long |
GenericRepositoryObjectWrapper.addAndReplaceFile(Client client,
java.io.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 |
GenericRepositoryObjectWrapper.addAndReplaceFile(Client client,
java.io.File file,
GenericRepositoryObjectWrapper.ReplacePolicy policy) |
Uploads a file, links it to the object and unlinks or deletes previous files with the same name.
|
void |
GenericRepositoryObjectWrapper.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 |
GenericRepositoryObjectWrapper.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.
|
DatasetWrapper |
ProjectWrapper.addDataset(Client client,
DatasetWrapper dataset) |
Adds a dataset to the project in OMERO.
|
DatasetWrapper |
ProjectWrapper.addDataset(Client client,
java.lang.String name,
java.lang.String description) |
Adds a dataset to the project in OMERO.
|
long |
GenericRepositoryObjectWrapper.addFile(Client client,
java.io.File file) |
Uploads a file and links it to the object
|
void |
GenericRepositoryObjectWrapper.addFileAnnotation(Client client,
FileAnnotationWrapper annotation) |
Deprecated.
|
void |
DatasetWrapper.addImage(Client client,
ImageWrapper image) |
Adds a single image to the dataset in OMERO
|
void |
DatasetWrapper.addImages(Client client,
java.util.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 |
GenericRepositoryObjectWrapper.addKeyValuePair(Client client,
java.lang.String key,
java.lang.String value) |
Adds a single Key-Value pair to the object.
|
void |
GenericRepositoryObjectWrapper.addMapAnnotation(Client client,
MapAnnotationWrapper mapAnnotation) |
Deprecated.
|
void |
GenericRepositoryObjectWrapper.addPairKeyValue(Client client,
java.lang.String key,
java.lang.String value) |
Deprecated.
|
void |
FolderWrapper.addROI(Client client,
ROIWrapper roi) |
Deprecated.
|
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.addTable(Client client,
TableWrapper table) |
Adds a table to the object in OMERO.
|
void |
GenericRepositoryObjectWrapper.addTag(Client client,
TagAnnotationWrapper tag) |
Deprecated.
|
void |
GenericRepositoryObjectWrapper.addTag(Client client,
java.lang.Long id) |
Adds a tag to the object in OMERO, if possible.
|
void |
GenericRepositoryObjectWrapper.addTag(Client client,
java.lang.String name,
java.lang.String description) |
Adds a newly created tag to the object in OMERO, if possible.
|
void |
GenericRepositoryObjectWrapper.addTags(Client client,
TagAnnotationWrapper... tags) |
Deprecated.
|
void |
GenericRepositoryObjectWrapper.addTags(Client client,
java.lang.Long... ids) |
Adds multiple tags by ID to the object in OMERO, if possible.
|
void |
GenericRepositoryObjectWrapper.copyAnnotationLinks(Client client,
GenericRepositoryObjectWrapper<?> object) |
Copies annotation links from some other object to this one
|
java.util.List<java.io.File> |
ImageWrapper.download(Client client,
java.lang.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
|
AnnotationList |
GenericRepositoryObjectWrapper.getAnnotations(Client client) |
Retrieves annotations linked to the object (of known types).
|
java.awt.Color |
ImageWrapper.getChannelColor(Client client,
int index) |
Gets the current color of the channel
|
java.awt.Color |
ImageWrapper.getChannelImportedColor(Client client,
int index) |
Gets the original color of the channel
|
java.lang.String |
ImageWrapper.getChannelName(Client client,
int index) |
Gets the name of the channel
|
java.util.List<ChannelWrapper> |
ImageWrapper.getChannels(Client client) |
Gets the image channels
|
java.util.List<DatasetWrapper> |
ImageWrapper.getDatasets(Client client) |
Retrieves the datasets containing this image
|
java.util.List<FileAnnotationWrapper> |
GenericRepositoryObjectWrapper.getFileAnnotations(Client client) |
Returns the file annotations
|
java.util.List<ImageWrapper> |
ImageWrapper.getFilesetImages(Client client) |
Returns the list of images sharing the same fileset as the current image.
|
FolderWrapper |
ImageWrapper.getFolder(Client client,
java.lang.Long folderId) |
Deprecated.
