChannelName(Client client, int index)	Gets the name of the channel.
List<ChannelWrapper>	ImageWrapper.getChannels(Client client)	Gets the image channels.
List<DatasetWrapper>	ImageWrapper.getDatasets(Client client)	Retrieves the datasets containing this image
List<ImageWrapper>	ImageWrapper.getFilesetImages(Client client)	Returns the list of images sharing the same fileset as the current image.
FolderWrapper	ImageWrapper.getFolder(Client client, Long folderId)	Deprecated. Gets the folder with the specified id on OMERO.
List<FolderWrapper>	ImageWrapper.getFolders(Client client)	Gets the list of folders linked to this image.
List<ImageWrapper>	DatasetWrapper.getImages(Client client)	Gets all images in the dataset available from OMERO.
List<ImageWrapper>	DatasetWrapper.getImages(Client client, String name)	Gets all images in the dataset with a certain name from OMERO.
List<ImageWrapper>	FolderWrapper.getImages(Client client)	Retrieves the images contained in this folder.
List<ImageWrapper>	PlateAcquisitionWrapper.getImages(Client client)	Retrieves the images contained in the wells in the parent plate.
List<ImageWrapper>	PlateWrapper.getImages(Client client)	Returns the images contained in the wells of this plate.
List<ImageWrapper>	ProjectWrapper.getImages(Client client)	Gets all images in the project available from OMERO.
List<ImageWrapper>	ProjectWrapper.getImages(Client client, String name)	Gets all images in the project with a certain name from OMERO.
List<ImageWrapper>	ProjectWrapper.getImages(Client client, String datasetName, String imageName)	Gets all images with a certain name from datasets with the specified name inside this project on OMERO.
List<ImageWrapper>	ScreenWrapper.getImages(Client client)	Retrieves the images contained in this screen.
List<ImageWrapper>	DatasetWrapper.getImagesKey(Client client, String key)	Deprecated. Gets all images in the dataset with a certain key
List<ImageWrapper>	ProjectWrapper.getImagesKey(Client client, String key)	Deprecated. Gets all images in the project with a certain key
List<ImageWrapper>	DatasetWrapper.getImagesLike(Client client, String motif)	Gets all images in the dataset with a certain motif in their name from OMERO.
List<ImageWrapper>	ProjectWrapper.getImagesLike(Client client, String motif)	Gets all images in the project with a certain motif in their name from OMERO.
List<ImageWrapper>	DatasetWrapper.getImagesPairKeyValue(Client client, String key, String value)	Deprecated. Gets all images in the dataset with a certain key value pair from OMERO
List<ImageWrapper>	ProjectWrapper.getImagesPairKeyValue(Client client, String key, String value)	Deprecated. Gets all images in the project with a certain key value pair from OMERO.
List<ImageWrapper>	DatasetWrapper.getImagesTagged(Client client, TagAnnotationWrapper tag)	Gets all images in the dataset tagged with a specified tag from OMERO.
List<ImageWrapper>	DatasetWrapper.getImagesTagged(Client client, Long tagId)	Gets all images in the dataset tagged with a specified tag from OMERO.
List<ImageWrapper>	ProjectWrapper.getImagesTagged(Client client, TagAnnotationWrapper tag)	Gets all images in the project tagged with a specified tag from OMERO.
List<ImageWrapper>	ProjectWrapper.getImagesTagged(Client client, Long tagId)	Gets all images in the project tagged with a specified tag from OMERO.
List<ImageWrapper>	DatasetWrapper.getImagesWithKey(Client client, String key)	Gets all images in the dataset with a certain key
List<ImageWrapper>	ProjectWrapper.getImagesWithKey(Client client, String key)	Gets all images in the project with a certain key
List<ImageWrapper>	DatasetWrapper.getImagesWithKeyValuePair(Client client, String key, String value)	Gets all images in the dataset with a certain key value pair from OMERO
List<ImageWrapper>	ProjectWrapper.getImagesWithKeyValuePair(Client client, String key, String value)	Gets all images in the project with a certain key value pair from OMERO.
List<PlateAcquisitionWrapper>	ImageWrapper.getPlateAcquisitions(Client client)	Returns the plate acquisitions linked to this image.
List<PlateAcquisitionWrapper>	ScreenWrapper.getPlateAcquisitions(Client client)	Returns the plate acquisitions linked to this object, either directly, or through parents/children.
List<PlateAcquisitionWrapper>	WellSampleWrapper.getPlateAcquisitions(Client client)	Returns the plate acquisitions linked to the parent Well.
List<PlateAcquisitionWrapper>	WellWrapper.getPlateAcquisitions(Client client)	Refreshes this well and returns the plate acquisitions linked to it.
List<PlateWrapper>	ImageWrapper.getPlates(Client client)	Retrieves the plates containing this image.
List<PlateWrapper>	PlateAcquisitionWrapper.getPlates(Client client)	Returns the (updated) parent plate as a singleton list.
List<PlateWrapper>	WellSampleWrapper.getPlates(Client client)	Returns the plates containing the parent Well.
List<ProjectWrapper>	DatasetWrapper.getProjects(Client client)	Retrieves the projects containing this dataset.
List<ProjectWrapper>	ImageWrapper.getProjects(Client client)	Retrieves the projects containing this image
byte[][][][]	PixelsWrapper.getRawPixels(Client client, int bpp)	Returns an array containing the raw values for each voxel for each planes
byte[][][][]	PixelsWrapper.getRawPixels(Client client, int[] xBounds, int[] yBounds, int[] cBounds, int[] zBounds, int[] tBounds, int bpp)	Returns an array containing the raw values for each voxel for each plane corresponding to the bounds
List<FolderWrapper>	ImageWrapper.getROIFolders(Client client)	Gets the list of folders linked to the ROIs in this image.
List<ROIWrapper>	FolderWrapper.getROIs(Client client)	Deprecated. Gets the ROI contained in the folder associated with the image id set (an image need to be associated)
List<ROIWrapper>	FolderWrapper.getROIs(Client client, long imageId)	Gets the ROIs contained in the folder associated with the provided image ID.
List<ROIWrapper>	FolderWrapper.getROIs(Client client, ImageWrapper image)	Gets the ROIs contained in the folder associated with the provided image.
List<ROIWrapper>	ImageWrapper.getROIs(Client client)	Gets all ROIs linked to the image in OMERO
List<ScreenWrapper>	ImageWrapper.getScreens(Client client)	Retrieves the screens containing this image
List<ScreenWrapper>	PlateAcquisitionWrapper.getScreens(Client client)	Retrieves the screens containing the parent plates.
List<ScreenWrapper>	PlateWrapper.getScreens(Client client)	Retrieves the screens containing this plate.
List<ScreenWrapper>	WellSampleWrapper.getScreens(Client client)	Returns the screens containing the parent Well.
List<ScreenWrapper>	WellWrapper.getScreens(Client client)	Refreshes this well and retrieves the screens containing it.
BufferedImage	ImageWrapper.getThumbnail(Client client, int size)	Retrieves the image thumbnail of the specified size.
WellWrapper	WellSampleWrapper.getWell(Client client)	Retrieves the well containing this well sample
List<WellWrapper>	ImageWrapper.getWells(Client client)	Retrieves the wells containing this image.
List<WellWrapper>	PlateAcquisitionWrapper.getWells(Client client)	Retrieves the wells contained in the parent plate.
List<WellWrapper>	PlateWrapper.getWells(Client client)	Gets all wells in the plate available from OMERO.
List<WellWrapper>	ScreenWrapper.getWells(Client client)	Retrieves the wells linked to this object, either directly, or through parents/children.
List<Long>	DatasetWrapper.importAndReplaceImages(Client client, 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.
List<Long>	DatasetWrapper.importAndReplaceImages(Client client, String path, GenericRepositoryObjectWrapper.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.