|
java.util.List<FolderWrapper> |
ImageWrapper.getFolders(Client client) |
Gets the list of folders linked to this image.
|
java.util.List<ImageWrapper> |
DatasetWrapper.getImages(Client client) |
Gets all images in the dataset available from OMERO.
|
java.util.List<ImageWrapper> |
DatasetWrapper.getImages(Client client,
java.lang.String name) |
Gets all images in the dataset with a certain name from OMERO.
|
java.util.List<ImageWrapper> |
FolderWrapper.getImages(Client client) |
Retrieves the images contained in this folder.
|
java.util.List<ImageWrapper> |
PlateAcquisitionWrapper.getImages(Client client) |
Retrieves the images contained in the wells in the parent plate.
|
java.util.List<ImageWrapper> |
PlateWrapper.getImages(Client client) |
Returns the images contained in the wells of this plate.
|
java.util.List<ImageWrapper> |
ProjectWrapper.getImages(Client client) |
Gets all images in the project available from OMERO.
|
java.util.List<ImageWrapper> |
ProjectWrapper.getImages(Client client,
java.lang.String name) |
Gets all images in the project with a certain name from OMERO.
|
java.util.List<ImageWrapper> |
ProjectWrapper.getImages(Client client,
java.lang.String datasetName,
java.lang.String imageName) |
Gets all images with a certain name from datasets with the specified name inside this project on OMERO.
|
java.util.List<ImageWrapper> |
ScreenWrapper.getImages(Client client) |
Retrieves the images contained in this screen.
|
java.util.List<ImageWrapper> |
DatasetWrapper.getImagesKey(Client client,
java.lang.String key) |
Deprecated.
|
java.util.List<ImageWrapper> |
ProjectWrapper.getImagesKey(Client client,
java.lang.String key) |
Deprecated.
|
java.util.List<ImageWrapper> |
DatasetWrapper.getImagesLike(Client client,
java.lang.String motif) |
Gets all images in the dataset with a certain motif in their name from OMERO.
|
java.util.List<ImageWrapper> |
ProjectWrapper.getImagesLike(Client client,
java.lang.String motif) |
Gets all images in the project with a certain motif in their name from OMERO.
|
java.util.List<ImageWrapper> |
DatasetWrapper.getImagesPairKeyValue(Client client,
java.lang.String key,
java.lang.String value) |
Deprecated.
|
java.util.List<ImageWrapper> |
ProjectWrapper.getImagesPairKeyValue(Client client,
java.lang.String key,
java.lang.String value) |
Deprecated.
|
java.util.List<ImageWrapper> |
DatasetWrapper.getImagesTagged(Client client,
TagAnnotationWrapper tag) |
Gets all images in the dataset tagged with a specified tag from OMERO.
|
java.util.List<ImageWrapper> |
DatasetWrapper.getImagesTagged(Client client,
java.lang.Long tagId) |
Gets all images in the dataset tagged with a specified tag from OMERO.
|
java.util.List<ImageWrapper> |
ProjectWrapper.getImagesTagged(Client client,
TagAnnotationWrapper tag) |
Gets all images in the project tagged with a specified tag from OMERO.
|
java.util.List<ImageWrapper> |
ProjectWrapper.getImagesTagged(Client client,
java.lang.Long tagId) |
Gets all images in the project tagged with a specified tag from OMERO.
|
java.util.List<ImageWrapper> |
DatasetWrapper.getImagesWithKey(Client client,
java.lang.String key) |
Gets all images in the dataset with a certain key
|
java.util.List<ImageWrapper> |
ProjectWrapper.getImagesWithKey(Client client,
java.lang.String key) |
Gets all images in the project with a certain key
|
java.util.List<ImageWrapper> |
DatasetWrapper.getImagesWithKeyValuePair(Client client,
java.lang.String key,
java.lang.String value) |
Gets all images in the dataset with a certain key value pair from OMERO
|
java.util.List<ImageWrapper> |
ProjectWrapper.getImagesWithKeyValuePair(Client client,
java.lang.String key,
java.lang.String value) |
Gets all images in the project with a certain key value pair from OMERO.