List<Long>	DatasetWrapper.importImage(Client client, String path)	Imports one image file to the dataset in OMERO.
boolean	DatasetWrapper.importImages(Client client, int threads, String... paths)	Imports all images candidates in the paths to the dataset in OMERO.
boolean	DatasetWrapper.importImages(Client client, String... paths)	Imports all images candidates in the paths to the dataset in OMERO.
boolean	ImageWrapper.isOrphaned(Client client)	Checks if image is orphaned (not in a WellSample nor linked to a dataset).
protected <A extends AnnotationData> void	FolderWrapper.link(Client client, A annotation)	Adds an annotation to the object in OMERO, if possible.
protected <A extends AnnotationData> void	PlateAcquisitionWrapper.link(Client client, A annotation)	Adds a tag to the object in OMERO, if possible.
void	PixelsWrapper.loadPlanesInfo(Client client)	Loads the planes information.
void	DatasetWrapper.refresh(Client client)	Reloads the dataset from OMERO.
void	PlateWrapper.refresh(Client client)	Reloads the plate from OMERO.
void	ProjectWrapper.refresh(Client client)	Reloads the project from OMERO.
void	WellWrapper.refresh(Client client)	Reloads the well from OMERO.
void	FolderWrapper.reload(Client client)	Reloads the folder from OMERO, to update all links.
void	ProjectWrapper.removeDataset(Client client, DatasetWrapper dataset)	Removes a dataset from the project in OMERO.
void	DatasetWrapper.removeImage(Client client, ImageWrapper image)	Removes an image from the dataset in OMERO.
List<ImageWrapper>	DatasetWrapper.replaceImages(Client client, Collection<? extends ImageWrapper> oldImages, ImageWrapper 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	ImageWrapper.saveROI(Client client, ROIWrapper roi)	Deprecated. Links a ROI to the image in OMERO
List<ROIWrapper>	ImageWrapper.saveROIs(Client client, ROIWrapper... rois)	Links ROIs to the image in OMERO.
List<ROIWrapper>	ImageWrapper.saveROIs(Client client, Collection<? extends ROIWrapper> rois)	Links ROIs to the image in OMERO.
ImagePlus	ImageWrapper.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	ImageWrapper.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.
ImagePlus	ImageWrapper.toImagePlus(Client client, ROIWrapper roi)	Gets the imagePlus from the image generated from the ROI.
void	FolderWrapper.unlinkAllROI(Client client)	Deprecated. Unlink all ROI, associated to the image set, in the folder.
void	FolderWrapper.unlinkAllROIs(Client client)	Unlink all ROIs associated to this folder.
void	FolderWrapper.unlinkAllROIs(Client client, long imageId)	Unlink all ROIs associated to the provided image ID from the folder.
void	FolderWrapper.unlinkAllROIs(Client client, ImageWrapper image)	Unlink all ROIs associated to the provided image from the folder.
void	FolderWrapper.unlinkROI(Client client, ROIWrapper roi)	Deprecated. Unlink an ROI, associated to the image set, in the folder.
void	FolderWrapper.unlinkROIs(Client client, ROIWrapper... rois)	Unlink ROIs from the folder.

Constructors in fr.igred.omero.repository with parameters of type Client

Constructor	Description
FolderWrapper(Client client, String name)	Constructor of the FolderWrapper class.
ProjectWrapper(Client client, String name, String description)	Constructor of the ProjectWrapper class.
ScreenWrapper(Client client, String name, String description)	Constructor of the ProjectWrapper class.

Uses of Client in fr.igred.omero.roi

Methods in fr.igred.omero.roi with parameters of type Client

Modifier and Type	Method	Description
<A extends AnnotationData> void	GenericShapeWrapper.link(Client client, A annotation)	Attach an AnnotationData to this object.
protected <A extends AnnotationData> void	ROIWrapper.link(Client client, A annotation)	Attach an AnnotationData to this object.
void	ROIWrapper.saveROI(Client client)	Saves the ROI.