|
java.util.Map<java.lang.String,java.lang.String> |
GenericRepositoryObjectWrapper.getKeyValuePairs(Client client) |
Gets the List of key-value pairs associated to an object as a map (no duplicate key should exist).
|
java.util.List<MapAnnotationWrapper> |
GenericRepositoryObjectWrapper.getMapAnnotations(Client client) |
Gets all map annotations linked to an object in OMERO, if possible.
|
int |
GenericRepositoryObjectWrapper.getMyRating(Client client) |
Returns the user rating for this object (averaged if multiple ratings are linked).
|
java.util.List<PlateAcquisitionWrapper> |
ImageWrapper.getPlateAcquisitions(Client client) |
Returns the plate acquisitions linked to this image.
|
java.util.List<PlateAcquisitionWrapper> |
ScreenWrapper.getPlateAcquisitions(Client client) |
Returns the plate acquisitions linked to this object, either directly, or through parents/children.
|
java.util.List<PlateAcquisitionWrapper> |
WellSampleWrapper.getPlateAcquisitions(Client client) |
Returns the plate acquisitions linked to the parent Well.
|
java.util.List<PlateAcquisitionWrapper> |
WellWrapper.getPlateAcquisitions(Client client) |
Refreshes this well and returns the plate acquisitions linked to it.
|
java.util.List<PlateWrapper> |
ImageWrapper.getPlates(Client client) |
Retrieves the plates containing this image.
|
java.util.List<PlateWrapper> |
PlateAcquisitionWrapper.getPlates(Client client) |
Returns the (updated) parent plate as a singleton list.
|
java.util.List<PlateWrapper> |
WellSampleWrapper.getPlates(Client client) |
Returns the plates containing the parent Well.
|
java.util.List<ProjectWrapper> |
DatasetWrapper.getProjects(Client client) |
Retrieves the projects containing this dataset.
|
java.util.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
|
java.util.List<FolderWrapper> |
ImageWrapper.getROIFolders(Client client) |
Gets the list of folders linked to the ROIs in this image.
|
java.util.List<ROIWrapper> |
FolderWrapper.getROIs(Client client) |
Deprecated.
|
java.util.List<ROIWrapper> |
FolderWrapper.getROIs(Client client,
long imageId) |
Gets the ROIs contained in the folder associated with the provided image ID.
|
java.util.List<ROIWrapper> |
FolderWrapper.getROIs(Client client,
ImageWrapper image) |
Gets the ROIs contained in the folder associated with the provided image.
|
java.util.List<ROIWrapper> |
ImageWrapper.getROIs(Client client) |
Gets all ROIs linked to the image in OMERO
|
java.util.List<ScreenWrapper> |
ImageWrapper.getScreens(Client client) |
Retrieves the screens containing this image
|
java.util.List<ScreenWrapper> |
PlateAcquisitionWrapper.getScreens(Client client) |
Retrieves the screens containing the parent plates.
|
java.util.List<ScreenWrapper> |
PlateWrapper.getScreens(Client client) |
Retrieves the screens containing this dataset.
|
java.util.List<ScreenWrapper> |
WellSampleWrapper.getScreens(Client client) |
Returns the screens containing the parent Well.
|
java.util.List<ScreenWrapper> |
WellWrapper.getScreens(Client client) |
Refreshes this well and retrieves the screens containing it.
|
TableWrapper |
GenericRepositoryObjectWrapper.getTable(Client client,
java.lang.Long fileId) |
Gets a certain table linked to the object in OMERO.
|
java.util.List<TableWrapper> |
GenericRepositoryObjectWrapper.getTables(Client client) |
Gets all tables linked to the object in OMERO.
|
java.util.List<TagAnnotationWrapper> |
GenericRepositoryObjectWrapper.getTags(Client client) |
Gets all tags linked to an object in OMERO, if possible.
|
java.awt.image.BufferedImage |
ImageWrapper.getThumbnail(Client client,
int size) |
Retrieves the image thumbnail of the specified size.
|
java.lang.String |
GenericRepositoryObjectWrapper.getValue(Client client,
java.lang.String key) |
Gets the value from a Key-Value pair associated to the object.
|
WellWrapper |
WellSampleWrapper.getWell(Client client) |
Retrieves the well containing this well sample
|
java.util.List<WellWrapper> |
ImageWrapper.getWells(Client client) |
Retrieves the wells containing this image.
|
java.util.List<WellWrapper> |
PlateAcquisitionWrapper.getWells(Client client) |
Retrieves the wells contained in the parent plate.
|
java.util.List<WellWrapper> |
PlateWrapper.getWells(Client client) |
Gets all wells in the plate available from OMERO.
|
java.util.List<WellWrapper> |
ScreenWrapper.getWells(Client client) |
Retrieves the wells linked to this object, either directly, or through parents/children.
|
java.util.List<java.lang.Long> |
DatasetWrapper.importAndReplaceImages(Client client,
java.lang.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.
|
java.util.List<java.lang.Long> |
DatasetWrapper.importAndReplaceImages(Client client,
java.lang.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.
|
java.util.List<java.lang.Long> |
DatasetWrapper.importImage(Client client,
java.lang.String path) |
Imports one image file to the dataset in OMERO.
|
boolean |
DatasetWrapper.importImages(Client client,
java.lang.String... paths) |
Imports all images candidates in the paths to the dataset in OMERO.
|
<A extends GenericAnnotationWrapper<?>>
boolean |
GenericRepositoryObjectWrapper.isLinked(Client client,
A annotation) |
Checks if a specific annotation is linked to the object.
|
boolean |
ImageWrapper.isOrphaned(Client client) |
Checks if image is orphaned (not in a WellSample nor linked to a dataset).
|
<A extends GenericAnnotationWrapper<?>>
void |
FolderWrapper.link(Client client,
A annotation) |
Adds an annotation to the object in OMERO, if possible.
|
<A extends GenericAnnotationWrapper<?>>
void |
GenericRepositoryObjectWrapper.link(Client client,
A annotation) |
Adds an annotation to the object in OMERO, if possible.
|
void |
GenericRepositoryObjectWrapper.link(Client client,
GenericAnnotationWrapper<?>... annotations) |
Adds multiple annotations to the object in OMERO, if possible.
|
<A extends GenericAnnotationWrapper<?>>
void |
PlateAcquisitionWrapper.link(Client client,
A annotation) |
Adds a tag to the object in OMERO, if possible.
|
void |
GenericRepositoryObjectWrapper.linkIfNotLinked(Client client,
GenericAnnotationWrapper<?>... annotations) |
Adds multiple annotations to the object in OMERO if they are not already linked.
|
void |
PixelsWrapper.loadPlanesInfo(Client client) |
Loads the planes information.
|
void |
GenericRepositoryObjectWrapper.rate(Client client,
int rating) |
Rates the object (using a rating annotation).
|
void |
DatasetWrapper.refresh(Client client) |
Refreshes the dataset.
|
void |
PlateWrapper.refresh(Client client) |
Refreshes the plate.
|
void |
ProjectWrapper.refresh(Client client) |
Refreshes the wrapped project.
|
void |
WellWrapper.refresh(Client client) |
Refreshes the well.
|
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.
|
protected void |
GenericRepositoryObjectWrapper.removeLink(Client client,
java.lang.String linkType,
long childId) |
Removes the link of the given type with the given child ID.
|
java.util.List<ImageWrapper> |
DatasetWrapper.replaceImages(Client client,
java.util.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.
|
java.util.List<ROIWrapper> |
ImageWrapper.saveROIs(Client client,
ROIWrapper... rois) |
Links ROIs to the image in OMERO.
|
java.util.List<ROIWrapper> |
ImageWrapper.saveROIs(Client client,
java.util.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.
|
<A extends GenericAnnotationWrapper<?>>
void |
GenericRepositoryObjectWrapper.unlink(Client client,
A annotation) |
Unlinks the given annotation from the current object.
|
void |
FolderWrapper.unlinkAllROI(Client client) |
Deprecated.
|
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.
|
void |
FolderWrapper.unlinkROIs(Client client,
ROIWrapper... rois) |
Unlink ROIs from the folder.
|